open my $results, '<', $outputfile
    or die "Cannot open '$outputfile' for reading: $!\n';

open my $cleaned, '>', $new_outputfile
    or die "Cannot open '$new_outputfile' for writing: $!\n";

{
    my %seen;
    local $_;
    while ( <$results> ) {
        chomp;

        next if $seen{ $_ }++;
        print $cleaned $_, "\n";
    }
}

# Always close in the reverse order of opening.
close $cleaned;
close $results;

unlink $results
    or die "Cannot unlink '$outputfile': $!\n";
File::Copy::move( $new_outputfile, $outputfile )
    or die "Cannot rename '$new_outputfile' to '$outputfile': $!\n";