Hello @Nicholas_Bokulich,
thank you for your reply. Verbose gives me this error log (see below). I think you are right - e.g. calculating beta-diversity is impossible with only one sample. I will retry once I collected more sequences.
Thank you for your helpful reply.
/Users/administrator/miniconda3/envs/qiime2-2019.1/lib/python3.6/site-packages/sklearn/utils/validation.py:595: DataConversionWarning: Data with input dtype float64 was converted to bool by check_pairwise_arrays.
warnings.warn(msg, DataConversionWarning)
/Users/administrator/miniconda3/envs/qiime2-2019.1/lib/python3.6/site-packages/skbio/stats/ordination/_principal_coordinate_analysis.py:188: RuntimeWarning: invalid value encountered in true_divide
proportion_explained = eigvals / sum_eigenvalues
/Users/administrator/miniconda3/envs/qiime2-2019.1/lib/python3.6/site-packages/emperor/core.py:614: RuntimeWarning: invalid value encountered in true_divide
c_data = (coords / np.max(np.abs(coords)))
Traceback (most recent call last):
File "/Users/administrator/miniconda3/envs/qiime2-2019.1/lib/python3.6/site-packages/q2cli/commands.py", line 274, in call
results = action(**arguments)
File "</Users/administrator/miniconda3/envs/qiime2-2019.1/lib/python3.6/site-packages/decorator.py:decorator-gen-375>", line 2, in core_metrics_phylogenetic
File "/Users/administrator/miniconda3/envs/qiime2-2019.1/lib/python3.6/site-packages/qiime2/sdk/action.py", line 231, in bound_callable
output_types, provenance)
File "/Users/administrator/miniconda3/envs/qiime2-2019.1/lib/python3.6/site-packages/qiime2/sdk/action.py", line 458, in callable_executor
outputs = self._callable(scope.ctx, **view_args)
File "/Users/administrator/miniconda3/envs/qiime2-2019.1/lib/python3.6/site-packages/q2_diversity/_core_metrics.py", line 59, in core_metrics_phylogenetic
metric='unweighted_unifrac', n_jobs=n_jobs)
File "</Users/administrator/miniconda3/envs/qiime2-2019.1/lib/python3.6/site-packages/decorator.py:decorator-gen-465>", line 2, in beta_phylogenetic
File "/Users/administrator/miniconda3/envs/qiime2-2019.1/lib/python3.6/site-packages/qiime2/sdk/action.py", line 231, in bound_callable
output_types, provenance)
File "/Users/administrator/miniconda3/envs/qiime2-2019.1/lib/python3.6/site-packages/qiime2/sdk/action.py", line 365, in callable_executor
output_views = self._callable(**view_args)
File "/Users/administrator/miniconda3/envs/qiime2-2019.1/lib/python3.6/site-packages/q2_diversity/_beta/_method.py", line 105, in beta_phylogenetic
variance_adjusted=variance_adjusted, bypass_tips=bypass_tips)
File "/Users/administrator/miniconda3/envs/qiime2-2019.1/lib/python3.6/site-packages/unifrac/_methods.py", line 103, in unweighted
variance_adjusted, 1.0, bypass_tips, threads)
File "unifrac/_api.pyx", line 83, in unifrac._api.ssu
File "stringsource", line 251, in View.MemoryView.array_cwrapper
File "stringsource", line 153, in View.MemoryView.array.cinit
ValueError: Invalid shape in axis 0: 0.
Plugin error from diversity:
Invalid shape in axis 0: 0.
See above for debug info.