Brent Pedersen

what does `bjobs -w` return for you when the job is running?

[this](https://github.com/brentp/bwa-meth/blob/master/bwameth.py#L398) is the only place it's adjust mapq and it's setting to 1. mapq 0 means it maps to multiple places equally which is more likely to occur with a...

if you can show that it performs better without that, I'll remove it. I've actually found (for non-BS-Seq data) that alignments/ regions with high NM are often bad as well.

still same criteria. if you can show that it is more accurate without, it can be removed. I'm hesitant to add more command-line flags.

It looks like a solution there is to build with htslib 1.9 instead of relying on the conda build. (You could also try htslib 1.11 which is released today). I...

yeah. that's not good. can you share the full command that you are running and the full stderr+stdout?

Hi, what is your question?

Hi, you can try the `--do-not-penalize-chimeras` argument.

Hi, without `--do-not-penalize-chimeras`, then bwameth does this: https://github.com/brentp/bwa-meth/blob/7c8e1eb2a3b17b1bc6ecbef62119bf422d131830/bwameth.py#L436-L444 so it find reads where there is a lot of soft-clipping. This can happen with BS-Seq and usually leads to lower quality...

A complete example (working in the template branch) would look like: ``` Python import re from bsub import bsub commands = 'bwameth.py --reference {ref} --read-group {sample} -p {results}/{name} {r1} {r2}'...