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Datasets:
scbirlab
/
cyc-pep-6-12mer-70M-2024

Tasks:
Fill-Mask
Text Classification
Text2Text Generation
Modalities:
Tabular
Text
Formats:
csv
Size:
100M - 1B
Tags:
chemistry
biology
Synthetic
SMILES
Libraries:
Datasets
Dask
License:
Dataset card Viewer Files Community
3
eachanjohnson commited on
Commit
0436f6c
•
1 Parent(s): 43c636a

Fix header (#2)

Browse files

- Fix headers and add calculated properties (b71c4cda22f2f2010ef1b5aaf5186a65a2d10b31)
- Add conversion logs (34cd67a52600f515d4e5fe244c6a72b37a548960)
- Update documentation and configs (1b7eb6335ec096d65ccf6d9610ec349695d60f4f)

This view is limited to 50 files because it contains too many changes.   See raw diff
Files changed (50) hide show
  1. README.md +23 -5
  2. test/cyc-pep-6-12mer-70M_00.csv.gz +2 -2
  3. test/cyc-pep-6-12mer-70M_00.log +337 -0
  4. test/cyc-pep-6-12mer-70M_01.csv.gz +2 -2
  5. test/cyc-pep-6-12mer-70M_01.log +337 -0
  6. test/cyc-pep-6-12mer-70M_02.csv.gz +2 -2
  7. test/cyc-pep-6-12mer-70M_02.log +337 -0
  8. test/cyc-pep-6-12mer-70M_03.csv.gz +2 -2
  9. test/cyc-pep-6-12mer-70M_03.log +337 -0
  10. test/cyc-pep-6-12mer-70M_04.csv.gz +2 -2
  11. test/cyc-pep-6-12mer-70M_04.log +337 -0
  12. test/cyc-pep-6-12mer-70M_05.csv.gz +2 -2
  13. test/cyc-pep-6-12mer-70M_05.log +337 -0
  14. test/cyc-pep-6-12mer-70M_06.csv.gz +2 -2
  15. test/cyc-pep-6-12mer-70M_06.log +337 -0
  16. test/cyc-pep-6-12mer-70M_07.csv.gz +2 -2
  17. test/cyc-pep-6-12mer-70M_07.log +337 -0
  18. test/cyc-pep-6-12mer-70M_08.csv.gz +2 -2
  19. test/cyc-pep-6-12mer-70M_08.log +337 -0
  20. test/cyc-pep-6-12mer-70M_09.csv.gz +2 -2
  21. test/cyc-pep-6-12mer-70M_09.log +337 -0
  22. test/cyc-pep-6-12mer-70M_10.csv.gz +2 -2
  23. test/cyc-pep-6-12mer-70M_10.log +337 -0
  24. test/cyc-pep-6-12mer-70M_11.csv.gz +2 -2
  25. test/cyc-pep-6-12mer-70M_11.log +337 -0
  26. train/cyc-pep-6-12mer-70M_00.csv.gz +2 -2
  27. train/cyc-pep-6-12mer-70M_00.log +337 -0
  28. train/cyc-pep-6-12mer-70M_01.csv.gz +2 -2
  29. train/cyc-pep-6-12mer-70M_01.log +337 -0
  30. train/cyc-pep-6-12mer-70M_02.csv.gz +2 -2
  31. train/cyc-pep-6-12mer-70M_02.log +337 -0
  32. train/cyc-pep-6-12mer-70M_03.csv.gz +2 -2
  33. train/cyc-pep-6-12mer-70M_03.log +337 -0
  34. train/cyc-pep-6-12mer-70M_04.csv.gz +2 -2
  35. train/cyc-pep-6-12mer-70M_04.log +337 -0
  36. train/cyc-pep-6-12mer-70M_05.csv.gz +2 -2
  37. train/cyc-pep-6-12mer-70M_05.log +337 -0
  38. train/cyc-pep-6-12mer-70M_06.csv.gz +2 -2
  39. train/cyc-pep-6-12mer-70M_06.log +337 -0
  40. train/cyc-pep-6-12mer-70M_07.csv.gz +2 -2
  41. train/cyc-pep-6-12mer-70M_07.log +337 -0
  42. train/cyc-pep-6-12mer-70M_08.csv.gz +2 -2
  43. train/cyc-pep-6-12mer-70M_08.log +337 -0
  44. train/cyc-pep-6-12mer-70M_09.csv.gz +2 -2
  45. train/cyc-pep-6-12mer-70M_09.log +337 -0
  46. train/cyc-pep-6-12mer-70M_10.csv.gz +2 -2
  47. train/cyc-pep-6-12mer-70M_10.log +337 -0
  48. train/cyc-pep-6-12mer-70M_11.csv.gz +2 -2
  49. train/cyc-pep-6-12mer-70M_11.log +337 -0
  50. train/cyc-pep-6-12mer-70M_12.csv.gz +2 -2
README.md CHANGED
@@ -1,11 +1,11 @@
1
  ---
2
  license: mit
3
  task_categories:
 
4
  - text-classification
 
5
  - translation
6
  - zero-shot-classification
7
- - text2text-generation
8
- - fill-mask
9
  tags:
10
  - chemistry
11
  - biology
@@ -13,10 +13,23 @@ tags:
13
  - SMILES
14
  size_categories:
15
  - 10M<n<100M
 
 
 
 
 
 
 
 
 
 
 
 
 
16
  ---
17
  # cyc-pep-6-12mer-70M-2024
18
 
19
- Set of 70 million (almost) unique cyclic and linear peptides comprising 6-12 amino acids.
20
 
21
  ## Dataset Details
22
 
@@ -26,11 +39,11 @@ Set of 70 million (almost) unique cyclic and linear peptides comprising 6-12 ami
26
  - **Funded by:** The Francis Crick Institute
27
  - **License:** MIT
28
 
29
- ### Dataset Sources [optional]
30
 
31
  <!-- Provide the basic links for the dataset. -->
32
 
33
- - **Repository:** [https://huggingface.co/datasets/scbirlab/cyc-pep-6-12mer-70M-2024]
34
  <!-- - **Paper [optional]:** [More Information Needed]
35
  - **Demo [optional]:** [More Information Needed] -->
36
 
@@ -56,7 +69,12 @@ Developing chemistry models around cyclic peptides.
56
  - **peptide_sequence**: Amino acid sequence of linear peptide
57
  - **SMILES**: SMILES string of linear peptide
58
  - **cyclic_id**: Identifier for cyclic peptide
 
59
  - **cysteine_to_N_cyclization**: SMILES string of cyclic peptide
 
 
 
 
60
 
61
  ## Dataset Creation
62
 
 
1
  ---
2
  license: mit
3
  task_categories:
4
+ - fill-mask
5
  - text-classification
6
+ - text2text-generation
7
  - translation
8
  - zero-shot-classification
 
 
9
  tags:
10
  - chemistry
11
  - biology
 
13
  - SMILES
14
  size_categories:
15
  - 10M<n<100M
16
+ pretty_name: 'Cyclic peptides (70 million)'
17
+ configs:
18
+ - config_name: full
19
+ data_files: "*/*.csv.gz"
20
+ default: true
21
+ - config_name: split
22
+ data_files:
23
+ - split: train
24
+ path: "train/*.csv.gz"
25
+ - split: test
26
+ path: "test/*.csv.gz"
27
+ - split: validation
28
+ path: "validation/*.csv.gz"
29
  ---
30
  # cyc-pep-6-12mer-70M-2024
31
 
32
+ Set of 70 million (almost) unique cyclic and linear peptides comprising 6-12 amino acids, each with some calculated molecular properties.
33
 
34
  ## Dataset Details
35
 
 
39
  - **Funded by:** The Francis Crick Institute
40
  - **License:** MIT
41
 
42
+ ### Dataset Sources
43
 
44
  <!-- Provide the basic links for the dataset. -->
45
 
46
+ - **Repository:** https://huggingface.co/datasets/scbirlab/cyc-pep-6-12mer-70M-2024
47
  <!-- - **Paper [optional]:** [More Information Needed]
48
  - **Demo [optional]:** [More Information Needed] -->
49
 
 
69
  - **peptide_sequence**: Amino acid sequence of linear peptide
70
  - **SMILES**: SMILES string of linear peptide
71
  - **cyclic_id**: Identifier for cyclic peptide
72
+ - **cyclic_inchikey**: Unique identifier for cyclic peptide
73
  - **cysteine_to_N_cyclization**: SMILES string of cyclic peptide
74
+ - **cyclic_scaffold**: Murcko scaffold of cyclic peptide
75
+ - **cyclic_mwt**: Molecular weight of cyclic peptide
76
+ - **cyclic_clogp**: Crippen LogP of cyclic peptide
77
+ - **cyclic_tpsa**: Topological polar surface area of cyclic peptide
78
 
79
  ## Dataset Creation
80
 
test/cyc-pep-6-12mer-70M_00.csv.gz CHANGED
@@ -1,3 +1,3 @@
1
  version https://git-lfs.github.com/spec/v1
2
- oid sha256:06be14f986a68a2a01779b93a50e5498b150a70cde2c34d7dbec192e727e7e67
3
- size 58256598
 
1
  version https://git-lfs.github.com/spec/v1
2
+ oid sha256:2e913c51083461027a3272b7fd2eb5f92b744cacdbca47607c4333750922a2fd
3
+ size 112845849
test/cyc-pep-6-12mer-70M_00.log ADDED
@@ -0,0 +1,337 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ + module purge
2
+ + '[' -z '' ']'
3
+ + case "$-" in
4
+ + __lmod_sh_dbg=x
5
+ + '[' -n x ']'
6
+ + set +x
7
+ Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output
8
+ Shell debugging restarted
9
+ + unset __lmod_sh_dbg
10
+ + return 0
11
+ + module load Anaconda3/2023.03
12
+ + '[' -z '' ']'
13
+ + case "$-" in
14
+ + __lmod_sh_dbg=x
15
+ + '[' -n x ']'
16
+ + set +x
17
+ Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output
18
+ Shell debugging restarted
19
+ + unset __lmod_sh_dbg
20
+ + return 0
21
+ + source /camp/home/johnsoe/.bashrc
22
+ ++ '[' '' = yes ']'
23
+ ++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '
24
+ +++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.bash hook
25
+ ++ __conda_setup='export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\''
26
+ export _CE_M='\'''\''
27
+ export _CE_CONDA='\'''\''
28
+ export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''
29
+
30
+ # Copyright (C) 2012 Anaconda, Inc
31
+ # SPDX-License-Identifier: BSD-3-Clause
32
+ __conda_exe() (
33
+ "$CONDA_EXE" $_CE_M $_CE_CONDA "$@"
34
+ )
35
+
36
+ __conda_hashr() {
37
+ if [ -n "${ZSH_VERSION:+x}" ]; then
38
+ \rehash
39
+ elif [ -n "${POSH_VERSION:+x}" ]; then
40
+ : # pass
41
+ else
42
+ \hash -r
43
+ fi
44
+ }
45
+
46
+ __conda_activate() {
47
+ if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then
48
+ # Handle transition from shell activated with conda <= 4.3 to a subsequent activation
49
+ # after conda updated to >= 4.4. See issue #6173.
50
+ PS1="$CONDA_PS1_BACKUP"
51
+ \unset CONDA_PS1_BACKUP
52
+ fi
53
+ \local ask_conda
54
+ ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return
55
+ \eval "$ask_conda"
56
+ __conda_hashr
57
+ }
58
+
59
+ __conda_reactivate() {
60
+ \local ask_conda
61
+ ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return
62
+ \eval "$ask_conda"
63
+ __conda_hashr
64
+ }
65
+
66
+ conda() {
67
+ \local cmd="${1-__missing__}"
68
+ case "$cmd" in
69
+ activate|deactivate)
70
+ __conda_activate "$@"
71
+ ;;
72
+ install|update|upgrade|remove|uninstall)
73
+ __conda_exe "$@" || \return
74
+ __conda_reactivate
75
+ ;;
76
+ *)
77
+ __conda_exe "$@"
78
+ ;;
79
+ esac
80
+ }
81
+
82
+ if [ -z "${CONDA_SHLVL+x}" ]; then
83
+ \export CONDA_SHLVL=0
84
+ # In dev-mode CONDA_EXE is python.exe and on Windows
85
+ # it is in a different relative location to condabin.
86
+ if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then
87
+ PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}"
88
+ else
89
+ PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}"
90
+ fi
91
+ \export PATH
92
+
93
+ # We'\''re not allowing PS1 to be unbound. It must at least be set.
94
+ # However, we'\''re not exporting it, which can cause problems when starting a second shell
95
+ # via a first shell (i.e. starting zsh from bash).
96
+ if [ -z "${PS1+x}" ]; then
97
+ PS1=
98
+ fi
99
+ fi
100
+
101
+ conda activate base'
102
+ ++ '[' 0 -eq 0 ']'
103
+ ++ eval 'export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\''
104
+ export _CE_M='\'''\''
105
+ export _CE_CONDA='\'''\''
106
+ export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''
107
+
108
+ # Copyright (C) 2012 Anaconda, Inc
109
+ # SPDX-License-Identifier: BSD-3-Clause
110
+ __conda_exe() (
111
+ "$CONDA_EXE" $_CE_M $_CE_CONDA "$@"
112
+ )
113
+
114
+ __conda_hashr() {
115
+ if [ -n "${ZSH_VERSION:+x}" ]; then
116
+ \rehash
117
+ elif [ -n "${POSH_VERSION:+x}" ]; then
118
+ : # pass
119
+ else
120
+ \hash -r
121
+ fi
122
+ }
123
+
124
+ __conda_activate() {
125
+ if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then
126
+ # Handle transition from shell activated with conda <= 4.3 to a subsequent activation
127
+ # after conda updated to >= 4.4. See issue #6173.
128
+ PS1="$CONDA_PS1_BACKUP"
129
+ \unset CONDA_PS1_BACKUP
130
+ fi
131
+ \local ask_conda
132
+ ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return
133
+ \eval "$ask_conda"
134
+ __conda_hashr
135
+ }
136
+
137
+ __conda_reactivate() {
138
+ \local ask_conda
139
+ ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return
140
+ \eval "$ask_conda"
141
+ __conda_hashr
142
+ }
143
+
144
+ conda() {
145
+ \local cmd="${1-__missing__}"
146
+ case "$cmd" in
147
+ activate|deactivate)
148
+ __conda_activate "$@"
149
+ ;;
150
+ install|update|upgrade|remove|uninstall)
151
+ __conda_exe "$@" || \return
152
+ __conda_reactivate
153
+ ;;
154
+ *)
155
+ __conda_exe "$@"
156
+ ;;
157
+ esac
158
+ }
159
+
160
+ if [ -z "${CONDA_SHLVL+x}" ]; then
161
+ \export CONDA_SHLVL=0
162
+ # In dev-mode CONDA_EXE is python.exe and on Windows
163
+ # it is in a different relative location to condabin.
164
+ if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then
165
+ PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}"
166
+ else
167
+ PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}"
168
+ fi
169
+ \export PATH
170
+
171
+ # We'\''re not allowing PS1 to be unbound. It must at least be set.
172
+ # However, we'\''re not exporting it, which can cause problems when starting a second shell
173
+ # via a first shell (i.e. starting zsh from bash).
174
+ if [ -z "${PS1+x}" ]; then
175
+ PS1=
176
+ fi
177
+ fi
178
+
179
+ conda activate base'
180
+ +++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda
181
+ +++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda
182
+ +++ export _CE_M=
183
+ +++ _CE_M=
184
+ +++ export _CE_CONDA=
185
+ +++ _CE_CONDA=
186
+ +++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python
187
+ +++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python
188
+ +++ '[' -z x ']'
189
+ +++ conda activate base
190
+ +++ local cmd=activate
191
+ +++ case "$cmd" in
192
+ +++ __conda_activate activate base
193
+ +++ '[' -n '' ']'
194
+ +++ local ask_conda
195
+ ++++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '
196
+ ++++ __conda_exe shell.posix activate base
197
+ ++++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate base
198
+ +++ ask_conda='PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\''
199
+ export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\''
200
+ export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\''
201
+ export CONDA_SHLVL='\''6'\''
202
+ export CONDA_DEFAULT_ENV='\''base'\''
203
+ export CONDA_PROMPT_MODIFIER='\''(base) '\''
204
+ export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\''
205
+ export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\''
206
+ export _CE_M='\'''\''
207
+ export _CE_CONDA='\'''\''
208
+ export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'''
209
+ +++ eval 'PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\''
210
+ export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\''
211
+ export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\''
212
+ export CONDA_SHLVL='\''6'\''
213
+ export CONDA_DEFAULT_ENV='\''base'\''
214
+ export CONDA_PROMPT_MODIFIER='\''(base) '\''
215
+ export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\''
216
+ export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\''
217
+ export _CE_M='\'''\''
218
+ export _CE_CONDA='\'''\''
219
+ export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'''
220
+ ++++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '
221
+ ++++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin
222
+ ++++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin
223
+ ++++ export CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0
224
+ ++++ CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0
225
+ ++++ export CONDA_SHLVL=6
226
+ ++++ CONDA_SHLVL=6
227
+ ++++ export CONDA_DEFAULT_ENV=base
228
+ ++++ CONDA_DEFAULT_ENV=base
229
+ ++++ export 'CONDA_PROMPT_MODIFIER=(base) '
230
+ ++++ CONDA_PROMPT_MODIFIER='(base) '
231
+ ++++ export CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev
232
+ ++++ CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev
233
+ ++++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda
234
+ ++++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda
235
+ ++++ export _CE_M=
236
+ ++++ _CE_M=
237
+ ++++ export _CE_CONDA=
238
+ ++++ _CE_CONDA=
239
+ ++++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python
240
+ ++++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python
241
+ +++ __conda_hashr
242
+ +++ '[' -n '' ']'
243
+ +++ '[' -n '' ']'
244
+ +++ hash -r
245
+ ++ unset __conda_setup
246
+ + conda activate schemist-dev
247
+ + local cmd=activate
248
+ + case "$cmd" in
249
+ + __conda_activate activate schemist-dev
250
+ + '[' -n '' ']'
251
+ + local ask_conda
252
+ ++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '
253
+ ++ __conda_exe shell.posix activate schemist-dev
254
+ ++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate schemist-dev
255
+ + ask_conda='PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\''
256
+ export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\''
257
+ export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\''
258
+ export CONDA_SHLVL='\''7'\''
259
+ export CONDA_DEFAULT_ENV='\''schemist-dev'\''
260
+ export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\''
261
+ export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\''
262
+ export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\''
263
+ export _CE_M='\'''\''
264
+ export _CE_CONDA='\'''\''
265
+ export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'''
266
+ + eval 'PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\''
267
+ export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\''
268
+ export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\''
269
+ export CONDA_SHLVL='\''7'\''
270
+ export CONDA_DEFAULT_ENV='\''schemist-dev'\''
271
+ export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\''
272
+ export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\''
273
+ export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\''
274
+ export _CE_M='\'''\''
275
+ export _CE_CONDA='\'''\''
276
+ export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'''
277
+ ++ PS1='(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '
278
+ ++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin
279
+ ++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin
280
+ ++ export CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev
281
+ ++ CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev
282
+ ++ export CONDA_SHLVL=7
283
+ ++ CONDA_SHLVL=7
284
+ ++ export CONDA_DEFAULT_ENV=schemist-dev
285
+ ++ CONDA_DEFAULT_ENV=schemist-dev
286
+ ++ export 'CONDA_PROMPT_MODIFIER=(schemist-dev) '
287
+ ++ CONDA_PROMPT_MODIFIER='(schemist-dev) '
288
+ ++ export CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0
289
+ ++ CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0
290
+ ++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda
291
+ ++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda
292
+ ++ export _CE_M=
293
+ ++ _CE_M=
294
+ ++ export _CE_CONDA=
295
+ ++ _CE_CONDA=
296
+ ++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python
297
+ ++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python
298
+ + __conda_hashr
299
+ + '[' -n '' ']'
300
+ + '[' -n '' ']'
301
+ + hash -r
302
+ + CHUNK_HEAD_FILE=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz
303
+ + INPUT=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/test/cyc-pep-6-12mer-70M_00.csv
304
+ + COLUMN=cysteine_to_N_cyclization
305
+ + PREFIX=cyclic_
306
+ + AWK='1 { print $8, $1, $2, $10, $3 }'
307
+ + '[' -z cysteine_to_N_cyclization ']'
308
+ + '[' -z cyclic_ ']'
309
+ + '[' -z '1 { print $8, $1, $2, $10, $3 }' ']'
310
+ + 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
311
+ + schemist convert -f csv --column cysteine_to_N_cyclization --to id inchikey scaffold mwt clogp tpsa --prefix cyclic_ --options prefix=SCB-
312
+ + gzip --best
313
+ + awk -F, -v OFS=, '1 { print $8, $1, $2, $10, $3 }'
314
+ ++ tr ' ' ,
315
+ ++ head -n1
316
+ ++ zcat /nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz
317
+ 🚀 Converting between string representations with the following parameters:
318
+ subcommand: convert
319
+ output: <_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>
320
+ format: csv
321
+ input: <_io.TextIOWrapper name='<stdin>' mode='r' encoding='utf-8'>
322
+ representation: SMILES
323
+ column: cysteine_to_N_cyclization
324
+ prefix: cyclic_
325
+ to: ['id', 'inchikey', 'scaffold', 'mwt', 'clogp', 'tpsa']
326
+ options: ['prefix=SCB-']
327
+ func: <function _convert at 0x7f120cbef240>
328
+
329
+ Error counts:
330
+ cyclic_id: 0
331
+ cyclic_inchikey: 0
332
+ cyclic_scaffold: 0
333
+ cyclic_mwt: 0
334
+ cyclic_clogp: 0
335
+ cyclic_tpsa: 0
336
+ ⏰ Completed process in 3:10:05.774172
337
+ + 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.csv.gz CHANGED
@@ -1,3 +1,3 @@
1
  version https://git-lfs.github.com/spec/v1
2
- oid sha256:2238d323e335426a55721bd5b6a68ce61cd7ed92f71fa7a5dfe2c80ce3dab975
3
- size 59576589
 
1
  version https://git-lfs.github.com/spec/v1
2
+ oid sha256:b12aa9b2723934da0ed96abb7517e5ca1e50ea6ed2ab4c54c5855b232bafa4ce
3
+ size 114559271
test/cyc-pep-6-12mer-70M_01.log ADDED
@@ -0,0 +1,337 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ + module purge
2
+ + '[' -z '' ']'
3
+ + case "$-" in
4
+ + __lmod_sh_dbg=x
5
+ + '[' -n x ']'
6
+ + set +x
7
+ Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output
8
+ Shell debugging restarted
9
+ + unset __lmod_sh_dbg
10
+ + return 0
11
+ + module load Anaconda3/2023.03
12
+ + '[' -z '' ']'
13
+ + case "$-" in
14
+ + __lmod_sh_dbg=x
15
+ + '[' -n x ']'
16
+ + set +x
17
+ Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output
18
+ Shell debugging restarted
19
+ + unset __lmod_sh_dbg
20
+ + return 0
21
+ + source /camp/home/johnsoe/.bashrc
22
+ ++ '[' '' = yes ']'
23
+ ++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '
24
+ +++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.bash hook
25
+ ++ __conda_setup='export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\''
26
+ export _CE_M='\'''\''
27
+ export _CE_CONDA='\'''\''
28
+ export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''
29
+
30
+ # Copyright (C) 2012 Anaconda, Inc
31
+ # SPDX-License-Identifier: BSD-3-Clause
32
+ __conda_exe() (
33
+ "$CONDA_EXE" $_CE_M $_CE_CONDA "$@"
34
+ )
35
+
36
+ __conda_hashr() {
37
+ if [ -n "${ZSH_VERSION:+x}" ]; then
38
+ \rehash
39
+ elif [ -n "${POSH_VERSION:+x}" ]; then
40
+ : # pass
41
+ else
42
+ \hash -r
43
+ fi
44
+ }
45
+
46
+ __conda_activate() {
47
+ if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then
48
+ # Handle transition from shell activated with conda <= 4.3 to a subsequent activation
49
+ # after conda updated to >= 4.4. See issue #6173.
50
+ PS1="$CONDA_PS1_BACKUP"
51
+ \unset CONDA_PS1_BACKUP
52
+ fi
53
+ \local ask_conda
54
+ ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return
55
+ \eval "$ask_conda"
56
+ __conda_hashr
57
+ }
58
+
59
+ __conda_reactivate() {
60
+ \local ask_conda
61
+ ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return
62
+ \eval "$ask_conda"
63
+ __conda_hashr
64
+ }
65
+
66
+ conda() {
67
+ \local cmd="${1-__missing__}"
68
+ case "$cmd" in
69
+ activate|deactivate)
70
+ __conda_activate "$@"
71
+ ;;
72
+ install|update|upgrade|remove|uninstall)
73
+ __conda_exe "$@" || \return
74
+ __conda_reactivate
75
+ ;;
76
+ *)
77
+ __conda_exe "$@"
78
+ ;;
79
+ esac
80
+ }
81
+
82
+ if [ -z "${CONDA_SHLVL+x}" ]; then
83
+ \export CONDA_SHLVL=0
84
+ # In dev-mode CONDA_EXE is python.exe and on Windows
85
+ # it is in a different relative location to condabin.
86
+ if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then
87
+ PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}"
88
+ else
89
+ PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}"
90
+ fi
91
+ \export PATH
92
+
93
+ # We'\''re not allowing PS1 to be unbound. It must at least be set.
94
+ # However, we'\''re not exporting it, which can cause problems when starting a second shell
95
+ # via a first shell (i.e. starting zsh from bash).
96
+ if [ -z "${PS1+x}" ]; then
97
+ PS1=
98
+ fi
99
+ fi
100
+
101
+ conda activate base'
102
+ ++ '[' 0 -eq 0 ']'
103
+ ++ eval 'export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\''
104
+ export _CE_M='\'''\''
105
+ export _CE_CONDA='\'''\''
106
+ export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''
107
+
108
+ # Copyright (C) 2012 Anaconda, Inc
109
+ # SPDX-License-Identifier: BSD-3-Clause
110
+ __conda_exe() (
111
+ "$CONDA_EXE" $_CE_M $_CE_CONDA "$@"
112
+ )
113
+
114
+ __conda_hashr() {
115
+ if [ -n "${ZSH_VERSION:+x}" ]; then
116
+ \rehash
117
+ elif [ -n "${POSH_VERSION:+x}" ]; then
118
+ : # pass
119
+ else
120
+ \hash -r
121
+ fi
122
+ }
123
+
124
+ __conda_activate() {
125
+ if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then
126
+ # Handle transition from shell activated with conda <= 4.3 to a subsequent activation
127
+ # after conda updated to >= 4.4. See issue #6173.
128
+ PS1="$CONDA_PS1_BACKUP"
129
+ \unset CONDA_PS1_BACKUP
130
+ fi
131
+ \local ask_conda
132
+ ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return
133
+ \eval "$ask_conda"
134
+ __conda_hashr
135
+ }
136
+
137
+ __conda_reactivate() {
138
+ \local ask_conda
139
+ ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return
140
+ \eval "$ask_conda"
141
+ __conda_hashr
142
+ }
143
+
144
+ conda() {
145
+ \local cmd="${1-__missing__}"
146
+ case "$cmd" in
147
+ activate|deactivate)
148
+ __conda_activate "$@"
149
+ ;;
150
+ install|update|upgrade|remove|uninstall)
151
+ __conda_exe "$@" || \return
152
+ __conda_reactivate
153
+ ;;
154
+ *)
155
+ __conda_exe "$@"
156
+ ;;
157
+ esac
158
+ }
159
+
160
+ if [ -z "${CONDA_SHLVL+x}" ]; then
161
+ \export CONDA_SHLVL=0
162
+ # In dev-mode CONDA_EXE is python.exe and on Windows
163
+ # it is in a different relative location to condabin.
164
+ if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then
165
+ PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}"
166
+ else
167
+ PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}"
168
+ fi
169
+ \export PATH
170
+
171
+ # We'\''re not allowing PS1 to be unbound. It must at least be set.
172
+ # However, we'\''re not exporting it, which can cause problems when starting a second shell
173
+ # via a first shell (i.e. starting zsh from bash).
174
+ if [ -z "${PS1+x}" ]; then
175
+ PS1=
176
+ fi
177
+ fi
178
+
179
+ conda activate base'
180
+ +++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda
181
+ +++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda
182
+ +++ export _CE_M=
183
+ +++ _CE_M=
184
+ +++ export _CE_CONDA=
185
+ +++ _CE_CONDA=
186
+ +++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python
187
+ +++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python
188
+ +++ '[' -z x ']'
189
+ +++ conda activate base
190
+ +++ local cmd=activate
191
+ +++ case "$cmd" in
192
+ +++ __conda_activate activate base
193
+ +++ '[' -n '' ']'
194
+ +++ local ask_conda
195
+ ++++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '
196
+ ++++ __conda_exe shell.posix activate base
197
+ ++++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate base
198
+ +++ ask_conda='PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\''
199
+ export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\''
200
+ export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\''
201
+ export CONDA_SHLVL='\''6'\''
202
+ export CONDA_DEFAULT_ENV='\''base'\''
203
+ export CONDA_PROMPT_MODIFIER='\''(base) '\''
204
+ export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\''
205
+ export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\''
206
+ export _CE_M='\'''\''
207
+ export _CE_CONDA='\'''\''
208
+ export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'''
209
+ +++ eval 'PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\''
210
+ export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\''
211
+ export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\''
212
+ export CONDA_SHLVL='\''6'\''
213
+ export CONDA_DEFAULT_ENV='\''base'\''
214
+ export CONDA_PROMPT_MODIFIER='\''(base) '\''
215
+ export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\''
216
+ export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\''
217
+ export _CE_M='\'''\''
218
+ export _CE_CONDA='\'''\''
219
+ export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'''
220
+ ++++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '
221
+ ++++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin
222
+ ++++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin
223
+ ++++ export CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0
224
+ ++++ CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0
225
+ ++++ export CONDA_SHLVL=6
226
+ ++++ CONDA_SHLVL=6
227
+ ++++ export CONDA_DEFAULT_ENV=base
228
+ ++++ CONDA_DEFAULT_ENV=base
229
+ ++++ export 'CONDA_PROMPT_MODIFIER=(base) '
230
+ ++++ CONDA_PROMPT_MODIFIER='(base) '
231
+ ++++ export CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev
232
+ ++++ CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev
233
+ ++++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda
234
+ ++++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda
235
+ ++++ export _CE_M=
236
+ ++++ _CE_M=
237
+ ++++ export _CE_CONDA=
238
+ ++++ _CE_CONDA=
239
+ ++++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python
240
+ ++++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python
241
+ +++ __conda_hashr
242
+ +++ '[' -n '' ']'
243
+ +++ '[' -n '' ']'
244
+ +++ hash -r
245
+ ++ unset __conda_setup
246
+ + conda activate schemist-dev
247
+ + local cmd=activate
248
+ + case "$cmd" in
249
+ + __conda_activate activate schemist-dev
250
+ + '[' -n '' ']'
251
+ + local ask_conda
252
+ ++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '
253
+ ++ __conda_exe shell.posix activate schemist-dev
254
+ ++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate schemist-dev
255
+ + ask_conda='PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\''
256
+ export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\''
257
+ export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\''
258
+ export CONDA_SHLVL='\''7'\''
259
+ export CONDA_DEFAULT_ENV='\''schemist-dev'\''
260
+ export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\''
261
+ export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\''
262
+ export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\''
263
+ export _CE_M='\'''\''
264
+ export _CE_CONDA='\'''\''
265
+ export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'''
266
+ + eval 'PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\''
267
+ export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\''
268
+ export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\''
269
+ export CONDA_SHLVL='\''7'\''
270
+ export CONDA_DEFAULT_ENV='\''schemist-dev'\''
271
+ export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\''
272
+ export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\''
273
+ export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\''
274
+ export _CE_M='\'''\''
275
+ export _CE_CONDA='\'''\''
276
+ export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'''
277
+ ++ PS1='(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '
278
+ ++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin
279
+ ++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin
280
+ ++ export CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev
281
+ ++ CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev
282
+ ++ export CONDA_SHLVL=7
283
+ ++ CONDA_SHLVL=7
284
+ ++ export CONDA_DEFAULT_ENV=schemist-dev
285
+ ++ CONDA_DEFAULT_ENV=schemist-dev
286
+ ++ export 'CONDA_PROMPT_MODIFIER=(schemist-dev) '
287
+ ++ CONDA_PROMPT_MODIFIER='(schemist-dev) '
288
+ ++ export CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0
289
+ ++ CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0
290
+ ++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda
291
+ ++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda
292
+ ++ export _CE_M=
293
+ ++ _CE_M=
294
+ ++ export _CE_CONDA=
295
+ ++ _CE_CONDA=
296
+ ++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python
297
+ ++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python
298
+ + __conda_hashr
299
+ + '[' -n '' ']'
300
+ + '[' -n '' ']'
301
+ + hash -r
302
+ + CHUNK_HEAD_FILE=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz
303
+ + INPUT=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/test/cyc-pep-6-12mer-70M_01.csv
304
+ + COLUMN=cysteine_to_N_cyclization
305
+ + PREFIX=cyclic_
306
+ + AWK='1 { print $8, $1, $2, $10, $3 }'
307
+ + '[' -z cysteine_to_N_cyclization ']'
308
+ + '[' -z cyclic_ ']'
309
+ + '[' -z '1 { print $8, $1, $2, $10, $3 }' ']'
310
+ + 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
311
+ + awk -F, -v OFS=, '1 { print $8, $1, $2, $10, $3 }'
312
+ + schemist convert -f csv --column cysteine_to_N_cyclization --to id inchikey scaffold mwt clogp tpsa --prefix cyclic_ --options prefix=SCB-
313
+ + gzip --best
314
+ ++ zcat /nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz
315
+ ++ head -n1
316
+ ++ tr ' ' ,
317
+ 🚀 Converting between string representations with the following parameters:
318
+ subcommand: convert
319
+ output: <_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>
320
+ format: csv
321
+ input: <_io.TextIOWrapper name='<stdin>' mode='r' encoding='utf-8'>
322
+ representation: SMILES
323
+ column: cysteine_to_N_cyclization
324
+ prefix: cyclic_
325
+ to: ['id', 'inchikey', 'scaffold', 'mwt', 'clogp', 'tpsa']
326
+ options: ['prefix=SCB-']
327
+ func: <function _convert at 0x7f27fe3a7240>
328
+
329
+ Error counts:
330
+ cyclic_id: 0
331
+ cyclic_inchikey: 0
332
+ cyclic_scaffold: 0
333
+ cyclic_mwt: 0
334
+ cyclic_clogp: 0
335
+ cyclic_tpsa: 0
336
+ ⏰ Completed process in 3:02:08.685108
337
+ + 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.csv.gz CHANGED
@@ -1,3 +1,3 @@
1
  version https://git-lfs.github.com/spec/v1
2
- oid sha256:6c5b61e10bdb3ce612dd195915920ef8391fedfda64089de9ad9f9f77f907c91
3
- size 61923971
 
