FailedConsole Output

Skipping 2,796 KB.. Full Log
qXrOEBpkDgMEMDIxMFQUlDDI2RQXJOYpFJdU5qTaKoEttlJQNjBwdnF2sVayAwD4vuoDpQAAAA==Discovery starting.
Discovery completed in 65 milliseconds.
Run starting. Expected test count is: 0
Run completed in 70 milliseconds.
Total number of tests run: 0
Suites: completed 0, aborted 0
Tests: succeeded 0, failed 0, canceled 0, ignored 0, pending 0
No tests were executed.
[INFO] 
[INFO] --- maven-jar-plugin:3.1.2:jar (default-jar) @ adam-codegen-spark2_2.12 ---
[INFO] Building jar: /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-codegen/target/adam-codegen-spark2_2.12-0.27.0-SNAPSHOT.jar
[INFO] 
[INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ adam-codegen-spark2_2.12 ---
[INFO] 
[INFO] --- maven-javadoc-plugin:3.1.0:jar (attach-javadoc) @ adam-codegen-spark2_2.12 ---
[INFO] Building jar: /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-codegen/target/adam-codegen-spark2_2.12-0.27.0-SNAPSHOT-javadoc.jar
[INFO] 
[INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) > generate-sources @ adam-codegen-spark2_2.12 >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-codegen-spark2_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-codegen-spark2_2.12 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ adam-codegen-spark2_2.12 ---
[INFO] Source directory: /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-codegen/src/main/scala added.
[INFO] 
[INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) < generate-sources @ adam-codegen-spark2_2.12 <<<
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ adam-codegen-spark2_2.12 ---
model contains 11 documentable templates
[INFO] Building jar: /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-codegen/target/adam-codegen-spark2_2.12-0.27.0-SNAPSHOT-javadoc.jar
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building ADAM_2.12: Core 0.27.0-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-core-spark2_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-core-spark2_2.12 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ adam-core-spark2_2.12 ---
[INFO] Source directory: /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala added.
[INFO] Source directory: /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/generated-sources/src/main/scala added.
[INFO] 
[INFO] --- exec-maven-plugin:1.5.0:java (generate-scala-products) @ adam-core-spark2_2.12 ---
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
[INFO] 
[INFO] --- exec-maven-plugin:1.5.0:java (generate-scala-projection-fields) @ adam-core-spark2_2.12 ---
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ adam-core-spark2_2.12 ---
[INFO] Modified 2 of 199 .scala files
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ adam-core-spark2_2.12 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ adam-core-spark2_2.12 ---
[INFO] /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/java:-1: info: compiling
[INFO] /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala:-1: info: compiling
[INFO] /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/generated-sources/src/main/scala:-1: info: compiling
[INFO] Compiling 136 source files to /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/2.12.8/classes at 1557958062789
[WARNING] warning: there were 21 deprecation warnings
[WARNING] warning: there were 31 deprecation warnings (since 0.21.0)
[WARNING] warning: there was one deprecation warning (since 1.0.6)
[WARNING] warning: there were 31 deprecation warnings (since 2.0.0)
[WARNING] warning: there was one deprecation warning (since 2.11.0)
[WARNING] warning: there were 170 deprecation warnings (since 2.12.0)
[WARNING] warning: there was one deprecation warning (since 2.12.7)
[WARNING] warning: there were 256 deprecation warnings in total; re-run with -deprecation for details
[WARNING] warning: there were 5 feature warnings; re-run with -feature for details
[WARNING] 9 warnings found
[INFO] prepare-compile in 0 s
[INFO] compile in 24 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ adam-core-spark2_2.12 ---
[INFO] Changes detected - recompiling the module!
[INFO] Compiling 6 source files to /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/2.12.8/classes
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ adam-core-spark2_2.12 ---
[INFO] Test Source directory: /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala added.
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ adam-core-spark2_2.12 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 150 resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ adam-core-spark2_2.12 ---
[INFO] /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala:-1: info: compiling
[INFO] Compiling 69 source files to /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/2.12.8/test-classes at 1557958089297
[WARNING] /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/algorithms/consensus/NormalizationUtilsSuite.scala:59: warning: method recordToRichRecord in object RichAlignmentRecord is deprecated (since 0.21.0): Use explicit conversion wherever possible in new development.
[WARNING]       .build()
[WARNING]             ^
[WARNING] /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/algorithms/consensus/NormalizationUtilsSuite.scala:61: warning: method richRecordToRecord in object RichAlignmentRecord is deprecated (since 0.21.0): Use explicit conversion wherever possible in new development.
[WARNING]     val new_cigar = NormalizationUtils.leftAlignIndel(read)
[WARNING]                                                       ^
[WARNING] /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/algorithms/consensus/NormalizationUtilsSuite.scala:66: warning: method richRecordToRecord in object RichAlignmentRecord is deprecated (since 0.21.0): Use explicit conversion wherever possible in new development.
[WARNING]     assert(RichAlignmentRecord(read).samtoolsCigar.getReadLength === new_cigar.getReadLength)
[WARNING]                                ^
[WARNING] /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/AlignmentRecordConverterSuite.scala:171: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     val newSAMRecord = newSAMReader.iterator().dropWhile(r => r.getReadName != readName)
[WARNING]                                             ^
[WARNING] /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/AlignmentRecordConverterSuite.scala:274: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       .setAlignments(seqAsJavaList(alignments))
[WARNING]                      ^
[WARNING] /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/AlignmentRecordConverterSuite.scala:311: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       .setAlignments(seqAsJavaList(alignments))
[WARNING]                      ^
[WARNING] /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/AlignmentRecordConverterSuite.scala:335: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     val fragment = Fragment.newBuilder().setAlignments(List(record)).build()
[WARNING]                                                            ^
[WARNING] /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/SAMRecordConverterSuite.scala:54: warning: method getNotPrimaryAlignmentFlag in class SAMRecord is deprecated: see corresponding Javadoc for more information.
[WARNING]     assert(!testAlignmentRecord.getPrimaryAlignment === testSAMRecord.getNotPrimaryAlignmentFlag)
[WARNING]                                                                       ^
[WARNING] /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/SAMRecordConverterSuite.scala:89: warning: method getNotPrimaryAlignmentFlag in class SAMRecord is deprecated: see corresponding Javadoc for more information.
[WARNING]     assert(!testAlignmentRecord.getPrimaryAlignment === testSAMRecord.getNotPrimaryAlignmentFlag)
[WARNING]                                                                       ^
[WARNING] /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/SAMRecordConverterSuite.scala:106: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       val samIter = asScalaIterator(newSAMReader.iterator())
[WARNING]                     ^
[WARNING] /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:53: warning: method extractDictionary in class SAMSequenceDictionaryExtractor is deprecated: see corresponding Javadoc for more information.
[WARNING]     SequenceDictionary(SAMSequenceDictionaryExtractor.extractDictionary(new File(path)))
[WARNING]                                                       ^
[WARNING] /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:63: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     .alleles(List(Allele.create("A", true), Allele.create("T")))
[WARNING]                  ^
[WARNING] /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:69: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     .alleles(List(Allele.create("A", true), Allele.create("T"), Allele.create("G")))
[WARNING]                  ^
[WARNING] /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:75: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     .alleles(List(Allele.create("A", true), Allele.create("<NON_REF>", false)))
[WARNING]                  ^
[WARNING] /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:81: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     .alleles(List(Allele.create("A", true), Allele.create("<CN0>", false)))
[WARNING]                  ^
[WARNING] /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:109: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       .alleles(List(Allele.create("A", true), Allele.create("T")))
[WARNING]                    ^
[WARNING] /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:143: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       GenotypeBuilder.create("NA12878", vcb.getAlleles(), genotypeAttributes))
[WARNING]                                                           ^
[WARNING] /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:154: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     assert(adamGT.getAlleles.sameElements(List(GenotypeAllele.REF, GenotypeAllele.ALT)))
[WARNING]                   ^
[WARNING] /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:184: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       assert(adamVariant.variant.getFiltersFailed.sameElements(List("LowMQ")))
[WARNING]                                  ^
[WARNING] /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:219: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       assert(adamGT.getVariantCallingAnnotations.getFiltersFailed.sameElements(List("LowMQ")))
[WARNING]                                                  ^
[WARNING] /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:234: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     assert(htsjdkVC.getAlternateAlleles.sameElements(List(Allele.create("T"))))
[WARNING]                     ^
[WARNING] /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:245: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       .setStrandBiasComponents(List(0, 2, 4, 6).map(i => i: java.lang.Integer))
[WARNING]                                                    ^
[WARNING] /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:246: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       .setAlleles(List(GenotypeAllele.REF, GenotypeAllele.ALT))
[WARNING]                       ^
[WARNING] /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:279: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       .setStrandBiasComponents(List(0, 2).map(i => i: java.lang.Integer))
[WARNING]                                              ^
[WARNING] /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:280: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       .setAlleles(List(GenotypeAllele.REF, GenotypeAllele.ALT))
[WARNING]                       ^
[WARNING] /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:298: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       .setStrandBiasComponents(List(0, 2).map(i => i: java.lang.Integer))
[WARNING]                                              ^
[WARNING] /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:299: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       .setAlleles(List(GenotypeAllele.REF, GenotypeAllele.ALT))
[WARNING]                       ^
[WARNING] /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:320: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     for ((allele, idx) <- vc.getAlternateAlleles.zipWithIndex) {
[WARNING]                              ^
[WARNING] /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:328: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     val gb = new GenotypeBuilder("NA12878", List(Allele.create("T"), Allele.create("G")))
[WARNING]                                                 ^
[WARNING] /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:347: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     assert(adamGT1.getAlleles.sameElements(List(GenotypeAllele.ALT, GenotypeAllele.OTHER_ALT)))
[WARNING]                    ^
[WARNING] /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:349: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     assert(adamGT1.getGenotypeLikelihoods
[WARNING]                    ^
[WARNING] /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:354: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     assert(adamGT2.getAlleles.sameElements(List(GenotypeAllele.OTHER_ALT, GenotypeAllele.ALT)))
[WARNING]                    ^
[WARNING] /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:356: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     assert(adamGT2.getGenotypeLikelihoods
[WARNING]                    ^
[WARNING] /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:380: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     val gb = new GenotypeBuilder("NA12878", List(Allele.create("A", true), Allele.create("A", true)))
[WARNING]                                                 ^
[WARNING] /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:393: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     assert(adamGT.getAlleles.sameElements(List(GenotypeAllele.REF, GenotypeAllele.REF)))
[WARNING]                   ^
[WARNING] /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:396: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     assert(adamGT.getNonReferenceLikelihoods
[WARNING]                   ^
[WARNING] /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:421: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     assert(variant.variant.getNames.length === 1)
[WARNING]                            ^
[WARNING] /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:433: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     assert(variant.variant.getNames.length === 2)
[WARNING]                            ^
[WARNING] /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:543: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       genotypeAttributes)))((bldr, fn) => {
[WARNING]       ^
[WARNING] /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:693: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     assert(gls(0) < -0.99e-1 && gls(0) > -1.1e-1)
[WARNING]            ^
[WARNING] /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:693: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     assert(gls(0) < -0.99e-1 && gls(0) > -1.1e-1)
[WARNING]                                 ^
[WARNING] /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:694: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     assert(gls(1) < -0.99e-3 && gls(1) > -1.1e-3)
[WARNING]            ^
[WARNING] /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:694: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     assert(gls(1) < -0.99e-3 && gls(1) > -1.1e-3)
[WARNING]                                 ^
[WARNING] /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:695: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     assert(gls(2) < -0.99e-6 && gls(2) > -1.1e-6)
[WARNING]            ^
[WARNING] /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:695: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     assert(gls(2) < -0.99e-6 && gls(2) > -1.1e-6)
[WARNING]                                 ^
[WARNING] /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:714: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     assert(sb(0) === 10)
[WARNING]            ^
[WARNING] /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:715: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     assert(sb(1) === 12)
[WARNING]            ^
[WARNING] /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:716: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     assert(sb(2) === 14)
[WARNING]            ^
[WARNING] /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:717: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     assert(sb(3) === 16)
[WARNING]            ^
[WARNING] /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:762: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     assert(failedFilters(0) === "FAILED_FILTER")
[WARNING]            ^
[WARNING] /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:776: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     assert(failedFilters(0) === "FAILED_FILTER1")
[WARNING]            ^
[WARNING] /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:777: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     assert(failedFilters(1) === "FAILED_FILTER2")
[WARNING]            ^
[WARNING] /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:778: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     assert(failedFilters(2) === "FAILED_FILTER3")
[WARNING]            ^
[WARNING] /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:930: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]         .map(d => d: java.lang.Double))
[WARNING]             ^
[WARNING] /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:954: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]           .map(i => i: java.lang.Integer))
[WARNING]               ^
