AbortedConsole Output

Skipping 483 KB.. Full Log
sfish.jersey.servlet.init.internal.LocalizationMessages
[WARNING] utils-metrics-spark2_2.11-0.2.13.jar, mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar define 407 overlapping classes: 
[WARNING]   - org.apache.spark.rdd.InstrumentedPairRDDFunctions$$anonfun$reduceByKey$2$$anonfun$apply$33
[WARNING]   - org.bdgenomics.utils.instrumentation.SimpleMonitorValueExtractor
[WARNING]   - org.apache.spark.rdd.InstrumentedPairRDDFunctions$$anonfun$fullOuterJoin$2
[WARNING]   - org.bdgenomics.utils.instrumentation.MetricsListener$$anonfun$onTaskEnd$2
[WARNING]   - org.bdgenomics.utils.metrics.Histogram$$anonfun$countSubset$1
[WARNING]   - org.bdgenomics.utils.instrumentation.Alignment$
[WARNING]   - org.apache.spark.rdd.InstrumentedPairRDDFunctions$$anonfun$saveAsHadoopFile$3
[WARNING]   - org.bdgenomics.utils.instrumentation.Metrics$TreeNode$$anonfun$6
[WARNING]   - org.apache.spark.rdd.InstrumentedRDD$$anonfun$reduce$1$$anonfun$apply$35
[WARNING]   - org.apache.spark.rdd.InstrumentedRDD$$anonfun$aggregate$1$$anonfun$apply$39$$anonfun$apply$40
[WARNING]   - 397 more...
[WARNING] avro-mapred-1.7.7-hadoop2.jar, mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar define 126 overlapping classes: 
[WARNING]   - org.apache.avro.mapreduce.AvroMultipleOutputs
[WARNING]   - org.apache.avro.mapreduce.AvroKeyValueOutputFormat
[WARNING]   - org.apache.avro.mapred.SequenceFileReader$8
[WARNING]   - org.apache.avro.hadoop.file.HadoopCodecFactory
[WARNING]   - org.apache.avro.mapred.Pair
[WARNING]   - org.apache.avro.mapred.AvroMultipleOutputs
[WARNING]   - org.apache.avro.mapred.FsInput
[WARNING]   - org.apache.avro.mapred.tether.InputProtocol$Callback
[WARNING]   - org.apache.avro.mapred.AvroOutputFormat$1
[WARNING]   - org.apache.avro.hadoop.file.SortedKeyValueFile$Reader$Options
[WARNING]   - 116 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar, metrics-core-3.1.5.jar define 115 overlapping classes: 
[WARNING]   - com.codahale.metrics.JmxReporter$JmxGaugeMBean
[WARNING]   - com.codahale.metrics.ThreadLocalRandomProxy$InternalProvider
[WARNING]   - com.codahale.metrics.JmxReporter
[WARNING]   - com.codahale.metrics.EWMA
[WARNING]   - com.codahale.metrics.Gauge
[WARNING]   - com.codahale.metrics.MetricRegistry$MetricBuilder$1
[WARNING]   - com.codahale.metrics.MetricFilter$1
[WARNING]   - com.codahale.metrics.JmxReporter$JmxCounterMBean
[WARNING]   - com.codahale.metrics.InstrumentedExecutorService$InstrumentedRunnable
[WARNING]   - com.codahale.metrics.RatioGauge$Ratio
[WARNING]   - 105 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, htsjdk-2.16.1.jar, mango-cli-0.0.3-SNAPSHOT.jar define 983 overlapping classes: 
[WARNING]   - htsjdk.samtools.cram.ref.ReferenceSource
[WARNING]   - htsjdk.samtools.HighAccuracyDownsamplingIterator
[WARNING]   - htsjdk.samtools.util.zip.DeflaterFactory
[WARNING]   - htsjdk.samtools.filter.DuplicateReadFilter
[WARNING]   - htsjdk.variant.vcf.VCFEncoder
[WARNING]   - htsjdk.samtools.util.CloserUtil
[WARNING]   - htsjdk.tribble.TribbleException$FeatureFileDoesntExist
[WARNING]   - htsjdk.tribble.index.tabix.TabixIndex
[WARNING]   - htsjdk.samtools.AbstractBAMFileIndex
[WARNING]   - htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder$1
[WARNING]   - 973 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar, metrics-jvm-3.1.5.jar define 38 overlapping classes: 
[WARNING]   - com.codahale.metrics.jvm.MemoryUsageGaugeSet$15
[WARNING]   - com.codahale.metrics.jvm.MemoryUsageGaugeSet$3
[WARNING]   - com.codahale.metrics.jvm.CachedThreadStatesGaugeSet
[WARNING]   - com.codahale.metrics.jvm.MemoryUsageGaugeSet
[WARNING]   - com.codahale.metrics.jvm.MemoryUsageGaugeSet$8
[WARNING]   - com.codahale.metrics.jvm.ClassLoadingGaugeSet$1
[WARNING]   - com.codahale.metrics.jvm.MemoryUsageGaugeSet$5
[WARNING]   - com.codahale.metrics.jvm.BufferPoolMetricSet
[WARNING]   - com.codahale.metrics.jvm.ThreadStatesGaugeSet
[WARNING]   - com.codahale.metrics.jvm.MemoryUsageGaugeSet$10
[WARNING]   - 28 more...
[WARNING] commons-logging-1.1.1.jar, mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar, jcl-over-slf4j-1.7.16.jar define 6 overlapping classes: 
[WARNING]   - org.apache.commons.logging.impl.SimpleLog$1
[WARNING]   - org.apache.commons.logging.Log
[WARNING]   - org.apache.commons.logging.impl.SimpleLog
[WARNING]   - org.apache.commons.logging.LogConfigurationException
[WARNING]   - org.apache.commons.logging.impl.NoOpLog
[WARNING]   - org.apache.commons.logging.LogFactory
[WARNING] xz-1.5.jar, mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar define 105 overlapping classes: 
[WARNING]   - org.tukaani.xz.lzma.LZMADecoder$LengthDecoder
[WARNING]   - org.tukaani.xz.index.IndexDecoder
[WARNING]   - org.tukaani.xz.lzma.LZMADecoder
[WARNING]   - org.tukaani.xz.lzma.LZMAEncoderFast
[WARNING]   - org.tukaani.xz.lzma.LZMAEncoder$LengthEncoder
[WARNING]   - org.tukaani.xz.BlockOutputStream
[WARNING]   - org.tukaani.xz.simple.SimpleFilter
[WARNING]   - org.tukaani.xz.rangecoder.RangeCoder
[WARNING]   - org.tukaani.xz.XZOutputStream
[WARNING]   - org.tukaani.xz.UncompressedLZMA2OutputStream
[WARNING]   - 95 more...
[WARNING] scalate-util_2.11-1.8.0.jar, mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar, scalate-core_2.11-1.8.0.jar define 222 overlapping classes: 
[WARNING]   - org.fusesource.scalate.util.StringResource
[WARNING]   - org.fusesource.scalate.util.SourceMap$SmapParser$$anonfun$12$$anonfun$apply$3$$anonfun$apply$19
[WARNING]   - org.fusesource.scalate.util.ClassPathBuilder$$anonfun$findManifestEntries$1$$anonfun$apply$3
[WARNING]   - org.fusesource.scalate.util.SourceMap$SmapParser$$anonfun$18
[WARNING]   - org.fusesource.scalate.util.SourceMap$SmapParser$$anonfun$12$$anonfun$apply$3$$anonfun$apply$5$$anonfun$apply$6$$anonfun$apply$9$$anonfun$apply$10
[WARNING]   - org.fusesource.scalate.util.ResourceLoader
[WARNING]   - org.fusesource.scalate.util.SourceMapStratum$$anonfun$7
[WARNING]   - org.fusesource.scalate.util.SourceMap$SmapParser$$anonfun$20$$anonfun$apply$45
[WARNING]   - org.fusesource.scalate.util.ProductReflector$
[WARNING]   - org.fusesource.scalate.util.ClassFinder$$anonfun$discoverCommandClasses$1
[WARNING]   - 212 more...
[WARNING] jersey-client-2.22.2.jar, mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar define 111 overlapping classes: 
[WARNING]   - org.glassfish.jersey.client.ChunkParser
[WARNING]   - org.glassfish.jersey.client.HttpUrlConnectorProvider
[WARNING]   - org.glassfish.jersey.client.JerseyInvocation$EntityPresence
[WARNING]   - org.glassfish.jersey.client.ResponseCallback
[WARNING]   - org.glassfish.jersey.client.authentication.RequestAuthenticationException
[WARNING]   - org.glassfish.jersey.client.JerseyInvocation$5
[WARNING]   - org.glassfish.jersey.client.ClientConfig$State$4
[WARNING]   - org.glassfish.jersey.client.ClientResponse$1
[WARNING]   - org.glassfish.jersey.client.InboundJaxrsResponse$2
[WARNING]   - org.glassfish.jersey.client.internal.HttpUrlConnector$5
[WARNING]   - 101 more...
[WARNING] commons-jexl-2.1.1.jar, mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar define 178 overlapping classes: 
[WARNING]   - org.apache.commons.jexl2.internal.AbstractExecutor$Get
[WARNING]   - org.apache.commons.jexl2.introspection.JexlPropertyGet
[WARNING]   - org.apache.commons.jexl2.parser.StringParser
[WARNING]   - org.apache.commons.jexl2.parser.ASTBitwiseOrNode
[WARNING]   - org.apache.commons.jexl2.internal.introspection.MethodKey$1
[WARNING]   - org.apache.commons.jexl2.Main
[WARNING]   - org.apache.commons.jexl2.parser.ASTForeachStatement
[WARNING]   - org.apache.commons.jexl2.introspection.Sandbox
[WARNING]   - org.apache.commons.jexl2.internal.introspection.ClassMap
[WARNING]   - org.apache.commons.jexl2.parser.ASTFunctionNode
[WARNING]   - 168 more...
[WARNING] compress-lzf-1.0.3.jar, mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar define 42 overlapping classes: 
[WARNING]   - com.ning.compress.lzf.LZFUncompressor
[WARNING]   - com.ning.compress.BufferRecycler
[WARNING]   - com.ning.compress.lzf.LZFEncoder
[WARNING]   - com.ning.compress.lzf.impl.UnsafeChunkEncoderBE
