in my experience, perl has some problems reading vary large amounts of data into a single variable. it may be better if you can load each line into an entry of an array, (if you've got plenty of memory) or better yet, try to just process a line at a time. For very large jobs like this, I find it preferrable to take one large job and make it in to several small jobs which usually just scan through the file. its probably work while to spend some time thinking of your algorithm to see if this is possible.
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