Closed nicola-palmieri closed 2 years ago
What version of sklearn do you have? Assuming you installed with conda, can you please post the result of running conda list
?
This may also be a problem with using these previous databases, which are not compatible with poppunk v2. New databases can be found here: https://poppunk.net/pages/databases.html
If you need to use an old database, you'll need to downgrade to poppunk 1.2.2 (https://poppunk.readthedocs.io/en/v1.2.2-docs/), but I wouldn't typically recommend this.
Many thanks for this, I will try to use the new database.
Versions
poppunk 2.4.0
Command used and output returned
poppunk_assign --db ecoli_poppunk_db --query list_of_genomes.txt --output poppunk-out --threads 14
Describe the bug
I have installed poppunk in a completely fresh conda environment, but got the error above after I tried to assign 4 new strains to a previously downloaded database from this paper (https://www.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.000499). I think the version is sklearn is not compatible with poppunk. How should I proceed?
Thank you! Nicola