[WARNING]   - com.ning.compress.lzf.impl.UnsafeChunkEncoderLE
[WARNING]   - com.ning.compress.gzip.OptimizedGZIPInputStream
[WARNING]   - com.ning.compress.lzf.util.LZFFileOutputStream$Wrapper
[WARNING]   - com.ning.compress.lzf.util.LZFFileInputStream$1
[WARNING]   - com.ning.compress.lzf.ChunkEncoder
[WARNING]   - com.ning.compress.lzf.impl.UnsafeChunkDecoder
[WARNING]   - 32 more...
[WARNING] java-xmlbuilder-1.1.jar, mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar define 5 overlapping classes: 
[WARNING]   - com.jamesmurty.utils.NamespaceContextImpl
[WARNING]   - com.jamesmurty.utils.BaseXMLBuilder
[WARNING]   - com.jamesmurty.utils.XMLBuilder
[WARNING]   - com.jamesmurty.utils.XMLBuilder2
[WARNING]   - com.jamesmurty.utils.XMLBuilderRuntimeException
[WARNING] jackson-module-scala_2.11-2.6.7.1.jar, mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar define 403 overlapping classes: 
[WARNING]   - com.fasterxml.jackson.module.scala.deser.UnsortedMapDeserializer$$anonfun$2
[WARNING]   - com.fasterxml.jackson.module.scala.deser.UnsortedSetDeserializerModule
[WARNING]   - com.fasterxml.jackson.module.scala.deser.UnsortedMapDeserializerModule$class
[WARNING]   - com.fasterxml.jackson.module.scala.JacksonModule$$anonfun$1
[WARNING]   - com.fasterxml.jackson.module.scala.deser.SortedSetDeserializer$$anonfun$4
[WARNING]   - com.fasterxml.jackson.module.scala.util.Options$class
[WARNING]   - com.fasterxml.jackson.module.scala.util.EnumResolver$
[WARNING]   - com.fasterxml.jackson.module.scala.ser.OptionSerializer$$anonfun$serialize$1
[WARNING]   - com.fasterxml.jackson.module.scala.ser.OptionSerializerModule
[WARNING]   - com.fasterxml.jackson.module.scala.modifiers.CollectionLikeTypeModifier$$anonfun$modifyType$3
[WARNING]   - 393 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, jets3t-0.9.4.jar, mango-cli-0.0.3-SNAPSHOT.jar define 616 overlapping classes: 
[WARNING]   - org.jets3t.service.acl.GroupGrantee
[WARNING]   - org.jets3t.service.multithread.CreateObjectsEvent
[WARNING]   - org.jets3t.service.model.S3BucketLoggingStatus
[WARNING]   - contribs.com.centerkey.utils.BareBonesBrowserLaunch
[WARNING]   - org.jets3t.service.impl.rest.CloudFrontXmlResponsesSaxParser$CacheBehaviorHandler
[WARNING]   - org.jets3t.apps.uploader.XmlGenerator$ObjectAndSignatureRequestDetails
[WARNING]   - org.jets3t.service.MultipartUploadChunk
[WARNING]   - org.jets3t.apps.cockpit.Cockpit$27
[WARNING]   - org.jets3t.service.model.S3DeleteMarker
[WARNING]   - org.jets3t.gui.TableSorter$Row
[WARNING]   - 606 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar, jetty-server-9.4.15.v20190215.jar define 302 overlapping classes: 
[WARNING]   - org.eclipse.jetty.server.handler.ThreadLimitHandler$RFC7239
[WARNING]   - org.eclipse.jetty.server.handler.ManagedAttributeListener
[WARNING]   - org.eclipse.jetty.server.ServletRequestHttpWrapper
[WARNING]   - org.eclipse.jetty.server.DebugListener$1
[WARNING]   - org.eclipse.jetty.server.ShutdownMonitor$1
[WARNING]   - org.eclipse.jetty.server.HttpInput$1
[WARNING]   - org.eclipse.jetty.server.UserIdentity$Scope
[WARNING]   - org.eclipse.jetty.server.AcceptRateLimit$1
[WARNING]   - org.eclipse.jetty.server.session.AbstractSessionDataStoreFactory
[WARNING]   - org.eclipse.jetty.server.AsyncContextState$1
[WARNING]   - 292 more...
[WARNING] servo-core-0.12.12.jar, mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar define 162 overlapping classes: 
[WARNING]   - com.netflix.servo.util.Objects
[WARNING]   - com.netflix.servo.util.Clock
[WARNING]   - com.netflix.servo.monitor.MaxGauge
[WARNING]   - com.netflix.servo.publish.LocalJmxConnector
[WARNING]   - com.netflix.servo.publish.MonitorRegistryMetricPoller$MonitorValueCallable
[WARNING]   - com.netflix.servo.util.ExpiringCache$Entry
[WARNING]   - com.netflix.servo.util.ThreadCpuStats$CpuUsage
[WARNING]   - com.netflix.servo.tag.SmallTagMap$Builder
[WARNING]   - com.netflix.servo.stats.StatsConfig
[WARNING]   - com.netflix.servo.monitor.Monitors$CounterFactory
[WARNING]   - 152 more...
[WARNING] commons-net-2.2.jar, mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar define 137 overlapping classes: 
[WARNING]   - org.apache.commons.net.telnet.SimpleOptionHandler
[WARNING]   - org.apache.commons.net.ftp.parser.FTPFileEntryParserFactory
[WARNING]   - org.apache.commons.net.DefaultDatagramSocketFactory
[WARNING]   - org.apache.commons.net.ftp.parser.ConfigurableFTPFileEntryParserImpl
[WARNING]   - org.apache.commons.net.ntp.NTPUDPClient
[WARNING]   - org.apache.commons.net.util.SubnetUtils$1
[WARNING]   - org.apache.commons.net.tftp.TFTP
[WARNING]   - org.apache.commons.net.ftp.FTPClient
[WARNING]   - org.apache.commons.net.echo.EchoTCPClient
[WARNING]   - org.apache.commons.net.telnet.Telnet
[WARNING]   - 127 more...
[WARNING] commons-codec-1.12.jar, mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar define 92 overlapping classes: 
[WARNING]   - org.apache.commons.codec.language.Nysiis
[WARNING]   - org.apache.commons.codec.language.bm.Rule$1
[WARNING]   - org.apache.commons.codec.language.bm.Rule$RPattern
[WARNING]   - org.apache.commons.codec.language.ColognePhonetic$CologneInputBuffer
[WARNING]   - org.apache.commons.codec.digest.HmacUtils
[WARNING]   - org.apache.commons.codec.language.bm.BeiderMorseEncoder
[WARNING]   - org.apache.commons.codec.digest.UnixCrypt
[WARNING]   - org.apache.commons.codec.language.Soundex
[WARNING]   - org.apache.commons.codec.binary.BinaryCodec
[WARNING]   - org.apache.commons.codec.language.bm.Languages$1
[WARNING]   - 82 more...
[WARNING] jetty-io-9.4.15.v20190215.jar, mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar define 96 overlapping classes: 
[WARNING]   - org.eclipse.jetty.io.ssl.ALPNProcessor
[WARNING]   - org.eclipse.jetty.io.CyclicTimeout$Wakeup
[WARNING]   - org.eclipse.jetty.io.AbstractEndPoint$2
[WARNING]   - org.eclipse.jetty.io.CyclicTimeout$Timeout
[WARNING]   - org.eclipse.jetty.io.ChannelEndPoint$1
[WARNING]   - org.eclipse.jetty.io.WriteFlusher$FailedState
[WARNING]   - org.eclipse.jetty.io.CyclicTimeout$1
[WARNING]   - org.eclipse.jetty.io.ManagedSelector$Acceptor
[WARNING]   - org.eclipse.jetty.io.ssl.SslClientConnectionFactory$1
[WARNING]   - org.eclipse.jetty.io.ByteBufferPool$Lease
[WARNING]   - 86 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, parquet-scala_2.10-1.8.3.jar, mango-cli-0.0.3-SNAPSHOT.jar define 19 overlapping classes: 
[WARNING]   - org.apache.parquet.filter2.dsl.Dsl$SupportsEqNotEq
[WARNING]   - org.apache.parquet.filter2.dsl.Dsl$FloatColumn$
[WARNING]   - org.apache.parquet.filter2.dsl.Dsl$DoubleColumn
[WARNING]   - org.apache.parquet.filter2.dsl.Dsl$Column$class
[WARNING]   - org.apache.parquet.filter2.dsl.Dsl
[WARNING]   - org.apache.parquet.filter2.dsl.Dsl$FloatColumn
[WARNING]   - org.apache.parquet.filter2.dsl.Dsl$LongColumn
[WARNING]   - org.apache.parquet.filter2.dsl.Dsl$BinaryColumn
[WARNING]   - org.apache.parquet.filter2.dsl.Dsl$IntColumn$
[WARNING]   - org.apache.parquet.filter2.dsl.Dsl$DoubleColumn$
[WARNING]   - 9 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar, jetty-webapp-9.4.15.v20190215.jar define 51 overlapping classes: 
[WARNING]   - org.eclipse.jetty.webapp.FragmentDescriptor
[WARNING]   - org.eclipse.jetty.webapp.CachingWebAppClassLoader
[WARNING]   - org.eclipse.jetty.webapp.ClasspathPattern$ClassEntry
[WARNING]   - org.eclipse.jetty.webapp.WebAppContext
[WARNING]   - org.eclipse.jetty.webapp.ClasspathPattern$ByClass
[WARNING]   - org.eclipse.jetty.webapp.CloneConfiguration
[WARNING]   - org.eclipse.jetty.webapp.RelativeOrdering$1
[WARNING]   - org.eclipse.jetty.webapp.Configuration$ClassList
[WARNING]   - org.eclipse.jetty.webapp.ClasspathPattern$ByModule
[WARNING]   - org.eclipse.jetty.webapp.StandardDescriptorProcessor$1
[WARNING]   - 41 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar, commons-io-2.6.jar define 127 overlapping classes: 
[WARNING]   - org.apache.commons.io.FileCleaningTracker
[WARNING]   - org.apache.commons.io.comparator.SizeFileComparator
[WARNING]   - org.apache.commons.io.input.CloseShieldInputStream
[WARNING]   - org.apache.commons.io.ByteOrderParser
[WARNING]   - org.apache.commons.io.filefilter.EmptyFileFilter
[WARNING]   - org.apache.commons.io.monitor.FileEntry
[WARNING]   - org.apache.commons.io.output.ThresholdingOutputStream
[WARNING]   - org.apache.commons.io.input.TailerListener
[WARNING]   - org.apache.commons.io.IOExceptionWithCause
[WARNING]   - org.apache.commons.io.filefilter.NotFileFilter
[WARNING]   - 117 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, guice-4.2.0.jar, mango-cli-0.0.3-SNAPSHOT.jar define 573 overlapping classes: 
[WARNING]   - com.google.inject.Scope
[WARNING]   - com.google.inject.Binding
[WARNING]   - com.google.inject.internal.cglib.core.$EmitUtils$3
[WARNING]   - com.google.inject.spi.TypeConverter
[WARNING]   - com.google.inject.internal.ConstructionProxy
[WARNING]   - com.google.inject.spi.InjectionPoint
[WARNING]   - com.google.inject.spi.StaticInjectionRequest
[WARNING]   - com.google.inject.internal.cglib.proxy.$FixedValueGenerator
[WARNING]   - com.google.inject.internal.cglib.proxy.$DispatcherGenerator
[WARNING]   - com.google.inject.spi.Elements$ElementsAsModule
[WARNING]   - 563 more...
[WARNING] ivy-2.4.0.jar, mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar define 744 overlapping classes: 
[WARNING]   - org.apache.ivy.ant.IvyDeliver
[WARNING]   - org.apache.ivy.plugins.resolver.util.ApacheHttpURLLister
[WARNING]   - org.apache.ivy.ant.BuildOBRTask
[WARNING]   - org.apache.ivy.osgi.p2.P2MetadataParser$UnitsHandler$1
[WARNING]   - org.apache.ivy.core.cache.ResolutionCacheManager
[WARNING]   - org.apache.ivy.osgi.repo.EditableRepoDescriptor
[WARNING]   - org.apache.ivy.plugins.parser.AbstractModuleDescriptorParser$AbstractParser
[WARNING]   - org.apache.ivy.plugins.latest.LatestLexicographicStrategy$1
[WARNING]   - org.apache.ivy.osgi.repo.FSManifestIterable$3
[WARNING]   - org.apache.ivy.util.url.HttpClientHandler
[WARNING]   - 734 more...
[WARNING] utils-cli-spark2_2.11-0.2.13.jar, mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar define 23 overlapping classes: 
[WARNING]   - org.bdgenomics.utils.cli.Args4j
[WARNING]   - org.bdgenomics.utils.cli.BDGSparkCommand$$anonfun$printMetrics$4
[WARNING]   - org.bdgenomics.utils.cli.ParquetArgs
[WARNING]   - org.bdgenomics.utils.cli.BDGSparkCommand$$anonfun$printMetrics$3
[WARNING]   - org.bdgenomics.utils.cli.BDGSparkCommand$class
[WARNING]   - org.bdgenomics.utils.cli.BDGSparkCommand$$anonfun$printMetrics$2
[WARNING]   - org.bdgenomics.utils.cli.BDGSparkCommand$$anonfun$run$1
[WARNING]   - org.bdgenomics.utils.cli.ParquetArgs$class
[WARNING]   - org.bdgenomics.utils.cli.BDGSparkCommand$$anonfun$printMetrics$1
[WARNING]   - org.bdgenomics.utils.cli.SaveArgs
[WARNING]   - 13 more...
[WARNING] activation-1.1.1.jar, mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar define 38 overlapping classes: 
[WARNING]   - javax.activation.DataContentHandlerFactory
[WARNING]   - javax.activation.ObjectDataContentHandler
[WARNING]   - javax.activation.DataContentHandler
[WARNING]   - com.sun.activation.registries.MimeTypeEntry
[WARNING]   - com.sun.activation.viewers.TextViewer
[WARNING]   - com.sun.activation.registries.LogSupport
[WARNING]   - javax.activation.CommandObject
[WARNING]   - javax.activation.SecuritySupport$2
[WARNING]   - com.sun.activation.viewers.TextEditor
[WARNING]   - com.sun.activation.viewers.ImageViewerCanvas
[WARNING]   - 28 more...
[WARNING] error_prone_annotations-2.2.0.jar, mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar define 22 overlapping classes: 
[WARNING]   - com.google.errorprone.annotations.NoAllocation
[WARNING]   - com.google.errorprone.annotations.Var
[WARNING]   - com.google.errorprone.annotations.IncompatibleModifiers
[WARNING]   - com.google.errorprone.annotations.CompatibleWith
[WARNING]   - com.google.errorprone.annotations.concurrent.LockMethod
[WARNING]   - com.google.errorprone.annotations.FormatString
[WARNING]   - com.google.errorprone.annotations.DoNotCall
[WARNING]   - com.google.errorprone.annotations.Immutable
[WARNING]   - com.google.errorprone.annotations.RestrictedApi
[WARNING]   - com.google.errorprone.annotations.CompileTimeConstant
[WARNING]   - 12 more...
[WARNING] bcprov-jdk15on-1.52.jar, mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar define 2430 overlapping classes: 
[WARNING]   - org.bouncycastle.crypto.modes.gcm.Tables8kGCMMultiplier
[WARNING]   - org.bouncycastle.crypto.tls.HeartbeatMode
[WARNING]   - org.bouncycastle.pqc.math.linearalgebra.GF2nPolynomialElement
[WARNING]   - org.bouncycastle.jcajce.provider.asymmetric.ecgost.KeyFactorySpi
[WARNING]   - org.bouncycastle.jcajce.provider.symmetric.AES$AlgParamsCCM
[WARNING]   - org.bouncycastle.asn1.tsp.TimeStampResp
[WARNING]   - org.bouncycastle.jcajce.provider.digest.SHA384$Mappings
[WARNING]   - org.bouncycastle.jcajce.provider.asymmetric.elgamal.AlgorithmParameterGeneratorSpi
[WARNING]   - org.bouncycastle.asn1.x509.CRLNumber
[WARNING]   - org.bouncycastle.jcajce.provider.digest.SM3
[WARNING]   - 2420 more...
[WARNING] spark-network-common_2.11-2.3.3.jar, mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar define 1697 overlapping classes: 
[WARNING]   - org.spark_project.guava.annotations.Beta
[WARNING]   - org.spark_project.guava.util.concurrent.UncaughtExceptionHandlers$Exiter
[WARNING]   - org.spark_project.guava.eventbus.Subscribe
[WARNING]   - org.spark_project.guava.collect.TreeRangeMap
[WARNING]   - org.spark_project.guava.collect.ImmutableList$SubList
[WARNING]   - org.spark_project.guava.cache.RemovalCause$1
[WARNING]   - org.spark_project.guava.collect.ForwardingMultimap
[WARNING]   - org.spark_project.guava.io.LimitInputStream
[WARNING]   - org.spark_project.guava.math.BigIntegerMath
[WARNING]   - org.spark_project.guava.collect.Tables
[WARNING]   - 1687 more...
[WARNING] jsr305-1.3.9.jar, mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar define 35 overlapping classes: 
[WARNING]   - javax.annotation.RegEx
[WARNING]   - javax.annotation.concurrent.Immutable
[WARNING]   - javax.annotation.meta.TypeQualifierDefault
[WARNING]   - javax.annotation.meta.TypeQualifier
[WARNING]   - javax.annotation.Syntax
[WARNING]   - javax.annotation.CheckReturnValue
[WARNING]   - javax.annotation.CheckForNull
[WARNING]   - javax.annotation.Nonnull
[WARNING]   - javax.annotation.meta.TypeQualifierNickname
[WARNING]   - javax.annotation.MatchesPattern
[WARNING]   - 25 more...
[WARNING] jersey-server-2.22.2.jar, mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar define 665 overlapping classes: 
[WARNING]   - org.glassfish.jersey.server.internal.inject.ParamConverters$TypeFromString
[WARNING]   - org.glassfish.jersey.server.internal.inject.QueryParamValueFactoryProvider
[WARNING]   - org.glassfish.jersey.server.internal.inject.ParamInjectionResolver
[WARNING]   - org.glassfish.jersey.server.internal.InternalServerProperties
[WARNING]   - org.glassfish.jersey.server.internal.inject.ParameterInjectionBinder$5
[WARNING]   - jersey.repackaged.org.objectweb.asm.FieldWriter
[WARNING]   - org.glassfish.jersey.server.internal.RuntimeDelegateImpl
[WARNING]   - org.glassfish.jersey.server.internal.inject.ParamConverterFactory
[WARNING]   - org.glassfish.jersey.server.internal.monitoring.RequestEventImpl$Builder
[WARNING]   - org.glassfish.jersey.server.ContainerRequest
[WARNING]   - 655 more...
[WARNING] lift-json_2.11-3.0.1.jar, mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar define 368 overlapping classes: 
[WARNING]   - net.liftweb.json.TypeHints$CompositeTypeHints$$anonfun$deserialize$2
[WARNING]   - net.liftweb.json.JsonAST$RenderSettings$$anonfun$2
[WARNING]   - net.liftweb.json.TypeInfo$
[WARNING]   - net.liftweb.json.JsonAST$JString$
[WARNING]   - net.liftweb.json.JsonAST$RenderSettings$
[WARNING]   - net.liftweb.json.JsonParser$OpenArr$
[WARNING]   - net.liftweb.json.Meta$
[WARNING]   - net.liftweb.json.TypeHints$CompositeTypeHints$$anonfun$net$liftweb$json$TypeHints$CompositeTypeHints$$hasClass$1$3
[WARNING]   - net.liftweb.json.JsonAST$JDouble$
[WARNING]   - net.liftweb.json.Extraction$$anonfun$net$liftweb$json$Extraction$$submap$1$1
[WARNING]   - 358 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar, jcl-over-slf4j-1.7.16.jar define 3 overlapping classes: 
[WARNING]   - org.apache.commons.logging.impl.SLF4JLogFactory
[WARNING]   - org.apache.commons.logging.impl.SLF4JLocationAwareLog
[WARNING]   - org.apache.commons.logging.impl.SLF4JLog
[WARNING] hk2-api-2.4.0-b34.jar, mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar define 165 overlapping classes: 
[WARNING]   - org.glassfish.hk2.api.ActiveDescriptor
[WARNING]   - org.glassfish.hk2.api.Proxiable
[WARNING]   - org.glassfish.hk2.utilities.InjecteeImpl
[WARNING]   - org.glassfish.hk2.api.ProxyCtl
[WARNING]   - org.glassfish.hk2.api.DynamicConfiguration
[WARNING]   - org.glassfish.hk2.internal.ImmediateHelper$1
[WARNING]   - org.glassfish.hk2.api.InjectionResolver
[WARNING]   - org.glassfish.hk2.utilities.ServiceLocatorUtilities$3
[WARNING]   - org.glassfish.hk2.api.Validator
[WARNING]   - org.glassfish.hk2.api.PopulatorPostProcessor
[WARNING]   - 155 more...
[WARNING] snappy-java-1.0.5.jar, mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar define 12 overlapping classes: 
[WARNING]   - org.xerial.snappy.SnappyLoader
[WARNING]   - org.xerial.snappy.SnappyOutputStream
[WARNING]   - org.xerial.snappy.SnappyErrorCode
[WARNING]   - org.xerial.snappy.SnappyBundleActivator
[WARNING]   - org.xerial.snappy.SnappyError
[WARNING]   - org.xerial.snappy.SnappyNativeAPI
[WARNING]   - org.xerial.snappy.SnappyException
[WARNING]   - org.xerial.snappy.Snappy
[WARNING]   - org.xerial.snappy.SnappyNative
[WARNING]   - org.xerial.snappy.OSInfo
[WARNING]   - 2 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, jul-to-slf4j-1.7.16.jar, mango-cli-0.0.3-SNAPSHOT.jar define 1 overlapping classes: 
[WARNING]   - org.slf4j.bridge.SLF4JBridgeHandler
[WARNING] checker-qual-2.5.2.jar, mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar define 302 overlapping classes: 
[WARNING]   - org.checkerframework.checker.formatter.FormatUtil
[WARNING]   - org.checkerframework.checker.units.qual.MixedUnits
[WARNING]   - org.checkerframework.checker.units.qual.PolyUnit
[WARNING]   - org.checkerframework.checker.regex.qual.PolyRegex
[WARNING]   - org.checkerframework.checker.units.qual.C
[WARNING]   - org.checkerframework.checker.formatter.FormatUtil$IllegalFormatConversionCategoryException
[WARNING]   - org.checkerframework.framework.qual.Unqualified
[WARNING]   - org.checkerframework.common.reflection.qual.UnknownMethod
[WARNING]   - org.checkerframework.framework.qual.EnsuresQualifierIf
[WARNING]   - org.checkerframework.checker.signedness.SignednessUtil
[WARNING]   - 292 more...
[WARNING] jetty-xml-9.4.15.v20190215.jar, mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar define 14 overlapping classes: 
[WARNING]   - org.eclipse.jetty.xml.ConfigurationProcessorFactory
[WARNING]   - org.eclipse.jetty.xml.XmlParser$Node
[WARNING]   - org.eclipse.jetty.xml.XmlConfiguration$JettyXmlConfiguration$AttrOrElementNode
[WARNING]   - org.eclipse.jetty.xml.XmlConfiguration$JettyXmlConfiguration
[WARNING]   - org.eclipse.jetty.xml.ConfigurationProcessor
[WARNING]   - org.eclipse.jetty.xml.XmlParser$Handler
[WARNING]   - org.eclipse.jetty.xml.XmlConfiguration
[WARNING]   - org.eclipse.jetty.xml.XmlConfiguration$1
[WARNING]   - org.eclipse.jetty.xml.XmlConfiguration$JettyXmlConfiguration$1
[WARNING]   - org.eclipse.jetty.xml.XmlParser
[WARNING]   - 4 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar, aopalliance-repackaged-2.4.0-b34.jar define 17 overlapping classes: 
[WARNING]   - org.aopalliance.reflect.ClassLocator
[WARNING]   - org.aopalliance.reflect.Metadata
[WARNING]   - org.aopalliance.instrument.Instrumentation
[WARNING]   - org.aopalliance.reflect.Field
[WARNING]   - org.aopalliance.intercept.FieldInterceptor
[WARNING]   - org.aopalliance.reflect.Method
[WARNING]   - org.aopalliance.reflect.CodeLocator
[WARNING]   - org.aopalliance.intercept.FieldAccess
[WARNING]   - org.aopalliance.reflect.ProgramUnit
[WARNING]   - org.aopalliance.instrument.UndoNotSupportedException
[WARNING]   - 7 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar, grizzled-slf4j_2.11-1.0.2.jar define 4 overlapping classes: 
[WARNING]   - grizzled.slf4j.Logger$
[WARNING]   - grizzled.slf4j.Logging
[WARNING]   - grizzled.slf4j.Logging$class
[WARNING]   - grizzled.slf4j.Logger
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar, fastutil-6.6.5.jar define 10700 overlapping classes: 
[WARNING]   - it.unimi.dsi.fastutil.doubles.Double2IntRBTreeMap$Submap$KeySet
[WARNING]   - it.unimi.dsi.fastutil.longs.Long2CharAVLTreeMap$2$1
[WARNING]   - it.unimi.dsi.fastutil.bytes.Byte2ObjectLinkedOpenHashMap$EntryIterator
[WARNING]   - it.unimi.dsi.fastutil.shorts.Short2FloatOpenCustomHashMap$KeySet
[WARNING]   - it.unimi.dsi.fastutil.ints.Int2ReferenceRBTreeMap$Submap
[WARNING]   - it.unimi.dsi.fastutil.bytes.Byte2BooleanRBTreeMap$Submap$1
[WARNING]   - it.unimi.dsi.fastutil.floats.AbstractFloat2ShortSortedMap$ValuesCollection
[WARNING]   - it.unimi.dsi.fastutil.longs.Long2ReferenceRBTreeMap$Submap$2
[WARNING]   - it.unimi.dsi.fastutil.chars.AbstractChar2LongSortedMap$ValuesIterator
[WARNING]   - it.unimi.dsi.fastutil.doubles.DoubleHeaps
[WARNING]   - 10690 more...
[WARNING] jackson-core-asl-1.9.13.jar, mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar define 121 overlapping classes: 
[WARNING]   - org.codehaus.jackson.annotate.JsonManagedReference
[WARNING]   - org.codehaus.jackson.util.DefaultPrettyPrinter$FixedSpaceIndenter
[WARNING]   - org.codehaus.jackson.JsonGenerationException
[WARNING]   - org.codehaus.jackson.util.BufferRecycler$CharBufferType
[WARNING]   - org.codehaus.jackson.io.UTF32Reader
[WARNING]   - org.codehaus.jackson.sym.Name1
[WARNING]   - org.codehaus.jackson.util.MinimalPrettyPrinter
[WARNING]   - org.codehaus.jackson.impl.JsonParserBase
[WARNING]   - org.codehaus.jackson.annotate.JsonValue
[WARNING]   - org.codehaus.jackson.sym.CharsToNameCanonicalizer$Bucket
[WARNING]   - 111 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, xbean-asm5-shaded-4.4.jar, mango-cli-0.0.3-SNAPSHOT.jar define 81 overlapping classes: 
[WARNING]   - org.apache.xbean.asm5.FieldWriter
[WARNING]   - org.apache.xbean.asm5.commons.GeneratorAdapter
[WARNING]   - org.apache.xbean.asm5.AnnotationWriter
[WARNING]   - org.apache.xbean.asm5.tree.IntInsnNode
[WARNING]   - org.apache.xbean.asm5.Type
[WARNING]   - org.apache.xbean.asm5.commons.RemappingClassAdapter
[WARNING]   - org.apache.xbean.asm5.tree.FieldInsnNode
[WARNING]   - org.apache.xbean.asm5.tree.MultiANewArrayInsnNode
[WARNING]   - org.apache.xbean.asm5.tree.IincInsnNode
[WARNING]   - org.apache.xbean.asm5.tree.InsnList$InsnListIterator
[WARNING]   - 71 more...
[WARNING] convert-0.6.0.jar, mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar define 23 overlapping classes: 
[WARNING]   - org.bdgenomics.convert.bdgenomics.SliceToRead
[WARNING]   - org.bdgenomics.convert.bdgenomics.SliceToSequence
[WARNING]   - org.bdgenomics.convert.bdgenomics.BdgenomicsModule
[WARNING]   - org.bdgenomics.convert.ConversionException
[WARNING]   - org.bdgenomics.convert.bdgenomics.OntologyTermToString
[WARNING]   - org.bdgenomics.convert.bdgenomics.StringToVariantAnnotationMessage
[WARNING]   - org.bdgenomics.convert.ConversionStringency
[WARNING]   - org.bdgenomics.convert.bdgenomics.ReadToSlice
[WARNING]   - org.bdgenomics.convert.Converter
[WARNING]   - org.bdgenomics.convert.bdgenomics.ReadToSequence
[WARNING]   - 13 more...
[WARNING] spark-unsafe_2.11-2.3.3.jar, mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar define 18 overlapping classes: 
[WARNING]   - org.apache.spark.unsafe.types.UTF8String
[WARNING]   - org.apache.spark.unsafe.memory.HeapMemoryAllocator
[WARNING]   - org.apache.spark.unsafe.array.LongArray
[WARNING]   - org.apache.spark.unsafe.types.UTF8String$LongWrapper
[WARNING]   - org.apache.spark.unsafe.bitset.BitSetMethods
[WARNING]   - org.apache.spark.unsafe.memory.UnsafeMemoryAllocator
[WARNING]   - org.apache.spark.sql.catalyst.expressions.HiveHasher
[WARNING]   - org.apache.spark.unsafe.KVIterator
[WARNING]   - org.apache.spark.unsafe.types.CalendarInterval
