I created txonomy.qza by running qiime feature-classifier classify-sklearn command
thne I tried running following command -
qiime metadata tabulate
–m-input-file taxonomy.qza
–o-visualization taxonomy
I got following debug information -
Traceback (most recent call last):
File “/home/amol2/volume/software/miniconda/miniconda2/envs/qiime2-2019.7/lib/python3.6/site-packages/q2cli/click/type.py”, line 170, in _convert_metadata
metadata = artifact.view(qiime2.Metadata)
File “/home/amol2/volume/software/miniconda/miniconda2/envs/qiime2-2019.7/lib/python3.6/site-packages/qiime2/sdk/result.py”, line 277, in view
return self._view(view_type)
File “/home/amol2/volume/software/miniconda/miniconda2/envs/qiime2-2019.7/lib/python3.6/site-packages/qiime2/sdk/result.py”, line 289, in _view
result = transformation(self._archiver.data_dir)
File “/home/amol2/volume/software/miniconda/miniconda2/envs/qiime2-2019.7/lib/python3.6/site-packages/qiime2/core/transform.py”, line 70, in transformation
new_view = transformer(view)
File “/home/amol2/volume/software/miniconda/miniconda2/envs/qiime2-2019.7/lib/python3.6/site-packages/qiime2/core/transform.py”, line 213, in wrapped
return transformer(view.file.view(self._wrapped_view_type))
File “/home/amol2/volume/software/miniconda/miniconda2/envs/qiime2-2019.7/lib/python3.6/site-packages/q2_types/feature_data/_transformer.py”, line 194, in _29
return qiime2.Metadata(df)
File “/home/amol2/volume/software/miniconda/miniconda2/envs/qiime2-2019.7/lib/python3.6/site-packages/qiime2/metadata/metadata.py”, line 364, in init
self._dataframe, self._columns = self._normalize_dataframe(dataframe)
File “/home/amol2/volume/software/miniconda/miniconda2/envs/qiime2-2019.7/lib/python3.6/site-packages/qiime2/metadata/metadata.py”, line 372, in _normalize_dataframe
metadata_column = self._metadata_column_factory(series)
File “/home/amol2/volume/software/miniconda/miniconda2/envs/qiime2-2019.7/lib/python3.6/site-packages/qiime2/metadata/metadata.py”, line 384, in _metadata_column_factory
column = CategoricalMetadataColumn(series)
File “/home/amol2/volume/software/miniconda/miniconda2/envs/qiime2-2019.7/lib/python3.6/site-packages/qiime2/metadata/metadata.py”, line 880, in init
self._series = self.normalize(series)
File “/home/amol2/volume/software/miniconda/miniconda2/envs/qiime2-2019.7/lib/python3.6/site-packages/qiime2/metadata/metadata.py”, line 1150, in normalize
return series.apply(normalize, convert_dtype=False)
File “/home/amol2/volume/software/miniconda/miniconda2/envs/qiime2-2019.7/lib/python3.6/site-packages/pandas/core/series.py”, line 3591, in apply
mapped = lib.map_infer(values, f, convert=convert_dtype)
File “pandas/_libs/lib.pyx”, line 2217, in pandas._libs.lib.map_infer
File “/home/amol2/volume/software/miniconda/miniconda2/envs/qiime2-2019.7/lib/python3.6/site-packages/qiime2/metadata/metadata.py”, line 1139, in normalize
“value: %r” % (cls.name, series.name, value))
ValueError: CategoricalMetadataColumn does not support values with leading or trailing whitespace characters. Column ‘Taxon’ has the following value: 'D_0__Bacteria;D_1__Actinobacteria;D_2__Thermoleophilia;D_3__Solirubrobacterales;D_4__67-14;D_5__uncultured bacterium ’
Looking at other posts it looks like a similar problem like this
wonder if it is a bug? I followed steps suggested by @thermokarst and it has worked well, Thanks