Console Output

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[INFO] 
[INFO] --- maven-license-plugin:1.10.b1:check (default) @ cannoli-core-spark3_2.12 ---
[INFO] Checking licenses...
[INFO] 
[INFO] --- maven-install-plugin:3.0.0-M1:install (default-install) @ cannoli-core-spark3_2.12 ---
[INFO] Installing /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/core/target/cannoli-core-spark3_2.12-0.12.0-SNAPSHOT.jar to /home/jenkins/.m2/repository/org/bdgenomics/cannoli/cannoli-core-spark3_2.12/0.12.0-SNAPSHOT/cannoli-core-spark3_2.12-0.12.0-SNAPSHOT.jar
[INFO] Installing /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/core/pom.xml to /home/jenkins/.m2/repository/org/bdgenomics/cannoli/cannoli-core-spark3_2.12/0.12.0-SNAPSHOT/cannoli-core-spark3_2.12-0.12.0-SNAPSHOT.pom
[INFO] Installing /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/core/target/cannoli-core-spark3_2.12-0.12.0-SNAPSHOT-sources.jar to /home/jenkins/.m2/repository/org/bdgenomics/cannoli/cannoli-core-spark3_2.12/0.12.0-SNAPSHOT/cannoli-core-spark3_2.12-0.12.0-SNAPSHOT-sources.jar
[INFO] Installing /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/core/target/cannoli-core-spark3_2.12-0.12.0-SNAPSHOT-javadoc.jar to /home/jenkins/.m2/repository/org/bdgenomics/cannoli/cannoli-core-spark3_2.12/0.12.0-SNAPSHOT/cannoli-core-spark3_2.12-0.12.0-SNAPSHOT-javadoc.jar
[INFO] Installing /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/core/target/cannoli-core-spark3_2.12-0.12.0-SNAPSHOT-javadoc.jar to /home/jenkins/.m2/repository/org/bdgenomics/cannoli/cannoli-core-spark3_2.12/0.12.0-SNAPSHOT/cannoli-core-spark3_2.12-0.12.0-SNAPSHOT-javadoc.jar
[INFO] 
[INFO] --- maven-deploy-plugin:3.0.0-M1:deploy (default-deploy) @ cannoli-core-spark3_2.12 ---
Downloading from sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-core-spark3_2.12/0.12.0-SNAPSHOT/maven-metadata.xml
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Downloaded from sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-core-spark3_2.12/0.12.0-SNAPSHOT/maven-metadata.xml (1.2 kB at 8.4 kB/s)
Uploading to sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-core-spark3_2.12/0.12.0-SNAPSHOT/cannoli-core-spark3_2.12-0.12.0-20210315.163949-22.jar
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Uploaded to sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-core-spark3_2.12/0.12.0-SNAPSHOT/cannoli-core-spark3_2.12-0.12.0-20210315.163949-22.jar (203 kB at 292 kB/s)
Uploading to sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-core-spark3_2.12/0.12.0-SNAPSHOT/cannoli-core-spark3_2.12-0.12.0-20210315.163949-22.pom
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Uploaded to sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-core-spark3_2.12/0.12.0-SNAPSHOT/cannoli-core-spark3_2.12-0.12.0-20210315.163949-22.pom (2.7 kB at 5.8 kB/s)
Uploading to sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-core-spark3_2.12/0.12.0-SNAPSHOT/cannoli-core-spark3_2.12-0.12.0-20210315.163949-22-sources.jar
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Uploaded to sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-core-spark3_2.12/0.12.0-SNAPSHOT/cannoli-core-spark3_2.12-0.12.0-20210315.163949-22-sources.jar (53 kB at 101 kB/s)
Uploading to sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-core-spark3_2.12/0.12.0-SNAPSHOT/cannoli-core-spark3_2.12-0.12.0-20210315.163949-22-javadoc.jar
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Uploaded to sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-core-spark3_2.12/0.12.0-SNAPSHOT/cannoli-core-spark3_2.12-0.12.0-20210315.163949-22-javadoc.jar (1.4 MB at 2.2 MB/s)
Uploading to sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-core-spark3_2.12/0.12.0-SNAPSHOT/cannoli-core-spark3_2.12-0.12.0-20210315.163949-22-javadoc.jar
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Uploaded to sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-core-spark3_2.12/0.12.0-SNAPSHOT/cannoli-core-spark3_2.12-0.12.0-20210315.163949-22-javadoc.jar (1.4 MB at 2.5 MB/s)
Downloading from sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-core-spark3_2.12/maven-metadata.xml
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Downloaded from sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-core-spark3_2.12/maven-metadata.xml (409 B at 2.7 kB/s)
Uploading to sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-core-spark3_2.12/0.12.0-SNAPSHOT/maven-metadata.xml
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Uploaded to sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-core-spark3_2.12/0.12.0-SNAPSHOT/maven-metadata.xml (1.2 kB at 2.6 kB/s)
Uploading to sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-core-spark3_2.12/maven-metadata.xml
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Uploaded to sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-core-spark3_2.12/maven-metadata.xml (409 B at 868 B/s)
[INFO] 
[INFO] -----------< org.bdgenomics.cannoli:cannoli-cli-spark3_2.12 >-----------
[INFO] Building Cannoli_2.12: CLI 0.12.0-SNAPSHOT                         [4/6]
[INFO] --------------------------------[ jar ]---------------------------------
[INFO] 
[INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-maven) @ cannoli-cli-spark3_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-java) @ cannoli-cli-spark3_2.12 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:timestamp-property (timestamp-property) @ cannoli-cli-spark3_2.12 ---
[INFO] 
[INFO] --- git-commit-id-plugin:2.2.2:revision (default) @ cannoli-cli-spark3_2.12 ---
[INFO] 
[INFO] --- templating-maven-plugin:1.0.0:filter-sources (filter-src) @ cannoli-cli-spark3_2.12 ---
[INFO] Coping files with filtering to temporary directory.
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 1 resource
[INFO] No files needs to be copied to output directory. Up to date: /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/cli/target/generated-sources/java-templates
[INFO] Source directory: /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/cli/target/generated-sources/java-templates added.
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ cannoli-cli-spark3_2.12 ---
[INFO] Source directory: /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/cli/src/main/scala added.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ cannoli-cli-spark3_2.12 ---
[INFO] Modified 0 of 27 .scala files
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ cannoli-cli-spark3_2.12 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/cli/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ cannoli-cli-spark3_2.12 ---
[WARNING]  Expected all dependencies to require Scala version: 2.12.10
[WARNING]  com.twitter:chill_2.12:0.9.5 requires scala version: 2.12.10
[WARNING]  org.apache.spark:spark-network-common_2.12:3.0.2 requires scala version: 2.12.10
[WARNING]  org.scala-lang.modules:scala-xml_2.12:1.2.0 requires scala version: 2.12.8
[WARNING] Multiple versions of scala libraries detected!
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ cannoli-cli-spark3_2.12 ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ cannoli-cli-spark3_2.12 ---
[INFO] Test Source directory: /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/cli/src/test/scala added.
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ cannoli-cli-spark3_2.12 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 5 resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ cannoli-cli-spark3_2.12 ---
[WARNING]  Expected all dependencies to require Scala version: 2.12.10
[WARNING]  com.twitter:chill_2.12:0.9.5 requires scala version: 2.12.10
[WARNING]  org.apache.spark:spark-network-common_2.12:3.0.2 requires scala version: 2.12.10
[WARNING]  org.scala-lang.modules:scala-xml_2.12:1.2.0 requires scala version: 2.12.8
[WARNING] Multiple versions of scala libraries detected!
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ cannoli-cli-spark3_2.12 ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ cannoli-cli-spark3_2.12 ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ cannoli-cli-spark3_2.12 ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- maven-jar-plugin:3.1.2:jar (default-jar) @ cannoli-cli-spark3_2.12 ---
[INFO] Building jar: /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/cli/target/cannoli-cli-spark3_2.12-0.12.0-SNAPSHOT.jar
[INFO] 
[INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ cannoli-cli-spark3_2.12 ---
[INFO] Building jar: /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/cli/target/cannoli-cli-spark3_2.12-0.12.0-SNAPSHOT-sources.jar
[INFO] 
[INFO] --- maven-javadoc-plugin:3.1.0:jar (attach-javadocs) @ cannoli-cli-spark3_2.12 ---
[INFO] The goal 'org.apache.maven.plugins:maven-javadoc-plugin:3.1.0:javadoc' has not been previously called for the module: 'org.bdgenomics.cannoli:cannoli-core-spark3_2.12:jar:0.12.0-SNAPSHOT'. Trying to invoke it...
[WARNING] Creating fake javadoc directory to prevent repeated invocations: /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/core/target/apidocs
[ERROR] Error fetching link: /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/core/target/apidocs. Ignored it.
[INFO] 
Loading source files for package org.bdgenomics.cannoli.cli...
Constructing Javadoc information...
Standard Doclet version 1.8.0_191
Building tree for all the packages and classes...
Generating /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/cli/target/apidocs/org/bdgenomics/cannoli/cli/About.html...
Generating /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/cli/target/apidocs/org/bdgenomics/cannoli/cli/package-frame.html...
Generating /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/cli/target/apidocs/org/bdgenomics/cannoli/cli/package-summary.html...
Generating /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/cli/target/apidocs/org/bdgenomics/cannoli/cli/package-tree.html...
Generating /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/cli/target/apidocs/constant-values.html...
Generating /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/cli/target/apidocs/org/bdgenomics/cannoli/cli/class-use/About.html...
Generating /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/cli/target/apidocs/org/bdgenomics/cannoli/cli/package-use.html...
Building index for all the packages and classes...
Generating /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/cli/target/apidocs/overview-tree.html...
Generating /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/cli/target/apidocs/index-all.html...
Generating /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/cli/target/apidocs/deprecated-list.html...
Building index for all classes...
Generating /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/cli/target/apidocs/allclasses-frame.html...
Generating /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/cli/target/apidocs/allclasses-noframe.html...
Generating /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/cli/target/apidocs/index.html...
Generating /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/cli/target/apidocs/help-doc.html...
[INFO] Building jar: /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/cli/target/cannoli-cli-spark3_2.12-0.12.0-SNAPSHOT-javadoc.jar
[INFO] 
[INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) > generate-sources @ cannoli-cli-spark3_2.12 >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-maven) @ cannoli-cli-spark3_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-java) @ cannoli-cli-spark3_2.12 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:timestamp-property (timestamp-property) @ cannoli-cli-spark3_2.12 ---
[INFO] 
[INFO] --- git-commit-id-plugin:2.2.2:revision (default) @ cannoli-cli-spark3_2.12 ---
[INFO] 
[INFO] --- templating-maven-plugin:1.0.0:filter-sources (filter-src) @ cannoli-cli-spark3_2.12 ---
[INFO] Coping files with filtering to temporary directory.
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 1 resource
[INFO] No files needs to be copied to output directory. Up to date: /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/cli/target/generated-sources/java-templates
[INFO] Source directory: /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/cli/target/generated-sources/java-templates added.
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ cannoli-cli-spark3_2.12 ---
[INFO] Source directory: /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/cli/src/main/scala added.
[INFO] 
[INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) < generate-sources @ cannoli-cli-spark3_2.12 <<<
[INFO] 
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ cannoli-cli-spark3_2.12 ---
[WARNING]  Expected all dependencies to require Scala version: 2.12.10
[WARNING]  com.twitter:chill_2.12:0.9.5 requires scala version: 2.12.10
[WARNING]  org.apache.spark:spark-network-common_2.12:3.0.2 requires scala version: 2.12.10
[WARNING]  org.scala-lang.modules:scala-xml_2.12:1.2.0 requires scala version: 2.12.8
[WARNING] Multiple versions of scala libraries detected!
