Open Blosberg opened 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
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/)?
Oh, I forgot to add the sample.fasta to the repo.
I'll fix that.
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?
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.