Matthew Schechter

Thanks @mooreryan for the detailed explanation! I've never debugged R like this so this was a great learning experience. I went ahead an implemented the`⁠stringsAsFactors = TRUE` in this branch:...

Great, looks like the different version of R was the culprit! I just merged this fix here: https://github.com/merenlab/anvio/pull/1973

Hi @meren, I am getting the same error as described in this issue. os: MacOS Catalina 10.15.4 anvio version ``` Anvi'o version ...............................: esther (v6.2-master) Profile DB version ...........................: 32...

Thanks for the suggestions @meren. I went back and filtered for a group of 70 SCGs using the combined homogeneity index and was successfully able to use `anvi-gen-phylogenomic-tree`

Thanks! Here is a reproducible way to set up a test case with amino acid sequences: ```bash cd INFANT-GUT-TUTORIAL # extract Ribosomal_L1 seqs anvi-get-sequences-for-hmm-hits -c CONTIGS.db \ -p PROFILE.db \...

blastp should be able to call both NCBI NR and refseq.

@meren thanks again for giving workflows a separate documentation infrastructure. I took a swing at this here: https://github.com/merenlab/anvio/tree/ecophylo-artifact-documentation Should I remove the [ecophylo artifact](https://anvio.org/help/main/artifacts/ecophylo-workflow/) in this branch or would we...

@meren can we also have an `artifacts_accepted` option? I think it's important to document which artifacts are the input to workflows as well e.g. the contigs-worklow should accept a [fasta](https://anvio.org/help/main/artifacts/fasta/)...

## February 23, 2023 - @isaacfink21 and I caught up and defined his timeline for participation in the project until he graduates - Back of the napkin, he has a...

Thanks for the ping everyone - I'll run through my current documentation and prepare commits. I know the release timeline is tight.