Hi there.
I'm having a similar issue to topics here and here. However, I don't think that the solutions posted there work for me, as I'm processing more than one sample here, and the sampling depth should be at the depth of my largest sample. I'm using qiime2-2018.11.
My command was:
qiime diversity core-metrics-phylogenetic
--i-phylogeny SAR-rooted-tree.qza
--i-table SAR_table_97.qza
--p-sampling-depth 210111
--m-metadata-file ../metadata_LSU_qiime2_2017_bb_only.tsv
--output-dir SAR-core-metrics-results
--verbose
Error message:
/opt/anaconda/anaconda3/envs/qiime2-2018.11/lib/python3.5/importlib/_bootstrap.py:222: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
return f(*args, **kwds)
/opt/anaconda/anaconda3/envs/qiime2-2018.11/lib/python3.5/importlib/_bootstrap.py:222: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
return f(*args, **kwds)
/opt/anaconda/anaconda3/envs/qiime2-2018.11/lib/python3.5/importlib/_bootstrap.py:222: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
return f(*args, **kwds)
/opt/anaconda/anaconda3/envs/qiime2-2018.11/lib/python3.5/site-packages/h5py/init.py:34: FutureWarning: Conversion of the second argument of issubdtype from float to np.floating is deprecated. In future, it will be treated as np.float64 == np.dtype(float).type.
from ._conv import register_converters as _register_converters
/opt/anaconda/anaconda3/envs/qiime2-2018.11/lib/python3.5/importlib/_bootstrap.py:222: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility
return f(*args, **kwds)
/opt/anaconda/anaconda3/envs/qiime2-2018.11/lib/python3.5/importlib/_bootstrap.py:222: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
return f(*args, **kwds)
/opt/anaconda/anaconda3/envs/qiime2-2018.11/lib/python3.5/importlib/_bootstrap.py:222: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
return f(*args, **kwds)
/opt/anaconda/anaconda3/envs/qiime2-2018.11/lib/python3.5/importlib/_bootstrap.py:222: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
return f(*args, **kwds)
/opt/anaconda/anaconda3/envs/qiime2-2018.11/lib/python3.5/importlib/_bootstrap.py:222: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility
return f(*args, **kwds)
/opt/anaconda/anaconda3/envs/qiime2-2018.11/lib/python3.5/site-packages/sklearn/ensemble/weight_boosting.py:29: DeprecationWarning: numpy.core.umath_tests is an internal NumPy module and should not be imported. It will be removed in a future NumPy release.
from numpy.core.umath_tests import inner1d
/opt/anaconda/anaconda3/envs/qiime2-2018.11/lib/python3.5/importlib/_bootstrap.py:222: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
return f(*args, **kwds)
Traceback (most recent call last):
File "/opt/anaconda/anaconda3/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 "/opt/anaconda/anaconda3/envs/qiime2-2018.11/lib/python3.5/site-packages/qiime2/sdk/action.py", line 231, in bound_callable
output_types, provenance)
File "/opt/anaconda/anaconda3/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 "/opt/anaconda/anaconda3/envs/qiime2-2018.11/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 "/opt/anaconda/anaconda3/envs/qiime2-2018.11/lib/python3.5/site-packages/qiime2/sdk/action.py", line 231, in bound_callable
output_types, provenance)
File "/opt/anaconda/anaconda3/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 "/opt/anaconda/anaconda3/envs/qiime2-2018.11/lib/python3.5/site-packages/q2_diversity/_core_metrics.py", line 22, in core_metrics
results += alpha(table=rarefied_table, metric=metric)
File "", line 2, in alpha
File "/opt/anaconda/anaconda3/envs/qiime2-2018.11/lib/python3.5/site-packages/qiime2/sdk/action.py", line 231, in bound_callable
output_types, provenance)
File "/opt/anaconda/anaconda3/envs/qiime2-2018.11/lib/python3.5/site-packages/qiime2/sdk/action.py", line 390, in callable_executor
spec.qiime_type, output_view, spec.view_type, prov)
File "/opt/anaconda/anaconda3/envs/qiime2-2018.11/lib/python3.5/site-packages/qiime2/sdk/result.py", line 265, in _from_view
result = transformation(view)
File "/opt/anaconda/anaconda3/envs/qiime2-2018.11/lib/python3.5/site-packages/qiime2/core/transform.py", line 70, in transformation
new_view = transformer(view)
File "/opt/anaconda/anaconda3/envs/qiime2-2018.11/lib/python3.5/site-packages/qiime2/core/transform.py", line 223, in wrapped
new_view.file.write_data(file_view, self._wrapped_view_type)
File "/opt/anaconda/anaconda3/envs/qiime2-2018.11/lib/python3.5/site-packages/qiime2/plugin/model/directory_format.py", line 86, in write_data
result = transformation(view)
File "/opt/anaconda/anaconda3/envs/qiime2-2018.11/lib/python3.5/site-packages/qiime2/core/transform.py", line 68, in transformation
self.validate(view)
File "/opt/anaconda/anaconda3/envs/qiime2-2018.11/lib/python3.5/site-packages/qiime2/core/transform.py", line 143, in validate
view.validate('min')
File "/opt/anaconda/anaconda3/envs/qiime2-2018.11/lib/python3.5/site-packages/qiime2/plugin/model/file_format.py", line 34, in validate
% (self.path, self.class.name))
qiime2.core.exceptions.ValidationError: /tmp/q2-AlphaDiversityFormat-8hfqbjyx is not a(n) AlphaDiversityFormat file
Plugin error from diversity:
/tmp/q2-AlphaDiversityFormat-8hfqbjyx is not a(n) AlphaDiversityFormat file
See above for debug info.
Please also find attached my feature table summarize visualization. SAR_table.qzv (1.8 MB)
Thanks!