Description:
Note: Check if the EMS client library path is present in the TRA file.

Symptoms:
The error similar to:
>>>>>>>>>>>>>>>>>>>>>>>
2014 Oct 10 09:57:45:774 GMT -0400 BW.inv_sys_instrument_adapters-InstrumentAdapterProcesses Error [BW-Core] BWENGINE-100001 process initialization failed for Process Definitions/Instrument Adapter/SmfUpdateRefresh.process
process initialization failed for Process Definitions/Instrument Adapter/SmfUpdateRefresh.process
        at com.tibco.pe.core.WorkflowBuilder.build(Unknown Source)
        at com.tibco.pe.core.WorkflowLoader.setWorkflows(Unknown Source)
        at com.tibco.pe.core.WorkflowLoader.loadWorkflows(Unknown Source)
        at com.tibco.pe.core.JobPoolConfigurator.a(Unknown Source)
        at com.tibco.pe.core.JobPoolConfigurator.if(Unknown Source)
        at com.tibco.pe.core.JobPool.<init>(Unknown Source)
        at com.tibco.pe.core.JobPoolCreator.init(Unknown Source)
        at com.tibco.pe.core.JobPoolCreator.<init>(Unknown Source)
        at com.tibco.pe.PEMain.a(Unknown Source)
        at com.tibco.pe.PEMain.do(Unknown Source)
        at com.tibco.pe.PEMain.a(Unknown Source)
        at com.tibco.pe.PEMain.<init>(Unknown Source)
        at com.tibco.pe.PEMain.main(Unknown Source)
caused by: Initialization error in [Process Definitions/Instrument Adapter/SmfUpdateRefresh.process/Adapter Subscriber]
        at com.tibco.pe.core.WorkflowBuilder.build(Unknown Source)
        at com.tibco.pe.core.WorkflowLoader.setWorkflows(Unknown Source)
        at com.tibco.pe.core.WorkflowLoader.loadWorkflows(Unknown Source)
        at com.tibco.pe.core.JobPoolConfigurator.a(Unknown Source)
        at com.tibco.pe.core.JobPoolConfigurator.if(Unknown Source)
        at com.tibco.pe.core.JobPool.<init>(Unknown Source)
        at com.tibco.pe.core.JobPoolCreator.init(Unknown Source)
        at com.tibco.pe.core.JobPoolCreator.<init>(Unknown Source)
        at com.tibco.pe.PEMain.a(Unknown Source)
        at com.tibco.pe.PEMain.do(Unknown Source)
        at com.tibco.pe.PEMain.a(Unknown Source)
        at com.tibco.pe.PEMain.<init>(Unknown Source)
        at com.tibco.pe.PEMain.main(Unknown Source)
caused by: Could not create connection with JMS server.[   Queue Connection Factory = QueueConnectionFactory
   User Name = abc
   JNDI User Name = abc
   JNDI Context URL = tcp://localhost:7222
   JNDI Context Factory = com.tibco.tibjms.naming.TibjmsInitialContextFactory
]
>>>>>>>>>>>>>>>>>>>>>>>

Cause:
EMS client libraries are no longer bundled in TIBCO Runtime Agent post 5.9.0.

Error: "Could not create connection with JMS server." after migration to TIBCO BusinessWorks version using TIBCO Runtime Agent 5.9.0 and onwards.

Add the EMS client libraries by running the traUpgradeManager utility with the –ems option.

traUpgradeManager -path C:\TIBCO_HOME -ems
C:\TIBCO_HOME\ems\<version>

Example:

traUpgradeManager -path C:\tibco -ems C:\tibco\ems\8.0

https://docs.tibco.com/pub/runtime_agent/5.9.0/TIB_TRA_5.9.0_relnotes.pdf