Add log

spark-species.log

@@ -0,0 +1,1375 @@
++ 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: openpyxl==3.1.0 in ./.schemist/lib/python3.10/site-packages (from schemist>=0.0.4.post1) (3.1.0)
+Requirement already satisfied: requests in ./.schemist/lib/python3.10/site-packages (from schemist>=0.0.4.post1) (2.32.3)
+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: nemony in ./.schemist/lib/python3.10/site-packages (from schemist>=0.0.4.post1) (0.0.2)
+Requirement already satisfied: selfies in ./.schemist/lib/python3.10/site-packages (from schemist>=0.0.4.post1) (2.2.0)
+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: 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: numpy>=1.22.4 in ./.schemist/lib/python3.10/site-packages (from pandas) (2.2.4)
+Requirement already satisfied: pytz>=2020.1 in ./.schemist/lib/python3.10/site-packages (from pandas) (2025.2)
+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: 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: 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: idna<4,>=2.5 in ./.schemist/lib/python3.10/site-packages (from requests->schemist>=0.0.4.post1) (3.10)
+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 -> 25.0.1
+[notice] To update, run: python -m pip install --upgrade pip
++ source .schemist/bin/activate
+++ deactivate nondestructive
+++ '[' -n '' ']'
+++ '[' -n '' ']'
+++ '[' -n /usr/bin/bash -o -n '' ']'
+++ hash -r
+++ '[' -n '' ']'
+++ unset VIRTUAL_ENV
+++ unset VIRTUAL_ENV_PROMPT
+++ '[' '!' nondestructive = nondestructive ']'
+++ VIRTUAL_ENV=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/.schemist
+++ export VIRTUAL_ENV
+++ _OLD_VIRTUAL_PATH=/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-ddc367ed5c8936efe395cffeec279b04ffd7db78/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-ddc367ed5c8936efe395cffeec279b04ffd7db78/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-ddc367ed5c8936efe395cffeec279b04ffd7db78/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/usr/lpp/mmfs/bin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin
+++ PATH=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/.schemist/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-ddc367ed5c8936efe395cffeec279b04ffd7db78/server/bin/remote-cli:/camp/home/johnsoe/.conda/envs/dev/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-ddc367ed5c8936efe395cffeec279b04ffd7db78/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/nemo/lab/johnsone/home/users/johnsoe/.vscode-server/cli/servers/Stable-ddc367ed5c8936efe395cffeec279b04ffd7db78/server/bin/remote-cli:/camp/apps/eb/software/Anaconda3/2023.09-0/bin:/camp/apps/eb/software/Anaconda3/2023.09-0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin:/usr/lpp/mmfs/bin:/usr/lpp/mmfs/bin:/camp/home/johnsoe/.local/bin:/camp/home/johnsoe/bin
+++ export PATH
+++ '[' -n '' ']'
+++ '[' -z '' ']'
+++ _OLD_VIRTUAL_PS1=
+++ PS1='(.schemist) '
+++ export PS1
+++ VIRTUAL_ENV_PROMPT='(.schemist) '
+++ export VIRTUAL_ENV_PROMPT
+++ '[' -n /usr/bin/bash -o -n '' ']'
+++ 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 $0 }'
++ schemist convert -2 id smiles inchikey scaffold mwt clogp tpsa -f CSV -x prefix=SCB-
++ local col=smiles
++ local val=
++ local sep=,
++ local 'op=!='
++ awk -F, -v field=smiles -v val= 'NR == 1 { for (i = 1; i <= NF; i++) { if ($i==field) { col=i } }; print $0 } ((NR > 1) && ($col != val)) { print $0 }'
++ local col=pmic
++ local val=
++ local sep=,
++ local 'op=!='
++ awk -F, -v field=pmic -v val= 'NR == 1 { for (i = 1; i <= NF; i++) { if ($i==field) { col=i } }; print $0 } ((NR > 1) && ($col != val)) { print $0 }'
+🚀 Converting between string representations with the following parameters:
+	subcommand: convert
+	output: <_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>
+	format: CSV
+	input: <_io.TextIOWrapper name='<stdin>' mode='r' encoding='utf-8'>
+	representation: SMILES
+	column: smiles
+	prefix: None
+	to: ['id', 'smiles', 'inchikey', 'scaffold', 'mwt', 'clogp', 'tpsa']
+	options: ['prefix=SCB-']
+	func: <function _convert at 0x7fb8cbe6df30>
+
+Error counts:
+	id: 0
+	smiles: 0
+	inchikey: 0
+	scaffold: 0
+	mwt: 0
+	clogp: 0
+	tpsa: 0
+⏰ Completed process in 0:01:46.483237
++ unique_values /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/spark-accumulation-wt.csv species
++ local sep=,
+++ get_column_number species
+++ local sep=,
+++ head -n1
+++ tr , '
+'
+++ grep -n '^species$'
+++ cut -f 1 -d :
++ local field=12
++ tail -n+2 /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/spark-accumulation-wt.csv
++ cut -f12 -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 "${unique_organisms[@]}"
++ species_safe=Acinetobacter-baumannii
++ output_data_dir=/nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Acinetobacter-baumannii
++ logger 'Processing Acinetobacter baumannii...'
++ local 'message=Processing Acinetobacter baumannii...'
+++ date
++ local '_date=Wed 26 Mar 22:16:31 GMT 2025'
++ local 'prefix=Wed 26 Mar 22:16:31 GMT 2025'
++ echo 'Wed 26 Mar 22:16:31 GMT 2025 :: Processing Acinetobacter baumannii...'
+Wed 26 Mar 22:16:31 GMT 2025 :: Processing Acinetobacter baumannii...
