Using profile slurm for setting default command line arguments. INFO snakemake.logging [2025-11-22T07:56:44+0000]: None host: compute-13-1 INFO snakemake.logging [2025-11-22T07:56:44+0000]: host: compute-13-1 Building DAG of jobs... INFO snakemake.logging [2025-11-22T07:56:44+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. Please run Snakemake directly on the login node. WARNING snakemake.logging [2025-11-22T07:56:44+0000]: You are running snakemake in a SLURM job context. This is not recommended, as it may lead to unexpected behavior. Please run Snakemake directly on the login node. SLURM run ID: 21d1b82b-160d-4a51-bf44-c2ff5d5bafb3 INFO snakemake.logging [2025-11-22T07:56:49+0000]: SLURM run ID: 21d1b82b-160d-4a51-bf44-c2ff5d5bafb3 Using shell: /usr/bin/bash INFO snakemake.logging [2025-11-22T07:56:49+0000]: Using shell: /usr/bin/bash Provided remote nodes: 50 INFO snakemake.logging [2025-11-22T07:56:49+0000]: Provided remote nodes: 50 Job stats: job count --------------------------------------------------------------- ------- all 1 all_duckdb_reports 1 all_outputs 1 all_reports 1 anatomy 1 anatomy_compendia 1 anatomy_go_ids 1 anatomy_mesh_ids 1 anatomy_umls_ids 1 cell_line 1 cell_line_compendia 1 check_activity 1 check_anatomical_entity 1 check_anatomy_completeness 1 check_cell 1 check_cell_line 1 check_cell_line_completeness 1 check_cellular_component 1 check_chemical_completeness 1 check_chemical_entity 1 check_chemical_mixture 1 check_compendia_files 1 check_complex_mixture 1 check_conflation_files 1 check_disease 1 check_disease_completeness 1 check_drug 1 check_for_duplicate_clique_leaders 1 check_for_duplicate_curies 1 check_for_identically_labeled_cliques 1 check_gene 1 check_gene_completeness 1 check_genefamily 1 check_genefamily_completeness 1 check_gross_anatomical_structure 1 check_macromolecular_complex 1 check_macromolecular_complex_completeness 1 check_molecular_mixture 1 check_pathway 1 check_phenotypic_feature 1 check_polypeptide 1 check_process 1 check_process_completeness 1 check_protein 1 check_protein_completeness 1 check_publications 1 check_publications_completeness 1 check_small_molecule 1 check_synonyms_gzipped_files 1 check_taxon 1 check_taxon_completeness 1 chembl_labels_and_smiles 1 chemical 1 chemical_chembl_ids 1 chemical_compendia 1 chemical_drugbank_ids 1 chemical_drugcentral_ids 1 chemical_gtopdb_ids 1 chemical_hmdb_ids 1 chemical_kegg_ids 1 chemical_mesh_ids 1 chemical_pubchem_ids 1 chemical_rxnorm_ids 1 chemical_umls_ids 1 chemical_unichem_concordia 1 chemical_unii_ids 1 compress_umls 1 disease 1 disease_compendia 1 disease_doid_ids 1 disease_efo_ids 1 disease_mesh_ids 1 disease_ncit_ids 1 disease_omim_ids 1 disease_orphanet_ids 1 disease_umls_ids 1 download_umls 1 drugchemical 1 drugchemical_conflated_synonyms 1 drugchemical_conflation 1 export_all_compendia_to_duckdb 1 export_all_synonyms_to_duckdb 1 export_all_to_duckdb 1 export_all_to_kgx 1 export_all_to_sapbert_training 1 export_compendia_to_duckdb 24 export_synonyms_to_duckdb 18 extract_taxon_ids_from_uniprotkb 1 filter_unichem 1 gene 1 gene_compendia 1 gene_ensembl_ids 1 gene_hgnc_ids 1 gene_mods_ids 1 gene_ncbi_ids 1 gene_omim_ids 1 gene_umls_ids 1 genefamily 1 genefamily_compendia 1 genefamily_hgncfamily_ids 1 genefamily_pantherfamily_ids 1 geneprotein 1 geneprotein_conflated_synonyms 1 geneprotein_conflation 1 geneprotein_uniprot_relationships 1 generate_content_report_for_compendium_AnatomicalEntity 1 generate_content_report_for_compendium_BiologicalProcess 1 generate_content_report_for_compendium_Cell 1 generate_content_report_for_compendium_CellLine 1 generate_content_report_for_compendium_CellularComponent 1 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_Disease 1 generate_content_report_for_compendium_Drug 1 generate_content_report_for_compendium_Gene 1 generate_content_report_for_compendium_GeneFamily 1 generate_content_report_for_compendium_GrossAnatomicalStructure 1 generate_content_report_for_compendium_MacromolecularComplex 1 generate_content_report_for_compendium_MolecularActivity 1 generate_content_report_for_compendium_MolecularMixture 1 generate_content_report_for_compendium_OrganismTaxon 1 generate_content_report_for_compendium_Pathway 1 generate_content_report_for_compendium_PhenotypicFeature 1 generate_content_report_for_compendium_Polypeptide 1 generate_content_report_for_compendium_Protein 1 generate_content_report_for_compendium_Publication 1 generate_content_report_for_compendium_SmallMolecule 1 generate_content_report_for_compendium_umls 1 generate_kgx 24 generate_prefix_report 1 generate_pubmed_compendia 1 generate_pubmed_concords 1 generate_sapbert_training_data 18 generate_summary_content_report_for_compendia 1 get_CLO_labels 1 get_EC 1 get_EC_labels 1 get_EFO 1 get_EFO_labels 1 get_SMPDB_labels 1 get_anatomy_umls_relationships 1 get_chebi_concord 1 get_chembl 1 get_chemical_drugcentral_relationships 1 get_chemical_mesh_relationships 1 get_chemical_pubchem_cas_concord 1 get_chemical_pubchem_mesh_concord 1 get_chemical_rxnorm_relationships 1 get_chemical_umls_relationships 1 get_chemical_unichem_relationships 1 get_clo_ids 1 get_complexportal_labels_and_synonyms 1 get_disease_doid_relationships 1 get_disease_efo_relationships 1 get_disease_umls_relationships 1 get_doid_labels_and_synonyms 1 get_drugbank_labels_and_synonyms 1 get_ensembl 1 get_gene_medgen_relationships 1 get_gene_ncbigene_ensembl_relationships 1 get_gene_ncbigene_relationships 1 get_gene_umls_relationships 1 get_gtopdb_inchikey_concord 1 get_hgnc 1 get_hgnc_labels_and_synonyms 1 get_hgncfamily_labels 1 get_icrdf 1 get_mesh_labels 1 get_mods_labels 1 get_ncbigene_labels_synonyms_and_taxa 1 get_orphanet_labels_and_synonyms 1 get_panther_pathway_labels 1 get_pantherfamily 1 get_pantherfamily_labels 1 get_process_go_relationships 1 get_process_rhea_relationships 1 get_process_umls_relationships 1 get_protein_ncit_umls_relationships 1 get_protein_ncit_uniprotkb_relationships 1 get_protein_pr_uniprotkb_relationships 1 get_protein_umls_relationships 1 get_protein_uniprotkb_ensembl_relationships 1 get_reactome_labels 1 get_rhea_labels 1 get_taxon_relationships 1 get_taxon_umls_relationships 1 get_umls_labels_and_synonyms 1 get_uniprotkb_labels 1 get_wikidata_cell_relationships 1 gtopdb_labels_and_synonyms 1 hmdb_labels_and_synonyms 1 keggcompound_labels 1 leftover_umls 1 macromolecular_complex 1 macromolecular_complex_compendia 1 macromolecular_complex_ids 1 ncbitaxon_labels_and_synonyms 1 process 1 process_compendia 1 process_ec_ids 1 process_panther_ids 1 process_reactome_ids 1 process_rhea_ids 1 process_smpdb_ids 1 process_umls_ids 1 protein 1 protein_compendia 1 protein_ensembl_ids 1 protein_umls_ids 1 protein_uniprotkb_ids 1 pubchem_labels 1 pubchem_rxnorm_relationships 1 pubchem_synonyms 1 publications 1 rxnorm_relationships 1 taxon 1 taxon_compendia 1 taxon_mesh_ids 1 taxon_ncbi_ids 1 taxon_umls_ids 1 umls_relationships 1 unii_labels_and_synonyms 1 untyped_chemical_compendia 1 verify_pubmed 1 total 305 INFO snakemake.logging [2025-11-22T07:56:49+0000]: Job stats: job count --------------------------------------------------------------- ------- all 1 all_duckdb_reports 1 all_outputs 1 all_reports 1 anatomy 1 anatomy_compendia 1 anatomy_go_ids 1 anatomy_mesh_ids 1 anatomy_umls_ids 1 cell_line 1 cell_line_compendia 1 check_activity 1 check_anatomical_entity 1 check_anatomy_completeness 1 check_cell 1 check_cell_line 1 check_cell_line_completeness 1 check_cellular_component 1 check_chemical_completeness 1 check_chemical_entity 1 check_chemical_mixture 1 check_compendia_files 1 check_complex_mixture 1 check_conflation_files 1 check_disease 1 check_disease_completeness 1 check_drug 1 check_for_duplicate_clique_leaders 1 check_for_duplicate_curies 1 check_for_identically_labeled_cliques 1 check_gene 1 check_gene_completeness 1 check_genefamily 1 check_genefamily_completeness 1 check_gross_anatomical_structure 1 check_macromolecular_complex 1 check_macromolecular_complex_completeness 1 check_molecular_mixture 1 check_pathway 1 check_phenotypic_feature 1 check_polypeptide 1 check_process 1 check_process_completeness 1 check_protein 1 check_protein_completeness 1 check_publications 1 check_publications_completeness 1 check_small_molecule 1 check_synonyms_gzipped_files 1 check_taxon 1 check_taxon_completeness 1 chembl_labels_and_smiles 1 chemical 1 chemical_chembl_ids 1 chemical_compendia 1 chemical_drugbank_ids 1 chemical_drugcentral_ids 1 chemical_gtopdb_ids 1 chemical_hmdb_ids 1 chemical_kegg_ids 1 chemical_mesh_ids 1 chemical_pubchem_ids 1 chemical_rxnorm_ids 1 chemical_umls_ids 1 chemical_unichem_concordia 1 chemical_unii_ids 1 compress_umls 1 disease 1 disease_compendia 1 disease_doid_ids 1 disease_efo_ids 1 disease_mesh_ids 1 disease_ncit_ids 1 disease_omim_ids 1 disease_orphanet_ids 1 disease_umls_ids 1 download_umls 1 drugchemical 1 drugchemical_conflated_synonyms 1 drugchemical_conflation 1 export_all_compendia_to_duckdb 1 export_all_synonyms_to_duckdb 1 export_all_to_duckdb 1 export_all_to_kgx 1 export_all_to_sapbert_training 1 export_compendia_to_duckdb 24 export_synonyms_to_duckdb 18 extract_taxon_ids_from_uniprotkb 1 filter_unichem 1 gene 1 gene_compendia 1 gene_ensembl_ids 1 gene_hgnc_ids 1 gene_mods_ids 1 gene_ncbi_ids 1 gene_omim_ids 1 gene_umls_ids 1 genefamily 1 genefamily_compendia 1 genefamily_hgncfamily_ids 1 genefamily_pantherfamily_ids 1 geneprotein 1 geneprotein_conflated_synonyms 1 geneprotein_conflation 1 geneprotein_uniprot_relationships 1 generate_content_report_for_compendium_AnatomicalEntity 1 generate_content_report_for_compendium_BiologicalProcess 1 generate_content_report_for_compendium_Cell 1 generate_content_report_for_compendium_CellLine 1 generate_content_report_for_compendium_CellularComponent 1 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_Disease 1 generate_content_report_for_compendium_Drug 1 generate_content_report_for_compendium_Gene 1 generate_content_report_for_compendium_GeneFamily 1 generate_content_report_for_compendium_GrossAnatomicalStructure 1 generate_content_report_for_compendium_MacromolecularComplex 1 generate_content_report_for_compendium_MolecularActivity 1 generate_content_report_for_compendium_MolecularMixture 1 generate_content_report_for_compendium_OrganismTaxon 1 generate_content_report_for_compendium_Pathway 1 generate_content_report_for_compendium_PhenotypicFeature 1 generate_content_report_for_compendium_Polypeptide 1 generate_content_report_for_compendium_Protein 