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Queue remains open when data is staged from an external source #2502

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ellisrichardj opened this issue Dec 17, 2021 · 1 comment
Closed

Queue remains open when data is staged from an external source #2502

ellisrichardj opened this issue Dec 17, 2021 · 1 comment
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@ellisrichardj
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Bug report

Expected behavior and actual behavior

Expected: Pipeline runs to completion without errors
Actual: Crashes due to open queue linked to collectfile

Steps to reproduce the problem

Github repo here: [https://github.com/APHA-CSU/btb-seq/tree/s3direct]
Run as follows:
nextflow run APHA-CSU/btb-seq -r s3direct --reads="s3://s3-bucket/*_{S*_R1,S*_R2}*.fastq.gz"

The pipeline runs as expected, but fails as the CombineOutput process cannot be initiated. The output attached below indicates that one of the collectFile operator queues is remains open. The offending snippet is here.

AssignCluster
	.collectFile( name: "${params.DataDir}_AssignedWGSCluster_${params.today}.csv", sort: true, storeDir: "$params.outdir/Results_${params.DataDir}_${params.today}", keepHeader: true )
	.set {Assigned}

QueryBovis
	.collectFile( name: "${params.DataDir}_BovPos_${params.today}.csv", sort: true, storeDir: "$params.outdir/Results_${params.DataDir}_${params.today}", keepHeader: true )
	.set {Qbovis}

process CombineOutput {
	publishDir "$params.outdir/Results_${params.DataDir}_${params.today}", mode: 'copy', pattern: '*.csv'
	
	input:
	file('Assigned.csv') from Assigned
	file('Qbovis.csv') from Qbovis

	output:
	file '*.csv' into FinalOut

	"""
	combineCsv.py Assigned.csv Qbovis.csv ${params.DataDir}
	"""
}

Program output

error.nextflow.log

Specifically, the error is shown here:

Caused by:
  Oops.. something wrong happened while creating task 'CombineOutput' unique id -- Offending keys: [
 - type=java.util.UUID value=0ad5d850-cdf0-4713-9f76-81413e61fdd0,
 - type=java.lang.String value=CombineOutput,
 - type=java.lang.String value="""
	combineCsv.py Assigned.csv Qbovis.csv ${params.DataDir}
	"""
,
 - type=java.lang.String value=Assigned.csv,
 - type=nextflow.util.ArrayBag value=[FileHolder(sourceObj:/processing/TestDec21/work/stage/6e/9e76fa42efffae5a0de0ec944d13af/NB552234_0093_AssignedWGSCluster_17Dec21.csv, storePath:/processing/TestDec21/work/stage/6e/9e76fa42efffae5a0de0ec944d13af/NB552234_0093_AssignedWGSCluster_17Dec21.csv, stageName:Assigned.csv)],
 - type=java.lang.String value=Qbovis.csv,
 - type=nextflow.util.ArrayBag value=[FileHolder(sourceObj:/processing/TestDec21/work/stage/6a/18d54fffd943dfbcb59fc063a57a77/NB552234_0093_BovPos_17Dec21.csv, storePath:/processing/TestDec21/work/stage/6a/18d54fffd943dfbcb59fc063a57a77/NB552234_0093_BovPos_17Dec21.csv, stageName:Qbovis.csv)],
 - type=java.lang.String value=$,
 - type=java.lang.Boolean value=true,
 - type=java.util.HashMap$EntrySet value=[params.DataDir=NB552234_0093],
 - type=sun.nio.fs.UnixPath value=/home/richardellis/btb-seq-2dev/btb-seq/bin/combineCsv.py]

