merfin doesnt respect -threads option

[bredeson]

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]

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

[arangrhie]

@brianwalenz could you take a look?

[brianwalenz]

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]

Also with -polish as well.

Thanks for the tip!