Question: bam-readcounts: despite partial bam file get segfault
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gravatar for damien.biotpelletier
6.1 years ago by
Canada
damien.biotpelletier0 wrote:

Hi all,

I'm trying to run bam-readcount on a MacOS X 10.9.5 machine.

I'm aware that bam-readcount returns a segfault when asked to process an entire bam file, that's why I order it to run one chromosome at a time.

Here's a example command I tried:

bam-readcount -f 7Dref_all.fa 7dmerge_dedup.bam XV > 7dmerge_dedup_chrXV.readcount

I get the following warnings, along with an empty output file:

Minimum mapping quality is set to 0
Expect library: 7d in BAM
Segmentation fault: 11

Anything wrong with my syntax ? I played with it a bit, to no avail. Tried several different bam files, all of them are fine in other applications, as far as I can tell. They were generated by picard.

 

Thanks a million

 

Damien

sequencing alignment • 2.1k views
ADD COMMENTlink modified 4.3 years ago by Biostar ♦♦ 20 • written 6.1 years ago by damien.biotpelletier0

OP

Ran same command on ubuntu, worked perfectly. I'm confused. Installation went smoothly in both cases.

Any known issues with Mac OS X and bam-readcount ?

I can run on ubuntu just fine, but it'd be great if I could do it on Mac OS X, too.

ADD REPLYlink written 6.1 years ago by damien.biotpelletier0

Yes, for reasons currently unknown, bam-readcount always segfaults on modern versions of OS X (Yosemite and Mavericks). There is an open issue on github https://github.com/genome/bam-readcount/issues/12 which I will update when we get around to fixing it, but I don't have a timeline for when I will get to this.

ADD REPLYlink written 6.1 years ago by ernfrid210

Thank you very much for your answer.

I'll run on Linux, then, it's far from being impractical.

And thanks for getting this great tool out there. Very appreciated, and very useful.

ADD REPLYlink written 6.1 years ago by damien.biotpelletier0
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