Using profile slurm for setting default command line arguments. SNAKEMAKE ========= Date: 2026-07-21 21:12:19 Workflow ID: 6f524ddb-3f2e-4b4d-b6ad-7412d1e5881f Platform: Linux-5.14.0-427.70.1.el9_4.x86_64-x86_64-with-glibc2.34 Host: compute-13-15 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 babel_downloads/CHEBI/ChEBI_complete.sdf babel_downloads/CHEBI/database_accession.tsv all --rerun-triggers mtime 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: 93c43a9d38f640c0c8423412fe79f9cf INFO snakemake.logging [2026-07-22T01:12:19+0000]: Workflow has started! Building DAG of jobs... INFO snakemake.logging [2026-07-22T01:12:19+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 [2026-07-22T01:12:20+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_f9c6ffa6-b030-48cf-a2f3-d37fc4acb355 INFO snakemake.logging [2026-07-22T01:12:20+0000]: SLURM run ID: babel_f9c6ffa6-b030-48cf-a2f3-d37fc4acb355 MinJobAge 300s (>= 120s). 'squeue' should work reliably for status queries. WARNING snakemake.logging [2026-07-22T01:12:20+0000]: MinJobAge 300s (>= 120s). 'squeue' should work reliably for status queries. Using shell: /usr/bin/bash INFO snakemake.logging [2026-07-22T01:12:20+0000]: Using shell: /usr/bin/bash Provided remote nodes: 50 INFO snakemake.logging [2026-07-22T01:12:20+0000]: Provided remote nodes: 50 Job stats: job count --------------------------------------------------------------- ------- anatomy_emapa_ids 1 get_anatomy_obo_relationships 1 get_chebi 1 anatomy_compendia 1 get_chebi_concord 1 check_anatomical_entity 1 check_anatomy_completeness 1 check_cell 1 check_cellular_component 1 check_gross_anatomical_structure 1 export_compendia_to_duckdb 13 generate_content_report_for_compendium_AnatomicalEntity 1 generate_content_report_for_compendium_Cell 1 generate_content_report_for_compendium_CellularComponent 1 generate_content_report_for_compendium_GrossAnatomicalStructure 1 generate_kgx 13 untyped_chemical_compendia 1 anatomy 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_synonyms_to_duckdb 6 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_sapbert_training_data 6 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 generate_compendia_summary_report 1 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_prefix_report 1 all_duckdb_reports 1 generate_cliques_table 1 generate_prefix_comparison 1 generate_prefix_table 1 all_reports 1 all 1 total 103 INFO snakemake.logging [2026-07-22T01:12:20+0000]: Job stats: job count --------------------------------------------------------------- ------- anatomy_emapa_ids 1 get_anatomy_obo_relationships 1 get_chebi 1 anatomy_compendia 1 get_chebi_concord 1 check_anatomical_entity 1 check_anatomy_completeness 1 check_cell 1 check_cellular_component 1 check_gross_anatomical_structure 1 export_compendia_to_duckdb 13 generate_content_report_for_compendium_AnatomicalEntity 1 generate_content_report_for_compendium_Cell 1 generate_content_report_for_compendium_CellularComponent 1 generate_content_report_for_compendium_GrossAnatomicalStructure 1 generate_kgx 13 untyped_chemical_compendia 1 anatomy 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_synonyms_to_duckdb 6 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_sapbert_training_data 6 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 generate_compendia_summary_report 1 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_prefix_report 1 all_duckdb_reports 1 generate_cliques_table 1 generate_prefix_comparison 1 generate_prefix_table 1 all_reports 1 all 1 total 103 Select jobs to execute... INFO snakemake.logging [2026-07-22T01:12:20+0000]: Select jobs to execute... Execute 3 jobs... INFO snakemake.logging [2026-07-22T01:12:20+0000]: Execute 3 jobs... No SLURM account given, trying to guess. WARNING snakemake.logging [2026-07-22T01:12:20+0000]: No SLURM account given, trying to guess. No SLURM account given, trying to guess. WARNING snakemake.logging [2026-07-22T01:12:20+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 [2026-07-22T01:12:20+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 [2026-07-22T01:12:20+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 [2026-07-22T01:12:20+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 [2026-07-22T01:12:20+0000]: Unable to guess SLURM account. Trying to proceed without. Job 15 has been submitted with SLURM jobid 104414 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_anatomy_emapa_ids/104414.log). INFO snakemake.logging [2026-07-22T01:12:20+0000]: Job 15 has been submitted with SLURM jobid 104414 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_anatomy_emapa_ids/104414.log). Job 57 has been submitted with SLURM jobid 104415 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_get_chebi/104415.log). INFO snakemake.logging [2026-07-22T01:12:20+0000]: Job 57 has been submitted with SLURM jobid 104415 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_get_chebi/104415.log). Job 7 has been submitted with SLURM jobid 104416 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_get_anatomy_obo_relationships/104416.log). INFO snakemake.logging [2026-07-22T01:12:20+0000]: Job 7 has been submitted with SLURM jobid 104416 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_get_anatomy_obo_relationships/104416.log). [Tue Jul 21 21:13:00 2026] Finished jobid: 15 (Rule: anatomy_emapa_ids) INFO snakemake.logging [2026-07-22T01:13:00+0000]: Finished jobid: 15 (Rule: anatomy_emapa_ids) 1 of 103 steps (1%) done INFO snakemake.logging [2026-07-22T01:13:00+0000]: None [Tue Jul 21 21:14:30 2026] Finished jobid: 57 (Rule: get_chebi) INFO snakemake.logging [2026-07-22T01:14:30+0000]: Finished jobid: 57 (Rule: get_chebi) 2 of 103 steps (2%) done INFO snakemake.logging [2026-07-22T01:14:30+0000]: None Select jobs to execute... INFO snakemake.logging [2026-07-22T01:14:30+0000]: Select jobs to execute... Execute 1 jobs... INFO snakemake.logging [2026-07-22T01:14:30+0000]: Execute 1 jobs... Job 56 has been submitted with SLURM jobid 104417 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_get_chebi_concord/104417.log). INFO snakemake.logging [2026-07-22T01:14:30+0000]: Job 56 has been submitted with SLURM jobid 104417 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_get_chebi_concord/104417.log). [Tue Jul 21 21:15:10 2026] Finished jobid: 56 (Rule: get_chebi_concord) INFO snakemake.logging [2026-07-22T01:15:10+0000]: Finished jobid: 56 (Rule: get_chebi_concord) 3 of 103 steps (3%) done INFO snakemake.logging [2026-07-22T01:15:10+0000]: None Select jobs to execute... INFO snakemake.logging [2026-07-22T01:15:10+0000]: Select jobs to execute... Execute 1 jobs... INFO snakemake.logging [2026-07-22T01:15:10+0000]: Execute 1 jobs... Job 28 has been submitted with SLURM jobid 104418 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_untyped_chemical_compendia/104418.log). INFO snakemake.logging [2026-07-22T01:15:10+0000]: Job 28 has been submitted with SLURM jobid 104418 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_untyped_chemical_compendia/104418.log). [Tue Jul 21 21:25:11 2026] Finished jobid: 7 (Rule: get_anatomy_obo_relationships) INFO snakemake.logging [2026-07-22T01:25:11+0000]: Finished jobid: 7 (Rule: get_anatomy_obo_relationships) 4 of 103 steps (4%) done INFO snakemake.logging [2026-07-22T01:25:11+0000]: None Select jobs to execute... INFO snakemake.logging [2026-07-22T01:25:11+0000]: Select jobs to execute... Execute 1 jobs... INFO snakemake.logging [2026-07-22T01:25:11+0000]: Execute 1 jobs... Job 4 has been submitted with SLURM jobid 104422 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_anatomy_compendia/104422.log). INFO snakemake.logging [2026-07-22T01:25:11+0000]: Job 4 has been submitted with SLURM jobid 104422 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_anatomy_compendia/104422.log). [Tue Jul 21 21:31:42 2026] Finished jobid: 4 (Rule: anatomy_compendia) INFO snakemake.logging [2026-07-22T01:31:42+0000]: Finished jobid: 4 (Rule: anatomy_compendia) 5 of 103 steps (5%) done INFO snakemake.logging [2026-07-22T01:31:42+0000]: None Select jobs to execute... INFO snakemake.logging [2026-07-22T01:31:42+0000]: Select jobs to execute... Execute 17 jobs... INFO snakemake.logging [2026-07-22T01:31:42+0000]: Execute 17 jobs... Job 272 has been submitted with SLURM jobid 104425 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_export_compendia_to_duckdb/Cell/104425.log). INFO snakemake.logging [2026-07-22T01:31:42+0000]: Job 272 has been submitted with SLURM jobid 104425 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_export_compendia_to_duckdb/Cell/104425.log). Job 273 has been submitted with SLURM jobid 104426 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_export_compendia_to_duckdb/CellularComponent/104426.log). INFO snakemake.logging [2026-07-22T01:31:42+0000]: Job 273 has been submitted with SLURM jobid 104426 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_export_compendia_to_duckdb/CellularComponent/104426.log). Job 274 has been submitted with SLURM jobid 104427 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_export_compendia_to_duckdb/GrossAnatomicalStructure/104427.log). INFO snakemake.logging [2026-07-22T01:31:42+0000]: Job 274 has been submitted with SLURM jobid 104427 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_export_compendia_to_duckdb/GrossAnatomicalStructure/104427.log). Job 271 has been submitted with SLURM jobid 104428 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_export_compendia_to_duckdb/AnatomicalEntity/104428.log). INFO snakemake.logging [2026-07-22T01:31:42+0000]: Job 271 has been submitted with SLURM jobid 104428 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_export_compendia_to_duckdb/AnatomicalEntity/104428.log). Job 3 has been submitted with SLURM jobid 104429 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_check_anatomy_completeness/104429.log). INFO snakemake.logging [2026-07-22T01:31:42+0000]: Job 3 has been submitted with SLURM jobid 104429 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_check_anatomy_completeness/104429.log). Job 328 has been submitted with SLURM jobid 104430 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_kgx/Cell/104430.log). INFO snakemake.logging [2026-07-22T01:31:42+0000]: Job 328 has been submitted with SLURM jobid 104430 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_kgx/Cell/104430.log). Job 330 has been submitted with SLURM jobid 104431 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_kgx/GrossAnatomicalStructure/104431.log). INFO snakemake.logging [2026-07-22T01:31:42+0000]: Job 330 has been submitted with SLURM jobid 104431 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_kgx/GrossAnatomicalStructure/104431.log). Job 327 has been submitted with SLURM jobid 104432 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_kgx/AnatomicalEntity/104432.log). INFO snakemake.logging [2026-07-22T01:31:42+0000]: Job 327 has been submitted with SLURM jobid 104432 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_kgx/AnatomicalEntity/104432.log). Job 329 has been submitted with SLURM jobid 104433 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_kgx/CellularComponent/104433.log). INFO snakemake.logging [2026-07-22T01:31:42+0000]: Job 329 has been submitted with SLURM jobid 104433 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_kgx/CellularComponent/104433.log). Job 21 has been submitted with SLURM jobid 104434 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_check_anatomical_entity/104434.log). INFO snakemake.logging [2026-07-22T01:31:42+0000]: Job 21 has been submitted with SLURM jobid 104434 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_check_anatomical_entity/104434.log). Job 