Issue #2 new
Tommy Tang
created an issue

Hi,

I was using

conda install -c bbglab oncodrivefml
Fetching package metadata ...................
Solving package specifications: .

# All requested packages already installed.
# packages in environment at /apps/conda/envs/oncodrive:
#
oncodrivefml              2.0.2                    py36_0    bbglab

oncodrivefml -i LUAD_oncodrive_input.tsv1 -e cds.regions.gz -c oncodrivefml.conf --type coding --sequencing wes -o LUAD_oncodrive
23:00:21 INFO: Using HG19 as reference genome
23:00:21 INFO: Running analysis
       Parsing elements 'cds.regions.gz': 100%|███████████████████████████████████████████████████████████████| 207139/207139 [00:08<00:00, 24270.52it/s]
23:00:37 INFO: Mapping mutations
* [0 muts]
**         [252341 muts]
23:00:44 INFO: Computing signatures
Traceback (most recent call last):
  File "/apps/conda/envs/oncodrive/bin/oncodrivefml", line 6, in <module>
    sys.exit(oncodrivefml.main.cmdline())
  File "/apps/conda/envs/oncodrive/lib/python3.6/site-packages/click/core.py", line 722, in __call__
    return self.main(*args, **kwargs)
  File "/apps/conda/envs/oncodrive/lib/python3.6/site-packages/click/core.py", line 697, in main
    rv = self.invoke(ctx)
  File "/apps/conda/envs/oncodrive/lib/python3.6/site-packages/click/core.py", line 895, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/apps/conda/envs/oncodrive/lib/python3.6/site-packages/click/core.py", line 535, in invoke
    return callback(*args, **kwargs)
  File "/apps/conda/envs/oncodrive/lib/python3.6/site-packages/oncodrivefml/main.py", line 382, in cmdline
    main(mutations_file, elements_file, output_folder, config_file, samples_blacklist, generate_pickle, override_config)
  File "/apps/conda/envs/oncodrive/lib/python3.6/site-packages/oncodrivefml/main.py", line 332, in main
    analysis.run()
  File "/apps/conda/envs/oncodrive/lib/python3.6/site-packages/oncodrivefml/main.py", line 194, in run
    self.__compute_signature()
  File "/apps/conda/envs/oncodrive/lib/python3.6/site-packages/oncodrivefml/main.py", line 135, in __compute_signature
    save_pickle=save_signature_pickle)
  File "/apps/conda/envs/oncodrive/lib/python3.6/site-packages/oncodrivefml/signature.py", line 331, in load_signature
    signature_dict = compute_signature(signature_function, classifier, collapse, include_mnp)
  File "/apps/conda/envs/oncodrive/lib/python3.6/site-packages/oncodrivefml/signature.py", line 224, in compute_signature
    logger.debug('Discrepancy in substitution at position %d of chr %s', pos, mut['CHROMOSOME'])
UnboundLocalError: local variable 'pos' referenced before assignment

this error was solved by https://bitbucket.org/bbglab/oncodrivefml/commits/271302acada6300f33eab45d5dae5e8bf238cce9 (thanks Loris for answering my email)

can you please add a new conda receipt for the new version?

Thanks! Tommy