Problems with Eggnog renaming from grouped table

Microbial community profiling HUMAnN
1

Hey team,

I’ve run HUMAnN (v3.7) and regrouped my UniRef90 table to Eggnog. Now, I’m trying to rename the Eggnog table to be more human readable, but humann_rename_table can’t find the Eggnog names mapping file.

What I have done:

I’ve successfully installed the utility mapping files (humann_databases --download utility_mapping full download_dir --update-config yes)

I’ve regrouped the table (humann_regroup_table -i <uniref90_genefams_table> -g uniref90_eggnog -o <eggnog_grouped_table>)

I’ve also been able to regroup and rename my tables based on GO and PFams.

What breaks:

humann_rename_table -i <eggnog_grouped_table> -n eggnog -o <eggnog_grouped_named_table>

Which results in a FileNotFound error:
FileNotFoundError: [Errno 2] No such file or directory: '/path/to/conda_environment/lib/python3.7/site-packages/humann/tools/../data/misc/map_eggnog_name.txt.gz'

Is there somewhere I can download map_eggnog_name.txt.gz?

2

That file should be part of the (full) HUMAnN utility mapping database if you have that downloaded?

5

Hi again,

I am using humann v3.9 installed in a mamba environment.
I used this to download the utility mapping
humann_databases --download utility_mapping full ./databases

I got the same error as @sterrettJD .

humann_config --print

HUMAnN Configuration ( Section : Name = Value )
database_folders : nucleotide = /media/akodon/ANDRES/databases/chocophlan
database_folders : protein = /media/akodon/ANDRES/databases/uniref
database_folders : utility_mapping = /media/akodon/ANDRES/databases/utility_mapping

The utility mapping database appears as correclty located… How can I reroute or fix this?
Thanks

Andrés

6

If you run humann_rename_table -h it should list out the naming options available to you. Do you see the eggNOG names in that list?

7

Hi Eric, thanks for your help, I hadn’t tried that here is the output:

-n {kegg-orthology,kegg-pathway,kegg-module,ec,metacyc-rxn,metacyc-pwy,pfam,eggnog,go,infogo1000,uniref50,uniref90}, --names {kegg-orthology,kegg-pathway,kegg-module,ec,metacyc-rxn,metacyc-pwy,pfam,eggnog,go,infogo1000,uniref50,uniref90}

These are the options but the -n option that I used was the same as the one listed above…

humann_rename_table --input humann_pathways.tsv --names eggnog --output humann_pathways_regroup.tsv --simplify

I got this result

Loading table from: humann_pathways.tsv
  Treating humann_pathways.tsv as stratified output, e.g. ['UNINTEGRATED', 'g__Acetobacter.s__Acetobacter_sp_CAG_267']
Loading mapping file from: /home/evolucion/mambaforge/envs/humano/lib/python3.12/site-packages/humann/tools/../data/misc/map_eggnog_name.txt.gz
Traceback (most recent call last):
  File "/home/evolucion/mambaforge/envs/humano/bin/humann_rename_table", line 8, in <module>
    sys.exit(main())
             ^^^^^^
  File "/home/evolucion/mambaforge/envs/humano/lib/python3.12/site-packages/humann/tools/rename_table.py", line 143, in main
    polymap = util.load_polymap( c_default_names[args.names].path, allowed_keys=allowed_keys )
              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/evolucion/mambaforge/envs/humano/lib/python3.12/site-packages/humann/tools/util.py", line 341, in load_polymap
    size_warn( path )
  File "/home/evolucion/mambaforge/envs/humano/lib/python3.12/site-packages/humann/tools/util.py", line 268, in size_warn
    if m * os.path.getsize( path ) > c_many_bytes:
           ^^^^^^^^^^^^^^^^^^^^^^^
  File "<frozen genericpath>", line 62, in getsize
FileNotFoundError: [Errno 2] No such file or directory: '/home/evolucion/mambaforge/envs/humano/lib/python3.12/site-packages/humann/tools/../data/misc/map_eggnog_name.txt.gz'

Thanks

A

8

Hmm, it’s strange that it can see the list of files but not load one. Must be something weird with how it’s been installed. The script allows you to pass a custom path for mapping IDs to names (--custom). If you can see the path to the names file and view it with less, then you could pass it manually to the script with that --custom flag. The script tries to automatically connect to available mapping files but something isn’t working there.

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9

Pointing to the database location worked! Thanks again for your help.

1 Like