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linminhtoo/gist:d897a2f4bda7c4315c202c19ad7e2e49

Created January 22, 2024 18:56
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java stack with jtrace
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gistfile1.txt
minhtoo@minhtoo:~/.nextflow/capsule/deps$ jstack 63923
2024-01-23 02:54:51
Full thread dump OpenJDK 64-Bit Server VM (17.0.6+10-LTS mixed mode, sharing):
Threads class SMR info:
_java_thread_list=0x00007f46f0001890, length=38, elements={
0x00007f4748028010, 0x00007f4748167420, 0x00007f4748168800, 0x00007f4748177b10,
0x00007f4748178ec0, 0x00007f474817a2d0, 0x00007f474817bd00, 0x00007f474817d230,
0x00007f474817e6a0, 0x00007f47481b30f0, 0x00007f47481b5050, 0x00007f4748fc0990,
0x00007f474892a1c0, 0x00007f4748de2880, 0x00007f4749203220, 0x00007f47494b6d80,
0x00007f47494bd840, 0x00007f4749498f20, 0x00007f47494ed380, 0x00007f474950e4e0,
0x00007f474952a810, 0x00007f474952c990, 0x00007f474952ec20, 0x00007f474952fd60,
0x00007f4749538a00, 0x00007f47495397a0, 0x00007f474953b760, 0x00007f474953eea0,
0x00007f4749540890, 0x00007f4749551050, 0x00007f474955fe70, 0x00007f4749561ba0,
0x00007f4749560c20, 0x00007f47495263d0, 0x00007f46500179b0, 0x00007f46500110d0,
0x00007f46000020f0, 0x00007f46f0000eb0
}
"main" #1 prio=5 os_prio=0 cpu=6865.98ms elapsed=916.97s tid=0x00007f4748028010 nid=0xfa05 waiting on condition [0x00007f474edfe000]
java.lang.Thread.State: WAITING (parking)
at jdk.internal.misc.Unsafe.park(java.base@17.0.6/Native Method)
- parking to wait for <0x000000060ff5d4b8> (a java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject)
at java.util.concurrent.locks.LockSupport.park(java.base@17.0.6/LockSupport.java:341)
at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionNode.block(java.base@17.0.6/AbstractQueuedSynchronizer.java:506)
at java.util.concurrent.ForkJoinPool.unmanagedBlock(java.base@17.0.6/ForkJoinPool.java:3463)
at java.util.concurrent.ForkJoinPool.managedBlock(java.base@17.0.6/ForkJoinPool.java:3434)
at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(java.base@17.0.6/AbstractQueuedSynchronizer.java:1623)
at nextflow.util.Barrier$_awaitCompletion_closure3.doCall(Barrier.groovy:92)
at nextflow.util.Barrier$_awaitCompletion_closure3.call(Barrier.groovy)
at nextflow.extension.Bolts.withLock(Bolts.groovy:337)
at nextflow.extension.Bolts.withLock(Bolts.groovy)
at nextflow.util.Barrier.awaitCompletion(Barrier.groovy:89)
at nextflow.Session.await(Session.groovy:659)
at nextflow.script.ScriptRunner.await(ScriptRunner.groovy:255)
at nextflow.script.ScriptRunner.execute(ScriptRunner.groovy:143)
at nextflow.cli.CmdRun.run(CmdRun.groovy:372)
at nextflow.cli.Launcher.run(Launcher.groovy:500)
at nextflow.cli.Launcher.main(Launcher.groovy:672)
"Reference Handler" #2 daemon prio=10 os_prio=0 cpu=1.36ms elapsed=916.96s tid=0x00007f4748167420 nid=0xfa0c waiting on condition [0x00007f470f5f1000]
java.lang.Thread.State: RUNNABLE
at java.lang.ref.Reference.waitForReferencePendingList(java.base@17.0.6/Native Method)
at java.lang.ref.Reference.processPendingReferences(java.base@17.0.6/Reference.java:253)
at java.lang.ref.Reference$ReferenceHandler.run(java.base@17.0.6/Reference.java:215)
"Finalizer" #3 daemon prio=8 os_prio=0 cpu=0.79ms elapsed=916.96s tid=0x00007f4748168800 nid=0xfa0d in Object.wait() [0x00007f470ebfe000]
java.lang.Thread.State: WAITING (on object monitor)
at java.lang.Object.wait(java.base@17.0.6/Native Method)
- waiting on <0x000000060ea1b688> (a java.lang.ref.ReferenceQueue$Lock)
at java.lang.ref.ReferenceQueue.remove(java.base@17.0.6/ReferenceQueue.java:155)
- locked <0x000000060ea1b688> (a java.lang.ref.ReferenceQueue$Lock)
at java.lang.ref.ReferenceQueue.remove(java.base@17.0.6/ReferenceQueue.java:176)
at java.lang.ref.Finalizer$FinalizerThread.run(java.base@17.0.6/Finalizer.java:172)
"Signal Dispatcher" #4 daemon prio=9 os_prio=0 cpu=0.25ms elapsed=916.96s tid=0x00007f4748177b10 nid=0xfa0e waiting on condition [0x0000000000000000]
java.lang.Thread.State: RUNNABLE
"Service Thread" #5 daemon prio=9 os_prio=0 cpu=1.72ms elapsed=916.96s tid=0x00007f4748178ec0 nid=0xfa0f runnable [0x0000000000000000]
java.lang.Thread.State: RUNNABLE
"Monitor Deflation Thread" #6 daemon prio=9 os_prio=0 cpu=29.15ms elapsed=916.96s tid=0x00007f474817a2d0 nid=0xfa10 runnable [0x0000000000000000]
java.lang.Thread.State: RUNNABLE
"C2 CompilerThread0" #7 daemon prio=9 os_prio=0 cpu=5231.61ms elapsed=916.96s tid=0x00007f474817bd00 nid=0xfa11 waiting on condition [0x0000000000000000]
java.lang.Thread.State: RUNNABLE
No compile task
"C1 CompilerThread0" #15 daemon prio=9 os_prio=0 cpu=824.16ms elapsed=916.96s tid=0x00007f474817d230 nid=0xfa12 waiting on condition [0x0000000000000000]
java.lang.Thread.State: RUNNABLE
No compile task
"Sweeper thread" #19 daemon prio=9 os_prio=0 cpu=153.35ms elapsed=916.96s tid=0x00007f474817e6a0 nid=0xfa13 runnable [0x0000000000000000]
java.lang.Thread.State: RUNNABLE
"Common-Cleaner" #20 daemon prio=8 os_prio=0 cpu=2.63ms elapsed=916.95s tid=0x00007f47481b30f0 nid=0xfa15 in Object.wait() [0x00007f470de86000]
java.lang.Thread.State: TIMED_WAITING (on object monitor)
at java.lang.Object.wait(java.base@17.0.6/Native Method)
- waiting on <no object reference available>
