filterBAM seg faults with A LOT of memory
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:
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
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
Just wondering if I should move this step to a cluster where I might use 120Gigs or even more.
Thanks
Philipp