FailedConsole Output

Skipping 132 KB.. Full Log
kDgMEMDIxMFQUlDDI2RQXJOYpFJdU5qTaKoEttlJQdnYxAAJrJTsAN/bC9aUAAAA=  org.bdgenomics.utils.misc.MathUtils.fpEquals(nonRefObservation.alleleLogLikelihoods.apply(0), BiallelicGenotyperSuite.this.os.logL(2, 2, 0.9999, 0.9999), org.bdgenomics.utils.misc.MathUtils.fpEquals$default$3) was false (BiallelicGenotyperSuite.scala:182)
  org.scalatest.exceptions.TestFailedException:
  at org.scalatest.Assertions$class.newAssertionFailedException(Assertions.scala:500)
  at org.scalatest.FunSuite.newAssertionFailedException(FunSuite.scala:1555)
  at org.scalatest.Assertions$AssertionsHelper.macroAssert(Assertions.scala:466)
  at org.bdgenomics.avocado.genotyping.BiallelicGenotyperSuite$$anonfun$7$$anonfun$apply$mcV$sp$1.apply(BiallelicGenotyperSuite.scala:182)
  at org.bdgenomics.avocado.genotyping.BiallelicGenotyperSuite$$anonfun$7$$anonfun$apply$mcV$sp$1.apply(BiallelicGenotyperSuite.scala:171)
  at scala.collection.immutable.List.foreach(List.scala:381)
  at org.bdgenomics.avocado.genotyping.BiallelicGenotyperSuite$$anonfun$7.apply$mcV$sp(BiallelicGenotyperSuite.scala:171)
  at org.bdgenomics.utils.misc.SparkFunSuite$$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.BiallelicGenotyperSuite.org$scalatest$BeforeAndAfter$$super$runTest(BiallelicGenotyperSuite.scala:43)
  at org.scalatest.BeforeAndAfter$class.runTest(BeforeAndAfter.scala:200)
  at org.bdgenomics.avocado.genotyping.BiallelicGenotyperSuite.runTest(BiallelicGenotyperSuite.scala:43)
  at org.scalatest.FunSuiteLike$$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$$anonfun$run$1.apply(FunSuiteLike.scala:212)
  at org.scalatest.SuperEngine.runImpl(Engine.scala:545)
  at org.scalatest.FunSuiteLike$class.run(FunSuiteLike.scala:212)
  at org.bdgenomics.avocado.genotyping.BiallelicGenotyperSuite.org$scalatest$BeforeAndAfter$$super$run(BiallelicGenotyperSuite.scala:43)
  at org.scalatest.BeforeAndAfter$class.run(BeforeAndAfter.scala:241)
  at org.bdgenomics.avocado.genotyping.BiallelicGenotyperSuite.run(BiallelicGenotyperSuite.scala:43)
  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)
- build genotype for het snp
- force call possible STR/indel !!! IGNORED !!!
- log space factorial
- fisher test for strand bias
2017-10-12 09:08:21 WARN  BiallelicGenotyper:157 - Input RDD is not persisted. Performance may be degraded.
2017-10-12 09:08:28 WARN  TaskSetManager:66 - Stage 5 contains a task of very large size (10540 KB). The maximum recommended task size is 100 KB.
- discover and call simple SNP
2017-10-12 09:09:37 WARN  BiallelicGenotyper:157 - Input RDD is not persisted. Performance may be degraded.
2017-10-12 09:09:43 WARN  TaskSetManager:66 - Stage 5 contains a task of very large size (10540 KB). The maximum recommended task size is 100 KB.
- discover and call simple SNP and score all sites
2017-10-12 09:10:53 WARN  BiallelicGenotyper:157 - Input RDD is not persisted. Performance may be degraded.
2017-10-12 09:11:00 WARN  TaskSetManager:66 - Stage 5 contains a task of very large size (10540 KB). The maximum recommended task size is 100 KB.
- discover and call short indel
2017-10-12 09:12:10 WARN  BiallelicGenotyper:157 - Input RDD is not persisted. Performance may be degraded.
2017-10-12 09:12:18 WARN  TaskSetManager:66 - Stage 5 contains a task of very large size (10540 KB). The maximum recommended task size is 100 KB.
