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Issue mapping trait #78

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Issue mapping trait#78
@aoshaver

Description

@aoshaver
aoshaver
opened on Aug 4, 2025

command run:

nextflow run andersenlab/nemascan
--vcf 20210803
--traitfile /home/ashaver5/vast-eande106/projects/Amanda/projects/NemaScan/traitfiles/ABZ_ASSAY1_medians.tsv
--sthresh EIGEN
--species c_briggsae
--finemap TRUE
--out /home/ashaver5/vast-eande106/projects/Amanda/projects/NemaScan/output

error message:
-- Check script '/home/ashaver5/.nextflow/assets/andersenlab/nemascan/main.nf' at line: 171 or see '.nextflow.log' file for more details

Netflow log:

Aug-04 14:33:32.577 [main] DEBUG nextflow.cli.Launcher - $> nextflow run andersenlab/nemascan --vcf 20210803 --traitfile /home/ashaver5/vast-eande106/projects/Amanda/projects/NemaScan/traitfiles/ABZ_ASSAY1_medians.tsv --sthresh EIGEN --species c_briggsae --finemap TRUE --out /home/ashaver5/vast-eande106/projects/Amanda/projects/NemaScan/output
Aug-04 14:33:33.972 [main] DEBUG nextflow.cli.CmdRun - N E X T F L O W  ~  version 24.10.1
Aug-04 14:33:34.072 [main] DEBUG nextflow.plugin.PluginsFacade - Setting up plugin manager > mode=prod; embedded=false; plugins-dir=/home/ashaver5/.nextflow/plugins; core-plugins: nf-amazon@2.9.1,nf-azure@1.10.2,nf-cloudcache@0.4.2,nf-codecommit@0.2.2,nf-console@1.1.4,nf-google@1.15.2,nf-tower@1.9.3,nf-wave@1.7.3
Aug-04 14:33:34.177 [main] INFO  o.pf4j.DefaultPluginStatusProvider - Enabled plugins: []
Aug-04 14:33:34.178 [main] INFO  o.pf4j.DefaultPluginStatusProvider - Disabled plugins: []
Aug-04 14:33:34.182 [main] INFO  org.pf4j.DefaultPluginManager - PF4J version 3.12.0 in 'deployment' mode
Aug-04 14:33:34.274 [main] INFO  org.pf4j.AbstractPluginManager - No plugins
Aug-04 14:33:34.286 [main] DEBUG nextflow.scm.ProviderConfig - Using SCM config path: /home/ashaver5/.nextflow/scm
Aug-04 14:33:37.370 [main] DEBUG nextflow.scm.AssetManager - Git config: /home/ashaver5/.nextflow/assets/andersenlab/nemascan/.git/config; branch: null; remote: origin; url: https://github.com/AndersenLab/NemaScan.git
Aug-04 14:33:37.481 [main] DEBUG nextflow.scm.RepositoryFactory - Found Git repository result: [RepositoryFactory]
Aug-04 14:33:37.572 [main] DEBUG nextflow.scm.AssetManager - Git config: /home/ashaver5/.nextflow/assets/andersenlab/nemascan/.git/config; branch: null; remote: origin; url: https://github.com/AndersenLab/NemaScan.git
Aug-04 14:33:39.876 [main] DEBUG nextflow.config.ConfigBuilder - Found config base: /home/ashaver5/.nextflow/assets/andersenlab/nemascan/nextflow.config
Aug-04 14:33:39.877 [main] DEBUG nextflow.config.ConfigBuilder - Found config local: /vast/eande106/projects/Amanda/projects/NemaScan/nextflow.config
Aug-04 14:33:39.878 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /home/ashaver5/.nextflow/assets/andersenlab/nemascan/nextflow.config
Aug-04 14:33:39.879 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /vast/eande106/projects/Amanda/projects/NemaScan/nextflow.config
Aug-04 14:33:39.969 [main] DEBUG n.secret.LocalSecretsProvider - Secrets store: /home/ashaver5/.nextflow/secrets/store.json
Aug-04 14:33:39.971 [main] DEBUG nextflow.secret.SecretsLoader - Discovered secrets providers: [nextflow.secret.LocalSecretsProvider@1bedc703] - activable => nextflow.secret.LocalSecretsProvider@1bedc703
Aug-04 14:33:40.066 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `standard`
Aug-04 14:33:41.165 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `standard`
