Console Output

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[INFO] Installing artifact /home/jenkins/.m2/repository/org/bdgenomics/utils/utils-misc-spark3_2.12/0.3.0/utils-misc-spark3_2.12-0.3.0.jar to /tmp/mangoTestpODQhLH/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/org/bdgenomics/utils/utils-misc-spark3_2.12/0.3.0/utils-misc-spark3_2.12-0.3.0.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/bdgenomics/utils/utils-intervalrdd-spark3_2.12/0.3.0/utils-intervalrdd-spark3_2.12-0.3.0.jar to /tmp/mangoTestpODQhLH/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/org/bdgenomics/utils/utils-intervalrdd-spark3_2.12/0.3.0/utils-intervalrdd-spark3_2.12-0.3.0.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/eclipse/jetty/jetty-server/9.4.17.v20190418/jetty-server-9.4.17.v20190418.jar to /tmp/mangoTestpODQhLH/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/org/eclipse/jetty/jetty-server/9.4.17.v20190418/jetty-server-9.4.17.v20190418.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/eclipse/jetty/jetty-http/9.4.17.v20190418/jetty-http-9.4.17.v20190418.jar to /tmp/mangoTestpODQhLH/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/org/eclipse/jetty/jetty-http/9.4.17.v20190418/jetty-http-9.4.17.v20190418.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/eclipse/jetty/jetty-util/9.4.17.v20190418/jetty-util-9.4.17.v20190418.jar to /tmp/mangoTestpODQhLH/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/org/eclipse/jetty/jetty-util/9.4.17.v20190418/jetty-util-9.4.17.v20190418.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/eclipse/jetty/jetty-io/9.4.17.v20190418/jetty-io-9.4.17.v20190418.jar to /tmp/mangoTestpODQhLH/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/org/eclipse/jetty/jetty-io/9.4.17.v20190418/jetty-io-9.4.17.v20190418.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/eclipse/jetty/jetty-webapp/9.4.17.v20190418/jetty-webapp-9.4.17.v20190418.jar to /tmp/mangoTestpODQhLH/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/org/eclipse/jetty/jetty-webapp/9.4.17.v20190418/jetty-webapp-9.4.17.v20190418.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/eclipse/jetty/jetty-xml/9.4.17.v20190418/jetty-xml-9.4.17.v20190418.jar to /tmp/mangoTestpODQhLH/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/org/eclipse/jetty/jetty-xml/9.4.17.v20190418/jetty-xml-9.4.17.v20190418.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/eclipse/jetty/jetty-servlet/9.4.17.v20190418/jetty-servlet-9.4.17.v20190418.jar to /tmp/mangoTestpODQhLH/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/org/eclipse/jetty/jetty-servlet/9.4.17.v20190418/jetty-servlet-9.4.17.v20190418.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/eclipse/jetty/jetty-security/9.4.17.v20190418/jetty-security-9.4.17.v20190418.jar to /tmp/mangoTestpODQhLH/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/org/eclipse/jetty/jetty-security/9.4.17.v20190418/jetty-security-9.4.17.v20190418.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/scalatra/scalatra_2.12/2.5.0/scalatra_2.12-2.5.0.jar to /tmp/mangoTestpODQhLH/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/org/scalatra/scalatra_2.12/2.5.0/scalatra_2.12-2.5.0.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/scalatra/scalatra-common_2.12/2.5.0/scalatra-common_2.12-2.5.0.jar to /tmp/mangoTestpODQhLH/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/org/scalatra/scalatra-common_2.12/2.5.0/scalatra-common_2.12-2.5.0.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/com/googlecode/juniversalchardet/juniversalchardet/1.0.3/juniversalchardet-1.0.3.jar to /tmp/mangoTestpODQhLH/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/com/googlecode/juniversalchardet/juniversalchardet/1.0.3/juniversalchardet-1.0.3.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/eu/medsea/mimeutil/mime-util/2.1.3/mime-util-2.1.3.jar to /tmp/mangoTestpODQhLH/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/eu/medsea/mimeutil/mime-util/2.1.3/mime-util-2.1.3.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/scala-lang/modules/scala-parser-combinators_2.12/1.0.4/scala-parser-combinators_2.12-1.0.4.jar to /tmp/mangoTestpODQhLH/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/org/scala-lang/modules/scala-parser-combinators_2.12/1.0.4/scala-parser-combinators_2.12-1.0.4.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/scalatra/scalate/scalate-core_2.12/1.9.1/scalate-core_2.12-1.9.1.jar to /tmp/mangoTestpODQhLH/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/org/scalatra/scalate/scalate-core_2.12/1.9.1/scalate-core_2.12-1.9.1.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/scala-lang/scala-compiler/2.12.8/scala-compiler-2.12.8.jar to /tmp/mangoTestpODQhLH/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/org/scala-lang/scala-compiler/2.12.8/scala-compiler-2.12.8.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/scalatra/scalate/scalate-util_2.12/1.9.1/scalate-util_2.12-1.9.1.jar to /tmp/mangoTestpODQhLH/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/org/scalatra/scalate/scalate-util_2.12/1.9.1/scalate-util_2.12-1.9.1.jar
