Innodb using key cache?
In addition to what Md Haidar Ali Khan said, ...
The "default storage engine" does not mean that you created all the tables in that engine.  You should verify with SHOW TABLE STATUS; for you database(s).  That will say, among other things, what Engine is being used.

innodb_buffer_pool_size, for an InnoDB-only system, should be set to about 70% of available RAM (if RAM is at least 4GB).  And set key_buffer_size to some small value, say, 20M because of system tables that are in MyISAM.  These system tables probably caused the spikes you saw.

More discussion of memory -- including what to do if you are using MyISAM.