[WARNING] /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:962: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]         .map(i => i: java.lang.Integer))
[WARNING]             ^
[WARNING] /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1089: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       .setFiltersFailed(Seq("lowmq"))
[WARNING]                            ^
[WARNING] /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1101: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       .setFiltersFailed(Seq("lowmq", "lowdp"))
[WARNING]                            ^
[WARNING] /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1195: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     assert(v.getNames.length === 1)
[WARNING]              ^
[WARNING] /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1205: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     assert(v.getNames.length === 2)
[WARNING]              ^
[WARNING] /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1262: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]         vcb.filters(Set("FAILED1", "FAILED2", "FAILED3"))
[WARNING]                        ^
[WARNING] /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1267: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     val failedSet = v.getFiltersFailed.toSet
[WARNING]                       ^
[WARNING] /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1285: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       .setNames(Seq("name"))
[WARNING]                    ^
[WARNING] /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1295: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       .setNames(Seq("name1", "name2"))
[WARNING]                    ^
[WARNING] /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1364: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       .setFiltersFailed(Seq("FAILED"))
[WARNING]                            ^
[WARNING] /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1378: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       .setFiltersFailed(Seq("FAILED1", "FAILED2"))
[WARNING]                            ^
[WARNING] /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1493: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       10).map(i => i: java.lang.Integer)
[WARNING]              ^
[WARNING] /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1501: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       10, 13, 16).map(i => i: java.lang.Integer)
[WARNING]                      ^
[WARNING] /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1516: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       0.1f).map(i => i: java.lang.Float)
[WARNING]                ^
[WARNING] /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1523: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     val acList: java.util.List[String] = List("+Inf")
[WARNING]                                              ^
[WARNING] /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1530: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     val acList: java.util.List[String] = List("-Inf")
[WARNING]                                              ^
[WARNING] /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1538: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       0.1f, 0.01f, 0.001f).map(i => i: java.lang.Float)
[WARNING]                               ^
[WARNING] /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1552: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     val acList: java.util.List[String] = List("10D90M")
[WARNING]                                              ^
[WARNING] /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1559: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     val acList: java.util.List[String] = List("10D90M", "100M", "90M10D")
[WARNING]                                              ^
[WARNING] /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1575: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       5, 10).map(i => i: java.lang.Integer)
[WARNING]                 ^
[WARNING] /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1584: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       5, 10, 13, 16).map(i => i: java.lang.Integer)
[WARNING]                         ^
[WARNING] /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1601: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       5, 10).map(i => i: java.lang.Integer)
[WARNING]                 ^
[WARNING] /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1610: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       5, 10, 13, 16).map(i => i: java.lang.Integer)
[WARNING]                         ^
[WARNING] /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1627: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       5, 10).map(i => i: java.lang.Integer)
[WARNING]                 ^
[WARNING] /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1636: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       5, 10, 13, 16).map(i => i: java.lang.Integer)
[WARNING]                         ^
[WARNING] /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:2436: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       Map[String, java.lang.Object](("ONE_INT", "42")))
[WARNING]                                    ^
[WARNING] /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:2459: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       Map[String, java.lang.Object](("FOUR_INTS", "5,10,15,20")))
[WARNING]                                    ^
[WARNING] /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:2482: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       Map[String, java.lang.Object](("FOUR_FLOATS", "5.0,10.1,15.2,20.3")))
[WARNING]                                    ^
[WARNING] /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:2505: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       Map[String, java.lang.Object](("A_INT", "10,15,20")))
[WARNING]                                    ^
[WARNING] /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:2528: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       Map[String, java.lang.Object](("R_INT", "5,10,15,20")))
[WARNING]                                    ^
[WARNING] /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:2551: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       Map[String, java.lang.Object](("R_STRING", "foo,bar,baz")))
[WARNING]                                    ^
[WARNING] /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:2574: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       Map[String, java.lang.Object](("STRING_G", "foo,bar,baz")))
[WARNING]                                    ^
[WARNING] /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/models/CoverageSuite.scala:37: warning: variable start in class Feature is deprecated: see corresponding Javadoc for more information.
[WARNING]     assert(coverageAfterConversion.start == featureToConvert.start)
[WARNING]                                                              ^
[WARNING] /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/models/CoverageSuite.scala:38: warning: variable end in class Feature is deprecated: see corresponding Javadoc for more information.
[WARNING]     assert(coverageAfterConversion.end == featureToConvert.end)
[WARNING]                                                            ^
[WARNING] /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/models/CoverageSuite.scala:40: warning: variable score in class Feature is deprecated: see corresponding Javadoc for more information.
[WARNING]     assert(coverageAfterConversion.count == featureToConvert.score)
[WARNING]                                                              ^
[WARNING] /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/models/CoverageSuite.scala:57: warning: variable start in class Feature is deprecated: see corresponding Javadoc for more information.
[WARNING]     assert(coverageAfterConversion.start == featureToConvert.start)
[WARNING]                                                              ^
[WARNING] /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/models/CoverageSuite.scala:58: warning: variable end in class Feature is deprecated: see corresponding Javadoc for more information.
[WARNING]     assert(coverageAfterConversion.end == featureToConvert.end)
[WARNING]                                                            ^
[WARNING] /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/models/CoverageSuite.scala:60: warning: variable score in class Feature is deprecated: see corresponding Javadoc for more information.
[WARNING]     assert(coverageAfterConversion.count == featureToConvert.score)
[WARNING]                                                              ^
[WARNING] /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/models/CoverageSuite.scala:61: warning: variable sampleId in class Feature is deprecated: see corresponding Javadoc for more information.
[WARNING]     assert(coverageAfterConversion.optSampleId == Some(featureToConvert.sampleId))
[WARNING]                                                                         ^
[WARNING] /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/models/MdTagSuite.scala:194: warning: method recordToRichRecord in object RichAlignmentRecord is deprecated (since 0.21.0): Use explicit conversion wherever possible in new development.
[WARNING]     assert(read.mdTag.get.end === read.getEnd)
[WARNING]            ^
[WARNING] /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/models/MdTagSuite.scala:475: warning: method recordToRichRecord in object RichAlignmentRecord is deprecated (since 0.21.0): Use explicit conversion wherever possible in new development.
[WARNING]     val tag = read.mdTag.get
[WARNING]               ^
[WARNING] /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/models/MdTagSuite.scala:482: warning: method recordToRichRecord in object RichAlignmentRecord is deprecated (since 0.21.0): Use explicit conversion wherever possible in new development.
[WARNING]     assert(tag.getReference(read) === "AAAAAAAAAAAAAAAAAAAAAAAAAAAAAGGGGGGGGGGAAAAAAAAAAGGGGGGGGGGAAAAAAAAAAA")
[WARNING]                             ^
[WARNING] /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/models/MdTagSuite.scala:495: warning: method recordToRichRecord in object RichAlignmentRecord is deprecated (since 0.21.0): Use explicit conversion wherever possible in new development.
[WARNING]     val tag = read.mdTag.get
[WARNING]               ^
[WARNING] /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/models/MdTagSuite.scala:496: warning: method recordToRichRecord in object RichAlignmentRecord is deprecated (since 0.21.0): Use explicit conversion wherever possible in new development.
[WARNING]     assert(tag.getReference(read, withGaps = true) === "AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGGGGGGGGGGAAAAAAAAAAA")
[WARNING]                             ^
[WARNING] /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/models/MdTagSuite.scala:510: warning: method recordToRichRecord in object RichAlignmentRecord is deprecated (since 0.21.0): Use explicit conversion wherever possible in new development.
[WARNING]     val newTag = MdTag.moveAlignment(read, newCigar)
[WARNING]                                      ^
[WARNING] 211 warnings found
[INFO] prepare-compile in 0 s
[INFO] compile in 27 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ adam-core-spark2_2.12 ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ adam-core-spark2_2.12 ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ adam-core-spark2_2.12 ---
Discovery starting.
Discovery completed in 544 milliseconds.
Run starting. Expected test count is: 0
Run completed in 552 milliseconds.
Total number of tests run: 0
Suites: completed 0, aborted 0
Tests: succeeded 0, failed 0, canceled 0, ignored 0, pending 0
No tests were executed.
[INFO] 
[INFO] --- maven-jar-plugin:3.1.2:jar (default-jar) @ adam-core-spark2_2.12 ---
[INFO] Building jar: /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/adam-core-spark2_2.12-0.27.0-SNAPSHOT.jar
[INFO] 
[INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ adam-core-spark2_2.12 ---
[INFO] Building jar: /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/adam-core-spark2_2.12-0.27.0-SNAPSHOT-sources.jar
[INFO] 
[INFO] --- maven-javadoc-plugin:3.1.0:jar (attach-javadoc) @ adam-core-spark2_2.12 ---
[ERROR] Error fetching link: /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-codegen/target/apidocs. Ignored it.
[INFO] 
Loading source files for package org.apache.parquet.avro...
Loading source files for package org.bdgenomics.adam.io...
Constructing Javadoc information...
Standard Doclet version 1.8.0_191
Building tree for all the packages and classes...
Generating /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/org/apache/parquet/avro/AvroSchemaConverter.html...
Generating /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/org/bdgenomics/adam/io/FastqInputFormat.html...
Generating /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/org/bdgenomics/adam/io/FastqRecordReader.html...
Generating /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/org/bdgenomics/adam/io/InterleavedFastqInputFormat.html...
Generating /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/org/bdgenomics/adam/io/SingleFastqInputFormat.html...
Generating /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/overview-frame.html...
Generating /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/org/apache/parquet/avro/package-frame.html...
Generating /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/org/apache/parquet/avro/package-summary.html...
Generating /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/org/apache/parquet/avro/package-tree.html...
Generating /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/org/bdgenomics/adam/io/package-frame.html...
Generating /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/org/bdgenomics/adam/io/package-summary.html...
Generating /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/org/bdgenomics/adam/io/package-tree.html...
Generating /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/constant-values.html...
Generating /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/org/apache/parquet/avro/class-use/AvroSchemaConverter.html...
Generating /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/org/bdgenomics/adam/io/class-use/InterleavedFastqInputFormat.html...
Generating /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/org/bdgenomics/adam/io/class-use/SingleFastqInputFormat.html...
Generating /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/org/bdgenomics/adam/io/class-use/FastqInputFormat.html...
Generating /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/org/bdgenomics/adam/io/class-use/FastqRecordReader.html...
Generating /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/org/apache/parquet/avro/package-use.html...
Generating /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/org/bdgenomics/adam/io/package-use.html...
Building index for all the packages and classes...
Generating /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/overview-tree.html...
Generating /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/index-all.html...
Generating /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/deprecated-list.html...
Building index for all classes...
Generating /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/allclasses-frame.html...
Generating /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/allclasses-noframe.html...
Generating /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/index.html...
Generating /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/overview-summary.html...
Generating /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/help-doc.html...
6 warnings
[WARNING] Javadoc Warnings
[WARNING] /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/java/org/bdgenomics/adam/io/FastqRecordReader.java:235: warning: no @param for codec
[WARNING] protected final int positionAtFirstRecord(final FSDataInputStream stream,
[WARNING] ^
[WARNING] /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/java/org/bdgenomics/adam/io/FastqRecordReader.java:235: warning: no @return
[WARNING] protected final int positionAtFirstRecord(final FSDataInputStream stream,
[WARNING] ^
[WARNING] /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/java/org/bdgenomics/adam/io/FastqRecordReader.java:235: warning: no @throws for java.io.IOException
[WARNING] protected final int positionAtFirstRecord(final FSDataInputStream stream,
[WARNING] ^
[WARNING] /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/java/org/bdgenomics/adam/io/FastqRecordReader.java:389: warning: no @throws for java.io.IOException
[WARNING] protected final boolean lowLevelFastqRead(final Text readName, final Text value)
[WARNING] ^
[WARNING] /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/java/org/bdgenomics/adam/io/FastqRecordReader.java:431: warning: no @throws for java.io.IOException
[WARNING] abstract protected boolean next(Text value) throws IOException;
[WARNING] ^
[WARNING] /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/java/org/bdgenomics/adam/io/FastqRecordReader.java:154: warning: no @throws for java.io.IOException
[WARNING] protected FastqRecordReader(final Configuration conf,
[WARNING] ^
[INFO] Building jar: /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/adam-core-spark2_2.12-0.27.0-SNAPSHOT-javadoc.jar
[INFO] 
[INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) > generate-sources @ adam-core-spark2_2.12 >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-core-spark2_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-core-spark2_2.12 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ adam-core-spark2_2.12 ---
[INFO] Source directory: /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala added.
[INFO] Source directory: /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/generated-sources/src/main/scala added.
