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Downloading: https://oss.sonatype.org/content/repositories/releases/com/github/fommil/netlib/netlib-native_system-linux-i686/1.1/netlib-native_system-linux-i686-1.1-natives.jar
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Downloaded: https://oss.sonatype.org/content/repositories/releases/com/github/fommil/netlib/netlib-native_system-win-i686/1.1/netlib-native_system-win-i686-1.1-natives.jar (549 KB at 2284.6 KB/sec)
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ deca-core_2.11 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-source (add-source) @ deca-core_2.11 ---
[INFO] Source directory: /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-core/src/main/scala added.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ deca-core_2.11 ---
[INFO] Modified 0 of 20 .scala files
[INFO] 
[INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ deca-core_2.11 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-core/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ deca-core_2.11 ---
[WARNING]  Expected all dependencies to require Scala version: 2.11.8
[WARNING]  org.bdgenomics.utils:utils-misc-spark2_2.11:0.2.11 requires scala version: 2.11.4
[WARNING] Multiple versions of scala libraries detected!
[WARNING] Zinc server is not available at port 3030 - reverting to normal incremental compile
[INFO] Using incremental compilation
[INFO] Compiling 15 Scala sources to /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-core/target/scala-2.11.8/classes...
[WARNING] /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-core/src/main/scala/org/bdgenomics/deca/util/MLibUtils.scala:46: non-variable type argument Int in type pattern breeze.linalg.SliceVector[Int,Double] is unchecked since it is eliminated by erasure
[WARNING]       case v: SliceVector[Int, Double] => breezeVectorToMLlib(v.toDenseVector)
[WARNING]               ^
[WARNING] there were 14 deprecation warnings; re-run with -deprecation for details
[WARNING] two warnings found
[INFO] 
[INFO] --- maven-compiler-plugin:3.5.1:compile (default-compile) @ deca-core_2.11 ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-test-source (add-test-source) @ deca-core_2.11 ---
[INFO] Test Source directory: /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-core/src/test/scala added.
[INFO] 
[INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ deca-core_2.11 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 11 resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ deca-core_2.11 ---
[WARNING]  Expected all dependencies to require Scala version: 2.11.8
[WARNING]  org.bdgenomics.utils:utils-misc-spark2_2.11:0.2.11 requires scala version: 2.11.4
[WARNING] Multiple versions of scala libraries detected!
[WARNING] Zinc server is not available at port 3030 - reverting to normal incremental compile
[INFO] Using incremental compilation
[INFO] Compiling 5 Scala sources to /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-core/target/scala-2.11.8/test-classes...
[INFO] 
[INFO] --- maven-compiler-plugin:3.5.1:testCompile (default-testCompile) @ deca-core_2.11 ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-surefire-plugin:2.7:test (default-test) @ deca-core_2.11 ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- scalatest-maven-plugin:1.0:test (test) @ deca-core_2.11 ---
Discovery starting.
Discovery completed in 638 milliseconds.
Run starting. Expected test count is: 16
NormalizationSuite:
2017-08-24 13:45:06 WARN  NativeCodeLoader:62 - Unable to load native-hadoop library for your platform... using builtin-java classes where applicable
2017-08-24 13:45:12 WARN  Executor:66 - 1 block locks were not released by TID = 7:
[rdd_0_3]
2017-08-24 13:45:12 WARN  Executor:66 - 1 block locks were not released by TID = 5:
[rdd_0_1]
- mean centers data by columns
- zScores data by rows
2017-08-24 13:45:13 WARN  Executor:66 - 1 block locks were not released by TID = 11:
[rdd_3_3]
2017-08-24 13:45:13 WARN  Executor:66 - 1 block locks were not released by TID = 9:
[rdd_3_1]
2017-08-24 13:45:14 WARN  BLAS:61 - Failed to load implementation from: com.github.fommil.netlib.NativeSystemBLAS
2017-08-24 13:45:14 WARN  BLAS:61 - Failed to load implementation from: com.github.fommil.netlib.NativeRefBLAS
2017-08-24 13:45:14 WARN  LAPACK:61 - Failed to load implementation from: com.github.fommil.netlib.NativeSystemLAPACK
2017-08-24 13:45:14 WARN  LAPACK:61 - Failed to load implementation from: com.github.fommil.netlib.NativeRefLAPACK
2017-08-24 13:45:14 WARN  Executor:66 - 1 block locks were not released by TID = 21:
[rdd_3_1]
2017-08-24 13:45:14 WARN  Executor:66 - 1 block locks were not released by TID = 23:
[rdd_3_3]
- removes top k components of data
2017-08-24 13:45:15 WARN  Executor:66 - 1 block locks were not released by TID = 0:
[rdd_1_0]
2017-08-24 13:45:15 WARN  Executor:66 - 1 block locks were not released by TID = 6:
[rdd_1_0]
2017-08-24 13:45:15 WARN  RowMatrix:66 - The input data is not directly cached, which may hurt performance if its parent RDDs are also uncached.
