Here's another way to do the task which doesn't require reading the entire file into memory.

#!/usr/bin/perl

use strict;
use warnings;

my %keeplist;
open my $rids, '<', 'rids_that_have_versions.txt' or die $!;
while (<$rids>) { chomp; $keeplist{$_} = 1;}
close $rids;

while (<STDIN>) {
  next unless /^##/;  # only deal with '##' lines
  my $rid = substr($_, 19, 10);

  print "$rid: " . ($keeplist{$rid} ? 'y' : 'n') . "\n";
}
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