基因数据处理72之GATK安装成功
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1.下载：
git clone https://github.com/broadgsa/gatk-protected.git2.安装：
git checkout 3.5mvn clean package -DskipTests3.安装成功：
[INFO] Reactor Summary:[INFO] [INFO] GATK Root .......................................... SUCCESS [ 0.590 s][INFO] GATK Aggregator .................................... SUCCESS [ 0.502 s][INFO] GATK GSALib ........................................ SUCCESS [ 0.863 s][INFO] GATK Utils ......................................... SUCCESS [ 32.395 s][INFO] GATK Engine ........................................ SUCCESS [ 9.264 s][INFO] GATK Tools Public .................................. SUCCESS [ 23.222 s][INFO] External Example ................................... SUCCESS [ 12.317 s][INFO] GATK Queue ......................................... SUCCESS [11:32 min][INFO] GATK Queue Extensions Generator .................... SUCCESS [ 0.128 s][INFO] GATK Queue Extensions Public ....................... SUCCESS [02:07 min][INFO] GATK Aggregator Public ............................. SUCCESS [ 0.003 s][INFO] GATK Tools Protected ............................... SUCCESS [ 32.863 s][INFO] GATK Package Distribution .......................... SUCCESS [01:08 min][INFO] GATK Queue Extensions Distribution ................. SUCCESS [01:34 min][INFO] GATK Queue Package Distribution .................... SUCCESS [02:37 min][INFO] GATK Aggregator Protected .......................... SUCCESS [ 0.005 s][INFO] ------------------------------------------------------------------------[INFO] BUILD SUCCESS[INFO] ------------------------------------------------------------------------参考：
【1】https://github.com/broadgsa/gatk-protected
【2】https://www.broadinstitute.org/gatk/download/
记录：（1）Master：
[WARNING] - org.apache.commons.httpclient.auth.AuthScope[WARNING] - org.apache.commons.httpclient.cookie.RFC2965Spec$CookieCommentUrlAttributeHandler[WARNING] - org.apache.commons.httpclient.HttpClientError[WARNING] - 157 more...[WARNING] gatk-package-distribution-3.5.jar, gatk-engine-3.5.jar define 305 overlappping classes: [WARNING] - org.broadinstitute.gatk.engine.iterators.BoundedReadIterator[WARNING] - org.broadinstitute.gatk.engine.filters.ReadNameFilter[WARNING] - org.broadinstitute.gatk.engine.datasources.providers.LocusReferenceView[WARNING] - org.broadinstitute.gatk.engine.alignment.reference.packing.BasePackedInputStream[WARNING] - org.broadinstitute.gatk.engine.io.NWaySAMFileWriter[WARNING] - org.broadinstitute.gatk.engine.filters.MissingReadGroupFilter[WARNING] - org.broadinstitute.gatk.engine.alignment.reference.bwt.SuffixArray$SuffixArrayComparator[WARNING] - org.broadinstitute.gatk.engine.filters.BadMateFilter[WARNING] - org.broadinstitute.gatk.engine.walkers.Allows[WARNING] - org.broadinstitute.gatk.engine.traversals.TraverseReadPairs[WARNING] - 295 more...[WARNING] gatk-tools-public-3.5.jar, gatk-package-distribution-3.5.jar define 228 overlappping classes: [WARNING] - org.broadinstitute.gatk.tools.walkers.variantutils.ConcordanceMetrics$SiteConcordanceType[WARNING] - org.broadinstitute.gatk.tools.walkers.variantutils.VariantsToTable$7[WARNING] - org.broadinstitute.gatk.tools.walkers.varianteval.evaluators.VariantSummary[WARNING] - org.broadinstitute.gatk.tools.walkers.varianteval.evaluators.MultiallelicSummary[WARNING] - org.broadinstitute.gatk.tools.walkers.annotator.interfaces.AnnotationInterfaceManager[WARNING] - org.broadinstitute.gatk.tools.walkers.variantutils.VariantsToTable[WARNING] - org.broadinstitute.gatk.tools.walkers.readutils.ClipReads[WARNING] - org.broadinstitute.gatk.tools.walkers.variantutils.VariantsToTable$1[WARNING] - org.broadinstitute.gatk.tools.walkers.variantutils.ValidateVariants$ValidationType[WARNING] - org.broadinstitute.gatk.tools.walkers.annotator.SnpEffUtil[WARNING] - 218 more...[WARNING] commons-logging-1.1.1.jar, gatk-package-distribution-3.5.jar define 28 overlappping classes: [WARNING] - org.apache.commons.logging.impl.LogFactoryImpl$2[WARNING] - org.apache.commons.logging.impl.LogFactoryImpl[WARNING] - org.apache.commons.logging.LogFactory$3[WARNING] - org.apache.commons.logging.impl.WeakHashtable$1[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.impl.AvalonLogger[WARNING] - org.apache.commons.logging.LogConfigurationException[WARNING] - 18 more...[WARNING] maven-shade-plugin has detected that some .class files[WARNING] are present in two or more JARs. When this happens, only[WARNING] one single version of the class is copied in the uberjar.[WARNING] Usually this is not harmful and you can skeep these[WARNING] warnings, otherwise try to manually exclude artifacts[WARNING] based on mvn dependency:tree -Ddetail=true and the above[WARNING] output[WARNING] See http://docs.codehaus.org/display/MAVENUSER/Shade+Plugin[INFO] Minimized 28439 -> 10985 (38%)[INFO] Replacing original artifact with shaded artifact.[INFO] Replacing /home/hadoop/xubo/tools/gatk-protected/protected/gatk-package-distribution/target/gatk-package-distribution-3.5.jar with /home/hadoop/xubo/tools/gatk-protected/protected/gatk-package-distribution/target/gatk-package-distribution-3.5-shaded.jar[INFO] [INFO] --- maven-assembly-plugin:2.4:single (binary-dist) @ gatk-package-distribution ---[INFO] Reading assembly descriptor: /home/hadoop/xubo/tools/gatk-protected/protected/gatk-package-distribution/../../public/src/main/assembly/binary-dist.xml[WARNING] Invalid POM for com.google.code.cofoja:cofoja:jar:1.2-20140817, transitive dependencies (if any) will not be available, enable debug logging for more details[INFO] Building tar: /home/hadoop/xubo/tools/gatk-protected/protected/gatk-package-distribution/target/gatk-package-distribution-3.5-binary-dist.tar.bz2[INFO] [INFO] --- maven-junction-plugin:1.0.3:link (link-executable-jar) @ gatk-package-distribution ---Downloading: https://repo.maven.apache.org/maven2/commons-io/commons-io/1.2/commons-io-1.2.pomDownloaded: https://repo.maven.apache.org/maven2/commons-io/commons-io/1.2/commons-io-1.2.pom (7 KB at 16.8 KB/sec)Downloading: https://repo.maven.apache.org/maven2/commons-io/commons-io/1.2/commons-io-1.2.jarDownloading: https://repo.maven.apache.org/maven2/org/apache/maven/maven-artifact/2.0/maven-artifact-2.0.jarDownloaded: https://repo.maven.apache.org/maven2/commons-io/commons-io/1.2/commons-io-1.2.jar (65 KB at 29.7 KB/sec)Downloaded: https://repo.maven.apache.org/maven2/org/apache/maven/maven-artifact/2.0/maven-artifact-2.0.jar (77 KB at 15.4 KB/sec)[INFO] [INFO] --- maven-junction-plugin:1.0.3:link (link-package-jar) @ gatk-package-distribution ---[INFO] [INFO] --- maven-junction-plugin:1.0.3:link (link-git-release) @ gatk-package-distribution ---[INFO] [INFO] ------------------------------------------------------------------------[INFO] Building GATK Queue Extensions Distribution 3.5[INFO] ------------------------------------------------------------------------[INFO] [INFO] --- maven-clean-plugin:2.5:clean (default-clean) @ gatk-queue-extensions-distribution ---[INFO] Deleting /home/hadoop/xubo/tools/gatk-protected/protected/gatk-queue-extensions-distribution (includes = [javadoc.sh, options, packages], excludes = [])[INFO] Deleting /home/hadoop/xubo/tools/gatk-protected/protected/gatk-queue-extensions-distribution (includes = [dependency-reduced-pom.xml], excludes = [])[INFO] [INFO] --- gitdescribe-maven-plugin:2.0:gitdescribe (gitdescribe-initialize) @ gatk-queue-extensions-distribution ---[INFO] [INFO] --- build-helper-maven-plugin:1.8:regex-property (fix-version-initialize) @ gatk-queue-extensions-distribution ---[INFO] [INFO] --- build-helper-maven-plugin:1.8:add-source (add-gatk-extensions) @ gatk-queue-extensions-distribution ---[INFO] Source directory: /home/hadoop/xubo/tools/gatk-protected/protected/gatk-queue-extensions-distribution/../../public/gatk-queue-extensions-public/src/main/scala added.[INFO] Source directory: /home/hadoop/xubo/tools/gatk-protected/protected/gatk-queue-extensions-distribution/target/generated-sources/gatk-extensions added.[INFO] [INFO] --- exec-maven-plugin:1.2.1:exec (generate-gatk-extensions) @ gatk-queue-extensions-distribution ---[INFO] [INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ gatk-queue-extensions-distribution ---[INFO] Using 'UTF-8' encoding to copy filtered resources.[INFO] skip non existing resourceDirectory /home/hadoop/xubo/tools/gatk-protected/protected/gatk-queue-extensions-distribution/src/main/resources[INFO] [INFO] --- maven-scala-plugin:2.15.2:compile (default) @ gatk-queue-extensions-distribution ---[INFO] Checking for multiple versions of scala[WARNING] Invalid POM for com.google.code.cofoja:cofoja:jar:1.2-20140817, transitive dependencies (if any) will not be available, enable debug logging for more details[WARNING] Invalid POM for com.google.code.cofoja:cofoja:jar:1.2-20140817, transitive dependencies (if any) will not be available, enable debug logging for more details[INFO] includes = [**/*.scala,**/*.java,][INFO] excludes = [][INFO] /home/hadoop/xubo/tools/gatk-protected/public/gatk-queue-extensions-public/src/main/scala:-1: info: compiling[INFO] /home/hadoop/xubo/tools/gatk-protected/protected/gatk-queue-extensions-distribution/target/generated-sources/gatk-extensions:-1: info: compiling[INFO] Compiling 148 source files to /home/hadoop/xubo/tools/gatk-protected/protected/gatk-queue-extensions-distribution/target/classes at 1465303337200[INFO] prepare-compile in 0 s[INFO] compile in 79 s[INFO] [INFO] --- maven-compiler-plugin:3.1:compile (compile-package-info) @ gatk-queue-extensions-distribution ---[INFO] Nothing to compile - all classes are up to date[INFO] [INFO] --- maven-compiler-plugin:3.1:compile (compile-java) @ gatk-queue-extensions-distribution ---[INFO] Nothing to compile - all classes are up to date[INFO] [INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ gatk-queue-extensions-distribution ---[INFO] Using 'UTF-8' encoding to copy filtered resources.[INFO] skip non existing resourceDirectory /home/hadoop/xubo/tools/gatk-protected/protected/gatk-queue-extensions-distribution/src/test/resources[INFO] [INFO] --- maven-scala-plugin:2.15.2:testCompile (default) @ gatk-queue-extensions-distribution ---[INFO] Checking for multiple versions of scala[INFO] includes = [**/*.scala,**/*.java,][INFO] excludes = [][INFO] /home/hadoop/xubo/tools/gatk-protected/protected/gatk-queue-extensions-distribution/src/test/scala:-1: info: compiling[INFO] Compiling 2 source files to /home/hadoop/xubo/tools/gatk-protected/protected/gatk-queue-extensions-distribution/target/test-classes at 1465303417190[INFO] prepare-compile in 0 s[INFO] compile in 6 s[INFO] [INFO] --- maven-compiler-plugin:3.1:testCompile (testCompile-java) @ gatk-queue-extensions-distribution ---[INFO] No sources to compile[INFO] [INFO] --- maven-surefire-plugin:2.16:test (unit-tests) @ gatk-queue-extensions-distribution ---[INFO] Tests are skipped.