++ For making this :)

Unless you are using autodie, I'd say: always use a temporary variable for the filename, to use both in the call to open and in the error message. This is to avoid having an error message that says that file A is missing, or can't be read, when you were actually trying to read file B, and to avoid looking in the wrong folder. Two examples (which I've both been guilty of):

open my $input, '<', "my_input.xml" or die "Can't open my_input.csv: $
+!"; # Whoops, my_input.xml does not exist by my_input.csv file does

my $input_file = "my_input.xml";
open my $input, '<', $input_file or die "Can't open $input_file: $!"; 
+# Still doesn't work but the error message is correct
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my $file = get_file(); 
my $folder = get_folder(); # The function returned an empty string by 
+mistake
open my $data, '<', "$folder/$file" or die "Can't open $file; $!"; # B
+ut I see the file my folder, why does it say it doesn't exist?

my $input_file = "$folder/$input";
open my $data, '<', $input_file or die "Can't open $input_file: $!"; #
+ You'll see straightaway that you the folder is empty
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Also, that's not really specific to open but try to give meaningful names to your variables. Having to use numbers is nearly always a sign that the name is wrong. $input and $output is always better than $file and $file2. $reference_data and $new_data is also better than $fh1 and $fh2.