Using profile slurm for setting default command line arguments. SNAKEMAKE ========= Date: 2026-07-14 05:00:26 Workflow ID: 98fe4fc5-4a04-43b4-ae33-40675c56e0de Platform: Linux-5.14.0-427.70.1.el9_4.x86_64-x86_64-with-glibc2.34 Host: compute-13-1 User: gaurav Snakemake version: 9.23.1 Python version: 3.13.9 (main, Oct 14 2025, 21:29:44) [Clang 20.1.4 ] Command: /projects/babel/runs/gaurav/babel-1.18/.venv/bin/snakemake --profile slurm Snakefile: /projects/babel/runs/gaurav/babel-1.18/Snakefile Base directory: /projects/babel/runs/gaurav/babel-1.18 Run directory: /projects/babel/runs/gaurav/babel-1.18 Working directory: /projects/babel/runs/gaurav/babel-1.18 Config file(s): ['config.yaml', 'config.yaml'] Config MD5: eda72a598cf6f8676e7be6b40ac56b9d INFO snakemake.logging [2026-07-14T09:00:26+0000]: Workflow has started! Building DAG of jobs... INFO snakemake.logging [2026-07-14T09:00:26+0000]: Building DAG of jobs... You are running snakemake in a SLURM job context. This is not recommended, as it may lead to unexpected behavior. If possible, please run Snakemake directly on the login node. WARNING snakemake.logging [2026-07-14T09:00:27+0000]: You are running snakemake in a SLURM job context. This is not recommended, as it may lead to unexpected behavior. If possible, please run Snakemake directly on the login node. SLURM run ID: babel_94b54343-095a-4c15-8bc0-529889394a60 INFO snakemake.logging [2026-07-14T09:00:27+0000]: SLURM run ID: babel_94b54343-095a-4c15-8bc0-529889394a60 MinJobAge 300s (>= 120s). 'squeue' should work reliably for status queries. WARNING snakemake.logging [2026-07-14T09:00:27+0000]: MinJobAge 300s (>= 120s). 'squeue' should work reliably for status queries. Using shell: /usr/bin/bash INFO snakemake.logging [2026-07-14T09:00:27+0000]: Using shell: /usr/bin/bash Provided remote nodes: 50 INFO snakemake.logging [2026-07-14T09:00:27+0000]: Provided remote nodes: 50 Job stats: job count -------------------------------------------------------------- ------- chemical_drugbank_food_extracts 1 get_drugbank_labels_and_synonyms 1 untyped_chemical_compendia 1 chemical_compendia 1 check_chemical_completeness 1 check_chemical_entity 1 check_chemical_mixture 1 check_complex_mixture 1 check_drug 1 check_food 1 check_molecular_mixture 1 check_polypeptide 1 check_small_molecule 1 drugchemical_conflation 1 export_compendia_to_duckdb 9 generate_content_report_for_compendium_ChemicalEntity 1 generate_content_report_for_compendium_ChemicalMixture 1 generate_content_report_for_compendium_ComplexMolecularMixture 1 generate_content_report_for_compendium_Drug 1 generate_content_report_for_compendium_Food 1 generate_content_report_for_compendium_MolecularMixture 1 generate_content_report_for_compendium_Polypeptide 1 generate_content_report_for_compendium_SmallMolecule 1 generate_kgx 9 leftover_umls 1 chemical 1 compress_umls 1 export_conflation_to_duckdb 1 generate_content_report_for_compendium_umls 1 generate_mapping_sources_table 1 drugchemical_conflated_synonyms 1 export_all_compendia_to_duckdb 1 export_all_conflations_to_duckdb 1 export_all_to_kgx 1 export_synonyms_to_duckdb 2 generate_compendia_summary_report 1 generate_sapbert_training_data 2 drugchemical 1 export_intermediate_files_to_duckdb 1 all_outputs 1 export_all_synonyms_to_duckdb 1 export_all_to_sapbert_training 1 check_compendia_files 1 check_conflation_files 1 check_synonyms_gzipped_files 1 export_all_to_duckdb 1 check_for_duplicate_clique_leaders 1 check_for_duplicate_curies 1 check_for_identically_labeled_cliques 1 generate_clique_leader_report 1 generate_curie_report 1 all_duckdb_reports 1 generate_cliques_table 1 generate_prefix_table 1 all_reports 1 all 1 total 74 INFO snakemake.logging [2026-07-14T09:00:27+0000]: Job stats: job count -------------------------------------------------------------- ------- chemical_drugbank_food_extracts 1 get_drugbank_labels_and_synonyms 1 untyped_chemical_compendia 1 chemical_compendia 1 check_chemical_completeness 1 check_chemical_entity 1 check_chemical_mixture 1 check_complex_mixture 1 check_drug 1 check_food 1 check_molecular_mixture 1 check_polypeptide 1 check_small_molecule 1 drugchemical_conflation 1 export_compendia_to_duckdb 9 generate_content_report_for_compendium_ChemicalEntity 1 generate_content_report_for_compendium_ChemicalMixture 1 generate_content_report_for_compendium_ComplexMolecularMixture 1 generate_content_report_for_compendium_Drug 1 generate_content_report_for_compendium_Food 1 generate_content_report_for_compendium_MolecularMixture 1 generate_content_report_for_compendium_Polypeptide 1 generate_content_report_for_compendium_SmallMolecule 1 generate_kgx 9 leftover_umls 1 chemical 1 compress_umls 1 export_conflation_to_duckdb 1 generate_content_report_for_compendium_umls 1 generate_mapping_sources_table 1 drugchemical_conflated_synonyms 1 export_all_compendia_to_duckdb 1 export_all_conflations_to_duckdb 1 export_all_to_kgx 1 export_synonyms_to_duckdb 2 generate_compendia_summary_report 1 generate_sapbert_training_data 2 drugchemical 1 export_intermediate_files_to_duckdb 1 all_outputs 1 export_all_synonyms_to_duckdb 1 export_all_to_sapbert_training 1 check_compendia_files 1 check_conflation_files 1 check_synonyms_gzipped_files 1 export_all_to_duckdb 1 check_for_duplicate_clique_leaders 1 check_for_duplicate_curies 1 check_for_identically_labeled_cliques 1 generate_clique_leader_report 1 generate_curie_report 1 all_duckdb_reports 1 generate_cliques_table 1 generate_prefix_table 1 all_reports 1 all 1 total 74 Select jobs to execute... INFO snakemake.logging [2026-07-14T09:00:27+0000]: Select jobs to execute... Execute 2 jobs... INFO snakemake.logging [2026-07-14T09:00:27+0000]: Execute 2 jobs... No SLURM account given, trying to guess. WARNING snakemake.logging [2026-07-14T09:00:27+0000]: No SLURM account given, trying to guess. No SLURM account given, trying to guess. WARNING snakemake.logging [2026-07-14T09:00:27+0000]: No SLURM account given, trying to guess. No account was given, not able to get a SLURM account via sacct: sacct: invalid option -- '1' WARNING snakemake.logging [2026-07-14T09:00:27+0000]: No account was given, not able to get a SLURM account via sacct: sacct: invalid option -- '1' Unable to guess SLURM account. Trying to proceed without. WARNING snakemake.logging [2026-07-14T09:00:27+0000]: Unable to guess SLURM account. Trying to proceed without. No account was given, not able to get a SLURM account via sacct: sacct: invalid option -- '1' WARNING snakemake.logging [2026-07-14T09:00:27+0000]: No account was given, not able to get a SLURM account via sacct: sacct: invalid option -- '1' Unable to guess SLURM account. Trying to proceed without. WARNING snakemake.logging [2026-07-14T09:00:27+0000]: Unable to guess SLURM account. Trying to proceed without. Job 72 has been submitted with SLURM jobid 53219 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_chemical_drugbank_food_extracts/53219.log). INFO snakemake.logging [2026-07-14T09:00:28+0000]: Job 72 has been submitted with SLURM jobid 53219 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_chemical_drugbank_food_extracts/53219.log). Job 40 has been submitted with SLURM jobid 53220 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_get_drugbank_labels_and_synonyms/53220.log). INFO snakemake.logging [2026-07-14T09:00:28+0000]: Job 40 has been submitted with SLURM jobid 53220 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_get_drugbank_labels_and_synonyms/53220.log). [Tue Jul 14 05:01:08 2026] Finished jobid: 72 (Rule: chemical_drugbank_food_extracts) INFO snakemake.logging [2026-07-14T09:01:08+0000]: Finished jobid: 72 (Rule: chemical_drugbank_food_extracts) 1 of 74 steps (1%) done INFO snakemake.logging [2026-07-14T09:01:08+0000]: None [Tue Jul 14 05:01:08 2026] Finished jobid: 40 (Rule: get_drugbank_labels_and_synonyms) INFO snakemake.logging [2026-07-14T09:01:08+0000]: Finished jobid: 40 (Rule: get_drugbank_labels_and_synonyms) 2 of 74 steps (3%) done INFO snakemake.logging [2026-07-14T09:01:08+0000]: None Select jobs to execute... INFO snakemake.logging [2026-07-14T09:01:08+0000]: Select jobs to execute... Execute 1 jobs... INFO snakemake.logging [2026-07-14T09:01:08+0000]: Execute 1 jobs... Job 27 has been submitted with SLURM jobid 53221 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_untyped_chemical_compendia/53221.log). INFO snakemake.logging [2026-07-14T09:01:08+0000]: Job 27 has been submitted with SLURM jobid 53221 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_untyped_chemical_compendia/53221.log). [Tue Jul 14 06:01:41 2026] Finished jobid: 27 (Rule: untyped_chemical_compendia) INFO snakemake.logging [2026-07-14T10:01:41+0000]: Finished jobid: 27 (Rule: untyped_chemical_compendia) 3 of 74 steps (4%) done INFO snakemake.logging [2026-07-14T10:01:41+0000]: None Select jobs to execute... INFO snakemake.logging [2026-07-14T10:01:41+0000]: Select jobs to execute... Execute 1 jobs... INFO snakemake.logging [2026-07-14T10:01:41+0000]: Execute 1 jobs... Job 26 has been submitted with SLURM jobid 53235 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_chemical_compendia/53235.log). INFO snakemake.logging [2026-07-14T10:01:41+0000]: Job 26 has been submitted with SLURM jobid 53235 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_chemical_compendia/53235.log). [Tue Jul 14 11:29:25 2026] Finished jobid: 26 (Rule: chemical_compendia) INFO snakemake.logging [2026-07-14T15:29:25+0000]: Finished jobid: 26 (Rule: chemical_compendia) 4 of 74 steps (5%) done INFO snakemake.logging [2026-07-14T15:29:25+0000]: None Select jobs to execute... INFO snakemake.logging [2026-07-14T15:29:25+0000]: Select jobs to execute... Execute 35 jobs... INFO snakemake.logging [2026-07-14T15:29:25+0000]: Execute 35 jobs... Job 277 has been submitted with SLURM jobid 53267 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_export_compendia_to_duckdb/ComplexMolecularMixture/53267.log). INFO snakemake.logging [2026-07-14T15:29:25+0000]: Job 277 has been submitted with SLURM jobid 53267 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_export_compendia_to_duckdb/ComplexMolecularMixture/53267.log). Job 278 has been submitted with SLURM jobid 53268 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_export_compendia_to_duckdb/ChemicalEntity/53268.log). INFO snakemake.logging [2026-07-14T15:29:25+0000]: Job 278 has been submitted with SLURM jobid 53268 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_export_compendia_to_duckdb/ChemicalEntity/53268.log). Job 279 has been submitted with SLURM jobid 53269 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_export_compendia_to_duckdb/ChemicalMixture/53269.log). INFO snakemake.logging [2026-07-14T15:29:25+0000]: Job 279 has been submitted with SLURM jobid 53269 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_export_compendia_to_duckdb/ChemicalMixture/53269.log). Job 280 has been submitted with SLURM jobid 53270 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_export_compendia_to_duckdb/Drug/53270.log). INFO snakemake.logging [2026-07-14T15:29:25+0000]: Job 280 has been submitted with SLURM jobid 53270 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_export_compendia_to_duckdb/Drug/53270.log). Job 281 has been submitted with SLURM jobid 53271 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_export_compendia_to_duckdb/Food/53271.log). INFO snakemake.logging [2026-07-14T15:29:25+0000]: Job 281 has been submitted with SLURM jobid 53271 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_export_compendia_to_duckdb/Food/53271.log). Job 274 has been submitted with SLURM jobid 53272 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_export_compendia_to_duckdb/MolecularMixture/53272.log). INFO snakemake.logging [2026-07-14T15:29:25+0000]: Job 274 has been submitted with SLURM jobid 53272 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_export_compendia_to_duckdb/MolecularMixture/53272.log). Job 275 has been submitted with SLURM jobid 53273 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_export_compendia_to_duckdb/SmallMolecule/53273.log). INFO snakemake.logging [2026-07-14T15:29:25+0000]: Job 275 has been submitted with SLURM jobid 53273 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_export_compendia_to_duckdb/SmallMolecule/53273.log). Job 276 has been submitted with SLURM jobid 53274 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_export_compendia_to_duckdb/Polypeptide/53274.log). INFO snakemake.logging [2026-07-14T15:29:25+0000]: Job 276 has been submitted with SLURM jobid 53274 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_export_compendia_to_duckdb/Polypeptide/53274.log). Job 245 has been submitted with SLURM jobid 53275 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_content_report_for_compendium_ComplexMolecularMixture/53275.log). INFO snakemake.logging [2026-07-14T15:29:25+0000]: Job 245 has been submitted with SLURM jobid 53275 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_content_report_for_compendium_ComplexMolecularMixture/53275.log). Job 227 has been submitted with SLURM jobid 53276 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_drugchemical_conflation/53276.log). INFO snakemake.logging [2026-07-14T15:29:25+0000]: Job 227 has been submitted with SLURM jobid 53276 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_drugchemical_conflation/53276.log). Job 79 has been submitted with SLURM jobid 53277 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_check_chemical_entity/53277.log). INFO snakemake.logging [2026-07-14T15:29:25+0000]: Job 79 has been submitted with SLURM jobid 53277 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_check_chemical_entity/53277.log). Job 337 has been submitted with SLURM jobid 53278 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_kgx/Food/53278.log). INFO snakemake.logging [2026-07-14T15:29:25+0000]: Job 337 has been submitted with SLURM jobid 53278 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_kgx/Food/53278.log). Job 330 has been submitted with SLURM jobid 53279 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_kgx/MolecularMixture/53279.log). INFO snakemake.logging [2026-07-14T15:29:25+0000]: Job 330 has been submitted with SLURM jobid 53279 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_kgx/MolecularMixture/53279.log). Job 332 has been submitted with SLURM jobid 53280 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_kgx/Polypeptide/53280.log). INFO snakemake.logging [2026-07-14T15:29:25+0000]: Job 332 has been submitted with SLURM jobid 53280 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_kgx/Polypeptide/53280.log). Job 331 has been submitted with SLURM jobid 53281 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_kgx/SmallMolecule/53281.log). INFO snakemake.logging [2026-07-14T15:29:25+0000]: Job 331 has been submitted with SLURM jobid 53281 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_kgx/SmallMolecule/53281.log). Job 333 has been submitted with SLURM jobid 53282 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_kgx/ComplexMolecularMixture/53282.log). INFO snakemake.logging [2026-07-14T15:29:25+0000]: Job 333 has been submitted with SLURM jobid 53282 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_kgx/ComplexMolecularMixture/53282.log). Job 334 has been submitted with SLURM jobid 53283 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_kgx/ChemicalEntity/53283.log). INFO snakemake.logging [2026-07-14T15:29:25+0000]: Job 334 has been submitted with SLURM jobid 53283 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_kgx/ChemicalEntity/53283.log). Job 336 has been submitted with SLURM jobid 53284 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_kgx/Drug/53284.log). INFO snakemake.logging [2026-07-14T15:29:26+0000]: Job 336 has been submitted with SLURM jobid 53284 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_kgx/Drug/53284.log). Job 335 has been submitted with SLURM jobid 53285 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_kgx/ChemicalMixture/53285.log). INFO snakemake.logging [2026-07-14T15:29:26+0000]: Job 335 has been submitted with SLURM jobid 53285 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_kgx/ChemicalMixture/53285.log). Job 246 has been submitted with SLURM jobid 53286 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_content_report_for_compendium_ChemicalEntity/53286.log). INFO snakemake.logging [2026-07-14T15:29:26+0000]: Job 246 has been submitted with SLURM jobid 53286 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_content_report_for_compendium_ChemicalEntity/53286.log). Job 80 has been submitted with SLURM jobid 53287 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_check_chemical_mixture/53287.log). INFO snakemake.logging [2026-07-14T15:29:26+0000]: Job 80 has been submitted with SLURM jobid 53287 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_check_chemical_mixture/53287.log). Job 25 has been submitted with SLURM jobid 53288 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_check_chemical_completeness/53288.log). INFO snakemake.logging [2026-07-14T15:29:26+0000]: Job 25 has been submitted with SLURM jobid 53288 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_check_chemical_completeness/53288.log). Job 247 has been submitted with SLURM jobid 53289 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_content_report_for_compendium_ChemicalMixture/53289.log). INFO snakemake.logging [2026-07-14T15:29:26+0000]: Job 247 has been submitted with SLURM jobid 53289 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_content_report_for_compendium_ChemicalMixture/53289.log). Job 81 has been submitted with SLURM jobid 53290 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_check_drug/53290.log). INFO snakemake.logging [2026-07-14T15:29:26+0000]: Job 81 has been submitted with SLURM jobid 53290 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_check_drug/53290.log). Job 248 has been submitted with SLURM jobid 53291 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_content_report_for_compendium_Drug/53291.log). INFO snakemake.logging [2026-07-14T15:29:26+0000]: Job 248 has been submitted with SLURM jobid 53291 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_content_report_for_compendium_Drug/53291.log). Job 82 has been submitted with SLURM jobid 53292 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_check_food/53292.log). INFO snakemake.logging [2026-07-14T15:29:26+0000]: Job 82 has been submitted with SLURM jobid 53292 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_check_food/53292.log). Job 215 has been submitted with SLURM jobid 53293 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_leftover_umls/53293.log). INFO snakemake.logging [2026-07-14T15:29:26+0000]: Job 215 has been submitted with SLURM jobid 53293 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_leftover_umls/53293.log). Job 75 has been submitted with SLURM jobid 53294 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_check_molecular_mixture/53294.log). INFO snakemake.logging [2026-07-14T15:29:26+0000]: Job 75 has been submitted with SLURM jobid 53294 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_check_molecular_mixture/53294.log). Job 249 has been submitted with SLURM jobid 53295 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_content_report_for_compendium_Food/53295.log). INFO snakemake.logging [2026-07-14T15:29:26+0000]: Job 249 has been submitted with SLURM jobid 53295 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_content_report_for_compendium_Food/53295.log). Job 242 has been submitted with SLURM jobid 53296 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_content_report_for_compendium_MolecularMixture/53296.log). INFO snakemake.logging [2026-07-14T15:29:26+0000]: Job 242 has been submitted with SLURM jobid 53296 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_content_report_for_compendium_MolecularMixture/53296.log). Job 76 has been submitted with SLURM jobid 53297 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_check_small_molecule/53297.log). INFO snakemake.logging [2026-07-14T15:29:26+0000]: Job 76 has been submitted with SLURM jobid 53297 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_check_small_molecule/53297.log). Job 243 has been submitted with SLURM jobid 53298 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_content_report_for_compendium_SmallMolecule/53298.log). INFO snakemake.logging [2026-07-14T15:29:26+0000]: Job 243 has been submitted with SLURM jobid 53298 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_content_report_for_compendium_SmallMolecule/53298.log). Job 77 has been submitted with SLURM jobid 53299 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_check_polypeptide/53299.log). INFO snakemake.logging [2026-07-14T15:29:26+0000]: Job 77 has been submitted with SLURM jobid 53299 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_check_polypeptide/53299.log). Job 244 has been submitted with SLURM jobid 53300 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_content_report_for_compendium_Polypeptide/53300.log). INFO snakemake.logging [2026-07-14T15:29:26+0000]: Job 244 has been submitted with SLURM jobid 53300 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_content_report_for_compendium_Polypeptide/53300.log). Job 78 has been submitted with SLURM jobid 53301 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_check_complex_mixture/53301.log). INFO snakemake.logging [2026-07-14T15:29:26+0000]: Job 78 has been submitted with SLURM jobid 53301 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_check_complex_mixture/53301.log). [Tue Jul 14 11:30:05 2026] Finished jobid: 277 (Rule: export_compendia_to_duckdb) INFO snakemake.logging [2026-07-14T15:30:05+0000]: Finished jobid: 277 (Rule: export_compendia_to_duckdb) 5 of 74 steps (7%) done INFO snakemake.logging [2026-07-14T15:30:05+0000]: None [Tue Jul 14 11:30:05 2026] Finished jobid: 278 (Rule: export_compendia_to_duckdb) INFO snakemake.logging [2026-07-14T15:30:05+0000]: Finished jobid: 278 (Rule: export_compendia_to_duckdb) 6 of 74 steps (8%) done INFO snakemake.logging [2026-07-14T15:30:05+0000]: None [Tue Jul 14 11:30:05 2026] Finished jobid: 279 (Rule: export_compendia_to_duckdb) INFO snakemake.logging [2026-07-14T15:30:05+0000]: Finished jobid: 279 (Rule: export_compendia_to_duckdb) 7 of 74 steps (9%) done INFO snakemake.logging [2026-07-14T15:30:05+0000]: None [Tue Jul 14 11:30:05 2026] Finished jobid: 280 (Rule: export_compendia_to_duckdb) INFO snakemake.logging [2026-07-14T15:30:05+0000]: Finished jobid: 280 (Rule: export_compendia_to_duckdb) 8 of 74 steps (11%) done INFO snakemake.logging [2026-07-14T15:30:05+0000]: None [Tue Jul 14 11:30:05 2026] Finished jobid: 281 (Rule: export_compendia_to_duckdb) INFO snakemake.logging [2026-07-14T15:30:05+0000]: Finished jobid: 281 (Rule: export_compendia_to_duckdb) 9 of 74 steps (12%) done INFO snakemake.logging [2026-07-14T15:30:05+0000]: None [Tue Jul 14 11:30:05 2026] Finished jobid: 276 (Rule: export_compendia_to_duckdb) INFO snakemake.logging [2026-07-14T15:30:05+0000]: Finished jobid: 276 (Rule: export_compendia_to_duckdb) 10 of 74 steps (14%) done INFO snakemake.logging [2026-07-14T15:30:05+0000]: None [Tue Jul 14 11:30:05 2026] Finished jobid: 245 (Rule: generate_content_report_for_compendium_ComplexMolecularMixture) INFO snakemake.logging [2026-07-14T15:30:05+0000]: Finished jobid: 245 (Rule: generate_content_report_for_compendium_ComplexMolecularMixture) 11 of 74 steps (15%) done INFO snakemake.logging [2026-07-14T15:30:05+0000]: None [Tue Jul 14 11:30:05 2026] Finished jobid: 79 (Rule: check_chemical_entity) INFO snakemake.logging [2026-07-14T15:30:05+0000]: Finished jobid: 79 (Rule: check_chemical_entity) 12 of 74 steps (16%) done INFO snakemake.logging [2026-07-14T15:30:05+0000]: None [Tue Jul 14 11:30:05 2026] Finished jobid: 337 (Rule: generate_kgx) INFO snakemake.logging [2026-07-14T15:30:05+0000]: Finished jobid: 337 (Rule: generate_kgx) 13 of 74 steps (18%) done INFO snakemake.logging [2026-07-14T15:30:05+0000]: None [Tue Jul 14 11:30:05 2026] Finished jobid: 332 (Rule: generate_kgx) INFO snakemake.logging [2026-07-14T15:30:05+0000]: Finished jobid: 332 (Rule: generate_kgx) 14 of 74 steps (19%) done INFO snakemake.logging [2026-07-14T15:30:05+0000]: None [Tue Jul 14 11:30:05 2026] Finished jobid: 333 (Rule: generate_kgx) INFO snakemake.logging [2026-07-14T15:30:05+0000]: Finished jobid: 333 (Rule: generate_kgx) 15 of 74 steps (20%) done INFO snakemake.logging [2026-07-14T15:30:05+0000]: None [Tue Jul 14 11:30:05 2026] Finished jobid: 334 (Rule: generate_kgx) INFO snakemake.logging [2026-07-14T15:30:05+0000]: Finished jobid: 334 (Rule: generate_kgx) 16 of 74 steps (22%) done INFO snakemake.logging [2026-07-14T15:30:05+0000]: None [Tue Jul 14 11:30:05 2026] Finished jobid: 336 (Rule: generate_kgx) INFO snakemake.logging [2026-07-14T15:30:05+0000]: Finished jobid: 336 (Rule: generate_kgx) 17 of 74 steps (23%) done INFO snakemake.logging [2026-07-14T15:30:05+0000]: None [Tue Jul 14 11:30:06 2026] Finished jobid: 335 (Rule: generate_kgx) INFO snakemake.logging [2026-07-14T15:30:06+0000]: Finished jobid: 335 (Rule: generate_kgx) 18 of 74 steps (24%) done INFO snakemake.logging [2026-07-14T15:30:06+0000]: None [Tue Jul 14 11:30:06 2026] Finished jobid: 246 (Rule: generate_content_report_for_compendium_ChemicalEntity) INFO snakemake.logging [2026-07-14T15:30:06+0000]: Finished jobid: 246 (Rule: generate_content_report_for_compendium_ChemicalEntity) 19 of 74 steps (26%) done INFO snakemake.logging [2026-07-14T15:30:06+0000]: None [Tue Jul 14 11:30:06 2026] Finished jobid: 80 (Rule: check_chemical_mixture) INFO snakemake.logging [2026-07-14T15:30:06+0000]: Finished jobid: 80 (Rule: check_chemical_mixture) 20 of 74 steps (27%) done INFO snakemake.logging [2026-07-14T15:30:06+0000]: None [Tue Jul 14 11:30:06 2026] Finished jobid: 247 (Rule: generate_content_report_for_compendium_ChemicalMixture) INFO snakemake.logging [2026-07-14T15:30:06+0000]: Finished jobid: 247 (Rule: generate_content_report_for_compendium_ChemicalMixture) 21 of 74 steps (28%) done INFO snakemake.logging [2026-07-14T15:30:06+0000]: None [Tue Jul 14 11:30:06 2026] Finished jobid: 81 (Rule: check_drug) INFO snakemake.logging [2026-07-14T15:30:06+0000]: Finished jobid: 81 (Rule: check_drug) 22 of 74 steps (30%) done INFO snakemake.logging [2026-07-14T15:30:06+0000]: None [Tue Jul 14 11:30:06 2026] Finished jobid: 248 (Rule: generate_content_report_for_compendium_Drug) INFO snakemake.logging [2026-07-14T15:30:06+0000]: Finished jobid: 248 (Rule: generate_content_report_for_compendium_Drug) 23 of 74 steps (31%) done INFO snakemake.logging [2026-07-14T15:30:06+0000]: None [Tue Jul 14 11:30:06 2026] Finished jobid: 82 (Rule: check_food) INFO snakemake.logging [2026-07-14T15:30:06+0000]: Finished jobid: 82 (Rule: check_food) 24 of 74 steps (32%) done INFO snakemake.logging [2026-07-14T15:30:06+0000]: None [Tue Jul 14 11:30:06 2026] Finished jobid: 249 (Rule: generate_content_report_for_compendium_Food) INFO snakemake.logging [2026-07-14T15:30:06+0000]: Finished jobid: 249 (Rule: generate_content_report_for_compendium_Food) 25 of 74 steps (34%) done INFO snakemake.logging [2026-07-14T15:30:06+0000]: None [Tue Jul 14 11:30:06 2026] Finished jobid: 77 (Rule: check_polypeptide) INFO snakemake.logging [2026-07-14T15:30:06+0000]: Finished jobid: 77 (Rule: check_polypeptide) 26 of 74 steps (35%) done INFO snakemake.logging [2026-07-14T15:30:06+0000]: None [Tue Jul 14 11:30:06 2026] Finished jobid: 244 (Rule: generate_content_report_for_compendium_Polypeptide) INFO snakemake.logging [2026-07-14T15:30:06+0000]: Finished jobid: 244 (Rule: generate_content_report_for_compendium_Polypeptide) 27 of 74 steps (36%) done INFO snakemake.logging [2026-07-14T15:30:06+0000]: None [Tue Jul 14 11:30:06 2026] Finished jobid: 78 (Rule: check_complex_mixture) INFO snakemake.logging [2026-07-14T15:30:06+0000]: Finished jobid: 78 (Rule: check_complex_mixture) 28 of 74 steps (38%) done INFO snakemake.logging [2026-07-14T15:30:06+0000]: None [Tue Jul 14 11:31:36 2026] Finished jobid: 75 (Rule: check_molecular_mixture) INFO snakemake.logging [2026-07-14T15:31:36+0000]: Finished jobid: 75 (Rule: check_molecular_mixture) 29 of 74 steps (39%) done INFO snakemake.logging [2026-07-14T15:31:36+0000]: None [Tue Jul 14 11:32:16 2026] Finished jobid: 242 (Rule: generate_content_report_for_compendium_MolecularMixture) INFO snakemake.logging [2026-07-14T15:32:16+0000]: Finished jobid: 242 (Rule: generate_content_report_for_compendium_MolecularMixture) 30 of 74 steps (41%) done INFO snakemake.logging [2026-07-14T15:32:16+0000]: None [Tue Jul 14 11:40:27 2026] Finished jobid: 274 (Rule: export_compendia_to_duckdb) INFO snakemake.logging [2026-07-14T15:40:27+0000]: Finished jobid: 274 (Rule: export_compendia_to_duckdb) 31 of 74 steps (42%) done INFO snakemake.logging [2026-07-14T15:40:27+0000]: None [Tue Jul 14 11:44:07 2026] Finished jobid: 25 (Rule: check_chemical_completeness) INFO snakemake.logging [2026-07-14T15:44:07+0000]: Finished jobid: 25 (Rule: check_chemical_completeness) 32 of 74 steps (43%) done INFO snakemake.logging [2026-07-14T15:44:07+0000]: None [Tue Jul 14 11:45:37 2026] Finished jobid: 76 (Rule: check_small_molecule) INFO snakemake.logging [2026-07-14T15:45:37+0000]: Finished jobid: 76 (Rule: check_small_molecule) 33 of 74 steps (45%) done INFO snakemake.logging [2026-07-14T15:45:37+0000]: None Select jobs to execute... INFO snakemake.logging [2026-07-14T15:45:37+0000]: Select jobs to execute... Execute 1 jobs... INFO snakemake.logging [2026-07-14T15:45:37+0000]: Execute 1 jobs... Job 24 has been submitted with SLURM jobid 53307 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_chemical/53307.log). INFO snakemake.logging [2026-07-14T15:45:37+0000]: Job 24 has been submitted with SLURM jobid 53307 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_chemical/53307.log). [Tue Jul 14 11:48:07 2026] Finished jobid: 243 (Rule: generate_content_report_for_compendium_SmallMolecule) INFO snakemake.logging [2026-07-14T15:48:07+0000]: Finished jobid: 243 (Rule: generate_content_report_for_compendium_SmallMolecule) 34 of 74 steps (46%) done INFO snakemake.logging [2026-07-14T15:48:07+0000]: None [Tue Jul 14 11:48:48 2026] Finished jobid: 330 (Rule: generate_kgx) INFO snakemake.logging [2026-07-14T15:48:48+0000]: Finished jobid: 330 (Rule: generate_kgx) 35 of 74 steps (47%) done INFO snakemake.logging [2026-07-14T15:48:48+0000]: None [Tue Jul 14 11:55:18 2026] Finished jobid: 227 (Rule: drugchemical_conflation) INFO snakemake.logging [2026-07-14T15:55:18+0000]: Finished jobid: 227 (Rule: drugchemical_conflation) 36 of 74 steps (49%) done INFO snakemake.logging [2026-07-14T15:55:18+0000]: None Select jobs to execute... INFO snakemake.logging [2026-07-14T15:55:18+0000]: Select jobs to execute... Execute 1 jobs... INFO snakemake.logging [2026-07-14T15:55:18+0000]: Execute 1 jobs... Job 316 has been submitted with SLURM jobid 53313 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_export_conflation_to_duckdb/DrugChemical/53313.log). INFO snakemake.logging [2026-07-14T15:55:18+0000]: Job 316 has been submitted with SLURM jobid 53313 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_export_conflation_to_duckdb/DrugChemical/53313.log). [Tue Jul 14 11:55:58 2026] Finished jobid: 316 (Rule: export_conflation_to_duckdb) INFO snakemake.logging [2026-07-14T15:55:58+0000]: Finished jobid: 316 (Rule: export_conflation_to_duckdb) 37 of 74 steps (50%) done INFO snakemake.logging [2026-07-14T15:55:58+0000]: None Select jobs to execute... INFO snakemake.logging [2026-07-14T15:55:58+0000]: Select jobs to execute... Execute 1 jobs... INFO snakemake.logging [2026-07-14T15:55:58+0000]: Execute 1 jobs... [Tue Jul 14 11:55:58 2026] localrule export_all_conflations_to_duckdb: input: babel_outputs/duckdb/parquet/filename=GeneProtein/Conflation.parquet, babel_outputs/duckdb/parquet/filename=DrugChemical/Conflation.parquet output: babel_outputs/duckdb/conflations_done jobid: 314 reason: Missing output files: babel_outputs/duckdb/conflations_done; Input files updated by another job: babel_outputs/duckdb/parquet/filename=DrugChemical/Conflation.parquet resources: tmpdir=/tmp, disk_mb=1047, disk=1.05 GB, disk_mib=999, mem_mb=16000, mem=16 GB, mem_mib=15259, runtime=120, cpus_per_task=1 INFO snakemake.logging [2026-07-14T15:55:58+0000]: Rule: export_all_conflations_to_duckdb, Jobid: 314 INFO snakemake.logging [2026-07-14T15:55:58+0000]: Shell command: echo 'done' >> babel_outputs/duckdb/conflations_done [Tue Jul 14 11:55:58 2026] Finished jobid: 314 (Rule: export_all_conflations_to_duckdb) INFO snakemake.logging [2026-07-14T15:55:58+0000]: Finished jobid: 314 (Rule: export_all_conflations_to_duckdb) 38 of 74 steps (51%) done INFO snakemake.logging [2026-07-14T15:55:58+0000]: None [Tue Jul 14 12:07:59 2026] Finished jobid: 215 (Rule: leftover_umls) INFO snakemake.logging [2026-07-14T16:07:59+0000]: Finished jobid: 215 (Rule: leftover_umls) 39 of 74 steps (53%) done INFO snakemake.logging [2026-07-14T16:07:59+0000]: None Select jobs to execute... INFO snakemake.logging [2026-07-14T16:07:59+0000]: Select jobs to execute... Execute 5 jobs... INFO snakemake.logging [2026-07-14T16:07:59+0000]: Execute 5 jobs... Job 260 has been submitted with SLURM jobid 53319 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_content_report_for_compendium_umls/53319.log). INFO snakemake.logging [2026-07-14T16:07:59+0000]: Job 260 has been submitted with SLURM jobid 53319 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_content_report_for_compendium_umls/53319.log). Job 292 has been submitted with SLURM jobid 53320 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_export_compendia_to_duckdb/umls/53320.log). INFO snakemake.logging [2026-07-14T16:07:59+0000]: Job 292 has been submitted with SLURM jobid 53320 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_export_compendia_to_duckdb/umls/53320.log). Job 348 has been submitted with SLURM jobid 53321 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_kgx/umls/53321.log). INFO snakemake.logging [2026-07-14T16:07:59+0000]: Job 348 has been submitted with SLURM jobid 53321 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_kgx/umls/53321.log). Job 214 has been submitted with SLURM jobid 53322 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_compress_umls/53322.log). INFO snakemake.logging [2026-07-14T16:07:59+0000]: Job 214 has been submitted with SLURM jobid 53322 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_compress_umls/53322.log). Job 320 has been submitted with SLURM jobid 53323 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_mapping_sources_table/53323.log). INFO snakemake.logging [2026-07-14T16:07:59+0000]: Job 320 has been submitted with SLURM jobid 53323 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_mapping_sources_table/53323.log). [Tue Jul 14 12:08:39 2026] Finished jobid: 260 (Rule: generate_content_report_for_compendium_umls) INFO snakemake.logging [2026-07-14T16:08:39+0000]: Finished jobid: 260 (Rule: generate_content_report_for_compendium_umls) 40 of 74 steps (54%) done INFO snakemake.logging [2026-07-14T16:08:39+0000]: None Select jobs to execute... INFO snakemake.logging [2026-07-14T16:08:39+0000]: Select jobs to execute... Execute 1 jobs... INFO snakemake.logging [2026-07-14T16:08:39+0000]: Execute 1 jobs... Job 237 has been submitted with SLURM jobid 53324 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_compendia_summary_report/53324.log). INFO snakemake.logging [2026-07-14T16:08:39+0000]: Job 237 has been submitted with SLURM jobid 53324 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_compendia_summary_report/53324.log). [Tue Jul 14 12:08:39 2026] Finished jobid: 320 (Rule: generate_mapping_sources_table) INFO snakemake.logging [2026-07-14T16:08:39+0000]: Finished jobid: 320 (Rule: generate_mapping_sources_table) 41 of 74 steps (55%) done INFO snakemake.logging [2026-07-14T16:08:39+0000]: None [Tue Jul 14 12:09:19 2026] Finished jobid: 348 (Rule: generate_kgx) INFO snakemake.logging [2026-07-14T16:09:19+0000]: Finished jobid: 348 (Rule: generate_kgx) 42 of 74 steps (57%) done INFO snakemake.logging [2026-07-14T16:09:19+0000]: None [Tue Jul 14 12:09:19 2026] Finished jobid: 214 (Rule: compress_umls) INFO snakemake.logging [2026-07-14T16:09:19+0000]: Finished jobid: 214 (Rule: compress_umls) 43 of 74 steps (58%) done INFO snakemake.logging [2026-07-14T16:09:19+0000]: None Removing temporary output babel_outputs/synonyms/umls.txt. INFO snakemake.logging [2026-07-14T16:09:19+0000]: Removing temporary output babel_outputs/synonyms/umls.txt. Select jobs to execute... INFO snakemake.logging [2026-07-14T16:09:19+0000]: Select jobs to execute... Execute 2 jobs... INFO snakemake.logging [2026-07-14T16:09:19+0000]: Execute 2 jobs... Job 312 has been submitted with SLURM jobid 53326 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_export_synonyms_to_duckdb/umls/53326.log). INFO snakemake.logging [2026-07-14T16:09:19+0000]: Job 312 has been submitted with SLURM jobid 53326 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_export_synonyms_to_duckdb/umls/53326.log). Job 368 has been submitted with SLURM jobid 53327 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_sapbert_training_data/umls.txt/53327.log). INFO snakemake.logging [2026-07-14T16:09:19+0000]: Job 368 has been submitted with SLURM jobid 53327 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_sapbert_training_data/umls.txt/53327.log). [Tue Jul 14 12:09:19 2026] Finished jobid: 237 (Rule: generate_compendia_summary_report) INFO snakemake.logging [2026-07-14T16:09:19+0000]: Finished jobid: 237 (Rule: generate_compendia_summary_report) 44 of 74 steps (59%) done INFO snakemake.logging [2026-07-14T16:09:19+0000]: None [Tue Jul 14 12:09:59 2026] Finished jobid: 292 (Rule: export_compendia_to_duckdb) INFO snakemake.logging [2026-07-14T16:09:59+0000]: Finished jobid: 292 (Rule: export_compendia_to_duckdb) 45 of 74 steps (61%) done INFO snakemake.logging [2026-07-14T16:09:59+0000]: None [Tue Jul 14 12:09:59 2026] Finished jobid: 312 (Rule: export_synonyms_to_duckdb) INFO snakemake.logging [2026-07-14T16:09:59+0000]: Finished jobid: 312 (Rule: export_synonyms_to_duckdb) 46 of 74 steps (62%) done INFO snakemake.logging [2026-07-14T16:09:59+0000]: None [Tue Jul 14 12:10:40 2026] Finished jobid: 368 (Rule: generate_sapbert_training_data) INFO snakemake.logging [2026-07-14T16:10:40+0000]: Finished jobid: 368 (Rule: generate_sapbert_training_data) 47 of 74 steps (64%) done INFO snakemake.logging [2026-07-14T16:10:40+0000]: None [Tue Jul 14 13:29:13 2026] Finished jobid: 275 (Rule: export_compendia_to_duckdb) INFO snakemake.logging [2026-07-14T17:29:13+0000]: Finished jobid: 275 (Rule: export_compendia_to_duckdb) 48 of 74 steps (65%) done INFO snakemake.logging [2026-07-14T17:29:13+0000]: None Select jobs to execute... INFO snakemake.logging [2026-07-14T17:29:13+0000]: Select jobs to execute... Execute 1 jobs... INFO snakemake.logging [2026-07-14T17:29:13+0000]: Execute 1 jobs... [Tue Jul 14 13:29:13 2026] localrule export_all_compendia_to_duckdb: input: babel_outputs/duckdb/duckdbs/filename=AnatomicalEntity/compendium.duckdb, babel_outputs/duckdb/duckdbs/filename=Cell/compendium.duckdb, babel_outputs/duckdb/duckdbs/filename=CellularComponent/compendium.duckdb, babel_outputs/duckdb/duckdbs/filename=GrossAnatomicalStructure/compendium.duckdb, babel_outputs/duckdb/duckdbs/filename=MolecularMixture/compendium.duckdb, babel_outputs/duckdb/duckdbs/filename=SmallMolecule/compendium.duckdb, babel_outputs/duckdb/duckdbs/filename=Polypeptide/compendium.duckdb, babel_outputs/duckdb/duckdbs/filename=ComplexMolecularMixture/compendium.duckdb, babel_outputs/duckdb/duckdbs/filename=ChemicalEntity/compendium.duckdb, babel_outputs/duckdb/duckdbs/filename=ChemicalMixture/compendium.duckdb, babel_outputs/duckdb/duckdbs/filename=Drug/compendium.duckdb, babel_outputs/duckdb/duckdbs/filename=Food/compendium.duckdb, babel_outputs/duckdb/duckdbs/filename=Disease/compendium.duckdb, babel_outputs/duckdb/duckdbs/filename=PhenotypicFeature/compendium.duckdb, babel_outputs/duckdb/duckdbs/filename=Gene/compendium.duckdb, babel_outputs/duckdb/duckdbs/filename=GeneFamily/compendium.duckdb, babel_outputs/duckdb/duckdbs/filename=Pathway/compendium.duckdb, babel_outputs/duckdb/duckdbs/filename=BiologicalProcess/compendium.duckdb, babel_outputs/duckdb/duckdbs/filename=MolecularActivity/compendium.duckdb, babel_outputs/duckdb/duckdbs/filename=Protein/compendium.duckdb, babel_outputs/duckdb/duckdbs/filename=OrganismTaxon/compendium.duckdb, babel_outputs/duckdb/duckdbs/filename=CellLine/compendium.duckdb, babel_outputs/duckdb/duckdbs/filename=umls/compendium.duckdb, babel_outputs/duckdb/duckdbs/filename=MacromolecularComplex/compendium.duckdb, babel_outputs/duckdb/duckdbs/filename=Publication/compendium.duckdb output: babel_outputs/duckdb/compendia_done jobid: 269 reason: Missing output files: babel_outputs/duckdb/compendia_done; Input files updated by another job: babel_outputs/duckdb/duckdbs/filename=Polypeptide/compendium.duckdb, babel_outputs/duckdb/duckdbs/filename=ComplexMolecularMixture/compendium.duckdb, babel_outputs/duckdb/duckdbs/filename=ChemicalEntity/compendium.duckdb, babel_outputs/duckdb/duckdbs/filename=SmallMolecule/compendium.duckdb, babel_outputs/duckdb/duckdbs/filename=umls/compendium.duckdb, babel_outputs/duckdb/duckdbs/filename=Food/compendium.duckdb, babel_outputs/duckdb/duckdbs/filename=Drug/compendium.duckdb, babel_outputs/duckdb/duckdbs/filename=ChemicalMixture/compendium.duckdb, babel_outputs/duckdb/duckdbs/filename=MolecularMixture/compendium.duckdb resources: tmpdir=/tmp, disk_mb=114764, disk=114.76 GB, disk_mib=109448, mem_mb=16000, mem=16 GB, mem_mib=15259, runtime=120, cpus_per_task=1 INFO snakemake.logging [2026-07-14T17:29:13+0000]: Rule: export_all_compendia_to_duckdb, Jobid: 269 INFO snakemake.logging [2026-07-14T17:29:13+0000]: Shell command: echo 'done' >> babel_outputs/duckdb/compendia_done [Tue Jul 14 13:29:13 2026] Finished jobid: 269 (Rule: export_all_compendia_to_duckdb) INFO snakemake.logging [2026-07-14T17:29:13+0000]: Finished jobid: 269 (Rule: export_all_compendia_to_duckdb) 49 of 74 steps (66%) done INFO snakemake.logging [2026-07-14T17:29:13+0000]: None Select jobs to execute... INFO snakemake.logging [2026-07-14T17:29:13+0000]: Select jobs to execute... Execute 1 jobs... INFO snakemake.logging [2026-07-14T17:29:13+0000]: Execute 1 jobs... Job 317 has been submitted with SLURM jobid 53345 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_export_intermediate_files_to_duckdb/53345.log). INFO snakemake.logging [2026-07-14T17:29:13+0000]: Job 317 has been submitted with SLURM jobid 53345 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_export_intermediate_files_to_duckdb/53345.log). [Tue Jul 14 13:39:14 2026] Finished jobid: 24 (Rule: chemical) INFO snakemake.logging [2026-07-14T17:39:14+0000]: Finished jobid: 24 (Rule: chemical) 50 of 74 steps (68%) done INFO snakemake.logging [2026-07-14T17:39:14+0000]: None Removing temporary output babel_outputs/synonyms/ChemicalMixture.txt. INFO snakemake.logging [2026-07-14T17:39:14+0000]: Removing temporary output babel_outputs/synonyms/ChemicalMixture.txt. Removing temporary output babel_outputs/synonyms/Drug.txt. INFO snakemake.logging [2026-07-14T17:39:14+0000]: Removing temporary output babel_outputs/synonyms/Drug.txt. Removing temporary output babel_outputs/synonyms/ComplexMolecularMixture.txt. INFO snakemake.logging [2026-07-14T17:39:14+0000]: Removing temporary output babel_outputs/synonyms/ComplexMolecularMixture.txt. Removing temporary output babel_outputs/synonyms/Polypeptide.txt. INFO snakemake.logging [2026-07-14T17:39:14+0000]: Removing temporary output babel_outputs/synonyms/Polypeptide.txt. Removing temporary output babel_outputs/synonyms/ChemicalEntity.txt. INFO snakemake.logging [2026-07-14T17:39:14+0000]: Removing temporary output babel_outputs/synonyms/ChemicalEntity.txt. Removing temporary output babel_outputs/synonyms/SmallMolecule.txt. INFO snakemake.logging [2026-07-14T17:39:14+0000]: Removing temporary output babel_outputs/synonyms/SmallMolecule.txt. Removing temporary output babel_outputs/synonyms/Food.txt. INFO snakemake.logging [2026-07-14T17:39:14+0000]: Removing temporary output babel_outputs/synonyms/Food.txt. Removing temporary output babel_outputs/synonyms/MolecularMixture.txt. INFO snakemake.logging [2026-07-14T17:39:14+0000]: Removing temporary output babel_outputs/synonyms/MolecularMixture.txt. Select jobs to execute... INFO snakemake.logging [2026-07-14T17:39:14+0000]: Select jobs to execute... Execute 1 jobs... INFO snakemake.logging [2026-07-14T17:39:14+0000]: Execute 1 jobs... Job 232 has been submitted with SLURM jobid 53348 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_drugchemical_conflated_synonyms/53348.log). INFO snakemake.logging [2026-07-14T17:39:14+0000]: Job 232 has been submitted with SLURM jobid 53348 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_drugchemical_conflated_synonyms/53348.log). [Tue Jul 14 13:51:15 2026] Finished jobid: 317 (Rule: export_intermediate_files_to_duckdb) INFO snakemake.logging [2026-07-14T17:51:15+0000]: Finished jobid: 317 (Rule: export_intermediate_files_to_duckdb) 51 of 74 steps (69%) done INFO snakemake.logging [2026-07-14T17:51:15+0000]: None Removing temporary output babel_outputs/duckdb/concords.duckdb. INFO snakemake.logging [2026-07-14T17:51:15+0000]: Removing temporary output babel_outputs/duckdb/concords.duckdb. [Tue Jul 14 14:15:47 2026] Finished jobid: 331 (Rule: generate_kgx) INFO snakemake.logging [2026-07-14T18:15:47+0000]: Finished jobid: 331 (Rule: generate_kgx) 52 of 74 steps (70%) done INFO snakemake.logging [2026-07-14T18:15:47+0000]: None Select jobs to execute... INFO snakemake.logging [2026-07-14T18:15:47+0000]: Select jobs to execute... Execute 1 jobs... INFO snakemake.logging [2026-07-14T18:15:47+0000]: Execute 1 jobs... [Tue Jul 14 14:15:47 2026] localrule export_all_to_kgx: input: babel_outputs/kgx/AnatomicalEntity_nodes.jsonl.gz, babel_outputs/kgx/Cell_nodes.jsonl.gz, babel_outputs/kgx/CellularComponent_nodes.jsonl.gz, babel_outputs/kgx/GrossAnatomicalStructure_nodes.jsonl.gz, babel_outputs/kgx/MolecularMixture_nodes.jsonl.gz, babel_outputs/kgx/SmallMolecule_nodes.jsonl.gz, babel_outputs/kgx/Polypeptide_nodes.jsonl.gz, babel_outputs/kgx/ComplexMolecularMixture_nodes.jsonl.gz, babel_outputs/kgx/ChemicalEntity_nodes.jsonl.gz, babel_outputs/kgx/ChemicalMixture_nodes.jsonl.gz, babel_outputs/kgx/Drug_nodes.jsonl.gz, babel_outputs/kgx/Food_nodes.jsonl.gz, babel_outputs/kgx/Disease_nodes.jsonl.gz, babel_outputs/kgx/PhenotypicFeature_nodes.jsonl.gz, babel_outputs/kgx/Gene_nodes.jsonl.gz, babel_outputs/kgx/GeneFamily_nodes.jsonl.gz, babel_outputs/kgx/Pathway_nodes.jsonl.gz, babel_outputs/kgx/BiologicalProcess_nodes.jsonl.gz, babel_outputs/kgx/MolecularActivity_nodes.jsonl.gz, babel_outputs/kgx/Protein_nodes.jsonl.gz, babel_outputs/kgx/OrganismTaxon_nodes.jsonl.gz, babel_outputs/kgx/CellLine_nodes.jsonl.gz, babel_outputs/kgx/umls_nodes.jsonl.gz, babel_outputs/kgx/MacromolecularComplex_nodes.jsonl.gz, babel_outputs/kgx/Publication_nodes.jsonl.gz, babel_outputs/kgx/AnatomicalEntity_edges.jsonl.gz, babel_outputs/kgx/Cell_edges.jsonl.gz, babel_outputs/kgx/CellularComponent_edges.jsonl.gz, babel_outputs/kgx/GrossAnatomicalStructure_edges.jsonl.gz, babel_outputs/kgx/MolecularMixture_edges.jsonl.gz, babel_outputs/kgx/SmallMolecule_edges.jsonl.gz, babel_outputs/kgx/Polypeptide_edges.jsonl.gz, babel_outputs/kgx/ComplexMolecularMixture_edges.jsonl.gz, babel_outputs/kgx/ChemicalEntity_edges.jsonl.gz, babel_outputs/kgx/ChemicalMixture_edges.jsonl.gz, babel_outputs/kgx/Drug_edges.jsonl.gz, babel_outputs/kgx/Food_edges.jsonl.gz, babel_outputs/kgx/Disease_edges.jsonl.gz, babel_outputs/kgx/PhenotypicFeature_edges.jsonl.gz, babel_outputs/kgx/Gene_edges.jsonl.gz, babel_outputs/kgx/GeneFamily_edges.jsonl.gz, babel_outputs/kgx/Pathway_edges.jsonl.gz, babel_outputs/kgx/BiologicalProcess_edges.jsonl.gz, babel_outputs/kgx/MolecularActivity_edges.jsonl.gz, babel_outputs/kgx/Protein_edges.jsonl.gz, babel_outputs/kgx/OrganismTaxon_edges.jsonl.gz, babel_outputs/kgx/CellLine_edges.jsonl.gz, babel_outputs/kgx/umls_edges.jsonl.gz, babel_outputs/kgx/MacromolecularComplex_edges.jsonl.gz, babel_outputs/kgx/Publication_edges.jsonl.gz output: babel_outputs/kgx/done jobid: 325 reason: Missing output files: babel_outputs/kgx/done; Input files updated by another job: babel_outputs/kgx/Polypeptide_edges.jsonl.gz, babel_outputs/kgx/Drug_nodes.jsonl.gz, babel_outputs/kgx/Food_edges.jsonl.gz, babel_outputs/kgx/MolecularMixture_nodes.jsonl.gz, babel_outputs/kgx/SmallMolecule_nodes.jsonl.gz, babel_outputs/kgx/umls_edges.jsonl.gz, babel_outputs/kgx/SmallMolecule_edges.jsonl.gz, babel_outputs/kgx/Food_nodes.jsonl.gz, babel_outputs/kgx/MolecularMixture_edges.jsonl.gz, babel_outputs/kgx/ChemicalEntity_edges.jsonl.gz, babel_outputs/kgx/ComplexMolecularMixture_nodes.jsonl.gz, babel_outputs/kgx/Drug_edges.jsonl.gz, babel_outputs/kgx/ChemicalEntity_nodes.jsonl.gz, babel_outputs/kgx/Polypeptide_nodes.jsonl.gz, babel_outputs/kgx/ChemicalMixture_edges.jsonl.gz, babel_outputs/kgx/ChemicalMixture_nodes.jsonl.gz, babel_outputs/kgx/umls_nodes.jsonl.gz, babel_outputs/kgx/ComplexMolecularMixture_edges.jsonl.gz resources: tmpdir=/tmp, disk_mb=52662, disk=52.66 GB, disk_mib=50223, mem_mb=16000, mem=16 GB, mem_mib=15259, runtime=120, cpus_per_task=1 INFO snakemake.logging [2026-07-14T18:15:47+0000]: Rule: export_all_to_kgx, Jobid: 325 INFO snakemake.logging [2026-07-14T18:15:47+0000]: Shell command: echo 'done' >> babel_outputs/kgx/done [Tue Jul 14 14:15:47 2026] Finished jobid: 325 (Rule: export_all_to_kgx) INFO snakemake.logging [2026-07-14T18:15:47+0000]: Finished jobid: 325 (Rule: export_all_to_kgx) 53 of 74 steps (72%) done INFO snakemake.logging [2026-07-14T18:15:47+0000]: None [Tue Jul 14 16:25:22 2026] Finished jobid: 232 (Rule: drugchemical_conflated_synonyms) INFO snakemake.logging [2026-07-14T20:25:22+0000]: Finished jobid: 232 (Rule: drugchemical_conflated_synonyms) 54 of 74 steps (73%) done INFO snakemake.logging [2026-07-14T20:25:22+0000]: None Select jobs to execute... INFO snakemake.logging [2026-07-14T20:25:22+0000]: Select jobs to execute... Execute 3 jobs... INFO snakemake.logging [2026-07-14T20:25:23+0000]: Execute 3 jobs... [Tue Jul 14 16:25:23 2026] localrule drugchemical: input: babel_outputs/conflation/DrugChemical.txt, babel_outputs/synonyms/DrugChemicalConflated.txt.gz output: babel_outputs/reports/drugchemical_done jobid: 226 reason: Missing output files: babel_outputs/reports/drugchemical_done; Input files updated by another job: babel_outputs/conflation/DrugChemical.txt, babel_outputs/synonyms/DrugChemicalConflated.txt.gz resources: tmpdir=/tmp, disk_mb=13007, disk=13.01 GB, disk_mib=12405, mem_mb=16000, mem=16 GB, mem_mib=15259, runtime=120, cpus_per_task=1 INFO snakemake.logging [2026-07-14T20:25:23+0000]: Rule: drugchemical, Jobid: 226 INFO snakemake.logging [2026-07-14T20:25:23+0000]: Shell command: None [Tue Jul 14 16:25:23 2026] Finished jobid: 226 (Rule: drugchemical) INFO snakemake.logging [2026-07-14T20:25:23+0000]: Finished jobid: 226 (Rule: drugchemical) 55 of 74 steps (74%) done INFO snakemake.logging [2026-07-14T20:25:23+0000]: None Select jobs to execute... INFO snakemake.logging [2026-07-14T20:25:23+0000]: Select jobs to execute... Job 310 has been submitted with SLURM jobid 53408 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_export_synonyms_to_duckdb/DrugChemicalConflated/53408.log). INFO snakemake.logging [2026-07-14T20:25:23+0000]: Job 310 has been submitted with SLURM jobid 53408 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_export_synonyms_to_duckdb/DrugChemicalConflated/53408.log). Job 366 has been submitted with SLURM jobid 53409 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_sapbert_training_data/DrugChemicalConflated.txt/53409.log). INFO snakemake.logging [2026-07-14T20:25:23+0000]: Job 366 has been submitted with SLURM jobid 53409 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_sapbert_training_data/DrugChemicalConflated.txt/53409.log). Execute 1 jobs... INFO snakemake.logging [2026-07-14T20:25:23+0000]: Execute 1 jobs... [Tue Jul 14 16:25:23 2026] localrule all_outputs: input: babel_outputs/reports/anatomy_done, babel_outputs/reports/chemicals_done, babel_outputs/reports/disease_done, babel_outputs/reports/gene_done, babel_outputs/reports/genefamily_done, babel_outputs/reports/geneprotein_done, babel_outputs/reports/process_done, babel_outputs/reports/protein_done, babel_outputs/reports/taxon_done, babel_outputs/reports/cell_line_done, babel_outputs/reports/umls_done, babel_outputs/reports/macromolecular_complex_done, babel_outputs/reports/drugchemical_done, babel_outputs/reports/publications_done output: babel_outputs/reports/outputs_done jobid: 1 reason: Missing output files: babel_outputs/reports/outputs_done; Input files updated by another job: babel_outputs/reports/umls_done, babel_outputs/reports/chemicals_done, babel_outputs/reports/drugchemical_done resources: tmpdir=/tmp, disk_mb=1000, disk=1 GB, disk_mib=954, mem_mb=16000, mem=16 GB, mem_mib=15259, runtime=120, cpus_per_task=1 INFO snakemake.logging [2026-07-14T20:25:23+0000]: Rule: all_outputs, Jobid: 1 INFO snakemake.logging [2026-07-14T20:25:23+0000]: Shell command: None [Tue Jul 14 16:25:23 2026] Finished jobid: 1 (Rule: all_outputs) INFO snakemake.logging [2026-07-14T20:25:23+0000]: Finished jobid: 1 (Rule: all_outputs) 56 of 74 steps (76%) done INFO snakemake.logging [2026-07-14T20:25:23+0000]: None Select jobs to execute... INFO snakemake.logging [2026-07-14T20:25:23+0000]: Select jobs to execute... Execute 3 jobs... INFO snakemake.logging [2026-07-14T20:25:23+0000]: Execute 3 jobs... Job 264 has been submitted with SLURM jobid 53410 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_check_synonyms_gzipped_files/53410.log). INFO snakemake.logging [2026-07-14T20:25:23+0000]: Job 264 has been submitted with SLURM jobid 53410 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_check_synonyms_gzipped_files/53410.log). Job 263 has been submitted with SLURM jobid 53411 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_check_compendia_files/53411.log). INFO snakemake.logging [2026-07-14T20:25:23+0000]: Job 263 has been submitted with SLURM jobid 53411 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_check_compendia_files/53411.log). Job 265 has been submitted with SLURM jobid 53412 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_check_conflation_files/53412.log). INFO snakemake.logging [2026-07-14T20:25:23+0000]: Job 265 has been submitted with SLURM jobid 53412 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_check_conflation_files/53412.log). [Tue Jul 14 16:26:03 2026] Finished jobid: 264 (Rule: check_synonyms_gzipped_files) INFO snakemake.logging [2026-07-14T20:26:03+0000]: Finished jobid: 264 (Rule: check_synonyms_gzipped_files) 57 of 74 steps (77%) done INFO snakemake.logging [2026-07-14T20:26:03+0000]: None [Tue Jul 14 16:26:03 2026] Finished