Aug-04 14:33:41.875 [main] DEBUG nextflow.cli.CmdRun - Applied DSL=2 from script declaration
Aug-04 14:33:41.876 [main] DEBUG nextflow.cli.CmdRun - Launching `https://github.com/andersenlab/nemascan` [focused_sinoussi] DSL2 - revision: 2f19f5f80d [master]
Aug-04 14:33:41.878 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins default=[]
Aug-04 14:33:41.878 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins resolved requirement=[]
Aug-04 14:33:42.084 [main] DEBUG nextflow.Session - Session UUID: a3f9dc08-2a09-4280-8781-d0911d875a3e
Aug-04 14:33:42.085 [main] DEBUG nextflow.Session - Run name: focused_sinoussi
Aug-04 14:33:42.085 [main] DEBUG nextflow.Session - Executor pool size: 2
Aug-04 14:33:42.170 [main] DEBUG nextflow.file.FilePorter - File porter settings maxRetries=3; maxTransfers=50; pollTimeout=null
Aug-04 14:33:42.174 [main] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'FileTransfer' minSize=10; maxSize=10; workQueue=LinkedBlockingQueue[10000]; allowCoreThreadTimeout=false
Aug-04 14:33:42.274 [main] DEBUG nextflow.cli.CmdRun - 
  Version: 24.10.1 build 5930
  Created: 18-11-2024 12:21 UTC (07:21 EDT)
  System: Linux 4.18.0-477.21.1.el8_8.x86_64
  Runtime: Groovy 4.0.23 on OpenJDK 64-Bit Server VM 17.0.13-internal+0-adhoc..src
  Encoding: UTF-8 (UTF-8)
  Process: 3015742@login03 [172.20.2.3]
  CPUs: 1 - Mem: 5 GB (4.1 GB) - Swap: 0 (0)
Aug-04 14:33:42.376 [main] DEBUG nextflow.Session - Work-dir: /scratch4/eande106/Amanda [gpfs]
Aug-04 14:33:42.671 [main] DEBUG nextflow.executor.ExecutorFactory - Extension executors providers=[]
Aug-04 14:33:42.680 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory
Aug-04 14:33:43.166 [main] DEBUG nextflow.cache.CacheFactory - Using Nextflow cache factory: nextflow.cache.DefaultCacheFactory
Aug-04 14:33:43.176 [main] DEBUG nextflow.util.CustomThreadPool - Creating default thread pool > poolSize: 2; maxThreads: 1000
Aug-04 14:33:43.482 [main] DEBUG nextflow.Session - Session start
Aug-04 14:33:48.473 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution
Aug-04 14:33:48.768 [main] DEBUG nextflow.script.ScriptRunner - Parsed script files:
  Script_42975fc9b318f7dc: /home/ashaver5/.nextflow/assets/andersenlab/nemascan/main.nf
Aug-04 14:33:48.768 [main] DEBUG nextflow.Session - Session aborted -- Cause: Cannot invoke method and() on null object
Aug-04 14:33:48.775 [main] DEBUG nextflow.Session - 
Thread[JGit-FileStoreAttributeReader-1,5,main]
  java.base@17.0.13-internal/jdk.internal.misc.Unsafe.park(Native Method)
  java.base@17.0.13-internal/java.util.concurrent.locks.LockSupport.park(LockSupport.java:341)
  java.base@17.0.13-internal/java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionNode.block(AbstractQueuedSynchronizer.java:506)
  java.base@17.0.13-internal/java.util.concurrent.ForkJoinPool.unmanagedBlock(ForkJoinPool.java:3465)
  java.base@17.0.13-internal/java.util.concurrent.ForkJoinPool.managedBlock(ForkJoinPool.java:3436)
  java.base@17.0.13-internal/java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:1630)
  java.base@17.0.13-internal/java.util.concurrent.LinkedBlockingQueue.take(LinkedBlockingQueue.java:435)
  java.base@17.0.13-internal/java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1062)
  java.base@17.0.13-internal/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1122)
  java.base@17.0.13-internal/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635)
  java.base@17.0.13-internal/java.lang.Thread.run(Thread.java:840)

Thread[Signal Dispatcher,9,system]

