An error occurred when using Greengenes2

[wfgui]

Hi,

When I was annotating the 16S sequence with Greengenes2, I was prompted with a database version error. Could you please tell me how to obtain the latest gg2 pre-trained classifier? The commands to be run are as follows：

#qiime2 version: 2025.7
qiime feature-classifier classify-sklearn \
                --i-classifier 2024.09.backbone.full-length.nb.sklearn-1.4.2.qza \
                --i-reads rep-seqs.qza \
                --o-classification taxonomy.qza \
                --p-n-jobs 12

[gregcaporaso]

@wfgui, can you share the error you received, and also the output of running qiime info? I think this should work as QIIME 2 2025.7 is still on scikit-learn 1.4.2.

[wfgui]

The error message is as follows：

There was a problem with the command:                     
 (1/1) Invalid value for '--i-classifier': 2024.09.backbone.full-length.nb.sklearn-1.4.2.qza was created by 'QIIME 2024.5.0'. The currently installed framework cannot
  interpret archive version '6'.

qiime info：

System versions
Python version: 3.10.14
QIIME 2 release: 2025.7
QIIME 2 version: 2025.7.0
q2cli version: 2025.7.0

Installed plugins
alignment: 2025.7.0
composition: 2025.7.0
cutadapt: 2025.7.0
dada2: 2025.7.0
deblur: 2025.7.0
demux: 2025.7.0
diversity: 2025.7.0
diversity-lib: 2025.7.0
emperor: 2025.7.0
feature-classifier: 2025.7.0
feature-table: 2025.7.0
fragment-insertion: 2025.7.0
longitudinal: 2025.7.0
metadata: 2025.7.0
phylogeny: 2025.7.0
quality-control: 2025.7.0
quality-filter: 2025.7.0
rescript: 2025.7.0
sample-classifier: 2025.7.0
stats: 2025.7.0
taxa: 2025.7.0
types: 2025.7.0
vizard: 0.0.1.dev

[lizgehret]

Hey @wfgui,

Hmm, interesting... this classifier should definitely be compatible with QIIME 2 2025.7. Could you re-run this command with the --verbose flag and provide the full traceback that you receive (either copy/paste or full page screenshot)? This might give us some more insight into where things are going sideways.

Thanks!

[wfgui]

Hi，

This classifier is really compatible with QIIME 2 2025.7. After I restarted the server and reactivated the QIIME2 environment, everything became normal. Thank you ！

[gregcaporaso]

Thanks for the update @wfgui, and glad it's working for you now. If this comes up again, will you follow up? We're uncertain why this would have come up so we just want to keep our eyes on it.

Happy ing!