Include full dataset with scaffold split (#6)

- Add logs and all with scaffold split (f054511e67dc1beae433c95982f6e9a06a5eba90)

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build.log

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++ DATA=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/spark-mic_cleaned.csv
++ DATA_OUTPUT_DIR=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt
++ FEATURE=smiles
++ LABEL=pmic
++ python -m venv .schemist
++ .schemist/bin/pip install 'schemist>=0.0.4.post1' pandas
+Requirement already satisfied: schemist>=0.0.4.post1 in ./.schemist/lib/python3.10/site-packages (0.0.4.post1)
+Requirement already satisfied: pandas in ./.schemist/lib/python3.10/site-packages (2.2.3)
+Requirement already satisfied: rdkit>=2022.09.5 in ./.schemist/lib/python3.10/site-packages (from schemist>=0.0.4.post1) (2024.9.6)
+Requirement already satisfied: carabiner-tools[pd]>=0.0.4 in ./.schemist/lib/python3.10/site-packages (from schemist>=0.0.4.post1) (0.0.4)
+Requirement already satisfied: requests in ./.schemist/lib/python3.10/site-packages (from schemist>=0.0.4.post1) (2.32.3)
+Requirement already satisfied: nemony in ./.schemist/lib/python3.10/site-packages (from schemist>=0.0.4.post1) (0.0.2)
+Requirement already satisfied: openpyxl==3.1.0 in ./.schemist/lib/python3.10/site-packages (from schemist>=0.0.4.post1) (3.1.0)
+Requirement already satisfied: descriptastorus>=2.7 in ./.schemist/lib/python3.10/site-packages (from schemist>=0.0.4.post1) (2.8.0)
+Requirement already satisfied: selfies in ./.schemist/lib/python3.10/site-packages (from schemist>=0.0.4.post1) (2.2.0)
+Requirement already satisfied: et-xmlfile in ./.schemist/lib/python3.10/site-packages (from openpyxl==3.1.0->schemist>=0.0.4.post1) (2.0.0)
+Requirement already satisfied: tzdata>=2022.7 in ./.schemist/lib/python3.10/site-packages (from pandas) (2025.2)
+Requirement already satisfied: python-dateutil>=2.8.2 in ./.schemist/lib/python3.10/site-packages (from pandas) (2.9.0.post0)
+Requirement already satisfied: pytz>=2020.1 in ./.schemist/lib/python3.10/site-packages (from pandas) (2025.2)
+Requirement already satisfied: numpy>=1.22.4 in ./.schemist/lib/python3.10/site-packages (from pandas) (2.2.4)
+Requirement already satisfied: tqdm in ./.schemist/lib/python3.10/site-packages (from carabiner-tools[pd]>=0.0.4->schemist>=0.0.4.post1) (4.67.1)
+Requirement already satisfied: scipy in ./.schemist/lib/python3.10/site-packages (from descriptastorus>=2.7->schemist>=0.0.4.post1) (1.15.2)
+Requirement already satisfied: pandas-flavor in ./.schemist/lib/python3.10/site-packages (from descriptastorus>=2.7->schemist>=0.0.4.post1) (0.6.0)
+Requirement already satisfied: six>=1.5 in ./.schemist/lib/python3.10/site-packages (from python-dateutil>=2.8.2->pandas) (1.17.0)
+Requirement already satisfied: Pillow in ./.schemist/lib/python3.10/site-packages (from rdkit>=2022.09.5->schemist>=0.0.4.post1) (11.1.0)
+Requirement already satisfied: pyyaml in ./.schemist/lib/python3.10/site-packages (from nemony->schemist>=0.0.4.post1) (6.0.2)
+Requirement already satisfied: idna<4,>=2.5 in ./.schemist/lib/python3.10/site-packages (from requests->schemist>=0.0.4.post1) (3.10)
+Requirement already satisfied: certifi>=2017.4.17 in ./.schemist/lib/python3.10/site-packages (from requests->schemist>=0.0.4.post1) (2025.1.31)
+Requirement already satisfied: charset-normalizer<4,>=2 in ./.schemist/lib/python3.10/site-packages (from requests->schemist>=0.0.4.post1) (3.4.1)
+Requirement already satisfied: urllib3<3,>=1.21.1 in ./.schemist/lib/python3.10/site-packages (from requests->schemist>=0.0.4.post1) (2.3.0)
+Requirement already satisfied: xarray in ./.schemist/lib/python3.10/site-packages (from pandas-flavor->descriptastorus>=2.7->schemist>=0.0.4.post1) (2025.3.0)
+Requirement already satisfied: packaging>=23.2 in ./.schemist/lib/python3.10/site-packages (from xarray->pandas-flavor->descriptastorus>=2.7->schemist>=0.0.4.post1) (24.2)
+
+[notice] A new release of pip is available: 23.0.1 -> 25.2
+[notice] To update, run: /nemo/lab/johnsone/home/users/johnsoe/data/datasets/.schemist/bin/python -m pip install --upgrade pip
++ source .schemist/bin/activate
+++ deactivate nondestructive
+++ '[' -n '' ']'
+++ '[' -n '' ']'
+++ hash -r
+++ '[' -n '' ']'
+++ unset VIRTUAL_ENV
+++ unset VIRTUAL_ENV_PROMPT
+++ '[' '!' nondestructive = nondestructive ']'
+++ case "$(uname)" in
++++ uname
+++ export VIRTUAL_ENV=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/.schemist
+++ VIRTUAL_ENV=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/.schemist
+++ _OLD_VIRTUAL_PATH=/camp/home/johnsoe/.conda/envs/duvida-dev2/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/share/Modules/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin
+++ PATH=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/.schemist/bin:/camp/home/johnsoe/.conda/envs/duvida-dev2/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/share/Modules/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin
+++ export PATH
+++ VIRTUAL_ENV_PROMPT='(.schemist) '
+++ export VIRTUAL_ENV_PROMPT
+++ '[' -n '' ']'
+++ '[' -z '' ']'
+++ _OLD_VIRTUAL_PS1=
+++ PS1='((.schemist) ) '
+++ export PS1
+++ hash -r
++ mkdir -p /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt
++ wt_data=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/spark-accumulation-wt.csv
++ sed '1s/^\xEF\xBB\xBF//' /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/spark-mic_cleaned.csv
++ filter_table accumulation_phenotype 'Wild type'
++ filter_table smiles '' , '!='
++ local col=accumulation_phenotype
++ local 'val=Wild type'
++ local sep=,
++ local op===
++ filter_table pmic '' , '!='
++ awk -F, -v field=accumulation_phenotype -v 'val=Wild type' 'NR == 1 { for (i = 1; i <= NF; i++) { if ($i==field) { col=i } }; print $0 } ((NR > 1) && ($col == val)) { print $0 }'
++ local col=smiles
++ pandas '.drop(columns=["pubmed_id"])'
++ local val=
++ local sep=,
++ local 'op=!='
++ awk -F, -v field=smiles -v val= 'NR == 1 { for (i = 1; i <= NF; i++) { if ($i==field) { col=i } }; print $0 } ((NR > 1) && ($col != val)) { print $0 }'
++ local col=pmic
++ local val=
++ local sep=,
++ local 'op=!='
++ schemist convert -2 id smiles inchikey scaffold mwt clogp tpsa -f CSV -x prefix=SCB-
++ schemist split -f CSV --type scaffold --train 0.7 --test 0.15 --seed 0 --output /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/spark-accumulation-wt.csv
++ awk -F, -v field=pmic -v val= 'NR == 1 { for (i = 1; i <= NF; i++) { if ($i==field) { col=i } }; print $0 } ((NR > 1) && ($col != val)) { print $0 }'
++ local 'cmd=.drop(columns=["pubmed_id"])'
++ local sep1=,
++ local idx=False
++ local sep2=,
++ python -c 'import sys; import pandas as pd; df = pd.read_csv(sys.stdin, sep=",", low_memory=False).drop(columns=["pubmed_id"]).to_csv(sys.stdout, index=False, sep=",")'
+🚀 Converting between string representations with the following parameters:
+	subcommand: convert
+	output: <_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>
+	format: CSV
+	input: <_io.TextIOWrapper name='<stdin>' mode='r' encoding='utf-8'>
+	representation: SMILES
+	column: smiles
+	prefix: None
+	to: ['id', 'smiles', 'inchikey', 'scaffold', 'mwt', 'clogp', 'tpsa']
+	options: ['prefix=SCB-']
+	func: <function _convert at 0x7f7416005f30>
+🚀 Splitting table with the following parameters:
+	subcommand: split
+	output: <_io.TextIOWrapper name='/nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/spark-accumulation-wt.csv' mode='w' encoding='UTF-8'>
+	format: CSV
+	input: <_io.TextIOWrapper name='<stdin>' mode='r' encoding='utf-8'>
+	representation: SMILES
+	column: smiles
+	prefix: None
+	type: scaffold
+	train: 0.7
+	test: 0.15
+	seed: 0
+	func: <function _split at 0x7f993b65e290>
+
+Error counts:
+	id: 0
+	smiles: 0
+	inchikey: 0
+	scaffold: 0
+	mwt: 0
+	clogp: 0
+	tpsa: 0
+⏰ Completed process in 0:01:48.736916
+
+
+Split counts:
+	train: 55181
+	test: 11825
+	validation: 11823
+⏰ Completed process in 0:03:07.793300
++ for split in "train" "test" "validation"
++ output_data_dir=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/all
++ mkdir -p /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/all
++ logger 'Processing /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/spark-accumulation-wt.csv train...'
++ local 'message=Processing /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/spark-accumulation-wt.csv train...'
+++ date
++ local '_date=Fri 17 Oct 16:30:03 BST 2025'
++ local 'prefix=Fri 17 Oct 16:30:03 BST 2025'
++ echo 'Fri 17 Oct 16:30:03 BST 2025 :: Processing /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/spark-accumulation-wt.csv train...'
+Fri 17 Oct 16:30:03 BST 2025 :: Processing /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/spark-accumulation-wt.csv train...
++ filter_table is_train True
++ local col=is_train
++ local val=True
++ local sep=,
++ local op===
++ awk -F, -v field=is_train -v val=True 'NR == 1 { for (i = 1; i <= NF; i++) { if ($i==field) { col=i } }; print $0 } ((NR > 1) && ($col == val)) { print $0 }'
++ gzip --best -f /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/all/scaffold-split-train.csv
++ for split in "train" "test" "validation"
++ output_data_dir=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/all
++ mkdir -p /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/all
++ logger 'Processing /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/spark-accumulation-wt.csv test...'
++ local 'message=Processing /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/spark-accumulation-wt.csv test...'
+++ date
++ local '_date=Fri 17 Oct 16:30:04 BST 2025'
++ local 'prefix=Fri 17 Oct 16:30:04 BST 2025'
++ echo 'Fri 17 Oct 16:30:04 BST 2025 :: Processing /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/spark-accumulation-wt.csv test...'
+Fri 17 Oct 16:30:04 BST 2025 :: Processing /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/spark-accumulation-wt.csv test...
