I am doing my first downstream analysis on metagenomic WGS data. I was classifying the taxonomy kraken2 (custom database - all refseqs) and calculating species abundances with bracken.
My Idea was to use qiime2 to calculate unifrac distances, since it provides nice plotting features. I obtained the pyhlogenetic tree in newick format from the kraken database using this script.
I tried to import this tree to qiime2 using the following commands:
qiime tools import --input-path ncbi_taxonomy.newick --type 'Phylogeny[Unrooted]' --output-path tax_tree.qza
qiime phylogeny midpoint-root --i-tree tax_tree.qza --o-rooted-tree tax_tree_rooted.qza
..and I get the following error:
Traceback (most recent call last):
File "/opt/conda/envs/qiime2-2018.11/lib/python3.5/site-packages/skbio/tree/_tree.py", line 2418, in get_max_distance
self._set_max_distance()
File "/opt/conda/envs/qiime2-2018.11/lib/python3.5/site-packages/skbio/tree/_tree.py", line 2359, in _set_max_distance
raise TreeError("No support for single descedent nodes")
skbio.tree._exception.TreeError: No support for single descedent nodes
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/opt/conda/envs/qiime2-2018.11/lib/python3.5/site-packages/q2cli/commands.py", line 274, in __call__
results = action(**arguments)
File "<decorator-gen-206>", line 2, in midpoint_root
File "/opt/conda/envs/qiime2-2018.11/lib/python3.5/site-packages/qiime2/sdk/action.py", line 231, in bound_callable
output_types, provenance)
File "/opt/conda/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 "/opt/conda/envs/qiime2-2018.11/lib/python3.5/site-packages/q2_phylogeny/_util.py", line 13, in midpoint_root
return tree.root_at_midpoint()
File "/opt/conda/envs/qiime2-2018.11/lib/python3.5/site-packages/skbio/tree/_tree.py", line 862, in root_at_midpoint
max_dist, tips = tree.get_max_distance()
File "/opt/conda/envs/qiime2-2018.11/lib/python3.5/site-packages/skbio/tree/_tree.py", line 2420, in get_max_distance
return self._get_max_distance_singledesc()
File "/opt/conda/envs/qiime2-2018.11/lib/python3.5/site-packages/skbio/tree/_tree.py", line 2376, in _get_max_distance_singledesc
distmtx = self.tip_tip_distances()
File "/opt/conda/envs/qiime2-2018.11/lib/python3.5/site-packages/skbio/tree/_tree.py", line 2501, in tip_tip_distances
result = np.zeros((num_tips, num_tips), float) # tip by tip matrix
MemoryError
I verified that the input tree is in valid Newick format. I was running the command on a +300GB RAM machine, so memory shouldn't be an issue. I don't know if I am getting something wrong? Does qiime require pyhlogentic trees to show some certain features. I would be glad if somone can give me Ideas or guidelines on how to get a my data into qiime.