at java.lang.ref.ReferenceQueue.remove(java.base@17.0.6/ReferenceQueue.java:155)
- locked <0x000000060ea32320> (a java.lang.ref.ReferenceQueue$Lock)
at jdk.internal.ref.CleanerImpl.run(java.base@17.0.6/CleanerImpl.java:140)
at java.lang.Thread.run(java.base@17.0.6/Thread.java:833)
at jdk.internal.misc.InnocuousThread.run(java.base@17.0.6/InnocuousThread.java:162)
"Notification Thread" #21 daemon prio=9 os_prio=0 cpu=0.04ms elapsed=916.95s tid=0x00007f47481b5050 nid=0xfa16 runnable [0x0000000000000000]
java.lang.Thread.State: RUNNABLE
"process reaper" #27 daemon prio=10 os_prio=0 cpu=1.33ms elapsed=914.14s tid=0x00007f4748fc0990 nid=0xfa46 runnable [0x00007f474e856000]
java.lang.Thread.State: RUNNABLE
at java.lang.ProcessHandleImpl.waitForProcessExit0(java.base@17.0.6/Native Method)
at java.lang.ProcessHandleImpl$1.run(java.base@17.0.6/ProcessHandleImpl.java:147)
at java.util.concurrent.ThreadPoolExecutor.runWorker(java.base@17.0.6/ThreadPoolExecutor.java:1136)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(java.base@17.0.6/ThreadPoolExecutor.java:635)
at java.lang.Thread.run(java.base@17.0.6/Thread.java:833)
"JGit-WorkQueue" #36 daemon prio=5 os_prio=0 cpu=0.56ms elapsed=889.99s tid=0x00007f474892a1c0 nid=0xfab0 waiting on condition [0x00007f470c2e8000]
java.lang.Thread.State: WAITING (parking)
at jdk.internal.misc.Unsafe.park(java.base@17.0.6/Native Method)
- parking to wait for <0x000000060ec01e88> (a java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject)
at java.util.concurrent.locks.LockSupport.park(java.base@17.0.6/LockSupport.java:341)
at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionNode.block(java.base@17.0.6/AbstractQueuedSynchronizer.java:506)
at java.util.concurrent.ForkJoinPool.unmanagedBlock(java.base@17.0.6/ForkJoinPool.java:3463)
at java.util.concurrent.ForkJoinPool.managedBlock(java.base@17.0.6/ForkJoinPool.java:3434)
at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(java.base@17.0.6/AbstractQueuedSynchronizer.java:1623)
at java.util.concurrent.ScheduledThreadPoolExecutor$DelayedWorkQueue.take(java.base@17.0.6/ScheduledThreadPoolExecutor.java:1170)
at java.util.concurrent.ScheduledThreadPoolExecutor$DelayedWorkQueue.take(java.base@17.0.6/ScheduledThreadPoolExecutor.java:899)
at java.util.concurrent.ThreadPoolExecutor.getTask(java.base@17.0.6/ThreadPoolExecutor.java:1062)
at java.util.concurrent.ThreadPoolExecutor.runWorker(java.base@17.0.6/ThreadPoolExecutor.java:1122)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(java.base@17.0.6/ThreadPoolExecutor.java:635)
at java.lang.Thread.run(java.base@17.0.6/Thread.java:833)
"Thread-5" #39 daemon prio=5 os_prio=0 cpu=234.59ms elapsed=886.77s tid=0x00007f4748de2880 nid=0xfad2 waiting on condition [0x00007f470df85000]
java.lang.Thread.State: TIMED_WAITING (parking)
at jdk.internal.misc.Unsafe.park(java.base@17.0.6/Native Method)
- parking to wait for <0x000000060fd158a8> (a java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject)
at java.util.concurrent.locks.LockSupport.parkNanos(java.base@17.0.6/LockSupport.java:252)
at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.awaitNanos(java.base@17.0.6/AbstractQueuedSynchronizer.java:1672)
at java.util.concurrent.LinkedBlockingDeque.pollFirst(java.base@17.0.6/LinkedBlockingDeque.java:515)
at java.util.concurrent.LinkedBlockingDeque.poll(java.base@17.0.6/LinkedBlockingDeque.java:677)
at nextflow.util.SimpleAgent.run(SimpleAgent.groovy:89)
at jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(java.base@17.0.6/Native Method)
at jdk.internal.reflect.NativeMethodAccessorImpl.invoke(java.base@17.0.6/NativeMethodAccessorImpl.java:77)
at jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(java.base@17.0.6/DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(java.base@17.0.6/Method.java:568)
at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:107)
at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:323)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1254)
at groovy.lang.MetaClassImpl.invokeMethodClosure(MetaClassImpl.java:1042)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1128)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1030)
at groovy.lang.Closure.call(Closure.java:427)
at groovy.lang.Closure.call(Closure.java:406)
at groovy.lang.Closure.run(Closure.java:498)
at java.lang.Thread.run(java.base@17.0.6/Thread.java:833)
"AnsiLogObserver" #40 daemon prio=5 os_prio=0 cpu=232.22ms elapsed=886.62s tid=0x00007f4749203220 nid=0xfad9 in Object.wait() [0x00007f468e2f7000]
java.lang.Thread.State: TIMED_WAITING (on object monitor)
at java.lang.Object.wait(java.base@17.0.6/Native Method)
- waiting on <no object reference available>
at nextflow.trace.AnsiLogObserver.render0(AnsiLogObserver.groovy:179)
- locked <0x000000060fd71ad0> (a nextflow.trace.AnsiLogObserver)
at jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(java.base@17.0.6/Native Method)
at jdk.internal.reflect.NativeMethodAccessorImpl.invoke(java.base@17.0.6/NativeMethodAccessorImpl.java:77)
at jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(java.base@17.0.6/DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(java.base@17.0.6/Method.java:568)
at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:107)
at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:323)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1254)
