Failing to run oncodrivefml

Issue #19 new
Former user created an issue

I try to run the following command:

oncodrivefml -i tcga_input_hg19_project_BRCA.tsv -e ../example/cds.regions.gz --type coding --sequencing wes

But get the following error:

/cs/phd/nadavb/my_storage/oncodrivefml_python_env/lib/python3.6/site-packages/oncodrivefml/main.py:101: DeprecationWarning: --type option is no longer supported. Edit the configuration file appropriately
  DeprecationWarning)
Traceback (most recent call last):
  File "/cs/phd/nadavb/my_storage/oncodrivefml_python_env/bin/oncodrivefml", line 10, in <module>
    sys.exit(cmdline())
  File "/cs/phd/nadavb/my_storage/oncodrivefml_python_env/lib/python3.6/site-packages/click/core.py", line 722, in __call__
    return self.main(*args, **kwargs)
  File "/cs/phd/nadavb/my_storage/oncodrivefml_python_env/lib/python3.6/site-packages/click/core.py", line 697, in main
    rv = self.invoke(ctx)
  File "/cs/phd/nadavb/my_storage/oncodrivefml_python_env/lib/python3.6/site-packages/click/core.py", line 895, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/cs/phd/nadavb/my_storage/oncodrivefml_python_env/lib/python3.6/site-packages/click/core.py", line 535, in invoke
    return callback(*args, **kwargs)
  File "/cs/phd/nadavb/my_storage/oncodrivefml_python_env/lib/python3.6/site-packages/oncodrivefml/main.py", line 118, in cmdline
    main(mutations_file, elements_file, output_folder, config_file, samples_blacklist, cores, seed, override_config)
  File "/cs/phd/nadavb/my_storage/oncodrivefml_python_env/lib/python3.6/site-packages/oncodrivefml/main.py", line 51, in main
    configuration = load_configuration(config_file, override=config_override_dict)
  File "/cs/phd/nadavb/my_storage/oncodrivefml_python_env/lib/python3.6/site-packages/oncodrivefml/config.py", line 33, in load_configuration
    return BGConfig(config_template, config_file=config_file, use_env_vars=True, override_values=override, unrepr=False)
  File "/cs/phd/nadavb/my_storage/oncodrivefml_python_env/lib/python3.6/site-packages/bgconfig.py", line 228, in __init__
    ConfigObj.__init__(self, config_file, configspec=config_spec, interpolation=interpolation, unrepr=unrepr)
  File "/cs/phd/nadavb/my_storage/oncodrivefml_python_env/lib/python3.6/site-packages/configobj.py", line 1229, in __init__
    self._load(infile, configspec)
  File "/cs/phd/nadavb/my_storage/oncodrivefml_python_env/lib/python3.6/site-packages/configobj.py", line 1318, in _load
    raise error
configobj.ParseError: Parse error in value at line 228.

It should be noted that I always get the same error (always complaining about line 228) no matter what input tsv file I'm giving it.

Comments (2)

  1. Iker Reyes

    Seems to be a compatibility problem with older configuration files. Can you provide your configuration file? It should be in ``~/.config/bbglab/oncodrivefml_v2.conf``

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