[INFO] Installing artifact /tmp/mangoTestpODQhLH/deleteMePleaseThisIsNoLongerNeeded/mango-core/target/mango-core-spark3_2.12-0.0.6-SNAPSHOT.jar to /tmp/mangoTestpODQhLH/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/org/bdgenomics/mango/mango-core-spark3_2.12/0.0.6-SNAPSHOT/mango-core-spark3_2.12-0.0.6-SNAPSHOT.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/bdgenomics/utils/utils-io-spark3_2.12/0.3.0/utils-io-spark3_2.12-0.3.0.jar to /tmp/mangoTestpODQhLH/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/org/bdgenomics/utils/utils-io-spark3_2.12/0.3.0/utils-io-spark3_2.12-0.3.0.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/com/google/protobuf/protobuf-java/3.0.0-beta-3/protobuf-java-3.0.0-beta-3.jar to /tmp/mangoTestpODQhLH/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/com/google/protobuf/protobuf-java/3.0.0-beta-3/protobuf-java-3.0.0-beta-3.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/com/google/protobuf/protobuf-java-util/3.0.0-beta-3/protobuf-java-util-3.0.0-beta-3.jar to /tmp/mangoTestpODQhLH/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/com/google/protobuf/protobuf-java-util/3.0.0-beta-3/protobuf-java-util-3.0.0-beta-3.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/ga4gh/ga4gh-schemas/0.6.0a10/ga4gh-schemas-0.6.0a10.jar to /tmp/mangoTestpODQhLH/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/org/ga4gh/ga4gh-schemas/0.6.0a10/ga4gh-schemas-0.6.0a10.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/bdgenomics/convert/convert-ga4gh/0.9.0/convert-ga4gh-0.9.0.jar to /tmp/mangoTestpODQhLH/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/org/bdgenomics/convert/convert-ga4gh/0.9.0/convert-ga4gh-0.9.0.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/bdgenomics/convert/convert-htsjdk/0.9.0/convert-htsjdk-0.9.0.jar to /tmp/mangoTestpODQhLH/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/org/bdgenomics/convert/convert-htsjdk/0.9.0/convert-htsjdk-0.9.0.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/com/google/inject/extensions/guice-assistedinject/4.2.2/guice-assistedinject-4.2.2.jar to /tmp/mangoTestpODQhLH/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/com/google/inject/extensions/guice-assistedinject/4.2.2/guice-assistedinject-4.2.2.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/bdgenomics/convert/convert/0.9.0/convert-0.9.0.jar to /tmp/mangoTestpODQhLH/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/org/bdgenomics/convert/convert/0.9.0/convert-0.9.0.jar
[INFO] Installing artifact /tmp/mangoTestpODQhLH/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/mango-cli-spark3_2.12-0.0.6-SNAPSHOT.jar to /tmp/mangoTestpODQhLH/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/org/bdgenomics/mango/mango-cli-spark3_2.12/0.0.6-SNAPSHOT/mango-cli-spark3_2.12-0.0.6-SNAPSHOT.jar
[INFO] 
[INFO] ----------< org.bdgenomics.mango:mango-assembly-spark3_2.12 >-----------
[INFO] Building Mango_2.12: Assembly 0.0.6-SNAPSHOT                       [3/5]
[INFO] --------------------------------[ jar ]---------------------------------
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Downloaded from central: https://repo.maven.apache.org/maven2/com/fasterxml/jackson/core/jackson-core/2.9.8/jackson-core-2.9.8.jar (326 kB at 2.9 MB/s)
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Downloaded from central: https://repo.maven.apache.org/maven2/com/fasterxml/jackson/core/jackson-databind/2.9.8/jackson-databind-2.9.8.jar (1.3 MB at 8.3 MB/s)
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ mango-assembly-spark3_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ mango-assembly-spark3_2.12 ---
[INFO] 
[INFO] --- git-commit-id-plugin:2.2.2:revision (default) @ mango-assembly-spark3_2.12 ---
[INFO] 
[INFO] --- templating-maven-plugin:1.0.0:filter-sources (filter-src) @ mango-assembly-spark3_2.12 ---
[INFO] Request to add '/tmp/mangoTestpODQhLH/deleteMePleaseThisIsNoLongerNeeded/mango-assembly/src/main/java-templates' folder. Not added since it does not exist.
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-source (add-source) @ mango-assembly-spark3_2.12 ---
[INFO] Source directory: /tmp/mangoTestpODQhLH/deleteMePleaseThisIsNoLongerNeeded/mango-assembly/src/main/scala added.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default) @ mango-assembly-spark3_2.12 ---
[INFO] Modified 0 of 1 .scala files
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ mango-assembly-spark3_2.12 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /tmp/mangoTestpODQhLH/deleteMePleaseThisIsNoLongerNeeded/mango-assembly/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ mango-assembly-spark3_2.12 ---
[WARNING]  Expected all dependencies to require Scala version: 2.12.8
[WARNING]  net.liftweb:lift-json_2.12:3.3.0 requires scala version: 2.12.6
[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) @ mango-assembly-spark3_2.12 ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-test-source (add-test-source) @ mango-assembly-spark3_2.12 ---
[INFO] Test Source directory: /tmp/mangoTestpODQhLH/deleteMePleaseThisIsNoLongerNeeded/mango-assembly/src/test/scala added.
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ mango-assembly-spark3_2.12 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /tmp/mangoTestpODQhLH/deleteMePleaseThisIsNoLongerNeeded/mango-assembly/src/test/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ mango-assembly-spark3_2.12 ---
[WARNING]  Expected all dependencies to require Scala version: 2.12.8
[WARNING]  net.liftweb:lift-json_2.12:3.3.0 requires scala version: 2.12.6
[WARNING] Multiple versions of scala libraries detected!
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ mango-assembly-spark3_2.12 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ mango-assembly-spark3_2.12 ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- maven-jar-plugin:3.1.2:jar (default-jar) @ mango-assembly-spark3_2.12 ---
[INFO] Building jar: /tmp/mangoTestpODQhLH/deleteMePleaseThisIsNoLongerNeeded/mango-assembly/target/mango-assembly-spark3_2.12-0.0.6-SNAPSHOT.jar
[INFO] 
[INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ mango-assembly-spark3_2.12 ---
[INFO] Building jar: /tmp/mangoTestpODQhLH/deleteMePleaseThisIsNoLongerNeeded/mango-assembly/target/mango-assembly-spark3_2.12-0.0.6-SNAPSHOT-sources.jar
[INFO] 
[INFO] --- maven-javadoc-plugin:3.1.0:jar (attach-javadocs) @ mango-assembly-spark3_2.12 ---
[INFO] 
[INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) > generate-sources @ mango-assembly-spark3_2.12 >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ mango-assembly-spark3_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ mango-assembly-spark3_2.12 ---
[INFO] 
[INFO] --- git-commit-id-plugin:2.2.2:revision (default) @ mango-assembly-spark3_2.12 ---
[INFO] 
[INFO] --- templating-maven-plugin:1.0.0:filter-sources (filter-src) @ mango-assembly-spark3_2.12 ---
[INFO] Request to add '/tmp/mangoTestpODQhLH/deleteMePleaseThisIsNoLongerNeeded/mango-assembly/src/main/java-templates' folder. Not added since it does not exist.
