'var_aa' error

Issue #114 resolved
chan created an issue

I ran Resfinder installed with pip in a conda environment. It returns the following error.

python -m resfinder -ifa ${fasta} -o ${outdir2}/${isolates} -j ${outdir2}/${isolates}/${isolates}_resfinder.json -s ${species} -u --acquired --disinfectant -c --ignore_missing_species -b ${blastn} -k ${kma} 
Traceback (most recent call last):
  File "/lustre1/applications/conda/env/resfinder/lib/python3.9/runpy.py", line 197, in _run_module_as_main
    return _run_code(code, main_globals, None,
  File "/lustre1/applications/conda/env/resfinder/lib/python3.9/runpy.py", line 87, in _run_code
    exec(code, run_globals)
  File "/lustre1/applications/conda/env/resfinder/pypkg/resfinder/__main__.py", line 5, in <module>
    sys.exit(main())
  File "/lustre1/applications/conda/env/resfinder/pypkg/resfinder/run_resfinder.py", line 511, in main
    isolate.load_finder_results(std_table=std_result,
  File "/lustre1/applications/conda/env/resfinder/pypkg/resfinder/cge/phenotype2genotype/isolate.py", line 269, in load_finder_results
    unique_id_nuc, unique_id_aa = Isolate.get_phenodb_id(feat_info,
  File "/lustre1/applications/conda/env/resfinder/pypkg/resfinder/cge/phenotype2genotype/isolate.py", line 237, in get_phenodb_id
    f"_{feat_res_dict['var_aa']}")
  File "/lustre1/applications/conda/env/resfinder/lib/python3.9/collections/__init__.py", line 1058, in __getitem__
    raise KeyError(key)
KeyError: 'var_aa'

What would be the error means?
(FYI my Resfinder version)

python -m resfinder --version
4.3.2 

Comments (3)

  1. Edison Alain von Matt

    Dear Chan,

    thank you for your message.

    Could you please append your input file to this post or send it to me at food-cgehelp@dtu.dk?

    And, what is your current version of resfinder_db and pointfinder_db?

    Best regards

    Eddy

  2. chan reporter

    Dear Eddy,

    My current version of resfinder_db is 2.1.1, pointfinder_db is 3.0.1, and disinfinder_db is 2.0.1
    I will send you the input file via email ASAP.

    Thank you very much.
    Best regards,

    David

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