A. Murat Eren (Meren)

If you were to send us a private email with download links for your files (profile-db, contigs-db) we could also double-check things here :)

Thanks for bringing this up, @philipwoods. Do you happen to have any insights whether changing that GA cutoff changes the rate of the recognition of 5S rRNA? We can also...

Can we use your 5S profile in anvi'o @xvazquezc? Would you consider sending a PR? We would love to update those models!

Thanks for this, @xvazquezc. I'll mark this as a small project with the hope that someone will pick it up and work on this :)

I run your command in @mschecht's branch, and got this error: ``` Functions found ..............................: EGGNOG_BEST_TAX, Pfam, COG20_CATEGORY, EGGNOG_BACT, COG20_FUNCTION, EGGNOG_PFAMs, EGGNOG_COG_CATEGORY, EGGNOG_BRITE, KEGG_BRITE, EGGNOG_KEGG_KO, KOfam, EGGNOG_GENE_FUNCTION_NAME, EGGNOG_KEGG_REACTION, EGGNOG_BiGG_REACTIONS, EGGNOG_KEGG_MODULE,...

I see a lot of pandas errors reported lately. I wonder if there was an update recently that causes all these incompatibility issues. Note for self: we should always finalize...

This is very interesting. @philipwoods, would you consider sharing your contigs-db file and the exact command you're running on it to get this error? Maybe we can try to reproduce...

Great point, Sam :) There should also be a sanity check over the self.max_retries variable since it shouldn't be ever set to something < 1.

It seems the DIAMOND failed to generate the search output resuts. Would you please run `anvi-self-test --suite pangenomics` on the same computer and post teh entire output it generates in...

Thank you very much for your input, @apcamargo. I will work on this and try to come up with a modular solution.