diff --git a/README.md b/README.md index 82dcee967138823d4da0d3e4feb6f6a0833423dc..82124fd8d7bacccfc60ec297866f2e74fcb68ea8 100644 --- a/README.md +++ b/README.md @@ -1,11 +1,11 @@ --- license: mit task_categories: +- fill-mask - text-classification +- text2text-generation - translation - zero-shot-classification -- text2text-generation -- fill-mask tags: - chemistry - biology @@ -13,10 +13,23 @@ tags: - SMILES size_categories: - 10M -- **Repository:** [https://huggingface.co/datasets/scbirlab/cyc-pep-6-12mer-70M-2024] +- **Repository:** https://huggingface.co/datasets/scbirlab/cyc-pep-6-12mer-70M-2024 @@ -56,7 +69,12 @@ Developing chemistry models around cyclic peptides. - **peptide_sequence**: Amino acid sequence of linear peptide - **SMILES**: SMILES string of linear peptide - **cyclic_id**: Identifier for cyclic peptide +- **cyclic_inchikey**: Unique identifier for cyclic peptide - **cysteine_to_N_cyclization**: SMILES string of cyclic peptide +- **cyclic_scaffold**: Murcko scaffold of cyclic peptide +- **cyclic_mwt**: Molecular weight of cyclic peptide +- **cyclic_clogp**: Crippen LogP of cyclic peptide +- **cyclic_tpsa**: Topological polar surface area of cyclic peptide ## Dataset Creation diff --git a/test/cyc-pep-6-12mer-70M_00.csv.gz b/test/cyc-pep-6-12mer-70M_00.csv.gz index f52e9eb35a7329599429c20aa3fccb8385bbfff1..967d64d85ba9910fc88b9be29755c63c288b2578 100644 --- a/test/cyc-pep-6-12mer-70M_00.csv.gz +++ b/test/cyc-pep-6-12mer-70M_00.csv.gz @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:06be14f986a68a2a01779b93a50e5498b150a70cde2c34d7dbec192e727e7e67 -size 58256598 +oid sha256:2e913c51083461027a3272b7fd2eb5f92b744cacdbca47607c4333750922a2fd +size 112845849 diff --git a/test/cyc-pep-6-12mer-70M_00.log b/test/cyc-pep-6-12mer-70M_00.log new file mode 100644 index 0000000000000000000000000000000000000000..8c9be24bde18d5fd2eb42e52353cebea190fa7f9 --- /dev/null +++ b/test/cyc-pep-6-12mer-70M_00.log @@ -0,0 +1,337 @@ ++ module purge ++ '[' -z '' ']' ++ case "$-" in ++ __lmod_sh_dbg=x ++ '[' -n x ']' ++ set +x +Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output +Shell debugging restarted ++ unset __lmod_sh_dbg ++ return 0 ++ module load Anaconda3/2023.03 ++ '[' -z '' ']' ++ case "$-" in ++ __lmod_sh_dbg=x ++ '[' -n x ']' ++ set +x +Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output +Shell debugging restarted ++ unset __lmod_sh_dbg ++ return 0 ++ source /camp/home/johnsoe/.bashrc +++ '[' '' = yes ']' +++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' ++++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.bash hook +++ __conda_setup='export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'' + +# Copyright (C) 2012 Anaconda, Inc +# SPDX-License-Identifier: BSD-3-Clause +__conda_exe() ( + "$CONDA_EXE" $_CE_M $_CE_CONDA "$@" +) + +__conda_hashr() { + if [ -n "${ZSH_VERSION:+x}" ]; then + \rehash + elif [ -n "${POSH_VERSION:+x}" ]; then + : # pass + else + \hash -r + fi +} + +__conda_activate() { + if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then + # Handle transition from shell activated with conda <= 4.3 to a subsequent activation + # after conda updated to >= 4.4. See issue #6173. + PS1="$CONDA_PS1_BACKUP" + \unset CONDA_PS1_BACKUP + fi + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return + \eval "$ask_conda" + __conda_hashr +} + +__conda_reactivate() { + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return + \eval "$ask_conda" + __conda_hashr +} + +conda() { + \local cmd="${1-__missing__}" + case "$cmd" in + activate|deactivate) + __conda_activate "$@" + ;; + install|update|upgrade|remove|uninstall) + __conda_exe "$@" || \return + __conda_reactivate + ;; + *) + __conda_exe "$@" + ;; + esac +} + +if [ -z "${CONDA_SHLVL+x}" ]; then + \export CONDA_SHLVL=0 + # In dev-mode CONDA_EXE is python.exe and on Windows + # it is in a different relative location to condabin. + if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then + PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}" + else + PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}" + fi + \export PATH + + # We'\''re not allowing PS1 to be unbound. It must at least be set. + # However, we'\''re not exporting it, which can cause problems when starting a second shell + # via a first shell (i.e. starting zsh from bash). + if [ -z "${PS1+x}" ]; then + PS1= + fi +fi + +conda activate base' +++ '[' 0 -eq 0 ']' +++ eval 'export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'' + +# Copyright (C) 2012 Anaconda, Inc +# SPDX-License-Identifier: BSD-3-Clause +__conda_exe() ( + "$CONDA_EXE" $_CE_M $_CE_CONDA "$@" +) + +__conda_hashr() { + if [ -n "${ZSH_VERSION:+x}" ]; then + \rehash + elif [ -n "${POSH_VERSION:+x}" ]; then + : # pass + else + \hash -r + fi +} + +__conda_activate() { + if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then + # Handle transition from shell activated with conda <= 4.3 to a subsequent activation + # after conda updated to >= 4.4. See issue #6173. + PS1="$CONDA_PS1_BACKUP" + \unset CONDA_PS1_BACKUP + fi + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return + \eval "$ask_conda" + __conda_hashr +} + +__conda_reactivate() { + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return + \eval "$ask_conda" + __conda_hashr +} + +conda() { + \local cmd="${1-__missing__}" + case "$cmd" in + activate|deactivate) + __conda_activate "$@" + ;; + install|update|upgrade|remove|uninstall) + __conda_exe "$@" || \return + __conda_reactivate + ;; + *) + __conda_exe "$@" + ;; + esac +} + +if [ -z "${CONDA_SHLVL+x}" ]; then + \export CONDA_SHLVL=0 + # In dev-mode CONDA_EXE is python.exe and on Windows + # it is in a different relative location to condabin. + if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then + PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}" + else + PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}" + fi + \export PATH + + # We'\''re not allowing PS1 to be unbound. It must at least be set. + # However, we'\''re not exporting it, which can cause problems when starting a second shell + # via a first shell (i.e. starting zsh from bash). + if [ -z "${PS1+x}" ]; then + PS1= + fi +fi + +conda activate base' ++++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda ++++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda ++++ export _CE_M= ++++ _CE_M= ++++ export _CE_CONDA= ++++ _CE_CONDA= ++++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ '[' -z x ']' ++++ conda activate base ++++ local cmd=activate ++++ case "$cmd" in ++++ __conda_activate activate base ++++ '[' -n '' ']' ++++ local ask_conda +++++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++++ __conda_exe shell.posix activate base +++++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate base ++++ ask_conda='PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_SHLVL='\''6'\'' +export CONDA_DEFAULT_ENV='\''base'\'' +export CONDA_PROMPT_MODIFIER='\''(base) '\'' +export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' ++++ eval 'PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_SHLVL='\''6'\'' +export CONDA_DEFAULT_ENV='\''base'\'' +export CONDA_PROMPT_MODIFIER='\''(base) '\'' +export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' +++++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++++ export CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0 +++++ CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0 +++++ export CONDA_SHLVL=6 +++++ CONDA_SHLVL=6 +++++ export CONDA_DEFAULT_ENV=base +++++ CONDA_DEFAULT_ENV=base +++++ export 'CONDA_PROMPT_MODIFIER=(base) ' +++++ CONDA_PROMPT_MODIFIER='(base) ' +++++ export CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev +++++ CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev +++++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++++ export _CE_M= +++++ _CE_M= +++++ export _CE_CONDA= +++++ _CE_CONDA= +++++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python +++++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ __conda_hashr ++++ '[' -n '' ']' ++++ '[' -n '' ']' ++++ hash -r +++ unset __conda_setup ++ conda activate schemist-dev ++ local cmd=activate ++ case "$cmd" in ++ __conda_activate activate schemist-dev ++ '[' -n '' ']' ++ local ask_conda +++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++ __conda_exe shell.posix activate schemist-dev +++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate schemist-dev ++ ask_conda='PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_SHLVL='\''7'\'' +export CONDA_DEFAULT_ENV='\''schemist-dev'\'' +export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\'' +export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' ++ eval 'PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_SHLVL='\''7'\'' +export CONDA_DEFAULT_ENV='\''schemist-dev'\'' +export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\'' +export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' +++ PS1='(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++ export CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev +++ CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev +++ export CONDA_SHLVL=7 +++ CONDA_SHLVL=7 +++ export CONDA_DEFAULT_ENV=schemist-dev +++ CONDA_DEFAULT_ENV=schemist-dev +++ export 'CONDA_PROMPT_MODIFIER=(schemist-dev) ' +++ CONDA_PROMPT_MODIFIER='(schemist-dev) ' +++ export CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0 +++ CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0 +++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++ export _CE_M= +++ _CE_M= +++ export _CE_CONDA= +++ _CE_CONDA= +++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python +++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++ __conda_hashr ++ '[' -n '' ']' ++ '[' -n '' ']' ++ hash -r ++ CHUNK_HEAD_FILE=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz ++ INPUT=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/test/cyc-pep-6-12mer-70M_00.csv ++ COLUMN=cysteine_to_N_cyclization ++ PREFIX=cyclic_ ++ AWK='1 { print $8, $1, $2, $10, $3 }' ++ '[' -z cysteine_to_N_cyclization ']' ++ '[' -z cyclic_ ']' ++ '[' -z '1 { print $8, $1, $2, $10, $3 }' ']' ++ cat /dev/fd/63 /nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/test/cyc-pep-6-12mer-70M_00.csv ++ schemist convert -f csv --column cysteine_to_N_cyclization --to id inchikey scaffold mwt clogp tpsa --prefix cyclic_ --options prefix=SCB- ++ gzip --best ++ awk -F, -v OFS=, '1 { print $8, $1, $2, $10, $3 }' +++ tr ' ' , +++ head -n1 +++ zcat /nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz +🚀 Converting between string representations with the following parameters: + subcommand: convert + output: <_io.TextIOWrapper name='' mode='w' encoding='utf-8'> + format: csv + input: <_io.TextIOWrapper name='' mode='r' encoding='utf-8'> + representation: SMILES + column: cysteine_to_N_cyclization + prefix: cyclic_ + to: ['id', 'inchikey', 'scaffold', 'mwt', 'clogp', 'tpsa'] + options: ['prefix=SCB-'] + func: + 0it [00:00, ?it/s] 1it [00:11, 11.78s/it] 2it [00:23, 11.64s/it] 3it [00:34, 11.62s/it] 4it [00:46, 11.62s/it] 5it [00:58, 11.63s/it] 6it [01:09, 11.64s/it] 7it [01:21, 11.63s/it] 8it [01:34, 11.92s/it] 9it [01:46, 12.06s/it] 10it [01:58, 12.02s/it] 11it [02:11, 12.27s/it] 12it [02:22, 12.14s/it] 13it [02:35, 12.28s/it] 14it [02:48, 12.55s/it] 15it [03:02, 12.80s/it] 16it [03:15, 12.92s/it] 17it [03:29, 13.16s/it] 18it [03:42, 13.13s/it] 19it [03:55, 13.15s/it] 20it [04:08, 13.31s/it] 21it [04:22, 13.34s/it] 22it [04:35, 13.18s/it] 23it [04:47, 13.02s/it] 24it [05:00, 12.91s/it] 25it [05:12, 12.78s/it] 26it [05:25, 12.69s/it] 27it [05:37, 12.54s/it] 28it [05:51, 12.83s/it] 29it [06:03, 12.81s/it] 30it [06:16, 12.71s/it] 31it [06:29, 12.75s/it] 32it [06:42, 12.77s/it] 33it [06:54, 12.66s/it] 34it [07:06, 12.59s/it] 35it [07:20, 12.83s/it] 36it [07:33, 12.82s/it] 37it [07:45, 12.74s/it] 38it [07:58, 12.64s/it] 39it [08:10, 12.62s/it] 40it [08:22, 12.53s/it] 41it [08:36, 12.90s/it] 42it [08:52, 13.78s/it] 43it [09:05, 13.49s/it] 44it [09:18, 13.50s/it] 45it [09:35, 14.44s/it] 46it [09:51, 14.93s/it] 47it [10:03, 14.16s/it] 48it [10:16, 13.59s/it] 49it [10:29, 13.39s/it] 50it [10:41, 13.04s/it] 51it [10:52, 12.49s/it] 52it [11:04, 12.43s/it] 53it [11:17, 12.60s/it] 54it [11:30, 12.61s/it] 55it [11:42, 12.40s/it] 56it [11:53, 11.97s/it] 57it [12:04, 11.71s/it] 58it [12:15, 11.58s/it] 59it [12:27, 11.53s/it] 60it [12:39, 11.66s/it] 61it [12:50, 11.73s/it] 62it [13:03, 11.92s/it] 63it [13:16, 12.40s/it] 64it [13:31, 13.00s/it] 65it [13:43, 12.84s/it] 66it [13:56, 12.93s/it] 67it [14:08, 12.66s/it] 68it [14:21, 12.52s/it] 69it [14:33, 12.34s/it] 70it [14:45, 12.26s/it] 71it [14:57, 12.19s/it] 72it [15:10, 12.49s/it] 73it [15:23, 12.75s/it] 74it [15:36, 12.87s/it] 75it [15:49, 12.78s/it] 76it [16:01, 12.61s/it] 77it [16:14, 12.69s/it] 78it [16:26, 12.46s/it] 79it [16:40, 12.99s/it] 80it [16:52, 12.81s/it] 81it [17:08, 13.48s/it] 82it [17:23, 14.07s/it] 83it [17:38, 14.38s/it] 84it [17:51, 13.93s/it] 85it [18:04, 13.79s/it] 86it [18:18, 13.58s/it] 87it [18:30, 13.34s/it] 88it [18:42, 12.81s/it] 89it [18:53, 12.31s/it] 90it [19:06, 12.59s/it] 91it [19:19, 12.74s/it] 92it [19:32, 12.65s/it] 93it [19:45, 12.92s/it] 94it [19:57, 12.41s/it] 95it [20:10, 12.77s/it] 96it [20:21, 12.30s/it] 97it [20:35, 12.58s/it] 98it [20:49, 13.12s/it] 99it [21:00, 12.56s/it] 100it [21:12, 12.18s/it] 101it [21:23, 11.96s/it] 102it [21:35, 11.92s/it] 103it [21:47, 11.92s/it] 104it [21:58, 11.82s/it] 105it [22:10, 11.77s/it] 106it [22:22, 11.98s/it] 107it [22:35, 12.16s/it] 108it [22:46, 11.93s/it] 109it [22:57, 11.61s/it] 110it [23:08, 11.48s/it] 111it [23:20, 11.40s/it] 112it [23:31, 11.33s/it] 113it [23:42, 11.33s/it] 114it [23:53, 11.31s/it] 115it [24:05, 11.28s/it] 116it [24:16, 11.24s/it] 117it [24:27, 11.22s/it] 118it [24:38, 11.17s/it] 119it [24:49, 11.17s/it] 120it [25:00, 11.14s/it] 121it [25:11, 11.12s/it] 122it [25:22, 11.08s/it] 123it [25:33, 11.06s/it] 124it [25:45, 11.10s/it] 125it [25:56, 11.10s/it] 126it [26:07, 11.13s/it] 127it [26:18, 11.08s/it] 128it [26:29, 11.07s/it] 129it [26:40, 11.10s/it] 130it [26:51, 11.13s/it] 131it [27:02, 11.17s/it] 132it [27:14, 11.19s/it] 133it [27:25, 11.18s/it] 134it [27:36, 11.21s/it] 135it [27:47, 11.20s/it] 136it [27:58, 11.10s/it] 137it [28:09, 11.09s/it] 138it [28:20, 11.06s/it] 139it [28:31, 11.06s/it] 140it [28:42, 11.07s/it] 141it [28:53, 11.07s/it] 142it [29:05, 11.10s/it] 143it [29:16, 11.17s/it] 144it [29:27, 11.11s/it] 145it [29:38, 11.15s/it] 146it [29:49, 11.15s/it] 147it [30:00, 11.15s/it] 148it [30:11, 11.12s/it] 149it [30:22, 11.03s/it] 150it [30:33, 11.03s/it] 151it [30:44, 11.06s/it] 152it [30:56, 11.08s/it] 153it [31:07, 11.05s/it] 154it [31:18, 11.04s/it] 155it [31:29, 11.03s/it] 156it [31:40, 11.06s/it] 157it [31:51, 11.07s/it] 158it [32:02, 11.07s/it] 159it [32:13, 11.04s/it] 160it [32:24, 11.04s/it] 161it [32:35, 11.08s/it] 162it [32:46, 11.09s/it] 163it [32:57, 11.05s/it] 164it [33:08, 11.05s/it] 165it [33:19, 11.06s/it] 166it [33:30, 11.04s/it] 167it [33:41, 11.02s/it] 168it [33:52, 11.01s/it] 169it [34:03, 11.02s/it] 170it [34:14, 11.02s/it] 171it [34:25, 11.01s/it] 172it [34:36, 11.01s/it] 173it [34:47, 10.99s/it] 174it [34:58, 10.99s/it] 175it [35:09, 11.01s/it] 176it [35:20, 11.03s/it] 177it [35:31, 10.98s/it] 178it [35:42, 10.98s/it] 179it [35:53, 11.00s/it] 180it [36:04, 11.01s/it] 181it [36:15, 11.03s/it] 182it [36:26, 11.05s/it] 183it [36:37, 11.04s/it] 184it [36:48, 11.02s/it] 185it [36:59, 11.01s/it] 186it [37:10, 11.02s/it] 187it [37:22, 11.02s/it] 188it [37:33, 11.01s/it] 189it [37:44, 11.01s/it] 190it [37:54, 10.94s/it] 191it [38:05, 10.91s/it] 192it [38:16, 10.88s/it] 193it [38:27, 10.92s/it] 194it [38:38, 10.91s/it] 195it [38:49, 10.85s/it] 196it [38:59, 10.80s/it] 197it [39:10, 10.90s/it] 198it [39:22, 11.00s/it] 199it [39:33, 11.04s/it] 200it [39:44, 11.16s/it] 201it [39:55, 11.10s/it] 202it [40:06, 11.09s/it] 203it [40:17, 11.06s/it] 204it [40:28, 11.03s/it] 205it [40:40, 11.15s/it] 206it [40:51, 11.19s/it] 207it [41:02, 11.17s/it] 208it [41:13, 11.24s/it] 209it [41:25, 11.21s/it] 210it [41:36, 11.14s/it] 211it [41:47, 11.11s/it] 212it [41:58, 11.09s/it] 213it [42:09, 11.09s/it] 214it [42:20, 11.10s/it] 215it [42:31, 11.08s/it] 216it [42:42, 11.10s/it] 217it [42:53, 11.08s/it] 218it [43:04, 11.10s/it] 219it [43:15, 11.11s/it] 220it [43:26, 11.12s/it] 221it [43:37, 11.10s/it] 222it [43:49, 11.09s/it] 223it [44:00, 11.07s/it] 224it [44:11, 11.07s/it] 225it [44:22, 11.06s/it] 226it [44:33, 11.05s/it] 227it [44:44, 11.06s/it] 228it [44:55, 11.06s/it] 229it [45:06, 11.05s/it] 230it [45:17, 11.04s/it] 231it [45:28, 11.05s/it] 232it [45:39, 11.05s/it] 233it [45:50, 11.07s/it] 234it [46:01, 11.05s/it] 235it [46:12, 11.04s/it] 236it [46:23, 11.09s/it] 237it [46:35, 11.11s/it] 238it [46:46, 11.18s/it] 239it [46:57, 11.11s/it] 240it [47:08, 11.14s/it] 241it [47:19, 11.14s/it] 242it [47:30, 11.11s/it] 243it [47:42, 11.25s/it] 244it [47:53, 11.37s/it] 245it [48:05, 11.29s/it] 246it [48:16, 11.24s/it] 247it [48:27, 11.24s/it] 248it [48:38, 11.27s/it] 249it [48:49, 11.24s/it] 250it [49:00, 11.17s/it] 251it [49:12, 11.20s/it] 252it [49:23, 11.16s/it] 253it [49:34, 11.15s/it] 254it [49:45, 11.14s/it] 255it [49:56, 11.10s/it] 256it [50:07, 11.07s/it] 257it [50:18, 11.06s/it] 258it [50:29, 11.08s/it] 259it [50:40, 11.07s/it] 260it [50:51, 11.07s/it] 261it [51:02, 11.09s/it] 262it [51:14, 11.14s/it] 263it [51:25, 11.11s/it] 264it [51:36, 11.07s/it] 265it [51:47, 11.05s/it] 266it [51:58, 11.10s/it] 267it [52:09, 11.12s/it] 268it [52:20, 11.08s/it] 269it [52:31, 11.07s/it] 270it [52:43, 11.16s/it] 271it [52:54, 11.22s/it] 272it [53:05, 11.18s/it] 273it [53:16, 11.16s/it] 274it [53:27, 11.15s/it] 275it [53:39, 11.22s/it] 276it [53:50, 11.22s/it] 277it [54:01, 11.19s/it] 278it [54:12, 11.24s/it] 279it [54:24, 11.25s/it] 280it [54:35, 11.21s/it] 281it [54:46, 11.15s/it] 282it [54:57, 11.15s/it] 283it [55:08, 11.11s/it] 284it [55:19, 11.09s/it] 285it [55:30, 11.05s/it] 286it [55:41, 11.10s/it] 287it [55:52, 11.09s/it] 288it [56:03, 11.09s/it] 289it [56:15, 11.15s/it] 290it [56:26, 11.13s/it] 291it [56:37, 11.14s/it] 292it [56:48, 11.16s/it] 293it [56:59, 11.18s/it] 294it [57:10, 11.15s/it] 295it [57:21, 11.16s/it] 296it [57:33, 11.17s/it] 297it [57:44, 11.18s/it] 298it [57:55, 11.13s/it] 299it [58:06, 11.11s/it] 300it [58:17, 11.12s/it] 301it [58:28, 11.06s/it] 302it [58:39, 11.04s/it] 303it [58:50, 11.04s/it] 304it [59:01, 11.02s/it] 305it [59:12, 11.07s/it] 306it [59:23, 11.08s/it] 307it [59:34, 11.07s/it] 308it [59:45, 11.06s/it] 309it [59:56, 11.07s/it] 310it [1:00:08, 11.07s/it] 311it [1:00:19, 11.05s/it] 312it [1:00:29, 11.02s/it] 313it [1:00:41, 11.05s/it] 314it [1:00:52, 11.09s/it] 315it [1:01:03, 11.09s/it] 316it [1:01:14, 11.15s/it] 317it [1:01:25, 11.12s/it] 318it [1:01:36, 11.11s/it] 319it [1:01:48, 11.16s/it] 320it [1:01:59, 11.14s/it] 321it [1:02:10, 11.15s/it] 322it [1:02:21, 11.11s/it] 323it [1:02:32, 11.09s/it] 324it [1:02:43, 11.07s/it] 325it [1:02:54, 11.07s/it] 326it [1:03:05, 11.07s/it] 327it [1:03:16, 11.13s/it] 328it [1:03:27, 11.11s/it] 329it [1:03:38, 11.09s/it] 330it [1:03:49, 11.07s/it] 331it [1:04:00, 11.03s/it] 332it [1:04:12, 11.15s/it] 333it [1:04:23, 11.20s/it] 334it [1:04:34, 11.23s/it] 335it [1:04:46, 11.20s/it] 336it [1:04:57, 11.21s/it] 337it [1:05:08, 11.17s/it] 338it [1:05:19, 11.15s/it] 339it [1:05:30, 11.11s/it] 340it [1:05:41, 11.05s/it] 341it [1:05:52, 11.03s/it] 342it [1:06:03, 11.01s/it] 343it [1:06:14, 11.10s/it] 344it [1:06:25, 11.07s/it] 345it [1:06:36, 11.05s/it] 346it [1:06:47, 11.06s/it] 347it [1:06:58, 11.05s/it] 348it [1:07:09, 11.06s/it] 349it [1:07:21, 11.09s/it] 350it [1:07:32, 11.06s/it] 351it [1:07:43, 11.05s/it] 352it [1:07:54, 11.05s/it] 353it [1:08:05, 11.03s/it] 354it [1:08:16, 11.22s/it] 355it [1:08:27, 11.18s/it] 356it [1:08:39, 11.18s/it] 357it [1:08:50, 11.20s/it] 358it [1:09:01, 11.12s/it] 359it [1:09:12, 11.07s/it] 360it [1:09:23, 11.04s/it] 361it [1:09:34, 11.01s/it] 362it [1:09:45, 11.12s/it] 363it [1:09:56, 11.09s/it] 364it [1:10:07, 11.10s/it] 365it [1:10:18, 11.18s/it] 366it [1:10:30, 11.16s/it] 367it [1:10:41, 11.13s/it] 368it [1:10:52, 11.11s/it] 369it [1:11:03, 11.08s/it] 370it [1:11:14, 11.13s/it] 371it [1:11:25, 11.11s/it] 372it [1:11:36, 11.10s/it] 373it [1:11:47, 11.06s/it] 374it [1:11:58, 11.02s/it] 375it [1:12:09, 11.06s/it] 376it [1:12:20, 11.09s/it] 377it [1:12:31, 11.09s/it] 378it [1:12:43, 11.17s/it] 379it [1:12:54, 11.19s/it] 380it [1:13:05, 11.15s/it] 381it [1:13:16, 11.16s/it] 382it [1:13:27, 11.13s/it] 383it [1:13:38, 11.13s/it] 384it [1:13:50, 11.16s/it] 385it [1:14:01, 11.12s/it] 386it [1:14:12, 11.18s/it] 387it [1:14:23, 11.19s/it] 388it [1:14:34, 11.17s/it] 389it [1:14:46, 11.22s/it] 390it [1:14:57, 11.17s/it] 391it [1:15:08, 11.17s/it] 392it [1:15:19, 11.22s/it] 393it [1:15:30, 11.19s/it] 394it [1:15:41, 11.19s/it] 395it [1:15:53, 11.16s/it] 396it [1:16:04, 11.14s/it] 397it [1:16:15, 11.17s/it] 398it [1:16:26, 11.15s/it] 399it [1:16:37, 11.13s/it] 400it [1:16:48, 11.20s/it] 401it [1:17:00, 11.22s/it] 402it [1:17:11, 11.21s/it] 403it [1:17:22, 11.22s/it] 404it [1:17:33, 11.17s/it] 405it [1:17:44, 11.20s/it] 406it [1:17:55, 11.14s/it] 407it [1:18:07, 11.13s/it] 408it [1:18:18, 11.18s/it] 409it [1:18:29, 11.13s/it] 410it [1:18:40, 11.14s/it] 411it [1:18:51, 11.13s/it] 412it [1:19:02, 11.10s/it] 413it [1:19:14, 11.16s/it] 414it [1:19:25, 11.12s/it] 415it [1:19:36, 11.11s/it] 416it [1:19:47, 11.23s/it] 417it [1:19:58, 11.22s/it] 418it [1:20:09, 11.18s/it] 419it [1:20:20, 11.13s/it] 420it [1:20:31, 11.10s/it] 421it [1:20:42, 11.05s/it] 422it [1:20:53, 11.02s/it] 423it [1:21:04, 11.01s/it] 424it [1:21:15, 10.99s/it] 425it [1:21:26, 11.00s/it] 426it [1:21:37, 11.03s/it] 427it [1:21:48, 11.00s/it] 428it [1:21:59, 11.00s/it] 429it [1:22:10, 11.00s/it] 430it [1:22:21, 11.02s/it] 431it [1:22:32, 11.00s/it] 432it [1:22:43, 10.99s/it] 433it [1:22:54, 11.00s/it] 434it [1:23:05, 10.99s/it] 435it [1:23:16, 11.00s/it] 436it [1:23:27, 11.01s/it] 437it [1:23:38, 11.01s/it] 438it [1:23:49, 11.00s/it] 439it 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[3:01:44, 11.00s/it] 958it [3:01:55, 11.00s/it] 959it [3:02:06, 11.00s/it] 960it [3:02:17, 10.98s/it] 961it [3:02:28, 10.97s/it] 962it [3:02:39, 10.99s/it] 963it [3:02:50, 10.98s/it] 964it [3:03:01, 10.99s/it] 965it [3:03:12, 10.99s/it] 966it [3:03:23, 10.98s/it] 967it [3:03:34, 10.99s/it] 968it [3:03:45, 10.97s/it] 969it [3:03:56, 11.00s/it] 970it [3:04:07, 10.99s/it] 971it [3:04:18, 10.98s/it] 972it [3:04:29, 10.98s/it] 973it [3:04:40, 10.99s/it] 974it [3:04:51, 11.00s/it] 975it [3:05:02, 10.98s/it] 976it [3:05:13, 11.00s/it] 977it [3:05:24, 11.00s/it] 978it [3:05:35, 11.02s/it] 979it [3:05:46, 11.02s/it] 980it [3:05:57, 10.99s/it] 981it [3:06:08, 10.99s/it] 982it [3:06:19, 11.00s/it] 983it [3:06:30, 11.00s/it] 984it [3:06:42, 11.45s/it] 985it [3:06:53, 11.30s/it] 986it [3:07:04, 11.30s/it] 987it [3:07:15, 11.20s/it] 988it [3:07:26, 11.14s/it] 989it [3:07:37, 11.10s/it] 990it [3:07:48, 11.05s/it] 991it [3:07:59, 11.04s/it] 992it [3:08:10, 11.00s/it] 993it [3:08:21, 11.00s/it] 994it [3:08:32, 10.99s/it] 995it [3:08:43, 11.02s/it] 996it [3:08:54, 11.02s/it] 997it [3:09:05, 11.00s/it] 998it [3:09:16, 11.00s/it] 999it [3:09:27, 10.99s/it] 1000it [3:09:38, 10.99s/it] 1000it [3:09:38, 11.38s/it] +Error counts: + cyclic_id: 0 + cyclic_inchikey: 0 + cyclic_scaffold: 0 + cyclic_mwt: 0 + cyclic_clogp: 0 + cyclic_tpsa: 0 +⏰ Completed process in 3:10:05.774172 ++ rm /nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/test/cyc-pep-6-12mer-70M_00.csv diff --git a/test/cyc-pep-6-12mer-70M_01.csv.gz b/test/cyc-pep-6-12mer-70M_01.csv.gz index 3dbf7871cdec4e28310bf2c949023ea01dd6c78b..329dec25ca59f8e50f72da3516c51661c8699433 100644 --- a/test/cyc-pep-6-12mer-70M_01.csv.gz +++ b/test/cyc-pep-6-12mer-70M_01.csv.gz @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:2238d323e335426a55721bd5b6a68ce61cd7ed92f71fa7a5dfe2c80ce3dab975 -size 59576589 +oid sha256:b12aa9b2723934da0ed96abb7517e5ca1e50ea6ed2ab4c54c5855b232bafa4ce +size 114559271 diff --git a/test/cyc-pep-6-12mer-70M_01.log b/test/cyc-pep-6-12mer-70M_01.log new file mode 100644 index 0000000000000000000000000000000000000000..4cf85934b715ec3bc8ec07d1bb99962942401a9b --- /dev/null +++ b/test/cyc-pep-6-12mer-70M_01.log @@ -0,0 +1,337 @@ ++ module purge ++ '[' -z '' ']' ++ case "$-" in ++ __lmod_sh_dbg=x ++ '[' -n x ']' ++ set +x +Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output +Shell debugging restarted ++ unset __lmod_sh_dbg ++ return 0 ++ module load Anaconda3/2023.03 ++ '[' -z '' ']' ++ case "$-" in ++ __lmod_sh_dbg=x ++ '[' -n x ']' ++ set +x +Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output +Shell debugging restarted ++ unset __lmod_sh_dbg ++ return 0 ++ source /camp/home/johnsoe/.bashrc +++ '[' '' = yes ']' +++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' ++++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.bash hook +++ __conda_setup='export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'' + +# Copyright (C) 2012 Anaconda, Inc +# SPDX-License-Identifier: BSD-3-Clause +__conda_exe() ( + "$CONDA_EXE" $_CE_M $_CE_CONDA "$@" +) + +__conda_hashr() { + if [ -n "${ZSH_VERSION:+x}" ]; then + \rehash + elif [ -n "${POSH_VERSION:+x}" ]; then + : # pass + else + \hash -r + fi +} + +__conda_activate() { + if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then + # Handle transition from shell activated with conda <= 4.3 to a subsequent activation + # after conda updated to >= 4.4. See issue #6173. + PS1="$CONDA_PS1_BACKUP" + \unset CONDA_PS1_BACKUP + fi + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return + \eval "$ask_conda" + __conda_hashr +} + +__conda_reactivate() { + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return + \eval "$ask_conda" + __conda_hashr +} + +conda() { + \local cmd="${1-__missing__}" + case "$cmd" in + activate|deactivate) + __conda_activate "$@" + ;; + install|update|upgrade|remove|uninstall) + __conda_exe "$@" || \return + __conda_reactivate + ;; + *) + __conda_exe "$@" + ;; + esac +} + +if [ -z "${CONDA_SHLVL+x}" ]; then + \export CONDA_SHLVL=0 + # In dev-mode CONDA_EXE is python.exe and on Windows + # it is in a different relative location to condabin. + if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then + PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}" + else + PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}" + fi + \export PATH + + # We'\''re not allowing PS1 to be unbound. It must at least be set. + # However, we'\''re not exporting it, which can cause problems when starting a second shell + # via a first shell (i.e. starting zsh from bash). + if [ -z "${PS1+x}" ]; then + PS1= + fi +fi + +conda activate base' +++ '[' 0 -eq 0 ']' +++ eval 'export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'' + +# Copyright (C) 2012 Anaconda, Inc +# SPDX-License-Identifier: BSD-3-Clause +__conda_exe() ( + "$CONDA_EXE" $_CE_M $_CE_CONDA "$@" +) + +__conda_hashr() { + if [ -n "${ZSH_VERSION:+x}" ]; then + \rehash + elif [ -n "${POSH_VERSION:+x}" ]; then + : # pass + else + \hash -r + fi +} + +__conda_activate() { + if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then + # Handle transition from shell activated with conda <= 4.3 to a subsequent activation + # after conda updated to >= 4.4. See issue #6173. + PS1="$CONDA_PS1_BACKUP" + \unset CONDA_PS1_BACKUP + fi + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return + \eval "$ask_conda" + __conda_hashr +} + +__conda_reactivate() { + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return + \eval "$ask_conda" + __conda_hashr +} + +conda() { + \local cmd="${1-__missing__}" + case "$cmd" in + activate|deactivate) + __conda_activate "$@" + ;; + install|update|upgrade|remove|uninstall) + __conda_exe "$@" || \return + __conda_reactivate + ;; + *) + __conda_exe "$@" + ;; + esac +} + +if [ -z "${CONDA_SHLVL+x}" ]; then + \export CONDA_SHLVL=0 + # In dev-mode CONDA_EXE is python.exe and on Windows + # it is in a different relative location to condabin. + if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then + PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}" + else + PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}" + fi + \export PATH + + # We'\''re not allowing PS1 to be unbound. It must at least be set. + # However, we'\''re not exporting it, which can cause problems when starting a second shell + # via a first shell (i.e. starting zsh from bash). + if [ -z "${PS1+x}" ]; then + PS1= + fi +fi + +conda activate base' ++++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda ++++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda ++++ export _CE_M= ++++ _CE_M= ++++ export _CE_CONDA= ++++ _CE_CONDA= ++++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ '[' -z x ']' ++++ conda activate base ++++ local cmd=activate ++++ case "$cmd" in ++++ __conda_activate activate base ++++ '[' -n '' ']' ++++ local ask_conda +++++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++++ __conda_exe shell.posix activate base +++++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate base ++++ ask_conda='PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_SHLVL='\''6'\'' +export CONDA_DEFAULT_ENV='\''base'\'' +export CONDA_PROMPT_MODIFIER='\''(base) '\'' +export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' ++++ eval 'PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_SHLVL='\''6'\'' +export CONDA_DEFAULT_ENV='\''base'\'' +export CONDA_PROMPT_MODIFIER='\''(base) '\'' +export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' +++++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++++ export CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0 +++++ CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0 +++++ export CONDA_SHLVL=6 +++++ CONDA_SHLVL=6 +++++ export CONDA_DEFAULT_ENV=base +++++ CONDA_DEFAULT_ENV=base +++++ export 'CONDA_PROMPT_MODIFIER=(base) ' +++++ CONDA_PROMPT_MODIFIER='(base) ' +++++ export CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev +++++ CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev +++++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++++ export _CE_M= +++++ _CE_M= +++++ export _CE_CONDA= +++++ _CE_CONDA= +++++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python +++++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ __conda_hashr ++++ '[' -n '' ']' ++++ '[' -n '' ']' ++++ hash -r +++ unset __conda_setup ++ conda activate schemist-dev ++ local cmd=activate ++ case "$cmd" in ++ __conda_activate activate schemist-dev ++ '[' -n '' ']' ++ local ask_conda +++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++ __conda_exe shell.posix activate schemist-dev +++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate schemist-dev ++ ask_conda='PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_SHLVL='\''7'\'' +export CONDA_DEFAULT_ENV='\''schemist-dev'\'' +export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\'' +export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' ++ eval 'PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_SHLVL='\''7'\'' +export CONDA_DEFAULT_ENV='\''schemist-dev'\'' +export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\'' +export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' +++ PS1='(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++ export CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev +++ CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev +++ export CONDA_SHLVL=7 +++ CONDA_SHLVL=7 +++ export CONDA_DEFAULT_ENV=schemist-dev +++ CONDA_DEFAULT_ENV=schemist-dev +++ export 'CONDA_PROMPT_MODIFIER=(schemist-dev) ' +++ CONDA_PROMPT_MODIFIER='(schemist-dev) ' +++ export CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0 +++ CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0 +++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++ export _CE_M= +++ _CE_M= +++ export _CE_CONDA= +++ _CE_CONDA= +++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python +++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++ __conda_hashr ++ '[' -n '' ']' ++ '[' -n '' ']' ++ hash -r ++ CHUNK_HEAD_FILE=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz ++ INPUT=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/test/cyc-pep-6-12mer-70M_01.csv ++ COLUMN=cysteine_to_N_cyclization ++ PREFIX=cyclic_ ++ AWK='1 { print $8, $1, $2, $10, $3 }' ++ '[' -z cysteine_to_N_cyclization ']' ++ '[' -z cyclic_ ']' ++ '[' -z '1 { print $8, $1, $2, $10, $3 }' ']' ++ cat /dev/fd/63 /nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/test/cyc-pep-6-12mer-70M_01.csv ++ awk -F, -v OFS=, '1 { print $8, $1, $2, $10, $3 }' ++ schemist convert -f csv --column cysteine_to_N_cyclization --to id inchikey scaffold mwt clogp tpsa --prefix cyclic_ --options prefix=SCB- ++ gzip --best +++ zcat /nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz +++ head -n1 +++ tr ' ' , +🚀 Converting between string representations with the following parameters: + subcommand: convert + output: <_io.TextIOWrapper name='' mode='w' encoding='utf-8'> + format: csv + input: <_io.TextIOWrapper name='' mode='r' encoding='utf-8'> + representation: SMILES + column: cysteine_to_N_cyclization + prefix: cyclic_ + to: ['id', 'inchikey', 'scaffold', 'mwt', 'clogp', 'tpsa'] + options: ['prefix=SCB-'] + func: + 0it [00:00, ?it/s] 1it [00:10, 10.82s/it] 2it [00:21, 10.59s/it] 3it [00:31, 10.56s/it] 4it [00:42, 10.53s/it] 5it [00:52, 10.51s/it] 6it 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11.48s/it] 960it [2:54:05, 11.47s/it] 961it [2:54:17, 11.49s/it] 962it [2:54:28, 11.49s/it] 963it [2:54:40, 11.50s/it] 964it [2:54:51, 11.49s/it] 965it [2:55:03, 11.47s/it] 966it [2:55:14, 11.48s/it] 967it [2:55:26, 11.49s/it] 968it [2:55:37, 11.49s/it] 969it [2:55:49, 11.52s/it] 970it [2:56:00, 11.51s/it] 971it [2:56:12, 11.50s/it] 972it [2:56:24, 11.57s/it] 973it [2:56:35, 11.58s/it] 974it [2:56:47, 11.57s/it] 975it [2:56:58, 11.55s/it] 976it [2:57:10, 11.53s/it] 977it [2:57:21, 11.50s/it] 978it [2:57:33, 11.49s/it] 979it [2:57:44, 11.48s/it] 980it [2:57:56, 11.50s/it] 981it [2:58:07, 11.49s/it] 982it [2:58:18, 11.46s/it] 983it [2:58:30, 11.48s/it] 984it [2:58:41, 11.48s/it] 985it [2:58:53, 11.50s/it] 986it [2:59:05, 11.50s/it] 987it [2:59:16, 11.50s/it] 988it [2:59:27, 11.48s/it] 989it [2:59:39, 11.48s/it] 990it [2:59:50, 11.49s/it] 991it [3:00:02, 11.49s/it] 992it [3:00:13, 11.49s/it] 993it [3:00:25, 11.47s/it] 994it [3:00:36, 11.49s/it] 995it [3:00:48, 11.49s/it] 996it [3:00:59, 11.49s/it] 997it [3:01:11, 11.49s/it] 998it [3:01:22, 11.50s/it] 999it [3:01:34, 11.49s/it] 1000it [3:01:45, 11.47s/it] 1000it [3:01:45, 10.91s/it] +Error counts: + cyclic_id: 0 + cyclic_inchikey: 0 + cyclic_scaffold: 0 + cyclic_mwt: 0 + cyclic_clogp: 0 + cyclic_tpsa: 0 +⏰ Completed process in 3:02:08.685108 ++ rm /nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/test/cyc-pep-6-12mer-70M_01.csv diff --git a/test/cyc-pep-6-12mer-70M_02.csv.gz b/test/cyc-pep-6-12mer-70M_02.csv.gz index 7cc0020bae3029771aa2ba89a1f7b4e75be347c6..aa8358e7dd8af78a850a511641b0fcc8207a423b 100644 --- a/test/cyc-pep-6-12mer-70M_02.csv.gz +++ b/test/cyc-pep-6-12mer-70M_02.csv.gz @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:6c5b61e10bdb3ce612dd195915920ef8391fedfda64089de9ad9f9f77f907c91 -size 61923971 +oid sha256:ab0474546e2ae83ec9107e251098b84a471047d033f4e7e958531f54c267415d +size 117618606 diff --git a/test/cyc-pep-6-12mer-70M_02.log b/test/cyc-pep-6-12mer-70M_02.log new file mode 100644 index 0000000000000000000000000000000000000000..74f66673f5476b0a39d42905b8d8dd9e5b06d4df --- /dev/null +++ b/test/cyc-pep-6-12mer-70M_02.log @@ -0,0 +1,337 @@ ++ module purge ++ '[' -z '' ']' ++ case "$-" in ++ __lmod_sh_dbg=x ++ '[' -n x ']' ++ set +x +Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output +Shell debugging restarted ++ unset __lmod_sh_dbg ++ return 0 ++ module load Anaconda3/2023.03 ++ '[' -z '' ']' ++ case "$-" in ++ __lmod_sh_dbg=x ++ '[' -n x ']' ++ set +x +Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output +Shell debugging restarted ++ unset __lmod_sh_dbg ++ return 0 ++ source /camp/home/johnsoe/.bashrc +++ '[' '' = yes ']' +++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' ++++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.bash hook +++ __conda_setup='export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'' + +# Copyright (C) 2012 Anaconda, Inc +# SPDX-License-Identifier: BSD-3-Clause +__conda_exe() ( + "$CONDA_EXE" $_CE_M $_CE_CONDA "$@" +) + +__conda_hashr() { + if [ -n "${ZSH_VERSION:+x}" ]; then + \rehash + elif [ -n "${POSH_VERSION:+x}" ]; then + : # pass + else + \hash -r + fi +} + +__conda_activate() { + if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then + # Handle transition from shell activated with conda <= 4.3 to a subsequent activation + # after conda updated to >= 4.4. See issue #6173. + PS1="$CONDA_PS1_BACKUP" + \unset CONDA_PS1_BACKUP + fi + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return + \eval "$ask_conda" + __conda_hashr +} + +__conda_reactivate() { + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return + \eval "$ask_conda" + __conda_hashr +} + +conda() { + \local cmd="${1-__missing__}" + case "$cmd" in + activate|deactivate) + __conda_activate "$@" + ;; + install|update|upgrade|remove|uninstall) + __conda_exe "$@" || \return + __conda_reactivate + ;; + *) + __conda_exe "$@" + ;; + esac +} + +if [ -z "${CONDA_SHLVL+x}" ]; then + \export CONDA_SHLVL=0 + # In dev-mode CONDA_EXE is python.exe and on Windows + # it is in a different relative location to condabin. + if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then + PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}" + else + PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}" + fi + \export PATH + + # We'\''re not allowing PS1 to be unbound. It must at least be set. + # However, we'\''re not exporting it, which can cause problems when starting a second shell + # via a first shell (i.e. starting zsh from bash). + if [ -z "${PS1+x}" ]; then + PS1= + fi +fi + +conda activate base' +++ '[' 0 -eq 0 ']' +++ eval 'export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'' + +# Copyright (C) 2012 Anaconda, Inc +# SPDX-License-Identifier: BSD-3-Clause +__conda_exe() ( + "$CONDA_EXE" $_CE_M $_CE_CONDA "$@" +) + +__conda_hashr() { + if [ -n "${ZSH_VERSION:+x}" ]; then + \rehash + elif [ -n "${POSH_VERSION:+x}" ]; then + : # pass + else + \hash -r + fi +} + +__conda_activate() { + if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then + # Handle transition from shell activated with conda <= 4.3 to a subsequent activation + # after conda updated to >= 4.4. See issue #6173. + PS1="$CONDA_PS1_BACKUP" + \unset CONDA_PS1_BACKUP + fi + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return + \eval "$ask_conda" + __conda_hashr +} + +__conda_reactivate() { + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return + \eval "$ask_conda" + __conda_hashr +} + +conda() { + \local cmd="${1-__missing__}" + case "$cmd" in + activate|deactivate) + __conda_activate "$@" + ;; + install|update|upgrade|remove|uninstall) + __conda_exe "$@" || \return + __conda_reactivate + ;; + *) + __conda_exe "$@" + ;; + esac +} + +if [ -z "${CONDA_SHLVL+x}" ]; then + \export CONDA_SHLVL=0 + # In dev-mode CONDA_EXE is python.exe and on Windows + # it is in a different relative location to condabin. + if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then + PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}" + else + PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}" + fi + \export PATH + + # We'\''re not allowing PS1 to be unbound. It must at least be set. + # However, we'\''re not exporting it, which can cause problems when starting a second shell + # via a first shell (i.e. starting zsh from bash). + if [ -z "${PS1+x}" ]; then + PS1= + fi +fi + +conda activate base' ++++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda ++++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda ++++ export _CE_M= ++++ _CE_M= ++++ export _CE_CONDA= ++++ _CE_CONDA= ++++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ '[' -z x ']' ++++ conda activate base ++++ local cmd=activate ++++ case "$cmd" in ++++ __conda_activate activate base ++++ '[' -n '' ']' ++++ local ask_conda +++++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++++ __conda_exe shell.posix activate base +++++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate base ++++ ask_conda='PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_SHLVL='\''6'\'' +export CONDA_DEFAULT_ENV='\''base'\'' +export CONDA_PROMPT_MODIFIER='\''(base) '\'' +export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' ++++ eval 'PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_SHLVL='\''6'\'' +export CONDA_DEFAULT_ENV='\''base'\'' +export CONDA_PROMPT_MODIFIER='\''(base) '\'' +export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' +++++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++++ export CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0 +++++ CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0 +++++ export CONDA_SHLVL=6 +++++ CONDA_SHLVL=6 +++++ export CONDA_DEFAULT_ENV=base +++++ CONDA_DEFAULT_ENV=base +++++ export 'CONDA_PROMPT_MODIFIER=(base) ' +++++ CONDA_PROMPT_MODIFIER='(base) ' +++++ export CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev +++++ CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev +++++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++++ export _CE_M= +++++ _CE_M= +++++ export _CE_CONDA= +++++ _CE_CONDA= +++++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python +++++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ __conda_hashr ++++ '[' -n '' ']' ++++ '[' -n '' ']' ++++ hash -r +++ unset __conda_setup ++ conda activate schemist-dev ++ local cmd=activate ++ case "$cmd" in ++ __conda_activate activate schemist-dev ++ '[' -n '' ']' ++ local ask_conda +++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++ __conda_exe shell.posix activate schemist-dev +++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate schemist-dev ++ ask_conda='PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_SHLVL='\''7'\'' +export CONDA_DEFAULT_ENV='\''schemist-dev'\'' +export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\'' +export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' ++ eval 'PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_SHLVL='\''7'\'' +export CONDA_DEFAULT_ENV='\''schemist-dev'\'' +export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\'' +export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' +++ PS1='(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++ export CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev +++ CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev +++ export CONDA_SHLVL=7 +++ CONDA_SHLVL=7 +++ export CONDA_DEFAULT_ENV=schemist-dev +++ CONDA_DEFAULT_ENV=schemist-dev +++ export 'CONDA_PROMPT_MODIFIER=(schemist-dev) ' +++ CONDA_PROMPT_MODIFIER='(schemist-dev) ' +++ export CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0 +++ CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0 +++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++ export _CE_M= +++ _CE_M= +++ export _CE_CONDA= +++ _CE_CONDA= +++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python +++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++ __conda_hashr ++ '[' -n '' ']' ++ '[' -n '' ']' ++ hash -r ++ CHUNK_HEAD_FILE=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz ++ INPUT=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/test/cyc-pep-6-12mer-70M_02.csv ++ COLUMN=cysteine_to_N_cyclization ++ PREFIX=cyclic_ ++ AWK='1 { print $8, $1, $2, $10, $3 }' ++ '[' -z cysteine_to_N_cyclization ']' ++ '[' -z cyclic_ ']' ++ '[' -z '1 { print $8, $1, $2, $10, $3 }' ']' ++ awk -F, -v OFS=, '1 { print $8, $1, $2, $10, $3 }' ++ cat /dev/fd/63 /nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/test/cyc-pep-6-12mer-70M_02.csv +++ zcat /nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz ++ gzip --best ++ schemist convert -f csv --column cysteine_to_N_cyclization --to id inchikey scaffold mwt clogp tpsa --prefix cyclic_ --options prefix=SCB- +++ head -n1 +++ tr ' ' , +🚀 Converting between string representations with the following parameters: + subcommand: convert + output: <_io.TextIOWrapper name='' mode='w' encoding='utf-8'> + format: csv + input: <_io.TextIOWrapper name='' mode='r' encoding='utf-8'> + representation: SMILES + column: cysteine_to_N_cyclization + prefix: cyclic_ + to: ['id', 'inchikey', 'scaffold', 'mwt', 'clogp', 'tpsa'] + options: ['prefix=SCB-'] + func: + 0it [00:00, ?it/s] 1it [00:12, 12.29s/it] 2it [00:23, 11.92s/it] 3it [00:35, 11.88s/it] 4it [00:47, 11.99s/it] 5it [01:00, 12.08s/it] 6it [01:12, 12.15s/it] 7it [01:24, 12.17s/it] 8it [01:36, 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[3:07:40, 11.64s/it] 919it [3:07:52, 11.64s/it] 920it [3:08:04, 11.63s/it] 921it [3:08:15, 11.65s/it] 922it [3:08:27, 11.62s/it] 923it [3:08:38, 11.61s/it] 924it [3:08:50, 11.61s/it] 925it [3:09:02, 11.62s/it] 926it [3:09:13, 11.62s/it] 927it [3:09:25, 11.61s/it] 928it [3:09:37, 11.62s/it] 929it [3:09:48, 11.65s/it] 930it [3:10:00, 11.65s/it] 931it [3:10:12, 11.68s/it] 932it [3:10:23, 11.69s/it] 933it [3:10:35, 11.67s/it] 934it [3:10:47, 11.68s/it] 935it [3:10:58, 11.68s/it] 936it [3:11:10, 11.67s/it] 937it [3:11:22, 11.67s/it] 938it [3:11:33, 11.68s/it] 939it [3:11:45, 11.69s/it] 940it [3:11:57, 11.69s/it] 941it [3:12:09, 11.71s/it] 942it [3:12:20, 11.70s/it] 943it [3:12:32, 11.69s/it] 944it [3:12:44, 11.68s/it] 945it [3:12:55, 11.69s/it] 946it [3:13:07, 11.68s/it] 947it [3:13:19, 11.70s/it] 948it [3:13:30, 11.70s/it] 949it [3:13:42, 11.70s/it] 950it [3:13:54, 11.71s/it] 951it [3:14:05, 11.69s/it] 952it [3:14:17, 11.69s/it] 953it [3:14:29, 11.71s/it] 954it [3:14:41, 11.71s/it] 955it [3:14:53, 11.78s/it] 956it [3:15:05, 11.91s/it] 957it [3:15:17, 11.99s/it] 958it [3:15:29, 12.05s/it] 959it [3:15:41, 12.08s/it] 960it [3:15:54, 12.12s/it] 961it [3:16:06, 12.12s/it] 962it [3:16:18, 12.13s/it] 963it [3:16:30, 12.15s/it] 964it [3:16:43, 12.30s/it] 965it [3:16:55, 12.35s/it] 966it [3:17:08, 12.42s/it] 967it [3:17:20, 12.35s/it] 968it [3:17:32, 12.36s/it] 969it [3:17:45, 12.38s/it] 970it [3:17:57, 12.34s/it] 971it [3:18:09, 12.18s/it] 972it [3:18:21, 12.14s/it] 973it [3:18:33, 12.05s/it] 974it [3:18:44, 11.97s/it] 975it [3:18:56, 11.90s/it] 976it [3:19:08, 11.83s/it] 977it [3:19:20, 11.80s/it] 978it [3:19:31, 11.81s/it] 979it [3:19:43, 11.79s/it] 980it [3:19:55, 11.78s/it] 981it [3:20:07, 11.76s/it] 982it [3:20:18, 11.75s/it] 983it [3:20:30, 11.76s/it] 984it [3:20:42, 11.76s/it] 985it [3:20:54, 11.75s/it] 986it [3:21:05, 11.76s/it] 987it [3:21:17, 11.75s/it] 988it [3:21:29, 11.77s/it] 989it [3:21:41, 11.74s/it] 990it [3:21:52, 11.73s/it] 991it [3:22:04, 11.74s/it] 992it [3:22:16, 11.72s/it] 993it [3:22:27, 11.71s/it] 994it [3:22:39, 11.66s/it] 995it [3:22:51, 11.64s/it] 996it [3:23:02, 11.67s/it] 997it [3:23:14, 11.65s/it] 998it [3:23:26, 11.66s/it] 999it [3:23:37, 11.67s/it] 1000it [3:23:49, 11.67s/it] 1000it [3:23:49, 12.23s/it] +Error counts: + cyclic_id: 0 + cyclic_inchikey: 0 + cyclic_scaffold: 0 + cyclic_mwt: 0 + cyclic_clogp: 0 + cyclic_tpsa: 0 +⏰ Completed process in 3:24:16.673804 ++ rm /nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/test/cyc-pep-6-12mer-70M_02.csv diff --git a/test/cyc-pep-6-12mer-70M_03.csv.gz b/test/cyc-pep-6-12mer-70M_03.csv.gz index de1585357830c61937f16348ee5a7f3f7e260b64..a324a16229f8fe8ad9d28f648e16e5538a16756a 100644 --- a/test/cyc-pep-6-12mer-70M_03.csv.gz +++ b/test/cyc-pep-6-12mer-70M_03.csv.gz @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:758cea96c5ad60d9a8f1a1958832c52d54839f5070c9d67fcac290b3ab63fd72 -size 64582471 +oid sha256:9a998db31deff36153cb620395dc97628d3c7d6b7c5ffed9fdc4482ca9e797df +size 121096790 diff --git a/test/cyc-pep-6-12mer-70M_03.log b/test/cyc-pep-6-12mer-70M_03.log new file mode 100644 index 0000000000000000000000000000000000000000..385ce23195d68e9f435fef79c3e65e56da393c83 --- /dev/null +++ b/test/cyc-pep-6-12mer-70M_03.log @@ -0,0 +1,337 @@ ++ module purge ++ '[' -z '' ']' ++ case "$-" in ++ __lmod_sh_dbg=x ++ '[' -n x ']' ++ set +x +Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output +Shell debugging restarted ++ unset __lmod_sh_dbg ++ return 0 ++ module load Anaconda3/2023.03 ++ '[' -z '' ']' ++ case "$-" in ++ __lmod_sh_dbg=x ++ '[' -n x ']' ++ set +x +Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output +Shell debugging restarted ++ unset __lmod_sh_dbg ++ return 0 ++ source /camp/home/johnsoe/.bashrc +++ '[' '' = yes ']' +++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' ++++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.bash hook +++ __conda_setup='export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'' + +# Copyright (C) 2012 Anaconda, Inc +# SPDX-License-Identifier: BSD-3-Clause +__conda_exe() ( + "$CONDA_EXE" $_CE_M $_CE_CONDA "$@" +) + +__conda_hashr() { + if [ -n "${ZSH_VERSION:+x}" ]; then + \rehash + elif [ -n "${POSH_VERSION:+x}" ]; then + : # pass + else + \hash -r + fi +} + +__conda_activate() { + if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then + # Handle transition from shell activated with conda <= 4.3 to a subsequent activation + # after conda updated to >= 4.4. See issue #6173. + PS1="$CONDA_PS1_BACKUP" + \unset CONDA_PS1_BACKUP + fi + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return + \eval "$ask_conda" + __conda_hashr +} + +__conda_reactivate() { + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return + \eval "$ask_conda" + __conda_hashr +} + +conda() { + \local cmd="${1-__missing__}" + case "$cmd" in + activate|deactivate) + __conda_activate "$@" + ;; + install|update|upgrade|remove|uninstall) + __conda_exe "$@" || \return + __conda_reactivate + ;; + *) + __conda_exe "$@" + ;; + esac +} + +if [ -z "${CONDA_SHLVL+x}" ]; then + \export CONDA_SHLVL=0 + # In dev-mode CONDA_EXE is python.exe and on Windows + # it is in a different relative location to condabin. + if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then + PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}" + else + PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}" + fi + \export PATH + + # We'\''re not allowing PS1 to be unbound. It must at least be set. + # However, we'\''re not exporting it, which can cause problems when starting a second shell + # via a first shell (i.e. starting zsh from bash). + if [ -z "${PS1+x}" ]; then + PS1= + fi +fi + +conda activate base' +++ '[' 0 -eq 0 ']' +++ eval 'export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'' + +# Copyright (C) 2012 Anaconda, Inc +# SPDX-License-Identifier: BSD-3-Clause +__conda_exe() ( + "$CONDA_EXE" $_CE_M $_CE_CONDA "$@" +) + +__conda_hashr() { + if [ -n "${ZSH_VERSION:+x}" ]; then + \rehash + elif [ -n "${POSH_VERSION:+x}" ]; then + : # pass + else + \hash -r + fi +} + +__conda_activate() { + if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then + # Handle transition from shell activated with conda <= 4.3 to a subsequent activation + # after conda updated to >= 4.4. See issue #6173. + PS1="$CONDA_PS1_BACKUP" + \unset CONDA_PS1_BACKUP + fi + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return + \eval "$ask_conda" + __conda_hashr +} + +__conda_reactivate() { + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return + \eval "$ask_conda" + __conda_hashr +} + +conda() { + \local cmd="${1-__missing__}" + case "$cmd" in + activate|deactivate) + __conda_activate "$@" + ;; + install|update|upgrade|remove|uninstall) + __conda_exe "$@" || \return + __conda_reactivate + ;; + *) + __conda_exe "$@" + ;; + esac +} + +if [ -z "${CONDA_SHLVL+x}" ]; then + \export CONDA_SHLVL=0 + # In dev-mode CONDA_EXE is python.exe and on Windows + # it is in a different relative location to condabin. + if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then + PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}" + else + PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}" + fi + \export PATH + + # We'\''re not allowing PS1 to be unbound. It must at least be set. + # However, we'\''re not exporting it, which can cause problems when starting a second shell + # via a first shell (i.e. starting zsh from bash). + if [ -z "${PS1+x}" ]; then + PS1= + fi +fi + +conda activate base' ++++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda ++++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda ++++ export _CE_M= ++++ _CE_M= ++++ export _CE_CONDA= ++++ _CE_CONDA= ++++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ '[' -z x ']' ++++ conda activate base ++++ local cmd=activate ++++ case "$cmd" in ++++ __conda_activate activate base ++++ '[' -n '' ']' ++++ local ask_conda +++++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++++ __conda_exe shell.posix activate base +++++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate base ++++ ask_conda='PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_SHLVL='\''6'\'' +export CONDA_DEFAULT_ENV='\''base'\'' +export CONDA_PROMPT_MODIFIER='\''(base) '\'' +export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' ++++ eval 'PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_SHLVL='\''6'\'' +export CONDA_DEFAULT_ENV='\''base'\'' +export CONDA_PROMPT_MODIFIER='\''(base) '\'' +export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' +++++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++++ export CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0 +++++ CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0 +++++ export CONDA_SHLVL=6 +++++ CONDA_SHLVL=6 +++++ export CONDA_DEFAULT_ENV=base +++++ CONDA_DEFAULT_ENV=base +++++ export 'CONDA_PROMPT_MODIFIER=(base) ' +++++ CONDA_PROMPT_MODIFIER='(base) ' +++++ export CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev +++++ CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev +++++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++++ export _CE_M= +++++ _CE_M= +++++ export _CE_CONDA= +++++ _CE_CONDA= +++++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python +++++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ __conda_hashr ++++ '[' -n '' ']' ++++ '[' -n '' ']' ++++ hash -r +++ unset __conda_setup ++ conda activate schemist-dev ++ local cmd=activate ++ case "$cmd" in ++ __conda_activate activate schemist-dev ++ '[' -n '' ']' ++ local ask_conda +++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++ __conda_exe shell.posix activate schemist-dev +++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate schemist-dev ++ ask_conda='PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_SHLVL='\''7'\'' +export CONDA_DEFAULT_ENV='\''schemist-dev'\'' +export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\'' +export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' ++ eval 'PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_SHLVL='\''7'\'' +export CONDA_DEFAULT_ENV='\''schemist-dev'\'' +export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\'' +export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' +++ PS1='(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++ export CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev +++ CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev +++ export CONDA_SHLVL=7 +++ CONDA_SHLVL=7 +++ export CONDA_DEFAULT_ENV=schemist-dev +++ CONDA_DEFAULT_ENV=schemist-dev +++ export 'CONDA_PROMPT_MODIFIER=(schemist-dev) ' +++ CONDA_PROMPT_MODIFIER='(schemist-dev) ' +++ export CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0 +++ CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0 +++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++ export _CE_M= +++ _CE_M= +++ export _CE_CONDA= +++ _CE_CONDA= +++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python +++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++ __conda_hashr ++ '[' -n '' ']' ++ '[' -n '' ']' ++ hash -r ++ CHUNK_HEAD_FILE=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz ++ INPUT=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/test/cyc-pep-6-12mer-70M_03.csv ++ COLUMN=cysteine_to_N_cyclization ++ PREFIX=cyclic_ ++ AWK='1 { print $8, $1, $2, $10, $3 }' ++ '[' -z cysteine_to_N_cyclization ']' ++ '[' -z cyclic_ ']' ++ '[' -z '1 { print $8, $1, $2, $10, $3 }' ']' ++ awk -F, -v OFS=, '1 { print $8, $1, $2, $10, $3 }' ++ cat /dev/fd/63 /nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/test/cyc-pep-6-12mer-70M_03.csv ++ gzip --best ++ schemist convert -f csv --column cysteine_to_N_cyclization --to id inchikey scaffold mwt clogp tpsa --prefix cyclic_ --options prefix=SCB- +++ zcat /nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz +++ head -n1 +++ tr ' ' , +🚀 Converting between string representations with the following parameters: + subcommand: convert + output: <_io.TextIOWrapper name='' mode='w' encoding='utf-8'> + format: csv + input: <_io.TextIOWrapper name='' mode='r' encoding='utf-8'> + representation: SMILES + column: cysteine_to_N_cyclization + prefix: cyclic_ + to: ['id', 'inchikey', 'scaffold', 'mwt', 'clogp', 'tpsa'] + options: ['prefix=SCB-'] + func: + 0it [00:00, ?it/s] 1it [00:12, 12.18s/it] 2it [00:23, 11.91s/it] 3it [00:35, 11.90s/it] 4it [00:47, 12.00s/it] 5it [01:00, 12.14s/it] 6it [01:12, 12.19s/it] 7it [01:24, 12.21s/it] 8it [01:37, 12.23s/it] 9it [01:49, 12.24s/it] 10it [02:01, 12.27s/it] 11it [02:13, 12.19s/it] 12it [02:25, 12.20s/it] 13it [02:38, 12.21s/it] 14it [02:50, 12.23s/it] 15it [03:02, 12.20s/it] 16it [03:14, 12.21s/it] 17it [03:27, 12.19s/it] 18it [03:39, 12.19s/it] 19it [03:51, 12.20s/it] 20it [04:03, 12.16s/it] 21it [04:15, 12.11s/it] 22it [04:27, 12.09s/it] 23it [04:39, 12.12s/it] 24it [04:51, 12.11s/it] 25it [05:04, 12.14s/it] 26it [05:16, 12.14s/it] 27it [05:28, 12.08s/it] 28it [05:40, 12.06s/it] 29it [05:52, 12.02s/it] 30it [06:04, 12.07s/it] 31it [06:16, 12.05s/it] 32it [06:28, 12.06s/it] 33it [06:40, 12.04s/it] 34it [06:52, 12.07s/it] 35it [07:04, 12.10s/it] 36it [07:16, 12.07s/it] 37it [07:28, 12.04s/it] 38it [07:40, 12.06s/it] 39it [07:52, 12.02s/it] 40it [08:04, 12.02s/it] 41it [08:16, 12.04s/it] 42it [08:28, 12.06s/it] 43it [08:40, 12.04s/it] 44it [08:52, 12.03s/it] 45it [09:04, 12.05s/it] 46it [09:16, 12.05s/it] 47it [09:28, 12.01s/it] 48it [09:40, 12.03s/it] 49it [09:52, 12.03s/it] 50it [10:05, 12.04s/it] 51it [10:16, 12.01s/it] 52it [10:29, 12.02s/it] 53it [10:41, 12.00s/it] 54it [10:53, 12.00s/it] 55it [11:05, 12.04s/it] 56it [11:17, 12.03s/it] 57it [11:29, 12.03s/it] 58it [11:41, 12.09s/it] 59it [11:53, 12.11s/it] 60it [12:05, 12.12s/it] 61it [12:17, 12.12s/it] 62it [12:29, 12.08s/it] 63it [12:41, 12.07s/it] 64it [12:53, 12.08s/it] 65it [13:06, 12.09s/it] 66it [13:18, 12.10s/it] 67it [13:30, 12.11s/it] 68it [13:42, 12.10s/it] 69it [13:54, 12.07s/it] 70it [14:06, 12.07s/it] 71it [14:18, 12.09s/it] 72it [14:30, 12.06s/it] 73it [14:42, 12.09s/it] 74it [14:54, 12.09s/it] 75it [15:06, 12.07s/it] 76it [15:18, 12.07s/it] 77it [15:30, 12.06s/it] 78it [15:43, 12.08s/it] 79it [15:55, 12.09s/it] 80it [16:07, 12.04s/it] 81it [16:19, 12.08s/it] 82it [16:31, 12.11s/it] 83it [16:44, 12.24s/it] 84it [16:56, 12.18s/it] 85it [17:08, 12.15s/it] 86it [17:20, 12.11s/it] 87it [17:32, 12.07s/it] 88it [17:44, 12.07s/it] 89it [17:56, 12.05s/it] 90it [18:08, 12.09s/it] 91it [18:20, 12.12s/it] 92it [18:32, 12.05s/it] 93it [18:44, 12.06s/it] 94it [18:56, 12.14s/it] 95it [19:08, 12.09s/it] 96it [19:20, 12.05s/it] 97it [19:32, 12.06s/it] 98it [19:44, 12.02s/it] 99it [19:57, 12.17s/it] 100it [20:10, 12.33s/it] 101it [20:22, 12.46s/it] 102it [20:35, 12.64s/it] 103it [20:49, 12.81s/it] 104it [21:02, 12.88s/it] 105it [21:15, 12.92s/it] 106it [21:28, 12.98s/it] 107it [21:42, 13.24s/it] 108it [21:55, 13.24s/it] 109it [22:08, 13.25s/it] 110it [22:21, 13.24s/it] 111it [22:36, 13.70s/it] 112it [22:53, 14.79s/it] 113it [23:11, 15.54s/it] 114it [23:27, 15.85s/it] 115it [23:45, 16.25s/it] 116it [24:00, 16.13s/it] 117it [24:17, 16.14s/it] 118it [24:34, 16.42s/it] 119it [24:50, 16.34s/it] 120it [25:06, 16.33s/it] 121it [25:22, 16.27s/it] 122it [25:38, 16.23s/it] 123it [25:55, 16.32s/it] 124it [26:13, 16.78s/it] 125it [26:31, 17.38s/it] 126it [26:51, 17.99s/it] 127it [27:11, 18.76s/it] 128it [27:33, 19.51s/it] 129it [27:53, 19.87s/it] 130it [28:14, 19.95s/it] 131it [28:36, 20.60s/it] 132it [28:57, 20.76s/it] 133it [29:16, 20.34s/it] 134it [29:36, 20.28s/it] 135it [29:57, 20.33s/it] 136it [30:17, 20.25s/it] 137it [30:37, 20.29s/it] 138it [30:58, 20.30s/it] 139it [31:18, 20.30s/it] 140it [31:38, 20.36s/it] 141it [31:58, 20.26s/it] 142it [32:19, 20.48s/it] 143it [32:39, 20.21s/it] 144it [32:59, 20.02s/it] 145it [33:18, 19.78s/it] 146it [33:37, 19.53s/it] 147it [33:55, 19.26s/it] 148it [34:14, 19.05s/it] 149it [34:33, 19.12s/it] 150it [34:52, 19.18s/it] 151it [35:11, 18.99s/it] 152it [35:29, 18.66s/it] 153it [35:47, 18.41s/it] 154it [36:04, 18.13s/it] 155it [36:21, 17.75s/it] 156it [36:37, 17.30s/it] 157it [36:53, 16.67s/it] 158it [37:09, 16.58s/it] 159it [37:25, 16.47s/it] 160it [37:40, 16.01s/it] 161it [37:55, 15.78s/it] 162it [38:10, 15.60s/it] 163it [38:26, 15.64s/it] 164it [38:42, 15.57s/it] 165it [38:56, 15.27s/it] 166it [39:10, 14.87s/it] 167it [39:24, 14.59s/it] 168it [39:38, 14.33s/it] 169it [39:52, 14.41s/it] 170it [40:07, 14.48s/it] 171it [40:22, 14.55s/it] 172it [40:36, 14.52s/it] 173it [40:50, 14.29s/it] 174it [41:05, 14.65s/it] 175it [41:20, 14.55s/it] 176it [41:34, 14.56s/it] 177it [41:48, 14.25s/it] 178it [42:02, 14.11s/it] 179it [42:16, 14.10s/it] 180it [42:30, 14.14s/it] 181it [42:44, 14.18s/it] 182it [42:59, 14.24s/it] 183it [43:13, 14.31s/it] 184it [43:28, 14.52s/it] 185it [43:44, 14.95s/it] 186it [44:00, 15.11s/it] 187it [44:15, 15.15s/it] 188it [44:30, 15.06s/it] 189it [44:44, 14.88s/it] 190it [44:58, 14.57s/it] 191it [45:13, 14.73s/it] 192it [45:27, 14.56s/it] 193it [45:42, 14.52s/it] 194it [45:56, 14.54s/it] 195it [46:11, 14.66s/it] 196it [46:25, 14.55s/it] 197it [46:40, 14.60s/it] 198it [46:56, 14.90s/it] 199it [47:10, 14.62s/it] 200it [47:24, 14.52s/it] 201it [47:38, 14.35s/it] 202it [47:52, 14.30s/it] 203it [48:07, 14.34s/it] 204it [48:20, 14.18s/it] 205it [48:34, 14.10s/it] 206it [48:48, 14.07s/it] 207it [49:02, 13.94s/it] 208it [49:15, 13.65s/it] 209it [49:28, 13.45s/it] 210it [49:41, 13.29s/it] 211it [49:54, 13.15s/it] 212it [50:07, 13.07s/it] 213it [50:20, 13.29s/it] 214it [50:34, 13.36s/it] 215it [50:47, 13.45s/it] 216it [51:01, 13.50s/it] 217it [51:15, 13.53s/it] 218it [51:28, 13.52s/it] 219it [51:42, 13.58s/it] 220it [51:55, 13.49s/it] 221it [52:09, 13.57s/it] 222it [52:22, 13.47s/it] 223it [52:35, 13.34s/it] 224it [52:48, 13.25s/it] 225it [53:01, 13.14s/it] 226it [53:14, 12.99s/it] 227it [53:27, 12.93s/it] 228it [53:40, 12.93s/it] 229it [53:52, 12.86s/it] 230it [54:05, 12.82s/it] 231it [54:18, 12.80s/it] 232it [54:30, 12.75s/it] 233it [54:43, 12.71s/it] 234it [54:55, 12.53s/it] 235it [55:07, 12.33s/it] 236it [55:19, 12.22s/it] 237it [55:31, 12.14s/it] 238it [55:43, 12.09s/it] 239it [55:55, 12.06s/it] 240it [56:07, 12.04s/it] 241it [56:19, 12.04s/it] 242it [56:31, 12.06s/it] 243it [56:43, 12.01s/it] 244it [56:55, 11.96s/it] 245it [57:06, 11.91s/it] 246it [57:18, 11.92s/it] 247it [57:30, 11.90s/it] 248it [57:43, 12.30s/it] 249it [57:55, 12.19s/it] 250it [58:07, 12.09s/it] 251it [58:19, 12.05s/it] 252it [58:31, 12.01s/it] 253it [58:43, 11.97s/it] 254it [58:55, 11.95s/it] 255it [59:07, 11.93s/it] 256it [59:19, 11.88s/it] 257it [59:30, 11.85s/it] 258it [59:42, 11.84s/it] 259it [59:54, 11.77s/it] 260it [1:00:06, 11.81s/it] 261it [1:00:17, 11.81s/it] 262it [1:00:29, 11.80s/it] 263it [1:00:41, 11.92s/it] 264it [1:00:53, 11.91s/it] 265it [1:01:05, 11.89s/it] 266it [1:01:17, 11.86s/it] 267it [1:01:29, 11.81s/it] 268it [1:01:41, 11.86s/it] 269it [1:01:52, 11.81s/it] 270it [1:02:04, 11.79s/it] 271it [1:02:16, 11.76s/it] 272it [1:02:28, 11.75s/it] 273it [1:02:39, 11.74s/it] 274it [1:02:51, 11.72s/it] 275it [1:03:03, 11.72s/it] 276it [1:03:14, 11.71s/it] 277it [1:03:26, 11.72s/it] 278it [1:03:38, 11.70s/it] 279it [1:03:49, 11.72s/it] 280it [1:04:01, 11.72s/it] 281it [1:04:14, 12.04s/it] 282it [1:04:27, 12.27s/it] 283it [1:04:40, 12.42s/it] 284it [1:04:52, 12.53s/it] 285it [1:05:05, 12.59s/it] 286it [1:05:18, 12.67s/it] 287it [1:05:31, 12.72s/it] 288it [1:05:44, 12.74s/it] 289it [1:05:56, 12.74s/it] 290it [1:06:09, 12.75s/it] 291it [1:06:22, 12.74s/it] 292it [1:06:34, 12.73s/it] 293it [1:06:47, 12.76s/it] 294it [1:07:00, 12.78s/it] 295it [1:07:13, 12.78s/it] 296it [1:07:26, 12.76s/it] 297it [1:07:38, 12.75s/it] 298it [1:07:51, 12.75s/it] 299it [1:08:04, 12.75s/it] 300it [1:08:17, 12.72s/it] 301it [1:08:29, 12.74s/it] 302it [1:08:42, 12.73s/it] 303it [1:08:55, 12.71s/it] 304it [1:09:08, 12.76s/it] 305it [1:09:20, 12.76s/it] 306it [1:09:33, 12.75s/it] 307it [1:09:46, 12.76s/it] 308it [1:09:59, 12.77s/it] 309it [1:10:11, 12.77s/it] 310it [1:10:24, 12.77s/it] 311it [1:10:37, 12.78s/it] 312it [1:10:50, 12.79s/it] 313it [1:11:03, 12.78s/it] 314it [1:11:15, 12.76s/it] 315it [1:11:28, 12.74s/it] 316it [1:11:41, 12.75s/it] 317it [1:11:53, 12.76s/it] 318it [1:12:06, 12.74s/it] 319it [1:12:19, 12.76s/it] 320it [1:12:32, 12.75s/it] 321it [1:12:45, 12.77s/it] 322it [1:12:57, 12.75s/it] 323it [1:13:10, 12.76s/it] 324it [1:13:23, 12.75s/it] 325it [1:13:35, 12.72s/it] 326it [1:13:48, 12.72s/it] 327it [1:14:01, 12.71s/it] 328it [1:14:14, 12.71s/it] 329it [1:14:26, 12.70s/it] 330it [1:14:39, 12.70s/it] 331it [1:14:52, 12.71s/it] 332it [1:15:04, 12.70s/it] 333it [1:15:17, 12.72s/it] 334it [1:15:30, 12.72s/it] 335it [1:15:43, 12.74s/it] 336it [1:15:55, 12.75s/it] 337it [1:16:08, 12.72s/it] 338it [1:16:21, 12.69s/it] 339it [1:16:33, 12.69s/it] 340it [1:16:46, 12.69s/it] 341it [1:16:59, 12.68s/it] 342it [1:17:11, 12.68s/it] 343it [1:17:24, 12.67s/it] 344it [1:17:37, 12.70s/it] 345it [1:17:49, 12.69s/it] 346it [1:18:02, 12.69s/it] 347it [1:18:15, 12.70s/it] 348it [1:18:27, 12.69s/it] 349it [1:18:40, 12.69s/it] 350it [1:18:53, 12.68s/it] 351it [1:19:06, 12.70s/it] 352it [1:19:18, 12.72s/it] 353it [1:19:31, 12.70s/it] 354it [1:19:44, 12.67s/it] 355it [1:19:56, 12.66s/it] 356it [1:20:09, 12.67s/it] 357it [1:20:22, 12.72s/it] 358it [1:20:34, 12.71s/it] 359it [1:20:47, 12.68s/it] 360it [1:21:00, 12.68s/it] 361it [1:21:12, 12.68s/it] 362it [1:21:25, 12.67s/it] 363it [1:21:38, 12.65s/it] 364it [1:21:50, 12.66s/it] 365it [1:22:03, 12.68s/it] 366it [1:22:16, 12.70s/it] 367it [1:22:28, 12.68s/it] 368it [1:22:41, 12.69s/it] 369it [1:22:54, 12.69s/it] 370it [1:23:07, 12.71s/it] 371it [1:23:19, 12.68s/it] 372it [1:23:32, 12.67s/it] 373it [1:23:45, 12.70s/it] 374it [1:23:57, 12.69s/it] 375it [1:24:10, 12.70s/it] 376it [1:24:23, 12.72s/it] 377it [1:24:35, 12.71s/it] 378it [1:24:48, 12.69s/it] 379it [1:25:01, 12.67s/it] 380it [1:25:13, 12.67s/it] 381it [1:25:26, 12.67s/it] 382it [1:25:39, 12.69s/it] 383it [1:25:51, 12.69s/it] 384it [1:26:04, 12.69s/it] 385it [1:26:17, 12.69s/it] 386it [1:26:29, 12.67s/it] 387it [1:26:42, 12.65s/it] 388it [1:26:55, 12.66s/it] 389it [1:27:07, 12.66s/it] 390it [1:27:20, 12.66s/it] 391it [1:27:33, 12.68s/it] 392it [1:27:46, 12.68s/it] 393it [1:27:58, 12.67s/it] 394it [1:28:11, 12.67s/it] 395it [1:28:24, 12.68s/it] 396it [1:28:36, 12.69s/it] 397it [1:28:49, 12.67s/it] 398it [1:29:02, 12.69s/it] 399it [1:29:14, 12.71s/it] 400it 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[3:27:31, 13.72s/it] 956it [3:27:45, 13.76s/it] 957it [3:27:59, 13.78s/it] 958it [3:28:13, 13.76s/it] 959it [3:28:26, 13.69s/it] 960it [3:28:39, 13.45s/it] 961it [3:28:52, 13.31s/it] 962it [3:29:05, 13.23s/it] 963it [3:29:18, 13.17s/it] 964it [3:29:31, 13.14s/it] 965it [3:29:44, 13.12s/it] 966it [3:29:58, 13.27s/it] 967it [3:30:11, 13.26s/it] 968it [3:30:24, 13.25s/it] 969it [3:30:38, 13.28s/it] 970it [3:30:51, 13.24s/it] 971it [3:31:04, 13.24s/it] 972it [3:31:17, 13.24s/it] 973it [3:31:31, 13.33s/it] 974it [3:31:45, 13.47s/it] 975it [3:31:59, 13.58s/it] 976it [3:32:12, 13.58s/it] 977it [3:32:26, 13.76s/it] 978it [3:32:41, 14.01s/it] 979it [3:32:55, 14.16s/it] 980it [3:33:10, 14.36s/it] 981it [3:33:25, 14.49s/it] 982it [3:33:40, 14.58s/it] 983it [3:33:54, 14.57s/it] 984it [3:34:09, 14.63s/it] 985it [3:34:24, 14.66s/it] 986it [3:34:39, 14.66s/it] 987it [3:34:53, 14.52s/it] 988it [3:35:07, 14.51s/it] 989it [3:35:22, 14.49s/it] 990it [3:35:36, 14.57s/it] 991it [3:35:51, 14.60s/it] 992it [3:36:06, 14.66s/it] 993it [3:36:21, 14.69s/it] 994it [3:36:35, 14.55s/it] 995it [3:36:50, 14.60s/it] 996it [3:37:04, 14.67s/it] 997it [3:37:19, 14.77s/it] 998it [3:37:34, 14.72s/it] 999it [3:37:49, 14.70s/it] 1000it [3:38:04, 14.85s/it] 1000it [3:38:04, 13.08s/it] +Error counts: + cyclic_id: 0 + cyclic_inchikey: 0 + cyclic_scaffold: 0 + cyclic_mwt: 0 + cyclic_clogp: 0 + cyclic_tpsa: 0 +⏰ Completed process in 3:38:32.888238 ++ rm /nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/test/cyc-pep-6-12mer-70M_03.csv diff --git a/test/cyc-pep-6-12mer-70M_04.csv.gz b/test/cyc-pep-6-12mer-70M_04.csv.gz index e25c5d14058f1513876e185378aa7a1e5644362d..6d91f3d30a3c4e79179449454c5f3ace7b124315 100644 --- a/test/cyc-pep-6-12mer-70M_04.csv.gz +++ b/test/cyc-pep-6-12mer-70M_04.csv.gz @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:c7163b34e785bf3a9d481d4ba7dfa9b0b94602ce9c888b1182a69f31fdb47cce -size 62712613 +oid sha256:bea05e48dd08aadf83a368b21f7548c8128584f3dd480e3758dbfc6ec00f55ff +size 118252402 diff --git a/test/cyc-pep-6-12mer-70M_04.log b/test/cyc-pep-6-12mer-70M_04.log new file mode 100644 index 0000000000000000000000000000000000000000..f68cb2f39b849428834b01572a7b5d8638edde5e --- /dev/null +++ b/test/cyc-pep-6-12mer-70M_04.log @@ -0,0 +1,337 @@ ++ module purge ++ '[' -z '' ']' ++ case "$-" in ++ __lmod_sh_dbg=x ++ '[' -n x ']' ++ set +x +Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output +Shell debugging restarted ++ unset __lmod_sh_dbg ++ return 0 ++ module load Anaconda3/2023.03 ++ '[' -z '' ']' ++ case "$-" in ++ __lmod_sh_dbg=x ++ '[' -n x ']' ++ set +x +Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output +Shell debugging restarted ++ unset __lmod_sh_dbg ++ return 0 ++ source /camp/home/johnsoe/.bashrc +++ '[' '' = yes ']' +++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' ++++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.bash hook +++ __conda_setup='export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'' + +# Copyright (C) 2012 Anaconda, Inc +# SPDX-License-Identifier: BSD-3-Clause +__conda_exe() ( + "$CONDA_EXE" $_CE_M $_CE_CONDA "$@" +) + +__conda_hashr() { + if [ -n "${ZSH_VERSION:+x}" ]; then + \rehash + elif [ -n "${POSH_VERSION:+x}" ]; then + : # pass + else + \hash -r + fi +} + +__conda_activate() { + if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then + # Handle transition from shell activated with conda <= 4.3 to a subsequent activation + # after conda updated to >= 4.4. See issue #6173. + PS1="$CONDA_PS1_BACKUP" + \unset CONDA_PS1_BACKUP + fi + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return + \eval "$ask_conda" + __conda_hashr +} + +__conda_reactivate() { + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return + \eval "$ask_conda" + __conda_hashr +} + +conda() { + \local cmd="${1-__missing__}" + case "$cmd" in + activate|deactivate) + __conda_activate "$@" + ;; + install|update|upgrade|remove|uninstall) + __conda_exe "$@" || \return + __conda_reactivate + ;; + *) + __conda_exe "$@" + ;; + esac +} + +if [ -z "${CONDA_SHLVL+x}" ]; then + \export CONDA_SHLVL=0 + # In dev-mode CONDA_EXE is python.exe and on Windows + # it is in a different relative location to condabin. + if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then + PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}" + else + PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}" + fi + \export PATH + + # We'\''re not allowing PS1 to be unbound. It must at least be set. + # However, we'\''re not exporting it, which can cause problems when starting a second shell + # via a first shell (i.e. starting zsh from bash). + if [ -z "${PS1+x}" ]; then + PS1= + fi +fi + +conda activate base' +++ '[' 0 -eq 0 ']' +++ eval 'export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'' + +# Copyright (C) 2012 Anaconda, Inc +# SPDX-License-Identifier: BSD-3-Clause +__conda_exe() ( + "$CONDA_EXE" $_CE_M $_CE_CONDA "$@" +) + +__conda_hashr() { + if [ -n "${ZSH_VERSION:+x}" ]; then + \rehash + elif [ -n "${POSH_VERSION:+x}" ]; then + : # pass + else + \hash -r + fi +} + +__conda_activate() { + if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then + # Handle transition from shell activated with conda <= 4.3 to a subsequent activation + # after conda updated to >= 4.4. See issue #6173. + PS1="$CONDA_PS1_BACKUP" + \unset CONDA_PS1_BACKUP + fi + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return + \eval "$ask_conda" + __conda_hashr +} + +__conda_reactivate() { + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return + \eval "$ask_conda" + __conda_hashr +} + +conda() { + \local cmd="${1-__missing__}" + case "$cmd" in + activate|deactivate) + __conda_activate "$@" + ;; + install|update|upgrade|remove|uninstall) + __conda_exe "$@" || \return + __conda_reactivate + ;; + *) + __conda_exe "$@" + ;; + esac +} + +if [ -z "${CONDA_SHLVL+x}" ]; then + \export CONDA_SHLVL=0 + # In dev-mode CONDA_EXE is python.exe and on Windows + # it is in a different relative location to condabin. + if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then + PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}" + else + PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}" + fi + \export PATH + + # We'\''re not allowing PS1 to be unbound. It must at least be set. + # However, we'\''re not exporting it, which can cause problems when starting a second shell + # via a first shell (i.e. starting zsh from bash). + if [ -z "${PS1+x}" ]; then + PS1= + fi +fi + +conda activate base' ++++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda ++++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda ++++ export _CE_M= ++++ _CE_M= ++++ export _CE_CONDA= ++++ _CE_CONDA= ++++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ '[' -z x ']' ++++ conda activate base ++++ local cmd=activate ++++ case "$cmd" in ++++ __conda_activate activate base ++++ '[' -n '' ']' ++++ local ask_conda +++++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++++ __conda_exe shell.posix activate base +++++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate base ++++ ask_conda='PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_SHLVL='\''6'\'' +export CONDA_DEFAULT_ENV='\''base'\'' +export CONDA_PROMPT_MODIFIER='\''(base) '\'' +export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' ++++ eval 'PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_SHLVL='\''6'\'' +export CONDA_DEFAULT_ENV='\''base'\'' +export CONDA_PROMPT_MODIFIER='\''(base) '\'' +export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' +++++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++++ export CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0 +++++ CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0 +++++ export CONDA_SHLVL=6 +++++ CONDA_SHLVL=6 +++++ export CONDA_DEFAULT_ENV=base +++++ CONDA_DEFAULT_ENV=base +++++ export 'CONDA_PROMPT_MODIFIER=(base) ' +++++ CONDA_PROMPT_MODIFIER='(base) ' +++++ export CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev +++++ CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev +++++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++++ export _CE_M= +++++ _CE_M= +++++ export _CE_CONDA= +++++ _CE_CONDA= +++++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python +++++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ __conda_hashr ++++ '[' -n '' ']' ++++ '[' -n '' ']' ++++ hash -r +++ unset __conda_setup ++ conda activate schemist-dev ++ local cmd=activate ++ case "$cmd" in ++ __conda_activate activate schemist-dev ++ '[' -n '' ']' ++ local ask_conda +++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++ __conda_exe shell.posix activate schemist-dev +++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate schemist-dev ++ ask_conda='PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_SHLVL='\''7'\'' +export CONDA_DEFAULT_ENV='\''schemist-dev'\'' +export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\'' +export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' ++ eval 'PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_SHLVL='\''7'\'' +export CONDA_DEFAULT_ENV='\''schemist-dev'\'' +export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\'' +export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' +++ PS1='(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++ export CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev +++ CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev +++ export CONDA_SHLVL=7 +++ CONDA_SHLVL=7 +++ export CONDA_DEFAULT_ENV=schemist-dev +++ CONDA_DEFAULT_ENV=schemist-dev +++ export 'CONDA_PROMPT_MODIFIER=(schemist-dev) ' +++ CONDA_PROMPT_MODIFIER='(schemist-dev) ' +++ export CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0 +++ CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0 +++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++ export _CE_M= +++ _CE_M= +++ export _CE_CONDA= +++ _CE_CONDA= +++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python +++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++ __conda_hashr ++ '[' -n '' ']' ++ '[' -n '' ']' ++ hash -r ++ CHUNK_HEAD_FILE=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz ++ INPUT=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/test/cyc-pep-6-12mer-70M_04.csv ++ COLUMN=cysteine_to_N_cyclization ++ PREFIX=cyclic_ ++ AWK='1 { print $8, $1, $2, $10, $3 }' ++ '[' -z cysteine_to_N_cyclization ']' ++ '[' -z cyclic_ ']' ++ '[' -z '1 { print $8, $1, $2, $10, $3 }' ']' ++ awk -F, -v OFS=, '1 { print $8, $1, $2, $10, $3 }' ++ cat /dev/fd/63 /nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/test/cyc-pep-6-12mer-70M_04.csv +++ zcat /nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz ++ schemist convert -f csv --column cysteine_to_N_cyclization --to id inchikey scaffold mwt clogp tpsa --prefix cyclic_ --options prefix=SCB- +++ head -n1 ++ gzip --best +++ tr ' ' , +🚀 Converting between string representations with the following parameters: + subcommand: convert + output: <_io.TextIOWrapper name='' mode='w' encoding='utf-8'> + format: csv + input: <_io.TextIOWrapper name='' mode='r' encoding='utf-8'> + representation: SMILES + column: cysteine_to_N_cyclization + prefix: cyclic_ + to: ['id', 'inchikey', 'scaffold', 'mwt', 'clogp', 'tpsa'] + options: ['prefix=SCB-'] + func: + 0it [00:00, ?it/s] 1it [00:12, 12.83s/it] 2it [00:25, 12.63s/it] 3it [00:37, 12.60s/it] 4it [00:50, 12.61s/it] 5it [01:03, 12.64s/it] 6it [01:15, 12.65s/it] 7it [01:28, 12.65s/it] 8it [01:41, 12.67s/it] 9it [01:53, 12.69s/it] 10it [02:06, 12.69s/it] 11it [02:19, 12.67s/it] 12it [02:31, 12.64s/it] 13it [02:44, 12.63s/it] 14it [02:57, 12.62s/it] 15it [03:09, 12.62s/it] 16it [03:22, 12.57s/it] 17it [03:34, 12.62s/it] 18it [03:47, 12.64s/it] 19it [04:00, 12.68s/it] 20it [04:12, 12.68s/it] 21it [04:25, 12.66s/it] 22it [04:38, 12.64s/it] 23it [04:50, 12.61s/it] 24it [05:03, 12.61s/it] 25it [05:15, 12.59s/it] 26it [05:28, 12.58s/it] 27it [05:41, 12.62s/it] 28it [05:53, 12.63s/it] 29it [06:06, 12.61s/it] 30it [06:19, 12.63s/it] 31it [06:31, 12.63s/it] 32it [06:44, 12.63s/it] 33it [06:56, 12.64s/it] 34it [07:09, 12.65s/it] 35it [07:22, 12.61s/it] 36it [07:34, 12.59s/it] 37it [07:47, 12.61s/it] 38it [08:00, 12.62s/it] 39it [08:12, 12.62s/it] 40it [08:25, 12.63s/it] 41it [08:37, 12.64s/it] 42it [08:50, 12.60s/it] 43it [09:03, 12.60s/it] 44it [09:15, 12.61s/it] 45it [09:28, 12.63s/it] 46it [09:41, 12.64s/it] 47it [09:53, 12.67s/it] 48it [10:06, 12.67s/it] 49it [10:19, 12.65s/it] 50it [10:31, 12.65s/it] 51it [10:44, 12.68s/it] 52it [10:57, 12.68s/it] 53it [11:09, 12.72s/it] 54it [11:22, 12.77s/it] 55it [11:35, 12.81s/it] 56it [11:48, 12.83s/it] 57it [12:01, 12.86s/it] 58it [12:14, 12.86s/it] 59it [12:27, 12.88s/it] 60it [12:40, 12.92s/it] 61it [12:53, 12.94s/it] 62it [13:06, 12.97s/it] 63it [13:19, 12.96s/it] 64it [13:32, 12.96s/it] 65it [13:45, 12.92s/it] 66it [13:57, 12.91s/it] 67it [14:10, 12.91s/it] 68it [14:23, 12.91s/it] 69it [14:36, 12.87s/it] 70it [14:49, 12.86s/it] 71it [15:02, 12.85s/it] 72it [15:15, 12.86s/it] 73it [15:27, 12.85s/it] 74it [15:40, 12.88s/it] 75it [15:53, 12.87s/it] 76it [16:06, 12.83s/it] 77it [16:19, 12.84s/it] 78it [16:32, 12.83s/it] 79it [16:45, 12.88s/it] 80it [16:58, 12.90s/it] 81it [17:10, 12.90s/it] 82it [17:23, 12.92s/it] 83it [17:36, 12.91s/it] 84it [17:49, 12.92s/it] 85it [18:02, 12.95s/it] 86it [18:15, 12.94s/it] 87it [18:28, 12.92s/it] 88it [18:41, 12.90s/it] 89it [18:54, 12.91s/it] 90it [19:07, 12.88s/it] 91it [19:20, 12.89s/it] 92it [19:33, 12.90s/it] 93it [19:45, 12.91s/it] 94it [19:58, 12.91s/it] 95it [20:11, 12.91s/it] 96it [20:24, 12.89s/it] 97it [20:37, 12.89s/it] 98it [20:50, 12.89s/it] 99it [21:03, 12.93s/it] 100it [21:16, 12.95s/it] 101it [21:29, 12.95s/it] 102it [21:42, 13.07s/it] 103it [21:56, 13.17s/it] 104it [22:09, 13.13s/it] 105it [22:22, 13.11s/it] 106it [22:35, 13.11s/it] 107it [22:48, 13.15s/it] 108it [23:01, 13.14s/it] 109it [23:14, 13.12s/it] 110it [23:27, 13.12s/it] 111it [23:41, 13.13s/it] 112it [23:54, 13.18s/it] 113it [24:07, 13.18s/it] 114it [24:20, 13.08s/it] 115it [24:33, 13.07s/it] 116it [24:46, 13.07s/it] 117it [24:59, 13.09s/it] 118it [25:12, 13.05s/it] 119it [25:25, 13.03s/it] 120it [25:38, 13.00s/it] 121it [25:51, 13.00s/it] 122it [26:04, 12.96s/it] 123it [26:17, 13.05s/it] 124it [26:30, 13.06s/it] 125it [26:43, 13.09s/it] 126it [26:57, 13.13s/it] 127it [27:10, 13.18s/it] 128it [27:23, 13.23s/it] 129it [27:37, 13.25s/it] 130it [27:50, 13.24s/it] 131it [28:03, 13.18s/it] 132it [28:16, 13.21s/it] 133it [28:29, 13.20s/it] 134it [28:42, 13.16s/it] 135it [28:55, 13.13s/it] 136it [29:08, 13.12s/it] 137it [29:22, 13.15s/it] 138it [29:35, 13.12s/it] 139it [29:48, 13.07s/it] 140it [30:01, 13.06s/it] 141it [30:14, 13.12s/it] 142it [30:27, 13.10s/it] 143it [30:40, 13.11s/it] 144it [30:53, 13.11s/it] 145it [31:06, 13.10s/it] 146it [31:19, 13.07s/it] 147it [31:32, 13.06s/it] 148it [31:45, 13.06s/it] 149it [31:59, 13.06s/it] 150it [32:12, 13.04s/it] 151it [32:24, 13.01s/it] 152it [32:38, 13.03s/it] 153it [32:51, 13.02s/it] 154it [33:03, 12.97s/it] 155it [33:16, 12.95s/it] 156it [33:29, 12.98s/it] 157it [33:42, 12.97s/it] 158it [33:55, 12.95s/it] 159it [34:08, 12.98s/it] 160it [34:21, 12.98s/it] 161it [34:34, 13.01s/it] 162it [34:47, 13.01s/it] 163it [35:00, 13.01s/it] 164it [35:14, 13.08s/it] 165it [35:27, 13.11s/it] 166it [35:40, 13.13s/it] 167it [35:53, 13.13s/it] 168it [36:06, 13.12s/it] 169it [36:19, 13.12s/it] 170it [36:32, 13.15s/it] 171it [36:45, 13.12s/it] 172it [36:58, 13.08s/it] 173it [37:12, 13.08s/it] 174it [37:25, 13.08s/it] 175it [37:38, 13.07s/it] 176it [37:51, 13.06s/it] 177it [38:04, 13.04s/it] 178it [38:17, 13.00s/it] 179it [38:30, 13.00s/it] 180it [38:43, 12.98s/it] 181it [38:56, 13.00s/it] 182it [39:09, 12.99s/it] 183it [39:22, 13.02s/it] 184it [39:35, 12.99s/it] 185it [39:47, 12.95s/it] 186it [40:00, 12.97s/it] 187it [40:14, 13.02s/it] 188it [40:27, 13.05s/it] 189it [40:40, 13.07s/it] 190it [40:53, 13.03s/it] 191it [41:06, 13.03s/it] 192it [41:19, 13.01s/it] 193it [41:32, 12.98s/it] 194it [41:45, 12.99s/it] 195it [41:58, 12.96s/it] 196it [42:11, 12.95s/it] 197it [42:24, 12.96s/it] 198it [42:36, 12.96s/it] 199it [42:50, 13.06s/it] 200it [43:03, 13.14s/it] 201it [43:16, 13.17s/it] 202it [43:29, 13.12s/it] 203it [43:42, 13.09s/it] 204it [43:55, 13.06s/it] 205it [44:08, 13.01s/it] 206it [44:21, 13.03s/it] 207it [44:34, 13.03s/it] 208it [44:47, 13.04s/it] 209it [45:00, 13.02s/it] 210it [45:13, 13.01s/it] 211it [45:26, 13.04s/it] 212it [45:39, 13.01s/it] 213it [45:52, 13.02s/it] 214it [46:06, 13.03s/it] 215it [46:19, 13.04s/it] 216it [46:32, 13.02s/it] 217it [46:45, 13.01s/it] 218it [46:58, 13.06s/it] 219it [47:11, 13.15s/it] 220it [47:25, 13.28s/it] 221it [47:38, 13.30s/it] 222it [47:52, 13.37s/it] 223it [48:05, 13.41s/it] 224it [48:19, 13.45s/it] 225it [48:32, 13.43s/it] 226it [48:45, 13.37s/it] 227it [48:58, 13.28s/it] 228it [49:11, 13.24s/it] 229it [49:24, 13.15s/it] 230it [49:37, 13.11s/it] 231it [49:50, 13.08s/it] 232it [50:03, 13.04s/it] 233it [50:16, 13.08s/it] 234it [50:30, 13.17s/it] 235it [50:43, 13.21s/it] 236it [50:56, 13.23s/it] 237it [51:10, 13.25s/it] 238it [51:23, 13.29s/it] 239it [51:37, 13.32s/it] 240it [51:50, 13.28s/it] 241it [52:03, 13.27s/it] 242it [52:16, 13.22s/it] 243it [52:29, 13.23s/it] 244it [52:43, 13.23s/it] 245it [52:56, 13.25s/it] 246it [53:09, 13.24s/it] 247it [53:22, 13.25s/it] 248it [53:36, 13.27s/it] 249it [53:49, 13.25s/it] 250it [54:02, 13.23s/it] 251it [54:15, 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12.94s/it] 920it [3:19:20, 12.95s/it] 921it [3:19:27, 11.00s/it] 922it [3:19:33, 9.61s/it] 923it [3:19:40, 8.78s/it] 924it [3:19:47, 8.12s/it] 925it [3:19:53, 7.63s/it] 926it [3:20:00, 7.28s/it] 927it [3:20:07, 7.19s/it] 928it [3:20:13, 7.02s/it] 929it [3:20:20, 6.94s/it] 930it [3:20:27, 6.91s/it] 931it [3:20:34, 7.01s/it] 932it [3:20:41, 7.02s/it] 933it [3:20:48, 6.94s/it] 934it [3:20:55, 6.91s/it] 935it [3:21:02, 6.98s/it] 936it [3:21:09, 6.98s/it] 937it [3:21:15, 6.91s/it] 938it [3:21:22, 6.85s/it] 939it [3:21:29, 6.88s/it] 940it [3:21:36, 6.92s/it] 941it [3:21:43, 6.84s/it] 942it [3:21:50, 6.80s/it] 943it [3:21:56, 6.82s/it] 944it [3:22:03, 6.87s/it] 945it [3:22:10, 6.79s/it] 946it [3:22:17, 6.73s/it] 947it [3:22:23, 6.71s/it] 948it [3:22:30, 6.78s/it] 949it [3:22:37, 6.74s/it] 950it [3:22:44, 6.75s/it] 951it [3:22:50, 6.75s/it] 952it [3:22:58, 6.88s/it] 953it [3:23:04, 6.83s/it] 954it [3:23:11, 6.69s/it] 955it [3:23:17, 6.60s/it] 956it [3:23:24, 6.68s/it] 957it [3:23:30, 6.65s/it] 958it [3:23:37, 6.67s/it] 959it [3:23:44, 6.67s/it] 960it [3:23:51, 6.82s/it] 961it [3:23:58, 6.84s/it] 962it [3:24:05, 6.92s/it] 963it [3:24:12, 7.00s/it] 964it [3:24:20, 7.19s/it] 965it [3:24:27, 7.24s/it] 966it [3:24:34, 7.24s/it] 967it [3:24:42, 7.24s/it] 968it [3:24:49, 7.38s/it] 969it [3:24:57, 7.40s/it] 970it [3:25:04, 7.40s/it] 971it [3:25:12, 7.39s/it] 972it [3:25:19, 7.53s/it] 973it [3:25:27, 7.58s/it] 974it [3:25:34, 7.47s/it] 975it [3:25:41, 7.35s/it] 976it [3:25:49, 7.36s/it] 977it [3:25:56, 7.33s/it] 978it [3:26:03, 7.20s/it] 979it [3:26:10, 7.10s/it] 980it [3:26:17, 7.10s/it] 981it [3:26:24, 7.10s/it] 982it [3:26:31, 7.04s/it] 983it [3:26:38, 7.05s/it] 984it [3:26:45, 7.11s/it] 985it [3:26:53, 7.20s/it] 986it [3:27:00, 7.13s/it] 987it [3:27:06, 7.05s/it] 988it [3:27:13, 7.01s/it] 989it [3:27:21, 7.07s/it] 990it [3:27:27, 7.01s/it] 991it [3:27:34, 6.98s/it] 992it [3:27:41, 6.99s/it] 993it [3:27:49, 7.11s/it] 994it [3:27:56, 7.06s/it] 995it [3:28:03, 6.99s/it] 996it [3:28:09, 6.93s/it] 997it [3:28:17, 7.02s/it] 998it [3:28:24, 7.00s/it] 999it [3:28:30, 6.96s/it] 1000it [3:28:37, 6.89s/it] 1000it [3:28:37, 12.52s/it] +Error counts: + cyclic_id: 0 + cyclic_inchikey: 0 + cyclic_scaffold: 0 + cyclic_mwt: 0 + cyclic_clogp: 0 + cyclic_tpsa: 0 +⏰ Completed process in 3:29:01.669280 ++ rm /nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/test/cyc-pep-6-12mer-70M_04.csv diff --git a/test/cyc-pep-6-12mer-70M_05.csv.gz b/test/cyc-pep-6-12mer-70M_05.csv.gz index bb5dadf169fa9c632424a6017c587f247cc57ea6..5098c3a2005c5e84e12d96e04888a733196dd1b1 100644 --- a/test/cyc-pep-6-12mer-70M_05.csv.gz +++ b/test/cyc-pep-6-12mer-70M_05.csv.gz @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:458c84baee025b66dcd2d989b276628f538ae76830dae896751ec11e7fb03849 -size 29476270 +oid sha256:2b854ad30333d2b0935f3e64d66b8b497d975915f30f7cb21008db529c945298 +size 70372794 diff --git a/test/cyc-pep-6-12mer-70M_05.log b/test/cyc-pep-6-12mer-70M_05.log new file mode 100644 index 0000000000000000000000000000000000000000..059f207ed8e188db8808aaa65e35fba910d210de --- /dev/null +++ b/test/cyc-pep-6-12mer-70M_05.log @@ -0,0 +1,337 @@ ++ module purge ++ '[' -z '' ']' ++ case "$-" in ++ __lmod_sh_dbg=x ++ '[' -n x ']' ++ set +x +Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output +Shell debugging restarted ++ unset __lmod_sh_dbg ++ return 0 ++ module load Anaconda3/2023.03 ++ '[' -z '' ']' ++ case "$-" in ++ __lmod_sh_dbg=x ++ '[' -n x ']' ++ set +x +Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output +Shell debugging restarted ++ unset __lmod_sh_dbg ++ return 0 ++ source /camp/home/johnsoe/.bashrc +++ '[' '' = yes ']' +++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' ++++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.bash hook +++ __conda_setup='export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'' + +# Copyright (C) 2012 Anaconda, Inc +# SPDX-License-Identifier: BSD-3-Clause +__conda_exe() ( + "$CONDA_EXE" $_CE_M $_CE_CONDA "$@" +) + +__conda_hashr() { + if [ -n "${ZSH_VERSION:+x}" ]; then + \rehash + elif [ -n "${POSH_VERSION:+x}" ]; then + : # pass + else + \hash -r + fi +} + +__conda_activate() { + if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then + # Handle transition from shell activated with conda <= 4.3 to a subsequent activation + # after conda updated to >= 4.4. See issue #6173. + PS1="$CONDA_PS1_BACKUP" + \unset CONDA_PS1_BACKUP + fi + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return + \eval "$ask_conda" + __conda_hashr +} + +__conda_reactivate() { + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return + \eval "$ask_conda" + __conda_hashr +} + +conda() { + \local cmd="${1-__missing__}" + case "$cmd" in + activate|deactivate) + __conda_activate "$@" + ;; + install|update|upgrade|remove|uninstall) + __conda_exe "$@" || \return + __conda_reactivate + ;; + *) + __conda_exe "$@" + ;; + esac +} + +if [ -z "${CONDA_SHLVL+x}" ]; then + \export CONDA_SHLVL=0 + # In dev-mode CONDA_EXE is python.exe and on Windows + # it is in a different relative location to condabin. + if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then + PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}" + else + PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}" + fi + \export PATH + + # We'\''re not allowing PS1 to be unbound. It must at least be set. + # However, we'\''re not exporting it, which can cause problems when starting a second shell + # via a first shell (i.e. starting zsh from bash). + if [ -z "${PS1+x}" ]; then + PS1= + fi +fi + +conda activate base' +++ '[' 0 -eq 0 ']' +++ eval 'export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'' + +# Copyright (C) 2012 Anaconda, Inc +# SPDX-License-Identifier: BSD-3-Clause +__conda_exe() ( + "$CONDA_EXE" $_CE_M $_CE_CONDA "$@" +) + +__conda_hashr() { + if [ -n "${ZSH_VERSION:+x}" ]; then + \rehash + elif [ -n "${POSH_VERSION:+x}" ]; then + : # pass + else + \hash -r + fi +} + +__conda_activate() { + if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then + # Handle transition from shell activated with conda <= 4.3 to a subsequent activation + # after conda updated to >= 4.4. See issue #6173. + PS1="$CONDA_PS1_BACKUP" + \unset CONDA_PS1_BACKUP + fi + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return + \eval "$ask_conda" + __conda_hashr +} + +__conda_reactivate() { + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return + \eval "$ask_conda" + __conda_hashr +} + +conda() { + \local cmd="${1-__missing__}" + case "$cmd" in + activate|deactivate) + __conda_activate "$@" + ;; + install|update|upgrade|remove|uninstall) + __conda_exe "$@" || \return + __conda_reactivate + ;; + *) + __conda_exe "$@" + ;; + esac +} + +if [ -z "${CONDA_SHLVL+x}" ]; then + \export CONDA_SHLVL=0 + # In dev-mode CONDA_EXE is python.exe and on Windows + # it is in a different relative location to condabin. + if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then + PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}" + else + PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}" + fi + \export PATH + + # We'\''re not allowing PS1 to be unbound. It must at least be set. + # However, we'\''re not exporting it, which can cause problems when starting a second shell + # via a first shell (i.e. starting zsh from bash). + if [ -z "${PS1+x}" ]; then + PS1= + fi +fi + +conda activate base' ++++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda ++++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda ++++ export _CE_M= ++++ _CE_M= ++++ export _CE_CONDA= ++++ _CE_CONDA= ++++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ '[' -z x ']' ++++ conda activate base ++++ local cmd=activate ++++ case "$cmd" in ++++ __conda_activate activate base ++++ '[' -n '' ']' ++++ local ask_conda +++++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++++ __conda_exe shell.posix activate base +++++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate base ++++ ask_conda='PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_SHLVL='\''6'\'' +export CONDA_DEFAULT_ENV='\''base'\'' +export CONDA_PROMPT_MODIFIER='\''(base) '\'' +export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' ++++ eval 'PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_SHLVL='\''6'\'' +export CONDA_DEFAULT_ENV='\''base'\'' +export CONDA_PROMPT_MODIFIER='\''(base) '\'' +export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' +++++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++++ export CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0 +++++ CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0 +++++ export CONDA_SHLVL=6 +++++ CONDA_SHLVL=6 +++++ export CONDA_DEFAULT_ENV=base +++++ CONDA_DEFAULT_ENV=base +++++ export 'CONDA_PROMPT_MODIFIER=(base) ' +++++ CONDA_PROMPT_MODIFIER='(base) ' +++++ export CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev +++++ CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev +++++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++++ export _CE_M= +++++ _CE_M= +++++ export _CE_CONDA= +++++ _CE_CONDA= +++++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python +++++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ __conda_hashr ++++ '[' -n '' ']' ++++ '[' -n '' ']' ++++ hash -r +++ unset __conda_setup ++ conda activate schemist-dev ++ local cmd=activate ++ case "$cmd" in ++ __conda_activate activate schemist-dev ++ '[' -n '' ']' ++ local ask_conda +++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++ __conda_exe shell.posix activate schemist-dev +++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate schemist-dev ++ ask_conda='PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_SHLVL='\''7'\'' +export CONDA_DEFAULT_ENV='\''schemist-dev'\'' +export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\'' +export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' ++ eval 'PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_SHLVL='\''7'\'' +export CONDA_DEFAULT_ENV='\''schemist-dev'\'' +export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\'' +export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' +++ PS1='(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++ export CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev +++ CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev +++ export CONDA_SHLVL=7 +++ CONDA_SHLVL=7 +++ export CONDA_DEFAULT_ENV=schemist-dev +++ CONDA_DEFAULT_ENV=schemist-dev +++ export 'CONDA_PROMPT_MODIFIER=(schemist-dev) ' +++ CONDA_PROMPT_MODIFIER='(schemist-dev) ' +++ export CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0 +++ CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0 +++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++ export _CE_M= +++ _CE_M= +++ export _CE_CONDA= +++ _CE_CONDA= +++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python +++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++ __conda_hashr ++ '[' -n '' ']' ++ '[' -n '' ']' ++ hash -r ++ CHUNK_HEAD_FILE=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz ++ INPUT=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/test/cyc-pep-6-12mer-70M_05.csv ++ COLUMN=cysteine_to_N_cyclization ++ PREFIX=cyclic_ ++ AWK='1 { print $8, $1, $2, $10, $3 }' ++ '[' -z cysteine_to_N_cyclization ']' ++ '[' -z cyclic_ ']' ++ '[' -z '1 { print $8, $1, $2, $10, $3 }' ']' ++ cat /dev/fd/63 /nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/test/cyc-pep-6-12mer-70M_05.csv ++ schemist convert -f csv --column cysteine_to_N_cyclization --to id inchikey scaffold mwt clogp tpsa --prefix cyclic_ --options prefix=SCB- +++ head -n1 ++ gzip --best +++ zcat /nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz ++ awk -F, -v OFS=, '1 { print $8, $1, $2, $10, $3 }' +++ tr ' ' , +🚀 Converting between string representations with the following parameters: + subcommand: convert + output: <_io.TextIOWrapper name='' mode='w' encoding='utf-8'> + format: csv + input: <_io.TextIOWrapper name='' mode='r' encoding='utf-8'> + representation: SMILES + column: cysteine_to_N_cyclization + prefix: cyclic_ + to: ['id', 'inchikey', 'scaffold', 'mwt', 'clogp', 'tpsa'] + options: ['prefix=SCB-'] + func: + 0it [00:00, ?it/s] 1it [00:07, 7.06s/it] 2it [00:13, 6.87s/it] 3it [00:20, 6.60s/it] 4it [00:26, 6.46s/it] 5it [00:33, 6.55s/it] 6it [00:39, 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[1:14:42, 7.29s/it] 624it [1:14:50, 7.44s/it] 625it [1:14:57, 7.48s/it] 626it [1:15:04, 7.46s/it] 627it [1:15:12, 7.45s/it] 628it [1:15:20, 7.60s/it] 629it [1:15:28, 7.62s/it] 630it [1:15:35, 7.52s/it] 631it [1:15:42, 7.38s/it] 632it [1:15:49, 7.40s/it] 633it [1:15:57, 7.37s/it] 634it [1:16:03, 7.22s/it] 635it [1:16:10, 7.12s/it] 636it [1:16:17, 7.10s/it] 637it [1:16:25, 7.11s/it] 638it [1:16:32, 7.06s/it] 639it [1:16:39, 7.08s/it] 640it [1:16:46, 7.12s/it] 641it [1:16:53, 7.23s/it] 642it [1:17:00, 7.17s/it] 643it [1:17:07, 7.08s/it] 644it [1:17:14, 7.03s/it] 645it [1:17:21, 7.11s/it] 646it [1:17:28, 7.05s/it] 647it [1:17:35, 6.99s/it] 648it [1:17:42, 6.96s/it] 649it [1:17:49, 7.07s/it] 650it [1:17:56, 7.06s/it] 651it [1:18:03, 6.97s/it] 652it [1:18:10, 6.89s/it] 653it [1:18:17, 6.99s/it] 654it [1:18:24, 6.97s/it] 655it [1:18:31, 6.91s/it] 656it [1:18:38, 6.89s/it] 657it [1:18:45, 7.02s/it] 658it [1:18:52, 7.03s/it] 659it [1:18:59, 7.00s/it] 660it [1:19:06, 6.91s/it] 661it [1:19:13, 7.01s/it] 662it [1:19:20, 7.00s/it] 663it [1:19:27, 6.94s/it] 664it [1:19:34, 6.92s/it] 665it [1:19:41, 7.03s/it] 666it [1:19:48, 7.04s/it] 667it [1:19:55, 7.06s/it] 668it [1:20:02, 7.11s/it] 669it [1:20:10, 7.25s/it] 670it [1:20:17, 7.28s/it] 671it [1:20:24, 7.22s/it] 672it [1:20:31, 7.17s/it] 673it [1:20:39, 7.25s/it] 674it [1:20:46, 7.31s/it] 675it [1:20:53, 7.23s/it] 676it [1:21:00, 7.19s/it] 677it [1:21:08, 7.21s/it] 678it [1:21:15, 7.27s/it] 679it [1:21:22, 7.21s/it] 680it [1:21:29, 7.15s/it] 681it [1:21:36, 7.14s/it] 682it [1:21:44, 7.22s/it] 683it [1:21:51, 7.15s/it] 684it [1:21:58, 7.10s/it] 685it [1:22:05, 7.07s/it] 686it [1:22:12, 7.13s/it] 687it [1:22:19, 7.09s/it] 688it [1:22:26, 7.09s/it] 689it [1:22:33, 7.08s/it] 690it [1:22:40, 7.20s/it] 691it [1:22:48, 7.17s/it] 692it [1:22:54, 7.03s/it] 693it [1:23:01, 6.94s/it] 694it [1:23:08, 7.01s/it] 695it [1:23:15, 6.99s/it] 696it [1:23:22, 6.99s/it] 697it [1:23:29, 7.00s/it] 698it [1:23:37, 7.16s/it] 699it [1:23:44, 7.16s/it] 700it [1:23:51, 7.27s/it] 701it [1:23:59, 7.33s/it] 702it [1:24:07, 7.56s/it] 703it [1:24:15, 7.60s/it] 704it [1:24:22, 7.61s/it] 705it [1:24:30, 7.62s/it] 706it [1:24:38, 7.77s/it] 707it [1:24:46, 7.80s/it] 708it [1:24:54, 7.78s/it] 709it [1:25:01, 7.79s/it] 710it [1:25:10, 7.92s/it] 711it [1:25:18, 7.95s/it] 712it [1:25:25, 7.83s/it] 713it [1:25:33, 7.69s/it] 714it [1:25:40, 7.70s/it] 715it [1:25:48, 7.68s/it] 716it [1:25:55, 7.56s/it] 717it [1:26:02, 7.43s/it] 718it [1:26:10, 7.43s/it] 719it [1:26:17, 7.46s/it] 720it [1:26:25, 7.39s/it] 721it [1:26:32, 7.41s/it] 722it [1:26:40, 7.45s/it] 723it [1:26:47, 7.56s/it] 724it [1:26:55, 7.51s/it] 725it [1:27:02, 7.41s/it] 726it [1:27:09, 7.36s/it] 727it [1:27:17, 7.40s/it] 728it [1:27:24, 7.33s/it] 729it [1:27:31, 7.30s/it] 730it [1:27:38, 7.26s/it] 731it [1:27:46, 7.38s/it] 732it [1:27:53, 7.33s/it] 733it [1:28:00, 7.24s/it] 734it [1:28:07, 7.18s/it] 735it [1:28:15, 7.28s/it] 736it [1:28:22, 7.26s/it] 737it [1:28:29, 7.21s/it] 738it [1:28:36, 7.16s/it] 739it [1:28:44, 7.31s/it] 740it [1:28:51, 7.30s/it] 741it [1:28:58, 7.27s/it] 742it [1:29:05, 7.23s/it] 743it [1:29:13, 7.37s/it] 744it [1:29:20, 7.38s/it] 745it [1:29:28, 7.33s/it] 746it [1:29:35, 7.30s/it] 747it [1:29:43, 7.40s/it] 748it [1:29:50, 7.40s/it] 749it [1:29:57, 7.43s/it] 750it [1:30:05, 7.49s/it] 751it [1:30:13, 7.67s/it] 752it [1:30:21, 7.73s/it] 753it [1:30:29, 7.67s/it] 754it [1:30:36, 7.63s/it] 755it [1:30:44, 7.69s/it] 756it [1:30:52, 7.73s/it] 757it [1:30:59, 7.66s/it] 758it [1:31:07, 7.64s/it] 759it [1:31:15, 7.66s/it] 760it [1:31:22, 7.71s/it] 761it [1:31:30, 7.63s/it] 762it [1:31:37, 7.59s/it] 763it [1:31:45, 7.58s/it] 764it [1:31:53, 7.65s/it] 765it [1:32:00, 7.60s/it] 766it [1:32:08, 7.54s/it] 767it [1:32:15, 7.49s/it] 768it [1:32:23, 7.59s/it] 769it [1:32:30, 7.55s/it] 770it [1:32:38, 7.54s/it] 771it [1:32:45, 7.53s/it] 772it [1:32:53, 7.67s/it] 773it [1:33:01, 7.66s/it] 774it [1:33:08, 7.50s/it] 775it [1:33:15, 7.40s/it] 776it [1:33:23, 7.47s/it] 777it [1:33:30, 7.42s/it] 778it [1:33:37, 7.42s/it] 779it [1:33:45, 7.42s/it] 780it [1:33:53, 7.58s/it] 781it [1:34:00, 7.60s/it] 782it [1:34:08, 7.69s/it] 783it [1:34:16, 7.77s/it] 784it [1:34:25, 7.99s/it] 785it [1:34:33, 8.05s/it] 786it [1:34:41, 8.04s/it] 787it [1:34:49, 8.03s/it] 788it [1:34:58, 8.18s/it] 789it [1:35:06, 8.21s/it] 790it [1:35:14, 8.20s/it] 791it [1:35:22, 8.20s/it] 792it [1:35:31, 8.34s/it] 793it [1:35:39, 8.38s/it] 794it [1:35:47, 8.27s/it] 795it [1:35:55, 8.14s/it] 796it [1:36:03, 8.12s/it] 797it [1:36:11, 8.11s/it] 798it [1:36:19, 7.98s/it] 799it [1:36:27, 7.88s/it] 800it [1:36:35, 7.85s/it] 801it [1:36:42, 7.89s/it] 802it [1:36:50, 7.80s/it] 803it [1:36:58, 7.81s/it] 804it [1:37:06, 7.85s/it] 805it [1:37:14, 7.97s/it] 806it [1:37:22, 7.92s/it] 807it [1:37:29, 7.82s/it] 808it [1:37:37, 7.78s/it] 809it [1:37:45, 7.85s/it] 810it [1:37:53, 7.79s/it] 811it [1:38:01, 7.75s/it] 812it [1:38:08, 7.70s/it] 813it [1:38:16, 7.83s/it] 814it [1:38:24, 7.79s/it] 815it [1:38:31, 7.71s/it] 816it [1:38:39, 7.64s/it] 817it [1:38:47, 7.75s/it] 818it [1:38:55, 7.73s/it] 819it [1:39:02, 7.67s/it] 820it [1:39:10, 7.64s/it] 821it [1:39:18, 7.76s/it] 822it [1:39:25, 7.75s/it] 823it [1:39:33, 7.61s/it] 824it [1:39:40, 7.49s/it] 825it [1:39:48, 7.57s/it] 826it [1:39:55, 7.52s/it] 827it [1:40:03, 7.48s/it] 828it [1:40:10, 7.42s/it] 829it [1:40:18, 7.54s/it] 830it [1:40:25, 7.55s/it] 831it [1:40:33, 7.56s/it] 832it [1:40:41, 7.61s/it] 833it [1:40:49, 7.78s/it] 834it [1:40:57, 7.83s/it] 835it [1:41:04, 7.77s/it] 836it [1:41:12, 7.73s/it] 837it [1:41:20, 7.83s/it] 838it [1:41:28, 7.83s/it] 839it [1:41:35, 7.77s/it] 840it [1:41:43, 7.72s/it] 841it [1:41:51, 7.77s/it] 842it [1:41:59, 7.80s/it] 843it [1:42:06, 7.71s/it] 844it [1:42:14, 7.68s/it] 845it [1:42:22, 7.69s/it] 846it [1:42:29, 7.75s/it] 847it [1:42:37, 7.68s/it] 848it [1:42:44, 7.60s/it] 849it [1:42:52, 7.59s/it] 850it [1:43:00, 7.66s/it] 851it [1:43:07, 7.61s/it] 852it [1:43:15, 7.61s/it] 853it [1:43:23, 7.61s/it] 854it [1:43:31, 7.75s/it] 855it [1:43:38, 7.70s/it] 856it [1:43:45, 7.57s/it] 857it [1:43:53, 7.48s/it] 858it [1:44:00, 7.55s/it] 859it [1:44:08, 7.51s/it] 860it [1:44:15, 7.52s/it] 861it [1:44:23, 7.53s/it] 862it [1:44:31, 7.69s/it] 863it [1:44:39, 7.70s/it] 864it [1:44:47, 7.79s/it] 865it [1:44:55, 7.85s/it] 866it [1:45:03, 8.08s/it] 867it [1:45:12, 8.13s/it] 868it [1:45:20, 8.14s/it] 869it [1:45:28, 8.12s/it] 870it [1:45:37, 8.31s/it] 871it [1:45:45, 8.34s/it] 872it [1:45:53, 8.33s/it] 873it [1:46:02, 8.31s/it] 874it [1:46:10, 8.46s/it] 875it [1:46:19, 8.48s/it] 876it [1:46:27, 8.36s/it] 877it [1:46:35, 8.23s/it] 878it [1:46:43, 8.23s/it] 879it [1:46:51, 8.22s/it] 880it [1:46:59, 8.08s/it] 881it [1:47:07, 7.96s/it] 882it [1:47:15, 7.96s/it] 883it [1:47:23, 7.97s/it] 884it [1:47:30, 7.91s/it] 885it [1:47:38, 7.93s/it] 886it [1:47:47, 8.00s/it] 887it [1:47:55, 8.08s/it] 888it [1:48:03, 8.00s/it] 889it [1:48:10, 7.92s/it] 890it [1:48:18, 7.88s/it] 891it [1:48:26, 7.93s/it] 892it [1:48:34, 7.86s/it] 893it [1:48:42, 7.84s/it] 894it [1:48:50, 7.84s/it] 895it [1:48:58, 7.95s/it] 896it [1:49:06, 7.89s/it] 897it [1:49:13, 7.81s/it] 898it [1:49:21, 7.77s/it] 899it [1:49:29, 7.86s/it] 900it [1:49:37, 7.83s/it] 901it [1:49:44, 7.80s/it] 902it [1:49:52, 7.75s/it] 903it [1:50:00, 7.88s/it] 904it [1:50:08, 7.86s/it] 905it [1:50:15, 7.73s/it] 906it [1:50:23, 7.62s/it] 907it [1:50:31, 7.71s/it] 908it [1:50:38, 7.67s/it] 909it [1:50:46, 7.59s/it] 910it [1:50:53, 7.55s/it] 911it [1:51:01, 7.67s/it] 912it [1:51:09, 7.68s/it] 913it [1:51:17, 7.71s/it] 914it [1:51:24, 7.75s/it] 915it [1:51:33, 7.94s/it] 916it [1:51:41, 7.98s/it] 917it [1:51:49, 7.93s/it] 918it [1:51:57, 7.89s/it] 919it [1:52:05, 7.99s/it] 920it [1:52:13, 8.01s/it] 921it [1:52:21, 7.93s/it] 922it [1:52:28, 7.88s/it] 923it [1:52:36, 7.90s/it] 924it [1:52:44, 7.94s/it] 925it [1:52:52, 7.88s/it] 926it [1:53:00, 7.84s/it] 927it [1:53:08, 7.85s/it] 928it [1:53:16, 7.91s/it] 929it [1:53:23, 7.82s/it] 930it [1:53:31, 7.76s/it] 931it [1:53:39, 7.77s/it] 932it [1:53:47, 7.84s/it] 933it [1:53:54, 7.80s/it] 934it [1:54:02, 7.79s/it] 935it [1:54:10, 7.80s/it] 936it [1:54:18, 7.92s/it] 937it [1:54:26, 7.88s/it] 938it [1:54:33, 7.76s/it] 939it [1:54:41, 7.67s/it] 940it [1:54:49, 7.76s/it] 941it [1:54:57, 7.71s/it] 942it [1:55:04, 7.73s/it] 943it [1:55:12, 7.72s/it] 944it [1:55:20, 7.86s/it] 945it [1:55:28, 7.88s/it] 946it [1:55:36, 7.97s/it] 947it [1:55:44, 8.04s/it] 948it [1:55:53, 8.25s/it] 949it [1:56:02, 8.32s/it] 950it [1:56:10, 8.31s/it] 951it [1:56:18, 8.31s/it] 952it [1:56:27, 8.47s/it] 953it [1:56:35, 8.43s/it] 954it [1:56:44, 8.40s/it] 955it [1:56:52, 8.37s/it] 956it [1:57:01, 8.53s/it] 957it [1:57:10, 8.55s/it] 958it [1:57:18, 8.41s/it] 959it [1:57:26, 8.27s/it] 960it [1:57:34, 8.31s/it] 961it [1:57:42, 8.28s/it] 962it [1:57:50, 8.15s/it] 963it [1:57:58, 8.03s/it] 964it [1:58:06, 8.03s/it] 965it [1:58:14, 8.03s/it] 966it [1:58:22, 7.98s/it] 967it [1:58:30, 8.00s/it] 968it [1:58:38, 8.07s/it] 969it [1:58:46, 8.18s/it] 970it [1:58:54, 8.09s/it] 971it [1:59:02, 8.01s/it] 972it [1:59:10, 8.00s/it] 973it [1:59:18, 8.01s/it] 974it [1:59:26, 7.94s/it] 975it [1:59:34, 7.89s/it] 976it [1:59:42, 7.91s/it] 977it [1:59:50, 8.03s/it] 978it [1:59:58, 7.97s/it] 979it [2:00:06, 7.89s/it] 980it [2:00:13, 7.85s/it] 981it [2:00:21, 7.95s/it] 982it [2:00:29, 7.88s/it] 983it [2:00:37, 7.87s/it] 984it [2:00:45, 7.84s/it] 985it [2:00:53, 7.97s/it] 986it [2:01:01, 7.94s/it] 987it [2:01:08, 7.64s/it] 988it [2:01:15, 7.43s/it] 989it [2:01:22, 7.40s/it] 990it [2:01:29, 7.31s/it] 991it [2:01:36, 7.20s/it] 992it [2:01:43, 7.11s/it] 993it [2:01:51, 7.23s/it] 994it [2:01:58, 7.22s/it] 995it [2:02:05, 7.25s/it] 996it [2:02:12, 7.28s/it] 997it [2:02:20, 7.46s/it] 998it [2:02:28, 7.49s/it] 999it [2:02:35, 7.44s/it] 1000it [2:02:43, 7.39s/it] 1000it [2:02:43, 7.36s/it] +Error counts: + cyclic_id: 0 + cyclic_inchikey: 0 + cyclic_scaffold: 0 + cyclic_mwt: 0 + cyclic_clogp: 0 + cyclic_tpsa: 0 +⏰ Completed process in 2:03:00.630330 ++ rm /nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/test/cyc-pep-6-12mer-70M_05.csv diff --git a/test/cyc-pep-6-12mer-70M_06.csv.gz b/test/cyc-pep-6-12mer-70M_06.csv.gz index a4ebad4b5079dc4576a97a69cdf71d48156c0fa2..b969a124bf30255ab40c419d4f33c5b2c8e6f747 100644 --- a/test/cyc-pep-6-12mer-70M_06.csv.gz +++ b/test/cyc-pep-6-12mer-70M_06.csv.gz @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:abaaee336080505b080b6be9c82a07deadfc403e1d3545703df3a979058f8d02 -size 31682076 +oid sha256:75aa920f6b77644561a323b4cbdaa7c41b4080d9850684c9121b12ffbccd8cc5 +size 74258503 diff --git a/test/cyc-pep-6-12mer-70M_06.log b/test/cyc-pep-6-12mer-70M_06.log new file mode 100644 index 0000000000000000000000000000000000000000..34d4ce6717f84aa400723c2c4bf7bd785d39cc63 --- /dev/null +++ b/test/cyc-pep-6-12mer-70M_06.log @@ -0,0 +1,337 @@ ++ module purge ++ '[' -z '' ']' ++ case "$-" in ++ __lmod_sh_dbg=x ++ '[' -n x ']' ++ set +x +Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output +Shell debugging restarted ++ unset __lmod_sh_dbg ++ return 0 ++ module load Anaconda3/2023.03 ++ '[' -z '' ']' ++ case "$-" in ++ __lmod_sh_dbg=x ++ '[' -n x ']' ++ set +x +Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output +Shell debugging restarted ++ unset __lmod_sh_dbg ++ return 0 ++ source /camp/home/johnsoe/.bashrc +++ '[' '' = yes ']' +++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' ++++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.bash hook +++ __conda_setup='export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'' + +# Copyright (C) 2012 Anaconda, Inc +# SPDX-License-Identifier: BSD-3-Clause +__conda_exe() ( + "$CONDA_EXE" $_CE_M $_CE_CONDA "$@" +) + +__conda_hashr() { + if [ -n "${ZSH_VERSION:+x}" ]; then + \rehash + elif [ -n "${POSH_VERSION:+x}" ]; then + : # pass + else + \hash -r + fi +} + +__conda_activate() { + if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then + # Handle transition from shell activated with conda <= 4.3 to a subsequent activation + # after conda updated to >= 4.4. See issue #6173. + PS1="$CONDA_PS1_BACKUP" + \unset CONDA_PS1_BACKUP + fi + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return + \eval "$ask_conda" + __conda_hashr +} + +__conda_reactivate() { + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return + \eval "$ask_conda" + __conda_hashr +} + +conda() { + \local cmd="${1-__missing__}" + case "$cmd" in + activate|deactivate) + __conda_activate "$@" + ;; + install|update|upgrade|remove|uninstall) + __conda_exe "$@" || \return + __conda_reactivate + ;; + *) + __conda_exe "$@" + ;; + esac +} + +if [ -z "${CONDA_SHLVL+x}" ]; then + \export CONDA_SHLVL=0 + # In dev-mode CONDA_EXE is python.exe and on Windows + # it is in a different relative location to condabin. + if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then + PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}" + else + PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}" + fi + \export PATH + + # We'\''re not allowing PS1 to be unbound. It must at least be set. + # However, we'\''re not exporting it, which can cause problems when starting a second shell + # via a first shell (i.e. starting zsh from bash). + if [ -z "${PS1+x}" ]; then + PS1= + fi +fi + +conda activate base' +++ '[' 0 -eq 0 ']' +++ eval 'export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'' + +# Copyright (C) 2012 Anaconda, Inc +# SPDX-License-Identifier: BSD-3-Clause +__conda_exe() ( + "$CONDA_EXE" $_CE_M $_CE_CONDA "$@" +) + +__conda_hashr() { + if [ -n "${ZSH_VERSION:+x}" ]; then + \rehash + elif [ -n "${POSH_VERSION:+x}" ]; then + : # pass + else + \hash -r + fi +} + +__conda_activate() { + if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then + # Handle transition from shell activated with conda <= 4.3 to a subsequent activation + # after conda updated to >= 4.4. See issue #6173. + PS1="$CONDA_PS1_BACKUP" + \unset CONDA_PS1_BACKUP + fi + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return + \eval "$ask_conda" + __conda_hashr +} + +__conda_reactivate() { + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return + \eval "$ask_conda" + __conda_hashr +} + +conda() { + \local cmd="${1-__missing__}" + case "$cmd" in + activate|deactivate) + __conda_activate "$@" + ;; + install|update|upgrade|remove|uninstall) + __conda_exe "$@" || \return + __conda_reactivate + ;; + *) + __conda_exe "$@" + ;; + esac +} + +if [ -z "${CONDA_SHLVL+x}" ]; then + \export CONDA_SHLVL=0 + # In dev-mode CONDA_EXE is python.exe and on Windows + # it is in a different relative location to condabin. + if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then + PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}" + else + PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}" + fi + \export PATH + + # We'\''re not allowing PS1 to be unbound. It must at least be set. + # However, we'\''re not exporting it, which can cause problems when starting a second shell + # via a first shell (i.e. starting zsh from bash). + if [ -z "${PS1+x}" ]; then + PS1= + fi +fi + +conda activate base' ++++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda ++++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda ++++ export _CE_M= ++++ _CE_M= ++++ export _CE_CONDA= ++++ _CE_CONDA= ++++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ '[' -z x ']' ++++ conda activate base ++++ local cmd=activate ++++ case "$cmd" in ++++ __conda_activate activate base ++++ '[' -n '' ']' ++++ local ask_conda +++++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++++ __conda_exe shell.posix activate base +++++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate base ++++ ask_conda='PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_SHLVL='\''6'\'' +export CONDA_DEFAULT_ENV='\''base'\'' +export CONDA_PROMPT_MODIFIER='\''(base) '\'' +export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' ++++ eval 'PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_SHLVL='\''6'\'' +export CONDA_DEFAULT_ENV='\''base'\'' +export CONDA_PROMPT_MODIFIER='\''(base) '\'' +export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' +++++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++++ export CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0 +++++ CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0 +++++ export CONDA_SHLVL=6 +++++ CONDA_SHLVL=6 +++++ export CONDA_DEFAULT_ENV=base +++++ CONDA_DEFAULT_ENV=base +++++ export 'CONDA_PROMPT_MODIFIER=(base) ' +++++ CONDA_PROMPT_MODIFIER='(base) ' +++++ export CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev +++++ CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev +++++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++++ export _CE_M= +++++ _CE_M= +++++ export _CE_CONDA= +++++ _CE_CONDA= +++++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python +++++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ __conda_hashr ++++ '[' -n '' ']' ++++ '[' -n '' ']' ++++ hash -r +++ unset __conda_setup ++ conda activate schemist-dev ++ local cmd=activate ++ case "$cmd" in ++ __conda_activate activate schemist-dev ++ '[' -n '' ']' ++ local ask_conda +++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++ __conda_exe shell.posix activate schemist-dev +++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate schemist-dev ++ ask_conda='PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_SHLVL='\''7'\'' +export CONDA_DEFAULT_ENV='\''schemist-dev'\'' +export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\'' +export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' ++ eval 'PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_SHLVL='\''7'\'' +export CONDA_DEFAULT_ENV='\''schemist-dev'\'' +export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\'' +export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' +++ PS1='(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++ export CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev +++ CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev +++ export CONDA_SHLVL=7 +++ CONDA_SHLVL=7 +++ export CONDA_DEFAULT_ENV=schemist-dev +++ CONDA_DEFAULT_ENV=schemist-dev +++ export 'CONDA_PROMPT_MODIFIER=(schemist-dev) ' +++ CONDA_PROMPT_MODIFIER='(schemist-dev) ' +++ export CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0 +++ CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0 +++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++ export _CE_M= +++ _CE_M= +++ export _CE_CONDA= +++ _CE_CONDA= +++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python +++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++ __conda_hashr ++ '[' -n '' ']' ++ '[' -n '' ']' ++ hash -r ++ CHUNK_HEAD_FILE=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz ++ INPUT=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/test/cyc-pep-6-12mer-70M_06.csv ++ COLUMN=cysteine_to_N_cyclization ++ PREFIX=cyclic_ ++ AWK='1 { print $8, $1, $2, $10, $3 }' ++ '[' -z cysteine_to_N_cyclization ']' ++ '[' -z cyclic_ ']' ++ '[' -z '1 { print $8, $1, $2, $10, $3 }' ']' ++ cat /dev/fd/63 /nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/test/cyc-pep-6-12mer-70M_06.csv +++ zcat /nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz +++ head -n1 ++ awk -F, -v OFS=, '1 { print $8, $1, $2, $10, $3 }' +++ tr ' ' , ++ schemist convert -f csv --column cysteine_to_N_cyclization --to id inchikey scaffold mwt clogp tpsa --prefix cyclic_ --options prefix=SCB- ++ gzip --best +🚀 Converting between string representations with the following parameters: + subcommand: convert + output: <_io.TextIOWrapper name='' mode='w' encoding='utf-8'> + format: csv + input: <_io.TextIOWrapper name='' mode='r' encoding='utf-8'> + representation: SMILES + column: cysteine_to_N_cyclization + prefix: cyclic_ + to: ['id', 'inchikey', 'scaffold', 'mwt', 'clogp', 'tpsa'] + options: ['prefix=SCB-'] + func: + 0it [00:00, ?it/s] 1it [00:07, 7.82s/it] 2it [00:15, 7.70s/it] 3it [00:22, 7.56s/it] 4it [00:30, 7.45s/it] 5it [00:37, 7.54s/it] 6it [00:45, 7.52s/it] 7it [00:52, 7.40s/it] 8it [00:59, 7.33s/it] 9it [01:07, 7.38s/it] 10it [01:14, 7.40s/it] 11it [01:21, 7.32s/it] 12it [01:28, 7.28s/it] 13it [01:36, 7.28s/it] 14it [01:43, 7.33s/it] 15it [01:50, 7.26s/it] 16it [01:57, 7.26s/it] 17it [02:05, 7.30s/it] 18it [02:13, 7.47s/it] 19it [02:20, 7.44s/it] 20it [02:27, 7.32s/it] 21it [02:34, 7.23s/it] 22it [02:42, 7.30s/it] 23it [02:49, 7.25s/it] 24it [02:56, 7.29s/it] 25it [03:03, 7.28s/it] 26it [03:11, 7.42s/it] 27it [03:19, 7.43s/it] 28it [03:26, 7.52s/it] 29it [03:34, 7.57s/it] 30it [03:43, 7.86s/it] 31it [03:51, 8.03s/it] 32it [03:59, 8.11s/it] 33it [04:07, 8.14s/it] 34it [04:16, 8.37s/it] 35it [04:25, 8.40s/it] 36it [04:33, 8.40s/it] 37it [04:42, 8.45s/it] 38it [04:51, 8.65s/it] 39it [05:00, 8.68s/it] 40it [05:08, 8.54s/it] 41it [05:16, 8.37s/it] 42it [05:24, 8.42s/it] 43it [05:33, 8.36s/it] 44it [05:41, 8.28s/it] 45it [05:49, 8.15s/it] 46it [05:56, 8.05s/it] 47it [06:04, 7.94s/it] 48it [06:12, 7.82s/it] 49it [06:19, 7.79s/it] 50it [06:27, 7.86s/it] 51it [06:35, 7.91s/it] 52it [06:43, 7.79s/it] 53it [06:50, 7.71s/it] 54it [06:58, 7.68s/it] 55it [07:06, 7.69s/it] 56it [07:13, 7.60s/it] 57it [07:21, 7.56s/it] 58it [07:28, 7.55s/it] 59it [07:36, 7.68s/it] 60it [07:44, 7.64s/it] 61it [07:51, 7.61s/it] 62it [07:59, 7.58s/it] 63it [08:07, 7.67s/it] 64it [08:14, 7.63s/it] 65it [08:22, 7.59s/it] 66it [08:29, 7.55s/it] 67it [08:37, 7.66s/it] 68it [08:45, 7.66s/it] 69it [08:51, 7.39s/it] 70it [08:58, 7.18s/it] 71it [09:05, 7.24s/it] 72it [09:12, 7.14s/it] 73it [09:19, 7.06s/it] 74it [09:26, 6.99s/it] 75it [09:34, 7.17s/it] 76it [09:41, 7.22s/it] 77it [09:48, 7.26s/it] 78it [09:56, 7.32s/it] 79it [10:04, 7.54s/it] 80it [10:12, 7.57s/it] 81it [10:19, 7.51s/it] 82it [10:26, 7.46s/it] 83it [10:34, 7.57s/it] 84it [10:42, 7.59s/it] 85it [10:49, 7.50s/it] 86it [10:56, 7.44s/it] 87it [11:04, 7.50s/it] 88it [11:11, 7.51s/it] 89it [11:19, 7.41s/it] 90it [11:26, 7.37s/it] 91it [11:33, 7.43s/it] 92it [11:41, 7.47s/it] 93it [11:48, 7.41s/it] 94it [11:56, 7.36s/it] 95it [12:03, 7.38s/it] 96it [12:11, 7.45s/it] 97it [12:18, 7.39s/it] 98it [12:25, 7.39s/it] 99it [12:33, 7.42s/it] 100it [12:40, 7.51s/it] 101it [12:48, 7.46s/it] 102it [12:55, 7.32s/it] 103it [13:02, 7.27s/it] 104it [13:09, 7.33s/it] 105it [13:17, 7.27s/it] 106it [13:24, 7.31s/it] 107it [13:31, 7.30s/it] 108it [13:39, 7.47s/it] 109it [13:47, 7.48s/it] 110it [13:54, 7.60s/it] 111it [14:02, 7.65s/it] 112it [14:11, 7.84s/it] 113it [14:19, 7.88s/it] 114it [14:26, 7.87s/it] 115it [14:34, 7.87s/it] 116it [14:43, 8.05s/it] 117it [14:51, 8.07s/it] 118it [14:59, 8.04s/it] 119it [15:07, 8.04s/it] 120it [15:15, 8.20s/it] 121it [15:24, 8.23s/it] 122it [15:32, 8.12s/it] 123it [15:39, 7.98s/it] 124it [15:47, 7.99s/it] 125it [15:55, 7.95s/it] 126it [16:02, 7.77s/it] 127it [16:10, 7.58s/it] 128it [16:17, 7.59s/it] 129it [16:25, 7.58s/it] 130it [16:32, 7.52s/it] 131it [16:40, 7.50s/it] 132it [16:47, 7.58s/it] 133it [16:55, 7.62s/it] 134it [17:02, 7.50s/it] 135it [17:09, 7.39s/it] 136it [17:17, 7.35s/it] 137it [17:24, 7.38s/it] 138it [17:31, 7.33s/it] 139it [17:39, 7.32s/it] 140it [17:46, 7.35s/it] 141it [17:54, 7.43s/it] 142it [18:01, 7.37s/it] 143it [18:08, 7.29s/it] 144it [18:15, 7.24s/it] 145it [18:23, 7.32s/it] 146it [18:30, 7.27s/it] 147it [18:37, 7.27s/it] 148it [18:44, 7.23s/it] 149it [18:52, 7.35s/it] 150it [18:59, 7.32s/it] 151it [19:06, 7.20s/it] 152it [19:13, 7.14s/it] 153it [19:20, 7.24s/it] 154it [19:28, 7.20s/it] 155it [19:35, 7.15s/it] 156it [19:42, 7.09s/it] 157it [19:49, 7.24s/it] 158it [19:56, 7.23s/it] 159it [20:04, 7.26s/it] 160it [20:11, 7.31s/it] 161it [20:19, 7.54s/it] 162it [20:27, 7.61s/it] 163it [20:34, 7.58s/it] 164it [20:42, 7.55s/it] 165it [20:50, 7.67s/it] 166it [20:57, 7.65s/it] 167it [21:05, 7.55s/it] 168it [21:12, 7.47s/it] 169it [21:20, 7.54s/it] 170it [21:27, 7.52s/it] 171it [21:34, 7.43s/it] 172it [21:42, 7.38s/it] 173it [21:49, 7.43s/it] 174it [21:57, 7.46s/it] 175it [22:04, 7.39s/it] 176it [22:11, 7.34s/it] 177it [22:19, 7.36s/it] 178it [22:26, 7.40s/it] 179it [22:33, 7.33s/it] 180it [22:41, 7.35s/it] 181it [22:48, 7.42s/it] 182it [22:56, 7.51s/it] 183it [23:03, 7.43s/it] 184it [23:10, 7.29s/it] 185it [23:17, 7.19s/it] 186it [23:25, 7.33s/it] 187it [23:32, 7.27s/it] 188it [23:39, 7.30s/it] 189it [23:47, 7.32s/it] 190it [23:54, 7.43s/it] 191it [24:02, 7.42s/it] 192it [24:10, 7.51s/it] 193it [24:18, 7.67s/it] 194it [24:26, 7.92s/it] 195it [24:34, 7.98s/it] 196it [24:42, 8.03s/it] 197it [24:50, 8.06s/it] 198it [24:59, 8.25s/it] 199it [25:08, 8.29s/it] 200it [25:16, 8.28s/it] 201it [25:24, 8.29s/it] 202it [25:33, 8.46s/it] 203it [25:42, 8.49s/it] 204it [25:50, 8.34s/it] 205it [25:57, 8.19s/it] 206it [26:06, 8.21s/it] 207it [26:14, 8.17s/it] 208it [26:21, 7.98s/it] 209it [26:29, 7.83s/it] 210it [26:37, 7.82s/it] 211it [26:44, 7.78s/it] 212it [26:52, 7.70s/it] 213it [26:59, 7.70s/it] 214it [27:07, 7.77s/it] 215it [27:15, 7.84s/it] 216it [27:23, 7.78s/it] 217it [27:30, 7.67s/it] 218it [27:38, 7.64s/it] 219it [27:46, 7.72s/it] 220it [27:54, 7.70s/it] 221it [28:01, 7.70s/it] 222it [28:09, 7.72s/it] 223it [28:17, 7.83s/it] 224it [28:25, 7.78s/it] 225it [28:32, 7.71s/it] 226it [28:40, 7.66s/it] 227it [28:48, 7.77s/it] 228it [28:56, 7.73s/it] 229it [29:03, 7.69s/it] 230it [29:11, 7.66s/it] 231it [29:19, 7.77s/it] 232it [29:26, 7.77s/it] 233it [29:33, 7.52s/it] 234it [29:40, 7.29s/it] 235it [29:48, 7.31s/it] 236it [29:55, 7.24s/it] 237it [30:02, 7.15s/it] 238it [30:08, 7.09s/it] 239it [30:16, 7.19s/it] 240it [30:23, 7.18s/it] 241it [30:30, 7.21s/it] 242it [30:38, 7.23s/it] 243it [30:45, 7.40s/it] 244it [30:53, 7.44s/it] 245it [31:00, 7.38s/it] 246it [31:08, 7.36s/it] 247it [31:15, 7.45s/it] 248it [31:23, 7.46s/it] 249it [31:30, 7.37s/it] 250it [31:37, 7.33s/it] 251it [31:45, 7.39s/it] 252it [31:52, 7.40s/it] 253it [31:59, 7.33s/it] 254it [32:06, 7.27s/it] 255it [32:14, 7.28s/it] 256it [32:21, 7.32s/it] 257it [32:28, 7.24s/it] 258it [32:35, 7.16s/it] 259it [32:42, 7.15s/it] 260it [32:50, 7.21s/it] 261it [32:57, 7.15s/it] 262it [33:04, 7.12s/it] 263it [33:11, 7.14s/it] 264it [33:18, 7.29s/it] 265it [33:26, 7.25s/it] 266it [33:32, 7.12s/it] 267it [33:39, 7.03s/it] 268it [33:47, 7.13s/it] 269it [33:54, 7.12s/it] 270it [34:01, 7.14s/it] 271it [34:08, 7.12s/it] 272it [34:16, 7.30s/it] 273it [34:23, 7.30s/it] 274it [34:31, 7.39s/it] 275it [34:38, 7.44s/it] 276it [34:46, 7.63s/it] 277it [34:54, 7.69s/it] 278it [35:02, 7.68s/it] 279it [35:09, 7.66s/it] 280it [35:17, 7.81s/it] 281it [35:25, 7.86s/it] 282it [35:33, 7.81s/it] 283it [35:41, 7.79s/it] 284it [35:49, 7.90s/it] 285it [35:57, 7.93s/it] 286it [36:05, 7.82s/it] 287it [36:12, 7.70s/it] 288it [36:20, 7.71s/it] 289it [36:27, 7.69s/it] 290it [36:35, 7.55s/it] 291it [36:42, 7.44s/it] 292it [36:49, 7.41s/it] 293it [36:57, 7.43s/it] 294it [37:04, 7.36s/it] 295it [37:11, 7.37s/it] 296it [37:19, 7.40s/it] 297it [37:26, 7.50s/it] 298it [37:34, 7.44s/it] 299it [37:41, 7.37s/it] 300it [37:48, 7.32s/it] 301it [37:56, 7.41s/it] 302it [38:03, 7.35s/it] 303it [38:10, 7.32s/it] 304it [38:18, 7.33s/it] 305it [38:25, 7.44s/it] 306it [38:33, 7.43s/it] 307it [38:40, 7.34s/it] 308it [38:47, 7.32s/it] 309it [38:55, 7.44s/it] 310it [39:02, 7.43s/it] 311it [39:09, 7.39s/it] 312it [39:17, 7.35s/it] 313it [39:25, 7.51s/it] 314it [39:32, 7.48s/it] 315it [39:39, 7.35s/it] 316it [39:46, 7.22s/it] 317it [39:53, 7.28s/it] 318it [40:00, 7.23s/it] 319it [40:07, 7.16s/it] 320it [40:14, 7.12s/it] 321it [40:22, 7.22s/it] 322it [40:29, 7.22s/it] 323it [40:37, 7.26s/it] 324it [40:44, 7.33s/it] 325it [40:52, 7.46s/it] 326it [40:59, 7.53s/it] 327it [41:07, 7.47s/it] 328it [41:14, 7.46s/it] 329it [41:22, 7.50s/it] 330it [41:30, 7.57s/it] 331it [41:37, 7.48s/it] 332it [41:44, 7.44s/it] 333it [41:52, 7.44s/it] 334it [41:59, 7.51s/it] 335it [42:07, 7.46s/it] 336it [42:14, 7.40s/it] 337it [42:21, 7.34s/it] 338it [42:29, 7.43s/it] 339it [42:36, 7.37s/it] 340it [42:43, 7.29s/it] 341it [42:50, 7.24s/it] 342it [42:58, 7.35s/it] 343it [43:05, 7.29s/it] 344it [43:12, 7.29s/it] 345it [43:20, 7.28s/it] 346it [43:27, 7.41s/it] 347it [43:35, 7.42s/it] 348it [43:42, 7.28s/it] 349it [43:49, 7.18s/it] 350it [43:56, 7.28s/it] 351it [44:03, 7.24s/it] 352it [44:10, 7.22s/it] 353it [44:18, 7.24s/it] 354it [44:25, 7.40s/it] 355it [44:33, 7.43s/it] 356it [44:41, 7.50s/it] 357it [44:48, 7.58s/it] 358it [44:57, 7.79s/it] 359it [45:05, 7.84s/it] 360it [45:12, 7.84s/it] 361it [45:20, 7.85s/it] 362it [45:29, 7.98s/it] 363it [45:37, 8.01s/it] 364it [45:45, 8.00s/it] 365it [45:53, 7.99s/it] 366it [46:01, 8.09s/it] 367it [46:09, 8.17s/it] 368it [46:17, 8.06s/it] 369it [46:25, 7.94s/it] 370it [46:33, 7.93s/it] 371it [46:41, 7.94s/it] 372it [46:48, 7.81s/it] 373it [46:56, 7.69s/it] 374it [47:03, 7.64s/it] 375it [47:11, 7.66s/it] 376it [47:18, 7.63s/it] 377it [47:26, 7.65s/it] 378it [47:34, 7.69s/it] 379it [47:42, 7.84s/it] 380it [47:50, 7.80s/it] 381it [47:57, 7.68s/it] 382it [48:04, 7.58s/it] 383it [48:12, 7.65s/it] 384it 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890it [1:53:31, 7.72s/it] 891it [1:53:39, 7.78s/it] 892it [1:53:47, 7.70s/it] 893it [1:53:54, 7.63s/it] 894it [1:54:02, 7.58s/it] 895it [1:54:10, 7.68s/it] 896it [1:54:17, 7.68s/it] 897it [1:54:25, 7.69s/it] 898it [1:54:33, 7.75s/it] 899it [1:54:41, 7.91s/it] 900it [1:54:49, 7.95s/it] 901it [1:54:57, 7.91s/it] 902it [1:55:05, 7.87s/it] 903it [1:55:13, 7.95s/it] 904it [1:55:21, 7.97s/it] 905it [1:55:29, 7.92s/it] 906it [1:55:36, 7.88s/it] 907it [1:55:44, 7.91s/it] 908it [1:55:53, 7.96s/it] 909it [1:56:00, 7.87s/it] 910it [1:56:08, 7.82s/it] 911it [1:56:16, 7.82s/it] 912it [1:56:24, 7.91s/it] 913it [1:56:32, 7.83s/it] 914it [1:56:39, 7.78s/it] 915it [1:56:47, 7.75s/it] 916it [1:56:55, 7.85s/it] 917it [1:57:03, 7.82s/it] 918it [1:57:10, 7.80s/it] 919it [1:57:18, 7.81s/it] 920it [1:57:26, 7.92s/it] 921it [1:57:34, 7.88s/it] 922it [1:57:42, 7.79s/it] 923it [1:57:49, 7.68s/it] 924it [1:57:57, 7.75s/it] 925it [1:58:05, 7.71s/it] 926it [1:58:13, 7.72s/it] 927it [1:58:20, 7.72s/it] 928it [1:58:28, 7.88s/it] 929it [1:58:36, 7.88s/it] 930it [1:58:45, 7.97s/it] 931it [1:58:53, 8.04s/it] 932it [1:59:01, 8.24s/it] 933it [1:59:10, 8.30s/it] 934it [1:59:18, 8.29s/it] 935it [1:59:26, 8.29s/it] 936it [1:59:35, 8.44s/it] 937it [1:59:44, 8.47s/it] 938it [1:59:52, 8.44s/it] 939it [2:00:01, 8.45s/it] 940it [2:00:10, 8.59s/it] 941it [2:00:18, 8.62s/it] 942it [2:00:26, 8.50s/it] 943it [2:00:34, 8.36s/it] 944it [2:00:43, 8.35s/it] 945it [2:00:51, 8.34s/it] 946it [2:00:59, 8.21s/it] 947it [2:01:07, 8.09s/it] 948it [2:01:15, 8.10s/it] 949it [2:01:23, 8.08s/it] 950it [2:01:31, 8.01s/it] 951it [2:01:39, 8.01s/it] 952it [2:01:47, 8.08s/it] 953it [2:01:56, 8.19s/it] 954it [2:02:03, 8.11s/it] 955it [2:02:11, 8.03s/it] 956it [2:02:19, 7.97s/it] 957it [2:02:27, 8.03s/it] 958it [2:02:35, 7.96s/it] 959it [2:02:43, 7.94s/it] 960it [2:02:51, 7.92s/it] 961it [2:02:59, 8.03s/it] 962it [2:03:07, 8.01s/it] 963it [2:03:15, 7.92s/it] 964it [2:03:22, 7.84s/it] 965it [2:03:31, 7.96s/it] 966it [2:03:39, 7.94s/it] 967it [2:03:46, 7.88s/it] 968it [2:03:54, 7.81s/it] 969it [2:04:02, 7.94s/it] 970it [2:04:10, 7.94s/it] 971it [2:04:18, 7.76s/it] 972it [2:04:25, 7.60s/it] 973it [2:04:32, 7.64s/it] 974it [2:04:40, 7.59s/it] 975it [2:04:47, 7.52s/it] 976it [2:04:55, 7.47s/it] 977it [2:05:02, 7.57s/it] 978it [2:05:10, 7.55s/it] 979it [2:05:18, 7.56s/it] 980it [2:05:25, 7.61s/it] 981it [2:05:33, 7.77s/it] 982it [2:05:41, 7.84s/it] 983it [2:05:49, 7.80s/it] 984it [2:05:57, 7.75s/it] 985it [2:06:05, 7.82s/it] 986it [2:06:13, 7.86s/it] 987it [2:06:20, 7.80s/it] 988it [2:06:28, 7.75s/it] 989it [2:06:36, 7.78s/it] 990it [2:06:44, 7.82s/it] 991it [2:06:51, 7.74s/it] 992it [2:06:59, 7.72s/it] 993it [2:07:07, 7.76s/it] 994it [2:07:15, 7.83s/it] 995it [2:07:22, 7.78s/it] 996it [2:07:30, 7.71s/it] 997it [2:07:38, 7.68s/it] 998it [2:07:46, 7.78s/it] 999it [2:07:53, 7.73s/it] 1000it [2:08:01, 7.75s/it] 1000it [2:08:01, 7.68s/it] +Error counts: + cyclic_id: 0 + cyclic_inchikey: 0 + cyclic_scaffold: 0 + cyclic_mwt: 0 + cyclic_clogp: 0 + cyclic_tpsa: 0 +⏰ Completed process in 2:08:19.491369 ++ rm /nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/test/cyc-pep-6-12mer-70M_06.csv diff --git a/test/cyc-pep-6-12mer-70M_07.csv.gz b/test/cyc-pep-6-12mer-70M_07.csv.gz index d31c69ef5974f9eb28bac640df98ed2560f63f2b..147eb69c7fc1f213b8a6d617f0759e51f504e50f 100644 --- a/test/cyc-pep-6-12mer-70M_07.csv.gz +++ b/test/cyc-pep-6-12mer-70M_07.csv.gz @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:201b456bab747100162f73dd54cd3066027760d9d3246d23bca725959784a321 -size 34198877 +oid sha256:0235bf78583cf8847a849cb826a05dc280a6a816dc8f758c84d0fd852f55a030 +size 78737230 diff --git a/test/cyc-pep-6-12mer-70M_07.log b/test/cyc-pep-6-12mer-70M_07.log new file mode 100644 index 0000000000000000000000000000000000000000..34dbd849b5a426dcb31922f045f4a2fe9dde474e --- /dev/null +++ b/test/cyc-pep-6-12mer-70M_07.log @@ -0,0 +1,337 @@ ++ module purge ++ '[' -z '' ']' ++ case "$-" in ++ __lmod_sh_dbg=x ++ '[' -n x ']' ++ set +x +Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output +Shell debugging restarted ++ unset __lmod_sh_dbg ++ return 0 ++ module load Anaconda3/2023.03 ++ '[' -z '' ']' ++ case "$-" in ++ __lmod_sh_dbg=x ++ '[' -n x ']' ++ set +x +Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output +Shell debugging restarted ++ unset __lmod_sh_dbg ++ return 0 ++ source /camp/home/johnsoe/.bashrc +++ '[' '' = yes ']' +++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' ++++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.bash hook +++ __conda_setup='export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'' + +# Copyright (C) 2012 Anaconda, Inc +# SPDX-License-Identifier: BSD-3-Clause +__conda_exe() ( + "$CONDA_EXE" $_CE_M $_CE_CONDA "$@" +) + +__conda_hashr() { + if [ -n "${ZSH_VERSION:+x}" ]; then + \rehash + elif [ -n "${POSH_VERSION:+x}" ]; then + : # pass + else + \hash -r + fi +} + +__conda_activate() { + if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then + # Handle transition from shell activated with conda <= 4.3 to a subsequent activation + # after conda updated to >= 4.4. See issue #6173. + PS1="$CONDA_PS1_BACKUP" + \unset CONDA_PS1_BACKUP + fi + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return + \eval "$ask_conda" + __conda_hashr +} + +__conda_reactivate() { + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return + \eval "$ask_conda" + __conda_hashr +} + +conda() { + \local cmd="${1-__missing__}" + case "$cmd" in + activate|deactivate) + __conda_activate "$@" + ;; + install|update|upgrade|remove|uninstall) + __conda_exe "$@" || \return + __conda_reactivate + ;; + *) + __conda_exe "$@" + ;; + esac +} + +if [ -z "${CONDA_SHLVL+x}" ]; then + \export CONDA_SHLVL=0 + # In dev-mode CONDA_EXE is python.exe and on Windows + # it is in a different relative location to condabin. + if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then + PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}" + else + PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}" + fi + \export PATH + + # We'\''re not allowing PS1 to be unbound. It must at least be set. + # However, we'\''re not exporting it, which can cause problems when starting a second shell + # via a first shell (i.e. starting zsh from bash). + if [ -z "${PS1+x}" ]; then + PS1= + fi +fi + +conda activate base' +++ '[' 0 -eq 0 ']' +++ eval 'export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'' + +# Copyright (C) 2012 Anaconda, Inc +# SPDX-License-Identifier: BSD-3-Clause +__conda_exe() ( + "$CONDA_EXE" $_CE_M $_CE_CONDA "$@" +) + +__conda_hashr() { + if [ -n "${ZSH_VERSION:+x}" ]; then + \rehash + elif [ -n "${POSH_VERSION:+x}" ]; then + : # pass + else + \hash -r + fi +} + +__conda_activate() { + if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then + # Handle transition from shell activated with conda <= 4.3 to a subsequent activation + # after conda updated to >= 4.4. See issue #6173. + PS1="$CONDA_PS1_BACKUP" + \unset CONDA_PS1_BACKUP + fi + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return + \eval "$ask_conda" + __conda_hashr +} + +__conda_reactivate() { + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return + \eval "$ask_conda" + __conda_hashr +} + +conda() { + \local cmd="${1-__missing__}" + case "$cmd" in + activate|deactivate) + __conda_activate "$@" + ;; + install|update|upgrade|remove|uninstall) + __conda_exe "$@" || \return + __conda_reactivate + ;; + *) + __conda_exe "$@" + ;; + esac +} + +if [ -z "${CONDA_SHLVL+x}" ]; then + \export CONDA_SHLVL=0 + # In dev-mode CONDA_EXE is python.exe and on Windows + # it is in a different relative location to condabin. + if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then + PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}" + else + PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}" + fi + \export PATH + + # We'\''re not allowing PS1 to be unbound. It must at least be set. + # However, we'\''re not exporting it, which can cause problems when starting a second shell + # via a first shell (i.e. starting zsh from bash). + if [ -z "${PS1+x}" ]; then + PS1= + fi +fi + +conda activate base' ++++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda ++++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda ++++ export _CE_M= ++++ _CE_M= ++++ export _CE_CONDA= ++++ _CE_CONDA= ++++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ '[' -z x ']' ++++ conda activate base ++++ local cmd=activate ++++ case "$cmd" in ++++ __conda_activate activate base ++++ '[' -n '' ']' ++++ local ask_conda +++++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++++ __conda_exe shell.posix activate base +++++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate base ++++ ask_conda='PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_SHLVL='\''6'\'' +export CONDA_DEFAULT_ENV='\''base'\'' +export CONDA_PROMPT_MODIFIER='\''(base) '\'' +export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' ++++ eval 'PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_SHLVL='\''6'\'' +export CONDA_DEFAULT_ENV='\''base'\'' +export CONDA_PROMPT_MODIFIER='\''(base) '\'' +export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' +++++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++++ export CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0 +++++ CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0 +++++ export CONDA_SHLVL=6 +++++ CONDA_SHLVL=6 +++++ export CONDA_DEFAULT_ENV=base +++++ CONDA_DEFAULT_ENV=base +++++ export 'CONDA_PROMPT_MODIFIER=(base) ' +++++ CONDA_PROMPT_MODIFIER='(base) ' +++++ export CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev +++++ CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev +++++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++++ export _CE_M= +++++ _CE_M= +++++ export _CE_CONDA= +++++ _CE_CONDA= +++++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python +++++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ __conda_hashr ++++ '[' -n '' ']' ++++ '[' -n '' ']' ++++ hash -r +++ unset __conda_setup ++ conda activate schemist-dev ++ local cmd=activate ++ case "$cmd" in ++ __conda_activate activate schemist-dev ++ '[' -n '' ']' ++ local ask_conda +++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++ __conda_exe shell.posix activate schemist-dev +++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate schemist-dev ++ ask_conda='PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_SHLVL='\''7'\'' +export CONDA_DEFAULT_ENV='\''schemist-dev'\'' +export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\'' +export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' ++ eval 'PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_SHLVL='\''7'\'' +export CONDA_DEFAULT_ENV='\''schemist-dev'\'' +export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\'' +export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' +++ PS1='(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++ export CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev +++ CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev +++ export CONDA_SHLVL=7 +++ CONDA_SHLVL=7 +++ export CONDA_DEFAULT_ENV=schemist-dev +++ CONDA_DEFAULT_ENV=schemist-dev +++ export 'CONDA_PROMPT_MODIFIER=(schemist-dev) ' +++ CONDA_PROMPT_MODIFIER='(schemist-dev) ' +++ export CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0 +++ CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0 +++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++ export _CE_M= +++ _CE_M= +++ export _CE_CONDA= +++ _CE_CONDA= +++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python +++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++ __conda_hashr ++ '[' -n '' ']' ++ '[' -n '' ']' ++ hash -r ++ CHUNK_HEAD_FILE=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz ++ INPUT=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/test/cyc-pep-6-12mer-70M_07.csv ++ COLUMN=cysteine_to_N_cyclization ++ PREFIX=cyclic_ ++ AWK='1 { print $8, $1, $2, $10, $3 }' ++ '[' -z cysteine_to_N_cyclization ']' ++ '[' -z cyclic_ ']' ++ '[' -z '1 { print $8, $1, $2, $10, $3 }' ']' ++ cat /dev/fd/63 /nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/test/cyc-pep-6-12mer-70M_07.csv ++ awk -F, -v OFS=, '1 { print $8, $1, $2, $10, $3 }' +++ zcat /nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz ++ schemist convert -f csv --column cysteine_to_N_cyclization --to id inchikey scaffold mwt clogp tpsa --prefix cyclic_ --options prefix=SCB- ++ gzip --best +++ head -n1 +++ tr ' ' , +🚀 Converting between string representations with the following parameters: + subcommand: convert + output: <_io.TextIOWrapper name='' mode='w' encoding='utf-8'> + format: csv + input: <_io.TextIOWrapper name='' mode='r' encoding='utf-8'> + representation: SMILES + column: cysteine_to_N_cyclization + prefix: cyclic_ + to: ['id', 'inchikey', 'scaffold', 'mwt', 'clogp', 'tpsa'] + options: ['prefix=SCB-'] + func: + 0it [00:00, ?it/s] 1it [00:07, 7.91s/it] 2it [00:16, 8.19s/it] 3it [00:24, 8.04s/it] 4it [00:31, 7.85s/it] 5it [00:39, 7.73s/it] 6it [00:47, 7.83s/it] 7it [00:54, 7.78s/it] 8it [01:02, 7.81s/it] 9it [01:10, 7.82s/it] 10it [01:19, 8.01s/it] 11it [01:27, 8.01s/it] 12it [01:35, 8.12s/it] 13it [01:43, 8.17s/it] 14it [01:52, 8.41s/it] 15it [02:01, 8.45s/it] 16it [02:09, 8.46s/it] 17it [02:18, 8.47s/it] 18it [02:27, 8.68s/it] 19it [02:36, 8.72s/it] 20it [02:45, 8.74s/it] 21it [02:53, 8.77s/it] 22it [03:03, 8.93s/it] 23it [03:12, 8.99s/it] 24it [03:20, 8.87s/it] 25it [03:29, 8.73s/it] 26it [03:38, 8.75s/it] 27it [03:46, 8.73s/it] 28it [03:55, 8.59s/it] 29it [04:03, 8.47s/it] 30it [04:11, 8.46s/it] 31it [04:20, 8.48s/it] 32it [04:28, 8.41s/it] 33it [04:36, 8.43s/it] 34it [04:45, 8.50s/it] 35it [04:54, 8.61s/it] 36it [05:02, 8.52s/it] 37it [05:10, 8.41s/it] 38it [05:19, 8.37s/it] 39it [05:27, 8.45s/it] 40it [05:35, 8.37s/it] 41it [05:44, 8.34s/it] 42it [05:52, 8.34s/it] 43it [06:01, 8.45s/it] 44it [06:09, 8.40s/it] 45it [06:17, 8.30s/it] 46it [06:25, 8.26s/it] 47it [06:34, 8.38s/it] 48it [06:42, 8.36s/it] 49it [06:50, 8.31s/it] 50it [06:59, 8.26s/it] 51it [07:07, 8.39s/it] 52it [07:16, 8.38s/it] 53it [07:23, 8.17s/it] 54it [07:31, 7.99s/it] 55it [07:39, 8.05s/it] 56it [07:47, 7.99s/it] 57it [07:55, 7.92s/it] 58it [08:02, 7.85s/it] 59it [08:11, 7.97s/it] 60it [08:19, 7.97s/it] 61it [08:27, 7.98s/it] 62it [08:35, 8.02s/it] 63it [08:43, 8.19s/it] 64it [08:52, 8.23s/it] 65it [09:00, 8.16s/it] 66it [09:08, 8.14s/it] 67it [09:16, 8.23s/it] 68it [09:24, 8.25s/it] 69it [09:32, 8.17s/it] 70it [09:40, 8.12s/it] 71it [09:49, 8.17s/it] 72it [09:57, 8.20s/it] 73it [10:05, 8.14s/it] 74it [10:13, 8.09s/it] 75it [10:21, 8.11s/it] 76it [10:29, 8.16s/it] 77it [10:37, 8.09s/it] 78it [10:45, 8.02s/it] 79it [10:53, 8.01s/it] 80it [11:01, 8.09s/it] 81it [11:09, 8.04s/it] 82it [11:17, 8.05s/it] 83it [11:25, 8.05s/it] 84it [11:34, 8.18s/it] 85it [11:42, 8.12s/it] 86it [11:50, 7.96s/it] 87it [11:57, 7.88s/it] 88it [12:05, 7.95s/it] 89it [12:13, 7.91s/it] 90it [12:21, 7.92s/it] 91it [12:29, 7.93s/it] 92it [12:38, 8.10s/it] 93it [12:46, 8.14s/it] 94it [12:54, 8.24s/it] 95it [13:03, 8.30s/it] 96it [13:12, 8.52s/it] 97it [13:20, 8.58s/it] 98it [13:29, 8.60s/it] 99it [13:38, 8.58s/it] 100it [13:47, 8.73s/it] 101it [13:56, 8.76s/it] 102it [14:04, 8.77s/it] 103it [14:13, 8.78s/it] 104it [14:22, 8.93s/it] 105it [14:31, 8.94s/it] 106it [14:40, 8.83s/it] 107it [14:48, 8.69s/it] 108it [14:57, 8.67s/it] 109it [15:06, 8.68s/it] 110it [15:14, 8.56s/it] 111it [15:22, 8.41s/it] 112it [15:30, 8.36s/it] 113it [15:39, 8.40s/it] 114it [15:47, 8.32s/it] 115it [15:55, 8.34s/it] 116it [16:04, 8.37s/it] 117it [16:12, 8.49s/it] 118it [16:21, 8.43s/it] 119it [16:29, 8.32s/it] 120it [16:37, 8.26s/it] 121it [16:45, 8.34s/it] 122it [16:53, 8.23s/it] 123it [17:01, 8.11s/it] 124it [17:09, 8.02s/it] 125it [17:18, 8.21s/it] 126it [17:26, 8.24s/it] 127it [17:34, 8.07s/it] 128it [17:41, 7.95s/it] 129it [17:50, 8.19s/it] 130it [17:58, 8.09s/it] 131it [18:06, 7.99s/it] 132it [18:14, 7.92s/it] 133it [18:22, 8.05s/it] 134it [18:30, 8.04s/it] 135it [18:37, 7.90s/it] 136it [18:45, 7.79s/it] 137it [18:53, 7.86s/it] 138it [19:01, 7.83s/it] 139it [19:08, 7.75s/it] 140it [19:16, 7.70s/it] 141it [19:24, 7.81s/it] 142it [19:32, 7.81s/it] 143it [19:40, 7.83s/it] 144it [19:48, 7.88s/it] 145it [19:56, 8.04s/it] 146it [20:04, 8.10s/it] 147it [20:12, 8.05s/it] 148it [20:20, 8.01s/it] 149it [20:28, 8.09s/it] 150it [20:37, 8.12s/it] 151it [20:44, 8.04s/it] 152it [20:52, 8.00s/it] 153it [21:01, 8.05s/it] 154it [21:09, 8.09s/it] 155it [21:17, 8.01s/it] 156it [21:24, 7.94s/it] 157it [21:32, 7.95s/it] 158it [21:40, 8.01s/it] 159it [21:48, 7.93s/it] 160it [21:56, 7.86s/it] 161it [22:04, 7.85s/it] 162it [22:12, 7.94s/it] 163it [22:20, 7.89s/it] 164it [22:28, 7.88s/it] 165it [22:35, 7.88s/it] 166it [22:44, 8.03s/it] 167it [22:52, 7.99s/it] 168it [22:59, 7.85s/it] 169it [23:07, 7.76s/it] 170it [23:15, 7.84s/it] 171it [23:22, 7.79s/it] 172it [23:30, 7.80s/it] 173it [23:38, 7.81s/it] 174it [23:46, 7.97s/it] 175it [23:55, 8.00s/it] 176it [24:03, 8.09s/it] 177it [24:11, 8.15s/it] 178it [24:20, 8.37s/it] 179it [24:29, 8.44s/it] 180it [24:37, 8.45s/it] 181it [24:45, 8.44s/it] 182it [24:55, 8.62s/it] 183it [25:03, 8.63s/it] 184it [25:12, 8.62s/it] 185it [25:20, 8.61s/it] 186it [25:29, 8.75s/it] 187it [25:38, 8.78s/it] 188it [25:47, 8.67s/it] 189it [25:55, 8.52s/it] 190it [26:03, 8.54s/it] 191it [26:12, 8.50s/it] 192it [26:20, 8.37s/it] 193it [26:28, 8.24s/it] 194it [26:36, 8.23s/it] 195it [26:44, 8.22s/it] 196it [26:52, 8.17s/it] 197it [27:01, 8.19s/it] 198it [27:09, 8.26s/it] 199it [27:18, 8.35s/it] 200it [27:26, 8.29s/it] 201it [27:34, 8.17s/it] 202it [27:42, 8.13s/it] 203it [27:50, 8.22s/it] 204it [27:58, 8.15s/it] 205it [28:06, 8.12s/it] 206it [28:14, 8.11s/it] 207it [28:23, 8.22s/it] 208it [28:31, 8.18s/it] 209it [28:39, 8.09s/it] 210it [28:46, 8.02s/it] 211it [28:55, 8.14s/it] 212it [29:03, 8.13s/it] 213it [29:11, 8.07s/it] 214it [29:19, 8.02s/it] 215it [29:27, 8.16s/it] 216it [29:35, 8.16s/it] 217it [29:43, 7.90s/it] 218it [29:50, 7.68s/it] 219it [29:58, 7.68s/it] 220it [30:05, 7.58s/it] 221it [30:12, 7.48s/it] 222it [30:20, 7.42s/it] 223it [30:27, 7.52s/it] 224it [30:35, 7.50s/it] 225it [30:42, 7.50s/it] 226it [30:50, 7.56s/it] 227it [30:58, 7.71s/it] 228it [31:06, 7.76s/it] 229it [31:13, 7.69s/it] 230it [31:21, 7.66s/it] 231it [31:29, 7.73s/it] 232it [31:37, 7.76s/it] 233it [31:44, 7.70s/it] 234it [31:52, 7.65s/it] 235it [32:00, 7.69s/it] 236it [32:07, 7.71s/it] 237it [32:15, 7.64s/it] 238it [32:22, 7.60s/it] 239it [32:30, 7.61s/it] 240it [32:38, 7.67s/it] 241it [32:45, 7.59s/it] 242it [32:53, 7.54s/it] 243it [33:00, 7.53s/it] 244it [33:08, 7.60s/it] 245it [33:15, 7.55s/it] 246it [33:23, 7.54s/it] 247it [33:30, 7.56s/it] 248it [33:38, 7.67s/it] 249it [33:46, 7.61s/it] 250it [33:53, 7.55s/it] 251it [34:01, 7.51s/it] 252it [34:08, 7.61s/it] 253it [34:16, 7.58s/it] 254it [34:23, 7.56s/it] 255it [34:31, 7.55s/it] 256it [34:39, 7.68s/it] 257it [34:47, 7.68s/it] 258it [34:55, 7.77s/it] 259it [35:03, 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8.19s/it] 887it [2:04:12, 8.20s/it] 888it [2:04:21, 8.30s/it] 889it [2:04:29, 8.27s/it] 890it [2:04:37, 8.20s/it] 891it [2:04:45, 8.15s/it] 892it [2:04:53, 8.25s/it] 893it [2:05:01, 8.22s/it] 894it [2:05:09, 8.16s/it] 895it [2:05:17, 8.09s/it] 896it [2:05:26, 8.20s/it] 897it [2:05:34, 8.19s/it] 898it [2:05:42, 8.10s/it] 899it [2:05:50, 8.01s/it] 900it [2:05:58, 8.11s/it] 901it [2:06:06, 8.10s/it] 902it [2:06:14, 8.02s/it] 903it [2:06:22, 7.97s/it] 904it [2:06:30, 8.14s/it] 905it [2:06:38, 8.13s/it] 906it [2:06:46, 8.01s/it] 907it [2:06:54, 7.89s/it] 908it [2:07:02, 7.98s/it] 909it [2:07:10, 7.97s/it] 910it [2:07:18, 7.97s/it] 911it [2:07:26, 8.00s/it] 912it [2:07:34, 8.16s/it] 913it [2:07:43, 8.26s/it] 914it [2:07:51, 8.31s/it] 915it [2:08:00, 8.41s/it] 916it [2:08:09, 8.59s/it] 917it [2:08:18, 8.72s/it] 918it [2:08:27, 8.72s/it] 919it [2:08:36, 8.73s/it] 920it [2:08:45, 8.82s/it] 921it [2:08:54, 8.93s/it] 922it [2:09:03, 8.90s/it] 923it [2:09:12, 8.93s/it] 924it [2:09:21, 9.03s/it] 925it [2:09:30, 9.13s/it] 926it [2:09:39, 9.02s/it] 927it [2:09:47, 8.85s/it] 928it [2:09:56, 8.80s/it] 929it [2:10:05, 8.85s/it] 930it [2:10:14, 8.76s/it] 931it [2:10:22, 8.73s/it] 932it [2:10:31, 8.60s/it] 933it [2:10:39, 8.60s/it] 934it [2:10:48, 8.51s/it] 935it [2:10:56, 8.51s/it] 936it [2:11:04, 8.49s/it] 937it [2:11:13, 8.63s/it] 938it [2:11:22, 8.61s/it] 939it [2:11:30, 8.45s/it] 940it [2:11:38, 8.37s/it] 941it [2:11:47, 8.50s/it] 942it [2:11:55, 8.44s/it] 943it [2:12:04, 8.37s/it] 944it [2:12:12, 8.30s/it] 945it [2:12:20, 8.44s/it] 946it [2:12:29, 8.41s/it] 947it [2:12:37, 8.30s/it] 948it [2:12:45, 8.19s/it] 949it [2:12:53, 8.30s/it] 950it [2:13:02, 8.27s/it] 951it [2:13:10, 8.24s/it] 952it [2:13:18, 8.26s/it] 953it [2:13:27, 8.39s/it] 954it [2:13:35, 8.39s/it] 955it [2:13:43, 8.21s/it] 956it [2:13:51, 8.07s/it] 957it [2:13:59, 8.09s/it] 958it [2:14:07, 8.12s/it] 959it [2:14:15, 8.03s/it] 960it [2:14:23, 7.98s/it] 961it [2:14:31, 8.05s/it] 962it [2:14:39, 8.08s/it] 963it [2:14:47, 8.08s/it] 964it [2:14:55, 8.18s/it] 965it [2:15:04, 8.28s/it] 966it [2:15:13, 8.38s/it] 967it [2:15:21, 8.36s/it] 968it [2:15:29, 8.37s/it] 969it [2:15:38, 8.39s/it] 970it [2:15:46, 8.49s/it] 971it [2:15:55, 8.43s/it] 972it [2:16:03, 8.37s/it] 973it [2:16:11, 8.34s/it] 974it [2:16:20, 8.45s/it] 975it [2:16:28, 8.41s/it] 976it [2:16:36, 8.35s/it] 977it [2:16:45, 8.29s/it] 978it [2:16:53, 8.39s/it] 979it [2:17:02, 8.36s/it] 980it [2:17:10, 8.26s/it] 981it [2:17:18, 8.18s/it] 982it [2:17:26, 8.27s/it] 983it [2:17:34, 8.25s/it] 984it [2:17:42, 8.21s/it] 985it [2:17:51, 8.19s/it] 986it [2:17:59, 8.32s/it] 987it [2:18:08, 8.34s/it] 988it [2:18:15, 8.17s/it] 989it [2:18:23, 8.04s/it] 990it [2:18:31, 8.13s/it] 991it [2:18:39, 8.07s/it] 992it [2:18:47, 8.10s/it] 993it [2:18:56, 8.09s/it] 994it [2:19:04, 8.27s/it] 995it [2:19:13, 8.27s/it] 996it [2:19:22, 8.60s/it] 997it [2:19:32, 8.97s/it] 998it [2:19:41, 9.19s/it] 999it [2:19:51, 9.20s/it] 1000it [2:20:00, 9.20s/it] 1000it [2:20:00, 8.40s/it] +Error counts: + cyclic_id: 0 + cyclic_inchikey: 0 + cyclic_scaffold: 0 + cyclic_mwt: 0 + cyclic_clogp: 0 + cyclic_tpsa: 0 +⏰ Completed process in 2:20:18.532640 ++ rm /nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/test/cyc-pep-6-12mer-70M_07.csv diff --git a/test/cyc-pep-6-12mer-70M_08.csv.gz b/test/cyc-pep-6-12mer-70M_08.csv.gz index 1c6439f07aa78c88758bf0830704617b56461ad3..ee33672d7048ecc8b6ef96ee6fbf5b950d88bc1c 100644 --- a/test/cyc-pep-6-12mer-70M_08.csv.gz +++ b/test/cyc-pep-6-12mer-70M_08.csv.gz @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:df735149229f974916fcea5350d5c953e1cd63d74d1eae987aed61c9133237f4 -size 47424767 +oid sha256:af512fb7d8573c2c07bed492e0c1e9256c901c9e71c7f466c2f2ef01dc84e625 +size 97937697 diff --git a/test/cyc-pep-6-12mer-70M_08.log b/test/cyc-pep-6-12mer-70M_08.log new file mode 100644 index 0000000000000000000000000000000000000000..4a10af193df67c0213f8a0169a84c6a4ae7b1434 --- /dev/null +++ b/test/cyc-pep-6-12mer-70M_08.log @@ -0,0 +1,337 @@ ++ module purge ++ '[' -z '' ']' ++ case "$-" in ++ __lmod_sh_dbg=x ++ '[' -n x ']' ++ set +x +Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output +Shell debugging restarted ++ unset __lmod_sh_dbg ++ return 0 ++ module load Anaconda3/2023.03 ++ '[' -z '' ']' ++ case "$-" in ++ __lmod_sh_dbg=x ++ '[' -n x ']' ++ set +x +Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output +Shell debugging restarted ++ unset __lmod_sh_dbg ++ return 0 ++ source /camp/home/johnsoe/.bashrc +++ '[' '' = yes ']' +++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' ++++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.bash hook +++ __conda_setup='export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'' + +# Copyright (C) 2012 Anaconda, Inc +# SPDX-License-Identifier: BSD-3-Clause +__conda_exe() ( + "$CONDA_EXE" $_CE_M $_CE_CONDA "$@" +) + +__conda_hashr() { + if [ -n "${ZSH_VERSION:+x}" ]; then + \rehash + elif [ -n "${POSH_VERSION:+x}" ]; then + : # pass + else + \hash -r + fi +} + +__conda_activate() { + if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then + # Handle transition from shell activated with conda <= 4.3 to a subsequent activation + # after conda updated to >= 4.4. See issue #6173. + PS1="$CONDA_PS1_BACKUP" + \unset CONDA_PS1_BACKUP + fi + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return + \eval "$ask_conda" + __conda_hashr +} + +__conda_reactivate() { + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return + \eval "$ask_conda" + __conda_hashr +} + +conda() { + \local cmd="${1-__missing__}" + case "$cmd" in + activate|deactivate) + __conda_activate "$@" + ;; + install|update|upgrade|remove|uninstall) + __conda_exe "$@" || \return + __conda_reactivate + ;; + *) + __conda_exe "$@" + ;; + esac +} + +if [ -z "${CONDA_SHLVL+x}" ]; then + \export CONDA_SHLVL=0 + # In dev-mode CONDA_EXE is python.exe and on Windows + # it is in a different relative location to condabin. + if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then + PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}" + else + PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}" + fi + \export PATH + + # We'\''re not allowing PS1 to be unbound. It must at least be set. + # However, we'\''re not exporting it, which can cause problems when starting a second shell + # via a first shell (i.e. starting zsh from bash). + if [ -z "${PS1+x}" ]; then + PS1= + fi +fi + +conda activate base' +++ '[' 0 -eq 0 ']' +++ eval 'export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'' + +# Copyright (C) 2012 Anaconda, Inc +# SPDX-License-Identifier: BSD-3-Clause +__conda_exe() ( + "$CONDA_EXE" $_CE_M $_CE_CONDA "$@" +) + +__conda_hashr() { + if [ -n "${ZSH_VERSION:+x}" ]; then + \rehash + elif [ -n "${POSH_VERSION:+x}" ]; then + : # pass + else + \hash -r + fi +} + +__conda_activate() { + if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then + # Handle transition from shell activated with conda <= 4.3 to a subsequent activation + # after conda updated to >= 4.4. See issue #6173. + PS1="$CONDA_PS1_BACKUP" + \unset CONDA_PS1_BACKUP + fi + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return + \eval "$ask_conda" + __conda_hashr +} + +__conda_reactivate() { + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return + \eval "$ask_conda" + __conda_hashr +} + +conda() { + \local cmd="${1-__missing__}" + case "$cmd" in + activate|deactivate) + __conda_activate "$@" + ;; + install|update|upgrade|remove|uninstall) + __conda_exe "$@" || \return + __conda_reactivate + ;; + *) + __conda_exe "$@" + ;; + esac +} + +if [ -z "${CONDA_SHLVL+x}" ]; then + \export CONDA_SHLVL=0 + # In dev-mode CONDA_EXE is python.exe and on Windows + # it is in a different relative location to condabin. + if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then + PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}" + else + PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}" + fi + \export PATH + + # We'\''re not allowing PS1 to be unbound. It must at least be set. + # However, we'\''re not exporting it, which can cause problems when starting a second shell + # via a first shell (i.e. starting zsh from bash). + if [ -z "${PS1+x}" ]; then + PS1= + fi +fi + +conda activate base' ++++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda ++++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda ++++ export _CE_M= ++++ _CE_M= ++++ export _CE_CONDA= ++++ _CE_CONDA= ++++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ '[' -z x ']' ++++ conda activate base ++++ local cmd=activate ++++ case "$cmd" in ++++ __conda_activate activate base ++++ '[' -n '' ']' ++++ local ask_conda +++++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++++ __conda_exe shell.posix activate base +++++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate base ++++ ask_conda='PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_SHLVL='\''6'\'' +export CONDA_DEFAULT_ENV='\''base'\'' +export CONDA_PROMPT_MODIFIER='\''(base) '\'' +export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' ++++ eval 'PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_SHLVL='\''6'\'' +export CONDA_DEFAULT_ENV='\''base'\'' +export CONDA_PROMPT_MODIFIER='\''(base) '\'' +export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' +++++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++++ export CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0 +++++ CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0 +++++ export CONDA_SHLVL=6 +++++ CONDA_SHLVL=6 +++++ export CONDA_DEFAULT_ENV=base +++++ CONDA_DEFAULT_ENV=base +++++ export 'CONDA_PROMPT_MODIFIER=(base) ' +++++ CONDA_PROMPT_MODIFIER='(base) ' +++++ export CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev +++++ CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev +++++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++++ export _CE_M= +++++ _CE_M= +++++ export _CE_CONDA= +++++ _CE_CONDA= +++++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python +++++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ __conda_hashr ++++ '[' -n '' ']' ++++ '[' -n '' ']' ++++ hash -r +++ unset __conda_setup ++ conda activate schemist-dev ++ local cmd=activate ++ case "$cmd" in ++ __conda_activate activate schemist-dev ++ '[' -n '' ']' ++ local ask_conda +++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++ __conda_exe shell.posix activate schemist-dev +++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate schemist-dev ++ ask_conda='PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_SHLVL='\''7'\'' +export CONDA_DEFAULT_ENV='\''schemist-dev'\'' +export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\'' +export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' ++ eval 'PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_SHLVL='\''7'\'' +export CONDA_DEFAULT_ENV='\''schemist-dev'\'' +export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\'' +export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' +++ PS1='(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++ export CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev +++ CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev +++ export CONDA_SHLVL=7 +++ CONDA_SHLVL=7 +++ export CONDA_DEFAULT_ENV=schemist-dev +++ CONDA_DEFAULT_ENV=schemist-dev +++ export 'CONDA_PROMPT_MODIFIER=(schemist-dev) ' +++ CONDA_PROMPT_MODIFIER='(schemist-dev) ' +++ export CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0 +++ CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0 +++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++ export _CE_M= +++ _CE_M= +++ export _CE_CONDA= +++ _CE_CONDA= +++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python +++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++ __conda_hashr ++ '[' -n '' ']' ++ '[' -n '' ']' ++ hash -r ++ CHUNK_HEAD_FILE=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz ++ INPUT=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/test/cyc-pep-6-12mer-70M_08.csv ++ COLUMN=cysteine_to_N_cyclization ++ PREFIX=cyclic_ ++ AWK='1 { print $8, $1, $2, $10, $3 }' ++ '[' -z cysteine_to_N_cyclization ']' ++ '[' -z cyclic_ ']' ++ '[' -z '1 { print $8, $1, $2, $10, $3 }' ']' ++ awk -F, -v OFS=, '1 { print $8, $1, $2, $10, $3 }' ++ cat /dev/fd/63 /nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/test/cyc-pep-6-12mer-70M_08.csv ++ schemist convert -f csv --column cysteine_to_N_cyclization --to id inchikey scaffold mwt clogp tpsa --prefix cyclic_ --options prefix=SCB- +++ head -n1 ++ gzip --best +++ tr ' ' , +++ zcat /nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz +🚀 Converting between string representations with the following parameters: + subcommand: convert + output: <_io.TextIOWrapper name='' mode='w' encoding='utf-8'> + format: csv + input: <_io.TextIOWrapper name='' mode='r' encoding='utf-8'> + representation: SMILES + column: cysteine_to_N_cyclization + prefix: cyclic_ + to: ['id', 'inchikey', 'scaffold', 'mwt', 'clogp', 'tpsa'] + options: ['prefix=SCB-'] + func: + 0it [00:00, ?it/s] 1it [00:08, 8.17s/it] 2it [00:16, 8.30s/it] 3it [00:24, 8.36s/it] 4it [00:33, 8.30s/it] 5it [00:41, 8.30s/it] 6it [00:50, 8.38s/it] 7it [00:58, 8.45s/it] 8it [01:06, 8.36s/it] 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8.62s/it] 621it [1:26:23, 8.63s/it] 622it [1:26:32, 8.63s/it] 623it [1:26:41, 8.64s/it] 624it [1:26:49, 8.62s/it] 625it [1:26:58, 8.62s/it] 626it [1:27:06, 8.60s/it] 627it [1:27:15, 8.60s/it] 628it [1:27:24, 8.60s/it] 629it [1:27:32, 8.60s/it] 630it [1:27:41, 8.61s/it] 631it [1:27:50, 8.60s/it] 632it [1:27:58, 8.60s/it] 633it [1:28:07, 8.59s/it] 634it [1:28:15, 8.61s/it] 635it [1:28:24, 8.62s/it] 636it [1:28:33, 8.61s/it] 637it [1:28:41, 8.60s/it] 638it [1:28:50, 8.60s/it] 639it [1:28:58, 8.59s/it] 640it [1:29:07, 8.58s/it] 641it [1:29:16, 8.60s/it] 642it [1:29:24, 8.59s/it] 643it [1:29:33, 8.60s/it] 644it [1:29:41, 8.59s/it] 645it [1:29:50, 8.61s/it] 646it [1:29:58, 8.60s/it] 647it [1:30:07, 8.61s/it] 648it [1:30:16, 8.60s/it] 649it [1:30:24, 8.61s/it] 650it [1:30:33, 8.62s/it] 651it [1:30:42, 8.61s/it] 652it [1:30:50, 8.62s/it] 653it [1:30:59, 8.62s/it] 654it [1:31:07, 8.61s/it] 655it [1:31:16, 8.62s/it] 656it [1:31:25, 8.59s/it] 657it [1:31:33, 8.59s/it] 658it [1:31:42, 8.60s/it] 659it [1:31:50, 8.60s/it] 660it [1:31:59, 8.61s/it] 661it [1:32:08, 8.60s/it] 662it [1:32:16, 8.62s/it] 663it [1:32:25, 8.61s/it] 664it [1:32:33, 8.61s/it] 665it [1:32:42, 8.61s/it] 666it [1:32:51, 8.60s/it] 667it [1:32:59, 8.60s/it] 668it [1:33:08, 8.60s/it] 669it [1:33:16, 8.60s/it] 670it [1:33:25, 8.60s/it] 671it [1:33:34, 8.61s/it] 672it [1:33:42, 8.62s/it] 673it [1:33:51, 8.62s/it] 674it [1:34:00, 8.62s/it] 675it [1:34:08, 8.62s/it] 676it [1:34:17, 8.63s/it] 677it [1:34:26, 8.64s/it] 678it [1:34:34, 8.64s/it] 679it [1:34:43, 8.63s/it] 680it [1:34:51, 8.63s/it] 681it [1:35:00, 8.62s/it] 682it [1:35:09, 8.61s/it] 683it [1:35:17, 8.61s/it] 684it [1:35:26, 8.61s/it] 685it [1:35:34, 8.62s/it] 686it [1:35:43, 8.61s/it] 687it [1:35:52, 8.63s/it] 688it [1:36:00, 8.62s/it] 689it [1:36:09, 8.61s/it] 690it [1:36:17, 8.59s/it] 691it [1:36:26, 8.60s/it] 692it [1:36:35, 8.62s/it] 693it [1:36:43, 8.64s/it] 694it [1:36:52, 8.63s/it] 695it [1:37:01, 8.63s/it] 696it [1:37:09, 8.62s/it] 697it [1:37:18, 8.63s/it] 698it [1:37:27, 8.64s/it] 699it [1:37:35, 8.63s/it] 700it [1:37:44, 8.62s/it] 701it [1:37:52, 8.63s/it] 702it [1:38:01, 8.62s/it] 703it [1:38:10, 8.61s/it] 704it [1:38:18, 8.61s/it] 705it [1:38:27, 8.61s/it] 706it [1:38:35, 8.62s/it] 707it [1:38:44, 8.62s/it] 708it [1:38:53, 8.60s/it] 709it [1:39:01, 8.61s/it] 710it [1:39:10, 8.62s/it] 711it [1:39:18, 8.60s/it] 712it [1:39:27, 8.61s/it] 713it [1:39:36, 8.62s/it] 714it [1:39:44, 8.61s/it] 715it [1:39:53, 8.62s/it] 716it [1:40:02, 8.61s/it] 717it [1:40:10, 8.62s/it] 718it [1:40:19, 8.61s/it] 719it [1:40:27, 8.60s/it] 720it [1:40:36, 8.61s/it] 721it [1:40:45, 8.63s/it] 722it [1:40:53, 8.64s/it] 723it [1:41:02, 8.65s/it] 724it [1:41:11, 8.63s/it] 725it [1:41:19, 8.62s/it] 726it [1:41:28, 8.63s/it] 727it [1:41:37, 8.64s/it] 728it [1:41:45, 8.63s/it] 729it [1:41:54, 8.63s/it] 730it [1:42:02, 8.63s/it] 731it [1:42:11, 8.63s/it] 732it [1:42:20, 8.64s/it] 733it [1:42:28, 8.64s/it] 734it [1:42:37, 8.65s/it] 735it [1:42:46, 8.62s/it] 736it [1:42:54, 8.64s/it] 737it [1:43:03, 8.63s/it] 738it [1:43:12, 8.64s/it] 739it [1:43:20, 8.64s/it] 740it [1:43:29, 8.64s/it] 741it [1:43:37, 8.62s/it] 742it [1:43:46, 8.64s/it] 743it [1:43:55, 8.64s/it] 744it [1:44:03, 8.65s/it] 745it [1:44:12, 8.64s/it] 746it [1:44:21, 8.64s/it] 747it [1:44:29, 8.63s/it] 748it [1:44:38, 8.63s/it] 749it [1:44:46, 8.62s/it] 750it [1:44:55, 8.62s/it] 751it [1:45:04, 8.61s/it] 752it [1:45:12, 8.62s/it] 753it [1:45:21, 8.62s/it] 754it [1:45:30, 8.63s/it] 755it [1:45:38, 8.64s/it] 756it [1:45:47, 8.63s/it] 757it [1:45:55, 8.62s/it] 758it [1:46:04, 8.60s/it] 759it [1:46:13, 8.62s/it] 760it [1:46:21, 8.61s/it] 761it [1:46:30, 8.62s/it] 762it [1:46:39, 8.62s/it] 763it [1:46:47, 8.63s/it] 764it [1:46:56, 8.63s/it] 765it [1:47:04, 8.63s/it] 766it [1:47:13, 8.63s/it] 767it [1:47:22, 8.63s/it] 768it [1:47:30, 8.61s/it] 769it [1:47:39, 8.65s/it] 770it [1:47:48, 8.63s/it] 771it [1:47:56, 8.64s/it] 772it [1:48:05, 8.63s/it] 773it [1:48:14, 8.65s/it] 774it [1:48:22, 8.63s/it] 775it [1:48:31, 8.64s/it] 776it [1:48:39, 8.63s/it] 777it [1:48:48, 8.64s/it] 778it [1:48:57, 8.63s/it] 779it [1:49:05, 8.63s/it] 780it [1:49:14, 8.62s/it] 781it [1:49:23, 8.63s/it] 782it [1:49:31, 8.63s/it] 783it [1:49:40, 8.62s/it] 784it [1:49:48, 8.62s/it] 785it [1:49:57, 8.63s/it] 786it [1:50:06, 8.64s/it] 787it [1:50:14, 8.62s/it] 788it [1:50:23, 8.64s/it] 789it [1:50:32, 8.65s/it] 790it [1:50:40, 8.64s/it] 791it [1:50:49, 8.63s/it] 792it [1:50:57, 8.63s/it] 793it [1:51:06, 8.63s/it] 794it [1:51:15, 8.63s/it] 795it [1:51:23, 8.63s/it] 796it [1:51:32, 8.63s/it] 797it [1:51:41, 8.61s/it] 798it [1:51:49, 8.62s/it] 799it [1:51:58, 8.60s/it] 800it [1:52:06, 8.61s/it] 801it [1:52:15, 8.60s/it] 802it [1:52:24, 8.60s/it] 803it [1:52:32, 8.60s/it] 804it [1:52:41, 8.61s/it] 805it [1:52:49, 8.59s/it] 806it [1:52:58, 8.61s/it] 807it [1:53:07, 8.61s/it] 808it [1:53:15, 8.62s/it] 809it [1:53:24, 8.61s/it] 810it [1:53:32, 8.61s/it] 811it [1:53:41, 8.62s/it] 812it [1:53:50, 8.64s/it] 813it [1:53:58, 8.62s/it] 814it [1:54:07, 8.62s/it] 815it [1:54:16, 8.61s/it] 816it [1:54:24, 8.61s/it] 817it [1:54:33, 8.62s/it] 818it [1:54:41, 8.62s/it] 819it [1:54:50, 8.63s/it] 820it [1:54:59, 8.62s/it] 821it [1:55:07, 8.63s/it] 822it [1:55:16, 8.62s/it] 823it [1:55:25, 8.63s/it] 824it [1:55:33, 8.63s/it] 825it [1:55:42, 8.61s/it] 826it [1:55:50, 8.62s/it] 827it [1:55:59, 8.61s/it] 828it [1:56:08, 8.63s/it] 829it [1:56:16, 8.63s/it] 830it [1:56:25, 8.64s/it] 831it [1:56:34, 8.64s/it] 832it [1:56:42, 8.64s/it] 833it [1:56:51, 8.63s/it] 834it [1:57:00, 8.64s/it] 835it [1:57:08, 8.62s/it] 836it [1:57:17, 8.62s/it] 837it [1:57:25, 8.62s/it] 838it [1:57:34, 8.63s/it] 839it [1:57:43, 8.63s/it] 840it [1:57:51, 8.63s/it] 841it [1:58:00, 8.64s/it] 842it [1:58:09, 8.64s/it] 843it [1:58:17, 8.61s/it] 844it [1:58:26, 8.62s/it] 845it [1:58:34, 8.62s/it] 846it [1:58:43, 8.62s/it] 847it [1:58:52, 8.65s/it] 848it [1:59:00, 8.65s/it] 849it [1:59:09, 8.68s/it] 850it [1:59:18, 8.68s/it] 851it [1:59:27, 8.70s/it] 852it [1:59:35, 8.69s/it] 853it [1:59:44, 8.71s/it] 854it [1:59:53, 8.71s/it] 855it [2:00:01, 8.70s/it] 856it [2:00:10, 8.69s/it] 857it [2:00:19, 8.70s/it] 858it [2:00:27, 8.69s/it] 859it [2:00:36, 8.70s/it] 860it [2:00:45, 8.70s/it] 861it [2:00:54, 8.72s/it] 862it [2:01:02, 8.70s/it] 863it [2:01:11, 8.71s/it] 864it [2:01:20, 8.71s/it] 865it [2:01:28, 8.70s/it] 866it [2:01:37, 8.69s/it] 867it [2:01:46, 8.67s/it] 868it [2:01:54, 8.67s/it] 869it [2:02:03, 8.68s/it] 870it [2:02:12, 8.67s/it] 871it [2:02:20, 8.68s/it] 872it [2:02:29, 8.70s/it] 873it [2:02:38, 8.69s/it] 874it [2:02:47, 8.70s/it] 875it [2:02:55, 8.69s/it] 876it [2:03:04, 8.70s/it] 877it [2:03:13, 8.70s/it] 878it [2:03:21, 8.71s/it] 879it [2:03:30, 8.70s/it] 880it [2:03:39, 8.71s/it] 881it [2:03:47, 8.69s/it] 882it [2:03:56, 8.70s/it] 883it [2:04:05, 8.69s/it] 884it [2:04:13, 8.69s/it] 885it [2:04:22, 8.68s/it] 886it [2:04:31, 8.70s/it] 887it [2:04:40, 8.71s/it] 888it [2:04:48, 8.72s/it] 889it [2:04:57, 8.71s/it] 890it [2:05:06, 8.69s/it] 891it [2:05:14, 8.69s/it] 892it [2:05:23, 8.68s/it] 893it [2:05:32, 8.68s/it] 894it [2:05:40, 8.67s/it] 895it [2:05:49, 8.65s/it] 896it [2:05:58, 8.65s/it] 897it [2:06:06, 8.66s/it] 898it [2:06:15, 8.65s/it] 899it [2:06:24, 8.65s/it] 900it [2:06:32, 8.65s/it] 901it [2:06:41, 8.64s/it] 902it [2:06:50, 8.65s/it] 903it [2:06:58, 8.65s/it] 904it [2:07:07, 8.64s/it] 905it [2:07:15, 8.63s/it] 906it [2:07:24, 8.64s/it] 907it [2:07:33, 8.66s/it] 908it [2:07:41, 8.63s/it] 909it [2:07:50, 8.64s/it] 910it [2:07:59, 8.64s/it] 911it [2:08:07, 8.66s/it] 912it [2:08:16, 8.65s/it] 913it [2:08:25, 8.65s/it] 914it [2:08:33, 8.65s/it] 915it [2:08:42, 8.64s/it] 916it [2:08:50, 8.63s/it] 917it [2:08:59, 8.63s/it] 918it [2:09:08, 8.64s/it] 919it [2:09:16, 8.62s/it] 920it [2:09:25, 8.63s/it] 921it [2:09:34, 8.62s/it] 922it [2:09:42, 8.63s/it] 923it [2:09:51, 8.62s/it] 924it [2:09:59, 8.63s/it] 925it [2:10:08, 8.63s/it] 926it [2:10:17, 8.64s/it] 927it [2:10:25, 8.62s/it] 928it [2:10:34, 8.62s/it] 929it [2:10:43, 8.63s/it] 930it [2:10:51, 8.64s/it] 931it [2:11:00, 8.61s/it] 932it [2:11:09, 8.62s/it] 933it [2:11:17, 8.64s/it] 934it [2:11:26, 8.65s/it] 935it [2:11:35, 8.65s/it] 936it [2:11:43, 8.66s/it] 937it [2:11:52, 8.65s/it] 938it [2:12:00, 8.64s/it] 939it [2:12:09, 8.62s/it] 940it [2:12:18, 8.63s/it] 941it [2:12:26, 8.64s/it] 942it [2:12:35, 8.65s/it] 943it [2:12:44, 8.66s/it] 944it [2:12:52, 8.65s/it] 945it [2:13:01, 8.66s/it] 946it [2:13:10, 8.67s/it] 947it [2:13:18, 8.68s/it] 948it [2:13:27, 8.68s/it] 949it [2:13:36, 8.67s/it] 950it [2:13:44, 8.67s/it] 951it [2:13:53, 8.67s/it] 952it [2:14:02, 8.67s/it] 953it [2:14:10, 8.66s/it] 954it [2:14:19, 8.67s/it] 955it [2:14:28, 8.67s/it] 956it [2:14:36, 8.65s/it] 957it [2:14:45, 8.65s/it] 958it [2:14:54, 8.65s/it] 959it [2:15:02, 8.67s/it] 960it [2:15:11, 8.66s/it] 961it [2:15:20, 8.66s/it] 962it [2:15:28, 8.65s/it] 963it [2:15:37, 8.67s/it] 964it [2:15:46, 8.69s/it] 965it [2:15:54, 8.68s/it] 966it [2:16:03, 8.67s/it] 967it [2:16:12, 8.67s/it] 968it [2:16:20, 8.64s/it] 969it [2:16:29, 8.66s/it] 970it [2:16:38, 8.67s/it] 971it [2:16:46, 8.66s/it] 972it [2:16:55, 8.66s/it] 973it [2:17:04, 8.65s/it] 974it [2:17:12, 8.68s/it] 975it [2:17:21, 8.67s/it] 976it [2:17:30, 8.66s/it] 977it [2:17:38, 8.66s/it] 978it [2:17:47, 8.65s/it] 979it [2:17:56, 8.66s/it] 980it [2:18:04, 8.64s/it] 981it [2:18:13, 8.64s/it] 982it [2:18:21, 8.64s/it] 983it [2:18:30, 8.63s/it] 984it [2:18:39, 8.64s/it] 985it [2:18:47, 8.64s/it] 986it [2:18:56, 8.64s/it] 987it [2:19:05, 8.64s/it] 988it [2:19:13, 8.64s/it] 989it [2:19:22, 8.65s/it] 990it [2:19:31, 8.66s/it] 991it [2:19:39, 8.64s/it] 992it [2:19:48, 8.64s/it] 993it [2:19:56, 8.64s/it] 994it [2:20:05, 8.65s/it] 995it [2:20:14, 8.66s/it] 996it [2:20:23, 8.67s/it] 997it [2:20:31, 8.68s/it] 998it [2:20:40, 8.67s/it] 999it [2:20:49, 8.67s/it] 1000it [2:20:57, 8.69s/it] 1000it [2:20:57, 8.46s/it] +Error counts: + cyclic_id: 0 + cyclic_inchikey: 0 + cyclic_scaffold: 0 + cyclic_mwt: 0 + cyclic_clogp: 0 + cyclic_tpsa: 0 +⏰ Completed process in 2:21:16.221649 ++ rm /nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/test/cyc-pep-6-12mer-70M_08.csv diff --git a/test/cyc-pep-6-12mer-70M_09.csv.gz b/test/cyc-pep-6-12mer-70M_09.csv.gz index 004386825b007255681ae8dd2d97cf0434b07e9d..bab137726ea510ac963fac5361366618beeb627a 100644 --- a/test/cyc-pep-6-12mer-70M_09.csv.gz +++ b/test/cyc-pep-6-12mer-70M_09.csv.gz @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:b53d7c0d1348a35bc409fd1afb0351f37bce96e5e4730eee0d35a3b7766e2bf6 -size 51295923 +oid sha256:d872389d791ed0567bc316360f0dfc97cc635e6006c1b0083486016b9e93071f +size 103498286 diff --git a/test/cyc-pep-6-12mer-70M_09.log b/test/cyc-pep-6-12mer-70M_09.log new file mode 100644 index 0000000000000000000000000000000000000000..3056fffddaf5715888c265151c993896e2dbf083 --- /dev/null +++ b/test/cyc-pep-6-12mer-70M_09.log @@ -0,0 +1,337 @@ ++ module purge ++ '[' -z '' ']' ++ case "$-" in ++ __lmod_sh_dbg=x ++ '[' -n x ']' ++ set +x +Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output +Shell debugging restarted ++ unset __lmod_sh_dbg ++ return 0 ++ module load Anaconda3/2023.03 ++ '[' -z '' ']' ++ case "$-" in ++ __lmod_sh_dbg=x ++ '[' -n x ']' ++ set +x +Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output +Shell debugging restarted ++ unset __lmod_sh_dbg ++ return 0 ++ source /camp/home/johnsoe/.bashrc +++ '[' '' = yes ']' +++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' ++++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.bash hook +++ __conda_setup='export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'' + +# Copyright (C) 2012 Anaconda, Inc +# SPDX-License-Identifier: BSD-3-Clause +__conda_exe() ( + "$CONDA_EXE" $_CE_M $_CE_CONDA "$@" +) + +__conda_hashr() { + if [ -n "${ZSH_VERSION:+x}" ]; then + \rehash + elif [ -n "${POSH_VERSION:+x}" ]; then + : # pass + else + \hash -r + fi +} + +__conda_activate() { + if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then + # Handle transition from shell activated with conda <= 4.3 to a subsequent activation + # after conda updated to >= 4.4. See issue #6173. + PS1="$CONDA_PS1_BACKUP" + \unset CONDA_PS1_BACKUP + fi + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return + \eval "$ask_conda" + __conda_hashr +} + +__conda_reactivate() { + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return + \eval "$ask_conda" + __conda_hashr +} + +conda() { + \local cmd="${1-__missing__}" + case "$cmd" in + activate|deactivate) + __conda_activate "$@" + ;; + install|update|upgrade|remove|uninstall) + __conda_exe "$@" || \return + __conda_reactivate + ;; + *) + __conda_exe "$@" + ;; + esac +} + +if [ -z "${CONDA_SHLVL+x}" ]; then + \export CONDA_SHLVL=0 + # In dev-mode CONDA_EXE is python.exe and on Windows + # it is in a different relative location to condabin. + if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then + PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}" + else + PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}" + fi + \export PATH + + # We'\''re not allowing PS1 to be unbound. It must at least be set. + # However, we'\''re not exporting it, which can cause problems when starting a second shell + # via a first shell (i.e. starting zsh from bash). + if [ -z "${PS1+x}" ]; then + PS1= + fi +fi + +conda activate base' +++ '[' 0 -eq 0 ']' +++ eval 'export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'' + +# Copyright (C) 2012 Anaconda, Inc +# SPDX-License-Identifier: BSD-3-Clause +__conda_exe() ( + "$CONDA_EXE" $_CE_M $_CE_CONDA "$@" +) + +__conda_hashr() { + if [ -n "${ZSH_VERSION:+x}" ]; then + \rehash + elif [ -n "${POSH_VERSION:+x}" ]; then + : # pass + else + \hash -r + fi +} + +__conda_activate() { + if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then + # Handle transition from shell activated with conda <= 4.3 to a subsequent activation + # after conda updated to >= 4.4. See issue #6173. + PS1="$CONDA_PS1_BACKUP" + \unset CONDA_PS1_BACKUP + fi + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return + \eval "$ask_conda" + __conda_hashr +} + +__conda_reactivate() { + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return + \eval "$ask_conda" + __conda_hashr +} + +conda() { + \local cmd="${1-__missing__}" + case "$cmd" in + activate|deactivate) + __conda_activate "$@" + ;; + install|update|upgrade|remove|uninstall) + __conda_exe "$@" || \return + __conda_reactivate + ;; + *) + __conda_exe "$@" + ;; + esac +} + +if [ -z "${CONDA_SHLVL+x}" ]; then + \export CONDA_SHLVL=0 + # In dev-mode CONDA_EXE is python.exe and on Windows + # it is in a different relative location to condabin. + if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then + PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}" + else + PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}" + fi + \export PATH + + # We'\''re not allowing PS1 to be unbound. It must at least be set. + # However, we'\''re not exporting it, which can cause problems when starting a second shell + # via a first shell (i.e. starting zsh from bash). + if [ -z "${PS1+x}" ]; then + PS1= + fi +fi + +conda activate base' ++++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda ++++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda ++++ export _CE_M= ++++ _CE_M= ++++ export _CE_CONDA= ++++ _CE_CONDA= ++++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ '[' -z x ']' ++++ conda activate base ++++ local cmd=activate ++++ case "$cmd" in ++++ __conda_activate activate base ++++ '[' -n '' ']' ++++ local ask_conda +++++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++++ __conda_exe shell.posix activate base +++++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate base ++++ ask_conda='PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_SHLVL='\''6'\'' +export CONDA_DEFAULT_ENV='\''base'\'' +export CONDA_PROMPT_MODIFIER='\''(base) '\'' +export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' ++++ eval 'PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_SHLVL='\''6'\'' +export CONDA_DEFAULT_ENV='\''base'\'' +export CONDA_PROMPT_MODIFIER='\''(base) '\'' +export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' +++++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++++ export CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0 +++++ CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0 +++++ export CONDA_SHLVL=6 +++++ CONDA_SHLVL=6 +++++ export CONDA_DEFAULT_ENV=base +++++ CONDA_DEFAULT_ENV=base +++++ export 'CONDA_PROMPT_MODIFIER=(base) ' +++++ CONDA_PROMPT_MODIFIER='(base) ' +++++ export CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev +++++ CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev +++++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++++ export _CE_M= +++++ _CE_M= +++++ export _CE_CONDA= +++++ _CE_CONDA= +++++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python +++++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ __conda_hashr ++++ '[' -n '' ']' ++++ '[' -n '' ']' ++++ hash -r +++ unset __conda_setup ++ conda activate schemist-dev ++ local cmd=activate ++ case "$cmd" in ++ __conda_activate activate schemist-dev ++ '[' -n '' ']' ++ local ask_conda +++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++ __conda_exe shell.posix activate schemist-dev +++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate schemist-dev ++ ask_conda='PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_SHLVL='\''7'\'' +export CONDA_DEFAULT_ENV='\''schemist-dev'\'' +export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\'' +export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' ++ eval 'PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_SHLVL='\''7'\'' +export CONDA_DEFAULT_ENV='\''schemist-dev'\'' +export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\'' +export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' +++ PS1='(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++ export CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev +++ CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev +++ export CONDA_SHLVL=7 +++ CONDA_SHLVL=7 +++ export CONDA_DEFAULT_ENV=schemist-dev +++ CONDA_DEFAULT_ENV=schemist-dev +++ export 'CONDA_PROMPT_MODIFIER=(schemist-dev) ' +++ CONDA_PROMPT_MODIFIER='(schemist-dev) ' +++ export CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0 +++ CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0 +++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++ export _CE_M= +++ _CE_M= +++ export _CE_CONDA= +++ _CE_CONDA= +++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python +++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++ __conda_hashr ++ '[' -n '' ']' ++ '[' -n '' ']' ++ hash -r ++ CHUNK_HEAD_FILE=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz ++ INPUT=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/test/cyc-pep-6-12mer-70M_09.csv ++ COLUMN=cysteine_to_N_cyclization ++ PREFIX=cyclic_ ++ AWK='1 { print $8, $1, $2, $10, $3 }' ++ '[' -z cysteine_to_N_cyclization ']' ++ '[' -z cyclic_ ']' ++ '[' -z '1 { print $8, $1, $2, $10, $3 }' ']' ++ cat /dev/fd/63 /nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/test/cyc-pep-6-12mer-70M_09.csv ++ awk -F, -v OFS=, '1 { print $8, $1, $2, $10, $3 }' +++ zcat /nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz ++ schemist convert -f csv --column cysteine_to_N_cyclization --to id inchikey scaffold mwt clogp tpsa --prefix cyclic_ --options prefix=SCB- ++ gzip --best +++ head -n1 +++ tr ' ' , +🚀 Converting between string representations with the following parameters: + subcommand: convert + output: <_io.TextIOWrapper name='' mode='w' encoding='utf-8'> + format: csv + input: <_io.TextIOWrapper name='' mode='r' encoding='utf-8'> + representation: SMILES + column: cysteine_to_N_cyclization + prefix: cyclic_ + to: ['id', 'inchikey', 'scaffold', 'mwt', 'clogp', 'tpsa'] + options: ['prefix=SCB-'] + func: + 0it [00:00, ?it/s] 1it [00:08, 8.98s/it] 2it [00:17, 8.96s/it] 3it [00:26, 8.97s/it] 4it [00:35, 8.98s/it] 5it [00:44, 8.98s/it] 6it [00:53, 8.98s/it] 7it [01:02, 8.99s/it] 8it [01:11, 9.00s/it] 9it [01:20, 8.99s/it] 10it [01:29, 8.99s/it] 11it [01:38, 8.97s/it] 12it [01:47, 8.99s/it] 13it [01:56, 9.00s/it] 14it [02:05, 8.96s/it] 15it [02:14, 8.96s/it] 16it [02:23, 8.93s/it] 17it [02:32, 8.94s/it] 18it [02:41, 8.95s/it] 19it [02:50, 8.96s/it] 20it [02:59, 9.00s/it] 21it [03:08, 8.98s/it] 22it [03:17, 8.99s/it] 23it [03:26, 8.99s/it] 24it [03:35, 9.00s/it] 25it [03:44, 9.02s/it] 26it [03:53, 9.01s/it] 27it [04:02, 9.05s/it] 28it [04:11, 9.02s/it] 29it [04:20, 9.02s/it] 30it [04:29, 9.00s/it] 31it [04:38, 8.98s/it] 32it [04:47, 8.97s/it] 33it [04:56, 8.97s/it] 34it [05:05, 8.96s/it] 35it [05:14, 8.95s/it] 36it [05:23, 8.95s/it] 37it [05:32, 8.95s/it] 38it [05:41, 8.93s/it] 39it [05:50, 8.93s/it] 40it [05:59, 8.95s/it] 41it [06:07, 8.94s/it] 42it [06:16, 8.95s/it] 43it [06:25, 8.94s/it] 44it [06:34, 8.95s/it] 45it [06:43, 8.96s/it] 46it [06:52, 8.95s/it] 47it [07:01, 8.95s/it] 48it [07:10, 8.95s/it] 49it [07:19, 8.95s/it] 50it [07:28, 8.96s/it] 51it [07:37, 8.95s/it] 52it [07:46, 8.98s/it] 53it [07:55, 8.96s/it] 54it [08:04, 8.96s/it] 55it [08:13, 8.96s/it] 56it [08:22, 8.95s/it] 57it [08:31, 8.96s/it] 58it [08:40, 8.96s/it] 59it [08:49, 8.97s/it] 60it [08:58, 8.96s/it] 61it [09:07, 8.94s/it] 62it [09:15, 8.95s/it] 63it [09:24, 8.94s/it] 64it [09:33, 8.96s/it] 65it [09:42, 8.95s/it] 66it [09:51, 8.94s/it] 67it [10:00, 8.94s/it] 68it [10:09, 8.94s/it] 69it [10:18, 8.94s/it] 70it [10:27, 8.94s/it] 71it [10:36, 8.93s/it] 72it [10:45, 8.94s/it] 73it [10:54, 8.93s/it] 74it [11:03, 8.95s/it] 75it [11:12, 8.94s/it] 76it [11:21, 8.94s/it] 77it [11:30, 8.95s/it] 78it [11:39, 8.96s/it] 79it [11:48, 8.97s/it] 80it [11:57, 8.96s/it] 81it [12:05, 8.95s/it] 82it [12:14, 8.96s/it] 83it [12:23, 8.96s/it] 84it [12:32, 8.96s/it] 85it [12:41, 8.96s/it] 86it [12:50, 8.96s/it] 87it [12:59, 8.96s/it] 88it [13:08, 8.96s/it] 89it [13:17, 8.96s/it] 90it [13:26, 8.96s/it] 91it [13:35, 8.96s/it] 92it [13:44, 8.96s/it] 93it [13:53, 8.94s/it] 94it [14:02, 8.94s/it] 95it [14:11, 8.96s/it] 96it [14:20, 8.93s/it] 97it [14:29, 8.93s/it] 98it [14:38, 8.93s/it] 99it [14:47, 8.96s/it] 100it [14:56, 8.95s/it] 101it [15:05, 8.95s/it] 102it [15:14, 8.96s/it] 103it [15:22, 8.96s/it] 104it [15:31, 8.96s/it] 105it [15:40, 8.97s/it] 106it [15:49, 8.96s/it] 107it [15:58, 8.96s/it] 108it [16:07, 8.96s/it] 109it [16:16, 8.96s/it] 110it [16:25, 8.94s/it] 111it [16:34, 8.97s/it] 112it [16:43, 8.96s/it] 113it [16:52, 8.98s/it] 114it [17:01, 8.97s/it] 115it [17:10, 8.97s/it] 116it [17:19, 8.96s/it] 117it [17:28, 8.95s/it] 118it [17:37, 8.94s/it] 119it [17:46, 8.92s/it] 120it [17:55, 8.90s/it] 121it [18:03, 8.91s/it] 122it [18:12, 8.90s/it] 123it [18:21, 8.90s/it] 124it [18:30, 8.92s/it] 125it [18:39, 8.92s/it] 126it [18:48, 8.92s/it] 127it [18:57, 8.91s/it] 128it [19:06, 8.91s/it] 129it [19:15, 8.92s/it] 130it [19:24, 8.92s/it] 131it [19:33, 8.92s/it] 132it [19:42, 8.92s/it] 133it [19:50, 8.93s/it] 134it [19:59, 8.92s/it] 135it [20:08, 8.93s/it] 136it [20:17, 8.93s/it] 137it [20:26, 8.94s/it] 138it [20:35, 8.93s/it] 139it [20:44, 8.95s/it] 140it [20:53, 8.94s/it] 141it [21:02, 8.95s/it] 142it [21:11, 8.94s/it] 143it [21:20, 8.94s/it] 144it [21:29, 8.95s/it] 145it [21:38, 8.94s/it] 146it [21:47, 8.95s/it] 147it [21:56, 8.93s/it] 148it [22:05, 8.93s/it] 149it [22:14, 8.94s/it] 150it [22:22, 8.93s/it] 151it [22:31, 8.94s/it] 152it [22:40, 8.93s/it] 153it [22:49, 8.92s/it] 154it [22:58, 8.93s/it] 155it [23:07, 8.94s/it] 156it [23:16, 8.93s/it] 157it [23:25, 8.91s/it] 158it [23:34, 8.91s/it] 159it [23:43, 8.91s/it] 160it [23:52, 8.90s/it] 161it [24:01, 8.91s/it] 162it [24:09, 8.92s/it] 163it [24:18, 8.92s/it] 164it [24:27, 8.94s/it] 165it [24:36, 8.97s/it] 166it [24:45, 8.95s/it] 167it [24:54, 8.96s/it] 168it [25:03, 8.94s/it] 169it [25:12, 8.96s/it] 170it [25:21, 8.95s/it] 171it [25:30, 8.96s/it] 172it [25:39, 8.94s/it] 173it [25:48, 8.94s/it] 174it [25:57, 8.94s/it] 175it [26:06, 8.94s/it] 176it [26:15, 8.96s/it] 177it [26:24, 8.95s/it] 178it [26:33, 8.96s/it] 179it [26:42, 8.97s/it] 180it [26:51, 8.97s/it] 181it [27:00, 8.95s/it] 182it [27:09, 8.94s/it] 183it [27:17, 8.91s/it] 184it [27:26, 8.93s/it] 185it [27:35, 8.93s/it] 186it [27:44, 8.95s/it] 187it [27:53, 8.94s/it] 188it [28:02, 8.94s/it] 189it [28:11, 8.94s/it] 190it [28:20, 8.94s/it] 191it [28:29, 8.95s/it] 192it [28:38, 8.93s/it] 193it [28:47, 8.95s/it] 194it [28:56, 8.95s/it] 195it [29:05, 8.95s/it] 196it [29:14, 8.93s/it] 197it [29:23, 8.93s/it] 198it [29:31, 8.93s/it] 199it [29:40, 8.94s/it] 200it [29:49, 8.94s/it] 201it [29:58, 8.94s/it] 202it [30:07, 8.93s/it] 203it [30:16, 8.95s/it] 204it [30:25, 8.93s/it] 205it [30:34, 8.94s/it] 206it [30:43, 8.94s/it] 207it [30:52, 8.92s/it] 208it [31:01, 8.92s/it] 209it [31:10, 8.92s/it] 210it [31:19, 8.93s/it] 211it [31:28, 8.99s/it] 212it [31:37, 9.00s/it] 213it [31:46, 8.98s/it] 214it [31:55, 8.97s/it] 215it [32:04, 8.97s/it] 216it [32:13, 8.99s/it] 217it [32:22, 8.97s/it] 218it [32:31, 8.97s/it] 219it [32:40, 8.95s/it] 220it [32:48, 8.95s/it] 221it [32:57, 8.93s/it] 222it [33:06, 8.93s/it] 223it [33:15, 8.93s/it] 224it [33:24, 8.93s/it] 225it [33:33, 8.92s/it] 226it [33:42, 8.92s/it] 227it [33:51, 8.94s/it] 228it [34:00, 8.93s/it] 229it [34:09, 8.95s/it] 230it [34:18, 8.94s/it] 231it [34:27, 8.94s/it] 232it [34:36, 8.92s/it] 233it [34:45, 8.95s/it] 234it [34:54, 8.96s/it] 235it [35:03, 8.95s/it] 236it [35:11, 8.95s/it] 237it [35:20, 8.95s/it] 238it [35:29, 8.96s/it] 239it [35:38, 8.93s/it] 240it [35:47, 8.96s/it] 241it [35:56, 8.95s/it] 242it [36:05, 8.96s/it] 243it [36:14, 8.95s/it] 244it [36:23, 8.95s/it] 245it [36:32, 8.94s/it] 246it [36:41, 8.97s/it] 247it [36:50, 8.96s/it] 248it [36:59, 8.95s/it] 249it [37:08, 8.93s/it] 250it [37:17, 8.94s/it] 251it [37:26, 8.93s/it] 252it [37:35, 8.93s/it] 253it [37:44, 8.94s/it] 254it [37:53, 8.95s/it] 255it [38:02, 8.96s/it] 256it [38:10, 8.95s/it] 257it [38:19, 8.96s/it] 258it [38:28, 8.97s/it] 259it [38:37, 8.96s/it] 260it [38:46, 8.96s/it] 261it [38:55, 8.97s/it] 262it [39:04, 8.96s/it] 263it [39:13, 8.95s/it] 264it [39:22, 8.94s/it] 265it [39:31, 8.95s/it] 266it [39:40, 8.95s/it] 267it [39:49, 8.95s/it] 268it [39:58, 8.95s/it] 269it [40:07, 8.95s/it] 270it [40:16, 8.97s/it] 271it [40:25, 8.96s/it] 272it [40:34, 8.95s/it] 273it [40:43, 8.94s/it] 274it [40:52, 8.97s/it] 275it [41:01, 8.97s/it] 276it [41:10, 8.99s/it] 277it [41:19, 9.00s/it] 278it [41:28, 9.00s/it] 279it [41:37, 8.98s/it] 280it [41:46, 8.96s/it] 281it [41:55, 8.97s/it] 282it [42:04, 8.98s/it] 283it [42:13, 8.98s/it] 284it [42:22, 8.98s/it] 285it [42:31, 8.98s/it] 286it [42:39, 8.97s/it] 287it [42:49, 8.99s/it] 288it [42:58, 9.01s/it] 289it [43:07, 9.01s/it] 290it [43:16, 8.99s/it] 291it [43:24, 8.98s/it] 292it [43:33, 8.97s/it] 293it [43:42, 8.97s/it] 294it [43:51, 8.96s/it] 295it [44:00, 8.96s/it] 296it [44:09, 8.96s/it] 297it [44:18, 8.96s/it] 298it [44:27, 8.98s/it] 299it [44:36, 8.97s/it] 300it [44:45, 8.98s/it] 301it 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8.97s/it] 343it [51:12, 8.99s/it] 344it [51:21, 8.98s/it] 345it [51:30, 8.98s/it] 346it [51:39, 8.98s/it] 347it [51:48, 8.99s/it] 348it [51:57, 8.98s/it] 349it [52:06, 8.97s/it] 350it [52:15, 8.96s/it] 351it [52:24, 8.96s/it] 352it [52:33, 8.98s/it] 353it [52:42, 8.99s/it] 354it [52:51, 8.99s/it] 355it [53:00, 9.00s/it] 356it [53:09, 9.00s/it] 357it [53:18, 8.99s/it] 358it [53:27, 8.98s/it] 359it [53:36, 8.98s/it] 360it [53:45, 8.98s/it] 361it [53:54, 8.97s/it] 362it [54:02, 8.97s/it] 363it [54:11, 8.98s/it] 364it [54:20, 8.96s/it] 365it [54:29, 8.97s/it] 366it [54:38, 8.97s/it] 367it [54:47, 8.99s/it] 368it [54:56, 8.98s/it] 369it [55:05, 9.00s/it] 370it [55:14, 8.99s/it] 371it [55:23, 9.01s/it] 372it [55:32, 9.00s/it] 373it [55:41, 9.00s/it] 374it [55:50, 8.99s/it] 375it [55:59, 9.00s/it] 376it [56:08, 8.99s/it] 377it [56:17, 8.98s/it] 378it [56:26, 8.99s/it] 379it [56:35, 8.98s/it] 380it [56:44, 8.98s/it] 381it [56:53, 8.97s/it] 382it [57:02, 8.98s/it] 383it [57:11, 8.99s/it] 384it 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10.25s/it] 957it [2:25:57, 10.27s/it] 958it [2:26:07, 10.30s/it] 959it [2:26:18, 10.30s/it] 960it [2:26:28, 10.30s/it] 961it [2:26:38, 10.31s/it] 962it [2:26:49, 10.31s/it] 963it [2:26:59, 10.31s/it] 964it [2:27:09, 10.30s/it] 965it [2:27:19, 10.26s/it] 966it [2:27:29, 10.21s/it] 967it [2:27:40, 10.21s/it] 968it [2:27:50, 10.17s/it] 969it [2:28:00, 10.18s/it] 970it [2:28:10, 10.16s/it] 971it [2:28:20, 10.14s/it] 972it [2:28:30, 10.13s/it] 973it [2:28:40, 10.13s/it] 974it [2:28:51, 10.13s/it] 975it [2:29:01, 10.14s/it] 976it [2:29:11, 10.14s/it] 977it [2:29:21, 10.14s/it] 978it [2:29:31, 10.13s/it] 979it [2:29:41, 10.14s/it] 980it [2:29:51, 10.12s/it] 981it [2:30:01, 10.12s/it] 982it [2:30:12, 10.14s/it] 983it [2:30:22, 10.13s/it] 984it [2:30:32, 10.16s/it] 985it [2:30:42, 10.14s/it] 986it [2:30:52, 10.14s/it] 987it [2:31:02, 10.13s/it] 988it [2:31:12, 10.11s/it] 989it [2:31:22, 10.11s/it] 990it [2:31:33, 10.13s/it] 991it [2:31:43, 10.15s/it] 992it [2:31:53, 10.14s/it] 993it [2:32:03, 10.14s/it] 994it [2:32:13, 10.18s/it] 995it [2:32:23, 10.16s/it] 996it [2:32:34, 10.16s/it] 997it [2:32:44, 10.14s/it] 998it [2:32:54, 10.14s/it] 999it [2:33:04, 10.14s/it] 1000it [2:33:14, 10.17s/it] 1000it [2:33:14, 9.19s/it] +Error counts: + cyclic_id: 0 + cyclic_inchikey: 0 + cyclic_scaffold: 0 + cyclic_mwt: 0 + cyclic_clogp: 0 + cyclic_tpsa: 0 +⏰ Completed process in 2:33:34.867497 ++ rm /nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/test/cyc-pep-6-12mer-70M_09.csv diff --git a/test/cyc-pep-6-12mer-70M_10.csv.gz b/test/cyc-pep-6-12mer-70M_10.csv.gz index 63509a88c9916ba8ae659aaf946c74317d4c00cb..4c7bc5106a90ca59e8194c1de6098e1e1003df71 100644 --- a/test/cyc-pep-6-12mer-70M_10.csv.gz +++ b/test/cyc-pep-6-12mer-70M_10.csv.gz @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:e67a2972bd0f92cbcc499bed7be8e7e77455b989bec94fe0f368da80749fa29a -size 54500817 +oid sha256:199e08245d441ed59444e81419b31363a8b65ea032f0c939860432fd5623149a +size 107802205 diff --git a/test/cyc-pep-6-12mer-70M_10.log b/test/cyc-pep-6-12mer-70M_10.log new file mode 100644 index 0000000000000000000000000000000000000000..2962c148b2b2a83201b7cdc97566c7f6937528fe --- /dev/null +++ b/test/cyc-pep-6-12mer-70M_10.log @@ -0,0 +1,337 @@ ++ module purge ++ '[' -z '' ']' ++ case "$-" in ++ __lmod_sh_dbg=x ++ '[' -n x ']' ++ set +x +Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output +Shell debugging restarted ++ unset __lmod_sh_dbg ++ return 0 ++ module load Anaconda3/2023.03 ++ '[' -z '' ']' ++ case "$-" in ++ __lmod_sh_dbg=x ++ '[' -n x ']' ++ set +x +Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output +Shell debugging restarted ++ unset __lmod_sh_dbg ++ return 0 ++ source /camp/home/johnsoe/.bashrc +++ '[' '' = yes ']' +++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' ++++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.bash hook +++ __conda_setup='export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'' + +# Copyright (C) 2012 Anaconda, Inc +# SPDX-License-Identifier: BSD-3-Clause +__conda_exe() ( + "$CONDA_EXE" $_CE_M $_CE_CONDA "$@" +) + +__conda_hashr() { + if [ -n "${ZSH_VERSION:+x}" ]; then + \rehash + elif [ -n "${POSH_VERSION:+x}" ]; then + : # pass + else + \hash -r + fi +} + +__conda_activate() { + if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then + # Handle transition from shell activated with conda <= 4.3 to a subsequent activation + # after conda updated to >= 4.4. See issue #6173. + PS1="$CONDA_PS1_BACKUP" + \unset CONDA_PS1_BACKUP + fi + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return + \eval "$ask_conda" + __conda_hashr +} + +__conda_reactivate() { + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return + \eval "$ask_conda" + __conda_hashr +} + +conda() { + \local cmd="${1-__missing__}" + case "$cmd" in + activate|deactivate) + __conda_activate "$@" + ;; + install|update|upgrade|remove|uninstall) + __conda_exe "$@" || \return + __conda_reactivate + ;; + *) + __conda_exe "$@" + ;; + esac +} + +if [ -z "${CONDA_SHLVL+x}" ]; then + \export CONDA_SHLVL=0 + # In dev-mode CONDA_EXE is python.exe and on Windows + # it is in a different relative location to condabin. + if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then + PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}" + else + PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}" + fi + \export PATH + + # We'\''re not allowing PS1 to be unbound. It must at least be set. + # However, we'\''re not exporting it, which can cause problems when starting a second shell + # via a first shell (i.e. starting zsh from bash). + if [ -z "${PS1+x}" ]; then + PS1= + fi +fi + +conda activate base' +++ '[' 0 -eq 0 ']' +++ eval 'export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'' + +# Copyright (C) 2012 Anaconda, Inc +# SPDX-License-Identifier: BSD-3-Clause +__conda_exe() ( + "$CONDA_EXE" $_CE_M $_CE_CONDA "$@" +) + +__conda_hashr() { + if [ -n "${ZSH_VERSION:+x}" ]; then + \rehash + elif [ -n "${POSH_VERSION:+x}" ]; then + : # pass + else + \hash -r + fi +} + +__conda_activate() { + if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then + # Handle transition from shell activated with conda <= 4.3 to a subsequent activation + # after conda updated to >= 4.4. See issue #6173. + PS1="$CONDA_PS1_BACKUP" + \unset CONDA_PS1_BACKUP + fi + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return + \eval "$ask_conda" + __conda_hashr +} + +__conda_reactivate() { + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return + \eval "$ask_conda" + __conda_hashr +} + +conda() { + \local cmd="${1-__missing__}" + case "$cmd" in + activate|deactivate) + __conda_activate "$@" + ;; + install|update|upgrade|remove|uninstall) + __conda_exe "$@" || \return + __conda_reactivate + ;; + *) + __conda_exe "$@" + ;; + esac +} + +if [ -z "${CONDA_SHLVL+x}" ]; then + \export CONDA_SHLVL=0 + # In dev-mode CONDA_EXE is python.exe and on Windows + # it is in a different relative location to condabin. + if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then + PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}" + else + PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}" + fi + \export PATH + + # We'\''re not allowing PS1 to be unbound. It must at least be set. + # However, we'\''re not exporting it, which can cause problems when starting a second shell + # via a first shell (i.e. starting zsh from bash). + if [ -z "${PS1+x}" ]; then + PS1= + fi +fi + +conda activate base' ++++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda ++++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda ++++ export _CE_M= ++++ _CE_M= ++++ export _CE_CONDA= ++++ _CE_CONDA= ++++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ '[' -z x ']' ++++ conda activate base ++++ local cmd=activate ++++ case "$cmd" in ++++ __conda_activate activate base ++++ '[' -n '' ']' ++++ local ask_conda +++++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++++ __conda_exe shell.posix activate base +++++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate base ++++ ask_conda='PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_SHLVL='\''6'\'' +export CONDA_DEFAULT_ENV='\''base'\'' +export CONDA_PROMPT_MODIFIER='\''(base) '\'' +export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' ++++ eval 'PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_SHLVL='\''6'\'' +export CONDA_DEFAULT_ENV='\''base'\'' +export CONDA_PROMPT_MODIFIER='\''(base) '\'' +export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' +++++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++++ export CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0 +++++ CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0 +++++ export CONDA_SHLVL=6 +++++ CONDA_SHLVL=6 +++++ export CONDA_DEFAULT_ENV=base +++++ CONDA_DEFAULT_ENV=base +++++ export 'CONDA_PROMPT_MODIFIER=(base) ' +++++ CONDA_PROMPT_MODIFIER='(base) ' +++++ export CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev +++++ CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev +++++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++++ export _CE_M= +++++ _CE_M= +++++ export _CE_CONDA= +++++ _CE_CONDA= +++++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python +++++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ __conda_hashr ++++ '[' -n '' ']' ++++ '[' -n '' ']' ++++ hash -r +++ unset __conda_setup ++ conda activate schemist-dev ++ local cmd=activate ++ case "$cmd" in ++ __conda_activate activate schemist-dev ++ '[' -n '' ']' ++ local ask_conda +++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++ __conda_exe shell.posix activate schemist-dev +++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate schemist-dev ++ ask_conda='PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_SHLVL='\''7'\'' +export CONDA_DEFAULT_ENV='\''schemist-dev'\'' +export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\'' +export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' ++ eval 'PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_SHLVL='\''7'\'' +export CONDA_DEFAULT_ENV='\''schemist-dev'\'' +export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\'' +export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' +++ PS1='(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++ export CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev +++ CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev +++ export CONDA_SHLVL=7 +++ CONDA_SHLVL=7 +++ export CONDA_DEFAULT_ENV=schemist-dev +++ CONDA_DEFAULT_ENV=schemist-dev +++ export 'CONDA_PROMPT_MODIFIER=(schemist-dev) ' +++ CONDA_PROMPT_MODIFIER='(schemist-dev) ' +++ export CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0 +++ CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0 +++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++ export _CE_M= +++ _CE_M= +++ export _CE_CONDA= +++ _CE_CONDA= +++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python +++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++ __conda_hashr ++ '[' -n '' ']' ++ '[' -n '' ']' ++ hash -r ++ CHUNK_HEAD_FILE=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz ++ INPUT=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/test/cyc-pep-6-12mer-70M_10.csv ++ COLUMN=cysteine_to_N_cyclization ++ PREFIX=cyclic_ ++ AWK='1 { print $8, $1, $2, $10, $3 }' ++ '[' -z cysteine_to_N_cyclization ']' ++ '[' -z cyclic_ ']' ++ '[' -z '1 { print $8, $1, $2, $10, $3 }' ']' ++ cat /dev/fd/63 /nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/test/cyc-pep-6-12mer-70M_10.csv +++ head -n1 ++ schemist convert -f csv --column cysteine_to_N_cyclization --to id inchikey scaffold mwt clogp tpsa --prefix cyclic_ --options prefix=SCB- +++ tr ' ' , ++ gzip --best +++ zcat /nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz ++ awk -F, -v OFS=, '1 { print $8, $1, $2, $10, $3 }' +🚀 Converting between string representations with the following parameters: + subcommand: convert + output: <_io.TextIOWrapper name='' mode='w' encoding='utf-8'> + format: csv + input: <_io.TextIOWrapper name='' mode='r' encoding='utf-8'> + representation: SMILES + column: cysteine_to_N_cyclization + prefix: cyclic_ + to: ['id', 'inchikey', 'scaffold', 'mwt', 'clogp', 'tpsa'] + options: ['prefix=SCB-'] + func: + 0it [00:00, ?it/s] 1it [00:10, 10.21s/it] 2it [00:20, 10.13s/it] 3it [00:30, 10.10s/it] 4it [00:40, 10.11s/it] 5it [00:50, 10.10s/it] 6it 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9.89s/it] 951it [2:36:56, 9.88s/it] 952it [2:37:06, 9.87s/it] 953it [2:37:16, 9.87s/it] 954it [2:37:26, 9.87s/it] 955it [2:37:36, 9.89s/it] 956it [2:37:46, 9.89s/it] 957it [2:37:56, 9.91s/it] 958it [2:38:06, 9.93s/it] 959it [2:38:16, 9.94s/it] 960it [2:38:26, 9.93s/it] 961it [2:38:36, 9.91s/it] 962it [2:38:45, 9.92s/it] 963it [2:38:55, 9.95s/it] 964it [2:39:05, 9.95s/it] 965it [2:39:15, 9.97s/it] 966it [2:39:25, 9.97s/it] 967it [2:39:35, 9.96s/it] 968it [2:39:45, 9.97s/it] 969it [2:39:55, 9.98s/it] 970it [2:40:05, 10.00s/it] 971it [2:40:15, 9.98s/it] 972it [2:40:25, 9.96s/it] 973it [2:40:35, 9.95s/it] 974it [2:40:45, 9.96s/it] 975it [2:40:55, 9.94s/it] 976it [2:41:05, 9.92s/it] 977it [2:41:15, 9.90s/it] 978it [2:41:25, 9.92s/it] 979it [2:41:35, 9.90s/it] 980it [2:41:44, 9.90s/it] 981it [2:41:54, 9.86s/it] 982it [2:42:04, 9.88s/it] 983it [2:42:14, 9.88s/it] 984it [2:42:24, 9.87s/it] 985it [2:42:34, 9.86s/it] 986it [2:42:44, 9.86s/it] 987it [2:42:53, 9.86s/it] 988it [2:43:03, 9.89s/it] 989it [2:43:13, 9.88s/it] 990it [2:43:23, 9.89s/it] 991it [2:43:33, 9.90s/it] 992it [2:43:43, 9.91s/it] 993it [2:43:53, 9.91s/it] 994it [2:44:03, 9.93s/it] 995it [2:44:13, 9.93s/it] 996it [2:44:23, 9.93s/it] 997it [2:44:33, 9.92s/it] 998it [2:44:43, 9.93s/it] 999it [2:44:53, 9.93s/it] 1000it [2:45:03, 9.93s/it] 1000it [2:45:03, 9.90s/it] +Error counts: + cyclic_id: 0 + cyclic_inchikey: 0 + cyclic_scaffold: 0 + cyclic_mwt: 0 + cyclic_clogp: 0 + cyclic_tpsa: 0 +⏰ Completed process in 2:45:25.905852 ++ rm /nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/test/cyc-pep-6-12mer-70M_10.csv diff --git a/test/cyc-pep-6-12mer-70M_11.csv.gz b/test/cyc-pep-6-12mer-70M_11.csv.gz index 6896b11dca4e31abece51aa34cf6f0a1f6ac3dfc..0ad1886cf9f59ea323cfa2d4c3c301f225147bd3 100644 --- a/test/cyc-pep-6-12mer-70M_11.csv.gz +++ b/test/cyc-pep-6-12mer-70M_11.csv.gz @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:391ad3a94a7a8b21c716673919c760276cfaae109b729d99c8f9fc67c8654644 -size 26168089 +oid sha256:504987739844f6673f4a60dfd82a638dcdbce8b19768eeac08a91dc59c53dea8 +size 51760158 diff --git a/test/cyc-pep-6-12mer-70M_11.log b/test/cyc-pep-6-12mer-70M_11.log new file mode 100644 index 0000000000000000000000000000000000000000..6273ea34606522f9ca3b91557dc8c5155bd9e92c --- /dev/null +++ b/test/cyc-pep-6-12mer-70M_11.log @@ -0,0 +1,337 @@ ++ module purge ++ '[' -z '' ']' ++ case "$-" in ++ __lmod_sh_dbg=x ++ '[' -n x ']' ++ set +x +Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output +Shell debugging restarted ++ unset __lmod_sh_dbg ++ return 0 ++ module load Anaconda3/2023.03 ++ '[' -z '' ']' ++ case "$-" in ++ __lmod_sh_dbg=x ++ '[' -n x ']' ++ set +x +Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output +Shell debugging restarted ++ unset __lmod_sh_dbg ++ return 0 ++ source /camp/home/johnsoe/.bashrc +++ '[' '' = yes ']' +++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' ++++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.bash hook +++ __conda_setup='export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'' + +# Copyright (C) 2012 Anaconda, Inc +# SPDX-License-Identifier: BSD-3-Clause +__conda_exe() ( + "$CONDA_EXE" $_CE_M $_CE_CONDA "$@" +) + +__conda_hashr() { + if [ -n "${ZSH_VERSION:+x}" ]; then + \rehash + elif [ -n "${POSH_VERSION:+x}" ]; then + : # pass + else + \hash -r + fi +} + +__conda_activate() { + if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then + # Handle transition from shell activated with conda <= 4.3 to a subsequent activation + # after conda updated to >= 4.4. See issue #6173. + PS1="$CONDA_PS1_BACKUP" + \unset CONDA_PS1_BACKUP + fi + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return + \eval "$ask_conda" + __conda_hashr +} + +__conda_reactivate() { + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return + \eval "$ask_conda" + __conda_hashr +} + +conda() { + \local cmd="${1-__missing__}" + case "$cmd" in + activate|deactivate) + __conda_activate "$@" + ;; + install|update|upgrade|remove|uninstall) + __conda_exe "$@" || \return + __conda_reactivate + ;; + *) + __conda_exe "$@" + ;; + esac +} + +if [ -z "${CONDA_SHLVL+x}" ]; then + \export CONDA_SHLVL=0 + # In dev-mode CONDA_EXE is python.exe and on Windows + # it is in a different relative location to condabin. + if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then + PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}" + else + PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}" + fi + \export PATH + + # We'\''re not allowing PS1 to be unbound. It must at least be set. + # However, we'\''re not exporting it, which can cause problems when starting a second shell + # via a first shell (i.e. starting zsh from bash). + if [ -z "${PS1+x}" ]; then + PS1= + fi +fi + +conda activate base' +++ '[' 0 -eq 0 ']' +++ eval 'export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'' + +# Copyright (C) 2012 Anaconda, Inc +# SPDX-License-Identifier: BSD-3-Clause +__conda_exe() ( + "$CONDA_EXE" $_CE_M $_CE_CONDA "$@" +) + +__conda_hashr() { + if [ -n "${ZSH_VERSION:+x}" ]; then + \rehash + elif [ -n "${POSH_VERSION:+x}" ]; then + : # pass + else + \hash -r + fi +} + +__conda_activate() { + if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then + # Handle transition from shell activated with conda <= 4.3 to a subsequent activation + # after conda updated to >= 4.4. See issue #6173. + PS1="$CONDA_PS1_BACKUP" + \unset CONDA_PS1_BACKUP + fi + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return + \eval "$ask_conda" + __conda_hashr +} + +__conda_reactivate() { + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return + \eval "$ask_conda" + __conda_hashr +} + +conda() { + \local cmd="${1-__missing__}" + case "$cmd" in + activate|deactivate) + __conda_activate "$@" + ;; + install|update|upgrade|remove|uninstall) + __conda_exe "$@" || \return + __conda_reactivate + ;; + *) + __conda_exe "$@" + ;; + esac +} + +if [ -z "${CONDA_SHLVL+x}" ]; then + \export CONDA_SHLVL=0 + # In dev-mode CONDA_EXE is python.exe and on Windows + # it is in a different relative location to condabin. + if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then + PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}" + else + PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}" + fi + \export PATH + + # We'\''re not allowing PS1 to be unbound. It must at least be set. + # However, we'\''re not exporting it, which can cause problems when starting a second shell + # via a first shell (i.e. starting zsh from bash). + if [ -z "${PS1+x}" ]; then + PS1= + fi +fi + +conda activate base' ++++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda ++++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda ++++ export _CE_M= ++++ _CE_M= ++++ export _CE_CONDA= ++++ _CE_CONDA= ++++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ '[' -z x ']' ++++ conda activate base ++++ local cmd=activate ++++ case "$cmd" in ++++ __conda_activate activate base ++++ '[' -n '' ']' ++++ local ask_conda +++++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++++ __conda_exe shell.posix activate base +++++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate base ++++ ask_conda='PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_SHLVL='\''6'\'' +export CONDA_DEFAULT_ENV='\''base'\'' +export CONDA_PROMPT_MODIFIER='\''(base) '\'' +export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' ++++ eval 'PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_SHLVL='\''6'\'' +export CONDA_DEFAULT_ENV='\''base'\'' +export CONDA_PROMPT_MODIFIER='\''(base) '\'' +export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' +++++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++++ export CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0 +++++ CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0 +++++ export CONDA_SHLVL=6 +++++ CONDA_SHLVL=6 +++++ export CONDA_DEFAULT_ENV=base +++++ CONDA_DEFAULT_ENV=base +++++ export 'CONDA_PROMPT_MODIFIER=(base) ' +++++ CONDA_PROMPT_MODIFIER='(base) ' +++++ export CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev +++++ CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev +++++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++++ export _CE_M= +++++ _CE_M= +++++ export _CE_CONDA= +++++ _CE_CONDA= +++++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python +++++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ __conda_hashr ++++ '[' -n '' ']' ++++ '[' -n '' ']' ++++ hash -r +++ unset __conda_setup ++ conda activate schemist-dev ++ local cmd=activate ++ case "$cmd" in ++ __conda_activate activate schemist-dev ++ '[' -n '' ']' ++ local ask_conda +++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++ __conda_exe shell.posix activate schemist-dev +++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate schemist-dev ++ ask_conda='PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_SHLVL='\''7'\'' +export CONDA_DEFAULT_ENV='\''schemist-dev'\'' +export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\'' +export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' ++ eval 'PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_SHLVL='\''7'\'' +export CONDA_DEFAULT_ENV='\''schemist-dev'\'' +export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\'' +export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' +++ PS1='(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++ export CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev +++ CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev +++ export CONDA_SHLVL=7 +++ CONDA_SHLVL=7 +++ export CONDA_DEFAULT_ENV=schemist-dev +++ CONDA_DEFAULT_ENV=schemist-dev +++ export 'CONDA_PROMPT_MODIFIER=(schemist-dev) ' +++ CONDA_PROMPT_MODIFIER='(schemist-dev) ' +++ export CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0 +++ CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0 +++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++ export _CE_M= +++ _CE_M= +++ export _CE_CONDA= +++ _CE_CONDA= +++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python +++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++ __conda_hashr ++ '[' -n '' ']' ++ '[' -n '' ']' ++ hash -r ++ CHUNK_HEAD_FILE=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz ++ INPUT=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/test/cyc-pep-6-12mer-70M_11.csv ++ COLUMN=cysteine_to_N_cyclization ++ PREFIX=cyclic_ ++ AWK='1 { print $8, $1, $2, $10, $3 }' ++ '[' -z cysteine_to_N_cyclization ']' ++ '[' -z cyclic_ ']' ++ '[' -z '1 { print $8, $1, $2, $10, $3 }' ']' ++ awk -F, -v OFS=, '1 { print $8, $1, $2, $10, $3 }' ++ cat /dev/fd/63 /nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/test/cyc-pep-6-12mer-70M_11.csv +++ zcat /nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz ++ schemist convert -f csv --column cysteine_to_N_cyclization --to id inchikey scaffold mwt clogp tpsa --prefix cyclic_ --options prefix=SCB- ++ gzip --best +++ tr ' ' , +++ head -n1 +🚀 Converting between string representations with the following parameters: + subcommand: convert + output: <_io.TextIOWrapper name='' mode='w' encoding='utf-8'> + format: csv + input: <_io.TextIOWrapper name='' mode='r' encoding='utf-8'> + representation: SMILES + column: cysteine_to_N_cyclization + prefix: cyclic_ + to: ['id', 'inchikey', 'scaffold', 'mwt', 'clogp', 'tpsa'] + options: ['prefix=SCB-'] + func: + 0it [00:00, ?it/s] 1it [00:10, 10.41s/it] 2it [00:20, 10.30s/it] 3it [00:31, 10.39s/it] 4it [00:41, 10.37s/it] 5it [00:51, 10.36s/it] 6it [01:02, 10.33s/it] 7it [01:12, 10.32s/it] 8it [01:22, 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481it [1:20:58, 10.10s/it] +Error counts: + cyclic_id: 0 + cyclic_inchikey: 0 + cyclic_scaffold: 0 + cyclic_mwt: 0 + cyclic_clogp: 0 + cyclic_tpsa: 0 +⏰ Completed process in 1:21:08.538847 ++ rm /nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/test/cyc-pep-6-12mer-70M_11.csv diff --git a/train/cyc-pep-6-12mer-70M_00.csv.gz b/train/cyc-pep-6-12mer-70M_00.csv.gz index 37cc7967bbc72b0976d9307b46220bb038d0b74f..5271ef3133338d52e84b57ddc8a98c7f39fbaf4c 100644 --- a/train/cyc-pep-6-12mer-70M_00.csv.gz +++ b/train/cyc-pep-6-12mer-70M_00.csv.gz @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:27a95b1f21d38e79c716e6af47e4fa44ead26226601926ce31fcf389b37c28ae -size 58249769 +oid sha256:1533dd518c32e080fe4b876e67f47d175cf22e83ed4081e5cf99bff0adf1931f +size 112828175 diff --git a/train/cyc-pep-6-12mer-70M_00.log b/train/cyc-pep-6-12mer-70M_00.log new file mode 100644 index 0000000000000000000000000000000000000000..0733f256a85de9d7d897ef99544590b9480a1f4f --- /dev/null +++ b/train/cyc-pep-6-12mer-70M_00.log @@ -0,0 +1,337 @@ ++ module purge ++ '[' -z '' ']' ++ case "$-" in ++ __lmod_sh_dbg=x ++ '[' -n x ']' ++ set +x +Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output +Shell debugging restarted ++ unset __lmod_sh_dbg ++ return 0 ++ module load Anaconda3/2023.03 ++ '[' -z '' ']' ++ case "$-" in ++ __lmod_sh_dbg=x ++ '[' -n x ']' ++ set +x +Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output +Shell debugging restarted ++ unset __lmod_sh_dbg ++ return 0 ++ source /camp/home/johnsoe/.bashrc +++ '[' '' = yes ']' +++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' ++++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.bash hook +++ __conda_setup='export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'' + +# Copyright (C) 2012 Anaconda, Inc +# SPDX-License-Identifier: BSD-3-Clause +__conda_exe() ( + "$CONDA_EXE" $_CE_M $_CE_CONDA "$@" +) + +__conda_hashr() { + if [ -n "${ZSH_VERSION:+x}" ]; then + \rehash + elif [ -n "${POSH_VERSION:+x}" ]; then + : # pass + else + \hash -r + fi +} + +__conda_activate() { + if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then + # Handle transition from shell activated with conda <= 4.3 to a subsequent activation + # after conda updated to >= 4.4. See issue #6173. + PS1="$CONDA_PS1_BACKUP" + \unset CONDA_PS1_BACKUP + fi + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return + \eval "$ask_conda" + __conda_hashr +} + +__conda_reactivate() { + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return + \eval "$ask_conda" + __conda_hashr +} + +conda() { + \local cmd="${1-__missing__}" + case "$cmd" in + activate|deactivate) + __conda_activate "$@" + ;; + install|update|upgrade|remove|uninstall) + __conda_exe "$@" || \return + __conda_reactivate + ;; + *) + __conda_exe "$@" + ;; + esac +} + +if [ -z "${CONDA_SHLVL+x}" ]; then + \export CONDA_SHLVL=0 + # In dev-mode CONDA_EXE is python.exe and on Windows + # it is in a different relative location to condabin. + if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then + PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}" + else + PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}" + fi + \export PATH + + # We'\''re not allowing PS1 to be unbound. It must at least be set. + # However, we'\''re not exporting it, which can cause problems when starting a second shell + # via a first shell (i.e. starting zsh from bash). + if [ -z "${PS1+x}" ]; then + PS1= + fi +fi + +conda activate base' +++ '[' 0 -eq 0 ']' +++ eval 'export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'' + +# Copyright (C) 2012 Anaconda, Inc +# SPDX-License-Identifier: BSD-3-Clause +__conda_exe() ( + "$CONDA_EXE" $_CE_M $_CE_CONDA "$@" +) + +__conda_hashr() { + if [ -n "${ZSH_VERSION:+x}" ]; then + \rehash + elif [ -n "${POSH_VERSION:+x}" ]; then + : # pass + else + \hash -r + fi +} + +__conda_activate() { + if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then + # Handle transition from shell activated with conda <= 4.3 to a subsequent activation + # after conda updated to >= 4.4. See issue #6173. + PS1="$CONDA_PS1_BACKUP" + \unset CONDA_PS1_BACKUP + fi + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return + \eval "$ask_conda" + __conda_hashr +} + +__conda_reactivate() { + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return + \eval "$ask_conda" + __conda_hashr +} + +conda() { + \local cmd="${1-__missing__}" + case "$cmd" in + activate|deactivate) + __conda_activate "$@" + ;; + install|update|upgrade|remove|uninstall) + __conda_exe "$@" || \return + __conda_reactivate + ;; + *) + __conda_exe "$@" + ;; + esac +} + +if [ -z "${CONDA_SHLVL+x}" ]; then + \export CONDA_SHLVL=0 + # In dev-mode CONDA_EXE is python.exe and on Windows + # it is in a different relative location to condabin. + if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then + PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}" + else + PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}" + fi + \export PATH + + # We'\''re not allowing PS1 to be unbound. It must at least be set. + # However, we'\''re not exporting it, which can cause problems when starting a second shell + # via a first shell (i.e. starting zsh from bash). + if [ -z "${PS1+x}" ]; then + PS1= + fi +fi + +conda activate base' ++++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda ++++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda ++++ export _CE_M= ++++ _CE_M= ++++ export _CE_CONDA= ++++ _CE_CONDA= ++++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ '[' -z x ']' ++++ conda activate base ++++ local cmd=activate ++++ case "$cmd" in ++++ __conda_activate activate base ++++ '[' -n '' ']' ++++ local ask_conda +++++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++++ __conda_exe shell.posix activate base +++++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate base ++++ ask_conda='PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_SHLVL='\''6'\'' +export CONDA_DEFAULT_ENV='\''base'\'' +export CONDA_PROMPT_MODIFIER='\''(base) '\'' +export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' ++++ eval 'PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_SHLVL='\''6'\'' +export CONDA_DEFAULT_ENV='\''base'\'' +export CONDA_PROMPT_MODIFIER='\''(base) '\'' +export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' +++++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++++ export CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0 +++++ CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0 +++++ export CONDA_SHLVL=6 +++++ CONDA_SHLVL=6 +++++ export CONDA_DEFAULT_ENV=base +++++ CONDA_DEFAULT_ENV=base +++++ export 'CONDA_PROMPT_MODIFIER=(base) ' +++++ CONDA_PROMPT_MODIFIER='(base) ' +++++ export CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev +++++ CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev +++++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++++ export _CE_M= +++++ _CE_M= +++++ export _CE_CONDA= +++++ _CE_CONDA= +++++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python +++++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ __conda_hashr ++++ '[' -n '' ']' ++++ '[' -n '' ']' ++++ hash -r +++ unset __conda_setup ++ conda activate schemist-dev ++ local cmd=activate ++ case "$cmd" in ++ __conda_activate activate schemist-dev ++ '[' -n '' ']' ++ local ask_conda +++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++ __conda_exe shell.posix activate schemist-dev +++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate schemist-dev ++ ask_conda='PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_SHLVL='\''7'\'' +export CONDA_DEFAULT_ENV='\''schemist-dev'\'' +export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\'' +export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' ++ eval 'PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_SHLVL='\''7'\'' +export CONDA_DEFAULT_ENV='\''schemist-dev'\'' +export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\'' +export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' +++ PS1='(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++ export CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev +++ CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev +++ export CONDA_SHLVL=7 +++ CONDA_SHLVL=7 +++ export CONDA_DEFAULT_ENV=schemist-dev +++ CONDA_DEFAULT_ENV=schemist-dev +++ export 'CONDA_PROMPT_MODIFIER=(schemist-dev) ' +++ CONDA_PROMPT_MODIFIER='(schemist-dev) ' +++ export CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0 +++ CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0 +++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++ export _CE_M= +++ _CE_M= +++ export _CE_CONDA= +++ _CE_CONDA= +++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python +++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++ __conda_hashr ++ '[' -n '' ']' ++ '[' -n '' ']' ++ hash -r ++ CHUNK_HEAD_FILE=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz ++ INPUT=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/train/cyc-pep-6-12mer-70M_00.csv ++ COLUMN=cysteine_to_N_cyclization ++ PREFIX=cyclic_ ++ AWK='1 { print $8, $1, $2, $10, $3 }' ++ '[' -z cysteine_to_N_cyclization ']' ++ '[' -z cyclic_ ']' ++ '[' -z '1 { print $8, $1, $2, $10, $3 }' ']' ++ cat /dev/fd/63 /nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/train/cyc-pep-6-12mer-70M_00.csv ++ gzip --best ++ schemist convert -f csv --column cysteine_to_N_cyclization --to id inchikey scaffold mwt clogp tpsa --prefix cyclic_ --options prefix=SCB- +++ tr ' ' , ++ awk -F, -v OFS=, '1 { print $8, $1, $2, $10, $3 }' +++ head -n1 +++ zcat /nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz +🚀 Converting between string representations with the following parameters: + subcommand: convert + output: <_io.TextIOWrapper name='' mode='w' encoding='utf-8'> + format: csv + input: <_io.TextIOWrapper name='' mode='r' encoding='utf-8'> + representation: SMILES + column: cysteine_to_N_cyclization + prefix: cyclic_ + to: ['id', 'inchikey', 'scaffold', 'mwt', 'clogp', 'tpsa'] + options: ['prefix=SCB-'] + func: + 0it [00:00, ?it/s] 1it [00:11, 11.24s/it] 2it [00:22, 11.12s/it] 3it [00:33, 11.19s/it] 4it [00:44, 11.18s/it] 5it [00:55, 11.15s/it] 6it 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[2:58:52, 10.70s/it] 997it [2:59:03, 10.69s/it] 998it [2:59:14, 10.70s/it] 999it [2:59:24, 10.69s/it] 1000it [2:59:35, 10.70s/it] 1000it [2:59:35, 10.78s/it] +Error counts: + cyclic_id: 0 + cyclic_inchikey: 0 + cyclic_scaffold: 0 + cyclic_mwt: 0 + cyclic_clogp: 0 + cyclic_tpsa: 0 +⏰ Completed process in 2:59:58.795561 ++ rm /nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/train/cyc-pep-6-12mer-70M_00.csv diff --git a/train/cyc-pep-6-12mer-70M_01.csv.gz b/train/cyc-pep-6-12mer-70M_01.csv.gz index 1b3cc5d76ab12741a1f012910854a5c8bdef66a1..ec9b1c33450f6b45553005bc4cc0f188159ec103 100644 --- a/train/cyc-pep-6-12mer-70M_01.csv.gz +++ b/train/cyc-pep-6-12mer-70M_01.csv.gz @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:d387ed185e88ecfdb4413a271ec111011b684f33e27244b5cd95d01da3a79dff -size 58249061 +oid sha256:13bc91d61c8e22cdda8434608fb531a5565694108ffc8b7dbeb6967e39b3a6a0 +size 112823965 diff --git a/train/cyc-pep-6-12mer-70M_01.log b/train/cyc-pep-6-12mer-70M_01.log new file mode 100644 index 0000000000000000000000000000000000000000..06bf43d666598402071f6e820f62f7ae487e576d --- /dev/null +++ b/train/cyc-pep-6-12mer-70M_01.log @@ -0,0 +1,337 @@ ++ module purge ++ '[' -z '' ']' ++ case "$-" in ++ __lmod_sh_dbg=x ++ '[' -n x ']' ++ set +x +Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output +Shell debugging restarted ++ unset __lmod_sh_dbg ++ return 0 ++ module load Anaconda3/2023.03 ++ '[' -z '' ']' ++ case "$-" in ++ __lmod_sh_dbg=x ++ '[' -n x ']' ++ set +x +Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output +Shell debugging restarted ++ unset __lmod_sh_dbg ++ return 0 ++ source /camp/home/johnsoe/.bashrc +++ '[' '' = yes ']' +++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' ++++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.bash hook +++ __conda_setup='export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'' + +# Copyright (C) 2012 Anaconda, Inc +# SPDX-License-Identifier: BSD-3-Clause +__conda_exe() ( + "$CONDA_EXE" $_CE_M $_CE_CONDA "$@" +) + +__conda_hashr() { + if [ -n "${ZSH_VERSION:+x}" ]; then + \rehash + elif [ -n "${POSH_VERSION:+x}" ]; then + : # pass + else + \hash -r + fi +} + +__conda_activate() { + if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then + # Handle transition from shell activated with conda <= 4.3 to a subsequent activation + # after conda updated to >= 4.4. See issue #6173. + PS1="$CONDA_PS1_BACKUP" + \unset CONDA_PS1_BACKUP + fi + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return + \eval "$ask_conda" + __conda_hashr +} + +__conda_reactivate() { + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return + \eval "$ask_conda" + __conda_hashr +} + +conda() { + \local cmd="${1-__missing__}" + case "$cmd" in + activate|deactivate) + __conda_activate "$@" + ;; + install|update|upgrade|remove|uninstall) + __conda_exe "$@" || \return + __conda_reactivate + ;; + *) + __conda_exe "$@" + ;; + esac +} + +if [ -z "${CONDA_SHLVL+x}" ]; then + \export CONDA_SHLVL=0 + # In dev-mode CONDA_EXE is python.exe and on Windows + # it is in a different relative location to condabin. + if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then + PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}" + else + PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}" + fi + \export PATH + + # We'\''re not allowing PS1 to be unbound. It must at least be set. + # However, we'\''re not exporting it, which can cause problems when starting a second shell + # via a first shell (i.e. starting zsh from bash). + if [ -z "${PS1+x}" ]; then + PS1= + fi +fi + +conda activate base' +++ '[' 0 -eq 0 ']' +++ eval 'export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'' + +# Copyright (C) 2012 Anaconda, Inc +# SPDX-License-Identifier: BSD-3-Clause +__conda_exe() ( + "$CONDA_EXE" $_CE_M $_CE_CONDA "$@" +) + +__conda_hashr() { + if [ -n "${ZSH_VERSION:+x}" ]; then + \rehash + elif [ -n "${POSH_VERSION:+x}" ]; then + : # pass + else + \hash -r + fi +} + +__conda_activate() { + if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then + # Handle transition from shell activated with conda <= 4.3 to a subsequent activation + # after conda updated to >= 4.4. See issue #6173. + PS1="$CONDA_PS1_BACKUP" + \unset CONDA_PS1_BACKUP + fi + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return + \eval "$ask_conda" + __conda_hashr +} + +__conda_reactivate() { + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return + \eval "$ask_conda" + __conda_hashr +} + +conda() { + \local cmd="${1-__missing__}" + case "$cmd" in + activate|deactivate) + __conda_activate "$@" + ;; + install|update|upgrade|remove|uninstall) + __conda_exe "$@" || \return + __conda_reactivate + ;; + *) + __conda_exe "$@" + ;; + esac +} + +if [ -z "${CONDA_SHLVL+x}" ]; then + \export CONDA_SHLVL=0 + # In dev-mode CONDA_EXE is python.exe and on Windows + # it is in a different relative location to condabin. + if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then + PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}" + else + PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}" + fi + \export PATH + + # We'\''re not allowing PS1 to be unbound. It must at least be set. + # However, we'\''re not exporting it, which can cause problems when starting a second shell + # via a first shell (i.e. starting zsh from bash). + if [ -z "${PS1+x}" ]; then + PS1= + fi +fi + +conda activate base' ++++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda ++++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda ++++ export _CE_M= ++++ _CE_M= ++++ export _CE_CONDA= ++++ _CE_CONDA= ++++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ '[' -z x ']' ++++ conda activate base ++++ local cmd=activate ++++ case "$cmd" in ++++ __conda_activate activate base ++++ '[' -n '' ']' ++++ local ask_conda +++++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++++ __conda_exe shell.posix activate base +++++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate base ++++ ask_conda='PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_SHLVL='\''6'\'' +export CONDA_DEFAULT_ENV='\''base'\'' +export CONDA_PROMPT_MODIFIER='\''(base) '\'' +export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' ++++ eval 'PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_SHLVL='\''6'\'' +export CONDA_DEFAULT_ENV='\''base'\'' +export CONDA_PROMPT_MODIFIER='\''(base) '\'' +export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' +++++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++++ export CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0 +++++ CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0 +++++ export CONDA_SHLVL=6 +++++ CONDA_SHLVL=6 +++++ export CONDA_DEFAULT_ENV=base +++++ CONDA_DEFAULT_ENV=base +++++ export 'CONDA_PROMPT_MODIFIER=(base) ' +++++ CONDA_PROMPT_MODIFIER='(base) ' +++++ export CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev +++++ CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev +++++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++++ export _CE_M= +++++ _CE_M= +++++ export _CE_CONDA= +++++ _CE_CONDA= +++++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python +++++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ __conda_hashr ++++ '[' -n '' ']' ++++ '[' -n '' ']' ++++ hash -r +++ unset __conda_setup ++ conda activate schemist-dev ++ local cmd=activate ++ case "$cmd" in ++ __conda_activate activate schemist-dev ++ '[' -n '' ']' ++ local ask_conda +++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++ __conda_exe shell.posix activate schemist-dev +++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate schemist-dev ++ ask_conda='PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_SHLVL='\''7'\'' +export CONDA_DEFAULT_ENV='\''schemist-dev'\'' +export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\'' +export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' ++ eval 'PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_SHLVL='\''7'\'' +export CONDA_DEFAULT_ENV='\''schemist-dev'\'' +export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\'' +export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' +++ PS1='(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++ export CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev +++ CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev +++ export CONDA_SHLVL=7 +++ CONDA_SHLVL=7 +++ export CONDA_DEFAULT_ENV=schemist-dev +++ CONDA_DEFAULT_ENV=schemist-dev +++ export 'CONDA_PROMPT_MODIFIER=(schemist-dev) ' +++ CONDA_PROMPT_MODIFIER='(schemist-dev) ' +++ export CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0 +++ CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0 +++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++ export _CE_M= +++ _CE_M= +++ export _CE_CONDA= +++ _CE_CONDA= +++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python +++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++ __conda_hashr ++ '[' -n '' ']' ++ '[' -n '' ']' ++ hash -r ++ CHUNK_HEAD_FILE=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz ++ INPUT=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/train/cyc-pep-6-12mer-70M_01.csv ++ COLUMN=cysteine_to_N_cyclization ++ PREFIX=cyclic_ ++ AWK='1 { print $8, $1, $2, $10, $3 }' ++ '[' -z cysteine_to_N_cyclization ']' ++ '[' -z cyclic_ ']' ++ '[' -z '1 { print $8, $1, $2, $10, $3 }' ']' ++ cat /dev/fd/63 /nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/train/cyc-pep-6-12mer-70M_01.csv ++ schemist convert -f csv --column cysteine_to_N_cyclization --to id inchikey scaffold mwt clogp tpsa --prefix cyclic_ --options prefix=SCB- ++ gzip --best +++ head -n1 ++ awk -F, -v OFS=, '1 { print $8, $1, $2, $10, $3 }' +++ zcat /nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz +++ tr ' ' , +🚀 Converting between string representations with the following parameters: + subcommand: convert + output: <_io.TextIOWrapper name='' mode='w' encoding='utf-8'> + format: csv + input: <_io.TextIOWrapper name='' mode='r' encoding='utf-8'> + representation: SMILES + column: cysteine_to_N_cyclization + prefix: cyclic_ + to: ['id', 'inchikey', 'scaffold', 'mwt', 'clogp', 'tpsa'] + options: ['prefix=SCB-'] + func: + 0it [00:00, ?it/s] 1it [00:10, 10.64s/it] 2it [00:21, 10.59s/it] 3it [00:31, 10.60s/it] 4it [00:42, 10.65s/it] 5it [00:53, 10.63s/it] 6it [01:03, 10.63s/it] 7it [01:14, 10.64s/it] 8it [01:25, 10.65s/it] 9it [01:35, 10.66s/it] 10it [01:46, 10.67s/it] 11it [01:57, 10.64s/it] 12it [02:07, 10.65s/it] 13it [02:18, 10.65s/it] 14it [02:29, 10.66s/it] 15it [02:39, 10.66s/it] 16it [02:50, 10.67s/it] 17it [03:01, 10.65s/it] 18it [03:11, 10.65s/it] 19it [03:22, 10.63s/it] 20it [03:32, 10.64s/it] 21it [03:43, 10.62s/it] 22it [03:54, 10.65s/it] 23it [04:04, 10.65s/it] 24it [04:15, 10.65s/it] 25it [04:26, 10.65s/it] 26it [04:36, 10.65s/it] 27it [04:47, 10.65s/it] 28it [04:58, 10.67s/it] 29it [05:08, 10.66s/it] 30it [05:19, 10.66s/it] 31it [05:30, 10.64s/it] 32it [05:40, 10.64s/it] 33it [05:51, 10.64s/it] 34it [06:01, 10.61s/it] 35it [06:12, 10.60s/it] 36it [06:23, 10.60s/it] 37it [06:33, 10.60s/it] 38it [06:44, 10.60s/it] 39it [06:54, 10.58s/it] 40it [07:05, 10.61s/it] 41it [07:16, 10.64s/it] 42it [07:26, 10.63s/it] 43it [07:37, 10.64s/it] 44it [07:48, 10.64s/it] 45it [07:58, 10.67s/it] 46it [08:09, 10.67s/it] 47it [08:20, 10.66s/it] 48it [08:30, 10.64s/it] 49it [08:41, 10.63s/it] 50it [08:51, 10.63s/it] 51it [09:02, 10.63s/it] 52it [09:13, 10.64s/it] 53it [09:23, 10.64s/it] 54it [09:34, 10.62s/it] 55it [09:45, 10.62s/it] 56it [09:55, 10.63s/it] 57it [10:06, 10.64s/it] 58it [10:17, 10.65s/it] 59it [10:27, 10.65s/it] 60it [10:38, 10.66s/it] 61it [10:48, 10.65s/it] 62it [10:59, 10.64s/it] 63it [11:10, 10.63s/it] 64it [11:20, 10.64s/it] 65it [11:31, 10.61s/it] 66it [11:42, 10.62s/it] 67it [11:52, 10.62s/it] 68it [12:03, 10.60s/it] 69it [12:13, 10.63s/it] 70it [12:24, 10.61s/it] 71it [12:35, 10.63s/it] 72it [12:45, 10.62s/it] 73it [12:56, 10.63s/it] 74it [13:07, 10.62s/it] 75it [13:17, 10.63s/it] 76it [13:28, 10.63s/it] 77it [13:38, 10.61s/it] 78it [13:49, 10.61s/it] 79it [14:00, 10.61s/it] 80it [14:10, 10.61s/it] 81it [14:21, 10.62s/it] 82it [14:31, 10.63s/it] 83it [14:42, 10.64s/it] 84it [14:53, 10.66s/it] 85it [15:03, 10.64s/it] 86it [15:14, 10.64s/it] 87it [15:25, 10.65s/it] 88it [15:35, 10.64s/it] 89it [15:46, 10.63s/it] 90it [15:57, 10.65s/it] 91it [16:07, 10.63s/it] 92it [16:18, 10.66s/it] 93it [16:29, 10.66s/it] 94it [16:39, 10.66s/it] 95it [16:50, 10.66s/it] 96it [17:01, 10.64s/it] 97it [17:11, 10.64s/it] 98it [17:22, 10.62s/it] 99it [17:32, 10.61s/it] 100it [17:43, 10.60s/it] 101it [17:54, 10.62s/it] 102it [18:04, 10.62s/it] 103it [18:15, 10.63s/it] 104it [18:26, 10.64s/it] 105it [18:36, 10.63s/it] 106it [18:47, 10.63s/it] 107it [18:57, 10.63s/it] 108it [19:08, 10.61s/it] 109it [19:19, 10.63s/it] 110it [19:29, 10.61s/it] 111it [19:40, 10.64s/it] 112it [19:51, 10.64s/it] 113it [20:01, 10.66s/it] 114it [20:12, 10.65s/it] 115it [20:23, 10.65s/it] 116it [20:33, 10.64s/it] 117it [20:44, 10.64s/it] 118it [20:54, 10.64s/it] 119it [21:05, 10.66s/it] 120it [21:16, 10.66s/it] 121it [21:26, 10.66s/it] 122it [21:37, 10.68s/it] 123it [21:48, 10.65s/it] 124it [21:58, 10.66s/it] 125it [22:09, 10.66s/it] 126it [22:20, 10.67s/it] 127it [22:31, 10.68s/it] 128it [22:41, 10.67s/it] 129it [22:52, 10.64s/it] 130it [23:02, 10.64s/it] 131it [23:13, 10.64s/it] 132it [23:24, 10.63s/it] 133it [23:34, 10.63s/it] 134it [23:45, 10.62s/it] 135it [23:55, 10.62s/it] 136it [24:06, 10.64s/it] 137it [24:17, 10.63s/it] 138it [24:27, 10.64s/it] 139it [24:38, 10.64s/it] 140it [24:49, 10.63s/it] 141it [24:59, 10.62s/it] 142it [25:10, 10.62s/it] 143it [25:21, 10.62s/it] 144it [25:31, 10.65s/it] 145it [25:42, 10.65s/it] 146it [25:53, 10.65s/it] 147it [26:03, 10.64s/it] 148it [26:14, 10.65s/it] 149it [26:24, 10.65s/it] 150it [26:35, 10.65s/it] 151it [26:46, 10.64s/it] 152it [26:56, 10.65s/it] 153it [27:07, 10.65s/it] 154it [27:18, 10.63s/it] 155it [27:28, 10.63s/it] 156it [27:39, 10.62s/it] 157it [27:50, 10.64s/it] 158it [28:00, 10.63s/it] 159it [28:11, 10.64s/it] 160it [28:22, 10.65s/it] 161it [28:32, 10.66s/it] 162it [28:43, 10.65s/it] 163it [28:54, 10.69s/it] 164it [29:04, 10.67s/it] 165it [29:15, 10.68s/it] 166it [29:26, 10.67s/it] 167it [29:36, 10.69s/it] 168it [29:47, 10.67s/it] 169it [29:58, 10.65s/it] 170it [30:08, 10.64s/it] 171it [30:19, 10.64s/it] 172it [30:29, 10.65s/it] 173it [30:40, 10.63s/it] 174it [30:51, 10.64s/it] 175it [31:01, 10.63s/it] 176it [31:12, 10.63s/it] 177it [31:23, 10.62s/it] 178it [31:33, 10.62s/it] 179it [31:44, 10.61s/it] 180it [31:54, 10.63s/it] 181it [32:05, 10.62s/it] 182it [32:16, 10.63s/it] 183it [32:26, 10.63s/it] 184it [32:37, 10.62s/it] 185it [32:48, 10.63s/it] 186it [32:58, 10.63s/it] 187it [33:09, 10.65s/it] 188it [33:20, 10.64s/it] 189it [33:30, 10.65s/it] 190it [33:41, 10.65s/it] 191it [33:51, 10.63s/it] 192it [34:02, 10.62s/it] 193it [34:13, 10.63s/it] 194it [34:23, 10.60s/it] 195it [34:34, 10.61s/it] 196it [34:44, 10.59s/it] 197it [34:55, 10.59s/it] 198it [35:06, 10.59s/it] 199it [35:16, 10.63s/it] 200it [35:27, 10.64s/it] 201it [35:38, 10.64s/it] 202it [35:48, 10.65s/it] 203it [35:59, 10.65s/it] 204it [36:09, 10.63s/it] 205it [36:20, 10.63s/it] 206it [36:31, 10.64s/it] 207it [36:41, 10.63s/it] 208it [36:52, 10.62s/it] 209it [37:03, 10.62s/it] 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290it [51:24, 10.66s/it] 291it [51:35, 10.67s/it] 292it [51:46, 10.66s/it] 293it [51:56, 10.68s/it] 294it [52:07, 10.69s/it] 295it [52:18, 10.68s/it] 296it [52:28, 10.65s/it] 297it [52:39, 10.67s/it] 298it [52:50, 10.67s/it] 299it [53:01, 10.67s/it] 300it [53:11, 10.65s/it] 301it [53:22, 10.66s/it] 302it [53:32, 10.66s/it] 303it [53:43, 10.67s/it] 304it [53:54, 10.66s/it] 305it [54:04, 10.68s/it] 306it [54:15, 10.66s/it] 307it [54:26, 10.67s/it] 308it [54:36, 10.66s/it] 309it [54:47, 10.68s/it] 310it [54:58, 10.65s/it] 311it [55:08, 10.65s/it] 312it [55:19, 10.64s/it] 313it [55:30, 10.64s/it] 314it [55:40, 10.64s/it] 315it [55:51, 10.65s/it] 316it [56:02, 10.65s/it] 317it [56:12, 10.66s/it] 318it [56:23, 10.67s/it] 319it [56:34, 10.67s/it] 320it [56:44, 10.67s/it] 321it [56:55, 10.66s/it] 322it [57:06, 10.65s/it] 323it [57:16, 10.66s/it] 324it [57:27, 10.65s/it] 325it [57:38, 10.66s/it] 326it [57:48, 10.70s/it] 327it [57:59, 10.70s/it] 328it [58:10, 10.71s/it] 329it [58:20, 10.69s/it] 330it [58:31, 10.69s/it] 331it [58:42, 10.69s/it] 332it [58:53, 10.70s/it] 333it [59:03, 10.70s/it] 334it [59:14, 10.68s/it] 335it [59:25, 10.69s/it] 336it [59:35, 10.67s/it] 337it [59:46, 10.67s/it] 338it [59:57, 10.69s/it] 339it [1:00:07, 10.68s/it] 340it [1:00:18, 10.65s/it] 341it [1:00:29, 10.67s/it] 342it [1:00:39, 10.68s/it] 343it [1:00:50, 10.66s/it] 344it [1:01:01, 10.67s/it] 345it [1:01:11, 10.69s/it] 346it [1:01:22, 10.68s/it] 347it [1:01:33, 10.68s/it] 348it [1:01:43, 10.69s/it] 349it [1:01:54, 10.69s/it] 350it [1:02:05, 10.67s/it] 351it [1:02:15, 10.67s/it] 352it [1:02:26, 10.66s/it] 353it [1:02:37, 10.66s/it] 354it [1:02:47, 10.67s/it] 355it [1:02:58, 10.68s/it] 356it [1:03:09, 10.69s/it] 357it [1:03:19, 10.68s/it] 358it [1:03:30, 10.65s/it] 359it [1:03:41, 10.66s/it] 360it [1:03:51, 10.66s/it] 361it [1:04:02, 10.66s/it] 362it [1:04:13, 10.68s/it] 363it [1:04:23, 10.68s/it] 364it [1:04:34, 10.68s/it] 365it [1:04:45, 10.69s/it] 366it [1:04:55, 10.69s/it] 367it [1:05:06, 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10.90s/it] 960it [2:51:10, 10.90s/it] 961it [2:51:21, 10.89s/it] 962it [2:51:32, 10.88s/it] 963it [2:51:42, 10.90s/it] 964it [2:51:53, 10.88s/it] 965it [2:52:04, 10.90s/it] 966it [2:52:15, 10.89s/it] 967it [2:52:26, 10.90s/it] 968it [2:52:37, 10.89s/it] 969it [2:52:48, 10.89s/it] 970it [2:52:59, 10.90s/it] 971it [2:53:10, 10.88s/it] 972it [2:53:20, 10.88s/it] 973it [2:53:31, 10.89s/it] 974it [2:53:42, 10.91s/it] 975it [2:53:53, 10.93s/it] 976it [2:54:04, 10.90s/it] 977it [2:54:15, 10.88s/it] 978it [2:54:26, 10.87s/it] 979it [2:54:37, 10.88s/it] 980it [2:54:48, 10.89s/it] 981it [2:54:59, 10.91s/it] 982it [2:55:09, 10.91s/it] 983it [2:55:20, 10.89s/it] 984it [2:55:31, 10.89s/it] 985it [2:55:42, 10.89s/it] 986it [2:55:53, 10.91s/it] 987it [2:56:04, 10.91s/it] 988it [2:56:15, 10.92s/it] 989it [2:56:26, 10.91s/it] 990it [2:56:37, 10.91s/it] 991it [2:56:48, 10.92s/it] 992it [2:56:59, 10.93s/it] 993it [2:57:09, 10.90s/it] 994it [2:57:20, 10.89s/it] 995it [2:57:31, 10.85s/it] 996it [2:57:42, 10.86s/it] 997it [2:57:53, 10.88s/it] 998it [2:58:04, 10.88s/it] 999it [2:58:15, 10.89s/it] 1000it [2:58:25, 10.88s/it] 1000it [2:58:25, 10.71s/it] +Error counts: + cyclic_id: 0 + cyclic_inchikey: 0 + cyclic_scaffold: 0 + cyclic_mwt: 0 + cyclic_clogp: 0 + cyclic_tpsa: 0 +⏰ Completed process in 2:58:48.975518 ++ rm /nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/train/cyc-pep-6-12mer-70M_01.csv diff --git a/train/cyc-pep-6-12mer-70M_02.csv.gz b/train/cyc-pep-6-12mer-70M_02.csv.gz index 97d5dd6c1eabcd6c7d01b1eb4b989a0e48ff3a37..1d1a975b740a5f45076ad0cb2470e89029e6efb8 100644 --- a/train/cyc-pep-6-12mer-70M_02.csv.gz +++ b/train/cyc-pep-6-12mer-70M_02.csv.gz @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:cccb9f6a7df61c7c02fd68f553cf9c426a38bf0b5c175c3f7c77f06c07daaeab -size 58253797 +oid sha256:00d2407f78ec4a79757633e04beb57d0fffb1035ccaa97940e3acc18a3a8f5e8 +size 112828179 diff --git a/train/cyc-pep-6-12mer-70M_02.log b/train/cyc-pep-6-12mer-70M_02.log new file mode 100644 index 0000000000000000000000000000000000000000..c111d6f75d3930614ddd5599f70fffaa09050aa5 --- /dev/null +++ b/train/cyc-pep-6-12mer-70M_02.log @@ -0,0 +1,337 @@ ++ module purge ++ '[' -z '' ']' ++ case "$-" in ++ __lmod_sh_dbg=x ++ '[' -n x ']' ++ set +x +Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output +Shell debugging restarted ++ unset __lmod_sh_dbg ++ return 0 ++ module load Anaconda3/2023.03 ++ '[' -z '' ']' ++ case "$-" in ++ __lmod_sh_dbg=x ++ '[' -n x ']' ++ set +x +Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output +Shell debugging restarted ++ unset __lmod_sh_dbg ++ return 0 ++ source /camp/home/johnsoe/.bashrc +++ '[' '' = yes ']' +++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' ++++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.bash hook +++ __conda_setup='export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'' + +# Copyright (C) 2012 Anaconda, Inc +# SPDX-License-Identifier: BSD-3-Clause +__conda_exe() ( + "$CONDA_EXE" $_CE_M $_CE_CONDA "$@" +) + +__conda_hashr() { + if [ -n "${ZSH_VERSION:+x}" ]; then + \rehash + elif [ -n "${POSH_VERSION:+x}" ]; then + : # pass + else + \hash -r + fi +} + +__conda_activate() { + if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then + # Handle transition from shell activated with conda <= 4.3 to a subsequent activation + # after conda updated to >= 4.4. See issue #6173. + PS1="$CONDA_PS1_BACKUP" + \unset CONDA_PS1_BACKUP + fi + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return + \eval "$ask_conda" + __conda_hashr +} + +__conda_reactivate() { + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return + \eval "$ask_conda" + __conda_hashr +} + +conda() { + \local cmd="${1-__missing__}" + case "$cmd" in + activate|deactivate) + __conda_activate "$@" + ;; + install|update|upgrade|remove|uninstall) + __conda_exe "$@" || \return + __conda_reactivate + ;; + *) + __conda_exe "$@" + ;; + esac +} + +if [ -z "${CONDA_SHLVL+x}" ]; then + \export CONDA_SHLVL=0 + # In dev-mode CONDA_EXE is python.exe and on Windows + # it is in a different relative location to condabin. + if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then + PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}" + else + PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}" + fi + \export PATH + + # We'\''re not allowing PS1 to be unbound. It must at least be set. + # However, we'\''re not exporting it, which can cause problems when starting a second shell + # via a first shell (i.e. starting zsh from bash). + if [ -z "${PS1+x}" ]; then + PS1= + fi +fi + +conda activate base' +++ '[' 0 -eq 0 ']' +++ eval 'export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'' + +# Copyright (C) 2012 Anaconda, Inc +# SPDX-License-Identifier: BSD-3-Clause +__conda_exe() ( + "$CONDA_EXE" $_CE_M $_CE_CONDA "$@" +) + +__conda_hashr() { + if [ -n "${ZSH_VERSION:+x}" ]; then + \rehash + elif [ -n "${POSH_VERSION:+x}" ]; then + : # pass + else + \hash -r + fi +} + +__conda_activate() { + if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then + # Handle transition from shell activated with conda <= 4.3 to a subsequent activation + # after conda updated to >= 4.4. See issue #6173. + PS1="$CONDA_PS1_BACKUP" + \unset CONDA_PS1_BACKUP + fi + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return + \eval "$ask_conda" + __conda_hashr +} + +__conda_reactivate() { + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return + \eval "$ask_conda" + __conda_hashr +} + +conda() { + \local cmd="${1-__missing__}" + case "$cmd" in + activate|deactivate) + __conda_activate "$@" + ;; + install|update|upgrade|remove|uninstall) + __conda_exe "$@" || \return + __conda_reactivate + ;; + *) + __conda_exe "$@" + ;; + esac +} + +if [ -z "${CONDA_SHLVL+x}" ]; then + \export CONDA_SHLVL=0 + # In dev-mode CONDA_EXE is python.exe and on Windows + # it is in a different relative location to condabin. + if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then + PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}" + else + PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}" + fi + \export PATH + + # We'\''re not allowing PS1 to be unbound. It must at least be set. + # However, we'\''re not exporting it, which can cause problems when starting a second shell + # via a first shell (i.e. starting zsh from bash). + if [ -z "${PS1+x}" ]; then + PS1= + fi +fi + +conda activate base' ++++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda ++++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda ++++ export _CE_M= ++++ _CE_M= ++++ export _CE_CONDA= ++++ _CE_CONDA= ++++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ '[' -z x ']' ++++ conda activate base ++++ local cmd=activate ++++ case "$cmd" in ++++ __conda_activate activate base ++++ '[' -n '' ']' ++++ local ask_conda +++++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++++ __conda_exe shell.posix activate base +++++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate base ++++ ask_conda='PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_SHLVL='\''6'\'' +export CONDA_DEFAULT_ENV='\''base'\'' +export CONDA_PROMPT_MODIFIER='\''(base) '\'' +export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' ++++ eval 'PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_SHLVL='\''6'\'' +export CONDA_DEFAULT_ENV='\''base'\'' +export CONDA_PROMPT_MODIFIER='\''(base) '\'' +export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' +++++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++++ export CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0 +++++ CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0 +++++ export CONDA_SHLVL=6 +++++ CONDA_SHLVL=6 +++++ export CONDA_DEFAULT_ENV=base +++++ CONDA_DEFAULT_ENV=base +++++ export 'CONDA_PROMPT_MODIFIER=(base) ' +++++ CONDA_PROMPT_MODIFIER='(base) ' +++++ export CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev +++++ CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev +++++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++++ export _CE_M= +++++ _CE_M= +++++ export _CE_CONDA= +++++ _CE_CONDA= +++++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python +++++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ __conda_hashr ++++ '[' -n '' ']' ++++ '[' -n '' ']' ++++ hash -r +++ unset __conda_setup ++ conda activate schemist-dev ++ local cmd=activate ++ case "$cmd" in ++ __conda_activate activate schemist-dev ++ '[' -n '' ']' ++ local ask_conda +++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++ __conda_exe shell.posix activate schemist-dev +++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate schemist-dev ++ ask_conda='PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_SHLVL='\''7'\'' +export CONDA_DEFAULT_ENV='\''schemist-dev'\'' +export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\'' +export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' ++ eval 'PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_SHLVL='\''7'\'' +export CONDA_DEFAULT_ENV='\''schemist-dev'\'' +export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\'' +export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' +++ PS1='(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++ export CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev +++ CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev +++ export CONDA_SHLVL=7 +++ CONDA_SHLVL=7 +++ export CONDA_DEFAULT_ENV=schemist-dev +++ CONDA_DEFAULT_ENV=schemist-dev +++ export 'CONDA_PROMPT_MODIFIER=(schemist-dev) ' +++ CONDA_PROMPT_MODIFIER='(schemist-dev) ' +++ export CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0 +++ CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0 +++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++ export _CE_M= +++ _CE_M= +++ export _CE_CONDA= +++ _CE_CONDA= +++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python +++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++ __conda_hashr ++ '[' -n '' ']' ++ '[' -n '' ']' ++ hash -r ++ CHUNK_HEAD_FILE=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz ++ INPUT=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/train/cyc-pep-6-12mer-70M_02.csv ++ COLUMN=cysteine_to_N_cyclization ++ PREFIX=cyclic_ ++ AWK='1 { print $8, $1, $2, $10, $3 }' ++ '[' -z cysteine_to_N_cyclization ']' ++ '[' -z cyclic_ ']' ++ '[' -z '1 { print $8, $1, $2, $10, $3 }' ']' ++ cat /dev/fd/63 /nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/train/cyc-pep-6-12mer-70M_02.csv ++ awk -F, -v OFS=, '1 { print $8, $1, $2, $10, $3 }' +++ zcat /nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz ++ schemist convert -f csv --column cysteine_to_N_cyclization --to id inchikey scaffold mwt clogp tpsa --prefix cyclic_ --options prefix=SCB- +++ head -n1 ++ gzip --best +++ tr ' ' , +🚀 Converting between string representations with the following parameters: + subcommand: convert + output: <_io.TextIOWrapper name='' mode='w' encoding='utf-8'> + format: csv + input: <_io.TextIOWrapper name='' mode='r' encoding='utf-8'> + representation: SMILES + column: cysteine_to_N_cyclization + prefix: cyclic_ + to: ['id', 'inchikey', 'scaffold', 'mwt', 'clogp', 'tpsa'] + options: ['prefix=SCB-'] + func: + 0it [00:00, ?it/s] 1it [00:11, 11.27s/it] 2it [00:22, 11.27s/it] 3it [00:33, 11.21s/it] 4it [00:44, 11.20s/it] 5it [00:56, 11.19s/it] 6it [01:07, 11.17s/it] 7it [01:18, 11.17s/it] 8it [01:29, 11.20s/it] 9it [01:40, 11.21s/it] 10it [01:52, 11.20s/it] 11it [02:03, 11.18s/it] 12it [02:14, 11.22s/it] 13it [02:25, 11.20s/it] 14it [02:36, 11.21s/it] 15it [02:48, 11.22s/it] 16it [02:59, 11.23s/it] 17it [03:10, 11.22s/it] 18it [03:21, 11.19s/it] 19it [03:32, 11.19s/it] 20it [03:43, 11.16s/it] 21it [03:55, 11.16s/it] 22it [04:06, 11.18s/it] 23it [04:17, 11.19s/it] 24it [04:28, 11.19s/it] 25it [04:39, 11.20s/it] 26it [04:51, 11.22s/it] 27it [05:02, 11.23s/it] 28it [05:13, 11.20s/it] 29it [05:24, 11.21s/it] 30it [05:36, 11.24s/it] 31it [05:47, 11.24s/it] 32it [05:58, 11.23s/it] 33it [06:09, 11.22s/it] 34it [06:21, 11.26s/it] 35it [06:32, 11.28s/it] 36it [06:43, 11.26s/it] 37it [06:54, 11.21s/it] 38it [07:05, 11.20s/it] 39it [07:17, 11.17s/it] 40it [07:28, 11.15s/it] 41it [07:39, 11.15s/it] 42it [07:50, 11.13s/it] 43it [08:01, 11.13s/it] 44it [08:12, 11.15s/it] 45it [08:23, 11.18s/it] 46it [08:35, 11.19s/it] 47it [08:46, 11.22s/it] 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10.97s/it] 90it [16:40, 10.99s/it] 91it [16:51, 10.98s/it] 92it [17:02, 10.99s/it] 93it [17:13, 10.97s/it] 94it [17:24, 10.98s/it] 95it [17:35, 10.98s/it] 96it [17:46, 10.97s/it] 97it [17:57, 10.97s/it] 98it [18:08, 10.97s/it] 99it [18:19, 10.96s/it] 100it [18:30, 10.95s/it] 101it [18:41, 10.95s/it] 102it [18:52, 10.97s/it] 103it [19:03, 11.00s/it] 104it [19:14, 10.98s/it] 105it [19:25, 10.98s/it] 106it [19:36, 10.99s/it] 107it [19:47, 11.00s/it] 108it [19:58, 11.00s/it] 109it [20:09, 11.02s/it] 110it [20:20, 10.97s/it] 111it [20:31, 10.92s/it] 112it [20:42, 10.91s/it] 113it [20:52, 10.92s/it] 114it [21:03, 10.93s/it] 115it [21:14, 10.94s/it] 116it [21:25, 10.95s/it] 117it [21:36, 10.95s/it] 118it [21:47, 10.96s/it] 119it [21:58, 10.96s/it] 120it [22:09, 10.98s/it] 121it [22:20, 10.94s/it] 122it [22:31, 10.94s/it] 123it [22:42, 10.93s/it] 124it [22:53, 10.94s/it] 125it [23:04, 10.94s/it] 126it [23:15, 10.95s/it] 127it [23:26, 10.95s/it] 128it [23:37, 10.95s/it] 129it [23:48, 10.94s/it] 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11.06s/it] 959it [2:53:49, 11.06s/it] 960it [2:54:00, 11.06s/it] 961it [2:54:11, 11.06s/it] 962it [2:54:22, 11.07s/it] 963it [2:54:33, 11.09s/it] 964it [2:54:44, 11.06s/it] 965it [2:54:56, 11.07s/it] 966it [2:55:07, 11.08s/it] 967it [2:55:18, 11.06s/it] 968it [2:55:29, 11.06s/it] 969it [2:55:40, 11.04s/it] 970it [2:55:51, 11.02s/it] 971it [2:56:02, 11.02s/it] 972it [2:56:13, 11.01s/it] 973it [2:56:24, 10.98s/it] 974it [2:56:34, 10.96s/it] 975it [2:56:45, 10.93s/it] 976it [2:56:56, 10.94s/it] 977it [2:57:07, 10.96s/it] 978it [2:57:18, 10.95s/it] 979it [2:57:29, 10.94s/it] 980it [2:57:40, 10.91s/it] 981it [2:57:51, 10.88s/it] 982it [2:58:02, 10.90s/it] 983it [2:58:13, 10.94s/it] 984it [2:58:24, 10.92s/it] 985it [2:58:34, 10.88s/it] 986it [2:58:45, 10.88s/it] 987it [2:58:56, 10.91s/it] 988it [2:59:07, 10.93s/it] 989it [2:59:18, 10.95s/it] 990it [2:59:29, 10.98s/it] 991it [2:59:40, 11.00s/it] 992it [2:59:51, 11.03s/it] 993it [3:00:03, 11.08s/it] 994it [3:00:14, 11.09s/it] 995it [3:00:25, 11.10s/it] 996it [3:00:36, 11.10s/it] 997it [3:00:47, 11.10s/it] 998it [3:00:58, 11.07s/it] 999it [3:01:09, 11.08s/it] 1000it [3:01:20, 11.12s/it] 1000it [3:01:20, 10.88s/it] +Error counts: + cyclic_id: 0 + cyclic_inchikey: 0 + cyclic_scaffold: 0 + cyclic_mwt: 0 + cyclic_clogp: 0 + cyclic_tpsa: 0 +⏰ Completed process in 3:01:43.044204 ++ rm /nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/train/cyc-pep-6-12mer-70M_02.csv diff --git a/train/cyc-pep-6-12mer-70M_03.csv.gz b/train/cyc-pep-6-12mer-70M_03.csv.gz index 6e3af32e1d0ce431a075d67e401a8cebed02a784..4a4f43da46d3360ef32e3e21dbe1de37a0db18c3 100644 --- a/train/cyc-pep-6-12mer-70M_03.csv.gz +++ b/train/cyc-pep-6-12mer-70M_03.csv.gz @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:340be6860ea52b67de160194816637a69c8db0baa8b40a33c66d8333c2cc8d7c -size 58252448 +oid sha256:1def9ffdfe1abdc5d1454df26ea49f9e8bb6b6b21841787044d956385ecca11a +size 112829110 diff --git a/train/cyc-pep-6-12mer-70M_03.log b/train/cyc-pep-6-12mer-70M_03.log new file mode 100644 index 0000000000000000000000000000000000000000..b055076c5506d78dedae51e1a52c4841de7c4099 --- /dev/null +++ b/train/cyc-pep-6-12mer-70M_03.log @@ -0,0 +1,337 @@ ++ module purge ++ '[' -z '' ']' ++ case "$-" in ++ __lmod_sh_dbg=x ++ '[' -n x ']' ++ set +x +Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output +Shell debugging restarted ++ unset __lmod_sh_dbg ++ return 0 ++ module load Anaconda3/2023.03 ++ '[' -z '' ']' ++ case "$-" in ++ __lmod_sh_dbg=x ++ '[' -n x ']' ++ set +x +Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output +Shell debugging restarted ++ unset __lmod_sh_dbg ++ return 0 ++ source /camp/home/johnsoe/.bashrc +++ '[' '' = yes ']' +++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' ++++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.bash hook +++ __conda_setup='export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'' + +# Copyright (C) 2012 Anaconda, Inc +# SPDX-License-Identifier: BSD-3-Clause +__conda_exe() ( + "$CONDA_EXE" $_CE_M $_CE_CONDA "$@" +) + +__conda_hashr() { + if [ -n "${ZSH_VERSION:+x}" ]; then + \rehash + elif [ -n "${POSH_VERSION:+x}" ]; then + : # pass + else + \hash -r + fi +} + +__conda_activate() { + if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then + # Handle transition from shell activated with conda <= 4.3 to a subsequent activation + # after conda updated to >= 4.4. See issue #6173. + PS1="$CONDA_PS1_BACKUP" + \unset CONDA_PS1_BACKUP + fi + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return + \eval "$ask_conda" + __conda_hashr +} + +__conda_reactivate() { + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return + \eval "$ask_conda" + __conda_hashr +} + +conda() { + \local cmd="${1-__missing__}" + case "$cmd" in + activate|deactivate) + __conda_activate "$@" + ;; + install|update|upgrade|remove|uninstall) + __conda_exe "$@" || \return + __conda_reactivate + ;; + *) + __conda_exe "$@" + ;; + esac +} + +if [ -z "${CONDA_SHLVL+x}" ]; then + \export CONDA_SHLVL=0 + # In dev-mode CONDA_EXE is python.exe and on Windows + # it is in a different relative location to condabin. + if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then + PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}" + else + PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}" + fi + \export PATH + + # We'\''re not allowing PS1 to be unbound. It must at least be set. + # However, we'\''re not exporting it, which can cause problems when starting a second shell + # via a first shell (i.e. starting zsh from bash). + if [ -z "${PS1+x}" ]; then + PS1= + fi +fi + +conda activate base' +++ '[' 0 -eq 0 ']' +++ eval 'export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'' + +# Copyright (C) 2012 Anaconda, Inc +# SPDX-License-Identifier: BSD-3-Clause +__conda_exe() ( + "$CONDA_EXE" $_CE_M $_CE_CONDA "$@" +) + +__conda_hashr() { + if [ -n "${ZSH_VERSION:+x}" ]; then + \rehash + elif [ -n "${POSH_VERSION:+x}" ]; then + : # pass + else + \hash -r + fi +} + +__conda_activate() { + if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then + # Handle transition from shell activated with conda <= 4.3 to a subsequent activation + # after conda updated to >= 4.4. See issue #6173. + PS1="$CONDA_PS1_BACKUP" + \unset CONDA_PS1_BACKUP + fi + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return + \eval "$ask_conda" + __conda_hashr +} + +__conda_reactivate() { + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return + \eval "$ask_conda" + __conda_hashr +} + +conda() { + \local cmd="${1-__missing__}" + case "$cmd" in + activate|deactivate) + __conda_activate "$@" + ;; + install|update|upgrade|remove|uninstall) + __conda_exe "$@" || \return + __conda_reactivate + ;; + *) + __conda_exe "$@" + ;; + esac +} + +if [ -z "${CONDA_SHLVL+x}" ]; then + \export CONDA_SHLVL=0 + # In dev-mode CONDA_EXE is python.exe and on Windows + # it is in a different relative location to condabin. + if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then + PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}" + else + PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}" + fi + \export PATH + + # We'\''re not allowing PS1 to be unbound. It must at least be set. + # However, we'\''re not exporting it, which can cause problems when starting a second shell + # via a first shell (i.e. starting zsh from bash). + if [ -z "${PS1+x}" ]; then + PS1= + fi +fi + +conda activate base' ++++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda ++++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda ++++ export _CE_M= ++++ _CE_M= ++++ export _CE_CONDA= ++++ _CE_CONDA= ++++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ '[' -z x ']' ++++ conda activate base ++++ local cmd=activate ++++ case "$cmd" in ++++ __conda_activate activate base ++++ '[' -n '' ']' ++++ local ask_conda +++++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++++ __conda_exe shell.posix activate base +++++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate base ++++ ask_conda='PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_SHLVL='\''6'\'' +export CONDA_DEFAULT_ENV='\''base'\'' +export CONDA_PROMPT_MODIFIER='\''(base) '\'' +export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' ++++ eval 'PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_SHLVL='\''6'\'' +export CONDA_DEFAULT_ENV='\''base'\'' +export CONDA_PROMPT_MODIFIER='\''(base) '\'' +export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' +++++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++++ export CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0 +++++ CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0 +++++ export CONDA_SHLVL=6 +++++ CONDA_SHLVL=6 +++++ export CONDA_DEFAULT_ENV=base +++++ CONDA_DEFAULT_ENV=base +++++ export 'CONDA_PROMPT_MODIFIER=(base) ' +++++ CONDA_PROMPT_MODIFIER='(base) ' +++++ export CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev +++++ CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev +++++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++++ export _CE_M= +++++ _CE_M= +++++ export _CE_CONDA= +++++ _CE_CONDA= +++++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python +++++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ __conda_hashr ++++ '[' -n '' ']' ++++ '[' -n '' ']' ++++ hash -r +++ unset __conda_setup ++ conda activate schemist-dev ++ local cmd=activate ++ case "$cmd" in ++ __conda_activate activate schemist-dev ++ '[' -n '' ']' ++ local ask_conda +++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++ __conda_exe shell.posix activate schemist-dev +++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate schemist-dev ++ ask_conda='PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_SHLVL='\''7'\'' +export CONDA_DEFAULT_ENV='\''schemist-dev'\'' +export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\'' +export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' ++ eval 'PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_SHLVL='\''7'\'' +export CONDA_DEFAULT_ENV='\''schemist-dev'\'' +export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\'' +export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' +++ PS1='(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++ export CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev +++ CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev +++ export CONDA_SHLVL=7 +++ CONDA_SHLVL=7 +++ export CONDA_DEFAULT_ENV=schemist-dev +++ CONDA_DEFAULT_ENV=schemist-dev +++ export 'CONDA_PROMPT_MODIFIER=(schemist-dev) ' +++ CONDA_PROMPT_MODIFIER='(schemist-dev) ' +++ export CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0 +++ CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0 +++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++ export _CE_M= +++ _CE_M= +++ export _CE_CONDA= +++ _CE_CONDA= +++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python +++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++ __conda_hashr ++ '[' -n '' ']' ++ '[' -n '' ']' ++ hash -r ++ CHUNK_HEAD_FILE=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz ++ INPUT=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/train/cyc-pep-6-12mer-70M_03.csv ++ COLUMN=cysteine_to_N_cyclization ++ PREFIX=cyclic_ ++ AWK='1 { print $8, $1, $2, $10, $3 }' ++ '[' -z cysteine_to_N_cyclization ']' ++ '[' -z cyclic_ ']' ++ '[' -z '1 { print $8, $1, $2, $10, $3 }' ']' ++ cat /dev/fd/63 /nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/train/cyc-pep-6-12mer-70M_03.csv ++ awk -F, -v OFS=, '1 { print $8, $1, $2, $10, $3 }' +++ zcat /nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz +++ head -n1 ++ schemist convert -f csv --column cysteine_to_N_cyclization --to id inchikey scaffold mwt clogp tpsa --prefix cyclic_ --options prefix=SCB- ++ gzip --best +++ tr ' ' , +🚀 Converting between string representations with the following parameters: + subcommand: convert + output: <_io.TextIOWrapper name='' mode='w' encoding='utf-8'> + format: csv + input: <_io.TextIOWrapper name='' mode='r' encoding='utf-8'> + representation: SMILES + column: cysteine_to_N_cyclization + prefix: cyclic_ + to: ['id', 'inchikey', 'scaffold', 'mwt', 'clogp', 'tpsa'] + options: ['prefix=SCB-'] + func: + 0it [00:00, ?it/s] 1it [00:11, 11.60s/it] 2it [00:23, 11.50s/it] 3it [00:34, 11.58s/it] 4it [00:46, 11.59s/it] 5it [00:57, 11.57s/it] 6it 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11.85s/it] 994it [3:18:16, 11.87s/it] 995it [3:18:28, 11.95s/it] 996it [3:18:40, 11.96s/it] 997it [3:18:53, 12.02s/it] 998it [3:19:05, 12.03s/it] 999it [3:19:17, 11.99s/it] 1000it [3:19:29, 12.00s/it] 1000it [3:19:29, 11.97s/it] +Error counts: + cyclic_id: 0 + cyclic_inchikey: 0 + cyclic_scaffold: 0 + cyclic_mwt: 0 + cyclic_clogp: 0 + cyclic_tpsa: 0 +⏰ Completed process in 3:19:53.014538 ++ rm /nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/train/cyc-pep-6-12mer-70M_03.csv diff --git a/train/cyc-pep-6-12mer-70M_04.csv.gz b/train/cyc-pep-6-12mer-70M_04.csv.gz index 674fec323dcba1cba78f95ebcc0e8506df31d5ce..90ac56fa5c8515fe3babbe850ca035616d0594c5 100644 --- a/train/cyc-pep-6-12mer-70M_04.csv.gz +++ b/train/cyc-pep-6-12mer-70M_04.csv.gz @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:b6f415213fd5d5fe9fbe0e63bee04fd673a2079e898b392fb7b5139377669890 -size 58254248 +oid sha256:71a5b2d69be31606128710921f1e0fe7f8cd96a818e6fbde78855a19c60fafc5 +size 112833751 diff --git a/train/cyc-pep-6-12mer-70M_04.log b/train/cyc-pep-6-12mer-70M_04.log new file mode 100644 index 0000000000000000000000000000000000000000..cf56ebd77dd41fb521216d2c288d5491a7437909 --- /dev/null +++ b/train/cyc-pep-6-12mer-70M_04.log @@ -0,0 +1,337 @@ ++ module purge ++ '[' -z '' ']' ++ case "$-" in ++ __lmod_sh_dbg=x ++ '[' -n x ']' ++ set +x +Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output +Shell debugging restarted ++ unset __lmod_sh_dbg ++ return 0 ++ module load Anaconda3/2023.03 ++ '[' -z '' ']' ++ case "$-" in ++ __lmod_sh_dbg=x ++ '[' -n x ']' ++ set +x +Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output +Shell debugging restarted ++ unset __lmod_sh_dbg ++ return 0 ++ source /camp/home/johnsoe/.bashrc +++ '[' '' = yes ']' +++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' ++++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.bash hook +++ __conda_setup='export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'' + +# Copyright (C) 2012 Anaconda, Inc +# SPDX-License-Identifier: BSD-3-Clause +__conda_exe() ( + "$CONDA_EXE" $_CE_M $_CE_CONDA "$@" +) + +__conda_hashr() { + if [ -n "${ZSH_VERSION:+x}" ]; then + \rehash + elif [ -n "${POSH_VERSION:+x}" ]; then + : # pass + else + \hash -r + fi +} + +__conda_activate() { + if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then + # Handle transition from shell activated with conda <= 4.3 to a subsequent activation + # after conda updated to >= 4.4. See issue #6173. + PS1="$CONDA_PS1_BACKUP" + \unset CONDA_PS1_BACKUP + fi + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return + \eval "$ask_conda" + __conda_hashr +} + +__conda_reactivate() { + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return + \eval "$ask_conda" + __conda_hashr +} + +conda() { + \local cmd="${1-__missing__}" + case "$cmd" in + activate|deactivate) + __conda_activate "$@" + ;; + install|update|upgrade|remove|uninstall) + __conda_exe "$@" || \return + __conda_reactivate + ;; + *) + __conda_exe "$@" + ;; + esac +} + +if [ -z "${CONDA_SHLVL+x}" ]; then + \export CONDA_SHLVL=0 + # In dev-mode CONDA_EXE is python.exe and on Windows + # it is in a different relative location to condabin. + if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then + PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}" + else + PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}" + fi + \export PATH + + # We'\''re not allowing PS1 to be unbound. It must at least be set. + # However, we'\''re not exporting it, which can cause problems when starting a second shell + # via a first shell (i.e. starting zsh from bash). + if [ -z "${PS1+x}" ]; then + PS1= + fi +fi + +conda activate base' +++ '[' 0 -eq 0 ']' +++ eval 'export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'' + +# Copyright (C) 2012 Anaconda, Inc +# SPDX-License-Identifier: BSD-3-Clause +__conda_exe() ( + "$CONDA_EXE" $_CE_M $_CE_CONDA "$@" +) + +__conda_hashr() { + if [ -n "${ZSH_VERSION:+x}" ]; then + \rehash + elif [ -n "${POSH_VERSION:+x}" ]; then + : # pass + else + \hash -r + fi +} + +__conda_activate() { + if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then + # Handle transition from shell activated with conda <= 4.3 to a subsequent activation + # after conda updated to >= 4.4. See issue #6173. + PS1="$CONDA_PS1_BACKUP" + \unset CONDA_PS1_BACKUP + fi + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return + \eval "$ask_conda" + __conda_hashr +} + +__conda_reactivate() { + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return + \eval "$ask_conda" + __conda_hashr +} + +conda() { + \local cmd="${1-__missing__}" + case "$cmd" in + activate|deactivate) + __conda_activate "$@" + ;; + install|update|upgrade|remove|uninstall) + __conda_exe "$@" || \return + __conda_reactivate + ;; + *) + __conda_exe "$@" + ;; + esac +} + +if [ -z "${CONDA_SHLVL+x}" ]; then + \export CONDA_SHLVL=0 + # In dev-mode CONDA_EXE is python.exe and on Windows + # it is in a different relative location to condabin. + if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then + PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}" + else + PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}" + fi + \export PATH + + # We'\''re not allowing PS1 to be unbound. It must at least be set. + # However, we'\''re not exporting it, which can cause problems when starting a second shell + # via a first shell (i.e. starting zsh from bash). + if [ -z "${PS1+x}" ]; then + PS1= + fi +fi + +conda activate base' ++++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda ++++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda ++++ export _CE_M= ++++ _CE_M= ++++ export _CE_CONDA= ++++ _CE_CONDA= ++++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ '[' -z x ']' ++++ conda activate base ++++ local cmd=activate ++++ case "$cmd" in ++++ __conda_activate activate base ++++ '[' -n '' ']' ++++ local ask_conda +++++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++++ __conda_exe shell.posix activate base +++++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate base ++++ ask_conda='PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_SHLVL='\''6'\'' +export CONDA_DEFAULT_ENV='\''base'\'' +export CONDA_PROMPT_MODIFIER='\''(base) '\'' +export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' ++++ eval 'PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_SHLVL='\''6'\'' +export CONDA_DEFAULT_ENV='\''base'\'' +export CONDA_PROMPT_MODIFIER='\''(base) '\'' +export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' +++++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++++ export CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0 +++++ CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0 +++++ export CONDA_SHLVL=6 +++++ CONDA_SHLVL=6 +++++ export CONDA_DEFAULT_ENV=base +++++ CONDA_DEFAULT_ENV=base +++++ export 'CONDA_PROMPT_MODIFIER=(base) ' +++++ CONDA_PROMPT_MODIFIER='(base) ' +++++ export CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev +++++ CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev +++++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++++ export _CE_M= +++++ _CE_M= +++++ export _CE_CONDA= +++++ _CE_CONDA= +++++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python +++++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ __conda_hashr ++++ '[' -n '' ']' ++++ '[' -n '' ']' ++++ hash -r +++ unset __conda_setup ++ conda activate schemist-dev ++ local cmd=activate ++ case "$cmd" in ++ __conda_activate activate schemist-dev ++ '[' -n '' ']' ++ local ask_conda +++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++ __conda_exe shell.posix activate schemist-dev +++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate schemist-dev ++ ask_conda='PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_SHLVL='\''7'\'' +export CONDA_DEFAULT_ENV='\''schemist-dev'\'' +export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\'' +export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' ++ eval 'PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_SHLVL='\''7'\'' +export CONDA_DEFAULT_ENV='\''schemist-dev'\'' +export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\'' +export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' +++ PS1='(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++ export CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev +++ CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev +++ export CONDA_SHLVL=7 +++ CONDA_SHLVL=7 +++ export CONDA_DEFAULT_ENV=schemist-dev +++ CONDA_DEFAULT_ENV=schemist-dev +++ export 'CONDA_PROMPT_MODIFIER=(schemist-dev) ' +++ CONDA_PROMPT_MODIFIER='(schemist-dev) ' +++ export CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0 +++ CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0 +++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++ export _CE_M= +++ _CE_M= +++ export _CE_CONDA= +++ _CE_CONDA= +++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python +++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++ __conda_hashr ++ '[' -n '' ']' ++ '[' -n '' ']' ++ hash -r ++ CHUNK_HEAD_FILE=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz ++ INPUT=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/train/cyc-pep-6-12mer-70M_04.csv ++ COLUMN=cysteine_to_N_cyclization ++ PREFIX=cyclic_ ++ AWK='1 { print $8, $1, $2, $10, $3 }' ++ '[' -z cysteine_to_N_cyclization ']' ++ '[' -z cyclic_ ']' ++ '[' -z '1 { print $8, $1, $2, $10, $3 }' ']' ++ cat /dev/fd/63 /nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/train/cyc-pep-6-12mer-70M_04.csv ++ schemist convert -f csv --column cysteine_to_N_cyclization --to id inchikey scaffold mwt clogp tpsa --prefix cyclic_ --options prefix=SCB- ++ gzip --best ++ awk -F, -v OFS=, '1 { print $8, $1, $2, $10, $3 }' +++ zcat /nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz +++ tr ' ' , +++ head -n1 +🚀 Converting between string representations with the following parameters: + subcommand: convert + output: <_io.TextIOWrapper name='' mode='w' encoding='utf-8'> + format: csv + input: <_io.TextIOWrapper name='' mode='r' encoding='utf-8'> + representation: SMILES + column: cysteine_to_N_cyclization + prefix: cyclic_ + to: ['id', 'inchikey', 'scaffold', 'mwt', 'clogp', 'tpsa'] + options: ['prefix=SCB-'] + func: + 0it [00:00, ?it/s] 1it [00:11, 11.60s/it] 2it [00:22, 11.43s/it] 3it [00:34, 11.59s/it] 4it [00:46, 11.54s/it] 5it [00:58, 11.77s/it] 6it [01:10, 11.82s/it] 7it [01:22, 11.89s/it] 8it [01:34, 11.90s/it] 9it [01:45, 11.73s/it] 10it [01:56, 11.61s/it] 11it [02:08, 11.63s/it] 12it [02:20, 11.60s/it] 13it [02:31, 11.53s/it] 14it [02:43, 11.70s/it] 15it [02:55, 11.78s/it] 16it [03:07, 11.82s/it] 17it [03:18, 11.70s/it] 18it [03:30, 11.62s/it] 19it [03:41, 11.62s/it] 20it [03:53, 11.53s/it] 21it [04:04, 11.54s/it] 22it [04:16, 11.58s/it] 23it [04:28, 11.67s/it] 24it [04:40, 11.81s/it] 25it [04:52, 11.88s/it] 26it [05:04, 11.94s/it] 27it [05:16, 11.96s/it] 28it [05:28, 11.98s/it] 29it [05:40, 12.04s/it] 30it [05:52, 12.00s/it] 31it [06:04, 12.03s/it] 32it [06:16, 12.04s/it] 33it [06:28, 12.03s/it] 34it [06:41, 12.08s/it] 35it [06:53, 12.06s/it] 36it [07:04, 11.86s/it] 37it [07:16, 11.76s/it] 38it [07:28, 11.82s/it] 39it [07:39, 11.85s/it] 40it [07:51, 11.87s/it] 41it [08:03, 11.73s/it] 42it [08:14, 11.65s/it] 43it [08:26, 11.60s/it] 44it [08:37, 11.55s/it] 45it [08:49, 11.55s/it] 46it [09:00, 11.55s/it] 47it [09:12, 11.55s/it] 48it [09:24, 11.70s/it] 49it [09:36, 11.84s/it] 50it [09:48, 11.89s/it] 51it [10:00, 11.95s/it] 52it [10:12, 12.00s/it] 53it [10:23, 11.67s/it] 54it [10:34, 11.42s/it] 55it [10:45, 11.25s/it] 56it [10:56, 11.14s/it] 57it [11:07, 11.07s/it] 58it [11:17, 11.02s/it] 59it [11:28, 10.98s/it] 60it [11:39, 10.94s/it] 61it [11:50, 10.92s/it] 62it [12:01, 10.91s/it] 63it [12:12, 10.89s/it] 64it [12:23, 10.88s/it] 65it [12:33, 10.85s/it] 66it [12:44, 10.85s/it] 67it [12:55, 10.83s/it] 68it [13:06, 10.82s/it] 69it [13:17, 10.80s/it] 70it [13:27, 10.80s/it] 71it [13:38, 10.82s/it] 72it [13:49, 10.85s/it] 73it [14:00, 10.85s/it] 74it [14:11, 10.84s/it] 75it [14:22, 10.85s/it] 76it [14:33, 10.84s/it] 77it [14:43, 10.83s/it] 78it [14:54, 10.80s/it] 79it [15:05, 10.79s/it] 80it [15:16, 10.80s/it] 81it [15:27, 10.80s/it] 82it [15:37, 10.82s/it] 83it [15:48, 10.83s/it] 84it [15:59, 10.83s/it] 85it [16:10, 10.82s/it] 86it [16:21, 10.81s/it] 87it [16:32, 10.83s/it] 88it [16:42, 10.85s/it] 89it [16:53, 10.86s/it] 90it [17:04, 10.84s/it] 91it [17:15, 10.86s/it] 92it [17:26, 10.84s/it] 93it [17:37, 10.85s/it] 94it [17:47, 10.83s/it] 95it [17:58, 10.86s/it] 96it [18:09, 10.84s/it] 97it [18:20, 10.84s/it] 98it [18:31, 10.83s/it] 99it [18:42, 10.81s/it] 100it [18:52, 10.82s/it] 101it [19:03, 10.82s/it] 102it [19:14, 10.81s/it] 103it [19:25, 10.83s/it] 104it [19:36, 10.83s/it] 105it [19:46, 10.79s/it] 106it [19:57, 10.80s/it] 107it [20:08, 10.80s/it] 108it [20:19, 10.81s/it] 109it [20:30, 10.80s/it] 110it [20:41, 10.82s/it] 111it [20:51, 10.81s/it] 112it [21:02, 10.83s/it] 113it [21:13, 10.82s/it] 114it [21:24, 10.84s/it] 115it [21:35, 10.84s/it] 116it [21:46, 10.84s/it] 117it [21:56, 10.84s/it] 118it [22:07, 10.84s/it] 119it [22:18, 10.85s/it] 120it [22:29, 10.83s/it] 121it [22:40, 10.82s/it] 122it [22:50, 10.81s/it] 123it [23:01, 10.84s/it] 124it [23:12, 10.82s/it] 125it [23:23, 10.85s/it] 126it [23:34, 10.84s/it] 127it [23:45, 10.85s/it] 128it [23:56, 10.83s/it] 129it [24:06, 10.85s/it] 130it [24:17, 10.83s/it] 131it [24:28, 10.85s/it] 132it [24:39, 10.86s/it] 133it [24:50, 10.86s/it] 134it [25:01, 10.82s/it] 135it [25:11, 10.83s/it] 136it [25:22, 10.83s/it] 137it [25:33, 10.83s/it] 138it [25:44, 10.82s/it] 139it [25:55, 10.84s/it] 140it [26:06, 10.85s/it] 141it [26:17, 10.85s/it] 142it [26:27, 10.84s/it] 143it [26:38, 10.85s/it] 144it [26:49, 10.87s/it] 145it [27:00, 10.80s/it] 146it [27:10, 10.76s/it] 147it [27:21, 10.76s/it] 148it [27:32, 10.78s/it] 149it [27:43, 10.78s/it] 150it [27:54, 10.79s/it] 151it [28:04, 10.80s/it] 152it [28:15, 10.82s/it] 153it [28:26, 10.81s/it] 154it [28:37, 10.82s/it] 155it [28:48, 10.81s/it] 156it [28:59, 10.81s/it] 157it [29:09, 10.83s/it] 158it [29:20, 10.83s/it] 159it [29:31, 10.84s/it] 160it [29:42, 10.85s/it] 161it [29:53, 10.87s/it] 162it [30:04, 10.85s/it] 163it [30:15, 10.89s/it] 164it [30:26, 10.88s/it] 165it [30:36, 10.87s/it] 166it [30:47, 10.87s/it] 167it [30:58, 10.86s/it] 168it [31:09, 10.86s/it] 169it [31:20, 10.86s/it] 170it [31:31, 10.87s/it] 171it [31:42, 10.88s/it] 172it [31:52, 10.88s/it] 173it [32:03, 10.86s/it] 174it [32:14, 10.88s/it] 175it [32:25, 10.85s/it] 176it [32:36, 10.87s/it] 177it [32:47, 10.86s/it] 178it [32:58, 10.85s/it] 179it [33:08, 10.86s/it] 180it [33:19, 10.84s/it] 181it [33:30, 10.84s/it] 182it [33:41, 10.83s/it] 183it [33:52, 10.83s/it] 184it [34:03, 10.84s/it] 185it [34:13, 10.84s/it] 186it [34:24, 10.82s/it] 187it [34:35, 10.83s/it] 188it [34:46, 10.91s/it] 189it [34:58, 11.05s/it] 190it [35:08, 10.99s/it] 191it [35:19, 10.93s/it] 192it [35:30, 10.90s/it] 193it [35:41, 10.88s/it] 194it [35:52, 10.84s/it] 195it [36:02, 10.85s/it] 196it [36:13, 10.85s/it] 197it [36:24, 10.85s/it] 198it [36:35, 10.85s/it] 199it [36:46, 10.84s/it] 200it [36:57, 10.88s/it] 201it [37:08, 10.87s/it] 202it [37:19, 10.87s/it] 203it [37:29, 10.88s/it] 204it [37:40, 10.86s/it] 205it [37:51, 10.83s/it] 206it [38:02, 10.87s/it] 207it [38:13, 10.85s/it] 208it [38:24, 10.85s/it] 209it [38:35, 10.87s/it] 210it [38:45, 10.84s/it] 211it [38:56, 10.85s/it] 212it [39:07, 10.86s/it] 213it [39:18, 10.85s/it] 214it [39:29, 10.86s/it] 215it [39:40, 10.86s/it] 216it [39:50, 10.86s/it] 217it [40:01, 10.87s/it] 218it [40:12, 10.86s/it] 219it [40:23, 10.87s/it] 220it [40:34, 10.86s/it] 221it [40:45, 10.86s/it] 222it [40:56, 10.86s/it] 223it [41:06, 10.85s/it] 224it [41:17, 10.82s/it] 225it [41:28, 10.84s/it] 226it [41:39, 10.84s/it] 227it [41:50, 10.83s/it] 228it [42:01, 10.82s/it] 229it [42:11, 10.83s/it] 230it [42:22, 10.82s/it] 231it [42:33, 10.80s/it] 232it [42:44, 10.80s/it] 233it [42:55, 10.80s/it] 234it [43:05, 10.80s/it] 235it [43:16, 10.82s/it] 236it [43:27, 10.85s/it] 237it [43:38, 10.86s/it] 238it [43:49, 10.84s/it] 239it [44:00, 10.85s/it] 240it [44:11, 10.87s/it] 241it [44:22, 10.91s/it] 242it [44:33, 10.92s/it] 243it [44:44, 10.94s/it] 244it [44:55, 11.07s/it] 245it [45:07, 11.33s/it] 246it [45:19, 11.51s/it] 247it [45:31, 11.66s/it] 248it [45:43, 11.76s/it] 249it [45:55, 11.96s/it] 250it [46:08, 12.25s/it] 251it [46:21, 12.47s/it] 252it [46:34, 12.64s/it] 253it [46:47, 12.73s/it] 254it [47:00, 12.79s/it] 255it [47:13, 12.86s/it] 256it [47:26, 12.90s/it] 257it [47:39, 12.90s/it] 258it [47:52, 12.91s/it] 259it [48:05, 12.95s/it] 260it [48:17, 12.72s/it] 261it [48:29, 12.51s/it] 262it [48:42, 12.59s/it] 263it [48:55, 12.67s/it] 264it [49:08, 12.73s/it] 265it [49:21, 12.79s/it] 266it [49:34, 12.86s/it] 267it [49:47, 12.92s/it] 268it [50:00, 12.96s/it] 269it [50:12, 12.72s/it] 270it [50:24, 12.51s/it] 271it [50:37, 12.66s/it] 272it [50:50, 12.82s/it] 273it [51:03, 12.89s/it] 274it [51:16, 12.88s/it] 275it [51:29, 12.93s/it] 276it [51:41, 12.66s/it] 277it [51:53, 12.45s/it] 278it [52:06, 12.65s/it] 279it [52:19, 12.73s/it] 280it [52:32, 12.76s/it] 281it [52:44, 12.51s/it] 282it [52:57, 12.62s/it] 283it [53:10, 12.73s/it] 284it [53:22, 12.73s/it] 285it [53:33, 12.21s/it] 286it [53:44, 11.82s/it] 287it [53:55, 11.58s/it] 288it [54:06, 11.42s/it] 289it [54:17, 11.27s/it] 290it [54:28, 11.17s/it] 291it [54:39, 11.10s/it] 292it [54:51, 11.36s/it] 293it [55:03, 11.53s/it] 294it [55:16, 11.96s/it] 295it [55:28, 12.01s/it] 296it [55:40, 12.02s/it] 297it [55:53, 12.26s/it] 298it [56:06, 12.42s/it] 299it [56:19, 12.62s/it] 300it [56:32, 12.75s/it] 301it [56:45, 12.80s/it] 302it [56:58, 12.83s/it] 303it [57:11, 12.86s/it] 304it [57:23, 12.57s/it] 305it [57:35, 12.40s/it] 306it [57:47, 12.26s/it] 307it [57:59, 12.17s/it] 308it [58:11, 12.11s/it] 309it [58:23, 12.21s/it] 310it [58:35, 12.15s/it] 311it [58:47, 12.09s/it] 312it [59:00, 12.34s/it] 313it [59:13, 12.49s/it] 314it [59:25, 12.38s/it] 315it [59:38, 12.52s/it] 316it [59:50, 12.60s/it] 317it [1:00:03, 12.71s/it] 318it [1:00:16, 12.74s/it] 319it [1:00:29, 12.76s/it] 320it [1:00:42, 12.80s/it] 321it [1:00:55, 12.85s/it] 322it [1:01:08, 12.81s/it] 323it [1:01:20, 12.82s/it] 324it [1:01:33, 12.61s/it] 325it [1:01:45, 12.53s/it] 326it [1:01:57, 12.40s/it] 327it [1:02:08, 11.96s/it] 328it [1:02:19, 11.64s/it] 329it [1:02:30, 11.43s/it] 330it [1:02:41, 11.28s/it] 331it [1:02:52, 11.14s/it] 332it [1:03:02, 11.07s/it] 333it [1:03:13, 10.99s/it] 334it [1:03:24, 10.95s/it] 335it [1:03:35, 10.95s/it] 336it [1:03:46, 10.91s/it] 337it [1:03:57, 10.88s/it] 338it [1:04:08, 10.89s/it] 339it [1:04:18, 10.89s/it] 340it [1:04:29, 10.89s/it] 341it [1:04:40, 10.90s/it] 342it [1:04:51, 10.87s/it] 343it [1:05:02, 10.87s/it] 344it [1:05:13, 10.88s/it] 345it [1:05:24, 10.88s/it] 346it [1:05:35, 10.87s/it] 347it [1:05:46, 10.89s/it] 348it [1:05:56, 10.88s/it] 349it [1:06:07, 10.86s/it] 350it [1:06:18, 10.87s/it] 351it [1:06:29, 10.88s/it] 352it [1:06:40, 10.88s/it] 353it [1:06:51, 10.87s/it] 354it [1:07:01, 10.85s/it] 355it [1:07:12, 10.84s/it] 356it [1:07:23, 10.86s/it] 357it [1:07:34, 10.87s/it] 358it [1:07:45, 10.88s/it] 359it [1:07:56, 10.80s/it] 360it [1:08:06, 10.79s/it] 361it [1:08:17, 10.83s/it] 362it [1:08:28, 10.85s/it] 363it [1:08:39, 10.85s/it] 364it [1:08:50, 10.85s/it] 365it [1:09:01, 10.88s/it] 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958it [2:59:30, 11.00s/it] 959it [2:59:42, 11.13s/it] 960it [2:59:53, 11.08s/it] 961it [3:00:04, 10.97s/it] 962it [3:00:14, 10.93s/it] 963it [3:00:25, 10.90s/it] 964it [3:00:36, 10.91s/it] 965it [3:00:47, 10.89s/it] 966it [3:00:58, 10.90s/it] 967it [3:01:09, 10.89s/it] 968it [3:01:20, 10.90s/it] 969it [3:01:31, 10.89s/it] 970it [3:01:41, 10.89s/it] 971it [3:01:52, 10.91s/it] 972it [3:02:03, 10.89s/it] 973it [3:02:14, 10.88s/it] 974it [3:02:25, 10.87s/it] 975it [3:02:36, 10.87s/it] 976it [3:02:47, 10.89s/it] 977it [3:02:58, 10.87s/it] 978it [3:03:09, 10.88s/it] 979it [3:03:19, 10.88s/it] 980it [3:03:30, 10.89s/it] 981it [3:03:41, 10.89s/it] 982it [3:03:52, 10.87s/it] 983it [3:04:03, 10.89s/it] 984it [3:04:14, 10.88s/it] 985it [3:04:25, 10.86s/it] 986it [3:04:36, 10.88s/it] 987it [3:04:46, 10.89s/it] 988it [3:04:57, 10.87s/it] 989it [3:05:08, 10.88s/it] 990it [3:05:19, 10.88s/it] 991it [3:05:30, 10.88s/it] 992it [3:05:41, 10.88s/it] 993it [3:05:52, 10.87s/it] 994it [3:06:02, 10.85s/it] 995it [3:06:13, 10.86s/it] 996it [3:06:24, 10.86s/it] 997it [3:06:35, 10.86s/it] 998it [3:06:46, 10.85s/it] 999it [3:06:56, 10.70s/it] 1000it [3:07:07, 10.60s/it] 1000it [3:07:07, 11.23s/it] +Error counts: + cyclic_id: 0 + cyclic_inchikey: 0 + cyclic_scaffold: 0 + cyclic_mwt: 0 + cyclic_clogp: 0 + cyclic_tpsa: 0 +⏰ Completed process in 3:07:30.395736 ++ rm /nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/train/cyc-pep-6-12mer-70M_04.csv diff --git a/train/cyc-pep-6-12mer-70M_05.csv.gz b/train/cyc-pep-6-12mer-70M_05.csv.gz index 99cf9818a4cf6a9ee584a093d47df74c9d562303..8e0cfefde8f42f7329d9881606a5d3464e1fe9dd 100644 --- a/train/cyc-pep-6-12mer-70M_05.csv.gz +++ b/train/cyc-pep-6-12mer-70M_05.csv.gz @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:fe26c7b18749498c9aa2739942dea3e1639ad863ade522efc2684254df272785 -size 58249398 +oid sha256:6bd762c2b6706e8ba084a6983569a0642bc5625cf36d7118d3c8346b0071a7d6 +size 112829355 diff --git a/train/cyc-pep-6-12mer-70M_05.log b/train/cyc-pep-6-12mer-70M_05.log new file mode 100644 index 0000000000000000000000000000000000000000..6e57ed689f2599e4174fceb55ffa15ce5384b41f --- /dev/null +++ b/train/cyc-pep-6-12mer-70M_05.log @@ -0,0 +1,337 @@ ++ module purge ++ '[' -z '' ']' ++ case "$-" in ++ __lmod_sh_dbg=x ++ '[' -n x ']' ++ set +x +Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output +Shell debugging restarted ++ unset __lmod_sh_dbg ++ return 0 ++ module load Anaconda3/2023.03 ++ '[' -z '' ']' ++ case "$-" in ++ __lmod_sh_dbg=x ++ '[' -n x ']' ++ set +x +Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output +Shell debugging restarted ++ unset __lmod_sh_dbg ++ return 0 ++ source /camp/home/johnsoe/.bashrc +++ '[' '' = yes ']' +++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' ++++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.bash hook +++ __conda_setup='export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'' + +# Copyright (C) 2012 Anaconda, Inc +# SPDX-License-Identifier: BSD-3-Clause +__conda_exe() ( + "$CONDA_EXE" $_CE_M $_CE_CONDA "$@" +) + +__conda_hashr() { + if [ -n "${ZSH_VERSION:+x}" ]; then + \rehash + elif [ -n "${POSH_VERSION:+x}" ]; then + : # pass + else + \hash -r + fi +} + +__conda_activate() { + if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then + # Handle transition from shell activated with conda <= 4.3 to a subsequent activation + # after conda updated to >= 4.4. See issue #6173. + PS1="$CONDA_PS1_BACKUP" + \unset CONDA_PS1_BACKUP + fi + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return + \eval "$ask_conda" + __conda_hashr +} + +__conda_reactivate() { + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return + \eval "$ask_conda" + __conda_hashr +} + +conda() { + \local cmd="${1-__missing__}" + case "$cmd" in + activate|deactivate) + __conda_activate "$@" + ;; + install|update|upgrade|remove|uninstall) + __conda_exe "$@" || \return + __conda_reactivate + ;; + *) + __conda_exe "$@" + ;; + esac +} + +if [ -z "${CONDA_SHLVL+x}" ]; then + \export CONDA_SHLVL=0 + # In dev-mode CONDA_EXE is python.exe and on Windows + # it is in a different relative location to condabin. + if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then + PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}" + else + PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}" + fi + \export PATH + + # We'\''re not allowing PS1 to be unbound. It must at least be set. + # However, we'\''re not exporting it, which can cause problems when starting a second shell + # via a first shell (i.e. starting zsh from bash). + if [ -z "${PS1+x}" ]; then + PS1= + fi +fi + +conda activate base' +++ '[' 0 -eq 0 ']' +++ eval 'export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'' + +# Copyright (C) 2012 Anaconda, Inc +# SPDX-License-Identifier: BSD-3-Clause +__conda_exe() ( + "$CONDA_EXE" $_CE_M $_CE_CONDA "$@" +) + +__conda_hashr() { + if [ -n "${ZSH_VERSION:+x}" ]; then + \rehash + elif [ -n "${POSH_VERSION:+x}" ]; then + : # pass + else + \hash -r + fi +} + +__conda_activate() { + if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then + # Handle transition from shell activated with conda <= 4.3 to a subsequent activation + # after conda updated to >= 4.4. See issue #6173. + PS1="$CONDA_PS1_BACKUP" + \unset CONDA_PS1_BACKUP + fi + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return + \eval "$ask_conda" + __conda_hashr +} + +__conda_reactivate() { + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return + \eval "$ask_conda" + __conda_hashr +} + +conda() { + \local cmd="${1-__missing__}" + case "$cmd" in + activate|deactivate) + __conda_activate "$@" + ;; + install|update|upgrade|remove|uninstall) + __conda_exe "$@" || \return + __conda_reactivate + ;; + *) + __conda_exe "$@" + ;; + esac +} + +if [ -z "${CONDA_SHLVL+x}" ]; then + \export CONDA_SHLVL=0 + # In dev-mode CONDA_EXE is python.exe and on Windows + # it is in a different relative location to condabin. + if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then + PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}" + else + PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}" + fi + \export PATH + + # We'\''re not allowing PS1 to be unbound. It must at least be set. + # However, we'\''re not exporting it, which can cause problems when starting a second shell + # via a first shell (i.e. starting zsh from bash). + if [ -z "${PS1+x}" ]; then + PS1= + fi +fi + +conda activate base' ++++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda ++++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda ++++ export _CE_M= ++++ _CE_M= ++++ export _CE_CONDA= ++++ _CE_CONDA= ++++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ '[' -z x ']' ++++ conda activate base ++++ local cmd=activate ++++ case "$cmd" in ++++ __conda_activate activate base ++++ '[' -n '' ']' ++++ local ask_conda +++++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++++ __conda_exe shell.posix activate base +++++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate base ++++ ask_conda='PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_SHLVL='\''6'\'' +export CONDA_DEFAULT_ENV='\''base'\'' +export CONDA_PROMPT_MODIFIER='\''(base) '\'' +export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' ++++ eval 'PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_SHLVL='\''6'\'' +export CONDA_DEFAULT_ENV='\''base'\'' +export CONDA_PROMPT_MODIFIER='\''(base) '\'' +export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' +++++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++++ export CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0 +++++ CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0 +++++ export CONDA_SHLVL=6 +++++ CONDA_SHLVL=6 +++++ export CONDA_DEFAULT_ENV=base +++++ CONDA_DEFAULT_ENV=base +++++ export 'CONDA_PROMPT_MODIFIER=(base) ' +++++ CONDA_PROMPT_MODIFIER='(base) ' +++++ export CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev +++++ CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev +++++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++++ export _CE_M= +++++ _CE_M= +++++ export _CE_CONDA= +++++ _CE_CONDA= +++++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python +++++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ __conda_hashr ++++ '[' -n '' ']' ++++ '[' -n '' ']' ++++ hash -r +++ unset __conda_setup ++ conda activate schemist-dev ++ local cmd=activate ++ case "$cmd" in ++ __conda_activate activate schemist-dev ++ '[' -n '' ']' ++ local ask_conda +++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++ __conda_exe shell.posix activate schemist-dev +++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate schemist-dev ++ ask_conda='PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_SHLVL='\''7'\'' +export CONDA_DEFAULT_ENV='\''schemist-dev'\'' +export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\'' +export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' ++ eval 'PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_SHLVL='\''7'\'' +export CONDA_DEFAULT_ENV='\''schemist-dev'\'' +export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\'' +export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' +++ PS1='(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++ export CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev +++ CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev +++ export CONDA_SHLVL=7 +++ CONDA_SHLVL=7 +++ export CONDA_DEFAULT_ENV=schemist-dev +++ CONDA_DEFAULT_ENV=schemist-dev +++ export 'CONDA_PROMPT_MODIFIER=(schemist-dev) ' +++ CONDA_PROMPT_MODIFIER='(schemist-dev) ' +++ export CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0 +++ CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0 +++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++ export _CE_M= +++ _CE_M= +++ export _CE_CONDA= +++ _CE_CONDA= +++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python +++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++ __conda_hashr ++ '[' -n '' ']' ++ '[' -n '' ']' ++ hash -r ++ CHUNK_HEAD_FILE=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz ++ INPUT=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/train/cyc-pep-6-12mer-70M_05.csv ++ COLUMN=cysteine_to_N_cyclization ++ PREFIX=cyclic_ ++ AWK='1 { print $8, $1, $2, $10, $3 }' ++ '[' -z cysteine_to_N_cyclization ']' ++ '[' -z cyclic_ ']' ++ '[' -z '1 { print $8, $1, $2, $10, $3 }' ']' ++ cat /dev/fd/63 /nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/train/cyc-pep-6-12mer-70M_05.csv ++ awk -F, -v OFS=, '1 { print $8, $1, $2, $10, $3 }' +++ zcat /nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz ++ schemist convert -f csv --column cysteine_to_N_cyclization --to id inchikey scaffold mwt clogp tpsa --prefix cyclic_ --options prefix=SCB- ++ gzip --best +++ head -n1 +++ tr ' ' , +🚀 Converting between string representations with the following parameters: + subcommand: convert + output: <_io.TextIOWrapper name='' mode='w' encoding='utf-8'> + format: csv + input: <_io.TextIOWrapper name='' mode='r' encoding='utf-8'> + representation: SMILES + column: cysteine_to_N_cyclization + prefix: cyclic_ + to: ['id', 'inchikey', 'scaffold', 'mwt', 'clogp', 'tpsa'] + options: ['prefix=SCB-'] + func: + 0it [00:00, ?it/s] 1it [00:11, 11.39s/it] 2it [00:22, 11.35s/it] 3it [00:33, 11.32s/it] 4it [00:45, 11.29s/it] 5it [00:56, 11.28s/it] 6it [01:07, 11.21s/it] 7it [01:18, 11.19s/it] 8it [01:29, 11.20s/it] 9it [01:41, 11.20s/it] 10it [01:52, 11.22s/it] 11it [02:03, 11.20s/it] 12it [02:14, 11.20s/it] 13it [02:26, 11.23s/it] 14it [02:37, 11.16s/it] 15it [02:48, 11.11s/it] 16it [02:58, 11.05s/it] 17it [03:09, 11.01s/it] 18it [03:20, 10.96s/it] 19it [03:31, 10.94s/it] 20it [03:42, 10.91s/it] 21it [03:53, 10.91s/it] 22it [04:04, 10.90s/it] 23it [04:15, 10.89s/it] 24it [04:25, 10.88s/it] 25it [04:36, 10.91s/it] 26it [04:47, 10.90s/it] 27it [04:58, 10.93s/it] 28it [05:09, 10.89s/it] 29it [05:20, 10.88s/it] 30it [05:31, 10.88s/it] 31it [05:42, 10.87s/it] 32it [05:53, 10.89s/it] 33it [06:03, 10.87s/it] 34it [06:14, 10.88s/it] 35it [06:25, 10.84s/it] 36it [06:36, 10.86s/it] 37it [06:47, 10.85s/it] 38it [06:58, 10.85s/it] 39it [07:08, 10.83s/it] 40it [07:19, 10.83s/it] 41it [07:30, 10.81s/it] 42it [07:41, 10.81s/it] 43it [07:52, 10.82s/it] 44it [08:03, 10.82s/it] 45it [08:13, 10.84s/it] 46it [08:24, 10.84s/it] 47it [08:35, 10.80s/it] 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10.82s/it] 90it [16:20, 10.82s/it] 91it [16:30, 10.83s/it] 92it [16:41, 10.82s/it] 93it [16:52, 10.81s/it] 94it [17:03, 10.81s/it] 95it [17:14, 10.81s/it] 96it [17:24, 10.80s/it] 97it [17:35, 10.81s/it] 98it [17:46, 10.79s/it] 99it [17:57, 10.79s/it] 100it [18:07, 10.78s/it] 101it [18:18, 10.80s/it] 102it [18:29, 10.79s/it] 103it [18:40, 10.81s/it] 104it [18:51, 10.78s/it] 105it [19:02, 10.81s/it] 106it [19:12, 10.80s/it] 107it [19:23, 10.80s/it] 108it [19:34, 10.82s/it] 109it [19:45, 10.89s/it] 110it [19:56, 10.97s/it] 111it [20:07, 10.98s/it] 112it [20:18, 11.01s/it] 113it [20:29, 11.01s/it] 114it [20:40, 11.04s/it] 115it [20:52, 11.06s/it] 116it [21:03, 11.10s/it] 117it [21:14, 11.10s/it] 118it [21:25, 11.11s/it] 119it [21:36, 11.12s/it] 120it [21:47, 11.10s/it] 121it [21:58, 11.12s/it] 122it [22:09, 11.10s/it] 123it [22:20, 11.10s/it] 124it [22:32, 11.09s/it] 125it [22:43, 11.12s/it] 126it [22:54, 11.09s/it] 127it [23:05, 11.10s/it] 128it [23:16, 11.09s/it] 129it [23:27, 11.12s/it] 130it [23:38, 11.10s/it] 131it [23:49, 11.10s/it] 132it [24:00, 11.10s/it] 133it [24:12, 11.12s/it] 134it [24:23, 11.11s/it] 135it [24:34, 11.11s/it] 136it [24:45, 11.10s/it] 137it [24:56, 11.13s/it] 138it [25:07, 11.12s/it] 139it [25:18, 11.13s/it] 140it [25:29, 11.12s/it] 141it [25:40, 11.14s/it] 142it [25:52, 11.12s/it] 143it [26:03, 11.13s/it] 144it [26:14, 11.15s/it] 145it [26:25, 11.15s/it] 146it [26:36, 11.15s/it] 147it [26:48, 11.28s/it] 148it [26:59, 11.25s/it] 149it [27:10, 11.19s/it] 150it [27:21, 11.20s/it] 151it [27:32, 11.17s/it] 152it [27:43, 11.14s/it] 153it [27:55, 11.14s/it] 154it [28:06, 11.15s/it] 155it [28:17, 11.15s/it] 156it [28:28, 11.15s/it] 157it [28:39, 11.15s/it] 158it [28:50, 11.16s/it] 159it [29:02, 11.17s/it] 160it [29:13, 11.14s/it] 161it [29:24, 11.13s/it] 162it [29:35, 11.13s/it] 163it [29:46, 11.14s/it] 164it [29:57, 11.14s/it] 165it [30:08, 11.12s/it] 166it [30:19, 11.11s/it] 167it [30:30, 11.11s/it] 168it [30:42, 11.11s/it] 169it [30:53, 11.08s/it] 170it [31:04, 11.11s/it] 171it [31:15, 11.09s/it] 172it [31:26, 11.12s/it] 173it [31:37, 11.10s/it] 174it [31:48, 11.11s/it] 175it [31:59, 11.12s/it] 176it [32:10, 11.09s/it] 177it [32:21, 11.10s/it] 178it [32:33, 11.08s/it] 179it [32:44, 11.08s/it] 180it [32:55, 11.10s/it] 181it [33:06, 11.08s/it] 182it [33:16, 10.96s/it] 183it [33:27, 10.92s/it] 184it [33:38, 10.88s/it] 185it [33:49, 10.86s/it] 186it [34:00, 10.84s/it] 187it [34:10, 10.80s/it] 188it [34:21, 10.81s/it] 189it [34:32, 10.80s/it] 190it [34:43, 10.81s/it] 191it [34:54, 10.80s/it] 192it [35:04, 10.81s/it] 193it [35:15, 10.78s/it] 194it [35:26, 10.78s/it] 195it [35:37, 10.77s/it] 196it [35:47, 10.78s/it] 197it [35:58, 10.76s/it] 198it [36:09, 10.79s/it] 199it [36:20, 10.77s/it] 200it [36:31, 10.80s/it] 201it [36:41, 10.80s/it] 202it [36:52, 10.80s/it] 203it [37:03, 10.80s/it] 204it [37:14, 10.89s/it] 205it [37:25, 10.96s/it] 206it [37:36, 10.99s/it] 207it [37:47, 11.01s/it] 208it [37:58, 11.03s/it] 209it [38:10, 11.07s/it] 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11.37s/it] 959it [2:55:37, 11.37s/it] 960it [2:55:48, 11.35s/it] 961it [2:56:00, 11.33s/it] 962it [2:56:11, 11.38s/it] 963it [2:56:23, 11.40s/it] 964it [2:56:34, 11.42s/it] 965it [2:56:45, 11.41s/it] 966it [2:56:57, 11.38s/it] 967it [2:57:08, 11.39s/it] 968it [2:57:20, 11.43s/it] 969it [2:57:31, 11.44s/it] 970it [2:57:43, 11.45s/it] 971it [2:57:54, 11.45s/it] 972it [2:58:05, 11.39s/it] 973it [2:58:17, 11.39s/it] 974it [2:58:28, 11.38s/it] 975it [2:58:40, 11.41s/it] 976it [2:58:51, 11.46s/it] 977it [2:59:02, 11.42s/it] 978it [2:59:14, 11.39s/it] 979it [2:59:25, 11.37s/it] 980it [2:59:36, 11.36s/it] 981it [2:59:48, 11.38s/it] 982it [3:00:00, 11.45s/it] 983it [3:00:11, 11.43s/it] 984it [3:00:22, 11.40s/it] 985it [3:00:34, 11.38s/it] 986it [3:00:45, 11.38s/it] 987it [3:00:57, 11.46s/it] 988it [3:01:08, 11.53s/it] 989it [3:01:20, 11.48s/it] 990it [3:01:31, 11.39s/it] 991it [3:01:42, 11.39s/it] 992it [3:01:54, 11.43s/it] 993it [3:02:05, 11.48s/it] 994it [3:02:17, 11.51s/it] 995it [3:02:28, 11.43s/it] 996it [3:02:39, 11.37s/it] 997it [3:02:51, 11.37s/it] 998it [3:03:02, 11.46s/it] 999it [3:03:14, 11.53s/it] 1000it [3:03:26, 11.53s/it] 1000it [3:03:26, 11.01s/it] +Error counts: + cyclic_id: 0 + cyclic_inchikey: 0 + cyclic_scaffold: 0 + cyclic_mwt: 0 + cyclic_clogp: 0 + cyclic_tpsa: 0 +⏰ Completed process in 3:03:48.458908 ++ rm /nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/train/cyc-pep-6-12mer-70M_05.csv diff --git a/train/cyc-pep-6-12mer-70M_06.csv.gz b/train/cyc-pep-6-12mer-70M_06.csv.gz index 11a953b4ef9f6eec0e990424e70f4a8c194e4909..6a32b800f6af7db4db452b264f34876c153ce0e8 100644 --- a/train/cyc-pep-6-12mer-70M_06.csv.gz +++ b/train/cyc-pep-6-12mer-70M_06.csv.gz @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:39475ca699e51b29c20eca9cc07b81d6ddacb1f4f7fe0ce93be606b4de358797 -size 59207060 +oid sha256:0f8c8b52c97b6c777c40a603d85d0e390dc5205d6bdd4f0ba1708b4bdbac8c96 +size 114077572 diff --git a/train/cyc-pep-6-12mer-70M_06.log b/train/cyc-pep-6-12mer-70M_06.log new file mode 100644 index 0000000000000000000000000000000000000000..b8626fc2da1c8efb0a2c3f4c3ede37da5d52dde5 --- /dev/null +++ b/train/cyc-pep-6-12mer-70M_06.log @@ -0,0 +1,337 @@ ++ module purge ++ '[' -z '' ']' ++ case "$-" in ++ __lmod_sh_dbg=x ++ '[' -n x ']' ++ set +x +Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output +Shell debugging restarted ++ unset __lmod_sh_dbg ++ return 0 ++ module load Anaconda3/2023.03 ++ '[' -z '' ']' ++ case "$-" in ++ __lmod_sh_dbg=x ++ '[' -n x ']' ++ set +x +Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output +Shell debugging restarted ++ unset __lmod_sh_dbg ++ return 0 ++ source /camp/home/johnsoe/.bashrc +++ '[' '' = yes ']' +++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' ++++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.bash hook +++ __conda_setup='export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'' + +# Copyright (C) 2012 Anaconda, Inc +# SPDX-License-Identifier: BSD-3-Clause +__conda_exe() ( + "$CONDA_EXE" $_CE_M $_CE_CONDA "$@" +) + +__conda_hashr() { + if [ -n "${ZSH_VERSION:+x}" ]; then + \rehash + elif [ -n "${POSH_VERSION:+x}" ]; then + : # pass + else + \hash -r + fi +} + +__conda_activate() { + if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then + # Handle transition from shell activated with conda <= 4.3 to a subsequent activation + # after conda updated to >= 4.4. See issue #6173. + PS1="$CONDA_PS1_BACKUP" + \unset CONDA_PS1_BACKUP + fi + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return + \eval "$ask_conda" + __conda_hashr +} + +__conda_reactivate() { + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return + \eval "$ask_conda" + __conda_hashr +} + +conda() { + \local cmd="${1-__missing__}" + case "$cmd" in + activate|deactivate) + __conda_activate "$@" + ;; + install|update|upgrade|remove|uninstall) + __conda_exe "$@" || \return + __conda_reactivate + ;; + *) + __conda_exe "$@" + ;; + esac +} + +if [ -z "${CONDA_SHLVL+x}" ]; then + \export CONDA_SHLVL=0 + # In dev-mode CONDA_EXE is python.exe and on Windows + # it is in a different relative location to condabin. + if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then + PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}" + else + PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}" + fi + \export PATH + + # We'\''re not allowing PS1 to be unbound. It must at least be set. + # However, we'\''re not exporting it, which can cause problems when starting a second shell + # via a first shell (i.e. starting zsh from bash). + if [ -z "${PS1+x}" ]; then + PS1= + fi +fi + +conda activate base' +++ '[' 0 -eq 0 ']' +++ eval 'export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'' + +# Copyright (C) 2012 Anaconda, Inc +# SPDX-License-Identifier: BSD-3-Clause +__conda_exe() ( + "$CONDA_EXE" $_CE_M $_CE_CONDA "$@" +) + +__conda_hashr() { + if [ -n "${ZSH_VERSION:+x}" ]; then + \rehash + elif [ -n "${POSH_VERSION:+x}" ]; then + : # pass + else + \hash -r + fi +} + +__conda_activate() { + if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then + # Handle transition from shell activated with conda <= 4.3 to a subsequent activation + # after conda updated to >= 4.4. See issue #6173. + PS1="$CONDA_PS1_BACKUP" + \unset CONDA_PS1_BACKUP + fi + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return + \eval "$ask_conda" + __conda_hashr +} + +__conda_reactivate() { + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return + \eval "$ask_conda" + __conda_hashr +} + +conda() { + \local cmd="${1-__missing__}" + case "$cmd" in + activate|deactivate) + __conda_activate "$@" + ;; + install|update|upgrade|remove|uninstall) + __conda_exe "$@" || \return + __conda_reactivate + ;; + *) + __conda_exe "$@" + ;; + esac +} + +if [ -z "${CONDA_SHLVL+x}" ]; then + \export CONDA_SHLVL=0 + # In dev-mode CONDA_EXE is python.exe and on Windows + # it is in a different relative location to condabin. + if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then + PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}" + else + PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}" + fi + \export PATH + + # We'\''re not allowing PS1 to be unbound. It must at least be set. + # However, we'\''re not exporting it, which can cause problems when starting a second shell + # via a first shell (i.e. starting zsh from bash). + if [ -z "${PS1+x}" ]; then + PS1= + fi +fi + +conda activate base' ++++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda ++++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda ++++ export _CE_M= ++++ _CE_M= ++++ export _CE_CONDA= ++++ _CE_CONDA= ++++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ '[' -z x ']' ++++ conda activate base ++++ local cmd=activate ++++ case "$cmd" in ++++ __conda_activate activate base ++++ '[' -n '' ']' ++++ local ask_conda +++++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++++ __conda_exe shell.posix activate base +++++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate base ++++ ask_conda='PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_SHLVL='\''6'\'' +export CONDA_DEFAULT_ENV='\''base'\'' +export CONDA_PROMPT_MODIFIER='\''(base) '\'' +export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' ++++ eval 'PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_SHLVL='\''6'\'' +export CONDA_DEFAULT_ENV='\''base'\'' +export CONDA_PROMPT_MODIFIER='\''(base) '\'' +export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' +++++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++++ export CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0 +++++ CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0 +++++ export CONDA_SHLVL=6 +++++ CONDA_SHLVL=6 +++++ export CONDA_DEFAULT_ENV=base +++++ CONDA_DEFAULT_ENV=base +++++ export 'CONDA_PROMPT_MODIFIER=(base) ' +++++ CONDA_PROMPT_MODIFIER='(base) ' +++++ export CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev +++++ CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev +++++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++++ export _CE_M= +++++ _CE_M= +++++ export _CE_CONDA= +++++ _CE_CONDA= +++++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python +++++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ __conda_hashr ++++ '[' -n '' ']' ++++ '[' -n '' ']' ++++ hash -r +++ unset __conda_setup ++ conda activate schemist-dev ++ local cmd=activate ++ case "$cmd" in ++ __conda_activate activate schemist-dev ++ '[' -n '' ']' ++ local ask_conda +++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++ __conda_exe shell.posix activate schemist-dev +++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate schemist-dev ++ ask_conda='PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_SHLVL='\''7'\'' +export CONDA_DEFAULT_ENV='\''schemist-dev'\'' +export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\'' +export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' ++ eval 'PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_SHLVL='\''7'\'' +export CONDA_DEFAULT_ENV='\''schemist-dev'\'' +export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\'' +export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' +++ PS1='(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++ export CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev +++ CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev +++ export CONDA_SHLVL=7 +++ CONDA_SHLVL=7 +++ export CONDA_DEFAULT_ENV=schemist-dev +++ CONDA_DEFAULT_ENV=schemist-dev +++ export 'CONDA_PROMPT_MODIFIER=(schemist-dev) ' +++ CONDA_PROMPT_MODIFIER='(schemist-dev) ' +++ export CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0 +++ CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0 +++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++ export _CE_M= +++ _CE_M= +++ export _CE_CONDA= +++ _CE_CONDA= +++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python +++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++ __conda_hashr ++ '[' -n '' ']' ++ '[' -n '' ']' ++ hash -r ++ CHUNK_HEAD_FILE=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz ++ INPUT=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/train/cyc-pep-6-12mer-70M_06.csv ++ COLUMN=cysteine_to_N_cyclization ++ PREFIX=cyclic_ ++ AWK='1 { print $8, $1, $2, $10, $3 }' ++ '[' -z cysteine_to_N_cyclization ']' ++ '[' -z cyclic_ ']' ++ '[' -z '1 { print $8, $1, $2, $10, $3 }' ']' ++ awk -F, -v OFS=, '1 { print $8, $1, $2, $10, $3 }' ++ cat /dev/fd/63 /nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/train/cyc-pep-6-12mer-70M_06.csv ++ schemist convert -f csv --column cysteine_to_N_cyclization --to id inchikey scaffold mwt clogp tpsa --prefix cyclic_ --options prefix=SCB- ++ gzip --best +++ zcat /nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz +++ head -n1 +++ tr ' ' , +🚀 Converting between string representations with the following parameters: + subcommand: convert + output: <_io.TextIOWrapper name='' mode='w' encoding='utf-8'> + format: csv + input: <_io.TextIOWrapper name='' mode='r' encoding='utf-8'> + representation: SMILES + column: cysteine_to_N_cyclization + prefix: cyclic_ + to: ['id', 'inchikey', 'scaffold', 'mwt', 'clogp', 'tpsa'] + options: ['prefix=SCB-'] + func: + 0it [00:00, ?it/s] 1it [00:11, 11.89s/it] 2it [00:23, 11.67s/it] 3it [00:34, 11.61s/it] 4it [00:46, 11.63s/it] 5it [00:58, 11.65s/it] 6it [01:09, 11.63s/it] 7it [01:21, 11.68s/it] 8it [01:33, 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[3:15:51, 13.17s/it] 959it [3:16:04, 13.16s/it] 960it [3:16:17, 13.18s/it] 961it [3:16:30, 13.19s/it] 962it [3:16:44, 13.25s/it] 963it [3:16:57, 13.30s/it] 964it [3:17:10, 13.26s/it] 965it [3:17:23, 13.23s/it] 966it [3:17:36, 13.14s/it] 967it [3:17:49, 13.16s/it] 968it [3:18:03, 13.20s/it] 969it [3:18:16, 13.20s/it] 970it [3:18:29, 13.27s/it] 971it [3:18:43, 13.24s/it] 972it [3:18:56, 13.25s/it] 973it [3:19:09, 13.30s/it] 974it [3:19:22, 13.28s/it] 975it [3:19:36, 13.27s/it] 976it [3:19:49, 13.30s/it] 977it [3:20:02, 13.32s/it] 978it [3:20:16, 13.30s/it] 979it [3:20:29, 13.30s/it] 980it [3:20:42, 13.28s/it] 981it [3:20:56, 13.28s/it] 982it [3:21:09, 13.25s/it] 983it [3:21:22, 13.21s/it] 984it [3:21:35, 13.22s/it] 985it [3:21:48, 13.22s/it] 986it [3:22:01, 13.19s/it] 987it [3:22:15, 13.20s/it] 988it [3:22:28, 13.20s/it] 989it [3:22:41, 13.20s/it] 990it [3:22:54, 13.19s/it] 991it [3:23:07, 13.17s/it] 992it [3:23:21, 13.19s/it] 993it [3:23:34, 13.18s/it] 994it [3:23:47, 13.24s/it] 995it [3:24:00, 13.21s/it] 996it [3:24:14, 13.24s/it] 997it [3:24:27, 13.26s/it] 998it [3:24:40, 13.20s/it] 999it [3:24:53, 13.19s/it] 1000it [3:25:06, 13.23s/it] 1000it [3:25:06, 12.31s/it] +Error counts: + cyclic_id: 0 + cyclic_inchikey: 0 + cyclic_scaffold: 0 + cyclic_mwt: 0 + cyclic_clogp: 0 + cyclic_tpsa: 0 +⏰ Completed process in 3:25:30.156492 ++ rm /nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/train/cyc-pep-6-12mer-70M_06.csv diff --git a/train/cyc-pep-6-12mer-70M_07.csv.gz b/train/cyc-pep-6-12mer-70M_07.csv.gz index e888da9a02c837646cc504250a4980ad9d50bced..7370c3ae32485e552bea40e0a65d907c2e229a75 100644 --- a/train/cyc-pep-6-12mer-70M_07.csv.gz +++ b/train/cyc-pep-6-12mer-70M_07.csv.gz @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:4bd24068f5ee5587c0b23a56ac79315e74c00011b78aaaec401c07678d0ecdbd -size 61920564 +oid sha256:bebd419015a0b7c988aadcb153e993dd807e3ce5f83749a73cff4a07a85f5b5a +size 117597869 diff --git a/train/cyc-pep-6-12mer-70M_07.log b/train/cyc-pep-6-12mer-70M_07.log new file mode 100644 index 0000000000000000000000000000000000000000..dc5bc7fe5d19c5a96ac290ed53fe728cf9c65aed --- /dev/null +++ b/train/cyc-pep-6-12mer-70M_07.log @@ -0,0 +1,337 @@ ++ module purge ++ '[' -z '' ']' ++ case "$-" in ++ __lmod_sh_dbg=x ++ '[' -n x ']' ++ set +x +Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output +Shell debugging restarted ++ unset __lmod_sh_dbg ++ return 0 ++ module load Anaconda3/2023.03 ++ '[' -z '' ']' ++ case "$-" in ++ __lmod_sh_dbg=x ++ '[' -n x ']' ++ set +x +Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output +Shell debugging restarted ++ unset __lmod_sh_dbg ++ return 0 ++ source /camp/home/johnsoe/.bashrc +++ '[' '' = yes ']' +++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' ++++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.bash hook +++ __conda_setup='export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'' + +# Copyright (C) 2012 Anaconda, Inc +# SPDX-License-Identifier: BSD-3-Clause +__conda_exe() ( + "$CONDA_EXE" $_CE_M $_CE_CONDA "$@" +) + +__conda_hashr() { + if [ -n "${ZSH_VERSION:+x}" ]; then + \rehash + elif [ -n "${POSH_VERSION:+x}" ]; then + : # pass + else + \hash -r + fi +} + +__conda_activate() { + if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then + # Handle transition from shell activated with conda <= 4.3 to a subsequent activation + # after conda updated to >= 4.4. See issue #6173. + PS1="$CONDA_PS1_BACKUP" + \unset CONDA_PS1_BACKUP + fi + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return + \eval "$ask_conda" + __conda_hashr +} + +__conda_reactivate() { + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return + \eval "$ask_conda" + __conda_hashr +} + +conda() { + \local cmd="${1-__missing__}" + case "$cmd" in + activate|deactivate) + __conda_activate "$@" + ;; + install|update|upgrade|remove|uninstall) + __conda_exe "$@" || \return + __conda_reactivate + ;; + *) + __conda_exe "$@" + ;; + esac +} + +if [ -z "${CONDA_SHLVL+x}" ]; then + \export CONDA_SHLVL=0 + # In dev-mode CONDA_EXE is python.exe and on Windows + # it is in a different relative location to condabin. + if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then + PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}" + else + PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}" + fi + \export PATH + + # We'\''re not allowing PS1 to be unbound. It must at least be set. + # However, we'\''re not exporting it, which can cause problems when starting a second shell + # via a first shell (i.e. starting zsh from bash). + if [ -z "${PS1+x}" ]; then + PS1= + fi +fi + +conda activate base' +++ '[' 0 -eq 0 ']' +++ eval 'export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'' + +# Copyright (C) 2012 Anaconda, Inc +# SPDX-License-Identifier: BSD-3-Clause +__conda_exe() ( + "$CONDA_EXE" $_CE_M $_CE_CONDA "$@" +) + +__conda_hashr() { + if [ -n "${ZSH_VERSION:+x}" ]; then + \rehash + elif [ -n "${POSH_VERSION:+x}" ]; then + : # pass + else + \hash -r + fi +} + +__conda_activate() { + if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then + # Handle transition from shell activated with conda <= 4.3 to a subsequent activation + # after conda updated to >= 4.4. See issue #6173. + PS1="$CONDA_PS1_BACKUP" + \unset CONDA_PS1_BACKUP + fi + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return + \eval "$ask_conda" + __conda_hashr +} + +__conda_reactivate() { + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return + \eval "$ask_conda" + __conda_hashr +} + +conda() { + \local cmd="${1-__missing__}" + case "$cmd" in + activate|deactivate) + __conda_activate "$@" + ;; + install|update|upgrade|remove|uninstall) + __conda_exe "$@" || \return + __conda_reactivate + ;; + *) + __conda_exe "$@" + ;; + esac +} + +if [ -z "${CONDA_SHLVL+x}" ]; then + \export CONDA_SHLVL=0 + # In dev-mode CONDA_EXE is python.exe and on Windows + # it is in a different relative location to condabin. + if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then + PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}" + else + PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}" + fi + \export PATH + + # We'\''re not allowing PS1 to be unbound. It must at least be set. + # However, we'\''re not exporting it, which can cause problems when starting a second shell + # via a first shell (i.e. starting zsh from bash). + if [ -z "${PS1+x}" ]; then + PS1= + fi +fi + +conda activate base' ++++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda ++++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda ++++ export _CE_M= ++++ _CE_M= ++++ export _CE_CONDA= ++++ _CE_CONDA= ++++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ '[' -z x ']' ++++ conda activate base ++++ local cmd=activate ++++ case "$cmd" in ++++ __conda_activate activate base ++++ '[' -n '' ']' ++++ local ask_conda +++++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++++ __conda_exe shell.posix activate base +++++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate base ++++ ask_conda='PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_SHLVL='\''6'\'' +export CONDA_DEFAULT_ENV='\''base'\'' +export CONDA_PROMPT_MODIFIER='\''(base) '\'' +export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' ++++ eval 'PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_SHLVL='\''6'\'' +export CONDA_DEFAULT_ENV='\''base'\'' +export CONDA_PROMPT_MODIFIER='\''(base) '\'' +export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' +++++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++++ export CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0 +++++ CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0 +++++ export CONDA_SHLVL=6 +++++ CONDA_SHLVL=6 +++++ export CONDA_DEFAULT_ENV=base +++++ CONDA_DEFAULT_ENV=base +++++ export 'CONDA_PROMPT_MODIFIER=(base) ' +++++ CONDA_PROMPT_MODIFIER='(base) ' +++++ export CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev +++++ CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev +++++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++++ export _CE_M= +++++ _CE_M= +++++ export _CE_CONDA= +++++ _CE_CONDA= +++++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python +++++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ __conda_hashr ++++ '[' -n '' ']' ++++ '[' -n '' ']' ++++ hash -r +++ unset __conda_setup ++ conda activate schemist-dev ++ local cmd=activate ++ case "$cmd" in ++ __conda_activate activate schemist-dev ++ '[' -n '' ']' ++ local ask_conda +++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++ __conda_exe shell.posix activate schemist-dev +++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate schemist-dev ++ ask_conda='PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_SHLVL='\''7'\'' +export CONDA_DEFAULT_ENV='\''schemist-dev'\'' +export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\'' +export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' ++ eval 'PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_SHLVL='\''7'\'' +export CONDA_DEFAULT_ENV='\''schemist-dev'\'' +export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\'' +export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' +++ PS1='(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++ export CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev +++ CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev +++ export CONDA_SHLVL=7 +++ CONDA_SHLVL=7 +++ export CONDA_DEFAULT_ENV=schemist-dev +++ CONDA_DEFAULT_ENV=schemist-dev +++ export 'CONDA_PROMPT_MODIFIER=(schemist-dev) ' +++ CONDA_PROMPT_MODIFIER='(schemist-dev) ' +++ export CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0 +++ CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0 +++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++ export _CE_M= +++ _CE_M= +++ export _CE_CONDA= +++ _CE_CONDA= +++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python +++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++ __conda_hashr ++ '[' -n '' ']' ++ '[' -n '' ']' ++ hash -r ++ CHUNK_HEAD_FILE=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz ++ INPUT=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/train/cyc-pep-6-12mer-70M_07.csv ++ COLUMN=cysteine_to_N_cyclization ++ PREFIX=cyclic_ ++ AWK='1 { print $8, $1, $2, $10, $3 }' ++ '[' -z cysteine_to_N_cyclization ']' ++ '[' -z cyclic_ ']' ++ '[' -z '1 { print $8, $1, $2, $10, $3 }' ']' ++ cat /dev/fd/63 /nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/train/cyc-pep-6-12mer-70M_07.csv ++ awk -F, -v OFS=, '1 { print $8, $1, $2, $10, $3 }' ++ schemist convert -f csv --column cysteine_to_N_cyclization --to id inchikey scaffold mwt clogp tpsa --prefix cyclic_ --options prefix=SCB- ++ gzip --best +++ tr ' ' , +++ head -n1 +++ zcat /nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz +🚀 Converting between string representations with the following parameters: + subcommand: convert + output: <_io.TextIOWrapper name='' mode='w' encoding='utf-8'> + format: csv + input: <_io.TextIOWrapper name='' mode='r' encoding='utf-8'> + representation: SMILES + column: cysteine_to_N_cyclization + prefix: cyclic_ + to: ['id', 'inchikey', 'scaffold', 'mwt', 'clogp', 'tpsa'] + options: ['prefix=SCB-'] + func: + 0it [00:00, ?it/s] 1it [00:12, 12.06s/it] 2it [00:24, 12.08s/it] 3it [00:36, 12.11s/it] 4it [00:48, 12.13s/it] 5it [01:00, 12.12s/it] 6it [01:12, 12.12s/it] 7it [01:24, 12.11s/it] 8it [01:36, 12.10s/it] 9it [01:48, 12.08s/it] 10it [02:00, 12.07s/it] 11it [02:13, 12.12s/it] 12it [02:25, 12.07s/it] 13it [02:37, 12.12s/it] 14it [02:49, 12.12s/it] 15it [03:01, 12.13s/it] 16it [03:13, 12.15s/it] 17it [03:25, 12.13s/it] 18it [03:38, 12.15s/it] 19it [03:50, 12.12s/it] 20it [04:02, 12.16s/it] 21it [04:14, 12.14s/it] 22it [04:26, 12.12s/it] 23it [04:38, 12.15s/it] 24it [04:50, 12.11s/it] 25it [05:03, 12.15s/it] 26it [05:15, 12.12s/it] 27it [05:27, 12.13s/it] 28it [05:39, 12.15s/it] 29it [05:51, 12.11s/it] 30it [06:03, 12.11s/it] 31it [06:15, 12.09s/it] 32it [06:27, 12.10s/it] 33it [06:39, 12.12s/it] 34it [06:52, 12.11s/it] 35it [07:04, 12.10s/it] 36it [07:15, 12.00s/it] 37it [07:27, 11.96s/it] 38it [07:39, 12.01s/it] 39it [07:51, 11.94s/it] 40it [08:03, 12.00s/it] 41it [08:15, 11.98s/it] 42it [08:27, 11.93s/it] 43it [08:39, 11.90s/it] 44it [08:51, 11.85s/it] 45it [09:02, 11.86s/it] 46it [09:14, 11.85s/it] 47it [09:26, 11.82s/it] 48it [09:38, 11.88s/it] 49it [09:50, 11.82s/it] 50it [10:02, 11.83s/it] 51it [10:14, 11.85s/it] 52it [10:25, 11.84s/it] 53it [10:37, 11.89s/it] 54it [10:49, 11.88s/it] 55it [11:01, 11.93s/it] 56it [11:13, 11.92s/it] 57it [11:25, 11.87s/it] 58it [11:37, 11.90s/it] 59it [11:49, 11.86s/it] 60it [12:01, 11.90s/it] 61it [12:13, 11.94s/it] 62it [12:24, 11.89s/it] 63it [12:36, 11.92s/it] 64it [12:48, 11.89s/it] 65it [13:00, 11.83s/it] 66it [13:12, 11.79s/it] 67it [13:23, 11.77s/it] 68it [13:35, 11.78s/it] 69it [13:47, 11.76s/it] 70it [13:59, 11.76s/it] 71it [14:10, 11.74s/it] 72it [14:22, 11.74s/it] 73it [14:34, 11.72s/it] 74it [14:46, 11.75s/it] 75it [14:57, 11.75s/it] 76it [15:09, 11.78s/it] 77it [15:21, 11.75s/it] 78it [15:33, 11.75s/it] 79it [15:44, 11.73s/it] 80it [15:56, 11.73s/it] 81it [16:08, 11.74s/it] 82it [16:20, 11.75s/it] 83it [16:31, 11.75s/it] 84it [16:43, 11.75s/it] 85it [16:55, 11.76s/it] 86it [17:07, 11.76s/it] 87it [17:18, 11.76s/it] 88it [17:30, 11.76s/it] 89it [17:42, 11.75s/it] 90it [17:54, 11.78s/it] 91it [18:05, 11.78s/it] 92it [18:17, 11.81s/it] 93it [18:29, 11.81s/it] 94it [18:41, 11.80s/it] 95it [18:53, 11.81s/it] 96it [19:05, 11.80s/it] 97it [19:16, 11.80s/it] 98it [19:28, 11.79s/it] 99it [19:40, 11.78s/it] 100it [19:52, 11.75s/it] 101it [20:03, 11.76s/it] 102it [20:15, 11.76s/it] 103it [20:27, 11.73s/it] 104it [20:39, 11.77s/it] 105it [20:50, 11.78s/it] 106it [21:02, 11.78s/it] 107it [21:14, 11.80s/it] 108it [21:26, 11.77s/it] 109it [21:37, 11.78s/it] 110it [21:49, 11.77s/it] 111it [22:01, 11.77s/it] 112it [22:13, 11.77s/it] 113it [22:25, 11.78s/it] 114it [22:36, 11.77s/it] 115it [22:48, 11.77s/it] 116it [23:00, 11.75s/it] 117it [23:12, 11.75s/it] 118it [23:23, 11.76s/it] 119it [23:35, 11.77s/it] 120it [23:47, 11.77s/it] 121it [23:59, 11.75s/it] 122it [24:10, 11.76s/it] 123it [24:22, 11.76s/it] 124it [24:34, 11.75s/it] 125it [24:46, 11.76s/it] 126it [24:57, 11.75s/it] 127it [25:09, 11.75s/it] 128it [25:21, 11.76s/it] 129it [25:33, 11.75s/it] 130it [25:44, 11.73s/it] 131it [25:56, 11.74s/it] 132it [26:08, 11.74s/it] 133it [26:20, 11.74s/it] 134it [26:31, 11.75s/it] 135it [26:43, 11.75s/it] 136it [26:55, 11.74s/it] 137it [27:07, 11.75s/it] 138it [27:18, 11.76s/it] 139it [27:30, 11.75s/it] 140it [27:42, 11.74s/it] 141it [27:54, 11.75s/it] 142it [28:05, 11.73s/it] 143it [28:17, 11.74s/it] 144it [28:29, 11.75s/it] 145it [28:41, 11.74s/it] 146it [28:52, 11.74s/it] 147it [29:04, 11.72s/it] 148it [29:16, 11.72s/it] 149it [29:27, 11.74s/it] 150it [29:39, 11.73s/it] 151it [29:51, 11.74s/it] 152it [30:03, 11.77s/it] 153it [30:14, 11.75s/it] 154it [30:26, 11.77s/it] 155it [30:38, 11.75s/it] 156it [30:50, 11.75s/it] 157it [31:02, 11.76s/it] 158it [31:13, 11.76s/it] 159it [31:25, 11.76s/it] 160it [31:37, 11.77s/it] 161it [31:49, 11.75s/it] 162it [32:00, 11.76s/it] 163it [32:12, 11.74s/it] 164it [32:24, 11.76s/it] 165it [32:36, 11.77s/it] 166it [32:47, 11.74s/it] 167it [32:59, 11.75s/it] 168it [33:11, 11.79s/it] 169it [33:23, 11.77s/it] 170it [33:34, 11.76s/it] 171it [33:46, 11.75s/it] 172it [33:58, 11.75s/it] 173it [34:10, 11.74s/it] 174it [34:21, 11.74s/it] 175it [34:33, 11.76s/it] 176it [34:45, 11.76s/it] 177it [34:57, 11.75s/it] 178it [35:08, 11.75s/it] 179it [35:20, 11.72s/it] 180it [35:32, 11.74s/it] 181it [35:44, 11.75s/it] 182it [35:55, 11.74s/it] 183it [36:07, 11.75s/it] 184it [36:19, 11.73s/it] 185it [36:31, 11.76s/it] 186it [36:42, 11.77s/it] 187it [36:54, 11.75s/it] 188it [37:06, 11.74s/it] 189it [37:18, 11.74s/it] 190it [37:29, 11.73s/it] 191it [37:41, 11.76s/it] 192it [37:53, 11.76s/it] 193it [38:05, 11.75s/it] 194it [38:16, 11.76s/it] 195it [38:28, 11.76s/it] 196it [38:40, 11.77s/it] 197it [38:52, 11.75s/it] 198it [39:03, 11.75s/it] 199it [39:15, 11.75s/it] 200it [39:27, 11.73s/it] 201it [39:39, 11.74s/it] 202it [39:50, 11.76s/it] 203it [40:02, 11.75s/it] 204it [40:14, 11.77s/it] 205it [40:26, 11.78s/it] 206it [40:38, 11.78s/it] 207it [40:49, 11.78s/it] 208it [41:01, 11.75s/it] 209it [41:13, 11.78s/it] 210it [41:25, 11.77s/it] 211it [41:36, 11.77s/it] 212it [41:48, 11.76s/it] 213it [42:00, 11.74s/it] 214it [42:12, 11.75s/it] 215it [42:23, 11.76s/it] 216it [42:35, 11.74s/it] 217it [42:47, 11.75s/it] 218it [42:59, 11.75s/it] 219it [43:10, 11.72s/it] 220it [43:22, 11.71s/it] 221it [43:34, 11.70s/it] 222it [43:45, 11.70s/it] 223it [43:57, 11.69s/it] 224it [44:09, 11.72s/it] 225it [44:20, 11.72s/it] 226it [44:32, 11.70s/it] 227it [44:44, 11.71s/it] 228it [44:56, 11.76s/it] 229it [45:08, 11.78s/it] 230it [45:19, 11.79s/it] 231it [45:31, 11.77s/it] 232it [45:43, 11.76s/it] 233it [45:55, 11.77s/it] 234it [46:06, 11.77s/it] 235it [46:18, 11.79s/it] 236it [46:30, 11.79s/it] 237it [46:42, 11.78s/it] 238it [46:54, 11.79s/it] 239it [47:05, 11.78s/it] 240it [47:17, 11.78s/it] 241it [47:29, 11.79s/it] 242it [47:41, 11.79s/it] 243it [47:52, 11.76s/it] 244it [48:04, 11.77s/it] 245it [48:16, 11.79s/it] 246it [48:28, 11.79s/it] 247it [48:40, 11.79s/it] 248it [48:51, 11.77s/it] 249it [49:03, 11.76s/it] 250it [49:15, 11.75s/it] 251it [49:27, 11.77s/it] 252it [49:38, 11.77s/it] 253it [49:50, 11.75s/it] 254it [50:02, 11.75s/it] 255it [50:14, 11.77s/it] 256it [50:25, 11.75s/it] 257it [50:37, 11.78s/it] 258it [50:49, 11.76s/it] 259it [51:01, 11.75s/it] 260it [51:12, 11.75s/it] 261it [51:24, 11.74s/it] 262it [51:36, 11.74s/it] 263it [51:48, 11.75s/it] 264it [51:59, 11.76s/it] 265it [52:11, 11.77s/it] 266it [52:23, 11.75s/it] 267it [52:35, 11.75s/it] 268it [52:46, 11.75s/it] 269it [52:58, 11.74s/it] 270it [53:10, 11.76s/it] 271it [53:22, 11.75s/it] 272it [53:33, 11.75s/it] 273it [53:45, 11.75s/it] 274it [53:57, 11.76s/it] 275it [54:09, 11.75s/it] 276it [54:20, 11.76s/it] 277it [54:32, 11.73s/it] 278it [54:44, 11.75s/it] 279it [54:56, 11.75s/it] 280it [55:07, 11.75s/it] 281it [55:19, 11.77s/it] 282it [55:31, 11.75s/it] 283it [55:43, 11.75s/it] 284it [55:54, 11.74s/it] 285it [56:06, 11.74s/it] 286it [56:18, 11.74s/it] 287it [56:30, 11.75s/it] 288it [56:41, 11.73s/it] 289it [56:53, 11.76s/it] 290it [57:05, 11.75s/it] 291it [57:17, 11.76s/it] 292it [57:28, 11.76s/it] 293it [57:40, 11.77s/it] 294it [57:52, 11.76s/it] 295it [58:04, 11.78s/it] 296it [58:16, 11.78s/it] 297it [58:27, 11.76s/it] 298it [58:39, 11.76s/it] 299it [58:51, 11.74s/it] 300it [59:02, 11.75s/it] 301it [59:14, 11.76s/it] 302it [59:26, 11.74s/it] 303it [59:38, 11.75s/it] 304it [59:49, 11.76s/it] 305it [1:00:01, 11.76s/it] 306it [1:00:13, 11.76s/it] 307it [1:00:25, 11.75s/it] 308it [1:00:37, 11.76s/it] 309it [1:00:48, 11.76s/it] 310it [1:01:00, 11.78s/it] 311it [1:01:12, 11.77s/it] 312it [1:01:24, 11.76s/it] 313it [1:01:35, 11.76s/it] 314it [1:01:47, 11.78s/it] 315it [1:01:59, 11.78s/it] 316it [1:02:11, 11.79s/it] 317it [1:02:23, 11.78s/it] 318it [1:02:34, 11.76s/it] 319it [1:02:46, 11.79s/it] 320it [1:02:58, 11.82s/it] 321it [1:03:10, 11.81s/it] 322it [1:03:22, 11.81s/it] 323it [1:03:33, 11.80s/it] 324it [1:03:45, 11.80s/it] 325it [1:03:57, 11.80s/it] 326it [1:04:09, 11.82s/it] 327it [1:04:21, 11.81s/it] 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957it [3:09:05, 12.09s/it] 958it [3:09:17, 12.02s/it] 959it [3:09:29, 12.02s/it] 960it [3:09:41, 12.03s/it] 961it [3:09:53, 12.08s/it] 962it [3:10:05, 12.10s/it] 963it [3:10:17, 12.09s/it] 964it [3:10:29, 12.09s/it] 965it [3:10:41, 12.05s/it] 966it [3:10:53, 12.05s/it] 967it [3:11:05, 12.11s/it] 968it [3:11:18, 12.12s/it] 969it [3:11:30, 12.11s/it] 970it [3:11:42, 12.12s/it] 971it [3:11:54, 12.12s/it] 972it [3:12:06, 12.08s/it] 973it [3:12:18, 12.08s/it] 974it [3:12:30, 12.10s/it] 975it [3:12:42, 12.11s/it] 976it [3:12:55, 12.15s/it] 977it [3:13:06, 12.10s/it] 978it [3:13:18, 12.03s/it] 979it [3:13:30, 12.04s/it] 980it [3:13:42, 12.05s/it] 981it [3:13:55, 12.08s/it] 982it [3:14:07, 12.07s/it] 983it [3:14:19, 12.06s/it] 984it [3:14:31, 12.06s/it] 985it [3:14:43, 12.03s/it] 986it [3:14:55, 12.07s/it] 987it [3:15:07, 12.08s/it] 988it [3:15:19, 12.07s/it] 989it [3:15:31, 12.09s/it] 990it [3:15:43, 12.06s/it] 991it [3:15:55, 12.02s/it] 992it [3:16:07, 12.04s/it] 993it [3:16:19, 12.03s/it] 994it [3:16:31, 12.07s/it] 995it [3:16:43, 12.07s/it] 996it [3:16:56, 12.06s/it] 997it [3:17:07, 12.03s/it] 998it [3:17:19, 12.01s/it] 999it [3:17:32, 12.08s/it] 1000it [3:17:44, 12.09s/it] 1000it [3:17:44, 11.86s/it] +Error counts: + cyclic_id: 0 + cyclic_inchikey: 0 + cyclic_scaffold: 0 + cyclic_mwt: 0 + cyclic_clogp: 0 + cyclic_tpsa: 0 +⏰ Completed process in 3:18:08.109675 ++ rm /nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/train/cyc-pep-6-12mer-70M_07.csv diff --git a/train/cyc-pep-6-12mer-70M_08.csv.gz b/train/cyc-pep-6-12mer-70M_08.csv.gz index afd0a3196aa3d8f9d12cfa54a2019993761132b1..2fe6a733a19752efd86f1053c5df1fd27653185b 100644 --- a/train/cyc-pep-6-12mer-70M_08.csv.gz +++ b/train/cyc-pep-6-12mer-70M_08.csv.gz @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:27ebb0665ac18ce05bcffcb8dd52223f98e6e6cf4c2d2422c0c04ff75474baa4 -size 61924935 +oid sha256:43b40bf86d8c8b1a9cda58d0c1084556a42db1f382bc346476b029874fc788cc +size 117605134 diff --git a/train/cyc-pep-6-12mer-70M_08.log b/train/cyc-pep-6-12mer-70M_08.log new file mode 100644 index 0000000000000000000000000000000000000000..988760cf9b0b066bc04179ce975785b2ac83d73f --- /dev/null +++ b/train/cyc-pep-6-12mer-70M_08.log @@ -0,0 +1,337 @@ ++ module purge ++ '[' -z '' ']' ++ case "$-" in ++ __lmod_sh_dbg=x ++ '[' -n x ']' ++ set +x +Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output +Shell debugging restarted ++ unset __lmod_sh_dbg ++ return 0 ++ module load Anaconda3/2023.03 ++ '[' -z '' ']' ++ case "$-" in ++ __lmod_sh_dbg=x ++ '[' -n x ']' ++ set +x +Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output +Shell debugging restarted ++ unset __lmod_sh_dbg ++ return 0 ++ source /camp/home/johnsoe/.bashrc +++ '[' '' = yes ']' +++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' ++++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.bash hook +++ __conda_setup='export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'' + +# Copyright (C) 2012 Anaconda, Inc +# SPDX-License-Identifier: BSD-3-Clause +__conda_exe() ( + "$CONDA_EXE" $_CE_M $_CE_CONDA "$@" +) + +__conda_hashr() { + if [ -n "${ZSH_VERSION:+x}" ]; then + \rehash + elif [ -n "${POSH_VERSION:+x}" ]; then + : # pass + else + \hash -r + fi +} + +__conda_activate() { + if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then + # Handle transition from shell activated with conda <= 4.3 to a subsequent activation + # after conda updated to >= 4.4. See issue #6173. + PS1="$CONDA_PS1_BACKUP" + \unset CONDA_PS1_BACKUP + fi + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return + \eval "$ask_conda" + __conda_hashr +} + +__conda_reactivate() { + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return + \eval "$ask_conda" + __conda_hashr +} + +conda() { + \local cmd="${1-__missing__}" + case "$cmd" in + activate|deactivate) + __conda_activate "$@" + ;; + install|update|upgrade|remove|uninstall) + __conda_exe "$@" || \return + __conda_reactivate + ;; + *) + __conda_exe "$@" + ;; + esac +} + +if [ -z "${CONDA_SHLVL+x}" ]; then + \export CONDA_SHLVL=0 + # In dev-mode CONDA_EXE is python.exe and on Windows + # it is in a different relative location to condabin. + if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then + PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}" + else + PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}" + fi + \export PATH + + # We'\''re not allowing PS1 to be unbound. It must at least be set. + # However, we'\''re not exporting it, which can cause problems when starting a second shell + # via a first shell (i.e. starting zsh from bash). + if [ -z "${PS1+x}" ]; then + PS1= + fi +fi + +conda activate base' +++ '[' 0 -eq 0 ']' +++ eval 'export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'' + +# Copyright (C) 2012 Anaconda, Inc +# SPDX-License-Identifier: BSD-3-Clause +__conda_exe() ( + "$CONDA_EXE" $_CE_M $_CE_CONDA "$@" +) + +__conda_hashr() { + if [ -n "${ZSH_VERSION:+x}" ]; then + \rehash + elif [ -n "${POSH_VERSION:+x}" ]; then + : # pass + else + \hash -r + fi +} + +__conda_activate() { + if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then + # Handle transition from shell activated with conda <= 4.3 to a subsequent activation + # after conda updated to >= 4.4. See issue #6173. + PS1="$CONDA_PS1_BACKUP" + \unset CONDA_PS1_BACKUP + fi + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return + \eval "$ask_conda" + __conda_hashr +} + +__conda_reactivate() { + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return + \eval "$ask_conda" + __conda_hashr +} + +conda() { + \local cmd="${1-__missing__}" + case "$cmd" in + activate|deactivate) + __conda_activate "$@" + ;; + install|update|upgrade|remove|uninstall) + __conda_exe "$@" || \return + __conda_reactivate + ;; + *) + __conda_exe "$@" + ;; + esac +} + +if [ -z "${CONDA_SHLVL+x}" ]; then + \export CONDA_SHLVL=0 + # In dev-mode CONDA_EXE is python.exe and on Windows + # it is in a different relative location to condabin. + if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then + PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}" + else + PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}" + fi + \export PATH + + # We'\''re not allowing PS1 to be unbound. It must at least be set. + # However, we'\''re not exporting it, which can cause problems when starting a second shell + # via a first shell (i.e. starting zsh from bash). + if [ -z "${PS1+x}" ]; then + PS1= + fi +fi + +conda activate base' ++++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda ++++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda ++++ export _CE_M= ++++ _CE_M= ++++ export _CE_CONDA= ++++ _CE_CONDA= ++++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ '[' -z x ']' ++++ conda activate base ++++ local cmd=activate ++++ case "$cmd" in ++++ __conda_activate activate base ++++ '[' -n '' ']' ++++ local ask_conda +++++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++++ __conda_exe shell.posix activate base +++++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate base ++++ ask_conda='PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_SHLVL='\''6'\'' +export CONDA_DEFAULT_ENV='\''base'\'' +export CONDA_PROMPT_MODIFIER='\''(base) '\'' +export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' ++++ eval 'PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_SHLVL='\''6'\'' +export CONDA_DEFAULT_ENV='\''base'\'' +export CONDA_PROMPT_MODIFIER='\''(base) '\'' +export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' +++++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++++ export CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0 +++++ CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0 +++++ export CONDA_SHLVL=6 +++++ CONDA_SHLVL=6 +++++ export CONDA_DEFAULT_ENV=base +++++ CONDA_DEFAULT_ENV=base +++++ export 'CONDA_PROMPT_MODIFIER=(base) ' +++++ CONDA_PROMPT_MODIFIER='(base) ' +++++ export CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev +++++ CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev +++++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++++ export _CE_M= +++++ _CE_M= +++++ export _CE_CONDA= +++++ _CE_CONDA= +++++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python +++++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ __conda_hashr ++++ '[' -n '' ']' ++++ '[' -n '' ']' ++++ hash -r +++ unset __conda_setup ++ conda activate schemist-dev ++ local cmd=activate ++ case "$cmd" in ++ __conda_activate activate schemist-dev ++ '[' -n '' ']' ++ local ask_conda +++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++ __conda_exe shell.posix activate schemist-dev +++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate schemist-dev ++ ask_conda='PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_SHLVL='\''7'\'' +export CONDA_DEFAULT_ENV='\''schemist-dev'\'' +export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\'' +export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' ++ eval 'PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_SHLVL='\''7'\'' +export CONDA_DEFAULT_ENV='\''schemist-dev'\'' +export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\'' +export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' +++ PS1='(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++ export CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev +++ CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev +++ export CONDA_SHLVL=7 +++ CONDA_SHLVL=7 +++ export CONDA_DEFAULT_ENV=schemist-dev +++ CONDA_DEFAULT_ENV=schemist-dev +++ export 'CONDA_PROMPT_MODIFIER=(schemist-dev) ' +++ CONDA_PROMPT_MODIFIER='(schemist-dev) ' +++ export CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0 +++ CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0 +++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++ export _CE_M= +++ _CE_M= +++ export _CE_CONDA= +++ _CE_CONDA= +++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python +++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++ __conda_hashr ++ '[' -n '' ']' ++ '[' -n '' ']' ++ hash -r ++ CHUNK_HEAD_FILE=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz ++ INPUT=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/train/cyc-pep-6-12mer-70M_08.csv ++ COLUMN=cysteine_to_N_cyclization ++ PREFIX=cyclic_ ++ AWK='1 { print $8, $1, $2, $10, $3 }' ++ '[' -z cysteine_to_N_cyclization ']' ++ '[' -z cyclic_ ']' ++ '[' -z '1 { print $8, $1, $2, $10, $3 }' ']' ++ cat /dev/fd/63 /nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/train/cyc-pep-6-12mer-70M_08.csv ++ awk -F, -v OFS=, '1 { print $8, $1, $2, $10, $3 }' +++ zcat /nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz ++ schemist convert -f csv --column cysteine_to_N_cyclization --to id inchikey scaffold mwt clogp tpsa --prefix cyclic_ --options prefix=SCB- ++ gzip --best +++ head -n1 +++ tr ' ' , +🚀 Converting between string representations with the following parameters: + subcommand: convert + output: <_io.TextIOWrapper name='' mode='w' encoding='utf-8'> + format: csv + input: <_io.TextIOWrapper name='' mode='r' encoding='utf-8'> + representation: SMILES + column: cysteine_to_N_cyclization + prefix: cyclic_ + to: ['id', 'inchikey', 'scaffold', 'mwt', 'clogp', 'tpsa'] + options: ['prefix=SCB-'] + func: + 0it [00:00, ?it/s] 1it [00:11, 11.87s/it] 2it [00:23, 11.78s/it] 3it [00:35, 11.77s/it] 4it [00:47, 11.81s/it] 5it [00:59, 11.84s/it] 6it 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957it [3:07:12, 11.21s/it] 958it [3:07:23, 11.23s/it] 959it [3:07:35, 11.23s/it] 960it [3:07:46, 11.23s/it] 961it [3:07:57, 11.24s/it] 962it [3:08:08, 11.24s/it] 963it [3:08:19, 11.23s/it] 964it [3:08:31, 11.26s/it] 965it [3:08:42, 11.27s/it] 966it [3:08:53, 11.25s/it] 967it [3:09:04, 11.25s/it] 968it [3:09:16, 11.25s/it] 969it [3:09:27, 11.27s/it] 970it [3:09:38, 11.29s/it] 971it [3:09:50, 11.29s/it] 972it [3:10:01, 11.29s/it] 973it [3:10:12, 11.27s/it] 974it [3:10:23, 11.28s/it] 975it [3:10:35, 11.28s/it] 976it [3:10:46, 11.29s/it] 977it [3:10:57, 11.29s/it] 978it [3:11:09, 11.28s/it] 979it [3:11:20, 11.29s/it] 980it [3:11:31, 11.29s/it] 981it [3:11:43, 11.30s/it] 982it [3:11:54, 11.29s/it] 983it [3:12:05, 11.28s/it] 984it [3:12:16, 11.28s/it] 985it [3:12:28, 11.29s/it] 986it [3:12:39, 11.31s/it] 987it [3:12:50, 11.30s/it] 988it [3:13:02, 11.43s/it] 989it [3:13:15, 11.89s/it] 990it [3:13:28, 12.31s/it] 991it [3:13:42, 12.62s/it] 992it [3:13:54, 12.53s/it] 993it [3:14:06, 12.34s/it] 994it [3:14:19, 12.53s/it] 995it [3:14:32, 12.70s/it] 996it [3:14:45, 12.76s/it] 997it [3:14:57, 12.61s/it] 998it [3:15:10, 12.67s/it] 999it [3:15:23, 12.85s/it] 1000it [3:15:37, 13.23s/it] 1000it [3:15:37, 11.74s/it] +Error counts: + cyclic_id: 0 + cyclic_inchikey: 0 + cyclic_scaffold: 0 + cyclic_mwt: 0 + cyclic_clogp: 0 + cyclic_tpsa: 0 +⏰ Completed process in 3:15:59.963602 ++ rm /nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/train/cyc-pep-6-12mer-70M_08.csv diff --git a/train/cyc-pep-6-12mer-70M_09.csv.gz b/train/cyc-pep-6-12mer-70M_09.csv.gz index 828560e677500e3179943672ac39d58956413555..d21ffae540285f79eeaaea8766e8f9e26d8e851b 100644 --- a/train/cyc-pep-6-12mer-70M_09.csv.gz +++ b/train/cyc-pep-6-12mer-70M_09.csv.gz @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:44656fbf5f8c2bbe29de3a22891fc07b1142f4fe60907ac5cfab4cce0984c079 -size 61925202 +oid sha256:be9ec4115b86dcee15f970658913b3a3fa115ad25d3eab2412f7c7eeb9477e0b +size 117606847 diff --git a/train/cyc-pep-6-12mer-70M_09.log b/train/cyc-pep-6-12mer-70M_09.log new file mode 100644 index 0000000000000000000000000000000000000000..8a423f3b37f361f628df958c2567cd796143de2b --- /dev/null +++ b/train/cyc-pep-6-12mer-70M_09.log @@ -0,0 +1,337 @@ ++ module purge ++ '[' -z '' ']' ++ case "$-" in ++ __lmod_sh_dbg=x ++ '[' -n x ']' ++ set +x +Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output +Shell debugging restarted ++ unset __lmod_sh_dbg ++ return 0 ++ module load Anaconda3/2023.03 ++ '[' -z '' ']' ++ case "$-" in ++ __lmod_sh_dbg=x ++ '[' -n x ']' ++ set +x +Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output +Shell debugging restarted ++ unset __lmod_sh_dbg ++ return 0 ++ source /camp/home/johnsoe/.bashrc +++ '[' '' = yes ']' +++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' ++++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.bash hook +++ __conda_setup='export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'' + +# Copyright (C) 2012 Anaconda, Inc +# SPDX-License-Identifier: BSD-3-Clause +__conda_exe() ( + "$CONDA_EXE" $_CE_M $_CE_CONDA "$@" +) + +__conda_hashr() { + if [ -n "${ZSH_VERSION:+x}" ]; then + \rehash + elif [ -n "${POSH_VERSION:+x}" ]; then + : # pass + else + \hash -r + fi +} + +__conda_activate() { + if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then + # Handle transition from shell activated with conda <= 4.3 to a subsequent activation + # after conda updated to >= 4.4. See issue #6173. + PS1="$CONDA_PS1_BACKUP" + \unset CONDA_PS1_BACKUP + fi + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return + \eval "$ask_conda" + __conda_hashr +} + +__conda_reactivate() { + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return + \eval "$ask_conda" + __conda_hashr +} + +conda() { + \local cmd="${1-__missing__}" + case "$cmd" in + activate|deactivate) + __conda_activate "$@" + ;; + install|update|upgrade|remove|uninstall) + __conda_exe "$@" || \return + __conda_reactivate + ;; + *) + __conda_exe "$@" + ;; + esac +} + +if [ -z "${CONDA_SHLVL+x}" ]; then + \export CONDA_SHLVL=0 + # In dev-mode CONDA_EXE is python.exe and on Windows + # it is in a different relative location to condabin. + if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then + PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}" + else + PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}" + fi + \export PATH + + # We'\''re not allowing PS1 to be unbound. It must at least be set. + # However, we'\''re not exporting it, which can cause problems when starting a second shell + # via a first shell (i.e. starting zsh from bash). + if [ -z "${PS1+x}" ]; then + PS1= + fi +fi + +conda activate base' +++ '[' 0 -eq 0 ']' +++ eval 'export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'' + +# Copyright (C) 2012 Anaconda, Inc +# SPDX-License-Identifier: BSD-3-Clause +__conda_exe() ( + "$CONDA_EXE" $_CE_M $_CE_CONDA "$@" +) + +__conda_hashr() { + if [ -n "${ZSH_VERSION:+x}" ]; then + \rehash + elif [ -n "${POSH_VERSION:+x}" ]; then + : # pass + else + \hash -r + fi +} + +__conda_activate() { + if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then + # Handle transition from shell activated with conda <= 4.3 to a subsequent activation + # after conda updated to >= 4.4. See issue #6173. + PS1="$CONDA_PS1_BACKUP" + \unset CONDA_PS1_BACKUP + fi + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return + \eval "$ask_conda" + __conda_hashr +} + +__conda_reactivate() { + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return + \eval "$ask_conda" + __conda_hashr +} + +conda() { + \local cmd="${1-__missing__}" + case "$cmd" in + activate|deactivate) + __conda_activate "$@" + ;; + install|update|upgrade|remove|uninstall) + __conda_exe "$@" || \return + __conda_reactivate + ;; + *) + __conda_exe "$@" + ;; + esac +} + +if [ -z "${CONDA_SHLVL+x}" ]; then + \export CONDA_SHLVL=0 + # In dev-mode CONDA_EXE is python.exe and on Windows + # it is in a different relative location to condabin. + if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then + PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}" + else + PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}" + fi + \export PATH + + # We'\''re not allowing PS1 to be unbound. It must at least be set. + # However, we'\''re not exporting it, which can cause problems when starting a second shell + # via a first shell (i.e. starting zsh from bash). + if [ -z "${PS1+x}" ]; then + PS1= + fi +fi + +conda activate base' ++++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda ++++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda ++++ export _CE_M= ++++ _CE_M= ++++ export _CE_CONDA= ++++ _CE_CONDA= ++++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ '[' -z x ']' ++++ conda activate base ++++ local cmd=activate ++++ case "$cmd" in ++++ __conda_activate activate base ++++ '[' -n '' ']' ++++ local ask_conda +++++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++++ __conda_exe shell.posix activate base +++++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate base ++++ ask_conda='PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_SHLVL='\''6'\'' +export CONDA_DEFAULT_ENV='\''base'\'' +export CONDA_PROMPT_MODIFIER='\''(base) '\'' +export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' ++++ eval 'PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_SHLVL='\''6'\'' +export CONDA_DEFAULT_ENV='\''base'\'' +export CONDA_PROMPT_MODIFIER='\''(base) '\'' +export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' +++++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++++ export CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0 +++++ CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0 +++++ export CONDA_SHLVL=6 +++++ CONDA_SHLVL=6 +++++ export CONDA_DEFAULT_ENV=base +++++ CONDA_DEFAULT_ENV=base +++++ export 'CONDA_PROMPT_MODIFIER=(base) ' +++++ CONDA_PROMPT_MODIFIER='(base) ' +++++ export CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev +++++ CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev +++++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++++ export _CE_M= +++++ _CE_M= +++++ export _CE_CONDA= +++++ _CE_CONDA= +++++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python +++++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ __conda_hashr ++++ '[' -n '' ']' ++++ '[' -n '' ']' ++++ hash -r +++ unset __conda_setup ++ conda activate schemist-dev ++ local cmd=activate ++ case "$cmd" in ++ __conda_activate activate schemist-dev ++ '[' -n '' ']' ++ local ask_conda +++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++ __conda_exe shell.posix activate schemist-dev +++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate schemist-dev ++ ask_conda='PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_SHLVL='\''7'\'' +export CONDA_DEFAULT_ENV='\''schemist-dev'\'' +export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\'' +export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' ++ eval 'PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_SHLVL='\''7'\'' +export CONDA_DEFAULT_ENV='\''schemist-dev'\'' +export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\'' +export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' +++ PS1='(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++ export CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev +++ CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev +++ export CONDA_SHLVL=7 +++ CONDA_SHLVL=7 +++ export CONDA_DEFAULT_ENV=schemist-dev +++ CONDA_DEFAULT_ENV=schemist-dev +++ export 'CONDA_PROMPT_MODIFIER=(schemist-dev) ' +++ CONDA_PROMPT_MODIFIER='(schemist-dev) ' +++ export CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0 +++ CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0 +++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++ export _CE_M= +++ _CE_M= +++ export _CE_CONDA= +++ _CE_CONDA= +++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python +++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++ __conda_hashr ++ '[' -n '' ']' ++ '[' -n '' ']' ++ hash -r ++ CHUNK_HEAD_FILE=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz ++ INPUT=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/train/cyc-pep-6-12mer-70M_09.csv ++ COLUMN=cysteine_to_N_cyclization ++ PREFIX=cyclic_ ++ AWK='1 { print $8, $1, $2, $10, $3 }' ++ '[' -z cysteine_to_N_cyclization ']' ++ '[' -z cyclic_ ']' ++ '[' -z '1 { print $8, $1, $2, $10, $3 }' ']' ++ cat /dev/fd/63 /nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/train/cyc-pep-6-12mer-70M_09.csv ++ awk -F, -v OFS=, '1 { print $8, $1, $2, $10, $3 }' +++ zcat /nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz ++ gzip --best ++ schemist convert -f csv --column cysteine_to_N_cyclization --to id inchikey scaffold mwt clogp tpsa --prefix cyclic_ --options prefix=SCB- +++ head -n1 +++ tr ' ' , +🚀 Converting between string representations with the following parameters: + subcommand: convert + output: <_io.TextIOWrapper name='' mode='w' encoding='utf-8'> + format: csv + input: <_io.TextIOWrapper name='' mode='r' encoding='utf-8'> + representation: SMILES + column: cysteine_to_N_cyclization + prefix: cyclic_ + to: ['id', 'inchikey', 'scaffold', 'mwt', 'clogp', 'tpsa'] + options: ['prefix=SCB-'] + func: + 0it [00:00, ?it/s] 1it [00:12, 12.07s/it] 2it [00:23, 11.88s/it] 3it [00:35, 11.80s/it] 4it [00:47, 11.73s/it] 5it [00:58, 11.69s/it] 6it 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11.57s/it] 958it [3:05:07, 11.59s/it] 959it [3:05:18, 11.55s/it] 960it [3:05:30, 11.55s/it] 961it [3:05:41, 11.55s/it] 962it [3:05:53, 11.57s/it] 963it [3:06:05, 11.60s/it] 964it [3:06:16, 11.60s/it] 965it [3:06:28, 11.59s/it] 966it [3:06:39, 11.59s/it] 967it [3:06:51, 11.61s/it] 968it [3:07:03, 11.59s/it] 969it [3:07:14, 11.59s/it] 970it [3:07:26, 11.60s/it] 971it [3:07:37, 11.60s/it] 972it [3:07:49, 11.58s/it] 973it [3:08:00, 11.58s/it] 974it [3:08:12, 11.57s/it] 975it [3:08:24, 11.58s/it] 976it [3:08:35, 11.58s/it] 977it [3:08:47, 11.59s/it] 978it [3:08:58, 11.60s/it] 979it [3:09:10, 11.58s/it] 980it [3:09:21, 11.57s/it] 981it [3:09:33, 11.55s/it] 982it [3:09:45, 11.58s/it] 983it [3:09:56, 11.61s/it] 984it [3:10:08, 11.63s/it] 985it [3:10:20, 11.64s/it] 986it [3:10:31, 11.62s/it] 987it [3:10:43, 11.60s/it] 988it [3:10:54, 11.60s/it] 989it [3:11:06, 11.60s/it] 990it [3:11:18, 11.59s/it] 991it [3:11:29, 11.61s/it] 992it [3:11:41, 11.61s/it] 993it [3:11:52, 11.59s/it] 994it [3:12:04, 11.57s/it] 995it [3:12:16, 11.59s/it] 996it [3:12:27, 11.60s/it] 997it [3:12:39, 11.58s/it] 998it [3:12:50, 11.60s/it] 999it [3:13:02, 11.59s/it] 1000it [3:13:13, 11.59s/it] 1000it [3:13:14, 11.59s/it] +Error counts: + cyclic_id: 0 + cyclic_inchikey: 0 + cyclic_scaffold: 0 + cyclic_mwt: 0 + cyclic_clogp: 0 + cyclic_tpsa: 0 +⏰ Completed process in 3:13:37.264983 ++ rm /nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/train/cyc-pep-6-12mer-70M_09.csv diff --git a/train/cyc-pep-6-12mer-70M_10.csv.gz b/train/cyc-pep-6-12mer-70M_10.csv.gz index 5ef0b5375b8050deeea8dc4a36aed091c05dc622..682d4633188d4b533def07f3bc4a1c413e2a3f34 100644 --- a/train/cyc-pep-6-12mer-70M_10.csv.gz +++ b/train/cyc-pep-6-12mer-70M_10.csv.gz @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:fd4424cf71a1c2a569f3777329ede153e6af66307e226c17d2f1e4c471929953 -size 61925397 +oid sha256:4f7a2f45c864c3f48009e5ffa565a2ca9d8ff6ab6723553e3a6c9d7bb59cfa9f +size 117603124 diff --git a/train/cyc-pep-6-12mer-70M_10.log b/train/cyc-pep-6-12mer-70M_10.log new file mode 100644 index 0000000000000000000000000000000000000000..90c1aff72a3408da1640abf7d74b30b3a30ed76f --- /dev/null +++ b/train/cyc-pep-6-12mer-70M_10.log @@ -0,0 +1,337 @@ ++ module purge ++ '[' -z '' ']' ++ case "$-" in ++ __lmod_sh_dbg=x ++ '[' -n x ']' ++ set +x +Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output +Shell debugging restarted ++ unset __lmod_sh_dbg ++ return 0 ++ module load Anaconda3/2023.03 ++ '[' -z '' ']' ++ case "$-" in ++ __lmod_sh_dbg=x ++ '[' -n x ']' ++ set +x +Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output +Shell debugging restarted ++ unset __lmod_sh_dbg ++ return 0 ++ source /camp/home/johnsoe/.bashrc +++ '[' '' = yes ']' +++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' ++++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.bash hook +++ __conda_setup='export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'' + +# Copyright (C) 2012 Anaconda, Inc +# SPDX-License-Identifier: BSD-3-Clause +__conda_exe() ( + "$CONDA_EXE" $_CE_M $_CE_CONDA "$@" +) + +__conda_hashr() { + if [ -n "${ZSH_VERSION:+x}" ]; then + \rehash + elif [ -n "${POSH_VERSION:+x}" ]; then + : # pass + else + \hash -r + fi +} + +__conda_activate() { + if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then + # Handle transition from shell activated with conda <= 4.3 to a subsequent activation + # after conda updated to >= 4.4. See issue #6173. + PS1="$CONDA_PS1_BACKUP" + \unset CONDA_PS1_BACKUP + fi + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return + \eval "$ask_conda" + __conda_hashr +} + +__conda_reactivate() { + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return + \eval "$ask_conda" + __conda_hashr +} + +conda() { + \local cmd="${1-__missing__}" + case "$cmd" in + activate|deactivate) + __conda_activate "$@" + ;; + install|update|upgrade|remove|uninstall) + __conda_exe "$@" || \return + __conda_reactivate + ;; + *) + __conda_exe "$@" + ;; + esac +} + +if [ -z "${CONDA_SHLVL+x}" ]; then + \export CONDA_SHLVL=0 + # In dev-mode CONDA_EXE is python.exe and on Windows + # it is in a different relative location to condabin. + if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then + PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}" + else + PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}" + fi + \export PATH + + # We'\''re not allowing PS1 to be unbound. It must at least be set. + # However, we'\''re not exporting it, which can cause problems when starting a second shell + # via a first shell (i.e. starting zsh from bash). + if [ -z "${PS1+x}" ]; then + PS1= + fi +fi + +conda activate base' +++ '[' 0 -eq 0 ']' +++ eval 'export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'' + +# Copyright (C) 2012 Anaconda, Inc +# SPDX-License-Identifier: BSD-3-Clause +__conda_exe() ( + "$CONDA_EXE" $_CE_M $_CE_CONDA "$@" +) + +__conda_hashr() { + if [ -n "${ZSH_VERSION:+x}" ]; then + \rehash + elif [ -n "${POSH_VERSION:+x}" ]; then + : # pass + else + \hash -r + fi +} + +__conda_activate() { + if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then + # Handle transition from shell activated with conda <= 4.3 to a subsequent activation + # after conda updated to >= 4.4. See issue #6173. + PS1="$CONDA_PS1_BACKUP" + \unset CONDA_PS1_BACKUP + fi + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return + \eval "$ask_conda" + __conda_hashr +} + +__conda_reactivate() { + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return + \eval "$ask_conda" + __conda_hashr +} + +conda() { + \local cmd="${1-__missing__}" + case "$cmd" in + activate|deactivate) + __conda_activate "$@" + ;; + install|update|upgrade|remove|uninstall) + __conda_exe "$@" || \return + __conda_reactivate + ;; + *) + __conda_exe "$@" + ;; + esac +} + +if [ -z "${CONDA_SHLVL+x}" ]; then + \export CONDA_SHLVL=0 + # In dev-mode CONDA_EXE is python.exe and on Windows + # it is in a different relative location to condabin. + if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then + PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}" + else + PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}" + fi + \export PATH + + # We'\''re not allowing PS1 to be unbound. It must at least be set. + # However, we'\''re not exporting it, which can cause problems when starting a second shell + # via a first shell (i.e. starting zsh from bash). + if [ -z "${PS1+x}" ]; then + PS1= + fi +fi + +conda activate base' ++++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda ++++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda ++++ export _CE_M= ++++ _CE_M= ++++ export _CE_CONDA= ++++ _CE_CONDA= ++++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ '[' -z x ']' ++++ conda activate base ++++ local cmd=activate ++++ case "$cmd" in ++++ __conda_activate activate base ++++ '[' -n '' ']' ++++ local ask_conda +++++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++++ __conda_exe shell.posix activate base +++++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate base ++++ ask_conda='PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_SHLVL='\''6'\'' +export CONDA_DEFAULT_ENV='\''base'\'' +export CONDA_PROMPT_MODIFIER='\''(base) '\'' +export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' ++++ eval 'PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_SHLVL='\''6'\'' +export CONDA_DEFAULT_ENV='\''base'\'' +export CONDA_PROMPT_MODIFIER='\''(base) '\'' +export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' +++++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++++ export CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0 +++++ CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0 +++++ export CONDA_SHLVL=6 +++++ CONDA_SHLVL=6 +++++ export CONDA_DEFAULT_ENV=base +++++ CONDA_DEFAULT_ENV=base +++++ export 'CONDA_PROMPT_MODIFIER=(base) ' +++++ CONDA_PROMPT_MODIFIER='(base) ' +++++ export CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev +++++ CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev +++++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++++ export _CE_M= +++++ _CE_M= +++++ export _CE_CONDA= +++++ _CE_CONDA= +++++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python +++++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ __conda_hashr ++++ '[' -n '' ']' ++++ '[' -n '' ']' ++++ hash -r +++ unset __conda_setup ++ conda activate schemist-dev ++ local cmd=activate ++ case "$cmd" in ++ __conda_activate activate schemist-dev ++ '[' -n '' ']' ++ local ask_conda +++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++ __conda_exe shell.posix activate schemist-dev +++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate schemist-dev ++ ask_conda='PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_SHLVL='\''7'\'' +export CONDA_DEFAULT_ENV='\''schemist-dev'\'' +export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\'' +export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' ++ eval 'PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_SHLVL='\''7'\'' +export CONDA_DEFAULT_ENV='\''schemist-dev'\'' +export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\'' +export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' +++ PS1='(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++ export CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev +++ CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev +++ export CONDA_SHLVL=7 +++ CONDA_SHLVL=7 +++ export CONDA_DEFAULT_ENV=schemist-dev +++ CONDA_DEFAULT_ENV=schemist-dev +++ export 'CONDA_PROMPT_MODIFIER=(schemist-dev) ' +++ CONDA_PROMPT_MODIFIER='(schemist-dev) ' +++ export CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0 +++ CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0 +++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++ export _CE_M= +++ _CE_M= +++ export _CE_CONDA= +++ _CE_CONDA= +++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python +++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++ __conda_hashr ++ '[' -n '' ']' ++ '[' -n '' ']' ++ hash -r ++ CHUNK_HEAD_FILE=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz ++ INPUT=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/train/cyc-pep-6-12mer-70M_10.csv ++ COLUMN=cysteine_to_N_cyclization ++ PREFIX=cyclic_ ++ AWK='1 { print $8, $1, $2, $10, $3 }' ++ '[' -z cysteine_to_N_cyclization ']' ++ '[' -z cyclic_ ']' ++ '[' -z '1 { print $8, $1, $2, $10, $3 }' ']' ++ cat /dev/fd/63 /nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/train/cyc-pep-6-12mer-70M_10.csv ++ awk -F, -v OFS=, '1 { print $8, $1, $2, $10, $3 }' +++ zcat /nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz ++ schemist convert -f csv --column cysteine_to_N_cyclization --to id inchikey scaffold mwt clogp tpsa --prefix cyclic_ --options prefix=SCB- +++ head -n1 ++ gzip --best +++ tr ' ' , +🚀 Converting between string representations with the following parameters: + subcommand: convert + output: <_io.TextIOWrapper name='' mode='w' encoding='utf-8'> + format: csv + input: <_io.TextIOWrapper name='' mode='r' encoding='utf-8'> + representation: SMILES + column: cysteine_to_N_cyclization + prefix: cyclic_ + to: ['id', 'inchikey', 'scaffold', 'mwt', 'clogp', 'tpsa'] + options: ['prefix=SCB-'] + func: + 0it [00:00, ?it/s] 1it [00:11, 11.72s/it] 2it [00:23, 11.68s/it] 3it [00:35, 11.70s/it] 4it [00:46, 11.75s/it] 5it [00:58, 11.73s/it] 6it [01:10, 11.74s/it] 7it [01:22, 11.76s/it] 8it [01:33, 11.73s/it] 9it [01:45, 11.72s/it] 10it [01:57, 11.72s/it] 11it [02:09, 11.75s/it] 12it [02:20, 11.73s/it] 13it [02:32, 11.74s/it] 14it [02:44, 11.72s/it] 15it [02:55, 11.71s/it] 16it [03:07, 11.71s/it] 17it [03:19, 11.68s/it] 18it [03:30, 11.67s/it] 19it [03:42, 11.70s/it] 20it [03:54, 11.71s/it] 21it [04:06, 11.72s/it] 22it [04:17, 11.74s/it] 23it [04:29, 11.73s/it] 24it [04:41, 11.72s/it] 25it [04:52, 11.70s/it] 26it [05:04, 11.70s/it] 27it [05:16, 11.69s/it] 28it [05:27, 11.67s/it] 29it [05:39, 11.68s/it] 30it [05:51, 11.70s/it] 31it [06:03, 11.71s/it] 32it [06:14, 11.72s/it] 33it [06:26, 11.68s/it] 34it [06:37, 11.63s/it] 35it [06:49, 11.63s/it] 36it [07:01, 11.64s/it] 37it [07:12, 11.65s/it] 38it [07:24, 11.64s/it] 39it [07:36, 11.64s/it] 40it [07:47, 11.65s/it] 41it [07:59, 11.66s/it] 42it [08:11, 11.67s/it] 43it [08:22, 11.64s/it] 44it [08:34, 11.63s/it] 45it [08:46, 11.64s/it] 46it [08:57, 11.60s/it] 47it [09:09, 11.61s/it] 48it [09:20, 11.60s/it] 49it [09:32, 11.61s/it] 50it [09:44, 11.63s/it] 51it [09:55, 11.63s/it] 52it [10:07, 11.65s/it] 53it [10:18, 11.63s/it] 54it [10:30, 11.62s/it] 55it [10:42, 11.62s/it] 56it [10:53, 11.61s/it] 57it [11:05, 11.66s/it] 58it [11:17, 11.66s/it] 59it [11:28, 11.67s/it] 60it [11:40, 11.67s/it] 61it [11:52, 11.65s/it] 62it [12:03, 11.65s/it] 63it [12:15, 11.65s/it] 64it [12:27, 11.66s/it] 65it [12:38, 11.67s/it] 66it [12:50, 11.68s/it] 67it [13:02, 11.68s/it] 68it [13:13, 11.68s/it] 69it [13:25, 11.64s/it] 70it [13:37, 11.64s/it] 71it [13:48, 11.62s/it] 72it [14:00, 11.61s/it] 73it [14:11, 11.65s/it] 74it [14:23, 11.63s/it] 75it [14:35, 11.63s/it] 76it [14:46, 11.64s/it] 77it [14:58, 11.67s/it] 78it [15:10, 11.67s/it] 79it [15:21, 11.64s/it] 80it [15:33, 11.65s/it] 81it [15:45, 11.67s/it] 82it [15:56, 11.65s/it] 83it [16:08, 11.67s/it] 84it [16:20, 11.65s/it] 85it [16:31, 11.64s/it] 86it [16:43, 11.66s/it] 87it [16:55, 11.65s/it] 88it [17:06, 11.69s/it] 89it [17:18, 11.70s/it] 90it [17:30, 11.71s/it] 91it [17:42, 11.70s/it] 92it [17:53, 11.70s/it] 93it [18:05, 11.70s/it] 94it [18:17, 11.73s/it] 95it [18:28, 11.72s/it] 96it [18:40, 11.72s/it] 97it [18:52, 11.71s/it] 98it [19:04, 11.70s/it] 99it [19:15, 11.69s/it] 100it [19:27, 11.69s/it] 101it [19:39, 11.70s/it] 102it [19:50, 11.67s/it] 103it [20:02, 11.66s/it] 104it [20:14, 11.69s/it] 105it [20:25, 11.71s/it] 106it [20:37, 11.71s/it] 107it [20:49, 11.70s/it] 108it [21:00, 11.70s/it] 109it [21:12, 11.71s/it] 110it [21:24, 11.66s/it] 111it [21:35, 11.66s/it] 112it [21:47, 11.65s/it] 113it [21:59, 11.64s/it] 114it [22:10, 11.65s/it] 115it [22:22, 11.64s/it] 116it [22:34, 11.65s/it] 117it [22:45, 11.69s/it] 118it [22:57, 11.70s/it] 119it [23:09, 11.70s/it] 120it [23:20, 11.68s/it] 121it [23:32, 11.70s/it] 122it [23:44, 11.70s/it] 123it [23:56, 11.70s/it] 124it [24:07, 11.71s/it] 125it [24:19, 11.70s/it] 126it [24:31, 11.70s/it] 127it [24:42, 11.70s/it] 128it [24:54, 11.69s/it] 129it [25:06, 11.70s/it] 130it [25:17, 11.69s/it] 131it [25:29, 11.68s/it] 132it [25:41, 11.69s/it] 133it [25:52, 11.69s/it] 134it [26:04, 11.68s/it] 135it [26:16, 11.68s/it] 136it [26:28, 11.70s/it] 137it [26:39, 11.70s/it] 138it [26:51, 11.70s/it] 139it [27:03, 11.68s/it] 140it [27:14, 11.68s/it] 141it [27:26, 11.69s/it] 142it [27:38, 11.71s/it] 143it [27:49, 11.72s/it] 144it [28:01, 11.72s/it] 145it [28:13, 11.71s/it] 146it [28:25, 11.70s/it] 147it [28:36, 11.70s/it] 148it [28:48, 11.67s/it] 149it [29:00, 11.67s/it] 150it [29:11, 11.67s/it] 151it [29:23, 11.64s/it] 152it [29:34, 11.64s/it] 153it [29:46, 11.65s/it] 154it [29:58, 11.65s/it] 155it [30:09, 11.66s/it] 156it [30:21, 11.66s/it] 157it [30:33, 11.67s/it] 158it [30:44, 11.68s/it] 159it [30:56, 11.68s/it] 160it [31:08, 11.69s/it] 161it [31:19, 11.66s/it] 162it [31:31, 11.65s/it] 163it [31:43, 11.65s/it] 164it [31:54, 11.65s/it] 165it [32:06, 11.66s/it] 166it [32:18, 11.68s/it] 167it [32:29, 11.67s/it] 168it [32:41, 11.68s/it] 169it [32:53, 11.66s/it] 170it [33:05, 11.69s/it] 171it [33:16, 11.70s/it] 172it [33:28, 11.67s/it] 173it [33:40, 11.67s/it] 174it [33:51, 11.67s/it] 175it [34:03, 11.65s/it] 176it [34:14, 11.66s/it] 177it [34:26, 11.65s/it] 178it [34:38, 11.67s/it] 179it [34:50, 11.68s/it] 180it [35:01, 11.68s/it] 181it [35:13, 11.69s/it] 182it [35:25, 11.68s/it] 183it [35:36, 11.68s/it] 184it [35:48, 11.69s/it] 185it [36:00, 11.66s/it] 186it [36:11, 11.67s/it] 187it [36:23, 11.70s/it] 188it [36:35, 11.70s/it] 189it [36:46, 11.69s/it] 190it [36:58, 11.69s/it] 191it [37:10, 11.68s/it] 192it [37:21, 11.71s/it] 193it [37:33, 11.68s/it] 194it [37:45, 11.67s/it] 195it [37:56, 11.66s/it] 196it [38:08, 11.68s/it] 197it [38:20, 11.68s/it] 198it [38:31, 11.67s/it] 199it [38:43, 11.69s/it] 200it [38:55, 11.64s/it] 201it [39:06, 11.68s/it] 202it [39:18, 11.67s/it] 203it [39:30, 11.68s/it] 204it [39:42, 11.69s/it] 205it [39:53, 11.71s/it] 206it [40:05, 11.68s/it] 207it [40:17, 11.66s/it] 208it [40:28, 11.67s/it] 209it [40:40, 11.67s/it] 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250it [48:38, 11.70s/it] 251it [48:50, 11.72s/it] 252it [49:01, 11.69s/it] 253it [49:13, 11.69s/it] 254it [49:25, 11.68s/it] 255it [49:36, 11.67s/it] 256it [49:48, 11.66s/it] 257it [50:00, 11.63s/it] 258it [50:11, 11.67s/it] 259it [50:23, 11.66s/it] 260it [50:35, 11.66s/it] 261it [50:46, 11.67s/it] 262it [50:58, 11.70s/it] 263it [51:10, 11.69s/it] 264it [51:21, 11.67s/it] 265it [51:33, 11.64s/it] 266it [51:45, 11.66s/it] 267it [51:56, 11.64s/it] 268it [52:08, 11.65s/it] 269it [52:20, 11.64s/it] 270it [52:31, 11.65s/it] 271it [52:43, 11.67s/it] 272it [52:55, 11.66s/it] 273it [53:06, 11.65s/it] 274it [53:18, 11.68s/it] 275it [53:30, 11.66s/it] 276it [53:41, 11.67s/it] 277it [53:53, 11.66s/it] 278it [54:05, 11.65s/it] 279it [54:16, 11.66s/it] 280it [54:28, 11.64s/it] 281it [54:40, 11.65s/it] 282it [54:51, 11.66s/it] 283it [55:03, 11.64s/it] 284it [55:15, 11.67s/it] 285it [55:26, 11.68s/it] 286it [55:38, 11.66s/it] 287it [55:50, 11.67s/it] 288it [56:01, 11.67s/it] 289it [56:13, 11.66s/it] 290it [56:24, 11.65s/it] 291it [56:36, 11.65s/it] 292it [56:48, 11.66s/it] 293it [57:00, 11.68s/it] 294it [57:11, 11.69s/it] 295it [57:23, 11.69s/it] 296it [57:35, 11.67s/it] 297it [57:46, 11.65s/it] 298it [57:58, 11.66s/it] 299it [58:10, 11.66s/it] 300it [58:21, 11.69s/it] 301it [58:33, 11.70s/it] 302it [58:45, 11.70s/it] 303it [58:56, 11.68s/it] 304it [59:08, 11.65s/it] 305it [59:20, 11.67s/it] 306it [59:31, 11.68s/it] 307it [59:43, 11.68s/it] 308it [59:55, 11.69s/it] 309it [1:00:06, 11.68s/it] 310it [1:00:18, 11.67s/it] 311it [1:00:30, 11.68s/it] 312it [1:00:41, 11.68s/it] 313it [1:00:53, 11.69s/it] 314it [1:01:05, 11.69s/it] 315it [1:01:16, 11.68s/it] 316it [1:01:28, 11.67s/it] 317it [1:01:40, 11.69s/it] 318it [1:01:52, 11.71s/it] 319it [1:02:03, 11.69s/it] 320it [1:02:15, 11.66s/it] 321it [1:02:27, 11.68s/it] 322it [1:02:38, 11.69s/it] 323it [1:02:50, 11.69s/it] 324it [1:03:02, 11.69s/it] 325it [1:03:13, 11.67s/it] 326it [1:03:25, 11.65s/it] 327it [1:03:37, 11.65s/it] 328it 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[3:06:27, 11.98s/it] 958it [3:06:39, 11.97s/it] 959it [3:06:51, 12.00s/it] 960it [3:07:03, 12.03s/it] 961it [3:07:15, 12.08s/it] 962it [3:07:27, 12.00s/it] 963it [3:07:39, 12.00s/it] 964it [3:07:51, 11.98s/it] 965it [3:08:03, 12.01s/it] 966it [3:08:15, 12.08s/it] 967it [3:08:27, 12.07s/it] 968it [3:08:39, 11.98s/it] 969it [3:08:51, 11.95s/it] 970it [3:09:03, 11.99s/it] 971it [3:09:15, 12.06s/it] 972it [3:09:27, 12.06s/it] 973it [3:09:39, 11.98s/it] 974it [3:09:51, 11.94s/it] 975it [3:10:03, 11.94s/it] 976it [3:10:15, 12.04s/it] 977it [3:10:27, 12.07s/it] 978it [3:10:39, 12.02s/it] 979it [3:10:51, 11.95s/it] 980it [3:11:03, 11.93s/it] 981it [3:11:15, 11.98s/it] 982it [3:11:27, 12.03s/it] 983it [3:11:39, 12.01s/it] 984it [3:11:51, 12.00s/it] 985it [3:12:03, 11.96s/it] 986it [3:12:15, 11.96s/it] 987it [3:12:27, 12.02s/it] 988it [3:12:39, 12.05s/it] 989it [3:12:51, 12.05s/it] 990it [3:13:03, 12.05s/it] 991it [3:13:15, 12.02s/it] 992it [3:13:27, 12.03s/it] 993it [3:13:39, 12.05s/it] 994it [3:13:51, 12.01s/it] 995it [3:14:03, 12.01s/it] 996it [3:14:15, 12.01s/it] 997it [3:14:27, 12.03s/it] 998it [3:14:39, 12.04s/it] 999it [3:14:51, 12.02s/it] 1000it [3:15:03, 12.00s/it] 1000it [3:15:03, 11.70s/it] +Error counts: + cyclic_id: 0 + cyclic_inchikey: 0 + cyclic_scaffold: 0 + cyclic_mwt: 0 + cyclic_clogp: 0 + cyclic_tpsa: 0 +⏰ Completed process in 3:15:26.501328 ++ rm /nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/train/cyc-pep-6-12mer-70M_10.csv diff --git a/train/cyc-pep-6-12mer-70M_11.csv.gz b/train/cyc-pep-6-12mer-70M_11.csv.gz index 5daf50dcd0b3f129f2f724d47f29b3dec927db77..71df478599c3e7957c0ca25a84e3926d8ff868b0 100644 --- a/train/cyc-pep-6-12mer-70M_11.csv.gz +++ b/train/cyc-pep-6-12mer-70M_11.csv.gz @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:753475102dd5334b0fe1e580afc1660e73674dad4d5240e142337b4814844fcf -size 61923784 +oid sha256:c7107dbca4e33cce6b922a562a44ebb3460b925265e7f82613935155e1be4743 +size 117607437 diff --git a/train/cyc-pep-6-12mer-70M_11.log b/train/cyc-pep-6-12mer-70M_11.log new file mode 100644 index 0000000000000000000000000000000000000000..cff4068732d63d2ab864d875b407a2d38cb95043 --- /dev/null +++ b/train/cyc-pep-6-12mer-70M_11.log @@ -0,0 +1,337 @@ ++ module purge ++ '[' -z '' ']' ++ case "$-" in ++ __lmod_sh_dbg=x ++ '[' -n x ']' ++ set +x +Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output +Shell debugging restarted ++ unset __lmod_sh_dbg ++ return 0 ++ module load Anaconda3/2023.03 ++ '[' -z '' ']' ++ case "$-" in ++ __lmod_sh_dbg=x ++ '[' -n x ']' ++ set +x +Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output +Shell debugging restarted ++ unset __lmod_sh_dbg ++ return 0 ++ source /camp/home/johnsoe/.bashrc +++ '[' '' = yes ']' +++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' ++++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.bash hook +++ __conda_setup='export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'' + +# Copyright (C) 2012 Anaconda, Inc +# SPDX-License-Identifier: BSD-3-Clause +__conda_exe() ( + "$CONDA_EXE" $_CE_M $_CE_CONDA "$@" +) + +__conda_hashr() { + if [ -n "${ZSH_VERSION:+x}" ]; then + \rehash + elif [ -n "${POSH_VERSION:+x}" ]; then + : # pass + else + \hash -r + fi +} + +__conda_activate() { + if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then + # Handle transition from shell activated with conda <= 4.3 to a subsequent activation + # after conda updated to >= 4.4. See issue #6173. + PS1="$CONDA_PS1_BACKUP" + \unset CONDA_PS1_BACKUP + fi + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return + \eval "$ask_conda" + __conda_hashr +} + +__conda_reactivate() { + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return + \eval "$ask_conda" + __conda_hashr +} + +conda() { + \local cmd="${1-__missing__}" + case "$cmd" in + activate|deactivate) + __conda_activate "$@" + ;; + install|update|upgrade|remove|uninstall) + __conda_exe "$@" || \return + __conda_reactivate + ;; + *) + __conda_exe "$@" + ;; + esac +} + +if [ -z "${CONDA_SHLVL+x}" ]; then + \export CONDA_SHLVL=0 + # In dev-mode CONDA_EXE is python.exe and on Windows + # it is in a different relative location to condabin. + if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then + PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}" + else + PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}" + fi + \export PATH + + # We'\''re not allowing PS1 to be unbound. It must at least be set. + # However, we'\''re not exporting it, which can cause problems when starting a second shell + # via a first shell (i.e. starting zsh from bash). + if [ -z "${PS1+x}" ]; then + PS1= + fi +fi + +conda activate base' +++ '[' 0 -eq 0 ']' +++ eval 'export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'' + +# Copyright (C) 2012 Anaconda, Inc +# SPDX-License-Identifier: BSD-3-Clause +__conda_exe() ( + "$CONDA_EXE" $_CE_M $_CE_CONDA "$@" +) + +__conda_hashr() { + if [ -n "${ZSH_VERSION:+x}" ]; then + \rehash + elif [ -n "${POSH_VERSION:+x}" ]; then + : # pass + else + \hash -r + fi +} + +__conda_activate() { + if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then + # Handle transition from shell activated with conda <= 4.3 to a subsequent activation + # after conda updated to >= 4.4. See issue #6173. + PS1="$CONDA_PS1_BACKUP" + \unset CONDA_PS1_BACKUP + fi + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return + \eval "$ask_conda" + __conda_hashr +} + +__conda_reactivate() { + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return + \eval "$ask_conda" + __conda_hashr +} + +conda() { + \local cmd="${1-__missing__}" + case "$cmd" in + activate|deactivate) + __conda_activate "$@" + ;; + install|update|upgrade|remove|uninstall) + __conda_exe "$@" || \return + __conda_reactivate + ;; + *) + __conda_exe "$@" + ;; + esac +} + +if [ -z "${CONDA_SHLVL+x}" ]; then + \export CONDA_SHLVL=0 + # In dev-mode CONDA_EXE is python.exe and on Windows + # it is in a different relative location to condabin. + if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then + PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}" + else + PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}" + fi + \export PATH + + # We'\''re not allowing PS1 to be unbound. It must at least be set. + # However, we'\''re not exporting it, which can cause problems when starting a second shell + # via a first shell (i.e. starting zsh from bash). + if [ -z "${PS1+x}" ]; then + PS1= + fi +fi + +conda activate base' ++++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda ++++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda ++++ export _CE_M= ++++ _CE_M= ++++ export _CE_CONDA= ++++ _CE_CONDA= ++++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ '[' -z x ']' ++++ conda activate base ++++ local cmd=activate ++++ case "$cmd" in ++++ __conda_activate activate base ++++ '[' -n '' ']' ++++ local ask_conda +++++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++++ __conda_exe shell.posix activate base +++++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate base ++++ ask_conda='PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_SHLVL='\''6'\'' +export CONDA_DEFAULT_ENV='\''base'\'' +export CONDA_PROMPT_MODIFIER='\''(base) '\'' +export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' ++++ eval 'PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_SHLVL='\''6'\'' +export CONDA_DEFAULT_ENV='\''base'\'' +export CONDA_PROMPT_MODIFIER='\''(base) '\'' +export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' +++++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++++ export CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0 +++++ CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0 +++++ export CONDA_SHLVL=6 +++++ CONDA_SHLVL=6 +++++ export CONDA_DEFAULT_ENV=base +++++ CONDA_DEFAULT_ENV=base +++++ export 'CONDA_PROMPT_MODIFIER=(base) ' +++++ CONDA_PROMPT_MODIFIER='(base) ' +++++ export CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev +++++ CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev +++++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++++ export _CE_M= +++++ _CE_M= +++++ export _CE_CONDA= +++++ _CE_CONDA= +++++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python +++++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ __conda_hashr ++++ '[' -n '' ']' ++++ '[' -n '' ']' ++++ hash -r +++ unset __conda_setup ++ conda activate schemist-dev ++ local cmd=activate ++ case "$cmd" in ++ __conda_activate activate schemist-dev ++ '[' -n '' ']' ++ local ask_conda +++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++ __conda_exe shell.posix activate schemist-dev +++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate schemist-dev ++ ask_conda='PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_SHLVL='\''7'\'' +export CONDA_DEFAULT_ENV='\''schemist-dev'\'' +export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\'' +export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' ++ eval 'PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_SHLVL='\''7'\'' +export CONDA_DEFAULT_ENV='\''schemist-dev'\'' +export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\'' +export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' +++ PS1='(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++ export CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev +++ CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev +++ export CONDA_SHLVL=7 +++ CONDA_SHLVL=7 +++ export CONDA_DEFAULT_ENV=schemist-dev +++ CONDA_DEFAULT_ENV=schemist-dev +++ export 'CONDA_PROMPT_MODIFIER=(schemist-dev) ' +++ CONDA_PROMPT_MODIFIER='(schemist-dev) ' +++ export CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0 +++ CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0 +++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++ export _CE_M= +++ _CE_M= +++ export _CE_CONDA= +++ _CE_CONDA= +++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python +++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++ __conda_hashr ++ '[' -n '' ']' ++ '[' -n '' ']' ++ hash -r ++ CHUNK_HEAD_FILE=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz ++ INPUT=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/train/cyc-pep-6-12mer-70M_11.csv ++ COLUMN=cysteine_to_N_cyclization ++ PREFIX=cyclic_ ++ AWK='1 { print $8, $1, $2, $10, $3 }' ++ '[' -z cysteine_to_N_cyclization ']' ++ '[' -z cyclic_ ']' ++ '[' -z '1 { print $8, $1, $2, $10, $3 }' ']' ++ cat /dev/fd/63 /nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/train/cyc-pep-6-12mer-70M_11.csv ++ schemist convert -f csv --column cysteine_to_N_cyclization --to id inchikey scaffold mwt clogp tpsa --prefix cyclic_ --options prefix=SCB- ++ gzip --best ++ awk -F, -v OFS=, '1 { print $8, $1, $2, $10, $3 }' +++ zcat /nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz +++ tr ' ' , +++ head -n1 +🚀 Converting between string representations with the following parameters: + subcommand: convert + output: <_io.TextIOWrapper name='' mode='w' encoding='utf-8'> + format: csv + input: <_io.TextIOWrapper name='' mode='r' encoding='utf-8'> + representation: SMILES + column: cysteine_to_N_cyclization + prefix: cyclic_ + to: ['id', 'inchikey', 'scaffold', 'mwt', 'clogp', 'tpsa'] + options: ['prefix=SCB-'] + func: + 0it [00:00, ?it/s] 1it [00:11, 11.85s/it] 2it [00:23, 11.72s/it] 3it [00:35, 11.78s/it] 4it [00:47, 11.79s/it] 5it [00:59, 11.84s/it] 6it 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[3:06:59, 11.84s/it] 958it [3:07:11, 11.84s/it] 959it [3:07:23, 11.83s/it] 960it [3:07:35, 11.83s/it] 961it [3:07:47, 11.82s/it] 962it [3:07:58, 11.82s/it] 963it [3:08:10, 11.82s/it] 964it [3:08:22, 11.86s/it] 965it [3:08:34, 11.86s/it] 966it [3:08:46, 11.89s/it] 967it [3:08:58, 11.86s/it] 968it [3:09:10, 11.85s/it] 969it [3:09:22, 11.87s/it] 970it [3:09:33, 11.88s/it] 971it [3:09:45, 11.90s/it] 972it [3:09:57, 11.89s/it] 973it [3:10:09, 11.87s/it] 974it [3:10:21, 11.89s/it] 975it [3:10:33, 11.88s/it] 976it [3:10:45, 11.88s/it] 977it [3:10:57, 11.90s/it] 978it [3:11:09, 11.89s/it] 979it [3:11:21, 11.90s/it] 980it [3:11:32, 11.90s/it] 981it [3:11:44, 11.88s/it] 982it [3:11:56, 11.90s/it] 983it [3:12:08, 11.90s/it] 984it [3:12:20, 11.88s/it] 985it [3:12:32, 11.92s/it] 986it [3:12:44, 11.90s/it] 987it [3:12:56, 11.90s/it] 988it [3:13:08, 11.90s/it] 989it [3:13:19, 11.87s/it] 990it [3:13:31, 11.87s/it] 991it [3:13:43, 11.84s/it] 992it [3:13:55, 11.84s/it] 993it [3:14:07, 11.85s/it] 994it [3:14:19, 11.86s/it] 995it [3:14:30, 11.84s/it] 996it [3:14:42, 11.82s/it] 997it [3:14:54, 11.81s/it] 998it [3:15:06, 11.86s/it] 999it [3:15:18, 11.86s/it] 1000it [3:15:30, 11.84s/it] 1000it [3:15:30, 11.73s/it] +Error counts: + cyclic_id: 0 + cyclic_inchikey: 0 + cyclic_scaffold: 0 + cyclic_mwt: 0 + cyclic_clogp: 0 + cyclic_tpsa: 0 +⏰ Completed process in 3:15:54.052880 ++ rm /nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/train/cyc-pep-6-12mer-70M_11.csv diff --git a/train/cyc-pep-6-12mer-70M_12.csv.gz b/train/cyc-pep-6-12mer-70M_12.csv.gz index 74f531a6f26d77fec2494d93d879cc2c57cfd314..08d236aa9f52cbaa348134b09d2afba6def4e3ff 100644 --- a/train/cyc-pep-6-12mer-70M_12.csv.gz +++ b/train/cyc-pep-6-12mer-70M_12.csv.gz @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:45d8bb6db82c27c8ec14c15ab4a988b0a70c624fd37989574c562b97d72ebeb0 -size 61932256 +oid sha256:c2a6cffc49021aee6ec6fc4c31b6dae8137a34e4375e1e93e7e6bc227e96161f +size 117606141 diff --git a/train/cyc-pep-6-12mer-70M_12.log b/train/cyc-pep-6-12mer-70M_12.log new file mode 100644 index 0000000000000000000000000000000000000000..42d30895fa3e5328be06567eb11af72bd54b2d6f --- /dev/null +++ b/train/cyc-pep-6-12mer-70M_12.log @@ -0,0 +1,337 @@ ++ module purge ++ '[' -z '' ']' ++ case "$-" in ++ __lmod_sh_dbg=x ++ '[' -n x ']' ++ set +x +Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output +Shell debugging restarted ++ unset __lmod_sh_dbg ++ return 0 ++ module load Anaconda3/2023.03 ++ '[' -z '' ']' ++ case "$-" in ++ __lmod_sh_dbg=x ++ '[' -n x ']' ++ set +x +Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output +Shell debugging restarted ++ unset __lmod_sh_dbg ++ return 0 ++ source /camp/home/johnsoe/.bashrc +++ '[' '' = yes ']' +++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' ++++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.bash hook +++ __conda_setup='export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'' + +# Copyright (C) 2012 Anaconda, Inc +# SPDX-License-Identifier: BSD-3-Clause +__conda_exe() ( + "$CONDA_EXE" $_CE_M $_CE_CONDA "$@" +) + +__conda_hashr() { + if [ -n "${ZSH_VERSION:+x}" ]; then + \rehash + elif [ -n "${POSH_VERSION:+x}" ]; then + : # pass + else + \hash -r + fi +} + +__conda_activate() { + if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then + # Handle transition from shell activated with conda <= 4.3 to a subsequent activation + # after conda updated to >= 4.4. See issue #6173. + PS1="$CONDA_PS1_BACKUP" + \unset CONDA_PS1_BACKUP + fi + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return + \eval "$ask_conda" + __conda_hashr +} + +__conda_reactivate() { + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return + \eval "$ask_conda" + __conda_hashr +} + +conda() { + \local cmd="${1-__missing__}" + case "$cmd" in + activate|deactivate) + __conda_activate "$@" + ;; + install|update|upgrade|remove|uninstall) + __conda_exe "$@" || \return + __conda_reactivate + ;; + *) + __conda_exe "$@" + ;; + esac +} + +if [ -z "${CONDA_SHLVL+x}" ]; then + \export CONDA_SHLVL=0 + # In dev-mode CONDA_EXE is python.exe and on Windows + # it is in a different relative location to condabin. + if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then + PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}" + else + PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}" + fi + \export PATH + + # We'\''re not allowing PS1 to be unbound. It must at least be set. + # However, we'\''re not exporting it, which can cause problems when starting a second shell + # via a first shell (i.e. starting zsh from bash). + if [ -z "${PS1+x}" ]; then + PS1= + fi +fi + +conda activate base' +++ '[' 0 -eq 0 ']' +++ eval 'export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'' + +# Copyright (C) 2012 Anaconda, Inc +# SPDX-License-Identifier: BSD-3-Clause +__conda_exe() ( + "$CONDA_EXE" $_CE_M $_CE_CONDA "$@" +) + +__conda_hashr() { + if [ -n "${ZSH_VERSION:+x}" ]; then + \rehash + elif [ -n "${POSH_VERSION:+x}" ]; then + : # pass + else + \hash -r + fi +} + +__conda_activate() { + if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then + # Handle transition from shell activated with conda <= 4.3 to a subsequent activation + # after conda updated to >= 4.4. See issue #6173. + PS1="$CONDA_PS1_BACKUP" + \unset CONDA_PS1_BACKUP + fi + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return + \eval "$ask_conda" + __conda_hashr +} + +__conda_reactivate() { + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return + \eval "$ask_conda" + __conda_hashr +} + +conda() { + \local cmd="${1-__missing__}" + case "$cmd" in + activate|deactivate) + __conda_activate "$@" + ;; + install|update|upgrade|remove|uninstall) + __conda_exe "$@" || \return + __conda_reactivate + ;; + *) + __conda_exe "$@" + ;; + esac +} + +if [ -z "${CONDA_SHLVL+x}" ]; then + \export CONDA_SHLVL=0 + # In dev-mode CONDA_EXE is python.exe and on Windows + # it is in a different relative location to condabin. + if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then + PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}" + else + PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}" + fi + \export PATH + + # We'\''re not allowing PS1 to be unbound. It must at least be set. + # However, we'\''re not exporting it, which can cause problems when starting a second shell + # via a first shell (i.e. starting zsh from bash). + if [ -z "${PS1+x}" ]; then + PS1= + fi +fi + +conda activate base' ++++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda ++++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda ++++ export _CE_M= ++++ _CE_M= ++++ export _CE_CONDA= ++++ _CE_CONDA= ++++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ '[' -z x ']' ++++ conda activate base ++++ local cmd=activate ++++ case "$cmd" in ++++ __conda_activate activate base ++++ '[' -n '' ']' ++++ local ask_conda +++++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++++ __conda_exe shell.posix activate base +++++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate base ++++ ask_conda='PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_SHLVL='\''6'\'' +export CONDA_DEFAULT_ENV='\''base'\'' +export CONDA_PROMPT_MODIFIER='\''(base) '\'' +export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' ++++ eval 'PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_SHLVL='\''6'\'' +export CONDA_DEFAULT_ENV='\''base'\'' +export CONDA_PROMPT_MODIFIER='\''(base) '\'' +export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' +++++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++++ export CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0 +++++ CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0 +++++ export CONDA_SHLVL=6 +++++ CONDA_SHLVL=6 +++++ export CONDA_DEFAULT_ENV=base +++++ CONDA_DEFAULT_ENV=base +++++ export 'CONDA_PROMPT_MODIFIER=(base) ' +++++ CONDA_PROMPT_MODIFIER='(base) ' +++++ export CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev +++++ CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev +++++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++++ export _CE_M= +++++ _CE_M= +++++ export _CE_CONDA= +++++ _CE_CONDA= +++++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python +++++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ __conda_hashr ++++ '[' -n '' ']' ++++ '[' -n '' ']' ++++ hash -r +++ unset __conda_setup ++ conda activate schemist-dev ++ local cmd=activate ++ case "$cmd" in ++ __conda_activate activate schemist-dev ++ '[' -n '' ']' ++ local ask_conda +++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++ __conda_exe shell.posix activate schemist-dev +++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate schemist-dev ++ ask_conda='PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_SHLVL='\''7'\'' +export CONDA_DEFAULT_ENV='\''schemist-dev'\'' +export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\'' +export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' ++ eval 'PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_SHLVL='\''7'\'' +export CONDA_DEFAULT_ENV='\''schemist-dev'\'' +export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\'' +export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' +++ PS1='(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++ export CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev +++ CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev +++ export CONDA_SHLVL=7 +++ CONDA_SHLVL=7 +++ export CONDA_DEFAULT_ENV=schemist-dev +++ CONDA_DEFAULT_ENV=schemist-dev +++ export 'CONDA_PROMPT_MODIFIER=(schemist-dev) ' +++ CONDA_PROMPT_MODIFIER='(schemist-dev) ' +++ export CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0 +++ CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0 +++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++ export _CE_M= +++ _CE_M= +++ export _CE_CONDA= +++ _CE_CONDA= +++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python +++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++ __conda_hashr ++ '[' -n '' ']' ++ '[' -n '' ']' ++ hash -r ++ CHUNK_HEAD_FILE=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz ++ INPUT=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/train/cyc-pep-6-12mer-70M_12.csv ++ COLUMN=cysteine_to_N_cyclization ++ PREFIX=cyclic_ ++ AWK='1 { print $8, $1, $2, $10, $3 }' ++ '[' -z cysteine_to_N_cyclization ']' ++ '[' -z cyclic_ ']' ++ '[' -z '1 { print $8, $1, $2, $10, $3 }' ']' ++ cat /dev/fd/63 /nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/train/cyc-pep-6-12mer-70M_12.csv ++ schemist convert -f csv --column cysteine_to_N_cyclization --to id inchikey scaffold mwt clogp tpsa --prefix cyclic_ --options prefix=SCB- ++ gzip --best +++ head -n1 ++ awk -F, -v OFS=, '1 { print $8, $1, $2, $10, $3 }' +++ zcat /nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz +++ tr ' ' , +🚀 Converting between string representations with the following parameters: + subcommand: convert + output: <_io.TextIOWrapper name='' mode='w' encoding='utf-8'> + format: csv + input: <_io.TextIOWrapper name='' mode='r' encoding='utf-8'> + representation: SMILES + column: cysteine_to_N_cyclization + prefix: cyclic_ + to: ['id', 'inchikey', 'scaffold', 'mwt', 'clogp', 'tpsa'] + options: ['prefix=SCB-'] + func: + 0it [00:00, ?it/s] 1it [00:11, 11.59s/it] 2it [00:23, 11.50s/it] 3it [00:34, 11.49s/it] 4it [00:46, 11.50s/it] 5it [00:57, 11.51s/it] 6it 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11.55s/it] 958it [3:04:08, 11.55s/it] 959it [3:04:20, 11.54s/it] 960it [3:04:31, 11.52s/it] 961it [3:04:43, 11.55s/it] 962it [3:04:54, 11.52s/it] 963it [3:05:06, 11.53s/it] 964it [3:05:18, 11.53s/it] 965it [3:05:29, 11.53s/it] 966it [3:05:41, 11.56s/it] 967it [3:05:52, 11.55s/it] 968it [3:06:04, 11.55s/it] 969it [3:06:15, 11.52s/it] 970it [3:06:27, 11.52s/it] 971it [3:06:38, 11.54s/it] 972it [3:06:50, 11.55s/it] 973it [3:07:01, 11.54s/it] 974it [3:07:13, 11.54s/it] 975it [3:07:24, 11.53s/it] 976it [3:07:36, 11.55s/it] 977it [3:07:48, 11.54s/it] 978it [3:07:59, 11.52s/it] 979it [3:08:11, 11.51s/it] 980it [3:08:22, 11.53s/it] 981it [3:08:34, 11.51s/it] 982it [3:08:45, 11.53s/it] 983it [3:08:57, 11.53s/it] 984it [3:09:08, 11.54s/it] 985it [3:09:20, 11.53s/it] 986it [3:09:31, 11.54s/it] 987it [3:09:43, 11.55s/it] 988it [3:09:54, 11.52s/it] 989it [3:10:06, 11.54s/it] 990it [3:10:17, 11.53s/it] 991it [3:10:29, 11.53s/it] 992it [3:10:41, 11.55s/it] 993it [3:10:52, 11.54s/it] 994it [3:11:04, 11.54s/it] 995it [3:11:15, 11.54s/it] 996it [3:11:27, 11.54s/it] 997it [3:11:38, 11.53s/it] 998it [3:11:50, 11.52s/it] 999it [3:12:01, 11.53s/it] 1000it [3:12:13, 11.54s/it] 1000it [3:12:13, 11.53s/it] +Error counts: + cyclic_id: 0 + cyclic_inchikey: 0 + cyclic_scaffold: 0 + cyclic_mwt: 0 + cyclic_clogp: 0 + cyclic_tpsa: 0 +⏰ Completed process in 3:12:37.374014 ++ rm /nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/train/cyc-pep-6-12mer-70M_12.csv diff --git a/train/cyc-pep-6-12mer-70M_13.csv.gz b/train/cyc-pep-6-12mer-70M_13.csv.gz index 361255f674c32a17c82c46f9c136e74b29da3195..d99fad546bc90f945698b12a17de72f0e437cdbb 100644 --- a/train/cyc-pep-6-12mer-70M_13.csv.gz +++ b/train/cyc-pep-6-12mer-70M_13.csv.gz @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:93376dab46ead5ef64e25eeeadf855d51ad0edef6f3e8c928f0a028d6167bd42 -size 63844476 +oid sha256:fa985fd6973ed59c6dc1b8ba58231f8fd179e9566f6c67a1f4aef8b5c3c854b1 +size 120132005 diff --git a/train/cyc-pep-6-12mer-70M_13.log b/train/cyc-pep-6-12mer-70M_13.log new file mode 100644 index 0000000000000000000000000000000000000000..41e533bc3da1eeccf46a8b1caba668a1fa4e1141 --- /dev/null +++ b/train/cyc-pep-6-12mer-70M_13.log @@ -0,0 +1,337 @@ ++ module purge ++ '[' -z '' ']' ++ case "$-" in ++ __lmod_sh_dbg=x ++ '[' -n x ']' ++ set +x +Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output +Shell debugging restarted ++ unset __lmod_sh_dbg ++ return 0 ++ module load Anaconda3/2023.03 ++ '[' -z '' ']' ++ case "$-" in ++ __lmod_sh_dbg=x ++ '[' -n x ']' ++ set +x +Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output +Shell debugging restarted ++ unset __lmod_sh_dbg ++ return 0 ++ source /camp/home/johnsoe/.bashrc +++ '[' '' = yes ']' +++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' ++++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.bash hook +++ __conda_setup='export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'' + +# Copyright (C) 2012 Anaconda, Inc +# SPDX-License-Identifier: BSD-3-Clause +__conda_exe() ( + "$CONDA_EXE" $_CE_M $_CE_CONDA "$@" +) + +__conda_hashr() { + if [ -n "${ZSH_VERSION:+x}" ]; then + \rehash + elif [ -n "${POSH_VERSION:+x}" ]; then + : # pass + else + \hash -r + fi +} + +__conda_activate() { + if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then + # Handle transition from shell activated with conda <= 4.3 to a subsequent activation + # after conda updated to >= 4.4. See issue #6173. + PS1="$CONDA_PS1_BACKUP" + \unset CONDA_PS1_BACKUP + fi + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return + \eval "$ask_conda" + __conda_hashr +} + +__conda_reactivate() { + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return + \eval "$ask_conda" + __conda_hashr +} + +conda() { + \local cmd="${1-__missing__}" + case "$cmd" in + activate|deactivate) + __conda_activate "$@" + ;; + install|update|upgrade|remove|uninstall) + __conda_exe "$@" || \return + __conda_reactivate + ;; + *) + __conda_exe "$@" + ;; + esac +} + +if [ -z "${CONDA_SHLVL+x}" ]; then + \export CONDA_SHLVL=0 + # In dev-mode CONDA_EXE is python.exe and on Windows + # it is in a different relative location to condabin. + if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then + PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}" + else + PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}" + fi + \export PATH + + # We'\''re not allowing PS1 to be unbound. It must at least be set. + # However, we'\''re not exporting it, which can cause problems when starting a second shell + # via a first shell (i.e. starting zsh from bash). + if [ -z "${PS1+x}" ]; then + PS1= + fi +fi + +conda activate base' +++ '[' 0 -eq 0 ']' +++ eval 'export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'' + +# Copyright (C) 2012 Anaconda, Inc +# SPDX-License-Identifier: BSD-3-Clause +__conda_exe() ( + "$CONDA_EXE" $_CE_M $_CE_CONDA "$@" +) + +__conda_hashr() { + if [ -n "${ZSH_VERSION:+x}" ]; then + \rehash + elif [ -n "${POSH_VERSION:+x}" ]; then + : # pass + else + \hash -r + fi +} + +__conda_activate() { + if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then + # Handle transition from shell activated with conda <= 4.3 to a subsequent activation + # after conda updated to >= 4.4. See issue #6173. + PS1="$CONDA_PS1_BACKUP" + \unset CONDA_PS1_BACKUP + fi + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return + \eval "$ask_conda" + __conda_hashr +} + +__conda_reactivate() { + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return + \eval "$ask_conda" + __conda_hashr +} + +conda() { + \local cmd="${1-__missing__}" + case "$cmd" in + activate|deactivate) + __conda_activate "$@" + ;; + install|update|upgrade|remove|uninstall) + __conda_exe "$@" || \return + __conda_reactivate + ;; + *) + __conda_exe "$@" + ;; + esac +} + +if [ -z "${CONDA_SHLVL+x}" ]; then + \export CONDA_SHLVL=0 + # In dev-mode CONDA_EXE is python.exe and on Windows + # it is in a different relative location to condabin. + if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then + PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}" + else + PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}" + fi + \export PATH + + # We'\''re not allowing PS1 to be unbound. It must at least be set. + # However, we'\''re not exporting it, which can cause problems when starting a second shell + # via a first shell (i.e. starting zsh from bash). + if [ -z "${PS1+x}" ]; then + PS1= + fi +fi + +conda activate base' ++++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda ++++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda ++++ export _CE_M= ++++ _CE_M= ++++ export _CE_CONDA= ++++ _CE_CONDA= ++++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ '[' -z x ']' ++++ conda activate base ++++ local cmd=activate ++++ case "$cmd" in ++++ __conda_activate activate base ++++ '[' -n '' ']' ++++ local ask_conda +++++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++++ __conda_exe shell.posix activate base +++++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate base ++++ ask_conda='PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_SHLVL='\''6'\'' +export CONDA_DEFAULT_ENV='\''base'\'' +export CONDA_PROMPT_MODIFIER='\''(base) '\'' +export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' ++++ eval 'PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_SHLVL='\''6'\'' +export CONDA_DEFAULT_ENV='\''base'\'' +export CONDA_PROMPT_MODIFIER='\''(base) '\'' +export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' +++++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++++ export CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0 +++++ CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0 +++++ export CONDA_SHLVL=6 +++++ CONDA_SHLVL=6 +++++ export CONDA_DEFAULT_ENV=base +++++ CONDA_DEFAULT_ENV=base +++++ export 'CONDA_PROMPT_MODIFIER=(base) ' +++++ CONDA_PROMPT_MODIFIER='(base) ' +++++ export CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev +++++ CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev +++++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++++ export _CE_M= +++++ _CE_M= +++++ export _CE_CONDA= +++++ _CE_CONDA= +++++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python +++++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ __conda_hashr ++++ '[' -n '' ']' ++++ '[' -n '' ']' ++++ hash -r +++ unset __conda_setup ++ conda activate schemist-dev ++ local cmd=activate ++ case "$cmd" in ++ __conda_activate activate schemist-dev ++ '[' -n '' ']' ++ local ask_conda +++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++ __conda_exe shell.posix activate schemist-dev +++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate schemist-dev ++ ask_conda='PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_SHLVL='\''7'\'' +export CONDA_DEFAULT_ENV='\''schemist-dev'\'' +export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\'' +export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' ++ eval 'PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_SHLVL='\''7'\'' +export CONDA_DEFAULT_ENV='\''schemist-dev'\'' +export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\'' +export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' +++ PS1='(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++ export CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev +++ CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev +++ export CONDA_SHLVL=7 +++ CONDA_SHLVL=7 +++ export CONDA_DEFAULT_ENV=schemist-dev +++ CONDA_DEFAULT_ENV=schemist-dev +++ export 'CONDA_PROMPT_MODIFIER=(schemist-dev) ' +++ CONDA_PROMPT_MODIFIER='(schemist-dev) ' +++ export CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0 +++ CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0 +++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++ export _CE_M= +++ _CE_M= +++ export _CE_CONDA= +++ _CE_CONDA= +++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python +++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++ __conda_hashr ++ '[' -n '' ']' ++ '[' -n '' ']' ++ hash -r ++ CHUNK_HEAD_FILE=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz ++ INPUT=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/train/cyc-pep-6-12mer-70M_13.csv ++ COLUMN=cysteine_to_N_cyclization ++ PREFIX=cyclic_ ++ AWK='1 { print $8, $1, $2, $10, $3 }' ++ '[' -z cysteine_to_N_cyclization ']' ++ '[' -z cyclic_ ']' ++ '[' -z '1 { print $8, $1, $2, $10, $3 }' ']' ++ cat /dev/fd/63 /nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/train/cyc-pep-6-12mer-70M_13.csv ++ schemist convert -f csv --column cysteine_to_N_cyclization --to id inchikey scaffold mwt clogp tpsa --prefix cyclic_ --options prefix=SCB- ++ gzip --best +++ head -n1 ++ awk -F, -v OFS=, '1 { print $8, $1, $2, $10, $3 }' +++ zcat /nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz +++ tr ' ' , +🚀 Converting between string representations with the following parameters: + subcommand: convert + output: <_io.TextIOWrapper name='' mode='w' encoding='utf-8'> + format: csv + input: <_io.TextIOWrapper name='' mode='r' encoding='utf-8'> + representation: SMILES + column: cysteine_to_N_cyclization + prefix: cyclic_ + to: ['id', 'inchikey', 'scaffold', 'mwt', 'clogp', 'tpsa'] + options: ['prefix=SCB-'] + func: + 0it [00:00, ?it/s] 1it [00:12, 12.09s/it] 2it [00:23, 11.95s/it] 3it [00:35, 11.96s/it] 4it [00:47, 11.97s/it] 5it [00:59, 12.02s/it] 6it [01:11, 11.98s/it] 7it [01:23, 11.98s/it] 8it [01:35, 11.98s/it] 9it [01:47, 11.99s/it] 10it [01:59, 11.95s/it] 11it [02:11, 11.93s/it] 12it [02:23, 11.92s/it] 13it [02:35, 11.91s/it] 14it [02:47, 11.92s/it] 15it [02:59, 11.94s/it] 16it [03:11, 11.94s/it] 17it [03:23, 11.94s/it] 18it [03:35, 11.96s/it] 19it [03:47, 11.94s/it] 20it [03:58, 11.92s/it] 21it [04:10, 11.93s/it] 22it [04:22, 11.93s/it] 23it [04:34, 11.93s/it] 24it [04:46, 11.94s/it] 25it [04:58, 11.94s/it] 26it [05:10, 11.92s/it] 27it [05:22, 11.96s/it] 28it [05:34, 11.95s/it] 29it [05:46, 11.96s/it] 30it [05:58, 11.94s/it] 31it [06:10, 11.91s/it] 32it [06:22, 11.91s/it] 33it [06:34, 11.93s/it] 34it [06:46, 11.93s/it] 35it [06:57, 11.92s/it] 36it [07:09, 11.92s/it] 37it [07:21, 11.94s/it] 38it [07:33, 11.95s/it] 39it [07:45, 11.93s/it] 40it [07:57, 11.94s/it] 41it [08:09, 11.93s/it] 42it [08:21, 11.93s/it] 43it [08:33, 11.93s/it] 44it [08:45, 11.91s/it] 45it [08:57, 11.95s/it] 46it [09:09, 12.01s/it] 47it [09:21, 12.00s/it] 48it [09:33, 11.97s/it] 49it [09:45, 11.98s/it] 50it [09:57, 11.95s/it] 51it [10:09, 11.95s/it] 52it [10:21, 11.95s/it] 53it [10:33, 11.95s/it] 54it [10:45, 11.95s/it] 55it [10:56, 11.92s/it] 56it [11:08, 11.95s/it] 57it [11:20, 11.94s/it] 58it [11:32, 11.94s/it] 59it [11:44, 11.93s/it] 60it [11:56, 11.94s/it] 61it [12:08, 11.95s/it] 62it [12:20, 11.95s/it] 63it [12:32, 11.94s/it] 64it [12:44, 11.94s/it] 65it [12:56, 11.92s/it] 66it [13:08, 11.92s/it] 67it [13:20, 11.94s/it] 68it [13:32, 11.94s/it] 69it [13:44, 11.95s/it] 70it [13:56, 11.94s/it] 71it [14:07, 11.92s/it] 72it [14:19, 11.91s/it] 73it [14:31, 11.90s/it] 74it [14:43, 11.93s/it] 75it [14:55, 11.90s/it] 76it [15:07, 11.90s/it] 77it [15:19, 11.91s/it] 78it [15:31, 11.91s/it] 79it [15:43, 11.92s/it] 80it [15:55, 11.96s/it] 81it [16:07, 12.02s/it] 82it [16:19, 12.02s/it] 83it [16:31, 12.00s/it] 84it [16:43, 12.02s/it] 85it [16:55, 11.97s/it] 86it [17:07, 11.96s/it] 87it [17:19, 11.94s/it] 88it [17:31, 11.93s/it] 89it [17:42, 11.92s/it] 90it [17:54, 11.94s/it] 91it [18:06, 11.94s/it] 92it [18:18, 11.94s/it] 93it [18:30, 11.93s/it] 94it [18:42, 11.92s/it] 95it [18:54, 11.94s/it] 96it [19:06, 11.94s/it] 97it [19:18, 11.91s/it] 98it [19:30, 11.94s/it] 99it [19:42, 11.91s/it] 100it [19:54, 11.89s/it] 101it [20:05, 11.86s/it] 102it [20:17, 11.83s/it] 103it [20:29, 11.82s/it] 104it [20:41, 11.81s/it] 105it [20:53, 11.81s/it] 106it [21:04, 11.80s/it] 107it [21:16, 11.81s/it] 108it [21:28, 11.80s/it] 109it [21:40, 11.83s/it] 110it [21:52, 11.84s/it] 111it [22:03, 11.82s/it] 112it [22:15, 11.82s/it] 113it [22:27, 11.82s/it] 114it [22:39, 11.85s/it] 115it [22:51, 11.83s/it] 116it [23:03, 11.82s/it] 117it [23:14, 11.81s/it] 118it [23:26, 11.81s/it] 119it [23:38, 11.82s/it] 120it [23:50, 11.78s/it] 121it [24:02, 11.80s/it] 122it [24:13, 11.77s/it] 123it [24:25, 11.79s/it] 124it [24:37, 11.82s/it] 125it [24:49, 11.82s/it] 126it [25:01, 11.82s/it] 127it [25:13, 11.82s/it] 128it [25:24, 11.81s/it] 129it [25:36, 11.80s/it] 130it [25:48, 11.81s/it] 131it [26:00, 11.80s/it] 132it [26:12, 11.82s/it] 133it [26:23, 11.82s/it] 134it [26:35, 11.79s/it] 135it [26:47, 11.79s/it] 136it [26:59, 11.80s/it] 137it [27:11, 11.83s/it] 138it [27:22, 11.81s/it] 139it [27:34, 11.83s/it] 140it [27:46, 11.84s/it] 141it [27:58, 11.81s/it] 142it [28:10, 11.83s/it] 143it [28:22, 11.83s/it] 144it [28:33, 11.81s/it] 145it [28:45, 11.82s/it] 146it [28:57, 11.84s/it] 147it [29:09, 11.84s/it] 148it [29:21, 11.86s/it] 149it [29:33, 11.84s/it] 150it [29:44, 11.84s/it] 151it [29:56, 11.83s/it] 152it [30:08, 11.82s/it] 153it [30:20, 11.82s/it] 154it [30:32, 11.82s/it] 155it [30:43, 11.80s/it] 156it [30:55, 11.79s/it] 157it [31:07, 11.82s/it] 158it [31:19, 11.81s/it] 159it [31:31, 11.81s/it] 160it [31:42, 11.81s/it] 161it [31:54, 11.80s/it] 162it [32:06, 11.82s/it] 163it [32:18, 11.83s/it] 164it [32:30, 11.83s/it] 165it [32:42, 11.83s/it] 166it [32:53, 11.83s/it] 167it [33:05, 11.84s/it] 168it [33:17, 11.87s/it] 169it [33:29, 11.90s/it] 170it [33:41, 11.87s/it] 171it [33:53, 11.87s/it] 172it [34:05, 11.89s/it] 173it [34:17, 11.89s/it] 174it [34:29, 11.86s/it] 175it [34:40, 11.85s/it] 176it [34:52, 11.85s/it] 177it [35:04, 11.83s/it] 178it [35:16, 11.86s/it] 179it [35:28, 11.86s/it] 180it [35:40, 11.83s/it] 181it [35:51, 11.86s/it] 182it [36:03, 11.87s/it] 183it [36:15, 11.85s/it] 184it [36:27, 11.86s/it] 185it [36:39, 11.85s/it] 186it [36:51, 11.84s/it] 187it [37:03, 11.85s/it] 188it [37:14, 11.85s/it] 189it [37:26, 11.83s/it] 190it [37:38, 11.82s/it] 191it [37:50, 11.83s/it] 192it [38:02, 11.82s/it] 193it [38:14, 11.84s/it] 194it [38:25, 11.84s/it] 195it [38:37, 11.84s/it] 196it [38:49, 11.83s/it] 197it [39:01, 11.82s/it] 198it [39:13, 11.84s/it] 199it [39:25, 11.82s/it] 200it [39:36, 11.82s/it] 201it [39:48, 11.82s/it] 202it [40:00, 11.85s/it] 203it [40:12, 11.84s/it] 204it [40:24, 11.85s/it] 205it [40:36, 11.87s/it] 206it [40:48, 11.86s/it] 207it [40:59, 11.84s/it] 208it [41:11, 11.85s/it] 209it [41:23, 11.84s/it] 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250it [49:28, 11.82s/it] 251it [49:39, 11.83s/it] 252it [49:51, 11.85s/it] 253it [50:03, 11.84s/it] 254it [50:15, 11.86s/it] 255it [50:27, 11.88s/it] 256it [50:39, 11.84s/it] 257it [50:51, 11.85s/it] 258it [51:02, 11.85s/it] 259it [51:14, 11.82s/it] 260it [51:26, 11.82s/it] 261it [51:38, 11.82s/it] 262it [51:50, 11.80s/it] 263it [52:01, 11.81s/it] 264it [52:13, 11.82s/it] 265it [52:25, 11.83s/it] 266it [52:37, 11.83s/it] 267it [52:49, 11.81s/it] 268it [53:01, 11.82s/it] 269it [53:12, 11.81s/it] 270it [53:24, 11.81s/it] 271it [53:36, 11.81s/it] 272it [53:48, 11.80s/it] 273it [54:00, 11.78s/it] 274it [54:11, 11.77s/it] 275it [54:23, 11.82s/it] 276it [54:35, 11.81s/it] 277it [54:47, 11.81s/it] 278it [54:59, 11.82s/it] 279it [55:10, 11.82s/it] 280it [55:22, 11.80s/it] 281it [55:34, 11.83s/it] 282it [55:46, 11.87s/it] 283it [55:58, 11.88s/it] 284it [56:10, 11.93s/it] 285it [56:22, 11.97s/it] 286it [56:34, 11.98s/it] 287it [56:46, 11.95s/it] 288it [56:58, 11.96s/it] 289it [57:10, 11.97s/it] 290it [57:22, 11.97s/it] 291it [57:34, 11.96s/it] 292it [57:46, 11.92s/it] 293it [57:58, 11.91s/it] 294it [58:09, 11.87s/it] 295it [58:21, 11.86s/it] 296it [58:33, 11.85s/it] 297it [58:45, 11.84s/it] 298it [58:57, 11.85s/it] 299it [59:09, 11.86s/it] 300it [59:20, 11.86s/it] 301it [59:32, 11.86s/it] 302it [59:44, 11.87s/it] 303it [59:56, 11.90s/it] 304it [1:00:08, 11.87s/it] 305it [1:00:20, 11.86s/it] 306it [1:00:32, 11.87s/it] 307it [1:00:44, 11.87s/it] 308it [1:00:55, 11.85s/it] 309it [1:01:07, 11.83s/it] 310it [1:01:19, 11.83s/it] 311it [1:01:31, 11.83s/it] 312it [1:01:43, 11.87s/it] 313it [1:01:55, 11.86s/it] 314it [1:02:06, 11.87s/it] 315it [1:02:18, 11.86s/it] 316it [1:02:30, 11.85s/it] 317it [1:02:42, 11.84s/it] 318it [1:02:54, 11.83s/it] 319it [1:03:06, 11.84s/it] 320it [1:03:18, 11.85s/it] 321it [1:03:29, 11.83s/it] 322it [1:03:41, 11.84s/it] 323it [1:03:53, 11.82s/it] 324it [1:04:05, 11.83s/it] 325it [1:04:17, 11.82s/it] 326it [1:04:28, 11.82s/it] 327it [1:04:40, 11.83s/it] 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957it [3:21:42, 13.79s/it] 958it [3:21:56, 13.78s/it] 959it [3:22:10, 13.84s/it] 960it [3:22:24, 13.87s/it] 961it [3:22:38, 13.84s/it] 962it [3:22:51, 13.79s/it] 963it [3:23:05, 13.80s/it] 964it [3:23:19, 13.90s/it] 965it [3:23:33, 13.86s/it] 966it [3:23:47, 13.80s/it] 967it [3:24:01, 13.82s/it] 968it [3:24:15, 13.89s/it] 969it [3:24:29, 13.89s/it] 970it [3:24:42, 13.83s/it] 971it [3:24:56, 13.77s/it] 972it [3:25:10, 13.80s/it] 973it [3:25:24, 13.82s/it] 974it [3:25:37, 13.83s/it] 975it [3:25:51, 13.83s/it] 976it [3:26:05, 13.84s/it] 977it [3:26:19, 13.85s/it] 978it [3:26:33, 13.89s/it] 979it [3:26:47, 13.86s/it] 980it [3:27:01, 13.86s/it] 981it [3:27:14, 13.80s/it] 982it [3:27:28, 13.67s/it] 983it [3:27:41, 13.56s/it] 984it [3:27:54, 13.44s/it] 985it [3:28:07, 13.42s/it] 986it [3:28:21, 13.40s/it] 987it [3:28:35, 13.51s/it] 988it [3:28:49, 13.65s/it] 989it [3:29:02, 13.72s/it] 990it [3:29:16, 13.77s/it] 991it [3:29:30, 13.80s/it] 992it [3:29:44, 13.90s/it] 993it [3:29:58, 13.90s/it] 994it [3:30:12, 13.84s/it] 995it [3:30:26, 13.82s/it] 996it [3:30:40, 13.89s/it] 997it [3:30:54, 13.98s/it] 998it [3:31:08, 13.91s/it] 999it [3:31:21, 13.85s/it] 1000it [3:31:35, 13.85s/it] 1000it [3:31:35, 12.70s/it] +Error counts: + cyclic_id: 0 + cyclic_inchikey: 0 + cyclic_scaffold: 0 + cyclic_mwt: 0 + cyclic_clogp: 0 + cyclic_tpsa: 0 +⏰ Completed process in 3:32:01.299828 ++ rm /nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/train/cyc-pep-6-12mer-70M_13.csv diff --git a/train/cyc-pep-6-12mer-70M_14.csv.gz b/train/cyc-pep-6-12mer-70M_14.csv.gz index 4ce00dc7e7dad9a6bb85ff20099ba33dbbe335c2..a4d436ca0f4bf9df13e372858a157088e4c71050 100644 --- a/train/cyc-pep-6-12mer-70M_14.csv.gz +++ b/train/cyc-pep-6-12mer-70M_14.csv.gz @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:1bc12f03e1cb87b8ba487f25bfef5abd7bc6c4a60006b2dc5f96914b51b24e4b -size 65619867 +oid sha256:caeeebdb034b8071e4f7a49023f3787a72afc2bd66455b5e3c7bec7e493d9368 +size 122458551 diff --git a/train/cyc-pep-6-12mer-70M_14.log b/train/cyc-pep-6-12mer-70M_14.log new file mode 100644 index 0000000000000000000000000000000000000000..973da05b9a197513c8a26ce89b45333dad2b9eeb --- /dev/null +++ b/train/cyc-pep-6-12mer-70M_14.log @@ -0,0 +1,337 @@ ++ module purge ++ '[' -z '' ']' ++ case "$-" in ++ __lmod_sh_dbg=x ++ '[' -n x ']' ++ set +x +Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output +Shell debugging restarted ++ unset __lmod_sh_dbg ++ return 0 ++ module load Anaconda3/2023.03 ++ '[' -z '' ']' ++ case "$-" in ++ __lmod_sh_dbg=x ++ '[' -n x ']' ++ set +x +Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output +Shell debugging restarted ++ unset __lmod_sh_dbg ++ return 0 ++ source /camp/home/johnsoe/.bashrc +++ '[' '' = yes ']' +++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' ++++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.bash hook +++ __conda_setup='export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'' + +# Copyright (C) 2012 Anaconda, Inc +# SPDX-License-Identifier: BSD-3-Clause +__conda_exe() ( + "$CONDA_EXE" $_CE_M $_CE_CONDA "$@" +) + +__conda_hashr() { + if [ -n "${ZSH_VERSION:+x}" ]; then + \rehash + elif [ -n "${POSH_VERSION:+x}" ]; then + : # pass + else + \hash -r + fi +} + +__conda_activate() { + if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then + # Handle transition from shell activated with conda <= 4.3 to a subsequent activation + # after conda updated to >= 4.4. See issue #6173. + PS1="$CONDA_PS1_BACKUP" + \unset CONDA_PS1_BACKUP + fi + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return + \eval "$ask_conda" + __conda_hashr +} + +__conda_reactivate() { + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return + \eval "$ask_conda" + __conda_hashr +} + +conda() { + \local cmd="${1-__missing__}" + case "$cmd" in + activate|deactivate) + __conda_activate "$@" + ;; + install|update|upgrade|remove|uninstall) + __conda_exe "$@" || \return + __conda_reactivate + ;; + *) + __conda_exe "$@" + ;; + esac +} + +if [ -z "${CONDA_SHLVL+x}" ]; then + \export CONDA_SHLVL=0 + # In dev-mode CONDA_EXE is python.exe and on Windows + # it is in a different relative location to condabin. + if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then + PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}" + else + PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}" + fi + \export PATH + + # We'\''re not allowing PS1 to be unbound. It must at least be set. + # However, we'\''re not exporting it, which can cause problems when starting a second shell + # via a first shell (i.e. starting zsh from bash). + if [ -z "${PS1+x}" ]; then + PS1= + fi +fi + +conda activate base' +++ '[' 0 -eq 0 ']' +++ eval 'export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'' + +# Copyright (C) 2012 Anaconda, Inc +# SPDX-License-Identifier: BSD-3-Clause +__conda_exe() ( + "$CONDA_EXE" $_CE_M $_CE_CONDA "$@" +) + +__conda_hashr() { + if [ -n "${ZSH_VERSION:+x}" ]; then + \rehash + elif [ -n "${POSH_VERSION:+x}" ]; then + : # pass + else + \hash -r + fi +} + +__conda_activate() { + if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then + # Handle transition from shell activated with conda <= 4.3 to a subsequent activation + # after conda updated to >= 4.4. See issue #6173. + PS1="$CONDA_PS1_BACKUP" + \unset CONDA_PS1_BACKUP + fi + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return + \eval "$ask_conda" + __conda_hashr +} + +__conda_reactivate() { + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return + \eval "$ask_conda" + __conda_hashr +} + +conda() { + \local cmd="${1-__missing__}" + case "$cmd" in + activate|deactivate) + __conda_activate "$@" + ;; + install|update|upgrade|remove|uninstall) + __conda_exe "$@" || \return + __conda_reactivate + ;; + *) + __conda_exe "$@" + ;; + esac +} + +if [ -z "${CONDA_SHLVL+x}" ]; then + \export CONDA_SHLVL=0 + # In dev-mode CONDA_EXE is python.exe and on Windows + # it is in a different relative location to condabin. + if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then + PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}" + else + PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}" + fi + \export PATH + + # We'\''re not allowing PS1 to be unbound. It must at least be set. + # However, we'\''re not exporting it, which can cause problems when starting a second shell + # via a first shell (i.e. starting zsh from bash). + if [ -z "${PS1+x}" ]; then + PS1= + fi +fi + +conda activate base' ++++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda ++++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda ++++ export _CE_M= ++++ _CE_M= ++++ export _CE_CONDA= ++++ _CE_CONDA= ++++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ '[' -z x ']' ++++ conda activate base ++++ local cmd=activate ++++ case "$cmd" in ++++ __conda_activate activate base ++++ '[' -n '' ']' ++++ local ask_conda +++++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++++ __conda_exe shell.posix activate base +++++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate base ++++ ask_conda='PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_SHLVL='\''6'\'' +export CONDA_DEFAULT_ENV='\''base'\'' +export CONDA_PROMPT_MODIFIER='\''(base) '\'' +export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' ++++ eval 'PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_SHLVL='\''6'\'' +export CONDA_DEFAULT_ENV='\''base'\'' +export CONDA_PROMPT_MODIFIER='\''(base) '\'' +export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' +++++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++++ export CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0 +++++ CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0 +++++ export CONDA_SHLVL=6 +++++ CONDA_SHLVL=6 +++++ export CONDA_DEFAULT_ENV=base +++++ CONDA_DEFAULT_ENV=base +++++ export 'CONDA_PROMPT_MODIFIER=(base) ' +++++ CONDA_PROMPT_MODIFIER='(base) ' +++++ export CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev +++++ CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev +++++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++++ export _CE_M= +++++ _CE_M= +++++ export _CE_CONDA= +++++ _CE_CONDA= +++++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python +++++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ __conda_hashr ++++ '[' -n '' ']' ++++ '[' -n '' ']' ++++ hash -r +++ unset __conda_setup ++ conda activate schemist-dev ++ local cmd=activate ++ case "$cmd" in ++ __conda_activate activate schemist-dev ++ '[' -n '' ']' ++ local ask_conda +++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++ __conda_exe shell.posix activate schemist-dev +++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate schemist-dev ++ ask_conda='PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_SHLVL='\''7'\'' +export CONDA_DEFAULT_ENV='\''schemist-dev'\'' +export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\'' +export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' ++ eval 'PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_SHLVL='\''7'\'' +export CONDA_DEFAULT_ENV='\''schemist-dev'\'' +export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\'' +export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' +++ PS1='(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++ export CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev +++ CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev +++ export CONDA_SHLVL=7 +++ CONDA_SHLVL=7 +++ export CONDA_DEFAULT_ENV=schemist-dev +++ CONDA_DEFAULT_ENV=schemist-dev +++ export 'CONDA_PROMPT_MODIFIER=(schemist-dev) ' +++ CONDA_PROMPT_MODIFIER='(schemist-dev) ' +++ export CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0 +++ CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0 +++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++ export _CE_M= +++ _CE_M= +++ export _CE_CONDA= +++ _CE_CONDA= +++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python +++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++ __conda_hashr ++ '[' -n '' ']' ++ '[' -n '' ']' ++ hash -r ++ CHUNK_HEAD_FILE=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz ++ INPUT=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/train/cyc-pep-6-12mer-70M_14.csv ++ COLUMN=cysteine_to_N_cyclization ++ PREFIX=cyclic_ ++ AWK='1 { print $8, $1, $2, $10, $3 }' ++ '[' -z cysteine_to_N_cyclization ']' ++ '[' -z cyclic_ ']' ++ '[' -z '1 { print $8, $1, $2, $10, $3 }' ']' ++ cat /dev/fd/63 /nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/train/cyc-pep-6-12mer-70M_14.csv ++ awk -F, -v OFS=, '1 { print $8, $1, $2, $10, $3 }' +++ zcat /nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz +++ head -n1 ++ schemist convert -f csv --column cysteine_to_N_cyclization --to id inchikey scaffold mwt clogp tpsa --prefix cyclic_ --options prefix=SCB- ++ gzip --best +++ tr ' ' , +🚀 Converting between string representations with the following parameters: + subcommand: convert + output: <_io.TextIOWrapper name='' mode='w' encoding='utf-8'> + format: csv + input: <_io.TextIOWrapper name='' mode='r' encoding='utf-8'> + representation: SMILES + column: cysteine_to_N_cyclization + prefix: cyclic_ + to: ['id', 'inchikey', 'scaffold', 'mwt', 'clogp', 'tpsa'] + options: ['prefix=SCB-'] + func: + 0it [00:00, ?it/s] 1it [00:30, 30.42s/it] 2it [00:59, 29.85s/it] 3it [01:29, 29.94s/it] 4it [01:59, 29.78s/it] 5it [02:28, 29.45s/it] 6it 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[8:03:02, 32.36s/it] 981it [8:03:36, 32.81s/it] 982it [8:04:12, 33.73s/it] 983it [8:04:45, 33.50s/it] 984it [8:05:18, 33.51s/it] 985it [8:05:54, 34.25s/it] 986it [8:06:23, 32.67s/it] 987it [8:06:54, 32.13s/it] 988it [8:07:30, 33.11s/it] 989it [8:08:01, 32.70s/it] 990it [8:08:29, 31.16s/it] 991it [8:08:57, 30.27s/it] 992it [8:09:24, 29.20s/it] 993it [8:09:50, 28.32s/it] 994it [8:10:16, 27.53s/it] 995it [8:10:40, 26.68s/it] 996it [8:11:07, 26.52s/it] 997it [8:11:34, 26.81s/it] 998it [8:12:03, 27.45s/it] 999it [8:12:33, 28.17s/it] 1000it [8:13:02, 28.40s/it] 1000it [8:13:02, 29.58s/it] +Error counts: + cyclic_id: 0 + cyclic_inchikey: 0 + cyclic_scaffold: 0 + cyclic_mwt: 0 + cyclic_clogp: 0 + cyclic_tpsa: 0 +⏰ Completed process in 8:13:33.626895 ++ rm /nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/train/cyc-pep-6-12mer-70M_14.csv diff --git a/train/cyc-pep-6-12mer-70M_15.csv.gz b/train/cyc-pep-6-12mer-70M_15.csv.gz index 85b0ab5b5d045554901e8339b10083f8d00fa696..1c6549607c5813e5e2ec2778b7385a12b38229f3 100644 --- a/train/cyc-pep-6-12mer-70M_15.csv.gz +++ b/train/cyc-pep-6-12mer-70M_15.csv.gz @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:b68f3735a2973cd8ec78698e446e21fd3a189964b75360a5705ae6cb28f71c41 -size 65616928 +oid sha256:565e968d39e465cbcb94b523872838ca0a8225d62199696414d547ec0a957de4 +size 122455904 diff --git a/train/cyc-pep-6-12mer-70M_15.log b/train/cyc-pep-6-12mer-70M_15.log new file mode 100644 index 0000000000000000000000000000000000000000..40a87b26f3518527c75e10976f54b82ddb9a3550 --- /dev/null +++ b/train/cyc-pep-6-12mer-70M_15.log @@ -0,0 +1,337 @@ ++ module purge ++ '[' -z '' ']' ++ case "$-" in ++ __lmod_sh_dbg=x ++ '[' -n x ']' ++ set +x +Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output +Shell debugging restarted ++ unset __lmod_sh_dbg ++ return 0 ++ module load Anaconda3/2023.03 ++ '[' -z '' ']' ++ case "$-" in ++ __lmod_sh_dbg=x ++ '[' -n x ']' ++ set +x +Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output +Shell debugging restarted ++ unset __lmod_sh_dbg ++ return 0 ++ source /camp/home/johnsoe/.bashrc +++ '[' '' = yes ']' +++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' ++++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.bash hook +++ __conda_setup='export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'' + +# Copyright (C) 2012 Anaconda, Inc +# SPDX-License-Identifier: BSD-3-Clause +__conda_exe() ( + "$CONDA_EXE" $_CE_M $_CE_CONDA "$@" +) + +__conda_hashr() { + if [ -n "${ZSH_VERSION:+x}" ]; then + \rehash + elif [ -n "${POSH_VERSION:+x}" ]; then + : # pass + else + \hash -r + fi +} + +__conda_activate() { + if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then + # Handle transition from shell activated with conda <= 4.3 to a subsequent activation + # after conda updated to >= 4.4. See issue #6173. + PS1="$CONDA_PS1_BACKUP" + \unset CONDA_PS1_BACKUP + fi + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return + \eval "$ask_conda" + __conda_hashr +} + +__conda_reactivate() { + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return + \eval "$ask_conda" + __conda_hashr +} + +conda() { + \local cmd="${1-__missing__}" + case "$cmd" in + activate|deactivate) + __conda_activate "$@" + ;; + install|update|upgrade|remove|uninstall) + __conda_exe "$@" || \return + __conda_reactivate + ;; + *) + __conda_exe "$@" + ;; + esac +} + +if [ -z "${CONDA_SHLVL+x}" ]; then + \export CONDA_SHLVL=0 + # In dev-mode CONDA_EXE is python.exe and on Windows + # it is in a different relative location to condabin. + if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then + PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}" + else + PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}" + fi + \export PATH + + # We'\''re not allowing PS1 to be unbound. It must at least be set. + # However, we'\''re not exporting it, which can cause problems when starting a second shell + # via a first shell (i.e. starting zsh from bash). + if [ -z "${PS1+x}" ]; then + PS1= + fi +fi + +conda activate base' +++ '[' 0 -eq 0 ']' +++ eval 'export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'' + +# Copyright (C) 2012 Anaconda, Inc +# SPDX-License-Identifier: BSD-3-Clause +__conda_exe() ( + "$CONDA_EXE" $_CE_M $_CE_CONDA "$@" +) + +__conda_hashr() { + if [ -n "${ZSH_VERSION:+x}" ]; then + \rehash + elif [ -n "${POSH_VERSION:+x}" ]; then + : # pass + else + \hash -r + fi +} + +__conda_activate() { + if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then + # Handle transition from shell activated with conda <= 4.3 to a subsequent activation + # after conda updated to >= 4.4. See issue #6173. + PS1="$CONDA_PS1_BACKUP" + \unset CONDA_PS1_BACKUP + fi + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return + \eval "$ask_conda" + __conda_hashr +} + +__conda_reactivate() { + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return + \eval "$ask_conda" + __conda_hashr +} + +conda() { + \local cmd="${1-__missing__}" + case "$cmd" in + activate|deactivate) + __conda_activate "$@" + ;; + install|update|upgrade|remove|uninstall) + __conda_exe "$@" || \return + __conda_reactivate + ;; + *) + __conda_exe "$@" + ;; + esac +} + +if [ -z "${CONDA_SHLVL+x}" ]; then + \export CONDA_SHLVL=0 + # In dev-mode CONDA_EXE is python.exe and on Windows + # it is in a different relative location to condabin. + if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then + PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}" + else + PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}" + fi + \export PATH + + # We'\''re not allowing PS1 to be unbound. It must at least be set. + # However, we'\''re not exporting it, which can cause problems when starting a second shell + # via a first shell (i.e. starting zsh from bash). + if [ -z "${PS1+x}" ]; then + PS1= + fi +fi + +conda activate base' ++++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda ++++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda ++++ export _CE_M= ++++ _CE_M= ++++ export _CE_CONDA= ++++ _CE_CONDA= ++++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ '[' -z x ']' ++++ conda activate base ++++ local cmd=activate ++++ case "$cmd" in ++++ __conda_activate activate base ++++ '[' -n '' ']' ++++ local ask_conda +++++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++++ __conda_exe shell.posix activate base +++++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate base ++++ ask_conda='PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_SHLVL='\''6'\'' +export CONDA_DEFAULT_ENV='\''base'\'' +export CONDA_PROMPT_MODIFIER='\''(base) '\'' +export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' ++++ eval 'PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_SHLVL='\''6'\'' +export CONDA_DEFAULT_ENV='\''base'\'' +export CONDA_PROMPT_MODIFIER='\''(base) '\'' +export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' +++++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++++ export CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0 +++++ CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0 +++++ export CONDA_SHLVL=6 +++++ CONDA_SHLVL=6 +++++ export CONDA_DEFAULT_ENV=base +++++ CONDA_DEFAULT_ENV=base +++++ export 'CONDA_PROMPT_MODIFIER=(base) ' +++++ CONDA_PROMPT_MODIFIER='(base) ' +++++ export CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev +++++ CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev +++++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++++ export _CE_M= +++++ _CE_M= +++++ export _CE_CONDA= +++++ _CE_CONDA= +++++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python +++++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ __conda_hashr ++++ '[' -n '' ']' ++++ '[' -n '' ']' ++++ hash -r +++ unset __conda_setup ++ conda activate schemist-dev ++ local cmd=activate ++ case "$cmd" in ++ __conda_activate activate schemist-dev ++ '[' -n '' ']' ++ local ask_conda +++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++ __conda_exe shell.posix activate schemist-dev +++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate schemist-dev ++ ask_conda='PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_SHLVL='\''7'\'' +export CONDA_DEFAULT_ENV='\''schemist-dev'\'' +export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\'' +export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' ++ eval 'PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_SHLVL='\''7'\'' +export CONDA_DEFAULT_ENV='\''schemist-dev'\'' +export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\'' +export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' +++ PS1='(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++ export CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev +++ CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev +++ export CONDA_SHLVL=7 +++ CONDA_SHLVL=7 +++ export CONDA_DEFAULT_ENV=schemist-dev +++ CONDA_DEFAULT_ENV=schemist-dev +++ export 'CONDA_PROMPT_MODIFIER=(schemist-dev) ' +++ CONDA_PROMPT_MODIFIER='(schemist-dev) ' +++ export CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0 +++ CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0 +++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++ export _CE_M= +++ _CE_M= +++ export _CE_CONDA= +++ _CE_CONDA= +++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python +++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++ __conda_hashr ++ '[' -n '' ']' ++ '[' -n '' ']' ++ hash -r ++ CHUNK_HEAD_FILE=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz ++ INPUT=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/train/cyc-pep-6-12mer-70M_15.csv ++ COLUMN=cysteine_to_N_cyclization ++ PREFIX=cyclic_ ++ AWK='1 { print $8, $1, $2, $10, $3 }' ++ '[' -z cysteine_to_N_cyclization ']' ++ '[' -z cyclic_ ']' ++ '[' -z '1 { print $8, $1, $2, $10, $3 }' ']' ++ cat /dev/fd/63 /nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/train/cyc-pep-6-12mer-70M_15.csv ++ awk -F, -v OFS=, '1 { print $8, $1, $2, $10, $3 }' ++ gzip --best +++ zcat /nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz ++ schemist convert -f csv --column cysteine_to_N_cyclization --to id inchikey scaffold mwt clogp tpsa --prefix cyclic_ --options prefix=SCB- +++ head -n1 +++ tr ' ' , +🚀 Converting between string representations with the following parameters: + subcommand: convert + output: <_io.TextIOWrapper name='' mode='w' encoding='utf-8'> + format: csv + input: <_io.TextIOWrapper name='' mode='r' encoding='utf-8'> + representation: SMILES + column: cysteine_to_N_cyclization + prefix: cyclic_ + to: ['id', 'inchikey', 'scaffold', 'mwt', 'clogp', 'tpsa'] + options: ['prefix=SCB-'] + func: + 0it [00:00, ?it/s] 1it [00:21, 21.57s/it] 2it [00:45, 23.17s/it] 3it [01:10, 23.99s/it] 4it [01:34, 23.73s/it] 5it [01:58, 23.94s/it] 6it [02:23, 24.43s/it] 7it [02:50, 25.31s/it] 8it [03:18, 25.87s/it] 9it [03:39, 24.59s/it] 10it [04:06, 25.39s/it] 11it [04:33, 25.76s/it] 12it [04:58, 25.40s/it] 13it [05:25, 25.89s/it] 14it [05:51, 26.07s/it] 15it [06:19, 26.71s/it] 16it [06:44, 26.00s/it] 17it [07:09, 25.74s/it] 18it [07:35, 25.82s/it] 19it [08:00, 25.70s/it] 20it [08:25, 25.51s/it] 21it [08:51, 25.67s/it] 22it [09:14, 24.87s/it] 23it [09:38, 24.46s/it] 24it [10:00, 23.67s/it] 25it [10:26, 24.53s/it] 26it [10:52, 24.94s/it] 27it [11:16, 24.53s/it] 28it [11:41, 24.81s/it] 29it [12:03, 23.84s/it] 30it [12:25, 23.49s/it] 31it [12:48, 23.28s/it] 32it [13:12, 23.44s/it] 33it [13:37, 23.86s/it] 34it [14:00, 23.70s/it] 35it [14:25, 23.98s/it] 36it [14:51, 24.56s/it] 37it [15:15, 24.34s/it] 38it [15:39, 24.28s/it] 39it [16:04, 24.67s/it] 40it [16:30, 24.84s/it] 41it [16:56, 25.27s/it] 42it [17:22, 25.45s/it] 43it [17:48, 25.63s/it] 44it [18:14, 25.81s/it] 45it [18:38, 25.14s/it] 46it [19:03, 25.15s/it] 47it [19:27, 25.01s/it] 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945it [6:27:27, 21.85s/it] 946it [6:27:51, 22.50s/it] 947it [6:28:12, 21.94s/it] 948it [6:28:31, 21.22s/it] 949it [6:28:53, 21.47s/it] 950it [6:29:15, 21.71s/it] 951it [6:29:37, 21.82s/it] 952it [6:30:00, 22.03s/it] 953it [6:30:22, 22.10s/it] 954it [6:30:44, 21.97s/it] 955it [6:31:06, 21.89s/it] 956it [6:31:29, 22.28s/it] 957it [6:31:51, 22.30s/it] 958it [6:32:12, 21.72s/it] 959it [6:32:32, 21.43s/it] 960it [6:32:53, 21.29s/it] 961it [6:33:17, 21.94s/it] 962it [6:33:39, 22.15s/it] 963it [6:34:00, 21.82s/it] 964it [6:34:24, 22.45s/it] 965it [6:34:48, 22.70s/it] 966it [6:35:10, 22.62s/it] 967it [6:35:34, 22.96s/it] 968it [6:35:57, 23.14s/it] 969it [6:36:18, 22.47s/it] 970it [6:36:40, 22.35s/it] 971it [6:37:04, 22.86s/it] 972it [6:37:29, 23.36s/it] 973it [6:37:50, 22.76s/it] 974it [6:38:13, 22.87s/it] 975it [6:38:37, 23.12s/it] 976it [6:39:00, 22.94s/it] 977it [6:39:23, 22.97s/it] 978it [6:39:47, 23.28s/it] 979it [6:40:11, 23.62s/it] 980it [6:40:36, 23.88s/it] 981it [6:41:00, 24.15s/it] 982it [6:41:25, 24.28s/it] 983it [6:41:49, 24.23s/it] 984it [6:42:11, 23.65s/it] 985it [6:42:34, 23.36s/it] 986it [6:42:58, 23.60s/it] 987it [6:43:21, 23.36s/it] 988it [6:43:43, 22.87s/it] 989it [6:44:07, 23.35s/it] 990it [6:44:29, 22.99s/it] 991it [6:44:53, 23.19s/it] 992it [6:45:15, 22.70s/it] 993it [6:45:37, 22.51s/it] 994it [6:46:00, 22.70s/it] 995it [6:46:21, 22.25s/it] 996it [6:46:43, 22.20s/it] 997it [6:47:06, 22.41s/it] 998it [6:47:27, 21.97s/it] 999it [6:47:49, 22.12s/it] 1000it [6:48:11, 22.09s/it] 1000it [6:48:11, 24.49s/it] +Error counts: + cyclic_id: 0 + cyclic_inchikey: 0 + cyclic_scaffold: 0 + cyclic_mwt: 0 + cyclic_clogp: 0 + cyclic_tpsa: 0 +⏰ Completed process in 6:48:40.533636 ++ rm /nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/train/cyc-pep-6-12mer-70M_15.csv diff --git a/train/cyc-pep-6-12mer-70M_16.csv.gz b/train/cyc-pep-6-12mer-70M_16.csv.gz index aca2e15a9bfa7ec2c844d3c603e595aaa442fa5e..53c903db15310e12e7a9f9aacc51eec305d53bca 100644 --- a/train/cyc-pep-6-12mer-70M_16.csv.gz +++ b/train/cyc-pep-6-12mer-70M_16.csv.gz @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:06dbcd8a6c85aa0592dfc90b44e01ed3b65fd5dcee73bdb32c098b966aba4647 -size 65613795 +oid sha256:109f70565c4ca8cff0475a4396a260abbfa294a3458207f081b1965e8eb84e3a +size 122453945 diff --git a/train/cyc-pep-6-12mer-70M_16.log b/train/cyc-pep-6-12mer-70M_16.log new file mode 100644 index 0000000000000000000000000000000000000000..d756a637747dd4a0883babaa888d652ecc493395 --- /dev/null +++ b/train/cyc-pep-6-12mer-70M_16.log @@ -0,0 +1,337 @@ ++ module purge ++ '[' -z '' ']' ++ case "$-" in ++ __lmod_sh_dbg=x ++ '[' -n x ']' ++ set +x +Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output +Shell debugging restarted ++ unset __lmod_sh_dbg ++ return 0 ++ module load Anaconda3/2023.03 ++ '[' -z '' ']' ++ case "$-" in ++ __lmod_sh_dbg=x ++ '[' -n x ']' ++ set +x +Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output +Shell debugging restarted ++ unset __lmod_sh_dbg ++ return 0 ++ source /camp/home/johnsoe/.bashrc +++ '[' '' = yes ']' +++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' ++++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.bash hook +++ __conda_setup='export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'' + +# Copyright (C) 2012 Anaconda, Inc +# SPDX-License-Identifier: BSD-3-Clause +__conda_exe() ( + "$CONDA_EXE" $_CE_M $_CE_CONDA "$@" +) + +__conda_hashr() { + if [ -n "${ZSH_VERSION:+x}" ]; then + \rehash + elif [ -n "${POSH_VERSION:+x}" ]; then + : # pass + else + \hash -r + fi +} + +__conda_activate() { + if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then + # Handle transition from shell activated with conda <= 4.3 to a subsequent activation + # after conda updated to >= 4.4. See issue #6173. + PS1="$CONDA_PS1_BACKUP" + \unset CONDA_PS1_BACKUP + fi + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return + \eval "$ask_conda" + __conda_hashr +} + +__conda_reactivate() { + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return + \eval "$ask_conda" + __conda_hashr +} + +conda() { + \local cmd="${1-__missing__}" + case "$cmd" in + activate|deactivate) + __conda_activate "$@" + ;; + install|update|upgrade|remove|uninstall) + __conda_exe "$@" || \return + __conda_reactivate + ;; + *) + __conda_exe "$@" + ;; + esac +} + +if [ -z "${CONDA_SHLVL+x}" ]; then + \export CONDA_SHLVL=0 + # In dev-mode CONDA_EXE is python.exe and on Windows + # it is in a different relative location to condabin. + if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then + PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}" + else + PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}" + fi + \export PATH + + # We'\''re not allowing PS1 to be unbound. It must at least be set. + # However, we'\''re not exporting it, which can cause problems when starting a second shell + # via a first shell (i.e. starting zsh from bash). + if [ -z "${PS1+x}" ]; then + PS1= + fi +fi + +conda activate base' +++ '[' 0 -eq 0 ']' +++ eval 'export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'' + +# Copyright (C) 2012 Anaconda, Inc +# SPDX-License-Identifier: BSD-3-Clause +__conda_exe() ( + "$CONDA_EXE" $_CE_M $_CE_CONDA "$@" +) + +__conda_hashr() { + if [ -n "${ZSH_VERSION:+x}" ]; then + \rehash + elif [ -n "${POSH_VERSION:+x}" ]; then + : # pass + else + \hash -r + fi +} + +__conda_activate() { + if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then + # Handle transition from shell activated with conda <= 4.3 to a subsequent activation + # after conda updated to >= 4.4. See issue #6173. + PS1="$CONDA_PS1_BACKUP" + \unset CONDA_PS1_BACKUP + fi + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return + \eval "$ask_conda" + __conda_hashr +} + +__conda_reactivate() { + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return + \eval "$ask_conda" + __conda_hashr +} + +conda() { + \local cmd="${1-__missing__}" + case "$cmd" in + activate|deactivate) + __conda_activate "$@" + ;; + install|update|upgrade|remove|uninstall) + __conda_exe "$@" || \return + __conda_reactivate + ;; + *) + __conda_exe "$@" + ;; + esac +} + +if [ -z "${CONDA_SHLVL+x}" ]; then + \export CONDA_SHLVL=0 + # In dev-mode CONDA_EXE is python.exe and on Windows + # it is in a different relative location to condabin. + if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then + PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}" + else + PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}" + fi + \export PATH + + # We'\''re not allowing PS1 to be unbound. It must at least be set. + # However, we'\''re not exporting it, which can cause problems when starting a second shell + # via a first shell (i.e. starting zsh from bash). + if [ -z "${PS1+x}" ]; then + PS1= + fi +fi + +conda activate base' ++++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda ++++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda ++++ export _CE_M= ++++ _CE_M= ++++ export _CE_CONDA= ++++ _CE_CONDA= ++++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ '[' -z x ']' ++++ conda activate base ++++ local cmd=activate ++++ case "$cmd" in ++++ __conda_activate activate base ++++ '[' -n '' ']' ++++ local ask_conda +++++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++++ __conda_exe shell.posix activate base +++++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate base ++++ ask_conda='PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_SHLVL='\''6'\'' +export CONDA_DEFAULT_ENV='\''base'\'' +export CONDA_PROMPT_MODIFIER='\''(base) '\'' +export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' ++++ eval 'PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_SHLVL='\''6'\'' +export CONDA_DEFAULT_ENV='\''base'\'' +export CONDA_PROMPT_MODIFIER='\''(base) '\'' +export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' +++++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++++ export CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0 +++++ CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0 +++++ export CONDA_SHLVL=6 +++++ CONDA_SHLVL=6 +++++ export CONDA_DEFAULT_ENV=base +++++ CONDA_DEFAULT_ENV=base +++++ export 'CONDA_PROMPT_MODIFIER=(base) ' +++++ CONDA_PROMPT_MODIFIER='(base) ' +++++ export CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev +++++ CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev +++++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++++ export _CE_M= +++++ _CE_M= +++++ export _CE_CONDA= +++++ _CE_CONDA= +++++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python +++++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ __conda_hashr ++++ '[' -n '' ']' ++++ '[' -n '' ']' ++++ hash -r +++ unset __conda_setup ++ conda activate schemist-dev ++ local cmd=activate ++ case "$cmd" in ++ __conda_activate activate schemist-dev ++ '[' -n '' ']' ++ local ask_conda +++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++ __conda_exe shell.posix activate schemist-dev +++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate schemist-dev ++ ask_conda='PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_SHLVL='\''7'\'' +export CONDA_DEFAULT_ENV='\''schemist-dev'\'' +export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\'' +export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' ++ eval 'PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_SHLVL='\''7'\'' +export CONDA_DEFAULT_ENV='\''schemist-dev'\'' +export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\'' +export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' +++ PS1='(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++ export CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev +++ CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev +++ export CONDA_SHLVL=7 +++ CONDA_SHLVL=7 +++ export CONDA_DEFAULT_ENV=schemist-dev +++ CONDA_DEFAULT_ENV=schemist-dev +++ export 'CONDA_PROMPT_MODIFIER=(schemist-dev) ' +++ CONDA_PROMPT_MODIFIER='(schemist-dev) ' +++ export CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0 +++ CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0 +++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++ export _CE_M= +++ _CE_M= +++ export _CE_CONDA= +++ _CE_CONDA= +++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python +++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++ __conda_hashr ++ '[' -n '' ']' ++ '[' -n '' ']' ++ hash -r ++ CHUNK_HEAD_FILE=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz ++ INPUT=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/train/cyc-pep-6-12mer-70M_16.csv ++ COLUMN=cysteine_to_N_cyclization ++ PREFIX=cyclic_ ++ AWK='1 { print $8, $1, $2, $10, $3 }' ++ '[' -z cysteine_to_N_cyclization ']' ++ '[' -z cyclic_ ']' ++ '[' -z '1 { print $8, $1, $2, $10, $3 }' ']' ++ awk -F, -v OFS=, '1 { print $8, $1, $2, $10, $3 }' ++ cat /dev/fd/63 /nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/train/cyc-pep-6-12mer-70M_16.csv +++ zcat /nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz ++ schemist convert -f csv --column cysteine_to_N_cyclization --to id inchikey scaffold mwt clogp tpsa --prefix cyclic_ --options prefix=SCB- ++ gzip --best +++ head -n1 +++ tr ' ' , +🚀 Converting between string representations with the following parameters: + subcommand: convert + output: <_io.TextIOWrapper name='' mode='w' encoding='utf-8'> + format: csv + input: <_io.TextIOWrapper name='' mode='r' encoding='utf-8'> + representation: SMILES + column: cysteine_to_N_cyclization + prefix: cyclic_ + to: ['id', 'inchikey', 'scaffold', 'mwt', 'clogp', 'tpsa'] + options: ['prefix=SCB-'] + func: + 0it [00:00, ?it/s] 1it [00:13, 13.06s/it] 2it [00:25, 12.92s/it] 3it [00:38, 12.89s/it] 4it [00:51, 12.90s/it] 5it [01:04, 12.87s/it] 6it [01:17, 12.88s/it] 7it [01:30, 12.87s/it] 8it [01:43, 12.87s/it] 9it [01:56, 12.91s/it] 10it [02:08, 12.90s/it] 11it [02:21, 12.90s/it] 12it [02:34, 12.88s/it] 13it [02:47, 12.88s/it] 14it [03:00, 12.91s/it] 15it [03:13, 12.91s/it] 16it [03:26, 12.91s/it] 17it [03:39, 12.87s/it] 18it [03:52, 12.88s/it] 19it [04:04, 12.85s/it] 20it [04:17, 12.86s/it] 21it [04:30, 12.87s/it] 22it [04:43, 12.83s/it] 23it [04:56, 12.83s/it] 24it [05:09, 12.88s/it] 25it [05:22, 12.89s/it] 26it [05:34, 12.89s/it] 27it [05:47, 12.87s/it] 28it [06:00, 12.85s/it] 29it [06:13, 12.84s/it] 30it [06:26, 12.85s/it] 31it [06:39, 12.88s/it] 32it [06:52, 12.88s/it] 33it [07:04, 12.87s/it] 34it [07:17, 12.89s/it] 35it [07:30, 12.87s/it] 36it [07:43, 12.85s/it] 37it [07:56, 12.86s/it] 38it [08:09, 12.87s/it] 39it [08:22, 12.87s/it] 40it [08:34, 12.84s/it] 41it [08:47, 12.84s/it] 42it [09:00, 12.85s/it] 43it [09:13, 12.82s/it] 44it [09:26, 12.83s/it] 45it [09:39, 12.82s/it] 46it [09:51, 12.85s/it] 47it [10:04, 12.82s/it] 48it [10:17, 12.82s/it] 49it [10:30, 12.83s/it] 50it [10:43, 12.85s/it] 51it [10:56, 12.87s/it] 52it [11:09, 12.87s/it] 53it [11:22, 12.89s/it] 54it [11:34, 12.88s/it] 55it [11:47, 12.88s/it] 56it [12:00, 12.86s/it] 57it [12:13, 12.86s/it] 58it [12:26, 12.82s/it] 59it [12:39, 12.86s/it] 60it [12:51, 12.85s/it] 61it [13:04, 12.87s/it] 62it [13:17, 12.85s/it] 63it [13:30, 12.85s/it] 64it [13:43, 12.85s/it] 65it [13:56, 12.85s/it] 66it [14:09, 12.84s/it] 67it [14:21, 12.84s/it] 68it [14:34, 12.83s/it] 69it [14:47, 12.84s/it] 70it [15:00, 12.85s/it] 71it [15:13, 12.85s/it] 72it [15:25, 12.81s/it] 73it [15:38, 12.81s/it] 74it [15:51, 12.82s/it] 75it [16:04, 12.83s/it] 76it [16:17, 12.84s/it] 77it [16:30, 12.86s/it] 78it [16:43, 12.87s/it] 79it [16:55, 12.85s/it] 80it [17:08, 12.89s/it] 81it [17:21, 12.90s/it] 82it [17:34, 12.90s/it] 83it [17:47, 12.91s/it] 84it [18:00, 12.88s/it] 85it [18:13, 12.89s/it] 86it [18:26, 12.88s/it] 87it [18:39, 12.86s/it] 88it [18:51, 12.87s/it] 89it [19:04, 12.87s/it] 90it [19:17, 12.85s/it] 91it [19:30, 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13.02s/it] 957it [3:26:18, 13.03s/it] 958it [3:26:31, 13.04s/it] 959it [3:26:44, 13.03s/it] 960it [3:26:58, 13.03s/it] 961it [3:27:11, 13.04s/it] 962it [3:27:24, 13.07s/it] 963it [3:27:37, 13.10s/it] 964it [3:27:50, 13.08s/it] 965it [3:28:03, 13.04s/it] 966it [3:28:16, 13.06s/it] 967it [3:28:29, 13.07s/it] 968it [3:28:42, 13.09s/it] 969it [3:28:55, 13.07s/it] 970it [3:29:08, 13.06s/it] 971it [3:29:21, 13.10s/it] 972it [3:29:35, 13.11s/it] 973it [3:29:48, 13.15s/it] 974it [3:30:01, 13.12s/it] 975it [3:30:14, 13.11s/it] 976it [3:30:27, 13.15s/it] 977it [3:30:40, 13.14s/it] 978it [3:30:53, 13.12s/it] 979it [3:31:06, 13.11s/it] 980it [3:31:19, 13.08s/it] 981it [3:31:33, 13.11s/it] 982it [3:31:46, 13.08s/it] 983it [3:31:59, 13.12s/it] 984it [3:32:12, 13.06s/it] 985it [3:32:25, 13.08s/it] 986it [3:32:38, 13.05s/it] 987it [3:32:51, 13.08s/it] 988it [3:33:04, 13.08s/it] 989it [3:33:17, 13.06s/it] 990it [3:33:30, 13.08s/it] 991it [3:33:43, 13.08s/it] 992it [3:33:56, 13.09s/it] 993it [3:34:10, 13.08s/it] 994it [3:34:23, 13.09s/it] 995it [3:34:36, 13.04s/it] 996it [3:34:49, 13.04s/it] 997it [3:35:02, 13.04s/it] 998it [3:35:15, 13.08s/it] 999it [3:35:28, 13.08s/it] 1000it [3:35:41, 13.05s/it] 1000it [3:35:41, 12.94s/it] +Error counts: + cyclic_id: 0 + cyclic_inchikey: 0 + cyclic_scaffold: 0 + cyclic_mwt: 0 + cyclic_clogp: 0 + cyclic_tpsa: 0 +⏰ Completed process in 3:36:06.095438 ++ rm /nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/train/cyc-pep-6-12mer-70M_16.csv diff --git a/train/cyc-pep-6-12mer-70M_17.csv.gz b/train/cyc-pep-6-12mer-70M_17.csv.gz index 6b394970f1cec16c8a0083a80be731a7021cf18e..d63a15476f8484e09a447cf2dbbe5868a2aff394 100644 --- a/train/cyc-pep-6-12mer-70M_17.csv.gz +++ b/train/cyc-pep-6-12mer-70M_17.csv.gz @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:425bf558aa8768237147bd35da187e9f5302fd5e11499057c8335bd87caf0dd8 -size 65621644 +oid sha256:0c46e682dddf11ceb670b4255a30fe1a79f3ee7a75e3123de68a93f511bf15c1 +size 122461529 diff --git a/train/cyc-pep-6-12mer-70M_17.log b/train/cyc-pep-6-12mer-70M_17.log new file mode 100644 index 0000000000000000000000000000000000000000..0379b37e18c7885748940a636017f69c8f611ece --- /dev/null +++ b/train/cyc-pep-6-12mer-70M_17.log @@ -0,0 +1,337 @@ ++ module purge ++ '[' -z '' ']' ++ case "$-" in ++ __lmod_sh_dbg=x ++ '[' -n x ']' ++ set +x +Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output +Shell debugging restarted ++ unset __lmod_sh_dbg ++ return 0 ++ module load Anaconda3/2023.03 ++ '[' -z '' ']' ++ case "$-" in ++ __lmod_sh_dbg=x ++ '[' -n x ']' ++ set +x +Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output +Shell debugging restarted ++ unset __lmod_sh_dbg ++ return 0 ++ source /camp/home/johnsoe/.bashrc +++ '[' '' = yes ']' +++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' ++++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.bash hook +++ __conda_setup='export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'' + +# Copyright (C) 2012 Anaconda, Inc +# SPDX-License-Identifier: BSD-3-Clause +__conda_exe() ( + "$CONDA_EXE" $_CE_M $_CE_CONDA "$@" +) + +__conda_hashr() { + if [ -n "${ZSH_VERSION:+x}" ]; then + \rehash + elif [ -n "${POSH_VERSION:+x}" ]; then + : # pass + else + \hash -r + fi +} + +__conda_activate() { + if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then + # Handle transition from shell activated with conda <= 4.3 to a subsequent activation + # after conda updated to >= 4.4. See issue #6173. + PS1="$CONDA_PS1_BACKUP" + \unset CONDA_PS1_BACKUP + fi + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return + \eval "$ask_conda" + __conda_hashr +} + +__conda_reactivate() { + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return + \eval "$ask_conda" + __conda_hashr +} + +conda() { + \local cmd="${1-__missing__}" + case "$cmd" in + activate|deactivate) + __conda_activate "$@" + ;; + install|update|upgrade|remove|uninstall) + __conda_exe "$@" || \return + __conda_reactivate + ;; + *) + __conda_exe "$@" + ;; + esac +} + +if [ -z "${CONDA_SHLVL+x}" ]; then + \export CONDA_SHLVL=0 + # In dev-mode CONDA_EXE is python.exe and on Windows + # it is in a different relative location to condabin. + if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then + PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}" + else + PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}" + fi + \export PATH + + # We'\''re not allowing PS1 to be unbound. It must at least be set. + # However, we'\''re not exporting it, which can cause problems when starting a second shell + # via a first shell (i.e. starting zsh from bash). + if [ -z "${PS1+x}" ]; then + PS1= + fi +fi + +conda activate base' +++ '[' 0 -eq 0 ']' +++ eval 'export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'' + +# Copyright (C) 2012 Anaconda, Inc +# SPDX-License-Identifier: BSD-3-Clause +__conda_exe() ( + "$CONDA_EXE" $_CE_M $_CE_CONDA "$@" +) + +__conda_hashr() { + if [ -n "${ZSH_VERSION:+x}" ]; then + \rehash + elif [ -n "${POSH_VERSION:+x}" ]; then + : # pass + else + \hash -r + fi +} + +__conda_activate() { + if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then + # Handle transition from shell activated with conda <= 4.3 to a subsequent activation + # after conda updated to >= 4.4. See issue #6173. + PS1="$CONDA_PS1_BACKUP" + \unset CONDA_PS1_BACKUP + fi + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return + \eval "$ask_conda" + __conda_hashr +} + +__conda_reactivate() { + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return + \eval "$ask_conda" + __conda_hashr +} + +conda() { + \local cmd="${1-__missing__}" + case "$cmd" in + activate|deactivate) + __conda_activate "$@" + ;; + install|update|upgrade|remove|uninstall) + __conda_exe "$@" || \return + __conda_reactivate + ;; + *) + __conda_exe "$@" + ;; + esac +} + +if [ -z "${CONDA_SHLVL+x}" ]; then + \export CONDA_SHLVL=0 + # In dev-mode CONDA_EXE is python.exe and on Windows + # it is in a different relative location to condabin. + if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then + PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}" + else + PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}" + fi + \export PATH + + # We'\''re not allowing PS1 to be unbound. It must at least be set. + # However, we'\''re not exporting it, which can cause problems when starting a second shell + # via a first shell (i.e. starting zsh from bash). + if [ -z "${PS1+x}" ]; then + PS1= + fi +fi + +conda activate base' ++++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda ++++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda ++++ export _CE_M= ++++ _CE_M= ++++ export _CE_CONDA= ++++ _CE_CONDA= ++++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ '[' -z x ']' ++++ conda activate base ++++ local cmd=activate ++++ case "$cmd" in ++++ __conda_activate activate base ++++ '[' -n '' ']' ++++ local ask_conda +++++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++++ __conda_exe shell.posix activate base +++++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate base ++++ ask_conda='PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_SHLVL='\''6'\'' +export CONDA_DEFAULT_ENV='\''base'\'' +export CONDA_PROMPT_MODIFIER='\''(base) '\'' +export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' ++++ eval 'PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_SHLVL='\''6'\'' +export CONDA_DEFAULT_ENV='\''base'\'' +export CONDA_PROMPT_MODIFIER='\''(base) '\'' +export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' +++++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++++ export CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0 +++++ CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0 +++++ export CONDA_SHLVL=6 +++++ CONDA_SHLVL=6 +++++ export CONDA_DEFAULT_ENV=base +++++ CONDA_DEFAULT_ENV=base +++++ export 'CONDA_PROMPT_MODIFIER=(base) ' +++++ CONDA_PROMPT_MODIFIER='(base) ' +++++ export CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev +++++ CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev +++++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++++ export _CE_M= +++++ _CE_M= +++++ export _CE_CONDA= +++++ _CE_CONDA= +++++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python +++++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ __conda_hashr ++++ '[' -n '' ']' ++++ '[' -n '' ']' ++++ hash -r +++ unset __conda_setup ++ conda activate schemist-dev ++ local cmd=activate ++ case "$cmd" in ++ __conda_activate activate schemist-dev ++ '[' -n '' ']' ++ local ask_conda +++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++ __conda_exe shell.posix activate schemist-dev +++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate schemist-dev ++ ask_conda='PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_SHLVL='\''7'\'' +export CONDA_DEFAULT_ENV='\''schemist-dev'\'' +export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\'' +export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' ++ eval 'PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_SHLVL='\''7'\'' +export CONDA_DEFAULT_ENV='\''schemist-dev'\'' +export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\'' +export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' +++ PS1='(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++ export CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev +++ CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev +++ export CONDA_SHLVL=7 +++ CONDA_SHLVL=7 +++ export CONDA_DEFAULT_ENV=schemist-dev +++ CONDA_DEFAULT_ENV=schemist-dev +++ export 'CONDA_PROMPT_MODIFIER=(schemist-dev) ' +++ CONDA_PROMPT_MODIFIER='(schemist-dev) ' +++ export CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0 +++ CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0 +++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++ export _CE_M= +++ _CE_M= +++ export _CE_CONDA= +++ _CE_CONDA= +++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python +++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++ __conda_hashr ++ '[' -n '' ']' ++ '[' -n '' ']' ++ hash -r ++ CHUNK_HEAD_FILE=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz ++ INPUT=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/train/cyc-pep-6-12mer-70M_17.csv ++ COLUMN=cysteine_to_N_cyclization ++ PREFIX=cyclic_ ++ AWK='1 { print $8, $1, $2, $10, $3 }' ++ '[' -z cysteine_to_N_cyclization ']' ++ '[' -z cyclic_ ']' ++ '[' -z '1 { print $8, $1, $2, $10, $3 }' ']' ++ cat /dev/fd/63 /nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/train/cyc-pep-6-12mer-70M_17.csv ++ awk -F, -v OFS=, '1 { print $8, $1, $2, $10, $3 }' +++ zcat /nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz ++ schemist convert -f csv --column cysteine_to_N_cyclization --to id inchikey scaffold mwt clogp tpsa --prefix cyclic_ --options prefix=SCB- ++ gzip --best +++ head -n1 +++ tr ' ' , +🚀 Converting between string representations with the following parameters: + subcommand: convert + output: <_io.TextIOWrapper name='' mode='w' encoding='utf-8'> + format: csv + input: <_io.TextIOWrapper name='' mode='r' encoding='utf-8'> + representation: SMILES + column: cysteine_to_N_cyclization + prefix: cyclic_ + to: ['id', 'inchikey', 'scaffold', 'mwt', 'clogp', 'tpsa'] + options: ['prefix=SCB-'] + func: + 0it [00:00, ?it/s] 1it [00:13, 13.36s/it] 2it [00:26, 13.17s/it] 3it [00:39, 13.06s/it] 4it [00:52, 13.01s/it] 5it [01:05, 12.95s/it] 6it 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[3:26:14, 13.07s/it] 956it [3:26:28, 13.10s/it] 957it [3:26:41, 13.10s/it] 958it [3:26:54, 13.13s/it] 959it [3:27:07, 13.15s/it] 960it [3:27:20, 13.19s/it] 961it [3:27:34, 13.22s/it] 962it [3:27:47, 13.19s/it] 963it [3:28:00, 13.19s/it] 964it [3:28:13, 13.18s/it] 965it [3:28:26, 13.20s/it] 966it [3:28:40, 13.21s/it] 967it [3:28:53, 13.19s/it] 968it [3:29:06, 13.26s/it] 969it [3:29:20, 13.36s/it] 970it [3:29:33, 13.36s/it] 971it [3:29:46, 13.35s/it] 972it [3:29:59, 13.27s/it] 973it [3:30:13, 13.32s/it] 974it [3:30:26, 13.33s/it] 975it [3:30:39, 13.29s/it] 976it [3:30:53, 13.26s/it] 977it [3:31:06, 13.30s/it] 978it [3:31:19, 13.34s/it] 979it [3:31:33, 13.50s/it] 980it [3:31:47, 13.50s/it] 981it [3:32:00, 13.54s/it] 982it [3:32:14, 13.44s/it] 983it [3:32:27, 13.46s/it] 984it [3:32:40, 13.37s/it] 985it [3:32:54, 13.31s/it] 986it [3:33:07, 13.28s/it] 987it [3:33:20, 13.23s/it] 988it [3:33:34, 13.45s/it] 989it [3:33:47, 13.43s/it] 990it [3:34:00, 13.38s/it] 991it [3:34:14, 13.32s/it] 992it [3:34:27, 13.34s/it] 993it [3:34:40, 13.26s/it] 994it [3:34:53, 13.29s/it] 995it [3:35:07, 13.33s/it] 996it [3:35:20, 13.28s/it] 997it [3:35:33, 13.30s/it] 998it [3:35:47, 13.30s/it] 999it [3:36:00, 13.28s/it] 1000it [3:36:13, 13.33s/it] 1000it [3:36:13, 12.97s/it] +Error counts: + cyclic_id: 0 + cyclic_inchikey: 0 + cyclic_scaffold: 0 + cyclic_mwt: 0 + cyclic_clogp: 0 + cyclic_tpsa: 0 +⏰ Completed process in 3:36:38.290184 ++ rm /nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/train/cyc-pep-6-12mer-70M_17.csv diff --git a/train/cyc-pep-6-12mer-70M_18.csv.gz b/train/cyc-pep-6-12mer-70M_18.csv.gz index c5f4ebc464bdb147249f338d470a43a1709430a9..088735f0c0f5142a8b2d0c5932adbebfb6a75157 100644 --- a/train/cyc-pep-6-12mer-70M_18.csv.gz +++ b/train/cyc-pep-6-12mer-70M_18.csv.gz @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:a2bd84313f18e2368facdea16d61856e864ce17fd082936d95180bff1596fcc9 -size 65623633 +oid sha256:fc815c886442acc164cf88c13ee5f9fa17a30d157b6eda00c5e63f5f1d588458 +size 122461716 diff --git a/train/cyc-pep-6-12mer-70M_18.log b/train/cyc-pep-6-12mer-70M_18.log new file mode 100644 index 0000000000000000000000000000000000000000..f0912cbc2890f898fa83081834bf1bca49bb172b --- /dev/null +++ b/train/cyc-pep-6-12mer-70M_18.log @@ -0,0 +1,337 @@ ++ module purge ++ '[' -z '' ']' ++ case "$-" in ++ __lmod_sh_dbg=x ++ '[' -n x ']' ++ set +x +Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output +Shell debugging restarted ++ unset __lmod_sh_dbg ++ return 0 ++ module load Anaconda3/2023.03 ++ '[' -z '' ']' ++ case "$-" in ++ __lmod_sh_dbg=x ++ '[' -n x ']' ++ set +x +Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output +Shell debugging restarted ++ unset __lmod_sh_dbg ++ return 0 ++ source /camp/home/johnsoe/.bashrc +++ '[' '' = yes ']' +++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' ++++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.bash hook +++ __conda_setup='export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'' + +# Copyright (C) 2012 Anaconda, Inc +# SPDX-License-Identifier: BSD-3-Clause +__conda_exe() ( + "$CONDA_EXE" $_CE_M $_CE_CONDA "$@" +) + +__conda_hashr() { + if [ -n "${ZSH_VERSION:+x}" ]; then + \rehash + elif [ -n "${POSH_VERSION:+x}" ]; then + : # pass + else + \hash -r + fi +} + +__conda_activate() { + if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then + # Handle transition from shell activated with conda <= 4.3 to a subsequent activation + # after conda updated to >= 4.4. See issue #6173. + PS1="$CONDA_PS1_BACKUP" + \unset CONDA_PS1_BACKUP + fi + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return + \eval "$ask_conda" + __conda_hashr +} + +__conda_reactivate() { + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return + \eval "$ask_conda" + __conda_hashr +} + +conda() { + \local cmd="${1-__missing__}" + case "$cmd" in + activate|deactivate) + __conda_activate "$@" + ;; + install|update|upgrade|remove|uninstall) + __conda_exe "$@" || \return + __conda_reactivate + ;; + *) + __conda_exe "$@" + ;; + esac +} + +if [ -z "${CONDA_SHLVL+x}" ]; then + \export CONDA_SHLVL=0 + # In dev-mode CONDA_EXE is python.exe and on Windows + # it is in a different relative location to condabin. + if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then + PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}" + else + PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}" + fi + \export PATH + + # We'\''re not allowing PS1 to be unbound. It must at least be set. + # However, we'\''re not exporting it, which can cause problems when starting a second shell + # via a first shell (i.e. starting zsh from bash). + if [ -z "${PS1+x}" ]; then + PS1= + fi +fi + +conda activate base' +++ '[' 0 -eq 0 ']' +++ eval 'export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'' + +# Copyright (C) 2012 Anaconda, Inc +# SPDX-License-Identifier: BSD-3-Clause +__conda_exe() ( + "$CONDA_EXE" $_CE_M $_CE_CONDA "$@" +) + +__conda_hashr() { + if [ -n "${ZSH_VERSION:+x}" ]; then + \rehash + elif [ -n "${POSH_VERSION:+x}" ]; then + : # pass + else + \hash -r + fi +} + +__conda_activate() { + if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then + # Handle transition from shell activated with conda <= 4.3 to a subsequent activation + # after conda updated to >= 4.4. See issue #6173. + PS1="$CONDA_PS1_BACKUP" + \unset CONDA_PS1_BACKUP + fi + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return + \eval "$ask_conda" + __conda_hashr +} + +__conda_reactivate() { + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return + \eval "$ask_conda" + __conda_hashr +} + +conda() { + \local cmd="${1-__missing__}" + case "$cmd" in + activate|deactivate) + __conda_activate "$@" + ;; + install|update|upgrade|remove|uninstall) + __conda_exe "$@" || \return + __conda_reactivate + ;; + *) + __conda_exe "$@" + ;; + esac +} + +if [ -z "${CONDA_SHLVL+x}" ]; then + \export CONDA_SHLVL=0 + # In dev-mode CONDA_EXE is python.exe and on Windows + # it is in a different relative location to condabin. + if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then + PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}" + else + PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}" + fi + \export PATH + + # We'\''re not allowing PS1 to be unbound. It must at least be set. + # However, we'\''re not exporting it, which can cause problems when starting a second shell + # via a first shell (i.e. starting zsh from bash). + if [ -z "${PS1+x}" ]; then + PS1= + fi +fi + +conda activate base' ++++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda ++++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda ++++ export _CE_M= ++++ _CE_M= ++++ export _CE_CONDA= ++++ _CE_CONDA= ++++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ '[' -z x ']' ++++ conda activate base ++++ local cmd=activate ++++ case "$cmd" in ++++ __conda_activate activate base ++++ '[' -n '' ']' ++++ local ask_conda +++++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++++ __conda_exe shell.posix activate base +++++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate base ++++ ask_conda='PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_SHLVL='\''6'\'' +export CONDA_DEFAULT_ENV='\''base'\'' +export CONDA_PROMPT_MODIFIER='\''(base) '\'' +export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' ++++ eval 'PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_SHLVL='\''6'\'' +export CONDA_DEFAULT_ENV='\''base'\'' +export CONDA_PROMPT_MODIFIER='\''(base) '\'' +export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' +++++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++++ export CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0 +++++ CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0 +++++ export CONDA_SHLVL=6 +++++ CONDA_SHLVL=6 +++++ export CONDA_DEFAULT_ENV=base +++++ CONDA_DEFAULT_ENV=base +++++ export 'CONDA_PROMPT_MODIFIER=(base) ' +++++ CONDA_PROMPT_MODIFIER='(base) ' +++++ export CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev +++++ CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev +++++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++++ export _CE_M= +++++ _CE_M= +++++ export _CE_CONDA= +++++ _CE_CONDA= +++++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python +++++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ __conda_hashr ++++ '[' -n '' ']' ++++ '[' -n '' ']' ++++ hash -r +++ unset __conda_setup ++ conda activate schemist-dev ++ local cmd=activate ++ case "$cmd" in ++ __conda_activate activate schemist-dev ++ '[' -n '' ']' ++ local ask_conda +++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++ __conda_exe shell.posix activate schemist-dev +++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate schemist-dev ++ ask_conda='PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_SHLVL='\''7'\'' +export CONDA_DEFAULT_ENV='\''schemist-dev'\'' +export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\'' +export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' ++ eval 'PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_SHLVL='\''7'\'' +export CONDA_DEFAULT_ENV='\''schemist-dev'\'' +export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\'' +export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' +++ PS1='(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++ export CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev +++ CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev +++ export CONDA_SHLVL=7 +++ CONDA_SHLVL=7 +++ export CONDA_DEFAULT_ENV=schemist-dev +++ CONDA_DEFAULT_ENV=schemist-dev +++ export 'CONDA_PROMPT_MODIFIER=(schemist-dev) ' +++ CONDA_PROMPT_MODIFIER='(schemist-dev) ' +++ export CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0 +++ CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0 +++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++ export _CE_M= +++ _CE_M= +++ export _CE_CONDA= +++ _CE_CONDA= +++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python +++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++ __conda_hashr ++ '[' -n '' ']' ++ '[' -n '' ']' ++ hash -r ++ CHUNK_HEAD_FILE=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz ++ INPUT=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/train/cyc-pep-6-12mer-70M_18.csv ++ COLUMN=cysteine_to_N_cyclization ++ PREFIX=cyclic_ ++ AWK='1 { print $8, $1, $2, $10, $3 }' ++ '[' -z cysteine_to_N_cyclization ']' ++ '[' -z cyclic_ ']' ++ '[' -z '1 { print $8, $1, $2, $10, $3 }' ']' ++ cat /dev/fd/63 /nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/train/cyc-pep-6-12mer-70M_18.csv ++ schemist convert -f csv --column cysteine_to_N_cyclization --to id inchikey scaffold mwt clogp tpsa --prefix cyclic_ --options prefix=SCB- ++ gzip --best ++ awk -F, -v OFS=, '1 { print $8, $1, $2, $10, $3 }' +++ zcat /nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz +++ tr ' ' , +++ head -n1 +🚀 Converting between string representations with the following parameters: + subcommand: convert + output: <_io.TextIOWrapper name='' mode='w' encoding='utf-8'> + format: csv + input: <_io.TextIOWrapper name='' mode='r' encoding='utf-8'> + representation: SMILES + column: cysteine_to_N_cyclization + prefix: cyclic_ + to: ['id', 'inchikey', 'scaffold', 'mwt', 'clogp', 'tpsa'] + options: ['prefix=SCB-'] + func: + 0it [00:00, ?it/s] 1it [00:12, 12.55s/it] 2it [00:25, 12.50s/it] 3it [00:37, 12.48s/it] 4it [00:50, 12.50s/it] 5it [01:02, 12.49s/it] 6it [01:14, 12.49s/it] 7it [01:27, 12.47s/it] 8it [01:39, 12.48s/it] 9it [01:52, 12.49s/it] 10it [02:04, 12.48s/it] 11it [02:17, 12.45s/it] 12it [02:29, 12.47s/it] 13it [02:42, 12.47s/it] 14it [02:54, 12.47s/it] 15it [03:07, 12.49s/it] 16it [03:19, 12.48s/it] 17it [03:32, 12.48s/it] 18it [03:44, 12.47s/it] 19it [03:57, 12.47s/it] 20it [04:09, 12.48s/it] 21it [04:22, 12.47s/it] 22it [04:34, 12.45s/it] 23it [04:46, 12.46s/it] 24it [04:59, 12.45s/it] 25it [05:11, 12.45s/it] 26it [05:24, 12.45s/it] 27it [05:36, 12.44s/it] 28it [05:49, 12.42s/it] 29it [06:01, 12.40s/it] 30it [06:13, 12.37s/it] 31it [06:26, 12.40s/it] 32it [06:38, 12.39s/it] 33it [06:50, 12.40s/it] 34it [07:03, 12.40s/it] 35it [07:15, 12.40s/it] 36it [07:28, 12.39s/it] 37it [07:40, 12.41s/it] 38it [07:52, 12.40s/it] 39it [08:05, 12.41s/it] 40it [08:17, 12.40s/it] 41it [08:30, 12.39s/it] 42it [08:42, 12.41s/it] 43it [08:54, 12.42s/it] 44it [09:07, 12.43s/it] 45it [09:19, 12.44s/it] 46it [09:32, 12.44s/it] 47it [09:44, 12.44s/it] 48it [09:57, 12.43s/it] 49it [10:09, 12.41s/it] 50it [10:21, 12.41s/it] 51it [10:34, 12.40s/it] 52it [10:46, 12.39s/it] 53it [10:59, 12.41s/it] 54it [11:11, 12.43s/it] 55it [11:24, 12.44s/it] 56it [11:36, 12.44s/it] 57it [11:49, 12.45s/it] 58it [12:01, 12.42s/it] 59it [12:13, 12.42s/it] 60it [12:26, 12.41s/it] 61it [12:38, 12.41s/it] 62it [12:51, 12.43s/it] 63it [13:03, 12.43s/it] 64it [13:15, 12.41s/it] 65it [13:28, 12.42s/it] 66it [13:40, 12.42s/it] 67it [13:53, 12.41s/it] 68it [14:05, 12.41s/it] 69it [14:17, 12.42s/it] 70it [14:30, 12.43s/it] 71it [14:42, 12.42s/it] 72it [14:55, 12.42s/it] 73it [15:07, 12.44s/it] 74it [15:20, 12.42s/it] 75it [15:32, 12.39s/it] 76it [15:44, 12.42s/it] 77it [15:57, 12.42s/it] 78it [16:09, 12.42s/it] 79it [16:22, 12.43s/it] 80it [16:34, 12.43s/it] 81it [16:47, 12.44s/it] 82it [16:59, 12.46s/it] 83it [17:12, 12.48s/it] 84it [17:24, 12.44s/it] 85it [17:36, 12.45s/it] 86it [17:49, 12.47s/it] 87it [18:01, 12.44s/it] 88it [18:14, 12.43s/it] 89it [18:26, 12.46s/it] 90it [18:39, 12.44s/it] 91it [18:51, 12.44s/it] 92it [19:04, 12.45s/it] 93it [19:16, 12.45s/it] 94it [19:28, 12.45s/it] 95it [19:41, 12.43s/it] 96it [19:53, 12.42s/it] 97it [20:06, 12.46s/it] 98it [20:18, 12.44s/it] 99it [20:31, 12.45s/it] 100it [20:43, 12.47s/it] 101it [20:56, 12.46s/it] 102it [21:08, 12.45s/it] 103it [21:20, 12.45s/it] 104it [21:33, 12.46s/it] 105it [21:45, 12.43s/it] 106it [21:58, 12.42s/it] 107it [22:10, 12.42s/it] 108it [22:23, 12.42s/it] 109it [22:35, 12.42s/it] 110it [22:47, 12.40s/it] 111it [23:00, 12.42s/it] 112it [23:12, 12.42s/it] 113it [23:25, 12.42s/it] 114it [23:37, 12.41s/it] 115it [23:49, 12.39s/it] 116it [24:02, 12.41s/it] 117it [24:14, 12.41s/it] 118it [24:27, 12.41s/it] 119it [24:39, 12.43s/it] 120it [24:52, 12.43s/it] 121it [25:04, 12.43s/it] 122it [25:16, 12.42s/it] 123it [25:29, 12.44s/it] 124it [25:41, 12.45s/it] 125it [25:54, 12.45s/it] 126it [26:06, 12.46s/it] 127it [26:19, 12.46s/it] 128it [26:31, 12.46s/it] 129it [26:44, 12.46s/it] 130it [26:56, 12.46s/it] 131it [27:09, 12.46s/it] 132it [27:21, 12.46s/it] 133it [27:33, 12.44s/it] 134it [27:46, 12.45s/it] 135it [27:58, 12.42s/it] 136it [28:11, 12.43s/it] 137it [28:23, 12.44s/it] 138it [28:36, 12.45s/it] 139it [28:48, 12.45s/it] 140it [29:01, 12.45s/it] 141it [29:13, 12.42s/it] 142it [29:25, 12.43s/it] 143it [29:38, 12.43s/it] 144it [29:50, 12.41s/it] 145it [30:03, 12.43s/it] 146it [30:15, 12.45s/it] 147it [30:28, 12.44s/it] 148it [30:40, 12.42s/it] 149it [30:52, 12.41s/it] 150it [31:05, 12.40s/it] 151it [31:17, 12.40s/it] 152it [31:30, 12.43s/it] 153it [31:42, 12.43s/it] 154it [31:54, 12.41s/it] 155it [32:07, 12.42s/it] 156it [32:19, 12.44s/it] 157it [32:32, 12.43s/it] 158it [32:44, 12.45s/it] 159it [32:57, 12.45s/it] 160it [33:09, 12.44s/it] 161it [33:21, 12.43s/it] 162it [33:34, 12.45s/it] 163it [33:46, 12.45s/it] 164it [33:59, 12.47s/it] 165it [34:11, 12.48s/it] 166it [34:24, 12.49s/it] 167it [34:36, 12.50s/it] 168it [34:49, 12.46s/it] 169it [35:01, 12.47s/it] 170it [35:14, 12.46s/it] 171it [35:26, 12.47s/it] 172it [35:39, 12.44s/it] 173it [35:51, 12.44s/it] 174it [36:04, 12.45s/it] 175it [36:16, 12.44s/it] 176it [36:28, 12.45s/it] 177it [36:41, 12.45s/it] 178it [36:53, 12.42s/it] 179it [37:06, 12.43s/it] 180it [37:18, 12.41s/it] 181it [37:31, 12.44s/it] 182it [37:43, 12.43s/it] 183it [37:55, 12.44s/it] 184it [38:08, 12.44s/it] 185it [38:20, 12.45s/it] 186it [38:33, 12.46s/it] 187it [38:45, 12.43s/it] 188it [38:58, 12.41s/it] 189it [39:10, 12.40s/it] 190it [39:22, 12.41s/it] 191it [39:35, 12.42s/it] 192it [39:47, 12.46s/it] 193it [40:00, 12.45s/it] 194it [40:12, 12.45s/it] 195it [40:25, 12.44s/it] 196it [40:37, 12.45s/it] 197it [40:50, 12.44s/it] 198it [41:02, 12.44s/it] 199it [41:14, 12.44s/it] 200it [41:27, 12.45s/it] 201it [41:39, 12.45s/it] 202it [41:52, 12.47s/it] 203it [42:04, 12.51s/it] 204it [42:17, 12.52s/it] 205it [42:30, 12.54s/it] 206it [42:42, 12.55s/it] 207it [42:55, 12.54s/it] 208it [43:07, 12.54s/it] 209it [43:20, 12.53s/it] 210it [43:32, 12.51s/it] 211it [43:45, 12.52s/it] 212it [43:57, 12.52s/it] 213it [44:10, 12.55s/it] 214it [44:22, 12.55s/it] 215it [44:35, 12.51s/it] 216it [44:47, 12.53s/it] 217it [45:00, 12.54s/it] 218it [45:12, 12.52s/it] 219it [45:25, 12.52s/it] 220it [45:37, 12.52s/it] 221it [45:50, 12.52s/it] 222it [46:02, 12.49s/it] 223it [46:15, 12.53s/it] 224it [46:28, 12.52s/it] 225it [46:40, 12.54s/it] 226it [46:53, 12.53s/it] 227it [47:05, 12.54s/it] 228it [47:18, 12.55s/it] 229it [47:30, 12.55s/it] 230it [47:43, 12.55s/it] 231it [47:55, 12.56s/it] 232it [48:08, 12.56s/it] 233it [48:21, 12.54s/it] 234it [48:33, 12.53s/it] 235it [48:45, 12.50s/it] 236it [48:58, 12.46s/it] 237it [49:10, 12.50s/it] 238it [49:23, 12.51s/it] 239it [49:35, 12.49s/it] 240it [49:48, 12.50s/it] 241it [50:00, 12.51s/it] 242it [50:13, 12.50s/it] 243it [50:25, 12.49s/it] 244it [50:38, 12.46s/it] 245it [50:50, 12.46s/it] 246it [51:03, 12.48s/it] 247it [51:15, 12.49s/it] 248it [51:28, 12.50s/it] 249it [51:40, 12.48s/it] 250it [51:53, 12.49s/it] 251it [52:05, 12.47s/it] 252it [52:18, 12.48s/it] 253it [52:30, 12.44s/it] 254it [52:43, 12.46s/it] 255it [52:55, 12.44s/it] 256it [53:07, 12.43s/it] 257it [53:20, 12.42s/it] 258it [53:32, 12.43s/it] 259it [53:45, 12.42s/it] 260it [53:57, 12.43s/it] 261it [54:10, 12.45s/it] 262it [54:22, 12.46s/it] 263it [54:34, 12.45s/it] 264it [54:47, 12.48s/it] 265it [54:59, 12.47s/it] 266it [55:12, 12.46s/it] 267it [55:24, 12.46s/it] 268it [55:37, 12.47s/it] 269it [55:49, 12.50s/it] 270it [56:02, 12.50s/it] 271it [56:14, 12.50s/it] 272it [56:27, 12.51s/it] 273it [56:39, 12.52s/it] 274it [56:52, 12.52s/it] 275it [57:04, 12.50s/it] 276it [57:17, 12.48s/it] 277it [57:29, 12.49s/it] 278it [57:42, 12.51s/it] 279it [57:54, 12.50s/it] 280it [58:07, 12.51s/it] 281it [58:19, 12.50s/it] 282it [58:32, 12.50s/it] 283it [58:44, 12.49s/it] 284it [58:57, 12.47s/it] 285it [59:09, 12.49s/it] 286it [59:22, 12.48s/it] 287it [59:34, 12.47s/it] 288it [59:47, 12.45s/it] 289it [59:59, 12.46s/it] 290it [1:00:12, 12.47s/it] 291it [1:00:24, 12.47s/it] 292it [1:00:37, 12.47s/it] 293it [1:00:49, 12.46s/it] 294it [1:01:02, 12.49s/it] 295it [1:01:14, 12.46s/it] 296it [1:01:26, 12.49s/it] 297it [1:01:39, 12.48s/it] 298it [1:01:51, 12.48s/it] 299it [1:02:04, 12.49s/it] 300it [1:02:16, 12.50s/it] 301it [1:02:29, 12.50s/it] 302it [1:02:41, 12.49s/it] 303it [1:02:54, 12.49s/it] 304it [1:03:06, 12.50s/it] 305it [1:03:19, 12.49s/it] 306it [1:03:31, 12.49s/it] 307it [1:03:44, 12.51s/it] 308it [1:03:56, 12.51s/it] 309it [1:04:09, 12.52s/it] 310it [1:04:22, 12.54s/it] 311it [1:04:34, 12.55s/it] 312it [1:04:47, 12.56s/it] 313it [1:04:59, 12.59s/it] 314it [1:05:12, 12.58s/it] 315it [1:05:24, 12.56s/it] 316it [1:05:37, 12.56s/it] 317it [1:05:50, 12.56s/it] 318it [1:06:02, 12.54s/it] 319it [1:06:15, 12.55s/it] 320it [1:06:27, 12.54s/it] 321it [1:06:40, 12.53s/it] 322it [1:06:52, 12.53s/it] 323it [1:07:05, 12.49s/it] 324it [1:07:17, 12.50s/it] 325it [1:07:30, 12.50s/it] 326it [1:07:42, 12.47s/it] 327it [1:07:55, 12.47s/it] 328it [1:08:07, 12.47s/it] 329it [1:08:20, 12.48s/it] 330it [1:08:32, 12.50s/it] 331it [1:08:45, 12.51s/it] 332it [1:08:57, 12.51s/it] 333it [1:09:10, 12.53s/it] 334it [1:09:22, 12.54s/it] 335it [1:09:35, 12.59s/it] 336it [1:09:48, 12.60s/it] 337it [1:10:00, 12.59s/it] 338it [1:10:13, 12.55s/it] 339it [1:10:25, 12.53s/it] 340it [1:10:38, 12.54s/it] 341it [1:10:50, 12.52s/it] 342it [1:11:03, 12.53s/it] 343it [1:11:15, 12.50s/it] 344it [1:11:28, 12.49s/it] 345it [1:11:40, 12.51s/it] 346it [1:11:53, 12.52s/it] 347it [1:12:05, 12.51s/it] 348it [1:12:18, 12.53s/it] 349it [1:12:30, 12.56s/it] 350it [1:12:43, 12.61s/it] 351it [1:12:56, 12.63s/it] 352it [1:13:08, 12.61s/it] 353it [1:13:21, 12.62s/it] 354it [1:13:33, 12.58s/it] 355it [1:13:46, 12.57s/it] 356it [1:13:58, 12.55s/it] 357it [1:14:11, 12.53s/it] 358it [1:14:23, 12.51s/it] 359it [1:14:36, 12.52s/it] 360it [1:14:49, 12.52s/it] 361it [1:15:01, 12.53s/it] 362it [1:15:14, 12.55s/it] 363it [1:15:26, 12.56s/it] 364it [1:15:39, 12.57s/it] 365it [1:15:51, 12.55s/it] 366it [1:16:04, 12.54s/it] 367it [1:16:17, 12.57s/it] 368it [1:16:29, 12.56s/it] 369it [1:16:42, 12.53s/it] 370it [1:16:54, 12.50s/it] 371it [1:17:06, 12.47s/it] 372it [1:17:19, 12.47s/it] 373it [1:17:31, 12.48s/it] 374it [1:17:44, 12.46s/it] 375it [1:17:56, 12.47s/it] 376it [1:18:09, 12.47s/it] 377it [1:18:21, 12.48s/it] 378it [1:18:34, 12.50s/it] 379it [1:18:46, 12.50s/it] 380it [1:18:59, 12.51s/it] 381it [1:19:11, 12.53s/it] 382it [1:19:24, 12.52s/it] 383it [1:19:36, 12.49s/it] 384it [1:19:49, 12.51s/it] 385it [1:20:01, 12.51s/it] 386it [1:20:14, 12.52s/it] 387it [1:20:26, 12.51s/it] 388it [1:20:39, 12.48s/it] 389it [1:20:51, 12.50s/it] 390it [1:21:04, 12.49s/it] 391it [1:21:16, 12.51s/it] 392it [1:21:29, 12.53s/it] 393it [1:21:42, 12.55s/it] 394it [1:21:54, 12.53s/it] 395it [1:22:06, 12.52s/it] 396it [1:22:19, 12.53s/it] 397it [1:22:32, 12.53s/it] 398it [1:22:44, 12.55s/it] 399it [1:22:57, 12.55s/it] 400it [1:23:09, 12.57s/it] 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919it [3:18:00, 13.74s/it] 920it [3:18:14, 13.84s/it] 921it [3:18:28, 13.87s/it] 922it [3:18:42, 13.88s/it] 923it [3:18:56, 13.95s/it] 924it [3:19:10, 13.94s/it] 925it [3:19:24, 13.85s/it] 926it [3:19:38, 13.84s/it] 927it [3:19:52, 13.89s/it] 928it [3:20:06, 13.90s/it] 929it [3:20:19, 13.83s/it] 930it [3:20:33, 13.78s/it] 931it [3:20:47, 13.85s/it] 932it [3:21:01, 13.83s/it] 933it [3:21:14, 13.78s/it] 934it [3:21:28, 13.76s/it] 935it [3:21:42, 13.77s/it] 936it [3:21:56, 13.86s/it] 937it [3:22:10, 13.87s/it] 938it [3:22:23, 13.82s/it] 939it [3:22:37, 13.81s/it] 940it [3:22:51, 13.90s/it] 941it [3:23:05, 13.95s/it] 942it [3:23:19, 13.87s/it] 943it [3:23:33, 13.75s/it] 944it [3:23:46, 13.72s/it] 945it [3:24:00, 13.80s/it] 946it [3:24:14, 13.82s/it] 947it [3:24:28, 13.76s/it] 948it [3:24:42, 13.79s/it] 949it [3:24:55, 13.80s/it] 950it [3:25:09, 13.78s/it] 951it [3:25:23, 13.78s/it] 952it [3:25:37, 13.80s/it] 953it [3:25:51, 13.83s/it] 954it [3:26:05, 13.88s/it] 955it [3:26:18, 13.84s/it] 956it [3:26:32, 13.83s/it] 957it [3:26:46, 13.80s/it] 958it [3:27:00, 13.79s/it] 959it [3:27:14, 13.81s/it] 960it [3:27:27, 13.79s/it] 961it [3:27:41, 13.78s/it] 962it [3:27:55, 13.79s/it] 963it [3:28:09, 13.85s/it] 964it [3:28:23, 13.85s/it] 965it [3:28:36, 13.80s/it] 966it [3:28:50, 13.74s/it] 967it [3:29:04, 13.72s/it] 968it [3:29:18, 13.83s/it] 969it [3:29:32, 13.84s/it] 970it [3:29:45, 13.83s/it] 971it [3:29:59, 13.79s/it] 972it [3:30:13, 13.80s/it] 973it [3:30:27, 13.88s/it] 974it [3:30:40, 13.74s/it] 975it [3:30:54, 13.72s/it] 976it [3:31:08, 13.72s/it] 977it [3:31:22, 13.79s/it] 978it [3:31:36, 13.84s/it] 979it [3:31:49, 13.81s/it] 980it [3:32:03, 13.75s/it] 981it [3:32:17, 13.73s/it] 982it [3:32:31, 13.79s/it] 983it [3:32:45, 13.82s/it] 984it [3:32:58, 13.79s/it] 985it [3:33:12, 13.79s/it] 986it [3:33:26, 13.78s/it] 987it [3:33:40, 13.84s/it] 988it [3:33:54, 13.88s/it] 989it [3:34:08, 13.87s/it] 990it [3:34:21, 13.86s/it] 991it [3:34:35, 13.85s/it] 992it [3:34:49, 13.91s/it] 993it [3:35:03, 13.85s/it] 994it [3:35:17, 13.81s/it] 995it [3:35:31, 13.82s/it] 996it [3:35:45, 13.87s/it] 997it [3:35:58, 13.84s/it] 998it [3:36:12, 13.78s/it] 999it [3:36:26, 13.79s/it] 1000it [3:36:40, 13.85s/it] 1000it [3:36:40, 13.00s/it] +Error counts: + cyclic_id: 0 + cyclic_inchikey: 0 + cyclic_scaffold: 0 + cyclic_mwt: 0 + cyclic_clogp: 0 + cyclic_tpsa: 0 +⏰ Completed process in 3:37:05.204538 ++ rm /nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/train/cyc-pep-6-12mer-70M_18.csv diff --git a/train/cyc-pep-6-12mer-70M_19.csv.gz b/train/cyc-pep-6-12mer-70M_19.csv.gz index 034829a4ebb1a7e2e02d8aee288d9eb810cb6aa1..e6666458d368899230739431c55efe128542c698 100644 --- a/train/cyc-pep-6-12mer-70M_19.csv.gz +++ b/train/cyc-pep-6-12mer-70M_19.csv.gz @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:e14a57944c05f39d362ad516f8f292aa8e04ae8953675f95467666f83a795230 -size 65624473 +oid sha256:817be2a7c6dbfd2465ef21a15df38ea3b0efb7c0440681131f359d7021b6e91a +size 122463465 diff --git a/train/cyc-pep-6-12mer-70M_19.log b/train/cyc-pep-6-12mer-70M_19.log new file mode 100644 index 0000000000000000000000000000000000000000..7e2614008c4c9c5eee0f8afd74dca42da0f72fd8 --- /dev/null +++ b/train/cyc-pep-6-12mer-70M_19.log @@ -0,0 +1,337 @@ ++ module purge ++ '[' -z '' ']' ++ case "$-" in ++ __lmod_sh_dbg=x ++ '[' -n x ']' ++ set +x +Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output +Shell debugging restarted ++ unset __lmod_sh_dbg ++ return 0 ++ module load Anaconda3/2023.03 ++ '[' -z '' ']' ++ case "$-" in ++ __lmod_sh_dbg=x ++ '[' -n x ']' ++ set +x +Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output +Shell debugging restarted ++ unset __lmod_sh_dbg ++ return 0 ++ source /camp/home/johnsoe/.bashrc +++ '[' '' = yes ']' +++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' ++++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.bash hook +++ __conda_setup='export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'' + +# Copyright (C) 2012 Anaconda, Inc +# SPDX-License-Identifier: BSD-3-Clause +__conda_exe() ( + "$CONDA_EXE" $_CE_M $_CE_CONDA "$@" +) + +__conda_hashr() { + if [ -n "${ZSH_VERSION:+x}" ]; then + \rehash + elif [ -n "${POSH_VERSION:+x}" ]; then + : # pass + else + \hash -r + fi +} + +__conda_activate() { + if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then + # Handle transition from shell activated with conda <= 4.3 to a subsequent activation + # after conda updated to >= 4.4. See issue #6173. + PS1="$CONDA_PS1_BACKUP" + \unset CONDA_PS1_BACKUP + fi + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return + \eval "$ask_conda" + __conda_hashr +} + +__conda_reactivate() { + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return + \eval "$ask_conda" + __conda_hashr +} + +conda() { + \local cmd="${1-__missing__}" + case "$cmd" in + activate|deactivate) + __conda_activate "$@" + ;; + install|update|upgrade|remove|uninstall) + __conda_exe "$@" || \return + __conda_reactivate + ;; + *) + __conda_exe "$@" + ;; + esac +} + +if [ -z "${CONDA_SHLVL+x}" ]; then + \export CONDA_SHLVL=0 + # In dev-mode CONDA_EXE is python.exe and on Windows + # it is in a different relative location to condabin. + if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then + PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}" + else + PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}" + fi + \export PATH + + # We'\''re not allowing PS1 to be unbound. It must at least be set. + # However, we'\''re not exporting it, which can cause problems when starting a second shell + # via a first shell (i.e. starting zsh from bash). + if [ -z "${PS1+x}" ]; then + PS1= + fi +fi + +conda activate base' +++ '[' 0 -eq 0 ']' +++ eval 'export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'' + +# Copyright (C) 2012 Anaconda, Inc +# SPDX-License-Identifier: BSD-3-Clause +__conda_exe() ( + "$CONDA_EXE" $_CE_M $_CE_CONDA "$@" +) + +__conda_hashr() { + if [ -n "${ZSH_VERSION:+x}" ]; then + \rehash + elif [ -n "${POSH_VERSION:+x}" ]; then + : # pass + else + \hash -r + fi +} + +__conda_activate() { + if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then + # Handle transition from shell activated with conda <= 4.3 to a subsequent activation + # after conda updated to >= 4.4. See issue #6173. + PS1="$CONDA_PS1_BACKUP" + \unset CONDA_PS1_BACKUP + fi + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return + \eval "$ask_conda" + __conda_hashr +} + +__conda_reactivate() { + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return + \eval "$ask_conda" + __conda_hashr +} + +conda() { + \local cmd="${1-__missing__}" + case "$cmd" in + activate|deactivate) + __conda_activate "$@" + ;; + install|update|upgrade|remove|uninstall) + __conda_exe "$@" || \return + __conda_reactivate + ;; + *) + __conda_exe "$@" + ;; + esac +} + +if [ -z "${CONDA_SHLVL+x}" ]; then + \export CONDA_SHLVL=0 + # In dev-mode CONDA_EXE is python.exe and on Windows + # it is in a different relative location to condabin. + if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then + PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}" + else + PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}" + fi + \export PATH + + # We'\''re not allowing PS1 to be unbound. It must at least be set. + # However, we'\''re not exporting it, which can cause problems when starting a second shell + # via a first shell (i.e. starting zsh from bash). + if [ -z "${PS1+x}" ]; then + PS1= + fi +fi + +conda activate base' ++++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda ++++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda ++++ export _CE_M= ++++ _CE_M= ++++ export _CE_CONDA= ++++ _CE_CONDA= ++++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ '[' -z x ']' ++++ conda activate base ++++ local cmd=activate ++++ case "$cmd" in ++++ __conda_activate activate base ++++ '[' -n '' ']' ++++ local ask_conda +++++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++++ __conda_exe shell.posix activate base +++++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate base ++++ ask_conda='PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_SHLVL='\''6'\'' +export CONDA_DEFAULT_ENV='\''base'\'' +export CONDA_PROMPT_MODIFIER='\''(base) '\'' +export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' ++++ eval 'PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_SHLVL='\''6'\'' +export CONDA_DEFAULT_ENV='\''base'\'' +export CONDA_PROMPT_MODIFIER='\''(base) '\'' +export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' +++++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++++ export CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0 +++++ CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0 +++++ export CONDA_SHLVL=6 +++++ CONDA_SHLVL=6 +++++ export CONDA_DEFAULT_ENV=base +++++ CONDA_DEFAULT_ENV=base +++++ export 'CONDA_PROMPT_MODIFIER=(base) ' +++++ CONDA_PROMPT_MODIFIER='(base) ' +++++ export CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev +++++ CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev +++++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++++ export _CE_M= +++++ _CE_M= +++++ export _CE_CONDA= +++++ _CE_CONDA= +++++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python +++++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ __conda_hashr ++++ '[' -n '' ']' ++++ '[' -n '' ']' ++++ hash -r +++ unset __conda_setup ++ conda activate schemist-dev ++ local cmd=activate ++ case "$cmd" in ++ __conda_activate activate schemist-dev ++ '[' -n '' ']' ++ local ask_conda +++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++ __conda_exe shell.posix activate schemist-dev +++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate schemist-dev ++ ask_conda='PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_SHLVL='\''7'\'' +export CONDA_DEFAULT_ENV='\''schemist-dev'\'' +export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\'' +export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' ++ eval 'PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_SHLVL='\''7'\'' +export CONDA_DEFAULT_ENV='\''schemist-dev'\'' +export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\'' +export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' +++ PS1='(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++ export CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev +++ CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev +++ export CONDA_SHLVL=7 +++ CONDA_SHLVL=7 +++ export CONDA_DEFAULT_ENV=schemist-dev +++ CONDA_DEFAULT_ENV=schemist-dev +++ export 'CONDA_PROMPT_MODIFIER=(schemist-dev) ' +++ CONDA_PROMPT_MODIFIER='(schemist-dev) ' +++ export CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0 +++ CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0 +++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++ export _CE_M= +++ _CE_M= +++ export _CE_CONDA= +++ _CE_CONDA= +++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python +++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++ __conda_hashr ++ '[' -n '' ']' ++ '[' -n '' ']' ++ hash -r ++ CHUNK_HEAD_FILE=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz ++ INPUT=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/train/cyc-pep-6-12mer-70M_19.csv ++ COLUMN=cysteine_to_N_cyclization ++ PREFIX=cyclic_ ++ AWK='1 { print $8, $1, $2, $10, $3 }' ++ '[' -z cysteine_to_N_cyclization ']' ++ '[' -z cyclic_ ']' ++ '[' -z '1 { print $8, $1, $2, $10, $3 }' ']' ++ cat /dev/fd/63 /nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/train/cyc-pep-6-12mer-70M_19.csv ++ awk -F, -v OFS=, '1 { print $8, $1, $2, $10, $3 }' ++ schemist convert -f csv --column cysteine_to_N_cyclization --to id inchikey scaffold mwt clogp tpsa --prefix cyclic_ --options prefix=SCB- +++ zcat /nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz ++ gzip --best +++ head -n1 +++ tr ' ' , +🚀 Converting between string representations with the following parameters: + subcommand: convert + output: <_io.TextIOWrapper name='' mode='w' encoding='utf-8'> + format: csv + input: <_io.TextIOWrapper name='' mode='r' encoding='utf-8'> + representation: SMILES + column: cysteine_to_N_cyclization + prefix: cyclic_ + to: ['id', 'inchikey', 'scaffold', 'mwt', 'clogp', 'tpsa'] + options: ['prefix=SCB-'] + func: + 0it [00:00, ?it/s] 1it [00:13, 13.06s/it] 2it [00:25, 12.99s/it] 3it [00:38, 12.95s/it] 4it [00:51, 12.92s/it] 5it [01:04, 12.93s/it] 6it [01:17, 12.97s/it] 7it [01:30, 12.94s/it] 8it [01:43, 12.91s/it] 9it [01:56, 12.89s/it] 10it [02:09, 12.89s/it] 11it [02:22, 12.92s/it] 12it [02:35, 12.92s/it] 13it [02:48, 12.94s/it] 14it [03:01, 12.94s/it] 15it [03:13, 12.93s/it] 16it [03:26, 12.92s/it] 17it [03:39, 12.92s/it] 18it [03:52, 12.92s/it] 19it [04:05, 12.91s/it] 20it [04:18, 12.90s/it] 21it [04:31, 12.90s/it] 22it [04:44, 12.88s/it] 23it [04:57, 12.89s/it] 24it [05:10, 12.89s/it] 25it [05:22, 12.89s/it] 26it [05:35, 12.89s/it] 27it [05:48, 12.90s/it] 28it [06:01, 12.91s/it] 29it [06:14, 12.91s/it] 30it [06:27, 12.90s/it] 31it [06:40, 12.91s/it] 32it [06:53, 12.91s/it] 33it [07:06, 12.86s/it] 34it [07:18, 12.88s/it] 35it [07:31, 12.90s/it] 36it [07:44, 12.92s/it] 37it [07:57, 12.93s/it] 38it [08:10, 12.93s/it] 39it [08:23, 12.92s/it] 40it [08:36, 12.92s/it] 41it [08:49, 12.90s/it] 42it [09:02, 12.91s/it] 43it [09:15, 12.90s/it] 44it [09:28, 12.91s/it] 45it [09:41, 12.90s/it] 46it [09:53, 12.90s/it] 47it [10:06, 12.90s/it] 48it [10:19, 12.91s/it] 49it [10:32, 12.86s/it] 50it [10:45, 12.89s/it] 51it [10:58, 12.87s/it] 52it [11:11, 12.87s/it] 53it [11:24, 12.85s/it] 54it [11:36, 12.85s/it] 55it [11:49, 12.88s/it] 56it [12:02, 12.88s/it] 57it [12:15, 12.91s/it] 58it [12:28, 12.94s/it] 59it [12:41, 12.91s/it] 60it [12:54, 12.89s/it] 61it [13:07, 12.91s/it] 62it [13:20, 12.92s/it] 63it [13:33, 12.91s/it] 64it [13:46, 12.90s/it] 65it [13:58, 12.90s/it] 66it [14:11, 12.91s/it] 67it [14:24, 12.91s/it] 68it [14:37, 12.92s/it] 69it [14:50, 12.92s/it] 70it [15:03, 12.89s/it] 71it [15:16, 12.88s/it] 72it [15:29, 12.90s/it] 73it [15:42, 12.90s/it] 74it [15:55, 12.89s/it] 75it [16:07, 12.89s/it] 76it [16:20, 12.91s/it] 77it [16:33, 12.89s/it] 78it [16:46, 12.88s/it] 79it [16:59, 12.87s/it] 80it [17:12, 12.88s/it] 81it [17:25, 12.86s/it] 82it [17:38, 12.89s/it] 83it [17:51, 12.92s/it] 84it [18:03, 12.90s/it] 85it [18:16, 12.87s/it] 86it [18:29, 12.86s/it] 87it [18:42, 12.85s/it] 88it [18:55, 12.83s/it] 89it [19:08, 12.83s/it] 90it [19:20, 12.85s/it] 91it [19:33, 12.84s/it] 92it [19:46, 12.85s/it] 93it [19:59, 12.87s/it] 94it [20:12, 12.89s/it] 95it [20:25, 12.89s/it] 96it [20:38, 12.90s/it] 97it [20:51, 12.88s/it] 98it [21:04, 12.89s/it] 99it [21:16, 12.89s/it] 100it [21:29, 12.90s/it] 101it [21:42, 12.88s/it] 102it [21:55, 12.87s/it] 103it [22:08, 12.87s/it] 104it [22:21, 12.83s/it] 105it [22:33, 12.83s/it] 106it [22:46, 12.85s/it] 107it [22:59, 12.88s/it] 108it [23:12, 12.88s/it] 109it [23:25, 12.88s/it] 110it [23:38, 12.86s/it] 111it [23:51, 12.87s/it] 112it [24:04, 12.86s/it] 113it [24:16, 12.83s/it] 114it [24:29, 12.86s/it] 115it [24:42, 12.87s/it] 116it [24:55, 12.86s/it] 117it [25:08, 12.84s/it] 118it [25:21, 12.81s/it] 119it [25:33, 12.84s/it] 120it [25:46, 12.83s/it] 121it [25:59, 12.83s/it] 122it [26:12, 12.81s/it] 123it [26:25, 12.80s/it] 124it [26:38, 12.83s/it] 125it [26:50, 12.83s/it] 126it [27:03, 12.86s/it] 127it [27:16, 12.82s/it] 128it [27:29, 12.79s/it] 129it [27:42, 12.80s/it] 130it [27:54, 12.78s/it] 131it [28:07, 12.79s/it] 132it [28:20, 12.81s/it] 133it [28:33, 12.83s/it] 134it [28:46, 12.86s/it] 135it [28:59, 12.84s/it] 136it [29:11, 12.84s/it] 137it [29:24, 12.86s/it] 138it [29:37, 12.85s/it] 139it [29:50, 12.85s/it] 140it [30:03, 12.86s/it] 141it [30:16, 12.87s/it] 142it [30:29, 12.88s/it] 143it [30:42, 12.87s/it] 144it [30:54, 12.89s/it] 145it [31:07, 12.90s/it] 146it [31:20, 12.89s/it] 147it [31:33, 12.92s/it] 148it [31:46, 12.93s/it] 149it [31:59, 12.92s/it] 150it [32:12, 12.91s/it] 151it [32:25, 12.90s/it] 152it [32:38, 12.88s/it] 153it [32:51, 12.87s/it] 154it [33:03, 12.87s/it] 155it [33:16, 12.90s/it] 156it [33:29, 12.92s/it] 157it [33:42, 12.91s/it] 158it [33:55, 12.93s/it] 159it [34:08, 12.95s/it] 160it [34:21, 12.95s/it] 161it [34:34, 12.94s/it] 162it [34:47, 12.95s/it] 163it [35:00, 12.97s/it] 164it [35:13, 12.95s/it] 165it [35:26, 12.92s/it] 166it [35:39, 12.89s/it] 167it [35:52, 12.91s/it] 168it [36:04, 12.90s/it] 169it [36:17, 12.93s/it] 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[3:29:26, 13.12s/it] 956it [3:29:39, 13.15s/it] 957it [3:29:52, 13.18s/it] 958it [3:30:05, 13.18s/it] 959it [3:30:19, 13.26s/it] 960it [3:30:32, 13.23s/it] 961it [3:30:45, 13.21s/it] 962it [3:30:58, 13.24s/it] 963it [3:31:12, 13.31s/it] 964it [3:31:25, 13.41s/it] 965it [3:31:39, 13.39s/it] 966it [3:31:52, 13.29s/it] 967it [3:32:05, 13.30s/it] 968it [3:32:19, 13.37s/it] 969it [3:32:32, 13.38s/it] 970it [3:32:45, 13.32s/it] 971it [3:32:58, 13.29s/it] 972it [3:33:12, 13.31s/it] 973it [3:33:25, 13.40s/it] 974it [3:33:39, 13.38s/it] 975it [3:33:52, 13.29s/it] 976it [3:34:05, 13.26s/it] 977it [3:34:18, 13.23s/it] 978it [3:34:32, 13.28s/it] 979it [3:34:45, 13.29s/it] 980it [3:34:58, 13.27s/it] 981it [3:35:11, 13.23s/it] 982it [3:35:25, 13.22s/it] 983it [3:35:38, 13.39s/it] 984it [3:35:52, 13.45s/it] 985it [3:36:05, 13.45s/it] 986it [3:36:19, 13.42s/it] 987it [3:36:32, 13.38s/it] 988it [3:36:45, 13.41s/it] 989it [3:36:59, 13.51s/it] 990it [3:37:13, 13.46s/it] 991it [3:37:26, 13.39s/it] 992it [3:37:39, 13.34s/it] 993it [3:37:52, 13.32s/it] 994it [3:38:06, 13.35s/it] 995it [3:38:19, 13.39s/it] 996it [3:38:33, 13.42s/it] 997it [3:38:46, 13.37s/it] 998it [3:38:59, 13.31s/it] 999it [3:39:12, 13.25s/it] 1000it [3:39:25, 13.24s/it] 1000it [3:39:25, 13.17s/it] +Error counts: + cyclic_id: 0 + cyclic_inchikey: 0 + cyclic_scaffold: 0 + cyclic_mwt: 0 + cyclic_clogp: 0 + cyclic_tpsa: 0 +⏰ Completed process in 3:39:50.782277 ++ rm /nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/train/cyc-pep-6-12mer-70M_19.csv diff --git a/train/cyc-pep-6-12mer-70M_20.csv.gz b/train/cyc-pep-6-12mer-70M_20.csv.gz index 61ad1eb7a4922c20423bb34e0a3eafdc9694d4e5..f989e89874baf60b6c7b699cab4e3f9843f33bfa 100644 --- a/train/cyc-pep-6-12mer-70M_20.csv.gz +++ b/train/cyc-pep-6-12mer-70M_20.csv.gz @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:4ce827e1ad8620533ef8ad56b3b8092a76b661a4fbaa9ff0da06fa630e4406b8 -size 35607663 +oid sha256:6dd8a5708fdb52cc506a853efdce0f695020d8d91bf70efcd3eec45d17783160 +size 77852695 diff --git a/train/cyc-pep-6-12mer-70M_20.log b/train/cyc-pep-6-12mer-70M_20.log new file mode 100644 index 0000000000000000000000000000000000000000..9793bed96041f21a6aff596c2a8240524993c65d --- /dev/null +++ b/train/cyc-pep-6-12mer-70M_20.log @@ -0,0 +1,337 @@ ++ module purge ++ '[' -z '' ']' ++ case "$-" in ++ __lmod_sh_dbg=x ++ '[' -n x ']' ++ set +x +Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output +Shell debugging restarted ++ unset __lmod_sh_dbg ++ return 0 ++ module load Anaconda3/2023.03 ++ '[' -z '' ']' ++ case "$-" in ++ __lmod_sh_dbg=x ++ '[' -n x ']' ++ set +x +Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output +Shell debugging restarted ++ unset __lmod_sh_dbg ++ return 0 ++ source /camp/home/johnsoe/.bashrc +++ '[' '' = yes ']' +++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' ++++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.bash hook +++ __conda_setup='export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'' + +# Copyright (C) 2012 Anaconda, Inc +# SPDX-License-Identifier: BSD-3-Clause +__conda_exe() ( + "$CONDA_EXE" $_CE_M $_CE_CONDA "$@" +) + +__conda_hashr() { + if [ -n "${ZSH_VERSION:+x}" ]; then + \rehash + elif [ -n "${POSH_VERSION:+x}" ]; then + : # pass + else + \hash -r + fi +} + +__conda_activate() { + if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then + # Handle transition from shell activated with conda <= 4.3 to a subsequent activation + # after conda updated to >= 4.4. See issue #6173. + PS1="$CONDA_PS1_BACKUP" + \unset CONDA_PS1_BACKUP + fi + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return + \eval "$ask_conda" + __conda_hashr +} + +__conda_reactivate() { + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return + \eval "$ask_conda" + __conda_hashr +} + +conda() { + \local cmd="${1-__missing__}" + case "$cmd" in + activate|deactivate) + __conda_activate "$@" + ;; + install|update|upgrade|remove|uninstall) + __conda_exe "$@" || \return + __conda_reactivate + ;; + *) + __conda_exe "$@" + ;; + esac +} + +if [ -z "${CONDA_SHLVL+x}" ]; then + \export CONDA_SHLVL=0 + # In dev-mode CONDA_EXE is python.exe and on Windows + # it is in a different relative location to condabin. + if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then + PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}" + else + PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}" + fi + \export PATH + + # We'\''re not allowing PS1 to be unbound. It must at least be set. + # However, we'\''re not exporting it, which can cause problems when starting a second shell + # via a first shell (i.e. starting zsh from bash). + if [ -z "${PS1+x}" ]; then + PS1= + fi +fi + +conda activate base' +++ '[' 0 -eq 0 ']' +++ eval 'export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'' + +# Copyright (C) 2012 Anaconda, Inc +# SPDX-License-Identifier: BSD-3-Clause +__conda_exe() ( + "$CONDA_EXE" $_CE_M $_CE_CONDA "$@" +) + +__conda_hashr() { + if [ -n "${ZSH_VERSION:+x}" ]; then + \rehash + elif [ -n "${POSH_VERSION:+x}" ]; then + : # pass + else + \hash -r + fi +} + +__conda_activate() { + if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then + # Handle transition from shell activated with conda <= 4.3 to a subsequent activation + # after conda updated to >= 4.4. See issue #6173. + PS1="$CONDA_PS1_BACKUP" + \unset CONDA_PS1_BACKUP + fi + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return + \eval "$ask_conda" + __conda_hashr +} + +__conda_reactivate() { + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return + \eval "$ask_conda" + __conda_hashr +} + +conda() { + \local cmd="${1-__missing__}" + case "$cmd" in + activate|deactivate) + __conda_activate "$@" + ;; + install|update|upgrade|remove|uninstall) + __conda_exe "$@" || \return + __conda_reactivate + ;; + *) + __conda_exe "$@" + ;; + esac +} + +if [ -z "${CONDA_SHLVL+x}" ]; then + \export CONDA_SHLVL=0 + # In dev-mode CONDA_EXE is python.exe and on Windows + # it is in a different relative location to condabin. + if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then + PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}" + else + PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}" + fi + \export PATH + + # We'\''re not allowing PS1 to be unbound. It must at least be set. + # However, we'\''re not exporting it, which can cause problems when starting a second shell + # via a first shell (i.e. starting zsh from bash). + if [ -z "${PS1+x}" ]; then + PS1= + fi +fi + +conda activate base' ++++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda ++++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda ++++ export _CE_M= ++++ _CE_M= ++++ export _CE_CONDA= ++++ _CE_CONDA= ++++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ '[' -z x ']' ++++ conda activate base ++++ local cmd=activate ++++ case "$cmd" in ++++ __conda_activate activate base ++++ '[' -n '' ']' ++++ local ask_conda +++++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++++ __conda_exe shell.posix activate base +++++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate base ++++ ask_conda='PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_SHLVL='\''6'\'' +export CONDA_DEFAULT_ENV='\''base'\'' +export CONDA_PROMPT_MODIFIER='\''(base) '\'' +export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' ++++ eval 'PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_SHLVL='\''6'\'' +export CONDA_DEFAULT_ENV='\''base'\'' +export CONDA_PROMPT_MODIFIER='\''(base) '\'' +export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' +++++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++++ export CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0 +++++ CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0 +++++ export CONDA_SHLVL=6 +++++ CONDA_SHLVL=6 +++++ export CONDA_DEFAULT_ENV=base +++++ CONDA_DEFAULT_ENV=base +++++ export 'CONDA_PROMPT_MODIFIER=(base) ' +++++ CONDA_PROMPT_MODIFIER='(base) ' +++++ export CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev +++++ CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev +++++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++++ export _CE_M= +++++ _CE_M= +++++ export _CE_CONDA= +++++ _CE_CONDA= +++++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python +++++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ __conda_hashr ++++ '[' -n '' ']' ++++ '[' -n '' ']' ++++ hash -r +++ unset __conda_setup ++ conda activate schemist-dev ++ local cmd=activate ++ case "$cmd" in ++ __conda_activate activate schemist-dev ++ '[' -n '' ']' ++ local ask_conda +++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++ __conda_exe shell.posix activate schemist-dev +++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate schemist-dev ++ ask_conda='PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_SHLVL='\''7'\'' +export CONDA_DEFAULT_ENV='\''schemist-dev'\'' +export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\'' +export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' ++ eval 'PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_SHLVL='\''7'\'' +export CONDA_DEFAULT_ENV='\''schemist-dev'\'' +export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\'' +export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' +++ PS1='(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++ export CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev +++ CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev +++ export CONDA_SHLVL=7 +++ CONDA_SHLVL=7 +++ export CONDA_DEFAULT_ENV=schemist-dev +++ CONDA_DEFAULT_ENV=schemist-dev +++ export 'CONDA_PROMPT_MODIFIER=(schemist-dev) ' +++ CONDA_PROMPT_MODIFIER='(schemist-dev) ' +++ export CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0 +++ CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0 +++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++ export _CE_M= +++ _CE_M= +++ export _CE_CONDA= +++ _CE_CONDA= +++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python +++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++ __conda_hashr ++ '[' -n '' ']' ++ '[' -n '' ']' ++ hash -r ++ CHUNK_HEAD_FILE=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz ++ INPUT=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/train/cyc-pep-6-12mer-70M_20.csv ++ COLUMN=cysteine_to_N_cyclization ++ PREFIX=cyclic_ ++ AWK='1 { print $8, $1, $2, $10, $3 }' ++ '[' -z cysteine_to_N_cyclization ']' ++ '[' -z cyclic_ ']' ++ '[' -z '1 { print $8, $1, $2, $10, $3 }' ']' ++ cat /dev/fd/63 /nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/train/cyc-pep-6-12mer-70M_20.csv ++ schemist convert -f csv --column cysteine_to_N_cyclization --to id inchikey scaffold mwt clogp tpsa --prefix cyclic_ --options prefix=SCB- ++ gzip --best +++ head -n1 ++ awk -F, -v OFS=, '1 { print $8, $1, $2, $10, $3 }' +++ zcat /nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz +++ tr ' ' , +🚀 Converting between string representations with the following parameters: + subcommand: convert + output: <_io.TextIOWrapper name='' mode='w' encoding='utf-8'> + format: csv + input: <_io.TextIOWrapper name='' mode='r' encoding='utf-8'> + representation: SMILES + column: cysteine_to_N_cyclization + prefix: cyclic_ + to: ['id', 'inchikey', 'scaffold', 'mwt', 'clogp', 'tpsa'] + options: ['prefix=SCB-'] + func: + 0it [00:00, ?it/s] 1it [00:13, 13.58s/it] 2it [00:26, 13.29s/it] 3it [00:39, 13.20s/it] 4it [00:52, 13.19s/it] 5it [01:06, 13.19s/it] 6it 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7.35s/it] 986it [2:20:02, 7.27s/it] 987it [2:20:09, 7.27s/it] 988it [2:20:17, 7.46s/it] 989it [2:20:25, 7.68s/it] 990it [2:20:33, 7.83s/it] 991it [2:20:41, 7.84s/it] 992it [2:20:49, 7.88s/it] 993it [2:20:57, 7.80s/it] 994it [2:21:04, 7.67s/it] 995it [2:21:11, 7.58s/it] 996it [2:21:19, 7.52s/it] 997it [2:21:26, 7.38s/it] 998it [2:21:33, 7.38s/it] 999it [2:21:41, 7.40s/it] 1000it [2:21:48, 7.40s/it] 1000it [2:21:48, 8.51s/it] +Error counts: + cyclic_id: 0 + cyclic_inchikey: 0 + cyclic_scaffold: 0 + cyclic_mwt: 0 + cyclic_clogp: 0 + cyclic_tpsa: 0 +⏰ Completed process in 2:22:11.409905 ++ rm /nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/train/cyc-pep-6-12mer-70M_20.csv diff --git a/train/cyc-pep-6-12mer-70M_21.csv.gz b/train/cyc-pep-6-12mer-70M_21.csv.gz index 33bafdf8093f3c4e17a2242ede0fc0184cb426c0..b96c0bac8cfa3674af3fd94cdc15cbf4a48187f9 100644 --- a/train/cyc-pep-6-12mer-70M_21.csv.gz +++ b/train/cyc-pep-6-12mer-70M_21.csv.gz @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:90b2da475d35f5791fbfbea15ac4a12555ccabc6a84f444ed8ccf128e708f4db -size 27227695 +oid sha256:9fc326e7360db35cd2dde43fdbfb3079fa98115e95181ec67d5c3e08be6cd40e +size 65657777 diff --git a/train/cyc-pep-6-12mer-70M_21.log b/train/cyc-pep-6-12mer-70M_21.log new file mode 100644 index 0000000000000000000000000000000000000000..e2d84c1116e5e16152c9e95444e878199f6a533c --- /dev/null +++ b/train/cyc-pep-6-12mer-70M_21.log @@ -0,0 +1,337 @@ ++ module purge ++ '[' -z '' ']' ++ case "$-" in ++ __lmod_sh_dbg=x ++ '[' -n x ']' ++ set +x +Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output +Shell debugging restarted ++ unset __lmod_sh_dbg ++ return 0 ++ module load Anaconda3/2023.03 ++ '[' -z '' ']' ++ case "$-" in ++ __lmod_sh_dbg=x ++ '[' -n x ']' ++ set +x +Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output +Shell debugging restarted ++ unset __lmod_sh_dbg ++ return 0 ++ source /camp/home/johnsoe/.bashrc +++ '[' '' = yes ']' +++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' ++++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.bash hook +++ __conda_setup='export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'' + +# Copyright (C) 2012 Anaconda, Inc +# SPDX-License-Identifier: BSD-3-Clause +__conda_exe() ( + "$CONDA_EXE" $_CE_M $_CE_CONDA "$@" +) + +__conda_hashr() { + if [ -n "${ZSH_VERSION:+x}" ]; then + \rehash + elif [ -n "${POSH_VERSION:+x}" ]; then + : # pass + else + \hash -r + fi +} + +__conda_activate() { + if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then + # Handle transition from shell activated with conda <= 4.3 to a subsequent activation + # after conda updated to >= 4.4. See issue #6173. + PS1="$CONDA_PS1_BACKUP" + \unset CONDA_PS1_BACKUP + fi + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return + \eval "$ask_conda" + __conda_hashr +} + +__conda_reactivate() { + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return + \eval "$ask_conda" + __conda_hashr +} + +conda() { + \local cmd="${1-__missing__}" + case "$cmd" in + activate|deactivate) + __conda_activate "$@" + ;; + install|update|upgrade|remove|uninstall) + __conda_exe "$@" || \return + __conda_reactivate + ;; + *) + __conda_exe "$@" + ;; + esac +} + +if [ -z "${CONDA_SHLVL+x}" ]; then + \export CONDA_SHLVL=0 + # In dev-mode CONDA_EXE is python.exe and on Windows + # it is in a different relative location to condabin. + if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then + PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}" + else + PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}" + fi + \export PATH + + # We'\''re not allowing PS1 to be unbound. It must at least be set. + # However, we'\''re not exporting it, which can cause problems when starting a second shell + # via a first shell (i.e. starting zsh from bash). + if [ -z "${PS1+x}" ]; then + PS1= + fi +fi + +conda activate base' +++ '[' 0 -eq 0 ']' +++ eval 'export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'' + +# Copyright (C) 2012 Anaconda, Inc +# SPDX-License-Identifier: BSD-3-Clause +__conda_exe() ( + "$CONDA_EXE" $_CE_M $_CE_CONDA "$@" +) + +__conda_hashr() { + if [ -n "${ZSH_VERSION:+x}" ]; then + \rehash + elif [ -n "${POSH_VERSION:+x}" ]; then + : # pass + else + \hash -r + fi +} + +__conda_activate() { + if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then + # Handle transition from shell activated with conda <= 4.3 to a subsequent activation + # after conda updated to >= 4.4. See issue #6173. + PS1="$CONDA_PS1_BACKUP" + \unset CONDA_PS1_BACKUP + fi + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return + \eval "$ask_conda" + __conda_hashr +} + +__conda_reactivate() { + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return + \eval "$ask_conda" + __conda_hashr +} + +conda() { + \local cmd="${1-__missing__}" + case "$cmd" in + activate|deactivate) + __conda_activate "$@" + ;; + install|update|upgrade|remove|uninstall) + __conda_exe "$@" || \return + __conda_reactivate + ;; + *) + __conda_exe "$@" + ;; + esac +} + +if [ -z "${CONDA_SHLVL+x}" ]; then + \export CONDA_SHLVL=0 + # In dev-mode CONDA_EXE is python.exe and on Windows + # it is in a different relative location to condabin. + if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then + PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}" + else + PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}" + fi + \export PATH + + # We'\''re not allowing PS1 to be unbound. It must at least be set. + # However, we'\''re not exporting it, which can cause problems when starting a second shell + # via a first shell (i.e. starting zsh from bash). + if [ -z "${PS1+x}" ]; then + PS1= + fi +fi + +conda activate base' ++++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda ++++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda ++++ export _CE_M= ++++ _CE_M= ++++ export _CE_CONDA= ++++ _CE_CONDA= ++++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ '[' -z x ']' ++++ conda activate base ++++ local cmd=activate ++++ case "$cmd" in ++++ __conda_activate activate base ++++ '[' -n '' ']' ++++ local ask_conda +++++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++++ __conda_exe shell.posix activate base +++++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate base ++++ ask_conda='PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_SHLVL='\''6'\'' +export CONDA_DEFAULT_ENV='\''base'\'' +export CONDA_PROMPT_MODIFIER='\''(base) '\'' +export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' ++++ eval 'PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_SHLVL='\''6'\'' +export CONDA_DEFAULT_ENV='\''base'\'' +export CONDA_PROMPT_MODIFIER='\''(base) '\'' +export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' +++++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++++ export CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0 +++++ CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0 +++++ export CONDA_SHLVL=6 +++++ CONDA_SHLVL=6 +++++ export CONDA_DEFAULT_ENV=base +++++ CONDA_DEFAULT_ENV=base +++++ export 'CONDA_PROMPT_MODIFIER=(base) ' +++++ CONDA_PROMPT_MODIFIER='(base) ' +++++ export CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev +++++ CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev +++++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++++ export _CE_M= +++++ _CE_M= +++++ export _CE_CONDA= +++++ _CE_CONDA= +++++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python +++++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ __conda_hashr ++++ '[' -n '' ']' ++++ '[' -n '' ']' ++++ hash -r +++ unset __conda_setup ++ conda activate schemist-dev ++ local cmd=activate ++ case "$cmd" in ++ __conda_activate activate schemist-dev ++ '[' -n '' ']' ++ local ask_conda +++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++ __conda_exe shell.posix activate schemist-dev +++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate schemist-dev ++ ask_conda='PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_SHLVL='\''7'\'' +export CONDA_DEFAULT_ENV='\''schemist-dev'\'' +export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\'' +export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' ++ eval 'PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_SHLVL='\''7'\'' +export CONDA_DEFAULT_ENV='\''schemist-dev'\'' +export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\'' +export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' +++ PS1='(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++ export CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev +++ CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev +++ export CONDA_SHLVL=7 +++ CONDA_SHLVL=7 +++ export CONDA_DEFAULT_ENV=schemist-dev +++ CONDA_DEFAULT_ENV=schemist-dev +++ export 'CONDA_PROMPT_MODIFIER=(schemist-dev) ' +++ CONDA_PROMPT_MODIFIER='(schemist-dev) ' +++ export CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0 +++ CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0 +++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++ export _CE_M= +++ _CE_M= +++ export _CE_CONDA= +++ _CE_CONDA= +++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python +++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++ __conda_hashr ++ '[' -n '' ']' ++ '[' -n '' ']' ++ hash -r ++ CHUNK_HEAD_FILE=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz ++ INPUT=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/train/cyc-pep-6-12mer-70M_21.csv ++ COLUMN=cysteine_to_N_cyclization ++ PREFIX=cyclic_ ++ AWK='1 { print $8, $1, $2, $10, $3 }' ++ '[' -z cysteine_to_N_cyclization ']' ++ '[' -z cyclic_ ']' ++ '[' -z '1 { print $8, $1, $2, $10, $3 }' ']' ++ cat /dev/fd/63 /nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/train/cyc-pep-6-12mer-70M_21.csv ++ schemist convert -f csv --column cysteine_to_N_cyclization --to id inchikey scaffold mwt clogp tpsa --prefix cyclic_ --options prefix=SCB- ++ gzip --best ++ awk -F, -v OFS=, '1 { print $8, $1, $2, $10, $3 }' +++ zcat /nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz +++ tr ' ' , +++ head -n1 +🚀 Converting between string representations with the following parameters: + subcommand: convert + output: <_io.TextIOWrapper name='' mode='w' encoding='utf-8'> + format: csv + input: <_io.TextIOWrapper name='' mode='r' encoding='utf-8'> + representation: SMILES + column: cysteine_to_N_cyclization + prefix: cyclic_ + to: ['id', 'inchikey', 'scaffold', 'mwt', 'clogp', 'tpsa'] + options: ['prefix=SCB-'] + func: + 0it [00:00, ?it/s] 1it [00:06, 6.83s/it] 2it [00:13, 6.80s/it] 3it [00:20, 6.66s/it] 4it [00:26, 6.72s/it] 5it [00:34, 6.91s/it] 6it [00:41, 7.11s/it] 7it [00:48, 7.14s/it] 8it [00:55, 7.05s/it] 9it [01:02, 7.02s/it] 10it [01:09, 6.95s/it] 11it [01:16, 6.95s/it] 12it [01:23, 6.92s/it] 13it [01:29, 6.82s/it] 14it [01:36, 6.80s/it] 15it [01:43, 6.85s/it] 16it [01:50, 6.88s/it] 17it [01:57, 6.89s/it] 18it [02:04, 6.86s/it] 19it [02:11, 6.85s/it] 20it [02:17, 6.83s/it] 21it [02:25, 6.95s/it] 22it [02:32, 7.11s/it] 23it [02:40, 7.26s/it] 24it [02:47, 7.23s/it] 25it [02:54, 7.19s/it] 26it [03:01, 7.17s/it] 27it [03:08, 7.12s/it] 28it [03:15, 7.09s/it] 29it [03:22, 7.00s/it] 30it [03:28, 6.80s/it] 31it [03:35, 6.73s/it] 32it [03:41, 6.72s/it] 33it [03:48, 6.69s/it] 34it [03:55, 6.63s/it] 35it [04:01, 6.58s/it] 36it [04:08, 6.56s/it] 37it [04:14, 6.57s/it] 38it [04:21, 6.70s/it] 39it [04:28, 6.84s/it] 40it [04:35, 6.94s/it] 41it [04:42, 6.90s/it] 42it [04:49, 6.88s/it] 43it [04:56, 6.85s/it] 44it [05:03, 6.80s/it] 45it [05:09, 6.74s/it] 46it [05:16, 6.72s/it] 47it [05:23, 6.71s/it] 48it [05:29, 6.77s/it] 49it [05:36, 6.80s/it] 50it [05:43, 6.82s/it] 51it [05:50, 6.82s/it] 52it [05:57, 6.83s/it] 53it [06:04, 6.78s/it] 54it [06:10, 6.81s/it] 55it [06:18, 6.99s/it] 56it [06:25, 7.15s/it] 57it [06:33, 7.22s/it] 58it [06:40, 7.17s/it] 59it [06:47, 7.15s/it] 60it [06:54, 7.09s/it] 61it [07:01, 7.05s/it] 62it [07:08, 7.02s/it] 63it [07:15, 7.04s/it] 64it [07:22, 7.06s/it] 65it [07:29, 7.16s/it] 66it [07:37, 7.22s/it] 67it [07:44, 7.25s/it] 68it [07:51, 7.27s/it] 69it [07:59, 7.29s/it] 70it [08:06, 7.24s/it] 71it [08:13, 7.30s/it] 72it [08:21, 7.48s/it] 73it [08:29, 7.67s/it] 74it [08:37, 7.72s/it] 75it [08:45, 7.65s/it] 76it [08:52, 7.64s/it] 77it [09:00, 7.57s/it] 78it [09:07, 7.54s/it] 79it [09:15, 7.52s/it] 80it [09:22, 7.44s/it] 81it [09:29, 7.38s/it] 82it [09:37, 7.42s/it] 83it [09:44, 7.43s/it] 84it [09:51, 7.44s/it] 85it [09:59, 7.41s/it] 86it [10:06, 7.41s/it] 87it [10:13, 7.36s/it] 88it [10:21, 7.44s/it] 89it [10:29, 7.63s/it] 90it [10:37, 7.81s/it] 91it [10:45, 7.79s/it] 92it [10:53, 7.74s/it] 93it [11:00, 7.72s/it] 94it [11:08, 7.70s/it] 95it [11:16, 7.67s/it] 96it [11:23, 7.64s/it] 97it [11:31, 7.55s/it] 98it [11:38, 7.51s/it] 99it [11:46, 7.55s/it] 100it [11:53, 7.59s/it] 101it [12:01, 7.58s/it] 102it [12:08, 7.56s/it] 103it [12:16, 7.55s/it] 104it [12:23, 7.51s/it] 105it [12:31, 7.61s/it] 106it [12:39, 7.79s/it] 107it [12:48, 7.97s/it] 108it [12:56, 7.92s/it] 109it [13:03, 7.88s/it] 110it [13:11, 7.84s/it] 111it [13:19, 7.82s/it] 112it [13:27, 7.80s/it] 113it [13:34, 7.74s/it] 114it [13:41, 7.49s/it] 115it [13:48, 7.36s/it] 116it [13:56, 7.34s/it] 117it [14:03, 7.31s/it] 118it [14:10, 7.26s/it] 119it [14:17, 7.20s/it] 120it [14:24, 7.17s/it] 121it [14:31, 7.16s/it] 122it [14:39, 7.28s/it] 123it [14:47, 7.43s/it] 124it [14:54, 7.57s/it] 125it [15:02, 7.53s/it] 126it [15:09, 7.47s/it] 127it [15:17, 7.47s/it] 128it [15:24, 7.43s/it] 129it [15:31, 7.38s/it] 130it [15:38, 7.32s/it] 131it [15:45, 7.12s/it] 132it [15:52, 7.06s/it] 133it [15:59, 7.07s/it] 134it [16:06, 7.04s/it] 135it [16:13, 6.98s/it] 136it [16:20, 6.94s/it] 137it [16:27, 6.93s/it] 138it [16:34, 6.94s/it] 139it [16:41, 7.07s/it] 140it [16:49, 7.23s/it] 141it [16:56, 7.32s/it] 142it [17:03, 7.30s/it] 143it [17:11, 7.28s/it] 144it [17:18, 7.22s/it] 145it [17:25, 7.18s/it] 146it [17:32, 7.13s/it] 147it [17:39, 7.11s/it] 148it [17:46, 7.07s/it] 149it [17:53, 7.14s/it] 150it [18:00, 7.15s/it] 151it [18:08, 7.15s/it] 152it [18:15, 7.14s/it] 153it [18:22, 7.17s/it] 154it [18:29, 7.14s/it] 155it [18:36, 7.15s/it] 156it [18:44, 7.31s/it] 157it [18:52, 7.46s/it] 158it [18:59, 7.55s/it] 159it [19:07, 7.50s/it] 160it [19:14, 7.50s/it] 161it [19:22, 7.44s/it] 162it [19:29, 7.39s/it] 163it [19:36, 7.36s/it] 164it [19:43, 7.25s/it] 165it [19:50, 7.08s/it] 166it [19:57, 7.08s/it] 167it [20:04, 7.06s/it] 168it [20:11, 7.01s/it] 169it [20:18, 6.98s/it] 170it [20:25, 7.02s/it] 171it [20:32, 6.96s/it] 172it [20:39, 6.98s/it] 173it [20:46, 7.16s/it] 174it [20:54, 7.33s/it] 175it [21:01, 7.34s/it] 176it [21:08, 7.26s/it] 177it [21:16, 7.23s/it] 178it [21:23, 7.17s/it] 179it [21:30, 7.13s/it] 180it [21:37, 7.11s/it] 181it [21:44, 7.04s/it] 182it [21:50, 6.97s/it] 183it [21:57, 7.00s/it] 184it [22:05, 7.02s/it] 185it [22:12, 7.03s/it] 186it [22:18, 6.99s/it] 187it [22:25, 7.00s/it] 188it [22:32, 6.94s/it] 189it [22:39, 7.01s/it] 190it [22:47, 7.20s/it] 191it [22:55, 7.36s/it] 192it [23:02, 7.37s/it] 193it [23:09, 7.29s/it] 194it [23:17, 7.28s/it] 195it [23:24, 7.25s/it] 196it [23:31, 7.20s/it] 197it [23:38, 7.18s/it] 198it [23:45, 7.02s/it] 199it [23:51, 6.94s/it] 200it [23:58, 6.96s/it] 201it [24:05, 6.96s/it] 202it [24:12, 6.94s/it] 203it [24:19, 6.88s/it] 204it [24:26, 6.89s/it] 205it [24:33, 6.84s/it] 206it [24:40, 6.97s/it] 207it [24:47, 7.14s/it] 208it [24:55, 7.28s/it] 209it [25:02, 7.25s/it] 210it [25:09, 7.19s/it] 211it [25:16, 7.16s/it] 212it [25:23, 7.13s/it] 213it [25:30, 7.09s/it] 214it [25:37, 7.04s/it] 215it [25:44, 6.94s/it] 216it [25:51, 6.94s/it] 217it [25:58, 6.97s/it] 218it [26:05, 6.98s/it] 219it [26:12, 6.96s/it] 220it [26:19, 6.93s/it] 221it [26:26, 6.91s/it] 222it [26:33, 6.93s/it] 223it [26:40, 7.05s/it] 224it [26:48, 7.20s/it] 225it [26:55, 7.33s/it] 226it [27:02, 7.30s/it] 227it [27:10, 7.26s/it] 228it [27:17, 7.24s/it] 229it [27:24, 7.22s/it] 230it [27:31, 7.16s/it] 231it [27:38, 7.09s/it] 232it [27:44, 6.85s/it] 233it [27:51, 6.73s/it] 234it [27:57, 6.70s/it] 235it [28:04, 6.66s/it] 236it [28:10, 6.58s/it] 237it [28:17, 6.52s/it] 238it [28:23, 6.50s/it] 239it [28:30, 6.50s/it] 240it [28:36, 6.62s/it] 241it [28:43, 6.76s/it] 242it [28:51, 6.87s/it] 243it [28:57, 6.82s/it] 244it [29:04, 6.82s/it] 245it [29:11, 6.78s/it] 246it [29:17, 6.73s/it] 247it [29:24, 6.68s/it] 248it [29:31, 6.63s/it] 249it [29:37, 6.54s/it] 250it [29:44, 6.57s/it] 251it [29:50, 6.60s/it] 252it [29:57, 6.59s/it] 253it [30:03, 6.58s/it] 254it [30:10, 6.56s/it] 255it [30:16, 6.54s/it] 256it [30:23, 6.55s/it] 257it [30:30, 6.70s/it] 258it [30:37, 6.84s/it] 259it [30:44, 6.93s/it] 260it [30:51, 6.91s/it] 261it [30:58, 6.89s/it] 262it [31:05, 6.83s/it] 263it [31:11, 6.79s/it] 264it [31:18, 6.74s/it] 265it [31:25, 6.75s/it] 266it [31:31, 6.75s/it] 267it [31:38, 6.79s/it] 268it [31:45, 6.83s/it] 269it [31:52, 6.84s/it] 270it [31:59, 6.84s/it] 271it [32:06, 6.86s/it] 272it [32:13, 6.80s/it] 273it [32:20, 6.86s/it] 274it [32:27, 7.02s/it] 275it [32:35, 7.20s/it] 276it [32:42, 7.25s/it] 277it [32:49, 7.18s/it] 278it [32:56, 7.17s/it] 279it [33:03, 7.12s/it] 280it [33:10, 7.08s/it] 281it [33:17, 7.06s/it] 282it [33:24, 6.95s/it] 283it [33:30, 6.84s/it] 284it [33:37, 6.84s/it] 285it [33:44, 6.85s/it] 286it [33:51, 6.84s/it] 287it [33:58, 6.79s/it] 288it [34:04, 6.79s/it] 289it [34:11, 6.73s/it] 290it [34:18, 6.84s/it] 291it [34:25, 7.01s/it] 292it [34:33, 7.16s/it] 293it [34:40, 7.14s/it] 294it [34:47, 7.09s/it] 295it [34:54, 7.05s/it] 296it [35:01, 7.03s/it] 297it [35:08, 6.97s/it] 298it [35:15, 6.93s/it] 299it [35:21, 6.81s/it] 300it [35:28, 6.75s/it] 301it [35:35, 6.78s/it] 302it [35:42, 6.82s/it] 303it [35:48, 6.80s/it] 304it [35:55, 6.76s/it] 305it [36:02, 6.76s/it] 306it [36:08, 6.70s/it] 307it [36:15, 6.80s/it] 308it [36:23, 6.98s/it] 309it [36:30, 7.14s/it] 310it [36:37, 7.13s/it] 311it [36:44, 7.07s/it] 312it [36:51, 7.03s/it] 313it [36:58, 7.01s/it] 314it [37:05, 6.97s/it] 315it [37:12, 6.94s/it] 316it [37:18, 6.78s/it] 317it [37:25, 6.73s/it] 318it [37:32, 6.75s/it] 319it [37:38, 6.76s/it] 320it [37:45, 6.75s/it] 321it [37:52, 6.70s/it] 322it [37:58, 6.68s/it] 323it [38:05, 6.65s/it] 324it [38:12, 6.75s/it] 325it [38:19, 6.92s/it] 326it [38:27, 7.08s/it] 327it [38:34, 7.05s/it] 328it [38:41, 7.00s/it] 329it [38:48, 6.97s/it] 330it [38:54, 6.94s/it] 331it [39:01, 6.91s/it] 332it [39:08, 6.88s/it] 333it [39:14, 6.73s/it] 334it [39:21, 6.66s/it] 335it [39:28, 6.68s/it] 336it [39:34, 6.70s/it] 337it [39:41, 6.68s/it] 338it [39:48, 6.63s/it] 339it [39:54, 6.62s/it] 340it [40:01, 6.59s/it] 341it [40:08, 6.68s/it] 342it [40:15, 6.85s/it] 343it [40:22, 7.00s/it] 344it [40:29, 6.98s/it] 345it [40:36, 6.93s/it] 346it [40:43, 6.90s/it] 347it [40:50, 6.88s/it] 348it [40:56, 6.84s/it] 349it [41:03, 6.80s/it] 350it [41:09, 6.70s/it] 351it [41:16, 6.70s/it] 352it [41:23, 6.76s/it] 353it [41:30, 6.78s/it] 354it [41:37, 6.78s/it] 355it [41:43, 6.74s/it] 356it [41:50, 6.73s/it] 357it [41:57, 6.74s/it] 358it [42:04, 6.86s/it] 359it [42:11, 7.02s/it] 360it [42:19, 7.15s/it] 361it [42:26, 7.13s/it] 362it [42:33, 7.08s/it] 363it [42:40, 7.07s/it] 364it [42:47, 7.04s/it] 365it [42:54, 6.99s/it] 366it [43:01, 6.94s/it] 367it [43:07, 6.73s/it] 368it [43:13, 6.63s/it] 369it [43:20, 6.62s/it] 370it [43:26, 6.59s/it] 371it [43:33, 6.55s/it] 372it [43:39, 6.50s/it] 373it [43:46, 6.48s/it] 374it [43:52, 6.49s/it] 375it [43:59, 6.60s/it] 376it [44:06, 6.75s/it] 377it [44:13, 6.85s/it] 378it [44:20, 6.83s/it] 379it [44:27, 6.79s/it] 380it [44:33, 6.77s/it] 381it [44:40, 6.74s/it] 382it [44:47, 6.68s/it] 383it [44:53, 6.66s/it] 384it 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7.06s/it] 969it [1:53:34, 7.04s/it] 970it [1:53:41, 6.99s/it] 971it [1:53:47, 6.98s/it] 972it [1:53:54, 6.96s/it] 973it [1:54:01, 6.81s/it] 974it [1:54:07, 6.75s/it] 975it [1:54:14, 6.79s/it] 976it [1:54:21, 6.80s/it] 977it [1:54:28, 6.76s/it] 978it [1:54:34, 6.72s/it] 979it [1:54:41, 6.68s/it] 980it [1:54:48, 6.67s/it] 981it [1:54:55, 6.80s/it] 982it [1:55:02, 6.94s/it] 983it [1:55:09, 7.07s/it] 984it [1:55:16, 7.02s/it] 985it [1:55:23, 6.98s/it] 986it [1:55:30, 6.96s/it] 987it [1:55:37, 6.92s/it] 988it [1:55:44, 6.87s/it] 989it [1:55:50, 6.82s/it] 990it [1:55:57, 6.69s/it] 991it [1:56:04, 6.70s/it] 992it [1:56:10, 6.70s/it] 993it [1:56:17, 6.68s/it] 994it [1:56:23, 6.66s/it] 995it [1:56:30, 6.64s/it] 996it [1:56:37, 6.61s/it] 997it [1:56:43, 6.61s/it] 998it [1:56:50, 6.73s/it] 999it [1:56:57, 6.85s/it] 1000it [1:57:05, 6.97s/it] 1000it [1:57:05, 7.03s/it] +Error counts: + cyclic_id: 0 + cyclic_inchikey: 0 + cyclic_scaffold: 0 + cyclic_mwt: 0 + cyclic_clogp: 0 + cyclic_tpsa: 0 +⏰ Completed process in 1:57:22.750854 ++ rm /nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/train/cyc-pep-6-12mer-70M_21.csv diff --git a/train/cyc-pep-6-12mer-70M_22.csv.gz b/train/cyc-pep-6-12mer-70M_22.csv.gz index 60dfe3cfde4f9ced12f4c2d1e994093502999bdc..f6915250a4ff43b8901ab551c13ad0e211072385 100644 --- a/train/cyc-pep-6-12mer-70M_22.csv.gz +++ b/train/cyc-pep-6-12mer-70M_22.csv.gz @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:b1eeaa7bbaa13f78a74f43e6616adabdd1d9a3e40f0e21dd0c9ebd07f40da3cb -size 27095855 +oid sha256:d1e0233da5cad5b2214314ad62c6a111656f95103bcb8bbada40342ec6c596a1 +size 65206312 diff --git a/train/cyc-pep-6-12mer-70M_22.log b/train/cyc-pep-6-12mer-70M_22.log new file mode 100644 index 0000000000000000000000000000000000000000..67392de97eb81f2a1ee64fe760bc16e5337a380f --- /dev/null +++ b/train/cyc-pep-6-12mer-70M_22.log @@ -0,0 +1,337 @@ ++ module purge ++ '[' -z '' ']' ++ case "$-" in ++ __lmod_sh_dbg=x ++ '[' -n x ']' ++ set +x +Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output +Shell debugging restarted ++ unset __lmod_sh_dbg ++ return 0 ++ module load Anaconda3/2023.03 ++ '[' -z '' ']' ++ case "$-" in ++ __lmod_sh_dbg=x ++ '[' -n x ']' ++ set +x +Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output +Shell debugging restarted ++ unset __lmod_sh_dbg ++ return 0 ++ source /camp/home/johnsoe/.bashrc +++ '[' '' = yes ']' +++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' ++++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.bash hook +++ __conda_setup='export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'' + +# Copyright (C) 2012 Anaconda, Inc +# SPDX-License-Identifier: BSD-3-Clause +__conda_exe() ( + "$CONDA_EXE" $_CE_M $_CE_CONDA "$@" +) + +__conda_hashr() { + if [ -n "${ZSH_VERSION:+x}" ]; then + \rehash + elif [ -n "${POSH_VERSION:+x}" ]; then + : # pass + else + \hash -r + fi +} + +__conda_activate() { + if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then + # Handle transition from shell activated with conda <= 4.3 to a subsequent activation + # after conda updated to >= 4.4. See issue #6173. + PS1="$CONDA_PS1_BACKUP" + \unset CONDA_PS1_BACKUP + fi + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return + \eval "$ask_conda" + __conda_hashr +} + +__conda_reactivate() { + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return + \eval "$ask_conda" + __conda_hashr +} + +conda() { + \local cmd="${1-__missing__}" + case "$cmd" in + activate|deactivate) + __conda_activate "$@" + ;; + install|update|upgrade|remove|uninstall) + __conda_exe "$@" || \return + __conda_reactivate + ;; + *) + __conda_exe "$@" + ;; + esac +} + +if [ -z "${CONDA_SHLVL+x}" ]; then + \export CONDA_SHLVL=0 + # In dev-mode CONDA_EXE is python.exe and on Windows + # it is in a different relative location to condabin. + if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then + PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}" + else + PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}" + fi + \export PATH + + # We'\''re not allowing PS1 to be unbound. It must at least be set. + # However, we'\''re not exporting it, which can cause problems when starting a second shell + # via a first shell (i.e. starting zsh from bash). + if [ -z "${PS1+x}" ]; then + PS1= + fi +fi + +conda activate base' +++ '[' 0 -eq 0 ']' +++ eval 'export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'' + +# Copyright (C) 2012 Anaconda, Inc +# SPDX-License-Identifier: BSD-3-Clause +__conda_exe() ( + "$CONDA_EXE" $_CE_M $_CE_CONDA "$@" +) + +__conda_hashr() { + if [ -n "${ZSH_VERSION:+x}" ]; then + \rehash + elif [ -n "${POSH_VERSION:+x}" ]; then + : # pass + else + \hash -r + fi +} + +__conda_activate() { + if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then + # Handle transition from shell activated with conda <= 4.3 to a subsequent activation + # after conda updated to >= 4.4. See issue #6173. + PS1="$CONDA_PS1_BACKUP" + \unset CONDA_PS1_BACKUP + fi + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return + \eval "$ask_conda" + __conda_hashr +} + +__conda_reactivate() { + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return + \eval "$ask_conda" + __conda_hashr +} + +conda() { + \local cmd="${1-__missing__}" + case "$cmd" in + activate|deactivate) + __conda_activate "$@" + ;; + install|update|upgrade|remove|uninstall) + __conda_exe "$@" || \return + __conda_reactivate + ;; + *) + __conda_exe "$@" + ;; + esac +} + +if [ -z "${CONDA_SHLVL+x}" ]; then + \export CONDA_SHLVL=0 + # In dev-mode CONDA_EXE is python.exe and on Windows + # it is in a different relative location to condabin. + if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then + PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}" + else + PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}" + fi + \export PATH + + # We'\''re not allowing PS1 to be unbound. It must at least be set. + # However, we'\''re not exporting it, which can cause problems when starting a second shell + # via a first shell (i.e. starting zsh from bash). + if [ -z "${PS1+x}" ]; then + PS1= + fi +fi + +conda activate base' ++++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda ++++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda ++++ export _CE_M= ++++ _CE_M= ++++ export _CE_CONDA= ++++ _CE_CONDA= ++++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ '[' -z x ']' ++++ conda activate base ++++ local cmd=activate ++++ case "$cmd" in ++++ __conda_activate activate base ++++ '[' -n '' ']' ++++ local ask_conda +++++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++++ __conda_exe shell.posix activate base +++++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate base ++++ ask_conda='PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_SHLVL='\''6'\'' +export CONDA_DEFAULT_ENV='\''base'\'' +export CONDA_PROMPT_MODIFIER='\''(base) '\'' +export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' ++++ eval 'PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_SHLVL='\''6'\'' +export CONDA_DEFAULT_ENV='\''base'\'' +export CONDA_PROMPT_MODIFIER='\''(base) '\'' +export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' +++++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++++ export CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0 +++++ CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0 +++++ export CONDA_SHLVL=6 +++++ CONDA_SHLVL=6 +++++ export CONDA_DEFAULT_ENV=base +++++ CONDA_DEFAULT_ENV=base +++++ export 'CONDA_PROMPT_MODIFIER=(base) ' +++++ CONDA_PROMPT_MODIFIER='(base) ' +++++ export CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev +++++ CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev +++++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++++ export _CE_M= +++++ _CE_M= +++++ export _CE_CONDA= +++++ _CE_CONDA= +++++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python +++++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ __conda_hashr ++++ '[' -n '' ']' ++++ '[' -n '' ']' ++++ hash -r +++ unset __conda_setup ++ conda activate schemist-dev ++ local cmd=activate ++ case "$cmd" in ++ __conda_activate activate schemist-dev ++ '[' -n '' ']' ++ local ask_conda +++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++ __conda_exe shell.posix activate schemist-dev +++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate schemist-dev ++ ask_conda='PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_SHLVL='\''7'\'' +export CONDA_DEFAULT_ENV='\''schemist-dev'\'' +export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\'' +export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' ++ eval 'PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_SHLVL='\''7'\'' +export CONDA_DEFAULT_ENV='\''schemist-dev'\'' +export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\'' +export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' +++ PS1='(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++ export CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev +++ CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev +++ export CONDA_SHLVL=7 +++ CONDA_SHLVL=7 +++ export CONDA_DEFAULT_ENV=schemist-dev +++ CONDA_DEFAULT_ENV=schemist-dev +++ export 'CONDA_PROMPT_MODIFIER=(schemist-dev) ' +++ CONDA_PROMPT_MODIFIER='(schemist-dev) ' +++ export CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0 +++ CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0 +++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++ export _CE_M= +++ _CE_M= +++ export _CE_CONDA= +++ _CE_CONDA= +++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python +++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++ __conda_hashr ++ '[' -n '' ']' ++ '[' -n '' ']' ++ hash -r ++ CHUNK_HEAD_FILE=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz ++ INPUT=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/train/cyc-pep-6-12mer-70M_22.csv ++ COLUMN=cysteine_to_N_cyclization ++ PREFIX=cyclic_ ++ AWK='1 { print $8, $1, $2, $10, $3 }' ++ '[' -z cysteine_to_N_cyclization ']' ++ '[' -z cyclic_ ']' ++ '[' -z '1 { print $8, $1, $2, $10, $3 }' ']' ++ awk -F, -v OFS=, '1 { print $8, $1, $2, $10, $3 }' ++ cat /dev/fd/63 /nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/train/cyc-pep-6-12mer-70M_22.csv +++ zcat /nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz ++ schemist convert -f csv --column cysteine_to_N_cyclization --to id inchikey scaffold mwt clogp tpsa --prefix cyclic_ --options prefix=SCB- ++ gzip --best +++ head -n1 +++ tr ' ' , +🚀 Converting between string representations with the following parameters: + subcommand: convert + output: <_io.TextIOWrapper name='' mode='w' encoding='utf-8'> + format: csv + input: <_io.TextIOWrapper name='' mode='r' encoding='utf-8'> + representation: SMILES + column: cysteine_to_N_cyclization + prefix: cyclic_ + to: ['id', 'inchikey', 'scaffold', 'mwt', 'clogp', 'tpsa'] + options: ['prefix=SCB-'] + func: + 0it [00:00, ?it/s] 1it [00:06, 6.89s/it] 2it [00:13, 6.90s/it] 3it [00:20, 6.85s/it] 4it [00:27, 6.80s/it] 5it [00:34, 6.77s/it] 6it [00:40, 6.70s/it] 7it [00:46, 6.59s/it] 8it [00:53, 6.61s/it] 9it [01:00, 6.63s/it] 10it [01:06, 6.61s/it] 11it [01:13, 6.58s/it] 12it [01:19, 6.58s/it] 13it [01:26, 6.53s/it] 14it [01:32, 6.54s/it] 15it [01:39, 6.70s/it] 16it [01:47, 6.84s/it] 17it [01:54, 6.92s/it] 18it [02:01, 6.86s/it] 19it [02:07, 6.87s/it] 20it [02:14, 6.79s/it] 21it [02:21, 6.76s/it] 22it [02:27, 6.73s/it] 23it [02:34, 6.69s/it] 24it [02:41, 6.65s/it] 25it [02:47, 6.71s/it] 26it [02:54, 6.73s/it] 27it [03:01, 6.72s/it] 28it [03:08, 6.72s/it] 29it [03:14, 6.73s/it] 30it [03:21, 6.70s/it] 31it [03:28, 6.79s/it] 32it [03:35, 6.98s/it] 33it [03:43, 7.18s/it] 34it [03:50, 7.24s/it] 35it [03:57, 7.17s/it] 36it [04:05, 7.16s/it] 37it [04:12, 7.11s/it] 38it [04:19, 7.10s/it] 39it [04:26, 7.09s/it] 40it [04:32, 6.87s/it] 41it [04:38, 6.73s/it] 42it [04:45, 6.71s/it] 43it [04:52, 6.70s/it] 44it [04:58, 6.64s/it] 45it [05:05, 6.59s/it] 46it [05:11, 6.57s/it] 47it [05:18, 6.53s/it] 48it [05:24, 6.60s/it] 49it [05:32, 6.78s/it] 50it [05:39, 6.93s/it] 51it [05:46, 6.93s/it] 52it [05:53, 6.87s/it] 53it [05:59, 6.85s/it] 54it [06:06, 6.81s/it] 55it [06:13, 6.79s/it] 56it [06:20, 6.76s/it] 57it [06:26, 6.70s/it] 58it [06:33, 6.69s/it] 59it [06:40, 6.76s/it] 60it [06:47, 6.79s/it] 61it [06:53, 6.76s/it] 62it [07:00, 6.73s/it] 63it [07:07, 6.72s/it] 64it [07:13, 6.67s/it] 65it [07:20, 6.79s/it] 66it [07:28, 6.99s/it] 67it [07:35, 7.13s/it] 68it [07:42, 7.11s/it] 69it [07:49, 7.06s/it] 70it [07:56, 7.03s/it] 71it [08:03, 7.02s/it] 72it [08:10, 6.96s/it] 73it [08:17, 6.93s/it] 74it [08:24, 6.94s/it] 75it [08:31, 7.02s/it] 76it [08:38, 7.15s/it] 77it [08:46, 7.23s/it] 78it [08:53, 7.24s/it] 79it [09:00, 7.21s/it] 80it [09:08, 7.23s/it] 81it [09:15, 7.21s/it] 82it [09:22, 7.35s/it] 83it [09:30, 7.51s/it] 84it [09:38, 7.67s/it] 85it [09:46, 7.63s/it] 86it [09:53, 7.59s/it] 87it [10:01, 7.56s/it] 88it [10:08, 7.54s/it] 89it [10:16, 7.49s/it] 90it [10:23, 7.45s/it] 91it [10:30, 7.35s/it] 92it [10:38, 7.40s/it] 93it [10:45, 7.46s/it] 94it [10:53, 7.50s/it] 95it [11:00, 7.48s/it] 96it [11:08, 7.45s/it] 97it [11:15, 7.44s/it] 98it [11:23, 7.46s/it] 99it [11:31, 7.63s/it] 100it [11:39, 7.77s/it] 101it [11:47, 7.89s/it] 102it [11:55, 7.85s/it] 103it [12:02, 7.81s/it] 104it [12:10, 7.79s/it] 105it [12:18, 7.75s/it] 106it [12:25, 7.68s/it] 107it [12:33, 7.63s/it] 108it [12:40, 7.53s/it] 109it [12:48, 7.54s/it] 110it [12:55, 7.61s/it] 111it [13:03, 7.64s/it] 112it [13:11, 7.61s/it] 113it [13:18, 7.55s/it] 114it [13:26, 7.53s/it] 115it [13:33, 7.54s/it] 116it [13:41, 7.68s/it] 117it [13:49, 7.81s/it] 118it [13:58, 7.93s/it] 119it [14:05, 7.86s/it] 120it [14:13, 7.82s/it] 121it [14:21, 7.80s/it] 122it [14:28, 7.74s/it] 123it [14:36, 7.69s/it] 124it [14:43, 7.60s/it] 125it [14:50, 7.39s/it] 126it [14:57, 7.32s/it] 127it [15:04, 7.29s/it] 128it [15:12, 7.22s/it] 129it [15:19, 7.16s/it] 130it [15:26, 7.10s/it] 131it [15:33, 7.08s/it] 132it [15:40, 7.09s/it] 133it [15:47, 7.21s/it] 134it [15:55, 7.36s/it] 135it [16:03, 7.44s/it] 136it [16:10, 7.40s/it] 137it [16:17, 7.38s/it] 138it [16:24, 7.32s/it] 139it [16:32, 7.28s/it] 140it [16:39, 7.22s/it] 141it [16:46, 7.14s/it] 142it [16:52, 7.01s/it] 143it [16:59, 6.97s/it] 144it [17:06, 6.96s/it] 145it [17:13, 6.92s/it] 146it [17:20, 6.87s/it] 147it [17:26, 6.85s/it] 148it [17:33, 6.82s/it] 149it [17:40, 6.82s/it] 150it [17:47, 6.96s/it] 151it [17:55, 7.10s/it] 152it [18:02, 7.21s/it] 153it [18:09, 7.15s/it] 154it [18:16, 7.16s/it] 155it [18:23, 7.12s/it] 156it [18:30, 7.06s/it] 157it [18:37, 7.00s/it] 158it [18:44, 6.95s/it] 159it [18:51, 6.94s/it] 160it [18:58, 7.01s/it] 161it [19:05, 7.06s/it] 162it [19:12, 7.05s/it] 163it [19:19, 7.03s/it] 164it [19:26, 7.03s/it] 165it [19:33, 7.01s/it] 166it [19:40, 7.00s/it] 167it [19:48, 7.14s/it] 168it [19:56, 7.33s/it] 169it [20:03, 7.46s/it] 170it [20:11, 7.44s/it] 171it [20:18, 7.42s/it] 172it [20:25, 7.37s/it] 173it [20:33, 7.33s/it] 174it [20:40, 7.30s/it] 175it [20:47, 7.20s/it] 176it [20:53, 7.04s/it] 177it [21:01, 7.05s/it] 178it [21:08, 7.05s/it] 179it [21:14, 7.00s/it] 180it [21:21, 6.95s/it] 181it [21:28, 6.94s/it] 182it [21:35, 6.88s/it] 183it [21:42, 6.88s/it] 184it [21:49, 7.02s/it] 185it [21:57, 7.18s/it] 186it [22:04, 7.26s/it] 187it [22:11, 7.25s/it] 188it [22:19, 7.23s/it] 189it [22:25, 7.13s/it] 190it [22:32, 7.08s/it] 191it [22:39, 7.02s/it] 192it [22:46, 6.94s/it] 193it [22:53, 6.87s/it] 194it [23:00, 6.90s/it] 195it [23:07, 6.91s/it] 196it [23:14, 6.94s/it] 197it [23:20, 6.88s/it] 198it [23:27, 6.89s/it] 199it [23:34, 6.86s/it] 200it [23:41, 6.85s/it] 201it [23:48, 7.02s/it] 202it [23:56, 7.15s/it] 203it [24:03, 7.25s/it] 204it [24:10, 7.22s/it] 205it [24:18, 7.20s/it] 206it [24:25, 7.12s/it] 207it [24:31, 7.05s/it] 208it [24:38, 7.02s/it] 209it [24:45, 6.91s/it] 210it [24:52, 6.81s/it] 211it [24:58, 6.82s/it] 212it [25:05, 6.83s/it] 213it [25:12, 6.80s/it] 214it [25:19, 6.79s/it] 215it [25:26, 6.77s/it] 216it [25:32, 6.70s/it] 217it [25:39, 6.74s/it] 218it [25:46, 6.89s/it] 219it [25:54, 7.07s/it] 220it [26:01, 7.14s/it] 221it [26:08, 7.07s/it] 222it [26:15, 7.07s/it] 223it [26:22, 7.00s/it] 224it [26:29, 6.97s/it] 225it [26:36, 6.94s/it] 226it [26:42, 6.83s/it] 227it [26:49, 6.78s/it] 228it [26:56, 6.84s/it] 229it [27:03, 6.86s/it] 230it [27:10, 6.89s/it] 231it [27:16, 6.84s/it] 232it [27:23, 6.85s/it] 233it [27:30, 6.79s/it] 234it [27:37, 6.88s/it] 235it [27:44, 7.03s/it] 236it [27:52, 7.19s/it] 237it [27:59, 7.21s/it] 238it [28:06, 7.13s/it] 239it [28:13, 7.11s/it] 240it [28:20, 7.04s/it] 241it [28:27, 7.03s/it] 242it [28:34, 7.01s/it] 243it [28:40, 6.75s/it] 244it [28:46, 6.60s/it] 245it [28:53, 6.57s/it] 246it [28:59, 6.56s/it] 247it [29:06, 6.50s/it] 248it [29:12, 6.44s/it] 249it [29:18, 6.43s/it] 250it [29:25, 6.37s/it] 251it [29:31, 6.48s/it] 252it [29:38, 6.65s/it] 253it [29:46, 6.79s/it] 254it [29:52, 6.75s/it] 255it [29:59, 6.71s/it] 256it [30:06, 6.69s/it] 257it [30:12, 6.63s/it] 258it [30:19, 6.60s/it] 259it [30:25, 6.56s/it] 260it [30:31, 6.47s/it] 261it [30:38, 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971it [1:56:25, 7.14s/it] 972it [1:56:32, 7.12s/it] 973it [1:56:39, 7.13s/it] 974it [1:56:46, 7.12s/it] 975it [1:56:53, 7.04s/it] 976it [1:57:00, 7.08s/it] 977it [1:57:08, 7.19s/it] 978it [1:57:16, 7.34s/it] 979it [1:57:23, 7.41s/it] 980it [1:57:30, 7.33s/it] 981it [1:57:38, 7.33s/it] 982it [1:57:45, 7.29s/it] 983it [1:57:52, 7.28s/it] 984it [1:57:59, 7.27s/it] 985it [1:58:06, 7.09s/it] 986it [1:58:13, 6.98s/it] 987it [1:58:20, 6.96s/it] 988it [1:58:26, 6.94s/it] 989it [1:58:33, 6.86s/it] 990it [1:58:40, 6.79s/it] 991it [1:58:47, 6.80s/it] 992it [1:58:54, 6.84s/it] 993it [1:59:01, 6.98s/it] 994it [1:59:08, 7.17s/it] 995it [1:59:16, 7.26s/it] 996it [1:59:23, 7.24s/it] 997it [1:59:30, 7.24s/it] 998it [1:59:38, 7.31s/it] 999it [1:59:45, 7.32s/it] 1000it [1:59:52, 7.21s/it] 1000it [1:59:52, 7.19s/it] +Error counts: + cyclic_id: 0 + cyclic_inchikey: 0 + cyclic_scaffold: 0 + cyclic_mwt: 0 + cyclic_clogp: 0 + cyclic_tpsa: 0 +⏰ Completed process in 2:00:09.191117 ++ rm /nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/train/cyc-pep-6-12mer-70M_22.csv diff --git a/train/cyc-pep-6-12mer-70M_23.csv.gz b/train/cyc-pep-6-12mer-70M_23.csv.gz index 7f2f2e67038583a9715dd0c49f6483f9e6a9065c..060e0abe87559281681b1ab7fa6e3feb48df943d 100644 --- a/train/cyc-pep-6-12mer-70M_23.csv.gz +++ b/train/cyc-pep-6-12mer-70M_23.csv.gz @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:a9f6401d41e6cf8c163a87c13f768d22e6bf08e2c19db4683fc40f2271f963d1 -size 26970190 +oid sha256:7b9ce243a542dfc753644ddd21548364ca98db7781b82093809bbfed747295c1 +size 64807226 diff --git a/train/cyc-pep-6-12mer-70M_23.log b/train/cyc-pep-6-12mer-70M_23.log new file mode 100644 index 0000000000000000000000000000000000000000..12aafa8c71c372ce93a37c418e61b8fac9b12ccd --- /dev/null +++ b/train/cyc-pep-6-12mer-70M_23.log @@ -0,0 +1,337 @@ ++ module purge ++ '[' -z '' ']' ++ case "$-" in ++ __lmod_sh_dbg=x ++ '[' -n x ']' ++ set +x +Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output +Shell debugging restarted ++ unset __lmod_sh_dbg ++ return 0 ++ module load Anaconda3/2023.03 ++ '[' -z '' ']' ++ case "$-" in ++ __lmod_sh_dbg=x ++ '[' -n x ']' ++ set +x +Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output +Shell debugging restarted ++ unset __lmod_sh_dbg ++ return 0 ++ source /camp/home/johnsoe/.bashrc +++ '[' '' = yes ']' +++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' ++++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.bash hook +++ __conda_setup='export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'' + +# Copyright (C) 2012 Anaconda, Inc +# SPDX-License-Identifier: BSD-3-Clause +__conda_exe() ( + "$CONDA_EXE" $_CE_M $_CE_CONDA "$@" +) + +__conda_hashr() { + if [ -n "${ZSH_VERSION:+x}" ]; then + \rehash + elif [ -n "${POSH_VERSION:+x}" ]; then + : # pass + else + \hash -r + fi +} + +__conda_activate() { + if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then + # Handle transition from shell activated with conda <= 4.3 to a subsequent activation + # after conda updated to >= 4.4. See issue #6173. + PS1="$CONDA_PS1_BACKUP" + \unset CONDA_PS1_BACKUP + fi + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return + \eval "$ask_conda" + __conda_hashr +} + +__conda_reactivate() { + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return + \eval "$ask_conda" + __conda_hashr +} + +conda() { + \local cmd="${1-__missing__}" + case "$cmd" in + activate|deactivate) + __conda_activate "$@" + ;; + install|update|upgrade|remove|uninstall) + __conda_exe "$@" || \return + __conda_reactivate + ;; + *) + __conda_exe "$@" + ;; + esac +} + +if [ -z "${CONDA_SHLVL+x}" ]; then + \export CONDA_SHLVL=0 + # In dev-mode CONDA_EXE is python.exe and on Windows + # it is in a different relative location to condabin. + if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then + PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}" + else + PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}" + fi + \export PATH + + # We'\''re not allowing PS1 to be unbound. It must at least be set. + # However, we'\''re not exporting it, which can cause problems when starting a second shell + # via a first shell (i.e. starting zsh from bash). + if [ -z "${PS1+x}" ]; then + PS1= + fi +fi + +conda activate base' +++ '[' 0 -eq 0 ']' +++ eval 'export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'' + +# Copyright (C) 2012 Anaconda, Inc +# SPDX-License-Identifier: BSD-3-Clause +__conda_exe() ( + "$CONDA_EXE" $_CE_M $_CE_CONDA "$@" +) + +__conda_hashr() { + if [ -n "${ZSH_VERSION:+x}" ]; then + \rehash + elif [ -n "${POSH_VERSION:+x}" ]; then + : # pass + else + \hash -r + fi +} + +__conda_activate() { + if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then + # Handle transition from shell activated with conda <= 4.3 to a subsequent activation + # after conda updated to >= 4.4. See issue #6173. + PS1="$CONDA_PS1_BACKUP" + \unset CONDA_PS1_BACKUP + fi + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return + \eval "$ask_conda" + __conda_hashr +} + +__conda_reactivate() { + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return + \eval "$ask_conda" + __conda_hashr +} + +conda() { + \local cmd="${1-__missing__}" + case "$cmd" in + activate|deactivate) + __conda_activate "$@" + ;; + install|update|upgrade|remove|uninstall) + __conda_exe "$@" || \return + __conda_reactivate + ;; + *) + __conda_exe "$@" + ;; + esac +} + +if [ -z "${CONDA_SHLVL+x}" ]; then + \export CONDA_SHLVL=0 + # In dev-mode CONDA_EXE is python.exe and on Windows + # it is in a different relative location to condabin. + if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then + PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}" + else + PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}" + fi + \export PATH + + # We'\''re not allowing PS1 to be unbound. It must at least be set. + # However, we'\''re not exporting it, which can cause problems when starting a second shell + # via a first shell (i.e. starting zsh from bash). + if [ -z "${PS1+x}" ]; then + PS1= + fi +fi + +conda activate base' ++++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda ++++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda ++++ export _CE_M= ++++ _CE_M= ++++ export _CE_CONDA= ++++ _CE_CONDA= ++++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ '[' -z x ']' ++++ conda activate base ++++ local cmd=activate ++++ case "$cmd" in ++++ __conda_activate activate base ++++ '[' -n '' ']' ++++ local ask_conda +++++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++++ __conda_exe shell.posix activate base +++++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate base ++++ ask_conda='PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_SHLVL='\''6'\'' +export CONDA_DEFAULT_ENV='\''base'\'' +export CONDA_PROMPT_MODIFIER='\''(base) '\'' +export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' ++++ eval 'PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_SHLVL='\''6'\'' +export CONDA_DEFAULT_ENV='\''base'\'' +export CONDA_PROMPT_MODIFIER='\''(base) '\'' +export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' +++++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++++ export CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0 +++++ CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0 +++++ export CONDA_SHLVL=6 +++++ CONDA_SHLVL=6 +++++ export CONDA_DEFAULT_ENV=base +++++ CONDA_DEFAULT_ENV=base +++++ export 'CONDA_PROMPT_MODIFIER=(base) ' +++++ CONDA_PROMPT_MODIFIER='(base) ' +++++ export CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev +++++ CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev +++++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++++ export _CE_M= +++++ _CE_M= +++++ export _CE_CONDA= +++++ _CE_CONDA= +++++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python +++++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ __conda_hashr ++++ '[' -n '' ']' ++++ '[' -n '' ']' ++++ hash -r +++ unset __conda_setup ++ conda activate schemist-dev ++ local cmd=activate ++ case "$cmd" in ++ __conda_activate activate schemist-dev ++ '[' -n '' ']' ++ local ask_conda +++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++ __conda_exe shell.posix activate schemist-dev +++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate schemist-dev ++ ask_conda='PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_SHLVL='\''7'\'' +export CONDA_DEFAULT_ENV='\''schemist-dev'\'' +export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\'' +export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' ++ eval 'PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_SHLVL='\''7'\'' +export CONDA_DEFAULT_ENV='\''schemist-dev'\'' +export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\'' +export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' +++ PS1='(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++ export CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev +++ CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev +++ export CONDA_SHLVL=7 +++ CONDA_SHLVL=7 +++ export CONDA_DEFAULT_ENV=schemist-dev +++ CONDA_DEFAULT_ENV=schemist-dev +++ export 'CONDA_PROMPT_MODIFIER=(schemist-dev) ' +++ CONDA_PROMPT_MODIFIER='(schemist-dev) ' +++ export CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0 +++ CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0 +++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++ export _CE_M= +++ _CE_M= +++ export _CE_CONDA= +++ _CE_CONDA= +++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python +++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++ __conda_hashr ++ '[' -n '' ']' ++ '[' -n '' ']' ++ hash -r ++ CHUNK_HEAD_FILE=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz ++ INPUT=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/train/cyc-pep-6-12mer-70M_23.csv ++ COLUMN=cysteine_to_N_cyclization ++ PREFIX=cyclic_ ++ AWK='1 { print $8, $1, $2, $10, $3 }' ++ '[' -z cysteine_to_N_cyclization ']' ++ '[' -z cyclic_ ']' ++ '[' -z '1 { print $8, $1, $2, $10, $3 }' ']' ++ cat /dev/fd/63 /nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/train/cyc-pep-6-12mer-70M_23.csv ++ awk -F, -v OFS=, '1 { print $8, $1, $2, $10, $3 }' ++ gzip --best +++ head -n1 +++ zcat /nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz ++ schemist convert -f csv --column cysteine_to_N_cyclization --to id inchikey scaffold mwt clogp tpsa --prefix cyclic_ --options prefix=SCB- +++ tr ' ' , +🚀 Converting between string representations with the following parameters: + subcommand: convert + output: <_io.TextIOWrapper name='' mode='w' encoding='utf-8'> + format: csv + input: <_io.TextIOWrapper name='' mode='r' encoding='utf-8'> + representation: SMILES + column: cysteine_to_N_cyclization + prefix: cyclic_ + to: ['id', 'inchikey', 'scaffold', 'mwt', 'clogp', 'tpsa'] + options: ['prefix=SCB-'] + func: + 0it [00:00, ?it/s] 1it [00:06, 6.58s/it] 2it [00:12, 6.26s/it] 3it [00:18, 6.28s/it] 4it [00:25, 6.35s/it] 5it [00:31, 6.38s/it] 6it 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7.61s/it] 970it [1:56:20, 7.76s/it] 971it [1:56:29, 7.92s/it] 972it [1:56:37, 8.05s/it] 973it [1:56:45, 7.99s/it] 974it [1:56:53, 7.91s/it] 975it [1:57:00, 7.89s/it] 976it [1:57:08, 7.85s/it] 977it [1:57:16, 7.79s/it] 978it [1:57:24, 7.77s/it] 979it [1:57:31, 7.64s/it] 980it [1:57:38, 7.61s/it] 981it [1:57:46, 7.62s/it] 982it [1:57:54, 7.66s/it] 983it [1:58:01, 7.62s/it] 984it [1:58:09, 7.59s/it] 985it [1:58:16, 7.56s/it] 986it [1:58:24, 7.53s/it] 987it [1:58:32, 7.64s/it] 988it [1:58:40, 7.76s/it] 989it [1:58:48, 7.89s/it] 990it [1:58:56, 7.88s/it] 991it [1:59:04, 7.90s/it] 992it [1:59:11, 7.86s/it] 993it [1:59:19, 7.81s/it] 994it [1:59:27, 7.75s/it] 995it [1:59:34, 7.69s/it] 996it [1:59:42, 7.58s/it] 997it [1:59:49, 7.60s/it] 998it [1:59:57, 7.57s/it] 999it [2:00:04, 7.54s/it] 1000it [2:00:12, 7.51s/it] 1000it [2:00:12, 7.21s/it] +Error counts: + cyclic_id: 0 + cyclic_inchikey: 0 + cyclic_scaffold: 0 + cyclic_mwt: 0 + cyclic_clogp: 0 + cyclic_tpsa: 0 +⏰ Completed process in 2:00:28.044039 ++ rm /nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/train/cyc-pep-6-12mer-70M_23.csv diff --git a/train/cyc-pep-6-12mer-70M_24.csv.gz b/train/cyc-pep-6-12mer-70M_24.csv.gz index a46422a12005b496839e7c0455b02b0263e127e4..ba3bc6e993d95e6b43cc9676abcc2dd14c71f8cb 100644 --- a/train/cyc-pep-6-12mer-70M_24.csv.gz +++ b/train/cyc-pep-6-12mer-70M_24.csv.gz @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:c6eb3005836008167b0d4e019da9277d7aaa92477a999937460bdacb26388c3d -size 27285058 +oid sha256:cc3469b73bf35515ae1ea999d8a035f38fd05ff0fd52fe67f92b01f9a942994e +size 65592278 diff --git a/train/cyc-pep-6-12mer-70M_24.log b/train/cyc-pep-6-12mer-70M_24.log new file mode 100644 index 0000000000000000000000000000000000000000..1e9dd5b015d088c0928d109b6ef12e83191073a4 --- /dev/null +++ b/train/cyc-pep-6-12mer-70M_24.log @@ -0,0 +1,337 @@ ++ module purge ++ '[' -z '' ']' ++ case "$-" in ++ __lmod_sh_dbg=x ++ '[' -n x ']' ++ set +x +Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output +Shell debugging restarted ++ unset __lmod_sh_dbg ++ return 0 ++ module load Anaconda3/2023.03 ++ '[' -z '' ']' ++ case "$-" in ++ __lmod_sh_dbg=x ++ '[' -n x ']' ++ set +x +Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output +Shell debugging restarted ++ unset __lmod_sh_dbg ++ return 0 ++ source /camp/home/johnsoe/.bashrc +++ '[' '' = yes ']' +++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' ++++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.bash hook +++ __conda_setup='export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'' + +# Copyright (C) 2012 Anaconda, Inc +# SPDX-License-Identifier: BSD-3-Clause +__conda_exe() ( + "$CONDA_EXE" $_CE_M $_CE_CONDA "$@" +) + +__conda_hashr() { + if [ -n "${ZSH_VERSION:+x}" ]; then + \rehash + elif [ -n "${POSH_VERSION:+x}" ]; then + : # pass + else + \hash -r + fi +} + +__conda_activate() { + if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then + # Handle transition from shell activated with conda <= 4.3 to a subsequent activation + # after conda updated to >= 4.4. See issue #6173. + PS1="$CONDA_PS1_BACKUP" + \unset CONDA_PS1_BACKUP + fi + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return + \eval "$ask_conda" + __conda_hashr +} + +__conda_reactivate() { + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return + \eval "$ask_conda" + __conda_hashr +} + +conda() { + \local cmd="${1-__missing__}" + case "$cmd" in + activate|deactivate) + __conda_activate "$@" + ;; + install|update|upgrade|remove|uninstall) + __conda_exe "$@" || \return + __conda_reactivate + ;; + *) + __conda_exe "$@" + ;; + esac +} + +if [ -z "${CONDA_SHLVL+x}" ]; then + \export CONDA_SHLVL=0 + # In dev-mode CONDA_EXE is python.exe and on Windows + # it is in a different relative location to condabin. + if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then + PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}" + else + PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}" + fi + \export PATH + + # We'\''re not allowing PS1 to be unbound. It must at least be set. + # However, we'\''re not exporting it, which can cause problems when starting a second shell + # via a first shell (i.e. starting zsh from bash). + if [ -z "${PS1+x}" ]; then + PS1= + fi +fi + +conda activate base' +++ '[' 0 -eq 0 ']' +++ eval 'export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'' + +# Copyright (C) 2012 Anaconda, Inc +# SPDX-License-Identifier: BSD-3-Clause +__conda_exe() ( + "$CONDA_EXE" $_CE_M $_CE_CONDA "$@" +) + +__conda_hashr() { + if [ -n "${ZSH_VERSION:+x}" ]; then + \rehash + elif [ -n "${POSH_VERSION:+x}" ]; then + : # pass + else + \hash -r + fi +} + +__conda_activate() { + if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then + # Handle transition from shell activated with conda <= 4.3 to a subsequent activation + # after conda updated to >= 4.4. See issue #6173. + PS1="$CONDA_PS1_BACKUP" + \unset CONDA_PS1_BACKUP + fi + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return + \eval "$ask_conda" + __conda_hashr +} + +__conda_reactivate() { + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return + \eval "$ask_conda" + __conda_hashr +} + +conda() { + \local cmd="${1-__missing__}" + case "$cmd" in + activate|deactivate) + __conda_activate "$@" + ;; + install|update|upgrade|remove|uninstall) + __conda_exe "$@" || \return + __conda_reactivate + ;; + *) + __conda_exe "$@" + ;; + esac +} + +if [ -z "${CONDA_SHLVL+x}" ]; then + \export CONDA_SHLVL=0 + # In dev-mode CONDA_EXE is python.exe and on Windows + # it is in a different relative location to condabin. + if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then + PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}" + else + PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}" + fi + \export PATH + + # We'\''re not allowing PS1 to be unbound. It must at least be set. + # However, we'\''re not exporting it, which can cause problems when starting a second shell + # via a first shell (i.e. starting zsh from bash). + if [ -z "${PS1+x}" ]; then + PS1= + fi +fi + +conda activate base' ++++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda ++++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda ++++ export _CE_M= ++++ _CE_M= ++++ export _CE_CONDA= ++++ _CE_CONDA= ++++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ '[' -z x ']' ++++ conda activate base ++++ local cmd=activate ++++ case "$cmd" in ++++ __conda_activate activate base ++++ '[' -n '' ']' ++++ local ask_conda +++++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++++ __conda_exe shell.posix activate base +++++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate base ++++ ask_conda='PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_SHLVL='\''6'\'' +export CONDA_DEFAULT_ENV='\''base'\'' +export CONDA_PROMPT_MODIFIER='\''(base) '\'' +export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' ++++ eval 'PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_SHLVL='\''6'\'' +export CONDA_DEFAULT_ENV='\''base'\'' +export CONDA_PROMPT_MODIFIER='\''(base) '\'' +export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' +++++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++++ export CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0 +++++ CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0 +++++ export CONDA_SHLVL=6 +++++ CONDA_SHLVL=6 +++++ export CONDA_DEFAULT_ENV=base +++++ CONDA_DEFAULT_ENV=base +++++ export 'CONDA_PROMPT_MODIFIER=(base) ' +++++ CONDA_PROMPT_MODIFIER='(base) ' +++++ export CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev +++++ CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev +++++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++++ export _CE_M= +++++ _CE_M= +++++ export _CE_CONDA= +++++ _CE_CONDA= +++++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python +++++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ __conda_hashr ++++ '[' -n '' ']' ++++ '[' -n '' ']' ++++ hash -r +++ unset __conda_setup ++ conda activate schemist-dev ++ local cmd=activate ++ case "$cmd" in ++ __conda_activate activate schemist-dev ++ '[' -n '' ']' ++ local ask_conda +++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++ __conda_exe shell.posix activate schemist-dev +++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate schemist-dev ++ ask_conda='PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_SHLVL='\''7'\'' +export CONDA_DEFAULT_ENV='\''schemist-dev'\'' +export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\'' +export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' ++ eval 'PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_SHLVL='\''7'\'' +export CONDA_DEFAULT_ENV='\''schemist-dev'\'' +export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\'' +export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' +++ PS1='(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++ export CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev +++ CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev +++ export CONDA_SHLVL=7 +++ CONDA_SHLVL=7 +++ export CONDA_DEFAULT_ENV=schemist-dev +++ CONDA_DEFAULT_ENV=schemist-dev +++ export 'CONDA_PROMPT_MODIFIER=(schemist-dev) ' +++ CONDA_PROMPT_MODIFIER='(schemist-dev) ' +++ export CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0 +++ CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0 +++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++ export _CE_M= +++ _CE_M= +++ export _CE_CONDA= +++ _CE_CONDA= +++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python +++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++ __conda_hashr ++ '[' -n '' ']' ++ '[' -n '' ']' ++ hash -r ++ CHUNK_HEAD_FILE=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz ++ INPUT=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/train/cyc-pep-6-12mer-70M_24.csv ++ COLUMN=cysteine_to_N_cyclization ++ PREFIX=cyclic_ ++ AWK='1 { print $8, $1, $2, $10, $3 }' ++ '[' -z cysteine_to_N_cyclization ']' ++ '[' -z cyclic_ ']' ++ '[' -z '1 { print $8, $1, $2, $10, $3 }' ']' ++ cat /dev/fd/63 /nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/train/cyc-pep-6-12mer-70M_24.csv ++ awk -F, -v OFS=, '1 { print $8, $1, $2, $10, $3 }' ++ schemist convert -f csv --column cysteine_to_N_cyclization --to id inchikey scaffold mwt clogp tpsa --prefix cyclic_ --options prefix=SCB- +++ zcat /nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz ++ gzip --best +++ tr ' ' , +++ head -n1 +🚀 Converting between string representations with the following parameters: + subcommand: convert + output: <_io.TextIOWrapper name='' mode='w' encoding='utf-8'> + format: csv + input: <_io.TextIOWrapper name='' mode='r' encoding='utf-8'> + representation: SMILES + column: cysteine_to_N_cyclization + prefix: cyclic_ + to: ['id', 'inchikey', 'scaffold', 'mwt', 'clogp', 'tpsa'] + options: ['prefix=SCB-'] + func: + 0it [00:00, ?it/s] 1it [00:07, 7.48s/it] 2it [00:14, 7.47s/it] 3it [00:22, 7.46s/it] 4it [00:30, 7.67s/it] 5it [00:38, 7.84s/it] 6it 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cyclic_inchikey: 0 + cyclic_scaffold: 0 + cyclic_mwt: 0 + cyclic_clogp: 0 + cyclic_tpsa: 0 +⏰ Completed process in 2:11:19.188644 ++ rm /nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/train/cyc-pep-6-12mer-70M_24.csv diff --git a/train/cyc-pep-6-12mer-70M_25.csv.gz b/train/cyc-pep-6-12mer-70M_25.csv.gz index 48770750059b1bed755ccfff2401db9e9251a023..bffebc45bf0cbb35cbd66418ec10af4ca9388e1b 100644 --- a/train/cyc-pep-6-12mer-70M_25.csv.gz +++ b/train/cyc-pep-6-12mer-70M_25.csv.gz @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:69cc30f6ed5f84c2b01f97844fc59ae605d164e500a8cee084e62244d6efc654 -size 27261100 +oid sha256:363e147cdde55c406e64648db58494389a525a11bea5dc7c7223f2de5f020c41 +size 65350787 diff --git a/train/cyc-pep-6-12mer-70M_25.log b/train/cyc-pep-6-12mer-70M_25.log new file mode 100644 index 0000000000000000000000000000000000000000..f671c939338d40e3f7aaa58afcdcdc4a6a6c6a13 --- /dev/null +++ b/train/cyc-pep-6-12mer-70M_25.log @@ -0,0 +1,337 @@ ++ module purge ++ '[' -z '' ']' ++ case "$-" in ++ __lmod_sh_dbg=x ++ '[' -n x ']' ++ set +x +Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output +Shell debugging restarted ++ unset __lmod_sh_dbg ++ return 0 ++ module load Anaconda3/2023.03 ++ '[' -z '' ']' ++ case "$-" in ++ __lmod_sh_dbg=x ++ '[' -n x ']' ++ set +x +Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output +Shell debugging restarted ++ unset __lmod_sh_dbg ++ return 0 ++ source /camp/home/johnsoe/.bashrc +++ '[' '' = yes ']' +++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' ++++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.bash hook +++ __conda_setup='export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'' + +# Copyright (C) 2012 Anaconda, Inc +# SPDX-License-Identifier: BSD-3-Clause +__conda_exe() ( + "$CONDA_EXE" $_CE_M $_CE_CONDA "$@" +) + +__conda_hashr() { + if [ -n "${ZSH_VERSION:+x}" ]; then + \rehash + elif [ -n "${POSH_VERSION:+x}" ]; then + : # pass + else + \hash -r + fi +} + +__conda_activate() { + if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then + # Handle transition from shell activated with conda <= 4.3 to a subsequent activation + # after conda updated to >= 4.4. See issue #6173. + PS1="$CONDA_PS1_BACKUP" + \unset CONDA_PS1_BACKUP + fi + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return + \eval "$ask_conda" + __conda_hashr +} + +__conda_reactivate() { + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return + \eval "$ask_conda" + __conda_hashr +} + +conda() { + \local cmd="${1-__missing__}" + case "$cmd" in + activate|deactivate) + __conda_activate "$@" + ;; + install|update|upgrade|remove|uninstall) + __conda_exe "$@" || \return + __conda_reactivate + ;; + *) + __conda_exe "$@" + ;; + esac +} + +if [ -z "${CONDA_SHLVL+x}" ]; then + \export CONDA_SHLVL=0 + # In dev-mode CONDA_EXE is python.exe and on Windows + # it is in a different relative location to condabin. + if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then + PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}" + else + PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}" + fi + \export PATH + + # We'\''re not allowing PS1 to be unbound. It must at least be set. + # However, we'\''re not exporting it, which can cause problems when starting a second shell + # via a first shell (i.e. starting zsh from bash). + if [ -z "${PS1+x}" ]; then + PS1= + fi +fi + +conda activate base' +++ '[' 0 -eq 0 ']' +++ eval 'export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'' + +# Copyright (C) 2012 Anaconda, Inc +# SPDX-License-Identifier: BSD-3-Clause +__conda_exe() ( + "$CONDA_EXE" $_CE_M $_CE_CONDA "$@" +) + +__conda_hashr() { + if [ -n "${ZSH_VERSION:+x}" ]; then + \rehash + elif [ -n "${POSH_VERSION:+x}" ]; then + : # pass + else + \hash -r + fi +} + +__conda_activate() { + if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then + # Handle transition from shell activated with conda <= 4.3 to a subsequent activation + # after conda updated to >= 4.4. See issue #6173. + PS1="$CONDA_PS1_BACKUP" + \unset CONDA_PS1_BACKUP + fi + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return + \eval "$ask_conda" + __conda_hashr +} + +__conda_reactivate() { + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return + \eval "$ask_conda" + __conda_hashr +} + +conda() { + \local cmd="${1-__missing__}" + case "$cmd" in + activate|deactivate) + __conda_activate "$@" + ;; + install|update|upgrade|remove|uninstall) + __conda_exe "$@" || \return + __conda_reactivate + ;; + *) + __conda_exe "$@" + ;; + esac +} + +if [ -z "${CONDA_SHLVL+x}" ]; then + \export CONDA_SHLVL=0 + # In dev-mode CONDA_EXE is python.exe and on Windows + # it is in a different relative location to condabin. + if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then + PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}" + else + PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}" + fi + \export PATH + + # We'\''re not allowing PS1 to be unbound. It must at least be set. + # However, we'\''re not exporting it, which can cause problems when starting a second shell + # via a first shell (i.e. starting zsh from bash). + if [ -z "${PS1+x}" ]; then + PS1= + fi +fi + +conda activate base' ++++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda ++++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda ++++ export _CE_M= ++++ _CE_M= ++++ export _CE_CONDA= ++++ _CE_CONDA= ++++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ '[' -z x ']' ++++ conda activate base ++++ local cmd=activate ++++ case "$cmd" in ++++ __conda_activate activate base ++++ '[' -n '' ']' ++++ local ask_conda +++++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++++ __conda_exe shell.posix activate base +++++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate base ++++ ask_conda='PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_SHLVL='\''6'\'' +export CONDA_DEFAULT_ENV='\''base'\'' +export CONDA_PROMPT_MODIFIER='\''(base) '\'' +export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' ++++ eval 'PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_SHLVL='\''6'\'' +export CONDA_DEFAULT_ENV='\''base'\'' +export CONDA_PROMPT_MODIFIER='\''(base) '\'' +export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' +++++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++++ export CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0 +++++ CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0 +++++ export CONDA_SHLVL=6 +++++ CONDA_SHLVL=6 +++++ export CONDA_DEFAULT_ENV=base +++++ CONDA_DEFAULT_ENV=base +++++ export 'CONDA_PROMPT_MODIFIER=(base) ' +++++ CONDA_PROMPT_MODIFIER='(base) ' +++++ export CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev +++++ CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev +++++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++++ export _CE_M= +++++ _CE_M= +++++ export _CE_CONDA= +++++ _CE_CONDA= +++++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python +++++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ __conda_hashr ++++ '[' -n '' ']' ++++ '[' -n '' ']' ++++ hash -r +++ unset __conda_setup ++ conda activate schemist-dev ++ local cmd=activate ++ case "$cmd" in ++ __conda_activate activate schemist-dev ++ '[' -n '' ']' ++ local ask_conda +++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++ __conda_exe shell.posix activate schemist-dev +++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate schemist-dev ++ ask_conda='PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_SHLVL='\''7'\'' +export CONDA_DEFAULT_ENV='\''schemist-dev'\'' +export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\'' +export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' ++ eval 'PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_SHLVL='\''7'\'' +export CONDA_DEFAULT_ENV='\''schemist-dev'\'' +export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\'' +export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' +++ PS1='(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++ export CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev +++ CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev +++ export CONDA_SHLVL=7 +++ CONDA_SHLVL=7 +++ export CONDA_DEFAULT_ENV=schemist-dev +++ CONDA_DEFAULT_ENV=schemist-dev +++ export 'CONDA_PROMPT_MODIFIER=(schemist-dev) ' +++ CONDA_PROMPT_MODIFIER='(schemist-dev) ' +++ export CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0 +++ CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0 +++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++ export _CE_M= +++ _CE_M= +++ export _CE_CONDA= +++ _CE_CONDA= +++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python +++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++ __conda_hashr ++ '[' -n '' ']' ++ '[' -n '' ']' ++ hash -r ++ CHUNK_HEAD_FILE=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz ++ INPUT=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/train/cyc-pep-6-12mer-70M_25.csv ++ COLUMN=cysteine_to_N_cyclization ++ PREFIX=cyclic_ ++ AWK='1 { print $8, $1, $2, $10, $3 }' ++ '[' -z cysteine_to_N_cyclization ']' ++ '[' -z cyclic_ ']' ++ '[' -z '1 { print $8, $1, $2, $10, $3 }' ']' ++ cat /dev/fd/63 /nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/train/cyc-pep-6-12mer-70M_25.csv ++ schemist convert -f csv --column cysteine_to_N_cyclization --to id inchikey scaffold mwt clogp tpsa --prefix cyclic_ --options prefix=SCB- ++ gzip --best +++ zcat /nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz ++ awk -F, -v OFS=, '1 { print $8, $1, $2, $10, $3 }' +++ head -n1 +++ tr ' ' , +🚀 Converting between string representations with the following parameters: + subcommand: convert + output: <_io.TextIOWrapper name='' mode='w' encoding='utf-8'> + format: csv + input: <_io.TextIOWrapper name='' mode='r' encoding='utf-8'> + representation: SMILES + column: cysteine_to_N_cyclization + prefix: cyclic_ + to: ['id', 'inchikey', 'scaffold', 'mwt', 'clogp', 'tpsa'] + options: ['prefix=SCB-'] + func: + 0it [00:00, ?it/s] 1it [00:07, 7.21s/it] 2it [00:14, 7.23s/it] 3it [00:21, 7.16s/it] 4it [00:28, 7.16s/it] 5it [00:35, 7.15s/it] 6it [00:42, 7.02s/it] 7it [00:49, 6.94s/it] 8it [00:56, 7.01s/it] 9it [01:03, 7.05s/it] 10it [01:10, 7.02s/it] 11it [01:17, 6.92s/it] 12it [01:24, 6.89s/it] 13it [01:30, 6.83s/it] 14it [01:37, 6.91s/it] 15it [01:45, 7.10s/it] 16it [01:53, 7.26s/it] 17it [02:00, 7.24s/it] 18it [02:07, 7.17s/it] 19it [02:14, 7.14s/it] 20it [02:21, 7.11s/it] 21it [02:28, 7.08s/it] 22it [02:35, 7.02s/it] 23it [02:41, 6.90s/it] 24it [02:48, 6.85s/it] 25it [02:55, 6.88s/it] 26it [03:02, 6.88s/it] 27it [03:09, 6.86s/it] 28it [03:16, 6.82s/it] 29it [03:22, 6.81s/it] 30it [03:29, 6.77s/it] 31it [03:36, 6.90s/it] 32it [03:44, 7.06s/it] 33it [03:51, 7.19s/it] 34it [03:58, 7.17s/it] 35it [04:05, 7.12s/it] 36it [04:12, 7.12s/it] 37it [04:19, 7.08s/it] 38it [04:26, 7.01s/it] 39it [04:33, 6.98s/it] 40it [04:40, 6.82s/it] 41it [04:46, 6.75s/it] 42it [04:53, 6.80s/it] 43it [05:00, 6.79s/it] 44it [05:07, 6.76s/it] 45it [05:13, 6.71s/it] 46it [05:20, 6.68s/it] 47it [05:26, 6.66s/it] 48it [05:33, 6.79s/it] 49it [05:41, 6.95s/it] 50it [05:48, 7.08s/it] 51it [05:55, 7.06s/it] 52it [06:02, 7.05s/it] 53it [06:09, 7.02s/it] 54it [06:16, 6.98s/it] 55it [06:23, 6.96s/it] 56it [06:30, 6.94s/it] 57it [06:36, 6.86s/it] 58it [06:43, 6.89s/it] 59it [06:50, 6.94s/it] 60it [06:58, 6.96s/it] 61it [07:04, 6.95s/it] 62it [07:11, 6.97s/it] 63it [07:18, 6.96s/it] 64it [07:25, 6.94s/it] 65it [07:33, 7.08s/it] 66it [07:40, 7.22s/it] 67it [07:48, 7.33s/it] 68it [07:55, 7.30s/it] 69it [08:02, 7.29s/it] 70it [08:09, 7.25s/it] 71it [08:16, 7.18s/it] 72it [08:23, 7.12s/it] 73it [08:30, 7.02s/it] 74it [08:37, 6.85s/it] 75it [08:43, 6.81s/it] 76it [08:50, 6.78s/it] 77it [08:57, 6.71s/it] 78it [09:03, 6.64s/it] 79it [09:10, 6.61s/it] 80it [09:16, 6.60s/it] 81it [09:23, 6.61s/it] 82it [09:30, 6.75s/it] 83it [09:37, 6.89s/it] 84it [09:44, 6.99s/it] 85it [09:51, 6.95s/it] 86it [09:58, 6.95s/it] 87it [10:05, 6.85s/it] 88it [10:12, 6.79s/it] 89it [10:18, 6.75s/it] 90it [10:25, 6.73s/it] 91it [10:32, 6.72s/it] 92it [10:39, 6.82s/it] 93it [10:46, 6.85s/it] 94it [10:52, 6.86s/it] 95it [10:59, 6.85s/it] 96it [11:06, 6.85s/it] 97it [11:13, 6.81s/it] 98it [11:20, 6.85s/it] 99it [11:27, 7.00s/it] 100it [11:35, 7.18s/it] 101it [11:42, 7.25s/it] 102it [11:49, 7.19s/it] 103it [11:56, 7.18s/it] 104it [12:03, 7.11s/it] 105it [12:10, 7.07s/it] 106it [12:17, 7.05s/it] 107it [12:24, 7.09s/it] 108it [12:32, 7.14s/it] 109it [12:39, 7.25s/it] 110it [12:47, 7.29s/it] 111it [12:54, 7.31s/it] 112it [13:01, 7.32s/it] 113it [13:09, 7.34s/it] 114it [13:16, 7.29s/it] 115it [13:23, 7.35s/it] 116it [13:31, 7.52s/it] 117it [13:39, 7.71s/it] 118it [13:47, 7.78s/it] 119it [13:55, 7.70s/it] 120it [14:03, 7.70s/it] 121it [14:10, 7.65s/it] 122it [14:18, 7.63s/it] 123it [14:25, 7.60s/it] 124it [14:33, 7.53s/it] 125it [14:40, 7.45s/it] 126it [14:48, 7.53s/it] 127it [14:55, 7.58s/it] 128it [15:03, 7.62s/it] 129it [15:10, 7.59s/it] 130it [15:18, 7.64s/it] 131it [15:26, 7.58s/it] 132it [15:33, 7.63s/it] 133it [15:42, 7.81s/it] 134it [15:50, 7.99s/it] 135it [15:58, 8.07s/it] 136it [16:06, 8.06s/it] 137it [16:14, 8.07s/it] 138it [16:22, 8.01s/it] 139it [16:30, 7.96s/it] 140it [16:38, 7.89s/it] 141it [16:46, 7.82s/it] 142it [16:53, 7.79s/it] 143it [17:02, 7.92s/it] 144it [17:10, 8.02s/it] 145it [17:18, 7.99s/it] 146it [17:25, 7.92s/it] 147it [17:33, 7.89s/it] 148it [17:41, 7.82s/it] 149it [17:49, 7.93s/it] 150it [17:58, 8.14s/it] 151it [18:07, 8.39s/it] 152it [18:15, 8.39s/it] 153it [18:23, 8.30s/it] 154it [18:31, 8.24s/it] 155it [18:39, 8.17s/it] 156it [18:47, 8.13s/it] 157it [18:55, 8.13s/it] 158it [19:03, 7.87s/it] 159it [19:11, 7.86s/it] 160it [19:18, 7.83s/it] 161it [19:26, 7.75s/it] 162it [19:33, 7.64s/it] 163it [19:41, 7.53s/it] 164it [19:48, 7.49s/it] 165it [19:55, 7.42s/it] 166it [20:03, 7.55s/it] 167it [20:11, 7.80s/it] 168it [20:20, 8.02s/it] 169it [20:28, 7.96s/it] 170it [20:35, 7.87s/it] 171it [20:43, 7.80s/it] 172it [20:51, 7.74s/it] 173it [20:58, 7.69s/it] 174it [21:06, 7.64s/it] 175it [21:13, 7.44s/it] 176it [21:20, 7.53s/it] 177it [21:28, 7.54s/it] 178it [21:35, 7.51s/it] 179it [21:43, 7.39s/it] 180it [21:50, 7.36s/it] 181it [21:57, 7.33s/it] 182it [22:04, 7.28s/it] 183it [22:12, 7.39s/it] 184it [22:20, 7.60s/it] 185it [22:28, 7.73s/it] 186it [22:36, 7.71s/it] 187it [22:43, 7.71s/it] 188it [22:51, 7.68s/it] 189it [22:59, 7.66s/it] 190it [23:06, 7.58s/it] 191it [23:13, 7.49s/it] 192it [23:21, 7.42s/it] 193it [23:28, 7.52s/it] 194it [23:36, 7.51s/it] 195it [23:43, 7.50s/it] 196it [23:51, 7.49s/it] 197it [23:59, 7.56s/it] 198it [24:06, 7.53s/it] 199it [24:14, 7.53s/it] 200it [24:22, 7.67s/it] 201it [24:30, 7.81s/it] 202it [24:38, 7.90s/it] 203it [24:46, 7.86s/it] 204it [24:53, 7.84s/it] 205it [25:01, 7.84s/it] 206it [25:09, 7.89s/it] 207it [25:17, 7.86s/it] 208it [25:24, 7.74s/it] 209it [25:32, 7.58s/it] 210it [25:39, 7.59s/it] 211it [25:47, 7.53s/it] 212it [25:54, 7.44s/it] 213it [26:01, 7.38s/it] 214it [26:09, 7.43s/it] 215it [26:16, 7.38s/it] 216it [26:23, 7.42s/it] 217it [26:31, 7.57s/it] 218it [26:39, 7.75s/it] 219it [26:47, 7.83s/it] 220it [26:55, 7.78s/it] 221it [27:03, 7.74s/it] 222it [27:11, 7.74s/it] 223it [27:18, 7.76s/it] 224it [27:26, 7.72s/it] 225it [27:33, 7.60s/it] 226it [27:41, 7.51s/it] 227it [27:48, 7.55s/it] 228it [27:56, 7.61s/it] 229it [28:04, 7.63s/it] 230it [28:11, 7.59s/it] 231it [28:19, 7.67s/it] 232it [28:27, 7.65s/it] 233it [28:34, 7.68s/it] 234it [28:43, 7.86s/it] 235it [28:51, 8.03s/it] 236it [28:59, 8.06s/it] 237it [29:07, 7.98s/it] 238it [29:15, 7.98s/it] 239it [29:23, 7.97s/it] 240it [29:31, 7.96s/it] 241it [29:39, 7.88s/it] 242it [29:46, 7.64s/it] 243it [29:53, 7.55s/it] 244it [30:00, 7.52s/it] 245it [30:08, 7.57s/it] 246it [30:16, 7.51s/it] 247it [30:23, 7.48s/it] 248it [30:31, 7.58s/it] 249it [30:38, 7.62s/it] 250it [30:46, 7.66s/it] 251it [30:54, 7.74s/it] 252it [31:02, 7.82s/it] 253it [31:10, 7.72s/it] 254it [31:17, 7.69s/it] 255it [31:25, 7.72s/it] 256it [31:33, 7.81s/it] 257it [31:41, 7.81s/it] 258it [31:49, 7.79s/it] 259it [31:56, 7.59s/it] 260it [32:03, 7.53s/it] 261it [32:10, 7.47s/it] 262it [32:18, 7.45s/it] 263it [32:25, 7.46s/it] 264it [32:33, 7.47s/it] 265it [32:41, 7.62s/it] 266it [32:48, 7.64s/it] 267it [32:56, 7.73s/it] 268it [33:04, 7.81s/it] 269it [33:12, 7.87s/it] 270it [33:20, 7.74s/it] 271it [33:28, 7.72s/it] 272it [33:35, 7.73s/it] 273it [33:43, 7.81s/it] 274it [33:51, 7.86s/it] 275it [33:59, 7.88s/it] 276it [34:06, 7.62s/it] 277it [34:14, 7.53s/it] 278it [34:21, 7.40s/it] 279it [34:28, 7.25s/it] 280it [34:35, 7.22s/it] 281it [34:42, 7.19s/it] 282it [34:49, 7.29s/it] 283it [34:57, 7.38s/it] 284it [35:05, 7.61s/it] 285it [35:13, 7.73s/it] 286it [35:21, 7.75s/it] 287it [35:28, 7.61s/it] 288it [35:35, 7.50s/it] 289it [35:43, 7.44s/it] 290it [35:50, 7.46s/it] 291it [35:58, 7.53s/it] 292it [36:06, 7.57s/it] 293it [36:13, 7.54s/it] 294it [36:21, 7.61s/it] 295it [36:28, 7.59s/it] 296it [36:36, 7.48s/it] 297it [36:43, 7.34s/it] 298it [36:50, 7.34s/it] 299it [36:57, 7.30s/it] 300it [37:05, 7.43s/it] 301it 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928it [1:58:13, 7.55s/it] 929it [1:58:20, 7.56s/it] 930it [1:58:28, 7.61s/it] 931it [1:58:35, 7.55s/it] 932it [1:58:43, 7.45s/it] 933it [1:58:50, 7.39s/it] 934it [1:58:57, 7.28s/it] 935it [1:59:04, 7.27s/it] 936it [1:59:12, 7.30s/it] 937it [1:59:19, 7.33s/it] 938it [1:59:26, 7.35s/it] 939it [1:59:34, 7.39s/it] 940it [1:59:41, 7.33s/it] 941it [1:59:48, 7.30s/it] 942it [1:59:56, 7.41s/it] 943it [2:00:03, 7.46s/it] 944it [2:00:12, 7.63s/it] 945it [2:00:19, 7.57s/it] 946it [2:00:27, 7.63s/it] 947it [2:00:34, 7.63s/it] 948it [2:00:42, 7.62s/it] 949it [2:00:49, 7.56s/it] 950it [2:00:56, 7.41s/it] 951it [2:01:03, 7.12s/it] 952it [2:01:10, 7.00s/it] 953it [2:01:16, 6.94s/it] 954it [2:01:24, 6.99s/it] 955it [2:01:31, 7.01s/it] 956it [2:01:38, 7.01s/it] 957it [2:01:45, 7.03s/it] 958it [2:01:52, 7.04s/it] 959it [2:01:59, 7.15s/it] 960it [2:02:06, 7.18s/it] 961it [2:02:14, 7.20s/it] 962it [2:02:21, 7.15s/it] 963it [2:02:28, 7.21s/it] 964it [2:02:35, 7.28s/it] 965it [2:02:43, 7.30s/it] 966it [2:02:50, 7.28s/it] 967it [2:02:57, 7.25s/it] 968it [2:03:04, 7.16s/it] 969it [2:03:11, 7.06s/it] 970it [2:03:18, 7.00s/it] 971it [2:03:25, 6.92s/it] 972it [2:03:32, 6.99s/it] 973it [2:03:39, 7.07s/it] 974it [2:03:46, 7.08s/it] 975it [2:03:53, 7.13s/it] 976it [2:04:01, 7.32s/it] 977it [2:04:09, 7.47s/it] 978it [2:04:16, 7.44s/it] 979it [2:04:23, 7.29s/it] 980it [2:04:30, 7.22s/it] 981it [2:04:38, 7.28s/it] 982it [2:04:45, 7.32s/it] 983it [2:04:52, 7.34s/it] 984it [2:05:00, 7.36s/it] 985it [2:05:07, 7.36s/it] 986it [2:05:15, 7.37s/it] 987it [2:05:22, 7.32s/it] 988it [2:05:29, 7.26s/it] 989it [2:05:36, 7.23s/it] 990it [2:05:43, 7.26s/it] 991it [2:05:51, 7.36s/it] 992it [2:05:59, 7.48s/it] 993it [2:06:07, 7.70s/it] 994it [2:06:15, 7.88s/it] 995it [2:06:23, 7.89s/it] 996it [2:06:31, 7.71s/it] 997it [2:06:38, 7.64s/it] 998it [2:06:45, 7.57s/it] 999it [2:06:53, 7.59s/it] 1000it [2:07:01, 7.71s/it] 1000it [2:07:01, 7.62s/it] +Error counts: + cyclic_id: 0 + cyclic_inchikey: 0 + cyclic_scaffold: 0 + cyclic_mwt: 0 + cyclic_clogp: 0 + cyclic_tpsa: 0 +⏰ Completed process in 2:07:19.178901 ++ rm /nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/train/cyc-pep-6-12mer-70M_25.csv diff --git a/train/cyc-pep-6-12mer-70M_26.csv.gz b/train/cyc-pep-6-12mer-70M_26.csv.gz index 7cfec7a53eca7aefac959e3761f65a0c7ec56d49..80733a4dca78c8141df016f3d735ddf552138f73 100644 --- a/train/cyc-pep-6-12mer-70M_26.csv.gz +++ b/train/cyc-pep-6-12mer-70M_26.csv.gz @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:f566eefb4f0ff967d5797771bdc76793f6620c38757f2663ea7e3f580644dafd -size 27461484 +oid sha256:06cdf93412e8dbd18015bcf42b211881e5e73d3f1229346a6bee90f51eb553b5 +size 65702600 diff --git a/train/cyc-pep-6-12mer-70M_26.log b/train/cyc-pep-6-12mer-70M_26.log new file mode 100644 index 0000000000000000000000000000000000000000..5a7dd10c67cc4314e8a1ce173c998f537b6e921f --- /dev/null +++ b/train/cyc-pep-6-12mer-70M_26.log @@ -0,0 +1,337 @@ ++ module purge ++ '[' -z '' ']' ++ case "$-" in ++ __lmod_sh_dbg=x ++ '[' -n x ']' ++ set +x +Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output +Shell debugging restarted ++ unset __lmod_sh_dbg ++ return 0 ++ module load Anaconda3/2023.03 ++ '[' -z '' ']' ++ case "$-" in ++ __lmod_sh_dbg=x ++ '[' -n x ']' ++ set +x +Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output +Shell debugging restarted ++ unset __lmod_sh_dbg ++ return 0 ++ source /camp/home/johnsoe/.bashrc +++ '[' '' = yes ']' +++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' ++++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.bash hook +++ __conda_setup='export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'' + +# Copyright (C) 2012 Anaconda, Inc +# SPDX-License-Identifier: BSD-3-Clause +__conda_exe() ( + "$CONDA_EXE" $_CE_M $_CE_CONDA "$@" +) + +__conda_hashr() { + if [ -n "${ZSH_VERSION:+x}" ]; then + \rehash + elif [ -n "${POSH_VERSION:+x}" ]; then + : # pass + else + \hash -r + fi +} + +__conda_activate() { + if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then + # Handle transition from shell activated with conda <= 4.3 to a subsequent activation + # after conda updated to >= 4.4. See issue #6173. + PS1="$CONDA_PS1_BACKUP" + \unset CONDA_PS1_BACKUP + fi + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return + \eval "$ask_conda" + __conda_hashr +} + +__conda_reactivate() { + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return + \eval "$ask_conda" + __conda_hashr +} + +conda() { + \local cmd="${1-__missing__}" + case "$cmd" in + activate|deactivate) + __conda_activate "$@" + ;; + install|update|upgrade|remove|uninstall) + __conda_exe "$@" || \return + __conda_reactivate + ;; + *) + __conda_exe "$@" + ;; + esac +} + +if [ -z "${CONDA_SHLVL+x}" ]; then + \export CONDA_SHLVL=0 + # In dev-mode CONDA_EXE is python.exe and on Windows + # it is in a different relative location to condabin. + if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then + PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}" + else + PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}" + fi + \export PATH + + # We'\''re not allowing PS1 to be unbound. It must at least be set. + # However, we'\''re not exporting it, which can cause problems when starting a second shell + # via a first shell (i.e. starting zsh from bash). + if [ -z "${PS1+x}" ]; then + PS1= + fi +fi + +conda activate base' +++ '[' 0 -eq 0 ']' +++ eval 'export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'' + +# Copyright (C) 2012 Anaconda, Inc +# SPDX-License-Identifier: BSD-3-Clause +__conda_exe() ( + "$CONDA_EXE" $_CE_M $_CE_CONDA "$@" +) + +__conda_hashr() { + if [ -n "${ZSH_VERSION:+x}" ]; then + \rehash + elif [ -n "${POSH_VERSION:+x}" ]; then + : # pass + else + \hash -r + fi +} + +__conda_activate() { + if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then + # Handle transition from shell activated with conda <= 4.3 to a subsequent activation + # after conda updated to >= 4.4. See issue #6173. + PS1="$CONDA_PS1_BACKUP" + \unset CONDA_PS1_BACKUP + fi + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return + \eval "$ask_conda" + __conda_hashr +} + +__conda_reactivate() { + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return + \eval "$ask_conda" + __conda_hashr +} + +conda() { + \local cmd="${1-__missing__}" + case "$cmd" in + activate|deactivate) + __conda_activate "$@" + ;; + install|update|upgrade|remove|uninstall) + __conda_exe "$@" || \return + __conda_reactivate + ;; + *) + __conda_exe "$@" + ;; + esac +} + +if [ -z "${CONDA_SHLVL+x}" ]; then + \export CONDA_SHLVL=0 + # In dev-mode CONDA_EXE is python.exe and on Windows + # it is in a different relative location to condabin. + if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then + PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}" + else + PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}" + fi + \export PATH + + # We'\''re not allowing PS1 to be unbound. It must at least be set. + # However, we'\''re not exporting it, which can cause problems when starting a second shell + # via a first shell (i.e. starting zsh from bash). + if [ -z "${PS1+x}" ]; then + PS1= + fi +fi + +conda activate base' ++++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda ++++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda ++++ export _CE_M= ++++ _CE_M= ++++ export _CE_CONDA= ++++ _CE_CONDA= ++++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ '[' -z x ']' ++++ conda activate base ++++ local cmd=activate ++++ case "$cmd" in ++++ __conda_activate activate base ++++ '[' -n '' ']' ++++ local ask_conda +++++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++++ __conda_exe shell.posix activate base +++++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate base ++++ ask_conda='PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_SHLVL='\''6'\'' +export CONDA_DEFAULT_ENV='\''base'\'' +export CONDA_PROMPT_MODIFIER='\''(base) '\'' +export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' ++++ eval 'PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_SHLVL='\''6'\'' +export CONDA_DEFAULT_ENV='\''base'\'' +export CONDA_PROMPT_MODIFIER='\''(base) '\'' +export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' +++++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++++ export CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0 +++++ CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0 +++++ export CONDA_SHLVL=6 +++++ CONDA_SHLVL=6 +++++ export CONDA_DEFAULT_ENV=base +++++ CONDA_DEFAULT_ENV=base +++++ export 'CONDA_PROMPT_MODIFIER=(base) ' +++++ CONDA_PROMPT_MODIFIER='(base) ' +++++ export CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev +++++ CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev +++++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++++ export _CE_M= +++++ _CE_M= +++++ export _CE_CONDA= +++++ _CE_CONDA= +++++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python +++++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ __conda_hashr ++++ '[' -n '' ']' ++++ '[' -n '' ']' ++++ hash -r +++ unset __conda_setup ++ conda activate schemist-dev ++ local cmd=activate ++ case "$cmd" in ++ __conda_activate activate schemist-dev ++ '[' -n '' ']' ++ local ask_conda +++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++ __conda_exe shell.posix activate schemist-dev +++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate schemist-dev ++ ask_conda='PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_SHLVL='\''7'\'' +export CONDA_DEFAULT_ENV='\''schemist-dev'\'' +export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\'' +export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' ++ eval 'PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_SHLVL='\''7'\'' +export CONDA_DEFAULT_ENV='\''schemist-dev'\'' +export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\'' +export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' +++ PS1='(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++ export CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev +++ CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev +++ export CONDA_SHLVL=7 +++ CONDA_SHLVL=7 +++ export CONDA_DEFAULT_ENV=schemist-dev +++ CONDA_DEFAULT_ENV=schemist-dev +++ export 'CONDA_PROMPT_MODIFIER=(schemist-dev) ' +++ CONDA_PROMPT_MODIFIER='(schemist-dev) ' +++ export CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0 +++ CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0 +++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++ export _CE_M= +++ _CE_M= +++ export _CE_CONDA= +++ _CE_CONDA= +++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python +++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++ __conda_hashr ++ '[' -n '' ']' ++ '[' -n '' ']' ++ hash -r ++ CHUNK_HEAD_FILE=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz ++ INPUT=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/train/cyc-pep-6-12mer-70M_26.csv ++ COLUMN=cysteine_to_N_cyclization ++ PREFIX=cyclic_ ++ AWK='1 { print $8, $1, $2, $10, $3 }' ++ '[' -z cysteine_to_N_cyclization ']' ++ '[' -z cyclic_ ']' ++ '[' -z '1 { print $8, $1, $2, $10, $3 }' ']' ++ cat /dev/fd/63 /nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/train/cyc-pep-6-12mer-70M_26.csv ++ awk -F, -v OFS=, '1 { print $8, $1, $2, $10, $3 }' +++ zcat /nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz ++ schemist convert -f csv --column cysteine_to_N_cyclization --to id inchikey scaffold mwt clogp tpsa --prefix cyclic_ --options prefix=SCB- +++ head -n1 ++ gzip --best +++ tr ' ' , +🚀 Converting between string representations with the following parameters: + subcommand: convert + output: <_io.TextIOWrapper name='' mode='w' encoding='utf-8'> + format: csv + input: <_io.TextIOWrapper name='' mode='r' encoding='utf-8'> + representation: SMILES + column: cysteine_to_N_cyclization + prefix: cyclic_ + to: ['id', 'inchikey', 'scaffold', 'mwt', 'clogp', 'tpsa'] + options: ['prefix=SCB-'] + func: + 0it [00:00, ?it/s] 1it [00:06, 6.96s/it] 2it [00:13, 6.82s/it] 3it [00:20, 6.88s/it] 4it [00:27, 6.89s/it] 5it [00:34, 6.88s/it] 6it 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7.13s/it] 50it [05:53, 7.08s/it] 51it [06:00, 7.04s/it] 52it [06:06, 6.88s/it] 53it [06:13, 6.84s/it] 54it [06:20, 6.90s/it] 55it [06:27, 6.91s/it] 56it [06:34, 6.91s/it] 57it [06:40, 6.87s/it] 58it [06:47, 6.85s/it] 59it [06:54, 6.83s/it] 60it [07:01, 6.91s/it] 61it [07:09, 7.05s/it] 62it [07:16, 7.18s/it] 63it [07:23, 7.12s/it] 64it [07:30, 7.10s/it] 65it [07:37, 7.08s/it] 66it [07:44, 7.05s/it] 67it [07:51, 7.01s/it] 68it [07:58, 6.98s/it] 69it [08:05, 6.91s/it] 70it [08:12, 6.97s/it] 71it [08:19, 7.01s/it] 72it [08:26, 6.97s/it] 73it [08:33, 6.94s/it] 74it [08:39, 6.91s/it] 75it [08:46, 6.89s/it] 76it [08:53, 6.88s/it] 77it [09:01, 7.05s/it] 78it [09:08, 7.25s/it] 79it [09:16, 7.33s/it] 80it [09:23, 7.32s/it] 81it [09:30, 7.32s/it] 82it [09:38, 7.25s/it] 83it [09:45, 7.20s/it] 84it [09:52, 7.12s/it] 85it [09:58, 7.00s/it] 86it [10:05, 6.82s/it] 87it [10:11, 6.80s/it] 88it [10:18, 6.80s/it] 89it [10:25, 6.75s/it] 90it [10:31, 6.72s/it] 91it [10:38, 6.73s/it] 92it [10:45, 6.70s/it] 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7.12s/it] 930it [1:52:33, 7.09s/it] 931it [1:52:40, 7.10s/it] 932it [1:52:47, 7.10s/it] 933it [1:52:54, 7.10s/it] 934it [1:53:01, 7.06s/it] 935it [1:53:08, 7.15s/it] 936it [1:53:16, 7.36s/it] 937it [1:53:24, 7.48s/it] 938it [1:53:31, 7.43s/it] 939it [1:53:38, 7.34s/it] 940it [1:53:46, 7.32s/it] 941it [1:53:53, 7.29s/it] 942it [1:54:00, 7.28s/it] 943it [1:54:07, 7.25s/it] 944it [1:54:14, 7.17s/it] 945it [1:54:21, 7.18s/it] 946it [1:54:29, 7.24s/it] 947it [1:54:36, 7.22s/it] 948it [1:54:43, 7.19s/it] 949it [1:54:50, 7.17s/it] 950it [1:54:57, 7.14s/it] 951it [1:55:05, 7.17s/it] 952it [1:55:12, 7.29s/it] 953it [1:55:20, 7.45s/it] 954it [1:55:28, 7.59s/it] 955it [1:55:35, 7.53s/it] 956it [1:55:43, 7.48s/it] 957it [1:55:50, 7.49s/it] 958it [1:55:57, 7.44s/it] 959it [1:56:05, 7.36s/it] 960it [1:56:12, 7.30s/it] 961it [1:56:19, 7.14s/it] 962it [1:56:26, 7.10s/it] 963it [1:56:33, 7.15s/it] 964it [1:56:40, 7.15s/it] 965it [1:56:47, 7.14s/it] 966it [1:56:54, 7.20s/it] 967it [1:57:02, 7.21s/it] 968it [1:57:09, 7.24s/it] 969it [1:57:17, 7.34s/it] 970it [1:57:24, 7.43s/it] 971it [1:57:32, 7.48s/it] 972it [1:57:39, 7.38s/it] 973it [1:57:46, 7.35s/it] 974it [1:57:54, 7.36s/it] 975it [1:58:01, 7.35s/it] 976it [1:58:08, 7.32s/it] 977it [1:58:15, 7.26s/it] 978it [1:58:22, 7.17s/it] 979it [1:58:30, 7.19s/it] 980it [1:58:37, 7.18s/it] 981it [1:58:44, 7.14s/it] 982it [1:58:51, 7.10s/it] 983it [1:58:58, 7.09s/it] 984it [1:59:05, 7.10s/it] 985it [1:59:12, 7.12s/it] 986it [1:59:20, 7.30s/it] 987it [1:59:28, 7.44s/it] 988it [1:59:35, 7.51s/it] 989it [1:59:43, 7.50s/it] 990it [1:59:50, 7.48s/it] 991it [1:59:57, 7.42s/it] 992it [2:00:05, 7.38s/it] 993it [2:00:12, 7.31s/it] 994it [2:00:19, 7.30s/it] 995it [2:00:26, 7.32s/it] 996it [2:00:34, 7.41s/it] 997it [2:00:42, 7.44s/it] 998it [2:00:49, 7.47s/it] 999it [2:00:57, 7.48s/it] 1000it [2:01:04, 7.52s/it] 1000it [2:01:04, 7.26s/it] +Error counts: + cyclic_id: 0 + cyclic_inchikey: 0 + cyclic_scaffold: 0 + cyclic_mwt: 0 + cyclic_clogp: 0 + cyclic_tpsa: 0 +⏰ Completed process in 2:01:21.327765 ++ rm /nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/train/cyc-pep-6-12mer-70M_26.csv diff --git a/train/cyc-pep-6-12mer-70M_27.csv.gz b/train/cyc-pep-6-12mer-70M_27.csv.gz index 9ea7750c2dc0ec7b280b08189250df1f4c0cc6c6..8eb5867545d3bea4425f82b061e5008403e0a197 100644 --- a/train/cyc-pep-6-12mer-70M_27.csv.gz +++ b/train/cyc-pep-6-12mer-70M_27.csv.gz @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:004d7cb15c0fe02958b403723a4a4922974f0d5dcc49f25f434aa7c9d5a1abaf -size 32267666 +oid sha256:39102e37ec309b48ad6f0a725e9ba4a0cb0253ec39481314654c7f5c9f2433a2 +size 75263837 diff --git a/train/cyc-pep-6-12mer-70M_27.log b/train/cyc-pep-6-12mer-70M_27.log new file mode 100644 index 0000000000000000000000000000000000000000..6c8175f031d3aef479b59d919d9f5868e9431aad --- /dev/null +++ b/train/cyc-pep-6-12mer-70M_27.log @@ -0,0 +1,337 @@ ++ module purge ++ '[' -z '' ']' ++ case "$-" in ++ __lmod_sh_dbg=x ++ '[' -n x ']' ++ set +x +Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output +Shell debugging restarted ++ unset __lmod_sh_dbg ++ return 0 ++ module load Anaconda3/2023.03 ++ '[' -z '' ']' ++ case "$-" in ++ __lmod_sh_dbg=x ++ '[' -n x ']' ++ set +x +Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output +Shell debugging restarted ++ unset __lmod_sh_dbg ++ return 0 ++ source /camp/home/johnsoe/.bashrc +++ '[' '' = yes ']' +++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' ++++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.bash hook +++ __conda_setup='export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'' + +# Copyright (C) 2012 Anaconda, Inc +# SPDX-License-Identifier: BSD-3-Clause +__conda_exe() ( + "$CONDA_EXE" $_CE_M $_CE_CONDA "$@" +) + +__conda_hashr() { + if [ -n "${ZSH_VERSION:+x}" ]; then + \rehash + elif [ -n "${POSH_VERSION:+x}" ]; then + : # pass + else + \hash -r + fi +} + +__conda_activate() { + if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then + # Handle transition from shell activated with conda <= 4.3 to a subsequent activation + # after conda updated to >= 4.4. See issue #6173. + PS1="$CONDA_PS1_BACKUP" + \unset CONDA_PS1_BACKUP + fi + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return + \eval "$ask_conda" + __conda_hashr +} + +__conda_reactivate() { + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return + \eval "$ask_conda" + __conda_hashr +} + +conda() { + \local cmd="${1-__missing__}" + case "$cmd" in + activate|deactivate) + __conda_activate "$@" + ;; + install|update|upgrade|remove|uninstall) + __conda_exe "$@" || \return + __conda_reactivate + ;; + *) + __conda_exe "$@" + ;; + esac +} + +if [ -z "${CONDA_SHLVL+x}" ]; then + \export CONDA_SHLVL=0 + # In dev-mode CONDA_EXE is python.exe and on Windows + # it is in a different relative location to condabin. + if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then + PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}" + else + PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}" + fi + \export PATH + + # We'\''re not allowing PS1 to be unbound. It must at least be set. + # However, we'\''re not exporting it, which can cause problems when starting a second shell + # via a first shell (i.e. starting zsh from bash). + if [ -z "${PS1+x}" ]; then + PS1= + fi +fi + +conda activate base' +++ '[' 0 -eq 0 ']' +++ eval 'export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'' + +# Copyright (C) 2012 Anaconda, Inc +# SPDX-License-Identifier: BSD-3-Clause +__conda_exe() ( + "$CONDA_EXE" $_CE_M $_CE_CONDA "$@" +) + +__conda_hashr() { + if [ -n "${ZSH_VERSION:+x}" ]; then + \rehash + elif [ -n "${POSH_VERSION:+x}" ]; then + : # pass + else + \hash -r + fi +} + +__conda_activate() { + if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then + # Handle transition from shell activated with conda <= 4.3 to a subsequent activation + # after conda updated to >= 4.4. See issue #6173. + PS1="$CONDA_PS1_BACKUP" + \unset CONDA_PS1_BACKUP + fi + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return + \eval "$ask_conda" + __conda_hashr +} + +__conda_reactivate() { + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return + \eval "$ask_conda" + __conda_hashr +} + +conda() { + \local cmd="${1-__missing__}" + case "$cmd" in + activate|deactivate) + __conda_activate "$@" + ;; + install|update|upgrade|remove|uninstall) + __conda_exe "$@" || \return + __conda_reactivate + ;; + *) + __conda_exe "$@" + ;; + esac +} + +if [ -z "${CONDA_SHLVL+x}" ]; then + \export CONDA_SHLVL=0 + # In dev-mode CONDA_EXE is python.exe and on Windows + # it is in a different relative location to condabin. + if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then + PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}" + else + PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}" + fi + \export PATH + + # We'\''re not allowing PS1 to be unbound. It must at least be set. + # However, we'\''re not exporting it, which can cause problems when starting a second shell + # via a first shell (i.e. starting zsh from bash). + if [ -z "${PS1+x}" ]; then + PS1= + fi +fi + +conda activate base' ++++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda ++++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda ++++ export _CE_M= ++++ _CE_M= ++++ export _CE_CONDA= ++++ _CE_CONDA= ++++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ '[' -z x ']' ++++ conda activate base ++++ local cmd=activate ++++ case "$cmd" in ++++ __conda_activate activate base ++++ '[' -n '' ']' ++++ local ask_conda +++++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++++ __conda_exe shell.posix activate base +++++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate base ++++ ask_conda='PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_SHLVL='\''6'\'' +export CONDA_DEFAULT_ENV='\''base'\'' +export CONDA_PROMPT_MODIFIER='\''(base) '\'' +export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' ++++ eval 'PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_SHLVL='\''6'\'' +export CONDA_DEFAULT_ENV='\''base'\'' +export CONDA_PROMPT_MODIFIER='\''(base) '\'' +export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' +++++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++++ export CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0 +++++ CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0 +++++ export CONDA_SHLVL=6 +++++ CONDA_SHLVL=6 +++++ export CONDA_DEFAULT_ENV=base +++++ CONDA_DEFAULT_ENV=base +++++ export 'CONDA_PROMPT_MODIFIER=(base) ' +++++ CONDA_PROMPT_MODIFIER='(base) ' +++++ export CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev +++++ CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev +++++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++++ export _CE_M= +++++ _CE_M= +++++ export _CE_CONDA= +++++ _CE_CONDA= +++++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python +++++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ __conda_hashr ++++ '[' -n '' ']' ++++ '[' -n '' ']' ++++ hash -r +++ unset __conda_setup ++ conda activate schemist-dev ++ local cmd=activate ++ case "$cmd" in ++ __conda_activate activate schemist-dev ++ '[' -n '' ']' ++ local ask_conda +++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++ __conda_exe shell.posix activate schemist-dev +++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate schemist-dev ++ ask_conda='PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_SHLVL='\''7'\'' +export CONDA_DEFAULT_ENV='\''schemist-dev'\'' +export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\'' +export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' ++ eval 'PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_SHLVL='\''7'\'' +export CONDA_DEFAULT_ENV='\''schemist-dev'\'' +export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\'' +export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' +++ PS1='(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++ export CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev +++ CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev +++ export CONDA_SHLVL=7 +++ CONDA_SHLVL=7 +++ export CONDA_DEFAULT_ENV=schemist-dev +++ CONDA_DEFAULT_ENV=schemist-dev +++ export 'CONDA_PROMPT_MODIFIER=(schemist-dev) ' +++ CONDA_PROMPT_MODIFIER='(schemist-dev) ' +++ export CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0 +++ CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0 +++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++ export _CE_M= +++ _CE_M= +++ export _CE_CONDA= +++ _CE_CONDA= +++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python +++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++ __conda_hashr ++ '[' -n '' ']' ++ '[' -n '' ']' ++ hash -r ++ CHUNK_HEAD_FILE=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz ++ INPUT=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/train/cyc-pep-6-12mer-70M_27.csv ++ COLUMN=cysteine_to_N_cyclization ++ PREFIX=cyclic_ ++ AWK='1 { print $8, $1, $2, $10, $3 }' ++ '[' -z cysteine_to_N_cyclization ']' ++ '[' -z cyclic_ ']' ++ '[' -z '1 { print $8, $1, $2, $10, $3 }' ']' ++ cat /dev/fd/63 /nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/train/cyc-pep-6-12mer-70M_27.csv ++ awk -F, -v OFS=, '1 { print $8, $1, $2, $10, $3 }' +++ zcat /nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz +++ head -n1 ++ gzip --best ++ schemist convert -f csv --column cysteine_to_N_cyclization --to id inchikey scaffold mwt clogp tpsa --prefix cyclic_ --options prefix=SCB- +++ tr ' ' , +🚀 Converting between string representations with the following parameters: + subcommand: convert + output: <_io.TextIOWrapper name='' mode='w' encoding='utf-8'> + format: csv + input: <_io.TextIOWrapper name='' mode='r' encoding='utf-8'> + representation: SMILES + column: cysteine_to_N_cyclization + prefix: cyclic_ + to: ['id', 'inchikey', 'scaffold', 'mwt', 'clogp', 'tpsa'] + options: ['prefix=SCB-'] + func: + 0it [00:00, ?it/s] 1it [00:07, 7.18s/it] 2it [00:14, 7.27s/it] 3it [00:22, 7.53s/it] 4it [00:30, 7.70s/it] 5it [00:38, 7.75s/it] 6it 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[2:05:36, 8.16s/it] 967it [2:05:44, 8.08s/it] 968it [2:05:52, 8.10s/it] 969it [2:06:00, 8.03s/it] 970it [2:06:08, 7.99s/it] 971it [2:06:16, 7.96s/it] 972it [2:06:23, 7.71s/it] 973it [2:06:30, 7.53s/it] 974it [2:06:38, 7.48s/it] 975it [2:06:45, 7.49s/it] 976it [2:06:53, 7.46s/it] 977it [2:07:00, 7.37s/it] 978it [2:07:07, 7.33s/it] 979it [2:07:14, 7.22s/it] 980it [2:07:21, 7.25s/it] 981it [2:07:29, 7.40s/it] 982it [2:07:37, 7.62s/it] 983it [2:07:45, 7.68s/it] 984it [2:07:52, 7.60s/it] 985it [2:08:00, 7.61s/it] 986it [2:08:07, 7.54s/it] 987it [2:08:15, 7.50s/it] 988it [2:08:22, 7.47s/it] 989it [2:08:29, 7.34s/it] 990it [2:08:36, 7.26s/it] 991it [2:08:44, 7.29s/it] 992it [2:08:51, 7.30s/it] 993it [2:08:59, 7.36s/it] 994it [2:09:06, 7.36s/it] 995it [2:09:13, 7.39s/it] 996it [2:09:20, 7.31s/it] 997it [2:09:28, 7.39s/it] 998it [2:09:36, 7.54s/it] 999it [2:09:44, 7.69s/it] 1000it [2:09:52, 7.70s/it] 1000it [2:09:52, 7.79s/it] +Error counts: + cyclic_id: 0 + cyclic_inchikey: 0 + cyclic_scaffold: 0 + cyclic_mwt: 0 + cyclic_clogp: 0 + cyclic_tpsa: 0 +⏰ Completed process in 2:10:09.854464 ++ rm /nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/train/cyc-pep-6-12mer-70M_27.csv diff --git a/train/cyc-pep-6-12mer-70M_28.csv.gz b/train/cyc-pep-6-12mer-70M_28.csv.gz index c33e838dfd327c03b76f8f95ed3b257ed2fd926f..ae8b97eb6466b27d11461e2edc66f819f457b1af 100644 --- a/train/cyc-pep-6-12mer-70M_28.csv.gz +++ b/train/cyc-pep-6-12mer-70M_28.csv.gz @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:f33a27a93eb9b8130029f256f1be16350dcf7cebc096ccadf9383bc2672352a1 -size 32213881 +oid sha256:f9a278d071d1e25a8daf17092a085cb8575f45b1228a8fff5aca397fc4357caf +size 75773269 diff --git a/train/cyc-pep-6-12mer-70M_28.log b/train/cyc-pep-6-12mer-70M_28.log new file mode 100644 index 0000000000000000000000000000000000000000..d08cd7a8acbc57780eef175e5acea0e13891f1fe --- /dev/null +++ b/train/cyc-pep-6-12mer-70M_28.log @@ -0,0 +1,337 @@ ++ module purge ++ '[' -z '' ']' ++ case "$-" in ++ __lmod_sh_dbg=x ++ '[' -n x ']' ++ set +x +Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output +Shell debugging restarted ++ unset __lmod_sh_dbg ++ return 0 ++ module load Anaconda3/2023.03 ++ '[' -z '' ']' ++ case "$-" in ++ __lmod_sh_dbg=x ++ '[' -n x ']' ++ set +x +Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output +Shell debugging restarted ++ unset __lmod_sh_dbg ++ return 0 ++ source /camp/home/johnsoe/.bashrc +++ '[' '' = yes ']' +++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' ++++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.bash hook +++ __conda_setup='export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'' + +# Copyright (C) 2012 Anaconda, Inc +# SPDX-License-Identifier: BSD-3-Clause +__conda_exe() ( + "$CONDA_EXE" $_CE_M $_CE_CONDA "$@" +) + +__conda_hashr() { + if [ -n "${ZSH_VERSION:+x}" ]; then + \rehash + elif [ -n "${POSH_VERSION:+x}" ]; then + : # pass + else + \hash -r + fi +} + +__conda_activate() { + if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then + # Handle transition from shell activated with conda <= 4.3 to a subsequent activation + # after conda updated to >= 4.4. See issue #6173. + PS1="$CONDA_PS1_BACKUP" + \unset CONDA_PS1_BACKUP + fi + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return + \eval "$ask_conda" + __conda_hashr +} + +__conda_reactivate() { + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return + \eval "$ask_conda" + __conda_hashr +} + +conda() { + \local cmd="${1-__missing__}" + case "$cmd" in + activate|deactivate) + __conda_activate "$@" + ;; + install|update|upgrade|remove|uninstall) + __conda_exe "$@" || \return + __conda_reactivate + ;; + *) + __conda_exe "$@" + ;; + esac +} + +if [ -z "${CONDA_SHLVL+x}" ]; then + \export CONDA_SHLVL=0 + # In dev-mode CONDA_EXE is python.exe and on Windows + # it is in a different relative location to condabin. + if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then + PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}" + else + PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}" + fi + \export PATH + + # We'\''re not allowing PS1 to be unbound. It must at least be set. + # However, we'\''re not exporting it, which can cause problems when starting a second shell + # via a first shell (i.e. starting zsh from bash). + if [ -z "${PS1+x}" ]; then + PS1= + fi +fi + +conda activate base' +++ '[' 0 -eq 0 ']' +++ eval 'export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'' + +# Copyright (C) 2012 Anaconda, Inc +# SPDX-License-Identifier: BSD-3-Clause +__conda_exe() ( + "$CONDA_EXE" $_CE_M $_CE_CONDA "$@" +) + +__conda_hashr() { + if [ -n "${ZSH_VERSION:+x}" ]; then + \rehash + elif [ -n "${POSH_VERSION:+x}" ]; then + : # pass + else + \hash -r + fi +} + +__conda_activate() { + if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then + # Handle transition from shell activated with conda <= 4.3 to a subsequent activation + # after conda updated to >= 4.4. See issue #6173. + PS1="$CONDA_PS1_BACKUP" + \unset CONDA_PS1_BACKUP + fi + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return + \eval "$ask_conda" + __conda_hashr +} + +__conda_reactivate() { + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return + \eval "$ask_conda" + __conda_hashr +} + +conda() { + \local cmd="${1-__missing__}" + case "$cmd" in + activate|deactivate) + __conda_activate "$@" + ;; + install|update|upgrade|remove|uninstall) + __conda_exe "$@" || \return + __conda_reactivate + ;; + *) + __conda_exe "$@" + ;; + esac +} + +if [ -z "${CONDA_SHLVL+x}" ]; then + \export CONDA_SHLVL=0 + # In dev-mode CONDA_EXE is python.exe and on Windows + # it is in a different relative location to condabin. + if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then + PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}" + else + PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}" + fi + \export PATH + + # We'\''re not allowing PS1 to be unbound. It must at least be set. + # However, we'\''re not exporting it, which can cause problems when starting a second shell + # via a first shell (i.e. starting zsh from bash). + if [ -z "${PS1+x}" ]; then + PS1= + fi +fi + +conda activate base' ++++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda ++++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda ++++ export _CE_M= ++++ _CE_M= ++++ export _CE_CONDA= ++++ _CE_CONDA= ++++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ '[' -z x ']' ++++ conda activate base ++++ local cmd=activate ++++ case "$cmd" in ++++ __conda_activate activate base ++++ '[' -n '' ']' ++++ local ask_conda +++++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++++ __conda_exe shell.posix activate base +++++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate base ++++ ask_conda='PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_SHLVL='\''6'\'' +export CONDA_DEFAULT_ENV='\''base'\'' +export CONDA_PROMPT_MODIFIER='\''(base) '\'' +export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' ++++ eval 'PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_SHLVL='\''6'\'' +export CONDA_DEFAULT_ENV='\''base'\'' +export CONDA_PROMPT_MODIFIER='\''(base) '\'' +export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' +++++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++++ export CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0 +++++ CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0 +++++ export CONDA_SHLVL=6 +++++ CONDA_SHLVL=6 +++++ export CONDA_DEFAULT_ENV=base +++++ CONDA_DEFAULT_ENV=base +++++ export 'CONDA_PROMPT_MODIFIER=(base) ' +++++ CONDA_PROMPT_MODIFIER='(base) ' +++++ export CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev +++++ CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev +++++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++++ export _CE_M= +++++ _CE_M= +++++ export _CE_CONDA= +++++ _CE_CONDA= +++++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python +++++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ __conda_hashr ++++ '[' -n '' ']' ++++ '[' -n '' ']' ++++ hash -r +++ unset __conda_setup ++ conda activate schemist-dev ++ local cmd=activate ++ case "$cmd" in ++ __conda_activate activate schemist-dev ++ '[' -n '' ']' ++ local ask_conda +++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++ __conda_exe shell.posix activate schemist-dev +++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate schemist-dev ++ ask_conda='PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_SHLVL='\''7'\'' +export CONDA_DEFAULT_ENV='\''schemist-dev'\'' +export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\'' +export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' ++ eval 'PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_SHLVL='\''7'\'' +export CONDA_DEFAULT_ENV='\''schemist-dev'\'' +export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\'' +export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' +++ PS1='(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++ export CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev +++ CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev +++ export CONDA_SHLVL=7 +++ CONDA_SHLVL=7 +++ export CONDA_DEFAULT_ENV=schemist-dev +++ CONDA_DEFAULT_ENV=schemist-dev +++ export 'CONDA_PROMPT_MODIFIER=(schemist-dev) ' +++ CONDA_PROMPT_MODIFIER='(schemist-dev) ' +++ export CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0 +++ CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0 +++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++ export _CE_M= +++ _CE_M= +++ export _CE_CONDA= +++ _CE_CONDA= +++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python +++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++ __conda_hashr ++ '[' -n '' ']' ++ '[' -n '' ']' ++ hash -r ++ CHUNK_HEAD_FILE=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz ++ INPUT=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/train/cyc-pep-6-12mer-70M_28.csv ++ COLUMN=cysteine_to_N_cyclization ++ PREFIX=cyclic_ ++ AWK='1 { print $8, $1, $2, $10, $3 }' ++ '[' -z cysteine_to_N_cyclization ']' ++ '[' -z cyclic_ ']' ++ '[' -z '1 { print $8, $1, $2, $10, $3 }' ']' ++ cat /dev/fd/63 /nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/train/cyc-pep-6-12mer-70M_28.csv ++ schemist convert -f csv --column cysteine_to_N_cyclization --to id inchikey scaffold mwt clogp tpsa --prefix cyclic_ --options prefix=SCB- ++ gzip --best ++ awk -F, -v OFS=, '1 { print $8, $1, $2, $10, $3 }' +++ zcat /nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz +++ tr ' ' , +++ head -n1 +🚀 Converting between string representations with the following parameters: + subcommand: convert + output: <_io.TextIOWrapper name='' mode='w' encoding='utf-8'> + format: csv + input: <_io.TextIOWrapper name='' mode='r' encoding='utf-8'> + representation: SMILES + column: cysteine_to_N_cyclization + prefix: cyclic_ + to: ['id', 'inchikey', 'scaffold', 'mwt', 'clogp', 'tpsa'] + options: ['prefix=SCB-'] + func: + 0it [00:00, ?it/s] 1it [00:07, 7.53s/it] 2it [00:15, 7.59s/it] 3it [00:22, 7.51s/it] 4it [00:30, 7.48s/it] 5it [00:37, 7.50s/it] 6it [00:44, 7.47s/it] 7it [00:52, 7.46s/it] 8it [01:00, 7.55s/it] 9it [01:07, 7.59s/it] 10it [01:15, 7.62s/it] 11it [01:23, 7.60s/it] 12it [01:30, 7.60s/it] 13it [01:38, 7.55s/it] 14it [01:46, 7.66s/it] 15it [01:54, 7.86s/it] 16it [02:02, 8.02s/it] 17it [02:10, 8.01s/it] 18it [02:18, 7.96s/it] 19it [02:26, 7.94s/it] 20it [02:34, 7.90s/it] 21it [02:42, 7.86s/it] 22it [02:49, 7.82s/it] 23it [02:56, 7.65s/it] 24it [03:04, 7.59s/it] 25it [03:12, 7.62s/it] 26it [03:19, 7.62s/it] 27it [03:27, 7.59s/it] 28it [03:34, 7.54s/it] 29it [03:42, 7.52s/it] 30it [03:49, 7.48s/it] 31it [03:57, 7.64s/it] 32it [04:05, 7.79s/it] 33it [04:14, 7.95s/it] 34it [04:21, 7.92s/it] 35it [04:29, 7.86s/it] 36it [04:37, 7.86s/it] 37it [04:45, 7.82s/it] 38it [04:52, 7.76s/it] 39it [05:00, 7.69s/it] 40it [05:07, 7.57s/it] 41it [05:15, 7.57s/it] 42it [05:22, 7.59s/it] 43it [05:30, 7.59s/it] 44it [05:37, 7.55s/it] 45it [05:45, 7.53s/it] 46it [05:52, 7.53s/it] 47it [06:00, 7.53s/it] 48it [06:08, 7.68s/it] 49it [06:16, 7.83s/it] 50it [06:24, 7.95s/it] 51it [06:32, 7.89s/it] 52it [06:40, 7.90s/it] 53it [06:48, 7.85s/it] 54it [06:55, 7.80s/it] 55it [07:03, 7.75s/it] 56it [07:11, 7.66s/it] 57it [07:18, 7.55s/it] 58it [07:25, 7.54s/it] 59it [07:33, 7.54s/it] 60it [07:40, 7.52s/it] 61it [07:48, 7.49s/it] 62it [07:55, 7.46s/it] 63it [08:03, 7.43s/it] 64it [08:10, 7.45s/it] 65it [08:18, 7.61s/it] 66it [08:26, 7.77s/it] 67it [08:34, 7.92s/it] 68it [08:42, 7.87s/it] 69it [08:50, 7.89s/it] 70it [08:58, 7.85s/it] 71it [09:06, 7.82s/it] 72it [09:13, 7.75s/it] 73it [09:21, 7.68s/it] 74it [09:28, 7.57s/it] 75it [09:36, 7.56s/it] 76it [09:43, 7.56s/it] 77it [09:51, 7.53s/it] 78it [09:58, 7.47s/it] 79it [10:05, 7.48s/it] 80it [10:13, 7.43s/it] 81it [10:20, 7.45s/it] 82it [10:28, 7.59s/it] 83it [10:36, 7.74s/it] 84it [10:44, 7.83s/it] 85it [10:52, 7.79s/it] 86it [11:00, 7.79s/it] 87it [11:07, 7.73s/it] 88it [11:15, 7.69s/it] 89it [11:22, 7.62s/it] 90it [11:30, 7.58s/it] 91it [11:37, 7.53s/it] 92it [11:45, 7.57s/it] 93it [11:53, 7.59s/it] 94it [12:00, 7.59s/it] 95it [12:08, 7.60s/it] 96it [12:16, 7.62s/it] 97it [12:23, 7.55s/it] 98it [12:31, 7.61s/it] 99it [12:39, 7.78s/it] 100it [12:47, 7.96s/it] 101it [12:55, 8.03s/it] 102it [13:03, 7.97s/it] 103it [13:11, 7.94s/it] 104it [13:19, 7.87s/it] 105it [13:27, 7.85s/it] 106it [13:34, 7.83s/it] 107it [13:42, 7.61s/it] 108it [13:49, 7.44s/it] 109it [13:56, 7.39s/it] 110it [14:03, 7.36s/it] 111it [14:10, 7.32s/it] 112it [14:18, 7.29s/it] 113it [14:25, 7.27s/it] 114it [14:32, 7.22s/it] 115it [14:39, 7.27s/it] 116it [14:47, 7.42s/it] 117it [14:55, 7.61s/it] 118it [15:03, 7.63s/it] 119it [15:10, 7.55s/it] 120it [15:18, 7.54s/it] 121it [15:25, 7.48s/it] 122it [15:32, 7.46s/it] 123it [15:40, 7.43s/it] 124it [15:47, 7.38s/it] 125it [15:54, 7.39s/it] 126it [16:02, 7.45s/it] 127it [16:10, 7.51s/it] 128it [16:17, 7.55s/it] 129it [16:25, 7.52s/it] 130it [16:32, 7.54s/it] 131it [16:40, 7.49s/it] 132it [16:48, 7.60s/it] 133it [16:56, 7.79s/it] 134it [17:04, 7.94s/it] 135it [17:12, 7.93s/it] 136it [17:20, 7.85s/it] 137it [17:28, 7.84s/it] 138it [17:35, 7.81s/it] 139it [17:43, 7.76s/it] 140it [17:51, 7.74s/it] 141it [17:58, 7.75s/it] 142it [18:06, 7.85s/it] 143it [18:15, 7.95s/it] 144it [18:23, 8.02s/it] 145it [18:31, 8.01s/it] 146it [18:39, 8.01s/it] 147it [18:47, 7.99s/it] 148it [18:55, 8.01s/it] 149it [19:03, 8.16s/it] 150it [19:12, 8.32s/it] 151it [19:21, 8.46s/it] 152it [19:29, 8.43s/it] 153it [19:38, 8.40s/it] 154it [19:46, 8.38s/it] 155it [19:54, 8.34s/it] 156it [20:02, 8.27s/it] 157it [20:10, 8.23s/it] 158it [20:18, 8.13s/it] 159it [20:27, 8.17s/it] 160it [20:35, 8.19s/it] 161it [20:43, 8.18s/it] 162it [20:51, 8.15s/it] 163it [20:59, 8.14s/it] 164it [21:07, 8.13s/it] 165it [21:15, 8.12s/it] 166it [21:24, 8.30s/it] 167it [21:33, 8.47s/it] 168it [21:42, 8.58s/it] 169it [21:50, 8.52s/it] 170it [21:59, 8.53s/it] 171it [22:07, 8.45s/it] 172it [22:15, 8.41s/it] 173it [22:23, 8.36s/it] 174it [22:32, 8.31s/it] 175it [22:40, 8.26s/it] 176it [22:48, 8.30s/it] 177it [22:57, 8.33s/it] 178it [23:05, 8.33s/it] 179it [23:13, 8.31s/it] 180it [23:22, 8.33s/it] 181it [23:30, 8.28s/it] 182it [23:38, 8.28s/it] 183it [23:47, 8.47s/it] 184it [23:56, 8.63s/it] 185it [24:05, 8.72s/it] 186it [24:14, 8.69s/it] 187it [24:22, 8.69s/it] 188it [24:31, 8.60s/it] 189it [24:39, 8.55s/it] 190it [24:47, 8.53s/it] 191it [24:55, 8.35s/it] 192it [25:03, 8.16s/it] 193it [25:11, 8.10s/it] 194it [25:19, 8.05s/it] 195it [25:27, 8.01s/it] 196it [25:35, 7.97s/it] 197it [25:43, 7.96s/it] 198it [25:50, 7.85s/it] 199it [25:59, 7.93s/it] 200it [26:07, 8.08s/it] 201it [26:16, 8.27s/it] 202it [26:24, 8.30s/it] 203it [26:32, 8.24s/it] 204it [26:40, 8.24s/it] 205it [26:48, 8.17s/it] 206it [26:56, 8.11s/it] 207it [27:04, 8.08s/it] 208it [27:12, 7.94s/it] 209it [27:19, 7.79s/it] 210it [27:27, 7.78s/it] 211it [27:35, 7.74s/it] 212it [27:42, 7.71s/it] 213it [27:50, 7.70s/it] 214it [27:58, 7.67s/it] 215it [28:05, 7.59s/it] 216it [28:13, 7.65s/it] 217it [28:21, 7.80s/it] 218it [28:30, 8.00s/it] 219it [28:38, 8.04s/it] 220it [28:45, 7.95s/it] 221it [28:53, 7.95s/it] 222it [29:01, 7.88s/it] 223it [29:09, 7.85s/it] 224it [29:17, 7.86s/it] 225it [29:24, 7.79s/it] 226it [29:32, 7.77s/it] 227it [29:40, 7.84s/it] 228it [29:48, 7.87s/it] 229it [29:56, 7.88s/it] 230it [30:04, 7.88s/it] 231it [30:12, 7.90s/it] 232it [30:19, 7.82s/it] 233it [30:28, 7.91s/it] 234it [30:36, 8.09s/it] 235it [30:45, 8.28s/it] 236it [30:53, 8.30s/it] 237it [31:01, 8.23s/it] 238it [31:09, 8.21s/it] 239it [31:17, 8.18s/it] 240it [31:26, 8.14s/it] 241it [31:34, 8.11s/it] 242it [31:41, 7.91s/it] 243it [31:48, 7.78s/it] 244it [31:56, 7.78s/it] 245it [32:04, 7.77s/it] 246it [32:12, 7.73s/it] 247it [32:19, 7.67s/it] 248it [32:27, 7.65s/it] 249it [32:34, 7.61s/it] 250it [32:42, 7.74s/it] 251it [32:51, 7.91s/it] 252it [32:59, 8.06s/it] 253it [33:07, 8.01s/it] 254it [33:15, 7.95s/it] 255it [33:23, 7.94s/it] 256it [33:31, 7.92s/it] 257it [33:38, 7.86s/it] 258it [33:46, 7.81s/it] 259it [33:53, 7.70s/it] 260it [34:01, 7.71s/it] 261it [34:09, 7.74s/it] 262it [34:17, 7.74s/it] 263it [34:24, 7.73s/it] 264it [34:32, 7.70s/it] 265it [34:40, 7.68s/it] 266it [34:47, 7.67s/it] 267it [34:55, 7.81s/it] 268it [35:04, 7.98s/it] 269it [35:12, 8.12s/it] 270it [35:20, 8.10s/it] 271it [35:28, 8.06s/it] 272it [35:36, 8.03s/it] 273it [35:44, 7.99s/it] 274it [35:52, 7.93s/it] 275it [36:00, 7.84s/it] 276it [36:07, 7.71s/it] 277it [36:15, 7.70s/it] 278it [36:22, 7.69s/it] 279it [36:30, 7.67s/it] 280it [36:37, 7.63s/it] 281it [36:45, 7.64s/it] 282it [36:53, 7.59s/it] 283it [37:00, 7.60s/it] 284it [37:08, 7.77s/it] 285it [37:17, 7.92s/it] 286it [37:25, 8.03s/it] 287it [37:33, 7.97s/it] 288it [37:41, 7.97s/it] 289it [37:48, 7.90s/it] 290it [37:56, 7.86s/it] 291it [38:04, 7.82s/it] 292it [38:12, 7.74s/it] 293it [38:19, 7.68s/it] 294it [38:27, 7.72s/it] 295it [38:35, 7.72s/it] 296it [38:42, 7.71s/it] 297it [38:50, 7.66s/it] 298it [38:58, 7.69s/it] 299it [39:05, 7.63s/it] 300it [39:13, 7.64s/it] 301it [39:21, 7.82s/it] 302it [39:29, 7.99s/it] 303it [39:38, 8.07s/it] 304it [39:45, 8.01s/it] 305it [39:54, 8.02s/it] 306it [40:01, 7.94s/it] 307it [40:09, 7.91s/it] 308it [40:17, 7.90s/it] 309it [40:24, 7.71s/it] 310it [40:31, 7.51s/it] 311it [40:39, 7.46s/it] 312it [40:46, 7.41s/it] 313it [40:53, 7.36s/it] 314it [41:00, 7.30s/it] 315it [41:08, 7.27s/it] 316it [41:14, 7.17s/it] 317it [41:22, 7.24s/it] 318it [41:30, 7.39s/it] 319it [41:38, 7.57s/it] 320it [41:45, 7.60s/it] 321it [41:53, 7.52s/it] 322it [42:00, 7.52s/it] 323it [42:07, 7.44s/it] 324it [42:15, 7.43s/it] 325it [42:22, 7.38s/it] 326it [42:29, 7.27s/it] 327it [42:36, 7.24s/it] 328it [42:44, 7.30s/it] 329it [42:51, 7.32s/it] 330it [42:58, 7.33s/it] 331it [43:06, 7.29s/it] 332it [43:13, 7.29s/it] 333it [43:20, 7.23s/it] 334it [43:27, 7.30s/it] 335it [43:35, 7.49s/it] 336it [43:43, 7.64s/it] 337it [43:51, 7.68s/it] 338it [43:59, 7.61s/it] 339it [44:06, 7.59s/it] 340it [44:14, 7.54s/it] 341it [44:21, 7.52s/it] 342it [44:28, 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[2:05:15, 7.71s/it] 966it [2:05:22, 7.64s/it] 967it [2:05:30, 7.57s/it] 968it [2:05:38, 7.61s/it] 969it [2:05:45, 7.63s/it] 970it [2:05:53, 7.60s/it] 971it [2:06:00, 7.60s/it] 972it [2:06:08, 7.60s/it] 973it [2:06:15, 7.52s/it] 974it [2:06:23, 7.59s/it] 975it [2:06:31, 7.75s/it] 976it [2:06:40, 7.95s/it] 977it [2:06:48, 7.97s/it] 978it [2:06:55, 7.89s/it] 979it [2:07:03, 7.90s/it] 980it [2:07:11, 7.82s/it] 981it [2:07:19, 7.82s/it] 982it [2:07:26, 7.78s/it] 983it [2:07:33, 7.53s/it] 984it [2:07:40, 7.36s/it] 985it [2:07:47, 7.31s/it] 986it [2:07:55, 7.30s/it] 987it [2:08:02, 7.24s/it] 988it [2:08:09, 7.16s/it] 989it [2:08:16, 7.12s/it] 990it [2:08:23, 7.07s/it] 991it [2:08:30, 7.18s/it] 992it [2:08:38, 7.33s/it] 993it [2:08:46, 7.48s/it] 994it [2:08:53, 7.44s/it] 995it [2:09:00, 7.40s/it] 996it [2:09:08, 7.39s/it] 997it [2:09:15, 7.36s/it] 998it [2:09:22, 7.30s/it] 999it [2:09:29, 7.25s/it] 1000it [2:09:36, 7.16s/it] 1000it [2:09:36, 7.78s/it] +Error counts: + cyclic_id: 0 + cyclic_inchikey: 0 + cyclic_scaffold: 0 + cyclic_mwt: 0 + cyclic_clogp: 0 + cyclic_tpsa: 0 +⏰ Completed process in 2:09:55.794212 ++ rm /nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/train/cyc-pep-6-12mer-70M_28.csv diff --git a/train/cyc-pep-6-12mer-70M_29.csv.gz b/train/cyc-pep-6-12mer-70M_29.csv.gz index 63611e868813b791fcb48b4edacfc2017593adde..02700efeb1038e8143e2b4cee0817ec032af0cf1 100644 --- a/train/cyc-pep-6-12mer-70M_29.csv.gz +++ b/train/cyc-pep-6-12mer-70M_29.csv.gz @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:7758bb45346e0a1b04bba122b1e8090f0878c4abe8c601c73c48cdfc80a4bd7a -size 31550559 +oid sha256:3b88e39cdb5f661e135eefe7c43f5e48701e7d7bb05d59543771a2dd58032016 +size 73866063 diff --git a/train/cyc-pep-6-12mer-70M_29.log b/train/cyc-pep-6-12mer-70M_29.log new file mode 100644 index 0000000000000000000000000000000000000000..2d8178bfab49164241af73643c162850ac9d7a60 --- /dev/null +++ b/train/cyc-pep-6-12mer-70M_29.log @@ -0,0 +1,337 @@ ++ module purge ++ '[' -z '' ']' ++ case "$-" in ++ __lmod_sh_dbg=x ++ '[' -n x ']' ++ set +x +Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output +Shell debugging restarted ++ unset __lmod_sh_dbg ++ return 0 ++ module load Anaconda3/2023.03 ++ '[' -z '' ']' ++ case "$-" in ++ __lmod_sh_dbg=x ++ '[' -n x ']' ++ set +x +Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output +Shell debugging restarted ++ unset __lmod_sh_dbg ++ return 0 ++ source /camp/home/johnsoe/.bashrc +++ '[' '' = yes ']' +++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' ++++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.bash hook +++ __conda_setup='export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'' + +# Copyright (C) 2012 Anaconda, Inc +# SPDX-License-Identifier: BSD-3-Clause +__conda_exe() ( + "$CONDA_EXE" $_CE_M $_CE_CONDA "$@" +) + +__conda_hashr() { + if [ -n "${ZSH_VERSION:+x}" ]; then + \rehash + elif [ -n "${POSH_VERSION:+x}" ]; then + : # pass + else + \hash -r + fi +} + +__conda_activate() { + if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then + # Handle transition from shell activated with conda <= 4.3 to a subsequent activation + # after conda updated to >= 4.4. See issue #6173. + PS1="$CONDA_PS1_BACKUP" + \unset CONDA_PS1_BACKUP + fi + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return + \eval "$ask_conda" + __conda_hashr +} + +__conda_reactivate() { + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return + \eval "$ask_conda" + __conda_hashr +} + +conda() { + \local cmd="${1-__missing__}" + case "$cmd" in + activate|deactivate) + __conda_activate "$@" + ;; + install|update|upgrade|remove|uninstall) + __conda_exe "$@" || \return + __conda_reactivate + ;; + *) + __conda_exe "$@" + ;; + esac +} + +if [ -z "${CONDA_SHLVL+x}" ]; then + \export CONDA_SHLVL=0 + # In dev-mode CONDA_EXE is python.exe and on Windows + # it is in a different relative location to condabin. + if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then + PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}" + else + PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}" + fi + \export PATH + + # We'\''re not allowing PS1 to be unbound. It must at least be set. + # However, we'\''re not exporting it, which can cause problems when starting a second shell + # via a first shell (i.e. starting zsh from bash). + if [ -z "${PS1+x}" ]; then + PS1= + fi +fi + +conda activate base' +++ '[' 0 -eq 0 ']' +++ eval 'export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'' + +# Copyright (C) 2012 Anaconda, Inc +# SPDX-License-Identifier: BSD-3-Clause +__conda_exe() ( + "$CONDA_EXE" $_CE_M $_CE_CONDA "$@" +) + +__conda_hashr() { + if [ -n "${ZSH_VERSION:+x}" ]; then + \rehash + elif [ -n "${POSH_VERSION:+x}" ]; then + : # pass + else + \hash -r + fi +} + +__conda_activate() { + if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then + # Handle transition from shell activated with conda <= 4.3 to a subsequent activation + # after conda updated to >= 4.4. See issue #6173. + PS1="$CONDA_PS1_BACKUP" + \unset CONDA_PS1_BACKUP + fi + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return + \eval "$ask_conda" + __conda_hashr +} + +__conda_reactivate() { + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return + \eval "$ask_conda" + __conda_hashr +} + +conda() { + \local cmd="${1-__missing__}" + case "$cmd" in + activate|deactivate) + __conda_activate "$@" + ;; + install|update|upgrade|remove|uninstall) + __conda_exe "$@" || \return + __conda_reactivate + ;; + *) + __conda_exe "$@" + ;; + esac +} + +if [ -z "${CONDA_SHLVL+x}" ]; then + \export CONDA_SHLVL=0 + # In dev-mode CONDA_EXE is python.exe and on Windows + # it is in a different relative location to condabin. + if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then + PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}" + else + PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}" + fi + \export PATH + + # We'\''re not allowing PS1 to be unbound. It must at least be set. + # However, we'\''re not exporting it, which can cause problems when starting a second shell + # via a first shell (i.e. starting zsh from bash). + if [ -z "${PS1+x}" ]; then + PS1= + fi +fi + +conda activate base' ++++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda ++++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda ++++ export _CE_M= ++++ _CE_M= ++++ export _CE_CONDA= ++++ _CE_CONDA= ++++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ '[' -z x ']' ++++ conda activate base ++++ local cmd=activate ++++ case "$cmd" in ++++ __conda_activate activate base ++++ '[' -n '' ']' ++++ local ask_conda +++++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++++ __conda_exe shell.posix activate base +++++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate base ++++ ask_conda='PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_SHLVL='\''6'\'' +export CONDA_DEFAULT_ENV='\''base'\'' +export CONDA_PROMPT_MODIFIER='\''(base) '\'' +export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' ++++ eval 'PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_SHLVL='\''6'\'' +export CONDA_DEFAULT_ENV='\''base'\'' +export CONDA_PROMPT_MODIFIER='\''(base) '\'' +export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' +++++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++++ export CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0 +++++ CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0 +++++ export CONDA_SHLVL=6 +++++ CONDA_SHLVL=6 +++++ export CONDA_DEFAULT_ENV=base +++++ CONDA_DEFAULT_ENV=base +++++ export 'CONDA_PROMPT_MODIFIER=(base) ' +++++ CONDA_PROMPT_MODIFIER='(base) ' +++++ export CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev +++++ CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev +++++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++++ export _CE_M= +++++ _CE_M= +++++ export _CE_CONDA= +++++ _CE_CONDA= +++++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python +++++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ __conda_hashr ++++ '[' -n '' ']' ++++ '[' -n '' ']' ++++ hash -r +++ unset __conda_setup ++ conda activate schemist-dev ++ local cmd=activate ++ case "$cmd" in ++ __conda_activate activate schemist-dev ++ '[' -n '' ']' ++ local ask_conda +++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++ __conda_exe shell.posix activate schemist-dev +++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate schemist-dev ++ ask_conda='PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_SHLVL='\''7'\'' +export CONDA_DEFAULT_ENV='\''schemist-dev'\'' +export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\'' +export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' ++ eval 'PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_SHLVL='\''7'\'' +export CONDA_DEFAULT_ENV='\''schemist-dev'\'' +export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\'' +export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' +++ PS1='(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++ export CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev +++ CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev +++ export CONDA_SHLVL=7 +++ CONDA_SHLVL=7 +++ export CONDA_DEFAULT_ENV=schemist-dev +++ CONDA_DEFAULT_ENV=schemist-dev +++ export 'CONDA_PROMPT_MODIFIER=(schemist-dev) ' +++ CONDA_PROMPT_MODIFIER='(schemist-dev) ' +++ export CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0 +++ CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0 +++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++ export _CE_M= +++ _CE_M= +++ export _CE_CONDA= +++ _CE_CONDA= +++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python +++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++ __conda_hashr ++ '[' -n '' ']' ++ '[' -n '' ']' ++ hash -r ++ CHUNK_HEAD_FILE=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz ++ INPUT=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/train/cyc-pep-6-12mer-70M_29.csv ++ COLUMN=cysteine_to_N_cyclization ++ PREFIX=cyclic_ ++ AWK='1 { print $8, $1, $2, $10, $3 }' ++ '[' -z cysteine_to_N_cyclization ']' ++ '[' -z cyclic_ ']' ++ '[' -z '1 { print $8, $1, $2, $10, $3 }' ']' ++ cat /dev/fd/63 /nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/train/cyc-pep-6-12mer-70M_29.csv ++ awk -F, -v OFS=, '1 { print $8, $1, $2, $10, $3 }' ++ gzip --best ++ schemist convert -f csv --column cysteine_to_N_cyclization --to id inchikey scaffold mwt clogp tpsa --prefix cyclic_ --options prefix=SCB- +++ zcat /nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz +++ head -n1 +++ tr ' ' , +🚀 Converting between string representations with the following parameters: + subcommand: convert + output: <_io.TextIOWrapper name='' mode='w' encoding='utf-8'> + format: csv + input: <_io.TextIOWrapper name='' mode='r' encoding='utf-8'> + representation: SMILES + column: cysteine_to_N_cyclization + prefix: cyclic_ + to: ['id', 'inchikey', 'scaffold', 'mwt', 'clogp', 'tpsa'] + options: ['prefix=SCB-'] + func: + 0it [00:00, ?it/s] 1it [00:08, 8.70s/it] 2it [00:17, 8.61s/it] 3it [00:25, 8.54s/it] 4it [00:34, 8.50s/it] 5it [00:42, 8.51s/it] 6it 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9.15s/it] 50it [07:34, 9.00s/it] 51it [07:43, 8.87s/it] 52it [07:51, 8.74s/it] 53it [08:00, 8.68s/it] 54it [08:09, 8.65s/it] 55it [08:17, 8.52s/it] 56it [08:25, 8.42s/it] 57it [08:33, 8.29s/it] 58it [08:41, 8.34s/it] 59it [08:50, 8.50s/it] 60it [08:59, 8.68s/it] 61it [09:09, 8.83s/it] 62it [09:17, 8.73s/it] 63it [09:26, 8.70s/it] 64it [09:34, 8.70s/it] 65it [09:43, 8.68s/it] 66it [09:52, 8.68s/it] 67it [10:00, 8.59s/it] 68it [10:09, 8.58s/it] 69it [10:17, 8.64s/it] 70it [10:26, 8.63s/it] 71it [10:35, 8.60s/it] 72it [10:43, 8.52s/it] 73it [10:51, 8.46s/it] 74it [11:00, 8.40s/it] 75it [11:09, 8.58s/it] 76it [11:18, 8.82s/it] 77it [11:27, 9.04s/it] 78it [11:37, 9.11s/it] 79it [11:45, 8.96s/it] 80it [11:54, 8.90s/it] 81it [12:03, 8.77s/it] 82it [12:11, 8.75s/it] 83it [12:20, 8.88s/it] 84it [12:29, 8.73s/it] 85it [12:37, 8.61s/it] 86it [12:46, 8.72s/it] 87it [12:55, 8.69s/it] 88it [13:03, 8.54s/it] 89it [13:11, 8.42s/it] 90it [13:20, 8.54s/it] 91it [13:28, 8.45s/it] 92it [13:37, 8.56s/it] 93it [13:46, 8.85s/it] 94it [13:56, 9.11s/it] 95it [14:05, 8.99s/it] 96it [14:13, 8.78s/it] 97it [14:22, 8.74s/it] 98it [14:30, 8.68s/it] 99it [14:39, 8.72s/it] 100it [14:48, 8.87s/it] 101it [14:57, 8.87s/it] 102it [15:06, 8.82s/it] 103it [15:15, 8.76s/it] 104it [15:23, 8.69s/it] 105it [15:32, 8.68s/it] 106it [15:40, 8.61s/it] 107it [15:49, 8.70s/it] 108it [15:58, 8.76s/it] 109it [16:07, 8.94s/it] 110it [16:17, 9.08s/it] 111it [16:26, 9.14s/it] 112it [16:35, 9.11s/it] 113it [16:44, 9.01s/it] 114it [16:53, 9.04s/it] 115it [17:02, 9.08s/it] 116it [17:11, 9.11s/it] 117it [17:20, 9.05s/it] 118it [17:28, 8.63s/it] 119it [17:36, 8.43s/it] 120it [17:44, 8.37s/it] 121it [17:53, 8.44s/it] 122it [18:01, 8.44s/it] 123it [18:10, 8.43s/it] 124it [18:18, 8.47s/it] 125it [18:27, 8.46s/it] 126it [18:35, 8.42s/it] 127it [18:44, 8.54s/it] 128it [18:53, 8.76s/it] 129it [19:02, 8.73s/it] 130it [19:10, 8.67s/it] 131it [19:19, 8.67s/it] 132it [19:27, 8.62s/it] 133it [19:35, 8.41s/it] 134it [19:43, 8.28s/it] 135it [19:51, 8.23s/it] 136it [20:00, 8.35s/it] 137it [20:09, 8.55s/it] 138it [20:18, 8.64s/it] 139it [20:26, 8.59s/it] 140it [20:34, 8.46s/it] 141it [20:43, 8.35s/it] 142it [20:51, 8.34s/it] 143it [21:00, 8.56s/it] 144it [21:09, 8.83s/it] 145it [21:19, 9.08s/it] 146it [21:28, 9.03s/it] 147it [21:36, 8.80s/it] 148it [21:45, 8.74s/it] 149it [21:54, 8.73s/it] 150it [22:02, 8.74s/it] 151it [22:11, 8.78s/it] 152it [22:20, 8.90s/it] 153it [22:30, 8.99s/it] 154it [22:38, 8.95s/it] 155it [22:47, 8.84s/it] 156it [22:56, 8.92s/it] 157it [23:05, 8.97s/it] 158it [23:14, 9.01s/it] 159it [23:24, 9.10s/it] 160it [23:33, 9.21s/it] 161it [23:42, 9.26s/it] 162it [23:52, 9.36s/it] 163it [24:01, 9.38s/it] 164it [24:11, 9.36s/it] 165it [24:20, 9.39s/it] 166it [24:30, 9.46s/it] 167it [24:39, 9.24s/it] 168it [24:47, 9.09s/it] 169it [24:56, 9.05s/it] 170it [25:06, 9.17s/it] 171it [25:15, 9.19s/it] 172it [25:24, 9.19s/it] 173it [25:33, 9.16s/it] 174it [25:42, 9.01s/it] 175it [25:51, 8.97s/it] 176it [26:00, 9.10s/it] 177it [26:10, 9.36s/it] 178it [26:20, 9.50s/it] 179it [26:30, 9.57s/it] 180it [26:39, 9.46s/it] 181it [26:48, 9.40s/it] 182it [26:58, 9.39s/it] 183it [27:07, 9.48s/it] 184it [27:17, 9.52s/it] 185it [27:26, 9.40s/it] 186it [27:35, 9.23s/it] 187it [27:44, 9.18s/it] 188it [27:53, 9.29s/it] 189it [28:03, 9.32s/it] 190it [28:12, 9.42s/it] 191it [28:22, 9.51s/it] 192it [28:31, 9.38s/it] 193it [28:40, 9.27s/it] 194it [28:50, 9.37s/it] 195it [29:00, 9.57s/it] 196it [29:10, 9.78s/it] 197it [29:20, 9.85s/it] 198it [29:30, 9.85s/it] 199it [29:39, 9.70s/it] 200it [29:49, 9.67s/it] 201it [29:58, 9.52s/it] 202it [30:07, 9.35s/it] 203it [30:16, 9.24s/it] 204it [30:25, 9.21s/it] 205it [30:34, 9.18s/it] 206it [30:43, 9.09s/it] 207it [30:52, 9.05s/it] 208it [31:01, 8.92s/it] 209it [31:09, 8.84s/it] 210it [31:18, 8.79s/it] 211it [31:27, 8.95s/it] 212it [31:37, 9.16s/it] 213it [31:47, 9.37s/it] 214it [31:56, 9.33s/it] 215it [32:05, 9.26s/it] 216it [32:14, 9.23s/it] 217it [32:24, 9.21s/it] 218it 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7.73s/it] 999it [2:25:15, 7.70s/it] 1000it [2:25:22, 7.70s/it] 1000it [2:25:22, 8.72s/it] +Error counts: + cyclic_id: 0 + cyclic_inchikey: 0 + cyclic_scaffold: 0 + cyclic_mwt: 0 + cyclic_clogp: 0 + cyclic_tpsa: 0 +⏰ Completed process in 2:25:43.707604 ++ rm /nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/train/cyc-pep-6-12mer-70M_29.csv diff --git a/train/cyc-pep-6-12mer-70M_30.csv.gz b/train/cyc-pep-6-12mer-70M_30.csv.gz index 88e0d1326906d43d89db7322968514c94599a063..b70fa44c8158fb0fda3402e9afc79c2014b84573 100644 --- a/train/cyc-pep-6-12mer-70M_30.csv.gz +++ b/train/cyc-pep-6-12mer-70M_30.csv.gz @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:ac2ee111ccbfd6a717001b7be386c133902ec6b6f98e00005275bdc3baeeaac2 -size 32260095 +oid sha256:1f4a0b047f24e10a92dce7e755a50f88e765ac0dd1a106dcb6c69ec9c1562064 +size 75343765 diff --git a/train/cyc-pep-6-12mer-70M_30.log b/train/cyc-pep-6-12mer-70M_30.log new file mode 100644 index 0000000000000000000000000000000000000000..7452e4ba970e90782ac83d80b3405a0ee9ac4672 --- /dev/null +++ b/train/cyc-pep-6-12mer-70M_30.log @@ -0,0 +1,337 @@ ++ module purge ++ '[' -z '' ']' ++ case "$-" in ++ __lmod_sh_dbg=x ++ '[' -n x ']' ++ set +x +Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output +Shell debugging restarted ++ unset __lmod_sh_dbg ++ return 0 ++ module load Anaconda3/2023.03 ++ '[' -z '' ']' ++ case "$-" in ++ __lmod_sh_dbg=x ++ '[' -n x ']' ++ set +x +Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output +Shell debugging restarted ++ unset __lmod_sh_dbg ++ return 0 ++ source /camp/home/johnsoe/.bashrc +++ '[' '' = yes ']' +++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' ++++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.bash hook +++ __conda_setup='export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'' + +# Copyright (C) 2012 Anaconda, Inc +# SPDX-License-Identifier: BSD-3-Clause +__conda_exe() ( + "$CONDA_EXE" $_CE_M $_CE_CONDA "$@" +) + +__conda_hashr() { + if [ -n "${ZSH_VERSION:+x}" ]; then + \rehash + elif [ -n "${POSH_VERSION:+x}" ]; then + : # pass + else + \hash -r + fi +} + +__conda_activate() { + if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then + # Handle transition from shell activated with conda <= 4.3 to a subsequent activation + # after conda updated to >= 4.4. See issue #6173. + PS1="$CONDA_PS1_BACKUP" + \unset CONDA_PS1_BACKUP + fi + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return + \eval "$ask_conda" + __conda_hashr +} + +__conda_reactivate() { + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return + \eval "$ask_conda" + __conda_hashr +} + +conda() { + \local cmd="${1-__missing__}" + case "$cmd" in + activate|deactivate) + __conda_activate "$@" + ;; + install|update|upgrade|remove|uninstall) + __conda_exe "$@" || \return + __conda_reactivate + ;; + *) + __conda_exe "$@" + ;; + esac +} + +if [ -z "${CONDA_SHLVL+x}" ]; then + \export CONDA_SHLVL=0 + # In dev-mode CONDA_EXE is python.exe and on Windows + # it is in a different relative location to condabin. + if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then + PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}" + else + PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}" + fi + \export PATH + + # We'\''re not allowing PS1 to be unbound. It must at least be set. + # However, we'\''re not exporting it, which can cause problems when starting a second shell + # via a first shell (i.e. starting zsh from bash). + if [ -z "${PS1+x}" ]; then + PS1= + fi +fi + +conda activate base' +++ '[' 0 -eq 0 ']' +++ eval 'export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'' + +# Copyright (C) 2012 Anaconda, Inc +# SPDX-License-Identifier: BSD-3-Clause +__conda_exe() ( + "$CONDA_EXE" $_CE_M $_CE_CONDA "$@" +) + +__conda_hashr() { + if [ -n "${ZSH_VERSION:+x}" ]; then + \rehash + elif [ -n "${POSH_VERSION:+x}" ]; then + : # pass + else + \hash -r + fi +} + +__conda_activate() { + if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then + # Handle transition from shell activated with conda <= 4.3 to a subsequent activation + # after conda updated to >= 4.4. See issue #6173. + PS1="$CONDA_PS1_BACKUP" + \unset CONDA_PS1_BACKUP + fi + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return + \eval "$ask_conda" + __conda_hashr +} + +__conda_reactivate() { + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return + \eval "$ask_conda" + __conda_hashr +} + +conda() { + \local cmd="${1-__missing__}" + case "$cmd" in + activate|deactivate) + __conda_activate "$@" + ;; + install|update|upgrade|remove|uninstall) + __conda_exe "$@" || \return + __conda_reactivate + ;; + *) + __conda_exe "$@" + ;; + esac +} + +if [ -z "${CONDA_SHLVL+x}" ]; then + \export CONDA_SHLVL=0 + # In dev-mode CONDA_EXE is python.exe and on Windows + # it is in a different relative location to condabin. + if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then + PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}" + else + PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}" + fi + \export PATH + + # We'\''re not allowing PS1 to be unbound. It must at least be set. + # However, we'\''re not exporting it, which can cause problems when starting a second shell + # via a first shell (i.e. starting zsh from bash). + if [ -z "${PS1+x}" ]; then + PS1= + fi +fi + +conda activate base' ++++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda ++++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda ++++ export _CE_M= ++++ _CE_M= ++++ export _CE_CONDA= ++++ _CE_CONDA= ++++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ '[' -z x ']' ++++ conda activate base ++++ local cmd=activate ++++ case "$cmd" in ++++ __conda_activate activate base ++++ '[' -n '' ']' ++++ local ask_conda +++++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++++ __conda_exe shell.posix activate base +++++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate base ++++ ask_conda='PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_SHLVL='\''6'\'' +export CONDA_DEFAULT_ENV='\''base'\'' +export CONDA_PROMPT_MODIFIER='\''(base) '\'' +export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' ++++ eval 'PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_SHLVL='\''6'\'' +export CONDA_DEFAULT_ENV='\''base'\'' +export CONDA_PROMPT_MODIFIER='\''(base) '\'' +export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' +++++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++++ export CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0 +++++ CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0 +++++ export CONDA_SHLVL=6 +++++ CONDA_SHLVL=6 +++++ export CONDA_DEFAULT_ENV=base +++++ CONDA_DEFAULT_ENV=base +++++ export 'CONDA_PROMPT_MODIFIER=(base) ' +++++ CONDA_PROMPT_MODIFIER='(base) ' +++++ export CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev +++++ CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev +++++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++++ export _CE_M= +++++ _CE_M= +++++ export _CE_CONDA= +++++ _CE_CONDA= +++++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python +++++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ __conda_hashr ++++ '[' -n '' ']' ++++ '[' -n '' ']' ++++ hash -r +++ unset __conda_setup ++ conda activate schemist-dev ++ local cmd=activate ++ case "$cmd" in ++ __conda_activate activate schemist-dev ++ '[' -n '' ']' ++ local ask_conda +++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++ __conda_exe shell.posix activate schemist-dev +++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate schemist-dev ++ ask_conda='PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_SHLVL='\''7'\'' +export CONDA_DEFAULT_ENV='\''schemist-dev'\'' +export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\'' +export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' ++ eval 'PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_SHLVL='\''7'\'' +export CONDA_DEFAULT_ENV='\''schemist-dev'\'' +export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\'' +export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' +++ PS1='(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++ export CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev +++ CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev +++ export CONDA_SHLVL=7 +++ CONDA_SHLVL=7 +++ export CONDA_DEFAULT_ENV=schemist-dev +++ CONDA_DEFAULT_ENV=schemist-dev +++ export 'CONDA_PROMPT_MODIFIER=(schemist-dev) ' +++ CONDA_PROMPT_MODIFIER='(schemist-dev) ' +++ export CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0 +++ CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0 +++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++ export _CE_M= +++ _CE_M= +++ export _CE_CONDA= +++ _CE_CONDA= +++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python +++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++ __conda_hashr ++ '[' -n '' ']' ++ '[' -n '' ']' ++ hash -r ++ CHUNK_HEAD_FILE=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz ++ INPUT=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/train/cyc-pep-6-12mer-70M_30.csv ++ COLUMN=cysteine_to_N_cyclization ++ PREFIX=cyclic_ ++ AWK='1 { print $8, $1, $2, $10, $3 }' ++ '[' -z cysteine_to_N_cyclization ']' ++ '[' -z cyclic_ ']' ++ '[' -z '1 { print $8, $1, $2, $10, $3 }' ']' ++ cat /dev/fd/63 /nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/train/cyc-pep-6-12mer-70M_30.csv ++ schemist convert -f csv --column cysteine_to_N_cyclization --to id inchikey scaffold mwt clogp tpsa --prefix cyclic_ --options prefix=SCB- ++ gzip --best ++ awk -F, -v OFS=, '1 { print $8, $1, $2, $10, $3 }' +++ head -n1 +++ tr ' ' , +++ zcat /nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz +🚀 Converting between string representations with the following parameters: + subcommand: convert + output: <_io.TextIOWrapper name='' mode='w' encoding='utf-8'> + format: csv + input: <_io.TextIOWrapper name='' mode='r' encoding='utf-8'> + representation: SMILES + column: cysteine_to_N_cyclization + prefix: cyclic_ + to: ['id', 'inchikey', 'scaffold', 'mwt', 'clogp', 'tpsa'] + options: ['prefix=SCB-'] + func: + 0it [00:00, ?it/s] 1it [00:07, 7.26s/it] 2it [00:14, 7.44s/it] 3it [00:22, 7.66s/it] 4it [00:30, 7.83s/it] 5it [00:38, 7.86s/it] 6it 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[2:29:15, 9.49s/it] 1000it [2:29:25, 9.63s/it] 1000it [2:29:25, 8.97s/it] +Error counts: + cyclic_id: 0 + cyclic_inchikey: 0 + cyclic_scaffold: 0 + cyclic_mwt: 0 + cyclic_clogp: 0 + cyclic_tpsa: 0 +⏰ Completed process in 2:29:44.509518 ++ rm /nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/train/cyc-pep-6-12mer-70M_30.csv diff --git a/train/cyc-pep-6-12mer-70M_31.csv.gz b/train/cyc-pep-6-12mer-70M_31.csv.gz index 5af59343dd0ad3862d25c7890bdd6e2ac31afe5b..3cbdfc1e8fe24f38be9a6ab24169fef52e68f680 100644 --- a/train/cyc-pep-6-12mer-70M_31.csv.gz +++ b/train/cyc-pep-6-12mer-70M_31.csv.gz @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:cc19b234265a856825a50a38c33c6f1ad8c6d6d1bad157ab0c7fbff8123c18d5 -size 32298493 +oid sha256:7ded0cc6ea91446a853c881e45311b622e11e1b477b19e4165d9f973510eccfa +size 75487771 diff --git a/train/cyc-pep-6-12mer-70M_31.log b/train/cyc-pep-6-12mer-70M_31.log new file mode 100644 index 0000000000000000000000000000000000000000..b61ba571a1a137c757eff07e75e9a35c30c9ad54 --- /dev/null +++ b/train/cyc-pep-6-12mer-70M_31.log @@ -0,0 +1,337 @@ ++ module purge ++ '[' -z '' ']' ++ case "$-" in ++ __lmod_sh_dbg=x ++ '[' -n x ']' ++ set +x +Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output +Shell debugging restarted ++ unset __lmod_sh_dbg ++ return 0 ++ module load Anaconda3/2023.03 ++ '[' -z '' ']' ++ case "$-" in ++ __lmod_sh_dbg=x ++ '[' -n x ']' ++ set +x +Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output +Shell debugging restarted ++ unset __lmod_sh_dbg ++ return 0 ++ source /camp/home/johnsoe/.bashrc +++ '[' '' = yes ']' +++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' ++++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.bash hook +++ __conda_setup='export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'' + +# Copyright (C) 2012 Anaconda, Inc +# SPDX-License-Identifier: BSD-3-Clause +__conda_exe() ( + "$CONDA_EXE" $_CE_M $_CE_CONDA "$@" +) + +__conda_hashr() { + if [ -n "${ZSH_VERSION:+x}" ]; then + \rehash + elif [ -n "${POSH_VERSION:+x}" ]; then + : # pass + else + \hash -r + fi +} + +__conda_activate() { + if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then + # Handle transition from shell activated with conda <= 4.3 to a subsequent activation + # after conda updated to >= 4.4. See issue #6173. + PS1="$CONDA_PS1_BACKUP" + \unset CONDA_PS1_BACKUP + fi + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return + \eval "$ask_conda" + __conda_hashr +} + +__conda_reactivate() { + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return + \eval "$ask_conda" + __conda_hashr +} + +conda() { + \local cmd="${1-__missing__}" + case "$cmd" in + activate|deactivate) + __conda_activate "$@" + ;; + install|update|upgrade|remove|uninstall) + __conda_exe "$@" || \return + __conda_reactivate + ;; + *) + __conda_exe "$@" + ;; + esac +} + +if [ -z "${CONDA_SHLVL+x}" ]; then + \export CONDA_SHLVL=0 + # In dev-mode CONDA_EXE is python.exe and on Windows + # it is in a different relative location to condabin. + if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then + PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}" + else + PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}" + fi + \export PATH + + # We'\''re not allowing PS1 to be unbound. It must at least be set. + # However, we'\''re not exporting it, which can cause problems when starting a second shell + # via a first shell (i.e. starting zsh from bash). + if [ -z "${PS1+x}" ]; then + PS1= + fi +fi + +conda activate base' +++ '[' 0 -eq 0 ']' +++ eval 'export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'' + +# Copyright (C) 2012 Anaconda, Inc +# SPDX-License-Identifier: BSD-3-Clause +__conda_exe() ( + "$CONDA_EXE" $_CE_M $_CE_CONDA "$@" +) + +__conda_hashr() { + if [ -n "${ZSH_VERSION:+x}" ]; then + \rehash + elif [ -n "${POSH_VERSION:+x}" ]; then + : # pass + else + \hash -r + fi +} + +__conda_activate() { + if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then + # Handle transition from shell activated with conda <= 4.3 to a subsequent activation + # after conda updated to >= 4.4. See issue #6173. + PS1="$CONDA_PS1_BACKUP" + \unset CONDA_PS1_BACKUP + fi + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return + \eval "$ask_conda" + __conda_hashr +} + +__conda_reactivate() { + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return + \eval "$ask_conda" + __conda_hashr +} + +conda() { + \local cmd="${1-__missing__}" + case "$cmd" in + activate|deactivate) + __conda_activate "$@" + ;; + install|update|upgrade|remove|uninstall) + __conda_exe "$@" || \return + __conda_reactivate + ;; + *) + __conda_exe "$@" + ;; + esac +} + +if [ -z "${CONDA_SHLVL+x}" ]; then + \export CONDA_SHLVL=0 + # In dev-mode CONDA_EXE is python.exe and on Windows + # it is in a different relative location to condabin. + if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then + PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}" + else + PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}" + fi + \export PATH + + # We'\''re not allowing PS1 to be unbound. It must at least be set. + # However, we'\''re not exporting it, which can cause problems when starting a second shell + # via a first shell (i.e. starting zsh from bash). + if [ -z "${PS1+x}" ]; then + PS1= + fi +fi + +conda activate base' ++++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda ++++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda ++++ export _CE_M= ++++ _CE_M= ++++ export _CE_CONDA= ++++ _CE_CONDA= ++++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ '[' -z x ']' ++++ conda activate base ++++ local cmd=activate ++++ case "$cmd" in ++++ __conda_activate activate base ++++ '[' -n '' ']' ++++ local ask_conda +++++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++++ __conda_exe shell.posix activate base +++++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate base ++++ ask_conda='PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_SHLVL='\''6'\'' +export CONDA_DEFAULT_ENV='\''base'\'' +export CONDA_PROMPT_MODIFIER='\''(base) '\'' +export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' ++++ eval 'PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_SHLVL='\''6'\'' +export CONDA_DEFAULT_ENV='\''base'\'' +export CONDA_PROMPT_MODIFIER='\''(base) '\'' +export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' +++++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++++ export CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0 +++++ CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0 +++++ export CONDA_SHLVL=6 +++++ CONDA_SHLVL=6 +++++ export CONDA_DEFAULT_ENV=base +++++ CONDA_DEFAULT_ENV=base +++++ export 'CONDA_PROMPT_MODIFIER=(base) ' +++++ CONDA_PROMPT_MODIFIER='(base) ' +++++ export CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev +++++ CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev +++++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++++ export _CE_M= +++++ _CE_M= +++++ export _CE_CONDA= +++++ _CE_CONDA= +++++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python +++++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ __conda_hashr ++++ '[' -n '' ']' ++++ '[' -n '' ']' ++++ hash -r +++ unset __conda_setup ++ conda activate schemist-dev ++ local cmd=activate ++ case "$cmd" in ++ __conda_activate activate schemist-dev ++ '[' -n '' ']' ++ local ask_conda +++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++ __conda_exe shell.posix activate schemist-dev +++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate schemist-dev ++ ask_conda='PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_SHLVL='\''7'\'' +export CONDA_DEFAULT_ENV='\''schemist-dev'\'' +export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\'' +export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' ++ eval 'PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_SHLVL='\''7'\'' +export CONDA_DEFAULT_ENV='\''schemist-dev'\'' +export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\'' +export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' +++ PS1='(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++ export CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev +++ CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev +++ export CONDA_SHLVL=7 +++ CONDA_SHLVL=7 +++ export CONDA_DEFAULT_ENV=schemist-dev +++ CONDA_DEFAULT_ENV=schemist-dev +++ export 'CONDA_PROMPT_MODIFIER=(schemist-dev) ' +++ CONDA_PROMPT_MODIFIER='(schemist-dev) ' +++ export CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0 +++ CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0 +++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++ export _CE_M= +++ _CE_M= +++ export _CE_CONDA= +++ _CE_CONDA= +++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python +++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++ __conda_hashr ++ '[' -n '' ']' ++ '[' -n '' ']' ++ hash -r ++ CHUNK_HEAD_FILE=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz ++ INPUT=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/train/cyc-pep-6-12mer-70M_31.csv ++ COLUMN=cysteine_to_N_cyclization ++ PREFIX=cyclic_ ++ AWK='1 { print $8, $1, $2, $10, $3 }' ++ '[' -z cysteine_to_N_cyclization ']' ++ '[' -z cyclic_ ']' ++ '[' -z '1 { print $8, $1, $2, $10, $3 }' ']' ++ awk -F, -v OFS=, '1 { print $8, $1, $2, $10, $3 }' ++ cat /dev/fd/63 /nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/train/cyc-pep-6-12mer-70M_31.csv ++ gzip --best +++ head -n1 ++ schemist convert -f csv --column cysteine_to_N_cyclization --to id inchikey scaffold mwt clogp tpsa --prefix cyclic_ --options prefix=SCB- +++ zcat /nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz +++ tr ' ' , +🚀 Converting between string representations with the following parameters: + subcommand: convert + output: <_io.TextIOWrapper name='' mode='w' encoding='utf-8'> + format: csv + input: <_io.TextIOWrapper name='' mode='r' encoding='utf-8'> + representation: SMILES + column: cysteine_to_N_cyclization + prefix: cyclic_ + to: ['id', 'inchikey', 'scaffold', 'mwt', 'clogp', 'tpsa'] + options: ['prefix=SCB-'] + func: + 0it [00:00, ?it/s] 1it [00:08, 8.87s/it] 2it [00:17, 8.88s/it] 3it [00:26, 8.78s/it] 4it [00:35, 8.76s/it] 5it [00:43, 8.70s/it] 6it [00:52, 8.59s/it] 7it [01:00, 8.41s/it] 8it [01:08, 8.42s/it] 9it [01:16, 8.39s/it] 10it [01:25, 8.35s/it] 11it [01:33, 8.28s/it] 12it [01:41, 8.24s/it] 13it [01:49, 8.15s/it] 14it [01:57, 8.13s/it] 15it [02:06, 8.31s/it] 16it [02:15, 8.51s/it] 17it [02:24, 8.62s/it] 18it [02:32, 8.58s/it] 19it [02:41, 8.59s/it] 20it [02:49, 8.49s/it] 21it [02:57, 8.43s/it] 22it [03:06, 8.41s/it] 23it [03:14, 8.33s/it] 24it [03:22, 8.27s/it] 25it [03:30, 8.35s/it] 26it [03:39, 8.37s/it] 27it [03:47, 8.34s/it] 28it [03:55, 8.34s/it] 29it [04:04, 8.33s/it] 30it [04:12, 8.25s/it] 31it [04:20, 8.29s/it] 32it [04:29, 8.46s/it] 33it [04:38, 8.62s/it] 34it [04:47, 8.69s/it] 35it [04:55, 8.62s/it] 36it [05:04, 8.62s/it] 37it [05:12, 8.58s/it] 38it [05:21, 8.54s/it] 39it [05:29, 8.52s/it] 40it [05:38, 8.49s/it] 41it [05:46, 8.46s/it] 42it [05:55, 8.53s/it] 43it [06:03, 8.55s/it] 44it [06:12, 8.60s/it] 45it [06:21, 8.63s/it] 46it [06:30, 8.64s/it] 47it [06:38, 8.60s/it] 48it [06:47, 8.69s/it] 49it [06:56, 8.87s/it] 50it [07:06, 9.09s/it] 51it [07:15, 9.10s/it] 52it [07:24, 9.04s/it] 53it [07:33, 9.04s/it] 54it [07:42, 8.99s/it] 55it [07:51, 8.97s/it] 56it [08:00, 8.94s/it] 57it [08:08, 8.81s/it] 58it [08:17, 8.72s/it] 59it [08:25, 8.72s/it] 60it [08:34, 8.72s/it] 61it [08:43, 8.69s/it] 62it [08:51, 8.65s/it] 63it [09:00, 8.63s/it] 64it [09:08, 8.60s/it] 65it [09:17, 8.68s/it] 66it [09:27, 8.91s/it] 67it [09:36, 9.08s/it] 68it [09:45, 9.07s/it] 69it [09:54, 8.99s/it] 70it [10:03, 8.95s/it] 71it [10:12, 8.90s/it] 72it [10:20, 8.86s/it] 73it [10:29, 8.84s/it] 74it [10:37, 8.69s/it] 75it [10:46, 8.62s/it] 76it [10:55, 8.64s/it] 77it [11:03, 8.70s/it] 78it [11:12, 8.67s/it] 79it [11:21, 8.62s/it] 80it [11:29, 8.59s/it] 81it [11:37, 8.51s/it] 82it [11:46, 8.62s/it] 83it [11:56, 8.81s/it] 84it [12:05, 8.99s/it] 85it [12:14, 8.97s/it] 86it [12:23, 8.90s/it] 87it [12:31, 8.87s/it] 88it [12:40, 8.84s/it] 89it [12:49, 8.77s/it] 90it [12:57, 8.74s/it] 91it [13:06, 8.59s/it] 92it [13:14, 8.55s/it] 93it [13:23, 8.61s/it] 94it [13:32, 8.61s/it] 95it [13:40, 8.57s/it] 96it [13:48, 8.50s/it] 97it [13:57, 8.48s/it] 98it [14:05, 8.43s/it] 99it [14:14, 8.57s/it] 100it [14:23, 8.77s/it] 101it [14:32, 8.91s/it] 102it [14:41, 8.87s/it] 103it [14:50, 8.84s/it] 104it [14:59, 8.83s/it] 105it [15:07, 8.78s/it] 106it [15:16, 8.70s/it] 107it [15:25, 8.65s/it] 108it [15:33, 8.47s/it] 109it [15:41, 8.47s/it] 110it [15:50, 8.49s/it] 111it [15:58, 8.47s/it] 112it [16:06, 8.41s/it] 113it [16:15, 8.37s/it] 114it [16:23, 8.33s/it] 115it [16:31, 8.32s/it] 116it [16:40, 8.48s/it] 117it [16:49, 8.64s/it] 118it [16:58, 8.76s/it] 119it [17:07, 8.72s/it] 120it [17:15, 8.72s/it] 121it [17:24, 8.66s/it] 122it [17:32, 8.60s/it] 123it [17:41, 8.55s/it] 124it [17:49, 8.52s/it] 125it [17:58, 8.47s/it] 126it [18:06, 8.57s/it] 127it [18:15, 8.61s/it] 128it [18:24, 8.61s/it] 129it [18:32, 8.54s/it] 130it [18:41, 8.54s/it] 131it [18:49, 8.52s/it] 132it [18:58, 8.55s/it] 133it [19:07, 8.73s/it] 134it [19:16, 8.90s/it] 135it [19:25, 9.01s/it] 136it [19:34, 8.96s/it] 137it [19:43, 8.93s/it] 138it [19:52, 8.86s/it] 139it [20:01, 8.81s/it] 140it [20:09, 8.80s/it] 141it [20:18, 8.67s/it] 142it [20:26, 8.48s/it] 143it [20:34, 8.44s/it] 144it [20:42, 8.39s/it] 145it [20:50, 8.33s/it] 146it [20:59, 8.28s/it] 147it [21:07, 8.27s/it] 148it [21:15, 8.25s/it] 149it [21:23, 8.27s/it] 150it [21:32, 8.42s/it] 151it [21:41, 8.57s/it] 152it [21:50, 8.67s/it] 153it [21:58, 8.59s/it] 154it [22:07, 8.59s/it] 155it [22:15, 8.52s/it] 156it [22:24, 8.47s/it] 157it [22:32, 8.45s/it] 158it [22:40, 8.42s/it] 159it [22:49, 8.41s/it] 160it [22:58, 8.53s/it] 161it [23:06, 8.56s/it] 162it [23:15, 8.58s/it] 163it [23:23, 8.53s/it] 164it [23:32, 8.53s/it] 165it [23:40, 8.45s/it] 166it [23:49, 8.51s/it] 167it [23:58, 8.68s/it] 168it [24:07, 8.90s/it] 169it [24:16, 8.97s/it] 170it [24:25, 8.88s/it] 171it [24:34, 8.86s/it] 172it [24:43, 8.80s/it] 173it [24:51, 8.78s/it] 174it [25:00, 8.77s/it] 175it [25:09, 8.76s/it] 176it [25:18, 8.78s/it] 177it [25:27, 8.94s/it] 178it [25:36, 9.00s/it] 179it [25:45, 9.05s/it] 180it [25:54, 9.03s/it] 181it [26:03, 9.04s/it] 182it [26:12, 8.97s/it] 183it [26:21, 9.07s/it] 184it [26:31, 9.28s/it] 185it [26:41, 9.49s/it] 186it [26:51, 9.49s/it] 187it [27:00, 9.43s/it] 188it [27:09, 9.43s/it] 189it [27:19, 9.37s/it] 190it [27:28, 9.34s/it] 191it [27:37, 9.32s/it] 192it [27:46, 9.19s/it] 193it [27:55, 9.13s/it] 194it [28:04, 9.20s/it] 195it [28:14, 9.24s/it] 196it [28:23, 9.21s/it] 197it [28:32, 9.17s/it] 198it [28:41, 9.18s/it] 199it [28:50, 9.17s/it] 200it [29:00, 9.25s/it] 201it [29:10, 9.47s/it] 202it [29:20, 9.65s/it] 203it [29:29, 9.62s/it] 204it [29:39, 9.56s/it] 205it [29:48, 9.52s/it] 206it [29:58, 9.52s/it] 207it [30:07, 9.47s/it] 208it [30:16, 9.41s/it] 209it [30:25, 9.29s/it] 210it [30:35, 9.30s/it] 211it [30:44, 9.40s/it] 212it [30:54, 9.41s/it] 213it [31:03, 9.40s/it] 214it [31:12, 9.38s/it] 215it [31:22, 9.37s/it] 216it [31:31, 9.34s/it] 217it [31:41, 9.51s/it] 218it [31:51, 9.72s/it] 219it [32:01, 9.89s/it] 220it [32:11, 9.86s/it] 221it [32:21, 9.83s/it] 222it [32:31, 9.83s/it] 223it [32:40, 9.77s/it] 224it [32:50, 9.69s/it] 225it [32:59, 9.61s/it] 226it [33:08, 9.31s/it] 227it [33:17, 9.24s/it] 228it [33:26, 9.22s/it] 229it [33:35, 9.14s/it] 230it [33:44, 9.07s/it] 231it [33:53, 8.99s/it] 232it [34:02, 8.93s/it] 233it [34:10, 8.91s/it] 234it [34:20, 9.08s/it] 235it [34:30, 9.25s/it] 236it [34:39, 9.36s/it] 237it [34:48, 9.32s/it] 238it [34:58, 9.30s/it] 239it [35:07, 9.20s/it] 240it [35:16, 9.14s/it] 241it [35:25, 9.10s/it] 242it [35:33, 8.98s/it] 243it [35:42, 8.88s/it] 244it [35:51, 8.86s/it] 245it [36:00, 8.83s/it] 246it [36:08, 8.75s/it] 247it [36:17, 8.68s/it] 248it [36:25, 8.67s/it] 249it [36:34, 8.60s/it] 250it [36:43, 8.65s/it] 251it [36:52, 8.83s/it] 252it [37:01, 9.01s/it] 253it [37:11, 9.12s/it] 254it [37:19, 9.03s/it] 255it [37:28, 9.01s/it] 256it [37:37, 8.94s/it] 257it [37:46, 8.90s/it] 258it [37:55, 8.87s/it] 259it [38:03, 8.84s/it] 260it [38:12, 8.81s/it] 261it [38:21, 8.88s/it] 262it [38:30, 8.90s/it] 263it [38:39, 8.86s/it] 264it [38:48, 8.84s/it] 265it [38:57, 8.87s/it] 266it [39:05, 8.84s/it] 267it [39:15, 8.89s/it] 268it [39:24, 9.08s/it] 269it [39:34, 9.28s/it] 270it [39:43, 9.35s/it] 271it [39:52, 9.27s/it] 272it [40:02, 9.26s/it] 273it [40:11, 9.21s/it] 274it [40:20, 9.17s/it] 275it [40:29, 9.18s/it] 276it [40:38, 8.99s/it] 277it [40:46, 8.82s/it] 278it [40:55, 8.79s/it] 279it [41:03, 8.73s/it] 280it [41:12, 8.71s/it] 281it [41:20, 8.65s/it] 282it [41:29, 8.64s/it] 283it [41:37, 8.56s/it] 284it [41:46, 8.65s/it] 285it [41:55, 8.82s/it] 286it [42:05, 9.02s/it] 287it [42:14, 9.02s/it] 288it [42:23, 8.92s/it] 289it [42:32, 8.92s/it] 290it [42:40, 8.89s/it] 291it [42:49, 8.86s/it] 292it [42:58, 8.84s/it] 293it [43:06, 8.71s/it] 294it [43:15, 8.66s/it] 295it [43:24, 8.67s/it] 296it [43:32, 8.71s/it] 297it [43:41, 8.69s/it] 298it [43:50, 8.66s/it] 299it [43:58, 8.64s/it] 300it [44:07, 8.63s/it] 301it [44:16, 8.74s/it] 302it [44:25, 8.94s/it] 303it [44:35, 9.10s/it] 304it [44:44, 9.06s/it] 305it [44:53, 9.00s/it] 306it [45:02, 9.02s/it] 307it [45:11, 8.99s/it] 308it [45:19, 8.94s/it] 309it [45:28, 8.87s/it] 310it [45:36, 8.68s/it] 311it [45:45, 8.66s/it] 312it [45:54, 8.68s/it] 313it [46:02, 8.67s/it] 314it [46:11, 8.63s/it] 315it [46:19, 8.61s/it] 316it [46:28, 8.57s/it] 317it [46:36, 8.57s/it] 318it [46:45, 8.70s/it] 319it [46:55, 8.87s/it] 320it [47:04, 8.99s/it] 321it [47:13, 8.94s/it] 322it [47:22, 8.96s/it] 323it [47:31, 8.91s/it] 324it [47:39, 8.87s/it] 325it [47:48, 8.80s/it] 326it [47:57, 8.73s/it] 327it [48:05, 8.67s/it] 328it [48:14, 8.69s/it] 329it [48:23, 8.69s/it] 330it [48:31, 8.68s/it] 331it [48:40, 8.66s/it] 332it [48:48, 8.65s/it] 333it [48:57, 8.62s/it] 334it [49:06, 8.62s/it] 335it [49:15, 8.79s/it] 336it [49:24, 8.96s/it] 337it [49:34, 9.08s/it] 338it [49:42, 9.03s/it] 339it [49:52, 9.04s/it] 340it [50:00, 8.96s/it] 341it [50:09, 8.92s/it] 342it [50:18, 8.89s/it] 343it [50:26, 8.68s/it] 344it [50:34, 8.37s/it] 345it [50:42, 8.23s/it] 346it [50:50, 8.13s/it] 347it [50:57, 8.04s/it] 348it [51:05, 7.93s/it] 349it [51:13, 7.90s/it] 350it [51:21, 7.81s/it] 351it [51:28, 7.82s/it] 352it [51:37, 7.97s/it] 353it [51:45, 8.12s/it] 354it [51:54, 8.21s/it] 355it [52:02, 8.18s/it] 356it [52:10, 8.14s/it] 357it [52:18, 8.06s/it] 358it [52:25, 8.01s/it] 359it [52:33, 7.99s/it] 360it [52:41, 7.94s/it] 361it [52:49, 7.87s/it] 362it [52:57, 7.91s/it] 363it [53:05, 7.95s/it] 364it [53:13, 7.91s/it] 365it [53:21, 7.90s/it] 366it [53:29, 7.88s/it] 367it [53:36, 7.79s/it] 368it [53:44, 7.86s/it] 369it [53:53, 8.05s/it] 370it [54:01, 8.26s/it] 371it [54:10, 8.30s/it] 372it [54:18, 8.22s/it] 373it [54:26, 8.20s/it] 374it [54:34, 8.14s/it] 375it [54:42, 8.09s/it] 376it [54:50, 8.06s/it] 377it [54:58, 8.03s/it] 378it [55:06, 8.07s/it] 379it [55:14, 8.14s/it] 380it [55:23, 8.22s/it] 381it [55:31, 8.25s/it] 382it [55:39, 8.24s/it] 383it [55:48, 8.24s/it] 384it [55:56, 8.19s/it] 385it [56:04, 8.25s/it] 386it 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8.47s/it] +Error counts: + cyclic_id: 0 + cyclic_inchikey: 0 + cyclic_scaffold: 0 + cyclic_mwt: 0 + cyclic_clogp: 0 + cyclic_tpsa: 0 +⏰ Completed process in 2:21:30.013258 ++ rm /nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/train/cyc-pep-6-12mer-70M_31.csv diff --git a/train/cyc-pep-6-12mer-70M_32.csv.gz b/train/cyc-pep-6-12mer-70M_32.csv.gz index ba8c56432947acce27f2997d3c949f12996ec2ff..41a72ddb5364584842d42494af8272db33568dff 100644 --- a/train/cyc-pep-6-12mer-70M_32.csv.gz +++ b/train/cyc-pep-6-12mer-70M_32.csv.gz @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:861cb210a2244686a4fc2551a6a72c711e02cd7eea7d06343f7fffa6ff1622d6 -size 32287243 +oid sha256:a1f8e9cbc4441bd215175cc7d7a8a3644729da3c5f42d70ee079323d2d2c2d22 +size 75300399 diff --git a/train/cyc-pep-6-12mer-70M_32.log b/train/cyc-pep-6-12mer-70M_32.log new file mode 100644 index 0000000000000000000000000000000000000000..02f2654569a7060f84a0f6b482b4c7e8ce6e7a16 --- /dev/null +++ b/train/cyc-pep-6-12mer-70M_32.log @@ -0,0 +1,337 @@ ++ module purge ++ '[' -z '' ']' ++ case "$-" in ++ __lmod_sh_dbg=x ++ '[' -n x ']' ++ set +x +Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output +Shell debugging restarted ++ unset __lmod_sh_dbg ++ return 0 ++ module load Anaconda3/2023.03 ++ '[' -z '' ']' ++ case "$-" in ++ __lmod_sh_dbg=x ++ '[' -n x ']' ++ set +x +Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output +Shell debugging restarted ++ unset __lmod_sh_dbg ++ return 0 ++ source /camp/home/johnsoe/.bashrc +++ '[' '' = yes ']' +++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' ++++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.bash hook +++ __conda_setup='export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'' + +# Copyright (C) 2012 Anaconda, Inc +# SPDX-License-Identifier: BSD-3-Clause +__conda_exe() ( + "$CONDA_EXE" $_CE_M $_CE_CONDA "$@" +) + +__conda_hashr() { + if [ -n "${ZSH_VERSION:+x}" ]; then + \rehash + elif [ -n "${POSH_VERSION:+x}" ]; then + : # pass + else + \hash -r + fi +} + +__conda_activate() { + if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then + # Handle transition from shell activated with conda <= 4.3 to a subsequent activation + # after conda updated to >= 4.4. See issue #6173. + PS1="$CONDA_PS1_BACKUP" + \unset CONDA_PS1_BACKUP + fi + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return + \eval "$ask_conda" + __conda_hashr +} + +__conda_reactivate() { + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return + \eval "$ask_conda" + __conda_hashr +} + +conda() { + \local cmd="${1-__missing__}" + case "$cmd" in + activate|deactivate) + __conda_activate "$@" + ;; + install|update|upgrade|remove|uninstall) + __conda_exe "$@" || \return + __conda_reactivate + ;; + *) + __conda_exe "$@" + ;; + esac +} + +if [ -z "${CONDA_SHLVL+x}" ]; then + \export CONDA_SHLVL=0 + # In dev-mode CONDA_EXE is python.exe and on Windows + # it is in a different relative location to condabin. + if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then + PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}" + else + PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}" + fi + \export PATH + + # We'\''re not allowing PS1 to be unbound. It must at least be set. + # However, we'\''re not exporting it, which can cause problems when starting a second shell + # via a first shell (i.e. starting zsh from bash). + if [ -z "${PS1+x}" ]; then + PS1= + fi +fi + +conda activate base' +++ '[' 0 -eq 0 ']' +++ eval 'export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'' + +# Copyright (C) 2012 Anaconda, Inc +# SPDX-License-Identifier: BSD-3-Clause +__conda_exe() ( + "$CONDA_EXE" $_CE_M $_CE_CONDA "$@" +) + +__conda_hashr() { + if [ -n "${ZSH_VERSION:+x}" ]; then + \rehash + elif [ -n "${POSH_VERSION:+x}" ]; then + : # pass + else + \hash -r + fi +} + +__conda_activate() { + if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then + # Handle transition from shell activated with conda <= 4.3 to a subsequent activation + # after conda updated to >= 4.4. See issue #6173. + PS1="$CONDA_PS1_BACKUP" + \unset CONDA_PS1_BACKUP + fi + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return + \eval "$ask_conda" + __conda_hashr +} + +__conda_reactivate() { + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return + \eval "$ask_conda" + __conda_hashr +} + +conda() { + \local cmd="${1-__missing__}" + case "$cmd" in + activate|deactivate) + __conda_activate "$@" + ;; + install|update|upgrade|remove|uninstall) + __conda_exe "$@" || \return + __conda_reactivate + ;; + *) + __conda_exe "$@" + ;; + esac +} + +if [ -z "${CONDA_SHLVL+x}" ]; then + \export CONDA_SHLVL=0 + # In dev-mode CONDA_EXE is python.exe and on Windows + # it is in a different relative location to condabin. + if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then + PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}" + else + PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}" + fi + \export PATH + + # We'\''re not allowing PS1 to be unbound. It must at least be set. + # However, we'\''re not exporting