SuccessConsole Output

Skipping 55 KB.. Full Log
vIKc0PTOvWC8xrzgzOT8nv0gvODO3ICfVoyQ3xy+/JNU2Yj/Tagmf50wMjD4M7CWJ6SCJEgYhn6zEskT9nMS8dP3gkqLMvHTriiIGKaihyfl5xfk5qXrOEBpkDgMEMDIxMFQUlDCw2+gXFyTm2QEAI9P8iI4AAAA=
- generate coverage observations for a mapped read
- generate coverage observations for several mapped reads, and an unaligned read
ContaminationEstimatorSuite:
- estimate contamination from a read dataset with 10% contamination reads
- estimate contamination from a read dataset with 5% contamination reads and misc other reads
TranscriptCountsSuite:
- run aggregate with one transcript
- run aggregate with two transcripts, where one is covered twice
AlleleFrequencySuite:
- no alts at a site --> minor allele frequency = 0.0
- half hom ref, half hom alt --> minor allele frequency = 0.5
- half hom ref, half het --> minor allele frequency = 0.25
- 70 hom ref, 20 het, 10 hom alt --> minor allele frequency = 0.2
Run completed in 15 seconds, 856 milliseconds.
Total number of tests run: 64
Suites: completed 17, aborted 0
Tests: succeeded 64, failed 0, canceled 0, ignored 0, pending 0
All tests passed.
[INFO] 
[INFO] --- maven-jar-plugin:2.6:jar (default-jar) @ quinine-core_2.10 ---
[INFO] Building jar: /home/jenkins/workspace/kumquat-prb/hadoop.version/2.2.0/label/centos/quinine-core/target/quinine-core_2.10-0.0.2-SNAPSHOT.jar
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building quinine: CLI 0.0.2-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[WARNING] The POM for org.bdgenomics.adam:adam-cli_2.10:jar:0.19.0 is invalid, transitive dependencies (if any) will not be available, enable debug logging for more details
[INFO] 
[INFO] --- maven-clean-plugin:2.6.1:clean (default-clean) @ quinine-cli_2.10 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ quinine-cli_2.10 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ quinine-cli_2.10 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:1.9.1:add-source (add-source) @ quinine-cli_2.10 ---
[INFO] Source directory: /home/jenkins/workspace/kumquat-prb/hadoop.version/2.2.0/label/centos/quinine-cli/src/main/scala added.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ quinine-cli_2.10 ---
[INFO] Modified 0 of 12 .scala files
[INFO] 
[INFO] --- maven-resources-plugin:2.7:resources (default-resources) @ quinine-cli_2.10 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/kumquat-prb/hadoop.version/2.2.0/label/centos/quinine-cli/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ quinine-cli_2.10 ---
[WARNING] Invalid POM for org.bdgenomics.adam:adam-cli_2.10:jar:0.19.0, transitive dependencies (if any) will not be available, enable debug logging for more details
[WARNING]  Expected all dependencies to require Scala version: 2.10.4
[WARNING]  org.scoverage:scalac-scoverage-plugin_2.10:1.1.1 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.utils:utils-io_2.10:0.2.4 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.adam:adam-core_2.10:0.19.0 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.quinine:quinine-core_2.10:0.0.2-SNAPSHOT requires scala version: 2.10.4
[WARNING]  org.bdgenomics.utils:utils-misc_2.10:0.2.4 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.adam:adam-core_2.10:0.19.0 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.utils:utils-misc_2.10:0.2.4 requires scala version: 2.10.4
[WARNING]  org.scalatest:scalatest_2.10:2.2.5 requires scala version: 2.10.4
[WARNING]  org.scala-lang:scala-reflect:2.10.5 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.utils:utils-cli_2.10:0.2.4 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.utils:utils-metrics_2.10:0.2.4 requires scala version: 2.10.4
[WARNING]  com.twitter:chill_2.10:0.5.0 requires scala version: 2.10.4
[WARNING]  com.typesafe.akka:akka-remote_2.10:2.3.11 requires scala version: 2.10.4
[WARNING]  com.typesafe.akka:akka-actor_2.10:2.3.11 requires scala version: 2.10.4
[WARNING]  com.typesafe.akka:akka-slf4j_2.10:2.3.11 requires scala version: 2.10.4
[WARNING]  org.apache.spark:spark-core_2.10:1.6.1 requires scala version: 2.10.4
[WARNING]  org.json4s:json4s-jackson_2.10:3.2.10 requires scala version: 2.10.4
[WARNING]  org.json4s:json4s-core_2.10:3.2.10 requires scala version: 2.10.4
[WARNING]  org.json4s:json4s-ast_2.10:3.2.10 requires scala version: 2.10.4
[WARNING]  org.json4s:json4s-core_2.10:3.2.10 requires scala version: 2.10.0
[WARNING] Multiple versions of scala libraries detected!
[INFO] /home/jenkins/workspace/kumquat-prb/hadoop.version/2.2.0/label/centos/quinine-cli/src/main/scala:-1: info: compiling
[INFO] Compiling 11 source files to /home/jenkins/workspace/kumquat-prb/hadoop.version/2.2.0/label/centos/quinine-cli/target/scala-2.10.4/classes at 1469515990621
[INFO] prepare-compile in 0 s
[INFO] compile in 7 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.3:compile (default-compile) @ quinine-cli_2.10 ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- build-helper-maven-plugin:1.9.1:add-test-source (add-test-source) @ quinine-cli_2.10 ---
[INFO] Test Source directory: /home/jenkins/workspace/kumquat-prb/hadoop.version/2.2.0/label/centos/quinine-cli/src/test/scala added.
[INFO] 
[INFO] --- maven-resources-plugin:2.7:testResources (default-testResources) @ quinine-cli_2.10 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/kumquat-prb/hadoop.version/2.2.0/label/centos/quinine-cli/src/test/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ quinine-cli_2.10 ---
[WARNING]  Expected all dependencies to require Scala version: 2.10.4
[WARNING]  org.scoverage:scalac-scoverage-plugin_2.10:1.1.1 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.utils:utils-io_2.10:0.2.4 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.adam:adam-core_2.10:0.19.0 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.quinine:quinine-core_2.10:0.0.2-SNAPSHOT requires scala version: 2.10.4
[WARNING]  org.bdgenomics.utils:utils-misc_2.10:0.2.4 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.adam:adam-core_2.10:0.19.0 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.utils:utils-misc_2.10:0.2.4 requires scala version: 2.10.4
[WARNING]  org.scalatest:scalatest_2.10:2.2.5 requires scala version: 2.10.4
[WARNING]  org.scala-lang:scala-reflect:2.10.5 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.utils:utils-cli_2.10:0.2.4 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.utils:utils-metrics_2.10:0.2.4 requires scala version: 2.10.4
[WARNING]  com.twitter:chill_2.10:0.5.0 requires scala version: 2.10.4
[WARNING]  com.typesafe.akka:akka-remote_2.10:2.3.11 requires scala version: 2.10.4
[WARNING]  com.typesafe.akka:akka-actor_2.10:2.3.11 requires scala version: 2.10.4
[WARNING]  com.typesafe.akka:akka-slf4j_2.10:2.3.11 requires scala version: 2.10.4
[WARNING]  org.apache.spark:spark-core_2.10:1.6.1 requires scala version: 2.10.4
[WARNING]  org.json4s:json4s-jackson_2.10:3.2.10 requires scala version: 2.10.4
[WARNING]  org.json4s:json4s-core_2.10:3.2.10 requires scala version: 2.10.4
[WARNING]  org.json4s:json4s-ast_2.10:3.2.10 requires scala version: 2.10.4
[WARNING]  org.json4s:json4s-core_2.10:3.2.10 requires scala version: 2.10.0
[WARNING] Multiple versions of scala libraries detected!
