J Andrew R Farrell

Yup, your Samtools isn’t working properly, you either don’t have it installed or you have a very old version. I’ve seen that invalid option T and O before when Sam...

https://pubmed.ncbi.nlm.nih.gov/23165927/ https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5903934/ ===================================== Andrew Farrell PhD Director of Research and Science Department of Human Genetics USTAR Center for Genetic Discovery Eccles Institute of Human Genetics University of Utah School of...

The first error your getting is from jellyfish "/tmp/RUFUS/scripts/RunJellyForRUFUS.sh: line 34: 62244 Killed $JELLYFISH count --disk -m $K -L $L -s 8G -t $T -o $GEN.Jhash -C $GEN.fq”. I believe...

That’s unfortunate. Since it’s a docker image, I assume that path never changes, you could ask them to change that line to just be whatever the RUFUS directory path is...

The error in your build is due to a 3rd party program FASTP which I actually don't use anymore and should remove from the make, thanks for the reminder. For...

So that a complex event which RUFUS is much better at calling than other methods because of our highly accurate breakpoints, but admediatly we probably aren't documenting the best, mainly...

I have been dealing with such situations so far by just soft linking the bams I want to use into a run directory. I create a directory in a place...