1 generate_content_report_for_compendium_Publication 1 generate_content_report_for_compendium_SmallMolecule 1 generate_content_report_for_compendium_umls 1 generate_kgx 24 generate_prefix_report 1 generate_pubmed_compendia 1 generate_pubmed_concords 1 generate_sapbert_training_data 18 generate_summary_content_report_for_compendia 1 get_CLO_labels 1 get_EC 1 get_EC_labels 1 get_EFO 1 get_EFO_labels 1 get_SMPDB_labels 1 get_anatomy_umls_relationships 1 get_chebi_concord 1 get_chembl 1 get_chemical_drugcentral_relationships 1 get_chemical_mesh_relationships 1 get_chemical_pubchem_cas_concord 1 get_chemical_pubchem_mesh_concord 1 get_chemical_rxnorm_relationships 1 get_chemical_umls_relationships 1 get_chemical_unichem_relationships 1 get_clo_ids 1 get_complexportal_labels_and_synonyms 1 get_disease_doid_relationships 1 get_disease_efo_relationships 1 get_disease_umls_relationships 1 get_doid_labels_and_synonyms 1 get_drugbank_labels_and_synonyms 1 get_ensembl 1 get_gene_medgen_relationships 1 get_gene_ncbigene_ensembl_relationships 1 get_gene_ncbigene_relationships 1 get_gene_umls_relationships 1 get_gtopdb_inchikey_concord 1 get_hgnc 1 get_hgnc_labels_and_synonyms 1 get_hgncfamily_labels 1 get_icrdf 1 get_mesh_labels 1 get_mods_labels 1 get_ncbigene_labels_synonyms_and_taxa 1 get_orphanet_labels_and_synonyms 1 get_panther_pathway_labels 1 get_pantherfamily 1 get_pantherfamily_labels 1 get_process_go_relationships 1 get_process_rhea_relationships 1 get_process_umls_relationships 1 get_protein_ncit_umls_relationships 1 get_protein_ncit_uniprotkb_relationships 1 get_protein_pr_uniprotkb_relationships 1 get_protein_umls_relationships 1 get_protein_uniprotkb_ensembl_relationships 1 get_reactome_labels 1 get_rhea_labels 1 get_taxon_relationships 1 get_taxon_umls_relationships 1 get_umls_labels_and_synonyms 1 get_uniprotkb_labels 1 get_wikidata_cell_relationships 1 gtopdb_labels_and_synonyms 1 hmdb_labels_and_synonyms 1 keggcompound_labels 1 leftover_umls 1 macromolecular_complex 1 macromolecular_complex_compendia 1 macromolecular_complex_ids 1 ncbitaxon_labels_and_synonyms 1 process 1 process_compendia 1 process_ec_ids 1 process_panther_ids 1 process_reactome_ids 1 process_rhea_ids 1 process_smpdb_ids 1 process_umls_ids 1 protein 1 protein_compendia 1 protein_ensembl_ids 1 protein_umls_ids 1 protein_uniprotkb_ids 1 pubchem_labels 1 pubchem_rxnorm_relationships 1 pubchem_synonyms 1 publications 1 rxnorm_relationships 1 taxon 1 taxon_compendia 1 taxon_mesh_ids 1 taxon_ncbi_ids 1 taxon_umls_ids 1 umls_relationships 1 unii_labels_and_synonyms 1 untyped_chemical_compendia 1 verify_pubmed 1 total 305 Select jobs to execute... INFO snakemake.logging [2025-11-22T07:56:49+0000]: Select jobs to execute... Execute 50 jobs... INFO snakemake.logging [2025-11-22T07:56:49+0000]: Execute 50 jobs... [Sat Nov 22 02:56:49 2025] rule keggcompound_labels: output: babel_downloads/KEGG.COMPOUND/labels jobid: 32 reason: Missing output files: babel_downloads/KEGG.COMPOUND/labels resources: mem_mb=64000, mem_mib=954, disk_mb=50000, disk_mib=47684, tmpdir=, mem=64G, runtime=120, cpus_per_task=4 INFO snakemake.logging [2025-11-22T07:56:49+0000]: Rule: keggcompound_labels, Jobid: 32 INFO snakemake.logging [2025-11-22T07:56:49+0000]: Shell command: None No SLURM account given, trying to guess. WARNING snakemake.logging [2025-11-22T07:56:49+0000]: No SLURM account given, trying to guess. Unable to guess SLURM account. Trying to proceed without. WARNING snakemake.logging [2025-11-22T07:56:49+0000]: Unable to guess SLURM account. Trying to proceed without. Job 32 has been submitted with SLURM jobid 45395 (log: babel_outputs/logs/rule_keggcompound_labels/45395.log). INFO snakemake.logging [2025-11-22T07:56:49+0000]: Job 32 has been submitted with SLURM jobid 45395 (log: babel_outputs/logs/rule_keggcompound_labels/45395.log). [Sat Nov 22 02:56:49 2025] rule get_protein_ncit_uniprotkb_relationships: input: babel_downloads/NCIT/NCIt-SwissProt_Mapping.txt output: babel_outputs/intermediate/protein/concords/NCIT_UniProtKB, babel_outputs/intermediate/protein/concords/metadata-NCIT_UniProtKB.yaml jobid: 147 reason: Missing output files: babel_outputs/intermediate/protein/concords/NCIT_UniProtKB, babel_outputs/intermediate/protein/concords/metadata-NCIT_UniProtKB.yaml resources: mem_mb=64000, mem_mib=954, disk_mb=1000, disk_mib=954, tmpdir=, mem=64G, runtime=120, cpus_per_task=4 INFO snakemake.logging [2025-11-22T07:56:49+0000]: Rule: get_protein_ncit_uniprotkb_relationships, Jobid: 147 INFO snakemake.logging [2025-11-22T07:56:50+0000]: Shell command: None Job 147 has been submitted with SLURM jobid 45396 (log: babel_outputs/logs/rule_get_protein_ncit_uniprotkb_relationships/45396.log). INFO snakemake.logging [2025-11-22T07:56:50+0000]: Job 147 has been submitted with SLURM jobid 45396 (log: babel_outputs/logs/rule_get_protein_ncit_uniprotkb_relationships/45396.log). [Sat Nov 22 02:56:50 2025] rule disease_ncit_ids: output: babel_outputs/intermediate/disease/ids/NCIT jobid: 94 reason: Missing output files: babel_outputs/intermediate/disease/ids/NCIT resources: mem_mb=64000, mem_mib=954, disk_mb=50000, disk_mib=47684, tmpdir=, mem=64G, runtime=120, cpus_per_task=4 INFO snakemake.logging [2025-11-22T07:56:50+0000]: Rule: disease_ncit_ids, Jobid: 94 INFO snakemake.logging [2025-11-22T07:56:50+0000]: Shell command: None Job 94 has been submitted with SLURM jobid 45397 (log: babel_outputs/logs/rule_disease_ncit_ids/45397.log). INFO snakemake.logging [2025-11-22T07:56:50+0000]: Job 94 has been submitted with SLURM jobid 45397 (log: babel_outputs/logs/rule_disease_ncit_ids/45397.log). [Sat Nov 22 02:56:50 2025] rule get_reactome_labels: input: babel_downloads/REACT/Events.json output: babel_downloads/REACT/labels jobid: 164 reason: Missing output files: babel_downloads/REACT/labels resources: mem_mb=64000, mem_mib=954, disk_mb=1000, disk_mib=954, tmpdir=, mem=64G, runtime=120, cpus_per_task=4 INFO snakemake.logging [2025-11-22T07:56:50+0000]: Rule: get_reactome_labels, Jobid: 164 INFO snakemake.logging [2025-11-22T07:56:50+0000]: Shell command: None Job 164 has been submitted with SLURM jobid 45398 (log: babel_outputs/logs/rule_get_reactome_labels/45398.log). INFO snakemake.logging [2025-11-22T07:56:50+0000]: Job 164 has been submitted with SLURM jobid 45398 (log: babel_outputs/logs/rule_get_reactome_labels/45398.log). [Sat Nov 22 02:56:50 2025] rule chemical_drugcentral_ids: input: babel_downloads/DrugCentral/structures output: babel_outputs/intermediate/chemicals/ids/DrugCentral jobid: 70 reason: Missing output files: babel_outputs/intermediate/chemicals/ids/DrugCentral resources: mem_mb=64000, mem_mib=954, disk_mb=1000, disk_mib=954, tmpdir=, mem=64G, runtime=120, cpus_per_task=4 INFO snakemake.logging [2025-11-22T07:56:50+0000]: Rule: chemical_drugcentral_ids, Jobid: 70 INFO snakemake.logging [2025-11-22T07:56:50+0000]: Shell command: None Job 70 has been submitted with SLURM jobid 45399 (log: babel_outputs/logs/rule_chemical_drugcentral_ids/45399.log). INFO snakemake.logging [2025-11-22T07:56:50+0000]: Job 70 has been submitted with SLURM jobid 45399 (log: babel_outputs/logs/rule_chemical_drugcentral_ids/45399.log). [Sat Nov 22 02:56:50 2025] rule unii_labels_and_synonyms: input: babel_downloads/UNII/Latest_UNII_Names.txt output: babel_downloads/UNII/labels, babel_downloads/UNII/synonyms jobid: 33 reason: Missing output files: babel_downloads/UNII/synonyms, babel_downloads/UNII/labels resources: mem_mb=64000, mem_mib=954, disk_mb=1000, disk_mib=954, tmpdir=, mem=64G, runtime=120, cpus_per_task=4 INFO snakemake.logging [2025-11-22T07:56:50+0000]: Rule: unii_labels_and_synonyms, Jobid: 33 INFO snakemake.logging [2025-11-22T07:56:50+0000]: Shell command: None Job 33 has been submitted with SLURM jobid 45400 (log: babel_outputs/logs/rule_unii_labels_and_synonyms/45400.log). INFO snakemake.logging [2025-11-22T07:56:50+0000]: Job 33 has been submitted with SLURM jobid 45400 (log: babel_outputs/logs/rule_unii_labels_and_synonyms/45400.log). [Sat Nov 22 02:56:50 2025] rule rxnorm_relationships: input: babel_downloads/RxNorm/RXNCONSO.RRF, babel_downloads/RxNorm/RXNREL.RRF output: babel_outputs/intermediate/drugchemical/concords/RXNORM, babel_outputs/intermediate/drugchemical/concords/metadata-RXNORM.yaml jobid: 220 reason: Missing output files: babel_outputs/intermediate/drugchemical/concords/metadata-RXNORM.yaml, babel_outputs/intermediate/drugchemical/concords/RXNORM resources: mem_mb=64000, mem_mib=1176, disk_mb=1233, disk_mib=1176, tmpdir=, mem=64G, runtime=120, cpus_per_task=4 INFO snakemake.logging [2025-11-22T07:56:50+0000]: Rule: rxnorm_relationships, Jobid: 220 INFO snakemake.logging [2025-11-22T07:56:50+0000]: Shell command: None Job 220 has been submitted with SLURM jobid 45401 (log: babel_outputs/logs/rule_rxnorm_relationships/45401.log). INFO snakemake.logging [2025-11-22T07:56:50+0000]: Job 220 has been submitted with SLURM jobid 45401 (log: babel_outputs/logs/rule_rxnorm_relationships/45401.log). [Sat Nov 22 02:56:50 2025] rule anatomy_go_ids: output: babel_outputs/intermediate/anatomy/ids/GO jobid: 13 reason: Missing output files: babel_outputs/intermediate/anatomy/ids/GO resources: mem_mb=64000, mem_mib=954, disk_mb=50000, disk_mib=47684, tmpdir=, mem=64G, runtime=120, cpus_per_task=4 INFO snakemake.logging [2025-11-22T07:56:50+0000]: Rule: anatomy_go_ids, Jobid: 13 INFO snakemake.logging [2025-11-22T07:56:50+0000]: Shell command: None Job 13 has been submitted with SLURM jobid 45402 (log: babel_outputs/logs/rule_anatomy_go_ids/45402.log). INFO snakemake.logging [2025-11-22T07:56:50+0000]: Job 13 has been submitted with SLURM jobid 45402 (log: babel_outputs/logs/rule_anatomy_go_ids/45402.log). [Sat Nov 22 02:56:50 2025] rule get_gene_medgen_relationships: input: babel_downloads/NCBIGene/mim2gene_medgen output: babel_outputs/intermediate/gene/concords/medgen, babel_outputs/intermediate/gene/concords/metadata-medgen.yaml jobid: 116 reason: Missing output files: babel_outputs/intermediate/gene/concords/metadata-medgen.yaml, babel_outputs/intermediate/gene/concords/medgen resources: mem_mb=64000, mem_mib=954, disk_mb=1000, disk_mib=954, tmpdir=, mem=64G, runtime=120, cpus_per_task=4 INFO snakemake.logging [2025-11-22T07:56:50+0000]: Rule: get_gene_medgen_relationships, Jobid: 116 INFO snakemake.logging [2025-11-22T07:56:50+0000]: Shell command: None Job 116 has been submitted with SLURM jobid 45403 (log: babel_outputs/logs/rule_get_gene_medgen_relationships/45403.log). INFO