Using Qiime2 to run core diversity analysis on Humann2 outputs


I am wanting to use Qiime2 to run core-diversity metrics on output from Humann2. I see on Humann2’s manual that Qiime1 supported this, and was wondering if Qiime 2 supported it as well? If so, how does one go about this? I’ve successfully converted my Humann2 outputs into .biom format, and subsequently converted the .biom files to Qiime2 artifacts, however, all downstream analyses that Qiime2 performs seem also to require that the physical sequences are input at some point (the rep-seq files is needed). Even if I could upload the WGS sequences, the features aren’t going to align with those created from the biom file. Is there a way around this that I’m just overlooking?


What actions are you trying to use? Very few actions that take a feature table as input also require reference sequences (or a phylogeny, for that matter).

My guess is that you are trying to run core-metrics-phylogenetic, which will require a phylogeny. Try core-metrics instead — unless if you really need phylogenetic diversity metrics and can construct a phylogeny for your features.

If you are trying a different action, let me know which and maybe I can recommend a workaround.