FYI, if that folder is the NFS share for transfer, you can hit odd permissions issues despite being root.
move the certificates keystore out to /tmp or something like that and try again as root. Also, you'll want to make your keysize at least 2048 ... since I think the default in java is still 1024.
Also, it looks like you're trying to execute the file rather than run the keytool command to update. I haven't tried doing something like this, but you should be running keytool like it shows in the documentation.