jobid: 263 (Rule: check_compendia_files) INFO snakemake.logging [2026-07-14T20:26:03+0000]: Finished jobid: 263 (Rule: check_compendia_files) 58 of 74 steps (78%) done INFO snakemake.logging [2026-07-14T20:26:03+0000]: None [Tue Jul 14 16:26:03 2026] Finished jobid: 265 (Rule: check_conflation_files) INFO snakemake.logging [2026-07-14T20:26:03+0000]: Finished jobid: 265 (Rule: check_conflation_files) 59 of 74 steps (80%) done INFO snakemake.logging [2026-07-14T20:26:03+0000]: None [Tue Jul 14 16:36:03 2026] Finished jobid: 310 (Rule: export_synonyms_to_duckdb) INFO snakemake.logging [2026-07-14T20:36:03+0000]: Finished jobid: 310 (Rule: export_synonyms_to_duckdb) 60 of 74 steps (81%) done INFO snakemake.logging [2026-07-14T20:36:03+0000]: None Select jobs to execute... INFO snakemake.logging [2026-07-14T20:36:03+0000]: Select jobs to execute... Execute 1 jobs... INFO snakemake.logging [2026-07-14T20:36:03+0000]: Execute 1 jobs... [Tue Jul 14 16:36:03 2026] localrule export_all_synonyms_to_duckdb: input: babel_outputs/duckdb/duckdbs/filename=AnatomicalEntity/synonyms.duckdb, babel_outputs/duckdb/duckdbs/filename=Cell/synonyms.duckdb, babel_outputs/duckdb/duckdbs/filename=CellularComponent/synonyms.duckdb, babel_outputs/duckdb/duckdbs/filename=GrossAnatomicalStructure/synonyms.duckdb, babel_outputs/duckdb/duckdbs/filename=Gene/synonyms.duckdb, babel_outputs/duckdb/duckdbs/filename=Protein/synonyms.duckdb, babel_outputs/duckdb/duckdbs/filename=Disease/synonyms.duckdb, babel_outputs/duckdb/duckdbs/filename=PhenotypicFeature/synonyms.duckdb, babel_outputs/duckdb/duckdbs/filename=Pathway/synonyms.duckdb, babel_outputs/duckdb/duckdbs/filename=BiologicalProcess/synonyms.duckdb, babel_outputs/duckdb/duckdbs/filename=MolecularActivity/synonyms.duckdb, babel_outputs/duckdb/duckdbs/filename=OrganismTaxon/synonyms.duckdb, babel_outputs/duckdb/duckdbs/filename=CellLine/synonyms.duckdb, babel_outputs/duckdb/duckdbs/filename=GeneFamily/synonyms.duckdb, babel_outputs/duckdb/duckdbs/filename=DrugChemicalConflated/synonyms.duckdb, babel_outputs/duckdb/duckdbs/filename=GeneProteinConflated/synonyms.duckdb, babel_outputs/duckdb/duckdbs/filename=umls/synonyms.duckdb, babel_outputs/duckdb/duckdbs/filename=MacromolecularComplex/synonyms.duckdb output: babel_outputs/duckdb/synonyms_done jobid: 295 reason: Missing output files: babel_outputs/duckdb/synonyms_done; Input files updated by another job: babel_outputs/duckdb/duckdbs/filename=umls/synonyms.duckdb, babel_outputs/duckdb/duckdbs/filename=DrugChemicalConflated/synonyms.duckdb resources: tmpdir=/tmp, disk_mb=1000, disk=1 GB, disk_mib=954, mem_mb=16000, mem=16 GB, mem_mib=15259, runtime=120, cpus_per_task=1 INFO snakemake.logging [2026-07-14T20:36:03+0000]: Rule: export_all_synonyms_to_duckdb, Jobid: 295 INFO snakemake.logging [2026-07-14T20:36:03+0000]: Shell command: echo 'done' >> babel_outputs/duckdb/synonyms_done [Tue Jul 14 16:36:03 2026] Finished jobid: 295 (Rule: export_all_synonyms_to_duckdb) INFO snakemake.logging [2026-07-14T20:36:03+0000]: Finished jobid: 295 (Rule: export_all_synonyms_to_duckdb) 61 of 74 steps (82%) done INFO snakemake.logging [2026-07-14T20:36:03+0000]: None Select jobs to execute... INFO snakemake.logging [2026-07-14T20:36:03+0000]: Select jobs to execute... Execute 1 jobs... INFO snakemake.logging [2026-07-14T20:36:03+0000]: Execute 1 jobs... [Tue Jul 14 16:36:03 2026] localrule export_all_to_duckdb: input: babel_outputs/duckdb/compendia_done, babel_outputs/duckdb/synonyms_done, babel_outputs/duckdb/conflations_done, babel_outputs/duckdb/Identifier.parquet, babel_outputs/duckdb/Concord.parquet, babel_outputs/duckdb/Metadata.parquet output: babel_outputs/duckdb/done jobid: 268 reason: Missing output files: babel_outputs/duckdb/done; Input files updated by another job: babel_outputs/duckdb/Identifier.parquet, babel_outputs/duckdb/synonyms_done, babel_outputs/duckdb/Metadata.parquet, babel_outputs/duckdb/conflations_done, babel_outputs/duckdb/Concord.parquet, babel_outputs/duckdb/compendia_done resources: tmpdir=/tmp, disk_mb=13329, disk=13.33 GB, disk_mib=12712, mem_mb=16000, mem=16 GB, mem_mib=15259, runtime=120, cpus_per_task=1 INFO snakemake.logging [2026-07-14T20:36:03+0000]: Rule: export_all_to_duckdb, Jobid: 268 INFO snakemake.logging [2026-07-14T20:36:03+0000]: Shell command: echo 'done' >> babel_outputs/duckdb/done [Tue Jul 14 16:36:04 2026] Finished jobid: 268 (Rule: export_all_to_duckdb) INFO snakemake.logging [2026-07-14T20:36:04+0000]: Finished jobid: 268 (Rule: export_all_to_duckdb) 62 of 74 steps (84%) done INFO snakemake.logging [2026-07-14T20:36:04+0000]: None Select jobs to execute... INFO snakemake.logging [2026-07-14T20:36:04+0000]: Select jobs to execute... Execute 5 jobs... INFO snakemake.logging [2026-07-14T20:36:04+0000]: Execute 5 jobs... Job 319 has been submitted with SLURM jobid 53419 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_clique_leader_report/53419.log). INFO snakemake.logging [2026-07-14T20:36:04+0000]: Job 319 has been submitted with SLURM jobid 53419 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_clique_leader_report/53419.log). Job 324 has been submitted with SLURM jobid 53420 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_check_for_duplicate_clique_leaders/53420.log). INFO snakemake.logging [2026-07-14T20:36:04+0000]: Job 324 has been submitted with SLURM jobid 53420 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_check_for_duplicate_clique_leaders/53420.log). Job 323 has been submitted with SLURM jobid 53421 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_check_for_duplicate_curies/53421.log). INFO snakemake.logging [2026-07-14T20:36:04+0000]: Job 323 has been submitted with SLURM jobid 53421 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_check_for_duplicate_curies/53421.log). Job 267 has been submitted with SLURM jobid 53422 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_curie_report/53422.log). INFO snakemake.logging [2026-07-14T20:36:04+0000]: Job 267 has been submitted with SLURM jobid 53422 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_curie_report/53422.log). Job 322 has been submitted with SLURM jobid 53423 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_check_for_identically_labeled_cliques/53423.log). INFO snakemake.logging [2026-07-14T20:36:04+0000]: Job 322 has been submitted with SLURM jobid 53423 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_check_for_identically_labeled_cliques/53423.log). [Tue Jul 14 16:41:04 2026] Finished jobid: 324 (Rule: check_for_duplicate_clique_leaders) INFO snakemake.logging [2026-07-14T20:41:04+0000]: Finished jobid: 324 (Rule: check_for_duplicate_clique_leaders) 63 of 74 steps (85%) done INFO snakemake.logging [2026-07-14T20:41:04+0000]: None Removing temporary output babel_outputs/duckdb/duckdbs/duplicate_clique_leaders.duckdb. INFO snakemake.logging [2026-07-14T20:41:04+0000]: Removing temporary output babel_outputs/duckdb/duckdbs/duplicate_clique_leaders.duckdb. [Tue Jul 14 16:41:44 2026] Finished jobid: 319 (Rule: generate_clique_leader_report) INFO snakemake.logging [2026-07-14T20:41:44+0000]: Finished jobid: 319 (Rule: generate_clique_leader_report) 64 of 74 steps (86%) done INFO snakemake.logging [2026-07-14T20:41:44+0000]: None Removing temporary output babel_outputs/duckdb/duckdbs/clique_leaders.duckdb. INFO snakemake.logging [2026-07-14T20:41:44+0000]: Removing temporary output babel_outputs/duckdb/duckdbs/clique_leaders.duckdb. Select jobs to execute... INFO snakemake.logging [2026-07-14T20:41:44+0000]: Select jobs to execute... Execute 1 jobs... INFO snakemake.logging [2026-07-14T20:41:44+0000]: Execute 1 jobs... Job 318 has been submitted with SLURM jobid 53425 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_cliques_table/53425.log). INFO snakemake.logging [2026-07-14T20:41:44+0000]: Job 318 has been submitted with SLURM jobid 53425 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_cliques_table/53425.log). [Tue Jul 14 16:42:24 2026] Finished jobid: 267 (Rule: generate_curie_report) INFO snakemake.logging [2026-07-14T20:42:24+0000]: Finished jobid: 267 (Rule: generate_curie_report) 65 of 74 steps (88%) done INFO snakemake.logging [2026-07-14T20:42:24+0000]: None Removing temporary output babel_outputs/duckdb/duckdbs/curie_report.duckdb. INFO snakemake.logging [2026-07-14T20:42:24+0000]: Removing temporary output babel_outputs/duckdb/duckdbs/curie_report.duckdb. Select jobs to execute... INFO snakemake.logging [2026-07-14T20:42:24+0000]: Select jobs to execute... Execute 1 jobs... INFO snakemake.logging [2026-07-14T20:42:24+0000]: Execute 1 jobs... Job 266 has been submitted with SLURM jobid 53426 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_prefix_table/53426.log). INFO snakemake.logging [2026-07-14T20:42:24+0000]: Job 266 has been submitted with SLURM jobid 53426 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_prefix_table/53426.log). [Tue Jul 14 16:42:24 2026] Finished jobid: 318 (Rule: generate_cliques_table) INFO snakemake.logging [2026-07-14T20:42:24+0000]: Finished jobid: 318 (Rule: generate_cliques_table) 66 of 74 steps (89%) done INFO snakemake.logging [2026-07-14T20:42:24+0000]: None [Tue Jul 14 16:43:04 2026] Finished jobid: 266 (Rule: generate_prefix_table) INFO snakemake.logging [2026-07-14T20:43:04+0000]: Finished jobid: 266 (Rule: generate_prefix_table) 67 of 74 steps (91%) done INFO snakemake.logging [2026-07-14T20:43:04+0000]: None Select jobs to execute... INFO snakemake.logging [2026-07-14T20:43:04+0000]: Select jobs to execute... Execute 1 jobs... INFO snakemake.logging [2026-07-14T20:43:04+0000]: Execute 1 jobs... [Tue Jul 14 16:43:04 2026] localrule all_reports: input: babel_outputs/reports/content/compendia_report.json, babel_outputs/reports/check_compendia_files.done, babel_outputs/reports/check_synonyms_files.done, babel_outputs/reports/check_conflation_files.done, babel_outputs/reports/tables/prefix_table.csv, babel_outputs/reports/tables/cliques_table.csv, babel_outputs/reports/tables/mapping_sources_table.csv output: babel_outputs/reports/reports_done jobid: 236 reason: Missing output files: babel_outputs/reports/reports_done; Input files updated by another job: babel_outputs/reports/tables/mapping_sources_table.csv, babel_outputs/reports/check_compendia_files.done, babel_outputs/reports/content/compendia_report.json, babel_outputs/reports/check_conflation_files.done, babel_outputs/reports/tables/prefix_table.csv, babel_outputs/reports/check_synonyms_files.done, babel_outputs/reports/tables/cliques_table.csv resources: tmpdir=/tmp, disk_mb=1000, disk=1 GB, disk_mib=954, mem_mb=16000, mem=16 GB, mem_mib=15259, runtime=120, cpus_per_task=1 INFO snakemake.logging [2026-07-14T20:43:04+0000]: Rule: all_reports, Jobid: 236 INFO snakemake.logging [2026-07-14T20:43:04+0000]: Shell command: echo 'done' >> babel_outputs/reports/reports_done [Tue Jul 14 16:43:04 2026] Finished jobid: 236 (Rule: all_reports) INFO snakemake.logging [2026-07-14T20:43:04+0000]: Finished jobid: 236 (Rule: all_reports) 68 of 74 steps (92%) done INFO snakemake.logging [2026-07-14T20:43:04+0000]: None [Tue Jul 14 16:49:35 2026] Finished jobid: 323 (Rule: check_for_duplicate_curies) INFO snakemake.logging [2026-07-14T20:49:35+0000]: Finished jobid: 323 (Rule: check_for_duplicate_curies) 69 of 74 steps (93%) done INFO snakemake.logging [2026-07-14T20:49:35+0000]: None Removing temporary output babel_outputs/duckdb/duckdbs/duplicate_curies.duckdb. INFO snakemake.logging [2026-07-14T20:49:35+0000]: Removing temporary output babel_outputs/duckdb/duckdbs/duplicate_curies.duckdb. [Tue Jul 14 16:49:35 2026] Finished jobid: 322 (Rule: check_for_identically_labeled_cliques) INFO snakemake.logging [2026-07-14T20:49:35+0000]: Finished jobid: 322 (Rule: check_for_identically_labeled_cliques) 70 of 74 steps (95%) done INFO snakemake.logging [2026-07-14T20:49:35+0000]: None Removing temporary output babel_outputs/duckdb/duckdbs/identically_labeled_clique.duckdb. INFO snakemake.logging [2026-07-14T20:49:35+0000]: Removing temporary output babel_outputs/duckdb/duckdbs/identically_labeled_clique.duckdb. Select jobs to execute... INFO snakemake.logging [2026-07-14T20:49:35+0000]: Select jobs to execute... Execute 1 jobs... INFO snakemake.logging [2026-07-14T20:49:35+0000]: Execute 1 jobs... [Tue Jul 14 16:49:35 2026] localrule all_duckdb_reports: input: babel_outputs/duckdb/done, babel_outputs/reports/duckdb/identically_labeled_cliques.tsv.gz, babel_outputs/reports/duckdb/duplicate_curies.tsv, babel_outputs/reports/duckdb/duplicate_clique_leaders.tsv, babel_outputs/reports/duckdb/curie_report.json, babel_outputs/reports/duckdb/clique_leaders.json output: babel_outputs/reports/duckdb/done jobid: 321 reason: Missing output files: babel_outputs/reports/duckdb/done; Input files updated by another job: babel_outputs/reports/duckdb/identically_labeled_cliques.tsv.gz, babel_outputs/reports/duckdb/duplicate_clique_leaders.tsv, babel_outputs/reports/duckdb/clique_leaders.json, babel_outputs/reports/duckdb/duplicate_curies.tsv, babel_outputs/reports/duckdb/curie_report.json, babel_outputs/duckdb/done resources: tmpdir=/tmp, disk_mb=1000, disk=1 GB, disk_mib=954, mem_mb=16000, mem=16 GB, mem_mib=15259, runtime=120, cpus_per_task=1 INFO snakemake.logging [2026-07-14T20:49:35+0000]: Rule: all_duckdb_reports, Jobid: 321 INFO snakemake.logging [2026-07-14T20:49:35+0000]: Shell command: echo 'done' >> babel_outputs/reports/duckdb/done [Tue Jul 14 16:49:35 2026] Finished jobid: 321 (Rule: all_duckdb_reports) INFO snakemake.logging [2026-07-14T20:49:35+0000]: Finished jobid: 321 (Rule: all_duckdb_reports) 71 of 74 steps (96%) done INFO snakemake.logging [2026-07-14T20:49:35+0000]: None [Tue Jul 14 18:02:08 2026] Finished jobid: 366 (Rule: generate_sapbert_training_data) INFO snakemake.logging [2026-07-14T22:02:08+0000]: Finished jobid: 366 (Rule: generate_sapbert_training_data) 72 of 74 steps (97%) done INFO snakemake.logging [2026-07-14T22:02:08+0000]: None Select jobs to execute... INFO snakemake.logging [2026-07-14T22:02:08+0000]: Select jobs to execute... Execute 1 jobs... INFO snakemake.logging [2026-07-14T22:02:08+0000]: Execute 1 jobs... [Tue Jul 14 18:02:08 2026] localrule export_all_to_sapbert_training: input: babel_outputs/sapbert-training-data/AnatomicalEntity.txt.gz, babel_outputs/sapbert-training-data/Cell.txt.gz, babel_outputs/sapbert-training-data/CellularComponent.txt.gz, babel_outputs/sapbert-training-data/GrossAnatomicalStructure.txt.gz, babel_outputs/sapbert-training-data/Gene.txt.gz, babel_outputs/sapbert-training-data/Protein.txt.gz, babel_outputs/sapbert-training-data/Disease.txt.gz, babel_outputs/sapbert-training-data/PhenotypicFeature.txt.gz, babel_outputs/sapbert-training-data/Pathway.txt.gz, babel_outputs/sapbert-training-data/BiologicalProcess.txt.gz, babel_outputs/sapbert-training-data/MolecularActivity.txt.gz, babel_outputs/sapbert-training-data/OrganismTaxon.txt.gz, babel_outputs/sapbert-training-data/CellLine.txt.gz, babel_outputs/sapbert-training-data/GeneFamily.txt.gz, babel_outputs/sapbert-training-data/DrugChemicalConflated.txt.gz, babel_outputs/sapbert-training-data/GeneProteinConflated.txt.gz, babel_outputs/sapbert-training-data/umls.txt.gz, babel_outputs/sapbert-training-data/MacromolecularComplex.txt.gz output: babel_outputs/sapbert-training-data/done jobid: 351 reason: Missing output files: babel_outputs/sapbert-training-data/done; Input files updated by another job: babel_outputs/sapbert-training-data/umls.txt.gz, babel_outputs/sapbert-training-data/DrugChemicalConflated.txt.gz resources: tmpdir=/tmp, disk_mb=41374, disk=41.37 GB, disk_mib=39458, mem_mb=16000, mem=16 GB, mem_mib=15259, runtime=120, cpus_per_task=1 INFO snakemake.logging [2026-07-14T22:02:08+0000]: Rule: export_all_to_sapbert_training, Jobid: 351 INFO snakemake.logging [2026-07-14T22:02:08+0000]: Shell command: echo 'done' >> babel_outputs/sapbert-training-data/done [Tue Jul 14 18:02:09 2026] Finished jobid: 351 (Rule: export_all_to_sapbert_training) INFO snakemake.logging [2026-07-14T22:02:09+0000]: Finished jobid: 351 (Rule: export_all_to_sapbert_training) 73 of 74 steps (99%) done INFO snakemake.logging [2026-07-14T22:02:09+0000]: None Select jobs to execute... INFO snakemake.logging [2026-07-14T22:02:09+0000]: Select jobs to execute... Execute 1 jobs... INFO snakemake.logging [2026-07-14T22:02:09+0000]: Execute 1 jobs... [Tue Jul 14 18:02:09 2026] localrule all: input: babel_outputs/reports/outputs_done, babel_outputs/reports/reports_done, babel_outputs/duckdb/done, babel_outputs/reports/duckdb/done, babel_outputs/kgx/done, babel_outputs/sapbert-training-data/done, config.yaml output: babel_outputs/reports/all_done, babel_outputs/config.yaml jobid: 0 reason: Input files updated by another job: babel_outputs/reports/outputs_done, babel_outputs/reports/reports_done, babel_outputs/sapbert-training-data/done, babel_outputs/reports/duckdb/done, babel_outputs/kgx/done, babel_outputs/duckdb/done resources: tmpdir=/tmp, disk_mb=1000, disk=1 GB, disk_mib=954, mem_mb=16000, mem=16 GB, mem_mib=15259, runtime=120, cpus_per_task=1 INFO snakemake.logging [2026-07-14T22:02:09+0000]: Rule: all, Jobid: 0 INFO snakemake.logging [2026-07-14T22:02:09+0000]: Shell command: None [Tue Jul 14 18:02:09 2026] Finished jobid: 0 (Rule: all) INFO snakemake.logging [2026-07-14T22:02:09+0000]: Finished jobid: 0 (Rule: all) 74 of 74 steps (100%) done INFO snakemake.logging [2026-07-14T22:02:09+0000]: None Job 53219.0 for rule 'rule_chemical_drugbank_food_extracts' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-14T22:02:49+0000]: Job 53219.0 for rule 'rule_chemical_drugbank_food_extracts' (python) has low CPU efficiency: 0.0%. Job 53220.0 for rule 'rule_get_drugbank_labels_and_synonyms' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-14T22:02:49+0000]: Job 53220.0 for rule 'rule_get_drugbank_labels_and_synonyms' (python) has low CPU efficiency: 0.0%. Job 53221.0 for rule 'rule_untyped_chemical_compendia' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-14T22:02:49+0000]: Job 53221.0 for rule 'rule_untyped_chemical_compendia' (python) has low CPU efficiency: 0.0%. Job 53235.0 for rule 'rule_chemical_compendia' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-14T22:02:49+0000]: Job 53235.0 for rule 'rule_chemical_compendia' (python) has low CPU efficiency: 0.0%. Job 53267.0 for rule 'rule_export_compendia_to_duckdb_wildcards_ComplexMolecularMixture' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-14T22:02:49+0000]: Job 53267.0 for rule 'rule_export_compendia_to_duckdb_wildcards_ComplexMolecularMixture' (python) has low CPU efficiency: 0.0%. Job 53268.0 for rule 'rule_export_compendia_to_duckdb_wildcards_ChemicalEntity' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-14T22:02:49+0000]: Job 53268.0 for rule 'rule_export_compendia_to_duckdb_wildcards_ChemicalEntity' (python) has low CPU efficiency: 0.0%. Job 53269.0 for rule 'rule_export_compendia_to_duckdb_wildcards_ChemicalMixture' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-14T22:02:49+0000]: Job 53269.0 for rule 'rule_export_compendia_to_duckdb_wildcards_ChemicalMixture' (python) has low CPU efficiency: 0.0%. Job 53270.0 for rule 'rule_export_compendia_to_duckdb_wildcards_Drug' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-14T22:02:49+0000]: Job 53270.0 for rule 'rule_export_compendia_to_duckdb_wildcards_Drug' (python) has low CPU efficiency: 0.0%. Job 53271.0 for rule 'rule_export_compendia_to_duckdb_wildcards_Food' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-14T22:02:49+0000]: Job 53271.0 for rule 'rule_export_compendia_to_duckdb_wildcards_Food' (python) has low CPU efficiency: 0.0%. Job 53272.0 for rule 'rule_export_compendia_to_duckdb_wildcards_MolecularMixture' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-14T22:02:49+0000]: Job 53272.0 for rule 'rule_export_compendia_to_duckdb_wildcards_MolecularMixture' (python) has low CPU efficiency: 0.0%. Job 53273.0 for rule 'rule_export_compendia_to_duckdb_wildcards_SmallMolecule' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-14T22:02:49+0000]: Job 53273.0 for rule 'rule_export_compendia_to_duckdb_wildcards_SmallMolecule' (python) has low CPU efficiency: 0.0%. Job 53274.0 for rule 'rule_export_compendia_to_duckdb_wildcards_Polypeptide' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-14T22:02:49+0000]: Job 53274.0 for rule 'rule_export_compendia_to_duckdb_wildcards_Polypeptide' (python) has low CPU efficiency: 0.0%. Job 53275.0 for rule 'rule_generate_content_report_for_compendium_ComplexMolecularMixture' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-14T22:02:49+0000]: Job 53275.0 for rule 'rule_generate_content_report_for_compendium_ComplexMolecularMixture' (python) has low CPU efficiency: 0.0%. Job 53276.0 for rule 'rule_drugchemical_conflation' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-14T22:02:49+0000]: Job 53276.0 for rule 'rule_drugchemical_conflation' (python) has low CPU efficiency: 0.0%. Job 53277.0 for rule 'rule_check_chemical_entity' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-14T22:02:49+0000]: Job 53277.0 for rule 'rule_check_chemical_entity' (python) has low CPU efficiency: 0.0%. Job 53278.0 for rule 'rule_generate_kgx_wildcards_Food' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-14T22:02:49+0000]: Job 53278.0 for rule 'rule_generate_kgx_wildcards_Food' (python) has low CPU efficiency: 0.0%. Job 53279.0 for rule 'rule_generate_kgx_wildcards_MolecularMixture' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-14T22:02:49+0000]: Job 53279.0 for rule 'rule_generate_kgx_wildcards_MolecularMixture' (python) has low CPU efficiency: 0.0%. Job 53280.0 for rule 'rule_generate_kgx_wildcards_Polypeptide' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-14T22:02:49+0000]: Job 53280.0 for rule 'rule_generate_kgx_wildcards_Polypeptide' (python) has low CPU efficiency: 0.0%. Job 53281.0 for rule 'rule_generate_kgx_wildcards_SmallMolecule' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-14T22:02:49+0000]: Job 53281.0 for rule 'rule_generate_kgx_wildcards_SmallMolecule' (python) has