[INFO] [INFO] --- maven-jar-plugin:2.4:jar (default-jar) @ gatk-queue-extensions-distribution ---[INFO] Building jar: /home/hadoop/xubo/tools/gatk-protected/protected/gatk-queue-extensions-distribution/target/gatk-queue-extensions-distribution-3.5.jar[INFO] [INFO] --- maven-jar-plugin:2.4:test-jar (test-jar) @ gatk-queue-extensions-distribution ---[INFO] Building jar: /home/hadoop/xubo/tools/gatk-protected/protected/gatk-queue-extensions-distribution/target/gatk-queue-extensions-distribution-3.5-tests.jar[INFO] [INFO] ------------------------------------------------------------------------[INFO] Building GATK Queue Package Distribution 3.5[INFO] ------------------------------------------------------------------------Downloading: file:/home/hadoop/xubo/tools/gatk-protected/protected/gatk-queue-package-distribution/../../public/repo/net/sf/snpeff/snpeff/2.0.5/snpeff-2.0.5.pom[WARNING] Could not validate integrity of download from file:/home/hadoop/xubo/tools/gatk-protected/protected/gatk-queue-package-distribution/../../public/repo/net/sf/snpeff/snpeff/2.0.5/snpeff-2.0.5.pom: Checksum validation failed, no checksums available[WARNING] Checksum validation failed, no checksums available for file:/home/hadoop/xubo/tools/gatk-protected/protected/gatk-queue-package-distribution/../../public/repo/net/sf/snpeff/snpeff/2.0.5/snpeff-2.0.5.pomDownloaded: file:/home/hadoop/xubo/tools/gatk-protected/protected/gatk-queue-package-distribution/../../public/repo/net/sf/snpeff/snpeff/2.0.5/snpeff-2.0.5.pom (363 B at 354.5 KB/sec)Downloading: file:/home/hadoop/xubo/tools/gatk-protected/protected/gatk-queue-package-distribution/../../public/repo/net/sf/snpeff/snpeff/2.0.5/snpeff-2.0.5.jar[WARNING] Could not validate integrity of download from file:/home/hadoop/xubo/tools/gatk-protected/protected/gatk-queue-package-distribution/../../public/repo/net/sf/snpeff/snpeff/2.0.5/snpeff-2.0.5.jar: Checksum validation failed, no checksums available[WARNING] Checksum validation failed, no checksums available for file:/home/hadoop/xubo/tools/gatk-protected/protected/gatk-queue-package-distribution/../../public/repo/net/sf/snpeff/snpeff/2.0.5/snpeff-2.0.5.jarDownloaded: file:/home/hadoop/xubo/tools/gatk-protected/protected/gatk-queue-package-distribution/../../public/repo/net/sf/snpeff/snpeff/2.0.5/snpeff-2.0.5.jar (4081 KB at 54405.5 KB/sec)[INFO] [INFO] --- maven-clean-plugin:2.5:clean (default-clean) @ gatk-queue-package-distribution ---[INFO] Deleting /home/hadoop/xubo/tools/gatk-protected/protected/gatk-queue-package-distribution (includes = [javadoc.sh, options, packages], excludes = [])[INFO] Deleting /home/hadoop/xubo/tools/gatk-protected/protected/gatk-queue-package-distribution (includes = [dependency-reduced-pom.xml], excludes = [])[INFO] [INFO] --- gitdescribe-maven-plugin:2.0:gitdescribe (gitdescribe-initialize) @ gatk-queue-package-distribution ---[INFO] [INFO] --- build-helper-maven-plugin:1.8:regex-property (fix-version-initialize) @ gatk-queue-package-distribution ---[INFO] [INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ gatk-queue-package-distribution ---[INFO] Using 'UTF-8' encoding to copy filtered resources.[INFO] skip non existing resourceDirectory /home/hadoop/xubo/tools/gatk-protected/protected/gatk-queue-package-distribution/src/main/resources[INFO] [INFO] --- maven-compiler-plugin:3.1:compile (compile-package-info) @ gatk-queue-package-distribution ---[INFO] No sources to compile[INFO] [INFO] --- maven-compiler-plugin:3.1:compile (compile-java) @ gatk-queue-package-distribution ---[INFO] No sources to compile[INFO] [INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ gatk-queue-package-distribution ---[INFO] Using 'UTF-8' encoding to copy filtered resources.[INFO] skip non existing resourceDirectory /home/hadoop/xubo/tools/gatk-protected/protected/gatk-queue-package-distribution/src/test/resources[INFO] [INFO] --- maven-compiler-plugin:3.1:testCompile (testCompile-java) @ gatk-queue-package-distribution ---[INFO] No sources to compile[INFO] [INFO] --- maven-surefire-plugin:2.16:test (unit-tests) @ gatk-queue-package-distribution ---[INFO] Tests are skipped.[INFO] [INFO] --- maven-dependency-plugin:2.8:unpack-dependencies (unpack-direct-dependencies) @ gatk-queue-package-distribution ---[INFO] Unpacking /home/hadoop/.m2/repository/org/scala-lang/scala-compiler/2.10.2/scala-compiler-2.10.2.jar to /home/hadoop/xubo/tools/gatk-protected/protected/gatk-queue-package-distribution/target/classes with includes "" and excludes "GATKText.properties"[INFO] Unpacking /home/hadoop/.m2/repository/net/java/dev/jna/jna/3.2.7/jna-3.2.7.jar to /home/hadoop/xubo/tools/gatk-protected/protected/gatk-queue-package-distribution/target/classes with includes "" and excludes "GATKText.properties"[INFO] Unpacking /home/hadoop/.m2/repository/com/google/code/cofoja/cofoja/1.2-20140817/cofoja-1.2-20140817.jar to /home/hadoop/xubo/tools/gatk-protected/protected/gatk-queue-package-distribution/target/classes with includes "" and excludes "GATKText.properties"[INFO] Unpacking /home/hadoop/xubo/tools/gatk-protected/protected/gatk-queue-extensions-distribution/target/gatk-queue-extensions-distribution-3.5.jar to /home/hadoop/xubo/tools/gatk-protected/protected/gatk-queue-package-distribution/target/classes with includes "" and excludes "GATKText.properties"[INFO] Unpacking /home/hadoop/.m2/repository/commons-httpclient/commons-httpclient/3.1/commons-httpclient-3.1.jar to /home/hadoop/xubo/tools/gatk-protected/protected/gatk-queue-package-distribution/target/classes with includes "" and excludes "GATKText.properties"[INFO] Unpacking /home/hadoop/xubo/tools/gatk-protected/protected/gatk-package-distribution/target/gatk-package-distribution-3.5.jar to /home/hadoop/xubo/tools/gatk-protected/protected/gatk-queue-package-distribution/target/classes with includes "" and excludes "GATKText.properties"[INFO] Unpacking /home/hadoop/.m2/repository/com/github/broadinstitute/picard/1.141/picard-1.141.jar to /home/hadoop/xubo/tools/gatk-protected/protected/gatk-queue-package-distribution/target/classes with includes "" and excludes "GATKText.properties"[INFO] Unpacking /home/hadoop/.m2/repository/net/sf/snpeff/snpeff/2.0.5/snpeff-2.0.5.jar to /home/hadoop/xubo/tools/gatk-protected/protected/gatk-queue-package-distribution/target/classes with includes "" and excludes "GATKText.properties"[INFO] Unpacking /home/hadoop/.m2/repository/org/scala-lang/scala-library/2.10.2/scala-library-2.10.2.jar to /home/hadoop/xubo/tools/gatk-protected/protected/gatk-queue-package-distribution/target/classes with includes "" and excludes "GATKText.properties"[INFO] Unpacking /home/hadoop/xubo/tools/gatk-protected/public/gatk-queue/target/gatk-queue-3.5.jar to /home/hadoop/xubo/tools/gatk-protected/protected/gatk-queue-package-distribution/target/classes with includes "" and excludes "GATKText.properties"[INFO] Unpacking /home/hadoop/.m2/repository/javax/mail/mail/1.4.4/mail-1.4.4.jar to /home/hadoop/xubo/tools/gatk-protected/protected/gatk-queue-package-distribution/target/classes with includes "" and excludes "GATKText.properties"[INFO] [INFO] --- maven-jar-plugin:2.4:jar (executable-jar) @ gatk-queue-package-distribution ---[WARNING] JAR will be empty - no content was marked for inclusion![INFO] Building jar: /home/hadoop/xubo/tools/gatk-protected/protected/gatk-queue-package-distribution/../../target/executable/Queue.jar[INFO] [INFO] --- maven-jar-plugin:2.4:jar (unshaded-default-jar) @ gatk-queue-package-distribution ---[INFO] Building jar: /home/hadoop/xubo/tools/gatk-protected/protected/gatk-queue-package-distribution/target/gatk-queue-package-distribution-3.5.jar[INFO] [INFO] --- maven-jar-plugin:2.4:test-jar (test-jar) @ gatk-queue-package-distribution ---[INFO] Skipping packaging of the test-jar[INFO] [INFO] --- maven-dependency-plugin:2.8:copy-dependencies (executable-jar-lib) @ gatk-queue-package-distribution ---[INFO] Copying scala-reflect-2.10.2.jar to /home/hadoop/xubo/tools/gatk-protected/protected/gatk-queue-package-distribution/../../target/executable/lib/scala-reflect-2.10.2.jar[INFO] Copying gatk-queue-extensions-public-3.5-example-resources.tar.bz2 to /home/hadoop/xubo/tools/gatk-protected/protected/gatk-queue-package-distribution/../../target/executable/lib/gatk-queue-extensions-public-3.5-example-resources.tar.bz2[INFO] Copying scala-compiler-2.10.2.jar to /home/hadoop/xubo/tools/gatk-protected/protected/gatk-queue-package-distribution/../../target/executable/lib/scala-compiler-2.10.2.jar[INFO] Copying gatk-queue-extensions-distribution-3.5.jar to /home/hadoop/xubo/tools/gatk-protected/protected/gatk-queue-package-distribution/../../target/executable/lib/gatk-queue-extensions-distribution-3.5.jar[INFO] Copying guava-18.0.jar to /home/hadoop/xubo/tools/gatk-protected/protected/gatk-queue-package-distribution/../../target/executable/lib/guava-18.0.jar[INFO] Copying gatk-package-distribution-3.5.jar to /home/hadoop/xubo/tools/gatk-protected/protected/gatk-queue-package-distribution/../../target/executable/lib/gatk-package-distribution-3.5.jar[INFO] Copying gatk-queue-extensions-generator-3.5.jar to /home/hadoop/xubo/tools/gatk-protected/protected/gatk-queue-package-distribution/../../target/executable/lib/gatk-queue-extensions-generator-3.5.jar[INFO] Copying snpeff-2.0.5.jar to /home/hadoop/xubo/tools/gatk-protected/protected/gatk-queue-package-distribution/../../target/executable/lib/snpeff-2.0.5.jar[INFO] Copying scala-library-2.10.2.jar to /home/hadoop/xubo/tools/gatk-protected/protected/gatk-queue-package-distribution/../../target/executable/lib/scala-library-2.10.2.jar[INFO] Copying gatk-queue-3.5.jar to /home/hadoop/xubo/tools/gatk-protected/protected/gatk-queue-package-distribution/../../target/executable/lib/gatk-queue-3.5.jar[INFO] Copying commons-email-1.2.jar to /home/hadoop/xubo/tools/gatk-protected/protected/gatk-queue-package-distribution/../../target/executable/lib/commons-email-1.2.jar[INFO] httpcore-4.1.jar already exists in destination.[INFO] google-api-client-1.19.0.jar already exists in destination.[INFO] jcommander-1.27.jar already exists in destination.[INFO] stax-api-1.0.1.jar already exists in destination.[INFO] commons-logging-1.1.1.jar already exists in destination.[INFO] gatk-tools-java-1.1.jar already exists in destination.[INFO] concurrent-1.3.4.jar already exists in destination.[INFO] stax-1.2.0.jar already exists in destination.[INFO] ant-1.8.2.jar already exists in destination.[INFO] picard-1.141.jar already exists in destination.[INFO] gson-2.2.2.jar already exists in destination.[INFO] google-oauth-client-java6-1.19.0.jar already exists in destination.[INFO] jgrapht-0.8.3.jar already exists in destination.[INFO] commons-io-2.1.jar already exists in destination.[INFO] jetty-util-6.1.26.jar already exists in destination.[INFO] ant-launcher-1.8.2.jar already exists in destination.[INFO] commons-httpclient-3.1.jar already exists in destination.[INFO] xml-apis-1.0.b2.jar already exists in destination.[INFO] commons-codec-1.2.jar already exists in destination.[INFO] activation-1.1.jar already exists in destination.[INFO] simple-xml-2.0.4.jar already exists in destination.[INFO] commons-lang-2.5.jar already exists in destination.[INFO] drmaa-gridengine-6.2u5.jar already exists in destination.[INFO] reflections-0.9.9-RC1.jar already exists in destination.[INFO] htsjdk-1.141.jar already exists in destination.[INFO] jna-3.2.7.jar already exists in destination.