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my @counts;
while (<>) {
...
      ++$counts[$col_num]{ $fields[$col_num] };
   }
}

for my $col_num (1..$#counts) {         # for my $col_num (0, 8) { ??
   my $col_counts = $counts[$col_num];
...
         map { join(',', @{ $by_count{$_} }) }
            keys(%by_count);
}