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Out of memory when using freebayes-parallel #312

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


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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.

On Thu, Aug 18, 2016, 20:17 jwickes wrote:

Closed #312 #312.

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