$total is the number of elements in @lines, not the last
array index. You're looping until $i <= $total, so the
last element that you're trying to access is beyond the
bounds of the array. So it's undefined.
Say that your array has 5 elements:
my @lines = qw/a b c d e/;
my $total = @lines;
$total is now 5, but the last array index is 4, because
the indices start at 0. In your
for loop, $i goes from
0 to 5, and when $i is 5, you're trying to access
$lines[5]
which doesn't exist.
The solution, of course, is to change your for loop:
for my $i (0..$total-1) {
...
Of course, if this is all you're doing, you may as well just
use
grep:
my $total = grep $_ ne "\n", @lines;
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