[WARNING]  Expected all dependencies to require Scala version: 2.12.10
[WARNING]  com.twitter:chill_2.12:0.9.5 requires scala version: 2.12.10
[WARNING]  org.apache.spark:spark-network-common_2.12:3.0.2 requires scala version: 2.12.10
[WARNING]  org.scala-lang.modules:scala-xml_2.12:1.2.0 requires scala version: 2.12.8
[WARNING] Multiple versions of scala libraries detected!
model contains 78 documentable templates
[INFO] Building jar: /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/cli/target/cannoli-cli-spark3_2.12-0.12.0-SNAPSHOT-javadoc.jar
[INFO] 
[INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-javadocs) > generate-sources @ cannoli-cli-spark3_2.12 >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-maven) @ cannoli-cli-spark3_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-java) @ cannoli-cli-spark3_2.12 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:timestamp-property (timestamp-property) @ cannoli-cli-spark3_2.12 ---
[INFO] 
[INFO] --- git-commit-id-plugin:2.2.2:revision (default) @ cannoli-cli-spark3_2.12 ---
[INFO] 
[INFO] --- templating-maven-plugin:1.0.0:filter-sources (filter-src) @ cannoli-cli-spark3_2.12 ---
[INFO] Coping files with filtering to temporary directory.
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 1 resource
[INFO] No files needs to be copied to output directory. Up to date: /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/cli/target/generated-sources/java-templates
[INFO] Source directory: /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/cli/target/generated-sources/java-templates added.
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ cannoli-cli-spark3_2.12 ---
[INFO] Source directory: /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/cli/src/main/scala added.
[INFO] 
[INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-javadocs) < generate-sources @ cannoli-cli-spark3_2.12 <<<
[INFO] 
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-javadocs) @ cannoli-cli-spark3_2.12 ---
[WARNING]  Expected all dependencies to require Scala version: 2.12.10
[WARNING]  com.twitter:chill_2.12:0.9.5 requires scala version: 2.12.10
[WARNING]  org.apache.spark:spark-network-common_2.12:3.0.2 requires scala version: 2.12.10
[WARNING]  org.scala-lang.modules:scala-xml_2.12:1.2.0 requires scala version: 2.12.8
[WARNING] Multiple versions of scala libraries detected!
[WARNING]  Expected all dependencies to require Scala version: 2.12.10
[WARNING]  com.twitter:chill_2.12:0.9.5 requires scala version: 2.12.10
[WARNING]  org.apache.spark:spark-network-common_2.12:3.0.2 requires scala version: 2.12.10
[WARNING]  org.scala-lang.modules:scala-xml_2.12:1.2.0 requires scala version: 2.12.8
[WARNING] Multiple versions of scala libraries detected!
model contains 78 documentable templates
[INFO] Building jar: /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/cli/target/cannoli-cli-spark3_2.12-0.12.0-SNAPSHOT-javadoc.jar
[INFO] 
[INFO] --- maven-license-plugin:1.10.b1:check (default) @ cannoli-cli-spark3_2.12 ---
[INFO] Checking licenses...
[INFO] 
[INFO] --- maven-install-plugin:3.0.0-M1:install (default-install) @ cannoli-cli-spark3_2.12 ---
[INFO] Installing /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/cli/target/cannoli-cli-spark3_2.12-0.12.0-SNAPSHOT.jar to /home/jenkins/.m2/repository/org/bdgenomics/cannoli/cannoli-cli-spark3_2.12/0.12.0-SNAPSHOT/cannoli-cli-spark3_2.12-0.12.0-SNAPSHOT.jar
[INFO] Installing /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/cli/pom.xml to /home/jenkins/.m2/repository/org/bdgenomics/cannoli/cannoli-cli-spark3_2.12/0.12.0-SNAPSHOT/cannoli-cli-spark3_2.12-0.12.0-SNAPSHOT.pom
[INFO] Installing /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/cli/target/cannoli-cli-spark3_2.12-0.12.0-SNAPSHOT-sources.jar to /home/jenkins/.m2/repository/org/bdgenomics/cannoli/cannoli-cli-spark3_2.12/0.12.0-SNAPSHOT/cannoli-cli-spark3_2.12-0.12.0-SNAPSHOT-sources.jar
[INFO] Installing /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/cli/target/cannoli-cli-spark3_2.12-0.12.0-SNAPSHOT-javadoc.jar to /home/jenkins/.m2/repository/org/bdgenomics/cannoli/cannoli-cli-spark3_2.12/0.12.0-SNAPSHOT/cannoli-cli-spark3_2.12-0.12.0-SNAPSHOT-javadoc.jar
[INFO] Installing /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/cli/target/cannoli-cli-spark3_2.12-0.12.0-SNAPSHOT-javadoc.jar to /home/jenkins/.m2/repository/org/bdgenomics/cannoli/cannoli-cli-spark3_2.12/0.12.0-SNAPSHOT/cannoli-cli-spark3_2.12-0.12.0-SNAPSHOT-javadoc.jar
[INFO] Installing /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/cli/target/cannoli-cli-spark3_2.12-0.12.0-SNAPSHOT-javadoc.jar to /home/jenkins/.m2/repository/org/bdgenomics/cannoli/cannoli-cli-spark3_2.12/0.12.0-SNAPSHOT/cannoli-cli-spark3_2.12-0.12.0-SNAPSHOT-javadoc.jar
[INFO] 
[INFO] --- maven-deploy-plugin:3.0.0-M1:deploy (default-deploy) @ cannoli-cli-spark3_2.12 ---
Downloading from sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-cli-spark3_2.12/0.12.0-SNAPSHOT/maven-metadata.xml
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Downloaded from sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-cli-spark3_2.12/0.12.0-SNAPSHOT/maven-metadata.xml (1.2 kB at 8.4 kB/s)
Uploading to sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-cli-spark3_2.12/0.12.0-SNAPSHOT/cannoli-cli-spark3_2.12-0.12.0-20210315.164020-22.jar
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Uploaded to sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-cli-spark3_2.12/0.12.0-SNAPSHOT/cannoli-cli-spark3_2.12-0.12.0-20210315.164020-22.jar (219 kB at 305 kB/s)
Uploading to sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-cli-spark3_2.12/0.12.0-SNAPSHOT/cannoli-cli-spark3_2.12-0.12.0-20210315.164020-22.pom
Progress (1): 3.7 kB
                    
Uploaded to sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-cli-spark3_2.12/0.12.0-SNAPSHOT/cannoli-cli-spark3_2.12-0.12.0-20210315.164020-22.pom (3.7 kB at 7.9 kB/s)
Uploading to sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-cli-spark3_2.12/0.12.0-SNAPSHOT/cannoli-cli-spark3_2.12-0.12.0-20210315.164020-22-sources.jar
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Uploaded to sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-cli-spark3_2.12/0.12.0-SNAPSHOT/cannoli-cli-spark3_2.12-0.12.0-20210315.164020-22-sources.jar (45 kB at 96 kB/s)
Uploading to sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-cli-spark3_2.12/0.12.0-SNAPSHOT/cannoli-cli-spark3_2.12-0.12.0-20210315.164020-22-javadoc.jar
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Uploaded to sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-cli-spark3_2.12/0.12.0-SNAPSHOT/cannoli-cli-spark3_2.12-0.12.0-20210315.164020-22-javadoc.jar (1.6 MB at 2.5 MB/s)
Uploading to sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-cli-spark3_2.12/0.12.0-SNAPSHOT/cannoli-cli-spark3_2.12-0.12.0-20210315.164020-22-javadoc.jar
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Uploaded to sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-cli-spark3_2.12/0.12.0-SNAPSHOT/cannoli-cli-spark3_2.12-0.12.0-20210315.164020-22-javadoc.jar (1.6 MB at 2.7 MB/s)
Uploading to sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-cli-spark3_2.12/0.12.0-SNAPSHOT/cannoli-cli-spark3_2.12-0.12.0-20210315.164020-22-javadoc.jar
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Uploaded to sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-cli-spark3_2.12/0.12.0-SNAPSHOT/cannoli-cli-spark3_2.12-0.12.0-20210315.164020-22-javadoc.jar (1.6 MB at 2.7 MB/s)
Downloading from sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-cli-spark3_2.12/maven-metadata.xml
Progress (1): 408 B
                   
Downloaded from sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-cli-spark3_2.12/maven-metadata.xml (408 B at 2.6 kB/s)
Uploading to sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-cli-spark3_2.12/0.12.0-SNAPSHOT/maven-metadata.xml
Progress (1): 1.2 kB
                    
Uploaded to sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-cli-spark3_2.12/0.12.0-SNAPSHOT/maven-metadata.xml (1.2 kB at 1.8 kB/s)
Uploading to sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-cli-spark3_2.12/maven-metadata.xml
Progress (1): 408 B
                   
Uploaded to sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-cli-spark3_2.12/maven-metadata.xml (408 B at 790 B/s)
[INFO] 
[INFO] --------< org.bdgenomics.cannoli:cannoli-assembly-spark3_2.12 >---------
[INFO] Building Cannoli_2.12: Assembly 0.12.0-SNAPSHOT                    [5/6]
[INFO] --------------------------------[ jar ]---------------------------------
[INFO] 
[INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-maven) @ cannoli-assembly-spark3_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-java) @ cannoli-assembly-spark3_2.12 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ cannoli-assembly-spark3_2.12 ---
[INFO] Source directory: /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/assembly/src/main/scala added.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ cannoli-assembly-spark3_2.12 ---
[INFO] Modified 0 of 1 .scala files
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ cannoli-assembly-spark3_2.12 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/assembly/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ cannoli-assembly-spark3_2.12 ---
[WARNING]  Expected all dependencies to require Scala version: 2.12.10
[WARNING]  org.bdgenomics.utils:utils-misc-spark3_2.12:0.3.0 requires scala version: 2.12.8
[WARNING] Multiple versions of scala libraries detected!
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ cannoli-assembly-spark3_2.12 ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ cannoli-assembly-spark3_2.12 ---
[INFO] Test Source directory: /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/assembly/src/test/scala added.
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ cannoli-assembly-spark3_2.12 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/assembly/src/test/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ cannoli-assembly-spark3_2.12 ---
[WARNING]  Expected all dependencies to require Scala version: 2.12.10
[WARNING]  org.bdgenomics.utils:utils-misc-spark3_2.12:0.3.0 requires scala version: 2.12.8
[WARNING] Multiple versions of scala libraries detected!
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ cannoli-assembly-spark3_2.12 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ cannoli-assembly-spark3_2.12 ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- maven-jar-plugin:3.1.2:jar (default-jar) @ cannoli-assembly-spark3_2.12 ---
[INFO] 
[INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ cannoli-assembly-spark3_2.12 ---
[INFO] Building jar: /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/assembly/target/cannoli-assembly-spark3_2.12-0.12.0-SNAPSHOT-sources.jar
[INFO] 
[INFO] --- maven-javadoc-plugin:3.1.0:jar (attach-javadocs) @ cannoli-assembly-spark3_2.12 ---
[INFO] 
[INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) > generate-sources @ cannoli-assembly-spark3_2.12 >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-maven) @ cannoli-assembly-spark3_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-java) @ cannoli-assembly-spark3_2.12 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ cannoli-assembly-spark3_2.12 ---
[INFO] Source directory: /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/assembly/src/main/scala added.
