Jan-08 15:06:35.136 [main] DEBUG nextflow.cli.Launcher - $> nextflow -log nextflow.log run SNP1.nf -resume Jan-08 15:06:35.472 [main] DEBUG nextflow.cli.CmdRun - N E X T F L O W ~ version 24.10.3 Jan-08 15:06:35.520 [main] DEBUG nextflow.plugin.PluginsFacade - Setting up plugin manager > mode=prod; embedded=false; plugins-dir=/root/.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@1.15.3,nf-tower@1.9.3,nf-wave@1.7.4 Jan-08 15:06:35.552 [main] INFO o.pf4j.DefaultPluginStatusProvider - Enabled plugins: [] Jan-08 15:06:35.553 [main] INFO o.pf4j.DefaultPluginStatusProvider - Disabled plugins: [] Jan-08 15:06:35.558 [main] INFO org.pf4j.DefaultPluginManager - PF4J version 3.12.0 in 'deployment' mode Jan-08 15:06:35.589 [main] INFO org.pf4j.AbstractPluginManager - No plugins Jan-08 15:06:35.780 [main] DEBUG nextflow.cli.CmdRun - Applied DSL=2 from script declaration Jan-08 15:06:35.817 [main] DEBUG nextflow.cli.CmdRun - Launching `SNP1.nf` [festering_newton] DSL2 - revision: c372e954ca Jan-08 15:06:35.823 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins default=[] Jan-08 15:06:35.825 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins resolved requirement=[] Jan-08 15:06:36.069 [main] DEBUG nextflow.Session - Session UUID: d040ee6e-960c-4d7e-9570-df7daed6928c Jan-08 15:06:36.077 [main] DEBUG nextflow.Session - Run name: festering_newton Jan-08 15:06:36.078 [main] DEBUG nextflow.Session - Executor pool size: 2 Jan-08 15:06:36.095 [main] DEBUG nextflow.file.FilePorter - File porter settings maxRetries=3; maxTransfers=50; pollTimeout=null Jan-08 15:06:36.113 [main] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'FileTransfer' minSize=10; maxSize=10; workQueue=LinkedBlockingQueue[10000]; allowCoreThreadTimeout=false Jan-08 15:06:36.191 [main] DEBUG nextflow.cli.CmdRun - Version: 24.10.3 build 5933 Created: 16-12-2024 15:34 UTC (21:04 IDT) System: Linux 5.4.0-88-generic Runtime: Groovy 4.0.23 on OpenJDK 64-Bit Server VM 11.0.13+7-b1751.21 Encoding: UTF-8 (UTF-8) Process: 359152@ab-openlab [127.0.1.1] CPUs: 1 - Mem: 62.8 GB (4.5 GB) - Swap: 16 GB (15.9 GB) Jan-08 15:06:36.277 [main] DEBUG nextflow.Session - Work-dir: /home/gpsr/webserver/cgidocs/anshu/RAPID-engine/work [btrfs] Jan-08 15:06:36.278 [main] DEBUG nextflow.Session - Script base path does not exist or is not a directory: /home/gpsr/webserver/cgidocs/anshu/RAPID-engine/bin Jan-08 15:06:36.321 [main] DEBUG nextflow.executor.ExecutorFactory - Extension executors providers=[] Jan-08 15:06:36.368 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory Jan-08 15:06:36.441 [main] DEBUG nextflow.cache.CacheFactory - Using Nextflow cache factory: nextflow.cache.DefaultCacheFactory Jan-08 15:06:36.487 [main] DEBUG nextflow.util.CustomThreadPool - Creating default thread pool > poolSize: 2; maxThreads: 1000 Jan-08 15:06:36.663 [main] DEBUG nextflow.Session - Session start Jan-08 15:06:39.813 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution Jan-08 15:06:39.837 [main] DEBUG n.secret.LocalSecretsProvider - Secrets store: /root/.nextflow/secrets/store.json Jan-08 15:06:39.859 [main] DEBUG nextflow.secret.SecretsLoader - Discovered secrets providers: [nextflow.secret.LocalSecretsProvider@5ce3409b] - activable => nextflow.secret.LocalSecretsProvider@5ce3409b Jan-08 15:06:39.893 [main] INFO nextflow.Nextflow - A C I N E T O B A C T E R A N A L Y S I S P I P E L I N E =================================================== Reference Genome: /home/gpsr/webserver/cgidocs/anshu/RAPID-engine/reference_genome/acinetobacter_genome.fa Reads Directory : /home/gpsr/webserver/cgidocs/anshu/RAPID-engine/upload Output Directory: /home/gpsr/webserver/cgidocs/anshu/RAPID-engine/result Threads : 32 Jan-08 15:06:40.350 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jan-08 