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NPE is thrown when checking LSF queue status #1234

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erichards52 opened this issue Jul 19, 2019 · 0 comments
Closed

NPE is thrown when checking LSF queue status #1234

erichards52 opened this issue Jul 19, 2019 · 0 comments

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@erichards52
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erichards52 commented Jul 19, 2019

Copying from here.

When attempting to run the script attached bigsiPipe.nf.txt, the very first process (retReadTxt) exits with the error:
Error executing process > 'retReadTxt'

Caused by:
java.lang.NullPointerException

This doesn't happen when I run this with the currently installed version (nextflow version 19.04.1.5072).

I've attached the log file associated with the error.

I've copied the error from the log file and posted it below:

Jul-18 16:24:02.611 [Task monitor] ERROR nextflow.processor.TaskProcessor - Error executing process > 'retReadTxt'

Caused by:
  java.lang.NullPointerException

java.lang.NullPointerException: null
        at nextflow.util.Throttle.cache(Throttle.groovy:208)
        at nextflow.executor.AbstractGridExecutor.getQueueStatus(AbstractGridExecutor.groovy:299)
        at nextflow.executor.AbstractGridExecutor.checkActiveStatus(AbstractGridExecutor.groovy:368)
        at nextflow.executor.AbstractGridExecutor$checkActiveStatus$0.call(Unknown Source)
        at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:47)
        at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:115)
        at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:135)
        at nextflow.executor.GridTaskHandler.readExitStatus(GridTaskHandler.groovy:205)
        at nextflow.executor.GridTaskHandler.checkIfCompleted(GridTaskHandler.groovy:330)
        at nextflow.processor.TaskPollingMonitor.checkTaskStatus(TaskPollingMonitor.groovy:601)
        at nextflow.processor.TaskPollingMonitor.checkAllTasks(TaskPollingMonitor.groovy:528)
        at nextflow.processor.TaskPollingMonitor.pollLoop(TaskPollingMonitor.groovy:407)
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.lang.reflect.Method.invoke(Method.java:498)
        at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:101)
        at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:323)
        at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1217)
        at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1041)
        at org.codehaus.groovy.runtime.InvokerHelper.invokePogoMethod(InvokerHelper.java:1011)
        at org.codehaus.groovy.runtime.InvokerHelper.invokeMethod(InvokerHelper.java:994)
        at org.codehaus.groovy.runtime.InvokerHelper.invokeMethodSafe(InvokerHelper.java:97)
        at nextflow.processor.TaskPollingMonitor$_start_closure2.doCall(TaskPollingMonitor.groovy:291)
        at nextflow.processor.TaskPollingMonitor$_start_closure2.call(TaskPollingMonitor.groovy)
        at groovy.lang.Closure.run(Closure.java:486)
        at java.lang.Thread.run(Thread.java:748)

If you've any time to look into this, that would be great!

nullPointerNextflowLog.txt

Thanks,
Edward.

@pditommaso pditommaso added the bug label Jul 23, 2019
@pditommaso pditommaso changed the title 19.07.0-edge Unprovoked java.lang.NullPointerException NPE is thrown when checking LSF queue status Jul 27, 2019
@pditommaso pditommaso added this to the v19.07.0 milestone Jul 27, 2019
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