Issue with Auto increment in MYSQL Current Structure in MYSQL: 

CREATE TABLE `JOB_ONPREM` (
       `JOB_ID` bigint(20) NOT NULL AUTO_INCREMENT,
       `JOB_NAME` varchar(255) NOT NULL DEFAULT '',
       `SANDBOX` varchar(100) NOT NULL DEFAULT '',
       `JOB_SUB_TYPE` varchar(500) DEFAULT NULL,
       `PARENT_JOB_NAME` varchar(255) NOT NULL DEFAULT '',
       PRIMARY KEY (JOB_ID,`JOB_NAME`,`SANDBOX`,`PARENT_JOB_NAME`)
     ) ENGINE=InnoDB AUTO_INCREMENT=10493 DEFAULT CHARSET=utf8



  I want to keep JOB_NAME,SANDBOX,PARENT_JOB_NAME as Primary KEY and
  JOB_ID as Auto Increment because I am using "ON DUPLICATE KEY UPDATE"
  and because of auto-increment it is inserting new rows and creating
  duplicate in table.
  
  And while removing job_id from primary key. I am getting error as
  "Incorrect table definition; there can be only one auto column and
  it must be defined as a key"
The CREATE TABLE documentation says much the same as what your error message says:


  There can be only one AUTO_INCREMENT column per table, it must be
  indexed, and it cannot have a DEFAULT value.


You need to index the JOB_ID column.

ALTER TABLE JOB_ONPREM
ADD INDEX `dba269102` (`JOB_ID`)


Try that and see if afterwards you can alter the primary key. You could also make it a unique index instead, to help avoid duplicates.

ALTER TABLE JOB_ONPREM
ADD UNIQUE INDEX `dba269102` (`JOB_ID`)