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foreach my $first (@first_directory){
  my @store_array = qw (1 2 3 4 5 6); # here
  while(my ($i,$j) = splice(@store_array,0,2)){
    my $second_directory = "$first/$i/$j";
  ..

#!/usr/bin/perl
use strict; use warnings;
...
  }    
}
close $fh_log;