FailedConsole Output

Skipping 2,029 KB.. Full Log
KoEttlJQdnYxAAJrJTsAN/bC9aUAAAA=  at org.scalatest.tools.Runner$.main(Runner.scala:860)
  at org.scalatest.tools.Runner.main(Runner.scala)
ObserverSuite:
- a fully clipped read will not generate any observations
- generate observations for a sequence match under diploid model
- generate observations for a read with an insertion under diploid model
- generate observations for a read with a deletion under diploid model
DiscoveredVariantSuite:
- round trip conversion to/from variant
SquareOffReferenceModelSuite:
- don't trim a snp
- trim a mnp
- trim an insertion
- don't trim a deletion
- extract variants finds sites with a called alt *** FAILED ***
  java.lang.reflect.InvocationTargetException:
  at sun.reflect.GeneratedMethodAccessor63.invoke(Unknown Source)
  at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
  at java.lang.reflect.Method.invoke(Method.java:498)
  at org.bdgenomics.utils.misc.HadoopUtil$.newJob(HadoopUtil.scala:35)
  at org.bdgenomics.utils.misc.HadoopUtil$.newJob(HadoopUtil.scala:48)
  at org.bdgenomics.adam.rdd.ADAMContext.org$bdgenomics$adam$rdd$ADAMContext$$readVcfRecords(ADAMContext.scala:2134)
  at org.bdgenomics.adam.rdd.ADAMContext$$anonfun$loadVcf$1.apply(ADAMContext.scala:2166)
  at org.bdgenomics.adam.rdd.ADAMContext$$anonfun$loadVcf$1.apply(ADAMContext.scala:2163)
  at scala.Option.fold(Option.scala:158)
  at org.apache.spark.rdd.Timer.time(Timer.scala:48)
  at org.bdgenomics.adam.rdd.ADAMContext.loadVcf(ADAMContext.scala:2163)
  at org.bdgenomics.adam.rdd.ADAMContext$$anonfun$loadGenotypes$1.apply(ADAMContext.scala:3185)
  at org.bdgenomics.adam.rdd.ADAMContext$$anonfun$loadGenotypes$1.apply(ADAMContext.scala:3183)
  at scala.Option.fold(Option.scala:158)
  at org.apache.spark.rdd.Timer.time(Timer.scala:48)
  at org.bdgenomics.adam.rdd.ADAMContext.loadGenotypes(ADAMContext.scala:3181)
  at org.bdgenomics.avocado.genotyping.SquareOffReferenceModelSuite$$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: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.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$$anonfun$runNestedSuites$1.apply(Suite.scala:1526)
  at scala.collection.IndexedSeqOptimized$class.foreach(IndexedSeqOptimized.scala:33)
  at scala.collection.mutable.ArrayOps$ofRef.foreach(ArrayOps.scala:186)
  at org.scalatest.Suite$class.runNestedSuites(Suite.scala:1526)
  at org.scalatest.tools.DiscoverySuite.runNestedSuites(DiscoverySuite.scala:29)
  at org.scalatest.Suite$class.run(Suite.scala:1421)
  at org.scalatest.tools.DiscoverySuite.run(DiscoverySuite.scala:29)
  at org.scalatest.tools.SuiteRunner.run(SuiteRunner.scala:55)
  at org.scalatest.tools.Runner$$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$$anonfun$runOptionallyWithPassFailReporter$2.apply(Runner.scala:1043)
  at org.scalatest.tools.Runner$.withClassLoaderAndDispatchReporter(Runner.scala:2722)
  at org.scalatest.tools.Runner$.runOptionallyWithPassFailReporter(Runner.scala:1043)
  at org.scalatest.tools.Runner$.main(Runner.scala:860)
  at org.scalatest.tools.Runner.main(Runner.scala)
  Cause: java.lang.NoClassDefFoundError: Could not initialize class org.apache.hadoop.security.Credentials
  at org.apache.hadoop.mapred.JobConf.<init>(JobConf.java:334)
  at org.apache.hadoop.mapreduce.Job.getInstance(Job.java:184)
  at sun.reflect.GeneratedMethodAccessor63.invoke(Unknown Source)
  at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
  at java.lang.reflect.Method.invoke(Method.java:498)
  at org.bdgenomics.utils.misc.HadoopUtil$.newJob(HadoopUtil.scala:35)
  at org.bdgenomics.utils.misc.HadoopUtil$.newJob(HadoopUtil.scala:48)
  at org.bdgenomics.adam.rdd.ADAMContext.org$bdgenomics$adam$rdd$ADAMContext$$readVcfRecords(ADAMContext.scala:2134)
  at org.bdgenomics.adam.rdd.ADAMContext$$anonfun$loadVcf$1.apply(ADAMContext.scala:2166)
  at org.bdgenomics.adam.rdd.ADAMContext$$anonfun$loadVcf$1.apply(ADAMContext.scala:2163)
  at scala.Option.fold(Option.scala:158)
  at org.apache.spark.rdd.Timer.time(Timer.scala:48)
  at org.bdgenomics.adam.rdd.ADAMContext.loadVcf(ADAMContext.scala:2163)
  at org.bdgenomics.adam.rdd.ADAMContext$$anonfun$loadGenotypes$1.apply(ADAMContext.scala:3185)
  at org.bdgenomics.adam.rdd.ADAMContext$$anonfun$loadGenotypes$1.apply(ADAMContext.scala:3183)
  at scala.Option.fold(Option.scala:158)