[INFO] 
[INFO] --- exec-maven-plugin:1.5.0:java (generate-scala-products) @ adam-core-spark2_2.12 ---
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
[INFO] 
[INFO] --- exec-maven-plugin:1.5.0:java (generate-scala-projection-fields) @ adam-core-spark2_2.12 ---
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
[INFO] 
[INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) < generate-sources @ adam-core-spark2_2.12 <<<
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ adam-core-spark2_2.12 ---
/tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/converters/FastaConverter.scala:230: warning: discarding unmoored doc comment
    /**
    ^
/tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/rdd/read/AlignmentRecordDataset.scala:803: warning: Octal escape literals are deprecated, use \u0001 instead.
      binaryCodec.writeBytes("BAM\001".getBytes())
                                 ^
/tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/rich/RichCigar.scala:43: warning: discarding unmoored doc comment
    /**
    ^
warning: there were 5 feature warnings; re-run with -feature for details
model contains 276 documentable templates
/tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/models/ReadGroupDictionary.scala:47: warning: Could not find any member to link for "IllegalArgumentException".
/**
^
/tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/util/AttributeUtils.scala:70: warning: Could not find any member to link for "IllegalArgumentException".
  /**
  ^
/tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/rdd/GenomicDataset.scala:755: warning: Variable x undefined in comment for method pipe in trait GenomicDataset
   * Files are substituted in to the command with a $x syntax. E.g., to invoke
                                                     ^
/tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/rdd/GenomicDataset.scala:756: warning: Variable 0 undefined in comment for method pipe in trait GenomicDataset
   * a command that uses the first file from the files Seq, use $0. To access
                                                                 ^
/tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/rdd/GenomicDataset.scala:757: warning: Variable root undefined in comment for method pipe in trait GenomicDataset
   * the path to the directory where the files are copied, use $root.
                                                                ^
/tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/rdd/contig/NucleotideContigFragmentDataset.scala:365: warning: Could not find any member to link for "UnsupportedOperationException".
  /**
  ^
/tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/rdd/GenomicPartitioners.scala:178: warning: Could not find any member to link for "IllegalArgumentException".
  /**
  ^
/tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/rdd/GenomicPartitioners.scala:75: warning: Could not find any member to link for "IllegalArgumentException".
  /**
  ^
/tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/rdd/ADAMContext.scala:3085: warning: Could not find any member to link for "IllegalArgumentException".
  /**
  ^
/tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/rdd/ADAMContext.scala:1388: warning: Could not find any member to link for "FileNotFoundException".
  /**
  ^
/tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/rdd/ADAMContext.scala:1368: warning: Could not find any member to link for "FileNotFoundException".
  /**
  ^
/tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/rdd/ADAMContext.scala:1339: warning: Could not find any member to link for "FileNotFoundException".
  /**
  ^
/tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/projections/Projection.scala:45: warning: Could not find any member to link for "IllegalArgumentException".
  /**
  ^
/tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/models/ReferenceRegion.scala:456: warning: Could not find any member to link for "IllegalArgumentException".
  /**
  ^
/tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/models/ReferenceRegion.scala:426: warning: Could not find any member to link for "IllegalArgumentException".
  /**
  ^
/tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/models/ReferenceRegion.scala:411: warning: Could not find any member to link for "IllegalArgumentException".
  /**
  ^
/tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/models/ReferenceRegion.scala:336: warning: Could not find any member to link for "IllegalArgumentException".
  /**
  ^
/tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/models/ReferenceRegion.scala:258: warning: Could not find any member to link for "IllegalArgumentException".
  /**
  ^
/tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/models/ReferenceRegion.scala:242: warning: Could not find any member to link for "IllegalArgumentException".
  /**
  ^
/tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/models/Alphabet.scala:44: warning: Could not find any member to link for "IllegalArgumentException".
  /**
  ^
/tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/java/org/bdgenomics/adam/io/FastqRecordReader.java:377: warning: Could not find any member to link for "RuntimeException".
    /**
    ^
25 warnings found
[INFO] Building jar: /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/adam-core-spark2_2.12-0.27.0-SNAPSHOT-javadoc.jar
[INFO] 
[INFO] --- maven-jar-plugin:3.1.2:test-jar (default) @ adam-core-spark2_2.12 ---
[INFO] Building jar: /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/adam-core-spark2_2.12-0.27.0-SNAPSHOT-tests.jar
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building ADAM_2.12: APIs for Java, Python 0.27.0-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-apis-spark2_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-apis-spark2_2.12 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ adam-apis-spark2_2.12 ---
[INFO] Source directory: /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-apis/src/main/scala added.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ adam-apis-spark2_2.12 ---
[INFO] Modified 0 of 5 .scala files
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ adam-apis-spark2_2.12 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-apis/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ adam-apis-spark2_2.12 ---
[INFO] /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-apis/src/main/scala:-1: info: compiling
[INFO] Compiling 4 source files to /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-apis/target/2.12.8/classes at 1557958152147
[WARNING] warning: there was one deprecation warning (since 2.12.0); re-run with -deprecation for details
[WARNING] warning: there were two feature warnings; re-run with -feature for details
[WARNING] two warnings found
[INFO] prepare-compile in 0 s
[INFO] compile in 5 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ adam-apis-spark2_2.12 ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ adam-apis-spark2_2.12 ---
[INFO] Test Source directory: /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-apis/src/test/scala added.
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ adam-apis-spark2_2.12 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 2 resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ adam-apis-spark2_2.12 ---
[INFO] /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-apis/src/test/java:-1: info: compiling
[INFO] /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-apis/src/test/scala:-1: info: compiling
[INFO] Compiling 8 source files to /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-apis/target/2.12.8/test-classes at 1557958157760
[INFO] prepare-compile in 0 s
[INFO] compile in 4 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ adam-apis-spark2_2.12 ---
[INFO] Changes detected - recompiling the module!
[INFO] Compiling 7 source files to /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-apis/target/2.12.8/test-classes
[INFO] 
[INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ adam-apis-spark2_2.12 ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ adam-apis-spark2_2.12 ---
Discovery starting.
Discovery completed in 137 milliseconds.
Run starting. Expected test count is: 0
Run completed in 146 milliseconds.
Total number of tests run: 0
Suites: completed 0, aborted 0
Tests: succeeded 0, failed 0, canceled 0, ignored 0, pending 0
No tests were executed.
[INFO] 
[INFO] --- maven-jar-plugin:3.1.2:jar (default-jar) @ adam-apis-spark2_2.12 ---
[INFO] Building jar: /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-apis/target/adam-apis-spark2_2.12-0.27.0-SNAPSHOT.jar
[INFO] 
[INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ adam-apis-spark2_2.12 ---
[INFO] 
[INFO] --- maven-javadoc-plugin:3.1.0:jar (attach-javadoc) @ adam-apis-spark2_2.12 ---
[INFO] Building jar: /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-apis/target/adam-apis-spark2_2.12-0.27.0-SNAPSHOT-javadoc.jar
[INFO] 
[INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) > generate-sources @ adam-apis-spark2_2.12 >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-apis-spark2_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-apis-spark2_2.12 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ adam-apis-spark2_2.12 ---
[INFO] Source directory: /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-apis/src/main/scala added.
[INFO] 
[INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) < generate-sources @ adam-apis-spark2_2.12 <<<
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ adam-apis-spark2_2.12 ---
warning: there were two feature warnings; re-run with -feature for details
model contains 124 documentable templates
one warning found
[INFO] Building jar: /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-apis/target/adam-apis-spark2_2.12-0.27.0-SNAPSHOT-javadoc.jar
[INFO] 
[INFO] --- maven-jar-plugin:3.1.2:test-jar (default) @ adam-apis-spark2_2.12 ---
[INFO] Building jar: /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-apis/target/adam-apis-spark2_2.12-0.27.0-SNAPSHOT-tests.jar
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building ADAM_2.12: CLI 0.27.0-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-cli-spark2_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-cli-spark2_2.12 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:timestamp-property (timestamp-property) @ adam-cli-spark2_2.12 ---
[INFO] 
[INFO] --- git-commit-id-plugin:2.2.2:revision (default) @ adam-cli-spark2_2.12 ---
[INFO] 
[INFO] --- templating-maven-plugin:1.0.0:filter-sources (filter-src) @ adam-cli-spark2_2.12 ---
[INFO] Coping files with filtering to temporary directory.
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 1 resource
[INFO] No files needs to be copied to output directory. Up to date: /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/generated-sources/java-templates
[INFO] Source directory: /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/generated-sources/java-templates added.
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ adam-cli-spark2_2.12 ---
[INFO] Source directory: /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-cli/src/main/scala added.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ adam-cli-spark2_2.12 ---
[INFO] Modified 0 of 31 .scala files
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ adam-cli-spark2_2.12 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-cli/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ adam-cli-spark2_2.12 ---
[INFO] /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/generated-sources/java-templates:-1: info: compiling
[INFO] /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-cli/src/main/scala:-1: info: compiling
[INFO] Compiling 18 source files to /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/2.12.8/classes at 1557958172176
[WARNING] warning: there was one deprecation warning
[WARNING] warning: there was one deprecation warning (since 2.12.0)
[WARNING] warning: there were two deprecation warnings in total; re-run with -deprecation for details
[WARNING] three warnings found
[INFO] prepare-compile in 0 s
[INFO] compile in 7 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ adam-cli-spark2_2.12 ---
[INFO] Changes detected - recompiling the module!
[INFO] Compiling 1 source file to /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/2.12.8/classes
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ adam-cli-spark2_2.12 ---
[INFO] Test Source directory: /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-cli/src/test/scala added.
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ adam-cli-spark2_2.12 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 15 resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ adam-cli-spark2_2.12 ---
[INFO] /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-cli/src/test/scala:-1: info: compiling
[INFO] Compiling 14 source files to /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/2.12.8/test-classes at 1557958180033
[INFO] prepare-compile in 0 s
[INFO] compile in 6 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ adam-cli-spark2_2.12 ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ adam-cli-spark2_2.12 ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ adam-cli-spark2_2.12 ---
Discovery starting.
Discovery completed in 137 milliseconds.
Run starting. Expected test count is: 0
Run completed in 143 milliseconds.
Total number of tests run: 0
Suites: completed 0, aborted 0
Tests: succeeded 0, failed 0, canceled 0, ignored 0, pending 0
No tests were executed.
[INFO] 
[INFO] --- maven-jar-plugin:3.1.2:jar (default-jar) @ adam-cli-spark2_2.12 ---
[INFO] Building jar: /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/adam-cli-spark2_2.12-0.27.0-SNAPSHOT.jar
[INFO] 
[INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ adam-cli-spark2_2.12 ---
[INFO] Building jar: /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/adam-cli-spark2_2.12-0.27.0-SNAPSHOT-sources.jar
[INFO] 
[INFO] --- maven-javadoc-plugin:3.1.0:jar (attach-javadoc) @ adam-cli-spark2_2.12 ---
[ERROR] Error fetching link: /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-apis/target/apidocs. Ignored it.
[INFO] 
Loading source files for package org.bdgenomics.adam.cli...
Constructing Javadoc information...
Standard Doclet version 1.8.0_191
Building tree for all the packages and classes...
Generating /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/apidocs/org/bdgenomics/adam/cli/About.html...
Generating /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/apidocs/org/bdgenomics/adam/cli/package-frame.html...
Generating /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/apidocs/org/bdgenomics/adam/cli/package-summary.html...
Generating /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/apidocs/org/bdgenomics/adam/cli/package-tree.html...
Generating /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/apidocs/constant-values.html...
Generating /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/apidocs/org/bdgenomics/adam/cli/class-use/About.html...
Generating /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/apidocs/org/bdgenomics/adam/cli/package-use.html...
Building index for all the packages and classes...
Generating /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/apidocs/overview-tree.html...
Generating /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/apidocs/index-all.html...
Generating /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/apidocs/deprecated-list.html...
Building index for all classes...
Generating /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/apidocs/allclasses-frame.html...
Generating /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/apidocs/allclasses-noframe.html...
Generating /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/apidocs/index.html...
Generating /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/apidocs/help-doc.html...
[INFO] Building jar: /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/adam-cli-spark2_2.12-0.27.0-SNAPSHOT-javadoc.jar
[INFO] 
[INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) > generate-sources @ adam-cli-spark2_2.12 >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-cli-spark2_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-cli-spark2_2.12 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:timestamp-property (timestamp-property) @ adam-cli-spark2_2.12 ---
[INFO] 
[INFO] --- git-commit-id-plugin:2.2.2:revision (default) @ adam-cli-spark2_2.12 ---
[INFO] 
[INFO] --- templating-maven-plugin:1.0.0:filter-sources (filter-src) @ adam-cli-spark2_2.12 ---
[INFO] Coping files with filtering to temporary directory.
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 1 resource
[INFO] No files needs to be copied to output directory. Up to date: /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/generated-sources/java-templates
[INFO] Source directory: /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/generated-sources/java-templates added.
