When running the command:
qiime diversity core-metrics-phylogenetic --i-phylogeny /Users/Becca/Box\ Sync/RAPID/biom/rooted-tree.qza --i-table /Users/Becca/Box\ Sync/RAPID/biom/otu-table-no-mitochondria-no-chloroplast-min2-names.qza --m-metadata-file /Users/Becca/Box\ Sync/RAPID/RAPID-analysis/data/map.txt --output-dir /Users/Becca/Box\ Sync/RAPID/rarefied-table-results/core-metrics-results --p-sampling-depth 1001
I get the error:
Plugin error from diversity:
init() got an unexpected keyword argument 'procrustes'
The full Debug info:
/Users/Becca/miniconda2/envs/qiime2-2018.8/lib/python3.5/site-packages/skbio/div
ersity/alpha/_base.py:793: RuntimeWarning: invalid value encountered in double_s
calars
return shannon(counts, base=np.e) / np.log(observed_otus(counts))
/Users/Becca/miniconda2/envs/qiime2-2018.8/lib/python3.5/site-packages/sklearn/u
tils/validation.py:475: DataConversionWarning: Data with input dtype float64 was
converted to bool by check_pairwise_arrays.
warnings.warn(msg, DataConversionWarning)
/Users/Becca/miniconda2/envs/qiime2-2018.8/lib/python3.5/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 -0.44991660503480524 and the largest is 10.340186068286494.
RuntimeWarning
Traceback (most recent call last):
File "/Users/Becca/miniconda2/envs/qiime2-2018.8/lib/python3.5/site-packages/q2cli/commands.py", line 274, in call
results = action(**arguments)
File "", line 2, in core_metrics_phylogenetic
File "/Users/Becca/miniconda2/envs/qiime2-2018.8/lib/python3.5/site-packages/qiime2/sdk/action.py", line 231, in bound_callable
output_types, provenance)
File "/Users/Becca/miniconda2/envs/qiime2-2018.8/lib/python3.5/site-packages/qiime2/sdk/action.py", line 455, in callable_executor
outputs = self._callable(scope.ctx, **view_args)
File "/Users/Becca/miniconda2/envs/qiime2-2018.8/lib/python3.5/site-packages/q2_diversity/_core_metrics.py", line 51, in core_metrics_phylogenetic
metadata=metadata, n_jobs=n_jobs)
File "", line 2, in core_metrics
File "/Users/Becca/miniconda2/envs/qiime2-2018.8/lib/python3.5/site-packages/qiime2/sdk/action.py", line 231, in bound_callable
output_types, provenance)
File "/Users/Becca/miniconda2/envs/qiime2-2018.8/lib/python3.5/site-packages/qiime2/sdk/action.py", line 455, in callable_executor
outputs = self._callable(scope.ctx, **view_args)
File "/Users/Becca/miniconda2/envs/qiime2-2018.8/lib/python3.5/site-packages/q2_diversity/_core_metrics.py", line 37, in core_metrics
results += emperor_plot(pcoa=pcoa, metadata=metadata)
File "", line 2, in plot
File "/Users/Becca/miniconda2/envs/qiime2-2018.8/lib/python3.5/site-packages/qiime2/sdk/action.py", line 231, in bound_callable
output_types, provenance)
File "/Users/Becca/miniconda2/envs/qiime2-2018.8/lib/python3.5/site-packages/qiime2/sdk/action.py", line 424, in callable_executor
ret_val = self._callable(output_dir=temp_dir, **view_args)
File "/Users/Becca/miniconda2/envs/qiime2-2018.8/lib/python3.5/site-packages/q2_emperor/_plot.py", line 58, in plot
custom_axes=custom_axes, plot_name='plot')
File "/Users/Becca/miniconda2/envs/qiime2-2018.8/lib/python3.5/site-packages/q2_emperor/_plot.py", line 38, in _generic_plot
procrustes=procrustes, remote='.')
TypeError: init() got an unexpected keyword argument 'procrustes'
Any suggestions on what could be going wrong?
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