Gneiss add-pseudocount: no taxa.qza generated


I am using Qiime2-2017.8
In the tutorial “Differential abundance analysis with gneiss”, the command:

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

with output artifacts:
composition.qza: view | download
table.qza: view | download
taxa.qza: view | download

When I am doing it with my data, only the composition.qza is generated. But in the tutorial, we are asked to download the taxa.qza file.

Am I missing one step to get this file?

Hi @Nathalie25! The gneiss add-psuedocount command only generates the one output (specified with the --o-composition flag), so you are right on track! The other files you referenced are other files necessary for running the tutorial on its own:

The files table.qza and taxa.qza came from the two download blocks above the command block you referenced. Sorry if that isn't very clear, but if you have some ideas on how to make that more noticeable please let us know, we will gladly make changes! :t_rex:

Hello, thanks for your quick answer!
The tutorial is clear, and it works well with the data you provided.

But I am confused : How did you generated the taxa.qza file?

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The files taxa.qza and table.qza are just files necessary for running the tutorial independently. The files were generated as part of another tutorial, and are just linked to here, so that this tutorial can stand on its own, without requiring you to run through something like the Moving Pictures Tutorial from start to finish.

I can’t find in the Moving picture tutorial the command lines to make the file taxa.qza.
Are taxa.qza and taxonomy.qza the same file?

QIIME 2 doesn't care what you name your Artifacts or Visualizations, it is entirely up to you to choose names that are meaningful to you! Provenance takes care of the rest (tracking who did what, when it was done, where it was done, and how it was done)!

No, they aren't the same file - you can tell by loading both (taxa.qza from Gneiss Tutorial & taxonomy.qza from Moving Pictures Tutorial) in and investigating their provenance. What matters to QIIME 2 (and to you, a user of QIIME 2) is that while both of those files are different, they both represent the same Semantic Type of data: FeatureData[Taxonomy]!

If you haven't had a chance to review the Core Concepts section of the docs, I would highly recommend it!

Thanks for your help! For sure I will read the core concepts. I am a newbie, I installed qiime2 last week, but your tutorials are really helpful.
I will try to figure out how to get the taxa file, to complete the gneiss analyses.

Have a nice day

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