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  • proteomania
    Member
    • Sep 2010
    • 11
    #1

    HMMSplicer "_scoreHalf" Error

    Hi all,

    Recently I came across a "_scoreHalf" error in HMMSplicer for several, but not all, datasets. All my datasets are 100nt single end. The input fastq was generated from unaligned reads after bowtie mapping. The error message looks like this.

    06:49:53 04/19/11: Running HMM and matching second half
    files combined
    Invalid input to _scoreHalf
    AGACGATGAAGAAGATGAT
    AGACGATGATGAATTT
    HHFHFHHHHHHHHHHHHHH
    Traceback (most recent call last):
    File "/Volumes/A_MPro2TB/softwareForNGS/myPerlScripts/pipeLines/allTheWayHomeRunner/resources/scripts/HMMSplicerScripts/runHMMSAMOut.py", line 927, in <module>
    sys.exit(main(None))
    File "/Volumes/A_MPro2TB/softwareForNGS/myPerlScripts/pipeLines/allTheWayHomeRunner/resources/scripts/HMMSplicerScripts/runHMMSAMOut.py", line 322, in main
    readLength, numMMinSeed, isLargeGenome, logfile, qualityFormat, deleteTmp)
    File "/Volumes/A_MPro2TB/softwareForNGS/myPerlScripts/pipeLines/allTheWayHomeRunner/resources/scripts/HMMSplicerScripts/runHMMSAMOut.py", line 730, in runHMM
    maxIntron, readLength, True)
    File "/Volumes/A_MPro2TB/softwareForNGS/myPerlScripts/pipeLines/allTheWayHomeRunner/resources/scripts/HMMSplicerScripts/junctionHMM.py", line 980, in rescueMultipleSeeds
    multiplier)
    File "/Volumes/A_MPro2TB/softwareForNGS/myPerlScripts/pipeLines/allTheWayHomeRunner/resources/scripts/HMMSplicerScripts/junctionHMM.py", line 675, in _calculateScore
    scoreSecond = _scoreHalf(readSecond, genomeSecond, qualSecond)
    File "/Volumes/A_MPro2TB/softwareForNGS/myPerlScripts/pipeLines/allTheWayHomeRunner/resources/scripts/HMMSplicerScripts/junctionHMM.py", line 718, in _scoreHalf
    raise hmmErrors.UnexpectedException("Invalid input into _scoreHalf")
    hmmErrors.UnexpectedException: Invalid input into _scoreHalf

    I grepped "AGACGATGAAGAAGATGAT" from the fastq and it seems to be coming from a gene with internal repeat.

    Any ideas?

    Thanks in advance.

    Chung
    Tags: None
  • proteomania
    Member
    • Sep 2010
    • 11
    #2
    Somehow I've found this error can be resolved by increasing the 2nd half anchor value. Any ideas?

    Comment

    • proteomania
      Member
      • Sep 2010
      • 11
      #3
      The problem was identified. The end of the second half of the junction somehow fell beyond the contig and the extracted contig sequence is shorter than the actual read seq and that create the problem. Disable the hmmErrors.UnexpectedException("Invalid input into _scoreHalf") of in _scoreHalf solves the problem.

      Comment

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