at groovy.lang.MetaClassImpl.invokeMethodClosure(MetaClassImpl.java:1042)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1128)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1030)
at groovy.lang.Closure.call(Closure.java:427)
at groovy.lang.Closure.call(Closure.java:406)
at groovy.lang.Closure.run(Closure.java:498)
at java.lang.Thread.run(java.base@17.0.6/Thread.java:833)
"Actor Thread 1" #41 daemon prio=5 os_prio=0 cpu=3.62ms elapsed=883.94s tid=0x00007f47494b6d80 nid=0xfadc waiting on condition [0x00007f468ebfe000]
java.lang.Thread.State: WAITING (parking)
at jdk.internal.misc.Unsafe.park(java.base@17.0.6/Native Method)
- parking to wait for <0x000000060ffaef38> (a java.util.concurrent.SynchronousQueue$TransferStack)
at java.util.concurrent.locks.LockSupport.park(java.base@17.0.6/LockSupport.java:341)
at java.util.concurrent.SynchronousQueue$TransferStack$SNode.block(java.base@17.0.6/SynchronousQueue.java:288)
at java.util.concurrent.ForkJoinPool.unmanagedBlock(java.base@17.0.6/ForkJoinPool.java:3463)
at java.util.concurrent.ForkJoinPool.managedBlock(java.base@17.0.6/ForkJoinPool.java:3434)
at java.util.concurrent.SynchronousQueue$TransferStack.transfer(java.base@17.0.6/SynchronousQueue.java:397)
at java.util.concurrent.SynchronousQueue.take(java.base@17.0.6/SynchronousQueue.java:886)
at java.util.concurrent.ThreadPoolExecutor.getTask(java.base@17.0.6/ThreadPoolExecutor.java:1062)
at java.util.concurrent.ThreadPoolExecutor.runWorker(java.base@17.0.6/ThreadPoolExecutor.java:1122)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(java.base@17.0.6/ThreadPoolExecutor.java:635)
at java.lang.Thread.run(java.base@17.0.6/Thread.java:833)
"Actor Thread 2" #42 daemon prio=5 os_prio=0 cpu=0.21ms elapsed=883.92s tid=0x00007f47494bd840 nid=0xfadd waiting on condition [0x00007f468e4f8000]
java.lang.Thread.State: WAITING (parking)
at jdk.internal.misc.Unsafe.park(java.base@17.0.6/Native Method)
- parking to wait for <0x000000060ffaef38> (a java.util.concurrent.SynchronousQueue$TransferStack)
at java.util.concurrent.locks.LockSupport.park(java.base@17.0.6/LockSupport.java:341)
at java.util.concurrent.SynchronousQueue$TransferStack$SNode.block(java.base@17.0.6/SynchronousQueue.java:288)
at java.util.concurrent.ForkJoinPool.unmanagedBlock(java.base@17.0.6/ForkJoinPool.java:3463)
at java.util.concurrent.ForkJoinPool.managedBlock(java.base@17.0.6/ForkJoinPool.java:3434)
at java.util.concurrent.SynchronousQueue$TransferStack.transfer(java.base@17.0.6/SynchronousQueue.java:397)
at java.util.concurrent.SynchronousQueue.take(java.base@17.0.6/SynchronousQueue.java:886)
at java.util.concurrent.ThreadPoolExecutor.getTask(java.base@17.0.6/ThreadPoolExecutor.java:1062)
at java.util.concurrent.ThreadPoolExecutor.runWorker(java.base@17.0.6/ThreadPoolExecutor.java:1122)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(java.base@17.0.6/ThreadPoolExecutor.java:635)
at java.lang.Thread.run(java.base@17.0.6/Thread.java:833)
"Task monitor" #43 daemon prio=5 os_prio=0 cpu=927.15ms elapsed=883.88s tid=0x00007f4749498f20 nid=0xfade waiting on condition [0x00007f468e3f7000]
java.lang.Thread.State: TIMED_WAITING (parking)
at jdk.internal.misc.Unsafe.park(java.base@17.0.6/Native Method)
- parking to wait for <0x00000006179d4d88> (a java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject)
at java.util.concurrent.locks.LockSupport.parkNanos(java.base@17.0.6/LockSupport.java:252)
at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(java.base@17.0.6/AbstractQueuedSynchronizer.java:1757)
at nextflow.processor.TaskPollingMonitor$_await_closure5.doCall(TaskPollingMonitor.groovy:493)
at nextflow.processor.TaskPollingMonitor$_await_closure5.call(TaskPollingMonitor.groovy)
at nextflow.extension.Bolts.withLock(Bolts.groovy:337)
at nextflow.extension.Bolts.withLock(Bolts.groovy)
at nextflow.processor.TaskPollingMonitor.await(TaskPollingMonitor.groovy:492)
at nextflow.processor.TaskPollingMonitor.pollLoop(TaskPollingMonitor.groovy:422)
at jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(java.base@17.0.6/Native Method)
at jdk.internal.reflect.NativeMethodAccessorImpl.invoke(java.base@17.0.6/NativeMethodAccessorImpl.java:77)
at jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(java.base@17.0.6/DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(java.base@17.0.6/Method.java:568)
at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:107)
at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:323)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1254)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1030)
at org.codehaus.groovy.runtime.InvokerHelper.invokePogoMethod(InvokerHelper.java:1036)
at org.codehaus.groovy.runtime.InvokerHelper.invokeMethod(InvokerHelper.java:1019)
at org.codehaus.groovy.runtime.InvokerHelper.invokeMethodSafe(InvokerHelper.java:97)
at nextflow.processor.TaskPollingMonitor$_start_closure2.doCall(TaskPollingMonitor.groovy:293)
at nextflow.processor.TaskPollingMonitor$_start_closure2.call(TaskPollingMonitor.groovy)
at groovy.lang.Closure.run(Closure.java:498)
at java.lang.Thread.run(java.base@17.0.6/Thread.java:833)
"Task submitter" #44 daemon prio=5 os_prio=0 cpu=29.80ms elapsed=883.88s tid=0x00007f47494ed380 nid=0xfadf waiting on condition [0x00007f468c3fd000]
