use strict;
use warnings;

my $second_file = "npn.txt";
open my $fh2, '<', $second_file or die "Can't write to '$second_file': $!\n";

my @contents;
chomp (@contents = (<$fh2>));
close $fh2;

my $first_file= "hi5res.txt";

open my $fh1, '<', $first_file or die "Can't write to '$first_file': $!\n";

while( my $eachLine=<$fh1>)
{
        chomp($eachLine);
        my @array = split(/,/,$eachLine);

        print $eachLine if (not defined $array[1]);

        if (grep {$_ eq $array[1]} @contents) {
                  print "$eachLine\n" ;
          }

}