Qiime 2 plugin gneiss error

Dear all,

I´m trying to perform the differential abundance analysis with gneiss but I can´t figure out the problem.
qiime gneiss add-pseudocount
–i-table table.qza
–p-pseudocount 1
–o-composition-table composition.qza

It says Error: QIIME 2 plugin ‘gneiss’ has no action ‘add-pseudocount’.

Hi there @ssbbrr -

This command was removed one year ago, and was replaced with inline-parameters for controlling the psuedocount value. Are you following an old tutorial somewhere? What version of QIIME 2 are you using?

yes I´m following the old tutorial from here: https://docs.qiime2.org/2018.2/tutorials/gneiss/
I´m using qiime 2, 2019.1 . So since the tutorial doesn’t work, can someone put up the new code or new tutorial??

you are following a very old tutorial that does not match the version of QIIME 2 that you are running.

On the left-hand side of the documentation page there is a button with a drop-down menu of different release versions:

use this button to choose the version of QIIME 2 that you are running:

or better yet always run the latest version of QIIME 2 and you will always match the latest documentation :smile:

The other option is to modify the URL to match the version you are running. SO:

Try this instead: QIIME 2 user documentation — QIIME 2 2019.1.0 documentation

Just a note of interest: the tutorials/documentation will always work because they are automatically run and tested as a part of every single release... this keeps us from accidentally releasing broken documentation! (some details of the text may get stale if we fail to catch it, but the code will always run fine since it is automatically tested)


Thank you so much for your help! I got the latest tutorial now! :slight_smile: