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Out of memory when using freebayes-parallel #312

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jwickes opened this Issue Aug 17, 2016 · 1 comment

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jwickes commented Aug 17, 2016

I have a sample of 1281 BAM files that I've been trying to process though many of the threads for freebayes are getting 'killed'.

I've been calling them using freebayes-parallel over regions of 1 million.
freebayes-parallel ref.fa.1M.regions 32 -f ref.fa -L bamlist>output.vcf

Another thing to note is that I had to add a --gnu flag to the freebayes-parallel script to get it to work.

Thanks for the help!

@jwickes jwickes closed this Aug 18, 2016

@ekg

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ekg commented Aug 21, 2016

It might help a lot to reduce the memory usage by merging the BAM files
using samtools or Picard first. It looks like the BamTools API is not very
memory efficient with many files.

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Closed #312 #312.


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