[INFO] colt-1.2.0.jar already exists in destination.[INFO] httpclient-4.1.1.jar already exists in destination.[INFO] xz-1.5.jar already exists in destination.[INFO] google-api-client-java6-1.19.0.jar already exists in destination.[INFO] jets3t-0.8.1.jar already exists in destination.[INFO] cofoja-1.2-20140817.jar already exists in destination.[INFO] google-oauth-client-1.19.0.jar already exists in destination.[INFO] google-oauth-client-jetty-1.19.0.jar already exists in destination.[INFO] jsr305-1.3.9.jar already exists in destination.[INFO] gatk-utils-3.5-example-resources.tar.bz2 already exists in destination.[INFO] gsalib-3.5.tar.gz already exists in destination.[INFO] gatk-utils-3.5.jar already exists in destination.[INFO] mail-1.4.4.jar already exists in destination.[INFO] commons-compress-1.4.1.jar already exists in destination.[INFO] snappy-java-1.0.3-rc3.jar already exists in destination.[INFO] javassist-3.16.1-GA.jar already exists in destination.[INFO] google-http-client-jackson2-1.19.0.jar already exists in destination.[INFO] servlet-api-2.5.jar already exists in destination.[INFO] fastutil-6.5.3.jar already exists in destination.[INFO] commons-collections-3.2.1.jar already exists in destination.[INFO] gatk-engine-3.5.jar already exists in destination.[INFO] freemarker-2.3.18.jar already exists in destination.[INFO] jama-1.0.2.jar already exists in destination.[INFO] commons-math-2.2.jar already exists in destination.[INFO] slf4j-log4j12-1.7.5.jar already exists in destination.[INFO] log4j-1.2.15.jar already exists in destination.[INFO] gov.nist.math.jama-1.1.1.jar already exists in destination.[INFO] gatk-tools-protected-3.5.jar already exists in destination.[INFO] slf4j-api-1.6.1.jar already exists in destination.[INFO] commons-jexl-2.1.1.jar already exists in destination.[INFO] google-genomics-utils-v1beta2-0.19.jar already exists in destination.[INFO] dom4j-1.6.1.jar already exists in destination.[INFO] google-api-services-genomics-v1beta2-rev9-1.19.0.jar already exists in destination.[INFO] jackson-core-2.1.3.jar already exists in destination.[INFO] drmaa-common-1.0.jar already exists in destination.[INFO] google-http-client-1.19.0.jar already exists in destination.[INFO] jetty-6.1.26.jar already exists in destination.[INFO] java-xmlbuilder-0.4.jar already exists in destination.[INFO] gatk-tools-public-3.5.jar already exists in destination.[INFO] [INFO] --- maven-shade-plugin:2.1:shade (package-jar) @ gatk-queue-package-distribution ---[WARNING] Map in class org.apache.maven.plugins.shade.resource.ManifestResourceTransformer declares value type as: class java.util.jar.Attributes but saw: class java.lang.String at runtime[INFO] Including org.broadinstitute.gatk:gatk-queue:jar:3.5 in the shaded jar.[INFO] Including org.broadinstitute.gatk:gatk-utils:jar:3.5 in the shaded jar.[INFO] Including log4j:log4j:jar:1.2.15 in the shaded jar.[INFO] Including net.sf.jgrapht:jgrapht:jar:0.8.3 in the shaded jar.[INFO] Including org.apache.commons:commons-email:jar:1.2 in the shaded jar.[INFO] Including org.broadinstitute.gatk:gatk-package-distribution:jar:3.5 in the shaded jar.[INFO] Including org.broadinstitute.gatk:gatk-engine:jar:3.5 in the shaded jar.[INFO] Including net.java.dev.jets3t:jets3t:jar:0.8.1 in the shaded jar.[INFO] Including com.jamesmurty.utils:java-xmlbuilder:jar:0.4 in the shaded jar.[INFO] Including org.simpleframework:simple-xml:jar:2.0.4 in the shaded jar.[INFO] Including stax:stax-api:jar:1.0.1 in the shaded jar.[INFO] Including stax:stax:jar:1.2.0 in the shaded jar.[INFO] Including org.broadinstitute.gatk:gatk-tools-public:jar:3.5 in the shaded jar.[INFO] Including org.apache.commons:commons-jexl:jar:2.1.1 in the shaded jar.[INFO] Including org.broadinstitute.gatk:gatk-tools-protected:jar:3.5 in the shaded jar.[INFO] Including gov.nist.math:jama:jar:1.0.2 in the shaded jar.[INFO] Including org.slf4j:slf4j-log4j12:jar:1.7.5 in the shaded jar.[INFO] Including com.github.samtools:htsjdk:jar:1.141 in the shaded jar.[INFO] Including org.xerial.snappy:snappy-java:jar:1.0.3-rc3 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:1.5 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 commons-logging:commons-logging:jar:1.1.1 in the shaded jar.[INFO] Including org.broadinstitute.gatk:gatk-queue-extensions-distribution:jar:3.5 in the shaded jar.[INFO] Including org.broadinstitute.gatk:gatk-queue-extensions-generator:jar:3.5 in the shaded jar.[INFO] Including org.scala-lang:scala-library:jar:2.10.2 in the shaded jar.[INFO] Including org.scala-lang:scala-compiler:jar:2.10.2 in the shaded jar.[INFO] Including org.scala-lang:scala-reflect:jar:2.10.2 in the shaded jar.[INFO] Including com.github.broadinstitute:picard:jar:1.141 in the shaded jar.[INFO] Including com.google.cloud.genomics:gatk-tools-java:jar:1.1 in the shaded jar.[INFO] Including com.google.api-client:google-api-client:jar:1.19.0 in the shaded jar.[INFO] Including com.google.oauth-client:google-oauth-client:jar:1.19.0 in the shaded jar.[INFO] Including com.google.oauth-client:google-oauth-client-jetty:jar:1.19.0 in the shaded jar.[INFO] Including com.google.oauth-client:google-oauth-client-java6:jar:1.19.0 in the shaded jar.[INFO] Including com.google.http-client:google-http-client:jar:1.19.0 in the shaded jar.[INFO] Including com.google.http-client:google-http-client-jackson2:jar:1.19.0 in the shaded jar.[INFO] Including com.fasterxml.jackson.core:jackson-core:jar:2.1.3 in the shaded jar.[INFO] Including com.google.apis:google-api-services-genomics:jar:v1beta2-rev9-1.19.0 in the shaded jar.[INFO] Including com.google.cloud.genomics:google-genomics-utils:jar:v1beta2-0.19 in the shaded jar.[INFO] Including com.google.api-client:google-api-client-java6:jar:1.19.0 in the shaded jar.[INFO] Including com.google.guava:guava:jar:18.0 in the shaded jar.[INFO] Including gov.nist.math.jama:gov.nist.math.jama:jar:1.1.1 in the shaded jar.[INFO] Including org.mortbay.jetty:jetty:jar:6.1.26 in the shaded jar.[INFO] Including org.mortbay.jetty:jetty-util:jar:6.1.26 in the shaded jar.[INFO] Including javax.servlet:servlet-api:jar:2.5 in the shaded jar.[INFO] Including javax.mail:mail:jar:1.4.4 in the shaded jar.[INFO] Including javax.activation:activation:jar:1.1 in the shaded jar.[INFO] Including net.java.dev.jna:jna:jar:3.2.7 in the shaded jar.[INFO] Including com.google.code.cofoja:cofoja:jar:1.2-20140817 in the shaded jar.[INFO] Including net.sf.snpeff:snpeff:jar:2.0.5 in the shaded jar.[INFO] Including commons-httpclient:commons-httpclient:jar:3.1 in the shaded jar.[INFO] Including commons-codec:commons-codec:jar:1.2 in the shaded jar.[INFO] Excluding org.broadinstitute.gatk:gatk-utils:tar.bz2:example-resources:3.5 from the shaded jar.[INFO] Including colt:colt:jar:1.2.0 in the shaded jar.[INFO] Including concurrent:concurrent:jar:1.3.4 in the shaded jar.[INFO] Including it.unimi.dsi:fastutil:jar:6.5.3 in the shaded jar.[INFO] Including org.reflections:reflections:jar:0.9.9-RC1 in the shaded jar.[INFO] Including org.javassist:javassist:jar:3.16.1-GA in the shaded jar.[INFO] Including dom4j:dom4j:jar:1.6.1 in the shaded jar.[INFO] Including xml-apis:xml-apis:jar:1.0.b2 in the shaded jar.[INFO] Including org.slf4j:slf4j-api:jar:1.6.1 in the shaded jar.[INFO] Including org.freemarker:freemarker:jar:2.3.18 in the shaded jar.[INFO] Including commons-lang:commons-lang:jar:2.5 in the shaded jar.[INFO] Including commons-io:commons-io:jar:2.1 in the shaded jar.[INFO] Including commons-collections:commons-collections:jar:3.2.1 in the shaded jar.[INFO] Including org.apache.commons:commons-math:jar:2.2 in the shaded jar.[INFO] Including us.levk:drmaa-gridengine:jar:6.2u5 in the shaded jar.[INFO] Including us.levk:drmaa-common:jar:1.0 in the shaded jar.[INFO] Including com.google.code.gson:gson:jar:2.2.2 in the shaded jar.[INFO] Including org.apache.httpcomponents:httpclient:jar:4.1.1 in the shaded jar.[INFO] Including org.apache.httpcomponents:httpcore:jar:4.1 in the shaded jar.[INFO] Excluding org.broadinstitute.gatk:gsalib:tar.gz:3.5 from the shaded jar.[INFO] Excluding org.broadinstitute.gatk:gatk-queue-extensions-public:tar.bz2:example-resources:3.5 from the shaded jar.[INFO] Including com.google.code.findbugs:jsr305:jar:1.3.9 in the shaded jar.[INFO] Including com.beust:jcommander:jar:1.27 in the shaded jar.[INFO] Minimizing jar org.broadinstitute.gatk:gatk-queue-package-distribution:jar:3.5[WARNING] gatk-queue-package-distribution-3.5.jar, gatk-package-distribution-3.5.jar, commons-codec-1.2.jar define 10 overlappping classes: [WARNING] - org.apache.commons.codec.BinaryEncoder[WARNING] - org.apache.commons.codec.BinaryDecoder[WARNING] - org.apache.commons.codec.Encoder[WARNING] - org.apache.commons.codec.binary.Base64[WARNING] - org.apache.commons.codec.Decoder[WARNING] - org.apache.commons.codec.net.URLCodec[WARNING] - org.apache.commons.codec.DecoderException[WARNING] - org.apache.commons.codec.EncoderException[WARNING] - org.apache.commons.codec.StringEncoder[WARNING] - org.apache.commons.codec.StringDecoder[WARNING] dom4j-1.6.1.jar, gatk-queue-package-distribution-3.5.jar, gatk-package-distribution-3.5.jar define 88 overlappping classes: [WARNING] - org.dom4j.io.DispatchHandler[WARNING] - org.dom4j.dtd.ElementDecl[WARNING] - org.dom4j.io.SAXHelper[WARNING] - org.dom4j.Branch[WARNING] - org.dom4j.DocumentException[WARNING] - org.dom4j.tree.ContentListFacade[WARNING] - org.dom4j.tree.ConcurrentReaderHashMap$1[WARNING] - org.dom4j.Visitor[WARNING] - org.dom4j.tree.AbstractDocumentType[WARNING] - org.dom4j.tree.NamespaceCache[WARNING] - 78 more...[WARNING] gatk-queue-package-distribution-3.5.jar, freemarker-2.3.18.jar, snpeff-2.0.5.jar define 172 overlappping classes: [WARNING] - freemarker.ext.xml.JdomNavigator[WARNING] - freemarker.ext.jdom.NodeListModel$NamedNodeOperator[WARNING] - freemarker.ext.xml.DomNavigator[WARNING] - freemarker.core.CommandLine[WARNING] - freemarker.ext.jdom.NodeListModel$QNameOp[WARNING] - freemarker.ext.jsp.FreeMarkerJspFactory[WARNING] - freemarker.ext.xml.Navigator$ParentOp[WARNING] - freemarker.core.RegexBuiltins$RegexMatchModel$2[WARNING] - freemarker.debug.DebuggerClient[WARNING] - freemarker.core.RegexBuiltins$ReplaceMethod[WARNING] - 162 more...[WARNING] gatk-queue-package-distribution-3.5.jar, gatk-package-distribution-3.5.jar, gatk-engine-3.5.jar define 305 overlappping classes: [WARNING] - org.broadinstitute.gatk.engine.iterators.BoundedReadIterator[WARNING] - org.broadinstitute.gatk.engine.filters.ReadNameFilter[WARNING] - org.broadinstitute.gatk.engine.datasources.providers.LocusReferenceView[WARNING] - org.broadinstitute.gatk.engine.alignment.reference.packing.BasePackedInputStream[WARNING] - org.broadinstitute.gatk.engine.io.NWaySAMFileWriter[WARNING] - org.broadinstitute.gatk.engine.filters.MissingReadGroupFilter[WARNING] - org.broadinstitute.gatk.engine.alignment.reference.bwt.SuffixArray$SuffixArrayComparator[WARNING] - org.broadinstitute.gatk.engine.filters.BadMateFilter[WARNING] - org.broadinstitute.gatk.engine.walkers.Allows[WARNING] - org.broadinstitute.gatk.engine.traversals.TraverseReadPairs[WARNING] - 295 more...