Trying to fix basic functionality again.
This commit is contained in:
511
.nextflow.log.1
Normal file
511
.nextflow.log.1
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@@ -0,0 +1,511 @@
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Mar-23 11:44:25.724 [main] DEBUG nextflow.cli.Launcher - $> nextflow run main.nf --disease_name 'Multiple Sclerosis' --population 10
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Mar-23 11:44:26.022 [main] DEBUG nextflow.cli.CmdRun - N E X T F L O W ~ version 24.10.5
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Mar-23 11:44:26.079 [main] DEBUG nextflow.plugin.PluginsFacade - Setting up plugin manager > mode=prod; embedded=false; plugins-dir=/Users/richman/.nextflow/plugins; core-plugins: nf-amazon@2.9.2,nf-azure@1.10.2,nf-cloudcache@0.4.2,nf-codecommit@0.2.2,nf-console@1.1.4,nf-google@1.15.4,nf-tower@1.9.3,nf-wave@1.7.4
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Mar-23 11:44:26.129 [main] INFO o.pf4j.DefaultPluginStatusProvider - Enabled plugins: []
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Mar-23 11:44:26.130 [main] INFO o.pf4j.DefaultPluginStatusProvider - Disabled plugins: []
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Mar-23 11:44:26.138 [main] INFO org.pf4j.DefaultPluginManager - PF4J version 3.12.0 in 'deployment' mode
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Mar-23 11:44:26.192 [main] INFO org.pf4j.AbstractPluginManager - No plugins
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Mar-23 11:44:26.303 [main] DEBUG nextflow.config.ConfigBuilder - Found config local: /Users/richman/workspace/synthea-alldiseases/nextflow.config
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Mar-23 11:44:26.317 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /Users/richman/workspace/synthea-alldiseases/nextflow.config
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Mar-23 11:44:26.466 [main] DEBUG n.secret.LocalSecretsProvider - Secrets store: /Users/richman/.nextflow/secrets/store.json
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Mar-23 11:44:26.474 [main] DEBUG nextflow.secret.SecretsLoader - Discovered secrets providers: [nextflow.secret.LocalSecretsProvider@c827db] - activable => nextflow.secret.LocalSecretsProvider@c827db
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Mar-23 11:44:26.570 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `standard`
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Mar-23 11:44:28.572 [main] DEBUG nextflow.cli.CmdRun - Applied DSL=2 from script declaration
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Mar-23 11:44:28.598 [main] DEBUG nextflow.cli.CmdRun - Launching `main.nf` [distracted_curran] DSL2 - revision: ab2562e4a1
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Mar-23 11:44:28.602 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins default=[]
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Mar-23 11:44:28.603 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins resolved requirement=[]
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Mar-23 11:44:28.705 [main] DEBUG nextflow.Session - Session UUID: ae62d0f9-dec1-462d-a18a-b4b9ebf0f702
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Mar-23 11:44:28.706 [main] DEBUG nextflow.Session - Run name: distracted_curran
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Mar-23 11:44:28.708 [main] DEBUG nextflow.Session - Executor pool size: 10
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Mar-23 11:44:28.723 [main] DEBUG nextflow.file.FilePorter - File porter settings maxRetries=3; maxTransfers=50; pollTimeout=null
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Mar-23 11:44:28.742 [main] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'FileTransfer' minSize=10; maxSize=30; workQueue=LinkedBlockingQueue[-1]; allowCoreThreadTimeout=false
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Mar-23 11:44:28.958 [main] DEBUG nextflow.cli.CmdRun -
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Version: 24.10.5 build 5935
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Created: 04-03-2025 17:55 UTC (09:55 PDT)
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System: Mac OS X 10.16
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Runtime: Groovy 4.0.23 on OpenJDK 64-Bit Server VM 15.0.2+7-27
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Encoding: UTF-8 (UTF-8)
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Process: 73685@MacBookPro.localdomain [192.168.1.157]
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CPUs: 10 - Mem: 32 GB (18.5 MB) - Swap: 6 GB (1.6 GB)
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Mar-23 11:44:29.023 [main] DEBUG nextflow.Session - Work-dir: /Users/richman/workspace/synthea-alldiseases/work [Mac OS X]
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Mar-23 11:44:29.024 [main] DEBUG nextflow.Session - Script base path does not exist or is not a directory: /Users/richman/workspace/synthea-alldiseases/bin
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Mar-23 11:44:29.044 [main] DEBUG nextflow.executor.ExecutorFactory - Extension executors providers=[]
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Mar-23 11:44:29.060 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory
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Mar-23 11:44:29.129 [main] DEBUG nextflow.cache.CacheFactory - Using Nextflow cache factory: nextflow.cache.DefaultCacheFactory
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Mar-23 11:44:29.162 [main] DEBUG nextflow.util.CustomThreadPool - Creating default thread pool > poolSize: 11; maxThreads: 1000
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Mar-23 11:44:29.230 [main] DEBUG nextflow.Session - Session start
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Mar-23 11:44:29.237 [main] DEBUG nextflow.trace.TraceFileObserver - Workflow started -- trace file: /Users/richman/workspace/synthea-alldiseases/trace.txt
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Mar-23 11:44:30.406 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution
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Mar-23 11:44:30.757 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: local
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Mar-23 11:44:30.758 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
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Mar-23 11:44:30.786 [main] DEBUG nextflow.executor.Executor - [warm up] executor > local
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Mar-23 11:44:30.795 [main] DEBUG n.processor.LocalPollingMonitor - Creating local task monitor for executor 'local' > cpus=10; memory=32 GB; capacity=10; pollInterval=100ms; dumpInterval=5m
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Mar-23 11:44:30.801 [main] DEBUG n.processor.TaskPollingMonitor - >>> barrier register (monitor: local)
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Mar-23 11:44:30.992 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: local
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Mar-23 11:44:30.993 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
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Mar-23 11:44:31.002 [main] DEBUG nextflow.Session - Workflow process names [dsl2]: checkAndGetModule, generatePatients
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Mar-23 11:44:31.004 [main] DEBUG nextflow.Session - Igniting dataflow network (2)
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Mar-23 11:44:31.005 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > checkAndGetModule
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Mar-23 11:44:31.005 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > generatePatients
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Mar-23 11:44:31.007 [main] DEBUG nextflow.script.ScriptRunner - Parsed script files:
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Script_b4244dfae6385692: /Users/richman/workspace/synthea-alldiseases/main.nf
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Mar-23 11:44:31.008 [main] DEBUG nextflow.script.ScriptRunner - > Awaiting termination
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Mar-23 11:44:31.010 [main] DEBUG nextflow.Session - Session await
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Mar-23 11:44:31.414 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
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Mar-23 11:44:31.419 [Task submitter] INFO nextflow.Session - [5f/61e0a1] Submitted process > checkAndGetModule
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Mar-23 11:44:32.587 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 1; name: checkAndGetModule; status: COMPLETED; exit: 1; error: -; workDir: /Users/richman/workspace/synthea-alldiseases/work/5f/61e0a106b3bf7b6d8599a7220c029c]
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Mar-23 11:44:32.591 [Task monitor] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'TaskFinalizer' minSize=10; maxSize=30; workQueue=LinkedBlockingQueue[-1]; allowCoreThreadTimeout=false
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Mar-23 11:44:32.609 [SIGINT handler] DEBUG nextflow.Session - Session aborted -- Cause: SIGINT
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Mar-23 11:44:32.610 [TaskFinalizer-1] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
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task: name=checkAndGetModule; work-dir=/Users/richman/workspace/synthea-alldiseases/work/5f/61e0a106b3bf7b6d8599a7220c029c
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error [nextflow.exception.ProcessFailedException]: Process `checkAndGetModule` terminated with an error exit status (1)
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Mar-23 11:44:32.634 [main] DEBUG nextflow.Session - Session await > all processes finished
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Mar-23 11:44:32.696 [SIGINT handler] DEBUG nextflow.Session -
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Thread[process reaper,10,system]
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java.base@15.0.2/jdk.internal.misc.Unsafe.park(Native Method)
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java.base@15.0.2/java.util.concurrent.locks.LockSupport.parkNanos(LockSupport.java:252)
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java.base@15.0.2/java.util.concurrent.SynchronousQueue$TransferStack.awaitFulfill(SynchronousQueue.java:462)
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java.base@15.0.2/java.util.concurrent.SynchronousQueue$TransferStack.transfer(SynchronousQueue.java:361)
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java.base@15.0.2/java.util.concurrent.SynchronousQueue.poll(SynchronousQueue.java:937)
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java.base@15.0.2/java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1055)
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java.base@15.0.2/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1116)
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java.base@15.0.2/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:630)
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java.base@15.0.2/java.lang.Thread.run(Thread.java:832)
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Thread[pool-2-thread-1,5,main]
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java.base@15.0.2/jdk.internal.misc.Unsafe.park(Native Method)
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java.base@15.0.2/java.util.concurrent.locks.LockSupport.park(LockSupport.java:341)
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java.base@15.0.2/java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionNode.block(AbstractQueuedSynchronizer.java:505)
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java.base@15.0.2/java.util.concurrent.ForkJoinPool.managedBlock(ForkJoinPool.java:3137)
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java.base@15.0.2/java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:1614)
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java.base@15.0.2/java.util.concurrent.LinkedBlockingQueue.take(LinkedBlockingQueue.java:435)
