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This repository has been archived by the owner on Aug 20, 2024. It is now read-only.
When resuming a pipeline with ImmutableMap meta, following warnings are given:
WARN: [CMGG_CMGGSTRUCTURAL:CMGGSTRUCTURAL:BAM_REPEAT_ESTIMATION_EXPANSIONHUNTER:EXPANSIONHUNTER (1)] Unable to resume cached task -- See log file for details
WARN: [CMGG_CMGGSTRUCTURAL:CMGGSTRUCTURAL:BAM_REPEAT_ESTIMATION_EXPANSIONHUNTER:EXPANSIONHUNTER (4)] Unable to resume cached task -- See log file for details
WARN: [CMGG_CMGGSTRUCTURAL:CMGGSTRUCTURAL:BAM_REPEAT_ESTIMATION_EXPANSIONHUNTER:EXPANSIONHUNTER (2)] Unable to resume cached task -- See log file for details
WARN: [CMGG_CMGGSTRUCTURAL:CMGGSTRUCTURAL:BAM_REPEAT_ESTIMATION_EXPANSIONHUNTER:EXPANSIONHUNTER (3)] Unable to resume cached task -- See log file for details
WARN: [CMGG_CMGGSTRUCTURAL:CMGGSTRUCTURAL:BAM_REPEAT_ESTIMATION_EXPANSIONHUNTER:EXPANSIONHUNTER (5)] Unable to resume cached task -- See log file for details
With this as error in .nextflow.log:
com.esotericsoftware.kryo.KryoException: Unable to find class: nextflow.validation.ImmutableMap
at com.esotericsoftware.kryo.util.DefaultClassResolver.readName(DefaultClassResolver.java:138)
at com.esotericsoftware.kryo.util.DefaultClassResolver.readClass(DefaultClassResolver.java:115)
at com.esotericsoftware.kryo.Kryo.readClass(Kryo.java:641)
at com.esotericsoftware.kryo.Kryo.readClassAndObject(Kryo.java:752)
at com.esotericsoftware.kryo.serializers.MapSerializer.read(MapSerializer.java:143)
at com.esotericsoftware.kryo.serializers.MapSerializer.read(MapSerializer.java:21)
at com.esotericsoftware.kryo.Kryo.readClassAndObject(Kryo.java:761)
at com.esotericsoftware.kryo.Kryo$readClassAndObject$8.call(Unknown Source)
at nextflow.util.KryoHelper.deserialize(SerializationHelper.groovy:181)
at nextflow.util.KryoHelper.deserialize(SerializationHelper.groovy)
at nextflow.util.KryoHelper$deserialize.call(Unknown Source)
at nextflow.processor.TaskContext.deserialize(TaskContext.groovy:202)
at nextflow.cache.CacheDB.getTaskEntry(CacheDB.groovy:88)
at nextflow.processor.TaskProcessor.checkCachedOrLaunchTask(TaskProcessor.groovy:770)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:568)
at org.codehaus.groovy.runtime.callsite.PlainObjectMetaMethodSite.doInvoke(PlainObjectMetaMethodSite.java:48)
at org.codehaus.groovy.runtime.callsite.PogoMetaMethodSite$PogoCachedMethodSiteNoUnwrapNoCoerce.invoke(PogoMetaMethodSite.java:189)
at org.codehaus.groovy.runtime.callsite.PogoMetaMethodSite.callCurrent(PogoMetaMethodSite.java:57)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:203)
at nextflow.processor.TaskProcessor.invokeTask(TaskProcessor.groovy:618)
at nextflow.processor.InvokeTaskAdapter.call(InvokeTaskAdapter.groovy:52)
at groovyx.gpars.dataflow.operator.DataflowOperatorActor.startTask(DataflowOperatorActor.java:120)
at groovyx.gpars.dataflow.operator.ForkingDataflowOperatorActor.access$001(ForkingDataflowOperatorActor.java:35)
at groovyx.gpars.dataflow.operator.ForkingDataflowOperatorActor$1.run(ForkingDataflowOperatorActor.java:58)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1136)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635)
at java.base/java.lang.Thread.run(Thread.java:833)
Caused by: java.lang.ClassNotFoundException: nextflow.validation.ImmutableMap
at java.base/jdk.internal.loader.BuiltinClassLoader.loadClass(BuiltinClassLoader.java:641)
at java.base/jdk.internal.loader.ClassLoaders$AppClassLoader.loadClass(ClassLoaders.java:188)
at java.base/java.lang.ClassLoader.loadClass(ClassLoader.java:520)
at java.base/java.lang.Class.forName0(Native Method)
at java.base/java.lang.Class.forName(Class.java:467)
at com.esotericsoftware.kryo.util.DefaultClassResolver.readName(DefaultClassResolver.java:136)
... 29 common frames omitted
Possible solution: try to find a way to make ImmutableMap available to the main flow
The text was updated successfully, but these errors were encountered:
I would suggest turning of the use of ImmutableMap for now until this is fixed, you can still use it when running production code that does not need to be resumed
When resuming a pipeline with ImmutableMap meta, following warnings are given:
With this as error in
.nextflow.log
:Possible solution: try to find a way to make
ImmutableMap
available to the main flowThe text was updated successfully, but these errors were encountered: