Migrate Jira to MySql - Unknown system variable 'storage_engine'
If you are using MySQL 5.6, InnoDB is already the default.

Please do not use storage-engine because it is deprecated and probably explains the error.

You should use default-storage-engine or default_storage_engine in my.cnf instead

[mysqld]
default-storage-engine = InnoDB


GIVE IT A TRY !!!