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Unclear error message when using an unknown entrypoint #5811

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DriesSchaumont opened this issue Feb 24, 2025 · 0 comments
Open

Unclear error message when using an unknown entrypoint #5811

DriesSchaumont opened this issue Feb 24, 2025 · 0 comments

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@DriesSchaumont
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Bug report

Expected behavior and actual behavior

When specifying an unknown entrypoint using -entry <entrypoint>, an error message describing the problem should be displayed. Currently, only ERROR ~ Strings must not be null is shown.

Steps to reproduce the problem

nextflow run nf-core/demultiplex -entry 'foo'

Program output

 N E X T F L O W   ~  version 24.10.4

Launching `https://github.com/nf-core/demultiplex` [disturbed_mendel] DSL2 - revision: 7c2040c5b9 [master]

ERROR ~ Strings must not be null

 -- Check '.nextflow.log' file for details

Feb-24 08:33:36.841 [main] DEBUG nextflow.cli.Launcher - $> nextflow run nf-core/demultiplex -entry foo
Feb-24 08:33:37.022 [main] DEBUG nextflow.cli.CmdRun - N E X T F L O W  ~  version 24.10.4
Feb-24 08:33:37.034 [main] DEBUG nextflow.plugin.PluginsFacade - Setting up plugin manager > mode=prod; embedded=false; plugins-dir=/home/di/.nextflow/plugins; core-plugins: [email protected],[email protected],[email protected],[email protected],[email protected],[email protected],[email protected],[email protected]
Feb-24 08:33:37.050 [main] INFO  o.pf4j.DefaultPluginStatusProvider - Enabled plugins: []
Feb-24 08:33:37.050 [main] INFO  o.pf4j.DefaultPluginStatusProvider - Disabled plugins: []
Feb-24 08:33:37.052 [main] INFO  org.pf4j.DefaultPluginManager - PF4J version 3.12.0 in 'deployment' mode
Feb-24 08:33:37.060 [main] INFO  org.pf4j.AbstractPluginManager - No pluginsx
Feb-24 08:33:37.424 [main] DEBUG nextflow.scm.RepositoryFactory - Found Git repository result: [RepositoryFactory]
Feb-24 08:33:37.665 [main] DEBUG nextflow.scm.AssetManager - Git config: /home/di/.nextflow/assets/nf-core/demultiplex/.git/config; branch: null; remote: origin; url: https://github.com/nf-core/demultiplex.git
Feb-24 08:33:37.674 [main] DEBUG nextflow.scm.AssetManager - Git config: /home/di/.nextflow/assets/nf-core/demultiplex/.git/config; branch: null; remote: origin; url: https://github.com/nf-core/demultiplex.git
Feb-24 08:33:38.174 [main] DEBUG nextflow.config.ConfigBuilder - Found config base: /home/di/.nextflow/assets/nf-core/demultiplex/nextflow.config
Feb-24 08:33:38.175 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /home/di/.nextflow/assets/nf-core/demultiplex/nextflow.config
Feb-24 08:33:38.180 [main] DEBUG n.secret.LocalSecretsProvider - Secrets store: /home/di/.nextflow/secrets/store.json
Feb-24 08:33:38.182 [main] DEBUG nextflow.secret.SecretsLoader - Discovered secrets providers: [nextflow.secret.LocalSecretsProvider@2506e949] - activable => nextflow.secret.LocalSecretsProvider@2506e949
Feb-24 08:33:38.184 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `standard`
Feb-24 08:33:38.612 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `standard`
Feb-24 08:33:38.637 [main] DEBUG nextflow.cli.CmdRun - Applied DSL=2 by global default
Feb-24 08:33:38.638 [main] DEBUG nextflow.cli.CmdRun - Launching `https://github.com/nf-core/demultiplex` [disturbed_mendel] DSL2 - revision: 7c2040c5b9 [master]
Feb-24 08:33:38.639 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins declared=[[email protected]]
Feb-24 08:33:38.640 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins default=[]
Feb-24 08:33:38.640 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins resolved requirement=[[email protected]]
Feb-24 08:33:38.640 [main] DEBUG nextflow.plugin.PluginUpdater - Installing plugin nf-schema version: 2.1.1
Feb-24 08:33:38.644 [main] INFO  org.pf4j.AbstractPluginManager - Plugin '[email protected]' resolved
Feb-24 08:33:38.644 [main] INFO  org.pf4j.AbstractPluginManager - Start plugin '[email protected]'
Feb-24 08:33:38.647 [main] DEBUG nextflow.plugin.BasePlugin - Plugin started [email protected]
