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Hello. I'm trying to run the test_full profile fo...
# taxprofiler
n
Hello. I'm trying to run the test_full profile for taxprofiler but got the error:
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Dec-05 13:22:17.351 [Actor Thread 193] ERROR nextflow.extension.OperatorImpl - @unknown
groovy.lang.MissingMethodException: No signature of method: groovyx.gpars.dataflow.DataflowBroadcast.getAt() is applicable for argument types: (Integer) values: [0]
Possible solutions: getAt(java.lang.String), putAt(java.lang.String, java.lang.Object), wait(), grep(), tap(groovy.lang.Closure), getClass()
	at org.codehaus.groovy.runtime.ScriptBytecodeAdapter.unwrap(ScriptBytecodeAdapter.java:72)
	at org.codehaus.groovy.vmplugin.v8.IndyGuardsFiltersAndSignatures.unwrap(IndyGuardsFiltersAndSignatures.java:163)
	at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321)
	at Script_cfae9702b3126798$_runScript_closure3$_closure5$_closure34.doCall(Script_cfae9702b3126798:345)
	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:343)
	at org.codehaus.groovy.runtime.metaclass.TransformMetaMethod.invoke(TransformMetaMethod.java:59)
	at groovy.lang.MetaClassImpl$3.invoke(MetaClassImpl.java:1374)
	at org.codehaus.groovy.runtime.metaclass.TransformMetaMethod.doMethodInvoke(TransformMetaMethod.java:66)
	at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:280)
	at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1007)
	at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321)
	at nextflow.extension.MapOp$_apply_closure1.doCall(MapOp.groovy:56)
	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:343)
	at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:328)
	at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:280)
	at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1007)
	at groovy.lang.Closure.call(Closure.java:433)
	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$1.handleMessage(AbstractLoopingActor.java:93)
	at groovyx.gpars.util.AsyncMessagingCore.run(AsyncMessagingCore.java:132)
	at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1144)
	at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:642)
	at java.base/java.lang.Thread.run(Thread.java:1583)
There are some related google results but not quite exactly the same thing. What is going on here? I'm using nextflow 25.04.06 and singularity 4.3.2. Command line: 
nextflow run nf-core/taxprofiler -r 1.2.5 -c htc_resourceLimits.config -profile test_full -resume  --outdir results
Config file:
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singularity {
  enabled = true
  autoMounts = true
  pullTimeout = '2h'   // 20m default is just not long enough sometimes
  // runOptions = "--bind /zfs1:/zfs1"
}

process {
  executor = 'slurm'
  clusterOptions = '' // { "${params.clusterOptions ?: ''}" }
  scratch = true
  resourceLimits = [
    cpus: 64,
    memory: '768.GB',
    time: '144.h'
  ]
}
// added this 10/14/25 because of this <https://nfcore.slack.com/archives/CE9MS66BS/p1760452204421589?thread_ts=1760448413.679689&cid=CE9MS66BS>
aws {
  client {
    anonymous = true
  }
}
I restarted the pipeline without 
resume
and it is working so far. Fingers crossed.
alas, no luck. Got same error:
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grep -A40 ERROR .nextflow.log
Dec-05 16:22:52.641 [Actor Thread 151] ERROR nextflow.extension.OperatorImpl - @unknown
groovy.lang.MissingMethodException: No signature of method: groovyx.gpars.dataflow.DataflowBroadcast.getAt() is applicable for argument types: (Integer) values: [0]
Possible solutions: getAt(java.lang.String), putAt(java.lang.String, java.lang.Object), wait(), grep(), tap(groovy.lang.Closure), getClass()
	at org.codehaus.groovy.runtime.ScriptBytecodeAdapter.unwrap(ScriptBytecodeAdapter.java:72)
	at org.codehaus.groovy.vmplugin.v8.IndyGuardsFiltersAndSignatures.unwrap(IndyGuardsFiltersAndSignatures.java:163)
	at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321)
	at Script_cfae9702b3126798$_runScript_closure3$_closure5$_closure34.doCall(Script_cfae9702b3126798:345)
	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:343)
	at org.codehaus.groovy.runtime.metaclass.TransformMetaMethod.invoke(TransformMetaMethod.java:59)
	at groovy.lang.MetaClassImpl$3.invoke(MetaClassImpl.java:1374)
	at org.codehaus.groovy.runtime.metaclass.TransformMetaMethod.doMethodInvoke(TransformMetaMethod.java:66)
	at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:280)
	at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1007)
	at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321)
	at nextflow.extension.MapOp$_apply_closure1.doCall(MapOp.groovy:56)
	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:343)
	at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:328)
	at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:280)
	at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1007)
	at groovy.lang.Closure.call(Closure.java:433)
	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$1.handleMessage(AbstractLoopingActor.java:93)
	at groovyx.gpars.util.AsyncMessagingCore.run(AsyncMessagingCore.java:132)
	at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1144)
	at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:642)
	at java.base/java.lang.Thread.run(Thread.java:1583)
s
Is this happening at krakenuniq process?
n
I don't think so but I cannot really tell from the log files. See attached.
execution_trace_2025-12-05_15-29-19.txt
s
Have you tried to check if you get the same error with 
1.2.4
?
n
1.2.4 is currently running without a problem and seems to be nearing the end of the pipeline. I'll report back when done.
1.2.4 just finished successfully:
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-[nf-core/taxprofiler] Pipeline completed successfully-

Completed at: 08-Dec-2025 11:30:16
Duration    : 2h 8m 37s
CPU hours   : 41.8
Succeeded   : 236
However, one caveat. The nfcore codes and singularity images that I used for 1.2.4 were predownloaded but for 1.2.5 they were not predownloaded. So, I'm pulling 1.2.5 code and images and will run 1.2.5 with the local files and keep you posted..
I pulled the 1.2.5 code and images yet I still got the same error:
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ERROR nextflow.extension.OperatorImpl - @unknown
groovy.lang.MissingMethodException: No signature of method: groovyx.gpars.dataflow.DataflowBroadcast.getAt() is applicable for argument types: (Integer) values: [0]
Do you need the .nexflow.log and execution_trace for this run? I can confirm that 1.2.4 works with local code and images.
s
Thank you, I will have a look tomorrow.
👍🏽 1
I think the issue is in the krakenuniq process, I had the same issue and I saw you got an error at the exact same line. Will try to fix the bug and then do a patch release. For the time being you can either try to run the 
1.2.5
version and ignore krakenuniq or run the 
1.2.4
. Sorry about the inconvenience.
And as @James Fellows Yates pointed out, it might be due to the nextflow version.
n
No worries. Thank you for your help. I used 
module load nextflow/25.04.6 singularity/4.3.2
for all my runs of the 1.2.4 and 1.2.5 versions of the pipeline.
s
Thank you for the additional info.
👍🏽 1
j
@novelvirus the log would still be helpful if you still have it
n
j
@novelvirus we are trying to investigate by replicating the issue. Sofia has a similar error but at a different part of the pipeline which is weird... the error messages are not desciprtive to where the issue is happened so it may take a bit of time
You could try on some real data in the meantime to see if it always happens (our normal small test doesn't have this issue)
n
👍🏽
j
@novelvirus small upodate, we found the issue last week, and hit a second downstream one just as I had to leave. The former is easy fix, the latter I will invstigate Tghrsday
👍🏽 1
Merged and will be in the next patch release (first thing after the holidays) https://github.com/nf-core/taxprofiler/pull/674
👍🏽 1
💯 1
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