Simon Sadedin

Hmm, just testing on my Mac I don't seem to have `pidof` - might have to do something cruder like `ps -efa | grep java`?

I've actually just committed a change which may be relevant to this. What is happening is that Bpipe thinks the last stage (humann2) seemingly not declaring an output. In such...

Hi, yes you are correct - Bazam will definitely output every read that has a mate and will not filter anything. However currently it does drop single ended reads. Potentially...

Very interesting - thanks for posting! I will try this out on some of our own large pipelines and merge after a little testing. Incidentally, if you are running pipelines...

I think that 4G is probably not enough RAM (depending on the structure of your BAM file Bazam will cache a lot of reads in memory). So I'd suggest trying...

Indeed, it looks like they should be to me. I am surprised this isn't causing wider issues! I will put a fix in for this. Thanks for reporting it.

Unfortunately this is currently the case: the "uses" construct only controls what jobs Bpipe itself will attempt to launch, and that throttling occurs before any interaction with resource managers occurs....

I just spent an hour trying to get their maven repo to deliver me the dependencies that our build depends on based on those instructions, and sadly failed. From what...

Can you look in the bpipe log file (.bpipe/bpipe.log) and search for the sbatch command? hopefully it should be logged in there and we can see exactly what is being...

Sorry about that ... don't quite know how it happened but hopefully fixed now. Can you try again?