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fix: reduce sentmm2 sort_thread_mem and mbuffer to fit Slurm mem
sort_thread_mem 4G * 32 threads = 128GB + mbuffer 128GB = 256GB, exceeding the 200GB Slurm mem_mb allocation. minimap2 streams slower than Sentieon BWA, so mbuffer fills up and OOMs the job, causing 'samtools sort: truncated file'. Changed: - sort_thread_mem: 4G -> 3G (32 * 3G = 96GB ceiling) - mbuffer: 128G -> 32G (plenty for I/O smoothing) - Total realistic peak: ~140-150GB, fits in 200GB allocation
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config/day_profiles/slurm/templates/rule_config.yaml

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -136,9 +136,9 @@ sentmm2_align_sort:
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minimap2_threads: 160
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sort_threads: 32
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mem_mb: 200000
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sort_thread_mem: "4G"
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sort_thread_mem: "3G"
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minimap2_opts: " -ax map-hifi "
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mbuffer: " | mbuffer -m 128G -q -s 2M "
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mbuffer: " | mbuffer -m 32G -q -s 2M "
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constraint: ""
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strobe_align_sort:

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