concoct in metawrap binning module - use all available threads instead of requested

Question

[shevch2009]

Hello, all!

I am trying to use metawrap and encountered an issue.

The code:

metawrap binning -o /pathtofolders/CONCOCT -t 16 -a /pathtofolders/contigs.fa --concoct /pathtofolders/CLEAN_READS_metawrap/*fastq

And I can see that it uses all available threads on the server, but we are not allowed to do that.

I can't find any explanation, there is a similar question on the concoct github page without an answer.

Also, one post says- CPU usage can be limited by setting the maximum number of threads via the OMP_THREAD_LIMIT environmental variable, but ideally the CONCOCT script should handle it without further user intervention.

I also don't think that posting this issue on metawrap github page will get the answer, because there are many unanswered posts.

Metabat2 and maxbin2 work perfectly, but concoct seems to have a bug.

I can't understand how to fix it!

I would be grateful for any help! Thanks, Alla

Answer 1

[GenoMax]

but ideally the CONCOCT script should handle it without further user intervention

That probably refers to threads the application is able to see (which would be the max available on server) and that is what must be happening in your case.

Set the environmental variable as suggested and see if that helps. This would need to be done in terminal you are running the code from or via a script if you are using a job scheduler. For bash shell

OMP_THREAD_LIMIT=N
export OMP_THREAD_LIMIT

Replace N with a number you are allowed to use.

[shevch2009]

Thank you for your suggestion! I will try it :)

Best, Alla

[shevch2009]

It looks like it's working, but before finishing the process concoct still takes all available threads for a several seconds, and then it's done. Really strange.