Open sunta3iouxos opened 1 month ago
I tested the same but using the bowtie2 and it seems that it does not through this error anymore.
So, it is a bwa specific issue, that migh be related to -R '@RG\tID:A006200402_224949_S7_L000\tDS:A006200402_224949_S7_L000\tPL:ILLUMINA\tSM:A006200402_224949_S7_L000'
Hi,
this error message from samtools means that the alignment has failed e.g. no proper bam was produced (and piped into samtools).
Do you mean that running the workflow with --aligner bowtie2
didn't reproduce the error?
Best wishes,
Katarzyna
Exactly, I used the same DNA-mapping command, and only changed the --al8gner entry to bowtie. Then the whole thing worked.
Hi all, I got an interesting and unexpected error. Unfortunately, I can not retrieve the bam file to see what it is about:
the log:
and this is the command