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Running the latest commit of scrnaseq with nextflow 23.10.1 results in: ERROR ~ PosixFileAttributeView right after the start of the pipeline.
Updating nextflow to 24.04.3 fixes the problem.
So, it appears that the latest version of scrnaseq is not backwards compatible. If this is the case, it would be best if the pipeline checked the nextflow version on start and raised an error if the nextflow version was <24.
Jul-11 02:04:39.330 [Actor Thread 126] ERROR nextflow.extension.OperatorImpl - @unknown
java.lang.UnsupportedOperationException: PosixFileAttributeView
at com.google.cloud.storage.contrib.nio.CloudStorageFileSystemProvider.getFileAttributeView(CloudStorageFileSystemProvider.java:855)
at java.base/java.nio.file.Files.getFileAttributeView(Files.java:1790)
at java.base/java.nio.file.CopyMoveHelper.copyToForeignTarget(CopyMoveHelper.java:151)
at java.base/java.nio.file.CopyMoveHelper.moveToForeignTarget(CopyMoveHelper.java:193)
at java.base/java.nio.file.Files.move(Files.java:1433)
at nextflow.file.SimpleFileCollector.saveFile(SimpleFileCollector.groovy:102)
at nextflow.file.FileCollector.saveTo0(FileCollector.groovy:228)
at nextflow.file.FileCollector.saveTo(FileCollector.groovy:251)
at nextflow.file.FileCollector$saveTo.call(Unknown Source)
at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:47)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:125)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:139)
at nextflow.extension.CollectFileOp.emitItems(CollectFileOp.groovy:187)
at java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:103)
at java.base/java.lang.reflect.Method.invoke(Method.java:580)
at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:107)
at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:323)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1254)
at groovy.lang.MetaClassImpl.invokeMethodClosure(MetaClassImpl.java:1042)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1128)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1030)
at groovy.lang.Closure.call(Closure.java:427)
at groovy.lang.Closure.call(Closure.java:416)
at groovy.lang.Closure$call.call(Unknown Source)
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:139)
at nextflow.extension.DataflowHelper$3.afterStop(DataflowHelper.groovy:257)
at groovyx.gpars.dataflow.operator.DataflowProcessor.fireAfterStop(DataflowProcessor.java:324)
at groovyx.gpars.dataflow.operator.DataflowProcessorActor.afterStop(DataflowProcessorActor.java:59)
at java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:103)
at java.base/java.lang.reflect.Method.invoke(Method.java:580)
at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:107)
at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:323)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1254)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1030)
at org.codehaus.groovy.runtime.InvokerHelper.invokePojoMethod(InvokerHelper.java:1024)
at org.codehaus.groovy.runtime.InvokerHelper.invokeMethod(InvokerHelper.java:1015)
at groovyx.gpars.actor.Actor.callDynamic(Actor.java:369)
at groovyx.gpars.actor.Actor.handleTermination(Actor.java:320)
at groovyx.gpars.actor.AbstractLoopingActor.terminate(AbstractLoopingActor.java:204)
at groovyx.gpars.dataflow.operator.DataflowProcessor.terminate(DataflowProcessor.java:147)
at groovyx.gpars.dataflow.operator.DataflowProcessor$terminate$1.call(Unknown Source)
at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:47)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:125)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:130)
at nextflow.extension.DataflowHelper$_subscribeImpl_closure2.doCall(DataflowHelper.groovy:290)
at java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:103)
at java.base/java.lang.reflect.Method.invoke(Method.java:580)
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 groovy.lang.Closure.call(Closure.java:427)
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$1.handleMessage(AbstractLoopingActor.java:93)
at groovyx.gpars.util.AsyncMessagingCore.run(AsyncMessagingCore.java:132)
at java.base/java.util.concurrent.ThreadPerTaskExecutor$TaskRunner.run(ThreadPerTaskExecutor.java:314)
at java.base/java.lang.Thread.run(Thread.java:1583)
Jul-11 02:04:39.339 [Actor Thread 126] DEBUG nextflow.Session - Session aborted -- Cause: PosixFileAttributeView
Jul-11 02:04:39.365 [Actor Thread 126] DEBUG nextflow.Session - The following nodes are still active:
System information
Hardware: GCP VM
Executor: tried both GCP and local
Container engine: Docker
OS: Linux
Pipeline version: latest commit in the master branch
The text was updated successfully, but these errors were encountered:
I believe this is more related to the cloud setup than the pipeline itself, judging from
CloudStorageFileSystemProvider.java:855
Probably there's a nextflow bug related to GCP file storage in nextflow < 24. The pipeline itself can run on 23.04 (which is the nf-core standard minimal version atm), this is ensured by CI.
Description of the bug
Running the latest commit of scrnaseq with nextflow 23.10.1 results in:
ERROR ~ PosixFileAttributeView
right after the start of the pipeline.Updating nextflow to 24.04.3 fixes the problem.
So, it appears that the latest version of scrnaseq is not backwards compatible. If this is the case, it would be best if the pipeline checked the nextflow version on start and raised an error if the nextflow version was <24.
Command used and terminal output
Relevant files
The relevant section of the
.nextflow.log
:System information
master
branchThe text was updated successfully, but these errors were encountered: