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polio-nanopore / piranha

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Lack of sequences from supplementary-datadir in trees generated by phylo module #224

Closed AShaw1802 closed 3 months ago

AShaw1802 commented 3 months ago

ReferenceDatabase_text.txt

Hi, I'm struggling to get the phylo module to add the supplementary-datadir to the trees that are generated (both report and .tre file)- I'm using the command

"piranha -b Demo_barcodes.csv -i demultiplexed/ -rp -sd ReferenceDatabase/ -o Output"

with the Piranaha v.1.2.2 and the updated conda environment. Everything is running to completion and I have the tree and report, but the sequences from the supp directory are missing. I've attached the fasta file that is in ReferenceDatabase/ which has ddns_group in the headers (Originally the file was ReferenceDatabase.fasta, which I converted to text so that I could upload it). Can you spot any error in my file or command? Thanks!

aineniamh commented 3 months ago
Screenshot 2024-03-05 at 16 46 34

I'm not sure what the issue is- I just ran your command on some example data I have and they got added in fine. Are there Sabin2-related and Sabin1-related phylogenies being made at all? Can you attach the output?

AShaw1802 commented 3 months ago

I did a few re-installations and cleared out the conda environments in case that made a difference, and whilst it's still the same pirahna version I got the SD sequences added in the end, so an update issue. Thanks for checking though!