Hi everyone,
I’m trying to run a panaroo using the following command: panaroo -i *.gff -o ./charlotte_new/ --clean-mode strict -a core --aligner clustal --core_threshold 0.98 -t 10 --remove-invalid-genes
But i get the following error instead:
Traceback (most recent call last):
File “/shared/team/conda/cerith-jones.bacterial-genom-3/panaroo/bin/panaroo”, line 6, in
from panaroo.main import main
File “/shared/team/conda/cerith-jones.bacterial-genom-3/panaroo/lib/python3.12/site-packages/panaroo/main.py”, line 14, in
from .generate_output import *
File “/shared/team/conda/cerith-jones.bacterial-genom-3/panaroo/lib/python3.12/site-packages/panaroo/generate_output.py”, line 10, in
from Bio.Alphabet import generic_dna
File “/shared/team/conda/cerith-jones.bacterial-genom-3/panaroo/lib/python3.12/site-packages/Bio/Alphabet/init.py”, line 20, in
raise ImportError(
ImportError: Bio.Alphabet has been removed from Biopython. In many cases, the alphabet can simply be ignored and removed from scripts. In a few cases, you may need to specify the molecule_type as an annotation on a SeqRecord for your script to work correctly. Please see History and replacement of Bio.Alphabet · Biopython for more information
I have used the same line of code before and it’s worked fine, I don’t understand the Bio.Alphabet has been removed from Biopython, as I’ve never had an alphabet in my code before??? Is there some new code I should be using?
the panaroo version i have installed is 1.1.2, biopython version i have installed is 1.83, conda version is 23.1.0
I have read that downgrading the biopython version can help solve this error but i’ve had no luck with this. I’ve tried uninstalling and reinstalling the panaroo
Kind of new to all this so any help would be appreciated thanks 