In this part of your code:

while (@arr2 = <CF>){

foreach $line (@arr2) {
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you are doing two nested loops, whereas you really need only one. And the first loop is actually faulty. You either want to do this:

my @arr2 = <CF>;
foreach $line (@arr2) {
# ...
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or that:

while (my $line = <CF>) {
# ...
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The second solution is simpler, slightly faster and, in my view, cleaner.