the class column for the LEfSe command is missing if the comparison is not pairwise. Happens on the Linux and Ubuntu versions with the most recent version of mothur (1.48.0) on Ubuntu 23.10 and Ubuntu 22.04. As soon as I add a third class to any analysis, the class column is gone. Tried also the example data from the MiSeq SOP (only change is that I included a third class in the design file for a few samples (early, late and test). Resulted in the same behavior.