Description:
This issue is seen when the Enterprise Messaging Service location is provided as part of the Tibco Runtime Agent 5.9.x installation and Domain utility is run to upgrade the domain to Tibco Runtime Agent 5.9.x. In this case the Domainutility fails to upgrade domains with a Null Pointer Exception.

Symptoms:
Domain Utility to upgrade the domain Task fails and below Null Pointer Exception appear in the domainutilty.log.
<------------------
2015 Apr 10 17:05:09:87 GMT -0400 DU Error [DomainUtility] AESDKJ-0000 java.lang.NullPointerException
at com.tibco.administrator.command.tool.TraUpgradeManager.a(TraUpgradeManager.java:804)
at com.tibco.administrator.command.tool.TraUpgradeManager.if(TraUpgradeManager.java:236)
at com.tibco.administrator.command.tool.TraUpgradeManager.doUpgrade(TraUpgradeManager.java:131)
at com.tibco.administrator.du.task.migration.UpgradeTo59.new(UpgradeTo59.java:442)
at com.tibco.administrator.du.task.migration.UpgradeTo59.upgrade(UpgradeTo59.java:187)
at com.tibco.administrator.du.task.migration.MigrateTo59Task.execute(MigrateTo59Task.java:63)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
at java.lang.reflect.Method.invoke(Unknown Source)
at com.tibco.administrator.wizard.progress.Trampoline.invoke(Trampoline.java:96)
at com.tibco.administrator.wizard.progress.BusyWait.run(BusyWait.java:267)
at java.lang.Thread.run(Unknown Source)
--------->
Cause:
When the Enterprise Messaging Service location is provided as part of the Tibco Runtime Agent 5.9.x installation, it updates all the files including the configuration files for the existing domains. This causes the domain upgrade via the domain utility to fail.