libgomp: Thread creation failed: Resource temporarily unavailable

[Vidhu Joshi]

Hi,

I am completing the PreFASTQC on ~350 million 151bp fwd and rev reads sequenced on the Illumina platform.

I ran the 'preprocess' function, followed by the sga index function which yielded 1) a combined fasta file and 2) a bwt file. 

However, the indexing step exited prematurely with the following error/message:

Building index for cam4_genome.fastq in memory using ropebwt

done bwt construction, generating .sai file

libgomp: Thread creation failed: Resource temporarily unavailable

Please advise. Any guidance would be much appreciated.

Regards,

Vidhu

[Jared Simpson]

Hi Vidhu,

How many threads did you try to run with? Is it possible you ran out of memory?

Jared

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[Vidhu Joshi]

Hi Jared,

First off, thank you so much for your prompt reply.

I was using 20 threads x 18G of memory per thread x 1G of stack memory.

I have not run into this error before on the cluster.

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[Vidhu Joshi]

I am contemplating converting my .fastq from the previous preprocess step to a FASTA, indexing that with BWA, and plugging it back into the third preprocess step (preqc).

What are your thoughts on this?

Kindly let me know, and thanks again for all your guidance.

Warm regards,

Vidhu

[Jared Simpson]

Hi Vidhu,

SGA and BWA use different bwt structures, so that won't work.

1GB of stack memory per thread sounds excessive, I suggest trying 8 threads with 32M of stack memory per thread.

Jared

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[Vidhu Joshi]

Hi Jared,

Again, thank you very much for the quick response.

I may as well ask now -- do any of the steps up until (and including) scaffolding require more than 10-20 threads x 18G memory? Is 32M of stack sufficient for each step?

If 8 threads x 32M stack yields the same error, what could be an alternative solution? 

My confusion is that the process generated a .bwt index file but failed when generating the .sai file.

Please advise, and thanks again for all your guidance.

[Vidhu Joshi]

Hi Jared,

Using fewer threads and less stack memory (as you advised) did the trick!

Thank you for your guidance!

Vidhu

[Jared Simpson]

Great, glad it helped.

Jared

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