1
  version https://git-lfs.github.com/spec/v1
2
+ oid sha256:ab0474546e2ae83ec9107e251098b84a471047d033f4e7e958531f54c267415d
3
+ size 117618606
test/cyc-pep-6-12mer-70M_02.log ADDED
@@ -0,0 +1,337 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ + module purge
2
+ + '[' -z '' ']'
3
+ + case "$-" in
4
+ + __lmod_sh_dbg=x
5
+ + '[' -n x ']'
6
+ + set +x
7
+ Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output
8
+ Shell debugging restarted
9
+ + unset __lmod_sh_dbg
10
+ + return 0
11
+ + module load Anaconda3/2023.03
12
+ + '[' -z '' ']'
13
+ + case "$-" in
14
+ + __lmod_sh_dbg=x
15
+ + '[' -n x ']'
16
+ + set +x
17
+ Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output
18
+ Shell debugging restarted
19
+ + unset __lmod_sh_dbg
20
+ + return 0
21
+ + source /camp/home/johnsoe/.bashrc
22
+ ++ '[' '' = yes ']'
23
+ ++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '
24
+ +++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.bash hook
25
+ ++ __conda_setup='export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\''
26
+ export _CE_M='\'''\''
27
+ export _CE_CONDA='\'''\''
28
+ export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''
29
+
30
+ # Copyright (C) 2012 Anaconda, Inc
31
+ # SPDX-License-Identifier: BSD-3-Clause
32
+ __conda_exe() (
33
+ "$CONDA_EXE" $_CE_M $_CE_CONDA "$@"
34
+ )
35
+
36
+ __conda_hashr() {
37
+ if [ -n "${ZSH_VERSION:+x}" ]; then
38
+ \rehash
39
+ elif [ -n "${POSH_VERSION:+x}" ]; then
40
+ : # pass
41
+ else
42
+ \hash -r
43
+ fi
44
+ }
45
+
46
+ __conda_activate() {
47
+ if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then
48
+ # Handle transition from shell activated with conda <= 4.3 to a subsequent activation
49
+ # after conda updated to >= 4.4. See issue #6173.
50
+ PS1="$CONDA_PS1_BACKUP"
51
+ \unset CONDA_PS1_BACKUP
52
+ fi
53
+ \local ask_conda
54
+ ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return
55
+ \eval "$ask_conda"
56
+ __conda_hashr
57
+ }
58
+
59
+ __conda_reactivate() {
60
+ \local ask_conda
61
+ ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return
62
+ \eval "$ask_conda"
63
+ __conda_hashr
64
+ }
65
+
66
+ conda() {
67
+ \local cmd="${1-__missing__}"
68
+ case "$cmd" in
69
+ activate|deactivate)
70
+ __conda_activate "$@"
71
+ ;;
72
+ install|update|upgrade|remove|uninstall)
73
+ __conda_exe "$@" || \return
74
+ __conda_reactivate
75
+ ;;
76
+ *)
77
+ __conda_exe "$@"
78
+ ;;
79
+ esac
80
+ }
81
+
82
+ if [ -z "${CONDA_SHLVL+x}" ]; then
83
+ \export CONDA_SHLVL=0
84
+ # In dev-mode CONDA_EXE is python.exe and on Windows
85
+ # it is in a different relative location to condabin.
86
+ if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then
87
+ PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}"
88
+ else
89
+ PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}"
90
+ fi
91
+ \export PATH
92
+
93
+ # We'\''re not allowing PS1 to be unbound. It must at least be set.
94
+ # However, we'\''re not exporting it, which can cause problems when starting a second shell
95
+ # via a first shell (i.e. starting zsh from bash).
96
+ if [ -z "${PS1+x}" ]; then
97
+ PS1=
98
+ fi
99
+ fi
100
+
101
+ conda activate base'
102
+ ++ '[' 0 -eq 0 ']'
103
+ ++ eval 'export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\''
104
+ export _CE_M='\'''\''
105
+ export _CE_CONDA='\'''\''
106
+ export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''
107
+
108
+ # Copyright (C) 2012 Anaconda, Inc
109
+ # SPDX-License-Identifier: BSD-3-Clause
110
+ __conda_exe() (
111
+ "$CONDA_EXE" $_CE_M $_CE_CONDA "$@"
112
+ )
113
+
114
+ __conda_hashr() {
115
+ if [ -n "${ZSH_VERSION:+x}" ]; then
116
+ \rehash
117
+ elif [ -n "${POSH_VERSION:+x}" ]; then
118
+ : # pass
119
+ else
120
+ \hash -r
121
+ fi
122
+ }
123
+
124
+ __conda_activate() {
125
+ if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then
126
+ # Handle transition from shell activated with conda <= 4.3 to a subsequent activation
127
+ # after conda updated to >= 4.4. See issue #6173.
128
+ PS1="$CONDA_PS1_BACKUP"
129
+ \unset CONDA_PS1_BACKUP
130
+ fi
131
+ \local ask_conda
132
+ ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return
133
+ \eval "$ask_conda"
134
+ __conda_hashr
135
+ }
136
+
137
+ __conda_reactivate() {
138
+ \local ask_conda
139
+ ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return
140
+ \eval "$ask_conda"
141
+ __conda_hashr
142
+ }
143
+
144
+ conda() {
145
+ \local cmd="${1-__missing__}"
146
+ case "$cmd" in
147
+ activate|deactivate)
148
+ __conda_activate "$@"
149
+ ;;
150
+ install|update|upgrade|remove|uninstall)
151
+ __conda_exe "$@" || \return
152
+ __conda_reactivate
153
+ ;;
154
+ *)
155
+ __conda_exe "$@"
156
+ ;;
157
+ esac
158
+ }
159
+
160
+ if [ -z "${CONDA_SHLVL+x}" ]; then
161
+ \export CONDA_SHLVL=0
162
+ # In dev-mode CONDA_EXE is python.exe and on Windows
163
+ # it is in a different relative location to condabin.
164
+ if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then
165
+ PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}"
166
+ else
167
+ PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}"
168
+ fi
169
+ \export PATH
170
+
171
+ # We'\''re not allowing PS1 to be unbound. It must at least be set.
172
+ # However, we'\''re not exporting it, which can cause problems when starting a second shell
173
+ # via a first shell (i.e. starting zsh from bash).
174
+ if [ -z "${PS1+x}" ]; then
175
+ PS1=
176
+ fi
177
+ fi
178
+
179
+ conda activate base'
180
+ +++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda
181
+ +++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda
182
+ +++ export _CE_M=
183
+ +++ _CE_M=
184
+ +++ export _CE_CONDA=
185
+ +++ _CE_CONDA=
186
+ +++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python
187
+ +++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python
188
+ +++ '[' -z x ']'
189
+ +++ conda activate base
190
+ +++ local cmd=activate
191
+ +++ case "$cmd" in
192
+ +++ __conda_activate activate base
193
+ +++ '[' -n '' ']'
194
+ +++ local ask_conda
195
+ ++++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '
196
+ ++++ __conda_exe shell.posix activate base
197
+ ++++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate base
198
+ +++ ask_conda='PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\''
199
+ export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\''
200
+ export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\''
201
+ export CONDA_SHLVL='\''6'\''
202
+ export CONDA_DEFAULT_ENV='\''base'\''
203
+ export CONDA_PROMPT_MODIFIER='\''(base) '\''
204
+ export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\''
205
+ export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\''
206
+ export _CE_M='\'''\''
207
+ export _CE_CONDA='\'''\''
208
+ export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'''
209
+ +++ eval 'PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\''
210
+ export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\''
211
+ export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\''
212
+ export CONDA_SHLVL='\''6'\''
213
+ export CONDA_DEFAULT_ENV='\''base'\''
214
+ export CONDA_PROMPT_MODIFIER='\''(base) '\''
215
+ export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\''
216
+ export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\''
217
+ export _CE_M='\'''\''
218
+ export _CE_CONDA='\'''\''
219
+ export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'''
220
+ ++++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '
221
+ ++++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin
222
+ ++++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin
223
+ ++++ export CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0
224
+ ++++ CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0
225
+ ++++ export CONDA_SHLVL=6
226
+ ++++ CONDA_SHLVL=6
227
+ ++++ export CONDA_DEFAULT_ENV=base
228
+ ++++ CONDA_DEFAULT_ENV=base
229
+ ++++ export 'CONDA_PROMPT_MODIFIER=(base) '
230
+ ++++ CONDA_PROMPT_MODIFIER='(base) '
231
+ ++++ export CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev
232
+ ++++ CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev
233
+ ++++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda
234
+ ++++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda
235
+ ++++ export _CE_M=
236
+ ++++ _CE_M=
237
+ ++++ export _CE_CONDA=
238
+ ++++ _CE_CONDA=
239
+ ++++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python
240
+ ++++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python
241
+ +++ __conda_hashr
242
+ +++ '[' -n '' ']'
243
+ +++ '[' -n '' ']'
244
+ +++ hash -r
245
+ ++ unset __conda_setup
246
+ + conda activate schemist-dev
247
+ + local cmd=activate
248
+ + case "$cmd" in
249
+ + __conda_activate activate schemist-dev
250
+ + '[' -n '' ']'
251
+ + local ask_conda
252
+ ++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '
253
+ ++ __conda_exe shell.posix activate schemist-dev
254
+ ++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate schemist-dev
255
+ + ask_conda='PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\''
256
+ export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\''
257
+ export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\''
258
+ export CONDA_SHLVL='\''7'\''
259
+ export CONDA_DEFAULT_ENV='\''schemist-dev'\''
260
+ export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\''
261
+ export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\''
262
+ export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\''
263
+ export _CE_M='\'''\''
264
+ export _CE_CONDA='\'''\''
265
+ export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'''
266
+ + eval 'PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\''
267
+ export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\''
268
+ export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\''
269
+ export CONDA_SHLVL='\''7'\''
270
+ export CONDA_DEFAULT_ENV='\''schemist-dev'\''
271
+ export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\''
272
+ export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\''
273
+ export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\''
274
+ export _CE_M='\'''\''
275
+ export _CE_CONDA='\'''\''
276
+ export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'''
277
+ ++ PS1='(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '
278
+ ++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin
279
+ ++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin
280
+ ++ export CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev
281
+ ++ CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev
282
+ ++ export CONDA_SHLVL=7
283
+ ++ CONDA_SHLVL=7
284
+ ++ export CONDA_DEFAULT_ENV=schemist-dev
285
+ ++ CONDA_DEFAULT_ENV=schemist-dev
286
+ ++ export 'CONDA_PROMPT_MODIFIER=(schemist-dev) '
287
+ ++ CONDA_PROMPT_MODIFIER='(schemist-dev) '
288
+ ++ export CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0
289
+ ++ CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0
290
+ ++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda
291
+ ++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda
292
+ ++ export _CE_M=
293
+ ++ _CE_M=
294
+ ++ export _CE_CONDA=
295
+ ++ _CE_CONDA=
296
+ ++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python
297
+ ++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python
298
+ + __conda_hashr
299
+ + '[' -n '' ']'
300
+ + '[' -n '' ']'
301
+ + hash -r
302
+ + CHUNK_HEAD_FILE=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz
303
+ + INPUT=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/test/cyc-pep-6-12mer-70M_02.csv
304
+ + COLUMN=cysteine_to_N_cyclization
305
+ + PREFIX=cyclic_
306
+ + AWK='1 { print $8, $1, $2, $10, $3 }'
307
+ + '[' -z cysteine_to_N_cyclization ']'
308
+ + '[' -z cyclic_ ']'
309
+ + '[' -z '1 { print $8, $1, $2, $10, $3 }' ']'
310
+ + awk -F, -v OFS=, '1 { print $8, $1, $2, $10, $3 }'
311
+ + 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
312
+ ++ zcat /nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz
313
+ + gzip --best
314
+ + schemist convert -f csv --column cysteine_to_N_cyclization --to id inchikey scaffold mwt clogp tpsa --prefix cyclic_ --options prefix=SCB-
315
+ ++ head -n1
316
+ ++ tr ' ' ,
317
+ 🚀 Converting between string representations with the following parameters:
318
+ subcommand: convert
319
+ output: <_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>
320
+ format: csv
321
+ input: <_io.TextIOWrapper name='<stdin>' mode='r' encoding='utf-8'>
322
+ representation: SMILES
323
+ column: cysteine_to_N_cyclization
324
+ prefix: cyclic_
325
+ to: ['id', 'inchikey', 'scaffold', 'mwt', 'clogp', 'tpsa']
326
+ options: ['prefix=SCB-']
327
+ func: <function _convert at 0x7ff3285db240>
328
+
329
+ Error counts:
330
+ cyclic_id: 0
331
+ cyclic_inchikey: 0
332
+ cyclic_scaffold: 0
333
+ cyclic_mwt: 0
334
+ cyclic_clogp: 0
335
+ cyclic_tpsa: 0
336
+ ⏰ Completed process in 3:24:16.673804
337
+ + 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.csv.gz CHANGED
@@ -1,3 +1,3 @@
1
  version https://git-lfs.github.com/spec/v1
2
- oid sha256:758cea96c5ad60d9a8f1a1958832c52d54839f5070c9d67fcac290b3ab63fd72
3
- size 64582471
 
1
  version https://git-lfs.github.com/spec/v1
2
+ oid sha256:9a998db31deff36153cb620395dc97628d3c7d6b7c5ffed9fdc4482ca9e797df
3
+ size 121096790
test/cyc-pep-6-12mer-70M_03.log ADDED
@@ -0,0 +1,337 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ + module purge
2
+ + '[' -z '' ']'
3
+ + case "$-" in
4
+ + __lmod_sh_dbg=x
5
+ + '[' -n x ']'
6
+ + set +x
7
+ Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output
8
+ Shell debugging restarted
9
+ + unset __lmod_sh_dbg
10
+ + return 0
11
+ + module load Anaconda3/2023.03
12
+ + '[' -z '' ']'
13
+ + case "$-" in
14
+ + __lmod_sh_dbg=x
15
+ + '[' -n x ']'
16
+ + set +x
17
+ Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output
18
+ Shell debugging restarted
19
+ + unset __lmod_sh_dbg
20
+ + return 0
21
+ + source /camp/home/johnsoe/.bashrc
22
+ ++ '[' '' = yes ']'
23
+ ++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '
24
+ +++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.bash hook
25
+ ++ __conda_setup='export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\''
26
+ export _CE_M='\'''\''
27
+ export _CE_CONDA='\'''\''
28
+ export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''
29
+
30
+ # Copyright (C) 2012 Anaconda, Inc
31
+ # SPDX-License-Identifier: BSD-3-Clause
32
+ __conda_exe() (
33
+ "$CONDA_EXE" $_CE_M $_CE_CONDA "$@"
34
+ )
35
+
36
+ __conda_hashr() {
37
+ if [ -n "${ZSH_VERSION:+x}" ]; then
38
+ \rehash
39
+ elif [ -n "${POSH_VERSION:+x}" ]; then
40
+ : # pass
41
+ else
42
+ \hash -r
43
+ fi
44
+ }
45
+
46
+ __conda_activate() {
47
+ if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then
48
+ # Handle transition from shell activated with conda <= 4.3 to a subsequent activation
49
+ # after conda updated to >= 4.4. See issue #6173.
50
+ PS1="$CONDA_PS1_BACKUP"
51
+ \unset CONDA_PS1_BACKUP
52
+ fi
53
+ \local ask_conda
54
+ ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return
55
+ \eval "$ask_conda"
56
+ __conda_hashr
57
+ }
58
+
59
+ __conda_reactivate() {
60
+ \local ask_conda
61
+ ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return
62
+ \eval "$ask_conda"
63
+ __conda_hashr
64
+ }
65
+
66
+ conda() {
67
+ \local cmd="${1-__missing__}"
68
+ case "$cmd" in
69
+ activate|deactivate)
70
+ __conda_activate "$@"
71
+ ;;
72
+ install|update|upgrade|remove|uninstall)
73
+ __conda_exe "$@" || \return
74
+ __conda_reactivate
75
+ ;;
76
+ *)
77
+ __conda_exe "$@"
78
+ ;;
79
+ esac
80
+ }
81
+
82
+ if [ -z "${CONDA_SHLVL+x}" ]; then
83
+ \export CONDA_SHLVL=0
84
+ # In dev-mode CONDA_EXE is python.exe and on Windows
85
+ # it is in a different relative location to condabin.
86
+ if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then
87
+ PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}"
88
+ else
89
+ PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}"
90
+ fi
91
+ \export PATH
92
+
93
+ # We'\''re not allowing PS1 to be unbound. It must at least be set.
94
+ # However, we'\''re not exporting it, which can cause problems when starting a second shell
95
+ # via a first shell (i.e. starting zsh from bash).
96
+ if [ -z "${PS1+x}" ]; then
97
+ PS1=
98
+ fi
99
+ fi
100
+
101
+ conda activate base'
102
+ ++ '[' 0 -eq 0 ']'
103
+ ++ eval 'export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\''
104
+ export _CE_M='\'''\''
105
+ export _CE_CONDA='\'''\''
106
+ export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''
107
+
108
+ # Copyright (C) 2012 Anaconda, Inc
109
+ # SPDX-License-Identifier: BSD-3-Clause
110
+ __conda_exe() (
111
+ "$CONDA_EXE" $_CE_M $_CE_CONDA "$@"
112
+ )
113
+
114
+ __conda_hashr() {
115
+ if [ -n "${ZSH_VERSION:+x}" ]; then
116
+ \rehash
117
+ elif [ -n "${POSH_VERSION:+x}" ]; then
118
+ : # pass
119
+ else
120
+ \hash -r
121
+ fi
122
+ }
123
+
124
+ __conda_activate() {
125
+ if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then
126
+ # Handle transition from shell activated with conda <= 4.3 to a subsequent activation
127
+ # after conda updated to >= 4.4. See issue #6173.
128
+ PS1="$CONDA_PS1_BACKUP"
129
+ \unset CONDA_PS1_BACKUP
130
+ fi
131
+ \local ask_conda
132
+ ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return
133
+ \eval "$ask_conda"
134
+ __conda_hashr
135
+ }
136
+
137
+ __conda_reactivate() {
138
+ \local ask_conda
139
+ ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return
140
+ \eval "$ask_conda"
141
+ __conda_hashr
142
+ }
143
+
144
+ conda() {
145
+ \local cmd="${1-__missing__}"
146
+ case "$cmd" in
147
+ activate|deactivate)
148
+ __conda_activate "$@"
149
+ ;;
150
+ install|update|upgrade|remove|uninstall)
151
+ __conda_exe "$@" || \return
152
+ __conda_reactivate
153
+ ;;
154
+ *)
155
+ __conda_exe "$@"
156
+ ;;
157
+ esac
158
+ }
159
+
160
+ if [ -z "${CONDA_SHLVL+x}" ]; then
161
+ \export CONDA_SHLVL=0
162
+ # In dev-mode CONDA_EXE is python.exe and on Windows
163
+ # it is in a different relative location to condabin.
164
+ if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then
165
+ PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}"
166
+ else
167
+ PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}"
168
+ fi
169
+ \export PATH
170
+
171
+ # We'\''re not allowing PS1 to be unbound. It must at least be set.
172
+ # However, we'\''re not exporting it, which can cause problems when starting a second shell
173
+ # via a first shell (i.e. starting zsh from bash).
174
+ if [ -z "${PS1+x}" ]; then
175
+ PS1=
176
+ fi
177
+ fi
178
+
179
+ conda activate base'
180
+ +++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda
181
+ +++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda
182
+ +++ export _CE_M=
183
+ +++ _CE_M=
184
+ +++ export _CE_CONDA=
185
+ +++ _CE_CONDA=
186
+ +++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python
187
+ +++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python
188
+ +++ '[' -z x ']'
189
+ +++ conda activate base
190
+ +++ local cmd=activate
191
+ +++ case "$cmd" in
192
+ +++ __conda_activate activate base
193
+ +++ '[' -n '' ']'
194
+ +++ local ask_conda
195
+ ++++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '
196
+ ++++ __conda_exe shell.posix activate base
197
+ ++++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate base
198
+ +++ ask_conda='PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\''
199
+ export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\''
200
+ export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\''
201
+ export CONDA_SHLVL='\''6'\''
202
+ export CONDA_DEFAULT_ENV='\''base'\''
203
+ export CONDA_PROMPT_MODIFIER='\''(base) '\''
204
+ export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\''
205
+ export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\''
206
+ export _CE_M='\'''\''
207
+ export _CE_CONDA='\'''\''
208
+ export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'''
209
+ +++ eval 'PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\''
210
+ export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\''
211
+ export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\''
212
+ export CONDA_SHLVL='\''6'\''
213
+ export CONDA_DEFAULT_ENV='\''base'\''
214
+ export CONDA_PROMPT_MODIFIER='\''(base) '\''
215
+ export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\''
216
+ export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\''
217
+ export _CE_M='\'''\''
218
+ export _CE_CONDA='\'''\''
219
+ export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'''
220
+ ++++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '
221
+ ++++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin
222
+ ++++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin
223
+ ++++ export CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0
224
+ ++++ CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0
225
+ ++++ export CONDA_SHLVL=6
226
+ ++++ CONDA_SHLVL=6
227
+ ++++ export CONDA_DEFAULT_ENV=base
228
+ ++++ CONDA_DEFAULT_ENV=base
229
+ ++++ export 'CONDA_PROMPT_MODIFIER=(base) '
230
+ ++++ CONDA_PROMPT_MODIFIER='(base) '
231
+ ++++ export CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev
232
+ ++++ CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev
233
+ ++++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda
234
+ ++++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda
235
+ ++++ export _CE_M=
236
+ ++++ _CE_M=
237
+ ++++ export _CE_CONDA=
238
+ ++++ _CE_CONDA=
239
+ ++++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python
240
+ ++++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python
241
+ +++ __conda_hashr
242
+ +++ '[' -n '' ']'
243
+ +++ '[' -n '' ']'
244
+ +++ hash -r
245
+ ++ unset __conda_setup
246
+ + conda activate schemist-dev
247
+ + local cmd=activate
248
+ + case "$cmd" in
249
+ + __conda_activate activate schemist-dev
250
+ + '[' -n '' ']'
251
+ + local ask_conda
252
+ ++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '
253
+ ++ __conda_exe shell.posix activate schemist-dev
254
+ ++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate schemist-dev
255
+ + ask_conda='PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\''
256
+ export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\''
257
+ export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\''
258
+ export CONDA_SHLVL='\''7'\''
259
+ export CONDA_DEFAULT_ENV='\''schemist-dev'\''
260
+ export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\''
261
+ export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\''
262
+ export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\''
263
+ export _CE_M='\'''\''
264
+ export _CE_CONDA='\'''\''
265
+ export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'''
266
+ + eval 'PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\''
267
+ export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\''
268
+ export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\''
269
+ export CONDA_SHLVL='\''7'\''
270
+ export CONDA_DEFAULT_ENV='\''schemist-dev'\''
271
+ export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\''
272
+ export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\''
273
+ export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\''
274
+ export _CE_M='\'''\''
275
+ export _CE_CONDA='\'''\''
276
+ export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'''
277
+ ++ PS1='(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '
278
+ ++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin
279
+ ++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin
280
+ ++ export CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev
281
+ ++ CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev
282
+ ++ export CONDA_SHLVL=7
283
+ ++ CONDA_SHLVL=7
284
+ ++ export CONDA_DEFAULT_ENV=schemist-dev
285
+ ++ CONDA_DEFAULT_ENV=schemist-dev
286
+ ++ export 'CONDA_PROMPT_MODIFIER=(schemist-dev) '
287
+ ++ CONDA_PROMPT_MODIFIER='(schemist-dev) '
288
+ ++ export CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0
289
+ ++ CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0
290
+ ++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda
291
+ ++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda
292
+ ++ export _CE_M=
293
+ ++ _CE_M=
294
+ ++ export _CE_CONDA=
295
+ ++ _CE_CONDA=
296
+ ++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python
297
+ ++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python
298
+ + __conda_hashr
299
+ + '[' -n '' ']'
300
+ + '[' -n '' ']'
301
+ + hash -r
302
+ + CHUNK_HEAD_FILE=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz
303
+ + INPUT=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/test/cyc-pep-6-12mer-70M_03.csv
304
+ + COLUMN=cysteine_to_N_cyclization
305
+ + PREFIX=cyclic_
306
+ + AWK='1 { print $8, $1, $2, $10, $3 }'
307
+ + '[' -z cysteine_to_N_cyclization ']'
308
+ + '[' -z cyclic_ ']'
309
+ + '[' -z '1 { print $8, $1, $2, $10, $3 }' ']'
310
+ + awk -F, -v OFS=, '1 { print $8, $1, $2, $10, $3 }'
311
+ + 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
312
+ + gzip --best
313
+ + schemist convert -f csv --column cysteine_to_N_cyclization --to id inchikey scaffold mwt clogp tpsa --prefix cyclic_ --options prefix=SCB-
314
+ ++ zcat /nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz
315
+ ++ head -n1
316
+ ++ tr ' ' ,
317
+ 🚀 Converting between string representations with the following parameters:
318
+ subcommand: convert
319
+ output: <_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>
320
+ format: csv
321
+ input: <_io.TextIOWrapper name='<stdin>' mode='r' encoding='utf-8'>
322
+ representation: SMILES
323
+ column: cysteine_to_N_cyclization
324
+ prefix: cyclic_
325
+ to: ['id', 'inchikey', 'scaffold', 'mwt', 'clogp', 'tpsa']
326
+ options: ['prefix=SCB-']
327
+ func: <function _convert at 0x7ffb82d8f240>
328
+
329
+ Error counts:
330
+ cyclic_id: 0
331
+ cyclic_inchikey: 0
332
+ cyclic_scaffold: 0
333
+ cyclic_mwt: 0
334
+ cyclic_clogp: 0
335
+ cyclic_tpsa: 0
336
+ ⏰ Completed process in 3:38:32.888238
337
+ + 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.csv.gz CHANGED
@@ -1,3 +1,3 @@
1
  version https://git-lfs.github.com/spec/v1
2
- oid sha256:c7163b34e785bf3a9d481d4ba7dfa9b0b94602ce9c888b1182a69f31fdb47cce
3
- size 62712613
 
1
  version https://git-lfs.github.com/spec/v1
2
+ oid sha256:bea05e48dd08aadf83a368b21f7548c8128584f3dd480e3758dbfc6ec00f55ff
3
+ size 118252402
test/cyc-pep-6-12mer-70M_04.log ADDED
@@ -0,0 +1,337 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ + module purge
2
+ + '[' -z '' ']'
3
+ + case "$-" in
4
+ + __lmod_sh_dbg=x
5
+ + '[' -n x ']'
6
+ + set +x
7
+ Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output
8
+ Shell debugging restarted
9
+ + unset __lmod_sh_dbg
10
+ + return 0
11
+ + module load Anaconda3/2023.03
12
+ + '[' -z '' ']'
13
+ + case "$-" in
14
+ + __lmod_sh_dbg=x
15
+ + '[' -n x ']'
16
+ + set +x
17
+ Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output
18
+ Shell debugging restarted
19
+ + unset __lmod_sh_dbg
20
+ + return 0
21
+ + source /camp/home/johnsoe/.bashrc
22
+ ++ '[' '' = yes ']'
23
+ ++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '
24
+ +++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.bash hook
25
+ ++ __conda_setup='export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\''
26
+ export _CE_M='\'''\''
27
+ export _CE_CONDA='\'''\''
28
+ export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''
29
+
30
+ # Copyright (C) 2012 Anaconda, Inc
31
+ # SPDX-License-Identifier: BSD-3-Clause
32
+ __conda_exe() (
33
+ "$CONDA_EXE" $_CE_M $_CE_CONDA "$@"
34
+ )
35
+
36
+ __conda_hashr() {
37
+ if [ -n "${ZSH_VERSION:+x}" ]; then
38
+ \rehash
39
+ elif [ -n "${POSH_VERSION:+x}" ]; then
40
+ : # pass
41
+ else
42
+ \hash -r
43
+ fi
44
+ }
45
+
46
+ __conda_activate() {
47
+ if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then
48
+ # Handle transition from shell activated with conda <= 4.3 to a subsequent activation
49
+ # after conda updated to >= 4.4. See issue #6173.
50
+ PS1="$CONDA_PS1_BACKUP"
51
+ \unset CONDA_PS1_BACKUP
52
+ fi
53
+ \local ask_conda
54
+ ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return
55
+ \eval "$ask_conda"
56
+ __conda_hashr
57
+ }
58
+
59
+ __conda_reactivate() {
60
+ \local ask_conda
61
+ ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return
62
+ \eval "$ask_conda"
63
+ __conda_hashr
64
+ }
65
+
66
+ conda() {
67
+ \local cmd="${1-__missing__}"
68
+ case "$cmd" in
69
+ activate|deactivate)
70
+ __conda_activate "$@"
71
+ ;;
72
+ install|update|upgrade|remove|uninstall)
73
+ __conda_exe "$@" || \return
74
+ __conda_reactivate
75
+ ;;
76
+ *)
77
+ __conda_exe "$@"
78
+ ;;
79
+ esac
80
+ }
81
+
82
+ if [ -z "${CONDA_SHLVL+x}" ]; then
83
+ \export CONDA_SHLVL=0
84
+ # In dev-mode CONDA_EXE is python.exe and on Windows
85
+ # it is in a different relative location to condabin.
86
+ if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then
87
+ PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}"
88
+ else
89
+ PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}"
90
+ fi
91
+ \export PATH
92
+
93
+ # We'\''re not allowing PS1 to be unbound. It must at least be set.
94
+ # However, we'\''re not exporting it, which can cause problems when starting a second shell
95
+ # via a first shell (i.e. starting zsh from bash).
96
+ if [ -z "${PS1+x}" ]; then
97
+ PS1=
98
+ fi
99
+ fi
100
+
101
+ conda activate base'
102
+ ++ '[' 0 -eq 0 ']'
103
+ ++ eval 'export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\''
104
+ export _CE_M='\'''\''
105
+ export _CE_CONDA='\'''\''
106
+ export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''
107
+
108
+ # Copyright (C) 2012 Anaconda, Inc
109
+ # SPDX-License-Identifier: BSD-3-Clause
110
+ __conda_exe() (
111
+ "$CONDA_EXE" $_CE_M $_CE_CONDA "$@"
112
+ )
113
+
114
+ __conda_hashr() {
115
+ if [ -n "${ZSH_VERSION:+x}" ]; then
116
+ \rehash
117
+ elif [ -n "${POSH_VERSION:+x}" ]; then
118
+ : # pass
119
+ else
120
+ \hash -r
121
+ fi
122
+ }
123
+
124
+ __conda_activate() {
125
+ if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then
126
+ # Handle transition from shell activated with conda <= 4.3 to a subsequent activation
127
+ # after conda updated to >= 4.4. See issue #6173.
128
+ PS1="$CONDA_PS1_BACKUP"
129
+ \unset CONDA_PS1_BACKUP
130
+ fi
131
+ \local ask_conda
132
+ ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return
133
+ \eval "$ask_conda"
134
+ __conda_hashr
135
+ }
136
+
137
+ __conda_reactivate() {
138
+ \local ask_conda
139
+ ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return
140
+ \eval "$ask_conda"
141
+ __conda_hashr
142
+ }
143
+
144
+ conda() {
145
+ \local cmd="${1-__missing__}"
146
+ case "$cmd" in
147
+ activate|deactivate)
148
+ __conda_activate "$@"
149
+ ;;
150
+ install|update|upgrade|remove|uninstall)
151
+ __conda_exe "$@" || \return
152
+ __conda_reactivate
153
+ ;;
154
+ *)
155
+ __conda_exe "$@"
156
+ ;;
157
+ esac
158
+ }
159
+
160
+ if [ -z "${CONDA_SHLVL+x}" ]; then
161
+ \export CONDA_SHLVL=0
162
+ # In dev-mode CONDA_EXE is python.exe and on Windows
163
+ # it is in a different relative location to condabin.
164
+ if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then
165
+ PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}"
166
+ else
167
+ PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}"
168
+ fi
169
+ \export PATH
170
+
171
+ # We'\''re not allowing PS1 to be unbound. It must at least be set.
172
+ # However, we'\''re not exporting it, which can cause problems when starting a second shell
173
+ # via a first shell (i.e. starting zsh from bash).
174
+ if [ -z "${PS1+x}" ]; then
175
+ PS1=
176
+ fi
177
+ fi
178
+
179
+ conda activate base'
180
+ +++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda
181
+ +++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda
182
+ +++ export _CE_M=
183
+ +++ _CE_M=
184
+ +++ export _CE_CONDA=
185
+ +++ _CE_CONDA=
186
+ +++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python
187
+ +++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python
188
+ +++ '[' -z x ']'
189
+ +++ conda activate base
190
+ +++ local cmd=activate
191
+ +++ case "$cmd" in
192
+ +++ __conda_activate activate base
193
+ +++ '[' -n '' ']'
194
+ +++ local ask_conda
195
+ ++++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '
196
+ ++++ __conda_exe shell.posix activate base
197
+ ++++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate base
198
+ +++ ask_conda='PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\''
199
+ export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\''
200
+ export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\''
201
+ export CONDA_SHLVL='\''6'\''
202
+ export CONDA_DEFAULT_ENV='\''base'\''
203
+ export CONDA_PROMPT_MODIFIER='\''(base) '\''
204
+ export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\''
205
+ export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\''
206
+ export _CE_M='\'''\''
207
+ export _CE_CONDA='\'''\''
208
+ export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'''
209
+ +++ eval 'PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\''
210
+ export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\''
211
+ export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\''
212
+ export CONDA_SHLVL='\''6'\''
213
+ export CONDA_DEFAULT_ENV='\''base'\''
214
+ export CONDA_PROMPT_MODIFIER='\''(base) '\''
215
+ export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\''
216
+ export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\''
217
+ export _CE_M='\'''\''
218
+ export _CE_CONDA='\'''\''
219
+ export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'''
220
+ ++++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '
221
+ ++++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin
222
+ ++++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin
223
+ ++++ export CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0
224
+ ++++ CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0
225
+ ++++ export CONDA_SHLVL=6
226
+ ++++ CONDA_SHLVL=6
227
+ ++++ export CONDA_DEFAULT_ENV=base
228
+ ++++ CONDA_DEFAULT_ENV=base
229
+ ++++ export 'CONDA_PROMPT_MODIFIER=(base) '
230
+ ++++ CONDA_PROMPT_MODIFIER='(base) '
231
+ ++++ export CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev
232
+ ++++ CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev
233
+ ++++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda
234
+ ++++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda
235
+ ++++ export _CE_M=
236
+ ++++ _CE_M=
237
+ ++++ export _CE_CONDA=
238
+ ++++ _CE_CONDA=
239
+ ++++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python
240
+ ++++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python
241
+ +++ __conda_hashr
242
+ +++ '[' -n '' ']'
243
+ +++ '[' -n '' ']'
244
+ +++ hash -r
245
+ ++ unset __conda_setup
246
+ + conda activate schemist-dev
247
+ + local cmd=activate
248
+ + case "$cmd" in
249
+ + __conda_activate activate schemist-dev
250
+ + '[' -n '' ']'
251
+ + local ask_conda
252
+ ++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '
253
+ ++ __conda_exe shell.posix activate schemist-dev
254
+ ++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate schemist-dev
255
+ + ask_conda='PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\''
256
+ export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\''
257
+ export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\''
258
+ export CONDA_SHLVL='\''7'\''
259
+ export CONDA_DEFAULT_ENV='\''schemist-dev'\''
260
+ export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\''
261
+ export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\''
262
+ export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\''
263
+ export _CE_M='\'''\''
264
+ export _CE_CONDA='\'''\''
265
+ export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'''
266
+ + eval 'PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\''
267
+ export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\''
268
+ export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\''
269
+ export CONDA_SHLVL='\''7'\''
270
+ export CONDA_DEFAULT_ENV='\''schemist-dev'\''
271
+ export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\''
272
+ export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\''
273
+ export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\''
274
+ export _CE_M='\'''\''
275
+ export _CE_CONDA='\'''\''
276
+ export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'''
277
+ ++ PS1='(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '
278
+ ++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin
279
+ ++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin
280
+ ++ export CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev
281
+ ++ CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev
282
+ ++ export CONDA_SHLVL=7
283
+ ++ CONDA_SHLVL=7
284
+ ++ export CONDA_DEFAULT_ENV=schemist-dev
285
+ ++ CONDA_DEFAULT_ENV=schemist-dev
286
+ ++ export 'CONDA_PROMPT_MODIFIER=(schemist-dev) '
287
+ ++ CONDA_PROMPT_MODIFIER='(schemist-dev) '
288
+ ++ export CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0
289
+ ++ CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0
290
+ ++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda
291
+ ++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda
292
+ ++ export _CE_M=
293
+ ++ _CE_M=
294
+ ++ export _CE_CONDA=
295
+ ++ _CE_CONDA=
296
+ ++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python
297
+ ++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python
298
+ + __conda_hashr
299
+ + '[' -n '' ']'
300
+ + '[' -n '' ']'
301
+ + hash -r
302
+ + CHUNK_HEAD_FILE=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz
303
+ + INPUT=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/test/cyc-pep-6-12mer-70M_04.csv
304
+ + COLUMN=cysteine_to_N_cyclization
305
+ + PREFIX=cyclic_
306
+ + AWK='1 { print $8, $1, $2, $10, $3 }'
307
+ + '[' -z cysteine_to_N_cyclization ']'
308
+ + '[' -z cyclic_ ']'
309
+ + '[' -z '1 { print $8, $1, $2, $10, $3 }' ']'
310
+ + awk -F, -v OFS=, '1 { print $8, $1, $2, $10, $3 }'
311
+ + 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
312
+ ++ zcat /nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz
313
+ + schemist convert -f csv --column cysteine_to_N_cyclization --to id inchikey scaffold mwt clogp tpsa --prefix cyclic_ --options prefix=SCB-
314
+ ++ head -n1
315
+ + gzip --best
316
+ ++ tr ' ' ,
317
+ 🚀 Converting between string representations with the following parameters:
318
+ subcommand: convert
319
+ output: <_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>
320
+ format: csv
321
+ input: <_io.TextIOWrapper name='<stdin>' mode='r' encoding='utf-8'>
322
+ representation: SMILES
323
+ column: cysteine_to_N_cyclization
324
+ prefix: cyclic_
325
+ to: ['id', 'inchikey', 'scaffold', 'mwt', 'clogp', 'tpsa']
326
+ options: ['prefix=SCB-']
327
+ func: <function _convert at 0x7f8ebdc23240>
328
+
329
+ Error counts:
330
+ cyclic_id: 0
331
+ cyclic_inchikey: 0
332
+ cyclic_scaffold: 0
333
+ cyclic_mwt: 0
334
+ cyclic_clogp: 0
335
+ cyclic_tpsa: 0
336
+ ⏰ Completed process in 3:29:01.669280
337
+ + 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.csv.gz CHANGED
@@ -1,3 +1,3 @@
1
  version https://git-lfs.github.com/spec/v1
2
- oid sha256:458c84baee025b66dcd2d989b276628f538ae76830dae896751ec11e7fb03849
3
- size 29476270
 
1
  version https://git-lfs.github.com/spec/v1
2
+ oid sha256:2b854ad30333d2b0935f3e64d66b8b497d975915f30f7cb21008db529c945298
3
+ size 70372794
test/cyc-pep-6-12mer-70M_05.log ADDED
@@ -0,0 +1,337 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ + module purge
2
+ + '[' -z '' ']'
3
+ + case "$-" in
4
+ + __lmod_sh_dbg=x
5
+ + '[' -n x ']'
6
+ + set +x
7
+ Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output
8
+ Shell debugging restarted
9
+ + unset __lmod_sh_dbg
10
+ + return 0
11
+ + module load Anaconda3/2023.03
12
+ + '[' -z '' ']'
13
+ + case "$-" in
14
+ + __lmod_sh_dbg=x
15
+ + '[' -n x ']'
16
+ + set +x
17
+ Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output
18
+ Shell debugging restarted
19
+ + unset __lmod_sh_dbg
20
+ + return 0
21
+ + source /camp/home/johnsoe/.bashrc
22
+ ++ '[' '' = yes ']'
23
+ ++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '
24
+ +++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.bash hook
25
+ ++ __conda_setup='export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\''
26
+ export _CE_M='\'''\''
27
+ export _CE_CONDA='\'''\''
28
+ export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''
29
+
30
+ # Copyright (C) 2012 Anaconda, Inc
31
+ # SPDX-License-Identifier: BSD-3-Clause
32
+ __conda_exe() (
33
+ "$CONDA_EXE" $_CE_M $_CE_CONDA "$@"
34
+ )
35
+
36
+ __conda_hashr() {
37
+ if [ -n "${ZSH_VERSION:+x}" ]; then
38
+ \rehash
39
+ elif [ -n "${POSH_VERSION:+x}" ]; then
40
+ : # pass
41
+ else
42
+ \hash -r
43
+ fi
44
+ }
45
+
46
+ __conda_activate() {
47
+ if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then
48
+ # Handle transition from shell activated with conda <= 4.3 to a subsequent activation
49
+ # after conda updated to >= 4.4. See issue #6173.
50
+ PS1="$CONDA_PS1_BACKUP"
51
+ \unset CONDA_PS1_BACKUP
52
+ fi
53
+ \local ask_conda
54
+ ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return
55
+ \eval "$ask_conda"
56
+ __conda_hashr
57
+ }
58
+
59
+ __conda_reactivate() {
60
+ \local ask_conda
61
+ ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return
62
+ \eval "$ask_conda"
63
+ __conda_hashr
64
+ }
65
+
66
+ conda() {
67
+ \local cmd="${1-__missing__}"
68
+ case "$cmd" in
69
+ activate|deactivate)
70
+ __conda_activate "$@"
71
+ ;;
72
+ install|update|upgrade|remove|uninstall)
73
+ __conda_exe "$@" || \return
74
+ __conda_reactivate
75
+ ;;
76
+ *)
77
+ __conda_exe "$@"
78
+ ;;
79
+ esac
80
+ }
81
+
82
+ if [ -z "${CONDA_SHLVL+x}" ]; then
83
+ \export CONDA_SHLVL=0
84
+ # In dev-mode CONDA_EXE is python.exe and on Windows
85
+ # it is in a different relative location to condabin.
86
+ if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then
87
+ PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}"
88
+ else
89
+ PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}"
90
+ fi
91
+ \export PATH
92
+
93
+ # We'\''re not allowing PS1 to be unbound. It must at least be set.
94
+ # However, we'\''re not exporting it, which can cause problems when starting a second shell
95
+ # via a first shell (i.e. starting zsh from bash).
96
+ if [ -z "${PS1+x}" ]; then
97
+ PS1=
98
+ fi
99
+ fi
100
+
101
+ conda activate base'
102
+ ++ '[' 0 -eq 0 ']'
103
+ ++ eval 'export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\''
104
+ export _CE_M='\'''\''
105
+ export _CE_CONDA='\'''\''
106
+ export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''
107
+
108
+ # Copyright (C) 2012 Anaconda, Inc
109
+ # SPDX-License-Identifier: BSD-3-Clause
110
+ __conda_exe() (
111
+ "$CONDA_EXE" $_CE_M $_CE_CONDA "$@"
112
+ )
113
+
114
+ __conda_hashr() {
115
+ if [ -n "${ZSH_VERSION:+x}" ]; then
116
+ \rehash
117
+ elif [ -n "${POSH_VERSION:+x}" ]; then
118
+ : # pass
119
+ else
120
+ \hash -r
121
+ fi
122
+ }
123
+
124
+ __conda_activate() {
125
+ if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then
126
+ # Handle transition from shell activated with conda <= 4.3 to a subsequent activation
127
+ # after conda updated to >= 4.4. See issue #6173.
128
+ PS1="$CONDA_PS1_BACKUP"
129
+ \unset CONDA_PS1_BACKUP
130
+ fi
131
+ \local ask_conda
132
+ ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return
133
+ \eval "$ask_conda"
134
+ __conda_hashr
135
+ }
136
+
137
+ __conda_reactivate() {
138
+ \local ask_conda
139
+ ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return
140
+ \eval "$ask_conda"
141
+ __conda_hashr
142
+ }
143
+
144
+ conda() {
145
+ \local cmd="${1-__missing__}"
146
+ case "$cmd" in
147
+ activate|deactivate)
148
+ __conda_activate "$@"
149
+ ;;
150
+ install|update|upgrade|remove|uninstall)
151
+ __conda_exe "$@" || \return
152
+ __conda_reactivate
153
+ ;;
154
+ *)
155
+ __conda_exe "$@"
156
+ ;;
157
+ esac
158
+ }
159
+
160
+ if [ -z "${CONDA_SHLVL+x}" ]; then
161
+ \export CONDA_SHLVL=0
162
+ # In dev-mode CONDA_EXE is python.exe and on Windows
163
+ # it is in a different relative location to condabin.
164
+ if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then
165
+ PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}"
166
+ else
167
+ PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}"
168
+ fi
169
+ \export PATH
170
+
171
+ # We'\''re not allowing PS1 to be unbound. It must at least be set.
172
+ # However, we'\''re not exporting it, which can cause problems when starting a second shell
173
+ # via a first shell (i.e. starting zsh from bash).
174
+ if [ -z "${PS1+x}" ]; then
175
+ PS1=
176
+ fi
177
+ fi
178
+
179
+ conda activate base'
180
+ +++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda
181
+ +++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda
182
+ +++ export _CE_M=
183
+ +++ _CE_M=
184
+ +++ export _CE_CONDA=
185
+ +++ _CE_CONDA=
186
+ +++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python
187
+ +++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python
188
+ +++ '[' -z x ']'
189
+ +++ conda activate base
190
+ +++ local cmd=activate
191
+ +++ case "$cmd" in
192
+ +++ __conda_activate activate base
193
+ +++ '[' -n '' ']'
194
+ +++ local ask_conda
195
+ ++++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '
196
+ ++++ __conda_exe shell.posix activate base
197
+ ++++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate base
198
+ +++ ask_conda='PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\''
199
+ export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\''
200
+ export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\''
201
+ export CONDA_SHLVL='\''6'\''
202
+ export CONDA_DEFAULT_ENV='\''base'\''
203
+ export CONDA_PROMPT_MODIFIER='\''(base) '\''
204
+ export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\''
205
+ export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\''
206
+ export _CE_M='\'''\''
207
+ export _CE_CONDA='\'''\''
208
+ export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'''
209
+ +++ eval 'PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\''
210
+ export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\''
211
+ export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\''
212
+ export CONDA_SHLVL='\''6'\''
213
+ export CONDA_DEFAULT_ENV='\''base'\''
214
+ export CONDA_PROMPT_MODIFIER='\''(base) '\''
215
+ export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\''
216
+ export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\''
217
+ export _CE_M='\'''\''
218
+ export _CE_CONDA='\'''\''
219
+ export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'''
220
+ ++++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '
221
+ ++++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin
222
+ ++++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin
223
+ ++++ export CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0
224
+ ++++ CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0
225
+ ++++ export CONDA_SHLVL=6
226
+ ++++ CONDA_SHLVL=6
227
+ ++++ export CONDA_DEFAULT_ENV=base
228
+ ++++ CONDA_DEFAULT_ENV=base
229
+ ++++ export 'CONDA_PROMPT_MODIFIER=(base) '
230
+ ++++ CONDA_PROMPT_MODIFIER='(base) '
231
+ ++++ export CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev
232
+ ++++ CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev
233
+ ++++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda
234
+ ++++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda
235
+ ++++ export _CE_M=
236
+ ++++ _CE_M=
237
+ ++++ export _CE_CONDA=
238
+ ++++ _CE_CONDA=
239
+ ++++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python
240
+ ++++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python
241
+ +++ __conda_hashr
242
+ +++ '[' -n '' ']'
243
+ +++ '[' -n '' ']'
244
+ +++ hash -r
245
+ ++ unset __conda_setup
246
+ + conda activate schemist-dev
247
+ + local cmd=activate
248
+ + case "$cmd" in
249
+ + __conda_activate activate schemist-dev
250
+ + '[' -n '' ']'
251
+ + local ask_conda
252
+ ++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '
253
+ ++ __conda_exe shell.posix activate schemist-dev
254
+ ++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate schemist-dev
255
+ + ask_conda='PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\''
256
+ export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\''
257
+ export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\''
258
+ export CONDA_SHLVL='\''7'\''
259
+ export CONDA_DEFAULT_ENV='\''schemist-dev'\''
260
+ export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\''
261
+ export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\''
262
+ export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\''
263
+ export _CE_M='\'''\''
264
+ export _CE_CONDA='\'''\''
265
+ export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'''
266
+ + eval 'PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\''
267
+ export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\''
268
+ export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\''
269
+ export CONDA_SHLVL='\''7'\''
270
+ export CONDA_DEFAULT_ENV='\''schemist-dev'\''
271
+ export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\''
272
+ export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\''
273
+ export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\''
274
+ export _CE_M='\'''\''
275
+ export _CE_CONDA='\'''\''
276
+ export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'''
277
+ ++ PS1='(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '
278
+ ++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin
279
+ ++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin
280
+ ++ export CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev
281
+ ++ CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev
282
+ ++ export CONDA_SHLVL=7
283
+ ++ CONDA_SHLVL=7
284
+ ++ export CONDA_DEFAULT_ENV=schemist-dev
285
+ ++ CONDA_DEFAULT_ENV=schemist-dev
286
+ ++ export 'CONDA_PROMPT_MODIFIER=(schemist-dev) '
287
+ ++ CONDA_PROMPT_MODIFIER='(schemist-dev) '
288
+ ++ export CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0
289
+ ++ CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0
290
+ ++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda
291
+ ++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda
292
+ ++ export _CE_M=
293
+ ++ _CE_M=
294
+ ++ export _CE_CONDA=
295
+ ++ _CE_CONDA=
296
+ ++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python
297
+ ++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python
298
+ + __conda_hashr
299
+ + '[' -n '' ']'
300
+ + '[' -n '' ']'
301
+ + hash -r
302
+ + CHUNK_HEAD_FILE=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz
303
+ + INPUT=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/test/cyc-pep-6-12mer-70M_05.csv
304
+ + COLUMN=cysteine_to_N_cyclization
305
+ + PREFIX=cyclic_
306
+ + AWK='1 { print $8, $1, $2, $10, $3 }'
307
+ + '[' -z cysteine_to_N_cyclization ']'
308
+ + '[' -z cyclic_ ']'
309
+ + '[' -z '1 { print $8, $1, $2, $10, $3 }' ']'
310
+ + 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
311
+ + schemist convert -f csv --column cysteine_to_N_cyclization --to id inchikey scaffold mwt clogp tpsa --prefix cyclic_ --options prefix=SCB-
312
+ ++ head -n1
313
+ + gzip --best
314
+ ++ zcat /nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz
315
+ + awk -F, -v OFS=, '1 { print $8, $1, $2, $10, $3 }'
316
+ ++ tr ' ' ,
317
+ 🚀 Converting between string representations with the following parameters:
318
+ subcommand: convert
319
+ output: <_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>
320
+ format: csv
321
+ input: <_io.TextIOWrapper name='<stdin>' mode='r' encoding='utf-8'>
322
+ representation: SMILES
323
+ column: cysteine_to_N_cyclization
324
+ prefix: cyclic_
325
+ to: ['id', 'inchikey', 'scaffold', 'mwt', 'clogp', 'tpsa']
326
+ options: ['prefix=SCB-']
327
+ func: <function _convert at 0x7f5863d47240>
328
+
329
+ Error counts:
330
+ cyclic_id: 0
331
+ cyclic_inchikey: 0
332
+ cyclic_scaffold: 0
333
+ cyclic_mwt: 0
334
+ cyclic_clogp: 0
335
+ cyclic_tpsa: 0
336
+ ⏰ Completed process in 2:03:00.630330
337
+ + 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.csv.gz CHANGED
@@ -1,3 +1,3 @@
1
  version https://git-lfs.github.com/spec/v1
2
- oid sha256:abaaee336080505b080b6be9c82a07deadfc403e1d3545703df3a979058f8d02
3
- size 31682076
 
1
  version https://git-lfs.github.com/spec/v1
2
+ oid sha256:75aa920f6b77644561a323b4cbdaa7c41b4080d9850684c9121b12ffbccd8cc5
3
+ size 74258503
test/cyc-pep-6-12mer-70M_06.log ADDED
@@ -0,0 +1,337 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ + module purge
2
+ + '[' -z '' ']'
3
+ + case "$-" in
4
+ + __lmod_sh_dbg=x
5
+ + '[' -n x ']'
6
+ + set +x
7
+ Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output
8
+ Shell debugging restarted
9
+ + unset __lmod_sh_dbg
10
+ + return 0
11
+ + module load Anaconda3/2023.03
12
+ + '[' -z '' ']'
13
+ + case "$-" in
14
+ + __lmod_sh_dbg=x
15
+ + '[' -n x ']'
16
+ + set +x
17
+ Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output
18
+ Shell debugging restarted
19
+ + unset __lmod_sh_dbg
20
+ + return 0
21
+ + source /camp/home/johnsoe/.bashrc
22
+ ++ '[' '' = yes ']'
23
+ ++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '
24
+ +++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.bash hook
25
+ ++ __conda_setup='export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\''
26
+ export _CE_M='\'''\''
27
+ export _CE_CONDA='\'''\''
28
+ export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''
29
+
30
+ # Copyright (C) 2012 Anaconda, Inc
31
+ # SPDX-License-Identifier: BSD-3-Clause
32
+ __conda_exe() (
33
+ "$CONDA_EXE" $_CE_M $_CE_CONDA "$@"
34
+ )
35
+
36
+ __conda_hashr() {
37
+ if [ -n "${ZSH_VERSION:+x}" ]; then
38
+ \rehash
39
+ elif [ -n "${POSH_VERSION:+x}" ]; then
40
+ : # pass
41
+ else
42
+ \hash -r
43
+ fi
44
+ }
45
+
46
+ __conda_activate() {
47
+ if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then
48
+ # Handle transition from shell activated with conda <= 4.3 to a subsequent activation
49
+ # after conda updated to >= 4.4. See issue #6173.
50
+ PS1="$CONDA_PS1_BACKUP"
51
+ \unset CONDA_PS1_BACKUP
52
+ fi
53
+ \local ask_conda
54
+ ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return
55
+ \eval "$ask_conda"
56
+ __conda_hashr
57
+ }
58
+
59
+ __conda_reactivate() {
60
+ \local ask_conda
61
+ ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return
62
+ \eval "$ask_conda"
63
+ __conda_hashr
64
+ }
65
+
66
+ conda() {
67
+ \local cmd="${1-__missing__}"
68
+ case "$cmd" in
69
+ activate|deactivate)
70
+ __conda_activate "$@"
71
+ ;;
72
+ install|update|upgrade|remove|uninstall)
73
+ __conda_exe "$@" || \return
74
+ __conda_reactivate
75
+ ;;
76
+ *)
77
+ __conda_exe "$@"
78
+ ;;
79
+ esac
80
+ }
81
+
82
+ if [ -z "${CONDA_SHLVL+x}" ]; then
83
+ \export CONDA_SHLVL=0
84
+ # In dev-mode CONDA_EXE is python.exe and on Windows
85
+ # it is in a different relative location to condabin.
86
+ if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then
87
+ PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}"
88
+ else
89
+ PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}"
90
+ fi
91
+ \export PATH
92
+
93
+ # We'\''re not allowing PS1 to be unbound. It must at least be set.
94
+ # However, we'\''re not exporting it, which can cause problems when starting a second shell
95
+ # via a first shell (i.e. starting zsh from bash).
96
+ if [ -z "${PS1+x}" ]; then
97
+ PS1=
98
+ fi
99
+ fi
100
+
101
+ conda activate base'
102
+ ++ '[' 0 -eq 0 ']'
103
+ ++ eval 'export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\''
104
+ export _CE_M='\'''\''
105
+ export _CE_CONDA='\'''\''
106
+ export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''
107
+
108
+ # Copyright (C) 2012 Anaconda, Inc
109
+ # SPDX-License-Identifier: BSD-3-Clause
110
+ __conda_exe() (
111
+ "$CONDA_EXE" $_CE_M $_CE_CONDA "$@"
112
+ )
113
+
114
+ __conda_hashr() {
115
+ if [ -n "${ZSH_VERSION:+x}" ]; then
116
+ \rehash
117
+ elif [ -n "${POSH_VERSION:+x}" ]; then
118
+ : # pass
119
+ else
120
+ \hash -r
121
+ fi
122
+ }
123
+
124
+ __conda_activate() {
125
+ if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then
126
+ # Handle transition from shell activated with conda <= 4.3 to a subsequent activation
127
+ # after conda updated to >= 4.4. See issue #6173.
128
+ PS1="$CONDA_PS1_BACKUP"
129
+ \unset CONDA_PS1_BACKUP
130
+ fi
131
+ \local ask_conda
132
+ ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return
133
+ \eval "$ask_conda"
134
+ __conda_hashr
135
+ }
136
+
137
+ __conda_reactivate() {
138
+ \local ask_conda
139
+ ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return
140
+ \eval "$ask_conda"
141
+ __conda_hashr
142
+ }
143
+
144
+ conda() {
145
+ \local cmd="${1-__missing__}"
146
+ case "$cmd" in
147
+ activate|deactivate)
148
+ __conda_activate "$@"
149
+ ;;
150
+ install|update|upgrade|remove|uninstall)
151
+ __conda_exe "$@" || \return
152
+ __conda_reactivate
153
+ ;;
154
+ *)
155
+ __conda_exe "$@"
156
+ ;;
157
+ esac
158
+ }
159
+
160
+ if [ -z "${CONDA_SHLVL+x}" ]; then
161
+ \export CONDA_SHLVL=0
162
+ # In dev-mode CONDA_EXE is python.exe and on Windows
163
+ # it is in a different relative location to condabin.
164
+ if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then
165
+ PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}"
166
+ else
167
+ PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}"
168
+ fi
169
+ \export PATH
170
+
171
+ # We'\''re not allowing PS1 to be unbound. It must at least be set.
172
+ # However, we'\''re not exporting it, which can cause problems when starting a second shell
173
+ # via a first shell (i.e. starting zsh from bash).
174
+ if [ -z "${PS1+x}" ]; then
175
+ PS1=
176
+ fi
177
+ fi
178
+
179
+ conda activate base'
180
+ +++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda
181
+ +++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda
182
+ +++ export _CE_M=
183
+ +++ _CE_M=
184
+ +++ export _CE_CONDA=
185
+ +++ _CE_CONDA=
186
+ +++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python
187
+ +++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python
188
+ +++ '[' -z x ']'
189
+ +++ conda activate base
190
+ +++ local cmd=activate
191
+ +++ case "$cmd" in
192
+ +++ __conda_activate activate base
193
+ +++ '[' -n '' ']'
194
+ +++ local ask_conda
195
+ ++++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '
196
+ ++++ __conda_exe shell.posix activate base
197
+ ++++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate base
198
+ +++ ask_conda='PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\''
199
+ export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\''
200
+ export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\''
201
+ export CONDA_SHLVL='\''6'\''
202
+ export CONDA_DEFAULT_ENV='\''base'\''
203
+ export CONDA_PROMPT_MODIFIER='\''(base) '\''
204
+ export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\''
205
+ export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\''
206
+ export _CE_M='\'''\''
207
+ export _CE_CONDA='\'''\''
208
+ export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'''
209
+ +++ eval 'PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\''
210
+ export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\''
211
+ export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\''
212
+ export CONDA_SHLVL='\''6'\''
213
+ export CONDA_DEFAULT_ENV='\''base'\''
214
+ export CONDA_PROMPT_MODIFIER='\''(base) '\''
215
+ export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\''
216
+ export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\''
217
+ export _CE_M='\'''\''
218
+ export _CE_CONDA='\'''\''
219
+ export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'''
220
+ ++++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '
221
+ ++++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin
222
+ ++++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin
223
+ ++++ export CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0
224
+ ++++ CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0
225
+ ++++ export CONDA_SHLVL=6
226
+ ++++ CONDA_SHLVL=6
227
+ ++++ export CONDA_DEFAULT_ENV=base
228
+ ++++ CONDA_DEFAULT_ENV=base
229
+ ++++ export 'CONDA_PROMPT_MODIFIER=(base) '
230
+ ++++ CONDA_PROMPT_MODIFIER='(base) '
231
+ ++++ export CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev
232
+ ++++ CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev
233
+ ++++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda
234
+ ++++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda
235
+ ++++ export _CE_M=
236
+ ++++ _CE_M=
237
+ ++++ export _CE_CONDA=
238
+ ++++ _CE_CONDA=
239
+ ++++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python
240
+ ++++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python
241
+ +++ __conda_hashr
242
+ +++ '[' -n '' ']'
243
+ +++ '[' -n '' ']'
244
+ +++ hash -r
245
+ ++ unset __conda_setup
246
+ + conda activate schemist-dev
247
+ + local cmd=activate
248
+ + case "$cmd" in
249
+ + __conda_activate activate schemist-dev
250
+ + '[' -n '' ']'
251
+ + local ask_conda
252
+ ++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '
253
+ ++ __conda_exe shell.posix activate schemist-dev
254
+ ++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate schemist-dev
255
+ + ask_conda='PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\''
256
+ export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\''
257
+ export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\''
258
+ export CONDA_SHLVL='\''7'\''
259
+ export CONDA_DEFAULT_ENV='\''schemist-dev'\''
260
+ export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\''
261
+ export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\''
262
+ export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\''
263
+ export _CE_M='\'''\''
264
+ export _CE_CONDA='\'''\''
265
+ export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'''
266
+ + eval 'PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\''
267
+ export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\''
268
+ export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\''
269
+ export CONDA_SHLVL='\''7'\''
270
+ export CONDA_DEFAULT_ENV='\''schemist-dev'\''
271
+ export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\''
272
+ export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\''
273
+ export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\''
274
+ export _CE_M='\'''\''
275
+ export _CE_CONDA='\'''\''
276
+ export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'''
277
+ ++ PS1='(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '
278
+ ++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin
279
+ ++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin
280
+ ++ export CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev
281
+ ++ CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev
282
+ ++ export CONDA_SHLVL=7
283
+ ++ CONDA_SHLVL=7
284
+ ++ export CONDA_DEFAULT_ENV=schemist-dev
285
+ ++ CONDA_DEFAULT_ENV=schemist-dev
286
+ ++ export 'CONDA_PROMPT_MODIFIER=(schemist-dev) '
287
+ ++ CONDA_PROMPT_MODIFIER='(schemist-dev) '
288
+ ++ export CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0
289
+ ++ CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0
290
+ ++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda
291
+ ++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda
292
+ ++ export _CE_M=
293
+ ++ _CE_M=
294
+ ++ export _CE_CONDA=
295
+ ++ _CE_CONDA=
296
+ ++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python
297
+ ++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python
298
+ + __conda_hashr
299
+ + '[' -n '' ']'
300
+ + '[' -n '' ']'
301
+ + hash -r
302
+ + CHUNK_HEAD_FILE=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz
303
+ + INPUT=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/test/cyc-pep-6-12mer-70M_06.csv
304
+ + COLUMN=cysteine_to_N_cyclization
305
+ + PREFIX=cyclic_
306
+ + AWK='1 { print $8, $1, $2, $10, $3 }'
307
+ + '[' -z cysteine_to_N_cyclization ']'
308
+ + '[' -z cyclic_ ']'
309
+ + '[' -z '1 { print $8, $1, $2, $10, $3 }' ']'
310
+ + 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
311
+ ++ zcat /nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz
312
+ ++ head -n1
313
+ + awk -F, -v OFS=, '1 { print $8, $1, $2, $10, $3 }'
314
+ ++ tr ' ' ,
315
+ + schemist convert -f csv --column cysteine_to_N_cyclization --to id inchikey scaffold mwt clogp tpsa --prefix cyclic_ --options prefix=SCB-
316
+ + gzip --best
317
+ 🚀 Converting between string representations with the following parameters:
318
+ subcommand: convert
319
+ output: <_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>
320
+ format: csv
321
+ input: <_io.TextIOWrapper name='<stdin>' mode='r' encoding='utf-8'>
322
+ representation: SMILES
323
+ column: cysteine_to_N_cyclization
324
+ prefix: cyclic_
325
+ to: ['id', 'inchikey', 'scaffold', 'mwt', 'clogp', 'tpsa']
326
+ options: ['prefix=SCB-']
327
+ func: <function _convert at 0x7f71dbc6b240>
328
+
329
+ Error counts:
330
+ cyclic_id: 0
331
+ cyclic_inchikey: 0
332
+ cyclic_scaffold: 0
333
+ cyclic_mwt: 0
334
+ cyclic_clogp: 0
335
+ cyclic_tpsa: 0
336
+ ⏰ Completed process in 2:08:19.491369
337
+ + 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.csv.gz CHANGED
@@ -1,3 +1,3 @@
1
  version https://git-lfs.github.com/spec/v1
2
- oid sha256:201b456bab747100162f73dd54cd3066027760d9d3246d23bca725959784a321
3
- size 34198877
 
1
  version https://git-lfs.github.com/spec/v1
2
+ oid sha256:0235bf78583cf8847a849cb826a05dc280a6a816dc8f758c84d0fd852f55a030
3
+ size 78737230
test/cyc-pep-6-12mer-70M_07.log ADDED
@@ -0,0 +1,337 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ + module purge
2
+ + '[' -z '' ']'
3
+ + case "$-" in
4
+ + __lmod_sh_dbg=x
5
+ + '[' -n x ']'
6
+ + set +x
7
+ Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output
8
+ Shell debugging restarted
9
+ + unset __lmod_sh_dbg
10
+ + return 0
11
+ + module load Anaconda3/2023.03
12
+ + '[' -z '' ']'
13
+ + case "$-" in
14
+ + __lmod_sh_dbg=x
15
+ + '[' -n x ']'
16
+ + set +x
17
+ Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output
18
+ Shell debugging restarted
19
+ + unset __lmod_sh_dbg
20
+ + return 0
21
+ + source /camp/home/johnsoe/.bashrc
22
+ ++ '[' '' = yes ']'
23
+ ++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '
24
+ +++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.bash hook
25
+ ++ __conda_setup='export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\''
26
+ export _CE_M='\'''\''
27
+ export _CE_CONDA='\'''\''
28
+ export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''
29
+
30
+ # Copyright (C) 2012 Anaconda, Inc
31
+ # SPDX-License-Identifier: BSD-3-Clause
32
+ __conda_exe() (
33
+ "$CONDA_EXE" $_CE_M $_CE_CONDA "$@"
34
+ )
35
+
36
+ __conda_hashr() {
37
+ if [ -n "${ZSH_VERSION:+x}" ]; then
38
+ \rehash
39
+ elif [ -n "${POSH_VERSION:+x}" ]; then
40
+ : # pass
41
+ else
42
+ \hash -r
43
+ fi
44
+ }
45
+
46
+ __conda_activate() {
47
+ if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then
48
+ # Handle transition from shell activated with conda <= 4.3 to a subsequent activation
49
+ # after conda updated to >= 4.4. See issue #6173.
50
+ PS1="$CONDA_PS1_BACKUP"
51
+ \unset CONDA_PS1_BACKUP
52
+ fi
53
+ \local ask_conda
54
+ ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return
55
+ \eval "$ask_conda"
56
+ __conda_hashr
57
+ }
58
+
59
+ __conda_reactivate() {
60
+ \local ask_conda
61
+ ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return
62
+ \eval "$ask_conda"
63
+ __conda_hashr
64
+ }
65
+
66
+ conda() {
67
+ \local cmd="${1-__missing__}"
68
+ case "$cmd" in
69
+ activate|deactivate)
70
+ __conda_activate "$@"
71
+ ;;
72
+ install|update|upgrade|remove|uninstall)
73
+ __conda_exe "$@" || \return
74
+ __conda_reactivate
75
+ ;;
76
+ *)
77
+ __conda_exe "$@"
78
+ ;;
79
+ esac
80
+ }
81
+
82
+ if [ -z "${CONDA_SHLVL+x}" ]; then
83
+ \export CONDA_SHLVL=0
84
+ # In dev-mode CONDA_EXE is python.exe and on Windows
85
+ # it is in a different relative location to condabin.
86
+ if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then
87
+ PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}"
88
+ else
89
+ PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}"
90
+ fi
91
+ \export PATH
92
+
93
+ # We'\''re not allowing PS1 to be unbound. It must at least be set.
94
+ # However, we'\''re not exporting it, which can cause problems when starting a second shell
95
+ # via a first shell (i.e. starting zsh from bash).
96
+ if [ -z "${PS1+x}" ]; then
97
+ PS1=
98
+ fi
99
+ fi
100
+
101
+ conda activate base'
102
+ ++ '[' 0 -eq 0 ']'
103
+ ++ eval 'export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\''
104
+ export _CE_M='\'''\''
105
+ export _CE_CONDA='\'''\''
106
+ export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''
107
+
108
+ # Copyright (C) 2012 Anaconda, Inc
109
+ # SPDX-License-Identifier: BSD-3-Clause
110
+ __conda_exe() (
111
+ "$CONDA_EXE" $_CE_M $_CE_CONDA "$@"
112
+ )
113
+
114
+ __conda_hashr() {
115
+ if [ -n "${ZSH_VERSION:+x}" ]; then
116
+ \rehash
117
+ elif [ -n "${POSH_VERSION:+x}" ]; then
118
+ : # pass
119
+ else
120
+ \hash -r
121
+ fi
122
+ }
123
+
124
+ __conda_activate() {
125
+ if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then
126
+ # Handle transition from shell activated with conda <= 4.3 to a subsequent activation
127
+ # after conda updated to >= 4.4. See issue #6173.
128
+ PS1="$CONDA_PS1_BACKUP"
129
+ \unset CONDA_PS1_BACKUP
130
+ fi
131
+ \local ask_conda
132
+ ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return
133
+ \eval "$ask_conda"
134
+ __conda_hashr
135
+ }
136
+
137
+ __conda_reactivate() {
138
+ \local ask_conda
139
+ ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return
140
+ \eval "$ask_conda"
141
+ __conda_hashr
142
+ }
143
+
144
+ conda() {
145
+ \local cmd="${1-__missing__}"
146
+ case "$cmd" in
147
+ activate|deactivate)
148
+ __conda_activate "$@"
149
+ ;;
150
+ install|update|upgrade|remove|uninstall)
151
+ __conda_exe "$@" || \return
152
+ __conda_reactivate
153
+ ;;
154
+ *)
155
+ __conda_exe "$@"
156
+ ;;
157
+ esac
158
+ }
159
+
160
+ if [ -z "${CONDA_SHLVL+x}" ]; then
161
+ \export CONDA_SHLVL=0
162
+ # In dev-mode CONDA_EXE is python.exe and on Windows
163
+ # it is in a different relative location to condabin.
164
+ if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then
165
+ PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}"
166
+ else
167
+ PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}"
168
+ fi
169
+ \export PATH
170
+
171
+ # We'\''re not allowing PS1 to be unbound. It must at least be set.
172
+ # However, we'\''re not exporting it, which can cause problems when starting a second shell
173
+ # via a first shell (i.e. starting zsh from bash).
174
+ if [ -z "${PS1+x}" ]; then
175
+ PS1=
176
+ fi
177
+ fi
178
+
179
+ conda activate base'
180
+ +++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda
181
+ +++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda
182
+ +++ export _CE_M=
183
+ +++ _CE_M=
184
+ +++ export _CE_CONDA=
185
+ +++ _CE_CONDA=
186
+ +++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python
187
+ +++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python
188
+ +++ '[' -z x ']'
189
+ +++ conda activate base
190
+ +++ local cmd=activate
191
+ +++ case "$cmd" in
192
+ +++ __conda_activate activate base
193
+ +++ '[' -n '' ']'
194
+ +++ local ask_conda
195
+ ++++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '
196
+ ++++ __conda_exe shell.posix activate base
197
+ ++++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate base
198
+ +++ ask_conda='PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\''
199
+ export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\''
200
+ export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\''
201
+ export CONDA_SHLVL='\''6'\''
202
+ export CONDA_DEFAULT_ENV='\''base'\''
203
+ export CONDA_PROMPT_MODIFIER='\''(base) '\''
204
+ export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\''
205
+ export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\''
206
+ export _CE_M='\'''\''
207
+ export _CE_CONDA='\'''\''
208
+ export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'''
209
+ +++ eval 'PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\''
210
+ export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\''
211
+ export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\''
212
+ export CONDA_SHLVL='\''6'\''
213
+ export CONDA_DEFAULT_ENV='\''base'\''
214
+ export CONDA_PROMPT_MODIFIER='\''(base) '\''
215
+ export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\''
216
+ export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\''
217
+ export _CE_M='\'''\''
218
+ export _CE_CONDA='\'''\''
219
+ export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'''
220
+ ++++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '
221
+ ++++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin
222
+ ++++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin
223
+ ++++ export CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0
224
+ ++++ CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0
225
+ ++++ export CONDA_SHLVL=6
226
+ ++++ CONDA_SHLVL=6
227
+ ++++ export CONDA_DEFAULT_ENV=base
228
+ ++++ CONDA_DEFAULT_ENV=base
229
+ ++++ export 'CONDA_PROMPT_MODIFIER=(base) '
230
+ ++++ CONDA_PROMPT_MODIFIER='(base) '
231
+ ++++ export CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev
232
+ ++++ CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev
233
+ ++++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda
234
+ ++++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda
235
+ ++++ export _CE_M=
236
+ ++++ _CE_M=
237
+ ++++ export _CE_CONDA=
238
+ ++++ _CE_CONDA=
239
+ ++++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python
240
+ ++++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python
241
+ +++ __conda_hashr
242
+ +++ '[' -n '' ']'
243
+ +++ '[' -n '' ']'
244
+ +++ hash -r
245
+ ++ unset __conda_setup
246
+ + conda activate schemist-dev
247
+ + local cmd=activate
248
+ + case "$cmd" in
249
+ + __conda_activate activate schemist-dev
250
+ + '[' -n '' ']'
251
+ + local ask_conda
252
+ ++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '
253
+ ++ __conda_exe shell.posix activate schemist-dev
254
+ ++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate schemist-dev
255
+ + ask_conda='PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\''
256
+ export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\''
257
+ export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\''
258
+ export CONDA_SHLVL='\''7'\''
259
+ export CONDA_DEFAULT_ENV='\''schemist-dev'\''
260
+ export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\''
261
+ export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\''
262
+ export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\''
263
+ export _CE_M='\'''\''
264
+ export _CE_CONDA='\'''\''
265
+ export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'''
266
+ + eval 'PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\''
267
+ export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\''
268
+ export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\''
269
+ export CONDA_SHLVL='\''7'\''
270
+ export CONDA_DEFAULT_ENV='\''schemist-dev'\''
271
+ export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\''
272
+ export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\''
273
+ export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\''
274
+ export _CE_M='\'''\''
275
+ export _CE_CONDA='\'''\''
276
+ export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'''
277
+ ++ PS1='(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '
278
+ ++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin
279
+ ++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin
280
+ ++ export CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev
281
+ ++ CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev
282
+ ++ export CONDA_SHLVL=7
283
+ ++ CONDA_SHLVL=7
284
+ ++ export CONDA_DEFAULT_ENV=schemist-dev
285
+ ++ CONDA_DEFAULT_ENV=schemist-dev
286
+ ++ export 'CONDA_PROMPT_MODIFIER=(schemist-dev) '
287
+ ++ CONDA_PROMPT_MODIFIER='(schemist-dev) '
288
+ ++ export CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0
289
+ ++ CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0
290
+ ++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda
291
+ ++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda
292
+ ++ export _CE_M=
293
+ ++ _CE_M=
294
+ ++ export _CE_CONDA=
295
+ ++ _CE_CONDA=
296
+ ++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python
297
+ ++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python
298
+ + __conda_hashr
299
+ + '[' -n '' ']'
300
+ + '[' -n '' ']'
301
+ + hash -r
302
+ + CHUNK_HEAD_FILE=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz
303
+ + INPUT=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/test/cyc-pep-6-12mer-70M_07.csv
304
+ + COLUMN=cysteine_to_N_cyclization
305
+ + PREFIX=cyclic_
306
+ + AWK='1 { print $8, $1, $2, $10, $3 }'
307
+ + '[' -z cysteine_to_N_cyclization ']'
308
+ + '[' -z cyclic_ ']'
309
+ + '[' -z '1 { print $8, $1, $2, $10, $3 }' ']'
310
+ + 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
311
+ + awk -F, -v OFS=, '1 { print $8, $1, $2, $10, $3 }'
312
+ ++ zcat /nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz
313
+ + schemist convert -f csv --column cysteine_to_N_cyclization --to id inchikey scaffold mwt clogp tpsa --prefix cyclic_ --options prefix=SCB-
314
+ + gzip --best
315
+ ++ head -n1
316
+ ++ tr ' ' ,
317
+ 🚀 Converting between string representations with the following parameters:
318
+ subcommand: convert
319
+ output: <_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>
320
+ format: csv
321
+ input: <_io.TextIOWrapper name='<stdin>' mode='r' encoding='utf-8'>
322
+ representation: SMILES
323
+ column: cysteine_to_N_cyclization
324
+ prefix: cyclic_
325
+ to: ['id', 'inchikey', 'scaffold', 'mwt', 'clogp', 'tpsa']
326
+ options: ['prefix=SCB-']
327
+ func: <function _convert at 0x7fe0c32d7240>
328
+
329
+ Error counts:
330
+ cyclic_id: 0
331
+ cyclic_inchikey: 0
332
+ cyclic_scaffold: 0
333
+ cyclic_mwt: 0
334
+ cyclic_clogp: 0
335
+ cyclic_tpsa: 0
336
+ ⏰ Completed process in 2:20:18.532640
337
+ + 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.csv.gz CHANGED
@@ -1,3 +1,3 @@
1
  version https://git-lfs.github.com/spec/v1
2
- oid sha256:df735149229f974916fcea5350d5c953e1cd63d74d1eae987aed61c9133237f4
3
- size 47424767
 
1
  version https://git-lfs.github.com/spec/v1
2
+ oid sha256:af512fb7d8573c2c07bed492e0c1e9256c901c9e71c7f466c2f2ef01dc84e625
3
+ size 97937697
test/cyc-pep-6-12mer-70M_08.log ADDED
@@ -0,0 +1,337 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ + module purge
2
+ + '[' -z '' ']'
3
+ + case "$-" in
4
+ + __lmod_sh_dbg=x
5
+ + '[' -n x ']'
6
+ + set +x
7
+ Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output
8
+ Shell debugging restarted
9
+ + unset __lmod_sh_dbg
10
+ + return 0
11
+ + module load Anaconda3/2023.03
12
+ + '[' -z '' ']'
13
+ + case "$-" in
14
+ + __lmod_sh_dbg=x
15
+ + '[' -n x ']'
16
+ + set +x
17
+ Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output
18
+ Shell debugging restarted
19
+ + unset __lmod_sh_dbg
20
+ + return 0
21
+ + source /camp/home/johnsoe/.bashrc
22
+ ++ '[' '' = yes ']'
23
+ ++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '
24
+ +++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.bash hook
25
+ ++ __conda_setup='export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\''
26
+ export _CE_M='\'''\''
27
+ export _CE_CONDA='\'''\''
28
+ export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''
29
+
30
+ # Copyright (C) 2012 Anaconda, Inc
31
+ # SPDX-License-Identifier: BSD-3-Clause
32
+ __conda_exe() (
33
+ "$CONDA_EXE" $_CE_M $_CE_CONDA "$@"
34
+ )
35
+
36
+ __conda_hashr() {
37
+ if [ -n "${ZSH_VERSION:+x}" ]; then
38
+ \rehash
39
+ elif [ -n "${POSH_VERSION:+x}" ]; then
40
+ : # pass
41
+ else
42
+ \hash -r
43
+ fi
44
+ }
45
+
46
+ __conda_activate() {
47
+ if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then
48
+ # Handle transition from shell activated with conda <= 4.3 to a subsequent activation
49
+ # after conda updated to >= 4.4. See issue #6173.
50
+ PS1="$CONDA_PS1_BACKUP"
51
+ \unset CONDA_PS1_BACKUP
52
+ fi
53
+ \local ask_conda
54
+ ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return
55
+ \eval "$ask_conda"
56
+ __conda_hashr
57
+ }
58
+
59
+ __conda_reactivate() {
60
+ \local ask_conda
61
+ ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return
62
+ \eval "$ask_conda"
63
+ __conda_hashr
64
+ }
65
+
66
+ conda() {
67
+ \local cmd="${1-__missing__}"
68
+ case "$cmd" in
69
+ activate|deactivate)
70
+ __conda_activate "$@"
71
+ ;;
72
+ install|update|upgrade|remove|uninstall)
73
+ __conda_exe "$@" || \return
74
+ __conda_reactivate
75
+ ;;
76
+ *)
77
+ __conda_exe "$@"
78
+ ;;
79
+ esac
80
+ }
81
+
82
+ if [ -z "${CONDA_SHLVL+x}" ]; then
83
+ \export CONDA_SHLVL=0
84
+ # In dev-mode CONDA_EXE is python.exe and on Windows
85
+ # it is in a different relative location to condabin.
86
+ if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then
87
+ PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}"
88
+ else
89
+ PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}"
90
+ fi
91
+ \export PATH
92
+
93
+ # We'\''re not allowing PS1 to be unbound. It must at least be set.
94
+ # However, we'\''re not exporting it, which can cause problems when starting a second shell
95
+ # via a first shell (i.e. starting zsh from bash).
96
+ if [ -z "${PS1+x}" ]; then
97
+ PS1=
98
+ fi
99
+ fi
100
+
101
+ conda activate base'
102
+ ++ '[' 0 -eq 0 ']'
103
+ ++ eval 'export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\''
104
+ export _CE_M='\'''\''
105
+ export _CE_CONDA='\'''\''
106
+ export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''
107
+
108
+ # Copyright (C) 2012 Anaconda, Inc
109
+ # SPDX-License-Identifier: BSD-3-Clause
110
+ __conda_exe() (
111
+ "$CONDA_EXE" $_CE_M $_CE_CONDA "$@"
112
+ )
113
+
114
+ __conda_hashr() {
115
+ if [ -n "${ZSH_VERSION:+x}" ]; then
116
+ \rehash
117
+ elif [ -n "${POSH_VERSION:+x}" ]; then
118
+ : # pass
119
+ else
120
+ \hash -r
121
+ fi
122
+ }
123
+
124
+ __conda_activate() {
125
+ if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then
126
+ # Handle transition from shell activated with conda <= 4.3 to a subsequent activation
127
+ # after conda updated to >= 4.4. See issue #6173.
128
+ PS1="$CONDA_PS1_BACKUP"
129
+ \unset CONDA_PS1_BACKUP
130
+ fi
131
+ \local ask_conda
132
+ ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return
133
+ \eval "$ask_conda"
134
+ __conda_hashr
135
+ }
136
+
137
+ __conda_reactivate() {
138
+ \local ask_conda
139
+ ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return
140
+ \eval "$ask_conda"
141
+ __conda_hashr
142
+ }
143
+
144
+ conda() {
145
+ \local cmd="${1-__missing__}"
146
+ case "$cmd" in
147
+ activate|deactivate)
148
+ __conda_activate "$@"
149
+ ;;
150
+ install|update|upgrade|remove|uninstall)
151
+ __conda_exe "$@" || \return
152
+ __conda_reactivate
153
+ ;;
154
+ *)
155
+ __conda_exe "$@"
156
+ ;;
157
+ esac
158
+ }
159
+
160
+ if [ -z "${CONDA_SHLVL+x}" ]; then
161
+ \export CONDA_SHLVL=0
162
+ # In dev-mode CONDA_EXE is python.exe and on Windows
163
+ # it is in a different relative location to condabin.
164
+ if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then
165
+ PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}"
166
+ else
167
+ PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}"
168
+ fi
169
+ \export PATH
170
+
171
+ # We'\''re not allowing PS1 to be unbound. It must at least be set.
172
+ # However, we'\''re not exporting it, which can cause problems when starting a second shell
173
+ # via a first shell (i.e. starting zsh from bash).
174
+ if [ -z "${PS1+x}" ]; then
175
+ PS1=
176
+ fi
177
+ fi
178
+
179
+ conda activate base'
180
+ +++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda
181
+ +++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda
182
+ +++ export _CE_M=
183
+ +++ _CE_M=
184
+ +++ export _CE_CONDA=
185
+ +++ _CE_CONDA=
186
+ +++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python
187
+ +++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python
188
+ +++ '[' -z x ']'
189
+ +++ conda activate base
190
+ +++ local cmd=activate
191
+ +++ case "$cmd" in
192
+ +++ __conda_activate activate base
193
+ +++ '[' -n '' ']'
194
+ +++ local ask_conda
195
+ ++++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '
196
+ ++++ __conda_exe shell.posix activate base
197
+ ++++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate base
198
+ +++ ask_conda='PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\''
199
+ export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\''
200
+ export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\''
201
+ export CONDA_SHLVL='\''6'\''
202
+ export CONDA_DEFAULT_ENV='\''base'\''
203
+ export CONDA_PROMPT_MODIFIER='\''(base) '\''
204
+ export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\''
205
+ export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\''
206
+ export _CE_M='\'''\''
207
+ export _CE_CONDA='\'''\''
208
+ export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'''
209
+ +++ eval 'PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\''
210
+ export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\''
211
+ export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\''
212
+ export CONDA_SHLVL='\''6'\''
213
+ export CONDA_DEFAULT_ENV='\''base'\''
214
+ export CONDA_PROMPT_MODIFIER='\''(base) '\''
215
+ export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\''
216
+ export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\''
217
+ export _CE_M='\'''\''
218
+ export _CE_CONDA='\'''\''
219
+ export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'''
220
+ ++++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '
221
+ ++++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin
222
+ ++++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin
223
+ ++++ export CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0
224
+ ++++ CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0
225
+ ++++ export CONDA_SHLVL=6
226
+ ++++ CONDA_SHLVL=6
227
+ ++++ export CONDA_DEFAULT_ENV=base
228
+ ++++ CONDA_DEFAULT_ENV=base
229
+ ++++ export 'CONDA_PROMPT_MODIFIER=(base) '
230
+ ++++ CONDA_PROMPT_MODIFIER='(base) '
231
+ ++++ export CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev
232
+ ++++ CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev
233
+ ++++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda
234
+ ++++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda
235
+ ++++ export _CE_M=
236
+ ++++ _CE_M=
237
+ ++++ export _CE_CONDA=
238
+ ++++ _CE_CONDA=
239
+ ++++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python
240
+ ++++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python
241
+ +++ __conda_hashr
242
+ +++ '[' -n '' ']'
243
+ +++ '[' -n '' ']'
244
+ +++ hash -r
245
+ ++ unset __conda_setup
246
+ + conda activate schemist-dev
247
+ + local cmd=activate
248
+ + case "$cmd" in
249
+ + __conda_activate activate schemist-dev
250
+ + '[' -n '' ']'
251
+ + local ask_conda
252
+ ++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '
253
+ ++ __conda_exe shell.posix activate schemist-dev
254
+ ++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate schemist-dev
255
+ + ask_conda='PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\''
256
+ export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\''
257
+ export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\''
258
+ export CONDA_SHLVL='\''7'\''
259
+ export CONDA_DEFAULT_ENV='\''schemist-dev'\''
260
+ export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\''
261
+ export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\''
262
+ export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\''
263
+ export _CE_M='\'''\''
264
+ export _CE_CONDA='\'''\''
265
+ export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'''
266
+ + eval 'PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\''
267
+ export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\''
268
+ export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\''
269
+ export CONDA_SHLVL='\''7'\''
270
+ export CONDA_DEFAULT_ENV='\''schemist-dev'\''
271
+ export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\''
272
+ export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\''
273
+ export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\''
274
+ export _CE_M='\'''\''
275
+ export _CE_CONDA='\'''\''
276
+ export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'''
277
+ ++ PS1='(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '
278
+ ++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin
279
+ ++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin
280
+ ++ export CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev
281
+ ++ CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev
282
+ ++ export CONDA_SHLVL=7
283
+ ++ CONDA_SHLVL=7
284
+ ++ export CONDA_DEFAULT_ENV=schemist-dev
285
+ ++ CONDA_DEFAULT_ENV=schemist-dev
286
+ ++ export 'CONDA_PROMPT_MODIFIER=(schemist-dev) '
287
+ ++ CONDA_PROMPT_MODIFIER='(schemist-dev) '
288
+ ++ export CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0
289
+ ++ CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0
290
+ ++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda
291
+ ++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda
292
+ ++ export _CE_M=
293
+ ++ _CE_M=
294
+ ++ export _CE_CONDA=
295
+ ++ _CE_CONDA=
296
+ ++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python
297
+ ++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python
298
+ + __conda_hashr
299
+ + '[' -n '' ']'
300
+ + '[' -n '' ']'
301
+ + hash -r
302
+ + CHUNK_HEAD_FILE=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz
303
+ + INPUT=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/test/cyc-pep-6-12mer-70M_08.csv
304
+ + COLUMN=cysteine_to_N_cyclization
305
+ + PREFIX=cyclic_
306
+ + AWK='1 { print $8, $1, $2, $10, $3 }'
307
+ + '[' -z cysteine_to_N_cyclization ']'
308
+ + '[' -z cyclic_ ']'
309
+ + '[' -z '1 { print $8, $1, $2, $10, $3 }' ']'
310
+ + awk -F, -v OFS=, '1 { print $8, $1, $2, $10, $3 }'
311
+ + 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
312
+ + schemist convert -f csv --column cysteine_to_N_cyclization --to id inchikey scaffold mwt clogp tpsa --prefix cyclic_ --options prefix=SCB-
313
+ ++ head -n1
314
+ + gzip --best
315
+ ++ tr ' ' ,
316
+ ++ zcat /nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz
317
+ 🚀 Converting between string representations with the following parameters:
318
+ subcommand: convert
319
+ output: <_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>
320
+ format: csv
321
+ input: <_io.TextIOWrapper name='<stdin>' mode='r' encoding='utf-8'>
322
+ representation: SMILES
323
+ column: cysteine_to_N_cyclization
324
+ prefix: cyclic_
325
+ to: ['id', 'inchikey', 'scaffold', 'mwt', 'clogp', 'tpsa']
326
+ options: ['prefix=SCB-']
327
+ func: <function _convert at 0x7f6753cc7240>
328
+
329
+ Error counts:
330
+ cyclic_id: 0
331
+ cyclic_inchikey: 0
332
+ cyclic_scaffold: 0
333
+ cyclic_mwt: 0
334
+ cyclic_clogp: 0
335
+ cyclic_tpsa: 0
336
+ ⏰ Completed process in 2:21:16.221649
337
+ + 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.csv.gz CHANGED
@@ -1,3 +1,3 @@
1
  version https://git-lfs.github.com/spec/v1
2
- oid sha256:b53d7c0d1348a35bc409fd1afb0351f37bce96e5e4730eee0d35a3b7766e2bf6
3
- size 51295923
 
