Closed DeondeJager closed 1 year ago
Hi Deon,
Thank you for the report!
You are not doing anything wrong; that is a bug in paleomix. I'll release a fixed version Thursday or Friday.
Best, Mikkel
Hi Mikkel,
OK, thanks for looking into it, and for pushing a fix soon - much appreciated!
Cheers, Deon
I've released a version of paleomix that fixes this (v1.3.8). Thanks for the report and let me know if you run into any other problems.
Cheers, Mikkel
Hi Mikkel,
I added additional options (
-n
and-o
) for bwa backtrack in the yaml file (bam pipeline), expecting them to be applied to thebwa aln
command (as stated in the yaml file), but instead they seem to be applied to thebwa samse
command (see log file), which then results in an error (I assume becausebwa samse
doesn't have a-o
option). I've attached the yaml and log files, and I'm using paleomix v1.3.7. Please can you have a look to see what's going wrong here?Cheers, Deon SCR_086_RmA009.yaml.txt bam_pipeline.20230515_151100_01.log