Installing QIIME on my Mac

Hello–I had installed QIIME back in June. Now I am trying to install again.

When I run:

(qiime2-2019.10) Andrews-Air:~ adinsmoor$ conda env create -n qiime2-2019.10 --file qiime2-2019.10-py36-osx-conda.yml

I get this error:

CondaValueError: prefix already exists: /Users/adinsmoor/opt/miniconda3/envs/qiime2-2019.10

It seems I may be having trouble activating the conda environment, following this:


Hi Andrew,

Could you try running conda info --envs in your terminal and paste the results here? This command will display a list of all the conda environments installed on your system.

My guess is that you already have an environment named qiime2-2019.10 installed on your system somehow (this could’ve happened in a few different ways – one likely scenario might be that QIIME 2 2019.10 is already (partially?) installed). Anyway, if this is the case, you should see qiime2-2019.10 show up in the output that the conda info --envs command gives you!

If you do see qiime2-2019.10 show up in the output, then you should be able to fix the problem by removing the environment using conda remove --name qiime2-2019.10 --all. From there you should be able to (re)-install :qiime2: properly.

Let us know if this works!


Thank you, that worked originally! However, when I close my terminal and re-run source “activate qiime2-2019.10” I get the following error:

(base) wirelessprv-10-194-185-112:~ adinsmoor$ source activate qiime2-2019.10

xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun

(qiime2-2019.10) wirelessprv-10-194-185-112:~ adinsmoor$

Hoping to do moving picture tutorial next.


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Hey @adinsmoor!

Check out this error message:

I don’t think this is related to your QIIME 2 environment. A quick search turns up:

Give that a shot, hopefully that’ll sort you out.

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