1
  version https://git-lfs.github.com/spec/v1
2
+ oid sha256:d872389d791ed0567bc316360f0dfc97cc635e6006c1b0083486016b9e93071f
3
+ size 103498286
test/cyc-pep-6-12mer-70M_09.log ADDED
@@ -0,0 +1,337 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ + module purge
2
+ + '[' -z '' ']'
3
+ + case "$-" in
4
+ + __lmod_sh_dbg=x
5
+ + '[' -n x ']'
6
+ + set +x
7
+ Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output
8
+ Shell debugging restarted
9
+ + unset __lmod_sh_dbg
10
+ + return 0
11
+ + module load Anaconda3/2023.03
12
+ + '[' -z '' ']'
13
+ + case "$-" in
14
+ + __lmod_sh_dbg=x
15
+ + '[' -n x ']'
16
+ + set +x
17
+ Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output
18
+ Shell debugging restarted
19
+ + unset __lmod_sh_dbg
20
+ + return 0
21
+ + source /camp/home/johnsoe/.bashrc
22
+ ++ '[' '' = yes ']'
23
+ ++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '
24
+ +++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.bash hook
25
+ ++ __conda_setup='export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\''
26
+ export _CE_M='\'''\''
27
+ export _CE_CONDA='\'''\''
28
+ export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''
29
+
30
+ # Copyright (C) 2012 Anaconda, Inc
31
+ # SPDX-License-Identifier: BSD-3-Clause
32
+ __conda_exe() (
33
+ "$CONDA_EXE" $_CE_M $_CE_CONDA "$@"
34
+ )
35
+
36
+ __conda_hashr() {
37
+ if [ -n "${ZSH_VERSION:+x}" ]; then
38
+ \rehash
39
+ elif [ -n "${POSH_VERSION:+x}" ]; then
40
+ : # pass
41
+ else
42
+ \hash -r
43
+ fi
44
+ }
45
+
46
+ __conda_activate() {
47
+ if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then
48
+ # Handle transition from shell activated with conda <= 4.3 to a subsequent activation
49
+ # after conda updated to >= 4.4. See issue #6173.
50
+ PS1="$CONDA_PS1_BACKUP"
51
+ \unset CONDA_PS1_BACKUP
52
+ fi
53
+ \local ask_conda
54
+ ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return
55
+ \eval "$ask_conda"
56
+ __conda_hashr
57
+ }
58
+
59
+ __conda_reactivate() {
60
+ \local ask_conda
61
+ ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return
62
+ \eval "$ask_conda"
63
+ __conda_hashr
64
+ }
65
+
66
+ conda() {
67
+ \local cmd="${1-__missing__}"
68
+ case "$cmd" in
69
+ activate|deactivate)
70
+ __conda_activate "$@"
71
+ ;;
72
+ install|update|upgrade|remove|uninstall)
73
+ __conda_exe "$@" || \return
74
+ __conda_reactivate
75
+ ;;
76
+ *)
77
+ __conda_exe "$@"
78
+ ;;
79
+ esac
80
+ }
81
+
82
+ if [ -z "${CONDA_SHLVL+x}" ]; then
83
+ \export CONDA_SHLVL=0
84
+ # In dev-mode CONDA_EXE is python.exe and on Windows
85
+ # it is in a different relative location to condabin.
86
+ if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then
87
+ PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}"
88
+ else
89
+ PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}"
90
+ fi
91
+ \export PATH
92
+
93
+ # We'\''re not allowing PS1 to be unbound. It must at least be set.
94
+ # However, we'\''re not exporting it, which can cause problems when starting a second shell
95
+ # via a first shell (i.e. starting zsh from bash).
96
+ if [ -z "${PS1+x}" ]; then
97
+ PS1=
98
+ fi
99
+ fi
100
+
101
+ conda activate base'
102
+ ++ '[' 0 -eq 0 ']'
103
+ ++ eval 'export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\''
104
+ export _CE_M='\'''\''
105
+ export _CE_CONDA='\'''\''
106
+ export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''
107
+
108
+ # Copyright (C) 2012 Anaconda, Inc
109
+ # SPDX-License-Identifier: BSD-3-Clause
110
+ __conda_exe() (
111
+ "$CONDA_EXE" $_CE_M $_CE_CONDA "$@"
112
+ )
113
+
114
+ __conda_hashr() {
115
+ if [ -n "${ZSH_VERSION:+x}" ]; then
116
+ \rehash
117
+ elif [ -n "${POSH_VERSION:+x}" ]; then
118
+ : # pass
119
+ else
120
+ \hash -r
121
+ fi
122
+ }
123
+
124
+ __conda_activate() {
125
+ if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then
126
+ # Handle transition from shell activated with conda <= 4.3 to a subsequent activation
127
+ # after conda updated to >= 4.4. See issue #6173.
128
+ PS1="$CONDA_PS1_BACKUP"
129
+ \unset CONDA_PS1_BACKUP
130
+ fi
131
+ \local ask_conda
132
+ ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return
133
+ \eval "$ask_conda"
134
+ __conda_hashr
135
+ }
136
+
137
+ __conda_reactivate() {
138
+ \local ask_conda
139
+ ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return
140
+ \eval "$ask_conda"
141
+ __conda_hashr
142
+ }
143
+
144
+ conda() {
145
+ \local cmd="${1-__missing__}"
146
+ case "$cmd" in
147
+ activate|deactivate)
148
+ __conda_activate "$@"
149
+ ;;
150
+ install|update|upgrade|remove|uninstall)
151
+ __conda_exe "$@" || \return
152
+ __conda_reactivate
153
+ ;;
154
+ *)
155
+ __conda_exe "$@"
156
+ ;;
157
+ esac
158
+ }
159
+
160
+ if [ -z "${CONDA_SHLVL+x}" ]; then
161
+ \export CONDA_SHLVL=0
162
+ # In dev-mode CONDA_EXE is python.exe and on Windows
163
+ # it is in a different relative location to condabin.
164
+ if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then
165
+ PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}"
166
+ else
167
+ PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}"
168
+ fi
169
+ \export PATH
170
+
171
+ # We'\''re not allowing PS1 to be unbound. It must at least be set.
172
+ # However, we'\''re not exporting it, which can cause problems when starting a second shell
173
+ # via a first shell (i.e. starting zsh from bash).
174
+ if [ -z "${PS1+x}" ]; then
175
+ PS1=
176
+ fi
177
+ fi
178
+
179
+ conda activate base'
180
+ +++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda
181
+ +++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda
182
+ +++ export _CE_M=
183
+ +++ _CE_M=
184
+ +++ export _CE_CONDA=
185
+ +++ _CE_CONDA=
186
+ +++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python
187
+ +++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python
188
+ +++ '[' -z x ']'
189
+ +++ conda activate base
190
+ +++ local cmd=activate
191
+ +++ case "$cmd" in
192
+ +++ __conda_activate activate base
193
+ +++ '[' -n '' ']'
194
+ +++ local ask_conda
195
+ ++++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '
196
+ ++++ __conda_exe shell.posix activate base
197
+ ++++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate base
198
+ +++ ask_conda='PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\''
199
+ export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\''
200
+ export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\''
201
+ export CONDA_SHLVL='\''6'\''
202
+ export CONDA_DEFAULT_ENV='\''base'\''
203
+ export CONDA_PROMPT_MODIFIER='\''(base) '\''
204
+ export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\''
205
+ export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\''
206
+ export _CE_M='\'''\''
207
+ export _CE_CONDA='\'''\''
208
+ export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'''
209
+ +++ eval 'PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\''
210
+ export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\''
211
+ export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\''
212
+ export CONDA_SHLVL='\''6'\''
213
+ export CONDA_DEFAULT_ENV='\''base'\''
214
+ export CONDA_PROMPT_MODIFIER='\''(base) '\''
215
+ export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\''
216
+ export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\''
217
+ export _CE_M='\'''\''
218
+ export _CE_CONDA='\'''\''
219
+ export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'''
220
+ ++++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '
221
+ ++++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin
222
+ ++++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin
223
+ ++++ export CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0
224
+ ++++ CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0
225
+ ++++ export CONDA_SHLVL=6
226
+ ++++ CONDA_SHLVL=6
227
+ ++++ export CONDA_DEFAULT_ENV=base
228
+ ++++ CONDA_DEFAULT_ENV=base
229
+ ++++ export 'CONDA_PROMPT_MODIFIER=(base) '
230
+ ++++ CONDA_PROMPT_MODIFIER='(base) '
231
+ ++++ export CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev
232
+ ++++ CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev
233
+ ++++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda
234
+ ++++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda
235
+ ++++ export _CE_M=
236
+ ++++ _CE_M=
237
+ ++++ export _CE_CONDA=
238
+ ++++ _CE_CONDA=
239
+ ++++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python
240
+ ++++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python
241
+ +++ __conda_hashr
242
+ +++ '[' -n '' ']'
243
+ +++ '[' -n '' ']'
244
+ +++ hash -r
245
+ ++ unset __conda_setup
246
+ + conda activate schemist-dev
247
+ + local cmd=activate
248
+ + case "$cmd" in
249
+ + __conda_activate activate schemist-dev
250
+ + '[' -n '' ']'
251
+ + local ask_conda
252
+ ++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '
253
+ ++ __conda_exe shell.posix activate schemist-dev
254
+ ++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate schemist-dev
255
+ + ask_conda='PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\''
256
+ export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\''
257
+ export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\''
258
+ export CONDA_SHLVL='\''7'\''
259
+ export CONDA_DEFAULT_ENV='\''schemist-dev'\''
260
+ export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\''
261
+ export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\''
262
+ export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\''
263
+ export _CE_M='\'''\''
264
+ export _CE_CONDA='\'''\''
265
+ export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'''
266
+ + eval 'PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\''
267
+ export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\''
268
+ export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\''
269
+ export CONDA_SHLVL='\''7'\''
270
+ export CONDA_DEFAULT_ENV='\''schemist-dev'\''
271
+ export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\''
272
+ export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\''
273
+ export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\''
274
+ export _CE_M='\'''\''
275
+ export _CE_CONDA='\'''\''
276
+ export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'''
277
+ ++ PS1='(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '
278
+ ++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin
279
+ ++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin
280
+ ++ export CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev
281
+ ++ CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev
282
+ ++ export CONDA_SHLVL=7
283
+ ++ CONDA_SHLVL=7
284
+ ++ export CONDA_DEFAULT_ENV=schemist-dev
285
+ ++ CONDA_DEFAULT_ENV=schemist-dev
286
+ ++ export 'CONDA_PROMPT_MODIFIER=(schemist-dev) '
287
+ ++ CONDA_PROMPT_MODIFIER='(schemist-dev) '
288
+ ++ export CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0
289
+ ++ CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0
290
+ ++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda
291
+ ++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda
292
+ ++ export _CE_M=
293
+ ++ _CE_M=
294
+ ++ export _CE_CONDA=
295
+ ++ _CE_CONDA=
296
+ ++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python
297
+ ++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python
298
+ + __conda_hashr
299
+ + '[' -n '' ']'
300
+ + '[' -n '' ']'
301
+ + hash -r
302
+ + CHUNK_HEAD_FILE=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz
303
+ + INPUT=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/test/cyc-pep-6-12mer-70M_09.csv
304
+ + COLUMN=cysteine_to_N_cyclization
305
+ + PREFIX=cyclic_
306
+ + AWK='1 { print $8, $1, $2, $10, $3 }'
307
+ + '[' -z cysteine_to_N_cyclization ']'
308
+ + '[' -z cyclic_ ']'
309
+ + '[' -z '1 { print $8, $1, $2, $10, $3 }' ']'
310
+ + 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
311
+ + awk -F, -v OFS=, '1 { print $8, $1, $2, $10, $3 }'
312
+ ++ zcat /nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz
313
+ + schemist convert -f csv --column cysteine_to_N_cyclization --to id inchikey scaffold mwt clogp tpsa --prefix cyclic_ --options prefix=SCB-
314
+ + gzip --best
315
+ ++ head -n1
316
+ ++ tr ' ' ,
317
+ 🚀 Converting between string representations with the following parameters:
318
+ subcommand: convert
319
+ output: <_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>
320
+ format: csv
321
+ input: <_io.TextIOWrapper name='<stdin>' mode='r' encoding='utf-8'>
322
+ representation: SMILES
323
+ column: cysteine_to_N_cyclization
324
+ prefix: cyclic_
325
+ to: ['id', 'inchikey', 'scaffold', 'mwt', 'clogp', 'tpsa']
326
+ options: ['prefix=SCB-']
327
+ func: <function _convert at 0x7f94dfb2f240>
328
+
329
+ Error counts:
330
+ cyclic_id: 0
331
+ cyclic_inchikey: 0
332
+ cyclic_scaffold: 0
333
+ cyclic_mwt: 0
334
+ cyclic_clogp: 0
335
+ cyclic_tpsa: 0
336
+ ⏰ Completed process in 2:33:34.867497
337
+ + 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.csv.gz CHANGED
@@ -1,3 +1,3 @@
1
  version https://git-lfs.github.com/spec/v1
2
- oid sha256:e67a2972bd0f92cbcc499bed7be8e7e77455b989bec94fe0f368da80749fa29a
3
- size 54500817
 
1
  version https://git-lfs.github.com/spec/v1
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+ oid sha256:199e08245d441ed59444e81419b31363a8b65ea032f0c939860432fd5623149a
3
+ size 107802205
test/cyc-pep-6-12mer-70M_10.log ADDED
@@ -0,0 +1,337 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ + module purge
2
+ + '[' -z '' ']'
3
+ + case "$-" in
4
+ + __lmod_sh_dbg=x
5
+ + '[' -n x ']'
6
+ + set +x
7
+ Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output
8
+ Shell debugging restarted
9
+ + unset __lmod_sh_dbg
10
+ + return 0
11
+ + module load Anaconda3/2023.03
12
+ + '[' -z '' ']'
13
+ + case "$-" in
14
+ + __lmod_sh_dbg=x
15
+ + '[' -n x ']'
16
+ + set +x
17
+ Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output
18
+ Shell debugging restarted
19
+ + unset __lmod_sh_dbg
20
+ + return 0
21
+ + source /camp/home/johnsoe/.bashrc
22
+ ++ '[' '' = yes ']'
23
+ ++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '
24
+ +++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.bash hook
25
+ ++ __conda_setup='export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\''
26
+ export _CE_M='\'''\''
27
+ export _CE_CONDA='\'''\''
28
+ export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''
29
+
30
+ # Copyright (C) 2012 Anaconda, Inc
31
+ # SPDX-License-Identifier: BSD-3-Clause
32
+ __conda_exe() (
33
+ "$CONDA_EXE" $_CE_M $_CE_CONDA "$@"
34
+ )
35
+
36
+ __conda_hashr() {
37
+ if [ -n "${ZSH_VERSION:+x}" ]; then
38
+ \rehash
39
+ elif [ -n "${POSH_VERSION:+x}" ]; then
40
+ : # pass
41
+ else
42
+ \hash -r
43
+ fi
44
+ }
45
+
46
+ __conda_activate() {
47
+ if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then
48
+ # Handle transition from shell activated with conda <= 4.3 to a subsequent activation
49
+ # after conda updated to >= 4.4. See issue #6173.
50
+ PS1="$CONDA_PS1_BACKUP"
51
+ \unset CONDA_PS1_BACKUP
52
+ fi
53
+ \local ask_conda
54
+ ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return
55
+ \eval "$ask_conda"
56
+ __conda_hashr
57
+ }
58
+
59
+ __conda_reactivate() {
60
+ \local ask_conda
61
+ ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return
62
+ \eval "$ask_conda"
63
+ __conda_hashr
64
+ }
65
+
66
+ conda() {
67
+ \local cmd="${1-__missing__}"
68
+ case "$cmd" in
69
+ activate|deactivate)
70
+ __conda_activate "$@"
71
+ ;;
72
+ install|update|upgrade|remove|uninstall)
73
+ __conda_exe "$@" || \return
74
+ __conda_reactivate
75
+ ;;
76
+ *)
77
+ __conda_exe "$@"
78
+ ;;
79
+ esac
80
+ }
81
+
82
+ if [ -z "${CONDA_SHLVL+x}" ]; then
83
+ \export CONDA_SHLVL=0
84
+ # In dev-mode CONDA_EXE is python.exe and on Windows
85
+ # it is in a different relative location to condabin.
86
+ if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then
87
+ PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}"
88
+ else
89
+ PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}"
90
+ fi
91
+ \export PATH
92
+
93
+ # We'\''re not allowing PS1 to be unbound. It must at least be set.
94
+ # However, we'\''re not exporting it, which can cause problems when starting a second shell
95
+ # via a first shell (i.e. starting zsh from bash).
96
+ if [ -z "${PS1+x}" ]; then
97
+ PS1=
98
+ fi
99
+ fi
100
+
101
+ conda activate base'
102
+ ++ '[' 0 -eq 0 ']'
103
+ ++ eval 'export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\''
104
+ export _CE_M='\'''\''
105
+ export _CE_CONDA='\'''\''
106
+ export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''
107
+
108
+ # Copyright (C) 2012 Anaconda, Inc
109
+ # SPDX-License-Identifier: BSD-3-Clause
110
+ __conda_exe() (
111
+ "$CONDA_EXE" $_CE_M $_CE_CONDA "$@"
112
+ )
113
+
114
+ __conda_hashr() {
115
+ if [ -n "${ZSH_VERSION:+x}" ]; then
116
+ \rehash
117
+ elif [ -n "${POSH_VERSION:+x}" ]; then
118
+ : # pass
119
+ else
120
+ \hash -r
121
+ fi
122
+ }
123
+
124
+ __conda_activate() {
125
+ if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then
126
+ # Handle transition from shell activated with conda <= 4.3 to a subsequent activation
127
+ # after conda updated to >= 4.4. See issue #6173.
128
+ PS1="$CONDA_PS1_BACKUP"
129
+ \unset CONDA_PS1_BACKUP
130
+ fi
131
+ \local ask_conda
132
+ ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return
133
+ \eval "$ask_conda"
134
+ __conda_hashr
135
+ }
136
+
137
+ __conda_reactivate() {
138
+ \local ask_conda
139
+ ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return
140
+ \eval "$ask_conda"
141
+ __conda_hashr
142
+ }
143
+
144
+ conda() {
145
+ \local cmd="${1-__missing__}"
146
+ case "$cmd" in
147
+ activate|deactivate)
148
+ __conda_activate "$@"
149
+ ;;
150
+ install|update|upgrade|remove|uninstall)
151
+ __conda_exe "$@" || \return
152
+ __conda_reactivate
153
+ ;;
154
+ *)
155
+ __conda_exe "$@"
156
+ ;;
157
+ esac
158
+ }
159
+
160
+ if [ -z "${CONDA_SHLVL+x}" ]; then
161
+ \export CONDA_SHLVL=0
162
+ # In dev-mode CONDA_EXE is python.exe and on Windows
163
+ # it is in a different relative location to condabin.
164
+ if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then
165
+ PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}"
166
+ else
167
+ PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}"
168
+ fi
169
+ \export PATH
170
+
171
+ # We'\''re not allowing PS1 to be unbound. It must at least be set.
172
+ # However, we'\''re not exporting it, which can cause problems when starting a second shell
173
+ # via a first shell (i.e. starting zsh from bash).
174
+ if [ -z "${PS1+x}" ]; then
175
+ PS1=
176
+ fi
177
+ fi
178
+
179
+ conda activate base'
180
+ +++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda
181
+ +++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda
182
+ +++ export _CE_M=
183
+ +++ _CE_M=
184
+ +++ export _CE_CONDA=
185
+ +++ _CE_CONDA=
186
+ +++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python
187
+ +++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python
188
+ +++ '[' -z x ']'
189
+ +++ conda activate base
190
+ +++ local cmd=activate
191
+ +++ case "$cmd" in
192
+ +++ __conda_activate activate base
193
+ +++ '[' -n '' ']'
194
+ +++ local ask_conda
195
+ ++++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '
196
+ ++++ __conda_exe shell.posix activate base
197
+ ++++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate base
198
+ +++ ask_conda='PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\''
199
+ export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\''
200
+ export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\''
201
+ export CONDA_SHLVL='\''6'\''
202
+ export CONDA_DEFAULT_ENV='\''base'\''
203
+ export CONDA_PROMPT_MODIFIER='\''(base) '\''
204
+ export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\''
205
+ export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\''
206
+ export _CE_M='\'''\''
207
+ export _CE_CONDA='\'''\''
208
+ export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'''
209
+ +++ eval 'PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\''
210
+ export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\''
211
+ export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\''
212
+ export CONDA_SHLVL='\''6'\''
213
+ export CONDA_DEFAULT_ENV='\''base'\''
214
+ export CONDA_PROMPT_MODIFIER='\''(base) '\''
215
+ export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\''
216
+ export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\''
217
+ export _CE_M='\'''\''
218
+ export _CE_CONDA='\'''\''
219
+ export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'''
220
+ ++++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '
221
+ ++++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin
222
+ ++++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin
223
+ ++++ export CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0
224
+ ++++ CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0
225
+ ++++ export CONDA_SHLVL=6
226
+ ++++ CONDA_SHLVL=6
227
+ ++++ export CONDA_DEFAULT_ENV=base
228
+ ++++ CONDA_DEFAULT_ENV=base
229
+ ++++ export 'CONDA_PROMPT_MODIFIER=(base) '
230
+ ++++ CONDA_PROMPT_MODIFIER='(base) '
231
+ ++++ export CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev
232
+ ++++ CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev
233
+ ++++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda
234
+ ++++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda
235
+ ++++ export _CE_M=
236
+ ++++ _CE_M=
237
+ ++++ export _CE_CONDA=
238
+ ++++ _CE_CONDA=
239
+ ++++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python
240
+ ++++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python
241
+ +++ __conda_hashr
242
+ +++ '[' -n '' ']'
243
+ +++ '[' -n '' ']'
244
+ +++ hash -r
245
+ ++ unset __conda_setup
246
+ + conda activate schemist-dev
247
+ + local cmd=activate
248
+ + case "$cmd" in
249
+ + __conda_activate activate schemist-dev
250
+ + '[' -n '' ']'
251
+ + local ask_conda
252
+ ++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '
253
+ ++ __conda_exe shell.posix activate schemist-dev
254
+ ++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate schemist-dev
255
+ + ask_conda='PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\''
256
+ export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\''
257
+ export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\''
258
+ export CONDA_SHLVL='\''7'\''
259
+ export CONDA_DEFAULT_ENV='\''schemist-dev'\''
260
+ export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\''
261
+ export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\''
262
+ export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\''
263
+ export _CE_M='\'''\''
264
+ export _CE_CONDA='\'''\''
265
+ export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'''
266
+ + eval 'PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\''
267
+ export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\''
268
+ export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\''
269
+ export CONDA_SHLVL='\''7'\''
270
+ export CONDA_DEFAULT_ENV='\''schemist-dev'\''
271
+ export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\''
272
+ export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\''
273
+ export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\''
274
+ export _CE_M='\'''\''
275
+ export _CE_CONDA='\'''\''
276
+ export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'''
277
+ ++ PS1='(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '
278
+ ++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin
279
+ ++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin
280
+ ++ export CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev
281
+ ++ CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev
282
+ ++ export CONDA_SHLVL=7
283
+ ++ CONDA_SHLVL=7
284
+ ++ export CONDA_DEFAULT_ENV=schemist-dev
285
+ ++ CONDA_DEFAULT_ENV=schemist-dev
286
+ ++ export 'CONDA_PROMPT_MODIFIER=(schemist-dev) '
287
+ ++ CONDA_PROMPT_MODIFIER='(schemist-dev) '
288
+ ++ export CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0
289
+ ++ CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0
290
+ ++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda
291
+ ++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda
292
+ ++ export _CE_M=
293
+ ++ _CE_M=
294
+ ++ export _CE_CONDA=
295
+ ++ _CE_CONDA=
296
+ ++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python
297
+ ++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python
298
+ + __conda_hashr
299
+ + '[' -n '' ']'
300
+ + '[' -n '' ']'
301
+ + hash -r
302
+ + CHUNK_HEAD_FILE=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz
303
+ + INPUT=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/test/cyc-pep-6-12mer-70M_10.csv
304
+ + COLUMN=cysteine_to_N_cyclization
305
+ + PREFIX=cyclic_
306
+ + AWK='1 { print $8, $1, $2, $10, $3 }'
307
+ + '[' -z cysteine_to_N_cyclization ']'
308
+ + '[' -z cyclic_ ']'
309
+ + '[' -z '1 { print $8, $1, $2, $10, $3 }' ']'
310
+ + 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
311
+ ++ head -n1
312
+ + schemist convert -f csv --column cysteine_to_N_cyclization --to id inchikey scaffold mwt clogp tpsa --prefix cyclic_ --options prefix=SCB-
313
+ ++ tr ' ' ,
314
+ + gzip --best
315
+ ++ zcat /nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz
316
+ + awk -F, -v OFS=, '1 { print $8, $1, $2, $10, $3 }'
317
+ 🚀 Converting between string representations with the following parameters:
318
+ subcommand: convert
319
+ output: <_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>
320
+ format: csv
321
+ input: <_io.TextIOWrapper name='<stdin>' mode='r' encoding='utf-8'>
322
+ representation: SMILES
323
+ column: cysteine_to_N_cyclization
324
+ prefix: cyclic_
325
+ to: ['id', 'inchikey', 'scaffold', 'mwt', 'clogp', 'tpsa']
326
+ options: ['prefix=SCB-']
327
+ func: <function _convert at 0x7f9537463240>
328
+
329
+ Error counts:
330
+ cyclic_id: 0
331
+ cyclic_inchikey: 0
332
+ cyclic_scaffold: 0
333
+ cyclic_mwt: 0
334
+ cyclic_clogp: 0
335
+ cyclic_tpsa: 0
336
+ ⏰ Completed process in 2:45:25.905852
337
+ + 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.csv.gz CHANGED
@@ -1,3 +1,3 @@
1
  version https://git-lfs.github.com/spec/v1
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- oid sha256:391ad3a94a7a8b21c716673919c760276cfaae109b729d99c8f9fc67c8654644
3
- size 26168089
 
1
  version https://git-lfs.github.com/spec/v1
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+ oid sha256:504987739844f6673f4a60dfd82a638dcdbce8b19768eeac08a91dc59c53dea8
3
+ size 51760158
test/cyc-pep-6-12mer-70M_11.log ADDED
@@ -0,0 +1,337 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ + module purge
2
+ + '[' -z '' ']'
3
+ + case "$-" in
4
+ + __lmod_sh_dbg=x
5
+ + '[' -n x ']'
6
+ + set +x
7
+ Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output
8
+ Shell debugging restarted
9
+ + unset __lmod_sh_dbg
10
+ + return 0
11
+ + module load Anaconda3/2023.03
12
+ + '[' -z '' ']'
13
+ + case "$-" in
14
+ + __lmod_sh_dbg=x
15
+ + '[' -n x ']'
16
+ + set +x
17
+ Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output
18
+ Shell debugging restarted
19
+ + unset __lmod_sh_dbg
20
+ + return 0
21
+ + source /camp/home/johnsoe/.bashrc
22
+ ++ '[' '' = yes ']'
23
+ ++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '
24
+ +++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.bash hook
25
+ ++ __conda_setup='export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\''
26
+ export _CE_M='\'''\''
27
+ export _CE_CONDA='\'''\''
28
+ export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''
29
+
30
+ # Copyright (C) 2012 Anaconda, Inc
31
+ # SPDX-License-Identifier: BSD-3-Clause
32
+ __conda_exe() (
33
+ "$CONDA_EXE" $_CE_M $_CE_CONDA "$@"
34
+ )
35
+
36
+ __conda_hashr() {
37
+ if [ -n "${ZSH_VERSION:+x}" ]; then
38
+ \rehash
39
+ elif [ -n "${POSH_VERSION:+x}" ]; then
40
+ : # pass
41
+ else
42
+ \hash -r
43
+ fi
44
+ }
45
+
46
+ __conda_activate() {
47
+ if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then
48
+ # Handle transition from shell activated with conda <= 4.3 to a subsequent activation
49
+ # after conda updated to >= 4.4. See issue #6173.
50
+ PS1="$CONDA_PS1_BACKUP"
51
+ \unset CONDA_PS1_BACKUP
52
+ fi
53
+ \local ask_conda
54
+ ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return
55
+ \eval "$ask_conda"
56
+ __conda_hashr
57
+ }
58
+
59
+ __conda_reactivate() {
60
+ \local ask_conda
61
+ ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return
62
+ \eval "$ask_conda"
63
+ __conda_hashr
64
+ }
65
+
66
+ conda() {
67
+ \local cmd="${1-__missing__}"
68
+ case "$cmd" in
69
+ activate|deactivate)
70
+ __conda_activate "$@"
71
+ ;;
72
+ install|update|upgrade|remove|uninstall)
73
+ __conda_exe "$@" || \return
74
+ __conda_reactivate
75
+ ;;
76
+ *)
77
+ __conda_exe "$@"
78
+ ;;
79
+ esac
80
+ }
81
+
82
+ if [ -z "${CONDA_SHLVL+x}" ]; then
83
+ \export CONDA_SHLVL=0
84
+ # In dev-mode CONDA_EXE is python.exe and on Windows
85
+ # it is in a different relative location to condabin.
86
+ if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then
87
+ PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}"
88
+ else
89
+ PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}"
90
+ fi
91
+ \export PATH
92
+
93
+ # We'\''re not allowing PS1 to be unbound. It must at least be set.
94
+ # However, we'\''re not exporting it, which can cause problems when starting a second shell
95
+ # via a first shell (i.e. starting zsh from bash).
96
+ if [ -z "${PS1+x}" ]; then
97
+ PS1=
98
+ fi
99
+ fi
100
+
101
+ conda activate base'
102
+ ++ '[' 0 -eq 0 ']'
103
+ ++ eval 'export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\''
104
+ export _CE_M='\'''\''
105
+ export _CE_CONDA='\'''\''
106
+ export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''
107
+
108
+ # Copyright (C) 2012 Anaconda, Inc
109
+ # SPDX-License-Identifier: BSD-3-Clause
110
+ __conda_exe() (
111
+ "$CONDA_EXE" $_CE_M $_CE_CONDA "$@"
112
+ )
113
+
114
+ __conda_hashr() {
115
+ if [ -n "${ZSH_VERSION:+x}" ]; then
116
+ \rehash
117
+ elif [ -n "${POSH_VERSION:+x}" ]; then
118
+ : # pass
119
+ else
120
+ \hash -r
121
+ fi
122
+ }
123
+
124
+ __conda_activate() {
125
+ if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then
126
+ # Handle transition from shell activated with conda <= 4.3 to a subsequent activation
127
+ # after conda updated to >= 4.4. See issue #6173.
128
+ PS1="$CONDA_PS1_BACKUP"
129
+ \unset CONDA_PS1_BACKUP
130
+ fi
131
+ \local ask_conda
132
+ ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return
133
+ \eval "$ask_conda"
134
+ __conda_hashr
135
+ }
136
+
137
+ __conda_reactivate() {
138
+ \local ask_conda
139
+ ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return
140
+ \eval "$ask_conda"
141
+ __conda_hashr
142
+ }
143
+
144
+ conda() {
145
+ \local cmd="${1-__missing__}"
146
+ case "$cmd" in
147
+ activate|deactivate)
148
+ __conda_activate "$@"
149
+ ;;
150
+ install|update|upgrade|remove|uninstall)
151
+ __conda_exe "$@" || \return
152
+ __conda_reactivate
153
+ ;;
154
+ *)
155
+ __conda_exe "$@"
156
+ ;;
157
+ esac
158
+ }
159
+
160
+ if [ -z "${CONDA_SHLVL+x}" ]; then
161
+ \export CONDA_SHLVL=0
162
+ # In dev-mode CONDA_EXE is python.exe and on Windows
163
+ # it is in a different relative location to condabin.
164
+ if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then
165
+ PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}"
166
+ else
167
+ PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}"
168
+ fi
169
+ \export PATH
170
+
171
+ # We'\''re not allowing PS1 to be unbound. It must at least be set.
172
+ # However, we'\''re not exporting it, which can cause problems when starting a second shell
173
+ # via a first shell (i.e. starting zsh from bash).
174
+ if [ -z "${PS1+x}" ]; then
175
+ PS1=
176
+ fi
177
+ fi
178
+
179
+ conda activate base'
180
+ +++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda
181
+ +++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda
182
+ +++ export _CE_M=
183
+ +++ _CE_M=
184
+ +++ export _CE_CONDA=
185
+ +++ _CE_CONDA=
186
+ +++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python
187
+ +++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python
188
+ +++ '[' -z x ']'
189
+ +++ conda activate base
190
+ +++ local cmd=activate
191
+ +++ case "$cmd" in
192
+ +++ __conda_activate activate base
193
+ +++ '[' -n '' ']'
194
+ +++ local ask_conda
195
+ ++++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '
196
+ ++++ __conda_exe shell.posix activate base
197
+ ++++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate base
198
+ +++ ask_conda='PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\''
199
+ export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\''
200
+ export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\''
201
+ export CONDA_SHLVL='\''6'\''
202
+ export CONDA_DEFAULT_ENV='\''base'\''
203
+ export CONDA_PROMPT_MODIFIER='\''(base) '\''
204
+ export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\''
205
+ export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\''
206
+ export _CE_M='\'''\''
207
+ export _CE_CONDA='\'''\''
208
+ export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'''
209
+ +++ eval 'PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\''
210
+ export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\''
211
+ export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\''
212
+ export CONDA_SHLVL='\''6'\''
213
+ export CONDA_DEFAULT_ENV='\''base'\''
214
+ export CONDA_PROMPT_MODIFIER='\''(base) '\''
215
+ export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\''
216
+ export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\''
217
+ export _CE_M='\'''\''
218
+ export _CE_CONDA='\'''\''
219
+ export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'''
220
+ ++++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '
221
+ ++++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin
222
+ ++++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin
223
+ ++++ export CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0
224
+ ++++ CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0
225
+ ++++ export CONDA_SHLVL=6
226
+ ++++ CONDA_SHLVL=6
227
+ ++++ export CONDA_DEFAULT_ENV=base
228
+ ++++ CONDA_DEFAULT_ENV=base
229
+ ++++ export 'CONDA_PROMPT_MODIFIER=(base) '
230
+ ++++ CONDA_PROMPT_MODIFIER='(base) '
231
+ ++++ export CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev
232
+ ++++ CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev
233
+ ++++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda
234
+ ++++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda
235
+ ++++ export _CE_M=
236
+ ++++ _CE_M=
237
+ ++++ export _CE_CONDA=
238
+ ++++ _CE_CONDA=
239
+ ++++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python
240
+ ++++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python
241
+ +++ __conda_hashr
242
+ +++ '[' -n '' ']'
243
+ +++ '[' -n '' ']'
244
+ +++ hash -r
245
+ ++ unset __conda_setup
246
+ + conda activate schemist-dev
247
+ + local cmd=activate
248
+ + case "$cmd" in
249
+ + __conda_activate activate schemist-dev
250
+ + '[' -n '' ']'
251
+ + local ask_conda
252
+ ++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '
253
+ ++ __conda_exe shell.posix activate schemist-dev
254
+ ++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate schemist-dev
255
+ + ask_conda='PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\''
256
+ export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\''
257
+ export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\''
258
+ export CONDA_SHLVL='\''7'\''
259
+ export CONDA_DEFAULT_ENV='\''schemist-dev'\''
260
+ export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\''
261
+ export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\''
262
+ export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\''
263
+ export _CE_M='\'''\''
264
+ export _CE_CONDA='\'''\''
265
+ export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'''
266
+ + eval 'PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\''
267
+ export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\''
268
+ export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\''
269
+ export CONDA_SHLVL='\''7'\''
270
+ export CONDA_DEFAULT_ENV='\''schemist-dev'\''
271
+ export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\''
272
+ export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\''
273
+ export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\''
274
+ export _CE_M='\'''\''
275
+ export _CE_CONDA='\'''\''
276
+ export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'''
277
+ ++ PS1='(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '
278
+ ++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin
279
+ ++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin
280
+ ++ export CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev
281
+ ++ CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev
282
+ ++ export CONDA_SHLVL=7
283
+ ++ CONDA_SHLVL=7
284
+ ++ export CONDA_DEFAULT_ENV=schemist-dev
285
+ ++ CONDA_DEFAULT_ENV=schemist-dev
286
+ ++ export 'CONDA_PROMPT_MODIFIER=(schemist-dev) '
287
+ ++ CONDA_PROMPT_MODIFIER='(schemist-dev) '
288
+ ++ export CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0
289
+ ++ CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0
290
+ ++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda
291
+ ++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda
292
+ ++ export _CE_M=
293
+ ++ _CE_M=
294
+ ++ export _CE_CONDA=
295
+ ++ _CE_CONDA=
296
+ ++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python
297
+ ++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python
298
+ + __conda_hashr
299
+ + '[' -n '' ']'
300
+ + '[' -n '' ']'
301
+ + hash -r
302
+ + CHUNK_HEAD_FILE=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz
303
+ + INPUT=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/test/cyc-pep-6-12mer-70M_11.csv
304
+ + COLUMN=cysteine_to_N_cyclization
305
+ + PREFIX=cyclic_
306
+ + AWK='1 { print $8, $1, $2, $10, $3 }'
307
+ + '[' -z cysteine_to_N_cyclization ']'
308
+ + '[' -z cyclic_ ']'
309
+ + '[' -z '1 { print $8, $1, $2, $10, $3 }' ']'
310
+ + awk -F, -v OFS=, '1 { print $8, $1, $2, $10, $3 }'
311
+ + 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
312
+ ++ zcat /nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz
313
+ + schemist convert -f csv --column cysteine_to_N_cyclization --to id inchikey scaffold mwt clogp tpsa --prefix cyclic_ --options prefix=SCB-
314
+ + gzip --best
315
+ ++ tr ' ' ,
316
+ ++ head -n1
317
+ 🚀 Converting between string representations with the following parameters:
318
+ subcommand: convert
319
+ output: <_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>
320
+ format: csv
321
+ input: <_io.TextIOWrapper name='<stdin>' mode='r' encoding='utf-8'>
322
+ representation: SMILES
323
+ column: cysteine_to_N_cyclization
324
+ prefix: cyclic_
325
+ to: ['id', 'inchikey', 'scaffold', 'mwt', 'clogp', 'tpsa']
326
+ options: ['prefix=SCB-']
327
+ func: <function _convert at 0x7f145a383240>
328
+
329
+ Error counts:
330
+ cyclic_id: 0
331
+ cyclic_inchikey: 0
332
+ cyclic_scaffold: 0
333
+ cyclic_mwt: 0
334
+ cyclic_clogp: 0
335
+ cyclic_tpsa: 0
336
+ ⏰ Completed process in 1:21:08.538847
337
+ + 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.csv.gz CHANGED
@@ -1,3 +1,3 @@
1
  version https://git-lfs.github.com/spec/v1
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- oid sha256:27a95b1f21d38e79c716e6af47e4fa44ead26226601926ce31fcf389b37c28ae
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- size 58249769
 