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ adam-cli-spark2_2.12 ---
[INFO] Source directory: /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-cli/src/main/scala added.
[INFO] 
[INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) < generate-sources @ adam-cli-spark2_2.12 <<<
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ adam-cli-spark2_2.12 ---
model contains 55 documentable templates
[INFO] Building jar: /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/adam-cli-spark2_2.12-0.27.0-SNAPSHOT-javadoc.jar
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[INFO] Building ADAM_2.12: Assembly 0.27.0-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-assembly-spark2_2.12 ---
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[INFO] --- git-commit-id-plugin:2.2.2:revision (default) @ adam-assembly-spark2_2.12 ---
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[INFO] --- templating-maven-plugin:1.0.0:filter-sources (filter-src) @ adam-assembly-spark2_2.12 ---
[INFO] Request to add '/tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/src/main/java-templates' folder. Not added since it does not exist.
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ adam-assembly-spark2_2.12 ---
[INFO] Source directory: /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/src/main/scala added.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ adam-assembly-spark2_2.12 ---
[INFO] Modified 0 of 1 .scala files
[INFO] 
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[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ adam-assembly-spark2_2.12 ---
[INFO] /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/src/main/scala:-1: info: compiling
[INFO] Compiling 1 source files to /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/target/2.12.8/classes at 1557958198688
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[INFO] Nothing to compile - all classes are up to date
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[INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ adam-assembly-spark2_2.12 ---
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[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/src/test/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ adam-assembly-spark2_2.12 ---
[INFO] No sources to compile
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[INFO] Tests are skipped.
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[INFO] Building jar: /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/target/adam-assembly-spark2_2.12-0.27.0-SNAPSHOT.jar
[INFO] 
[INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ adam-assembly-spark2_2.12 ---
[INFO] 
[INFO] --- maven-javadoc-plugin:3.1.0:jar (attach-javadoc) @ adam-assembly-spark2_2.12 ---
[INFO] 
[INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) > generate-sources @ adam-assembly-spark2_2.12 >>>
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[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-assembly-spark2_2.12 ---
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[INFO] --- git-commit-id-plugin:2.2.2:revision (default) @ adam-assembly-spark2_2.12 ---
[INFO] 
[INFO] --- templating-maven-plugin:1.0.0:filter-sources (filter-src) @ adam-assembly-spark2_2.12 ---
[INFO] Request to add '/tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/src/main/java-templates' folder. Not added since it does not exist.
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ adam-assembly-spark2_2.12 ---
[INFO] Source directory: /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/src/main/scala added.
[INFO] 
[INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) < generate-sources @ adam-assembly-spark2_2.12 <<<
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ adam-assembly-spark2_2.12 ---
model contains 6 documentable templates
[INFO] Building jar: /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/target/adam-assembly-spark2_2.12-0.27.0-SNAPSHOT-javadoc.jar
[INFO] 
[INFO] --- maven-shade-plugin:3.2.0:shade (default) @ adam-assembly-spark2_2.12 ---
[INFO] Including org.bdgenomics.adam:adam-cli-spark2_2.12:jar:0.27.0-SNAPSHOT in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-misc-spark2_2.12:jar:0.2.15 in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-io-spark2_2.12:jar:0.2.15 in the shaded jar.
[INFO] Including org.apache.httpcomponents:httpclient:jar:4.5.7 in the shaded jar.
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[INFO] Including org.bdgenomics.utils:utils-cli-spark2_2.12:jar:0.2.15 in the shaded jar.
[INFO] Including org.clapper:grizzled-slf4j_2.12:jar:1.3.3 in the shaded jar.
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[INFO] Including org.bdgenomics.utils:utils-metrics-spark2_2.12:jar:0.2.15 in the shaded jar.
[INFO] Including com.netflix.servo:servo-core:jar:0.12.25 in the shaded jar.
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[INFO] Including org.slf4j:slf4j-api:jar:1.7.25 in the shaded jar.
[INFO] Including org.bdgenomics.bdg-formats:bdg-formats:jar:0.12.0 in the shaded jar.
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[INFO] Including org.tukaani:xz:jar:1.5 in the shaded jar.
[INFO] Including org.bdgenomics.adam:adam-core-spark2_2.12:jar:0.27.0-SNAPSHOT in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-intervalrdd-spark2_2.12:jar:0.2.15 in the shaded jar.
[INFO] Including com.esotericsoftware.kryo:kryo:jar:2.24.0 in the shaded jar.
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[INFO] Including com.google.guava:listenablefuture:jar:9999.0-empty-to-avoid-conflict-with-guava in the shaded jar.
[INFO] Including org.checkerframework:checker-qual:jar:2.5.2 in the shaded jar.
[INFO] Including com.google.errorprone:error_prone_annotations:jar:2.2.0 in the shaded jar.
[INFO] Including com.google.j2objc:j2objc-annotations:jar:1.1 in the shaded jar.
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[INFO] Including org.bdgenomics.adam:adam-codegen-spark2_2.12:jar:0.27.0-SNAPSHOT in the shaded jar.
[INFO] Including org.bdgenomics.adam:adam-apis-spark2_2.12:jar:0.27.0-SNAPSHOT in the shaded jar.
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[INFO] Including com.google.code.findbugs:jsr305:jar:1.3.9 in the shaded jar.
[WARNING] WORKAROUND:  refusing to add class org/apache/parquet/avro/AvroSchemaConverter$2.class from jar /home/jenkins/.m2/repository/org/apache/parquet/parquet-avro/1.10.1/parquet-avro-1.10.1.jar
[WARNING] WORKAROUND:  refusing to add class org/apache/parquet/avro/AvroSchemaConverter.class from jar /home/jenkins/.m2/repository/org/apache/parquet/parquet-avro/1.10.1/parquet-avro-1.10.1.jar
[WARNING] WORKAROUND:  refusing to add class org/apache/parquet/avro/AvroSchemaConverter$1.class from jar /home/jenkins/.m2/repository/org/apache/parquet/parquet-avro/1.10.1/parquet-avro-1.10.1.jar
[WARNING] guava-27.0-jre.jar, failureaccess-1.0.jar define 2 overlapping classes: 
[WARNING]   - com.google.common.util.concurrent.internal.InternalFutureFailureAccess
[WARNING]   - com.google.common.util.concurrent.internal.InternalFutures
[WARNING] maven-shade-plugin has detected that some class files are
[WARNING] present in two or more JARs. When this happens, only one
[WARNING] single version of the class is copied to the uber jar.
[WARNING] Usually this is not harmful and you can skip these warnings,
[WARNING] otherwise try to manually exclude artifacts based on
[WARNING] mvn dependency:tree -Ddetail=true and the above output.
[WARNING] See http://maven.apache.org/plugins/maven-shade-plugin/
[INFO] Replacing original artifact with shaded artifact.
[INFO] Replacing /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/target/adam-assembly-spark2_2.12-0.27.0-SNAPSHOT.jar with /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/target/adam-assembly-spark2_2.12-0.27.0-SNAPSHOT-shaded.jar
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building ADAM_2.12: Python APIs 0.27.0-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-python-spark2_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-python-spark2_2.12 ---
[INFO] 
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[INFO] Modified 0 of 0 .scala files
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[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-python/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ adam-python-spark2_2.12 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- exec-maven-plugin:1.5.0:exec (dev-python) @ adam-python-spark2_2.12 ---
pip install -e .
DEPRECATION: Python 2.7 will reach the end of its life on January 1st, 2020. Please upgrade your Python as Python 2.7 won't be maintained after that date. A future version of pip will drop support for Python 2.7.
Obtaining file:///tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-python
Collecting pyspark>=1.6.0 (from bdgenomics.adam==0.26.0a0)
  Downloading https://files.pythonhosted.org/packages/37/98/244399c0daa7894cdf387e7007d5e8b3710a79b67f3fd991c0b0b644822d/pyspark-2.4.3.tar.gz (215.6MB)
Collecting py4j==0.10.7 (from pyspark>=1.6.0->bdgenomics.adam==0.26.0a0)
  Using cached https://files.pythonhosted.org/packages/e3/53/c737818eb9a7dc32a7cd4f1396e787bd94200c3997c72c1dbe028587bd76/py4j-0.10.7-py2.py3-none-any.whl
Building wheels for collected packages: pyspark
  Building wheel for pyspark (setup.py): started
  Building wheel for pyspark (setup.py): finished with status 'done'
  Stored in directory: /home/jenkins/.cache/pip/wheels/8d/20/f0/b30e2024226dc112e256930dd2cd4f06d00ab053c86278dcf3
Successfully built pyspark
Installing collected packages: py4j, pyspark, bdgenomics.adam
  Running setup.py develop for bdgenomics.adam
Successfully installed bdgenomics.adam py4j-0.10.7 pyspark-2.4.3
python setup.py bdist_egg
Could not import pypandoc - required to package bdgenomics.adam
running bdist_egg
running egg_info
writing requirements to bdgenomics.adam.egg-info/requires.txt
writing bdgenomics.adam.egg-info/PKG-INFO
writing top-level names to bdgenomics.adam.egg-info/top_level.txt
writing dependency_links to bdgenomics.adam.egg-info/dependency_links.txt
package init file 'deps/jars/__init__.py' not found (or not a regular file)
package init file 'deps/bin/__init__.py' not found (or not a regular file)
reading manifest file 'bdgenomics.adam.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no previously-included files matching '*.py[cod]' found anywhere in distribution
warning: no previously-included files matching '__pycache__' found anywhere in distribution
warning: no previously-included files matching '.DS_Store' found anywhere in distribution
writing manifest file 'bdgenomics.adam.egg-info/SOURCES.txt'
installing library code to build/bdist.linux-x86_64/egg
running install_lib
running build_py
creating build
creating build/lib
creating build/lib/bdgenomics
copying bdgenomics/__init__.py -> build/lib/bdgenomics
creating build/lib/bdgenomics/adam
copying bdgenomics/adam/rdd.py -> build/lib/bdgenomics/adam
copying bdgenomics/adam/find_adam_home.py -> build/lib/bdgenomics/adam
copying bdgenomics/adam/models.py -> build/lib/bdgenomics/adam
copying bdgenomics/adam/stringency.py -> build/lib/bdgenomics/adam
copying bdgenomics/adam/__init__.py -> build/lib/bdgenomics/adam
copying bdgenomics/adam/adamContext.py -> build/lib/bdgenomics/adam
creating build/lib/bdgenomics/adam/test
copying bdgenomics/adam/test/variantDataset_test.py -> build/lib/bdgenomics/adam/test
copying bdgenomics/adam/test/coverageDataset_test.py -> build/lib/bdgenomics/adam/test
copying bdgenomics/adam/test/adamContext_test.py -> build/lib/bdgenomics/adam/test
copying bdgenomics/adam/test/featureDataset_test.py -> build/lib/bdgenomics/adam/test
copying bdgenomics/adam/test/genotypeDataset_test.py -> build/lib/bdgenomics/adam/test
copying bdgenomics/adam/test/__init__.py -> build/lib/bdgenomics/adam/test
copying bdgenomics/adam/test/alignmentRecordDataset_test.py -> build/lib/bdgenomics/adam/test
creating build/lib/bdgenomics/adam/jars
copying deps/jars/adam.jar -> build/lib/bdgenomics/adam/jars