[INFO] /home/jenkins/workspace/kumquat-prb/hadoop.version/2.2.0/label/centos/quinine-cli/src/test/scala:-1: info: compiling
[INFO] Compiling 1 source files to /home/jenkins/workspace/kumquat-prb/hadoop.version/2.2.0/label/centos/quinine-cli/target/scala-2.10.4/test-classes at 1469515998252
[INFO] prepare-compile in 0 s
[INFO] compile in 3 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.3:testCompile (default-testCompile) @ quinine-cli_2.10 ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-surefire-plugin:2.18.1:test (default-test) @ quinine-cli_2.10 ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- scalatest-maven-plugin:1.0:test (test) @ quinine-cli_2.10 ---
Discovery starting.
Discovery completed in 155 milliseconds.
Run starting. Expected test count is: 1
StatWriterSuite:
SLF4J: Class path contains multiple SLF4J bindings.
SLF4J: Found binding in [jar:file:/home/jenkins/.m2/repository/org/slf4j/slf4j-log4j12/1.7.12/slf4j-log4j12-1.7.12.jar!/org/slf4j/impl/StaticLoggerBinder.class]
SLF4J: Found binding in [jar:file:/home/jenkins/.m2/repository/org/bdgenomics/adam/adam-cli_2.10/0.19.0/adam-cli_2.10-0.19.0.jar!/org/slf4j/impl/StaticLoggerBinder.class]
SLF4J: See http://www.slf4j.org/codes.html#multiple_bindings for an explanation.
SLF4J: Actual binding is of type [org.slf4j.impl.Log4jLoggerFactory]
2016-07-25 23:53:23 WARN  NativeCodeLoader:62 - Unable to load native-hadoop library for your platform... using builtin-java classes where applicable
- write something to a file
Run completed in 2 seconds, 495 milliseconds.
Total number of tests run: 1
Suites: completed 2, aborted 0
Tests: succeeded 1, failed 0, canceled 0, ignored 0, pending 0
All tests passed.
[INFO] 
[INFO] --- maven-jar-plugin:2.6:jar (default-jar) @ quinine-cli_2.10 ---
[INFO] Building jar: /home/jenkins/workspace/kumquat-prb/hadoop.version/2.2.0/label/centos/quinine-cli/target/quinine-cli_2.10-0.0.2-SNAPSHOT.jar
[INFO] 
[INFO] --- maven-shade-plugin:2.4.1:shade (default) @ quinine-cli_2.10 ---
[INFO] Including org.bdgenomics.quinine:quinine-core_2.10:jar:0.0.2-SNAPSHOT in the shaded jar.
[INFO] Including org.scoverage:scalac-scoverage-plugin_2.10:jar:1.1.1 in the shaded jar.
[INFO] Including org.bdgenomics.adam:adam-core_2.10:jar:0.19.0 in the shaded jar.
[INFO] Including org.scala-lang:scala-library:jar:2.10.4 in the shaded jar.
[INFO] Including org.slf4j:slf4j-log4j12:jar:1.7.12 in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-misc_2.10:jar:0.2.4 in the shaded jar.
[INFO] Including org.bdgenomics.adam:adam-cli_2.10:jar:0.19.0 in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-io_2.10:jar:0.2.4 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 org.bdgenomics.bdg-formats:bdg-formats:jar:0.7.0 in the shaded jar.
[INFO] Including commons-io:commons-io:jar:1.3.2 in the shaded jar.
[INFO] Including it.unimi.dsi:fastutil:jar:6.6.5 in the shaded jar.
[INFO] Including org.apache.avro:avro:jar:1.7.7 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:2.3 in the shaded jar.
[INFO] Including org.apache.commons:commons-compress:jar:1.4.1 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-avro:jar:1.8.1 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-format:jar:2.3.0-incubating in the shaded jar.
[INFO] Including org.apache.parquet:parquet-scala_2.10:jar:1.8.1 in the shaded jar.
[INFO] Including org.seqdoop:hadoop-bam:jar:7.1.0 in the shaded jar.
[INFO] Including commons-cli:commons-cli:jar:1.2 in the shaded jar.
[INFO] Including commons-httpclient:commons-httpclient:jar:3.1 in the shaded jar.
[INFO] Including com.github.samtools:htsjdk:jar:1.139 in the shaded jar.
[INFO] Including org.apache.commons:commons-jexl:jar:2.1.1 in the shaded jar.
[INFO] Including commons-logging:commons-logging:jar:1.1.1 in the shaded jar.
[INFO] Including org.tukaani:xz:jar:1.5 in the shaded jar.
[INFO] Including org.apache.ant:ant:jar:1.8.2 in the shaded jar.
[INFO] Including org.apache.ant:ant-launcher:jar:1.8.2 in the shaded jar.
[INFO] Including org.apache.httpcomponents:httpclient:jar:4.5.1 in the shaded jar.
[INFO] Including org.apache.httpcomponents:httpcore:jar:4.4.3 in the shaded jar.
[INFO] Including commons-codec:commons-codec:jar:1.9 in the shaded jar.
[INFO] Including com.netflix.servo:servo-core:jar:0.10.0 in the shaded jar.
[INFO] Including com.google.code.findbugs:annotations:jar:2.0.0 in the shaded jar.
[INFO] Including com.netflix.servo:servo-internal:jar:0.10.0 in the shaded jar.
[INFO] Including com.google.guava:guava:jar:16.0.1 in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-cli_2.10:jar:0.2.4 in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-metrics_2.10:jar:0.2.4 in the shaded jar.
[INFO] Including org.slf4j:slf4j-api:jar:1.7.10 in the shaded jar.
[INFO] Including log4j:log4j:jar:1.2.17 in the shaded jar.
[INFO] Including org.xerial.snappy:snappy-java:jar:1.1.2 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-column:jar:1.7.0 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-common:jar:1.7.0 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-encoding:jar:1.7.0 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-generator:jar:1.7.0 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-hadoop:jar:1.7.0 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-jackson:jar:1.7.0 in the shaded jar.
[INFO] Including args4j:args4j:jar:2.0.31 in the shaded jar.
[WARNING] adam-cli_2.10-0.19.0.jar, minlog-1.2.jar define 2 overlapping classes: 
[WARNING]   - com.esotericsoftware.minlog.Log$Logger
[WARNING]   - com.esotericsoftware.minlog.Log
[WARNING] commons-cli-1.2.jar, adam-cli_2.10-0.19.0.jar define 22 overlapping classes: 
[WARNING]   - org.apache.commons.cli.PosixParser
[WARNING]   - org.apache.commons.cli.OptionBuilder
[WARNING]   - org.apache.commons.cli.AlreadySelectedException
[WARNING]   - org.apache.commons.cli.Options
[WARNING]   - org.apache.commons.cli.UnrecognizedOptionException
[WARNING]   - org.apache.commons.cli.Option
[WARNING]   - org.apache.commons.cli.Parser
[WARNING]   - org.apache.commons.cli.TypeHandler
[WARNING]   - org.apache.commons.cli.OptionGroup
[WARNING]   - org.apache.commons.cli.MissingArgumentException
[WARNING]   - 12 more...
