Hi there. I’m using humann3 and trying to convert uniref90 to EC.

the script I’m running is:

humann_regroup_table --input normalized_rel_abd/AA10_relab.tsv --output EC_normalized/AA10_relab_EC_norm.tsv --groups uniref90_level4ec --custom /lustre/homes/unina.it053/utility_mapping/map_level4ec_uniref90.txt

but I’m having the following error:

humann_regroup_table: error: argument -g/–groups: invalid choice: ‘uniref90_level4ec’ (choose from ‘uniref90_rxn’, ‘uniref50_rxn’)
usage: humann_regroup_table [-h] [-i INPUT] [-g {uniref90_rxn,uniref50_rxn}]

In the folder /lustre/homes/unina.it053/utility_mapping/ I have downloaded all conversion files but I don’t have the permissions to write the human config files. Is there any other way to specify the path to the files?
Could you please help?


Hi Francesca, I think if you remove the --groups uniref90_level4ec from your command and just use the custom option it should resolve the error you are seeing.


It works! Thank you!

Hi all, this is still an issue when trying to use biobakery workflows because of this issue that the bot auto-closed: groups: invalid choice: 'uniref90_level4ec' (choose from 'uniref90_rxn', 'uniref50_rxn')\n"` · Issue #16 · biobakery/biobakery_workflows · GitHub. It seems like an easy fix, I can submit a PR if you give some guidance on how to resolve this