Biom add txonomy not working

[chiara (Chiara Conte)]

Hello everyone,

Thank you for this responsive forum.

I have an issue with adding taxonomy to biom file. I followed the posts are alredy here about this topic but noting worked and I keep receiving an empty taxonomy column or the text below.
I'd need to do it to run faprotax.

Do you have any further uiggestion regarding this, please?

Thank you very much in advance,
Chiara

HDF

ÿÿÿÿÿÿÿÿ ÿÿÿÿÿÿÿÿ ` ˆ ¨
˜ TREE ÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿ x HEAP X È observation sample 8 ˆ ¨ @ id
@ type H
format-url P format-version @ H
generated-by H creation-date H shape @ · 0 nnz @ æ à TREE ÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿ € GCOL
No Table ID http://biom-format.org BIOM-Format 2.1.10 2023-09-10T11:23:44.507637

Please find below the flow I followed:
Export
qiime tools export --input-path /g100_scratch/userexternal/USER/xxxx/EMS/faprotax_preparation/rar_EMS_halo_table.qza --output-path /g100_scratch/userexternal/USER/xxxx/EMS/faprotax_preparation/exported_rar_EMS_table.qza

qiime tools export --input-path /g100_scratch/userexternal/USER/xxxx/EMS/faprotax_preparation/ems_taxonomy_rar.qza --output-path /g100_scratch/userexternal/USER/xxxx/EMS/faprotax_preparation/exported_ems_tax_rar.qza

biom convert -i /g100_scratch/userexternal/USER/xxxx/EMS/faprotax_preparation/exported_rar_EMS_table.qza/feature-table.biom -o /g100_scratch/userexternal/USER/xxxx/EMS/faprotax_preparation/exported_rar_EMS_table.qza/feature-table.tsv --to-tsv

biom add-metadata -i /g100_scratch/userexternal/USER/xxxx/EMS/faprotax_preparation/exported_rar_EMS_table.qza/feature-table.biom -o /g100_scratch/userexternal/USER/xxxx/EMS/faprotax_preparation/exported_rar_EMS_table.qza/feature-with-taxonomy.biom --observation-metadata-fp /g100_scratch/userexternal/USER/xxxx/EMS/faprotax_preparation/exported_ems_tax_rar.qza/taxonomy.tsv --sc-separated taxonomy

biom convert -i /g100_scratch/userexternal/USER/xxxx/EMS/faprotax_preparation/exported_rar_EMS_table.qza/feature-with-taxonomy.biom -o /g100_scratch/userexternal/USER/xxxx/EMS/faprotax_preparation/exported_rar_EMS_table.qza/feature-with-taxonomy-table.tsv --to-tsv

THE OUTPUT WAS A FEATURE TABLE WITHOUT TAXONOMY

[llenzi (Luca)]

Hi @chiara,

I suspect the taxonomy is in the biom but was not exported in the final tsv file.

biom add-metadata -i ./feature-table.biom -o table-with-taxonomy.biom
–observation-metadata-fp biom-taxonomy.tsv --sc-separated taxonomy

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

In particular, try adding the '--header-key taxonomy' parameter to outoput what you need!

Hope it helps
Luca