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biod / sambamba

Tools for working with SAM/BAM data
http://thebird.nl/blog/D_Dragon.html
GNU General Public License v2.0
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core dump in 0.5.5 and 0.5.8 #181

Closed RichardCorbett closed 8 years ago

RichardCorbett commented 8 years ago

Hi. When I try and merge some bisulfite novoalign bams I get a core dump. I've tried this on Centos5 and Centos 6 with the 2 versions above and I consistently get this error soon after the run begins.

xhost11 /projects/rcorbettprj2/novoAlignBioQC/A27712 $

/gsc/software/linux-x86_64/sambamba-0.5.5/sambamba_v0.5.5 merge -p A27712.bam ./*sorted.bam; Segmentation fault

any ideas?

RichardCorbett commented 8 years ago

Hmmm. I was able to run some other samples successfully. There is quite likely a problem with one of the bams I am trying to merge.

lomereiter commented 8 years ago

Does any of your files contain long reads (~10K bases)? They weren't handled properly until recently (#182).

RichardCorbett commented 8 years ago

Hi Artem, Nope, just 125bp illumina reads. I suspect one of the bams were truncated (we've had some network errors lately). I'll try re-running the alignment and see if that fixes things. It might take a few days (novoalign after all).

RichardCorbett commented 8 years ago

Hi Artem, As expected, having re-run the alignments allows me to successfully to merge/dupmark the bams. There must have been something wrong with my original bams.