#263 Bowtie2 version 2.0.3 crashes silently on HiSeq data

closed-accepted
nobody
bowtie (178)
7
2013-01-09
2012-12-27
No

Hi,

I have had bowtie2 crash repeatedly on HiSeq data, both paired end and single end. Each time, no errors are reported, and the SAM file is truncated. I am including a sample data set, which has this problem reproducibly (forward and reverse reads from a large experiment chopped up by split): https://dl.dropbox.com/u/5275622/test.tar.gz

I've tried changing threading and mapping algorithms, but no luck. This is a rare and insidious error.

Any help would be appreciated!

Thank you,

Sasha

Discussion

  • Alexander Mikheyev

    • priority: 5 --> 7
     
  • Ben Langmead

    Ben Langmead - 2013-01-08

    I fixed a bug very much like the one you report in version 2.0.5. Could you please re-test with that version and let me know what happens? If not, I will certainly look further into this.

    Best,
    Ben

     
  • Ben Langmead

    Ben Langmead - 2013-01-08
    • status: open --> pending
     
  • Alexander Mikheyev

    Yep, this seems to have fixed the problem.

    Thank you!

     
  • Alexander Mikheyev

    • status: pending --> closed-accepted
     

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