[WARNING] gatk-queue-package-distribution-3.5.jar, gatk-package-distribution-3.5.jar, jgrapht-0.8.3.jar define 63 overlappping classes: [WARNING] - org.jgrapht.graph.DefaultDirectedGraph[WARNING] - org.jgrapht.traverse.CrossComponentIterator$FlyweightEdgeEvent[WARNING] - org.jgrapht.graph.IntrusiveEdge[WARNING] - org.jgrapht.graph.AbstractBaseGraph[WARNING] - org.jgrapht.alg.CycleDetector$1[WARNING] - org.jgrapht.alg.StrongConnectivityInspector$1[WARNING] - org.jgrapht.graph.Subgraph$BaseGraphListener[WARNING] - org.jgrapht.EdgeFactory[WARNING] - org.jgrapht.event.TraversalListener[WARNING] - org.jgrapht.graph.AbstractBaseGraph$DirectedSpecifics[WARNING] - 53 more...[WARNING] gatk-queue-package-distribution-3.5.jar, gatk-package-distribution-3.5.jar, commons-io-2.1.jar define 32 overlappping classes: [WARNING] - org.apache.commons.io.filefilter.FalseFileFilter[WARNING] - org.apache.commons.io.filefilter.SuffixFileFilter[WARNING] - org.apache.commons.io.filefilter.TrueFileFilter[WARNING] - org.apache.commons.io.input.ClosedInputStream[WARNING] - org.apache.commons.io.filefilter.NotFileFilter[WARNING] - org.apache.commons.io.filefilter.ConditionalFileFilter[WARNING] - org.apache.commons.io.filefilter.IOFileFilter[WARNING] - org.apache.commons.io.filefilter.OrFileFilter[WARNING] - org.apache.commons.io.comparator.LastModifiedFileComparator[WARNING] - org.apache.commons.io.filefilter.PrefixFileFilter[WARNING] - 22 more...[WARNING] gatk-queue-package-distribution-3.5.jar, commons-jexl-2.1.1.jar, gatk-package-distribution-3.5.jar define 158 overlappping 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.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] - org.apache.commons.jexl2.introspection.JexlPropertySet[WARNING] - 148 more...[WARNING] gatk-queue-package-distribution-3.5.jar, scala-compiler-2.10.2.jar define 8560 overlappping classes: [WARNING] - scala.tools.nsc.transform.patmat.MatchTranslation$MatchTranslator$ExtractorCallProd[WARNING] - scala.tools.nsc.ast.DocComments$DocComment$$anonfun$defineVariables$2[WARNING] - ch.epfl.lamp.compiler.msil.emit.ConstructorBuilder[WARNING] - scala.tools.nsc.backend.msil.GenMSIL$BytecodeGenerator$$anonfun$scala$tools$nsc$backend$msil$GenMSIL$BytecodeGenerator$$genMethod$3$$anonfun$apply$5[WARNING] - scala.tools.nsc.transform.Constructors$ConstructorTransformer$$anonfun$8[WARNING] - scala.tools.nsc.backend.msil.GenMSIL$BytecodeGenerator$$anonfun$customModifiers$1[WARNING] - scala.tools.nsc.backend.MSILPlatform$class[WARNING] - scala.tools.nsc.ast.DocComments$$anonfun$expandInternal$1$1$$anonfun$apply$5[WARNING] - scala.tools.nsc.CommonRunner[WARNING] - scala.tools.nsc.interpreter.Power$ReplUtilities$$anonfun$clazz$1[WARNING] - 8550 more...[WARNING] gatk-queue-package-distribution-3.5.jar, gatk-tools-protected-3.5.jar, gatk-package-distribution-3.5.jar define 524 overlappping classes: [WARNING] - org.broadinstitute.gatk.tools.walkers.variantutils.CombineGVCFs$OverallState[WARNING] - org.broadinstitute.gatk.tools.walkers.diagnostics.diagnosetargets.CallableStatus[WARNING] - org.broadinstitute.gatk.tools.walkers.haplotypecaller.PairHMMLikelihoodCalculationEngine$PCR_ERROR_MODEL[WARNING] - org.broadinstitute.gatk.utils.collections.CountSet[WARNING] - org.broadinstitute.gatk.tools.walkers.haplotypecaller.LDMerger$LDMergeData[WARNING] - org.broadinstitute.gatk.utils.variant.TandemRepeatFinder$Result[WARNING] - org.broadinstitute.gatk.tools.walkers.annotator.DepthPerAlleleBySample[WARNING] - org.broadinstitute.gatk.tools.walkers.bqsr.ReadRecalibrationInfo[WARNING] - org.broadinstitute.gatk.tools.walkers.haplotypecaller.graphs.TestGraph[WARNING] - org.broadinstitute.gatk.tools.walkers.validation.validationsiteselector.KeepAFSpectrumFrequencySelector[WARNING] - 514 more...[WARNING] gatk-queue-package-distribution-3.5.jar, commons-lang-2.5.jar, gatk-package-distribution-3.5.jar define 45 overlappping classes: [WARNING] - org.apache.commons.lang.ObjectUtils[WARNING] - org.apache.commons.lang.builder.IDKey[WARNING] - org.apache.commons.lang.exception.NestableRuntimeException[WARNING] - org.apache.commons.lang.builder.ToStringStyle$MultiLineToStringStyle[WARNING] - org.apache.commons.lang.StringEscapeUtils[WARNING] - org.apache.commons.lang.CharRange[WARNING] - org.apache.commons.lang.IntHashMap[WARNING] - org.apache.commons.lang.builder.EqualsBuilder[WARNING] - org.apache.commons.lang.Entities$ArrayEntityMap[WARNING] - org.apache.commons.lang.Entities$BinaryEntityMap[WARNING] - 35 more...[WARNING] gatk-queue-package-distribution-3.5.jar, snpeff-2.0.5.jar define 1319 overlappping classes: [WARNING] - flanagan.physprop.IonicRadii[WARNING] - junit.awtui.TestRunner$2[WARNING] - gnu.trove.THashMap$EqProcedure[WARNING] - gnu.trove.TFloatStack[WARNING] - gnu.trove.decorator.TDoubleByteHashMapDecorator$1[WARNING] - gnu.trove.decorator.TDoubleShortHashMapDecorator$1$1[WARNING] - gnu.trove.decorator.TLongDoubleHashMapDecorator$1[WARNING] - flanagan.analysis.RegressionFunction2[WARNING] - gnu.trove.TShortHashSet$1[WARNING] - ca.mcgill.mcb.pcingola.interval.codonChange.CodonChangeSnp[WARNING] - 1309 more...[WARNING] gatk-queue-package-distribution-3.5.jar, gatk-package-distribution-3.5.jar, slf4j-log4j12-1.7.5.jar define 6 overlappping 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] jna-3.2.7.jar, gatk-queue-package-distribution-3.5.jar define 16 overlappping classes: [WARNING] - com.sun.jna.win32.StdCallLibrary$StdCallCallback[WARNING] - com.sun.jna.win32.W32APIOptions$1[WARNING] - com.sun.jna.win32.W32APIFunctionMapper[WARNING] - com.sun.jna.win32.StdCall[WARNING] - com.sun.jna.DefaultTypeMapper[WARNING] - com.sun.jna.win32.W32APITypeMapper[WARNING] - com.sun.jna.DefaultTypeMapper$Entry[WARNING] - com.sun.jna.win32.StdCallLibrary[WARNING] - com.sun.jna.ptr.ShortByReference[WARNING] - com.sun.jna.win32.W32APITypeMapper$2[WARNING] - 6 more...[WARNING] gatk-queue-package-distribution-3.5.jar, guava-18.0.jar, gatk-package-distribution-3.5.jar define 477 overlappping classes: [WARNING] - com.google.common.collect.MapMakerInternalMap$SoftEvictableEntry[WARNING] - com.google.common.collect.Iterators$12[WARNING] - com.google.common.base.Predicates$InstanceOfPredicate[WARNING] - com.google.common.collect.ImmutableMultiset$1[WARNING] - com.google.common.collect.MapMaker$RemovalCause$4[WARNING] - com.google.common.collect.MapMakerInternalMap$WeakValueReference[WARNING] - com.google.common.collect.Maps$TransformedEntriesSortedMap[WARNING] - com.google.common.base.Predicates$AndPredicate[WARNING] - com.google.common.collect.Multimaps$Keys$KeysEntrySet[WARNING] - com.google.common.collect.ImmutableSortedSet$Builder[WARNING] - 467 more...[WARNING] gatk-queue-package-distribution-3.5.jar, mail-1.4.4.jar define 286 overlappping classes: [WARNING] - javax.mail.internet.ContentDisposition[WARNING] - com.sun.mail.pop3.Protocol[WARNING] - com.sun.mail.iap.Response[WARNING] - com.sun.mail.smtp.DigestMD5[WARNING] - javax.mail.internet.MimePart[WARNING] - com.sun.mail.imap.IMAPMessage[WARNING] - javax.mail.Message[WARNING] - com.sun.mail.imap.Rights[WARNING] - com.sun.mail.util.SocketFetcher[WARNING] - com.sun.mail.pop3.POP3Store[WARNING] - 276 more...[WARNING] stax-api-1.0.1.jar, gatk-queue-package-distribution-3.5.jar, gatk-package-distribution-3.5.jar define 24 overlappping classes: [WARNING] - javax.xml.stream.FactoryFinder[WARNING] - javax.xml.stream.events.StartElement[WARNING] - javax.xml.stream.Location[WARNING] - javax.xml.stream.EventFilter[WARNING] - javax.xml.stream.XMLInputFactory[WARNING] - javax.xml.stream.XMLEventReader[WARNING] - javax.xml.stream.events.Attribute[WARNING] - javax.xml.stream.events.Characters[WARNING] - javax.xml.stream.XMLStreamException[WARNING] - javax.xml.stream.XMLStreamReader[WARNING] - 14 more...[WARNING] gatk-queue-package-distribution-3.5.jar, picard-1.141.jar define 574 overlappping classes: [WARNING] - picard.illumina.parser.BarcodeParser$BarcodeDataIterator$1[WARNING] - picard.illumina.parser.readers.BclQualityEvaluationStrategy$1[WARNING] - picard.illumina.parser.PerTileCycleParser[WARNING] - picard.sam.SamToFastq$FastqWriters$1[WARNING] - picard.illumina.IlluminaBasecallsConverter[WARNING] - picard.analysis.CountingFilter[WARNING] - picard.analysis.InsertSizeMetrics[WARNING] - picard.illumina.quality.CollectHiSeqXPfFailMetrics$ReadClassifier[WARNING] - picard.analysis.AlignmentSummaryMetrics$Category[WARNING] - picard.illumina.parser.PosParser$2[WARNING] - 564 more...[WARNING] gatk-queue-package-distribution-3.5.jar, commons-collections-3.2.1.jar, gatk-package-distribution-3.5.jar define 37 overlappping classes: [WARNING] - org.apache.commons.collections.list.TransformedList$TransformedListIterator[WARNING] - org.apache.commons.collections.collection.TypedCollection[WARNING] - org.apache.commons.collections.collection.UnmodifiableCollection[WARNING] - org.apache.commons.collections.collection.UnmodifiableBoundedCollection[WARNING] - org.apache.commons.collections.list.UnmodifiableList[WARNING] - org.apache.commons.collections.BoundedCollection[WARNING] - org.apache.commons.collections.iterators.AbstractEmptyIterator[WARNING] - org.apache.commons.collections.iterators.UnmodifiableListIterator[WARNING] - org.apache.commons.collections.collection.SynchronizedCollection[WARNING] - org.apache.commons.collections.Factory[WARNING] - 27 more...[WARNING] gatk-queue-package-distribution-3.5.jar, freemarker-2.3.18.jar, gatk-package-distribution-3.5.jar define 24 overlappping classes: [WARNING] - freemarker.core.DateBuiltins$iso_BI$Result[WARNING] - freemarker.core.TemplateClassResolver$4[WARNING] - freemarker.core.TemplateClassResolver[WARNING] - freemarker.core.TemplateClassResolver$2[WARNING] - freemarker.core.DateBuiltins[WARNING] - freemarker.core.TemplateClassResolver$1[WARNING] - freemarker.core.DateBuiltins$iso_BI[WARNING] - freemarker.ext.beans.BeansWrapper$MethodAppearanceDecision[WARNING] - freemarker.core.TemplateClassResolver$3[WARNING] - freemarker.template.utility.DateUtil[WARNING] - 14 more...[WARNING] gatk-queue-package-distribution-3.5.jar, ant-1.8.2.jar, gatk-package-distribution-3.5.jar define 4 overlappping classes: [WARNING] - org.apache.tools.bzip2.CBZip2InputStream$Data[WARNING] - org.apache.tools.bzip2.CBZip2InputStream[WARNING] - org.apache.tools.bzip2.CRC[WARNING] - org.apache.tools.bzip2.BZip2Constants[WARNING] servlet-api-2.5.jar, gatk-queue-package-distribution-3.5.jar, gatk-package-distribution-3.5.jar define 11 overlappping classes: [WARNING] - javax.servlet.ServletInputStream[WARNING] - javax.servlet.ServletConfig[WARNING] - javax.servlet.RequestDispatcher[WARNING] - javax.servlet.ServletRequest[WARNING] - javax.servlet.ServletResponse[WARNING] - javax.servlet.ServletException[WARNING] - javax.servlet.ServletContext[WARNING] - javax.servlet.ServletContextListener[WARNING] - javax.servlet.ServletOutputStream[WARNING] - javax.servlet.Servlet[WARNING] - 1 more...