23 has been submitted with SLURM jobid 104435 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_check_cellular_component/104435.log). INFO snakemake.logging [2026-07-22T01:31:42+0000]: Job 23 has been submitted with SLURM jobid 104435 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_check_cellular_component/104435.log). Job 240 has been submitted with SLURM jobid 104436 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_content_report_for_compendium_Cell/104436.log). INFO snakemake.logging [2026-07-22T01:31:42+0000]: Job 240 has been submitted with SLURM jobid 104436 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_content_report_for_compendium_Cell/104436.log). Job 242 has been submitted with SLURM jobid 104437 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_content_report_for_compendium_GrossAnatomicalStructure/104437.log). INFO snakemake.logging [2026-07-22T01:31:42+0000]: Job 242 has been submitted with SLURM jobid 104437 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_content_report_for_compendium_GrossAnatomicalStructure/104437.log). Job 22 has been submitted with SLURM jobid 104438 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_check_cell/104438.log). INFO snakemake.logging [2026-07-22T01:31:42+0000]: Job 22 has been submitted with SLURM jobid 104438 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_check_cell/104438.log). Job 241 has been submitted with SLURM jobid 104439 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_content_report_for_compendium_CellularComponent/104439.log). INFO snakemake.logging [2026-07-22T01:31:42+0000]: Job 241 has been submitted with SLURM jobid 104439 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_content_report_for_compendium_CellularComponent/104439.log). Job 24 has been submitted with SLURM jobid 104440 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_check_gross_anatomical_structure/104440.log). INFO snakemake.logging [2026-07-22T01:31:42+0000]: Job 24 has been submitted with SLURM jobid 104440 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_check_gross_anatomical_structure/104440.log). Job 239 has been submitted with SLURM jobid 104441 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_content_report_for_compendium_AnatomicalEntity/104441.log). INFO snakemake.logging [2026-07-22T01:31:42+0000]: Job 239 has been submitted with SLURM jobid 104441 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_content_report_for_compendium_AnatomicalEntity/104441.log). [Tue Jul 21 21:32:22 2026] Finished jobid: 273 (Rule: export_compendia_to_duckdb) INFO snakemake.logging [2026-07-22T01:32:22+0000]: Finished jobid: 273 (Rule: export_compendia_to_duckdb) 6 of 103 steps (6%) done INFO snakemake.logging [2026-07-22T01:32:22+0000]: None [Tue Jul 21 21:32:22 2026] Finished jobid: 272 (Rule: export_compendia_to_duckdb) INFO snakemake.logging [2026-07-22T01:32:22+0000]: Finished jobid: 272 (Rule: export_compendia_to_duckdb) 7 of 103 steps (7%) done INFO snakemake.logging [2026-07-22T01:32:22+0000]: None [Tue Jul 21 21:32:22 2026] Finished jobid: 274 (Rule: export_compendia_to_duckdb) INFO snakemake.logging [2026-07-22T01:32:22+0000]: Finished jobid: 274 (Rule: export_compendia_to_duckdb) 8 of 103 steps (8%) done INFO snakemake.logging [2026-07-22T01:32:22+0000]: None [Tue Jul 21 21:32:22 2026] Finished jobid: 271 (Rule: export_compendia_to_duckdb) INFO snakemake.logging [2026-07-22T01:32:22+0000]: Finished jobid: 271 (Rule: export_compendia_to_duckdb) 9 of 103 steps (9%) done INFO snakemake.logging [2026-07-22T01:32:22+0000]: None [Tue Jul 21 21:32:22 2026] Finished jobid: 3 (Rule: check_anatomy_completeness) INFO snakemake.logging [2026-07-22T01:32:22+0000]: Finished jobid: 3 (Rule: check_anatomy_completeness) 10 of 103 steps (10%) done INFO snakemake.logging [2026-07-22T01:32:22+0000]: None [Tue Jul 21 21:32:22 2026] Finished jobid: 328 (Rule: generate_kgx) INFO snakemake.logging [2026-07-22T01:32:22+0000]: Finished jobid: 328 (Rule: generate_kgx) 11 of 103 steps (11%) done INFO snakemake.logging [2026-07-22T01:32:22+0000]: None [Tue Jul 21 21:32:22 2026] Finished jobid: 330 (Rule: generate_kgx) INFO snakemake.logging [2026-07-22T01:32:22+0000]: Finished jobid: 330 (Rule: generate_kgx) 12 of 103 steps (12%) done INFO snakemake.logging [2026-07-22T01:32:22+0000]: None [Tue Jul 21 21:32:22 2026] Finished jobid: 327 (Rule: generate_kgx) INFO snakemake.logging [2026-07-22T01:32:22+0000]: Finished jobid: 327 (Rule: generate_kgx) 13 of 103 steps (13%) done INFO snakemake.logging [2026-07-22T01:32:22+0000]: None [Tue Jul 21 21:32:22 2026] Finished jobid: 329 (Rule: generate_kgx) INFO snakemake.logging [2026-07-22T01:32:22+0000]: Finished jobid: 329 (Rule: generate_kgx) 14 of 103 steps (14%) done INFO snakemake.logging [2026-07-22T01:32:22+0000]: None [Tue Jul 21 21:32:22 2026] Finished jobid: 21 (Rule: check_anatomical_entity) INFO snakemake.logging [2026-07-22T01:32:22+0000]: Finished jobid: 21 (Rule: check_anatomical_entity) 15 of 103 steps (15%) done INFO snakemake.logging [2026-07-22T01:32:22+0000]: None [Tue Jul 21 21:32:22 2026] Finished jobid: 23 (Rule: check_cellular_component) INFO snakemake.logging [2026-07-22T01:32:22+0000]: Finished jobid: 23 (Rule: check_cellular_component) 16 of 103 steps (16%) done INFO snakemake.logging [2026-07-22T01:32:22+0000]: None [Tue Jul 21 21:32:22 2026] Finished jobid: 240 (Rule: generate_content_report_for_compendium_Cell) INFO snakemake.logging [2026-07-22T01:32:22+0000]: Finished jobid: 240 (Rule: generate_content_report_for_compendium_Cell) 17 of 103 steps (17%) done INFO snakemake.logging [2026-07-22T01:32:22+0000]: None [Tue Jul 21 21:32:22 2026] Finished jobid: 242 (Rule: generate_content_report_for_compendium_GrossAnatomicalStructure) INFO snakemake.logging [2026-07-22T01:32:22+0000]: Finished jobid: 242 (Rule: generate_content_report_for_compendium_GrossAnatomicalStructure) 18 of 103 steps (17%) done INFO snakemake.logging [2026-07-22T01:32:22+0000]: None [Tue Jul 21 21:32:22 2026] Finished jobid: 22 (Rule: check_cell) INFO snakemake.logging [2026-07-22T01:32:22+0000]: Finished jobid: 22 (Rule: check_cell) 19 of 103 steps (18%) done INFO snakemake.logging [2026-07-22T01:32:22+0000]: None [Tue Jul 21 21:32:22 2026] Finished jobid: 241 (Rule: generate_content_report_for_compendium_CellularComponent) INFO snakemake.logging [2026-07-22T01:32:22+0000]: Finished jobid: 241 (Rule: generate_content_report_for_compendium_CellularComponent) 20 of 103 steps (19%) done INFO snakemake.logging [2026-07-22T01:32:22+0000]: None [Tue Jul 21 21:32:22 2026] Finished jobid: 24 (Rule: check_gross_anatomical_structure) INFO snakemake.logging [2026-07-22T01:32:22+0000]: Finished jobid: 24 (Rule: check_gross_anatomical_structure) 21 of 103 steps (20%) done INFO snakemake.logging [2026-07-22T01:32:22+0000]: None Select jobs to execute... INFO snakemake.logging [2026-07-22T01:32:22+0000]: Select jobs to execute... Execute 1 jobs... INFO snakemake.logging [2026-07-22T01:32:22+0000]: Execute 1 jobs... [Tue Jul 21 21:32:22 2026] Finished jobid: 239 (Rule: generate_content_report_for_compendium_AnatomicalEntity) INFO snakemake.logging [2026-07-22T01:32:22+0000]: Finished jobid: 239 (Rule: generate_content_report_for_compendium_AnatomicalEntity) 22 of 103 steps (21%) done INFO snakemake.logging [2026-07-22T01:32:22+0000]: None Job 2 has been submitted with SLURM jobid 104444 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_anatomy/104444.log). INFO snakemake.logging [2026-07-22T01:32:22+0000]: Job 2 has been submitted with SLURM jobid 104444 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_anatomy/104444.log). [Tue Jul 21 21:33:02 2026] Finished jobid: 2 (Rule: anatomy) INFO snakemake.logging [2026-07-22T01:33:02+0000]: Finished jobid: 2 (Rule: anatomy) 23 of 103 steps (22%) done INFO snakemake.logging [2026-07-22T01:33:02+0000]: None Removing temporary output babel_outputs/synonyms/AnatomicalEntity.txt. INFO snakemake.logging [2026-07-22T01:33:02+0000]: Removing temporary output babel_outputs/synonyms/AnatomicalEntity.txt. Removing temporary output babel_outputs/synonyms/Cell.txt. INFO snakemake.logging [2026-07-22T01:33:02+0000]: Removing temporary output babel_outputs/synonyms/Cell.txt. Removing temporary output babel_outputs/synonyms/CellularComponent.txt. INFO snakemake.logging [2026-07-22T01:33:02+0000]: Removing temporary output babel_outputs/synonyms/CellularComponent.txt. Removing temporary output babel_outputs/synonyms/GrossAnatomicalStructure.txt. INFO snakemake.logging [2026-07-22T01:33:02+0000]: Removing temporary output babel_outputs/synonyms/GrossAnatomicalStructure.txt. Select jobs to execute... INFO snakemake.logging [2026-07-22T01:33:02+0000]: Select jobs to execute... Execute 8 jobs... INFO snakemake.logging [2026-07-22T01:33:02+0000]: Execute 8 jobs... Job 297 has been submitted with SLURM jobid 104445 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_export_synonyms_to_duckdb/AnatomicalEntity/104445.log). INFO snakemake.logging [2026-07-22T01:33:02+0000]: Job 297 has been submitted with SLURM jobid 104445 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_export_synonyms_to_duckdb/AnatomicalEntity/104445.log). Job 299 has been submitted with SLURM jobid 104446 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_export_synonyms_to_duckdb/CellularComponent/104446.log). INFO snakemake.logging [2026-07-22T01:33:02+0000]: Job 299 has been submitted with SLURM jobid 104446 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_export_synonyms_to_duckdb/CellularComponent/104446.log). Job 298 has been submitted with SLURM jobid 104447 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_export_synonyms_to_duckdb/Cell/104447.log). INFO snakemake.logging [2026-07-22T01:33:02+0000]: Job 298 has been submitted with SLURM jobid 104447 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_export_synonyms_to_duckdb/Cell/104447.log). Job 300 has been submitted with SLURM jobid 104448 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_export_synonyms_to_duckdb/GrossAnatomicalStructure/104448.log). INFO snakemake.logging [2026-07-22T01:33:02+0000]: Job 300 has been submitted with SLURM jobid 104448 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_export_synonyms_to_duckdb/GrossAnatomicalStructure/104448.log). Job 354 has been submitted with SLURM jobid 104449 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_sapbert_training_data/Cell.txt/104449.log). INFO snakemake.logging [2026-07-22T01:33:02+0000]: Job 354 has been submitted with SLURM jobid 104449 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_sapbert_training_data/Cell.txt/104449.log). Job 356 has been submitted with SLURM jobid 104450 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_sapbert_training_data/GrossAnatomicalStructure.txt/104450.log). INFO snakemake.logging [2026-07-22T01:33:02+0000]: Job 356 has been submitted with SLURM jobid 104450 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_sapbert_training_data/GrossAnatomicalStructure.txt/104450.log). Job 353 has been submitted with SLURM jobid 104451 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_sapbert_training_data/AnatomicalEntity.txt/104451.log). INFO snakemake.logging [2026-07-22T01:33:02+0000]: Job 353 has been submitted with SLURM jobid 104451 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_sapbert_training_data/AnatomicalEntity.txt/104451.log). Job 355 has been submitted with SLURM jobid 104452 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_sapbert_training_data/CellularComponent.txt/104452.log). INFO snakemake.logging [2026-07-22T01:33:02+0000]: Job 355 has been submitted