++ mkdir -p /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Acinetobacter-baumannii
++ filter_table species 'Acinetobacter baumannii'
++ local col=species
++ local 'val=Acinetobacter baumannii'
++ local sep=,
++ local op===
++ awk -F, -v field=species -v 'val=Acinetobacter baumannii' 'NR == 1 { for (i = 1; i <= NF; i++) { if ($i==field) { col=i } }; print $0 } ((NR > 1) && ($col == val)) { print $0 }'
+++ tail -n+2 /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Acinetobacter-baumannii/full.csv
+++ wc -l
++ data_size=2148
++ logger 'Data for Acinetobacter baumannii has 2148 rows'
++ local 'message=Data for Acinetobacter baumannii has 2148 rows'
+++ date
++ local '_date=Wed 26 Mar 22:16:31 GMT 2025'
++ local 'prefix=Wed 26 Mar 22:16:31 GMT 2025'
++ echo 'Wed 26 Mar 22:16:31 GMT 2025 :: Data for Acinetobacter baumannii has 2148 rows'
+Wed 26 Mar 22:16:31 GMT 2025 :: Data for Acinetobacter baumannii has 2148 rows
++ '[' 2148 -gt 1000 ']'
++ printf 'Acinetobacter baumannii\t2148\n'
++ schemist split /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Acinetobacter-baumannii/full.csv --type scaffold --train 0.7 --test 0.15 --seed 0 --output /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Acinetobacter-baumannii/scaffold-split.csv
+🚀 Splitting table with the following parameters:
+	subcommand: split
+	output: <_io.TextIOWrapper name='/nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Acinetobacter-baumannii/scaffold-split.csv' mode='w' encoding='UTF-8'>
+	format: None
+	input: <_io.TextIOWrapper name='/nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Acinetobacter-baumannii/full.csv' mode='r' encoding='UTF-8'>
+	representation: SMILES
+	column: smiles
+	prefix: None
+	type: scaffold
+	train: 0.7
+	test: 0.15
+	seed: 0
+	func: <function _split at 0x7fea87d16170>
+
+
+Split counts:
+	train: 1504
+	test: 323
+	validation: 321
+⏰ Completed process in 0:00:01.745583
++ for split in "train" "test" "validation"
++ filter_table is_train True
++ local col=is_train
++ local val=True
++ local sep=,
++ local op===
++ awk -F, -v field=is_train -v val=True 'NR == 1 { for (i = 1; i <= NF; i++) { if ($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=Wed 26 Mar 22:16:35 GMT 2025'
++ local 'prefix=Wed 26 Mar 22:16:35 GMT 2025'
++ echo 'Wed 26 Mar 22:16:35 GMT 2025 :: Processing Bacillus subtilis...'
+Wed 26 Mar 22:16:35 GMT 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 $0 }'
+++ tail -n+2 /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Bacillus-subtilis/full.csv
+++ wc -l
++ data_size=13
++ logger 'Data for Bacillus subtilis has 13 rows'
++ local 'message=Data for Bacillus subtilis has 13 rows'
+++ date
++ local '_date=Wed 26 Mar 22:16:35 GMT 2025'
++ local 'prefix=Wed 26 Mar 22:16:35 GMT 2025'
++ echo 'Wed 26 Mar 22:16:35 GMT 2025 :: Data for Bacillus subtilis has 13 rows'
+Wed 26 Mar 22:16:35 GMT 2025 :: Data for Bacillus subtilis has 13 rows
++ '[' 13 -gt 1000 ']'
++ rm -r /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Bacillus-subtilis
++ for species in "${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=Wed 26 Mar 22:16:35 GMT 2025'
++ local 'prefix=Wed 26 Mar 22:16:35 GMT 2025'
++ echo 'Wed 26 Mar 22:16:35 GMT 2025 :: Processing Brucella abortus...'
+Wed 26 Mar 22:16:35 GMT 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 $0 }'
+++ tail -n+2 /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Brucella-abortus/full.csv
+++ wc -l
++ data_size=9946
++ logger 'Data for Brucella abortus has 9946 rows'
++ local 'message=Data for Brucella abortus has 9946 rows'
+++ date
++ local '_date=Wed 26 Mar 22:16:35 GMT 2025'
++ local 'prefix=Wed 26 Mar 22:16:35 GMT 2025'
++ echo 'Wed 26 Mar 22:16:35 GMT 2025 :: Data for Brucella abortus has 9946 rows'
+Wed 26 Mar 22:16:35 GMT 2025 :: Data for Brucella abortus has 9946 rows
++ '[' 9946 -gt 1000 ']'
++ printf 'Brucella abortus\t9946\n'
++ schemist split /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Brucella-abortus/full.csv --type scaffold --train 0.7 --test 0.15 --seed 0 --output /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Brucella-abortus/scaffold-split.csv
+🚀 Splitting table with the following parameters:
+	subcommand: split
+	output: <_io.TextIOWrapper name='/nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Brucella-abortus/scaffold-split.csv' mode='w' encoding='UTF-8'>
+	format: None
+	input: <_io.TextIOWrapper name='/nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Brucella-abortus/full.csv' mode='r' encoding='UTF-8'>
+	representation: SMILES
+	column: smiles
+	prefix: None
+	type: scaffold
+	train: 0.7
+	test: 0.15
+	seed: 0
+	func: <function _split at 0x7fa660baa290>
+
+
+Split counts:
+	train: 6963
+	test: 1492
+	validation: 1491
+⏰ Completed process in 0:00:05.882432
++ for split in "train" "test" "validation"
++ filter_table is_train True
++ local col=is_train
++ local val=True
++ local sep=,
++ local op===
++ awk -F, -v field=is_train -v val=True 'NR == 1 { for (i = 1; i <= NF; i++) { if ($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=Wed 26 Mar 22:16:43 GMT 2025'
++ local 'prefix=Wed 26 Mar 22:16:43 GMT 2025'
++ echo 'Wed 26 Mar 22:16:43 GMT 2025 :: Processing Burkholderia thailandensis...'