[INFO] 
[INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) < generate-sources @ cannoli-assembly-spark3_2.12 <<<
[INFO] 
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ cannoli-assembly-spark3_2.12 ---
[WARNING]  Expected all dependencies to require Scala version: 2.12.10
[WARNING]  org.bdgenomics.utils:utils-misc-spark3_2.12:0.3.0 requires scala version: 2.12.8
[WARNING] Multiple versions of scala libraries detected!
[WARNING]  Expected all dependencies to require Scala version: 2.12.10
[WARNING]  org.bdgenomics.utils:utils-misc-spark3_2.12:0.3.0 requires scala version: 2.12.8
[WARNING] Multiple versions of scala libraries detected!
model contains 6 documentable templates
[INFO] Building jar: /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/assembly/target/cannoli-assembly-spark3_2.12-0.12.0-SNAPSHOT-javadoc.jar
[INFO] 
[INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-javadocs) > generate-sources @ cannoli-assembly-spark3_2.12 >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-maven) @ cannoli-assembly-spark3_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-java) @ cannoli-assembly-spark3_2.12 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ cannoli-assembly-spark3_2.12 ---
[INFO] Source directory: /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/assembly/src/main/scala added.
[INFO] 
[INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-javadocs) < generate-sources @ cannoli-assembly-spark3_2.12 <<<
[INFO] 
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-javadocs) @ cannoli-assembly-spark3_2.12 ---
[WARNING]  Expected all dependencies to require Scala version: 2.12.10
[WARNING]  org.bdgenomics.utils:utils-misc-spark3_2.12:0.3.0 requires scala version: 2.12.8
[WARNING] Multiple versions of scala libraries detected!
[WARNING]  Expected all dependencies to require Scala version: 2.12.10
[WARNING]  org.bdgenomics.utils:utils-misc-spark3_2.12:0.3.0 requires scala version: 2.12.8
[WARNING] Multiple versions of scala libraries detected!
model contains 6 documentable templates
[INFO] Building jar: /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/assembly/target/cannoli-assembly-spark3_2.12-0.12.0-SNAPSHOT-javadoc.jar
[INFO] 
[INFO] --- maven-shade-plugin:3.2.0:shade (default) @ cannoli-assembly-spark3_2.12 ---
[INFO] Including org.bdgenomics.cannoli:cannoli-cli-spark3_2.12:jar:0.12.0-SNAPSHOT in the shaded jar.
[INFO] Including org.bdgenomics.adam:adam-cli-spark3_2.12:jar:0.34.0 in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-misc-spark3_2.12:jar:0.3.0 in the shaded jar.
[INFO] Including org.scala-lang:scala-library:jar:2.12.8 in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-io-spark3_2.12:jar:0.3.0 in the shaded jar.
[INFO] Including org.apache.httpcomponents:httpclient:jar:4.5.7 in the shaded jar.
[INFO] Including org.apache.httpcomponents:httpcore:jar:4.4.11 in the shaded jar.
[INFO] Including commons-logging:commons-logging:jar:1.2 in the shaded jar.
[INFO] Including commons-codec:commons-codec:jar:1.11 in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-cli-spark3_2.12:jar:0.3.0 in the shaded jar.
[INFO] Including org.clapper:grizzled-slf4j_2.12:jar:1.3.4 in the shaded jar.
[INFO] Including org.slf4j:slf4j-api:jar:1.7.9 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-avro:jar:1.10.1 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-column:jar:1.10.1 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-common:jar:1.10.1 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-encoding:jar:1.10.1 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-hadoop:jar:1.10.1 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-jackson:jar:1.10.1 in the shaded jar.
[INFO] Including commons-pool:commons-pool:jar:1.6 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-format:jar:2.4.0 in the shaded jar.
[INFO] Including org.bdgenomics.bdg-formats:bdg-formats:jar:0.15.0 in the shaded jar.
[INFO] Including org.apache.avro:avro:jar:1.8.2 in the shaded jar.
[INFO] Including org.codehaus.jackson:jackson-core-asl:jar:1.9.13 in the shaded jar.
[INFO] Including org.codehaus.jackson:jackson-mapper-asl:jar:1.9.13 in the shaded jar.
[INFO] Including com.thoughtworks.paranamer:paranamer:jar:2.7 in the shaded jar.
[INFO] Including org.xerial.snappy:snappy-java:jar:1.1.1.3 in the shaded jar.
[INFO] Including org.apache.commons:commons-compress:jar:1.8.1 in the shaded jar.
[INFO] Including org.tukaani:xz:jar:1.5 in the shaded jar.
[INFO] Including org.bdgenomics.adam:adam-core-spark3_2.12:jar:0.34.0 in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-intervalrdd-spark3_2.12:jar:0.3.0 in the shaded jar.
[INFO] Including com.esotericsoftware.kryo:kryo:jar:2.24.0 in the shaded jar.
[INFO] Including com.esotericsoftware.minlog:minlog:jar:1.2 in the shaded jar.
[INFO] Including org.objenesis:objenesis:jar:2.1 in the shaded jar.
[INFO] Including commons-io:commons-io:jar:2.6 in the shaded jar.
[INFO] Including it.unimi.dsi:fastutil:jar:6.6.5 in the shaded jar.
[INFO] Including org.seqdoop:hadoop-bam:jar:7.9.2 in the shaded jar.
[INFO] Including com.github.jsr203hadoop:jsr203hadoop:jar:1.0.3 in the shaded jar.
[INFO] Including com.github.samtools:htsjdk:jar:2.19.0 in the shaded jar.
[INFO] Including org.apache.commons:commons-jexl:jar:2.1.1 in the shaded jar.
[INFO] Including gov.nih.nlm.ncbi:ngs-java:jar:2.9.0 in the shaded jar.
[INFO] Including com.google.guava:guava:jar:27.0.1-jre in the shaded jar.
[INFO] Including com.google.guava:failureaccess:jar:1.0.1 in the shaded jar.
[INFO] Including com.google.guava:listenablefuture:jar:9999.0-empty-to-avoid-conflict-with-guava in the shaded jar.
[INFO] Including org.checkerframework:checker-qual:jar:2.5.2 in the shaded jar.
[INFO] Including com.google.errorprone:error_prone_annotations:jar:2.2.0 in the shaded jar.
[INFO] Including com.google.j2objc:j2objc-annotations:jar:1.1 in the shaded jar.
[INFO] Including org.codehaus.mojo:animal-sniffer-annotations:jar:1.17 in the shaded jar.
[INFO] Including org.bdgenomics.adam:adam-codegen-spark3_2.12:jar:0.34.0 in the shaded jar.
[INFO] Including org.bdgenomics.adam:adam-apis-spark3_2.12:jar:0.34.0 in the shaded jar.
[INFO] Including args4j:args4j:jar:2.33 in the shaded jar.
[INFO] Including net.codingwell:scala-guice_2.12:jar:4.2.1 in the shaded jar.
[INFO] Including com.google.inject:guice:jar:4.2.0 in the shaded jar.
[INFO] Including javax.inject:javax.inject:jar:1 in the shaded jar.
[INFO] Including aopalliance:aopalliance:jar:1.0 in the shaded jar.
[INFO] Including org.scala-lang:scala-reflect:jar:2.12.6 in the shaded jar.
[INFO] Including com.google.code.findbugs:jsr305:jar:1.3.9 in the shaded jar.
[INFO] Including org.bdgenomics.cannoli:cannoli-core-spark3_2.12:jar:0.12.0-SNAPSHOT in the shaded jar.
[INFO] Including org.bdgenomics.cannoli:cannoli-builder-spark3_2.12:jar:0.12.0-SNAPSHOT in the shaded jar.
[WARNING] cannoli-assembly-spark3_2.12-0.12.0-SNAPSHOT.jar, bdg-formats-0.15.0.jar define 58 overlapping classes: 
[WARNING]   - org.bdgenomics.formats.avro.VariantCallingAnnotations$Builder
[WARNING]   - org.bdgenomics.formats.avro.VariantAnnotation$Builder
[WARNING]   - org.bdgenomics.formats.avro.Reference$1
[WARNING]   - org.bdgenomics.formats.avro.VariantAnnotationMessage
[WARNING]   - org.bdgenomics.formats.avro.Alignment$Builder
[WARNING]   - org.bdgenomics.formats.avro.OntologyTerm$1
[WARNING]   - org.bdgenomics.formats.avro.Alignment$1
[WARNING]   - org.bdgenomics.formats.avro.Feature$1
[WARNING]   - org.bdgenomics.formats.avro.Sequence$1
[WARNING]   - org.bdgenomics.formats.avro.ReadGroup$Builder
[WARNING]   - 48 more...
[WARNING] cannoli-assembly-spark3_2.12-0.12.0-SNAPSHOT.jar, parquet-column-1.10.1.jar define 792 overlapping classes: 
[WARNING]   - org.apache.parquet.it.unimi.dsi.fastutil.longs.LongComparator
[WARNING]   - org.apache.parquet.column.values.dictionary.DictionaryValuesWriter$PlainIntegerDictionaryValuesWriter
[WARNING]   - org.apache.parquet.io.PrimitiveColumnIO
[WARNING]   - org.apache.parquet.io.api.Binary$ByteBufferBackedBinary
[WARNING]   - org.apache.parquet.it.unimi.dsi.fastutil.doubles.DoubleSortedSet
[WARNING]   - org.apache.parquet.io.BaseRecordReader
[WARNING]   - org.apache.parquet.column.ParquetProperties$1
[WARNING]   - org.apache.parquet.column.UnknownColumnException
[WARNING]   - org.apache.parquet.filter.ColumnPredicates$12
[WARNING]   - org.apache.parquet.schema.Types$BaseMapBuilder$ListValueBuilder
[WARNING]   - 782 more...
[WARNING] cannoli-assembly-spark3_2.12-0.12.0-SNAPSHOT.jar, commons-jexl-2.1.1.jar define 178 overlapping classes: 
[WARNING]   - org.apache.commons.jexl2.internal.AbstractExecutor$Get
[WARNING]   - org.apache.commons.jexl2.introspection.JexlPropertyGet
[WARNING]   - org.apache.commons.jexl2.parser.StringParser
[WARNING]   - org.apache.commons.jexl2.parser.ASTBitwiseOrNode
[WARNING]   - org.apache.commons.jexl2.internal.introspection.MethodKey$1
[WARNING]   - org.apache.commons.jexl2.Main
[WARNING]   - org.apache.commons.jexl2.parser.ASTForeachStatement
[WARNING]   - org.apache.commons.jexl2.introspection.Sandbox
[WARNING]   - org.apache.commons.jexl2.internal.introspection.ClassMap
[WARNING]   - org.apache.commons.jexl2.parser.ASTFunctionNode
[WARNING]   - 168 more...
[WARNING] cannoli-assembly-spark3_2.12-0.12.0-SNAPSHOT.jar, j2objc-annotations-1.1.jar define 12 overlapping classes: 
[WARNING]   - com.google.j2objc.annotations.Property
[WARNING]   - com.google.j2objc.annotations.RetainedWith
[WARNING]   - com.google.j2objc.annotations.RetainedLocalRef
[WARNING]   - com.google.j2objc.annotations.J2ObjCIncompatible
[WARNING]   - com.google.j2objc.annotations.AutoreleasePool
[WARNING]   - com.google.j2objc.annotations.LoopTranslation$LoopStyle
[WARNING]   - com.google.j2objc.annotations.ReflectionSupport$Level
[WARNING]   - com.google.j2objc.annotations.ReflectionSupport
[WARNING]   - com.google.j2objc.annotations.WeakOuter
[WARNING]   - com.google.j2objc.annotations.Weak
[WARNING]   - 2 more...
