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assigned issue to
Failing to run oncodrivefml
Issue #19
new
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)
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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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