+Wed 26 Mar 22:16:43 GMT 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 $0 }'
+++ tail -n+2 /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Burkholderia-thailandensis/full.csv
+++ wc -l
++ data_size=725
++ logger 'Data for Burkholderia thailandensis has 725 rows'
++ local 'message=Data for Burkholderia thailandensis has 725 rows'
+++ date
++ local '_date=Wed 26 Mar 22:16:43 GMT 2025'
++ local 'prefix=Wed 26 Mar 22:16:43 GMT 2025'
++ echo 'Wed 26 Mar 22:16:43 GMT 2025 :: Data for Burkholderia thailandensis has 725 rows'
+Wed 26 Mar 22:16:43 GMT 2025 :: Data for Burkholderia thailandensis has 725 rows
++ '[' 725 -gt 1000 ']'
++ rm -r /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Burkholderia-thailandensis
++ for species in "${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=Wed 26 Mar 22:16:43 GMT 2025'
++ local 'prefix=Wed 26 Mar 22:16:43 GMT 2025'
++ echo 'Wed 26 Mar 22:16:43 GMT 2025 :: Processing Caulobacter crescentus...'
+Wed 26 Mar 22:16:43 GMT 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 $0 }'
+++ tail -n+2 /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Caulobacter-crescentus/full.csv
+++ wc -l
++ data_size=37
++ logger 'Data for Caulobacter crescentus has 37 rows'
++ local 'message=Data for Caulobacter crescentus has 37 rows'
+++ date
++ local '_date=Wed 26 Mar 22:16:44 GMT 2025'
++ local 'prefix=Wed 26 Mar 22:16:44 GMT 2025'
++ echo 'Wed 26 Mar 22:16:44 GMT 2025 :: Data for Caulobacter crescentus has 37 rows'
+Wed 26 Mar 22:16:44 GMT 2025 :: Data for Caulobacter crescentus has 37 rows
++ '[' 37 -gt 1000 ']'
++ rm -r /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Caulobacter-crescentus
++ for species in "${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=Wed 26 Mar 22:16:44 GMT 2025'
++ local 'prefix=Wed 26 Mar 22:16:44 GMT 2025'
++ echo 'Wed 26 Mar 22:16:44 GMT 2025 :: Processing Enterobacter cloacae...'
+Wed 26 Mar 22:16:44 GMT 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 $0 }'
+++ tail -n+2 /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Enterobacter-cloacae/full.csv
+++ wc -l
++ data_size=101
++ logger 'Data for Enterobacter cloacae has 101 rows'
++ local 'message=Data for Enterobacter cloacae has 101 rows'
+++ date
++ local '_date=Wed 26 Mar 22:16:44 GMT 2025'
++ local 'prefix=Wed 26 Mar 22:16:44 GMT 2025'
++ echo 'Wed 26 Mar 22:16:44 GMT 2025 :: Data for Enterobacter cloacae has 101 rows'
+Wed 26 Mar 22:16:44 GMT 2025 :: Data for Enterobacter cloacae has 101 rows
++ '[' 101 -gt 1000 ']'
++ rm -r /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Enterobacter-cloacae
++ for species in "${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=Wed 26 Mar 22:16:44 GMT 2025'
++ local 'prefix=Wed 26 Mar 22:16:44 GMT 2025'
++ echo 'Wed 26 Mar 22:16:44 GMT 2025 :: Processing Enterococcus faecalis...'
+Wed 26 Mar 22:16:44 GMT 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 $0 }'
+++ tail -n+2 /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Enterococcus-faecalis/full.csv
+++ wc -l
++ data_size=961
++ logger 'Data for Enterococcus faecalis has 961 rows'
++ local 'message=Data for Enterococcus faecalis has 961 rows'
+++ date
++ local '_date=Wed 26 Mar 22:16:44 GMT 2025'
++ local 'prefix=Wed 26 Mar 22:16:44 GMT 2025'
++ echo 'Wed 26 Mar 22:16:44 GMT 2025 :: Data for Enterococcus faecalis has 961 rows'
+Wed 26 Mar 22:16:44 GMT 2025 :: Data for Enterococcus faecalis has 961 rows
++ '[' 961 -gt 1000 ']'
++ rm -r /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Enterococcus-faecalis
++ for species in "${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=Wed 26 Mar 22:16:44 GMT 2025'
++ local 'prefix=Wed 26 Mar 22:16:44 GMT 2025'
++ echo 'Wed 26 Mar 22:16:44 GMT 2025 :: Processing Escherichia coli...'
+Wed 26 Mar 22:16:44 GMT 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 $0 }'
+++ tail -n+2 /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Escherichia-coli/full.csv
+++ wc -l
++ data_size=20451
++ logger 'Data for Escherichia coli has 20451 rows'
++ local 'message=Data for Escherichia coli has 20451 rows'
+++ date
++ local '_date=Wed 26 Mar 22:16:44 GMT 2025'
++ local 'prefix=Wed 26 Mar 22:16:44 GMT 2025'
++ echo 'Wed 26 Mar 22:16:44 GMT 2025 :: Data for Escherichia coli has 20451 rows'
+Wed 26 Mar 22:16:44 GMT 2025 :: Data for Escherichia coli has 20451 rows
++ '[' 20451 -gt 1000 ']'
++ printf 'Escherichia coli\t20451\n'
++ schemist split /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Escherichia-coli/full.csv --type scaffold --train 0.7 --test 0.15 --seed 0 --output /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Escherichia-coli/scaffold-split.csv
+🚀 Splitting table with the following parameters:
+	subcommand: split
+	output: <_io.TextIOWrapper name='/nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Escherichia-coli/scaffold-split.csv' mode='w' encoding='UTF-8'>
+	format: None
+	input: <_io.TextIOWrapper name='/nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Escherichia-coli/full.csv' mode='r' encoding='UTF-8'>
+	representation: SMILES
+	column: smiles
+	prefix: None
+	type: scaffold
+	train: 0.7
+	test: 0.15
+	seed: 0
+	func: <function _split at 0x7f1a9b34e290>
+
+
+Split counts:
+	train: 14316
+	test: 3068
+	validation: 3067
+⏰ Completed process in 0:00:18.054209
++ for split in "train" "test" "validation"
++ filter_table is_train True
++ local col=is_train
++ local val=True
++ local sep=,
++ local op===
++ awk -F, -v field=is_train -v val=True 'NR == 1 { for (i = 1; i <= NF; i++) { if ($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=Wed 26 Mar 22:17:05 GMT 2025'
++ local 'prefix=Wed 26 Mar 22:17:05 GMT 2025'
++ echo 'Wed 26 Mar 22:17:05 GMT 2025 :: Processing Francisella novicida...'
