As others have mentioned above, this may be because the file has not yet finished writing. I would use a "stable" file concept and check that the file has not been modified since X time period.

# check if the file has stablized for over 30 seconds
if (is_stable_file($file, 30)) {
   process($file);
}

sub is_stable_file {

    my $file                  = shift;
    my $wait_seconds          = shift || 0;

    my $result                = 1;

    if ($wait_seconds > 0) {

       my ($mtime)            = (stat($file))[9];
       my $secs_since_mod     = (time - $mtime);

       if ($secs_since_mod < $wait_seconds) {
          $result             = 0;
       }

    }

    return $result;

}
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