plugin feature-classifier

Hi everyone!

I have this code:
INPUT_DIR=/Users/valentinagirardi/Downloads/Bioinf-enero/20_dada2

OUTPUT_DIR=/Users/valentinagirardi/Downloads/Bioinf-enero/30_taxonomy_assignment

mkdir ${OUTPUT_DIR}

qiime feature-classifier classify-sklearn --i-reads 20_dada2/dada2-rep-seqs.qza --i-classifier classifier_16S_V3-V4.qza --p-n-jobs 1 --p-reads-per-batch 1000 --o-classification classified_rep_seqs.qza

mv classified_rep_seqs.qza ${OUTPUT_DIR}/.

and I get this error: Error: QIIME 2 has no plugin/command named 'feature-classifier'. And when I put qiime info into the terminal the plugin 'feature-classifier' doesn't appear.

I already tried:

  • updating conda:
    conda update -n base conda

  • removing and creating again the conda environment:
    conda deactivate
    conda remove --name qiime2-2020.8 --all
    conda create -n qiime2-2020.8 python=3.6
    conda activate qiime2-2020.8
    conda install -c qiime2/label/r2020.8 -c conda-forge -c bioconda qiime2

  • checking the channels configuration:
    conda config --show channels
    (and qiime appears first on the list)

  • creating a new Conda environment without predefined channels:
    conda create -n nuevo_entorno python=3.6
    conda activate nuevo_entorno
    conda install -c qiime2/label/r2020.8 -c conda-forge -c bioconda qiime2

Hello @Valentina_Girardi,

Are you submitting the script you posted to a cluster by chance? If so, you may need to activate the conda environment inside of the script. If not, can you run conda activate qiime2-2020.8 and then qiime info and post the output?

3 Likes

Hi!! I recently found a solution creating a new conda environment and updating qiime2 to the 2023 version and the plugin magical had appeared, thank you for your help!!

1 Like