If you have mysqladmin
available, you may get the list of queries with:
> mysqladmin -uUSERNAME -pPASSWORD pr
+-----+------+-----------------+--------+---------+------+--------------+------------------+
| Id | User | Host | db | Command | Time | State | Info |
+-----+------+-----------------+--------+---------+------+--------------+------------------+
| 137 | beet | localhost:53535 | people | Query | 292 | Sending data | DELETE FROM |
| 145 | root | localhost:55745 | | Query | 0 | | show processlist |
+-----+------+-----------------+--------+---------+------+--------------+------------------+
Then you may stop the mysql process that is hosting the long running query:
> mysqladmin -uUSERNAME -pPASSWORD kill 137