Failed

org.bdgenomics.gnocchi.models.LinearGnocchiModelSuite.LinearGnocchiModel correctly combines GnocchiModels

Failing for the past 1 build (Since Failed#20 )
Took 0.56 sec.

Error Message

Job aborted due to stage failure: Task 0 in stage 3.0 failed 1 times, most recent failure: Lost task 0.0 in stage 3.0 (TID 3, localhost, executor driver): java.lang.IllegalArgumentException: No overlap between phenotype and genotype state sample IDs.
 at org.bdgenomics.gnocchi.algorithms.siteregression.LinearSiteRegression$class.prepareDesignMatrix(LinearSiteRegression.scala:118)
 at org.bdgenomics.gnocchi.algorithms.siteregression.LinearSiteRegression$.prepareDesignMatrix(LinearSiteRegression.scala:145)
 at org.bdgenomics.gnocchi.algorithms.siteregression.LinearSiteRegression$class.applyToSite(LinearSiteRegression.scala:53)
 at org.bdgenomics.gnocchi.algorithms.siteregression.LinearSiteRegression$.applyToSite(LinearSiteRegression.scala:145)
 at org.bdgenomics.gnocchi.algorithms.siteregression.LinearSiteRegression$$anonfun$apply$1.apply(LinearSiteRegression.scala:44)
 at org.bdgenomics.gnocchi.algorithms.siteregression.LinearSiteRegression$$anonfun$apply$1.apply(LinearSiteRegression.scala:43)
 at org.apache.spark.sql.catalyst.expressions.GeneratedClass$GeneratedIterator.processNext(Unknown Source)
 at org.apache.spark.sql.execution.BufferedRowIterator.hasNext(BufferedRowIterator.java:43)
 at org.apache.spark.sql.execution.WholeStageCodegenExec$$anonfun$8$$anon$1.hasNext(WholeStageCodegenExec.scala:395)
 at org.apache.spark.sql.execution.SparkPlan$$anonfun$2.apply(SparkPlan.scala:234)
 at org.apache.spark.sql.execution.SparkPlan$$anonfun$2.apply(SparkPlan.scala:228)
 at org.apache.spark.rdd.RDD$$anonfun$mapPartitionsInternal$1$$anonfun$apply$25.apply(RDD.scala:827)
 at org.apache.spark.rdd.RDD$$anonfun$mapPartitionsInternal$1$$anonfun$apply$25.apply(RDD.scala:827)
 at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
 at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:323)
 at org.apache.spark.rdd.RDD.iterator(RDD.scala:287)
 at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:87)
 at org.apache.spark.scheduler.Task.run(Task.scala:108)
 at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:335)
 at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
 at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
 at java.lang.Thread.run(Thread.java:745)

Driver stacktrace:

Stacktrace

      org.apache.spark.SparkException: Job aborted due to stage failure: Task 0 in stage 3.0 failed 1 times, most recent failure: Lost task 0.0 in stage 3.0 (TID 3, localhost, executor driver): java.lang.IllegalArgumentException: No overlap between phenotype and genotype state sample IDs.
	at org.bdgenomics.gnocchi.algorithms.siteregression.LinearSiteRegression$class.prepareDesignMatrix(LinearSiteRegression.scala:118)
	at org.bdgenomics.gnocchi.algorithms.siteregression.LinearSiteRegression$.prepareDesignMatrix(LinearSiteRegression.scala:145)
	at org.bdgenomics.gnocchi.algorithms.siteregression.LinearSiteRegression$class.applyToSite(LinearSiteRegression.scala:53)
	at org.bdgenomics.gnocchi.algorithms.siteregression.LinearSiteRegression$.applyToSite(LinearSiteRegression.scala:145)
	at org.bdgenomics.gnocchi.algorithms.siteregression.LinearSiteRegression$$anonfun$apply$1.apply(LinearSiteRegression.scala:44)
	at org.bdgenomics.gnocchi.algorithms.siteregression.LinearSiteRegression$$anonfun$apply$1.apply(LinearSiteRegression.scala:43)
	at org.apache.spark.sql.catalyst.expressions.GeneratedClass$GeneratedIterator.processNext(Unknown Source)
	at org.apache.spark.sql.execution.BufferedRowIterator.hasNext(BufferedRowIterator.java:43)
	at org.apache.spark.sql.execution.WholeStageCodegenExec$$anonfun$8$$anon$1.hasNext(WholeStageCodegenExec.scala:395)
	at org.apache.spark.sql.execution.SparkPlan$$anonfun$2.apply(SparkPlan.scala:234)
	at org.apache.spark.sql.execution.SparkPlan$$anonfun$2.apply(SparkPlan.scala:228)
	at org.apache.spark.rdd.RDD$$anonfun$mapPartitionsInternal$1$$anonfun$apply$25.apply(RDD.scala:827)
	at org.apache.spark.rdd.RDD$$anonfun$mapPartitionsInternal$1$$anonfun$apply$25.apply(RDD.scala:827)
	at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
	at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:323)
	at org.apache.spark.rdd.RDD.iterator(RDD.scala:287)
	at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:87)
	at org.apache.spark.scheduler.Task.run(Task.scala:108)
	at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:335)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
	at java.lang.Thread.run(Thread.java:745)