+Wed 26 Mar 22:17:05 GMT 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 $0 }'
+++ tail -n+2 /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Francisella-novicida/full.csv
+++ wc -l
++ data_size=4
++ logger 'Data for Francisella novicida has 4 rows'
++ local 'message=Data for Francisella novicida has 4 rows'
+++ date
++ local '_date=Wed 26 Mar 22:17:05 GMT 2025'
++ local 'prefix=Wed 26 Mar 22:17:05 GMT 2025'
++ echo 'Wed 26 Mar 22:17:05 GMT 2025 :: Data for Francisella novicida has 4 rows'
+Wed 26 Mar 22:17:05 GMT 2025 :: Data for Francisella novicida has 4 rows
++ '[' 4 -gt 1000 ']'
++ rm -r /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Francisella-novicida
++ for species in "${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=Wed 26 Mar 22:17:05 GMT 2025'
++ local 'prefix=Wed 26 Mar 22:17:05 GMT 2025'
++ echo 'Wed 26 Mar 22:17:05 GMT 2025 :: Processing Francisella tularensis...'
+Wed 26 Mar 22:17:05 GMT 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 $0 }'
+++ tail -n+2 /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Francisella-tularensis/full.csv
+++ wc -l
++ data_size=9671
++ logger 'Data for Francisella tularensis has 9671 rows'
++ local 'message=Data for Francisella tularensis has 9671 rows'
+++ date
++ local '_date=Wed 26 Mar 22:17:05 GMT 2025'
++ local 'prefix=Wed 26 Mar 22:17:05 GMT 2025'
++ echo 'Wed 26 Mar 22:17:05 GMT 2025 :: Data for Francisella tularensis has 9671 rows'
+Wed 26 Mar 22:17:05 GMT 2025 :: Data for Francisella tularensis has 9671 rows
++ '[' 9671 -gt 1000 ']'
++ printf 'Francisella tularensis\t9671\n'
++ schemist split /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Francisella-tularensis/full.csv --type scaffold --train 0.7 --test 0.15 --seed 0 --output /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Francisella-tularensis/scaffold-split.csv
+🚀 Splitting table with the following parameters:
+	subcommand: split
+	output: <_io.TextIOWrapper name='/nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Francisella-tularensis/scaffold-split.csv' mode='w' encoding='UTF-8'>
+	format: None
+	input: <_io.TextIOWrapper name='/nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Francisella-tularensis/full.csv' mode='r' encoding='UTF-8'>
+	representation: SMILES
+	column: smiles
+	prefix: None
+	type: scaffold
+	train: 0.7
+	test: 0.15
+	seed: 0
+	func: <function _split at 0x7f0d87072170>
+
+
+Split counts:
+	train: 6770
+	test: 1451
+	validation: 1450
+⏰ Completed process in 0:00:05.703710
++ for split in "train" "test" "validation"
++ filter_table is_train True
++ local col=is_train
++ local val=True
++ local sep=,
++ local op===
++ awk -F, -v field=is_train -v val=True 'NR == 1 { for (i = 1; i <= NF; i++) { if ($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=Wed 26 Mar 22:17:13 GMT 2025'
++ local 'prefix=Wed 26 Mar 22:17:13 GMT 2025'
++ echo 'Wed 26 Mar 22:17:13 GMT 2025 :: Processing Haemophilus influenzae...'
+Wed 26 Mar 22:17:13 GMT 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 $0 }'
+++ tail -n+2 /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Haemophilus-influenzae/full.csv
+++ wc -l
++ data_size=27
++ logger 'Data for Haemophilus influenzae has 27 rows'
++ local 'message=Data for Haemophilus influenzae has 27 rows'
+++ date
++ local '_date=Wed 26 Mar 22:17:13 GMT 2025'
++ local 'prefix=Wed 26 Mar 22:17:13 GMT 2025'
++ echo 'Wed 26 Mar 22:17:13 GMT 2025 :: Data for Haemophilus influenzae has 27 rows'
+Wed 26 Mar 22:17:13 GMT 2025 :: Data for Haemophilus influenzae has 27 rows
++ '[' 27 -gt 1000 ']'
++ rm -r /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Haemophilus-influenzae
++ for species in "${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=Wed 26 Mar 22:17:13 GMT 2025'
++ local 'prefix=Wed 26 Mar 22:17:13 GMT 2025'
++ echo 'Wed 26 Mar 22:17:13 GMT 2025 :: Processing Klebsiella pneumoniae...'
