FailedConsole Output

Skipping 2,196 KB.. Full Log
 object RichAlignmentRecord is deprecated: Use explicit conversion wherever possible in new development.
[WARNING]     val newTag = MdTag.moveAlignment(read, newCigar, "AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA", 100L)
[WARNING]                                      ^
[WARNING] /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/models/MdTagSuite.scala:544: warning: method recordToRichRecord in object RichAlignmentRecord is deprecated: Use explicit conversion wherever possible in new development.
[WARNING]     val newTag = MdTag.moveAlignment(read, newCigar, "GGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA", 100L)
[WARNING]                                      ^
[WARNING] /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/models/MdTagSuite.scala:562: warning: method recordToRichRecord in object RichAlignmentRecord is deprecated: Use explicit conversion wherever possible in new development.
[WARNING]     val newTag = MdTag.moveAlignment(read, newCigar, "AAAAAAAAAAGGGGGGGGGGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA", 100L)
[WARNING]                                      ^
[WARNING] /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/models/MdTagSuite.scala:580: warning: method recordToRichRecord in object RichAlignmentRecord is deprecated: Use explicit conversion wherever possible in new development.
[WARNING]     val newTag = MdTag.moveAlignment(read, newCigar, "AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA", 100L)
[WARNING]                                      ^
[WARNING] /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/models/SequenceDictionarySuite.scala:48: warning: method extractDictionary in object SAMSequenceDictionaryExtractor is deprecated: see corresponding Javadoc for more information.
[WARNING]     val ssd = SAMSequenceDictionaryExtractor.extractDictionary(new File(path))
[WARNING]                                              ^
[WARNING] /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/models/SequenceDictionarySuite.scala:62: warning: method extractDictionary in object SAMSequenceDictionaryExtractor is deprecated: see corresponding Javadoc for more information.
[WARNING]     val ssd = SAMSequenceDictionaryExtractor.extractDictionary(new File(path))
[WARNING]                                              ^
[WARNING] /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/models/SequenceDictionarySuite.scala:75: warning: method extractDictionary in object SAMSequenceDictionaryExtractor is deprecated: see corresponding Javadoc for more information.
[WARNING]     val ssd = SAMSequenceDictionaryExtractor.extractDictionary(new File(path))
[WARNING]                                              ^
[WARNING] /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/contig/NucleotideContigFragmentDatasetSuite.scala:742: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead
[WARNING]     val sqlContext = SQLContext.getOrCreate(sc)
[WARNING]                                 ^
[WARNING] /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/contig/NucleotideContigFragmentDatasetSuite.scala:770: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead
[WARNING]     val sqlContext = SQLContext.getOrCreate(sc)
[WARNING]                                 ^
[WARNING] /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/contig/NucleotideContigFragmentDatasetSuite.scala:801: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead
[WARNING]     val sqlContext = SQLContext.getOrCreate(sc)
[WARNING]                                 ^
[WARNING] /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/contig/NucleotideContigFragmentDatasetSuite.scala:832: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead
[WARNING]     val sqlContext = SQLContext.getOrCreate(sc)
[WARNING]                                 ^
[WARNING] /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/contig/NucleotideContigFragmentDatasetSuite.scala:863: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead
[WARNING]     val sqlContext = SQLContext.getOrCreate(sc)
[WARNING]                                 ^
[WARNING] /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/contig/NucleotideContigFragmentDatasetSuite.scala:894: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead
[WARNING]     val sqlContext = SQLContext.getOrCreate(sc)
[WARNING]                                 ^
[WARNING] /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/feature/CoverageDatasetSuite.scala:309: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead
[WARNING]     val sqlContext = SQLContext.getOrCreate(sc)
[WARNING]                                 ^
[WARNING] /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/feature/CoverageDatasetSuite.scala:340: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead
[WARNING]     val sqlContext = SQLContext.getOrCreate(sc)
[WARNING]                                 ^
[WARNING] /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/feature/CoverageDatasetSuite.scala:371: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead
[WARNING]     val sqlContext = SQLContext.getOrCreate(sc)
[WARNING]                                 ^
[WARNING] /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/feature/CoverageDatasetSuite.scala:402: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead
[WARNING]     val sqlContext = SQLContext.getOrCreate(sc)
[WARNING]                                 ^
[WARNING] /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/feature/CoverageDatasetSuite.scala:433: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead
[WARNING]     val sqlContext = SQLContext.getOrCreate(sc)
[WARNING]                                 ^
[WARNING] /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/feature/CoverageDatasetSuite.scala:464: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead
[WARNING]     val sqlContext = SQLContext.getOrCreate(sc)
[WARNING]                                 ^
[WARNING] /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/feature/FeatureDatasetSuite.scala:1022: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead
[WARNING]     val sqlContext = SQLContext.getOrCreate(sc)
[WARNING]                                 ^
[WARNING] /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/feature/FeatureDatasetSuite.scala:1053: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead
[WARNING]     val sqlContext = SQLContext.getOrCreate(sc)
[WARNING]                                 ^
[WARNING] /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/feature/FeatureDatasetSuite.scala:1081: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead
[WARNING]     val sqlContext = SQLContext.getOrCreate(sc)
[WARNING]                                 ^
[WARNING] /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/feature/FeatureDatasetSuite.scala:1112: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead
[WARNING]     val sqlContext = SQLContext.getOrCreate(sc)
[WARNING]                                 ^
[WARNING] /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/feature/FeatureDatasetSuite.scala:1143: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead
[WARNING]     val sqlContext = SQLContext.getOrCreate(sc)
[WARNING]                                 ^
[WARNING] /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/feature/FeatureDatasetSuite.scala:1174: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead
[WARNING]     val sqlContext = SQLContext.getOrCreate(sc)
[WARNING]                                 ^
[WARNING] /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/fragment/FragmentDatasetSuite.scala:400: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead
[WARNING]     val sqlContext = SQLContext.getOrCreate(sc)
[WARNING]                                 ^
[WARNING] /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/fragment/FragmentDatasetSuite.scala:431: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead
[WARNING]     val sqlContext = SQLContext.getOrCreate(sc)
[WARNING]                                 ^
[WARNING] /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/fragment/FragmentDatasetSuite.scala:459: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead
[WARNING]     val sqlContext = SQLContext.getOrCreate(sc)
[WARNING]                                 ^
[WARNING] /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/fragment/FragmentDatasetSuite.scala:490: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead
[WARNING]     val sqlContext = SQLContext.getOrCreate(sc)
[WARNING]                                 ^
[WARNING] /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/fragment/FragmentDatasetSuite.scala:521: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead
[WARNING]     val sqlContext = SQLContext.getOrCreate(sc)
[WARNING]                                 ^
[WARNING] /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/fragment/FragmentDatasetSuite.scala:552: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead
[WARNING]     val sqlContext = SQLContext.getOrCreate(sc)
[WARNING]                                 ^
[WARNING] /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/read/AlignmentRecordDatasetSuite.scala:1438: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead
[WARNING]     val sqlContext = SQLContext.getOrCreate(sc)
[WARNING]                                 ^
[WARNING] /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/read/AlignmentRecordDatasetSuite.scala:1460: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead
[WARNING]     val sqlContext = SQLContext.getOrCreate(sc)
[WARNING]                                 ^
[WARNING] /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/read/AlignmentRecordDatasetSuite.scala:1491: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead
[WARNING]     val sqlContext = SQLContext.getOrCreate(sc)
[WARNING]                                 ^
[WARNING] /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/read/AlignmentRecordDatasetSuite.scala:1519: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead
[WARNING]     val sqlContext = SQLContext.getOrCreate(sc)
[WARNING]                                 ^
[WARNING] /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/read/AlignmentRecordDatasetSuite.scala:1550: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead
[WARNING]     val sqlContext = SQLContext.getOrCreate(sc)
[WARNING]                                 ^
[WARNING] /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/read/AlignmentRecordDatasetSuite.scala:1581: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead
[WARNING]     val sqlContext = SQLContext.getOrCreate(sc)
[WARNING]                                 ^
[WARNING] /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/read/AlignmentRecordDatasetSuite.scala:1613: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead
[WARNING]     val sqlContext = SQLContext.getOrCreate(sc)
[WARNING]                                 ^
[WARNING] /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/read/realignment/IndelRealignmentTargetSuite.scala:83: warning: method richRecordToRecord in object RichAlignmentRecord is deprecated: Use explicit conversion wherever possible in new development.