2017-08-24 13:45:15 WARN  ARPACK:61 - Failed to load implementation from: com.github.fommil.netlib.NativeSystemARPACK
2017-08-24 13:45:15 WARN  ARPACK:61 - Failed to load implementation from: com.github.fommil.netlib.NativeRefARPACK
2017-08-24 13:45:16 WARN  RowMatrix:66 - The input data was not directly cached, which may hurt performance if its parent RDDs are also uncached.
2017-08-24 13:45:16 WARN  Executor:66 - 1 block locks were not released by TID = 35:
[rdd_23_0]
2017-08-24 13:45:16 WARN  Executor:66 - 1 block locks were not released by TID = 41:
[rdd_23_0]
2017-08-24 13:45:16 WARN  Executor:66 - 1 block locks were not released by TID = 44:
[rdd_4_0]
- produces same results with fixed k
2017-08-24 13:45:16 WARN  Executor:66 - 1 block locks were not released by TID = 0:
[rdd_1_0]
2017-08-24 13:45:16 WARN  Executor:66 - 1 block locks were not released by TID = 6:
[rdd_1_0]
2017-08-24 13:45:16 WARN  Executor:66 - 1 block locks were not released by TID = 7:
[rdd_7_0]
2017-08-24 13:45:16 WARN  Executor:66 - 1 block locks were not released by TID = 13:
[rdd_7_0]
2017-08-24 13:45:17 WARN  Executor:66 - 1 block locks were not released by TID = 18:
[rdd_4_0]
- filters and centers SVD results
2017-08-24 13:45:17 WARN  Executor:66 - 1 block locks were not released by TID = 0:
[rdd_1_0]
2017-08-24 13:45:17 WARN  Executor:66 - 1 block locks were not released by TID = 8:
[rdd_1_0]
2017-08-24 13:45:17 WARN  Executor:66 - 1 block locks were not released by TID = 9:
[rdd_10_0]
2017-08-24 13:45:17 WARN  Executor:66 - 1 block locks were not released by TID = 15:
[rdd_10_0]
2017-08-24 13:45:17 WARN  Executor:66 - 1 block locks were not released by TID = 24:
[rdd_21_0]
2017-08-24 13:45:17 WARN  RowMatrix:66 - The input data is not directly cached, which may hurt performance if its parent RDDs are also uncached.
2017-08-24 13:45:18 WARN  RowMatrix:66 - The input data was not directly cached, which may hurt performance if its parent RDDs are also uncached.
2017-08-24 13:45:18 WARN  RowMatrix:66 - The input data is not directly cached, which may hurt performance if its parent RDDs are also uncached.
2017-08-24 13:45:19 WARN  RowMatrix:66 - The input data was not directly cached, which may hurt performance if its parent RDDs are also uncached.
2017-08-24 13:45:19 WARN  Executor:66 - 1 block locks were not released by TID = 99:
[rdd_64_0]
- filters and normalizes read depth data
HMMSuite:
2017-08-24 13:45:19 WARN  Executor:66 - 1 block locks were not released by TID = 0:
[rdd_1_0]
2017-08-24 13:45:19 WARN  Executor:66 - 1 block locks were not released by TID = 6:
[rdd_1_0]
- Generates transition matrix for array of distances
- Handles contig boundaries in computing transition matrix
2017-08-24 13:45:19 WARN  Executor:66 - 1 block locks were not released by TID = 0:
[rdd_1_0]
2017-08-24 13:45:20 WARN  Executor:66 - 1 block locks were not released by TID = 6:
[rdd_1_0]
- Discovers CNVs
DecaSuite:
2017-08-24 13:45:20 WARN  Executor:66 - 1 block locks were not released by TID = 0:
[rdd_1_0]
2017-08-24 13:45:21 WARN  Executor:66 - 1 block locks were not released by TID = 6:
[rdd_1_0]
- read XHMM matrix
2017-08-24 13:45:21 WARN  Executor:66 - 1 block locks were not released by TID = 0:
[rdd_1_0]
2017-08-24 13:45:21 WARN  Executor:66 - 1 block locks were not released by TID = 6:
[rdd_1_0]
2017-08-24 13:45:21 WARN  Executor:66 - 1 block locks were not released by TID = 9:
[rdd_9_0]
2017-08-24 13:45:21 WARN  Executor:66 - 1 block locks were not released by TID = 15:
[rdd_9_0]
- write XHMM matrix
CoverageSuite:
- Finds correct first target
- computes coverage for targets
- counts fragments not just reads *** FAILED ***
  java.lang.NullPointerException:
  at org.bdgenomics.deca.CoverageSuite$$anonfun$3.apply$mcV$sp(CoverageSuite.scala:54)
  at org.bdgenomics.utils.misc.SparkFunSuite$$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.deca.CoverageSuite.org$scalatest$BeforeAndAfter$$super$runTest(CoverageSuite.scala:11)
