How to convert txt to qzv

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1

I need to convert taxonomy.txt to taxonomy .qzv. The following conmand does not work.

Error information:

taxonomy.txt (2.1 MB)

TypeError: classifier.txt does not appear to be a BIOM file!

biom convert -i taxonomy.txt -o taxonomy.biom --table-type "Table" --to-hdf5
2

Hi @SouthGateProject,

To go from a taxonomy.txt to a taxonomy.qza, there are a few steps.

  1. Import the taxonomy.txt into QIIME 2 so you can get a taxonomy.qza
qiime tools import --input-path <path to taxonomy.txt> --output-path taxonomy.qza --type 'FeatureData[Taxonomy]'
  1. Next, you will need to visualize your taxonomy.qza to get it to be a taxonomy.qzv
qiime metadata tabulate \
  --m-input-file taxonomy.qza \
  --o-visualization taxonomy.qzv

I hope this helps!

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3

There was a problem importing taxonomy.txt:

taxonomy.txt is not a(n) TSVTaxonomyFormat file:

['Feature ID', 'Taxon'] must be the first two header values. The first two header values provided are: ['OTUID', 'Domain'] (on line 1).

It must be tsv format?

4

Hi @SouthGateProject,
Yes, a Taxonomy file in QIIME 2 is a TSV.

What that error is saying is that QIIME 2 expects the header of your file to be "'Feature ID' and 'Taxon' but yours says 'OTUID' and 'Domain'.

Can you edit your file so that the header says 'Feature ID' and 'Taxon', and try to import?

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5

@cherman2 Thanks. The error has been solved.

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