基因数据处理44之cloud-scale-bwamem安装

原创

KeepLearningAI 2023-01-04 10:58:09 博主文章分类：基因数据处理 ©著作权

文章标签 cloud-scal maven hadoop apache 文章分类 虚拟化云计算

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cloud-scale-bwamem是在spark等云环境上实现bwa-mem算法，加速对全基因组匹配的处理
1.下载：

git clone  https://github.com/ytchen0323/cloud-scale-bwamem.git

2.编译：

mvn clean package

3.编译成功：

[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 35:49 min
[INFO] Finished at: 2016-06-01T23:41:50+08:00
[INFO] Final Memory: 62M/375M
[INFO] ------------------------------------------------------------------------

参考：
【1】 https://github.com/ytchen0323/cloud-scale-bwamem
【2】 http://vast.cs.ucla.edu/publications/cs-bwamem-fast-and-scalable-read-aligner-cloud-scale-whole-genome-sequencing

安装记录：

xubo@xubo:~/xubo/tools$ git clone  https://github.com/ytchen0323/cloud-scale-bwamem.git
Cloning into 'cloud-scale-bwamem'...
remote: Counting objects: 1425, done.
remote: Total 1425 (delta 0), reused 0 (delta 0), pack-reused 1425
Receiving objects: 100% (1425/1425), 526.98 KiB | 170.00 KiB/s, done.
Resolving deltas: 100% (661/661), done.
Checking connectivity... done.
xubo@xubo:~/xubo/tools$ cd cloud-scale-bwamem/
xubo@xubo:~/xubo/tools/cloud-scale-bwamem$ ls
compile.pl  license.md  pom.xml  README.md  run_test.sh  src
xubo@xubo:~/xubo/tools/cloud-scale-bwamem$ mvn clean package
[INFO] Scanning for projects...
[WARNING] 
[WARNING] Some problems were encountered while building the effective model for cs.ucla.edu:cloud-scale-bwamem:jar:0.2.2
[WARNING] 'build.plugins.plugin.version' for org.apache.maven.plugins:maven-shade-plugin is missing. @ line 151, column 21
[WARNING] 'build.plugins.plugin.version' for org.scala-tools:maven-scala-plugin is missing. @ line 95, column 21
[WARNING] 
[WARNING] It is highly recommended to fix these problems because they threaten the stability of your build.
[WARNING] 
[WARNING] For this reason, future Maven versions might no longer support building such malformed projects.
[WARNING] 
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building Cloud-Scale-BWAMEM 0.2.2
[INFO] ------------------------------------------------------------------------
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[INFO] Checking for multiple versions of scala
[WARNING]  Expected all dependencies to require Scala version: 2.10.4
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[INFO] includes = [**/*.scala,**/*.java,]
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[WARNING] warning: there were 22 deprecation warning(s); re-run with -deprecation for details
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[INFO] Copying jackson-databind-2.4.4.jar to /home/xubo/xubo/tools/cloud-scale-bwamem/target/lib/jackson-databind-2.4.4.jar
[INFO] Copying lz4-1.3.0.jar to /home/xubo/xubo/tools/cloud-scale-bwamem/target/lib/lz4-1.3.0.jar
[INFO] Copying hadoop-yarn-client-2.5.2.jar to /home/xubo/xubo/tools/cloud-scale-bwamem/target/lib/hadoop-yarn-client-2.5.2.jar
[INFO] Copying scalac-scoverage-plugin_2.10-1.1.1.jar to /home/xubo/xubo/tools/cloud-scale-bwamem/target/lib/scalac-scoverage-plugin_2.10-1.1.1.jar
[INFO] Copying commons-configuration-1.6.jar to /home/xubo/xubo/tools/cloud-scale-bwamem/target/lib/commons-configuration-1.6.jar
[INFO] Copying httpcore-4.3.1.jar to /home/xubo/xubo/tools/cloud-scale-bwamem/target/lib/httpcore-4.3.1.jar