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java.base@15.0.2/java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1056)
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java.base@15.0.2/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1116)
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java.base@15.0.2/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:630)
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java.base@15.0.2/java.lang.Thread.run(Thread.java:832)
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Thread[Task submitter,5,main]
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java.base@15.0.2/jdk.internal.misc.Unsafe.park(Native Method)
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java.base@15.0.2/java.util.concurrent.locks.LockSupport.park(LockSupport.java:341)
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java.base@15.0.2/java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionNode.block(AbstractQueuedSynchronizer.java:505)
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java.base@15.0.2/java.util.concurrent.ForkJoinPool.managedBlock(ForkJoinPool.java:3137)
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java.base@15.0.2/java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:1614)
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app//nextflow.processor.TaskPollingMonitor.awaitTasks(TaskPollingMonitor.groovy:388)
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app//nextflow.processor.TaskPollingMonitor.submitLoop(TaskPollingMonitor.groovy:412)
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java.base@15.0.2/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
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java.base@15.0.2/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:64)
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java.base@15.0.2/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
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java.base@15.0.2/java.lang.reflect.Method.invoke(Method.java:564)
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app//org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:343)
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app//groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:328)
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app//groovy.lang.MetaClassImpl.doInvokeMethod(MetaClassImpl.java:1333)
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app//groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1088)
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app//groovy.lang.MetaClassImpl.invokeMethodClosure(MetaClassImpl.java:1017)
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app//groovy.lang.MetaClassImpl.doInvokeMethod(MetaClassImpl.java:1207)
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app//groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1088)
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app//groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1007)
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app//groovy.lang.Closure.call(Closure.java:433)
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app//groovy.lang.Closure.call(Closure.java:412)
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app//groovy.lang.Closure.run(Closure.java:505)
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java.base@15.0.2/java.lang.Thread.run(Thread.java:832)
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Thread[Actor Thread 5,5,main]
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java.base@15.0.2/jdk.internal.misc.Unsafe.park(Native Method)
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java.base@15.0.2/java.util.concurrent.locks.LockSupport.park(LockSupport.java:211)
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java.base@15.0.2/java.util.concurrent.SynchronousQueue$TransferStack.awaitFulfill(SynchronousQueue.java:460)
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java.base@15.0.2/java.util.concurrent.SynchronousQueue$TransferStack.transfer(SynchronousQueue.java:361)
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java.base@15.0.2/java.util.concurrent.SynchronousQueue.take(SynchronousQueue.java:920)
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java.base@15.0.2/java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1056)
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java.base@15.0.2/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1116)
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java.base@15.0.2/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:630)
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java.base@15.0.2/java.lang.Thread.run(Thread.java:832)
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Thread[Actor Thread 2,5,main]
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||||
java.base@15.0.2/jdk.internal.misc.Unsafe.park(Native Method)
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java.base@15.0.2/java.util.concurrent.locks.LockSupport.park(LockSupport.java:211)
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java.base@15.0.2/java.util.concurrent.SynchronousQueue$TransferStack.awaitFulfill(SynchronousQueue.java:460)
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java.base@15.0.2/java.util.concurrent.SynchronousQueue$TransferStack.transfer(SynchronousQueue.java:361)
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java.base@15.0.2/java.util.concurrent.SynchronousQueue.take(SynchronousQueue.java:920)
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java.base@15.0.2/java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1056)
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java.base@15.0.2/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1116)
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java.base@15.0.2/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:630)
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java.base@15.0.2/java.lang.Thread.run(Thread.java:832)
