FailedConsole Output

Skipping 148 KB.. Full Log
QT2jNKU4P0+vIKc0PTOvWC8xrzgzOT8nv0gvODO3ICfVoyQ3xy+/JNU2Yj/Tagmf50wMjD4M7CWJ6SCJEgYhn6zEskT9nMS8dP3gkqLMvHTriiIGKaihyfl5xfk5qXrOEBpkDgMEMDIxMFQUlDCw2+gXFyTm2QEAI9P8iI4AAAA=
  at org.apache.xbean.asm5.ClassReader.<init>(Unknown Source)
  at org.apache.spark.util.ClosureCleaner$.getClassReader(ClosureCleaner.scala:42)
  at org.apache.spark.util.ClosureCleaner$.getInnerClosureClasses(ClosureCleaner.scala:83)
  at org.apache.spark.util.ClosureCleaner$.org$apache$spark$util$ClosureCleaner$$clean(ClosureCleaner.scala:173)
  at org.apache.spark.util.ClosureCleaner$.clean(ClosureCleaner.scala:108)
  at org.apache.spark.SparkContext.clean(SparkContext.scala:2094)
  at org.apache.spark.rdd.RDD$$anonfun$flatMap$1.apply(RDD.scala:379)
  at org.apache.spark.rdd.RDD$$anonfun$flatMap$1.apply(RDD.scala:378)
  at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:151)
  at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:112)
  at org.apache.spark.rdd.RDD.withScope(RDD.scala:362)
  at org.apache.spark.rdd.RDD.flatMap(RDD.scala:378)
  at org.bdgenomics.adam.rdd.ADAMContext$$anonfun$loadVcf$1.apply(ADAMContext.scala:2050)
  at org.bdgenomics.adam.rdd.ADAMContext$$anonfun$loadVcf$1.apply(ADAMContext.scala:2038)
  at scala.Option.fold(Option.scala:157)
  at org.apache.spark.rdd.Timer.time(Timer.scala:48)
  at org.bdgenomics.adam.rdd.ADAMContext.loadVcf(ADAMContext.scala:2038)
  at org.bdgenomics.adam.rdd.ADAMContext$$anonfun$loadGenotypes$1.apply(ADAMContext.scala:2842)
  at org.bdgenomics.adam.rdd.ADAMContext$$anonfun$loadGenotypes$1.apply(ADAMContext.scala:2840)
  at scala.Option.fold(Option.scala:157)
  at org.apache.spark.rdd.Timer.time(Timer.scala:48)
  at org.bdgenomics.adam.rdd.ADAMContext.loadGenotypes(ADAMContext.scala:2838)
  at org.bdgenomics.avocado.genotyping.SquareOffReferenceModelSuite$$anonfun$5.apply$mcV$sp(SquareOffReferenceModelSuite.scala:54)
  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$$anonfun$runTest$1.apply(FunSuiteLike.scala:175)
  at org.scalatest.SuperEngine.runTestImpl(Engine.scala:306)
  at org.scalatest.FunSuiteLike$class.runTest(FunSuiteLike.scala:175)
  at org.bdgenomics.avocado.genotyping.SquareOffReferenceModelSuite.org$scalatest$BeforeAndAfter$$super$runTest(SquareOffReferenceModelSuite.scala:29)
  at org.scalatest.BeforeAndAfter$class.runTest(BeforeAndAfter.scala:200)
  at org.bdgenomics.avocado.genotyping.SquareOffReferenceModelSuite.runTest(SquareOffReferenceModelSuite.scala:29)
  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:318)
  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.avocado.genotyping.SquareOffReferenceModelSuite.org$scalatest$BeforeAndAfter$$super$run(SquareOffReferenceModelSuite.scala:29)
  at org.scalatest.BeforeAndAfter$class.run(BeforeAndAfter.scala:241)
  at org.bdgenomics.avocado.genotyping.SquareOffReferenceModelSuite.run(SquareOffReferenceModelSuite.scala:29)
  at org.scalatest.Suite$class.callExecuteOnSuite$1(Suite.scala:1492)
  at org.scalatest.Suite$$anonfun$runNestedSuites$1.apply(Suite.scala:1528)
  at org.scalatest.Suite$$anonfun$runNestedSuites$1.apply(Suite.scala:1526)
  at scala.collection.IndexedSeqOptimized$class.foreach(IndexedSeqOptimized.scala:33)
  at scala.collection.mutable.ArrayOps$ofRef.foreach(ArrayOps.scala:108)
  at org.scalatest.Suite$class.runNestedSuites(Suite.scala:1526)
  at org.scalatest.tools.DiscoverySuite.runNestedSuites(DiscoverySuite.scala:29)
  at org.scalatest.Suite$class.run(Suite.scala:1421)