nextflow.exception.UnexpectedException: Oops.. something wrong happened while creating task 'CombineOutput' unique id -- Offending keys: [
 - type=java.util.UUID value=0ad5d850-cdf0-4713-9f76-81413e61fdd0,
 - type=java.lang.String value=CombineOutput,
 - type=java.lang.String value="""
	combineCsv.py Assigned.csv Qbovis.csv ${params.DataDir}
	"""
,
 - type=java.lang.String value=Assigned.csv,
 - type=nextflow.util.ArrayBag value=[FileHolder(sourceObj:/processing/TestDec21/work/stage/6e/9e76fa42efffae5a0de0ec944d13af/NB552234_0093_AssignedWGSCluster_17Dec21.csv, storePath:/processing/TestDec21/work/stage/6e/9e76fa42efffae5a0de0ec944d13af/NB552234_0093_AssignedWGSCluster_17Dec21.csv, stageName:Assigned.csv)],
 - type=java.lang.String value=Qbovis.csv,
 - type=nextflow.util.ArrayBag value=[FileHolder(sourceObj:/processing/TestDec21/work/stage/6a/18d54fffd943dfbcb59fc063a57a77/NB552234_0093_BovPos_17Dec21.csv, storePath:/processing/TestDec21/work/stage/6a/18d54fffd943dfbcb59fc063a57a77/NB552234_0093_BovPos_17Dec21.csv, stageName:Qbovis.csv)],
 - type=java.lang.String value=$,
 - type=java.lang.Boolean value=true,
 - type=java.util.HashMap$EntrySet value=[params.DataDir=NB552234_0093],
 - type=sun.nio.fs.UnixPath value=/home/richardellis/btb-seq-2dev/btb-seq/bin/combineCsv.py]
	at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
	at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
	at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
	at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:490)
	at org.codehaus.groovy.reflection.CachedConstructor.invoke(CachedConstructor.java:72)
	at org.codehaus.groovy.reflection.CachedConstructor.doConstructorInvoke(CachedConstructor.java:59)
	at org.codehaus.groovy.runtime.callsite.ConstructorSite$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:286)
	at nextflow.processor.TaskProcessor.computeHash(TaskProcessor.groovy:1988)
	at nextflow.processor.TaskProcessor$computeHash$5.callCurrent(Unknown Source)
	at nextflow.processor.TaskProcessor.createTaskHashKey(TaskProcessor.groovy:1975)
	at jdk.internal.reflect.GeneratedMethodAccessor220.invoke(Unknown Source)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.base/java.lang.reflect.Method.invoke(Method.java:566)
	at org.codehaus.groovy.runtime.callsite.PlainObjectMetaMethodSite.doInvoke(PlainObjectMetaMethodSite.java:43)
	at org.codehaus.groovy.runtime.callsite.PogoMetaMethodSite$PogoCachedMethodSiteNoUnwrapNoCoerce.invoke(PogoMetaMethodSite.java:193)
	at org.codehaus.groovy.runtime.callsite.PogoMetaMethodSite.callCurrent(PogoMetaMethodSite.java:61)
	at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:185)
	at nextflow.processor.TaskProcessor.invokeTask(TaskProcessor.groovy:591)
	at nextflow.processor.InvokeTaskAdapter.call(InvokeTaskAdapter.groovy:59)
	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$1.run(ForkingDataflowOperatorActor.java:58)
	at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)
	at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
	at java.base/java.lang.Thread.run(Thread.java:829)
Caused by: java.lang.IllegalArgumentException: The bucket name parameter must be specified when listing objects in a bucket
	at com.amazonaws.services.s3.AmazonS3Client.rejectNull(AmazonS3Client.java:3839)
	at com.amazonaws.services.s3.AmazonS3Client.listObjects(AmazonS3Client.java:861)
	at com.upplication.s3fs.AmazonS3Client.listObjects(AmazonS3Client.java:105)
	at com.upplication.s3fs.util.S3ObjectSummaryLookup.lookup(S3ObjectSummaryLookup.java:113)