2017-10-12 09:12:30 ERROR BiallelicGenotyper:358 - Processing read H06JUADXX130110:1:1109:10925:52628 failed with exception java.lang.StringIndexOutOfBoundsException: String index out of range: 0. Skipping...
2017-10-12 09:12:30 ERROR BiallelicGenotyper:358 - Processing read H06JUADXX130110:1:1116:7369:15293 failed with exception java.lang.StringIndexOutOfBoundsException: String index out of range: 0. Skipping...
2017-10-12 09:12:30 ERROR BiallelicGenotyper:358 - Processing read H06HDADXX130110:2:1115:12347:40533 failed with exception java.lang.StringIndexOutOfBoundsException: String index out of range: 0. Skipping...
2017-10-12 09:12:30 ERROR BiallelicGenotyper:358 - Processing read H06HDADXX130110:1:2110:7844:95190 failed with exception java.lang.StringIndexOutOfBoundsException: String index out of range: 0. Skipping...
2017-10-12 09:12:30 ERROR BiallelicGenotyper:358 - Processing read H06HDADXX130110:1:2203:13041:33390 failed with exception java.lang.StringIndexOutOfBoundsException: String index out of range: 0. Skipping...
- discover and call het and hom snps
2017-10-12 09:13:30 WARN  Executor:66 - 1 block locks were not released by TID = 202:
[rdd_2_0]
- score a single read covering a deletion
2017-10-12 09:13:37 WARN  TaskSetManager:66 - Stage 7 contains a task of very large size (10540 KB). The maximum recommended task size is 100 KB.
- discover and force call hom alt deletion
2017-10-12 09:14:53 WARN  TaskSetManager:66 - Stage 7 contains a task of very large size (10540 KB). The maximum recommended task size is 100 KB.
- call hom alt AGCCAGTGGACGCCGACCT->A deletion at 1/875159
2017-10-12 09:16:01 WARN  BiallelicGenotyper:157 - Input RDD is not persisted. Performance may be degraded.
2017-10-12 09:16:08 WARN  TaskSetManager:66 - Stage 5 contains a task of very large size (10540 KB). The maximum recommended task size is 100 KB.
- call hom alt TACACACACACACACACACACACACACACAC->T deletion at 1/1777263
2017-10-12 09:17:16 WARN  BiallelicGenotyper:157 - Input RDD is not persisted. Performance may be degraded.
2017-10-12 09:17:23 WARN  TaskSetManager:66 - Stage 5 contains a task of very large size (10540 KB). The maximum recommended task size is 100 KB.
- call hom alt CAG->C deletion at 1/1067596
2017-10-12 09:18:33 WARN  BiallelicGenotyper:157 - Input RDD is not persisted. Performance may be degraded.
2017-10-12 09:18:39 WARN  TaskSetManager:66 - Stage 5 contains a task of very large size (10540 KB). The maximum recommended task size is 100 KB.
- call hom alt C->G snp at 1/877715
2017-10-12 09:19:48 WARN  BiallelicGenotyper:157 - Input RDD is not persisted. Performance may be degraded.
2017-10-12 09:19:55 WARN  TaskSetManager:66 - Stage 5 contains a task of very large size (10540 KB). The maximum recommended task size is 100 KB.
- call hom alt ACAG->A deletion at 1/886049
2017-10-12 09:21:07 WARN  BiallelicGenotyper:157 - Input RDD is not persisted. Performance may be degraded.
2017-10-12 09:21:14 WARN  TaskSetManager:66 - Stage 5 contains a task of very large size (10540 KB). The maximum recommended task size is 100 KB.
- call hom alt GA->CC mnp at 1/889158?9
2017-10-12 09:22:24 WARN  BiallelicGenotyper:157 - Input RDD is not persisted. Performance may be degraded.
2017-10-12 09:22:32 WARN  TaskSetManager:66 - Stage 14 contains a task of very large size (10540 KB). The maximum recommended task size is 100 KB.
- call hom alt C->CCCCT insertion at 1/866511
2017-10-12 09:22:37 WARN  BiallelicGenotyper:157 - Input RDD is not persisted. Performance may be degraded.
