Coding problem with "qiime gneiss"


I am learning gneiss analysis using gimme. I followed the online tutorial:

I am using qiime2-2019.4 which was installed with conda under macOS system. I found some problems with the codes of gneiss analysis:

  1. There is no “qiime gneiss add-pseudocount”. I think it should be “qiime composition add-pseudocount”?

  2. I used “qiime composition add-pseudocount” to add a pseudocount to all of the counts and got a table in qza format. However, when I run:

qiime gneiss correlation-clustering
–i-table pseudo.qza
–o-clustering pseudo.hierarchy.qza

I got the error: Invalid value for “–i-table”: Expected an artifact of at least type
FeatureTable[Frequency]. An artifact of type FeatureTable[Composition] was

However, I downloaded the example from the tutorial, the “composition.qza” is also in FeatureTable[Composition] type. I am a bit confused. Could you please help me with it? Thank you a lot!

Since you are using the latest version of the Qiime2-2019.4, it would be better to use the updated GNEISS tutorial:
This step was already included as default and you are not required to do it by yourself. So it’s asking you to provide an original table

Good luck!


Hi Timanix,

I see. Thank you very much for help!