@thermokarst thanks for looking into this for me. I agree with your comment about the feature IDs not matching, but that was later when she was trying to build a custom tree after the pre-built tree use failed for her.
Earlier in the thread (on her first file upload, not the second one) there is still an issue that she identified that is possibly caused by underscores in the IDs. I'm having the same issue she is where I see the IDs matching between her feature table and the pre-built ghost tree .nwk but it's still failing when we run qiime diversity. I tried escaping the underscores but it still failed. This part should be super simple for users because they're just using the qiime diversity plugin with a pre-built ghost tree .nwk file, not q2-ghost-tree. Any ghost tree .nwk is just a phylogenetic tree that they can use in qiime diversity analysis. Do you or any of the team have any insight about this underscore issue? Thank you!