[WARNING] servo-internal-0.10.0.jar, adam-cli_2.10-0.19.0.jar define 91 overlapping classes: 
[WARNING]   - com.netflix.servo.jsr166e.ConcurrentHashMapV8$ConcurrentHashMapSpliterator
[WARNING]   - com.netflix.servo.jsr166e.ConcurrentHashMapV8$ForEachTransformedKeyTask
[WARNING]   - com.netflix.servo.jsr166e.ConcurrentHashMapV8$KeySpliterator
[WARNING]   - com.netflix.servo.jsr166e.ForkJoinTask$AdaptedCallable
[WARNING]   - com.netflix.servo.jsr166e.ConcurrentHashMapV8$MapReduceKeysToLongTask
[WARNING]   - com.netflix.servo.jsr166e.ThreadLocalRandom$1
[WARNING]   - com.netflix.servo.jsr166e.ConcurrentHashMapV8$TreeNode
[WARNING]   - com.netflix.servo.jsr166e.ConcurrentHashMapV8$ObjectToDouble
[WARNING]   - com.netflix.servo.jsr166e.ConcurrentHashMapV8$ObjectByObjectToInt
[WARNING]   - com.netflix.servo.jsr166e.ForkJoinPool$1
[WARNING]   - 81 more...
[WARNING] adam-cli_2.10-0.19.0.jar, hadoop-bam-7.1.0.jar define 166 overlapping classes: 
[WARNING]   - org.seqdoop.hadoop_bam.cli.plugins.chipster.SummarizeInputFormat
[WARNING]   - org.seqdoop.hadoop_bam.BCFStoppableOutputStream
[WARNING]   - org.seqdoop.hadoop_bam.LazyBAMRecord
[WARNING]   - org.seqdoop.hadoop_bam.LazyParsingGenotypesContext$Parser
[WARNING]   - org.seqdoop.hadoop_bam.VCFRecordWriter
[WARNING]   - org.seqdoop.hadoop_bam.cli.plugins.View$1
[WARNING]   - hadoop.org.apache.hadoop.mapreduce.lib.partition.TotalOrderPartitioner
[WARNING]   - org.seqdoop.hadoop_bam.SAMRecordWritable
[WARNING]   - org.seqdoop.hadoop_bam.VCFInputFormat
[WARNING]   - org.seqdoop.hadoop_bam.BCFSplitGuesser
[WARNING]   - 156 more...
[WARNING] httpcore-4.4.3.jar, adam-cli_2.10-0.19.0.jar define 254 overlapping classes: 
[WARNING]   - org.apache.http.ConnectionReuseStrategy
[WARNING]   - org.apache.http.params.AbstractHttpParams
[WARNING]   - org.apache.http.ConnectionClosedException
[WARNING]   - org.apache.http.params.HttpAbstractParamBean
[WARNING]   - org.apache.http.pool.AbstractConnPool$2
[WARNING]   - org.apache.http.protocol.HttpResponseInterceptorList
[WARNING]   - org.apache.http.impl.io.ChunkedOutputStream
[WARNING]   - org.apache.http.message.BasicHttpResponse
[WARNING]   - org.apache.http.pool.AbstractConnPool$3
[WARNING]   - org.apache.http.impl.io.DefaultHttpResponseWriterFactory
[WARNING]   - 244 more...
[WARNING] adam-cli_2.10-0.19.0.jar, jackson-mapper-asl-1.9.13.jar define 502 overlapping classes: 
[WARNING]   - org.codehaus.jackson.map.ser.impl.SerializerCache$TypeKey
[WARNING]   - org.codehaus.jackson.map.DeserializerProvider
[WARNING]   - org.codehaus.jackson.map.deser.std.StdKeyDeserializer$LongKD
[WARNING]   - org.codehaus.jackson.node.ValueNode
[WARNING]   - org.codehaus.jackson.map.ser.std.CollectionSerializer
[WARNING]   - org.codehaus.jackson.map.ser.impl.PropertySerializerMap$Double
[WARNING]   - org.codehaus.jackson.map.deser.FromStringDeserializer
[WARNING]   - org.codehaus.jackson.map.deser.std.StdKeyDeserializer$FloatKD
[WARNING]   - org.codehaus.jackson.map.Deserializers
[WARNING]   - org.codehaus.jackson.map.ser.StdSerializers$SerializableSerializer
[WARNING]   - 492 more...
[WARNING] adam-cli_2.10-0.19.0.jar, kryo-2.24.0.jar define 193 overlapping classes: 
[WARNING]   - com.esotericsoftware.kryo.serializers.FieldSerializer$CachedField
[WARNING]   - com.esotericsoftware.kryo.util.ListReferenceResolver
[WARNING]   - com.esotericsoftware.kryo.io.KryoDataInput
[WARNING]   - com.esotericsoftware.kryo.serializers.DefaultSerializers$BigIntegerSerializer
[WARNING]   - com.esotericsoftware.kryo.NotNull
[WARNING]   - com.esotericsoftware.reflectasm.shaded.org.objectweb.asm.Edge
[WARNING]   - com.esotericsoftware.kryo.serializers.AsmCacheFields$AsmBooleanField
[WARNING]   - com.esotericsoftware.reflectasm.shaded.org.objectweb.asm.ClassVisitor
[WARNING]   - com.esotericsoftware.kryo.serializers.DefaultArraySerializers$CharArraySerializer
[WARNING]   - com.esotericsoftware.kryo.serializers.ObjectField
[WARNING]   - 183 more...
[WARNING] adam-cli_2.10-0.19.0.jar, scala-library-2.10.4.jar define 4899 overlapping classes: 
[WARNING]   - scala.Function2$mcIJI$sp$class
[WARNING]   - scala.xml.parsing.TokenTests
[WARNING]   - scala.runtime.NonLocalReturnControl$mcF$sp
[WARNING]   - scala.runtime.RichFloat
[WARNING]   - scala.collection.mutable.ArrayBuilder$ofLong
[WARNING]   - scala.util.parsing.combinator.Parsers$$anonfun$elem$1
[WARNING]   - scala.concurrent.impl.Promise$KeptPromise
[WARNING]   - scala.collection.IterableViewLike$$anonfun$sliding$1$$anonfun$apply$2
[WARNING]   - scala.collection.parallel.ParIterableLike$Composite
[WARNING]   - scala.concurrent.duration.package$span$
[WARNING]   - 4889 more...
[WARNING] commons-logging-1.1.1.jar, adam-cli_2.10-0.19.0.jar define 28 overlapping classes: 
[WARNING]   - org.apache.commons.logging.impl.LogFactoryImpl$2
[WARNING]   - org.apache.commons.logging.impl.LogFactoryImpl
[WARNING]   - org.apache.commons.logging.impl.WeakHashtable$1
[WARNING]   - org.apache.commons.logging.LogFactory$3
[WARNING]   - org.apache.commons.logging.impl.LogFactoryImpl$3
[WARNING]   - org.apache.commons.logging.impl.LogFactoryImpl$1
[WARNING]   - org.apache.commons.logging.LogFactory$6
[WARNING]   - org.apache.commons.logging.impl.WeakHashtable
[WARNING]   - org.apache.commons.logging.LogConfigurationException
[WARNING]   - org.apache.commons.logging.impl.AvalonLogger
[WARNING]   - 18 more...
[WARNING] commons-compress-1.4.1.jar, adam-cli_2.10-0.19.0.jar define 129 overlapping classes: 
[WARNING]   - org.apache.commons.compress.archivers.dump.DumpArchiveEntry$PERMISSION
[WARNING]   - org.apache.commons.compress.compressors.xz.XZCompressorInputStream
[WARNING]   - org.apache.commons.compress.archivers.zip.ZipEncodingHelper
[WARNING]   - org.apache.commons.compress.archivers.ar.ArArchiveOutputStream
[WARNING]   - org.apache.commons.compress.utils.CountingOutputStream
[WARNING]   - org.apache.commons.compress.archivers.tar.TarUtils
[WARNING]   - org.apache.commons.compress.compressors.pack200.Pack200CompressorOutputStream
[WARNING]   - org.apache.commons.compress.utils.ArchiveUtils
[WARNING]   - org.apache.commons.compress.archivers.dump.DumpArchiveEntry
[WARNING]   - org.apache.commons.compress.archivers.dump.DumpArchiveException
[WARNING]   - 119 more...
