Gneiss command not found, though qiime2 is loaded


I am running qiime 2 from the command line (q2cli version 2017.12.0).

I am using the chronic fatigue syndrome tutorial ( and when I run the following line:

qiime gneiss add-pseudocount --i-table table.qza --p-pseudocount 1 --o-composition-table composition.qza

I get this error:

Usage: qiime [OPTIONS] COMMAND [ARGS]…

Error: No such command “gneiss”.

Prior to running this line, I activated qiime2
source activate qiime2-2017.12

I am also working within a virtual environment.

When I run qiime --info I get:
System versions
Python version: 3.5.4
QIIME 2 release: 2017.12
QIIME 2 version: 2017.12.1
q2cli version: 2017.12.0

Installed plugins
No plugins are currently installed.
You can browse the official QIIME 2 plugins at

Application config directory

Getting help
To get help with QIIME 2, visit

Citing QIIME 2
If you use QIIME 2 in any published work, you should cite QIIME 2 and the plugins that you used. To display the citations for QIIME 2 and all installed plugins, run:

qiime info --citations

Any help figuring out why I can’t run gneiss would be much appreciated!
Thank you

Hi @Calliope_Holingue! How did you install QIIME 2? For example, did you perform a native installation, or are you using one of the virtual machine options (e.g. VirtualBox, Docker, AWS)?

What kind of virtual environment are you using (e.g. Python virtualenv, conda environment, something else)? Depending on what you have set up, the virtual environment could be causing issues with the QIIME 2 installation.

Hi @jairideout, thanks for your help.

I installed QIIME 2 using native installation, as described in the link you provided. I am running QIIME 2 within a conda environment, again based on the link above (source activate qiime2-2017.12),


Thanks for the info! I’m not sure why none of the QIIME 2 plugins are installed, something must have gone awry during the install process. Can you please try removing your qiime2-2017.12 environment and reinstall QIIME 2 following the native installation guide? After removing the qiime2-2017.12 environment, and before installing the environment again, please run these commands to clear conda’s cache and update conda:

conda clean -y --all
conda update conda

If reinstalling QIIME 2 doesn’t solve the problem, can you please send me the exact install commands you’re running, and all of the output they produce? Also let me know what operating system you’re using (macOS or Linux). Thanks!

Hi @jairideout, thanks for the help! The issue was resolved. I’m working from a cluster and had a to create a user specific conda environment to run qiime2, because the cluster version didn’t allow for all the qiime2 dependencies.

It’s working great now. Thanks!

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