Plugin error from gneiss:
Debug info has been saved to /tmp/qiime2-q2cli-err-1d7j37cq.log
I can only suspect that the error is within the composition and/or hierarchy artefact, as my feature table worked fine throughout other qiime2 analysis, but then again I don't know :)
The log files indicate some sort of memory error, which has been raised in a previous post here. However no troubleshoot was given. Is this a simple case of disk space?
/home/qiime2/miniconda/envs/qiime2-2017.12/lib/python3.5/site-packages/gneiss-0.4.2-py3.5.egg/gneiss/util.py:181: FutureWarning: '.reindex_axis' is deprecated and will be removed in a future version. Use '.reindex' instead.
Traceback (most recent call last):
File "/home/qiime2/miniconda/envs/qiime2-2017.12/lib/python3.5/site-packages/q2cli/commands.py", line 224, in __call__
results = action(**arguments)
File "<decorator-gen-208>", line 2, in ilr_transform
File "/home/qiime2/miniconda/envs/qiime2-2017.12/lib/python3.5/site-packages/qiime2/sdk/action.py", line 228, in bound_callable
output_types, provenance)
File "/home/qiime2/miniconda/envs/qiime2-2017.12/lib/python3.5/site-packages/qiime2/sdk/action.py", line 363, in _callable_executor_
output_views = self._callable(**view_args)
File "/home/qiime2/miniconda/envs/qiime2-2017.12/lib/python3.5/site-packages/gneiss-0.4.2-py3.5.egg/gneiss/composition/_composition.py", line 18, in ilr_transform
balances = ilr(_table.values, basis)
File "/home/qiime2/miniconda/envs/qiime2-2017.12/lib/python3.5/site-packages/skbio/stats/composition.py", line 570, in ilr
_check_orthogonality(basis)
File "/home/qiime2/miniconda/envs/qiime2-2017.12/lib/python3.5/site-packages/skbio/stats/composition.py", line 1119, in _check_orthogonality
if not np.allclose(inner(basis, basis), np.identity(len(basis)),
File "/home/qiime2/miniconda/envs/qiime2-2017.12/lib/python3.5/site-packages/skbio/stats/composition.py", line 413, in inner
a, b = clr(x), clr(y)
File "/home/qiime2/miniconda/envs/qiime2-2017.12/lib/python3.5/site-packages/skbio/stats/composition.py", line 461, in clr
lmat = np.log(mat)
MemoryError