Thanks @karren_owl --- I found the culprit. q2-phylogeny is using scikit-bio behind the scenes to do the midpoint rooting --- I was reading up on the Newick file format (used to represent the tree here), check this tidbit out:
In this format, underscores are treated as spaces --- in order to include a literal underscore, you must precede the underscore with a single-quote '. You can also surround the entire ID with single quotes.
I tried the qiime importing again using new biomtable and tree file with id quoted with single quotes. However, it runs to the same error again:
All feature_ids must be present as tip names in phylogeny. feature_ids not corresponding to tip names (n=515): ‘May12.50v_1549’ ‘Jul11.25v_4600’ ‘Jun22.0v_544
2’ ‘Aug5.50v_20401’ ‘May12.75v_1961’ ‘Jul11.50v_9708’ ‘Jul27.25v_4983’ ‘Jul27.50v_1972’
Are you sure you have your files in order? I just successfully ran the core-metrics-phylo command from above using the feature table (from above) (UUID e43d8331-06d5-4444-8835-70bec0bacf56) and the tree you just posted — worked as expected. Make sure you have everything in order and give it a shot again!
