mysql CPU usage too high

Myserver CPU: Intel Xeon W3520 (4 cores / 8 Threads) 2.66GHz (3.4GHz Turbo Boost) Ram: 32 GB DDR3 hard disk: 2 x 2TB SATA3 hard raid 1 my.cnf [PHP][mysqld] default-storage-engine=MyISAM innodb_file_per_table=1 local-infile=0 port=3306 socket=/var/lib/mysql/mysql.sock max_connections=600 max_user_connections=30 max_connect_errors=15 key_buffer=512M myisam_sort_buffer_size=64M join_buffer_size=1M read_buffer_size=128K sort_buffer_size=256K table_cache=10000 thread_cache_size=50 wait_timeout=300 connect_timeout=30 max_allowed_packet=16M query_cache_limit=4M query_cache_size=128M query_cache_type=1 tmp_table_size=128M max_heap_table_size=128M innodb_buffer_pool_size=1300M slow_query_log=1 delayed_insert_timeout=1 tmpdir=/mysqltmp open_files_limit=24440 [mysql.server] user=mysql [safe_mysqld] err-log=mysqld.log pid-file=/var/lib/mysql/mysql.pid [mysqldump] quick max_allowed_packet = 16M [mysql] no-auto-rehash[/PHP] Here is the output of mysqltuner: [PHP] >> MySQLTuner 1.1.1 - Major Hayden >> Bug reports, feature requests, and downloads at http://mysqltuner.com/ >> Run with '--help' for additional options and output filtering -------- General Statistics -------------------------------------------------- [--] Skipped version check for MySQLTuner script [OK] Currently running supported MySQL version 5.5.34-cll [OK] Operating on 64-bit architecture -------- Storage Engine Statistics ------------------------------------------- [--] Status: -Archive -BDB -Federated +InnoDB -ISAM -NDBCluster [--] Data in MyISAM tables: 105M (Tables: 249) [--] Data in InnoDB tables: 928K (Tables: 58) [--] Data in PERFORMANCE_SCHEMA tables: 0B (Tables: 17) [!!] Total fragmented tables: 12 -------- Security Recommendations ------------------------------------------- [OK] All database users have passwords assigned -------- Performance Metrics ------------------------------------------------- [--] Up for: 2d 20h 7m 16s (44M q [182.628 qps], 2M conn, TX: 26B, RX: 3B) [--] Reads / Writes: 70% / 30% [--] Total buffers: 2.0G global + 1.9M per thread (600 max threads) [OK] Maximum possible memory usage: 3.1G (9% of installed RAM) [OK] Slow queries: 0% (0/44M) [OK] Highest usage of available connections: 5% (34/600) [OK] Key buffer size / total MyISAM indexes: 512.0M/13.3M [OK] Key buffer hit rate: 100.0% (31M cached / 5K reads) [OK] Query cache efficiency: 70.9% (23M cached / 33M selects) [!!] Query cache prunes per day: 135331 [OK] Sorts requiring temporary tables: 0% (880 temp sorts / 2M sorts) [OK] Temporary tables created on disk: 1% (38K on disk / 2M total) [OK] Thread cache hit rate: 99% (34 created / 2M connections) [!!] Table cache hit rate: 0% (660 open / 285K opened) [OK] Open file limit used: 3% (852/24K) [!!] Table locks acquired immediately: 93% [OK] InnoDB data size / buffer pool: 928.0K/1.3G -------- Recommendations ----------------------------------------------------- General recommendations: Run OPTIMIZE TABLE to defragment tables for better performance Increase table_cache gradually to avoid file descriptor limits Optimize queries and/or use InnoDB to reduce lock wait Variables to adjust: query_cache_size (> 128M) table_cache (> 10000)[/PHP]