import a feature table in .tsv

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1

I am trying to import a feature table in .tsv format and am getting the error below. What should I do? Thank you!

(qiime2-2021.4) FVFCW3NGP3Y0:QUIIME_try natalia_palacios$ qiime tools import --type 'FeatureTable[Frequency]' --input-path feature_table_for_quiime-4.tsv --input-format TSVTaxonomyFormat --output-path taxonomy.qza
Traceback (most recent call last):
File "/Users/natalia_palacios/opt/anaconda3/envs/qiime2-2021.4/lib/python3.8/site-packages/q2cli/builtin/tools.py", line 157, in import_data
artifact = qiime2.sdk.Artifact.import_data(type, input_path,
File "/Users/natalia_palacios/opt/anaconda3/envs/qiime2-2021.4/lib/python3.8/site-packages/qiime2/sdk/result.py", line 240, in import_data
return cls.from_view(type, view, view_type, provenance_capture,
File "/Users/natalia_palacios/opt/anaconda3/envs/qiime2-2021.4/lib/python3.8/site-packages/qiime2/sdk/result.py", line 265, in _from_view
transformation = from_type.make_transformation(to_type,
File "/Users/natalia_palacios/opt/anaconda3/envs/qiime2-2021.4/lib/python3.8/site-packages/qiime2/core/transform.py", line 58, in make_transformation
raise Exception("No transformation from %r to %r" %
Exception: No transformation from <class 'q2_types.feature_data._format.TSVTaxonomyFormat'> to <class 'q2_types.feature_table._format.BIOMV210DirFmt'>

An unexpected error has occurred:

No transformation from <class 'q2_types.feature_data._format.TSVTaxonomyFormat'> to <class 'q2_types.feature_table._format.BIOMV210DirFmt'>

  • Have you reviewed the QIIME 2 Forum Glossary?
  • Version of QIIME 2 you are running, and how it is installed (e.g. Virtualbox, conda, etc.)
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2

Hi @Natasha_Palacios

Looks like you are trying to import a feature-table.tsv (judging by its name, it contains read counts by samples) as a taxonomy artifact, which should contain information about taxa assignments.

3

Yes, I am trying to import a feature table (abundance of each species by sample). How do I do this?

4

Hi!
As I understood, you have a .tsv file that needed to be imported to Qiime2.
If yes, you should convert a .tsv file to biom first:

biom convert -i feature-table.tsv -o feature-table.biom --table-type="OTU table" --to-hdf5

Now you should be able to import it:

qiime tools import \
  --input-path feature-table.biom \
  --type 'FeatureTable[Frequency]' \
  --input-format BIOMV210Format \
  --output-path feature-table.qza
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5

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