Another caveat of ITS data is that it's hard to produce a meaningful phylogenetic tree that works well with phylogenetic diversity metrics such as Faith's PD or UniFrac. When performing diversity analyses with ITS data you'll need to use non-phylogenetic metrics for alpha and beta diversity (e.g. Observed OTUs/Species, Shannon, Bray-Curtis, Jaccard, etc.).
Unfortunately the qiime diversity core-metrics workflow requires a phylogenetic tree, so you won't be able to use that command with your data. We have an open issue to make core-metrics work without a phylogenetic tree -- it'll likely be in the upcoming 2017.8 release which will go live next week. We'll follow up here when it's available!
In the meantime, you can run each of the steps individually instead of using core-metrics -- see @ebolyen's suggestions in this topic.