gistfile1.txt

-bash-4.1$ jstack -l 13606
Picked up _JAVA_OPTIONS: -Dhttp.proxyHost=proxy.swmed.edu -Dhttp.proxyPort=3128
2016-06-29 22:19:09
Full thread dump Java HotSpot(TM) 64-Bit Server VM (24.51-b03 mixed mode):

"Attach Listener" daemon prio=10 tid=0x00007fa478001000 nid=0x35cc waiting on condition [0x0000000000000000]
   java.lang.Thread.State: RUNNABLE

   Locked ownable synchronizers:
	- None

"Actor Thread 1" daemon prio=10 tid=0x00007fa4cc6c0000 nid=0x3574 waiting on condition [0x00007fa4bd7a3000]
   java.lang.Thread.State: WAITING (parking)
	at sun.misc.Unsafe.park(Native Method)
	- parking to wait for  <0x00000007aef0e4d0> (a java.util.concurrent.SynchronousQueue$TransferStack)
	at java.util.concurrent.locks.LockSupport.park(LockSupport.java:186)
	at java.util.concurrent.SynchronousQueue$TransferStack.awaitFulfill(SynchronousQueue.java:458)
	at java.util.concurrent.SynchronousQueue$TransferStack.transfer(SynchronousQueue.java:359)
	at java.util.concurrent.SynchronousQueue.take(SynchronousQueue.java:925)
	at java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1068)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1130)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
	at java.lang.Thread.run(Thread.java:744)

   Locked ownable synchronizers:
	- None

"Thread-2" prio=10 tid=0x00007fa4cc6ae000 nid=0x3573 waiting on condition [0x00007fa4bd8a3000]
   java.lang.Thread.State: TIMED_WAITING (parking)
	at sun.misc.Unsafe.park(Native Method)
	- parking to wait for  <0x00000007aecd0fb8> (a java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject)
	at java.util.concurrent.locks.LockSupport.parkNanos(LockSupport.java:226)
	at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:2176)
	at nextflow.processor.TaskPollingMonitor$_await_closure8.doCall(TaskPollingMonitor.groovy:372)
	at nextflow.processor.TaskPollingMonitor$_await_closure8.call(TaskPollingMonitor.groovy)
	at nextflow.extension.Bolts.withLock(Bolts.groovy:304)
	at nextflow.extension.Bolts.withLock(Bolts.groovy)
	at nextflow.processor.TaskPollingMonitor.await(TaskPollingMonitor.groovy:371)
	at nextflow.processor.TaskPollingMonitor.pollLoop(TaskPollingMonitor.groovy:346)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:606)
	at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:93)
	at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:325)
	at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1215)
	at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1024)
	at org.codehaus.groovy.runtime.InvokerHelper.invokePogoMethod(InvokerHelper.java:923)
	at org.codehaus.groovy.runtime.InvokerHelper.invokeMethod(InvokerHelper.java:906)
	at org.codehaus.groovy.runtime.InvokerHelper.invokeMethodSafe(InvokerHelper.java:74)
	at nextflow.processor.TaskPollingMonitor$_start_closure6.doCall(TaskPollingMonitor.groovy:319)
	at nextflow.processor.TaskPollingMonitor$_start_closure6.call(TaskPollingMonitor.groovy)
	at groovy.lang.Closure.run(Closure.java:495)
	at java.lang.Thread.run(Thread.java:744)

   Locked ownable synchronizers:
	- None

"Service Thread" daemon prio=10 tid=0x00007fa4cc0a6800 nid=0x3571 runnable [0x0000000000000000]
   java.lang.Thread.State: RUNNABLE

   Locked ownable synchronizers:
	- None

"C1 CompilerThread3" daemon prio=10 tid=0x00007fa4cc0a4000 nid=0x3570 waiting on condition [0x0000000000000000]
   java.lang.Thread.State: RUNNABLE

   Locked ownable synchronizers:
	- None

"C2 CompilerThread2" daemon prio=10 tid=0x00007fa4cc0a2000 nid=0x356f waiting on condition [0x0000000000000000]
   java.lang.Thread.State: RUNNABLE

   Locked ownable synchronizers:
	- None

"C2 CompilerThread1" daemon prio=10 tid=0x00007fa4cc0a0000 nid=0x356e waiting on condition [0x0000000000000000]
   java.lang.Thread.State: RUNNABLE