15:06:40.350 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jan-08 15:06:40.365 [main] DEBUG nextflow.executor.Executor - [warm up] executor > local Jan-08 15:06:40.390 [main] DEBUG n.processor.LocalPollingMonitor - Creating local task monitor for executor 'local' > cpus=1; memory=62.8 GB; capacity=1; pollInterval=100ms; dumpInterval=5m Jan-08 15:06:40.399 [main] DEBUG n.processor.TaskPollingMonitor - >>> barrier register (monitor: local) Jan-08 15:06:40.764 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jan-08 15:06:40.764 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jan-08 15:06:40.789 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jan-08 15:06:40.789 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jan-08 15:06:40.811 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jan-08 15:06:40.811 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jan-08 15:06:40.833 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jan-08 15:06:40.835 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jan-08 15:06:40.859 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jan-08 15:06:40.859 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jan-08 15:06:40.882 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jan-08 15:06:40.883 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jan-08 15:06:40.896 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jan-08 15:06:40.896 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jan-08 15:06:40.912 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jan-08 15:06:40.912 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jan-08 15:06:40.921 [main] DEBUG nextflow.Session - Workflow process names [dsl2]: FASTQC_RAW, PROCESS_VCF, ANALYZE_RESULTS, CALL_VARIANTS, INDEX_REFERENCE, FASTP, FASTQC_TRIMMED, FILTER_VARIANTS, ALIGN_READS Jan-08 15:06:40.922 [main] DEBUG nextflow.Session - Igniting dataflow network (10) Jan-08 15:06:40.936 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > FASTQC_RAW Jan-08 15:06:40.941 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > FASTP Jan-08 15:06:40.941 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > FASTQC_TRIMMED Jan-08 15:06:40.942 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > INDEX_REFERENCE Jan-08 15:06:40.964 [PathVisitor-1] DEBUG nextflow.file.PathVisitor - files for syntax: glob; folder: /home/gpsr/webserver/cgidocs/anshu/RAPID-engine/upload/; pattern: *_{1,2}.fastq*.gz; options: [checkIfExists:true] Jan-08 15:06:40.971 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > ALIGN_READS Jan-08 15:06:40.972 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > CALL_VARIANTS Jan-08 15:06:40.977 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PROCESS_VCF Jan-08 15:06:40.978 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > FILTER_VARIANTS Jan-08 15:06:40.978 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > ANALYZE_RESULTS Jan-08 15:06:40.980 [main] DEBUG nextflow.script.ScriptRunner - Parsed script files: Script_fa877a98c7edd501: /home/gpsr/webserver/cgidocs/anshu/RAPID-engine/SNP1.nf Jan-08 15:06:40.980 [main] DEBUG nextflow.script.ScriptRunner - > Awaiting termination Jan-08 15:06:40.980 [main] DEBUG nextflow.Session - Session await Jan-08 15:06:41.455 [Actor Thread 3] INFO nextflow.processor.TaskProcessor - [cc/e3a774] Cached process > INDEX_REFERENCE Jan-08 15:06:41.460 [Actor Thread 5] INFO nextflow.processor.TaskProcessor - [34/4bd32d] Cached process > FASTQC_RAW (1) Jan-08 15:06:41.472 [Actor Thread 2] INFO nextflow.processor.TaskProcessor - [40/e2b802] Cached process > FASTP (1) Jan-08 15:06:41.617 [Actor Thread 3] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'PublishDir' minSize=10; maxSize=10; workQueue=LinkedBlockingQueue[10000]; allowCoreThreadTimeout=false