The problem here is the array @c1_uniq_cog_ids and the scalar variable $name1 have got flattened and will be stored in the variable @c1_uniq_cog_ids inside your subroutine. So inorder to retain the values you need to pass the array as reference.

cog_class(\@c1_uniq_cog_ids, $name1);
sub cog_class {                                                       
+      my ($c1_uniq_cog_ids, $name) = @_;
  ### you can use @$c1_uniq_cog_ids to get the contents array
}
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In your case even you can reverse the way in which your parameters are passed.

cog_class($name1,@c1_uniq_cog_ids);
sub cog_class {
    my ($name,@c1_uniq_cog_ids)=@_;
}
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Hope this may shed some light....