Your problem appears to be that the data file is too big. That would indicate you are reading the whole file into memory and then processing. You need to switch to an alogrithm that processes each line as it is read (if possible). If this is the case, post the code you have so far.
I don't know about the -Duselargefiles switch, but it appears to refer to the perl scrpt size. Can anyone clarify?
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