merfin doesnt respect -threads option

arangrhie / merfin

Evaluate variant calls and its combination with k-mer multiplicity

Apache License 2.0

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merfin doesnt respect -threads option #8

Closed bredeson closed 1 year ago

bredeson commented 3 years ago

Hi!

FYI, I'm running merfin -dump -threads 8 at the moment, and it is currently running the meryl count step on the genome sequence fasta with 16 threads. Is this a bug?

Best, Jessen

bredeson commented 3 years ago

Ah, and the -hist function does this as well.

arangrhie commented 3 years ago

@brianwalenz could you take a look?

brianwalenz commented 3 years ago

It looks like the threads parameter doesn't propagate to the meryl subprocess. A quick workaround is to set environment variable OMP_NUM_THREADS to what you want.

The code has been updated to fix this, too.

bredeson commented 3 years ago

Also with -polish as well.

Thanks for the tip!