Cameron Reid

I'm also using 2.3.4. Got it to run by pip installing dendropy then adding it to my path. Still don't know why it didn't work from regular installation though.

Thanks guys!

@anugos @maxibor I had the same problem running via slurm on HPC and was able to resolve it by switching the prokka container to this one https://depot.galaxyproject.org/singularity/prokka%3A1.14.6--pl5321hdfd78af_4

Hi there, I've think I've run into this issue but as I have ~60k MAGs, CheckM is taking a long time and the Bdb.csv file is not present. As an...

Hi Matt, I ran checkM2 outside of dRep and formatted it as described above for dRep. It worked on once I added the .fna extension to the names in the...

I had the same issue. @MicroSeq 's solution worked for me but I guess it's not preferable in the long run. Maybe making it possible to download the CheckM2 db...

Update: I removed the Checkm2Database rule and modified Checkm2ContigAnalysis to take a pre-downloaded DIAMOND database, then ran with the original checkm2.yaml conda env (i.e. not the workaround described by @MicroSeq...