Increase picard_markdup maxtime from 30 min to 4 h#48
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The picard_markdup rule has maxtime="30:00", which is insufficient for larger BAMs. In a 12-sample mouse run (paired, HISAT2, ~5-6 GB sorted BAMs), 3 of 12 samples hit the 30-min wall and were killed mid-write while MarkDuplicates was still streaming records. Because cluster_profile/config.yaml does not define a status script, the Snakemake driver did not detect the SLURM TIMEOUTs and never exercised restart-times: 5 - the pipeline silently hung at 89% with no log activity until manually investigated. Bumping to 4:00:00 covers BAMs we've observed in practice (successful runs took 19-28 min) with comfortable headroom; users can still tune lower for small datasets via the resources override. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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Summary
The
picard_markduprule inSnakefile(line 293) hasmaxtime="30:00", which is insufficient for larger BAMs and causes silent pipeline hangs.What we observed
On a 12-sample mouse run (paired-end, HISAT2, ~5–6 GB sorted BAMs), 3 of 12 samples hit the 30-minute wall and were killed mid-write while
MarkDuplicateswas still streaming records (last positions on chr19 etc., ~190M+ records written).Because
cluster_profile/config.yamldoes not define a status script, the Snakemake driver did not detect the SLURMTIMEOUTstates and never exercisedrestart-times: 5— the pipeline silently hung at 56/63 (89%) steps done with no log activity until investigated manually.Change
4 h is comfortably above what we've seen on real data (
picard_markdupjobs that succeeded on this run took 19–28 min) while leaving headroom for larger libraries. Users with small datasets can still override via--set-resourcesif they want tighter scheduling.Test plan
maxtime="4:00:00"— the 3 previously-timed-out markdups complete in ~25–30 minpicard_collectmetricsandmultiqcstill complete on the reruncluster_profile/so SLURMTIMEOUT/FAILEDstates are surfaced to Snakemake andrestart-timesactually fires🤖 Generated with Claude Code