GoDaddy file manager file permission icon
Maybe there is a permission problem.
After consulting with GoDaddy, I still couldn't run a script. They weren't any help, but they tried. Even though I had changed attributes in Wise-FTP to 755, I figured I still had a permission problem. Finally I found a grayed out permissions icon that is only available if a file is selected (checked) in the GoDaddy file manager.
The script ran after I checked the permission option shown below.
Executable: Allows users to execute files as scripts.
There are other options too. Maybe one of them will solve your problem.