Add conversion logs

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='<stdout>' mode='w' encoding='utf-8'>
+	format: csv
+	input: <_io.TextIOWrapper name='<stdin>' 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: <function _convert at 0x7f120cbef240>
+
+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

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='<stdout>' mode='w' encoding='utf-8'>
+	format: csv
+	input: <_io.TextIOWrapper name='<stdin>' 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: <function _convert at 0x7f27fe3a7240>
+
+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

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='<stdout>' mode='w' encoding='utf-8'>
+	format: csv
+	input: <_io.TextIOWrapper name='<stdin>' 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: <function _convert at 0x7ff3285db240>
+
+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

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='<stdout>' mode='w' encoding='utf-8'>
+	format: csv
+	input: <_io.TextIOWrapper name='<stdin>' 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: <function _convert at 0x7ffb82d8f240>
+
+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

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='<stdout>' mode='w' encoding='utf-8'>
+	format: csv
+	input: <_io.TextIOWrapper name='<stdin>' 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: <function _convert at 0x7f8ebdc23240>
+
+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

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='<stdout>' mode='w' encoding='utf-8'>
+	format: csv
+	input: <_io.TextIOWrapper name='<stdin>' 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: <function _convert at 0x7f5863d47240>
+
+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

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='<stdout>' mode='w' encoding='utf-8'>
+	format: csv
+	input: <_io.TextIOWrapper name='<stdin>' 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: <function _convert at 0x7f71dbc6b240>
+
+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

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='<stdout>' mode='w' encoding='utf-8'>
+	format: csv
+	input: <_io.TextIOWrapper name='<stdin>' 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: <function _convert at 0x7fe0c32d7240>
+
+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

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='<stdout>' mode='w' encoding='utf-8'>
+	format: csv
+	input: <_io.TextIOWrapper name='<stdin>' 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: <function _convert at 0x7f6753cc7240>
+
+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

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='<stdout>' mode='w' encoding='utf-8'>
+	format: csv
+	input: <_io.TextIOWrapper name='<stdin>' 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: <function _convert at 0x7f94dfb2f240>
+
+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

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='<stdout>' mode='w' encoding='utf-8'>
+	format: csv
+	input: <_io.TextIOWrapper name='<stdin>' 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: <function _convert at 0x7f9537463240>
+
+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

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='<stdout>' mode='w' encoding='utf-8'>
+	format: csv
+	input: <_io.TextIOWrapper name='<stdin>' 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: <function _convert at 0x7f145a383240>
+
+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

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='<stdout>' mode='w' encoding='utf-8'>
+	format: csv
+	input: <_io.TextIOWrapper name='<stdin>' 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: <function _convert at 0x7f967c3a7240>
+
+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

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='<stdout>' mode='w' encoding='utf-8'>
+	format: csv
+	input: <_io.TextIOWrapper name='<stdin>' 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: <function _convert at 0x7f7db174b240>
+
+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

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='<stdout>' mode='w' encoding='utf-8'>
+	format: csv
+	input: <_io.TextIOWrapper name='<stdin>' 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: <function _convert at 0x7ff086203240>
+
+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

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='<stdout>' mode='w' encoding='utf-8'>
+	format: csv
+	input: <_io.TextIOWrapper name='<stdin>' 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: <function _convert at 0x7f7e3726f240>
+
+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

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='<stdout>' mode='w' encoding='utf-8'>
+	format: csv
+	input: <_io.TextIOWrapper name='<stdin>' 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: <function _convert at 0x7f44e4bcb240>
+
+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

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='<stdout>' mode='w' encoding='utf-8'>
+	format: csv
+	input: <_io.TextIOWrapper name='<stdin>' 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: <function _convert at 0x7f6e76fb7240>
+
+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

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='<stdout>' mode='w' encoding='utf-8'>
+	format: csv
+	input: <_io.TextIOWrapper name='<stdin>' 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: <function _convert at 0x7f673477b240>
+
+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

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='<stdout>' mode='w' encoding='utf-8'>
+	format: csv
+	input: <_io.TextIOWrapper name='<stdin>' 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: <function _convert at 0x7fcb30feb240>
+
+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

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='<stdout>' mode='w' encoding='utf-8'>
+	format: csv
+	input: <_io.TextIOWrapper name='<stdin>' 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: <function _convert at 0x7f0910a93240>
+
+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

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='<stdout>' mode='w' encoding='utf-8'>
+	format: csv
+	input: <_io.TextIOWrapper name='<stdin>' 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: <function _convert at 0x7f2099aeb240>
+
+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

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='<stdout>' mode='w' encoding='utf-8'>
+	format: csv
+	input: <_io.TextIOWrapper name='<stdin>' 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: <function _convert at 0x7f377f5ef240>
+
+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

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='<stdout>' mode='w' encoding='utf-8'>
+	format: csv
+	input: <_io.TextIOWrapper name='<stdin>' 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: <function _convert at 0x7f9298a7f240>
+
+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

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='<stdout>' mode='w' encoding='utf-8'>
+	format: csv
+	input: <_io.TextIOWrapper name='<stdin>' 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: <function _convert at 0x7f5ad0003240>
+
+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

