James

I am having the same error, actually. Below is my output. ------------------------------------------------------------------- Polishing alignment and re-aligning. ------------------------------------------------------------------- muscle 5.1.linux64 [] 396Gb RAM, 40 cores Built Feb 24 2022 03:16:15 (C)...

I followed the instructions above, and still ran into the same error. The terminal output is attached: [Terminal SavedOutpiut.txt](https://github.com/harmslab/topiary/files/10891943/Terminal.SavedOutpiut.txt)

Yes, here it is. [04_aligned-dataframe.csv](https://github.com/harmslab/topiary/files/10951723/04_aligned-dataframe.csv)

Yes, I was able to progress past the alignment! I think this issue can be closed. Unfortunately, I will need to open another for what appears to be the same...

[Terminal Saved Output Mar 15.txt](https://github.com/harmslab/topiary/files/10976158/Terminal.Saved.Output.Mar.15.txt) I have attached the whole terminal session, but below is the relevant part. It says the issue is that my alignment is too small, and...

The input file was the output of the seed_to_alignment, i thought. I used the 05_clean-aligned-dataframe.csv as the input for ali_to_anc, without any cleaning.

No, that's what I did. I was hoping Topiary would 'fill in' around that sequence, but it seems like it's looking for that to be the 'edge' of sequence space...

I've filed out the seed alignment, and ran into an error that I suspect is because of the format of my seed alignment. I have attached the seed alignment. Do...

I changed the species name in the seed alignment, which advanced me further than I have been able to get before. Unfortunately, the alignment hit a critical error again. I...