Diversity core-metrics ValueError: "tree" must be rooted

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:

Plugin error from diversity:

tree must be rooted.

Any suggestions?


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Here is the error report:

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.

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!

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