'var_aa' error
Issue #114
resolved
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)
-
-
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
-
- changed status to resolved
Issue has been fixed in ResFinder version 4.4.0
- Log in to comment
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