Jan-08 15:06:41.649 [Actor Thread 7] INFO nextflow.processor.TaskProcessor - [f2/96401b] Cached process > FASTQC_TRIMMED (1) Jan-08 15:06:41.755 [Actor Thread 11] INFO nextflow.processor.TaskProcessor - [2d/04e89b] Cached process > ALIGN_READS (1) Jan-08 15:06:41.925 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jan-08 15:06:41.932 [Task submitter] INFO nextflow.Session - [0c/c28253] Submitted process > CALL_VARIANTS (1) Jan-08 15:06:42.041 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 6; name: CALL_VARIANTS (1); status: COMPLETED; exit: 127; error: -; workDir: /home/gpsr/webserver/cgidocs/anshu/RAPID-engine/work/0c/c282531125834d5bb7dfb9932e428e] Jan-08 15:06:42.042 [Task monitor] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'TaskFinalizer' minSize=10; maxSize=10; workQueue=LinkedBlockingQueue[10000]; allowCoreThreadTimeout=false Jan-08 15:06:42.064 [TaskFinalizer-1] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for task: name=CALL_VARIANTS (1); work-dir=/home/gpsr/webserver/cgidocs/anshu/RAPID-engine/work/0c/c282531125834d5bb7dfb9932e428e error [nextflow.exception.ProcessFailedException]: Process `CALL_VARIANTS (1)` terminated with an error exit status (127) Jan-08 15:06:42.117 [TaskFinalizer-1] ERROR nextflow.processor.TaskProcessor - Error executing process > 'CALL_VARIANTS (1)' Caused by: Process `CALL_VARIANTS (1)` terminated with an error exit status (127) Command executed: bcftools mpileup -f acinetobacter_genome.fa SRR21995810.bam | bcftools call -mv -Ov -o SRR21995810.variants.vcf Command exit status: 127 Command output: (empty) Command error: bcftools: error while loading shared libraries: libcrypto.so.1.0.0: cannot open shared object file: No such file or directory bcftools: error while loading shared libraries: libcrypto.so.1.0.0: cannot open shared object file: No such file or directory Work dir: /home/gpsr/webserver/cgidocs/anshu/RAPID-engine/work/0c/c282531125834d5bb7dfb9932e428e Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out` Jan-08 15:06:42.132 [main] DEBUG nextflow.Session - Session await > all processes finished Jan-08 15:06:42.145 [TaskFinalizer-1] DEBUG nextflow.Session - Session aborted -- Cause: Process `CALL_VARIANTS (1)` terminated with an error exit status (127) Jan-08 15:06:42.181 [Task monitor] DEBUG n.processor.TaskPollingMonitor - <<< barrier arrives (monitor: local) - terminating tasks monitor poll loop Jan-08 15:06:42.181 [main] DEBUG nextflow.Session - Session await > all barriers passed Jan-08 15:06:42.192 [main] INFO nextflow.Nextflow - Pipeline failed. Check the logs. Jan-08 15:06:42.201 [TaskFinalizer-1] DEBUG nextflow.Session - Thread[PathVisitor-1,5,main] java.base@11.0.13/jdk.internal.misc.Unsafe.park(Native Method) java.base@11.0.13/java.util.concurrent.locks.LockSupport.parkNanos(LockSupport.java:234) java.base@11.0.13/java.util.concurrent.SynchronousQueue$TransferStack.awaitFulfill(SynchronousQueue.java:462) java.base@11.0.13/java.util.concurrent.SynchronousQueue$TransferStack.transfer(SynchronousQueue.java:361) java.base@11.0.13/java.util.concurrent.SynchronousQueue.poll(SynchronousQueue.java:937) java.base@11.0.13/java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1053) java.base@11.0.13/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1114) java.base@11.0.13/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) java.base@11.0.13/java.lang.Thread.run(Thread.java:829) Thread[Actor Thread 12,5,main] java.base@11.0.13/jdk.internal.misc.Unsafe.park(Native