++ filter_table is_test True
++ local col=is_test
++ local val=True
++ local sep=,
++ local op===
++ awk -F, -v field=is_test -v val=True 'NR == 1 { for (i = 1; i <= NF; i++) { if ($i==field) { col=i } }; print $0 } ((NR > 1) && ($col == val)) { print $0 }'
++ gzip --best -f /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/all/scaffold-split-test.csv
++ for split in "train" "test" "validation"
++ output_data_dir=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/all
++ mkdir -p /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/all
++ logger 'Processing /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/spark-accumulation-wt.csv validation...'
++ local 'message=Processing /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/spark-accumulation-wt.csv validation...'
+++ date
++ local '_date=Fri 17 Oct 16:30:05 BST 2025'
++ local 'prefix=Fri 17 Oct 16:30:05 BST 2025'
++ echo 'Fri 17 Oct 16:30:05 BST 2025 :: Processing /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/spark-accumulation-wt.csv validation...'
+Fri 17 Oct 16:30:05 BST 2025 :: Processing /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/spark-accumulation-wt.csv validation...
++ filter_table is_validation True
++ local col=is_validation
++ local val=True
++ local sep=,
++ local op===
++ awk -F, -v field=is_validation -v val=True 'NR == 1 { for (i = 1; i <= NF; i++) { if ($i==field) { col=i } }; print $0 } ((NR > 1) && ($col == val)) { print $0 }'
++ gzip --best -f /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/all/scaffold-split-validation.csv
++ unique_values /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/spark-accumulation-wt.csv species
++ local sep=,
+++ get_column_number species
+++ local sep=,
+++ head -n1
+++ tr , '
+'
+++ grep -n '^species$'
+++ cut -f 1 -d :
++ local field=11
++ tail -n+2 /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/spark-accumulation-wt.csv
++ cut -f11 -d,
++ sort -u
++ readarray -t unique_organisms
++ printf 'species_name\tn_rows\n'
++ echo 'Acinetobacter baumannii' 'Bacillus subtilis' 'Brucella abortus' 'Burkholderia thailandensis' 'Caulobacter crescentus' 'Enterobacter cloacae' 'Enterococcus faecalis' 'Escherichia coli' 'Francisella novicida' 'Francisella tularensis' 'Haemophilus influenzae' 'Klebsiella pneumoniae' 'Moraxella catarrhalis' 'Mycobacterium vaccae' 'Proteus hauseri' 'Proteus mirabilis' 'Pseudomonas aeruginosa' 'Pseudomonas fluorescens' 'Pseudomonas syringae' 'Salmonella enterica serovar Typhimurium' 'Staphylococcus aureus' 'Stenotrophomonas maltophilia' 'Streptococcus pneumoniae' 'Vibrio cholerae' 'Yersinia enterocolitica' 'Yersinia pestis' 'Yersinia pseudotuberculosis'
+Acinetobacter baumannii Bacillus subtilis Brucella abortus Burkholderia thailandensis Caulobacter crescentus Enterobacter cloacae Enterococcus faecalis Escherichia coli Francisella novicida Francisella tularensis Haemophilus influenzae Klebsiella pneumoniae Moraxella catarrhalis Mycobacterium vaccae Proteus hauseri Proteus mirabilis Pseudomonas aeruginosa Pseudomonas fluorescens Pseudomonas syringae Salmonella enterica serovar Typhimurium Staphylococcus aureus Stenotrophomonas maltophilia Streptococcus pneumoniae Vibrio cholerae Yersinia enterocolitica Yersinia pestis Yersinia pseudotuberculosis
++ for species in "${unique_organisms[@]}"
++ species_safe=Acinetobacter-baumannii
++ output_data_dir=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Acinetobacter-baumannii
++ logger 'Processing Acinetobacter baumannii...'
++ local 'message=Processing Acinetobacter baumannii...'
+++ date
++ local '_date=Fri 17 Oct 16:30:05 BST 2025'
++ local 'prefix=Fri 17 Oct 16:30:05 BST 2025'
++ echo 'Fri 17 Oct 16:30:05 BST 2025 :: Processing Acinetobacter baumannii...'
+Fri 17 Oct 16:30:05 BST 2025 :: Processing Acinetobacter baumannii...
++ mkdir -p /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Acinetobacter-baumannii
++ filter_table species 'Acinetobacter baumannii'
++ local col=species
++ local 'val=Acinetobacter baumannii'
++ local sep=,
++ local op===
++ awk -F, -v field=species -v 'val=Acinetobacter baumannii' 'NR == 1 { for (i = 1; i <= NF; i++) { if ($i==field) { col=i } }; print $0 } ((NR > 1) && ($col == val)) { print $0 }'
+++ tail -n+2 /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Acinetobacter-baumannii/full.csv
+++ wc -l
++ data_size=2148
++ logger 'Data for Acinetobacter baumannii has 2148 rows'
++ local 'message=Data for Acinetobacter baumannii has 2148 rows'
+++ date
++ local '_date=Fri 17 Oct 16:30:06 BST 2025'
++ local 'prefix=Fri 17 Oct 16:30:06 BST 2025'
++ echo 'Fri 17 Oct 16:30:06 BST 2025 :: Data for Acinetobacter baumannii has 2148 rows'
+Fri 17 Oct 16:30:06 BST 2025 :: Data for Acinetobacter baumannii has 2148 rows
++ '[' 2148 -gt 1000 ']'
++ printf 'Acinetobacter baumannii\t2148\n'
++ schemist split /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Acinetobacter-baumannii/full.csv --type scaffold --train 0.7 --test 0.15 --seed 0 --output /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Acinetobacter-baumannii/scaffold-split.csv
+🚀 Splitting table with the following parameters:
+	subcommand: split
+	output: <_io.TextIOWrapper name='/nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Acinetobacter-baumannii/scaffold-split.csv' mode='w' encoding='UTF-8'>
+	format: None
+	input: <_io.TextIOWrapper name='/nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Acinetobacter-baumannii/full.csv' mode='r' encoding='UTF-8'>
+	representation: SMILES
+	column: smiles
+	prefix: None
+	type: scaffold
+	train: 0.7
+	test: 0.15
+	seed: 0
+	func: <function _split at 0x7f4f1f396170>
+
+
+Split counts:
+	train: 1504
+	test: 323
+	validation: 321
+⏰ Completed process in 0:00:01.848351
++ for split in "train" "test" "validation"
++ filter_table is_train True
++ local col=is_train
++ local val=True
++ local sep=,
++ local op===
++ awk -F, -v field=is_train -v val=True 'NR == 1 { for (i = 1; i <= NF; i++) { if ($i==field) { col=i } }; print $0 } ((NR > 1) && ($col == val)) { print $0 }'
++ gzip --best -f /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Acinetobacter-baumannii/scaffold-split-train.csv
++ for split in "train" "test" "validation"
++ filter_table is_test True
++ local col=is_test
++ local val=True
++ local sep=,
++ local op===
++ awk -F, -v field=is_test -v val=True 'NR == 1 { for (i = 1; i <= NF; i++) { if ($i==field) { col=i } }; print $0 } ((NR > 1) && ($col == val)) { print $0 }'
++ gzip --best -f /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Acinetobacter-baumannii/scaffold-split-test.csv
++ for split in "train" "test" "validation"
++ filter_table is_validation True
++ local col=is_validation
++ local val=True
++ local sep=,
++ local op===
++ awk -F, -v field=is_validation -v val=True 'NR == 1 { for (i = 1; i <= NF; i++) { if ($i==field) { col=i } }; print $0 } ((NR > 1) && ($col == val)) { print $0 }'
++ gzip --best -f /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Acinetobacter-baumannii/scaffold-split-validation.csv
++ gzip --best -f /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Acinetobacter-baumannii/scaffold-split.csv
++ rm /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Acinetobacter-baumannii/full.csv
++ for species in "${unique_organisms[@]}"
++ species_safe=Bacillus-subtilis
++ output_data_dir=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Bacillus-subtilis
++ logger 'Processing Bacillus subtilis...'
++ local 'message=Processing Bacillus subtilis...'
+++ date
++ local '_date=Fri 17 Oct 16:30:26 BST 2025'
++ local 'prefix=Fri 17 Oct 16:30:26 BST 2025'
++ echo 'Fri 17 Oct 16:30:26 BST 2025 :: Processing Bacillus subtilis...'
+Fri 17 Oct 16:30:26 BST 2025 :: Processing Bacillus subtilis...
++ mkdir -p /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Bacillus-subtilis
++ filter_table species 'Bacillus subtilis'
++ local col=species
++ local 'val=Bacillus subtilis'
++ local sep=,
++ local op===
++ awk -F, -v field=species -v 'val=Bacillus subtilis' 'NR == 1 { for (i = 1; i <= NF; i++) { if ($i==field) { col=i } }; print $0 } ((NR > 1) && ($col == val)) { print $0 }'
+++ tail -n+2 /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Bacillus-subtilis/full.csv
+++ wc -l
++ data_size=13
++ logger 'Data for Bacillus subtilis has 13 rows'
++ local 'message=Data for Bacillus subtilis has 13 rows'
+++ date
++ local '_date=Fri 17 Oct 16:30:27 BST 2025'
++ local 'prefix=Fri 17 Oct 16:30:27 BST 2025'
++ echo 'Fri 17 Oct 16:30:27 BST 2025 :: Data for Bacillus subtilis has 13 rows'
+Fri 17 Oct 16:30:27 BST 2025 :: Data for Bacillus subtilis has 13 rows
++ '[' 13 -gt 1000 ']'
++ rm -r /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Bacillus-subtilis
++ for species in "${unique_organisms[@]}"
++ species_safe=Brucella-abortus
++ output_data_dir=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Brucella-abortus
++ logger 'Processing Brucella abortus...'
++ local 'message=Processing Brucella abortus...'
+++ date
++ local '_date=Fri 17 Oct 16:30:27 BST 2025'
++ local 'prefix=Fri 17 Oct 16:30:27 BST 2025'
++ echo 'Fri 17 Oct 16:30:27 BST 2025 :: Processing Brucella abortus...'
+Fri 17 Oct 16:30:27 BST 2025 :: Processing Brucella abortus...
