Issue with humann_regroup_table in biobakery_workflows wmgx

Infrastructure and utilities bioBakery workflows
1

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
      action_func(task)
    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
it__.py", 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.
  Out:
  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')

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?

2

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!
Lauren

3

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

4

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

Thanks!
Lauren