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reshape default mem for depletion tasks #67

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dpark01 opened this issue May 14, 2020 · 1 comment · Fixed by #74
Closed

reshape default mem for depletion tasks #67

dpark01 opened this issue May 14, 2020 · 1 comment · Fixed by #74

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@dpark01
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dpark01 commented May 14, 2020

Until we replace Picard FilterSamReads upstream, for the short term, we should increase default mem allocation to depletion steps.

Currently, the deplete_taxa and filter_to_taxon tasks are allocated 8 cores & 15GB CPU (both GCE & DNAnexus). May want to consider 8 core 32GB (mem2_ssd1_v2_x8 / n1-highmem-8).

On the kraken-side, the filter_bam_to_taxa task is currently 2-core 7GB but we may want to bump to 2-core 13GB (n1-highmem-2 / mem3_ssd1_v2_x2)

@dpark01
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dpark01 commented May 18, 2020

Actually, filter_bam_to_taxa probably doesn't need more RAM since it's likely giving enough to Picard, but deplete_taxa is only giving 50% RAM to the JVM. Maybe we should just bump that fraction a bit

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