[WARNING] gatk-queue-package-distribution-3.5.jar, colt-1.2.0.jar, gatk-package-distribution-3.5.jar define 15 overlappping classes: [WARNING] - cern.jet.math.Constants[WARNING] - cern.jet.random.Normal[WARNING] - cern.jet.stat.Gamma[WARNING] - cern.colt.function.DoubleFunction[WARNING] - cern.jet.random.AbstractContinousDistribution[WARNING] - cern.colt.function.IntFunction[WARNING] - cern.jet.random.engine.MersenneTwister[WARNING] - cern.colt.PersistentObject[WARNING] - cern.jet.math.Arithmetic[WARNING] - cern.jet.stat.Probability[WARNING] - 5 more...[WARNING] gatk-queue-package-distribution-3.5.jar, xz-1.5.jar, gatk-package-distribution-3.5.jar define 84 overlappping classes: [WARNING] - org.tukaani.xz.lzma.Optimum[WARNING] - org.tukaani.xz.index.IndexBase[WARNING] - org.tukaani.xz.lzma.LZMAEncoderNormal[WARNING] - org.tukaani.xz.delta.DeltaDecoder[WARNING] - org.tukaani.xz.DeltaCoder[WARNING] - org.tukaani.xz.simple.SPARC[WARNING] - org.tukaani.xz.LZMA2Coder[WARNING] - org.tukaani.xz.common.DecoderUtil[WARNING] - org.tukaani.xz.XZOutputStream[WARNING] - org.tukaani.xz.UnsupportedOptionsException[WARNING] - 74 more...[WARNING] gatk-queue-package-distribution-3.5.jar, commons-httpclient-3.1.jar, gatk-package-distribution-3.5.jar define 167 overlappping 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] gatk-queue-package-distribution-3.5.jar, httpcore-4.1.jar, gatk-package-distribution-3.5.jar define 121 overlappping classes: [WARNING] - org.apache.http.ConnectionReuseStrategy[WARNING] - org.apache.http.params.AbstractHttpParams[WARNING] - org.apache.http.util.VersionInfo[WARNING] - org.apache.http.MalformedChunkCodingException[WARNING] - org.apache.http.HttpClientConnection[WARNING] - org.apache.http.params.BasicHttpParams[WARNING] - org.apache.http.impl.io.AbstractSessionOutputBuffer[WARNING] - org.apache.http.impl.io.ContentLengthInputStream[WARNING] - org.apache.http.impl.AbstractHttpClientConnection[WARNING] - org.apache.http.protocol.HttpResponseInterceptorList[WARNING] - 111 more...[WARNING] gatk-queue-package-distribution-3.5.jar, gatk-queue-extensions-distribution-3.5.jar define 405 overlappping classes: [WARNING] - org.broadinstitute.gatk.queue.extensions.gatk.DocumentationTest$$anonfun$2[WARNING] - org.broadinstitute.gatk.queue.extensions.gatk.RealignerTargetCreator$$anonfun$1[WARNING] - org.broadinstitute.gatk.queue.extensions.gatk.GATKScatterFunction$$anonfun$1[WARNING] - org.broadinstitute.gatk.queue.extensions.gatk.VariantEval[WARNING] - org.broadinstitute.gatk.queue.extensions.gatk.Sample$class[WARNING] - org.broadinstitute.gatk.queue.extensions.gatk.ASEReadCounter$$anonfun$1[WARNING] - org.broadinstitute.gatk.queue.extensions.gatk.MergeVCFs[WARNING] - org.broadinstitute.gatk.queue.extensions.gatk.UnifiedGenotyper$$anonfun$1[WARNING] - org.broadinstitute.gatk.queue.extensions.gatk.RodSystemValidation$$anonfun$freezeFieldValues$1[WARNING] - org.broadinstitute.gatk.queue.extensions.gatk.PrepareTargets[WARNING] - 395 more...[WARNING] gatk-queue-package-distribution-3.5.jar, xml-apis-1.0.b2.jar, gatk-package-distribution-3.5.jar define 68 overlappping classes: [WARNING] - javax.xml.parsers.FactoryConfigurationError[WARNING] - javax.xml.parsers.SAXParserFactory[WARNING] - javax.xml.parsers.SAXParser[WARNING] - org.w3c.dom.Document[WARNING] - javax.xml.transform.TransformerException[WARNING] - javax.xml.transform.SourceLocator[WARNING] - org.w3c.dom.Node[WARNING] - org.xml.sax.helpers.AttributesImpl[WARNING] - org.xml.sax.DTDHandler[WARNING] - javax.xml.transform.TransformerConfigurationException[WARNING] - 58 more...[WARNING] gatk-queue-package-distribution-3.5.jar, gatk-package-distribution-3.5.jar define 183 overlappping classes: [WARNING] - com.google.common.collect.Multisets$SetMultiset$ElementSet[WARNING] - com.google.common.collect.Multimaps$FilteredMultimap$AsMap$Values$2[WARNING] - com.google.common.collect.SortedIterables$2[WARNING] - com.google.common.collect.ImmutableMultimap$Values$1[WARNING] - com.google.common.collect.Maps$AbstractFilteredMap$Values$1[WARNING] - com.google.common.collect.Sets$PowerSet$BitFilteredSetIterator[WARNING] - com.google.common.collect.BstRangeOps$1[WARNING] - com.google.common.collect.RegularImmutableMultiset$1[WARNING] - com.google.common.collect.Multimaps$UnmodifiableAsMapValues[WARNING] - com.google.common.collect.Multimaps$FilteredMultimap$AsMap$Values[WARNING] - 173 more...[WARNING] gov.nist.math.jama-1.1.1.jar, gatk-queue-package-distribution-3.5.jar, gatk-package-distribution-3.5.jar, jama-1.0.2.jar define 7 overlappping classes: [WARNING] - Jama.SingularValueDecomposition[WARNING] - Jama.EigenvalueDecomposition[WARNING] - Jama.CholeskyDecomposition[WARNING] - Jama.util.Maths[WARNING] - Jama.Matrix[WARNING] - Jama.LUDecomposition[WARNING] - Jama.QRDecomposition[WARNING] gatk-queue-package-distribution-3.5.jar, commons-compress-1.4.1.jar, gatk-package-distribution-3.5.jar define 10 overlappping classes: [WARNING] - org.apache.commons.compress.compressors.xz.XZCompressorInputStream[WARNING] - org.apache.commons.compress.compressors.bzip2.BZip2CompressorInputStream[WARNING] - org.apache.commons.compress.compressors.bzip2.BZip2CompressorInputStream$Data[WARNING] - org.apache.commons.compress.utils.CountingOutputStream[WARNING] - org.apache.commons.compress.compressors.xz.XZCompressorOutputStream[WARNING] - org.apache.commons.compress.compressors.bzip2.BZip2Constants[WARNING] - org.apache.commons.compress.compressors.CompressorOutputStream[WARNING] - org.apache.commons.compress.compressors.CompressorInputStream[WARNING] - org.apache.commons.compress.compressors.bzip2.CRC[WARNING] - org.apache.commons.compress.compressors.bzip2.Rand[WARNING] gatk-queue-package-distribution-3.5.jar, gatk-package-distribution-3.5.jar, java-xmlbuilder-0.4.jar define 4 overlappping classes: [WARNING] - net.iharder.base64.Base64$OutputStream[WARNING] - net.iharder.base64.Base64[WARNING] - net.iharder.base64.Base64$InputStream[WARNING] - com.jamesmurty.utils.XMLBuilder[WARNING] gatk-queue-package-distribution-3.5.jar, fastutil-6.5.3.jar, gatk-package-distribution-3.5.jar define 124 overlappping classes: [WARNING] - it.unimi.dsi.fastutil.ints.AbstractIntList$1[WARNING] - it.unimi.dsi.fastutil.objects.ObjectIterators$UnmodifiableIterator[WARNING] - it.unimi.dsi.fastutil.objects.Object2IntMap[WARNING] - it.unimi.dsi.fastutil.objects.ObjectArrayList$1[WARNING] - it.unimi.dsi.fastutil.objects.Object2IntOpenHashMap$KeyIterator[WARNING] - it.unimi.dsi.fastutil.objects.Object2ObjectOpenHashMap$MapEntry[WARNING] - it.unimi.dsi.fastutil.Arrays[WARNING] - it.unimi.dsi.fastutil.objects.ObjectIterators[WARNING] - it.unimi.dsi.fastutil.objects.Object2ObjectMap$FastEntrySet[WARNING] - it.unimi.dsi.fastutil.objects.ObjectBidirectionalIterator[WARNING] - 114 more...[WARNING] gatk-queue-package-distribution-3.5.jar, freemarker-2.3.18.jar, gatk-package-distribution-3.5.jar, snpeff-2.0.5.jar define 457 overlappping classes: [WARNING] - freemarker.ext.jython.JythonWrapper[WARNING] - freemarker.ext.dom.CharacterDataNodeModel[WARNING] - freemarker.template.SimpleCollection$SimpleTemplateModelIterator[WARNING] - freemarker.debug.impl.DebuggerService[WARNING] - freemarker.core.CollectionAndSequence$SequenceIterator[WARNING] - freemarker.template.EmptyMap[WARNING] - freemarker.ext.beans.CollectionAdapter$1[WARNING] - freemarker.debug.impl.DebuggerService$NoOpDebuggerService[WARNING] - freemarker.core.FMParserTokenManager[WARNING] - freemarker.core.NumericalBuiltins$longBI[WARNING] - 447 more...[WARNING] commons-logging-1.1.1.jar, gatk-queue-package-distribution-3.5.jar, gatk-package-distribution-3.5.jar define 28 overlappping 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] gatk-queue-package-distribution-3.5.jar, picard-1.141.jar, gatk-package-distribution-3.5.jar define 16 overlappping classes: [WARNING] - picard.cmdline.CommandLineParseException[WARNING] - picard.cmdline.CommandLineParser$ChildOptionArg[WARNING] - picard.cmdline.NestedOptions[WARNING] - picard.cmdline.CommandLineParserDefinitionException[WARNING] - picard.cmdline.programgroups.None[WARNING] - picard.cmdline.Option[WARNING] - picard.cmdline.PositionalArguments[WARNING] - picard.cmdline.CommandLineProgramProperties[WARNING] - picard.cmdline.CommandLineProgram[WARNING] - picard.cmdline.CommandLineProgramGroup[WARNING] - 6 more...[WARNING] gatk-queue-package-distribution-3.5.jar, gatk-package-distribution-3.5.jar, jets3t-0.8.1.jar define 157 overlappping classes: [WARNING] - org.jets3t.service.multi.event.ServiceEvent[WARNING] - org.jets3t.service.impl.rest.XmlResponsesSaxParser$ListBucketHandler[WARNING] - org.jets3t.service.io.OutputStreamWrapper[WARNING] - org.jets3t.service.multi.ThreadedStorageService$3[WARNING] - org.jets3t.service.io.RepeatableFileInputStream[WARNING] - org.jets3t.service.model.BaseVersionOrDeleteMarker[WARNING] - org.jets3t.service.impl.rest.XmlResponsesSaxParser$ListMultipartUploadsResultHandler[WARNING] - org.jets3t.service.utils.MultipartUtils[WARNING] - org.jets3t.service.multi.ThreadedStorageService$AbstractRunnable[WARNING] - org.jets3t.service.utils.RestUtils$1[WARNING] - 147 more...[WARNING] gatk-queue-package-distribution-3.5.jar, gatk-package-distribution-3.5.jar, reflections-0.9.9-RC1.jar define 82 overlappping classes: [WARNING] - org.reflections.vfs.SystemFile[WARNING] - org.reflections.vfs.Vfs$DefaultUrlTypes[WARNING] - org.reflections.vfs.Vfs$DefaultUrlTypes$3[WARNING] - org.reflections.vfs.Vfs$DefaultUrlTypes$2[WARNING] - org.reflections.util.FilterBuilder$Exclude[WARNING] - org.reflections.vfs.ZipDir$1[WARNING] - org.reflections.vfs.JarInputDir$1$1[WARNING] - org.reflections.ReflectionUtils$2[WARNING] - org.reflections.Store[WARNING] - org.reflections.ReflectionUtils$5[WARNING] - 72 more...[WARNING] gatk-queue-package-distribution-3.5.jar, gatk-package-distribution-3.5.jar, log4j-1.2.15.jar define 72 overlappping classes: [WARNING] - org.apache.log4j.or.ObjectRenderer[WARNING] - org.apache.log4j.helpers.AbsoluteTimeDateFormat[WARNING] - org.apache.log4j.helpers.FileWatchdog[WARNING] - org.apache.log4j.Priority[WARNING] - org.apache.log4j.WriterAppender[WARNING] - org.apache.log4j.helpers.PatternParser$NamedPatternConverter[WARNING] - org.apache.log4j.spi.NOPLogger[WARNING] - org.apache.log4j.NDC$DiagnosticContext[WARNING] - org.apache.log4j.spi.ErrorHandler[WARNING] - org.apache.log4j.spi.AppenderAttachable[WARNING] - 62 more...[WARNING] gatk-tools-public-3.5.jar, gatk-queue-package-distribution-3.5.jar, gatk-package-distribution-3.5.jar define 228 overlappping classes: [WARNING] - org.broadinstitute.gatk.tools.walkers.variantutils.ConcordanceMetrics$SiteConcordanceType[WARNING] - org.broadinstitute.gatk.tools.walkers.variantutils.VariantsToTable$7[WARNING] - org.broadinstitute.gatk.tools.walkers.varianteval.evaluators.MultiallelicSummary[WARNING] - org.broadinstitute.gatk.tools.walkers.varianteval.evaluators.VariantSummary[WARNING] - org.broadinstitute.gatk.tools.walkers.annotator.interfaces.AnnotationInterfaceManager[WARNING] - org.broadinstitute.gatk.tools.walkers.variantutils.VariantsToTable[WARNING] - org.broadinstitute.gatk.tools.walkers.readutils.ClipReads[WARNING] - org.broadinstitute.gatk.tools.walkers.variantutils.VariantsToTable$1[WARNING] - org.broadinstitute.gatk.tools.walkers.variantutils.ValidateVariants$ValidationType[WARNING] - org.broadinstitute.gatk.tools.walkers.annotator.SnpEffUtil[WARNING] - 218 more...