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filter-fasta.py runs out of memory #669

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terrycojones opened this issue Jan 25, 2019 · 0 comments
Open

filter-fasta.py runs out of memory #669

terrycojones opened this issue Jan 25, 2019 · 0 comments
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A command like this filter-fasta.py --quiet --fastq --idLambda 'lambda r: "-1 ".join(r.split(None, 1))' (or something simpler) runs out of memory (or causes SLURM to think so) on the csd3 cluster. It shouldn't. Somewhere there must be a leak or Python objects are not being garbage collected, etc. I've looked at this before, monitoring a long-running process using top and not seeing it grow, so I'm not sure what's going on.
@terrycojones terrycojones self-assigned this Jan 25, 2019
@terrycojones terrycojones changed the title filterFasta runs out of memory filter-fasta.py runs out of memory Jan 25, 2019
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