for (my $y = 0; $y < $num; $y++) {
      for (my $x = $y+1; $x < $num; $x++) {
         if (($scores->[$y]->[$x] >= 0.96)) {
            if ($blast_par->{$cleancodes->[$x]}->{"taxon"} eq
                $blast_par->{$cleancodes->[$y]}->{"taxon"}) {
               if (($blast_par->{$cleancodes->[$y]}->{"defline"} =~ m/refseq/i) &&
                   ($blast_par->{$cleancodes->[$x]}->{"defline"} =~ m/refseq/i)) {
                  if ($blast_par->{$cleancodes->[$y]}->{"defline"} =~ m/NP_/) { # this line produces the error
                     $to_keep = $y;
                     $to_kill = $x;
                  }
                  elsif (($blast_par->{$cleancodes->[$y]}->{"defline"}->[$y] !~ m/NP_/) &&
                         ($blast_par->{$cleancodes->[$x]}->{"defline"}->[$x] =~ m/NP_/)) {
                     $to_keep = $x;
                     $to_kill = $y;
                  }
               }
               &generic_sub($to_kill, $to_keep);
            }
         }
      }
   }