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Has anyone tried running this pipeline recently? I...
# hgtseq
m
Has anyone tried running this pipeline recently? I tried running the hgtseq pipeline with the test data but I’m having trouble (see thread).
Command run:
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nextflow run nf-core/hgtseq -r 1.1.0 -c nextflow.config -profile singularity,test --outdir results_hgtseq
Output:
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DEBUG nextflow.processor.TaskProcessor - Process NFCORE_HGTSEQ:HGTSEQ:SORTBAM:SAMTOOLS_INDEX > Skipping output binding because one or more optional files are missing: fileoutparam<2:1>
Sep.-05 09:24:41.490 [Actor Thread 26] ERROR nextflow.extension.OperatorImpl - @unknown
java.lang.NullPointerException: Cannot invoke "java.util.Map.get(Object)" because "self" is null
        at org.codehaus.groovy.runtime.DefaultGroovyMethods.getAt(DefaultGroovyMethods.java:8581)
        at nextflow.extension.JoinOp.checkRemainder(JoinOp.groovy:237)
        at nextflow.extension.JoinOp.access$0(JoinOp.groovy)
        at nextflow.extension.JoinOp$_handler_closure2.doCall(JoinOp.groovy:133)
        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.reflection.CachedMethod.invoke(CachedMethod.java:343)
        at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:328)
        at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:279)
        at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1007)
        at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321)
        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 jdk.internal.reflect.GeneratedMethodAccessor96.invoke(Unknown Source)
        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.reflection.CachedMethod.invoke(CachedMethod.java:343)
        at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:328)
        at groovy.lang.MetaClassImpl.doInvokeMethod(MetaClassImpl.java:1333)
        at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1088)
        at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1007)
        at org.codehaus.groovy.runtime.InvokerHelper.invokePojoMethod(InvokerHelper.java:633)
        at org.codehaus.groovy.runtime.InvokerHelper.invokeMethod(InvokerHelper.java:624)
        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.DataflowProcessorActor.checkPoison(DataflowProcessorActor.java:115)
        at groovyx.gpars.dataflow.operator.DataflowOperatorActor.onMessage(DataflowOperatorActor.java:83)
        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$1.handleMessage(AbstractLoopingActor.java:93)
        at groovyx.gpars.util.AsyncMessagingCore.run(AsyncMessagingCore.java:132)
        at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1136)
        at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635)
        at java.base/java.lang.Thread.run(Thread.java:840)
Sep.-05 09:24:41.500 [Actor Thread 26] DEBUG nextflow.Session - Session aborted -- Cause: Cannot invoke "java.util.Map.get(Object)" because "self" is null
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