++ mkdir -p /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Brucella-abortus
++ filter_table species 'Brucella abortus'
++ local col=species
++ local 'val=Brucella abortus'
++ local sep=,
++ local op===
++ awk -F, -v field=species -v 'val=Brucella abortus' 'NR == 1 { for (i = 1; i <= NF; i++) { if ($i==field) { col=i } }; print $0 } ((NR > 1) && ($col == val)) { print $0 }'
+++ tail -n+2 /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Brucella-abortus/full.csv
+++ wc -l
++ data_size=9946
++ logger 'Data for Brucella abortus has 9946 rows'
++ local 'message=Data for Brucella abortus has 9946 rows'
+++ date
++ local '_date=Fri 17 Oct 16:30:27 BST 2025'
++ local 'prefix=Fri 17 Oct 16:30:27 BST 2025'
++ echo 'Fri 17 Oct 16:30:27 BST 2025 :: Data for Brucella abortus has 9946 rows'
+Fri 17 Oct 16:30:27 BST 2025 :: Data for Brucella abortus has 9946 rows
++ '[' 9946 -gt 1000 ']'
++ printf 'Brucella abortus\t9946\n'
++ schemist split /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Brucella-abortus/full.csv --type scaffold --train 0.7 --test 0.15 --seed 0 --output /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Brucella-abortus/scaffold-split.csv
+🚀 Splitting table with the following parameters:
+	subcommand: split
+	output: <_io.TextIOWrapper name='/nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Brucella-abortus/scaffold-split.csv' mode='w' encoding='UTF-8'>
+	format: None
+	input: <_io.TextIOWrapper name='/nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Brucella-abortus/full.csv' mode='r' encoding='UTF-8'>
+	representation: SMILES
+	column: smiles
+	prefix: None
+	type: scaffold
+	train: 0.7
+	test: 0.15
+	seed: 0
+	func: <function _split at 0x7f8f43352290>
+
+
+Split counts:
+	train: 6963
+	test: 1492
+	validation: 1491
+⏰ Completed process in 0:00:06.049017
++ for split in "train" "test" "validation"
++ filter_table is_train True
++ local col=is_train
++ local val=True
++ local sep=,
++ local op===
++ awk -F, -v field=is_train -v val=True 'NR == 1 { for (i = 1; i <= NF; i++) { if ($i==field) { col=i } }; print $0 } ((NR > 1) && ($col == val)) { print $0 }'
++ gzip --best -f /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Brucella-abortus/scaffold-split-train.csv
++ for split in "train" "test" "validation"
++ filter_table is_test True
++ local col=is_test
++ local val=True
++ local sep=,
++ local op===
++ awk -F, -v field=is_test -v val=True 'NR == 1 { for (i = 1; i <= NF; i++) { if ($i==field) { col=i } }; print $0 } ((NR > 1) && ($col == val)) { print $0 }'
++ gzip --best -f /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Brucella-abortus/scaffold-split-test.csv
++ for split in "train" "test" "validation"
++ filter_table is_validation True
++ local col=is_validation
++ local val=True
++ local sep=,
++ local op===
++ awk -F, -v field=is_validation -v val=True 'NR == 1 { for (i = 1; i <= NF; i++) { if ($i==field) { col=i } }; print $0 } ((NR > 1) && ($col == val)) { print $0 }'
++ gzip --best -f /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Brucella-abortus/scaffold-split-validation.csv
++ gzip --best -f /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Brucella-abortus/scaffold-split.csv
++ rm /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Brucella-abortus/full.csv
++ for species in "${unique_organisms[@]}"
++ species_safe=Burkholderia-thailandensis
++ output_data_dir=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Burkholderia-thailandensis
++ logger 'Processing Burkholderia thailandensis...'
++ local 'message=Processing Burkholderia thailandensis...'
+++ date
++ local '_date=Fri 17 Oct 16:30:36 BST 2025'
++ local 'prefix=Fri 17 Oct 16:30:36 BST 2025'
++ echo 'Fri 17 Oct 16:30:36 BST 2025 :: Processing Burkholderia thailandensis...'
+Fri 17 Oct 16:30:36 BST 2025 :: Processing Burkholderia thailandensis...
++ mkdir -p /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Burkholderia-thailandensis
++ filter_table species 'Burkholderia thailandensis'
++ local col=species
++ local 'val=Burkholderia thailandensis'
++ local sep=,
++ local op===
++ awk -F, -v field=species -v 'val=Burkholderia thailandensis' 'NR == 1 { for (i = 1; i <= NF; i++) { if ($i==field) { col=i } }; print $0 } ((NR > 1) && ($col == val)) { print $0 }'
+++ tail -n+2 /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Burkholderia-thailandensis/full.csv
+++ wc -l
++ data_size=725
++ logger 'Data for Burkholderia thailandensis has 725 rows'
++ local 'message=Data for Burkholderia thailandensis has 725 rows'
+++ date
++ local '_date=Fri 17 Oct 16:30:37 BST 2025'
++ local 'prefix=Fri 17 Oct 16:30:37 BST 2025'
++ echo 'Fri 17 Oct 16:30:37 BST 2025 :: Data for Burkholderia thailandensis has 725 rows'
+Fri 17 Oct 16:30:37 BST 2025 :: Data for Burkholderia thailandensis has 725 rows
++ '[' 725 -gt 1000 ']'
++ rm -r /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Burkholderia-thailandensis
++ for species in "${unique_organisms[@]}"
++ species_safe=Caulobacter-crescentus
++ output_data_dir=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Caulobacter-crescentus
++ logger 'Processing Caulobacter crescentus...'
++ local 'message=Processing Caulobacter crescentus...'
+++ date
++ local '_date=Fri 17 Oct 16:30:37 BST 2025'
++ local 'prefix=Fri 17 Oct 16:30:37 BST 2025'
++ echo 'Fri 17 Oct 16:30:37 BST 2025 :: Processing Caulobacter crescentus...'
+Fri 17 Oct 16:30:37 BST 2025 :: Processing Caulobacter crescentus...
++ mkdir -p /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Caulobacter-crescentus
++ filter_table species 'Caulobacter crescentus'
++ local col=species
++ local 'val=Caulobacter crescentus'
++ local sep=,
++ local op===
++ awk -F, -v field=species -v 'val=Caulobacter crescentus' 'NR == 1 { for (i = 1; i <= NF; i++) { if ($i==field) { col=i } }; print $0 } ((NR > 1) && ($col == val)) { print $0 }'
+++ tail -n+2 /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Caulobacter-crescentus/full.csv
+++ wc -l
++ data_size=37
++ logger 'Data for Caulobacter crescentus has 37 rows'
++ local 'message=Data for Caulobacter crescentus has 37 rows'
+++ date
++ local '_date=Fri 17 Oct 16:30:37 BST 2025'
++ local 'prefix=Fri 17 Oct 16:30:37 BST 2025'
++ echo 'Fri 17 Oct 16:30:37 BST 2025 :: Data for Caulobacter crescentus has 37 rows'
+Fri 17 Oct 16:30:37 BST 2025 :: Data for Caulobacter crescentus has 37 rows
++ '[' 37 -gt 1000 ']'
++ rm -r /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Caulobacter-crescentus
++ for species in "${unique_organisms[@]}"
++ species_safe=Enterobacter-cloacae
++ output_data_dir=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Enterobacter-cloacae
++ logger 'Processing Enterobacter cloacae...'
++ local 'message=Processing Enterobacter cloacae...'
+++ date
++ local '_date=Fri 17 Oct 16:30:37 BST 2025'
++ local 'prefix=Fri 17 Oct 16:30:37 BST 2025'
++ echo 'Fri 17 Oct 16:30:37 BST 2025 :: Processing Enterobacter cloacae...'
+Fri 17 Oct 16:30:37 BST 2025 :: Processing Enterobacter cloacae...
++ mkdir -p /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Enterobacter-cloacae
++ filter_table species 'Enterobacter cloacae'
++ local col=species
++ local 'val=Enterobacter cloacae'
++ local sep=,
++ local op===
++ awk -F, -v field=species -v 'val=Enterobacter cloacae' 'NR == 1 { for (i = 1; i <= NF; i++) { if ($i==field) { col=i } }; print $0 } ((NR > 1) && ($col == val)) { print $0 }'
+++ tail -n+2 /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Enterobacter-cloacae/full.csv
+++ wc -l
++ data_size=101
++ logger 'Data for Enterobacter cloacae has 101 rows'
++ local 'message=Data for Enterobacter cloacae has 101 rows'
+++ date
++ local '_date=Fri 17 Oct 16:30:37 BST 2025'
++ local 'prefix=Fri 17 Oct 16:30:37 BST 2025'
++ echo 'Fri 17 Oct 16:30:37 BST 2025 :: Data for Enterobacter cloacae has 101 rows'
+Fri 17 Oct 16:30:37 BST 2025 :: Data for Enterobacter cloacae has 101 rows
++ '[' 101 -gt 1000 ']'
++ rm -r /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Enterobacter-cloacae
++ for species in "${unique_organisms[@]}"
++ species_safe=Enterococcus-faecalis
++ output_data_dir=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Enterococcus-faecalis
++ logger 'Processing Enterococcus faecalis...'
++ local 'message=Processing Enterococcus faecalis...'
+++ date
++ local '_date=Fri 17 Oct 16:30:37 BST 2025'
++ local 'prefix=Fri 17 Oct 16:30:37 BST 2025'
++ echo 'Fri 17 Oct 16:30:37 BST 2025 :: Processing Enterococcus faecalis...'
+Fri 17 Oct 16:30:37 BST 2025 :: Processing Enterococcus faecalis...
++ mkdir -p /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Enterococcus-faecalis
++ filter_table species 'Enterococcus faecalis'
++ local col=species
++ local 'val=Enterococcus faecalis'
++ local sep=,
++ local op===
++ awk -F, -v field=species -v 'val=Enterococcus faecalis' 'NR == 1 { for (i = 1; i <= NF; i++) { if ($i==field) { col=i } }; print $0 } ((NR > 1) && ($col == val)) { print $0 }'
+++ tail -n+2 /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Enterococcus-faecalis/full.csv
+++ wc -l
++ data_size=961
++ logger 'Data for Enterococcus faecalis has 961 rows'
++ local 'message=Data for Enterococcus faecalis has 961 rows'
+++ date
++ local '_date=Fri 17 Oct 16:30:37 BST 2025'
++ local 'prefix=Fri 17 Oct 16:30:37 BST 2025'
++ echo 'Fri 17 Oct 16:30:37 BST 2025 :: Data for Enterococcus faecalis has 961 rows'
+Fri 17 Oct 16:30:37 BST 2025 :: Data for Enterococcus faecalis has 961 rows
++ '[' 961 -gt 1000 ']'
++ rm -r /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Enterococcus-faecalis
++ for species in "${unique_organisms[@]}"
++ species_safe=Escherichia-coli
++ output_data_dir=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Escherichia-coli
++ logger 'Processing Escherichia coli...'
++ local 'message=Processing Escherichia coli...'
+++ date
++ local '_date=Fri 17 Oct 16:30:37 BST 2025'
++ local 'prefix=Fri 17 Oct 16:30:37 BST 2025'
++ echo 'Fri 17 Oct 16:30:37 BST 2025 :: Processing Escherichia coli...'
+Fri 17 Oct 16:30:37 BST 2025 :: Processing Escherichia coli...
