I downloaded new classifiers from Silva 144 version. I used qiime2-amplicon-2025.10 because I wanted to see how much different the results were from a previous run when I got intoo a sequence of issues as soon as I started DADA2 denoising, which makes a quick test time consuming.
- First I got a version error when attempting to run feature-classifier classify-sklearn.
- To fix this I wanted to install rachis-qiime2-2026.7 that I did not use for my old data, and therefore I did not have it installed. That ended in another version conflict.
- Then I set
conda config --set channel_priority flexibleas indicated above, I wanted to clean conda and got other error messages. Likely this is because at the time I installed conda system wide in /opt/miniconda3 (to give access to more users, and it sucks, to say it mildly, it needs a lot of adaptations, over and over again). - It is friday evening, I did not want to waste my weekend with troubleshooting, so I gave up.
I am an occasional user of Qiime2 and have no time to keep up with the high-frequency flow of method-breaking updates. Would an "LTS" version be an idea?
output:
Plugin error from feature-classifier:
The scikit-learn version (1.7.1) 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.
user@I251:/media/data/Amplicon/run144$ conda update conda
2 channel Terms of Service accepted
Retrieving notices: done
DirectoryNotACondaEnvironmentError: The target directory exists, but it is not a conda environment.
Use 'conda create' to convert the directory to a conda environment.
target directory: /opt/miniconda3/envs
user@I251:/media/data/Amplicon/run144$ conda env create
--name rachis-qiime2-2026.7
--file https://raw.githubusercontent.com/qiime2/distributions/refs/heads/dev/2026.7/qiime2/released/rachis-qiime2-linux-64-conda.yml
2 channel Terms of Service accepted
Retrieving notices: done
Channels:
conda-forge
bioconda
defaults
Platform: linux-64
Collecting package metadata (repodata.json): done
Solving environment: failed
LibMambaUnsatisfiableError: Encountered problems while solving:
package deblur-1.1.1-pyhdfd78af_0 requires sortmerna 2.0, but none of the providers can be installed
Could not solve for environment specs
The following package could not be installed
└─ deblur =1.1.1 * is not installable because it requires
└─ sortmerna ==2.0 *, which conflicts with any installable versions previously reported.
user@I251:/media/data/Amplicon/run144$ conda config --set channel_priority flexible
user@I251:/media/data/Amplicon/run144$ conda clean --all
Will remove 208 (773.7 MB) tarball(s).
Proceed ([y]/n)? y
Will remove 1 index cache(s).
Proceed ([y]/n)? y
WARNING: cannot remove, file permissions: /opt/miniconda3/pkgs/cache
Will remove 93 (1.30 GB) package(s).
Proceed ([y]/n)? y
WARNING: cannot remove, file permissions: /opt/miniconda3/pkgs/libcurl-8.16.0-heebcbe5_0
WARNING: cannot remove, file permissions: /opt/miniconda3/pkgs/conda-25.11.1-py313h06a4308_0
WARNING: cannot remove, file permissions: /opt/miniconda3/pkgs/libunistring-1.3-hb25bd0a_0
WARNING: cannot remove, file permissions: /opt/miniconda3/pkgs/libidn2-2.3.8-hf80d704_0
There are no tempfile(s) to remove.
There are no logfile(s) to remove.