Use of uninitialized value in subtraction (-) at line 117, <$IN2> line
+ 4148567.
Use of uninitialized value in numeric gt (>) at line 118, <$IN2> line 
+4148567.
Use of uninitialized value $F2[2] in hash element at line 119, <$IN2> 
+line 4148567.
Argument "" isn't numeric in sort at line 127, <$IN2> line 4148567.
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Instead of randomly reshuffling the file, could you not extract that 1 line (head -4148567 <file> | tail -1) and then run your script against that 1 line? If I head to guess, seeing that $F[2] is the culprit, I'm guessing you have a double tab on that particular line.

update:Nevermind ... I shouldn't answer questions without first reading the whole thing and second not having finished my morning cup of coffee.