Daan Speth

here's the `--debug` output from the moment anvi-run-kegg-kofams throws an error. Nothing quite as obvious as the problem with anvi-run-hmms seems to be happening, but I might be checking the...

@meren, thanks! I emailed iva the contigs db. As I mentioned buried somewhere above,. I generated this particular db from a public mag (GCA_003647425), but in a previous version of...

@meren the normal runtime for anvi-run-kegg-kofams is ballpark 2 minutes with these settings on our server, so i run into this issue with this particular db before that time. when...

thanks @meren and @ivagljiva! did you still want the contigs db for the anvi-run-hmm issue to see whether there is an upstream problem in anvio or in the data? I...

didn't have time to run tests today, will get back to you in a few days

Here's a different dataset (forward reads from SRR2605792) used as query to search a nirK protein database. The axes show the raw score, not the bit score. with `--no-ranking` flag...

setting the `--no-ranking` parameter did not change anything, and setting a much higher minimum score also did not resolve the issue.

Hi Meren, your proposed general solution is much more expansive than what I suggested. If that's doable, i'd of course be happy with that. Otherwise, having the option treat the...

Hi @meren, I was running anvi-export-functions, and was wondering whether the "--defline-format F-STRING" could also easily be implemented in that program. While the file generated is not a fasta file,...