[WARNING] adam-cli_2.10-0.19.0.jar, parquet-common-1.7.0.jar define 11 overlapping classes: 
[WARNING]   - org.apache.parquet.Ints
[WARNING]   - org.apache.parquet.ParquetRuntimeException
[WARNING]   - org.apache.parquet.hadoop.metadata.ColumnPath
[WARNING]   - org.apache.parquet.Log$1
[WARNING]   - org.apache.parquet.hadoop.metadata.Canonicalizer
[WARNING]   - org.apache.parquet.Log
[WARNING]   - org.apache.parquet.Preconditions
[WARNING]   - org.apache.parquet.hadoop.metadata.ColumnPath$1
[WARNING]   - org.apache.parquet.Closeables
[WARNING]   - org.apache.parquet.bytes.BytesUtils
[WARNING]   - 1 more...
[WARNING] adam-cli_2.10-0.19.0.jar, xz-1.5.jar define 105 overlapping classes: 
[WARNING]   - org.tukaani.xz.PowerPCOptions
[WARNING]   - org.tukaani.xz.index.IndexBase
[WARNING]   - org.tukaani.xz.DeltaEncoder
[WARNING]   - org.tukaani.xz.lzma.LZMAEncoderNormal
[WARNING]   - org.tukaani.xz.DeltaCoder
[WARNING]   - org.tukaani.xz.delta.DeltaDecoder
[WARNING]   - org.tukaani.xz.common.DecoderUtil
[WARNING]   - org.tukaani.xz.LZMA2InputStream
[WARNING]   - org.tukaani.xz.DeltaOutputStream
[WARNING]   - org.tukaani.xz.lz.HC4
[WARNING]   - 95 more...
[WARNING] annotations-2.0.0.jar, adam-cli_2.10-0.19.0.jar define 62 overlapping classes: 
[WARNING]   - edu.umd.cs.findbugs.annotations.PossiblyNull
[WARNING]   - net.jcip.annotations.Immutable
[WARNING]   - javax.annotation.Nonnegative
[WARNING]   - javax.annotation.CheckForSigned
[WARNING]   - javax.annotation.CheckForNull
[WARNING]   - javax.annotation.Tainted
[WARNING]   - net.jcip.annotations.NotThreadSafe
[WARNING]   - edu.umd.cs.findbugs.annotations.SuppressWarnings
[WARNING]   - javax.annotation.Detainted
[WARNING]   - javax.annotation.Nonnull$Checker
[WARNING]   - 52 more...
[WARNING] parquet-encoding-1.7.0.jar, adam-cli_2.10-0.19.0.jar define 184 overlapping classes: 
[WARNING]   - org.apache.parquet.column.values.bitpacking.LemireBitPackingLE$Packer9
[WARNING]   - org.apache.parquet.column.values.bitpacking.ByteBitPackingLE$Packer2
[WARNING]   - org.apache.parquet.column.values.bitpacking.BaseBitPackingReader
[WARNING]   - org.apache.parquet.column.values.bitpacking.ByteBitPackingBE$Packer16
[WARNING]   - org.apache.parquet.column.values.bitpacking.ByteBitPackingBE$1
[WARNING]   - org.apache.parquet.column.values.bitpacking.LemireBitPackingBE$Packer0
[WARNING]   - org.apache.parquet.column.values.bitpacking.ByteBitPackingLE$Packer22
[WARNING]   - org.apache.parquet.column.values.bitpacking.ByteBitPackingLE$1
[WARNING]   - org.apache.parquet.column.values.bitpacking.LemireBitPackingLE$1
[WARNING]   - org.apache.parquet.column.values.bitpacking.LemireBitPackingLE$Packer30
[WARNING]   - 174 more...
[WARNING] servo-core-0.10.0.jar, adam-cli_2.10-0.19.0.jar define 172 overlapping classes: 
[WARNING]   - com.netflix.servo.util.UnmodifiableList
[WARNING]   - com.netflix.servo.monitor.BasicCompositeMonitor
[WARNING]   - com.netflix.servo.util.Clock$1
[WARNING]   - com.netflix.servo.monitor.AnnotatedNumberMonitor
[WARNING]   - com.netflix.servo.publish.MonitorRegistryMetricPoller$MonitorValueCallable
[WARNING]   - com.netflix.servo.tag.Tag
[WARNING]   - com.netflix.servo.tag.InjectableTag
[WARNING]   - com.netflix.servo.util.ExpiringCache$Entry
[WARNING]   - com.netflix.servo.monitor.MonitorConfig$Builder
[WARNING]   - com.netflix.servo.publish.AsyncMetricObserver$1
[WARNING]   - 162 more...
[WARNING] parquet-hadoop-1.7.0.jar, adam-cli_2.10-0.19.0.jar define 117 overlapping classes: 
[WARNING]   - org.apache.parquet.hadoop.example.GroupReadSupport
[WARNING]   - org.apache.parquet.hadoop.ParquetFileWriter$STATE$2
[WARNING]   - org.apache.parquet.hadoop.mapred.MapredParquetOutputCommitter
[WARNING]   - org.apache.parquet.hadoop.ParquetFileReader$3
[WARNING]   - org.apache.parquet.hadoop.util.counters.mapred.MapRedCounterAdapter
[WARNING]   - org.apache.parquet.filter2.statisticslevel.StatisticsFilter
[WARNING]   - org.apache.parquet.hadoop.metadata.EncodingList
[WARNING]   - org.apache.parquet.hadoop.ClientSideMetadataSplitStrategy$1
[WARNING]   - org.apache.parquet.hadoop.util.counters.BenchmarkCounter$NullCounter
[WARNING]   - org.apache.parquet.hadoop.ColumnChunkPageWriteStore$1
[WARNING]   - 107 more...
[WARNING] adam-cli_2.10-0.19.0.jar, scalac-scoverage-plugin_2.10-1.1.1.jar define 172 overlapping classes: 
[WARNING]   - scoverage.report.ScoverageHtmlWriter$$anonfun$classRow$1
[WARNING]   - scoverage.ClassCoverage
[WARNING]   - scoverage.Statement
[WARNING]   - scoverage.PackageBuilders$class
[WARNING]   - scoverage.ScoverageInstrumentationComponent$Transformer$$anonfun$allConstArgs$1
[WARNING]   - scoverage.ScoverageInstrumentationComponent$Transformer$$anonfun$safeEnd$2
[WARNING]   - scoverage.report.NoData$
[WARNING]   - scoverage.MeasuredFile
[WARNING]   - scoverage.Location$$anonfun$apply$1$$anonfun$scoverage$Location$$anonfun$$enclosingMethod$1$1
[WARNING]   - scoverage.Location$$anonfun$apply$1$$anonfun$apply$2
[WARNING]   - 162 more...
[WARNING] commons-httpclient-3.1.jar, adam-cli_2.10-0.19.0.jar define 167 overlapping classes: 
[WARNING]   - org.apache.commons.httpclient.util.URIUtil$Coder
[WARNING]   - org.apache.commons.httpclient.HttpMethodDirector
[WARNING]   - org.apache.commons.httpclient.cookie.CookiePolicy
[WARNING]   - org.apache.commons.httpclient.MethodRetryHandler
[WARNING]   - org.apache.commons.httpclient.auth.NTLMScheme
[WARNING]   - org.apache.commons.httpclient.auth.AuthChallengeParser
[WARNING]   - org.apache.commons.httpclient.methods.multipart.ByteArrayPartSource
[WARNING]   - org.apache.commons.httpclient.cookie.RFC2965Spec$CookieCommentUrlAttributeHandler
[WARNING]   - org.apache.commons.httpclient.auth.AuthScope
[WARNING]   - org.apache.commons.httpclient.HttpClientError
[WARNING]   - 157 more...
