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Problem with -r Random

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This topic contains 4 replies, has 2 voices, and was last updated by  Colin Hercus 8 years, 6 months ago.

Viewing 5 posts - 1 through 5 (of 5 total)
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  • April 1, 2016 at 10:43 pm #1857

    top1214
    Participant

    Running this command:
    $ novoalign -r Random -d D_rerio_RNA.nix -f run_1826_s_7_withindex_sequence.txt_TAATCATAA.fq > test.starve1.novout
    generates this output:

    Assertion failed: (tgt[tposn] != '\0'), function rptmismatch, file src/rptNative.cc, line 239.
Abort trap: 6

    It seems to sort of be working, as the output file includes several tags with the R in the 5th column.

    I tried -r All, and that seems to work fine (at least, it didn’t die as quickly; I did not run it to completion).

    April 2, 2016 at 12:27 am #1858

    Colin Hercus
    Keymaster

    What version of Novoalign are you using?

    April 4, 2016 at 1:49 am #1859

    Colin Hercus
    Keymaster

    There is an issue in V3.04 where changes we made to support alternate scaffolds of GRC38 could result in a n invalid CIGAR for SAM format reports. The problem was caused by a failure to detail the correct alignment when using -r Random or -r All and could affect Native report format as well so as first step if you are using V3.04 could you upgrade to V3.04.04 which has a fix.

    April 4, 2016 at 4:51 pm #1860

    top1214
    Participant

    I was running 3.04.01, upgraded, and it seems to be working fine.

    April 5, 2016 at 12:47 am #1861

    Colin Hercus
    Keymaster

    That’s excellent. Thanks for the update.

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