Hello Irene,
I have had a chance to look into this and unfortunately I haven’t been able to get to the bottom of it yet. 
I’m also getting “All feature_ids must be present as tip names in phylogeny . feature_ids not corresponding to tip names” error when running qiime diversity that I believe are related to underscores in the names of Newick files. The IDs definitely match! I can see them. See this issue if you’re interested: Errors when importing biomtable and tree files created by Ucluster into QIIME2
Previously, the UNITE files I have used did not have underscores, so I wasn’t aware that this would be a problem within the QIIME 2 environment. Underscores in names and IDs are pretty common. I tried to replace all _ with '_ in the Newick tree ghost tree (the ' is the escape character that was recommended) and rerun your diversity analysis, but I still got a failure. This time it is a new failure unrelated to the IDs not matching. I’m getting the following traceback now which is ultimately list index out of range plugin error from the qiime diversity plugin.
/Users/jenniferfouquier/anaconda3/envs/qiime2-2019.1/lib/python3.6/site-packages/sklearn/utils/validation.py:595: DataConversionWarning: Data with input dtype float64 was converted to bool by check_pairwise_arrays.
warnings.warn(msg, DataConversionWarning)
/Users/jenniferfouquier/anaconda3/envs/qiime2-2019.1/lib/python3.6/site-packages/skbio/stats/ordination/_principal_coordinate_analysis.py:152: RuntimeWarning: The result contains negative eigenvalues. Please compare their magnitude with the magnitude of some of the largest positive eigenvalues. If the negative ones are smaller, it's probably safe to ignore them, but if they are large in magnitude, the results won't be useful. See the Notes section for more details. The smallest eigenvalue is -0.07012680524153422 and the largest is 3.719931633058869.
RuntimeWarning
Traceback (most recent call last):
File "/Users/jenniferfouquier/anaconda3/envs/qiime2-2019.1/lib/python3.6/site-packages/q2cli/commands.py", line 274, in __call__
results = action(**arguments)
File "</Users/jenniferfouquier/anaconda3/envs/qiime2-2019.1/lib/python3.6/site-packages/decorator.py:decorator-gen-375>", line 2, in core_metrics_phylogenetic
File "/Users/jenniferfouquier/anaconda3/envs/qiime2-2019.1/lib/python3.6/site-packages/qiime2/sdk/action.py", line 231, in bound_callable
output_types, provenance)
File "/Users/jenniferfouquier/anaconda3/envs/qiime2-2019.1/lib/python3.6/site-packages/qiime2/sdk/action.py", line 458, in _callable_executor_
outputs = self._callable(scope.ctx, **view_args)
File "/Users/jenniferfouquier/anaconda3/envs/qiime2-2019.1/lib/python3.6/site-packages/q2_diversity/_core_metrics.py", line 55, in core_metrics_phylogenetic
metric='faith_pd')
File "</Users/jenniferfouquier/anaconda3/envs/qiime2-2019.1/lib/python3.6/site-packages/decorator.py:decorator-gen-482>", line 2, in alpha_phylogenetic
File "/Users/jenniferfouquier/anaconda3/envs/qiime2-2019.1/lib/python3.6/site-packages/qiime2/sdk/action.py", line 225, in bound_callable
spec.view_type, recorder)
File "/Users/jenniferfouquier/anaconda3/envs/qiime2-2019.1/lib/python3.6/site-packages/qiime2/sdk/result.py", line 287, in _view
result = transformation(self._archiver.data_dir)
File "/Users/jenniferfouquier/anaconda3/envs/qiime2-2019.1/lib/python3.6/site-packages/qiime2/core/transform.py", line 70, in transformation
new_view = transformer(view)
File "/Users/jenniferfouquier/anaconda3/envs/qiime2-2019.1/lib/python3.6/site-packages/qiime2/core/transform.py", line 213, in wrapped
return transformer(view.file.view(self._wrapped_view_type))
File "/Users/jenniferfouquier/anaconda3/envs/qiime2-2019.1/lib/python3.6/site-packages/q2_types/tree/_transformer.py", line 26, in _2
return skbio.TreeNode.read(fh, format='newick', verify=False)
File "/Users/jenniferfouquier/anaconda3/envs/qiime2-2019.1/lib/python3.6/site-packages/skbio/io/registry.py", line 652, in read
return registry.read(file, into=cls, format=format, **kwargs)
File "/Users/jenniferfouquier/anaconda3/envs/qiime2-2019.1/lib/python3.6/site-packages/skbio/io/registry.py", line 513, in read
return self._read_ret(file, format, into, verify, kwargs)
File "/Users/jenniferfouquier/anaconda3/envs/qiime2-2019.1/lib/python3.6/site-packages/skbio/io/registry.py", line 520, in _read_ret
return reader(file, **kwargs)
File "/Users/jenniferfouquier/anaconda3/envs/qiime2-2019.1/lib/python3.6/site-packages/skbio/io/registry.py", line 998, in wrapped_reader
return reader_function(fhs[-1], **kwargs)
File "/Users/jenniferfouquier/anaconda3/envs/qiime2-2019.1/lib/python3.6/site-packages/skbio/io/format/newick.py", line 307, in _newick_to_tree_node
while current_depth == tree_stack[-1][1]:
IndexError: list index out of range
Maybe @thermokarst or @ebolyen know what this issue is or can point me somwhere
Regarding running ghost-tree. It looks like you’re using qiime ghost-tree scaffold-hybrid-tree-foundation-alignment command correctly. I’m sorry you’re having so much trouble with all of this. It’s definitely not you. I would love to see these files. Can you attach all of these or send to jennifer.fouquier (at) ucdenver.edu?