  at org.scalatest.tools.DiscoverySuite.run(DiscoverySuite.scala:29)
  at org.scalatest.tools.SuiteRunner.run(SuiteRunner.scala:55)
  at org.scalatest.tools.Runner$$anonfun$doRunRunRunDaDoRunRun$3.apply(Runner.scala:2563)
  at org.scalatest.tools.Runner$$anonfun$doRunRunRunDaDoRunRun$3.apply(Runner.scala:2557)
  at scala.collection.immutable.List.foreach(List.scala:318)
  at org.scalatest.tools.Runner$.doRunRunRunDaDoRunRun(Runner.scala:2557)
  at org.scalatest.tools.Runner$$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)
- find genotype if variant is present
- don't find genotype if variant is not present
- excise a genotype from a reference block
- square off a site with data from multiple samples
DiscoverVariantsSuite:
- no variants in unaligned read
- no variants in rdd with unaligned read
- no variants in read that is a perfect sequence match
2018-01-01 04:39:49 WARN  SparkContext:66 - Support for Scala 2.10 is deprecated as of Spark 2.1.0
- no variants in rdd with sequence match reads
- find snp in read with a 1bp sequence mismatch
2018-01-01 04:39:50 WARN  SparkContext:66 - Support for Scala 2.10 is deprecated as of Spark 2.1.0
- find one snp in reads with 1bp sequence mismatch
- find insertion in read
2018-01-01 04:39:51 WARN  SparkContext:66 - Support for Scala 2.10 is deprecated as of Spark 2.1.0
- find insertion in reads
- find deletion in read
2018-01-01 04:39:51 WARN  SparkContext:66 - Support for Scala 2.10 is deprecated as of Spark 2.1.0
- find deletion in reads
2018-01-01 04:39:52 WARN  SparkContext:66 - Support for Scala 2.10 is deprecated as of Spark 2.1.0
- find variants in alignment record rdd
- break TT->CA mnp into two snps
ObservationOperatorSuite:
- zero operators are empty
- non-zero operators are non-empty
- cannot build mismatch with wrong ref length
- collapsing a non repeated set of operators should eliminate 0 ops
- collapsing a repeated set of operators with mixed match/mismatch
- collapse a set of operators with repeats
- collapse a set of operators with repeats and clips
- make a cigar and md tag from a single sequence match
- make a cigar and md tag from a single sequence mismatch
- make a cigar and md tag from a single multi-base sequence match
- make a cigar and md tag from a single deletion
- make a cigar and md tag from a single insertion
- make a cigar for a match followed by a deletion
- make a cigar for an insertion flanked by matches
- make a cigar for a match followed by a mismatch
- make a cigar for a multi-base mismatch flanked by matches
- make a cigar for a match after a clip
- make a cigar for a mismatch after a clip
- extract reference from a single snp
- extract reference from a single deletion
- extract reference from a single insertion
- extract reference from a soft clipped sequence
- extract reference from a hard clipped sequence
- extract reference from a match flanked deletion
- extract reference from a match flanked insertion
- read must be mapped to extract alignment operators
- extracting alignment operators will fail if cigar is unset
- extracting alignment operators will fail if cigar is *
- extracting alignment operators will fail if MD tag is unset
- extract alignment operators from a perfect read
- extract alignment operators from a read with a single mismatch
- extract alignment operators from a read with a single deletion
- extract alignment operators from a read with a single insertion
LogUtilsSuite:
- test our nifty log summer
- can we compute the sum of logs correctly?
- can we compute the additive inverse of logs correctly?
