I've just re-run all those commands and, as a second test, the command below alone:
qiime diversity core-metrics-phylogenetic --i-phylogeny rooted-tree.qza --i-table table.ftd.noUnassigned.qza --p-sampling-depth 20000 --m-metadata-file metadata3 --output-dir core-metrics-output --p-n-jobs 7
and now that error I've mentioned from here Qiime diversity beta-phylogenetic Data must be symmetric and cannot contain NaNs error returned:
Plugin error from diversity:
Data must be symmetric and cannot contain NaNs.
Is that possible that somehow the numbers (counts) in the table are being interpreted as float even if they are integer? I highlighted it
/home/leonardo.alves/miniconda2/envs/qiime2-2018.11/lib/python3.5/site-packages/sklearn/utils/validation.py:475: DataConversionWarning: Data with inp
ut dtype float64 was converted to bool by check_pairwise_arrays.
warnings.warn(msg, DataConversionWarning)
Traceback (most recent call last):
File "/home/leonardo.alves/miniconda2/envs/qiime2-2018.11/lib/python3.5/site-packages/q2cli/commands.py", line 274, in call
results = action(**arguments)
File "", line 2, in core_metrics_phylogenetic
File "/home/leonardo.alves/miniconda2/envs/qiime2-2018.11/lib/python3.5/site-packages/qiime2/sdk/action.py", line 231, in bound_callable
output_types, provenance)
File "/home/leonardo.alves/miniconda2/envs/qiime2-2018.11/lib/python3.5/site-packages/qiime2/sdk/action.py", line 455, in callable_executor
outputs = self._callable(scope.ctx, **view_args)
File "/home/leonardo.alves/miniconda2/envs/qiime2-2018.11/lib/python3.5/site-packages/q2_diversity/_core_metrics.py", line 59, in core_metrics_phyl
ogenetic
metric='unweighted_unifrac', n_jobs=n_jobs)
File "", line 2, in beta_phylogenetic
File "/home/leonardo.alves/miniconda2/envs/qiime2-2018.11/lib/python3.5/site-packages/qiime2/sdk/action.py", line 231, in bound_callable
output_types, provenance)
File "/home/leonardo.alves/miniconda2/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 "/home/leonardo.alves/miniconda2/envs/qiime2-2018.11/lib/python3.5/site-packages/q2_diversity/_beta/_method.py", line 99, in beta_phylogenetic
variance_adjusted=variance_adjusted, bypass_tips=bypass_tips)
File "/home/leonardo.alves/miniconda2/envs/qiime2-2018.11/lib/python3.5/site-packages/unifrac/_methods.py", line 103, in unweighted
variance_adjusted, 1.0, bypass_tips, threads)
File "unifrac/_api.pyx", line 90, in unifrac._api.ssu
File "/home/leonardo.alves/miniconda2/envs/qiime2-2018.11/lib/python3.5/site-packages/skbio/stats/distance/_base.py", line 106, in init
self._validate(data, ids)
File "/home/leonardo.alves/miniconda2/envs/qiime2-2018.11/lib/python3.5/site-packages/skbio/stats/distance/_base.py", line 873, in _validate
"Data must be symmetric and cannot contain NaNs.")
skbio.stats.distance._base.DistanceMatrixError: Data must be symmetric and cannot contain NaNs.