snakemake.logging [2025-11-22T07:56:50+0000]: Job 116 has been submitted with SLURM jobid 45403 (log: babel_outputs/logs/rule_get_gene_medgen_relationships/45403.log). [Sat Nov 22 02:56:50 2025] rule get_rhea_labels: input: babel_downloads/RHEA/rhea.rdf output: babel_downloads/RHEA/labels jobid: 166 reason: Missing output files: babel_downloads/RHEA/labels resources: mem_mb=64000, mem_mib=954, disk_mb=1000, disk_mib=954, tmpdir=, mem=64G, runtime=120, cpus_per_task=4 INFO snakemake.logging [2025-11-22T07:56:50+0000]: Rule: get_rhea_labels, Jobid: 166 INFO snakemake.logging [2025-11-22T07:56:50+0000]: Shell command: None Job 166 has been submitted with SLURM jobid 45404 (log: babel_outputs/logs/rule_get_rhea_labels/45404.log). INFO snakemake.logging [2025-11-22T07:56:50+0000]: Job 166 has been submitted with SLURM jobid 45404 (log: babel_outputs/logs/rule_get_rhea_labels/45404.log). [Sat Nov 22 02:56:50 2025] rule verify_pubmed: input: babel_downloads/PubMed/downloaded output: babel_downloads/PubMed/verified jobid: 213 reason: Missing output files: babel_downloads/PubMed/verified resources: mem_mb=64000, mem_mib=954, disk_mb=1000, disk_mib=954, tmpdir=, mem=64G, runtime=120, cpus_per_task=4 INFO snakemake.logging [2025-11-22T07:56:50+0000]: Rule: verify_pubmed, Jobid: 213 INFO snakemake.logging [2025-11-22T07:56:50+0000]: Shell command: None Job 213 has been submitted with SLURM jobid 45405 (log: babel_outputs/logs/rule_verify_pubmed/45405.log). INFO snakemake.logging [2025-11-22T07:56:50+0000]: Job 213 has been submitted with SLURM jobid 45405 (log: babel_outputs/logs/rule_verify_pubmed/45405.log). [Sat Nov 22 02:56:50 2025] rule hmdb_labels_and_synonyms: input: babel_downloads/HMDB/hmdb_metabolites.xml output: babel_downloads/HMDB/labels, babel_downloads/HMDB/synonyms, babel_downloads/HMDB/smiles jobid: 35 reason: Missing output files: babel_downloads/HMDB/synonyms, babel_downloads/HMDB/smiles, babel_downloads/HMDB/labels resources: mem_mb=64000, mem_mib=7630, disk_mb=12373, disk_mib=11800, tmpdir=, mem=64G, runtime=120, cpus_per_task=4 INFO snakemake.logging [2025-11-22T07:56:50+0000]: Rule: hmdb_labels_and_synonyms, Jobid: 35 INFO snakemake.logging [2025-11-22T07:56:50+0000]: Shell command: None Job 35 has been submitted with SLURM jobid 45406 (log: babel_outputs/logs/rule_hmdb_labels_and_synonyms/45406.log). INFO snakemake.logging [2025-11-22T07:56:50+0000]: Job 35 has been submitted with SLURM jobid 45406 (log: babel_outputs/logs/rule_hmdb_labels_and_synonyms/45406.log). [Sat Nov 22 02:56:50 2025] rule get_doid_labels_and_synonyms: input: babel_downloads/DOID/doid.json output: babel_downloads/DOID/labels, babel_downloads/DOID/synonyms jobid: 83 reason: Missing output files: babel_downloads/DOID/synonyms, babel_downloads/DOID/labels resources: mem_mb=64000, mem_mib=954, disk_mb=1000, disk_mib=954, tmpdir=, mem=64G, runtime=120, cpus_per_task=4 INFO snakemake.logging [2025-11-22T07:56:50+0000]: Rule: get_doid_labels_and_synonyms, Jobid: 83 INFO snakemake.logging [2025-11-22T07:56:50+0000]: Shell command: None Job 83 has been submitted with SLURM jobid 45407 (log: babel_outputs/logs/rule_get_doid_labels_and_synonyms/45407.log). INFO snakemake.logging [2025-11-22T07:56:50+0000]: Job 83 has been submitted with SLURM jobid 45407 (log: babel_outputs/logs/rule_get_doid_labels_and_synonyms/45407.log). [Sat Nov 22 02:56:50 2025] rule disease_omim_ids: input: babel_downloads/OMIM/mim2gene.txt output: babel_outputs/intermediate/disease/ids/OMIM jobid: 92 reason: Missing output files: babel_outputs/intermediate/disease/ids/OMIM resources: mem_mb=64000, mem_mib=954, disk_mb=1000, disk_mib=954, tmpdir=, mem=64G, runtime=120, cpus_per_task=4 INFO snakemake.logging [2025-11-22T07:56:50+0000]: Rule: disease_omim_ids, Jobid: 92 INFO snakemake.logging [2025-11-22T07:56:50+0000]: Shell command: None Job 92 has been submitted with SLURM jobid 45408 (log: babel_outputs/logs/rule_disease_omim_ids/45408.log). INFO snakemake.logging [2025-11-22T07:56:50+0000]: Job 92 has been submitted with SLURM jobid 45408 (log: babel_outputs/logs/rule_disease_omim_ids/45408.log). [Sat Nov 22 02:56:50 2025] rule gene_omim_ids: input: babel_downloads/OMIM/mim2gene.txt output: babel_outputs/intermediate/gene/ids/OMIM jobid: 123 reason: Missing output files: babel_outputs/intermediate/gene/ids/OMIM resources: mem_mb=64000, mem_mib=954, disk_mb=1000, disk_mib=954, tmpdir=, mem=64G, runtime=120, cpus_per_task=4 INFO snakemake.logging [2025-11-22T07:56:50+0000]: Rule: gene_omim_ids, Jobid: 123 INFO snakemake.logging [2025-11-22T07:56:50+0000]: Shell command: None Job 123 has been submitted with SLURM jobid 45409 (log: babel_outputs/logs/rule_gene_omim_ids/45409.log). INFO snakemake.logging [2025-11-22T07:56:50+0000]: Job 123 has been submitted with SLURM jobid 45409 (log: babel_outputs/logs/rule_gene_omim_ids/45409.log). [Sat Nov 22 02:56:50 2025] rule process_reactome_ids: input: babel_downloads/REACT/Events.json output: babel_outputs/intermediate/process/ids/REACT jobid: 179 reason: Missing output files: babel_outputs/intermediate/process/ids/REACT resources: mem_mb=64000, mem_mib=954, disk_mb=1000, disk_mib=954, tmpdir=, mem=64G, runtime=120, cpus_per_task=4 INFO snakemake.logging [2025-11-22T07:56:50+0000]: Rule: process_reactome_ids, Jobid: 179 INFO snakemake.logging [2025-11-22T07:56:50+0000]: Shell command: None Job 179 has been submitted with SLURM jobid 45410 (log: babel_outputs/logs/rule_process_reactome_ids/45410.log). INFO snakemake.logging [2025-11-22T07:56:50+0000]: Job 179 has been submitted with SLURM jobid 45410 (log: babel_outputs/logs/rule_process_reactome_ids/45410.log). [Sat Nov 22 02:56:50 2025] rule ncbitaxon_labels_and_synonyms: input: babel_downloads/NCBITaxon/taxdump.tar output: babel_downloads/NCBITaxon/labels, babel_downloads/NCBITaxon/synonyms, babel_downloads/NCBITaxon/properties.tsv.gz jobid: 190 reason: Missing output files: babel_downloads/NCBITaxon/synonyms, babel_downloads/NCBITaxon/labels resources: mem_mb=64000, mem_mib=954, disk_mb=1000, disk_mib=954, tmpdir=, mem=64G, runtime=120, cpus_per_task=4 INFO snakemake.logging [2025-11-22T07:56:50+0000]: Rule: ncbitaxon_labels_and_synonyms, Jobid: 190 INFO snakemake.logging [2025-11-22T07:56:50+0000]: Shell command: None Job 190 has been submitted with SLURM jobid 45411 (log: babel_outputs/logs/rule_ncbitaxon_labels_and_synonyms/45411.log). INFO snakemake.logging [2025-11-22T07:56:50+0000]: Job 190 has been submitted with SLURM jobid 45411 (log: babel_outputs/logs/rule_ncbitaxon_labels_and_synonyms/45411.log). [Sat Nov 22 02:56:50 2025] rule get_ensembl: output: babel_downloads/ENSEMBL, babel_downloads/ENSEMBL/BioMartDownloadComplete jobid: 121 reason: Forced execution resources: mem_mb=64000, mem_mib=954, disk_mb=50000, disk_mib=47684, tmpdir=, mem=64G, runtime=120, cpus_per_task=4 INFO snakemake.logging [2025-11-22T07:56:50+0000]: Rule: get_ensembl, Jobid: 121 INFO snakemake.logging [2025-11-22T07:56:50+0000]: Shell command: None Job 121 has been submitted with SLURM jobid 45412 (log: babel_outputs/logs/rule_get_ensembl/45412.log). INFO snakemake.logging [2025-11-22T07:56:50+0000]: Job 121 has been submitted with SLURM jobid 45412 (log: babel_outputs/logs/rule_get_ensembl/45412.log). [Sat Nov 22 02:56:50 2025] rule chemical_mesh_ids: input: babel_downloads/MESH/mesh.nt output: babel_outputs/intermediate/chemicals/ids/MESH jobid: 51 reason: Missing output files: babel_outputs/intermediate/chemicals/ids/MESH resources: mem_mb=64000, mem_mib=4171, disk_mb=4373, disk_mib=4171, tmpdir=, mem=64G, runtime=120, cpus_per_task=4 INFO snakemake.logging [2025-11-22T07:56:50+0000]: Rule: chemical_mesh_ids, Jobid: 51 INFO snakemake.logging [2025-11-22T07:56:50+0000]: Shell command: None Job 51 has been submitted with SLURM jobid 45413 (log: babel_outputs/logs/rule_chemical_mesh_ids/45413.log). INFO snakemake.logging [2025-11-22T07:56:50+0000]: Job 51 has been submitted with SLURM jobid 45413 (log: babel_outputs/logs/rule_chemical_mesh_ids/45413.log). [Sat Nov 22 02:56:50 2025] rule get_EC: output: babel_downloads/EC/enzyme.rdf jobid: 169 reason: Missing output files: babel_downloads/EC/enzyme.rdf resources: mem_mb=64000, mem_mib=954, disk_mb=50000, disk_mib=47684, tmpdir=, mem=64G, runtime=120, cpus_per_task=4 INFO snakemake.logging [2025-11-22T07:56:50+0000]: Rule: get_EC, Jobid: 169 INFO snakemake.logging [2025-11-22T07:56:50+0000]: Shell command: None Job 169 has been submitted with SLURM jobid 45414 (log: babel_outputs/logs/rule_get_EC/45414.log). INFO snakemake.logging [2025-11-22T07:56:50+0000]: Job 169 has been submitted with SLURM jobid 45414 (log: babel_outputs/logs/rule_get_EC/45414.log). [Sat Nov 22 02:56:50 2025] rule pubchem_labels: input: babel_downloads/PUBCHEM.COMPOUND/CID-Title.gz output: babel_downloads/PUBCHEM.COMPOUND/labels jobid: 37 reason: Missing output files: babel_downloads/PUBCHEM.COMPOUND/labels resources: mem_mb=64000, mem_mib=3359, disk_mb=3522, disk_mib=3359, tmpdir=, mem=64G, runtime=120, cpus_per_task=4 INFO snakemake.logging [2025-11-22T07:56:50+0000]: Rule: pubchem_labels, Jobid: 37 INFO snakemake.logging [2025-11-22T07:56:50+0000]: Shell command: None Job 37 has been submitted with SLURM jobid 45415 (log: babel_outputs/logs/rule_pubchem_labels/45415.log). INFO snakemake.logging [2025-11-22T07:56:50+0000]: Job 37 has been submitted with SLURM jobid 45415 (log: babel_outputs/logs/rule_pubchem_labels/45415.log). [Sat Nov 22 02:56:50 2025] rule chemical_gtopdb_ids: input: babel_downloads/GTOPDB/ligands.tsv output: babel_outputs/intermediate/chemicals/ids/GTOPDB jobid: 63 reason: Missing output files: babel_outputs/intermediate/chemicals/ids/GTOPDB resources: mem_mb=64000, mem_mib=954, disk_mb=1000, disk_mib=954, tmpdir=, mem=64G, runtime=120, cpus_per_task=4 INFO snakemake.logging [2025-11-22T07:56:50+0000]: Rule: chemical_gtopdb_ids, Jobid: 63 INFO snakemake.logging [2025-11-22T07:56:50+0000]: Shell command: None Job 63 has been submitted with SLURM jobid 45416 (log: babel_outputs/logs/rule_chemical_gtopdb_ids/45416.log). INFO snakemake.logging [2025-11-22T07:56:50+0000]: Job 63 has been submitted with SLURM jobid 45416 (log: babel_outputs/logs/rule_chemical_gtopdb_ids/45416.log). [Sat Nov 22 02:56:50 2025] rule get_orphanet_labels_and_synonyms: input: babel_downloads/Orphanet/Orphanet_Nomenclature_Pack_EN.zip output: babel_downloads/Orphanet/labels, babel_downloads/Orphanet/synonyms jobid: 85 reason: Missing output files: babel_downloads/Orphanet/labels, babel_downloads/Orphanet/synonyms resources: mem_mb=64000, mem_mib=954, disk_mb=1000, disk_mib=954, tmpdir=, mem=64G, runtime=120, cpus_per_task=4 INFO snakemake.logging [2025-11-22T07:56:50+0000]: Rule: get_orphanet_labels_and_synonyms, Jobid: 85 INFO snakemake.logging [2025-11-22T07:56:50+0000]: Shell command: None Job 85 has been submitted with SLURM jobid 45417 (log: babel_outputs/logs/rule_get_orphanet_labels_and_synonyms/45417.log). INFO snakemake.logging [2025-11-22T07:56:50+0000]: Job 85 has been submitted with SLURM jobid 45417 (log: babel_outputs/logs/rule_get_orphanet_labels_and_synonyms/45417.log). [Sat Nov 22 02:56:50 2025] rule disease_efo_ids: output: babel_outputs/intermediate/disease/ids/EFO jobid: 97 reason: Missing output files: babel_outputs/intermediate/disease/ids/EFO resources: mem_mb=64000, mem_mib=954, disk_mb=50000, disk_mib=47684, tmpdir=, mem=64G, runtime=120, cpus_per_task=4 INFO snakemake.logging [2025-11-22T07:56:50+0000]: Rule: disease_efo_ids, Jobid: 97 INFO snakemake.logging [2025-11-22T07:56:50+0000]: Shell command: None Job 97 has been submitted with SLURM jobid 45418 (log: babel_outputs/logs/rule_disease_efo_ids/45418.log). INFO snakemake.logging [2025-11-22T07:56:50+0000]: Job 97 has been submitted with SLURM jobid 45418 (log: babel_outputs/logs/rule_disease_efo_ids/45418.log). [Sat Nov 22 02:56:50 2025] rule get_hgncfamily_labels: input: babel_downloads/HGNC.FAMILY/family.csv output: babel_downloads/HGNC.FAMILY/labels, babel_downloads/HGNC.FAMILY/descriptions, babel_downloads/HGNC.FAMILY/metadata.yaml jobid: 133 reason: Missing output files: babel_downloads/HGNC.FAMILY/metadata.yaml, babel_downloads/HGNC.FAMILY/labels resources: mem_mb=64000, mem_mib=954, disk_mb=1000, disk_mib=954, tmpdir=, mem=64G, runtime=120, cpus_per_task=4 INFO snakemake.logging [2025-11-22T07:56:50+0000]: Rule: get_hgncfamily_labels, Jobid: 133 INFO snakemake.logging [2025-11-22T07:56:50+0000]: Shell command: None Job 133 has been submitted with SLURM jobid 45419 (log: babel_outputs/logs/rule_get_hgncfamily_labels/45419.log). INFO snakemake.logging [2025-11-22T07:56:50+0000]: Job 133 has been submitted with SLURM jobid 45419 (log: babel_outputs/logs/rule_get_hgncfamily_labels/45419.log). [Sat Nov 22 02:56:50 2025] rule chemical_rxnorm_ids: input: babel_downloads/RxNorm/RXNCONSO.RRF output: babel_outputs/intermediate/chemicals/ids/RXNORM jobid: 60 reason: Missing output files: babel_outputs/intermediate/chemicals/ids/RXNORM resources: mem_mb=64000, mem_mib=954, disk_mb=1000, disk_mib=954, tmpdir=, mem=64G, runtime=120, cpus_per_task=4 INFO snakemake.logging [2025-11-22T07:56:50+0000]: Rule: chemical_rxnorm_ids, Jobid: 60 INFO snakemake.logging [2025-11-22T07:56:50+0000]: Shell command: None Job 60 has been submitted with SLURM jobid 45420 (log: babel_outputs/logs/rule_chemical_rxnorm_ids/45420.log). INFO snakemake.logging [2025-11-22T07:56:50+0000]: Job 60 has been submitted with SLURM jobid 45420 (log: babel_outputs/logs/rule_chemical_rxnorm_ids/45420.log). [Sat Nov 22 02:56:50 2025] rule get_complexportal_labels_and_synonyms: input: babel_downloads/ComplexPortal/559292.tsv output: babel_downloads/ComplexPortal/559292_labels.tsv, babel_downloads/ComplexPortal/559292_synonyms.tsv, babel_downloads/ComplexPortal/metadata.yaml jobid: 208 reason: Missing output files: babel_downloads/ComplexPortal/metadata.yaml, babel_downloads/ComplexPortal/559292_labels.tsv, babel_downloads/ComplexPortal/559292_synonyms.tsv resources: mem_mb=64000, mem_mib=954, disk_mb=1000, disk_mib=954, tmpdir=, mem=64G, runtime=120, cpus_per_task=4 INFO snakemake.logging [2025-11-22T07:56:50+0000]: Rule: get_complexportal_labels_and_synonyms, Jobid: 208 INFO snakemake.logging [2025-11-22T07:56:50+0000]: Shell command: None Job 208 has been submitted with SLURM jobid 45421 (log: babel_outputs/logs/rule_get_complexportal_labels_and_synonyms/45421.log). INFO snakemake.logging [2025-11-22T07:56:50+0000]: Job 208 has been submitted with SLURM jobid 45421 (log: babel_outputs/logs/rule_get_complexportal_labels_and_synonyms/45421.log). [Sat Nov 22 02:56:50 2025] rule filter_unichem: input: babel_downloads/UNICHEM/reference.tsv.gz output: babel_downloads/UNICHEM/reference.filtered.tsv jobid: 46 reason: Missing output files: babel_downloads/UNICHEM/reference.filtered.tsv resources: mem_mb=64000, mem_mib=3699, disk_mb=3878, disk_mib=3699, tmpdir=, mem=64G, runtime=120, cpus_per_task=4 INFO snakemake.logging [2025-11-22T07:56:50+0000]: Rule: filter_unichem, Jobid: 46 INFO snakemake.logging [2025-11-22T07:56:50+0000]: Shell command: None Job 46 has been submitted with SLURM jobid 45422 (log: babel_outputs/logs/rule_filter_unichem/45422.log). INFO snakemake.logging [2025-11-22T07:56:50+0000]: Job 46 has been submitted with SLURM jobid 45422 (log: babel_outputs/logs/rule_filter_unichem/45422.log). [Sat Nov 22 02:56:50 2025] rule chemical_unii_ids: input: babel_downloads/UNII/Latest_UNII_Records.txt output: babel_outputs/intermediate/chemicals/ids/UNII jobid: 66 reason: Missing output files: babel_outputs/intermediate/chemicals/ids/UNII resources: mem_mb=64000, mem_mib=954, disk_mb=1000, disk_mib=954, tmpdir=, mem=64G, runtime=120, cpus_per_task=4 INFO snakemake.logging [2025-11-22T07:56:50+0000]: Rule: chemical_unii_ids, Jobid: 66 INFO snakemake.logging [2025-11-22T07:56:50+0000]: Shell command: None Job 66 has been submitted with SLURM jobid 45423 (log: babel_outputs/logs/rule_chemical_unii_ids/45423.log). INFO snakemake.logging [2025-11-22T07:56:50+0000]: Job 66 has been submitted with SLURM jobid 45423 (log: babel_outputs/logs/rule_chemical_unii_ids/45423.log). [Sat Nov 22 02:56:50 2025] rule get_ncbigene_labels_synonyms_and_taxa: input: babel_downloads/NCBIGene/gene_info.gz output: babel_downloads/NCBIGene/labels, babel_downloads/NCBIGene/synonyms, babel_downloads/NCBIGene/taxa, babel_downloads/NCBIGene/descriptions jobid: 111 reason: Missing output files: babel_downloads/NCBIGene/labels, babel_downloads/NCBIGene/synonyms resources: mem_mb=64000, mem_mib=2523, disk_mb=2645, disk_mib=2523, tmpdir=, mem=64G, runtime=120, cpus_per_task=4 INFO snakemake.logging [2025-11-22T07:56:50+0000]: Rule: get_ncbigene_labels_synonyms_and_taxa, Jobid: 111 INFO snakemake.logging [2025-11-22T07:56:50+0000]: Shell command: None Job 111 has been submitted with SLURM jobid 45424 (log: babel_outputs/logs/rule_get_ncbigene_labels_synonyms_and_taxa/45424.log). INFO snakemake.logging [2025-11-22T07:56:50+0000]: Job 111 has been submitted with SLURM jobid 45424 (log: babel_outputs/logs/rule_get_ncbigene_labels_synonyms_and_taxa/45424.log). [Sat Nov 22 02:56:50 2025] rule get_gtopdb_inchikey_concord: input: babel_downloads/GTOPDB/ligands.tsv output: babel_outputs/intermediate/chemicals/concords/GTOPDB, babel_outputs/intermediate/chemicals/concords/metadata-GTOPDB.yaml jobid: 53 reason: Missing output files: babel_outputs/intermediate/chemicals/concords/metadata-GTOPDB.yaml, babel_outputs/intermediate/chemicals/concords/GTOPDB resources: mem_mb=64000, mem_mib=954, disk_mb=1000, disk_mib=954, tmpdir=, mem=64G, runtime=120, cpus_per_task=4 INFO snakemake.logging [2025-11-22T07:56:50+0000]: Rule: get_gtopdb_inchikey_concord, Jobid: 53 INFO snakemake.logging [2025-11-22T07:56:50+0000]: Shell command: None Job 53 has been submitted with SLURM jobid 45425 (log: babel_outputs/logs/rule_get_gtopdb_inchikey_concord/45425.log). INFO snakemake.logging [2025-11-22T07:56:50+0000]: Job 53 has been submitted with SLURM jobid 45425 (log: babel_outputs/logs/rule_get_gtopdb_inchikey_concord/45425.log). [Sat Nov 22 02:56:50 2025] rule get_protein_uniprotkb_ensembl_relationships: input: babel_downloads/UniProtKB/idmapping.dat output: babel_outputs/intermediate/protein/concords/UniProtKB, babel_outputs/intermediate/protein/concords/metadata-UniProtKB.yaml jobid: 144 reason: Missing output files: babel_outputs/intermediate/protein/concords/metadata-UniProtKB.yaml, babel_outputs/intermediate/protein/concords/UniProtKB resources: mem_mb=64000, mem_mib=7630, disk_mb=165563, disk_mib=157894, tmpdir=, mem=64G, runtime=120, cpus_per_task=4 INFO snakemake.logging [2025-11-22T07:56:50+0000]: Rule: get_protein_uniprotkb_ensembl_relationships, Jobid: 144 INFO snakemake.logging [2025-11-22T07:56:50+0000]: Shell command: None Job 144 has been submitted with SLURM jobid 45426 (log: babel_outputs/logs/rule_get_protein_uniprotkb_ensembl_relationships/45426.log). INFO snakemake.logging [2025-11-22T07:56:50+0000]: Job 144 has been submitted with SLURM jobid 45426 (log: babel_outputs/logs/rule_get_protein_uniprotkb_ensembl_relationships/45426.log). [Sat Nov 22 02:56:50 2025] rule get_chembl: output: babel_downloads/CHEMBL.COMPOUND/chembl_latest_molecule.ttl, babel_downloads/CHEMBL.COMPOUND/cco.ttl jobid: 29 reason: Missing output files: babel_downloads/CHEMBL.COMPOUND/chembl_latest_molecule.ttl, babel_downloads/CHEMBL.COMPOUND/cco.ttl resources: mem_mb=64000, mem_mib=954, disk_mb=50000, disk_mib=47684, tmpdir=, mem=64G, runtime=120, cpus_per_task=4 INFO snakemake.logging [2025-11-22T07:56:50+0000]: Rule: get_chembl, Jobid: 29 INFO snakemake.logging [2025-11-22T07:56:50+0000]: Shell command: None Job 29 has been submitted with SLURM jobid 45427 (log: babel_outputs/logs/rule_get_chembl/45427.log). INFO snakemake.logging [2025-11-22T07:56:50+0000]: Job 29 has been submitted with SLURM jobid 45427 (log: babel_outputs/logs/rule_get_chembl/45427.log). [Sat Nov 22 02:56:50 2025] rule get_process_go_relationships: output: babel_outputs/intermediate/process/concords/GO, babel_outputs/intermediate/process/concords/metadata-GO.yaml jobid: 174 reason: Missing output files: babel_outputs/intermediate/process/concords/GO, babel_outputs/intermediate/process/concords/metadata-GO.yaml resources: mem_mb=64000, mem_mib=954, disk_mb=50000, disk_mib=47684, tmpdir=, mem=64G, runtime=120, cpus_per_task=4 INFO snakemake.logging [2025-11-22T07:56:50+0000]: Rule: get_process_go_relationships, Jobid: 174 INFO snakemake.logging [2025-11-22T07:56:50+0000]: Shell command: None Job 174 has been submitted with SLURM jobid 45428 (log: babel_outputs/logs/rule_get_process_go_relationships/45428.log). INFO snakemake.logging [2025-11-22T07:56:50+0000]: Job 174 has been submitted with SLURM jobid 45428 (log: babel_outputs/logs/rule_get_process_go_relationships/45428.log). [Sat Nov 22 02:56:50 2025] rule get_clo_ids: input: babel_downloads/CLO/clo.owl output: babel_outputs/intermediate/cell_line/ids/CLO jobid: 201 reason: Missing