I checked the permissions and it has all the necessary permissions. Here is an example of the code, I'm probably way off first time trying to do something like this:

$filekey = $cgi->param("doc_file"); 
unlink($filekey) if -e $pubFile_path$filekey;

if ($filekey) {
  if ($filekey =~ /([^\/\\]+)$/) {
    $filename = $1;
    ($ext) = $filename =~ /(\.\w+)$/;
  } 
  else {
return "You attempted to upload <B>$filekey</B> that isn't properly fo
+rmatted. Please rename the file on your computer, and attempt to uplo
+ad it again. Files may not have forward or backward slashes in their 
+names. Also, they may not be prefixed with one (or more) periods.";
}


$path = $pubFile_path . "/" . $count . $ext;

open(OUTFILE, ">$path") or &script_err("Unable to open $path  \nReason
+: $!");;

binmode(OUTFILE); 
  while ($bytes = read($filekey,$buffer,1024)) {
    $totalbytes += $bytes;
    print OUTFILE $buffer;
  }

close(OUTFILE);
}
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