Feb-24 08:33:38.687 [main] DEBUG nextflow.Session - Session UUID: ef8dc132-5123-4d6a-aa90-5c8e5d9bb235
Feb-24 08:33:38.687 [main] DEBUG nextflow.Session - Run name: disturbed_mendel
Feb-24 08:33:38.687 [main] DEBUG nextflow.Session - Executor pool size: 16
Feb-24 08:33:38.691 [main] DEBUG nextflow.file.FilePorter - File porter settings maxRetries=3; maxTransfers=50; pollTimeout=null
Feb-24 08:33:38.694 [main] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'FileTransfer' minSize=10; maxSize=48; workQueue=LinkedBlockingQueue[10000]; allowCoreThreadTimeout=false
Feb-24 08:33:38.703 [main] DEBUG nextflow.cli.CmdRun - 
  Version: 24.10.4 build 5934
  Created: 20-01-2025 16:47 UTC 
  System: Linux 6.8.0-53-generic
  Runtime: Groovy 4.0.23 on OpenJDK 64-Bit Server VM 21.0.6+7-Ubuntu-124.04.1
  Encoding: UTF-8 (UTF-8)
  Process: 1593230@di-server [127.0.1.1]
  CPUs: 16 - Mem: 31.3 GB (6.5 GB) - Swap: 20 GB (19.7 GB)
Feb-24 08:33:38.713 [main] DEBUG nextflow.Session - Work-dir: /home/workdir [ext2/ext3]
Feb-24 08:33:38.740 [main] DEBUG nextflow.executor.ExecutorFactory - Extension executors providers=[]
Feb-24 08:33:38.746 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory
Feb-24 08:33:38.777 [main] DEBUG nextflow.cache.CacheFactory - Using Nextflow cache factory: nextflow.cache.DefaultCacheFactory
Feb-24 08:33:38.783 [main] DEBUG nextflow.util.CustomThreadPool - Creating default thread pool > poolSize: 17; maxThreads: 1000
Feb-24 08:33:38.818 [main] DEBUG nextflow.Session - Session start
Feb-24 08:33:38.823 [main] DEBUG nextflow.Session - Using default localLib path: /home/di/.nextflow/assets/nf-core/demultiplex/lib
Feb-24 08:33:38.825 [main] DEBUG nextflow.Session - Adding to the classpath library: /home/di/.nextflow/assets/nf-core/demultiplex/lib
Feb-24 08:33:38.900 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution
Feb-24 08:33:40.124 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [paramsSummaryMap:paramsSummaryMap]; plugin Id: nf-schema
Feb-24 08:33:40.301 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [paramsSummaryLog:paramsSummaryLog]; plugin Id: nf-schema
Feb-24 08:33:40.302 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [validateParameters:validateParameters]; plugin Id: nf-schema
Feb-24 08:33:40.303 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [paramsSummaryMap:paramsSummaryMap]; plugin Id: nf-schema
Feb-24 08:33:40.304 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [samplesheetToList:samplesheetToList]; plugin Id: nf-schema
Feb-24 08:33:40.407 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [paramsSummaryLog:paramsSummaryLog]; plugin Id: nf-schema
Feb-24 08:33:40.408 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [validateParameters:validateParameters]; plugin Id: nf-schema
Feb-24 08:33:40.409 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [paramsSummaryMap:paramsSummaryMap]; plugin Id: nf-schema
Feb-24 08:33:40.409 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [samplesheetToList:samplesheetToList]; plugin Id: nf-schema
Feb-24 08:33:40.462 [main] DEBUG nextflow.script.ScriptRunner - Parsed script files:
  Script_4c9f9bc851987489: /home/di/.nextflow/assets/nf-core/demultiplex/./workflows/../subworkflows/local/mkfastq_demultiplex/../../../modules/nf-core/cellranger/mkfastq/main.nf
  Script_135f64b745a80044: /home/di/.nextflow/assets/nf-core/demultiplex/./workflows/../modules/local/fastq_to_samplesheet/main.nf
  Script_0ce72e734ad77725: /home/di/.nextflow/assets/nf-core/demultiplex/./workflows/../subworkflows/local/utils_nfcore_demultiplex_pipeline/../../nf-core/utils_nextflow_pipeline/main.nf
  Script_78a38f6af741a872: /home/di/.nextflow/assets/nf-core/demultiplex/./workflows/../subworkflows/nf-core/fastq_contam_seqtk_kraken/../../../modules/nf-core/seqtk/sample/main.nf
  Script_de639b9212d9f01b: /home/di/.nextflow/assets/nf-core/demultiplex/./workflows/../subworkflows/nf-core/fastq_contam_seqtk_kraken/../../../modules/nf-core/kraken2/kraken2/main.nf
  Script_215a636da7ab24a2: /home/di/.nextflow/assets/nf-core/demultiplex/./subworkflows/local/utils_nfcore_demultiplex_pipeline/../../nf-core/utils_nfschema_plugin/main.nf