java.lang.Thread.State: WAITING (parking)
at jdk.internal.misc.Unsafe.park(java.base@17.0.6/Native Method)
- parking to wait for <0x0000000617a32908> (a java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject)
at java.util.concurrent.locks.LockSupport.park(java.base@17.0.6/LockSupport.java:341)
at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionNode.block(java.base@17.0.6/AbstractQueuedSynchronizer.java:506)
at java.util.concurrent.ForkJoinPool.unmanagedBlock(java.base@17.0.6/ForkJoinPool.java:3463)
at java.util.concurrent.ForkJoinPool.managedBlock(java.base@17.0.6/ForkJoinPool.java:3434)
at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(java.base@17.0.6/AbstractQueuedSynchronizer.java:1623)
at nextflow.processor.TaskPollingMonitor.awaitTasks(TaskPollingMonitor.groovy:363)
at nextflow.processor.TaskPollingMonitor.submitLoop(TaskPollingMonitor.groovy:387)
at jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(java.base@17.0.6/Native Method)
at jdk.internal.reflect.NativeMethodAccessorImpl.invoke(java.base@17.0.6/NativeMethodAccessorImpl.java:77)
at jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(java.base@17.0.6/DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(java.base@17.0.6/Method.java:568)
at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:107)
at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:323)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1254)
at groovy.lang.MetaClassImpl.invokeMethodClosure(MetaClassImpl.java:1042)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1128)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1030)
at groovy.lang.Closure.call(Closure.java:427)
at groovy.lang.Closure.call(Closure.java:406)
at groovy.lang.Closure.run(Closure.java:498)
at java.lang.Thread.run(java.base@17.0.6/Thread.java:833)
"Actor Thread 3" #45 daemon prio=5 os_prio=0 cpu=0.19ms elapsed=883.85s tid=0x00007f474950e4e0 nid=0xfae0 waiting on condition [0x00007f468c2fe000]
java.lang.Thread.State: WAITING (parking)
at jdk.internal.misc.Unsafe.park(java.base@17.0.6/Native Method)
- parking to wait for <0x000000060ffaef38> (a java.util.concurrent.SynchronousQueue$TransferStack)
at java.util.concurrent.locks.LockSupport.park(java.base@17.0.6/LockSupport.java:341)
at java.util.concurrent.SynchronousQueue$TransferStack$SNode.block(java.base@17.0.6/SynchronousQueue.java:288)
at java.util.concurrent.ForkJoinPool.unmanagedBlock(java.base@17.0.6/ForkJoinPool.java:3463)
at java.util.concurrent.ForkJoinPool.managedBlock(java.base@17.0.6/ForkJoinPool.java:3434)
at java.util.concurrent.SynchronousQueue$TransferStack.transfer(java.base@17.0.6/SynchronousQueue.java:397)
at java.util.concurrent.SynchronousQueue.take(java.base@17.0.6/SynchronousQueue.java:886)
at java.util.concurrent.ThreadPoolExecutor.getTask(java.base@17.0.6/ThreadPoolExecutor.java:1062)
at java.util.concurrent.ThreadPoolExecutor.runWorker(java.base@17.0.6/ThreadPoolExecutor.java:1122)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(java.base@17.0.6/ThreadPoolExecutor.java:635)
at java.lang.Thread.run(java.base@17.0.6/Thread.java:833)
"Actor Thread 4" #46 daemon prio=5 os_prio=0 cpu=0.29ms elapsed=883.83s tid=0x00007f474952a810 nid=0xfae1 waiting on condition [0x00007f468c1fe000]
java.lang.Thread.State: WAITING (parking)
at jdk.internal.misc.Unsafe.park(java.base@17.0.6/Native Method)
- parking to wait for <0x000000060ffaef38> (a java.util.concurrent.SynchronousQueue$TransferStack)
at java.util.concurrent.locks.LockSupport.park(java.base@17.0.6/LockSupport.java:341)
at java.util.concurrent.SynchronousQueue$TransferStack$SNode.block(java.base@17.0.6/SynchronousQueue.java:288)
at java.util.concurrent.ForkJoinPool.unmanagedBlock(java.base@17.0.6/ForkJoinPool.java:3463)
at java.util.concurrent.ForkJoinPool.managedBlock(java.base@17.0.6/ForkJoinPool.java:3434)
at java.util.concurrent.SynchronousQueue$TransferStack.transfer(java.base@17.0.6/SynchronousQueue.java:397)
at java.util.concurrent.SynchronousQueue.take(java.base@17.0.6/SynchronousQueue.java:886)
at java.util.concurrent.ThreadPoolExecutor.getTask(java.base@17.0.6/ThreadPoolExecutor.java:1062)
at java.util.concurrent.ThreadPoolExecutor.runWorker(java.base@17.0.6/ThreadPoolExecutor.java:1122)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(java.base@17.0.6/ThreadPoolExecutor.java:635)
at java.lang.Thread.run(java.base@17.0.6/Thread.java:833)
"Actor Thread 5" #47 daemon prio=5 os_prio=0 cpu=0.20ms elapsed=883.83s tid=0x00007f474952c990 nid=0xfae2 waiting on condition [0x00007f468c0fe000]
java.lang.Thread.State: WAITING (parking)
at jdk.internal.misc.Unsafe.park(java.base@17.0.6/Native Method)
- parking to wait for <0x000000060ffaef38> (a java.util.concurrent.SynchronousQueue$TransferStack)
at java.util.concurrent.locks.LockSupport.park(java.base@17.0.6/LockSupport.java:341)
at java.util.concurrent.SynchronousQueue$TransferStack$SNode.block(java.base@17.0.6/SynchronousQueue.java:288)
at java.util.concurrent.ForkJoinPool.unmanagedBlock(java.base@17.0.6/ForkJoinPool.java:3463)
at java.util.concurrent.ForkJoinPool.managedBlock(java.base@17.0.6/ForkJoinPool.java:3434)
at java.util.concurrent.SynchronousQueue$TransferStack.transfer(java.base@17.0.6/SynchronousQueue.java:397)