Driver stacktrace:
      at org.apache.spark.scheduler.DAGScheduler.org$apache$spark$scheduler$DAGScheduler$$failJobAndIndependentStages(DAGScheduler.scala:1499)
      at org.apache.spark.scheduler.DAGScheduler$$anonfun$abortStage$1.apply(DAGScheduler.scala:1487)
      at org.apache.spark.scheduler.DAGScheduler$$anonfun$abortStage$1.apply(DAGScheduler.scala:1486)
      at scala.collection.mutable.ResizableArray$class.foreach(ResizableArray.scala:59)
      at scala.collection.mutable.ArrayBuffer.foreach(ArrayBuffer.scala:48)
      at org.apache.spark.scheduler.DAGScheduler.abortStage(DAGScheduler.scala:1486)
      at org.apache.spark.scheduler.DAGScheduler$$anonfun$handleTaskSetFailed$1.apply(DAGScheduler.scala:814)
      at org.apache.spark.scheduler.DAGScheduler$$anonfun$handleTaskSetFailed$1.apply(DAGScheduler.scala:814)
      at scala.Option.foreach(Option.scala:257)
      at org.apache.spark.scheduler.DAGScheduler.handleTaskSetFailed(DAGScheduler.scala:814)
      at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.doOnReceive(DAGScheduler.scala:1714)
      at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:1669)
      at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:1658)
      at org.apache.spark.util.EventLoop$$anon$1.run(EventLoop.scala:48)
      at org.apache.spark.scheduler.DAGScheduler.runJob(DAGScheduler.scala:630)
      at org.apache.spark.SparkContext.runJob(SparkContext.scala:2022)
      at org.apache.spark.SparkContext.runJob(SparkContext.scala:2043)
      at org.apache.spark.SparkContext.runJob(SparkContext.scala:2062)
      at org.apache.spark.SparkContext.runJob(SparkContext.scala:2087)
      at org.apache.spark.rdd.RDD$$anonfun$collect$1.apply(RDD.scala:936)
      at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:151)
      at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:112)
      at org.apache.spark.rdd.RDD.withScope(RDD.scala:362)
      at org.apache.spark.rdd.RDD.collect(RDD.scala:935)
      at org.apache.spark.sql.execution.SparkPlan.executeCollect(SparkPlan.scala:278)
      at org.apache.spark.sql.Dataset.org$apache$spark$sql$Dataset$$collectFromPlan(Dataset.scala:2853)
      at org.apache.spark.sql.Dataset$$anonfun$collect$1.apply(Dataset.scala:2390)
      at org.apache.spark.sql.Dataset$$anonfun$collect$1.apply(Dataset.scala:2390)
      at org.apache.spark.sql.Dataset$$anonfun$55.apply(Dataset.scala:2837)
      at org.apache.spark.sql.execution.SQLExecution$.withNewExecutionId(SQLExecution.scala:65)
      at org.apache.spark.sql.Dataset.withAction(Dataset.scala:2836)
      at org.apache.spark.sql.Dataset.collect(Dataset.scala:2390)
      at org.bdgenomics.gnocchi.models.LinearGnocchiModelFactory$.apply(LinearGnocchiModel.scala:68)
      at org.bdgenomics.gnocchi.models.LinearGnocchiModelSuite$$anonfun$2.apply$mcV$sp(LinearGnocchiModelSuite.scala:37)
      at org.bdgenomics.utils.misc.SparkFunSuite$$anonfun$sparkTest$1.apply$mcV$sp(SparkFunSuite.scala:102)
      at org.bdgenomics.utils.misc.SparkFunSuite$$anonfun$sparkTest$1.apply(SparkFunSuite.scala:98)
      at org.bdgenomics.utils.misc.SparkFunSuite$$anonfun$sparkTest$1.apply(SparkFunSuite.scala:98)
      at org.scalatest.Transformer$$anonfun$apply$1.apply$mcV$sp(Transformer.scala:22)