++ mkdir -p /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Escherichia-coli
++ filter_table species 'Escherichia coli'
++ local col=species
++ local 'val=Escherichia coli'
++ local sep=,
++ local op===
++ awk -F, -v field=species -v 'val=Escherichia coli' 'NR == 1 { for (i = 1; i <= NF; i++) { if ($i==field) { col=i } }; print $0 } ((NR > 1) && ($col == val)) { print $0 }'
+++ tail -n+2 /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Escherichia-coli/full.csv
+++ wc -l
++ data_size=20451
++ logger 'Data for Escherichia coli has 20451 rows'
++ local 'message=Data for Escherichia coli has 20451 rows'
+++ date
++ local '_date=Fri 17 Oct 16:30:38 BST 2025'
++ local 'prefix=Fri 17 Oct 16:30:38 BST 2025'
++ echo 'Fri 17 Oct 16:30:38 BST 2025 :: Data for Escherichia coli has 20451 rows'
+Fri 17 Oct 16:30:38 BST 2025 :: Data for Escherichia coli has 20451 rows
++ '[' 20451 -gt 1000 ']'
++ printf 'Escherichia coli\t20451\n'
++ schemist split /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Escherichia-coli/full.csv --type scaffold --train 0.7 --test 0.15 --seed 0 --output /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Escherichia-coli/scaffold-split.csv
+🚀 Splitting table with the following parameters:
+	subcommand: split
+	output: <_io.TextIOWrapper name='/nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Escherichia-coli/scaffold-split.csv' mode='w' encoding='UTF-8'>
+	format: None
+	input: <_io.TextIOWrapper name='/nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Escherichia-coli/full.csv' mode='r' encoding='UTF-8'>
+	representation: SMILES
+	column: smiles
+	prefix: None
+	type: scaffold
+	train: 0.7
+	test: 0.15
+	seed: 0
+	func: <function _split at 0x7f239aaa2290>
+
+
+Split counts:
+	train: 14316
+	test: 3068
+	validation: 3067
+⏰ Completed process in 0:00:18.888909
++ for split in "train" "test" "validation"
++ filter_table is_train True
++ local col=is_train
++ local val=True
++ local sep=,
++ local op===
++ awk -F, -v field=is_train -v val=True 'NR == 1 { for (i = 1; i <= NF; i++) { if ($i==field) { col=i } }; print $0 } ((NR > 1) && ($col == val)) { print $0 }'
++ gzip --best -f /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Escherichia-coli/scaffold-split-train.csv
++ for split in "train" "test" "validation"
++ filter_table is_test True
++ local col=is_test
++ local val=True
++ local sep=,
++ local op===
++ awk -F, -v field=is_test -v val=True 'NR == 1 { for (i = 1; i <= NF; i++) { if ($i==field) { col=i } }; print $0 } ((NR > 1) && ($col == val)) { print $0 }'
++ gzip --best -f /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Escherichia-coli/scaffold-split-test.csv
++ for split in "train" "test" "validation"
++ filter_table is_validation True
++ local col=is_validation
++ local val=True
++ local sep=,
++ local op===
++ awk -F, -v field=is_validation -v val=True 'NR == 1 { for (i = 1; i <= NF; i++) { if ($i==field) { col=i } }; print $0 } ((NR > 1) && ($col == val)) { print $0 }'
++ gzip --best -f /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Escherichia-coli/scaffold-split-validation.csv
++ gzip --best -f /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Escherichia-coli/scaffold-split.csv
++ rm /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Escherichia-coli/full.csv
++ for species in "${unique_organisms[@]}"
++ species_safe=Francisella-novicida
++ output_data_dir=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Francisella-novicida
++ logger 'Processing Francisella novicida...'
++ local 'message=Processing Francisella novicida...'
+++ date
++ local '_date=Fri 17 Oct 16:31:00 BST 2025'
++ local 'prefix=Fri 17 Oct 16:31:00 BST 2025'
++ echo 'Fri 17 Oct 16:31:00 BST 2025 :: Processing Francisella novicida...'
+Fri 17 Oct 16:31:00 BST 2025 :: Processing Francisella novicida...
++ mkdir -p /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Francisella-novicida
++ filter_table species 'Francisella novicida'
++ local col=species
++ local 'val=Francisella novicida'
++ local sep=,
++ local op===
++ awk -F, -v field=species -v 'val=Francisella novicida' 'NR == 1 { for (i = 1; i <= NF; i++) { if ($i==field) { col=i } }; print $0 } ((NR > 1) && ($col == val)) { print $0 }'
+++ tail -n+2 /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Francisella-novicida/full.csv
+++ wc -l
++ data_size=4
++ logger 'Data for Francisella novicida has 4 rows'
++ local 'message=Data for Francisella novicida has 4 rows'
+++ date
++ local '_date=Fri 17 Oct 16:31:00 BST 2025'
++ local 'prefix=Fri 17 Oct 16:31:00 BST 2025'
++ echo 'Fri 17 Oct 16:31:00 BST 2025 :: Data for Francisella novicida has 4 rows'
+Fri 17 Oct 16:31:00 BST 2025 :: Data for Francisella novicida has 4 rows
++ '[' 4 -gt 1000 ']'
++ rm -r /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Francisella-novicida
++ for species in "${unique_organisms[@]}"
++ species_safe=Francisella-tularensis
++ output_data_dir=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Francisella-tularensis
++ logger 'Processing Francisella tularensis...'
++ local 'message=Processing Francisella tularensis...'
+++ date
++ local '_date=Fri 17 Oct 16:31:00 BST 2025'
++ local 'prefix=Fri 17 Oct 16:31:00 BST 2025'
++ echo 'Fri 17 Oct 16:31:00 BST 2025 :: Processing Francisella tularensis...'
+Fri 17 Oct 16:31:00 BST 2025 :: Processing Francisella tularensis...
++ mkdir -p /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Francisella-tularensis
++ filter_table species 'Francisella tularensis'
++ local col=species
++ local 'val=Francisella tularensis'
++ local sep=,
++ local op===
++ awk -F, -v field=species -v 'val=Francisella tularensis' 'NR == 1 { for (i = 1; i <= NF; i++) { if ($i==field) { col=i } }; print $0 } ((NR > 1) && ($col == val)) { print $0 }'
+++ tail -n+2 /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Francisella-tularensis/full.csv
+++ wc -l
++ data_size=9671
++ logger 'Data for Francisella tularensis has 9671 rows'
++ local 'message=Data for Francisella tularensis has 9671 rows'
+++ date
++ local '_date=Fri 17 Oct 16:31:00 BST 2025'
++ local 'prefix=Fri 17 Oct 16:31:00 BST 2025'
++ echo 'Fri 17 Oct 16:31:00 BST 2025 :: Data for Francisella tularensis has 9671 rows'
+Fri 17 Oct 16:31:00 BST 2025 :: Data for Francisella tularensis has 9671 rows
++ '[' 9671 -gt 1000 ']'
++ printf 'Francisella tularensis\t9671\n'
++ schemist split /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Francisella-tularensis/full.csv --type scaffold --train 0.7 --test 0.15 --seed 0 --output /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Francisella-tularensis/scaffold-split.csv
+🚀 Splitting table with the following parameters:
+	subcommand: split
+	output: <_io.TextIOWrapper name='/nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Francisella-tularensis/scaffold-split.csv' mode='w' encoding='UTF-8'>
+	format: None
+	input: <_io.TextIOWrapper name='/nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Francisella-tularensis/full.csv' mode='r' encoding='UTF-8'>
+	representation: SMILES
+	column: smiles
+	prefix: None
+	type: scaffold
+	train: 0.7
+	test: 0.15
+	seed: 0
+	func: <function _split at 0x7f381d022170>
+
+
+Split counts:
+	train: 6770
+	test: 1451
+	validation: 1450
+⏰ Completed process in 0:00:05.736728
++ for split in "train" "test" "validation"
++ filter_table is_train True
++ local col=is_train
++ local val=True
++ local sep=,
++ local op===
++ awk -F, -v field=is_train -v val=True 'NR == 1 { for (i = 1; i <= NF; i++) { if ($i==field) { col=i } }; print $0 } ((NR > 1) && ($col == val)) { print $0 }'
++ gzip --best -f /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Francisella-tularensis/scaffold-split-train.csv
++ for split in "train" "test" "validation"
++ filter_table is_test True
++ local col=is_test
++ local val=True
++ local sep=,
++ local op===
++ awk -F, -v field=is_test -v val=True 'NR == 1 { for (i = 1; i <= NF; i++) { if ($i==field) { col=i } }; print $0 } ((NR > 1) && ($col == val)) { print $0 }'
++ gzip --best -f /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Francisella-tularensis/scaffold-split-test.csv
++ for split in "train" "test" "validation"
++ filter_table is_validation True
++ local col=is_validation
++ local val=True
++ local sep=,
++ local op===
++ awk -F, -v field=is_validation -v val=True 'NR == 1 { for (i = 1; i <= NF; i++) { if ($i==field) { col=i } }; print $0 } ((NR > 1) && ($col == val)) { print $0 }'
++ gzip --best -f /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Francisella-tularensis/scaffold-split-validation.csv
++ gzip --best -f /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Francisella-tularensis/scaffold-split.csv
++ rm /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Francisella-tularensis/full.csv
++ for species in "${unique_organisms[@]}"
++ species_safe=Haemophilus-influenzae
++ output_data_dir=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Haemophilus-influenzae
++ logger 'Processing Haemophilus influenzae...'
++ local 'message=Processing Haemophilus influenzae...'
+++ date
++ local '_date=Fri 17 Oct 16:31:08 BST 2025'
++ local 'prefix=Fri 17 Oct 16:31:08 BST 2025'
++ echo 'Fri 17 Oct 16:31:08 BST 2025 :: Processing Haemophilus influenzae...'
+Fri 17 Oct 16:31:08 BST 2025 :: Processing Haemophilus influenzae...
++ mkdir -p /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Haemophilus-influenzae
++ filter_table species 'Haemophilus influenzae'
++ local col=species
++ local 'val=Haemophilus influenzae'
++ local sep=,
++ local op===
++ awk -F, -v field=species -v 'val=Haemophilus influenzae' 'NR == 1 { for (i = 1; i <= NF; i++) { if ($i==field) { col=i } }; print $0 } ((NR > 1) && ($col == val)) { print $0 }'
+++ tail -n+2 /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Haemophilus-influenzae/full.csv
+++ wc -l
++ data_size=27
++ logger 'Data for Haemophilus influenzae has 27 rows'
++ local 'message=Data for Haemophilus influenzae has 27 rows'
+++ date
++ local '_date=Fri 17 Oct 16:31:09 BST 2025'
++ local 'prefix=Fri 17 Oct 16:31:09 BST 2025'
++ echo 'Fri 17 Oct 16:31:09 BST 2025 :: Data for Haemophilus influenzae has 27 rows'
+Fri 17 Oct 16:31:09 BST 2025 :: Data for Haemophilus influenzae has 27 rows
++ '[' 27 -gt 1000 ']'
++ rm -r /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Haemophilus-influenzae
++ for species in "${unique_organisms[@]}"
++ species_safe=Klebsiella-pneumoniae
++ output_data_dir=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Klebsiella-pneumoniae
++ logger 'Processing Klebsiella pneumoniae...'
++ local 'message=Processing Klebsiella pneumoniae...'
+++ date
++ local '_date=Fri 17 Oct 16:31:09 BST 2025'
++ local 'prefix=Fri 17 Oct 16:31:09 BST 2025'
++ echo 'Fri 17 Oct 16:31:09 BST 2025 :: Processing Klebsiella pneumoniae...'
+Fri 17 Oct 16:31:09 BST 2025 :: Processing Klebsiella pneumoniae...
