Analyzing PICRUSt output in QIIME using gneiss

Hi QIIME support team,

I’ve recently been working on processing some PICRUSt data, and I’ve been trying to process my metagenome predictions in QIIME through gneiss to try and get differentially abundant KOs. So far, this is what I’ve done:

#convert txt to biom
biom convert -i metagenome_predictions_QIIMEedited.txt -o metagenome_predictions_QIIMEedited_hdf5.biom --table-type=“OTU table” --to-hdf5

#import biom table into QIIME2
qiime tools import
–input-path metagenome_predictions_QIIMEedited_hdf5.biom
–type ‘FeatureTable[Frequency]’
–input-format BIOMV210Format
–output-path metagenome_predictions_QIIMEedited.qza

#add pseudocount
qiime composition add-pseudocount
–i-table metagenome_predictions_QIIMEedited.qza
–o-composition-table metagenome_predictions_QIIMEedited_pseudocount.qza

qiime gneiss gradient-clustering
–i-table metagenome_predictions_QIIMEedited_pseudocount.qza
–m-gradient-file /Users/heatherdeel/Dropbox/PMI_3_analyses/bone/02_metadata/maps/map3_no_blanks.txt
–m-gradient-column ADD_0
–o-clustering gradient-hierarchy.qza

All of the above was completed successfully, and I was able to summarize the feature table as well and it was converted correctly. However, when I try to perform gneiss using the following, I get this error:

qiime gneiss ilr-hierarchical
–i-table metagenome_predictions_QIIMEedited_pseudocount.qza
–i-tree gradient-hierarchy.qza
–o-balances balances.qza

Plugin error from gneiss:

Argument to parameter ‘table’ is not a subtype of FeatureTable[Frequency].

Does anyone know what the problem may be? Also, it is entirely possible that this isn’t a good way to visualize my PICRUSt data, does anyone have any insight about whether this is a good strategy or not?

Thank you so much in advance!

1 Like

Hi @hdeel!
The issue is this command:

Pseudocount is now automatically added by gneiss, and does not (should not) be run prior to gneiss. See the latest gneiss tutorial for examples (I expect you were following an older tutorial or someone else’s commands).

So in other words, metagenome_predictions_QIIMEedited.qza should be the input table for ilr-hierarchical.

I hope that helps!

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