[WARNING] adam-cli_2.10-0.19.0.jar, ant-launcher-1.8.2.jar define 5 overlapping classes: 
[WARNING]   - org.apache.tools.ant.launch.Launcher
[WARNING]   - org.apache.tools.ant.launch.LaunchException
[WARNING]   - org.apache.tools.ant.launch.AntMain
[WARNING]   - org.apache.tools.ant.launch.Locator$1
[WARNING]   - org.apache.tools.ant.launch.Locator
[WARNING] adam-cli_2.10-0.19.0.jar, httpclient-4.5.1.jar define 461 overlapping classes: 
[WARNING]   - org.apache.http.conn.routing.RouteInfo$TunnelType
[WARNING]   - org.apache.http.conn.ssl.SSLInitializationException
[WARNING]   - org.apache.http.impl.client.FutureRequestExecutionService
[WARNING]   - org.apache.http.client.methods.HttpUriRequest
[WARNING]   - org.apache.http.client.methods.RequestBuilder
[WARNING]   - org.apache.http.client.entity.DeflateInputStream
[WARNING]   - org.apache.http.impl.cookie.RFC2965SpecFactory
[WARNING]   - org.apache.http.auth.ChallengeState
[WARNING]   - org.apache.http.impl.client.DefaultTargetAuthenticationHandler
[WARNING]   - org.apache.http.impl.client.BasicResponseHandler
[WARNING]   - 451 more...
[WARNING] adam-cli_2.10-0.19.0.jar, utils-metrics_2.10-0.2.4.jar define 440 overlapping classes: 
[WARNING]   - org.bdgenomics.utils.metrics.Histogram
[WARNING]   - org.apache.spark.rdd.InstrumentedRDD$$anonfun$zipPartitions$5$$anonfun$apply$48$$anonfun$apply$49
[WARNING]   - org.apache.spark.rdd.InstrumentedRDD$$anonfun$aggregate$1$$anonfun$apply$59
[WARNING]   - org.apache.spark.rdd.InstrumentedPairRDDFunctions$$anonfun$cogroup$8
[WARNING]   - org.apache.spark.rdd.InstrumentedPairRDDFunctions$$anonfun$reduceByKey$1$$anonfun$apply$31$$anonfun$apply$32
[WARNING]   - org.apache.spark.rdd.InstrumentedRDD$$anonfun$max$1
[WARNING]   - org.apache.spark.rdd.InstrumentedRDD$$anonfun$groupBy$2$$anonfun$apply$16$$anonfun$apply$17
[WARNING]   - org.apache.spark.rdd.InstrumentedPairRDDFunctions$$anonfun$foldByKey$1
[WARNING]   - org.apache.spark.rdd.InstrumentedRDD$$anonfun$foreachPartition$1$$anonfun$apply$mcV$sp$4$$anonfun$apply$5
[WARNING]   - org.apache.spark.rdd.InstrumentedRDD$$anonfun$intersection$2
[WARNING]   - 430 more...
[WARNING] adam-cli_2.10-0.19.0.jar, bdg-formats-0.7.0.jar define 46 overlapping classes: 
[WARNING]   - org.bdgenomics.formats.avro.BDG$Callback
[WARNING]   - org.bdgenomics.formats.avro.AlignmentRecord$Builder
[WARNING]   - org.bdgenomics.formats.avro.Genotype$1
[WARNING]   - org.bdgenomics.formats.avro.AlignmentRecord
[WARNING]   - org.bdgenomics.formats.avro.VariantCallingAnnotations$Builder
[WARNING]   - org.bdgenomics.formats.avro.Dbxref$Builder
[WARNING]   - org.bdgenomics.formats.avro.Feature$1
[WARNING]   - org.bdgenomics.formats.avro.DatabaseVariantAnnotation
[WARNING]   - org.bdgenomics.formats.avro.Feature$Builder
[WARNING]   - org.bdgenomics.formats.avro.RecordGroupMetadata$1
[WARNING]   - 36 more...
[WARNING] snappy-java-1.1.2.jar, adam-cli_2.10-0.19.0.jar define 25 overlapping classes: 
[WARNING]   - org.xerial.snappy.OSInfo
[WARNING]   - org.xerial.snappy.SnappyOutputStream
[WARNING]   - org.xerial.snappy.buffer.BufferAllocator
[WARNING]   - org.xerial.snappy.SnappyLoader
[WARNING]   - org.xerial.snappy.SnappyFramed
[WARNING]   - org.xerial.snappy.SnappyFramedInputStream$FrameMetaData
[WARNING]   - org.xerial.snappy.buffer.CachedBufferAllocator$1
[WARNING]   - org.xerial.snappy.SnappyException
[WARNING]   - org.xerial.snappy.SnappyBundleActivator
[WARNING]   - org.xerial.snappy.SnappyFramedOutputStream
[WARNING]   - 15 more...
[WARNING] adam-cli_2.10-0.19.0.jar, paranamer-2.3.jar define 15 overlapping classes: 
[WARNING]   - com.thoughtworks.paranamer.ParameterNamesNotFoundException
[WARNING]   - com.thoughtworks.paranamer.AdaptiveParanamer
[WARNING]   - com.thoughtworks.paranamer.BytecodeReadingParanamer$ClassReader
[WARNING]   - com.thoughtworks.paranamer.AnnotationParanamer$Jsr330Helper
[WARNING]   - com.thoughtworks.paranamer.BytecodeReadingParanamer$MethodCollector
[WARNING]   - com.thoughtworks.paranamer.BytecodeReadingParanamer$1
[WARNING]   - com.thoughtworks.paranamer.DefaultParanamer
[WARNING]   - com.thoughtworks.paranamer.BytecodeReadingParanamer
[WARNING]   - com.thoughtworks.paranamer.Paranamer
[WARNING]   - com.thoughtworks.paranamer.BytecodeReadingParanamer$TypeCollector
[WARNING]   - 5 more...
[WARNING] adam-cli_2.10-0.19.0.jar, args4j-2.0.31.jar define 71 overlapping classes: 
[WARNING]   - org.kohsuke.args4j.spi.PatternOptionHandler
[WARNING]   - org.kohsuke.args4j.spi.AnnotationImpl
[WARNING]   - org.kohsuke.args4j.spi.EnumOptionHandler
[WARNING]   - org.kohsuke.args4j.spi.ArgumentImpl
[WARNING]   - org.kohsuke.args4j.spi.SubCommand
[WARNING]   - org.kohsuke.args4j.spi.MethodSetter
[WARNING]   - org.kohsuke.args4j.spi.InetAddressOptionHandler
[WARNING]   - org.kohsuke.args4j.Messages
[WARNING]   - org.kohsuke.args4j.spi.OptionHandler
[WARNING]   - org.kohsuke.args4j.spi.ConfigElement
[WARNING]   - 61 more...
[WARNING] adam-cli_2.10-0.19.0.jar, objenesis-2.1.jar define 37 overlapping classes: 
[WARNING]   - org.objenesis.Objenesis
[WARNING]   - org.objenesis.strategy.StdInstantiatorStrategy
[WARNING]   - org.objenesis.instantiator.android.AndroidSerializationInstantiator
[WARNING]   - org.objenesis.instantiator.basic.ObjectStreamClassInstantiator
[WARNING]   - org.objenesis.instantiator.sun.SunReflectionFactorySerializationInstantiator
[WARNING]   - org.objenesis.instantiator.perc.PercSerializationInstantiator
[WARNING]   - org.objenesis.instantiator.jrockit.JRockitLegacyInstantiator
[WARNING]   - org.objenesis.instantiator.gcj.GCJInstantiatorBase
[WARNING]   - org.objenesis.ObjenesisException
[WARNING]   - org.objenesis.instantiator.basic.ObjectInputStreamInstantiator$MockStream
[WARNING]   - 27 more...
[WARNING] ant-1.8.2.jar, adam-cli_2.10-0.19.0.jar define 1090 overlapping classes: 
[WARNING]   - org.apache.tools.ant.filters.LineContainsRegExp
[WARNING]   - org.apache.tools.ant.util.SymbolicLinkUtils
[WARNING]   - org.apache.tools.ant.property.LocalPropertyStack
[WARNING]   - org.apache.tools.ant.types.selectors.MajoritySelector
[WARNING]   - org.apache.tools.ant.taskdefs.optional.depend.ClassFileUtils
[WARNING]   - org.apache.tools.ant.taskdefs.condition.HasMethod
[WARNING]   - org.apache.tools.ant.taskdefs.optional.native2ascii.SunNative2Ascii
[WARNING]   - org.apache.tools.ant.taskdefs.Local
[WARNING]   - org.apache.tools.ant.loader.AntClassLoader2
[WARNING]   - org.apache.tools.ant.taskdefs.optional.vss.MSVSS$CurrentModUpdated
[WARNING]   - 1080 more...
[WARNING] adam-cli_2.10-0.19.0.jar, parquet-format-2.3.0-incubating.jar define 232 overlapping classes: 
[WARNING]   - parquet.org.apache.thrift.protocol.TCompactProtocol$Types
[WARNING]   - org.apache.parquet.format.ConvertedType
[WARNING]   - org.apache.parquet.format.DataPageHeaderV2
[WARNING]   - parquet.org.apache.thrift.TSerializer
[WARNING]   - org.apache.parquet.format.event.TypedConsumer$ListConsumer
[WARNING]   - parquet.org.apache.thrift.protocol.TJSONProtocol
[WARNING]   - parquet.org.apache.thrift.transport.TSeekableFile
[WARNING]   - parquet.org.apache.thrift.TServiceClientFactory
[WARNING]   - parquet.org.apache.thrift.transport.THttpClient
[WARNING]   - parquet.org.apache.thrift.protocol.TProtocolUtil
[WARNING]   - 222 more...
[WARNING] adam-cli_2.10-0.19.0.jar, parquet-avro-1.8.1.jar define 83 overlapping classes: 
[WARNING]   - org.apache.parquet.avro.AvroIndexedRecordConverter
[WARNING]   - org.apache.parquet.avro.AvroParquetReader$1
[WARNING]   - org.apache.parquet.avro.GenericDataSupplier
[WARNING]   - org.apache.parquet.avro.AvroConverters$FieldByteConverter
[WARNING]   - org.apache.parquet.avro.AvroConverters$AvroGroupConverter
[WARNING]   - org.apache.parquet.avro.AvroConverters$FieldEnumConverter
[WARNING]   - org.apache.parquet.avro.AvroConverters$FieldIntegerConverter
[WARNING]   - org.apache.parquet.avro.AvroWriteSupport
[WARNING]   - org.apache.parquet.avro.AvroIndexedRecordConverter$MapConverter$MapKeyValueConverter
[WARNING]   - org.apache.parquet.avro.AvroRecordMaterializer
[WARNING]   - 73 more...
[WARNING] jackson-core-asl-1.9.13.jar, adam-cli_2.10-0.19.0.jar define 121 overlapping classes: 
[WARNING]   - org.codehaus.jackson.util.DefaultPrettyPrinter
[WARNING]   - org.codehaus.jackson.impl.JsonWriteContext
[WARNING]   - org.codehaus.jackson.annotate.JsonSubTypes
[WARNING]   - org.codehaus.jackson.io.IOContext
[WARNING]   - org.codehaus.jackson.impl.JsonParserMinimalBase$1
[WARNING]   - org.codehaus.jackson.annotate.JsonTypeInfo$None
[WARNING]   - org.codehaus.jackson.sym.NameN
[WARNING]   - org.codehaus.jackson.util.JsonParserDelegate
[WARNING]   - org.codehaus.jackson.util.MinimalPrettyPrinter
[WARNING]   - org.codehaus.jackson.util.DefaultPrettyPrinter$Lf2SpacesIndenter
[WARNING]   - 111 more...
[WARNING] commons-jexl-2.1.1.jar, adam-cli_2.10-0.19.0.jar define 178 overlapping classes: 
[WARNING]   - org.apache.commons.jexl2.ExpressionImpl$1
[WARNING]   - org.apache.commons.jexl2.parser.ASTNotNode
[WARNING]   - org.apache.commons.jexl2.parser.Parser$JJCalls
[WARNING]   - org.apache.commons.jexl2.parser.ASTReference
[WARNING]   - org.apache.commons.jexl2.introspection.Sandbox
[WARNING]   - org.apache.commons.jexl2.parser.Token
[WARNING]   - org.apache.commons.jexl2.internal.introspection.MethodMap
[WARNING]   - org.apache.commons.jexl2.parser.ASTSizeFunction
[WARNING]   - org.apache.commons.jexl2.ExpressionImpl
[WARNING]   - org.apache.commons.jexl2.parser.ASTForeachStatement
[WARNING]   - 168 more...
[WARNING] adam-cli_2.10-0.19.0.jar, utils-io_2.10-0.2.4.jar define 23 overlapping classes: 
[WARNING]   - org.bdgenomics.utils.io.ByteAccess$class
[WARNING]   - org.bdgenomics.utils.io.LocalFileByteAccess$$anonfun$3
[WARNING]   - org.bdgenomics.utils.io.HTTPRangedByteAccess$
[WARNING]   - org.bdgenomics.utils.io.HTTPRangedByteAccess$$anonfun$3
[WARNING]   - org.bdgenomics.utils.io.HTTPRangedByteAccess
[WARNING]   - org.bdgenomics.utils.io.LocalFileByteAccess
[WARNING]   - org.bdgenomics.utils.io.ByteArrayByteAccess$$anonfun$1
[WARNING]   - org.bdgenomics.utils.io.LocalFileByteAccess$$anonfun$2
[WARNING]   - org.bdgenomics.utils.io.HTTPRangedByteAccess$$anonfun$readByteStream$1
[WARNING]   - org.bdgenomics.utils.io.ByteAccess$$anonfun$readFully$1
[WARNING]   - 13 more...
[WARNING] adam-cli_2.10-0.19.0.jar, commons-codec-1.9.jar define 30 overlapping classes: 
[WARNING]   - org.apache.commons.codec.net.BCodec
[WARNING]   - org.apache.commons.codec.binary.BinaryCodec
[WARNING]   - org.apache.commons.codec.language.DoubleMetaphone
[WARNING]   - org.apache.commons.codec.net.Utils
[WARNING]   - org.apache.commons.codec.Encoder
[WARNING]   - org.apache.commons.codec.binary.Base64
[WARNING]   - org.apache.commons.codec.binary.Hex
[WARNING]   - org.apache.commons.codec.Decoder
[WARNING]   - org.apache.commons.codec.language.Metaphone
[WARNING]   - org.apache.commons.codec.net.URLCodec
[WARNING]   - 20 more...
