java.lang.RuntimeException: JobStoreResultSimpletonEntry(metrics,"gs://broad-gotc-prod-cromwell-execution/PairedEndSingleSampleWorkflow/5b7f21d8-0a96-4bbe-a96b-aa68c0454fd7/call-CollectQualityYieldMetrics/shard-8/HV2J2CCXX.8.Pond-555028.unmapped.quality_yield_metrics",File,892420,Some(287367)): unrecognized WDL type: File

GitHub | mcovarr | 8 months ago
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    GitHub comment 1349#242840472

    GitHub | 8 months ago | mcovarr
    java.lang.RuntimeException: JobStoreResultSimpletonEntry(metrics,"gs://broad-gotc-prod-cromwell-execution/PairedEndSingleSampleWorkflow/5b7f21d8-0a96-4bbe-a96b-aa68c0454fd7/call-CollectQualityYieldMetrics/shard-8/HV2J2CCXX.8.Pond-555028.unmapped.quality_yield_metrics",File,892420,Some(287367)): unrecognized WDL type: File

    Root Cause Analysis

    1. java.lang.RuntimeException

      JobStoreResultSimpletonEntry(metrics,"gs://broad-gotc-prod-cromwell-execution/PairedEndSingleSampleWorkflow/5b7f21d8-0a96-4bbe-a96b-aa68c0454fd7/call-CollectQualityYieldMetrics/shard-8/HV2J2CCXX.8.Pond-555028.unmapped.quality_yield_metrics",File,892420,Some(287367)): unrecognized WDL type: File

