Hi again @Nicholas_Bokulich !
In my attempt to train a v4 silva 138.2 classifier on qiime2-amplicon-2024.10, I run into a scikit-bio error:
pkg_resources.ContextualVersionConflict: (scikit-bio 0.6.0 (/projects/lindsval@colostate.edu/software/anaconda/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages), Requirement.parse('scikit-bio<0.6.0,>=0.5.0'), {'iow'})
I think I get this error because (from what I can find from this post) the current workaround for greengenes2 compatibility with qiime2 2024.10 in order to avoid downgrading scikit-bio is to run:
conda install "cython<1.0"
pip install q2-greengenes2 "scikit-bio>=0.6.0"
I found that if you dont strictly install scikit-bio>=0.6.0, it results in this error:
**Plugin error from diversity:**
** module 'skbio.diversity.alpha' has no attribute 'sobs'**
So it seems like if you want to classify using greengenes2 and proceed with core-metrics, you must have scikit-bio>=0.6.0, but in order to build a silva classifier for qiime2 2024.10 you need to have scikit-bio 0.5.9 or earlier. @timanix did you run into any issues like this (that is, if you use both silva and gg2 for classification)
Does this seem correct? Can you help me figure out a way in which I can use qiime2 2024.10 to generate a silva 138.2 v4 classifier and be able to run gg2 all the way through to core-metrics?
thanks!