at java.util.concurrent.SynchronousQueue.take(java.base@17.0.6/SynchronousQueue.java:886)
at java.util.concurrent.ThreadPoolExecutor.getTask(java.base@17.0.6/ThreadPoolExecutor.java:1062)
at java.util.concurrent.ThreadPoolExecutor.runWorker(java.base@17.0.6/ThreadPoolExecutor.java:1122)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(java.base@17.0.6/ThreadPoolExecutor.java:635)
at java.lang.Thread.run(java.base@17.0.6/Thread.java:833)
"Actor Thread 6" #48 daemon prio=5 os_prio=0 cpu=68.07ms elapsed=883.83s tid=0x00007f474952ec20 nid=0xfae3 waiting on condition [0x00007f46577fe000]
java.lang.Thread.State: WAITING (parking)
at jdk.internal.misc.Unsafe.park(java.base@17.0.6/Native Method)
- parking to wait for <0x000000060ffaef38> (a java.util.concurrent.SynchronousQueue$TransferStack)
at java.util.concurrent.locks.LockSupport.park(java.base@17.0.6/LockSupport.java:341)
at java.util.concurrent.SynchronousQueue$TransferStack$SNode.block(java.base@17.0.6/SynchronousQueue.java:288)
at java.util.concurrent.ForkJoinPool.unmanagedBlock(java.base@17.0.6/ForkJoinPool.java:3463)
at java.util.concurrent.ForkJoinPool.managedBlock(java.base@17.0.6/ForkJoinPool.java:3434)
at java.util.concurrent.SynchronousQueue$TransferStack.transfer(java.base@17.0.6/SynchronousQueue.java:397)
at java.util.concurrent.SynchronousQueue.take(java.base@17.0.6/SynchronousQueue.java:886)
at java.util.concurrent.ThreadPoolExecutor.getTask(java.base@17.0.6/ThreadPoolExecutor.java:1062)
at java.util.concurrent.ThreadPoolExecutor.runWorker(java.base@17.0.6/ThreadPoolExecutor.java:1122)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(java.base@17.0.6/ThreadPoolExecutor.java:635)
at java.lang.Thread.run(java.base@17.0.6/Thread.java:833)
"Actor Thread 7" #49 daemon prio=5 os_prio=0 cpu=0.55ms elapsed=883.83s tid=0x00007f474952fd60 nid=0xfae4 waiting on condition [0x00007f46576fe000]
java.lang.Thread.State: WAITING (parking)
at jdk.internal.misc.Unsafe.park(java.base@17.0.6/Native Method)
- parking to wait for <0x000000060ffaef38> (a java.util.concurrent.SynchronousQueue$TransferStack)
at java.util.concurrent.locks.LockSupport.park(java.base@17.0.6/LockSupport.java:341)
at java.util.concurrent.SynchronousQueue$TransferStack$SNode.block(java.base@17.0.6/SynchronousQueue.java:288)
at java.util.concurrent.ForkJoinPool.unmanagedBlock(java.base@17.0.6/ForkJoinPool.java:3463)
at java.util.concurrent.ForkJoinPool.managedBlock(java.base@17.0.6/ForkJoinPool.java:3434)
at java.util.concurrent.SynchronousQueue$TransferStack.transfer(java.base@17.0.6/SynchronousQueue.java:397)
at java.util.concurrent.SynchronousQueue.take(java.base@17.0.6/SynchronousQueue.java:886)
at java.util.concurrent.ThreadPoolExecutor.getTask(java.base@17.0.6/ThreadPoolExecutor.java:1062)
at java.util.concurrent.ThreadPoolExecutor.runWorker(java.base@17.0.6/ThreadPoolExecutor.java:1122)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(java.base@17.0.6/ThreadPoolExecutor.java:635)
at java.lang.Thread.run(java.base@17.0.6/Thread.java:833)
"Actor Thread 8" #50 daemon prio=5 os_prio=0 cpu=0.55ms elapsed=883.82s tid=0x00007f4749538a00 nid=0xfae5 waiting on condition [0x00007f46575fe000]
java.lang.Thread.State: WAITING (parking)
at jdk.internal.misc.Unsafe.park(java.base@17.0.6/Native Method)
- parking to wait for <0x000000060ffaef38> (a java.util.concurrent.SynchronousQueue$TransferStack)
at java.util.concurrent.locks.LockSupport.park(java.base@17.0.6/LockSupport.java:341)
at java.util.concurrent.SynchronousQueue$TransferStack$SNode.block(java.base@17.0.6/SynchronousQueue.java:288)
at java.util.concurrent.ForkJoinPool.unmanagedBlock(java.base@17.0.6/ForkJoinPool.java:3463)
at java.util.concurrent.ForkJoinPool.managedBlock(java.base@17.0.6/ForkJoinPool.java:3434)
at java.util.concurrent.SynchronousQueue$TransferStack.transfer(java.base@17.0.6/SynchronousQueue.java:397)
at java.util.concurrent.SynchronousQueue.take(java.base@17.0.6/SynchronousQueue.java:886)
at java.util.concurrent.ThreadPoolExecutor.getTask(java.base@17.0.6/ThreadPoolExecutor.java:1062)
at java.util.concurrent.ThreadPoolExecutor.runWorker(java.base@17.0.6/ThreadPoolExecutor.java:1122)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(java.base@17.0.6/ThreadPoolExecutor.java:635)
at java.lang.Thread.run(java.base@17.0.6/Thread.java:833)
"Actor Thread 9" #51 daemon prio=5 os_prio=0 cpu=0.29ms elapsed=883.82s tid=0x00007f47495397a0 nid=0xfae6 waiting on condition [0x00007f46574fe000]
java.lang.Thread.State: WAITING (parking)
at jdk.internal.misc.Unsafe.park(java.base@17.0.6/Native Method)
- parking to wait for <0x000000060ffaef38> (a java.util.concurrent.SynchronousQueue$TransferStack)
at java.util.concurrent.locks.LockSupport.park(java.base@17.0.6/LockSupport.java:341)
at java.util.concurrent.SynchronousQueue$TransferStack$SNode.block(java.base@17.0.6/SynchronousQueue.java:288)
at java.util.concurrent.ForkJoinPool.unmanagedBlock(java.base@17.0.6/ForkJoinPool.java:3463)
at java.util.concurrent.ForkJoinPool.managedBlock(java.base@17.0.6/ForkJoinPool.java:3434)
at java.util.concurrent.SynchronousQueue$TransferStack.transfer(java.base@17.0.6/SynchronousQueue.java:397)
at java.util.concurrent.SynchronousQueue.take(java.base@17.0.6/SynchronousQueue.java:886)
