Regarding OTu count table generation with taxonomy details using biom commands in qiime2

I am a PhD student working on bacterial diversity of different Arctic ecosystems. I am in the learning phase of Qiime2. I could successfully do the data processing as per the instructions given in the qiime2 tutorials following Atacama and moving picture tutorials. I was trying to make the otu count table from the table.qza file using the commands mentioned in the forum: Exporting and modifying BIOM tables (e.g. adding taxonomy annotations).
I could successfully retrieve the count table but while trying to add the taxonomy information to the OTU count table, I was not able to get the result. I am still getting the same OTU count table without any taxonomy information.
Here are the commands that I have used:
qiime tools export --input-path table-nonchimeric-wo-borderline.qza --output-path exported_table-nc-wobl-new
biom head -i exported_table-nc-wobl-new/feature-table.tsv
qiime tools export --input-path nc-wobl-trained-taxonomy.qza --output-path exported_table-nc-wobl-new
cp exported_table-nc-wobl-new/taxonomy.tsv biom-new-taxonomy.tsv
the headers of biom-new-taxonomy.tsv was
Feature ID Taxon Confidence
This was changed to : #OTUID taxonomy confidence
saved and did the following steps.
biom add-metadata -i exported_table-nc-wobl-new/feature-table.biom -o table-with-taxonomy-nc-wobl-new.biom -m sample_metadata.tsv --observation-metadata-fp biom-new-taxonomy.tsv --sc-separated taxonomy --observation-header OTUID,taxonomy,confidence

biom convert -i table-with-taxonomy-nc-wobl-new.biom -o feature-table-nc-wobl-new-with-taxonomy.tsv -m sample_metadata.tsv --to-tsv

There is no error message generated. The command is getting executed but no taxonomy is added to the count table.

Can anyone suggest how to rectify this issue.


Femi Thomas

Hi @Femi_Thomas

You forget a key parameter.
biom convert -i table-with-taxonomy-nc-wobl-new.biom -o feature-table-nc-wobl-new-with-taxonomy.tsv -m sample_metadata.tsv --to-tsv –header-key taxonomy
Try it and let us know if it work out.


Hi @sixvable
Thank you for your suggestion. Your suggestion was helpful. Plus I had made a mistake while converting the biom-new-taxonomy.tsv headers to #OTUID which I realized. Now I have finally got the OTU count table with taxonomy info.