creating build/lib/bdgenomics/adam/bin
copying deps/bin/adam-shell -> build/lib/bdgenomics/adam/bin
copying deps/bin/adam-submit -> build/lib/bdgenomics/adam/bin
copying deps/bin/adamR -> build/lib/bdgenomics/adam/bin
copying deps/bin/find-adam-assembly.sh -> build/lib/bdgenomics/adam/bin
copying deps/bin/find-adam-egg.sh -> build/lib/bdgenomics/adam/bin
copying deps/bin/find-adam-home -> build/lib/bdgenomics/adam/bin
copying deps/bin/find-spark.sh -> build/lib/bdgenomics/adam/bin
copying deps/bin/pyadam -> build/lib/bdgenomics/adam/bin
creating build/bdist.linux-x86_64
creating build/bdist.linux-x86_64/egg
creating build/bdist.linux-x86_64/egg/bdgenomics
copying build/lib/bdgenomics/__init__.py -> build/bdist.linux-x86_64/egg/bdgenomics
creating build/bdist.linux-x86_64/egg/bdgenomics/adam
copying build/lib/bdgenomics/adam/rdd.py -> build/bdist.linux-x86_64/egg/bdgenomics/adam
copying build/lib/bdgenomics/adam/find_adam_home.py -> build/bdist.linux-x86_64/egg/bdgenomics/adam
creating build/bdist.linux-x86_64/egg/bdgenomics/adam/bin
copying build/lib/bdgenomics/adam/bin/adam-shell -> build/bdist.linux-x86_64/egg/bdgenomics/adam/bin
copying build/lib/bdgenomics/adam/bin/adam-submit -> build/bdist.linux-x86_64/egg/bdgenomics/adam/bin
copying build/lib/bdgenomics/adam/bin/pyadam -> build/bdist.linux-x86_64/egg/bdgenomics/adam/bin
copying build/lib/bdgenomics/adam/bin/adamR -> build/bdist.linux-x86_64/egg/bdgenomics/adam/bin
copying build/lib/bdgenomics/adam/bin/find-adam-home -> build/bdist.linux-x86_64/egg/bdgenomics/adam/bin
copying build/lib/bdgenomics/adam/bin/find-adam-assembly.sh -> build/bdist.linux-x86_64/egg/bdgenomics/adam/bin
copying build/lib/bdgenomics/adam/bin/find-spark.sh -> build/bdist.linux-x86_64/egg/bdgenomics/adam/bin
copying build/lib/bdgenomics/adam/bin/find-adam-egg.sh -> build/bdist.linux-x86_64/egg/bdgenomics/adam/bin
creating build/bdist.linux-x86_64/egg/bdgenomics/adam/jars
copying build/lib/bdgenomics/adam/jars/adam.jar -> build/bdist.linux-x86_64/egg/bdgenomics/adam/jars
copying build/lib/bdgenomics/adam/models.py -> build/bdist.linux-x86_64/egg/bdgenomics/adam
copying build/lib/bdgenomics/adam/stringency.py -> build/bdist.linux-x86_64/egg/bdgenomics/adam
copying build/lib/bdgenomics/adam/__init__.py -> build/bdist.linux-x86_64/egg/bdgenomics/adam
copying build/lib/bdgenomics/adam/adamContext.py -> build/bdist.linux-x86_64/egg/bdgenomics/adam
creating build/bdist.linux-x86_64/egg/bdgenomics/adam/test
copying build/lib/bdgenomics/adam/test/variantDataset_test.py -> build/bdist.linux-x86_64/egg/bdgenomics/adam/test
copying build/lib/bdgenomics/adam/test/coverageDataset_test.py -> build/bdist.linux-x86_64/egg/bdgenomics/adam/test
copying build/lib/bdgenomics/adam/test/adamContext_test.py -> build/bdist.linux-x86_64/egg/bdgenomics/adam/test
copying build/lib/bdgenomics/adam/test/featureDataset_test.py -> build/bdist.linux-x86_64/egg/bdgenomics/adam/test
copying build/lib/bdgenomics/adam/test/genotypeDataset_test.py -> build/bdist.linux-x86_64/egg/bdgenomics/adam/test
copying build/lib/bdgenomics/adam/test/__init__.py -> build/bdist.linux-x86_64/egg/bdgenomics/adam/test
copying build/lib/bdgenomics/adam/test/alignmentRecordDataset_test.py -> build/bdist.linux-x86_64/egg/bdgenomics/adam/test
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/__init__.py to __init__.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/adam/rdd.py to rdd.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/adam/find_adam_home.py to find_adam_home.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/adam/models.py to models.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/adam/stringency.py to stringency.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/adam/__init__.py to __init__.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/adam/adamContext.py to adamContext.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/adam/test/variantDataset_test.py to variantDataset_test.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/adam/test/coverageDataset_test.py to coverageDataset_test.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/adam/test/adamContext_test.py to adamContext_test.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/adam/test/featureDataset_test.py to featureDataset_test.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/adam/test/genotypeDataset_test.py to genotypeDataset_test.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/adam/test/__init__.py to __init__.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/adam/test/alignmentRecordDataset_test.py to alignmentRecordDataset_test.pyc
creating build/bdist.linux-x86_64/egg/EGG-INFO
installing scripts to build/bdist.linux-x86_64/egg/EGG-INFO/scripts
running install_scripts
running build_scripts
creating build/scripts-2.7
copying deps/bin/adam-shell -> build/scripts-2.7
copying deps/bin/adam-submit -> build/scripts-2.7
copying deps/bin/pyadam -> build/scripts-2.7
copying deps/bin/adamR -> build/scripts-2.7
copying deps/bin/find-adam-home -> build/scripts-2.7
copying deps/bin/find-adam-assembly.sh -> build/scripts-2.7
copying deps/bin/find-spark.sh -> build/scripts-2.7
copying deps/bin/find-adam-egg.sh -> build/scripts-2.7
copying and adjusting bdgenomics/adam/find_adam_home.py -> build/scripts-2.7
changing mode of build/scripts-2.7/find_adam_home.py from 664 to 775
creating build/bdist.linux-x86_64/egg/EGG-INFO/scripts
copying build/scripts-2.7/adam-shell -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts
copying build/scripts-2.7/adam-submit -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts
copying build/scripts-2.7/pyadam -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts
copying build/scripts-2.7/find_adam_home.py -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts
copying build/scripts-2.7/adamR -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts
copying build/scripts-2.7/find-adam-home -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts
copying build/scripts-2.7/find-adam-assembly.sh -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts
copying build/scripts-2.7/find-spark.sh -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts
copying build/scripts-2.7/find-adam-egg.sh -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts
changing mode of build/bdist.linux-x86_64/egg/EGG-INFO/scripts/adam-shell to 775
changing mode of build/bdist.linux-x86_64/egg/EGG-INFO/scripts/adam-submit to 775
changing mode of build/bdist.linux-x86_64/egg/EGG-INFO/scripts/pyadam to 775
changing mode of build/bdist.linux-x86_64/egg/EGG-INFO/scripts/find_adam_home.py to 775
changing mode of build/bdist.linux-x86_64/egg/EGG-INFO/scripts/adamR to 775
changing mode of build/bdist.linux-x86_64/egg/EGG-INFO/scripts/find-adam-home to 775
changing mode of build/bdist.linux-x86_64/egg/EGG-INFO/scripts/find-adam-assembly.sh to 775
changing mode of build/bdist.linux-x86_64/egg/EGG-INFO/scripts/find-spark.sh to 775
changing mode of build/bdist.linux-x86_64/egg/EGG-INFO/scripts/find-adam-egg.sh to 775
copying bdgenomics.adam.egg-info/PKG-INFO -> build/bdist.linux-x86_64/egg/EGG-INFO
copying bdgenomics.adam.egg-info/SOURCES.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying bdgenomics.adam.egg-info/dependency_links.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying bdgenomics.adam.egg-info/requires.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying bdgenomics.adam.egg-info/top_level.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
zip_safe flag not set; analyzing archive contents...
bdgenomics.__init__: module references __path__
bdgenomics.adam.find_adam_home: module references __file__
creating dist
creating 'dist/bdgenomics.adam-0.26.0a0-py2.7.egg' and adding 'build/bdist.linux-x86_64/egg' to it
removing 'build/bdist.linux-x86_64/egg' (and everything under it)
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ adam-python-spark2_2.12 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ adam-python-spark2_2.12 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-python/src/test/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ adam-python-spark2_2.12 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- exec-maven-plugin:1.5.0:exec (test-python) @ adam-python-spark2_2.12 ---
mkdir -p target
python -m pytest -vv --junitxml target/pytest-reports/tests.xml bdgenomics
============================= test session starts ==============================
platform linux2 -- Python 2.7.16, pytest-3.9.1, py-1.8.0, pluggy-0.11.0 -- /home/jenkins/anaconda2/envs/adam-build-d5e50896-fb2e-46f4-9160-de97745f77c9/bin/python
cachedir: .pytest_cache
rootdir: /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-python, inifile:
collecting ... collected 62 items

bdgenomics/adam/test/adamContext_test.py::ADAMContextTest::test_load_alignments PASSED [  1%]
bdgenomics/adam/test/adamContext_test.py::ADAMContextTest::test_load_bed PASSED [  3%]
bdgenomics/adam/test/adamContext_test.py::ADAMContextTest::test_load_contig_fragments PASSED [  4%]
bdgenomics/adam/test/adamContext_test.py::ADAMContextTest::test_load_coverage PASSED [  6%]
bdgenomics/adam/test/adamContext_test.py::ADAMContextTest::test_load_genotypes PASSED [  8%]
bdgenomics/adam/test/adamContext_test.py::ADAMContextTest::test_load_gtf PASSED [  9%]
bdgenomics/adam/test/adamContext_test.py::ADAMContextTest::test_load_indexed_bam PASSED [ 11%]
bdgenomics/adam/test/adamContext_test.py::ADAMContextTest::test_load_interval_list PASSED [ 12%]
bdgenomics/adam/test/adamContext_test.py::ADAMContextTest::test_load_narrowPeak PASSED [ 14%]
bdgenomics/adam/test/adamContext_test.py::ADAMContextTest::test_load_variants PASSED [ 16%]
bdgenomics/adam/test/alignmentRecordDataset_test.py::AlignmentRecordDatasetTest::test_broadcast_inner_join PASSED [ 17%]
bdgenomics/adam/test/alignmentRecordDataset_test.py::AlignmentRecordDatasetTest::test_broadcast_right_outer_join PASSED [ 19%]
bdgenomics/adam/test/alignmentRecordDataset_test.py::AlignmentRecordDatasetTest::test_caching PASSED [ 20%]
bdgenomics/adam/test/alignmentRecordDataset_test.py::AlignmentRecordDatasetTest::test_count_kmers PASSED [ 22%]
bdgenomics/adam/test/alignmentRecordDataset_test.py::AlignmentRecordDatasetTest::test_filterByOverlappingRegion PASSED [ 24%]
bdgenomics/adam/test/alignmentRecordDataset_test.py::AlignmentRecordDatasetTest::test_filterByOverlappingRegions PASSED [ 25%]
bdgenomics/adam/test/alignmentRecordDataset_test.py::AlignmentRecordDatasetTest::test_load_indexed_bam PASSED [ 27%]
bdgenomics/adam/test/alignmentRecordDataset_test.py::AlignmentRecordDatasetTest::test_persisting PASSED [ 29%]
bdgenomics/adam/test/alignmentRecordDataset_test.py::AlignmentRecordDatasetTest::test_pipe_as_sam PASSED [ 30%]
bdgenomics/adam/test/alignmentRecordDataset_test.py::AlignmentRecordDatasetTest::test_realignIndels_known_indels PASSED [ 32%]
bdgenomics/adam/test/alignmentRecordDataset_test.py::AlignmentRecordDatasetTest::test_realignIndels_reads PASSED [ 33%]
bdgenomics/adam/test/alignmentRecordDataset_test.py::AlignmentRecordDatasetTest::test_save_as_bam PASSED [ 35%]
bdgenomics/adam/test/alignmentRecordDataset_test.py::AlignmentRecordDatasetTest::test_save_sorted_sam PASSED [ 37%]
bdgenomics/adam/test/alignmentRecordDataset_test.py::AlignmentRecordDatasetTest::test_save_unordered_sam PASSED [ 38%]
bdgenomics/adam/test/alignmentRecordDataset_test.py::AlignmentRecordDatasetTest::test_shuffle_full_outer_join PASSED [ 40%]
bdgenomics/adam/test/alignmentRecordDataset_test.py::AlignmentRecordDatasetTest::test_shuffle_inner_join PASSED [ 41%]
bdgenomics/adam/test/alignmentRecordDataset_test.py::AlignmentRecordDatasetTest::test_shuffle_inner_join_groupBy_left PASSED [ 43%]
bdgenomics/adam/test/alignmentRecordDataset_test.py::AlignmentRecordDatasetTest::test_shuffle_left_outer_join PASSED [ 45%]
bdgenomics/adam/test/alignmentRecordDataset_test.py::AlignmentRecordDatasetTest::test_shuffle_right_outer_join PASSED [ 46%]