  Script_07ae51119a6c5038: /home/di/.nextflow/assets/nf-core/demultiplex/./workflows/../subworkflows/local/utils_nfcore_demultiplex_pipeline/../../nf-core/utils_nfcore_pipeline/main.nf
  Script_17b87265ecee922b: /home/di/.nextflow/assets/nf-core/demultiplex/./workflows/../subworkflows/nf-core/bcl_demultiplex/../../../modules/nf-core/bcl2fastq/main.nf
  Script_019b159e147f660f: /home/di/.nextflow/assets/nf-core/demultiplex/./workflows/../subworkflows/local/rundir_checkqc/../../../modules/nf-core/checkqc/main.nf
  Script_f28c7753320c73d3: /home/di/.nextflow/assets/nf-core/demultiplex/./workflows/../subworkflows/nf-core/bcl_demultiplex/main.nf
  Script_9f6ce129b29ed4a5: /home/di/.nextflow/assets/nf-core/demultiplex/./workflows/../modules/nf-core/fastp/main.nf
  Script_b23775daa269f1d5: /home/di/.nextflow/assets/nf-core/demultiplex/main.nf
  Script_931625db3bd17421: /home/di/.nextflow/assets/nf-core/demultiplex/./workflows/../subworkflows/local/bases_demultiplex/../../../modules/nf-core/bases2fastq/main.nf
  Script_4955288afd8ca61e: /home/di/.nextflow/assets/nf-core/demultiplex/./workflows/../modules/nf-core/multiqc/main.nf
  Script_ffbda26a6f1f93c6: /home/di/.nextflow/assets/nf-core/demultiplex/./workflows/../subworkflows/local/fqtk_demultiplex/../../../modules/nf-core/fqtk/main.nf
  Script_653e37925c366fd2: /home/di/.nextflow/assets/nf-core/demultiplex/./workflows/../subworkflows/local/bases_demultiplex/main.nf
  Script_3b12337d465898c8: /home/di/.nextflow/assets/nf-core/demultiplex/./subworkflows/local/utils_nfcore_demultiplex_pipeline/main.nf
  Script_223ca400878df5b0: /home/di/.nextflow/assets/nf-core/demultiplex/./workflows/../modules/nf-core/untar/main.nf
  Script_be7998a8dba04dbe: /home/di/.nextflow/assets/nf-core/demultiplex/./workflows/../subworkflows/local/mkfastq_demultiplex/main.nf
  Script_9d77a340ae7efb93: /home/di/.nextflow/assets/nf-core/demultiplex/./workflows/../subworkflows/nf-core/bcl_demultiplex/../../../modules/nf-core/bclconvert/main.nf
  Script_1666ce5f669c3956: /home/di/.nextflow/assets/nf-core/demultiplex/./workflows/../subworkflows/local/fqtk_demultiplex/main.nf
  Script_42ef361bc0cc2a26: /home/di/.nextflow/assets/nf-core/demultiplex/./workflows/../subworkflows/nf-core/fastq_contam_seqtk_kraken/main.nf
  Script_826df5eb1c762ecf: /home/di/.nextflow/assets/nf-core/demultiplex/./workflows/../subworkflows/local/rundir_checkqc/main.nf
  Script_3638011c9808828b: /home/di/.nextflow/assets/nf-core/demultiplex/./workflows/../modules/nf-core/falco/main.nf
  Script_e8b6f4d8b7600a31: /home/di/.nextflow/assets/nf-core/demultiplex/./workflows/../subworkflows/local/fqtk_demultiplex/../../../modules/local/csv2tsv.nf
  Script_00f4e4139227314c: /home/di/.nextflow/assets/nf-core/demultiplex/./workflows/../modules/nf-core/samshee/main.nf
  Script_8dbd043e852b6710: /home/di/.nextflow/assets/nf-core/demultiplex/./workflows/demultiplex.nf
  Script_3ef78d626b5182df: /home/di/.nextflow/assets/nf-core/demultiplex/./workflows/../subworkflows/local/singular_demultiplex/../../../modules/nf-core/sgdemux/main.nf
  Script_780d594c2de06cfc: /home/di/.nextflow/assets/nf-core/demultiplex/./workflows/../modules/nf-core/md5sum/main.nf
  Script_996721420bcb8936: /home/di/.nextflow/assets/nf-core/demultiplex/./workflows/../subworkflows/local/singular_demultiplex/main.nf
  Script_c9854d042b852d83: /home/di/.nextflow/assets/nf-core/demultiplex/./workflows/../subworkflows/local/rundir_checkqc/../../../modules/local/checkqc_dir/main.nf
Feb-24 08:33:40.462 [main] DEBUG nextflow.Session - Session aborted -- Cause: Strings must not be null
Feb-24 08:33:40.464 [main] DEBUG nextflow.Session - 
Thread[#10,Finalizer,8,system]
  [email protected]/java.lang.Object.wait0(Native Method)
  [email protected]/java.lang.Object.wait(Object.java:366)
  [email protected]/java.lang.Object.wait(Object.java:339)
  [email protected]/java.lang.ref.NativeReferenceQueue.await(NativeReferenceQueue.java:48)
  [email protected]/java.lang.ref.ReferenceQueue.remove0(ReferenceQueue.java:158)
  [email protected]/java.lang.ref.NativeReferenceQueue.remove(NativeReferenceQueue.java:89)
  [email protected]/java.lang.ref.Finalizer$FinalizerThread.run(Finalizer.java:173)