+Wed 26 Mar 22:17:13 GMT 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 $0 }'
+++ tail -n+2 /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Klebsiella-pneumoniae/full.csv
+++ wc -l
++ data_size=3920
++ logger 'Data for Klebsiella pneumoniae has 3920 rows'
++ local 'message=Data for Klebsiella pneumoniae has 3920 rows'
+++ date
++ local '_date=Wed 26 Mar 22:17:13 GMT 2025'
++ local 'prefix=Wed 26 Mar 22:17:13 GMT 2025'
++ echo 'Wed 26 Mar 22:17:13 GMT 2025 :: Data for Klebsiella pneumoniae has 3920 rows'
+Wed 26 Mar 22:17:13 GMT 2025 :: Data for Klebsiella pneumoniae has 3920 rows
++ '[' 3920 -gt 1000 ']'
++ printf 'Klebsiella pneumoniae\t3920\n'
++ schemist split /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Klebsiella-pneumoniae/full.csv --type scaffold --train 0.7 --test 0.15 --seed 0 --output /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Klebsiella-pneumoniae/scaffold-split.csv
+🚀 Splitting table with the following parameters:
+	subcommand: split
+	output: <_io.TextIOWrapper name='/nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Klebsiella-pneumoniae/scaffold-split.csv' mode='w' encoding='UTF-8'>
+	format: None
+	input: <_io.TextIOWrapper name='/nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Klebsiella-pneumoniae/full.csv' mode='r' encoding='UTF-8'>
+	representation: SMILES
+	column: smiles
+	prefix: None
+	type: scaffold
+	train: 0.7
+	test: 0.15
+	seed: 0
+	func: <function _split at 0x7fe59819e170>
+
+
+Split counts:
+	train: 2744
+	test: 588
+	validation: 588
+⏰ Completed process in 0:00:02.743941
++ for split in "train" "test" "validation"
++ filter_table is_train True
++ local col=is_train
++ local val=True
++ local sep=,
++ local op===
++ awk -F, -v field=is_train -v val=True 'NR == 1 { for (i = 1; i <= NF; i++) { if ($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=Wed 26 Mar 22:17:18 GMT 2025'
++ local 'prefix=Wed 26 Mar 22:17:18 GMT 2025'
++ echo 'Wed 26 Mar 22:17:18 GMT 2025 :: Processing Moraxella catarrhalis...'
+Wed 26 Mar 22:17:18 GMT 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 $0 }'
+++ tail -n+2 /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Moraxella-catarrhalis/full.csv
+++ wc -l
++ data_size=2
++ logger 'Data for Moraxella catarrhalis has 2 rows'
++ local 'message=Data for Moraxella catarrhalis has 2 rows'
+++ date
++ local '_date=Wed 26 Mar 22:17:18 GMT 2025'
++ local 'prefix=Wed 26 Mar 22:17:18 GMT 2025'
++ echo 'Wed 26 Mar 22:17:18 GMT 2025 :: Data for Moraxella catarrhalis has 2 rows'
+Wed 26 Mar 22:17:18 GMT 2025 :: Data for Moraxella catarrhalis has 2 rows
++ '[' 2 -gt 1000 ']'
++ rm -r /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Moraxella-catarrhalis
++ for species in "${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=Wed 26 Mar 22:17:18 GMT 2025'
++ local 'prefix=Wed 26 Mar 22:17:18 GMT 2025'
++ echo 'Wed 26 Mar 22:17:18 GMT 2025 :: Processing Mycobacterium vaccae...'
+Wed 26 Mar 22:17:18 GMT 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 $0 }'
+++ tail -n+2 /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Mycobacterium-vaccae/full.csv
+++ wc -l
++ data_size=7
++ logger 'Data for Mycobacterium vaccae has 7 rows'
++ local 'message=Data for Mycobacterium vaccae has 7 rows'
+++ date
++ local '_date=Wed 26 Mar 22:17:18 GMT 2025'
++ local 'prefix=Wed 26 Mar 22:17:18 GMT 2025'
++ echo 'Wed 26 Mar 22:17:18 GMT 2025 :: Data for Mycobacterium vaccae has 7 rows'
+Wed 26 Mar 22:17:18 GMT 2025 :: Data for Mycobacterium vaccae has 7 rows
++ '[' 7 -gt 1000 ']'
++ rm -r /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Mycobacterium-vaccae
++ for species in "${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=Wed 26 Mar 22:17:18 GMT 2025'
++ local 'prefix=Wed 26 Mar 22:17:18 GMT 2025'
++ echo 'Wed 26 Mar 22:17:18 GMT 2025 :: Processing Proteus hauseri...'
+Wed 26 Mar 22:17:18 GMT 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 $0 }'
+++ tail -n+2 /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Proteus-hauseri/full.csv
+++ wc -l
++ data_size=4
++ logger 'Data for Proteus hauseri has 4 rows'
++ local 'message=Data for Proteus hauseri has 4 rows'
+++ date
++ local '_date=Wed 26 Mar 22:17:18 GMT 2025'
++ local 'prefix=Wed 26 Mar 22:17:18 GMT 2025'
++ echo 'Wed 26 Mar 22:17:18 GMT 2025 :: Data for Proteus hauseri has 4 rows'
+Wed 26 Mar 22:17:18 GMT 2025 :: Data for Proteus hauseri has 4 rows
++ '[' 4 -gt 1000 ']'
++ rm -r /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Proteus-hauseri
++ for species in "${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=Wed 26 Mar 22:17:18 GMT 2025'
++ local 'prefix=Wed 26 Mar 22:17:18 GMT 2025'
++ echo 'Wed 26 Mar 22:17:18 GMT 2025 :: Processing Proteus mirabilis...'
+Wed 26 Mar 22:17:18 GMT 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 $0 }'
+++ tail -n+2 /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Proteus-mirabilis/full.csv
+++ wc -l
++ data_size=20
++ logger 'Data for Proteus mirabilis has 20 rows'
++ local 'message=Data for Proteus mirabilis has 20 rows'
+++ date
++ local '_date=Wed 26 Mar 22:17:19 GMT 2025'
++ local 'prefix=Wed 26 Mar 22:17:19 GMT 2025'
++ echo 'Wed 26 Mar 22:17:19 GMT 2025 :: Data for Proteus mirabilis has 20 rows'
+Wed 26 Mar 22:17:19 GMT 2025 :: Data for Proteus mirabilis has 20 rows
++ '[' 20 -gt 1000 ']'
++ rm -r /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Proteus-mirabilis
++ for species in "${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=Wed 26 Mar 22:17:19 GMT 2025'
++ local 'prefix=Wed 26 Mar 22:17:19 GMT 2025'
++ echo 'Wed 26 Mar 22:17:19 GMT 2025 :: Processing Pseudomonas aeruginosa...'