it, which can cause problems when starting a second shell + # via a first shell (i.e. starting zsh from bash). + if [ -z "${PS1+x}" ]; then + PS1= + fi +fi + +conda activate base' ++++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda ++++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda ++++ export _CE_M= ++++ _CE_M= ++++ export _CE_CONDA= ++++ _CE_CONDA= ++++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ '[' -z x ']' ++++ conda activate base ++++ local cmd=activate ++++ case "$cmd" in ++++ __conda_activate activate base ++++ '[' -n '' ']' ++++ local ask_conda +++++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++++ __conda_exe shell.posix activate base +++++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate base ++++ ask_conda='PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_SHLVL='\''6'\'' +export CONDA_DEFAULT_ENV='\''base'\'' +export CONDA_PROMPT_MODIFIER='\''(base) '\'' +export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' ++++ eval 'PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_SHLVL='\''6'\'' +export CONDA_DEFAULT_ENV='\''base'\'' +export CONDA_PROMPT_MODIFIER='\''(base) '\'' +export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' +++++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++++ export CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0 +++++ CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0 +++++ export CONDA_SHLVL=6 +++++ CONDA_SHLVL=6 +++++ export CONDA_DEFAULT_ENV=base +++++ CONDA_DEFAULT_ENV=base +++++ export 'CONDA_PROMPT_MODIFIER=(base) ' +++++ CONDA_PROMPT_MODIFIER='(base) ' +++++ export CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev +++++ CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev +++++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++++ export _CE_M= +++++ _CE_M= +++++ export _CE_CONDA= +++++ _CE_CONDA= +++++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python +++++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ __conda_hashr ++++ '[' -n '' ']' ++++ '[' -n '' ']' ++++ hash -r +++ unset __conda_setup ++ conda activate schemist-dev ++ local cmd=activate ++ case "$cmd" in ++ __conda_activate activate schemist-dev ++ '[' -n '' ']' ++ local ask_conda +++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++ __conda_exe shell.posix activate schemist-dev +++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate schemist-dev ++ ask_conda='PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_SHLVL='\''7'\'' +export CONDA_DEFAULT_ENV='\''schemist-dev'\'' +export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\'' +export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' ++ eval 'PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_SHLVL='\''7'\'' +export CONDA_DEFAULT_ENV='\''schemist-dev'\'' +export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\'' +export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' +++ PS1='(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++ export CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev +++ CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev +++ export CONDA_SHLVL=7 +++ CONDA_SHLVL=7 +++ export CONDA_DEFAULT_ENV=schemist-dev +++ CONDA_DEFAULT_ENV=schemist-dev +++ export 'CONDA_PROMPT_MODIFIER=(schemist-dev) ' +++ CONDA_PROMPT_MODIFIER='(schemist-dev) ' +++ export CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0 +++ CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0 +++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++ export _CE_M= +++ _CE_M= +++ export _CE_CONDA= +++ _CE_CONDA= +++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python +++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++ __conda_hashr ++ '[' -n '' ']' ++ '[' -n '' ']' ++ hash -r ++ CHUNK_HEAD_FILE=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz ++ INPUT=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/train/cyc-pep-6-12mer-70M_32.csv ++ COLUMN=cysteine_to_N_cyclization ++ PREFIX=cyclic_ ++ AWK='1 { print $8, $1, $2, $10, $3 }' ++ '[' -z cysteine_to_N_cyclization ']' ++ '[' -z cyclic_ ']' ++ '[' -z '1 { print $8, $1, $2, $10, $3 }' ']' ++ awk -F, -v OFS=, '1 { print $8, $1, $2, $10, $3 }' ++ cat /dev/fd/63 /nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/train/cyc-pep-6-12mer-70M_32.csv ++ schemist convert -f csv --column cysteine_to_N_cyclization --to id inchikey scaffold mwt clogp tpsa --prefix cyclic_ --options prefix=SCB- ++ gzip --best +++ zcat /nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz +++ head -n1 +++ tr ' ' , +🚀 Converting between string representations with the following parameters: + subcommand: convert + output: <_io.TextIOWrapper name='' mode='w' encoding='utf-8'> + format: csv + input: <_io.TextIOWrapper name='' mode='r' encoding='utf-8'> + representation: SMILES + column: cysteine_to_N_cyclization + prefix: cyclic_ + to: ['id', 'inchikey', 'scaffold', 'mwt', 'clogp', 'tpsa'] + options: ['prefix=SCB-'] + func: + 0it [00:00, ?it/s] 1it [00:08, 8.56s/it] 2it [00:17, 8.67s/it] 3it [00:26, 8.81s/it] 4it [00:35, 8.81s/it] 5it [00:43, 8.80s/it] 6it [00:52, 8.74s/it] 7it [01:01, 8.73s/it] 8it [01:09, 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52it [07:36, 8.80s/it] 53it [07:46, 8.92s/it] 54it [07:55, 8.94s/it] 55it [08:04, 8.99s/it] 56it [08:13, 9.00s/it] 57it [08:22, 9.04s/it] 58it [08:31, 8.96s/it] 59it [08:40, 9.03s/it] 60it [08:49, 9.16s/it] 61it [08:59, 9.43s/it] 62it [09:09, 9.44s/it] 63it [09:18, 9.35s/it] 64it [09:27, 9.35s/it] 65it [09:36, 9.29s/it] 66it [09:46, 9.26s/it] 67it [09:55, 9.26s/it] 68it [10:03, 9.05s/it] 69it [10:12, 8.95s/it] 70it [10:21, 8.95s/it] 71it [10:30, 8.91s/it] 72it [10:39, 8.90s/it] 73it [10:48, 8.91s/it] 74it [10:57, 8.94s/it] 75it [11:06, 8.87s/it] 76it [11:15, 8.95s/it] 77it [11:24, 9.17s/it] 78it [11:34, 9.34s/it] 79it [11:43, 9.37s/it] 80it [11:53, 9.28s/it] 81it [12:02, 9.31s/it] 82it [12:11, 9.26s/it] 83it [12:20, 9.22s/it] 84it [12:29, 9.17s/it] 85it [12:38, 8.97s/it] 86it [12:46, 8.86s/it] 87it [12:55, 8.93s/it] 88it [13:04, 8.95s/it] 89it [13:13, 8.95s/it] 90it [13:22, 8.88s/it] 91it [13:31, 8.86s/it] 92it [13:40, 8.80s/it] 93it [13:49, 9.03s/it] 94it [13:59, 9.26s/it] 95it 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137it [20:25, 8.81s/it] 138it [20:34, 8.84s/it] 139it [20:43, 8.79s/it] 140it [20:52, 8.72s/it] 141it [21:00, 8.77s/it] 142it [21:09, 8.78s/it] 143it [21:18, 8.81s/it] 144it [21:28, 9.02s/it] 145it [21:37, 9.19s/it] 146it [21:47, 9.31s/it] 147it [21:56, 9.28s/it] 148it [22:05, 9.29s/it] 149it [22:14, 9.24s/it] 150it [22:24, 9.17s/it] 151it [22:32, 9.10s/it] 152it [22:41, 8.97s/it] 153it [22:49, 8.77s/it] 154it [22:58, 8.72s/it] 155it [23:07, 8.66s/it] 156it [23:15, 8.62s/it] 157it [23:23, 8.55s/it] 158it [23:32, 8.57s/it] 159it [23:40, 8.52s/it] 160it [23:49, 8.55s/it] 161it [23:58, 8.76s/it] 162it [24:08, 8.95s/it] 163it [24:17, 9.05s/it] 164it [24:26, 8.96s/it] 165it [24:35, 8.95s/it] 166it [24:43, 8.85s/it] 167it [24:52, 8.80s/it] 168it [25:01, 8.75s/it] 169it [25:09, 8.74s/it] 170it [25:18, 8.70s/it] 171it [25:27, 8.83s/it] 172it [25:36, 8.85s/it] 173it [25:45, 8.89s/it] 174it [25:54, 8.86s/it] 175it [26:03, 8.88s/it] 176it [26:11, 8.73s/it] 177it [26:20, 8.74s/it] 178it [26:29, 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1000it [2:30:54, 8.92s/it] 1000it [2:30:54, 9.05s/it] +Error counts: + cyclic_id: 0 + cyclic_inchikey: 0 + cyclic_scaffold: 0 + cyclic_mwt: 0 + cyclic_clogp: 0 + cyclic_tpsa: 0 +⏰ Completed process in 2:31:13.908528 ++ rm /nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/train/cyc-pep-6-12mer-70M_32.csv diff --git a/train/cyc-pep-6-12mer-70M_33.csv.gz b/train/cyc-pep-6-12mer-70M_33.csv.gz index c671eea6f1d1fbb9cc33a45b836608e98033ea97..2c253473a382cf8dc9783f076eef1df9f612f193 100644 --- a/train/cyc-pep-6-12mer-70M_33.csv.gz +++ b/train/cyc-pep-6-12mer-70M_33.csv.gz @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:a5b523a39a649018b9b667dc5d218f61ef80528e2e9520e8e4855c3581e7c932 -size 37797392 +oid sha256:04bcb62c87abda61b76f13419ae08ec2a616d8b71136d234ac96ff793db71468 +size 83472905 diff --git a/train/cyc-pep-6-12mer-70M_33.log b/train/cyc-pep-6-12mer-70M_33.log new file mode 100644 index 0000000000000000000000000000000000000000..d614a231b60ba0ff6e78cd4b90c27583fb086a58 --- /dev/null +++ b/train/cyc-pep-6-12mer-70M_33.log @@ -0,0 +1,337 @@ ++ module purge ++ '[' -z '' ']' ++ case "$-" in ++ __lmod_sh_dbg=x ++ '[' -n x ']' ++ set +x +Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output +Shell debugging restarted ++ unset __lmod_sh_dbg ++ return 0 ++ module load Anaconda3/2023.03 ++ '[' -z '' ']' ++ case "$-" in ++ __lmod_sh_dbg=x ++ '[' -n x ']' ++ set +x +Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output +Shell debugging restarted ++ unset __lmod_sh_dbg ++ return 0 ++ source /camp/home/johnsoe/.bashrc +++ '[' '' = yes ']' +++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' ++++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.bash hook +++ __conda_setup='export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'' + +# Copyright (C) 2012 Anaconda, Inc +# SPDX-License-Identifier: BSD-3-Clause +__conda_exe() ( + "$CONDA_EXE" $_CE_M $_CE_CONDA "$@" +) + +__conda_hashr() { + if [ -n "${ZSH_VERSION:+x}" ]; then + \rehash + elif [ -n "${POSH_VERSION:+x}" ]; then + : # pass + else + \hash -r + fi +} + +__conda_activate() { + if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then + # Handle transition from shell activated with conda <= 4.3 to a subsequent activation + # after conda updated to >= 4.4. See issue #6173. + PS1="$CONDA_PS1_BACKUP" + \unset CONDA_PS1_BACKUP + fi + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return + \eval "$ask_conda" + __conda_hashr +} + +__conda_reactivate() { + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return + \eval "$ask_conda" + __conda_hashr +} + +conda() { + \local cmd="${1-__missing__}" + case "$cmd" in + activate|deactivate) + __conda_activate "$@" + ;; + install|update|upgrade|remove|uninstall) + __conda_exe "$@" || \return + __conda_reactivate + ;; + *) + __conda_exe "$@" + ;; + esac +} + +if [ -z "${CONDA_SHLVL+x}" ]; then + \export CONDA_SHLVL=0 + # In dev-mode CONDA_EXE is python.exe and on Windows + # it is in a different relative location to condabin. + if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then + PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}" + else + PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}" + fi + \export PATH + + # We'\''re not allowing PS1 to be unbound. It must at least be set. + # However, we'\''re not exporting it, which can cause problems when starting a second shell + # via a first shell (i.e. starting zsh from bash). + if [ -z "${PS1+x}" ]; then + PS1= + fi +fi + +conda activate base' +++ '[' 0 -eq 0 ']' +++ eval 'export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'' + +# Copyright (C) 2012 Anaconda, Inc +# SPDX-License-Identifier: BSD-3-Clause +__conda_exe() ( + "$CONDA_EXE" $_CE_M $_CE_CONDA "$@" +) + +__conda_hashr() { + if [ -n "${ZSH_VERSION:+x}" ]; then + \rehash + elif [ -n "${POSH_VERSION:+x}" ]; then + : # pass + else + \hash -r + fi +} + +__conda_activate() { + if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then + # Handle transition from shell activated with conda <= 4.3 to a subsequent activation + # after conda updated to >= 4.4. See issue #6173. + PS1="$CONDA_PS1_BACKUP" + \unset CONDA_PS1_BACKUP + fi + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return + \eval "$ask_conda" + __conda_hashr +} + +__conda_reactivate() { + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return + \eval "$ask_conda" + __conda_hashr +} + +conda() { + \local cmd="${1-__missing__}" + case "$cmd" in + activate|deactivate) + __conda_activate "$@" + ;; + install|update|upgrade|remove|uninstall) + __conda_exe "$@" || \return + __conda_reactivate + ;; + *) + __conda_exe "$@" + ;; + esac +} + +if [ -z "${CONDA_SHLVL+x}" ]; then + \export CONDA_SHLVL=0 + # In dev-mode CONDA_EXE is python.exe and on Windows + # it is in a different relative location to condabin. + if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then + PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}" + else + PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}" + fi + \export PATH + + # We'\''re not allowing PS1 to be unbound. It must at least be set. + # However, we'\''re not exporting it, which can cause problems when starting a second shell + # via a first shell (i.e. starting zsh from bash). + if [ -z "${PS1+x}" ]; then + PS1= + fi +fi + +conda activate base' ++++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda ++++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda ++++ export _CE_M= ++++ _CE_M= ++++ export _CE_CONDA= ++++ _CE_CONDA= ++++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ '[' -z x ']' ++++ conda activate base ++++ local cmd=activate ++++ case "$cmd" in ++++ __conda_activate activate base ++++ '[' -n '' ']' ++++ local ask_conda +++++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++++ __conda_exe shell.posix activate base +++++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate base ++++ ask_conda='PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_SHLVL='\''6'\'' +export CONDA_DEFAULT_ENV='\''base'\'' +export CONDA_PROMPT_MODIFIER='\''(base) '\'' +export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' ++++ eval 'PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_SHLVL='\''6'\'' +export CONDA_DEFAULT_ENV='\''base'\'' +export CONDA_PROMPT_MODIFIER='\''(base) '\'' +export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' +++++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++++ export CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0 +++++ CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0 +++++ export CONDA_SHLVL=6 +++++ CONDA_SHLVL=6 +++++ export CONDA_DEFAULT_ENV=base +++++ CONDA_DEFAULT_ENV=base +++++ export 'CONDA_PROMPT_MODIFIER=(base) ' +++++ CONDA_PROMPT_MODIFIER='(base) ' +++++ export CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev +++++ CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev +++++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++++ export _CE_M= +++++ _CE_M= +++++ export _CE_CONDA= +++++ _CE_CONDA= +++++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python +++++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ __conda_hashr ++++ '[' -n '' ']' ++++ '[' -n '' ']' ++++ hash -r +++ unset __conda_setup ++ conda activate schemist-dev ++ local cmd=activate ++ case "$cmd" in ++ __conda_activate activate schemist-dev ++ '[' -n '' ']' ++ local ask_conda +++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++ __conda_exe shell.posix activate schemist-dev +++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate schemist-dev ++ ask_conda='PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_SHLVL='\''7'\'' +export CONDA_DEFAULT_ENV='\''schemist-dev'\'' +export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\'' +export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' ++ eval 'PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_SHLVL='\''7'\'' +export CONDA_DEFAULT_ENV='\''schemist-dev'\'' +export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\'' +export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' +++ PS1='(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++ export CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev +++ CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev +++ export CONDA_SHLVL=7 +++ CONDA_SHLVL=7 +++ export CONDA_DEFAULT_ENV=schemist-dev +++ CONDA_DEFAULT_ENV=schemist-dev +++ export 'CONDA_PROMPT_MODIFIER=(schemist-dev) ' +++ CONDA_PROMPT_MODIFIER='(schemist-dev) ' +++ export CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0 +++ CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0 +++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++ export _CE_M= +++ _CE_M= +++ export _CE_CONDA= +++ _CE_CONDA= +++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python +++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++ __conda_hashr ++ '[' -n '' ']' ++ '[' -n '' ']' ++ hash -r ++ CHUNK_HEAD_FILE=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz ++ INPUT=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/train/cyc-pep-6-12mer-70M_33.csv ++ COLUMN=cysteine_to_N_cyclization ++ PREFIX=cyclic_ ++ AWK='1 { print $8, $1, $2, $10, $3 }' ++ '[' -z cysteine_to_N_cyclization ']' ++ '[' -z cyclic_ ']' ++ '[' -z '1 { print $8, $1, $2, $10, $3 }' ']' ++ cat /dev/fd/63 /nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/train/cyc-pep-6-12mer-70M_33.csv ++ schemist convert -f csv --column cysteine_to_N_cyclization --to id inchikey scaffold mwt clogp tpsa --prefix cyclic_ --options prefix=SCB- ++ awk -F, -v OFS=, '1 { print $8, $1, $2, $10, $3 }' ++ gzip --best +++ zcat /nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz +++ head -n1 +++ tr ' ' , +🚀 Converting between string representations with the following parameters: + subcommand: convert + output: <_io.TextIOWrapper name='' mode='w' encoding='utf-8'> + format: csv + input: <_io.TextIOWrapper name='' mode='r' encoding='utf-8'> + representation: SMILES + column: cysteine_to_N_cyclization + prefix: cyclic_ + to: ['id', 'inchikey', 'scaffold', 'mwt', 'clogp', 'tpsa'] + options: ['prefix=SCB-'] + func: + 0it [00:00, ?it/s] 1it [00:12, 12.01s/it] 2it [00:24, 12.20s/it] 3it [00:35, 11.53s/it] 4it [00:46, 11.47s/it] 5it [00:56, 11.06s/it] 6it 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[2:46:36, 8.80s/it] 976it [2:46:45, 8.79s/it] 977it [2:46:54, 8.78s/it] 978it [2:47:02, 8.77s/it] 979it [2:47:11, 8.75s/it] 980it [2:47:20, 8.73s/it] 981it [2:47:29, 8.76s/it] 982it [2:47:37, 8.75s/it] 983it [2:47:46, 8.74s/it] 984it [2:47:55, 8.73s/it] 985it [2:48:03, 8.73s/it] 986it [2:48:12, 8.73s/it] 987it [2:48:21, 8.74s/it] 988it [2:48:30, 8.74s/it] 989it [2:48:38, 8.75s/it] 990it [2:48:47, 8.74s/it] 991it [2:48:56, 8.73s/it] 992it [2:49:05, 8.71s/it] 993it [2:49:13, 8.70s/it] 994it [2:49:22, 8.69s/it] 995it [2:49:31, 8.70s/it] 996it [2:49:39, 8.70s/it] 997it [2:49:48, 8.70s/it] 998it [2:49:57, 8.70s/it] 999it [2:50:05, 8.70s/it] 1000it [2:50:14, 8.70s/it] 1000it [2:50:14, 10.21s/it] +Error counts: + cyclic_id: 0 + cyclic_inchikey: 0 + cyclic_scaffold: 0 + cyclic_mwt: 0 + cyclic_clogp: 0 + cyclic_tpsa: 0 +⏰ Completed process in 2:50:44.525887 ++ rm /nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/train/cyc-pep-6-12mer-70M_33.csv diff --git a/train/cyc-pep-6-12mer-70M_34.csv.gz b/train/cyc-pep-6-12mer-70M_34.csv.gz index d9c53f8bd00116b1586df56133540322d9bb3c48..fd6638bd833d1860a4fb8c4cc67ce4845bd645c3 100644 --- a/train/cyc-pep-6-12mer-70M_34.csv.gz +++ b/train/cyc-pep-6-12mer-70M_34.csv.gz @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:e19e60ee2b6d2987026aeb97c13ca8335a7f3fa83a8ae3a973555025513623f9 -size 50685626 +oid sha256:73662a6a368e602cd9dff1895b000c48f67b3337f076ae3c6a7091e9ef4c7a7f +size 102675674 diff --git a/train/cyc-pep-6-12mer-70M_34.log b/train/cyc-pep-6-12mer-70M_34.log new file mode 100644 index 0000000000000000000000000000000000000000..6010c3d6f65d7b7ad8c5004b1c620ef49f9faf75 --- /dev/null +++ b/train/cyc-pep-6-12mer-70M_34.log @@ -0,0 +1,337 @@ ++ module purge ++ '[' -z '' ']' ++ case "$-" in ++ __lmod_sh_dbg=x ++ '[' -n x ']' ++ set +x +Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output +Shell debugging restarted ++ unset __lmod_sh_dbg ++ return 0 ++ module load Anaconda3/2023.03 ++ '[' -z '' ']' ++ case "$-" in ++ __lmod_sh_dbg=x ++ '[' -n x ']' ++ set +x +Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output +Shell debugging restarted ++ unset __lmod_sh_dbg ++ return 0 ++ source /camp/home/johnsoe/.bashrc +++ '[' '' = yes ']' +++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' ++++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.bash hook +++ __conda_setup='export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'' + +# Copyright (C) 2012 Anaconda, Inc +# SPDX-License-Identifier: BSD-3-Clause +__conda_exe() ( + "$CONDA_EXE" $_CE_M $_CE_CONDA "$@" +) + +__conda_hashr() { + if [ -n "${ZSH_VERSION:+x}" ]; then + \rehash + elif [ -n "${POSH_VERSION:+x}" ]; then + : # pass + else + \hash -r + fi +} + +__conda_activate() { + if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then + # Handle transition from shell activated with conda <= 4.3 to a subsequent activation + # after conda updated to >= 4.4. See issue #6173. + PS1="$CONDA_PS1_BACKUP" + \unset CONDA_PS1_BACKUP + fi + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return + \eval "$ask_conda" + __conda_hashr +} + +__conda_reactivate() { + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return + \eval "$ask_conda" + __conda_hashr +} + +conda() { + \local cmd="${1-__missing__}" + case "$cmd" in + activate|deactivate) + __conda_activate "$@" + ;; + install|update|upgrade|remove|uninstall) + __conda_exe "$@" || \return + __conda_reactivate + ;; + *) + __conda_exe "$@" + ;; + esac +} + +if [ -z "${CONDA_SHLVL+x}" ]; then + \export CONDA_SHLVL=0 + # In dev-mode CONDA_EXE is python.exe and on Windows + # it is in a different relative location to condabin. + if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then + PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}" + else + PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}" + fi + \export PATH + + # We'\''re not allowing PS1 to be unbound. It must at least be set. + # However, we'\''re not exporting it, which can cause problems when starting a second shell + # via a first shell (i.e. starting zsh from bash). + if [ -z "${PS1+x}" ]; then + PS1= + fi +fi + +conda activate base' +++ '[' 0 -eq 0 ']' +++ eval 'export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'' + +# Copyright (C) 2012 Anaconda, Inc +# SPDX-License-Identifier: BSD-3-Clause +__conda_exe() ( + "$CONDA_EXE" $_CE_M $_CE_CONDA "$@" +) + +__conda_hashr() { + if [ -n "${ZSH_VERSION:+x}" ]; then + \rehash + elif [ -n "${POSH_VERSION:+x}" ]; then + : # pass + else + \hash -r + fi +} + +__conda_activate() { + if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then + # Handle transition from shell activated with conda <= 4.3 to a subsequent activation + # after conda updated to >= 4.4. See issue #6173. + PS1="$CONDA_PS1_BACKUP" + \unset CONDA_PS1_BACKUP + fi + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return + \eval "$ask_conda" + __conda_hashr +} + +__conda_reactivate() { + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return + \eval "$ask_conda" + __conda_hashr +} + +conda() { + \local cmd="${1-__missing__}" + case "$cmd" in + activate|deactivate) + __conda_activate "$@" + ;; + install|update|upgrade|remove|uninstall) + __conda_exe "$@" || \return + __conda_reactivate + ;; + *) + __conda_exe "$@" + ;; + esac +} + +if [ -z "${CONDA_SHLVL+x}" ]; then + \export CONDA_SHLVL=0 + # In dev-mode CONDA_EXE is python.exe and on Windows + # it is in a different relative location to condabin. + if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then + PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}" + else + PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}" + fi + \export PATH + + # We'\''re not allowing PS1 to be unbound. It must at least be set. + # However, we'\''re not exporting it, which can cause problems when starting a second shell + # via a first shell (i.e. starting zsh from bash). + if [ -z "${PS1+x}" ]; then + PS1= + fi +fi + +conda activate base' ++++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda ++++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda ++++ export _CE_M= ++++ _CE_M= ++++ export _CE_CONDA= ++++ _CE_CONDA= ++++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ '[' -z x ']' ++++ conda activate base ++++ local cmd=activate ++++ case "$cmd" in ++++ __conda_activate activate base ++++ '[' -n '' ']' ++++ local ask_conda +++++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++++ __conda_exe shell.posix activate base +++++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate base ++++ ask_conda='PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_SHLVL='\''6'\'' +export CONDA_DEFAULT_ENV='\''base'\'' +export CONDA_PROMPT_MODIFIER='\''(base) '\'' +export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' ++++ eval 'PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_SHLVL='\''6'\'' +export CONDA_DEFAULT_ENV='\''base'\'' +export CONDA_PROMPT_MODIFIER='\''(base) '\'' +export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' +++++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++++ export CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0 +++++ CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0 +++++ export CONDA_SHLVL=6 +++++ CONDA_SHLVL=6 +++++ export CONDA_DEFAULT_ENV=base +++++ CONDA_DEFAULT_ENV=base +++++ export 'CONDA_PROMPT_MODIFIER=(base) ' +++++ CONDA_PROMPT_MODIFIER='(base) ' +++++ export CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev +++++ CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev +++++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++++ export _CE_M= +++++ _CE_M= +++++ export _CE_CONDA= +++++ _CE_CONDA= +++++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python +++++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ __conda_hashr ++++ '[' -n '' ']' ++++ '[' -n '' ']' ++++ hash -r +++ unset __conda_setup ++ conda activate schemist-dev ++ local cmd=activate ++ case "$cmd" in ++ __conda_activate activate schemist-dev ++ '[' -n '' ']' ++ local ask_conda +++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++ __conda_exe shell.posix activate schemist-dev +++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate schemist-dev ++ ask_conda='PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_SHLVL='\''7'\'' +export CONDA_DEFAULT_ENV='\''schemist-dev'\'' +export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\'' +export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' ++ eval 'PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_SHLVL='\''7'\'' +export CONDA_DEFAULT_ENV='\''schemist-dev'\'' +export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\'' +export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' +++ PS1='(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++ export CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev +++ CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev +++ export CONDA_SHLVL=7 +++ CONDA_SHLVL=7 +++ export CONDA_DEFAULT_ENV=schemist-dev +++ CONDA_DEFAULT_ENV=schemist-dev +++ export 'CONDA_PROMPT_MODIFIER=(schemist-dev) ' +++ CONDA_PROMPT_MODIFIER='(schemist-dev) ' +++ export CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0 +++ CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0 +++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++ export _CE_M= +++ _CE_M= +++ export _CE_CONDA= +++ _CE_CONDA= +++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python +++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++ __conda_hashr ++ '[' -n '' ']' ++ '[' -n '' ']' ++ hash -r ++ CHUNK_HEAD_FILE=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz ++ INPUT=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/train/cyc-pep-6-12mer-70M_34.csv ++ COLUMN=cysteine_to_N_cyclization ++ PREFIX=cyclic_ ++ AWK='1 { print $8, $1, $2, $10, $3 }' ++ '[' -z cysteine_to_N_cyclization ']' ++ '[' -z cyclic_ ']' ++ '[' -z '1 { print $8, $1, $2, $10, $3 }' ']' ++ cat /dev/fd/63 /nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/train/cyc-pep-6-12mer-70M_34.csv ++ awk -F, -v OFS=, '1 { print $8, $1, $2, $10, $3 }' ++ gzip --best ++ schemist convert -f csv --column cysteine_to_N_cyclization --to id inchikey scaffold mwt clogp tpsa --prefix cyclic_ --options prefix=SCB- +++ head -n1 +++ zcat /nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz +++ tr ' ' , +🚀 Converting between string representations with the following parameters: + subcommand: convert + output: <_io.TextIOWrapper name='' mode='w' encoding='utf-8'> + format: csv + input: <_io.TextIOWrapper name='' mode='r' encoding='utf-8'> + representation: SMILES + column: cysteine_to_N_cyclization + prefix: cyclic_ + to: ['id', 'inchikey', 'scaffold', 'mwt', 'clogp', 'tpsa'] + options: ['prefix=SCB-'] + func: + 0it [00:00, ?it/s] 1it [00:09, 9.80s/it] 2it [00:19, 9.69s/it] 3it [00:29, 9.68s/it] 4it [00:38, 9.63s/it] 5it [00:48, 9.62s/it] 6it [00:57, 9.55s/it] 7it [01:07, 9.57s/it] 8it [01:16, 9.57s/it] 9it [01:26, 9.58s/it] 10it [01:36, 9.60s/it] 11it [01:45, 9.65s/it] 12it [01:55, 9.63s/it] 13it [02:04, 9.58s/it] 14it [02:14, 9.59s/it] 15it [02:24, 9.63s/it] 16it [02:33, 9.67s/it] 17it [02:43, 9.72s/it] 18it [02:53, 9.83s/it] 19it [03:03, 9.87s/it] 20it [03:13, 9.83s/it] 21it [03:23, 9.72s/it] 22it [03:32, 9.70s/it] 23it [03:42, 9.67s/it] 24it [03:51, 9.65s/it] 25it [04:01, 9.67s/it] 26it [04:11, 9.66s/it] 27it [04:20, 9.62s/it] 28it [04:30, 9.60s/it] 29it [04:40, 9.63s/it] 30it [04:49, 9.70s/it] 31it [04:59, 9.79s/it] 32it [05:10, 9.94s/it] 33it [05:20, 10.07s/it] 34it [05:30, 10.08s/it] 35it [05:40, 10.01s/it] 36it [05:50, 9.88s/it] 37it [05:59, 9.82s/it] 38it [06:09, 9.80s/it] 39it [06:19, 9.83s/it] 40it [06:29, 9.80s/it] 41it [06:39, 9.90s/it] 42it [06:49, 9.88s/it] 43it [06:59, 9.91s/it] 44it [07:08, 9.89s/it] 45it [07:18, 9.81s/it] 46it [07:28, 9.73s/it] 47it [07:38, 9.84s/it] 48it [07:48, 9.89s/it] 49it [07:58, 9.88s/it] 50it [08:08, 9.89s/it] 51it [08:17, 9.89s/it] 52it [08:27, 9.85s/it] 53it [08:37, 9.72s/it] 54it [08:47, 10.05s/it] 55it [08:57, 10.06s/it] 56it [09:07, 10.03s/it] 57it [09:17, 10.02s/it] 58it [09:28, 10.05s/it] 59it [09:38, 10.07s/it] 60it [09:48, 10.06s/it] 61it [09:58, 10.03s/it] 62it [10:07, 9.94s/it] 63it [10:17, 9.86s/it] 64it [10:27, 9.80s/it] 65it [10:37, 9.83s/it] 66it [10:46, 9.85s/it] 67it [10:57, 10.05s/it] 68it [11:07, 10.16s/it] 69it [11:17, 10.10s/it] 70it [11:27, 10.01s/it] 71it [11:37, 9.96s/it] 72it [11:47, 10.01s/it] 73it [11:58, 10.13s/it] 74it [12:08, 10.25s/it] 75it [12:18, 10.22s/it] 76it [12:28, 10.15s/it] 77it [12:38, 10.05s/it] 78it [12:48, 9.93s/it] 79it [12:58, 10.00s/it] 80it [13:09, 10.20s/it] 81it [13:19, 10.33s/it] 82it [13:29, 10.28s/it] 83it [13:39, 10.23s/it] 84it [13:49, 10.13s/it] 85it [13:59, 10.01s/it] 86it [14:09, 9.94s/it] 87it [14:19, 9.96s/it] 88it [14:29, 9.98s/it] 89it [14:39, 10.04s/it] 90it [14:49, 10.14s/it] 91it [15:00, 10.19s/it] 92it [15:10, 10.26s/it] 93it [15:20, 10.24s/it] 94it [15:31, 10.22s/it] 95it [15:40, 10.12s/it] 96it [15:50, 10.05s/it] 97it [16:00, 9.95s/it] 98it [16:10, 9.90s/it] 99it [16:20, 9.93s/it] 100it [16:30, 10.00s/it] 101it [16:40, 10.02s/it] 102it [16:50, 9.92s/it] 103it [16:59, 9.88s/it] 104it [17:09, 9.90s/it] 105it [17:19, 9.86s/it] 106it [17:29, 9.96s/it] 107it [17:39, 9.94s/it] 108it [17:49, 9.91s/it] 109it [17:59, 9.86s/it] 110it [18:09, 9.85s/it] 111it [18:18, 9.83s/it] 112it [18:28, 9.83s/it] 113it [18:38, 9.79s/it] 114it [18:48, 9.84s/it] 115it [18:58, 9.84s/it] 116it [19:07, 9.78s/it] 117it [19:18, 9.89s/it] 118it [19:28, 10.13s/it] 119it [19:38, 10.10s/it] 120it [19:48, 9.98s/it] 121it [19:58, 9.89s/it] 122it [20:07, 9.86s/it] 123it [20:17, 9.90s/it] 124it [20:27, 9.91s/it] 125it [20:38, 9.98s/it] 126it [20:48, 10.00s/it] 127it [20:58, 10.04s/it] 128it [21:08, 10.13s/it] 129it [21:18, 10.09s/it] 130it [21:28, 10.03s/it] 131it [21:38, 9.96s/it] 132it [21:48, 10.12s/it] 133it [21:58, 10.06s/it] 134it [22:08, 10.04s/it] 135it [22:18, 10.04s/it] 136it [22:29, 10.14s/it] 137it [22:39, 10.17s/it] 138it [22:49, 10.10s/it] 139it [22:59, 10.02s/it] 140it [23:09, 10.02s/it] 141it [23:19, 10.02s/it] 142it [23:29, 10.04s/it] 143it [23:38, 9.96s/it] 144it [23:48, 9.91s/it] 145it [23:58, 9.96s/it] 146it [24:09, 10.10s/it] 147it [24:20, 10.34s/it] 148it [24:31, 10.54s/it] 149it [24:41, 10.56s/it] 150it [24:52, 10.65s/it] 151it [25:03, 10.62s/it] 152it [25:13, 10.57s/it] 153it [25:23, 10.45s/it] 154it [25:33, 10.32s/it] 155it [25:44, 10.34s/it] 156it [25:54, 10.42s/it] 157it [26:05, 10.42s/it] 158it [26:15, 10.46s/it] 159it [26:26, 10.44s/it] 160it [26:37, 10.60s/it] 161it [26:47, 10.58s/it] 162it [26:57, 10.43s/it] 163it [27:07, 10.22s/it] 164it [27:17, 10.12s/it] 165it [27:27, 10.16s/it] 166it [27:37, 10.15s/it] 167it [27:47, 10.10s/it] 168it [27:57, 10.07s/it] 169it [28:08, 10.14s/it] 170it [28:18, 10.15s/it] 171it [28:27, 10.02s/it] 172it [28:37, 9.92s/it] 173it [28:47, 9.85s/it] 174it [28:57, 9.80s/it] 175it [29:07, 9.92s/it] 176it [29:17, 9.91s/it] 177it [29:26, 9.89s/it] 178it [29:36, 9.87s/it] 179it [29:46, 9.82s/it] 180it [29:56, 9.79s/it] 181it [30:05, 9.77s/it] 182it [30:15, 9.75s/it] 183it [30:25, 9.76s/it] 184it [30:35, 9.80s/it] 185it [30:45, 9.78s/it] 186it [30:54, 9.81s/it] 187it [31:04, 9.86s/it] 188it [31:14, 9.93s/it] 189it [31:25, 9.97s/it] 190it [31:34, 9.93s/it] 191it [31:44, 9.86s/it] 192it [31:54, 9.82s/it] 193it [32:03, 9.77s/it] 194it [32:13, 9.66s/it] 195it [32:22, 9.58s/it] 196it [32:32, 9.61s/it] 197it [32:42, 9.70s/it] 198it [32:52, 9.72s/it] 199it [33:01, 9.74s/it] 200it [33:11, 9.70s/it] 201it [33:21, 9.66s/it] 202it [33:30, 9.56s/it] 203it [33:39, 9.53s/it] 204it [33:50, 9.75s/it] 205it [34:00, 9.80s/it] 206it [34:09, 9.83s/it] 207it [34:19, 9.81s/it] 208it [34:29, 9.73s/it] 209it [34:38, 9.64s/it] 210it [34:49, 9.90s/it] 211it [34:59, 9.92s/it] 212it [35:09, 9.92s/it] 213it [35:18, 9.89s/it] 214it [35:29, 9.99s/it] 215it [35:38, 9.95s/it] 216it [35:48, 9.91s/it] 217it [35:58, 9.92s/it] 218it [36:08, 9.93s/it] 219it [36:18, 10.02s/it] 220it [36:28, 9.99s/it] 221it [36:38, 9.89s/it] 222it [36:48, 9.85s/it] 223it [36:57, 9.72s/it] 224it [37:07, 9.70s/it] 225it [37:17, 9.82s/it] 226it [37:27, 9.90s/it] 227it [37:37, 9.89s/it] 228it [37:46, 9.81s/it] 229it [37:56, 9.74s/it] 230it [38:06, 9.66s/it] 231it [38:16, 9.83s/it] 232it [38:26, 9.90s/it] 233it [38:35, 9.81s/it] 234it [38:46, 9.96s/it] 235it [38:56, 10.05s/it] 236it [39:06, 10.05s/it] 237it [39:16, 10.00s/it] 238it [39:26, 9.94s/it] 239it [39:36, 10.00s/it] 240it [39:46, 10.11s/it] 241it [39:56, 10.15s/it] 242it [40:07, 10.15s/it] 243it [40:17, 10.11s/it] 244it [40:27, 10.09s/it] 245it [40:37, 10.04s/it] 246it [40:47, 10.08s/it] 247it [40:57, 10.21s/it] 248it [41:08, 10.28s/it] 249it [41:18, 10.33s/it] 250it [41:28, 10.23s/it] 251it [41:38, 10.04s/it] 252it [41:48, 10.00s/it] 253it [41:58, 10.01s/it] 254it [42:08, 10.14s/it] 255it [42:19, 10.26s/it] 256it [42:29, 10.25s/it] 257it [42:39, 10.25s/it] 258it [42:49, 10.12s/it] 259it [42:59, 10.04s/it] 260it [43:09, 9.96s/it] 261it [43:19, 10.13s/it] 262it [43:30, 10.32s/it] 263it [43:40, 10.34s/it] 264it [43:50, 10.29s/it] 265it [44:00, 10.15s/it] 266it [44:10, 10.04s/it] 267it [44:20, 9.93s/it] 268it [44:30, 9.99s/it] 269it [44:40, 10.14s/it] 270it [44:51, 10.17s/it] 271it [45:00, 10.04s/it] 272it [45:10, 10.02s/it] 273it [45:20, 9.96s/it] 274it [45:30, 9.84s/it] 275it [45:40, 9.85s/it] 276it [45:50, 9.99s/it] 277it [46:00, 10.02s/it] 278it [46:10, 10.02s/it] 279it [46:20, 10.01s/it] 280it [46:30, 9.97s/it] 281it [46:40, 9.93s/it] 282it [46:50, 10.00s/it] 283it [47:00, 10.14s/it] 284it [47:11, 10.21s/it] 285it [47:21, 10.19s/it] 286it [47:31, 10.21s/it] 287it [47:41, 10.15s/it] 288it [47:51, 10.08s/it] 289it [48:01, 10.08s/it] 290it [48:11, 10.11s/it] 291it [48:22, 10.17s/it] 292it [48:32, 10.17s/it] 293it [48:42, 10.13s/it] 294it [48:52, 10.11s/it] 295it 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979it [2:41:29, 9.18s/it] 980it [2:41:38, 9.19s/it] 981it [2:41:47, 9.21s/it] 982it [2:41:57, 9.21s/it] 983it [2:42:06, 9.17s/it] 984it [2:42:15, 9.13s/it] 985it [2:42:24, 9.13s/it] 986it [2:42:33, 9.14s/it] 987it [2:42:42, 9.13s/it] 988it [2:42:51, 9.15s/it] 989it [2:43:00, 9.14s/it] 990it [2:43:10, 9.14s/it] 991it [2:43:19, 9.10s/it] 992it [2:43:28, 9.11s/it] 993it [2:43:37, 9.16s/it] 994it [2:43:46, 9.15s/it] 995it [2:43:55, 9.18s/it] 996it [2:44:04, 9.14s/it] 997it [2:44:13, 9.12s/it] 998it [2:44:23, 9.11s/it] 999it [2:44:32, 9.12s/it] 1000it [2:44:41, 9.14s/it] 1000it [2:44:41, 9.88s/it] +Error counts: + cyclic_id: 0 + cyclic_inchikey: 0 + cyclic_scaffold: 0 + cyclic_mwt: 0 + cyclic_clogp: 0 + cyclic_tpsa: 0 +⏰ Completed process in 2:45:02.766384 ++ rm /nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/train/cyc-pep-6-12mer-70M_34.csv diff --git a/train/cyc-pep-6-12mer-70M_35.csv.gz b/train/cyc-pep-6-12mer-70M_35.csv.gz index f2eaa5474bc41159b9d681038b0a3f24a93331dc..27143a5f0165dfec2209f663fd3ed1f1eca3e8c8 100644 --- a/train/cyc-pep-6-12mer-70M_35.csv.gz +++ b/train/cyc-pep-6-12mer-70M_35.csv.gz @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:1bafab4406830037f1635f65b943df2043bdb06219ed7c295e43841f844e64e5 -size 50681991 +oid sha256:a00bf6e668d6cb296ff77daf2e8a8d5d7043b2869185cd4a9cc3876c26b9e4a3 +size 102667168 diff --git a/train/cyc-pep-6-12mer-70M_35.log b/train/cyc-pep-6-12mer-70M_35.log new file mode 100644 index 0000000000000000000000000000000000000000..59617e77f9ad1d48f27f12e1010ad629de1593f6 --- /dev/null +++ b/train/cyc-pep-6-12mer-70M_35.log @@ -0,0 +1,337 @@ ++ module purge ++ '[' -z '' ']' ++ case "$-" in ++ __lmod_sh_dbg=x ++ '[' -n x ']' ++ set +x +Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output +Shell debugging restarted ++ unset __lmod_sh_dbg ++ return 0 ++ module load Anaconda3/2023.03 ++ '[' -z '' ']' ++ case "$-" in ++ __lmod_sh_dbg=x ++ '[' -n x ']' ++ set +x +Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output +Shell debugging restarted ++ unset __lmod_sh_dbg ++ return 0 ++ source /camp/home/johnsoe/.bashrc +++ '[' '' = yes ']' +++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' ++++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.bash hook +++ __conda_setup='export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'' + +# Copyright (C) 2012 Anaconda, Inc +# SPDX-License-Identifier: BSD-3-Clause +__conda_exe() ( + "$CONDA_EXE" $_CE_M $_CE_CONDA "$@" +) + +__conda_hashr() { + if [ -n "${ZSH_VERSION:+x}" ]; then + \rehash + elif [ -n "${POSH_VERSION:+x}" ]; then + : # pass + else + \hash -r + fi +} + +__conda_activate() { + if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then + # Handle transition from shell activated with conda <= 4.3 to a subsequent activation + # after conda updated to >= 4.4. See issue #6173. + PS1="$CONDA_PS1_BACKUP" + \unset CONDA_PS1_BACKUP + fi + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return + \eval "$ask_conda" + __conda_hashr +} + +__conda_reactivate() { + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return + \eval "$ask_conda" + __conda_hashr +} + +conda() { + \local cmd="${1-__missing__}" + case "$cmd" in + activate|deactivate) + __conda_activate "$@" + ;; + install|update|upgrade|remove|uninstall) + __conda_exe "$@" || \return + __conda_reactivate + ;; + *) + __conda_exe "$@" + ;; + esac +} + +if [ -z "${CONDA_SHLVL+x}" ]; then + \export CONDA_SHLVL=0 + # In dev-mode CONDA_EXE is python.exe and on Windows + # it is in a different relative location to condabin. + if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then + PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}" + else + PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}" + fi + \export PATH + + # We'\''re not allowing PS1 to be unbound. It must at least be set. + # However, we'\''re not exporting it, which can cause problems when starting a second shell + # via a first shell (i.e. starting zsh from bash). + if [ -z "${PS1+x}" ]; then + PS1= + fi +fi + +conda activate base' +++ '[' 0 -eq 0 ']' +++ eval 'export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'' + +# Copyright (C) 2012 Anaconda, Inc +# SPDX-License-Identifier: BSD-3-Clause +__conda_exe() ( + "$CONDA_EXE" $_CE_M $_CE_CONDA "$@" +) + +__conda_hashr() { + if [ -n "${ZSH_VERSION:+x}" ]; then + \rehash + elif [ -n "${POSH_VERSION:+x}" ]; then + : # pass + else + \hash -r + fi +} + +__conda_activate() { + if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then + # Handle transition from shell activated with conda <= 4.3 to a subsequent activation + # after conda updated to >= 4.4. See issue #6173. + PS1="$CONDA_PS1_BACKUP" + \unset CONDA_PS1_BACKUP + fi + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return + \eval "$ask_conda" + __conda_hashr +} + +__conda_reactivate() { + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return + \eval "$ask_conda" + __conda_hashr +} + +conda() { + \local cmd="${1-__missing__}" + case "$cmd" in + activate|deactivate) + __conda_activate "$@" + ;; + install|update|upgrade|remove|uninstall) + __conda_exe "$@" || \return + __conda_reactivate + ;; + *) + __conda_exe "$@" + ;; + esac +} + +if [ -z "${CONDA_SHLVL+x}" ]; then + \export CONDA_SHLVL=0 + # In dev-mode CONDA_EXE is python.exe and on Windows + # it is in a different relative location to condabin. + if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then + PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}" + else + PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}" + fi + \export PATH + + # We'\''re not allowing PS1 to be unbound. It must at least be set. + # However, we'\''re not exporting it, which can cause problems when starting a second shell + # via a first shell (i.e. starting zsh from bash). + if [ -z "${PS1+x}" ]; then + PS1= + fi +fi + +conda activate base' ++++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda ++++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda ++++ export _CE_M= ++++ _CE_M= ++++ export _CE_CONDA= ++++ _CE_CONDA= ++++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ '[' -z x ']' ++++ conda activate base ++++ local cmd=activate ++++ case "$cmd" in ++++ __conda_activate activate base ++++ '[' -n '' ']' ++++ local ask_conda +++++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++++ __conda_exe shell.posix activate base +++++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate base ++++ ask_conda='PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_SHLVL='\''6'\'' +export CONDA_DEFAULT_ENV='\''base'\'' +export CONDA_PROMPT_MODIFIER='\''(base) '\'' +export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' ++++ eval 'PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_SHLVL='\''6'\'' +export CONDA_DEFAULT_ENV='\''base'\'' +export CONDA_PROMPT_MODIFIER='\''(base) '\'' +export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' +++++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++++ export CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0 +++++ CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0 +++++ export CONDA_SHLVL=6 +++++ CONDA_SHLVL=6 +++++ export CONDA_DEFAULT_ENV=base +++++ CONDA_DEFAULT_ENV=base +++++ export 'CONDA_PROMPT_MODIFIER=(base) ' +++++ CONDA_PROMPT_MODIFIER='(base) ' +++++ export CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev +++++ CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev +++++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++++ export _CE_M= +++++ _CE_M= +++++ export _CE_CONDA= +++++ _CE_CONDA= +++++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python +++++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ __conda_hashr ++++ '[' -n '' ']' ++++ '[' -n '' ']' ++++ hash -r +++ unset __conda_setup ++ conda activate schemist-dev ++ local cmd=activate ++ case "$cmd" in ++ __conda_activate activate schemist-dev ++ '[' -n '' ']' ++ local ask_conda +++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++ __conda_exe shell.posix activate schemist-dev +++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate schemist-dev ++ ask_conda='PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_SHLVL='\''7'\'' +export CONDA_DEFAULT_ENV='\''schemist-dev'\'' +export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\'' +export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' ++ eval 'PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_SHLVL='\''7'\'' +export CONDA_DEFAULT_ENV='\''schemist-dev'\'' +export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\'' +export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' +++ PS1='(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++ export CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev +++ CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev +++ export CONDA_SHLVL=7 +++ CONDA_SHLVL=7 +++ export CONDA_DEFAULT_ENV=schemist-dev +++ CONDA_DEFAULT_ENV=schemist-dev +++ export 'CONDA_PROMPT_MODIFIER=(schemist-dev) ' +++ CONDA_PROMPT_MODIFIER='(schemist-dev) ' +++ export CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0 +++ CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0 +++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++ export _CE_M= +++ _CE_M= +++ export _CE_CONDA= +++ _CE_CONDA= +++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python +++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++ __conda_hashr ++ '[' -n '' ']' ++ '[' -n '' ']' ++ hash -r ++ CHUNK_HEAD_FILE=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz ++ INPUT=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/train/cyc-pep-6-12mer-70M_35.csv ++ COLUMN=cysteine_to_N_cyclization ++ PREFIX=cyclic_ ++ AWK='1 { print $8, $1, $2, $10, $3 }' ++ '[' -z cysteine_to_N_cyclization ']' ++ '[' -z cyclic_ ']' ++ '[' -z '1 { print $8, $1, $2, $10, $3 }' ']' ++ cat /dev/fd/63 /nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/train/cyc-pep-6-12mer-70M_35.csv ++ schemist convert -f csv --column cysteine_to_N_cyclization --to id inchikey scaffold mwt clogp tpsa --prefix cyclic_ --options prefix=SCB- ++ gzip --best ++ awk -F, -v OFS=, '1 { print $8, $1, $2, $10, $3 }' +++ head -n1 +++ tr ' ' , +++ zcat /nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz +🚀 Converting between string representations with the following parameters: + subcommand: convert + output: <_io.TextIOWrapper name='' mode='w' encoding='utf-8'> + format: csv + input: <_io.TextIOWrapper name='' mode='r' encoding='utf-8'> + representation: SMILES + column: cysteine_to_N_cyclization + prefix: cyclic_ + to: ['id', 'inchikey', 'scaffold', 'mwt', 'clogp', 'tpsa'] + options: ['prefix=SCB-'] + func: + 0it [00:00, ?it/s] 1it [00:09, 9.34s/it] 2it [00:18, 9.22s/it] 3it [00:27, 9.20s/it] 4it [00:36, 9.22s/it] 5it [00:45, 9.17s/it] 6it 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9.01s/it] 922it [2:22:53, 9.03s/it] 923it [2:23:02, 9.00s/it] 924it [2:23:11, 8.97s/it] 925it [2:23:20, 8.98s/it] 926it [2:23:29, 9.00s/it] 927it [2:23:38, 9.02s/it] 928it [2:23:47, 9.03s/it] 929it [2:23:56, 9.02s/it] 930it [2:24:05, 9.00s/it] 931it [2:24:14, 8.97s/it] 932it [2:24:23, 8.99s/it] 933it [2:24:32, 9.01s/it] 934it [2:24:41, 9.02s/it] 935it [2:24:50, 9.03s/it] 936it [2:24:59, 8.98s/it] 937it [2:25:08, 8.95s/it] 938it [2:25:17, 8.96s/it] 939it [2:25:26, 9.00s/it] 940it [2:25:35, 9.01s/it] 941it [2:25:44, 8.99s/it] 942it [2:25:53, 8.98s/it] 943it [2:26:02, 8.94s/it] 944it [2:26:11, 8.93s/it] 945it [2:26:20, 8.97s/it] 946it [2:26:29, 8.99s/it] 947it [2:26:38, 9.03s/it] 948it [2:26:47, 8.99s/it] 949it [2:26:56, 8.98s/it] 950it [2:27:05, 8.96s/it] 951it [2:27:14, 8.96s/it] 952it [2:27:23, 8.97s/it] 953it [2:27:32, 9.02s/it] 954it [2:27:41, 9.00s/it] 955it [2:27:50, 9.01s/it] 956it [2:27:59, 8.97s/it] 957it [2:28:08, 8.97s/it] 958it [2:28:16, 8.96s/it] 959it [2:28:26, 9.00s/it] 960it [2:28:35, 9.00s/it] 961it [2:28:43, 8.98s/it] 962it [2:28:52, 8.97s/it] 963it [2:29:01, 8.99s/it] 964it [2:29:10, 9.00s/it] 965it [2:29:20, 9.01s/it] 966it [2:29:29, 9.00s/it] 967it [2:29:37, 8.99s/it] 968it [2:29:46, 8.94s/it] 969it [2:29:55, 8.92s/it] 970it [2:30:04, 8.92s/it] 971it [2:30:13, 8.94s/it] 972it [2:30:22, 8.97s/it] 973it [2:30:31, 8.97s/it] 974it [2:30:40, 8.96s/it] 975it [2:30:49, 8.94s/it] 976it [2:30:58, 8.90s/it] 977it [2:31:07, 8.91s/it] 978it [2:31:16, 8.93s/it] 979it [2:31:25, 8.97s/it] 980it [2:31:34, 8.96s/it] 981it [2:31:43, 8.95s/it] 982it [2:31:51, 8.94s/it] 983it [2:32:00, 8.92s/it] 984it [2:32:09, 8.93s/it] 985it [2:32:18, 8.93s/it] 986it [2:32:27, 8.93s/it] 987it [2:32:36, 8.96s/it] 988it [2:32:45, 8.96s/it] 989it [2:32:54, 8.96s/it] 990it [2:33:03, 8.95s/it] 991it [2:33:12, 8.94s/it] 992it [2:33:21, 8.96s/it] 993it [2:33:30, 8.92s/it] 994it [2:33:39, 8.89s/it] 995it [2:33:47, 8.87s/it] 996it [2:33:56, 8.86s/it] 997it [2:34:05, 8.86s/it] 998it [2:34:14, 8.86s/it] 999it [2:34:23, 8.86s/it] 1000it [2:34:32, 8.86s/it] 1000it [2:34:32, 9.27s/it] +Error counts: + cyclic_id: 0 + cyclic_inchikey: 0 + cyclic_scaffold: 0 + cyclic_mwt: 0 + cyclic_clogp: 0 + cyclic_tpsa: 0 +⏰ Completed process in 2:34:53.179210 ++ rm /nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/train/cyc-pep-6-12mer-70M_35.csv diff --git a/train/cyc-pep-6-12mer-70M_36.csv.gz b/train/cyc-pep-6-12mer-70M_36.csv.gz index fc8d073c823d6e44816cce41931b05d93148353a..444c678043e96add66d2def8b5406b044db776ad 100644 --- a/train/cyc-pep-6-12mer-70M_36.csv.gz +++ b/train/cyc-pep-6-12mer-70M_36.csv.gz @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:8cf7e67cd32595ede0e864fa3809558ff2754be27b52027449ef55750f5e733a -size 50682051 +oid sha256:0f180dc6c131c6160bec8788b2353e4919390372187675bb4d55b449458ef9ac +size 102679596 diff --git a/train/cyc-pep-6-12mer-70M_36.log b/train/cyc-pep-6-12mer-70M_36.log new file mode 100644 index 0000000000000000000000000000000000000000..a3b45c768ef179613edf1f96701843c3f08dcb06 --- /dev/null +++ b/train/cyc-pep-6-12mer-70M_36.log @@ -0,0 +1,337 @@ ++ module purge ++ '[' -z '' ']' ++ case "$-" in ++ __lmod_sh_dbg=x ++ '[' -n x ']' ++ set +x +Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output +Shell debugging restarted ++ unset __lmod_sh_dbg ++ return 0 ++ module load Anaconda3/2023.03 ++ '[' -z '' ']' ++ case "$-" in ++ __lmod_sh_dbg=x ++ '[' -n x ']' ++ set +x +Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output +Shell debugging restarted ++ unset __lmod_sh_dbg ++ return 0 ++ source /camp/home/johnsoe/.bashrc +++ '[' '' = yes ']' +++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' ++++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.bash hook +++ __conda_setup='export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'' + +# Copyright (C) 2012 Anaconda, Inc +# SPDX-License-Identifier: BSD-3-Clause +__conda_exe() ( + "$CONDA_EXE" $_CE_M $_CE_CONDA "$@" +) + +__conda_hashr() { + if [ -n "${ZSH_VERSION:+x}" ]; then + \rehash + elif [ -n "${POSH_VERSION:+x}" ]; then + : # pass + else + \hash -r + fi +} + +__conda_activate() { + if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then + # Handle transition from shell activated with conda <= 4.3 to a subsequent activation + # after conda updated to >= 4.4. See issue #6173. + PS1="$CONDA_PS1_BACKUP" + \unset CONDA_PS1_BACKUP + fi + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return + \eval "$ask_conda" + __conda_hashr +} + +__conda_reactivate() { + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return + \eval "$ask_conda" + __conda_hashr +} + +conda() { + \local cmd="${1-__missing__}" + case "$cmd" in + activate|deactivate) + __conda_activate "$@" + ;; + install|update|upgrade|remove|uninstall) + __conda_exe "$@" || \return + __conda_reactivate + ;; + *) + __conda_exe "$@" + ;; + esac +} + +if [ -z "${CONDA_SHLVL+x}" ]; then + \export CONDA_SHLVL=0 + # In dev-mode CONDA_EXE is python.exe and on Windows + # it is in a different relative location to condabin. + if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then + PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}" + else + PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}" + fi + \export PATH + + # We'\''re not allowing PS1 to be unbound. It must at least be set. + # However, we'\''re not exporting it, which can cause problems when starting a second shell + # via a first shell (i.e. starting zsh from bash). + if [ -z "${PS1+x}" ]; then + PS1= + fi +fi + +conda activate base' +++ '[' 0 -eq 0 ']' +++ eval 'export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'' + +# Copyright (C) 2012 Anaconda, Inc +# SPDX-License-Identifier: BSD-3-Clause +__conda_exe() ( + "$CONDA_EXE" $_CE_M $_CE_CONDA "$@" +) + +__conda_hashr() { + if [ -n "${ZSH_VERSION:+x}" ]; then + \rehash + elif [ -n "${POSH_VERSION:+x}" ]; then + : # pass + else + \hash -r + fi +} + +__conda_activate() { + if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then + # Handle transition from shell activated with conda <= 4.3 to a subsequent activation + # after conda updated to >= 4.4. See issue #6173. + PS1="$CONDA_PS1_BACKUP" + \unset CONDA_PS1_BACKUP + fi + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return + \eval "$ask_conda" + __conda_hashr +} + +__conda_reactivate() { + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return + \eval "$ask_conda" + __conda_hashr +} + +conda() { + \local cmd="${1-__missing__}" + case "$cmd" in + activate|deactivate) + __conda_activate "$@" + ;; + install|update|upgrade|remove|uninstall) + __conda_exe "$@" || \return + __conda_reactivate + ;; + *) + __conda_exe "$@" + ;; + esac +} + +if [ -z "${CONDA_SHLVL+x}" ]; then + \export CONDA_SHLVL=0 + # In dev-mode CONDA_EXE is python.exe and on Windows + # it is in a different relative location to condabin. + if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then + PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}" + else + PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}" + fi + \export PATH + + # We'\''re not allowing PS1 to be unbound. It must at least be set. + # However, we'\''re not exporting it, which can cause problems when starting a second shell + # via a first shell (i.e. starting zsh from bash). + if [ -z "${PS1+x}" ]; then + PS1= + fi +fi + +conda activate base' ++++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda ++++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda ++++ export _CE_M= ++++ _CE_M= ++++ export _CE_CONDA= ++++ _CE_CONDA= ++++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ '[' -z x ']' ++++ conda activate base ++++ local cmd=activate ++++ case "$cmd" in ++++ __conda_activate activate base ++++ '[' -n '' ']' ++++ local ask_conda +++++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++++ __conda_exe shell.posix activate base +++++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate base ++++ ask_conda='PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_SHLVL='\''6'\'' +export CONDA_DEFAULT_ENV='\''base'\'' +export CONDA_PROMPT_MODIFIER='\''(base) '\'' +export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' ++++ eval 'PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_SHLVL='\''6'\'' +export CONDA_DEFAULT_ENV='\''base'\'' +export CONDA_PROMPT_MODIFIER='\''(base) '\'' +export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' +++++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++++ export CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0 +++++ CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0 +++++ export CONDA_SHLVL=6 +++++ CONDA_SHLVL=6 +++++ export CONDA_DEFAULT_ENV=base +++++ CONDA_DEFAULT_ENV=base +++++ export 'CONDA_PROMPT_MODIFIER=(base) ' +++++ CONDA_PROMPT_MODIFIER='(base) ' +++++ export CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev +++++ CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev +++++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++++ export _CE_M= +++++ _CE_M= +++++ export _CE_CONDA= +++++ _CE_CONDA= +++++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python +++++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ __conda_hashr ++++ '[' -n '' ']' ++++ '[' -n '' ']' ++++ hash -r +++ unset __conda_setup ++ conda activate schemist-dev ++ local cmd=activate ++ case "$cmd" in ++ __conda_activate activate schemist-dev ++ '[' -n '' ']' ++ local ask_conda +++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++ __conda_exe shell.posix activate schemist-dev +++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate schemist-dev ++ ask_conda='PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_SHLVL='\''7'\'' +export CONDA_DEFAULT_ENV='\''schemist-dev'\'' +export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\'' +export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' ++ eval 'PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_SHLVL='\''7'\'' +export CONDA_DEFAULT_ENV='\''schemist-dev'\'' +export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\'' +export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' +++ PS1='(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++ export CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev +++ CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev +++ export CONDA_SHLVL=7 +++ CONDA_SHLVL=7 +++ export CONDA_DEFAULT_ENV=schemist-dev +++ CONDA_DEFAULT_ENV=schemist-dev +++ export 'CONDA_PROMPT_MODIFIER=(schemist-dev) ' +++ CONDA_PROMPT_MODIFIER='(schemist-dev) ' +++ export CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0 +++ CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0 +++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++ export _CE_M= +++ _CE_M= +++ export _CE_CONDA= +++ _CE_CONDA= +++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python +++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++ __conda_hashr ++ '[' -n '' ']' ++ '[' -n '' ']' ++ hash -r ++ CHUNK_HEAD_FILE=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz ++ INPUT=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/train/cyc-pep-6-12mer-70M_36.csv ++ COLUMN=cysteine_to_N_cyclization ++ PREFIX=cyclic_ ++ AWK='1 { print $8, $1, $2, $10, $3 }' ++ '[' -z cysteine_to_N_cyclization ']' ++ '[' -z cyclic_ ']' ++ '[' -z '1 { print $8, $1, $2, $10, $3 }' ']' ++ cat /dev/fd/63 /nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/train/cyc-pep-6-12mer-70M_36.csv ++ awk -F, -v OFS=, '1 { print $8, $1, $2, $10, $3 }' +++ zcat /nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz ++ gzip --best +++ head -n1 +++ tr ' ' , ++ schemist convert -f csv --column cysteine_to_N_cyclization --to id inchikey scaffold mwt clogp tpsa --prefix cyclic_ --options prefix=SCB- +🚀 Converting between string representations with the following parameters: + subcommand: convert + output: <_io.TextIOWrapper name='' mode='w' encoding='utf-8'> + format: csv + input: <_io.TextIOWrapper name='' mode='r' encoding='utf-8'> + representation: SMILES + column: cysteine_to_N_cyclization + prefix: cyclic_ + to: ['id', 'inchikey', 'scaffold', 'mwt', 'clogp', 'tpsa'] + options: ['prefix=SCB-'] + func: + 0it [00:00, ?it/s] 1it [00:10, 10.32s/it] 2it [00:20, 10.18s/it] 3it [00:30, 10.25s/it] 4it [00:41, 10.39s/it] 5it [00:51, 10.48s/it] 6it [01:02, 10.57s/it] 7it [01:13, 10.57s/it] 8it [01:23, 10.47s/it] 9it [01:33, 10.38s/it] 10it [01:44, 10.50s/it] 11it [01:55, 10.55s/it] 12it [02:05, 10.61s/it] 13it [02:16, 10.61s/it] 14it [02:26, 10.55s/it] 15it [02:37, 10.49s/it] 16it [02:47, 10.49s/it] 17it [02:58, 10.59s/it] 18it [03:09, 10.65s/it] 19it [03:20, 10.66s/it] 20it [03:30, 10.58s/it] 21it [03:40, 10.49s/it] 22it [03:51, 10.47s/it] 23it [04:01, 10.33s/it] 24it [04:11, 10.22s/it] 25it [04:21, 10.36s/it] 26it [04:32, 10.48s/it] 27it [04:43, 10.47s/it] 28it [04:53, 10.33s/it] 29it [05:03, 10.24s/it] 30it [05:13, 10.15s/it] 31it [05:23, 10.28s/it] 32it [05:34, 10.41s/it] 33it [05:44, 10.46s/it] 34it [05:55, 10.52s/it] 35it [06:06, 10.52s/it] 36it [06:16, 10.52s/it] 37it [06:26, 10.44s/it] 38it [06:37, 10.42s/it] 39it [06:47, 10.38s/it] 40it [06:57, 10.39s/it] 41it [07:08, 10.35s/it] 42it [07:18, 10.40s/it] 43it [07:28, 10.29s/it] 44it [07:38, 10.15s/it] 45it [07:48, 10.14s/it] 46it [07:59, 10.25s/it] 47it [08:09, 10.31s/it] 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10.39s/it] 368it [1:05:29, 10.45s/it] 369it [1:05:40, 10.38s/it] 370it [1:05:50, 10.26s/it] 371it [1:06:00, 10.24s/it] 372it [1:06:10, 10.28s/it] 373it [1:06:20, 10.30s/it] 374it [1:06:31, 10.35s/it] 375it [1:06:41, 10.29s/it] 376it [1:06:51, 10.16s/it] 377it [1:07:01, 10.12s/it] 378it [1:07:11, 10.17s/it] 379it [1:07:22, 10.28s/it] 380it [1:07:32, 10.33s/it] 381it [1:07:42, 10.29s/it] 382it [1:07:52, 10.19s/it] 383it [1:08:03, 10.18s/it] 384it [1:08:12, 10.09s/it] 385it [1:08:23, 10.13s/it] 386it [1:08:33, 10.28s/it] 387it [1:08:43, 10.22s/it] 388it [1:08:53, 10.09s/it] 389it [1:09:03, 10.09s/it] 390it [1:09:13, 10.09s/it] 391it [1:09:24, 10.14s/it] 392it [1:09:34, 10.12s/it] 393it [1:09:44, 10.07s/it] 394it [1:09:53, 9.96s/it] 395it [1:10:03, 9.96s/it] 396it [1:10:13, 10.00s/it] 397it [1:10:24, 10.05s/it] 398it [1:10:34, 10.04s/it] 399it [1:10:43, 9.96s/it] 400it [1:10:53, 9.93s/it] 401it [1:11:03, 9.96s/it] 402it [1:11:13, 9.99s/it] 403it [1:11:23, 10.00s/it] 404it [1:11:33, 9.94s/it] 405it [1:11:43, 9.88s/it] 406it [1:11:53, 9.89s/it] 407it [1:12:03, 9.99s/it] 408it [1:12:13, 10.10s/it] 409it [1:12:23, 10.09s/it] 410it [1:12:33, 9.94s/it] 411it [1:12:42, 9.80s/it] 412it [1:12:52, 9.83s/it] 413it [1:13:02, 9.91s/it] 414it [1:13:13, 10.06s/it] 415it [1:13:23, 10.08s/it] 416it [1:13:33, 9.99s/it] 417it [1:13:43, 9.92s/it] 418it [1:13:52, 9.89s/it] 419it [1:14:02, 9.93s/it] 420it [1:14:13, 10.05s/it] 421it [1:14:23, 10.02s/it] 422it [1:14:33, 10.03s/it] 423it [1:14:43, 10.00s/it] 424it [1:14:53, 9.97s/it] 425it [1:15:03, 9.98s/it] 426it [1:15:13, 10.08s/it] 427it [1:15:23, 10.12s/it] 428it [1:15:33, 10.13s/it] 429it [1:15:43, 10.03s/it] 430it [1:15:53, 10.02s/it] 431it [1:16:03, 10.06s/it] 432it [1:16:13, 10.13s/it] 433it [1:16:23, 10.07s/it] 434it [1:16:33, 10.05s/it] 435it [1:16:43, 10.01s/it] 436it [1:16:53, 9.95s/it] 437it [1:17:03, 9.98s/it] 438it [1:17:13, 9.97s/it] 439it [1:17:23, 9.89s/it] 440it [1:17:33, 9.87s/it] 441it [1:17:42, 9.83s/it] 442it 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979it [2:38:35, 8.52s/it] 980it [2:38:43, 8.51s/it] 981it [2:38:52, 8.52s/it] 982it [2:39:00, 8.53s/it] 983it [2:39:09, 8.52s/it] 984it [2:39:17, 8.50s/it] 985it [2:39:26, 8.50s/it] 986it [2:39:34, 8.50s/it] 987it [2:39:43, 8.51s/it] 988it [2:39:51, 8.51s/it] 989it [2:40:00, 8.50s/it] 990it [2:40:08, 8.51s/it] 991it [2:40:17, 8.51s/it] 992it [2:40:25, 8.51s/it] 993it [2:40:34, 8.50s/it] 994it [2:40:42, 8.51s/it] 995it [2:40:51, 8.51s/it] 996it [2:40:59, 8.52s/it] 997it [2:41:08, 8.52s/it] 998it [2:41:16, 8.52s/it] 999it [2:41:25, 8.52s/it] 1000it [2:41:33, 8.52s/it] 1000it [2:41:33, 9.69s/it] +Error counts: + cyclic_id: 0 + cyclic_inchikey: 0 + cyclic_scaffold: 0 + cyclic_mwt: 0 + cyclic_clogp: 0 + cyclic_tpsa: 0 +⏰ Completed process in 2:41:54.507710 ++ rm /nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/train/cyc-pep-6-12mer-70M_36.csv diff --git a/train/cyc-pep-6-12mer-70M_37.csv.gz b/train/cyc-pep-6-12mer-70M_37.csv.gz index a0470699d958627f6b8c1a2c4808f9430912d9be..1b1e304c848eedec61269fb6d5b48dfcfb691bbd 100644 --- a/train/cyc-pep-6-12mer-70M_37.csv.gz +++ b/train/cyc-pep-6-12mer-70M_37.csv.gz @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:b22c3cb49fe7bfb276193e6e56a8893a29619e325b344d5de1d4da6f3bbb317d -size 50678955 +oid sha256:6ba34e8af9dfb666c174e9f9fd166232f14b5ead8bf413b222a29bbf8a04a4bc +size 102672832 diff --git a/train/cyc-pep-6-12mer-70M_37.log b/train/cyc-pep-6-12mer-70M_37.log new file mode 100644 index 0000000000000000000000000000000000000000..7b0d5ca90bd04ed83f96eafee6e81b0502cbf4ec --- /dev/null +++ b/train/cyc-pep-6-12mer-70M_37.log @@ -0,0 +1,337 @@ ++ module purge ++ '[' -z '' ']' ++ case "$-" in ++ __lmod_sh_dbg=x ++ '[' -n x ']' ++ set +x +Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output +Shell debugging restarted ++ unset __lmod_sh_dbg ++ return 0 ++ module load Anaconda3/2023.03 ++ '[' -z '' ']' ++ case "$-" in ++ __lmod_sh_dbg=x ++ '[' -n x ']' ++ set +x +Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output +Shell debugging restarted ++ unset __lmod_sh_dbg ++ return 0 ++ source /camp/home/johnsoe/.bashrc +++ '[' '' = yes ']' +++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' ++++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.bash hook +++ __conda_setup='export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'' + +# Copyright (C) 2012 Anaconda, Inc +# SPDX-License-Identifier: BSD-3-Clause +__conda_exe() ( + "$CONDA_EXE" $_CE_M $_CE_CONDA "$@" +) + +__conda_hashr() { + if [ -n "${ZSH_VERSION:+x}" ]; then + \rehash + elif [ -n "${POSH_VERSION:+x}" ]; then + : # pass + else + \hash -r + fi +} + +__conda_activate() { + if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then + # Handle transition from shell activated with conda <= 4.3 to a subsequent activation + # after conda updated to >= 4.4. See issue #6173. + PS1="$CONDA_PS1_BACKUP" + \unset CONDA_PS1_BACKUP + fi + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return + \eval "$ask_conda" + __conda_hashr +} + +__conda_reactivate() { + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return + \eval "$ask_conda" + __conda_hashr +} + +conda() { + \local cmd="${1-__missing__}" + case "$cmd" in + activate|deactivate) + __conda_activate "$@" + ;; + install|update|upgrade|remove|uninstall) + __conda_exe "$@" || \return + __conda_reactivate + ;; + *) + __conda_exe "$@" + ;; + esac +} + +if [ -z "${CONDA_SHLVL+x}" ]; then + \export CONDA_SHLVL=0 + # In dev-mode CONDA_EXE is python.exe and on Windows + # it is in a different relative location to condabin. + if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then + PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}" + else + PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}" + fi + \export PATH + + # We'\''re not allowing PS1 to be unbound. It must at least be set. + # However, we'\''re not exporting it, which can cause problems when starting a second shell + # via a first shell (i.e. starting zsh from bash). + if [ -z "${PS1+x}" ]; then + PS1= + fi +fi + +conda activate base' +++ '[' 0 -eq 0 ']' +++ eval 'export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'' + +# Copyright (C) 2012 Anaconda, Inc +# SPDX-License-Identifier: BSD-3-Clause +__conda_exe() ( + "$CONDA_EXE" $_CE_M $_CE_CONDA "$@" +) + +__conda_hashr() { + if [ -n "${ZSH_VERSION:+x}" ]; then + \rehash + elif [ -n "${POSH_VERSION:+x}" ]; then + : # pass + else + \hash -r + fi +} + +__conda_activate() { + if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then + # Handle transition from shell activated with conda <= 4.3 to a subsequent activation + # after conda updated to >= 4.4. See issue #6173. + PS1="$CONDA_PS1_BACKUP" + \unset CONDA_PS1_BACKUP + fi + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return + \eval "$ask_conda" + __conda_hashr +} + +__conda_reactivate() { + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return + \eval "$ask_conda" + __conda_hashr +} + +conda() { + \local cmd="${1-__missing__}" + case "$cmd" in + activate|deactivate) + __conda_activate "$@" + ;; + install|update|upgrade|remove|uninstall) + __conda_exe "$@" || \return + __conda_reactivate + ;; + *) + __conda_exe "$@" + ;; + esac +} + +if [ -z "${CONDA_SHLVL+x}" ]; then + \export CONDA_SHLVL=0 + # In dev-mode CONDA_EXE is python.exe and on Windows + # it is in a different relative location to condabin. + if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then + PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}" + else + PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}" + fi + \export PATH + + # We'\''re not allowing PS1 to be unbound. It must at least be set. + # However, we'\''re not exporting it, which can cause problems when starting a second shell + # via a first shell (i.e. starting zsh from bash). + if [ -z "${PS1+x}" ]; then + PS1= + fi +fi + +conda activate base' ++++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda ++++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda ++++ export _CE_M= ++++ _CE_M= ++++ export _CE_CONDA= ++++ _CE_CONDA= ++++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ '[' -z x ']' ++++ conda activate base ++++ local cmd=activate ++++ case "$cmd" in ++++ __conda_activate activate base ++++ '[' -n '' ']' ++++ local ask_conda +++++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++++ __conda_exe shell.posix activate base +++++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate base ++++ ask_conda='PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_SHLVL='\''6'\'' +export CONDA_DEFAULT_ENV='\''base'\'' +export CONDA_PROMPT_MODIFIER='\''(base) '\'' +export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' ++++ eval 'PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_SHLVL='\''6'\'' +export CONDA_DEFAULT_ENV='\''base'\'' +export CONDA_PROMPT_MODIFIER='\''(base) '\'' +export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' +++++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++++ export CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0 +++++ CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0 +++++ export CONDA_SHLVL=6 +++++ CONDA_SHLVL=6 +++++ export CONDA_DEFAULT_ENV=base +++++ CONDA_DEFAULT_ENV=base +++++ export 'CONDA_PROMPT_MODIFIER=(base) ' +++++ CONDA_PROMPT_MODIFIER='(base) ' +++++ export CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev +++++ CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev +++++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++++ export _CE_M= +++++ _CE_M= +++++ export _CE_CONDA= +++++ _CE_CONDA= +++++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python +++++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ __conda_hashr ++++ '[' -n '' ']' ++++ '[' -n '' ']' ++++ hash -r +++ unset __conda_setup ++ conda activate schemist-dev ++ local cmd=activate ++ case "$cmd" in ++ __conda_activate activate schemist-dev ++ '[' -n '' ']' ++ local ask_conda +++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++ __conda_exe shell.posix activate schemist-dev +++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate schemist-dev ++ ask_conda='PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_SHLVL='\''7'\'' +export CONDA_DEFAULT_ENV='\''schemist-dev'\'' +export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\'' +export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' ++ eval 'PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_SHLVL='\''7'\'' +export CONDA_DEFAULT_ENV='\''schemist-dev'\'' +export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\'' +export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' +++ PS1='(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++ export CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev +++ CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev +++ export CONDA_SHLVL=7 +++ CONDA_SHLVL=7 +++ export CONDA_DEFAULT_ENV=schemist-dev +++ CONDA_DEFAULT_ENV=schemist-dev +++ export 'CONDA_PROMPT_MODIFIER=(schemist-dev) ' +++ CONDA_PROMPT_MODIFIER='(schemist-dev) ' +++ export CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0 +++ CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0 +++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++ export _CE_M= +++ _CE_M= +++ export _CE_CONDA= +++ _CE_CONDA= +++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python +++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++ __conda_hashr ++ '[' -n '' ']' ++ '[' -n '' ']' ++ hash -r ++ CHUNK_HEAD_FILE=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz ++ INPUT=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/train/cyc-pep-6-12mer-70M_37.csv ++ COLUMN=cysteine_to_N_cyclization ++ PREFIX=cyclic_ ++ AWK='1 { print $8, $1, $2, $10, $3 }' ++ '[' -z cysteine_to_N_cyclization ']' ++ '[' -z cyclic_ ']' ++ '[' -z '1 { print $8, $1, $2, $10, $3 }' ']' ++ cat /dev/fd/63 /nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/train/cyc-pep-6-12mer-70M_37.csv ++ awk -F, -v OFS=, '1 { print $8, $1, $2, $10, $3 }' +++ zcat /nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz ++ schemist convert -f csv --column cysteine_to_N_cyclization --to id inchikey scaffold mwt clogp tpsa --prefix cyclic_ --options prefix=SCB- +++ head -n1 ++ gzip --best +++ tr ' ' , +🚀 Converting between string representations with the following parameters: + subcommand: convert + output: <_io.TextIOWrapper name='' mode='w' encoding='utf-8'> + format: csv + input: <_io.TextIOWrapper name='' mode='r' encoding='utf-8'> + representation: SMILES + column: cysteine_to_N_cyclization + prefix: cyclic_ + to: ['id', 'inchikey', 'scaffold', 'mwt', 'clogp', 'tpsa'] + options: ['prefix=SCB-'] + func: + 0it [00:00, ?it/s] 1it [00:08, 8.85s/it] 2it [00:17, 8.79s/it] 3it [00:26, 8.81s/it] 4it [00:35, 8.89s/it] 5it [00:44, 8.89s/it] 6it 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999it [2:27:57, 8.57s/it] 1000it [2:28:05, 8.57s/it] 1000it [2:28:05, 8.89s/it] +Error counts: + cyclic_id: 0 + cyclic_inchikey: 0 + cyclic_scaffold: 0 + cyclic_mwt: 0 + cyclic_clogp: 0 + cyclic_tpsa: 0 +⏰ Completed process in 2:28:25.095202 ++ rm /nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/train/cyc-pep-6-12mer-70M_37.csv diff --git a/train/cyc-pep-6-12mer-70M_38.csv.gz b/train/cyc-pep-6-12mer-70M_38.csv.gz index e10e17681f0a38bef6c35a831fe7d6f0ae9d4468..5f892662d7236419c771d3a2a294cb9b10b23469 100644 --- a/train/cyc-pep-6-12mer-70M_38.csv.gz +++ b/train/cyc-pep-6-12mer-70M_38.csv.gz @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:240884feebc0e685c6e1056be676cc59efbf22867a4a0e6f6b53d34806db3156 -size 50683148 +oid sha256:19482181809def1d17e3235ccf18d8f0d27d2eb905c756b45a8be87eddd43db2 +size 102676660 diff --git a/train/cyc-pep-6-12mer-70M_38.log b/train/cyc-pep-6-12mer-70M_38.log new file mode 100644 index 0000000000000000000000000000000000000000..f25f3a533e9c802abf25c62e860764cccf616f49 --- /dev/null +++ b/train/cyc-pep-6-12mer-70M_38.log @@ -0,0 +1,337 @@ ++ module purge ++ '[' -z '' ']' ++ case "$-" in ++ __lmod_sh_dbg=x ++ '[' -n x ']' ++ set +x +Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output +Shell debugging restarted ++ unset __lmod_sh_dbg ++ return 0 ++ module load Anaconda3/2023.03 ++ '[' -z '' ']' ++ case "$-" in ++ __lmod_sh_dbg=x ++ '[' -n x ']' ++ set +x +Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output +Shell debugging restarted ++ unset __lmod_sh_dbg ++ return 0 ++ source /camp/home/johnsoe/.bashrc +++ '[' '' = yes ']' +++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' ++++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.bash hook +++ __conda_setup='export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'' + +# Copyright (C) 2012 Anaconda, Inc +# SPDX-License-Identifier: BSD-3-Clause +__conda_exe() ( + "$CONDA_EXE" $_CE_M $_CE_CONDA "$@" +) + +__conda_hashr() { + if [ -n "${ZSH_VERSION:+x}" ]; then + \rehash + elif [ -n "${POSH_VERSION:+x}" ]; then + : # pass + else + \hash -r + fi +} + +__conda_activate() { + if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then + # Handle transition from shell activated with conda <= 4.3 to a subsequent activation + # after conda updated to >= 4.4. See issue #6173. + PS1="$CONDA_PS1_BACKUP" + \unset CONDA_PS1_BACKUP + fi + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return + \eval "$ask_conda" + __conda_hashr +} + +__conda_reactivate() { + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return + \eval "$ask_conda" + __conda_hashr +} + +conda() { + \local cmd="${1-__missing__}" + case "$cmd" in + activate|deactivate) + __conda_activate "$@" + ;; + install|update|upgrade|remove|uninstall) + __conda_exe "$@" || \return + __conda_reactivate + ;; + *) + __conda_exe "$@" + ;; + esac +} + +if [ -z "${CONDA_SHLVL+x}" ]; then + \export CONDA_SHLVL=0 + # In dev-mode CONDA_EXE is python.exe and on Windows + # it is in a different relative location to condabin. + if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then + PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}" + else + PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}" + fi + \export PATH + + # We'\''re not allowing PS1 to be unbound. It must at least be set. + # However, we'\''re not exporting it, which can cause problems when starting a second shell + # via a first shell (i.e. starting zsh from bash). + if [ -z "${PS1+x}" ]; then + PS1= + fi +fi + +conda activate base' +++ '[' 0 -eq 0 ']' +++ eval 'export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'' + +# Copyright (C) 2012 Anaconda, Inc +# SPDX-License-Identifier: BSD-3-Clause +__conda_exe() ( + "$CONDA_EXE" $_CE_M $_CE_CONDA "$@" +) + +__conda_hashr() { + if [ -n "${ZSH_VERSION:+x}" ]; then + \rehash + elif [ -n "${POSH_VERSION:+x}" ]; then + : # pass + else + \hash -r + fi +} + +__conda_activate() { + if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then + # Handle transition from shell activated with conda <= 4.3 to a subsequent activation + # after conda updated to >= 4.4. See issue #6173. + PS1="$CONDA_PS1_BACKUP" + \unset CONDA_PS1_BACKUP + fi + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return + \eval "$ask_conda" + __conda_hashr +} + +__conda_reactivate() { + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return + \eval "$ask_conda" + __conda_hashr +} + +conda() { + \local cmd="${1-__missing__}" + case "$cmd" in + activate|deactivate) + __conda_activate "$@" + ;; + install|update|upgrade|remove|uninstall) + __conda_exe "$@" || \return + __conda_reactivate + ;; + *) + __conda_exe "$@" + ;; + esac +} + +if [ -z "${CONDA_SHLVL+x}" ]; then + \export CONDA_SHLVL=0 + # In dev-mode CONDA_EXE is python.exe and on Windows + # it is in a different relative location to condabin. + if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then + PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}" + else + PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}" + fi + \export PATH + + # We'\''re not allowing PS1 to be unbound. It must at least be set. + # However, we'\''re not exporting it, which can cause problems when starting a second shell + # via a first shell (i.e. starting zsh from bash). + if [ -z "${PS1+x}" ]; then + PS1= + fi +fi + +conda activate base' ++++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda ++++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda ++++ export _CE_M= ++++ _CE_M= ++++ export _CE_CONDA= ++++ _CE_CONDA= ++++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ '[' -z x ']' ++++ conda activate base ++++ local cmd=activate ++++ case "$cmd" in ++++ __conda_activate activate base ++++ '[' -n '' ']' ++++ local ask_conda +++++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++++ __conda_exe shell.posix activate base +++++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate base ++++ ask_conda='PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_SHLVL='\''6'\'' +export CONDA_DEFAULT_ENV='\''base'\'' +export CONDA_PROMPT_MODIFIER='\''(base) '\'' +export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' ++++ eval 'PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_SHLVL='\''6'\'' +export CONDA_DEFAULT_ENV='\''base'\'' +export CONDA_PROMPT_MODIFIER='\''(base) '\'' +export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' +++++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++++ export CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0 +++++ CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0 +++++ export CONDA_SHLVL=6 +++++ CONDA_SHLVL=6 +++++ export CONDA_DEFAULT_ENV=base +++++ CONDA_DEFAULT_ENV=base +++++ export 'CONDA_PROMPT_MODIFIER=(base) ' +++++ CONDA_PROMPT_MODIFIER='(base) ' +++++ export CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev +++++ CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev +++++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++++ export _CE_M= +++++ _CE_M= +++++ export _CE_CONDA= +++++ _CE_CONDA= +++++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python +++++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ __conda_hashr ++++ '[' -n '' ']' ++++ '[' -n '' ']' ++++ hash -r +++ unset __conda_setup ++ conda activate schemist-dev ++ local cmd=activate ++ case "$cmd" in ++ __conda_activate activate schemist-dev ++ '[' -n '' ']' ++ local ask_conda +++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++ __conda_exe shell.posix activate schemist-dev +++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate schemist-dev ++ ask_conda='PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_SHLVL='\''7'\'' +export CONDA_DEFAULT_ENV='\''schemist-dev'\'' +export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\'' +export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' ++ eval 'PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_SHLVL='\''7'\'' +export CONDA_DEFAULT_ENV='\''schemist-dev'\'' +export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\'' +export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' +++ PS1='(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++ export CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev +++ CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev +++ export CONDA_SHLVL=7 +++ CONDA_SHLVL=7 +++ export CONDA_DEFAULT_ENV=schemist-dev +++ CONDA_DEFAULT_ENV=schemist-dev +++ export 'CONDA_PROMPT_MODIFIER=(schemist-dev) ' +++ CONDA_PROMPT_MODIFIER='(schemist-dev) ' +++ export CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0 +++ CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0 +++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++ export _CE_M= +++ _CE_M= +++ export _CE_CONDA= +++ _CE_CONDA= +++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python +++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++ __conda_hashr ++ '[' -n '' ']' ++ '[' -n '' ']' ++ hash -r ++ CHUNK_HEAD_FILE=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz ++ INPUT=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/train/cyc-pep-6-12mer-70M_38.csv ++ COLUMN=cysteine_to_N_cyclization ++ PREFIX=cyclic_ ++ AWK='1 { print $8, $1, $2, $10, $3 }' ++ '[' -z cysteine_to_N_cyclization ']' ++ '[' -z cyclic_ ']' ++ '[' -z '1 { print $8, $1, $2, $10, $3 }' ']' ++ awk -F, -v OFS=, '1 { print $8, $1, $2, $10, $3 }' ++ schemist convert -f csv --column cysteine_to_N_cyclization --to id inchikey scaffold mwt clogp tpsa --prefix cyclic_ --options prefix=SCB- ++ cat /dev/fd/63 /nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/train/cyc-pep-6-12mer-70M_38.csv +++ zcat /nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz +++ head -n1 +++ tr ' ' , ++ gzip --best +🚀 Converting between string representations with the following parameters: + subcommand: convert + output: <_io.TextIOWrapper name='' mode='w' encoding='utf-8'> + format: csv + input: <_io.TextIOWrapper name='' mode='r' encoding='utf-8'> + representation: SMILES + column: cysteine_to_N_cyclization + prefix: cyclic_ + to: ['id', 'inchikey', 'scaffold', 'mwt', 'clogp', 'tpsa'] + options: ['prefix=SCB-'] + func: + 0it [00:00, ?it/s] 1it [00:09, 9.36s/it] 2it [00:18, 9.21s/it] 3it [00:27, 9.11s/it] 4it [00:36, 9.10s/it] 5it [00:46, 9.25s/it] 6it [00:55, 9.22s/it] 7it [01:04, 9.22s/it] 8it [01:13, 9.29s/it] 9it 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998it [2:36:22, 8.78s/it] 999it [2:36:31, 8.84s/it] 1000it [2:36:40, 8.91s/it] 1000it [2:36:40, 9.40s/it] +Error counts: + cyclic_id: 0 + cyclic_inchikey: 0 + cyclic_scaffold: 0 + cyclic_mwt: 0 + cyclic_clogp: 0 + cyclic_tpsa: 0 +⏰ Completed process in 2:37:01.169965 ++ rm /nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/train/cyc-pep-6-12mer-70M_38.csv diff --git a/train/cyc-pep-6-12mer-70M_39.csv.gz b/train/cyc-pep-6-12mer-70M_39.csv.gz index 2fce278afa11794aaeab0e948a6252d49fd62059..e986193a4d215220e52ebc1805c258a4f4c367d0 100644 --- a/train/cyc-pep-6-12mer-70M_39.csv.gz +++ b/train/cyc-pep-6-12mer-70M_39.csv.gz @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:1549aa11a9cbedbab9a7d76835feba5e4254ec5d31ab7d979f18709a3337160f -size 50679337 +oid sha256:779925e53305b7928feaba5bcca419417e5b282e3f4b1e7b197ba8ee4a260c7f +size 102671705 diff --git a/train/cyc-pep-6-12mer-70M_39.log b/train/cyc-pep-6-12mer-70M_39.log new file mode 100644 index 0000000000000000000000000000000000000000..e7de6b9b3afa7276422fe089282818806946294e --- /dev/null +++ b/train/cyc-pep-6-12mer-70M_39.log @@ -0,0 +1,337 @@ ++ module purge ++ '[' -z '' ']' ++ case "$-" in ++ __lmod_sh_dbg=x ++ '[' -n x ']' ++ set +x +Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output +Shell debugging restarted ++ unset __lmod_sh_dbg ++ return 0 ++ module load Anaconda3/2023.03 ++ '[' -z '' ']' ++ case "$-" in ++ __lmod_sh_dbg=x ++ '[' -n x ']' ++ set +x +Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output +Shell debugging restarted ++ unset __lmod_sh_dbg ++ return 0 ++ source /camp/home/johnsoe/.bashrc +++ '[' '' = yes ']' +++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' ++++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.bash hook +++ __conda_setup='export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'' + +# Copyright (C) 2012 Anaconda, Inc +# SPDX-License-Identifier: BSD-3-Clause +__conda_exe() ( + "$CONDA_EXE" $_CE_M $_CE_CONDA "$@" +) + +__conda_hashr() { + if [ -n "${ZSH_VERSION:+x}" ]; then + \rehash + elif [ -n "${POSH_VERSION:+x}" ]; then + : # pass + else + \hash -r + fi +} + +__conda_activate() { + if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then + # Handle transition from shell activated with conda <= 4.3 to a subsequent activation + # after conda updated to >= 4.4. See issue #6173. + PS1="$CONDA_PS1_BACKUP" + \unset CONDA_PS1_BACKUP + fi + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return + \eval "$ask_conda" + __conda_hashr +} + +__conda_reactivate() { + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return + \eval "$ask_conda" + __conda_hashr +} + +conda() { + \local cmd="${1-__missing__}" + case "$cmd" in + activate|deactivate) + __conda_activate "$@" + ;; + install|update|upgrade|remove|uninstall) + __conda_exe "$@" || \return + __conda_reactivate + ;; + *) + __conda_exe "$@" + ;; + esac +} + +if [ -z "${CONDA_SHLVL+x}" ]; then + \export CONDA_SHLVL=0 + # In dev-mode CONDA_EXE is python.exe and on Windows + # it is in a different relative location to condabin. + if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then + PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}" + else + PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}" + fi + \export PATH + + # We'\''re not allowing PS1 to be unbound. It must at least be set. + # However, we'\''re not exporting it, which can cause problems when starting a second shell + # via a first shell (i.e. starting zsh from bash). + if [ -z "${PS1+x}" ]; then + PS1= + fi +fi + +conda activate base' +++ '[' 0 -eq 0 ']' +++ eval 'export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'' + +# Copyright (C) 2012 Anaconda, Inc +# SPDX-License-Identifier: BSD-3-Clause +__conda_exe() ( + "$CONDA_EXE" $_CE_M $_CE_CONDA "$@" +) + +__conda_hashr() { + if [ -n "${ZSH_VERSION:+x}" ]; then + \rehash + elif [ -n "${POSH_VERSION:+x}" ]; then + : # pass + else + \hash -r + fi +} + +__conda_activate() { + if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then + # Handle transition from shell activated with conda <= 4.3 to a subsequent activation + # after conda updated to >= 4.4. See issue #6173. + PS1="$CONDA_PS1_BACKUP" + \unset CONDA_PS1_BACKUP + fi + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return + \eval "$ask_conda" + __conda_hashr +} + +__conda_reactivate() { + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return + \eval "$ask_conda" + __conda_hashr +} + +conda() { + \local cmd="${1-__missing__}" + case "$cmd" in + activate|deactivate) + __conda_activate "$@" + ;; + install|update|upgrade|remove|uninstall) + __conda_exe "$@" || \return + __conda_reactivate + ;; + *) + __conda_exe "$@" + ;; + esac +} + +if [ -z "${CONDA_SHLVL+x}" ]; then + \export CONDA_SHLVL=0 + # In dev-mode CONDA_EXE is python.exe and on Windows + # it is in a different relative location to condabin. + if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then + PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}" + else + PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}" + fi + \export PATH + + # We'\''re not allowing PS1 to be unbound. It must at least be set. + # However, we'\''re not exporting it, which can cause problems when starting a second shell + # via a first shell (i.e. starting zsh from bash). + if [ -z "${PS1+x}" ]; then + PS1= + fi +fi + +conda activate base' ++++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda ++++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda ++++ export _CE_M= ++++ _CE_M= ++++ export _CE_CONDA= ++++ _CE_CONDA= ++++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ '[' -z x ']' ++++ conda activate base ++++ local cmd=activate ++++ case "$cmd" in ++++ __conda_activate activate base ++++ '[' -n '' ']' ++++ local ask_conda +++++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++++ __conda_exe shell.posix activate base +++++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate base ++++ ask_conda='PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_SHLVL='\''6'\'' +export CONDA_DEFAULT_ENV='\''base'\'' +export CONDA_PROMPT_MODIFIER='\''(base) '\'' +export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' ++++ eval 'PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_SHLVL='\''6'\'' +export CONDA_DEFAULT_ENV='\''base'\'' +export CONDA_PROMPT_MODIFIER='\''(base) '\'' +export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' +++++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++++ export CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0 +++++ CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0 +++++ export CONDA_SHLVL=6 +++++ CONDA_SHLVL=6 +++++ export CONDA_DEFAULT_ENV=base +++++ CONDA_DEFAULT_ENV=base +++++ export 'CONDA_PROMPT_MODIFIER=(base) ' +++++ CONDA_PROMPT_MODIFIER='(base) ' +++++ export CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev +++++ CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev +++++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++++ export _CE_M= +++++ _CE_M= +++++ export _CE_CONDA= +++++ _CE_CONDA= +++++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python +++++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ __conda_hashr ++++ '[' -n '' ']' ++++ '[' -n '' ']' ++++ hash -r +++ unset __conda_setup ++ conda activate schemist-dev ++ local cmd=activate ++ case "$cmd" in ++ __conda_activate activate schemist-dev ++ '[' -n '' ']' ++ local ask_conda +++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++ __conda_exe shell.posix activate schemist-dev +++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate schemist-dev ++ ask_conda='PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_SHLVL='\''7'\'' +export CONDA_DEFAULT_ENV='\''schemist-dev'\'' +export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\'' +export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' ++ eval 'PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_SHLVL='\''7'\'' +export CONDA_DEFAULT_ENV='\''schemist-dev'\'' +export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\'' +export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' +++ PS1='(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++ export CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev +++ CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev +++ export CONDA_SHLVL=7 +++ CONDA_SHLVL=7 +++ export CONDA_DEFAULT_ENV=schemist-dev +++ CONDA_DEFAULT_ENV=schemist-dev +++ export 'CONDA_PROMPT_MODIFIER=(schemist-dev) ' +++ CONDA_PROMPT_MODIFIER='(schemist-dev) ' +++ export CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0 +++ CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0 +++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++ export _CE_M= +++ _CE_M= +++ export _CE_CONDA= +++ _CE_CONDA= +++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python +++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++ __conda_hashr ++ '[' -n '' ']' ++ '[' -n '' ']' ++ hash -r ++ CHUNK_HEAD_FILE=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz ++ INPUT=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/train/cyc-pep-6-12mer-70M_39.csv ++ COLUMN=cysteine_to_N_cyclization ++ PREFIX=cyclic_ ++ AWK='1 { print $8, $1, $2, $10, $3 }' ++ '[' -z cysteine_to_N_cyclization ']' ++ '[' -z cyclic_ ']' ++ '[' -z '1 { print $8, $1, $2, $10, $3 }' ']' ++ cat /dev/fd/63 /nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/train/cyc-pep-6-12mer-70M_39.csv ++ awk -F, -v OFS=, '1 { print $8, $1, $2, $10, $3 }' ++ schemist convert -f csv --column cysteine_to_N_cyclization --to id inchikey scaffold mwt clogp tpsa --prefix cyclic_ --options prefix=SCB- +++ head -n1 ++ gzip --best +++ zcat /nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz +++ tr ' ' , +🚀 Converting between string representations with the following parameters: + subcommand: convert + output: <_io.TextIOWrapper name='' mode='w' encoding='utf-8'> + format: csv + input: <_io.TextIOWrapper name='' mode='r' encoding='utf-8'> + representation: SMILES + column: cysteine_to_N_cyclization + prefix: cyclic_ + to: ['id', 'inchikey', 'scaffold', 'mwt', 'clogp', 'tpsa'] + options: ['prefix=SCB-'] + func: + 0it [00:00, ?it/s] 1it [00:09, 9.33s/it] 2it [00:18, 9.23s/it] 3it [00:27, 9.27s/it] 4it [00:37, 9.33s/it] 5it [00:46, 9.34s/it] 6it [00:55, 9.31s/it] 7it [01:04, 9.23s/it] 8it [01:14, 9.19s/it] 9it [01:23, 9.21s/it] 10it [01:32, 9.27s/it] 11it [01:42, 9.30s/it] 12it [01:51, 9.32s/it] 13it [02:00, 9.31s/it] 14it [02:09, 9.23s/it] 15it [02:18, 9.20s/it] 16it [02:28, 9.25s/it] 17it [02:37, 9.39s/it] 18it [02:47, 9.45s/it] 19it [02:57, 9.49s/it] 20it [03:06, 9.51s/it] 21it [03:15, 9.42s/it] 22it [03:25, 9.34s/it] 23it [03:34, 9.33s/it] 24it [03:44, 9.45s/it] 25it [03:53, 9.50s/it] 26it [04:03, 9.58s/it] 27it [04:13, 9.65s/it] 28it [04:22, 9.52s/it] 29it [04:31, 9.45s/it] 30it [04:41, 9.42s/it] 31it [04:50, 9.52s/it] 32it [05:00, 9.54s/it] 33it [05:10, 9.57s/it] 34it [05:19, 9.57s/it] 35it [05:29, 9.49s/it] 36it [05:38, 9.40s/it] 37it [05:47, 9.36s/it] 38it [05:57, 9.45s/it] 39it [06:06, 9.51s/it] 40it [06:16, 9.56s/it] 41it [06:26, 9.60s/it] 42it [06:35, 9.52s/it] 43it [06:44, 9.41s/it] 44it [06:53, 9.34s/it] 45it [07:03, 9.44s/it] 46it [07:13, 9.52s/it] 47it [07:22, 9.60s/it] 48it [07:32, 9.63s/it] 49it [07:42, 9.54s/it] 50it [07:51, 9.47s/it] 51it [08:00, 9.44s/it] 52it [08:10, 9.57s/it] 53it [08:20, 9.60s/it] 54it [08:29, 9.64s/it] 55it [08:39, 9.64s/it] 56it [08:48, 9.55s/it] 57it [08:58, 9.45s/it] 58it [09:07, 9.39s/it] 59it [09:17, 9.47s/it] 60it [09:26, 9.52s/it] 61it [09:36, 9.57s/it] 62it [09:46, 9.61s/it] 63it [09:55, 9.53s/it] 64it [10:04, 9.44s/it] 65it [10:13, 9.35s/it] 66it [10:23, 9.45s/it] 67it [10:33, 9.53s/it] 68it [10:42, 9.58s/it] 69it [10:52, 9.70s/it] 70it [11:02, 9.65s/it] 71it [11:12, 9.65s/it] 72it [11:21, 9.53s/it] 73it [11:30, 9.53s/it] 74it [11:40, 9.50s/it] 75it [11:49, 9.47s/it] 76it [11:58, 9.41s/it] 77it [12:08, 9.31s/it] 78it [12:17, 9.22s/it] 79it [12:26, 9.19s/it] 80it [12:35, 9.36s/it] 81it [12:45, 9.45s/it] 82it [12:55, 9.53s/it] 83it [13:04, 9.57s/it] 84it [13:14, 9.56s/it] 85it [13:23, 9.46s/it] 86it [13:32, 9.36s/it] 87it [13:42, 9.46s/it] 88it [13:52, 9.53s/it] 89it [14:01, 9.60s/it] 90it [14:11, 9.63s/it] 91it [14:21, 9.57s/it] 92it [14:30, 9.46s/it] 93it [14:39, 9.39s/it] 94it [14:49, 9.53s/it] 95it [14:59, 9.61s/it] 96it [15:08, 9.65s/it] 97it [15:18, 9.64s/it] 98it [15:27, 9.57s/it] 99it [15:37, 9.46s/it] 100it [15:46, 9.40s/it] 101it [15:56, 9.46s/it] 102it [16:05, 9.53s/it] 103it [16:15, 9.58s/it] 104it [16:25, 9.59s/it] 105it [16:34, 9.61s/it] 106it [16:44, 9.53s/it] 107it [16:53, 9.46s/it] 108it [17:02, 9.51s/it] 109it [17:12, 9.59s/it] 110it [17:22, 9.64s/it] 111it [17:32, 9.68s/it] 112it [17:42, 9.71s/it] 113it [17:51, 9.56s/it] 114it [18:00, 9.46s/it] 115it [18:09, 9.46s/it] 116it [18:19, 9.55s/it] 117it [18:29, 9.59s/it] 118it [18:39, 9.64s/it] 119it [18:48, 9.62s/it] 120it [18:58, 9.53s/it] 121it [19:07, 9.46s/it] 122it [19:16, 9.45s/it] 123it [19:26, 9.51s/it] 124it [19:36, 9.62s/it] 125it [19:45, 9.63s/it] 126it [19:55, 9.67s/it] 127it [20:05, 9.56s/it] 128it [20:14, 9.45s/it] 129it [20:23, 9.44s/it] 130it [20:33, 9.52s/it] 131it [20:43, 9.57s/it] 132it [20:52, 9.60s/it] 133it [21:02, 9.63s/it] 134it [21:11, 9.52s/it] 135it [21:20, 9.44s/it] 136it [21:30, 9.38s/it] 137it [21:39, 9.39s/it] 138it [21:49, 9.51s/it] 139it [21:59, 9.60s/it] 140it [22:09, 9.72s/it] 141it [22:18, 9.69s/it] 142it [22:27, 9.53s/it] 143it [22:37, 9.43s/it] 144it [22:46, 9.50s/it] 145it [22:56, 9.62s/it] 146it [23:06, 9.69s/it] 147it [23:16, 9.75s/it] 148it [23:25, 9.66s/it] 149it [23:35, 9.50s/it] 150it [23:44, 9.39s/it] 151it [23:53, 9.47s/it] 152it [24:03, 9.57s/it] 153it [24:13, 9.64s/it] 154it [24:23, 9.73s/it] 155it [24:32, 9.68s/it] 156it [24:42, 9.52s/it] 157it [24:51, 9.41s/it] 158it [25:00, 9.46s/it] 159it [25:10, 9.59s/it] 160it [25:20, 9.68s/it] 161it [25:30, 9.74s/it] 162it [25:40, 9.69s/it] 163it [25:49, 9.54s/it] 164it [25:58, 9.41s/it] 165it [26:07, 9.47s/it] 166it [26:17, 9.60s/it] 167it [26:27, 9.69s/it] 168it [26:37, 9.77s/it] 169it [26:47, 9.71s/it] 170it [26:56, 9.54s/it] 171it [27:05, 9.43s/it] 172it [27:15, 9.51s/it] 173it [27:25, 9.65s/it] 174it [27:35, 9.75s/it] 175it [27:45, 9.80s/it] 176it [27:54, 9.70s/it] 177it [28:03, 9.53s/it] 178it [28:13, 9.46s/it] 179it [28:22, 9.51s/it] 180it [28:32, 9.67s/it] 181it [28:42, 9.74s/it] 182it [28:52, 9.80s/it] 183it [29:02, 9.74s/it] 184it [29:11, 9.65s/it] 185it [29:20, 9.53s/it] 186it [29:30, 9.54s/it] 187it [29:40, 9.67s/it] 188it [29:50, 9.74s/it] 189it [30:00, 9.81s/it] 190it [30:09, 9.72s/it] 191it [30:18, 9.55s/it] 192it [30:28, 9.45s/it] 193it [30:37, 9.51s/it] 194it [30:47, 9.69s/it] 195it [30:57, 9.77s/it] 196it [31:07, 9.82s/it] 197it [31:17, 9.72s/it] 198it [31:26, 9.53s/it] 199it [31:35, 9.43s/it] 200it [31:45, 9.49s/it] 201it [31:55, 9.62s/it] 202it [32:05, 9.71s/it] 203it [32:14, 9.77s/it] 204it [32:24, 9.74s/it] 205it [32:34, 9.63s/it] 206it [32:43, 9.52s/it] 207it [32:52, 9.58s/it] 208it [33:03, 9.75s/it] 209it [33:13, 9.86s/it] 210it [33:23, 9.90s/it] 211it [33:32, 9.80s/it] 212it [33:42, 9.68s/it] 213it [33:51, 9.58s/it] 214it [34:01, 9.59s/it] 215it [34:11, 9.74s/it] 216it [34:21, 9.87s/it] 217it [34:31, 9.91s/it] 218it [34:41, 9.89s/it] 219it [34:50, 9.74s/it] 220it [35:00, 9.66s/it] 221it [35:09, 9.65s/it] 222it [35:20, 9.86s/it] 223it [35:30, 9.96s/it] 224it [35:40, 9.96s/it] 225it [35:50, 9.91s/it] 226it [35:59, 9.78s/it] 227it [36:09, 9.71s/it] 228it [36:18, 9.67s/it] 229it [36:28, 9.82s/it] 230it [36:39, 9.93s/it] 231it [36:48, 9.93s/it] 232it [36:58, 9.89s/it] 233it [37:08, 9.78s/it] 234it [37:17, 9.70s/it] 235it [37:27, 9.66s/it] 236it [37:37, 9.82s/it] 237it [37:47, 9.91s/it] 238it [37:57, 9.93s/it] 239it [38:07, 9.89s/it] 240it [38:16, 9.77s/it] 241it [38:26, 9.71s/it] 242it [38:36, 9.68s/it] 243it [38:46, 9.80s/it] 244it [38:56, 9.90s/it] 245it [39:06, 9.87s/it] 246it [39:15, 9.84s/it] 247it [39:25, 9.74s/it] 248it [39:34, 9.68s/it] 249it [39:44, 9.64s/it] 250it [39:54, 9.73s/it] 251it [40:04, 9.89s/it] 252it [40:14, 9.92s/it] 253it [40:24, 9.93s/it] 254it [40:34, 9.83s/it] 255it [40:43, 9.73s/it] 256it [40:53, 9.66s/it] 257it [41:03, 9.80s/it] 258it [41:13, 9.97s/it] 259it [41:23, 9.97s/it] 260it [41:33, 9.91s/it] 261it [41:43, 9.84s/it] 262it [41:52, 9.77s/it] 263it [42:02, 9.71s/it] 264it [42:12, 9.76s/it] 265it [42:22, 9.89s/it] 266it [42:32, 9.93s/it] 267it [42:42, 9.91s/it] 268it [42:52, 9.89s/it] 269it [43:01, 9.80s/it] 270it [43:11, 9.82s/it] 271it [43:21, 9.90s/it] 272it [43:32, 10.07s/it] 273it [43:42, 10.02s/it] 274it [43:51, 9.98s/it] 275it [44:01, 9.85s/it] 276it [44:11, 9.79s/it] 277it [44:20, 9.73s/it] 278it [44:30, 9.82s/it] 279it [44:40, 9.91s/it] 280it [44:50, 9.89s/it] 281it [45:00, 9.96s/it] 282it [45:10, 9.81s/it] 283it [45:19, 9.72s/it] 284it [45:29, 9.70s/it] 285it [45:39, 9.85s/it] 286it [45:49, 9.98s/it] 287it [45:59, 9.99s/it] 288it [46:09, 9.93s/it] 289it [46:19, 9.77s/it] 290it [46:28, 9.75s/it] 291it [46:38, 9.62s/it] 292it [46:47, 9.62s/it] 293it [46:57, 9.62s/it] 294it [47:06, 9.59s/it] 295it [47:16, 9.65s/it] 296it [47:26, 9.61s/it] 297it [47:35, 9.54s/it] 298it [47:44, 9.43s/it] 299it [47:54, 9.49s/it] 300it [48:04, 9.56s/it] 301it [48:13, 9.63s/it] 302it [48:23, 9.59s/it] 303it [48:32, 9.49s/it] 304it [48:41, 9.41s/it] 305it [48:51, 9.44s/it] 306it [49:01, 9.58s/it] 307it [49:11, 9.66s/it] 308it [49:20, 9.69s/it] 309it [49:30, 9.69s/it] 310it [49:40, 9.66s/it] 311it [49:49, 9.56s/it] 312it [49:58, 9.47s/it] 313it [50:08, 9.46s/it] 314it [50:17, 9.49s/it] 315it [50:27, 9.53s/it] 316it [50:37, 9.58s/it] 317it [50:46, 9.63s/it] 318it [50:56, 9.56s/it] 319it [51:05, 9.58s/it] 320it [51:15, 9.63s/it] 321it [51:25, 9.70s/it] 322it [51:35, 9.71s/it] 323it [51:44, 9.73s/it] 324it [51:54, 9.74s/it] 325it [52:04, 9.62s/it] 326it [52:13, 9.53s/it] 327it [52:22, 9.48s/it] 328it [52:32, 9.55s/it] 329it [52:41, 9.53s/it] 330it [52:51, 9.58s/it] 331it [53:01, 9.58s/it] 332it [53:10, 9.47s/it] 333it [53:19, 9.42s/it] 334it [53:29, 9.43s/it] 335it [53:38, 9.53s/it] 336it [53:48, 9.63s/it] 337it [53:58, 9.66s/it] 338it [54:08, 9.70s/it] 339it [54:17, 9.54s/it] 340it [54:26, 9.45s/it] 341it [54:36, 9.40s/it] 342it [54:45, 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[2:29:22, 8.95s/it] 959it [2:29:31, 8.90s/it] 960it [2:29:40, 8.85s/it] 961it [2:29:49, 8.86s/it] 962it [2:29:57, 8.82s/it] 963it [2:30:06, 8.79s/it] 964it [2:30:15, 8.78s/it] 965it [2:30:24, 8.80s/it] 966it [2:30:32, 8.81s/it] 967it [2:30:41, 8.77s/it] 968it [2:30:50, 8.81s/it] 969it [2:30:59, 8.80s/it] 970it [2:31:08, 8.78s/it] 971it [2:31:16, 8.76s/it] 972it [2:31:25, 8.77s/it] 973it [2:31:34, 8.76s/it] 974it [2:31:43, 8.77s/it] 975it [2:31:51, 8.79s/it] 976it [2:32:00, 8.79s/it] 977it [2:32:09, 8.75s/it] 978it [2:32:18, 8.76s/it] 979it [2:32:27, 8.81s/it] 980it [2:32:35, 8.76s/it] 981it [2:32:44, 8.75s/it] 982it [2:32:53, 8.74s/it] 983it [2:33:01, 8.74s/it] 984it [2:33:10, 8.74s/it] 985it [2:33:19, 8.72s/it] 986it [2:33:28, 8.75s/it] 987it [2:33:36, 8.75s/it] 988it [2:33:45, 8.74s/it] 989it [2:33:54, 8.74s/it] 990it [2:34:03, 8.72s/it] 991it [2:34:11, 8.77s/it] 992it [2:34:20, 8.77s/it] 993it [2:34:29, 8.77s/it] 994it [2:34:38, 8.78s/it] 995it [2:34:47, 8.80s/it] 996it [2:34:55, 8.79s/it] 997it [2:35:04, 8.76s/it] 998it [2:35:13, 8.78s/it] 999it [2:35:22, 8.77s/it] 1000it [2:35:30, 8.75s/it] 1000it [2:35:30, 9.33s/it] +Error counts: + cyclic_id: 0 + cyclic_inchikey: 0 + cyclic_scaffold: 0 + cyclic_mwt: 0 + cyclic_clogp: 0 + cyclic_tpsa: 0 +⏰ Completed process in 2:35:53.974098 ++ rm /nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/train/cyc-pep-6-12mer-70M_39.csv diff --git a/train/cyc-pep-6-12mer-70M_40.csv.gz b/train/cyc-pep-6-12mer-70M_40.csv.gz index edf6099387415adc31424b53fe8a28a58968603b..d4b71700646d3140906e1cd9b4c58bc8cf1c1819 100644 --- a/train/cyc-pep-6-12mer-70M_40.csv.gz +++ b/train/cyc-pep-6-12mer-70M_40.csv.gz @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:79cedb6abbab3a89cb5d7383bbc3522c8e1587fe3e820b3d450b893ed547f3bd -size 52814706 +oid sha256:eca53078d55ff88f40c15933261fe19060f08fa520fb2bb278786529533f1287 +size 105535344 diff --git a/train/cyc-pep-6-12mer-70M_40.log b/train/cyc-pep-6-12mer-70M_40.log new file mode 100644 index 0000000000000000000000000000000000000000..a398049f8e216c808592379c2180d45de7a40f90 --- /dev/null +++ b/train/cyc-pep-6-12mer-70M_40.log @@ -0,0 +1,337 @@ ++ module purge ++ '[' -z '' ']' ++ case "$-" in ++ __lmod_sh_dbg=x ++ '[' -n x ']' ++ set +x +Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output +Shell debugging restarted ++ unset __lmod_sh_dbg ++ return 0 ++ module load Anaconda3/2023.03 ++ '[' -z '' ']' ++ case "$-" in ++ __lmod_sh_dbg=x ++ '[' -n x ']' ++ set +x +Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output +Shell debugging restarted ++ unset __lmod_sh_dbg ++ return 0 ++ source /camp/home/johnsoe/.bashrc +++ '[' '' = yes ']' +++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' ++++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.bash hook +++ __conda_setup='export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'' + +# Copyright (C) 2012 Anaconda, Inc +# SPDX-License-Identifier: BSD-3-Clause +__conda_exe() ( + "$CONDA_EXE" $_CE_M $_CE_CONDA "$@" +) + +__conda_hashr() { + if [ -n "${ZSH_VERSION:+x}" ]; then + \rehash + elif [ -n "${POSH_VERSION:+x}" ]; then + : # pass + else + \hash -r + fi +} + +__conda_activate() { + if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then + # Handle transition from shell activated with conda <= 4.3 to a subsequent activation + # after conda updated to >= 4.4. See issue #6173. + PS1="$CONDA_PS1_BACKUP" + \unset CONDA_PS1_BACKUP + fi + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return + \eval "$ask_conda" + __conda_hashr +} + +__conda_reactivate() { + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return + \eval "$ask_conda" + __conda_hashr +} + +conda() { + \local cmd="${1-__missing__}" + case "$cmd" in + activate|deactivate) + __conda_activate "$@" + ;; + install|update|upgrade|remove|uninstall) + __conda_exe "$@" || \return + __conda_reactivate + ;; + *) + __conda_exe "$@" + ;; + esac +} + +if [ -z "${CONDA_SHLVL+x}" ]; then + \export CONDA_SHLVL=0 + # In dev-mode CONDA_EXE is python.exe and on Windows + # it is in a different relative location to condabin. + if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then + PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}" + else + PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}" + fi + \export PATH + + # We'\''re not allowing PS1 to be unbound. It must at least be set. + # However, we'\''re not exporting it, which can cause problems when starting a second shell + # via a first shell (i.e. starting zsh from bash). + if [ -z "${PS1+x}" ]; then + PS1= + fi +fi + +conda activate base' +++ '[' 0 -eq 0 ']' +++ eval 'export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'' + +# Copyright (C) 2012 Anaconda, Inc +# SPDX-License-Identifier: BSD-3-Clause +__conda_exe() ( + "$CONDA_EXE" $_CE_M $_CE_CONDA "$@" +) + +__conda_hashr() { + if [ -n "${ZSH_VERSION:+x}" ]; then + \rehash + elif [ -n "${POSH_VERSION:+x}" ]; then + : # pass + else + \hash -r + fi +} + +__conda_activate() { + if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then + # Handle transition from shell activated with conda <= 4.3 to a subsequent activation + # after conda updated to >= 4.4. See issue #6173. + PS1="$CONDA_PS1_BACKUP" + \unset CONDA_PS1_BACKUP + fi + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return + \eval "$ask_conda" + __conda_hashr +} + +__conda_reactivate() { + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return + \eval "$ask_conda" + __conda_hashr +} + +conda() { + \local cmd="${1-__missing__}" + case "$cmd" in + activate|deactivate) + __conda_activate "$@" + ;; + install|update|upgrade|remove|uninstall) + __conda_exe "$@" || \return + __conda_reactivate + ;; + *) + __conda_exe "$@" + ;; + esac +} + +if [ -z "${CONDA_SHLVL+x}" ]; then + \export CONDA_SHLVL=0 + # In dev-mode CONDA_EXE is python.exe and on Windows + # it is in a different relative location to condabin. + if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then + PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}" + else + PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}" + fi + \export PATH + + # We'\''re not allowing PS1 to be unbound. It must at least be set. + # However, we'\''re not exporting it, which can cause problems when starting a second shell + # via a first shell (i.e. starting zsh from bash). + if [ -z "${PS1+x}" ]; then + PS1= + fi +fi + +conda activate base' ++++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda ++++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda ++++ export _CE_M= ++++ _CE_M= ++++ export _CE_CONDA= ++++ _CE_CONDA= ++++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ '[' -z x ']' ++++ conda activate base ++++ local cmd=activate ++++ case "$cmd" in ++++ __conda_activate activate base ++++ '[' -n '' ']' ++++ local ask_conda +++++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++++ __conda_exe shell.posix activate base +++++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate base ++++ ask_conda='PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_SHLVL='\''6'\'' +export CONDA_DEFAULT_ENV='\''base'\'' +export CONDA_PROMPT_MODIFIER='\''(base) '\'' +export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' ++++ eval 'PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_SHLVL='\''6'\'' +export CONDA_DEFAULT_ENV='\''base'\'' +export CONDA_PROMPT_MODIFIER='\''(base) '\'' +export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' +++++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++++ export CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0 +++++ CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0 +++++ export CONDA_SHLVL=6 +++++ CONDA_SHLVL=6 +++++ export CONDA_DEFAULT_ENV=base +++++ CONDA_DEFAULT_ENV=base +++++ export 'CONDA_PROMPT_MODIFIER=(base) ' +++++ CONDA_PROMPT_MODIFIER='(base) ' +++++ export CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev +++++ CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev +++++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++++ export _CE_M= +++++ _CE_M= +++++ export _CE_CONDA= +++++ _CE_CONDA= +++++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python +++++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ __conda_hashr ++++ '[' -n '' ']' ++++ '[' -n '' ']' ++++ hash -r +++ unset __conda_setup ++ conda activate schemist-dev ++ local cmd=activate ++ case "$cmd" in ++ __conda_activate activate schemist-dev ++ '[' -n '' ']' ++ local ask_conda +++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++ __conda_exe shell.posix activate schemist-dev +++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate schemist-dev ++ ask_conda='PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_SHLVL='\''7'\'' +export CONDA_DEFAULT_ENV='\''schemist-dev'\'' +export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\'' +export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' ++ eval 'PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_SHLVL='\''7'\'' +export CONDA_DEFAULT_ENV='\''schemist-dev'\'' +export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\'' +export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' +++ PS1='(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++ export CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev +++ CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev +++ export CONDA_SHLVL=7 +++ CONDA_SHLVL=7 +++ export CONDA_DEFAULT_ENV=schemist-dev +++ CONDA_DEFAULT_ENV=schemist-dev +++ export 'CONDA_PROMPT_MODIFIER=(schemist-dev) ' +++ CONDA_PROMPT_MODIFIER='(schemist-dev) ' +++ export CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0 +++ CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0 +++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++ export _CE_M= +++ _CE_M= +++ export _CE_CONDA= +++ _CE_CONDA= +++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python +++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++ __conda_hashr ++ '[' -n '' ']' ++ '[' -n '' ']' ++ hash -r ++ CHUNK_HEAD_FILE=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz ++ INPUT=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/train/cyc-pep-6-12mer-70M_40.csv ++ COLUMN=cysteine_to_N_cyclization ++ PREFIX=cyclic_ ++ AWK='1 { print $8, $1, $2, $10, $3 }' ++ '[' -z cysteine_to_N_cyclization ']' ++ '[' -z cyclic_ ']' ++ '[' -z '1 { print $8, $1, $2, $10, $3 }' ']' ++ cat /dev/fd/63 /nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/train/cyc-pep-6-12mer-70M_40.csv ++ awk -F, -v OFS=, '1 { print $8, $1, $2, $10, $3 }' ++ schemist convert -f csv --column cysteine_to_N_cyclization --to id inchikey scaffold mwt clogp tpsa --prefix cyclic_ --options prefix=SCB- ++ gzip --best +++ head -n1 +++ tr ' ' , +++ zcat /nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz +🚀 Converting between string representations with the following parameters: + subcommand: convert + output: <_io.TextIOWrapper name='' mode='w' encoding='utf-8'> + format: csv + input: <_io.TextIOWrapper name='' mode='r' encoding='utf-8'> + representation: SMILES + column: cysteine_to_N_cyclization + prefix: cyclic_ + to: ['id', 'inchikey', 'scaffold', 'mwt', 'clogp', 'tpsa'] + options: ['prefix=SCB-'] + func: + 0it [00:00, ?it/s] 1it [00:12, 12.30s/it] 2it [00:23, 11.74s/it] 3it [00:34, 11.43s/it] 4it [00:47, 11.80s/it] 5it [00:57, 11.42s/it] 6it 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[2:45:54, 9.73s/it] 977it [2:46:03, 9.70s/it] 978it [2:46:13, 9.72s/it] 979it [2:46:23, 9.73s/it] 980it [2:46:33, 9.72s/it] 981it [2:46:42, 9.69s/it] 982it [2:46:52, 9.66s/it] 983it [2:47:02, 9.66s/it] 984it [2:47:11, 9.67s/it] 985it [2:47:21, 9.67s/it] 986it [2:47:31, 9.67s/it] 987it [2:47:40, 9.64s/it] 988it [2:47:50, 9.61s/it] 989it [2:47:59, 9.62s/it] 990it [2:48:09, 9.64s/it] 991it [2:48:19, 9.64s/it] 992it [2:48:28, 9.66s/it] 993it [2:48:38, 9.64s/it] 994it [2:48:48, 9.63s/it] 995it [2:48:57, 9.63s/it] 996it [2:49:07, 9.63s/it] 997it [2:49:17, 9.66s/it] 998it [2:49:26, 9.68s/it] 999it [2:49:36, 9.67s/it] 1000it [2:49:46, 9.66s/it] 1000it [2:49:46, 10.19s/it] +Error counts: + cyclic_id: 0 + cyclic_inchikey: 0 + cyclic_scaffold: 0 + cyclic_mwt: 0 + cyclic_clogp: 0 + cyclic_tpsa: 0 +⏰ Completed process in 2:50:10.649625 ++ rm /nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/train/cyc-pep-6-12mer-70M_40.csv diff --git a/train/cyc-pep-6-12mer-70M_41.csv.gz b/train/cyc-pep-6-12mer-70M_41.csv.gz index baedc1fe55fc208aa972df703d0f5db064e6dd82..bbac69dd2c40c406681e47e421d9ab7bdfe749fc 100644 --- a/train/cyc-pep-6-12mer-70M_41.csv.gz +++ b/train/cyc-pep-6-12mer-70M_41.csv.gz @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:994507497dbb5b13393cac3951cae17ef31524e0271faaec727f8b23cc306800 -size 54494420 +oid sha256:e849a49bf6d5a1e436c70645af6642e0f358f046756c1f49f8c9340233203b17 +size 107782628 diff --git a/train/cyc-pep-6-12mer-70M_41.log b/train/cyc-pep-6-12mer-70M_41.log new file mode 100644 index 0000000000000000000000000000000000000000..b333d5219777764048af18531644498bebb4ce30 --- /dev/null +++ b/train/cyc-pep-6-12mer-70M_41.log @@ -0,0 +1,337 @@ ++ module purge ++ '[' -z '' ']' ++ case "$-" in ++ __lmod_sh_dbg=x ++ '[' -n x ']' ++ set +x +Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output +Shell debugging restarted ++ unset __lmod_sh_dbg ++ return 0 ++ module load Anaconda3/2023.03 ++ '[' -z '' ']' ++ case "$-" in ++ __lmod_sh_dbg=x ++ '[' -n x ']' ++ set +x +Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output +Shell debugging restarted ++ unset __lmod_sh_dbg ++ return 0 ++ source /camp/home/johnsoe/.bashrc +++ '[' '' = yes ']' +++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' ++++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.bash hook +++ __conda_setup='export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'' + +# Copyright (C) 2012 Anaconda, Inc +# SPDX-License-Identifier: BSD-3-Clause +__conda_exe() ( + "$CONDA_EXE" $_CE_M $_CE_CONDA "$@" +) + +__conda_hashr() { + if [ -n "${ZSH_VERSION:+x}" ]; then + \rehash + elif [ -n "${POSH_VERSION:+x}" ]; then + : # pass + else + \hash -r + fi +} + +__conda_activate() { + if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then + # Handle transition from shell activated with conda <= 4.3 to a subsequent activation + # after conda updated to >= 4.4. See issue #6173. + PS1="$CONDA_PS1_BACKUP" + \unset CONDA_PS1_BACKUP + fi + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return + \eval "$ask_conda" + __conda_hashr +} + +__conda_reactivate() { + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return + \eval "$ask_conda" + __conda_hashr +} + +conda() { + \local cmd="${1-__missing__}" + case "$cmd" in + activate|deactivate) + __conda_activate "$@" + ;; + install|update|upgrade|remove|uninstall) + __conda_exe "$@" || \return + __conda_reactivate + ;; + *) + __conda_exe "$@" + ;; + esac +} + +if [ -z "${CONDA_SHLVL+x}" ]; then + \export CONDA_SHLVL=0 + # In dev-mode CONDA_EXE is python.exe and on Windows + # it is in a different relative location to condabin. + if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then + PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}" + else + PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}" + fi + \export PATH + + # We'\''re not allowing PS1 to be unbound. It must at least be set. + # However, we'\''re not exporting it, which can cause problems when starting a second shell + # via a first shell (i.e. starting zsh from bash). + if [ -z "${PS1+x}" ]; then + PS1= + fi +fi + +conda activate base' +++ '[' 0 -eq 0 ']' +++ eval 'export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'' + +# Copyright (C) 2012 Anaconda, Inc +# SPDX-License-Identifier: BSD-3-Clause +__conda_exe() ( + "$CONDA_EXE" $_CE_M $_CE_CONDA "$@" +) + +__conda_hashr() { + if [ -n "${ZSH_VERSION:+x}" ]; then + \rehash + elif [ -n "${POSH_VERSION:+x}" ]; then + : # pass + else + \hash -r + fi +} + +__conda_activate() { + if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then + # Handle transition from shell activated with conda <= 4.3 to a subsequent activation + # after conda updated to >= 4.4. See issue #6173. + PS1="$CONDA_PS1_BACKUP" + \unset CONDA_PS1_BACKUP + fi + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return + \eval "$ask_conda" + __conda_hashr +} + +__conda_reactivate() { + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return + \eval "$ask_conda" + __conda_hashr +} + +conda() { + \local cmd="${1-__missing__}" + case "$cmd" in + activate|deactivate) + __conda_activate "$@" + ;; + install|update|upgrade|remove|uninstall) + __conda_exe "$@" || \return + __conda_reactivate + ;; + *) + __conda_exe "$@" + ;; + esac +} + +if [ -z "${CONDA_SHLVL+x}" ]; then + \export CONDA_SHLVL=0 + # In dev-mode CONDA_EXE is python.exe and on Windows + # it is in a different relative location to condabin. + if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then + PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}" + else + PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}" + fi + \export PATH + + # We'\''re not allowing PS1 to be unbound. It must at least be set. + # However, we'\''re not exporting it, which can cause problems when starting a second shell + # via a first shell (i.e. starting zsh from bash). + if [ -z "${PS1+x}" ]; then + PS1= + fi +fi + +conda activate base' ++++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda ++++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda ++++ export _CE_M= ++++ _CE_M= ++++ export _CE_CONDA= ++++ _CE_CONDA= ++++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ '[' -z x ']' ++++ conda activate base ++++ local cmd=activate ++++ case "$cmd" in ++++ __conda_activate activate base ++++ '[' -n '' ']' ++++ local ask_conda +++++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++++ __conda_exe shell.posix activate base +++++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate base ++++ ask_conda='PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_SHLVL='\''6'\'' +export CONDA_DEFAULT_ENV='\''base'\'' +export CONDA_PROMPT_MODIFIER='\''(base) '\'' +export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' ++++ eval 'PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_SHLVL='\''6'\'' +export CONDA_DEFAULT_ENV='\''base'\'' +export CONDA_PROMPT_MODIFIER='\''(base) '\'' +export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' +++++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++++ export CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0 +++++ CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0 +++++ export CONDA_SHLVL=6 +++++ CONDA_SHLVL=6 +++++ export CONDA_DEFAULT_ENV=base +++++ CONDA_DEFAULT_ENV=base +++++ export 'CONDA_PROMPT_MODIFIER=(base) ' +++++ CONDA_PROMPT_MODIFIER='(base) ' +++++ export CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev +++++ CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev +++++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++++ export _CE_M= +++++ _CE_M= +++++ export _CE_CONDA= +++++ _CE_CONDA= +++++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python +++++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ __conda_hashr ++++ '[' -n '' ']' ++++ '[' -n '' ']' ++++ hash -r +++ unset __conda_setup ++ conda activate schemist-dev ++ local cmd=activate ++ case "$cmd" in ++ __conda_activate activate schemist-dev ++ '[' -n '' ']' ++ local ask_conda +++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++ __conda_exe shell.posix activate schemist-dev +++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate schemist-dev ++ ask_conda='PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_SHLVL='\''7'\'' +export CONDA_DEFAULT_ENV='\''schemist-dev'\'' +export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\'' +export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' ++ eval 'PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_SHLVL='\''7'\'' +export CONDA_DEFAULT_ENV='\''schemist-dev'\'' +export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\'' +export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' +++ PS1='(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++ export CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev +++ CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev +++ export CONDA_SHLVL=7 +++ CONDA_SHLVL=7 +++ export CONDA_DEFAULT_ENV=schemist-dev +++ CONDA_DEFAULT_ENV=schemist-dev +++ export 'CONDA_PROMPT_MODIFIER=(schemist-dev) ' +++ CONDA_PROMPT_MODIFIER='(schemist-dev) ' +++ export CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0 +++ CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0 +++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++ export _CE_M= +++ _CE_M= +++ export _CE_CONDA= +++ _CE_CONDA= +++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python +++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++ __conda_hashr ++ '[' -n '' ']' ++ '[' -n '' ']' ++ hash -r ++ CHUNK_HEAD_FILE=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz ++ INPUT=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/train/cyc-pep-6-12mer-70M_41.csv ++ COLUMN=cysteine_to_N_cyclization ++ PREFIX=cyclic_ ++ AWK='1 { print $8, $1, $2, $10, $3 }' ++ '[' -z cysteine_to_N_cyclization ']' ++ '[' -z cyclic_ ']' ++ '[' -z '1 { print $8, $1, $2, $10, $3 }' ']' ++ awk -F, -v OFS=, '1 { print $8, $1, $2, $10, $3 }' ++ cat /dev/fd/63 /nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/train/cyc-pep-6-12mer-70M_41.csv ++ gzip --best ++ schemist convert -f csv --column cysteine_to_N_cyclization --to id inchikey scaffold mwt clogp tpsa --prefix cyclic_ --options prefix=SCB- +++ head -n1 +++ zcat /nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz +++ tr ' ' , +🚀 Converting between string representations with the following parameters: + subcommand: convert + output: <_io.TextIOWrapper name='' mode='w' encoding='utf-8'> + format: csv + input: <_io.TextIOWrapper name='' mode='r' encoding='utf-8'> + representation: SMILES + column: cysteine_to_N_cyclization + prefix: cyclic_ + to: ['id', 'inchikey', 'scaffold', 'mwt', 'clogp', 'tpsa'] + options: ['prefix=SCB-'] + func: + 0it [00:00, ?it/s] 1it [00:10, 10.02s/it] 2it [00:20, 10.26s/it] 3it [00:31, 10.52s/it] 4it [00:42, 10.73s/it] 5it [00:52, 10.68s/it] 6it [01:02, 10.38s/it] 7it [01:12, 10.20s/it] 8it [01:22, 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10.62s/it] 593it [1:42:28, 10.69s/it] 594it [1:42:38, 10.50s/it] 595it [1:42:49, 10.45s/it] 596it [1:42:59, 10.44s/it] 597it [1:43:10, 10.46s/it] 598it [1:43:21, 10.58s/it] 599it [1:43:31, 10.60s/it] 600it [1:43:42, 10.70s/it] 601it [1:43:53, 10.67s/it] 602it [1:44:03, 10.56s/it] 603it [1:44:14, 10.66s/it] 604it [1:44:25, 10.79s/it] 605it [1:44:36, 10.88s/it] 606it [1:44:47, 10.86s/it] 607it [1:44:57, 10.65s/it] 608it [1:45:07, 10.47s/it] 609it [1:45:18, 10.61s/it] 610it [1:45:30, 10.87s/it] 611it [1:45:40, 10.81s/it] 612it [1:45:51, 10.92s/it] 613it [1:46:02, 10.76s/it] 614it [1:46:12, 10.50s/it] 615it [1:46:21, 10.27s/it] 616it [1:46:31, 10.20s/it] 617it [1:46:42, 10.22s/it] 618it [1:46:52, 10.37s/it] 619it [1:47:03, 10.30s/it] 620it [1:47:13, 10.20s/it] 621it [1:47:23, 10.19s/it] 622it [1:47:33, 10.30s/it] 623it [1:47:44, 10.43s/it] 624it [1:47:54, 10.39s/it] 625it [1:48:04, 10.29s/it] 626it [1:48:15, 10.27s/it] 627it [1:48:25, 10.24s/it] 628it [1:48:35, 10.35s/it] 629it [1:48:46, 10.50s/it] 630it [1:48:57, 10.45s/it] 631it [1:49:06, 10.29s/it] 632it [1:49:17, 10.24s/it] 633it [1:49:28, 10.46s/it] 634it [1:49:38, 10.60s/it] 635it [1:49:49, 10.68s/it] 636it [1:50:00, 10.59s/it] 637it [1:50:10, 10.45s/it] 638it [1:50:20, 10.31s/it] 639it [1:50:30, 10.28s/it] 640it [1:50:41, 10.40s/it] 641it [1:50:51, 10.51s/it] 642it [1:51:02, 10.47s/it] 643it [1:51:12, 10.44s/it] 644it [1:51:22, 10.31s/it] 645it [1:51:33, 10.32s/it] 646it [1:51:43, 10.34s/it] 647it [1:51:54, 10.45s/it] 648it [1:52:04, 10.36s/it] 649it [1:52:14, 10.28s/it] 650it [1:52:24, 10.26s/it] 651it [1:52:34, 10.10s/it] 652it [1:52:44, 10.17s/it] 653it [1:52:56, 10.58s/it] 654it [1:53:07, 10.87s/it] 655it [1:53:18, 10.80s/it] 656it [1:53:28, 10.71s/it] 657it [1:53:39, 10.60s/it] 658it [1:53:49, 10.60s/it] 659it [1:54:00, 10.72s/it] 660it [1:54:12, 10.87s/it] 661it [1:54:22, 10.73s/it] 662it [1:54:32, 10.66s/it] 663it [1:54:43, 10.68s/it] 664it [1:54:54, 10.61s/it] 665it [1:55:04, 10.56s/it] 666it [1:55:15, 10.73s/it] 667it [1:55:26, 10.64s/it] 668it [1:55:36, 10.57s/it] 669it [1:55:46, 10.50s/it] 670it [1:55:57, 10.50s/it] 671it [1:56:07, 10.52s/it] 672it [1:56:18, 10.57s/it] 673it [1:56:29, 10.77s/it] 674it [1:56:40, 10.74s/it] 675it [1:56:50, 10.65s/it] 676it [1:57:01, 10.61s/it] 677it [1:57:11, 10.48s/it] 678it [1:57:22, 10.44s/it] 679it [1:57:33, 10.67s/it] 680it [1:57:44, 10.88s/it] 681it [1:57:55, 10.75s/it] 682it [1:58:05, 10.61s/it] 683it [1:58:15, 10.62s/it] 684it [1:58:26, 10.62s/it] 685it [1:58:37, 10.61s/it] 686it [1:58:48, 10.86s/it] 687it [1:58:59, 10.88s/it] 688it [1:59:09, 10.73s/it] 689it [1:59:20, 10.61s/it] 690it [1:59:30, 10.50s/it] 691it [1:59:40, 10.40s/it] 692it [1:59:51, 10.39s/it] 693it [2:00:02, 10.58s/it] 694it [2:00:12, 10.62s/it] 695it [2:00:23, 10.54s/it] 696it [2:00:33, 10.47s/it] 697it [2:00:43, 10.47s/it] 698it [2:00:53, 10.33s/it] 699it [2:01:04, 10.35s/it] 700it [2:01:14, 10.26s/it] 701it [2:01:24, 10.14s/it] 702it [2:01:33, 10.01s/it] 703it [2:01:43, 9.97s/it] 704it [2:01:53, 9.99s/it] 705it [2:02:04, 10.07s/it] 706it [2:02:14, 10.17s/it] 707it [2:02:24, 10.14s/it] 708it [2:02:34, 10.00s/it] 709it [2:02:44, 9.95s/it] 710it [2:02:53, 9.93s/it] 711it [2:03:03, 9.89s/it] 712it [2:03:13, 9.93s/it] 713it [2:03:23, 10.01s/it] 714it [2:03:34, 10.04s/it] 715it [2:03:43, 9.96s/it] 716it [2:03:53, 9.89s/it] 717it [2:04:04, 10.24s/it] 718it [2:04:16, 10.61s/it] 719it [2:04:27, 10.90s/it] 720it [2:04:38, 10.94s/it] 721it [2:04:49, 10.82s/it] 722it [2:04:58, 10.47s/it] 723it [2:05:08, 10.26s/it] 724it [2:05:19, 10.30s/it] 725it [2:05:29, 10.33s/it] 726it [2:05:39, 10.35s/it] 727it [2:05:50, 10.32s/it] 728it [2:06:00, 10.20s/it] 729it [2:06:09, 10.00s/it] 730it [2:06:19, 9.94s/it] 731it [2:06:29, 9.95s/it] 732it [2:06:39, 10.03s/it] 733it [2:06:50, 10.18s/it] 734it [2:07:00, 10.12s/it] 735it [2:07:09, 9.95s/it] 736it [2:07:19, 9.84s/it] 737it [2:07:28, 9.76s/it] 738it [2:07:38, 9.80s/it] 739it [2:07:48, 9.86s/it] 740it [2:07:58, 9.93s/it] 741it [2:08:08, 9.98s/it] 742it [2:08:18, 9.90s/it] 743it [2:08:28, 9.81s/it] 744it [2:08:37, 9.73s/it] 745it [2:08:47, 9.75s/it] 746it [2:08:57, 9.81s/it] 747it [2:09:07, 9.85s/it] 748it [2:09:17, 9.93s/it] 749it [2:09:27, 9.85s/it] 750it [2:09:36, 9.72s/it] 751it [2:09:46, 9.65s/it] 752it [2:09:55, 9.71s/it] 753it [2:10:06, 9.81s/it] 754it [2:10:15, 9.86s/it] 755it [2:10:25, 9.89s/it] 756it [2:10:35, 9.84s/it] 757it [2:10:45, 9.79s/it] 758it [2:10:54, 9.70s/it] 759it [2:11:04, 9.74s/it] 760it [2:11:14, 9.84s/it] 761it [2:11:24, 9.87s/it] 762it [2:11:34, 9.91s/it] 763it [2:11:44, 9.87s/it] 764it [2:11:54, 9.79s/it] 765it [2:12:03, 9.78s/it] 766it [2:12:13, 9.83s/it] 767it [2:12:23, 9.84s/it] 768it [2:12:33, 9.87s/it] 769it [2:12:44, 10.13s/it] 770it [2:12:54, 10.25s/it] 771it [2:13:04, 10.06s/it] 772it [2:13:13, 9.90s/it] 773it [2:13:23, 9.80s/it] 774it [2:13:33, 9.74s/it] 775it [2:13:43, 9.79s/it] 776it [2:13:52, 9.78s/it] 777it [2:14:02, 9.75s/it] 778it [2:14:12, 9.81s/it] 779it [2:14:22, 9.79s/it] 780it [2:14:31, 9.74s/it] 781it [2:14:41, 9.72s/it] 782it [2:14:51, 9.73s/it] 783it [2:15:01, 9.78s/it] 784it [2:15:11, 9.82s/it] 785it [2:15:21, 9.89s/it] 786it [2:15:30, 9.82s/it] 787it [2:15:40, 9.74s/it] 788it [2:15:49, 9.70s/it] 789it [2:15:59, 9.69s/it] 790it [2:16:09, 9.73s/it] 791it [2:16:19, 9.77s/it] 792it [2:16:29, 9.83s/it] 793it [2:16:39, 9.86s/it] 794it [2:16:48, 9.79s/it] 795it [2:16:58, 9.67s/it] 796it [2:17:07, 9.65s/it] 797it [2:17:17, 9.60s/it] 798it [2:17:26, 9.57s/it] 799it [2:17:36, 9.66s/it] 800it [2:17:46, 9.70s/it] 801it [2:17:56, 9.78s/it] 802it [2:18:06, 9.79s/it] 803it [2:18:15, 9.75s/it] 804it [2:18:25, 9.70s/it] 805it [2:18:34, 9.64s/it] 806it [2:18:44, 9.61s/it] 807it [2:18:54, 9.66s/it] 808it [2:19:04, 9.76s/it] 809it [2:19:14, 9.83s/it] 810it [2:19:24, 9.90s/it] 811it [2:19:34, 9.86s/it] 812it [2:19:43, 9.76s/it] 813it [2:19:53, 9.76s/it] 814it [2:20:03, 9.72s/it] 815it [2:20:12, 9.74s/it] 816it [2:20:22, 9.75s/it] 817it [2:20:32, 9.84s/it] 818it [2:20:42, 9.99s/it] 819it [2:20:52, 9.88s/it] 820it [2:21:02, 9.83s/it] 821it [2:21:12, 9.88s/it] 822it [2:21:23, 10.13s/it] 823it [2:21:33, 10.22s/it] 824it [2:21:44, 10.31s/it] 825it [2:21:53, 10.12s/it] 826it [2:22:03, 9.99s/it] 827it [2:22:13, 10.00s/it] 828it [2:22:23, 9.95s/it] 829it [2:22:32, 9.85s/it] 830it [2:22:42, 9.79s/it] 831it [2:22:52, 9.78s/it] 832it [2:23:02, 9.80s/it] 833it [2:23:12, 9.85s/it] 834it [2:23:21, 9.76s/it] 835it [2:23:31, 9.66s/it] 836it [2:23:40, 9.68s/it] 837it [2:23:50, 9.69s/it] 838it [2:23:59, 9.63s/it] 839it [2:24:09, 9.61s/it] 840it [2:24:19, 9.62s/it] 841it [2:24:28, 9.61s/it] 842it [2:24:38, 9.55s/it] 843it [2:24:47, 9.54s/it] 844it [2:24:57, 9.55s/it] 845it [2:25:06, 9.53s/it] 846it [2:25:16, 9.58s/it] 847it [2:25:26, 9.63s/it] 848it [2:25:35, 9.60s/it] 849it [2:25:45, 9.54s/it] 850it [2:25:54, 9.52s/it] 851it [2:26:04, 9.56s/it] 852it [2:26:13, 9.58s/it] 853it [2:26:23, 9.57s/it] 854it [2:26:33, 9.59s/it] 855it [2:26:42, 9.61s/it] 856it [2:26:52, 9.65s/it] 857it [2:27:02, 9.77s/it] 858it [2:27:12, 9.73s/it] 859it [2:27:21, 9.66s/it] 860it [2:27:31, 9.58s/it] 861it [2:27:40, 9.53s/it] 862it [2:27:49, 9.51s/it] 863it [2:27:59, 9.51s/it] 864it [2:28:08, 9.51s/it] 865it [2:28:18, 9.50s/it] 866it [2:28:27, 9.50s/it] 867it [2:28:37, 9.50s/it] 868it [2:28:46, 9.50s/it] 869it [2:28:56, 9.51s/it] 870it [2:29:05, 9.48s/it] 871it [2:29:15, 9.48s/it] 872it [2:29:24, 9.46s/it] 873it [2:29:34, 9.45s/it] 874it [2:29:43, 9.45s/it] 875it [2:29:53, 9.45s/it] 876it [2:30:02, 9.48s/it] 877it [2:30:12, 9.49s/it] 878it [2:30:21, 9.48s/it] 879it [2:30:31, 9.48s/it] 880it [2:30:40, 9.49s/it] 881it [2:30:50, 9.47s/it] 882it [2:30:59, 9.46s/it] 883it [2:31:08, 9.47s/it] 884it [2:31:18, 9.43s/it] 885it [2:31:27, 9.46s/it] 886it [2:31:37, 9.49s/it] 887it [2:31:46, 9.49s/it] 888it [2:31:56, 9.47s/it] 889it [2:32:05, 9.48s/it] 890it [2:32:15, 9.47s/it] 891it [2:32:24, 9.45s/it] 892it [2:32:34, 9.46s/it] 893it [2:32:43, 9.44s/it] 894it [2:32:52, 9.45s/it] 895it [2:33:02, 9.44s/it] 896it [2:33:11, 9.44s/it] 897it [2:33:21, 9.53s/it] 898it [2:33:31, 9.54s/it] 899it [2:33:40, 9.57s/it] 900it [2:33:50, 9.57s/it] 901it [2:34:00, 9.62s/it] 902it [2:34:09, 9.66s/it] 903it [2:34:19, 9.68s/it] 904it [2:34:29, 9.65s/it] 905it [2:34:38, 9.60s/it] 906it [2:34:48, 9.57s/it] 907it [2:34:57, 9.59s/it] 908it [2:35:07, 9.60s/it] 909it [2:35:17, 9.61s/it] 910it [2:35:26, 9.64s/it] 911it [2:35:36, 9.63s/it] 912it [2:35:45, 9.60s/it] 913it [2:35:55, 9.62s/it] 914it [2:36:05, 9.62s/it] 915it [2:36:14, 9.61s/it] 916it [2:36:24, 9.58s/it] 917it [2:36:33, 9.58s/it] 918it [2:36:43, 9.59s/it] 919it [2:36:53, 9.60s/it] 920it [2:37:02, 9.62s/it] 921it [2:37:12, 9.63s/it] 922it [2:37:22, 9.64s/it] 923it [2:37:31, 9.62s/it] 924it [2:37:41, 9.65s/it] 925it [2:37:51, 9.65s/it] 926it [2:38:00, 9.71s/it] 927it [2:38:10, 9.73s/it] 928it [2:38:20, 9.71s/it] 929it [2:38:29, 9.69s/it] 930it [2:38:39, 9.70s/it] 931it [2:38:49, 9.69s/it] 932it [2:38:58, 9.67s/it] 933it [2:39:08, 9.66s/it] 934it [2:39:18, 9.66s/it] 935it [2:39:27, 9.67s/it] 936it [2:39:37, 9.67s/it] 937it [2:39:47, 9.66s/it] 938it [2:39:56, 9.67s/it] 939it [2:40:06, 9.65s/it] 940it [2:40:16, 9.64s/it] 941it [2:40:25, 9.61s/it] 942it [2:40:35, 9.62s/it] 943it [2:40:44, 9.61s/it] 944it [2:40:54, 9.65s/it] 945it [2:41:04, 9.66s/it] 946it [2:41:13, 9.63s/it] 947it [2:41:23, 9.63s/it] 948it [2:41:33, 9.63s/it] 949it [2:41:42, 9.62s/it] 950it [2:41:52, 9.58s/it] 951it [2:42:01, 9.56s/it] 952it [2:42:11, 9.54s/it] 953it [2:42:20, 9.58s/it] 954it [2:42:30, 9.55s/it] 955it [2:42:40, 9.58s/it] 956it [2:42:49, 9.60s/it] 957it [2:42:59, 9.61s/it] 958it [2:43:08, 9.59s/it] 959it [2:43:18, 9.60s/it] 960it [2:43:28, 9.62s/it] 961it [2:43:37, 9.60s/it] 962it [2:43:47, 9.60s/it] 963it [2:43:56, 9.61s/it] 964it [2:44:06, 9.60s/it] 965it [2:44:16, 9.61s/it] 966it [2:44:25, 9.65s/it] 967it [2:44:35, 9.65s/it] 968it [2:44:45, 9.62s/it] 969it [2:44:54, 9.60s/it] 970it [2:45:04, 9.63s/it] 971it [2:45:14, 9.64s/it] 972it [2:45:23, 9.59s/it] 973it [2:45:33, 9.59s/it] 974it [2:45:42, 9.58s/it] 975it [2:45:52, 9.61s/it] 976it [2:46:01, 9.61s/it] 977it [2:46:11, 9.63s/it] 978it [2:46:21, 9.61s/it] 979it [2:46:30, 9.58s/it] 980it [2:46:40, 9.61s/it] 981it [2:46:50, 9.61s/it] 982it [2:46:59, 9.64s/it] 983it [2:47:09, 9.65s/it] 984it [2:47:18, 9.64s/it] 985it [2:47:28, 9.67s/it] 986it [2:47:38, 9.66s/it] 987it [2:47:48, 9.66s/it] 988it [2:47:57, 9.65s/it] 989it [2:48:07, 9.61s/it] 990it [2:48:16, 9.61s/it] 991it [2:48:26, 9.65s/it] 992it [2:48:36, 9.68s/it] 993it [2:48:46, 9.70s/it] 994it [2:48:55, 9.69s/it] 995it [2:49:05, 9.66s/it] 996it [2:49:14, 9.62s/it] 997it [2:49:24, 9.67s/it] 998it [2:49:34, 9.64s/it] 999it [2:49:43, 9.64s/it] 1000it [2:49:53, 9.66s/it] 1000it [2:49:53, 10.19s/it] +Error counts: + cyclic_id: 0 + cyclic_inchikey: 0 + cyclic_scaffold: 0 + cyclic_mwt: 0 + cyclic_clogp: 0 + cyclic_tpsa: 0 +⏰ Completed process in 2:50:14.550729 ++ rm /nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/train/cyc-pep-6-12mer-70M_41.csv diff --git a/train/cyc-pep-6-12mer-70M_42.csv.gz b/train/cyc-pep-6-12mer-70M_42.csv.gz index 24e633e64db8d773fe39e69736cbeb2bada588c8..6557c5df414bc352905b1f21e33f20b24db62599 100644 --- a/train/cyc-pep-6-12mer-70M_42.csv.gz +++ b/train/cyc-pep-6-12mer-70M_42.csv.gz @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:2913c157b5c5979b3eeebfccf1ec5206e05cfd15d0955ef88ac47ab60db1811b -size 54504729 +oid sha256:52a40049c74ed894deb2bcb1ea4804e5abad062b89af915e003343992d5bf9c6 +size 107810721 diff --git a/train/cyc-pep-6-12mer-70M_42.log b/train/cyc-pep-6-12mer-70M_42.log new file mode 100644 index 0000000000000000000000000000000000000000..cf5c1339978b2d9c0559ad1a994930847c8603e1 --- /dev/null +++ b/train/cyc-pep-6-12mer-70M_42.log @@ -0,0 +1,337 @@ ++ module purge ++ '[' -z '' ']' ++ case "$-" in ++ __lmod_sh_dbg=x ++ '[' -n x ']' ++ set +x +Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output +Shell debugging restarted ++ unset __lmod_sh_dbg ++ return 0 ++ module load Anaconda3/2023.03 ++ '[' -z '' ']' ++ case "$-" in ++ __lmod_sh_dbg=x ++ '[' -n x ']' ++ set +x +Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output +Shell debugging restarted ++ unset __lmod_sh_dbg ++ return 0 ++ source /camp/home/johnsoe/.bashrc +++ '[' '' = yes ']' +++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' ++++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.bash