Fantastico is not installed at the default location

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The error was 

Fantastico is not installed at the default location
/usr/local/cpanel/3rdparty/fantastico. Either move the Fantastico directory
from it's current location to /usr/local/cpanel/3rdparty/fantastico OR
enable ioncube loaders in WHM -> Tweak settings.

Enabling ioncube did not fix it for me. Maybe it will for you. After looking I found cpanel now uses /var/cpanel/3rdparty/bin/php NOT /usr/local/cpanel/3rdparty/bin/php

After doing a php info I saw it did not have a php.ini file in the new location. The fix was: 

cp /usr/local/cpanel/3rdparty/etc/php.ini /var/cpanel/3rdparty/etc

Other Possible Fixes

You may want to first try enabling ioncube in WHM->Tweak Settings

Second you may want to try to update fantastico with cd /usr/local/cpanel/whostmgr/docroot/cgi/fantastico/scripts/ ; /usr/local/cpanel/3rdparty/bin/php cron.php

Third you may want to rebuild cpanel's php with /scripts/makecpphp

Fourth you may want to try a cpanel update with /scripts/upcp --force

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