Using profile slurm for setting default command line arguments. SNAKEMAKE ========= Date: 2026-07-21 04:28:16 Workflow ID: 52a5b391-1719-4011-aa29-45f4c5d013e0 Platform: Linux-5.14.0-427.70.1.el9_4.x86_64-x86_64-with-glibc2.34 Host: compute-13-9 User: gaurav Snakemake version: 9.23.1 Python version: 3.13.9 (main, Oct 14 2025, 21:29:44) [Clang 20.1.4 ] Command: /projects/babel/runs/gaurav/babel-1.18/.venv/bin/snakemake --profile slurm Snakefile: /projects/babel/runs/gaurav/babel-1.18/Snakefile Base directory: /projects/babel/runs/gaurav/babel-1.18 Run directory: /projects/babel/runs/gaurav/babel-1.18 Working directory: /projects/babel/runs/gaurav/babel-1.18 Config file(s): ['config.yaml', 'config.yaml'] Config MD5: 04989925d6ddec565b70ca1b17aa0d02 INFO snakemake.logging [2026-07-21T08:28:16+0000]: Workflow has started! Building DAG of jobs... INFO snakemake.logging [2026-07-21T08:28:16+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 [2026-07-21T08:28:18+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_46bf1da2-51f9-4a94-a2f6-333cff151341 INFO snakemake.logging [2026-07-21T08:28:18+0000]: SLURM run ID: babel_46bf1da2-51f9-4a94-a2f6-333cff151341 MinJobAge 300s (>= 120s). 'squeue' should work reliably for status queries. WARNING snakemake.logging [2026-07-21T08:28:18+0000]: MinJobAge 300s (>= 120s). 'squeue' should work reliably for status queries. Using shell: /usr/bin/bash INFO snakemake.logging [2026-07-21T08:28:18+0000]: Using shell: /usr/bin/bash Provided remote nodes: 50 INFO snakemake.logging [2026-07-21T08:28:18+0000]: Provided remote nodes: 50 Job stats: job count -------------------------------------------------------------- ------- chemical_compendia 1 check_chemical_completeness 1 check_chemical_entity 1 check_chemical_mixture 1 check_complex_mixture 1 check_drug 1 check_food 1 check_molecular_mixture 1 check_polypeptide 1 check_small_molecule 1 drugchemical_conflation 1 export_compendia_to_duckdb 9 generate_content_report_for_compendium_ChemicalEntity 1 generate_content_report_for_compendium_ChemicalMixture 1 generate_content_report_for_compendium_ComplexMolecularMixture 1 generate_content_report_for_compendium_Drug 1 generate_content_report_for_compendium_Food 1 generate_content_report_for_compendium_MolecularMixture 1 generate_content_report_for_compendium_Polypeptide 1 generate_content_report_for_compendium_SmallMolecule 1 generate_kgx 9 leftover_umls 1 chemical 1 compress_umls 1 export_conflation_to_duckdb 1 generate_content_report_for_compendium_umls 1 generate_mapping_sources_table 1 drugchemical_conflated_synonyms 1 export_all_compendia_to_duckdb 1 export_all_conflations_to_duckdb 1 export_all_to_kgx 1 export_synonyms_to_duckdb 2 generate_compendia_summary_report 1 generate_sapbert_training_data 2 drugchemical 1 export_intermediate_files_to_duckdb 1 all_outputs 1 export_all_synonyms_to_duckdb 1 export_all_to_sapbert_training 1 check_compendia_files 1 check_conflation_files 1 check_synonyms_gzipped_files 1 export_all_to_duckdb 1 check_for_duplicate_clique_leaders 1 check_for_duplicate_curies 1 check_for_identically_labeled_cliques 1 generate_clique_leader_report 1 generate_curie_report 1 all_duckdb_reports 1 generate_cliques_table 1 generate_prefix_table 1 all_reports 1 all 1 total 71 INFO snakemake.logging [2026-07-21T08:28:18+0000]: Job stats: job count -------------------------------------------------------------- ------- chemical_compendia 1 check_chemical_completeness 1 check_chemical_entity 1 check_chemical_mixture 1 check_complex_mixture 1 check_drug 1 check_food 1 check_molecular_mixture 1 check_polypeptide 1 check_small_molecule 1 drugchemical_conflation 1 export_compendia_to_duckdb 9 generate_content_report_for_compendium_ChemicalEntity 1 generate_content_report_for_compendium_ChemicalMixture 1 generate_content_report_for_compendium_ComplexMolecularMixture 1 generate_content_report_for_compendium_Drug 1 generate_content_report_for_compendium_Food 1 generate_content_report_for_compendium_MolecularMixture 1 generate_content_report_for_compendium_Polypeptide 1 generate_content_report_for_compendium_SmallMolecule 1 generate_kgx 9 leftover_umls 1 chemical 1 compress_umls 1 export_conflation_to_duckdb 1 generate_content_report_for_compendium_umls 1 generate_mapping_sources_table 1 drugchemical_conflated_synonyms 1 export_all_compendia_to_duckdb 1 export_all_conflations_to_duckdb 1 export_all_to_kgx 1 export_synonyms_to_duckdb 2 generate_compendia_summary_report 1 generate_sapbert_training_data 2 drugchemical 1 export_intermediate_files_to_duckdb 1 all_outputs 1 export_all_synonyms_to_duckdb 1 export_all_to_sapbert_training 1 check_compendia_files 1 check_conflation_files 1 check_synonyms_gzipped_files 1 export_all_to_duckdb 1 check_for_duplicate_clique_leaders 1 check_for_duplicate_curies 1 check_for_identically_labeled_cliques 1 generate_clique_leader_report 1 generate_curie_report 1 all_duckdb_reports 1 generate_cliques_table 1 generate_prefix_table 1 all_reports 1 all 1 total 71 Select jobs to execute... INFO snakemake.logging [2026-07-21T08:28:18+0000]: Select jobs to execute... Execute 1 jobs... INFO snakemake.logging [2026-07-21T08:28:18+0000]: Execute 1 jobs... No SLURM account given, trying to guess. WARNING snakemake.logging [2026-07-21T08:28:18+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 [2026-07-21T08:28:18+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 [2026-07-21T08:28:18+0000]: Unable to guess SLURM account. Trying to proceed without. Job 26 has been submitted with SLURM jobid 103915 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_chemical_compendia/103915.log). INFO snakemake.logging [2026-07-21T08:28:18+0000]: Job 26 has been submitted with SLURM jobid 103915 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_chemical_compendia/103915.log). [Tue Jul 21 09:47:01 2026] Finished jobid: 26 (Rule: chemical_compendia) INFO snakemake.logging [2026-07-21T13:47:01+0000]: Finished jobid: 26 (Rule: chemical_compendia) 1 of 71 steps (1%) done INFO snakemake.logging [2026-07-21T13:47:01+0000]: None Select jobs to execute... INFO snakemake.logging [2026-07-21T13:47:01+0000]: Select jobs to execute... Execute 35 jobs... INFO snakemake.logging [2026-07-21T13:47:01+0000]: Execute 35 jobs... Job 277 has been submitted with SLURM jobid 104006 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_export_compendia_to_duckdb/ComplexMolecularMixture/104006.log). INFO snakemake.logging [2026-07-21T13:47:01+0000]: Job 277 has been submitted with SLURM jobid 104006 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_export_compendia_to_duckdb/ComplexMolecularMixture/104006.log). Job 276 has been submitted with SLURM jobid 104007 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_export_compendia_to_duckdb/Polypeptide/104007.log). INFO snakemake.logging [2026-07-21T13:47:01+0000]: Job 276 has been submitted with SLURM jobid 104007 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_export_compendia_to_duckdb/Polypeptide/104007.log). Job 278 has been submitted with SLURM jobid 104008 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_export_compendia_to_duckdb/ChemicalEntity/104008.log). INFO snakemake.logging [2026-07-21T13:47:01+0000]: Job 278 has been submitted with SLURM jobid 104008 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_export_compendia_to_duckdb/ChemicalEntity/104008.log). Job 279 has been submitted with SLURM jobid 104009 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_export_compendia_to_duckdb/ChemicalMixture/104009.log). INFO snakemake.logging [2026-07-21T13:47:01+0000]: Job 279 has been submitted with SLURM jobid 104009 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_export_compendia_to_duckdb/ChemicalMixture/104009.log). Job 280 has been submitted with SLURM jobid 104010 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_export_compendia_to_duckdb/Drug/104010.log). INFO snakemake.logging [2026-07-21T13:47:01+0000]: Job 280 has been submitted with SLURM jobid 104010 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_export_compendia_to_duckdb/Drug/104010.log). Job 281 has been submitted with SLURM jobid 104011 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_export_compendia_to_duckdb/Food/104011.log). INFO snakemake.logging [2026-07-21T13:47:01+0000]: Job 281 has been submitted with SLURM jobid 104011 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_export_compendia_to_duckdb/Food/104011.log). Job 274 has been submitted with SLURM jobid 104012 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_export_compendia_to_duckdb/MolecularMixture/104012.log). INFO snakemake.logging [2026-07-21T13:47:01+0000]: Job 274 has been submitted with SLURM jobid 104012 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_export_compendia_to_duckdb/MolecularMixture/104012.log). Job 275 has been submitted with SLURM jobid 104013 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_export_compendia_to_duckdb/SmallMolecule/104013.log). INFO snakemake.logging [2026-07-21T13:47:01+0000]: Job 275 has been submitted with SLURM jobid 104013 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_export_compendia_to_duckdb/SmallMolecule/104013.log). Job 244 has been submitted with SLURM jobid 104014 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_content_report_for_compendium_Polypeptide/104014.log). INFO snakemake.logging [2026-07-21T13:47:02+0000]: Job 244 has been submitted with SLURM jobid 104014 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_content_report_for_compendium_Polypeptide/104014.log). Job 336 has been submitted with SLURM jobid 104015 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_kgx/Drug/104015.log). INFO snakemake.logging [2026-07-21T13:47:02+0000]: Job 336 has been submitted with SLURM jobid 104015 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_kgx/Drug/104015.log). Job 337 has been submitted with SLURM jobid 104016 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_kgx/Food/104016.log). INFO snakemake.logging [2026-07-21T13:47:02+0000]: Job 337 has been submitted with SLURM jobid 104016 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_kgx/Food/104016.log). Job 330 has been submitted with SLURM jobid 104017 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_kgx/MolecularMixture/104017.log). INFO