MutSigCV: mutation_type_dictionary_file is missing error despite providing file

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casxue

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Oct 20, 2021, 4:23:36 AM10/20/21
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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

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Oct 20, 2021, 6:46:57 PM10/20/21
to GenePattern Help Forum
Hello, 

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


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

All the best
-Barbara
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