On 15 Jun 2015, at 17:46, Lo, Chien-Chi <chien...@lanl.gov> 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.
Do your bam files have many many headers? Samtools 1.2 merge could run for a
very long time on such headers on some platforms [1]; thanks to Nathan Weeks,
this problem has been fixed and the next samtools release should merge such
files as fast as 0.1.x samtools.
Giuseppe Aprea <giuseppe.ap...@gmail.com> wrote previously:
> 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
Giuseppe's problem appears to be different, and it would indeed be useful to
see a stack trace.
John
[1] https://github.com/samtools/samtools/pull/337
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