johnlees
commented
3 years ago Apologies for this, I think most likely the Salmonella database you have downloaded is from version 1 of poppunk, and no longer compatible with version 2 which you have installed. You could downgrade, but to be honest I wouldn't recommend doing this partly because the original Salmonella fit isn't likely to give the resolution you'd likely desire.
We will soon release an updated Salmonella fit in the coming weeks/months compatible with the new version, and at a higher resolution. I can post here when that is available. Alternatively you could fit your own model to the Salmonella data you have downloaded.
andreaniml
Versions " conda list" output :
Command used and output returned I'm trying to run poppunk on a set of reference genomes of Salmonella Typhimurium downloaded from ncbi. I've downloaded and extracted the salmonella enterica database and tried running poppunk_assing with the following command line:
nohup poppunk_assign --db salmonella_poppunk --query teste.txt --output teste_ncbi_poppunk_clusters --threads 8 &where teste.txt has the path to the .fna files (genome_name "tab" path/to/file)I've tried running referencing the path of the folder and in the upper level (ex: running the line --db salmonella_poppunk in "Somefolder/mydata" where both my data and the database are stored and running the line with "--db Somefolder/mydata/salmonella_poppunk" when running from another folder, both outputs are the same)
The program seems to be crashing really early on, here's the output:
Describe the bug
It's my first time running poppunk, I'm not sure if this is my installation being messed up (I installed via conda) or the error is on my side. I think I would expect that a folder with the output to be created, however, this crashes too early for that.