gneiss balance-taxonomy & taxonomy issues

I am having the same issue. I had taken my freq. table and collapsed the taxa to L6 prior to gneiss analysis. I had used the taxa collapse script as described in the ANCOM section of the Moving Pictures tutorial. All of the gneiss scripts worked well- until the ‘balance-taxonomy’ portion. I got the same error as Jewelna. After looking around the forum, it seems like others have experienced this, but I was unable to find a solution.

The problem looks to be what ebolyen suggested- the taxonomy artifact does not match the collapsed taxonomy in the gneiss analysis. What seems to be needed to solve the issue is a taxonomy artifact that is at the same taxonomic level (in my case, I need it at L6). I am not sure how to do this. Do I make a new taxonomy file from gg and set it at L6? Can I collapse the taxonomy file I already have to L6? I am going to try these approaches- but if anyone has fix, please let me know!

I think you are right, the issue here is that the FeatureTable[Frequency] IDs are the collapsed taxonomy strings, while the FeatureData[Taxonomy] IDs are still the hashed sequence values. We don’t have a method in QIIME 2 currently to collapse the FeatureData[Taxonomy], so you will have to do that manually (I would write some kind of script for that, personally).

Taking a step back, why can’t you use the uncollapsed table here?