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|
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Thread[Thread-1,5,main]
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java.base@15.0.2/jdk.internal.misc.Unsafe.park(Native Method)
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java.base@15.0.2/java.util.concurrent.locks.LockSupport.parkNanos(LockSupport.java:252)
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java.base@15.0.2/java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.awaitNanos(AbstractQueuedSynchronizer.java:1661)
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java.base@15.0.2/java.util.concurrent.LinkedBlockingDeque.pollFirst(LinkedBlockingDeque.java:515)
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java.base@15.0.2/java.util.concurrent.LinkedBlockingDeque.poll(LinkedBlockingDeque.java:677)
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app//nextflow.util.SimpleAgent.run(SimpleAgent.groovy:89)
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java.base@15.0.2/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
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java.base@15.0.2/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:64)
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||||
java.base@15.0.2/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
|
||||
java.base@15.0.2/java.lang.reflect.Method.invoke(Method.java:564)
|
||||
app//org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:343)
|
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app//groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:328)
|
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app//groovy.lang.MetaClassImpl.doInvokeMethod(MetaClassImpl.java:1333)
|
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app//groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1088)
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||||
app//groovy.lang.MetaClassImpl.invokeMethodClosure(MetaClassImpl.java:1017)
|
||||
app//groovy.lang.MetaClassImpl.doInvokeMethod(MetaClassImpl.java:1207)
|
||||
app//groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1088)
|
||||
app//groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1007)
|
||||
app//groovy.lang.Closure.call(Closure.java:433)
|
||||
app//groovy.lang.Closure.call(Closure.java:412)
|
||||
app//groovy.lang.Closure.run(Closure.java:505)
|
||||
java.base@15.0.2/java.lang.Thread.run(Thread.java:832)
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||||
|
||||
Thread[main,5,main]
|
||||
java.base@15.0.2/jdk.internal.misc.Unsafe.park(Native Method)
|
||||
java.base@15.0.2/java.util.concurrent.locks.LockSupport.park(LockSupport.java:341)
|
||||
java.base@15.0.2/java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionNode.block(AbstractQueuedSynchronizer.java:505)
|
||||
java.base@15.0.2/java.util.concurrent.ForkJoinPool.managedBlock(ForkJoinPool.java:3137)
|
||||
java.base@15.0.2/java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:1614)
|
||||
app//nextflow.util.Barrier$_awaitCompletion_closure3.doCall(Barrier.groovy:92)
|
||||
app//nextflow.util.Barrier$_awaitCompletion_closure3.call(Barrier.groovy)
|
||||
app//nextflow.extension.Bolts.withLock(Bolts.groovy:337)
|
||||
app//nextflow.extension.Bolts.withLock(Bolts.groovy)
|
||||
app//nextflow.util.Barrier.awaitCompletion(Barrier.groovy:89)
|
||||
app//nextflow.Session.await(Session.groovy:679)
|
||||
app//nextflow.script.ScriptRunner.await(ScriptRunner.groovy:256)
|
||||
app//nextflow.script.ScriptRunner.execute(ScriptRunner.groovy:144)
|
||||
app//nextflow.cli.CmdRun.run(CmdRun.groovy:376)
|
||||
app//nextflow.cli.Launcher.run(Launcher.groovy:503)
|
||||
app//nextflow.cli.Launcher.main(Launcher.groovy:658)
|
||||
|
||||
Thread[Notification Thread,9,system]
|
||||
|
||||
Thread[Reference Handler,10,system]
|
||||
java.base@15.0.2/java.lang.ref.Reference.waitForReferencePendingList(Native Method)
|
||||
java.base@15.0.2/java.lang.ref.Reference.processPendingReferences(Reference.java:241)
|
||||
java.base@15.0.2/java.lang.ref.Reference$ReferenceHandler.run(Reference.java:213)
|
||||
|
||||
Thread[Actor Thread 10,5,main]
|
||||
java.base@15.0.2/jdk.internal.misc.Unsafe.park(Native Method)
|
||||
java.base@15.0.2/java.util.concurrent.locks.LockSupport.park(LockSupport.java:211)
|
||||
java.base@15.0.2/java.util.concurrent.SynchronousQueue$TransferStack.awaitFulfill(SynchronousQueue.java:460)
|
||||
java.base@15.0.2/java.util.concurrent.SynchronousQueue$TransferStack.transfer(SynchronousQueue.java:361)
|
||||
java.base@15.0.2/java.util.concurrent.SynchronousQueue.take(SynchronousQueue.java:920)
|
||||
java.base@15.0.2/java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1056)
|
||||
java.base@15.0.2/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1116)
|
||||
java.base@15.0.2/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:630)
|
||||
java.base@15.0.2/java.lang.Thread.run(Thread.java:832)
|
||||
|
||||
Thread[Actor Thread 8,5,main]
|
||||
java.base@15.0.2/jdk.internal.misc.Unsafe.park(Native Method)
|
||||
java.base@15.0.2/java.util.concurrent.locks.LockSupport.park(LockSupport.java:211)
|
||||
java.base@15.0.2/java.util.concurrent.SynchronousQueue$TransferStack.awaitFulfill(SynchronousQueue.java:460)
|
||||
java.base@15.0.2/java.util.concurrent.SynchronousQueue$TransferStack.transfer(SynchronousQueue.java:361)
|
||||
java.base@15.0.2/java.util.concurrent.SynchronousQueue.take(SynchronousQueue.java:920)
|
||||
java.base@15.0.2/java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1056)
|
||||
java.base@15.0.2/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1116)
|
||||
java.base@15.0.2/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:630)
|
||||
java.base@15.0.2/java.lang.Thread.run(Thread.java:832)
|
||||
|
||||
Thread[Actor Thread 1,5,main]
|
||||
java.base@15.0.2/jdk.internal.misc.Unsafe.park(Native Method)
|
||||
java.base@15.0.2/java.util.concurrent.locks.LockSupport.park(LockSupport.java:211)
|
||||
java.base@15.0.2/java.util.concurrent.SynchronousQueue$TransferStack.awaitFulfill(SynchronousQueue.java:460)