[WARNING]     assert(TargetOrdering.contains(targets.head, read))
[WARNING]                                                  ^
[WARNING] /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/read/realignment/IndelRealignmentTargetSuite.scala:191: warning: method richRecordToRecord in object RichAlignmentRecord is deprecated: Use explicit conversion wherever possible in new development.
[WARNING]         if (read.getStart < 105) {
[WARNING]             ^
[WARNING] /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/read/realignment/IndelRealignmentTargetSuite.scala:194: warning: method richRecordToRecord in object RichAlignmentRecord is deprecated: Use explicit conversion wherever possible in new development.
[WARNING]           assert(targets.head.readRange.start === read.getStart)
[WARNING]                                                   ^
[WARNING] /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/read/realignment/IndelRealignmentTargetSuite.scala:195: warning: method richRecordToRecord in object RichAlignmentRecord is deprecated: Use explicit conversion wherever possible in new development.
[WARNING]           assert(targets.head.readRange.end === read.getEnd)
[WARNING]                                                 ^
[WARNING] /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/read/realignment/IndelRealignmentTargetSuite.scala:196: warning: method richRecordToRecord in object RichAlignmentRecord is deprecated: Use explicit conversion wherever possible in new development.
[WARNING]           assert(check_indel(targets.head, read))
[WARNING]                                            ^
[WARNING] /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/variant/GenotypeDatasetSuite.scala:406: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead
[WARNING]     val sqlContext = SQLContext.getOrCreate(sc)
[WARNING]                                 ^
[WARNING] /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/variant/GenotypeDatasetSuite.scala:437: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead
[WARNING]     val sqlContext = SQLContext.getOrCreate(sc)
[WARNING]                                 ^
[WARNING] /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/variant/GenotypeDatasetSuite.scala:465: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead
[WARNING]     val sqlContext = SQLContext.getOrCreate(sc)
[WARNING]                                 ^
[WARNING] /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/variant/GenotypeDatasetSuite.scala:496: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead
[WARNING]     val sqlContext = SQLContext.getOrCreate(sc)
[WARNING]                                 ^
[WARNING] /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/variant/GenotypeDatasetSuite.scala:527: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead
[WARNING]     val sqlContext = SQLContext.getOrCreate(sc)
[WARNING]                                 ^
[WARNING] /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/variant/GenotypeDatasetSuite.scala:558: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead
[WARNING]     val sqlContext = SQLContext.getOrCreate(sc)
[WARNING]                                 ^
[WARNING] /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/variant/GenotypeDatasetSuite.scala:697: warning: variable end in class Genotype is deprecated: see corresponding Javadoc for more information.
[WARNING]     assert(first.end === 16157602L)
[WARNING]                  ^
[WARNING] /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/variant/GenotypeDatasetSuite.scala:698: warning: variable end in class Variant is deprecated: see corresponding Javadoc for more information.
[WARNING]     assert(first.variant.end === 16157602L)
[WARNING]                          ^
[WARNING] /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/variant/GenotypeDatasetSuite.scala:698: warning: variable variant in class Genotype is deprecated: see corresponding Javadoc for more information.
[WARNING]     assert(first.variant.end === 16157602L)
[WARNING]                  ^
[WARNING] /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/variant/GenotypeDatasetSuite.scala:699: warning: variable annotation in class Variant is deprecated: see corresponding Javadoc for more information.
[WARNING]     assert(first.variant.annotation === null)
[WARNING]                          ^
[WARNING] /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/variant/GenotypeDatasetSuite.scala:699: warning: variable variant in class Genotype is deprecated: see corresponding Javadoc for more information.
[WARNING]     assert(first.variant.annotation === null)
[WARNING]                  ^
[WARNING] /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/variant/GenotypeDatasetSuite.scala:710: warning: variable end in class Genotype is deprecated: see corresponding Javadoc for more information.
[WARNING]     assert(firstVcfGenotype.end === 16157602L)
[WARNING]                             ^
[WARNING] /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/variant/GenotypeDatasetSuite.scala:712: warning: variable end in class Variant is deprecated: see corresponding Javadoc for more information.
[WARNING]     assert(firstVcfGenotype.variant.end === 16157602L)
[WARNING]                                     ^
[WARNING] /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/variant/GenotypeDatasetSuite.scala:712: warning: variable variant in class Genotype is deprecated: see corresponding Javadoc for more information.
[WARNING]     assert(firstVcfGenotype.variant.end === 16157602L)
[WARNING]                             ^
[WARNING] /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/variant/GenotypeDatasetSuite.scala:714: warning: variable annotation in class Variant is deprecated: see corresponding Javadoc for more information.
[WARNING]     assert(firstVcfGenotype.variant.annotation === null)
[WARNING]                                     ^
[WARNING] /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/variant/GenotypeDatasetSuite.scala:714: warning: variable variant in class Genotype is deprecated: see corresponding Javadoc for more information.
[WARNING]     assert(firstVcfGenotype.variant.annotation === null)
[WARNING]                             ^
[WARNING] /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/variant/GenotypeDatasetSuite.scala:745: warning: variable end in class Genotype is deprecated: see corresponding Javadoc for more information.
[WARNING]     assert(first.end === 16157602L)
[WARNING]                  ^
[WARNING] /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/variant/GenotypeDatasetSuite.scala:746: warning: variable end in class Variant is deprecated: see corresponding Javadoc for more information.
[WARNING]     assert(first.variant.end === 16157602L)
[WARNING]                          ^
[WARNING] /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/variant/GenotypeDatasetSuite.scala:746: warning: variable variant in class Genotype is deprecated: see corresponding Javadoc for more information.
[WARNING]     assert(first.variant.end === 16157602L)
[WARNING]                  ^
[WARNING] /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/variant/GenotypeDatasetSuite.scala:747: warning: variable attributes in class VariantAnnotation is deprecated: see corresponding Javadoc for more information.
[WARNING]     assert(first.variant.annotation.attributes.get("END") === "16157602")
[WARNING]                                     ^
[WARNING] /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/variant/GenotypeDatasetSuite.scala:747: warning: variable annotation in class Variant is deprecated: see corresponding Javadoc for more information.
[WARNING]     assert(first.variant.annotation.attributes.get("END") === "16157602")
[WARNING]                          ^
[WARNING] /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/variant/GenotypeDatasetSuite.scala:747: warning: variable variant in class Genotype is deprecated: see corresponding Javadoc for more information.
[WARNING]     assert(first.variant.annotation.attributes.get("END") === "16157602")
[WARNING]                  ^
[WARNING] /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/variant/GenotypeDatasetSuite.scala:758: warning: variable end in class Genotype is deprecated: see corresponding Javadoc for more information.
[WARNING]     assert(firstVcfGenotype.end === 16157602L)
[WARNING]                             ^
[WARNING] /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/variant/GenotypeDatasetSuite.scala:759: warning: variable end in class Variant is deprecated: see corresponding Javadoc for more information.
[WARNING]     assert(firstVcfGenotype.variant.end === 16157602L)
[WARNING]                                     ^
[WARNING] /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/variant/GenotypeDatasetSuite.scala:759: warning: variable variant in class Genotype is deprecated: see corresponding Javadoc for more information.
[WARNING]     assert(firstVcfGenotype.variant.end === 16157602L)
[WARNING]                             ^
[WARNING] /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/variant/GenotypeDatasetSuite.scala:760: warning: variable attributes in class VariantAnnotation is deprecated: see corresponding Javadoc for more information.
[WARNING]     assert(firstVcfGenotype.variant.annotation.attributes.get("END") === "16157602")
[WARNING]                                                ^
[WARNING] /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/variant/GenotypeDatasetSuite.scala:760: warning: variable annotation in class Variant is deprecated: see corresponding Javadoc for more information.
[WARNING]     assert(firstVcfGenotype.variant.annotation.attributes.get("END") === "16157602")
[WARNING]                                     ^
[WARNING] /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/variant/GenotypeDatasetSuite.scala:760: warning: variable variant in class Genotype is deprecated: see corresponding Javadoc for more information.
[WARNING]     assert(firstVcfGenotype.variant.annotation.attributes.get("END") === "16157602")
[WARNING]                             ^
[WARNING] /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/variant/VariantContextDatasetSuite.scala:181: warning: variable start in class Genotype is deprecated: see corresponding Javadoc for more information.
[WARNING]     val filtered = vcs.toGenotypes().rdd.filter(_.start == 66631043)
[WARNING]                                                   ^
[WARNING] /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/variant/VariantDatasetSuite.scala:422: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead
[WARNING]     val sqlContext = SQLContext.getOrCreate(sc)
[WARNING]                                 ^
[WARNING] /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/variant/VariantDatasetSuite.scala:453: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead
[WARNING]     val sqlContext = SQLContext.getOrCreate(sc)
[WARNING]                                 ^
[WARNING] /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/variant/VariantDatasetSuite.scala:481: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead
[WARNING]     val sqlContext = SQLContext.getOrCreate(sc)
[WARNING]                                 ^
[WARNING] /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/variant/VariantDatasetSuite.scala:512: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead
[WARNING]     val sqlContext = SQLContext.getOrCreate(sc)
[WARNING]                                 ^
[WARNING] /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/variant/VariantDatasetSuite.scala:543: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead
[WARNING]     val sqlContext = SQLContext.getOrCreate(sc)
[WARNING]                                 ^
[WARNING] /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/variant/VariantDatasetSuite.scala:574: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead
[WARNING]     val sqlContext = SQLContext.getOrCreate(sc)
[WARNING]                                 ^
[WARNING] /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rich/RichAlignmentRecordSuite.scala:31: warning: method recordToRichRecord in object RichAlignmentRecord is deprecated: Use explicit conversion wherever possible in new development.
[WARNING]     assert(recordWithoutClipping.unclippedStart == 42L)
[WARNING]            ^
[WARNING] /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rich/RichAlignmentRecordSuite.scala:32: warning: method recordToRichRecord in object RichAlignmentRecord is deprecated: Use explicit conversion wherever possible in new development.
[WARNING]     assert(recordWithClipping.unclippedStart == 40L)
[WARNING]            ^
[WARNING] /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rich/RichAlignmentRecordSuite.scala:33: warning: method recordToRichRecord in object RichAlignmentRecord is deprecated: Use explicit conversion wherever possible in new development.
[WARNING]     assert(recordWithHardClipping.unclippedStart == 37L)
[WARNING]            ^
[WARNING] /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rich/RichAlignmentRecordSuite.scala:41: warning: method recordToRichRecord in object RichAlignmentRecord is deprecated: Use explicit conversion wherever possible in new development.
[WARNING]     assert(recordWithoutClipping.unclippedEnd == 20L)
[WARNING]            ^
[WARNING] /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rich/RichAlignmentRecordSuite.scala:42: warning: method recordToRichRecord in object RichAlignmentRecord is deprecated: Use explicit conversion wherever possible in new development.
[WARNING]     assert(recordWithClipping.unclippedEnd == 20L)
[WARNING]            ^
[WARNING] /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rich/RichAlignmentRecordSuite.scala:43: warning: method recordToRichRecord in object RichAlignmentRecord is deprecated: Use explicit conversion wherever possible in new development.
[WARNING]     assert(recordWithHardClipping.unclippedEnd == 20L)
[WARNING]            ^
[WARNING] /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rich/RichAlignmentRecordSuite.scala:49: warning: method recordToRichRecord in object RichAlignmentRecord is deprecated: Use explicit conversion wherever possible in new development.
[WARNING]     assert(rec.tags.size === 2)
[WARNING]            ^
[WARNING] /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rich/RichAlignmentRecordSuite.scala:50: warning: method recordToRichRecord in object RichAlignmentRecord is deprecated: Use explicit conversion wherever possible in new development.
[WARNING]     assert(rec.tags(0) === Attribute("XX", TagType.Integer, 3))
[WARNING]            ^
[WARNING] /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rich/RichAlignmentRecordSuite.scala:51: warning: method recordToRichRecord in object RichAlignmentRecord is deprecated: Use explicit conversion wherever possible in new development.
[WARNING]     assert(rec.tags(1) === Attribute("YY", TagType.String, "foo"))
[WARNING]            ^
[WARNING] /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rich/RichAlignmentRecordSuite.scala:57: warning: method recordToRichRecord in object RichAlignmentRecord is deprecated: Use explicit conversion wherever possible in new development.
[WARNING]     val overlaps = unmappedRead.overlapsReferencePosition(ReferencePosition("chr1", 10))
[WARNING]                    ^
[WARNING] /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rich/RichCigarSuite.scala:34: warning: method recordToRichRecord in object RichAlignmentRecord is deprecated: Use explicit conversion wherever possible in new development.
[WARNING]     val newCigar = RichCigar(new Cigar(read.samtoolsCigar.getCigarElements)).moveLeft(1)
[WARNING]                                        ^
[WARNING] /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rich/RichCigarSuite.scala:37: warning: method recordToRichRecord in object RichAlignmentRecord is deprecated: Use explicit conversion wherever possible in new development.
[WARNING]     assert(newCigar2.cigar.getReadLength == read.samtoolsCigar.getReadLength)
[WARNING]                                             ^
[WARNING] /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rich/RichCigarSuite.scala:49: warning: method recordToRichRecord in object RichAlignmentRecord is deprecated: Use explicit conversion wherever possible in new development.
[WARNING]     val newCigar = RichCigar(new Cigar(read.samtoolsCigar.getCigarElements)).moveLeft(1)
[WARNING]                                        ^
[WARNING] /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rich/RichCigarSuite.scala:52: warning: method recordToRichRecord in object RichAlignmentRecord is deprecated: Use explicit conversion wherever possible in new development.
[WARNING]     assert(newCigar2.cigar.getReadLength == read.samtoolsCigar.getReadLength)
[WARNING]                                             ^
[WARNING] /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rich/RichCigarSuite.scala:64: warning: method recordToRichRecord in object RichAlignmentRecord is deprecated: Use explicit conversion wherever possible in new development.
[WARNING]     val newCigar = RichCigar(new Cigar(read.samtoolsCigar.getCigarElements)).moveLeft(1)
[WARNING]                                        ^
[WARNING] /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rich/RichCigarSuite.scala:66: warning: method recordToRichRecord in object RichAlignmentRecord is deprecated: Use explicit conversion wherever possible in new development.
[WARNING]     assert(newCigar.cigar.getReadLength == read.samtoolsCigar.getReadLength)
[WARNING]                                            ^
[WARNING] /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rich/RichCigarSuite.scala:78: warning: method recordToRichRecord in object RichAlignmentRecord is deprecated: Use explicit conversion wherever possible in new development.
[WARNING]     val newCigar = RichCigar(new Cigar(read.samtoolsCigar.getCigarElements)).moveLeft(1)
[WARNING]                                        ^
[WARNING] /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rich/RichCigarSuite.scala:80: warning: method recordToRichRecord in object RichAlignmentRecord is deprecated: Use explicit conversion wherever possible in new development.
