基因数据处理72之GATK安装成功

git clone https://github.com/broadgsa/gatk-protected.git

git checkout 3.5
mvn clean package -DskipTests

[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] ------------------------------------------------------------------------

记录：

[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.pom Downloaded: 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.jar Downloading: https://repo.maven.apache.org/maven2/org/apache/maven/maven-artifact/2.0/maven-artifact-2.0.jar Downloaded: 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.pom
Downloaded: 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.jar
Downloaded: 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] ------------------------------------------------------------------------

[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.pom Downloaded: 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.jar Downloading: https://repo.maven.apache.org/maven2/org/apache/maven/maven-artifact/2.0/maven-artifact-2.0.jar Downloading: https://repo.maven.apache.org/maven2/org/codehaus/plexus/plexus-utils/1.0.4/plexus-utils-1.0.4.jar Downloaded: 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.pom
Downloaded: 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.jar
Downloaded: 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]
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[INFO] Building jar: /home/xubo/xubo/tools/gatk-protected/protected/gatk-queue-package-distribution/target/gatk-queue-package-distribution-3.5.jar
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[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
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[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
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[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
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[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
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