[WARNING] cannoli-assembly-spark3_2.12-0.12.0-SNAPSHOT.jar, parquet-encoding-1.10.1.jar define 305 overlapping classes: 
[WARNING]   - org.apache.parquet.column.values.bitpacking.ByteBitPackingForLongBE$Packer25
[WARNING]   - org.apache.parquet.column.values.bitpacking.ByteBitPackingBE$Packer14
[WARNING]   - org.apache.parquet.column.values.bitpacking.BytePackerForLong
[WARNING]   - org.apache.parquet.column.values.bitpacking.ByteBitPackingLE$Packer10
[WARNING]   - org.apache.parquet.column.values.bitpacking.ByteBitPackingForLongLE$Packer54
[WARNING]   - org.apache.parquet.column.values.bitpacking.ByteBitPackingForLongLE$Packer41
[WARNING]   - org.apache.parquet.column.values.bitpacking.ByteBitPackingLE$Packer30
[WARNING]   - org.apache.parquet.column.values.bitpacking.ByteBitPackingLE$Packer23
[WARNING]   - org.apache.parquet.column.values.bitpacking.LemireBitPackingLE$Packer19
[WARNING]   - org.apache.parquet.column.values.bitpacking.ByteBitPackingForLongLE$Packer21
[WARNING]   - 295 more...
[WARNING] cannoli-assembly-spark3_2.12-0.12.0-SNAPSHOT.jar, failureaccess-1.0.1.jar define 2 overlapping classes: 
[WARNING]   - com.google.common.util.concurrent.internal.InternalFutureFailureAccess
[WARNING]   - com.google.common.util.concurrent.internal.InternalFutures
[WARNING] cannoli-assembly-spark3_2.12-0.12.0-SNAPSHOT.jar, args4j-2.33.jar define 74 overlapping classes: 
[WARNING]   - org.kohsuke.args4j.spi.DoubleOptionHandler
[WARNING]   - org.kohsuke.args4j.spi.MethodSetter
[WARNING]   - org.kohsuke.args4j.spi.MacAddressOptionHandler
[WARNING]   - org.kohsuke.args4j.spi.StringArrayOptionHandler
[WARNING]   - org.kohsuke.args4j.spi.SubCommand
[WARNING]   - org.kohsuke.args4j.spi.PatternOptionHandler
[WARNING]   - org.kohsuke.args4j.ParserProperties$1
[WARNING]   - org.kohsuke.args4j.OptionHandlerFilter$2
[WARNING]   - org.kohsuke.args4j.spi.MultiFileOptionHandler
[WARNING]   - org.kohsuke.args4j.OptionHandlerRegistry$DefaultConstructorHandlerFactory
[WARNING]   - 64 more...
[WARNING] cannoli-assembly-spark3_2.12-0.12.0-SNAPSHOT.jar, utils-misc-spark3_2.12-0.3.0.jar define 2 overlapping classes: 
[WARNING]   - org.bdgenomics.utils.misc.MathUtils
[WARNING]   - org.bdgenomics.utils.misc.MathUtils$
[WARNING] cannoli-assembly-spark3_2.12-0.12.0-SNAPSHOT.jar, commons-pool-1.6.jar define 55 overlapping classes: 
[WARNING]   - org.apache.commons.pool.PoolUtils$PoolableObjectFactoryAdaptor
[WARNING]   - org.apache.commons.pool.impl.GenericObjectPool$1
[WARNING]   - org.apache.commons.pool.impl.GenericObjectPool$Latch
[WARNING]   - org.apache.commons.pool.PoolUtils$ErodingFactor
[WARNING]   - org.apache.commons.pool.BasePoolableObjectFactory
[WARNING]   - org.apache.commons.pool.PoolUtils$KeyedPoolableObjectFactoryAdaptor
[WARNING]   - org.apache.commons.pool.impl.EvictionTimer$PrivilegedGetTccl
[WARNING]   - org.apache.commons.pool.impl.StackKeyedObjectPool
[WARNING]   - org.apache.commons.pool.BaseKeyedPoolableObjectFactory
[WARNING]   - org.apache.commons.pool.impl.GenericKeyedObjectPool$ObjectQueue
[WARNING]   - 45 more...
[WARNING] cannoli-assembly-spark3_2.12-0.12.0-SNAPSHOT.jar, parquet-hadoop-1.10.1.jar define 162 overlapping classes: 
[WARNING]   - org.apache.parquet.hadoop.mapred.DeprecatedParquetOutputFormat
[WARNING]   - org.apache.parquet.hadoop.api.WriteSupport$WriteContext
[WARNING]   - org.apache.parquet.format.converter.ParquetMetadataConverter$RangeMetadataFilter
[WARNING]   - org.apache.parquet.hadoop.ColumnChunkPageReadStore$ColumnChunkPageReader$1
[WARNING]   - org.apache.parquet.format.converter.ParquetMetadataConverter$2
[WARNING]   - org.apache.parquet.hadoop.metadata.ColumnChunkMetaData
[WARNING]   - org.apache.parquet.hadoop.api.WriteSupport$FinalizedWriteContext
[WARNING]   - org.apache.parquet.hadoop.util.HadoopPositionOutputStream
[WARNING]   - org.apache.parquet.HadoopReadOptions$1
[WARNING]   - org.apache.parquet.format.converter.ParquetMetadataConverter$NoFilter
[WARNING]   - 152 more...
[WARNING] cannoli-assembly-spark3_2.12-0.12.0-SNAPSHOT.jar, commons-compress-1.8.1.jar define 191 overlapping classes: 
[WARNING]   - org.apache.commons.compress.archivers.sevenz.SevenZArchiveEntry
[WARNING]   - org.apache.commons.compress.archivers.dump.ShortFileException
[WARNING]   - org.apache.commons.compress.utils.CountingInputStream
[WARNING]   - org.apache.commons.compress.compressors.bzip2.CRC
[WARNING]   - org.apache.commons.compress.compressors.bzip2.BZip2CompressorOutputStream
[WARNING]   - org.apache.commons.compress.archivers.dump.DumpArchiveEntry
[WARNING]   - org.apache.commons.compress.changes.ChangeSetPerformer$ArchiveEntryIterator
[WARNING]   - org.apache.commons.compress.compressors.bzip2.BlockSort
[WARNING]   - org.apache.commons.compress.archivers.tar.TarArchiveEntry
[WARNING]   - org.apache.commons.compress.archivers.dump.UnsupportedCompressionAlgorithmException
[WARNING]   - 181 more...
[WARNING] cannoli-assembly-spark3_2.12-0.12.0-SNAPSHOT.jar, error_prone_annotations-2.2.0.jar define 22 overlapping classes: 
[WARNING]   - com.google.errorprone.annotations.NoAllocation
[WARNING]   - com.google.errorprone.annotations.Var
[WARNING]   - com.google.errorprone.annotations.IncompatibleModifiers
[WARNING]   - com.google.errorprone.annotations.CompatibleWith
[WARNING]   - com.google.errorprone.annotations.concurrent.LockMethod
[WARNING]   - com.google.errorprone.annotations.FormatString
[WARNING]   - com.google.errorprone.annotations.DoNotCall
[WARNING]   - com.google.errorprone.annotations.Immutable
[WARNING]   - com.google.errorprone.annotations.RestrictedApi
[WARNING]   - com.google.errorprone.annotations.ForOverride
[WARNING]   - 12 more...
[WARNING] cannoli-assembly-spark3_2.12-0.12.0-SNAPSHOT.jar, scala-library-2.12.8.jar define 2503 overlapping classes: 
[WARNING]   - scala.collection.package$$anon$1
[WARNING]   - scala.FallbackArrayBuilding
[WARNING]   - scala.collection.immutable.IndexedSeq
[WARNING]   - scala.collection.mutable.ArrayOps$ofShort
[WARNING]   - scala.Function2$mcDID$sp
[WARNING]   - scala.collection.immutable.IntMapValueIterator
[WARNING]   - scala.collection.SeqViewLike$$anon$11
[WARNING]   - scala.runtime.AbstractFunction1$mcIF$sp
[WARNING]   - scala.annotation.meta.field
[WARNING]   - scala.collection.MapLike$DefaultKeySet
[WARNING]   - 2493 more...
[WARNING] cannoli-assembly-spark3_2.12-0.12.0-SNAPSHOT.jar, httpcore-4.4.11.jar define 252 overlapping classes: 
[WARNING]   - org.apache.http.protocol.HttpRequestHandler
[WARNING]   - org.apache.http.impl.io.ChunkedOutputStream
[WARNING]   - org.apache.http.protocol.ChainBuilder
[WARNING]   - org.apache.http.impl.entity.DisallowIdentityContentLengthStrategy
[WARNING]   - org.apache.http.impl.ConnSupport
[WARNING]   - org.apache.http.impl.io.DefaultHttpResponseParserFactory
[WARNING]   - org.apache.http.HttpClientConnection
[WARNING]   - org.apache.http.NameValuePair
[WARNING]   - org.apache.http.protocol.HttpExpectationVerifier
[WARNING]   - org.apache.http.impl.io.AbstractMessageWriter
[WARNING]   - 242 more...
[WARNING] cannoli-assembly-spark3_2.12-0.12.0-SNAPSHOT.jar, utils-intervalrdd-spark3_2.12-0.3.0.jar define 15 overlapping classes: 
[WARNING]   - org.bdgenomics.utils.interval.array.IntervalArray$
[WARNING]   - org.bdgenomics.utils.interval.rdd.IntervalPartition$
[WARNING]   - org.bdgenomics.utils.interval.array.ConcreteIntervalArray$
[WARNING]   - org.bdgenomics.utils.interval.array.Interval
[WARNING]   - org.bdgenomics.utils.interval.array.IntervalArray
[WARNING]   - org.bdgenomics.utils.interval.rdd.IntervalRDD$
[WARNING]   - org.bdgenomics.utils.interval.rdd.intervalrdd.package$
[WARNING]   - org.bdgenomics.utils.interval.rdd.IntervalPartition
[WARNING]   - org.bdgenomics.utils.interval.rdd.PartitionMerger
[WARNING]   - org.bdgenomics.utils.interval.rdd.intervalrdd.package
[WARNING]   - 5 more...
[WARNING] cannoli-assembly-spark3_2.12-0.12.0-SNAPSHOT.jar, parquet-avro-1.10.1.jar define 95 overlapping classes: 
[WARNING]   - org.apache.parquet.avro.AvroParquetInputFormat
[WARNING]   - org.apache.parquet.avro.AvroRecordConverter$AvroCollectionConverter$1
[WARNING]   - org.apache.parquet.avro.AvroRecordConverter$AvroArrayConverter$7
[WARNING]   - org.apache.parquet.avro.AvroConverters$AvroPrimitiveConverter
[WARNING]   - org.apache.parquet.avro.AvroWriteSupport$TwoLevelListWriter
[WARNING]   - org.apache.parquet.avro.ParentValueContainer$10
[WARNING]   - org.apache.parquet.avro.ParentValueContainer$13
[WARNING]   - org.apache.parquet.avro.AvroConverters$FieldIntegerConverter
[WARNING]   - org.apache.parquet.avro.AvroCompatRecordMaterializer
[WARNING]   - org.apache.parquet.avro.AvroWriteSupport$ListWriter
[WARNING]   - 85 more...