snakemake.logging [2026-07-21T13:47:02+0000]: Job 330 has been submitted with SLURM jobid 104017 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_kgx/MolecularMixture/104017.log). Job 331 has been submitted with SLURM jobid 104018 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_kgx/SmallMolecule/104018.log). INFO snakemake.logging [2026-07-21T13:47:02+0000]: Job 331 has been submitted with SLURM jobid 104018 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_kgx/SmallMolecule/104018.log). Job 332 has been submitted with SLURM jobid 104019 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_kgx/Polypeptide/104019.log). INFO snakemake.logging [2026-07-21T13:47:02+0000]: Job 332 has been submitted with SLURM jobid 104019 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_kgx/Polypeptide/104019.log). Job 333 has been submitted with SLURM jobid 104020 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_kgx/ComplexMolecularMixture/104020.log). INFO snakemake.logging [2026-07-21T13:47:02+0000]: Job 333 has been submitted with SLURM jobid 104020 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_kgx/ComplexMolecularMixture/104020.log). Job 334 has been submitted with SLURM jobid 104021 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_kgx/ChemicalEntity/104021.log). INFO snakemake.logging [2026-07-21T13:47:02+0000]: Job 334 has been submitted with SLURM jobid 104021 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_kgx/ChemicalEntity/104021.log). Job 335 has been submitted with SLURM jobid 104022 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_kgx/ChemicalMixture/104022.log). INFO snakemake.logging [2026-07-21T13:47:02+0000]: Job 335 has been submitted with SLURM jobid 104022 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_kgx/ChemicalMixture/104022.log). Job 78 has been submitted with SLURM jobid 104023 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_check_complex_mixture/104023.log). INFO snakemake.logging [2026-07-21T13:47:02+0000]: Job 78 has been submitted with SLURM jobid 104023 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_check_complex_mixture/104023.log). Job 245 has been submitted with SLURM jobid 104024 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_content_report_for_compendium_ComplexMolecularMixture/104024.log). INFO snakemake.logging [2026-07-21T13:47:02+0000]: Job 245 has been submitted with SLURM jobid 104024 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_content_report_for_compendium_ComplexMolecularMixture/104024.log). Job 227 has been submitted with SLURM jobid 104025 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_drugchemical_conflation/104025.log). INFO snakemake.logging [2026-07-21T13:47:02+0000]: Job 227 has been submitted with SLURM jobid 104025 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_drugchemical_conflation/104025.log). Job 79 has been submitted with SLURM jobid 104026 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_check_chemical_entity/104026.log). INFO snakemake.logging [2026-07-21T13:47:02+0000]: Job 79 has been submitted with SLURM jobid 104026 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_check_chemical_entity/104026.log). Job 246 has been submitted with SLURM jobid 104027 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_content_report_for_compendium_ChemicalEntity/104027.log). INFO snakemake.logging [2026-07-21T13:47:02+0000]: Job 246 has been submitted with SLURM jobid 104027 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_content_report_for_compendium_ChemicalEntity/104027.log). Job 80 has been submitted with SLURM jobid 104028 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_check_chemical_mixture/104028.log). INFO snakemake.logging [2026-07-21T13:47:02+0000]: Job 80 has been submitted with SLURM jobid 104028 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_check_chemical_mixture/104028.log). Job 25 has been submitted with SLURM jobid 104029 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_check_chemical_completeness/104029.log). INFO snakemake.logging [2026-07-21T13:47:02+0000]: Job 25 has been submitted with SLURM jobid 104029 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_check_chemical_completeness/104029.log). Job 247 has been submitted with SLURM jobid 104030 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_content_report_for_compendium_ChemicalMixture/104030.log). INFO snakemake.logging [2026-07-21T13:47:02+0000]: Job 247 has been submitted with SLURM jobid 104030 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_content_report_for_compendium_ChemicalMixture/104030.log). Job 81 has been submitted with SLURM jobid 104031 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_check_drug/104031.log). INFO snakemake.logging [2026-07-21T13:47:02+0000]: Job 81 has been submitted with SLURM jobid 104031 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_check_drug/104031.log). Job 248 has been submitted with SLURM jobid 104032 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_content_report_for_compendium_Drug/104032.log). INFO snakemake.logging [2026-07-21T13:47:02+0000]: Job 248 has been submitted with SLURM jobid 104032 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_content_report_for_compendium_Drug/104032.log). Job 82 has been submitted with SLURM jobid 104033 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_check_food/104033.log). INFO snakemake.logging [2026-07-21T13:47:02+0000]: Job 82 has been submitted with SLURM jobid 104033 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_check_food/104033.log). Job 215 has been submitted with SLURM jobid 104034 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_leftover_umls/104034.log). INFO snakemake.logging [2026-07-21T13:47:02+0000]: Job 215 has been submitted with SLURM jobid 104034 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_leftover_umls/104034.log). Job 75 has been submitted with SLURM jobid 104035 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_check_molecular_mixture/104035.log). INFO snakemake.logging [2026-07-21T13:47:02+0000]: Job 75 has been submitted with SLURM jobid 104035 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_check_molecular_mixture/104035.log). Job 249 has been submitted with SLURM jobid 104036 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_content_report_for_compendium_Food/104036.log). INFO snakemake.logging [2026-07-21T13:47:02+0000]: Job 249 has been submitted with SLURM jobid 104036 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_content_report_for_compendium_Food/104036.log). Job 242 has been submitted with SLURM jobid 104037 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_content_report_for_compendium_MolecularMixture/104037.log). INFO snakemake.logging [2026-07-21T13:47:02+0000]: Job 242 has been submitted with SLURM jobid 104037 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_content_report_for_compendium_MolecularMixture/104037.log). Job 76 has been submitted with SLURM jobid 104038 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_check_small_molecule/104038.log). INFO snakemake.logging [2026-07-21T13:47:02+0000]: Job 76 has been submitted with SLURM jobid 104038 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_check_small_molecule/104038.log). Job 243 has been submitted with SLURM jobid 104039 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_content_report_for_compendium_SmallMolecule/104039.log). INFO snakemake.logging [2026-07-21T13:47:02+0000]: Job 243 has been submitted with SLURM jobid 104039 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_content_report_for_compendium_SmallMolecule/104039.log). Job 77 has been submitted with SLURM jobid 104040 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_check_polypeptide/104040.log). INFO snakemake.logging [2026-07-21T13:47:02+0000]: Job 77 has been submitted with SLURM jobid 104040 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_check_polypeptide/104040.log). [Tue Jul 21 09:47:42 2026] Finished jobid: 277 (Rule: export_compendia_to_duckdb) INFO snakemake.logging [2026-07-21T13:47:42+0000]: Finished jobid: 277 (Rule: export_compendia_to_duckdb) 2 of 71 steps (3%) done INFO snakemake.logging [2026-07-21T13:47:42+0000]: None [Tue Jul 21 09:47:42 2026] Finished jobid: 276 (Rule: export_compendia_to_duckdb) INFO snakemake.logging [2026-07-21T13:47:42+0000]: Finished jobid: 276 (Rule: export_compendia_to_duckdb) 3 of 71 steps (4%) done INFO snakemake.logging [2026-07-21T13:47:42+0000]: None [Tue Jul 21 09:47:42 2026] Finished jobid: 279 (Rule: export_compendia_to_duckdb) INFO snakemake.logging [2026-07-21T13:47:42+0000]: Finished jobid: 279 (Rule: export_compendia_to_duckdb) 4 of 71 steps (6%) done INFO snakemake.logging [2026-07-21T13:47:42+0000]: None [Tue Jul 21 09:47:42 2026] Finished jobid: 280 (Rule: export_compendia_to_duckdb) INFO snakemake.logging [2026-07-21T13:47:42+0000]: Finished jobid: 280 (Rule: export_compendia_to_duckdb) 5 of 71 steps (7%) done INFO snakemake.logging [2026-07-21T13:47:42+0000]: None [Tue Jul 21 09:47:42 2026] Finished jobid: 281 (Rule: export_compendia_to_duckdb) INFO snakemake.logging [2026-07-21T13:47:42+0000]: Finished jobid: 281 (Rule: export_compendia_to_duckdb) 6 of 71 steps (8%) done INFO snakemake.logging [2026-07-21T13:47:42+0000]: None [Tue Jul 21 09:47:42 2026] Finished jobid: 244 (Rule: generate_content_report_for_compendium_Polypeptide) INFO snakemake.logging [2026-07-21T13:47:42+0000]: Finished jobid: 244 (Rule: generate_content_report_for_compendium_Polypeptide) 7 of 71 steps (10%) done INFO snakemake.logging [2026-07-21T13:47:42+0000]: None [Tue Jul 21 09:47:42 2026] Finished jobid: 336 (Rule: generate_kgx) INFO snakemake.logging [2026-07-21T13:47:42+0000]: Finished jobid: 336 (Rule: generate_kgx) 8 of 71 steps (11%) done INFO snakemake.logging [2026-07-21T13:47:42+0000]: None [Tue Jul 21 09:47:42 2026] Finished jobid: 337 (Rule: generate_kgx) INFO snakemake.logging [2026-07-21T13:47:42+0000]: Finished jobid: 337 (Rule: generate_kgx) 9 of 71 steps (13%) done INFO snakemake.logging [2026-07-21T13:47:42+0000]: None [Tue Jul 21 09:47:42 2026] Finished jobid: 332 (Rule: generate_kgx) INFO snakemake.logging [2026-07-21T13:47:42+0000]: Finished jobid: 332 (Rule: generate_kgx) 10 of 71 steps (14%) done INFO snakemake.logging [2026-07-21T13:47:42+0000]: None [Tue Jul 21 09:47:42 2026] Finished jobid: 333 (Rule: generate_kgx) INFO snakemake.logging [2026-07-21T13:47:42+0000]: Finished jobid: 333 (Rule: generate_kgx) 11 of 71 steps (15%) done INFO snakemake.logging [2026-07-21T13:47:42+0000]: None [Tue Jul 21 09:47:42 2026] Finished jobid: 335 (Rule: generate_kgx) INFO snakemake.logging [2026-07-21T13:47:42+0000]: Finished jobid: 335 (Rule: generate_kgx) 12 of 71 steps (17%) done INFO snakemake.logging [2026-07-21T13:47:42+0000]: None [Tue Jul 21 09:47:42 2026] Finished jobid: 78 (Rule: check_complex_mixture) INFO snakemake.logging [2026-07-21T13:47:42+0000]: Finished jobid: 78 (Rule: check_complex_mixture) 13 of 71 steps (18%) done INFO snakemake.logging [2026-07-21T13:47:42+0000]: None [Tue Jul 21 09:47:42 2026] Finished jobid: 245 (Rule: generate_content_report_for_compendium_ComplexMolecularMixture) INFO snakemake.logging [2026-07-21T13:47:42+0000]: Finished jobid: 245 (Rule: generate_content_report_for_compendium_ComplexMolecularMixture) 14 of 71 steps (20%) done INFO snakemake.logging [2026-07-21T13:47:42+0000]: None [Tue Jul 21 09:47:42 2026] Finished jobid: 79 (Rule: check_chemical_entity) INFO snakemake.logging [2026-07-21T13:47:42+0000]: Finished jobid: 79 (Rule: check_chemical_entity) 15 of 71 steps (21%) done INFO snakemake.logging [2026-07-21T13:47:42+0000]: None [Tue Jul 21 09:47:42 2026] Finished jobid: 246 (Rule: generate_content_report_for_compendium_ChemicalEntity) INFO snakemake.logging [2026-07-21T13:47:42+0000]: Finished jobid: 246 (Rule: generate_content_report_for_compendium_ChemicalEntity) 16 of 71 steps (23%) done INFO snakemake.logging [2026-07-21T13:47:42+0000]: None [Tue Jul 21 09:47:42 2026] Finished jobid: 80 (Rule: check_chemical_mixture) INFO snakemake.logging [2026-07-21T13:47:42+0000]: Finished jobid: 80 (Rule: check_chemical_mixture) 17 of 71 steps (24%) done INFO snakemake.logging [2026-07-21T13:47:42+0000]: None [Tue Jul 21 09:47:42 2026] Finished jobid: 247 (Rule: generate_content_report_for_compendium_ChemicalMixture) INFO snakemake.logging [2026-07-21T13:47:42+0000]: Finished jobid: 247 (Rule: generate_content_report_for_compendium_ChemicalMixture) 18 of 71 steps (25%) done INFO snakemake.logging [2026-07-21T13:47:42+0000]: None [Tue Jul 21 09:47:42 2026] Finished jobid: 81 (Rule: check_drug) INFO snakemake.logging [2026-07-21T13:47:42+0000]: Finished jobid: 81 (Rule: check_drug) 19 of 71 steps (27%) done INFO snakemake.logging [2026-07-21T13:47:42+0000]: None [Tue Jul 21 09:47:42 2026] Finished jobid: 248 (Rule: generate_content_report_for_compendium_Drug) INFO snakemake.logging [2026-07-21T13:47:42+0000]: Finished jobid: 248 (Rule: generate_content_report_for_compendium_Drug) 20 of 71 steps (28%) done INFO snakemake.logging [2026-07-21T13:47:42+0000]: None [Tue Jul 21 09:47:42 2026] Finished jobid: 82 (Rule: check_food) INFO snakemake.logging [2026-07-21T13:47:42+0000]: Finished jobid: 82 (Rule: check_food) 21 of 71 steps (30%) done INFO snakemake.logging [2026-07-21T13:47:42+0000]: None [Tue Jul 21 09:47:42 2026] Finished jobid: 249 (Rule: generate_content_report_for_compendium_Food) INFO snakemake.logging [2026-07-21T13:47:42+0000]: Finished jobid: 249 (Rule: generate_content_report_for_compendium_Food) 22 of 71 steps (31%) done INFO snakemake.logging [2026-07-21T13:47:42+0000]: None [Tue Jul 21 09:47:42 2026] Finished jobid: 77 (Rule: check_polypeptide) INFO snakemake.logging [2026-07-21T13:47:42+0000]: Finished jobid: 77 (Rule: check_polypeptide) 23 of 71 steps (32%) done INFO snakemake.logging [2026-07-21T13:47:42+0000]: None [Tue Jul 21 09:48:22 2026] Finished jobid: 278 (Rule: export_compendia_to_duckdb) INFO snakemake.logging [2026-07-21T13:48:22+0000]: Finished jobid: 278 (Rule: export_compendia_to_duckdb) 24 of 71 steps (34%) done INFO snakemake.logging [2026-07-21T13:48:22+0000]: None [Tue Jul 21 09:48:22 2026] Finished jobid: 334 (Rule: generate_kgx) INFO snakemake.logging [2026-07-21T13:48:22+0000]: Finished jobid: 334 (Rule: generate_kgx) 25 of 71 steps (35%) done INFO snakemake.logging [2026-07-21T13:48:22+0000]: None [Tue Jul 21 09:49:52 2026] Finished jobid: 75 (Rule: check_molecular_mixture) INFO snakemake.logging [2026-07-21T13:49:52+0000]: Finished jobid: 75 (Rule: check_molecular_mixture) 26 of 71 steps (37%) done INFO snakemake.logging [2026-07-21T13:49:52+0000]: None [Tue Jul 21 09:49:52 2026] Finished jobid: 242 (Rule: generate_content_report_for_compendium_MolecularMixture) INFO snakemake.logging [2026-07-21T13:49:52+0000]: Finished jobid: 242 (Rule: generate_content_report_for_compendium_MolecularMixture) 27 of 71 steps (38%) done INFO snakemake.logging [2026-07-21T13:49:52+0000]: None [Tue Jul 21 09:58:03 2026] Finished jobid: 274 (Rule: export_compendia_to_duckdb) INFO snakemake.logging [2026-07-21T13:58:03+0000]: Finished jobid: 274 (Rule: export_compendia_to_duckdb) 28 of 71 steps (39%) done INFO snakemake.logging [2026-07-21T13:58:03+0000]: None [Tue Jul 21 10:03:04 2026] Finished jobid: 25 (Rule: check_chemical_completeness) INFO snakemake.logging [2026-07-21T14:03:04+0000]: Finished jobid: 25 (Rule: check_chemical_completeness) 29 of 71 steps (41%) done INFO snakemake.logging [2026-07-21T14:03:04+0000]: None [Tue Jul 21 10:03:04 2026] Finished jobid: 76 (Rule: check_small_molecule) INFO snakemake.logging [2026-07-21T14:03:04+0000]: Finished jobid: 76 (Rule: check_small_molecule) 30 of 71 steps (42%) done INFO snakemake.logging [2026-07-21T14:03:04+0000]: None Select jobs to execute... INFO snakemake.logging [2026-07-21T14:03:04+0000]: Select jobs to execute... Execute 1 jobs... INFO snakemake.logging [2026-07-21T14:03:04+0000]: Execute 1 jobs... Job 24 has been submitted with SLURM jobid 104047 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_chemical/104047.log). INFO snakemake.logging [2026-07-21T14:03:04+0000]: Job 24 has been submitted with SLURM jobid 104047 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_chemical/104047.log). [Tue Jul 21 10:06:44 2026] Finished jobid: 330 (Rule: generate_kgx) INFO snakemake.logging [2026-07-21T14:06:44+0000]: Finished jobid: 330 (Rule: generate_kgx) 31 of 71 steps (44%) done INFO snakemake.logging [2026-07-21T14:06:44+0000]: None [Tue Jul 21 10:06:44 2026] Finished jobid: 243 (Rule: generate_content_report_for_compendium_SmallMolecule) INFO snakemake.logging [2026-07-21T14:06:44+0000]: Finished jobid: 243 (Rule: generate_content_report_for_compendium_SmallMolecule) 32 of 71 steps (45%) done INFO snakemake.logging [2026-07-21T14:06:44+0000]: None [Tue Jul 21 10:10:24 2026] Finished jobid: 227 (Rule: drugchemical_conflation) INFO snakemake.logging [2026-07-21T14:10:24+0000]: Finished jobid: 227 (Rule: drugchemical_conflation) 33 of 71 steps (46%) done INFO snakemake.logging [2026-07-21T14:10:24+0000]: None Select jobs to execute... INFO snakemake.logging [2026-07-21T14:10:24+0000]: Select jobs to execute... Execute 1 jobs... INFO snakemake.logging [2026-07-21T14:10:25+0000]: Execute 1 jobs... Job 316 has been submitted with SLURM jobid 104052 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_export_conflation_to_duckdb/DrugChemical/104052.log). INFO snakemake.logging [2026-07-21T14:10:25+0000]: Job 316 has been submitted with SLURM jobid 104052 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_export_conflation_to_duckdb/DrugChemical/104052.log). [Tue Jul 21 10:11:05 2026] Finished jobid: 316 (Rule: export_conflation_to_duckdb) INFO snakemake.logging [2026-07-21T14:11:05+0000]: Finished jobid: 316 (Rule: export_conflation_to_duckdb) 34 of 71 steps (48%) done INFO snakemake.logging [2026-07-21T14:11:05+0000]: None Select jobs to execute... INFO snakemake.logging [2026-07-21T14:11:05+0000]: Select jobs to execute... Execute 1 jobs... INFO snakemake.logging [2026-07-21T14:11:05+0000]: Execute 1 jobs... [Tue Jul 21 10:11:05 2026] localrule export_all_conflations_to_duckdb: input: babel_outputs/duckdb/parquet/filename=GeneProtein/Conflation.parquet, babel_outputs/duckdb/parquet/filename=DrugChemical/Conflation.parquet output: babel_outputs/duckdb/conflations_done jobid: 314 reason: 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 [2026-07-21T14:11:05+0000]: Rule: export_all_conflations_to_duckdb, Jobid: 314 INFO snakemake.logging [2026-07-21T14:11:05+0000]: Shell command: echo 'done' >> babel_outputs/duckdb/conflations_done [Tue Jul 21 10:11:05 2026] Finished jobid: 314 (Rule: export_all_conflations_to_duckdb) INFO snakemake.logging [2026-07-21T14:11:05+0000]: Finished jobid: 314 (Rule: export_all_conflations_to_duckdb) 35 of 71 steps (49%) done INFO snakemake.logging [2026-07-21T14:11:05+0000]: None [Tue Jul 21 10:25:16 2026] Finished jobid: 215 (Rule: leftover_umls) INFO snakemake.logging [2026-07-21T14:25:16+0000]: Finished jobid: 215 (Rule: leftover_umls) 36 of 71 steps (51%) done INFO snakemake.logging [2026-07-21T14:25:16+0000]: None Select jobs to execute... INFO snakemake.logging [2026-07-21T14:25:16+0000]: Select jobs to execute... Execute 5 jobs... INFO snakemake.logging [2026-07-21T14:25:16+0000]: Execute 5 jobs... Job 292 has been submitted with SLURM jobid 104054 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_export_compendia_to_duckdb/umls/104054.log). INFO snakemake.logging [2026-07-21T14:25:16+0000]: Job 292 has been submitted with SLURM jobid 104054 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_export_compendia_to_duckdb/umls/104054.log). Job 320 has been submitted with SLURM jobid 104055 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_mapping_sources_table/104055.log). INFO snakemake.logging [2026-07-21T14:25:16+0000]: Job 320 has been submitted with SLURM jobid 104055 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_mapping_sources_table/104055.log). Job 260 has been submitted with SLURM jobid 104056 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_content_report_for_compendium_umls/104056.log). INFO snakemake.logging [2026-07-21T14:25:16+0000]: Job 260 has been submitted with SLURM jobid 104056 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_content_report_for_compendium_umls/104056.log). Job 348 has been submitted with SLURM jobid 104057 