[INFO] Copying hadoop-mapreduce-client-jobclient-2.5.2.jar to /home/xubo/xubo/tools/cloud-scale-bwamem/target/lib/hadoop-mapreduce-client-jobclient-2.5.2.jar
[INFO] Copying jackson-core-2.4.4.jar to /home/xubo/xubo/tools/cloud-scale-bwamem/target/lib/jackson-core-2.4.4.jar
[INFO] Copying slf4j-log4j12-1.7.10.jar to /home/xubo/xubo/tools/cloud-scale-bwamem/target/lib/slf4j-log4j12-1.7.10.jar
[INFO] Copying spark-launcher_2.10-1.5.1.jar to /home/xubo/xubo/tools/cloud-scale-bwamem/target/lib/spark-launcher_2.10-1.5.1.jar
[INFO] Copying parquet-avro-1.8.1.jar to /home/xubo/xubo/tools/cloud-scale-bwamem/target/lib/parquet-avro-1.8.1.jar
[INFO] Copying chill_2.10-0.5.0.jar to /home/xubo/xubo/tools/cloud-scale-bwamem/target/lib/chill_2.10-0.5.0.jar
[INFO] Copying akka-actor_2.10-2.3.11.jar to /home/xubo/xubo/tools/cloud-scale-bwamem/target/lib/akka-actor_2.10-2.3.11.jar
[INFO] Copying jersey-server-1.9.jar to /home/xubo/xubo/tools/cloud-scale-bwamem/target/lib/jersey-server-1.9.jar
[INFO] Copying asm-4.0.jar to /home/xubo/xubo/tools/cloud-scale-bwamem/target/lib/asm-4.0.jar
[INFO] Copying scala-library-2.10.4.jar to /home/xubo/xubo/tools/cloud-scale-bwamem/target/lib/scala-library-2.10.4.jar
[INFO] Copying parquet-column-1.6.0.jar to /home/xubo/xubo/tools/cloud-scale-bwamem/target/lib/parquet-column-1.6.0.jar
[INFO] Copying spark-network-shuffle_2.10-1.5.1.jar to /home/xubo/xubo/tools/cloud-scale-bwamem/target/lib/spark-network-shuffle_2.10-1.5.1.jar
[INFO] Copying RoaringBitmap-0.4.5.jar to /home/xubo/xubo/tools/cloud-scale-bwamem/target/lib/RoaringBitmap-0.4.5.jar
[INFO] Copying netty-all-4.0.29.Final.jar to /home/xubo/xubo/tools/cloud-scale-bwamem/target/lib/netty-all-4.0.29.Final.jar
[INFO] Copying tachyon-client-0.7.1.jar to /home/xubo/xubo/tools/cloud-scale-bwamem/target/lib/tachyon-client-0.7.1.jar
[INFO] 
[INFO] --- maven-shade-plugin:2.4.3:shade (default) @ cloud-scale-bwamem ---
[INFO] Including org.scala-lang:scala-library:jar:2.10.4 in the shaded jar.
[INFO] Including org.apache.hadoop:hadoop-client:jar:2.5.2 in the shaded jar.
[INFO] Including org.apache.hadoop:hadoop-common:jar:2.5.2 in the shaded jar.
[INFO] Including commons-cli:commons-cli:jar:1.2 in the shaded jar.
[INFO] Including xmlenc:xmlenc:jar:0.52 in the shaded jar.
[INFO] Including commons-httpclient:commons-httpclient:jar:3.1 in the shaded jar.
[INFO] Including commons-codec:commons-codec:jar:1.4 in the shaded jar.
[INFO] Including commons-collections:commons-collections:jar:3.2.1 in the shaded jar.
[INFO] Including commons-lang:commons-lang:jar:2.6 in the shaded jar.
[INFO] Including commons-configuration:commons-configuration:jar:1.6 in the shaded jar.
[INFO] Including commons-digester:commons-digester:jar:1.8 in the shaded jar.
[INFO] Including commons-beanutils:commons-beanutils:jar:1.7.0 in the shaded jar.
[INFO] Including commons-beanutils:commons-beanutils-core:jar:1.8.0 in the shaded jar.
[INFO] Including com.google.protobuf:protobuf-java:jar:2.5.0 in the shaded jar.
[INFO] Including org.apache.hadoop:hadoop-auth:jar:2.5.2 in the shaded jar.
[INFO] Including org.apache.directory.server:apacheds-kerberos-codec:jar:2.0.0-M15 in the shaded jar.
[INFO] Including org.apache.directory.server:apacheds-i18n:jar:2.0.0-M15 in the shaded jar.
[INFO] Including org.apache.directory.api:api-asn1-api:jar:1.0.0-M20 in the shaded jar.
[INFO] Including org.apache.directory.api:api-util:jar:1.0.0-M20 in the shaded jar.