ObservationSuite:
- cannot create an observation with empty likelihoods
- cannot create an observation with 1-length likelihoods
- cannot create an observation with mismatching likelihood lengths
- forward strand must be >= 0
- forward strand cannot exceed coverage
- square map-q must be >= 0
- coverage is strictly positive
- invert an observation
- null an observation
RealignmentBlockSuite:
- folding over a clip returns the clip operator, soft clip
- folding over a clip returns the clip operator, hard clip
- folding over a canonical block returns the original alignment
- violate an invariant of the fold function, part 1
- violate an invariant of the fold function, part 2
- apply the fold function on a realignable block
- having a clip in the middle of a read is illegal
- can't have two soft clips back to back
- a read that is an exact sequence match is canonical
- hard clip before soft clip is ok at start of read
- hard clip after soft clip is ok at end of read
- a read with a single snp is canonical
- a read containing an indel with exact flanks is wholly realignable
- a read containing an indel with exact flanks is wholly realignable, with soft clipped bases
- a read containing an indel with longer flanks can be split into multiple blocks
- a read containing an indel with longer flanks on both sides can be split into multiple blocks
- properly handle a read that starts with a long soft clip
JointAnnotatorCallerSuite:
*** RUN ABORTED ***
  java.lang.NoClassDefFoundError: org/bdgenomics/adam/models/ReferencePosition$$anonfun$1
  at org.bdgenomics.adam.models.ReferencePosition$.apply(ReferencePosition.scala:89)
  at org.bdgenomics.adam.models.VariantContext$.buildFromGenotypes(VariantContext.scala:62)
  at org.bdgenomics.avocado.genotyping.JointAnnotatorCallerSuite$$anonfun$1.apply$mcV$sp(JointAnnotatorCallerSuite.scala:50)
  at org.bdgenomics.avocado.genotyping.JointAnnotatorCallerSuite$$anonfun$1.apply(JointAnnotatorCallerSuite.scala:43)
  at org.bdgenomics.avocado.genotyping.JointAnnotatorCallerSuite$$anonfun$1.apply(JointAnnotatorCallerSuite.scala:43)
  at org.scalatest.Transformer$$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$$anonfun$runTest$1.apply(FunSuiteLike.scala:175)
  at org.scalatest.SuperEngine.runTestImpl(Engine.scala:306)
  at org.scalatest.FunSuiteLike$class.runTest(FunSuiteLike.scala:175)
  at org.bdgenomics.avocado.genotyping.JointAnnotatorCallerSuite.org$scalatest$BeforeAndAfter$$super$runTest(JointAnnotatorCallerSuite.scala:31)
  at org.scalatest.BeforeAndAfter$class.runTest(BeforeAndAfter.scala:200)
  at org.bdgenomics.avocado.genotyping.JointAnnotatorCallerSuite.runTest(JointAnnotatorCallerSuite.scala:31)
  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:318)
  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.avocado.genotyping.JointAnnotatorCallerSuite.org$scalatest$BeforeAndAfter$$super$run(JointAnnotatorCallerSuite.scala:31)
  at org.scalatest.BeforeAndAfter$class.run(BeforeAndAfter.scala:241)
  at org.bdgenomics.avocado.genotyping.JointAnnotatorCallerSuite.run(JointAnnotatorCallerSuite.scala:31)
  at org.scalatest.Suite$class.callExecuteOnSuite$1(Suite.scala:1492)
  at org.scalatest.Suite$$anonfun$runNestedSuites$1.apply(Suite.scala:1528)
  at org.scalatest.Suite$$anonfun$runNestedSuites$1.apply(Suite.scala:1526)
  at scala.collection.IndexedSeqOptimized$class.foreach(IndexedSeqOptimized.scala:33)
  at scala.collection.mutable.ArrayOps$ofRef.foreach(ArrayOps.scala:108)
  at org.scalatest.Suite$class.runNestedSuites(Suite.scala:1526)
  at org.scalatest.tools.DiscoverySuite.runNestedSuites(DiscoverySuite.scala:29)
  at org.scalatest.Suite$class.run(Suite.scala:1421)
  at org.scalatest.tools.DiscoverySuite.run(DiscoverySuite.scala:29)
  at org.scalatest.tools.SuiteRunner.run(SuiteRunner.scala:55)
  at org.scalatest.tools.Runner$$anonfun$doRunRunRunDaDoRunRun$3.apply(Runner.scala:2563)
  at org.scalatest.tools.Runner$$anonfun$doRunRunRunDaDoRunRun$3.apply(Runner.scala:2557)
  at scala.collection.immutable.List.foreach(List.scala:318)
  at org.scalatest.tools.Runner$.doRunRunRunDaDoRunRun(Runner.scala:2557)
  at org.scalatest.tools.Runner$$anonfun$runOptionallyWithPassFailReporter$2.apply(Runner.scala:1044)
  at org.scalatest.tools.Runner$$anonfun$runOptionallyWithPassFailReporter$2.apply(Runner.scala:1043)
  at org.scalatest.tools.Runner$.withClassLoaderAndDispatchReporter(Runner.scala:2722)
  at org.scalatest.tools.Runner$.runOptionallyWithPassFailReporter(Runner.scala:1043)
  at org.scalatest.tools.Runner$.main(Runner.scala:860)
  at org.scalatest.tools.Runner.main(Runner.scala)
