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sc932 / ALE

Assembly Likelihood Estimator
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ALEhelpers.c:84: getQtoLogP: Assertion `idx >= 0 && idx < 63' failed. #5

Closed sauloal closed 10 years ago

sauloal commented 11 years ago

Dear developer, I've found this error. My guess is: my bam file is a merging of 3 libraries of different sizes (170, 500 and 2k). Am I correct? if so, isn't it possible to make ALE able to deal with that? Regards

Found FR sample avg insert length to be 385.974038 from 690198042 mapped reads Found FR sample insert length std to be 535.046583 stddev is too large (> 0.666700 * insertLength). This orientation is invalid There were 760420402 total reads with 0 proper mates, 4263 proper singles, 760416139 improper reads (39395299 chimeric). (0 reads were unmapped) Saved library parameters to sp3.ale.param Computing read placements and depths ALE: ALEhelpers.c:84: getQtoLogP: Assertion `idx >= 0 && idx < 63' failed.

sauloal commented 11 years ago

Confirmed. When running with only one library size ALE does work.

sc932 commented 10 years ago

It looks like ALE is encountering a Q score that is out of range. I'm not sure what you are using to generate these libraries, it may be possible that the quality score is encoded in a format that ALE is not expecting.

If you run ./ALE --qOff this allows you to set a custom Q score offset. Illumina, PACB and other sequencing technologies use different values (common ones are 33 (default) or 64).