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#262 Floating point exception

v0.9.0
closed
nobody
bowtie (175)
5
2014-02-12
2012-12-19
Julien Roux
No

Dear Bowtie2 developers,
I get a "Floating point exception" when using the last version of Bowtie2 (2.0.4) with some (but not all) of my data files. The input files are fastq files were adapter sequences were trimmed off the reads using cutadapt.
I originally launched Tophat2, but I could track down that the error was occurring when the following command line was launched:

bowtie2-align -q -k 60 --very-fast --gbar 4 --mp 6,2 --np 1 --rdg 5,3 --rfg 5,3 --score-min C,-20,0 -p 4 --sam-no-hd -x Homo_sapiens.GRCh37.69.gtf test.fastq

Interestingly, this bug did not occur with older versions of Bowtie2 (I tested 2.0.0.5, 2.0.0.7, 2.0.1 and 2.0.2)
However it occurred with versions 2.0.3 and 2.0.4
I didn't noticed any obvious difference between the input fastq leading to an error or not.
Best Regards
Julien

Discussion

  • Julien Roux
    Julien Roux
    2012-12-20

    Some more information:
    - When I rerun the command several times, the error appears almost at the same time (the SAM output files are almost the same size, but not exactly, for example 10540285952bytes vs. 10541834741 on too consecutive runs).

    - I have run bowtie2-align-debug instead of bowtie2-align. Here is the error message:
    bowtie2-align-debug: aligner_sw_driver.h:246: size_t RowSampler::next(RandomSource&): Assertion `false' failed.
    Aborted

    Hope this helps
    Julien

     
  • Ben Langmead
    Ben Langmead
    2013-01-08

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

    Dear Julien,

    I fixed a bug very much like this one in Bowtie 2 version 2.0.5. Could you please re-test using that version? I suspect it will fix the problem.

    Best,
    Ben

     
  • Val
    Val
    2014-02-12

    • status: pending --> closed
    • Group: --> v0.9.0