+Wed 26 Mar 22:17:19 GMT 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 $0 }'
+++ tail -n+2 /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Pseudomonas-aeruginosa/full.csv
+++ wc -l
++ data_size=15677
++ logger 'Data for Pseudomonas aeruginosa has 15677 rows'
++ local 'message=Data for Pseudomonas aeruginosa has 15677 rows'
+++ date
++ local '_date=Wed 26 Mar 22:17:19 GMT 2025'
++ local 'prefix=Wed 26 Mar 22:17:19 GMT 2025'
++ echo 'Wed 26 Mar 22:17:19 GMT 2025 :: Data for Pseudomonas aeruginosa has 15677 rows'
+Wed 26 Mar 22:17:19 GMT 2025 :: Data for Pseudomonas aeruginosa has 15677 rows
++ '[' 15677 -gt 1000 ']'
++ printf 'Pseudomonas aeruginosa\t15677\n'
++ schemist split /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Pseudomonas-aeruginosa/full.csv --type scaffold --train 0.7 --test 0.15 --seed 0 --output /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Pseudomonas-aeruginosa/scaffold-split.csv
+🚀 Splitting table with the following parameters:
+	subcommand: split
+	output: <_io.TextIOWrapper name='/nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Pseudomonas-aeruginosa/scaffold-split.csv' mode='w' encoding='UTF-8'>
+	format: None
+	input: <_io.TextIOWrapper name='/nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Pseudomonas-aeruginosa/full.csv' mode='r' encoding='UTF-8'>
+	representation: SMILES
+	column: smiles
+	prefix: None
+	type: scaffold
+	train: 0.7
+	test: 0.15
+	seed: 0
+	func: <function _split at 0x7fdf38cf2170>
+
+
+Split counts:
+	train: 10974
+	test: 2352
+	validation: 2351
+⏰ Completed process in 0:00:10.903278
++ for split in "train" "test" "validation"
++ filter_table is_train True
++ local col=is_train
++ local val=True
++ local sep=,
++ local op===
++ awk -F, -v field=is_train -v val=True 'NR == 1 { for (i = 1; i <= NF; i++) { if ($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=Wed 26 Mar 22:17:32 GMT 2025'
++ local 'prefix=Wed 26 Mar 22:17:32 GMT 2025'
++ echo 'Wed 26 Mar 22:17:32 GMT 2025 :: Processing Pseudomonas fluorescens...'
+Wed 26 Mar 22:17:32 GMT 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 $0 }'
+++ tail -n+2 /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Pseudomonas-fluorescens/full.csv
+++ wc -l
++ data_size=219
++ logger 'Data for Pseudomonas fluorescens has 219 rows'
++ local 'message=Data for Pseudomonas fluorescens has 219 rows'
+++ date
++ local '_date=Wed 26 Mar 22:17:32 GMT 2025'
++ local 'prefix=Wed 26 Mar 22:17:32 GMT 2025'
++ echo 'Wed 26 Mar 22:17:32 GMT 2025 :: Data for Pseudomonas fluorescens has 219 rows'
+Wed 26 Mar 22:17:32 GMT 2025 :: Data for Pseudomonas fluorescens has 219 rows
++ '[' 219 -gt 1000 ']'
++ rm -r /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Pseudomonas-fluorescens
++ for species in "${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=Wed 26 Mar 22:17:32 GMT 2025'
++ local 'prefix=Wed 26 Mar 22:17:32 GMT 2025'
++ echo 'Wed 26 Mar 22:17:32 GMT 2025 :: Processing Pseudomonas syringae...'
+Wed 26 Mar 22:17:32 GMT 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 $0 }'
+++ tail -n+2 /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Pseudomonas-syringae/full.csv
+++ wc -l
++ data_size=16
++ logger 'Data for Pseudomonas syringae has 16 rows'
++ local 'message=Data for Pseudomonas syringae has 16 rows'
+++ date
++ local '_date=Wed 26 Mar 22:17:32 GMT 2025'
++ local 'prefix=Wed 26 Mar 22:17:32 GMT 2025'
++ echo 'Wed 26 Mar 22:17:32 GMT 2025 :: Data for Pseudomonas syringae has 16 rows'
+Wed 26 Mar 22:17:32 GMT 2025 :: Data for Pseudomonas syringae has 16 rows
++ '[' 16 -gt 1000 ']'
++ rm -r /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Pseudomonas-syringae
++ for species in "${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=Wed 26 Mar 22:17:32 GMT 2025'
++ local 'prefix=Wed 26 Mar 22:17:32 GMT 2025'
++ echo 'Wed 26 Mar 22:17:32 GMT 2025 :: Processing Salmonella enterica serovar Typhimurium...'
+Wed 26 Mar 22:17:32 GMT 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 $0 }'
+++ tail -n+2 /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Salmonella-enterica-serovar-Typhimurium/full.csv
+++ wc -l
++ data_size=66
++ logger 'Data for Salmonella enterica serovar Typhimurium has 66 rows'
++ local 'message=Data for Salmonella enterica serovar Typhimurium has 66 rows'
+++ date
++ local '_date=Wed 26 Mar 22:17:32 GMT 2025'
++ local 'prefix=Wed 26 Mar 22:17:32 GMT 2025'
++ echo 'Wed 26 Mar 22:17:32 GMT 2025 :: Data for Salmonella enterica serovar Typhimurium has 66 rows'
+Wed 26 Mar 22:17:32 GMT 2025 :: Data for Salmonella enterica serovar Typhimurium has 66 rows
++ '[' 66 -gt 1000 ']'
++ rm -r /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Salmonella-enterica-serovar-Typhimurium
++ for species in "${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=Wed 26 Mar 22:17:32 GMT 2025'
++ local 'prefix=Wed 26 Mar 22:17:32 GMT 2025'
++ echo 'Wed 26 Mar 22:17:32 GMT 2025 :: Processing Staphylococcus aureus...'
