have 64Gb RAM - has to run everything
innodb_buffer_pool_size=41.2G ...
With that buffer pool setting MySQL should be using 42Gig of memory
If you actually get your server to use that.
64G - 42G = 12G to run everything else ... including apache (how ever that's configured) + anything else operating system wise. Including the cron job which when set to run only once a day, will have to work hard to 'catch up'.
And the following items in Tuner output should verify 'calculation' above:
Physical Memory
Max MySQL memory
Maximum reached memory usage:Maximum possible memory usage:
Overall possible memory usage with other process is compatible with memory available
Cron job ... not running frequently enough ... once every minute.
You mentioned you saw a lot of php-fpm processes. How many is a lot?
'SoS', Ken