Error Message-Default File

[Siti Nurmilah]

I have a trouble when using this command:

pathway_pipeline.py \
> -i KO_metagenome_out/pred_metagenome_contrib.tsv.gz \
> -o KEGG_pathways_out \
> -p 1 \
> --no_regroup \
> --map ~/miniconda3/envs/picrust2/lib/python3.6/sitepackages/picrust2/default_files/pathway_mapfiles/KEGG_pathways_to_KO.tsv

Traceback (most recent call last):
  File "/home/buah2023/miniconda3/envs/picrust2/bin/pathway_pipeline.py", line 7, in <module>
    exec(compile(f.read(), __file__, 'exec'))
  File "/mnt/c/biogas/picrust2-2.4.1/scripts/pathway_pipeline.py", line 272, in <module>
    main()
  File "/mnt/c/biogas/picrust2-2.4.1/scripts/pathway_pipeline.py", line 155, in main
    check_files_exist([args.input, args.map])
  File "/mnt/c/biogas/picrust2-2.4.1/picrust2/util.py", line 406, in check_files_exist
    raise ValueError("This input file was not found: " + missing_files[0])
ValueError: This input file was not found: /home/buah2023/miniconda3/envs/picrust2/lib/python3.6/sitepackages/picrust2/default_files/pathway_mapfiles/KEGG_pathways_to_KO.tsv

can someone help me?

[Robyn Wright]

Hi there,

That error message is suggesting that the files needed for PICRUSt2 to run aren't present in the folder that the script is expecting them to be in. Can you check whether they are actually at the file path given? (/home/buah2023/miniconda3/envs/picrust2/lib/python3.6/sitepackages/picrust2/default_files/pathway_mapfiles/KEGG_pathways_to_KO.tsv)

Robyn