I fixed the problem. So when I was executing the script the /path/ it doesnt load the data files opened by the script because I didnt have the path included to the data files in the script since I assumed they were in the same directory. However, I think the shell script executes the files from a different directory, so I just added

cd /pathofdirectory/
/pathofperl/perl /pathofscript/script.pl
[download]

and it worked. Thanks a lot though!