[WARNING]   - org.apache.spark.unsafe.memory.MemoryBlock
[WARNING]   - 8 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, curator-recipes-2.6.0.jar, mango-cli-0.0.3-SNAPSHOT.jar define 190 overlapping classes: 
[WARNING]   - org.apache.curator.framework.recipes.atomic.DistributedAtomicNumber
[WARNING]   - org.apache.curator.framework.recipes.locks.Reaper$State
[WARNING]   - org.apache.curator.framework.recipes.locks.InterProcessReadWriteLock
[WARNING]   - org.apache.curator.framework.recipes.queue.QueueBase
[WARNING]   - org.apache.curator.framework.recipes.locks.ChildReaper$1
[WARNING]   - org.apache.curator.framework.recipes.cache.Operation
[WARNING]   - org.apache.curator.framework.recipes.shared.SharedValue$1
[WARNING]   - org.apache.curator.framework.recipes.locks.Revoker
[WARNING]   - org.apache.curator.framework.recipes.queue.QueueSharderPolicies
[WARNING]   - org.apache.curator.framework.recipes.locks.StandardLockInternalsDriver
[WARNING]   - 180 more...
[WARNING] guava-27.0-jre.jar, mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar define 1955 overlapping classes: 
[WARNING]   - com.google.common.collect.CompactHashMap$Itr
[WARNING]   - com.google.common.collect.ImmutableMapValues$1
[WARNING]   - com.google.common.util.concurrent.AbstractService$5
[WARNING]   - com.google.common.io.LineProcessor
[WARNING]   - com.google.common.io.BaseEncoding$StandardBaseEncoding$2
[WARNING]   - com.google.common.io.ByteProcessor
[WARNING]   - com.google.common.math.package-info
[WARNING]   - com.google.common.util.concurrent.SimpleTimeLimiter
[WARNING]   - com.google.common.cache.AbstractCache$StatsCounter
[WARNING]   - com.google.common.util.concurrent.CycleDetectingLockFactory$Policies
[WARNING]   - 1945 more...
[WARNING] commons-math3-3.4.1.jar, mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar define 1215 overlapping classes: 
[WARNING]   - org.apache.commons.math3.optim.linear.LinearOptimizer
[WARNING]   - org.apache.commons.math3.linear.LUDecomposition$Solver
[WARNING]   - org.apache.commons.math3.analysis.function.Gaussian$Parametric
[WARNING]   - org.apache.commons.math3.stat.descriptive.WeightedEvaluation
[WARNING]   - org.apache.commons.math3.analysis.FunctionUtils$3
[WARNING]   - org.apache.commons.math3.stat.descriptive.AbstractStorelessUnivariateStatistic
[WARNING]   - org.apache.commons.math3.ml.clustering.FuzzyKMeansClusterer
[WARNING]   - org.apache.commons.math3.analysis.FunctionUtils$3$1
[WARNING]   - org.apache.commons.math3.ode.nonstiff.MidpointStepInterpolator
[WARNING]   - org.apache.commons.math3.ode.ParameterConfiguration
[WARNING]   - 1205 more...
[WARNING] jackson-module-paranamer-2.7.9.jar, mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar define 26 overlapping classes: 
[WARNING]   - com.fasterxml.jackson.module.paranamer.shaded.NullParanamer
[WARNING]   - com.fasterxml.jackson.module.paranamer.shaded.ParameterNamesNotFoundException
[WARNING]   - com.fasterxml.jackson.module.paranamer.shaded.BytecodeReadingParanamer$1
[WARNING]   - com.fasterxml.jackson.module.paranamer.shaded.BytecodeReadingParanamer$MethodCollector
[WARNING]   - com.fasterxml.jackson.module.paranamer.SerializableParanamer
[WARNING]   - com.fasterxml.jackson.module.paranamer.shaded.JavadocParanamer$DirJavadocProvider
[WARNING]   - com.fasterxml.jackson.module.paranamer.shaded.BytecodeReadingParanamer$Type
[WARNING]   - com.fasterxml.jackson.module.paranamer.ParanamerAnnotationIntrospector
[WARNING]   - com.fasterxml.jackson.module.paranamer.shaded.CachingParanamer$WithoutWeakReferences
[WARNING]   - com.fasterxml.jackson.module.paranamer.ParanamerOnJacksonAnnotationIntrospector
[WARNING]   - 16 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://maven.apache.org/plugins/maven-shade-plugin/
[INFO] Replacing original artifact with shaded artifact.
[INFO] Replacing /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-assembly/target/mango-assembly-0.0.3-SNAPSHOT.jar with /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-assembly/target/mango-assembly-0.0.3-SNAPSHOT-shaded.jar
[INFO] 
[INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ mango-assembly ---
[INFO] Building jar: /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-assembly/target/mango-assembly-0.0.3-SNAPSHOT-sources.jar
[INFO] 
[INFO] --- maven-javadoc-plugin:3.1.0:jar (attach-javadocs) @ mango-assembly ---
[INFO] 
[INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) > generate-sources @ mango-assembly >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ mango-assembly ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ mango-assembly ---
[INFO] 
[INFO] --- git-commit-id-plugin:2.2.1:revision (default) @ mango-assembly ---
[INFO] 
[INFO] --- templating-maven-plugin:1.0.0:filter-sources (filter-src) @ mango-assembly ---
[INFO] Request to add '/home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-assembly/src/main/java-templates' folder. Not added since it does not exist.
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-source (add-source) @ mango-assembly ---
[INFO] Source directory: /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-assembly/src/main/scala added.
[INFO] 
[INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) < generate-sources @ mango-assembly <<<
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ mango-assembly ---
model contains 6 documentable templates
[INFO] Building jar: /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-assembly/target/mango-assembly-0.0.3-SNAPSHOT-javadoc.jar
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building mango: Distribution 0.0.3-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ mango-distribution ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ mango-distribution ---
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default) @ mango-distribution ---
[INFO] Modified 0 of 0 .scala files
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ mango-distribution ---
[INFO] No sources to compile
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ mango-distribution ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-shade-plugin:3.1.0:shade (default) @ mango-distribution ---
[INFO] Replacing original artifact with shaded artifact.
[INFO] 
[INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ mango-distribution ---
[INFO] 
[INFO] --- maven-javadoc-plugin:3.1.0:jar (attach-javadocs) @ mango-distribution ---
[INFO] 
[INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) > generate-sources @ mango-distribution >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ mango-distribution ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ mango-distribution ---
[INFO] 
[INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) < generate-sources @ mango-distribution <<<
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ mango-distribution ---
[INFO] No source files found
[INFO] 
[INFO] --- maven-assembly-plugin:2.4.1:single (default) @ mango-distribution ---
[INFO] Reading assembly descriptor: src/main/assembly/assembly.xml
[INFO] Building tar: /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-distribution/target/mango-distribution-0.0.3-SNAPSHOT-bin.tar.gz
[INFO] Building tar: /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-distribution/target/mango-distribution-0.0.3-SNAPSHOT-bin.tar.bz2
[INFO] Building zip: /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-distribution/target/mango-distribution-0.0.3-SNAPSHOT-bin.zip
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary:
[INFO] 
[INFO] mango .............................................. SUCCESS [  3.528 s]
[INFO] mango: CORE ........................................ SUCCESS [ 46.836 s]
[INFO] mango: CLI ......................................... SUCCESS [01:05 min]
[INFO] Mango: Assembly .................................... SUCCESS [01:00 min]
[INFO] mango: Distribution ................................ SUCCESS [ 41.506 s]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 03:38 min
[INFO] Finished at: 2019-05-15T19:13:50-07:00
[INFO] Final Memory: 93M/1519M
[INFO] ------------------------------------------------------------------------

# make sure that the distribution package contains an assembly jar
# if no assembly jar is found, this will exit with code 1 and fail the build
tar tzvf mango-distribution/target/mango-distribution*-bin.tar.gz | \
    grep mango-assembly | \
    grep jar | \
    grep -v -e sources -e javadoc
+ grep mango-assembly
+ tar tzvf mango-distribution/target/mango-distribution-0.0.3-SNAPSHOT-bin.tar.gz
+ grep jar
+ grep -v -e sources -e javadoc
-rw-r--r-- jenkins/jenkins 126912024 2019-05-15 19:13 mango-distribution-0.0.3-SNAPSHOT/repo/mango-assembly-0.0.3-SNAPSHOT.jar

# we are done with maven, so clean up the maven temp dir
find ${MANGO_MVN_TMP_DIR}
+ find /tmp/mangoTestMvn99nKL1a
/tmp/mangoTestMvn99nKL1a
/tmp/mangoTestMvn99nKL1a/invalidBuild.genome813207388445121856
/tmp/mangoTestMvn99nKL1a/TempSuite5483406994438056876.adam
/tmp/mangoTestMvn99nKL1a/TempSuite5483406994438056876.adam/._references.avro.crc
/tmp/mangoTestMvn99nKL1a/TempSuite5483406994438056876.adam/._readGroups.avro.crc
/tmp/mangoTestMvn99nKL1a/TempSuite5483406994438056876.adam/_readGroups.avro
/tmp/mangoTestMvn99nKL1a/TempSuite5483406994438056876.adam/._partitionedByStartPos.crc
/tmp/mangoTestMvn99nKL1a/TempSuite5483406994438056876.adam/_references.avro
/tmp/mangoTestMvn99nKL1a/TempSuite5483406994438056876.adam/_partitionedByStartPos
/tmp/mangoTestMvn99nKL1a/TempSuite5483406994438056876.adam/._SUCCESS.crc
/tmp/mangoTestMvn99nKL1a/TempSuite5483406994438056876.adam/_SUCCESS
/tmp/mangoTestMvn99nKL1a/TempSuite5483406994438056876.adam/_processingSteps.avro
/tmp/mangoTestMvn99nKL1a/TempSuite5483406994438056876.adam/referenceName=1
/tmp/mangoTestMvn99nKL1a/TempSuite5483406994438056876.adam/referenceName=1/positionBin=26
/tmp/mangoTestMvn99nKL1a/TempSuite5483406994438056876.adam/referenceName=1/positionBin=26/.part-00000-8caa821b-507a-4e2e-830a-bcda0ec0903b.c000.snappy.parquet.crc
/tmp/mangoTestMvn99nKL1a/TempSuite5483406994438056876.adam/referenceName=1/positionBin=26/part-00000-8caa821b-507a-4e2e-830a-bcda0ec0903b.c000.snappy.parquet
/tmp/mangoTestMvn99nKL1a/TempSuite5483406994438056876.adam/referenceName=1/positionBin=240
/tmp/mangoTestMvn99nKL1a/TempSuite5483406994438056876.adam/referenceName=1/positionBin=240/.part-00000-8caa821b-507a-4e2e-830a-bcda0ec0903b.c000.snappy.parquet.crc
/tmp/mangoTestMvn99nKL1a/TempSuite5483406994438056876.adam/referenceName=1/positionBin=240/part-00000-8caa821b-507a-4e2e-830a-bcda0ec0903b.c000.snappy.parquet
/tmp/mangoTestMvn99nKL1a/TempSuite5483406994438056876.adam/._processingSteps.avro.crc
/tmp/mangoTestMvn99nKL1a/TempSuite5483406994438056876.adam/referenceName=2
/tmp/mangoTestMvn99nKL1a/TempSuite5483406994438056876.adam/referenceName=2/positionBin=189
/tmp/mangoTestMvn99nKL1a/TempSuite5483406994438056876.adam/referenceName=2/positionBin=189/.part-00000-8caa821b-507a-4e2e-830a-bcda0ec0903b.c000.snappy.parquet.crc
/tmp/mangoTestMvn99nKL1a/TempSuite5483406994438056876.adam/referenceName=2/positionBin=189/part-00000-8caa821b-507a-4e2e-830a-bcda0ec0903b.c000.snappy.parquet
/tmp/mangoTestMvn99nKL1a/TempSuite963826628074766370.adam
/tmp/mangoTestMvn99nKL1a/TempSuite963826628074766370.adam/_header
/tmp/mangoTestMvn99nKL1a/TempSuite963826628074766370.adam/._references.avro.crc
/tmp/mangoTestMvn99nKL1a/TempSuite963826628074766370.adam/_samples.avro
/tmp/mangoTestMvn99nKL1a/TempSuite963826628074766370.adam/._partitionedByStartPos.crc
/tmp/mangoTestMvn99nKL1a/TempSuite963826628074766370.adam/_references.avro
/tmp/mangoTestMvn99nKL1a/TempSuite963826628074766370.adam/_partitionedByStartPos
/tmp/mangoTestMvn99nKL1a/TempSuite963826628074766370.adam/._SUCCESS.crc
/tmp/mangoTestMvn99nKL1a/TempSuite963826628074766370.adam/_SUCCESS
/tmp/mangoTestMvn99nKL1a/TempSuite963826628074766370.adam/referenceName=1
/tmp/mangoTestMvn99nKL1a/TempSuite963826628074766370.adam/referenceName=1/positionBin=0
/tmp/mangoTestMvn99nKL1a/TempSuite963826628074766370.adam/referenceName=1/positionBin=0/part-00000-588db984-0d47-417b-b8b0-21ce6890ee29.c000.snappy.parquet
/tmp/mangoTestMvn99nKL1a/TempSuite963826628074766370.adam/referenceName=1/positionBin=0/.part-00000-588db984-0d47-417b-b8b0-21ce6890ee29.c000.snappy.parquet.crc
/tmp/mangoTestMvn99nKL1a/TempSuite963826628074766370.adam/._header.crc
/tmp/mangoTestMvn99nKL1a/TempSuite963826628074766370.adam/._samples.avro.crc
/tmp/mangoTestMvn99nKL1a/TempSuite1976304055392292816.adam
/tmp/mangoTestMvn99nKL1a/TempSuite1976304055392292816.adam/._references.avro.crc
/tmp/mangoTestMvn99nKL1a/TempSuite1976304055392292816.adam/._readGroups.avro.crc
/tmp/mangoTestMvn99nKL1a/TempSuite1976304055392292816.adam/_readGroups.avro
/tmp/mangoTestMvn99nKL1a/TempSuite1976304055392292816.adam/._partitionedByStartPos.crc
/tmp/mangoTestMvn99nKL1a/TempSuite1976304055392292816.adam/_references.avro
/tmp/mangoTestMvn99nKL1a/TempSuite1976304055392292816.adam/_partitionedByStartPos
/tmp/mangoTestMvn99nKL1a/TempSuite1976304055392292816.adam/._SUCCESS.crc
/tmp/mangoTestMvn99nKL1a/TempSuite1976304055392292816.adam/_SUCCESS
/tmp/mangoTestMvn99nKL1a/TempSuite1976304055392292816.adam/_processingSteps.avro
/tmp/mangoTestMvn99nKL1a/TempSuite1976304055392292816.adam/referenceName=1
/tmp/mangoTestMvn99nKL1a/TempSuite1976304055392292816.adam/referenceName=1/positionBin=26
/tmp/mangoTestMvn99nKL1a/TempSuite1976304055392292816.adam/referenceName=1/positionBin=26/.part-00000-d7bea983-6248-4ffa-b7cb-041f68f337fc.c000.snappy.parquet.crc
/tmp/mangoTestMvn99nKL1a/TempSuite1976304055392292816.adam/referenceName=1/positionBin=26/part-00000-d7bea983-6248-4ffa-b7cb-041f68f337fc.c000.snappy.parquet
/tmp/mangoTestMvn99nKL1a/TempSuite1976304055392292816.adam/referenceName=1/positionBin=240
/tmp/mangoTestMvn99nKL1a/TempSuite1976304055392292816.adam/referenceName=1/positionBin=240/.part-00000-d7bea983-6248-4ffa-b7cb-041f68f337fc.c000.snappy.parquet.crc
/tmp/mangoTestMvn99nKL1a/TempSuite1976304055392292816.adam/referenceName=1/positionBin=240/part-00000-d7bea983-6248-4ffa-b7cb-041f68f337fc.c000.snappy.parquet
/tmp/mangoTestMvn99nKL1a/TempSuite1976304055392292816.adam/._processingSteps.avro.crc
/tmp/mangoTestMvn99nKL1a/TempSuite1976304055392292816.adam/referenceName=2
/tmp/mangoTestMvn99nKL1a/TempSuite1976304055392292816.adam/referenceName=2/positionBin=189
/tmp/mangoTestMvn99nKL1a/TempSuite1976304055392292816.adam/referenceName=2/positionBin=189/.part-00000-d7bea983-6248-4ffa-b7cb-041f68f337fc.c000.snappy.parquet.crc
/tmp/mangoTestMvn99nKL1a/TempSuite1976304055392292816.adam/referenceName=2/positionBin=189/part-00000-d7bea983-6248-4ffa-b7cb-041f68f337fc.c000.snappy.parquet
/tmp/mangoTestMvn99nKL1a/TempSuite963826628074766370
/tmp/mangoTestMvn99nKL1a/6650199691445751956
/tmp/mangoTestMvn99nKL1a/invalidBuild.genome3538195827397235108
/tmp/mangoTestMvn99nKL1a/TempSuite5483406994438056876
/tmp/mangoTestMvn99nKL1a/TempSuite8767569084920184252.adam
/tmp/mangoTestMvn99nKL1a/TempSuite8767569084920184252.adam/_header
/tmp/mangoTestMvn99nKL1a/TempSuite8767569084920184252.adam/._references.avro.crc
/tmp/mangoTestMvn99nKL1a/TempSuite8767569084920184252.adam/_samples.avro
/tmp/mangoTestMvn99nKL1a/TempSuite8767569084920184252.adam/._partitionedByStartPos.crc
/tmp/mangoTestMvn99nKL1a/TempSuite8767569084920184252.adam/_references.avro
/tmp/mangoTestMvn99nKL1a/TempSuite8767569084920184252.adam/_partitionedByStartPos
/tmp/mangoTestMvn99nKL1a/TempSuite8767569084920184252.adam/._SUCCESS.crc
/tmp/mangoTestMvn99nKL1a/TempSuite8767569084920184252.adam/_SUCCESS
/tmp/mangoTestMvn99nKL1a/TempSuite8767569084920184252.adam/referenceName=1
/tmp/mangoTestMvn99nKL1a/TempSuite8767569084920184252.adam/referenceName=1/positionBin=0
/tmp/mangoTestMvn99nKL1a/TempSuite8767569084920184252.adam/referenceName=1/positionBin=0/part-00000-24223aa8-b797-41dc-b7f7-72e4b73a2e55.c000.snappy.parquet
/tmp/mangoTestMvn99nKL1a/TempSuite8767569084920184252.adam/referenceName=1/positionBin=0/.part-00000-24223aa8-b797-41dc-b7f7-72e4b73a2e55.c000.snappy.parquet.crc
/tmp/mangoTestMvn99nKL1a/TempSuite8767569084920184252.adam/._header.crc
/tmp/mangoTestMvn99nKL1a/TempSuite8767569084920184252.adam/._samples.avro.crc
/tmp/mangoTestMvn99nKL1a/genomes3707345242038748434
/tmp/mangoTestMvn99nKL1a/genomes3707345242038748434/hg19.genome
/tmp/mangoTestMvn99nKL1a/TempSuite1976304055392292816
/tmp/mangoTestMvn99nKL1a/genomes7619365875940664769
/tmp/mangoTestMvn99nKL1a/genomes7619365875940664769/hg19.genome
/tmp/mangoTestMvn99nKL1a/mmbroken2435401772730376369.genome
/tmp/mangoTestMvn99nKL1a/mmbroken4034087988933117464.genome
/tmp/mangoTestMvn99nKL1a/5764130671875577863
/tmp/mangoTestMvn99nKL1a/TempSuite8767569084920184252
/tmp/mangoTestMvn99nKL1a/6047802438852419763
/tmp/mangoTestMvn99nKL1a/6047802438852419763/anoGam1.genome
/tmp/mangoTestMvn99nKL1a/3124812392552132116
/tmp/mangoTestMvn99nKL1a/3124812392552132116/anoGam1.genome
/tmp/mangoTestMvn99nKL1a/snappy-1.0.5-libsnappyjava.so
rm -rf ${MANGO_MVN_TMP_DIR}
+ rm -rf /tmp/mangoTestMvn99nKL1a

