Issue with humann_regroup_table in biobakery_workflows wmgx

Issue with biobakery_workflows wmgx

Task 23 failed
  Name: humann_regroup_UniRef2EC____22002010590008.gz
  Original error:
  Error executing action 0. Original Exception:
  Traceback (most recent call last):
    File "/home/.local/lib/python3.10/site-packages/anadama2/runners.p
y", line 200, in _run_task_locally
    File "/home/.local/lib/python3.10/site-packages/anadama2/helpers.p
y", line 107, in actually_sh
      ret = _sh(s, **kwargs)
    File "/home/.local/lib/python3.10/site-packages/anadama2/util/__in", line 320, in sh
      raise ShellException(proc.returncode, msg.format(cmd, ret[0].decode('utf
-8'), ret[1].decode('utf-8')))
  anadama2.util.ShellException: [Errno 2] Command `humann_regroup_table --inpu
t /home/PDMB/Test_output/humann/main/22002010590008_genefamilies.tsv -
-output /home/PDMB/Test_output/humann/regrouped/22002010590008_ecs.tsv
 --groups uniref90_level4ec' failed.
  Err: usage: humann_regroup_table [-h] [-i INPUT] [-g {uniref90_rxn,uniref50_
                              [-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')

ls biobakery_workflows_databases/humann/utility_mapping/ :

map_ec_name.txt.gz          map_level4ec_uniref50.txt.gz
map_eggnog_name.txt.gz      map_level4ec_uniref90.txt.gz
map_eggnog_uniref50.txt.gz  map_pfam_name.txt.gz
map_eggnog_uniref90.txt.gz  map_pfam_uniref50.txt.gz
map_go_name.txt.gz          map_pfam_uniref90.txt.gz
map_go_uniref50.txt.gz      map_uniref50_name.txt.bz2
map_go_uniref90.txt.gz      map_uniref50_uniref90.txt.gz
map_ko_name.txt.gz          map_uniref90_name.txt.bz2
map_ko_uniref50.txt.gz      uniref50-tol-lca.dat.bz2
map_ko_uniref90.txt.gz      uniref90-tol-lca.dat.bz2

Is there a way to supply the --groups argument to biobakery_workflows?

Hello, Thank you for the detailed post! It looks like HUMAnN is possibly using the default set of utility mapping files instead of those included in your database folder. Try running $ humann_config --print to check and $ humann_config --update $SECTION $NAME $VALUE to update the location if needed.

Thank you!

Oh jeez, that seems so obvious in retrospect. Fixed!

No worries! So glad to hear it is fixed. Please post if you run into any other issues!