at java.util.concurrent.ThreadPoolExecutor.getTask(java.base@17.0.6/ThreadPoolExecutor.java:1062)
at java.util.concurrent.ThreadPoolExecutor.runWorker(java.base@17.0.6/ThreadPoolExecutor.java:1122)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(java.base@17.0.6/ThreadPoolExecutor.java:635)
at java.lang.Thread.run(java.base@17.0.6/Thread.java:833)
"Actor Thread 10" #52 daemon prio=5 os_prio=0 cpu=7.98ms elapsed=883.82s tid=0x00007f474953b760 nid=0xfae7 waiting on condition [0x00007f46573fe000]
java.lang.Thread.State: WAITING (parking)
at jdk.internal.misc.Unsafe.park(java.base@17.0.6/Native Method)
- parking to wait for <0x000000060ffaef38> (a java.util.concurrent.SynchronousQueue$TransferStack)
at java.util.concurrent.locks.LockSupport.park(java.base@17.0.6/LockSupport.java:341)
at java.util.concurrent.SynchronousQueue$TransferStack$SNode.block(java.base@17.0.6/SynchronousQueue.java:288)
at java.util.concurrent.ForkJoinPool.unmanagedBlock(java.base@17.0.6/ForkJoinPool.java:3463)
at java.util.concurrent.ForkJoinPool.managedBlock(java.base@17.0.6/ForkJoinPool.java:3434)
at java.util.concurrent.SynchronousQueue$TransferStack.transfer(java.base@17.0.6/SynchronousQueue.java:397)
at java.util.concurrent.SynchronousQueue.take(java.base@17.0.6/SynchronousQueue.java:886)
at java.util.concurrent.ThreadPoolExecutor.getTask(java.base@17.0.6/ThreadPoolExecutor.java:1062)
at java.util.concurrent.ThreadPoolExecutor.runWorker(java.base@17.0.6/ThreadPoolExecutor.java:1122)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(java.base@17.0.6/ThreadPoolExecutor.java:635)
at java.lang.Thread.run(java.base@17.0.6/Thread.java:833)
"Actor Thread 11" #53 daemon prio=5 os_prio=0 cpu=0.43ms elapsed=883.80s tid=0x00007f474953eea0 nid=0xfae9 waiting on condition [0x00007f46572fe000]
java.lang.Thread.State: WAITING (parking)
at jdk.internal.misc.Unsafe.park(java.base@17.0.6/Native Method)
- parking to wait for <0x000000060ffaef38> (a java.util.concurrent.SynchronousQueue$TransferStack)
at java.util.concurrent.locks.LockSupport.park(java.base@17.0.6/LockSupport.java:341)
at java.util.concurrent.SynchronousQueue$TransferStack$SNode.block(java.base@17.0.6/SynchronousQueue.java:288)
at java.util.concurrent.ForkJoinPool.unmanagedBlock(java.base@17.0.6/ForkJoinPool.java:3463)
at java.util.concurrent.ForkJoinPool.managedBlock(java.base@17.0.6/ForkJoinPool.java:3434)
at java.util.concurrent.SynchronousQueue$TransferStack.transfer(java.base@17.0.6/SynchronousQueue.java:397)
at java.util.concurrent.SynchronousQueue.take(java.base@17.0.6/SynchronousQueue.java:886)
at java.util.concurrent.ThreadPoolExecutor.getTask(java.base@17.0.6/ThreadPoolExecutor.java:1062)
at java.util.concurrent.ThreadPoolExecutor.runWorker(java.base@17.0.6/ThreadPoolExecutor.java:1122)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(java.base@17.0.6/ThreadPoolExecutor.java:635)
at java.lang.Thread.run(java.base@17.0.6/Thread.java:833)
"Actor Thread 12" #54 daemon prio=5 os_prio=0 cpu=49.12ms elapsed=883.80s tid=0x00007f4749540890 nid=0xfaea waiting on condition [0x00007f46571fe000]
java.lang.Thread.State: WAITING (parking)
at jdk.internal.misc.Unsafe.park(java.base@17.0.6/Native Method)
- parking to wait for <0x000000060ffaef38> (a java.util.concurrent.SynchronousQueue$TransferStack)
at java.util.concurrent.locks.LockSupport.park(java.base@17.0.6/LockSupport.java:341)
at java.util.concurrent.SynchronousQueue$TransferStack$SNode.block(java.base@17.0.6/SynchronousQueue.java:288)
at java.util.concurrent.ForkJoinPool.unmanagedBlock(java.base@17.0.6/ForkJoinPool.java:3463)
at java.util.concurrent.ForkJoinPool.managedBlock(java.base@17.0.6/ForkJoinPool.java:3434)
at java.util.concurrent.SynchronousQueue$TransferStack.transfer(java.base@17.0.6/SynchronousQueue.java:397)
at java.util.concurrent.SynchronousQueue.take(java.base@17.0.6/SynchronousQueue.java:886)
at java.util.concurrent.ThreadPoolExecutor.getTask(java.base@17.0.6/ThreadPoolExecutor.java:1062)
at java.util.concurrent.ThreadPoolExecutor.runWorker(java.base@17.0.6/ThreadPoolExecutor.java:1122)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(java.base@17.0.6/ThreadPoolExecutor.java:635)
at java.lang.Thread.run(java.base@17.0.6/Thread.java:833)
"Actor Thread 13" #56 daemon prio=5 os_prio=0 cpu=6.07ms elapsed=883.79s tid=0x00007f4749551050 nid=0xfaf0 waiting on condition [0x00007f46570fe000]
java.lang.Thread.State: WAITING (parking)
at jdk.internal.misc.Unsafe.park(java.base@17.0.6/Native Method)
- parking to wait for <0x000000060ffaef38> (a java.util.concurrent.SynchronousQueue$TransferStack)
at java.util.concurrent.locks.LockSupport.park(java.base@17.0.6/LockSupport.java:341)
at java.util.concurrent.SynchronousQueue$TransferStack$SNode.block(java.base@17.0.6/SynchronousQueue.java:288)
at java.util.concurrent.ForkJoinPool.unmanagedBlock(java.base@17.0.6/ForkJoinPool.java:3463)
at java.util.concurrent.ForkJoinPool.managedBlock(java.base@17.0.6/ForkJoinPool.java:3434)
at java.util.concurrent.SynchronousQueue$TransferStack.transfer(java.base@17.0.6/SynchronousQueue.java:397)
at java.util.concurrent.SynchronousQueue.take(java.base@17.0.6/SynchronousQueue.java:886)
at java.util.concurrent.ThreadPoolExecutor.getTask(java.base@17.0.6/ThreadPoolExecutor.java:1062)
