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tpshea2claude
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Fix Skani OOM: dynamic mem_gb scaled to bin sizes
Replace fixed 16 GB with 32 + 4*size(bins) so light samples stay cheap and heavy samples (many/large bins) get enough headroom for the GTDB r226 marker hash table load. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
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wdl/tasks/MAG/Skani.wdl

Lines changed: 2 additions & 1 deletion
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@@ -33,6 +33,7 @@ task Skani {
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}
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Int disk_size = 20 + ceil(3.0 * size(skani_db_tgz, "GB")) + ceil(2.0 * size(bins, "GB"))
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Int mem_size = 32 + ceil(4.0 * size(bins, "GB"))
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command <<<
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set -euxo pipefail
@@ -69,7 +70,7 @@ task Skani {
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RuntimeAttr default_attr = object {
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cpu_cores: 24,
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mem_gb: 16,
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mem_gb: mem_size,
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disk_gb: disk_size,
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boot_disk_gb: 25,
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preemptible_tries: 2,

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