Mutsig Error

Does anyone know what is causing this error
I am running mutsig on gene pattern from a maf created using oncotator.

Error using fgets
Invalid file identifier. Use fopen to generate a valid file identifier.

Error in fgetl (line 34)

Error in gp_MutSigCV>load_struct (line 1441)

Error in gp_MutSigCV>MutSig_preprocess (line 304)

Error in gp_MutSigCV (line 184)

MATLAB:FileIO:InvalidFid
Traceback (most recent call last):
File "/xchip/gpprod/servers/genepattern/taskLib/MutSigCV.1.12591/run_matlab.py", line 65, in
subprocess.check_call(matlabCommand)
File "/broad/software/free/Linux/redhat_5_x86_64/pkgs/python_2.6.5/lib/python2.6/subprocess.py", line 498, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['/xchip/gpprod/servers/genepattern/taskLib/MutSigCV.1.12591/gp_MutSigCV', '/xchip/gpprod-upload/servers/genepattern/users/vyellapa/uploads/tmp/run7186293850752403022.tmp/mutation.table.file/1/master.maf', '/xchip/gpprod/shared_data/example_files/MutSigCV_1.3/exome_full192.coverage.txt', '/xchip/gpprod/servers/genepattern/jobResults/838685/gene.covariates.txt', 'masterhmcl', '/xchip/gpprod/shared_data/cga/annotation/ucsc/hg19']' returned non-zero exit status 255

Error using fgets

ok I found the problem/solution: give full paths to mutation_type_dictionary_file.txt and chr_files_hg19 outputTest.txt , instead of using ../

That eliminated the problem for me, thanks

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Hi,

I am facing a similar problem, the difference is I am using MutSig from the command line. Any pointers on the possible cause (and how to resolve) will be much appreciated! thank you

../MutSigCV_1.4/run_MutSigCV.sh ~/software/MATLAB_Compiler_Runtime/v81/ LUSC.mutations.maf LUSC.coverage.txt gene.covariates.txt ../mutation_type_dictionary_file.txt ../chr_files_hg19 outputTest.txt
------------------------------------------

MutSigCV
v1.4

(c) Mike Lawrence and Gaddy Getz
Broad Institute of MIT and Harvard
======================================

MutSigCV: PREPROCESS
--------------------
Loading mutation_file...
Loading coverage file...
Processing mutation "effect"...
NOTE: This version now ignores "is_coding" and "is_silent".
Requires Variant_Classification/type column and mutation_type_dictionary so we can assign nulls.
Error using fgets
Invalid file identifier. Use fopen to generate a valid file identifier.

Error in fgetl (line 34)

Error in MutSigCV>load_struct (line 1445)

Error in MutSigCV>MutSig_preprocess (line 293)

Error in MutSigCV (line 184)

MATLAB:FileIO:InvalidFid