I am using Qiime Version 2017.10. I imported my rep_set.tre from Qiime1 to Qiime2 with the qiime tools import command and the flag --type 'Phylogeny[Rooted]'. rep_set-tree.qza (40.1 KB)
When I run the qiime diversity core-metrics-phylogenetic with the rep_set-tree.qza I get the error:
File “/~/local/bin/miniconda3/envs/qiime2-2017.10/lib/python3.5/site-packages/skbio/diversity/_util.py”, line 81, in _validate_otu_ids_and_tree
raise ValueError("tree must be rooted.")
ValueError: tree must be rooted.
I think the issue is that the import is saying that the tree is rooted, when it actually isn’t. Fortunately the fix is straight-forward. You’ll need to re-import your tree with a the same command as before, but instead of making the type Phylogeny[Rooted], just make it Phylogeny[Unrooted].
Then you can run qiime phylogeny midpoint-root on your new tree to get a rooted tree that core-metrics-phylogeny should like.
Let me know if that works, or if you need more detailed directions!