[WARNING]     assert(newCigar.cigar.getReadLength == read.samtoolsCigar.getReadLength)
[WARNING]                                            ^
[WARNING] 115 warnings found
[INFO] prepare-compile in 0 s
[INFO] compile in 33 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ adam-core-spark2_2.11 ---
[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_2.11 ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ adam-core-spark2_2.11 ---
Discovery starting.
Discovery completed in 1 second, 247 milliseconds.
Run starting. Expected test count is: 0
Run completed in 1 second, 252 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_2.11 ---
[INFO] Building jar: /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/adam-core-spark2_2.11-0.27.0-SNAPSHOT.jar
[INFO] 
[INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ adam-core-spark2_2.11 ---
[INFO] Building jar: /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/adam-core-spark2_2.11-0.27.0-SNAPSHOT-sources.jar
[INFO] 
[INFO] --- maven-javadoc-plugin:3.1.0:jar (attach-javadoc) @ adam-core-spark2_2.11 ---
[ERROR] Error fetching link: /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-codegen/target/apidocs. Ignored it.
[INFO] 
Loading source files for package org.bdgenomics.adam.io...
Loading source files for package org.apache.parquet.avro...
Constructing Javadoc information...
Standard Doclet version 1.8.0_191
Building tree for all the packages and classes...
Generating /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/org/bdgenomics/adam/io/FastqInputFormat.html...
Generating /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/org/bdgenomics/adam/io/FastqRecordReader.html...
Generating /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/org/bdgenomics/adam/io/InterleavedFastqInputFormat.html...
Generating /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/org/bdgenomics/adam/io/SingleFastqInputFormat.html...
Generating /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/org/apache/parquet/avro/AvroSchemaConverter.html...
Generating /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/overview-frame.html...
Generating /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/org/apache/parquet/avro/package-frame.html...
Generating /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/org/apache/parquet/avro/package-summary.html...
Generating /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/org/apache/parquet/avro/package-tree.html...
Generating /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/org/bdgenomics/adam/io/package-frame.html...
Generating /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/org/bdgenomics/adam/io/package-summary.html...
Generating /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/org/bdgenomics/adam/io/package-tree.html...
Generating /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/constant-values.html...
Generating /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/org/bdgenomics/adam/io/class-use/InterleavedFastqInputFormat.html...
Generating /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/org/bdgenomics/adam/io/class-use/SingleFastqInputFormat.html...
Generating /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/org/bdgenomics/adam/io/class-use/FastqRecordReader.html...
Generating /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/org/bdgenomics/adam/io/class-use/FastqInputFormat.html...
Generating /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/org/apache/parquet/avro/class-use/AvroSchemaConverter.html...
Generating /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/org/apache/parquet/avro/package-use.html...
Generating /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/org/bdgenomics/adam/io/package-use.html...
Building index for all the packages and classes...
Generating /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/overview-tree.html...
Generating /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/index-all.html...
Generating /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/deprecated-list.html...
Building index for all classes...
Generating /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/allclasses-frame.html...
Generating /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/allclasses-noframe.html...
Generating /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/index.html...
Generating /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/overview-summary.html...
Generating /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/help-doc.html...
6 warnings
[WARNING] Javadoc Warnings
[WARNING] /tmp/adamTestBCgudXi/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/adamTestBCgudXi/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/adamTestBCgudXi/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/adamTestBCgudXi/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/adamTestBCgudXi/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/adamTestBCgudXi/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/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/adam-core-spark2_2.11-0.27.0-SNAPSHOT-javadoc.jar
[INFO] 
[INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) > generate-sources @ adam-core-spark2_2.11 >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-core-spark2_2.11 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-core-spark2_2.11 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ adam-core-spark2_2.11 ---
[INFO] Source directory: /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala added.
[INFO] Source directory: /tmp/adamTestBCgudXi/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_2.11 ---
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_2.11 ---
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_2.11 <<<
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ adam-core-spark2_2.11 ---
/tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/converters/FastaConverter.scala:230: warning: discarding unmoored doc comment
    /**
    ^
/tmp/adamTestBCgudXi/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/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/rich/RichCigar.scala:43: warning: discarding unmoored doc comment
    /**
    ^
/tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/rdd/GenomicDataset.scala:3099: warning: no valid targets for annotation on value uTag - it is discarded unused. You may specify targets with meta-annotations, e.g. @(transient @getter)
  @transient val uTag: TypeTag[U]
   ^
warning: there were 5 feature warnings; re-run with -feature for details
model contains 276 documentable templates
/tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/util/AttributeUtils.scala:70: warning: Could not find any member to link for "IllegalArgumentException".
  /**
  ^
/tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/projections/Projection.scala:45: warning: Could not find any member to link for "IllegalArgumentException".
  /**
  ^
/tmp/adamTestBCgudXi/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/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/rdd/ADAMContext.scala:1339: warning: Could not find any member to link for "FileNotFoundException".
  /**
  ^
/tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/rdd/ADAMContext.scala:1368: warning: Could not find any member to link for "FileNotFoundException".
  /**
  ^
/tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/rdd/ADAMContext.scala:1388: warning: Could not find any member to link for "FileNotFoundException".
  /**
  ^
/tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/rdd/GenomicPartitioners.scala:75: warning: Could not find any member to link for "IllegalArgumentException".
  /**
  ^
/tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/rdd/GenomicPartitioners.scala:178: warning: Could not find any member to link for "IllegalArgumentException".
  /**
  ^
/tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/models/ReferenceRegion.scala:456: warning: Could not find any member to link for "IllegalArgumentException".
  /**
  ^
/tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/rdd/ADAMContext.scala:3085: warning: Could not find any member to link for "IllegalArgumentException".
  /**
  ^
/tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/models/ReferenceRegion.scala:411: warning: Could not find any member to link for "IllegalArgumentException".
  /**
  ^
/tmp/adamTestBCgudXi/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/adamTestBCgudXi/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/adamTestBCgudXi/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/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/models/ReadGroupDictionary.scala:47: warning: Could not find any member to link for "IllegalArgumentException".
/**
^
/tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/models/Alphabet.scala:44: warning: Could not find any member to link for "IllegalArgumentException".
  /**
  ^
/tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/models/ReferenceRegion.scala:258: warning: Could not find any member to link for "IllegalArgumentException".
  /**
  ^
/tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/models/ReferenceRegion.scala:242: warning: Could not find any member to link for "IllegalArgumentException".
  /**
  ^
/tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/models/ReferenceRegion.scala:426: warning: Could not find any member to link for "IllegalArgumentException".
  /**
  ^
/tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/models/ReferenceRegion.scala:336: warning: Could not find any member to link for "IllegalArgumentException".
  /**
  ^
25 warnings found
[INFO] Building jar: /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/adam-core-spark2_2.11-0.27.0-SNAPSHOT-javadoc.jar
[INFO] 
[INFO] --- maven-jar-plugin:3.1.2:test-jar (default) @ adam-core-spark2_2.11 ---
[INFO] Building jar: /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/adam-core-spark2_2.11-0.27.0-SNAPSHOT-tests.jar
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building ADAM_2.11: APIs for Java, Python 0.27.0-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-apis-spark2_2.11 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-apis-spark2_2.11 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ adam-apis-spark2_2.11 ---
[INFO] Source directory: /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-apis/src/main/scala added.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ adam-apis-spark2_2.11 ---
[INFO] Modified 0 of 5 .scala files
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ adam-apis-spark2_2.11 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-apis/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ adam-apis-spark2_2.11 ---
[INFO] /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-apis/src/main/scala:-1: info: compiling
[INFO] Compiling 4 source files to /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-apis/target/2.11.12/classes at 1557952829618
[WARNING] warning: there were two feature warnings; re-run with -feature for details
[WARNING] one warning found
[INFO] prepare-compile in 0 s
[INFO] compile in 4 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ adam-apis-spark2_2.11 ---
[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_2.11 ---
[INFO] Test Source directory: /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-apis/src/test/scala added.
