Hi ~,
when i try to use the taxa filter-table, i got plug error:
"Plugin error from taxa:
CategoricalMetadataColumn does not support strings with leading or trailing whitespace characters: 'D_0__Bacteria;D_1__Chloroflexi;D_2__Gitt-GS-136;D_3__uncultured bacterium ’
Debug info has been saved to /tmp/qiime2-q2cli-err-xm1a_ve7.log"
my commands are:
qiime taxa filter-table
–i-table unfiltered-table.qza
–i-taxonomy taxonomy.qza
–p-include 0__Bacteria
–o-filtered-table table.qza
I want to keep all sequences which contain Bacteria. According to Qiime taxa filter-table filtering multiple taxa, i need to use 0__Bacteria.
When i go to the debug log:
part of it looks like this(It is long, i only copied part of it here):File “/mnt/research/germs/softwares/miniconda2/envs/qiime2-2018.2/lib/python3.5/site-packages/qiime2/metadata/metadata.py”, line 218, in normalize
dataframe
metadata_column = self._metadata_column_factory(series)
File “/mnt/research/germs/softwares/miniconda2/envs/qiime2-2018.2/lib/python3.5/site-packages/qiime2/metadata/metadata.py”, line 230, in _metadata_c
olumn_factory
column = CategoricalMetadataColumn(series)
File “/mnt/research/germs/softwares/miniconda2/envs/qiime2-2018.2/lib/python3.5/site-packages/qiime2/metadata/metadata.py”, line 632, in init
self._series = self.normalize(series)
File “/mnt/research/germs/softwares/miniconda2/envs/qiime2-2018.2/lib/python3.5/site-packages/qiime2/metadata/metadata.py”, line 758, in normalize
return series.apply(normalize, convert_dtype=False)
File “/mnt/research/germs/softwares/miniconda2/envs/qiime2-2018.2/lib/python3.5/site-packages/pandas/core/series.py”, line 2551, in apply
mapped = lib.map_infer(values, f, convert=convert_dtype)
File “pandas/_libs/src/inference.pyx”, line 1521, in pandas._libs.lib.map_infer
File “/mnt/research/germs/softwares/miniconda2/envs/qiime2-2018.2/lib/python3.5/site-packages/qiime2/metadata/metadata.py”, line 748, in normalize
“whitespace characters: %r” % (cls.name, value))
ValueError: CategoricalMetadataColumn does not support strings with leading or trailing whitespace characters: 'D_0__Bacteria;D_1__Chloroflexi;D_2__Gi
tt-GS-136;D_3__uncultured bacterium ’
The taxonomy.qza which contains these 'D_0__Bacteria;D_1__Chloroflexi;D_2__Gitt-GS-136;D_3__uncultured bacterium ’ was generated by qiime2 after the following commands:
qiime feature-classifier classify-consensus-blast
–i-query rep-seqs.qza
–i-reference-taxonomy majority_taxonomy_7_levels.qza
–i-reference-reads 97_otus_16S.qza
–o-classification taxonomy
–p-perc-identity 0.90
–p-maxaccepts 1
Anybody has any idea to solve this error?
Thanks