find . -name pom.xml \
    -exec sed -i.bak \
    -e "s:sun.io.serialization.extendedDebugInfo=true -Djava.io.tmpdir=${MANGO_MVN_TMP_DIR}:sun.io.serialization.extendedDebugInfo=true:g" \
    {} \;
+ find . -name pom.xml -exec sed -i.bak -e 's:sun.io.serialization.extendedDebugInfo=true -Djava.io.tmpdir=/tmp/mangoTestMvn99nKL1a:sun.io.serialization.extendedDebugInfo=true:g' '{}' ';'
find . -name "*.bak" -exec rm -f {} \;
+ find . -name '*.bak' -exec rm -f '{}' ';'

# run integration tests
# prebuilt spark distributions are scala 2.11 for spark 2.x
if [[ ${SCALAVER} == 2.11 ]];
then

    # make a temp directory
    MANGO_TMP_DIR=$(mktemp -d -t mangoTestXXXXXXX)

    MANGO_TMP_DIR=$MANGO_TMP_DIR/deleteMePleaseThisIsNoLongerNeeded
    mkdir $MANGO_TMP_DIR

    # set the TMPDIR envar, which is used by python to choose where to make temp directories
    export TMPDIR=${MANGO_TMP_DIR}

    pushd $PROJECT_ROOT

    # Copy the jar into our temp space for testing
    cp -r . $MANGO_TMP_DIR
    popd

    pushd $MANGO_TMP_DIR

    # what hadoop version are we on? format string for downloading spark assembly
    if [[ $HADOOP_VERSION =~ ^2\.6 ]]; then
        HADOOP=hadoop2.6
    elif [[ $HADOOP_VERSION =~ ^2\.7 ]]; then
        HADOOP=hadoop2.7
    else
        echo "Unknown Hadoop version."
        exit 1
    fi

    # set spark artifact string for downloading assembly
    SPARK=spark-${SPARK_VERSION}

    # download prepackaged spark assembly
    curl \
        -L "https://www.apache.org/dyn/mirrors/mirrors.cgi?action=download&filename=spark/${SPARK}/${SPARK}-bin-${HADOOP}.tgz" \
        -o ${SPARK}-bin-${HADOOP}.tgz

    tar xzvf ${SPARK}-bin-${HADOOP}.tgz
    export SPARK_HOME=${MANGO_TMP_DIR}/${SPARK}-bin-${HADOOP}

    # add pyspark to the python path
    PY4J_ZIP="$(ls -1 "${SPARK_HOME}/python/lib" | grep py4j)"
    export PYTHONPATH=${SPARK_HOME}/python:${SPARK_HOME}/python/lib/${PY4J_ZIP}:${PYTHONPATH}

    # put mango jar on the pyspark path
    ASSEMBLY_DIR="${MANGO_TMP_DIR}/mango-assembly/target"
    ASSEMBLY_JAR="$(ls -1 "$ASSEMBLY_DIR" | grep "^mango-assembly[0-9A-Za-z\_\.-]*\.jar$" | grep -v javadoc | grep -v sources || true)"
    export PYSPARK_SUBMIT_ARGS="--jars ${ASSEMBLY_DIR}/${ASSEMBLY_JAR} --driver-class-path ${ASSEMBLY_DIR}/${ASSEMBLY_JAR} pyspark-shell"