Thread[#26,Common-Cleaner,8,InnocuousThreadGroup]
  [email protected]/jdk.internal.misc.Unsafe.park(Native Method)
  [email protected]/java.util.concurrent.locks.LockSupport.parkNanos(LockSupport.java:269)
  [email protected]/java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:1852)
  [email protected]/java.lang.ref.ReferenceQueue.await(ReferenceQueue.java:71)
  [email protected]/java.lang.ref.ReferenceQueue.remove0(ReferenceQueue.java:143)
  [email protected]/java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:218)
  [email protected]/jdk.internal.ref.CleanerImpl.run(CleanerImpl.java:140)
  [email protected]/java.lang.Thread.runWith(Thread.java:1596)
  [email protected]/java.lang.Thread.run(Thread.java:1583)
  [email protected]/jdk.internal.misc.InnocuousThread.run(InnocuousThread.java:186)

Thread[#50,Keep-Alive-Timer,8,InnocuousThreadGroup]
  [email protected]/java.lang.Thread.sleep0(Native Method)
  [email protected]/java.lang.Thread.sleep(Thread.java:509)
  [email protected]/sun.net.www.http.KeepAliveCache.run(KeepAliveCache.java:238)
  [email protected]/java.lang.Thread.runWith(Thread.java:1596)
  [email protected]/java.lang.Thread.run(Thread.java:1583)
  [email protected]/jdk.internal.misc.InnocuousThread.run(InnocuousThread.java:186)

