local nextflow.conf caused error

[mictadlo]

Hi, Thank you. I tried to override the resource settings with the below file for this workflow.

> cat nextflow.config
process {
  withName: 'deseq2' {
    memory = 60 GB
    CPU = 24
    time = 15 h
  }
}

Unfortuntely, I got this error:

$ nextflow run hoelzer-lab/rnaflow -r pbspro -profile test,singularity,pbspro --cores 1 --max_cores 1 -resume --singularityCacheDir /home/lorencm/.nextflow/NXF_SINGULARITY_CACHEDIR


Feb-21 09:58:43.188 [main] ERROR nextflow.cli.Launcher - Unable to parse config file: '/mnt/hpccs01/scratch/waterhouse_team/chamilka/qld/test/nextflow.config'

  No signature of method: java.lang.Integer.call() is applicable for argument types: (ConfigObject) values: [[:]]
  Possible solutions: wait(), any(), abs(), wait(long), tap(groovy.lang.Closure), any(groovy.lang.Closure)

groovy.lang.MissingMethodException: No signature of method: java.lang.Integer.call() is applicable for argument types: (ConfigObject) values: [[:]]
Possible solutions: wait(), any(), abs(), wait(long), tap(groovy.lang.Closure), any(groovy.lang.Closure)
        at org.codehaus.groovy.runtime.ScriptBytecodeAdapter.unwrap(ScriptBytecodeAdapter.java:70)
        at org.codehaus.groovy.runtime.callsite.PojoMetaClassSite.call(PojoMetaClassSite.java:46)
        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 _nf_config_91a5c13c$_run_closure1$_closure2.doCall(_nf_config_91a5c13c:3)
        at _nf_config_91a5c13c$_run_closure1$_closure2.doCall(_nf_config_91a5c13c)
        at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
        at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.base/java.lang.reflect.Method.invoke(Method.java:566)
        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:274)
        at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1030)
        at org.codehaus.groovy.runtime.callsite.PogoMetaClassSite.call(PogoMetaClassSite.java:38)
        at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:47)
        at org.codehaus.groovy.runtime.callsite.PogoMetaClassSite.call(PogoMetaClassSite.java:53)
        at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:130)
        at nextflow.config.ConfigParser$_parse_closure5.doCall(ConfigParser.groovy:427)
        at jdk.internal.reflect.GeneratedMethodAccessor7.invoke(Unknown Source)
        at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.base/java.lang.reflect.Method.invoke(Method.java:566)
        at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:107)
        at org.codehaus.groovy.runtime.metaclass.ClosureMetaMethod.invoke(ClosureMetaMethod.java:83)
        at groovy.lang.ExpandoMetaClass.invokeMethod(ExpandoMetaClass.java:1118)
        at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1030)
        at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:814)
        at groovy.lang.DelegatingMetaClass.invokeMethod(DelegatingMetaClass.java:140)
        at groovy.lang.GroovyObject.invokeMethod(GroovyObject.java:39)
        at groovy.lang.Script.invokeMethod(Script.java:96)
        at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeOnDelegationObjects(ClosureMetaClass.java:408)
        at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:348)
        at org.codehaus.groovy.runtime.callsite.PogoMetaClassSite.callCurrent(PogoMetaClassSite.java:61)
        at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallCurrent(CallSiteArray.java:51)
        at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:171)
        at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:185)
        at _nf_config_91a5c13c$_run_closure1.doCall(_nf_config_91a5c13c:2)
        at _nf_config_91a5c13c$_run_closure1.doCall(_nf_config_91a5c13c)
        at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
        at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.base/java.lang.reflect.Method.invoke(Method.java:566)
        at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:107)
        at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:323)
        at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:274)
        at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1030)
        at org.codehaus.groovy.runtime.callsite.PogoMetaClassSite.call(PogoMetaClassSite.java:38)
        at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:47)
        at org.codehaus.groovy.runtime.callsite.PogoMetaClassSite.call(PogoMetaClassSite.java:53)
        at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:130)
        at nextflow.config.ConfigParser$_parse_closure5.doCall(ConfigParser.groovy:427)
        at jdk.internal.reflect.GeneratedMethodAccessor7.invoke(Unknown Source)
        at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.base/java.lang.reflect.Method.invoke(Method.java:566)
        at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:107)
        at org.codehaus.groovy.runtime.metaclass.ClosureMetaMethod.invoke(ClosureMetaMethod.java:83)
        at groovy.lang.ExpandoMetaClass.invokeMethod(ExpandoMetaClass.java:1118)

Please find attached the log file (
nextflow.log.txt
)

I also open an github issues here

What did I miss?

Michal

[pditommaso]

You need to use either time = '15 h' or time = 15.h

[mictadlo]

Hi,
Thank you, I changed it to:

> cat nextflow.config 
process {
  withName: 'deseq2' {
    memory = 60.GB
    CPU = 24
    time = 15.h
  }
}

but unfortunately, I got this error:

Mar-01 09:50:09.659 [main] DEBUG nextflow.Session - Session start
Mar-01 09:50:09.690 [main] DEBUG nextflow.cli.Launcher - Operation aborted
nextflow.exception.AbortOperationException: Report file already exists: /mnt/hpccs01/scratch/waterhouse_team/chamilka/qld/test/results/Logs/execution_report.html -- enable the 'report.overwrite' option in your config file to overwrite existing files
        at nextflow.trace.ReportObserver.onFlowCreate(ReportObserver.groovy:133)
        at nextflow.Session$_notifyFlowCreate_closure23.doCall(Session.groovy:1087)
        at nextflow.Session$_notifyFlowCreate_closure23.call(Session.groovy)
        at org.codehaus.groovy.runtime.DefaultGroovyMethods.each(DefaultGroovyMethods.java:2357)
        at org.codehaus.groovy.runtime.DefaultGroovyMethods.each(DefaultGroovyMethods.java:2342)
        at org.codehaus.groovy.runtime.DefaultGroovyMethods.each(DefaultGroovyMethods.java:2383)
        at nextflow.Session.notifyFlowCreate(Session.groovy:1087)
        at nextflow.Session.start(Session.groovy:549)
        at nextflow.script.ScriptRunner.execute(ScriptRunner.groovy:131)
        at nextflow.cli.CmdRun.run(CmdRun.groovy:372)
        at nextflow.cli.Launcher.run(Launcher.groovy:500)
        at nextflow.cli.Launcher.main(Launcher.groovy:672)

What did I miss?

Michal

[bentsherman]

The solution is in the error message 😄

[mictadlo]

Thank you, but where can I find the config file to enable the 'report.overwrite' option?