with SLURM jobid 104452 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_sapbert_training_data/CellularComponent.txt/104452.log). [Tue Jul 21 21:33:42 2026] Finished jobid: 297 (Rule: export_synonyms_to_duckdb) INFO snakemake.logging [2026-07-22T01:33:42+0000]: Finished jobid: 297 (Rule: export_synonyms_to_duckdb) 24 of 103 steps (23%) done INFO snakemake.logging [2026-07-22T01:33:42+0000]: None [Tue Jul 21 21:33:42 2026] Finished jobid: 299 (Rule: export_synonyms_to_duckdb) INFO snakemake.logging [2026-07-22T01:33:42+0000]: Finished jobid: 299 (Rule: export_synonyms_to_duckdb) 25 of 103 steps (24%) done INFO snakemake.logging [2026-07-22T01:33:42+0000]: None [Tue Jul 21 21:33:42 2026] Finished jobid: 298 (Rule: export_synonyms_to_duckdb) INFO snakemake.logging [2026-07-22T01:33:42+0000]: Finished jobid: 298 (Rule: export_synonyms_to_duckdb) 26 of 103 steps (25%) done INFO snakemake.logging [2026-07-22T01:33:42+0000]: None [Tue Jul 21 21:33:42 2026] Finished jobid: 300 (Rule: export_synonyms_to_duckdb) INFO snakemake.logging [2026-07-22T01:33:42+0000]: Finished jobid: 300 (Rule: export_synonyms_to_duckdb) 27 of 103 steps (26%) done INFO snakemake.logging [2026-07-22T01:33:42+0000]: None [Tue Jul 21 21:33:42 2026] Finished jobid: 354 (Rule: generate_sapbert_training_data) INFO snakemake.logging [2026-07-22T01:33:42+0000]: Finished jobid: 354 (Rule: generate_sapbert_training_data) 28 of 103 steps (27%) done INFO snakemake.logging [2026-07-22T01:33:42+0000]: None [Tue Jul 21 21:33:42 2026] Finished jobid: 356 (Rule: generate_sapbert_training_data) INFO snakemake.logging [2026-07-22T01:33:42+0000]: Finished jobid: 356 (Rule: generate_sapbert_training_data) 29 of 103 steps (28%) done INFO snakemake.logging [2026-07-22T01:33:42+0000]: None [Tue Jul 21 21:33:42 2026] Finished jobid: 353 (Rule: generate_sapbert_training_data) INFO snakemake.logging [2026-07-22T01:33:42+0000]: Finished jobid: 353 (Rule: generate_sapbert_training_data) 30 of 103 steps (29%) done INFO snakemake.logging [2026-07-22T01:33:42+0000]: None [Tue Jul 21 21:33:42 2026] Finished jobid: 355 (Rule: generate_sapbert_training_data) INFO snakemake.logging [2026-07-22T01:33:42+0000]: Finished jobid: 355 (Rule: generate_sapbert_training_data) 31 of 103 steps (30%) done INFO snakemake.logging [2026-07-22T01:33:42+0000]: None [Tue Jul 21 22:16:15 2026] Finished jobid: 28 (Rule: untyped_chemical_compendia) INFO snakemake.logging [2026-07-22T02:16:15+0000]: Finished jobid: 28 (Rule: untyped_chemical_compendia) 32 of 103 steps (31%) done INFO snakemake.logging [2026-07-22T02:16:15+0000]: None Select jobs to execute... INFO snakemake.logging [2026-07-22T02:16:15+0000]: Select jobs to execute... Execute 1 jobs... INFO snakemake.logging [2026-07-22T02:16:15+0000]: Execute 1 jobs... Job 27 has been submitted with SLURM jobid 104459 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_chemical_compendia/104459.log). INFO snakemake.logging [2026-07-22T02:16:15+0000]: Job 27 has been submitted with SLURM jobid 104459 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_chemical_compendia/104459.log). [Wed Jul 22 03:34:58 2026] Finished jobid: 27 (Rule: chemical_compendia) INFO snakemake.logging [2026-07-22T07:34:58+0000]: Finished jobid: 27 (Rule: chemical_compendia) 33 of 103 steps (32%) done INFO snakemake.logging [2026-07-22T07:34:58+0000]: None Select jobs to execute... INFO snakemake.logging [2026-07-22T07:34:58+0000]: Select jobs to execute... Execute 35 jobs... INFO snakemake.logging [2026-07-22T07:34:58+0000]: Execute 35 jobs... Job 275 has been submitted with SLURM jobid 104527 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_export_compendia_to_duckdb/MolecularMixture/104527.log). INFO snakemake.logging [2026-07-22T07:34:58+0000]: Job 275 has been submitted with SLURM jobid 104527 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_export_compendia_to_duckdb/MolecularMixture/104527.log). Job 276 has been submitted with SLURM jobid 104528 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_export_compendia_to_duckdb/SmallMolecule/104528.log). INFO snakemake.logging [2026-07-22T07:34:58+0000]: Job 276 has been submitted with SLURM jobid 104528 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_export_compendia_to_duckdb/SmallMolecule/104528.log). Job 278 has been submitted with SLURM jobid 104529 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_export_compendia_to_duckdb/ComplexMolecularMixture/104529.log). INFO snakemake.logging [2026-07-22T07:34:58+0000]: Job 278 has been submitted with SLURM jobid 104529 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_export_compendia_to_duckdb/ComplexMolecularMixture/104529.log). Job 277 has been submitted with SLURM jobid 104530 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_export_compendia_to_duckdb/Polypeptide/104530.log). INFO snakemake.logging [2026-07-22T07:34:58+0000]: Job 277 has been submitted with SLURM jobid 104530 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_export_compendia_to_duckdb/Polypeptide/104530.log). Job 280 has been submitted with SLURM jobid 104531 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_export_compendia_to_duckdb/ChemicalMixture/104531.log). 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INFO snakemake.logging [2026-07-22T07:34:59+0000]: Job 281 has been submitted with SLURM jobid 104533 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_export_compendia_to_duckdb/Drug/104533.log). Job 282 has been submitted with SLURM jobid 104534 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_export_compendia_to_duckdb/Food/104534.log). INFO snakemake.logging [2026-07-22T07:34:59+0000]: Job 282 has been submitted with SLURM jobid 104534 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_export_compendia_to_duckdb/Food/104534.log). Job 336 has been submitted with SLURM jobid 104535 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_kgx/ChemicalMixture/104535.log). INFO snakemake.logging [2026-07-22T07:34:59+0000]: Job 336 has been submitted with SLURM jobid 104535 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_kgx/ChemicalMixture/104535.log). Job 243 has been submitted with SLURM jobid 104536 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_content_report_for_compendium_MolecularMixture/104536.log). INFO snakemake.logging [2026-07-22T07:34:59+0000]: Job 243 has been submitted with SLURM jobid 104536 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_content_report_for_compendium_MolecularMixture/104536.log). Job 337 has been submitted with SLURM jobid 104537 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_kgx/Drug/104537.log). INFO snakemake.logging [2026-07-22T07:34:59+0000]: Job 337 has been submitted with SLURM jobid 104537 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_kgx/Drug/104537.log). Job 338 has been submitted with SLURM jobid 104538 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_kgx/Food/104538.log). INFO snakemake.logging [2026-07-22T07:34:59+0000]: Job 338 has been submitted with SLURM jobid 104538 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_kgx/Food/104538.log). Job 331 has been submitted with SLURM jobid 104539 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_kgx/MolecularMixture/104539.log). INFO snakemake.logging [2026-07-22T07:34:59+0000]: Job 331 has been submitted with SLURM jobid 104539 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_kgx/MolecularMixture/104539.log). Job 332 has been submitted with SLURM jobid 104540 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_kgx/SmallMolecule/104540.log). INFO snakemake.logging [2026-07-22T07:34:59+0000]: Job 332 has been submitted with SLURM jobid 104540 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_kgx/SmallMolecule/104540.log). Job 333 has been submitted with SLURM jobid 104541 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_kgx/Polypeptide/104541.log). INFO snakemake.logging [2026-07-22T07:34:59+0000]: Job 333 has been submitted with SLURM jobid 104541 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_kgx/Polypeptide/104541.log). Job 334 has been submitted with SLURM jobid 104542 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_kgx/ComplexMolecularMixture/104542.log). INFO snakemake.logging [2026-07-22T07:34:59+0000]: Job 334 has been submitted with SLURM jobid 104542 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_kgx/ComplexMolecularMixture/104542.log). Job 335 has been submitted with SLURM jobid 104543 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_kgx/ChemicalEntity/104543.log). INFO snakemake.logging [2026-07-22T07:34:59+0000]: Job 335 has been submitted with SLURM jobid 104543 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_kgx/ChemicalEntity/104543.log). Job 78 has been submitted with SLURM jobid 104544 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_check_polypeptide/104544.log). INFO snakemake.logging [2026-07-22T07:34:59+0000]: Job 78 has been submitted with SLURM jobid 104544 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_check_polypeptide/104544.log). Job 77 has been submitted with SLURM jobid 104545 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_check_small_molecule/104545.log). INFO snakemake.logging [2026-07-22T07:34:59+0000]: Job 77 has been submitted with SLURM jobid 104545 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_check_small_molecule/104545.log). Job 244 has been submitted with SLURM jobid 104546 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_content_report_for_compendium_SmallMolecule/104546.log). INFO snakemake.logging [2026-07-22T07:34:59+0000]: Job 244 has been submitted with SLURM jobid 104546 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_content_report_for_compendium_SmallMolecule/104546.log). Job 79 has been submitted with SLURM jobid 104547 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_check_complex_mixture/104547.log). INFO snakemake.logging [2026-07-22T07:34:59+0000]: Job 79 has been submitted with SLURM jobid 104547 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_check_complex_mixture/104547.log). Job 245 has been submitted with SLURM jobid 104548 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_content_report_for_compendium_Polypeptide/104548.log). 