   Locked ownable synchronizers:
	- None

"C2 CompilerThread0" daemon prio=10 tid=0x00007fa4cc09d000 nid=0x356d waiting on condition [0x0000000000000000]
   java.lang.Thread.State: RUNNABLE

   Locked ownable synchronizers:
	- None

"Signal Dispatcher" daemon prio=10 tid=0x00007fa4cc092800 nid=0x356c runnable [0x0000000000000000]
   java.lang.Thread.State: RUNNABLE

   Locked ownable synchronizers:
	- None

"Finalizer" daemon prio=10 tid=0x00007fa4cc07b000 nid=0x356b in Object.wait() [0x00007fa4be7df000]
   java.lang.Thread.State: WAITING (on object monitor)
	at java.lang.Object.wait(Native Method)
	- waiting on <0x00000007b0e00588> (a java.lang.ref.ReferenceQueue$Lock)
	at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:135)
	- locked <0x00000007b0e00588> (a java.lang.ref.ReferenceQueue$Lock)
	at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:151)
	at java.lang.ref.Finalizer$FinalizerThread.run(Finalizer.java:189)

   Locked ownable synchronizers:
	- None

"Reference Handler" daemon prio=10 tid=0x00007fa4cc077000 nid=0x356a in Object.wait() [0x00007fa4be8e0000]
   java.lang.Thread.State: WAITING (on object monitor)
	at java.lang.Object.wait(Native Method)
	- waiting on <0x00000007b0e00620> (a java.lang.ref.Reference$Lock)
	at java.lang.Object.wait(Object.java:503)
	at java.lang.ref.Reference$ReferenceHandler.run(Reference.java:133)
	- locked <0x00000007b0e00620> (a java.lang.ref.Reference$Lock)

   Locked ownable synchronizers:
	- None

"main" prio=10 tid=0x00007fa4cc00b800 nid=0x3560 waiting on condition [0x00007fa4d1485000]
   java.lang.Thread.State: WAITING (parking)
	at sun.misc.Unsafe.park(Native Method)
	- parking to wait for  <0x00000007acef7ef8> (a java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject)
	at java.util.concurrent.locks.LockSupport.park(LockSupport.java:186)
	at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:2043)
	at nextflow.util.Barrier$_awaitCompletion_closure3.doCall(Barrier.groovy:96)
	at nextflow.util.Barrier$_awaitCompletion_closure3.call(Barrier.groovy)
	at nextflow.extension.Bolts.withLock(Bolts.groovy:304)
	at nextflow.extension.Bolts.withLock(Bolts.groovy)
	at nextflow.util.Barrier.awaitCompletion(Barrier.groovy:93)
	at nextflow.Session.await(Session.groovy:415)
	at nextflow.script.ScriptRunner.terminate(ScriptRunner.groovy:327)
	at nextflow.script.ScriptRunner.execute(ScriptRunner.groovy:158)
	at nextflow.cli.CmdRun.run(CmdRun.groovy:198)
	at nextflow.cli.Launcher.run(Launcher.groovy:385)
	at nextflow.cli.Launcher.main(Launcher.groovy:534)

   Locked ownable synchronizers:
	- None

"VM Thread" prio=10 tid=0x00007fa4cc074800 nid=0x3569 runnable 

"GC task thread#0 (ParallelGC)" prio=10 tid=0x00007fa4cc021800 nid=0x3561 runnable 

"GC task thread#1 (ParallelGC)" prio=10 tid=0x00007fa4cc023800 nid=0x3562 runnable 

"GC task thread#2 (ParallelGC)" prio=10 tid=0x00007fa4cc025800 nid=0x3563 runnable 

"GC task thread#3 (ParallelGC)" prio=10 tid=0x00007fa4cc027800 nid=0x3564 runnable 

"GC task thread#4 (ParallelGC)" prio=10 tid=0x00007fa4cc029800 nid=0x3565 runnable 

"GC task thread#5 (ParallelGC)" prio=10 tid=0x00007fa4cc02b000 nid=0x3566 runnable 

"GC task thread#6 (ParallelGC)" prio=10 tid=0x00007fa4cc02d000 nid=0x3567 runnable 

"GC task thread#7 (ParallelGC)" prio=10 tid=0x00007fa4cc02f000 nid=0x3568 runnable 

"VM Periodic Task Thread" prio=10 tid=0x00007fa4cc0b1800 nid=0x3572 waiting on condition 

JNI global references: 173