Error when run DEICODE plugin


I am using qiime2-2020.2 and want to use DEICODE plugin.

I followed installation steps in this link.

When I installed DEICODE plugin,I runned this code.

conda install -c condo-forge deicode

I wanted to run this code↓

     qiime deicode rpca \
        --i-table table.qza \
        --p-min-feature-count 10 \
        --p-min-sample-count 500 \
        --o-biplot ordination.qza \
        --o-distance-matrix distance.qza

but this error message appeared↓

Error: QIIME 2 has no plugin/command named 'deicode'.

I am glad if you can tell me the solution.

Hi @yoshikisuzu!

There are a few reasons you may be getting that error message.

First, it looks like there's a typo in the installation command: you've written

conda install -c condo-forge deicode

but the correct command should be

conda install -c conda-forge deicode

(note the "a" in "conda-forge").

If you're still getting a no plugin/command named 'deicode' error message from QIIME 2 after trying that second command, I would suggest running qiime dev refresh-cache before attempting to run the qiime deicode rpca ... command. That might fix that problem.

If things still aren't working out, let us know and we can look into this further! :qiime2:

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Thank you for your polite advice !!
I tried as you pointed out.

but that did not go well.
Please see the actual screen.

If you'd like,please tell me the solution.

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Thanks for sharing this screenshot! It looks like you’ve installed DEICODE into your “base” conda environment (see the (base) off to the left side of the screen?) – the problem with doing this is that you won’t be able to use this installation of DEICODE from within your qiime2-2020.2 environment. These environments are separated from each other – this is also why, for example, we can’t use qiime commands from outside of QIIME 2 environments. Does that make sense?

So: could you try activating your QIIME 2 conda environment and then running conda install -c conda-forge deicode? I think that should solve this problem.



Dear Mr.fedarko

I was able to understand your advise.
I am glad to inform you that problem is now solved !
I am very grateful to you for your help!
Thank you very much!