segmentation fault with wham-bam

[sahilseth]

I am seeing a segmentation fault:

$wham_dir/bin/WHAM-BAM -m 2 -q 15 -p 10 -x 4 -t $tbam -f $reflib \
  1> ${oprefix}_wham.vcf 2> ${oprefix}_wham.out

Aborted (core dumped)

less ${vcf}.out
INFO: WHAM-BAM requires : 2 soft-clips to score breakpoint
INFO: WHAM-BAM skip soft-clips with average base quality below: 15
INFO: WHAM-BAM skip soft-clips with mapping quaity below: 10
INFO: OpenMP will roughly use 4 threads
INFO: target bams:

....

INFO: running region: 1:65000500-66000500
INFO: running region: 1:66000500-67000500
INFO: running region: 1:69000500-70000500
INFO: running region: 1:70000500-71000500
INFO: running region: 1:67000500-68000500
INFO: running region: 1:71000500-72000500
src/seqan/core/include/seqan/basic/basic_exception.h:236 FAILED!  (Uncaught exception of type St12out_of_range: basic_string::substr)

I am primarily running for SVs.

Thanks!

[zeeev]

@sahilseth Sorry for the late reply. Can you send me a small test bam?

[sahilseth]

Hi Zeev,

It seems to work well for bwa mem bams, but not star aligned (RNA seq) bams. These are MD Anderson internal samples - don't have permission to share...

On Apr 19, 2016, at 11:23 AM, Zev Kronenberg [email protected] wrote:

@sahilseth Sorry for the late reply. Can you send me a small test bam?

— You are receiving this because you were mentioned. Reply to this email directly or view it on GitHub

[zeeev]

@sahilseth Thanks for reporting the bug. I understand protecting your data. Is there no chance of sharing a tiny slice that generates the same error?

[sahilseth]

Wish they were cell lines and not patient samples - IRB restriction. If I see the same error with other samples, will contact you.

One a side note, I was wondering if SV classifier supports translocations? I only got DEL, INV etc. no ITX or CTX.

Thanks!