Using profile slurm for setting default command line arguments. SNAKEMAKE ========= Date: 2026-07-15 03:46:12 Workflow ID: e379d330-fa62-48b2-ac8a-bf06608da1d4 Platform: Linux-5.14.0-427.70.1.el9_4.x86_64-x86_64-with-glibc2.34 Host: compute-13-1 User: gaurav Snakemake version: 9.23.1 Python version: 3.13.9 (main, Oct 14 2025, 21:29:44) [Clang 20.1.4 ] Command: /projects/babel/runs/gaurav/babel-1.18/.venv/bin/snakemake --profile slurm all_reports 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: 7d9670a395d9c1bfaaa4f0ccc57ce099 INFO snakemake.logging [2026-07-15T07:46:12+0000]: Workflow has started! Building DAG of jobs... INFO snakemake.logging [2026-07-15T07:46:12+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 [2026-07-15T07:46:17+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_1a84767d-2704-4ac1-83bd-7e3f9caa5c39 INFO snakemake.logging [2026-07-15T07:46:17+0000]: SLURM run ID: babel_1a84767d-2704-4ac1-83bd-7e3f9caa5c39 MinJobAge 300s (>= 120s). 'squeue' should work reliably for status queries. WARNING snakemake.logging [2026-07-15T07:46:17+0000]: MinJobAge 300s (>= 120s). 'squeue' should work reliably for status queries. Using shell: /usr/bin/bash INFO snakemake.logging [2026-07-15T07:46:17+0000]: Using shell: /usr/bin/bash Provided remote nodes: 50 INFO snakemake.logging [2026-07-15T07:46:17+0000]: Provided remote nodes: 50 Job stats: job count -------------------------- ------- generate_prefix_report 1 generate_cliques_table 1 generate_prefix_comparison 1 generate_prefix_table 1 all_reports 1 total 5 INFO snakemake.logging [2026-07-15T07:46:17+0000]: Job stats: job count -------------------------- ------- generate_prefix_report 1 generate_cliques_table 1 generate_prefix_comparison 1 generate_prefix_table 1 all_reports 1 total 5 Select jobs to execute... INFO snakemake.logging [2026-07-15T07:46:17+0000]: Select jobs to execute... Execute 1 jobs... INFO snakemake.logging [2026-07-15T07:46:17+0000]: Execute 1 jobs... No SLURM account given, trying to guess. WARNING snakemake.logging [2026-07-15T07:46:17+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 [2026-07-15T07:46:17+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 [2026-07-15T07:46:17+0000]: Unable to guess SLURM account. Trying to proceed without. Job 266 has been submitted with SLURM jobid 53591 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_prefix_report/53591.log). INFO snakemake.logging [2026-07-15T07:46:17+0000]: Job 266 has been submitted with SLURM jobid 53591 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_prefix_report/53591.log). [Wed Jul 15 04:02:48 2026] Finished jobid: 266 (Rule: generate_prefix_report) INFO snakemake.logging [2026-07-15T08:02:48+0000]: Finished jobid: 266 (Rule: generate_prefix_report) 1 of 5 steps (20%) done INFO snakemake.logging [2026-07-15T08:02:48+0000]: None Removing temporary output babel_outputs/duckdb/duckdbs/prefix_report.duckdb. INFO snakemake.logging [2026-07-15T08:02:48+0000]: Removing temporary output babel_outputs/duckdb/duckdbs/prefix_report.duckdb. Select jobs to execute... INFO snakemake.logging [2026-07-15T08:02:48+0000]: Select jobs to execute... Execute 3 jobs... INFO snakemake.logging [2026-07-15T08:02:48+0000]: Execute 3 jobs... Job 317 has been submitted with SLURM jobid 53599 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_cliques_table/53599.log). INFO snakemake.logging [2026-07-15T08:02:48+0000]: Job 317 has been submitted with SLURM jobid 53599 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_cliques_table/53599.log). Job 265 has been submitted with SLURM jobid 53600 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_prefix_table/53600.log). INFO snakemake.logging [2026-07-15T08:02:48+0000]: Job 265 has been submitted with SLURM jobid 53600 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_prefix_table/53600.log). Job 319 has been submitted with SLURM jobid 53601 