bdgenomics/adam/test/alignmentRecordDataset_test.py::AlignmentRecordDatasetTest::test_shuffle_right_outer_join_groupBy_left PASSED [ 48%]
bdgenomics/adam/test/alignmentRecordDataset_test.py::AlignmentRecordDatasetTest::test_to_coverage PASSED [ 50%]
bdgenomics/adam/test/alignmentRecordDataset_test.py::AlignmentRecordDatasetTest::test_to_fragments PASSED [ 51%]
bdgenomics/adam/test/alignmentRecordDataset_test.py::AlignmentRecordDatasetTest::test_transform PASSED [ 53%]
bdgenomics/adam/test/alignmentRecordDataset_test.py::AlignmentRecordDatasetTest::test_transmute_to_coverage PASSED [ 54%]
bdgenomics/adam/test/alignmentRecordDataset_test.py::AlignmentRecordDatasetTest::test_union PASSED [ 56%]
bdgenomics/adam/test/coverageDataset_test.py::CoverageDatasetTest::test_aggregatedCoverage PASSED [ 58%]
bdgenomics/adam/test/coverageDataset_test.py::CoverageDatasetTest::test_collapse PASSED [ 59%]
bdgenomics/adam/test/coverageDataset_test.py::CoverageDatasetTest::test_flatten FAILED [ 61%]
bdgenomics/adam/test/coverageDataset_test.py::CoverageDatasetTest::test_save PASSED [ 62%]
bdgenomics/adam/test/coverageDataset_test.py::CoverageDatasetTest::test_toFeatures PASSED [ 64%]
bdgenomics/adam/test/featureDataset_test.py::FeatureDatasetTest::test_round_trip_bed PASSED [ 66%]
bdgenomics/adam/test/featureDataset_test.py::FeatureDatasetTest::test_round_trip_gtf PASSED [ 67%]
bdgenomics/adam/test/featureDataset_test.py::FeatureDatasetTest::test_round_trip_interval_list PASSED [ 69%]
bdgenomics/adam/test/featureDataset_test.py::FeatureDatasetTest::test_round_trip_narrowPeak PASSED [ 70%]
bdgenomics/adam/test/featureDataset_test.py::FeatureDatasetTest::test_transform PASSED [ 72%]
bdgenomics/adam/test/genotypeDataset_test.py::GenotypeDatasetTest::test_to_variants PASSED [ 74%]
bdgenomics/adam/test/genotypeDataset_test.py::GenotypeDatasetTest::test_transform PASSED [ 75%]
bdgenomics/adam/test/genotypeDataset_test.py::GenotypeDatasetTest::test_vcf_add_filter PASSED [ 77%]
bdgenomics/adam/test/genotypeDataset_test.py::GenotypeDatasetTest::test_vcf_add_format_all_array PASSED [ 79%]
bdgenomics/adam/test/genotypeDataset_test.py::GenotypeDatasetTest::test_vcf_add_format_alts_array PASSED [ 80%]
bdgenomics/adam/test/genotypeDataset_test.py::GenotypeDatasetTest::test_vcf_add_format_array PASSED [ 82%]
bdgenomics/adam/test/genotypeDataset_test.py::GenotypeDatasetTest::test_vcf_add_format_genotype_array PASSED [ 83%]
bdgenomics/adam/test/genotypeDataset_test.py::GenotypeDatasetTest::test_vcf_add_format_scalar PASSED [ 85%]
bdgenomics/adam/test/genotypeDataset_test.py::GenotypeDatasetTest::test_vcf_add_info_all_array PASSED [ 87%]
bdgenomics/adam/test/genotypeDataset_test.py::GenotypeDatasetTest::test_vcf_add_info_alts_array PASSED [ 88%]
bdgenomics/adam/test/genotypeDataset_test.py::GenotypeDatasetTest::test_vcf_add_info_array PASSED [ 90%]
bdgenomics/adam/test/genotypeDataset_test.py::GenotypeDatasetTest::test_vcf_add_info_scalar PASSED [ 91%]
bdgenomics/adam/test/genotypeDataset_test.py::GenotypeDatasetTest::test_vcf_round_trip PASSED [ 93%]
bdgenomics/adam/test/genotypeDataset_test.py::GenotypeDatasetTest::test_vcf_sort PASSED [ 95%]
bdgenomics/adam/test/genotypeDataset_test.py::GenotypeDatasetTest::test_vcf_sort_lex PASSED [ 96%]
bdgenomics/adam/test/variantDataset_test.py::VariantDatasetTest::test_transform PASSED [ 98%]
bdgenomics/adam/test/variantDataset_test.py::VariantDatasetTest::test_vcf_round_trip PASSED [100%]

=================================== FAILURES ===================================
_______________________ CoverageDatasetTest.test_flatten _______________________

self = <bdgenomics.adam.test.coverageDataset_test.CoverageDatasetTest testMethod=test_flatten>

    def test_flatten(self):
        testFile = self.resourceFile("small.sam")
        ac = ADAMContext(self.ss)
    
        reads = ac.loadAlignments(testFile)
        coverage = reads.toCoverage()
        flattened = coverage.flatten()
>       self.assertEqual(flattened.toDF().count(), 1500)

bdgenomics/adam/test/coverageDataset_test.py:77: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
../spark-2.4.3-bin-without-hadoop-scala-2.12/python/pyspark/sql/dataframe.py:522: in count
    return int(self._jdf.count())
/tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.3-bin-without-hadoop-scala-2.12/python/lib/py4j-0.10.7-src.zip/py4j/java_gateway.py:1257: in __call__
    answer, self.gateway_client, self.target_id, self.name)
../spark-2.4.3-bin-without-hadoop-scala-2.12/python/pyspark/sql/utils.py:63: in deco
    return f(*a, **kw)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

answer = 'xro1978'
gateway_client = <py4j.java_gateway.GatewayClient object at 0x7f1689809550>
target_id = 'o1971', name = 'count'

    def get_return_value(answer, gateway_client, target_id=None, name=None):
        """Converts an answer received from the Java gateway into a Python object.
    
        For example, string representation of integers are converted to Python
        integer, string representation of objects are converted to JavaObject
        instances, etc.
    
        :param answer: the string returned by the Java gateway
        :param gateway_client: the gateway client used to communicate with the Java
            Gateway. Only necessary if the answer is a reference (e.g., object,
            list, map)
        :param target_id: the name of the object from which the answer comes from
            (e.g., *object1* in `object1.hello()`). Optional.
        :param name: the name of the member from which the answer comes from
            (e.g., *hello* in `object1.hello()`). Optional.
        """
        if is_error(answer)[0]:
            if len(answer) > 1:
                type = answer[1]
                value = OUTPUT_CONVERTER[type](answer[2:], gateway_client)
                if answer[1] == REFERENCE_TYPE:
                    raise Py4JJavaError(
                        "An error occurred while calling {0}{1}{2}.\n".
>                       format(target_id, ".", name), value)
E                   Py4JJavaError: An error occurred while calling o1971.count.
E                   : org.apache.spark.SparkException: Job aborted due to stage failure: Task 0 in stage 0.0 failed 1 times, most recent failure: Lost task 0.0 in stage 0.0 (TID 0, localhost, executor driver): java.io.IOException: Connection from /192.168.10.27:37117 closed
E                   	at org.apache.spark.network.client.TransportResponseHandler.channelInactive(TransportResponseHandler.java:146)
E                   	at org.apache.spark.network.server.TransportChannelHandler.channelInactive(TransportChannelHandler.java:108)
E                   	at io.netty.channel.AbstractChannelHandlerContext.invokeChannelInactive(AbstractChannelHandlerContext.java:245)
E                   	at io.netty.channel.AbstractChannelHandlerContext.invokeChannelInactive(AbstractChannelHandlerContext.java:231)
E                   	at io.netty.channel.AbstractChannelHandlerContext.fireChannelInactive(AbstractChannelHandlerContext.java:224)
E                   	at io.netty.channel.ChannelInboundHandlerAdapter.channelInactive(ChannelInboundHandlerAdapter.java:75)
E                   	at io.netty.handler.timeout.IdleStateHandler.channelInactive(IdleStateHandler.java:277)
E                   	at io.netty.channel.AbstractChannelHandlerContext.invokeChannelInactive(AbstractChannelHandlerContext.java:245)
E                   	at io.netty.channel.AbstractChannelHandlerContext.invokeChannelInactive(AbstractChannelHandlerContext.java:231)
E                   	at io.netty.channel.AbstractChannelHandlerContext.fireChannelInactive(AbstractChannelHandlerContext.java:224)
E                   	at io.netty.channel.ChannelInboundHandlerAdapter.channelInactive(ChannelInboundHandlerAdapter.java:75)
E                   	at io.netty.channel.AbstractChannelHandlerContext.invokeChannelInactive(AbstractChannelHandlerContext.java:245)
E                   	at io.netty.channel.AbstractChannelHandlerContext.invokeChannelInactive(AbstractChannelHandlerContext.java:231)
E                   	at io.netty.channel.AbstractChannelHandlerContext.fireChannelInactive(AbstractChannelHandlerContext.java:224)
E                   	at io.netty.channel.ChannelInboundHandlerAdapter.channelInactive(ChannelInboundHandlerAdapter.java:75)
E                   	at org.apache.spark.network.util.TransportFrameDecoder.channelInactive(TransportFrameDecoder.java:182)
E                   	at io.netty.channel.AbstractChannelHandlerContext.invokeChannelInactive(AbstractChannelHandlerContext.java:245)
E                   	at io.netty.channel.AbstractChannelHandlerContext.invokeChannelInactive(AbstractChannelHandlerContext.java:231)
E                   	at io.netty.channel.AbstractChannelHandlerContext.fireChannelInactive(AbstractChannelHandlerContext.java:224)
E                   	at io.netty.channel.DefaultChannelPipeline$HeadContext.channelInactive(DefaultChannelPipeline.java:1354)
E                   	at io.netty.channel.AbstractChannelHandlerContext.invokeChannelInactive(AbstractChannelHandlerContext.java:245)
E                   	at io.netty.channel.AbstractChannelHandlerContext.invokeChannelInactive(AbstractChannelHandlerContext.java:231)
E                   	at io.netty.channel.DefaultChannelPipeline.fireChannelInactive(DefaultChannelPipeline.java:917)
E                   	at io.netty.channel.AbstractChannel$AbstractUnsafe$8.run(AbstractChannel.java:822)
E                   	at io.netty.util.concurrent.AbstractEventExecutor.safeExecute(AbstractEventExecutor.java:163)
E                   	at io.netty.util.concurrent.SingleThreadEventExecutor.runAllTasks(SingleThreadEventExecutor.java:403)
E                   	at io.netty.channel.nio.NioEventLoop.run(NioEventLoop.java:463)
E                   	at io.netty.util.concurrent.SingleThreadEventExecutor$5.run(SingleThreadEventExecutor.java:858)
E                   	at io.netty.util.concurrent.DefaultThreadFactory$DefaultRunnableDecorator.run(DefaultThreadFactory.java:138)
E                   	at java.lang.Thread.run(Thread.java:748)
E                   
E                   Driver stacktrace:
E                   	at org.apache.spark.scheduler.DAGScheduler.failJobAndIndependentStages(DAGScheduler.scala:1889)
E                   	at org.apache.spark.scheduler.DAGScheduler.$anonfun$abortStage$2(DAGScheduler.scala:1877)
E                   	at org.apache.spark.scheduler.DAGScheduler.$anonfun$abortStage$2$adapted(DAGScheduler.scala:1876)
E                   	at scala.collection.mutable.ResizableArray.foreach(ResizableArray.scala:62)
E                   	at scala.collection.mutable.ResizableArray.foreach$(ResizableArray.scala:55)
E                   	at scala.collection.mutable.ArrayBuffer.foreach(ArrayBuffer.scala:49)
E                   	at org.apache.spark.scheduler.DAGScheduler.abortStage(DAGScheduler.scala:1876)
E                   	at org.apache.spark.scheduler.DAGScheduler.$anonfun$handleTaskSetFailed$1(DAGScheduler.scala:926)
E                   	at org.apache.spark.scheduler.DAGScheduler.$anonfun$handleTaskSetFailed$1$adapted(DAGScheduler.scala:926)
E                   	at scala.Option.foreach(Option.scala:274)
E                   	at org.apache.spark.scheduler.DAGScheduler.handleTaskSetFailed(DAGScheduler.scala:926)
E                   	at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.doOnReceive(DAGScheduler.scala:2110)
E                   	at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:2059)
E                   	at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:2048)
E                   	at org.apache.spark.util.EventLoop$$anon$1.run(EventLoop.scala:49)
E                   	at org.apache.spark.scheduler.DAGScheduler.runJob(DAGScheduler.scala:737)
E                   	at org.apache.spark.SparkContext.runJob(SparkContext.scala:2061)
E                   	at org.apache.spark.SparkContext.runJob(SparkContext.scala:2082)
E                   	at org.apache.spark.SparkContext.runJob(SparkContext.scala:2101)
E                   	at org.apache.spark.SparkContext.runJob(SparkContext.scala:2126)