Method) java.base@11.0.13/java.util.concurrent.locks.LockSupport.parkNanos(LockSupport.java:234) java.base@11.0.13/java.util.concurrent.SynchronousQueue$TransferStack.awaitFulfill(SynchronousQueue.java:462) java.base@11.0.13/java.util.concurrent.SynchronousQueue$TransferStack.transfer(SynchronousQueue.java:361) java.base@11.0.13/java.util.concurrent.SynchronousQueue.poll(SynchronousQueue.java:937) java.base@11.0.13/java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1053) java.base@11.0.13/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1114) java.base@11.0.13/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) java.base@11.0.13/java.lang.Thread.run(Thread.java:829) Thread[Finalizer,8,system] java.base@11.0.13/java.lang.Object.wait(Native Method) java.base@11.0.13/java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:155) java.base@11.0.13/java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:176) java.base@11.0.13/java.lang.ref.Finalizer$FinalizerThread.run(Finalizer.java:170) Thread[Actor Thread 3,5,main] java.base@11.0.13/jdk.internal.misc.Unsafe.park(Native Method) java.base@11.0.13/java.util.concurrent.locks.LockSupport.parkNanos(LockSupport.java:234) java.base@11.0.13/java.util.concurrent.SynchronousQueue$TransferStack.awaitFulfill(SynchronousQueue.java:462) java.base@11.0.13/java.util.concurrent.SynchronousQueue$TransferStack.transfer(SynchronousQueue.java:361) java.base@11.0.13/java.util.concurrent.SynchronousQueue.poll(SynchronousQueue.java:937) java.base@11.0.13/java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1053) java.base@11.0.13/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1114) java.base@11.0.13/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) java.base@11.0.13/java.lang.Thread.run(Thread.java:829) Thread[Actor Thread 6,5,main] java.base@11.0.13/jdk.internal.misc.Unsafe.park(Native Method) java.base@11.0.13/java.util.concurrent.locks.LockSupport.parkNanos(LockSupport.java:234) java.base@11.0.13/java.util.concurrent.SynchronousQueue$TransferStack.awaitFulfill(SynchronousQueue.java:462) java.base@11.0.13/java.util.concurrent.SynchronousQueue$TransferStack.transfer(SynchronousQueue.java:361) java.base@11.0.13/java.util.concurrent.SynchronousQueue.poll(SynchronousQueue.java:937) java.base@11.0.13/java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1053) java.base@11.0.13/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1114) java.base@11.0.13/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) java.base@11.0.13/java.lang.Thread.run(Thread.java:829) Thread[Reference Handler,10,system] java.base@11.0.13/java.lang.ref.Reference.waitForReferencePendingList(Native Method) java.base@11.0.13/java.lang.ref.Reference.processPendingReferences(Reference.java:241) java.base@11.0.13/java.lang.ref.Reference$ReferenceHandler.run(Reference.java:213) Thread[Thread-1,5,main] java.base@11.0.13/jdk.internal.misc.Unsafe.park(Native Method) java.base@11.0.13/java.util.concurrent.locks.LockSupport.parkNanos(LockSupport.java:234) java.base@11.0.13/java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.awaitNanos(AbstractQueuedSynchronizer.java:2123) java.base@11.0.13/java.util.concurrent.LinkedBlockingDeque.pollFirst(LinkedBlockingDeque.java:513) java.base@11.0.13/java.util.concurrent.LinkedBlockingDeque.poll(LinkedBlockingDeque.java:675) app//nextflow.util.SimpleAgent.run(SimpleAgent.groovy:89) java.base@11.0.13/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) java.base@11.0.13/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) java.base@11.0.13/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) java.base@11.0.13/java.lang.reflect.Method.invoke(Method.java:566) 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@11.0.13/java.lang.Thread.run(Thread.java:829) Thread[process reaper,10,system] java.base@11.0.13/jdk.internal.misc.Unsafe.park(Native