biom add-metadata: merging feature table with taxonomy

[Zango (Sauban Musa Jibril)]

Hello and good day, NEED URGENT HELP PLEASE. I am trying to merge my feature table created from DADA2 with its taxonomy but after i run the command the following error popup

my taxonomy.tsv file appears like this

Your help is highly appreciated

[llenzi (Luca)]

Hi @Zango,

maybe some command in the following thread could help you:

Exporting feature table with taxonomy added not working

Hello! I am a newbie on the qiime2 world and I am having isues exporting the feature table with the taxonomy annotations added for my data. I have followed the Exporting and modifying BIOM tables (e.g. adding taxonomy annotations) tutorial, and have tried some other codes/ suggestions made on the forum, but nothing has worked. If anyone can point out what I could be doing wrong, or if there is any other way to export the OTU table with its taxonomy, it will be appreciated! For reference I am …

Other than that, how did you create 'obs_md.txt' file?

Cheers
Luca

[Zango (Sauban Musa Jibril)]

Thanks for the quick reply, I actually used taxonomy file as obs_md.txt' file

[llenzi (Luca)]

Hi @Zango,
did you try the command frm the thread Ilinked above?
Did it work?

Luca

[Zango (Sauban Musa Jibril)]

Thank you, I tried it, it showed No data found in mapping file.

[llenzi (Luca)]

Hi @Zango,
let see, what files do you have in the path where you run the command? Do you have both 'obs_md.txt' as well as 'taxonomy.tsv'? (which are in fact the same file with tdifferent name?)
The error seems to point to an empty 'taxonomy.tsv' file, if I understand it well.

My other question is, how did you obtained the 'feature-table.biom'? Was it exported from the denoising artefact, or were filtered/processed in any way before the exporting step?

Luca

[Zango (Sauban Musa Jibril)]

Thank you for prompt reply, I have taxonomy.tsv file but do not have obs_md.txt file. The feature-table.biom was obtained from DADA2 and exported as .biom file

[colinbrislawn (Colin J Brislawn)]

@Zango

but do not have obs_md.txt file

Later on in that thread, we tried this and it worked for the last person.

@colinbrislawn

biom convert -i table.biom -o table.from_biom_w_taxonomy.txt --to-tsv --header-key taxonomy

Try that and report back!