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_kgx/umls/104057.log). INFO snakemake.logging [2026-07-21T14:25:16+0000]: Job 348 has been submitted with SLURM jobid 104057 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_kgx/umls/104057.log). Job 214 has been submitted with SLURM jobid 104058 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_compress_umls/104058.log). INFO snakemake.logging [2026-07-21T14:25:16+0000]: Job 214 has been submitted with SLURM jobid 104058 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_compress_umls/104058.log). [Tue Jul 21 10:25:56 2026] Finished jobid: 320 (Rule: generate_mapping_sources_table) INFO snakemake.logging [2026-07-21T14:25:56+0000]: Finished jobid: 320 (Rule: generate_mapping_sources_table) 37 of 71 steps (52%) done INFO snakemake.logging [2026-07-21T14:25:56+0000]: None [Tue Jul 21 10:25:56 2026] Finished jobid: 260 (Rule: generate_content_report_for_compendium_umls) INFO snakemake.logging [2026-07-21T14:25:56+0000]: Finished jobid: 260 (Rule: generate_content_report_for_compendium_umls) 38 of 71 steps (54%) done INFO snakemake.logging [2026-07-21T14:25:56+0000]: None Select jobs to execute... INFO snakemake.logging [2026-07-21T14:25:56+0000]: Select jobs to execute... Execute 1 jobs... INFO snakemake.logging [2026-07-21T14:25:56+0000]: Execute 1 jobs... Job 237 has been submitted with SLURM jobid 104059 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_compendia_summary_report/104059.log). INFO snakemake.logging [2026-07-21T14:25:56+0000]: Job 237 has been submitted with SLURM jobid 104059 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_compendia_summary_report/104059.log). [Tue Jul 21 10:26:36 2026] Finished jobid: 292 (Rule: export_compendia_to_duckdb) INFO snakemake.logging [2026-07-21T14:26:36+0000]: Finished jobid: 292 (Rule: export_compendia_to_duckdb) 39 of 71 steps (55%) done INFO snakemake.logging [2026-07-21T14:26:36+0000]: None [Tue Jul 21 10:26:36 2026] Finished jobid: 348 (Rule: generate_kgx) INFO snakemake.logging [2026-07-21T14:26:36+0000]: Finished jobid: 348 (Rule: generate_kgx) 40 of 71 steps (56%) done INFO snakemake.logging [2026-07-21T14:26:36+0000]: None [Tue Jul 21 10:26:36 2026] Finished jobid: 214 (Rule: compress_umls) INFO snakemake.logging [2026-07-21T14:26:36+0000]: Finished jobid: 214 (Rule: compress_umls) 41 of 71 steps (58%) done INFO snakemake.logging [2026-07-21T14:26:36+0000]: None Removing temporary output babel_outputs/synonyms/umls.txt. INFO snakemake.logging [2026-07-21T14:26:36+0000]: Removing temporary output babel_outputs/synonyms/umls.txt. Select jobs to execute... INFO snakemake.logging [2026-07-21T14:26:36+0000]: Select jobs to execute... Execute 2 jobs... INFO snakemake.logging [2026-07-21T14:26:36+0000]: Execute 2 jobs... Job 368 has been submitted with SLURM jobid 104060 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_sapbert_training_data/umls.txt/104060.log). INFO snakemake.logging [2026-07-21T14:26:36+0000]: Job 368 has been submitted with SLURM jobid 104060 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_sapbert_training_data/umls.txt/104060.log). Job 312 has been submitted with SLURM jobid 104061 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_export_synonyms_to_duckdb/umls/104061.log). INFO snakemake.logging [2026-07-21T14:26:36+0000]: Job 312 has been submitted with SLURM jobid 104061 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_export_synonyms_to_duckdb/umls/104061.log). [Tue Jul 21 10:26:36 2026] Finished jobid: 237 (Rule: generate_compendia_summary_report) INFO snakemake.logging [2026-07-21T14:26:36+0000]: Finished jobid: 237 (Rule: generate_compendia_summary_report) 42 of 71 steps (59%) done INFO snakemake.logging [2026-07-21T14:26:36+0000]: None [Tue Jul 21 10:27:16 2026] Finished jobid: 312 (Rule: export_synonyms_to_duckdb) INFO snakemake.logging [2026-07-21T14:27:16+0000]: Finished jobid: 312 (Rule: export_synonyms_to_duckdb) 43 of 71 steps (61%) done INFO snakemake.logging [2026-07-21T14:27:16+0000]: None [Tue Jul 21 10:27:56 2026] Finished jobid: 368 (Rule: generate_sapbert_training_data) INFO snakemake.logging [2026-07-21T14:27:56+0000]: Finished jobid: 368 (Rule: generate_sapbert_training_data) 44 of 71 steps (62%) done INFO snakemake.logging [2026-07-21T14:27:56+0000]: None [Tue Jul 21 11:55:30 2026] Finished jobid: 275 (Rule: export_compendia_to_duckdb) INFO snakemake.logging [2026-07-21T15:55:30+0000]: Finished jobid: 275 (Rule: export_compendia_to_duckdb) 45 of 71 steps (63%) done INFO snakemake.logging [2026-07-21T15:55:30+0000]: None Select jobs to execute... INFO snakemake.logging [2026-07-21T15:55:30+0000]: Select jobs to execute... Execute 1 jobs... INFO snakemake.logging [2026-07-21T15:55:30+0000]: Execute 1 jobs... [Tue Jul 21 11:55:30 2026] localrule export_all_compendia_to_duckdb: input: babel_outputs/duckdb/duckdbs/filename=AnatomicalEntity/compendium.duckdb, babel_outputs/duckdb/duckdbs/filename=Cell/compendium.duckdb, babel_outputs/duckdb/duckdbs/filename=CellularComponent/compendium.duckdb, babel_outputs/duckdb/duckdbs/filename=GrossAnatomicalStructure/compendium.duckdb, babel_outputs/duckdb/duckdbs/filename=MolecularMixture/compendium.duckdb, babel_outputs/duckdb/duckdbs/filename=SmallMolecule/compendium.duckdb, babel_outputs/duckdb/duckdbs/filename=Polypeptide/compendium.duckdb, babel_outputs/duckdb/duckdbs/filename=ComplexMolecularMixture/compendium.duckdb, babel_outputs/duckdb/duckdbs/filename=ChemicalEntity/compendium.duckdb, babel_outputs/duckdb/duckdbs/filename=ChemicalMixture/compendium.duckdb, babel_outputs/duckdb/duckdbs/filename=Drug/compendium.duckdb, babel_outputs/duckdb/duckdbs/filename=Food/compendium.duckdb, babel_outputs/duckdb/duckdbs/filename=Disease/compendium.duckdb, babel_outputs/duckdb/duckdbs/filename=PhenotypicFeature/compendium.duckdb, babel_outputs/duckdb/duckdbs/filename=Gene/compendium.duckdb, babel_outputs/duckdb/duckdbs/filename=GeneFamily/compendium.duckdb, babel_outputs/duckdb/duckdbs/filename=Pathway/compendium.duckdb, babel_outputs/duckdb/duckdbs/filename=BiologicalProcess/compendium.duckdb, babel_outputs/duckdb/duckdbs/filename=MolecularActivity/compendium.duckdb, babel_outputs/duckdb/duckdbs/filename=Protein/compendium.duckdb, babel_outputs/duckdb/duckdbs/filename=OrganismTaxon/compendium.duckdb, babel_outputs/duckdb/duckdbs/filename=CellLine/compendium.duckdb, babel_outputs/duckdb/duckdbs/filename=umls/compendium.duckdb, babel_outputs/duckdb/duckdbs/filename=MacromolecularComplex/compendium.duckdb, babel_outputs/duckdb/duckdbs/filename=Publication/compendium.duckdb output: babel_outputs/duckdb/compendia_done jobid: 269 reason: Input files updated by another job: babel_outputs/duckdb/duckdbs/filename=Drug/compendium.duckdb, babel_outputs/duckdb/duckdbs/filename=Food/compendium.duckdb, babel_outputs/duckdb/duckdbs/filename=ChemicalEntity/compendium.duckdb, babel_outputs/duckdb/duckdbs/filename=umls/compendium.duckdb, babel_outputs/duckdb/duckdbs/filename=ComplexMolecularMixture/compendium.duckdb, babel_outputs/duckdb/duckdbs/filename=Polypeptide/compendium.duckdb, babel_outputs/duckdb/duckdbs/filename=SmallMolecule/compendium.duckdb, babel_outputs/duckdb/duckdbs/filename=MolecularMixture/compendium.duckdb, babel_outputs/duckdb/duckdbs/filename=ChemicalMixture/compendium.duckdb resources: tmpdir=/tmp, mem_mb=16000, mem=16 GB, mem_mib=15259, disk_mb=114745, disk=114.75 GB, disk_mib=109430, runtime=120, cpus_per_task=1 INFO snakemake.logging [2026-07-21T15:55:30+0000]: Rule: export_all_compendia_to_duckdb, Jobid: 269 INFO snakemake.logging [2026-07-21T15:55:30+0000]: Shell command: echo 'done' >> babel_outputs/duckdb/compendia_done [Tue Jul 21 11:55:31 2026] Finished jobid: 24 (Rule: chemical) INFO snakemake.logging [2026-07-21T15:55:31+0000]: Finished jobid: 24 (Rule: chemical) 46 of 71 steps (65%) done INFO snakemake.logging [2026-07-21T15:55:31+0000]: None Removing temporary output babel_outputs/synonyms/Food.txt. INFO snakemake.logging [2026-07-21T15:55:31+0000]: Removing temporary output babel_outputs/synonyms/Food.txt. Removing temporary output babel_outputs/synonyms/Polypeptide.txt. INFO snakemake.logging [2026-07-21T15:55:31+0000]: Removing temporary output babel_outputs/synonyms/Polypeptide.txt. Removing temporary output babel_outputs/synonyms/ChemicalEntity.txt. INFO snakemake.logging [2026-07-21T15:55:31+0000]: Removing temporary output babel_outputs/synonyms/ChemicalEntity.txt. Removing temporary output babel_outputs/synonyms/ComplexMolecularMixture.txt. INFO snakemake.logging [2026-07-21T15:55:31+0000]: Removing temporary output babel_outputs/synonyms/ComplexMolecularMixture.txt. Removing temporary output babel_outputs/synonyms/MolecularMixture.txt. INFO snakemake.logging [2026-07-21T15:55:31+0000]: Removing temporary output babel_outputs/synonyms/MolecularMixture.txt. Removing temporary output babel_outputs/synonyms/ChemicalMixture.txt. INFO snakemake.logging [2026-07-21T15:55:31+0000]: Removing temporary output babel_outputs/synonyms/ChemicalMixture.txt. Removing temporary output babel_outputs/synonyms/Drug.txt. INFO snakemake.logging [2026-07-21T15:55:31+0000]: Removing temporary output babel_outputs/synonyms/Drug.txt. Removing temporary output babel_outputs/synonyms/SmallMolecule.txt. INFO snakemake.logging [2026-07-21T15:55:31+0000]: Removing temporary output babel_outputs/synonyms/SmallMolecule.txt. [Tue Jul 21 11:55:31 2026] Finished jobid: 269 (Rule: export_all_compendia_to_duckdb) INFO snakemake.logging [2026-07-21T15:55:31+0000]: Finished jobid: 269 (Rule: export_all_compendia_to_duckdb) 47 of 71 steps (66%) done INFO snakemake.logging [2026-07-21T15:55:31+0000]: None Select jobs to execute... INFO snakemake.logging [2026-07-21T15:55:31+0000]: Select jobs to execute... Execute 2 jobs... INFO snakemake.logging [2026-07-21T15:55:31+0000]: Execute 2 jobs... Job 232 has been submitted with SLURM jobid 104088 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_drugchemical_conflated_synonyms/104088.log). INFO snakemake.logging [2026-07-21T15:55:31+0000]: Job 232 has been submitted with SLURM jobid 104088 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_drugchemical_conflated_synonyms/104088.log). Job 317 has been submitted with SLURM jobid 104089 