2017-10-12 09:22:43 WARN  TaskSetManager:66 - Stage 5 contains a task of very large size (10540 KB). The maximum recommended task size is 100 KB.
- call het ATG->A deletion at 1/905130
2017-10-12 09:23:53 WARN  BiallelicGenotyper:157 - Input RDD is not persisted. Performance may be degraded.
2017-10-12 09:24:00 WARN  TaskSetManager:66 - Stage 5 contains a task of very large size (10540 KB). The maximum recommended task size is 100 KB.
- call het ATG->A deletion at 1/905130 while scoring all sites
2017-10-12 09:25:13 WARN  BiallelicGenotyper:157 - Input RDD is not persisted. Performance may be degraded.
2017-10-12 09:25:20 WARN  TaskSetManager:66 - Stage 5 contains a task of very large size (10540 KB). The maximum recommended task size is 100 KB.
- call het AG->A deletion at 1/907170
2017-10-12 09:26:28 WARN  BiallelicGenotyper:157 - Input RDD is not persisted. Performance may be degraded.
2017-10-12 09:26:35 WARN  TaskSetManager:66 - Stage 5 contains a task of very large size (10540 KB). The maximum recommended task size is 100 KB.
- call het T->G snp at 1/240898
2017-10-12 09:27:45 WARN  BiallelicGenotyper:157 - Input RDD is not persisted. Performance may be degraded.
2017-10-12 09:27:51 WARN  TaskSetManager:66 - Stage 5 contains a task of very large size (10540 KB). The maximum recommended task size is 100 KB.
- make het alt calls at biallelic snp locus
2017-10-12 09:29:01 WARN  BiallelicGenotyper:157 - Input RDD is not persisted. Performance may be degraded.
2017-10-12 09:29:07 WARN  TaskSetManager:66 - Stage 5 contains a task of very large size (10540 KB). The maximum recommended task size is 100 KB.
- call hom alt T->TAAA insertion at 1/4120185
2017-10-12 09:30:17 WARN  BiallelicGenotyper:157 - Input RDD is not persisted. Performance may be degraded.
2017-10-12 09:30:22 WARN  TaskSetManager:66 - Stage 5 contains a task of very large size (10540 KB). The maximum recommended task size is 100 KB.
{"variant": {"contigName": "1", "start": 5274546, "end": 5274551, "names": [], "splitFromMultiAllelic": false, "referenceAllele": "TTATA", "alternateAllele": "T", "quality": null, "filtersApplied": null, "filtersPassed": null, "filtersFailed": [], "annotation": null}, "contigName": "1", "start": 5274546, "end": 5274551, "variantCallingAnnotations": {"filtersApplied": null, "filtersPassed": null, "filtersFailed": [], "downsampled": null, "baseQRankSum": null, "fisherStrandBiasPValue": -0.0, "rmsMapQ": 97.46794, "mapq0Reads": null, "mqRankSum": null, "readPositionRankSum": null, "genotypePriors": [], "genotypePosteriors": [], "vqslod": null, "culprit": null, "attributes": {}}, "sampleId": "NA12878", "sampleDescription": null, "processingDescription": null, "alleles": ["ALT", "OTHER_ALT"], "expectedAlleleDosage": null, "referenceReadDepth": 0, "alternateReadDepth": 17, "readDepth": 38, "minReadDepth": null, "genotypeQuality": 249, "genotypeLikelihoods": [-70.87324901033372, 0.0, 9.157569518503912], "nonReferenceLikelihoods": [0.46526149370831527, 0.0, -0.6073937268968032], "strandBiasComponents": [0, 0, 8, 9], "splitFromMultiAllelic": false, "phased": false, "phaseSetId": null, "phaseQuality": null}