++ mkdir -p /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Klebsiella-pneumoniae
++ filter_table species 'Klebsiella pneumoniae'
++ local col=species
++ local 'val=Klebsiella pneumoniae'
++ local sep=,
++ local op===
++ awk -F, -v field=species -v 'val=Klebsiella pneumoniae' 'NR == 1 { for (i = 1; i <= NF; i++) { if ($i==field) { col=i } }; print $0 } ((NR > 1) && ($col == val)) { print $0 }'
+++ tail -n+2 /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Klebsiella-pneumoniae/full.csv
+++ wc -l
++ data_size=3920
++ logger 'Data for Klebsiella pneumoniae has 3920 rows'
++ local 'message=Data for Klebsiella pneumoniae has 3920 rows'
+++ date
++ local '_date=Fri 17 Oct 16:31:09 BST 2025'
++ local 'prefix=Fri 17 Oct 16:31:09 BST 2025'
++ echo 'Fri 17 Oct 16:31:09 BST 2025 :: Data for Klebsiella pneumoniae has 3920 rows'
+Fri 17 Oct 16:31:09 BST 2025 :: Data for Klebsiella pneumoniae has 3920 rows
++ '[' 3920 -gt 1000 ']'
++ printf 'Klebsiella pneumoniae\t3920\n'
++ schemist split /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Klebsiella-pneumoniae/full.csv --type scaffold --train 0.7 --test 0.15 --seed 0 --output /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Klebsiella-pneumoniae/scaffold-split.csv
+🚀 Splitting table with the following parameters:
+	subcommand: split
+	output: <_io.TextIOWrapper name='/nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Klebsiella-pneumoniae/scaffold-split.csv' mode='w' encoding='UTF-8'>
+	format: None
+	input: <_io.TextIOWrapper name='/nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Klebsiella-pneumoniae/full.csv' mode='r' encoding='UTF-8'>
+	representation: SMILES
+	column: smiles
+	prefix: None
+	type: scaffold
+	train: 0.7
+	test: 0.15
+	seed: 0
+	func: <function _split at 0x7f32d7e32170>
+
+
+Split counts:
+	train: 2744
+	test: 588
+	validation: 588
+⏰ Completed process in 0:00:02.797004
++ for split in "train" "test" "validation"
++ filter_table is_train True
++ local col=is_train
++ local val=True
++ local sep=,
++ local op===
++ awk -F, -v field=is_train -v val=True 'NR == 1 { for (i = 1; i <= NF; i++) { if ($i==field) { col=i } }; print $0 } ((NR > 1) && ($col == val)) { print $0 }'
++ gzip --best -f /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Klebsiella-pneumoniae/scaffold-split-train.csv
++ for split in "train" "test" "validation"
++ filter_table is_test True
++ local col=is_test
++ local val=True
++ local sep=,
++ local op===
++ awk -F, -v field=is_test -v val=True 'NR == 1 { for (i = 1; i <= NF; i++) { if ($i==field) { col=i } }; print $0 } ((NR > 1) && ($col == val)) { print $0 }'
++ gzip --best -f /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Klebsiella-pneumoniae/scaffold-split-test.csv
++ for split in "train" "test" "validation"
++ filter_table is_validation True
++ local col=is_validation
++ local val=True
++ local sep=,
++ local op===
++ awk -F, -v field=is_validation -v val=True 'NR == 1 { for (i = 1; i <= NF; i++) { if ($i==field) { col=i } }; print $0 } ((NR > 1) && ($col == val)) { print $0 }'
++ gzip --best -f /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Klebsiella-pneumoniae/scaffold-split-validation.csv
++ gzip --best -f /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Klebsiella-pneumoniae/scaffold-split.csv
++ rm /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Klebsiella-pneumoniae/full.csv
++ for species in "${unique_organisms[@]}"
++ species_safe=Moraxella-catarrhalis
++ output_data_dir=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Moraxella-catarrhalis
++ logger 'Processing Moraxella catarrhalis...'
++ local 'message=Processing Moraxella catarrhalis...'
+++ date
++ local '_date=Fri 17 Oct 16:31:13 BST 2025'
++ local 'prefix=Fri 17 Oct 16:31:13 BST 2025'
++ echo 'Fri 17 Oct 16:31:13 BST 2025 :: Processing Moraxella catarrhalis...'
+Fri 17 Oct 16:31:13 BST 2025 :: Processing Moraxella catarrhalis...
++ mkdir -p /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Moraxella-catarrhalis
++ filter_table species 'Moraxella catarrhalis'
++ local col=species
++ local 'val=Moraxella catarrhalis'
++ local sep=,
++ local op===
++ awk -F, -v field=species -v 'val=Moraxella catarrhalis' 'NR == 1 { for (i = 1; i <= NF; i++) { if ($i==field) { col=i } }; print $0 } ((NR > 1) && ($col == val)) { print $0 }'
+++ tail -n+2 /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Moraxella-catarrhalis/full.csv
+++ wc -l
++ data_size=2
++ logger 'Data for Moraxella catarrhalis has 2 rows'
++ local 'message=Data for Moraxella catarrhalis has 2 rows'
+++ date
++ local '_date=Fri 17 Oct 16:31:13 BST 2025'
++ local 'prefix=Fri 17 Oct 16:31:13 BST 2025'
++ echo 'Fri 17 Oct 16:31:13 BST 2025 :: Data for Moraxella catarrhalis has 2 rows'
+Fri 17 Oct 16:31:13 BST 2025 :: Data for Moraxella catarrhalis has 2 rows
++ '[' 2 -gt 1000 ']'
++ rm -r /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Moraxella-catarrhalis
++ for species in "${unique_organisms[@]}"
++ species_safe=Mycobacterium-vaccae
++ output_data_dir=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Mycobacterium-vaccae
++ logger 'Processing Mycobacterium vaccae...'
++ local 'message=Processing Mycobacterium vaccae...'
+++ date
++ local '_date=Fri 17 Oct 16:31:13 BST 2025'
++ local 'prefix=Fri 17 Oct 16:31:13 BST 2025'
++ echo 'Fri 17 Oct 16:31:13 BST 2025 :: Processing Mycobacterium vaccae...'
+Fri 17 Oct 16:31:13 BST 2025 :: Processing Mycobacterium vaccae...
++ mkdir -p /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Mycobacterium-vaccae
++ filter_table species 'Mycobacterium vaccae'
++ local col=species
++ local 'val=Mycobacterium vaccae'
++ local sep=,
++ local op===
++ awk -F, -v field=species -v 'val=Mycobacterium vaccae' 'NR == 1 { for (i = 1; i <= NF; i++) { if ($i==field) { col=i } }; print $0 } ((NR > 1) && ($col == val)) { print $0 }'
+++ tail -n+2 /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Mycobacterium-vaccae/full.csv
+++ wc -l
++ data_size=7
++ logger 'Data for Mycobacterium vaccae has 7 rows'
++ local 'message=Data for Mycobacterium vaccae has 7 rows'
+++ date
++ local '_date=Fri 17 Oct 16:31:14 BST 2025'
++ local 'prefix=Fri 17 Oct 16:31:14 BST 2025'
++ echo 'Fri 17 Oct 16:31:14 BST 2025 :: Data for Mycobacterium vaccae has 7 rows'
+Fri 17 Oct 16:31:14 BST 2025 :: Data for Mycobacterium vaccae has 7 rows
++ '[' 7 -gt 1000 ']'
++ rm -r /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Mycobacterium-vaccae
++ for species in "${unique_organisms[@]}"
++ species_safe=Proteus-hauseri
++ output_data_dir=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Proteus-hauseri
++ logger 'Processing Proteus hauseri...'
++ local 'message=Processing Proteus hauseri...'
+++ date
++ local '_date=Fri 17 Oct 16:31:14 BST 2025'
++ local 'prefix=Fri 17 Oct 16:31:14 BST 2025'
++ echo 'Fri 17 Oct 16:31:14 BST 2025 :: Processing Proteus hauseri...'
+Fri 17 Oct 16:31:14 BST 2025 :: Processing Proteus hauseri...
++ mkdir -p /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Proteus-hauseri
++ filter_table species 'Proteus hauseri'
++ local col=species
++ local 'val=Proteus hauseri'
++ local sep=,
++ local op===
++ awk -F, -v field=species -v 'val=Proteus hauseri' 'NR == 1 { for (i = 1; i <= NF; i++) { if ($i==field) { col=i } }; print $0 } ((NR > 1) && ($col == val)) { print $0 }'
+++ tail -n+2 /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Proteus-hauseri/full.csv
+++ wc -l
++ data_size=4
++ logger 'Data for Proteus hauseri has 4 rows'
++ local 'message=Data for Proteus hauseri has 4 rows'
+++ date
++ local '_date=Fri 17 Oct 16:31:14 BST 2025'
++ local 'prefix=Fri 17 Oct 16:31:14 BST 2025'
++ echo 'Fri 17 Oct 16:31:14 BST 2025 :: Data for Proteus hauseri has 4 rows'
+Fri 17 Oct 16:31:14 BST 2025 :: Data for Proteus hauseri has 4 rows
++ '[' 4 -gt 1000 ']'
++ rm -r /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Proteus-hauseri
++ for species in "${unique_organisms[@]}"
++ species_safe=Proteus-mirabilis
++ output_data_dir=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Proteus-mirabilis
++ logger 'Processing Proteus mirabilis...'
++ local 'message=Processing Proteus mirabilis...'
+++ date
++ local '_date=Fri 17 Oct 16:31:14 BST 2025'
++ local 'prefix=Fri 17 Oct 16:31:14 BST 2025'
++ echo 'Fri 17 Oct 16:31:14 BST 2025 :: Processing Proteus mirabilis...'
+Fri 17 Oct 16:31:14 BST 2025 :: Processing Proteus mirabilis...
++ mkdir -p /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Proteus-mirabilis
++ filter_table species 'Proteus mirabilis'
++ local col=species
++ local 'val=Proteus mirabilis'
++ local sep=,
++ local op===
++ awk -F, -v field=species -v 'val=Proteus mirabilis' 'NR == 1 { for (i = 1; i <= NF; i++) { if ($i==field) { col=i } }; print $0 } ((NR > 1) && ($col == val)) { print $0 }'
+++ tail -n+2 /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Proteus-mirabilis/full.csv
+++ wc -l
++ data_size=20
++ logger 'Data for Proteus mirabilis has 20 rows'
++ local 'message=Data for Proteus mirabilis has 20 rows'
+++ date
++ local '_date=Fri 17 Oct 16:31:14 BST 2025'
++ local 'prefix=Fri 17 Oct 16:31:14 BST 2025'
++ echo 'Fri 17 Oct 16:31:14 BST 2025 :: Data for Proteus mirabilis has 20 rows'
+Fri 17 Oct 16:31:14 BST 2025 :: Data for Proteus mirabilis has 20 rows
++ '[' 20 -gt 1000 ']'
++ rm -r /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Proteus-mirabilis
++ for species in "${unique_organisms[@]}"
++ species_safe=Pseudomonas-aeruginosa
++ output_data_dir=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Pseudomonas-aeruginosa
++ logger 'Processing Pseudomonas aeruginosa...'