  at org.apache.spark.rdd.Timer.time(Timer.scala:48)
  at org.bdgenomics.adam.rdd.ADAMContext.loadGenotypes(ADAMContext.scala:3181)
  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$$anonfun$traverseSubNodes$1$1.apply(Engine.scala:401)
  at scala.collection.immutable.List.foreach(List.scala:381)
  at org.scalatest.SuperEngine.traverseSubNodes$1(Engine.scala:401)
  at org.scalatest.SuperEngine.org$scalatest$SuperEngine$$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$$anonfun$run$1.apply(FunSuiteLike.scala:212)
  at org.scalatest.SuperEngine.runImpl(Engine.scala:545)
  at org.scalatest.FunSuiteLike$class.run(FunSuiteLike.scala:212)
  at org.bdgenomics.avocado.genotyping.SquareOffReferenceModelSuite.org$scalatest$BeforeAndAfter$$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$ofRef.foreach(ArrayOps.scala:186)
  at org.scalatest.Suite$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)
- 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
- no variants in rdd with sequence match reads
- find snp in read with a 1bp sequence mismatch
- find one snp in reads with 1bp sequence mismatch
- find insertion in read
- find insertion in reads
- find deletion in read
- find deletion in reads
- 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:
- discard reference site
- calculate MAF for all called genotypes
- calculate MAF ignoring uncalled genotypes
- roll up variant annotations from a single genotype
- roll up variant annotations across multiple genotypes
- recalling genotypes is a no-op for no calls and complex hets
- recall a genotype so that the state changes
- allele frequency being outside of (0.0, 1.0) just computes posteriors
- compute variant quality from a single genotype
- compute variant quality from multiple genotypes
CopyNumberMapSuite:
- create an empty map
- create a map with only diploid features
- create a map with a mix of features
PrefilterReadsSuite:
- filter on read uniqueness
- filter unmapped reads
- filter autosomal chromosomes with grc names
- filter sex chromosomes with grc names
- filter mitochondrial chromosome with a grc names
- filter autosomal chromosomes with hg names
- filter sex chromosomes with hg names
- filter mitochondrial chromosome with a hg names
- filter autosomal chromosomes from generator
- filter autosomal + sex chromosomes from generator
- filter all chromosomes from generator
- update a read whose mate is mapped to a filtered contig
- filter reads mapped to autosomal chromosomes from generator
- filter reads mapped to autosomal + sex chromosomes from generator
- filter reads mapped to all chromosomes from generator
- filter reads uniquely mapped to autosomal chromosomes from generator
- filter reads uniquely mapped to autosomal + sex chromosomes from generator
- filter reads uniquely mapped to all chromosomes from generator
- filter rdd of reads mapped to autosomal chromosomes from generator
- filter rdd of reads mapped to autosomal + sex chromosomes from generator
- filter rdd of reads mapped to all chromosomes from generator
- filter rdd of reads uniquely mapped to autosomal chromosomes from generator
- filter rdd of reads uniquely mapped to autosomal + sex chromosomes from generator
- filter rdd of reads uniquely mapped to all chromosomes from generator
Run completed in 1 minute, 11 seconds.
Total number of tests run: 282
Suites: completed 23, aborted 0
Tests: succeeded 257, failed 25, canceled 0, ignored 1, pending 0
*** 25 TESTS FAILED ***
[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 [  4.739 s]
[INFO] avocado-core: Core variant calling algorithms ...... FAILURE [02:04 min]
[INFO] avocado-cli: Command line interface for a distributed variant caller SKIPPED
[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 02:09 min
[INFO] Finished at: 2018-11-13T15:40:23-08:00
[INFO] Final Memory: 40M/1492M
[INFO] ------------------------------------------------------------------------
[ERROR] Failed to execute goal org.scalatest:scalatest-maven-plugin:1.0:test (test) on project avocado-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 :avocado-core_2.11
Build step 'Execute shell' marked build as failure
Recording test results
Publishing Scoverage XML and HTML report...
null
Setting commit status on GitHub for https://github.com/bigdatagenomics/avocado/commit/463dfedc7f7a836505ab7825e885dd972aec2fb3
Finished: FAILURE