+Wed 26 Mar 22:17:32 GMT 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 $0 }'
+++ tail -n+2 /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Staphylococcus-aureus/full.csv
+++ wc -l
++ data_size=2115
++ logger 'Data for Staphylococcus aureus has 2115 rows'
++ local 'message=Data for Staphylococcus aureus has 2115 rows'
+++ date
++ local '_date=Wed 26 Mar 22:17:33 GMT 2025'
++ local 'prefix=Wed 26 Mar 22:17:33 GMT 2025'
++ echo 'Wed 26 Mar 22:17:33 GMT 2025 :: Data for Staphylococcus aureus has 2115 rows'
+Wed 26 Mar 22:17:33 GMT 2025 :: Data for Staphylococcus aureus has 2115 rows
++ '[' 2115 -gt 1000 ']'
++ printf 'Staphylococcus aureus\t2115\n'
++ schemist split /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Staphylococcus-aureus/full.csv --type scaffold --train 0.7 --test 0.15 --seed 0 --output /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Staphylococcus-aureus/scaffold-split.csv
+🚀 Splitting table with the following parameters:
+	subcommand: split
+	output: <_io.TextIOWrapper name='/nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Staphylococcus-aureus/scaffold-split.csv' mode='w' encoding='UTF-8'>
+	format: None
+	input: <_io.TextIOWrapper name='/nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Staphylococcus-aureus/full.csv' mode='r' encoding='UTF-8'>
+	representation: SMILES
+	column: smiles
+	prefix: None
+	type: scaffold
+	train: 0.7
+	test: 0.15
+	seed: 0
+	func: <function _split at 0x7fa5c147a170>
+
+
+Split counts:
+	train: 1481
+	test: 318
+	validation: 316
+⏰ Completed process in 0:00:01.461816
++ for split in "train" "test" "validation"
++ filter_table is_train True
++ local col=is_train
++ local val=True
++ local sep=,
++ local op===
++ awk -F, -v field=is_train -v val=True 'NR == 1 { for (i = 1; i <= NF; i++) { if ($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=Wed 26 Mar 22:17:36 GMT 2025'
++ local 'prefix=Wed 26 Mar 22:17:36 GMT 2025'
++ echo 'Wed 26 Mar 22:17:36 GMT 2025 :: Processing Stenotrophomonas maltophilia...'
+Wed 26 Mar 22:17:36 GMT 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 $0 }'
+++ tail -n+2 /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Stenotrophomonas-maltophilia/full.csv
+++ wc -l
++ data_size=13
++ logger 'Data for Stenotrophomonas maltophilia has 13 rows'
++ local 'message=Data for Stenotrophomonas maltophilia has 13 rows'
+++ date
++ local '_date=Wed 26 Mar 22:17:36 GMT 2025'
++ local 'prefix=Wed 26 Mar 22:17:36 GMT 2025'
++ echo 'Wed 26 Mar 22:17:36 GMT 2025 :: Data for Stenotrophomonas maltophilia has 13 rows'
+Wed 26 Mar 22:17:36 GMT 2025 :: Data for Stenotrophomonas maltophilia has 13 rows
++ '[' 13 -gt 1000 ']'
++ rm -r /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Stenotrophomonas-maltophilia
++ for species in "${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=Wed 26 Mar 22:17:36 GMT 2025'
++ local 'prefix=Wed 26 Mar 22:17:36 GMT 2025'
++ echo 'Wed 26 Mar 22:17:36 GMT 2025 :: Processing Streptococcus pneumoniae...'
+Wed 26 Mar 22:17:36 GMT 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 $0 }'
+++ tail -n+2 /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Streptococcus-pneumoniae/full.csv
+++ wc -l
++ data_size=1254
++ logger 'Data for Streptococcus pneumoniae has 1254 rows'
++ local 'message=Data for Streptococcus pneumoniae has 1254 rows'
+++ date
++ local '_date=Wed 26 Mar 22:17:36 GMT 2025'
++ local 'prefix=Wed 26 Mar 22:17:36 GMT 2025'
++ echo 'Wed 26 Mar 22:17:36 GMT 2025 :: Data for Streptococcus pneumoniae has 1254 rows'
+Wed 26 Mar 22:17:36 GMT 2025 :: Data for Streptococcus pneumoniae has 1254 rows
++ '[' 1254 -gt 1000 ']'
++ printf 'Streptococcus pneumoniae\t1254\n'
++ schemist split /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Streptococcus-pneumoniae/full.csv --type scaffold --train 0.7 --test 0.15 --seed 0 --output /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Streptococcus-pneumoniae/scaffold-split.csv
+🚀 Splitting table with the following parameters:
+	subcommand: split
+	output: <_io.TextIOWrapper name='/nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Streptococcus-pneumoniae/scaffold-split.csv' mode='w' encoding='UTF-8'>
+	format: None
+	input: <_io.TextIOWrapper name='/nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Streptococcus-pneumoniae/full.csv' mode='r' encoding='UTF-8'>
+	representation: SMILES
+	column: smiles
+	prefix: None
+	type: scaffold
+	train: 0.7
+	test: 0.15
+	seed: 0
+	func: <function _split at 0x7fd9911b6170>
+
+
+Split counts:
+	train: 878
+	test: 189
+	validation: 187
+⏰ Completed process in 0:00:00.924644
++ for split in "train" "test" "validation"
++ filter_table is_train True
++ local col=is_train
++ local val=True
++ local sep=,
++ local op===
++ awk -F, -v field=is_train -v val=True 'NR == 1 { for (i = 1; i <= NF; i++) { if ($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=Wed 26 Mar 22:17:38 GMT 2025'
++ local 'prefix=Wed 26 Mar 22:17:38 GMT 2025'
++ echo 'Wed 26 Mar 22:17:38 GMT 2025 :: Processing Vibrio cholerae...'