[WARNING] cannoli-assembly-spark3_2.12-0.12.0-SNAPSHOT.jar, animal-sniffer-annotations-1.17.jar define 1 overlapping classes: 
[WARNING]   - org.codehaus.mojo.animal_sniffer.IgnoreJRERequirement
[WARNING] cannoli-assembly-spark3_2.12-0.12.0-SNAPSHOT.jar, xz-1.5.jar define 105 overlapping classes: 
[WARNING]   - org.tukaani.xz.lzma.LZMADecoder$LengthDecoder
[WARNING]   - org.tukaani.xz.index.IndexDecoder
[WARNING]   - org.tukaani.xz.lzma.LZMADecoder
[WARNING]   - org.tukaani.xz.lzma.LZMAEncoderFast
[WARNING]   - org.tukaani.xz.lzma.LZMAEncoder$LengthEncoder
[WARNING]   - org.tukaani.xz.BlockOutputStream
[WARNING]   - org.tukaani.xz.simple.SimpleFilter
[WARNING]   - org.tukaani.xz.rangecoder.RangeCoder
[WARNING]   - org.tukaani.xz.XZOutputStream
[WARNING]   - org.tukaani.xz.UncompressedLZMA2OutputStream
[WARNING]   - 95 more...
[WARNING] cannoli-assembly-spark3_2.12-0.12.0-SNAPSHOT.jar, scala-reflect-2.12.6.jar define 1372 overlapping classes: 
[WARNING]   - scala.reflect.internal.tpe.TypeMaps$CollectTypeCollector
[WARNING]   - scala.reflect.runtime.ReflectionUtils
[WARNING]   - scala.reflect.internal.Scopes$LookupInaccessible$
[WARNING]   - scala.reflect.internal.Types$LazyType
[WARNING]   - scala.reflect.internal.SymbolPairs$Cursor
[WARNING]   - scala.reflect.internal.Types$StaticallyAnnotatedType$
[WARNING]   - scala.reflect.internal.tpe.TypeMaps
[WARNING]   - scala.reflect.api.TypeTags$TypeTagImpl
[WARNING]   - scala.reflect.api.StandardLiftables$StandardUnliftableInstances$$anonfun$unliftTuple18$1
[WARNING]   - scala.reflect.runtime.SynchronizedSymbols$SynchronizedClassSymbol
[WARNING]   - 1362 more...
[WARNING] cannoli-assembly-spark3_2.12-0.12.0-SNAPSHOT.jar, paranamer-2.7.jar define 21 overlapping classes: 
[WARNING]   - com.thoughtworks.paranamer.PositionalParanamer
[WARNING]   - com.thoughtworks.paranamer.JavadocParanamer
[WARNING]   - com.thoughtworks.paranamer.BytecodeReadingParanamer
[WARNING]   - com.thoughtworks.paranamer.BytecodeReadingParanamer$Type
[WARNING]   - com.thoughtworks.paranamer.BytecodeReadingParanamer$1
[WARNING]   - com.thoughtworks.paranamer.JavadocParanamer$DirJavadocProvider
[WARNING]   - com.thoughtworks.paranamer.AnnotationParanamer$Jsr330Helper
[WARNING]   - com.thoughtworks.paranamer.BytecodeReadingParanamer$TypeCollector
[WARNING]   - com.thoughtworks.paranamer.AnnotationParanamer
[WARNING]   - com.thoughtworks.paranamer.NullParanamer
[WARNING]   - 11 more...
[WARNING] cannoli-assembly-spark3_2.12-0.12.0-SNAPSHOT.jar, jsr203hadoop-1.0.3.jar define 27 overlapping classes: 
[WARNING]   - hdfs.jsr203.HadoopDirectoryStream
[WARNING]   - hdfs.jsr203.HadoopPath
[WARNING]   - hdfs.jsr203.HadoopFileSystem$1
[WARNING]   - hdfs.jsr203.HadoopFileOwnerAttributeView
[WARNING]   - hdfs.jsr203.HadoopUserPrincipal
[WARNING]   - hdfs.jsr203.IAttributeReader
[WARNING]   - hdfs.jsr203.HadoopPath$1
[WARNING]   - hdfs.jsr203.HadoopBasicFileAttributes
[WARNING]   - hdfs.jsr203.HadoopDirectoryStream$1
[WARNING]   - hdfs.jsr203.package-info
[WARNING]   - 17 more...
[WARNING] cannoli-assembly-spark3_2.12-0.12.0-SNAPSHOT.jar, objenesis-2.1.jar define 37 overlapping classes: 
[WARNING]   - org.objenesis.ObjenesisBase
[WARNING]   - org.objenesis.instantiator.gcj.GCJInstantiator
[WARNING]   - org.objenesis.strategy.SingleInstantiatorStrategy
[WARNING]   - org.objenesis.ObjenesisHelper
[WARNING]   - org.objenesis.instantiator.sun.SunReflectionFactoryHelper
[WARNING]   - org.objenesis.instantiator.jrockit.JRockitLegacyInstantiator
[WARNING]   - org.objenesis.instantiator.sun.SunReflectionFactoryInstantiator
[WARNING]   - org.objenesis.instantiator.basic.NullInstantiator
[WARNING]   - org.objenesis.instantiator.android.Android17Instantiator
[WARNING]   - org.objenesis.instantiator.ObjectInstantiator
[WARNING]   - 27 more...
[WARNING] cannoli-assembly-spark3_2.12-0.12.0-SNAPSHOT.jar, aopalliance-1.0.jar define 9 overlapping classes: 
[WARNING]   - org.aopalliance.intercept.ConstructorInterceptor
[WARNING]   - org.aopalliance.intercept.MethodInvocation
[WARNING]   - org.aopalliance.intercept.MethodInterceptor
[WARNING]   - org.aopalliance.intercept.Invocation
[WARNING]   - org.aopalliance.aop.AspectException
[WARNING]   - org.aopalliance.intercept.Interceptor
[WARNING]   - org.aopalliance.intercept.Joinpoint
[WARNING]   - org.aopalliance.aop.Advice
[WARNING]   - org.aopalliance.intercept.ConstructorInvocation
[WARNING] cannoli-assembly-spark3_2.12-0.12.0-SNAPSHOT.jar, kryo-2.24.0.jar define 193 overlapping classes: 
[WARNING]   - com.esotericsoftware.kryo.serializers.BeanSerializer$1
[WARNING]   - com.esotericsoftware.kryo.Registration
[WARNING]   - com.esotericsoftware.reflectasm.shaded.org.objectweb.asm.Handler
[WARNING]   - com.esotericsoftware.reflectasm.shaded.org.objectweb.asm.ByteVector
[WARNING]   - com.esotericsoftware.reflectasm.shaded.org.objectweb.asm.FieldVisitor
[WARNING]   - com.esotericsoftware.kryo.util.IntMap$Values
[WARNING]   - com.esotericsoftware.kryo.serializers.DefaultSerializers$IntSerializer
[WARNING]   - com.esotericsoftware.kryo.serializers.FieldSerializerUnsafeUtilImpl
[WARNING]   - com.esotericsoftware.kryo.serializers.JavaSerializer
[WARNING]   - com.esotericsoftware.kryo.serializers.ObjectField$ObjectIntField
[WARNING]   - 183 more...
[WARNING] cannoli-assembly-spark3_2.12-0.12.0-SNAPSHOT.jar, utils-io-spark3_2.12-0.3.0.jar define 11 overlapping classes: 
[WARNING]   - org.bdgenomics.utils.io.FileLocator
[WARNING]   - org.bdgenomics.utils.io.ByteAccess
[WARNING]   - org.bdgenomics.utils.io.HTTPRangedByteAccess
[WARNING]   - org.bdgenomics.utils.io.LocalFileByteAccess
[WARNING]   - org.bdgenomics.utils.io.HTTPFileLocator$
[WARNING]   - org.bdgenomics.utils.io.HTTPFileLocator
[WARNING]   - org.bdgenomics.utils.io.LocalFileLocator
[WARNING]   - org.bdgenomics.utils.io.FileLocator$
[WARNING]   - org.bdgenomics.utils.io.HTTPRangedByteAccess$
[WARNING]   - org.bdgenomics.utils.io.ByteArrayByteAccess
[WARNING]   - 1 more...
[WARNING] cannoli-assembly-spark3_2.12-0.12.0-SNAPSHOT.jar, parquet-jackson-1.10.1.jar define 623 overlapping classes: 
[WARNING]   - shaded.parquet.org.codehaus.jackson.map.InjectableValues$Std
[WARNING]   - shaded.parquet.org.codehaus.jackson.map.introspect.POJOPropertyBuilder$Node
[WARNING]   - shaded.parquet.org.codehaus.jackson.util.TokenBuffer$1
[WARNING]   - shaded.parquet.org.codehaus.jackson.type.TypeReference
[WARNING]   - shaded.parquet.org.codehaus.jackson.map.deser.std.FromStringDeserializer$LocaleDeserializer
[WARNING]   - shaded.parquet.org.codehaus.jackson.map.ser.BasicSerializerFactory
[WARNING]   - shaded.parquet.org.codehaus.jackson.map.deser.StdKeyDeserializer
[WARNING]   - shaded.parquet.org.codehaus.jackson.map.deser.std.StdKeyDeserializer$EnumKD
[WARNING]   - shaded.parquet.org.codehaus.jackson.map.ser.std.InetAddressSerializer
[WARNING]   - shaded.parquet.org.codehaus.jackson.map.jsontype.impl.StdTypeResolverBuilder
[WARNING]   - 613 more...
[WARNING] cannoli-assembly-spark3_2.12-0.12.0-SNAPSHOT.jar, scala-guice_2.12-4.2.1.jar define 77 overlapping classes: 
[WARNING]   - net.codingwell.scalaguice.ScalaModule$
[WARNING]   - net.codingwell.scalaguice.ScalaModule$ScalaLinkedBindingBuilder$$anon$3$$typecreator5$1
[WARNING]   - net.codingwell.scalaguice.ScalaModule$ScalaScopedBindingBuilder
[WARNING]   - net.codingwell.scalaguice.InjectorExtensions$ScalaInjector$$typecreator2$1
[WARNING]   - net.codingwell.scalaguice.binder.ScopedBindingBuilderProxy
[WARNING]   - net.codingwell.scalaguice.ScalaPrivateModule$ElementBuilder
[WARNING]   - net.codingwell.scalaguice.ScalaModule$ScalaAnnotatedBindingBuilder
[WARNING]   - net.codingwell.scalaguice.InternalModule
[WARNING]   - net.codingwell.scalaguice.TypeConversions$ArrayType$
[WARNING]   - net.codingwell.scalaguice.ScalaOptionBinder
[WARNING]   - 67 more...
[WARNING] cannoli-assembly-spark3_2.12-0.12.0-SNAPSHOT.jar, adam-cli-spark3_2.12-0.34.0.jar define 55 overlapping classes: 
[WARNING]   - org.bdgenomics.adam.cli.PrintADAMArgs
[WARNING]   - org.bdgenomics.adam.cli.PrintADAM$
[WARNING]   - org.bdgenomics.adam.cli.FlagStat$
[WARNING]   - org.bdgenomics.adam.cli.View
[WARNING]   - org.bdgenomics.adam.cli.FlagStat
[WARNING]   - org.bdgenomics.adam.cli.TransformVariantsArgs
[WARNING]   - org.bdgenomics.adam.cli.TransformVariants$
[WARNING]   - org.bdgenomics.adam.cli.TransformFragments
[WARNING]   - org.bdgenomics.adam.cli.TransformSequences
[WARNING]   - org.bdgenomics.adam.cli.ADAMMain$
[WARNING]   - 45 more...
