Hey all, I'm messing around with a pipe similar to mag for my own uses (and for ONT data) and I've run into issues with BUSCO, it seems to error out if any of the individual bins fail for whatever reason and I can't see a good way to handle this, it's especially annoying when you have the case of most contig bins working absolutely fine but no results for the whole assembly just because one didn't......

Hi there, not a mag dev but on my pipelines I use transpose on my bins channel so each bin gets passed as a separate process in BUSCO. I then set the error strategy to ignore. BUSCO also fails a lot due to memory limitations so having a flexible retry strategy on memory also helps a lot. This ensures that only the individual bins exit with errors and not all of them.

Yeah I was worried somebody might say that 🙃

I actually also recently have problems with BUSCO in version 5.0.0+, earlier versions handled each bin in one process and it seemed much more stable that way.