Java error

[gurpreet-bioinfo]

Hi @hoelzer ,

Keep on getting the following error:

[Actor Thread 3] ERROR nextflow.extension.OperatorEx - @unknown
java.lang.IllegalArgumentException: Argument of `file` function cannot be null
	at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
	at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
	at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
	at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:490)
	at org.codehaus.groovy.reflection.CachedConstructor.invoke(CachedConstructor.java:72)
	at org.codehaus.groovy.reflection.CachedConstructor.doConstructorInvoke(CachedConstructor.java:59)
	at org.codehaus.groovy.runtime.callsite.ConstructorSite$ConstructorSiteNoUnwrap.callConstructor(ConstructorSite.java:84)
	at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallConstructor(CallSiteArray.java:59)
	at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callConstructor(AbstractCallSite.java:263)
	at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callConstructor(AbstractCallSite.java:277)
	at nextflow.Nextflow.file(Nextflow.groovy:146)
	at nextflow.Nextflow$file.callStatic(Unknown Source)
	at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallStatic(CallSiteArray.java:55)
	at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callStatic(AbstractCallSite.java:217)
	at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callStatic(AbstractCallSite.java:240)
	at Script_00383379$_runScript_closure1.doCall(Script_00383379:148)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.base/java.lang.reflect.Method.invoke(Method.java:566)
	at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:107)
	at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:323)
	at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:263)
	at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1026)
	at org.codehaus.groovy.runtime.callsite.PogoMetaClassSite.call(PogoMetaClassSite.java:38)
	at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:47)
	at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:125)
	at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:139)
	at nextflow.extension.MapOp$_apply_closure1.doCall(MapOp.groovy:57)
	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:263)
	at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1026)
	at groovy.lang.Closure.call(Closure.java:412)
	at groovyx.gpars.dataflow.operator.DataflowOperatorActor.startTask(DataflowOperatorActor.java:120)
	at groovyx.gpars.dataflow.operator.DataflowOperatorActor.onMessage(DataflowOperatorActor.java:108)
	at groovyx.gpars.actor.impl.SDAClosure$1.call(SDAClosure.java:43)
	at groovyx.gpars.actor.AbstractLoopingActor.runEnhancedWithoutRepliesOnMessages(AbstractLoopingActor.java:293)
	at groovyx.gpars.actor.AbstractLoopingActor.access$400(AbstractLoopingActor.java:30)
	at groovyx.gpars.actor.AbstractLoopingActor$1.handleMessage(AbstractLoopingActor.java:93)
	at groovyx.gpars.util.AsyncMessagingCore.run(AsyncMessagingCore.java:132)
	at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)
	at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
	at java.base/java.lang.Thread.run(Thread.java:834)

Even though loaded Java module, still the error persists.
Any pointers?

My commands from bash script (on slurm):

module load Singularity/3.5.2-GCC-5.4.0-2.26

nextflow run hoelzer-lab/rnaflow -r 1.2.2 --reads /rnaseq/project1/samples.csv --autodownload hsa --pathway hsa -resume
    --output /rnaseq/project1 

Also tried:

module load Singularity/3.5.2-GCC-5.4.0-2.26

nextflow run hoelzer-lab/rnaflow -r 1.2.2 --reads /rnaseq/project1/samples.csv --autodownload hsa --pathway hsa -resume
    --output /rnaseq/project1  -profile slurm,singularity

Thanks.

[hoelzer]

Hi @gurpreet-bioinfo !

What's your java --version?

I can not directly pinpoint what's going on here. Is nextflow generally working? So what if you try to run another pipeline? So for example:

nextflow run replikation/What_the_Phage -r v1.0.1 --cores 8 -profile smalltest,slurm,singularity

(I think this workflow is quite stable on SLURM+Singularity so it would be interesting if it runs through)

I think we did some tests on an HPC w/ SLURM (but likely using Conda and not Singularity) and it was working.

[gurpreet-bioinfo]

@hoelzer Java version is 11.0.2

Yes, nextflow is working as I am running another pipeline offline due to error with singularity images so downloaded the images and it's running smoothly.

[gurpreet-bioinfo]

@hoelzer Any pointers please? Thanks.

[hoelzer]

@gurpreet-bioinfo can you try the integrated test run for RNAflow?

nextflow run hoelzer-lab/rnaflow -r 1.2.2 -profile test,slurm,conda

and if this is working please try Singularity (if you don't want to continue w/ conda):

nextflow run hoelzer-lab/rnaflow -r 1.2.2 -profile test,slurm,singularity

If you run into issues while downloading the singularity images the first time, please try:

nextflow run hoelzer-lab/rnaflow -r 1.2.2 -profile test,slurm,singularity --cores 1 --max_cores 1

for the first setup and all container downloads.We experienced issues in particular on HPCs when images are downloaded and converted in parallel.

[hoelzer]

@gurpreet-bioinfo were you able to solve the problem?