E                   	at org.apache.spark.rdd.RDD.$anonfun$collect$1(RDD.scala:945)
E                   	at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:151)
E                   	at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:112)
E                   	at org.apache.spark.rdd.RDD.withScope(RDD.scala:363)
E                   	at org.apache.spark.rdd.RDD.collect(RDD.scala:944)
E                   	at org.apache.spark.sql.execution.SparkPlan.executeCollect(SparkPlan.scala:299)
E                   	at org.apache.spark.sql.Dataset.$anonfun$count$1(Dataset.scala:2830)
E                   	at org.apache.spark.sql.Dataset.$anonfun$count$1$adapted(Dataset.scala:2829)
E                   	at org.apache.spark.sql.Dataset.$anonfun$withAction$2(Dataset.scala:3364)
E                   	at org.apache.spark.sql.execution.SQLExecution$.$anonfun$withNewExecutionId$1(SQLExecution.scala:78)
E                   	at org.apache.spark.sql.execution.SQLExecution$.withSQLConfPropagated(SQLExecution.scala:125)
E                   	at org.apache.spark.sql.execution.SQLExecution$.withNewExecutionId(SQLExecution.scala:73)
E                   	at org.apache.spark.sql.Dataset.withAction(Dataset.scala:3364)
E                   	at org.apache.spark.sql.Dataset.count(Dataset.scala:2829)
E                   	at sun.reflect.GeneratedMethodAccessor116.invoke(Unknown Source)
E                   	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
E                   	at java.lang.reflect.Method.invoke(Method.java:498)
E                   	at py4j.reflection.MethodInvoker.invoke(MethodInvoker.java:244)
E                   	at py4j.reflection.ReflectionEngine.invoke(ReflectionEngine.java:357)
E                   	at py4j.Gateway.invoke(Gateway.java:282)
E                   	at py4j.commands.AbstractCommand.invokeMethod(AbstractCommand.java:132)
E                   	at py4j.commands.CallCommand.execute(CallCommand.java:79)
E                   	at py4j.GatewayConnection.run(GatewayConnection.java:238)
E                   	at java.lang.Thread.run(Thread.java:748)
E                   Caused by: java.io.IOException: Connection from /192.168.10.27:37117 closed
E                   	at org.apache.spark.network.client.TransportResponseHandler.channelInactive(TransportResponseHandler.java:146)
E                   	at org.apache.spark.network.server.TransportChannelHandler.channelInactive(TransportChannelHandler.java:108)
E                   	at io.netty.channel.AbstractChannelHandlerContext.invokeChannelInactive(AbstractChannelHandlerContext.java:245)
E                   	at io.netty.channel.AbstractChannelHandlerContext.invokeChannelInactive(AbstractChannelHandlerContext.java:231)
E                   	at io.netty.channel.AbstractChannelHandlerContext.fireChannelInactive(AbstractChannelHandlerContext.java:224)
E                   	at io.netty.channel.ChannelInboundHandlerAdapter.channelInactive(ChannelInboundHandlerAdapter.java:75)
E                   	at io.netty.handler.timeout.IdleStateHandler.channelInactive(IdleStateHandler.java:277)
E                   	at io.netty.channel.AbstractChannelHandlerContext.invokeChannelInactive(AbstractChannelHandlerContext.java:245)
E                   	at io.netty.channel.AbstractChannelHandlerContext.invokeChannelInactive(AbstractChannelHandlerContext.java:231)
E                   	at io.netty.channel.AbstractChannelHandlerContext.fireChannelInactive(AbstractChannelHandlerContext.java:224)
E                   	at io.netty.channel.ChannelInboundHandlerAdapter.channelInactive(ChannelInboundHandlerAdapter.java:75)
E                   	at io.netty.channel.AbstractChannelHandlerContext.invokeChannelInactive(AbstractChannelHandlerContext.java:245)
E                   	at io.netty.channel.AbstractChannelHandlerContext.invokeChannelInactive(AbstractChannelHandlerContext.java:231)
E                   	at io.netty.channel.AbstractChannelHandlerContext.fireChannelInactive(AbstractChannelHandlerContext.java:224)
E                   	at io.netty.channel.ChannelInboundHandlerAdapter.channelInactive(ChannelInboundHandlerAdapter.java:75)
E                   	at org.apache.spark.network.util.TransportFrameDecoder.channelInactive(TransportFrameDecoder.java:182)
E                   	at io.netty.channel.AbstractChannelHandlerContext.invokeChannelInactive(AbstractChannelHandlerContext.java:245)
E                   	at io.netty.channel.AbstractChannelHandlerContext.invokeChannelInactive(AbstractChannelHandlerContext.java:231)
E                   	at io.netty.channel.AbstractChannelHandlerContext.fireChannelInactive(AbstractChannelHandlerContext.java:224)
E                   	at io.netty.channel.DefaultChannelPipeline$HeadContext.channelInactive(DefaultChannelPipeline.java:1354)
E                   	at io.netty.channel.AbstractChannelHandlerContext.invokeChannelInactive(AbstractChannelHandlerContext.java:245)
E                   	at io.netty.channel.AbstractChannelHandlerContext.invokeChannelInactive(AbstractChannelHandlerContext.java:231)
E                   	at io.netty.channel.DefaultChannelPipeline.fireChannelInactive(DefaultChannelPipeline.java:917)
E                   	at io.netty.channel.AbstractChannel$AbstractUnsafe$8.run(AbstractChannel.java:822)
E                   	at io.netty.util.concurrent.AbstractEventExecutor.safeExecute(AbstractEventExecutor.java:163)
E                   	at io.netty.util.concurrent.SingleThreadEventExecutor.runAllTasks(SingleThreadEventExecutor.java:403)
E                   	at io.netty.channel.nio.NioEventLoop.run(NioEventLoop.java:463)
E                   	at io.netty.util.concurrent.SingleThreadEventExecutor$5.run(SingleThreadEventExecutor.java:858)
E                   	at io.netty.util.concurrent.DefaultThreadFactory$DefaultRunnableDecorator.run(DefaultThreadFactory.java:138)
E                   	... 1 more

/tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.3-bin-without-hadoop-scala-2.12/python/lib/py4j-0.10.7-src.zip/py4j/protocol.py:328: Py4JJavaError
----------------------------- Captured stderr call -----------------------------

[Stage 0:>                                                          (0 + 1) / 1]2019-05-15 15:11:42 ERROR TransportRequestHandler:292 - Error sending result StreamResponse{streamId=/jars/adam-assembly-spark2_2.12-0.27.0-SNAPSHOT.jar, byteCount=40587876, body=FileSegmentManagedBuffer{file=/tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/target/adam-assembly-spark2_2.12-0.27.0-SNAPSHOT.jar, offset=0, length=40587876}} to /192.168.10.27:45718; closing connection
io.netty.handler.codec.EncoderException: java.lang.OutOfMemoryError: Java heap space
	at io.netty.handler.codec.MessageToMessageEncoder.write(MessageToMessageEncoder.java:106)
	at io.netty.channel.AbstractChannelHandlerContext.invokeWrite0(AbstractChannelHandlerContext.java:738)
	at io.netty.channel.AbstractChannelHandlerContext.invokeWrite(AbstractChannelHandlerContext.java:730)
	at io.netty.channel.AbstractChannelHandlerContext.write(AbstractChannelHandlerContext.java:816)
	at io.netty.channel.AbstractChannelHandlerContext.write(AbstractChannelHandlerContext.java:723)
	at io.netty.handler.timeout.IdleStateHandler.write(IdleStateHandler.java:302)
	at io.netty.channel.AbstractChannelHandlerContext.invokeWrite0(AbstractChannelHandlerContext.java:738)
	at io.netty.channel.AbstractChannelHandlerContext.invokeWriteAndFlush(AbstractChannelHandlerContext.java:801)
	at io.netty.channel.AbstractChannelHandlerContext.write(AbstractChannelHandlerContext.java:814)
	at io.netty.channel.AbstractChannelHandlerContext.writeAndFlush(AbstractChannelHandlerContext.java:794)
	at io.netty.channel.AbstractChannelHandlerContext.writeAndFlush(AbstractChannelHandlerContext.java:831)
	at io.netty.channel.DefaultChannelPipeline.writeAndFlush(DefaultChannelPipeline.java:1041)
	at io.netty.channel.AbstractChannel.writeAndFlush(AbstractChannel.java:300)
	at org.apache.spark.network.server.TransportRequestHandler.respond(TransportRequestHandler.java:288)
	at org.apache.spark.network.server.TransportRequestHandler.processStreamRequest(TransportRequestHandler.java:169)
	at org.apache.spark.network.server.TransportRequestHandler.handle(TransportRequestHandler.java:107)
	at org.apache.spark.network.server.TransportChannelHandler.channelRead(TransportChannelHandler.java:118)
	at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:362)
	at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:348)
	at io.netty.channel.AbstractChannelHandlerContext.fireChannelRead(AbstractChannelHandlerContext.java:340)
	at io.netty.handler.timeout.IdleStateHandler.channelRead(IdleStateHandler.java:286)
	at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:362)
	at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:348)
	at io.netty.channel.AbstractChannelHandlerContext.fireChannelRead(AbstractChannelHandlerContext.java:340)
	at io.netty.handler.codec.MessageToMessageDecoder.channelRead(MessageToMessageDecoder.java:102)
	at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:362)
	at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:348)
	at io.netty.channel.AbstractChannelHandlerContext.fireChannelRead(AbstractChannelHandlerContext.java:340)
	at org.apache.spark.network.util.TransportFrameDecoder.channelRead(TransportFrameDecoder.java:85)
	at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:362)
	at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:348)
	at io.netty.channel.AbstractChannelHandlerContext.fireChannelRead(AbstractChannelHandlerContext.java:340)
	at io.netty.channel.DefaultChannelPipeline$HeadContext.channelRead(DefaultChannelPipeline.java:1359)
	at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:362)
	at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:348)
	at io.netty.channel.DefaultChannelPipeline.fireChannelRead(DefaultChannelPipeline.java:935)
	at io.netty.channel.nio.AbstractNioByteChannel$NioByteUnsafe.read(AbstractNioByteChannel.java:138)
	at io.netty.channel.nio.NioEventLoop.processSelectedKey(NioEventLoop.java:645)
	at io.netty.channel.nio.NioEventLoop.processSelectedKeysOptimized(NioEventLoop.java:580)
	at io.netty.channel.nio.NioEventLoop.processSelectedKeys(NioEventLoop.java:497)
	at io.netty.channel.nio.NioEventLoop.run(NioEventLoop.java:459)
	at io.netty.util.concurrent.SingleThreadEventExecutor$5.run(SingleThreadEventExecutor.java:858)
	at io.netty.util.concurrent.DefaultThreadFactory$DefaultRunnableDecorator.run(DefaultThreadFactory.java:138)
	at java.lang.Thread.run(Thread.java:748)
Caused by: java.lang.OutOfMemoryError: Java heap space
	at io.netty.util.internal.PlatformDependent.allocateUninitializedArray(PlatformDependent.java:200)
	at io.netty.buffer.PoolArena$HeapArena.newByteArray(PoolArena.java:676)
	at io.netty.buffer.PoolArena$HeapArena.newChunk(PoolArena.java:686)
	at io.netty.buffer.PoolArena.allocateNormal(PoolArena.java:244)
	at io.netty.buffer.PoolArena.allocate(PoolArena.java:214)
	at io.netty.buffer.PoolArena.allocate(PoolArena.java:146)
	at io.netty.buffer.PooledByteBufAllocator.newHeapBuffer(PooledByteBufAllocator.java:307)
	at io.netty.buffer.AbstractByteBufAllocator.heapBuffer(AbstractByteBufAllocator.java:166)
	at io.netty.buffer.AbstractByteBufAllocator.heapBuffer(AbstractByteBufAllocator.java:157)
	at org.apache.spark.network.protocol.MessageEncoder.encode(MessageEncoder.java:82)
	at org.apache.spark.network.protocol.MessageEncoder.encode(MessageEncoder.java:33)
	at io.netty.handler.codec.MessageToMessageEncoder.write(MessageToMessageEncoder.java:88)
	at io.netty.channel.AbstractChannelHandlerContext.invokeWrite0(AbstractChannelHandlerContext.java:738)
	at io.netty.channel.AbstractChannelHandlerContext.invokeWrite(AbstractChannelHandlerContext.java:730)
	at io.netty.channel.AbstractChannelHandlerContext.write(AbstractChannelHandlerContext.java:816)
	at io.netty.channel.AbstractChannelHandlerContext.write(AbstractChannelHandlerContext.java:723)
	at io.netty.handler.timeout.IdleStateHandler.write(IdleStateHandler.java:302)