at java.util.concurrent.ThreadPoolExecutor.runWorker(java.base@17.0.6/ThreadPoolExecutor.java:1122)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(java.base@17.0.6/ThreadPoolExecutor.java:635)
at java.lang.Thread.run(java.base@17.0.6/Thread.java:833)
"Actor Thread 14" #57 daemon prio=5 os_prio=0 cpu=5.80ms elapsed=883.77s tid=0x00007f474955fe70 nid=0xfaf5 waiting on condition [0x00007f4656ffe000]
java.lang.Thread.State: WAITING (parking)
at jdk.internal.misc.Unsafe.park(java.base@17.0.6/Native Method)
- parking to wait for <0x000000060ffaef38> (a java.util.concurrent.SynchronousQueue$TransferStack)
at java.util.concurrent.locks.LockSupport.park(java.base@17.0.6/LockSupport.java:341)
at java.util.concurrent.SynchronousQueue$TransferStack$SNode.block(java.base@17.0.6/SynchronousQueue.java:288)
at java.util.concurrent.ForkJoinPool.unmanagedBlock(java.base@17.0.6/ForkJoinPool.java:3463)
at java.util.concurrent.ForkJoinPool.managedBlock(java.base@17.0.6/ForkJoinPool.java:3434)
at java.util.concurrent.SynchronousQueue$TransferStack.transfer(java.base@17.0.6/SynchronousQueue.java:397)
at java.util.concurrent.SynchronousQueue.take(java.base@17.0.6/SynchronousQueue.java:886)
at java.util.concurrent.ThreadPoolExecutor.getTask(java.base@17.0.6/ThreadPoolExecutor.java:1062)
at java.util.concurrent.ThreadPoolExecutor.runWorker(java.base@17.0.6/ThreadPoolExecutor.java:1122)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(java.base@17.0.6/ThreadPoolExecutor.java:635)
at java.lang.Thread.run(java.base@17.0.6/Thread.java:833)
"Actor Thread 15" #58 daemon prio=5 os_prio=0 cpu=0.99ms elapsed=883.77s tid=0x00007f4749561ba0 nid=0xfaf6 waiting on condition [0x00007f4656efe000]
java.lang.Thread.State: WAITING (parking)
at jdk.internal.misc.Unsafe.park(java.base@17.0.6/Native Method)
- parking to wait for <0x000000060ffaef38> (a java.util.concurrent.SynchronousQueue$TransferStack)
at java.util.concurrent.locks.LockSupport.park(java.base@17.0.6/LockSupport.java:341)
at java.util.concurrent.SynchronousQueue$TransferStack$SNode.block(java.base@17.0.6/SynchronousQueue.java:288)
at java.util.concurrent.ForkJoinPool.unmanagedBlock(java.base@17.0.6/ForkJoinPool.java:3463)
at java.util.concurrent.ForkJoinPool.managedBlock(java.base@17.0.6/ForkJoinPool.java:3434)
at java.util.concurrent.SynchronousQueue$TransferStack.transfer(java.base@17.0.6/SynchronousQueue.java:397)
at java.util.concurrent.SynchronousQueue.take(java.base@17.0.6/SynchronousQueue.java:886)
at java.util.concurrent.ThreadPoolExecutor.getTask(java.base@17.0.6/ThreadPoolExecutor.java:1062)
at java.util.concurrent.ThreadPoolExecutor.runWorker(java.base@17.0.6/ThreadPoolExecutor.java:1122)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(java.base@17.0.6/ThreadPoolExecutor.java:635)
at java.lang.Thread.run(java.base@17.0.6/Thread.java:833)
"Actor Thread 16" #59 daemon prio=5 os_prio=0 cpu=1.42ms elapsed=883.77s tid=0x00007f4749560c20 nid=0xfaf7 waiting on condition [0x00007f4656dfe000]
java.lang.Thread.State: WAITING (parking)
at jdk.internal.misc.Unsafe.park(java.base@17.0.6/Native Method)
- parking to wait for <0x000000060ffaef38> (a java.util.concurrent.SynchronousQueue$TransferStack)
at java.util.concurrent.locks.LockSupport.park(java.base@17.0.6/LockSupport.java:341)
at java.util.concurrent.SynchronousQueue$TransferStack$SNode.block(java.base@17.0.6/SynchronousQueue.java:288)
at java.util.concurrent.ForkJoinPool.unmanagedBlock(java.base@17.0.6/ForkJoinPool.java:3463)
at java.util.concurrent.ForkJoinPool.managedBlock(java.base@17.0.6/ForkJoinPool.java:3434)
at java.util.concurrent.SynchronousQueue$TransferStack.transfer(java.base@17.0.6/SynchronousQueue.java:397)
at java.util.concurrent.SynchronousQueue.take(java.base@17.0.6/SynchronousQueue.java:886)
at java.util.concurrent.ThreadPoolExecutor.getTask(java.base@17.0.6/ThreadPoolExecutor.java:1062)
at java.util.concurrent.ThreadPoolExecutor.runWorker(java.base@17.0.6/ThreadPoolExecutor.java:1122)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(java.base@17.0.6/ThreadPoolExecutor.java:635)
at java.lang.Thread.run(java.base@17.0.6/Thread.java:833)
"Actor Thread 17" #60 daemon prio=5 os_prio=0 cpu=1.27ms elapsed=883.75s tid=0x00007f47495263d0 nid=0xfafd waiting on condition [0x00007f4656cfe000]
java.lang.Thread.State: WAITING (parking)
at jdk.internal.misc.Unsafe.park(java.base@17.0.6/Native Method)
- parking to wait for <0x000000060ffaef38> (a java.util.concurrent.SynchronousQueue$TransferStack)
at java.util.concurrent.locks.LockSupport.park(java.base@17.0.6/LockSupport.java:341)
at java.util.concurrent.SynchronousQueue$TransferStack$SNode.block(java.base@17.0.6/SynchronousQueue.java:288)
at java.util.concurrent.ForkJoinPool.unmanagedBlock(java.base@17.0.6/ForkJoinPool.java:3463)
at java.util.concurrent.ForkJoinPool.managedBlock(java.base@17.0.6/ForkJoinPool.java:3434)
at java.util.concurrent.SynchronousQueue$TransferStack.transfer(java.base@17.0.6/SynchronousQueue.java:397)
at java.util.concurrent.SynchronousQueue.take(java.base@17.0.6/SynchronousQueue.java:886)
at java.util.concurrent.ThreadPoolExecutor.getTask(java.base@17.0.6/ThreadPoolExecutor.java:1062)
at java.util.concurrent.ThreadPoolExecutor.runWorker(java.base@17.0.6/ThreadPoolExecutor.java:1122)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(java.base@17.0.6/ThreadPoolExecutor.java:635)
