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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!
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:
If you've any time to look into this, that would be great!
nullPointerNextflowLog.txt
Thanks,
Edward.
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