203967.metadata.tsv (702 Bytes) table-trim55126.qza (58.4 KB) rooted-tree.qza (76.7 KB)
I have qiime 2020.2 and qiime 2021.4 installed via conda.
Using the attached files, I ran the following command which succeeded in both qiime version 2020.2 and version 2021.4:
qiime diversity core-metrics-phylogenetic --verbose --i-phylogeny rooted-tree.qza --i-table table-trim55126.qza --m-metadata-file 203967.metadata.tsv --p-sampling-depth 300 --output-dir ./output/
.../site-packages/sklearn/metrics/pairwise.py:1735: DataConversionWarning: Data was converted to boolean for metric jaccard
warnings.warn(msg, DataConversionWarning)
.../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 -0.00311433891175376 and the largest is 0.5898033715594031.
RuntimeWarning
Saved FeatureTable[Frequency] to: ./output/rarefied_table.qza
Saved SampleData[AlphaDiversity] % Properties('phylogenetic') to: ./output/faith_pd_vector.qza
Saved SampleData[AlphaDiversity] to: ./output/observed_otus_vector.qza
Saved SampleData[AlphaDiversity] to: ./output/shannon_vector.qza
Saved SampleData[AlphaDiversity] to: ./output/evenness_vector.qza
Saved DistanceMatrix % Properties('phylogenetic') to: ./output/unweighted_unifrac_distance_matrix.qza
Saved DistanceMatrix % Properties('phylogenetic') to: ./output/weighted_unifrac_distance_matrix.qza
Saved DistanceMatrix to: ./output/jaccard_distance_matrix.qza
Saved DistanceMatrix to: ./output/bray_curtis_distance_matrix.qza
Saved PCoAResults to: ./output/unweighted_unifrac_pcoa_results.qza
Saved PCoAResults to: ./output/weighted_unifrac_pcoa_results.qza
Saved PCoAResults to: ./output/jaccard_pcoa_results.qza
Saved PCoAResults to: ./output/bray_curtis_pcoa_results.qza
Saved Visualization to: ./output/unweighted_unifrac_emperor.qzv
Saved Visualization to: ./output/weighted_unifrac_emperor.qzv
Saved Visualization to: ./output/jaccard_emperor.qzv
Saved Visualization to: ./output/bray_curtis_emperor.qzv
Then, I ran this command:
qiime diversity bioenv --verbose --i-distance-matrix ./output/unweighted_unifrac_distance_matrix.qza --m-metadata-file 203967.metadata.tsv --o-visualization ./output/unweighted-unifrac-bioenv.qzv
In qiime version 2020.2, I saw the output:
Saved Visualization to: ./output/unweighted-unifrac-bioenv.qzv
But in qiime version 2021.4, I saw the output:
Traceback (most recent call last):
File "/home/jacobs/miniconda3/envs/qiime2-2021.4/lib/python3.8/site-packages/q2cli/commands.py", line 329, in __call__
results = action(**arguments)
File "<decorator-gen-495>", line 2, in bioenv
File "/home/jacobs/miniconda3/envs/qiime2-2021.4/lib/python3.8/site-packages/qiime2/sdk/action.py", line 244, in bound_callable
outputs = self._callable_executor_(scope, callable_args,
File "/home/jacobs/miniconda3/envs/qiime2-2021.4/lib/python3.8/site-packages/qiime2/sdk/action.py", line 452, in _callable_executor_
ret_val = self._callable(output_dir=temp_dir, **view_args)
File "/home/jacobs/miniconda3/envs/qiime2-2021.4/lib/python3.8/site-packages/q2_diversity/_beta/_visualizer.py", line 47, in bioenv
metadata = qiime2.Metadata(df)
File "/home/jacobs/miniconda3/envs/qiime2-2021.4/lib/python3.8/site-packages/qiime2/metadata/metadata.py", line 357, in __init__
super().__init__(dataframe.index)
File "/home/jacobs/miniconda3/envs/qiime2-2021.4/lib/python3.8/site-packages/qiime2/metadata/metadata.py", line 92, in __init__
raise ValueError(
ValueError: Metadata must contain at least one ID.
Plugin error from diversity:
Metadata must contain at least one ID.
See above for debug info.
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