filterBAM seg faults with A LOT of memory

Discussions about predicting genes with AUGUSTUS. Not covered here: WebAUGUSTUS and BRAKER1

Moderator: bioinf

Post Reply
User avatar
katharina
Site Admin
Posts: 531
Joined: Wed Nov 18, 2015 6:14 pm
Location: Greifswald
Contact:

filterBAM seg faults with A LOT of memory

Post by katharina »

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:

Code: Select all

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
User avatar
katharina
Site Admin
Posts: 531
Joined: Wed Nov 18, 2015 6:14 pm
Location: Greifswald
Contact:

Re: filterBAM seg faults with A LOT of memory

Post by katharina »

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

Code: Select all

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
User avatar
katharina
Site Admin
Posts: 531
Joined: Wed Nov 18, 2015 6:14 pm
Location: Greifswald
Contact:

Re: filterBAM seg faults with A LOT of memory

Post by katharina »

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
Post Reply