Open DSchreyer opened 1 year ago
The last step findCancerMutations finishes with an error due to the missing columns in the CosmicMutantExportCensus.tsv file.
findCancerMutations
Error:
INFO: Converting SIF file to temporary sandbox... Traceback (most recent call last): File ".command.sh", line 14, in <module> mutations = mutations[['Tier','GENOMIC_MUTATION_ID', 'Mutation AA', 'Mutation Description', 'FATHMM prediction','FATHMM score']] File "/usr/local/lib/python3.8/dist-packages/pandas/core/frame.py", line 3030, in __getitem__ indexer = self.loc._get_listlike_indexer(key, axis=1, raise_missing=True)[1] File "/usr/local/lib/python3.8/dist-packages/pandas/core/indexing.py", line 1266, in _get_listlike_indexer self._validate_read_indexer(keyarr, indexer, axis, raise_missing=raise_missing) File "/usr/local/lib/python3.8/dist-packages/pandas/core/indexing.py", line 1316, in _validate_read_indexer raise KeyError(f"{not_found} not in index") KeyError: "['FATHMM score', 'FATHMM prediction'] not in index" INFO: Cleaning up image...
Did the version change?
Version v96 does not contain FATHMM information, but v95 does. To download v95 - https://cancer.sanger.ac.uk/cosmic/file_download/GRCh38/cosmic/v95/CosmicMutantExportCensus.tsv.gz
The last step
findCancerMutations
finishes with an error due to the missing columns in the CosmicMutantExportCensus.tsv file.Error:
Did the version change?