output files: babel_outputs/intermediate/cell_line/ids/CLO resources: mem_mb=64000, mem_mib=954, disk_mb=1000, disk_mib=954, tmpdir=, mem=64G, runtime=120, cpus_per_task=4 INFO snakemake.logging [2025-11-22T07:56:50+0000]: Rule: get_clo_ids, Jobid: 201 INFO snakemake.logging [2025-11-22T07:56:50+0000]: Shell command: None Job 201 has been submitted with SLURM jobid 45429 (log: babel_outputs/logs/rule_get_clo_ids/45429.log). INFO snakemake.logging [2025-11-22T07:56:50+0000]: Job 201 has been submitted with SLURM jobid 45429 (log: babel_outputs/logs/rule_get_clo_ids/45429.log). [Sat Nov 22 02:56:50 2025] rule get_drugbank_labels_and_synonyms: output: babel_downloads/DRUGBANK/drugbank vocabulary.csv, babel_downloads/DRUGBANK/labels, babel_downloads/DRUGBANK/synonyms jobid: 41 reason: Missing output files: babel_downloads/DRUGBANK/labels, babel_downloads/DRUGBANK/synonyms resources: mem_mb=64000, mem_mib=954, disk_mb=50000, disk_mib=47684, tmpdir=, mem=64G, runtime=120, cpus_per_task=4 INFO snakemake.logging [2025-11-22T07:56:50+0000]: Rule: get_drugbank_labels_and_synonyms, Jobid: 41 INFO snakemake.logging [2025-11-22T07:56:50+0000]: Shell command: None Job 41 has been submitted with SLURM jobid 45430 (log: babel_outputs/logs/rule_get_drugbank_labels_and_synonyms/45430.log). INFO snakemake.logging [2025-11-22T07:56:50+0000]: Job 41 has been submitted with SLURM jobid 45430 (log: babel_outputs/logs/rule_get_drugbank_labels_and_synonyms/45430.log). [Sat Nov 22 02:56:50 2025] rule get_EFO: output: babel_downloads/EFO/efo.owl jobid: 88 reason: Missing output files: babel_downloads/EFO/efo.owl resources: mem_mb=64000, mem_mib=954, disk_mb=50000, disk_mib=47684, tmpdir=, mem=64G, runtime=120, cpus_per_task=4 INFO snakemake.logging [2025-11-22T07:56:50+0000]: Rule: get_EFO, Jobid: 88 INFO snakemake.logging [2025-11-22T07:56:50+0000]: Shell command: None Job 88 has been submitted with SLURM jobid 45431 (log: babel_outputs/logs/rule_get_EFO/45431.log). INFO snakemake.logging [2025-11-22T07:56:50+0000]: Job 88 has been submitted with SLURM jobid 45431 (log: babel_outputs/logs/rule_get_EFO/45431.log). [Sat Nov 22 02:56:50 2025] rule get_icrdf: input: babel_downloads/common/ubergraph/labels, babel_downloads/common/ubergraph/synonyms.jsonl, babel_downloads/common/ubergraph/descriptions.jsonl output: babel_downloads/icRDF.tsv jobid: 18 reason: Missing output files: babel_downloads/icRDF.tsv resources: mem_mb=64000, mem_mib=1454, disk_mb=1524, disk_mib=1454, tmpdir=, mem=64G, runtime=120, cpus_per_task=4 INFO snakemake.logging [2025-11-22T07:56:50+0000]: Rule: get_icrdf, Jobid: 18 INFO snakemake.logging [2025-11-22T07:56:50+0000]: Shell command: None Job 18 has been submitted with SLURM jobid 45432 (log: babel_outputs/logs/rule_get_icrdf/45432.log). INFO snakemake.logging [2025-11-22T07:56:50+0000]: Job 18 has been submitted with SLURM jobid 45432 (log: babel_outputs/logs/rule_get_icrdf/45432.log). [Sat Nov 22 02:56:50 2025] rule get_mesh_labels: input: babel_downloads/MESH/mesh.nt output: babel_downloads/MESH/labels jobid: 49 reason: Missing output files: babel_downloads/MESH/labels resources: mem_mb=64000, mem_mib=4171, disk_mb=4373, disk_mib=4171, tmpdir=, mem=64G, runtime=120, cpus_per_task=4 INFO snakemake.logging [2025-11-22T07:56:50+0000]: Rule: get_mesh_labels, Jobid: 49 INFO snakemake.logging [2025-11-22T07:56:50+0000]: Shell command: None Job 49 has been submitted with SLURM jobid 45433 (log: babel_outputs/logs/rule_get_mesh_labels/45433.log). INFO snakemake.logging [2025-11-22T07:56:50+0000]: Job 49 has been submitted with SLURM jobid 45433 (log: babel_outputs/logs/rule_get_mesh_labels/45433.log). [Sat Nov 22 02:56:50 2025] rule taxon_mesh_ids: input: babel_downloads/MESH/mesh.nt output: babel_outputs/intermediate/taxon/ids/MESH jobid: 193 reason: Missing output files: babel_outputs/intermediate/taxon/ids/MESH resources: mem_mb=64000, mem_mib=4171, disk_mb=4373, disk_mib=4171, tmpdir=, mem=64G, runtime=120, cpus_per_task=4 INFO snakemake.logging [2025-11-22T07:56:50+0000]: Rule: taxon_mesh_ids, Jobid: 193 INFO snakemake.logging [2025-11-22T07:56:50+0000]: Shell command: None Job 193 has been submitted with SLURM jobid 45434 (log: babel_outputs/logs/rule_taxon_mesh_ids/45434.log). INFO snakemake.logging [2025-11-22T07:56:50+0000]: Job 193 has been submitted with SLURM jobid 45434 (log: babel_outputs/logs/rule_taxon_mesh_ids/45434.log). [Sat Nov 22 02:56:50 2025] rule get_pantherfamily: output: babel_downloads/PANTHER.FAMILY/family.csv jobid: 132 reason: Missing output files: babel_downloads/PANTHER.FAMILY/family.csv resources: mem_mb=64000, mem_mib=954, disk_mb=50000, disk_mib=47684, tmpdir=, mem=64G, runtime=120, cpus_per_task=4 INFO snakemake.logging [2025-11-22T07:56:50+0000]: Rule: get_pantherfamily, Jobid: 132 INFO snakemake.logging [2025-11-22T07:56:50+0000]: Shell command: None Job 132 has been submitted with SLURM jobid 45435 (log: babel_outputs/logs/rule_get_pantherfamily/45435.log). INFO snakemake.logging [2025-11-22T07:56:50+0000]: Job 132 has been submitted with SLURM jobid 45435 (log: babel_outputs/logs/rule_get_pantherfamily/45435.log). [Sat Nov 22 02:56:50 2025] rule get_process_rhea_relationships: input: babel_downloads/RHEA/rhea.rdf output: babel_outputs/intermediate/process/concords/RHEA, babel_outputs/intermediate/process/concords/metadata-RHEA.yaml jobid: 175 reason: Missing output files: babel_outputs/intermediate/process/concords/RHEA, babel_outputs/intermediate/process/concords/metadata-RHEA.yaml resources: mem_mb=64000, mem_mib=954, disk_mb=1000, disk_mib=954, tmpdir=, mem=64G, runtime=120, cpus_per_task=4 INFO snakemake.logging [2025-11-22T07:56:50+0000]: Rule: get_process_rhea_relationships, Jobid: 175 INFO snakemake.logging [2025-11-22T07:56:50+0000]: Shell command: None Job 175 has been submitted with SLURM jobid 45436 (log: babel_outputs/logs/rule_get_process_rhea_relationships/45436.log). INFO snakemake.logging [2025-11-22T07:56:50+0000]: Job 175 has been submitted with SLURM jobid 45436 (log: babel_outputs/logs/rule_get_process_rhea_relationships/45436.log). [Sat Nov 22 02:56:50 2025] rule gtopdb_labels_and_synonyms: input: babel_downloads/GTOPDB/ligands.tsv output: babel_downloads/GTOPDB/labels, babel_downloads/GTOPDB/synonyms jobid: 30 reason: Missing output files: babel_downloads/GTOPDB/labels, babel_downloads/GTOPDB/synonyms resources: mem_mb=64000, mem_mib=954, disk_mb=1000, disk_mib=954, tmpdir=, mem=64G, runtime=120, cpus_per_task=4 INFO snakemake.logging [2025-11-22T07:56:50+0000]: Rule: gtopdb_labels_and_synonyms, Jobid: 30 INFO snakemake.logging [2025-11-22T07:56:50+0000]: Shell command: None Job 30 has been submitted with SLURM jobid 45437 (log: babel_outputs/logs/rule_gtopdb_labels_and_synonyms/45437.log). INFO snakemake.logging [2025-11-22T07:56:50+0000]: Job 30 has been submitted with SLURM jobid 45437 (log: babel_outputs/logs/rule_gtopdb_labels_and_synonyms/45437.log). [Sat Nov 22 02:56:50 2025] rule disease_mesh_ids: input: babel_downloads/MESH/mesh.nt output: babel_outputs/intermediate/disease/ids/MESH jobid: 103 reason: Missing output files: babel_outputs/intermediate/disease/ids/MESH resources: mem_mb=64000, mem_mib=4171, disk_mb=4373, disk_mib=4171, tmpdir=, mem=64G, runtime=120, cpus_per_task=4 INFO snakemake.logging [2025-11-22T07:56:50+0000]: Rule: disease_mesh_ids, Jobid: 103 INFO snakemake.logging [2025-11-22T07:56:50+0000]: Shell command: None Job 103 has been submitted with SLURM jobid 45438 (log: babel_outputs/logs/rule_disease_mesh_ids/45438.log). INFO snakemake.logging [2025-11-22T07:56:50+0000]: Job 103 has been submitted with SLURM jobid 45438 (log: babel_outputs/logs/rule_disease_mesh_ids/45438.log). [Sat Nov 22 02:56:50 2025] rule get_wikidata_cell_relationships: output: babel_outputs/intermediate/anatomy/concords/WIKIDATA, babel_outputs/intermediate/anatomy/concords/metadata-WIKIDATA.yaml jobid: 11 reason: Missing output files: babel_outputs/intermediate/anatomy/concords/WIKIDATA, babel_outputs/intermediate/anatomy/concords/metadata-WIKIDATA.yaml resources: mem_mb=64000, mem_mib=954, disk_mb=50000, disk_mib=47684, tmpdir=, mem=64G, runtime=120, cpus_per_task=4 INFO snakemake.logging [2025-11-22T07:56:50+0000]: Rule: get_wikidata_cell_relationships, Jobid: 11 INFO snakemake.logging [2025-11-22T07:56:50+0000]: Shell command: None Job 11 has been submitted with SLURM jobid 45439 (log: babel_outputs/logs/rule_get_wikidata_cell_relationships/45439.log). INFO snakemake.logging [2025-11-22T07:56:50+0000]: Job 11 has been submitted with SLURM jobid 45439 (log: babel_outputs/logs/rule_get_wikidata_cell_relationships/45439.log). [Sat Nov 22 02:56:50 2025] rule get_protein_pr_uniprotkb_relationships: output: babel_outputs/intermediate/protein/concords/PR, babel_outputs/intermediate/protein/concords/metadata-PR.yaml jobid: 146 reason: Missing output files: babel_outputs/intermediate/protein/concords/metadata-PR.yaml, babel_outputs/intermediate/protein/concords/PR resources: mem_mb=64000, mem_mib=954, disk_mb=50000, disk_mib=47684, tmpdir=, mem=64G, runtime=120, cpus_per_task=4 INFO snakemake.logging [2025-11-22T07:56:50+0000]: Rule: get_protein_pr_uniprotkb_relationships, Jobid: 146 INFO snakemake.logging [2025-11-22T07:56:50+0000]: Shell command: None Job 146 has been submitted with SLURM jobid 45440 (log: babel_outputs/logs/rule_get_protein_pr_uniprotkb_relationships/45440.log). INFO snakemake.logging [2025-11-22T07:56:50+0000]: Job 146 has been submitted with SLURM jobid 45440 (log: babel_outputs/logs/rule_get_protein_pr_uniprotkb_relationships/45440.log). [Sat Nov 22 02:56:50 2025] rule get_CLO_labels: input: babel_downloads/CLO/clo.owl output: babel_downloads/CLO/labels, babel_downloads/CLO/synonyms jobid: 203 reason: Missing output files: babel_downloads/CLO/synonyms, babel_downloads/CLO/labels resources: mem_mb=64000, mem_mib=954, disk_mb=1000, disk_mib=954, tmpdir=, mem=64G, runtime=120, cpus_per_task=4 INFO snakemake.logging [2025-11-22T07:56:50+0000]: Rule: get_CLO_labels, Jobid: 203 INFO snakemake.logging [2025-11-22T07:56:50+0000]: Shell command: None Job 203 has been submitted with SLURM jobid 45441 (log: babel_outputs/logs/rule_get_CLO_labels/45441.log). INFO snakemake.logging [2025-11-22T07:56:50+0000]: Job 203 has been submitted with SLURM jobid 45441 (log: babel_outputs/logs/rule_get_CLO_labels/45441.log). [Sat Nov 22 02:56:50 2025] rule pubchem_synonyms: input: babel_downloads/PUBCHEM.COMPOUND/CID-Synonym-filtered.gz output: babel_downloads/PUBCHEM.COMPOUND/synonyms