[WARNING] gatk-queue-package-distribution-3.5.jar, gatk-package-distribution-3.5.jar, jsr305-1.3.9.jar define 11 overlappping classes: [WARNING] - javax.annotation.meta.When[WARNING] - javax.annotation.concurrent.Immutable[WARNING] - javax.annotation.CheckForNull[WARNING] - javax.annotation.meta.TypeQualifierValidator[WARNING] - javax.annotation.Nonnull[WARNING] - javax.annotation.Nullable[WARNING] - javax.annotation.meta.TypeQualifier[WARNING] - javax.annotation.concurrent.GuardedBy[WARNING] - javax.annotation.Nonnull$Checker[WARNING] - javax.annotation.CheckReturnValue[WARNING] - 1 more...[WARNING] gatk-queue-package-distribution-3.5.jar, gatk-package-distribution-3.5.jar, slf4j-api-1.6.1.jar define 19 overlappping classes: [WARNING] - org.slf4j.spi.MarkerFactoryBinder[WARNING] - org.slf4j.helpers.BasicMarker[WARNING] - org.slf4j.helpers.Util[WARNING] - org.slf4j.LoggerFactory[WARNING] - org.slf4j.Marker[WARNING] - org.slf4j.helpers.NamedLoggerBase[WARNING] - org.slf4j.Logger[WARNING] - org.slf4j.spi.LocationAwareLogger[WARNING] - org.slf4j.ILoggerFactory[WARNING] - org.slf4j.helpers.BasicMarkerFactory[WARNING] - 9 more...[WARNING] scala-library-2.10.2.jar, gatk-queue-package-distribution-3.5.jar define 4894 overlappping 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] - 4884 more...[WARNING] gatk-queue-package-distribution-3.5.jar, htsjdk-1.141.jar, gatk-package-distribution-3.5.jar define 913 overlappping 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$1[WARNING] - 903 more...[WARNING] gatk-queue-package-distribution-3.5.jar, httpclient-4.1.1.jar, gatk-package-distribution-3.5.jar define 206 overlappping classes: [WARNING] - org.apache.http.conn.routing.RouteInfo$TunnelType[WARNING] - org.apache.http.client.methods.HttpUriRequest[WARNING] - org.apache.http.impl.client.RedirectLocations[WARNING] - org.apache.http.conn.scheme.SchemeSocketFactoryAdaptor[WARNING] - org.apache.http.impl.cookie.BrowserCompatSpecFactory[WARNING] - org.apache.http.conn.ssl.AbstractVerifier[WARNING] - org.apache.http.client.protocol.RequestDefaultHeaders[WARNING] - org.apache.http.impl.cookie.RFC2965SpecFactory[WARNING] - org.apache.http.annotation.ThreadSafe[WARNING] - org.apache.http.client.methods.HttpRequestBase[WARNING] - 196 more...[WARNING] gatk-queue-package-distribution-3.5.jar, cofoja-1.2-20140817.jar, gatk-package-distribution-3.5.jar define 144 overlappping classes: [WARNING] - com.google.java.contract.util.Iterables[WARNING] - com.google.java.contract.core.apt.MethodContractCreator$PostMethodCreationTrait[WARNING] - com.google.java.contract.core.apt.SourcePreprocessor[WARNING] - com.google.java.contract.core.util.JavaTokenizer[WARNING] - com.google.java.contract.core.apt.AnnotationProcessor$1[WARNING] - com.google.java.contract.core.util.JavaTokenizer$TokenKind[WARNING] - com.google.java.contract.core.util.SyntheticJavaFile[WARNING] - com.google.java.contract.core.apt.MethodContractCreator[WARNING] - com.google.java.contract.ContractImport[WARNING] - com.google.java.contract.util.Predicates$11[WARNING] - 134 more...[WARNING] gatk-queue-3.5.jar, gatk-queue-package-distribution-3.5.jar define 405 overlappping classes: [WARNING] - org.broadinstitute.gatk.queue.library.ipf.SortByRef$$anonfun$contigVal$2[WARNING] - org.broadinstitute.gatk.queue.engine.CommandLineJobRunner$$anonfun$init$1[WARNING] - org.broadinstitute.gatk.queue.library.clf.vcf.VCFExtractIntervals[WARNING] - org.broadinstitute.gatk.queue.engine.QGraph$$anonfun$addFailedFunctions$2[WARNING] - org.broadinstitute.gatk.queue.engine.QGraph$$anonfun$getReadyJobs$1[WARNING] - org.broadinstitute.gatk.queue.QCommandLine$$anonfun$execute$8$$anonfun$5[WARNING] - org.broadinstitute.gatk.queue.engine.CommandLineJobManager$class[WARNING] - org.broadinstitute.gatk.queue.engine.lsf.Lsf706JobRunner$$anonfun$tryStop$2[WARNING] - org.broadinstitute.gatk.queue.engine.QGraph$$anonfun$logFailed$1[WARNING] - org.broadinstitute.gatk.queue.function.RetryMemoryLimit$$anonfun$isMemoryError$1[WARNING] - 395 more...[WARNING] gatk-utils-3.5.jar, gatk-queue-package-distribution-3.5.jar, gatk-package-distribution-3.5.jar define 1208 overlappping classes: [WARNING] - org.broadinstitute.gatk.utils.help.GATKDocWorkUnit[WARNING] - org.broadinstitute.gatk.utils.jna.lsf.v7_0_6.LibLsf$lsSharedResourceInfo$ByReference[WARNING] - org.broadinstitute.gatk.utils.variant.GATKVariantContextUtils$AlleleMapper[WARNING] - org.broadinstitute.gatk.utils.downsampling.SimplePositionalDownsamplerFactory[WARNING] - org.broadinstitute.gatk.utils.jna.lsf.v7_0_6.LibBat$jgrpCtrl$ByReference[WARNING] - org.broadinstitute.gatk.utils.R.RUtils[WARNING] - org.broadinstitute.gatk.utils.jna.lsf.v7_0_6.LibBat$_limitConsumer$ByValue[WARNING] - org.broadinstitute.gatk.utils.jna.lsf.v7_0_6.LibBat$addRsvRequest$ByValue[WARNING] - org.broadinstitute.gatk.utils.codecs.refseq.RefSeqFeature[WARNING] - org.broadinstitute.gatk.utils.jna.lsf.v7_0_6.LibBat$hostPartInfoEnt[WARNING] - 1198 more...[WARNING] gatk-queue-package-distribution-3.5.jar, simple-xml-2.0.4.jar, gatk-package-distribution-3.5.jar define 187 overlappping classes: [WARNING] - org.simpleframework.xml.stream.OutputStack[WARNING] - org.simpleframework.xml.transform.BigIntegerTransform[WARNING] - org.simpleframework.xml.transform.PackageMatcher[WARNING] - org.simpleframework.xml.stream.OutputNodeMap[WARNING] - org.simpleframework.xml.core.GetPart[WARNING] - org.simpleframework.xml.core.CompositeValue[WARNING] - org.simpleframework.xml.stream.Formatter[WARNING] - org.simpleframework.xml.core.Contact[WARNING] - org.simpleframework.xml.transform.DoubleTransform[WARNING] - org.simpleframework.xml.Namespace[WARNING] - 177 more...[WARNING] gatk-queue-package-distribution-3.5.jar, gatk-package-distribution-3.5.jar, drmaa-common-1.0.jar define 33 overlappping classes: [WARNING] - org.ggf.drmaa.DrmsInitException[WARNING] - org.ggf.drmaa.InvalidAttributeFormatException[WARNING] - org.ggf.drmaa.ReleaseInconsistentStateException[WARNING] - org.ggf.drmaa.TryLaterException[WARNING] - org.ggf.drmaa.SessionFactory$NewFactoryAction[WARNING] - org.ggf.drmaa.AlreadyActiveSessionException[WARNING] - org.ggf.drmaa.JobInfo[WARNING] - org.ggf.drmaa.FileTransferMode[WARNING] - org.ggf.drmaa.ResumeInconsistentStateException[WARNING] - org.ggf.drmaa.InvalidContactStringException[WARNING] - 23 more...[WARNING] javassist-3.16.1-GA.jar, gatk-queue-package-distribution-3.5.jar, gatk-package-distribution-3.5.jar define 285 overlappping classes: [WARNING] - javassist.bytecode.CodeIterator$Jump32[WARNING] - javassist.CtMember$Cache[WARNING] - javassist.bytecode.LineNumberAttribute[WARNING] - javassist.expr.NewArray[WARNING] - javassist.bytecode.SignatureAttribute$1[WARNING] - javassist.bytecode.SignatureAttribute$BaseType[WARNING] - javassist.CtField$LongInitializer[WARNING] - javassist.compiler.ast.BinExpr[WARNING] - javassist.bytecode.StackMap$Writer[WARNING] - javassist.CodeConverter$DefaultArrayAccessReplacementMethodNames[WARNING] - 275 more...[WARNING] gatk-queue-package-distribution-3.5.jar, gatk-package-distribution-3.5.jar, snappy-java-1.0.3-rc3.jar define 11 overlappping classes: [WARNING] - org.xerial.snappy.OSInfo[WARNING] - org.xerial.snappy.SnappyOutputStream[WARNING] - org.xerial.snappy.SnappyInputStream[WARNING] - org.xerial.snappy.SnappyErrorCode[WARNING] - org.xerial.snappy.SnappyCodec[WARNING] - org.xerial.snappy.SnappyException[WARNING] - org.xerial.snappy.SnappyNative[WARNING] - org.xerial.snappy.Snappy[WARNING] - org.xerial.snappy.LoadSnappy[WARNING] - org.xerial.snappy.SnappyError[WARNING] - 1 more...[WARNING] jna-3.2.7.jar, gatk-queue-package-distribution-3.5.jar, gatk-package-distribution-3.5.jar define 79 overlappping classes: [WARNING] - com.sun.jna.NativeLong[WARNING] - com.sun.jna.Structure$FFIType$size_t[WARNING] - com.sun.jna.Structure$StructField[WARNING] - com.sun.jna.InvocationMapper[WARNING] - com.sun.jna.StructureWriteContext[WARNING] - com.sun.jna.Callback$UncaughtExceptionHandler[WARNING] - com.sun.jna.StringArray[WARNING] - com.sun.jna.ptr.LongByReference[WARNING] - com.sun.jna.Callback[WARNING] - com.sun.jna.TypeMapper[WARNING] - 69 more...[WARNING] gatk-queue-package-distribution-3.5.jar, commons-math-2.2.jar, gatk-package-distribution-3.5.jar define 247 overlappping classes: [WARNING] - org.apache.commons.math.stat.descriptive.moment.Kurtosis[WARNING] - org.apache.commons.math.MathRuntimeException$6[WARNING] - org.apache.commons.math.distribution.GammaDistribution[WARNING] - org.apache.commons.math.distribution.ExponentialDistributionImpl[WARNING] - org.apache.commons.math.linear.FieldVector[WARNING] - org.apache.commons.math.exception.DimensionMismatchException[WARNING] - org.apache.commons.math.linear.AbstractRealMatrix$4[WARNING] - org.apache.commons.math.analysis.ComposableFunction$2[WARNING] - org.apache.commons.math.fraction.FractionField$LazyHolder[WARNING] - org.apache.commons.math.special.Beta[WARNING] - 237 more...[WARNING] gatk-queue-package-distribution-3.5.jar, gson-2.2.2.jar, gatk-package-distribution-3.5.jar define 153 overlappping classes: [WARNING] - com.google.gson.internal.bind.TypeAdapters$27[WARNING] - com.google.gson.internal.bind.TypeAdapters$10[WARNING] - com.google.gson.TreeTypeAdapter[WARNING] - com.google.gson.internal.bind.TypeAdapters$15[WARNING] - com.google.gson.JsonIOException[WARNING] - com.google.gson.internal.StringMap[WARNING] - com.google.gson.internal.StringMap$LinkedHashIterator[WARNING] - com.google.gson.annotations.Until[WARNING] - com.google.gson.internal.bind.TypeAdapterRuntimeTypeWrapper[WARNING] - com.google.gson.stream.JsonReader$2[WARNING] - 143 more...[WARNING] maven-shade-plugin has detected that some .class files[WARNING] are present in two or more JARs. When this happens, only[WARNING] one single version of the class is copied in the uberjar.[WARNING] Usually this is not harmful and you can skeep these[WARNING] warnings, otherwise try to manually exclude artifacts[WARNING] based on mvn dependency:tree -Ddetail=true and the above[WARNING] output[WARNING] See http://docs.codehaus.org/display/MAVENUSER/Shade+Plugin[INFO] Minimized 75339 -> 58916 (78%)[INFO] Replacing original artifact with shaded artifact.