[INFO] Including org.apache.zookeeper:zookeeper:jar:3.4.6 in the shaded jar.
[INFO] Including org.apache.hadoop:hadoop-hdfs:jar:2.5.2 in the shaded jar.
[INFO] Including org.mortbay.jetty:jetty-util:jar:6.1.26 in the shaded jar.
[INFO] Including io.netty:netty:jar:3.6.2.Final in the shaded jar.
[INFO] Including org.apache.hadoop:hadoop-mapreduce-client-app:jar:2.5.2 in the shaded jar.
[INFO] Including org.apache.hadoop:hadoop-mapreduce-client-common:jar:2.5.2 in the shaded jar.
[INFO] Including org.apache.hadoop:hadoop-yarn-client:jar:2.5.2 in the shaded jar.
[INFO] Including com.sun.jersey:jersey-client:jar:1.9 in the shaded jar.
[INFO] Including org.apache.hadoop:hadoop-yarn-server-common:jar:2.5.2 in the shaded jar.
[INFO] Including org.apache.hadoop:hadoop-mapreduce-client-shuffle:jar:2.5.2 in the shaded jar.
[INFO] Including org.fusesource.leveldbjni:leveldbjni-all:jar:1.8 in the shaded jar.
[INFO] Including org.apache.hadoop:hadoop-yarn-api:jar:2.5.2 in the shaded jar.
[INFO] Including org.apache.hadoop:hadoop-mapreduce-client-core:jar:2.5.2 in the shaded jar.
[INFO] Including org.apache.hadoop:hadoop-yarn-common:jar:2.5.2 in the shaded jar.
[INFO] Including javax.xml.bind:jaxb-api:jar:2.2.2 in the shaded jar.
[INFO] Including javax.xml.stream:stax-api:jar:1.0-2 in the shaded jar.
[INFO] Including javax.activation:activation:jar:1.1 in the shaded jar.
[INFO] Including org.apache.hadoop:hadoop-mapreduce-client-jobclient:jar:2.5.2 in the shaded jar.
[INFO] Including org.apache.hadoop:hadoop-annotations:jar:2.5.2 in the shaded jar.
[INFO] Including org.apache.spark:spark-core_2.10:jar:1.5.1 in the shaded jar.
[INFO] Including org.apache.avro:avro-mapred:jar:hadoop2:1.7.7 in the shaded jar.
[INFO] Including org.apache.avro:avro-ipc:jar:1.7.7 in the shaded jar.
[INFO] Including org.apache.avro:avro-ipc:jar:tests:1.7.7 in the shaded jar.
[INFO] Including com.twitter:chill_2.10:jar:0.5.0 in the shaded jar.
[INFO] Including com.twitter:chill-java:jar:0.5.0 in the shaded jar.
[INFO] Including org.apache.spark:spark-launcher_2.10:jar:1.5.1 in the shaded jar.
[INFO] Including org.apache.spark:spark-network-common_2.10:jar:1.5.1 in the shaded jar.
[INFO] Including org.apache.spark:spark-network-shuffle_2.10:jar:1.5.1 in the shaded jar.
[INFO] Including org.apache.spark:spark-unsafe_2.10:jar:1.5.1 in the shaded jar.
[INFO] Including net.java.dev.jets3t:jets3t:jar:0.7.1 in the shaded jar.
[INFO] Including org.apache.curator:curator-recipes:jar:2.4.0 in the shaded jar.
[INFO] Including org.apache.curator:curator-framework:jar:2.4.0 in the shaded jar.
[INFO] Including org.eclipse.jetty.orbit:javax.servlet:jar:3.0.0.v201112011016 in the shaded jar.
[INFO] Including org.apache.commons:commons-lang3:jar:3.3.2 in the shaded jar.
[INFO] Including org.apache.commons:commons-math3:jar:3.4.1 in the shaded jar.
[INFO] Including com.google.code.findbugs:jsr305:jar:1.3.9 in the shaded jar.
[INFO] Including org.slf4j:slf4j-api:jar:1.7.10 in the shaded jar.
[INFO] Including org.slf4j:jul-to-slf4j:jar:1.7.10 in the shaded jar.
[INFO] Including org.slf4j:jcl-over-slf4j:jar:1.7.10 in the shaded jar.
[INFO] Including log4j:log4j:jar:1.2.17 in the shaded jar.
[INFO] Including org.slf4j:slf4j-log4j12:jar:1.7.10 in the shaded jar.
[INFO] Including com.ning:compress-lzf:jar:1.0.3 in the shaded jar.
[INFO] Including org.xerial.snappy:snappy-java:jar:1.1.1.7 in the shaded jar.
[INFO] Including net.jpountz.lz4:lz4:jar:1.3.0 in the shaded jar.
[INFO] Including org.roaringbitmap:RoaringBitmap:jar:0.4.5 in the shaded jar.
[INFO] Including commons-net:commons-net:jar:2.2 in the shaded jar.
[INFO] Including com.typesafe.akka:akka-remote_2.10:jar:2.3.11 in the shaded jar.
[INFO] Including com.typesafe.akka:akka-actor_2.10:jar:2.3.11 in the shaded jar.
[INFO] Including com.typesafe:config:jar:1.2.1 in the shaded jar.
[INFO] Including org.uncommons.maths:uncommons-maths:jar:1.2.2a in the shaded jar.
[INFO] Including com.typesafe.akka:akka-slf4j_2.10:jar:2.3.11 in the shaded jar.
[INFO] Including org.json4s:json4s-jackson_2.10:jar:3.2.10 in the shaded jar.
[INFO] Including org.json4s:json4s-core_2.10:jar:3.2.10 in the shaded jar.
[INFO] Including org.json4s:json4s-ast_2.10:jar:3.2.10 in the shaded jar.
[INFO] Including org.scala-lang:scalap:jar:2.10.0 in the shaded jar.
[INFO] Including org.scala-lang:scala-compiler:jar:2.10.0 in the shaded jar.
[INFO] Including com.sun.jersey:jersey-server:jar:1.9 in the shaded jar.
[INFO] Including asm:asm:jar:3.1 in the shaded jar.
[INFO] Including com.sun.jersey:jersey-core:jar:1.9 in the shaded jar.
[INFO] Including org.apache.mesos:mesos:jar:shaded-protobuf:0.21.1 in the shaded jar.
[INFO] Including io.netty:netty-all:jar:4.0.29.Final in the shaded jar.
[INFO] Including com.clearspring.analytics:stream:jar:2.7.0 in the shaded jar.
[INFO] Including io.dropwizard.metrics:metrics-core:jar:3.1.2 in the shaded jar.
[INFO] Including io.dropwizard.metrics:metrics-jvm:jar:3.1.2 in the shaded jar.
[INFO] Including io.dropwizard.metrics:metrics-json:jar:3.1.2 in the shaded jar.
[INFO] Including io.dropwizard.metrics:metrics-graphite:jar:3.1.2 in the shaded jar.
[INFO] Including com.fasterxml.jackson.core:jackson-databind:jar:2.4.4 in the shaded jar.
[INFO] Including com.fasterxml.jackson.core:jackson-annotations:jar:2.4.0 in the shaded jar.
[INFO] Including com.fasterxml.jackson.core:jackson-core:jar:2.4.4 in the shaded jar.
[INFO] Including com.fasterxml.jackson.module:jackson-module-scala_2.10:jar:2.4.4 in the shaded jar.
[INFO] Including org.scala-lang:scala-reflect:jar:2.10.4 in the shaded jar.
[INFO] Including org.apache.ivy:ivy:jar:2.4.0 in the shaded jar.
[INFO] Including oro:oro:jar:2.0.8 in the shaded jar.
[INFO] Including org.tachyonproject:tachyon-client:jar:0.7.1 in the shaded jar.
[INFO] Including org.apache.curator:curator-client:jar:2.1.0-incubating in the shaded jar.
[INFO] Including org.tachyonproject:tachyon-underfs-hdfs:jar:0.7.1 in the shaded jar.
[INFO] Including org.tachyonproject:tachyon-underfs-local:jar:0.7.1 in the shaded jar.
[INFO] Including net.razorvine:pyrolite:jar:4.4 in the shaded jar.
[INFO] Including net.sf.py4j:py4j:jar:0.8.2.1 in the shaded jar.
[INFO] Including org.spark-project.spark:unused:jar:1.0.0 in the shaded jar.
[INFO] Including org.apache.avro:avro:jar:1.7.6 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.tukaani:xz:jar:1.0 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-column:jar:1.8.1 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-common:jar:1.8.1 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-encoding:jar:1.8.1 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-hadoop:jar:1.8.1 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-jackson: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 it.unimi.dsi:fastutil:jar:6.5.7 in the shaded jar.