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_export_intermediate_files_to_duckdb/104089.log). INFO snakemake.logging [2026-07-21T15:55:31+0000]: Job 317 has been submitted with SLURM jobid 104089 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_export_intermediate_files_to_duckdb/104089.log). [Tue Jul 21 12:20:02 2026] Finished jobid: 317 (Rule: export_intermediate_files_to_duckdb) INFO snakemake.logging [2026-07-21T16:20:02+0000]: Finished jobid: 317 (Rule: export_intermediate_files_to_duckdb) 48 of 71 steps (68%) done INFO snakemake.logging [2026-07-21T16:20:02+0000]: None Removing temporary output babel_outputs/duckdb/concords.duckdb. INFO snakemake.logging [2026-07-21T16:20:02+0000]: Removing temporary output babel_outputs/duckdb/concords.duckdb. [Tue Jul 21 12:32:03 2026] Finished jobid: 331 (Rule: generate_kgx) INFO snakemake.logging [2026-07-21T16:32:03+0000]: Finished jobid: 331 (Rule: generate_kgx) 49 of 71 steps (69%) done INFO snakemake.logging [2026-07-21T16:32:03+0000]: None Select jobs to execute... INFO snakemake.logging [2026-07-21T16:32:03+0000]: Select jobs to execute... Execute 1 jobs... INFO snakemake.logging [2026-07-21T16:32:03+0000]: Execute 1 jobs... [Tue Jul 21 12:32:03 2026] localrule export_all_to_kgx: input: babel_outputs/kgx/AnatomicalEntity_nodes.jsonl.gz, babel_outputs/kgx/Cell_nodes.jsonl.gz, babel_outputs/kgx/CellularComponent_nodes.jsonl.gz, babel_outputs/kgx/GrossAnatomicalStructure_nodes.jsonl.gz, babel_outputs/kgx/MolecularMixture_nodes.jsonl.gz, babel_outputs/kgx/SmallMolecule_nodes.jsonl.gz, babel_outputs/kgx/Polypeptide_nodes.jsonl.gz, babel_outputs/kgx/ComplexMolecularMixture_nodes.jsonl.gz, babel_outputs/kgx/ChemicalEntity_nodes.jsonl.gz, babel_outputs/kgx/ChemicalMixture_nodes.jsonl.gz, babel_outputs/kgx/Drug_nodes.jsonl.gz, babel_outputs/kgx/Food_nodes.jsonl.gz, babel_outputs/kgx/Disease_nodes.jsonl.gz, babel_outputs/kgx/PhenotypicFeature_nodes.jsonl.gz, babel_outputs/kgx/Gene_nodes.jsonl.gz, babel_outputs/kgx/GeneFamily_nodes.jsonl.gz, babel_outputs/kgx/Pathway_nodes.jsonl.gz, babel_outputs/kgx/BiologicalProcess_nodes.jsonl.gz, babel_outputs/kgx/MolecularActivity_nodes.jsonl.gz, babel_outputs/kgx/Protein_nodes.jsonl.gz, babel_outputs/kgx/OrganismTaxon_nodes.jsonl.gz, babel_outputs/kgx/CellLine_nodes.jsonl.gz, babel_outputs/kgx/umls_nodes.jsonl.gz, babel_outputs/kgx/MacromolecularComplex_nodes.jsonl.gz, babel_outputs/kgx/Publication_nodes.jsonl.gz, babel_outputs/kgx/AnatomicalEntity_edges.jsonl.gz, babel_outputs/kgx/Cell_edges.jsonl.gz, babel_outputs/kgx/CellularComponent_edges.jsonl.gz, babel_outputs/kgx/GrossAnatomicalStructure_edges.jsonl.gz, babel_outputs/kgx/MolecularMixture_edges.jsonl.gz, babel_outputs/kgx/SmallMolecule_edges.jsonl.gz, babel_outputs/kgx/Polypeptide_edges.jsonl.gz, babel_outputs/kgx/ComplexMolecularMixture_edges.jsonl.gz, babel_outputs/kgx/ChemicalEntity_edges.jsonl.gz, babel_outputs/kgx/ChemicalMixture_edges.jsonl.gz, babel_outputs/kgx/Drug_edges.jsonl.gz, babel_outputs/kgx/Food_edges.jsonl.gz, babel_outputs/kgx/Disease_edges.jsonl.gz, babel_outputs/kgx/PhenotypicFeature_edges.jsonl.gz, babel_outputs/kgx/Gene_edges.jsonl.gz, babel_outputs/kgx/GeneFamily_edges.jsonl.gz, babel_outputs/kgx/Pathway_edges.jsonl.gz, babel_outputs/kgx/BiologicalProcess_edges.jsonl.gz, babel_outputs/kgx/MolecularActivity_edges.jsonl.gz, babel_outputs/kgx/Protein_edges.jsonl.gz, babel_outputs/kgx/OrganismTaxon_edges.jsonl.gz, babel_outputs/kgx/CellLine_edges.jsonl.gz, babel_outputs/kgx/umls_edges.jsonl.gz, babel_outputs/kgx/MacromolecularComplex_edges.jsonl.gz, babel_outputs/kgx/Publication_edges.jsonl.gz output: babel_outputs/kgx/done jobid: 325 reason: Input files updated by another job: babel_outputs/kgx/Drug_nodes.jsonl.gz, babel_outputs/kgx/ChemicalEntity_nodes.jsonl.gz, babel_outputs/kgx/MolecularMixture_edges.jsonl.gz, babel_outputs/kgx/MolecularMixture_nodes.jsonl.gz, babel_outputs/kgx/Drug_edges.jsonl.gz, babel_outputs/kgx/umls_edges.jsonl.gz, babel_outputs/kgx/Food_nodes.jsonl.gz, babel_outputs/kgx/ChemicalEntity_edges.jsonl.gz, babel_outputs/kgx/ComplexMolecularMixture_edges.jsonl.gz, babel_outputs/kgx/Polypeptide_edges.jsonl.gz, babel_outputs/kgx/ChemicalMixture_nodes.jsonl.gz, babel_outputs/kgx/SmallMolecule_nodes.jsonl.gz, babel_outputs/kgx/Polypeptide_nodes.jsonl.gz, babel_outputs/kgx/ChemicalMixture_edges.jsonl.gz, babel_outputs/kgx/umls_nodes.jsonl.gz, babel_outputs/kgx/ComplexMolecularMixture_nodes.jsonl.gz, babel_outputs/kgx/Food_edges.jsonl.gz, babel_outputs/kgx/SmallMolecule_edges.jsonl.gz resources: tmpdir=/tmp, mem_mb=16000, mem=16 GB, mem_mib=15259, disk_mb=52662, disk=52.66 GB, disk_mib=50223, runtime=120, cpus_per_task=1 INFO snakemake.logging [2026-07-21T16:32:03+0000]: Rule: export_all_to_kgx, Jobid: 325 INFO snakemake.logging [2026-07-21T16:32:03+0000]: Shell command: echo 'done' >> babel_outputs/kgx/done [Tue Jul 21 12:32:04 2026] Finished jobid: 325 (Rule: export_all_to_kgx) INFO snakemake.logging [2026-07-21T16:32:04+0000]: Finished jobid: 325 (Rule: export_all_to_kgx) 50 of 71 steps (70%) done INFO snakemake.logging [2026-07-21T16:32:04+0000]: None [Tue Jul 21 14:41:39 2026] Finished jobid: 232 (Rule: drugchemical_conflated_synonyms) INFO snakemake.logging [2026-07-21T18:41:39+0000]: Finished jobid: 232 (Rule: drugchemical_conflated_synonyms) 51 of 71 steps (72%) done INFO snakemake.logging [2026-07-21T18:41:39+0000]: None Select jobs to execute... INFO snakemake.logging [2026-07-21T18:41:39+0000]: Select jobs to execute... Execute 3 jobs... INFO snakemake.logging [2026-07-21T18:41:39+0000]: Execute 3 jobs... [Tue Jul 21 14:41:39 2026] localrule drugchemical: input: babel_outputs/conflation/DrugChemical.txt, babel_outputs/synonyms/DrugChemicalConflated.txt.gz output: babel_outputs/reports/drugchemical_done jobid: 226 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 [2026-07-21T18:41:39+0000]: Rule: drugchemical, Jobid: 226 INFO snakemake.logging [2026-07-21T18:41:39+0000]: Shell command: None Job 310 has been submitted with SLURM jobid 104147 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_export_synonyms_to_duckdb/DrugChemicalConflated/104147.log). INFO snakemake.logging [2026-07-21T18:41:39+0000]: Job 310 has been submitted with SLURM jobid 104147 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_export_synonyms_to_duckdb/DrugChemicalConflated/104147.log). Job 366 has been submitted with SLURM jobid 104148 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_sapbert_training_data/DrugChemicalConflated.txt/104148.log). INFO snakemake.logging [2026-07-21T18:41:39+0000]: Job 366 has been submitted with SLURM jobid 104148 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_sapbert_training_data/DrugChemicalConflated.txt/104148.log). [Tue Jul 21 14:41:39 2026] Finished jobid: 226 (Rule: drugchemical) INFO snakemake.logging [2026-07-21T18:41:39+0000]: Finished jobid: 226 (Rule: drugchemical) 52 of 71 steps (73%) done INFO snakemake.logging [2026-07-21T18:41:39+0000]: None Select jobs to execute... INFO snakemake.logging [2026-07-21T18:41:39+0000]: Select jobs to execute... Execute 1 jobs... INFO snakemake.logging [2026-07-21T18:41:39+0000]: Execute 1 jobs... [Tue Jul 21 14:41:39 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/drugchemical_done, babel_outputs/reports/chemicals_done, babel_outputs/reports/umls_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 [2026-07-21T18:41:39+0000]: Rule: all_outputs, Jobid: 1 INFO snakemake.logging [2026-07-21T18:41:39+0000]: Shell command: None [Tue Jul 21 14:41:39 2026] Finished jobid: 1 (Rule: all_outputs) INFO snakemake.logging [2026-07-21T18:41:39+0000]: Finished jobid: 1 (Rule: all_outputs) 53 of 71 steps (75%) done INFO snakemake.logging [2026-07-21T18:41:39+0000]: None Select jobs to execute... INFO snakemake.logging [2026-07-21T18:41:39+0000]: Select jobs to execute... Execute 3 jobs... INFO snakemake.logging [2026-07-21T18:41:39+0000]: Execute 3 jobs... Job 264 has been submitted with SLURM jobid 104149 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_check_synonyms_gzipped_files/104149.log). INFO snakemake.logging [2026-07-21T18:41:39+0000]: Job 264 has been submitted with SLURM jobid 104149 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_check_synonyms_gzipped_files/104149.log). Job 263 has been submitted with SLURM jobid 104150 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_check_compendia_files/104150.log). INFO snakemake.logging [2026-07-21T18:41:39+0000]: Job 263 has been submitted with SLURM jobid 104150 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_check_compendia_files/104150.log). Job 265 has been submitted with SLURM jobid 104151 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_check_conflation_files/104151.log). INFO snakemake.logging [2026-07-21T18:41:39+0000]: Job 265 has been submitted with SLURM jobid 104151 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_check_conflation_files/104151.log). [Tue Jul 21 14:42:19 2026] Finished jobid: 264 (Rule: check_synonyms_gzipped_files) INFO snakemake.logging [2026-07-21T18:42:19+0000]: Finished jobid: 264 (Rule: check_synonyms_gzipped_files) 54 of 71 steps (76%) done INFO snakemake.logging [2026-07-21T18:42:19+0000]: None [Tue Jul 21 14:42:19 2026] Finished jobid: 263 (Rule: check_compendia_files) INFO snakemake.logging [2026-07-21T18:42:19+0000]: Finished jobid: 263 (Rule: check_compendia_files) 55 of 71 steps (77%) done INFO snakemake.logging [2026-07-21T18:42:19+0000]: None [Tue Jul 21 14:42:19 2026] Finished jobid: 265 (Rule: check_conflation_files) INFO snakemake.logging [2026-07-21T18:42:19+0000]: Finished jobid: 265 (Rule: check_conflation_files) 56 of 71 steps (79%) done INFO snakemake.logging [2026-07-21T18:42:19+0000]: None [Tue Jul 21 14:52:20 2026] Finished jobid: 310 (Rule: export_synonyms_to_duckdb) INFO snakemake.logging [2026-07-21T18:52:20+0000]: Finished jobid: 310 (Rule: export_synonyms_to_duckdb) 57 of 71 steps (80%) done INFO snakemake.logging [2026-07-21T18:52:20+0000]: None Select jobs to execute... INFO snakemake.logging [2026-07-21T18:52:20+0000]: Select jobs to execute... Execute 1 jobs... INFO snakemake.logging [2026-07-21T18:52:20+0000]: Execute 1 jobs... [Tue Jul 21 14:52:20 2026] localrule export_all_synonyms_to_duckdb: input: babel_outputs/duckdb/duckdbs/filename=AnatomicalEntity/synonyms.duckdb, babel_outputs/duckdb/duckdbs/filename=Cell/synonyms.duckdb, babel_outputs/duckdb/duckdbs/filename=CellularComponent/synonyms.duckdb, babel_outputs/duckdb/duckdbs/filename=GrossAnatomicalStructure/synonyms.duckdb, babel_outputs/duckdb/duckdbs/filename=Gene/synonyms.duckdb, babel_outputs/duckdb/duckdbs/filename=Protein/synonyms.duckdb, babel_outputs/duckdb/duckdbs/filename=Disease/synonyms.duckdb, babel_outputs/duckdb/duckdbs/filename=PhenotypicFeature/synonyms.duckdb, babel_outputs/duckdb/duckdbs/filename=Pathway/synonyms.duckdb, babel_outputs/duckdb/duckdbs/filename=BiologicalProcess/synonyms.duckdb, babel_outputs/duckdb/duckdbs/filename=MolecularActivity/synonyms.duckdb, babel_outputs/duckdb/duckdbs/filename=OrganismTaxon/synonyms.duckdb, babel_outputs/duckdb/duckdbs/filename=CellLine/synonyms.duckdb, babel_outputs/duckdb/duckdbs/filename=GeneFamily/synonyms.duckdb, babel_outputs/duckdb/duckdbs/filename=DrugChemicalConflated/synonyms.duckdb, babel_outputs/duckdb/duckdbs/filename=GeneProteinConflated/synonyms.duckdb, babel_outputs/duckdb/duckdbs/filename=umls/synonyms.duckdb, babel_outputs/duckdb/duckdbs/filename=MacromolecularComplex/synonyms.duckdb output: babel_outputs/duckdb/synonyms_done jobid: 295 reason: Input files updated by another job: babel_outputs/duckdb/duckdbs/filename=umls/synonyms.duckdb, babel_outputs/duckdb/duckdbs/filename=DrugChemicalConflated/synonyms.duckdb resources: tmpdir=/tmp, 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 [2026-07-21T18:52:20+0000]: Rule: export_all_synonyms_to_duckdb, Jobid: 295 INFO snakemake.logging [2026-07-21T18:52:20+0000]: Shell command: echo 'done' >> babel_outputs/duckdb/synonyms_done [Tue Jul 21 14:52:20 2026] Finished jobid: 295 (Rule: export_all_synonyms_to_duckdb) INFO snakemake.logging [2026-07-21T18:52:20+0000]: Finished jobid: 295 (Rule: export_all_synonyms_to_duckdb) 58 of 71 steps (82%) done INFO snakemake.logging [2026-07-21T18:52:20+0000]: None Select jobs to execute... INFO snakemake.logging [2026-07-21T18:52:20+0000]: Select jobs to execute... Execute 1 jobs... INFO snakemake.logging [2026-07-21T18:52:20+0000]: Execute 1 jobs... [Tue Jul 21 14:52:20 2026] localrule export_all_to_duckdb: input: babel_outputs/duckdb/compendia_done, babel_outputs/duckdb/synonyms_done, babel_outputs/duckdb/conflations_done, babel_outputs/duckdb/Identifier.parquet, babel_outputs/duckdb/Concord.parquet, babel_outputs/duckdb/Metadata.parquet output: babel_outputs/duckdb/done jobid: 268 reason: Input files updated by another job: babel_outputs/duckdb/Metadata.parquet, babel_outputs/duckdb/conflations_done, babel_outputs/duckdb/compendia_done, babel_outputs/duckdb/Identifier.parquet, babel_outputs/duckdb/Concord.parquet, babel_outputs/duckdb/synonyms_done resources: tmpdir=/tmp, mem_mb=16000, mem=16 GB, mem_mib=15259, disk_mb=13329, disk=13.33 GB, disk_mib=12712, runtime=120, cpus_per_task=1 INFO snakemake.logging [2026-07-21T18:52:20+0000]: Rule: export_all_to_duckdb, Jobid: 268 INFO snakemake.logging [2026-07-21T18:52:20+0000]: Shell command: echo 'done' >> babel_outputs/duckdb/done [Tue Jul 21 14:52:20 2026] Finished jobid: 268 (Rule: export_all_to_duckdb) INFO snakemake.logging [2026-07-21T18:52:20+0000]: Finished jobid: 268 (Rule: export_all_to_duckdb) 59 of 71 steps (83%) done INFO snakemake.logging [2026-07-21T18:52:20+0000]: None Select jobs to execute... INFO snakemake.logging [2026-07-21T18:52:20+0000]: Select jobs to execute... Execute 5 jobs... INFO snakemake.logging [2026-07-21T18:52:20+0000]: Execute 5 jobs... Job 323 has been submitted with SLURM jobid 104154 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_check_for_duplicate_curies/104154.log). INFO snakemake.logging [2026-07-21T18:52:20+0000]: Job 323 has been submitted with SLURM jobid 104154 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_check_for_duplicate_curies/104154.log). Job 267 has been submitted with SLURM jobid 104155 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_curie_report/104155.log). INFO snakemake.logging [2026-07-21T18:52:20+0000]: Job 267 has been submitted with SLURM jobid 104155 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_curie_report/104155.log). Job 322 has been submitted with SLURM jobid 104156 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_check_for_identically_labeled_cliques/104156.log). INFO snakemake.logging [2026-07-21T18:52:20+0000]: Job 322 has been submitted with SLURM jobid 104156 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_check_for_identically_labeled_cliques/104156.log). Job 324 has been submitted with SLURM jobid 104157 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_check_for_duplicate_clique_leaders/104157.log). INFO snakemake.logging [2026-07-21T18:52:20+0000]: Job 324 has been submitted with SLURM jobid 104157 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_check_for_duplicate_clique_leaders/104157.log). Job 319 has been submitted with SLURM jobid 104158 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_clique_leader_report/104158.log). INFO snakemake.logging [2026-07-21T18:52:20+0000]: Job 319 has been submitted with SLURM jobid 104158 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_clique_leader_report/104158.log). [Tue Jul 21 14:57:20 2026] Finished jobid: 324 (Rule: check_for_duplicate_clique_leaders) INFO snakemake.logging [2026-07-21T18:57:20+0000]: Finished jobid: 324 (Rule: check_for_duplicate_clique_leaders) 60 of 71 steps (85%) done INFO snakemake.logging [2026-07-21T18:57:20+0000]: None Removing temporary output babel_outputs/duckdb/duckdbs/duplicate_clique_leaders.duckdb. INFO snakemake.logging [2026-07-21T18:57:20+0000]: Removing temporary output babel_outputs/duckdb/duckdbs/duplicate_clique_leaders.duckdb. [Tue Jul 21 14:58:50 2026] Finished jobid: 267 (Rule: generate_curie_report) INFO snakemake.logging [2026-07-21T18:58:50+0000]: Finished jobid: 267 (Rule: generate_curie_report) 61 of 71 steps (86%) done INFO snakemake.logging [2026-07-21T18:58:50+0000]: None Removing temporary output babel_outputs/duckdb/duckdbs/curie_report.duckdb. INFO snakemake.logging [2026-07-21T18:58:50+0000]: Removing temporary output babel_outputs/duckdb/duckdbs/curie_report.duckdb. Select jobs to execute... INFO snakemake.logging [2026-07-21T18:58:50+0000]: Select jobs to execute... Execute 1 jobs... INFO snakemake.logging [2026-07-21T18:58:50+0000]: Execute 1 jobs... Job 266 has been submitted with SLURM jobid 104159 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_prefix_table/104159.log). INFO snakemake.logging [2026-07-21T18:58:50+0000]: Job 266 has been submitted with SLURM jobid 104159 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_prefix_table/104159.log). [Tue Jul 21 14:59:31 2026] Finished jobid: 266 (Rule: generate_prefix_table) INFO snakemake.logging [2026-07-21T18:59:31+0000]: Finished jobid: 266 (Rule: generate_prefix_table) 62 of 71 steps (87%) done INFO snakemake.logging [2026-07-21T18:59:31+0000]: None [Tue Jul 21 15:02:01 2026] Finished jobid: 323 (Rule: check_for_duplicate_curies) INFO snakemake.logging [2026-07-21T19:02:01+0000]: Finished jobid: 323 (Rule: check_for_duplicate_curies) 63 of 71 steps (89%) done INFO snakemake.logging [2026-07-21T19:02:01+0000]: None Removing temporary output babel_outputs/duckdb/duckdbs/duplicate_curies.duckdb. INFO snakemake.logging [2026-07-21T19:02:01+0000]: Removing temporary output babel_outputs/duckdb/duckdbs/duplicate_curies.duckdb. [Tue Jul 21 15:02:41 2026] Finished jobid: 319 (Rule: generate_clique_leader_report) INFO snakemake.logging [2026-07-21T19:02:41+0000]: Finished jobid: 319 (Rule: generate_clique_leader_report) 64 of 71 steps (90%) done INFO snakemake.logging [2026-07-21T19:02:41+0000]: None Removing temporary output babel_outputs/duckdb/duckdbs/clique_leaders.duckdb. INFO snakemake.logging [2026-07-21T19:02:41+0000]: Removing temporary output babel_outputs/duckdb/duckdbs/clique_leaders.duckdb. Select jobs to execute... INFO snakemake.logging [2026-07-21T19:02:41+0000]: Select jobs to execute... Execute 1 jobs... INFO snakemake.logging [2026-07-21T19:02:41+0000]: Execute 1 jobs... Job 318 has been submitted with SLURM jobid 104160 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_cliques_table/104160.log). INFO snakemake.logging [2026-07-21T19:02:41+0000]: Job 318 has been submitted with SLURM jobid 104160 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_cliques_table/104160.log). [Tue Jul 21 15:03:21 2026] Finished jobid: 318 (Rule: generate_cliques_table) INFO snakemake.logging [2026-07-21T19:03:21+0000]: Finished jobid: 318 (Rule: generate_cliques_table) 65 of 71 steps (92%) done INFO snakemake.logging [2026-07-21T19:03:21+0000]: None Select jobs to execute... INFO snakemake.logging [2026-07-21T19:03:21+0000]: Select jobs to execute... Execute 1 jobs... INFO snakemake.logging [2026-07-21T19:03:21+0000]: Execute 1 jobs... [Tue Jul 21 15:03:21 2026] localrule all_reports: input: babel_outputs/reports/content/compendia_report.json, babel_outputs/reports/check_compendia_files.done, babel_outputs/reports/check_synonyms_files.done, babel_outputs/reports/check_conflation_files.done, babel_outputs/reports/tables/prefix_table.csv, babel_outputs/reports/tables/cliques_table.csv, babel_outputs/reports/tables/mapping_sources_table.csv output: babel_outputs/reports/reports_done jobid: 236 reason: Input files updated by another job: babel_outputs/reports/check_synonyms_files.done, babel_outputs/reports/tables/prefix_table.csv, babel_outputs/reports/tables/mapping_sources_table.csv, babel_outputs/reports/check_compendia_files.done, babel_outputs/reports/content/compendia_report.json, babel_outputs/reports/check_conflation_files.done, babel_outputs/reports/tables/cliques_table.csv 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 [2026-07-21T19:03:21+0000]: Rule: all_reports, Jobid: 236 INFO snakemake.logging [2026-07-21T19:03:21+0000]: Shell command: echo 'done' >> babel_outputs/reports/reports_done [Tue Jul 21 15:03:21 2026] Finished jobid: 236 (Rule: all_reports) INFO snakemake.logging [2026-07-21T19:03:21+0000]: Finished jobid: 236 (Rule: all_reports) 66 of 71 steps (93%) done INFO snakemake.logging [2026-07-21T19:03:21+0000]: None [Tue Jul 21 15:13:22 2026] Finished