This is completely unrelated to your issue, but these suggestions may be useful in the future:

Use the strictures:

use warnings;
use strict;
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Amongst other things, this will warn you that

Scalar value @in_items[0] better written as $in_items[0]
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chomp can chomp all elements of a list at once, so there is no need to explicitly chomp each one:

chomp (my @in_items = @_);
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It is a good practice to check the return value of open, opendir and system.

Avoid using $a and $b since they have special meaning for sort.