[WARNING] slf4j-api-1.7.10.jar, adam-cli_2.10-0.19.0.jar define 28 overlapping classes: 
[WARNING]   - org.slf4j.spi.MarkerFactoryBinder
[WARNING]   - org.slf4j.MDC$MDCCloseable
[WARNING]   - org.slf4j.helpers.SubstituteLogger
[WARNING]   - org.slf4j.helpers.BasicMarker
[WARNING]   - org.slf4j.LoggerFactory
[WARNING]   - org.slf4j.helpers.Util$1
[WARNING]   - org.slf4j.IMarkerFactory
[WARNING]   - org.slf4j.helpers.NOPMDCAdapter
[WARNING]   - org.slf4j.spi.LoggerFactoryBinder
[WARNING]   - org.slf4j.spi.MDCAdapter
[WARNING]   - 18 more...
[WARNING] adam-cli_2.10-0.19.0.jar, slf4j-log4j12-1.7.12.jar define 6 overlapping classes: 
[WARNING]   - org.slf4j.impl.StaticMarkerBinder
[WARNING]   - org.slf4j.impl.Log4jLoggerFactory
[WARNING]   - org.slf4j.impl.StaticLoggerBinder
[WARNING]   - org.slf4j.impl.Log4jMDCAdapter
[WARNING]   - org.slf4j.impl.Log4jLoggerAdapter
[WARNING]   - org.slf4j.impl.StaticMDCBinder
[WARNING] utils-cli_2.10-0.2.4.jar, adam-cli_2.10-0.19.0.jar define 23 overlapping classes: 
[WARNING]   - org.bdgenomics.utils.cli.BDGCommand
[WARNING]   - org.bdgenomics.utils.cli.LoadFileArgs$class
[WARNING]   - org.bdgenomics.utils.cli.ParquetSaveArgs
[WARNING]   - org.bdgenomics.utils.cli.BDGSparkCommand$$anonfun$printMetrics$1
[WARNING]   - org.bdgenomics.utils.cli.ParquetArgs$class
[WARNING]   - org.bdgenomics.utils.cli.BDGSparkCommand$$anonfun$run$1
[WARNING]   - org.bdgenomics.utils.cli.BDGSparkCommand$$anonfun$printMetrics$2
[WARNING]   - org.bdgenomics.utils.cli.BDGCommandCompanion
[WARNING]   - org.bdgenomics.utils.cli.BDGSparkCommand
[WARNING]   - org.bdgenomics.utils.cli.ParquetLoadSaveArgs
[WARNING]   - 13 more...
[WARNING] adam-cli_2.10-0.19.0.jar, adam-core_2.10-0.19.0.jar define 1217 overlapping classes: 
[WARNING]   - org.bdgenomics.adam.rdd.variation.VariantContextRDDFunctions$$anonfun$saveAsVcf$1
[WARNING]   - org.bdgenomics.adam.rdd.read.AlignmentRecordRDDFunctions$$anonfun$22
[WARNING]   - org.bdgenomics.adam.models.RecordGroup$$anonfun$toMetadata$5
[WARNING]   - org.bdgenomics.adam.util.Flattener$$anonfun$org$bdgenomics$adam$util$Flattener$$flatten$1
[WARNING]   - org.bdgenomics.adam.models.SequenceRecord$$anonfun$toSAMSequenceRecord$9
[WARNING]   - org.bdgenomics.adam.converters.FastaConverter$FastaDescriptionLine$$anonfun$parseDescriptionLine$1$$anonfun$apply$1
[WARNING]   - org.bdgenomics.adam.models.RecordGroup$$anonfun$apply$9
[WARNING]   - org.bdgenomics.adam.rdd.ADAMContext$
[WARNING]   - org.bdgenomics.adam.rdd.read.AlignmentRecordRDDFunctions$$anonfun$adamCharacterizeTagValues$1$$anonfun$apply$8
[WARNING]   - org.bdgenomics.adam.rich.RichAlignmentRecord$$anonfun$getReferenceBase$1$1
[WARNING]   - 1207 more...
[WARNING] adam-cli_2.10-0.19.0.jar, avro-1.7.7.jar define 320 overlapping classes: 
[WARNING]   - org.apache.avro.SchemaBuilderException
[WARNING]   - org.apache.avro.io.BinaryData
[WARNING]   - org.apache.avro.reflect.Stringable
[WARNING]   - org.apache.avro.Schema$5
[WARNING]   - org.apache.avro.file.NullCodec$Option
[WARNING]   - org.apache.avro.SchemaBuilder$EnumDefault
[WARNING]   - org.apache.avro.data.RecordBuilder
[WARNING]   - org.apache.avro.SchemaBuilder$BaseFieldTypeBuilder
[WARNING]   - org.apache.avro.util.WeakIdentityHashMap$IdentityWeakReference
[WARNING]   - org.apache.avro.io.BinaryDecoder
[WARNING]   - 310 more...
[WARNING] adam-cli_2.10-0.19.0.jar, utils-misc_2.10-0.2.4.jar define 7 overlapping classes: 
[WARNING]   - org.bdgenomics.utils.misc.MathUtils$$anonfun$aggregateArray$1
[WARNING]   - org.bdgenomics.utils.misc.HadoopUtil$
[WARNING]   - org.bdgenomics.utils.misc.MathUtils$$anonfun$scalarArrayMultiply$1
[WARNING]   - org.bdgenomics.utils.misc.HadoopUtil
[WARNING]   - org.bdgenomics.utils.misc.MathUtils$$anonfun$softmax$1
[WARNING]   - org.bdgenomics.utils.misc.MathUtils$
[WARNING]   - org.bdgenomics.utils.misc.MathUtils
[WARNING] fastutil-6.6.5.jar, adam-cli_2.10-0.19.0.jar define 10700 overlapping classes: 
[WARNING]   - it.unimi.dsi.fastutil.doubles.Double2CharAVLTreeMap$Submap
[WARNING]   - it.unimi.dsi.fastutil.floats.FloatIterators$ListIteratorWrapper
[WARNING]   - it.unimi.dsi.fastutil.objects.Object2ReferenceMap$Entry
[WARNING]   - it.unimi.dsi.fastutil.ints.Int2IntMaps$SynchronizedMap
[WARNING]   - it.unimi.dsi.fastutil.floats.Float2LongSortedMaps$EmptySortedMap
[WARNING]   - it.unimi.dsi.fastutil.objects.Reference2ObjectOpenHashMap
[WARNING]   - it.unimi.dsi.fastutil.bytes.AbstractByte2ShortMap$1
[WARNING]   - it.unimi.dsi.fastutil.objects.Object2IntSortedMaps$UnmodifiableSortedMap
[WARNING]   - it.unimi.dsi.fastutil.bytes.Byte2DoubleRBTreeMap$Submap
[WARNING]   - it.unimi.dsi.fastutil.floats.Float2ObjectOpenHashMap$KeyIterator
[WARNING]   - 10690 more...
[WARNING] adam-cli_2.10-0.19.0.jar, parquet-column-1.7.0.jar define 696 overlapping classes: 
[WARNING]   - org.apache.parquet.column.values.RequiresFallback
[WARNING]   - org.apache.parquet.it.unimi.dsi.fastutil.doubles.DoubleArrays
[WARNING]   - org.apache.parquet.it.unimi.dsi.fastutil.ints.IntIterators$ArrayIterator
[WARNING]   - org.apache.parquet.example.data.simple.FloatValue
[WARNING]   - org.apache.parquet.it.unimi.dsi.fastutil.longs.LongIterators$IntIteratorWrapper
[WARNING]   - org.apache.parquet.column.page.DataPageV1
[WARNING]   - org.apache.parquet.filter.ColumnPredicates$DoublePredicateFunction
[WARNING]   - org.apache.parquet.it.unimi.dsi.fastutil.floats.AbstractFloatSet
[WARNING]   - org.apache.parquet.it.unimi.dsi.fastutil.ints.IntArrays$1
[WARNING]   - org.apache.parquet.it.unimi.dsi.fastutil.floats.Float2IntLinkedOpenHashMap$1
[WARNING]   - 686 more...