at java.lang.Thread.run(java.base@17.0.6/Thread.java:833)
"pool-4-thread-1" #62 prio=5 os_prio=0 cpu=0.44ms elapsed=883.61s tid=0x00007f46500179b0 nid=0xfb00 in Object.wait() [0x00007f46569fe000]
java.lang.Thread.State: WAITING (on object monitor)
at java.lang.Object.wait(java.base@17.0.6/Native Method)
- waiting on <0x0000000620667cc0> (a java.lang.ProcessImpl)
at java.lang.Object.wait(java.base@17.0.6/Object.java:338)
at java.lang.ProcessImpl.waitFor(java.base@17.0.6/ProcessImpl.java:434)
- locked <0x0000000620667cc0> (a java.lang.ProcessImpl)
at nextflow.executor.local.LocalTaskHandler$_submit_closure1.doCall(LocalTaskHandler.groovy:109)
at nextflow.executor.local.LocalTaskHandler$_submit_closure1.call(LocalTaskHandler.groovy)
at groovy.lang.Closure.run(Closure.java:498)
at java.util.concurrent.Executors$RunnableAdapter.call(java.base@17.0.6/Executors.java:539)
at java.util.concurrent.FutureTask.run(java.base@17.0.6/FutureTask.java:264)
at java.util.concurrent.ThreadPoolExecutor.runWorker(java.base@17.0.6/ThreadPoolExecutor.java:1136)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(java.base@17.0.6/ThreadPoolExecutor.java:635)
at java.lang.Thread.run(java.base@17.0.6/Thread.java:833)
"pool-4-thread-2" #63 prio=5 os_prio=0 cpu=0.54ms elapsed=883.60s tid=0x00007f46500110d0 nid=0xfb0a in Object.wait() [0x00007f46568fe000]
java.lang.Thread.State: WAITING (on object monitor)
at java.lang.Object.wait(java.base@17.0.6/Native Method)
- waiting on <0x0000000620000180> (a java.lang.ProcessImpl)
at java.lang.Object.wait(java.base@17.0.6/Object.java:338)
at java.lang.ProcessImpl.waitFor(java.base@17.0.6/ProcessImpl.java:434)
- locked <0x0000000620000180> (a java.lang.ProcessImpl)
at nextflow.executor.local.LocalTaskHandler$_submit_closure1.doCall(LocalTaskHandler.groovy:109)
at nextflow.executor.local.LocalTaskHandler$_submit_closure1.call(LocalTaskHandler.groovy)
at groovy.lang.Closure.run(Closure.java:498)
at java.util.concurrent.Executors$RunnableAdapter.call(java.base@17.0.6/Executors.java:539)
at java.util.concurrent.FutureTask.run(java.base@17.0.6/FutureTask.java:264)
at java.util.concurrent.ThreadPoolExecutor.runWorker(java.base@17.0.6/ThreadPoolExecutor.java:1136)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(java.base@17.0.6/ThreadPoolExecutor.java:635)
at java.lang.Thread.run(java.base@17.0.6/Thread.java:833)
"process reaper" #64 daemon prio=10 os_prio=0 cpu=0.10ms elapsed=883.60s tid=0x00007f46000020f0 nid=0xfb0e runnable [0x00007f474cc78000]
java.lang.Thread.State: RUNNABLE
at java.lang.ProcessHandleImpl.waitForProcessExit0(java.base@17.0.6/Native Method)
at java.lang.ProcessHandleImpl$1.run(java.base@17.0.6/ProcessHandleImpl.java:147)
at java.util.concurrent.ThreadPoolExecutor.runWorker(java.base@17.0.6/ThreadPoolExecutor.java:1136)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(java.base@17.0.6/ThreadPoolExecutor.java:635)
at java.lang.Thread.run(java.base@17.0.6/Thread.java:833)
"Attach Listener" #65 daemon prio=9 os_prio=0 cpu=0.26ms elapsed=0.10s tid=0x00007f46f0000eb0 nid=0x10056 waiting on condition [0x0000000000000000]
java.lang.Thread.State: RUNNABLE
"VM Thread" os_prio=0 cpu=51.47ms elapsed=916.97s tid=0x00007f4748163370 nid=0xfa0b runnable
"GC Thread#0" os_prio=0 cpu=114.34ms elapsed=916.97s tid=0x00007f4748057430 nid=0xfa06 runnable
"GC Thread#1" os_prio=0 cpu=45.11ms elapsed=916.74s tid=0x00007f4704006cd0 nid=0xfa1d runnable
"GC Thread#2" os_prio=0 cpu=71.54ms elapsed=916.74s tid=0x00007f4704007700 nid=0xfa1e runnable
"GC Thread#3" os_prio=0 cpu=95.83ms elapsed=916.74s tid=0x00007f4704008130 nid=0xfa1f runnable
"GC Thread#4" os_prio=0 cpu=67.81ms elapsed=916.74s tid=0x00007f4704008b60 nid=0xfa20 runnable
"GC Thread#5" os_prio=0 cpu=64.12ms elapsed=916.74s tid=0x00007f4704009590 nid=0xfa21 runnable
"GC Thread#6" os_prio=0 cpu=47.90ms elapsed=916.74s tid=0x00007f4704009fc0 nid=0xfa22 runnable
"GC Thread#7" os_prio=0 cpu=63.92ms elapsed=916.74s tid=0x00007f470400ade0 nid=0xfa23 runnable
"GC Thread#8" os_prio=0 cpu=65.70ms elapsed=916.74s tid=0x00007f470400bc00 nid=0xfa24 runnable
"GC Thread#9" os_prio=0 cpu=58.90ms elapsed=916.74s tid=0x00007f470400ca40 nid=0xfa25 runnable
"GC Thread#10" os_prio=0 cpu=78.01ms elapsed=916.74s tid=0x00007f470400d8a0 nid=0xfa26 runnable
"GC Thread#11" os_prio=0 cpu=71.09ms elapsed=916.74s tid=0x00007f470400e700 nid=0xfa27 runnable
"GC Thread#12" os_prio=0 cpu=87.73ms elapsed=915.55s tid=0x00007f4704014060 nid=0xfa36 runnable
"G1 Main Marker" os_prio=0 cpu=0.55ms elapsed=916.97s tid=0x00007f4748068310 nid=0xfa07 runnable
"G1 Conc#0" os_prio=0 cpu=24.77ms elapsed=916.97s tid=0x00007f4748069270 nid=0xfa08 runnable
"G1 Conc#1" os_prio=0 cpu=22.82ms elapsed=915.55s tid=0x00007f4710000eb0 nid=0xfa37 runnable
"G1 Conc#2" os_prio=0 cpu=25.77ms elapsed=915.55s tid=0x00007f4710001640 nid=0xfa38 runnable
"G1 Refine#0" os_prio=0 cpu=1.45ms elapsed=916.97s tid=0x00007f47481335d0 nid=0xfa09 runnable
"G1 Service" os_prio=0 cpu=195.37ms elapsed=916.97s tid=0x00007f47481344c0 nid=0xfa0a runnable
"VM Periodic Task Thread" os_prio=0 cpu=697.30ms elapsed=916.95s tid=0x00007f47481b6990 nid=0xfa17 waiting on condition
JNI global refs: 26, weak refs: 0
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