  Cause: java.lang.ClassNotFoundException: org.bdgenomics.adam.models.ReferencePosition$$anonfun$1
  at java.net.URLClassLoader.findClass(URLClassLoader.java:381)
  at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
  at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:331)
  at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
  at org.bdgenomics.adam.models.ReferencePosition$.apply(ReferencePosition.scala:89)
  at org.bdgenomics.adam.models.VariantContext$.buildFromGenotypes(VariantContext.scala:62)
  at org.bdgenomics.avocado.genotyping.JointAnnotatorCallerSuite$$anonfun$1.apply$mcV$sp(JointAnnotatorCallerSuite.scala:50)
  at org.bdgenomics.avocado.genotyping.JointAnnotatorCallerSuite$$anonfun$1.apply(JointAnnotatorCallerSuite.scala:43)
  at org.bdgenomics.avocado.genotyping.JointAnnotatorCallerSuite$$anonfun$1.apply(JointAnnotatorCallerSuite.scala:43)
  at org.scalatest.Transformer$$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$$anonfun$runTest$1.apply(FunSuiteLike.scala:175)
  at org.scalatest.SuperEngine.runTestImpl(Engine.scala:306)
  at org.scalatest.FunSuiteLike$class.runTest(FunSuiteLike.scala:175)
  at org.bdgenomics.avocado.genotyping.JointAnnotatorCallerSuite.org$scalatest$BeforeAndAfter$$super$runTest(JointAnnotatorCallerSuite.scala:31)
  at org.scalatest.BeforeAndAfter$class.runTest(BeforeAndAfter.scala:200)
  at org.bdgenomics.avocado.genotyping.JointAnnotatorCallerSuite.runTest(JointAnnotatorCallerSuite.scala:31)
  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:318)
  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.avocado.genotyping.JointAnnotatorCallerSuite.org$scalatest$BeforeAndAfter$$super$run(JointAnnotatorCallerSuite.scala:31)
  at org.scalatest.BeforeAndAfter$class.run(BeforeAndAfter.scala:241)
  at org.bdgenomics.avocado.genotyping.JointAnnotatorCallerSuite.run(JointAnnotatorCallerSuite.scala:31)
  at org.scalatest.Suite$class.callExecuteOnSuite$1(Suite.scala:1492)
  at org.scalatest.Suite$$anonfun$runNestedSuites$1.apply(Suite.scala:1528)
  at org.scalatest.Suite$$anonfun$runNestedSuites$1.apply(Suite.scala:1526)
  at scala.collection.IndexedSeqOptimized$class.foreach(IndexedSeqOptimized.scala:33)
  at scala.collection.mutable.ArrayOps$ofRef.foreach(ArrayOps.scala:108)
  at org.scalatest.Suite$class.runNestedSuites(Suite.scala:1526)
  at org.scalatest.tools.DiscoverySuite.runNestedSuites(DiscoverySuite.scala:29)
  at org.scalatest.Suite$class.run(Suite.scala:1421)
  at org.scalatest.tools.DiscoverySuite.run(DiscoverySuite.scala:29)
  at org.scalatest.tools.SuiteRunner.run(SuiteRunner.scala:55)
  at org.scalatest.tools.Runner$$anonfun$doRunRunRunDaDoRunRun$3.apply(Runner.scala:2563)
  at org.scalatest.tools.Runner$$anonfun$doRunRunRunDaDoRunRun$3.apply(Runner.scala:2557)
  at scala.collection.immutable.List.foreach(List.scala:318)
  at org.scalatest.tools.Runner$.doRunRunRunDaDoRunRun(Runner.scala:2557)
  at org.scalatest.tools.Runner$$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)
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Skipping avocado: A Variant Caller, Distributed
[INFO] This project has been banned from the build due to previous failures.
[INFO] ------------------------------------------------------------------------
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary:
[INFO] 
[INFO] avocado: A Variant Caller, Distributed ............ SUCCESS [3.653s]
[INFO] avocado-core: Core variant calling algorithms ..... FAILURE [24:10.983s]
[INFO] avocado-cli: Command line interface for a distributed variant caller  SKIPPED
[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 24:14.836s
[INFO] Finished at: Mon Jan 01 04:39:53 PST 2018
[INFO] Final Memory: 33M/1109M
[INFO] ------------------------------------------------------------------------
[ERROR] Failed to execute goal org.scalatest:scalatest-maven-plugin:1.0:test (test) on project avocado-core-spark2_2.10: There are test failures -> [Help 1]
[ERROR] 
[ERROR] To see the full stack trace of the errors, re-run Maven with the -e switch.
[ERROR] Re-run Maven using the -X switch to enable full debug logging.
[ERROR] 
[ERROR] For more information about the errors and possible solutions, please read the following articles:
[ERROR] [Help 1] http://cwiki.apache.org/confluence/display/MAVEN/MojoFailureException
[ERROR] 
[ERROR] After correcting the problems, you can resume the build with the command
[ERROR]   mvn <goals> -rf :avocado-core-spark2_2.10
Build step 'Execute shell' marked build as failure
Recording test results
ERROR: Step ?Publish JUnit test result report? failed: No test report files were found. Configuration error?
Sending e-mails to: fnothaft@berkeley.edu
Finished: FAILURE