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  • Bowtie2 error "Error reading _offs[] array"

    I've used Bowtie2-build to make 2 indexes of the same genome (mm9). The first index uses all default settings for Bowtie2-build. The second index uses custom settings that should hopefully make the alignment process faster:

    --bmaxdivn 2 instead of 4
    --dvc 256 instead of 1024
    --offrate 2 instead of 5
    --ftabchars 14 instead of 10

    Both indexes build successfully. The default index aligns successfully. When I try to do the same alignment but using the custom index I get an error:

    Code:
    "Error reading _offs[] array: 4092, 2620353516"
    and then,

    Code:
    "Error: Encountered internal Bowtie 2 exception (#1)"
    Then Bowtie2 exits. What what does this error message mean?

    [Edit] I made another index using:

    --bmaxdivn 3
    --dvc 256
    --offrate 3
    --ftabchars 12

    And it seems to be working (it is currently aligning). So either the particular custom settings I used in the first one caused the problem, or something went wrong during the build process. I will try remaking the first custom index.
    Last edited by biznatch; 09-05-2013, 09:16 AM.

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