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ adam-apis-spark2_2.11 ---
[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_2.11 ---
[INFO] /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-apis/src/test/java:-1: info: compiling
[INFO] /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-apis/src/test/scala:-1: info: compiling
[INFO] Compiling 8 source files to /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-apis/target/2.11.12/test-classes at 1557952834397
[INFO] prepare-compile in 0 s
[INFO] compile in 6 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ adam-apis-spark2_2.11 ---
[INFO] Changes detected - recompiling the module!
[INFO] Compiling 7 source files to /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-apis/target/2.11.12/test-classes
[INFO] 
[INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ adam-apis-spark2_2.11 ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ adam-apis-spark2_2.11 ---
Discovery starting.
Discovery completed in 218 milliseconds.
Run starting. Expected test count is: 0
Run completed in 229 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_2.11 ---
[INFO] Building jar: /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-apis/target/adam-apis-spark2_2.11-0.27.0-SNAPSHOT.jar
[INFO] 
[INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ adam-apis-spark2_2.11 ---
[INFO] 
[INFO] --- maven-javadoc-plugin:3.1.0:jar (attach-javadoc) @ adam-apis-spark2_2.11 ---
[INFO] Building jar: /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-apis/target/adam-apis-spark2_2.11-0.27.0-SNAPSHOT-javadoc.jar
[INFO] 
[INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) > generate-sources @ adam-apis-spark2_2.11 >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-apis-spark2_2.11 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-apis-spark2_2.11 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ adam-apis-spark2_2.11 ---
[INFO] Source directory: /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-apis/src/main/scala added.
[INFO] 
[INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) < generate-sources @ adam-apis-spark2_2.11 <<<
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ adam-apis-spark2_2.11 ---
warning: there were two feature warnings; re-run with -feature for details
model contains 124 documentable templates
one warning found
[INFO] Building jar: /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-apis/target/adam-apis-spark2_2.11-0.27.0-SNAPSHOT-javadoc.jar
[INFO] 
[INFO] --- maven-jar-plugin:3.1.2:test-jar (default) @ adam-apis-spark2_2.11 ---
[INFO] Building jar: /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-apis/target/adam-apis-spark2_2.11-0.27.0-SNAPSHOT-tests.jar
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building ADAM_2.11: CLI 0.27.0-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-cli-spark2_2.11 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-cli-spark2_2.11 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:timestamp-property (timestamp-property) @ adam-cli-spark2_2.11 ---
[INFO] 
[INFO] --- git-commit-id-plugin:2.2.2:revision (default) @ adam-cli-spark2_2.11 ---
[INFO] 
[INFO] --- templating-maven-plugin:1.0.0:filter-sources (filter-src) @ adam-cli-spark2_2.11 ---
[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/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/generated-sources/java-templates
[INFO] Source directory: /tmp/adamTestBCgudXi/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_2.11 ---
[INFO] Source directory: /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-cli/src/main/scala added.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ adam-cli-spark2_2.11 ---
[INFO] Modified 0 of 31 .scala files
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ adam-cli-spark2_2.11 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-cli/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ adam-cli-spark2_2.11 ---
[INFO] /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/generated-sources/java-templates:-1: info: compiling
[INFO] /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-cli/src/main/scala:-1: info: compiling
[INFO] Compiling 18 source files to /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/2.11.12/classes at 1557952854549
[WARNING] warning: there was one deprecation warning; re-run with -deprecation for details
[WARNING] one warning found
[INFO] prepare-compile in 0 s
[INFO] compile in 10 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ adam-cli-spark2_2.11 ---
[INFO] Changes detected - recompiling the module!
[INFO] Compiling 1 source file to /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/2.11.12/classes
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ adam-cli-spark2_2.11 ---
[INFO] Test Source directory: /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-cli/src/test/scala added.
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ adam-cli-spark2_2.11 ---
[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_2.11 ---
[INFO] /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-cli/src/test/scala:-1: info: compiling
[INFO] Compiling 14 source files to /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/2.11.12/test-classes at 1557952865188
[INFO] prepare-compile in 0 s
[INFO] compile in 11 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ adam-cli-spark2_2.11 ---
[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_2.11 ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ adam-cli-spark2_2.11 ---
Discovery starting.
Discovery completed in 184 milliseconds.
Run starting. Expected test count is: 0
Run completed in 191 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_2.11 ---
[INFO] Building jar: /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/adam-cli-spark2_2.11-0.27.0-SNAPSHOT.jar
[INFO] 
[INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ adam-cli-spark2_2.11 ---
[INFO] Building jar: /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/adam-cli-spark2_2.11-0.27.0-SNAPSHOT-sources.jar
[INFO] 
[INFO] --- maven-javadoc-plugin:3.1.0:jar (attach-javadoc) @ adam-cli-spark2_2.11 ---
[ERROR] Error fetching link: /tmp/adamTestBCgudXi/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/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/apidocs/org/bdgenomics/adam/cli/About.html...
Generating /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/apidocs/org/bdgenomics/adam/cli/package-frame.html...
Generating /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/apidocs/org/bdgenomics/adam/cli/package-summary.html...
Generating /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/apidocs/org/bdgenomics/adam/cli/package-tree.html...
Generating /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/apidocs/constant-values.html...
Generating /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/apidocs/org/bdgenomics/adam/cli/class-use/About.html...
Generating /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/apidocs/org/bdgenomics/adam/cli/package-use.html...
Building index for all the packages and classes...
Generating /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/apidocs/overview-tree.html...
Generating /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/apidocs/index-all.html...
Generating /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/apidocs/deprecated-list.html...
Building index for all classes...
Generating /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/apidocs/allclasses-frame.html...
Generating /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/apidocs/allclasses-noframe.html...
Generating /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/apidocs/index.html...
Generating /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/apidocs/help-doc.html...
[INFO] Building jar: /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/adam-cli-spark2_2.11-0.27.0-SNAPSHOT-javadoc.jar
[INFO] 
[INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) > generate-sources @ adam-cli-spark2_2.11 >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-cli-spark2_2.11 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-cli-spark2_2.11 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:timestamp-property (timestamp-property) @ adam-cli-spark2_2.11 ---
[INFO] 
[INFO] --- git-commit-id-plugin:2.2.2:revision (default) @ adam-cli-spark2_2.11 ---
[INFO] 
[INFO] --- templating-maven-plugin:1.0.0:filter-sources (filter-src) @ adam-cli-spark2_2.11 ---
[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/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/generated-sources/java-templates
[INFO] Source directory: /tmp/adamTestBCgudXi/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_2.11 ---
[INFO] Source directory: /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-cli/src/main/scala added.
[INFO] 
[INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) < generate-sources @ adam-cli-spark2_2.11 <<<
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ adam-cli-spark2_2.11 ---
model contains 55 documentable templates
[INFO] Building jar: /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/adam-cli-spark2_2.11-0.27.0-SNAPSHOT-javadoc.jar
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building ADAM_2.11: Assembly 0.27.0-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-assembly-spark2_2.11 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-assembly-spark2_2.11 ---
[INFO] 
[INFO] --- git-commit-id-plugin:2.2.2:revision (default) @ adam-assembly-spark2_2.11 ---
[INFO] 
[INFO] --- templating-maven-plugin:1.0.0:filter-sources (filter-src) @ adam-assembly-spark2_2.11 ---
[INFO] Request to add '/tmp/adamTestBCgudXi/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_2.11 ---
[INFO] Source directory: /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/src/main/scala added.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ adam-assembly-spark2_2.11 ---
[INFO] Modified 0 of 1 .scala files
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ adam-assembly-spark2_2.11 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ adam-assembly-spark2_2.11 ---
[INFO] /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/src/main/scala:-1: info: compiling
[INFO] Compiling 1 source files to /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/target/2.11.12/classes at 1557952890813
[INFO] prepare-compile in 0 s
[INFO] compile in 2 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ adam-assembly-spark2_2.11 ---
[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-assembly-spark2_2.11 ---
[INFO] Test Source directory: /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/src/test/scala added.
