use strict;
use warnings;

use MCE::Flow;
use MCE::Shared;

mce_open my $out_fh, '>', \*STDOUT or die "open error: $!\n";

mce_flow {
   max_workers => 4,
   chunk_size  => '2m',
   input_data  => "input_file.fasta",
   RS          => "\n>",
},
sub {
   my ( $mce, $chunk_ref, $chunk_id ) = @_;
   my ( $name, $output );

   for ( @{ $chunk_ref } ) {
      /^>(\w+)/; $name = $1;
      tr/\t\r\n //d; # trim white space

      while ( $_ =~ /(?<=(.....))CCCC(.{10})AGA(?=(.....))/g ) {
         $output .= "$name: $1, $2, $3\n";
      }
   }

   print $out_fh $output if length($output);
};