	at com.upplication.s3fs.S3FileSystemProvider.readAttributes(S3FileSystemProvider.java:669)
	at java.base/java.nio.file.Files.readAttributes(Files.java:1764)
	at nextflow.util.CacheHelper.hashFile(CacheHelper.java:239)
	at nextflow.util.CacheHelper.hasher(CacheHelper.java:186)
	at nextflow.util.CacheHelper.hasher(CacheHelper.java:169)
	at nextflow.util.CacheHelper.hasher(CacheHelper.java:111)
	at nextflow.util.CacheHelper.hasher(CacheHelper.java:107)
	at nextflow.util.CacheHelper.hashUnorderedCollection(CacheHelper.java:376)
	at nextflow.util.CacheHelper.hasher(CacheHelper.java:174)
	at nextflow.util.CacheHelper.hasher(CacheHelper.java:178)
	at nextflow.util.CacheHelper.hasher(CacheHelper.java:111)
	at nextflow.util.CacheHelper.hasher(CacheHelper.java:107)
	at nextflow.util.CacheHelper$hasher.call(Unknown Source)
	at nextflow.processor.TaskProcessor.computeHash(TaskProcessor.groovy:1984)
	... 17 common frames omitted
Dec-17 13:23:18.336 [Actor Thread 55] DEBUG nextflow.Session - Session aborted -- Cause: Oops.. something wrong happened while creating task 'CombineOutput' unique id -- Offending keys: [
 - type=java.util.UUID value=0ad5d850-cdf0-4713-9f76-81413e61fdd0,
 - type=java.lang.String value=CombineOutput,
 - type=java.lang.String value="""
	combineCsv.py Assigned.csv Qbovis.csv ${params.DataDir}
	"""
,
 - type=java.lang.String value=Assigned.csv,
 - type=nextflow.util.ArrayBag value=[FileHolder(sourceObj:/processing/TestDec21/work/stage/6e/9e76fa42efffae5a0de0ec944d13af/NB552234_0093_AssignedWGSCluster_17Dec21.csv, storePath:/processing/TestDec21/work/stage/6e/9e76fa42efffae5a0de0ec944d13af/NB552234_0093_AssignedWGSCluster_17Dec21.csv, stageName:Assigned.csv)],
 - type=java.lang.String value=Qbovis.csv,
 - type=nextflow.util.ArrayBag value=[FileHolder(sourceObj:/processing/TestDec21/work/stage/6a/18d54fffd943dfbcb59fc063a57a77/NB552234_0093_BovPos_17Dec21.csv, storePath:/processing/TestDec21/work/stage/6a/18d54fffd943dfbcb59fc063a57a77/NB552234_0093_BovPos_17Dec21.csv, stageName:Qbovis.csv)],
 - type=java.lang.String value=$,
 - type=java.lang.Boolean value=true,
 - type=java.util.HashMap$EntrySet value=[params.DataDir=NB552234_0093],
 - type=sun.nio.fs.UnixPath value=/home/richardellis/btb-seq-2dev/btb-seq/bin/combineCsv.py]
Dec-17 13:23:18.351 [Actor Thread 55] DEBUG nextflow.Session - The following nodes are still active:
[process] CombineOutput
  status=ACTIVE
  port 0: (queue) closed; channel: Assigned.csv
  port 1: (queue) OPEN  ; channel: Qbovis.csv
  port 2: (cntrl) -     ; channel: $

Environment

  • Nextflow version: 21.04.1
  • Java version: openjdk version "11.0.11"
  • Operating system: ubuntu 18.04.4 LTS
  • Bash version: GNU bash, version 4.4.20(1)-release (x86_64-pc-linux-gnu)

Additional context

Whilst this appears to be linked to collectFile, I think its more likely to be an upstream process linked to external downloads, and so I think this may be related to #1230 and possibly nf-core/sarek#130. This is because I can run the exact same process when the (exact same) input files are stored locally and the issue does not occur.
@ellisrichardj ellisrichardj mentioned this issue May 6, 2022
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stale bot commented Jun 11, 2022

This issue has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs. Thank you for your contributions.

@stale stale bot added the stale label Jun 11, 2022
@stale stale bot closed this as completed Sep 21, 2022
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