#240 Bowtie2 crashes silently

v0.9.0
closed
nobody
None
5
2014-07-23
2012-09-12
Ka Ming Nip
No

Hello,

I have been aligning reads to transcriptome assemblies with bowtie2-beta7 a few times. My experiences with bowtie2 have been great so far. However, bowtie2 crashed silently (with core-dumps) for one of my datasets.

This is the command that I used:
bowtie2 -a --fast -q -p 12 --score-min L,0,0 -x $contigs -1 $read1 -2 $read2 -S $output.sam

I have also run bowtie2 without the score-min function, but it also crashed.

I ran the same command again in debug mode and I got this message:
bowtie2-align-debug: aligner_sw_driver.h:246: size_t RowSampler::next(RandomSource&): Assertion `false' failed.

There were no errors from bowtie2-build.

Thanks,
Ka Ming

Discussion

  • Ben Langmead

    Ben Langmead - 2012-12-14
    • status: open --> pending
     
  • Ben Langmead

    Ben Langmead - 2012-12-14

    Dear Ka Ming,

    Does the latest version of Bowtie 2 still crash like this?

    Best,
    Ben

     
  • Val

    Val - 2014-07-23

    I assume the latest versions are working for this case now.

     
  • Val

    Val - 2014-07-23
    • status: pending --> closed
    • Group: --> v0.9.0
     

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