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='<stdout>' mode='w' encoding='utf-8'>
+	format: csv
+	input: <_io.TextIOWrapper name='<stdin>' 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: <function _convert at 0x7f65ea97b240>
+
+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

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='<stdout>' mode='w' encoding='utf-8'>
+	format: csv
+	input: <_io.TextIOWrapper name='<stdin>' 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: <function _convert at 0x7f35aa49b240>
+
+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

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='<stdout>' mode='w' encoding='utf-8'>
+	format: csv
+	input: <_io.TextIOWrapper name='<stdin>' 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: <function _convert at 0x7f8525723240>
+
+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

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='<stdout>' mode='w' encoding='utf-8'>
+	format: csv
+	input: <_io.TextIOWrapper name='<stdin>' 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: <function _convert at 0x7f5cefbe3240>
+
+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

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='<stdout>' mode='w' encoding='utf-8'>
+	format: csv
+	input: <_io.TextIOWrapper name='<stdin>' 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: <function _convert at 0x7fed0c327240>
+
+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

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='<stdout>' mode='w' encoding='utf-8'>
+	format: csv
+	input: <_io.TextIOWrapper name='<stdin>' 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: <function _convert at 0x7fd74f7db240>
+
+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

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='<stdout>' mode='w' encoding='utf-8'>
+	format: csv
+	input: <_io.TextIOWrapper name='<stdin>' 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: <function _convert at 0x7f7809557240>
+
+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

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='<stdout>' mode='w' encoding='utf-8'>
+	format: csv
+	input: <_io.TextIOWrapper name='<stdin>' 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: <function _convert at 0x7fa5667d7240>
+
+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

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='<stdout>' mode='w' encoding='utf-8'>
+	format: csv
+	input: <_io.TextIOWrapper name='<stdin>' 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: <function _convert at 0x7fb955ddf240>
+
+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

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='<stdout>' mode='w' encoding='utf-8'>
+	format: csv
+	input: <_io.TextIOWrapper name='<stdin>' 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: <function _convert at 0x7f6630b5b240>
+
+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

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='<stdout>' mode='w' encoding='utf-8'>
+	format: csv
+	input: <_io.TextIOWrapper name='<stdin>' 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: <function _convert at 0x7f965051b240>
+
+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

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='<stdout>' mode='w' encoding='utf-8'>
+	format: csv
+	input: <_io.TextIOWrapper name='<stdin>' 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: <function _convert at 0x7f899414f240>
+
+Error counts:
+	cyclic_id: 0
+	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

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='<stdout>' mode='w' encoding='utf-8'>
+	format: csv
+	input: <_io.TextIOWrapper name='<stdin>' 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: <function _convert at 0x7fe1ab60f240>
+
+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

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='<stdout>' mode='w' encoding='utf-8'>
+	format: csv
+	input: <_io.TextIOWrapper name='<stdin>' 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: <function _convert at 0x7f91c12bb240>
+
+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

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='<stdout>' mode='w' encoding='utf-8'>
+	format: csv
+	input: <_io.TextIOWrapper name='<stdin>' 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: <function _convert at 0x7faace5cb240>
+
+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

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='<stdout>' mode='w' encoding='utf-8'>
+	format: csv
+	input: <_io.TextIOWrapper name='<stdin>' 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: <function _convert at 0x7fe67f0ab240>
+
+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

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='<stdout>' mode='w' encoding='utf-8'>
+	format: csv
+	input: <_io.TextIOWrapper name='<stdin>' 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: <function _convert at 0x7ff2fd20f240>
+
+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

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='<stdout>' mode='w' encoding='utf-8'>
+	format: csv
+	input: <_io.TextIOWrapper name='<stdin>' 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: <function _convert at 0x7f3dc115b240>
+
+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

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='<stdout>' mode='w' encoding='utf-8'>
+	format: csv
+	input: <_io.TextIOWrapper name='<stdin>' 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: <function _convert at 0x7f09a5733240>
+
+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

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='<stdout>' mode='w' encoding='utf-8'>
+	format: csv
+	input: <_io.TextIOWrapper name='<stdin>' 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: <function _convert at 0x7f037ef0f240>
+
+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

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='<stdout>' mode='w' encoding='utf-8'>
+	format: csv
+	input: <_io.TextIOWrapper name='<stdin>' 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: <function _convert at 0x7f8b11817240>
+
+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

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='<stdout>' mode='w' encoding='utf-8'>
+	format: csv
+	input: <_io.TextIOWrapper name='<stdin>' 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: <function _convert at 0x7f362c75f240>
+
+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

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='<stdout>' mode='w' encoding='utf-8'>
+	format: csv
+	input: <_io.TextIOWrapper name='<stdin>' 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: <function _convert at 0x7f6e669a7240>
+
+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

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='<stdout>' mode='w' encoding='utf-8'>
+	format: csv
+	input: <_io.TextIOWrapper name='<stdin>' 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: <function _convert at 0x7f2a31063240>
+
+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

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='<stdout>' mode='w' encoding='utf-8'>
+	format: csv
+	input: <_io.TextIOWrapper name='<stdin>' 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: <function _convert at 0x7ff8f6e03240>
+
+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