[WARNING] commons-io-1.3.2.jar, adam-cli_2.10-0.19.0.jar define 59 overlapping classes: 
[WARNING]   - org.apache.commons.io.filefilter.ConditionalFileFilter
[WARNING]   - org.apache.commons.io.output.CountingOutputStream
[WARNING]   - org.apache.commons.io.output.NullWriter
[WARNING]   - org.apache.commons.io.filefilter.IOFileFilter
[WARNING]   - org.apache.commons.io.DirectoryWalker
[WARNING]   - org.apache.commons.io.FileDeleteStrategy
[WARNING]   - org.apache.commons.io.filefilter.PrefixFileFilter
[WARNING]   - org.apache.commons.io.FileSystemUtils
[WARNING]   - org.apache.commons.io.DirectoryWalker$CancelException
[WARNING]   - org.apache.commons.io.LineIterator
[WARNING]   - 49 more...
[WARNING] parquet-jackson-1.7.0.jar, adam-cli_2.10-0.19.0.jar define 623 overlapping classes: 
[WARNING]   - shaded.parquet.org.codehaus.jackson.map.deser.std.PrimitiveArrayDeserializers
[WARNING]   - shaded.parquet.org.codehaus.jackson.map.deser.std.StdDeserializer$DoubleDeserializer
[WARNING]   - shaded.parquet.org.codehaus.jackson.map.deser.impl.ValueInjector
[WARNING]   - shaded.parquet.org.codehaus.jackson.map.ser.PropertyBuilder
[WARNING]   - shaded.parquet.org.codehaus.jackson.sym.Name2
[WARNING]   - shaded.parquet.org.codehaus.jackson.map.deser.std.StdKeyDeserializer$ByteKD
[WARNING]   - shaded.parquet.org.codehaus.jackson.map.introspect.BasicClassIntrospector$1
[WARNING]   - shaded.parquet.org.codehaus.jackson.map.jsontype.impl.AsPropertyTypeSerializer
[WARNING]   - shaded.parquet.org.codehaus.jackson.map.BeanPropertyDefinition
[WARNING]   - shaded.parquet.org.codehaus.jackson.map.module.SimpleSerializers
[WARNING]   - 613 more...
[WARNING] adam-cli_2.10-0.19.0.jar, guava-16.0.1.jar define 1678 overlapping classes: 
[WARNING]   - com.google.common.collect.DenseImmutableTable$ImmutableArrayMap$1
[WARNING]   - com.google.common.collect.StandardTable$TableSet
[WARNING]   - com.google.common.collect.Iterators$12
[WARNING]   - com.google.common.collect.ImmutableMultiset$1
[WARNING]   - com.google.common.collect.Maps$TransformedEntriesSortedMap
[WARNING]   - com.google.common.collect.Multimaps$Keys$KeysEntrySet
[WARNING]   - com.google.common.collect.Maps$BiMapConverter
[WARNING]   - com.google.common.escape.Platform$1
[WARNING]   - com.google.common.collect.Sets$DescendingSet
[WARNING]   - com.google.common.collect.ImmutableMultiset$EntrySet$1
[WARNING]   - 1668 more...
[WARNING] adam-cli_2.10-0.19.0.jar, parquet-scala_2.10-1.8.1.jar define 19 overlapping classes: 
[WARNING]   - org.apache.parquet.filter2.dsl.Dsl$FloatColumn
[WARNING]   - org.apache.parquet.filter2.dsl.Dsl$SupportsLtGt
[WARNING]   - org.apache.parquet.filter2.dsl.Dsl$
[WARNING]   - org.apache.parquet.filter2.dsl.Dsl$BooleanColumn$
[WARNING]   - org.apache.parquet.filter2.dsl.Dsl
[WARNING]   - org.apache.parquet.filter2.dsl.Dsl$FloatColumn$
[WARNING]   - org.apache.parquet.filter2.dsl.Dsl$Column$class
[WARNING]   - org.apache.parquet.filter2.dsl.Dsl$BinaryColumn
[WARNING]   - org.apache.parquet.filter2.dsl.Dsl$LongColumn
[WARNING]   - org.apache.parquet.filter2.dsl.Dsl$SupportsEqNotEq
[WARNING]   - 9 more...
[WARNING] adam-cli_2.10-0.19.0.jar, log4j-1.2.17.jar define 314 overlapping classes: 
[WARNING]   - org.apache.log4j.net.DefaultEvaluator
[WARNING]   - org.apache.log4j.helpers.FileWatchdog
[WARNING]   - org.apache.log4j.xml.DOMConfigurator$5
[WARNING]   - org.apache.log4j.net.SyslogAppender
[WARNING]   - org.apache.log4j.chainsaw.ControlPanel$4
[WARNING]   - org.apache.log4j.chainsaw.LoggingReceiver
[WARNING]   - org.apache.log4j.NDC$DiagnosticContext
[WARNING]   - org.apache.log4j.lf5.viewer.configure.ConfigurationManager
[WARNING]   - org.apache.log4j.lf5.viewer.LogBrokerMonitor$14
[WARNING]   - org.apache.log4j.spi.ErrorHandler
[WARNING]   - 304 more...
[WARNING] htsjdk-1.139.jar, adam-cli_2.10-0.19.0.jar define 903 overlapping classes: 
[WARNING]   - htsjdk.samtools.Bin
[WARNING]   - htsjdk.samtools.util.ftp.FTPStream
[WARNING]   - htsjdk.tribble.example.ProfileIndexReading
[WARNING]   - htsjdk.samtools.cram.encoding.writer.Writer
[WARNING]   - htsjdk.samtools.util.CoordMath
[WARNING]   - htsjdk.samtools.cram.encoding.ByteArrayStopEncoding$ByteArrayStopCodec
[WARNING]   - htsjdk.samtools.CoordinateSortedPairInfoMap$1
[WARNING]   - htsjdk.samtools.util.Tuple
[WARNING]   - htsjdk.samtools.cram.encoding.writer.DataWriter
[WARNING]   - htsjdk.samtools.cram.encoding.huffman.codec.HuffmanIntHelper$1
[WARNING]   - 893 more...
[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://docs.codehaus.org/display/MAVENUSER/Shade+Plugin
[INFO] Replacing original artifact with shaded artifact.
[INFO] Replacing /home/jenkins/workspace/kumquat-prb/hadoop.version/2.2.0/label/centos/quinine-cli/target/quinine-cli_2.10-0.0.2-SNAPSHOT.jar with /home/jenkins/workspace/kumquat-prb/hadoop.version/2.2.0/label/centos/quinine-cli/target/quinine-cli_2.10-0.0.2-SNAPSHOT-shaded.jar
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary:
[INFO] 
[INFO] quinine ........................................... SUCCESS [3.388s]
[INFO] quinine: Core ..................................... SUCCESS [48.625s]
[INFO] quinine: CLI ...................................... SUCCESS [21.176s]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 1:13.349s
[INFO] Finished at: Mon Jul 25 23:53:31 PDT 2016
[INFO] Final Memory: 42M/2528M
[INFO] ------------------------------------------------------------------------
Recording test results
Finished: SUCCESS