hook +++ __conda_setup='export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'' + +# Copyright (C) 2012 Anaconda, Inc +# SPDX-License-Identifier: BSD-3-Clause +__conda_exe() ( + "$CONDA_EXE" $_CE_M $_CE_CONDA "$@" +) + +__conda_hashr() { + if [ -n "${ZSH_VERSION:+x}" ]; then + \rehash + elif [ -n "${POSH_VERSION:+x}" ]; then + : # pass + else + \hash -r + fi +} + +__conda_activate() { + if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then + # Handle transition from shell activated with conda <= 4.3 to a subsequent activation + # after conda updated to >= 4.4. See issue #6173. + PS1="$CONDA_PS1_BACKUP" + \unset CONDA_PS1_BACKUP + fi + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return + \eval "$ask_conda" + __conda_hashr +} + +__conda_reactivate() { + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return + \eval "$ask_conda" + __conda_hashr +} + +conda() { + \local cmd="${1-__missing__}" + case "$cmd" in + activate|deactivate) + __conda_activate "$@" + ;; + install|update|upgrade|remove|uninstall) + __conda_exe "$@" || \return + __conda_reactivate + ;; + *) + __conda_exe "$@" + ;; + esac +} + +if [ -z "${CONDA_SHLVL+x}" ]; then + \export CONDA_SHLVL=0 + # In dev-mode CONDA_EXE is python.exe and on Windows + # it is in a different relative location to condabin. + if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then + PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}" + else + PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}" + fi + \export PATH + + # We'\''re not allowing PS1 to be unbound. It must at least be set. + # However, we'\''re not exporting it, which can cause problems when starting a second shell + # via a first shell (i.e. starting zsh from bash). + if [ -z "${PS1+x}" ]; then + PS1= + fi +fi + +conda activate base' +++ '[' 0 -eq 0 ']' +++ eval 'export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'' + +# Copyright (C) 2012 Anaconda, Inc +# SPDX-License-Identifier: BSD-3-Clause +__conda_exe() ( + "$CONDA_EXE" $_CE_M $_CE_CONDA "$@" +) + +__conda_hashr() { + if [ -n "${ZSH_VERSION:+x}" ]; then + \rehash + elif [ -n "${POSH_VERSION:+x}" ]; then + : # pass + else + \hash -r + fi +} + +__conda_activate() { + if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then + # Handle transition from shell activated with conda <= 4.3 to a subsequent activation + # after conda updated to >= 4.4. See issue #6173. + PS1="$CONDA_PS1_BACKUP" + \unset CONDA_PS1_BACKUP + fi + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return + \eval "$ask_conda" + __conda_hashr +} + +__conda_reactivate() { + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return + \eval "$ask_conda" + __conda_hashr +} + +conda() { + \local cmd="${1-__missing__}" + case "$cmd" in + activate|deactivate) + __conda_activate "$@" + ;; + install|update|upgrade|remove|uninstall) + __conda_exe "$@" || \return + __conda_reactivate + ;; + *) + __conda_exe "$@" + ;; + esac +} + +if [ -z "${CONDA_SHLVL+x}" ]; then + \export CONDA_SHLVL=0 + # In dev-mode CONDA_EXE is python.exe and on Windows + # it is in a different relative location to condabin. + if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then + PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}" + else + PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}" + fi + \export PATH + + # We'\''re not allowing PS1 to be unbound. It must at least be set. + # However, we'\''re not exporting it, which can cause problems when starting a second shell + # via a first shell (i.e. starting zsh from bash). + if [ -z "${PS1+x}" ]; then + PS1= + fi +fi + +conda activate base' ++++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda ++++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda ++++ export _CE_M= ++++ _CE_M= ++++ export _CE_CONDA= ++++ _CE_CONDA= ++++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ '[' -z x ']' ++++ conda activate base ++++ local cmd=activate ++++ case "$cmd" in ++++ __conda_activate activate base ++++ '[' -n '' ']' ++++ local ask_conda +++++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++++ __conda_exe shell.posix activate base +++++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate base ++++ ask_conda='PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_SHLVL='\''6'\'' +export CONDA_DEFAULT_ENV='\''base'\'' +export CONDA_PROMPT_MODIFIER='\''(base) '\'' +export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' ++++ eval 'PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_SHLVL='\''6'\'' +export CONDA_DEFAULT_ENV='\''base'\'' +export CONDA_PROMPT_MODIFIER='\''(base) '\'' +export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' +++++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++++ export CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0 +++++ CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0 +++++ export CONDA_SHLVL=6 +++++ CONDA_SHLVL=6 +++++ export CONDA_DEFAULT_ENV=base +++++ CONDA_DEFAULT_ENV=base +++++ export 'CONDA_PROMPT_MODIFIER=(base) ' +++++ CONDA_PROMPT_MODIFIER='(base) ' +++++ export CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev +++++ CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev +++++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++++ export _CE_M= +++++ _CE_M= +++++ export _CE_CONDA= +++++ _CE_CONDA= +++++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python +++++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ __conda_hashr ++++ '[' -n '' ']' ++++ '[' -n '' ']' ++++ hash -r +++ unset __conda_setup ++ conda activate schemist-dev ++ local cmd=activate ++ case "$cmd" in ++ __conda_activate activate schemist-dev ++ '[' -n '' ']' ++ local ask_conda +++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++ __conda_exe shell.posix activate schemist-dev +++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate schemist-dev ++ ask_conda='PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_SHLVL='\''7'\'' +export CONDA_DEFAULT_ENV='\''schemist-dev'\'' +export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\'' +export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' ++ eval 'PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_SHLVL='\''7'\'' +export CONDA_DEFAULT_ENV='\''schemist-dev'\'' +export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\'' +export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' +++ PS1='(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++ export CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev +++ CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev +++ export CONDA_SHLVL=7 +++ CONDA_SHLVL=7 +++ export CONDA_DEFAULT_ENV=schemist-dev +++ CONDA_DEFAULT_ENV=schemist-dev +++ export 'CONDA_PROMPT_MODIFIER=(schemist-dev) ' +++ CONDA_PROMPT_MODIFIER='(schemist-dev) ' +++ export CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0 +++ CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0 +++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++ export _CE_M= +++ _CE_M= +++ export _CE_CONDA= +++ _CE_CONDA= +++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python +++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++ __conda_hashr ++ '[' -n '' ']' ++ '[' -n '' ']' ++ hash -r ++ CHUNK_HEAD_FILE=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz ++ INPUT=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/train/cyc-pep-6-12mer-70M_42.csv ++ COLUMN=cysteine_to_N_cyclization ++ PREFIX=cyclic_ ++ AWK='1 { print $8, $1, $2, $10, $3 }' ++ '[' -z cysteine_to_N_cyclization ']' ++ '[' -z cyclic_ ']' ++ '[' -z '1 { print $8, $1, $2, $10, $3 }' ']' ++ cat /dev/fd/63 /nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/train/cyc-pep-6-12mer-70M_42.csv ++ awk -F, -v OFS=, '1 { print $8, $1, $2, $10, $3 }' +++ zcat /nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz ++ schemist convert -f csv --column cysteine_to_N_cyclization --to id inchikey scaffold mwt clogp tpsa --prefix cyclic_ --options prefix=SCB- +++ head -n1 ++ gzip --best +++ tr ' ' , +🚀 Converting between string representations with the following parameters: + subcommand: convert + output: <_io.TextIOWrapper name='' mode='w' encoding='utf-8'> + format: csv + input: <_io.TextIOWrapper name='' mode='r' encoding='utf-8'> + representation: SMILES + column: cysteine_to_N_cyclization + prefix: cyclic_ + to: ['id', 'inchikey', 'scaffold', 'mwt', 'clogp', 'tpsa'] + options: ['prefix=SCB-'] + func: + 0it [00:00, ?it/s] 1it [00:10, 10.02s/it] 2it [00:19, 9.95s/it] 3it [00:29, 9.89s/it] 4it [00:39, 9.93s/it] 5it [00:49, 9.94s/it] 6it 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9.93s/it] 50it [08:16, 9.94s/it] 51it [08:26, 9.87s/it] 52it [08:35, 9.86s/it] 53it [08:45, 9.89s/it] 54it [08:55, 9.91s/it] 55it [09:05, 9.93s/it] 56it [09:15, 9.93s/it] 57it [09:25, 9.90s/it] 58it [09:35, 9.87s/it] 59it [09:45, 9.88s/it] 60it [09:55, 9.88s/it] 61it [10:05, 9.93s/it] 62it [10:15, 9.93s/it] 63it [10:24, 9.88s/it] 64it [10:34, 9.86s/it] 65it [10:44, 9.89s/it] 66it [10:54, 9.90s/it] 67it [11:04, 9.93s/it] 68it [11:14, 9.93s/it] 69it [11:24, 9.91s/it] 70it [11:34, 9.86s/it] 71it [11:44, 9.90s/it] 72it [11:53, 9.89s/it] 73it [12:03, 9.91s/it] 74it [12:13, 9.93s/it] 75it [12:23, 9.92s/it] 76it [12:33, 9.87s/it] 77it [12:43, 9.88s/it] 78it [12:53, 9.89s/it] 79it [13:03, 9.91s/it] 80it [13:13, 9.91s/it] 81it [13:23, 9.89s/it] 82it [13:32, 9.86s/it] 83it [13:42, 9.83s/it] 84it [13:52, 9.87s/it] 85it [14:02, 9.89s/it] 86it [14:12, 9.90s/it] 87it [14:22, 9.88s/it] 88it [14:32, 9.87s/it] 89it [14:41, 9.85s/it] 90it [14:51, 9.87s/it] 91it [15:01, 9.89s/it] 92it [15:11, 9.92s/it] 93it [15:21, 9.93s/it] 94it [15:31, 9.91s/it] 95it [15:41, 9.87s/it] 96it [15:51, 9.88s/it] 97it [16:01, 9.91s/it] 98it [16:11, 9.93s/it] 99it [16:21, 9.91s/it] 100it [16:30, 9.89s/it] 101it [16:40, 9.87s/it] 102it [16:50, 9.88s/it] 103it [17:00, 9.88s/it] 104it [17:10, 9.91s/it] 105it [17:20, 9.91s/it] 106it [17:30, 9.91s/it] 107it [17:40, 9.87s/it] 108it [17:49, 9.85s/it] 109it [17:59, 9.89s/it] 110it [18:09, 9.90s/it] 111it [18:19, 9.92s/it] 112it [18:29, 9.88s/it] 113it [18:39, 9.86s/it] 114it [18:49, 9.85s/it] 115it [18:59, 9.89s/it] 116it [19:09, 9.91s/it] 117it [19:19, 9.98s/it] 118it [19:29, 9.97s/it] 119it [19:39, 9.93s/it] 120it [19:49, 9.94s/it] 121it [19:58, 9.93s/it] 122it [20:08, 9.90s/it] 123it [20:18, 9.88s/it] 124it [20:28, 9.87s/it] 125it [20:38, 9.89s/it] 126it [20:48, 9.93s/it] 127it [20:58, 9.92s/it] 128it [21:08, 9.92s/it] 129it [21:18, 9.89s/it] 130it [21:27, 9.88s/it] 131it [21:37, 9.88s/it] 132it [21:47, 9.92s/it] 133it [21:57, 9.92s/it] 134it [22:07, 9.86s/it] 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9.77s/it] 177it [29:07, 9.78s/it] 178it [29:17, 9.77s/it] 179it [29:27, 9.77s/it] 180it [29:37, 9.78s/it] 181it [29:47, 9.78s/it] 182it [29:56, 9.79s/it] 183it [30:06, 9.78s/it] 184it [30:16, 9.81s/it] 185it [30:26, 9.81s/it] 186it [30:36, 9.80s/it] 187it [30:45, 9.79s/it] 188it [30:55, 9.78s/it] 189it [31:05, 9.76s/it] 190it [31:15, 9.78s/it] 191it [31:24, 9.77s/it] 192it [31:34, 9.78s/it] 193it [31:44, 9.77s/it] 194it [31:54, 9.76s/it] 195it [32:03, 9.77s/it] 196it [32:13, 9.76s/it] 197it [32:23, 9.75s/it] 198it [32:33, 9.77s/it] 199it [32:43, 9.80s/it] 200it [32:52, 9.79s/it] 201it [33:02, 9.79s/it] 202it [33:12, 9.78s/it] 203it [33:22, 9.79s/it] 204it [33:32, 9.79s/it] 205it [33:41, 9.78s/it] 206it [33:51, 9.79s/it] 207it [34:01, 9.80s/it] 208it [34:11, 9.79s/it] 209it [34:21, 9.82s/it] 210it [34:30, 9.83s/it] 211it [34:40, 9.81s/it] 212it [34:50, 9.83s/it] 213it [35:00, 9.84s/it] 214it [35:10, 9.82s/it] 215it [35:20, 9.82s/it] 216it [35:29, 9.78s/it] 217it [35:39, 9.80s/it] 218it [35:49, 9.78s/it] 219it [35:59, 9.79s/it] 220it [36:08, 9.80s/it] 221it [36:18, 9.78s/it] 222it [36:28, 9.79s/it] 223it [36:38, 9.79s/it] 224it [36:48, 9.77s/it] 225it [36:57, 9.78s/it] 226it [37:07, 9.79s/it] 227it [37:17, 9.79s/it] 228it [37:27, 9.80s/it] 229it [37:36, 9.78s/it] 230it [37:46, 9.78s/it] 231it [37:56, 9.79s/it] 232it [38:06, 9.79s/it] 233it [38:16, 9.79s/it] 234it [38:25, 9.80s/it] 235it [38:35, 9.78s/it] 236it [38:45, 9.78s/it] 237it [38:55, 9.76s/it] 238it [39:04, 9.76s/it] 239it [39:14, 9.79s/it] 240it [39:24, 9.79s/it] 241it [39:34, 9.78s/it] 242it [39:44, 9.78s/it] 243it [39:53, 9.77s/it] 244it [40:03, 9.76s/it] 245it [40:13, 9.76s/it] 246it [40:23, 9.78s/it] 247it [40:32, 9.78s/it] 248it [40:42, 9.79s/it] 249it [40:52, 9.78s/it] 250it [41:02, 9.78s/it] 251it [41:12, 9.78s/it] 252it [41:21, 9.80s/it] 253it [41:31, 9.82s/it] 254it [41:41, 9.81s/it] 255it [41:51, 9.81s/it] 256it [42:01, 9.79s/it] 257it [42:11, 9.82s/it] 258it [42:20, 9.83s/it] 259it [42:30, 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9.78s/it] 958it [2:36:36, 9.76s/it] 959it [2:36:45, 9.77s/it] 960it [2:36:55, 9.77s/it] 961it [2:37:05, 9.79s/it] 962it [2:37:15, 9.79s/it] 963it [2:37:25, 9.79s/it] 964it [2:37:34, 9.77s/it] 965it [2:37:44, 9.78s/it] 966it [2:37:54, 9.77s/it] 967it [2:38:04, 9.77s/it] 968it [2:38:13, 9.77s/it] 969it [2:38:23, 9.79s/it] 970it [2:38:33, 9.77s/it] 971it [2:38:43, 9.77s/it] 972it [2:38:53, 9.76s/it] 973it [2:39:02, 9.76s/it] 974it [2:39:12, 9.77s/it] 975it [2:39:22, 9.76s/it] 976it [2:39:32, 9.76s/it] 977it [2:39:41, 9.77s/it] 978it [2:39:51, 9.78s/it] 979it [2:40:01, 9.79s/it] 980it [2:40:11, 9.78s/it] 981it [2:40:21, 9.77s/it] 982it [2:40:30, 9.76s/it] 983it [2:40:40, 9.77s/it] 984it [2:40:50, 9.78s/it] 985it [2:41:00, 9.75s/it] 986it [2:41:09, 9.76s/it] 987it [2:41:19, 9.76s/it] 988it [2:41:29, 9.76s/it] 989it [2:41:39, 9.76s/it] 990it [2:41:48, 9.77s/it] 991it [2:41:58, 9.75s/it] 992it [2:42:08, 9.76s/it] 993it [2:42:18, 9.74s/it] 994it [2:42:27, 9.76s/it] 995it [2:42:37, 9.77s/it] 996it [2:42:47, 9.82s/it] 997it [2:42:57, 9.84s/it] 998it [2:43:07, 9.82s/it] 999it [2:43:17, 9.80s/it] 1000it [2:43:26, 9.81s/it] 1000it [2:43:26, 9.81s/it] +Error counts: + cyclic_id: 0 + cyclic_inchikey: 0 + cyclic_scaffold: 0 + cyclic_mwt: 0 + cyclic_clogp: 0 + cyclic_tpsa: 0 +⏰ Completed process in 2:43:47.502580 ++ rm /nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/train/cyc-pep-6-12mer-70M_42.csv diff --git a/train/cyc-pep-6-12mer-70M_43.csv.gz b/train/cyc-pep-6-12mer-70M_43.csv.gz index 9829e93c7711a84840625f36651266e03d882987..8213243040065ccf842aca4c013c085f7beeca88 100644 --- a/train/cyc-pep-6-12mer-70M_43.csv.gz +++ b/train/cyc-pep-6-12mer-70M_43.csv.gz @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:7aabf9e193ca3025f8a7c28cb854fe79116fc8dbb93dd6b298ad26b66ee2868b -size 54495791 +oid sha256:9b8f92dc4eff28d12355ac4019e5529b010cfed66a9d6f96a3f6bd98201c9acb +size 107796753 diff --git a/train/cyc-pep-6-12mer-70M_43.log b/train/cyc-pep-6-12mer-70M_43.log new file mode 100644 index 0000000000000000000000000000000000000000..9f809c949dba65daeb97e87e79f9532d7ef97fda --- /dev/null +++ b/train/cyc-pep-6-12mer-70M_43.log @@ -0,0 +1,337 @@ ++ module purge ++ '[' -z '' ']' ++ case "$-" in ++ __lmod_sh_dbg=x ++ '[' -n x ']' ++ set +x +Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output +Shell debugging restarted ++ unset __lmod_sh_dbg ++ return 0 ++ module load Anaconda3/2023.03 ++ '[' -z '' ']' ++ case "$-" in ++ __lmod_sh_dbg=x ++ '[' -n x ']' ++ set +x +Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output +Shell debugging restarted ++ unset __lmod_sh_dbg ++ return 0 ++ source /camp/home/johnsoe/.bashrc +++ '[' '' = yes ']' +++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' ++++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.bash hook +++ __conda_setup='export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'' + +# Copyright (C) 2012 Anaconda, Inc +# SPDX-License-Identifier: BSD-3-Clause +__conda_exe() ( + "$CONDA_EXE" $_CE_M $_CE_CONDA "$@" +) + +__conda_hashr() { + if [ -n "${ZSH_VERSION:+x}" ]; then + \rehash + elif [ -n "${POSH_VERSION:+x}" ]; then + : # pass + else + \hash -r + fi +} + +__conda_activate() { + if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then + # Handle transition from shell activated with conda <= 4.3 to a subsequent activation + # after conda updated to >= 4.4. See issue #6173. + PS1="$CONDA_PS1_BACKUP" + \unset CONDA_PS1_BACKUP + fi + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return + \eval "$ask_conda" + __conda_hashr +} + +__conda_reactivate() { + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return + \eval "$ask_conda" + __conda_hashr +} + +conda() { + \local cmd="${1-__missing__}" + case "$cmd" in + activate|deactivate) + __conda_activate "$@" + ;; + install|update|upgrade|remove|uninstall) + __conda_exe "$@" || \return + __conda_reactivate + ;; + *) + __conda_exe "$@" + ;; + esac +} + +if [ -z "${CONDA_SHLVL+x}" ]; then + \export CONDA_SHLVL=0 + # In dev-mode CONDA_EXE is python.exe and on Windows + # it is in a different relative location to condabin. + if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then + PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}" + else + PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}" + fi + \export PATH + + # We'\''re not allowing PS1 to be unbound. It must at least be set. + # However, we'\''re not exporting it, which can cause problems when starting a second shell + # via a first shell (i.e. starting zsh from bash). + if [ -z "${PS1+x}" ]; then + PS1= + fi +fi + +conda activate base' +++ '[' 0 -eq 0 ']' +++ eval 'export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'' + +# Copyright (C) 2012 Anaconda, Inc +# SPDX-License-Identifier: BSD-3-Clause +__conda_exe() ( + "$CONDA_EXE" $_CE_M $_CE_CONDA "$@" +) + +__conda_hashr() { + if [ -n "${ZSH_VERSION:+x}" ]; then + \rehash + elif [ -n "${POSH_VERSION:+x}" ]; then + : # pass + else + \hash -r + fi +} + +__conda_activate() { + if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then + # Handle transition from shell activated with conda <= 4.3 to a subsequent activation + # after conda updated to >= 4.4. See issue #6173. + PS1="$CONDA_PS1_BACKUP" + \unset CONDA_PS1_BACKUP + fi + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return + \eval "$ask_conda" + __conda_hashr +} + +__conda_reactivate() { + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return + \eval "$ask_conda" + __conda_hashr +} + +conda() { + \local cmd="${1-__missing__}" + case "$cmd" in + activate|deactivate) + __conda_activate "$@" + ;; + install|update|upgrade|remove|uninstall) + __conda_exe "$@" || \return + __conda_reactivate + ;; + *) + __conda_exe "$@" + ;; + esac +} + +if [ -z "${CONDA_SHLVL+x}" ]; then + \export CONDA_SHLVL=0 + # In dev-mode CONDA_EXE is python.exe and on Windows + # it is in a different relative location to condabin. + if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then + PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}" + else + PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}" + fi + \export PATH + + # We'\''re not allowing PS1 to be unbound. It must at least be set. + # However, we'\''re not exporting it, which can cause problems when starting a second shell + # via a first shell (i.e. starting zsh from bash). + if [ -z "${PS1+x}" ]; then + PS1= + fi +fi + +conda activate base' ++++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda ++++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda ++++ export _CE_M= ++++ _CE_M= ++++ export _CE_CONDA= ++++ _CE_CONDA= ++++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ '[' -z x ']' ++++ conda activate base ++++ local cmd=activate ++++ case "$cmd" in ++++ __conda_activate activate base ++++ '[' -n '' ']' ++++ local ask_conda +++++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++++ __conda_exe shell.posix activate base +++++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate base ++++ ask_conda='PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_SHLVL='\''6'\'' +export CONDA_DEFAULT_ENV='\''base'\'' +export CONDA_PROMPT_MODIFIER='\''(base) '\'' +export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' ++++ eval 'PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_SHLVL='\''6'\'' +export CONDA_DEFAULT_ENV='\''base'\'' +export CONDA_PROMPT_MODIFIER='\''(base) '\'' +export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' +++++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++++ export CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0 +++++ CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0 +++++ export CONDA_SHLVL=6 +++++ CONDA_SHLVL=6 +++++ export CONDA_DEFAULT_ENV=base +++++ CONDA_DEFAULT_ENV=base +++++ export 'CONDA_PROMPT_MODIFIER=(base) ' +++++ CONDA_PROMPT_MODIFIER='(base) ' +++++ export CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev +++++ CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev +++++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++++ export _CE_M= +++++ _CE_M= +++++ export _CE_CONDA= +++++ _CE_CONDA= +++++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python +++++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ __conda_hashr ++++ '[' -n '' ']' ++++ '[' -n '' ']' ++++ hash -r +++ unset __conda_setup ++ conda activate schemist-dev ++ local cmd=activate ++ case "$cmd" in ++ __conda_activate activate schemist-dev ++ '[' -n '' ']' ++ local ask_conda +++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++ __conda_exe shell.posix activate schemist-dev +++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate schemist-dev ++ ask_conda='PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_SHLVL='\''7'\'' +export CONDA_DEFAULT_ENV='\''schemist-dev'\'' +export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\'' +export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' ++ eval 'PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_SHLVL='\''7'\'' +export CONDA_DEFAULT_ENV='\''schemist-dev'\'' +export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\'' +export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' +++ PS1='(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++ export CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev +++ CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev +++ export CONDA_SHLVL=7 +++ CONDA_SHLVL=7 +++ export CONDA_DEFAULT_ENV=schemist-dev +++ CONDA_DEFAULT_ENV=schemist-dev +++ export 'CONDA_PROMPT_MODIFIER=(schemist-dev) ' +++ CONDA_PROMPT_MODIFIER='(schemist-dev) ' +++ export CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0 +++ CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0 +++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++ export _CE_M= +++ _CE_M= +++ export _CE_CONDA= +++ _CE_CONDA= +++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python +++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++ __conda_hashr ++ '[' -n '' ']' ++ '[' -n '' ']' ++ hash -r ++ CHUNK_HEAD_FILE=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz ++ INPUT=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/train/cyc-pep-6-12mer-70M_43.csv ++ COLUMN=cysteine_to_N_cyclization ++ PREFIX=cyclic_ ++ AWK='1 { print $8, $1, $2, $10, $3 }' ++ '[' -z cysteine_to_N_cyclization ']' ++ '[' -z cyclic_ ']' ++ '[' -z '1 { print $8, $1, $2, $10, $3 }' ']' ++ cat /dev/fd/63 /nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/train/cyc-pep-6-12mer-70M_43.csv ++ awk -F, -v OFS=, '1 { print $8, $1, $2, $10, $3 }' ++ schemist convert -f csv --column cysteine_to_N_cyclization --to id inchikey scaffold mwt clogp tpsa --prefix cyclic_ --options prefix=SCB- +++ zcat /nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz ++ gzip --best +++ head -n1 +++ tr ' ' , +🚀 Converting between string representations with the following parameters: + subcommand: convert + output: <_io.TextIOWrapper name='' mode='w' encoding='utf-8'> + format: csv + input: <_io.TextIOWrapper name='' mode='r' encoding='utf-8'> + representation: SMILES + column: cysteine_to_N_cyclization + prefix: cyclic_ + to: ['id', 'inchikey', 'scaffold', 'mwt', 'clogp', 'tpsa'] + options: ['prefix=SCB-'] + func: + 0it [00:00, ?it/s] 1it [00:11, 11.20s/it] 2it [00:22, 11.01s/it] 3it [00:33, 11.11s/it] 4it [00:44, 11.09s/it] 5it [00:55, 11.10s/it] 6it [01:06, 11.20s/it] 7it [01:17, 11.03s/it] 8it [01:27, 10.82s/it] 9it [01:38, 10.73s/it] 10it [01:49, 10.72s/it] 11it [01:59, 10.66s/it] 12it [02:10, 10.66s/it] 13it [02:21, 10.70s/it] 14it [02:31, 10.69s/it] 15it [02:42, 10.64s/it] 16it [02:53, 10.67s/it] 17it [03:03, 10.69s/it] 18it [03:14, 10.71s/it] 19it [03:25, 10.78s/it] 20it [03:36, 10.80s/it] 21it [03:46, 10.73s/it] 22it [03:57, 10.70s/it] 23it [04:07, 10.62s/it] 24it [04:18, 10.58s/it] 25it [04:29, 10.68s/it] 26it [04:40, 10.73s/it] 27it [04:51, 10.82s/it] 28it [05:02, 10.81s/it] 29it [05:12, 10.73s/it] 30it [05:23, 10.66s/it] 31it [05:34, 10.78s/it] 32it [05:45, 10.95s/it] 33it [05:56, 11.10s/it] 34it [06:08, 11.15s/it] 35it [06:19, 11.18s/it] 36it [06:30, 11.05s/it] 37it [06:40, 10.96s/it] 38it [06:51, 10.96s/it] 39it [07:02, 10.96s/it] 40it [07:14, 11.02s/it] 41it [07:25, 11.09s/it] 42it [07:36, 11.23s/it] 43it [07:48, 11.32s/it] 44it [07:59, 11.38s/it] 45it [08:10, 11.29s/it] 46it [08:22, 11.26s/it] 47it [08:33, 11.36s/it] 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11.26s/it] 90it [16:34, 11.30s/it] 91it [16:45, 11.30s/it] 92it [16:57, 11.48s/it] 93it [17:09, 11.53s/it] 94it [17:20, 11.44s/it] 95it [17:32, 11.48s/it] 96it [17:43, 11.49s/it] 97it [17:55, 11.57s/it] 98it [18:06, 11.46s/it] 99it [18:18, 11.48s/it] 100it [18:29, 11.44s/it] 101it [18:40, 11.43s/it] 102it [18:52, 11.58s/it] 103it [19:04, 11.66s/it] 104it [19:16, 11.65s/it] 105it [19:27, 11.50s/it] 106it [19:38, 11.38s/it] 107it [19:49, 11.32s/it] 108it [20:01, 11.48s/it] 109it [20:13, 11.63s/it] 110it [20:25, 11.72s/it] 111it [20:36, 11.63s/it] 112it [20:47, 11.44s/it] 113it [20:58, 11.34s/it] 114it [21:10, 11.54s/it] 115it [21:22, 11.68s/it] 116it [21:34, 11.74s/it] 117it [21:46, 11.76s/it] 118it [21:57, 11.56s/it] 119it [22:08, 11.40s/it] 120it [22:20, 11.47s/it] 121it [22:32, 11.54s/it] 122it [22:44, 11.67s/it] 123it [22:55, 11.71s/it] 124it [23:07, 11.58s/it] 125it [23:18, 11.45s/it] 126it [23:29, 11.49s/it] 127it [23:41, 11.53s/it] 128it [23:53, 11.58s/it] 129it [24:04, 11.64s/it] 130it [24:16, 11.51s/it] 131it [24:27, 11.45s/it] 132it [24:38, 11.41s/it] 133it [24:50, 11.42s/it] 134it [25:01, 11.46s/it] 135it [25:13, 11.49s/it] 136it [25:24, 11.38s/it] 137it [25:35, 11.32s/it] 138it [25:47, 11.42s/it] 139it [25:59, 11.57s/it] 140it [26:11, 11.64s/it] 141it [26:22, 11.57s/it] 142it [26:33, 11.47s/it] 143it [26:44, 11.42s/it] 144it [26:56, 11.49s/it] 145it [27:08, 11.64s/it] 146it [27:20, 11.73s/it] 147it [27:32, 11.65s/it] 148it [27:43, 11.53s/it] 149it [27:54, 11.42s/it] 150it [28:05, 11.45s/it] 151it [28:17, 11.52s/it] 152it [28:29, 11.68s/it] 153it [28:41, 11.63s/it] 154it [28:52, 11.61s/it] 155it [29:04, 11.56s/it] 156it [29:15, 11.53s/it] 157it [29:27, 11.49s/it] 158it [29:38, 11.60s/it] 159it [29:50, 11.64s/it] 160it [30:02, 11.63s/it] 161it [30:14, 11.77s/it] 162it [30:26, 11.77s/it] 163it [30:37, 11.69s/it] 164it [30:49, 11.66s/it] 165it [31:00, 11.61s/it] 166it [31:12, 11.61s/it] 167it [31:24, 11.75s/it] 168it [31:36, 11.76s/it] 169it [31:47, 11.76s/it] 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[2:57:44, 11.26s/it] 1000it [2:57:44, 10.66s/it] +Error counts: + cyclic_id: 0 + cyclic_inchikey: 0 + cyclic_scaffold: 0 + cyclic_mwt: 0 + cyclic_clogp: 0 + cyclic_tpsa: 0 +⏰ Completed process in 2:58:08.129997 ++ rm /nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/train/cyc-pep-6-12mer-70M_43.csv diff --git a/train/cyc-pep-6-12mer-70M_44.csv.gz b/train/cyc-pep-6-12mer-70M_44.csv.gz index a68d946c3782285f296130c3e958def6e285250f..6a6b996441a1063fb7ccdf896d80d31c45dae6bd 100644 --- a/train/cyc-pep-6-12mer-70M_44.csv.gz +++ b/train/cyc-pep-6-12mer-70M_44.csv.gz @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:a8c0f41225117fc78e20e3784082ed24dec27fccfe09baec035add7baa2ec628 -size 54498979 +oid sha256:12649a505f771f90317f96bd6c18d638548cd2a4d66ef9930bddc5bc8effd980 +size 107797622 diff --git a/train/cyc-pep-6-12mer-70M_44.log b/train/cyc-pep-6-12mer-70M_44.log new file mode 100644 index 0000000000000000000000000000000000000000..4b3ddac9fa4d50a395757e90e855991c2e5f1005 --- /dev/null +++ b/train/cyc-pep-6-12mer-70M_44.log @@ -0,0 +1,337 @@ ++ module purge ++ '[' -z '' ']' ++ case "$-" in ++ __lmod_sh_dbg=x ++ '[' -n x ']' ++ set +x +Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output +Shell debugging restarted ++ unset __lmod_sh_dbg ++ return 0 ++ module load Anaconda3/2023.03 ++ '[' -z '' ']' ++ case "$-" in ++ __lmod_sh_dbg=x ++ '[' -n x ']' ++ set +x +Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output +Shell debugging restarted ++ unset __lmod_sh_dbg ++ return 0 ++ source /camp/home/johnsoe/.bashrc +++ '[' '' = yes ']' +++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' ++++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.bash hook +++ __conda_setup='export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'' + +# Copyright (C) 2012 Anaconda, Inc +# SPDX-License-Identifier: BSD-3-Clause +__conda_exe() ( + "$CONDA_EXE" $_CE_M $_CE_CONDA "$@" +) + +__conda_hashr() { + if [ -n "${ZSH_VERSION:+x}" ]; then + \rehash + elif [ -n "${POSH_VERSION:+x}" ]; then + : # pass + else + \hash -r + fi +} + +__conda_activate() { + if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then + # Handle transition from shell activated with conda <= 4.3 to a subsequent activation + # after conda updated to >= 4.4. See issue #6173. + PS1="$CONDA_PS1_BACKUP" + \unset CONDA_PS1_BACKUP + fi + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return + \eval "$ask_conda" + __conda_hashr +} + +__conda_reactivate() { + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return + \eval "$ask_conda" + __conda_hashr +} + +conda() { + \local cmd="${1-__missing__}" + case "$cmd" in + activate|deactivate) + __conda_activate "$@" + ;; + install|update|upgrade|remove|uninstall) + __conda_exe "$@" || \return + __conda_reactivate + ;; + *) + __conda_exe "$@" + ;; + esac +} + +if [ -z "${CONDA_SHLVL+x}" ]; then + \export CONDA_SHLVL=0 + # In dev-mode CONDA_EXE is python.exe and on Windows + # it is in a different relative location to condabin. + if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then + PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}" + else + PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}" + fi + \export PATH + + # We'\''re not allowing PS1 to be unbound. It must at least be set. + # However, we'\''re not exporting it, which can cause problems when starting a second shell + # via a first shell (i.e. starting zsh from bash). + if [ -z "${PS1+x}" ]; then + PS1= + fi +fi + +conda activate base' +++ '[' 0 -eq 0 ']' +++ eval 'export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'' + +# Copyright (C) 2012 Anaconda, Inc +# SPDX-License-Identifier: BSD-3-Clause +__conda_exe() ( + "$CONDA_EXE" $_CE_M $_CE_CONDA "$@" +) + +__conda_hashr() { + if [ -n "${ZSH_VERSION:+x}" ]; then + \rehash + elif [ -n "${POSH_VERSION:+x}" ]; then + : # pass + else + \hash -r + fi +} + +__conda_activate() { + if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then + # Handle transition from shell activated with conda <= 4.3 to a subsequent activation + # after conda updated to >= 4.4. See issue #6173. + PS1="$CONDA_PS1_BACKUP" + \unset CONDA_PS1_BACKUP + fi + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return + \eval "$ask_conda" + __conda_hashr +} + +__conda_reactivate() { + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return + \eval "$ask_conda" + __conda_hashr +} + +conda() { + \local cmd="${1-__missing__}" + case "$cmd" in + activate|deactivate) + __conda_activate "$@" + ;; + install|update|upgrade|remove|uninstall) + __conda_exe "$@" || \return + __conda_reactivate + ;; + *) + __conda_exe "$@" + ;; + esac +} + +if [ -z "${CONDA_SHLVL+x}" ]; then + \export CONDA_SHLVL=0 + # In dev-mode CONDA_EXE is python.exe and on Windows + # it is in a different relative location to condabin. + if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then + PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}" + else + PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}" + fi + \export PATH + + # We'\''re not allowing PS1 to be unbound. It must at least be set. + # However, we'\''re not exporting it, which can cause problems when starting a second shell + # via a first shell (i.e. starting zsh from bash). + if [ -z "${PS1+x}" ]; then + PS1= + fi +fi + +conda activate base' ++++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda ++++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda ++++ export _CE_M= ++++ _CE_M= ++++ export _CE_CONDA= ++++ _CE_CONDA= ++++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ '[' -z x ']' ++++ conda activate base ++++ local cmd=activate ++++ case "$cmd" in ++++ __conda_activate activate base ++++ '[' -n '' ']' ++++ local ask_conda +++++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++++ __conda_exe shell.posix activate base +++++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate base ++++ ask_conda='PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_SHLVL='\''6'\'' +export CONDA_DEFAULT_ENV='\''base'\'' +export CONDA_PROMPT_MODIFIER='\''(base) '\'' +export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' ++++ eval 'PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_SHLVL='\''6'\'' +export CONDA_DEFAULT_ENV='\''base'\'' +export CONDA_PROMPT_MODIFIER='\''(base) '\'' +export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' +++++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++++ export CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0 +++++ CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0 +++++ export CONDA_SHLVL=6 +++++ CONDA_SHLVL=6 +++++ export CONDA_DEFAULT_ENV=base +++++ CONDA_DEFAULT_ENV=base +++++ export 'CONDA_PROMPT_MODIFIER=(base) ' +++++ CONDA_PROMPT_MODIFIER='(base) ' +++++ export CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev +++++ CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev +++++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++++ export _CE_M= +++++ _CE_M= +++++ export _CE_CONDA= +++++ _CE_CONDA= +++++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python +++++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ __conda_hashr ++++ '[' -n '' ']' ++++ '[' -n '' ']' ++++ hash -r +++ unset __conda_setup ++ conda activate schemist-dev ++ local cmd=activate ++ case "$cmd" in ++ __conda_activate activate schemist-dev ++ '[' -n '' ']' ++ local ask_conda +++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++ __conda_exe shell.posix activate schemist-dev +++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate schemist-dev ++ ask_conda='PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_SHLVL='\''7'\'' +export CONDA_DEFAULT_ENV='\''schemist-dev'\'' +export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\'' +export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' ++ eval 'PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_SHLVL='\''7'\'' +export CONDA_DEFAULT_ENV='\''schemist-dev'\'' +export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\'' +export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' +++ PS1='(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++ export CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev +++ CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev +++ export CONDA_SHLVL=7 +++ CONDA_SHLVL=7 +++ export CONDA_DEFAULT_ENV=schemist-dev +++ CONDA_DEFAULT_ENV=schemist-dev +++ export 'CONDA_PROMPT_MODIFIER=(schemist-dev) ' +++ CONDA_PROMPT_MODIFIER='(schemist-dev) ' +++ export CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0 +++ CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0 +++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++ export _CE_M= +++ _CE_M= +++ export _CE_CONDA= +++ _CE_CONDA= +++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python +++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++ __conda_hashr ++ '[' -n '' ']' ++ '[' -n '' ']' ++ hash -r ++ CHUNK_HEAD_FILE=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz ++ INPUT=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/train/cyc-pep-6-12mer-70M_44.csv ++ COLUMN=cysteine_to_N_cyclization ++ PREFIX=cyclic_ ++ AWK='1 { print $8, $1, $2, $10, $3 }' ++ '[' -z cysteine_to_N_cyclization ']' ++ '[' -z cyclic_ ']' ++ '[' -z '1 { print $8, $1, $2, $10, $3 }' ']' ++ cat /dev/fd/63 /nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/train/cyc-pep-6-12mer-70M_44.csv ++ awk -F, -v OFS=, '1 { print $8, $1, $2, $10, $3 }' ++ schemist convert -f csv --column cysteine_to_N_cyclization --to id inchikey scaffold mwt clogp tpsa --prefix cyclic_ --options prefix=SCB- ++ gzip --best +++ zcat /nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz +++ head -n1 +++ tr ' ' , +🚀 Converting between string representations with the following parameters: + subcommand: convert + output: <_io.TextIOWrapper name='' mode='w' encoding='utf-8'> + format: csv + input: <_io.TextIOWrapper name='' mode='r' encoding='utf-8'> + representation: SMILES + column: cysteine_to_N_cyclization + prefix: cyclic_ + to: ['id', 'inchikey', 'scaffold', 'mwt', 'clogp', 'tpsa'] + options: ['prefix=SCB-'] + func: + 0it [00:00, ?it/s] 1it [00:10, 10.07s/it] 2it [00:20, 9.99s/it] 3it [00:30, 10.22s/it] 4it [00:40, 10.12s/it] 5it [00:50, 10.02s/it] 6it 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[2:41:49, 9.57s/it] 985it [2:41:59, 9.56s/it] 986it [2:42:08, 9.57s/it] 987it [2:42:18, 9.56s/it] 988it [2:42:27, 9.56s/it] 989it [2:42:37, 9.54s/it] 990it [2:42:47, 9.55s/it] 991it [2:42:56, 9.55s/it] 992it [2:43:06, 9.55s/it] 993it [2:43:15, 9.54s/it] 994it [2:43:25, 9.57s/it] 995it [2:43:34, 9.57s/it] 996it [2:43:44, 9.56s/it] 997it [2:43:54, 9.56s/it] 998it [2:44:03, 9.55s/it] 999it [2:44:13, 9.54s/it] 1000it [2:44:22, 9.54s/it] 1000it [2:44:22, 9.86s/it] +Error counts: + cyclic_id: 0 + cyclic_inchikey: 0 + cyclic_scaffold: 0 + cyclic_mwt: 0 + cyclic_clogp: 0 + cyclic_tpsa: 0 +⏰ Completed process in 2:44:44.257637 ++ rm /nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/train/cyc-pep-6-12mer-70M_44.csv diff --git a/train/cyc-pep-6-12mer-70M_45.csv.gz b/train/cyc-pep-6-12mer-70M_45.csv.gz index a6e0992c6ea6efd7e314189f09021166e7793c69..7237940a6afaaf16cf8fe612b0db2893a0f7dfd6 100644 --- a/train/cyc-pep-6-12mer-70M_45.csv.gz +++ b/train/cyc-pep-6-12mer-70M_45.csv.gz @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:a5623c041675716655665ea6cfae4f470a973d23555e5bdee9d2a232230d4c99 -size 54502059 +oid sha256:d6acfdd9b8b03c96ca4bf0623c974ee9a0e4e99c17b889f99137f091fbbc48c5 +size 107802238 diff --git a/train/cyc-pep-6-12mer-70M_45.log b/train/cyc-pep-6-12mer-70M_45.log new file mode 100644 index 0000000000000000000000000000000000000000..513cc7368f17a469bd03565b47b26af306b92da5 --- /dev/null +++ b/train/cyc-pep-6-12mer-70M_45.log @@ -0,0 +1,337 @@ ++ module purge ++ '[' -z '' ']' ++ case "$-" in ++ __lmod_sh_dbg=x ++ '[' -n x ']' ++ set +x +Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output +Shell debugging restarted ++ unset __lmod_sh_dbg ++ return 0 ++ module load Anaconda3/2023.03 ++ '[' -z '' ']' ++ case "$-" in ++ __lmod_sh_dbg=x ++ '[' -n x ']' ++ set +x +Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output +Shell debugging restarted ++ unset __lmod_sh_dbg ++ return 0 ++ source /camp/home/johnsoe/.bashrc +++ '[' '' = yes ']' +++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' ++++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.bash hook +++ __conda_setup='export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'' + +# Copyright (C) 2012 Anaconda, Inc +# SPDX-License-Identifier: BSD-3-Clause +__conda_exe() ( + "$CONDA_EXE" $_CE_M $_CE_CONDA "$@" +) + +__conda_hashr() { + if [ -n "${ZSH_VERSION:+x}" ]; then + \rehash + elif [ -n "${POSH_VERSION:+x}" ]; then + : # pass + else + \hash -r + fi +} + +__conda_activate() { + if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then + # Handle transition from shell activated with conda <= 4.3 to a subsequent activation + # after conda updated to >= 4.4. See issue #6173. + PS1="$CONDA_PS1_BACKUP" + \unset CONDA_PS1_BACKUP + fi + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return + \eval "$ask_conda" + __conda_hashr +} + +__conda_reactivate() { + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return + \eval "$ask_conda" + __conda_hashr +} + +conda() { + \local cmd="${1-__missing__}" + case "$cmd" in + activate|deactivate) + __conda_activate "$@" + ;; + install|update|upgrade|remove|uninstall) + __conda_exe "$@" || \return + __conda_reactivate + ;; + *) + __conda_exe "$@" + ;; + esac +} + +if [ -z "${CONDA_SHLVL+x}" ]; then + \export CONDA_SHLVL=0 + # In dev-mode CONDA_EXE is python.exe and on Windows + # it is in a different relative location to condabin. + if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then + PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}" + else + PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}" + fi + \export PATH + + # We'\''re not allowing PS1 to be unbound. It must at least be set. + # However, we'\''re not exporting it, which can cause problems when starting a second shell + # via a first shell (i.e. starting zsh from bash). + if [ -z "${PS1+x}" ]; then + PS1= + fi +fi + +conda activate base' +++ '[' 0 -eq 0 ']' +++ eval 'export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'' + +# Copyright (C) 2012 Anaconda, Inc +# SPDX-License-Identifier: BSD-3-Clause +__conda_exe() ( + "$CONDA_EXE" $_CE_M $_CE_CONDA "$@" +) + +__conda_hashr() { + if [ -n "${ZSH_VERSION:+x}" ]; then + \rehash + elif [ -n "${POSH_VERSION:+x}" ]; then + : # pass + else + \hash -r + fi +} + +__conda_activate() { + if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then + # Handle transition from shell activated with conda <= 4.3 to a subsequent activation + # after conda updated to >= 4.4. See issue #6173. + PS1="$CONDA_PS1_BACKUP" + \unset CONDA_PS1_BACKUP + fi + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return + \eval "$ask_conda" + __conda_hashr +} + +__conda_reactivate() { + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return + \eval "$ask_conda" + __conda_hashr +} + +conda() { + \local cmd="${1-__missing__}" + case "$cmd" in + activate|deactivate) + __conda_activate "$@" + ;; + install|update|upgrade|remove|uninstall) + __conda_exe "$@" || \return + __conda_reactivate + ;; + *) + __conda_exe "$@" + ;; + esac +} + +if [ -z "${CONDA_SHLVL+x}" ]; then + \export CONDA_SHLVL=0 + # In dev-mode CONDA_EXE is python.exe and on Windows + # it is in a different relative location to condabin. + if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then + PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}" + else + PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}" + fi + \export PATH + + # We'\''re not allowing PS1 to be unbound. It must at least be set. + # However, we'\''re not exporting it, which can cause problems when starting a second shell + # via a first shell (i.e. starting zsh from bash). + if [ -z "${PS1+x}" ]; then + PS1= + fi +fi + +conda activate base' ++++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda ++++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda ++++ export _CE_M= ++++ _CE_M= ++++ export _CE_CONDA= ++++ _CE_CONDA= ++++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ '[' -z x ']' ++++ conda activate base ++++ local cmd=activate ++++ case "$cmd" in ++++ __conda_activate activate base ++++ '[' -n '' ']' ++++ local ask_conda +++++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++++ __conda_exe shell.posix activate base +++++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate base ++++ ask_conda='PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_SHLVL='\''6'\'' +export CONDA_DEFAULT_ENV='\''base'\'' +export CONDA_PROMPT_MODIFIER='\''(base) '\'' +export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' ++++ eval 'PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_SHLVL='\''6'\'' +export CONDA_DEFAULT_ENV='\''base'\'' +export CONDA_PROMPT_MODIFIER='\''(base) '\'' +export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' +++++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++++ export CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0 +++++ CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0 +++++ export CONDA_SHLVL=6 +++++ CONDA_SHLVL=6 +++++ export CONDA_DEFAULT_ENV=base +++++ CONDA_DEFAULT_ENV=base +++++ export 'CONDA_PROMPT_MODIFIER=(base) ' +++++ CONDA_PROMPT_MODIFIER='(base) ' +++++ export CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev +++++ CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev +++++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++++ export _CE_M= +++++ _CE_M= +++++ export _CE_CONDA= +++++ _CE_CONDA= +++++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python +++++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ __conda_hashr ++++ '[' -n '' ']' ++++ '[' -n '' ']' ++++ hash -r +++ unset __conda_setup ++ conda activate schemist-dev ++ local cmd=activate ++ case "$cmd" in ++ __conda_activate activate schemist-dev ++ '[' -n '' ']' ++ local ask_conda +++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++ __conda_exe shell.posix activate schemist-dev +++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate schemist-dev ++ ask_conda='PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_SHLVL='\''7'\'' +export CONDA_DEFAULT_ENV='\''schemist-dev'\'' +export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\'' +export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' ++ eval 'PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_SHLVL='\''7'\'' +export CONDA_DEFAULT_ENV='\''schemist-dev'\'' +export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\'' +export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' +++ PS1='(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++ export CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev +++ CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev +++ export CONDA_SHLVL=7 +++ CONDA_SHLVL=7 +++ export CONDA_DEFAULT_ENV=schemist-dev +++ CONDA_DEFAULT_ENV=schemist-dev +++ export 'CONDA_PROMPT_MODIFIER=(schemist-dev) ' +++ CONDA_PROMPT_MODIFIER='(schemist-dev) ' +++ export CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0 +++ CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0 +++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++ export _CE_M= +++ _CE_M= +++ export _CE_CONDA= +++ _CE_CONDA= +++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python +++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++ __conda_hashr ++ '[' -n '' ']' ++ '[' -n '' ']' ++ hash -r ++ CHUNK_HEAD_FILE=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz ++ INPUT=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/train/cyc-pep-6-12mer-70M_45.csv ++ COLUMN=cysteine_to_N_cyclization ++ PREFIX=cyclic_ ++ AWK='1 { print $8, $1, $2, $10, $3 }' ++ '[' -z cysteine_to_N_cyclization ']' ++ '[' -z cyclic_ ']' ++ '[' -z '1 { print $8, $1, $2, $10, $3 }' ']' ++ awk -F, -v OFS=, '1 { print $8, $1, $2, $10, $3 }' ++ schemist convert -f csv --column cysteine_to_N_cyclization --to id inchikey scaffold mwt clogp tpsa --prefix cyclic_ --options prefix=SCB- ++ cat /dev/fd/63 /nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/train/cyc-pep-6-12mer-70M_45.csv ++ gzip --best +++ zcat /nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz +++ tr ' ' , +++ head -n1 +🚀 Converting between string representations with the following parameters: + subcommand: convert + output: <_io.TextIOWrapper name='' mode='w' encoding='utf-8'> + format: csv + input: <_io.TextIOWrapper name='' mode='r' encoding='utf-8'> + representation: SMILES + column: cysteine_to_N_cyclization + prefix: cyclic_ + to: ['id', 'inchikey', 'scaffold', 'mwt', 'clogp', 'tpsa'] + options: ['prefix=SCB-'] + func: + 0it [00:00, ?it/s] 1it [00:10, 10.28s/it] 2it [00:20, 10.32s/it] 3it [00:30, 10.26s/it] 4it [00:41, 10.31s/it] 5it [00:51, 10.35s/it] 6it [01:01, 10.26s/it] 7it [01:11, 10.23s/it] 8it [01:22, 10.28s/it] 9it [01:32, 10.28s/it] 10it [01:42, 10.33s/it] 11it [01:53, 10.35s/it] 12it [02:03, 10.31s/it] 13it [02:13, 10.25s/it] 14it [02:24, 10.30s/it] 15it [02:34, 10.33s/it] 16it [02:44, 10.35s/it] 17it [02:55, 10.40s/it] 18it [03:05, 10.37s/it] 19it [03:15, 10.32s/it] 20it [03:26, 10.27s/it] 21it [03:36, 10.31s/it] 22it [03:46, 10.27s/it] 23it [03:57, 10.32s/it] 24it [04:07, 10.32s/it] 25it [04:17, 10.28s/it] 26it [04:27, 10.25s/it] 27it [04:38, 10.31s/it] 28it [04:48, 10.29s/it] 29it [04:58, 10.34s/it] 30it [05:09, 10.36s/it] 31it [05:19, 10.32s/it] 32it [05:29, 10.28s/it] 33it [05:40, 10.28s/it] 34it [05:50, 10.26s/it] 35it [06:00, 10.31s/it] 36it [06:11, 10.36s/it] 37it [06:21, 10.32s/it] 38it [06:31, 10.28s/it] 39it [06:41, 10.25s/it] 40it [06:52, 10.26s/it] 41it [07:02, 10.27s/it] 42it [07:12, 10.30s/it] 43it [07:22, 10.26s/it] 44it [07:33, 10.23s/it] 45it [07:43, 10.20s/it] 46it [07:53, 10.24s/it] 47it [08:03, 10.23s/it] 48it [08:13, 10.24s/it] 49it [08:24, 10.24s/it] 50it [08:34, 10.19s/it] 51it [08:44, 10.16s/it] 52it [08:54, 10.21s/it] 53it [09:04, 10.23s/it] 54it [09:15, 10.24s/it] 55it [09:25, 10.23s/it] 56it [09:35, 10.20s/it] 57it [09:45, 10.20s/it] 58it [09:56, 10.27s/it] 59it [10:06, 10.31s/it] 60it [10:16, 10.32s/it] 61it [10:27, 10.27s/it] 62it [10:37, 10.23s/it] 63it [10:47, 10.21s/it] 64it [10:57, 10.25s/it] 65it [11:08, 10.28s/it] 66it [11:18, 10.27s/it] 67it [11:28, 10.26s/it] 68it [11:38, 10.24s/it] 69it [11:48, 10.23s/it] 70it [11:59, 10.27s/it] 71it [12:09, 10.29s/it] 72it [12:19, 10.28s/it] 73it [12:30, 10.25s/it] 74it [12:40, 10.21s/it] 75it [12:50, 10.18s/it] 76it [13:00, 10.22s/it] 77it [13:11, 10.27s/it] 78it [13:21, 10.32s/it] 79it [13:31, 10.35s/it] 80it [13:42, 10.30s/it] 81it [13:52, 10.26s/it] 82it [14:02, 10.24s/it] 83it [14:12, 10.28s/it] 84it [14:23, 10.30s/it] 85it [14:33, 10.38s/it] 86it [14:43, 10.31s/it] 87it [14:53, 10.25s/it] 88it [15:04, 10.26s/it] 89it [15:14, 10.29s/it] 90it [15:24, 10.28s/it] 91it [15:35, 10.28s/it] 92it [15:45, 10.24s/it] 93it [15:55, 10.18s/it] 94it [16:05, 10.18s/it] 95it [16:15, 10.20s/it] 96it [16:26, 10.21s/it] 97it [16:36, 10.24s/it] 98it [16:46, 10.17s/it] 99it [16:56, 10.19s/it] 100it [17:06, 10.19s/it] 101it [17:17, 10.22s/it] 102it [17:27, 10.21s/it] 103it [17:37, 10.24s/it] 104it [17:47, 10.24s/it] 105it [17:58, 10.27s/it] 106it [18:08, 10.27s/it] 107it [18:18, 10.30s/it] 108it [18:29, 10.32s/it] 109it [18:39, 10.35s/it] 110it [18:49, 10.35s/it] 111it [19:00, 10.34s/it] 112it [19:10, 10.30s/it] 113it [19:20, 10.29s/it] 114it [19:30, 10.27s/it] 115it [19:41, 10.27s/it] 116it [19:51, 10.24s/it] 117it [20:01, 10.24s/it] 118it [20:11, 10.20s/it] 119it [20:21, 10.21s/it] 120it [20:32, 10.17s/it] 121it [20:42, 10.16s/it] 122it [20:52, 10.16s/it] 123it [21:02, 10.16s/it] 124it [21:12, 10.17s/it] 125it [21:22, 10.18s/it] 126it [21:33, 10.19s/it] 127it [21:43, 10.20s/it] 128it [21:53, 10.19s/it] 129it [22:03, 10.22s/it] 130it [22:13, 10.21s/it] 131it [22:24, 10.25s/it] 132it [22:34, 10.28s/it] 133it [22:44, 10.28s/it] 134it [22:55, 10.22s/it] 135it [23:05, 10.30s/it] 136it [23:15, 10.33s/it] 137it [23:26, 10.35s/it] 138it [23:36, 10.37s/it] 139it [23:46, 10.33s/it] 140it [23:57, 10.28s/it] 141it [24:07, 10.31s/it] 142it [24:17, 10.33s/it] 143it [24:28, 10.33s/it] 144it [24:38, 10.35s/it] 145it [24:48, 10.30s/it] 146it [24:58, 10.24s/it] 147it [25:09, 10.29s/it] 148it [25:19, 10.30s/it] 149it [25:29, 10.30s/it] 150it [25:40, 10.34s/it] 151it [25:50, 10.31s/it] 152it [26:00, 10.26s/it] 153it [26:10, 10.27s/it] 154it [26:21, 10.27s/it] 155it [26:31, 10.28s/it] 156it [26:41, 10.29s/it] 157it [26:52, 10.28s/it] 158it [27:02, 10.24s/it] 159it [27:12, 10.23s/it] 160it [27:22, 10.23s/it] 161it [27:32, 10.17s/it] 162it [27:42, 10.14s/it] 163it [27:52, 10.13s/it] 164it [28:02, 10.10s/it] 165it [28:13, 10.13s/it] 166it [28:23, 10.15s/it] 167it [28:33, 10.14s/it] 168it [28:43, 10.11s/it] 169it [28:53, 10.07s/it] 170it [29:03, 10.09s/it] 171it [29:13, 10.10s/it] 172it [29:23, 10.13s/it] 173it [29:34, 10.14s/it] 174it [29:44, 10.08s/it] 175it [29:54, 10.04s/it] 176it [30:04, 10.08s/it] 177it [30:14, 10.12s/it] 178it [30:24, 10.14s/it] 179it [30:34, 10.16s/it] 180it [30:44, 10.10s/it] 181it [30:54, 10.05s/it] 182it [31:04, 10.04s/it] 183it [31:14, 10.07s/it] 184it [31:25, 10.11s/it] 185it [31:35, 10.12s/it] 186it [31:45, 10.09s/it] 187it [31:55, 10.09s/it] 188it [32:05, 10.05s/it] 189it [32:15, 10.08s/it] 190it [32:25, 10.12s/it] 191it [32:35, 10.14s/it] 192it [32:45, 10.12s/it] 193it [32:55, 10.10s/it] 194it [33:05, 10.08s/it] 195it [33:16, 10.07s/it] 196it [33:26, 10.13s/it] 197it [33:36, 10.13s/it] 198it [33:46, 10.13s/it] 199it [33:56, 10.13s/it] 200it [34:06, 10.11s/it] 201it [34:16, 10.10s/it] 202it [34:26, 10.11s/it] 203it [34:37, 10.12s/it] 204it [34:47, 10.11s/it] 205it [34:57, 10.08s/it] 206it [35:07, 10.05s/it] 207it [35:17, 10.07s/it] 208it [35:27, 10.09s/it] 209it [35:37, 10.10s/it] 210it [35:47, 10.11s/it] 211it [35:57, 10.13s/it] 212it [36:07, 10.11s/it] 213it [36:17, 10.07s/it] 214it [36:27, 10.07s/it] 215it [36:38, 10.09s/it] 216it [36:48, 10.11s/it] 217it [36:58, 10.12s/it] 218it [37:08, 10.08s/it] 219it [37:18, 10.09s/it] 220it [37:28, 10.08s/it] 221it [37:38, 10.08s/it] 222it [37:48, 10.08s/it] 223it [37:58, 10.09s/it] 224it [38:08, 10.07s/it] 225it [38:18, 10.06s/it] 226it [38:28, 10.06s/it] 227it [38:38, 10.06s/it] 228it [38:49, 10.09s/it] 229it [38:59, 10.09s/it] 230it [39:09, 10.07s/it] 231it [39:19, 10.06s/it] 232it [39:29, 10.08s/it] 233it [39:39, 10.09s/it] 234it [39:49, 10.12s/it] 235it [39:59, 10.12s/it] 236it [40:09, 10.11s/it] 237it [40:19, 10.07s/it] 238it [40:29, 10.05s/it] 239it [40:39, 10.05s/it] 240it [40:50, 10.05s/it] 241it [41:00, 10.08s/it] 242it [41:10, 10.10s/it] 243it [41:20, 10.05s/it] 244it [41:30, 10.02s/it] 245it [41:40, 10.06s/it] 246it [41:50, 10.09s/it] 247it [42:00, 10.11s/it] 248it [42:10, 10.14s/it] 249it [42:20, 10.09s/it] 250it [42:30, 10.05s/it] 251it [42:40, 10.03s/it] 252it [42:50, 10.05s/it] 253it [43:01, 10.08s/it] 254it [43:11, 10.13s/it] 255it [43:21, 10.10s/it] 256it [43:31, 10.07s/it] 257it [43:41, 10.02s/it] 258it [43:51, 10.07s/it] 259it [44:01, 10.10s/it] 260it [44:11, 10.14s/it] 261it [44:21, 10.14s/it] 262it [44:31, 10.10s/it] 263it [44:41, 10.06s/it] 264it [44:52, 10.07s/it] 265it [45:02, 10.11s/it] 266it [45:12, 10.17s/it] 267it [45:22, 10.15s/it] 268it [45:32, 10.11s/it] 269it [45:42, 10.06s/it] 270it [45:52, 10.03s/it] 271it [46:02, 10.09s/it] 272it [46:12, 10.09s/it] 273it [46:23, 10.10s/it] 274it [46:33, 10.12s/it] 275it [46:43, 10.08s/it] 276it [46:53, 10.05s/it] 277it [47:03, 10.10s/it] 278it [47:13, 10.09s/it] 279it [47:23, 10.11s/it] 280it [47:33, 10.13s/it] 281it [47:43, 10.09s/it] 282it [47:53, 10.04s/it] 283it [48:03, 10.04s/it] 284it [48:13, 10.06s/it] 285it [48:23, 10.07s/it] 286it [48:34, 10.09s/it] 287it [48:44, 10.09s/it] 288it [48:54, 10.04s/it] 289it [49:04, 10.02s/it] 290it [49:14, 10.05s/it] 291it [49:24, 10.10s/it] 292it [49:34, 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9.77s/it] 973it [2:43:04, 9.76s/it] 974it [2:43:13, 9.75s/it] 975it [2:43:23, 9.78s/it] 976it [2:43:33, 9.80s/it] 977it [2:43:43, 9.79s/it] 978it [2:43:53, 9.80s/it] 979it [2:44:03, 9.81s/it] 980it [2:44:12, 9.82s/it] 981it [2:44:22, 9.84s/it] 982it [2:44:32, 9.83s/it] 983it [2:44:42, 9.86s/it] 984it [2:44:52, 9.87s/it] 985it [2:45:02, 9.88s/it] 986it [2:45:12, 9.84s/it] 987it [2:45:21, 9.83s/it] 988it [2:45:31, 9.80s/it] 989it [2:45:41, 9.82s/it] 990it [2:45:51, 9.81s/it] 991it [2:46:01, 9.83s/it] 992it [2:46:10, 9.83s/it] 993it [2:46:20, 9.83s/it] 994it [2:46:30, 9.84s/it] 995it [2:46:40, 9.85s/it] 996it [2:46:50, 9.85s/it] 997it [2:47:00, 9.87s/it] 998it [2:47:10, 9.86s/it] 999it [2:47:20, 9.87s/it] 1000it [2:47:29, 9.84s/it] 1000it [2:47:29, 10.05s/it] +Error counts: + cyclic_id: 0 + cyclic_inchikey: 0 + cyclic_scaffold: 0 + cyclic_mwt: 0 + cyclic_clogp: 0 + cyclic_tpsa: 0 +⏰ Completed process in 2:47:55.930886 ++ rm /nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/train/cyc-pep-6-12mer-70M_45.csv diff --git a/train/cyc-pep-6-12mer-70M_46.csv.gz b/train/cyc-pep-6-12mer-70M_46.csv.gz index d61b387a17095cdde061d418e2655e290d13eaa0..2fa280016425cd41d063a5e865401cf873564c3d 100644 --- a/train/cyc-pep-6-12mer-70M_46.csv.gz +++ b/train/cyc-pep-6-12mer-70M_46.csv.gz @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:34f89e5fa868745e792217d3eda6d3b5e16fda65953a1a567ed2b130808d0ee4 -size 54500278 +oid sha256:c17a0ee87ef96ad175af22aa7ff3ab86509af1981ef2225ec46755df26fdc09f +size 107807575 diff --git a/train/cyc-pep-6-12mer-70M_46.log b/train/cyc-pep-6-12mer-70M_46.log new file mode 100644 index 0000000000000000000000000000000000000000..f3ad08f763cd17e0d0b853de287c38373b7da1ad --- /dev/null +++ b/train/cyc-pep-6-12mer-70M_46.log @@ -0,0 +1,337 @@ ++ module purge ++ '[' -z '' ']' ++ case "$-" in ++ __lmod_sh_dbg=x ++ '[' -n x ']' ++ set +x +Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output +Shell debugging restarted ++ unset __lmod_sh_dbg ++ return 0 ++ module load Anaconda3/2023.03 ++ '[' -z '' ']' ++ case "$-" in ++ __lmod_sh_dbg=x ++ '[' -n x ']' ++ set +x +Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output +Shell debugging restarted ++ unset __lmod_sh_dbg ++ return 0 ++ source /camp/home/johnsoe/.bashrc +++ '[' '' = yes ']' +++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' ++++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.bash hook +++ __conda_setup='export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'' + +# Copyright (C) 2012 Anaconda, Inc +# SPDX-License-Identifier: BSD-3-Clause +__conda_exe() ( + "$CONDA_EXE" $_CE_M $_CE_CONDA "$@" +) + +__conda_hashr() { + if [ -n "${ZSH_VERSION:+x}" ]; then + \rehash + elif [ -n "${POSH_VERSION:+x}" ]; then + : # pass + else + \hash -r + fi +} + +__conda_activate() { + if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then + # Handle transition from shell activated with conda <= 4.3 to a subsequent activation + # after conda updated to >= 4.4. See issue #6173. + PS1="$CONDA_PS1_BACKUP" + \unset CONDA_PS1_BACKUP + fi + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return + \eval "$ask_conda" + __conda_hashr +} + +__conda_reactivate() { + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return + \eval "$ask_conda" + __conda_hashr +} + +conda() { + \local cmd="${1-__missing__}" + case "$cmd" in + activate|deactivate) + __conda_activate "$@" + ;; + install|update|upgrade|remove|uninstall) + __conda_exe "$@" || \return + __conda_reactivate + ;; + *) + __conda_exe "$@" + ;; + esac +} + +if [ -z "${CONDA_SHLVL+x}" ]; then + \export CONDA_SHLVL=0 + # In dev-mode CONDA_EXE is python.exe and on Windows + # it is in a different relative location to condabin. + if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then + PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}" + else + PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}" + fi + \export PATH + + # We'\''re not allowing PS1 to be unbound. It must at least be set. + # However, we'\''re not exporting it, which can cause problems when starting a second shell + # via a first shell (i.e. starting zsh from bash). + if [ -z "${PS1+x}" ]; then + PS1= + fi +fi + +conda activate base' +++ '[' 0 -eq 0 ']' +++ eval 'export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'' + +# Copyright (C) 2012 Anaconda, Inc +# SPDX-License-Identifier: BSD-3-Clause +__conda_exe() ( + "$CONDA_EXE" $_CE_M $_CE_CONDA "$@" +) + +__conda_hashr() { + if [ -n "${ZSH_VERSION:+x}" ]; then + \rehash + elif [ -n "${POSH_VERSION:+x}" ]; then + : # pass + else + \hash -r + fi +} + +__conda_activate() { + if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then + # Handle transition from shell activated with conda <= 4.3 to a subsequent activation + # after conda updated to >= 4.4. See issue #6173. + PS1="$CONDA_PS1_BACKUP" + \unset CONDA_PS1_BACKUP + fi + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return + \eval "$ask_conda" + __conda_hashr +} + +__conda_reactivate() { + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return + \eval "$ask_conda" + __conda_hashr +} + +conda() { + \local cmd="${1-__missing__}" + case "$cmd" in + activate|deactivate) + __conda_activate "$@" + ;; + install|update|upgrade|remove|uninstall) + __conda_exe "$@" || \return + __conda_reactivate + ;; + *) + __conda_exe "$@" + ;; + esac +} + +if [ -z "${CONDA_SHLVL+x}" ]; then + \export CONDA_SHLVL=0 + # In dev-mode CONDA_EXE is python.exe and on Windows + # it is in a different relative location to condabin. + if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then + PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}" + else + PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}" + fi + \export PATH + + # We'\''re not allowing PS1 to be unbound. It must at least be set. + # However, we'\''re not exporting it, which can cause problems when starting a second shell + # via a first shell (i.e. starting zsh from bash). + if [ -z "${PS1+x}" ]; then + PS1= + fi +fi + +conda activate base' ++++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda ++++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda ++++ export _CE_M= ++++ _CE_M= ++++ export _CE_CONDA= ++++ _CE_CONDA= ++++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ '[' -z x ']' ++++ conda activate base ++++ local cmd=activate ++++ case "$cmd" in ++++ __conda_activate activate base ++++ '[' -n '' ']' ++++ local ask_conda +++++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++++ __conda_exe shell.posix activate base +++++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate base ++++ ask_conda='PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_SHLVL='\''6'\'' +export CONDA_DEFAULT_ENV='\''base'\'' +export CONDA_PROMPT_MODIFIER='\''(base) '\'' +export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' ++++ eval 'PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_SHLVL='\''6'\'' +export CONDA_DEFAULT_ENV='\''base'\'' +export CONDA_PROMPT_MODIFIER='\''(base) '\'' +export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' +++++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++++ export CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0 +++++ CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0 +++++ export CONDA_SHLVL=6 +++++ CONDA_SHLVL=6 +++++ export CONDA_DEFAULT_ENV=base +++++ CONDA_DEFAULT_ENV=base +++++ export 'CONDA_PROMPT_MODIFIER=(base) ' +++++ CONDA_PROMPT_MODIFIER='(base) ' +++++ export CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev +++++ CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev +++++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++++ export _CE_M= +++++ _CE_M= +++++ export _CE_CONDA= +++++ _CE_CONDA= +++++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python +++++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ __conda_hashr ++++ '[' -n '' ']' ++++ '[' -n '' ']' ++++ hash -r +++ unset __conda_setup ++ conda activate schemist-dev ++ local cmd=activate ++ case "$cmd" in ++ __conda_activate activate schemist-dev ++ '[' -n '' ']' ++ local ask_conda +++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++ __conda_exe shell.posix activate schemist-dev +++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate schemist-dev ++ ask_conda='PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_SHLVL='\''7'\'' +export CONDA_DEFAULT_ENV='\''schemist-dev'\'' +export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\'' +export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' ++ eval 'PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_SHLVL='\''7'\'' +export CONDA_DEFAULT_ENV='\''schemist-dev'\'' +export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\'' +export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' +++ PS1='(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++ export CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev +++ CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev +++ export CONDA_SHLVL=7 +++ CONDA_SHLVL=7 +++ export CONDA_DEFAULT_ENV=schemist-dev +++ CONDA_DEFAULT_ENV=schemist-dev +++ export 'CONDA_PROMPT_MODIFIER=(schemist-dev) ' +++ CONDA_PROMPT_MODIFIER='(schemist-dev) ' +++ export CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0 +++ CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0 +++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++ export _CE_M= +++ _CE_M= +++ export _CE_CONDA= +++ _CE_CONDA= +++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python +++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++ __conda_hashr ++ '[' -n '' ']' ++ '[' -n '' ']' ++ hash -r ++ CHUNK_HEAD_FILE=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz ++ INPUT=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/train/cyc-pep-6-12mer-70M_46.csv ++ COLUMN=cysteine_to_N_cyclization ++ PREFIX=cyclic_ ++ AWK='1 { print $8, $1, $2, $10, $3 }' ++ '[' -z cysteine_to_N_cyclization ']' ++ '[' -z cyclic_ ']' ++ '[' -z '1 { print $8, $1, $2, $10, $3 }' ']' ++ cat /dev/fd/63 /nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/train/cyc-pep-6-12mer-70M_46.csv ++ awk -F, -v OFS=, '1 { print $8, $1, $2, $10, $3 }' ++ schemist convert -f csv --column cysteine_to_N_cyclization --to id inchikey scaffold mwt clogp tpsa --prefix cyclic_ --options prefix=SCB- +++ zcat /nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz +++ head -n1 ++ gzip --best +++ tr ' ' , +🚀 Converting between string representations with the following parameters: + subcommand: convert + output: <_io.TextIOWrapper name='' mode='w' encoding='utf-8'> + format: csv + input: <_io.TextIOWrapper name='' mode='r' encoding='utf-8'> + representation: SMILES + column: cysteine_to_N_cyclization + prefix: cyclic_ + to: ['id', 'inchikey', 'scaffold', 'mwt', 'clogp', 'tpsa'] + options: ['prefix=SCB-'] + func: + 0it [00:00, ?it/s] 1it [00:10, 10.13s/it] 2it [00:20, 10.07s/it] 3it [00:30, 10.08s/it] 4it [00:40, 10.06s/it] 5it [00:50, 10.02s/it] 6it 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9.60s/it] 952it [2:36:01, 9.58s/it] 953it [2:36:11, 9.57s/it] 954it [2:36:21, 9.56s/it] 955it [2:36:30, 9.58s/it] 956it [2:36:40, 9.57s/it] 957it [2:36:49, 9.56s/it] 958it [2:36:59, 9.55s/it] 959it [2:37:08, 9.55s/it] 960it [2:37:18, 9.58s/it] 961it [2:37:28, 9.57s/it] 962it [2:37:37, 9.57s/it] 963it [2:37:47, 9.59s/it] 964it [2:37:56, 9.58s/it] 965it [2:38:06, 9.58s/it] 966it [2:38:15, 9.57s/it] 967it [2:38:25, 9.55s/it] 968it [2:38:35, 9.58s/it] 969it [2:38:44, 9.58s/it] 970it [2:38:54, 9.56s/it] 971it [2:39:03, 9.55s/it] 972it [2:39:13, 9.57s/it] 973it [2:39:22, 9.54s/it] 974it [2:39:32, 9.55s/it] 975it [2:39:41, 9.58s/it] 976it [2:39:51, 9.62s/it] 977it [2:40:01, 9.64s/it] 978it [2:40:10, 9.64s/it] 979it [2:40:20, 9.62s/it] 980it [2:40:30, 9.66s/it] 981it [2:40:40, 9.71s/it] 982it [2:40:49, 9.69s/it] 983it [2:40:59, 9.66s/it] 984it [2:41:09, 9.67s/it] 985it [2:41:18, 9.68s/it] 986it [2:41:28, 9.67s/it] 987it [2:41:38, 9.66s/it] 988it [2:41:47, 9.63s/it] 989it [2:41:57, 9.65s/it] 990it [2:42:06, 9.63s/it] 991it [2:42:16, 9.64s/it] 992it [2:42:26, 9.67s/it] 993it [2:42:35, 9.64s/it] 994it [2:42:45, 9.62s/it] 995it [2:42:55, 9.62s/it] 996it [2:43:04, 9.60s/it] 997it [2:43:14, 9.58s/it] 998it [2:43:23, 9.59s/it] 999it [2:43:33, 9.58s/it] 1000it [2:43:42, 9.60s/it] 1000it [2:43:42, 9.82s/it] +Error counts: + cyclic_id: 0 + cyclic_inchikey: 0 + cyclic_scaffold: 0 + cyclic_mwt: 0 + cyclic_clogp: 0 + cyclic_tpsa: 0 +⏰ Completed process in 2:44:04.878653 ++ rm /nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/train/cyc-pep-6-12mer-70M_46.csv diff --git a/train/cyc-pep-6-12mer-70M_47.csv.gz b/train/cyc-pep-6-12mer-70M_47.csv.gz index ffd311a72e9159abaf192ef43fb2190c508ce682..7b91e450d88b3ec55bed7051dac8c7a57e9b4a60 100644 --- a/train/cyc-pep-6-12mer-70M_47.csv.gz +++ b/train/cyc-pep-6-12mer-70M_47.csv.gz @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:226fb3475dab5a70fbf92f757e68a4fe56df0562f738415fc2da6fb36bea7b39 -size 9831309 +oid sha256:f70ebc90bb3c2a40f4262f7e9cbcc87bcd36d7d1ef6bd383c6d30fb997ae0487 +size 19442443 diff --git a/train/cyc-pep-6-12mer-70M_47.log b/train/cyc-pep-6-12mer-70M_47.log new file mode 100644 index 0000000000000000000000000000000000000000..0a8ac2454003d04f06d02221e181ed1a22b049ec --- /dev/null +++ b/train/cyc-pep-6-12mer-70M_47.log @@ -0,0 +1,337 @@ ++ module purge ++ '[' -z '' ']' ++ case "$-" in ++ __lmod_sh_dbg=x ++ '[' -n x ']' ++ set +x +Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output +Shell debugging restarted ++ unset __lmod_sh_dbg ++ return 0 ++ module load Anaconda3/2023.03 ++ '[' -z '' ']' ++ case "$-" in ++ __lmod_sh_dbg=x ++ '[' -n x ']' ++ set +x +Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output +Shell debugging restarted ++ unset __lmod_sh_dbg ++ return 0 ++ source /camp/home/johnsoe/.bashrc +++ '[' '' = yes ']' +++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' ++++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.bash hook +++ __conda_setup='export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'' + +# Copyright (C) 2012 Anaconda, Inc +# SPDX-License-Identifier: BSD-3-Clause +__conda_exe() ( + "$CONDA_EXE" $_CE_M $_CE_CONDA "$@" +) + +__conda_hashr() { + if [ -n "${ZSH_VERSION:+x}" ]; then + \rehash + elif [ -n "${POSH_VERSION:+x}" ]; then + : # pass + else + \hash -r + fi +} + +__conda_activate() { + if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then + # Handle transition from shell activated with conda <= 4.3 to a subsequent activation + # after conda updated to >= 4.4. See issue #6173. + PS1="$CONDA_PS1_BACKUP" + \unset CONDA_PS1_BACKUP + fi + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return + \eval "$ask_conda" + __conda_hashr +} + +__conda_reactivate() { + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return + \eval "$ask_conda" + __conda_hashr +} + +conda() { + \local cmd="${1-__missing__}" + case "$cmd" in + activate|deactivate) + __conda_activate "$@" + ;; + install|update|upgrade|remove|uninstall) + __conda_exe "$@" || \return + __conda_reactivate + ;; + *) + __conda_exe "$@" + ;; + esac +} + +if [ -z "${CONDA_SHLVL+x}" ]; then + \export CONDA_SHLVL=0 + # In dev-mode CONDA_EXE is python.exe and on Windows + # it is in a different relative location to condabin. + if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then + PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}" + else + PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}" + fi + \export PATH + + # We'\''re not allowing PS1 to be unbound. It must at least be set. + # However, we'\''re not exporting it, which can cause problems when starting a second shell + # via a first shell (i.e. starting zsh from bash). + if [ -z "${PS1+x}" ]; then + PS1= + fi +fi + +conda activate base' +++ '[' 0 -eq 0 ']' +++ eval 'export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'' + +# Copyright (C) 2012 Anaconda, Inc +# SPDX-License-Identifier: BSD-3-Clause +__conda_exe() ( + "$CONDA_EXE" $_CE_M $_CE_CONDA "$@" +) + +__conda_hashr() { + if [ -n "${ZSH_VERSION:+x}" ]; then + \rehash + elif [ -n "${POSH_VERSION:+x}" ]; then + : # pass + else + \hash -r + fi +} + +__conda_activate() { + if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then + # Handle transition from shell activated with conda <= 4.3 to a subsequent activation + # after conda updated to >= 4.4. See issue #6173. + PS1="$CONDA_PS1_BACKUP" + \unset CONDA_PS1_BACKUP + fi + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return + \eval "$ask_conda" + __conda_hashr +} + +__conda_reactivate() { + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return + \eval "$ask_conda" + __conda_hashr +} + +conda() { + \local cmd="${1-__missing__}" + case "$cmd" in + activate|deactivate) + __conda_activate "$@" + ;; + install|update|upgrade|remove|uninstall) + __conda_exe "$@" || \return + __conda_reactivate + ;; + *) + __conda_exe "$@" + ;; + esac +} + +if [ -z "${CONDA_SHLVL+x}" ]; then + \export CONDA_SHLVL=0 + # In dev-mode CONDA_EXE is python.exe and on Windows + # it is in a different relative location to condabin. + if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then + PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}" + else + PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}" + fi + \export PATH + + # We'\''re not allowing PS1 to be unbound. It must at least be set. + # However, we'\''re not exporting it, which can cause problems when starting a second shell + # via a first shell (i.e. starting zsh from bash). + if [ -z "${PS1+x}" ]; then + PS1= + fi +fi + +conda activate base' ++++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda ++++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda ++++ export _CE_M= ++++ _CE_M= ++++ export _CE_CONDA= ++++ _CE_CONDA= ++++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ '[' -z x ']' ++++ conda activate base ++++ local cmd=activate ++++ case "$cmd" in ++++ __conda_activate activate base ++++ '[' -n '' ']' ++++ local ask_conda +++++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++++ __conda_exe shell.posix activate base +++++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate base ++++ ask_conda='PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_SHLVL='\''6'\'' +export CONDA_DEFAULT_ENV='\''base'\'' +export CONDA_PROMPT_MODIFIER='\''(base) '\'' +export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' ++++ eval 'PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_SHLVL='\''6'\'' +export CONDA_DEFAULT_ENV='\''base'\'' +export CONDA_PROMPT_MODIFIER='\''(base) '\'' +export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' +++++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++++ export CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0 +++++ CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0 +++++ export CONDA_SHLVL=6 +++++ CONDA_SHLVL=6 +++++ export CONDA_DEFAULT_ENV=base +++++ CONDA_DEFAULT_ENV=base +++++ export 'CONDA_PROMPT_MODIFIER=(base) ' +++++ CONDA_PROMPT_MODIFIER='(base) ' +++++ export CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev +++++ CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev +++++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++++ export _CE_M= +++++ _CE_M= +++++ export _CE_CONDA= +++++ _CE_CONDA= +++++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python +++++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ __conda_hashr ++++ '[' -n '' ']' ++++ '[' -n '' ']' ++++ hash -r +++ unset __conda_setup ++ conda activate schemist-dev ++ local cmd=activate ++ case "$cmd" in ++ __conda_activate activate schemist-dev ++ '[' -n '' ']' ++ local ask_conda +++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++ __conda_exe shell.posix activate schemist-dev +++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate schemist-dev ++ ask_conda='PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_SHLVL='\''7'\'' +export CONDA_DEFAULT_ENV='\''schemist-dev'\'' +export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\'' +export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' ++ eval 'PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_SHLVL='\''7'\'' +export CONDA_DEFAULT_ENV='\''schemist-dev'\'' +export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\'' +export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' +++ PS1='(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++ export CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev +++ CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev +++ export CONDA_SHLVL=7 +++ CONDA_SHLVL=7 +++ export CONDA_DEFAULT_ENV=schemist-dev +++ CONDA_DEFAULT_ENV=schemist-dev +++ export 'CONDA_PROMPT_MODIFIER=(schemist-dev) ' +++ CONDA_PROMPT_MODIFIER='(schemist-dev) ' +++ export CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0 +++ CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0 +++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++ export _CE_M= +++ _CE_M= +++ export _CE_CONDA= +++ _CE_CONDA= +++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python +++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++ __conda_hashr ++ '[' -n '' ']' ++ '[' -n '' ']' ++ hash -r ++ CHUNK_HEAD_FILE=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz ++ INPUT=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/train/cyc-pep-6-12mer-70M_47.csv ++ COLUMN=cysteine_to_N_cyclization ++ PREFIX=cyclic_ ++ AWK='1 { print $8, $1, $2, $10, $3 }' ++ '[' -z cysteine_to_N_cyclization ']' ++ '[' -z cyclic_ ']' ++ '[' -z '1 { print $8, $1, $2, $10, $3 }' ']' ++ cat /dev/fd/63 /nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/train/cyc-pep-6-12mer-70M_47.csv ++ awk -F, -v OFS=, '1 { print $8, $1, $2, $10, $3 }' +++ zcat /nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz +++ head -n1 ++ gzip --best +++ tr ' ' , ++ schemist convert -f csv --column cysteine_to_N_cyclization --to id inchikey scaffold mwt clogp tpsa --prefix cyclic_ --options prefix=SCB- +🚀 Converting between string representations with the following parameters: + subcommand: convert + output: <_io.TextIOWrapper name='' mode='w' encoding='utf-8'> + format: csv + input: <_io.TextIOWrapper name='' mode='r' encoding='utf-8'> + representation: SMILES + column: cysteine_to_N_cyclization + prefix: cyclic_ + to: ['id', 'inchikey', 'scaffold', 'mwt', 'clogp', 'tpsa'] + options: ['prefix=SCB-'] + func: + 0it [00:00, ?it/s] 1it [00:10, 10.21s/it] 2it [00:20, 10.13s/it] 3it [00:30, 10.03s/it] 4it [00:40, 9.96s/it] 5it [00:49, 9.91s/it] 6it [00:59, 9.93s/it] 7it [01:09, 9.91s/it] 8it [01:19, 9.89s/it] 9it [01:29, 9.88s/it] 10it [01:39, 9.84s/it] 11it [01:49, 9.85s/it] 12it [01:58, 9.86s/it] 13it [02:08, 9.89s/it] 14it [02:18, 9.91s/it] 15it [02:28, 9.88s/it] 16it [02:38, 9.85s/it] 17it [02:48, 9.81s/it] 18it [02:57, 9.82s/it] 19it [03:07, 9.84s/it] 20it [03:17, 9.86s/it] 21it [03:27, 9.87s/it] 22it [03:37, 9.83s/it] 23it [03:46, 9.76s/it] 24it [03:56, 9.73s/it] 25it [04:06, 9.76s/it] 26it [04:16, 9.80s/it] 27it [04:26, 9.80s/it] 28it [04:36, 9.89s/it] 29it [04:46, 9.97s/it] 30it [04:56, 10.04s/it] 31it [05:06, 10.01s/it] 32it [05:16, 9.97s/it] 33it [05:26, 9.95s/it] 34it [05:36, 9.88s/it] 35it [05:45, 9.84s/it] 36it [05:55, 9.84s/it] 37it [06:05, 9.81s/it] 38it [06:15, 9.82s/it] 39it [06:25, 9.83s/it] 40it [06:34, 9.84s/it] 41it [06:44, 9.81s/it] 42it [06:54, 9.78s/it] 43it [07:04, 9.77s/it] 44it [07:14, 9.82s/it] 45it [07:24, 9.87s/it] 46it [07:33, 9.86s/it] 47it [07:43, 9.80s/it] 48it [07:53, 9.75s/it] 49it [08:03, 9.79s/it] 50it [08:13, 9.83s/it] 51it [08:22, 9.86s/it] 52it [08:32, 9.88s/it] 53it [08:42, 9.84s/it] 54it [08:52, 9.81s/it] 55it [09:02, 9.78s/it] 56it [09:11, 9.81s/it] 57it [09:21, 9.83s/it] 58it [09:31, 9.85s/it] 59it [09:41, 9.86s/it] 60it [09:51, 9.83s/it] 61it [10:01, 9.80s/it] 62it [10:11, 9.83s/it] 63it [10:20, 9.86s/it] 64it [10:30, 9.85s/it] 65it [10:40, 9.83s/it] 66it [10:50, 9.81s/it] 67it [11:00, 9.77s/it] 68it [11:09, 9.80s/it] 69it [11:19, 9.84s/it] 70it [11:29, 9.82s/it] 71it [11:39, 9.97s/it] 72it [11:49, 9.99s/it] 73it [11:59, 9.92s/it] 74it [12:09, 9.88s/it] 75it [12:19, 9.86s/it] 76it [12:29, 9.84s/it] 77it [12:38, 9.85s/it] 78it [12:48, 9.83s/it] 79it [12:58, 9.82s/it] 80it [13:08, 9.83s/it] 81it [13:18, 9.82s/it] 82it [13:28, 9.84s/it] 83it [13:37, 9.82s/it] 84it [13:47, 9.80s/it] 85it [13:57, 9.77s/it] 86it [14:07, 9.78s/it] 87it [14:16, 9.77s/it] 88it [14:26, 9.80s/it] 89it [14:36, 9.80s/it] 90it [14:46, 9.81s/it] 91it [14:56, 9.82s/it] 92it [15:05, 9.80s/it] 93it [15:15, 9.77s/it] 94it [15:25, 9.78s/it] 95it [15:35, 9.76s/it] 96it [15:44, 9.77s/it] 97it [15:54, 9.75s/it] 98it [16:04, 9.74s/it] 99it [16:14, 9.73s/it] 100it [16:23, 9.73s/it] 101it [16:33, 9.71s/it] 102it [16:43, 9.70s/it] 103it [16:52, 9.70s/it] 104it [17:02, 9.69s/it] 105it [17:12, 9.66s/it] 106it [17:21, 9.67s/it] 107it [17:31, 9.69s/it] 108it [17:41, 9.70s/it] 109it [17:50, 9.71s/it] 110it [18:00, 9.72s/it] 111it [18:10, 9.70s/it] 112it [18:20, 9.71s/it] 113it [18:29, 9.71s/it] 114it [18:39, 9.72s/it] 115it [18:49, 9.73s/it] 116it [18:59, 9.74s/it] 117it [19:08, 9.72s/it] 118it [19:18, 9.71s/it] 119it [19:28, 9.71s/it] 120it [19:37, 9.70s/it] 121it [19:47, 9.71s/it] 122it [19:57, 9.73s/it] 123it [20:06, 9.70s/it] 124it [20:16, 9.68s/it] 125it [20:26, 9.71s/it] 126it [20:36, 9.74s/it] 127it [20:45, 9.73s/it] 128it [20:55, 9.78s/it] 129it [21:05, 9.74s/it] 130it [21:15, 9.73s/it] 131it [21:24, 9.73s/it] 132it [21:34, 9.74s/it] 133it [21:44, 9.74s/it] 134it [21:54, 9.72s/it] 135it [22:03, 9.70s/it] 136it [22:13, 9.69s/it] 137it [22:23, 9.70s/it] 138it [22:32, 9.72s/it] 139it [22:42, 9.76s/it] 140it [22:52, 9.78s/it] 141it [23:02, 9.76s/it] 142it [23:11, 9.72s/it] 143it [23:21, 9.70s/it] 144it [23:31, 9.71s/it] 145it [23:41, 9.75s/it] 146it [23:50, 9.75s/it] 147it [24:00, 9.73s/it] 148it [24:10, 9.72s/it] 149it [24:19, 9.73s/it] 150it [24:29, 9.73s/it] 151it [24:39, 9.74s/it] 152it [24:49, 9.72s/it] 153it [24:58, 9.73s/it] 154it [25:08, 9.74s/it] 155it [25:18, 9.73s/it] 156it [25:28, 9.75s/it] 157it [25:37, 9.74s/it] 158it [25:47, 9.74s/it] 159it [25:57, 9.75s/it] 160it [26:07, 9.72s/it] 161it [26:16, 9.70s/it] 162it [26:26, 9.71s/it] 163it [26:36, 9.73s/it] 164it [26:45, 9.75s/it] 165it [26:55, 9.73s/it] 166it [27:05, 9.74s/it] 167it [27:15, 9.75s/it] 168it [27:25, 9.77s/it] 169it [27:34, 9.76s/it] 170it [27:44, 9.76s/it] 171it [27:54, 9.78s/it] 172it [28:04, 9.75s/it] 173it [28:13, 9.75s/it] 174it [28:23, 9.76s/it] 175it [28:33, 9.77s/it] 176it [28:43, 9.77s/it] 177it [28:52, 9.73s/it] 178it [29:02, 9.70s/it] 179it [29:12, 9.71s/it] 180it [29:21, 9.73s/it] 181it [29:25, 7.94s/it] 181it [29:25, 9.76s/it] +Error counts: + cyclic_id: 0 + cyclic_inchikey: 0 + cyclic_scaffold: 0 + cyclic_mwt: 0 + cyclic_clogp: 0 + cyclic_tpsa: 0 +⏰ Completed process in 0:29:29.402888 ++ rm /nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/train/cyc-pep-6-12mer-70M_47.csv diff --git a/validation/cyc-pep-6-12mer-70M_00.csv.gz b/validation/cyc-pep-6-12mer-70M_00.csv.gz index 297857525ddf4e76b63a6f3a8e7c0813b565ff5c..2a345cfa056d7c05ec5966bf89b778f906bf8332 100644 --- a/validation/cyc-pep-6-12mer-70M_00.csv.gz +++ b/validation/cyc-pep-6-12mer-70M_00.csv.gz @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:6aee6ffc3c8ab44e70eb770db405cb793b8de34650e427c94f40b67480a3c0d7 -size 58250562 +oid sha256:5508aa346473021697537fc3bf8323100f1f1e1be24773890b140bf34a731224 +size 112826220 diff --git a/validation/cyc-pep-6-12mer-70M_00.log b/validation/cyc-pep-6-12mer-70M_00.log new file mode 100644 index 0000000000000000000000000000000000000000..306f2ccd3896ee93f37e0d56bfa3762a9a877426 --- /dev/null +++ b/validation/cyc-pep-6-12mer-70M_00.log @@ -0,0 +1,337 @@ ++ module purge ++ '[' -z '' ']' ++ case "$-" in ++ __lmod_sh_dbg=x ++ '[' -n x ']' ++ set +x +Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output +Shell debugging restarted ++ unset __lmod_sh_dbg ++ return 0 ++ module load Anaconda3/2023.03 ++ '[' -z '' ']' ++ case "$-" in ++ __lmod_sh_dbg=x ++ '[' -n x ']' ++ set +x +Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output +Shell debugging restarted ++ unset __lmod_sh_dbg ++ return 0 ++ source /camp/home/johnsoe/.bashrc +++ '[' '' = yes ']' +++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' ++++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.bash hook +++ __conda_setup='export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'' + +# Copyright (C) 2012 Anaconda, Inc +# SPDX-License-Identifier: BSD-3-Clause +__conda_exe() ( + "$CONDA_EXE" $_CE_M $_CE_CONDA "$@" +) + +__conda_hashr() { + if [ -n "${ZSH_VERSION:+x}" ]; then + \rehash + elif [ -n "${POSH_VERSION:+x}" ]; then + : # pass + else + \hash -r + fi +} + +__conda_activate() { + if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then + # Handle transition from shell activated with conda <= 4.3 to a subsequent activation + # after conda updated to >= 4.4. See issue #6173. + PS1="$CONDA_PS1_BACKUP" + \unset CONDA_PS1_BACKUP + fi + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return + \eval "$ask_conda" + __conda_hashr +} + +__conda_reactivate() { + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return + \eval "$ask_conda" + __conda_hashr +} + +conda() { + \local cmd="${1-__missing__}" + case "$cmd" in + activate|deactivate) + __conda_activate "$@" + ;; + install|update|upgrade|remove|uninstall) + __conda_exe "$@" || \return + __conda_reactivate + ;; + *) + __conda_exe "$@" + ;; + esac +} + +if [ -z "${CONDA_SHLVL+x}" ]; then + \export CONDA_SHLVL=0 + # In dev-mode CONDA_EXE is python.exe and on Windows + # it is in a different relative location to condabin. + if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then + PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}" + else + PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}" + fi + \export PATH + + # We'\''re not allowing PS1 to be unbound. It must at least be set. + # However, we'\''re not exporting it, which can cause problems when starting a second shell + # via a first shell (i.e. starting zsh from bash). + if [ -z "${PS1+x}" ]; then + PS1= + fi +fi + +conda activate base' +++ '[' 0 -eq 0 ']' +++ eval 'export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'' + +# Copyright (C) 2012 Anaconda, Inc +# SPDX-License-Identifier: BSD-3-Clause +__conda_exe() ( + "$CONDA_EXE" $_CE_M $_CE_CONDA "$@" +) + +__conda_hashr() { + if [ -n "${ZSH_VERSION:+x}" ]; then + \rehash + elif [ -n "${POSH_VERSION:+x}" ]; then + : # pass + else + \hash -r + fi +} + +__conda_activate() { + if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then + # Handle transition from shell activated with conda <= 4.3 to a subsequent activation + # after conda updated to >= 4.4. See issue #6173. + PS1="$CONDA_PS1_BACKUP" + \unset CONDA_PS1_BACKUP + fi + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return + \eval "$ask_conda" + __conda_hashr +} + +__conda_reactivate() { + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return + \eval "$ask_conda" + __conda_hashr +} + +conda() { + \local cmd="${1-__missing__}" + case "$cmd" in + activate|deactivate) + __conda_activate "$@" + ;; + install|update|upgrade|remove|uninstall) + __conda_exe "$@" || \return + __conda_reactivate + ;; + *) + __conda_exe "$@" + ;; + esac +} + +if [ -z "${CONDA_SHLVL+x}" ]; then + \export CONDA_SHLVL=0 + # In dev-mode CONDA_EXE is python.exe and on Windows + # it is in a different relative location to condabin. + if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then + PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}" + else + PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}" + fi + \export PATH + + # We'\''re not allowing PS1 to be unbound. It must at least be set. + # However, we'\''re not exporting it, which can cause problems when starting a second shell + # via a first shell (i.e. starting zsh from bash). + if [ -z "${PS1+x}" ]; then + PS1= + fi +fi + +conda activate base' ++++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda ++++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda ++++ export _CE_M= ++++ _CE_M= ++++ export _CE_CONDA= ++++ _CE_CONDA= ++++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ '[' -z x ']' ++++ conda activate base ++++ local cmd=activate ++++ case "$cmd" in ++++ __conda_activate activate base ++++ '[' -n '' ']' ++++ local ask_conda +++++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++++ __conda_exe shell.posix activate base +++++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate base ++++ ask_conda='PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_SHLVL='\''6'\'' +export CONDA_DEFAULT_ENV='\''base'\'' +export CONDA_PROMPT_MODIFIER='\''(base) '\'' +export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' ++++ eval 'PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_SHLVL='\''6'\'' +export CONDA_DEFAULT_ENV='\''base'\'' +export CONDA_PROMPT_MODIFIER='\''(base) '\'' +export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' +++++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++++ export CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0 +++++ CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0 +++++ export CONDA_SHLVL=6 +++++ CONDA_SHLVL=6 +++++ export CONDA_DEFAULT_ENV=base +++++ CONDA_DEFAULT_ENV=base +++++ export 'CONDA_PROMPT_MODIFIER=(base) ' +++++ CONDA_PROMPT_MODIFIER='(base) ' +++++ export CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev +++++ CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev +++++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++++ export _CE_M= +++++ _CE_M= +++++ export _CE_CONDA= +++++ _CE_CONDA= +++++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python +++++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ __conda_hashr ++++ '[' -n '' ']' ++++ '[' -n '' ']' ++++ hash -r +++ unset __conda_setup ++ conda activate schemist-dev ++ local cmd=activate ++ case "$cmd" in ++ __conda_activate activate schemist-dev ++ '[' -n '' ']' ++ local ask_conda +++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++ __conda_exe shell.posix activate schemist-dev +++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate schemist-dev ++ ask_conda='PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_SHLVL='\''7'\'' +export CONDA_DEFAULT_ENV='\''schemist-dev'\'' +export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\'' +export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' ++ eval 'PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_SHLVL='\''7'\'' +export CONDA_DEFAULT_ENV='\''schemist-dev'\'' +export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\'' +export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' +++ PS1='(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++ export CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev +++ CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev +++ export CONDA_SHLVL=7 +++ CONDA_SHLVL=7 +++ export CONDA_DEFAULT_ENV=schemist-dev +++ CONDA_DEFAULT_ENV=schemist-dev +++ export 'CONDA_PROMPT_MODIFIER=(schemist-dev) ' +++ CONDA_PROMPT_MODIFIER='(schemist-dev) ' +++ export CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0 +++ CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0 +++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++ export _CE_M= +++ _CE_M= +++ export _CE_CONDA= +++ _CE_CONDA= +++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python +++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++ __conda_hashr ++ '[' -n '' ']' ++ '[' -n '' ']' ++ hash -r ++ CHUNK_HEAD_FILE=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz ++ INPUT=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/validation/cyc-pep-6-12mer-70M_00.csv ++ COLUMN=cysteine_to_N_cyclization ++ PREFIX=cyclic_ ++ AWK='1 { print $8, $1, $2, $10, $3 }' ++ '[' -z cysteine_to_N_cyclization ']' ++ '[' -z cyclic_ ']' ++ '[' -z '1 { print $8, $1, $2, $10, $3 }' ']' ++ cat /dev/fd/63 /nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/validation/cyc-pep-6-12mer-70M_00.csv ++ schemist convert -f csv --column cysteine_to_N_cyclization --to id inchikey scaffold mwt clogp tpsa --prefix cyclic_ --options prefix=SCB- ++ gzip --best ++ awk -F, -v OFS=, '1 { print $8, $1, $2, $10, $3 }' +++ head -n1 +++ zcat /nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz +++ tr ' ' , +🚀 Converting between string representations with the following parameters: + subcommand: convert + output: <_io.TextIOWrapper name='' mode='w' encoding='utf-8'> + format: csv + input: <_io.TextIOWrapper name='' mode='r' encoding='utf-8'> + representation: SMILES + column: cysteine_to_N_cyclization + prefix: cyclic_ + to: ['id', 'inchikey', 'scaffold', 'mwt', 'clogp', 'tpsa'] + options: ['prefix=SCB-'] + func: + 0it [00:00, ?it/s] 1it [00:10, 10.87s/it] 2it [00:21, 10.82s/it] 3it [00:32, 10.78s/it] 4it [00:43, 10.83s/it] 5it [00:54, 10.84s/it] 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10.69s/it] 922it [2:47:08, 10.67s/it] 923it [2:47:19, 10.70s/it] 924it [2:47:30, 10.69s/it] 925it [2:47:40, 10.68s/it] 926it [2:47:51, 10.70s/it] 927it [2:48:02, 10.70s/it] 928it [2:48:13, 10.71s/it] 929it [2:48:23, 10.72s/it] 930it [2:48:34, 10.72s/it] 931it [2:48:45, 10.71s/it] 932it [2:48:56, 10.73s/it] 933it [2:49:06, 10.72s/it] 934it [2:49:17, 10.73s/it] 935it [2:49:28, 10.71s/it] 936it [2:49:38, 10.71s/it] 937it [2:49:49, 10.72s/it] 938it [2:50:00, 10.71s/it] 939it [2:50:10, 10.70s/it] 940it [2:50:21, 10.77s/it] 941it [2:50:32, 10.78s/it] 942it [2:50:43, 10.74s/it] 943it [2:50:54, 10.73s/it] 944it [2:51:04, 10.76s/it] 945it [2:51:15, 10.78s/it] 946it [2:51:26, 10.78s/it] 947it [2:51:37, 10.78s/it] 948it [2:51:47, 10.75s/it] 949it [2:51:58, 10.76s/it] 950it [2:52:09, 10.72s/it] 951it [2:52:20, 10.74s/it] 952it [2:52:30, 10.75s/it] 953it [2:52:41, 10.78s/it] 954it [2:52:52, 10.87s/it] 955it [2:53:03, 10.84s/it] 956it [2:53:14, 10.82s/it] 957it [2:53:25, 10.78s/it] 958it [2:53:35, 10.74s/it] 959it [2:53:46, 10.70s/it] 960it [2:53:57, 10.72s/it] 961it [2:54:07, 10.71s/it] 962it [2:54:18, 10.69s/it] 963it [2:54:29, 10.69s/it] 964it [2:54:39, 10.72s/it] 965it [2:54:50, 10.71s/it] 966it [2:55:01, 10.71s/it] 967it [2:55:12, 10.75s/it] 968it [2:55:22, 10.73s/it] 969it [2:55:33, 10.76s/it] 970it [2:55:44, 10.77s/it] 971it [2:55:55, 10.74s/it] 972it [2:56:05, 10.77s/it] 973it [2:56:16, 10.77s/it] 974it [2:56:27, 10.80s/it] 975it [2:56:38, 10.80s/it] 976it [2:56:49, 10.83s/it] 977it [2:57:00, 10.88s/it] 978it [2:57:11, 10.90s/it] 979it [2:57:22, 10.90s/it] 980it [2:57:33, 10.92s/it] 981it [2:57:43, 10.86s/it] 982it [2:57:54, 10.82s/it] 983it [2:58:05, 10.86s/it] 984it [2:58:16, 10.86s/it] 985it [2:58:27, 10.94s/it] 986it [2:58:38, 11.02s/it] 987it [2:58:49, 11.01s/it] 988it [2:59:00, 10.97s/it] 989it [2:59:11, 11.05s/it] 990it [2:59:23, 11.15s/it] 991it [2:59:35, 11.54s/it] 992it [2:59:47, 11.54s/it] 993it [2:59:58, 11.60s/it] 994it [3:00:09, 11.44s/it] 995it [3:00:20, 11.25s/it] 996it [3:00:31, 11.13s/it] 997it [3:00:42, 11.01s/it] 998it [3:00:53, 11.00s/it] 999it [3:01:04, 10.91s/it] 1000it [3:01:14, 10.84s/it] 1000it [3:01:14, 10.87s/it] +Error counts: + cyclic_id: 0 + cyclic_inchikey: 0 + cyclic_scaffold: 0 + cyclic_mwt: 0 + cyclic_clogp: 0 + cyclic_tpsa: 0 +⏰ Completed process in 3:01:37.676095 ++ rm /nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/validation/cyc-pep-6-12mer-70M_00.csv diff --git a/validation/cyc-pep-6-12mer-70M_01.csv.gz b/validation/cyc-pep-6-12mer-70M_01.csv.gz index d27859dd0f37f370bcad1b7352b5950cb1778bfc..09d7dde1d42fa4e57c88188f30381787206154cf 100644 --- a/validation/cyc-pep-6-12mer-70M_01.csv.gz +++ b/validation/cyc-pep-6-12mer-70M_01.csv.gz @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:83d582f6c20da2918c0ca15f1601008680f3a908947508b1eeaccbff7c98a19e -size 59644749 +oid sha256:5ba37c665f6c8cca07abc30d237493f5e870d4a6e839a2551bb1d5725d5102ea +size 114643168 diff --git a/validation/cyc-pep-6-12mer-70M_01.log b/validation/cyc-pep-6-12mer-70M_01.log new file mode 100644 index 0000000000000000000000000000000000000000..8deef8f6e43dbc2efe0a4d41cb63211381993fdf --- /dev/null +++ b/validation/cyc-pep-6-12mer-70M_01.log @@ -0,0 +1,337 @@ ++ module purge ++ '[' -z '' ']' ++ case "$-" in ++ __lmod_sh_dbg=x ++ '[' -n x ']' ++ set +x +Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output +Shell debugging restarted ++ unset __lmod_sh_dbg ++ return 0 ++ module load Anaconda3/2023.03 ++ '[' -z '' ']' ++ case "$-" in ++ __lmod_sh_dbg=x ++ '[' -n x ']' ++ set +x +Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output +Shell debugging restarted ++ unset __lmod_sh_dbg ++ return 0 ++ source /camp/home/johnsoe/.bashrc +++ '[' '' = yes ']' +++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' ++++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.bash hook +++ __conda_setup='export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'' + +# Copyright (C) 2012 Anaconda, Inc +# SPDX-License-Identifier: BSD-3-Clause +__conda_exe() ( + "$CONDA_EXE" $_CE_M $_CE_CONDA "$@" +) + +__conda_hashr() { + if [ -n "${ZSH_VERSION:+x}" ]; then + \rehash + elif [ -n "${POSH_VERSION:+x}" ]; then + : # pass + else + \hash -r + fi +} + +__conda_activate() { + if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then + # Handle transition from shell activated with conda <= 4.3 to a subsequent activation + # after conda updated to >= 4.4. See issue #6173. + PS1="$CONDA_PS1_BACKUP" + \unset CONDA_PS1_BACKUP + fi + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return + \eval "$ask_conda" + __conda_hashr +} + +__conda_reactivate() { + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return + \eval "$ask_conda" + __conda_hashr +} + +conda() { + \local cmd="${1-__missing__}" + case "$cmd" in + activate|deactivate) + __conda_activate "$@" + ;; + install|update|upgrade|remove|uninstall) + __conda_exe "$@" || \return + __conda_reactivate + ;; + *) + __conda_exe "$@" + ;; + esac +} + +if [ -z "${CONDA_SHLVL+x}" ]; then + \export CONDA_SHLVL=0 + # In dev-mode CONDA_EXE is python.exe and on Windows + # it is in a different relative location to condabin. + if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then + PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}" + else + PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}" + fi + \export PATH + + # We'\''re not allowing PS1 to be unbound. It must at least be set. + # However, we'\''re not exporting it, which can cause problems when starting a second shell + # via a first shell (i.e. starting zsh from bash). + if [ -z "${PS1+x}" ]; then + PS1= + fi +fi + +conda activate base' +++ '[' 0 -eq 0 ']' +++ eval 'export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'' + +# Copyright (C) 2012 Anaconda, Inc +# SPDX-License-Identifier: BSD-3-Clause +__conda_exe() ( + "$CONDA_EXE" $_CE_M $_CE_CONDA "$@" +) + +__conda_hashr() { + if [ -n "${ZSH_VERSION:+x}" ]; then + \rehash + elif [ -n "${POSH_VERSION:+x}" ]; then + : # pass + else + \hash -r + fi +} + +__conda_activate() { + if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then + # Handle transition from shell activated with conda <= 4.3 to a subsequent activation + # after conda updated to >= 4.4. See issue #6173. + PS1="$CONDA_PS1_BACKUP" + \unset CONDA_PS1_BACKUP + fi + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return + \eval "$ask_conda" + __conda_hashr +} + +__conda_reactivate() { + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return + \eval "$ask_conda" + __conda_hashr +} + +conda() { + \local cmd="${1-__missing__}" + case "$cmd" in + activate|deactivate) + __conda_activate "$@" + ;; + install|update|upgrade|remove|uninstall) + __conda_exe "$@" || \return + __conda_reactivate + ;; + *) + __conda_exe "$@" + ;; + esac +} + +if [ -z "${CONDA_SHLVL+x}" ]; then + \export CONDA_SHLVL=0 + # In dev-mode CONDA_EXE is python.exe and on Windows + # it is in a different relative location to condabin. + if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then + PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}" + else + PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}" + fi + \export PATH + + # We'\''re not allowing PS1 to be unbound. It must at least be set. + # However, we'\''re not exporting it, which can cause problems when starting a second shell + # via a first shell (i.e. starting zsh from bash). + if [ -z "${PS1+x}" ]; then + PS1= + fi +fi + +conda activate base' ++++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda ++++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda ++++ export _CE_M= ++++ _CE_M= ++++ export _CE_CONDA= ++++ _CE_CONDA= ++++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ '[' -z x ']' ++++ conda activate base ++++ local cmd=activate ++++ case "$cmd" in ++++ __conda_activate activate base ++++ '[' -n '' ']' ++++ local ask_conda +++++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++++ __conda_exe shell.posix activate base +++++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate base ++++ ask_conda='PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_SHLVL='\''6'\'' +export CONDA_DEFAULT_ENV='\''base'\'' +export CONDA_PROMPT_MODIFIER='\''(base) '\'' +export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' ++++ eval 'PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_SHLVL='\''6'\'' +export CONDA_DEFAULT_ENV='\''base'\'' +export CONDA_PROMPT_MODIFIER='\''(base) '\'' +export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' +++++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++++ export CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0 +++++ CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0 +++++ export CONDA_SHLVL=6 +++++ CONDA_SHLVL=6 +++++ export CONDA_DEFAULT_ENV=base +++++ CONDA_DEFAULT_ENV=base +++++ export 'CONDA_PROMPT_MODIFIER=(base) ' +++++ CONDA_PROMPT_MODIFIER='(base) ' +++++ export CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev +++++ CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev +++++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++++ export _CE_M= +++++ _CE_M= +++++ export _CE_CONDA= +++++ _CE_CONDA= +++++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python +++++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ __conda_hashr ++++ '[' -n '' ']' ++++ '[' -n '' ']' ++++ hash -r +++ unset __conda_setup ++ conda activate schemist-dev ++ local cmd=activate ++ case "$cmd" in ++ __conda_activate activate schemist-dev ++ '[' -n '' ']' ++ local ask_conda +++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++ __conda_exe shell.posix activate schemist-dev +++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate schemist-dev ++ ask_conda='PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_SHLVL='\''7'\'' +export CONDA_DEFAULT_ENV='\''schemist-dev'\'' +export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\'' +export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' ++ eval 'PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_SHLVL='\''7'\'' +export CONDA_DEFAULT_ENV='\''schemist-dev'\'' +export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\'' +export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' +++ PS1='(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++ export CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev +++ CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev +++ export CONDA_SHLVL=7 +++ CONDA_SHLVL=7 +++ export CONDA_DEFAULT_ENV=schemist-dev +++ CONDA_DEFAULT_ENV=schemist-dev +++ export 'CONDA_PROMPT_MODIFIER=(schemist-dev) ' +++ CONDA_PROMPT_MODIFIER='(schemist-dev) ' +++ export CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0 +++ CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0 +++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++ export _CE_M= +++ _CE_M= +++ export _CE_CONDA= +++ _CE_CONDA= +++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python +++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++ __conda_hashr ++ '[' -n '' ']' ++ '[' -n '' ']' ++ hash -r ++ CHUNK_HEAD_FILE=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz ++ INPUT=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/validation/cyc-pep-6-12mer-70M_01.csv ++ COLUMN=cysteine_to_N_cyclization ++ PREFIX=cyclic_ ++ AWK='1 { print $8, $1, $2, $10, $3 }' ++ '[' -z cysteine_to_N_cyclization ']' ++ '[' -z cyclic_ ']' ++ '[' -z '1 { print $8, $1, $2, $10, $3 }' ']' ++ cat /dev/fd/63 /nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/validation/cyc-pep-6-12mer-70M_01.csv ++ awk -F, -v OFS=, '1 { print $8, $1, $2, $10, $3 }' ++ schemist convert -f csv --column cysteine_to_N_cyclization --to id inchikey scaffold mwt clogp tpsa --prefix cyclic_ --options prefix=SCB- ++ gzip --best +++ zcat /nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz +++ head -n1 +++ tr ' ' , +🚀 Converting between string representations with the following parameters: + subcommand: convert + output: <_io.TextIOWrapper name='' mode='w' encoding='utf-8'> + format: csv + input: <_io.TextIOWrapper name='' mode='r' encoding='utf-8'> + representation: SMILES + column: cysteine_to_N_cyclization + prefix: cyclic_ + to: ['id', 'inchikey', 'scaffold', 'mwt', 'clogp', 'tpsa'] + options: ['prefix=SCB-'] + func: + 0it [00:00, ?it/s] 1it [00:10, 10.56s/it] 2it [00:20, 10.48s/it] 3it [00:31, 10.49s/it] 4it [00:41, 10.49s/it] 5it [00:52, 10.47s/it] 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[2:55:03, 11.24s/it] 960it [2:55:14, 11.25s/it] 961it [2:55:25, 11.26s/it] 962it [2:55:36, 11.26s/it] 963it [2:55:48, 11.27s/it] 964it [2:55:59, 11.27s/it] 965it [2:56:10, 11.25s/it] 966it [2:56:22, 11.26s/it] 967it [2:56:33, 11.26s/it] 968it [2:56:44, 11.26s/it] 969it [2:56:55, 11.25s/it] 970it [2:57:06, 11.25s/it] 971it [2:57:18, 11.24s/it] 972it [2:57:29, 11.25s/it] 973it [2:57:40, 11.25s/it] 974it [2:57:51, 11.25s/it] 975it [2:58:03, 11.25s/it] 976it [2:58:14, 11.26s/it] 977it [2:58:25, 11.25s/it] 978it [2:58:37, 11.27s/it] 979it [2:58:48, 11.25s/it] 980it [2:58:59, 11.24s/it] 981it [2:59:10, 11.24s/it] 982it [2:59:21, 11.22s/it] 983it [2:59:33, 11.24s/it] 984it [2:59:44, 11.25s/it] 985it [2:59:55, 11.25s/it] 986it [3:00:07, 11.28s/it] 987it [3:00:18, 11.30s/it] 988it [3:00:29, 11.29s/it] 989it [3:00:40, 11.28s/it] 990it [3:00:52, 11.28s/it] 991it [3:01:03, 11.30s/it] 992it [3:01:14, 11.29s/it] 993it [3:01:26, 11.27s/it] 994it [3:01:37, 11.28s/it] 995it [3:01:48, 11.26s/it] 996it [3:01:59, 11.24s/it] 997it [3:02:10, 11.24s/it] 998it [3:02:22, 11.24s/it] 999it [3:02:33, 11.24s/it] 1000it [3:02:44, 11.23s/it] 1000it [3:02:44, 10.96s/it] +Error counts: + cyclic_id: 0 + cyclic_inchikey: 0 + cyclic_scaffold: 0 + cyclic_mwt: 0 + cyclic_clogp: 0 + cyclic_tpsa: 0 +⏰ Completed process in 3:03:06.976305 ++ rm /nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/validation/cyc-pep-6-12mer-70M_01.csv diff --git a/validation/cyc-pep-6-12mer-70M_02.csv.gz b/validation/cyc-pep-6-12mer-70M_02.csv.gz index 5d25b32528a98720b3b7512995e202022659d460..a71e62c2066e984b401260a781487af1e956ea64 100644 --- a/validation/cyc-pep-6-12mer-70M_02.csv.gz +++ b/validation/cyc-pep-6-12mer-70M_02.csv.gz @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:a16b18226eea14a6bf2d9ec5e83498e7833d741983392c23c8b3a2ddc11655d8 -size 61929347 +oid sha256:2772fe08c3af86135366239168b1d1574ed796e262a3caef0779cbbff8915551 +size 117616316 diff --git a/validation/cyc-pep-6-12mer-70M_02.log b/validation/cyc-pep-6-12mer-70M_02.log new file mode 100644 index 0000000000000000000000000000000000000000..70411e32fd83fcd2982631559ba73e8c6c9ca263 --- /dev/null +++ b/validation/cyc-pep-6-12mer-70M_02.log @@ -0,0 +1,337 @@ ++ module purge ++ '[' -z '' ']' ++ case "$-" in ++ __lmod_sh_dbg=x ++ '[' -n x ']' ++ set +x +Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output +Shell debugging restarted ++ unset __lmod_sh_dbg ++ return 0 ++ module load Anaconda3/2023.03 ++ '[' -z '' ']' ++ case "$-" in ++ __lmod_sh_dbg=x ++ '[' -n x ']' ++ set +x +Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output +Shell debugging restarted ++ unset __lmod_sh_dbg ++ return 0 ++ source /camp/home/johnsoe/.bashrc +++ '[' '' = yes ']' +++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' ++++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.bash hook +++ __conda_setup='export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'' + +# Copyright (C) 2012 Anaconda, Inc +# SPDX-License-Identifier: BSD-3-Clause +__conda_exe() ( + "$CONDA_EXE" $_CE_M $_CE_CONDA "$@" +) + +__conda_hashr() { + if [ -n "${ZSH_VERSION:+x}" ]; then + \rehash + elif [ -n "${POSH_VERSION:+x}" ]; then + : # pass + else + \hash -r + fi +} + +__conda_activate() { + if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then + # Handle transition from shell activated with conda <= 4.3 to a subsequent activation + # after conda updated to >= 4.4. See issue #6173. + PS1="$CONDA_PS1_BACKUP" + \unset CONDA_PS1_BACKUP + fi + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return + \eval "$ask_conda" + __conda_hashr +} + +__conda_reactivate() { + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return + \eval "$ask_conda" + __conda_hashr +} + +conda() { + \local cmd="${1-__missing__}" + case "$cmd" in + activate|deactivate) + __conda_activate "$@" + ;; + install|update|upgrade|remove|uninstall) + __conda_exe "$@" || \return + __conda_reactivate + ;; + *) + __conda_exe "$@" + ;; + esac +} + +if [ -z "${CONDA_SHLVL+x}" ]; then + \export CONDA_SHLVL=0 + # In dev-mode CONDA_EXE is python.exe and on Windows + # it is in a different relative location to condabin. + if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then + PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}" + else + PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}" + fi + \export PATH + + # We'\''re not allowing PS1 to be unbound. It must at least be set. + # However, we'\''re not exporting it, which can cause problems when starting a second shell + # via a first shell (i.e. starting zsh from bash). + if [ -z "${PS1+x}" ]; then + PS1= + fi +fi + +conda activate base' +++ '[' 0 -eq 0 ']' +++ eval 'export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'' + +# Copyright (C) 2012 Anaconda, Inc +# SPDX-License-Identifier: BSD-3-Clause +__conda_exe() ( + "$CONDA_EXE" $_CE_M $_CE_CONDA "$@" +) + +__conda_hashr() { + if [ -n "${ZSH_VERSION:+x}" ]; then + \rehash + elif [ -n "${POSH_VERSION:+x}" ]; then + : # pass + else + \hash -r + fi +} + +__conda_activate() { + if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then + # Handle transition from shell activated with conda <= 4.3 to a subsequent activation + # after conda updated to >= 4.4. See issue #6173. + PS1="$CONDA_PS1_BACKUP" + \unset CONDA_PS1_BACKUP + fi + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return + \eval "$ask_conda" + __conda_hashr +} + +__conda_reactivate() { + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return + \eval "$ask_conda" + __conda_hashr +} + +conda() { + \local cmd="${1-__missing__}" + case "$cmd" in + activate|deactivate) + __conda_activate "$@" + ;; + install|update|upgrade|remove|uninstall) + __conda_exe "$@" || \return + __conda_reactivate + ;; + *) + __conda_exe "$@" + ;; + esac +} + +if [ -z "${CONDA_SHLVL+x}" ]; then + \export CONDA_SHLVL=0 + # In dev-mode CONDA_EXE is python.exe and on Windows + # it is in a different relative location to condabin. + if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then + PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}" + else + PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}" + fi + \export PATH + + # We'\''re not allowing PS1 to be unbound. It must at least be set. + # However, we'\''re not exporting it, which can cause problems when starting a second shell + # via a first shell (i.e. starting zsh from bash). + if [ -z "${PS1+x}" ]; then + PS1= + fi +fi + +conda activate base' ++++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda ++++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda ++++ export _CE_M= ++++ _CE_M= ++++ export _CE_CONDA= ++++ _CE_CONDA= ++++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ '[' -z x ']' ++++ conda activate base ++++ local cmd=activate ++++ case "$cmd" in ++++ __conda_activate activate base ++++ '[' -n '' ']' ++++ local ask_conda +++++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++++ __conda_exe shell.posix activate base +++++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate base ++++ ask_conda='PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_SHLVL='\''6'\'' +export CONDA_DEFAULT_ENV='\''base'\'' +export CONDA_PROMPT_MODIFIER='\''(base) '\'' +export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' ++++ eval 'PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_SHLVL='\''6'\'' +export CONDA_DEFAULT_ENV='\''base'\'' +export CONDA_PROMPT_MODIFIER='\''(base) '\'' +export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' +++++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++++ export CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0 +++++ CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0 +++++ export CONDA_SHLVL=6 +++++ CONDA_SHLVL=6 +++++ export CONDA_DEFAULT_ENV=base +++++ CONDA_DEFAULT_ENV=base +++++ export 'CONDA_PROMPT_MODIFIER=(base) ' +++++ CONDA_PROMPT_MODIFIER='(base) ' +++++ export CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev +++++ CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev +++++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++++ export _CE_M= +++++ _CE_M= +++++ export _CE_CONDA= +++++ _CE_CONDA= +++++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python +++++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ __conda_hashr ++++ '[' -n '' ']' ++++ '[' -n '' ']' ++++ hash -r +++ unset __conda_setup ++ conda activate schemist-dev ++ local cmd=activate ++ case "$cmd" in ++ __conda_activate activate schemist-dev ++ '[' -n '' ']' ++ local ask_conda +++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++ __conda_exe shell.posix activate schemist-dev +++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate schemist-dev ++ ask_conda='PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_SHLVL='\''7'\'' +export CONDA_DEFAULT_ENV='\''schemist-dev'\'' +export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\'' +export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' ++ eval 'PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_SHLVL='\''7'\'' +export CONDA_DEFAULT_ENV='\''schemist-dev'\'' +export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\'' +export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' +++ PS1='(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++ export CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev +++ CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev +++ export CONDA_SHLVL=7 +++ CONDA_SHLVL=7 +++ export CONDA_DEFAULT_ENV=schemist-dev +++ CONDA_DEFAULT_ENV=schemist-dev +++ export 'CONDA_PROMPT_MODIFIER=(schemist-dev) ' +++ CONDA_PROMPT_MODIFIER='(schemist-dev) ' +++ export CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0 +++ CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0 +++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++ export _CE_M= +++ _CE_M= +++ export _CE_CONDA= +++ _CE_CONDA= +++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python +++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++ __conda_hashr ++ '[' -n '' ']' ++ '[' -n '' ']' ++ hash -r ++ CHUNK_HEAD_FILE=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz ++ INPUT=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/validation/cyc-pep-6-12mer-70M_02.csv ++ COLUMN=cysteine_to_N_cyclization ++ PREFIX=cyclic_ ++ AWK='1 { print $8, $1, $2, $10, $3 }' ++ '[' -z cysteine_to_N_cyclization ']' ++ '[' -z cyclic_ ']' ++ '[' -z '1 { print $8, $1, $2, $10, $3 }' ']' ++ cat /dev/fd/63 /nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/validation/cyc-pep-6-12mer-70M_02.csv ++ schemist convert -f csv --column cysteine_to_N_cyclization --to id inchikey scaffold mwt clogp tpsa --prefix cyclic_ --options prefix=SCB- ++ gzip --best +++ head -n1 ++ awk -F, -v OFS=, '1 { print $8, $1, $2, $10, $3 }' +++ zcat /nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz +++ tr ' ' , +🚀 Converting between string representations with the following parameters: + subcommand: convert + output: <_io.TextIOWrapper name='' mode='w' encoding='utf-8'> + format: csv + input: <_io.TextIOWrapper name='' mode='r' encoding='utf-8'> + representation: SMILES + column: cysteine_to_N_cyclization + prefix: cyclic_ + to: ['id', 'inchikey', 'scaffold', 'mwt', 'clogp', 'tpsa'] + options: ['prefix=SCB-'] + func: + 0it [00:00, ?it/s] 1it [00:14, 14.57s/it] 2it [00:28, 14.34s/it] 3it [00:42, 14.15s/it] 4it [00:56, 14.17s/it] 5it [01:11, 14.27s/it] 6it [01:25, 14.32s/it] 7it [01:40, 14.31s/it] 8it [01:54, 14.23s/it] 9it [02:08, 14.36s/it] 10it [02:20, 13.67s/it] 11it [02:33, 13.24s/it] 12it [02:45, 12.87s/it] 13it [02:57, 12.61s/it] 14it [03:09, 12.54s/it] 15it [03:21, 12.46s/it] 16it [03:34, 12.41s/it] 17it [03:46, 12.29s/it] 18it [03:58, 12.18s/it] 19it [04:10, 12.20s/it] 20it [04:22, 12.26s/it] 21it [04:35, 12.31s/it] 22it [04:47, 12.31s/it] 23it [04:59, 12.25s/it] 24it [05:11, 12.22s/it] 25it [05:23, 12.23s/it] 26it [05:36, 12.25s/it] 27it [05:48, 12.24s/it] 28it [06:00, 12.19s/it] 29it [06:12, 12.14s/it] 30it [06:25, 12.23s/it] 31it [06:37, 12.26s/it] 32it [06:49, 12.27s/it] 33it [07:01, 12.21s/it] 34it [07:13, 12.17s/it] 35it [07:26, 12.21s/it] 36it [07:38, 12.26s/it] 37it [07:50, 12.33s/it] 38it [08:03, 12.35s/it] 39it [08:15, 12.30s/it] 40it [08:29, 12.95s/it] 41it [08:44, 13.47s/it] 42it [08:59, 13.75s/it] 43it [09:11, 13.31s/it] 44it [09:23, 13.07s/it] 45it [09:37, 13.37s/it] 46it [09:52, 13.65s/it] 47it [10:06, 13.91s/it] 48it [10:20, 13.93s/it] 49it [10:34, 13.95s/it] 50it [10:49, 14.10s/it] 51it [11:03, 14.20s/it] 52it [11:17, 14.18s/it] 53it [11:30, 13.60s/it] 54it [11:42, 13.22s/it] 55it [11:54, 12.98s/it] 56it [12:07, 12.84s/it] 57it [12:19, 12.72s/it] 58it [12:31, 12.58s/it] 59it [12:44, 12.54s/it] 60it [12:56, 12.53s/it] 61it [13:09, 12.54s/it] 62it [13:22, 12.54s/it] 63it [13:34, 12.47s/it] 64it [13:46, 12.47s/it] 65it [13:59, 12.57s/it] 66it [14:12, 12.59s/it] 67it [14:27, 13.52s/it] 68it [14:44, 14.36s/it] 69it [15:00, 14.91s/it] 70it [15:17, 15.50s/it] 71it [15:33, 15.82s/it] 72it [15:46, 14.76s/it] 73it [15:58, 13.98s/it] 74it [16:10, 13.52s/it] 75it [16:23, 13.22s/it] 76it [16:35, 12.97s/it] 77it [16:47, 12.77s/it] 78it [17:00, 12.60s/it] 79it [17:12, 12.53s/it] 80it [17:25, 12.52s/it] 81it [17:37, 12.52s/it] 82it [17:50, 12.64s/it] 83it [18:03, 12.67s/it] 84it [18:15, 12.55s/it] 85it [18:27, 12.52s/it] 86it [18:40, 12.49s/it] 87it [18:52, 12.48s/it] 88it [19:05, 12.43s/it] 89it [19:17, 12.37s/it] 90it [19:29, 12.34s/it] 91it [19:42, 12.37s/it] 92it [19:54, 12.39s/it] 93it [20:06, 12.41s/it] 94it [20:19, 12.37s/it] 95it [20:31, 12.35s/it] 96it [20:43, 12.36s/it] 97it [20:56, 12.36s/it] 98it [21:08, 12.39s/it] 99it [21:20, 12.27s/it] 100it [21:32, 12.26s/it] 101it [21:45, 12.28s/it] 102it [21:57, 12.31s/it] 103it [22:10, 12.34s/it] 104it [22:22, 12.28s/it] 105it [22:34, 12.34s/it] 106it [22:47, 12.35s/it] 107it [22:59, 12.36s/it] 108it [23:12, 12.41s/it] 109it [23:24, 12.40s/it] 110it [23:36, 12.39s/it] 111it [23:49, 12.39s/it] 112it [24:01, 12.45s/it] 113it [24:14, 12.53s/it] 114it [24:27, 12.58s/it] 115it [24:39, 12.51s/it] 116it [24:51, 12.48s/it] 117it [25:04, 12.53s/it] 118it [25:17, 12.52s/it] 119it [25:29, 12.56s/it] 120it [25:42, 12.51s/it] 121it [25:54, 12.45s/it] 122it [26:06, 12.49s/it] 123it [26:19, 12.45s/it] 124it [26:31, 12.49s/it] 125it [26:44, 12.49s/it] 126it [26:56, 12.44s/it] 127it [27:09, 12.48s/it] 128it [27:21, 12.49s/it] 129it [27:34, 12.50s/it] 130it [27:46, 12.52s/it] 131it [27:59, 12.47s/it] 132it [28:11, 12.47s/it] 133it [28:25, 12.95s/it] 134it [28:40, 13.39s/it] 135it [28:52, 13.13s/it] 136it [29:05, 12.90s/it] 137it [29:17, 12.75s/it] 138it [29:30, 12.73s/it] 139it [29:42, 12.71s/it] 140it [29:55, 12.65s/it] 141it [30:07, 12.56s/it] 142it [30:20, 12.51s/it] 143it [30:32, 12.53s/it] 144it [30:45, 12.55s/it] 145it [30:57, 12.58s/it] 146it [31:10, 12.52s/it] 147it [31:22, 12.45s/it] 148it [31:34, 12.41s/it] 149it [31:49, 12.96s/it] 150it [32:01, 12.87s/it] 151it [32:14, 12.73s/it] 152it [32:26, 12.59s/it] 153it [32:38, 12.51s/it] 154it [32:51, 12.48s/it] 155it [33:03, 12.51s/it] 156it [33:16, 12.50s/it] 157it [33:28, 12.46s/it] 158it [33:41, 12.53s/it] 159it [33:54, 12.60s/it] 160it [34:06, 12.61s/it] 161it [34:19, 12.55s/it] 162it [34:31, 12.42s/it] 163it [34:43, 12.35s/it] 164it [34:55, 12.34s/it] 165it [35:08, 12.35s/it] 166it [35:20, 12.33s/it] 167it [35:32, 12.30s/it] 168it [35:44, 12.26s/it] 169it [35:57, 12.30s/it] 170it [36:09, 12.27s/it] 171it [36:21, 12.26s/it] 172it [36:33, 12.21s/it] 173it [36:45, 12.20s/it] 174it [37:00, 12.79s/it] 175it [37:14, 13.21s/it] 176it [37:26, 12.92s/it] 177it [37:38, 12.66s/it] 178it [37:50, 12.52s/it] 179it [38:03, 12.48s/it] 180it [38:15, 12.48s/it] 181it [38:27, 12.43s/it] 182it [38:39, 12.30s/it] 183it [38:51, 12.21s/it] 184it [39:04, 12.24s/it] 185it [39:16, 12.31s/it] 186it [39:29, 12.32s/it] 187it [39:41, 12.28s/it] 188it [39:53, 12.19s/it] 189it [40:05, 12.22s/it] 190it [40:18, 12.33s/it] 191it [40:30, 12.36s/it] 192it [40:42, 12.39s/it] 193it [40:55, 12.32s/it] 194it [41:07, 12.32s/it] 195it [41:19, 12.29s/it] 196it [41:32, 12.33s/it] 197it [41:44, 12.31s/it] 198it [41:56, 12.23s/it] 199it [42:08, 12.27s/it] 200it [42:21, 12.29s/it] 201it [42:33, 12.31s/it] 202it [42:45, 12.21s/it] 203it [42:57, 12.13s/it] 204it [43:09, 12.08s/it] 205it [43:21, 12.14s/it] 206it [43:33, 12.19s/it] 207it [43:46, 12.18s/it] 208it [43:58, 12.14s/it] 209it [44:10, 12.09s/it] 210it [44:22, 12.10s/it] 211it [44:34, 12.15s/it] 212it [44:46, 12.16s/it] 213it [44:58, 12.16s/it] 214it [45:11, 12.31s/it] 215it [45:24, 12.51s/it] 216it [45:37, 12.63s/it] 217it [45:49, 12.58s/it] 218it [46:02, 12.54s/it] 219it [46:14, 12.57s/it] 220it [46:27, 12.60s/it] 221it [46:40, 12.68s/it] 222it [46:52, 12.62s/it] 223it [47:05, 12.55s/it] 224it [47:17, 12.46s/it] 225it [47:29, 12.42s/it] 226it [47:42, 12.44s/it] 227it [47:54, 12.45s/it] 228it [48:07, 12.46s/it] 229it [48:19, 12.45s/it] 230it [48:32, 12.40s/it] 231it [48:44, 12.43s/it] 232it [48:57, 12.50s/it] 233it [49:09, 12.49s/it] 234it [49:22, 12.55s/it] 235it [49:34, 12.57s/it] 236it [49:47, 12.49s/it] 237it [49:59, 12.44s/it] 238it [50:12, 12.51s/it] 239it [50:24, 12.51s/it] 240it [50:37, 12.54s/it] 241it [50:49, 12.54s/it] 242it [51:02, 12.51s/it] 243it [51:14, 12.53s/it] 244it [51:27, 12.50s/it] 245it [51:40, 12.58s/it] 246it [51:52, 12.44s/it] 247it [52:04, 12.37s/it] 248it [52:16, 12.29s/it] 249it [52:28, 12.27s/it] 250it [52:41, 12.27s/it] 251it [52:53, 12.24s/it] 252it [53:06, 12.62s/it] 253it [53:20, 13.03s/it] 254it [53:34, 13.34s/it] 255it [53:49, 13.59s/it] 256it [54:03, 13.73s/it] 257it [54:17, 13.87s/it] 258it [54:31, 13.93s/it] 259it [54:45, 13.96s/it] 260it [54:59, 13.94s/it] 261it [55:13, 14.07s/it] 262it [55:27, 14.09s/it] 263it [55:41, 13.88s/it] 264it [55:55, 14.00s/it] 265it [56:09, 14.04s/it] 266it [56:23, 14.08s/it] 267it [56:37, 14.10s/it] 268it [56:52, 14.14s/it] 269it [57:06, 14.13s/it] 270it [57:20, 14.09s/it] 271it [57:34, 14.07s/it] 272it [57:48, 14.11s/it] 273it [58:02, 14.16s/it] 274it [58:16, 14.10s/it] 275it [58:30, 14.13s/it] 276it [58:45, 14.16s/it] 277it [58:58, 14.08s/it] 278it [59:13, 14.06s/it] 279it [59:27, 14.06s/it] 280it [59:42, 14.55s/it] 281it [59:56, 14.26s/it] 282it [1:00:10, 14.24s/it] 283it [1:00:24, 14.20s/it] 284it [1:00:38, 14.05s/it] 285it [1:00:52, 14.04s/it] 286it [1:01:04, 13.45s/it] 287it [1:01:16, 13.01s/it] 288it [1:01:28, 12.73s/it] 289it [1:01:40, 12.49s/it] 290it [1:01:52, 12.35s/it] 291it [1:02:04, 12.25s/it] 292it [1:02:16, 12.17s/it] 293it [1:02:28, 12.12s/it] 294it [1:02:40, 12.10s/it] 295it [1:02:52, 12.09s/it] 296it [1:03:04, 12.05s/it] 297it [1:03:16, 12.03s/it] 298it [1:03:28, 12.06s/it] 299it [1:03:40, 12.05s/it] 300it [1:03:52, 12.01s/it] 301it [1:04:04, 12.01s/it] 302it [1:04:16, 12.03s/it] 303it [1:04:28, 12.03s/it] 304it [1:04:40, 12.05s/it] 305it [1:04:53, 12.21s/it] 306it [1:05:05, 12.21s/it] 307it [1:05:17, 12.17s/it] 308it [1:05:29, 12.15s/it] 309it [1:05:41, 12.10s/it] 310it [1:05:53, 12.04s/it] 311it [1:06:05, 12.02s/it] 312it [1:06:17, 11.97s/it] 313it [1:06:29, 11.91s/it] 314it [1:06:40, 11.86s/it] 315it [1:06:52, 11.86s/it] 316it [1:07:04, 11.82s/it] 317it [1:07:16, 11.83s/it] 318it [1:07:28, 11.80s/it] 319it [1:07:40, 11.83s/it] 320it [1:07:51, 11.84s/it] 321it [1:08:03, 11.86s/it] 322it [1:08:15, 11.83s/it] 323it [1:08:27, 11.83s/it] 324it [1:08:39, 11.86s/it] 325it [1:08:51, 11.91s/it] 326it [1:09:03, 11.97s/it] 327it [1:09:15, 12.03s/it] 328it [1:09:27, 12.08s/it] 329it [1:09:39, 12.09s/it] 330it [1:09:52, 12.09s/it] 331it [1:10:04, 12.06s/it] 332it [1:10:15, 11.99s/it] 333it [1:10:27, 11.89s/it] 334it [1:10:39, 11.84s/it] 335it [1:10:51, 11.86s/it] 336it [1:11:02, 11.83s/it] 337it [1:11:14, 11.87s/it] 338it [1:11:26, 11.89s/it] 339it [1:11:41, 12.63s/it] 340it [1:11:56, 13.48s/it] 341it [1:12:12, 14.09s/it] 342it [1:12:27, 14.51s/it] 343it [1:12:40, 13.88s/it] 344it [1:12:52, 13.39s/it] 345it [1:13:04, 13.02s/it] 346it [1:13:17, 12.91s/it] 347it [1:13:29, 12.73s/it] 348it [1:13:41, 12.64s/it] 349it [1:13:54, 12.59s/it] 350it [1:14:07, 12.90s/it] 351it [1:14:23, 13.64s/it] 352it [1:14:38, 14.22s/it] 353it [1:14:54, 14.52s/it] 354it [1:15:09, 14.82s/it] 355it [1:15:24, 14.96s/it] 356it [1:15:40, 15.01s/it] 357it [1:15:55, 15.13s/it] 358it [1:16:10, 15.15s/it] 359it [1:16:25, 15.16s/it] 360it [1:16:41, 15.22s/it] 361it [1:16:56, 15.24s/it] 362it [1:17:11, 15.05s/it] 363it [1:17:26, 15.29s/it] 364it [1:17:40, 14.82s/it] 365it [1:17:54, 14.45s/it] 366it [1:18:07, 14.14s/it] 367it [1:18:21, 13.94s/it] 368it [1:18:35, 13.96s/it] 369it [1:18:49, 14.16s/it] 370it [1:19:03, 13.91s/it] 371it [1:19:17, 13.98s/it] 372it [1:19:29, 13.31s/it] 373it [1:19:40, 12.86s/it] 374it [1:19:52, 12.52s/it] 375it [1:20:04, 12.31s/it] 376it [1:20:16, 12.16s/it] 377it [1:20:27, 12.06s/it] 378it [1:20:39, 12.01s/it] 379it [1:20:51, 11.94s/it] 380it [1:21:03, 11.90s/it] 381it [1:21:15, 11.93s/it] 382it [1:21:27, 11.92s/it] 383it [1:21:39, 11.88s/it] 384it [1:21:51, 11.88s/it] 385it [1:22:02, 11.86s/it] 386it [1:22:14, 11.87s/it] 387it [1:22:26, 11.88s/it] 388it [1:22:38, 11.86s/it] 389it [1:22:50, 11.91s/it] 390it [1:23:02, 11.85s/it] 391it [1:23:14, 11.84s/it] 392it [1:23:25, 11.84s/it] 393it [1:23:37, 11.79s/it] 394it [1:23:49, 11.89s/it] 395it [1:24:01, 11.89s/it] 396it [1:24:13, 11.91s/it] 397it [1:24:25, 11.89s/it] 398it [1:24:37, 11.84s/it] 399it [1:24:49, 11.90s/it] 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881it [3:01:55, 12.58s/it] 882it [3:02:08, 12.51s/it] 883it [3:02:20, 12.51s/it] 884it [3:02:32, 12.33s/it] 885it [3:02:44, 12.36s/it] 886it [3:02:57, 12.45s/it] 887it [3:03:10, 12.52s/it] 888it [3:03:22, 12.48s/it] 889it [3:03:34, 12.39s/it] 890it [3:03:47, 12.32s/it] 891it [3:03:59, 12.29s/it] 892it [3:04:11, 12.26s/it] 893it [3:04:23, 12.28s/it] 894it [3:04:36, 12.29s/it] 895it [3:04:48, 12.34s/it] 896it [3:05:01, 12.43s/it] 897it [3:05:13, 12.49s/it] 898it [3:05:26, 12.52s/it] 899it [3:05:39, 12.59s/it] 900it [3:05:51, 12.62s/it] 901it [3:06:05, 13.00s/it] 902it [3:06:17, 12.59s/it] 903it [3:06:28, 12.28s/it] 904it [3:06:40, 12.05s/it] 905it [3:06:52, 11.91s/it] 906it [3:07:04, 11.92s/it] 907it [3:07:16, 12.07s/it] 908it [3:07:28, 12.15s/it] 909it [3:07:40, 12.17s/it] 910it [3:07:53, 12.19s/it] 911it [3:08:05, 12.09s/it] 912it [3:08:17, 12.17s/it] 913it [3:08:29, 12.22s/it] 914it [3:08:42, 12.26s/it] 915it [3:08:54, 12.31s/it] 916it [3:09:06, 12.33s/it] 917it [3:09:19, 12.33s/it] 918it [3:09:31, 12.34s/it] 919it [3:09:43, 12.35s/it] 920it [3:09:56, 12.35s/it] 921it [3:10:08, 12.35s/it] 922it [3:10:21, 12.39s/it] 923it [3:10:33, 12.37s/it] 924it [3:10:45, 12.40s/it] 925it [3:10:58, 12.41s/it] 926it [3:11:10, 12.40s/it] 927it [3:11:23, 12.43s/it] 928it [3:11:35, 12.43s/it] 929it [3:11:48, 12.42s/it] 930it [3:12:00, 12.42s/it] 931it [3:12:12, 12.39s/it] 932it [3:12:25, 12.39s/it] 933it [3:12:37, 12.37s/it] 934it [3:12:49, 12.39s/it] 935it [3:13:02, 12.43s/it] 936it [3:13:14, 12.42s/it] 937it [3:13:27, 12.42s/it] 938it [3:13:39, 12.48s/it] 939it [3:13:52, 12.52s/it] 940it [3:14:05, 12.55s/it] 941it [3:14:16, 12.31s/it] 942it [3:14:29, 12.39s/it] 943it [3:14:41, 12.36s/it] 944it [3:14:54, 12.48s/it] 945it [3:15:07, 12.49s/it] 946it [3:15:19, 12.54s/it] 947it [3:15:32, 12.58s/it] 948it [3:15:44, 12.53s/it] 949it [3:15:57, 12.55s/it] 950it [3:16:09, 12.46s/it] 951it [3:16:22, 12.48s/it] 952it [3:16:34, 12.52s/it] 953it [3:16:47, 12.55s/it] 954it [3:16:59, 12.48s/it] 955it [3:17:12, 12.48s/it] 956it [3:17:24, 12.48s/it] 957it [3:17:37, 12.50s/it] 958it [3:17:49, 12.50s/it] 959it [3:18:01, 12.40s/it] 960it [3:18:14, 12.32s/it] 961it [3:18:26, 12.38s/it] 962it [3:18:39, 12.51s/it] 963it [3:18:51, 12.50s/it] 964it [3:19:04, 12.47s/it] 965it [3:19:16, 12.41s/it] 966it [3:19:28, 12.38s/it] 967it [3:19:41, 12.35s/it] 968it [3:19:53, 12.36s/it] 969it [3:20:05, 12.31s/it] 970it [3:20:17, 12.29s/it] 971it [3:20:30, 12.29s/it] 972it [3:20:42, 12.27s/it] 973it [3:20:54, 12.29s/it] 974it [3:21:06, 12.25s/it] 975it [3:21:19, 12.25s/it] 976it [3:21:31, 12.29s/it] 977it [3:21:43, 12.31s/it] 978it [3:21:56, 12.32s/it] 979it [3:22:08, 12.35s/it] 980it [3:22:20, 12.29s/it] 981it [3:22:33, 12.32s/it] 982it [3:22:45, 12.30s/it] 983it [3:22:57, 12.30s/it] 984it [3:23:10, 12.33s/it] 985it [3:23:22, 12.31s/it] 986it [3:23:34, 12.32s/it] 987it [3:23:47, 12.30s/it] 988it [3:23:59, 12.32s/it] 989it [3:24:11, 12.36s/it] 990it [3:24:24, 12.34s/it] 991it [3:24:37, 12.67s/it] 992it [3:24:49, 12.60s/it] 993it [3:25:02, 12.45s/it] 994it [3:25:14, 12.42s/it] 995it [3:25:26, 12.40s/it] 996it [3:25:39, 12.37s/it] 997it [3:25:51, 12.36s/it] 998it [3:26:03, 12.37s/it] 999it [3:26:15, 12.10s/it] 1000it [3:26:27, 12.17s/it] 1000it [3:26:27, 12.39s/it] +Error counts: + cyclic_id: 0 + cyclic_inchikey: 0 + cyclic_scaffold: 0 + cyclic_mwt: 0 + cyclic_clogp: 0 + cyclic_tpsa: 0 +⏰ Completed process in 3:26:52.961739 ++ rm /nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/validation/cyc-pep-6-12mer-70M_02.csv diff --git a/validation/cyc-pep-6-12mer-70M_03.csv.gz b/validation/cyc-pep-6-12mer-70M_03.csv.gz index 263ada77c2440fd0dbeff80a1c981dbfee3522f3..b415d1c2a5b6cf434b65aeaf77527f653cdd0828 100644 --- a/validation/cyc-pep-6-12mer-70M_03.csv.gz +++ b/validation/cyc-pep-6-12mer-70M_03.csv.gz @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:59fc2d27f12181b400052de9196be6e4d52aa65c0fe854267c521a23e0e3ad94 -size 64723264 +oid sha256:3de757422d6f8f230bd5dacd649b9a7153167433bc3ca0e6fd49b8d8acc4bfa0 +size 121276892 diff --git a/validation/cyc-pep-6-12mer-70M_03.log b/validation/cyc-pep-6-12mer-70M_03.log new file mode 100644 index 0000000000000000000000000000000000000000..8b7bca15b1eede825c7f78d7f0dd69c6bcd4583d --- /dev/null +++ b/validation/cyc-pep-6-12mer-70M_03.log @@ -0,0 +1,337 @@ ++ module purge ++ '[' -z '' ']' ++ case "$-" in ++ __lmod_sh_dbg=x ++ '[' -n x ']' ++ set +x +Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output +Shell debugging restarted ++ unset __lmod_sh_dbg ++ return 0 ++ module load Anaconda3/2023.03 ++ '[' -z '' ']' ++ case "$-" in ++ __lmod_sh_dbg=x ++ '[' -n x ']' ++ set +x +Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output +Shell debugging restarted ++ unset __lmod_sh_dbg ++ return 0 ++ source /camp/home/johnsoe/.bashrc +++ '[' '' = yes ']' +++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' ++++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.bash hook +++ __conda_setup='export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'' + +# Copyright (C) 2012 Anaconda, Inc +# SPDX-License-Identifier: BSD-3-Clause +__conda_exe() ( + "$CONDA_EXE" $_CE_M $_CE_CONDA "$@" +) + +__conda_hashr() { + if [ -n "${ZSH_VERSION:+x}" ]; then + \rehash + elif [ -n "${POSH_VERSION:+x}" ]; then + : # pass + else + \hash -r + fi +} + +__conda_activate() { + if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then + # Handle transition from shell activated with conda <= 4.3 to a subsequent activation + # after conda updated to >= 4.4. See issue #6173. + PS1="$CONDA_PS1_BACKUP" + \unset CONDA_PS1_BACKUP + fi + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return + \eval "$ask_conda" + __conda_hashr +} + +__conda_reactivate() { + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return + \eval "$ask_conda" + __conda_hashr +} + +conda() { + \local cmd="${1-__missing__}" + case "$cmd" in + activate|deactivate) + __conda_activate "$@" + ;; + install|update|upgrade|remove|uninstall) + __conda_exe "$@" || \return + __conda_reactivate + ;; + *) + __conda_exe "$@" + ;; + esac +} + +if [ -z "${CONDA_SHLVL+x}" ]; then + \export CONDA_SHLVL=0 + # In dev-mode CONDA_EXE is python.exe and on Windows + # it is in a different relative location to condabin. + if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then + PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}" + else + PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}" + fi + \export PATH + + # We'\''re not allowing PS1 to be unbound. It must at least be set. + # However, we'\''re not exporting it, which can cause problems when starting a second shell + # via a first shell (i.e. starting zsh from bash). + if [ -z "${PS1+x}" ]; then + PS1= + fi +fi + +conda activate base' +++ '[' 0 -eq 0 ']' +++ eval 'export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'' + +# Copyright (C) 2012 Anaconda, Inc +# SPDX-License-Identifier: BSD-3-Clause +__conda_exe() ( + "$CONDA_EXE" $_CE_M $_CE_CONDA "$@" +) + +__conda_hashr() { + if [ -n "${ZSH_VERSION:+x}" ]; then + \rehash + elif [ -n "${POSH_VERSION:+x}" ]; then + : # pass + else + \hash -r + fi +} + +__conda_activate() { + if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then + # Handle transition from shell activated with conda <= 4.3 to a subsequent activation + # after conda updated to >= 4.4. See issue #6173. + PS1="$CONDA_PS1_BACKUP" + \unset CONDA_PS1_BACKUP + fi + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return + \eval "$ask_conda" + __conda_hashr +} + +__conda_reactivate() { + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return + \eval "$ask_conda" + __conda_hashr +} + +conda() { + \local cmd="${1-__missing__}" + case "$cmd" in + activate|deactivate) + __conda_activate "$@" + ;; + install|update|upgrade|remove|uninstall) + __conda_exe "$@" || \return + __conda_reactivate + ;; + *) + __conda_exe "$@" + ;; + esac +} + +if [ -z "${CONDA_SHLVL+x}" ]; then + \export CONDA_SHLVL=0 + # In dev-mode CONDA_EXE is python.exe and on Windows + # it is in a different relative location to condabin. + if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then + PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}" + else + PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}" + fi + \export PATH + + # We'\''re not allowing PS1 to be unbound. It must at least be set. + # However, we'\''re not exporting it, which can cause problems when starting a second shell + # via a first shell (i.e. starting zsh from bash). + if [ -z "${PS1+x}" ]; then + PS1= + fi +fi + +conda activate base' ++++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda ++++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda ++++ export _CE_M= ++++ _CE_M= ++++ export _CE_CONDA= ++++ _CE_CONDA= ++++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ '[' -z x ']' ++++ conda activate base ++++ local cmd=activate ++++ case "$cmd" in ++++ __conda_activate activate base ++++ '[' -n '' ']' ++++ local ask_conda +++++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++++ __conda_exe shell.posix activate base +++++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate base ++++ ask_conda='PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_SHLVL='\''6'\'' +export CONDA_DEFAULT_ENV='\''base'\'' +export CONDA_PROMPT_MODIFIER='\''(base) '\'' +export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' ++++ eval 'PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_SHLVL='\''6'\'' +export CONDA_DEFAULT_ENV='\''base'\'' +export CONDA_PROMPT_MODIFIER='\''(base) '\'' +export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' +++++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++++ export CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0 +++++ CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0 +++++ export CONDA_SHLVL=6 +++++ CONDA_SHLVL=6 +++++ export CONDA_DEFAULT_ENV=base +++++ CONDA_DEFAULT_ENV=base +++++ export 'CONDA_PROMPT_MODIFIER=(base) ' +++++ CONDA_PROMPT_MODIFIER='(base) ' +++++ export CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev +++++ CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev +++++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++++ export _CE_M= +++++ _CE_M= +++++ export _CE_CONDA= +++++ _CE_CONDA= +++++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python +++++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ __conda_hashr ++++ '[' -n '' ']' ++++ '[' -n '' ']' ++++ hash -r +++ unset __conda_setup ++ conda activate schemist-dev ++ local cmd=activate ++ case "$cmd" in ++ __conda_activate activate schemist-dev ++ '[' -n '' ']' ++ local ask_conda +++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++ __conda_exe shell.posix activate schemist-dev +++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate schemist-dev ++ ask_conda='PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_SHLVL='\''7'\'' +export CONDA_DEFAULT_ENV='\''schemist-dev'\'' +export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\'' +export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' ++ eval 'PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_SHLVL='\''7'\'' +export CONDA_DEFAULT_ENV='\''schemist-dev'\'' +export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\'' +export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' +++ PS1='(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++ export CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev +++ CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev +++ export CONDA_SHLVL=7 +++ CONDA_SHLVL=7 +++ export CONDA_DEFAULT_ENV=schemist-dev +++ CONDA_DEFAULT_ENV=schemist-dev +++ export 'CONDA_PROMPT_MODIFIER=(schemist-dev) ' +++ CONDA_PROMPT_MODIFIER='(schemist-dev) ' +++ export CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0 +++ CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0 +++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++ export _CE_M= +++ _CE_M= +++ export _CE_CONDA= +++ _CE_CONDA= +++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python +++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++ __conda_hashr ++ '[' -n '' ']' ++ '[' -n '' ']' ++ hash -r ++ CHUNK_HEAD_FILE=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz ++ INPUT=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/validation/cyc-pep-6-12mer-70M_03.csv ++ COLUMN=cysteine_to_N_cyclization ++ PREFIX=cyclic_ ++ AWK='1 { print $8, $1, $2, $10, $3 }' ++ '[' -z cysteine_to_N_cyclization ']' ++ '[' -z cyclic_ ']' ++ '[' -z '1 { print $8, $1, $2, $10, $3 }' ']' ++ cat /dev/fd/63 /nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/validation/cyc-pep-6-12mer-70M_03.csv ++ awk -F, -v OFS=, '1 { print $8, $1, $2, $10, $3 }' +++ zcat /nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz ++ gzip --best ++ schemist convert -f csv --column cysteine_to_N_cyclization --to id inchikey scaffold mwt clogp tpsa --prefix cyclic_ --options prefix=SCB- +++ head -n1 +++ tr ' ' , +🚀 Converting between string representations with the following parameters: + subcommand: convert + output: <_io.TextIOWrapper name='' mode='w' encoding='utf-8'> + format: csv + input: <_io.TextIOWrapper name='' mode='r' encoding='utf-8'> + representation: SMILES + column: cysteine_to_N_cyclization + prefix: cyclic_ + to: ['id', 'inchikey', 'scaffold', 'mwt', 'clogp', 'tpsa'] + options: ['prefix=SCB-'] + func: + 0it [00:00, ?it/s] 1it [00:11, 11.62s/it] 2it [00:23, 11.55s/it] 3it [00:34, 11.51s/it] 4it [00:46, 11.51s/it] 5it [00:57, 11.51s/it] 6it [01:09, 11.49s/it] 7it [01:20, 11.50s/it] 8it [01:32, 11.52s/it] 9it [01:43, 11.51s/it] 10it [01:55, 11.51s/it] 11it [02:06, 11.50s/it] 12it [02:18, 11.49s/it] 13it [02:29, 11.48s/it] 14it [02:41, 11.48s/it] 15it [02:52, 11.49s/it] 16it [03:03, 11.48s/it] 17it [03:15, 11.46s/it] 18it [03:26, 11.45s/it] 19it [03:38, 11.46s/it] 20it [03:49, 11.48s/it] 21it [04:01, 11.46s/it] 22it [04:12, 11.49s/it] 23it [04:24, 11.52s/it] 24it [04:35, 11.51s/it] 25it [04:47, 11.50s/it] 26it [04:58, 11.49s/it] 27it [05:10, 11.48s/it] 28it [05:21, 11.48s/it] 29it [05:33, 11.48s/it] 30it [05:44, 11.49s/it] 31it [05:56, 11.50s/it] 32it [06:07, 11.49s/it] 33it [06:19, 11.47s/it] 34it [06:30, 11.47s/it] 35it [06:42, 11.47s/it] 36it [06:53, 11.48s/it] 37it [07:05, 11.50s/it] 38it [07:16, 11.51s/it] 39it [07:28, 11.51s/it] 40it [07:39, 11.50s/it] 41it [07:51, 11.49s/it] 42it [08:02, 11.48s/it] 43it [08:13, 11.45s/it] 44it [08:25, 11.44s/it] 45it [08:36, 11.42s/it] 46it [08:48, 11.42s/it] 47it [08:59, 11.45s/it] 48it [09:11, 11.47s/it] 49it [09:22, 11.48s/it] 50it [09:34, 11.49s/it] 51it [09:45, 11.49s/it] 52it [09:57, 11.48s/it] 53it [10:08, 11.57s/it] 54it [10:20, 11.70s/it] 55it [10:32, 11.76s/it] 56it [10:44, 11.86s/it] 57it [10:56, 11.75s/it] 58it [11:07, 11.65s/it] 59it [11:19, 11.61s/it] 60it [11:30, 11.56s/it] 61it [11:42, 11.55s/it] 62it [11:53, 11.53s/it] 63it [12:05, 11.52s/it] 64it [12:16, 11.51s/it] 65it [12:28, 11.51s/it] 66it [12:39, 11.49s/it] 67it [12:51, 11.50s/it] 68it [13:02, 11.50s/it] 69it [13:14, 11.49s/it] 70it [13:25, 11.50s/it] 71it [13:37, 11.49s/it] 72it [13:48, 11.49s/it] 73it [14:00, 11.51s/it] 74it [14:12, 11.63s/it] 75it [14:24, 11.75s/it] 76it [14:36, 11.86s/it] 77it [14:48, 11.95s/it] 78it [15:00, 12.04s/it] 79it [15:12, 12.02s/it] 80it [15:24, 11.93s/it] 81it [15:36, 11.94s/it] 82it [15:48, 11.86s/it] 83it [16:00, 11.89s/it] 84it [16:12, 11.96s/it] 85it [16:24, 12.03s/it] 86it [16:36, 12.05s/it] 87it [16:48, 11.90s/it] 88it [16:59, 11.75s/it] 89it [17:11, 11.75s/it] 90it [17:23, 11.87s/it] 91it [17:35, 11.91s/it] 92it [17:47, 11.87s/it] 93it [17:58, 11.76s/it] 94it [18:10, 11.66s/it] 95it [18:21, 11.60s/it] 96it [18:32, 11.56s/it] 97it [18:44, 11.52s/it] 98it [18:55, 11.51s/it] 99it [19:07, 11.49s/it] 100it [19:18, 11.50s/it] 101it [19:30, 11.49s/it] 102it [19:41, 11.47s/it] 103it [19:53, 11.48s/it] 104it [20:04, 11.48s/it] 105it [20:16, 11.48s/it] 106it [20:27, 11.50s/it] 107it [20:39, 11.51s/it] 108it [20:50, 11.49s/it] 109it [21:02, 11.50s/it] 110it [21:13, 11.49s/it] 111it [21:25, 11.48s/it] 112it [21:36, 11.48s/it] 113it [21:48, 11.49s/it] 114it [21:59, 11.50s/it] 115it [22:11, 11.63s/it] 116it [22:23, 11.70s/it] 117it [22:35, 11.71s/it] 118it [22:46, 11.67s/it] 119it [22:58, 11.66s/it] 120it [23:09, 11.60s/it] 121it [23:21, 11.68s/it] 122it [23:33, 11.65s/it] 123it [23:44, 11.58s/it] 124it [23:56, 11.54s/it] 125it [24:07, 11.50s/it] 126it [24:19, 11.54s/it] 127it [24:30, 11.60s/it] 128it [24:42, 11.58s/it] 129it [24:53, 11.54s/it] 130it [25:05, 11.48s/it] 131it [25:16, 11.47s/it] 132it [25:28, 11.55s/it] 133it [25:40, 11.61s/it] 134it [25:51, 11.60s/it] 135it [26:03, 11.56s/it] 136it [26:14, 11.54s/it] 137it [26:26, 11.51s/it] 138it [26:37, 11.49s/it] 139it [26:49, 11.47s/it] 140it [27:00, 11.45s/it] 141it [27:12, 11.47s/it] 142it [27:23, 11.47s/it] 143it [27:34, 11.47s/it] 144it [27:46, 11.47s/it] 145it [27:57, 11.47s/it] 146it [28:09, 11.46s/it] 147it [28:20, 11.44s/it] 148it [28:32, 11.43s/it] 149it [28:43, 11.43s/it] 150it [28:55, 11.50s/it] 151it [29:06, 11.49s/it] 152it [29:18, 11.48s/it] 153it [29:29, 11.44s/it] 154it [29:41, 11.47s/it] 155it [29:52, 11.47s/it] 156it [30:03, 11.46s/it] 157it [30:15, 11.46s/it] 158it [30:26, 11.46s/it] 159it [30:38, 11.45s/it] 160it [30:49, 11.46s/it] 161it [31:01, 11.46s/it] 162it [31:12, 11.46s/it] 163it [31:24, 11.48s/it] 164it [31:35, 11.49s/it] 165it [31:47, 11.47s/it] 166it [31:58, 11.47s/it] 167it [32:10, 11.48s/it] 168it [32:21, 11.48s/it] 169it [32:33, 11.48s/it] 170it [32:44, 11.49s/it] 171it [32:56, 11.47s/it] 172it [33:07, 11.48s/it] 173it [33:19, 11.49s/it] 174it [33:30, 11.49s/it] 175it [33:42, 11.50s/it] 176it [33:53, 11.48s/it] 177it [34:04, 11.45s/it] 178it [34:16, 11.48s/it] 179it [34:27, 11.46s/it] 180it [34:39, 11.44s/it] 181it [34:50, 11.43s/it] 182it [35:02, 11.43s/it] 183it [35:13, 11.43s/it] 184it [35:24, 11.44s/it] 185it [35:36, 11.45s/it] 186it [35:47, 11.48s/it] 187it [35:59, 11.59s/it] 188it [36:11, 11.66s/it] 189it [36:23, 11.68s/it] 190it [36:35, 11.72s/it] 191it [36:47, 11.75s/it] 192it [36:58, 11.82s/it] 193it [37:10, 11.84s/it] 194it [37:22, 11.81s/it] 195it [37:34, 11.74s/it] 196it [37:45, 11.65s/it] 197it [37:57, 11.61s/it] 198it [38:08, 11.56s/it] 199it [38:20, 11.53s/it] 200it [38:31, 11.52s/it] 201it [38:42, 11.49s/it] 202it [38:54, 11.49s/it] 203it [39:05, 11.45s/it] 204it [39:17, 11.45s/it] 205it [39:28, 11.45s/it] 206it [39:40, 11.43s/it] 207it [39:51, 11.43s/it] 208it [40:02, 11.43s/it] 209it [40:14, 11.42s/it] 210it [40:25, 11.45s/it] 211it [40:37, 11.44s/it] 212it [40:48, 11.46s/it] 213it [41:00, 11.44s/it] 214it [41:11, 11.44s/it] 215it [41:23, 11.44s/it] 216it [41:34, 11.44s/it] 217it [41:45, 11.44s/it] 218it [41:57, 11.45s/it] 219it [42:08, 11.46s/it] 220it [42:20, 11.43s/it] 221it [42:31, 11.46s/it] 222it [42:43, 11.45s/it] 223it [42:54, 11.46s/it] 224it [43:06, 11.44s/it] 225it [43:17, 11.44s/it] 226it [43:29, 11.44s/it] 227it [43:40, 11.43s/it] 228it [43:51, 11.44s/it] 229it [44:03, 11.48s/it] 230it [44:14, 11.50s/it] 231it [44:26, 11.53s/it] 232it [44:38, 11.59s/it] 233it [44:50, 11.64s/it] 234it [45:01, 11.62s/it] 235it [45:13, 11.62s/it] 236it [45:25, 11.71s/it] 237it [45:37, 11.77s/it] 238it [45:49, 11.88s/it] 239it [46:01, 11.97s/it] 240it [46:13, 12.00s/it] 241it [46:26, 12.34s/it] 242it [46:39, 12.57s/it] 243it [46:52, 12.73s/it] 244it [47:05, 12.80s/it] 245it [47:19, 12.94s/it] 246it [47:32, 13.04s/it] 247it [47:45, 13.10s/it] 248it [47:58, 13.14s/it] 249it [48:12, 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12.22s/it] 957it [3:19:27, 12.22s/it] 958it [3:19:39, 12.20s/it] 959it [3:19:51, 12.19s/it] 960it [3:20:03, 12.20s/it] 961it [3:20:15, 12.18s/it] 962it [3:20:27, 12.18s/it] 963it [3:20:40, 12.17s/it] 964it [3:20:52, 12.18s/it] 965it [3:21:04, 12.17s/it] 966it [3:21:16, 12.19s/it] 967it [3:21:28, 12.21s/it] 968it [3:21:41, 12.19s/it] 969it [3:21:53, 12.22s/it] 970it [3:22:05, 12.23s/it] 971it [3:22:17, 12.19s/it] 972it [3:22:29, 12.19s/it] 973it [3:22:42, 12.19s/it] 974it [3:22:54, 12.21s/it] 975it [3:23:06, 12.19s/it] 976it [3:23:18, 12.20s/it] 977it [3:23:30, 12.20s/it] 978it [3:23:43, 12.18s/it] 979it [3:23:55, 12.19s/it] 980it [3:24:07, 12.19s/it] 981it [3:24:19, 12.19s/it] 982it [3:24:31, 12.22s/it] 983it [3:24:44, 12.22s/it] 984it [3:24:56, 12.23s/it] 985it [3:25:08, 12.21s/it] 986it [3:25:20, 12.20s/it] 987it [3:25:32, 12.21s/it] 988it [3:25:45, 12.21s/it] 989it [3:25:57, 12.20s/it] 990it [3:26:09, 12.20s/it] 991it [3:26:21, 12.21s/it] 992it [3:26:34, 12.21s/it] 993it [3:26:46, 12.20s/it] 994it [3:26:58, 12.20s/it] 995it [3:27:10, 12.20s/it] 996it [3:27:22, 12.20s/it] 997it [3:27:34, 12.18s/it] 998it [3:27:47, 12.17s/it] 999it [3:27:59, 12.18s/it] 1000it [3:28:11, 12.19s/it] 1000it [3:28:11, 12.49s/it] +Error counts: + cyclic_id: 0 + cyclic_inchikey: 0 + cyclic_scaffold: 0 + cyclic_mwt: 0 + cyclic_clogp: 0 + cyclic_tpsa: 0 +⏰ Completed process in 3:28:35.465184 ++ rm /nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/validation/cyc-pep-6-12mer-70M_03.csv diff --git a/validation/cyc-pep-6-12mer-70M_04.csv.gz b/validation/cyc-pep-6-12mer-70M_04.csv.gz index b0f31f1d881b59269ca9628ca3993cea71c7bf79..433ed90236b38da2f0df0b778f89b017c656e4f8 100644 --- a/validation/cyc-pep-6-12mer-70M_04.csv.gz +++ b/validation/cyc-pep-6-12mer-70M_04.csv.gz @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:661aebd9b10b2cb840136800ff9f0de385069bc001f566765df0b0f70d46d591 -size 60559070 +oid sha256:d785b5c2941b0413cff011cf0d67676d3989e52dedff1e2c81ef70ff5d9bacf7 +size 115167643 diff --git a/validation/cyc-pep-6-12mer-70M_04.log b/validation/cyc-pep-6-12mer-70M_04.log new file mode 100644 index 0000000000000000000000000000000000000000..415d1701b15264af92282a6c0e455bedc856e6e8 --- /dev/null +++ b/validation/cyc-pep-6-12mer-70M_04.log @@ -0,0 +1,337 @@ ++ module purge ++ '[' -z '' ']' ++ case "$-" in ++ __lmod_sh_dbg=x ++ '[' -n x ']' ++ set +x +Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output +Shell debugging restarted ++ unset __lmod_sh_dbg ++ return 0 ++ module load Anaconda3/2023.03 ++ '[' -z '' ']' ++ case "$-" in ++ __lmod_sh_dbg=x ++ '[' -n x ']' ++ set +x +Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output +Shell debugging restarted ++ unset __lmod_sh_dbg ++ return 0 ++ source /camp/home/johnsoe/.bashrc +++ '[' '' = yes ']' +++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' ++++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.bash hook +++ __conda_setup='export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'' + +# Copyright (C) 2012 Anaconda, Inc +# SPDX-License-Identifier: BSD-3-Clause +__conda_exe() ( + "$CONDA_EXE" $_CE_M $_CE_CONDA "$@" +) + +__conda_hashr() { + if [ -n "${ZSH_VERSION:+x}" ]; then + \rehash + elif [ -n "${POSH_VERSION:+x}" ]; then + : # pass + else + \hash -r + fi +} + +__conda_activate() { + if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then + # Handle transition from shell activated with conda <= 4.3 to a subsequent activation + # after conda updated to >= 4.4. See issue #6173. + PS1="$CONDA_PS1_BACKUP" + \unset CONDA_PS1_BACKUP + fi + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return + \eval "$ask_conda" + __conda_hashr +} + +__conda_reactivate() { + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return + \eval "$ask_conda" + __conda_hashr +} + +conda() { + \local cmd="${1-__missing__}" + case "$cmd" in + activate|deactivate) + __conda_activate "$@" + ;; + install|update|upgrade|remove|uninstall) + __conda_exe "$@" || \return + __conda_reactivate + ;; + *) + __conda_exe "$@" + ;; + esac +} + +if [ -z "${CONDA_SHLVL+x}" ]; then + \export CONDA_SHLVL=0 + # In dev-mode CONDA_EXE is python.exe and on Windows + # it is in a different relative location to condabin. + if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then + PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}" + else + PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}" + fi + \export PATH + + # We'\''re not allowing PS1 to be unbound. It must at least be set. + # However, we'\''re not exporting it, which can cause problems when starting a second shell + # via a first shell (i.e. starting zsh from bash). + if [ -z "${PS1+x}" ]; then + PS1= + fi +fi + +conda activate base' +++ '[' 0 -eq 0 ']' +++ eval 'export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'' + +# Copyright (C) 2012 Anaconda, Inc +# SPDX-License-Identifier: BSD-3-Clause +__conda_exe() ( + "$CONDA_EXE" $_CE_M $_CE_CONDA "$@" +) + +__conda_hashr() { + if [ -n "${ZSH_VERSION:+x}" ]; then + \rehash + elif [ -n "${POSH_VERSION:+x}" ]; then + : # pass + else + \hash -r + fi +} + +__conda_activate() { + if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then + # Handle transition from shell activated with conda <= 4.3 to a subsequent activation + # after conda updated to >= 4.4. See issue #6173. + PS1="$CONDA_PS1_BACKUP" + \unset CONDA_PS1_BACKUP + fi + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return + \eval "$ask_conda" + __conda_hashr +} + +__conda_reactivate() { + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return + \eval "$ask_conda" + __conda_hashr +} + +conda() { + \local cmd="${1-__missing__}" + case "$cmd" in + activate|deactivate) + __conda_activate "$@" + ;; + install|update|upgrade|remove|uninstall) + __conda_exe "$@" || \return + __conda_reactivate + ;; + *) + __conda_exe "$@" + ;; + esac +} + +if [ -z "${CONDA_SHLVL+x}" ]; then + \export CONDA_SHLVL=0 + # In dev-mode CONDA_EXE is python.exe and on Windows + # it is in a different relative location to condabin. + if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then + PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}" + else + PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}" + fi + \export PATH + + # We'\''re not allowing PS1 to be unbound. It must at least be set. + # However, we'\''re not exporting it, which can cause problems when starting a second shell + # via a first shell (i.e. starting zsh from bash). + if [ -z "${PS1+x}" ]; then + PS1= + fi +fi + +conda activate base' ++++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda ++++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda ++++ export _CE_M= ++++ _CE_M= ++++ export _CE_CONDA= ++++ _CE_CONDA= ++++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ '[' -z x ']' ++++ conda activate base ++++ local cmd=activate ++++ case "$cmd" in ++++ __conda_activate activate base ++++ '[' -n '' ']' ++++ local ask_conda +++++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++++ __conda_exe shell.posix activate base +++++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate base ++++ ask_conda='PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_SHLVL='\''6'\'' +export CONDA_DEFAULT_ENV='\''base'\'' +export CONDA_PROMPT_MODIFIER='\''(base) '\'' +export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' ++++ eval 'PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_SHLVL='\''6'\'' +export CONDA_DEFAULT_ENV='\''base'\'' +export CONDA_PROMPT_MODIFIER='\''(base) '\'' +export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' +++++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++++ export CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0 +++++ CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0 +++++ export CONDA_SHLVL=6 +++++ CONDA_SHLVL=6 +++++ export CONDA_DEFAULT_ENV=base +++++ CONDA_DEFAULT_ENV=base +++++ export 'CONDA_PROMPT_MODIFIER=(base) ' +++++ CONDA_PROMPT_MODIFIER='(base) ' +++++ export CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev +++++ CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev +++++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++++ export _CE_M= +++++ _CE_M= +++++ export _CE_CONDA= +++++ _CE_CONDA= +++++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python +++++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ __conda_hashr ++++ '[' -n '' ']' ++++ '[' -n '' ']' ++++ hash -r +++ unset __conda_setup ++ conda activate schemist-dev ++ local cmd=activate ++ case "$cmd" in ++ __conda_activate activate schemist-dev ++ '[' -n '' ']' ++ local ask_conda +++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++ __conda_exe shell.posix activate schemist-dev +++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate schemist-dev ++ ask_conda='PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_SHLVL='\''7'\'' +export CONDA_DEFAULT_ENV='\''schemist-dev'\'' +export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\'' +export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' ++ eval 'PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_SHLVL='\''7'\'' +export CONDA_DEFAULT_ENV='\''schemist-dev'\'' +export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\'' +export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' +++ PS1='(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++ export CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev +++ CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev +++ export CONDA_SHLVL=7 +++ CONDA_SHLVL=7 +++ export CONDA_DEFAULT_ENV=schemist-dev +++ CONDA_DEFAULT_ENV=schemist-dev +++ export 'CONDA_PROMPT_MODIFIER=(schemist-dev) ' +++ CONDA_PROMPT_MODIFIER='(schemist-dev) ' +++ export CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0 +++ CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0 +++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++ export _CE_M= +++ _CE_M= +++ export _CE_CONDA= +++ _CE_CONDA= +++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python +++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++ __conda_hashr ++ '[' -n '' ']' ++ '[' -n '' ']' ++ hash -r ++ CHUNK_HEAD_FILE=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz ++ INPUT=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/validation/cyc-pep-6-12mer-70M_04.csv ++ COLUMN=cysteine_to_N_cyclization ++ PREFIX=cyclic_ ++ AWK='1 { print $8, $1, $2, $10, $3 }' ++ '[' -z cysteine_to_N_cyclization ']' ++ '[' -z cyclic_ ']' ++ '[' -z '1 { print $8, $1, $2, $10, $3 }' ']' ++ cat /dev/fd/63 /nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/validation/cyc-pep-6-12mer-70M_04.csv ++ awk -F, -v OFS=, '1 { print $8, $1, $2, $10, $3 }' +++ zcat /nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz ++ gzip --best ++ schemist convert -f csv --column cysteine_to_N_cyclization --to id inchikey scaffold mwt clogp tpsa --prefix cyclic_ --options prefix=SCB- +++ head -n1 +++ tr ' ' , +🚀 Converting between string representations with the following parameters: + subcommand: convert + output: <_io.TextIOWrapper name='' mode='w' encoding='utf-8'> + format: csv + input: <_io.TextIOWrapper name='' mode='r' encoding='utf-8'> + representation: SMILES + column: cysteine_to_N_cyclization + prefix: cyclic_ + to: ['id', 'inchikey', 'scaffold', 'mwt', 'clogp', 'tpsa'] + options: ['prefix=SCB-'] + func: + 0it [00:00, ?it/s] 1it [00:12, 12.57s/it] 2it [00:25, 12.56s/it] 3it [00:37, 12.54s/it] 4it [00:50, 12.51s/it] 5it [01:02, 12.54s/it] 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6.51s/it] 959it [3:11:42, 6.47s/it] 960it [3:11:49, 6.55s/it] 961it [3:11:55, 6.55s/it] 962it [3:12:01, 6.47s/it] 963it [3:12:08, 6.43s/it] 964it [3:12:14, 6.49s/it] 965it [3:12:21, 6.49s/it] 966it [3:12:27, 6.41s/it] 967it [3:12:33, 6.35s/it] 968it [3:12:40, 6.40s/it] 969it [3:12:46, 6.41s/it] 970it [3:12:52, 6.36s/it] 971it [3:12:59, 6.36s/it] 972it [3:13:05, 6.42s/it] 973it [3:13:12, 6.48s/it] 974it [3:13:18, 6.39s/it] 975it [3:13:24, 6.31s/it] 976it [3:13:31, 6.31s/it] 977it [3:13:37, 6.31s/it] 978it [3:13:43, 6.27s/it] 979it [3:13:49, 6.31s/it] 980it [3:13:56, 6.38s/it] 981it [3:14:03, 6.46s/it] 982it [3:14:09, 6.48s/it] 983it [3:14:16, 6.58s/it] 984it [3:14:23, 6.70s/it] 985it [3:14:30, 6.83s/it] 986it [3:14:37, 6.84s/it] 987it [3:14:44, 6.86s/it] 988it [3:14:51, 6.92s/it] 989it [3:14:58, 7.01s/it] 990it [3:15:05, 6.99s/it] 991it [3:15:12, 7.02s/it] 992it [3:15:19, 7.06s/it] 993it [3:15:27, 7.15s/it] 994it [3:15:34, 7.08s/it] 995it [3:15:40, 6.95s/it] 996it [3:15:47, 6.90s/it] 997it [3:15:54, 6.93s/it] 998it [3:16:01, 6.84s/it] 999it [3:16:07, 6.72s/it] 1000it [3:16:14, 6.66s/it] 1000it [3:16:14, 11.77s/it] +Error counts: + cyclic_id: 0 + cyclic_inchikey: 0 + cyclic_scaffold: 0 + cyclic_mwt: 0 + cyclic_clogp: 0 + cyclic_tpsa: 0 +⏰ Completed process in 3:16:36.739137 ++ rm /nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/validation/cyc-pep-6-12mer-70M_04.csv diff --git a/validation/cyc-pep-6-12mer-70M_05.csv.gz b/validation/cyc-pep-6-12mer-70M_05.csv.gz index 477ac23f5df69aec638df2787eefeeabffd31325..2da2d762f80bc67947ddaea4223a2941686d8d5c 100644 --- a/validation/cyc-pep-6-12mer-70M_05.csv.gz +++ b/validation/cyc-pep-6-12mer-70M_05.csv.gz @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:84dacf39109472ff408d23ff580f1c57f2fa5c4951c71c0cc6a377d5b2307fe0 -size 29561368 +oid sha256:5736cbc22df6bacd3b73511fa9d8ef735a80de57cebf1c0917f4a87f2d828a23 +size 70459714 diff --git a/validation/cyc-pep-6-12mer-70M_05.log b/validation/cyc-pep-6-12mer-70M_05.log new file mode 100644 index 0000000000000000000000000000000000000000..a92ac5292d41ba73c3cd99cd571d12ae2feb102f --- /dev/null +++ b/validation/cyc-pep-6-12mer-70M_05.log @@ -0,0 +1,337 @@ ++ module purge ++ '[' -z '' ']' ++ case "$-" in ++ __lmod_sh_dbg=x ++ '[' -n x ']' ++ set +x +Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output +Shell debugging restarted ++ unset __lmod_sh_dbg ++ return 0 ++ module load Anaconda3/2023.03 ++ '[' -z '' ']' ++ case "$-" in ++ __lmod_sh_dbg=x ++ '[' -n x ']' ++ set +x +Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output +Shell debugging restarted ++ unset __lmod_sh_dbg ++ return 0 ++ source /camp/home/johnsoe/.bashrc +++ '[' '' = yes ']' +++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' ++++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.bash hook +++ __conda_setup='export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'' + +# Copyright (C) 2012 Anaconda, Inc +# SPDX-License-Identifier: BSD-3-Clause +__conda_exe() ( + "$CONDA_EXE" $_CE_M $_CE_CONDA "$@" +) + +__conda_hashr() { + if [ -n "${ZSH_VERSION:+x}" ]; then + \rehash + elif [ -n "${POSH_VERSION:+x}" ]; then + : # pass + else + \hash -r + fi +} + +__conda_activate() { + if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then + # Handle transition from shell activated with conda <= 4.3 to a subsequent activation + # after conda updated to >= 4.4. See issue #6173. + PS1="$CONDA_PS1_BACKUP" + \unset CONDA_PS1_BACKUP + fi + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return + \eval "$ask_conda" + __conda_hashr +} + +__conda_reactivate() { + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return + \eval "$ask_conda" + __conda_hashr +} + +conda() { + \local cmd="${1-__missing__}" + case "$cmd" in + activate|deactivate) + __conda_activate "$@" + ;; + install|update|upgrade|remove|uninstall) + __conda_exe "$@" || \return + __conda_reactivate + ;; + *) + __conda_exe "$@" + ;; + esac +} + +if [ -z "${CONDA_SHLVL+x}" ]; then + \export CONDA_SHLVL=0 + # In dev-mode CONDA_EXE is python.exe and on Windows + # it is in a different relative location to condabin. + if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then + PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}" + else + PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}" + fi + \export PATH + + # We'\''re not allowing PS1 to be unbound. It must at least be set. + # However, we'\''re not exporting it, which can cause problems when starting a second shell + # via a first shell (i.e. starting zsh from bash). + if [ -z "${PS1+x}" ]; then + PS1= + fi +fi + +conda activate base' +++ '[' 0 -eq 0 ']' +++ eval 'export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'' + +# Copyright (C) 2012 Anaconda, Inc +# SPDX-License-Identifier: BSD-3-Clause +__conda_exe() ( + "$CONDA_EXE" $_CE_M $_CE_CONDA "$@" +) + +__conda_hashr() { + if [ -n "${ZSH_VERSION:+x}" ]; then + \rehash + elif [ -n "${POSH_VERSION:+x}" ]; then + : # pass + else + \hash -r + fi +} + +__conda_activate() { + if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then + # Handle transition from shell activated with conda <= 4.3 to a subsequent activation + # after conda updated to >= 4.4. See issue #6173. + PS1="$CONDA_PS1_BACKUP" + \unset CONDA_PS1_BACKUP + fi + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return + \eval "$ask_conda" + __conda_hashr +} + +__conda_reactivate() { + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return + \eval "$ask_conda" + __conda_hashr +} + +conda() { + \local cmd="${1-__missing__}" + case "$cmd" in + activate|deactivate) + __conda_activate "$@" + ;; + install|update|upgrade|remove|uninstall) + __conda_exe "$@" || \return + __conda_reactivate + ;; + *) + __conda_exe "$@" + ;; + esac +} + +if [ -z "${CONDA_SHLVL+x}" ]; then + \export CONDA_SHLVL=0 + # In dev-mode CONDA_EXE is python.exe and on Windows + # it is in a different relative location to condabin. + if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then + PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}" + else + PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}" + fi + \export PATH + + # We'\''re not allowing PS1 to be unbound. It must at least be set. + # However, we'\''re not exporting it, which can cause problems when starting a second shell + # via a first shell (i.e. starting zsh from bash). + if [ -z "${PS1+x}" ]; then + PS1= + fi +fi + +conda activate base' ++++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda ++++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda ++++ export _CE_M= ++++ _CE_M= ++++ export _CE_CONDA= ++++ _CE_CONDA= ++++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ '[' -z x ']' ++++ conda activate base ++++ local cmd=activate ++++ case "$cmd" in ++++ __conda_activate activate base ++++ '[' -n '' ']' ++++ local ask_conda +++++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++++ __conda_exe shell.posix activate base +++++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate base ++++ ask_conda='PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_SHLVL='\''6'\'' +export CONDA_DEFAULT_ENV='\''base'\'' +export CONDA_PROMPT_MODIFIER='\''(base) '\'' +export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' ++++ eval 'PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_SHLVL='\''6'\'' +export CONDA_DEFAULT_ENV='\''base'\'' +export CONDA_PROMPT_MODIFIER='\''(base) '\'' +export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' +++++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++++ export CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0 +++++ CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0 +++++ export CONDA_SHLVL=6 +++++ CONDA_SHLVL=6 +++++ export CONDA_DEFAULT_ENV=base +++++ CONDA_DEFAULT_ENV=base +++++ export 'CONDA_PROMPT_MODIFIER=(base) ' +++++ CONDA_PROMPT_MODIFIER='(base) ' +++++ export CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev +++++ CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev +++++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++++ export _CE_M= +++++ _CE_M= +++++ export _CE_CONDA= +++++ _CE_CONDA= +++++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python +++++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ __conda_hashr ++++ '[' -n '' ']' ++++ '[' -n '' ']' ++++ hash -r +++ unset __conda_setup ++ conda activate schemist-dev ++ local cmd=activate ++ case "$cmd" in ++ __conda_activate activate schemist-dev ++ '[' -n '' ']' ++ local ask_conda +++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++ __conda_exe shell.posix activate schemist-dev +++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate schemist-dev ++ ask_conda='PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_SHLVL='\''7'\'' +export CONDA_DEFAULT_ENV='\''schemist-dev'\'' +export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\'' +export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' ++ eval 'PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_SHLVL='\''7'\'' +export CONDA_DEFAULT_ENV='\''schemist-dev'\'' +export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\'' +export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' +++ PS1='(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++ export CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev +++ CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev +++ export CONDA_SHLVL=7 +++ CONDA_SHLVL=7 +++ export CONDA_DEFAULT_ENV=schemist-dev +++ CONDA_DEFAULT_ENV=schemist-dev +++ export 'CONDA_PROMPT_MODIFIER=(schemist-dev) ' +++ CONDA_PROMPT_MODIFIER='(schemist-dev) ' +++ export CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0 +++ CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0 +++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++ export _CE_M= +++ _CE_M= +++ export _CE_CONDA= +++ _CE_CONDA= +++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python +++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++ __conda_hashr ++ '[' -n '' ']' ++ '[' -n '' ']' ++ hash -r ++ CHUNK_HEAD_FILE=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz ++ INPUT=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/validation/cyc-pep-6-12mer-70M_05.csv ++ COLUMN=cysteine_to_N_cyclization ++ PREFIX=cyclic_ ++ AWK='1 { print $8, $1, $2, $10, $3 }' ++ '[' -z cysteine_to_N_cyclization ']' ++ '[' -z cyclic_ ']' ++ '[' -z '1 { print $8, $1, $2, $10, $3 }' ']' ++ cat /dev/fd/63 /nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/validation/cyc-pep-6-12mer-70M_05.csv ++ schemist convert -f csv --column cysteine_to_N_cyclization --to id inchikey scaffold mwt clogp tpsa --prefix cyclic_ --options prefix=SCB- ++ gzip --best +++ head -n1 ++ awk -F, -v OFS=, '1 { print $8, $1, $2, $10, $3 }' +++ zcat /nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz +++ tr ' ' , +🚀 Converting between string representations with the following parameters: + subcommand: convert + output: <_io.TextIOWrapper name='' mode='w' encoding='utf-8'> + format: csv + input: <_io.TextIOWrapper name='' mode='r' encoding='utf-8'> + representation: SMILES + column: cysteine_to_N_cyclization + prefix: cyclic_ + to: ['id', 'inchikey', 'scaffold', 'mwt', 'clogp', 'tpsa'] + options: ['prefix=SCB-'] + func: + 0it [00:00, ?it/s] 1it [00:07, 7.10s/it] 2it [00:13, 6.88s/it] 3it [00:20, 6.88s/it] 4it [00:27, 6.91s/it] 5it [00:35, 7.07s/it] 6it [00:41, 7.00s/it] 7it [00:48, 6.90s/it] 8it [00:55, 6.82s/it] 9it [01:02, 6.90s/it] 10it [01:09, 6.86s/it] 11it [01:15, 6.82s/it] 12it [01:22, 6.78s/it] 13it [01:29, 6.90s/it] 14it [01:36, 6.89s/it] 15it [01:43, 6.80s/it] 16it [01:49, 6.73s/it] 17it [01:56, 6.82s/it] 18it [02:03, 6.80s/it] 19it [02:10, 6.76s/it] 20it [02:16, 6.70s/it] 21it [02:23, 6.84s/it] 22it [02:30, 6.83s/it] 23it [02:37, 6.76s/it] 24it [02:43, 6.71s/it] 25it [02:50, 6.82s/it] 26it [02:57, 6.81s/it] 27it [03:04, 6.77s/it] 28it [03:11, 6.73s/it] 29it [03:18, 6.86s/it] 30it [03:25, 6.85s/it] 31it [03:31, 6.86s/it] 32it [03:38, 6.90s/it] 33it [03:46, 7.06s/it] 34it [03:53, 7.08s/it] 35it [04:00, 7.03s/it] 36it [04:07, 6.97s/it] 37it [04:14, 7.08s/it] 38it [04:21, 7.08s/it] 39it [04:28, 7.02s/it] 40it [04:35, 6.99s/it] 41it [04:42, 7.08s/it] 42it [04:49, 7.09s/it] 43it [04:56, 7.00s/it] 44it [05:03, 6.95s/it] 45it [05:10, 7.02s/it] 46it [05:17, 7.02s/it] 47it [05:24, 6.94s/it] 48it [05:31, 6.89s/it] 49it [05:38, 6.96s/it] 50it [05:45, 6.96s/it] 51it [05:52, 6.93s/it] 52it [05:59, 6.92s/it] 53it [06:06, 7.04s/it] 54it [06:13, 7.06s/it] 55it [06:20, 6.94s/it] 56it [06:26, 6.84s/it] 57it [06:33, 6.87s/it] 58it [06:40, 6.86s/it] 59it [06:47, 6.85s/it] 60it [06:54, 6.86s/it] 61it [07:01, 6.96s/it] 62it [07:08, 6.99s/it] 63it [07:15, 7.03s/it] 64it [07:22, 7.13s/it] 65it [07:30, 7.28s/it] 66it [07:38, 7.39s/it] 67it [07:45, 7.39s/it] 68it [07:53, 7.42s/it] 69it [08:00, 7.52s/it] 70it [08:08, 7.59s/it] 71it [08:16, 7.57s/it] 72it [08:23, 7.58s/it] 73it [08:31, 7.63s/it] 74it [08:39, 7.73s/it] 75it [08:46, 7.63s/it] 76it [08:54, 7.51s/it] 77it [09:01, 7.47s/it] 78it [09:08, 7.49s/it] 79it [09:16, 7.40s/it] 80it [09:23, 7.26s/it] 81it [09:30, 7.21s/it] 82it [09:37, 7.24s/it] 83it [09:44, 7.17s/it] 84it [09:51, 7.18s/it] 85it [09:59, 7.22s/it] 86it [10:06, 7.33s/it] 87it [10:13, 7.28s/it] 88it [10:20, 7.19s/it] 89it [10:27, 7.14s/it] 90it [10:35, 7.21s/it] 91it [10:42, 7.14s/it] 92it [10:49, 7.09s/it] 93it [10:56, 7.07s/it] 94it [11:03, 7.17s/it] 95it [11:10, 7.15s/it] 96it [11:17, 7.07s/it] 97it [11:24, 7.04s/it] 98it [11:31, 7.13s/it] 99it [11:38, 7.08s/it] 100it [11:45, 7.05s/it] 101it [11:52, 7.03s/it] 102it [12:00, 7.15s/it] 103it [12:07, 7.12s/it] 104it [12:13, 6.92s/it] 105it [12:20, 6.78s/it] 106it [12:27, 6.82s/it] 107it [12:33, 6.78s/it] 108it [12:40, 6.72s/it] 109it [12:46, 6.67s/it] 110it [12:53, 6.77s/it] 111it [13:00, 6.76s/it] 112it [13:07, 6.77s/it] 113it [13:14, 6.79s/it] 114it [13:21, 6.94s/it] 115it [13:28, 6.96s/it] 116it [13:35, 6.91s/it] 117it [13:42, 6.87s/it] 118it [13:49, 6.99s/it] 119it [13:56, 6.98s/it] 120it [14:03, 6.92s/it] 121it [14:09, 6.88s/it] 122it [14:17, 6.99s/it] 123it [14:24, 6.97s/it] 124it [14:30, 6.90s/it] 125it [14:37, 6.82s/it] 126it [14:44, 6.94s/it] 127it [14:51, 6.93s/it] 128it [14:58, 6.85s/it] 129it [15:04, 6.77s/it] 130it [15:11, 6.85s/it] 131it [15:18, 6.84s/it] 132it [15:25, 6.81s/it] 133it [15:32, 6.79s/it] 134it [15:39, 6.91s/it] 135it [15:46, 6.93s/it] 136it [15:52, 6.82s/it] 137it [15:59, 6.73s/it] 138it [16:06, 6.76s/it] 139it [16:12, 6.76s/it] 140it [16:19, 6.74s/it] 141it [16:26, 6.77s/it] 142it [16:33, 6.86s/it] 143it [16:40, 6.93s/it] 144it [16:47, 6.94s/it] 145it [16:54, 7.05s/it] 146it [17:02, 7.19s/it] 147it [17:10, 7.31s/it] 148it [17:17, 7.30s/it] 149it [17:24, 7.32s/it] 150it [17:32, 7.41s/it] 151it [17:40, 7.51s/it] 152it [17:47, 7.50s/it] 153it [17:55, 7.52s/it] 154it [18:02, 7.55s/it] 155it [18:10, 7.64s/it] 156it [18:17, 7.57s/it] 157it [18:25, 7.44s/it] 158it [18:32, 7.37s/it] 159it [18:39, 7.42s/it] 160it [18:47, 7.34s/it] 161it [18:53, 7.20s/it] 162it [19:00, 7.12s/it] 163it [19:08, 7.18s/it] 164it [19:15, 7.11s/it] 165it [19:22, 7.11s/it] 166it [19:29, 7.09s/it] 167it [19:36, 7.23s/it] 168it [19:44, 7.23s/it] 169it [19:50, 7.12s/it] 170it [19:57, 7.05s/it] 171it [20:05, 7.13s/it] 172it [20:12, 7.09s/it] 173it [20:18, 7.04s/it] 174it [20:25, 6.98s/it] 175it [20:33, 7.11s/it] 176it [20:40, 7.09s/it] 177it [20:47, 6.99s/it] 178it [20:53, 6.93s/it] 179it [21:01, 7.04s/it] 180it [21:08, 7.03s/it] 181it [21:15, 6.98s/it] 182it [21:21, 6.93s/it] 183it [21:29, 7.06s/it] 184it [21:36, 7.06s/it] 185it [21:42, 6.86s/it] 186it [21:49, 6.73s/it] 187it [21:55, 6.77s/it] 188it [22:02, 6.72s/it] 189it [22:09, 6.66s/it] 190it [22:15, 6.60s/it] 191it [22:22, 6.71s/it] 192it [22:29, 6.68s/it] 193it [22:35, 6.70s/it] 194it [22:42, 6.74s/it] 195it [22:50, 6.91s/it] 196it [22:57, 6.95s/it] 197it [23:03, 6.88s/it] 198it [23:10, 6.83s/it] 199it [23:17, 6.97s/it] 200it [23:24, 6.96s/it] 201it [23:31, 6.89s/it] 202it [23:38, 6.83s/it] 203it [23:45, 6.93s/it] 204it [23:52, 6.92s/it] 205it [23:58, 6.84s/it] 206it [24:05, 6.77s/it] 207it [24:12, 6.87s/it] 208it [24:19, 6.84s/it] 209it [24:25, 6.76s/it] 210it [24:32, 6.70s/it] 211it [24:39, 6.77s/it] 212it [24:46, 6.76s/it] 213it [24:52, 6.74s/it] 214it [24:59, 6.74s/it] 215it [25:06, 6.84s/it] 216it [25:13, 6.86s/it] 217it [25:20, 6.75s/it] 218it [25:26, 6.66s/it] 219it [25:33, 6.69s/it] 220it [25:39, 6.67s/it] 221it [25:46, 6.65s/it] 222it [25:53, 6.67s/it] 223it [26:00, 6.77s/it] 224it [26:07, 6.83s/it] 225it [26:14, 6.86s/it] 226it [26:21, 6.97s/it] 227it [26:28, 7.11s/it] 228it [26:36, 7.20s/it] 229it [26:43, 7.22s/it] 230it [26:50, 7.23s/it] 231it [26:58, 7.33s/it] 232it [27:05, 7.39s/it] 233it [27:13, 7.37s/it] 234it [27:20, 7.39s/it] 235it [27:28, 7.48s/it] 236it [27:35, 7.54s/it] 237it [27:43, 7.44s/it] 238it [27:50, 7.33s/it] 239it [27:57, 7.30s/it] 240it [28:04, 7.30s/it] 241it [28:11, 7.19s/it] 242it [28:18, 7.09s/it] 243it [28:25, 7.06s/it] 244it [28:32, 7.09s/it] 245it [28:39, 7.02s/it] 246it [28:46, 7.03s/it] 247it [28:53, 7.08s/it] 248it [29:01, 7.17s/it] 249it [29:08, 7.11s/it] 250it [29:14, 7.01s/it] 251it [29:21, 6.98s/it] 252it [29:28, 7.04s/it] 253it [29:35, 6.97s/it] 254it [29:42, 6.95s/it] 255it [29:49, 6.94s/it] 256it [29:56, 7.03s/it] 257it [30:03, 6.99s/it] 258it [30:10, 6.91s/it] 259it [30:17, 6.88s/it] 260it [30:24, 6.97s/it] 261it [30:31, 6.93s/it] 262it [30:38, 6.90s/it] 263it [30:44, 6.88s/it] 264it [30:52, 6.98s/it] 265it [30:59, 6.96s/it] 266it [31:05, 6.78s/it] 267it [31:11, 6.66s/it] 268it [31:18, 6.71s/it] 269it [31:25, 6.65s/it] 270it [31:31, 6.59s/it] 271it [31:38, 6.53s/it] 272it [31:44, 6.64s/it] 273it [31:51, 6.63s/it] 274it [31:58, 6.66s/it] 275it [32:04, 6.67s/it] 276it [32:12, 6.84s/it] 277it [32:19, 6.86s/it] 278it [32:25, 6.81s/it] 279it [32:32, 6.77s/it] 280it [32:39, 6.88s/it] 281it [32:46, 6.88s/it] 282it [32:53, 6.82s/it] 283it [32:59, 6.75s/it] 284it [33:06, 6.85s/it] 285it [33:13, 6.84s/it] 286it [33:20, 6.78s/it] 287it [33:26, 6.69s/it] 288it [33:33, 6.80s/it] 289it [33:40, 6.79s/it] 290it [33:47, 6.72s/it] 291it [33:53, 6.63s/it] 292it [34:00, 6.74s/it] 293it [34:07, 6.71s/it] 294it [34:13, 6.68s/it] 295it [34:20, 6.66s/it] 296it [34:27, 6.78s/it] 297it [34:34, 6.80s/it] 298it [34:40, 6.68s/it] 299it [34:47, 6.58s/it] 300it [34:53, 6.63s/it] 301it 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6.87s/it] 343it [39:55, 6.83s/it] 344it [40:02, 6.80s/it] 345it [40:09, 6.93s/it] 346it [40:16, 6.93s/it] 347it [40:23, 6.74s/it] 348it [40:29, 6.58s/it] 349it [40:35, 6.63s/it] 350it [40:42, 6.58s/it] 351it [40:48, 6.52s/it] 352it [40:55, 6.47s/it] 353it [41:02, 6.59s/it] 354it [41:08, 6.56s/it] 355it [41:15, 6.60s/it] 356it [41:21, 6.63s/it] 357it [41:29, 6.80s/it] 358it [41:36, 6.83s/it] 359it [41:42, 6.77s/it] 360it [41:49, 6.72s/it] 361it [41:56, 6.85s/it] 362it [42:03, 6.84s/it] 363it [42:09, 6.77s/it] 364it [42:16, 6.70s/it] 365it [42:23, 6.81s/it] 366it [42:30, 6.82s/it] 367it [42:36, 6.72s/it] 368it [42:43, 6.65s/it] 369it [42:50, 6.74s/it] 370it [42:56, 6.73s/it] 371it [43:03, 6.65s/it] 372it [43:09, 6.60s/it] 373it [43:16, 6.67s/it] 374it [43:23, 6.67s/it] 375it [43:29, 6.62s/it] 376it [43:36, 6.61s/it] 377it [43:43, 6.72s/it] 378it [43:50, 6.75s/it] 379it [43:56, 6.64s/it] 380it [44:02, 6.54s/it] 381it [44:09, 6.56s/it] 382it [44:16, 6.55s/it] 383it [44:22, 6.52s/it] 384it [44:29, 6.56s/it] 385it [44:35, 6.63s/it] 386it [44:42, 6.71s/it] 387it [44:49, 6.74s/it] 388it [44:56, 6.84s/it] 389it [45:03, 6.95s/it] 390it [45:11, 7.10s/it] 391it [45:18, 7.09s/it] 392it [45:25, 7.12s/it] 393it [45:32, 7.16s/it] 394it [45:40, 7.28s/it] 395it [45:47, 7.26s/it] 396it [45:55, 7.28s/it] 397it [46:02, 7.32s/it] 398it [46:10, 7.42s/it] 399it [46:17, 7.38s/it] 400it [46:24, 7.25s/it] 401it [46:31, 7.16s/it] 402it [46:38, 7.21s/it] 403it [46:45, 7.13s/it] 404it [46:52, 7.01s/it] 405it [46:58, 6.91s/it] 406it [47:06, 6.99s/it] 407it [47:12, 6.94s/it] 408it [47:19, 6.94s/it] 409it [47:26, 6.95s/it] 410it [47:34, 7.08s/it] 411it [47:41, 7.07s/it] 412it [47:47, 6.95s/it] 413it [47:54, 6.87s/it] 414it [48:01, 6.96s/it] 415it [48:08, 6.92s/it] 416it [48:15, 6.89s/it] 417it [48:22, 6.85s/it] 418it [48:29, 6.95s/it] 419it [48:36, 6.95s/it] 420it [48:43, 6.88s/it] 421it [48:49, 6.81s/it] 422it [48:56, 6.92s/it] 423it [49:03, 6.88s/it] 424it [49:10, 6.85s/it] 425it [49:17, 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[1:55:42, 7.70s/it] 970it [1:55:50, 7.60s/it] 971it [1:55:57, 7.48s/it] 972it [1:56:04, 7.42s/it] 973it [1:56:12, 7.47s/it] 974it [1:56:19, 7.42s/it] 975it [1:56:26, 7.43s/it] 976it [1:56:34, 7.44s/it] 977it [1:56:42, 7.56s/it] 978it [1:56:49, 7.50s/it] 979it [1:56:56, 7.41s/it] 980it [1:57:03, 7.34s/it] 981it [1:57:11, 7.41s/it] 982it [1:57:18, 7.37s/it] 983it [1:57:26, 7.33s/it] 984it [1:57:33, 7.33s/it] 985it [1:57:40, 7.43s/it] 986it [1:57:48, 7.39s/it] 987it [1:57:55, 7.32s/it] 988it [1:58:02, 7.28s/it] 989it [1:58:10, 7.37s/it] 990it [1:58:17, 7.33s/it] 991it [1:58:24, 7.30s/it] 992it [1:58:31, 7.28s/it] 993it [1:58:39, 7.40s/it] 994it [1:58:46, 7.39s/it] 995it [1:58:53, 7.15s/it] 996it [1:59:00, 6.97s/it] 997it [1:59:07, 7.01s/it] 998it [1:59:13, 6.93s/it] 999it [1:59:20, 6.84s/it] 1000it [1:59:27, 6.78s/it] 1000it [1:59:27, 7.17s/it] +Error counts: + cyclic_id: 0 + cyclic_inchikey: 0 + cyclic_scaffold: 0 + cyclic_mwt: 0 + cyclic_clogp: 0 + cyclic_tpsa: 0 +⏰ Completed process in 1:59:44.382063 ++ rm /nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/validation/cyc-pep-6-12mer-70M_05.csv diff --git a/validation/cyc-pep-6-12mer-70M_06.csv.gz b/validation/cyc-pep-6-12mer-70M_06.csv.gz index 441385d975e281ab17b3c37daf0f81fc43c35b58..877e36486604c49a4878c459c5a131ad61330549 100644 --- a/validation/cyc-pep-6-12mer-70M_06.csv.gz +++ b/validation/cyc-pep-6-12mer-70M_06.csv.gz @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:acceb0090cf9b9d698c4570a5b9df439de5c92838f4b57ce1fd919e87ea0181d -size 32138104 +oid sha256:788e16722750c15e6d4077403b2e3cb34ca33307798745364da86385b835a6ba +size 75075327 diff --git a/validation/cyc-pep-6-12mer-70M_06.log b/validation/cyc-pep-6-12mer-70M_06.log new file mode 100644 index 0000000000000000000000000000000000000000..bb629be78005d0981f54688cf47caa1c5a0012ef --- /dev/null +++ b/validation/cyc-pep-6-12mer-70M_06.log @@ -0,0 +1,337 @@ ++ module purge ++ '[' -z '' ']' ++ case "$-" in ++ __lmod_sh_dbg=x ++ '[' -n x ']' ++ set +x +Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output +Shell debugging restarted ++ unset __lmod_sh_dbg ++ return 0 ++ module load Anaconda3/2023.03 ++ '[' -z '' ']' ++ case "$-" in ++ __lmod_sh_dbg=x ++ '[' -n x ']' ++ set +x +Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output +Shell debugging restarted ++ unset __lmod_sh_dbg ++ return 0 ++ source /camp/home/johnsoe/.bashrc +++ '[' '' = yes ']' +++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' ++++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.bash hook +++ __conda_setup='export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'' + +# Copyright (C) 2012 Anaconda, Inc +# SPDX-License-Identifier: BSD-3-Clause +__conda_exe() ( + "$CONDA_EXE" $_CE_M $_CE_CONDA "$@" +) + +__conda_hashr() { + if [ -n "${ZSH_VERSION:+x}" ]; then + \rehash + elif [ -n "${POSH_VERSION:+x}" ]; then + : # pass + else + \hash -r + fi +} + +__conda_activate() { + if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then + # Handle transition from shell activated with conda <= 4.3 to a subsequent activation + # after conda updated to >= 4.4. See issue #6173. + PS1="$CONDA_PS1_BACKUP" + \unset CONDA_PS1_BACKUP + fi + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return + \eval "$ask_conda" + __conda_hashr +} + +__conda_reactivate() { + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return + \eval "$ask_conda" + __conda_hashr +} + +conda() { + \local cmd="${1-__missing__}" + case "$cmd" in + activate|deactivate) + __conda_activate "$@" + ;; + install|update|upgrade|remove|uninstall) + __conda_exe "$@" || \return + __conda_reactivate + ;; + *) + __conda_exe "$@" + ;; + esac +} + +if [ -z "${CONDA_SHLVL+x}" ]; then + \export CONDA_SHLVL=0 + # In dev-mode CONDA_EXE is python.exe and on Windows + # it is in a different relative location to condabin. + if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then + PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}" + else + PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}" + fi + \export PATH + + # We'\''re not allowing PS1 to be unbound. It must at least be set. + # However, we'\''re not exporting it, which can cause problems when starting a second shell + # via a first shell (i.e. starting zsh from bash). + if [ -z "${PS1+x}" ]; then + PS1= + fi +fi + +conda activate base' +++ '[' 0 -eq 0 ']' +++ eval 'export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'' + +# Copyright (C) 2012 Anaconda, Inc +# SPDX-License-Identifier: BSD-3-Clause +__conda_exe() ( + "$CONDA_EXE" $_CE_M $_CE_CONDA "$@" +) + +__conda_hashr() { + if [ -n "${ZSH_VERSION:+x}" ]; then + \rehash + elif [ -n "${POSH_VERSION:+x}" ]; then + : # pass + else + \hash -r + fi +} + +__conda_activate() { + if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then + # Handle transition from shell activated with conda <= 4.3 to a subsequent activation + # after conda updated to >= 4.4. See issue #6173. + PS1="$CONDA_PS1_BACKUP" + \unset CONDA_PS1_BACKUP + fi + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return + \eval "$ask_conda" + __conda_hashr +} + +__conda_reactivate() { + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return + \eval "$ask_conda" + __conda_hashr +} + +conda() { + \local cmd="${1-__missing__}" + case "$cmd" in + activate|deactivate) + __conda_activate "$@" + ;; + install|update|upgrade|remove|uninstall) + __conda_exe "$@" || \return + __conda_reactivate + ;; + *) + __conda_exe "$@" + ;; + esac +} + +if [ -z "${CONDA_SHLVL+x}" ]; then + \export CONDA_SHLVL=0 + # In dev-mode CONDA_EXE is python.exe and on Windows + # it is in a different relative location to condabin. + if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then + PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}" + else + PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}" + fi + \export PATH + + # We'\''re not allowing PS1 to be unbound. It must at least be set. + # However, we'\''re not exporting it, which can cause problems when starting a second shell + # via a first shell (i.e. starting zsh from bash). + if [ -z "${PS1+x}" ]; then + PS1= + fi +fi + +conda activate base' ++++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda ++++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda ++++ export _CE_M= ++++ _CE_M= ++++ export _CE_CONDA= ++++ _CE_CONDA= ++++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ '[' -z x ']' ++++ conda activate base ++++ local cmd=activate ++++ case "$cmd" in ++++ __conda_activate activate base ++++ '[' -n '' ']' ++++ local ask_conda +++++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++++ __conda_exe shell.posix activate base +++++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate base ++++ ask_conda='PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_SHLVL='\''6'\'' +export CONDA_DEFAULT_ENV='\''base'\'' +export CONDA_PROMPT_MODIFIER='\''(base) '\'' +export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' ++++ eval 'PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_SHLVL='\''6'\'' +export CONDA_DEFAULT_ENV='\''base'\'' +export CONDA_PROMPT_MODIFIER='\''(base) '\'' +export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' +++++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++++ export CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0 +++++ CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0 +++++ export CONDA_SHLVL=6 +++++ CONDA_SHLVL=6 +++++ export CONDA_DEFAULT_ENV=base +++++ CONDA_DEFAULT_ENV=base +++++ export 'CONDA_PROMPT_MODIFIER=(base) ' +++++ CONDA_PROMPT_MODIFIER='(base) ' +++++ export CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev +++++ CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev +++++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++++ export _CE_M= +++++ _CE_M= +++++ export _CE_CONDA= +++++ _CE_CONDA= +++++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python +++++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ __conda_hashr ++++ '[' -n '' ']' ++++ '[' -n '' ']' ++++ hash -r +++ unset __conda_setup ++ conda activate schemist-dev ++ local cmd=activate ++ case "$cmd" in ++ __conda_activate activate schemist-dev ++ '[' -n '' ']' ++ local ask_conda +++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++ __conda_exe shell.posix activate schemist-dev +++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate schemist-dev ++ ask_conda='PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_SHLVL='\''7'\'' +export CONDA_DEFAULT_ENV='\''schemist-dev'\'' +export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\'' +export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' ++ eval 'PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_SHLVL='\''7'\'' +export CONDA_DEFAULT_ENV='\''schemist-dev'\'' +export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\'' +export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' +++ PS1='(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++ export CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev +++ CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev +++ export CONDA_SHLVL=7 +++ CONDA_SHLVL=7 +++ export CONDA_DEFAULT_ENV=schemist-dev +++ CONDA_DEFAULT_ENV=schemist-dev +++ export 'CONDA_PROMPT_MODIFIER=(schemist-dev) ' +++ CONDA_PROMPT_MODIFIER='(schemist-dev) ' +++ export CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0 +++ CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0 +++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++ export _CE_M= +++ _CE_M= +++ export _CE_CONDA= +++ _CE_CONDA= +++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python +++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++ __conda_hashr ++ '[' -n '' ']' ++ '[' -n '' ']' ++ hash -r ++ CHUNK_HEAD_FILE=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz ++ INPUT=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/validation/cyc-pep-6-12mer-70M_06.csv ++ COLUMN=cysteine_to_N_cyclization ++ PREFIX=cyclic_ ++ AWK='1 { print $8, $1, $2, $10, $3 }' ++ '[' -z cysteine_to_N_cyclization ']' ++ '[' -z cyclic_ ']' ++ '[' -z '1 { print $8, $1, $2, $10, $3 }' ']' ++ awk -F, -v OFS=, '1 { print $8, $1, $2, $10, $3 }' ++ cat /dev/fd/63 /nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/validation/cyc-pep-6-12mer-70M_06.csv ++ schemist convert -f csv --column cysteine_to_N_cyclization --to id inchikey scaffold mwt clogp tpsa --prefix cyclic_ --options prefix=SCB- +++ zcat /nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz ++ gzip --best +++ head -n1 +++ tr ' ' , +🚀 Converting between string representations with the following parameters: + subcommand: convert + output: <_io.TextIOWrapper name='' mode='w' encoding='utf-8'> + format: csv + input: <_io.TextIOWrapper name='' mode='r' encoding='utf-8'> + representation: SMILES + column: cysteine_to_N_cyclization + prefix: cyclic_ + to: ['id', 'inchikey', 'scaffold', 'mwt', 'clogp', 'tpsa'] + options: ['prefix=SCB-'] + func: + 0it [00:00, ?it/s] 1it [00:07, 7.19s/it] 2it [00:13, 6.96s/it] 3it [00:20, 6.95s/it] 4it [00:27, 6.96s/it] 5it [00:35, 7.15s/it] 6it [00:42, 7.15s/it] 7it [00:49, 7.07s/it] 8it [00:56, 7.01s/it] 9it [01:03, 7.13s/it] 10it [01:10, 7.12s/it] 11it [01:17, 7.05s/it] 12it [01:24, 6.99s/it] 13it [01:31, 7.09s/it] 14it [01:38, 7.06s/it] 15it [01:45, 6.99s/it] 16it [01:52, 6.93s/it] 17it [01:59, 7.03s/it] 18it [02:06, 7.00s/it] 19it [02:13, 6.91s/it] 20it [02:20, 6.83s/it] 21it [02:27, 6.92s/it] 22it [02:34, 6.91s/it] 23it [02:40, 6.87s/it] 24it [02:47, 6.88s/it] 25it [02:54, 6.97s/it] 26it [03:01, 6.99s/it] 27it [03:08, 6.89s/it] 28it [03:15, 6.77s/it] 29it [03:22, 6.82s/it] 30it [03:28, 6.79s/it] 31it [03:35, 6.77s/it] 32it [03:42, 6.81s/it] 33it [03:49, 6.91s/it] 34it [03:56, 6.95s/it] 35it [04:03, 6.99s/it] 36it [04:10, 7.07s/it] 37it [04:18, 7.23s/it] 38it [04:26, 7.33s/it] 39it [04:33, 7.34s/it] 40it [04:40, 7.39s/it] 41it [04:48, 7.48s/it] 42it [04:56, 7.56s/it] 43it [05:03, 7.52s/it] 44it [05:11, 7.55s/it] 45it [05:19, 7.60s/it] 46it [05:27, 7.69s/it] 47it [05:34, 7.60s/it] 48it [05:41, 7.48s/it] 49it [05:48, 7.43s/it] 50it [05:56, 7.46s/it] 51it [06:03, 7.36s/it] 52it [06:10, 7.23s/it] 53it [06:17, 7.17s/it] 54it [06:24, 7.21s/it] 55it [06:31, 7.14s/it] 56it [06:38, 7.15s/it] 57it [06:46, 7.19s/it] 58it [06:53, 7.29s/it] 59it [07:00, 7.24s/it] 60it [07:07, 7.14s/it] 61it [07:14, 7.08s/it] 62it [07:22, 7.15s/it] 63it [07:28, 7.08s/it] 64it [07:35, 7.05s/it] 65it [07:42, 7.04s/it] 66it [07:50, 7.14s/it] 67it [07:57, 7.09s/it] 68it [08:04, 7.02s/it] 69it [08:11, 6.98s/it] 70it [08:18, 7.07s/it] 71it [08:25, 7.02s/it] 72it [08:32, 6.99s/it] 73it [08:39, 6.96s/it] 74it [08:46, 7.08s/it] 75it [08:53, 7.08s/it] 76it [09:00, 6.98s/it] 77it [09:06, 6.90s/it] 78it [09:14, 7.00s/it] 79it [09:21, 6.96s/it] 80it [09:27, 6.93s/it] 81it [09:34, 6.88s/it] 82it [09:41, 7.00s/it] 83it [09:48, 7.01s/it] 84it [09:56, 7.05s/it] 85it [10:03, 7.09s/it] 86it [10:10, 7.27s/it] 87it [10:18, 7.30s/it] 88it [10:25, 7.25s/it] 89it [10:32, 7.18s/it] 90it [10:40, 7.31s/it] 91it [10:47, 7.29s/it] 92it [10:54, 7.21s/it] 93it [11:01, 7.16s/it] 94it [11:08, 7.25s/it] 95it [11:16, 7.26s/it] 96it [11:23, 7.17s/it] 97it [11:30, 7.10s/it] 98it [11:37, 7.21s/it] 99it [11:44, 7.19s/it] 100it [11:51, 7.12s/it] 101it [11:58, 7.04s/it] 102it [12:05, 7.11s/it] 103it [12:12, 7.11s/it] 104it [12:19, 7.06s/it] 105it [12:26, 7.06s/it] 106it [12:34, 7.19s/it] 107it [12:41, 7.21s/it] 108it [12:48, 7.12s/it] 109it [12:55, 7.01s/it] 110it [13:02, 7.05s/it] 111it [13:09, 7.04s/it] 112it [13:16, 7.00s/it] 113it [13:23, 7.03s/it] 114it [13:30, 7.12s/it] 115it [13:38, 7.18s/it] 116it [13:45, 7.22s/it] 117it [13:53, 7.32s/it] 118it [14:00, 7.49s/it] 119it [14:08, 7.60s/it] 120it [14:16, 7.59s/it] 121it [14:23, 7.61s/it] 122it [14:31, 7.68s/it] 123it [14:39, 7.79s/it] 124it [14:47, 7.77s/it] 125it [14:55, 7.80s/it] 126it [15:03, 7.85s/it] 127it [15:11, 7.95s/it] 128it [15:19, 7.86s/it] 129it [15:26, 7.73s/it] 130it [15:34, 7.67s/it] 131it [15:41, 7.69s/it] 132it [15:49, 7.57s/it] 133it [15:56, 7.45s/it] 134it [16:03, 7.39s/it] 135it [16:11, 7.45s/it] 136it [16:18, 7.40s/it] 137it [16:26, 7.42s/it] 138it [16:33, 7.47s/it] 139it [16:41, 7.62s/it] 140it [16:49, 7.57s/it] 141it [16:56, 7.47s/it] 142it [17:03, 7.39s/it] 143it [17:11, 7.45s/it] 144it [17:18, 7.38s/it] 145it [17:25, 7.35s/it] 146it [17:32, 7.34s/it] 147it [17:40, 7.46s/it] 148it [17:47, 7.41s/it] 149it [17:55, 7.33s/it] 150it [18:02, 7.25s/it] 151it [18:09, 7.34s/it] 152it [18:16, 7.30s/it] 153it [18:24, 7.27s/it] 154it [18:31, 7.23s/it] 155it [18:38, 7.36s/it] 156it [18:46, 7.35s/it] 157it [18:52, 7.11s/it] 158it [18:59, 6.93s/it] 159it [19:06, 6.95s/it] 160it [19:12, 6.85s/it] 161it [19:19, 6.77s/it] 162it [19:25, 6.69s/it] 163it [19:33, 6.80s/it] 164it [19:39, 6.79s/it] 165it [19:46, 6.83s/it] 166it [19:53, 6.86s/it] 167it [20:01, 7.04s/it] 168it [20:08, 7.06s/it] 169it [20:15, 7.01s/it] 170it [20:21, 6.96s/it] 171it [20:29, 7.08s/it] 172it [20:36, 7.06s/it] 173it [20:43, 6.97s/it] 174it [20:49, 6.92s/it] 175it [20:57, 7.03s/it] 176it [21:04, 7.02s/it] 177it [21:10, 6.95s/it] 178it [21:17, 6.88s/it] 179it [21:24, 6.97s/it] 180it [21:31, 6.95s/it] 181it [21:38, 6.88s/it] 182it [21:45, 6.81s/it] 183it [21:52, 6.86s/it] 184it [21:58, 6.88s/it] 185it [22:05, 6.84s/it] 186it [22:12, 6.84s/it] 187it [22:19, 6.92s/it] 188it [22:26, 6.95s/it] 189it [22:33, 6.86s/it] 190it [22:39, 6.76s/it] 191it [22:46, 6.76s/it] 192it [22:53, 6.78s/it] 193it [23:00, 6.74s/it] 194it [23:06, 6.77s/it] 195it [23:14, 6.85s/it] 196it [23:21, 6.93s/it] 197it [23:28, 6.94s/it] 198it [23:35, 7.06s/it] 199it [23:42, 7.19s/it] 200it [23:50, 7.33s/it] 201it [23:57, 7.33s/it] 202it [24:05, 7.36s/it] 203it [24:12, 7.39s/it] 204it [24:20, 7.51s/it] 205it [24:28, 7.50s/it] 206it [24:35, 7.52s/it] 207it [24:43, 7.55s/it] 208it [24:51, 7.67s/it] 209it [24:58, 7.61s/it] 210it [25:05, 7.49s/it] 211it [25:13, 7.41s/it] 212it [25:20, 7.45s/it] 213it [25:27, 7.34s/it] 214it [25:34, 7.21s/it] 215it [25:41, 7.14s/it] 216it [25:48, 7.19s/it] 217it [25:55, 7.13s/it] 218it [26:03, 7.13s/it] 219it [26:10, 7.12s/it] 220it [26:17, 7.26s/it] 221it [26:24, 7.25s/it] 222it [26:31, 7.14s/it] 223it [26:38, 7.05s/it] 224it [26:45, 7.13s/it] 225it [26:52, 7.10s/it] 226it [26:59, 7.04s/it] 227it [27:06, 7.00s/it] 228it [27:14, 7.13s/it] 229it [27:21, 7.11s/it] 230it [27:28, 7.03s/it] 231it [27:34, 6.95s/it] 232it [27:42, 7.05s/it] 233it [27:49, 7.04s/it] 234it [27:56, 6.99s/it] 235it [28:02, 6.95s/it] 236it [28:10, 7.08s/it] 237it [28:17, 7.07s/it] 238it [28:24, 6.95s/it] 239it [28:30, 6.82s/it] 240it [28:37, 6.89s/it] 241it [28:44, 6.87s/it] 242it [28:51, 6.82s/it] 243it [28:57, 6.77s/it] 244it [29:04, 6.85s/it] 245it [29:11, 6.83s/it] 246it [29:18, 6.87s/it] 247it [29:25, 6.90s/it] 248it [29:32, 7.05s/it] 249it [29:40, 7.10s/it] 250it [29:47, 7.05s/it] 251it [29:54, 7.02s/it] 252it [30:01, 7.11s/it] 253it [30:08, 7.12s/it] 254it [30:15, 7.05s/it] 255it [30:22, 7.02s/it] 256it [30:29, 7.06s/it] 257it [30:36, 7.09s/it] 258it [30:43, 7.01s/it] 259it [30:50, 6.96s/it] 260it [30:57, 6.99s/it] 261it [31:04, 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7.46s/it] 894it [1:50:17, 7.49s/it] 895it [1:50:25, 7.52s/it] 896it [1:50:33, 7.70s/it] 897it [1:50:41, 7.74s/it] 898it [1:50:48, 7.67s/it] 899it [1:50:56, 7.63s/it] 900it [1:51:04, 7.74s/it] 901it [1:51:11, 7.75s/it] 902it [1:51:19, 7.68s/it] 903it [1:51:26, 7.62s/it] 904it [1:51:34, 7.72s/it] 905it [1:51:42, 7.70s/it] 906it [1:51:49, 7.61s/it] 907it [1:51:57, 7.56s/it] 908it [1:52:05, 7.63s/it] 909it [1:52:12, 7.63s/it] 910it [1:52:20, 7.54s/it] 911it [1:52:27, 7.48s/it] 912it [1:52:35, 7.56s/it] 913it [1:52:42, 7.56s/it] 914it [1:52:50, 7.52s/it] 915it [1:52:57, 7.51s/it] 916it [1:53:05, 7.60s/it] 917it [1:53:13, 7.64s/it] 918it [1:53:20, 7.54s/it] 919it [1:53:27, 7.43s/it] 920it [1:53:35, 7.44s/it] 921it [1:53:42, 7.44s/it] 922it [1:53:49, 7.40s/it] 923it [1:53:57, 7.43s/it] 924it [1:54:05, 7.55s/it] 925it [1:54:12, 7.62s/it] 926it [1:54:20, 7.64s/it] 927it [1:54:28, 7.75s/it] 928it [1:54:36, 7.89s/it] 929it [1:54:45, 8.02s/it] 930it [1:54:53, 8.01s/it] 931it [1:55:01, 8.04s/it] 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[2:00:06, 7.35s/it] 971it [2:00:13, 7.27s/it] 972it [2:00:20, 7.21s/it] 973it [2:00:28, 7.33s/it] 974it [2:00:35, 7.31s/it] 975it [2:00:43, 7.35s/it] 976it [2:00:50, 7.38s/it] 977it [2:00:58, 7.55s/it] 978it [2:01:06, 7.58s/it] 979it [2:01:13, 7.52s/it] 980it [2:01:20, 7.47s/it] 981it [2:01:28, 7.59s/it] 982it [2:01:36, 7.59s/it] 983it [2:01:43, 7.53s/it] 984it [2:01:51, 7.45s/it] 985it [2:01:58, 7.56s/it] 986it [2:02:06, 7.54s/it] 987it [2:02:13, 7.47s/it] 988it [2:02:20, 7.40s/it] 989it [2:02:28, 7.49s/it] 990it [2:02:36, 7.49s/it] 991it [2:02:43, 7.40s/it] 992it [2:02:50, 7.33s/it] 993it [2:02:58, 7.42s/it] 994it [2:03:05, 7.41s/it] 995it [2:03:12, 7.38s/it] 996it [2:03:20, 7.37s/it] 997it [2:03:27, 7.48s/it] 998it [2:03:35, 7.51s/it] 999it [2:03:42, 7.39s/it] 1000it [2:03:49, 7.29s/it] 1000it [2:03:49, 7.43s/it] +Error counts: + cyclic_id: 0 + cyclic_inchikey: 0 + cyclic_scaffold: 0 + cyclic_mwt: 0 + cyclic_clogp: 0 + cyclic_tpsa: 0 +⏰ Completed process in 2:04:06.681304 ++ rm /nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/validation/cyc-pep-6-12mer-70M_06.csv diff --git a/validation/cyc-pep-6-12mer-70M_07.csv.gz b/validation/cyc-pep-6-12mer-70M_07.csv.gz index 9c55d4ce07256c3180d0f6ab06ce695908af0def..e92c57beb2d0080f82d2e7cec470829e44b3d012 100644 --- a/validation/cyc-pep-6-12mer-70M_07.csv.gz +++ b/validation/cyc-pep-6-12mer-70M_07.csv.gz @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:af1b776e751bfc034f56c588a192d5d9503f977be5d2cdd037aa68902c05ea4f -size 34258677 +oid sha256:d02138190e70c6bba628f4c8cb7d6623a14ab03f2316b89458cec5b40e1ce8d2 +size 78780153 diff --git a/validation/cyc-pep-6-12mer-70M_07.log b/validation/cyc-pep-6-12mer-70M_07.log new file mode 100644 index 0000000000000000000000000000000000000000..fe41bafe147695285fc5aaaa49920adb31d4d0ec --- /dev/null +++ b/validation/cyc-pep-6-12mer-70M_07.log @@ -0,0 +1,337 @@ ++ module purge ++ '[' -z '' ']' ++ case "$-" in ++ __lmod_sh_dbg=x ++ '[' -n x ']' ++ set +x +Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output +Shell debugging restarted ++ unset __lmod_sh_dbg ++ return 0 ++ module load Anaconda3/2023.03 ++ '[' -z '' ']' ++ case "$-" in ++ __lmod_sh_dbg=x ++ '[' -n x ']' ++ set +x +Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output +Shell debugging restarted ++ unset __lmod_sh_dbg ++ return 0 ++ source /camp/home/johnsoe/.bashrc +++ '[' '' = yes ']' +++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' ++++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.bash hook +++ __conda_setup='export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'' + +# Copyright (C) 2012 Anaconda, Inc +# SPDX-License-Identifier: BSD-3-Clause +__conda_exe() ( + "$CONDA_EXE" $_CE_M $_CE_CONDA "$@" +) + +__conda_hashr() { + if [ -n "${ZSH_VERSION:+x}" ]; then + \rehash + elif [ -n "${POSH_VERSION:+x}" ]; then + : # pass + else + \hash -r + fi +} + +__conda_activate() { + if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then + # Handle transition from shell activated with conda <= 4.3 to a subsequent activation + # after conda updated to >= 4.4. See issue #6173. + PS1="$CONDA_PS1_BACKUP" + \unset CONDA_PS1_BACKUP + fi + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return + \eval "$ask_conda" + __conda_hashr +} + +__conda_reactivate() { + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return + \eval "$ask_conda" + __conda_hashr +} + +conda() { + \local cmd="${1-__missing__}" + case "$cmd" in + activate|deactivate) + __conda_activate "$@" + ;; + install|update|upgrade|remove|uninstall) + __conda_exe "$@" || \return + __conda_reactivate + ;; + *) + __conda_exe "$@" + ;; + esac +} + +if [ -z "${CONDA_SHLVL+x}" ]; then + \export CONDA_SHLVL=0 + # In dev-mode CONDA_EXE is python.exe and on Windows + # it is in a different relative location to condabin. + if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then + PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}" + else + PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}" + fi + \export PATH + + # We'\''re not allowing PS1 to be unbound. It must at least be set. + # However, we'\''re not exporting it, which can cause problems when starting a second shell + # via a first shell (i.e. starting zsh from bash). + if [ -z "${PS1+x}" ]; then + PS1= + fi +fi + +conda activate base' +++ '[' 0 -eq 0 ']' +++ eval 'export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'' + +# Copyright (C) 2012 Anaconda, Inc +# SPDX-License-Identifier: BSD-3-Clause +__conda_exe() ( + "$CONDA_EXE" $_CE_M $_CE_CONDA "$@" +) + +__conda_hashr() { + if [ -n "${ZSH_VERSION:+x}" ]; then + \rehash + elif [ -n "${POSH_VERSION:+x}" ]; then + : # pass + else + \hash -r + fi +} + +__conda_activate() { + if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then + # Handle transition from shell activated with conda <= 4.3 to a subsequent activation + # after conda updated to >= 4.4. See issue #6173. + PS1="$CONDA_PS1_BACKUP" + \unset CONDA_PS1_BACKUP + fi + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return + \eval "$ask_conda" + __conda_hashr +} + +__conda_reactivate() { + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return + \eval "$ask_conda" + __conda_hashr +} + +conda() { + \local cmd="${1-__missing__}" + case "$cmd" in + activate|deactivate) + __conda_activate "$@" + ;; + install|update|upgrade|remove|uninstall) + __conda_exe "$@" || \return + __conda_reactivate + ;; + *) + __conda_exe "$@" + ;; + esac +} + +if [ -z "${CONDA_SHLVL+x}" ]; then + \export CONDA_SHLVL=0 + # In dev-mode CONDA_EXE is python.exe and on Windows + # it is in a different relative location to condabin. + if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then + PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}" + else + PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}" + fi + \export PATH + + # We'\''re not allowing PS1 to be unbound. It must at least be set. + # However, we'\''re not exporting it, which can cause problems when starting a second shell + # via a first shell (i.e. starting zsh from bash). + if [ -z "${PS1+x}" ]; then + PS1= + fi +fi + +conda activate base' ++++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda ++++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda ++++ export _CE_M= ++++ _CE_M= ++++ export _CE_CONDA= ++++ _CE_CONDA= ++++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ '[' -z x ']' ++++ conda activate base ++++ local cmd=activate ++++ case "$cmd" in ++++ __conda_activate activate base ++++ '[' -n '' ']' ++++ local ask_conda +++++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++++ __conda_exe shell.posix activate base +++++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate base ++++ ask_conda='PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_SHLVL='\''6'\'' +export CONDA_DEFAULT_ENV='\''base'\'' +export CONDA_PROMPT_MODIFIER='\''(base) '\'' +export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' ++++ eval 'PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_SHLVL='\''6'\'' +export CONDA_DEFAULT_ENV='\''base'\'' +export CONDA_PROMPT_MODIFIER='\''(base) '\'' +export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' +++++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++++ export CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0 +++++ CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0 +++++ export CONDA_SHLVL=6 +++++ CONDA_SHLVL=6 +++++ export CONDA_DEFAULT_ENV=base +++++ CONDA_DEFAULT_ENV=base +++++ export 'CONDA_PROMPT_MODIFIER=(base) ' +++++ CONDA_PROMPT_MODIFIER='(base) ' +++++ export CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev +++++ CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev +++++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++++ export _CE_M= +++++ _CE_M= +++++ export _CE_CONDA= +++++ _CE_CONDA= +++++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python +++++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ __conda_hashr ++++ '[' -n '' ']' ++++ '[' -n '' ']' ++++ hash -r +++ unset __conda_setup ++ conda activate schemist-dev ++ local cmd=activate ++ case "$cmd" in ++ __conda_activate activate schemist-dev ++ '[' -n '' ']' ++ local ask_conda +++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++ __conda_exe shell.posix activate schemist-dev +++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate schemist-dev ++ ask_conda='PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_SHLVL='\''7'\'' +export CONDA_DEFAULT_ENV='\''schemist-dev'\'' +export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\'' +export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' ++ eval 'PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_SHLVL='\''7'\'' +export CONDA_DEFAULT_ENV='\''schemist-dev'\'' +export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\'' +export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' +++ PS1='(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++ export CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev +++ CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev +++ export CONDA_SHLVL=7 +++ CONDA_SHLVL=7 +++ export CONDA_DEFAULT_ENV=schemist-dev +++ CONDA_DEFAULT_ENV=schemist-dev +++ export 'CONDA_PROMPT_MODIFIER=(schemist-dev) ' +++ CONDA_PROMPT_MODIFIER='(schemist-dev) ' +++ export CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0 +++ CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0 +++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++ export _CE_M= +++ _CE_M= +++ export _CE_CONDA= +++ _CE_CONDA= +++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python +++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++ __conda_hashr ++ '[' -n '' ']' ++ '[' -n '' ']' ++ hash -r ++ CHUNK_HEAD_FILE=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz ++ INPUT=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/validation/cyc-pep-6-12mer-70M_07.csv ++ COLUMN=cysteine_to_N_cyclization ++ PREFIX=cyclic_ ++ AWK='1 { print $8, $1, $2, $10, $3 }' ++ '[' -z cysteine_to_N_cyclization ']' ++ '[' -z cyclic_ ']' ++ '[' -z '1 { print $8, $1, $2, $10, $3 }' ']' ++ cat /dev/fd/63 /nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/validation/cyc-pep-6-12mer-70M_07.csv ++ awk -F, -v OFS=, '1 { print $8, $1, $2, $10, $3 }' +++ zcat /nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz ++ schemist convert -f csv --column cysteine_to_N_cyclization --to id inchikey scaffold mwt clogp tpsa --prefix cyclic_ --options prefix=SCB- ++ gzip --best +++ head -n1 +++ tr ' ' , +🚀 Converting between string representations with the following parameters: + subcommand: convert + output: <_io.TextIOWrapper name='' mode='w' encoding='utf-8'> + format: csv + input: <_io.TextIOWrapper name='' mode='r' encoding='utf-8'> + representation: SMILES + column: cysteine_to_N_cyclization + prefix: cyclic_ + to: ['id', 'inchikey', 'scaffold', 'mwt', 'clogp', 'tpsa'] + options: ['prefix=SCB-'] + func: + 0it [00:00, ?it/s] 1it [00:07, 7.51s/it] 2it [00:14, 7.42s/it] 3it [00:22, 7.38s/it] 4it [00:29, 7.44s/it] 5it [00:37, 7.57s/it] 6it 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888it [1:58:21, 7.85s/it] 889it [1:58:29, 7.96s/it] 890it [1:58:37, 7.85s/it] 891it [1:58:44, 7.73s/it] 892it [1:58:52, 7.70s/it] 893it [1:59:00, 7.71s/it] 894it [1:59:07, 7.67s/it] 895it [1:59:15, 7.70s/it] 896it [1:59:23, 7.75s/it] 897it [1:59:31, 7.87s/it] 898it [1:59:39, 7.88s/it] 899it [1:59:47, 8.02s/it] 900it [1:59:55, 8.12s/it] 901it [2:00:04, 8.32s/it] 902it [2:00:13, 8.33s/it] 903it [2:00:21, 8.35s/it] 904it [2:00:29, 8.34s/it] 905it [2:00:38, 8.51s/it] 906it [2:00:47, 8.51s/it] 907it [2:00:55, 8.51s/it] 908it [2:01:04, 8.49s/it] 909it [2:01:13, 8.66s/it] 910it [2:01:21, 8.66s/it] 911it [2:01:30, 8.50s/it] 912it [2:01:38, 8.37s/it] 913it [2:01:46, 8.42s/it] 914it [2:01:54, 8.38s/it] 915it [2:02:02, 8.20s/it] 916it [2:02:10, 8.07s/it] 917it [2:02:18, 8.15s/it] 918it [2:02:26, 8.12s/it] 919it [2:02:34, 8.10s/it] 920it [2:02:42, 8.07s/it] 921it [2:02:51, 8.24s/it] 922it [2:02:59, 8.26s/it] 923it [2:03:07, 8.14s/it] 924it [2:03:15, 8.01s/it] 925it [2:03:23, 8.12s/it] 926it [2:03:31, 8.07s/it] 927it [2:03:39, 8.00s/it] 928it [2:03:47, 7.93s/it] 929it [2:03:55, 8.03s/it] 930it [2:04:03, 8.03s/it] 931it [2:04:11, 7.93s/it] 932it [2:04:19, 7.84s/it] 933it [2:04:27, 7.95s/it] 934it [2:04:35, 7.91s/it] 935it [2:04:42, 7.84s/it] 936it [2:04:50, 7.78s/it] 937it [2:04:58, 7.90s/it] 938it [2:05:06, 7.91s/it] 939it [2:05:13, 7.73s/it] 940it [2:05:20, 7.54s/it] 941it [2:05:28, 7.56s/it] 942it [2:05:35, 7.49s/it] 943it [2:05:42, 7.40s/it] 944it [2:05:50, 7.32s/it] 945it [2:05:57, 7.41s/it] 946it [2:06:05, 7.40s/it] 947it [2:06:12, 7.40s/it] 948it [2:06:20, 7.45s/it] 949it [2:06:28, 7.60s/it] 950it [2:06:35, 7.65s/it] 951it [2:06:43, 7.60s/it] 952it [2:06:50, 7.58s/it] 953it [2:06:58, 7.67s/it] 954it [2:07:06, 7.69s/it] 955it [2:07:13, 7.63s/it] 956it [2:07:21, 7.58s/it] 957it [2:07:29, 7.63s/it] 958it [2:07:36, 7.66s/it] 959it [2:07:44, 7.58s/it] 960it [2:07:51, 7.53s/it] 961it [2:07:59, 7.58s/it] 962it [2:08:07, 7.62s/it] 963it [2:08:14, 7.53s/it] 964it [2:08:21, 7.50s/it] 965it [2:08:29, 7.50s/it] 966it [2:08:37, 7.56s/it] 967it [2:08:44, 7.49s/it] 968it [2:08:51, 7.49s/it] 969it [2:08:59, 7.53s/it] 970it [2:09:07, 7.64s/it] 971it [2:09:14, 7.55s/it] 972it [2:09:21, 7.43s/it] 973it [2:09:29, 7.37s/it] 974it [2:09:36, 7.41s/it] 975it [2:09:43, 7.35s/it] 976it [2:09:51, 7.40s/it] 977it [2:09:58, 7.43s/it] 978it [2:10:06, 7.57s/it] 979it [2:10:14, 7.56s/it] 980it [2:10:22, 7.67s/it] 981it [2:10:30, 7.75s/it] 982it [2:10:38, 7.94s/it] 983it [2:10:46, 7.97s/it] 984it [2:10:54, 7.99s/it] 985it [2:11:02, 7.99s/it] 986it [2:11:11, 8.15s/it] 987it [2:11:19, 8.17s/it] 988it [2:11:27, 8.17s/it] 989it [2:11:35, 8.18s/it] 990it [2:11:44, 8.34s/it] 991it [2:11:52, 8.32s/it] 992it [2:12:00, 8.15s/it] 993it [2:12:08, 8.01s/it] 994it [2:12:16, 8.07s/it] 995it [2:12:24, 8.03s/it] 996it [2:12:31, 7.87s/it] 997it [2:12:39, 7.75s/it] 998it [2:12:47, 7.83s/it] 999it [2:12:54, 7.79s/it] 1000it [2:13:02, 7.77s/it] 1000it [2:13:02, 7.98s/it] +Error counts: + cyclic_id: 0 + cyclic_inchikey: 0 + cyclic_scaffold: 0 + cyclic_mwt: 0 + cyclic_clogp: 0 + cyclic_tpsa: 0 +⏰ Completed process in 2:13:20.859728 ++ rm /nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/validation/cyc-pep-6-12mer-70M_07.csv diff --git a/validation/cyc-pep-6-12mer-70M_08.csv.gz b/validation/cyc-pep-6-12mer-70M_08.csv.gz index e2086f37e92d70319b5e7d197026c9852d1524f7..a76bb69427da36d6d9e092d7eaa2d4bdaca81928 100644 --- a/validation/cyc-pep-6-12mer-70M_08.csv.gz +++ b/validation/cyc-pep-6-12mer-70M_08.csv.gz @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:5aae3a0adbbf771b1309575905a0d60a7d8c744390304c97c13d4fd61c97b557 -size 49059745 +oid sha256:57a578802ce2d521592916ac23adfaf9e682e6a77e47c58bf9406a1a945c2098 +size 100311950 diff --git a/validation/cyc-pep-6-12mer-70M_08.log b/validation/cyc-pep-6-12mer-70M_08.log new file mode 100644 index 0000000000000000000000000000000000000000..e0734a8e702640ee2237f1d5d3f1872ca84f5909 --- /dev/null +++ b/validation/cyc-pep-6-12mer-70M_08.log @@ -0,0 +1,337 @@ ++ module purge ++ '[' -z '' ']' ++ case "$-" in ++ __lmod_sh_dbg=x ++ '[' -n x ']' ++ set +x +Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output +Shell debugging restarted ++ unset __lmod_sh_dbg ++ return 0 ++ module load Anaconda3/2023.03 ++ '[' -z '' ']' ++ case "$-" in ++ __lmod_sh_dbg=x ++ '[' -n x ']' ++ set +x +Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output +Shell debugging restarted ++ unset __lmod_sh_dbg ++ return 0 ++ source /camp/home/johnsoe/.bashrc +++ '[' '' = yes ']' +++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' ++++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.bash hook +++ __conda_setup='export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'' + +# Copyright (C) 2012 Anaconda, Inc +# SPDX-License-Identifier: BSD-3-Clause +__conda_exe() ( + "$CONDA_EXE" $_CE_M $_CE_CONDA "$@" +) + +__conda_hashr() { + if [ -n "${ZSH_VERSION:+x}" ]; then + \rehash + elif [ -n "${POSH_VERSION:+x}" ]; then + : # pass + else + \hash -r + fi +} + +__conda_activate() { + if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then + # Handle transition from shell activated with conda <= 4.3 to a subsequent activation + # after conda updated to >= 4.4. See issue #6173. + PS1="$CONDA_PS1_BACKUP" + \unset CONDA_PS1_BACKUP + fi + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return + \eval "$ask_conda" + __conda_hashr +} + +__conda_reactivate() { + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return + \eval "$ask_conda" + __conda_hashr +} + +conda() { + \local cmd="${1-__missing__}" + case "$cmd" in + activate|deactivate) + __conda_activate "$@" + ;; + install|update|upgrade|remove|uninstall) + __conda_exe "$@" || \return + __conda_reactivate + ;; + *) + __conda_exe "$@" + ;; + esac +} + +if [ -z "${CONDA_SHLVL+x}" ]; then + \export CONDA_SHLVL=0 + # In dev-mode CONDA_EXE is python.exe and on Windows + # it is in a different relative location to condabin. + if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then + PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}" + else + PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}" + fi + \export PATH + + # We'\''re not allowing PS1 to be unbound. It must at least be set. + # However, we'\''re not exporting it, which can cause problems when starting a second shell + # via a first shell (i.e. starting zsh from bash). + if [ -z "${PS1+x}" ]; then + PS1= + fi +fi + +conda activate base' +++ '[' 0 -eq 0 ']' +++ eval 'export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'' + +# Copyright (C) 2012 Anaconda, Inc +# SPDX-License-Identifier: BSD-3-Clause +__conda_exe() ( + "$CONDA_EXE" $_CE_M $_CE_CONDA "$@" +) + +__conda_hashr() { + if [ -n "${ZSH_VERSION:+x}" ]; then + \rehash + elif [ -n "${POSH_VERSION:+x}" ]; then + : # pass + else + \hash -r + fi +} + +__conda_activate() { + if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then + # Handle transition from shell activated with conda <= 4.3 to a subsequent activation + # after conda updated to >= 4.4. See issue #6173. + PS1="$CONDA_PS1_BACKUP" + \unset CONDA_PS1_BACKUP + fi + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return + \eval "$ask_conda" + __conda_hashr +} + +__conda_reactivate() { + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return + \eval "$ask_conda" + __conda_hashr +} + +conda() { + \local cmd="${1-__missing__}" + case "$cmd" in + activate|deactivate) + __conda_activate "$@" + ;; + install|update|upgrade|remove|uninstall) + __conda_exe "$@" || \return + __conda_reactivate + ;; + *) + __conda_exe "$@" + ;; + esac +} + +if [ -z "${CONDA_SHLVL+x}" ]; then + \export CONDA_SHLVL=0 + # In dev-mode CONDA_EXE is python.exe and on Windows + # it is in a different relative location to condabin. + if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then + PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}" + else + PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}" + fi + \export PATH + + # We'\''re not allowing PS1 to be unbound. It must at least be set. + # However, we'\''re not exporting it, which can cause problems when starting a second shell + # via a first shell (i.e. starting zsh from bash). + if [ -z "${PS1+x}" ]; then + PS1= + fi +fi + +conda activate base' ++++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda ++++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda ++++ export _CE_M= ++++ _CE_M= ++++ export _CE_CONDA= ++++ _CE_CONDA= ++++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ '[' -z x ']' ++++ conda activate base ++++ local cmd=activate ++++ case "$cmd" in ++++ __conda_activate activate base ++++ '[' -n '' ']' ++++ local ask_conda +++++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++++ __conda_exe shell.posix activate base +++++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate base ++++ ask_conda='PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_SHLVL='\''6'\'' +export CONDA_DEFAULT_ENV='\''base'\'' +export CONDA_PROMPT_MODIFIER='\''(base) '\'' +export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' ++++ eval 'PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_SHLVL='\''6'\'' +export CONDA_DEFAULT_ENV='\''base'\'' +export CONDA_PROMPT_MODIFIER='\''(base) '\'' +export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' +++++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++++ export CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0 +++++ CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0 +++++ export CONDA_SHLVL=6 +++++ CONDA_SHLVL=6 +++++ export CONDA_DEFAULT_ENV=base +++++ CONDA_DEFAULT_ENV=base +++++ export 'CONDA_PROMPT_MODIFIER=(base) ' +++++ CONDA_PROMPT_MODIFIER='(base) ' +++++ export CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev +++++ CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev +++++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++++ export _CE_M= +++++ _CE_M= +++++ export _CE_CONDA= +++++ _CE_CONDA= +++++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python +++++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ __conda_hashr ++++ '[' -n '' ']' ++++ '[' -n '' ']' ++++ hash -r +++ unset __conda_setup ++ conda activate schemist-dev ++ local cmd=activate ++ case "$cmd" in ++ __conda_activate activate schemist-dev ++ '[' -n '' ']' ++ local ask_conda +++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++ __conda_exe shell.posix activate schemist-dev +++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate schemist-dev ++ ask_conda='PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_SHLVL='\''7'\'' +export CONDA_DEFAULT_ENV='\''schemist-dev'\'' +export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\'' +export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' ++ eval 'PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_SHLVL='\''7'\'' +export CONDA_DEFAULT_ENV='\''schemist-dev'\'' +export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\'' +export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' +++ PS1='(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++ export CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev +++ CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev +++ export CONDA_SHLVL=7 +++ CONDA_SHLVL=7 +++ export CONDA_DEFAULT_ENV=schemist-dev +++ CONDA_DEFAULT_ENV=schemist-dev +++ export 'CONDA_PROMPT_MODIFIER=(schemist-dev) ' +++ CONDA_PROMPT_MODIFIER='(schemist-dev) ' +++ export CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0 +++ CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0 +++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++ export _CE_M= +++ _CE_M= +++ export _CE_CONDA= +++ _CE_CONDA= +++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python +++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++ __conda_hashr ++ '[' -n '' ']' ++ '[' -n '' ']' ++ hash -r ++ CHUNK_HEAD_FILE=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz ++ INPUT=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/validation/cyc-pep-6-12mer-70M_08.csv ++ COLUMN=cysteine_to_N_cyclization ++ PREFIX=cyclic_ ++ AWK='1 { print $8, $1, $2, $10, $3 }' ++ '[' -z cysteine_to_N_cyclization ']' ++ '[' -z cyclic_ ']' ++ '[' -z '1 { print $8, $1, $2, $10, $3 }' ']' ++ awk -F, -v OFS=, '1 { print $8, $1, $2, $10, $3 }' ++ cat /dev/fd/63 /nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/validation/cyc-pep-6-12mer-70M_08.csv +++ zcat /nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz ++ gzip --best ++ schemist convert -f csv --column cysteine_to_N_cyclization --to id inchikey scaffold mwt clogp tpsa --prefix cyclic_ --options prefix=SCB- +++ tr ' ' , +++ head -n1 +🚀 Converting between string representations with the following parameters: + subcommand: convert + output: <_io.TextIOWrapper name='' mode='w' encoding='utf-8'> + format: csv + input: <_io.TextIOWrapper name='' mode='r' encoding='utf-8'> + representation: SMILES + column: cysteine_to_N_cyclization + prefix: cyclic_ + to: ['id', 'inchikey', 'scaffold', 'mwt', 'clogp', 'tpsa'] + options: ['prefix=SCB-'] + func: + 0it [00:00, ?it/s] 1it [00:08, 8.18s/it] 2it [00:16, 8.49s/it] 3it [00:25, 8.45s/it] 4it [00:33, 8.27s/it] 5it [00:41, 8.13s/it] 6it [00:49, 8.24s/it] 7it [00:57, 8.19s/it] 8it [01:05, 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8.66s/it] 926it [2:14:00, 8.68s/it] 927it [2:14:09, 8.66s/it] 928it [2:14:17, 8.66s/it] 929it [2:14:26, 8.69s/it] 930it [2:14:35, 8.69s/it] 931it [2:14:43, 8.67s/it] 932it [2:14:52, 8.67s/it] 933it [2:15:01, 8.67s/it] 934it [2:15:09, 8.67s/it] 935it [2:15:18, 8.66s/it] 936it [2:15:27, 8.67s/it] 937it [2:15:35, 8.68s/it] 938it [2:15:44, 8.67s/it] 939it [2:15:53, 8.69s/it] 940it [2:16:01, 8.68s/it] 941it [2:16:10, 8.67s/it] 942it [2:16:19, 8.68s/it] 943it [2:16:27, 8.67s/it] 944it [2:16:36, 8.67s/it] 945it [2:16:45, 8.65s/it] 946it [2:16:53, 8.65s/it] 947it [2:17:02, 8.66s/it] 948it [2:17:11, 8.66s/it] 949it [2:17:19, 8.65s/it] 950it [2:17:28, 8.67s/it] 951it [2:17:37, 8.68s/it] 952it [2:17:45, 8.68s/it] 953it [2:17:54, 8.66s/it] 954it [2:18:03, 8.66s/it] 955it [2:18:11, 8.67s/it] 956it [2:18:20, 8.66s/it] 957it [2:18:29, 8.67s/it] 958it [2:18:37, 8.68s/it] 959it [2:18:46, 8.68s/it] 960it [2:18:55, 8.69s/it] 961it [2:19:03, 8.67s/it] 962it [2:19:12, 8.67s/it] 963it [2:19:21, 8.68s/it] 964it [2:19:30, 8.69s/it] 965it [2:19:38, 8.69s/it] 966it [2:19:47, 8.68s/it] 967it [2:19:56, 8.70s/it] 968it [2:20:04, 8.69s/it] 969it [2:20:13, 8.67s/it] 970it [2:20:22, 8.66s/it] 971it [2:20:30, 8.66s/it] 972it [2:20:39, 8.67s/it] 973it [2:20:48, 8.69s/it] 974it [2:20:56, 8.67s/it] 975it [2:21:05, 8.67s/it] 976it [2:21:14, 8.67s/it] 977it [2:21:22, 8.66s/it] 978it [2:21:31, 8.67s/it] 979it [2:21:40, 8.66s/it] 980it [2:21:48, 8.66s/it] 981it [2:21:57, 8.65s/it] 982it [2:22:06, 8.65s/it] 983it [2:22:14, 8.67s/it] 984it [2:22:23, 8.65s/it] 985it [2:22:32, 8.67s/it] 986it [2:22:40, 8.67s/it] 987it [2:22:49, 8.67s/it] 988it [2:22:58, 8.68s/it] 989it [2:23:06, 8.65s/it] 990it [2:23:15, 8.65s/it] 991it [2:23:24, 8.66s/it] 992it [2:23:32, 8.66s/it] 993it [2:23:41, 8.65s/it] 994it [2:23:49, 8.65s/it] 995it [2:23:58, 8.65s/it] 996it [2:24:07, 8.67s/it] 997it [2:24:15, 8.67s/it] 998it [2:24:24, 8.67s/it] 999it [2:24:33, 8.66s/it] 1000it [2:24:41, 8.67s/it] 1000it [2:24:41, 8.68s/it] +Error counts: + cyclic_id: 0 + cyclic_inchikey: 0 + cyclic_scaffold: 0 + cyclic_mwt: 0 + cyclic_clogp: 0 + cyclic_tpsa: 0 +⏰ Completed process in 2:25:01.134683 ++ rm /nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/validation/cyc-pep-6-12mer-70M_08.csv diff --git a/validation/cyc-pep-6-12mer-70M_09.csv.gz b/validation/cyc-pep-6-12mer-70M_09.csv.gz index ff43a7efaff824507d51c59706956b0add531948..84fe425c7c2d28c7a26c1cbe257d7199e0029b25 100644 --- a/validation/cyc-pep-6-12mer-70M_09.csv.gz +++ b/validation/cyc-pep-6-12mer-70M_09.csv.gz @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:93653c4d0b36709689960878db330f753378f798b61cde57922854c5fffc4856 -size 51750785 +oid sha256:ee57035b83bcf77011c1f66441d1cf85b52f73790ad3c7afe32cc6dfbb887657 +size 104111373 diff --git a/validation/cyc-pep-6-12mer-70M_09.log b/validation/cyc-pep-6-12mer-70M_09.log new file mode 100644 index 0000000000000000000000000000000000000000..e0211c7d3d67d3ed0bb05b6b69ff96f7f502a76e --- /dev/null +++ b/validation/cyc-pep-6-12mer-70M_09.log @@ -0,0 +1,337 @@ ++ module purge ++ '[' -z '' ']' ++ case "$-" in ++ __lmod_sh_dbg=x ++ '[' -n x ']' ++ set +x +Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output +Shell debugging restarted ++ unset __lmod_sh_dbg ++ return 0 ++ module load Anaconda3/2023.03 ++ '[' -z '' ']' ++ case "$-" in ++ __lmod_sh_dbg=x ++ '[' -n x ']' ++ set +x +Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output +Shell debugging restarted ++ unset __lmod_sh_dbg ++ return 0 ++ source /camp/home/johnsoe/.bashrc +++ '[' '' = yes ']' +++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' ++++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.bash hook +++ __conda_setup='export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'' + +# Copyright (C) 2012 Anaconda, Inc +# SPDX-License-Identifier: BSD-3-Clause +__conda_exe() ( + "$CONDA_EXE" $_CE_M $_CE_CONDA "$@" +) + +__conda_hashr() { + if [ -n "${ZSH_VERSION:+x}" ]; then + \rehash + elif [ -n "${POSH_VERSION:+x}" ]; then + : # pass + else + \hash -r + fi +} + +__conda_activate() { + if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then + # Handle transition from shell activated with conda <= 4.3 to a subsequent activation + # after conda updated to >= 4.4. See issue #6173. + PS1="$CONDA_PS1_BACKUP" + \unset CONDA_PS1_BACKUP + fi + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return + \eval "$ask_conda" + __conda_hashr +} + +__conda_reactivate() { + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return + \eval "$ask_conda" + __conda_hashr +} + +conda() { + \local cmd="${1-__missing__}" + case "$cmd" in + activate|deactivate) + __conda_activate "$@" + ;; + install|update|upgrade|remove|uninstall) + __conda_exe "$@" || \return + __conda_reactivate + ;; + *) + __conda_exe "$@" + ;; + esac +} + +if [ -z "${CONDA_SHLVL+x}" ]; then + \export CONDA_SHLVL=0 + # In dev-mode CONDA_EXE is python.exe and on Windows + # it is in a different relative location to condabin. + if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then + PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}" + else + PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}" + fi + \export PATH + + # We'\''re not allowing PS1 to be unbound. It must at least be set. + # However, we'\''re not exporting it, which can cause problems when starting a second shell + # via a first shell (i.e. starting zsh from bash). + if [ -z "${PS1+x}" ]; then + PS1= + fi +fi + +conda activate base' +++ '[' 0 -eq 0 ']' +++ eval 'export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'' + +# Copyright (C) 2012 Anaconda, Inc +# SPDX-License-Identifier: BSD-3-Clause +__conda_exe() ( + "$CONDA_EXE" $_CE_M $_CE_CONDA "$@" +) + +__conda_hashr() { + if [ -n "${ZSH_VERSION:+x}" ]; then + \rehash + elif [ -n "${POSH_VERSION:+x}" ]; then + : # pass + else + \hash -r + fi +} + +__conda_activate() { + if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then + # Handle transition from shell activated with conda <= 4.3 to a subsequent activation + # after conda updated to >= 4.4. See issue #6173. + PS1="$CONDA_PS1_BACKUP" + \unset CONDA_PS1_BACKUP + fi + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return + \eval "$ask_conda" + __conda_hashr +} + +__conda_reactivate() { + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return + \eval "$ask_conda" + __conda_hashr +} + +conda() { + \local cmd="${1-__missing__}" + case "$cmd" in + activate|deactivate) + __conda_activate "$@" + ;; + install|update|upgrade|remove|uninstall) + __conda_exe "$@" || \return + __conda_reactivate + ;; + *) + __conda_exe "$@" + ;; + esac +} + +if [ -z "${CONDA_SHLVL+x}" ]; then + \export CONDA_SHLVL=0 + # In dev-mode CONDA_EXE is python.exe and on Windows + # it is in a different relative location to condabin. + if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then + PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}" + else + PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}" + fi + \export PATH + + # We'\''re not allowing PS1 to be unbound. It must at least be set. + # However, we'\''re not exporting it, which can cause problems when starting a second shell + # via a first shell (i.e. starting zsh from bash). + if [ -z "${PS1+x}" ]; then + PS1= + fi +fi + +conda activate base' ++++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda ++++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda ++++ export _CE_M= ++++ _CE_M= ++++ export _CE_CONDA= ++++ _CE_CONDA= ++++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ '[' -z x ']' ++++ conda activate base ++++ local cmd=activate ++++ case "$cmd" in ++++ __conda_activate activate base ++++ '[' -n '' ']' ++++ local ask_conda +++++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++++ __conda_exe shell.posix activate base +++++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate base ++++ ask_conda='PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_SHLVL='\''6'\'' +export CONDA_DEFAULT_ENV='\''base'\'' +export CONDA_PROMPT_MODIFIER='\''(base) '\'' +export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' ++++ eval 'PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_SHLVL='\''6'\'' +export CONDA_DEFAULT_ENV='\''base'\'' +export CONDA_PROMPT_MODIFIER='\''(base) '\'' +export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' +++++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++++ export CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0 +++++ CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0 +++++ export CONDA_SHLVL=6 +++++ CONDA_SHLVL=6 +++++ export CONDA_DEFAULT_ENV=base +++++ CONDA_DEFAULT_ENV=base +++++ export 'CONDA_PROMPT_MODIFIER=(base) ' +++++ CONDA_PROMPT_MODIFIER='(base) ' +++++ export CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev +++++ CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev +++++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++++ export _CE_M= +++++ _CE_M= +++++ export _CE_CONDA= +++++ _CE_CONDA= +++++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python +++++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ __conda_hashr ++++ '[' -n '' ']' ++++ '[' -n '' ']' ++++ hash -r +++ unset __conda_setup ++ conda activate schemist-dev ++ local cmd=activate ++ case "$cmd" in ++ __conda_activate activate schemist-dev ++ '[' -n '' ']' ++ local ask_conda +++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++ __conda_exe shell.posix activate schemist-dev +++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate schemist-dev ++ ask_conda='PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_SHLVL='\''7'\'' +export CONDA_DEFAULT_ENV='\''schemist-dev'\'' +export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\'' +export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' ++ eval 'PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_SHLVL='\''7'\'' +export CONDA_DEFAULT_ENV='\''schemist-dev'\'' +export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\'' +export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' +++ PS1='(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++ export CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev +++ CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev +++ export CONDA_SHLVL=7 +++ CONDA_SHLVL=7 +++ export CONDA_DEFAULT_ENV=schemist-dev +++ CONDA_DEFAULT_ENV=schemist-dev +++ export 'CONDA_PROMPT_MODIFIER=(schemist-dev) ' +++ CONDA_PROMPT_MODIFIER='(schemist-dev) ' +++ export CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0 +++ CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0 +++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++ export _CE_M= +++ _CE_M= +++ export _CE_CONDA= +++ _CE_CONDA= +++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python +++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++ __conda_hashr ++ '[' -n '' ']' ++ '[' -n '' ']' ++ hash -r ++ CHUNK_HEAD_FILE=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz ++ INPUT=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/validation/cyc-pep-6-12mer-70M_09.csv ++ COLUMN=cysteine_to_N_cyclization ++ PREFIX=cyclic_ ++ AWK='1 { print $8, $1, $2, $10, $3 }' ++ '[' -z cysteine_to_N_cyclization ']' ++ '[' -z cyclic_ ']' ++ '[' -z '1 { print $8, $1, $2, $10, $3 }' ']' ++ awk -F, -v OFS=, '1 { print $8, $1, $2, $10, $3 }' ++ cat /dev/fd/63 /nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/validation/cyc-pep-6-12mer-70M_09.csv ++ gzip --best +++ head -n1 +++ zcat /nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz ++ schemist convert -f csv --column cysteine_to_N_cyclization --to id inchikey scaffold mwt clogp tpsa --prefix cyclic_ --options prefix=SCB- +++ tr ' ' , +🚀 Converting between string representations with the following parameters: + subcommand: convert + output: <_io.TextIOWrapper name='' mode='w' encoding='utf-8'> + format: csv + input: <_io.TextIOWrapper name='' mode='r' encoding='utf-8'> + representation: SMILES + column: cysteine_to_N_cyclization + prefix: cyclic_ + to: ['id', 'inchikey', 'scaffold', 'mwt', 'clogp', 'tpsa'] + options: ['prefix=SCB-'] + func: + 0it [00:00, ?it/s] 1it [00:08, 8.74s/it] 2it [00:17, 8.76s/it] 3it [00:26, 8.79s/it] 4it [00:35, 8.80s/it] 5it [00:43, 8.81s/it] 6it [00:52, 8.80s/it] 7it [01:01, 8.75s/it] 8it [01:10, 8.73s/it] 9it [01:18, 8.76s/it] 10it [01:27, 8.76s/it] 11it [01:36, 8.77s/it] 12it [01:45, 8.80s/it] 13it [01:54, 8.80s/it] 14it [02:02, 8.77s/it] 15it [02:11, 8.77s/it] 16it [02:20, 8.75s/it] 17it [02:29, 8.75s/it] 18it [02:37, 8.79s/it] 19it [02:46, 8.79s/it] 20it [02:55, 8.79s/it] 21it [03:04, 8.79s/it] 22it [03:13, 8.77s/it] 23it [03:21, 8.78s/it] 24it [03:30, 8.78s/it] 25it [03:39, 8.79s/it] 26it [03:48, 8.75s/it] 27it [03:56, 8.73s/it] 28it [04:05, 8.73s/it] 29it [04:14, 8.74s/it] 30it [04:23, 8.77s/it] 31it [04:31, 8.76s/it] 32it [04:40, 8.76s/it] 33it [04:49, 8.79s/it] 34it [04:58, 8.77s/it] 35it [05:06, 8.77s/it] 36it [05:15, 8.80s/it] 37it [05:24, 8.81s/it] 38it [05:33, 8.81s/it] 39it [05:42, 8.79s/it] 40it [05:51, 8.81s/it] 41it [05:59, 8.81s/it] 42it [06:08, 8.82s/it] 43it [06:17, 8.83s/it] 44it [06:26, 8.80s/it] 45it [06:35, 8.80s/it] 46it [06:43, 8.77s/it] 47it [06:52, 8.75s/it] 48it [07:01, 8.77s/it] 49it [07:10, 8.76s/it] 50it [07:18, 8.75s/it] 51it [07:27, 8.72s/it] 52it [07:36, 8.72s/it] 53it [07:44, 8.73s/it] 54it [07:53, 8.72s/it] 55it [08:02, 8.73s/it] 56it [08:11, 8.74s/it] 57it [08:19, 8.72s/it] 58it [08:28, 8.71s/it] 59it [08:37, 8.69s/it] 60it [08:45, 8.68s/it] 61it [08:54, 8.73s/it] 62it [09:03, 8.75s/it] 63it [09:12, 8.75s/it] 64it [09:20, 8.72s/it] 65it [09:29, 8.72s/it] 66it [09:38, 8.74s/it] 67it [09:47, 8.74s/it] 68it [09:55, 8.78s/it] 69it [10:04, 8.79s/it] 70it [10:13, 8.78s/it] 71it [10:22, 8.78s/it] 72it [10:31, 8.77s/it] 73it [10:39, 8.76s/it] 74it [10:48, 8.74s/it] 75it [10:57, 8.74s/it] 76it [11:06, 8.77s/it] 77it [11:14, 8.79s/it] 78it [11:23, 8.79s/it] 79it [11:32, 8.77s/it] 80it [11:41, 8.72s/it] 81it [11:49, 8.72s/it] 82it [11:58, 8.75s/it] 83it [12:07, 8.74s/it] 84it [12:16, 8.75s/it] 85it [12:24, 8.75s/it] 86it [12:33, 8.74s/it] 87it [12:42, 8.71s/it] 88it [12:50, 8.72s/it] 89it [12:59, 8.74s/it] 90it [13:08, 8.75s/it] 91it [13:17, 8.76s/it] 92it [13:25, 8.75s/it] 93it [13:34, 8.73s/it] 94it [13:43, 8.74s/it] 95it [13:52, 8.74s/it] 96it [14:00, 8.75s/it] 97it [14:09, 8.73s/it] 98it [14:18, 8.74s/it] 99it [14:27, 8.73s/it] 100it [14:35, 8.74s/it] 101it [14:44, 8.75s/it] 102it [14:53, 8.75s/it] 103it [15:02, 8.74s/it] 104it [15:10, 8.73s/it] 105it [15:19, 8.74s/it] 106it [15:28, 8.75s/it] 107it [15:37, 8.74s/it] 108it [15:45, 8.76s/it] 109it [15:54, 8.75s/it] 110it [16:03, 8.75s/it] 111it [16:11, 8.72s/it] 112it [16:20, 8.72s/it] 113it [16:29, 8.72s/it] 114it [16:38, 8.74s/it] 115it [16:46, 8.73s/it] 116it [16:55, 8.73s/it] 117it [17:04, 8.71s/it] 118it [17:13, 8.71s/it] 119it [17:21, 8.71s/it] 120it [17:30, 8.71s/it] 121it [17:39, 8.72s/it] 122it [17:47, 8.70s/it] 123it [17:56, 8.69s/it] 124it [18:05, 8.67s/it] 125it [18:13, 8.68s/it] 126it [18:22, 8.69s/it] 127it [18:31, 8.71s/it] 128it [18:39, 8.68s/it] 129it [18:48, 8.69s/it] 130it [18:57, 8.69s/it] 131it [19:06, 8.70s/it] 132it [19:14, 8.70s/it] 133it [19:23, 8.71s/it] 134it [19:32, 8.70s/it] 135it [19:40, 8.70s/it] 136it [19:49, 8.67s/it] 137it [19:58, 8.68s/it] 138it [20:06, 8.69s/it] 139it [20:15, 8.70s/it] 140it [20:24, 8.69s/it] 141it [20:32, 8.69s/it] 142it [20:41, 8.68s/it] 143it [20:50, 8.68s/it] 144it [20:58, 8.69s/it] 145it [21:07, 8.69s/it] 146it [21:16, 8.69s/it] 147it [21:25, 8.68s/it] 148it [21:33, 8.69s/it] 149it [21:42, 8.68s/it] 150it [21:51, 8.68s/it] 151it [21:59, 8.67s/it] 152it [22:08, 8.69s/it] 153it [22:17, 8.68s/it] 154it [22:25, 8.71s/it] 155it [22:34, 8.70s/it] 156it [22:43, 8.70s/it] 157it [22:51, 8.68s/it] 158it [23:00, 8.69s/it] 159it [23:09, 8.69s/it] 160it [23:17, 8.68s/it] 161it [23:26, 8.68s/it] 162it [23:35, 8.70s/it] 163it [23:44, 8.68s/it] 164it [23:52, 8.66s/it] 165it [24:01, 8.66s/it] 166it [24:10, 8.70s/it] 167it [24:18, 8.73s/it] 168it [24:27, 8.72s/it] 169it [24:36, 8.71s/it] 170it [24:44, 8.70s/it] 171it [24:53, 8.70s/it] 172it [25:02, 8.68s/it] 173it [25:10, 8.68s/it] 174it [25:19, 8.68s/it] 175it [25:28, 8.67s/it] 176it [25:36, 8.67s/it] 177it [25:45, 8.68s/it] 178it [25:54, 8.67s/it] 179it [26:02, 8.68s/it] 180it [26:11, 8.66s/it] 181it [26:20, 8.65s/it] 182it [26:28, 8.64s/it] 183it [26:37, 8.65s/it] 184it [26:46, 8.63s/it] 185it [26:54, 8.64s/it] 186it [27:03, 8.64s/it] 187it [27:12, 8.63s/it] 188it [27:20, 8.64s/it] 189it [27:29, 8.64s/it] 190it [27:37, 8.63s/it] 191it [27:46, 8.62s/it] 192it [27:55, 8.61s/it] 193it [28:03, 8.60s/it] 194it [28:12, 8.61s/it] 195it [28:20, 8.61s/it] 196it [28:29, 8.62s/it] 197it [28:38, 8.62s/it] 198it [28:46, 8.64s/it] 199it [28:55, 8.66s/it] 200it [29:04, 8.66s/it] 201it [29:12, 8.66s/it] 202it [29:21, 8.66s/it] 203it [29:30, 8.66s/it] 204it [29:38, 8.66s/it] 205it [29:47, 8.66s/it] 206it [29:56, 8.64s/it] 207it [30:04, 8.65s/it] 208it [30:13, 8.65s/it] 209it [30:22, 8.65s/it] 210it [30:30, 8.66s/it] 211it [30:39, 8.68s/it] 212it [30:48, 8.66s/it] 213it [30:56, 8.65s/it] 214it [31:05, 8.67s/it] 215it [31:14, 8.66s/it] 216it [31:22, 8.67s/it] 217it [31:31, 8.69s/it] 218it [31:40, 8.67s/it] 219it [31:48, 8.67s/it] 220it [31:57, 8.66s/it] 221it [32:06, 8.64s/it] 222it [32:14, 8.65s/it] 223it [32:23, 8.65s/it] 224it [32:32, 8.65s/it] 225it [32:40, 8.65s/it] 226it [32:49, 8.66s/it] 227it [32:58, 8.65s/it] 228it [33:06, 8.66s/it] 229it [33:15, 8.64s/it] 230it [33:23, 8.64s/it] 231it [33:32, 8.63s/it] 232it [33:41, 8.64s/it] 233it [33:49, 8.64s/it] 234it [33:58, 8.65s/it] 235it [34:07, 8.65s/it] 236it [34:15, 8.66s/it] 237it [34:24, 8.65s/it] 238it [34:33, 8.66s/it] 239it [34:41, 8.65s/it] 240it [34:50, 8.66s/it] 241it [34:59, 8.65s/it] 242it [35:07, 8.64s/it] 243it [35:16, 8.64s/it] 244it [35:24, 8.62s/it] 245it [35:33, 8.64s/it] 246it [35:42, 8.62s/it] 247it [35:50, 8.63s/it] 248it [35:59, 8.62s/it] 249it [36:08, 8.62s/it] 250it [36:16, 8.62s/it] 251it [36:25, 8.61s/it] 252it [36:33, 8.61s/it] 253it [36:42, 8.62s/it] 254it [36:51, 8.64s/it] 255it [36:59, 8.64s/it] 256it [37:08, 8.64s/it] 257it [37:17, 8.64s/it] 258it [37:25, 8.62s/it] 259it [37:34, 8.63s/it] 260it [37:42, 8.63s/it] 261it [37:51, 8.64s/it] 262it [38:00, 8.63s/it] 263it [38:08, 8.61s/it] 264it [38:17, 8.61s/it] 265it [38:26, 8.62s/it] 266it [38:34, 8.62s/it] 267it [38:43, 8.62s/it] 268it [38:51, 8.62s/it] 269it [39:00, 8.62s/it] 270it [39:09, 8.63s/it] 271it [39:17, 8.64s/it] 272it [39:26, 8.65s/it] 273it [39:35, 8.64s/it] 274it [39:43, 8.67s/it] 275it [39:52, 8.65s/it] 276it [40:01, 8.66s/it] 277it [40:09, 8.64s/it] 278it [40:18, 8.64s/it] 279it [40:27, 8.63s/it] 280it [40:35, 8.66s/it] 281it [40:44, 8.64s/it] 282it [40:53, 8.65s/it] 283it [41:01, 8.65s/it] 284it [41:10, 8.65s/it] 285it [41:18, 8.64s/it] 286it [41:27, 8.65s/it] 287it [41:36, 8.66s/it] 288it [41:44, 8.67s/it] 289it [41:53, 8.66s/it] 290it [42:02, 8.66s/it] 291it [42:10, 8.64s/it] 292it [42:19, 8.64s/it] 293it [42:28, 8.64s/it] 294it [42:36, 8.63s/it] 295it [42:45, 8.62s/it] 296it [42:53, 8.61s/it] 297it [43:02, 8.64s/it] 298it [43:11, 8.66s/it] 299it [43:20, 8.67s/it] 300it [43:28, 8.66s/it] 301it [43:37, 8.65s/it] 302it [43:45, 8.64s/it] 303it 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9.48s/it] 925it [2:18:21, 9.47s/it] 926it [2:18:30, 9.45s/it] 927it [2:18:40, 9.44s/it] 928it [2:18:49, 9.44s/it] 929it [2:18:59, 9.45s/it] 930it [2:19:08, 9.44s/it] 931it [2:19:17, 9.42s/it] 932it [2:19:27, 9.43s/it] 933it [2:19:36, 9.44s/it] 934it [2:19:46, 9.46s/it] 935it [2:19:55, 9.47s/it] 936it [2:20:05, 9.47s/it] 937it [2:20:14, 9.47s/it] 938it [2:20:24, 9.47s/it] 939it [2:20:33, 9.47s/it] 940it [2:20:43, 9.47s/it] 941it [2:20:52, 9.46s/it] 942it [2:21:01, 9.45s/it] 943it [2:21:11, 9.47s/it] 944it [2:21:20, 9.46s/it] 945it [2:21:30, 9.45s/it] 946it [2:21:39, 9.44s/it] 947it [2:21:49, 9.45s/it] 948it [2:21:58, 9.46s/it] 949it [2:22:08, 9.46s/it] 950it [2:22:17, 9.46s/it] 951it [2:22:27, 9.46s/it] 952it [2:22:36, 9.48s/it] 953it [2:22:46, 9.50s/it] 954it [2:22:55, 9.49s/it] 955it [2:23:05, 9.53s/it] 956it [2:23:14, 9.51s/it] 957it [2:23:24, 9.50s/it] 958it [2:23:33, 9.50s/it] 959it [2:23:43, 9.49s/it] 960it [2:23:52, 9.50s/it] 961it [2:24:02, 9.51s/it] 962it [2:24:11, 9.50s/it] 963it [2:24:21, 9.51s/it] 964it [2:24:30, 9.50s/it] 965it [2:24:40, 9.48s/it] 966it [2:24:49, 9.49s/it] 967it [2:24:59, 9.50s/it] 968it [2:25:08, 9.51s/it] 969it [2:25:18, 9.52s/it] 970it [2:25:27, 9.53s/it] 971it [2:25:37, 9.55s/it] 972it [2:25:46, 9.55s/it] 973it [2:25:56, 9.53s/it] 974it [2:26:05, 9.52s/it] 975it [2:26:15, 9.52s/it] 976it [2:26:24, 9.52s/it] 977it [2:26:34, 9.51s/it] 978it [2:26:44, 9.54s/it] 979it [2:26:53, 9.56s/it] 980it [2:27:03, 9.57s/it] 981it [2:27:12, 9.58s/it] 982it [2:27:22, 9.57s/it] 983it [2:27:31, 9.56s/it] 984it [2:27:41, 9.57s/it] 985it [2:27:51, 9.57s/it] 986it [2:28:00, 9.57s/it] 987it [2:28:10, 9.60s/it] 988it [2:28:19, 9.59s/it] 989it [2:28:29, 9.58s/it] 990it [2:28:39, 9.59s/it] 991it [2:28:48, 9.59s/it] 992it [2:28:58, 9.58s/it] 993it [2:29:07, 9.59s/it] 994it [2:29:17, 9.58s/it] 995it [2:29:26, 9.58s/it] 996it [2:29:36, 9.58s/it] 997it [2:29:46, 9.58s/it] 998it [2:29:55, 9.58s/it] 999it [2:30:05, 9.58s/it] 1000it [2:30:14, 9.60s/it] 1000it [2:30:14, 9.01s/it] +Error counts: + cyclic_id: 0 + cyclic_inchikey: 0 + cyclic_scaffold: 0 + cyclic_mwt: 0 + cyclic_clogp: 0 + cyclic_tpsa: 0 +⏰ Completed process in 2:30:34.532964 ++ rm /nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/validation/cyc-pep-6-12mer-70M_09.csv diff --git a/validation/cyc-pep-6-12mer-70M_10.csv.gz b/validation/cyc-pep-6-12mer-70M_10.csv.gz index 0e51e9011210b66a79f41c53b61307f75d37afcf..cf4a71a739cdd825de5d406c2aafd52d9a1d1d4b 100644 --- a/validation/cyc-pep-6-12mer-70M_10.csv.gz +++ b/validation/cyc-pep-6-12mer-70M_10.csv.gz @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:6e1ea027c3a229da722d8be1a0804ee3a6491636431fb699e6a50de984f0f484 -size 54503820 +oid sha256:db88872f4a1e7bd4083a1b0138beda8f3856c2d1e33c031f33b5f5e01d57feac +size 107791989 diff --git a/validation/cyc-pep-6-12mer-70M_10.log b/validation/cyc-pep-6-12mer-70M_10.log new file mode 100644 index 0000000000000000000000000000000000000000..9521d49e335a02c0d86f9b69b3e92d24ba366913 --- /dev/null +++ b/validation/cyc-pep-6-12mer-70M_10.log @@ -0,0 +1,337 @@ ++ module purge ++ '[' -z '' ']' ++ case "$-" in ++ __lmod_sh_dbg=x ++ '[' -n x ']' ++ set +x +Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output +Shell debugging restarted ++ unset __lmod_sh_dbg ++ return 0 ++ module load Anaconda3/2023.03 ++ '[' -z '' ']' ++ case "$-" in ++ __lmod_sh_dbg=x ++ '[' -n x ']' ++ set +x +Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output +Shell debugging restarted ++ unset __lmod_sh_dbg ++ return 0 ++ source /camp/home/johnsoe/.bashrc +++ '[' '' = yes ']' +++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' ++++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.bash hook +++ __conda_setup='export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'' + +# Copyright (C) 2012 Anaconda, Inc +# SPDX-License-Identifier: BSD-3-Clause +__conda_exe() ( + "$CONDA_EXE" $_CE_M $_CE_CONDA "$@" +) + +__conda_hashr() { + if [ -n "${ZSH_VERSION:+x}" ]; then + \rehash + elif [ -n "${POSH_VERSION:+x}" ]; then + : # pass + else + \hash -r + fi +} + +__conda_activate() { + if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then + # Handle transition from shell activated with conda <= 4.3 to a subsequent activation + # after conda updated to >= 4.4. See issue #6173. + PS1="$CONDA_PS1_BACKUP" + \unset CONDA_PS1_BACKUP + fi + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return + \eval "$ask_conda" + __conda_hashr +} + +__conda_reactivate() { + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return + \eval "$ask_conda" + __conda_hashr +} + +conda() { + \local cmd="${1-__missing__}" + case "$cmd" in + activate|deactivate) + __conda_activate "$@" + ;; + install|update|upgrade|remove|uninstall) + __conda_exe "$@" || \return + __conda_reactivate + ;; + *) + __conda_exe "$@" + ;; + esac +} + +if [ -z "${CONDA_SHLVL+x}" ]; then + \export CONDA_SHLVL=0 + # In dev-mode CONDA_EXE is python.exe and on Windows + # it is in a different relative location to condabin. + if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then + PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}" + else + PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}" + fi + \export PATH + + # We'\''re not allowing PS1 to be unbound. It must at least be set. + # However, we'\''re not exporting it, which can cause problems when starting a second shell + # via a first shell (i.e. starting zsh from bash). + if [ -z "${PS1+x}" ]; then + PS1= + fi +fi + +conda activate base' +++ '[' 0 -eq 0 ']' +++ eval 'export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'' + +# Copyright (C) 2012 Anaconda, Inc +# SPDX-License-Identifier: BSD-3-Clause +__conda_exe() ( + "$CONDA_EXE" $_CE_M $_CE_CONDA "$@" +) + +__conda_hashr() { + if [ -n "${ZSH_VERSION:+x}" ]; then + \rehash + elif [ -n "${POSH_VERSION:+x}" ]; then + : # pass + else + \hash -r + fi +} + +__conda_activate() { + if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then + # Handle transition from shell activated with conda <= 4.3 to a subsequent activation + # after conda updated to >= 4.4. See issue #6173. + PS1="$CONDA_PS1_BACKUP" + \unset CONDA_PS1_BACKUP + fi + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return + \eval "$ask_conda" + __conda_hashr +} + +__conda_reactivate() { + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return + \eval "$ask_conda" + __conda_hashr +} + +conda() { + \local cmd="${1-__missing__}" + case "$cmd" in + activate|deactivate) + __conda_activate "$@" + ;; + install|update|upgrade|remove|uninstall) + __conda_exe "$@" || \return + __conda_reactivate + ;; + *) + __conda_exe "$@" + ;; + esac +} + +if [ -z "${CONDA_SHLVL+x}" ]; then + \export CONDA_SHLVL=0 + # In dev-mode CONDA_EXE is python.exe and on Windows + # it is in a different relative location to condabin. + if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then + PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}" + else + PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}" + fi + \export PATH + + # We'\''re not allowing PS1 to be unbound. It must at least be set. + # However, we'\''re not exporting it, which can cause problems when starting a second shell + # via a first shell (i.e. starting zsh from bash). + if [ -z "${PS1+x}" ]; then + PS1= + fi +fi + +conda activate base' ++++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda ++++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda ++++ export _CE_M= ++++ _CE_M= ++++ export _CE_CONDA= ++++ _CE_CONDA= ++++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ '[' -z x ']' ++++ conda activate base ++++ local cmd=activate ++++ case "$cmd" in ++++ __conda_activate activate base ++++ '[' -n '' ']' ++++ local ask_conda +++++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++++ __conda_exe shell.posix activate base +++++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate base ++++ ask_conda='PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_SHLVL='\''6'\'' +export CONDA_DEFAULT_ENV='\''base'\'' +export CONDA_PROMPT_MODIFIER='\''(base) '\'' +export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' ++++ eval 'PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_SHLVL='\''6'\'' +export CONDA_DEFAULT_ENV='\''base'\'' +export CONDA_PROMPT_MODIFIER='\''(base) '\'' +export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' +++++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++++ export CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0 +++++ CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0 +++++ export CONDA_SHLVL=6 +++++ CONDA_SHLVL=6 +++++ export CONDA_DEFAULT_ENV=base +++++ CONDA_DEFAULT_ENV=base +++++ export 'CONDA_PROMPT_MODIFIER=(base) ' +++++ CONDA_PROMPT_MODIFIER='(base) ' +++++ export CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev +++++ CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev +++++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++++ export _CE_M= +++++ _CE_M= +++++ export _CE_CONDA= +++++ _CE_CONDA= +++++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python +++++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ __conda_hashr ++++ '[' -n '' ']' ++++ '[' -n '' ']' ++++ hash -r +++ unset __conda_setup ++ conda activate schemist-dev ++ local cmd=activate ++ case "$cmd" in ++ __conda_activate activate schemist-dev ++ '[' -n '' ']' ++ local ask_conda +++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++ __conda_exe shell.posix activate schemist-dev +++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate schemist-dev ++ ask_conda='PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_SHLVL='\''7'\'' +export CONDA_DEFAULT_ENV='\''schemist-dev'\'' +export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\'' +export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' ++ eval 'PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_SHLVL='\''7'\'' +export CONDA_DEFAULT_ENV='\''schemist-dev'\'' +export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\'' +export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' +++ PS1='(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++ export CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev +++ CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev +++ export CONDA_SHLVL=7 +++ CONDA_SHLVL=7 +++ export CONDA_DEFAULT_ENV=schemist-dev +++ CONDA_DEFAULT_ENV=schemist-dev +++ export 'CONDA_PROMPT_MODIFIER=(schemist-dev) ' +++ CONDA_PROMPT_MODIFIER='(schemist-dev) ' +++ export CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0 +++ CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0 +++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++ export _CE_M= +++ _CE_M= +++ export _CE_CONDA= +++ _CE_CONDA= +++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python +++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++ __conda_hashr ++ '[' -n '' ']' ++ '[' -n '' ']' ++ hash -r ++ CHUNK_HEAD_FILE=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz ++ INPUT=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/validation/cyc-pep-6-12mer-70M_10.csv ++ COLUMN=cysteine_to_N_cyclization ++ PREFIX=cyclic_ ++ AWK='1 { print $8, $1, $2, $10, $3 }' ++ '[' -z cysteine_to_N_cyclization ']' ++ '[' -z cyclic_ ']' ++ '[' -z '1 { print $8, $1, $2, $10, $3 }' ']' ++ cat /dev/fd/63 /nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/validation/cyc-pep-6-12mer-70M_10.csv ++ schemist convert -f csv --column cysteine_to_N_cyclization --to id inchikey scaffold mwt clogp tpsa --prefix cyclic_ --options prefix=SCB- ++ gzip --best +++ zcat /nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz ++ awk -F, -v OFS=, '1 { print $8, $1, $2, $10, $3 }' +++ head -n1 +++ tr ' ' , +🚀 Converting between string representations with the following parameters: + subcommand: convert + output: <_io.TextIOWrapper name='' mode='w' encoding='utf-8'> + format: csv + input: <_io.TextIOWrapper name='' mode='r' encoding='utf-8'> + representation: SMILES + column: cysteine_to_N_cyclization + prefix: cyclic_ + to: ['id', 'inchikey', 'scaffold', 'mwt', 'clogp', 'tpsa'] + options: ['prefix=SCB-'] + func: + 0it [00:00, ?it/s] 1it [00:09, 9.91s/it] 2it [00:19, 9.86s/it] 3it [00:29, 9.80s/it] 4it [00:39, 9.82s/it] 5it [00:49, 9.82s/it] 6it 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[2:36:34, 9.65s/it] 951it [2:36:44, 9.67s/it] 952it [2:36:53, 9.67s/it] 953it [2:37:03, 9.68s/it] 954it [2:37:13, 9.69s/it] 955it [2:37:22, 9.68s/it] 956it [2:37:32, 9.67s/it] 957it [2:37:42, 9.68s/it] 958it [2:37:51, 9.66s/it] 959it [2:38:01, 9.66s/it] 960it [2:38:11, 9.68s/it] 961it [2:38:20, 9.68s/it] 962it [2:38:30, 9.69s/it] 963it [2:38:40, 9.69s/it] 964it [2:38:49, 9.68s/it] 965it [2:38:59, 9.66s/it] 966it [2:39:09, 9.65s/it] 967it [2:39:18, 9.64s/it] 968it [2:39:28, 9.66s/it] 969it [2:39:38, 9.66s/it] 970it [2:39:47, 9.68s/it] 971it [2:39:57, 9.68s/it] 972it [2:40:07, 9.70s/it] 973it [2:40:16, 9.70s/it] 974it [2:40:26, 9.70s/it] 975it [2:40:36, 9.70s/it] 976it [2:40:46, 9.70s/it] 977it [2:40:55, 9.69s/it] 978it [2:41:05, 9.68s/it] 979it [2:41:15, 9.69s/it] 980it [2:41:24, 9.73s/it] 981it [2:41:34, 9.79s/it] 982it [2:41:44, 9.82s/it] 983it [2:41:54, 9.87s/it] 984it [2:42:04, 9.87s/it] 985it [2:42:14, 9.89s/it] 986it [2:42:24, 9.89s/it] 987it [2:42:34, 9.90s/it] 988it [2:42:44, 9.89s/it] 989it [2:42:54, 9.91s/it] 990it [2:43:04, 9.90s/it] 991it [2:43:14, 9.90s/it] 992it [2:43:23, 9.86s/it] 993it [2:43:33, 9.85s/it] 994it [2:43:43, 9.83s/it] 995it [2:43:53, 9.83s/it] 996it [2:44:03, 9.83s/it] 997it [2:44:13, 9.90s/it] 998it [2:44:22, 9.87s/it] 999it [2:44:32, 9.80s/it] 1000it [2:44:42, 9.80s/it] 1000it [2:44:42, 9.88s/it] +Error counts: + cyclic_id: 0 + cyclic_inchikey: 0 + cyclic_scaffold: 0 + cyclic_mwt: 0 + cyclic_clogp: 0 + cyclic_tpsa: 0 +⏰ Completed process in 2:45:04.046273 ++ rm /nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/validation/cyc-pep-6-12mer-70M_10.csv diff --git a/validation/cyc-pep-6-12mer-70M_11.csv.gz b/validation/cyc-pep-6-12mer-70M_11.csv.gz index 677ef9f8c203fdb7087ec62f13b71cf3acf27855..081e3b0a990b2add75921e1ee50837cb5d5c707d 100644 --- a/validation/cyc-pep-6-12mer-70M_11.csv.gz +++ b/validation/cyc-pep-6-12mer-70M_11.csv.gz @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:bc39110ec6cf2da84de371f511b4cbb78ec4ac2fec008e473b5dffb06fc2325d -size 18534854 +oid sha256:532bb8edee0f873737cef34d83b99582789b1d6cbe854a07eb8ec565982b8b6e +size 36662479 diff --git a/validation/cyc-pep-6-12mer-70M_11.log b/validation/cyc-pep-6-12mer-70M_11.log new file mode 100644 index 0000000000000000000000000000000000000000..0898c5d0322207c6d782da09c8e9cd8e8a296af0 --- /dev/null +++ b/validation/cyc-pep-6-12mer-70M_11.log @@ -0,0 +1,337 @@ ++ module purge ++ '[' -z '' ']' ++ case "$-" in ++ __lmod_sh_dbg=x ++ '[' -n x ']' ++ set +x +Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output +Shell debugging restarted ++ unset __lmod_sh_dbg ++ return 0 ++ module load Anaconda3/2023.03 ++ '[' -z '' ']' ++ case "$-" in ++ __lmod_sh_dbg=x ++ '[' -n x ']' ++ set +x +Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output +Shell debugging restarted ++ unset __lmod_sh_dbg ++ return 0 ++ source /camp/home/johnsoe/.bashrc +++ '[' '' = yes ']' +++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' ++++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.bash hook +++ __conda_setup='export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'' + +# Copyright (C) 2012 Anaconda, Inc +# SPDX-License-Identifier: BSD-3-Clause +__conda_exe() ( + "$CONDA_EXE" $_CE_M $_CE_CONDA "$@" +) + +__conda_hashr() { + if [ -n "${ZSH_VERSION:+x}" ]; then + \rehash + elif [ -n "${POSH_VERSION:+x}" ]; then + : # pass + else + \hash -r + fi +} + +__conda_activate() { + if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then + # Handle transition from shell activated with conda <= 4.3 to a subsequent activation + # after conda updated to >= 4.4. See issue #6173. + PS1="$CONDA_PS1_BACKUP" + \unset CONDA_PS1_BACKUP + fi + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return + \eval "$ask_conda" + __conda_hashr +} + +__conda_reactivate() { + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return + \eval "$ask_conda" + __conda_hashr +} + +conda() { + \local cmd="${1-__missing__}" + case "$cmd" in + activate|deactivate) + __conda_activate "$@" + ;; + install|update|upgrade|remove|uninstall) + __conda_exe "$@" || \return + __conda_reactivate + ;; + *) + __conda_exe "$@" + ;; + esac +} + +if [ -z "${CONDA_SHLVL+x}" ]; then + \export CONDA_SHLVL=0 + # In dev-mode CONDA_EXE is python.exe and on Windows + # it is in a different relative location to condabin. + if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then + PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}" + else + PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}" + fi + \export PATH + + # We'\''re not allowing PS1 to be unbound. It must at least be set. + # However, we'\''re not exporting it, which can cause problems when starting a second shell + # via a first shell (i.e. starting zsh from bash). + if [ -z "${PS1+x}" ]; then + PS1= + fi +fi + +conda activate base' +++ '[' 0 -eq 0 ']' +++ eval 'export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'' + +# Copyright (C) 2012 Anaconda, Inc +# SPDX-License-Identifier: BSD-3-Clause +__conda_exe() ( + "$CONDA_EXE" $_CE_M $_CE_CONDA "$@" +) + +__conda_hashr() { + if [ -n "${ZSH_VERSION:+x}" ]; then + \rehash + elif [ -n "${POSH_VERSION:+x}" ]; then + : # pass + else + \hash -r + fi +} + +__conda_activate() { + if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then + # Handle transition from shell activated with conda <= 4.3 to a subsequent activation + # after conda updated to >= 4.4. See issue #6173. + PS1="$CONDA_PS1_BACKUP" + \unset CONDA_PS1_BACKUP + fi + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return + \eval "$ask_conda" + __conda_hashr +} + +__conda_reactivate() { + \local ask_conda + ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return + \eval "$ask_conda" + __conda_hashr +} + +conda() { + \local cmd="${1-__missing__}" + case "$cmd" in + activate|deactivate) + __conda_activate "$@" + ;; + install|update|upgrade|remove|uninstall) + __conda_exe "$@" || \return + __conda_reactivate + ;; + *) + __conda_exe "$@" + ;; + esac +} + +if [ -z "${CONDA_SHLVL+x}" ]; then + \export CONDA_SHLVL=0 + # In dev-mode CONDA_EXE is python.exe and on Windows + # it is in a different relative location to condabin. + if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then + PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}" + else + PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}" + fi + \export PATH + + # We'\''re not allowing PS1 to be unbound. It must at least be set. + # However, we'\''re not exporting it, which can cause problems when starting a second shell + # via a first shell (i.e. starting zsh from bash). + if [ -z "${PS1+x}" ]; then + PS1= + fi +fi + +conda activate base' ++++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda ++++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda ++++ export _CE_M= ++++ _CE_M= ++++ export _CE_CONDA= ++++ _CE_CONDA= ++++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ '[' -z x ']' ++++ conda activate base ++++ local cmd=activate ++++ case "$cmd" in ++++ __conda_activate activate base ++++ '[' -n '' ']' ++++ local ask_conda +++++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++++ __conda_exe shell.posix activate base +++++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate base ++++ ask_conda='PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_SHLVL='\''6'\'' +export CONDA_DEFAULT_ENV='\''base'\'' +export CONDA_PROMPT_MODIFIER='\''(base) '\'' +export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' ++++ eval 'PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_SHLVL='\''6'\'' +export CONDA_DEFAULT_ENV='\''base'\'' +export CONDA_PROMPT_MODIFIER='\''(base) '\'' +export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' +++++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++++ export CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0 +++++ CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0 +++++ export CONDA_SHLVL=6 +++++ CONDA_SHLVL=6 +++++ export CONDA_DEFAULT_ENV=base +++++ CONDA_DEFAULT_ENV=base +++++ export 'CONDA_PROMPT_MODIFIER=(base) ' +++++ CONDA_PROMPT_MODIFIER='(base) ' +++++ export CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev +++++ CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev +++++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++++ export _CE_M= +++++ _CE_M= +++++ export _CE_CONDA= +++++ _CE_CONDA= +++++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python +++++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++++ __conda_hashr ++++ '[' -n '' ']' ++++ '[' -n '' ']' ++++ hash -r +++ unset __conda_setup ++ conda activate schemist-dev ++ local cmd=activate ++ case "$cmd" in ++ __conda_activate activate schemist-dev ++ '[' -n '' ']' ++ local ask_conda +++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++ __conda_exe shell.posix activate schemist-dev +++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate schemist-dev ++ ask_conda='PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_SHLVL='\''7'\'' +export CONDA_DEFAULT_ENV='\''schemist-dev'\'' +export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\'' +export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' ++ eval 'PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\'' +export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\'' +export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\'' +export CONDA_SHLVL='\''7'\'' +export CONDA_DEFAULT_ENV='\''schemist-dev'\'' +export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\'' +export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\'' +export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\'' +export _CE_M='\'''\'' +export _CE_CONDA='\'''\'' +export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''' +++ PS1='(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ ' +++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin +++ export CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev +++ CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev +++ export CONDA_SHLVL=7 +++ CONDA_SHLVL=7 +++ export CONDA_DEFAULT_ENV=schemist-dev +++ CONDA_DEFAULT_ENV=schemist-dev +++ export 'CONDA_PROMPT_MODIFIER=(schemist-dev) ' +++ CONDA_PROMPT_MODIFIER='(schemist-dev) ' +++ export CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0 +++ CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0 +++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda +++ export _CE_M= +++ _CE_M= +++ export _CE_CONDA= +++ _CE_CONDA= +++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python +++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python ++ __conda_hashr ++ '[' -n '' ']' ++ '[' -n '' ']' ++ hash -r ++ CHUNK_HEAD_FILE=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz ++ INPUT=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/validation/cyc-pep-6-12mer-70M_11.csv ++ COLUMN=cysteine_to_N_cyclization ++ PREFIX=cyclic_ ++ AWK='1 { print $8, $1, $2, $10, $3 }' ++ '[' -z cysteine_to_N_cyclization ']' ++ '[' -z cyclic_ ']' ++ '[' -z '1 { print $8, $1, $2, $10, $3 }' ']' ++ cat /dev/fd/63 /nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/validation/cyc-pep-6-12mer-70M_11.csv ++ awk -F, -v OFS=, '1 { print $8, $1, $2, $10, $3 }' +++ zcat /nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz ++ schemist convert -f csv --column cysteine_to_N_cyclization --to id inchikey scaffold mwt clogp tpsa --prefix cyclic_ --options prefix=SCB- +++ head -n1 ++ gzip --best +++ tr ' ' , +🚀 Converting between string representations with the following parameters: + subcommand: convert + output: <_io.TextIOWrapper name='' mode='w' encoding='utf-8'> + format: csv + input: <_io.TextIOWrapper name='' mode='r' encoding='utf-8'> + representation: SMILES + column: cysteine_to_N_cyclization + prefix: cyclic_ + to: ['id', 'inchikey', 'scaffold', 'mwt', 'clogp', 'tpsa'] + options: ['prefix=SCB-'] + func: + 0it [00:00, ?it/s] 1it [00:09, 9.55s/it] 2it [00:19, 9.54s/it] 3it [00:28, 9.57s/it] 4it [00:38, 9.58s/it] 5it [00:47, 9.59s/it] 6it [00:57, 9.61s/it] 7it [01:07, 9.59s/it] 8it [01:16, 9.55s/it] 9it [01:26, 9.54s/it] 10it [01:35, 9.53s/it] 11it [01:45, 9.54s/it] 12it [01:54, 9.55s/it] 13it [02:04, 9.56s/it] 14it [02:13, 9.54s/it] 15it [02:23, 9.52s/it] 16it [02:32, 9.49s/it] 17it [02:42, 9.50s/it] 18it [02:51, 9.53s/it] 19it [03:01, 9.55s/it] 20it [03:10, 9.56s/it] 21it [03:20, 9.54s/it] 22it [03:29, 9.52s/it] 23it [03:39, 9.52s/it] 24it [03:48, 9.51s/it] 25it [03:58, 9.53s/it] 26it [04:07, 9.50s/it] 27it [04:17, 9.52s/it] 28it [04:27, 9.55s/it] 29it [04:36, 9.53s/it] 30it [04:46, 9.54s/it] 31it [04:55, 9.55s/it] 32it [05:05, 9.54s/it] 33it [05:14, 9.55s/it] 34it [05:24, 9.55s/it] 35it [05:33, 9.56s/it] 36it [05:43, 9.53s/it] 37it [05:52, 9.51s/it] 38it [06:02, 9.51s/it] 39it [06:11, 9.51s/it] 40it [06:21, 9.52s/it] 41it [06:30, 9.51s/it] 42it [06:40, 9.53s/it] 43it [06:50, 9.53s/it] 44it [06:59, 9.53s/it] 45it [07:09, 9.52s/it] 46it [07:18, 9.53s/it] 47it [07:28, 9.54s/it] 48it [07:37, 9.57s/it] 49it [07:47, 9.57s/it] 50it [07:57, 9.59s/it] 51it [08:06, 9.58s/it] 52it [08:16, 9.57s/it] 53it [08:25, 9.56s/it] 54it [08:35, 9.54s/it] 55it [08:44, 9.55s/it] 56it [08:54, 9.54s/it] 57it [09:03, 9.55s/it] 58it [09:13, 9.54s/it] 59it [09:22, 9.54s/it] 60it [09:32, 9.53s/it] 61it [09:42, 9.57s/it] 62it [09:51, 9.57s/it] 63it [10:01, 9.56s/it] 64it [10:10, 9.56s/it] 65it [10:20, 9.57s/it] 66it [10:29, 9.56s/it] 67it [10:39, 9.53s/it] 68it [10:48, 9.56s/it] 69it [10:58, 9.58s/it] 70it [11:08, 9.58s/it] 71it [11:17, 9.59s/it] 72it [11:27, 9.59s/it] 73it [11:36, 9.59s/it] 74it [11:46, 9.56s/it] 75it [11:55, 9.54s/it] 76it [12:05, 9.53s/it] 77it [12:15, 9.57s/it] 78it [12:24, 9.57s/it] 79it [12:34, 9.57s/it] 80it [12:43, 9.57s/it] 81it [12:53, 9.57s/it] 82it [13:03, 9.58s/it] 83it [13:12, 9.57s/it] 84it [13:22, 9.55s/it] 85it [13:31, 9.54s/it] 86it [13:41, 9.56s/it] 87it [13:50, 9.57s/it] 88it [14:00, 9.56s/it] 89it [14:09, 9.55s/it] 90it [14:19, 9.56s/it] 91it [14:28, 9.55s/it] 92it [14:38, 9.54s/it] 93it [14:48, 9.56s/it] 94it [14:57, 9.55s/it] 95it [15:07, 9.56s/it] 96it [15:16, 9.56s/it] 97it [15:26, 9.57s/it] 98it [15:35, 9.58s/it] 99it [15:45, 9.55s/it] 100it [15:55, 9.58s/it] 101it [16:04, 9.60s/it] 102it [16:14, 9.60s/it] 103it [16:23, 9.58s/it] 104it [16:33, 9.58s/it] 105it [16:43, 9.58s/it] 106it [16:52, 9.55s/it] 107it [17:02, 9.56s/it] 108it [17:11, 9.58s/it] 109it [17:21, 9.57s/it] 110it [17:30, 9.56s/it] 111it [17:40, 9.55s/it] 112it [17:49, 9.56s/it] 113it [17:59, 9.52s/it] 114it [18:08, 9.54s/it] 115it [18:18, 9.54s/it] 116it [18:28, 9.56s/it] 117it [18:37, 9.56s/it] 118it [18:47, 9.56s/it] 119it [18:56, 9.53s/it] 120it [19:06, 9.54s/it] 121it [19:15, 9.55s/it] 122it [19:25, 9.59s/it] 123it [19:34, 9.56s/it] 124it [19:44, 9.56s/it] 125it [19:54, 9.57s/it] 126it [20:03, 9.56s/it] 127it [20:13, 9.56s/it] 128it [20:22, 9.55s/it] 129it [20:32, 9.55s/it] 130it [20:41, 9.54s/it] 131it [20:51, 9.54s/it] 132it [21:00, 9.54s/it] 133it [21:10, 9.54s/it] 134it [21:20, 9.56s/it] 135it [21:29, 9.58s/it] 136it [21:39, 9.56s/it] 137it [21:48, 9.54s/it] 138it [21:58, 9.57s/it] 139it [22:07, 9.57s/it] 140it [22:17, 9.57s/it] 141it [22:26, 9.56s/it] 142it [22:36, 9.54s/it] 143it [22:46, 9.54s/it] 144it [22:55, 9.54s/it] 145it [23:05, 9.52s/it] 146it [23:14, 9.51s/it] 147it [23:24, 9.52s/it] 148it [23:33, 9.52s/it] 149it [23:43, 9.52s/it] 150it [23:52, 9.54s/it] 151it [24:02, 9.53s/it] 152it [24:11, 9.52s/it] 153it [24:21, 9.51s/it] 154it [24:30, 9.51s/it] 155it [24:40, 9.53s/it] 156it [24:49, 9.52s/it] 157it [24:59, 9.52s/it] 158it [25:08, 9.54s/it] 159it [25:18, 9.55s/it] 160it [25:28, 9.56s/it] 161it [25:37, 9.58s/it] 162it [25:47, 9.58s/it] 163it [25:56, 9.56s/it] 164it [26:06, 9.57s/it] 165it [26:15, 9.57s/it] 166it [26:25, 9.56s/it] 167it [26:35, 9.58s/it] 168it [26:44, 9.59s/it] 169it [26:54, 9.57s/it] 170it [27:03, 9.56s/it] 171it [27:13, 9.57s/it] 172it [27:22, 9.56s/it] 173it [27:32, 9.55s/it] 174it [27:41, 9.56s/it] 175it [27:51, 9.55s/it] 176it [28:01, 9.57s/it] 177it [28:10, 9.55s/it] 178it [28:20, 9.59s/it] 179it [28:29, 9.57s/it] 180it [28:39, 9.56s/it] 181it [28:48, 9.54s/it] 182it [28:58, 9.56s/it] 183it [29:08, 9.56s/it] 184it [29:17, 9.56s/it] 185it [29:27, 9.57s/it] 186it [29:36, 9.59s/it] 187it [29:46, 9.59s/it] 188it [29:55, 9.58s/it] 189it [30:05, 9.56s/it] 190it [30:15, 9.56s/it] 191it [30:24, 9.57s/it] 192it [30:34, 9.57s/it] 193it [30:43, 9.59s/it] 194it [30:53, 9.59s/it] 195it [31:02, 9.58s/it] 196it [31:12, 9.59s/it] 197it [31:22, 9.58s/it] 198it [31:31, 9.57s/it] 199it [31:41, 9.57s/it] 200it [31:50, 9.60s/it] 201it [32:00, 9.61s/it] 202it [32:10, 9.60s/it] 203it [32:19, 9.57s/it] 204it [32:29, 9.56s/it] 205it [32:38, 9.57s/it] 206it [32:48, 9.57s/it] 207it [32:57, 9.56s/it] 208it [33:07, 9.57s/it] 209it [33:17, 9.57s/it] 210it [33:26, 9.59s/it] 211it [33:36, 9.60s/it] 212it [33:45, 9.57s/it] 213it [33:55, 9.57s/it] 214it [34:04, 9.56s/it] 215it [34:14, 9.56s/it] 216it [34:24, 9.55s/it] 217it [34:33, 9.58s/it] 218it [34:43, 9.58s/it] 219it [34:52, 9.57s/it] 220it [35:02, 9.59s/it] 221it [35:11, 9.59s/it] 222it [35:21, 9.57s/it] 223it [35:30, 9.54s/it] 224it [35:40, 9.57s/it] 225it [35:50, 9.56s/it] 226it [35:59, 9.56s/it] 227it [36:09, 9.55s/it] 228it [36:18, 9.56s/it] 229it [36:28, 9.56s/it] 230it [36:37, 9.55s/it] 231it [36:47, 9.54s/it] 232it [36:57, 9.56s/it] 233it [37:06, 9.55s/it] 234it [37:16, 9.55s/it] 235it [37:25, 9.54s/it] 236it [37:35, 9.53s/it] 237it [37:44, 9.55s/it] 238it [37:54, 9.55s/it] 239it [38:03, 9.54s/it] 240it [38:13, 9.56s/it] 241it [38:22, 9.56s/it] 242it [38:32, 9.53s/it] 243it [38:41, 9.51s/it] 244it [38:51, 9.52s/it] 245it [39:00, 9.52s/it] 246it [39:10, 9.52s/it] 247it [39:20, 9.53s/it] 248it [39:29, 9.55s/it] 249it [39:39, 9.53s/it] 250it [39:48, 9.53s/it] 251it [39:58, 9.53s/it] 252it [40:07, 9.55s/it] 253it [40:17, 9.56s/it] 254it [40:26, 9.55s/it] 255it [40:36, 9.55s/it] 256it [40:45, 9.54s/it] 257it [40:55, 9.55s/it] 258it [41:05, 9.57s/it] 259it [41:14, 9.57s/it] 260it [41:24, 9.58s/it] 261it [41:33, 9.58s/it] 262it [41:43, 9.58s/it] 263it [41:53, 9.58s/it] 264it [42:02, 9.59s/it] 265it [42:12, 9.59s/it] 266it [42:21, 9.59s/it] 267it [42:31, 9.58s/it] 268it [42:41, 9.59s/it] 269it [42:50, 9.62s/it] 270it [43:00, 9.66s/it] 271it [43:10, 9.71s/it] 272it [43:20, 9.77s/it] 273it [43:30, 9.79s/it] 274it [43:39, 9.82s/it] 275it [43:49, 9.84s/it] 276it [43:59, 9.83s/it] 277it [44:09, 9.79s/it] 278it [44:19, 9.81s/it] 279it [44:28, 9.82s/it] 280it [44:38, 9.85s/it] 281it [44:48, 9.85s/it] 282it [44:58, 9.88s/it] 283it [45:08, 9.89s/it] 284it [45:18, 9.91s/it] 285it [45:28, 9.89s/it] 286it [45:38, 9.86s/it] 287it [45:48, 9.87s/it] 288it [45:58, 9.88s/it] 289it [46:07, 9.90s/it] 290it [46:17, 9.90s/it] 291it [46:27, 9.90s/it] 292it [46:37, 9.88s/it] 293it [46:47, 9.86s/it] 294it [46:57, 9.88s/it] 295it [47:07, 9.86s/it] 296it [47:16, 9.81s/it] 297it [47:26, 9.80s/it] 298it [47:36, 9.82s/it] 299it [47:46, 9.83s/it] 300it [47:56, 9.85s/it] 301it [48:05, 9.83s/it] 302it [48:15, 9.82s/it] 303it [48:25, 9.80s/it] 304it [48:35, 9.80s/it] 305it [48:45, 9.81s/it] 306it [48:54, 9.80s/it] 307it [49:04, 9.78s/it] 308it [49:14, 9.76s/it] 309it [49:24, 9.79s/it] 310it [49:34, 9.82s/it] 311it [49:43, 9.80s/it] 312it [49:53, 9.78s/it] 313it [50:03, 9.77s/it] 314it [50:13, 9.76s/it] 315it [50:22, 9.77s/it] 316it [50:32, 9.77s/it] 317it [50:42, 9.82s/it] 318it [50:52, 9.79s/it] 319it [51:02, 9.80s/it] 320it [51:12, 9.82s/it] 321it [51:21, 9.84s/it] 322it [51:31, 9.79s/it] 323it [51:41, 9.77s/it] 324it [51:50, 9.73s/it] 325it [52:00, 9.69s/it] 326it [52:10, 9.65s/it] 327it [52:19, 9.63s/it] 328it [52:29, 9.64s/it] 329it [52:38, 9.63s/it] 330it [52:48, 9.65s/it] 331it [52:58, 9.70s/it] 332it [53:08, 9.73s/it] 333it [53:18, 9.75s/it] 334it [53:27, 9.78s/it] 335it [53:37, 9.78s/it] 336it [53:47, 9.79s/it] 337it [53:57, 9.81s/it] 338it [54:07, 9.80s/it] 339it [54:16, 9.80s/it] 340it [54:26, 9.82s/it] 341it [54:27, 7.07s/it] 341it [54:27, 9.58s/it] +Error counts: + cyclic_id: 0 + cyclic_inchikey: 0 + cyclic_scaffold: 0 + cyclic_mwt: 0 + cyclic_clogp: 0 + cyclic_tpsa: 0 +⏰ Completed process in 0:54:34.072277 ++ rm /nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/validation/cyc-pep-6-12mer-70M_11.csv