Zach Reitz

Have you tried using a different euk/prok classifier? This one came out recently: https://www.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.000823 https://github.com/LottePronk/whokaryote You could try it instead of EukRep and see if you get better results. Keep...

FYI, I had a similar error with --mix and --cutoffs above ~0.4. ``` /lustre/BIF/nobackup/reitz001/mambaforge/envs/bigscape/lib/python3.6/site-packages/sklearn/cluster/_affinity_propagation.py:247: ConvergenceWarning: Affinity propagation did not converge, this model will not have any cluster centers. "will not...

I encountered the same cryptic error after I initialized the motif with the wrong alphabet (uppercase vs lowercase). All of the counts are indeed zero in that case. It would...