groups: invalid choice: 'uniref90_level4ec' (choose from 'uniref90_rxn', 'uniref50_rxn')\n"`

Infrastructure and utilities bioBakery workflows
1

There is an error to run “biobakery_workflows wmgx xxx”. Error message is as below. It looks like humann3 should use “uniref90_rxn” but in the shotgun.py code, it use uniref90_level4ec.

Task 29 failed Name: humann_renorm_ecs_relab____HD42R4_subsample Original error: Task failed because parent task 20’ failed
Task 19 failed
Name: humann_regroup_UniRef2EC____HD32R1_subsample
Original error:
Error executing action 0. Original Exception:
Traceback (most recent call last):
File “/usr/local/lib/python3.6/dist-packages/anadama2/runners.py”, line 201, in _run_task_locally
action_func(task)
File “/usr/local/lib/python3.6/dist-packages/anadama2/helpers.py”, line 89, in actually_sh
ret = _sh(s, **kwargs)
File “/usr/local/lib/python3.6/dist-packages/anadama2/util/ init .py”, line 320, in sh
raise ShellException(proc.returncode, msg.format(cmd, ret[0], ret[1]))
anadama2.util.ShellException: [Errno 2] Command humann_regroup_table --input /data/result_wmgs_1/humann/main/HD32R1_subsample_genefamilies.tsv --output /data/result_wmgs_1/humann/regrouped/HD32R1_subsample_ecs.tsv --groups uniref90_level4ec' failed. Out: b'' Err: b"usage: humann_regroup_table [-h] [-i INPUT] [-g {uniref90_rxn,uniref50_rxn}]\n [-c CUSTOM] [-r] [-f {sum,mean}] [-e PRECISION]\n [-u {Y,N}] [-p {Y,N}] [-o OUTPUT]\nhumann_regroup_table: error: argument -g/--groups: invalid choice: 'uniref90_level4ec' (choose from 'uniref90_rxn', 'uniref50_rxn')\n"

2 Likes
2

Same issue here. uniref90_level4ec is not a valid option, apparently.

1 Like
3

You have to download the full utility_mapping database in order to use any other functional category, like ‘uniref90_level4ec’.
The full mapping database is not included by default since it is quite big in size.

Have a look on how to install the full utility_mapping db.
e.g.
humann_databases --download utility_mapping full <path_to_humann_dbs>

best regards.

4

I’ve downloaded the full database, and it is in the default location. I still get this same error

5

Hello everyone,
I have the same error,

Err: usage: humann_regroup_table [-h] [-i INPUT] [-g {uniref90_rxn,uniref50_rxn}]
[-c CUSTOM] [-r] [-f {sum,mean}] [-e PRECISION]
[-u {Y,N}] [-p {Y,N}] [-o OUTPUT]
humann_regroup_table: error: argument -g/–groups: invalid choice: ‘uniref90_level4ec’ (choose from ‘uniref90_rxn’, ‘uniref50_rxn’)

Could you please let me know, how did you solve this issue?

Thank you in advance,

Regards!

6

I have the same error. Do we have a solution for this?
If I run:
humann_regroup_table --input LC6_pathabundance.tsv --groups uniref90_ko --output TABLE2

I get:
usage: humann_regroup_table [-h] [-i INPUT] [-g {uniref90_rxn,uniref50_rxn}] [-c CUSTOM] [-r] [-f {sum,mean}] [-e PRECISION] [-u {Y,N}] [-p {Y,N}] [-o OUTPUT]
humann_regroup_table: error: argument -g/–groups: invalid choice: ‘uniref90_ko’ (choose from ‘uniref90_rxn’, ‘uniref50_rxn’)

But when I change it to:

(base) javad@Javad1:~$ humann_regroup_table --input LC6_pathabundance.tsv --groups uniref90_rxn --output TABLE2

I get (no error):

Loading table from: LC6_pathabundance.tsv

  • Treating LC6_pathabundance.tsv as stratified output, e.g. [‘UNINTEGRATED’, ‘unclassified’]*
    Loading mapping file from: /home/javad/miniconda3/lib/python3.10/site-packages/humann/tools/…/data/pathways/metacyc_reactions_level4ec_only.uniref.bz2
    Original Feature Count: 223; Grouped 1+ times: 2 (0.9%); Grouped 2+ times: 0 (0.0%)
7

I found the solution. I do not know if I needed to update my utility mapping folder or when you install humann will automatically update your utility mapping folder. However, to solve the issue simply update your utility_mapping

humann_config --update database_folders utility_mapping (path/to/your/folder/for/utility/mapping/files)