Hi @Jennifer_Fouquier ,
thanks for the reply, I attached the files. The table is the non-filtered table. I've been using the same versions of the ghost-tree, UNITE, and accessions file (01.12.2017), but the table doesn't seem to match the accessions file even though the format is the same. I am sure the issue is probably just some file is not quite the right version. I'm about to try again.
Also, I tried making a custom tree using the plugin following the tutorial, and got a confusing error. Just wondering if this looks like an error resulting from one of the files or an error from maybe an incomplete download or something?
qiime ghost-tree scaffold-hybrid-tree-foundation-alignment
--i-otu-map extensions_otu_map_90.qza
--i-extension-taxonomy m2taxonomy2.qza \
--i-extension-sequences sh_refs_qiime_ver7_dynamic_01.12.2017.qza
--i-foundation-alignment silva_fungi_only_full_aligned_132_FILTERED.qza
--o-ghost-tree ghost-tree-foundation-allignment-90-otus.qza
--verbose
Traceback (most recent call last):
File "/Users/ihoxie/miniconda3/envs/qiime2-2018.11/lib/python3.5/site-packages/q2cli/commands.py", line 274, in call
results = action(**arguments)
File "<decorator-gen-458>", line 2, in scaffold_hybrid_tree_foundation_alignment
File "/Users/ihoxie/miniconda3/envs/qiime2-2018.11/lib/python3.5/site-packages/qiime2/sdk/action.py", line 231, in bound_callable
output_types, provenance)
File "/Users/ihoxie/miniconda3/envs/qiime2-2018.11/lib/python3.5/site-packages/qiime2/sdk/action.py", line 362, in callable_executor
output_views = self._callable(**view_args)
File "/Users/ihoxie/q2-ghost-tree/q2_ghost_tree/_scaffold_hybrid_tree_foundation_alignment.py", line 44, in scaffold_hybrid_tree_foundation_alignment
gt_path, graft_level, None)[0]
File "/Users/ihoxie/miniconda3/envs/qiime2-2018.11/lib/python3.5/site-packages/ghosttree/scaffold/hybridtree.py", line 104, in extensions_onto_foundation
graft_level)
File "/Users/ihoxie/miniconda3/envs/qiime2-2018.11/lib/python3.5/site-packages/ghosttree/scaffold/hybridtree.py", line 205, in _extension_genus_accession_dict
taxonomy = accession_taxonomy_dic[i]
KeyError: '296d0566e223449e84f48b2f3fafded4'
Plugin error from ghost-tree:
'296d0566e223449e84f48b2f3fafded4'
See above for debug info.
Thanks for the help!
table-cr-973.qza (263.0 KB)
ghost-tree-midpoint-root2.qza (493.8 KB)
Metadatajustsamples.tsv (2.7 KB)