1
  version https://git-lfs.github.com/spec/v1
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+ oid sha256:1533dd518c32e080fe4b876e67f47d175cf22e83ed4081e5cf99bff0adf1931f
3
+ size 112828175
train/cyc-pep-6-12mer-70M_00.log ADDED
@@ -0,0 +1,337 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ + module purge
2
+ + '[' -z '' ']'
3
+ + case "$-" in
4
+ + __lmod_sh_dbg=x
5
+ + '[' -n x ']'
6
+ + set +x
7
+ Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output
8
+ Shell debugging restarted
9
+ + unset __lmod_sh_dbg
10
+ + return 0
11
+ + module load Anaconda3/2023.03
12
+ + '[' -z '' ']'
13
+ + case "$-" in
14
+ + __lmod_sh_dbg=x
15
+ + '[' -n x ']'
16
+ + set +x
17
+ Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output
18
+ Shell debugging restarted
19
+ + unset __lmod_sh_dbg
20
+ + return 0
21
+ + source /camp/home/johnsoe/.bashrc
22
+ ++ '[' '' = yes ']'
23
+ ++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '
24
+ +++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.bash hook
25
+ ++ __conda_setup='export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\''
26
+ export _CE_M='\'''\''
27
+ export _CE_CONDA='\'''\''
28
+ export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''
29
+
30
+ # Copyright (C) 2012 Anaconda, Inc
31
+ # SPDX-License-Identifier: BSD-3-Clause
32
+ __conda_exe() (
33
+ "$CONDA_EXE" $_CE_M $_CE_CONDA "$@"
34
+ )
35
+
36
+ __conda_hashr() {
37
+ if [ -n "${ZSH_VERSION:+x}" ]; then
38
+ \rehash
39
+ elif [ -n "${POSH_VERSION:+x}" ]; then
40
+ : # pass
41
+ else
42
+ \hash -r
43
+ fi
44
+ }
45
+
46
+ __conda_activate() {
47
+ if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then
48
+ # Handle transition from shell activated with conda <= 4.3 to a subsequent activation
49
+ # after conda updated to >= 4.4. See issue #6173.
50
+ PS1="$CONDA_PS1_BACKUP"
51
+ \unset CONDA_PS1_BACKUP
52
+ fi
53
+ \local ask_conda
54
+ ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return
55
+ \eval "$ask_conda"
56
+ __conda_hashr
57
+ }
58
+
59
+ __conda_reactivate() {
60
+ \local ask_conda
61
+ ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return
62
+ \eval "$ask_conda"
63
+ __conda_hashr
64
+ }
65
+
66
+ conda() {
67
+ \local cmd="${1-__missing__}"
68
+ case "$cmd" in
69
+ activate|deactivate)
70
+ __conda_activate "$@"
71
+ ;;
72
+ install|update|upgrade|remove|uninstall)
73
+ __conda_exe "$@" || \return
74
+ __conda_reactivate
75
+ ;;
76
+ *)
77
+ __conda_exe "$@"
78
+ ;;
79
+ esac
80
+ }
81
+
82
+ if [ -z "${CONDA_SHLVL+x}" ]; then
83
+ \export CONDA_SHLVL=0
84
+ # In dev-mode CONDA_EXE is python.exe and on Windows
85
+ # it is in a different relative location to condabin.
86
+ if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then
87
+ PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}"
88
+ else
89
+ PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}"
90
+ fi
91
+ \export PATH
92
+
93
+ # We'\''re not allowing PS1 to be unbound. It must at least be set.
94
+ # However, we'\''re not exporting it, which can cause problems when starting a second shell
95
+ # via a first shell (i.e. starting zsh from bash).
96
+ if [ -z "${PS1+x}" ]; then
97
+ PS1=
98
+ fi
99
+ fi
100
+
101
+ conda activate base'
102
+ ++ '[' 0 -eq 0 ']'
103
+ ++ eval 'export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\''
104
+ export _CE_M='\'''\''
105
+ export _CE_CONDA='\'''\''
106
+ export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''
107
+
108
+ # Copyright (C) 2012 Anaconda, Inc
109
+ # SPDX-License-Identifier: BSD-3-Clause
110
+ __conda_exe() (
111
+ "$CONDA_EXE" $_CE_M $_CE_CONDA "$@"
112
+ )
113
+
114
+ __conda_hashr() {
115
+ if [ -n "${ZSH_VERSION:+x}" ]; then
116
+ \rehash
117
+ elif [ -n "${POSH_VERSION:+x}" ]; then
118
+ : # pass
119
+ else
120
+ \hash -r
121
+ fi
122
+ }
123
+
124
+ __conda_activate() {
125
+ if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then
126
+ # Handle transition from shell activated with conda <= 4.3 to a subsequent activation
127
+ # after conda updated to >= 4.4. See issue #6173.
128
+ PS1="$CONDA_PS1_BACKUP"
129
+ \unset CONDA_PS1_BACKUP
130
+ fi
131
+ \local ask_conda
132
+ ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return
133
+ \eval "$ask_conda"
134
+ __conda_hashr
135
+ }
136
+
137
+ __conda_reactivate() {
138
+ \local ask_conda
139
+ ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return
140
+ \eval "$ask_conda"
141
+ __conda_hashr
142
+ }
143
+
144
+ conda() {
145
+ \local cmd="${1-__missing__}"
146
+ case "$cmd" in
147
+ activate|deactivate)
148
+ __conda_activate "$@"
149
+ ;;
150
+ install|update|upgrade|remove|uninstall)
151
+ __conda_exe "$@" || \return
152
+ __conda_reactivate
153
+ ;;
154
+ *)
155
+ __conda_exe "$@"
156
+ ;;
157
+ esac
158
+ }
159
+
160
+ if [ -z "${CONDA_SHLVL+x}" ]; then
161
+ \export CONDA_SHLVL=0
162
+ # In dev-mode CONDA_EXE is python.exe and on Windows
163
+ # it is in a different relative location to condabin.
164
+ if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then
165
+ PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}"
166
+ else
167
+ PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}"
168
+ fi
169
+ \export PATH
170
+
171
+ # We'\''re not allowing PS1 to be unbound. It must at least be set.
172
+ # However, we'\''re not exporting it, which can cause problems when starting a second shell
173
+ # via a first shell (i.e. starting zsh from bash).
174
+ if [ -z "${PS1+x}" ]; then
175
+ PS1=
176
+ fi
177
+ fi
178
+
179
+ conda activate base'
180
+ +++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda
181
+ +++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda
182
+ +++ export _CE_M=
183
+ +++ _CE_M=
184
+ +++ export _CE_CONDA=
185
+ +++ _CE_CONDA=
186
+ +++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python
187
+ +++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python
188
+ +++ '[' -z x ']'
189
+ +++ conda activate base
190
+ +++ local cmd=activate
191
+ +++ case "$cmd" in
192
+ +++ __conda_activate activate base
193
+ +++ '[' -n '' ']'
194
+ +++ local ask_conda
195
+ ++++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '
196
+ ++++ __conda_exe shell.posix activate base
197
+ ++++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate base
198
+ +++ ask_conda='PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\''
199
+ export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\''
200
+ export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\''
201
+ export CONDA_SHLVL='\''6'\''
202
+ export CONDA_DEFAULT_ENV='\''base'\''
203
+ export CONDA_PROMPT_MODIFIER='\''(base) '\''
204
+ export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\''
205
+ export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\''
206
+ export _CE_M='\'''\''
207
+ export _CE_CONDA='\'''\''
208
+ export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'''
209
+ +++ eval 'PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\''
210
+ export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\''
211
+ export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\''
212
+ export CONDA_SHLVL='\''6'\''
213
+ export CONDA_DEFAULT_ENV='\''base'\''
214
+ export CONDA_PROMPT_MODIFIER='\''(base) '\''
215
+ export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\''
216
+ export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\''
217
+ export _CE_M='\'''\''
218
+ export _CE_CONDA='\'''\''
219
+ export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'''
220
+ ++++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '
221
+ ++++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin
222
+ ++++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin
223
+ ++++ export CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0
224
+ ++++ CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0
225
+ ++++ export CONDA_SHLVL=6
226
+ ++++ CONDA_SHLVL=6
227
+ ++++ export CONDA_DEFAULT_ENV=base
228
+ ++++ CONDA_DEFAULT_ENV=base
229
+ ++++ export 'CONDA_PROMPT_MODIFIER=(base) '
230
+ ++++ CONDA_PROMPT_MODIFIER='(base) '
231
+ ++++ export CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev
232
+ ++++ CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev
233
+ ++++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda
234
+ ++++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda
235
+ ++++ export _CE_M=
236
+ ++++ _CE_M=
237
+ ++++ export _CE_CONDA=
238
+ ++++ _CE_CONDA=
239
+ ++++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python
240
+ ++++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python
241
+ +++ __conda_hashr
242
+ +++ '[' -n '' ']'
243
+ +++ '[' -n '' ']'
244
+ +++ hash -r
245
+ ++ unset __conda_setup
246
+ + conda activate schemist-dev
247
+ + local cmd=activate
248
+ + case "$cmd" in
249
+ + __conda_activate activate schemist-dev
250
+ + '[' -n '' ']'
251
+ + local ask_conda
252
+ ++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '
253
+ ++ __conda_exe shell.posix activate schemist-dev
254
+ ++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate schemist-dev
255
+ + ask_conda='PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\''
256
+ export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\''
257
+ export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\''
258
+ export CONDA_SHLVL='\''7'\''
259
+ export CONDA_DEFAULT_ENV='\''schemist-dev'\''
260
+ export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\''
261
+ export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\''
262
+ export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\''
263
+ export _CE_M='\'''\''
264
+ export _CE_CONDA='\'''\''
265
+ export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'''
266
+ + eval 'PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\''
267
+ export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\''
268
+ export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\''
269
+ export CONDA_SHLVL='\''7'\''
270
+ export CONDA_DEFAULT_ENV='\''schemist-dev'\''
271
+ export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\''
272
+ export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\''
273
+ export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\''
274
+ export _CE_M='\'''\''
275
+ export _CE_CONDA='\'''\''
276
+ export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'''
277
+ ++ PS1='(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '
278
+ ++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin
279
+ ++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin
280
+ ++ export CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev
281
+ ++ CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev
282
+ ++ export CONDA_SHLVL=7
283
+ ++ CONDA_SHLVL=7
284
+ ++ export CONDA_DEFAULT_ENV=schemist-dev
285
+ ++ CONDA_DEFAULT_ENV=schemist-dev
286
+ ++ export 'CONDA_PROMPT_MODIFIER=(schemist-dev) '
287
+ ++ CONDA_PROMPT_MODIFIER='(schemist-dev) '
288
+ ++ export CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0
289
+ ++ CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0
290
+ ++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda
291
+ ++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda
292
+ ++ export _CE_M=
293
+ ++ _CE_M=
294
+ ++ export _CE_CONDA=
295
+ ++ _CE_CONDA=
296
+ ++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python
297
+ ++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python
298
+ + __conda_hashr
299
+ + '[' -n '' ']'
300
+ + '[' -n '' ']'
301
+ + hash -r
302
+ + CHUNK_HEAD_FILE=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz
303
+ + INPUT=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/train/cyc-pep-6-12mer-70M_00.csv
304
+ + COLUMN=cysteine_to_N_cyclization
305
+ + PREFIX=cyclic_
306
+ + AWK='1 { print $8, $1, $2, $10, $3 }'
307
+ + '[' -z cysteine_to_N_cyclization ']'
308
+ + '[' -z cyclic_ ']'
309
+ + '[' -z '1 { print $8, $1, $2, $10, $3 }' ']'
310
+ + 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
311
+ + gzip --best
312
+ + schemist convert -f csv --column cysteine_to_N_cyclization --to id inchikey scaffold mwt clogp tpsa --prefix cyclic_ --options prefix=SCB-
313
+ ++ tr ' ' ,
314
+ + awk -F, -v OFS=, '1 { print $8, $1, $2, $10, $3 }'
315
+ ++ head -n1
316
+ ++ zcat /nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz
317
+ 🚀 Converting between string representations with the following parameters:
318
+ subcommand: convert
319
+ output: <_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>
320
+ format: csv
321
+ input: <_io.TextIOWrapper name='<stdin>' mode='r' encoding='utf-8'>
322
+ representation: SMILES
323
+ column: cysteine_to_N_cyclization
324
+ prefix: cyclic_
325
+ to: ['id', 'inchikey', 'scaffold', 'mwt', 'clogp', 'tpsa']
326
+ options: ['prefix=SCB-']
327
+ func: <function _convert at 0x7f967c3a7240>
328
+
329
+ Error counts:
330
+ cyclic_id: 0
331
+ cyclic_inchikey: 0
332
+ cyclic_scaffold: 0
333
+ cyclic_mwt: 0
334
+ cyclic_clogp: 0
335
+ cyclic_tpsa: 0
336
+ ⏰ Completed process in 2:59:58.795561
337
+ + 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.csv.gz CHANGED
@@ -1,3 +1,3 @@
1
  version https://git-lfs.github.com/spec/v1
2
- oid sha256:d387ed185e88ecfdb4413a271ec111011b684f33e27244b5cd95d01da3a79dff
3
- size 58249061
 
1
  version https://git-lfs.github.com/spec/v1
2
+ oid sha256:13bc91d61c8e22cdda8434608fb531a5565694108ffc8b7dbeb6967e39b3a6a0
3
+ size 112823965
train/cyc-pep-6-12mer-70M_01.log ADDED
@@ -0,0 +1,337 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ + module purge
2
+ + '[' -z '' ']'
3
+ + case "$-" in
4
+ + __lmod_sh_dbg=x
5
+ + '[' -n x ']'
6
+ + set +x
7
+ Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output
8
+ Shell debugging restarted
9
+ + unset __lmod_sh_dbg
10
+ + return 0
11
+ + module load Anaconda3/2023.03
12
+ + '[' -z '' ']'
13
+ + case "$-" in
14
+ + __lmod_sh_dbg=x
15
+ + '[' -n x ']'
16
+ + set +x
17
+ Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output
18
+ Shell debugging restarted
19
+ + unset __lmod_sh_dbg
20
+ + return 0
21
+ + source /camp/home/johnsoe/.bashrc
22
+ ++ '[' '' = yes ']'
23
+ ++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '
24
+ +++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.bash hook
25
+ ++ __conda_setup='export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\''
26
+ export _CE_M='\'''\''
27
+ export _CE_CONDA='\'''\''
28
+ export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''
29
+
30
+ # Copyright (C) 2012 Anaconda, Inc
31
+ # SPDX-License-Identifier: BSD-3-Clause
32
+ __conda_exe() (
33
+ "$CONDA_EXE" $_CE_M $_CE_CONDA "$@"
34
+ )
35
+
36
+ __conda_hashr() {
37
+ if [ -n "${ZSH_VERSION:+x}" ]; then
38
+ \rehash
39
+ elif [ -n "${POSH_VERSION:+x}" ]; then
40
+ : # pass
41
+ else
42
+ \hash -r
43
+ fi
44
+ }
45
+
46
+ __conda_activate() {
47
+ if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then
48
+ # Handle transition from shell activated with conda <= 4.3 to a subsequent activation
49
+ # after conda updated to >= 4.4. See issue #6173.
50
+ PS1="$CONDA_PS1_BACKUP"
51
+ \unset CONDA_PS1_BACKUP
52
+ fi
53
+ \local ask_conda
54
+ ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return
55
+ \eval "$ask_conda"
56
+ __conda_hashr
57
+ }
58
+
59
+ __conda_reactivate() {
60
+ \local ask_conda
61
+ ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return
62
+ \eval "$ask_conda"
63
+ __conda_hashr
64
+ }
65
+
66
+ conda() {
67
+ \local cmd="${1-__missing__}"
68
+ case "$cmd" in
69
+ activate|deactivate)
70
+ __conda_activate "$@"
71
+ ;;
72
+ install|update|upgrade|remove|uninstall)
73
+ __conda_exe "$@" || \return
74
+ __conda_reactivate
75
+ ;;
76
+ *)
77
+ __conda_exe "$@"
78
+ ;;
79
+ esac
80
+ }
81
+
82
+ if [ -z "${CONDA_SHLVL+x}" ]; then
83
+ \export CONDA_SHLVL=0
84
+ # In dev-mode CONDA_EXE is python.exe and on Windows
85
+ # it is in a different relative location to condabin.
86
+ if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then
87
+ PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}"
88
+ else
89
+ PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}"
90
+ fi
91
+ \export PATH
92
+
93
+ # We'\''re not allowing PS1 to be unbound. It must at least be set.
94
+ # However, we'\''re not exporting it, which can cause problems when starting a second shell
95
+ # via a first shell (i.e. starting zsh from bash).
96
+ if [ -z "${PS1+x}" ]; then
97
+ PS1=
98
+ fi
99
+ fi
100
+
101
+ conda activate base'
102
+ ++ '[' 0 -eq 0 ']'
103
+ ++ eval 'export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\''
104
+ export _CE_M='\'''\''
105
+ export _CE_CONDA='\'''\''
106
+ export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''
107
+
108
+ # Copyright (C) 2012 Anaconda, Inc
109
+ # SPDX-License-Identifier: BSD-3-Clause
110
+ __conda_exe() (
111
+ "$CONDA_EXE" $_CE_M $_CE_CONDA "$@"
112
+ )
113
+
114
+ __conda_hashr() {
115
+ if [ -n "${ZSH_VERSION:+x}" ]; then
116
+ \rehash
117
+ elif [ -n "${POSH_VERSION:+x}" ]; then
118
+ : # pass
119
+ else
120
+ \hash -r
121
+ fi
122
+ }
123
+
124
+ __conda_activate() {
125
+ if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then
126
+ # Handle transition from shell activated with conda <= 4.3 to a subsequent activation
127
+ # after conda updated to >= 4.4. See issue #6173.
128
+ PS1="$CONDA_PS1_BACKUP"
129
+ \unset CONDA_PS1_BACKUP
130
+ fi
131
+ \local ask_conda
132
+ ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return
133
+ \eval "$ask_conda"
134
+ __conda_hashr
135
+ }
136
+
137
+ __conda_reactivate() {
138
+ \local ask_conda
139
+ ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return
140
+ \eval "$ask_conda"
141
+ __conda_hashr
142
+ }
143
+
144
+ conda() {
145
+ \local cmd="${1-__missing__}"
146
+ case "$cmd" in
147
+ activate|deactivate)
148
+ __conda_activate "$@"
149
+ ;;
150
+ install|update|upgrade|remove|uninstall)
151
+ __conda_exe "$@" || \return
152
+ __conda_reactivate
153
+ ;;
154
+ *)
155
+ __conda_exe "$@"
156
+ ;;
157
+ esac
158
+ }
159
+
160
+ if [ -z "${CONDA_SHLVL+x}" ]; then
161
+ \export CONDA_SHLVL=0
162
+ # In dev-mode CONDA_EXE is python.exe and on Windows
163
+ # it is in a different relative location to condabin.
164
+ if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then
165
+ PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}"
166
+ else
167
+ PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}"
168
+ fi
169
+ \export PATH
170
+
171
+ # We'\''re not allowing PS1 to be unbound. It must at least be set.
172
+ # However, we'\''re not exporting it, which can cause problems when starting a second shell
173
+ # via a first shell (i.e. starting zsh from bash).
174
+ if [ -z "${PS1+x}" ]; then
175
+ PS1=
176
+ fi
177
+ fi
178
+
179
+ conda activate base'
180
+ +++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda
181
+ +++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda
182
+ +++ export _CE_M=
183
+ +++ _CE_M=
184
+ +++ export _CE_CONDA=
185
+ +++ _CE_CONDA=
186
+ +++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python
187
+ +++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python
188
+ +++ '[' -z x ']'
189
+ +++ conda activate base
190
+ +++ local cmd=activate
191
+ +++ case "$cmd" in
192
+ +++ __conda_activate activate base
193
+ +++ '[' -n '' ']'
194
+ +++ local ask_conda
195
+ ++++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '
196
+ ++++ __conda_exe shell.posix activate base
197
+ ++++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate base
198
+ +++ ask_conda='PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\''
199
+ export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\''
200
+ export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\''
201
+ export CONDA_SHLVL='\''6'\''
202
+ export CONDA_DEFAULT_ENV='\''base'\''
203
+ export CONDA_PROMPT_MODIFIER='\''(base) '\''
204
+ export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\''
205
+ export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\''
206
+ export _CE_M='\'''\''
207
+ export _CE_CONDA='\'''\''
208
+ export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'''
209
+ +++ eval 'PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\''
210
+ export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\''
211
+ export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\''
212
+ export CONDA_SHLVL='\''6'\''
213
+ export CONDA_DEFAULT_ENV='\''base'\''
214
+ export CONDA_PROMPT_MODIFIER='\''(base) '\''
215
+ export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\''
216
+ export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\''
217
+ export _CE_M='\'''\''
218
+ export _CE_CONDA='\'''\''
219
+ export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'''
220
+ ++++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '
221
+ ++++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin
222
+ ++++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin
223
+ ++++ export CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0
224
+ ++++ CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0
225
+ ++++ export CONDA_SHLVL=6
226
+ ++++ CONDA_SHLVL=6
227
+ ++++ export CONDA_DEFAULT_ENV=base
228
+ ++++ CONDA_DEFAULT_ENV=base
229
+ ++++ export 'CONDA_PROMPT_MODIFIER=(base) '
230
+ ++++ CONDA_PROMPT_MODIFIER='(base) '
231
+ ++++ export CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev
232
+ ++++ CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev
233
+ ++++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda
234
+ ++++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda
235
+ ++++ export _CE_M=
236
+ ++++ _CE_M=
237
+ ++++ export _CE_CONDA=
238
+ ++++ _CE_CONDA=
239
+ ++++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python
240
+ ++++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python
241
+ +++ __conda_hashr
242
+ +++ '[' -n '' ']'
243
+ +++ '[' -n '' ']'
244
+ +++ hash -r
245
+ ++ unset __conda_setup
246
+ + conda activate schemist-dev
247
+ + local cmd=activate
248
+ + case "$cmd" in
249
+ + __conda_activate activate schemist-dev
250
+ + '[' -n '' ']'
251
+ + local ask_conda
252
+ ++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '
253
+ ++ __conda_exe shell.posix activate schemist-dev
254
+ ++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate schemist-dev
255
+ + ask_conda='PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\''
256
+ export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\''
257
+ export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\''
258
+ export CONDA_SHLVL='\''7'\''
259
+ export CONDA_DEFAULT_ENV='\''schemist-dev'\''
260
+ export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\''
261
+ export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\''
262
+ export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\''
263
+ export _CE_M='\'''\''
264
+ export _CE_CONDA='\'''\''
265
+ export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'''
266
+ + eval 'PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\''
267
+ export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\''
268
+ export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\''
269
+ export CONDA_SHLVL='\''7'\''
270
+ export CONDA_DEFAULT_ENV='\''schemist-dev'\''
271
+ export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\''
272
+ export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\''
273
+ export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\''
274
+ export _CE_M='\'''\''
275
+ export _CE_CONDA='\'''\''
276
+ export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'''
277
+ ++ PS1='(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '
278
+ ++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin
279
+ ++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin
280
+ ++ export CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev
281
+ ++ CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev
282
+ ++ export CONDA_SHLVL=7
283
+ ++ CONDA_SHLVL=7
284
+ ++ export CONDA_DEFAULT_ENV=schemist-dev
285
+ ++ CONDA_DEFAULT_ENV=schemist-dev
286
+ ++ export 'CONDA_PROMPT_MODIFIER=(schemist-dev) '
287
+ ++ CONDA_PROMPT_MODIFIER='(schemist-dev) '
288
+ ++ export CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0
289
+ ++ CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0
290
+ ++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda
291
+ ++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda
292
+ ++ export _CE_M=
293
+ ++ _CE_M=
294
+ ++ export _CE_CONDA=
295
+ ++ _CE_CONDA=
296
+ ++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python
297
+ ++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python
298
+ + __conda_hashr
299
+ + '[' -n '' ']'
300
+ + '[' -n '' ']'
301
+ + hash -r
302
+ + CHUNK_HEAD_FILE=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz
303
+ + INPUT=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/train/cyc-pep-6-12mer-70M_01.csv
304
+ + COLUMN=cysteine_to_N_cyclization
305
+ + PREFIX=cyclic_
306
+ + AWK='1 { print $8, $1, $2, $10, $3 }'
307
+ + '[' -z cysteine_to_N_cyclization ']'
308
+ + '[' -z cyclic_ ']'
309
+ + '[' -z '1 { print $8, $1, $2, $10, $3 }' ']'
310
+ + 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
311
+ + schemist convert -f csv --column cysteine_to_N_cyclization --to id inchikey scaffold mwt clogp tpsa --prefix cyclic_ --options prefix=SCB-
312
+ + gzip --best
313
+ ++ head -n1
314
+ + awk -F, -v OFS=, '1 { print $8, $1, $2, $10, $3 }'
315
+ ++ zcat /nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz
316
+ ++ tr ' ' ,
317
+ 🚀 Converting between string representations with the following parameters:
318
+ subcommand: convert
319
+ output: <_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>
320
+ format: csv
321
+ input: <_io.TextIOWrapper name='<stdin>' mode='r' encoding='utf-8'>
322
+ representation: SMILES
323
+ column: cysteine_to_N_cyclization
324
+ prefix: cyclic_
325
+ to: ['id', 'inchikey', 'scaffold', 'mwt', 'clogp', 'tpsa']
326
+ options: ['prefix=SCB-']
327
+ func: <function _convert at 0x7f7db174b240>
328
+
329
+ Error counts:
330
+ cyclic_id: 0
331
+ cyclic_inchikey: 0
332
+ cyclic_scaffold: 0
333
+ cyclic_mwt: 0
334
+ cyclic_clogp: 0
335
+ cyclic_tpsa: 0
336
+ ⏰ Completed process in 2:58:48.975518
337
+ + 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.csv.gz CHANGED
@@ -1,3 +1,3 @@
1
  version https://git-lfs.github.com/spec/v1
2
- oid sha256:cccb9f6a7df61c7c02fd68f553cf9c426a38bf0b5c175c3f7c77f06c07daaeab
3
- size 58253797
 
1
  version https://git-lfs.github.com/spec/v1
2
+ oid sha256:00d2407f78ec4a79757633e04beb57d0fffb1035ccaa97940e3acc18a3a8f5e8
3
+ size 112828179
train/cyc-pep-6-12mer-70M_02.log ADDED
@@ -0,0 +1,337 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ + module purge
2
+ + '[' -z '' ']'
3
+ + case "$-" in
4
+ + __lmod_sh_dbg=x
5
+ + '[' -n x ']'
6
+ + set +x
7
+ Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output
8
+ Shell debugging restarted
9
+ + unset __lmod_sh_dbg
10
+ + return 0
11
+ + module load Anaconda3/2023.03
12
+ + '[' -z '' ']'
13
+ + case "$-" in
14
+ + __lmod_sh_dbg=x
15
+ + '[' -n x ']'
16
+ + set +x
17
+ Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output
18
+ Shell debugging restarted
19
+ + unset __lmod_sh_dbg
20
+ + return 0
21
+ + source /camp/home/johnsoe/.bashrc
22
+ ++ '[' '' = yes ']'
23
+ ++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '
24
+ +++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.bash hook
25
+ ++ __conda_setup='export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\''
26
+ export _CE_M='\'''\''
27
+ export _CE_CONDA='\'''\''
28
+ export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''
29
+
30
+ # Copyright (C) 2012 Anaconda, Inc
31
+ # SPDX-License-Identifier: BSD-3-Clause
32
+ __conda_exe() (
33
+ "$CONDA_EXE" $_CE_M $_CE_CONDA "$@"
34
+ )
35
+
36
+ __conda_hashr() {
37
+ if [ -n "${ZSH_VERSION:+x}" ]; then
38
+ \rehash
39
+ elif [ -n "${POSH_VERSION:+x}" ]; then
40
+ : # pass
41
+ else
42
+ \hash -r
43
+ fi
44
+ }
45
+
46
+ __conda_activate() {
47
+ if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then
48
+ # Handle transition from shell activated with conda <= 4.3 to a subsequent activation
49
+ # after conda updated to >= 4.4. See issue #6173.
50
+ PS1="$CONDA_PS1_BACKUP"
51
+ \unset CONDA_PS1_BACKUP
52
+ fi
53
+ \local ask_conda
54
+ ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return
55
+ \eval "$ask_conda"
56
+ __conda_hashr
57
+ }
58
+
59
+ __conda_reactivate() {
60
+ \local ask_conda
61
+ ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return
62
+ \eval "$ask_conda"
63
+ __conda_hashr
64
+ }
65
+
66
+ conda() {
67
+ \local cmd="${1-__missing__}"
68
+ case "$cmd" in
69
+ activate|deactivate)
70
+ __conda_activate "$@"
71
+ ;;
72
+ install|update|upgrade|remove|uninstall)
73
+ __conda_exe "$@" || \return
74
+ __conda_reactivate
75
+ ;;
76
+ *)
77
+ __conda_exe "$@"
78
+ ;;
79
+ esac
80
+ }
81
+
82
+ if [ -z "${CONDA_SHLVL+x}" ]; then
83
+ \export CONDA_SHLVL=0
84
+ # In dev-mode CONDA_EXE is python.exe and on Windows
85
+ # it is in a different relative location to condabin.
86
+ if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then
87
+ PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}"
88
+ else
89
+ PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}"
90
+ fi
91
+ \export PATH
92
+
93
+ # We'\''re not allowing PS1 to be unbound. It must at least be set.
94
+ # However, we'\''re not exporting it, which can cause problems when starting a second shell
95
+ # via a first shell (i.e. starting zsh from bash).
96
+ if [ -z "${PS1+x}" ]; then
97
+ PS1=
98
+ fi
99
+ fi
100
+
101
+ conda activate base'
102
+ ++ '[' 0 -eq 0 ']'
103
+ ++ eval 'export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\''
104
+ export _CE_M='\'''\''
105
+ export _CE_CONDA='\'''\''
106
+ export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''
107
+
108
+ # Copyright (C) 2012 Anaconda, Inc
109
+ # SPDX-License-Identifier: BSD-3-Clause
110
+ __conda_exe() (
111
+ "$CONDA_EXE" $_CE_M $_CE_CONDA "$@"
112
+ )
113
+
114
+ __conda_hashr() {
115
+ if [ -n "${ZSH_VERSION:+x}" ]; then
116
+ \rehash
117
+ elif [ -n "${POSH_VERSION:+x}" ]; then
118
+ : # pass
119
+ else
120
+ \hash -r
121
+ fi
122
+ }
123
+
124
+ __conda_activate() {
125
+ if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then
126
+ # Handle transition from shell activated with conda <= 4.3 to a subsequent activation
127
+ # after conda updated to >= 4.4. See issue #6173.
128
+ PS1="$CONDA_PS1_BACKUP"
129
+ \unset CONDA_PS1_BACKUP
130
+ fi
131
+ \local ask_conda
132
+ ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return
133
+ \eval "$ask_conda"
134
+ __conda_hashr
135
+ }
136
+
137
+ __conda_reactivate() {
138
+ \local ask_conda
139
+ ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return
140
+ \eval "$ask_conda"
141
+ __conda_hashr
142
+ }
143
+
144
+ conda() {
145
+ \local cmd="${1-__missing__}"
146
+ case "$cmd" in
147
+ activate|deactivate)
148
+ __conda_activate "$@"
149
+ ;;
150
+ install|update|upgrade|remove|uninstall)
151
+ __conda_exe "$@" || \return
152
+ __conda_reactivate
153
+ ;;
154
+ *)
155
+ __conda_exe "$@"
156
+ ;;
157
+ esac
158
+ }
159
+
160
+ if [ -z "${CONDA_SHLVL+x}" ]; then
161
+ \export CONDA_SHLVL=0
162
+ # In dev-mode CONDA_EXE is python.exe and on Windows
163
+ # it is in a different relative location to condabin.
164
+ if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then
165
+ PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}"
166
+ else
167
+ PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}"
168
+ fi
169
+ \export PATH
170
+
171
+ # We'\''re not allowing PS1 to be unbound. It must at least be set.
172
+ # However, we'\''re not exporting it, which can cause problems when starting a second shell
173
+ # via a first shell (i.e. starting zsh from bash).
174
+ if [ -z "${PS1+x}" ]; then
175
+ PS1=
176
+ fi
177
+ fi
178
+
179
+ conda activate base'
180
+ +++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda
181
+ +++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda
182
+ +++ export _CE_M=
183
+ +++ _CE_M=
184
+ +++ export _CE_CONDA=
185
+ +++ _CE_CONDA=
186
+ +++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python
187
+ +++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python
188
+ +++ '[' -z x ']'
189
+ +++ conda activate base
190
+ +++ local cmd=activate
191
+ +++ case "$cmd" in
192
+ +++ __conda_activate activate base
193
+ +++ '[' -n '' ']'
194
+ +++ local ask_conda
195
+ ++++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '
196
+ ++++ __conda_exe shell.posix activate base
197
+ ++++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate base
198
+ +++ ask_conda='PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\''
199
+ export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\''
200
+ export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\''
201
+ export CONDA_SHLVL='\''6'\''
202
+ export CONDA_DEFAULT_ENV='\''base'\''
203
+ export CONDA_PROMPT_MODIFIER='\''(base) '\''
204
+ export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\''
205
+ export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\''
206
+ export _CE_M='\'''\''
207
+ export _CE_CONDA='\'''\''
208
+ export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'''
209
+ +++ eval 'PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\''
210
+ export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\''
211
+ export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\''
212
+ export CONDA_SHLVL='\''6'\''
213
+ export CONDA_DEFAULT_ENV='\''base'\''
214
+ export CONDA_PROMPT_MODIFIER='\''(base) '\''
215
+ export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\''
216
+ export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\''
217
+ export _CE_M='\'''\''
218
+ export _CE_CONDA='\'''\''
219
+ export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'''
220
+ ++++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '
221
+ ++++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin
222
+ ++++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin
223
+ ++++ export CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0
224
+ ++++ CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0
225
+ ++++ export CONDA_SHLVL=6
226
+ ++++ CONDA_SHLVL=6
227
+ ++++ export CONDA_DEFAULT_ENV=base
228
+ ++++ CONDA_DEFAULT_ENV=base
229
+ ++++ export 'CONDA_PROMPT_MODIFIER=(base) '
230
+ ++++ CONDA_PROMPT_MODIFIER='(base) '
231
+ ++++ export CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev
232
+ ++++ CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev
233
+ ++++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda
234
+ ++++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda
235
+ ++++ export _CE_M=
236
+ ++++ _CE_M=
237
+ ++++ export _CE_CONDA=
238
+ ++++ _CE_CONDA=
239
+ ++++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python
240
+ ++++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python
241
+ +++ __conda_hashr
242
+ +++ '[' -n '' ']'
243
+ +++ '[' -n '' ']'
244
+ +++ hash -r
245
+ ++ unset __conda_setup
246
+ + conda activate schemist-dev
247
+ + local cmd=activate
248
+ + case "$cmd" in
249
+ + __conda_activate activate schemist-dev
250
+ + '[' -n '' ']'
251
+ + local ask_conda
252
+ ++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '
253
+ ++ __conda_exe shell.posix activate schemist-dev
254
+ ++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate schemist-dev
255
+ + ask_conda='PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\''
256
+ export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\''
257
+ export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\''
258
+ export CONDA_SHLVL='\''7'\''
259
+ export CONDA_DEFAULT_ENV='\''schemist-dev'\''
260
+ export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\''
261
+ export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\''
262
+ export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\''
263
+ export _CE_M='\'''\''
264
+ export _CE_CONDA='\'''\''
265
+ export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'''
266
+ + eval 'PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\''
267
+ export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\''
268
+ export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\''
269
+ export CONDA_SHLVL='\''7'\''
270
+ export CONDA_DEFAULT_ENV='\''schemist-dev'\''
271
+ export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\''
272
+ export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\''
273
+ export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\''
274
+ export _CE_M='\'''\''
275
+ export _CE_CONDA='\'''\''
276
+ export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'''
277
+ ++ PS1='(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '
278
+ ++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin
279
+ ++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin
280
+ ++ export CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev
281
+ ++ CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev
282
+ ++ export CONDA_SHLVL=7
283
+ ++ CONDA_SHLVL=7
284
+ ++ export CONDA_DEFAULT_ENV=schemist-dev
285
+ ++ CONDA_DEFAULT_ENV=schemist-dev
286
+ ++ export 'CONDA_PROMPT_MODIFIER=(schemist-dev) '
287
+ ++ CONDA_PROMPT_MODIFIER='(schemist-dev) '
288
+ ++ export CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0
289
+ ++ CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0
290
+ ++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda
291
+ ++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda
292
+ ++ export _CE_M=
293
+ ++ _CE_M=
294
+ ++ export _CE_CONDA=
295
+ ++ _CE_CONDA=
296
+ ++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python
297
+ ++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python
298
+ + __conda_hashr
299
+ + '[' -n '' ']'
300
+ + '[' -n '' ']'
301
+ + hash -r
302
+ + CHUNK_HEAD_FILE=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz
303
+ + INPUT=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/train/cyc-pep-6-12mer-70M_02.csv
304
+ + COLUMN=cysteine_to_N_cyclization
305
+ + PREFIX=cyclic_
306
+ + AWK='1 { print $8, $1, $2, $10, $3 }'
307
+ + '[' -z cysteine_to_N_cyclization ']'
308
+ + '[' -z cyclic_ ']'
309
+ + '[' -z '1 { print $8, $1, $2, $10, $3 }' ']'
310
+ + 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
311
+ + awk -F, -v OFS=, '1 { print $8, $1, $2, $10, $3 }'
312
+ ++ zcat /nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz
313
+ + schemist convert -f csv --column cysteine_to_N_cyclization --to id inchikey scaffold mwt clogp tpsa --prefix cyclic_ --options prefix=SCB-
314
+ ++ head -n1
315
+ + gzip --best
316
+ ++ tr ' ' ,
317
+ 🚀 Converting between string representations with the following parameters:
318
+ subcommand: convert
319
+ output: <_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>
320
+ format: csv
321
+ input: <_io.TextIOWrapper name='<stdin>' mode='r' encoding='utf-8'>
322
+ representation: SMILES
323
+ column: cysteine_to_N_cyclization
324
+ prefix: cyclic_
325
+ to: ['id', 'inchikey', 'scaffold', 'mwt', 'clogp', 'tpsa']
326
+ options: ['prefix=SCB-']
327
+ func: <function _convert at 0x7ff086203240>
328
+
329
+ Error counts:
330
+ cyclic_id: 0
331
+ cyclic_inchikey: 0
332
+ cyclic_scaffold: 0
333
+ cyclic_mwt: 0
334
+ cyclic_clogp: 0
335
+ cyclic_tpsa: 0
336
+ ⏰ Completed process in 3:01:43.044204
337
+ + 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.csv.gz CHANGED
@@ -1,3 +1,3 @@
1
  version https://git-lfs.github.com/spec/v1
2
- oid sha256:340be6860ea52b67de160194816637a69c8db0baa8b40a33c66d8333c2cc8d7c
3
- size 58252448
 