jobid: 322 (Rule: check_for_identically_labeled_cliques) INFO snakemake.logging [2026-07-21T19:13:22+0000]: Finished jobid: 322 (Rule: check_for_identically_labeled_cliques) 67 of 71 steps (94%) done INFO snakemake.logging [2026-07-21T19:13:22+0000]: None Removing temporary output babel_outputs/duckdb/duckdbs/identically_labeled_clique.duckdb. INFO snakemake.logging [2026-07-21T19:13:22+0000]: Removing temporary output babel_outputs/duckdb/duckdbs/identically_labeled_clique.duckdb. Select jobs to execute... INFO snakemake.logging [2026-07-21T19:13:22+0000]: Select jobs to execute... Execute 1 jobs... INFO snakemake.logging [2026-07-21T19:13:22+0000]: Execute 1 jobs... [Tue Jul 21 15:13:22 2026] localrule all_duckdb_reports: input: babel_outputs/duckdb/done, babel_outputs/reports/duckdb/identically_labeled_cliques.tsv.gz, babel_outputs/reports/duckdb/duplicate_curies.tsv, babel_outputs/reports/duckdb/duplicate_clique_leaders.tsv, babel_outputs/reports/duckdb/curie_report.json, babel_outputs/reports/duckdb/clique_leaders.json output: babel_outputs/reports/duckdb/done jobid: 321 reason: Input files updated by another job: babel_outputs/reports/duckdb/duplicate_clique_leaders.tsv, babel_outputs/reports/duckdb/duplicate_curies.tsv, babel_outputs/reports/duckdb/clique_leaders.json, babel_outputs/duckdb/done, babel_outputs/reports/duckdb/identically_labeled_cliques.tsv.gz, babel_outputs/reports/duckdb/curie_report.json 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 [2026-07-21T19:13:22+0000]: Rule: all_duckdb_reports, Jobid: 321 INFO snakemake.logging [2026-07-21T19:13:22+0000]: Shell command: echo 'done' >> babel_outputs/reports/duckdb/done [Tue Jul 21 15:13:22 2026] Finished jobid: 321 (Rule: all_duckdb_reports) INFO snakemake.logging [2026-07-21T19:13:22+0000]: Finished jobid: 321 (Rule: all_duckdb_reports) 68 of 71 steps (96%) done INFO snakemake.logging [2026-07-21T19:13:22+0000]: None [Tue Jul 21 16:19:55 2026] Finished jobid: 366 (Rule: generate_sapbert_training_data) INFO snakemake.logging [2026-07-21T20:19:55+0000]: Finished jobid: 366 (Rule: generate_sapbert_training_data) 69 of 71 steps (97%) done INFO snakemake.logging [2026-07-21T20:19:55+0000]: None Select jobs to execute... INFO snakemake.logging [2026-07-21T20:19:55+0000]: Select jobs to execute... Execute 1 jobs... INFO snakemake.logging [2026-07-21T20:19:55+0000]: Execute 1 jobs... [Tue Jul 21 16:19:55 2026] localrule export_all_to_sapbert_training: input: babel_outputs/sapbert-training-data/AnatomicalEntity.txt.gz, babel_outputs/sapbert-training-data/Cell.txt.gz, babel_outputs/sapbert-training-data/CellularComponent.txt.gz, babel_outputs/sapbert-training-data/GrossAnatomicalStructure.txt.gz, babel_outputs/sapbert-training-data/Gene.txt.gz, babel_outputs/sapbert-training-data/Protein.txt.gz, babel_outputs/sapbert-training-data/Disease.txt.gz, babel_outputs/sapbert-training-data/PhenotypicFeature.txt.gz, babel_outputs/sapbert-training-data/Pathway.txt.gz, babel_outputs/sapbert-training-data/BiologicalProcess.txt.gz, babel_outputs/sapbert-training-data/MolecularActivity.txt.gz, babel_outputs/sapbert-training-data/OrganismTaxon.txt.gz, babel_outputs/sapbert-training-data/CellLine.txt.gz, babel_outputs/sapbert-training-data/GeneFamily.txt.gz, babel_outputs/sapbert-training-data/DrugChemicalConflated.txt.gz, babel_outputs/sapbert-training-data/GeneProteinConflated.txt.gz, babel_outputs/sapbert-training-data/umls.txt.gz, babel_outputs/sapbert-training-data/MacromolecularComplex.txt.gz output: babel_outputs/sapbert-training-data/done jobid: 351 reason: Input files updated by another job: babel_outputs/sapbert-training-data/DrugChemicalConflated.txt.gz, babel_outputs/sapbert-training-data/umls.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 [2026-07-21T20:19:55+0000]: Rule: export_all_to_sapbert_training, Jobid: 351 INFO snakemake.logging [2026-07-21T20:19:55+0000]: Shell command: echo 'done' >> babel_outputs/sapbert-training-data/done [Tue Jul 21 16:19:56 2026] Finished jobid: 351 (Rule: export_all_to_sapbert_training) INFO snakemake.logging [2026-07-21T20:19:56+0000]: Finished jobid: 351 (Rule: export_all_to_sapbert_training) 70 of 71 steps (99%) done INFO snakemake.logging [2026-07-21T20:19:56+0000]: None Select jobs to execute... INFO snakemake.logging [2026-07-21T20:19:56+0000]: Select jobs to execute... Execute 1 jobs... INFO snakemake.logging [2026-07-21T20:19:56+0000]: Execute 1 jobs... [Tue Jul 21 16:19:56 2026] localrule all: input: babel_outputs/reports/outputs_done, babel_outputs/reports/reports_done, babel_outputs/duckdb/done, babel_outputs/reports/duckdb/done, babel_outputs/kgx/done, babel_outputs/sapbert-training-data/done, config.yaml output: babel_outputs/reports/all_done, babel_outputs/config.yaml jobid: 0 reason: Input files updated by another job: babel_outputs/reports/reports_done, babel_outputs/kgx/done, babel_outputs/sapbert-training-data/done, babel_outputs/duckdb/done, babel_outputs/reports/outputs_done, babel_outputs/reports/duckdb/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 [2026-07-21T20:19:56+0000]: Rule: all, Jobid: 0 INFO snakemake.logging [2026-07-21T20:19:56+0000]: Shell command: None [Tue Jul 21 16:19:56 2026] Finished jobid: 0 (Rule: all) INFO snakemake.logging [2026-07-21T20:19:56+0000]: Finished jobid: 0 (Rule: all) 71 of 71 steps (100%) done INFO snakemake.logging [2026-07-21T20:19:56+0000]: None Job 103915.0 for rule 'rule_chemical_compendia' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-21T20:20:36+0000]: Job 103915.0 for rule 'rule_chemical_compendia' (python) has low CPU efficiency: 0.0%. Job 104006.0 for rule 'rule_export_compendia_to_duckdb_wildcards_ComplexMolecularMixture' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-21T20:20:36+0000]: Job 104006.0 for rule 'rule_export_compendia_to_duckdb_wildcards_ComplexMolecularMixture' (python) has low CPU efficiency: 0.0%. Job 104007.0 for rule 'rule_export_compendia_to_duckdb_wildcards_Polypeptide' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-21T20:20:36+0000]: Job 104007.0 for rule 'rule_export_compendia_to_duckdb_wildcards_Polypeptide' (python) has low CPU efficiency: 0.0%. Job 104008.0 for rule 'rule_export_compendia_to_duckdb_wildcards_ChemicalEntity' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-21T20:20:36+0000]: Job 104008.0 for rule 'rule_export_compendia_to_duckdb_wildcards_ChemicalEntity' (python) has low CPU efficiency: 0.0%. Job 104009.0 for rule 'rule_export_compendia_to_duckdb_wildcards_ChemicalMixture' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-21T20:20:36+0000]: Job 104009.0 for rule 'rule_export_compendia_to_duckdb_wildcards_ChemicalMixture' (python) has low CPU efficiency: 0.0%. Job 104010.0 for rule 'rule_export_compendia_to_duckdb_wildcards_Drug' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-21T20:20:36+0000]: Job 104010.0 for rule 'rule_export_compendia_to_duckdb_wildcards_Drug' (python) has low CPU efficiency: 0.0%. Job 104011.0 for rule 'rule_export_compendia_to_duckdb_wildcards_Food' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-21T20:20:36+0000]: Job 104011.0 for rule 'rule_export_compendia_to_duckdb_wildcards_Food' (python) has low CPU efficiency: 0.0%. Job 104012.0 for rule 'rule_export_compendia_to_duckdb_wildcards_MolecularMixture' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-21T20:20:36+0000]: Job 104012.0 for rule 'rule_export_compendia_to_duckdb_wildcards_MolecularMixture' (python) has low CPU efficiency: 0.0%. Job 104013.0 for rule 'rule_export_compendia_to_duckdb_wildcards_SmallMolecule' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-21T20:20:36+0000]: Job 104013.0 for rule 'rule_export_compendia_to_duckdb_wildcards_SmallMolecule' (python) has low CPU efficiency: 0.0%. Job 104014.0 for rule 'rule_generate_content_report_for_compendium_Polypeptide' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-21T20:20:36+0000]: Job 104014.0 for rule 'rule_generate_content_report_for_compendium_Polypeptide' (python) has low CPU efficiency: 0.0%. Job 104015.0 for rule 'rule_generate_kgx_wildcards_Drug' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-21T20:20:36+0000]: Job 104015.0 for rule 'rule_generate_kgx_wildcards_Drug' (python) has low CPU efficiency: 0.0%. Job 104016.0 for rule 'rule_generate_kgx_wildcards_Food' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-21T20:20:36+0000]: Job 104016.0 for rule 'rule_generate_kgx_wildcards_Food' (python) has low CPU efficiency: 0.0%. Job 104017.0 for rule 'rule_generate_kgx_wildcards_MolecularMixture' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-21T20:20:36+0000]: Job 104017.0 for rule 'rule_generate_kgx_wildcards_MolecularMixture' (python) has low CPU efficiency: 0.0%. Job 104018.0 for rule 'rule_generate_kgx_wildcards_SmallMolecule' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-21T20:20:36+0000]: Job 104018.0 for rule 'rule_generate_kgx_wildcards_SmallMolecule' (python) has low CPU efficiency: 0.0%. Job 104019.0 for rule 'rule_generate_kgx_wildcards_Polypeptide' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-21T20:20:36+0000]: Job 104019.0 for rule 'rule_generate_kgx_wildcards_Polypeptide' (python) has low CPU efficiency: 0.0%. Job 104020.0 for rule 'rule_generate_kgx_wildcards_ComplexMolecularMixture' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-21T20:20:36+0000]: Job 104020.0 for rule 'rule_generate_kgx_wildcards_ComplexMolecularMixture' (python) has low CPU efficiency: 0.0%. Job 104021.0 for rule 'rule_generate_kgx_wildcards_ChemicalEntity' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-21T20:20:36+0000]: Job 104021.0 for rule 'rule_generate_kgx_wildcards_ChemicalEntity' (python) has low CPU efficiency: 0.0%. Job 104022.0 for rule 'rule_generate_kgx_wildcards_ChemicalMixture' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-21T20:20:36+0000]: Job 104022.0 for rule 'rule_generate_kgx_wildcards_ChemicalMixture' (python) has low CPU efficiency: 0.0%. Job 104023.0 for rule 'rule_check_complex_mixture' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-21T20:20:36+0000]: Job 104023.0 for rule 'rule_check_complex_mixture' (python) has low CPU efficiency: 0.0%. Job 104024.0 for rule 'rule_generate_content_report_for_compendium_ComplexMolecularMixture' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-21T20:20:36+0000]: Job 104024.0 for rule 'rule_generate_content_report_for_compendium_ComplexMolecularMixture' (python) has low CPU efficiency: 0.0%. Job 104025.0 for rule 'rule_drugchemical_conflation' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-21T20:20:36+0000]: Job 104025.0 for rule 'rule_drugchemical_conflation' (python) has low CPU efficiency: 0.0%. Job 104026.0 for rule 'rule_check_chemical_entity' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-21T20:20:36+0000]: Job 104026.0 for rule 'rule_check_chemical_entity' (python) has low CPU efficiency: 0.0%. Job 104027.0 for rule 'rule_generate_content_report_for_compendium_ChemicalEntity' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-21T20:20:36+0000]: Job 104027.0 for rule 'rule_generate_content_report_for_compendium_ChemicalEntity' (python) has low CPU efficiency: 0.0%. Job 104028.0 for rule 'rule_check_chemical_mixture' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-21T20:20:36+0000]: Job 104028.0 for rule 'rule_check_chemical_mixture' (python) has low CPU efficiency: 0.0%. Job 104029.0 for rule 'rule_check_chemical_completeness' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-21T20:20:36+0000]: Job 104029.0 for rule 'rule_check_chemical_completeness' (python) has low CPU efficiency: 0.0%. Job 104030.0 for rule 'rule_generate_content_report_for_compendium_ChemicalMixture' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-21T20:20:36+0000]: Job 104030.0 for rule 'rule_generate_content_report_for_compendium_ChemicalMixture' (python) has low CPU efficiency: 0.0%. Job 104031.0 for rule 'rule_check_drug' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-21T20:20:36+0000]: Job 104031.0 for rule 'rule_check_drug' (python) has low CPU efficiency: 0.0%. Job 104032.0 for rule 'rule_generate_content_report_for_compendium_Drug' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-21T20:20:36+0000]: Job 104032.0 for rule 'rule_generate_content_report_for_compendium_Drug' (python) has low CPU efficiency: 0.0%. Job 104033.0 for rule 'rule_check_food' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-21T20:20:36+0000]: Job 104033.0 for rule 'rule_check_food' (python) has low CPU efficiency: 0.0%. Job 104034.0 for rule 'rule_leftover_umls' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-21T20:20:36+0000]: Job 104034.0 for rule 'rule_leftover_umls' (python) has low CPU efficiency: 0.0%. Job 104035.0 for rule 'rule_check_molecular_mixture' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-21T20:20:36+0000]: Job 104035.0 for rule 'rule_check_molecular_mixture' (python) has low CPU efficiency: 0.0%. Job 104036.0 for rule 'rule_generate_content_report_for_compendium_Food' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-21T20:20:36+0000]: Job 104036.0 for rule 'rule_generate_content_report_for_compendium_Food' (python) has low CPU efficiency: 0.0%. Job 104037.0 for rule 'rule_generate_content_report_for_compendium_MolecularMixture' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-21T20:20:36+0000]: Job 104037.0 for rule 'rule_generate_content_report_for_compendium_MolecularMixture' (python) has low CPU efficiency: 0.0%. Job 104038.0 for rule 'rule_check_small_molecule' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-21T20:20:36+0000]: Job 104038.0 for rule 'rule_check_small_molecule' (python) has low CPU efficiency: 0.0%. Job 104039.0 for rule 'rule_generate_content_report_for_compendium_SmallMolecule' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-21T20:20:36+0000]: Job 104039.0 for rule 'rule_generate_content_report_for_compendium_SmallMolecule' (python) has low CPU efficiency: 0.0%. Job 104040.0 for rule 'rule_check_polypeptide' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-21T20:20:36+0000]: Job 104040.0 for rule 'rule_check_polypeptide' (python) has low CPU efficiency: 0.0%. Job 104047.0 for rule 'rule_chemical' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-21T20:20:36+0000]: Job 104047.0 for rule 'rule_chemical' (python) has low CPU efficiency: 0.0%. Job 104052.0 for rule 'rule_export_conflation_to_duckdb_wildcards_DrugChemical' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-21T20:20:36+0000]: Job 104052.0 for rule 'rule_export_conflation_to_duckdb_wildcards_DrugChemical' (python) has low CPU efficiency: 0.0%. Job 104054.0 for rule 'rule_export_compendia_to_duckdb_wildcards_umls' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-21T20:20:36+0000]: Job 104054.0 for rule 'rule_export_compendia_to_duckdb_wildcards_umls' (python) has low CPU efficiency: 0.0%. Job 104055.0 for rule 'rule_generate_mapping_sources_table' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-21T20:20:36+0000]: Job 104055.0 for rule 'rule_generate_mapping_sources_table' (python) has low CPU efficiency: 0.0%. Job 104056.0 for rule 'rule_generate_content_report_for_compendium_umls' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-21T20:20:36+0000]: Job 104056.0 for rule 'rule_generate_content_report_for_compendium_umls' (python) has low CPU efficiency: 0.0%. Job 104057.0 for rule 'rule_generate_kgx_wildcards_umls' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-21T20:20:36+0000]: Job 104057.0 for rule 'rule_generate_kgx_wildcards_umls' (python) has low CPU efficiency: 0.0%. Job 104058.0 for rule 'rule_compress_umls' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-21T20:20:36+0000]: Job 104058.0 for rule 'rule_compress_umls' (python) has low CPU efficiency: 0.0%. Job 104059.0 for rule 'rule_generate_compendia_summary_report' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-21T20:20:36+0000]: Job 104059.0 for rule 'rule_generate_compendia_summary_report' (python) has low CPU efficiency: 0.0%. Job 104060.0 for rule 'rule_generate_sapbert_training_data_wildcards_umls.txt' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-21T20:20:36+0000]: Job 104060.0 for rule 'rule_generate_sapbert_training_data_wildcards_umls.txt' (python) has low CPU efficiency: 0.0%. Job 104061.0 for rule 'rule_export_synonyms_to_duckdb_wildcards_umls' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-21T20:20:36+0000]: Job 104061.0 for rule 'rule_export_synonyms_to_duckdb_wildcards_umls' (python) has low CPU efficiency: 0.0%. Job 104088.0 for rule 'rule_drugchemical_conflated_synonyms' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-21T20:20:36+0000]: Job 104088.0 for rule 'rule_drugchemical_conflated_synonyms' (python) has low CPU efficiency: 0.0%. Job 104089.0 for rule 'rule_export_intermediate_files_to_duckdb' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-21T20:20:36+0000]: Job 104089.0 for rule 'rule_export_intermediate_files_to_duckdb' (python) has low CPU efficiency: 0.0%. Job 104147.0 for rule 'rule_export_synonyms_to_duckdb_wildcards_DrugChemicalConflated' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-21T20:20:36+0000]: Job 104147.0 for rule 'rule_export_synonyms_to_duckdb_wildcards_DrugChemicalConflated' (python) has low CPU efficiency: 0.0%. Job 104148.0 for rule 'rule_generate_sapbert_training_data_wildcards_DrugChemicalConflated.txt' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-21T20:20:36+0000]: Job 104148.0 for rule 'rule_generate_sapbert_training_data_wildcards_DrugChemicalConflated.txt' (python) has low CPU efficiency: 0.0%. Job 104149.0 for rule 'rule_check_synonyms_gzipped_files' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-21T20:20:36+0000]: Job 104149.0 for rule 'rule_check_synonyms_gzipped_files' (python) has low CPU efficiency: 0.0%. Job 104150.0 for rule 'rule_check_compendia_files' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-21T20:20:36+0000]: Job 104150.0 for rule 'rule_check_compendia_files' (python) has low CPU efficiency: 0.0%. Job 104151.0 for rule 'rule_check_conflation_files' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-21T20:20:36+0000]: Job 104151.0 for rule 'rule_check_conflation_files' (python) has low CPU efficiency: 0.0%. Job 104154.0 for rule 'rule_check_for_duplicate_curies' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-21T20:20:36+0000]: Job 104154.0 for rule 'rule_check_for_duplicate_curies' (python) has low CPU efficiency: 0.0%. Job 104155.0 for rule 'rule_generate_curie_report' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-21T20:20:36+0000]: Job 104155.0 for rule 'rule_generate_curie_report' (python) has low CPU efficiency: 0.0%. Job 104156.0 for rule 'rule_check_for_identically_labeled_cliques' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-21T20:20:36+0000]: Job 104156.0 for rule 'rule_check_for_identically_labeled_cliques' (python) has low CPU efficiency: 0.0%. Job 104157.0 for rule 'rule_check_for_duplicate_clique_leaders' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-21T20:20:36+0000]: Job 104157.0 for rule 'rule_check_for_duplicate_clique_leaders' (python) has low CPU efficiency: 0.0%. Job 104158.0 for rule 'rule_generate_clique_leader_report' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-21T20:20:36+0000]: Job 104158.0 for rule 'rule_generate_clique_leader_report' (python) has low CPU efficiency: 0.0%. Job 104159.0 for rule 'rule_generate_prefix_table' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-21T20:20:36+0000]: Job 104159.0 for rule 'rule_generate_prefix_table' (python) has low CPU efficiency: 0.0%. Job 104160.0 for rule 'rule_generate_cliques_table' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-21T20:20:36+0000]: Job 104160.0 for rule 'rule_generate_cliques_table' (python) has low CPU efficiency: 0.0%. Efficiency report for workflow babel_46bf1da2-51f9-4a94-a2f6-333cff151341 saved to babel_outputs/reports/slurm/slurm_efficiency_reports/efficiency_report_babel_46bf1da2-51f9-4a94-a2f6-333cff151341.csv. INFO snakemake.logging [2026-07-21T20:20:36+0000]: Efficiency report for workflow babel_46bf1da2-51f9-4a94-a2f6-333cff151341 saved to babel_outputs/reports/slurm/slurm_efficiency_reports/efficiency_report_babel_46bf1da2-51f9-4a94-a2f6-333cff151341.csv. Complete log(s): /projects/babel/runs/gaurav/babel-1.18/.snakemake/log/2026-07-21T042814.447684.snakemake.log INFO snakemake.logging [2026-07-21T20:20:36+0000]: Complete log(s): /projects/babel/runs/gaurav/babel-1.18/.snakemake/log/2026-07-21T042814.447684.snakemake.log