AUGUSTUS Forum

Posted: **Thu Nov 19, 2015 7:33 pm**

Originally posted in the old forum by Philipp Schiffer on 28.01.2014 - 14:25
Hi everybody,
I am running the filterBAM module as described here: http://bioinf.uni-greifswald.de/bioinf/ ... Aseq.GSNAP.
Thus I do:

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filterBam --uniq --paired --in rnaseq.ss.bam --out rnaseq.f.bam

When I ran it on several bam files in parallel it seg faulted. On error message indicated insufficient virtual men (this is on a 48Gig machine). So rerunning a single process now I note that it eats up more and more memory while reading in the READS. Could anybody give an indication of how the process scales? Is there a way to calculate how much mem I will need for a given number of READS in the sam/bam?
Just wondering if I should move this step to a cluster where I might use 120Gigs or even more.
Thanks
Philipp

Posted: **Thu Nov 19, 2015 7:33 pm**

by Philipp Schiffer on 28.01.2014 - 15:32
it died again

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Virtual memory exhausted. 
terminate called after throwing an instance of 'std::bad_alloc'
  what():  std::bad_alloc
[1] 7685 abort ~/bioProgs/augustus-3.0.1/auxprogs/filterBam/bin/filterBam --uniq --paired --in Ju0II_UNclean_shuf.gsnap.JU765_velvet_16k13.scb.500bp.fna.masked.sorted.s.bam --out Ju0II_UNclean_shuf.gsnap.JU765_velvet_16k13.scb.500bp.fna.masked.sorted.s.f.bam --verboseq

Posted: **Thu Nov 19, 2015 7:34 pm**

by Philipp Schiffer on 29.01.2014 - 10:23
solved
Hi!
Think I solved the issue. There was a problem with the READS not being indexed with -1/-2, which I guess will give a problem with filterBam.
Thanks!
Philipp

AUGUSTUS Forum

filterBAM seg faults with A LOT of memory

filterBAM seg faults with A LOT of memory

Re: filterBAM seg faults with A LOT of memory

Re: filterBAM seg faults with A LOT of memory