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  • sandhya
    replied
    Posting the reply from Novocraft's forum for this thread from zayed
    **********
    On Tue 14 of Sep., 2010 12:48 MYT, by zayed
    OK, it looks as though you may not have built your database index before doing the alignment step.

    First ensure that you index your fasta database sequence(s) using novoindex:

    ./novoindex HIV1.nix HIV1.fas



    Now do the alignment as before

    ./novoalign -F STDFQ -r0.2 -d HIV1.nix -f read1.fq read2.fq > paired.novoalign
    ***************
    And it worked

    Leave a comment:


  • Novoalign error message:- Interrupted..11 Obtained 7 stack frames.

    Hi,

    I receive the following error while aligning paired-end reads using novoalign.

    Interrupted..11
    Obtained 7 stack frames.
    0x400348
    0x4003cd
    0x43d860
    0x40df50
    0x400d07
    0x4d03f6
    0x400239

    The command I ran was ./novoalign -F STDFQ -r0.2 -d HIV1.fas -f read1.fq read2.fq > paired.novoalign

    If this is an OS/CPU related problem with a fix or if there is anything else I need to check please advise.

    P.S - I have posted the same query in Novocraft's forum but since there has not been a reply I decided to post it here as well. Sorry for cross-posting.

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