      at org.scalatest.OutcomeOf$class.outcomeOf(OutcomeOf.scala:85)
      at org.scalatest.OutcomeOf$.outcomeOf(OutcomeOf.scala:104)
      at org.scalatest.Transformer.apply(Transformer.scala:22)
      at org.scalatest.Transformer.apply(Transformer.scala:20)
      at org.scalatest.FunSuiteLike$$anon$1.apply(FunSuiteLike.scala:166)
      at org.scalatest.Suite$class.withFixture(Suite.scala:1122)
      at org.scalatest.FunSuite.withFixture(FunSuite.scala:1555)
      at org.scalatest.FunSuiteLike$class.invokeWithFixture$1(FunSuiteLike.scala:163)
      at org.scalatest.FunSuiteLike$$anonfun$runTest$1.apply(FunSuiteLike.scala:175)
      at org.scalatest.FunSuiteLike$$anonfun$runTest$1.apply(FunSuiteLike.scala:175)
      at org.scalatest.SuperEngine.runTestImpl(Engine.scala:306)
      at org.scalatest.FunSuiteLike$class.runTest(FunSuiteLike.scala:175)
      at org.bdgenomics.gnocchi.models.LinearGnocchiModelSuite.org$scalatest$BeforeAndAfter$$super$runTest(LinearGnocchiModelSuite.scala:13)
      at org.scalatest.BeforeAndAfter$class.runTest(BeforeAndAfter.scala:200)
      at org.bdgenomics.gnocchi.models.LinearGnocchiModelSuite.runTest(LinearGnocchiModelSuite.scala:13)
      at org.scalatest.FunSuiteLike$$anonfun$runTests$1.apply(FunSuiteLike.scala:208)
      at org.scalatest.FunSuiteLike$$anonfun$runTests$1.apply(FunSuiteLike.scala:208)
      at org.scalatest.SuperEngine$$anonfun$traverseSubNodes$1$1.apply(Engine.scala:413)
      at org.scalatest.SuperEngine$$anonfun$traverseSubNodes$1$1.apply(Engine.scala:401)
      at scala.collection.immutable.List.foreach(List.scala:381)
      at org.scalatest.SuperEngine.traverseSubNodes$1(Engine.scala:401)
      at org.scalatest.SuperEngine.org$scalatest$SuperEngine$$runTestsInBranch(Engine.scala:396)
      at org.scalatest.SuperEngine.runTestsImpl(Engine.scala:483)
      at org.scalatest.FunSuiteLike$class.runTests(FunSuiteLike.scala:208)
      at org.scalatest.FunSuite.runTests(FunSuite.scala:1555)
      at org.scalatest.Suite$class.run(Suite.scala:1424)
      at org.scalatest.FunSuite.org$scalatest$FunSuiteLike$$super$run(FunSuite.scala:1555)
      at org.scalatest.FunSuiteLike$$anonfun$run$1.apply(FunSuiteLike.scala:212)
      at org.scalatest.FunSuiteLike$$anonfun$run$1.apply(FunSuiteLike.scala:212)
      at org.scalatest.SuperEngine.runImpl(Engine.scala:545)
      at org.scalatest.FunSuiteLike$class.run(FunSuiteLike.scala:212)
      at org.bdgenomics.gnocchi.models.LinearGnocchiModelSuite.org$scalatest$BeforeAndAfter$$super$run(LinearGnocchiModelSuite.scala:13)
      at org.scalatest.BeforeAndAfter$class.run(BeforeAndAfter.scala:241)
      at org.bdgenomics.gnocchi.models.LinearGnocchiModelSuite.run(LinearGnocchiModelSuite.scala:13)
      at org.scalatest.Suite$class.callExecuteOnSuite$1(Suite.scala:1492)
      at org.scalatest.Suite$$anonfun$runNestedSuites$1.apply(Suite.scala:1528)
      at org.scalatest.Suite$$anonfun$runNestedSuites$1.apply(Suite.scala:1526)
      at scala.collection.IndexedSeqOptimized$class.foreach(IndexedSeqOptimized.scala:33)
      at scala.collection.mutable.ArrayOps$ofRef.foreach(ArrayOps.scala:186)
      at org.scalatest.Suite$class.runNestedSuites(Suite.scala:1526)
      at org.scalatest.tools.DiscoverySuite.runNestedSuites(DiscoverySuite.scala:29)
