open( BEST, "< $best_file") || die "Sorry, can't open $best_file: $!";


@best_array = ();
@NewRow = ();

while( <BEST> ) {
   print STDOUT "\t Reading next line...\n";
   $Record = $_;
   chomp($Record);
   $Record =~ s/^\s+//;
   @NewRow = split(/\s+/, $Record);
   print STDOUT @NewRow[0], " ", @NewRow[1], "\n";
   push( @best_array, [@NewRow] );
   print STDOUT "\t Proceeding to next line...\n";
}

print STDOUT "Processing BEST for duplicates";

...