[INFO] Including com.twitter:parquet-avro:jar:1.6.0 in the shaded jar.
[INFO] Including com.twitter:parquet-column:jar:1.6.0 in the shaded jar.
[INFO] Including com.twitter:parquet-common:jar:1.6.0 in the shaded jar.
[INFO] Including com.twitter:parquet-encoding:jar:1.6.0 in the shaded jar.
[INFO] Including com.twitter:parquet-generator:jar:1.6.0 in the shaded jar.
[INFO] Including com.twitter:parquet-hadoop:jar:1.6.0 in the shaded jar.
[INFO] Including com.twitter:parquet-jackson:jar:1.6.0 in the shaded jar.
[INFO] Including com.twitter:parquet-format:jar:2.2.0-rc1 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-scala_2.10:jar:1.8.1 in the shaded jar.
[INFO] Including org.bdgenomics.bdg-formats:bdg-formats:jar:0.6.1 in the shaded jar.
[INFO] Including org.bdgenomics.adam:adam-core_2.10:jar:0.18.0 in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-metrics_2.10:jar:0.2.3 in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-misc_2.10:jar:0.2.3 in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-io_2.10:jar:0.2.3 in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-cli_2.10:jar:0.2.3 in the shaded jar.
[INFO] Including args4j:args4j:jar:2.0.23 in the shaded jar.
[INFO] Including com.esotericsoftware.kryo:kryo:jar:2.21 in the shaded jar.
[INFO] Including com.esotericsoftware.reflectasm:reflectasm:jar:shaded:1.07 in the shaded jar.
[INFO] Including org.ow2.asm:asm:jar:4.0 in the shaded jar.
[INFO] Including com.esotericsoftware.minlog:minlog:jar:1.2 in the shaded jar.
[INFO] Including org.objenesis:objenesis:jar:1.2 in the shaded jar.
[INFO] Including org.scoverage:scalac-scoverage-plugin_2.10:jar:1.1.1 in the shaded jar.
[INFO] Including commons-io:commons-io:jar:1.3.2 in the shaded jar.
[INFO] Including org.seqdoop:hadoop-bam:jar:7.0.0 in the shaded jar.
[INFO] Including com.github.samtools:htsjdk:jar:1.133 in the shaded jar.
[INFO] Including org.apache.httpcomponents:httpclient:jar:4.3.2 in the shaded jar.
[INFO] Including org.apache.httpcomponents:httpcore:jar:4.3.1 in the shaded jar.
[INFO] Including com.netflix.servo:servo-core:jar:0.5.5 in the shaded jar.
[INFO] Including com.google.code.findbugs:annotations:jar:2.0.0 in the shaded jar.
[INFO] Including com.google.guava:guava:jar:14.0.1 in the shaded jar.
[INFO] Including org.seqdoop:htsjdk:jar:1.118 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.bcel:bcel:jar:5.2 in the shaded jar.
[INFO] Including jakarta-regexp:jakarta-regexp:jar:1.4 in the shaded jar.
[INFO] Including org.seqdoop:cofoja:jar:1.1-r150 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.testng:testng:jar:6.8.8 in the shaded jar.
[INFO] Including org.beanshell:bsh:jar:2.0b4 in the shaded jar.
[INFO] Including com.beust:jcommander:jar:1.27 in the shaded jar.