Method) java.base@11.0.13/java.util.concurrent.locks.LockSupport.parkNanos(LockSupport.java:234) java.base@11.0.13/java.util.concurrent.SynchronousQueue$TransferStack.awaitFulfill(SynchronousQueue.java:462) java.base@11.0.13/java.util.concurrent.SynchronousQueue$TransferStack.transfer(SynchronousQueue.java:361) java.base@11.0.13/java.util.concurrent.SynchronousQueue.poll(SynchronousQueue.java:937) java.base@11.0.13/java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1053) java.base@11.0.13/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1114) java.base@11.0.13/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) java.base@11.0.13/java.lang.Thread.run(Thread.java:829) Thread[pool-2-thread-1,5,main] java.base@11.0.13/jdk.internal.misc.Unsafe.park(Native Method) java.base@11.0.13/java.util.concurrent.locks.LockSupport.park(LockSupport.java:194) java.base@11.0.13/java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:2081) java.base@11.0.13/java.util.concurrent.LinkedBlockingQueue.take(LinkedBlockingQueue.java:433) java.base@11.0.13/java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1054) java.base@11.0.13/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1114) java.base@11.0.13/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) java.base@11.0.13/java.lang.Thread.run(Thread.java:829) Thread[Actor Thread 4,5,main] java.base@11.0.13/jdk.internal.misc.Unsafe.park(Native Method) java.base@11.0.13/java.util.concurrent.locks.LockSupport.parkNanos(LockSupport.java:234) java.base@11.0.13/java.util.concurrent.SynchronousQueue$TransferStack.awaitFulfill(SynchronousQueue.java:462) java.base@11.0.13/java.util.concurrent.SynchronousQueue$TransferStack.transfer(SynchronousQueue.java:361) java.base@11.0.13/java.util.concurrent.SynchronousQueue.poll(SynchronousQueue.java:937) java.base@11.0.13/java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1053) java.base@11.0.13/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1114) java.base@11.0.13/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) java.base@11.0.13/java.lang.Thread.run(Thread.java:829) Thread[Task submitter,5,main] java.base@11.0.13/jdk.internal.misc.Unsafe.park(Native Method) java.base@11.0.13/java.util.concurrent.locks.LockSupport.park(LockSupport.java:194) java.base@11.0.13/java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:2081) app//nextflow.processor.TaskPollingMonitor.awaitTasks(TaskPollingMonitor.groovy:388) app//nextflow.processor.TaskPollingMonitor.submitLoop(TaskPollingMonitor.groovy:412) java.base@11.0.13/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) java.base@11.0.13/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) java.base@11.0.13/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) java.base@11.0.13/java.lang.reflect.Method.invoke(Method.java:566) app//org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:343) app//groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:328) app//groovy.lang.MetaClassImpl.doInvokeMethod(MetaClassImpl.java:1333) app//groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1088) app//groovy.lang.MetaClassImpl.invokeMethodClosure(MetaClassImpl.java:1017) app//groovy.lang.MetaClassImpl.doInvokeMethod(MetaClassImpl.java:1207) app//groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1088) app//groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1007) app//groovy.lang.Closure.call(Closure.java:433) app//groovy.lang.Closure.call(Closure.java:412) app//groovy.lang.Closure.run(Closure.java:505) java.base@11.0.13/java.lang.Thread.run(Thread.java:829) Thread[Actor Thread 2,5,main] java.base@11.0.13/jdk.internal.misc.Unsafe.park(Native