1
  version https://git-lfs.github.com/spec/v1
2
+ oid sha256:1def9ffdfe1abdc5d1454df26ea49f9e8bb6b6b21841787044d956385ecca11a
3
+ size 112829110
train/cyc-pep-6-12mer-70M_03.log ADDED
@@ -0,0 +1,337 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ + module purge
2
+ + '[' -z '' ']'
3
+ + case "$-" in
4
+ + __lmod_sh_dbg=x
5
+ + '[' -n x ']'
6
+ + set +x
7
+ Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output
8
+ Shell debugging restarted
9
+ + unset __lmod_sh_dbg
10
+ + return 0
11
+ + module load Anaconda3/2023.03
12
+ + '[' -z '' ']'
13
+ + case "$-" in
14
+ + __lmod_sh_dbg=x
15
+ + '[' -n x ']'
16
+ + set +x
17
+ Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output
18
+ Shell debugging restarted
19
+ + unset __lmod_sh_dbg
20
+ + return 0
21
+ + source /camp/home/johnsoe/.bashrc
22
+ ++ '[' '' = yes ']'
23
+ ++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '
24
+ +++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.bash hook
25
+ ++ __conda_setup='export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\''
26
+ export _CE_M='\'''\''
27
+ export _CE_CONDA='\'''\''
28
+ export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''
29
+
30
+ # Copyright (C) 2012 Anaconda, Inc
31
+ # SPDX-License-Identifier: BSD-3-Clause
32
+ __conda_exe() (
33
+ "$CONDA_EXE" $_CE_M $_CE_CONDA "$@"
34
+ )
35
+
36
+ __conda_hashr() {
37
+ if [ -n "${ZSH_VERSION:+x}" ]; then
38
+ \rehash
39
+ elif [ -n "${POSH_VERSION:+x}" ]; then
40
+ : # pass
41
+ else
42
+ \hash -r
43
+ fi
44
+ }
45
+
46
+ __conda_activate() {
47
+ if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then
48
+ # Handle transition from shell activated with conda <= 4.3 to a subsequent activation
49
+ # after conda updated to >= 4.4. See issue #6173.
50
+ PS1="$CONDA_PS1_BACKUP"
51
+ \unset CONDA_PS1_BACKUP
52
+ fi
53
+ \local ask_conda
54
+ ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return
55
+ \eval "$ask_conda"
56
+ __conda_hashr
57
+ }
58
+
59
+ __conda_reactivate() {
60
+ \local ask_conda
61
+ ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return
62
+ \eval "$ask_conda"
63
+ __conda_hashr
64
+ }
65
+
66
+ conda() {
67
+ \local cmd="${1-__missing__}"
68
+ case "$cmd" in
69
+ activate|deactivate)
70
+ __conda_activate "$@"
71
+ ;;
72
+ install|update|upgrade|remove|uninstall)
73
+ __conda_exe "$@" || \return
74
+ __conda_reactivate
75
+ ;;
76
+ *)
77
+ __conda_exe "$@"
78
+ ;;
79
+ esac
80
+ }
81
+
82
+ if [ -z "${CONDA_SHLVL+x}" ]; then
83
+ \export CONDA_SHLVL=0
84
+ # In dev-mode CONDA_EXE is python.exe and on Windows
85
+ # it is in a different relative location to condabin.
86
+ if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then
87
+ PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}"
88
+ else
89
+ PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}"
90
+ fi
91
+ \export PATH
92
+
93
+ # We'\''re not allowing PS1 to be unbound. It must at least be set.
94
+ # However, we'\''re not exporting it, which can cause problems when starting a second shell
95
+ # via a first shell (i.e. starting zsh from bash).
96
+ if [ -z "${PS1+x}" ]; then
97
+ PS1=
98
+ fi
99
+ fi
100
+
101
+ conda activate base'
102
+ ++ '[' 0 -eq 0 ']'
103
+ ++ eval 'export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\''
104
+ export _CE_M='\'''\''
105
+ export _CE_CONDA='\'''\''
106
+ export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''
107
+
108
+ # Copyright (C) 2012 Anaconda, Inc
109
+ # SPDX-License-Identifier: BSD-3-Clause
110
+ __conda_exe() (
111
+ "$CONDA_EXE" $_CE_M $_CE_CONDA "$@"
112
+ )
113
+
114
+ __conda_hashr() {
115
+ if [ -n "${ZSH_VERSION:+x}" ]; then
116
+ \rehash
117
+ elif [ -n "${POSH_VERSION:+x}" ]; then
118
+ : # pass
119
+ else
120
+ \hash -r
121
+ fi
122
+ }
123
+
124
+ __conda_activate() {
125
+ if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then
126
+ # Handle transition from shell activated with conda <= 4.3 to a subsequent activation
127
+ # after conda updated to >= 4.4. See issue #6173.
128
+ PS1="$CONDA_PS1_BACKUP"
129
+ \unset CONDA_PS1_BACKUP
130
+ fi
131
+ \local ask_conda
132
+ ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return
133
+ \eval "$ask_conda"
134
+ __conda_hashr
135
+ }
136
+
137
+ __conda_reactivate() {
138
+ \local ask_conda
139
+ ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return
140
+ \eval "$ask_conda"
141
+ __conda_hashr
142
+ }
143
+
144
+ conda() {
145
+ \local cmd="${1-__missing__}"
146
+ case "$cmd" in
147
+ activate|deactivate)
148
+ __conda_activate "$@"
149
+ ;;
150
+ install|update|upgrade|remove|uninstall)
151
+ __conda_exe "$@" || \return
152
+ __conda_reactivate
153
+ ;;
154
+ *)
155
+ __conda_exe "$@"
156
+ ;;
157
+ esac
158
+ }
159
+
160
+ if [ -z "${CONDA_SHLVL+x}" ]; then
161
+ \export CONDA_SHLVL=0
162
+ # In dev-mode CONDA_EXE is python.exe and on Windows
163
+ # it is in a different relative location to condabin.
164
+ if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then
165
+ PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}"
166
+ else
167
+ PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}"
168
+ fi
169
+ \export PATH
170
+
171
+ # We'\''re not allowing PS1 to be unbound. It must at least be set.
172
+ # However, we'\''re not exporting it, which can cause problems when starting a second shell
173
+ # via a first shell (i.e. starting zsh from bash).
174
+ if [ -z "${PS1+x}" ]; then
175
+ PS1=
176
+ fi
177
+ fi
178
+
179
+ conda activate base'
180
+ +++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda
181
+ +++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda
182
+ +++ export _CE_M=
183
+ +++ _CE_M=
184
+ +++ export _CE_CONDA=
185
+ +++ _CE_CONDA=
186
+ +++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python
187
+ +++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python
188
+ +++ '[' -z x ']'
189
+ +++ conda activate base
190
+ +++ local cmd=activate
191
+ +++ case "$cmd" in
192
+ +++ __conda_activate activate base
193
+ +++ '[' -n '' ']'
194
+ +++ local ask_conda
195
+ ++++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '
196
+ ++++ __conda_exe shell.posix activate base
197
+ ++++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate base
198
+ +++ ask_conda='PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\''
199
+ export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\''
200
+ export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\''
201
+ export CONDA_SHLVL='\''6'\''
202
+ export CONDA_DEFAULT_ENV='\''base'\''
203
+ export CONDA_PROMPT_MODIFIER='\''(base) '\''
204
+ export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\''
205
+ export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\''
206
+ export _CE_M='\'''\''
207
+ export _CE_CONDA='\'''\''
208
+ export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'''
209
+ +++ eval 'PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\''
210
+ export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\''
211
+ export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\''
212
+ export CONDA_SHLVL='\''6'\''
213
+ export CONDA_DEFAULT_ENV='\''base'\''
214
+ export CONDA_PROMPT_MODIFIER='\''(base) '\''
215
+ export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\''
216
+ export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\''
217
+ export _CE_M='\'''\''
218
+ export _CE_CONDA='\'''\''
219
+ export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'''
220
+ ++++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '
221
+ ++++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin
222
+ ++++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin
223
+ ++++ export CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0
224
+ ++++ CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0
225
+ ++++ export CONDA_SHLVL=6
226
+ ++++ CONDA_SHLVL=6
227
+ ++++ export CONDA_DEFAULT_ENV=base
228
+ ++++ CONDA_DEFAULT_ENV=base
229
+ ++++ export 'CONDA_PROMPT_MODIFIER=(base) '
230
+ ++++ CONDA_PROMPT_MODIFIER='(base) '
231
+ ++++ export CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev
232
+ ++++ CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev
233
+ ++++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda
234
+ ++++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda
235
+ ++++ export _CE_M=
236
+ ++++ _CE_M=
237
+ ++++ export _CE_CONDA=
238
+ ++++ _CE_CONDA=
239
+ ++++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python
240
+ ++++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python
241
+ +++ __conda_hashr
242
+ +++ '[' -n '' ']'
243
+ +++ '[' -n '' ']'
244
+ +++ hash -r
245
+ ++ unset __conda_setup
246
+ + conda activate schemist-dev
247
+ + local cmd=activate
248
+ + case "$cmd" in
249
+ + __conda_activate activate schemist-dev
250
+ + '[' -n '' ']'
251
+ + local ask_conda
252
+ ++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '
253
+ ++ __conda_exe shell.posix activate schemist-dev
254
+ ++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate schemist-dev
255
+ + ask_conda='PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\''
256
+ export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\''
257
+ export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\''
258
+ export CONDA_SHLVL='\''7'\''
259
+ export CONDA_DEFAULT_ENV='\''schemist-dev'\''
260
+ export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\''
261
+ export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\''
262
+ export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\''
263
+ export _CE_M='\'''\''
264
+ export _CE_CONDA='\'''\''
265
+ export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'''
266
+ + eval 'PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\''
267
+ export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\''
268
+ export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\''
269
+ export CONDA_SHLVL='\''7'\''
270
+ export CONDA_DEFAULT_ENV='\''schemist-dev'\''
271
+ export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\''
272
+ export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\''
273
+ export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\''
274
+ export _CE_M='\'''\''
275
+ export _CE_CONDA='\'''\''
276
+ export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'''
277
+ ++ PS1='(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '
278
+ ++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin
279
+ ++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin
280
+ ++ export CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev
281
+ ++ CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev
282
+ ++ export CONDA_SHLVL=7
283
+ ++ CONDA_SHLVL=7
284
+ ++ export CONDA_DEFAULT_ENV=schemist-dev
285
+ ++ CONDA_DEFAULT_ENV=schemist-dev
286
+ ++ export 'CONDA_PROMPT_MODIFIER=(schemist-dev) '
287
+ ++ CONDA_PROMPT_MODIFIER='(schemist-dev) '
288
+ ++ export CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0
289
+ ++ CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0
290
+ ++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda
291
+ ++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda
292
+ ++ export _CE_M=
293
+ ++ _CE_M=
294
+ ++ export _CE_CONDA=
295
+ ++ _CE_CONDA=
296
+ ++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python
297
+ ++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python
298
+ + __conda_hashr
299
+ + '[' -n '' ']'
300
+ + '[' -n '' ']'
301
+ + hash -r
302
+ + CHUNK_HEAD_FILE=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz
303
+ + INPUT=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/train/cyc-pep-6-12mer-70M_03.csv
304
+ + COLUMN=cysteine_to_N_cyclization
305
+ + PREFIX=cyclic_
306
+ + AWK='1 { print $8, $1, $2, $10, $3 }'
307
+ + '[' -z cysteine_to_N_cyclization ']'
308
+ + '[' -z cyclic_ ']'
309
+ + '[' -z '1 { print $8, $1, $2, $10, $3 }' ']'
310
+ + 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
311
+ + awk -F, -v OFS=, '1 { print $8, $1, $2, $10, $3 }'
312
+ ++ zcat /nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz
313
+ ++ head -n1
314
+ + schemist convert -f csv --column cysteine_to_N_cyclization --to id inchikey scaffold mwt clogp tpsa --prefix cyclic_ --options prefix=SCB-
315
+ + gzip --best
316
+ ++ tr ' ' ,
317
+ 🚀 Converting between string representations with the following parameters:
318
+ subcommand: convert
319
+ output: <_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>
320
+ format: csv
321
+ input: <_io.TextIOWrapper name='<stdin>' mode='r' encoding='utf-8'>
322
+ representation: SMILES
323
+ column: cysteine_to_N_cyclization
324
+ prefix: cyclic_
325
+ to: ['id', 'inchikey', 'scaffold', 'mwt', 'clogp', 'tpsa']
326
+ options: ['prefix=SCB-']
327
+ func: <function _convert at 0x7f7e3726f240>
328
+
329
+ Error counts:
330
+ cyclic_id: 0
331
+ cyclic_inchikey: 0
332
+ cyclic_scaffold: 0
333
+ cyclic_mwt: 0
334
+ cyclic_clogp: 0
335
+ cyclic_tpsa: 0
336
+ ⏰ Completed process in 3:19:53.014538
337
+ + 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.csv.gz CHANGED
@@ -1,3 +1,3 @@
1
  version https://git-lfs.github.com/spec/v1
2
- oid sha256:b6f415213fd5d5fe9fbe0e63bee04fd673a2079e898b392fb7b5139377669890
3
- size 58254248
 
1
  version https://git-lfs.github.com/spec/v1
2
+ oid sha256:71a5b2d69be31606128710921f1e0fe7f8cd96a818e6fbde78855a19c60fafc5
3
+ size 112833751
train/cyc-pep-6-12mer-70M_04.log ADDED
@@ -0,0 +1,337 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ + module purge
2
+ + '[' -z '' ']'
3
+ + case "$-" in
4
+ + __lmod_sh_dbg=x
5
+ + '[' -n x ']'
6
+ + set +x
7
+ Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output
8
+ Shell debugging restarted
9
+ + unset __lmod_sh_dbg
10
+ + return 0
11
+ + module load Anaconda3/2023.03
12
+ + '[' -z '' ']'
13
+ + case "$-" in
14
+ + __lmod_sh_dbg=x
15
+ + '[' -n x ']'
16
+ + set +x
17
+ Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output
18
+ Shell debugging restarted
19
+ + unset __lmod_sh_dbg
20
+ + return 0
21
+ + source /camp/home/johnsoe/.bashrc
22
+ ++ '[' '' = yes ']'
23
+ ++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '
24
+ +++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.bash hook
25
+ ++ __conda_setup='export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\''
26
+ export _CE_M='\'''\''
27
+ export _CE_CONDA='\'''\''
28
+ export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''
29
+
30
+ # Copyright (C) 2012 Anaconda, Inc
31
+ # SPDX-License-Identifier: BSD-3-Clause
32
+ __conda_exe() (
33
+ "$CONDA_EXE" $_CE_M $_CE_CONDA "$@"
34
+ )
35
+
36
+ __conda_hashr() {
37
+ if [ -n "${ZSH_VERSION:+x}" ]; then
38
+ \rehash
39
+ elif [ -n "${POSH_VERSION:+x}" ]; then
40
+ : # pass
41
+ else
42
+ \hash -r
43
+ fi
44
+ }
45
+
46
+ __conda_activate() {
47
+ if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then
48
+ # Handle transition from shell activated with conda <= 4.3 to a subsequent activation
49
+ # after conda updated to >= 4.4. See issue #6173.
50
+ PS1="$CONDA_PS1_BACKUP"
51
+ \unset CONDA_PS1_BACKUP
52
+ fi
53
+ \local ask_conda
54
+ ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return
55
+ \eval "$ask_conda"
56
+ __conda_hashr
57
+ }
58
+
59
+ __conda_reactivate() {
60
+ \local ask_conda
61
+ ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return
62
+ \eval "$ask_conda"
63
+ __conda_hashr
64
+ }
65
+
66
+ conda() {
67
+ \local cmd="${1-__missing__}"
68
+ case "$cmd" in
69
+ activate|deactivate)
70
+ __conda_activate "$@"
71
+ ;;
72
+ install|update|upgrade|remove|uninstall)
73
+ __conda_exe "$@" || \return
74
+ __conda_reactivate
75
+ ;;
76
+ *)
77
+ __conda_exe "$@"
78
+ ;;
79
+ esac
80
+ }
81
+
82
+ if [ -z "${CONDA_SHLVL+x}" ]; then
83
+ \export CONDA_SHLVL=0
84
+ # In dev-mode CONDA_EXE is python.exe and on Windows
85
+ # it is in a different relative location to condabin.
86
+ if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then
87
+ PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}"
88
+ else
89
+ PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}"
90
+ fi
91
+ \export PATH
92
+
93
+ # We'\''re not allowing PS1 to be unbound. It must at least be set.
94
+ # However, we'\''re not exporting it, which can cause problems when starting a second shell
95
+ # via a first shell (i.e. starting zsh from bash).
96
+ if [ -z "${PS1+x}" ]; then
97
+ PS1=
98
+ fi
99
+ fi
100
+
101
+ conda activate base'
102
+ ++ '[' 0 -eq 0 ']'
103
+ ++ eval 'export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\''
104
+ export _CE_M='\'''\''
105
+ export _CE_CONDA='\'''\''
106
+ export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''
107
+
108
+ # Copyright (C) 2012 Anaconda, Inc
109
+ # SPDX-License-Identifier: BSD-3-Clause
110
+ __conda_exe() (
111
+ "$CONDA_EXE" $_CE_M $_CE_CONDA "$@"
112
+ )
113
+
114
+ __conda_hashr() {
115
+ if [ -n "${ZSH_VERSION:+x}" ]; then
116
+ \rehash
117
+ elif [ -n "${POSH_VERSION:+x}" ]; then
118
+ : # pass
119
+ else
120
+ \hash -r
121
+ fi
122
+ }
123
+
124
+ __conda_activate() {
125
+ if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then
126
+ # Handle transition from shell activated with conda <= 4.3 to a subsequent activation
127
+ # after conda updated to >= 4.4. See issue #6173.
128
+ PS1="$CONDA_PS1_BACKUP"
129
+ \unset CONDA_PS1_BACKUP
130
+ fi
131
+ \local ask_conda
132
+ ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return
133
+ \eval "$ask_conda"
134
+ __conda_hashr
135
+ }
136
+
137
+ __conda_reactivate() {
138
+ \local ask_conda
139
+ ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return
140
+ \eval "$ask_conda"
141
+ __conda_hashr
142
+ }
143
+
144
+ conda() {
145
+ \local cmd="${1-__missing__}"
146
+ case "$cmd" in
147
+ activate|deactivate)
148
+ __conda_activate "$@"
149
+ ;;
150
+ install|update|upgrade|remove|uninstall)
151
+ __conda_exe "$@" || \return
152
+ __conda_reactivate
153
+ ;;
154
+ *)
155
+ __conda_exe "$@"
156
+ ;;
157
+ esac
158
+ }
159
+
160
+ if [ -z "${CONDA_SHLVL+x}" ]; then
161
+ \export CONDA_SHLVL=0
162
+ # In dev-mode CONDA_EXE is python.exe and on Windows
163
+ # it is in a different relative location to condabin.
164
+ if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then
165
+ PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}"
166
+ else
167
+ PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}"
168
+ fi
169
+ \export PATH
170
+
171
+ # We'\''re not allowing PS1 to be unbound. It must at least be set.
172
+ # However, we'\''re not exporting it, which can cause problems when starting a second shell
173
+ # via a first shell (i.e. starting zsh from bash).
174
+ if [ -z "${PS1+x}" ]; then
175
+ PS1=
176
+ fi
177
+ fi
178
+
179
+ conda activate base'
180
+ +++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda
181
+ +++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda
182
+ +++ export _CE_M=
183
+ +++ _CE_M=
184
+ +++ export _CE_CONDA=
185
+ +++ _CE_CONDA=
186
+ +++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python
187
+ +++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python
188
+ +++ '[' -z x ']'
189
+ +++ conda activate base
190
+ +++ local cmd=activate
191
+ +++ case "$cmd" in
192
+ +++ __conda_activate activate base
193
+ +++ '[' -n '' ']'
194
+ +++ local ask_conda
195
+ ++++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '
196
+ ++++ __conda_exe shell.posix activate base
197
+ ++++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate base
198
+ +++ ask_conda='PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\''
199
+ export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\''
200
+ export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\''
201
+ export CONDA_SHLVL='\''6'\''
202
+ export CONDA_DEFAULT_ENV='\''base'\''
203
+ export CONDA_PROMPT_MODIFIER='\''(base) '\''
204
+ export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\''
205
+ export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\''
206
+ export _CE_M='\'''\''
207
+ export _CE_CONDA='\'''\''
208
+ export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'''
209
+ +++ eval 'PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\''
210
+ export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\''
211
+ export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\''
212
+ export CONDA_SHLVL='\''6'\''
213
+ export CONDA_DEFAULT_ENV='\''base'\''
214
+ export CONDA_PROMPT_MODIFIER='\''(base) '\''
215
+ export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\''
216
+ export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\''
217
+ export _CE_M='\'''\''
218
+ export _CE_CONDA='\'''\''
219
+ export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'''
220
+ ++++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '
221
+ ++++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin
222
+ ++++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin
223
+ ++++ export CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0
224
+ ++++ CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0
225
+ ++++ export CONDA_SHLVL=6
226
+ ++++ CONDA_SHLVL=6
227
+ ++++ export CONDA_DEFAULT_ENV=base
228
+ ++++ CONDA_DEFAULT_ENV=base
229
+ ++++ export 'CONDA_PROMPT_MODIFIER=(base) '
230
+ ++++ CONDA_PROMPT_MODIFIER='(base) '
231
+ ++++ export CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev
232
+ ++++ CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev
233
+ ++++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda
234
+ ++++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda
235
+ ++++ export _CE_M=
236
+ ++++ _CE_M=
237
+ ++++ export _CE_CONDA=
238
+ ++++ _CE_CONDA=
239
+ ++++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python
240
+ ++++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python
241
+ +++ __conda_hashr
242
+ +++ '[' -n '' ']'
243
+ +++ '[' -n '' ']'
244
+ +++ hash -r
245
+ ++ unset __conda_setup
246
+ + conda activate schemist-dev
247
+ + local cmd=activate
248
+ + case "$cmd" in
249
+ + __conda_activate activate schemist-dev
250
+ + '[' -n '' ']'
251
+ + local ask_conda
252
+ ++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '
253
+ ++ __conda_exe shell.posix activate schemist-dev
254
+ ++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate schemist-dev
255
+ + ask_conda='PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\''
256
+ export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\''
257
+ export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\''
258
+ export CONDA_SHLVL='\''7'\''
259
+ export CONDA_DEFAULT_ENV='\''schemist-dev'\''
260
+ export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\''
261
+ export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\''
262
+ export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\''
263
+ export _CE_M='\'''\''
264
+ export _CE_CONDA='\'''\''
265
+ export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'''
266
+ + eval 'PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\''
267
+ export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\''
268
+ export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\''
269
+ export CONDA_SHLVL='\''7'\''
270
+ export CONDA_DEFAULT_ENV='\''schemist-dev'\''
271
+ export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\''
272
+ export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\''
273
+ export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\''
274
+ export _CE_M='\'''\''
275
+ export _CE_CONDA='\'''\''
276
+ export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'''
277
+ ++ PS1='(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '
278
+ ++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin
279
+ ++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin
280
+ ++ export CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev
281
+ ++ CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev
282
+ ++ export CONDA_SHLVL=7
283
+ ++ CONDA_SHLVL=7
284
+ ++ export CONDA_DEFAULT_ENV=schemist-dev
285
+ ++ CONDA_DEFAULT_ENV=schemist-dev
286
+ ++ export 'CONDA_PROMPT_MODIFIER=(schemist-dev) '
287
+ ++ CONDA_PROMPT_MODIFIER='(schemist-dev) '
288
+ ++ export CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0
289
+ ++ CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0
290
+ ++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda
291
+ ++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda
292
+ ++ export _CE_M=
293
+ ++ _CE_M=
294
+ ++ export _CE_CONDA=
295
+ ++ _CE_CONDA=
296
+ ++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python
297
+ ++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python
298
+ + __conda_hashr
299
+ + '[' -n '' ']'
300
+ + '[' -n '' ']'
301
+ + hash -r
302
+ + CHUNK_HEAD_FILE=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz
303
+ + INPUT=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/train/cyc-pep-6-12mer-70M_04.csv
304
+ + COLUMN=cysteine_to_N_cyclization
305
+ + PREFIX=cyclic_
306
+ + AWK='1 { print $8, $1, $2, $10, $3 }'
307
+ + '[' -z cysteine_to_N_cyclization ']'
308
+ + '[' -z cyclic_ ']'
309
+ + '[' -z '1 { print $8, $1, $2, $10, $3 }' ']'
310
+ + 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
311
+ + schemist convert -f csv --column cysteine_to_N_cyclization --to id inchikey scaffold mwt clogp tpsa --prefix cyclic_ --options prefix=SCB-
312
+ + gzip --best
313
+ + awk -F, -v OFS=, '1 { print $8, $1, $2, $10, $3 }'
314
+ ++ zcat /nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz
315
+ ++ tr ' ' ,
316
+ ++ head -n1
317
+ 🚀 Converting between string representations with the following parameters:
318
+ subcommand: convert
319
+ output: <_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>
320
+ format: csv
321
+ input: <_io.TextIOWrapper name='<stdin>' mode='r' encoding='utf-8'>
322
+ representation: SMILES
323
+ column: cysteine_to_N_cyclization
324
+ prefix: cyclic_
325
+ to: ['id', 'inchikey', 'scaffold', 'mwt', 'clogp', 'tpsa']
326
+ options: ['prefix=SCB-']
327
+ func: <function _convert at 0x7f44e4bcb240>
328
+
329
+ Error counts:
330
+ cyclic_id: 0
331
+ cyclic_inchikey: 0
332
+ cyclic_scaffold: 0
333
+ cyclic_mwt: 0
334
+ cyclic_clogp: 0
335
+ cyclic_tpsa: 0
336
+ ⏰ Completed process in 3:07:30.395736
337
+ + 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.csv.gz CHANGED
@@ -1,3 +1,3 @@
1
  version https://git-lfs.github.com/spec/v1
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- oid sha256:fe26c7b18749498c9aa2739942dea3e1639ad863ade522efc2684254df272785
3
- size 58249398
 
1
  version https://git-lfs.github.com/spec/v1
2
+ oid sha256:6bd762c2b6706e8ba084a6983569a0642bc5625cf36d7118d3c8346b0071a7d6
3
+ size 112829355
train/cyc-pep-6-12mer-70M_05.log ADDED
@@ -0,0 +1,337 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ + module purge
2
+ + '[' -z '' ']'
3
+ + case "$-" in
4
+ + __lmod_sh_dbg=x
5
+ + '[' -n x ']'
6
+ + set +x
7
+ Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output
8
+ Shell debugging restarted
9
+ + unset __lmod_sh_dbg
10
+ + return 0
11
+ + module load Anaconda3/2023.03
12
+ + '[' -z '' ']'
13
+ + case "$-" in
14
+ + __lmod_sh_dbg=x
15
+ + '[' -n x ']'
16
+ + set +x
17
+ Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output
18
+ Shell debugging restarted
19
+ + unset __lmod_sh_dbg
20
+ + return 0
21
+ + source /camp/home/johnsoe/.bashrc
22
+ ++ '[' '' = yes ']'
23
+ ++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '
24
+ +++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.bash hook
25
+ ++ __conda_setup='export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\''
26
+ export _CE_M='\'''\''
27
+ export _CE_CONDA='\'''\''
28
+ export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''
29
+
30
+ # Copyright (C) 2012 Anaconda, Inc
31
+ # SPDX-License-Identifier: BSD-3-Clause
32
+ __conda_exe() (
33
+ "$CONDA_EXE" $_CE_M $_CE_CONDA "$@"
34
+ )
35
+
36
+ __conda_hashr() {
37
+ if [ -n "${ZSH_VERSION:+x}" ]; then
38
+ \rehash
39
+ elif [ -n "${POSH_VERSION:+x}" ]; then
40
+ : # pass
41
+ else
42
+ \hash -r
43
+ fi
44
+ }
45
+
46
+ __conda_activate() {
47
+ if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then
48
+ # Handle transition from shell activated with conda <= 4.3 to a subsequent activation
49
+ # after conda updated to >= 4.4. See issue #6173.
50
+ PS1="$CONDA_PS1_BACKUP"
51
+ \unset CONDA_PS1_BACKUP
52
+ fi
53
+ \local ask_conda
54
+ ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return
55
+ \eval "$ask_conda"
56
+ __conda_hashr
57
+ }
58
+
59
+ __conda_reactivate() {
60
+ \local ask_conda
61
+ ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return
62
+ \eval "$ask_conda"
63
+ __conda_hashr
64
+ }
65
+
66
+ conda() {
67
+ \local cmd="${1-__missing__}"
68
+ case "$cmd" in
69
+ activate|deactivate)
70
+ __conda_activate "$@"
71
+ ;;
72
+ install|update|upgrade|remove|uninstall)
73
+ __conda_exe "$@" || \return
74
+ __conda_reactivate
75
+ ;;
76
+ *)
77
+ __conda_exe "$@"
78
+ ;;
79
+ esac
80
+ }
81
+
82
+ if [ -z "${CONDA_SHLVL+x}" ]; then
83
+ \export CONDA_SHLVL=0
84
+ # In dev-mode CONDA_EXE is python.exe and on Windows
85
+ # it is in a different relative location to condabin.
86
+ if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then
87
+ PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}"
88
+ else
89
+ PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}"
90
+ fi
91
+ \export PATH
92
+
93
+ # We'\''re not allowing PS1 to be unbound. It must at least be set.
94
+ # However, we'\''re not exporting it, which can cause problems when starting a second shell
95
+ # via a first shell (i.e. starting zsh from bash).
96
+ if [ -z "${PS1+x}" ]; then
97
+ PS1=
98
+ fi
99
+ fi
100
+
101
+ conda activate base'
102
+ ++ '[' 0 -eq 0 ']'
103
+ ++ eval 'export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\''
104
+ export _CE_M='\'''\''
105
+ export _CE_CONDA='\'''\''
106
+ export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''
107
+
108
+ # Copyright (C) 2012 Anaconda, Inc
109
+ # SPDX-License-Identifier: BSD-3-Clause
110
+ __conda_exe() (
111
+ "$CONDA_EXE" $_CE_M $_CE_CONDA "$@"
112
+ )
113
+
114
+ __conda_hashr() {
115
+ if [ -n "${ZSH_VERSION:+x}" ]; then
116
+ \rehash
117
+ elif [ -n "${POSH_VERSION:+x}" ]; then
118
+ : # pass
119
+ else
120
+ \hash -r
121
+ fi
122
+ }
123
+
124
+ __conda_activate() {
125
+ if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then
126
+ # Handle transition from shell activated with conda <= 4.3 to a subsequent activation
127
+ # after conda updated to >= 4.4. See issue #6173.
128
+ PS1="$CONDA_PS1_BACKUP"
129
+ \unset CONDA_PS1_BACKUP
130
+ fi
131
+ \local ask_conda
132
+ ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return
133
+ \eval "$ask_conda"
134
+ __conda_hashr
135
+ }
136
+
137
+ __conda_reactivate() {
138
+ \local ask_conda
139
+ ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return
140
+ \eval "$ask_conda"
141
+ __conda_hashr
142
+ }
143
+
144
+ conda() {
145
+ \local cmd="${1-__missing__}"
146
+ case "$cmd" in
147
+ activate|deactivate)
148
+ __conda_activate "$@"
149
+ ;;
150
+ install|update|upgrade|remove|uninstall)
151
+ __conda_exe "$@" || \return
152
+ __conda_reactivate
153
+ ;;
154
+ *)
155
+ __conda_exe "$@"
156
+ ;;
157
+ esac
158
+ }
159
+
160
+ if [ -z "${CONDA_SHLVL+x}" ]; then
161
+ \export CONDA_SHLVL=0
162
+ # In dev-mode CONDA_EXE is python.exe and on Windows
163
+ # it is in a different relative location to condabin.
164
+ if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then
165
+ PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}"
166
+ else
167
+ PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}"
168
+ fi
169
+ \export PATH
170
+
171
+ # We'\''re not allowing PS1 to be unbound. It must at least be set.
172
+ # However, we'\''re not exporting it, which can cause problems when starting a second shell
173
+ # via a first shell (i.e. starting zsh from bash).
174
+ if [ -z "${PS1+x}" ]; then
175
+ PS1=
176
+ fi
177
+ fi
178
+
179
+ conda activate base'
180
+ +++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda
181
+ +++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda
182
+ +++ export _CE_M=
183
+ +++ _CE_M=
184
+ +++ export _CE_CONDA=
185
+ +++ _CE_CONDA=
186
+ +++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python
187
+ +++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python
188
+ +++ '[' -z x ']'
189
+ +++ conda activate base
190
+ +++ local cmd=activate
191
+ +++ case "$cmd" in
192
+ +++ __conda_activate activate base
193
+ +++ '[' -n '' ']'
194
+ +++ local ask_conda
195
+ ++++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '
196
+ ++++ __conda_exe shell.posix activate base
197
+ ++++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate base
198
+ +++ ask_conda='PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\''
199
+ export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\''
200
+ export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\''
201
+ export CONDA_SHLVL='\''6'\''
202
+ export CONDA_DEFAULT_ENV='\''base'\''
203
+ export CONDA_PROMPT_MODIFIER='\''(base) '\''
204
+ export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\''
205
+ export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\''
206
+ export _CE_M='\'''\''
207
+ export _CE_CONDA='\'''\''
208
+ export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'''
209
+ +++ eval 'PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\''
210
+ export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\''
211
+ export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\''
212
+ export CONDA_SHLVL='\''6'\''
213
+ export CONDA_DEFAULT_ENV='\''base'\''
214
+ export CONDA_PROMPT_MODIFIER='\''(base) '\''
215
+ export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\''
216
+ export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\''
217
+ export _CE_M='\'''\''
218
+ export _CE_CONDA='\'''\''
219
+ export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'''
220
+ ++++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '
221
+ ++++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin
222
+ ++++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin
223
+ ++++ export CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0
224
+ ++++ CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0
225
+ ++++ export CONDA_SHLVL=6
226
+ ++++ CONDA_SHLVL=6
227
+ ++++ export CONDA_DEFAULT_ENV=base
228
+ ++++ CONDA_DEFAULT_ENV=base
229
+ ++++ export 'CONDA_PROMPT_MODIFIER=(base) '
230
+ ++++ CONDA_PROMPT_MODIFIER='(base) '
231
+ ++++ export CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev
232
+ ++++ CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev
233
+ ++++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda
234
+ ++++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda
235
+ ++++ export _CE_M=
236
+ ++++ _CE_M=
237
+ ++++ export _CE_CONDA=
238
+ ++++ _CE_CONDA=
239
+ ++++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python
240
+ ++++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python
241
+ +++ __conda_hashr
242
+ +++ '[' -n '' ']'
243
+ +++ '[' -n '' ']'
244
+ +++ hash -r
245
+ ++ unset __conda_setup
246
+ + conda activate schemist-dev
247
+ + local cmd=activate
248
+ + case "$cmd" in
249
+ + __conda_activate activate schemist-dev
250
+ + '[' -n '' ']'
251
+ + local ask_conda
252
+ ++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '
253
+ ++ __conda_exe shell.posix activate schemist-dev
254
+ ++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate schemist-dev
255
+ + ask_conda='PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\''
256
+ export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\''
257
+ export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\''
258
+ export CONDA_SHLVL='\''7'\''
259
+ export CONDA_DEFAULT_ENV='\''schemist-dev'\''
260
+ export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\''
261
+ export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\''
262
+ export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\''
263
+ export _CE_M='\'''\''
264
+ export _CE_CONDA='\'''\''
265
+ export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'''
266
+ + eval 'PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\''
267
+ export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\''
268
+ export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\''
269
+ export CONDA_SHLVL='\''7'\''
270
+ export CONDA_DEFAULT_ENV='\''schemist-dev'\''
271
+ export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\''
272
+ export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\''
273
+ export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\''
274
+ export _CE_M='\'''\''
275
+ export _CE_CONDA='\'''\''
276
+ export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'''
277
+ ++ PS1='(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '
278
+ ++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin
279
+ ++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin
280
+ ++ export CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev
281
+ ++ CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev
282
+ ++ export CONDA_SHLVL=7
283
+ ++ CONDA_SHLVL=7
284
+ ++ export CONDA_DEFAULT_ENV=schemist-dev
285
+ ++ CONDA_DEFAULT_ENV=schemist-dev
286
+ ++ export 'CONDA_PROMPT_MODIFIER=(schemist-dev) '
287
+ ++ CONDA_PROMPT_MODIFIER='(schemist-dev) '
288
+ ++ export CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0
289
+ ++ CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0
290
+ ++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda
291
+ ++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda
292
+ ++ export _CE_M=
293
+ ++ _CE_M=
294
+ ++ export _CE_CONDA=
295
+ ++ _CE_CONDA=
296
+ ++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python
297
+ ++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python
298
+ + __conda_hashr
299
+ + '[' -n '' ']'
300
+ + '[' -n '' ']'
301
+ + hash -r
302
+ + CHUNK_HEAD_FILE=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz
303
+ + INPUT=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/train/cyc-pep-6-12mer-70M_05.csv
304
+ + COLUMN=cysteine_to_N_cyclization
305
+ + PREFIX=cyclic_
306
+ + AWK='1 { print $8, $1, $2, $10, $3 }'
307
+ + '[' -z cysteine_to_N_cyclization ']'
308
+ + '[' -z cyclic_ ']'
309
+ + '[' -z '1 { print $8, $1, $2, $10, $3 }' ']'
310
+ + 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
311
+ + awk -F, -v OFS=, '1 { print $8, $1, $2, $10, $3 }'
312
+ ++ zcat /nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz
313
+ + schemist convert -f csv --column cysteine_to_N_cyclization --to id inchikey scaffold mwt clogp tpsa --prefix cyclic_ --options prefix=SCB-
314
+ + gzip --best
315
+ ++ head -n1
316
+ ++ tr ' ' ,
317
+ 🚀 Converting between string representations with the following parameters:
318
+ subcommand: convert
319
+ output: <_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>
320
+ format: csv
321
+ input: <_io.TextIOWrapper name='<stdin>' mode='r' encoding='utf-8'>
322
+ representation: SMILES
323
+ column: cysteine_to_N_cyclization
324
+ prefix: cyclic_
325
+ to: ['id', 'inchikey', 'scaffold', 'mwt', 'clogp', 'tpsa']
326
+ options: ['prefix=SCB-']
327
+ func: <function _convert at 0x7f6e76fb7240>
328
+
329
+ Error counts:
330
+ cyclic_id: 0
331
+ cyclic_inchikey: 0
332
+ cyclic_scaffold: 0
333
+ cyclic_mwt: 0
334
+ cyclic_clogp: 0
335
+ cyclic_tpsa: 0
336
+ ⏰ Completed process in 3:03:48.458908
337
+ + 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.csv.gz CHANGED
@@ -1,3 +1,3 @@
1
  version https://git-lfs.github.com/spec/v1
2
- oid sha256:39475ca699e51b29c20eca9cc07b81d6ddacb1f4f7fe0ce93be606b4de358797
3
- size 59207060
 
