Converted biom table does not contain taxonomy


I am trying to obtain a classic OTU table with taxonomy using the biom functions from qiime2. I have followed the post by @thermokarst (Exporting and modifying BIOM tables (e.g. adding taxonomy annotations)) and when I obtain the biom table with taxonomy, I try to convert that biom table to tsv format and the taxonomy annotations are not added!

I have checked other posts with similar problems:

TypeError: can only join an iterable

So, could anybody tell me how to fix this issue?


Hi @Pablo_V,
I haven’t actually looked into your specific error/case here but a while back I did write a mini-tutorial on how to go from a qiime2 feature-table to a BugBase compatible OTU table and the first portion of it I think does what you want to do. Do you want to try that and if that doesn’t work for you then we’ll come back to troubleshoot this properly.

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Hi, @Mehrbod_Estaki,

I have followed the indications from the link you suggested and now it works perfectly! Thanks a lot.


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