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BIMSBbioinfo / pigx_bsseq

bisulfite sequencing pipeline from fastq to methylation reports
https://bioinformatics.mdc-berlin.de/pigx/
GNU General Public License v3.0
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Tests fail on bwameth_align_trimmed #161

Open Blosberg opened 4 years ago

Blosberg commented 4 years ago

Current tests with sample_sheet in tests break on bwameth_align_trimmed.

Logfile says

Exception: bad or empty fastqs

Seems reminiscent of this issue, but happening upstream of the samtools view.

alexg9010 commented 4 years ago

HI @Blosberg ,

Nice to hear from you, hope you are doing well :)

Could you verify that the pipeline is using the latest versions of bwameth? Maybe check in the generated config.json that the version is >= 0.2.2, which is the version I used for testing.

Best, Alex

Blosberg commented 4 years ago

Hi Alex. All is well 👍

$bwa-meth.py --version returns: bwa-meth.py 0.2.2

I noticed that the shortened fasta reference has been removed from the repo at /tests/genome/ --are tests now aligning against the full hg19 (somewhere outside of /tests/)?

alexg9010 commented 4 years ago

Oh, I forgot to add the sample.fasta to the repo.

I'll fix that.

Blosberg commented 4 years ago

Hi Alex. Thanks for adding sample.fasta to the repo. I'm fine with the name (so ignore the other comment), but the error that is encountered on rule bwameth_align_trimmed is unchanged: command exits with non-zero status The bottom of the bwameth_mapping.log file reads Exception: bad or empty fastqs. The corresponding files are not empty in 02_trimming, but perhaps there are simply zero alignments?