1
  version https://git-lfs.github.com/spec/v1
2
+ oid sha256:0f8c8b52c97b6c777c40a603d85d0e390dc5205d6bdd4f0ba1708b4bdbac8c96
3
+ size 114077572
train/cyc-pep-6-12mer-70M_06.log ADDED
@@ -0,0 +1,337 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ + module purge
2
+ + '[' -z '' ']'
3
+ + case "$-" in
4
+ + __lmod_sh_dbg=x
5
+ + '[' -n x ']'
6
+ + set +x
7
+ Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output
8
+ Shell debugging restarted
9
+ + unset __lmod_sh_dbg
10
+ + return 0
11
+ + module load Anaconda3/2023.03
12
+ + '[' -z '' ']'
13
+ + case "$-" in
14
+ + __lmod_sh_dbg=x
15
+ + '[' -n x ']'
16
+ + set +x
17
+ Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output
18
+ Shell debugging restarted
19
+ + unset __lmod_sh_dbg
20
+ + return 0
21
+ + source /camp/home/johnsoe/.bashrc
22
+ ++ '[' '' = yes ']'
23
+ ++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '
24
+ +++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.bash hook
25
+ ++ __conda_setup='export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\''
26
+ export _CE_M='\'''\''
27
+ export _CE_CONDA='\'''\''
28
+ export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''
29
+
30
+ # Copyright (C) 2012 Anaconda, Inc
31
+ # SPDX-License-Identifier: BSD-3-Clause
32
+ __conda_exe() (
33
+ "$CONDA_EXE" $_CE_M $_CE_CONDA "$@"
34
+ )
35
+
36
+ __conda_hashr() {
37
+ if [ -n "${ZSH_VERSION:+x}" ]; then
38
+ \rehash
39
+ elif [ -n "${POSH_VERSION:+x}" ]; then
40
+ : # pass
41
+ else
42
+ \hash -r
43
+ fi
44
+ }
45
+
46
+ __conda_activate() {
47
+ if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then
48
+ # Handle transition from shell activated with conda <= 4.3 to a subsequent activation
49
+ # after conda updated to >= 4.4. See issue #6173.
50
+ PS1="$CONDA_PS1_BACKUP"
51
+ \unset CONDA_PS1_BACKUP
52
+ fi
53
+ \local ask_conda
54
+ ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return
55
+ \eval "$ask_conda"
56
+ __conda_hashr
57
+ }
58
+
59
+ __conda_reactivate() {
60
+ \local ask_conda
61
+ ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return
62
+ \eval "$ask_conda"
63
+ __conda_hashr
64
+ }
65
+
66
+ conda() {
67
+ \local cmd="${1-__missing__}"
68
+ case "$cmd" in
69
+ activate|deactivate)
70
+ __conda_activate "$@"
71
+ ;;
72
+ install|update|upgrade|remove|uninstall)
73
+ __conda_exe "$@" || \return
74
+ __conda_reactivate
75
+ ;;
76
+ *)
77
+ __conda_exe "$@"
78
+ ;;
79
+ esac
80
+ }
81
+
82
+ if [ -z "${CONDA_SHLVL+x}" ]; then
83
+ \export CONDA_SHLVL=0
84
+ # In dev-mode CONDA_EXE is python.exe and on Windows
85
+ # it is in a different relative location to condabin.
86
+ if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then
87
+ PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}"
88
+ else
89
+ PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}"
90
+ fi
91
+ \export PATH
92
+
93
+ # We'\''re not allowing PS1 to be unbound. It must at least be set.
94
+ # However, we'\''re not exporting it, which can cause problems when starting a second shell
95
+ # via a first shell (i.e. starting zsh from bash).
96
+ if [ -z "${PS1+x}" ]; then
97
+ PS1=
98
+ fi
99
+ fi
100
+
101
+ conda activate base'
102
+ ++ '[' 0 -eq 0 ']'
103
+ ++ eval 'export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\''
104
+ export _CE_M='\'''\''
105
+ export _CE_CONDA='\'''\''
106
+ export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''
107
+
108
+ # Copyright (C) 2012 Anaconda, Inc
109
+ # SPDX-License-Identifier: BSD-3-Clause
110
+ __conda_exe() (
111
+ "$CONDA_EXE" $_CE_M $_CE_CONDA "$@"
112
+ )
113
+
114
+ __conda_hashr() {
115
+ if [ -n "${ZSH_VERSION:+x}" ]; then
116
+ \rehash
117
+ elif [ -n "${POSH_VERSION:+x}" ]; then
118
+ : # pass
119
+ else
120
+ \hash -r
121
+ fi
122
+ }
123
+
124
+ __conda_activate() {
125
+ if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then
126
+ # Handle transition from shell activated with conda <= 4.3 to a subsequent activation
127
+ # after conda updated to >= 4.4. See issue #6173.
128
+ PS1="$CONDA_PS1_BACKUP"
129
+ \unset CONDA_PS1_BACKUP
130
+ fi
131
+ \local ask_conda
132
+ ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return
133
+ \eval "$ask_conda"
134
+ __conda_hashr
135
+ }
136
+
137
+ __conda_reactivate() {
138
+ \local ask_conda
139
+ ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return
140
+ \eval "$ask_conda"
141
+ __conda_hashr
142
+ }
143
+
144
+ conda() {
145
+ \local cmd="${1-__missing__}"
146
+ case "$cmd" in
147
+ activate|deactivate)
148
+ __conda_activate "$@"
149
+ ;;
150
+ install|update|upgrade|remove|uninstall)
151
+ __conda_exe "$@" || \return
152
+ __conda_reactivate
153
+ ;;
154
+ *)
155
+ __conda_exe "$@"
156
+ ;;
157
+ esac
158
+ }
159
+
160
+ if [ -z "${CONDA_SHLVL+x}" ]; then
161
+ \export CONDA_SHLVL=0
162
+ # In dev-mode CONDA_EXE is python.exe and on Windows
163
+ # it is in a different relative location to condabin.
164
+ if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then
165
+ PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}"
166
+ else
167
+ PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}"
168
+ fi
169
+ \export PATH
170
+
171
+ # We'\''re not allowing PS1 to be unbound. It must at least be set.
172
+ # However, we'\''re not exporting it, which can cause problems when starting a second shell
173
+ # via a first shell (i.e. starting zsh from bash).
174
+ if [ -z "${PS1+x}" ]; then
175
+ PS1=
176
+ fi
177
+ fi
178
+
179
+ conda activate base'
180
+ +++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda
181
+ +++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda
182
+ +++ export _CE_M=
183
+ +++ _CE_M=
184
+ +++ export _CE_CONDA=
185
+ +++ _CE_CONDA=
186
+ +++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python
187
+ +++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python
188
+ +++ '[' -z x ']'
189
+ +++ conda activate base
190
+ +++ local cmd=activate
191
+ +++ case "$cmd" in
192
+ +++ __conda_activate activate base
193
+ +++ '[' -n '' ']'
194
+ +++ local ask_conda
195
+ ++++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '
196
+ ++++ __conda_exe shell.posix activate base
197
+ ++++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate base
198
+ +++ ask_conda='PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\''
199
+ export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\''
200
+ export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\''
201
+ export CONDA_SHLVL='\''6'\''
202
+ export CONDA_DEFAULT_ENV='\''base'\''
203
+ export CONDA_PROMPT_MODIFIER='\''(base) '\''
204
+ export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\''
205
+ export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\''
206
+ export _CE_M='\'''\''
207
+ export _CE_CONDA='\'''\''
208
+ export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'''
209
+ +++ eval 'PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\''
210
+ export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\''
211
+ export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\''
212
+ export CONDA_SHLVL='\''6'\''
213
+ export CONDA_DEFAULT_ENV='\''base'\''
214
+ export CONDA_PROMPT_MODIFIER='\''(base) '\''
215
+ export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\''
216
+ export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\''
217
+ export _CE_M='\'''\''
218
+ export _CE_CONDA='\'''\''
219
+ export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'''
220
+ ++++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '
221
+ ++++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin
222
+ ++++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin
223
+ ++++ export CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0
224
+ ++++ CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0
225
+ ++++ export CONDA_SHLVL=6
226
+ ++++ CONDA_SHLVL=6
227
+ ++++ export CONDA_DEFAULT_ENV=base
228
+ ++++ CONDA_DEFAULT_ENV=base
229
+ ++++ export 'CONDA_PROMPT_MODIFIER=(base) '
230
+ ++++ CONDA_PROMPT_MODIFIER='(base) '
231
+ ++++ export CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev
232
+ ++++ CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev
233
+ ++++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda
234
+ ++++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda
235
+ ++++ export _CE_M=
236
+ ++++ _CE_M=
237
+ ++++ export _CE_CONDA=
238
+ ++++ _CE_CONDA=
239
+ ++++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python
240
+ ++++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python
241
+ +++ __conda_hashr
242
+ +++ '[' -n '' ']'
243
+ +++ '[' -n '' ']'
244
+ +++ hash -r
245
+ ++ unset __conda_setup
246
+ + conda activate schemist-dev
247
+ + local cmd=activate
248
+ + case "$cmd" in
249
+ + __conda_activate activate schemist-dev
250
+ + '[' -n '' ']'
251
+ + local ask_conda
252
+ ++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '
253
+ ++ __conda_exe shell.posix activate schemist-dev
254
+ ++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate schemist-dev
255
+ + ask_conda='PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\''
256
+ export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\''
257
+ export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\''
258
+ export CONDA_SHLVL='\''7'\''
259
+ export CONDA_DEFAULT_ENV='\''schemist-dev'\''
260
+ export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\''
261
+ export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\''
262
+ export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\''
263
+ export _CE_M='\'''\''
264
+ export _CE_CONDA='\'''\''
265
+ export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'''
266
+ + eval 'PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\''
267
+ export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\''
268
+ export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\''
269
+ export CONDA_SHLVL='\''7'\''
270
+ export CONDA_DEFAULT_ENV='\''schemist-dev'\''
271
+ export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\''
272
+ export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\''
273
+ export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\''
274
+ export _CE_M='\'''\''
275
+ export _CE_CONDA='\'''\''
276
+ export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'''
277
+ ++ PS1='(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '
278
+ ++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin
279
+ ++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin
280
+ ++ export CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev
281
+ ++ CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev
282
+ ++ export CONDA_SHLVL=7
283
+ ++ CONDA_SHLVL=7
284
+ ++ export CONDA_DEFAULT_ENV=schemist-dev
285
+ ++ CONDA_DEFAULT_ENV=schemist-dev
286
+ ++ export 'CONDA_PROMPT_MODIFIER=(schemist-dev) '
287
+ ++ CONDA_PROMPT_MODIFIER='(schemist-dev) '
288
+ ++ export CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0
289
+ ++ CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0
290
+ ++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda
291
+ ++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda
292
+ ++ export _CE_M=
293
+ ++ _CE_M=
294
+ ++ export _CE_CONDA=
295
+ ++ _CE_CONDA=
296
+ ++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python
297
+ ++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python
298
+ + __conda_hashr
299
+ + '[' -n '' ']'
300
+ + '[' -n '' ']'
301
+ + hash -r
302
+ + CHUNK_HEAD_FILE=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz
303
+ + INPUT=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/train/cyc-pep-6-12mer-70M_06.csv
304
+ + COLUMN=cysteine_to_N_cyclization
305
+ + PREFIX=cyclic_
306
+ + AWK='1 { print $8, $1, $2, $10, $3 }'
307
+ + '[' -z cysteine_to_N_cyclization ']'
308
+ + '[' -z cyclic_ ']'
309
+ + '[' -z '1 { print $8, $1, $2, $10, $3 }' ']'
310
+ + awk -F, -v OFS=, '1 { print $8, $1, $2, $10, $3 }'
311
+ + 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
312
+ + schemist convert -f csv --column cysteine_to_N_cyclization --to id inchikey scaffold mwt clogp tpsa --prefix cyclic_ --options prefix=SCB-
313
+ + gzip --best
314
+ ++ zcat /nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz
315
+ ++ head -n1
316
+ ++ tr ' ' ,
317
+ 🚀 Converting between string representations with the following parameters:
318
+ subcommand: convert
319
+ output: <_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>
320
+ format: csv
321
+ input: <_io.TextIOWrapper name='<stdin>' mode='r' encoding='utf-8'>
322
+ representation: SMILES
323
+ column: cysteine_to_N_cyclization
324
+ prefix: cyclic_
325
+ to: ['id', 'inchikey', 'scaffold', 'mwt', 'clogp', 'tpsa']
326
+ options: ['prefix=SCB-']
327
+ func: <function _convert at 0x7f673477b240>
328
+
329
+ Error counts:
330
+ cyclic_id: 0
331
+ cyclic_inchikey: 0
332
+ cyclic_scaffold: 0
333
+ cyclic_mwt: 0
334
+ cyclic_clogp: 0
335
+ cyclic_tpsa: 0
336
+ ⏰ Completed process in 3:25:30.156492
337
+ + 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.csv.gz CHANGED
@@ -1,3 +1,3 @@
1
  version https://git-lfs.github.com/spec/v1
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- oid sha256:4bd24068f5ee5587c0b23a56ac79315e74c00011b78aaaec401c07678d0ecdbd
3
- size 61920564
 
1
  version https://git-lfs.github.com/spec/v1
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+ oid sha256:bebd419015a0b7c988aadcb153e993dd807e3ce5f83749a73cff4a07a85f5b5a
3
+ size 117597869
train/cyc-pep-6-12mer-70M_07.log ADDED
@@ -0,0 +1,337 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ + module purge
2
+ + '[' -z '' ']'
3
+ + case "$-" in
4
+ + __lmod_sh_dbg=x
5
+ + '[' -n x ']'
6
+ + set +x
7
+ Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output
8
+ Shell debugging restarted
9
+ + unset __lmod_sh_dbg
10
+ + return 0
11
+ + module load Anaconda3/2023.03
12
+ + '[' -z '' ']'
13
+ + case "$-" in
14
+ + __lmod_sh_dbg=x
15
+ + '[' -n x ']'
16
+ + set +x
17
+ Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output
18
+ Shell debugging restarted
19
+ + unset __lmod_sh_dbg
20
+ + return 0
21
+ + source /camp/home/johnsoe/.bashrc
22
+ ++ '[' '' = yes ']'
23
+ ++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '
24
+ +++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.bash hook
25
+ ++ __conda_setup='export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\''
26
+ export _CE_M='\'''\''
27
+ export _CE_CONDA='\'''\''
28
+ export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''
29
+
30
+ # Copyright (C) 2012 Anaconda, Inc
31
+ # SPDX-License-Identifier: BSD-3-Clause
32
+ __conda_exe() (
33
+ "$CONDA_EXE" $_CE_M $_CE_CONDA "$@"
34
+ )
35
+
36
+ __conda_hashr() {
37
+ if [ -n "${ZSH_VERSION:+x}" ]; then
38
+ \rehash
39
+ elif [ -n "${POSH_VERSION:+x}" ]; then
40
+ : # pass
41
+ else
42
+ \hash -r
43
+ fi
44
+ }
45
+
46
+ __conda_activate() {
47
+ if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then
48
+ # Handle transition from shell activated with conda <= 4.3 to a subsequent activation
49
+ # after conda updated to >= 4.4. See issue #6173.
50
+ PS1="$CONDA_PS1_BACKUP"
51
+ \unset CONDA_PS1_BACKUP
52
+ fi
53
+ \local ask_conda
54
+ ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return
55
+ \eval "$ask_conda"
56
+ __conda_hashr
57
+ }
58
+
59
+ __conda_reactivate() {
60
+ \local ask_conda
61
+ ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return
62
+ \eval "$ask_conda"
63
+ __conda_hashr
64
+ }
65
+
66
+ conda() {
67
+ \local cmd="${1-__missing__}"
68
+ case "$cmd" in
69
+ activate|deactivate)
70
+ __conda_activate "$@"
71
+ ;;
72
+ install|update|upgrade|remove|uninstall)
73
+ __conda_exe "$@" || \return
74
+ __conda_reactivate
75
+ ;;
76
+ *)
77
+ __conda_exe "$@"
78
+ ;;
79
+ esac
80
+ }
81
+
82
+ if [ -z "${CONDA_SHLVL+x}" ]; then
83
+ \export CONDA_SHLVL=0
84
+ # In dev-mode CONDA_EXE is python.exe and on Windows
85
+ # it is in a different relative location to condabin.
86
+ if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then
87
+ PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}"
88
+ else
89
+ PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}"
90
+ fi
91
+ \export PATH
92
+
93
+ # We'\''re not allowing PS1 to be unbound. It must at least be set.
94
+ # However, we'\''re not exporting it, which can cause problems when starting a second shell
95
+ # via a first shell (i.e. starting zsh from bash).
96
+ if [ -z "${PS1+x}" ]; then
97
+ PS1=
98
+ fi
99
+ fi
100
+
101
+ conda activate base'
102
+ ++ '[' 0 -eq 0 ']'
103
+ ++ eval 'export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\''
104
+ export _CE_M='\'''\''
105
+ export _CE_CONDA='\'''\''
106
+ export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''
107
+
108
+ # Copyright (C) 2012 Anaconda, Inc
109
+ # SPDX-License-Identifier: BSD-3-Clause
110
+ __conda_exe() (
111
+ "$CONDA_EXE" $_CE_M $_CE_CONDA "$@"
112
+ )
113
+
114
+ __conda_hashr() {
115
+ if [ -n "${ZSH_VERSION:+x}" ]; then
116
+ \rehash
117
+ elif [ -n "${POSH_VERSION:+x}" ]; then
118
+ : # pass
119
+ else
120
+ \hash -r
121
+ fi
122
+ }
123
+
124
+ __conda_activate() {
125
+ if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then
126
+ # Handle transition from shell activated with conda <= 4.3 to a subsequent activation
127
+ # after conda updated to >= 4.4. See issue #6173.
128
+ PS1="$CONDA_PS1_BACKUP"
129
+ \unset CONDA_PS1_BACKUP
130
+ fi
131
+ \local ask_conda
132
+ ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return
133
+ \eval "$ask_conda"
134
+ __conda_hashr
135
+ }
136
+
137
+ __conda_reactivate() {
138
+ \local ask_conda
139
+ ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return
140
+ \eval "$ask_conda"
141
+ __conda_hashr
142
+ }
143
+
144
+ conda() {
145
+ \local cmd="${1-__missing__}"
146
+ case "$cmd" in
147
+ activate|deactivate)
148
+ __conda_activate "$@"
149
+ ;;
150
+ install|update|upgrade|remove|uninstall)
151
+ __conda_exe "$@" || \return
152
+ __conda_reactivate
153
+ ;;
154
+ *)
155
+ __conda_exe "$@"
156
+ ;;
157
+ esac
158
+ }
159
+
160
+ if [ -z "${CONDA_SHLVL+x}" ]; then
161
+ \export CONDA_SHLVL=0
162
+ # In dev-mode CONDA_EXE is python.exe and on Windows
163
+ # it is in a different relative location to condabin.
164
+ if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then
165
+ PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}"
166
+ else
167
+ PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}"
168
+ fi
169
+ \export PATH
170
+
171
+ # We'\''re not allowing PS1 to be unbound. It must at least be set.
172
+ # However, we'\''re not exporting it, which can cause problems when starting a second shell
173
+ # via a first shell (i.e. starting zsh from bash).
174
+ if [ -z "${PS1+x}" ]; then
175
+ PS1=
176
+ fi
177
+ fi
178
+
179
+ conda activate base'
180
+ +++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda
181
+ +++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda
182
+ +++ export _CE_M=
183
+ +++ _CE_M=
184
+ +++ export _CE_CONDA=
185
+ +++ _CE_CONDA=
186
+ +++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python
187
+ +++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python
188
+ +++ '[' -z x ']'
189
+ +++ conda activate base
190
+ +++ local cmd=activate
191
+ +++ case "$cmd" in
192
+ +++ __conda_activate activate base
193
+ +++ '[' -n '' ']'
194
+ +++ local ask_conda
195
+ ++++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '
196
+ ++++ __conda_exe shell.posix activate base
197
+ ++++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate base
198
+ +++ ask_conda='PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\''
199
+ export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\''
200
+ export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\''
201
+ export CONDA_SHLVL='\''6'\''
202
+ export CONDA_DEFAULT_ENV='\''base'\''
203
+ export CONDA_PROMPT_MODIFIER='\''(base) '\''
204
+ export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\''
205
+ export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\''
206
+ export _CE_M='\'''\''
207
+ export _CE_CONDA='\'''\''
208
+ export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'''
209
+ +++ eval 'PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\''
210
+ export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\''
211
+ export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\''
212
+ export CONDA_SHLVL='\''6'\''
213
+ export CONDA_DEFAULT_ENV='\''base'\''
214
+ export CONDA_PROMPT_MODIFIER='\''(base) '\''
215
+ export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\''
216
+ export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\''
217
+ export _CE_M='\'''\''
218
+ export _CE_CONDA='\'''\''
219
+ export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'''
220
+ ++++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '
221
+ ++++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin
222
+ ++++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin
223
+ ++++ export CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0
224
+ ++++ CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0
225
+ ++++ export CONDA_SHLVL=6
226
+ ++++ CONDA_SHLVL=6
227
+ ++++ export CONDA_DEFAULT_ENV=base
228
+ ++++ CONDA_DEFAULT_ENV=base
229
+ ++++ export 'CONDA_PROMPT_MODIFIER=(base) '
230
+ ++++ CONDA_PROMPT_MODIFIER='(base) '
231
+ ++++ export CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev
232
+ ++++ CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev
233
+ ++++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda
234
+ ++++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda
235
+ ++++ export _CE_M=
236
+ ++++ _CE_M=
237
+ ++++ export _CE_CONDA=
238
+ ++++ _CE_CONDA=
239
+ ++++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python
240
+ ++++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python
241
+ +++ __conda_hashr
242
+ +++ '[' -n '' ']'
243
+ +++ '[' -n '' ']'
244
+ +++ hash -r
245
+ ++ unset __conda_setup
246
+ + conda activate schemist-dev
247
+ + local cmd=activate
248
+ + case "$cmd" in
249
+ + __conda_activate activate schemist-dev
250
+ + '[' -n '' ']'
251
+ + local ask_conda
252
+ ++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '
253
+ ++ __conda_exe shell.posix activate schemist-dev
254
+ ++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate schemist-dev
255
+ + ask_conda='PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\''
256
+ export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\''
257
+ export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\''
258
+ export CONDA_SHLVL='\''7'\''
259
+ export CONDA_DEFAULT_ENV='\''schemist-dev'\''
260
+ export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\''
261
+ export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\''
262
+ export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\''
263
+ export _CE_M='\'''\''
264
+ export _CE_CONDA='\'''\''
265
+ export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'''
266
+ + eval 'PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\''
267
+ export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\''
268
+ export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\''
269
+ export CONDA_SHLVL='\''7'\''
270
+ export CONDA_DEFAULT_ENV='\''schemist-dev'\''
271
+ export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\''
272
+ export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\''
273
+ export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\''
274
+ export _CE_M='\'''\''
275
+ export _CE_CONDA='\'''\''
276
+ export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'''
277
+ ++ PS1='(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '
278
+ ++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin
279
+ ++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin
280
+ ++ export CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev
281
+ ++ CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev
282
+ ++ export CONDA_SHLVL=7
283
+ ++ CONDA_SHLVL=7
284
+ ++ export CONDA_DEFAULT_ENV=schemist-dev
285
+ ++ CONDA_DEFAULT_ENV=schemist-dev
286
+ ++ export 'CONDA_PROMPT_MODIFIER=(schemist-dev) '
287
+ ++ CONDA_PROMPT_MODIFIER='(schemist-dev) '
288
+ ++ export CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0
289
+ ++ CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0
290
+ ++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda
291
+ ++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda
292
+ ++ export _CE_M=
293
+ ++ _CE_M=
294
+ ++ export _CE_CONDA=
295
+ ++ _CE_CONDA=
296
+ ++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python
297
+ ++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python
298
+ + __conda_hashr
299
+ + '[' -n '' ']'
300
+ + '[' -n '' ']'
301
+ + hash -r
302
+ + CHUNK_HEAD_FILE=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz
303
+ + INPUT=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/train/cyc-pep-6-12mer-70M_07.csv
304
+ + COLUMN=cysteine_to_N_cyclization
305
+ + PREFIX=cyclic_
306
+ + AWK='1 { print $8, $1, $2, $10, $3 }'
307
+ + '[' -z cysteine_to_N_cyclization ']'
308
+ + '[' -z cyclic_ ']'
309
+ + '[' -z '1 { print $8, $1, $2, $10, $3 }' ']'
310
+ + 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
311
+ + awk -F, -v OFS=, '1 { print $8, $1, $2, $10, $3 }'
312
+ + schemist convert -f csv --column cysteine_to_N_cyclization --to id inchikey scaffold mwt clogp tpsa --prefix cyclic_ --options prefix=SCB-
313
+ + gzip --best
314
+ ++ tr ' ' ,
315
+ ++ head -n1
316
+ ++ zcat /nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz
317
+ 🚀 Converting between string representations with the following parameters:
318
+ subcommand: convert
319
+ output: <_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>
320
+ format: csv
321
+ input: <_io.TextIOWrapper name='<stdin>' mode='r' encoding='utf-8'>
322
+ representation: SMILES
323
+ column: cysteine_to_N_cyclization
324
+ prefix: cyclic_
325
+ to: ['id', 'inchikey', 'scaffold', 'mwt', 'clogp', 'tpsa']
326
+ options: ['prefix=SCB-']
327
+ func: <function _convert at 0x7fcb30feb240>
328
+
329
+ Error counts:
330
+ cyclic_id: 0
331
+ cyclic_inchikey: 0
332
+ cyclic_scaffold: 0
333
+ cyclic_mwt: 0
334
+ cyclic_clogp: 0
335
+ cyclic_tpsa: 0
336
+ ⏰ Completed process in 3:18:08.109675
337
+ + 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.csv.gz CHANGED
@@ -1,3 +1,3 @@
1
  version https://git-lfs.github.com/spec/v1
2
- oid sha256:27ebb0665ac18ce05bcffcb8dd52223f98e6e6cf4c2d2422c0c04ff75474baa4
3
- size 61924935
 
1
  version https://git-lfs.github.com/spec/v1
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+ oid sha256:43b40bf86d8c8b1a9cda58d0c1084556a42db1f382bc346476b029874fc788cc
3
+ size 117605134
train/cyc-pep-6-12mer-70M_08.log ADDED
@@ -0,0 +1,337 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ + module purge
2
+ + '[' -z '' ']'
3
+ + case "$-" in
4
+ + __lmod_sh_dbg=x
5
+ + '[' -n x ']'
6
+ + set +x
7
+ Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output
8
+ Shell debugging restarted
9
+ + unset __lmod_sh_dbg
10
+ + return 0
11
+ + module load Anaconda3/2023.03
12
+ + '[' -z '' ']'
13
+ + case "$-" in
14
+ + __lmod_sh_dbg=x
15
+ + '[' -n x ']'
16
+ + set +x
17
+ Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output
18
+ Shell debugging restarted
19
+ + unset __lmod_sh_dbg
20
+ + return 0
21
+ + source /camp/home/johnsoe/.bashrc
22
+ ++ '[' '' = yes ']'
23
+ ++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '
24
+ +++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.bash hook
25
+ ++ __conda_setup='export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\''
26
+ export _CE_M='\'''\''
27
+ export _CE_CONDA='\'''\''
28
+ export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''
29
+
30
+ # Copyright (C) 2012 Anaconda, Inc
31
+ # SPDX-License-Identifier: BSD-3-Clause
32
+ __conda_exe() (
33
+ "$CONDA_EXE" $_CE_M $_CE_CONDA "$@"
34
+ )
35
+
36
+ __conda_hashr() {
37
+ if [ -n "${ZSH_VERSION:+x}" ]; then
38
+ \rehash
39
+ elif [ -n "${POSH_VERSION:+x}" ]; then
40
+ : # pass
41
+ else
42
+ \hash -r
43
+ fi
44
+ }
45
+
46
+ __conda_activate() {
47
+ if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then
48
+ # Handle transition from shell activated with conda <= 4.3 to a subsequent activation
49
+ # after conda updated to >= 4.4. See issue #6173.
50
+ PS1="$CONDA_PS1_BACKUP"
51
+ \unset CONDA_PS1_BACKUP
52
+ fi
53
+ \local ask_conda
54
+ ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return
55
+ \eval "$ask_conda"
56
+ __conda_hashr
57
+ }
58
+
59
+ __conda_reactivate() {
60
+ \local ask_conda
61
+ ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return
62
+ \eval "$ask_conda"
63
+ __conda_hashr
64
+ }
65
+
66
+ conda() {
67
+ \local cmd="${1-__missing__}"
68
+ case "$cmd" in
69
+ activate|deactivate)
70
+ __conda_activate "$@"
71
+ ;;
72
+ install|update|upgrade|remove|uninstall)
73
+ __conda_exe "$@" || \return
74
+ __conda_reactivate
75
+ ;;
76
+ *)
77
+ __conda_exe "$@"
78
+ ;;
79
+ esac
80
+ }
81
+
82
+ if [ -z "${CONDA_SHLVL+x}" ]; then
83
+ \export CONDA_SHLVL=0
84
+ # In dev-mode CONDA_EXE is python.exe and on Windows
85
+ # it is in a different relative location to condabin.
86
+ if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then
87
+ PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}"
88
+ else
89
+ PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}"
90
+ fi
91
+ \export PATH
92
+
93
+ # We'\''re not allowing PS1 to be unbound. It must at least be set.
94
+ # However, we'\''re not exporting it, which can cause problems when starting a second shell
95
+ # via a first shell (i.e. starting zsh from bash).
96
+ if [ -z "${PS1+x}" ]; then
97
+ PS1=
98
+ fi
99
+ fi
100
+
101
+ conda activate base'
102
+ ++ '[' 0 -eq 0 ']'
103
+ ++ eval 'export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\''
104
+ export _CE_M='\'''\''
105
+ export _CE_CONDA='\'''\''
106
+ export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''
107
+
108
+ # Copyright (C) 2012 Anaconda, Inc
109
+ # SPDX-License-Identifier: BSD-3-Clause
110
+ __conda_exe() (
111
+ "$CONDA_EXE" $_CE_M $_CE_CONDA "$@"
112
+ )
113
+
114
+ __conda_hashr() {
115
+ if [ -n "${ZSH_VERSION:+x}" ]; then
116
+ \rehash
117
+ elif [ -n "${POSH_VERSION:+x}" ]; then
118
+ : # pass
119
+ else
120
+ \hash -r
121
+ fi
122
+ }
123
+
124
+ __conda_activate() {
125
+ if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then
126
+ # Handle transition from shell activated with conda <= 4.3 to a subsequent activation
127
+ # after conda updated to >= 4.4. See issue #6173.
128
+ PS1="$CONDA_PS1_BACKUP"
129
+ \unset CONDA_PS1_BACKUP
130
+ fi
131
+ \local ask_conda
132
+ ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return
133
+ \eval "$ask_conda"
134
+ __conda_hashr
135
+ }
136
+
137
+ __conda_reactivate() {
138
+ \local ask_conda
139
+ ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return
140
+ \eval "$ask_conda"
141
+ __conda_hashr
142
+ }
143
+
144
+ conda() {
145
+ \local cmd="${1-__missing__}"
146
+ case "$cmd" in
147
+ activate|deactivate)
148
+ __conda_activate "$@"
149
+ ;;
150
+ install|update|upgrade|remove|uninstall)
151
+ __conda_exe "$@" || \return
152
+ __conda_reactivate
153
+ ;;
154
+ *)
155
+ __conda_exe "$@"
156
+ ;;
157
+ esac
158
+ }
159
+
160
+ if [ -z "${CONDA_SHLVL+x}" ]; then
161
+ \export CONDA_SHLVL=0
162
+ # In dev-mode CONDA_EXE is python.exe and on Windows
163
+ # it is in a different relative location to condabin.
164
+ if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then
165
+ PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}"
166
+ else
167
+ PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}"
168
+ fi
169
+ \export PATH
170
+
171
+ # We'\''re not allowing PS1 to be unbound. It must at least be set.
172
+ # However, we'\''re not exporting it, which can cause problems when starting a second shell
173
+ # via a first shell (i.e. starting zsh from bash).
174
+ if [ -z "${PS1+x}" ]; then
175
+ PS1=
176
+ fi
177
+ fi
178
+
179
+ conda activate base'
180
+ +++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda
181
+ +++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda
182
+ +++ export _CE_M=
183
+ +++ _CE_M=
184
+ +++ export _CE_CONDA=
185
+ +++ _CE_CONDA=
186
+ +++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python
187
+ +++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python
188
+ +++ '[' -z x ']'
189
+ +++ conda activate base
190
+ +++ local cmd=activate
191
+ +++ case "$cmd" in
192
+ +++ __conda_activate activate base
193
+ +++ '[' -n '' ']'
194
+ +++ local ask_conda
195
+ ++++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '
196
+ ++++ __conda_exe shell.posix activate base
197
+ ++++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate base
198
+ +++ ask_conda='PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\''
199
+ export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\''
200
+ export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\''
201
+ export CONDA_SHLVL='\''6'\''
202
+ export CONDA_DEFAULT_ENV='\''base'\''
203
+ export CONDA_PROMPT_MODIFIER='\''(base) '\''
204
+ export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\''
205
+ export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\''
206
+ export _CE_M='\'''\''
207
+ export _CE_CONDA='\'''\''
208
+ export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'''
209
+ +++ eval 'PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\''
210
+ export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\''
211
+ export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\''
212
+ export CONDA_SHLVL='\''6'\''
213
+ export CONDA_DEFAULT_ENV='\''base'\''
214
+ export CONDA_PROMPT_MODIFIER='\''(base) '\''
215
+ export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\''
216
+ export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\''
217
+ export _CE_M='\'''\''
218
+ export _CE_CONDA='\'''\''
219
+ export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'''
220
+ ++++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '
221
+ ++++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin
222
+ ++++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin
223
+ ++++ export CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0
224
+ ++++ CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0
225
+ ++++ export CONDA_SHLVL=6
226
+ ++++ CONDA_SHLVL=6
227
+ ++++ export CONDA_DEFAULT_ENV=base
228
+ ++++ CONDA_DEFAULT_ENV=base
229
+ ++++ export 'CONDA_PROMPT_MODIFIER=(base) '
230
+ ++++ CONDA_PROMPT_MODIFIER='(base) '
231
+ ++++ export CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev
232
+ ++++ CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev
233
+ ++++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda
234
+ ++++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda
235
+ ++++ export _CE_M=
236
+ ++++ _CE_M=
237
+ ++++ export _CE_CONDA=
238
+ ++++ _CE_CONDA=
239
+ ++++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python
240
+ ++++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python
241
+ +++ __conda_hashr
242
+ +++ '[' -n '' ']'
243
+ +++ '[' -n '' ']'
244
+ +++ hash -r
245
+ ++ unset __conda_setup
246
+ + conda activate schemist-dev
247
+ + local cmd=activate
248
+ + case "$cmd" in
249
+ + __conda_activate activate schemist-dev
250
+ + '[' -n '' ']'
251
+ + local ask_conda
252
+ ++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '
253
+ ++ __conda_exe shell.posix activate schemist-dev
254
+ ++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate schemist-dev
255
+ + ask_conda='PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\''
256
+ export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\''
257
+ export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\''
258
+ export CONDA_SHLVL='\''7'\''
259
+ export CONDA_DEFAULT_ENV='\''schemist-dev'\''
260
+ export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\''
261
+ export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\''
262
+ export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\''
263
+ export _CE_M='\'''\''
264
+ export _CE_CONDA='\'''\''
265
+ export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'''
266
+ + eval 'PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\''
267
+ export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\''
268
+ export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\''
269
+ export CONDA_SHLVL='\''7'\''
270
+ export CONDA_DEFAULT_ENV='\''schemist-dev'\''
271
+ export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\''
272
+ export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\''
273
+ export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\''
274
+ export _CE_M='\'''\''
275
+ export _CE_CONDA='\'''\''
276
+ export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'''
277
+ ++ PS1='(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '
278
+ ++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin
279
+ ++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin
280
+ ++ export CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev
281
+ ++ CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev
282
+ ++ export CONDA_SHLVL=7
283
+ ++ CONDA_SHLVL=7
284
+ ++ export CONDA_DEFAULT_ENV=schemist-dev
285
+ ++ CONDA_DEFAULT_ENV=schemist-dev
286
+ ++ export 'CONDA_PROMPT_MODIFIER=(schemist-dev) '
287
+ ++ CONDA_PROMPT_MODIFIER='(schemist-dev) '
288
+ ++ export CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0
289
+ ++ CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0
290
+ ++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda
291
+ ++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda
292
+ ++ export _CE_M=
293
+ ++ _CE_M=
294
+ ++ export _CE_CONDA=
295
+ ++ _CE_CONDA=
296
+ ++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python
297
+ ++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python
298
+ + __conda_hashr
299
+ + '[' -n '' ']'
300
+ + '[' -n '' ']'
301
+ + hash -r
302
+ + CHUNK_HEAD_FILE=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz
303
+ + INPUT=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/train/cyc-pep-6-12mer-70M_08.csv
304
+ + COLUMN=cysteine_to_N_cyclization
305
+ + PREFIX=cyclic_
306
+ + AWK='1 { print $8, $1, $2, $10, $3 }'
307
+ + '[' -z cysteine_to_N_cyclization ']'
308
+ + '[' -z cyclic_ ']'
309
+ + '[' -z '1 { print $8, $1, $2, $10, $3 }' ']'
310
+ + 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
311
+ + awk -F, -v OFS=, '1 { print $8, $1, $2, $10, $3 }'
312
+ ++ zcat /nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz
313
+ + schemist convert -f csv --column cysteine_to_N_cyclization --to id inchikey scaffold mwt clogp tpsa --prefix cyclic_ --options prefix=SCB-
314
+ + gzip --best
315
+ ++ head -n1
316
+ ++ tr ' ' ,
317
+ 🚀 Converting between string representations with the following parameters:
318
+ subcommand: convert
319
+ output: <_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>
320
+ format: csv
321
+ input: <_io.TextIOWrapper name='<stdin>' mode='r' encoding='utf-8'>
322
+ representation: SMILES
323
+ column: cysteine_to_N_cyclization
324
+ prefix: cyclic_
325
+ to: ['id', 'inchikey', 'scaffold', 'mwt', 'clogp', 'tpsa']
326
+ options: ['prefix=SCB-']
327
+ func: <function _convert at 0x7f0910a93240>
328
+
329
+ Error counts:
330
+ cyclic_id: 0
331
+ cyclic_inchikey: 0
332
+ cyclic_scaffold: 0
333
+ cyclic_mwt: 0
334
+ cyclic_clogp: 0
335
+ cyclic_tpsa: 0
336
+ ⏰ Completed process in 3:15:59.963602
337
+ + 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.csv.gz CHANGED
@@ -1,3 +1,3 @@
1
  version https://git-lfs.github.com/spec/v1
2
- oid sha256:44656fbf5f8c2bbe29de3a22891fc07b1142f4fe60907ac5cfab4cce0984c079
3
- size 61925202
 
1
  version https://git-lfs.github.com/spec/v1
2
+ oid sha256:be9ec4115b86dcee15f970658913b3a3fa115ad25d3eab2412f7c7eeb9477e0b
3
+ size 117606847
train/cyc-pep-6-12mer-70M_09.log ADDED
@@ -0,0 +1,337 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ + module purge
2
+ + '[' -z '' ']'
3
+ + case "$-" in
4
+ + __lmod_sh_dbg=x
5
+ + '[' -n x ']'
6
+ + set +x
7
+ Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output
8
+ Shell debugging restarted
9
+ + unset __lmod_sh_dbg
10
+ + return 0
11
+ + module load Anaconda3/2023.03
12
+ + '[' -z '' ']'
13
+ + case "$-" in
14
+ + __lmod_sh_dbg=x
15
+ + '[' -n x ']'
16
+ + set +x
17
+ Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output
18
+ Shell debugging restarted
19
+ + unset __lmod_sh_dbg
20
+ + return 0
21
+ + source /camp/home/johnsoe/.bashrc
22
+ ++ '[' '' = yes ']'
23
+ ++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '
24
+ +++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.bash hook
25
+ ++ __conda_setup='export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\''
26
+ export _CE_M='\'''\''
27
+ export _CE_CONDA='\'''\''
28
+ export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''
29
+
30
+ # Copyright (C) 2012 Anaconda, Inc
31
+ # SPDX-License-Identifier: BSD-3-Clause
32
+ __conda_exe() (
33
+ "$CONDA_EXE" $_CE_M $_CE_CONDA "$@"
34
+ )
35
+
36
+ __conda_hashr() {
37
+ if [ -n "${ZSH_VERSION:+x}" ]; then
38
+ \rehash
39
+ elif [ -n "${POSH_VERSION:+x}" ]; then
40
+ : # pass
41
+ else
42
+ \hash -r
43
+ fi
44
+ }
45
+
46
+ __conda_activate() {
47
+ if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then
48
+ # Handle transition from shell activated with conda <= 4.3 to a subsequent activation
49
+ # after conda updated to >= 4.4. See issue #6173.
50
+ PS1="$CONDA_PS1_BACKUP"
51
+ \unset CONDA_PS1_BACKUP
52
+ fi
53
+ \local ask_conda
54
+ ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return
55
+ \eval "$ask_conda"
56
+ __conda_hashr
57
+ }
58
+
59
+ __conda_reactivate() {
60
+ \local ask_conda
61
+ ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return
62
+ \eval "$ask_conda"
63
+ __conda_hashr
64
+ }
65
+
66
+ conda() {
67
+ \local cmd="${1-__missing__}"
68
+ case "$cmd" in
69
+ activate|deactivate)
70
+ __conda_activate "$@"
71
+ ;;
72
+ install|update|upgrade|remove|uninstall)
73
+ __conda_exe "$@" || \return
74
+ __conda_reactivate
75
+ ;;
76
+ *)
77
+ __conda_exe "$@"
78
+ ;;
79
+ esac
80
+ }
81
+
82
+ if [ -z "${CONDA_SHLVL+x}" ]; then
83
+ \export CONDA_SHLVL=0
84
+ # In dev-mode CONDA_EXE is python.exe and on Windows
85
+ # it is in a different relative location to condabin.
86
+ if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then
87
+ PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}"
88
+ else
89
+ PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}"
90
+ fi
91
+ \export PATH
92
+
93
+ # We'\''re not allowing PS1 to be unbound. It must at least be set.
94
+ # However, we'\''re not exporting it, which can cause problems when starting a second shell
95
+ # via a first shell (i.e. starting zsh from bash).
96
+ if [ -z "${PS1+x}" ]; then
97
+ PS1=
98
+ fi
99
+ fi
100
+
101
+ conda activate base'
102
+ ++ '[' 0 -eq 0 ']'
103
+ ++ eval 'export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\''
104
+ export _CE_M='\'''\''
105
+ export _CE_CONDA='\'''\''
106
+ export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''
107
+
108
+ # Copyright (C) 2012 Anaconda, Inc
109
+ # SPDX-License-Identifier: BSD-3-Clause
110
+ __conda_exe() (
111
+ "$CONDA_EXE" $_CE_M $_CE_CONDA "$@"
112
+ )
113
+
114
+ __conda_hashr() {
115
+ if [ -n "${ZSH_VERSION:+x}" ]; then
116
+ \rehash
117
+ elif [ -n "${POSH_VERSION:+x}" ]; then
118
+ : # pass
119
+ else
120
+ \hash -r
121
+ fi
122
+ }
123
+
124
+ __conda_activate() {
125
+ if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then
126
+ # Handle transition from shell activated with conda <= 4.3 to a subsequent activation
127
+ # after conda updated to >= 4.4. See issue #6173.
128
+ PS1="$CONDA_PS1_BACKUP"
129
+ \unset CONDA_PS1_BACKUP
130
+ fi
131
+ \local ask_conda
132
+ ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return
133
+ \eval "$ask_conda"
134
+ __conda_hashr
135
+ }
136
+
137
+ __conda_reactivate() {
138
+ \local ask_conda
139
+ ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return
140
+ \eval "$ask_conda"
141
+ __conda_hashr
142
+ }
143
+
144
+ conda() {
145
+ \local cmd="${1-__missing__}"
146
+ case "$cmd" in
147
+ activate|deactivate)
148
+ __conda_activate "$@"
149
+ ;;
150
+ install|update|upgrade|remove|uninstall)
151
+ __conda_exe "$@" || \return
152
+ __conda_reactivate
153
+ ;;
154
+ *)
155
+ __conda_exe "$@"
156
+ ;;
157
+ esac
158
+ }
159
+
160
+ if [ -z "${CONDA_SHLVL+x}" ]; then
161
+ \export CONDA_SHLVL=0
162
+ # In dev-mode CONDA_EXE is python.exe and on Windows
163
+ # it is in a different relative location to condabin.
164
+ if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then
165
+ PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}"
166
+ else
167
+ PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}"
168
+ fi
169
+ \export PATH
170
+
171
+ # We'\''re not allowing PS1 to be unbound. It must at least be set.
172
+ # However, we'\''re not exporting it, which can cause problems when starting a second shell
173
+ # via a first shell (i.e. starting zsh from bash).
174
+ if [ -z "${PS1+x}" ]; then
175
+ PS1=
176
+ fi
177
+ fi
178
+
179
+ conda activate base'
180
+ +++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda
181
+ +++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda
182
+ +++ export _CE_M=
183
+ +++ _CE_M=
184
+ +++ export _CE_CONDA=
185
+ +++ _CE_CONDA=
186
+ +++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python
187
+ +++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python
188
+ +++ '[' -z x ']'
189
+ +++ conda activate base
190
+ +++ local cmd=activate
191
+ +++ case "$cmd" in
192
+ +++ __conda_activate activate base
193
+ +++ '[' -n '' ']'
194
+ +++ local ask_conda
195
+ ++++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '
196
+ ++++ __conda_exe shell.posix activate base
197
+ ++++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate base
198
+ +++ ask_conda='PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\''
199
+ export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\''
200
+ export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\''
201
+ export CONDA_SHLVL='\''6'\''
202
+ export CONDA_DEFAULT_ENV='\''base'\''
203
+ export CONDA_PROMPT_MODIFIER='\''(base) '\''
204
+ export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\''
205
+ export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\''
206
+ export _CE_M='\'''\''
207
+ export _CE_CONDA='\'''\''
208
+ export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'''
209
+ +++ eval 'PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\''
210
+ export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\''
211
+ export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\''
212
+ export CONDA_SHLVL='\''6'\''
213
+ export CONDA_DEFAULT_ENV='\''base'\''
214
+ export CONDA_PROMPT_MODIFIER='\''(base) '\''
215
+ export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\''
216
+ export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\''
217
+ export _CE_M='\'''\''
218
+ export _CE_CONDA='\'''\''
219
+ export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'''
220
+ ++++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '
221
+ ++++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin
222
+ ++++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin
223
+ ++++ export CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0
224
+ ++++ CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0
225
+ ++++ export CONDA_SHLVL=6
226
+ ++++ CONDA_SHLVL=6
227
+ ++++ export CONDA_DEFAULT_ENV=base
228
+ ++++ CONDA_DEFAULT_ENV=base
229
+ ++++ export 'CONDA_PROMPT_MODIFIER=(base) '
230
+ ++++ CONDA_PROMPT_MODIFIER='(base) '
231
+ ++++ export CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev
232
+ ++++ CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev
233
+ ++++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda
234
+ ++++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda
235
+ ++++ export _CE_M=
236
+ ++++ _CE_M=
237
+ ++++ export _CE_CONDA=
238
+ ++++ _CE_CONDA=
239
+ ++++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python
240
+ ++++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python
241
+ +++ __conda_hashr
242
+ +++ '[' -n '' ']'
243
+ +++ '[' -n '' ']'
244
+ +++ hash -r
245
+ ++ unset __conda_setup
246
+ + conda activate schemist-dev
247
+ + local cmd=activate
248
+ + case "$cmd" in
249
+ + __conda_activate activate schemist-dev
250
+ + '[' -n '' ']'
251
+ + local ask_conda
252
+ ++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '
253
+ ++ __conda_exe shell.posix activate schemist-dev
254
+ ++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate schemist-dev
255
+ + ask_conda='PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\''
256
+ export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\''
257
+ export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\''
258
+ export CONDA_SHLVL='\''7'\''
259
+ export CONDA_DEFAULT_ENV='\''schemist-dev'\''
260
+ export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\''
261
+ export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\''
262
+ export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\''
263
+ export _CE_M='\'''\''
264
+ export _CE_CONDA='\'''\''
265
+ export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'''
266
+ + eval 'PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\''
267
+ export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\''
268
+ export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\''
269
+ export CONDA_SHLVL='\''7'\''
270
+ export CONDA_DEFAULT_ENV='\''schemist-dev'\''
271
+ export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\''
272
+ export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\''
273
+ export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\''
274
+ export _CE_M='\'''\''
275
+ export _CE_CONDA='\'''\''
276
+ export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'''
277
+ ++ PS1='(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '
278
+ ++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin
279
+ ++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin
280
+ ++ export CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev
281
+ ++ CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev
282
+ ++ export CONDA_SHLVL=7
283
+ ++ CONDA_SHLVL=7
284
+ ++ export CONDA_DEFAULT_ENV=schemist-dev
285
+ ++ CONDA_DEFAULT_ENV=schemist-dev
286
+ ++ export 'CONDA_PROMPT_MODIFIER=(schemist-dev) '
287
+ ++ CONDA_PROMPT_MODIFIER='(schemist-dev) '
288
+ ++ export CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0
289
+ ++ CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0
290
+ ++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda
291
+ ++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda
292
+ ++ export _CE_M=
293
+ ++ _CE_M=
294
+ ++ export _CE_CONDA=
295
+ ++ _CE_CONDA=
296
+ ++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python
297
+ ++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python
298
+ + __conda_hashr
299
+ + '[' -n '' ']'
300
+ + '[' -n '' ']'
301
+ + hash -r
302
+ + CHUNK_HEAD_FILE=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz
303
+ + INPUT=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/train/cyc-pep-6-12mer-70M_09.csv
304
+ + COLUMN=cysteine_to_N_cyclization
305
+ + PREFIX=cyclic_
306
+ + AWK='1 { print $8, $1, $2, $10, $3 }'
307
+ + '[' -z cysteine_to_N_cyclization ']'
308
+ + '[' -z cyclic_ ']'
309
+ + '[' -z '1 { print $8, $1, $2, $10, $3 }' ']'
310
+ + 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
311
+ + awk -F, -v OFS=, '1 { print $8, $1, $2, $10, $3 }'
312
+ ++ zcat /nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz
313
+ + gzip --best
314
+ + schemist convert -f csv --column cysteine_to_N_cyclization --to id inchikey scaffold mwt clogp tpsa --prefix cyclic_ --options prefix=SCB-
315
+ ++ head -n1
316
+ ++ tr ' ' ,
317
+ 🚀 Converting between string representations with the following parameters:
318
+ subcommand: convert
319
+ output: <_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>
320
+ format: csv
321
+ input: <_io.TextIOWrapper name='<stdin>' mode='r' encoding='utf-8'>
322
+ representation: SMILES
323
+ column: cysteine_to_N_cyclization
324
+ prefix: cyclic_
325
+ to: ['id', 'inchikey', 'scaffold', 'mwt', 'clogp', 'tpsa']
326
+ options: ['prefix=SCB-']
327
+ func: <function _convert at 0x7f2099aeb240>
328
+
329
+ Error counts:
330
+ cyclic_id: 0
331
+ cyclic_inchikey: 0
332
+ cyclic_scaffold: 0
333
+ cyclic_mwt: 0
334
+ cyclic_clogp: 0
335
+ cyclic_tpsa: 0
336
+ ⏰ Completed process in 3:13:37.264983
337
+ + 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.csv.gz CHANGED
@@ -1,3 +1,3 @@
1
  version https://git-lfs.github.com/spec/v1
2
- oid sha256:fd4424cf71a1c2a569f3777329ede153e6af66307e226c17d2f1e4c471929953
3
- size 61925397
 
1
  version https://git-lfs.github.com/spec/v1
2
+ oid sha256:4f7a2f45c864c3f48009e5ffa565a2ca9d8ff6ab6723553e3a6c9d7bb59cfa9f
3
+ size 117603124
train/cyc-pep-6-12mer-70M_10.log ADDED
@@ -0,0 +1,337 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ + module purge
2
+ + '[' -z '' ']'
3
+ + case "$-" in
4
+ + __lmod_sh_dbg=x
5
+ + '[' -n x ']'
6
+ + set +x
7
+ Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output
8
+ Shell debugging restarted
9
+ + unset __lmod_sh_dbg
10
+ + return 0
11
+ + module load Anaconda3/2023.03
12
+ + '[' -z '' ']'
13
+ + case "$-" in
14
+ + __lmod_sh_dbg=x
15
+ + '[' -n x ']'
16
+ + set +x
17
+ Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output
18
+ Shell debugging restarted
19
+ + unset __lmod_sh_dbg
20
+ + return 0
21
+ + source /camp/home/johnsoe/.bashrc
22
+ ++ '[' '' = yes ']'
23
+ ++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '
24
+ +++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.bash hook
25
+ ++ __conda_setup='export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\''
26
+ export _CE_M='\'''\''
27
+ export _CE_CONDA='\'''\''
28
+ export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''
29
+
30
+ # Copyright (C) 2012 Anaconda, Inc
31
+ # SPDX-License-Identifier: BSD-3-Clause
32
+ __conda_exe() (
33
+ "$CONDA_EXE" $_CE_M $_CE_CONDA "$@"
34
+ )
35
+
36
+ __conda_hashr() {
37
+ if [ -n "${ZSH_VERSION:+x}" ]; then
38
+ \rehash
39
+ elif [ -n "${POSH_VERSION:+x}" ]; then
40
+ : # pass
41
+ else
42
+ \hash -r
43
+ fi
44
+ }
45
+
46
+ __conda_activate() {
47
+ if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then
48
+ # Handle transition from shell activated with conda <= 4.3 to a subsequent activation
49
+ # after conda updated to >= 4.4. See issue #6173.
50
+ PS1="$CONDA_PS1_BACKUP"
51
+ \unset CONDA_PS1_BACKUP
52
+ fi
53
+ \local ask_conda
54
+ ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return
55
+ \eval "$ask_conda"
56
+ __conda_hashr
57
+ }
58
+
59
+ __conda_reactivate() {
60
+ \local ask_conda
61
+ ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return
62
+ \eval "$ask_conda"
63
+ __conda_hashr
64
+ }
65
+
66
+ conda() {
67
+ \local cmd="${1-__missing__}"
68
+ case "$cmd" in
69
+ activate|deactivate)
70
+ __conda_activate "$@"
71
+ ;;
72
+ install|update|upgrade|remove|uninstall)
73
+ __conda_exe "$@" || \return
74
+ __conda_reactivate
75
+ ;;
76
+ *)
77
+ __conda_exe "$@"
78
+ ;;
79
+ esac
80
+ }
81
+
82
+ if [ -z "${CONDA_SHLVL+x}" ]; then
83
+ \export CONDA_SHLVL=0
84
+ # In dev-mode CONDA_EXE is python.exe and on Windows
85
+ # it is in a different relative location to condabin.
86
+ if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then
87
+ PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}"
88
+ else
89
+ PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}"
90
+ fi
91
+ \export PATH
92
+
93
+ # We'\''re not allowing PS1 to be unbound. It must at least be set.
94
+ # However, we'\''re not exporting it, which can cause problems when starting a second shell
95
+ # via a first shell (i.e. starting zsh from bash).
96
+ if [ -z "${PS1+x}" ]; then
97
+ PS1=
98
+ fi
99
+ fi
100
+
101
+ conda activate base'
102
+ ++ '[' 0 -eq 0 ']'
103
+ ++ eval 'export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\''
104
+ export _CE_M='\'''\''
105
+ export _CE_CONDA='\'''\''
106
+ export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''
107
+
108
+ # Copyright (C) 2012 Anaconda, Inc
109
+ # SPDX-License-Identifier: BSD-3-Clause
110
+ __conda_exe() (
111
+ "$CONDA_EXE" $_CE_M $_CE_CONDA "$@"
112
+ )
113
+
114
+ __conda_hashr() {
115
+ if [ -n "${ZSH_VERSION:+x}" ]; then
116
+ \rehash
117
+ elif [ -n "${POSH_VERSION:+x}" ]; then
118
+ : # pass
119
+ else
120
+ \hash -r
121
+ fi
122
+ }
123
+
124
+ __conda_activate() {
125
+ if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then
126
+ # Handle transition from shell activated with conda <= 4.3 to a subsequent activation
127
+ # after conda updated to >= 4.4. See issue #6173.
128
+ PS1="$CONDA_PS1_BACKUP"
129
+ \unset CONDA_PS1_BACKUP
130
+ fi
131
+ \local ask_conda
132
+ ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return
133
+ \eval "$ask_conda"
134
+ __conda_hashr
135
+ }
136
+
137
+ __conda_reactivate() {
138
+ \local ask_conda
139
+ ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return
140
+ \eval "$ask_conda"
141
+ __conda_hashr
142
+ }
143
+
144
+ conda() {
145
+ \local cmd="${1-__missing__}"
146
+ case "$cmd" in
147
+ activate|deactivate)
148
+ __conda_activate "$@"
149
+ ;;
150
+ install|update|upgrade|remove|uninstall)
151
+ __conda_exe "$@" || \return
152
+ __conda_reactivate
153
+ ;;
154
+ *)
155
+ __conda_exe "$@"
156
+ ;;
157
+ esac
158
+ }
159
+
160
+ if [ -z "${CONDA_SHLVL+x}" ]; then
161
+ \export CONDA_SHLVL=0
162
+ # In dev-mode CONDA_EXE is python.exe and on Windows
163
+ # it is in a different relative location to condabin.
164
+ if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then
165
+ PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}"
166
+ else
167
+ PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}"
168
+ fi
169
+ \export PATH
170
+
171
+ # We'\''re not allowing PS1 to be unbound. It must at least be set.
172
+ # However, we'\''re not exporting it, which can cause problems when starting a second shell
173
+ # via a first shell (i.e. starting zsh from bash).
174
+ if [ -z "${PS1+x}" ]; then
175
+ PS1=
176
+ fi
177
+ fi
178
+
179
+ conda activate base'
180
+ +++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda
181
+ +++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda
182
+ +++ export _CE_M=
183
+ +++ _CE_M=
184
+ +++ export _CE_CONDA=
185
+ +++ _CE_CONDA=
186
+ +++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python
187
+ +++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python
188
+ +++ '[' -z x ']'
189
+ +++ conda activate base
190
+ +++ local cmd=activate
191
+ +++ case "$cmd" in
192
+ +++ __conda_activate activate base
193
+ +++ '[' -n '' ']'
194
+ +++ local ask_conda
195
+ ++++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '
196
+ ++++ __conda_exe shell.posix activate base
197
+ ++++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate base
198
+ +++ ask_conda='PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\''
199
+ export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\''
200
+ export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\''
201
+ export CONDA_SHLVL='\''6'\''
202
+ export CONDA_DEFAULT_ENV='\''base'\''
203
+ export CONDA_PROMPT_MODIFIER='\''(base) '\''
204
+ export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\''
205
+ export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\''
206
+ export _CE_M='\'''\''
207
+ export _CE_CONDA='\'''\''
208
+ export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'''
209
+ +++ eval 'PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\''
210
+ export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\''
211
+ export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\''
212
+ export CONDA_SHLVL='\''6'\''
213
+ export CONDA_DEFAULT_ENV='\''base'\''
214
+ export CONDA_PROMPT_MODIFIER='\''(base) '\''
215
+ export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\''
216
+ export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\''
217
+ export _CE_M='\'''\''
218
+ export _CE_CONDA='\'''\''
219
+ export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'''
220
+ ++++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '
221
+ ++++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin
222
+ ++++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin
223
+ ++++ export CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0
224
+ ++++ CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0
225
+ ++++ export CONDA_SHLVL=6
226
+ ++++ CONDA_SHLVL=6
227
+ ++++ export CONDA_DEFAULT_ENV=base
228
+ ++++ CONDA_DEFAULT_ENV=base
229
+ ++++ export 'CONDA_PROMPT_MODIFIER=(base) '
230
+ ++++ CONDA_PROMPT_MODIFIER='(base) '
231
+ ++++ export CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev
232
+ ++++ CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev
233
+ ++++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda
234
+ ++++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda
235
+ ++++ export _CE_M=
236
+ ++++ _CE_M=
237
+ ++++ export _CE_CONDA=
238
+ ++++ _CE_CONDA=
239
+ ++++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python
240
+ ++++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python
241
+ +++ __conda_hashr
242
+ +++ '[' -n '' ']'
243
+ +++ '[' -n '' ']'
244
+ +++ hash -r
245
+ ++ unset __conda_setup
246
+ + conda activate schemist-dev
247
+ + local cmd=activate
248
+ + case "$cmd" in
249
+ + __conda_activate activate schemist-dev
250
+ + '[' -n '' ']'
251
+ + local ask_conda
252
+ ++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '
253
+ ++ __conda_exe shell.posix activate schemist-dev
254
+ ++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate schemist-dev
255
+ + ask_conda='PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\''
256
+ export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\''
257
+ export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\''
258
+ export CONDA_SHLVL='\''7'\''
259
+ export CONDA_DEFAULT_ENV='\''schemist-dev'\''
260
+ export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\''
261
+ export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\''
262
+ export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\''
263
+ export _CE_M='\'''\''
264
+ export _CE_CONDA='\'''\''
265
+ export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'''
266
+ + eval 'PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\''
267
+ export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\''
268
+ export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\''
269
+ export CONDA_SHLVL='\''7'\''
270
+ export CONDA_DEFAULT_ENV='\''schemist-dev'\''
271
+ export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\''
272
+ export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\''
273
+ export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\''
274
+ export _CE_M='\'''\''
275
+ export _CE_CONDA='\'''\''
276
+ export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'''
277
+ ++ PS1='(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '
278
+ ++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin
279
+ ++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin
280
+ ++ export CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev
281
+ ++ CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev
282
+ ++ export CONDA_SHLVL=7
283
+ ++ CONDA_SHLVL=7
284
+ ++ export CONDA_DEFAULT_ENV=schemist-dev
285
+ ++ CONDA_DEFAULT_ENV=schemist-dev
286
+ ++ export 'CONDA_PROMPT_MODIFIER=(schemist-dev) '
287
+ ++ CONDA_PROMPT_MODIFIER='(schemist-dev) '
288
+ ++ export CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0
289
+ ++ CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0
290
+ ++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda
291
+ ++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda
292
+ ++ export _CE_M=
293
+ ++ _CE_M=
294
+ ++ export _CE_CONDA=
295
+ ++ _CE_CONDA=
296
+ ++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python
297
+ ++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python
298
+ + __conda_hashr
299
+ + '[' -n '' ']'
300
+ + '[' -n '' ']'
301
+ + hash -r
302
+ + CHUNK_HEAD_FILE=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz
303
+ + INPUT=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/train/cyc-pep-6-12mer-70M_10.csv
304
+ + COLUMN=cysteine_to_N_cyclization
305
+ + PREFIX=cyclic_
306
+ + AWK='1 { print $8, $1, $2, $10, $3 }'
307
+ + '[' -z cysteine_to_N_cyclization ']'
308
+ + '[' -z cyclic_ ']'
309
+ + '[' -z '1 { print $8, $1, $2, $10, $3 }' ']'
310
+ + 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
311
+ + awk -F, -v OFS=, '1 { print $8, $1, $2, $10, $3 }'
312
+ ++ zcat /nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz
313
+ + schemist convert -f csv --column cysteine_to_N_cyclization --to id inchikey scaffold mwt clogp tpsa --prefix cyclic_ --options prefix=SCB-
314
+ ++ head -n1
315
+ + gzip --best
316
+ ++ tr ' ' ,
317
+ 🚀 Converting between string representations with the following parameters:
318
+ subcommand: convert
319
+ output: <_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>
320
+ format: csv
321
+ input: <_io.TextIOWrapper name='<stdin>' mode='r' encoding='utf-8'>
322
+ representation: SMILES
323
+ column: cysteine_to_N_cyclization
324
+ prefix: cyclic_
325
+ to: ['id', 'inchikey', 'scaffold', 'mwt', 'clogp', 'tpsa']
326
+ options: ['prefix=SCB-']
327
+ func: <function _convert at 0x7f377f5ef240>
328
+
329
+ Error counts:
330
+ cyclic_id: 0
331
+ cyclic_inchikey: 0
332
+ cyclic_scaffold: 0
333
+ cyclic_mwt: 0
334
+ cyclic_clogp: 0
335
+ cyclic_tpsa: 0
336
+ ⏰ Completed process in 3:15:26.501328
337
+ + 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.csv.gz CHANGED
@@ -1,3 +1,3 @@
1
  version https://git-lfs.github.com/spec/v1
2
- oid sha256:753475102dd5334b0fe1e580afc1660e73674dad4d5240e142337b4814844fcf
3
- size 61923784
 
1
  version https://git-lfs.github.com/spec/v1
2
+ oid sha256:c7107dbca4e33cce6b922a562a44ebb3460b925265e7f82613935155e1be4743
3
+ size 117607437
train/cyc-pep-6-12mer-70M_11.log ADDED
@@ -0,0 +1,337 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ + module purge
2
+ + '[' -z '' ']'
3
+ + case "$-" in
4
+ + __lmod_sh_dbg=x
5
+ + '[' -n x ']'
6
+ + set +x
7
+ Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output
8
+ Shell debugging restarted
9
+ + unset __lmod_sh_dbg
10
+ + return 0
11
+ + module load Anaconda3/2023.03
12
+ + '[' -z '' ']'
13
+ + case "$-" in
14
+ + __lmod_sh_dbg=x
15
+ + '[' -n x ']'
16
+ + set +x
17
+ Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output
18
+ Shell debugging restarted
19
+ + unset __lmod_sh_dbg
20
+ + return 0
21
+ + source /camp/home/johnsoe/.bashrc
22
+ ++ '[' '' = yes ']'
23
+ ++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '
24
+ +++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.bash hook
25
+ ++ __conda_setup='export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\''
26
+ export _CE_M='\'''\''
27
+ export _CE_CONDA='\'''\''
28
+ export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''
29
+
30
+ # Copyright (C) 2012 Anaconda, Inc
31
+ # SPDX-License-Identifier: BSD-3-Clause
32
+ __conda_exe() (
33
+ "$CONDA_EXE" $_CE_M $_CE_CONDA "$@"
34
+ )
35
+
36
+ __conda_hashr() {
37
+ if [ -n "${ZSH_VERSION:+x}" ]; then
38
+ \rehash
39
+ elif [ -n "${POSH_VERSION:+x}" ]; then
40
+ : # pass
41
+ else
42
+ \hash -r
43
+ fi
44
+ }
45
+
46
+ __conda_activate() {
47
+ if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then
48
+ # Handle transition from shell activated with conda <= 4.3 to a subsequent activation
49
+ # after conda updated to >= 4.4. See issue #6173.
50
+ PS1="$CONDA_PS1_BACKUP"
51
+ \unset CONDA_PS1_BACKUP
52
+ fi
53
+ \local ask_conda
54
+ ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return
55
+ \eval "$ask_conda"
56
+ __conda_hashr
57
+ }
58
+
59
+ __conda_reactivate() {
60
+ \local ask_conda
61
+ ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return
62
+ \eval "$ask_conda"
63
+ __conda_hashr
64
+ }
65
+
66
+ conda() {
67
+ \local cmd="${1-__missing__}"
68
+ case "$cmd" in
69
+ activate|deactivate)
70
+ __conda_activate "$@"
71
+ ;;
72
+ install|update|upgrade|remove|uninstall)
73
+ __conda_exe "$@" || \return
74
+ __conda_reactivate
75
+ ;;
76
+ *)
77
+ __conda_exe "$@"
78
+ ;;
79
+ esac
80
+ }
81
+
82
+ if [ -z "${CONDA_SHLVL+x}" ]; then
83
+ \export CONDA_SHLVL=0
84
+ # In dev-mode CONDA_EXE is python.exe and on Windows
85
+ # it is in a different relative location to condabin.
86
+ if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then
87
+ PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}"
88
+ else
89
+ PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}"
90
+ fi
91
+ \export PATH
92
+
93
+ # We'\''re not allowing PS1 to be unbound. It must at least be set.
94
+ # However, we'\''re not exporting it, which can cause problems when starting a second shell
95
+ # via a first shell (i.e. starting zsh from bash).
96
+ if [ -z "${PS1+x}" ]; then
97
+ PS1=
98
+ fi
99
+ fi
100
+
101
+ conda activate base'
102
+ ++ '[' 0 -eq 0 ']'
103
+ ++ eval 'export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\''
104
+ export _CE_M='\'''\''
105
+ export _CE_CONDA='\'''\''
106
+ export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\''
107
+
108
+ # Copyright (C) 2012 Anaconda, Inc
109
+ # SPDX-License-Identifier: BSD-3-Clause
110
+ __conda_exe() (
111
+ "$CONDA_EXE" $_CE_M $_CE_CONDA "$@"
112
+ )
113
+
114
+ __conda_hashr() {
115
+ if [ -n "${ZSH_VERSION:+x}" ]; then
116
+ \rehash
117
+ elif [ -n "${POSH_VERSION:+x}" ]; then
118
+ : # pass
119
+ else
120
+ \hash -r
121
+ fi
122
+ }
123
+
124
+ __conda_activate() {
125
+ if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then
126
+ # Handle transition from shell activated with conda <= 4.3 to a subsequent activation
127
+ # after conda updated to >= 4.4. See issue #6173.
128
+ PS1="$CONDA_PS1_BACKUP"
129
+ \unset CONDA_PS1_BACKUP
130
+ fi
131
+ \local ask_conda
132
+ ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return
133
+ \eval "$ask_conda"
134
+ __conda_hashr
135
+ }
136
+
137
+ __conda_reactivate() {
138
+ \local ask_conda
139
+ ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return
140
+ \eval "$ask_conda"
141
+ __conda_hashr
142
+ }
143
+
144
+ conda() {
145
+ \local cmd="${1-__missing__}"
146
+ case "$cmd" in
147
+ activate|deactivate)
148
+ __conda_activate "$@"
149
+ ;;
150
+ install|update|upgrade|remove|uninstall)
151
+ __conda_exe "$@" || \return
152
+ __conda_reactivate
153
+ ;;
154
+ *)
155
+ __conda_exe "$@"
156
+ ;;
157
+ esac
158
+ }
159
+
160
+ if [ -z "${CONDA_SHLVL+x}" ]; then
161
+ \export CONDA_SHLVL=0
162
+ # In dev-mode CONDA_EXE is python.exe and on Windows
163
+ # it is in a different relative location to condabin.
164
+ if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then
165
+ PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}"
166
+ else
167
+ PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}"
168
+ fi
169
+ \export PATH
170
+
171
+ # We'\''re not allowing PS1 to be unbound. It must at least be set.
172
+ # However, we'\''re not exporting it, which can cause problems when starting a second shell
173
+ # via a first shell (i.e. starting zsh from bash).
174
+ if [ -z "${PS1+x}" ]; then
175
+ PS1=
176
+ fi
177
+ fi
178
+
179
+ conda activate base'
180
+ +++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda
181
+ +++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda
182
+ +++ export _CE_M=
183
+ +++ _CE_M=
184
+ +++ export _CE_CONDA=
185
+ +++ _CE_CONDA=
186
+ +++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python
187
+ +++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python
188
+ +++ '[' -z x ']'
189
+ +++ conda activate base
190
+ +++ local cmd=activate
191
+ +++ case "$cmd" in
192
+ +++ __conda_activate activate base
193
+ +++ '[' -n '' ']'
194
+ +++ local ask_conda
195
+ ++++ PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '
196
+ ++++ __conda_exe shell.posix activate base
197
+ ++++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate base
198
+ +++ ask_conda='PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\''
199
+ export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\''
200
+ export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\''
201
+ export CONDA_SHLVL='\''6'\''
202
+ export CONDA_DEFAULT_ENV='\''base'\''
203
+ export CONDA_PROMPT_MODIFIER='\''(base) '\''
204
+ export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\''
205
+ export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\''
206
+ export _CE_M='\'''\''
207
+ export _CE_CONDA='\'''\''
208
+ export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'''
209
+ +++ eval 'PS1='\''(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\''
210
+ export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\''
211
+ export CONDA_PREFIX='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\''
212
+ export CONDA_SHLVL='\''6'\''
213
+ export CONDA_DEFAULT_ENV='\''base'\''
214
+ export CONDA_PROMPT_MODIFIER='\''(base) '\''
215
+ export CONDA_PREFIX_5='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\''
216
+ export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\''
217
+ export _CE_M='\'''\''
218
+ export _CE_CONDA='\'''\''
219
+ export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'''
220
+ ++++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '
221
+ ++++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin
222
+ ++++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin
223
+ ++++ export CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0
224
+ ++++ CONDA_PREFIX=/camp/apps/eb/software/Anaconda3/2023.09-0
225
+ ++++ export CONDA_SHLVL=6
226
+ ++++ CONDA_SHLVL=6
227
+ ++++ export CONDA_DEFAULT_ENV=base
228
+ ++++ CONDA_DEFAULT_ENV=base
229
+ ++++ export 'CONDA_PROMPT_MODIFIER=(base) '
230
+ ++++ CONDA_PROMPT_MODIFIER='(base) '
231
+ ++++ export CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev
232
+ ++++ CONDA_PREFIX_5=/camp/home/johnsoe/.conda/envs/schemist-dev
233
+ ++++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda
234
+ ++++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda
235
+ ++++ export _CE_M=
236
+ ++++ _CE_M=
237
+ ++++ export _CE_CONDA=
238
+ ++++ _CE_CONDA=
239
+ ++++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python
240
+ ++++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python
241
+ +++ __conda_hashr
242
+ +++ '[' -n '' ']'
243
+ +++ '[' -n '' ']'
244
+ +++ hash -r
245
+ ++ unset __conda_setup
246
+ + conda activate schemist-dev
247
+ + local cmd=activate
248
+ + case "$cmd" in
249
+ + __conda_activate activate schemist-dev
250
+ + '[' -n '' ']'
251
+ + local ask_conda
252
+ ++ PS1='(base) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '
253
+ ++ __conda_exe shell.posix activate schemist-dev
254
+ ++ /camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda shell.posix activate schemist-dev
255
+ + ask_conda='PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\''
256
+ export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\''
257
+ export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\''
258
+ export CONDA_SHLVL='\''7'\''
259
+ export CONDA_DEFAULT_ENV='\''schemist-dev'\''
260
+ export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\''
261
+ export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\''
262
+ export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\''
263
+ export _CE_M='\'''\''
264
+ export _CE_CONDA='\'''\''
265
+ export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'''
266
+ + eval 'PS1='\''(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '\''
267
+ export PATH='\''/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin'\''
268
+ export CONDA_PREFIX='\''/camp/home/johnsoe/.conda/envs/schemist-dev'\''
269
+ export CONDA_SHLVL='\''7'\''
270
+ export CONDA_DEFAULT_ENV='\''schemist-dev'\''
271
+ export CONDA_PROMPT_MODIFIER='\''(schemist-dev) '\''
272
+ export CONDA_PREFIX_6='\''/camp/apps/eb/software/Anaconda3/2023.09-0'\''
273
+ export CONDA_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda'\''
274
+ export _CE_M='\'''\''
275
+ export _CE_CONDA='\'''\''
276
+ export CONDA_PYTHON_EXE='\''/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python'\'''
277
+ ++ PS1='(schemist-dev) ${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '
278
+ ++ export PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin
279
+ ++ PATH=/camp/apps/eb/software/Anaconda3/2023.03:/camp/apps/eb/software/Anaconda3/2023.03/sbin:/camp/apps/eb/software/Anaconda3/2023.03/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-384ff7382de624fb94dbaf6da11977bba1ecd427/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/schemist-dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/bin
280
+ ++ export CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev
281
+ ++ CONDA_PREFIX=/camp/home/johnsoe/.conda/envs/schemist-dev
282
+ ++ export CONDA_SHLVL=7
283
+ ++ CONDA_SHLVL=7
284
+ ++ export CONDA_DEFAULT_ENV=schemist-dev
285
+ ++ CONDA_DEFAULT_ENV=schemist-dev
286
+ ++ export 'CONDA_PROMPT_MODIFIER=(schemist-dev) '
287
+ ++ CONDA_PROMPT_MODIFIER='(schemist-dev) '
288
+ ++ export CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0
289
+ ++ CONDA_PREFIX_6=/camp/apps/eb/software/Anaconda3/2023.09-0
290
+ ++ export CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda
291
+ ++ CONDA_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/conda
292
+ ++ export _CE_M=
293
+ ++ _CE_M=
294
+ ++ export _CE_CONDA=
295
+ ++ _CE_CONDA=
296
+ ++ export CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python
297
+ ++ CONDA_PYTHON_EXE=/camp/apps/eb/software/Anaconda3/2023.09-0/bin/python
298
+ + __conda_hashr
299
+ + '[' -n '' ']'
300
+ + '[' -n '' ']'
301
+ + hash -r
302
+ + CHUNK_HEAD_FILE=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz
303
+ + INPUT=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/cyc-pep-6-12mer-70M-2024/train/cyc-pep-6-12mer-70M_11.csv
304
+ + COLUMN=cysteine_to_N_cyclization
305
+ + PREFIX=cyclic_
306
+ + AWK='1 { print $8, $1, $2, $10, $3 }'
307
+ + '[' -z cysteine_to_N_cyclization ']'
308
+ + '[' -z cyclic_ ']'
309
+ + '[' -z '1 { print $8, $1, $2, $10, $3 }' ']'
310
+ + 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
311
+ + schemist convert -f csv --column cysteine_to_N_cyclization --to id inchikey scaffold mwt clogp tpsa --prefix cyclic_ --options prefix=SCB-
312
+ + gzip --best
313
+ + awk -F, -v OFS=, '1 { print $8, $1, $2, $10, $3 }'
314
+ ++ zcat /nemo/lab/johnsone/home/users/johnsoe/data/datasets/rapid_6-12b/240425_rapid_6-12.tsv.gz
315
+ ++ tr ' ' ,
316
+ ++ head -n1
317
+ 🚀 Converting between string representations with the following parameters:
318
+ subcommand: convert
319
+ output: <_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>
320
+ format: csv
321
+ input: <_io.TextIOWrapper name='<stdin>' mode='r' encoding='utf-8'>
322
+ representation: SMILES
323
+ column: cysteine_to_N_cyclization
324
+ prefix: cyclic_
325
+ to: ['id', 'inchikey', 'scaffold', 'mwt', 'clogp', 'tpsa']
326
+ options: ['prefix=SCB-']
327
+ func: <function _convert at 0x7f9298a7f240>
328
+
329
+ Error counts:
330
+ cyclic_id: 0
331
+ cyclic_inchikey: 0
332
+ cyclic_scaffold: 0
333
+ cyclic_mwt: 0
334
+ cyclic_clogp: 0
335
+ cyclic_tpsa: 0
336
+ ⏰ Completed process in 3:15:54.052880
337
+ + 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.csv.gz CHANGED
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