Error: Alignment must have at least 3 sequences

Hello,

It’s been awhile since I’ve run the local build of nextstrain on my computer, so I went ahead and updated everything, first from github, then from the CLI using “conda update --all”

Ever since the update, I have not been able to successfully run the analysis, looks like a lot has changed, and I was wondering if someone could help me nail down where this issue is coming from.

I am not sure why it is asking for 3 sequences in the alignment. Is it saying that none of my sequences passed the quality checks, and now only the two reference sequences (Wuhan/Hu-1/2019 and Wuhan/WHO1/2019) remain?

If it helps, those two reference sequences are the only sequences in my aligned-delim.fasta file in the results folder. Almost all of the sequences I have passed to nextstrain have passed the quality checks in the past. I’m not sure where to look next.

Thanks for your help,
Jonathan