Brent Pedersen
Brent Pedersen
Hi Justin, It defaults to using the sample id as the family name. First col is family name and second col is sample name. So, it appears twice. I would...
The --infer stuff is less battle-tested. I think the best way is to run without infer and evaluate the HTML. If you share it here or to me privately, I...
I would check if you have tabs or single spaces in your pedigree file. Maybe there is some formatting issue. Otherwise, your output html looks good to me. YOu can...
oh. did you use --sample-prefix when you ran extract? That would be where the duplicated names came from. You only need that if you have for example, sequenced P0003626 two...
you could run your docker in interactive mode ("-it") to debug. Also make sure that: `/home/mferreira/genomeinabotle/HG002_son/alignments_joined/post_processed/*.bam` exists on your system outside of docker.
maybe you need to do `chmod a+r *.bam*` on the files on that directory since your docker user will need access. when you run with -it, don't send the extra...
You can try escaping the `*` but probably the simplest way is to put the command you want to run in a shell script then: ``` docker run ... bash...
exit status 137 means not enough memory. So you'll need to tell slurm or whatever is managing your jobs to allow more memory.
Hi, "MD" is added by bwa mem for the original alignment and not modified by bwa-meth so it won't be correct. For your other questions, are you using a directional...
adding zip here for Jason to test [fraguracy_dev.zip](https://github.com/user-attachments/files/17835425/fraguracy_dev.zip)