Error installing ITSxpress: ImportError: No module named 'q2cli'


I hope that you are all doing well.

Im having a hard time installing ITSxpress the following this tutorial.

When I ran conda install -c bioconda itsxpress

The output is:

Solving environment: done

==> WARNING: A newer version of conda exists. <==
  current version: 4.5.11
  latest version: 4.7.5

Please update conda by running

    $ conda update -n base conda

# All requested packages already installed.

Traceback (most recent call last):
  File "/home/aneth.david/.conda/envs/qiime2-2019.4/bin/qiime", line 7, in <module>
    from q2cli.__main__ import qiime
ImportError: No module named 'q2cli'

I have tried to re-install QIIME2 but when I repeat the process I get the same error.

Please help.


Hi @anethdavid! Does that post represent all the commands run? For example, did you activate a conda env first? Which one?

Are you removing the conda env before reinstalling? That might be the easiest way to ensure the install is working correctly.


Thank you for the response.

Yes, I activated qiime2-2019.4.

I was also running dada2 denoise paired on another screen while doing the install and uninstall part (probably shouldnt have done this), it ended with an error about a package as well. I unfortunately didn’t copy the error before restarting terminal.

No, how do I remove the conda environment before reinstalling?

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You’re welcome!

Check this post for removal instructions:

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It worked, I have ITSxpress installed!

I did:

  1. Follow instructions to remove the conda environment
  2. Reinstalled conda environment
  3. Instal qiime2
  4. Then install ITSexpress.

Thank you very much!