[INFO] Replacing /home/hadoop/xubo/tools/gatk-protected/protected/gatk-queue-package-distribution/target/gatk-queue-package-distribution-3.5.jar with /home/hadoop/xubo/tools/gatk-protected/protected/gatk-queue-package-distribution/target/gatk-queue-package-distribution-3.5-shaded.jar[INFO] [INFO] --- maven-assembly-plugin:2.4:single (binary-dist) @ gatk-queue-package-distribution ---[INFO] Reading assembly descriptor: /home/hadoop/xubo/tools/gatk-protected/protected/gatk-queue-package-distribution/../../public/src/main/assembly/binary-dist.xml[WARNING] Invalid POM for com.google.code.cofoja:cofoja:jar:1.2-20140817, transitive dependencies (if any) will not be available, enable debug logging for more details[INFO] Building tar: /home/hadoop/xubo/tools/gatk-protected/protected/gatk-queue-package-distribution/target/gatk-queue-package-distribution-3.5-binary-dist.tar.bz2[INFO] [INFO] --- maven-junction-plugin:1.0.3:link (link-executable-jar) @ gatk-queue-package-distribution ---[INFO] [INFO] --- maven-junction-plugin:1.0.3:link (link-package-jar) @ gatk-queue-package-distribution ---[INFO] [INFO] --- maven-junction-plugin:1.0.3:link (link-git-release) @ gatk-queue-package-distribution ---[INFO] [INFO] ------------------------------------------------------------------------[INFO] Building GATK Aggregator Protected 3.5[INFO] ------------------------------------------------------------------------[INFO] [INFO] --- maven-clean-plugin:2.5:clean (default-clean) @ gatk-aggregator-protected ---[INFO] [INFO] --- gitdescribe-maven-plugin:2.0:gitdescribe (gitdescribe-initialize) @ gatk-aggregator-protected ---[INFO] [INFO] --- build-helper-maven-plugin:1.8:regex-property (fix-version-initialize) @ gatk-aggregator-protected ---[INFO] ------------------------------------------------------------------------[INFO] Reactor Summary:[INFO] [INFO] GATK Root .......................................... SUCCESS [ 0.590 s][INFO] GATK Aggregator .................................... SUCCESS [ 0.502 s][INFO] GATK GSALib ........................................ SUCCESS [ 0.863 s][INFO] GATK Utils ......................................... SUCCESS [ 32.395 s][INFO] GATK Engine ........................................ SUCCESS [ 9.264 s][INFO] GATK Tools Public .................................. SUCCESS [ 23.222 s][INFO] External Example ................................... SUCCESS [ 12.317 s][INFO] GATK Queue ......................................... SUCCESS [11:32 min][INFO] GATK Queue Extensions Generator .................... SUCCESS [ 0.128 s][INFO] GATK Queue Extensions Public ....................... SUCCESS [02:07 min][INFO] GATK Aggregator Public ............................. SUCCESS [ 0.003 s][INFO] GATK Tools Protected ............................... SUCCESS [ 32.863 s][INFO] GATK Package Distribution .......................... SUCCESS [01:08 min][INFO] GATK Queue Extensions Distribution ................. SUCCESS [01:34 min][INFO] GATK Queue Package Distribution .................... SUCCESS [02:37 min][INFO] GATK Aggregator Protected .......................... SUCCESS [ 0.005 s][INFO] ------------------------------------------------------------------------[INFO] BUILD SUCCESS[INFO] ------------------------------------------------------------------------[INFO] Total time: 20:52 min[INFO] Finished at: 2016-06-07T20:46:21+08:00[INFO] Final Memory: 73M/988M[INFO] ------------------------------------------------------------------------（2）xubo：
[WARNING] - org.broadinstitute.gatk.tools.walkers.varianteval.evaluators.MultiallelicSummary[WARNING] - org.broadinstitute.gatk.tools.walkers.varianteval.evaluators.VariantSummary[WARNING] - org.broadinstitute.gatk.tools.walkers.annotator.interfaces.AnnotationInterfaceManager[WARNING] - org.broadinstitute.gatk.tools.walkers.variantutils.VariantsToTable[WARNING] - org.broadinstitute.gatk.tools.walkers.readutils.ClipReads[WARNING] - org.broadinstitute.gatk.tools.walkers.variantutils.VariantsToTable$1[WARNING] - org.broadinstitute.gatk.tools.walkers.variantutils.ValidateVariants$ValidationType[WARNING] - org.broadinstitute.gatk.tools.walkers.annotator.SnpEffUtil[WARNING] - 218 more...[WARNING] gatk-package-distribution-3.5.jar, slf4j-log4j12-1.7.5.jar define 6 overlappping 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] htsjdk-1.141.jar, gatk-package-distribution-3.5.jar define 913 overlappping 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] - 903 more...[WARNING] maven-shade-plugin has detected that some .class files[WARNING] are present in two or more JARs. When this happens, only[WARNING] one single version of the class is copied in the uberjar.[WARNING] Usually this is not harmful and you can skeep these[WARNING] warnings, otherwise try to manually exclude artifacts[WARNING] based on mvn dependency:tree -Ddetail=true and the above[WARNING] output[WARNING] See http://docs.codehaus.org/display/MAVENUSER/Shade+Plugin[INFO] Minimized 28606 -> 11039 (38%)[INFO] Replacing original artifact with shaded artifact.[INFO] Replacing /home/xubo/xubo/tools/gatk-protected/protected/gatk-package-distribution/target/gatk-package-distribution-3.5.jar with /home/xubo/xubo/tools/gatk-protected/protected/gatk-package-distribution/target/gatk-package-distribution-3.5-shaded.jar[INFO] [INFO] --- maven-assembly-plugin:2.4:single (binary-dist) @ gatk-package-distribution ---[INFO] Reading assembly descriptor: /home/xubo/xubo/tools/gatk-protected/protected/gatk-package-distribution/../../public/src/main/assembly/binary-dist.xml[INFO] Building tar: /home/xubo/xubo/tools/gatk-protected/protected/gatk-package-distribution/target/gatk-package-distribution-3.5-binary-dist.tar.bz2[INFO] [INFO] --- maven-junction-plugin:1.0.3:link (link-executable-jar) @ gatk-package-distribution ---Downloading: https://repo.maven.apache.org/maven2/commons-io/commons-io/1.2/commons-io-1.2.pomDownloaded: https://repo.maven.apache.org/maven2/commons-io/commons-io/1.2/commons-io-1.2.pom (7 KB at 10.1 KB/sec)Downloading: https://repo.maven.apache.org/maven2/commons-io/commons-io/1.2/commons-io-1.2.jarDownloading: https://repo.maven.apache.org/maven2/org/apache/maven/maven-artifact/2.0/maven-artifact-2.0.jarDownloading: https://repo.maven.apache.org/maven2/org/codehaus/plexus/plexus-utils/1.0.4/plexus-utils-1.0.4.jarDownloaded: https://repo.maven.apache.org/maven2/org/codehaus/plexus/plexus-utils/1.0.4/plexus-utils-1.0.4.jar (160 KB at 82.2 KB/sec)Downloaded: https://repo.maven.apache.org/maven2/org/apache/maven/maven-artifact/2.0/maven-artifact-2.0.jar (77 KB at 33.6 KB/sec)Downloaded: https://repo.maven.apache.org/maven2/commons-io/commons-io/1.2/commons-io-1.2.jar (65 KB at 25.7 KB/sec)[INFO] [INFO] --- maven-junction-plugin:1.0.3:link (link-package-jar) @ gatk-package-distribution ---[INFO] [INFO] --- maven-junction-plugin:1.0.3:link (link-git-release) @ gatk-package-distribution ---[INFO] [INFO] ------------------------------------------------------------------------[INFO] Building GATK Queue Extensions Distribution 3.5[INFO] ------------------------------------------------------------------------[INFO] [INFO] --- maven-clean-plugin:2.5:clean (default-clean) @ gatk-queue-extensions-distribution ---[INFO] Deleting /home/xubo/xubo/tools/gatk-protected/protected/gatk-queue-extensions-distribution (includes = [javadoc.sh, options, packages], excludes = [])[INFO] Deleting /home/xubo/xubo/tools/gatk-protected/protected/gatk-queue-extensions-distribution (includes = [dependency-reduced-pom.xml], excludes = [])[INFO] [INFO] --- gitdescribe-maven-plugin:2.0:gitdescribe (gitdescribe-initialize) @ gatk-queue-extensions-distribution ---[INFO] [INFO] --- build-helper-maven-plugin:1.8:regex-property (fix-version-initialize) @ gatk-queue-extensions-distribution ---[INFO] [INFO] --- build-helper-maven-plugin:1.8:add-source (add-gatk-extensions) @ gatk-queue-extensions-distribution ---[INFO] Source directory: /home/xubo/xubo/tools/gatk-protected/protected/gatk-queue-extensions-distribution/../../public/gatk-queue-extensions-public/src/main/scala added.[INFO] Source directory: /home/xubo/xubo/tools/gatk-protected/protected/gatk-queue-extensions-distribution/target/generated-sources/gatk-extensions added.[INFO] [INFO] --- exec-maven-plugin:1.2.1:exec (generate-gatk-extensions) @ gatk-queue-extensions-distribution ---[INFO] [INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ gatk-queue-extensions-distribution ---[INFO] Using 'UTF-8' encoding to copy filtered resources.[INFO] skip non existing resourceDirectory /home/xubo/xubo/tools/gatk-protected/protected/gatk-queue-extensions-distribution/src/main/resources[INFO] [INFO] --- maven-scala-plugin:2.15.2:compile (default) @ gatk-queue-extensions-distribution ---[INFO] Checking for multiple versions of scala[INFO] includes = [**/*.scala,**/*.java,][INFO] excludes = [][INFO] /home/xubo/xubo/tools/gatk-protected/public/gatk-queue-extensions-public/src/main/scala:-1: info: compiling[INFO] /home/xubo/xubo/tools/gatk-protected/protected/gatk-queue-extensions-distribution/target/generated-sources/gatk-extensions:-1: info: compiling[INFO] Compiling 148 source files to /home/xubo/xubo/tools/gatk-protected/protected/gatk-queue-extensions-distribution/target/classes at 1465304334840[INFO] prepare-compile in 0 s[INFO] compile in 114 s[INFO] [INFO] --- maven-compiler-plugin:3.1:compile (compile-package-info) @ gatk-queue-extensions-distribution ---[INFO] Nothing to compile - all classes are up to date[INFO] [INFO] --- maven-compiler-plugin:3.1:compile (compile-java) @ gatk-queue-extensions-distribution ---[INFO] Nothing to compile - all classes are up to date[INFO] [INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ gatk-queue-extensions-distribution ---[INFO] Using 'UTF-8' encoding to copy filtered resources.[INFO] skip non existing resourceDirectory /home/xubo/xubo/tools/gatk-protected/protected/gatk-queue-extensions-distribution/src/test/resources[INFO] [INFO] --- maven-scala-plugin:2.15.2:testCompile (default) @ gatk-queue-extensions-distribution ---[INFO] Checking for multiple versions of scala[INFO] includes = [**/*.scala,**/*.java,][INFO] excludes = [][INFO] /home/xubo/xubo/tools/gatk-protected/protected/gatk-queue-extensions-distribution/src/test/scala:-1: info: compiling[INFO] Compiling 2 source files to /home/xubo/xubo/tools/gatk-protected/protected/gatk-queue-extensions-distribution/target/test-classes at 1465304449319[INFO] prepare-compile in 0 s[INFO] compile in 11 s[INFO] [INFO] --- maven-compiler-plugin:3.1:testCompile (testCompile-java) @ gatk-queue-extensions-distribution ---[INFO] No sources to compile[INFO] [INFO] --- maven-surefire-plugin:2.16:test (unit-tests) @ gatk-queue-extensions-distribution ---[INFO] Tests are skipped.