Unable to analyse this particular genome using official Docker container

Issue #99 resolved
Jonathan Abrahams created an issue

Hi,

I am using this command $ docker run -v "${pwd}:/app" genomicepidemiology/resfinder -ifa /app/input_genome.fasta -o test1_res_image -s "mycobacterium tuberculosis" --acquired --point

I have tried in so many different ways to get this working with my genome (submitted to the resfinder server with ID 63C5582B000066E6751A2C21,although i accidently ran for Camplyobacter mutations), but it has not been working. It has been giving odd messages about keys (when a local installation is run). This only happens when looking for point mutations.

`

Traceback (most recent call last):
  File "/miniconda3/envs/Isolate_seq/lib/python3.10/runpy.py", line 196, in _run_module_as_main
    return _run_code(code, main_globals, None,
  File "/miniconda3/envs/Isolate_seq/lib/python3.10/runpy.py", line 86, in _run_code
    exec(code, run_globals)
  File "/miniconda3/envs/Isolate_seq/lib/python3.10/site-packages/resfinder/__main__.py", line 5, in <module>
    sys.exit(main())
  File "/miniconda3/envs/Isolate_seq/lib/python3.10/site-packages/resfinder/run_resfinder.py", line 460, in main
    PointFinderResultHandler.standardize_results(std_result,
  File "/miniconda3/envs/Isolate_seq/lib/python3.10/site-packages/resfinder/cge/output/std_results.py", line 162, in standardize_results
    res_collection.add_class(cl="seq_regions", **gene_result)
  File "/miniconda3/envs/Isolate_seq/lib/python3.10/site-packages/cgelib/output/result.py", line 122, in add_class
    self._add_class_dict(cl, res, clobber, clobber_warn)
  File "/miniconda3/envs/Isolate_seq/lib/python3.10/site-packages/cgelib/output/result.py", line 130, in _add_class_dict
    val = self[cl].get(res["key"], None)
  File "/miniconda3/envs/Isolate_seq/lib/python3.10/collections/__init__.py", line 1106, in __getitem__
    raise KeyError(key)
KeyError: 'key'

However, it works on this publicly available genome (just as a random example) . I am not sure if it is to do with a particular point mutation that occurs in some samples or not. https://www.ncbi.nlm.nih.gov/nuccore/NZ_MVHL01000001.1

My assembly was from Nanopore reads, if that makes any difference.

Any help on this would be much appreciated.

Comments (2)

  1. Edison Alain von Matt

    Dear Jonathan,

    thank you for your message and I apologize for the late reply.

    You are correct - we plan to fix this error for point mutations in the next release.

    Until then, I appended the correct results of your input genome that I found in your job https://cge.food.dtu.dk/cgi-bin/webface.fcgi?jobid=63C5582B000066E6751A2C21 with the default threshold values of coverage 60 and identity 80 against the Mycobacterium tuberculosis species to this post.

    Please let me know if you have additional questions.

    Best regards

    Eddy

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