Fri 1 Nov 16:08:12 GMT 2024 > Generating peptides on cn076 GNU bash, version 4.4.20(1)-release (x86_64-redhat-linux-gnu) Copyright (C) 2016 Free Software Foundation, Inc. License GPLv3+: GNU GPL version 3 or later This is free software; you are free to change and redistribute it. There is NO WARRANTY, to the extent permitted by law. Fri 1 Nov 16:08:12 GMT 2024 > Running /camp/apps/eb/software/Anaconda3/2023.03/bin/python : Python 3.10.10 Fri 1 Nov 16:08:12 GMT 2024 > Using Conda from . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Fri 1 Nov 16:08:12 GMT 2024 > Seed = 1; length = 10; max. number = 100000000; slice = 100000000 to 101000000; output dir. = 20241101_peptides_6-12x100M Fri 1 Nov 16:08:12 GMT 2024 > There are 10240000000000 peptides of length 10; generating 100000000 (0.000976563 %) Fri 1 Nov 16:08:12 GMT 2024 > Saving a slice to 20241101_peptides_6-12x100M/peptides_length-10_n-100000000_slice-100000000-101000000.csv.gz... + schemist enumerate --seed 1 --max-length 10 --prefix GY --suffix CGSGSGS --number 9.76563e-06 --slice 100000000 101000000 + schemist convert --column cysteine_to_N_cyclization --to id inchikey scaffold mwt clogp tpsa --prefix cyclic_ --options prefix=SCB- + tr ' ' , + schemist react --column SMILES --reaction cysteine_to_N_cyclization + schemist split --type random --train 0.7 --test 0.15 --column cysteine_to_N_cyclization --seed 1 + gzip --best + schemist convert --column SMILES --to id inchikey scaffold mwt clogp tpsa --prefix linear_ --options prefix=SCB- 🚀 Splitting table with the following parameters: subcommand: split output: <_io.TextIOWrapper name='' mode='w' encoding='utf-8'> format: None input: <_io.TextIOWrapper name='' mode='r' encoding='utf-8'> representation: SMILES column: cysteine_to_N_cyclization prefix: None type: random train: 0.7 test: 0.15 seed: 1 func: 🚀 Reacting peptides with the following parameters: subcommand: react output: <_io.TextIOWrapper name='' mode='w' encoding='utf-8'> format: None input: <_io.TextIOWrapper name='' mode='r' encoding='utf-8'> representation: SMILES column: SMILES name: None reaction: ['cysteine_to_N_cyclization'] func: 🚀 Enumerating peptides with the following parameters: subcommand: enumerate output: <_io.TextIOWrapper name='' mode='w' encoding='utf-8'> format: None to: SMILES options: None alphabet: GALVITSMCPFYWHKRDENQ max_length: 10 min_length: None number: 9.76563e-06 slice: ['100000000', '101000000'] seed: 1 prefix: GY suffix: CGSGSGS type: aa d_aa_only: False include_d_aa: False func: Sampling 100000051 (0.000976562998046875 %) peptides from length 10 to 10 (10240000000000 combinations). Probability of collision if drawing randomly is 1.0, with 976.9924758407456 (0.000976991977574837 %) collisions on average. > Executing naive sampling. 🚀 Converting between string representations with the following parameters: subcommand: convert output: <_io.TextIOWrapper name='' mode='w' encoding='utf-8'> format: None input: <_io.TextIOWrapper name='' mode='r' encoding='utf-8'> representation: SMILES column: cysteine_to_N_cyclization prefix: cyclic_ to: ['id', 'inchikey', 'scaffold', 'mwt', 'clogp', 'tpsa'] options: ['prefix=SCB-'] func: 🚀 Converting between string representations with the following parameters: subcommand: convert output: <_io.TextIOWrapper name='' mode='w' encoding='utf-8'> format: None input: <_io.TextIOWrapper name='' mode='r' encoding='utf-8'> representation: SMILES column: SMILES prefix: linear_ to: ['id', 'inchikey', 'scaffold', 'mwt', 'clogp', 'tpsa'] options: ['prefix=SCB-'] func: 0it [00:00, ?it/s] 1it [02:48, 168.59s/it] 1it [02:48, 168.59s/it] Enumerated peptides: Number of peptides: 51 Conversion errors: SMILES: 0 ⏰ Completed process in 0:02:48.599034 0it [00:00, ?it/s] 1it [00:00, 1.88it/s] 1it [00:00, 1.88it/s] Error counts: linear_id: 0 linear_inchikey: 0 linear_scaffold: 0 linear_mwt: 0 linear_clogp: 0 linear_tpsa: 0 ⏰ Completed process in 0:02:49.321494 0it [00:00, ?it/s] 1it [00:00, 2.38it/s] 1it [00:00, 2.37it/s] Error counts: cysteine_to_N_cyclization: 0 ⏰ Completed process in 0:02:49.912195 0it [00:00, ?it/s] 1it [00:00, 1.81it/s] 1it [00:00, 1.81it/s] Error counts: cyclic_id: 0 cyclic_inchikey: 0 cyclic_scaffold: 0 cyclic_mwt: 0 cyclic_clogp: 0 cyclic_tpsa: 0 ⏰ Completed process in 0:02:50.627683 0it [00:00, ?it/s] 1it [00:00, 152.87it/s] Split counts: train: 35 test: 10 validation: 6 ⏰ Completed process in 0:02:50.828585 ++ date + echo 'Fri 1 Nov 16:11:11 GMT 2024 :: 20241101_peptides_6-12x100M/peptides_length-10_n-100000000_slice-100000000-101000000.csv.gz' + AWK_SCRIPT='NR == 1 { n=split($0,h); for(i=1;i<=n;i++) col[h[i]]=i; print $0 }; ( NR > 1 && $col[c1] == "True" ) { print $0 }' + for split in train test validation ++ dirname 20241101_peptides_6-12x100M/peptides_length-10_n-100000000_slice-100000000-101000000.csv.gz + split_dir=20241101_peptides_6-12x100M/train ++ basename 20241101_peptides_6-12x100M/peptides_length-10_n-100000000_slice-100000000-101000000.csv.gz .csv.gz + split_file=20241101_peptides_6-12x100M/train/peptides_length-10_n-100000000_slice-100000000-101000000.csv.gz + mkdir -p 20241101_peptides_6-12x100M/train ++ date + echo 'Fri 1 Nov 16:11:11 GMT 2024 :: Saving train...' Fri 1 Nov 16:11:11 GMT 2024 :: Saving train... + zcat 20241101_peptides_6-12x100M/peptides_length-10_n-100000000_slice-100000000-101000000.csv.gz + gzip --best + awk -F, -v OFS=, -v c1=is_train 'NR == 1 { n=split($0,h); for(i=1;i<=n;i++) col[h[i]]=i; print $0 }; ( NR > 1 && $col[c1] == "True" ) { print $0 }' ++ date + echo 'Fri 1 Nov 16:11:11 GMT 2024 :: 20241101_peptides_6-12x100M/train/peptides_length-10_n-100000000_slice-100000000-101000000.csv.gz' + for split in train test validation ++ dirname 20241101_peptides_6-12x100M/peptides_length-10_n-100000000_slice-100000000-101000000.csv.gz + split_dir=20241101_peptides_6-12x100M/test ++ basename 20241101_peptides_6-12x100M/peptides_length-10_n-100000000_slice-100000000-101000000.csv.gz .csv.gz + split_file=20241101_peptides_6-12x100M/test/peptides_length-10_n-100000000_slice-100000000-101000000.csv.gz + mkdir -p 20241101_peptides_6-12x100M/test ++ date + echo 'Fri 1 Nov 16:11:11 GMT 2024 :: Saving test...' Fri 1 Nov 16:11:11 GMT 2024 :: Saving test... + zcat 20241101_peptides_6-12x100M/peptides_length-10_n-100000000_slice-100000000-101000000.csv.gz + gzip --best + awk -F, -v OFS=, -v c1=is_test 'NR == 1 { n=split($0,h); for(i=1;i<=n;i++) col[h[i]]=i; print $0 }; ( NR > 1 && $col[c1] == "True" ) { print $0 }' ++ date + echo 'Fri 1 Nov 16:11:11 GMT 2024 :: 20241101_peptides_6-12x100M/test/peptides_length-10_n-100000000_slice-100000000-101000000.csv.gz' + for split in train test validation ++ dirname 20241101_peptides_6-12x100M/peptides_length-10_n-100000000_slice-100000000-101000000.csv.gz + split_dir=20241101_peptides_6-12x100M/validation ++ basename 20241101_peptides_6-12x100M/peptides_length-10_n-100000000_slice-100000000-101000000.csv.gz .csv.gz + split_file=20241101_peptides_6-12x100M/validation/peptides_length-10_n-100000000_slice-100000000-101000000.csv.gz + mkdir -p 20241101_peptides_6-12x100M/validation ++ date + echo 'Fri 1 Nov 16:11:11 GMT 2024 :: Saving validation...' Fri 1 Nov 16:11:11 GMT 2024 :: Saving validation... + zcat 20241101_peptides_6-12x100M/peptides_length-10_n-100000000_slice-100000000-101000000.csv.gz + gzip --best + awk -F, -v OFS=, -v c1=is_validation 'NR == 1 { n=split($0,h); for(i=1;i<=n;i++) col[h[i]]=i; print $0 }; ( NR > 1 && $col[c1] == "True" ) { print $0 }' ++ date + echo 'Fri 1 Nov 16:11:11 GMT 2024 :: 20241101_peptides_6-12x100M/validation/peptides_length-10_n-100000000_slice-100000000-101000000.csv.gz' + '[' -e 20241101_peptides_6-12x100M/validation/peptides_length-10_n-100000000_slice-100000000-101000000.csv.gz.success ']' + rm 20241101_peptides_6-12x100M/peptides_length-10_n-100000000_slice-100000000-101000000.csv.gz 20241101_peptides_6-12x100M/peptides_length-10_n-100000000_slice-100000000-101000000.csv.gz.success + set +x Fri 1 Nov 16:11:11 GMT 2024 > Peptide generation complete