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_prefix_comparison/53601.log). INFO snakemake.logging [2026-07-15T08:02:48+0000]: Job 319 has been submitted with SLURM jobid 53601 (log: /projects/babel/runs/gaurav/babel-1.18/babel_outputs/logs/rule_generate_prefix_comparison/53601.log). [Wed Jul 15 04:03:28 2026] Finished jobid: 317 (Rule: generate_cliques_table) INFO snakemake.logging [2026-07-15T08:03:28+0000]: Finished jobid: 317 (Rule: generate_cliques_table) 2 of 5 steps (40%) done INFO snakemake.logging [2026-07-15T08:03:28+0000]: None [Wed Jul 15 04:03:28 2026] Finished jobid: 265 (Rule: generate_prefix_table) INFO snakemake.logging [2026-07-15T08:03:28+0000]: Finished jobid: 265 (Rule: generate_prefix_table) 3 of 5 steps (60%) done INFO snakemake.logging [2026-07-15T08:03:28+0000]: None [Wed Jul 15 04:03:28 2026] Finished jobid: 319 (Rule: generate_prefix_comparison) INFO snakemake.logging [2026-07-15T08:03:28+0000]: Finished jobid: 319 (Rule: generate_prefix_comparison) 4 of 5 steps (80%) done INFO snakemake.logging [2026-07-15T08:03:28+0000]: None Select jobs to execute... INFO snakemake.logging [2026-07-15T08:03:28+0000]: Select jobs to execute... Execute 1 jobs... INFO snakemake.logging [2026-07-15T08:03:28+0000]: Execute 1 jobs... [Wed Jul 15 04:03:28 2026] localrule all_reports: input: babel_outputs/reports/content/compendia_report.json, babel_outputs/reports/check_compendia_files.done, babel_outputs/reports/check_synonyms_files.done, babel_outputs/reports/check_conflation_files.done, babel_outputs/reports/tables/prefix_table.csv, babel_outputs/reports/tables/cliques_table.csv, babel_outputs/reports/tables/mapping_sources_table.csv, babel_outputs/reports/tables/prefix_comparison.md output: babel_outputs/reports/reports_done jobid: 0 reason: Input files updated by another job: babel_outputs/reports/tables/prefix_comparison.md, babel_outputs/reports/tables/prefix_table.csv, 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 [2026-07-15T08:03:28+0000]: Rule: all_reports, Jobid: 0 INFO snakemake.logging [2026-07-15T08:03:28+0000]: Shell command: echo 'done' >> babel_outputs/reports/reports_done [Wed Jul 15 04:03:28 2026] Finished jobid: 0 (Rule: all_reports) INFO snakemake.logging [2026-07-15T08:03:28+0000]: Finished jobid: 0 (Rule: all_reports) 5 of 5 steps (100%) done INFO snakemake.logging [2026-07-15T08:03:28+0000]: None Job 53591.0 for rule 'rule_generate_prefix_report' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-15T08:04:09+0000]: Job 53591.0 for rule 'rule_generate_prefix_report' (python) has low CPU efficiency: 0.0%. Job 53599.0 for rule 'rule_generate_cliques_table' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-15T08:04:09+0000]: Job 53599.0 for rule 'rule_generate_cliques_table' (python) has low CPU efficiency: 0.0%. Job 53600.0 for rule 'rule_generate_prefix_table' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-15T08:04:09+0000]: Job 53600.0 for rule 'rule_generate_prefix_table' (python) has low CPU efficiency: 0.0%. Job 53601.0 for rule 'rule_generate_prefix_comparison' (python) has low CPU efficiency: 0.0%. WARNING snakemake.logging [2026-07-15T08:04:09+0000]: Job 53601.0 for rule 'rule_generate_prefix_comparison' (python) has low CPU efficiency: 0.0%. Efficiency report for workflow babel_1a84767d-2704-4ac1-83bd-7e3f9caa5c39 saved to babel_outputs/reports/slurm/slurm_efficiency_reports/efficiency_report_babel_1a84767d-2704-4ac1-83bd-7e3f9caa5c39.csv. INFO snakemake.logging [2026-07-15T08:04:09+0000]: Efficiency report for workflow babel_1a84767d-2704-4ac1-83bd-7e3f9caa5c39 saved to babel_outputs/reports/slurm/slurm_efficiency_reports/efficiency_report_babel_1a84767d-2704-4ac1-83bd-7e3f9caa5c39.csv. Complete log(s): /projects/babel/runs/gaurav/babel-1.18/.snakemake/log/2026-07-15T034608.507734.snakemake.log INFO snakemake.logging [2026-07-15T08:04:09+0000]: Complete log(s): /projects/babel/runs/gaurav/babel-1.18/.snakemake/log/2026-07-15T034608.507734.snakemake.log