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ adam-assembly-spark2_2.11 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/src/test/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ adam-assembly-spark2_2.11 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ adam-assembly-spark2_2.11 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ adam-assembly-spark2_2.11 ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- maven-jar-plugin:3.1.2:jar (default-jar) @ adam-assembly-spark2_2.11 ---
[INFO] Building jar: /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/target/adam-assembly-spark2_2.11-0.27.0-SNAPSHOT.jar
[INFO] 
[INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ adam-assembly-spark2_2.11 ---
[INFO] 
[INFO] --- maven-javadoc-plugin:3.1.0:jar (attach-javadoc) @ adam-assembly-spark2_2.11 ---
[INFO] 
[INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) > generate-sources @ adam-assembly-spark2_2.11 >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-assembly-spark2_2.11 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-assembly-spark2_2.11 ---
[INFO] 
[INFO] --- git-commit-id-plugin:2.2.2:revision (default) @ adam-assembly-spark2_2.11 ---
[INFO] 
[INFO] --- templating-maven-plugin:1.0.0:filter-sources (filter-src) @ adam-assembly-spark2_2.11 ---
[INFO] Request to add '/tmp/adamTestBCgudXi/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_2.11 ---
[INFO] Source directory: /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/src/main/scala added.
[INFO] 
[INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) < generate-sources @ adam-assembly-spark2_2.11 <<<
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ adam-assembly-spark2_2.11 ---
model contains 6 documentable templates
[INFO] Building jar: /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/target/adam-assembly-spark2_2.11-0.27.0-SNAPSHOT-javadoc.jar
[INFO] 
[INFO] --- maven-shade-plugin:3.2.0:shade (default) @ adam-assembly-spark2_2.11 ---
[INFO] Including org.bdgenomics.adam:adam-cli-spark2_2.11:jar:0.27.0-SNAPSHOT in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-misc-spark2_2.11:jar:0.2.15 in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-io-spark2_2.11:jar:0.2.15 in the shaded jar.
[INFO] Including org.apache.httpcomponents:httpclient:jar:4.5.7 in the shaded jar.
[INFO] Including org.apache.httpcomponents:httpcore:jar:4.4.11 in the shaded jar.
[INFO] Including commons-logging:commons-logging:jar:1.2 in the shaded jar.
[INFO] Including commons-codec:commons-codec:jar:1.11 in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-cli-spark2_2.11:jar:0.2.15 in the shaded jar.
[INFO] Including org.clapper:grizzled-slf4j_2.11:jar:1.3.3 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-avro:jar:1.10.1 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-column:jar:1.10.1 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-common:jar:1.10.1 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-encoding:jar:1.10.1 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-hadoop:jar:1.10.1 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-jackson:jar:1.10.1 in the shaded jar.
[INFO] Including commons-pool:commons-pool:jar:1.6 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-format:jar:2.4.0 in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-metrics-spark2_2.11:jar:0.2.15 in the shaded jar.
[INFO] Including com.netflix.servo:servo-core:jar:0.12.25 in the shaded jar.
[INFO] Including com.netflix.spectator:spectator-api:jar:0.67.0 in the shaded jar.
[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.
[INFO] Including org.apache.avro:avro:jar:1.8.2 in the shaded jar.
[INFO] Including org.codehaus.jackson:jackson-core-asl:jar:1.9.13 in the shaded jar.
[INFO] Including org.codehaus.jackson:jackson-mapper-asl:jar:1.9.13 in the shaded jar.
[INFO] Including com.thoughtworks.paranamer:paranamer:jar:2.7 in the shaded jar.
[INFO] Including org.xerial.snappy:snappy-java:jar:1.1.1.3 in the shaded jar.
[INFO] Including org.apache.commons:commons-compress:jar:1.8.1 in the shaded jar.
[INFO] Including org.tukaani:xz:jar:1.5 in the shaded jar.
[INFO] Including org.bdgenomics.adam:adam-core-spark2_2.11:jar:0.27.0-SNAPSHOT in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-intervalrdd-spark2_2.11:jar:0.2.15 in the shaded jar.
[INFO] Including com.esotericsoftware.kryo:kryo:jar:2.24.0 in the shaded jar.
[INFO] Including com.esotericsoftware.minlog:minlog:jar:1.2 in the shaded jar.
[INFO] Including org.objenesis:objenesis:jar:2.1 in the shaded jar.
[INFO] Including commons-io:commons-io:jar:2.6 in the shaded jar.
[INFO] Including it.unimi.dsi:fastutil:jar:6.6.5 in the shaded jar.
[INFO] Including org.seqdoop:hadoop-bam:jar:7.9.2 in the shaded jar.
[INFO] Including com.github.jsr203hadoop:jsr203hadoop:jar:1.0.3 in the shaded jar.
[INFO] Including com.github.samtools:htsjdk:jar:2.18.2 in the shaded jar.
[INFO] Including org.apache.commons:commons-jexl:jar:2.1.1 in the shaded jar.
[INFO] Including gov.nih.nlm.ncbi:ngs-java:jar:2.9.0 in the shaded jar.
[INFO] Including com.google.guava:guava:jar:27.0-jre in the shaded jar.
[INFO] Including com.google.guava:failureaccess:jar:1.0 in the shaded jar.
[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.
[INFO] Including org.codehaus.mojo:animal-sniffer-annotations:jar:1.17 in the shaded jar.
[INFO] Including org.bdgenomics.adam:adam-codegen-spark2_2.11:jar:0.27.0-SNAPSHOT in the shaded jar.
[INFO] Including org.bdgenomics.adam:adam-apis-spark2_2.11:jar:0.27.0-SNAPSHOT in the shaded jar.
[INFO] Including args4j:args4j:jar:2.33 in the shaded jar.
[INFO] Including net.codingwell:scala-guice_2.11:jar:4.2.1 in the shaded jar.
[INFO] Including com.google.inject:guice:jar:4.2.0 in the shaded jar.
[INFO] Including javax.inject:javax.inject:jar:1 in the shaded jar.
[INFO] Including aopalliance:aopalliance:jar:1.0 in the shaded jar.
[INFO] Including org.scala-lang:scala-reflect:jar:2.11.12 in the shaded jar.
