Adding qiime2 taxonomy data to a .biom file


I’ve been trying these steps in order to import the biom file to Qiime1 and summarize the taxa barplot by categories. The export parts worked fine, I think, but when trying to add the metadata values to the biom file this error is returned:

biom.exception.BiomParseException: No header line was found in mapping file.


I have changed the biom-taxonomy.tsv file header line in order to reproduce what you wrote on your answer, like this:

#OTUID taxonomy confidence

This way, when running the code line, the error I reproduced before appears:

biom add-metadata -i exported/feature-table.biom -o table-with-taxonomy.biom --observation-metadata-fp biom-taxonomy.tsv --sc-separated taxonomy

Do you know where the error could be? Maybe with the table.qza file I am using? I tried using the table file obtained after the trimming step, maybe I should use another one?

Thank you very much in advance!

Hi @mc92! Can you double-check that #OTUID, taxonomy, and confidence are separated by tab characters instead of spaces? If that doesn’t work, can you send me the biom-taxonomy.tsv file so I can take a look?

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I tried writting the header line from zero and now it worked, so I assume I had some space I didn’t see previously.

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