jobid: 42 reason: Missing output files: babel_downloads/PUBCHEM.COMPOUND/synonyms resources: mem_mb=64000, mem_mib=1690, disk_mb=1772, disk_mib=1690, tmpdir=, mem=64G, runtime=120, cpus_per_task=4 INFO snakemake.logging [2025-11-22T07:56:50+0000]: Rule: pubchem_synonyms, Jobid: 42 INFO snakemake.logging [2025-11-22T07:56:50+0000]: Shell command: None Job 42 has been submitted with SLURM jobid 45442 (log: babel_outputs/logs/rule_pubchem_synonyms/45442.log). INFO snakemake.logging [2025-11-22T07:56:50+0000]: Job 42 has been submitted with SLURM jobid 45442 (log: babel_outputs/logs/rule_pubchem_synonyms/45442.log). [Sat Nov 22 02:56:50 2025] rule get_disease_doid_relationships: input: babel_downloads/DOID/doid.json output: babel_outputs/intermediate/disease/concords/DOID, babel_outputs/intermediate/disease/concords/metadata-DOID.yaml jobid: 95 reason: Missing output files: babel_outputs/intermediate/disease/concords/metadata-DOID.yaml, babel_outputs/intermediate/disease/concords/DOID resources: mem_mb=64000, mem_mib=954, disk_mb=1000, disk_mib=954, tmpdir=, mem=64G, runtime=120, cpus_per_task=4 INFO snakemake.logging [2025-11-22T07:56:50+0000]: Rule: get_disease_doid_relationships, Jobid: 95 INFO snakemake.logging [2025-11-22T07:56:50+0000]: Shell command: None Job 95 has been submitted with SLURM jobid 45443 (log: babel_outputs/logs/rule_get_disease_doid_relationships/45443.log). INFO snakemake.logging [2025-11-22T07:56:50+0000]: Job 95 has been submitted with SLURM jobid 45443 (log: babel_outputs/logs/rule_get_disease_doid_relationships/45443.log). [Sat Nov 22 02:56:50 2025] rule download_umls: output: babel_downloads/UMLS/MRCONSO.RRF, babel_downloads/UMLS/MRSTY.RRF, babel_downloads/UMLS/MRREL.RRF jobid: 9 reason: Missing output files: babel_downloads/UMLS/MRCONSO.RRF, babel_downloads/UMLS/MRREL.RRF, babel_downloads/UMLS/MRSTY.RRF resources: mem_mb=64000, mem_mib=954, disk_mb=50000, disk_mib=47684, tmpdir=, mem=64G, runtime=120, cpus_per_task=4 INFO snakemake.logging [2025-11-22T07:56:50+0000]: Rule: download_umls, Jobid: 9 INFO snakemake.logging [2025-11-22T07:56:50+0000]: Shell command: None Job 9 has been submitted with SLURM jobid 45444 (log: babel_outputs/logs/rule_download_umls/45444.log). INFO snakemake.logging [2025-11-22T07:56:50+0000]: Job 9 has been submitted with SLURM jobid 45444 (log: babel_outputs/logs/rule_download_umls/45444.log). Select jobs to execute... INFO snakemake.logging [2025-11-22T07:56:51+0000]: Select jobs to execute... Waiting at most 60 seconds for missing files: babel_outputs/intermediate/protein/concords/NCIT_UniProtKB (missing locally) babel_outputs/intermediate/protein/concords/metadata-NCIT_UniProtKB.yaml (missing locally) INFO snakemake.logging [2025-11-22T07:57:24+0000]: Waiting at most 60 seconds for missing files: babel_outputs/intermediate/protein/concords/NCIT_UniProtKB (missing locally) babel_outputs/intermediate/protein/concords/metadata-NCIT_UniProtKB.yaml (missing locally) [Sat Nov 22 02:57:48 2025] Finished jobid: 147 (Rule: get_protein_ncit_uniprotkb_relationships) INFO snakemake.logging [2025-11-22T07:57:48+0000]: Finished jobid: 147 (Rule: get_protein_ncit_uniprotkb_relationships) 1 of 305 steps (0.3%) done INFO snakemake.logging [2025-11-22T07:57:48+0000]: None Execute 1 jobs... INFO snakemake.logging [2025-11-22T07:57:49+0000]: Execute 1 jobs... [Sat Nov 22 02:57:49 2025] rule extract_taxon_ids_from_uniprotkb: input: babel_downloads/UniProtKB/idmapping.dat output: babel_downloads/UniProtKB/taxa jobid: 155 reason: Missing output files: babel_downloads/UniProtKB/taxa resources: mem_mb=64000, mem_mib=7630, disk_mb=165563, disk_mib=157894, tmpdir=, mem=64G, runtime=120, cpus_per_task=4 INFO snakemake.logging [2025-11-22T07:57:49+0000]: Rule: extract_taxon_ids_from_uniprotkb, Jobid: 155 INFO snakemake.logging [2025-11-22T07:57:49+0000]: Shell command: None [Sat Nov 22 02:57:49 2025] Error in rule disease_efo_ids: message: SLURM-job '45418' failed, SLURM status is: 'FAILED'. For further error details see the cluster/cloud log and the log files of the involved rule(s). jobid: 97 output: babel_outputs/intermediate/disease/ids/EFO log: babel_outputs/logs/rule_disease_efo_ids/45418.log (check log file(s) for error details) external_jobid: 45418 ERROR snakemake.logging [2025-11-22T07:57:49+0000]: Error in rule disease_efo_ids, jobid: 97 Job 155 has been submitted with SLURM jobid 45445 (log: babel_outputs/logs/rule_extract_taxon_ids_from_uniprotkb/45445.log). INFO snakemake.logging [2025-11-22T07:57:49+0000]: Job 155 has been submitted with SLURM jobid 45445 (log: babel_outputs/logs/rule_extract_taxon_ids_from_uniprotkb/45445.log). [Sat Nov 22 02:57:49 2025] Finished jobid: 94 (Rule: disease_ncit_ids) INFO snakemake.logging [2025-11-22T07:57:49+0000]: Finished jobid: 94 (Rule: disease_ncit_ids) 2 of 305 steps (1%) done INFO snakemake.logging [2025-11-22T07:57:49+0000]: None [Sat Nov 22 02:57:49 2025] Finished jobid: 164 (Rule: get_reactome_labels) INFO snakemake.logging [2025-11-22T07:57:49+0000]: Finished jobid: 164 (Rule: get_reactome_labels) 3 of 305 steps (1%) done INFO snakemake.logging [2025-11-22T07:57:49+0000]: None [Sat Nov 22 02:57:49 2025] Finished jobid: 70 (Rule: chemical_drugcentral_ids) INFO snakemake.logging [2025-11-22T07:57:50+0000]: Finished jobid: 70 (Rule: chemical_drugcentral_ids) 4 of 305 steps (1%) done INFO snakemake.logging [2025-11-22T07:57:50+0000]: None [Sat Nov 22 02:57:50 2025] Finished jobid: 33 (Rule: unii_labels_and_synonyms) INFO snakemake.logging [2025-11-22T07:57:50+0000]: Finished jobid: 33 (Rule: unii_labels_and_synonyms) 5 of 305 steps (2%) done INFO snakemake.logging [2025-11-22T07:57:50+0000]: None [Sat Nov 22 02:57:50 2025] Finished jobid: 220 (Rule: rxnorm_relationships) INFO snakemake.logging [2025-11-22T07:57:50+0000]: Finished jobid: 220 (Rule: rxnorm_relationships) 6 of 305 steps (2%) done INFO snakemake.logging [2025-11-22T07:57:50+0000]: None [Sat Nov 22 02:57:50 2025] Finished jobid: 13 (Rule: anatomy_go_ids) INFO snakemake.logging [2025-11-22T07:57:50+0000]: Finished jobid: 13 (Rule: anatomy_go_ids) 7 of 305 steps (2%) done INFO snakemake.logging [2025-11-22T07:57:50+0000]: None [Sat Nov 22 02:57:50 2025] Finished jobid: 116 (Rule: get_gene_medgen_relationships) INFO snakemake.logging [2025-11-22T07:57:50+0000]: Finished jobid: 116 (Rule: get_gene_medgen_relationships) 8 of 305 steps (3%) done INFO snakemake.logging [2025-11-22T07:57:50+0000]: None [Sat Nov 22 02:57:50 2025] Finished jobid: 166 (Rule: get_rhea_labels) INFO snakemake.logging [2025-11-22T07:57:50+0000]: Finished jobid: 166 (Rule: get_rhea_labels) 9 of 305 steps (3%) done INFO snakemake.logging [2025-11-22T07:57:50+0000]: None [Sat Nov 22 02:57:50 2025] Finished jobid: 83 (Rule: get_doid_labels_and_synonyms) INFO snakemake.logging [2025-11-22T07:57:50+0000]: Finished jobid: 83 (Rule: get_doid_labels_and_synonyms) 10 of 305 steps (3%) done INFO snakemake.logging [2025-11-22T07:57:50+0000]: None [Sat Nov 22 02:57:50 2025] Finished jobid: 92 (Rule: disease_omim_ids) INFO snakemake.logging [2025-11-22T07:57:50+0000]: Finished jobid: 92 (Rule: disease_omim_ids) 11 of 305 steps (4%) done INFO snakemake.logging [2025-11-22T07:57:50+0000]: None [Sat Nov 22 02:57:50 2025] Finished jobid: 123 (Rule: gene_omim_ids) INFO snakemake.logging [2025-11-22T07:57:50+0000]: Finished jobid: 123 (Rule: gene_omim_ids) 12 of 305 steps (4%) done INFO snakemake.logging [2025-11-22T07:57:50+0000]: None [Sat Nov 22 02:57:50 2025] Finished jobid: 179 (Rule: process_reactome_ids) INFO snakemake.logging [2025-11-22T07:57:50+0000]: Finished jobid: 179 (Rule: process_reactome_ids) 13 of 305 steps (4%) done INFO snakemake.logging [2025-11-22T07:57:50+0000]: None [Sat Nov 22 02:57:50 2025] Finished jobid: 169 (Rule: get_EC) INFO snakemake.logging [2025-11-22T07:57:50+0000]: Finished jobid: 169 (Rule: get_EC) 14 of 305 steps (5%) done INFO snakemake.logging [2025-11-22T07:57:50+0000]: None [Sat Nov 22 02:57:50 2025] Finished jobid: 63 (Rule: chemical_gtopdb_ids) INFO snakemake.logging [2025-11-22T07:57:50+0000]: Finished jobid: 63 (Rule: chemical_gtopdb_ids) 15 of 305 steps (5%) done INFO snakemake.logging [2025-11-22T07:57:50+0000]: None [Sat Nov 22 02:57:50 2025] Finished jobid: 85 (Rule: get_orphanet_labels_and_synonyms) INFO snakemake.logging [2025-11-22T07:57:50+0000]: Finished jobid: 85 (Rule: get_orphanet_labels_and_synonyms) 16 of 305 steps (5%) done INFO snakemake.logging [2025-11-22T07:57:50+0000]: None [Sat Nov 22 02:57:50 2025] Finished jobid: 133 (Rule: get_hgncfamily_labels) INFO snakemake.logging [2025-11-22T07:57:50+0000]: Finished jobid: 133 (Rule: get_hgncfamily_labels) 17 of 305 steps (6%) done INFO snakemake.logging [2025-11-22T07:57:50+0000]: None [Sat Nov 22 02:57:50 2025] Finished jobid: 60 (Rule: chemical_rxnorm_ids) INFO snakemake.logging [2025-11-22T07:57:50+0000]: Finished jobid: 60 (Rule: chemical_rxnorm_ids) 18 of 305 steps (6%) done INFO snakemake.logging [2025-11-22T07:57:50+0000]: None [Sat Nov 22 02:57:50 2025] Finished jobid: 208 (Rule: get_complexportal_labels_and_synonyms) INFO snakemake.logging [2025-11-22T07:57:50+0000]: Finished jobid: 208 (Rule: get_complexportal_labels_and_synonyms) 19 of 305 steps (6%) done INFO snakemake.logging [2025-11-22T07:57:50+0000]: None [Sat Nov 22 02:57:50 2025] Finished jobid: 66 (Rule: chemical_unii_ids) INFO snakemake.logging [2025-11-22T07:57:50+0000]: Finished jobid: 66 (Rule: chemical_unii_ids) 20 of 305 steps (7%) done INFO snakemake.logging [2025-11-22T07:57:50+0000]: None [Sat Nov 22 02:57:50 2025] Finished jobid: 53 (Rule: get_gtopdb_inchikey_concord) INFO snakemake.logging [2025-11-22T07:57:50+0000]: Finished jobid: 53 (Rule: get_gtopdb_inchikey_concord) 21 of 305 steps (7%) done INFO snakemake.logging [2025-11-22T07:57:50+0000]: None [Sat Nov 22 02:57:50 2025] Finished jobid: 201 (Rule: get_clo_ids) INFO snakemake.logging [2025-11-22T07:57:50+0000]: Finished jobid: 201 (Rule: get_clo_ids) 22 of 305 steps (7%) done INFO snakemake.logging [2025-11-22T07:57:50+0000]: None [Sat Nov 22 02:57:50 2025] Finished jobid: 41 (Rule: get_drugbank_labels_and_synonyms) INFO snakemake.logging [2025-11-22T07:57:50+0000]: Finished jobid: 41 (Rule: get_drugbank_labels_and_synonyms) 23 of 305 steps (8%) done INFO snakemake.logging [2025-11-22T07:57:50+0000]: None [Sat Nov 22 02:57:50 2025] Finished jobid: 88 (Rule: get_EFO) INFO snakemake.logging [2025-11-22T07:57:50+0000]: Finished jobid: 88 (Rule: get_EFO) 24 of 305 