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  • amos bank-transact show err

    Anyone tell me why ?

    running:

    bank-transact -c -b S1-S2.bnk -m S1-S2.afg

    log file show:

    AFG ..ERROR: Sequence and quality lengths disagree
    could not parse 'RED' message with iid:1, message ignored
    ERROR: Sequence and quality lengths disagree
    could not parse 'RED' message with iid:2, message ignored
    ERROR: Sequence and quality lengths disagree
    ERROR: Sequence and quality lengths disagree
    could not parse 'RED' message with iid:4, message ignored
    ERROR: Sequence and quality lengths disagree
    could not parse 'RED' message with iid:5, message ignored
    ERROR: Sequence and quality lengths disagree
    could not parse 'RED' message with iid:6, message ignored
    ERROR: Sequence and quality lengths disagree
    could not parse 'RED' message with iid:7, message ignored
    ERROR: Sequence and quality lengths disagree
    could not parse 'RED' message with iid:8, message ignored
    ERROR: Sequence and quality lengths disagree
    could not parse 'RED' message with iid:9, message ignored
    ERROR: Sequence and quality lengths disagree
    could not parse 'RED' message with iid:10, message ignored
    ERROR: Sequence and quality lengths disagree
    could not parse 'RED' message with iid:11, message ignored
    ERROR: Sequence and quality lengths disagree
    could not parse 'RED' message with iid:12, message ignored
    ERROR: Sequence and quality lengths disagree
    could not parse 'RED' message with iid:13, message ignored
    ERROR: Sequence and quality lengths disagree
    could not parse 'RED' message with iid:14, message ignored
    ERROR: Sequence and quality lengths disagree
    could not parse 'RED' message with iid:15, message ignored
    .
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    Last edited by bah; 02-22-2011, 01:35 PM.

  • #2
    afg file :

    {RED
    iid:8680569
    eid:ChrX_ctg150561
    seq:
    CTAGCCTCTGTACCTTTGCAGTAATTTAAAGTGTTAGCCAATGTGAGCATTCTAAGTATG
    TAATTCTCTTTCTGTGTCATTTGGACTATTCCAATACTCGGTGTGTCAGTAAACGTTGTA
    AAATTGTCTT
    .
    qlt:
    NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
    NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
    NNNNNNNNNN
    .
    frg:24678678
    clr:0,130
    }

    Comment


    • #3
      Did you changed the iid?? Perhaps that is the error when you're running the bank-transact. The programm not founded the iid to execute the parsing. Change the iid by 1, 2, 3, and so on. A little script in PERL can handle with this. But what is the size of the afg file?? The assembly file was generated by what assembler??


      Best regards,
      André

      Comment


      • #4
        yes, you are right. Each read name in the fasta file have two whitespace which lead to err. I had renamed them , then reproduced AFG file and the err was disappear.
        Thanks
        Hengxing

        Comment


        • #5
          We're welcome

          Comment

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