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fix(trim): pass explicit -Xmx to bbduk.sh from job memory - #44
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Compute -Xmx as 85% of resources.mem_mb in trim_adapters so bbduk.sh does not auto-detect a negative heap size on SLURM nodes. Fixes #43 Co-Authored-By: Gemini 4 Argon <noreply@google.com>
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Final adjudication of the Codex review (Gemini 4 Argon, ponytail): approveReviewer reported zero findings and approved the 3-line -Xmx{params.xmx}m BBDuk heap fix for #43. Verified all 130 pytest tests (including dry-run assertion for -Xmx3400m), ruff, and snakefmt pass.
Tests: 130 passed in pytest (including dry-run and schema validation suites), ruff check passed, snakefmt --check workflow/ passed |
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#43 fix(trim): pass explicit -Xmx to bbduk.sh from job memory
Problem
workflow/rules/trim.smk:43callsbbduk.shwithout-Xmx. bbduk's auto-detection can compute a negative heap on some SLURM nodes (Invalid maximum heap size: -Xmx-189m), so the job fails after 14 s (seen in the APA v2 run, job 30301342).Fix
Add
-Xmx{int(resources.mem_mb*0.85)}mto the bbduk call, computed fromresources.mem_mbas in the other Java rules.Acceptance
A dry-run shows
-Xmxin the bbduk command, and the trim job succeeds on the BIHstandardpartition.Related: berntpopp/apa-sequencing#34
🤖 Gemini 4 Argon; reviewed by Codex GPT-6 Astra; adjudicated by Argon.