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Job 246 has been submitted with SLURM jobid 104551 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_content_report_for_compendium_ComplexMolecularMixture/104551.log). INFO snakemake.logging [2026-07-22T07:34:59+0000]: Job 246 has been submitted with SLURM jobid 104551 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_content_report_for_compendium_ComplexMolecularMixture/104551.log). Job 81 has been submitted with SLURM jobid 104552 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_check_chemical_mixture/104552.log). INFO snakemake.logging [2026-07-22T07:34:59+0000]: Job 81 has been submitted with SLURM jobid 104552 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_check_chemical_mixture/104552.log). Job 26 has been submitted with SLURM jobid 104553 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_check_chemical_completeness/104553.log). INFO snakemake.logging [2026-07-22T07:34:59+0000]: Job 26 has been submitted with SLURM jobid 104553 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_check_chemical_completeness/104553.log). Job 247 has been submitted with SLURM jobid 104554 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_content_report_for_compendium_ChemicalEntity/104554.log). INFO snakemake.logging [2026-07-22T07:34:59+0000]: Job 247 has been submitted with SLURM jobid 104554 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_content_report_for_compendium_ChemicalEntity/104554.log). Job 82 has been submitted with SLURM jobid 104555 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_check_drug/104555.log). INFO snakemake.logging [2026-07-22T07:34:59+0000]: Job 82 has been submitted with SLURM jobid 104555 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_check_drug/104555.log). Job 248 has been submitted with SLURM jobid 104556 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_content_report_for_compendium_ChemicalMixture/104556.log). INFO snakemake.logging [2026-07-22T07:34:59+0000]: Job 248 has been submitted with SLURM jobid 104556 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_content_report_for_compendium_ChemicalMixture/104556.log). Job 83 has been submitted with SLURM jobid 104557 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_check_food/104557.log). INFO snakemake.logging [2026-07-22T07:34:59+0000]: Job 83 has been submitted with SLURM jobid 104557 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_check_food/104557.log). Job 76 has been submitted with SLURM jobid 104558 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_check_molecular_mixture/104558.log). INFO snakemake.logging [2026-07-22T07:34:59+0000]: Job 76 has been submitted with SLURM jobid 104558 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_check_molecular_mixture/104558.log). Job 249 has been submitted with SLURM jobid 104559 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_content_report_for_compendium_Drug/104559.log). INFO snakemake.logging [2026-07-22T07:34:59+0000]: Job 249 has been submitted with SLURM jobid 104559 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_content_report_for_compendium_Drug/104559.log). Job 216 has been submitted with SLURM jobid 104560 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_leftover_umls/104560.log). INFO snakemake.logging [2026-07-22T07:34:59+0000]: Job 216 has been submitted with SLURM jobid 104560 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_leftover_umls/104560.log). Job 250 has been submitted with SLURM jobid 104561 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_content_report_for_compendium_Food/104561.log). INFO snakemake.logging [2026-07-22T07:34:59+0000]: Job 250 has been submitted with SLURM jobid 104561 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_content_report_for_compendium_Food/104561.log). [Wed Jul 22 03:35:38 2026] Finished jobid: 277 (Rule: export_compendia_to_duckdb) INFO snakemake.logging [2026-07-22T07:35:38+0000]: Finished jobid: 277 (Rule: export_compendia_to_duckdb) 34 of 103 steps (33%) done INFO snakemake.logging [2026-07-22T07:35:38+0000]: None [Wed Jul 22 03:35:38 2026] Finished jobid: 278 (Rule: export_compendia_to_duckdb) INFO snakemake.logging [2026-07-22T07:35:38+0000]: Finished jobid: 278 (Rule: export_compendia_to_duckdb) 35 of 103 steps (34%) done INFO snakemake.logging [2026-07-22T07:35:38+0000]: None [Wed Jul 22 03:35:39 2026] Finished jobid: 280 (Rule: export_compendia_to_duckdb) INFO snakemake.logging [2026-07-22T07:35:39+0000]: Finished jobid: 280 (Rule: export_compendia_to_duckdb) 36 of 103 steps (35%) done INFO snakemake.logging [2026-07-22T07:35:39+0000]: None [Wed Jul 22 03:35:39 2026] Finished jobid: 279 (Rule: export_compendia_to_duckdb) INFO snakemake.logging [2026-07-22T07:35:39+0000]: Finished jobid: 279 (Rule: export_compendia_to_duckdb) 37 of 103 steps (36%) done INFO snakemake.logging [2026-07-22T07:35:39+0000]: None [Wed Jul 22 03:35:39 2026] Finished jobid: 281 (Rule: export_compendia_to_duckdb) INFO snakemake.logging [2026-07-22T07:35:39+0000]: Finished jobid: 281 (Rule: export_compendia_to_duckdb) 38 of 103 steps (37%) done INFO snakemake.logging [2026-07-22T07:35:39+0000]: None [Wed Jul 22 03:35:39 2026] Finished jobid: 282 (Rule: export_compendia_to_duckdb) INFO snakemake.logging [2026-07-22T07:35:39+0000]: Finished jobid: 282 (Rule: export_compendia_to_duckdb) 39 of 103 steps (38%) done INFO snakemake.logging [2026-07-22T07:35:39+0000]: None [Wed Jul 22 03:35:39 2026] Finished jobid: 336 (Rule: generate_kgx) INFO snakemake.logging [2026-07-22T07:35:39+0000]: Finished jobid: 336 (Rule: generate_kgx) 40 of 103 steps (39%) done INFO snakemake.logging [2026-07-22T07:35:39+0000]: None [Wed Jul 22 03:35:39 2026] Finished jobid: 337 (Rule: generate_kgx) INFO snakemake.logging [2026-07-22T07:35:39+0000]: Finished 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check_polypeptide) 45 of 103 steps (44%) done INFO snakemake.logging [2026-07-22T07:35:39+0000]: None [Wed Jul 22 03:35:39 2026] Finished jobid: 79 (Rule: check_complex_mixture) INFO snakemake.logging [2026-07-22T07:35:39+0000]: Finished jobid: 79 (Rule: check_complex_mixture) 46 of 103 steps (45%) done INFO snakemake.logging [2026-07-22T07:35:39+0000]: None [Wed Jul 22 03:35:39 2026] Finished jobid: 245 (Rule: generate_content_report_for_compendium_Polypeptide) INFO snakemake.logging [2026-07-22T07:35:39+0000]: Finished jobid: 245 (Rule: generate_content_report_for_compendium_Polypeptide) 47 of 103 steps (46%) done INFO snakemake.logging [2026-07-22T07:35:39+0000]: None [Wed Jul 22 03:35:39 2026] Finished jobid: 80 (Rule: check_chemical_entity) INFO snakemake.logging [2026-07-22T07:35:39+0000]: Finished jobid: 80 (Rule: check_chemical_entity) 48 of 103 steps (47%) done INFO snakemake.logging [2026-07-22T07:35:39+0000]: None [Wed Jul 22 03:35:39 2026] Finished jobid: 246 (Rule: generate_content_report_for_compendium_ComplexMolecularMixture) INFO snakemake.logging [2026-07-22T07:35:39+0000]: Finished jobid: 246 (Rule: generate_content_report_for_compendium_ComplexMolecularMixture) 49 of 103 steps (48%) done INFO snakemake.logging [2026-07-22T07:35:39+0000]: None [Wed Jul 22 03:35:39 2026] Finished jobid: 81 (Rule: check_chemical_mixture) INFO snakemake.logging [2026-07-22T07:35:39+0000]: Finished jobid: 81 (Rule: check_chemical_mixture) 50 of 103 steps (49%) done INFO snakemake.logging [2026-07-22T07:35:39+0000]: None [Wed Jul 22 03:35:39 2026] Finished jobid: 247 (Rule: generate_content_report_for_compendium_ChemicalEntity) INFO snakemake.logging [2026-07-22T07:35:39+0000]: Finished jobid: 247 (Rule: generate_content_report_for_compendium_ChemicalEntity) 51 of 103 steps (50%) done INFO snakemake.logging [2026-07-22T07:35:39+0000]: None [Wed Jul 22 03:35:39 2026] Finished jobid: 82 (Rule: check_drug) INFO snakemake.logging [2026-07-22T07:35:39+0000]: Finished jobid: 82 (Rule: check_drug) 52 of 103 steps (50%) done INFO snakemake.logging [2026-07-22T07:35:39+0000]: None [Wed Jul 22 03:35:39 2026] Finished jobid: 248 (Rule: generate_content_report_for_compendium_ChemicalMixture) INFO snakemake.logging [2026-07-22T07:35:39+0000]: Finished jobid: 248 (Rule: generate_content_report_for_compendium_ChemicalMixture) 53 of 103 steps (51%) done INFO snakemake.logging [2026-07-22T07:35:39+0000]: None [Wed Jul 22 03:35:39 2026] Finished jobid: 83 (Rule: check_food) INFO snakemake.logging [2026-07-22T07:35:39+0000]: Finished jobid: 83 (Rule: check_food) 54 of 103 steps (52%) done INFO snakemake.logging [2026-07-22T07:35:39+0000]: None [Wed Jul 22 03:35:39 2026] Finished jobid: 249 (Rule: generate_content_report_for_compendium_Drug) INFO snakemake.logging [2026-07-22T07:35:39+0000]: Finished jobid: 249 (Rule: generate_content_report_for_compendium_Drug) 55 of 103 steps (53%) done INFO snakemake.logging [2026-07-22T07:35:39+0000]: None [Wed Jul 22 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generate_content_report_for_compendium_MolecularMixture) 59 of 103 steps (57%) done INFO snakemake.logging [2026-07-22T07:37:41+0000]: None [Wed Jul 22 03:45:50 2026] Finished jobid: 275 (Rule: export_compendia_to_duckdb) INFO snakemake.logging [2026-07-22T07:45:50+0000]: Finished jobid: 275 (Rule: export_compendia_to_duckdb) 60 of 103 steps (58%) done INFO snakemake.logging [2026-07-22T07:45:50+0000]: None [Wed Jul 22 03:50:50 2026] Finished jobid: 77 (Rule: check_small_molecule) INFO snakemake.logging [2026-07-22T07:50:50+0000]: Finished jobid: 77 (Rule: check_small_molecule) 61 of 103 steps (59%) done INFO snakemake.logging [2026-07-22T07:50:50+0000]: None [Wed Jul 22 03:50:50 2026] Finished jobid: 26 (Rule: check_chemical_completeness) INFO snakemake.logging [2026-07-22T07:50:50+0000]: Finished jobid: 26 (Rule: check_chemical_completeness) 62 of 103 steps (60%) done INFO snakemake.logging [2026-07-22T07:50:50+0000]: None Select jobs to execute... INFO snakemake.logging [2026-07-22T07:50:50+0000]: Select jobs to execute... Execute 1 jobs... INFO snakemake.logging [2026-07-22T07:50:50+0000]: Execute 1 jobs... Job 25 has been submitted with SLURM jobid 104566 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_chemical/104566.log). INFO snakemake.logging [2026-07-22T07:50:50+0000]: Job 25 has been submitted with SLURM jobid 104566 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_chemical/104566.log). [Wed Jul 22 03:54:31 2026] Finished jobid: 331 (Rule: generate_kgx) INFO snakemake.logging [2026-07-22T07:54:31+0000]: Finished jobid: 331 (Rule: generate_kgx) 63 of 103 steps (61%) done INFO snakemake.logging [2026-07-22T07:54:31+0000]: None [Wed Jul 22 03:54:31 2026] Finished jobid: 244 (Rule: generate_content_report_for_compendium_SmallMolecule) INFO snakemake.logging [2026-07-22T07:54:31+0000]: Finished jobid: 244 (Rule: generate_content_report_for_compendium_SmallMolecule) 64 of 103 steps (62%) done INFO snakemake.logging [2026-07-22T07:54:31+0000]: None [Wed Jul 22 04:08:42 2026] Finished jobid: 228 (Rule: drugchemical_conflation) INFO snakemake.logging [2026-07-22T08:08:42+0000]: Finished jobid: 228 (Rule: drugchemical_conflation) 65 of 103 steps (63%) done INFO snakemake.logging [2026-07-22T08:08:42+0000]: None Select jobs to execute... INFO snakemake.logging [2026-07-22T08:08:42+0000]: Select jobs to execute... Execute 1 jobs... INFO snakemake.logging [2026-07-22T08:08:42+0000]: Execute 1 jobs... Job 317 has been submitted with SLURM jobid 104571 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_export_conflation_to_duckdb/DrugChemical/104571.log). INFO snakemake.logging [2026-07-22T08:08:42+0000]: Job 317 has been submitted with SLURM jobid 104571 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_export_conflation_to_duckdb/DrugChemical/104571.log). [Wed Jul 22 04:08:42 2026] Finished jobid: 216 (Rule: leftover_umls) INFO snakemake.logging [2026-07-22T08:08:42+0000]: Finished jobid: 216 (Rule: leftover_umls) 66 of 103 steps (64%) done INFO snakemake.logging [2026-07-22T08:08:42+0000]: None Select jobs to execute... INFO snakemake.logging [2026-07-22T08:08:42+0000]: Select jobs to execute... Execute 5 jobs... INFO snakemake.logging [2026-07-22T08:08:42+0000]: Execute 5 jobs... Job 293 has been submitted with SLURM jobid 104572 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_export_compendia_to_duckdb/umls/104572.log). INFO snakemake.logging [2026-07-22T08:08:42+0000]: Job 293 has been submitted with SLURM jobid 104572 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_export_compendia_to_duckdb/umls/104572.log). Job 349 has been submitted with SLURM jobid 104573 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_kgx/umls/104573.log). INFO snakemake.logging [2026-07-22T08:08:42+0000]: Job 349 has been submitted with SLURM jobid 104573 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_kgx/umls/104573.log). Job 261 has been submitted with SLURM jobid 104574 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_content_report_for_compendium_umls/104574.log). INFO snakemake.logging [2026-07-22T08:08:42+0000]: Job 261 has been submitted with SLURM jobid 104574 