Thread[#48,JGit-FileStoreAttributeReader-1,5,main]
  [email protected]/jdk.internal.misc.Unsafe.park(Native Method)
  [email protected]/java.util.concurrent.locks.LockSupport.park(LockSupport.java:371)
  [email protected]/java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionNode.block(AbstractQueuedSynchronizer.java:519)
  [email protected]/java.util.concurrent.ForkJoinPool.unmanagedBlock(ForkJoinPool.java:3780)
  [email protected]/java.util.concurrent.ForkJoinPool.managedBlock(ForkJoinPool.java:3725)
  [email protected]/java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:1712)
  [email protected]/java.util.concurrent.LinkedBlockingQueue.take(LinkedBlockingQueue.java:435)
  [email protected]/java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1070)
  [email protected]/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1130)
  [email protected]/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:642)
  [email protected]/java.lang.Thread.runWith(Thread.java:1596)
  [email protected]/java.lang.Thread.run(Thread.java:1583)

Thread[#53,Actor Thread 1,5,main]
  [email protected]/jdk.internal.misc.Unsafe.park(Native Method)
  [email protected]/java.util.concurrent.locks.LockSupport.park(LockSupport.java:371)
  [email protected]/java.util.concurrent.LinkedTransferQueue$DualNode.await(LinkedTransferQueue.java:458)
  [email protected]/java.util.concurrent.SynchronousQueue$Transferer.xferLifo(SynchronousQueue.java:194)
  [email protected]/java.util.concurrent.SynchronousQueue.xfer(SynchronousQueue.java:235)
  [email protected]/java.util.concurrent.SynchronousQueue.take(SynchronousQueue.java:318)
  [email protected]/java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1070)
  [email protected]/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1130)
  [email protected]/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:642)
  [email protected]/java.lang.Thread.runWith(Thread.java:1596)
  [email protected]/java.lang.Thread.run(Thread.java:1583)

Thread[#54,AnsiLogObserver,5,main]
  [email protected]/java.lang.Object.wait0(Native Method)
  [email protected]/java.lang.Object.wait(Object.java:366)
  app//nextflow.trace.AnsiLogObserver.render0(AnsiLogObserver.groovy:185)
  [email protected]/java.lang.invoke.DirectMethodHandle$Holder.invokeVirtual(DirectMethodHandle$Holder)
  [email protected]/java.lang.invoke.LambdaForm$MH/0x0000774ee8405800.invoke(LambdaForm$MH)
  [email protected]/java.lang.invoke.Invokers$Holder.invokeExact_MT(Invokers$Holder)
  [email protected]/jdk.internal.reflect.DirectMethodHandleAccessor.invokeImpl(DirectMethodHandleAccessor.java:154)
  [email protected]/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:103)
  [email protected]/java.lang.reflect.Method.invoke(Method.java:580)
  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)
  [email protected]/java.lang.Thread.runWith(Thread.java:1596)
  [email protected]/java.lang.Thread.run(Thread.java:1583)

Thread[#1,main,5,main]
  [email protected]/java.lang.Thread.dumpThreads(Native Method)
  [email protected]/java.lang.Thread.getAllStackTraces(Thread.java:2522)
  app//nextflow.util.SysHelper.dumpThreads(SysHelper.groovy:188)
  app//nextflow.Session.abort(Session.groovy:800)
  app//nextflow.script.ScriptRunner.execute(ScriptRunner.groovy:149)
  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[#11,Signal Dispatcher,9,system]

Thread[#9,Reference Handler,10,system]
  [email protected]/java.lang.ref.Reference.waitForReferencePendingList(Native Method)
  [email protected]/java.lang.ref.Reference.processPendingReferences(Reference.java:246)
  [email protected]/java.lang.ref.Reference$ReferenceHandler.run(Reference.java:208)

Thread[#45,process reaper,10,InnocuousThreadGroup]
  [email protected]/jdk.internal.misc.Unsafe.park(Native Method)
  [email protected]/java.util.concurrent.locks.LockSupport.parkNanos(LockSupport.java:410)
  [email protected]/java.util.concurrent.LinkedTransferQueue$DualNode.await(LinkedTransferQueue.java:452)
  [email protected]/java.util.concurrent.SynchronousQueue$Transferer.xferLifo(SynchronousQueue.java:194)
  [email protected]/java.util.concurrent.SynchronousQueue.xfer(SynchronousQueue.java:235)
  [email protected]/java.util.concurrent.SynchronousQueue.poll(SynchronousQueue.java:338)
  [email protected]/java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1069)
  [email protected]/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1130)
  [email protected]/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:642)
  [email protected]/java.lang.Thread.runWith(Thread.java:1596)
  [email protected]/java.lang.Thread.run(Thread.java:1583)
  [email protected]/jdk.internal.misc.InnocuousThread.run(InnocuousThread.java:186)

Thread[#27,Notification Thread,9,system]

Thread[#52,Thread-4,5,main]
  [email protected]/jdk.internal.misc.Unsafe.park(Native Method)
  [email protected]/java.util.concurrent.locks.LockSupport.parkNanos(LockSupport.java:269)
  [email protected]/java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.awaitNanos(AbstractQueuedSynchronizer.java:1763)
  [email protected]/java.util.concurrent.LinkedBlockingDeque.pollFirst(LinkedBlockingDeque.java:515)
  [email protected]/java.util.concurrent.LinkedBlockingDeque.poll(LinkedBlockingDeque.java:677)
  app//nextflow.util.SimpleAgent.run(SimpleAgent.groovy:89)
  [email protected]/java.lang.invoke.LambdaForm$DMH/0x0000774ee81b3400.invokeVirtual(LambdaForm$DMH)
  [email protected]/java.lang.invoke.LambdaForm$MH/0x0000774ee84a0000.invoke(LambdaForm$MH)
  [email protected]/java.lang.invoke.Invokers$Holder.invokeExact_MT(Invokers$Holder)
  [email protected]/jdk.internal.reflect.DirectMethodHandleAccessor.invokeImpl(DirectMethodHandleAccessor.java:153)
  [email protected]/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:103)
  [email protected]/java.lang.reflect.Method.invoke(Method.java:580)
  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)
  [email protected]/java.lang.Thread.runWith(Thread.java:1596)
  [email protected]/java.lang.Thread.run(Thread.java:1583)

Feb-24 08:33:40.468 [main] ERROR nextflow.cli.Launcher - Strings must not be null
java.lang.IllegalArgumentException: Strings must not be null
	at org.apache.commons.lang.StringUtils.getLevenshteinDistance(StringUtils.java:6256)
	at org.codehaus.groovy.vmplugin.v8.IndyInterface.selectMethod(IndyInterface.java:355)
	at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321)
	at nextflow.extension.Bolts$_closest_closure8.doCall(Bolts.groovy:748)
	at java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:103)
	at java.base/java.lang.reflect.Method.invoke(Method.java:580)
	at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:343)
	at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:328)
	at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:279)
	at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1007)
	at groovy.lang.Closure.call(Closure.java:433)
	at groovy.lang.Closure.call(Closure.java:422)
	at org.codehaus.groovy.runtime.DefaultGroovyMethods.each(DefaultGroovyMethods.java:2394)
	at org.codehaus.groovy.runtime.DefaultGroovyMethods.each(DefaultGroovyMethods.java:2379)
	at org.codehaus.groovy.runtime.DefaultGroovyMethods.each(DefaultGroovyMethods.java:2432)
	at org.codehaus.groovy.runtime.dgm$209.doMethodInvoke(Unknown Source)
	at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321)
	at nextflow.extension.Bolts.closest(Bolts.groovy:747)
	at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321)
	at nextflow.script.BaseScript.run0(BaseScript.groovy:168)
	at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321)
	at nextflow.script.BaseScript.run(BaseScript.groovy:209)
	at nextflow.script.ScriptParser.runScript(ScriptParser.groovy:236)
	at nextflow.script.ScriptRunner.run(ScriptRunner.groovy:243)
	at nextflow.script.ScriptRunner.execute(ScriptRunner.groovy:138)
	at nextflow.cli.CmdRun.run(CmdRun.groovy:376)
	at nextflow.cli.Launcher.run(Launcher.groovy:503)
	at nextflow.cli.Launcher.main(Launcher.groovy:658)

Environment

  • Nextflow version: 24.10.4
  • Java version: openjdk 21.0.6 2025-01-21
  • Operating system: Ubuntu 24.04.1
  • Bash version: GNU bash, version 5.2.21(1)-release (x86_64-pc-linux-gnu)
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@DriesSchaumont