Hi @rlm!
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!