# Converted biom table does not contain taxonomy

**URL:** https://forum.qiime2.org/t/converted-biom-table-does-not-contain-taxonomy/13969
**Category:** Other Bioinformatics Tools
**Tags:** taxonomy, biom
**Created:** [March 10, 2020, 1:54pm UTC](https://forum.qiime2.org/t/converted-biom-table-does-not-contain-taxonomy/13969 "2020-03-10T13:54:32Z")
**Posts on this page:** 4
**Page:** 1

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### Author: ![Pablo\_V](https://forum.qiime2.org/user_avatar/forum.qiime2.org/pablo_v/32/4898_2.png) [@Pablo\_V](https://forum.qiime2.org/u/Pablo_V)
#### Post date: [March 10, 2020, 1:54pm UTC](https://forum.qiime2.org/t/converted-biom-table-does-not-contain-taxonomy/13969/1 "2020-03-10T13:54:32Z")

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Hi,

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)](https://forum.qiime2.org/t/exporting-and-modifying-biom-tables-e-g-adding-taxonomy-annotations/3630)) 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:

- [Basic questions regarding classic OTU table in QIIME2](https://forum.qiime2.org/t/basic-questions-regarding-classic-otu-table-in-qiime2/4189) --\> Here the error was not adding "#OTUID taxonomy confidence" to the taxonomy.tsv file. However, I have changed the headers accordingly.
- [Exporting feature table and adding taxonomy and converting to tsv - #2 by Nicholas\_Bokulich](https://forum.qiime2.org/t/exporting-feature-table-and-adding-taxonomy-and-converting-to-tsv/6104/2) --\> Here the error was not adding "--header-key taxonomy" when converting the biom table into txt format. However, I have added "--header-key taxonomy" when converting the biom table with taxonomy into txt format and I get the following error:  
...  
'sc\_separated': lambda x: '; '.join(x),

TypeError: can only join an iterable

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

Cheers,  
Pablo

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### Author: ![Mehrbod\_Estaki](https://forum.qiime2.org/user_avatar/forum.qiime2.org/mehrbod_estaki/32/4001_2.png) [@Mehrbod\_Estaki](https://forum.qiime2.org/u/Mehrbod_Estaki)
#### Post date: [March 10, 2020, 8:11pm UTC](https://forum.qiime2.org/t/converted-biom-table-does-not-contain-taxonomy/13969/2 "2020-03-10T20:11:30Z")

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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](https://github.com/mestaki/qiime2-to-BugBase) 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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### Author: ![Pablo\_V](https://forum.qiime2.org/user_avatar/forum.qiime2.org/pablo_v/32/4898_2.png) [@Pablo\_V](https://forum.qiime2.org/u/Pablo_V)
#### Post date: [March 20, 2020, 4:44pm UTC](https://forum.qiime2.org/t/converted-biom-table-does-not-contain-taxonomy/13969/3 "2020-03-20T16:44:50Z")

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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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### Author: ![system](https://forum-qiime2-org.s3.dualstack.us-west-2.amazonaws.com/original/3X/2/1/21af5fe23cb6f4579467c66a9ed94e55274ca7bd.svg) [@system](https://forum.qiime2.org/u/system)
#### Post date: [April 20, 2020, 10:47pm UTC](https://forum.qiime2.org/t/converted-biom-table-does-not-contain-taxonomy/13969/4 "2020-04-20T22:47:01Z")

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