low CPU efficiency: 0.0%. Job 53282.0 for rule 'rule_generate_kgx_wildcards_ComplexMolecularMixture' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-14T22:02:49+0000]: Job 53282.0 for rule 'rule_generate_kgx_wildcards_ComplexMolecularMixture' (python) has low CPU efficiency: 0.0%. Job 53283.0 for rule 'rule_generate_kgx_wildcards_ChemicalEntity' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-14T22:02:49+0000]: Job 53283.0 for rule 'rule_generate_kgx_wildcards_ChemicalEntity' (python) has low CPU efficiency: 0.0%. Job 53284.0 for rule 'rule_generate_kgx_wildcards_Drug' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-14T22:02:49+0000]: Job 53284.0 for rule 'rule_generate_kgx_wildcards_Drug' (python) has low CPU efficiency: 0.0%. Job 53285.0 for rule 'rule_generate_kgx_wildcards_ChemicalMixture' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-14T22:02:49+0000]: Job 53285.0 for rule 'rule_generate_kgx_wildcards_ChemicalMixture' (python) has low CPU efficiency: 0.0%. Job 53286.0 for rule 'rule_generate_content_report_for_compendium_ChemicalEntity' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-14T22:02:49+0000]: Job 53286.0 for rule 'rule_generate_content_report_for_compendium_ChemicalEntity' (python) has low CPU efficiency: 0.0%. Job 53287.0 for rule 'rule_check_chemical_mixture' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-14T22:02:49+0000]: Job 53287.0 for rule 'rule_check_chemical_mixture' (python) has low CPU efficiency: 0.0%. Job 53288.0 for rule 'rule_check_chemical_completeness' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-14T22:02:49+0000]: Job 53288.0 for rule 'rule_check_chemical_completeness' (python) has low CPU efficiency: 0.0%. Job 53289.0 for rule 'rule_generate_content_report_for_compendium_ChemicalMixture' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-14T22:02:49+0000]: Job 53289.0 for rule 'rule_generate_content_report_for_compendium_ChemicalMixture' (python) has low CPU efficiency: 0.0%. Job 53290.0 for rule 'rule_check_drug' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-14T22:02:49+0000]: Job 53290.0 for rule 'rule_check_drug' (python) has low CPU efficiency: 0.0%. Job 53291.0 for rule 'rule_generate_content_report_for_compendium_Drug' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-14T22:02:49+0000]: Job 53291.0 for rule 'rule_generate_content_report_for_compendium_Drug' (python) has low CPU efficiency: 0.0%. Job 53292.0 for rule 'rule_check_food' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-14T22:02:49+0000]: Job 53292.0 for rule 'rule_check_food' (python) has low CPU efficiency: 0.0%. Job 53293.0 for rule 'rule_leftover_umls' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-14T22:02:49+0000]: Job 53293.0 for rule 'rule_leftover_umls' (python) has low CPU efficiency: 0.0%. Job 53294.0 for rule 'rule_check_molecular_mixture' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-14T22:02:49+0000]: Job 53294.0 for rule 'rule_check_molecular_mixture' (python) has low CPU efficiency: 0.0%. Job 53295.0 for rule 'rule_generate_content_report_for_compendium_Food' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-14T22:02:49+0000]: Job 53295.0 for rule 'rule_generate_content_report_for_compendium_Food' (python) has low CPU efficiency: 0.0%. Job 53296.0 for rule 'rule_generate_content_report_for_compendium_MolecularMixture' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-14T22:02:49+0000]: Job 53296.0 for rule 'rule_generate_content_report_for_compendium_MolecularMixture' (python) has low CPU efficiency: 0.0%. Job 53297.0 for rule 'rule_check_small_molecule' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-14T22:02:49+0000]: Job 53297.0 for rule 'rule_check_small_molecule' (python) has low CPU efficiency: 0.0%. Job 53298.0 for rule 'rule_generate_content_report_for_compendium_SmallMolecule' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-14T22:02:49+0000]: Job 53298.0 for rule 'rule_generate_content_report_for_compendium_SmallMolecule' (python) has low CPU efficiency: 0.0%. Job 53299.0 for rule 'rule_check_polypeptide' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-14T22:02:49+0000]: Job 53299.0 for rule 'rule_check_polypeptide' (python) has low CPU efficiency: 0.0%. Job 53300.0 for rule 'rule_generate_content_report_for_compendium_Polypeptide' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-14T22:02:49+0000]: Job 53300.0 for rule 'rule_generate_content_report_for_compendium_Polypeptide' (python) has low CPU efficiency: 0.0%. Job 53301.0 for rule 'rule_check_complex_mixture' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-14T22:02:49+0000]: Job 53301.0 for rule 'rule_check_complex_mixture' (python) has low CPU efficiency: 0.0%. Job 53307.0 for rule 'rule_chemical' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-14T22:02:49+0000]: Job 53307.0 for rule 'rule_chemical' (python) has low CPU efficiency: 0.0%. Job 53313.0 for rule 'rule_export_conflation_to_duckdb_wildcards_DrugChemical' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-14T22:02:49+0000]: Job 53313.0 for rule 'rule_export_conflation_to_duckdb_wildcards_DrugChemical' (python) has low CPU efficiency: 0.0%. Job 53319.0 for rule 'rule_generate_content_report_for_compendium_umls' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-14T22:02:49+0000]: Job 53319.0 for rule 'rule_generate_content_report_for_compendium_umls' (python) has low CPU efficiency: 0.0%. Job 53320.0 for rule 'rule_export_compendia_to_duckdb_wildcards_umls' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-14T22:02:49+0000]: Job 53320.0 for rule 'rule_export_compendia_to_duckdb_wildcards_umls' (python) has low CPU efficiency: 0.0%. Job 53321.0 for rule 'rule_generate_kgx_wildcards_umls' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-14T22:02:49+0000]: Job 53321.0 for rule 'rule_generate_kgx_wildcards_umls' (python) has low CPU efficiency: 0.0%. Job 53322.0 for rule 'rule_compress_umls' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-14T22:02:49+0000]: Job 53322.0 for rule 'rule_compress_umls' (python) has low CPU efficiency: 0.0%. Job 53323.0 for rule 'rule_generate_mapping_sources_table' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-14T22:02:49+0000]: Job 53323.0 for rule 'rule_generate_mapping_sources_table' (python) has low CPU efficiency: 0.0%. Job 53324.0 for rule 'rule_generate_compendia_summary_report' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-14T22:02:49+0000]: Job 53324.0 for rule 'rule_generate_compendia_summary_report' (python) has low CPU efficiency: 0.0%. Job 53326.0 for rule 'rule_export_synonyms_to_duckdb_wildcards_umls' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-14T22:02:49+0000]: Job 53326.0 for rule 'rule_export_synonyms_to_duckdb_wildcards_umls' (python) has low CPU efficiency: 0.0%. Job 53327.0 for rule 'rule_generate_sapbert_training_data_wildcards_umls.txt' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-14T22:02:49+0000]: Job 53327.0 for rule 'rule_generate_sapbert_training_data_wildcards_umls.txt' (python) has low CPU efficiency: 0.0%. Job 53345.0 for rule 'rule_export_intermediate_files_to_duckdb' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-14T22:02:49+0000]: Job 53345.0 for rule 'rule_export_intermediate_files_to_duckdb' (python) has low CPU efficiency: 0.0%. Job 53348.0 for rule 'rule_drugchemical_conflated_synonyms' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-14T22:02:49+0000]: Job 53348.0 for rule 'rule_drugchemical_conflated_synonyms' (python) has low CPU efficiency: 0.0%. Job 53408.0 for rule 'rule_export_synonyms_to_duckdb_wildcards_DrugChemicalConflated' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-14T22:02:49+0000]: Job 53408.0 for rule 'rule_export_synonyms_to_duckdb_wildcards_DrugChemicalConflated' (python) has low CPU efficiency: 0.0%. Job 53409.0 for rule 'rule_generate_sapbert_training_data_wildcards_DrugChemicalConflated.txt' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-14T22:02:49+0000]: Job 53409.0 for rule 'rule_generate_sapbert_training_data_wildcards_DrugChemicalConflated.txt' (python) has low CPU efficiency: 0.0%. Job 53410.0 for rule 'rule_check_synonyms_gzipped_files' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-14T22:02:49+0000]: Job 53410.0 for rule 'rule_check_synonyms_gzipped_files' (python) has low CPU efficiency: 0.0%. Job 53411.0 for rule 'rule_check_compendia_files' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-14T22:02:49+0000]: Job 53411.0 for rule 'rule_check_compendia_files' (python) has low CPU efficiency: 0.0%. Job 53412.0 for rule 'rule_check_conflation_files' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-14T22:02:49+0000]: Job 53412.0 for rule 'rule_check_conflation_files' (python) has low CPU efficiency: 0.0%. Job 53419.0 for rule 'rule_generate_clique_leader_report' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-14T22:02:49+0000]: Job 53419.0 for rule 'rule_generate_clique_leader_report' (python) has low CPU efficiency: 0.0%. Job 53420.0 for rule 'rule_check_for_duplicate_clique_leaders' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-14T22:02:49+0000]: Job 53420.0 for rule 'rule_check_for_duplicate_clique_leaders' (python) has low CPU efficiency: 0.0%. Job 53421.0 for rule 'rule_check_for_duplicate_curies' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-14T22:02:49+0000]: Job 53421.0 for rule 'rule_check_for_duplicate_curies' (python) has low CPU efficiency: 0.0%. Job 53422.0 for rule 'rule_generate_curie_report' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-14T22:02:49+0000]: Job 53422.0 for rule 'rule_generate_curie_report' (python) has low CPU efficiency: 0.0%. Job 53423.0 for rule 'rule_check_for_identically_labeled_cliques' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-14T22:02:49+0000]: Job 53423.0 for rule 'rule_check_for_identically_labeled_cliques' (python) has low CPU efficiency: 0.0%. Job 53425.0 for rule 'rule_generate_cliques_table' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-14T22:02:49+0000]: Job 53425.0 for rule 'rule_generate_cliques_table' (python) has low CPU efficiency: 0.0%. Job 53426.0 for rule 'rule_generate_prefix_table' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-14T22:02:49+0000]: Job 53426.0 for rule 'rule_generate_prefix_table' (python) has low CPU efficiency: 0.0%. Efficiency report for workflow babel_94b54343-095a-4c15-8bc0-529889394a60 saved to babel_outputs/reports/slurm/slurm_efficiency_reports/efficiency_report_babel_94b54343-095a-4c15-8bc0-529889394a60.csv. INFO snakemake.logging [2026-07-14T22:02:49+0000]: Efficiency report for workflow babel_94b54343-095a-4c15-8bc0-529889394a60 saved to babel_outputs/reports/slurm/slurm_efficiency_reports/efficiency_report_babel_94b54343-095a-4c15-8bc0-529889394a60.csv. Complete log(s): /projects/babel/runs/gaurav/babel-1.18/.snakemake/log/2026-07-14T050023.888281.snakemake.log INFO snakemake.logging [2026-07-14T22:02:49+0000]: Complete log(s): /projects/babel/runs/gaurav/babel-1.18/.snakemake/log/2026-07-14T050023.888281.snakemake.log