Hello,
I believe that, in the StrainPhlan tutorial, in step 5, the first part of the strainphlan command should be : " strainphlan -s consensus_markers/*.json.bz2… and not strainphlan -s consensus_markers/*.json. Otherwise, the sample files will not be recognized and it will give an error along the lines of: “samples + reference files <4”.
Great work with MetaPhlan and StrainPhlan, btw.