merfin doesnt respect -threads option
Closed this issue · 4 comments
bredeson commented
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
Ah, and the -hist
function does this as well.
arangrhie commented
@brianwalenz could you take a look?
brianwalenz commented
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
Also with -polish
as well.
Thanks for the tip!