Daan Speth

hmm, I think it is not limited to small genomes, but rather to genomes with a small number of contigs. I maintain anvio dbs for a large set of genomes...

I've manually split the A ciliaticola db in 11 contigs by arbitrarily inserting fasta headers, and ran @meren's `test_issue_1748` script on the new database with a varying number of threads....

Hi @meren, ah no worries about the logging. i won't create a feature request then, and patiently await 7.1 :P To your credit, I had noticed the lack of db...

I'll get you the contigs db in about 5hrs @meren I keep a local copy of the gtdb species representatives as anvio dbs for easy use in phylogenomics, pangenomics etc....

hold up, forgot to add something. While the error seems the same in both anvi-run-hmms and anvi-run-kegg-kofams, the handling of the progress after the keyboard interrupt is different. anvi-run-kegg-kofams, being...

and on the `-I` flag: yes, that was exactly what I was asking. That way, it becomes easier to update the "Ribosomal RNAs" hmm to the new ones with 6...

I had looked, and there are genes with many many X residues in it, just didn't think it was over 100K. But now I'm second guessing myself and checked properly,...

Still, doesn't seem to solve the anvi-run-kegg-kofams issue. Possibly unrelated. Let me see if I can run this with --debug to preserve temp files

as for the other one, I'll tell you later today :D but since it is a gtdb genome that shoudn't be the case. Otherwise I can go complain with donovan...

ah, @meren the failure for anvi-run-kegg-kofams was on an unrelated project, with only 427 genomes in it, and there I do know the culprit db specifically. Ironically, anvi-run-hmms runs smoothly...