steps (8%) done INFO snakemake.logging [2025-11-22T07:57:50+0000]: None [Sat Nov 22 02:57:50 2025] Finished jobid: 175 (Rule: get_process_rhea_relationships) INFO snakemake.logging [2025-11-22T07:57:50+0000]: Finished jobid: 175 (Rule: get_process_rhea_relationships) 25 of 305 steps (8%) done INFO snakemake.logging [2025-11-22T07:57:50+0000]: None [Sat Nov 22 02:57:50 2025] Finished jobid: 30 (Rule: gtopdb_labels_and_synonyms) INFO snakemake.logging [2025-11-22T07:57:50+0000]: Finished jobid: 30 (Rule: gtopdb_labels_and_synonyms) 26 of 305 steps (9%) done INFO snakemake.logging [2025-11-22T07:57:50+0000]: None [Sat Nov 22 02:57:50 2025] Finished jobid: 11 (Rule: get_wikidata_cell_relationships) INFO snakemake.logging [2025-11-22T07:57:50+0000]: Finished jobid: 11 (Rule: get_wikidata_cell_relationships) 27 of 305 steps (9%) done INFO snakemake.logging [2025-11-22T07:57:50+0000]: None [Sat Nov 22 02:57:50 2025] Finished jobid: 203 (Rule: get_CLO_labels) INFO snakemake.logging [2025-11-22T07:57:50+0000]: Finished jobid: 203 (Rule: get_CLO_labels) 28 of 305 steps (9%) done INFO snakemake.logging [2025-11-22T07:57:50+0000]: None [Sat Nov 22 02:57:50 2025] Finished jobid: 95 (Rule: get_disease_doid_relationships) INFO snakemake.logging [2025-11-22T07:57:50+0000]: Finished jobid: 95 (Rule: get_disease_doid_relationships) 29 of 305 steps (10%) done INFO snakemake.logging [2025-11-22T07:57:50+0000]: None [Sat Nov 22 02:58:30 2025] Finished jobid: 190 (Rule: ncbitaxon_labels_and_synonyms) INFO snakemake.logging [2025-11-22T07:58:30+0000]: Finished jobid: 190 (Rule: ncbitaxon_labels_and_synonyms) 30 of 305 steps (10%) done INFO snakemake.logging [2025-11-22T07:58:30+0000]: None [Sat Nov 22 02:58:30 2025] Finished jobid: 51 (Rule: chemical_mesh_ids) INFO snakemake.logging [2025-11-22T07:58:30+0000]: Finished jobid: 51 (Rule: chemical_mesh_ids) 31 of 305 steps (10%) done INFO snakemake.logging [2025-11-22T07:58:30+0000]: None [Sat Nov 22 02:58:30 2025] Finished jobid: 174 (Rule: get_process_go_relationships) INFO snakemake.logging [2025-11-22T07:58:30+0000]: Finished jobid: 174 (Rule: get_process_go_relationships) 32 of 305 steps (10%) done INFO snakemake.logging [2025-11-22T07:58:30+0000]: None [Sat Nov 22 02:58:30 2025] Finished jobid: 193 (Rule: taxon_mesh_ids) INFO snakemake.logging [2025-11-22T07:58:30+0000]: Finished jobid: 193 (Rule: taxon_mesh_ids) 33 of 305 steps (11%) done INFO snakemake.logging [2025-11-22T07:58:30+0000]: None [Sat Nov 22 02:58:30 2025] Finished jobid: 103 (Rule: disease_mesh_ids) INFO snakemake.logging [2025-11-22T07:58:30+0000]: Finished jobid: 103 (Rule: disease_mesh_ids) 34 of 305 steps (11%) done INFO snakemake.logging [2025-11-22T07:58:30+0000]: None [Sat Nov 22 02:59:10 2025] Error in rule get_protein_pr_uniprotkb_relationships: message: SLURM-job '45440' failed, SLURM status is: 'FAILED'. For further error details see the cluster/cloud log and the log files of the involved rule(s). jobid: 146 output: babel_outputs/intermediate/protein/concords/PR, babel_outputs/intermediate/protein/concords/metadata-PR.yaml log: babel_outputs/logs/rule_get_protein_pr_uniprotkb_relationships/45440.log (check log file(s) for error details) external_jobid: 45440 ERROR snakemake.logging [2025-11-22T07:59:10+0000]: Error in rule get_protein_pr_uniprotkb_relationships, jobid: 146 [Sat Nov 22 02:59:10 2025] Finished jobid: 49 (Rule: get_mesh_labels) INFO snakemake.logging [2025-11-22T07:59:10+0000]: Finished jobid: 49 (Rule: get_mesh_labels) 35 of 305 steps (11%) done INFO snakemake.logging [2025-11-22T07:59:10+0000]: None [Sat Nov 22 02:59:10 2025] Finished jobid: 42 (Rule: pubchem_synonyms) INFO snakemake.logging [2025-11-22T07:59:10+0000]: Finished jobid: 42 (Rule: pubchem_synonyms) 36 of 305 steps (12%) done INFO snakemake.logging [2025-11-22T07:59:10+0000]: None [Sat Nov 22 03:00:40 2025] Finished jobid: 37 (Rule: pubchem_labels) INFO snakemake.logging [2025-11-22T08:00:40+0000]: Finished jobid: 37 (Rule: pubchem_labels) 37 of 305 steps (12%) done INFO snakemake.logging [2025-11-22T08:00:40+0000]: None [Sat Nov 22 03:01:20 2025] Finished jobid: 46 (Rule: filter_unichem) INFO snakemake.logging [2025-11-22T08:01:20+0000]: Finished jobid: 46 (Rule: filter_unichem) 38 of 305 steps (12%) done INFO snakemake.logging [2025-11-22T08:01:20+0000]: None [Sat Nov 22 03:01:20 2025] Finished jobid: 9 (Rule: download_umls) INFO snakemake.logging [2025-11-22T08:01:20+0000]: Finished jobid: 9 (Rule: download_umls) 39 of 305 steps (13%) done INFO snakemake.logging [2025-11-22T08:01:20+0000]: None [Sat Nov 22 03:03:51 2025] Finished jobid: 18 (Rule: get_icrdf) INFO snakemake.logging [2025-11-22T08:03:51+0000]: Finished jobid: 18 (Rule: get_icrdf) 40 of 305 steps (13%) done INFO snakemake.logging [2025-11-22T08:03:51+0000]: None [Sat Nov 22 03:03:51 2025] Finished jobid: 132 (Rule: get_pantherfamily) INFO snakemake.logging [2025-11-22T08:03:51+0000]: Finished jobid: 132 (Rule: get_pantherfamily) 41 of 305 steps (13%) done INFO snakemake.logging [2025-11-22T08:03:51+0000]: None [Sat Nov 22 03:04:31 2025] Finished jobid: 32 (Rule: keggcompound_labels) INFO snakemake.logging [2025-11-22T08:04:31+0000]: Finished jobid: 32 (Rule: keggcompound_labels) 42 of 305 steps (14%) done INFO snakemake.logging [2025-11-22T08:04:31+0000]: None [Sat Nov 22 03:04:31 2025] Finished jobid: 111 (Rule: get_ncbigene_labels_synonyms_and_taxa) INFO snakemake.logging [2025-11-22T08:04:31+0000]: Finished jobid: 111 (Rule: get_ncbigene_labels_synonyms_and_taxa) 43 of 305 steps (14%) done INFO snakemake.logging [2025-11-22T08:04:31+0000]: None [Sat Nov 22 03:07:01 2025] Finished jobid: 35 (Rule: hmdb_labels_and_synonyms) INFO snakemake.logging [2025-11-22T08:07:01+0000]: Finished jobid: 35 (Rule: hmdb_labels_and_synonyms) 44 of 305 steps (14%) done INFO snakemake.logging [2025-11-22T08:07:01+0000]: None [Sat Nov 22 03:10:41 2025] Finished jobid: 29 (Rule: get_chembl) INFO snakemake.logging [2025-11-22T08:10:41+0000]: Finished jobid: 29 (Rule: get_chembl) 45 of 305 steps (15%) done INFO snakemake.logging [2025-11-22T08:10:41+0000]: None [Sat Nov 22 03:12:11 2025] Finished jobid: 213 (Rule: verify_pubmed) INFO snakemake.logging [2025-11-22T08:12:11+0000]: Finished jobid: 213 (Rule: verify_pubmed) 46 of 305 steps (15%) done INFO snakemake.logging [2025-11-22T08:12:11+0000]: None [Sat Nov 22 03:12:52 2025] Finished jobid: 144 (Rule: get_protein_uniprotkb_ensembl_relationships) INFO snakemake.logging [2025-11-22T08:12:52+0000]: Finished jobid: 144 (Rule: get_protein_uniprotkb_ensembl_relationships) 47 of 305 steps (15%) done INFO snakemake.logging [2025-11-22T08:12:52+0000]: None [Sat Nov 22 03:17:52 2025] Finished jobid: 155 (Rule: extract_taxon_ids_from_uniprotkb) INFO snakemake.logging [2025-11-22T08:17:52+0000]: Finished jobid: 155 (Rule: extract_taxon_ids_from_uniprotkb) 48 of 305 steps (16%) done INFO snakemake.logging [2025-11-22T08:17:52+0000]: None [Sat Nov 22 04:57:27 2025] Error in rule get_ensembl: message: SLURM-job '45412' failed, SLURM status is: 'TIMEOUT'. For further error details see the cluster/cloud log and the log files of the involved rule(s). jobid: 121 output: babel_downloads/ENSEMBL, babel_downloads/ENSEMBL/BioMartDownloadComplete log: babel_outputs/logs/rule_get_ensembl/45412.log (check log file(s) for error details) external_jobid: 45412 ERROR snakemake.logging [2025-11-22T09:57:27+0000]: Error in rule get_ensembl, jobid: 121 Removing output files of failed job get_ensembl since they might be corrupted: babel_downloads/ENSEMBL INFO snakemake.logging [2025-11-22T09:57:27+0000]: Removing output files of failed job get_ensembl since they might be corrupted: babel_downloads/ENSEMBL Shutting down, this might take some time. INFO snakemake.logging [2025-11-22T09:57:27+0000]: Shutting down, this might take some time. Cleaning up log files older than 10 day(s). INFO snakemake.logging [2025-11-22T10:00:27+0000]: Cleaning up log files older than 10 day(s). Job 45395.0 for rule 'rule_keggcompound_labels' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2025-11-22T10:00:29+0000]: Job 45395.0 for rule 'rule_keggcompound_labels' (python) has low CPU efficiency: 0.0%. Job 45396.0 for rule 'rule_get_protein_ncit_uniprotkb_relationships' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2025-11-22T10:00:29+0000]: Job 45396.0 for rule 'rule_get_protein_ncit_uniprotkb_relationships' (python) has low CPU efficiency: 0.0%. Job 45397.0 for rule 'rule_disease_ncit_ids' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2025-11-22T10:00:29+0000]: Job 45397.0 for rule 'rule_disease_ncit_ids' (python) has low CPU efficiency: 0.0%. Job 45398.0 for rule 'rule_get_reactome_labels' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2025-11-22T10:00:29+0000]: Job 45398.0 for rule 'rule_get_reactome_labels' (python) has low CPU efficiency: 0.0%. Job 45399.0 for rule 'rule_chemical_drugcentral_ids' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2025-11-22T10:00:29+0000]: Job 45399.0 for rule 'rule_chemical_drugcentral_ids' (python) has low CPU efficiency: 0.0%. Job 45400.0 for rule 'rule_unii_labels_and_synonyms' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2025-11-22T10:00:29+0000]: Job 45400.0 for rule 'rule_unii_labels_and_synonyms' (python) has low CPU efficiency: 0.0%. Job 45401.0 for rule 'rule_rxnorm_relationships' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2025-11-22T10:00:29+0000]: Job 45401.0 for rule 'rule_rxnorm_relationships' (python) has low CPU efficiency: 0.0%. Job 45402.0 for rule 'rule_anatomy_go_ids' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2025-11-22T10:00:29+0000]: Job 45402.0 for rule 'rule_anatomy_go_ids' (python) has low CPU efficiency: 0.0%. Job 45403.0 for rule 'rule_get_gene_medgen_relationships' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2025-11-22T10:00:29+0000]: Job 45403.0 for rule 'rule_get_gene_medgen_relationships' (python) has low CPU efficiency: 0.0%. Job 45404.0 for rule 'rule_get_rhea_labels' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2025-11-22T10:00:29+0000]: Job 45404.0 for rule 'rule_get_rhea_labels' (python) has low CPU efficiency: 0.0%. Job 45405.0 for rule 'rule_verify_pubmed' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2025-11-22T10:00:29+0000]: Job 45405.0 for rule 'rule_verify_pubmed' (python) has low CPU efficiency: 0.0%. Job 45406.0 for rule 'rule_hmdb_labels_and_synonyms' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2025-11-22T10:00:29+0000]: Job 