Human_regroup_table

Microbial community profiling HUMAnN
1

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?

Thanks
Francesca

2

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.

Thanks!
Lauren

3

It works! Thank you!

4

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

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