MutSigCV: mutation_type_dictionary_file is missing error despite providing file

[casxue]

When running MutSigCV from just a maf, I consistently get an error saying that the mutation_type_dictionary_file is missing. 

Error using gp_MutSigCV>MutSig_preprocess (line 302) 

missing mutation_type_dictionary_file 

Error in gp_MutSigCV (line 184)

I have tried both using the FTP link (e.g., job 386479) and uploading a local copy of the same file (e.g., job 386492), and both result in this same error.

Could you please advise how to proceed? Thanks!

[Barbara Hill]

Hello, 

The issue is that you have changed a substitution variable that GenePattern needs, in order to name your output file.

Please see this thread for more information.

Let us know if this helps to resolve the issue for you.

All the best

-Barbara