installing qiime for first time

I followed the instructions to install Qiime2 that are found here ( Natively installing QIIME 2 — QIIME 2 2023.9.2 documentation ) on Linux (subsystem).
and after insulation and activation when i check QIIME using <qiime --help>, i get error: qiime: command not found

Hi @Mostafa_Younis :smiley:

Just double checking so we can help you - Did you do all of the following;

fetch the file you need from the web:


create a conda environment for your new qiime2 amplicon distribution and tell it what file to use:

conda env create -n qiime2-amplicon-2023.9 --file qiime2-amplicon-2023.9-py38-linux-conda.yml

remove the file as a clean up step:

rm qiime2-amplicon-2023.9-py38-linux-conda.yml

then activate the conda environment:

conda activate qiime2-amplicon-2023.9

then check your install?

qiime --help

As you went along this path of instructions, what printouts did you get? Any errors etc?




Hi @buzic
Thank you for ur response
I did these steps twice but unfortunately, it is the same result.

Hello @Mostafa_Younis, in both attempts at creating the environment there you are getting the error:

CondaValueError prefix already exists: /home/munis/miniconda3/envs/qiime2-amplicon-2023.9

It looks like at some point you created an environment that was in some way corrupted and need to remove it and recreate it. Please run the command conda env remove -n qiime2-amplicon-2023.9 then follow the instructions given by @buzic again.


oooh, thank you @Oddant1 it works.

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