Thread[process reaper,10,system]
  java.base@17.0.13-internal/jdk.internal.misc.Unsafe.park(Native Method)
  java.base@17.0.13-internal/java.util.concurrent.locks.LockSupport.parkNanos(LockSupport.java:252)
  java.base@17.0.13-internal/java.util.concurrent.SynchronousQueue$TransferStack.transfer(SynchronousQueue.java:401)
  java.base@17.0.13-internal/java.util.concurrent.SynchronousQueue.poll(SynchronousQueue.java:903)
  java.base@17.0.13-internal/java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1061)
  java.base@17.0.13-internal/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1122)
  java.base@17.0.13-internal/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635)
  java.base@17.0.13-internal/java.lang.Thread.run(Thread.java:840)

Thread[Thread-4,5,main]
  java.base@17.0.13-internal/jdk.internal.misc.Unsafe.park(Native Method)
  java.base@17.0.13-internal/java.util.concurrent.locks.LockSupport.parkNanos(LockSupport.java:252)
  java.base@17.0.13-internal/java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.awaitNanos(AbstractQueuedSynchronizer.java:1679)
  java.base@17.0.13-internal/java.util.concurrent.LinkedBlockingDeque.pollFirst(LinkedBlockingDeque.java:515)
  java.base@17.0.13-internal/java.util.concurrent.LinkedBlockingDeque.poll(LinkedBlockingDeque.java:677)
  app//nextflow.util.SimpleAgent.run(SimpleAgent.groovy:89)
  java.base@17.0.13-internal/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
  java.base@17.0.13-internal/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
  java.base@17.0.13-internal/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
  java.base@17.0.13-internal/java.lang.reflect.Method.invoke(Method.java:569)
  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@17.0.13-internal/java.lang.Thread.run(Thread.java:840)

Thread[AnsiLogObserver,5,main]
  java.base@17.0.13-internal/java.lang.Object.wait(Native Method)
  app//nextflow.trace.AnsiLogObserver.render0(AnsiLogObserver.groovy:185)
  java.base@17.0.13-internal/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
  java.base@17.0.13-internal/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
  java.base@17.0.13-internal/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
  java.base@17.0.13-internal/java.lang.reflect.Method.invoke(Method.java:569)
  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@17.0.13-internal/java.lang.Thread.run(Thread.java:840)

Thread[Finalizer,8,system]
  java.base@17.0.13-internal/java.lang.Object.wait(Native Method)
  java.base@17.0.13-internal/java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:155)
  java.base@17.0.13-internal/java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:176)
  java.base@17.0.13-internal/java.lang.ref.Finalizer$FinalizerThread.run(Finalizer.java:172)

Thread[Common-Cleaner,8,InnocuousThreadGroup]
  java.base@17.0.13-internal/java.lang.Object.wait(Native Method)
  java.base@17.0.13-internal/java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:155)
  java.base@17.0.13-internal/jdk.internal.ref.CleanerImpl.run(CleanerImpl.java:140)
  java.base@17.0.13-internal/java.lang.Thread.run(Thread.java:840)
  java.base@17.0.13-internal/jdk.internal.misc.InnocuousThread.run(InnocuousThread.java:162)

Thread[main,5,main]
  java.base@17.0.13-internal/java.lang.Thread.dumpThreads(Native Method)
  java.base@17.0.13-internal/java.lang.Thread.getAllStackTraces(Thread.java:1671)
  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[Reference Handler,10,system]
  java.base@17.0.13-internal/java.lang.ref.Reference.waitForReferencePendingList(Native Method)
  java.base@17.0.13-internal/java.lang.ref.Reference.processPendingReferences(Reference.java:253)
  java.base@17.0.13-internal/java.lang.ref.Reference$ReferenceHandler.run(Reference.java:215)

Thread[Notification Thread,9,system]

Aug-04 14:33:48.781 [main] ERROR nextflow.cli.Launcher - @unknown
java.lang.NullPointerException: Cannot invoke method and() on null object
	at org.codehaus.groovy.runtime.NullObject.invokeMethod(NullObject.java:113)
	at org.codehaus.groovy.vmplugin.v8.IndyGuardsFiltersAndSignatures.invokeGroovyObjectInvoker(IndyGuardsFiltersAndSignatures.java:151)
	at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321)
	at Script_42975fc9b318f7dc.runScript(Script_42975fc9b318f7dc:171)
	at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321)
	at nextflow.script.BaseScript.run0(BaseScript.groovy:159)
	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)
(/data/eande106/software/conda_envs/nf24_env) [ashaver5@login03 NemaScan]$

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