# add metadata taxonomy problem

**URL:** https://forum.qiime2.org/t/add-metadata-taxonomy-problem/14172
**Category:** Other Bioinformatics Tools
**Created:** [March 23, 2020, 8:20pm UTC](https://forum.qiime2.org/t/add-metadata-taxonomy-problem/14172 "2020-03-23T20:20:40Z")
**Posts on this page:** 1
**Page:** 1

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### Author: ![MirjamBloem](https://forum.qiime2.org/letter_avatar_proxy/v4/letter/m/6bbea6/32.png) [@MirjamBloem](https://forum.qiime2.org/u/MirjamBloem)
#### Post date: [March 23, 2020, 8:20pm UTC](https://forum.qiime2.org/t/add-metadata-taxonomy-problem/14172/1 "2020-03-23T20:20:40Z")

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Hi,

Despite looking into several topics on the qiime forum, e.g. [Biom add metadata problem](https://forum.qiime2.org/t/biom-add-metadata-problem/8302) i did not manage to solve this.

I tried to add the taxonomy information to the biom file. I changed the header in the taxonomy file to #OTUID but i do not see my taxonomy information when i open the .txt file converted from the .biom file.  
I tried this:  
qiime tools export --input-path ./tableWesternDietSert.qza --output-path ./  
qiime tools export --input-path ./taxonomy\_rep-seqs.qza --output-path ./  
biom add-metadata -i feature-table.biom -o table-with-taxonomy.biom --observation-metadata-fp taxonomy.tsv --observation-header OTUID,Taxon,Confidence

biom convert -i table-with-taxonomy.biom -o table.from\_biom\_with\_taxonomy.txt --to-tsv

In the above topic i saw you need to add **--header-key taxonomy** so i tried this:

biom convert -i table-with-taxonomy.biom -o table.from\_biom\_with\_taxonomy.txt --to-tsv --header-key taxonomy

but when i do this i get a phyton related error message:

Traceback (most recent call last):  
File "/sw/arch/RedHatEnterpriseServer7/EB\_production/2019/software/QIIME2/2019.4/bin/biom", line 11, in   
sys.exit(cli())  
File "/sw/arch/RedHatEnterpriseServer7/EB\_production/2019/software/QIIME2/2019.4/lib/python3.6/site-packages/click/core.py", line 76n **call**  
return self.main(\*args, \*\*kwargs)  
File "/sw/arch/RedHatEnterpriseServer7/EB\_production/2019/software/QIIME2/2019.4/lib/python3.6/site-packages/click/core.py", line 71n main  
rv = self.invoke(ctx)  
File "/sw/arch/RedHatEnterpriseServer7/EB\_production/2019/software/QIIME2/2019.4/lib/python3.6/site-packages/click/core.py", line 11in invoke  
return \_process\_result(sub\_ctx.command.invoke(sub\_ctx))  
File "/sw/arch/RedHatEnterpriseServer7/EB\_production/2019/software/QIIME2/2019.4/lib/python3.6/site-packages/click/core.py", line 95n invoke  
return ctx.invoke(self.callback, \*\*ctx.params)  
File "/sw/arch/RedHatEnterpriseServer7/EB\_production/2019/software/QIIME2/2019.4/lib/python3.6/site-packages/click/core.py", line 55n invoke  
return callback(\*args, \*\*kwargs)  
File "/sw/arch/RedHatEnterpriseServer7/EB\_production/2019/software/QIIME2/2019.4/lib/python3.6/site-packages/biom/cli/table\_converte", line 129, in convert  
table\_type, process\_obs\_metadata, tsv\_metadata\_formatter)  
File "/sw/arch/RedHatEnterpriseServer7/EB\_production/2019/software/QIIME2/2019.4/lib/python3.6/site-packages/biom/cli/table\_converte", line 185, in \_convert  
metadata\_formatter=obs\_md\_fmt\_f)  
File "/sw/arch/RedHatEnterpriseServer7/EB\_production/2019/software/QIIME2/2019.4/lib/python3.6/site-packages/biom/table.py", line 48in to\_tsv  
observation\_column\_name)  
File "/sw/arch/RedHatEnterpriseServer7/EB\_production/2019/software/QIIME2/2019.4/lib/python3.6/site-packages/biom/table.py", line 16in delimited\_self  
md\_out = metadata\_formatter(md.get(header\_key, None))  
File "/sw/arch/RedHatEnterpriseServer7/EB\_production/2019/software/QIIME2/2019.4/lib/python3.6/site-packages/biom/cli/table\_converte", line 36, in   
'sc\_separated': lambda x: '; '.join(x),  
TypeError: can only join an iterable

Do you have advice on how to add the taxonomic information?

Thank you.  
Bests Mirjam