[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/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/target/adam-assembly-spark2_2.11-0.27.0-SNAPSHOT.jar with /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/target/adam-assembly-spark2_2.11-0.27.0-SNAPSHOT-shaded.jar
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building ADAM_2.11: Python APIs 0.27.0-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-python-spark2_2.11 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-python-spark2_2.11 ---
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[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ adam-python-spark2_2.11 ---
[INFO] Modified 0 of 0 .scala files
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ adam-python-spark2_2.11 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-python/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ adam-python-spark2_2.11 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- exec-maven-plugin:1.5.0:exec (dev-python) @ adam-python-spark2_2.11 ---
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/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-python
Requirement already satisfied: pyspark>=1.6.0 in /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.3-bin-hadoop2.7/python (from bdgenomics.adam==0.26.0a0) (2.4.3)
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
Installing collected packages: bdgenomics.adam, py4j
  Running setup.py develop for bdgenomics.adam
Successfully installed bdgenomics.adam py4j-0.10.7
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)
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
reading manifest file 'bdgenomics.adam.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
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/adamContext.py -> build/lib/bdgenomics/adam
copying bdgenomics/adam/rdd.py -> build/lib/bdgenomics/adam
copying bdgenomics/adam/models.py -> build/lib/bdgenomics/adam
copying bdgenomics/adam/find_adam_home.py -> build/lib/bdgenomics/adam
copying bdgenomics/adam/__init__.py -> build/lib/bdgenomics/adam
copying bdgenomics/adam/stringency.py -> build/lib/bdgenomics/adam
creating build/lib/bdgenomics/adam/test
copying bdgenomics/adam/test/genotypeDataset_test.py -> build/lib/bdgenomics/adam/test
copying bdgenomics/adam/test/variantDataset_test.py -> build/lib/bdgenomics/adam/test
copying bdgenomics/adam/test/alignmentRecordDataset_test.py -> build/lib/bdgenomics/adam/test
copying bdgenomics/adam/test/coverageDataset_test.py -> build/lib/bdgenomics/adam/test
copying bdgenomics/adam/test/__init__.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
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
creating build/bdist.linux-x86_64/egg/bdgenomics/adam
copying build/lib/bdgenomics/adam/adamContext.py -> build/bdist.linux-x86_64/egg/bdgenomics/adam
copying build/lib/bdgenomics/adam/rdd.py -> build/bdist.linux-x86_64/egg/bdgenomics/adam
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
creating 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-spark.sh -> 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/find-adam-egg.sh -> 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/find-adam-assembly.sh -> 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/adamR -> build/bdist.linux-x86_64/egg/bdgenomics/adam/bin
copying build/lib/bdgenomics/adam/find_adam_home.py -> build/bdist.linux-x86_64/egg/bdgenomics/adam
copying build/lib/bdgenomics/adam/__init__.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/genotypeDataset_test.py -> 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/alignmentRecordDataset_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/__init__.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/stringency.py -> build/bdist.linux-x86_64/egg/bdgenomics/adam
copying build/lib/bdgenomics/__init__.py -> build/bdist.linux-x86_64/egg/bdgenomics
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/rdd.py to rdd.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/find_adam_home.py to find_adam_home.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/test/genotypeDataset_test.py to genotypeDataset_test.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/alignmentRecordDataset_test.py to alignmentRecordDataset_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/__init__.py to __init__.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/stringency.py to stringency.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/__init__.py to __init__.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/find-adam-home -> build/scripts-2.7
copying deps/bin/find-spark.sh -> build/scripts-2.7
copying deps/bin/adam-shell -> build/scripts-2.7
copying deps/bin/find-adam-egg.sh -> build/scripts-2.7
copying deps/bin/pyadam -> build/scripts-2.7
copying deps/bin/find-adam-assembly.sh -> build/scripts-2.7
copying deps/bin/adam-submit -> build/scripts-2.7
copying deps/bin/adamR -> 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/find-adam-home -> 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/adam-shell -> 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
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/find-adam-assembly.sh -> 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/adamR -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts
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-spark.sh to 775
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/find-adam-egg.sh 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/find-adam-assembly.sh 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/adamR 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_2.11 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ adam-python-spark2_2.11 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-python/src/test/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ adam-python-spark2_2.11 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- exec-maven-plugin:1.5.0:exec (test-python) @ adam-python-spark2_2.11 ---
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-3cc6c2fc-e06a-4d30-8974-6e70069546aa/bin/python
cachedir: .pytest_cache
rootdir: /tmp/adamTestBCgudXi/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 PASSED [ 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 FAILED [ 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 ===================================
______________ GenotypeDatasetTest.test_vcf_add_format_alts_array ______________

self = <bdgenomics.adam.test.genotypeDataset_test.GenotypeDatasetTest testMethod=test_vcf_add_format_alts_array>

    def test_vcf_add_format_alts_array(self):
    
        testFile = self.resourceFile("small.vcf")
        ac = ADAMContext(self.ss)
    
        genotypes = ac.loadGenotypes(testFile)
    
        tmpPath = self.tmpFile() + ".vcf"
        genotypes.toVariantContexts().addAlternateAlleleArrayFormatHeaderLine("AA",
                                                                              "Array with # alts.",
>                                                                             chr).saveAsVcf(tmpPath)

bdgenomics/adam/test/genotypeDataset_test.py:130: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
bdgenomics/adam/rdd.py:1650: in saveAsVcf
    _toJava(stringency, self.sc._jvm))
/tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.3-bin-hadoop2.7/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-hadoop2.7/python/pyspark/sql/utils.py:63: in deco
    return f(*a, **kw)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

answer = 'xro2584'
gateway_client = <py4j.java_gateway.GatewayClient object at 0x7ffa37b2bad0>
target_id = 'o2582', name = 'saveAsVcf'

    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 o2582.saveAsVcf.
E                   : org.apache.spark.SparkException: Job aborted.
E                   	at org.apache.spark.internal.io.SparkHadoopWriter$.write(SparkHadoopWriter.scala:100)
E                   	at org.apache.spark.rdd.PairRDDFunctions$$anonfun$saveAsNewAPIHadoopDataset$1.apply$mcV$sp(PairRDDFunctions.scala:1083)
E                   	at org.apache.spark.rdd.PairRDDFunctions$$anonfun$saveAsNewAPIHadoopDataset$1.apply(PairRDDFunctions.scala:1081)
E                   	at org.apache.spark.rdd.PairRDDFunctions$$anonfun$saveAsNewAPIHadoopDataset$1.apply(PairRDDFunctions.scala:1081)
E                   	at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:151)
E                   	at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:112)
E                   	at org.apache.spark.rdd.RDD.withScope(RDD.scala:363)
E                   	at org.apache.spark.rdd.PairRDDFunctions.saveAsNewAPIHadoopDataset(PairRDDFunctions.scala:1081)
E                   	at org.apache.spark.rdd.PairRDDFunctions$$anonfun$saveAsNewAPIHadoopFile$2.apply$mcV$sp(PairRDDFunctions.scala:1000)
E                   	at org.apache.spark.rdd.PairRDDFunctions$$anonfun$saveAsNewAPIHadoopFile$2.apply(PairRDDFunctions.scala:991)
E                   	at org.apache.spark.rdd.PairRDDFunctions$$anonfun$saveAsNewAPIHadoopFile$2.apply(PairRDDFunctions.scala:991)
E                   	at org.apache.spark.rdd.RDDOperationScope$.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.PairRDDFunctions.saveAsNewAPIHadoopFile(PairRDDFunctions.scala:991)
E                   	at org.bdgenomics.adam.rdd.variant.VariantContextDataset$$anonfun$saveAsVcf$1.apply(VariantContextDataset.scala:420)
E                   	at scala.Option.fold(Option.scala:158)
E                   	at org.apache.spark.rdd.Timer.time(Timer.scala:48)
E                   	at org.bdgenomics.adam.rdd.variant.VariantContextDataset.saveAsVcf(VariantContextDataset.scala:351)
E                   	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
E                   	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
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: 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 /192.168.10.31:34776 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.org$apache$spark$scheduler$DAGScheduler$$failJobAndIndependentStages(DAGScheduler.scala:1889)
E                   	at org.apache.spark.scheduler.DAGScheduler$$anonfun$abortStage$1.apply(DAGScheduler.scala:1877)
E                   	at org.apache.spark.scheduler.DAGScheduler$$anonfun$abortStage$1.apply(DAGScheduler.scala:1876)
E                   	at scala.collection.mutable.ResizableArray$class.foreach(ResizableArray.scala:59)
E                   	at scala.collection.mutable.ArrayBuffer.foreach(ArrayBuffer.scala:48)
E                   	at org.apache.spark.scheduler.DAGScheduler.abortStage(DAGScheduler.scala:1876)
E                   	at org.apache.spark.scheduler.DAGScheduler$$anonfun$handleTaskSetFailed$1.apply(DAGScheduler.scala:926)
E                   	at org.apache.spark.scheduler.DAGScheduler$$anonfun$handleTaskSetFailed$1.apply(DAGScheduler.scala:926)
E                   	at scala.Option.foreach(Option.scala:257)
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$1.run(EventLoop.scala:49)
E                   	at org.apache.spark.scheduler.DAGScheduler.runJob(DAGScheduler.scala:737)
E                   	at org.apache.spark.SparkContext.runJob(SparkContext.scala:2061)
E                   	at org.apache.spark.SparkContext.runJob(SparkContext.scala:2082)
E                   	at org.apache.spark.SparkContext.runJob(SparkContext.scala:2114)
E                   	at org.apache.spark.internal.io.SparkHadoopWriter$.write(SparkHadoopWriter.scala:78)
E                   	... 29 more
E                   Caused by: java.io.IOException: Connection from /192.168.10.31:34776 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/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.3-bin-hadoop2.7/python/lib/py4j-0.10.7-src.zip/py4j/protocol.py:328: Py4JJavaError
----------------------------- Captured stderr call -----------------------------

[Stage 0:>                                                          (0 + 1) / 1]2019-05-15 13:43:25 ERROR TransportRequestHandler:292 - Error sending result StreamResponse{streamId=/jars/adam-assembly-spark2_2.11-0.27.0-SNAPSHOT.jar, byteCount=44167537, body=FileSegmentManagedBuffer{file=/tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/target/adam-assembly-spark2_2.11-0.27.0-SNAPSHOT.jar, offset=0, length=44167537}} to /192.168.10.31:43048; 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 13:43:25 ERROR TransportResponseHandler:144 - Still have 1 requests outstanding when connection from /192.168.10.31:34776 is closed
2019-05-15 13:43:25 ERROR Executor:91 - Exception in task 0.0 in stage 0.0 (TID 0)
java.io.IOException: Connection from /192.168.10.31:34776 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 13:43:25 WARN  TaskSetManager:66 - Lost task 0.0 in stage 0.0 (TID 0, localhost, executor driver): java.io.IOException: Connection from /192.168.10.31:34776 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 13:43:25 ERROR TaskSetManager:70 - Task 0 in stage 0.0 failed 1 times; aborting job
2019-05-15 13:43:25 ERROR SparkHadoopWriter:91 - Aborting job job_20190515134323_0006.
