Error executing MutSigCV with Large Files

We're having trouble executing MutSigCV with large files. Is there any restriction of the dimension of the data?

We have 625 MAF files and we joined to get a single file to execute MutSigCV. The resultant file is 25GBytes and we get the following error:

------------------------------------------
Setting up environment variables

LD_LIBRARY_PATH is .:/info/jaume/matlab/v901/runtime/glnxa64:/info/jaume/matlab/v901/bin/glnxa64:/info/jaume/matlab/v901/sys/os/glnxa64:/info/jaume/matlab/v901/sys/opengl/lib/glnxa64
"/home/jaume/LUAD/PLINK/MAF/LUAD_1.maf" "exome_full192.coverage.txt" "gene.covariates.txt" "/home/jaume/LUAD/PLINK/MAF/LUAD_1.outputMutSigCV" "mutation_type_dictionary_file.txt" "chr_files_hg19"

======================================
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"...
Warning: deprecated use of slength for structure with fields of nonuniform length
WARNING: 246/5439575 mutations could not be mapped to effect using mutation_type_dictionary_file:

: [123]
Variant_Classification: [123]
----TOTAL: [246]
They will be removed from the analysis.
Warning: deprecated use of slength for structure with fields of nonuniform length
Index exceeds matrix dimensions.

Error in MutSigCV>reorder_struct (line 1854)

Error in MutSigCV>reorder_struct_exclude (line 3885)

Error in MutSigCV>MutSig_preprocess (line 301)

Error in MutSigCV (line 184)

MATLAB:badsubscript
/bin/bash: error reading input file: Bad file descriptor

We tried reducing the dimension of the file and partitioning the MAF file into 5 new files resulting 5GBytes each adn we get the same error.

However, if we join only 2 MAF files, getting a new file of 90Mbytes, we can run MutSigCV without problems.

How can we execute MutSigCV with large files?

We kindly appreciate your help.

Thanks in advance.