[WARNING] commons-beanutils-1.7.0.jar, commons-beanutils-core-1.8.0.jar, commons-collections-3.2.1.jar define 10 overlapping classes: 
[WARNING]   - org.apache.commons.collections.FastHashMap$EntrySet
[WARNING]   - org.apache.commons.collections.ArrayStack
[WARNING]   - org.apache.commons.collections.FastHashMap$1
[WARNING]   - org.apache.commons.collections.FastHashMap$KeySet
[WARNING]   - org.apache.commons.collections.FastHashMap$CollectionView
[WARNING]   - org.apache.commons.collections.BufferUnderflowException
[WARNING]   - org.apache.commons.collections.Buffer
[WARNING]   - org.apache.commons.collections.FastHashMap$CollectionView$CollectionViewIterator
[WARNING]   - org.apache.commons.collections.FastHashMap$Values
[WARNING]   - org.apache.commons.collections.FastHashMap
[WARNING] minlog-1.2.jar, kryo-2.21.jar define 2 overlapping classes: 
[WARNING]   - com.esotericsoftware.minlog.Log$Logger
[WARNING]   - com.esotericsoftware.minlog.Log
[WARNING] asm-4.0.jar, cofoja-1.1-r150.jar define 1 overlapping classes: 
[WARNING]   - org.objectweb.asm.Handle
[WARNING] objenesis-1.2.jar, kryo-2.21.jar define 32 overlapping classes: 
[WARNING]   - org.objenesis.Objenesis
[WARNING]   - org.objenesis.strategy.StdInstantiatorStrategy
[WARNING]   - org.objenesis.instantiator.basic.ObjectStreamClassInstantiator
[WARNING]   - org.objenesis.instantiator.sun.SunReflectionFactorySerializationInstantiator
[WARNING]   - org.objenesis.instantiator.perc.PercSerializationInstantiator
[WARNING]   - org.objenesis.instantiator.NullInstantiator
[WARNING]   - org.objenesis.instantiator.jrockit.JRockitLegacyInstantiator
[WARNING]   - org.objenesis.instantiator.gcj.GCJInstantiatorBase
[WARNING]   - org.objenesis.ObjenesisException
[WARNING]   - org.objenesis.instantiator.basic.ObjectInputStreamInstantiator$MockStream
[WARNING]   - 22 more...
[WARNING] htsjdk-1.133.jar, htsjdk-1.118.jar define 644 overlapping classes: 
[WARNING]   - htsjdk.samtools.Bin
[WARNING]   - htsjdk.samtools.util.ftp.FTPStream
[WARNING]   - htsjdk.variant.variantcontext.VariantJEXLContext$11
[WARNING]   - htsjdk.tribble.example.ProfileIndexReading
[WARNING]   - htsjdk.tribble.index.tabix.TabixIndexCreator$TabixFeature
[WARNING]   - htsjdk.samtools.SAMFileHeader
[WARNING]   - htsjdk.samtools.util.CoordMath
[WARNING]   - htsjdk.samtools.CoordinateSortedPairInfoMap$1
[WARNING]   - htsjdk.tribble.readers.TabixReader$TIndex
[WARNING]   - htsjdk.samtools.util.Tuple
[WARNING]   - 634 more...
[WARNING] reflectasm-1.07-shaded.jar, kryo-2.21.jar define 23 overlapping classes: 
[WARNING]   - com.esotericsoftware.reflectasm.shaded.org.objectweb.asm.Opcodes
[WARNING]   - com.esotericsoftware.reflectasm.shaded.org.objectweb.asm.Frame
[WARNING]   - com.esotericsoftware.reflectasm.shaded.org.objectweb.asm.Label
[WARNING]   - com.esotericsoftware.reflectasm.shaded.org.objectweb.asm.FieldWriter
[WARNING]   - com.esotericsoftware.reflectasm.shaded.org.objectweb.asm.AnnotationVisitor
[WARNING]   - com.esotericsoftware.reflectasm.shaded.org.objectweb.asm.FieldVisitor
[WARNING]   - com.esotericsoftware.reflectasm.shaded.org.objectweb.asm.Item
[WARNING]   - com.esotericsoftware.reflectasm.AccessClassLoader
[WARNING]   - com.esotericsoftware.reflectasm.shaded.org.objectweb.asm.Edge
[WARNING]   - com.esotericsoftware.reflectasm.shaded.org.objectweb.asm.ClassVisitor
[WARNING]   - 13 more...
[WARNING] parquet-format-2.3.0-incubating.jar, parquet-format-2.2.0-rc1.jar define 151 overlapping classes: 
[WARNING]   - parquet.org.apache.thrift.protocol.TCompactProtocol$Types
[WARNING]   - parquet.org.slf4j.helpers.BasicMarkerFactory
[WARNING]   - parquet.org.apache.thrift.TSerializer
[WARNING]   - parquet.org.apache.thrift.protocol.TJSONProtocol
[WARNING]   - parquet.org.apache.thrift.protocol.TProtocolException
[WARNING]   - parquet.org.apache.thrift.transport.TSaslTransport$NegotiationStatus
[WARNING]   - parquet.org.apache.thrift.transport.TSeekableFile
[WARNING]   - parquet.org.apache.thrift.TServiceClientFactory
[WARNING]   - parquet.org.apache.thrift.transport.THttpClient
[WARNING]   - parquet.org.slf4j.ILoggerFactory
[WARNING]   - 141 more...
