Hi everyone, I’m trying to run taxonomy classification using the SILVA V3 classifier (for forward read only analysis), but I keep running into a scikit-learn version mismatch error in QIIME2-amplicon-2025.7. Here is the error I get: Plugin error from feature-classifier:
The scikit-learn version (0.24.1) used to generate this artifact does not match
the current version of scikit-learn installed (1.4.2). Please retrain your classifier
for your current deployment to prevent data-corruption errors.
I understand why the version mismatch occurs, but I am unsure how to proceed for the SILVA V3 region specifically. My questions:
- Is there an officially supported SILVA V3 classifier compatible with QIIME2-amplicon-2025.7 (scikit-learn 1.4.2)?
- If not, what is the recommended workflow to retrain a SILVA V3 classifier?
- Are there updated SILVA reference sequences/taxonomies recommended for this version of QIIME2?
- Is there any chance that the QIIME2 team plans to release updated region-specific classifiers (e.g., V3, V4, V3–V4) for 2025.x distributions?
I want to ensure that I follow the correct procedure rather than manually downgrading scikit-learn or breaking my environment.