  at org.scalatest.BeforeAndAfter$class.runTest(BeforeAndAfter.scala:200)
  at org.bdgenomics.deca.CoverageSuite.runTest(CoverageSuite.scala:11)
  at org.scalatest.FunSuiteLike$$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$$anonfun$run$1.apply(FunSuiteLike.scala:212)
  at org.scalatest.SuperEngine.runImpl(Engine.scala:545)
  at org.scalatest.FunSuiteLike$class.run(FunSuiteLike.scala:212)
  at org.bdgenomics.deca.CoverageSuite.org$scalatest$BeforeAndAfter$$super$run(CoverageSuite.scala:11)
  at org.scalatest.BeforeAndAfter$class.run(BeforeAndAfter.scala:241)
  at org.bdgenomics.deca.CoverageSuite.run(CoverageSuite.scala:11)
  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)
- counts imperfectly paired fragments *** FAILED ***
  java.lang.NullPointerException:
  at org.bdgenomics.deca.CoverageSuite$$anonfun$4.apply$mcV$sp(CoverageSuite.scala:69)
  at org.bdgenomics.utils.misc.SparkFunSuite$$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.deca.CoverageSuite.org$scalatest$BeforeAndAfter$$super$runTest(CoverageSuite.scala:11)
  at org.scalatest.BeforeAndAfter$class.runTest(BeforeAndAfter.scala:200)
  at org.bdgenomics.deca.CoverageSuite.runTest(CoverageSuite.scala:11)
  at org.scalatest.FunSuiteLike$$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$$anonfun$run$1.apply(FunSuiteLike.scala:212)
  at org.scalatest.SuperEngine.runImpl(Engine.scala:545)
  at org.scalatest.FunSuiteLike$class.run(FunSuiteLike.scala:212)
  at org.bdgenomics.deca.CoverageSuite.org$scalatest$BeforeAndAfter$$super$run(CoverageSuite.scala:11)
  at org.scalatest.BeforeAndAfter$class.run(BeforeAndAfter.scala:241)
  at org.bdgenomics.deca.CoverageSuite.run(CoverageSuite.scala:11)
  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)
- incorporates CIGAR into fragment analysis *** FAILED ***
  java.lang.NullPointerException:
  at org.bdgenomics.deca.CoverageSuite$$anonfun$5.apply$mcV$sp(CoverageSuite.scala:84)
  at org.bdgenomics.utils.misc.SparkFunSuite$$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.deca.CoverageSuite.org$scalatest$BeforeAndAfter$$super$runTest(CoverageSuite.scala:11)
  at org.scalatest.BeforeAndAfter$class.runTest(BeforeAndAfter.scala:200)
  at org.bdgenomics.deca.CoverageSuite.runTest(CoverageSuite.scala:11)
  at org.scalatest.FunSuiteLike$$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$$anonfun$run$1.apply(FunSuiteLike.scala:212)
  at org.scalatest.SuperEngine.runImpl(Engine.scala:545)
  at org.scalatest.FunSuiteLike$class.run(FunSuiteLike.scala:212)
  at org.bdgenomics.deca.CoverageSuite.org$scalatest$BeforeAndAfter$$super$run(CoverageSuite.scala:11)
  at org.scalatest.BeforeAndAfter$class.run(BeforeAndAfter.scala:241)
  at org.bdgenomics.deca.CoverageSuite.run(CoverageSuite.scala:11)
  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)
Run completed in 17 seconds, 864 milliseconds.
Total number of tests run: 16
Suites: completed 5, aborted 0
Tests: succeeded 13, failed 3, canceled 0, ignored 0, pending 0
*** 3 TESTS FAILED ***
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary:
[INFO] 
[INFO] deca: Distributed Exome CNV Analyzer .............. SUCCESS [2.393s]
[INFO] deca-core: Core variant calling algorithms ........ FAILURE [1:07.250s]
[INFO] deca-cli: Command line interface for a distributed variant caller  SKIPPED
[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 1:09.841s
[INFO] Finished at: Thu Aug 24 13:45:23 PDT 2017
[INFO] Final Memory: 42M/1406M
[INFO] ------------------------------------------------------------------------
[ERROR] Failed to execute goal org.scalatest:scalatest-maven-plugin:1.0:test (test) on project deca-core_2.11: 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 :deca-core_2.11
Build step 'Execute shell' marked build as failure
Recording test results
Publishing Scoverage XML and HTML report...
null
Finished: FAILURE