    # create a conda environment for python build, if necessary
    pythons=( 2.7 3.6 )
    for python in ${pythons[*]}
    do
        uuid=$(uuidgen)
        conda create -y -q -n mango-build-${uuid} python=${python}
        source activate mango-build-${uuid}

        # install npm and node in the venv for mango-viz
        conda install -y nodejs

        # prepare mango python
        pushd mango-python
        make prepare
        popd

        # we can run the python build, now that we have a spark executable
        mvn -U \
            -P python,distribution \
            package \
            -DskipTests \
            -Dhadoop.version=${HADOOP_VERSION} \
            -Dspark.version=${SPARK_VERSION}

        # clean mango python
        pushd mango-python
        make clean
        popd

        # prepare mango viz
        pushd mango-viz
        make prepare
        popd

        # run the widgets tests (mango-viz)
        mvn -P widgets test

        # clean mango viz
        pushd mango-viz
        make clean
        popd

        # make sure that the distribution package contains an egg
        # if no assembly jar is found, this will exit with code 1 and fail the build
        tar tzvf mango-distribution/target/mango-distribution*-bin.tar.gz | \
            grep bdgenomics.mango | \
            grep egg

        # test mango notebook, output to temporary log file
        MANGO_NOTEBOOK_LOGS=${MANGO_TMP_DIR}/mango-notebook.log
        bash -xv ${PROJECT_ROOT}/bin/mango-notebook  &> ${MANGO_NOTEBOOK_LOGS} &

        # sleep for 2 seconds to let mango-notebook start up
        sleep 2

        # if mango-notebook fails, then trying to kill the process will fail
        if kill $! ; then
            echo "Mango Notebook Succeeded"
        else
            echo "Mango Notebook failed with logs:"
            cat ${MANGO_NOTEBOOK_LOGS}
            # clean up
            rm -rf ${MANGO_TMP_DIR}
            exit 1
        fi

        # copy python targets back
        cp -r mango-python/target ${PROJECT_ROOT}/mango-python/

        # deactivate and remove the conda env
        source deactivate
        conda remove -y --name mango-build-${uuid} --all

    done

    # test mango submit
    MANGO_BROWSER_LOGS=mango-submit.log
    bash -xv ${PROJECT_ROOT}/example-files/browser-scripts/run-example.sh &> ${MANGO_BROWSER_LOGS} &

    # sleep for 10 seconds to let mango-browser start up
    sleep 10

    # make sure server responds to POST for reads and variants
    curl \
    --header "Content-type: application/json" \
    --request POST \
    --data "{\"pageToken\":null,\"pageSize\":200,\"readGroupIds\":[\"chr17_7500000-7515000_sam\"],\"referenceId\":\"chr17\",\"start\":1,\"end\":100}"  \
    http://localhost:8080/reads/search

    curl \
    --header "Content-type: application/json" \
    --request POST \
    --data "{\"variantSetId\":\"ALL_chr17_7500000-7515000_phase3_shapeit2_mvncall_integrated_v5a_20130502_genotypes_vcf\",\"pageToken\":null,\"pageSize\":400,\"referenceName\":\"chr17\",\"callSetIds\":[],\"start\":7500000,\"end\":7515000}"  \
    http://localhost:8080/variants/search

    # get processes with mango prefix
    PROCESSES=( $(ps aux | grep -F 'browser-scripts/run-example.sh' | grep -v -F 'grep' | awk '{ print $2 }') )

    # There should be processes running for mango-browser
    if [ "${#PROCESSES[@]}" -gt 0 ] ; then
        echo "Mango Browser Succeeded"
        # kill all Mango Browser related processes
        kill ${PROCESSES}; 
    else
        echo "Mango Browser failed with logs:"
        cat ${MANGO_BROWSER_LOGS}
        # clean up
        rm -rf ${MANGO_TMP_DIR}
        exit 1
    fi

    # test genome builds
    TEST_GENOME="anoGam1"
    bash -xv ${PROJECT_ROOT}/bin/make_genome ${TEST_GENOME} ${MANGO_TMP_DIR}

    unzip ${MANGO_TMP_DIR}/${TEST_GENOME}.genome -d ${MANGO_TMP_DIR}/${TEST_GENOME}

    pushd ${MANGO_TMP_DIR}/${TEST_GENOME}
    cat properties.txt
    cat ${TEST_GENOME}.chrom.sizes
    popd

    rm -rf ${MANGO_TMP_DIR}/${TEST_GENOME}*

    # clean up
    rm -rf ${MANGO_TMP_DIR}

fi
+ [[ 2.11 == 2.11 ]]
mktemp -d -t mangoTestXXXXXXX
++ mktemp -d -t mangoTestXXXXXXX
+ MANGO_TMP_DIR=/tmp/mangoTestdv9ZuJK
+ MANGO_TMP_DIR=/tmp/mangoTestdv9ZuJK/deleteMePleaseThisIsNoLongerNeeded
+ mkdir /tmp/mangoTestdv9ZuJK/deleteMePleaseThisIsNoLongerNeeded
+ export TMPDIR=/tmp/mangoTestdv9ZuJK/deleteMePleaseThisIsNoLongerNeeded
+ TMPDIR=/tmp/mangoTestdv9ZuJK/deleteMePleaseThisIsNoLongerNeeded
+ pushd /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/scripts/..
~/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu ~/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu
+ cp -r . /tmp/mangoTestdv9ZuJK/deleteMePleaseThisIsNoLongerNeeded
+ popd
~/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu
+ pushd /tmp/mangoTestdv9ZuJK/deleteMePleaseThisIsNoLongerNeeded
/tmp/mangoTestdv9ZuJK/deleteMePleaseThisIsNoLongerNeeded ~/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu
+ [[ 2.7.5 =~ ^2\.6 ]]
+ [[ 2.7.5 =~ ^2\.7 ]]
+ HADOOP=hadoop2.7
+ SPARK=spark-2.3.3
+ curl -L 'https://www.apache.org/dyn/mirrors/mirrors.cgi?action=download&filename=spark/spark-2.3.3/spark-2.3.3-bin-hadoop2.7.tgz' -o spark-2.3.3-bin-hadoop2.7.tgz
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0

  0     0    0     0    0     0      0      0 --:--:--  0:00:01 --:--:--     0
  0     0    0     0    0     0      0      0 --:--:--  0:00:03 --:--:--     0
  0     0    0     0    0     0      0      0 --:--:--  0:00:04 --:--:--     0
  0     0    0     0    0     0      0      0 --:--:--  0:00:05 --:--:--     0
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  0     0    0     0    0     0      0      0 --:--:--  0:00:07 --:--:--     0
  0     0    0     0    0     0      0      0 --:--:--  0:00:08 --:--:--     0
  0     0    0     0    0     0      0      0 --:--:--  0:00:09 --:--:--     0
  0     0    0     0    0     0      0      0 --:--:--  0:00:10 --:--:--     0
  0  215M    0  4112    0     0    375      0   6d 23h  0:00:10   6d 23h   830
  0  215M    0 86648    0     0   7154      0  8:46:34  0:00:12  8:46:22 16969
  0  215M    0  177k    0     0  13348      0  4:42:13  0:00:13  4:42:00 32284
  0  215M    0  177k    0     0  12436      0  5:02:55  0:00:14  5:02:41 32284
  0  215M    0  177k    0     0  11641      0  5:23:36  0:00:15  5:23:21 32284
  0  215M    0  180k    0     0  11310      0  5:33:04  0:00:16  5:32:48 33438
  0  215M    0  275k    0     0  16244      0  3:51:54  0:00:17  3:51:37 37191
  0  215M    0  275k    0     0  15359      0  4:05:16  0:00:18  4:04:58 21172
  0  215M    0  275k    0     0  14565      0  4:18:38  0:00:19  4:18:19 21172
  0  215M    0  275k    0     0  13849      0  4:32:00  0:00:20  4:31:40 21172
  0  215M    0  275k    0     0  13201      0  4:45:21  0:00:21  4:45:00 19383
  0  215M    0  275k    0     0  12610      0  4:58:44  0:00:22  4:58:22     0
  0  215M    0  275k    0     0  12070      0  5:12:06  0:00:23  5:11:43     0
  0  215M    0  275k    0     0  11574      0  5:25:28  0:00:24  5:25:04     0
  0  215M    0  275k    0     0  11118      0  5:38:49  0:00:25  5:38:24     0
  0  215M    0  281k    0     0  10917      0  5:45:04  0:00:26  5:44:38  1158
  0  215M    0  377k    0     0  14114      0  4:26:54  0:00:27  4:26:27 20842
  0  215M    0  377k    0     0  13616      0  4:36:40  0:00:28  4:36:12 20842
  0  215M    0  377k    0     0  13152      0  4:46:25  0:00:29  4:45:56 20838
  0  215M    0  377k    0     0  12719      0  4:56:10  0:00:30  4:55:40 20838
  0  215M    0  377k    0     0  12313      0  5:05:56  0:00:31  5:05:25 19673
  0  215M    0  377k    0     0  11932      0  5:15:42  0:00:32  5:15:10     0
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Build was aborted
Finished: ABORTED