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X! Tandem fails to run

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X! Tandem fails to run rwf  2010-04-08 08:34
Status: Closed
Assigned To: jeckels
 
The X! Tandem fails to run with the following entry in the labkey-errors.log

org.labkey.api.pipeline.PipelineJobException: Failed running C:\Program Files (x86)\LabKey Server\bin\tandem.exe, exit code 1
    at org.labkey.api.pipeline.PipelineJob.runSubProcess(PipelineJob.java:1098)
    at org.labkey.api.pipeline.PipelineJob.runSubProcess(PipelineJob.java:962)
    at org.labkey.ms2.pipeline.tandem.XTandemSearchTask.run(XTandemSearchTask.java:161)
    at org.labkey.api.pipeline.PipelineJob.runActiveTask(PipelineJob.java:624)
    at org.labkey.api.pipeline.PipelineJob.run(PipelineJob.java:847)
    at org.labkey.pipeline.mule.PipelineJobRunner.run(PipelineJobRunner.java:31)
    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 org.mule.impl.model.resolvers.DynamicEntryPoint.invokeMethod(DynamicEntryPoint.java:312)
    at org.mule.impl.model.resolvers.DynamicEntryPoint.invoke(DynamicEntryPoint.java:259)
    at org.mule.impl.DefaultLifecycleAdapter.intercept(DefaultLifecycleAdapter.java:193)
    at org.mule.impl.InterceptorsInvoker.execute(InterceptorsInvoker.java:47)
    at org.mule.impl.model.DefaultMuleProxy.run(DefaultMuleProxy.java:470)
    at org.mule.impl.work.WorkerContext.run(WorkerContext.java:310)
    at edu.emory.mathcs.backport.java.util.concurrent.ThreadPoolExecutor$CallerRunsPolicy.rejectedExecution(ThreadPoolExecutor.java:1895)
    at edu.emory.mathcs.backport.java.util.concurrent.ThreadPoolExecutor.reject(ThreadPoolExecutor.java:765)
    at edu.emory.mathcs.backport.java.util.concurrent.ThreadPoolExecutor.execute(ThreadPoolExecutor.java:1288)
    at org.mule.impl.work.ScheduleWorkExecutor.doExecute(ScheduleWorkExecutor.java:39)
    at org.mule.impl.work.MuleWorkManager.executeWork(MuleWorkManager.java:277)
    at org.mule.impl.work.MuleWorkManager.scheduleWork(MuleWorkManager.java:244)
    at org.mule.impl.model.seda.SedaComponent.run(SedaComponent.java:483)
    at org.mule.impl.work.WorkerContext.run(WorkerContext.java:310)
    at edu.emory.mathcs.backport.java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1061)
    at edu.emory.mathcs.backport.java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:575)
    at java.lang.Thread.run(Unknown Source)


Any assistance would be greatly appreciated.

Ron
 
 
jeckels responded:  2010-04-08 10:49
Hi Ron,

Can you attach the full log file for that individual job? It should contain some additional info that will help in tracking down the underlying problem.

Thanks,
Josh
 
rwf responded:  2010-04-08 16:08
Josh,

Attached is the full log file.

Ron
 
jeckels responded:  2010-04-08 17:27
Hi Ron,

Thanks. Can you also include the individual job's log file? From the content in your labkey.log, it looks like it should be in C:\RAW Data\Project2\xtandem\dbTest.

Thanks,
Josh
 
rwf responded:  2010-04-09 08:48
Hi Josh,

Attached is the individual job's log file. Unfortunately, there is not much in it since the X! Tandem search seems to be hanging with no apparent errors being thrown.

Ron
 
rwf responded:  2010-04-15 14:41
This problem has been resolved. There was a hard <CR> at the end of the labkey.xml file.

This extra line of blank space was preventing the Enterprise pipeline from running properly.

Please close out this thread.

thanks

Ron