8000 LongReads: Inefficient use of ressources in `me`-step · Issue #386 · imgag/megSAP · GitHub
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LongReads: Inefficient use of ressources in me-step #386

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BeneKenobi opened this issue May 6, 2025 · 0 comments
Open

LongReads: Inefficient use of ressources in me-step #386

BeneKenobi opened this issue May 6, 2025 · 0 comments
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@BeneKenobi
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In this step, modkit (and some samtools fixing afterward) is repeated a couple hundred times. Modkit runs for ~8 min and does not use the cores it gets allocated (because the chunks are so small?). This brings us to a runtime of 16 hours without using almost no resources at all:

Image

I think it would be better to call these in parallel to make use of given resources.
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