Supplemented sequences not appearing on phylo tree

[CatherineTroman]

Alex noticed this issue and I tested it quickly again today. When I selected a directory for supplementary data for the phylo module (with renamed fasta sequences from the same run), the sequences did not appear on the tree in the final report and it only had the samples and Sabin. Alex said this doesn't happen when running on the command line so not sure if it is something to do with how the GUI is processing the files in the directory.

If you need anything from me to help figure it out, just let me know.

Thanks!

[CorwinAnsley]

Hi Catherine, thanks for raising this issue. I haven't been able to recreate this error on my end yet, could you share the log file? (and test the problem again if you've used the gui again since, as the log resets each time); on windows it should be saved to Users<username>\AppData\Local\piranhaGUI\log.txt

[CatherineTroman]

Hi Corey,
I've attached the log and also the directory that I provided with the supplementary sequences, just in case it is something to do with the formatting of that.
[log.txt](https://gith
test-fasta-piranha.zip
ub.com/polio-nanopore/piranhaGUI/files/15274400/log.txt)

[aineniamh]

Can you try running it with the ddns_group=Sabin3-related (or whatever the group of the supp sequences are) in the header? I suspect the issue is piranha doesn't know what tree to put the supplementary sequences in.

https://github.com/polio-nanopore/piranha?tab=readme-ov-file#optional-phylogenetics-module-new-feature

[CatherineTroman]

Sorry, I should have checked they were definitely in the right format first.

I have rerun the analysis with the appropriate ddns_group= in the headers but the sequences still haven't appeared in the tree in the report.

I've attached the log from this attempt, just in case it might show anything different.
log.txt

[aineniamh]

If you run with the same supplementary data on the command line is it working okay?

[CatherineTroman]

I ran on the command line and it was ok and they appeared in the trees. Realised two of the files weren't saved as fasta, so I tried again on the GUI just in case but it still didn't have the supplemented sequences in the tree.

On running the GUI again I noticed when I started the analysis it popped up with a line saying "Cannot import pyabpoa, some features may not be available". Not sure if that has anything to do with it?