HMMSplicer "_scoreHalf" Error

[proteomania]

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

[proteomania]

Somehow I've found this error can be resolved by increasing the 2nd half anchor value. Any ideas?

[proteomania]

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.