philipwoods

The HMMs do come from Barrnap, but the Anvio readme file about how they imported them says they arbitrarily added a GA cutoff of 750 bitscore that wasn't present in...

My apologies for the slow response! When I ran the 5S HMM independently of Anvi'o, the lowest bitscore I saw from circularized reference genomes was about 47-48, so I would...

Sorry for the delay! Here is the file and the command I used (I forget whether `--annotation-source` is necessary when using gene clusters as the ngram source, but if it...

For what it's worth, I can verify that pandas 1.4.4 is installed in the environment: ``` (anvio-8) [pwoods@ocean revision]$ conda list | grep pandas pandas 1.4.4 pypi_0 pypi ```

I get the error while running `anvi-get-codon-frequencies -c ANME-2a_sp._Agg-19359.db -o test.txt` with the attached contigs database. [ANME-2a_sp._Agg-19359.zip](https://github.com/user-attachments/files/16422579/ANME-2a_sp._Agg-19359.zip)

I just finished installing an `anvio-dev` environment and the command above ran with no issue, which is confusing but possibly also useful debugging information.