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molikd / otb

Only The Best (Genome Assembly Tools)
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memory limits with hifiasm #22

Closed molikd closed 2 years ago

molikd commented 2 years ago

large datasets can currently cause out of memory errors while running hifiasm, limit (in part) with -f

molikd commented 2 years ago

hotfix on usda systems is to reduce cores utilized by hifiasm by half.

molikd commented 2 years ago

same as chhylp123/hifiasm/issues/93 and chhylp123/hifiasm/issues/239

what's going on here is that because of the number of sequences we are running out of memory on the machine.

molikd commented 2 years ago

my thoughts so far are to change “-f” (default is 37, higher could reduce memory useage) and reduce the threads used by hifiasm by some percentage, as most HPC scale memory with cores, and we want to over provision memory

github-actions[bot] commented 2 years ago

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