As Anonymous Monk has indicated, you have seriously abused "$x" to the point where your code deteriorates to nonsense, and IMHO, unmaintainable, probably unworkable.

I would suggest a complete overhaul, using strict and warnings, declaring meaningful variable names.

To optimize memory consumpion, read the 1000-line file into memory, then read and process each 50-line file (1000 < 50 * 50).

Please re-post when you have a new outline, and request review when you have something that compiles, but may have a specific problem (which I'm sure you will encounter). This is part of the learning process.