45406.0 for rule 'rule_hmdb_labels_and_synonyms' (python) has low CPU efficiency: 0.0%. Job 45407.0 for rule 'rule_get_doid_labels_and_synonyms' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2025-11-22T10:00:29+0000]: Job 45407.0 for rule 'rule_get_doid_labels_and_synonyms' (python) has low CPU efficiency: 0.0%. Job 45408.0 for rule 'rule_disease_omim_ids' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2025-11-22T10:00:29+0000]: Job 45408.0 for rule 'rule_disease_omim_ids' (python) has low CPU efficiency: 0.0%. Job 45409.0 for rule 'rule_gene_omim_ids' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2025-11-22T10:00:29+0000]: Job 45409.0 for rule 'rule_gene_omim_ids' (python) has low CPU efficiency: 0.0%. Job 45410.0 for rule 'rule_process_reactome_ids' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2025-11-22T10:00:29+0000]: Job 45410.0 for rule 'rule_process_reactome_ids' (python) has low CPU efficiency: 0.0%. Job 45411.0 for rule 'rule_ncbitaxon_labels_and_synonyms' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2025-11-22T10:00:29+0000]: Job 45411.0 for rule 'rule_ncbitaxon_labels_and_synonyms' (python) has low CPU efficiency: 0.0%. Job 45412.0 for rule 'rule_get_ensembl' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2025-11-22T10:00:29+0000]: Job 45412.0 for rule 'rule_get_ensembl' (python) has low CPU efficiency: 0.0%. Job 45413.0 for rule 'rule_chemical_mesh_ids' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2025-11-22T10:00:29+0000]: Job 45413.0 for rule 'rule_chemical_mesh_ids' (python) has low CPU efficiency: 0.0%. Job 45414.0 for rule 'rule_get_EC' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2025-11-22T10:00:29+0000]: Job 45414.0 for rule 'rule_get_EC' (python) has low CPU efficiency: 0.0%. Job 45415.0 for rule 'rule_pubchem_labels' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2025-11-22T10:00:29+0000]: Job 45415.0 for rule 'rule_pubchem_labels' (python) has low CPU efficiency: 0.0%. Job 45416.0 for rule 'rule_chemical_gtopdb_ids' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2025-11-22T10:00:29+0000]: Job 45416.0 for rule 'rule_chemical_gtopdb_ids' (python) has low CPU efficiency: 0.0%. Job 45417.0 for rule 'rule_get_orphanet_labels_and_synonyms' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2025-11-22T10:00:29+0000]: Job 45417.0 for rule 'rule_get_orphanet_labels_and_synonyms' (python) has low CPU efficiency: 0.0%. Job 45418.0 for rule 'rule_disease_efo_ids' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2025-11-22T10:00:29+0000]: Job 45418.0 for rule 'rule_disease_efo_ids' (python) has low CPU efficiency: 0.0%. Job 45419.0 for rule 'rule_get_hgncfamily_labels' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2025-11-22T10:00:29+0000]: Job 45419.0 for rule 'rule_get_hgncfamily_labels' (python) has low CPU efficiency: 0.0%. Job 45420.0 for rule 'rule_chemical_rxnorm_ids' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2025-11-22T10:00:29+0000]: Job 45420.0 for rule 'rule_chemical_rxnorm_ids' (python) has low CPU efficiency: 0.0%. Job 45421.0 for rule 'rule_get_complexportal_labels_and_synonyms' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2025-11-22T10:00:29+0000]: Job 45421.0 for rule 'rule_get_complexportal_labels_and_synonyms' (python) has low CPU efficiency: 0.0%. Job 45422.0 for rule 'rule_filter_unichem' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2025-11-22T10:00:29+0000]: Job 45422.0 for rule 'rule_filter_unichem' (python) has low CPU efficiency: 0.0%. Job 45423.0 for rule 'rule_chemical_unii_ids' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2025-11-22T10:00:29+0000]: Job 45423.0 for rule 'rule_chemical_unii_ids' (python) has low CPU efficiency: 0.0%. Job 45424.0 for rule 'rule_get_ncbigene_labels_synonyms_and_taxa' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2025-11-22T10:00:29+0000]: Job 45424.0 for rule 'rule_get_ncbigene_labels_synonyms_and_taxa' (python) has low CPU efficiency: 0.0%. Job 45425.0 for rule 'rule_get_gtopdb_inchikey_concord' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2025-11-22T10:00:29+0000]: Job 45425.0 for rule 'rule_get_gtopdb_inchikey_concord' (python) has low CPU efficiency: 0.0%. Job 45426.0 for rule 'rule_get_protein_uniprotkb_ensembl_relationships' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2025-11-22T10:00:29+0000]: Job 45426.0 for rule 'rule_get_protein_uniprotkb_ensembl_relationships' (python) has low CPU efficiency: 0.0%. Job 45427.0 for rule 'rule_get_chembl' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2025-11-22T10:00:29+0000]: Job 45427.0 for rule 'rule_get_chembl' (python) has low CPU efficiency: 0.0%. Job 45428.0 for rule 'rule_get_process_go_relationships' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2025-11-22T10:00:29+0000]: Job 45428.0 for rule 'rule_get_process_go_relationships' (python) has low CPU efficiency: 0.0%. Job 45429.0 for rule 'rule_get_clo_ids' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2025-11-22T10:00:29+0000]: Job 45429.0 for rule 'rule_get_clo_ids' (python) has low CPU efficiency: 0.0%. Job 45430.0 for rule 'rule_get_drugbank_labels_and_synonyms' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2025-11-22T10:00:29+0000]: Job 45430.0 for rule 'rule_get_drugbank_labels_and_synonyms' (python) has low CPU efficiency: 0.0%. Job 45431.0 for rule 'rule_get_EFO' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2025-11-22T10:00:29+0000]: Job 45431.0 for rule 'rule_get_EFO' (python) has low CPU efficiency: 0.0%. Job 45432.0 for rule 'rule_get_icrdf' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2025-11-22T10:00:29+0000]: Job 45432.0 for rule 'rule_get_icrdf' (python) has low CPU efficiency: 0.0%. Job 45433.0 for rule 'rule_get_mesh_labels' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2025-11-22T10:00:29+0000]: Job 45433.0 for rule 'rule_get_mesh_labels' (python) has low CPU efficiency: 0.0%. Job 45434.0 for rule 'rule_taxon_mesh_ids' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2025-11-22T10:00:29+0000]: Job 45434.0 for rule 'rule_taxon_mesh_ids' (python) has low CPU efficiency: 0.0%. Job 45435.0 for rule 'rule_get_pantherfamily' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2025-11-22T10:00:29+0000]: Job 45435.0 for rule 'rule_get_pantherfamily' (python) has low CPU efficiency: 0.0%. Job 45436.0 for rule 'rule_get_process_rhea_relationships' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2025-11-22T10:00:29+0000]: Job 45436.0 for rule 'rule_get_process_rhea_relationships' (python) has low CPU efficiency: 0.0%. Job 45437.0 for rule 'rule_gtopdb_labels_and_synonyms' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2025-11-22T10:00:29+0000]: Job 45437.0 for rule 'rule_gtopdb_labels_and_synonyms' (python) has low CPU efficiency: 0.0%. Job 45438.0 for rule 'rule_disease_mesh_ids' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2025-11-22T10:00:29+0000]: Job 45438.0 for rule 'rule_disease_mesh_ids' (python) has low CPU efficiency: 0.0%. Job 45439.0 for rule 'rule_get_wikidata_cell_relationships' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2025-11-22T10:00:29+0000]: Job 45439.0 for rule 'rule_get_wikidata_cell_relationships' (python) has low CPU efficiency: 0.0%. Job 45440.0 for rule 'rule_get_protein_pr_uniprotkb_relationships' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2025-11-22T10:00:29+0000]: Job 45440.0 for rule 'rule_get_protein_pr_uniprotkb_relationships' (python) has low CPU efficiency: 0.0%. Job 45441.0 for rule 'rule_get_CLO_labels' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2025-11-22T10:00:29+0000]: Job 45441.0 for rule 'rule_get_CLO_labels' (python) has low CPU efficiency: 0.0%. Job 45442.0 for rule 'rule_pubchem_synonyms' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2025-11-22T10:00:29+0000]: Job 45442.0 for rule 'rule_pubchem_synonyms' (python) has low CPU efficiency: 0.0%. Job 45443.0 for rule 'rule_get_disease_doid_relationships' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2025-11-22T10:00:29+0000]: Job 45443.0 for rule 'rule_get_disease_doid_relationships' (python) has low CPU efficiency: 0.0%. Job 45444.0 for rule 'rule_download_umls' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2025-11-22T10:00:29+0000]: Job 45444.0 for rule 'rule_download_umls' (python) has low CPU efficiency: 0.0%. Job 45445.0 for rule 'rule_extract_taxon_ids_from_uniprotkb' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2025-11-22T10:00:29+0000]: Job 45445.0 for rule 'rule_extract_taxon_ids_from_uniprotkb' (python) has low CPU efficiency: 0.0%. Efficiency report for workflow 21d1b82b-160d-4a51-bf44-c2ff5d5bafb3 saved to babel_outputs/reports/slurm/slurm_efficiency_report.csv/efficiency_report_21d1b82b-160d-4a51-bf44-c2ff5d5bafb3.csv. INFO snakemake.logging [2025-11-22T10:00:29+0000]: Efficiency report for workflow 21d1b82b-160d-4a51-bf44-c2ff5d5bafb3 saved to babel_outputs/reports/slurm/slurm_efficiency_report.csv/efficiency_report_21d1b82b-160d-4a51-bf44-c2ff5d5bafb3.csv. Exiting because a job execution failed. Look below for error messages ERROR snakemake.logging [2025-11-22T10:00:29+0000]: Exiting because a job execution failed. Look below for error messages [Sat Nov 22 05:00:29 2025] Error in rule get_protein_pr_uniprotkb_relationships: message: None jobid: 146 output: babel_outputs/intermediate/protein/concords/PR, babel_outputs/intermediate/protein/concords/metadata-PR.yaml ERROR snakemake.logging [2025-11-22T10:00:29+0000]: Error in rule get_protein_pr_uniprotkb_relationships, jobid: 146 [Sat Nov 22 05:00:29 2025] Error in rule disease_efo_ids: message: None jobid: 97 output: babel_outputs/intermediate/disease/ids/EFO ERROR snakemake.logging [2025-11-22T10:00:29+0000]: Error in rule disease_efo_ids, jobid: 97 [Sat Nov 22 05:00:29 2025] Error in rule get_ensembl: message: None jobid: 121 output: babel_downloads/ENSEMBL, babel_downloads/ENSEMBL/BioMartDownloadComplete ERROR snakemake.logging [2025-11-22T10:00:29+0000]: Error in rule get_ensembl, jobid: 121 Complete log(s): /projects/babel/runs/gaurav/babel-1.14-umls-level-0/.snakemake/log/2025-11-22T025642.543274.snakemake.log INFO snakemake.logging [2025-11-22T10:00:29+0000]: Complete log(s): /projects/babel/runs/gaurav/babel-1.14-umls-level-0/.snakemake/log/2025-11-22T025642.543274.snakemake.log WorkflowError: At least one job did not complete successfully. ERROR snakemake.logging [2025-11-22T10:00:29+0000]: WorkflowError: At least one job did not complete successfully.