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reader.nextLine();

Here.... and i hope you read the whole post......

Sure, it doesn't seem to be a memory issue as no such error generated by JVM, well, you might give it a try without buffering into the memory and check the results. Good Luck.

Well, the problem may be the lack of the memory but JVM must throw an exception about OutofMemory.
Well, JVM is memory limited so i guess there are different memory limits for 32 bit and 64 bit...

Well, why don't you try converting your file date to byteArray and then start parsing it?