Hi,
I'm having the same problem when I use the diversity plugin. I am analyzing ITS readings that particularly do not show problems to merge, but the use of ghost-tree sounds very interesting and I would like to compare its diversity results with a FastTree generated tree.
I've tried the Method 2 from the tutorial and I managed to make a ghost-tree with Silva 138 and UNITE 2020-02-20 release but I couldn't root it neither with qiime phylogeny midpoint-root nor with midpoint.root function on r ('phytools' package).
The former gives the following error:
Traceback (most recent call last):
File "/home/qiime/miniconda2/envs/qiime2-2018.8/lib/python3.5/site-packages/q2cli/commands.py", line 274, in call
results = action(**arguments)
File "", line 2, in midpoint_root
File "/home/qiime/miniconda2/envs/qiime2-2018.8/lib/python3.5/site-packages/qiime2/sdk/action.py", line 199, in bound_callable
self.signature.check_types(**user_input)
File "/home/qiime/miniconda2/envs/qiime2-2018.8/lib/python3.5/site-packages/qiime2/core/type/signature.py", line 299, in check_types
"subtype of %r." % (name, spec.qiime_type))
Plugin error from phylogeny:
Argument to parameter 'tree' is not a subtype of Phylogeny[Unrooted].
The latter:
Error in double(nm * nm) : vector size cannot be NA
In addition: Warning message:
In nm * nm : NAs produced by integer overflow
Here is the artifact of my first ghost-tree: ghost-tree-foundation-allignment-80-otus.qza (1.2 MB) (also happens at 90% and 100% similarity. I'd like to compare those too)
I tried re-importing the tree as suggested in this post but didn't work.
Finally, I decided to generate the ghost tree using a pre- and non-pre rooted foundation .nwk tree with the following command:
qiime ghost-tree scaffold-hybrid-tree-foundation-tree
> --i-otu-map extensions_otu_map_80.qza
> --i-extension-taxonomy sh_taxonomy_qiime_ver8_dynamic_s_04.02.2020.qza
> --i-extension-sequences sh_refs_qiime_ver8_dynamic_s_04.02.2020.qza
> --i-foundation-tree tree-tax_slv_ssu_138.qza
> --i-foundation-taxonomy taxonomy_foundation.qza
> --o-ghost-tree ghost-tree-foundation-tree-80-otus.qza
but sandly I received the following error:
Traceback (most recent call last):
File "/home/qiime/miniconda2/envs/qiime2-2018.8/lib/python3.5/site-packages/q2cli/commands.py", line 274, in call
results = action(**arguments)
File "", line 2, in scaffold_hybrid_tree_foundation_tree
File "/home/qiime/miniconda2/envs/qiime2-2018.8/lib/python3.5/site-packages/qiime2/sdk/action.py", line 231, in bound_callable
output_types, provenance)
File "/home/qiime/miniconda2/envs/qiime2-2018.8/lib/python3.5/site-packages/qiime2/sdk/action.py", line 362, in callable_executor
output_views = self._callable(**view_args)
File "/slowdata/smcgreig/q2-ghost-tree/q2_ghost_tree/_scaffold_hybrid_tree_foundation_tree.py", line 49, in scaffold_hybrid_tree_foundation_tree
foundation_taxonomy_fh)[0]
File "/home/qiime/miniconda2/envs/qiime2-2018.8/lib/python3.5/site-packages/ghosttree/scaffold/hybridtree.py", line 116, in extensions_onto_foundation
graft_letter, foundation_taxonomy)
File "/home/qiime/miniconda2/envs/qiime2-2018.8/lib/python3.5/site-packages/ghosttree/scaffold/hybridtree.py", line 275, in _make_nr_foundation_newick
sheared_tree = foundation_tree.shear(foundation_unique_accessions)
File "/home/qiime/miniconda2/envs/qiime2-2018.8/lib/python3.5/site-packages/skbio/tree/_tree.py", line 468, in shear
node.parent.remove(node)
AttributeError: 'NoneType' object has no attribute 'remove'
Plugin error from ghost-tree:
'NoneType' object has no attribute 'remove'
Here are the artifacts used there: extensions_otu_map_80.qza (790.4 KB) sh_refs_qiime_ver8_dynamic_s_04.02.2020.qza (7.6 MB) sh_taxonomy_qiime_ver8_dynamic_s_04.02.2020.qza (1.4 MB) taxonomy_foundation.qza (117.9 KB) tree-tax_slv_ssu_138.qza (28.6 KB) .
I'm no more than a very beginner in bioinformatics and I ran out of ideas. I hope I've been clear enough.
Thank you very much for any help and thank you for developing this interesting tool. I hope the errors are caused by a mistake I've done.
If you cannot get ghost tree to work, you would be better off using Bray Curtis or Binary Jaccard metrics to look at the differences in your samples rather than a phylogenetic metric with no meaning. I attached my paper where I used those non-phylogenetic distance metrics before I published ghost-tree. It's usually a pay only article (bummer) so I attached it here. Just to show that I did not use FastTree on my ITS seqs. 