|
||||
java.base@15.0.2/java.util.concurrent.SynchronousQueue$TransferStack.transfer(SynchronousQueue.java:361)
|
||||
java.base@15.0.2/java.util.concurrent.SynchronousQueue.take(SynchronousQueue.java:920)
|
||||
java.base@15.0.2/java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1056)
|
||||
java.base@15.0.2/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1116)
|
||||
java.base@15.0.2/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:630)
|
||||
java.base@15.0.2/java.lang.Thread.run(Thread.java:832)
|
||||
|
||||
Thread[Actor Thread 6,5,main]
|
||||
java.base@15.0.2/jdk.internal.misc.Unsafe.park(Native Method)
|
||||
java.base@15.0.2/java.util.concurrent.locks.LockSupport.park(LockSupport.java:211)
|
||||
java.base@15.0.2/java.util.concurrent.SynchronousQueue$TransferStack.awaitFulfill(SynchronousQueue.java:460)
|
||||
java.base@15.0.2/java.util.concurrent.SynchronousQueue$TransferStack.transfer(SynchronousQueue.java:361)
|
||||
java.base@15.0.2/java.util.concurrent.SynchronousQueue.take(SynchronousQueue.java:920)
|
||||
java.base@15.0.2/java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1056)
|
||||
java.base@15.0.2/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1116)
|
||||
java.base@15.0.2/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:630)
|
||||
java.base@15.0.2/java.lang.Thread.run(Thread.java:832)
|
||||
|
||||
Thread[SIGINT handler,9,system]
|
||||
java.base@15.0.2/java.lang.Thread.dumpThreads(Native Method)
|
||||
java.base@15.0.2/java.lang.Thread.getAllStackTraces(Thread.java:1649)
|
||||
app//nextflow.util.SysHelper.dumpThreads(SysHelper.groovy:188)
|
||||
app//nextflow.Session.abort(Session.groovy:800)
|
||||
app//nextflow.Session$_registerSignalHandlers_closure17.doCall(Session.groovy:489)
|
||||
java.base@15.0.2/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
|
||||
java.base@15.0.2/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:64)
|
||||
java.base@15.0.2/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
|
||||
java.base@15.0.2/java.lang.reflect.Method.invoke(Method.java:564)
|
||||
app//org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:343)
|
||||
app//groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:328)
|
||||
app//org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:279)
|
||||
app//groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1007)
|
||||
app//groovy.lang.Closure.call(Closure.java:433)
|
||||
app//org.codehaus.groovy.runtime.ConvertedClosure.invokeCustom(ConvertedClosure.java:52)
|
||||
app//org.codehaus.groovy.runtime.ConversionHandler.invoke(ConversionHandler.java:113)
|
||||
com.sun.proxy.$Proxy26.handle(Unknown Source)
|
||||
jdk.unsupported@15.0.2/sun.misc.Signal$InternalMiscHandler.handle(Signal.java:198)
|
||||
java.base@15.0.2/jdk.internal.misc.Signal$1.run(Signal.java:220)
|
||||
java.base@15.0.2/java.lang.Thread.run(Thread.java:832)
|
||||
|
||||
Thread[Actor Thread 9,5,main]
|
||||
java.base@15.0.2/java.lang.ClassLoader.defineClass1(Native Method)
|
||||
java.base@15.0.2/java.lang.ClassLoader.defineClass(ClassLoader.java:1016)
|
||||
java.base@15.0.2/java.security.SecureClassLoader.defineClass(SecureClassLoader.java:151)
|
||||
java.base@15.0.2/jdk.internal.loader.BuiltinClassLoader.defineClass(BuiltinClassLoader.java:825)
|
||||
java.base@15.0.2/jdk.internal.loader.BuiltinClassLoader.findClassOnClassPathOrNull(BuiltinClassLoader.java:723)
|
||||
java.base@15.0.2/jdk.internal.loader.BuiltinClassLoader.loadClassOrNull(BuiltinClassLoader.java:646)
|
||||
java.base@15.0.2/jdk.internal.loader.BuiltinClassLoader.loadClass(BuiltinClassLoader.java:604)
|
||||
java.base@15.0.2/jdk.internal.loader.ClassLoaders$AppClassLoader.loadClass(ClassLoaders.java:168)
|
||||
java.base@15.0.2/java.lang.ClassLoader.loadClass(ClassLoader.java:522)
|
||||
app//com.esotericsoftware.kryo.Kryo.<init>(Kryo.java:188)
|
||||
app//com.esotericsoftware.kryo.Kryo.<init>(Kryo.java:132)
|
||||
java.base@15.0.2/java.lang.invoke.DirectMethodHandle$Holder.newInvokeSpecial(DirectMethodHandle$Holder)
|
||||
java.base@15.0.2/java.lang.invoke.LambdaForm$MH/0x0000000800c2b440.invoke(LambdaForm$MH)
|
||||
java.base@15.0.2/java.lang.invoke.LambdaForm$MH/0x0000000800c2ac40.guardWithCatch(LambdaForm$MH)
|
||||
java.base@15.0.2/java.lang.invoke.LambdaForm$MH/0x0000000800bfbc40.reinvoke(LambdaForm$MH)
|
||||
java.base@15.0.2/java.lang.invoke.LambdaForm$MH/0x0000000800bfc040.guard(LambdaForm$MH)
|
||||
java.base@15.0.2/java.lang.invoke.LambdaForm$MH/0x0000000800bfbc40.reinvoke(LambdaForm$MH)
|
||||
java.base@15.0.2/java.lang.invoke.LambdaForm$MH/0x0000000800c2dc40.invoke(LambdaForm$MH)
|
||||
java.base@15.0.2/java.lang.invoke.LambdaForm$MH/0x0000000800c0a440.invokeExact_MT(LambdaForm$MH)
|
||||
app//org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321)
|
||||
java.base@15.0.2/java.lang.invoke.LambdaForm$DMH/0x0000000800bdd440.invokeStatic(LambdaForm$DMH)
|
||||
java.base@15.0.2/java.lang.invoke.LambdaForm$MH/0x0000000800bfa440.invoke(LambdaForm$MH)
|
||||
java.base@15.0.2/java.lang.invoke.Invokers$Holder.linkToCallSite(Invokers$Holder)
|
||||
app//nextflow.util.KryoHelper.newInstance(SerializationHelper.groovy:87)
|
||||
java.base@15.0.2/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
|
||||
java.base@15.0.2/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:64)
|
||||
java.base@15.0.2/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
|
||||
java.base@15.0.2/java.lang.reflect.Method.invoke(Method.java:564)
|
||||
app//org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:343)
|
||||
app//groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:328)
|
||||
app//groovy.lang.MetaClassImpl.invokeStaticMethod(MetaClassImpl.java:1586)
|
||||
app//org.codehaus.groovy.runtime.InvokerHelper.invokeMethod(InvokerHelper.java:611)
|
||||
app//org.codehaus.groovy.runtime.ScriptBytecodeAdapter.invokeMethodN(ScriptBytecodeAdapter.java:182)
|
||||
app//nextflow.util.KryoHelper$1.methodMissing(SerializationHelper.groovy)
|
||||
java.base@15.0.2/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
|
||||