+Wed 26 Mar 22:17:38 GMT 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 $0 }'
+++ tail -n+2 /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Vibrio-cholerae/full.csv
+++ wc -l
++ data_size=9
++ logger 'Data for Vibrio cholerae has 9 rows'
++ local 'message=Data for Vibrio cholerae has 9 rows'
+++ date
++ local '_date=Wed 26 Mar 22:17:39 GMT 2025'
++ local 'prefix=Wed 26 Mar 22:17:39 GMT 2025'
++ echo 'Wed 26 Mar 22:17:39 GMT 2025 :: Data for Vibrio cholerae has 9 rows'
+Wed 26 Mar 22:17:39 GMT 2025 :: Data for Vibrio cholerae has 9 rows
++ '[' 9 -gt 1000 ']'
++ rm -r /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Vibrio-cholerae
++ for species in "${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=Wed 26 Mar 22:17:39 GMT 2025'
++ local 'prefix=Wed 26 Mar 22:17:39 GMT 2025'
++ echo 'Wed 26 Mar 22:17:39 GMT 2025 :: Processing Yersinia enterocolitica...'
+Wed 26 Mar 22:17:39 GMT 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 $0 }'
+++ tail -n+2 /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Yersinia-enterocolitica/full.csv
+++ wc -l
++ data_size=1405
++ logger 'Data for Yersinia enterocolitica has 1405 rows'
++ local 'message=Data for Yersinia enterocolitica has 1405 rows'
+++ date
++ local '_date=Wed 26 Mar 22:17:39 GMT 2025'
++ local 'prefix=Wed 26 Mar 22:17:39 GMT 2025'
++ echo 'Wed 26 Mar 22:17:39 GMT 2025 :: Data for Yersinia enterocolitica has 1405 rows'
+Wed 26 Mar 22:17:39 GMT 2025 :: Data for Yersinia enterocolitica has 1405 rows
++ '[' 1405 -gt 1000 ']'
++ printf 'Yersinia enterocolitica\t1405\n'
++ schemist split /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Yersinia-enterocolitica/full.csv --type scaffold --train 0.7 --test 0.15 --seed 0 --output /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Yersinia-enterocolitica/scaffold-split.csv
+🚀 Splitting table with the following parameters:
+	subcommand: split
+	output: <_io.TextIOWrapper name='/nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Yersinia-enterocolitica/scaffold-split.csv' mode='w' encoding='UTF-8'>
+	format: None
+	input: <_io.TextIOWrapper name='/nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Yersinia-enterocolitica/full.csv' mode='r' encoding='UTF-8'>
+	representation: SMILES
+	column: smiles
+	prefix: None
+	type: scaffold
+	train: 0.7
+	test: 0.15
+	seed: 0
+	func: <function _split at 0x7f4cf51be170>
+
+
+Split counts:
+	train: 984
+	test: 211
+	validation: 210
+⏰ Completed process in 0:00:00.917110
++ for split in "train" "test" "validation"
++ filter_table is_train True
++ local col=is_train
++ local val=True
++ local sep=,
++ local op===
++ awk -F, -v field=is_train -v val=True 'NR == 1 { for (i = 1; i <= NF; i++) { if ($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=Wed 26 Mar 22:17:41 GMT 2025'
++ local 'prefix=Wed 26 Mar 22:17:41 GMT 2025'
++ echo 'Wed 26 Mar 22:17:41 GMT 2025 :: Processing Yersinia pestis...'
+Wed 26 Mar 22:17:41 GMT 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 $0 }'
+++ tail -n+2 /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Yersinia-pestis/full.csv
+++ wc -l
++ data_size=10002
++ logger 'Data for Yersinia pestis has 10002 rows'
++ local 'message=Data for Yersinia pestis has 10002 rows'
+++ date
++ local '_date=Wed 26 Mar 22:17:42 GMT 2025'
++ local 'prefix=Wed 26 Mar 22:17:42 GMT 2025'
++ echo 'Wed 26 Mar 22:17:42 GMT 2025 :: Data for Yersinia pestis has 10002 rows'
+Wed 26 Mar 22:17:42 GMT 2025 :: Data for Yersinia pestis has 10002 rows
++ '[' 10002 -gt 1000 ']'
++ printf 'Yersinia pestis\t10002\n'
++ schemist split /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Yersinia-pestis/full.csv --type scaffold --train 0.7 --test 0.15 --seed 0 --output /nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Yersinia-pestis/scaffold-split.csv
+🚀 Splitting table with the following parameters:
+	subcommand: split
+	output: <_io.TextIOWrapper name='/nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Yersinia-pestis/scaffold-split.csv' mode='w' encoding='UTF-8'>
+	format: None
+	input: <_io.TextIOWrapper name='/nemo/lab/johnsone/home/users/johnsoe/data/datasets/spark/species-wt/Yersinia-pestis/full.csv' mode='r' encoding='UTF-8'>
+	representation: SMILES
+	column: smiles
+	prefix: None
+	type: scaffold
+	train: 0.7
+	test: 0.15
+	seed: 0
+	func: <function _split at 0x7f7a32dde290>
+
+
+Split counts:
+	train: 7002
+	test: 1501
+	validation: 1499
+⏰ Completed process in 0:00:05.914599
++ for split in "train" "test" "validation"
++ filter_table is_train True
++ local col=is_train
++ local val=True
++ local sep=,
++ local op===
++ awk -F, -v field=is_train -v val=True 'NR == 1 { for (i = 1; i <= NF; i++) { if ($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=Wed 26 Mar 22:17:49 GMT 2025'
++ local 'prefix=Wed 26 Mar 22:17:49 GMT 2025'
++ echo 'Wed 26 Mar 22:17:49 GMT 2025 :: Processing Yersinia pseudotuberculosis...'
+Wed 26 Mar 22:17:49 GMT 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=Wed 26 Mar 22:17:50 GMT 2025'
++ local 'prefix=Wed 26 Mar 22:17:50 GMT 2025'
++ echo 'Wed 26 Mar 22:17:50 GMT 2025 :: Data for Yersinia pseudotuberculosis has 16 rows'
+Wed 26 Mar 22:17:50 GMT 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
+Wed 26 Mar 22:17:51 GMT 2025 :: Done!