	at io.netty.channel.AbstractChannelHandlerContext.invokeWrite0(AbstractChannelHandlerContext.java:738)
	at io.netty.channel.AbstractChannelHandlerContext.invokeWriteAndFlush(AbstractChannelHandlerContext.java:801)
	at io.netty.channel.AbstractChannelHandlerContext.write(AbstractChannelHandlerContext.java:814)
	at io.netty.channel.AbstractChannelHandlerContext.writeAndFlush(AbstractChannelHandlerContext.java:794)
	at io.netty.channel.AbstractChannelHandlerContext.writeAndFlush(AbstractChannelHandlerContext.java:831)
	at io.netty.channel.DefaultChannelPipeline.writeAndFlush(DefaultChannelPipeline.java:1041)
	at io.netty.channel.AbstractChannel.writeAndFlush(AbstractChannel.java:300)
	at org.apache.spark.network.server.TransportRequestHandler.respond(TransportRequestHandler.java:288)
	at org.apache.spark.network.server.TransportRequestHandler.processStreamRequest(TransportRequestHandler.java:169)
	at org.apache.spark.network.server.TransportRequestHandler.handle(TransportRequestHandler.java:107)
	at org.apache.spark.network.server.TransportChannelHandler.channelRead(TransportChannelHandler.java:118)
	at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:362)
	at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:348)
	at io.netty.channel.AbstractChannelHandlerContext.fireChannelRead(AbstractChannelHandlerContext.java:340)
	at io.netty.handler.timeout.IdleStateHandler.channelRead(IdleStateHandler.java:286)
2019-05-15 15:11:42 ERROR TransportResponseHandler:144 - Still have 1 requests outstanding when connection from /192.168.10.27:37117 is closed
2019-05-15 15:11:42 ERROR Executor:91 - Exception in task 0.0 in stage 0.0 (TID 0)
java.io.IOException: Connection from /192.168.10.27:37117 closed
	at org.apache.spark.network.client.TransportResponseHandler.channelInactive(TransportResponseHandler.java:146)
	at org.apache.spark.network.server.TransportChannelHandler.channelInactive(TransportChannelHandler.java:108)
	at io.netty.channel.AbstractChannelHandlerContext.invokeChannelInactive(AbstractChannelHandlerContext.java:245)
	at io.netty.channel.AbstractChannelHandlerContext.invokeChannelInactive(AbstractChannelHandlerContext.java:231)
	at io.netty.channel.AbstractChannelHandlerContext.fireChannelInactive(AbstractChannelHandlerContext.java:224)
	at io.netty.channel.ChannelInboundHandlerAdapter.channelInactive(ChannelInboundHandlerAdapter.java:75)
	at io.netty.handler.timeout.IdleStateHandler.channelInactive(IdleStateHandler.java:277)
	at io.netty.channel.AbstractChannelHandlerContext.invokeChannelInactive(AbstractChannelHandlerContext.java:245)
	at io.netty.channel.AbstractChannelHandlerContext.invokeChannelInactive(AbstractChannelHandlerContext.java:231)
	at io.netty.channel.AbstractChannelHandlerContext.fireChannelInactive(AbstractChannelHandlerContext.java:224)
	at io.netty.channel.ChannelInboundHandlerAdapter.channelInactive(ChannelInboundHandlerAdapter.java:75)
	at io.netty.channel.AbstractChannelHandlerContext.invokeChannelInactive(AbstractChannelHandlerContext.java:245)
	at io.netty.channel.AbstractChannelHandlerContext.invokeChannelInactive(AbstractChannelHandlerContext.java:231)
	at io.netty.channel.AbstractChannelHandlerContext.fireChannelInactive(AbstractChannelHandlerContext.java:224)
	at io.netty.channel.ChannelInboundHandlerAdapter.channelInactive(ChannelInboundHandlerAdapter.java:75)
	at org.apache.spark.network.util.TransportFrameDecoder.channelInactive(TransportFrameDecoder.java:182)
	at io.netty.channel.AbstractChannelHandlerContext.invokeChannelInactive(AbstractChannelHandlerContext.java:245)
	at io.netty.channel.AbstractChannelHandlerContext.invokeChannelInactive(AbstractChannelHandlerContext.java:231)
	at io.netty.channel.AbstractChannelHandlerContext.fireChannelInactive(AbstractChannelHandlerContext.java:224)
	at io.netty.channel.DefaultChannelPipeline$HeadContext.channelInactive(DefaultChannelPipeline.java:1354)
	at io.netty.channel.AbstractChannelHandlerContext.invokeChannelInactive(AbstractChannelHandlerContext.java:245)
	at io.netty.channel.AbstractChannelHandlerContext.invokeChannelInactive(AbstractChannelHandlerContext.java:231)
	at io.netty.channel.DefaultChannelPipeline.fireChannelInactive(DefaultChannelPipeline.java:917)
	at io.netty.channel.AbstractChannel$AbstractUnsafe$8.run(AbstractChannel.java:822)
	at io.netty.util.concurrent.AbstractEventExecutor.safeExecute(AbstractEventExecutor.java:163)
	at io.netty.util.concurrent.SingleThreadEventExecutor.runAllTasks(SingleThreadEventExecutor.java:403)
	at io.netty.channel.nio.NioEventLoop.run(NioEventLoop.java:463)
	at io.netty.util.concurrent.SingleThreadEventExecutor$5.run(SingleThreadEventExecutor.java:858)
	at io.netty.util.concurrent.DefaultThreadFactory$DefaultRunnableDecorator.run(DefaultThreadFactory.java:138)
	at java.lang.Thread.run(Thread.java:748)
2019-05-15 15:11:42 WARN  TaskSetManager:66 - Lost task 0.0 in stage 0.0 (TID 0, localhost, executor driver): java.io.IOException: Connection from /192.168.10.27:37117 closed
	at org.apache.spark.network.client.TransportResponseHandler.channelInactive(TransportResponseHandler.java:146)
	at org.apache.spark.network.server.TransportChannelHandler.channelInactive(TransportChannelHandler.java:108)
	at io.netty.channel.AbstractChannelHandlerContext.invokeChannelInactive(AbstractChannelHandlerContext.java:245)
	at io.netty.channel.AbstractChannelHandlerContext.invokeChannelInactive(AbstractChannelHandlerContext.java:231)
	at io.netty.channel.AbstractChannelHandlerContext.fireChannelInactive(AbstractChannelHandlerContext.java:224)
	at io.netty.channel.ChannelInboundHandlerAdapter.channelInactive(ChannelInboundHandlerAdapter.java:75)
	at io.netty.handler.timeout.IdleStateHandler.channelInactive(IdleStateHandler.java:277)
	at io.netty.channel.AbstractChannelHandlerContext.invokeChannelInactive(AbstractChannelHandlerContext.java:245)
	at io.netty.channel.AbstractChannelHandlerContext.invokeChannelInactive(AbstractChannelHandlerContext.java:231)
	at io.netty.channel.AbstractChannelHandlerContext.fireChannelInactive(AbstractChannelHandlerContext.java:224)
	at io.netty.channel.ChannelInboundHandlerAdapter.channelInactive(ChannelInboundHandlerAdapter.java:75)
	at io.netty.channel.AbstractChannelHandlerContext.invokeChannelInactive(AbstractChannelHandlerContext.java:245)
	at io.netty.channel.AbstractChannelHandlerContext.invokeChannelInactive(AbstractChannelHandlerContext.java:231)
	at io.netty.channel.AbstractChannelHandlerContext.fireChannelInactive(AbstractChannelHandlerContext.java:224)
	at io.netty.channel.ChannelInboundHandlerAdapter.channelInactive(ChannelInboundHandlerAdapter.java:75)
	at org.apache.spark.network.util.TransportFrameDecoder.channelInactive(TransportFrameDecoder.java:182)
	at io.netty.channel.AbstractChannelHandlerContext.invokeChannelInactive(AbstractChannelHandlerContext.java:245)
	at io.netty.channel.AbstractChannelHandlerContext.invokeChannelInactive(AbstractChannelHandlerContext.java:231)
	at io.netty.channel.AbstractChannelHandlerContext.fireChannelInactive(AbstractChannelHandlerContext.java:224)
	at io.netty.channel.DefaultChannelPipeline$HeadContext.channelInactive(DefaultChannelPipeline.java:1354)
	at io.netty.channel.AbstractChannelHandlerContext.invokeChannelInactive(AbstractChannelHandlerContext.java:245)
	at io.netty.channel.AbstractChannelHandlerContext.invokeChannelInactive(AbstractChannelHandlerContext.java:231)
	at io.netty.channel.DefaultChannelPipeline.fireChannelInactive(DefaultChannelPipeline.java:917)
	at io.netty.channel.AbstractChannel$AbstractUnsafe$8.run(AbstractChannel.java:822)
	at io.netty.util.concurrent.AbstractEventExecutor.safeExecute(AbstractEventExecutor.java:163)
	at io.netty.util.concurrent.SingleThreadEventExecutor.runAllTasks(SingleThreadEventExecutor.java:403)
	at io.netty.channel.nio.NioEventLoop.run(NioEventLoop.java:463)
	at io.netty.util.concurrent.SingleThreadEventExecutor$5.run(SingleThreadEventExecutor.java:858)
	at io.netty.util.concurrent.DefaultThreadFactory$DefaultRunnableDecorator.run(DefaultThreadFactory.java:138)
	at java.lang.Thread.run(Thread.java:748)

2019-05-15 15:11:42 ERROR TaskSetManager:70 - Task 0 in stage 0.0 failed 1 times; aborting job
- generated xml file: /tmp/adamTestbs8UC1b/deleteMePleaseThisIsNoLongerNeeded/adam-python/target/pytest-reports/tests.xml -
===================== 1 failed, 61 passed in 88.29 seconds =====================
Makefile:83: recipe for target 'test' failed
make: *** [test] Error 1
[ERROR] Command execution failed.
org.apache.commons.exec.ExecuteException: Process exited with an error: 2 (Exit value: 2)
	at org.apache.commons.exec.DefaultExecutor.executeInternal(DefaultExecutor.java:404)
	at org.apache.commons.exec.DefaultExecutor.execute(DefaultExecutor.java:166)
	at org.codehaus.mojo.exec.ExecMojo.executeCommandLine(ExecMojo.java:764)
	at org.codehaus.mojo.exec.ExecMojo.executeCommandLine(ExecMojo.java:711)
	at org.codehaus.mojo.exec.ExecMojo.execute(ExecMojo.java:289)
	at org.apache.maven.plugin.DefaultBuildPluginManager.executeMojo(DefaultBuildPluginManager.java:134)
	at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:207)
	at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:153)
	at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:145)
	at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject(LifecycleModuleBuilder.java:116)
	at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject(LifecycleModuleBuilder.java:80)
	at org.apache.maven.lifecycle.internal.builder.singlethreaded.SingleThreadedBuilder.build(SingleThreadedBuilder.java:51)
	at org.apache.maven.lifecycle.internal.LifecycleStarter.execute(LifecycleStarter.java:128)
	at org.apache.maven.DefaultMaven.doExecute(DefaultMaven.java:307)
	at org.apache.maven.DefaultMaven.doExecute(DefaultMaven.java:193)
	at org.apache.maven.DefaultMaven.execute(DefaultMaven.java:106)
	at org.apache.maven.cli.MavenCli.execute(MavenCli.java:863)
	at org.apache.maven.cli.MavenCli.doMain(MavenCli.java:288)
	at org.apache.maven.cli.MavenCli.main(MavenCli.java:199)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at org.codehaus.plexus.classworlds.launcher.Launcher.launchEnhanced(Launcher.java:289)
	at org.codehaus.plexus.classworlds.launcher.Launcher.launch(Launcher.java:229)
	at org.codehaus.plexus.classworlds.launcher.Launcher.mainWithExitCode(Launcher.java:415)
	at org.codehaus.plexus.classworlds.launcher.Launcher.main(Launcher.java:356)
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary:
[INFO] 
[INFO] ADAM_2.12 .......................................... SUCCESS [  9.150 s]
[INFO] ADAM_2.12: Shader workaround ....................... SUCCESS [  7.535 s]
[INFO] ADAM_2.12: Avro-to-Dataset codegen utils ........... SUCCESS [  9.376 s]
[INFO] ADAM_2.12: Core .................................... SUCCESS [01:36 min]
[INFO] ADAM_2.12: APIs for Java, Python ................... SUCCESS [ 18.618 s]
[INFO] ADAM_2.12: CLI ..................................... SUCCESS [ 26.958 s]
[INFO] ADAM_2.12: Assembly ................................ SUCCESS [ 15.221 s]
[INFO] ADAM_2.12: Python APIs ............................. FAILURE [02:01 min]
[INFO] ADAM_2.12: R APIs .................................. SKIPPED
[INFO] ADAM_2.12: Distribution ............................ SKIPPED
[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 05:06 min
[INFO] Finished at: 2019-05-15T15:12:14-07:00
[INFO] Final Memory: 85M/1479M
[INFO] ------------------------------------------------------------------------
[ERROR] Failed to execute goal org.codehaus.mojo:exec-maven-plugin:1.5.0:exec (test-python) on project adam-python-spark2_2.12: Command execution failed. Process exited with an error: 2 (Exit value: 2) -> [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/MojoExecutionException
[ERROR] 
[ERROR] After correcting the problems, you can resume the build with the command
[ERROR]   mvn <goals> -rf :adam-python-spark2_2.12
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/adam/commit/646d138fa281f24592dba23dfac1851c61b354f8
Finished: FAILURE