[WARNING] cannoli-assembly-spark3_2.12-0.12.0-SNAPSHOT.jar, parquet-common-1.10.1.jar define 83 overlapping classes: 
[WARNING]   - org.apache.parquet.SemanticVersion$SemanticVersionParseException
[WARNING]   - org.apache.parquet.bytes.SingleBufferInputStream
[WARNING]   - org.apache.parquet.Ints
[WARNING]   - org.apache.parquet.Version
[WARNING]   - org.apache.parquet.SemanticVersion$NumberOrString
[WARNING]   - org.apache.parquet.glob.GlobNode$Atom
[WARNING]   - org.apache.parquet.util.DynMethods$Builder
[WARNING]   - org.apache.parquet.bytes.BytesInput$EmptyBytesInput
[WARNING]   - org.apache.parquet.Exceptions
[WARNING]   - org.apache.parquet.bytes.MultiBufferInputStream$ConcatIterator
[WARNING]   - 73 more...
[WARNING] cannoli-assembly-spark3_2.12-0.12.0-SNAPSHOT.jar, hadoop-bam-7.9.2.jar define 115 overlapping classes: 
[WARNING]   - org.seqdoop.hadoop_bam.BAMSplitGuesser
[WARNING]   - org.seqdoop.hadoop_bam.util.SAMHeaderReader
[WARNING]   - org.seqdoop.hadoop_bam.QseqInputFormat
[WARNING]   - org.seqdoop.hadoop_bam.KeyIgnoringBCFRecordWriter
[WARNING]   - org.seqdoop.hadoop_bam.FastaInputFormat$1
[WARNING]   - org.seqdoop.hadoop_bam.util.SAMOutputPreparer$1
[WARNING]   - org.seqdoop.hadoop_bam.QseqOutputFormat$QseqRecordWriter
[WARNING]   - org.seqdoop.hadoop_bam.FastaInputFormat
[WARNING]   - org.seqdoop.hadoop_bam.LineReader
[WARNING]   - org.seqdoop.hadoop_bam.util.BGZFCodec
[WARNING]   - 105 more...
[WARNING] cannoli-assembly-spark3_2.12-0.12.0-SNAPSHOT.jar, checker-qual-2.5.2.jar define 302 overlapping classes: 
[WARNING]   - org.checkerframework.checker.formatter.FormatUtil
[WARNING]   - org.checkerframework.checker.units.qual.MixedUnits
[WARNING]   - org.checkerframework.checker.regex.qual.PolyRegex
[WARNING]   - org.checkerframework.checker.units.qual.PolyUnit
[WARNING]   - org.checkerframework.checker.formatter.FormatUtil$IllegalFormatConversionCategoryException
[WARNING]   - org.checkerframework.framework.qual.Unqualified
[WARNING]   - org.checkerframework.checker.units.qual.C
[WARNING]   - org.checkerframework.common.reflection.qual.UnknownMethod
[WARNING]   - org.checkerframework.framework.qual.EnsuresQualifierIf
[WARNING]   - org.checkerframework.checker.signedness.SignednessUtil
[WARNING]   - 292 more...
[WARNING] cannoli-assembly-spark3_2.12-0.12.0-SNAPSHOT.jar, commons-codec-1.11.jar define 96 overlapping classes: 
[WARNING]   - org.apache.commons.codec.language.Nysiis
[WARNING]   - org.apache.commons.codec.language.bm.Rule$1
[WARNING]   - org.apache.commons.codec.language.bm.Rule$RPattern
[WARNING]   - org.apache.commons.codec.language.ColognePhonetic$CologneInputBuffer
[WARNING]   - org.apache.commons.codec.digest.HmacUtils
[WARNING]   - org.apache.commons.codec.language.bm.BeiderMorseEncoder
[WARNING]   - org.apache.commons.codec.digest.UnixCrypt
[WARNING]   - org.apache.commons.codec.language.Soundex
[WARNING]   - org.apache.commons.codec.cli.Digest
[WARNING]   - org.apache.commons.codec.binary.BinaryCodec
[WARNING]   - 86 more...
[WARNING] cannoli-assembly-spark3_2.12-0.12.0-SNAPSHOT.jar, adam-apis-spark3_2.12-0.34.0.jar define 195 overlapping classes: 
[WARNING]   - org.bdgenomics.adam.api.java.FeaturesToFragmentsConverter
[WARNING]   - org.bdgenomics.adam.api.java.FeaturesToVariantsDatasetConverter
[WARNING]   - org.bdgenomics.adam.api.java.AlignmentsToFeaturesConverter
[WARNING]   - org.bdgenomics.adam.api.java.FeaturesToReadsDatasetConverter
[WARNING]   - org.bdgenomics.adam.api.java.VariantsToVariantsConverter
[WARNING]   - org.bdgenomics.adam.api.java.CoverageToReadsDatasetConverter
[WARNING]   - org.bdgenomics.adam.api.java.SequencesToGenotypesConverter
[WARNING]   - org.bdgenomics.adam.api.java.ReadsToSlicesDatasetConverter
[WARNING]   - org.bdgenomics.adam.api.java.SequencesToFeaturesConverter
[WARNING]   - org.bdgenomics.adam.api.java.GenotypesToSlicesConverter
[WARNING]   - 185 more...
[WARNING] cannoli-assembly-spark3_2.12-0.12.0-SNAPSHOT.jar, adam-core-spark3_2.12-0.34.0.jar define 608 overlapping classes: 
[WARNING]   - org.bdgenomics.adam.ds.variant.RDDBoundVariantContextDataset$
[WARNING]   - org.bdgenomics.adam.io.InterleavedFastqInputFormat
[WARNING]   - org.bdgenomics.adam.ds.sequence.RDDBoundSequenceDataset$
[WARNING]   - org.bdgenomics.adam.ds.InnerShuffleRegionJoin$
[WARNING]   - org.bdgenomics.adam.models.ReferenceRegion
[WARNING]   - org.bdgenomics.adam.ds.sequence.DatasetBoundSliceDataset
[WARNING]   - org.bdgenomics.adam.ds.read.realignment.ModPartitioner
[WARNING]   - org.bdgenomics.adam.ds.read.RepairPartitions
[WARNING]   - org.bdgenomics.adam.ds.GenomicDataset$$typecreator1$5
[WARNING]   - org.bdgenomics.adam.projections.SequenceField$
[WARNING]   - 598 more...
[WARNING] cannoli-assembly-spark3_2.12-0.12.0-SNAPSHOT.jar, commons-logging-1.2.jar define 28 overlapping classes: 
[WARNING]   - org.apache.commons.logging.LogSource
[WARNING]   - org.apache.commons.logging.impl.ServletContextCleaner
[WARNING]   - org.apache.commons.logging.Log
[WARNING]   - org.apache.commons.logging.LogFactory$3
[WARNING]   - org.apache.commons.logging.impl.LogFactoryImpl$2
[WARNING]   - org.apache.commons.logging.impl.LogKitLogger
[WARNING]   - org.apache.commons.logging.impl.Jdk14Logger
[WARNING]   - org.apache.commons.logging.LogConfigurationException
[WARNING]   - org.apache.commons.logging.impl.WeakHashtable$Referenced
[WARNING]   - org.apache.commons.logging.impl.WeakHashtable$WeakKey
[WARNING]   - 18 more...
[WARNING] cannoli-assembly-spark3_2.12-0.12.0-SNAPSHOT.jar, commons-io-2.6.jar define 127 overlapping classes: 
[WARNING]   - org.apache.commons.io.FileCleaningTracker
[WARNING]   - org.apache.commons.io.comparator.SizeFileComparator
[WARNING]   - org.apache.commons.io.input.CloseShieldInputStream
[WARNING]   - org.apache.commons.io.ByteOrderParser
[WARNING]   - org.apache.commons.io.filefilter.EmptyFileFilter
[WARNING]   - org.apache.commons.io.monitor.FileEntry
[WARNING]   - org.apache.commons.io.output.ThresholdingOutputStream
[WARNING]   - org.apache.commons.io.input.TailerListener
[WARNING]   - org.apache.commons.io.IOExceptionWithCause
[WARNING]   - org.apache.commons.io.filefilter.NotFileFilter
[WARNING]   - 117 more...
[WARNING] cannoli-assembly-spark3_2.12-0.12.0-SNAPSHOT.jar, parquet-avro-1.10.1.jar, adam-core-spark3_2.12-0.34.0.jar define 3 overlapping classes: 
[WARNING]   - org.apache.parquet.avro.AvroSchemaConverter$2
[WARNING]   - org.apache.parquet.avro.AvroSchemaConverter
[WARNING]   - org.apache.parquet.avro.AvroSchemaConverter$1
[WARNING] cannoli-assembly-spark3_2.12-0.12.0-SNAPSHOT.jar, fastutil-6.6.5.jar define 10700 overlapping classes: 
[WARNING]   - it.unimi.dsi.fastutil.doubles.Double2IntRBTreeMap$Submap$KeySet
[WARNING]   - it.unimi.dsi.fastutil.longs.Long2CharAVLTreeMap$2$1
[WARNING]   - it.unimi.dsi.fastutil.bytes.Byte2ObjectLinkedOpenHashMap$EntryIterator
[WARNING]   - it.unimi.dsi.fastutil.ints.Int2ReferenceRBTreeMap$Submap
[WARNING]   - it.unimi.dsi.fastutil.shorts.Short2FloatOpenCustomHashMap$KeySet
[WARNING]   - it.unimi.dsi.fastutil.bytes.Byte2BooleanRBTreeMap$Submap$1
[WARNING]   - it.unimi.dsi.fastutil.floats.AbstractFloat2ShortSortedMap$ValuesCollection
[WARNING]   - it.unimi.dsi.fastutil.longs.Long2ReferenceRBTreeMap$Submap$2
[WARNING]   - it.unimi.dsi.fastutil.chars.AbstractChar2LongSortedMap$ValuesIterator
[WARNING]   - it.unimi.dsi.fastutil.doubles.DoubleHeaps
[WARNING]   - 10690 more...
[WARNING] cannoli-assembly-spark3_2.12-0.12.0-SNAPSHOT.jar, htsjdk-2.19.0.jar define 993 overlapping classes: 
[WARNING]   - htsjdk.samtools.cram.ref.ReferenceSource
[WARNING]   - htsjdk.samtools.cram.compression.ExternalCompressor$3
[WARNING]   - htsjdk.samtools.HighAccuracyDownsamplingIterator
[WARNING]   - htsjdk.samtools.util.zip.DeflaterFactory
[WARNING]   - htsjdk.samtools.filter.DuplicateReadFilter
[WARNING]   - htsjdk.samtools.cram.encoding.core.huffmanUtils.HuffmanCode$1
[WARNING]   - htsjdk.samtools.cram.encoding.core.SubexponentialIntegerEncoding
[WARNING]   - htsjdk.variant.vcf.VCFEncoder
[WARNING]   - htsjdk.samtools.util.CloserUtil
[WARNING]   - htsjdk.tribble.TribbleException$FeatureFileDoesntExist
[WARNING]   - 983 more...
[WARNING] cannoli-assembly-spark3_2.12-0.12.0-SNAPSHOT.jar, avro-1.8.2.jar define 1172 overlapping classes: 
[WARNING]   - org.apache.avro.message.SchemaStore
[WARNING]   - avro.shaded.com.google.common.collect.SingletonImmutableList
[WARNING]   - org.apache.avro.io.EncoderFactory$DefaultEncoderFactory
[WARNING]   - avro.shaded.com.google.common.collect.Iterables$15
[WARNING]   - org.apache.avro.GuavaClasses
[WARNING]   - avro.shaded.com.google.common.collect.Sets$PowerSet$1$1
[WARNING]   - avro.shaded.com.google.common.collect.RegularImmutableMap
[WARNING]   - org.apache.avro.generic.GenericDatumReader$2
[WARNING]   - avro.shaded.com.google.common.collect.Synchronized$SynchronizedSortedSet
[WARNING]   - org.apache.avro.file.BZip2Codec
[WARNING]   - 1162 more...