Method) java.base@11.0.13/java.util.concurrent.locks.LockSupport.parkNanos(LockSupport.java:234) java.base@11.0.13/java.util.concurrent.SynchronousQueue$TransferStack.awaitFulfill(SynchronousQueue.java:462) java.base@11.0.13/java.util.concurrent.SynchronousQueue$TransferStack.transfer(SynchronousQueue.java:361) java.base@11.0.13/java.util.concurrent.SynchronousQueue.poll(SynchronousQueue.java:937) java.base@11.0.13/java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1053) java.base@11.0.13/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1114) java.base@11.0.13/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) java.base@11.0.13/java.lang.Thread.run(Thread.java:829) Thread[Actor Thread 1,5,main] java.base@11.0.13/jdk.internal.misc.Unsafe.park(Native Method) java.base@11.0.13/java.util.concurrent.locks.LockSupport.parkNanos(LockSupport.java:234) java.base@11.0.13/java.util.concurrent.SynchronousQueue$TransferStack.awaitFulfill(SynchronousQueue.java:462) java.base@11.0.13/java.util.concurrent.SynchronousQueue$TransferStack.transfer(SynchronousQueue.java:361) java.base@11.0.13/java.util.concurrent.SynchronousQueue.poll(SynchronousQueue.java:937) java.base@11.0.13/java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1053) java.base@11.0.13/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1114) java.base@11.0.13/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) java.base@11.0.13/java.lang.Thread.run(Thread.java:829) Thread[Actor Thread 7,5,main] java.base@11.0.13/jdk.internal.misc.Unsafe.park(Native Method) java.base@11.0.13/java.util.concurrent.locks.LockSupport.parkNanos(LockSupport.java:234) java.base@11.0.13/java.util.concurrent.SynchronousQueue$TransferStack.awaitFulfill(SynchronousQueue.java:462) java.base@11.0.13/java.util.concurrent.SynchronousQueue$TransferStack.transfer(SynchronousQueue.java:361) java.base@11.0.13/java.util.concurrent.SynchronousQueue.poll(SynchronousQueue.java:937) java.base@11.0.13/java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1053) java.base@11.0.13/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1114) java.base@11.0.13/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) java.base@11.0.13/java.lang.Thread.run(Thread.java:829) Thread[main,5,main] java.base@11.0.13/jdk.internal.misc.Unsafe.park(Native Method) java.base@11.0.13/java.util.concurrent.locks.LockSupport.park(LockSupport.java:194) java.base@11.0.13/java.util.concurrent.locks.AbstractQueuedSynchronizer.parkAndCheckInterrupt(AbstractQueuedSynchronizer.java:885) java.base@11.0.13/java.util.concurrent.locks.AbstractQueuedSynchronizer.doAcquireSharedInterruptibly(AbstractQueuedSynchronizer.java:1039) java.base@11.0.13/java.util.concurrent.locks.AbstractQueuedSynchronizer.acquireSharedInterruptibly(AbstractQueuedSynchronizer.java:1345) java.base@11.0.13/java.util.concurrent.CountDownLatch.await(CountDownLatch.java:232) app//nextflow.util.SimpleAgent$RetrieveValueClosure.getResult(SimpleAgent.groovy:132) app//nextflow.util.SimpleAgent.getValue(SimpleAgent.groovy:83) app//nextflow.trace.WorkflowStatsObserver.getStats(WorkflowStatsObserver.groovy:94) app//nextflow.script.WorkflowMetadata.getWorkflowStats(WorkflowMetadata.groovy:512) app//nextflow.script.WorkflowMetadata.invokeOnComplete(WorkflowMetadata.groovy:422) java.base@11.0.13/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) java.base@11.0.13/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) java.base@11.0.13/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) java.base@11.0.13/java.lang.reflect.Method.invoke(Method.java:566) app//org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:343) app//groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:328) app//groovy.lang.MetaClassImpl.doInvokeMethod(MetaClassImpl.java:1333) app//groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1088) app//groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1007) app//org.codehaus.groovy.runtime.InvokerHelper.invokePogoMethod(InvokerHelper.java:645) app//org.codehaus.groovy.runtime.InvokerHelper.invokeMethod(InvokerHelper.java:628) app//org.codehaus.groovy.runtime.InvokerHelper.invokeMethodSafe(InvokerHelper.java:82) app//nextflow.script.WorkflowMetadata$_closure2.doCall(WorkflowMetadata.groovy:286) app//nextflow.script.WorkflowMetadata$_closure2.call(WorkflowMetadata.groovy) app//groovy.lang.Closure.run(Closure.java:505) app//nextflow.Session.shutdown0(Session.groovy:741) app//nextflow.Session.destroy(Session.groovy:694) app//nextflow.script.ScriptRunner.shutdown(ScriptRunner.groovy:260) app//nextflow.script.ScriptRunner.execute(ScriptRunner.groovy:146) app//nextflow.cli.CmdRun.run(CmdRun.groovy:376) app//nextflow.cli.Launcher.run(Launcher.groovy:503) app//nextflow.cli.Launcher.main(Launcher.groovy:658) Thread[Actor Thread 5,5,main] java.base@11.0.13/jdk.internal.misc.Unsafe.park(Native Method) java.base@11.0.13/java.util.concurrent.locks.LockSupport.parkNanos(LockSupport.java:234) java.base@11.0.13/java.util.concurrent.SynchronousQueue$TransferStack.awaitFulfill(SynchronousQueue.java:462) java.base@11.0.13/java.util.concurrent.SynchronousQueue$TransferStack.transfer(SynchronousQueue.java:361) java.base@11.0.13/java.util.concurrent.SynchronousQueue.poll(SynchronousQueue.java:937) java.base@11.0.13/java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1053) java.base@11.0.13/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1114) java.base@11.0.13/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) java.base@11.0.13/java.lang.Thread.run(Thread.java:829) Thread[Common-Cleaner,8,InnocuousThreadGroup] java.base@11.0.13/java.lang.Object.wait(Native Method) java.base@11.0.13/java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:155) java.base@11.0.13/jdk.internal.ref.CleanerImpl.run(CleanerImpl.java:148) java.base@11.0.13/java.lang.Thread.run(Thread.java:829) java.base@11.0.13/jdk.internal.misc.InnocuousThread.run(InnocuousThread.java:134) Thread[TaskFinalizer-1,5,main] java.base@11.0.13/java.lang.Thread.dumpThreads(Native Method) java.base@11.0.13/java.lang.Thread.getAllStackTraces(Thread.java:1653) app//nextflow.util.SysHelper.dumpThreads(SysHelper.groovy:188) app//nextflow.Session.abort(Session.groovy:800) app//nextflow.Session.fault(Session.groovy:766) app//nextflow.processor.TaskPollingMonitor.finalizeTask(TaskPollingMonitor.groovy:695) app//nextflow.processor.TaskPollingMonitor.safeFinalizeTask(TaskPollingMonitor.groovy:678) java.base@11.0.13/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) java.base@11.0.13/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) java.base@11.0.13/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) java.base@11.0.13/java.lang.reflect.Method.invoke(Method.java:566) 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$_checkTaskStatus_lambda8.doCall(TaskPollingMonitor.groovy:668) app//nextflow.processor.TaskPollingMonitor$$Lambda$421/0x000000080058e040.run(Unknown Source) java.base@11.0.13/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) java.base@11.0.13/java.util.concurrent.FutureTask.run(FutureTask.java:264) java.base@11.0.13/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) java.base@11.0.13/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) java.base@11.0.13/java.lang.Thread.run(Thread.java:829) Thread[Actor Thread 10,5,main] java.base@11.0.13/jdk.internal.misc.Unsafe.park(Native Method) java.base@11.0.13/java.util.concurrent.locks.LockSupport.parkNanos(LockSupport.java:234) java.base@11.0.13/java.util.concurrent.SynchronousQueue$TransferStack.awaitFulfill(SynchronousQueue.java:462) java.base@11.0.13/java.util.concurrent.SynchronousQueue$TransferStack.transfer(SynchronousQueue.java:361) java.base@11.0.13/java.util.concurrent.SynchronousQueue.poll(SynchronousQueue.java:937) java.base@11.0.13/java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1053) java.base@11.0.13/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1114) java.base@11.0.13/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) java.base@11.0.13/java.lang.Thread.run(Thread.java:829) Thread[Signal