For (IMO) the most likely meaning of the message you quote, Ln 59 of your data file is the second of two lines, each of which contains an newline and nothing else.

And there is a more idiomatic (because it's more concise) way to get must the first line:

use strict;
use warnings;

open (IN, "1108644.txt") or die;

my $line = <IN>;
print "$line\n";
close IN;
[download]

... and that won't care a lick about line-endings at the bottom of the file.

updated by s/jmust/must/; above.