As noted here and there, it has been a nightmare to configure Akeeba Backup on the Godaddy server one of my clients insisted on using, but I've managed.
Just to let everybody know. The account was made last week (recently) and I found that the information about using the alternative script for a CRON-job here:
https://www.akeebabackup.com/documentation/akeeba-backup-documentation/automating-your-backup.html#frontend-backup
was no longer valid (for this particular account).
I still used the alternative script for the CRON-job. However the path had to be altered. The command I used to get it working is
/usr/bin/php5 "$HOME/public_html/cli/akeeba-altbackup.php" --profile=YOURPROFILE_ID
where YOURPROFILE_ID = the profile of the backup configuration
Hope this helps...