++ local 'message=Processing Pseudomonas aeruginosa...'
+++ date
++ local '_date=Fri 17 Oct 16:31:14 BST 2025'
++ local 'prefix=Fri 17 Oct 16:31:14 BST 2025'
++ echo 'Fri 17 Oct 16:31:14 BST 2025 :: Processing Pseudomonas aeruginosa...'
+Fri 17 Oct 16:31:14 BST 2025 :: Processing Pseudomonas aeruginosa...
++ mkdir -p /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Pseudomonas-aeruginosa
++ filter_table species 'Pseudomonas aeruginosa'
++ local col=species
++ local 'val=Pseudomonas aeruginosa'
++ local sep=,
++ local op===
++ awk -F, -v field=species -v 'val=Pseudomonas aeruginosa' 'NR == 1 { for (i = 1; i <= NF; i++) { if ($i==field) { col=i } }; print $0 } ((NR > 1) && ($col == val)) { print $0 }'
+++ tail -n+2 /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Pseudomonas-aeruginosa/full.csv
+++ wc -l
++ data_size=15677
++ logger 'Data for Pseudomonas aeruginosa has 15677 rows'
++ local 'message=Data for Pseudomonas aeruginosa has 15677 rows'
+++ date
++ local '_date=Fri 17 Oct 16:31:14 BST 2025'
++ local 'prefix=Fri 17 Oct 16:31:14 BST 2025'
++ echo 'Fri 17 Oct 16:31:14 BST 2025 :: Data for Pseudomonas aeruginosa has 15677 rows'
+Fri 17 Oct 16:31:14 BST 2025 :: Data for Pseudomonas aeruginosa has 15677 rows
++ '[' 15677 -gt 1000 ']'
++ printf 'Pseudomonas aeruginosa\t15677\n'
++ schemist split /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Pseudomonas-aeruginosa/full.csv --type scaffold --train 0.7 --test 0.15 --seed 0 --output /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Pseudomonas-aeruginosa/scaffold-split.csv
+🚀 Splitting table with the following parameters:
+	subcommand: split
+	output: <_io.TextIOWrapper name='/nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Pseudomonas-aeruginosa/scaffold-split.csv' mode='w' encoding='UTF-8'>
+	format: None
+	input: <_io.TextIOWrapper name='/nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Pseudomonas-aeruginosa/full.csv' mode='r' encoding='UTF-8'>
+	representation: SMILES
+	column: smiles
+	prefix: None
+	type: scaffold
+	train: 0.7
+	test: 0.15
+	seed: 0
+	func: <function _split at 0x7f7a4f136170>
+
+
+Split counts:
+	train: 10974
+	test: 2352
+	validation: 2351
+⏰ Completed process in 0:00:11.118282
++ for split in "train" "test" "validation"
++ filter_table is_train True
++ local col=is_train
++ local val=True
++ local sep=,
++ local op===
++ awk -F, -v field=is_train -v val=True 'NR == 1 { for (i = 1; i <= NF; i++) { if ($i==field) { col=i } }; print $0 } ((NR > 1) && ($col == val)) { print $0 }'
++ gzip --best -f /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Pseudomonas-aeruginosa/scaffold-split-train.csv
++ for split in "train" "test" "validation"
++ filter_table is_test True
++ local col=is_test
++ local val=True
++ local sep=,
++ local op===
++ awk -F, -v field=is_test -v val=True 'NR == 1 { for (i = 1; i <= NF; i++) { if ($i==field) { col=i } }; print $0 } ((NR > 1) && ($col == val)) { print $0 }'
++ gzip --best -f /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Pseudomonas-aeruginosa/scaffold-split-test.csv
++ for split in "train" "test" "validation"
++ filter_table is_validation True
++ local col=is_validation
++ local val=True
++ local sep=,
++ local op===
++ awk -F, -v field=is_validation -v val=True 'NR == 1 { for (i = 1; i <= NF; i++) { if ($i==field) { col=i } }; print $0 } ((NR > 1) && ($col == val)) { print $0 }'
++ gzip --best -f /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Pseudomonas-aeruginosa/scaffold-split-validation.csv
++ gzip --best -f /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Pseudomonas-aeruginosa/scaffold-split.csv
++ rm /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Pseudomonas-aeruginosa/full.csv
++ for species in "${unique_organisms[@]}"
++ species_safe=Pseudomonas-fluorescens
++ output_data_dir=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Pseudomonas-fluorescens
++ logger 'Processing Pseudomonas fluorescens...'
++ local 'message=Processing Pseudomonas fluorescens...'
+++ date
++ local '_date=Fri 17 Oct 16:31:27 BST 2025'
++ local 'prefix=Fri 17 Oct 16:31:27 BST 2025'
++ echo 'Fri 17 Oct 16:31:27 BST 2025 :: Processing Pseudomonas fluorescens...'
+Fri 17 Oct 16:31:27 BST 2025 :: Processing Pseudomonas fluorescens...
++ mkdir -p /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Pseudomonas-fluorescens
++ filter_table species 'Pseudomonas fluorescens'
++ local col=species
++ local 'val=Pseudomonas fluorescens'
++ local sep=,
++ local op===
++ awk -F, -v field=species -v 'val=Pseudomonas fluorescens' 'NR == 1 { for (i = 1; i <= NF; i++) { if ($i==field) { col=i } }; print $0 } ((NR > 1) && ($col == val)) { print $0 }'
+++ tail -n+2 /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Pseudomonas-fluorescens/full.csv
+++ wc -l
++ data_size=219
++ logger 'Data for Pseudomonas fluorescens has 219 rows'
++ local 'message=Data for Pseudomonas fluorescens has 219 rows'
+++ date
++ local '_date=Fri 17 Oct 16:31:28 BST 2025'
++ local 'prefix=Fri 17 Oct 16:31:28 BST 2025'
++ echo 'Fri 17 Oct 16:31:28 BST 2025 :: Data for Pseudomonas fluorescens has 219 rows'
+Fri 17 Oct 16:31:28 BST 2025 :: Data for Pseudomonas fluorescens has 219 rows
++ '[' 219 -gt 1000 ']'
++ rm -r /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Pseudomonas-fluorescens
++ for species in "${unique_organisms[@]}"
++ species_safe=Pseudomonas-syringae
++ output_data_dir=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Pseudomonas-syringae
++ logger 'Processing Pseudomonas syringae...'
++ local 'message=Processing Pseudomonas syringae...'
+++ date
++ local '_date=Fri 17 Oct 16:31:28 BST 2025'
++ local 'prefix=Fri 17 Oct 16:31:28 BST 2025'
++ echo 'Fri 17 Oct 16:31:28 BST 2025 :: Processing Pseudomonas syringae...'
+Fri 17 Oct 16:31:28 BST 2025 :: Processing Pseudomonas syringae...
++ mkdir -p /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Pseudomonas-syringae
++ filter_table species 'Pseudomonas syringae'
++ local col=species
++ local 'val=Pseudomonas syringae'
++ local sep=,
++ local op===
++ awk -F, -v field=species -v 'val=Pseudomonas syringae' 'NR == 1 { for (i = 1; i <= NF; i++) { if ($i==field) { col=i } }; print $0 } ((NR > 1) && ($col == val)) { print $0 }'
+++ tail -n+2 /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Pseudomonas-syringae/full.csv
+++ wc -l
++ data_size=16
++ logger 'Data for Pseudomonas syringae has 16 rows'
++ local 'message=Data for Pseudomonas syringae has 16 rows'
+++ date
++ local '_date=Fri 17 Oct 16:31:28 BST 2025'
++ local 'prefix=Fri 17 Oct 16:31:28 BST 2025'
++ echo 'Fri 17 Oct 16:31:28 BST 2025 :: Data for Pseudomonas syringae has 16 rows'
+Fri 17 Oct 16:31:28 BST 2025 :: Data for Pseudomonas syringae has 16 rows
++ '[' 16 -gt 1000 ']'
++ rm -r /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Pseudomonas-syringae
++ for species in "${unique_organisms[@]}"
++ species_safe=Salmonella-enterica-serovar-Typhimurium
++ output_data_dir=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Salmonella-enterica-serovar-Typhimurium
++ logger 'Processing Salmonella enterica serovar Typhimurium...'
++ local 'message=Processing Salmonella enterica serovar Typhimurium...'
+++ date
++ local '_date=Fri 17 Oct 16:31:28 BST 2025'
++ local 'prefix=Fri 17 Oct 16:31:28 BST 2025'
++ echo 'Fri 17 Oct 16:31:28 BST 2025 :: Processing Salmonella enterica serovar Typhimurium...'
+Fri 17 Oct 16:31:28 BST 2025 :: Processing Salmonella enterica serovar Typhimurium...
++ mkdir -p /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Salmonella-enterica-serovar-Typhimurium
++ filter_table species 'Salmonella enterica serovar Typhimurium'
++ local col=species
++ local 'val=Salmonella enterica serovar Typhimurium'
++ local sep=,
++ local op===
++ awk -F, -v field=species -v 'val=Salmonella enterica serovar Typhimurium' 'NR == 1 { for (i = 1; i <= NF; i++) { if ($i==field) { col=i } }; print $0 } ((NR > 1) && ($col == val)) { print $0 }'
+++ tail -n+2 /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Salmonella-enterica-serovar-Typhimurium/full.csv
+++ wc -l
++ data_size=66
++ logger 'Data for Salmonella enterica serovar Typhimurium has 66 rows'
++ local 'message=Data for Salmonella enterica serovar Typhimurium has 66 rows'
+++ date
++ local '_date=Fri 17 Oct 16:31:28 BST 2025'
++ local 'prefix=Fri 17 Oct 16:31:28 BST 2025'
++ echo 'Fri 17 Oct 16:31:28 BST 2025 :: Data for Salmonella enterica serovar Typhimurium has 66 rows'
+Fri 17 Oct 16:31:28 BST 2025 :: Data for Salmonella enterica serovar Typhimurium has 66 rows
++ '[' 66 -gt 1000 ']'
++ rm -r /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Salmonella-enterica-serovar-Typhimurium
++ for species in "${unique_organisms[@]}"
++ species_safe=Staphylococcus-aureus
++ output_data_dir=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Staphylococcus-aureus
++ logger 'Processing Staphylococcus aureus...'
++ local 'message=Processing Staphylococcus aureus...'
+++ date
++ local '_date=Fri 17 Oct 16:31:28 BST 2025'
++ local 'prefix=Fri 17 Oct 16:31:28 BST 2025'
++ echo 'Fri 17 Oct 16:31:28 BST 2025 :: Processing Staphylococcus aureus...'
+Fri 17 Oct 16:31:28 BST 2025 :: Processing Staphylococcus aureus...
