GreenGene2 Corrupting Qiime

[Chance (Chance Roberts)]

Hello,

I have been attempting to install Greengene2. After installing the most recent version of qiime and then installing greengene2, qiime no longer works. When uninstalling greengene2 qiime begins to work again. I am wondering where the issue is occurring as I can install other packages (like deblur) and nothing goes awry. Here is the error that is thrown when trying “qiime –help”

Traceback (most recent call last):
  File "/Users/NA/miniconda3/envs/qiime2-amplicon-2025.7/lib/python3.10/site-packages/q2cli/util.py", line 275, in get_plugin_manager
    return qiime2.sdk.PluginManager.reuse_existing()
  File "/Users/NA/miniconda3/envs/qiime2-amplicon-2025.7/lib/python3.10/site-packages/qiime2/sdk/plugin_manager.py", line 58, in reuse_existing
    raise UninitializedPluginManagerError
qiime2.sdk.plugin_manager.UninitializedPluginManagerError

Best,

Chance

[Oddant1 (Anthony Simard)]

Hello @Chance ,

Can you tell me what exactly you’re doing that’s leading to this error? The specific commands you are running to install/uninstall greengene2? Thank you.

[Chance (Chance Roberts)]

Hey @Oddant1 ,

I begin with installing greengenes2 using

pip install q2-greengenes2

I would then run

qiime --help

to see if something went wrong during the install, which would then prompt the error I got above.

I then uninstall greengenes2 using

pip uninstall q2-greengenes2

and re-run the help command to see if greengenes2 is what is leading to the issue

qiime --help

which then prints the standard help output that qiime has, leading me to believe this is an issue with the installation of greengenes2.

[Chance (Chance Roberts)]

I just fixed it (thank you AI and the lovely Qiime forums community)

It appears what was happening is an older version of Qiime I had installed (which I had deleted and then updated before attempting the Greengenes2 install) had some residual effect. I needed to force update sci-kit.

conda install -c conda-forge scikit-bio --force-reinstall

This appeared to have fixed my issues and I am now able to properly run everything I need.