Importing FeatureData[Taxonomy]

[five]

Hello

I would interested if anyone can solve a problem I have run into while using qiime tools import FeatureData[Taxonomy].

Passing the following commands:

qiime tools import
--type FeatureData[Taxonomy]
--input-path Data/Classifiers/Silva_128_release/SILVA_128_QIIME_release/taxonomy/16S_only/90/consensus_taxonomy_7_levels.txt
--output-path Data/Classifiers/Silva90_16STaxonomy.qza

or

qiime tools import
--type FeatureData[Taxonomy]
--input-path Data/Classifiers/Silva_128_release/SILVA_128_QIIME_release/taxonomy/16S_only/97/consensus_taxonomy_7_levels.txt
--output-path Data/Classifiers/Silva97_16STaxonomy.qza

In 2017_4 worked successfully, generating reference taxonomy artifacts I could use when using a qiime feature-classifier workflow.

However trialing these commands since moving to 2017_6 has generated errors such as

Traceback (most recent call last):
File "/home/qiime2/miniconda/envs/qiime2-2017.6/bin/qiime", line 6, in
sys.exit(q2cli.main.qiime())
File "/home/qiime2/miniconda/envs/qiime2-2017.6/lib/python3.5/site-packages/click/core.py", line 722, in call
return self.main(*args, **kwargs)
File "/home/qiime2/miniconda/envs/qiime2-2017.6/lib/python3.5/site-packages/click/core.py", line 697, in main
rv = self.invoke(ctx)
File "/home/qiime2/miniconda/envs/qiime2-2017.6/lib/python3.5/site-packages/click/core.py", line 1066, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/home/qiime2/miniconda/envs/qiime2-2017.6/lib/python3.5/site-packages/click/core.py", line 1066, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/home/qiime2/miniconda/envs/qiime2-2017.6/lib/python3.5/site-packages/click/core.py", line 895, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/home/qiime2/miniconda/envs/qiime2-2017.6/lib/python3.5/site-packages/click/core.py", line 535, in invoke
return callback(*args, **kwargs)
File "/home/qiime2/miniconda/envs/qiime2-2017.6/lib/python3.5/site-packages/q2cli/tools.py", line 111, in import_data
view_type=source_format)
File "/home/qiime2/miniconda/envs/qiime2-2017.6/lib/python3.5/site-packages/qiime2/sdk/result.py", line 192, in import_data
return cls.from_view(type, view, view_type, provenance_capture)
File "/home/qiime2/miniconda/envs/qiime2-2017.6/lib/python3.5/site-packages/qiime2/sdk/result.py", line 217, in _from_view
result = transformation(view)
File "/home/qiime2/miniconda/envs/qiime2-2017.6/lib/python3.5/site-packages/qiime2/core/transform.py", line 57, in transformation
self.validate(view)
File "/home/qiime2/miniconda/envs/qiime2-2017.6/lib/python3.5/site-packages/qiime2/core/transform.py", line 131, in validate
view.validate()
File "/home/qiime2/miniconda/envs/qiime2-2017.6/lib/python3.5/site-packages/qiime2/plugin/model/file_format.py", line 31, in validate
% (self.path, self.class.name))
ValueError: InPath('Data/Classifiers/Silva_128_release/SILVA_128_QIIME_release/taxonomy/16S_only/97/consensus_taxonomy_7_levels.txt') is not formatted as a TSVTaxonomyFormat file.

Any insight on what the problem is would be appreciated.

Thanks

[thermokarst]

Hi @five, we updated the TSVTaxonomyFormat in a recent release. Since the SILVA data you are attempting to import doesn’t contain a TSV header row, you will need to specify the source-format of the data on import to utilize the HeaderlessTSVTaxonomyFormat, instead of the default, TSVTaxonomyFormat:

qiime tools import \
 --type FeatureData[Taxonomy] \
 --input-path Data/Classifiers/Silva_128_release/SILVA_128_QIIME_release/taxonomy/16S_only/90/consensus_taxonomy_7_levels.txt \
 --source-format HeaderlessTSVTaxonomyFormat \
 --output-path Data/Classifiers/Silva90_16STaxonomy.qza

Hope that helps!