++ mkdir -p /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Staphylococcus-aureus
++ filter_table species 'Staphylococcus aureus'
++ local col=species
++ local 'val=Staphylococcus aureus'
++ local sep=,
++ local op===
++ awk -F, -v field=species -v 'val=Staphylococcus aureus' 'NR == 1 { for (i = 1; i <= NF; i++) { if ($i==field) { col=i } }; print $0 } ((NR > 1) && ($col == val)) { print $0 }'
+++ tail -n+2 /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Staphylococcus-aureus/full.csv
+++ wc -l
++ data_size=2115
++ logger 'Data for Staphylococcus aureus has 2115 rows'
++ local 'message=Data for Staphylococcus aureus has 2115 rows'
+++ date
++ local '_date=Fri 17 Oct 16:31:28 BST 2025'
++ local 'prefix=Fri 17 Oct 16:31:28 BST 2025'
++ echo 'Fri 17 Oct 16:31:28 BST 2025 :: Data for Staphylococcus aureus has 2115 rows'
+Fri 17 Oct 16:31:28 BST 2025 :: Data for Staphylococcus aureus has 2115 rows
++ '[' 2115 -gt 1000 ']'
++ printf 'Staphylococcus aureus\t2115\n'
++ schemist split /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Staphylococcus-aureus/full.csv --type scaffold --train 0.7 --test 0.15 --seed 0 --output /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Staphylococcus-aureus/scaffold-split.csv
+🚀 Splitting table with the following parameters:
+	subcommand: split
+	output: <_io.TextIOWrapper name='/nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Staphylococcus-aureus/scaffold-split.csv' mode='w' encoding='UTF-8'>
+	format: None
+	input: <_io.TextIOWrapper name='/nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Staphylococcus-aureus/full.csv' mode='r' encoding='UTF-8'>
+	representation: SMILES
+	column: smiles
+	prefix: None
+	type: scaffold
+	train: 0.7
+	test: 0.15
+	seed: 0
+	func: <function _split at 0x7f08beed2170>
+
+
+Split counts:
+	train: 1481
+	test: 318
+	validation: 316
+⏰ Completed process in 0:00:01.451083
++ for split in "train" "test" "validation"
++ filter_table is_train True
++ local col=is_train
++ local val=True
++ local sep=,
++ local op===
++ awk -F, -v field=is_train -v val=True 'NR == 1 { for (i = 1; i <= NF; i++) { if ($i==field) { col=i } }; print $0 } ((NR > 1) && ($col == val)) { print $0 }'
++ gzip --best -f /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Staphylococcus-aureus/scaffold-split-train.csv
++ for split in "train" "test" "validation"
++ filter_table is_test True
++ local col=is_test
++ local val=True
++ local sep=,
++ local op===
++ awk -F, -v field=is_test -v val=True 'NR == 1 { for (i = 1; i <= NF; i++) { if ($i==field) { col=i } }; print $0 } ((NR > 1) && ($col == val)) { print $0 }'
++ gzip --best -f /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Staphylococcus-aureus/scaffold-split-test.csv
++ for split in "train" "test" "validation"
++ filter_table is_validation True
++ local col=is_validation
++ local val=True
++ local sep=,
++ local op===
++ awk -F, -v field=is_validation -v val=True 'NR == 1 { for (i = 1; i <= NF; i++) { if ($i==field) { col=i } }; print $0 } ((NR > 1) && ($col == val)) { print $0 }'
++ gzip --best -f /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Staphylococcus-aureus/scaffold-split-validation.csv
++ gzip --best -f /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Staphylococcus-aureus/scaffold-split.csv
++ rm /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Staphylococcus-aureus/full.csv
++ for species in "${unique_organisms[@]}"
++ species_safe=Stenotrophomonas-maltophilia
++ output_data_dir=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Stenotrophomonas-maltophilia
++ logger 'Processing Stenotrophomonas maltophilia...'
++ local 'message=Processing Stenotrophomonas maltophilia...'
+++ date
++ local '_date=Fri 17 Oct 16:31:31 BST 2025'
++ local 'prefix=Fri 17 Oct 16:31:31 BST 2025'
++ echo 'Fri 17 Oct 16:31:31 BST 2025 :: Processing Stenotrophomonas maltophilia...'
+Fri 17 Oct 16:31:31 BST 2025 :: Processing Stenotrophomonas maltophilia...
++ mkdir -p /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Stenotrophomonas-maltophilia
++ filter_table species 'Stenotrophomonas maltophilia'
++ local col=species
++ local 'val=Stenotrophomonas maltophilia'
++ local sep=,
++ local op===
++ awk -F, -v field=species -v 'val=Stenotrophomonas maltophilia' 'NR == 1 { for (i = 1; i <= NF; i++) { if ($i==field) { col=i } }; print $0 } ((NR > 1) && ($col == val)) { print $0 }'
+++ tail -n+2 /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Stenotrophomonas-maltophilia/full.csv
+++ wc -l
++ data_size=13
++ logger 'Data for Stenotrophomonas maltophilia has 13 rows'
++ local 'message=Data for Stenotrophomonas maltophilia has 13 rows'
+++ date
++ local '_date=Fri 17 Oct 16:31:32 BST 2025'
++ local 'prefix=Fri 17 Oct 16:31:32 BST 2025'
++ echo 'Fri 17 Oct 16:31:32 BST 2025 :: Data for Stenotrophomonas maltophilia has 13 rows'
+Fri 17 Oct 16:31:32 BST 2025 :: Data for Stenotrophomonas maltophilia has 13 rows
++ '[' 13 -gt 1000 ']'
++ rm -r /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Stenotrophomonas-maltophilia
++ for species in "${unique_organisms[@]}"
++ species_safe=Streptococcus-pneumoniae
++ output_data_dir=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Streptococcus-pneumoniae
++ logger 'Processing Streptococcus pneumoniae...'
++ local 'message=Processing Streptococcus pneumoniae...'
+++ date
++ local '_date=Fri 17 Oct 16:31:32 BST 2025'
++ local 'prefix=Fri 17 Oct 16:31:32 BST 2025'
++ echo 'Fri 17 Oct 16:31:32 BST 2025 :: Processing Streptococcus pneumoniae...'
+Fri 17 Oct 16:31:32 BST 2025 :: Processing Streptococcus pneumoniae...
++ mkdir -p /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Streptococcus-pneumoniae
++ filter_table species 'Streptococcus pneumoniae'
++ local col=species
++ local 'val=Streptococcus pneumoniae'
++ local sep=,
++ local op===
++ awk -F, -v field=species -v 'val=Streptococcus pneumoniae' 'NR == 1 { for (i = 1; i <= NF; i++) { if ($i==field) { col=i } }; print $0 } ((NR > 1) && ($col == val)) { print $0 }'
+++ tail -n+2 /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Streptococcus-pneumoniae/full.csv
+++ wc -l
++ data_size=1254
++ logger 'Data for Streptococcus pneumoniae has 1254 rows'
++ local 'message=Data for Streptococcus pneumoniae has 1254 rows'
+++ date
++ local '_date=Fri 17 Oct 16:31:32 BST 2025'
++ local 'prefix=Fri 17 Oct 16:31:32 BST 2025'
++ echo 'Fri 17 Oct 16:31:32 BST 2025 :: Data for Streptococcus pneumoniae has 1254 rows'
+Fri 17 Oct 16:31:32 BST 2025 :: Data for Streptococcus pneumoniae has 1254 rows
++ '[' 1254 -gt 1000 ']'
++ printf 'Streptococcus pneumoniae\t1254\n'
++ schemist split /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Streptococcus-pneumoniae/full.csv --type scaffold --train 0.7 --test 0.15 --seed 0 --output /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Streptococcus-pneumoniae/scaffold-split.csv
+🚀 Splitting table with the following parameters:
+	subcommand: split
+	output: <_io.TextIOWrapper name='/nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Streptococcus-pneumoniae/scaffold-split.csv' mode='w' encoding='UTF-8'>
+	format: None
+	input: <_io.TextIOWrapper name='/nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Streptococcus-pneumoniae/full.csv' mode='r' encoding='UTF-8'>
+	representation: SMILES
+	column: smiles
+	prefix: None
+	type: scaffold
+	train: 0.7
+	test: 0.15
+	seed: 0
+	func: <function _split at 0x7f758c6f2170>
+
+
+Split counts:
+	train: 878
+	test: 189
+	validation: 187
+⏰ Completed process in 0:00:00.932421
++ for split in "train" "test" "validation"
++ filter_table is_train True
++ local col=is_train
++ local val=True
++ local sep=,
++ local op===
++ awk -F, -v field=is_train -v val=True 'NR == 1 { for (i = 1; i <= NF; i++) { if ($i==field) { col=i } }; print $0 } ((NR > 1) && ($col == val)) { print $0 }'
++ gzip --best -f /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Streptococcus-pneumoniae/scaffold-split-train.csv
++ for split in "train" "test" "validation"
++ filter_table is_test True
++ local col=is_test
++ local val=True
++ local sep=,
++ local op===
++ awk -F, -v field=is_test -v val=True 'NR == 1 { for (i = 1; i <= NF; i++) { if ($i==field) { col=i } }; print $0 } ((NR > 1) && ($col == val)) { print $0 }'
++ gzip --best -f /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Streptococcus-pneumoniae/scaffold-split-test.csv
++ for split in "train" "test" "validation"
++ filter_table is_validation True
++ local col=is_validation
++ local val=True
++ local sep=,
++ local op===
++ awk -F, -v field=is_validation -v val=True 'NR == 1 { for (i = 1; i <= NF; i++) { if ($i==field) { col=i } }; print $0 } ((NR > 1) && ($col == val)) { print $0 }'
++ gzip --best -f /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Streptococcus-pneumoniae/scaffold-split-validation.csv
++ gzip --best -f /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Streptococcus-pneumoniae/scaffold-split.csv
++ rm /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Streptococcus-pneumoniae/full.csv
++ for species in "${unique_organisms[@]}"
++ species_safe=Vibrio-cholerae
++ output_data_dir=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Vibrio-cholerae
++ logger 'Processing Vibrio cholerae...'
++ local 'message=Processing Vibrio cholerae...'
+++ date
++ local '_date=Fri 17 Oct 16:31:34 BST 2025'
++ local 'prefix=Fri 17 Oct 16:31:34 BST 2025'
++ echo 'Fri 17 Oct 16:31:34 BST 2025 :: Processing Vibrio cholerae...'
+Fri 17 Oct 16:31:34 BST 2025 :: Processing Vibrio cholerae...
++ mkdir -p /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Vibrio-cholerae
++ filter_table species 'Vibrio cholerae'
++ local col=species
++ local 'val=Vibrio cholerae'
++ local sep=,
++ local op===
++ awk -F, -v field=species -v 'val=Vibrio cholerae' 'NR == 1 { for (i = 1; i <= NF; i++) { if ($i==field) { col=i } }; print $0 } ((NR > 1) && ($col == val)) { print $0 }'
+++ tail -n+2 /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Vibrio-cholerae/full.csv
+++ wc -l
++ data_size=9
++ logger 'Data for Vibrio cholerae has 9 rows'
++ local 'message=Data for Vibrio cholerae has 9 rows'
+++ date
++ local '_date=Fri 17 Oct 16:31:34 BST 2025'
++ local 'prefix=Fri 17 Oct 16:31:34 BST 2025'
++ echo 'Fri 17 Oct 16:31:34 BST 2025 :: Data for Vibrio cholerae has 9 rows'
+Fri 17 Oct 16:31:34 BST 2025 :: Data for Vibrio cholerae has 9 rows
++ '[' 9 -gt 1000 ']'
++ rm -r /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Vibrio-cholerae
++ for species in "${unique_organisms[@]}"
++ species_safe=Yersinia-enterocolitica
++ output_data_dir=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Yersinia-enterocolitica
++ logger 'Processing Yersinia enterocolitica...'