[INFO] [INFO] --- maven-jar-plugin:2.4:jar (default-jar) @ gatk-queue-extensions-distribution ---[INFO] Building jar: /home/xubo/xubo/tools/gatk-protected/protected/gatk-queue-extensions-distribution/target/gatk-queue-extensions-distribution-3.5.jar[INFO] [INFO] --- maven-jar-plugin:2.4:test-jar (test-jar) @ gatk-queue-extensions-distribution ---[INFO] Building jar: /home/xubo/xubo/tools/gatk-protected/protected/gatk-queue-extensions-distribution/target/gatk-queue-extensions-distribution-3.5-tests.jar[INFO] [INFO] ------------------------------------------------------------------------[INFO] Building GATK Queue Package Distribution 3.5[INFO] ------------------------------------------------------------------------Downloading: file:/home/xubo/xubo/tools/gatk-protected/protected/gatk-queue-package-distribution/../../public/repo/net/sf/snpeff/snpeff/2.0.5/snpeff-2.0.5.pom[WARNING] Could not validate integrity of download from file:/home/xubo/xubo/tools/gatk-protected/protected/gatk-queue-package-distribution/../../public/repo/net/sf/snpeff/snpeff/2.0.5/snpeff-2.0.5.pom: Checksum validation failed, no checksums available[WARNING] Checksum validation failed, no checksums available for file:/home/xubo/xubo/tools/gatk-protected/protected/gatk-queue-package-distribution/../../public/repo/net/sf/snpeff/snpeff/2.0.5/snpeff-2.0.5.pomDownloaded: file:/home/xubo/xubo/tools/gatk-protected/protected/gatk-queue-package-distribution/../../public/repo/net/sf/snpeff/snpeff/2.0.5/snpeff-2.0.5.pom (363 B at 14.8 KB/sec)Downloading: file:/home/xubo/xubo/tools/gatk-protected/protected/gatk-queue-package-distribution/../../public/repo/net/sf/snpeff/snpeff/2.0.5/snpeff-2.0.5.jar[WARNING] Could not validate integrity of download from file:/home/xubo/xubo/tools/gatk-protected/protected/gatk-queue-package-distribution/../../public/repo/net/sf/snpeff/snpeff/2.0.5/snpeff-2.0.5.jar: Checksum validation failed, no checksums available[WARNING] Checksum validation failed, no checksums available for file:/home/xubo/xubo/tools/gatk-protected/protected/gatk-queue-package-distribution/../../public/repo/net/sf/snpeff/snpeff/2.0.5/snpeff-2.0.5.jarDownloaded: file:/home/xubo/xubo/tools/gatk-protected/protected/gatk-queue-package-distribution/../../public/repo/net/sf/snpeff/snpeff/2.0.5/snpeff-2.0.5.jar (4081 KB at 9027.5 KB/sec)[INFO] [INFO] --- maven-clean-plugin:2.5:clean (default-clean) @ gatk-queue-package-distribution ---[INFO] Deleting /home/xubo/xubo/tools/gatk-protected/protected/gatk-queue-package-distribution (includes = [javadoc.sh, options, packages], excludes = [])[INFO] Deleting /home/xubo/xubo/tools/gatk-protected/protected/gatk-queue-package-distribution (includes = [dependency-reduced-pom.xml], excludes = [])[INFO] [INFO] --- gitdescribe-maven-plugin:2.0:gitdescribe (gitdescribe-initialize) @ gatk-queue-package-distribution ---[INFO] [INFO] --- build-helper-maven-plugin:1.8:regex-property (fix-version-initialize) @ gatk-queue-package-distribution ---[INFO] [INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ gatk-queue-package-distribution ---[INFO] Using 'UTF-8' encoding to copy filtered resources.[INFO] skip non existing resourceDirectory /home/xubo/xubo/tools/gatk-protected/protected/gatk-queue-package-distribution/src/main/resources[INFO] [INFO] --- maven-compiler-plugin:3.1:compile (compile-package-info) @ gatk-queue-package-distribution ---[INFO] No sources to compile[INFO] [INFO] --- maven-compiler-plugin:3.1:compile (compile-java) @ gatk-queue-package-distribution ---[INFO] No sources to compile[INFO] [INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ gatk-queue-package-distribution ---[INFO] Using 'UTF-8' encoding to copy filtered resources.[INFO] skip non existing resourceDirectory /home/xubo/xubo/tools/gatk-protected/protected/gatk-queue-package-distribution/src/test/resources[INFO] [INFO] --- maven-compiler-plugin:3.1:testCompile (testCompile-java) @ gatk-queue-package-distribution ---[INFO] No sources to compile[INFO] [INFO] --- maven-surefire-plugin:2.16:test (unit-tests) @ gatk-queue-package-distribution ---[INFO] Tests are skipped.[INFO] [INFO] --- maven-dependency-plugin:2.8:unpack-dependencies (unpack-direct-dependencies) @ gatk-queue-package-distribution ---[INFO] Unpacking /home/xubo/.m2/repository/org/scala-lang/scala-compiler/2.10.2/scala-compiler-2.10.2.jar to /home/xubo/xubo/tools/gatk-protected/protected/gatk-queue-package-distribution/target/classes with includes "" and excludes "GATKText.properties"[INFO] Unpacking /home/xubo/.m2/repository/net/java/dev/jna/jna/3.2.7/jna-3.2.7.jar to /home/xubo/xubo/tools/gatk-protected/protected/gatk-queue-package-distribution/target/classes with includes "" and excludes "GATKText.properties"[INFO] Unpacking /home/xubo/.m2/repository/com/google/code/cofoja/cofoja/1.2-20140817/cofoja-1.2-20140817.jar to /home/xubo/xubo/tools/gatk-protected/protected/gatk-queue-package-distribution/target/classes with includes "" and excludes "GATKText.properties"[INFO] Unpacking /home/xubo/xubo/tools/gatk-protected/protected/gatk-queue-extensions-distribution/target/gatk-queue-extensions-distribution-3.5.jar to /home/xubo/xubo/tools/gatk-protected/protected/gatk-queue-package-distribution/target/classes with includes "" and excludes "GATKText.properties"[INFO] Unpacking /home/xubo/.m2/repository/commons-httpclient/commons-httpclient/3.1/commons-httpclient-3.1.jar to /home/xubo/xubo/tools/gatk-protected/protected/gatk-queue-package-distribution/target/classes with includes "" and excludes "GATKText.properties"[INFO] Unpacking /home/xubo/xubo/tools/gatk-protected/protected/gatk-package-distribution/target/gatk-package-distribution-3.5.jar to /home/xubo/xubo/tools/gatk-protected/protected/gatk-queue-package-distribution/target/classes with includes "" and excludes "GATKText.properties"[INFO] Unpacking /home/xubo/.m2/repository/com/github/broadinstitute/picard/1.141/picard-1.141.jar to /home/xubo/xubo/tools/gatk-protected/protected/gatk-queue-package-distribution/target/classes with includes "" and excludes "GATKText.properties"[INFO] Unpacking /home/xubo/.m2/repository/net/sf/snpeff/snpeff/2.0.5/snpeff-2.0.5.jar to /home/xubo/xubo/tools/gatk-protected/protected/gatk-queue-package-distribution/target/classes with includes "" and excludes "GATKText.properties"[INFO] Unpacking /home/xubo/.m2/repository/org/scala-lang/scala-library/2.10.2/scala-library-2.10.2.jar to /home/xubo/xubo/tools/gatk-protected/protected/gatk-queue-package-distribution/target/classes with includes "" and excludes "GATKText.properties"[INFO] Unpacking /home/xubo/xubo/tools/gatk-protected/public/gatk-queue/target/gatk-queue-3.5.jar to /home/xubo/xubo/tools/gatk-protected/protected/gatk-queue-package-distribution/target/classes with includes "" and excludes "GATKText.properties"[INFO] Unpacking /home/xubo/.m2/repository/javax/mail/mail/1.4.4/mail-1.4.4.jar to /home/xubo/xubo/tools/gatk-protected/protected/gatk-queue-package-distribution/target/classes with includes "" and excludes "GATKText.properties"[INFO] [INFO] --- maven-jar-plugin:2.4:jar (executable-jar) @ gatk-queue-package-distribution ---[WARNING] JAR will be empty - no content was marked for inclusion![INFO] Building jar: /home/xubo/xubo/tools/gatk-protected/protected/gatk-queue-package-distribution/../../target/executable/Queue.jar[INFO] [INFO] --- maven-jar-plugin:2.4:jar (unshaded-default-jar) @ gatk-queue-package-distribution ---[INFO] Building jar: /home/xubo/xubo/tools/gatk-protected/protected/gatk-queue-package-distribution/target/gatk-queue-package-distribution-3.5.jar[INFO] [INFO] --- maven-jar-plugin:2.4:test-jar (test-jar) @ gatk-queue-package-distribution ---[INFO] Skipping packaging of the test-jar[INFO] [INFO] --- maven-dependency-plugin:2.8:copy-dependencies (executable-jar-lib) @ gatk-queue-package-distribution ---[INFO] Copying scala-reflect-2.10.2.jar to /home/xubo/xubo/tools/gatk-protected/protected/gatk-queue-package-distribution/../../target/executable/lib/scala-reflect-2.10.2.jar[INFO] Copying gatk-queue-extensions-public-3.5-example-resources.tar.bz2 to /home/xubo/xubo/tools/gatk-protected/protected/gatk-queue-package-distribution/../../target/executable/lib/gatk-queue-extensions-public-3.5-example-resources.tar.bz2[INFO] Copying scala-compiler-2.10.2.jar to /home/xubo/xubo/tools/gatk-protected/protected/gatk-queue-package-distribution/../../target/executable/lib/scala-compiler-2.10.2.jar[INFO] Copying gatk-queue-extensions-distribution-3.5.jar to /home/xubo/xubo/tools/gatk-protected/protected/gatk-queue-package-distribution/../../target/executable/lib/gatk-queue-extensions-distribution-3.5.jar[INFO] Copying guava-18.0.jar to /home/xubo/xubo/tools/gatk-protected/protected/gatk-queue-package-distribution/../../target/executable/lib/guava-18.0.jar[INFO] Copying gatk-package-distribution-3.5.jar to /home/xubo/xubo/tools/gatk-protected/protected/gatk-queue-package-distribution/../../target/executable/lib/gatk-package-distribution-3.5.jar[INFO] Copying gatk-queue-extensions-generator-3.5.jar to /home/xubo/xubo/tools/gatk-protected/protected/gatk-queue-package-distribution/../../target/executable/lib/gatk-queue-extensions-generator-3.5.jar[INFO] Copying snpeff-2.0.5.jar to /home/xubo/xubo/tools/gatk-protected/protected/gatk-queue-package-distribution/../../target/executable/lib/snpeff-2.0.5.jar[INFO] Copying scala-library-2.10.2.jar to /home/xubo/xubo/tools/gatk-protected/protected/gatk-queue-package-distribution/../../target/executable/lib/scala-library-2.10.2.jar[INFO] Copying gatk-queue-3.5.jar to /home/xubo/xubo/tools/gatk-protected/protected/gatk-queue-package-distribution/../../target/executable/lib/gatk-queue-3.5.jar[INFO] Copying commons-email-1.2.jar to /home/xubo/xubo/tools/gatk-protected/protected/gatk-queue-package-distribution/../../target/executable/lib/commons-email-1.2.jar[INFO] httpcore-4.1.jar already exists in destination.[INFO] google-api-client-1.19.0.jar already exists in destination.[INFO] jcommander-1.27.jar already exists in destination.[INFO] 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simple-xml-2.0.4.jar already exists in destination.[INFO] commons-lang-2.5.jar already exists in destination.[INFO] drmaa-gridengine-6.2u5.jar already exists in destination.[INFO] reflections-0.9.9-RC1.jar already exists in destination.[INFO] htsjdk-1.141.jar already exists in destination.[INFO] jna-3.2.7.jar already exists in destination.[INFO] colt-1.2.0.jar already exists in destination.[INFO] httpclient-4.1.1.jar already exists in destination.[INFO] xz-1.5.jar already exists in destination.[INFO] google-api-client-java6-1.19.0.jar already exists in destination.[INFO] asm-all-5.0.4.jar already exists in destination.[INFO] jets3t-0.8.1.jar already exists in destination.[INFO] cofoja-1.2-20140817.jar already exists in destination.[INFO] google-oauth-client-1.19.0.jar already exists in destination.[INFO] google-oauth-client-jetty-1.19.0.jar already exists in destination.[INFO] jsr305-1.3.9.jar already exists in destination.[INFO] gatk-utils-3.5-example-resources.tar.bz2 already exists in destination.[INFO] gsalib-3.5.tar.gz already exists in destination.[INFO] gatk-utils-3.5.jar already exists in destination.[INFO] mail-1.4.4.jar already exists in destination.[INFO] commons-compress-1.4.1.jar already exists in destination.[INFO] snappy-java-1.0.3-rc3.jar already exists in destination.[INFO] javassist-3.16.1-GA.jar already exists in destination.[INFO] google-http-client-jackson2-1.19.0.jar already exists in destination.[INFO] servlet-api-2.5.jar already exists in destination.[INFO] fastutil-6.5.3.jar already exists in destination.[INFO] commons-collections-3.2.1.jar already exists in destination.[INFO] gatk-engine-3.5.jar already exists in destination.[INFO] freemarker-2.3.18.jar already exists in destination.[INFO] jama-1.0.2.jar already exists in destination.[INFO] commons-math-2.2.jar already exists in destination.[INFO] slf4j-log4j12-1.7.5.jar already exists in destination.[INFO] log4j-1.2.15.jar already exists in destination.[INFO] gov.nist.math.jama-1.1.1.jar already exists in destination.[INFO] gatk-tools-protected-3.5.jar already exists in destination.[INFO] slf4j-api-1.6.1.jar already exists in destination.[INFO] commons-jexl-2.1.1.jar already exists in destination.[INFO] google-genomics-utils-v1beta2-0.19.jar already exists in destination.[INFO] dom4j-1.6.1.jar already exists in destination.[INFO] google-api-services-genomics-v1beta2-rev9-1.1阅读全文
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