java.base@15.0.2/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:64)
|
||||
java.base@15.0.2/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
|
||||
java.base@15.0.2/java.lang.reflect.Method.invoke(Method.java:564)
|
||||
app//org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:343)
|
||||
app//groovy.lang.MetaClassImpl.invokeMissingMethod(MetaClassImpl.java:924)
|
||||
app//groovy.lang.MetaClassImpl.invokePropertyOrMissing(MetaClassImpl.java:1413)
|
||||
app//groovy.lang.MetaClassImpl.doInvokeMethod(MetaClassImpl.java:1335)
|
||||
app//groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1088)
|
||||
app//groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1007)
|
||||
java.base@15.0.2/java.lang.invoke.LambdaForm$DMH/0x0000000800bff440.invokeInterface(LambdaForm$DMH)
|
||||
java.base@15.0.2/java.lang.invoke.LambdaForm$MH/0x0000000800c9f840.invoke(LambdaForm$MH)
|
||||
java.base@15.0.2/java.lang.invoke.LambdaForm$MH/0x0000000800cac040.invoke(LambdaForm$MH)
|
||||
java.base@15.0.2/java.lang.invoke.LambdaForm$MH/0x0000000800c2ac40.guardWithCatch(LambdaForm$MH)
|
||||
java.base@15.0.2/java.lang.invoke.LambdaForm$MH/0x0000000800bfbc40.reinvoke(LambdaForm$MH)
|
||||
java.base@15.0.2/java.lang.invoke.LambdaForm$MH/0x0000000800bfc040.guard(LambdaForm$MH)
|
||||
java.base@15.0.2/java.lang.invoke.LambdaForm$MH/0x0000000800bfbc40.reinvoke(LambdaForm$MH)
|
||||
java.base@15.0.2/java.lang.invoke.LambdaForm$MH/0x0000000800bfc040.guard(LambdaForm$MH)
|
||||
java.base@15.0.2/java.lang.invoke.LambdaForm$MH/0x0000000800bfbc40.reinvoke(LambdaForm$MH)
|
||||
java.base@15.0.2/java.lang.invoke.LambdaForm$MH/0x0000000800c2dc40.invoke(LambdaForm$MH)
|
||||
java.base@15.0.2/java.lang.invoke.LambdaForm$MH/0x0000000800c0a440.invokeExact_MT(LambdaForm$MH)
|
||||
app//org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321)
|
||||
java.base@15.0.2/java.lang.invoke.LambdaForm$DMH/0x0000000800bdd440.invokeStatic(LambdaForm$DMH)
|
||||
java.base@15.0.2/java.lang.invoke.LambdaForm$MH/0x0000000800bfa440.invoke(LambdaForm$MH)
|
||||
java.base@15.0.2/java.lang.invoke.Invokers$Holder.linkToCallSite(Invokers$Holder)
|
||||
app//nextflow.util.KryoHelper$1.initialValue(SerializationHelper.groovy:60)
|
||||
app//nextflow.util.KryoHelper$1.initialValue(SerializationHelper.groovy)
|
||||
java.base@15.0.2/java.lang.ThreadLocal.setInitialValue(ThreadLocal.java:195)
|
||||
java.base@15.0.2/java.lang.ThreadLocal.get(ThreadLocal.java:172)
|
||||
java.base@15.0.2/java.lang.invoke.DirectMethodHandle$Holder.invokeVirtual(DirectMethodHandle$Holder)
|
||||
java.base@15.0.2/java.lang.invoke.LambdaForm$MH/0x0000000800c2ac40.guardWithCatch(LambdaForm$MH)
|
||||
java.base@15.0.2/java.lang.invoke.LambdaForm$MH/0x0000000800bfbc40.reinvoke(LambdaForm$MH)
|
||||
java.base@15.0.2/java.lang.invoke.LambdaForm$MH/0x0000000800bfc040.guard(LambdaForm$MH)
|
||||
java.base@15.0.2/java.lang.invoke.LambdaForm$MH/0x0000000800bfbc40.reinvoke(LambdaForm$MH)
|
||||
java.base@15.0.2/java.lang.invoke.LambdaForm$MH/0x0000000800bfc040.guard(LambdaForm$MH)
|
||||
java.base@15.0.2/java.lang.invoke.LambdaForm$MH/0x0000000800bfbc40.reinvoke(LambdaForm$MH)
|
||||
java.base@15.0.2/java.lang.invoke.LambdaForm$MH/0x0000000800c2dc40.invoke(LambdaForm$MH)
|
||||
java.base@15.0.2/java.lang.invoke.LambdaForm$MH/0x0000000800c0a440.invokeExact_MT(LambdaForm$MH)
|
||||
app//org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321)
|
||||
java.base@15.0.2/java.lang.invoke.LambdaForm$DMH/0x0000000800bdd440.invokeStatic(LambdaForm$DMH)
|
||||
java.base@15.0.2/java.lang.invoke.LambdaForm$MH/0x0000000800bfa440.invoke(LambdaForm$MH)
|
||||
java.base@15.0.2/java.lang.invoke.Invokers$Holder.linkToCallSite(Invokers$Holder)
|
||||
app//nextflow.util.KryoHelper.kryo(SerializationHelper.groovy:79)
|
||||
java.base@15.0.2/java.lang.invoke.LambdaForm$DMH/0x0000000800b8fc40.invokeStatic(LambdaForm$DMH)
|
||||
java.base@15.0.2/java.lang.invoke.LambdaForm$MH/0x0000000800c2b440.invoke(LambdaForm$MH)
|
||||
java.base@15.0.2/java.lang.invoke.LambdaForm$MH/0x0000000800c2ac40.guardWithCatch(LambdaForm$MH)
|
||||
java.base@15.0.2/java.lang.invoke.LambdaForm$MH/0x0000000800bfbc40.reinvoke(LambdaForm$MH)
|
||||
java.base@15.0.2/java.lang.invoke.LambdaForm$MH/0x0000000800bfc040.guard(LambdaForm$MH)
|
||||
java.base@15.0.2/java.lang.invoke.LambdaForm$MH/0x0000000800bfbc40.reinvoke(LambdaForm$MH)
|
||||
java.base@15.0.2/java.lang.invoke.LambdaForm$MH/0x0000000800c2dc40.invoke(LambdaForm$MH)
|
||||
java.base@15.0.2/java.lang.invoke.LambdaForm$MH/0x0000000800c0a440.invokeExact_MT(LambdaForm$MH)
|
||||
app//org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321)
|
||||
java.base@15.0.2/java.lang.invoke.LambdaForm$DMH/0x0000000800bdd440.invokeStatic(LambdaForm$DMH)
|
||||
java.base@15.0.2/java.lang.invoke.LambdaForm$MH/0x0000000800bfa440.invoke(LambdaForm$MH)
|
||||
java.base@15.0.2/java.lang.invoke.Invokers$Holder.linkToCallSite(Invokers$Holder)
|
||||
app//nextflow.util.KryoHelper.serialize(SerializationHelper.groovy:166)
|
||||
app//nextflow.trace.TraceRecord.serialize(TraceRecord.groovy:573)
|
||||
app//nextflow.cache.CacheDB.writeTaskEntry0(CacheDB.groovy:147)
|
||||
java.base@15.0.2/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
|
||||
java.base@15.0.2/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:64)
|
||||
java.base@15.0.2/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
|
||||
java.base@15.0.2/java.lang.reflect.Method.invoke(Method.java:564)
|
||||
app//org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:343)
|
||||
app//groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:328)
|
||||
app//groovy.lang.MetaClassImpl.doInvokeMethod(MetaClassImpl.java:1333)
|
||||
app//groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1088)
|
||||
app//groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1007)
|
||||
app//org.codehaus.groovy.runtime.InvokerHelper.invokePogoMethod(InvokerHelper.java:645)
|
||||
app//org.codehaus.groovy.runtime.InvokerHelper.invokeMethod(InvokerHelper.java:628)
|
||||
app//org.codehaus.groovy.runtime.InvokerHelper.invokeMethodSafe(InvokerHelper.java:82)