Dispatcher,9,system] Thread[AnsiLogObserver,5,main] java.base@11.0.13/java.lang.Object.wait(Native Method) app//nextflow.trace.AnsiLogObserver.render0(AnsiLogObserver.groovy:185) java.base@11.0.13/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) java.base@11.0.13/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) java.base@11.0.13/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) java.base@11.0.13/java.lang.reflect.Method.invoke(Method.java:566) 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@11.0.13/java.lang.Thread.run(Thread.java:829) Thread[Actor Thread 11,5,main] java.base@11.0.13/jdk.internal.misc.Unsafe.park(Native Method) java.base@11.0.13/java.util.concurrent.locks.LockSupport.parkNanos(LockSupport.java:234) java.base@11.0.13/java.util.concurrent.SynchronousQueue$TransferStack.awaitFulfill(SynchronousQueue.java:462) java.base@11.0.13/java.util.concurrent.SynchronousQueue$TransferStack.transfer(SynchronousQueue.java:361) java.base@11.0.13/java.util.concurrent.SynchronousQueue.poll(SynchronousQueue.java:937) java.base@11.0.13/java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1053) java.base@11.0.13/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1114) java.base@11.0.13/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) java.base@11.0.13/java.lang.Thread.run(Thread.java:829) Thread[Actor Thread 8,5,main] java.base@11.0.13/jdk.internal.misc.Unsafe.park(Native Method) java.base@11.0.13/java.util.concurrent.locks.LockSupport.parkNanos(LockSupport.java:234) java.base@11.0.13/java.util.concurrent.SynchronousQueue$TransferStack.awaitFulfill(SynchronousQueue.java:462) java.base@11.0.13/java.util.concurrent.SynchronousQueue$TransferStack.transfer(SynchronousQueue.java:361) java.base@11.0.13/java.util.concurrent.SynchronousQueue.poll(SynchronousQueue.java:937) java.base@11.0.13/java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1053) java.base@11.0.13/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1114) java.base@11.0.13/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) java.base@11.0.13/java.lang.Thread.run(Thread.java:829) Thread[Actor Thread 9,5,main] java.base@11.0.13/jdk.internal.misc.Unsafe.park(Native Method) java.base@11.0.13/java.util.concurrent.locks.LockSupport.parkNanos(LockSupport.java:234) java.base@11.0.13/java.util.concurrent.SynchronousQueue$TransferStack.awaitFulfill(SynchronousQueue.java:462) java.base@11.0.13/java.util.concurrent.SynchronousQueue$TransferStack.transfer(SynchronousQueue.java:361) java.base@11.0.13/java.util.concurrent.SynchronousQueue.poll(SynchronousQueue.java:937) java.base@11.0.13/java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1053) java.base@11.0.13/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1114) java.base@11.0.13/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) java.base@11.0.13/java.lang.Thread.run(Thread.java:829) Jan-08 15:06:42.202 [TaskFinalizer-1] WARN nextflow.util.SimpleAgent - Got an interrupted exception while taking agent result | java.lang.InterruptedException Jan-08 15:06:42.205 [main] DEBUG n.trace.WorkflowStatsObserver - Workflow completed > WorkflowStats[succeededCount=0; failedCount=1; ignoredCount=0; cachedCount=5; pendingCount=0; submittedCount=0; runningCount=0; retriesCount=0; abortedCount=0; succeedDuration=0ms; failedDuration=47ms; cachedDuration=20m 6s;loadCpus=0; loadMemory=0; peakRunning=1; peakCpus=1; peakMemory=0; ] Jan-08 15:06:42.364 [main] DEBUG nextflow.cache.CacheDB - Closing CacheDB done Jan-08 15:06:42.391 [main] DEBUG nextflow.script.ScriptRunner - > Execution complete -- Goodbye