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 /192.168.10.31:34776 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)

Driver stacktrace:
	at org.apache.spark.scheduler.DAGScheduler.org$apache$spark$scheduler$DAGScheduler$$failJobAndIndependentStages(DAGScheduler.scala:1889)
	at org.apache.spark.scheduler.DAGScheduler$$anonfun$abortStage$1.apply(DAGScheduler.scala:1877)
	at org.apache.spark.scheduler.DAGScheduler$$anonfun$abortStage$1.apply(DAGScheduler.scala:1876)
	at scala.collection.mutable.ResizableArray$class.foreach(ResizableArray.scala:59)
	at scala.collection.mutable.ArrayBuffer.foreach(ArrayBuffer.scala:48)
	at org.apache.spark.scheduler.DAGScheduler.abortStage(DAGScheduler.scala:1876)
	at org.apache.spark.scheduler.DAGScheduler$$anonfun$handleTaskSetFailed$1.apply(DAGScheduler.scala:926)
	at org.apache.spark.scheduler.DAGScheduler$$anonfun$handleTaskSetFailed$1.apply(DAGScheduler.scala:926)
	at scala.Option.foreach(Option.scala:257)
	at org.apache.spark.scheduler.DAGScheduler.handleTaskSetFailed(DAGScheduler.scala:926)
	at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.doOnReceive(DAGScheduler.scala:2110)
	at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:2059)
	at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:2048)
	at org.apache.spark.util.EventLoop$$anon$1.run(EventLoop.scala:49)
	at org.apache.spark.scheduler.DAGScheduler.runJob(DAGScheduler.scala:737)
	at org.apache.spark.SparkContext.runJob(SparkContext.scala:2061)
	at org.apache.spark.SparkContext.runJob(SparkContext.scala:2082)
	at org.apache.spark.SparkContext.runJob(SparkContext.scala:2114)
	at org.apache.spark.internal.io.SparkHadoopWriter$.write(SparkHadoopWriter.scala:78)
	at org.apache.spark.rdd.PairRDDFunctions$$anonfun$saveAsNewAPIHadoopDataset$1.apply$mcV$sp(PairRDDFunctions.scala:1083)
	at org.apache.spark.rdd.PairRDDFunctions$$anonfun$saveAsNewAPIHadoopDataset$1.apply(PairRDDFunctions.scala:1081)
	at org.apache.spark.rdd.PairRDDFunctions$$anonfun$saveAsNewAPIHadoopDataset$1.apply(PairRDDFunctions.scala:1081)
	at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:151)
	at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:112)
	at org.apache.spark.rdd.RDD.withScope(RDD.scala:363)
	at org.apache.spark.rdd.PairRDDFunctions.saveAsNewAPIHadoopDataset(PairRDDFunctions.scala:1081)
	at org.apache.spark.rdd.PairRDDFunctions$$anonfun$saveAsNewAPIHadoopFile$2.apply$mcV$sp(PairRDDFunctions.scala:1000)
	at org.apache.spark.rdd.PairRDDFunctions$$anonfun$saveAsNewAPIHadoopFile$2.apply(PairRDDFunctions.scala:991)
	at org.apache.spark.rdd.PairRDDFunctions$$anonfun$saveAsNewAPIHadoopFile$2.apply(PairRDDFunctions.scala:991)
	at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:151)
	at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:112)
	at org.apache.spark.rdd.RDD.withScope(RDD.scala:363)
	at org.apache.spark.rdd.PairRDDFunctions.saveAsNewAPIHadoopFile(PairRDDFunctions.scala:991)
	at org.bdgenomics.adam.rdd.variant.VariantContextDataset$$anonfun$saveAsVcf$1.apply(VariantContextDataset.scala:420)
	at scala.Option.fold(Option.scala:158)
	at org.apache.spark.rdd.Timer.time(Timer.scala:48)
	at org.bdgenomics.adam.rdd.variant.VariantContextDataset.saveAsVcf(VariantContextDataset.scala:351)
	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 py4j.reflection.MethodInvoker.invoke(MethodInvoker.java:244)
	at py4j.reflection.ReflectionEngine.invoke(ReflectionEngine.java:357)
	at py4j.Gateway.invoke(Gateway.java:282)
	at py4j.commands.AbstractCommand.invokeMethod(AbstractCommand.java:132)
	at py4j.commands.CallCommand.execute(CallCommand.java:79)
	at py4j.GatewayConnection.run(GatewayConnection.java:238)
	at java.lang.Thread.run(Thread.java:748)
Caused by: java.io.IOException: Connection from /192.168.10.31:34776 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)
	... 1 more
- generated xml file: /tmp/adamTestBCgudXi/deleteMePleaseThisIsNoLongerNeeded/adam-python/target/pytest-reports/tests.xml -
===================== 1 failed, 61 passed in 95.86 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_2.11 .......................................... SUCCESS [  7.701 s]
[INFO] ADAM_2.11: Shader workaround ....................... SUCCESS [  5.549 s]
[INFO] ADAM_2.11: Avro-to-Dataset codegen utils ........... SUCCESS [  7.369 s]
[INFO] ADAM_2.11: Core .................................... SUCCESS [01:43 min]
[INFO] ADAM_2.11: APIs for Java, Python ................... SUCCESS [ 23.718 s]
[INFO] ADAM_2.11: CLI ..................................... SUCCESS [ 36.838 s]
[INFO] ADAM_2.11: Assembly ................................ SUCCESS [ 25.211 s]
[INFO] ADAM_2.11: Python APIs ............................. FAILURE [01:41 min]
[INFO] ADAM_2.11: R APIs .................................. SKIPPED
[INFO] ADAM_2.11: Distribution ............................ SKIPPED
[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 05:11 min
[INFO] Finished at: 2019-05-15T13:43:36-07:00
[INFO] Final Memory: 92M/1448M
[INFO] ------------------------------------------------------------------------
[ERROR] Failed to execute goal org.codehaus.mojo:exec-maven-plugin:1.5.0:exec (test-python) on project adam-python-spark2_2.11: 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_2.11
Build step 'Execute shell' marked build as failure
Recording test results
Publishing Scoverage XML and HTML report...
Setting commit status on GitHub for https://github.com/bigdatagenomics/adam/commit/8f09a5504fee4f06243a20b42b534b17aef33d46
Finished: FAILURE