my @report;
while (my $line = <$log_file>) {
   my @fields = (split / /, $line);
   $report[$_]{$fields[$_]}++  for 2,4,5,9,7,1;
}
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should do! (untested)

But I would rather use names for each column in a HoH (since you are skipping indices), so

   $report{ $column[$_] }{ $fields[$_] }++  for 2,4,5,9,7,1;

might be better! (for a hash my %report of course)

UPDATE

using column-numbers as names/keys in a HoH

use strict;
use warnings;
use Data::Dump qw/dd/;

my %report;
while (my $line = <DATA>) {
  next if $line =~ /^\s*$/;                     # skip empty lines
  my @fields = (split / /, $line);
  $report{$_}{$fields[$_]}++  for 2,4,5,9,7,1;
}

dd \%report;

__DATA__
483 OS dx-32 1 charles list4 aardvark.com ty-off lx-on C 01
483 DS dx-14 1 james list3 23.456.12.7 ty-on lx-on B 01
769 XO dx-32 5 sully nolist widgets.com ty-on lx-on V 07
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thats what you want?

{
  1 => { DS => 1, OS => 1, XO => 1 },
  2 => { "dx-14" => 1, "dx-32" => 2 },
  4 => { charles => 1, james => 1, sully => 1 },
  5 => { list3 => 1, list4 => 1, nolist => 1 },
  7 => { "ty-off" => 1, "ty-on" => 2 },
  9 => { B => 1, C => 1, V => 1 },
}
[download]