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I forgot to mention that within the Matlab function, there are UNIX commands that create and remove files, such as

run = 'rm temp.file'
unix(run)

Perhaps this is the source of the problem?

I am trying to run a Matlab function, file.m, with qsub. Here is a portion of my .sge file:

echo Starting to run Matlab
matlab -nojvm -nodesktop -r "file('${inputfile}');exit;"
echo finished...