[WARNING] cannoli-assembly-spark3_2.12-0.12.0-SNAPSHOT.jar, guice-4.2.0.jar define 573 overlapping classes: 
[WARNING]   - com.google.inject.Scope
[WARNING]   - com.google.inject.Binding
[WARNING]   - com.google.inject.internal.cglib.core.$EmitUtils$3
[WARNING]   - com.google.inject.spi.TypeConverter
[WARNING]   - com.google.inject.internal.ConstructionProxy
[WARNING]   - com.google.inject.spi.InjectionPoint
[WARNING]   - com.google.inject.spi.StaticInjectionRequest
[WARNING]   - com.google.inject.internal.cglib.proxy.$FixedValueGenerator
[WARNING]   - com.google.inject.internal.cglib.proxy.$DispatcherGenerator
[WARNING]   - com.google.inject.spi.Elements$ElementsAsModule
[WARNING]   - 563 more...
[WARNING] cannoli-assembly-spark3_2.12-0.12.0-SNAPSHOT.jar, cannoli-core-spark3_2.12-0.12.0-SNAPSHOT.jar define 66 overlapping classes: 
[WARNING]   - org.bdgenomics.cannoli.Vep
[WARNING]   - org.bdgenomics.cannoli.Cannoli$
[WARNING]   - org.bdgenomics.cannoli.BwaMem2Args
[WARNING]   - org.bdgenomics.cannoli.BcftoolsMpileupArgs
[WARNING]   - org.bdgenomics.cannoli.Cannoli
[WARNING]   - org.bdgenomics.cannoli.util.QuerynameGrouper
[WARNING]   - org.bdgenomics.cannoli.VtNormalize
[WARNING]   - org.bdgenomics.cannoli.BedtoolsIntersect
[WARNING]   - org.bdgenomics.cannoli.GemArgs
[WARNING]   - org.bdgenomics.cannoli.SamtoolsMpileupArgs
[WARNING]   - 56 more...
[WARNING] cannoli-assembly-spark3_2.12-0.12.0-SNAPSHOT.jar, cannoli-cli-spark3_2.12-0.12.0-SNAPSHOT.jar define 75 overlapping classes: 
[WARNING]   - org.bdgenomics.cannoli.cli.BcftoolsCall$
[WARNING]   - org.bdgenomics.cannoli.cli.InterleaveFastqArgs
[WARNING]   - org.bdgenomics.cannoli.cli.BedtoolsIntersectArgs
[WARNING]   - org.bdgenomics.cannoli.cli.GemArgs
[WARNING]   - org.bdgenomics.cannoli.cli.Minimap2Args
[WARNING]   - org.bdgenomics.cannoli.cli.VepArgs
[WARNING]   - org.bdgenomics.cannoli.cli.SingleEndStar$
[WARNING]   - org.bdgenomics.cannoli.cli.Minimap2$
[WARNING]   - org.bdgenomics.cannoli.cli.Freebayes$
[WARNING]   - org.bdgenomics.cannoli.cli.FreebayesArgs
[WARNING]   - 65 more...
[WARNING] cannoli-assembly-spark3_2.12-0.12.0-SNAPSHOT.jar, ngs-java-2.9.0.jar define 73 overlapping classes: 
[WARNING]   - ngs.itf.ReadItf
[WARNING]   - gov.nih.nlm.ncbi.ngs.error.cause.JvmErrorCause
[WARNING]   - ngs.ReferenceIterator
[WARNING]   - gov.nih.nlm.ncbi.ngs.Manager$1
[WARNING]   - gov.nih.nlm.ncbi.ngs.LMProperties
[WARNING]   - gov.nih.nlm.ncbi.ngs.error.LibraryLoadError
[WARNING]   - gov.nih.nlm.ncbi.ngs.LibDependencies
[WARNING]   - gov.nih.nlm.ncbi.ngs.error.cause.ConnectionProblemCause
[WARNING]   - ngs.itf.PileupEventItf
[WARNING]   - gov.nih.nlm.ncbi.ngs.LibManager$Location
[WARNING]   - 63 more...
[WARNING] cannoli-assembly-spark3_2.12-0.12.0-SNAPSHOT.jar, minlog-1.2.jar define 2 overlapping classes: 
[WARNING]   - com.esotericsoftware.minlog.Log
[WARNING]   - com.esotericsoftware.minlog.Log$Logger
[WARNING] cannoli-assembly-spark3_2.12-0.12.0-SNAPSHOT.jar, jsr305-1.3.9.jar define 35 overlapping classes: 
[WARNING]   - javax.annotation.RegEx
[WARNING]   - javax.annotation.concurrent.Immutable
[WARNING]   - javax.annotation.meta.TypeQualifierDefault
[WARNING]   - javax.annotation.meta.TypeQualifier
[WARNING]   - javax.annotation.Syntax
[WARNING]   - javax.annotation.CheckForNull
[WARNING]   - javax.annotation.Nonnull
[WARNING]   - javax.annotation.CheckReturnValue
[WARNING]   - javax.annotation.meta.TypeQualifierNickname
[WARNING]   - javax.annotation.MatchesPattern
[WARNING]   - 25 more...
[WARNING] cannoli-assembly-spark3_2.12-0.12.0-SNAPSHOT.jar, guava-27.0.1-jre.jar define 1955 overlapping classes: 
[WARNING]   - com.google.common.collect.CompactHashMap$Itr
[WARNING]   - com.google.common.collect.ImmutableMapValues$1
[WARNING]   - com.google.common.util.concurrent.AbstractService$5
[WARNING]   - com.google.common.io.LineProcessor
[WARNING]   - com.google.common.io.BaseEncoding$StandardBaseEncoding$2
[WARNING]   - com.google.common.io.ByteProcessor
[WARNING]   - com.google.common.math.package-info
[WARNING]   - com.google.common.util.concurrent.SimpleTimeLimiter
[WARNING]   - com.google.common.cache.AbstractCache$StatsCounter
[WARNING]   - com.google.common.util.concurrent.CycleDetectingLockFactory$Policies
[WARNING]   - 1945 more...
[WARNING] cannoli-assembly-spark3_2.12-0.12.0-SNAPSHOT.jar, httpclient-4.5.7.jar define 467 overlapping classes: 
[WARNING]   - org.apache.http.impl.cookie.RFC2109Spec
[WARNING]   - org.apache.http.impl.execchain.MainClientExec
[WARNING]   - org.apache.http.conn.routing.RouteInfo$TunnelType
[WARNING]   - org.apache.http.client.methods.HttpGet
[WARNING]   - org.apache.http.impl.cookie.BrowserCompatSpecFactory
[WARNING]   - org.apache.http.impl.client.HttpAuthenticator
[WARNING]   - org.apache.http.conn.ManagedClientConnection
[WARNING]   - org.apache.http.client.protocol.RequestAuthCache
[WARNING]   - org.apache.http.conn.params.ConnConnectionParamBean
[WARNING]   - org.apache.http.impl.client.IdleConnectionEvictor
[WARNING]   - 457 more...
[WARNING] cannoli-assembly-spark3_2.12-0.12.0-SNAPSHOT.jar, javax.inject-1.jar define 6 overlapping classes: 
[WARNING]   - javax.inject.Inject
[WARNING]   - javax.inject.Singleton
[WARNING]   - javax.inject.Scope
[WARNING]   - javax.inject.Named
[WARNING]   - javax.inject.Provider
[WARNING]   - javax.inject.Qualifier
[WARNING] cannoli-assembly-spark3_2.12-0.12.0-SNAPSHOT.jar, adam-codegen-spark3_2.12-0.34.0.jar define 7 overlapping classes: 
[WARNING]   - org.bdgenomics.adam.codegen.DumpSchemasToProjectionEnums$
[WARNING]   - org.bdgenomics.adam.codegen.DumpSchemasToProjectionEnums
[WARNING]   - org.bdgenomics.adam.codegen.DumpSchemasToProduct
[WARNING]   - org.bdgenomics.adam.codegen.DumpSchemasToProduct$
[WARNING]   - org.bdgenomics.adam.codegen.Generator
[WARNING]   - org.bdgenomics.adam.codegen.ReflectSchema
[WARNING]   - org.bdgenomics.adam.codegen.ReflectSchema$
[WARNING] cannoli-assembly-spark3_2.12-0.12.0-SNAPSHOT.jar, jackson-core-asl-1.9.13.jar define 121 overlapping classes: 
[WARNING]   - org.codehaus.jackson.annotate.JsonManagedReference
[WARNING]   - org.codehaus.jackson.util.DefaultPrettyPrinter$FixedSpaceIndenter
[WARNING]   - org.codehaus.jackson.JsonGenerationException
[WARNING]   - org.codehaus.jackson.util.BufferRecycler$CharBufferType
[WARNING]   - org.codehaus.jackson.io.UTF32Reader
[WARNING]   - org.codehaus.jackson.sym.Name1
[WARNING]   - org.codehaus.jackson.util.MinimalPrettyPrinter
[WARNING]   - org.codehaus.jackson.impl.JsonParserBase
[WARNING]   - org.codehaus.jackson.sym.CharsToNameCanonicalizer$Bucket
[WARNING]   - org.codehaus.jackson.annotate.JsonValue
[WARNING]   - 111 more...
[WARNING] cannoli-assembly-spark3_2.12-0.12.0-SNAPSHOT.jar, slf4j-api-1.7.9.jar define 28 overlapping classes: 
[WARNING]   - org.slf4j.helpers.SubstituteLogger
[WARNING]   - org.slf4j.helpers.NamedLoggerBase
[WARNING]   - org.slf4j.helpers.NOPMDCAdapter
[WARNING]   - org.slf4j.MarkerFactory
[WARNING]   - org.slf4j.spi.LoggerFactoryBinder
[WARNING]   - org.slf4j.helpers.BasicMarker
[WARNING]   - org.slf4j.MDC$MDCCloseable
[WARNING]   - org.slf4j.spi.LocationAwareLogger
[WARNING]   - org.slf4j.helpers.MessageFormatter
[WARNING]   - org.slf4j.helpers.Util$ClassContextSecurityManager
[WARNING]   - 18 more...
[WARNING] cannoli-assembly-spark3_2.12-0.12.0-SNAPSHOT.jar, utils-cli-spark3_2.12-0.3.0.jar define 13 overlapping classes: 
[WARNING]   - org.bdgenomics.utils.cli.Args4j
[WARNING]   - org.bdgenomics.utils.cli.ParquetArgs
[WARNING]   - org.bdgenomics.utils.cli.SaveArgs
[WARNING]   - org.bdgenomics.utils.cli.Args4jBase
[WARNING]   - org.bdgenomics.utils.cli.ParquetSaveArgs
[WARNING]   - org.bdgenomics.utils.cli.ParquetLoadSaveArgs
[WARNING]   - org.bdgenomics.utils.cli.BDGCommandCompanion
[WARNING]   - org.bdgenomics.utils.cli.ParquetRDDArgs
[WARNING]   - org.bdgenomics.utils.cli.BDGSparkCommand
[WARNING]   - org.bdgenomics.utils.cli.SaveFileArgs
[WARNING]   - 3 more...
