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MikeAxtell / ShortStack

ShortStack: Comprehensive annotation and quantification of small RNA genes
MIT License
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Trouble with SOLiD reads #82

Closed BioFalcon closed 3 years ago

BioFalcon commented 5 years ago

Hi Mike,

I have been trying to run ShortStack using SOLiD reads, but it seems to be having trouble reading the reads on the get_read_s_aln subroutine, here is the last part of the log.

Adapter trimming input reads file Sample1.csfasta.gz with adapter CTGTAGGC Complete: 9711 out of 9994211 reads successfully trimmed
FATAL in sub-routine get_read_s_aln : Could not determine format of reads file ShortStack_Sample1/Sample1.c_trimmedsfasta.gz

Any idea of what might be the problem?

Thanks

MikeAxtell commented 5 years ago

Wow, SOLiD data. Haven't thought about SOLiD in many years and that part of the code base has not been maintained at all.

One thing I noticed from your output is a very small percentage of input reads that were successfully trimmed. Is that what you expected? It seems like an issue (although not one related to this bug).

I don't have any example SOLiD data to work with here. I think for me to properly de-bug this, I'd need some SOLiD data. Do you want to share yours (you could post on dropbox or whatever), and let me know what genome assembly you're working with? That way I could reproduce the bug here and try to fix it.

Thanks, Mike

On Wed, Sep 26, 2018 at 5:23 PM Francisco Falcon notifications@github.com wrote:

Hi Mike,

I have been trying to run ShortStack using SOLiD reads, but it seems to be having trouble reading the reads on the get_read_s_aln subroutine, here is the last part of the log.

Adapter trimming input reads file Sample1.csfasta.gz with adapter CTGTAGGC Complete: 9711 out of 9994211 reads successfully trimmed FATAL in sub-routine get_read_s_aln : Could not determine format of reads file ShortStack_Sample1/Sample1.c_trimmedsfasta.gz

Any idea of what might be the problem?

Thanks

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MikeAxtell commented 3 years ago

Will be dropping support for colorspace data altogether in the next major release.