|
||||
app//nextflow.cache.CacheDB$_putTaskAsync_closure1.doCall(CacheDB.groovy:157)
|
||||
app//nextflow.cache.CacheDB$_putTaskAsync_closure1.call(CacheDB.groovy)
|
||||
app//groovyx.gpars.agent.AgentBase.onMessage(AgentBase.java:102)
|
||||
app//groovyx.gpars.agent.Agent.handleMessage(Agent.java:84)
|
||||
app//groovyx.gpars.agent.AgentCore$1.handleMessage(AgentCore.java:48)
|
||||
app//groovyx.gpars.util.AsyncMessagingCore.run(AsyncMessagingCore.java:132)
|
||||
java.base@15.0.2/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1130)
|
||||
java.base@15.0.2/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:630)
|
||||
java.base@15.0.2/java.lang.Thread.run(Thread.java:832)
|
||||
|
||||
Thread[AnsiLogObserver,5,main]
|
||||
java.base@15.0.2/java.util.regex.Pattern$BmpCharProperty.match(Pattern.java:4020)
|
||||
java.base@15.0.2/java.util.regex.Pattern$GroupHead.match(Pattern.java:4855)
|
||||
java.base@15.0.2/java.util.regex.Pattern$Branch.match(Pattern.java:4798)
|
||||
java.base@15.0.2/java.util.regex.Pattern$Branch.match(Pattern.java:4798)
|
||||
java.base@15.0.2/java.util.regex.Pattern$Branch.match(Pattern.java:4798)
|
||||
java.base@15.0.2/java.util.regex.Pattern$BranchConn.match(Pattern.java:4763)
|
||||
java.base@15.0.2/java.util.regex.Pattern$GroupTail.match(Pattern.java:4886)
|
||||
java.base@15.0.2/java.util.regex.Pattern$BmpCharPropertyGreedy.match(Pattern.java:4394)
|
||||
java.base@15.0.2/java.util.regex.Pattern$GroupHead.match(Pattern.java:4855)
|
||||
java.base@15.0.2/java.util.regex.Pattern$Branch.match(Pattern.java:4800)
|
||||
java.base@15.0.2/java.util.regex.Pattern$Branch.match(Pattern.java:4798)
|
||||
java.base@15.0.2/java.util.regex.Pattern$BmpCharProperty.match(Pattern.java:4020)
|
||||
java.base@15.0.2/java.util.regex.Pattern$Start.match(Pattern.java:3673)
|
||||
java.base@15.0.2/java.util.regex.Matcher.search(Matcher.java:1729)
|
||||
java.base@15.0.2/java.util.regex.Matcher.find(Matcher.java:773)
|
||||
java.base@15.0.2/java.util.Formatter.parse(Formatter.java:2702)
|
||||
java.base@15.0.2/java.util.Formatter.format(Formatter.java:2655)
|
||||
java.base@15.0.2/java.util.Formatter.format(Formatter.java:2609)
|
||||
java.base@15.0.2/java.lang.String.format(String.java:3292)
|
||||
app//jline.internal.TerminalLineSettings.stty(TerminalLineSettings.java:168)
|
||||
app//jline.internal.TerminalLineSettings.get(TerminalLineSettings.java:72)
|
||||
app//jline.internal.TerminalLineSettings.getProperty(TerminalLineSettings.java:92)
|
||||
app//jline.UnixTerminal.getWidth(UnixTerminal.java:77)
|
||||
app//nextflow.trace.AnsiLogObserver.renderProcesses(AnsiLogObserver.groovy:257)
|
||||
app//nextflow.trace.AnsiLogObserver.renderProgress(AnsiLogObserver.groovy:312)
|
||||
app//nextflow.trace.AnsiLogObserver.render0(AnsiLogObserver.groovy:183)
|
||||
java.base@15.0.2/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
|
||||
java.base@15.0.2/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:64)
|
||||
java.base@15.0.2/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
|
||||
java.base@15.0.2/java.lang.reflect.Method.invoke(Method.java:564)
|
||||
app//org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:343)
|
||||
app//groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:328)
|
||||
app//groovy.lang.MetaClassImpl.doInvokeMethod(MetaClassImpl.java:1333)
|
||||
app//groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1088)
|
||||
app//groovy.lang.MetaClassImpl.invokeMethodClosure(MetaClassImpl.java:1017)
|
||||
app//groovy.lang.MetaClassImpl.doInvokeMethod(MetaClassImpl.java:1207)
|
||||
app//groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1088)
|
||||
app//groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1007)
|
||||
app//groovy.lang.Closure.call(Closure.java:433)
|
||||
app//groovy.lang.Closure.call(Closure.java:412)
|
||||
app//groovy.lang.Closure.run(Closure.java:505)
|
||||
java.base@15.0.2/java.lang.Thread.run(Thread.java:832)
|
||||
|
||||
Thread[TaskFinalizer-1,5,main]
|
||||
java.base@15.0.2/jdk.internal.misc.Unsafe.park(Native Method)
|
||||
java.base@15.0.2/java.util.concurrent.locks.LockSupport.park(LockSupport.java:341)
|
||||
java.base@15.0.2/java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionNode.block(AbstractQueuedSynchronizer.java:505)
|
||||
java.base@15.0.2/java.util.concurrent.ForkJoinPool.managedBlock(ForkJoinPool.java:3137)
|
||||
java.base@15.0.2/java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:1614)
|
||||
java.base@15.0.2/java.util.concurrent.LinkedBlockingQueue.take(LinkedBlockingQueue.java:435)
|
||||
java.base@15.0.2/java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1056)
|
||||
java.base@15.0.2/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1116)
|
||||
java.base@15.0.2/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:630)
|
||||
java.base@15.0.2/java.lang.Thread.run(Thread.java:832)
|
||||
|
||||
Thread[Actor Thread 4,5,main]
|
||||
java.base@15.0.2/jdk.internal.misc.Unsafe.park(Native Method)
|
||||
java.base@15.0.2/java.util.concurrent.locks.LockSupport.park(LockSupport.java:211)
|
||||
java.base@15.0.2/java.util.concurrent.SynchronousQueue$TransferStack.awaitFulfill(SynchronousQueue.java:460)
|
||||
java.base@15.0.2/java.util.concurrent.SynchronousQueue$TransferStack.transfer(SynchronousQueue.java:361)
|
||||
java.base@15.0.2/java.util.concurrent.SynchronousQueue.take(SynchronousQueue.java:920)
|
||||
java.base@15.0.2/java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1056)
|
||||
java.base@15.0.2/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1116)
|
||||
java.base@15.0.2/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:630)
|
||||
java.base@15.0.2/java.lang.Thread.run(Thread.java:832)
|
||||
|
||||
Thread[Task monitor,5,main]
|
||||
java.base@15.0.2/jdk.internal.misc.Unsafe.park(Native Method)
|
||||
java.base@15.0.2/java.util.concurrent.locks.LockSupport.parkNanos(LockSupport.java:252)
|
||||
java.base@15.0.2/java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:1746)
|
||||