[WARNING] cannoli-assembly-spark3_2.12-0.12.0-SNAPSHOT.jar, jackson-mapper-asl-1.9.13.jar define 502 overlapping classes: 
[WARNING]   - org.codehaus.jackson.map.ext.DOMSerializer
[WARNING]   - org.codehaus.jackson.node.POJONode
[WARNING]   - org.codehaus.jackson.map.ser.StdSerializers$UtilDateSerializer
[WARNING]   - org.codehaus.jackson.map.deser.std.JsonNodeDeserializer$ArrayDeserializer
[WARNING]   - org.codehaus.jackson.map.ext.JodaDeserializers$LocalDateDeserializer
[WARNING]   - org.codehaus.jackson.map.deser.std.PrimitiveArrayDeserializers$StringDeser
[WARNING]   - org.codehaus.jackson.map.util.Comparators$1
[WARNING]   - org.codehaus.jackson.map.util.StdDateFormat
[WARNING]   - org.codehaus.jackson.map.KeyDeserializer
[WARNING]   - org.codehaus.jackson.map.MapperConfig$Impl
[WARNING]   - 492 more...
[WARNING] cannoli-assembly-spark3_2.12-0.12.0-SNAPSHOT.jar, grizzled-slf4j_2.12-1.3.4.jar define 3 overlapping classes: 
[WARNING]   - grizzled.slf4j.Logger$
[WARNING]   - grizzled.slf4j.Logging
[WARNING]   - grizzled.slf4j.Logger
[WARNING] cannoli-assembly-spark3_2.12-0.12.0-SNAPSHOT.jar, cannoli-builder-spark3_2.12-0.12.0-SNAPSHOT.jar define 6 overlapping classes: 
[WARNING]   - org.bdgenomics.cannoli.builder.CommandBuilder
[WARNING]   - org.bdgenomics.cannoli.builder.LocalBuilder
[WARNING]   - org.bdgenomics.cannoli.builder.SingularityBuilder
[WARNING]   - org.bdgenomics.cannoli.builder.CommandBuilders
[WARNING]   - org.bdgenomics.cannoli.builder.DockerBuilder
[WARNING]   - org.bdgenomics.cannoli.builder.ContainerBuilder
[WARNING] cannoli-assembly-spark3_2.12-0.12.0-SNAPSHOT.jar, parquet-format-2.4.0.jar define 461 overlapping classes: 
[WARNING]   - shaded.parquet.org.apache.thrift.transport.TSimpleFileTransport
[WARNING]   - shaded.parquet.org.apache.thrift.transport.TServerSocket
[WARNING]   - shaded.parquet.org.apache.thrift.transport.TFileTransport$TruncableBufferedInputStream
[WARNING]   - shaded.parquet.org.apache.thrift.TFieldIdEnum
[WARNING]   - org.apache.parquet.format.SchemaElement$SchemaElementStandardScheme
[WARNING]   - shaded.parquet.org.apache.thrift.server.AbstractNonblockingServer$AbstractSelectThread
[WARNING]   - shaded.parquet.org.apache.thrift.TEnumHelper
[WARNING]   - org.apache.parquet.format.JsonType$JsonTypeStandardScheme
[WARNING]   - org.apache.parquet.format.DictionaryPageHeader$DictionaryPageHeaderTupleScheme
[WARNING]   - org.apache.parquet.format.UUIDType$1
[WARNING]   - 451 more...
[WARNING] cannoli-assembly-spark3_2.12-0.12.0-SNAPSHOT.jar, snappy-java-1.1.1.3.jar define 19 overlapping classes: 
[WARNING]   - org.xerial.snappy.SnappyLoader
[WARNING]   - org.xerial.snappy.SnappyFramedInputStream$FrameMetaData
[WARNING]   - org.xerial.snappy.SnappyFramedInputStream
[WARNING]   - org.xerial.snappy.SnappyOutputStream
[WARNING]   - org.xerial.snappy.SnappyErrorCode
[WARNING]   - org.xerial.snappy.SnappyBundleActivator
[WARNING]   - org.xerial.snappy.SnappyFramedOutputStream
[WARNING]   - org.xerial.snappy.BufferRecycler
[WARNING]   - org.xerial.snappy.SnappyError
[WARNING]   - org.xerial.snappy.SnappyFramedInputStream$FrameAction
[WARNING]   - 9 more...
[WARNING] maven-shade-plugin has detected that some class files are
[WARNING] present in two or more JARs. When this happens, only one
[WARNING] single version of the class is copied to the uber jar.
[WARNING] Usually this is not harmful and you can skip these warnings,
[WARNING] otherwise try to manually exclude artifacts based on
[WARNING] mvn dependency:tree -Ddetail=true and the above output.
[WARNING] See http://maven.apache.org/plugins/maven-shade-plugin/
[INFO] Replacing original artifact with shaded artifact.
[INFO] Replacing /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/assembly/target/cannoli-assembly-spark3_2.12-0.12.0-SNAPSHOT.jar with /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/assembly/target/cannoli-assembly-spark3_2.12-0.12.0-SNAPSHOT-shaded.jar
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[INFO] --- maven-license-plugin:1.10.b1:check (default) @ cannoli-assembly-spark3_2.12 ---
[INFO] Checking licenses...
[INFO] 
[INFO] --- maven-install-plugin:3.0.0-M1:install (default-install) @ cannoli-assembly-spark3_2.12 ---
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[INFO] Installing /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/assembly/pom.xml to /home/jenkins/.m2/repository/org/bdgenomics/cannoli/cannoli-assembly-spark3_2.12/0.12.0-SNAPSHOT/cannoli-assembly-spark3_2.12-0.12.0-SNAPSHOT.pom
[INFO] Installing /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/assembly/target/cannoli-assembly-spark3_2.12-0.12.0-SNAPSHOT-sources.jar to /home/jenkins/.m2/repository/org/bdgenomics/cannoli/cannoli-assembly-spark3_2.12/0.12.0-SNAPSHOT/cannoli-assembly-spark3_2.12-0.12.0-SNAPSHOT-sources.jar
[INFO] Installing /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/assembly/target/cannoli-assembly-spark3_2.12-0.12.0-SNAPSHOT-javadoc.jar to /home/jenkins/.m2/repository/org/bdgenomics/cannoli/cannoli-assembly-spark3_2.12/0.12.0-SNAPSHOT/cannoli-assembly-spark3_2.12-0.12.0-SNAPSHOT-javadoc.jar
[INFO] Installing /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/assembly/target/cannoli-assembly-spark3_2.12-0.12.0-SNAPSHOT-javadoc.jar to /home/jenkins/.m2/repository/org/bdgenomics/cannoli/cannoli-assembly-spark3_2.12/0.12.0-SNAPSHOT/cannoli-assembly-spark3_2.12-0.12.0-SNAPSHOT-javadoc.jar
[INFO] 
[INFO] --- maven-deploy-plugin:3.0.0-M1:deploy (default-deploy) @ cannoli-assembly-spark3_2.12 ---
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Uploading to sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-assembly-spark3_2.12/0.12.0-SNAPSHOT/cannoli-assembly-spark3_2.12-0.12.0-20210315.164038-22.pom
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Uploaded to sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-assembly-spark3_2.12/0.12.0-SNAPSHOT/cannoli-assembly-spark3_2.12-0.12.0-20210315.164038-22-javadoc.jar (1.1 MB at 1.8 MB/s)
Uploading to sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-assembly-spark3_2.12/0.12.0-SNAPSHOT/cannoli-assembly-spark3_2.12-0.12.0-20210315.164038-22-javadoc.jar
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Uploaded to sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-assembly-spark3_2.12/0.12.0-SNAPSHOT/cannoli-assembly-spark3_2.12-0.12.0-20210315.164038-22-javadoc.jar (1.1 MB at 2.0 MB/s)
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Uploading to sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-assembly-spark3_2.12/0.12.0-SNAPSHOT/maven-metadata.xml
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[INFO] 
[INFO] ------< org.bdgenomics.cannoli:cannoli-distribution-spark3_2.12 >-------
[INFO] Building Cannoli_2.12: Distribution 0.12.0-SNAPSHOT                [6/6]
[INFO] --------------------------------[ pom ]---------------------------------
[INFO] 
[INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-maven) @ cannoli-distribution-spark3_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-java) @ cannoli-distribution-spark3_2.12 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ cannoli-distribution-spark3_2.12 ---
[INFO] Source directory: /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/distribution/src/main/scala added.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ cannoli-distribution-spark3_2.12 ---
[INFO] Modified 0 of 0 .scala files
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ cannoli-distribution-spark3_2.12 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ cannoli-distribution-spark3_2.12 ---
[INFO] Test Source directory: /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/distribution/src/test/scala added.
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ cannoli-distribution-spark3_2.12 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ cannoli-distribution-spark3_2.12 ---
[INFO] 
[INFO] --- maven-javadoc-plugin:3.1.0:jar (attach-javadocs) @ cannoli-distribution-spark3_2.12 ---
[INFO] 
[INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) > generate-sources @ cannoli-distribution-spark3_2.12 >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-maven) @ cannoli-distribution-spark3_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-java) @ cannoli-distribution-spark3_2.12 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ cannoli-distribution-spark3_2.12 ---
[INFO] Source directory: /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/distribution/src/main/scala added.
[INFO] 
[INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) < generate-sources @ cannoli-distribution-spark3_2.12 <<<
[INFO] 
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ cannoli-distribution-spark3_2.12 ---
[INFO] No source files found
[INFO] 
[INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-javadocs) > generate-sources @ cannoli-distribution-spark3_2.12 >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-maven) @ cannoli-distribution-spark3_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-java) @ cannoli-distribution-spark3_2.12 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ cannoli-distribution-spark3_2.12 ---
[INFO] Source directory: /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/distribution/src/main/scala added.
[INFO] 
[INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-javadocs) < generate-sources @ cannoli-distribution-spark3_2.12 <<<
[INFO] 
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-javadocs) @ cannoli-distribution-spark3_2.12 ---
[INFO] No source files found
[INFO] 
[INFO] --- maven-assembly-plugin:3.1.0:single (default) @ cannoli-distribution-spark3_2.12 ---
[INFO] Reading assembly descriptor: src/main/assembly/assembly.xml
[INFO] Building tar: /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/distribution/target/cannoli-distribution-spark3_2.12-0.12.0-SNAPSHOT-bin.tar.gz
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[WARNING] Resulting tar file can only be processed successfully by GNU compatible tar commands
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[INFO] Building tar: /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/distribution/target/cannoli-distribution-spark3_2.12-0.12.0-SNAPSHOT-bin.tar.bz2
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[WARNING] Resulting tar file can only be processed successfully by GNU compatible tar commands
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[INFO] Building zip: /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/distribution/target/cannoli-distribution-spark3_2.12-0.12.0-SNAPSHOT-bin.zip
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[INFO] Checking licenses...
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[INFO] Installing /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/distribution/target/cannoli-distribution-spark3_2.12-0.12.0-SNAPSHOT-bin.tar.gz to /home/jenkins/.m2/repository/org/bdgenomics/cannoli/cannoli-distribution-spark3_2.12/0.12.0-SNAPSHOT/cannoli-distribution-spark3_2.12-0.12.0-SNAPSHOT-bin.tar.gz
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[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary for Cannoli_2.12 0.12.0-SNAPSHOT:
[INFO] 
[INFO] Cannoli_2.12 ....................................... SUCCESS [  6.498 s]
[INFO] Cannoli_2.12: Builder .............................. SUCCESS [ 17.341 s]
[INFO] Cannoli_2.12: Core ................................. SUCCESS [ 25.750 s]
[INFO] Cannoli_2.12: CLI .................................. SUCCESS [ 32.392 s]
[INFO] Cannoli_2.12: Assembly ............................. SUCCESS [ 19.858 s]
[INFO] Cannoli_2.12: Distribution ......................... SUCCESS [ 29.863 s]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time:  02:11 min
[INFO] Finished at: 2021-03-15T09:41:15-07:00
[INFO] ------------------------------------------------------------------------
Recording test results
[Checks API] No suitable checks publisher found.
Finished: SUCCESS