The most likely case is that

  $breakpoint{$chr}{$i}
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is undefined at the time you are getting those messages.

The way I would debug that is to use the perl debugger:
perl -d <your-script>
and add a "conditional breakpoint" at that line:

b 132 !defined($breakpoint{$chr}{$i})
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once the debugger is stopped , you can examine("x") the values in $chr, $i etc, and analyze why they are not what you expect.