Initial upload

20241101_peptides_6-12x100M_l-10_n-100000000_slice-100000000-101000000.log

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+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 <http://gnu.org/licenses/gpl.html>
+
+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 .
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+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='<stdout>' mode='w' encoding='utf-8'>
+	format: None
+	input: <_io.TextIOWrapper name='<stdin>' 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: <function _split at 0x7f95827af4c0>
+🚀 Reacting peptides with the following parameters:
+	subcommand: react
+	output: <_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>
+	format: None
+	input: <_io.TextIOWrapper name='<stdin>' mode='r' encoding='utf-8'>
+	representation: SMILES
+	column: SMILES
+	name: None
+	reaction: ['cysteine_to_N_cyclization']
+	func: <function _react at 0x7fd3c2bcf9c0>
+🚀 Enumerating peptides with the following parameters:
+	subcommand: enumerate
+	output: <_io.TextIOWrapper name='<stdout>' 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: <function _enum at 0x7fbfdb37b880>
+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='<stdout>' mode='w' encoding='utf-8'>
+	format: None
+	input: <_io.TextIOWrapper name='<stdin>' mode='r' encoding='utf-8'>
+	representation: SMILES
+	column: cysteine_to_N_cyclization
+	prefix: cyclic_
+	to: ['id', 'inchikey', 'scaffold', 'mwt', 'clogp', 'tpsa']
+	options: ['prefix=SCB-']
+	func: <function _convert at 0x7f7703877240>
+🚀 Converting between string representations with the following parameters:
+	subcommand: convert
+	output: <_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>
+	format: None
+	input: <_io.TextIOWrapper name='<stdin>' mode='r' encoding='utf-8'>
+	representation: SMILES
+	column: SMILES
+	prefix: linear_
+	to: ['id', 'inchikey', 'scaffold', 'mwt', 'clogp', 'tpsa']
+	options: ['prefix=SCB-']
+	func: <function _convert at 0x7fa10f0ef240>
+
+Enumerated peptides:
+	Number of peptides: 51
+Conversion errors:
+	SMILES: 0
+⏰ Completed process in 0:02:48.599034
+
+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
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+Error counts:
+	cysteine_to_N_cyclization: 0
+⏰ Completed process in 0:02:49.912195
+
+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
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+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
+