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McMahonLab / geodes

Diel transcriptomics of freshwater lakes
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Empty Phred scores in .sam files #10

Closed alexlinz closed 7 years ago

alexlinz commented 7 years ago

Each of my files has a few lines with "*" instead of a Phred score in the QUAL column (11). When htseq-count encounters these lines, it throws the error:

Error occured when processing SAM input (record #285895 in file GEODES002_nonrRNA.all.sam): object of type 'NoneType' has no len() [Exception type: TypeError, raised in _HTSeq.pyx:771]

The only thing I could find with a similar message is here: https://sourceforge.net/p/htseq/bugs/12/ and it seems to just skip those lines, if I'm understanding their code right.

There's only about 15-20 of these lines out of 500,000ish in each sam file, so I'm removing them for now. Is there a better way to deal with this? Why does this happen?

alexlinz commented 7 years ago

Switched from bwa to bbmap (using SAM version 1.3 instead of 1.4) and no longer have this issue.