{"variant": {"contigName": "1", "start": 5274546, "end": 5274549, "names": [], "splitFromMultiAllelic": false, "referenceAllele": "TTA", "alternateAllele": "T", "quality": null, "filtersApplied": null, "filtersPassed": null, "filtersFailed": [], "annotation": null}, "contigName": "1", "start": 5274546, "end": 5274549, "variantCallingAnnotations": {"filtersApplied": null, "filtersPassed": null, "filtersFailed": [], "downsampled": null, "baseQRankSum": null, "fisherStrandBiasPValue": -0.0, "rmsMapQ": 83.795815, "mapq0Reads": null, "mqRankSum": null, "readPositionRankSum": null, "genotypePriors": [], "genotypePosteriors": [], "vqslod": null, "culprit": null, "attributes": {}}, "sampleId": "NA12878", "sampleDescription": null, "processingDescription": null, "alleles": ["ALT", "OTHER_ALT"], "expectedAlleleDosage": null, "referenceReadDepth": 0, "alternateReadDepth": 23, "readDepth": 38, "minReadDepth": null, "genotypeQuality": 249, "genotypeLikelihoods": [-126.58664682399018, 0.0, 13.440146510587008], "nonReferenceLikelihoods": [0.46526149370831527, 0.0, -0.6073937268968032], "strandBiasComponents": [0, 0, 11, 12], "splitFromMultiAllelic": false, "phased": false, "phaseSetId": null, "phaseQuality": null}
- call het alt TTATA,TTA->T insertion at 1/5274547
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
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 *** FAILED ***
  optC.isDefined was false (DiscoverVariantsSuite.scala:256)
  org.scalatest.exceptions.TestFailedException:
  at org.scalatest.Assertions$class.newAssertionFailedException(Assertions.scala:500)
  at org.scalatest.FunSuite.newAssertionFailedException(FunSuite.scala:1555)
  at org.scalatest.Assertions$AssertionsHelper.macroAssert(Assertions.scala:466)
  at org.bdgenomics.avocado.genotyping.DiscoverVariantsSuite$$anonfun$12.apply$mcV$sp(DiscoverVariantsSuite.scala:256)
  at org.bdgenomics.avocado.genotyping.DiscoverVariantsSuite$$anonfun$12.apply(DiscoverVariantsSuite.scala:250)
  at org.bdgenomics.avocado.genotyping.DiscoverVariantsSuite$$anonfun$12.apply(DiscoverVariantsSuite.scala:250)
  at org.scalatest.Transformer$$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$$anonfun$runTest$1.apply(FunSuiteLike.scala:175)
  at org.scalatest.SuperEngine.runTestImpl(Engine.scala:306)
  at org.scalatest.FunSuiteLike$class.runTest(FunSuiteLike.scala:175)
  at org.bdgenomics.avocado.genotyping.DiscoverVariantsSuite.org$scalatest$BeforeAndAfter$$super$runTest(DiscoverVariantsSuite.scala:29)
  at org.scalatest.BeforeAndAfter$class.runTest(BeforeAndAfter.scala:200)
  at org.bdgenomics.avocado.genotyping.DiscoverVariantsSuite.runTest(DiscoverVariantsSuite.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.DiscoverVariantsSuite.org$scalatest$BeforeAndAfter$$super$run(DiscoverVariantsSuite.scala:29)
  at org.scalatest.BeforeAndAfter$class.run(BeforeAndAfter.scala:241)
  at org.bdgenomics.avocado.genotyping.DiscoverVariantsSuite.run(DiscoverVariantsSuite.scala:29)
  at org.scalatest.Suite$class.callExecuteOnSuite$1(Suite.scala:1492)
  at org.scalatest.Suite$$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)
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
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 23 minutes, 30 seconds.
Total number of tests run: 267
Suites: completed 21, aborted 0
Tests: succeeded 264, failed 3, canceled 0, ignored 1, pending 0
*** 3 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 [3.647s]
[INFO] avocado-core: Core variant calling algorithms ..... FAILURE [24:01.235s]
[INFO] avocado-cli: Command line interface for a distributed variant caller  SKIPPED
[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 24:05.115s
[INFO] Finished at: Thu Oct 12 09:31:40 PDT 2017
[INFO] Final Memory: 34M/1080M
[INFO] ------------------------------------------------------------------------
[ERROR] Failed to execute goal org.scalatest:scalatest-maven-plugin:1.0:test (test) on project avocado-core-spark2_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-spark2_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/417f88eac88514c4864bac92b8aad89368784402
Finished: FAILURE