++ local 'message=Processing Yersinia enterocolitica...'
+++ date
++ local '_date=Fri 17 Oct 16:31:34 BST 2025'
++ local 'prefix=Fri 17 Oct 16:31:34 BST 2025'
++ echo 'Fri 17 Oct 16:31:34 BST 2025 :: Processing Yersinia enterocolitica...'
+Fri 17 Oct 16:31:34 BST 2025 :: Processing Yersinia enterocolitica...
++ mkdir -p /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Yersinia-enterocolitica
++ filter_table species 'Yersinia enterocolitica'
++ local col=species
++ local 'val=Yersinia enterocolitica'
++ local sep=,
++ local op===
++ awk -F, -v field=species -v 'val=Yersinia enterocolitica' 'NR == 1 { for (i = 1; i <= NF; i++) { if ($i==field) { col=i } }; print $0 } ((NR > 1) && ($col == val)) { print $0 }'
+++ tail -n+2 /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Yersinia-enterocolitica/full.csv
+++ wc -l
++ data_size=1405
++ logger 'Data for Yersinia enterocolitica has 1405 rows'
++ local 'message=Data for Yersinia enterocolitica has 1405 rows'
+++ date
++ local '_date=Fri 17 Oct 16:31:35 BST 2025'
++ local 'prefix=Fri 17 Oct 16:31:35 BST 2025'
++ echo 'Fri 17 Oct 16:31:35 BST 2025 :: Data for Yersinia enterocolitica has 1405 rows'
+Fri 17 Oct 16:31:35 BST 2025 :: Data for Yersinia enterocolitica has 1405 rows
++ '[' 1405 -gt 1000 ']'
++ printf 'Yersinia enterocolitica\t1405\n'
++ schemist split /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Yersinia-enterocolitica/full.csv --type scaffold --train 0.7 --test 0.15 --seed 0 --output /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Yersinia-enterocolitica/scaffold-split.csv
+🚀 Splitting table with the following parameters:
+	subcommand: split
+	output: <_io.TextIOWrapper name='/nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Yersinia-enterocolitica/scaffold-split.csv' mode='w' encoding='UTF-8'>
+	format: None
+	input: <_io.TextIOWrapper name='/nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Yersinia-enterocolitica/full.csv' mode='r' encoding='UTF-8'>
+	representation: SMILES
+	column: smiles
+	prefix: None
+	type: scaffold
+	train: 0.7
+	test: 0.15
+	seed: 0
+	func: <function _split at 0x7f19b3532170>
+
+
+Split counts:
+	train: 984
+	test: 211
+	validation: 210
+⏰ Completed process in 0:00:00.925223
++ for split in "train" "test" "validation"
++ filter_table is_train True
++ local col=is_train
++ local val=True
++ local sep=,
++ local op===
++ awk -F, -v field=is_train -v val=True 'NR == 1 { for (i = 1; i <= NF; i++) { if ($i==field) { col=i } }; print $0 } ((NR > 1) && ($col == val)) { print $0 }'
++ gzip --best -f /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Yersinia-enterocolitica/scaffold-split-train.csv
++ for split in "train" "test" "validation"
++ filter_table is_test True
++ local col=is_test
++ local val=True
++ local sep=,
++ local op===
++ awk -F, -v field=is_test -v val=True 'NR == 1 { for (i = 1; i <= NF; i++) { if ($i==field) { col=i } }; print $0 } ((NR > 1) && ($col == val)) { print $0 }'
++ gzip --best -f /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Yersinia-enterocolitica/scaffold-split-test.csv
++ for split in "train" "test" "validation"
++ filter_table is_validation True
++ local col=is_validation
++ local val=True
++ local sep=,
++ local op===
++ awk -F, -v field=is_validation -v val=True 'NR == 1 { for (i = 1; i <= NF; i++) { if ($i==field) { col=i } }; print $0 } ((NR > 1) && ($col == val)) { print $0 }'
++ gzip --best -f /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Yersinia-enterocolitica/scaffold-split-validation.csv
++ gzip --best -f /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Yersinia-enterocolitica/scaffold-split.csv
++ rm /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Yersinia-enterocolitica/full.csv
++ for species in "${unique_organisms[@]}"
++ species_safe=Yersinia-pestis
++ output_data_dir=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Yersinia-pestis
++ logger 'Processing Yersinia pestis...'
++ local 'message=Processing Yersinia pestis...'
+++ date
++ local '_date=Fri 17 Oct 16:31:38 BST 2025'
++ local 'prefix=Fri 17 Oct 16:31:38 BST 2025'
++ echo 'Fri 17 Oct 16:31:38 BST 2025 :: Processing Yersinia pestis...'
+Fri 17 Oct 16:31:38 BST 2025 :: Processing Yersinia pestis...
++ mkdir -p /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Yersinia-pestis
++ filter_table species 'Yersinia pestis'
++ local col=species
++ local 'val=Yersinia pestis'
++ local sep=,
++ local op===
++ awk -F, -v field=species -v 'val=Yersinia pestis' 'NR == 1 { for (i = 1; i <= NF; i++) { if ($i==field) { col=i } }; print $0 } ((NR > 1) && ($col == val)) { print $0 }'
+++ tail -n+2 /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Yersinia-pestis/full.csv
+++ wc -l
++ data_size=10002
++ logger 'Data for Yersinia pestis has 10002 rows'
++ local 'message=Data for Yersinia pestis has 10002 rows'
+++ date
++ local '_date=Fri 17 Oct 16:31:38 BST 2025'
++ local 'prefix=Fri 17 Oct 16:31:38 BST 2025'
++ echo 'Fri 17 Oct 16:31:38 BST 2025 :: Data for Yersinia pestis has 10002 rows'
+Fri 17 Oct 16:31:38 BST 2025 :: Data for Yersinia pestis has 10002 rows
++ '[' 10002 -gt 1000 ']'
++ printf 'Yersinia pestis\t10002\n'
++ schemist split /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Yersinia-pestis/full.csv --type scaffold --train 0.7 --test 0.15 --seed 0 --output /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Yersinia-pestis/scaffold-split.csv
+🚀 Splitting table with the following parameters:
+	subcommand: split
+	output: <_io.TextIOWrapper name='/nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Yersinia-pestis/scaffold-split.csv' mode='w' encoding='UTF-8'>
+	format: None
+	input: <_io.TextIOWrapper name='/nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Yersinia-pestis/full.csv' mode='r' encoding='UTF-8'>
+	representation: SMILES
+	column: smiles
+	prefix: None
+	type: scaffold
+	train: 0.7
+	test: 0.15
+	seed: 0
+	func: <function _split at 0x7f1717a16290>
+
+
+Split counts:
+	train: 7002
+	test: 1501
+	validation: 1499
+⏰ Completed process in 0:00:06.110671
++ for split in "train" "test" "validation"
++ filter_table is_train True
++ local col=is_train
++ local val=True
++ local sep=,
++ local op===
++ awk -F, -v field=is_train -v val=True 'NR == 1 { for (i = 1; i <= NF; i++) { if ($i==field) { col=i } }; print $0 } ((NR > 1) && ($col == val)) { print $0 }'
++ gzip --best -f /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Yersinia-pestis/scaffold-split-train.csv
++ for split in "train" "test" "validation"
++ filter_table is_test True
++ local col=is_test
++ local val=True
++ local sep=,
++ local op===
++ awk -F, -v field=is_test -v val=True 'NR == 1 { for (i = 1; i <= NF; i++) { if ($i==field) { col=i } }; print $0 } ((NR > 1) && ($col == val)) { print $0 }'
++ gzip --best -f /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Yersinia-pestis/scaffold-split-test.csv
++ for split in "train" "test" "validation"
++ filter_table is_validation True
++ local col=is_validation
++ local val=True
++ local sep=,
++ local op===
++ awk -F, -v field=is_validation -v val=True 'NR == 1 { for (i = 1; i <= NF; i++) { if ($i==field) { col=i } }; print $0 } ((NR > 1) && ($col == val)) { print $0 }'
++ gzip --best -f /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Yersinia-pestis/scaffold-split-validation.csv
++ gzip --best -f /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Yersinia-pestis/scaffold-split.csv
++ rm /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Yersinia-pestis/full.csv
++ for species in "${unique_organisms[@]}"
++ species_safe=Yersinia-pseudotuberculosis
++ output_data_dir=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Yersinia-pseudotuberculosis
++ logger 'Processing Yersinia pseudotuberculosis...'
++ local 'message=Processing Yersinia pseudotuberculosis...'
+++ date
++ local '_date=Fri 17 Oct 16:31:47 BST 2025'
++ local 'prefix=Fri 17 Oct 16:31:47 BST 2025'
++ echo 'Fri 17 Oct 16:31:47 BST 2025 :: Processing Yersinia pseudotuberculosis...'
+Fri 17 Oct 16:31:47 BST 2025 :: Processing Yersinia pseudotuberculosis...
++ mkdir -p /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Yersinia-pseudotuberculosis
++ filter_table species 'Yersinia pseudotuberculosis'
++ local col=species
++ local 'val=Yersinia pseudotuberculosis'
++ local sep=,
++ local op===
++ awk -F, -v field=species -v 'val=Yersinia pseudotuberculosis' 'NR == 1 { for (i = 1; i <= NF; i++) { if ($i==field) { col=i } }; print $0 } ((NR > 1) && ($col == val)) { print $0 }'
+++ tail -n+2 /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Yersinia-pseudotuberculosis/full.csv
+++ wc -l
++ data_size=16
++ logger 'Data for Yersinia pseudotuberculosis has 16 rows'
++ local 'message=Data for Yersinia pseudotuberculosis has 16 rows'
+++ date
++ local '_date=Fri 17 Oct 16:31:47 BST 2025'
++ local 'prefix=Fri 17 Oct 16:31:47 BST 2025'
++ echo 'Fri 17 Oct 16:31:47 BST 2025 :: Data for Yersinia pseudotuberculosis has 16 rows'
+Fri 17 Oct 16:31:47 BST 2025 :: Data for Yersinia pseudotuberculosis has 16 rows
++ '[' 16 -gt 1000 ']'
++ rm -r /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Yersinia-pseudotuberculosis
++ gzip --best -f /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/spark-accumulation-wt.csv
++ set +x
+Fri 17 Oct 16:31:48 BST 2025 :: Done!

spark-accumulation-wt.csv.gz

@@ -1,3 +1,3 @@
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-size 5210031
+oid sha256:611028ec7aef76876c4213b583708a47c54d13bce4f8e01125b0d680ca04ef4d
+size 5220839