It would help if you could get a stack trace out of the core dump, or better still if this is something you can reproduce on public data then it'll give us a way of reproducing the errors locally.
I don't think we're aware of any known bugs in v1.2 merging. (At least I personally am not and I don't see issues on github for it.) James On Mon, Jun 15, 2015 at 04:46:12PM +0000, Lo, Chien-Chi wrote: > Samtools (v1.2) merge doesn't output any file of my two bam file and no > message throwing out. It just hang there and reserved ~2.0g memory. However, > 0.1.18 version finish the merging in ~2 mins. > > The two sorted bam files are 449M and 448M in size. > > v1.2 > samtools merge out.bam tmp/tmp.0000.bam tmp/tmp.0001.bam > > Version: 0.1.18 > samtools merge out.bam tmp/tmp.0000.bam tmp/tmp.0001.bam > > real 2m26.713s > user 2m20.100s > sys 0m6.530s > > Any insight or similar issue with error message from community? > > Thanks, > Chienchi > > > From: Giuseppe Aprea > <giuseppe.ap...@gmail.com<mailto:giuseppe.ap...@gmail.com>> > Date: Friday, February 6, 2015 at 10:13 AM > To: > "samtools-help@lists.sourceforge.net<mailto:samtools-help@lists.sourceforge.net>" > > <samtools-help@lists.sourceforge.net<mailto:samtools-help@lists.sourceforge.net>> > Subject: [Samtools-help] samtools merge > > Hi all. > > Is there any known limitation for bam merging? > > I am trying to merge 4 sorted bam files with samtools (v 1.2) but I get the > following error: > > > 39656 Segmentation fault (core dumped) samtools merge merging.bam > *.sorted.realigned.nodup.sorted.bam > > > *.sorted.realigned.nodup.sorted.bam are 4 files with sizes: 6.1G, 6.2G, 3.9G > and 4.0G > > > Any suggestion, please? > > > Thanks in advance, > > Giuseppe > ------------------------------------------------------------------------------ > _______________________________________________ > Samtools-help mailing list > Samtools-help@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/samtools-help -- James Bonfield (j...@sanger.ac.uk) | Hora aderat briligi. Nunc et Slythia Tova | Plurima gyrabant gymbolitare vabo; A Staden Package developer: | Et Borogovorum mimzebant undique formae, https://sf.net/projects/staden/ | Momiferique omnes exgrabure Rathi. -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. ------------------------------------------------------------------------------ _______________________________________________ Samtools-help mailing list Samtools-help@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/samtools-help
