Hi,

you've found your problem and its solution by now, but just two debugging tips that may help you in the future.

#Open the output file for saving the results;  
  open my $fh_out, '>', $write_dir.'/'.$filename
      or die "failed to open '$filename' for write";
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Your error message could be improved by replacing the bare filename with the full name with path, and also by printing the $! special variable which will tells you the error reported by the operating system. So, something like this:

  my $full_filename = $write_dir.'/'.$filename;
  open my $fh_out, '>', $full_filename 
      or die "failed to open $full_filename for write $!";
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would probably have led you to find the error by yourself.