      at org.scalatest.Suite$class.run(Suite.scala:1421)
      at org.scalatest.tools.DiscoverySuite.run(DiscoverySuite.scala:29)
      at org.scalatest.tools.SuiteRunner.run(SuiteRunner.scala:55)
      at org.scalatest.tools.Runner$$anonfun$doRunRunRunDaDoRunRun$3.apply(Runner.scala:2563)
      at org.scalatest.tools.Runner$$anonfun$doRunRunRunDaDoRunRun$3.apply(Runner.scala:2557)
      at scala.collection.immutable.List.foreach(List.scala:381)
      at org.scalatest.tools.Runner$.doRunRunRunDaDoRunRun(Runner.scala:2557)
      at org.scalatest.tools.Runner$$anonfun$runOptionallyWithPassFailReporter$2.apply(Runner.scala:1044)
      at org.scalatest.tools.Runner$$anonfun$runOptionallyWithPassFailReporter$2.apply(Runner.scala:1043)
      at org.scalatest.tools.Runner$.withClassLoaderAndDispatchReporter(Runner.scala:2722)
      at org.scalatest.tools.Runner$.runOptionallyWithPassFailReporter(Runner.scala:1043)
      at org.scalatest.tools.Runner$.main(Runner.scala:860)
      at org.scalatest.tools.Runner.main(Runner.scala)
      Cause: java.lang.IllegalArgumentException: No overlap between phenotype and genotype state sample IDs.
      at org.bdgenomics.gnocchi.algorithms.siteregression.LinearSiteRegression$class.prepareDesignMatrix(LinearSiteRegression.scala:118)
      at org.bdgenomics.gnocchi.algorithms.siteregression.LinearSiteRegression$.prepareDesignMatrix(LinearSiteRegression.scala:145)
      at org.bdgenomics.gnocchi.algorithms.siteregression.LinearSiteRegression$class.applyToSite(LinearSiteRegression.scala:53)
      at org.bdgenomics.gnocchi.algorithms.siteregression.LinearSiteRegression$.applyToSite(LinearSiteRegression.scala:145)
      at org.bdgenomics.gnocchi.algorithms.siteregression.LinearSiteRegression$$anonfun$apply$1.apply(LinearSiteRegression.scala:44)
      at org.bdgenomics.gnocchi.algorithms.siteregression.LinearSiteRegression$$anonfun$apply$1.apply(LinearSiteRegression.scala:43)
      at org.apache.spark.sql.catalyst.expressions.GeneratedClass$GeneratedIterator.processNext(Unknown Source)
      at org.apache.spark.sql.execution.BufferedRowIterator.hasNext(BufferedRowIterator.java:43)
      at org.apache.spark.sql.execution.WholeStageCodegenExec$$anonfun$8$$anon$1.hasNext(WholeStageCodegenExec.scala:395)
      at org.apache.spark.sql.execution.SparkPlan$$anonfun$2.apply(SparkPlan.scala:234)
      at org.apache.spark.sql.execution.SparkPlan$$anonfun$2.apply(SparkPlan.scala:228)
      at org.apache.spark.rdd.RDD$$anonfun$mapPartitionsInternal$1$$anonfun$apply$25.apply(RDD.scala:827)
      at org.apache.spark.rdd.RDD$$anonfun$mapPartitionsInternal$1$$anonfun$apply$25.apply(RDD.scala:827)
      at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
      at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:323)
      at org.apache.spark.rdd.RDD.iterator(RDD.scala:287)
      at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:87)
      at org.apache.spark.scheduler.Task.run(Task.scala:108)
      at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:335)
      at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
      at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
      at java.lang.Thread.run(Thread.java:745)