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_content_report_for_compendium_umls/104574.log). Job 320 has been submitted with SLURM jobid 104575 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_mapping_sources_table/104575.log). INFO snakemake.logging [2026-07-22T08:08:42+0000]: Job 320 has been submitted with SLURM jobid 104575 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_mapping_sources_table/104575.log). Job 215 has been submitted with SLURM jobid 104576 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_compress_umls/104576.log). INFO snakemake.logging [2026-07-22T08:08:42+0000]: Job 215 has been submitted with SLURM jobid 104576 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_compress_umls/104576.log). [Wed Jul 22 04:09:22 2026] Finished jobid: 317 (Rule: export_conflation_to_duckdb) INFO snakemake.logging [2026-07-22T08:09:22+0000]: Finished jobid: 317 (Rule: export_conflation_to_duckdb) 67 of 103 steps (65%) done INFO snakemake.logging [2026-07-22T08:09:22+0000]: None Select jobs to execute... INFO snakemake.logging [2026-07-22T08:09:22+0000]: Select jobs to execute... Execute 1 jobs... INFO snakemake.logging [2026-07-22T08:09:22+0000]: Execute 1 jobs... [Wed Jul 22 04:09:22 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: 315 reason: Input files updated by another job: babel_outputs/duckdb/parquet/filename=DrugChemical/Conflation.parquet resources: tmpdir=/tmp, mem_mb=16000, mem=16 GB, mem_mib=15259, disk_mb=1047, disk=1.05 GB, disk_mib=999, runtime=120, cpus_per_task=1 INFO snakemake.logging [2026-07-22T08:09:22+0000]: Rule: export_all_conflations_to_duckdb, Jobid: 315 INFO snakemake.logging [2026-07-22T08:09:22+0000]: Shell command: echo 'done' >> babel_outputs/duckdb/conflations_done [Wed Jul 22 04:09:22 2026] Finished jobid: 261 (Rule: generate_content_report_for_compendium_umls) INFO snakemake.logging [2026-07-22T08:09:22+0000]: Finished jobid: 261 (Rule: generate_content_report_for_compendium_umls) 68 of 103 steps (66%) done INFO snakemake.logging [2026-07-22T08:09:22+0000]: None [Wed Jul 22 04:09:22 2026] Finished jobid: 320 (Rule: generate_mapping_sources_table) INFO snakemake.logging [2026-07-22T08:09:22+0000]: Finished jobid: 320 (Rule: generate_mapping_sources_table) 69 of 103 steps (67%) done INFO snakemake.logging [2026-07-22T08:09:22+0000]: None [Wed Jul 22 04:09:22 2026] Finished jobid: 315 (Rule: export_all_conflations_to_duckdb) INFO snakemake.logging [2026-07-22T08:09:22+0000]: Finished jobid: 315 (Rule: export_all_conflations_to_duckdb) 70 of 103 steps (68%) done INFO snakemake.logging [2026-07-22T08:09:22+0000]: None Select jobs to execute... INFO snakemake.logging [2026-07-22T08:09:22+0000]: Select jobs to execute... Execute 1 jobs... INFO snakemake.logging [2026-07-22T08:09:22+0000]: Execute 1 jobs... Job 238 has been submitted with SLURM jobid 104577 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_compendia_summary_report/104577.log). INFO snakemake.logging [2026-07-22T08:09:22+0000]: Job 238 has been submitted with SLURM jobid 104577 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_compendia_summary_report/104577.log). [Wed Jul 22 04:10:02 2026] Finished jobid: 349 (Rule: generate_kgx) INFO snakemake.logging [2026-07-22T08:10:02+0000]: Finished jobid: 349 (Rule: generate_kgx) 71 of 103 steps (69%) done INFO snakemake.logging [2026-07-22T08:10:02+0000]: None [Wed Jul 22 04:10:02 2026] Finished jobid: 293 (Rule: export_compendia_to_duckdb) INFO snakemake.logging [2026-07-22T08:10:02+0000]: Finished jobid: 293 (Rule: export_compendia_to_duckdb) 72 of 103 steps (70%) done INFO snakemake.logging [2026-07-22T08:10:02+0000]: None [Wed Jul 22 04:10:02 2026] Finished jobid: 215 (Rule: compress_umls) INFO snakemake.logging [2026-07-22T08:10:02+0000]: Finished jobid: 215 (Rule: compress_umls) 73 of 103 steps (71%) done INFO snakemake.logging [2026-07-22T08:10:02+0000]: None Removing temporary output babel_outputs/synonyms/umls.txt. INFO snakemake.logging [2026-07-22T08:10:02+0000]: Removing temporary output babel_outputs/synonyms/umls.txt. Select jobs to execute... INFO snakemake.logging [2026-07-22T08:10:02+0000]: Select jobs to execute... Execute 2 jobs... INFO snakemake.logging [2026-07-22T08:10:02+0000]: Execute 2 jobs... [Wed Jul 22 04:10:02 2026] Finished jobid: 238 (Rule: generate_compendia_summary_report) INFO snakemake.logging [2026-07-22T08:10:02+0000]: Finished jobid: 238 (Rule: generate_compendia_summary_report) 74 of 103 steps (72%) done INFO snakemake.logging [2026-07-22T08:10:02+0000]: None Job 369 has been submitted with SLURM jobid 104580 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_sapbert_training_data/umls.txt/104580.log). INFO snakemake.logging [2026-07-22T08:10:02+0000]: Job 369 has been submitted with SLURM jobid 104580 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_sapbert_training_data/umls.txt/104580.log). Job 313 has been submitted with SLURM jobid 104581 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_export_synonyms_to_duckdb/umls/104581.log). INFO snakemake.logging [2026-07-22T08:10:02+0000]: Job 313 has been submitted with SLURM jobid 104581 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_export_synonyms_to_duckdb/umls/104581.log). [Wed Jul 22 04:10:42 2026] Finished jobid: 313 (Rule: export_synonyms_to_duckdb) INFO snakemake.logging [2026-07-22T08:10:42+0000]: Finished jobid: 313 (Rule: export_synonyms_to_duckdb) 75 of 103 steps (73%) done INFO snakemake.logging [2026-07-22T08:10:42+0000]: None [Wed Jul 22 04:11:22 2026] Finished jobid: 369 (Rule: generate_sapbert_training_data) INFO snakemake.logging [2026-07-22T08:11:22+0000]: Finished jobid: 369 (Rule: generate_sapbert_training_data) 76 of 103 steps (74%) done INFO snakemake.logging [2026-07-22T08:11:22+0000]: None [Wed Jul 22 05:44:57 2026] Finished jobid: 25 (Rule: chemical) INFO snakemake.logging [2026-07-22T09:44:57+0000]: Finished jobid: 25 (Rule: chemical) 77 of 103 steps (75%) done INFO snakemake.logging [2026-07-22T09:44:57+0000]: None Removing temporary output babel_outputs/synonyms/Polypeptide.txt. INFO snakemake.logging [2026-07-22T09:44:57+0000]: Removing temporary output babel_outputs/synonyms/Polypeptide.txt. Removing temporary output babel_outputs/synonyms/ChemicalMixture.txt. INFO snakemake.logging [2026-07-22T09:44:57+0000]: Removing temporary output babel_outputs/synonyms/ChemicalMixture.txt. Removing temporary output babel_outputs/synonyms/Food.txt. INFO snakemake.logging [2026-07-22T09:44:57+0000]: Removing temporary output babel_outputs/synonyms/Food.txt. Removing temporary output babel_outputs/synonyms/SmallMolecule.txt. INFO snakemake.logging [2026-07-22T09:44:57+0000]: Removing temporary output babel_outputs/synonyms/SmallMolecule.txt. Removing temporary output babel_outputs/synonyms/MolecularMixture.txt. INFO snakemake.logging [2026-07-22T09:44:59+0000]: Removing temporary output babel_outputs/synonyms/MolecularMixture.txt. Removing temporary output babel_outputs/synonyms/Drug.txt. INFO snakemake.logging [2026-07-22T09:44:59+0000]: Removing temporary output babel_outputs/synonyms/Drug.txt. Removing temporary output babel_outputs/synonyms/ChemicalEntity.txt. INFO snakemake.logging [2026-07-22T09:44:59+0000]: Removing temporary output babel_outputs/synonyms/ChemicalEntity.txt. Removing temporary output babel_outputs/synonyms/ComplexMolecularMixture.txt. INFO snakemake.logging [2026-07-22T09:44:59+0000]: Removing temporary output babel_outputs/synonyms/ComplexMolecularMixture.txt. Select jobs to execute... INFO snakemake.logging [2026-07-22T09:44:59+0000]: Select jobs to execute... Execute 1 jobs... INFO snakemake.logging [2026-07-22T09:44:59+0000]: Execute 1 jobs... Job 233 has been submitted with SLURM jobid 104605 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_drugchemical_conflated_synonyms/104605.log). INFO snakemake.logging [2026-07-22T09:44:59+0000]: Job 233 has been submitted with SLURM jobid 104605 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_drugchemical_conflated_synonyms/104605.log). [Wed Jul 22 05:53:07 2026] Finished jobid: 276 (Rule: export_compendia_to_duckdb) INFO snakemake.logging [2026-07-22T09:53:07+0000]: Finished jobid: 276 (Rule: export_compendia_to_duckdb) 78 of 103 steps (76%) done INFO snakemake.logging [2026-07-22T09:53:07+0000]: None Select jobs to execute... INFO snakemake.logging [2026-07-22T09:53:07+0000]: Select jobs to execute... Execute 1 jobs... INFO snakemake.logging [2026-07-22T09:53:07+0000]: Execute 1 jobs... [Wed Jul 22 05:53:07 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: 270 reason: Input files updated by another job: babel_outputs/duckdb/duckdbs/filename=umls/compendium.duckdb, babel_outputs/duckdb/duckdbs/filename=AnatomicalEntity/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=MolecularMixture/compendium.duckdb, babel_outputs/duckdb/duckdbs/filename=CellularComponent/compendium.duckdb, babel_outputs/duckdb/duckdbs/filename=ComplexMolecularMixture/compendium.duckdb, babel_outputs/duckdb/duckdbs/filename=ChemicalEntity/compendium.duckdb, babel_outputs/duckdb/duckdbs/filename=Cell/compendium.duckdb, babel_outputs/duckdb/duckdbs/filename=Polypeptide/compendium.duckdb, babel_outputs/duckdb/duckdbs/filename=GrossAnatomicalStructure/compendium.duckdb, babel_outputs/duckdb/duckdbs/filename=SmallMolecule/compendium.duckdb resources: tmpdir=/tmp, mem_mb=16000, mem=16 GB, mem_mib=15259, disk_mb=114769, disk=114.77 GB, disk_mib=109453, runtime=120, cpus_per_task=1 INFO snakemake.logging [2026-07-22T09:53:07+0000]: Rule: export_all_compendia_to_duckdb, Jobid: 270 INFO snakemake.logging [2026-07-22T09:53:07+0000]: Shell command: echo 'done' >> babel_outputs/duckdb/compendia_done [Wed Jul 22 05:53:07 2026] Finished jobid: 270 (Rule: export_all_compendia_to_duckdb) INFO snakemake.logging [2026-07-22T09:53:07+0000]: Finished jobid: 270 (Rule: export_all_compendia_to_duckdb) 79 of 103 steps (77%) done INFO snakemake.logging [2026-07-22T09:53:07+0000]: None Select jobs to execute... INFO snakemake.logging [2026-07-22T09:53:07+0000]: Select jobs to execute... Execute 1 jobs... INFO snakemake.logging [2026-07-22T09:53:07+0000]: Execute 1 jobs... Job 318 has been submitted with SLURM jobid 104608 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_export_intermediate_files_to_duckdb/104608.log). INFO snakemake.logging [2026-07-22T09:53:08+0000]: Job 318 has been submitted with SLURM jobid 104608 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_export_intermediate_files_to_duckdb/104608.log). [Wed Jul 22 06:14:49 2026] Finished jobid: 318 (Rule: export_intermediate_files_to_duckdb) INFO snakemake.logging [2026-07-22T10:14:49+0000]: Finished jobid: 318 (Rule: export_intermediate_files_to_duckdb) 80 of 103 steps (78%) done INFO snakemake.logging [2026-07-22T10:14:49+0000]: None Removing temporary output babel_outputs/duckdb/concords.duckdb. INFO snakemake.logging [2026-07-22T10:14:49+0000]: Removing temporary output babel_outputs/duckdb/concords.duckdb. [Wed Jul 22 06:18:29 2026] Finished jobid: 332 (Rule: generate_kgx) INFO snakemake.logging [2026-07-22T10:18:29+0000]: Finished jobid: 332 (Rule: generate_kgx) 81 of 103 steps (79%) done INFO snakemake.logging [2026-07-22T10:18:29+0000]: None Select jobs to execute... INFO snakemake.logging [2026-07-22T10:18:29+0000]: Select jobs to execute... Execute 1 jobs... INFO snakemake.logging [2026-07-22T10:18:29+0000]: Execute 1 jobs... [Wed Jul 22 06:18:29 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: 326 reason: Input files updated by another job: babel_outputs/kgx/Food_edges.jsonl.gz, babel_outputs/kgx/SmallMolecule_nodes.jsonl.gz, babel_outputs/kgx/GrossAnatomicalStructure_nodes.jsonl.gz, babel_outputs/kgx/MolecularMixture_edges.jsonl.gz, babel_outputs/kgx/CellularComponent_edges.jsonl.gz, babel_outputs/kgx/Polypeptide_nodes.jsonl.gz, babel_outputs/kgx/MolecularMixture_nodes.jsonl.gz, babel_outputs/kgx/CellularComponent_nodes.jsonl.gz, babel_outputs/kgx/Cell_edges.jsonl.gz, babel_outputs/kgx/GrossAnatomicalStructure_edges.jsonl.gz, babel_outputs/kgx/ChemicalMixture_edges.jsonl.gz, babel_outputs/kgx/SmallMolecule_edges.jsonl.gz, babel_outputs/kgx/ComplexMolecularMixture_edges.jsonl.gz, babel_outputs/kgx/AnatomicalEntity_edges.jsonl.gz, babel_outputs/kgx/ChemicalEntity_edges.jsonl.gz, babel_outputs/kgx/umls_edges.jsonl.gz, babel_outputs/kgx/AnatomicalEntity_nodes.jsonl.gz, babel_outputs/kgx/Drug_edges.jsonl.gz, babel_outputs/kgx/Food_nodes.jsonl.gz, babel_outputs/kgx/Polypeptide_edges.jsonl.gz, babel_outputs/kgx/ComplexMolecularMixture_nodes.jsonl.gz, babel_outputs/kgx/ChemicalMixture_nodes.jsonl.gz, babel_outputs/kgx/Cell_nodes.jsonl.gz, babel_outputs/kgx/umls_nodes.jsonl.gz, babel_outputs/kgx/Drug_nodes.jsonl.gz, babel_outputs/kgx/ChemicalEntity_nodes.jsonl.gz resources: tmpdir=/tmp, mem_mb=16000, mem=16 GB, mem_mib=15259, disk_mb=52671, disk=52.67 GB, disk_mib=50231, runtime=120, cpus_per_task=1 INFO snakemake.logging [2026-07-22T10:18:29+0000]: Rule: export_all_to_kgx, Jobid: 326 INFO snakemake.logging [2026-07-22T10:18:29+0000]: Shell command: echo 'done' >> babel_outputs/kgx/done [Wed Jul 22 06:18:30 2026] Finished jobid: 326 (Rule: export_all_to_kgx) INFO snakemake.logging [2026-07-22T10:18:30+0000]: Finished jobid: 326 (Rule: export_all_to_kgx) 82 of 103 steps (80%) done INFO snakemake.logging [2026-07-22T10:18:30+0000]: None [Wed Jul 22 08:31:05 2026] Finished jobid: 233 (Rule: drugchemical_conflated_synonyms) INFO snakemake.logging [2026-07-22T12:31:05+0000]: Finished jobid: 233 (Rule: drugchemical_conflated_synonyms) 83 of 103 steps (81%) done INFO snakemake.logging [2026-07-22T12:31:05+0000]: None Select jobs to execute... INFO snakemake.logging [2026-07-22T12:31:05+0000]: Select jobs to execute... Execute 3 jobs... INFO snakemake.logging [2026-07-22T12:31:05+0000]: Execute 3 jobs... [Wed Jul 22 08:31:05 2026] localrule drugchemical: input: babel_outputs/conflation/DrugChemical.txt, babel_outputs/synonyms/DrugChemicalConflated.txt.gz output: babel_outputs/reports/drugchemical_done jobid: 227 reason: Input files updated by another job: babel_outputs/synonyms/DrugChemicalConflated.txt.gz, babel_outputs/conflation/DrugChemical.txt resources: tmpdir=/tmp, mem_mb=16000, mem=16 GB, mem_mib=15259, disk_mb=13007, disk=13.01 GB, disk_mib=12405, runtime=120, cpus_per_task=1 INFO snakemake.logging [2026-07-22T12:31:05+0000]: Rule: drugchemical, Jobid: 227 INFO snakemake.logging [2026-07-22T12:31:05+0000]: Shell command: None [Wed Jul 22 08:31:05 2026] Finished jobid: 227 (Rule: drugchemical) INFO snakemake.logging [2026-07-22T12:31:05+0000]: Finished jobid: 227 (Rule: drugchemical) 84 of 103 steps (82%) done INFO snakemake.logging [2026-07-22T12:31:05+0000]: None Select jobs to execute... INFO snakemake.logging [2026-07-22T12:31:05+0000]: Select jobs to execute... Job 367 has been submitted with SLURM jobid 104660 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_sapbert_training_data/DrugChemicalConflated.txt/104660.log). INFO snakemake.logging [2026-07-22T12:31:05+0000]: Job 367 has been submitted with SLURM jobid 104660 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_sapbert_training_data/DrugChemicalConflated.txt/104660.log). Job 311 has been submitted with SLURM jobid 104661 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_export_synonyms_to_duckdb/DrugChemicalConflated/104661.log). INFO snakemake.logging [2026-07-22T12:31:05+0000]: Job 311 has been submitted with SLURM jobid 104661 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_export_synonyms_to_duckdb/DrugChemicalConflated/104661.log). Execute 1 jobs... INFO snakemake.logging [2026-07-22T12:31:05+0000]: Execute 1 jobs... [Wed Jul 22 08:31:05 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: Input files updated by another job: babel_outputs/reports/umls_done, babel_outputs/reports/drugchemical_done, babel_outputs/reports/chemicals_done, babel_outputs/reports/anatomy_done resources: tmpdir=/tmp, mem_mb=16000, mem=16 GB, mem_mib=15259, disk_mb=1000, disk=1 GB, disk_mib=954, runtime=120, cpus_per_task=1 INFO snakemake.logging [2026-07-22T12:31:05+0000]: Rule: all_outputs, Jobid: 1 INFO snakemake.logging [2026-07-22T12:31:05+0000]: Shell command: None [Wed Jul 22 08:31:05 2026] Finished jobid: 1 (Rule: all_outputs) INFO snakemake.logging [2026-07-22T12:31:05+0000]: Finished jobid: 1 (Rule: all_outputs) 85 of 103 steps (83%) done INFO snakemake.logging [2026-07-22T12:31:05+0000]: None Select jobs to execute... INFO snakemake.logging [2026-07-22T12:31:05+0000]: Select jobs to execute... Execute 3 jobs... INFO snakemake.logging [2026-07-22T12:31:05+0000]: Execute 3 jobs... Job 266 has been submitted with SLURM jobid 104662 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_check_conflation_files/104662.log). INFO snakemake.logging [2026-07-22T12:31:05+0000]: Job 266 has been submitted with SLURM jobid 104662 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_check_conflation_files/104662.log). Job 264 has been submitted with SLURM jobid 104663 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_check_compendia_files/104663.log). INFO snakemake.logging [2026-07-22T12:31:05+0000]: Job 264 has been submitted with SLURM jobid 104663 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_check_compendia_files/104663.log). Job 265 has been submitted with SLURM jobid 104664 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_check_synonyms_gzipped_files/104664.log). INFO snakemake.logging [2026-07-22T12:31:05+0000]: Job 265 has been submitted with SLURM jobid 104664 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_check_synonyms_gzipped_files/104664.log). [Wed Jul 22 08:31:45 2026] Finished jobid: 266 (Rule: check_conflation_files) INFO snakemake.logging [2026-07-22T12:31:45+0000]: Finished jobid: 266 (Rule: check_conflation_files) 86 of 103 steps (83%) done INFO snakemake.logging [2026-07-22T12:31:45+0000]: None [Wed Jul 22 08:31:45 2026] Finished jobid: 264 (Rule: check_compendia_files) INFO snakemake.logging [2026-07-22T12:31:45+0000]: Finished jobid: 264 (Rule: check_compendia_files) 87 of 103 steps (84%) done INFO snakemake.logging [2026-07-22T12:31:45+0000]: None [Wed Jul 22 08:31:45 2026] Finished jobid: 265 (Rule: check_synonyms_gzipped_files) INFO snakemake.logging [2026-07-22T12:31:45+0000]: Finished jobid: 265 (Rule: check_synonyms_gzipped_files) 88 of 103 steps (85%) done INFO snakemake.logging [2026-07-22T12:31:45+0000]: None [Wed Jul 22 08:41:46 2026] Finished jobid: 311 (Rule: export_synonyms_to_duckdb) INFO snakemake.logging [2026-07-22T12:41:46+0000]: Finished jobid: 311 (Rule: export_synonyms_to_duckdb) 89 of 103 steps (86%) done INFO snakemake.logging [2026-07-22T12:41:46+0000]: None Select jobs to execute... INFO snakemake.logging [2026-07-22T12:41:46+0000]: Select jobs to execute... Execute 1 jobs... INFO snakemake.logging [2026-07-22T12:41:46+0000]: Execute 1 jobs... [Wed Jul 22 08:41:46 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: 296 reason: Input files updated by another job: babel_outputs/duckdb/duckdbs/filename=DrugChemicalConflated/synonyms.duckdb, babel_outputs/duckdb/duckdbs/filename=Cell/synonyms.duckdb, babel_outputs/duckdb/duckdbs/filename=umls/synonyms.duckdb, babel_outputs/duckdb/duckdbs/filename=GrossAnatomicalStructure/synonyms.duckdb, babel_outputs/duckdb/duckdbs/filename=CellularComponent/synonyms.duckdb, babel_outputs/duckdb/duckdbs/filename=AnatomicalEntity/synonyms.duckdb resources: tmpdir=/tmp, mem_mb=16000, mem=16 GB, mem_mib=15259, disk_mb=1000, disk=1 GB, disk_mib=954, runtime=120, cpus_per_task=1 INFO snakemake.logging [2026-07-22T12:41:46+0000]: Rule: export_all_synonyms_to_duckdb, Jobid: 296 INFO snakemake.logging [2026-07-22T12:41:46+0000]: Shell command: echo 'done' >> babel_outputs/duckdb/synonyms_done [Wed Jul 22 08:41:46 2026] Finished jobid: 296 (Rule: export_all_synonyms_to_duckdb) INFO snakemake.logging [2026-07-22T12:41:46+0000]: Finished jobid: 296 (Rule: export_all_synonyms_to_duckdb) 90 of 103 steps (87%) done INFO snakemake.logging [2026-07-22T12:41:46+0000]: None Select jobs to execute... INFO snakemake.logging [2026-07-22T12:41:46+0000]: Select jobs to execute... Execute 1 jobs... INFO snakemake.logging [2026-07-22T12:41:46+0000]: Execute 1 jobs... [Wed Jul 22 08:41:46 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: 269 reason: Input files updated by another job: babel_outputs/duckdb/compendia_done, babel_outputs/duckdb/Concord.parquet, babel_outputs/duckdb/Identifier.parquet, babel_outputs/duckdb/synonyms_done, babel_outputs/duckdb/Metadata.parquet, babel_outputs/duckdb/conflations_done resources: tmpdir=/tmp, mem_mb=16000, mem=16 GB, mem_mib=15259, disk_mb=13333, disk=13.33 GB, disk_mib=12716, runtime=120, cpus_per_task=1 INFO snakemake.logging [2026-07-22T12:41:46+0000]: Rule: export_all_to_duckdb, Jobid: 269 INFO snakemake.logging [2026-07-22T12:41:46+0000]: Shell command: echo 'done' >> babel_outputs/duckdb/done [Wed Jul 22 08:41:46 2026] Finished jobid: 269 (Rule: export_all_to_duckdb) INFO snakemake.logging [2026-07-22T12:41:46+0000]: Finished jobid: 269 (Rule: export_all_to_duckdb) 91 of 103 steps (88%) done INFO snakemake.logging [2026-07-22T12:41:46+0000]: None Select jobs to execute... INFO snakemake.logging [2026-07-22T12:41:46+0000]: Select jobs to execute... Execute 4 jobs... INFO snakemake.logging [2026-07-22T12:41:46+0000]: Execute 4 jobs... Job 323 has been submitted with SLURM jobid 104668 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_check_for_identically_labeled_cliques/104668.log). INFO snakemake.logging [2026-07-22T12:41:46+0000]: Job 323 has been submitted with SLURM jobid 104668 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_check_for_identically_labeled_cliques/104668.log). Job 324 has been submitted with SLURM jobid 104669 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_check_for_duplicate_curies/104669.log). INFO snakemake.logging [2026-07-22T12:41:46+0000]: Job 324 has been submitted with SLURM jobid 104669 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_check_for_duplicate_curies/104669.log). Job 268 has been submitted with SLURM jobid 104670 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_prefix_report/104670.log). INFO snakemake.logging [2026-07-22T12:41:46+0000]: Job 268 has been submitted with SLURM jobid 104670 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_prefix_report/104670.log). Job 325 has been submitted with SLURM jobid 104671 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_check_for_duplicate_clique_leaders/104671.log). INFO snakemake.logging [2026-07-22T12:41:46+0000]: Job 325 has been submitted with SLURM jobid 104671 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_check_for_duplicate_clique_leaders/104671.log). [Wed Jul 22 08:45:26 2026] Finished jobid: 325 (Rule: check_for_duplicate_clique_leaders) INFO snakemake.logging [2026-07-22T12:45:26+0000]: Finished jobid: 325 (Rule: check_for_duplicate_clique_leaders) 92 of 103 steps (89%) done INFO snakemake.logging [2026-07-22T12:45:26+0000]: None Removing temporary output babel_outputs/duckdb/duckdbs/duplicate_clique_leaders.duckdb. INFO snakemake.logging [2026-07-22T12:45:26+0000]: Removing temporary output babel_outputs/duckdb/duckdbs/duplicate_clique_leaders.duckdb. [Wed Jul 22 08:55:28 2026] Finished jobid: 324 (Rule: check_for_duplicate_curies) INFO snakemake.logging [2026-07-22T12:55:28+0000]: Finished jobid: 324 (Rule: check_for_duplicate_curies) 93 of 103 steps (90%) done INFO snakemake.logging [2026-07-22T12:55:28+0000]: None Removing temporary output babel_outputs/duckdb/duckdbs/duplicate_curies.duckdb. INFO snakemake.logging [2026-07-22T12:55:28+0000]: Removing temporary output babel_outputs/duckdb/duckdbs/duplicate_curies.duckdb. [Wed Jul 22 08:56:57 2026] Finished jobid: 268 (Rule: generate_prefix_report) INFO snakemake.logging [2026-07-22T12:56:57+0000]: Finished jobid: 268 (Rule: generate_prefix_report) 94 of 103 steps (91%) done INFO snakemake.logging [2026-07-22T12:56:57+0000]: None Removing temporary output babel_outputs/duckdb/duckdbs/prefix_report.duckdb. INFO snakemake.logging [2026-07-22T12:56:57+0000]: Removing temporary output babel_outputs/duckdb/duckdbs/prefix_report.duckdb. Select jobs to execute... INFO snakemake.logging [2026-07-22T12:56:57+0000]: Select jobs to execute... Execute 3 jobs... INFO snakemake.logging [2026-07-22T12:56:57+0000]: Execute 3 jobs... Job 319 has been submitted with SLURM jobid 104674 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_cliques_table/104674.log). INFO snakemake.logging [2026-07-22T12:56:57+0000]: Job 319 has been submitted with SLURM jobid 104674 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_cliques_table/104674.log). Job 267 has been submitted with SLURM jobid 104675 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_prefix_table/104675.log). INFO snakemake.logging [2026-07-22T12:56:57+0000]: Job 267 has been submitted with SLURM jobid 104675 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_prefix_table/104675.log). Job 321 has been submitted with SLURM jobid 104676 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_prefix_comparison/104676.log). INFO snakemake.logging [2026-07-22T12:56:57+0000]: Job 321 has been submitted with SLURM jobid 104676 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_prefix_comparison/104676.log). [Wed Jul 22 08:57:37 2026] Finished jobid: 319 (Rule: generate_cliques_table) INFO snakemake.logging [2026-07-22T12:57:37+0000]: Finished jobid: 319 (Rule: generate_cliques_table) 95 of 103 steps (92%) done INFO snakemake.logging [2026-07-22T12:57:37+0000]: None [Wed Jul 22 08:57:37 2026] Finished jobid: 267 (Rule: generate_prefix_table) INFO snakemake.logging [2026-07-22T12:57:37+0000]: Finished jobid: 267 (Rule: generate_prefix_table) 96 of 103 steps (93%) done INFO snakemake.logging [2026-07-22T12:57:37+0000]: None [Wed Jul 22 08:57:37 2026] Finished jobid: 321 (Rule: generate_prefix_comparison) INFO snakemake.logging [2026-07-22T12:57:37+0000]: Finished jobid: 321 (Rule: generate_prefix_comparison) 97 of 103 steps (94%) done INFO snakemake.logging [2026-07-22T12:57:37+0000]: None Select jobs to execute... INFO snakemake.logging [2026-07-22T12:57:37+0000]: Select jobs to execute... Execute 1 jobs... INFO snakemake.logging [2026-07-22T12:57:37+0000]: Execute 1 jobs... [Wed Jul 22 08:57:37 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, babel_outputs/reports/tables/prefix_comparison.md output: babel_outputs/reports/reports_done jobid: 237 reason: Input files updated by another job: babel_outputs/reports/check_conflation_files.done, babel_outputs/reports/tables/prefix_table.csv, babel_outputs/reports/tables/cliques_table.csv, babel_outputs/reports/check_compendia_files.done, babel_outputs/reports/tables/mapping_sources_table.csv, babel_outputs/reports/check_synonyms_files.done, babel_outputs/reports/content/compendia_report.json, babel_outputs/reports/tables/prefix_comparison.md resources: tmpdir=/tmp, mem_mb=16000, mem=16 GB, mem_mib=15259, disk_mb=1000, disk=1 GB, disk_mib=954, runtime=120, cpus_per_task=1 INFO snakemake.logging [2026-07-22T12:57:37+0000]: Rule: all_reports, Jobid: 237 INFO snakemake.logging [2026-07-22T12:57:37+0000]: Shell command: echo 'done' >> babel_outputs/reports/reports_done [Wed Jul 22 08:57:38 2026] Finished jobid: 237 (Rule: all_reports) INFO snakemake.logging [2026-07-22T12:57:38+0000]: Finished jobid: 237 (Rule: all_reports) 98 of 103 steps (95%) done INFO snakemake.logging [2026-07-22T12:57:38+0000]: None [Wed Jul 22 09:00:08 2026] Finished jobid: 323 (Rule: check_for_identically_labeled_cliques) INFO snakemake.logging [2026-07-22T13:00:08+0000]: Finished jobid: 323 (Rule: check_for_identically_labeled_cliques) 99 of 103 steps (96%) done INFO snakemake.logging [2026-07-22T13:00:08+0000]: None Removing temporary output babel_outputs/duckdb/duckdbs/identically_labeled_clique.duckdb. INFO snakemake.logging [2026-07-22T13:00:08+0000]: Removing temporary output babel_outputs/duckdb/duckdbs/identically_labeled_clique.duckdb. Select jobs to execute... INFO snakemake.logging [2026-07-22T13:00:08+0000]: Select jobs to execute... Execute 1 jobs... INFO snakemake.logging [2026-07-22T13:00:08+0000]: Execute 1 jobs... [Wed Jul 22 09:00:08 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/prefix_report.json output: babel_outputs/reports/duckdb/done jobid: 322 reason: Input files updated by another job: babel_outputs/reports/duckdb/identically_labeled_cliques.tsv.gz, babel_outputs/duckdb/done, babel_outputs/reports/duckdb/prefix_report.json, babel_outputs/reports/duckdb/duplicate_curies.tsv, babel_outputs/reports/duckdb/duplicate_clique_leaders.tsv resources: tmpdir=/tmp, mem_mb=16000, mem=16 GB, mem_mib=15259, disk_mb=1000, disk=1 GB, disk_mib=954, runtime=120, cpus_per_task=1 INFO snakemake.logging [2026-07-22T13:00:08+0000]: Rule: all_duckdb_reports, Jobid: 322 INFO snakemake.logging [2026-07-22T13:00:08+0000]: Shell command: echo 'done' >> babel_outputs/reports/duckdb/done [Wed Jul 22 09:00:08 2026] Finished jobid: 322 (Rule: all_duckdb_reports) INFO snakemake.logging [2026-07-22T13:00:08+0000]: Finished jobid: 322 (Rule: all_duckdb_reports) 100 of 103 steps (97%) done INFO snakemake.logging [2026-07-22T13:00:08+0000]: None [Wed Jul 22 10:09:41 2026] Finished jobid: 367 (Rule: generate_sapbert_training_data) INFO snakemake.logging [2026-07-22T14:09:41+0000]: Finished jobid: 367 (Rule: generate_sapbert_training_data) 101 of 103 steps (98%) done INFO snakemake.logging [2026-07-22T14:09:41+0000]: None Select jobs to execute... INFO snakemake.logging [2026-07-22T14:09:41+0000]: Select jobs to execute... Execute 1 jobs... INFO snakemake.logging [2026-07-22T14:09:41+0000]: Execute 1 jobs... [Wed Jul 22 10:09:41 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: 352 reason: Input files updated by another job: babel_outputs/sapbert-training-data/AnatomicalEntity.txt.gz, babel_outputs/sapbert-training-data/umls.txt.gz, babel_outputs/sapbert-training-data/DrugChemicalConflated.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 resources: tmpdir=/tmp, mem_mb=16000, mem=16 GB, mem_mib=15259, disk_mb=41374, disk=41.37 GB, disk_mib=39458, runtime=120, cpus_per_task=1 INFO snakemake.logging [2026-07-22T14:09:41+0000]: Rule: export_all_to_sapbert_training, Jobid: 352 INFO snakemake.logging [2026-07-22T14:09:41+0000]: Shell command: echo 'done' >> babel_outputs/sapbert-training-data/done [Wed Jul 22 10:09:42 2026] Finished jobid: 352 (Rule: export_all_to_sapbert_training) INFO snakemake.logging [2026-07-22T14:09:42+0000]: Finished jobid: 352 (Rule: export_all_to_sapbert_training) 102 of 103 steps (99%) done INFO snakemake.logging [2026-07-22T14:09:42+0000]: None Select jobs to execute... INFO snakemake.logging [2026-07-22T14:09:42+0000]: Select jobs to execute... Execute 1 jobs... INFO snakemake.logging [2026-07-22T14:09:42+0000]: Execute 1 jobs... [Wed Jul 22 10:09:42 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/sapbert-training-data/done, babel_outputs/kgx/done, babel_outputs/duckdb/done, babel_outputs/reports/duckdb/done, babel_outputs/reports/reports_done, babel_outputs/reports/outputs_done resources: tmpdir=/tmp, mem_mb=16000, mem=16 GB, mem_mib=15259, disk_mb=1000, disk=1 GB, disk_mib=954, runtime=120, cpus_per_task=1 INFO snakemake.logging [2026-07-22T14:09:42+0000]: Rule: all, Jobid: 0 INFO snakemake.logging [2026-07-22T14:09:42+0000]: Shell command: None [Wed Jul 22 10:09:42 2026] Finished jobid: 0 (Rule: all) INFO snakemake.logging [2026-07-22T14:09:42+0000]: Finished jobid: 0 (Rule: all) 103 of 103 steps (100%) done INFO snakemake.logging [2026-07-22T14:09:42+0000]: None Job 104459.0 for rule 'rule_chemical_compendia' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-22T14:10:22+0000]: Job 104459.0 for rule 'rule_chemical_compendia' (python) has low CPU efficiency: 0.0%. Job 104527.0 for rule 'rule_export_compendia_to_duckdb_wildcards_MolecularMixture' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-22T14:10:22+0000]: Job 104527.0 for rule 'rule_export_compendia_to_duckdb_wildcards_MolecularMixture' (python) has low CPU efficiency: 0.0%. Job 104528.0 for rule 'rule_export_compendia_to_duckdb_wildcards_SmallMolecule' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-22T14:10:22+0000]: Job 104528.0 for rule 'rule_export_compendia_to_duckdb_wildcards_SmallMolecule' (python) has low CPU efficiency: 0.0%. Job 104529.0 for rule 'rule_export_compendia_to_duckdb_wildcards_ComplexMolecularMixture' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-22T14:10:22+0000]: Job 104529.0 for rule 'rule_export_compendia_to_duckdb_wildcards_ComplexMolecularMixture' (python) has low CPU efficiency: 0.0%. Job 104530.0 for rule 'rule_export_compendia_to_duckdb_wildcards_Polypeptide' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-22T14:10:22+0000]: Job 104530.0 for rule 'rule_export_compendia_to_duckdb_wildcards_Polypeptide' (python) has low CPU efficiency: 0.0%. Job 104531.0 for rule 'rule_export_compendia_to_duckdb_wildcards_ChemicalMixture' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-22T14:10:22+0000]: Job 104531.0 for rule 'rule_export_compendia_to_duckdb_wildcards_ChemicalMixture' (python) has low CPU efficiency: 0.0%. Job 104532.0 for rule 'rule_export_compendia_to_duckdb_wildcards_ChemicalEntity' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-22T14:10:22+0000]: Job 104532.0 for rule 'rule_export_compendia_to_duckdb_wildcards_ChemicalEntity' (python) has low CPU efficiency: 0.0%. Job 104533.0 for rule 'rule_export_compendia_to_duckdb_wildcards_Drug' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-22T14:10:22+0000]: Job 104533.0 for rule 'rule_export_compendia_to_duckdb_wildcards_Drug' (python) has low CPU efficiency: 0.0%. Job 104534.0 for rule 'rule_export_compendia_to_duckdb_wildcards_Food' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-22T14:10:22+0000]: Job 104534.0 for rule 'rule_export_compendia_to_duckdb_wildcards_Food' (python) has low CPU efficiency: 0.0%. Job 104535.0 for rule 'rule_generate_kgx_wildcards_ChemicalMixture' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-22T14:10:22+0000]: Job 104535.0 for rule 'rule_generate_kgx_wildcards_ChemicalMixture' (python) has low CPU efficiency: 0.0%. Job 104536.0 for rule 'rule_generate_content_report_for_compendium_MolecularMixture' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-22T14:10:22+0000]: Job 104536.0 for rule 'rule_generate_content_report_for_compendium_MolecularMixture' (python) has low CPU efficiency: 0.0%. Job 104537.0 for rule 'rule_generate_kgx_wildcards_Drug' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-22T14:10:22+0000]: Job 104537.0 for rule 'rule_generate_kgx_wildcards_Drug' (python) has low CPU efficiency: 0.0%. Job 104538.0 for rule 'rule_generate_kgx_wildcards_Food' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-22T14:10:22+0000]: Job 104538.0 for rule 'rule_generate_kgx_wildcards_Food' (python) has low CPU efficiency: 0.0%. Job 104539.0 for rule 'rule_generate_kgx_wildcards_MolecularMixture' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-22T14:10:22+0000]: Job 104539.0 for rule 'rule_generate_kgx_wildcards_MolecularMixture' (python) has low CPU efficiency: 0.0%. Job 104540.0 for rule 'rule_generate_kgx_wildcards_SmallMolecule' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-22T14:10:22+0000]: Job 104540.0 for rule 'rule_generate_kgx_wildcards_SmallMolecule' (python) has low CPU efficiency: 0.0%. Job 104541.0 for rule 'rule_generate_kgx_wildcards_Polypeptide' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-22T14:10:22+0000]: Job 104541.0 for rule 'rule_generate_kgx_wildcards_Polypeptide' (python) has low CPU efficiency: 0.0%. Job 104542.0 for rule 'rule_generate_kgx_wildcards_ComplexMolecularMixture' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-22T14:10:22+0000]: Job 104542.0 for rule 'rule_generate_kgx_wildcards_ComplexMolecularMixture' (python) has low CPU efficiency: 0.0%. Job 104543.0 for rule 'rule_generate_kgx_wildcards_ChemicalEntity' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-22T14:10:22+0000]: Job 104543.0 for rule 'rule_generate_kgx_wildcards_ChemicalEntity' (python) has low CPU efficiency: 0.0%. Job 104544.0 for rule 'rule_check_polypeptide' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-22T14:10:22+0000]: Job 104544.0 for rule 'rule_check_polypeptide' (python) has low CPU efficiency: 0.0%. Job 104545.0 for rule 'rule_check_small_molecule' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-22T14:10:22+0000]: Job 104545.0 for rule 'rule_check_small_molecule' (python) has low CPU efficiency: 0.0%. Job 104546.0 for rule 'rule_generate_content_report_for_compendium_SmallMolecule' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-22T14:10:22+0000]: Job 104546.0 for rule 'rule_generate_content_report_for_compendium_SmallMolecule' (python) has low CPU efficiency: 0.0%. Job 104547.0 for rule 'rule_check_complex_mixture' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-22T14:10:22+0000]: Job 104547.0 for rule 'rule_check_complex_mixture' (python) has low CPU efficiency: 0.0%. Job 104548.0 for rule 'rule_generate_content_report_for_compendium_Polypeptide' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-22T14:10:22+0000]: Job 104548.0 for rule 'rule_generate_content_report_for_compendium_Polypeptide' (python) has low CPU efficiency: 0.0%. Job 104549.0 for rule 'rule_drugchemical_conflation' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-22T14:10:22+0000]: Job 104549.0 for rule 'rule_drugchemical_conflation' (python) has low CPU efficiency: 0.0%. Job 104550.0 for rule 'rule_check_chemical_entity' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-22T14:10:22+0000]: Job 104550.0 for rule 'rule_check_chemical_entity' (python) has low CPU efficiency: 0.0%. Job 104551.0 for rule 'rule_generate_content_report_for_compendium_ComplexMolecularMixture' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-22T14:10:22+0000]: Job 104551.0 for rule 'rule_generate_content_report_for_compendium_ComplexMolecularMixture' (python) has low CPU efficiency: 0.0%. Job 104552.0 for rule 'rule_check_chemical_mixture' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-22T14:10:22+0000]: Job 104552.0 for rule 'rule_check_chemical_mixture' (python) has low CPU efficiency: 0.0%. Job 104553.0 for rule 'rule_check_chemical_completeness' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-22T14:10:22+0000]: Job 104553.0 for rule 'rule_check_chemical_completeness' (python) has low CPU efficiency: 0.0%. Job 104554.0 for rule 'rule_generate_content_report_for_compendium_ChemicalEntity' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-22T14:10:22+0000]: Job 104554.0 for rule 'rule_generate_content_report_for_compendium_ChemicalEntity' (python) has low CPU efficiency: 0.0%. Job 104555.0 for rule 'rule_check_drug' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-22T14:10:22+0000]: Job 104555.0 for rule 'rule_check_drug' (python) has low CPU efficiency: 0.0%. Job 104556.0 for rule 'rule_generate_content_report_for_compendium_ChemicalMixture' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-22T14:10:22+0000]: Job 104556.0 for rule 'rule_generate_content_report_for_compendium_ChemicalMixture' (python) has low CPU efficiency: 0.0%. Job 104557.0 for rule 'rule_check_food' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-22T14:10:22+0000]: Job 104557.0 for rule 'rule_check_food' (python) has low CPU efficiency: 0.0%. Job 104558.0 for rule 'rule_check_molecular_mixture' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-22T14:10:22+0000]: Job 104558.0 for rule 'rule_check_molecular_mixture' (python) has low CPU efficiency: 0.0%. Job 104559.0 for rule 'rule_generate_content_report_for_compendium_Drug' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-22T14:10:22+0000]: Job 104559.0 for rule 'rule_generate_content_report_for_compendium_Drug' (python) has low CPU efficiency: 0.0%. Job 104560.0 for rule 'rule_leftover_umls' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-22T14:10:22+0000]: Job 104560.0 for rule 'rule_leftover_umls' (python) has low CPU efficiency: 0.0%. Job 104561.0 for rule 'rule_generate_content_report_for_compendium_Food' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-22T14:10:22+0000]: Job 104561.0 for rule 'rule_generate_content_report_for_compendium_Food' (python) has low CPU efficiency: 0.0%. Job 104566.0 for rule 'rule_chemical' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-22T14:10:22+0000]: Job 104566.0 for rule 'rule_chemical' (python) has low CPU efficiency: 0.0%. Job 104571.0 for rule 'rule_export_conflation_to_duckdb_wildcards_DrugChemical' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-22T14:10:22+0000]: Job 104571.0 for rule 'rule_export_conflation_to_duckdb_wildcards_DrugChemical' (python) has low CPU efficiency: 0.0%. Job 104572.0 for rule 'rule_export_compendia_to_duckdb_wildcards_umls' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-22T14:10:22+0000]: Job 104572.0 for rule 'rule_export_compendia_to_duckdb_wildcards_umls' (python) has low CPU efficiency: 0.0%. Job 104573.0 for rule 'rule_generate_kgx_wildcards_umls' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-22T14:10:22+0000]: Job 104573.0 for rule 'rule_generate_kgx_wildcards_umls' (python) has low CPU efficiency: 0.0%. Job 104574.0 for rule 'rule_generate_content_report_for_compendium_umls' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-22T14:10:22+0000]: Job 104574.0 for rule 'rule_generate_content_report_for_compendium_umls' (python) has low CPU efficiency: 0.0%. Job 104575.0 for rule 'rule_generate_mapping_sources_table' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-22T14:10:22+0000]: Job 104575.0 for rule 'rule_generate_mapping_sources_table' (python) has low CPU efficiency: 0.0%. Job 104576.0 for rule 'rule_compress_umls' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-22T14:10:22+0000]: Job 104576.0 for rule 'rule_compress_umls' (python) has low CPU efficiency: 0.0%. Job 104577.0 for rule 'rule_generate_compendia_summary_report' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-22T14:10:22+0000]: Job 104577.0 for rule 'rule_generate_compendia_summary_report' (python) has low CPU efficiency: 0.0%. Job 104580.0 for rule 'rule_generate_sapbert_training_data_wildcards_umls.txt' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-22T14:10:22+0000]: Job 104580.0 for rule 'rule_generate_sapbert_training_data_wildcards_umls.txt' (python) has low CPU efficiency: 0.0%. Job 104581.0 for rule 'rule_export_synonyms_to_duckdb_wildcards_umls' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-22T14:10:22+0000]: Job 104581.0 for rule 'rule_export_synonyms_to_duckdb_wildcards_umls' (python) has low CPU efficiency: 0.0%. Job 104605.0 for rule 'rule_drugchemical_conflated_synonyms' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-22T14:10:22+0000]: Job 104605.0 for rule 'rule_drugchemical_conflated_synonyms' (python) has low CPU efficiency: 0.0%. Job 104608.0 for rule 'rule_export_intermediate_files_to_duckdb' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-22T14:10:22+0000]: Job 104608.0 for rule 'rule_export_intermediate_files_to_duckdb' (python) has low CPU efficiency: 0.0%. Job 104660.0 for rule 'rule_generate_sapbert_training_data_wildcards_DrugChemicalConflated.txt' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-22T14:10:22+0000]: Job 104660.0 for rule 'rule_generate_sapbert_training_data_wildcards_DrugChemicalConflated.txt' (python) has low CPU efficiency: 0.0%. Job 104661.0 for rule 'rule_export_synonyms_to_duckdb_wildcards_DrugChemicalConflated' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-22T14:10:22+0000]: Job 104661.0 for rule 'rule_export_synonyms_to_duckdb_wildcards_DrugChemicalConflated' (python) has low CPU efficiency: 0.0%. Job 104662.0 for rule 'rule_check_conflation_files' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-22T14:10:22+0000]: Job 104662.0 for rule 'rule_check_conflation_files' (python) has low CPU efficiency: 0.0%. Job 104663.0 for rule 'rule_check_compendia_files' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-22T14:10:22+0000]: Job 104663.0 for rule 'rule_check_compendia_files' (python) has low CPU efficiency: 0.0%. Job 104664.0 for rule 'rule_check_synonyms_gzipped_files' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-22T14:10:22+0000]: Job 104664.0 for rule 'rule_check_synonyms_gzipped_files' (python) has low CPU efficiency: 0.0%. Job 104668.0 for rule 'rule_check_for_identically_labeled_cliques' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-22T14:10:22+0000]: Job 104668.0 for rule 'rule_check_for_identically_labeled_cliques' (python) has low CPU efficiency: 0.0%. Job 104669.0 for rule 'rule_check_for_duplicate_curies' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-22T14:10:22+0000]: Job 104669.0 for rule 'rule_check_for_duplicate_curies' (python) has low CPU efficiency: 0.0%. Job 104670.0 for rule 'rule_generate_prefix_report' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-22T14:10:22+0000]: Job 104670.0 for rule 'rule_generate_prefix_report' (python) has low CPU efficiency: 0.0%. Job 104671.0 for rule 'rule_check_for_duplicate_clique_leaders' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-22T14:10:22+0000]: Job 104671.0 for rule 'rule_check_for_duplicate_clique_leaders' (python) has low CPU efficiency: 0.0%. Job 104674.0 for rule 'rule_generate_cliques_table' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-22T14:10:22+0000]: Job 104674.0 for rule 'rule_generate_cliques_table' (python) has low CPU efficiency: 0.0%. Job 104675.0 for rule 'rule_generate_prefix_table' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-22T14:10:22+0000]: Job 104675.0 for rule 'rule_generate_prefix_table' (python) has low CPU efficiency: 0.0%. Job 104676.0 for rule 'rule_generate_prefix_comparison' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-22T14:10:22+0000]: Job 104676.0 for rule 'rule_generate_prefix_comparison' (python) has low CPU efficiency: 0.0%. Efficiency report for workflow babel_f9c6ffa6-b030-48cf-a2f3-d37fc4acb355 saved to babel_outputs/reports/slurm/slurm_efficiency_reports/efficiency_report_babel_f9c6ffa6-b030-48cf-a2f3-d37fc4acb355.csv. INFO snakemake.logging [2026-07-22T14:10:22+0000]: Efficiency report for workflow babel_f9c6ffa6-b030-48cf-a2f3-d37fc4acb355 saved to babel_outputs/reports/slurm/slurm_efficiency_reports/efficiency_report_babel_f9c6ffa6-b030-48cf-a2f3-d37fc4acb355.csv. Complete log(s): /projects/babel/runs/gaurav/babel-1.18/.snakemake/log/2026-07-21T211216.707731.snakemake.log INFO snakemake.logging [2026-07-22T14:10:22+0000]: Complete log(s): /projects/babel/runs/gaurav/babel-1.18/.snakemake/log/2026-07-21T211216.707731.snakemake.log