      at cromwell.jobstore.SqlJobStore.cromwell$jobstore$SqlJobStore$$toSimpleton()
    2. cromwell.jobstore
      SqlJobStore$$anonfun$readJobResult$1$$anonfun$apply$5$$anonfun$3.apply
      1. cromwell.jobstore.SqlJobStore.cromwell$jobstore$SqlJobStore$$toSimpleton(SqlJobStore.scala:59)[classes/:na]
      2. cromwell.jobstore.SqlJobStore$$anonfun$readJobResult$1$$anonfun$apply$5$$anonfun$3.apply(SqlJobStore.scala:69)[classes/:na]
      3. cromwell.jobstore.SqlJobStore$$anonfun$readJobResult$1$$anonfun$apply$5$$anonfun$3.apply(SqlJobStore.scala:69)[classes/:na]
      3 frames
    3. Scala
      AbstractTraversable.map
      1. scala.collection.TraversableLike$$anonfun$map$1.apply(TraversableLike.scala:245)[scala-library-2.11.7.jar:1.0.0-M1]
      2. scala.collection.TraversableLike$$anonfun$map$1.apply(TraversableLike.scala:245)[scala-library-2.11.7.jar:1.0.0-M1]
      3. scala.collection.Iterator$class.foreach(Iterator.scala:742)[scala-library-2.11.7.jar:1.0.0-M1]
      4. scala.collection.AbstractIterator.foreach(Iterator.scala:1194)[scala-library-2.11.7.jar:1.0.0-M1]
      5. scala.collection.IterableLike$class.foreach(IterableLike.scala:72)[scala-library-2.11.7.jar:1.0.0-M1]
      6. scala.collection.AbstractIterable.foreach(Iterable.scala:54)[scala-library-2.11.7.jar:1.0.0-M1]
      7. scala.collection.TraversableLike$class.map(TraversableLike.scala:245)[scala-library-2.11.7.jar:1.0.0-M1]
      8. scala.collection.AbstractTraversable.map(Traversable.scala:104)[scala-library-2.11.7.jar:1.0.0-M1]
      8 frames
    4. cromwell.jobstore
      SqlJobStore$$anonfun$readJobResult$1$$anonfun$apply$5.apply
      1. cromwell.jobstore.SqlJobStore$$anonfun$readJobResult$1$$anonfun$apply$5.apply(SqlJobStore.scala:69)[classes/:na]
      2. cromwell.jobstore.SqlJobStore$$anonfun$readJobResult$1$$anonfun$apply$5.apply(SqlJobStore.scala:66)[classes/:na]
      2 frames
    5. Scala
      Option.map
      1. scala.Option.map(Option.scala:146)[scala-library-2.11.7.jar:1.0.0-M1]
      1 frame
    6. cromwell.jobstore
      SqlJobStore$$anonfun$readJobResult$1.apply
      1. cromwell.jobstore.SqlJobStore$$anonfun$readJobResult$1.apply(SqlJobStore.scala:66)[classes/:na]
      2. cromwell.jobstore.SqlJobStore$$anonfun$readJobResult$1.apply(SqlJobStore.scala:66)[classes/:na]
      2 frames
    7. Scala
      CallbackRunnable.run
      1. scala.util.Success$$anonfun$map$1.apply(Try.scala:237)[scala-library-2.11.7.jar:1.0.0-M1]
      2. scala.util.Try$.apply(Try.scala:192)[scala-library-2.11.7.jar:1.0.0-M1]
      3. scala.util.Success.map(Try.scala:237)[scala-library-2.11.7.jar:1.0.0-M1]
      4. scala.concurrent.Future$$anonfun$map$1.apply(Future.scala:235)[scala-library-2.11.7.jar:na]
      5. scala.concurrent.Future$$anonfun$map$1.apply(Future.scala:235)[scala-library-2.11.7.jar:na]
      6. scala.concurrent.impl.CallbackRunnable.run(Promise.scala:32)[scala-library-2.11.7.jar:na]
      6 frames
    8. Akka Actor
      BatchingExecutor$BlockableBatch$$anonfun$run$1.apply
      1. akka.dispatch.BatchingExecutor$AbstractBatch.processBatch(BatchingExecutor.scala:55)[akka-actor_2.11-2.3.15.jar:na]
      2. akka.dispatch.BatchingExecutor$BlockableBatch$$anonfun$run$1.apply$mcV$sp(BatchingExecutor.scala:91)[akka-actor_2.11-2.3.15.jar:na]
      3. akka.dispatch.BatchingExecutor$BlockableBatch$$anonfun$run$1.apply(BatchingExecutor.scala:91)[akka-actor_2.11-2.3.15.jar:na]
      4. akka.dispatch.BatchingExecutor$BlockableBatch$$anonfun$run$1.apply(BatchingExecutor.scala:91)[akka-actor_2.11-2.3.15.jar:na]
      4 frames
    9. Scala
      BlockContext$.withBlockContext
      1. scala.concurrent.BlockContext$.withBlockContext(BlockContext.scala:72)[scala-library-2.11.7.jar:na]
      1 frame
    10. Akka Actor
      ForkJoinExecutorConfigurator$AkkaForkJoinTask.exec
      1. akka.dispatch.BatchingExecutor$BlockableBatch.run(BatchingExecutor.scala:90)[akka-actor_2.11-2.3.15.jar:na]
      2. akka.dispatch.TaskInvocation.run(AbstractDispatcher.scala:40)[akka-actor_2.11-2.3.15.jar:na]
      3. akka.dispatch.ForkJoinExecutorConfigurator$AkkaForkJoinTask.exec(AbstractDispatcher.scala:397)[akka-actor_2.11-2.3.15.jar:na]
      3 frames
    11. Scala
      ForkJoinWorkerThread.run
      1. scala.concurrent.forkjoin.ForkJoinTask.doExec(ForkJoinTask.java:260)[scala-library-2.11.7.jar:na]
      2. scala.concurrent.forkjoin.ForkJoinPool$WorkQueue.runTask(ForkJoinPool.java:1339)[scala-library-2.11.7.jar:na]
      3. scala.concurrent.forkjoin.ForkJoinPool.runWorker(ForkJoinPool.java:1979)[scala-library-2.11.7.jar:na]
      4. scala.concurrent.forkjoin.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:107)[scala-library-2.11.7.jar:na]
      4 frames