[BUG] Cannot invoke method containsKey() on null object

[HocheolJang426]

Hi

I'm trying vsn-pipelines following your vignette here: https://vsn-pipelines-examples.readthedocs.io/en/latest/index.html

But when I'm running config, error comes;

In log file;
Apr-08 18:14:38.832 [main] DEBUG nextflow.cli.Launcher - $> nextflow -c com.config run vib-singlecell-nf/vsn-pipelines -entry scenic -r v0.25.0
Apr-08 18:14:39.057 [main] INFO nextflow.cli.CmdRun - N E X T F L O W ~ version 21.04.3
Apr-08 18:14:42.062 [main] DEBUG nextflow.scm.AssetManager - Git config: /home/users/hcjangimmuno/.nextflow/assets/vib-singlecell-nf/vsn-pipelines/.git/config; branch: master; remote: origin; url: https://github.com/vib-singlecell-nf/vsn-pipelines.git
Apr-08 18:14:42.107 [main] DEBUG nextflow.scm.AssetManager - Git config: /home/users/hcjangimmuno/.nextflow/assets/vib-singlecell-nf/vsn-pipelines/.git/config; branch: master; remote: origin; url: https://github.com/vib-singlecell-nf/vsn-pipelines.git
Apr-08 18:14:43.330 [main] INFO nextflow.cli.CmdRun - Launching vib-singlecell-nf/vsn-pipelines [hopeful_bassi] - revision: 721c42f [v0.25.0]
Apr-08 18:14:44.234 [main] DEBUG nextflow.config.ConfigBuilder - Found config base: /home/users/hcjangimmuno/.nextflow/assets/vib-singlecell-nf/vsn-pipelines/nextflow.config
Apr-08 18:14:44.244 [main] DEBUG nextflow.config.ConfigBuilder - User config file: /home/users/hcjangimmuno/com.config
Apr-08 18:14:44.245 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /home/users/hcjangimmuno/.nextflow/assets/vib-singlecell-nf/vsn-pipelines/nextflow.config
Apr-08 18:14:44.245 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /home/users/hcjangimmuno/com.config
Apr-08 18:14:44.266 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: standard
Apr-08 18:14:45.447 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: standard
Apr-08 18:14:45.975 [main] DEBUG nextflow.plugin.PluginsFacade - Setting up plugin manager > mode=prod; plugins-dir=/home/users/hcjangimmuno/.nextflow/plugins
Apr-08 18:14:46.007 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins default=[]
Apr-08 18:14:46.019 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins local root: .nextflow/plr/empty
Apr-08 18:14:46.041 [main] INFO org.pf4j.DefaultPluginStatusProvider - Enabled plugins: []
Apr-08 18:14:46.043 [main] INFO org.pf4j.DefaultPluginStatusProvider - Disabled plugins: []
Apr-08 18:14:46.056 [main] INFO org.pf4j.DefaultPluginManager - PF4J version 3.4.1 in 'deployment' mode
Apr-08 18:14:46.101 [main] INFO org.pf4j.AbstractPluginManager - No plugins
Apr-08 18:14:46.228 [main] DEBUG nextflow.Session - Session uuid: b72845a8-d20e-4657-84c4-e7c38509d0da
Apr-08 18:14:46.228 [main] DEBUG nextflow.Session - Run name: hopeful_bassi
Apr-08 18:14:46.255 [main] DEBUG nextflow.Session - Executor pool size: 24
Apr-08 18:14:46.322 [main] DEBUG nextflow.cli.CmdRun -
Version: 21.04.3 build 5560
Created: 21-07-2021 15:09 UTC (22-07-2021 00:09 KDT)
System: Linux 3.10.0-862.el7.x86_64
Runtime: Groovy 3.0.7 on OpenJDK 64-Bit Server VM 1.8.0_292-b10
Encoding: UTF-8 (ANSI_X3.4-1968)
Process: 192293@bnode15 [10.0.2.15]
CPUs: 24 - Mem: 1007.8 GB (66.5 GB) - Swap: 0 (0)
Apr-08 18:14:46.406 [main] DEBUG nextflow.Session - Work-dir: /home/users/hcjangimmuno/work [lustre]
Apr-08 18:14:46.407 [main] DEBUG nextflow.Session - Script base path does not exist or is not a directory: /home/users/hcjangimmuno/.nextflow/assets/vib-singlecell-nf/vsn-pipelines/bin
Apr-08 18:14:46.431 [main] DEBUG nextflow.executor.ExecutorFactory - Extension executors providers=[]
Apr-08 18:14:46.461 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory
Apr-08 18:14:47.736 [main] DEBUG nextflow.Session - Session start invoked
Apr-08 18:14:47.741 [main] DEBUG nextflow.trace.TraceFileObserver - Flow starting -- trace file: /home/users/hcjangimmuno/out/nextflow_reports/execution_trace.txt
Apr-08 18:14:49.572 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution
Apr-08 18:14:53.640 [main] DEBUG nextflow.Session - Workflow process names [dsl2]: COMPRESS_HDF5, SC__FILE_CONVERTER_FROM_SCE, SC__FILE_CONCATENATOR, SC__PUBLISH, SC__STAR_CONCATENATOR, SC__FILE_CONVERTER
Apr-08 18:14:53.990 [main] DEBUG nextflow.Session - Session aborted -- Cause: Cannot invoke method containsKey() on null object
Apr-08 18:14:54.021 [main] DEBUG nextflow.Session - The following nodes are still active:
[operator] view

Apr-08 18:14:54.043 [main] ERROR nextflow.cli.Launcher - @unknown
java.lang.NullPointerException: Cannot invoke method containsKey() on null object
at org.codehaus.groovy.runtime.NullObject.invokeMethod(NullObject.java:91)
at org.codehaus.groovy.runtime.callsite.PogoMetaClassSite.call(PogoMetaClassSite.java:44)
at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:47)
at org.codehaus.groovy.runtime.callsite.NullCallSite.call(NullCallSite.java:34)
at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:47)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:125)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:139)
at Script_7c29aa5e.runScript(Script_7c29aa5e:9)
at nextflow.script.BaseScript.runDsl2(BaseScript.groovy:170)
at nextflow.script.BaseScript.run(BaseScript.groovy:200)
at nextflow.script.ScriptParser.runScript(ScriptParser.groovy:221)
at nextflow.script.ScriptParser.runScript(ScriptParser.groovy:207)
at nextflow.script.ScriptParser.runScript(ScriptParser.groovy:201)
at nextflow.script.IncludeDef.memoizedMethodPriv$loadModule0PathMapSession(IncludeDef.groovy:142)
at nextflow.script.IncludeDef.access$0(IncludeDef.groovy)
at nextflow.script.IncludeDef$__clinit__closure1.doCall(IncludeDef.groovy)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:107)
at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:323)
at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:263)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1035)
at groovy.lang.Closure.call(Closure.java:412)
at org.codehaus.groovy.runtime.memoize.Memoize$MemoizeFunction.lambda$call$0(Memoize.java:137)
at org.codehaus.groovy.runtime.memoize.ConcurrentCommonCache.getAndPut(ConcurrentCommonCache.java:137)
at org.codehaus.groovy.runtime.memoize.ConcurrentCommonCache.getAndPut(ConcurrentCommonCache.java:113)
at org.codehaus.groovy.runtime.memoize.Memoize$MemoizeFunction.call(Memoize.java:136)
at nextflow.script.IncludeDef.loadModule0(IncludeDef.groovy)
at nextflow.script.IncludeDef.load0(IncludeDef.groovy:114)
at nextflow.script.IncludeDef$load0$2.call(Unknown Source)
at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:47)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:125)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:139)
at Script_fc2ccf76$_runScript_closure21$_closure75.doCall(Script_fc2ccf76:735)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:107)
at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:323)
at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:263)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1035)
at groovy.lang.Closure.call(Closure.java:412)
at groovy.lang.Closure.call(Closure.java:406)
at nextflow.script.WorkflowDef.run0(WorkflowDef.groovy:186)
at nextflow.script.WorkflowDef.run(WorkflowDef.groovy:170)
at nextflow.script.BindableDef.invoke_a(BindableDef.groovy:52)
at nextflow.script.ChainableDef$invoke_a.call(Unknown Source)
at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:47)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:125)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:139)
at nextflow.script.BaseScript.runDsl2(BaseScript.groovy:191)
at nextflow.script.BaseScript.run(BaseScript.groovy:200)
at nextflow.script.ScriptParser.runScript(ScriptParser.groovy:221)
at nextflow.script.ScriptRunner.run(ScriptRunner.groovy:212)
at nextflow.script.ScriptRunner.execute(ScriptRunner.groovy:120)
at nextflow.cli.CmdRun.run(CmdRun.groovy:302)
at nextflow.cli.Launcher.run(Launcher.groovy:475)
at nextflow.cli.Launcher.main(Launcher.groovy:657)

How can I solve this problem?
my nextflow version 21.04.3, and pipelines is [v0.25.0]

[mellyS]

Hi @HocheolJang426
I am experiencing the same issue. Were you able to solve it ?

[HocheolJang426]

No, I did not solved this issue.
Actually, I gave up this code