#262 Floating point exception

bowtie (178)
Julien Roux

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,, 2.0.1 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 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.

    Hope this helps

  • 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.


  • Val

    Val - 2014-02-12
    • status: pending --> closed
    • Group: --> v0.9.0

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