merfin doesnt respect -threads option

Question

merfin doesnt respect -threads option

Closed this issue 2 years ago · 4 comments

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

Answer 1 · 2021-07-27T16:54:21.000Z

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

Answer 2 · 2021-07-28T18:22:59.000Z

@brianwalenz could you take a look?

Answer 3 · 2021-07-28T23:51:03.000Z

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.

Answer 4 · 2021-07-31T06:23:33.000Z

Also with -polish as well.

Thanks for the tip!