[WARNING] hadoop-yarn-api-2.5.2.jar, hadoop-yarn-common-2.5.2.jar define 3 overlapping classes: 
[WARNING]   - org.apache.hadoop.yarn.factories.package-info
[WARNING]   - org.apache.hadoop.yarn.util.package-info
[WARNING]   - org.apache.hadoop.yarn.factory.providers.package-info
[WARNING] commons-logging-1.1.1.jar, jcl-over-slf4j-1.7.10.jar define 6 overlapping classes: 
[WARNING]   - org.apache.commons.logging.impl.NoOpLog
[WARNING]   - org.apache.commons.logging.impl.SimpleLog
[WARNING]   - org.apache.commons.logging.LogFactory
[WARNING]   - org.apache.commons.logging.LogConfigurationException
[WARNING]   - org.apache.commons.logging.impl.SimpleLog$1
[WARNING]   - org.apache.commons.logging.Log
[WARNING] commons-beanutils-1.7.0.jar, commons-beanutils-core-1.8.0.jar define 82 overlapping classes: 
[WARNING]   - org.apache.commons.beanutils.WrapDynaBean
[WARNING]   - org.apache.commons.beanutils.Converter
[WARNING]   - org.apache.commons.beanutils.converters.IntegerConverter
[WARNING]   - org.apache.commons.beanutils.locale.LocaleBeanUtilsBean
[WARNING]   - org.apache.commons.beanutils.locale.converters.DecimalLocaleConverter
[WARNING]   - org.apache.commons.beanutils.locale.converters.DoubleLocaleConverter
[WARNING]   - org.apache.commons.beanutils.converters.ShortConverter
[WARNING]   - org.apache.commons.beanutils.converters.StringArrayConverter
[WARNING]   - org.apache.commons.beanutils.locale.LocaleConvertUtilsBean
[WARNING]   - org.apache.commons.beanutils.LazyDynaClass
[WARNING]   - 72 more...
[WARNING] annotations-2.0.0.jar, jsr305-1.3.9.jar define 34 overlapping classes: 
[WARNING]   - javax.annotation.Nonnegative
[WARNING]   - javax.annotation.CheckForSigned
[WARNING]   - javax.annotation.CheckForNull
[WARNING]   - javax.annotation.Tainted
[WARNING]   - javax.annotation.meta.TypeQualifierValidator
[WARNING]   - javax.annotation.meta.TypeQualifier
[WARNING]   - javax.annotation.Syntax
[WARNING]   - javax.annotation.Detainted
[WARNING]   - javax.annotation.Nonnull$Checker
[WARNING]   - javax.annotation.meta.TypeQualifierNickname
[WARNING]   - 24 more...
[WARNING] spark-unsafe_2.10-1.5.1.jar, spark-launcher_2.10-1.5.1.jar, unused-1.0.0.jar, spark-network-shuffle_2.10-1.5.1.jar, spark-core_2.10-1.5.1.jar, spark-network-common_2.10-1.5.1.jar define 1 overlapping classes: 
[WARNING]   - org.apache.spark.unused.UnusedStubClass
[WARNING] asm-4.0.jar, cofoja-1.1-r150.jar, asm-3.1.jar define 21 overlapping classes: 
[WARNING]   - org.objectweb.asm.Item
[WARNING]   - org.objectweb.asm.signature.SignatureWriter
[WARNING]   - org.objectweb.asm.MethodWriter
[WARNING]   - org.objectweb.asm.Type
[WARNING]   - org.objectweb.asm.Opcodes
[WARNING]   - org.objectweb.asm.Handler
[WARNING]   - org.objectweb.asm.MethodVisitor
[WARNING]   - org.objectweb.asm.Label
[WARNING]   - org.objectweb.asm.FieldWriter
[WARNING]   - org.objectweb.asm.signature.SignatureVisitor
[WARNING]   - 11 more...
[WARNING] guava-14.0.1.jar, spark-network-common_2.10-1.5.1.jar define 7 overlapping classes: 
[WARNING]   - com.google.common.base.Optional$1$1
[WARNING]   - com.google.common.base.Supplier
[WARNING]   - com.google.common.base.Function
[WARNING]   - com.google.common.base.Optional
[WARNING]   - com.google.common.base.Optional$1
[WARNING]   - com.google.common.base.Absent
[WARNING]   - com.google.common.base.Present
[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] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 35:49 min
[INFO] Finished at: 2016-06-01T23:41:50+08:00
[INFO] Final Memory: 62M/375M
[INFO] ------------------------------------------------------------------------