app//nextflow.processor.TaskPollingMonitor$_await_closure5.doCall(TaskPollingMonitor.groovy:529)
|
||||
app//nextflow.processor.TaskPollingMonitor$_await_closure5.call(TaskPollingMonitor.groovy)
|
||||
app//nextflow.extension.Bolts.withLock(Bolts.groovy:337)
|
||||
app//nextflow.extension.Bolts.withLock(Bolts.groovy)
|
||||
app//nextflow.processor.TaskPollingMonitor.await(TaskPollingMonitor.groovy:528)
|
||||
app//nextflow.processor.TaskPollingMonitor.pollLoop(TaskPollingMonitor.groovy:453)
|
||||
java.base@15.0.2/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
|
||||
java.base@15.0.2/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:64)
|
||||
java.base@15.0.2/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
|
||||
java.base@15.0.2/java.lang.reflect.Method.invoke(Method.java:564)
|
||||
app//org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:343)
|
||||
app//groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:328)
|
||||
app//groovy.lang.MetaClassImpl.doInvokeMethod(MetaClassImpl.java:1333)
|
||||
app//groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1088)
|
||||
app//groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1007)
|
||||
app//org.codehaus.groovy.runtime.InvokerHelper.invokePogoMethod(InvokerHelper.java:645)
|
||||
app//org.codehaus.groovy.runtime.InvokerHelper.invokeMethod(InvokerHelper.java:628)
|
||||
app//org.codehaus.groovy.runtime.InvokerHelper.invokeMethodSafe(InvokerHelper.java:82)
|
||||
app//nextflow.processor.TaskPollingMonitor$_start_closure2.doCall(TaskPollingMonitor.groovy:318)
|
||||
app//nextflow.processor.TaskPollingMonitor$_start_closure2.call(TaskPollingMonitor.groovy)
|
||||
app//groovy.lang.Closure.run(Closure.java:505)
|
||||
java.base@15.0.2/java.lang.Thread.run(Thread.java:832)
|
||||
|
||||
Thread[Actor Thread 11,5,main]
|
||||
java.base@15.0.2/jdk.internal.misc.Unsafe.park(Native Method)
|
||||
java.base@15.0.2/java.util.concurrent.locks.LockSupport.park(LockSupport.java:211)
|
||||
java.base@15.0.2/java.util.concurrent.SynchronousQueue$TransferStack.awaitFulfill(SynchronousQueue.java:460)
|
||||
java.base@15.0.2/java.util.concurrent.SynchronousQueue$TransferStack.transfer(SynchronousQueue.java:361)
|
||||
java.base@15.0.2/java.util.concurrent.SynchronousQueue.take(SynchronousQueue.java:920)
|
||||
java.base@15.0.2/java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1056)
|
||||
java.base@15.0.2/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1116)
|
||||
java.base@15.0.2/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:630)
|
||||
java.base@15.0.2/java.lang.Thread.run(Thread.java:832)
|
||||
|
||||
Thread[Actor Thread 7,5,main]
|
||||
java.base@15.0.2/jdk.internal.misc.Unsafe.park(Native Method)
|
||||
java.base@15.0.2/java.util.concurrent.locks.LockSupport.park(LockSupport.java:211)
|
||||
java.base@15.0.2/java.util.concurrent.SynchronousQueue$TransferStack.awaitFulfill(SynchronousQueue.java:460)
|
||||
java.base@15.0.2/java.util.concurrent.SynchronousQueue$TransferStack.transfer(SynchronousQueue.java:361)
|
||||
java.base@15.0.2/java.util.concurrent.SynchronousQueue.take(SynchronousQueue.java:920)
|
||||
java.base@15.0.2/java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1056)
|
||||
java.base@15.0.2/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1116)
|
||||
java.base@15.0.2/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:630)
|
||||
java.base@15.0.2/java.lang.Thread.run(Thread.java:832)
|
||||
|
||||
Thread[Signal Dispatcher,9,system]
|
||||
|
||||
Thread[Actor Thread 3,5,main]
|
||||
java.base@15.0.2/jdk.internal.misc.Unsafe.park(Native Method)
|
||||
java.base@15.0.2/java.util.concurrent.locks.LockSupport.park(LockSupport.java:211)
|
||||
java.base@15.0.2/java.util.concurrent.SynchronousQueue$TransferStack.awaitFulfill(SynchronousQueue.java:460)
|
||||
java.base@15.0.2/java.util.concurrent.SynchronousQueue$TransferStack.transfer(SynchronousQueue.java:361)
|
||||
java.base@15.0.2/java.util.concurrent.SynchronousQueue.take(SynchronousQueue.java:920)
|
||||
java.base@15.0.2/java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1056)
|
||||
java.base@15.0.2/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1116)
|
||||
java.base@15.0.2/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:630)
|
||||
java.base@15.0.2/java.lang.Thread.run(Thread.java:832)
|
||||
|
||||
Thread[Common-Cleaner,8,InnocuousThreadGroup]
|
||||
java.base@15.0.2/java.lang.Object.wait(Native Method)
|
||||
java.base@15.0.2/java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:155)
|
||||
java.base@15.0.2/jdk.internal.ref.CleanerImpl.run(CleanerImpl.java:148)
|
||||
java.base@15.0.2/java.lang.Thread.run(Thread.java:832)
|
||||
java.base@15.0.2/jdk.internal.misc.InnocuousThread.run(InnocuousThread.java:134)
|
||||
|
||||
Thread[Finalizer,8,system]
|
||||
java.base@15.0.2/java.lang.Object.wait(Native Method)
|
||||
java.base@15.0.2/java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:155)
|
||||
java.base@15.0.2/java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:176)
|
||||
java.base@15.0.2/java.lang.ref.Finalizer$FinalizerThread.run(Finalizer.java:170)
|
||||
|
||||
Mar-23 11:44:32.701 [main] DEBUG nextflow.Session - Session await > all barriers passed
|
||||
Mar-23 11:44:32.701 [Task monitor] DEBUG n.processor.TaskPollingMonitor - <<< barrier arrives (monitor: local) - terminating tasks monitor poll loop
|
||||
Mar-23 11:44:32.736 [main] DEBUG n.trace.WorkflowStatsObserver - Workflow completed > WorkflowStats[succeededCount=0; failedCount=1; ignoredCount=0; cachedCount=0; pendingCount=0; submittedCount=0; runningCount=0; retriesCount=0; abortedCount=0; succeedDuration=0ms; failedDuration=1s; cachedDuration=0ms;loadCpus=0; loadMemory=0; peakRunning=1; peakCpus=1; peakMemory=0; ]
|
||||
Mar-23 11:44:32.741 [main] DEBUG nextflow.trace.TraceFileObserver - Workflow completed -- saving trace file
|
||||
Mar-23 11:44:33.181 [main] DEBUG nextflow.cache.CacheDB - Closing CacheDB done
|
||||
Mar-23 11:44:33.291 [main] DEBUG nextflow.script.ScriptRunner - > Execution complete -- Goodbye
|
||||
Reference in New Issue
Block a user