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-source (add-source) @ mango-assembly-spark3_2.12 ---
[INFO] Source directory: /tmp/mangoTestpODQhLH/deleteMePleaseThisIsNoLongerNeeded/mango-assembly/src/main/scala added.
[INFO] 
[INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) < generate-sources @ mango-assembly-spark3_2.12 <<<
[INFO] 
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ mango-assembly-spark3_2.12 ---
[WARNING]  Expected all dependencies to require Scala version: 2.12.8
[WARNING]  net.liftweb:lift-json_2.12:3.3.0 requires scala version: 2.12.6
[WARNING] Multiple versions of scala libraries detected!
[WARNING]  Expected all dependencies to require Scala version: 2.12.8
[WARNING]  net.liftweb:lift-json_2.12:3.3.0 requires scala version: 2.12.6
[WARNING] Multiple versions of scala libraries detected!
model contains 6 documentable templates
[INFO] Building jar: /tmp/mangoTestpODQhLH/deleteMePleaseThisIsNoLongerNeeded/mango-assembly/target/mango-assembly-spark3_2.12-0.0.6-SNAPSHOT-javadoc.jar
[INFO] 
[INFO] --- maven-shade-plugin:3.2.0:shade (default) @ mango-assembly-spark3_2.12 ---
Downloading from central: https://repo.maven.apache.org/maven2/org/bdgenomics/adam/adam-shade-spark3_2.12/0.32.0/adam-shade-spark3_2.12-0.32.0.pom
Progress (1): 1.5 kB
                    
Downloaded from central: https://repo.maven.apache.org/maven2/org/bdgenomics/adam/adam-shade-spark3_2.12/0.32.0/adam-shade-spark3_2.12-0.32.0.pom (1.5 kB at 124 kB/s)
Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/plugins/maven-shade-plugin/3.2.1/maven-shade-plugin-3.2.1.pom
Progress (1): 4.1/9.3 kB
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Progress (1): 9.3 kB    
                    
Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/maven/plugins/maven-shade-plugin/3.2.1/maven-shade-plugin-3.2.1.pom (9.3 kB at 718 kB/s)
Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/shared/maven-artifact-transfer/0.10.0/maven-artifact-transfer-0.10.0.pom
Progress (1): 4.1/12 kB
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[INFO] Including org.bdgenomics.mango:mango-cli-spark3_2.12:jar:0.0.6-SNAPSHOT in the shaded jar.
[INFO] Including net.liftweb:lift-json_2.12:jar:3.3.0 in the shaded jar.
[INFO] Including org.scala-lang:scala-library:jar:2.12.6 in the shaded jar.
[INFO] Including org.scala-lang:scalap:jar:2.12.6 in the shaded jar.
[INFO] Including com.thoughtworks.paranamer:paranamer:jar:2.8 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 org.xerial.snappy:snappy-java:jar:1.0.5 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.slf4j:slf4j-api:jar:1.7.7 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 commons-codec:commons-codec:jar:1.10 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 it.unimi.dsi:fastutil:jar:7.0.13 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-scala_2.10:jar:1.10.1 in the shaded jar.
[INFO] Including org.bdgenomics.adam:adam-cli-spark3_2.12:jar:0.32.0 in the shaded jar.
[INFO] Including org.bdgenomics.adam:adam-apis-spark3_2.12:jar:0.32.0 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.adam:adam-core-spark3_2.12:jar:0.32.0 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 org.clapper:grizzled-slf4j_2.12:jar:1.3.4 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 commons-logging:commons-logging:jar:1.1.1 in the shaded jar.
[INFO] Including gov.nih.nlm.ncbi:ngs-java:jar:2.9.0 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 com.google.guava:guava:jar:27.0-jre in the shaded jar.
[INFO] Including com.google.guava:failureaccess:jar:1.0 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:0.32.0 in the shaded jar.
[INFO] Including org.bdgenomics.bdg-formats:bdg-formats:jar:0.15.0 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.bdgenomics.utils:utils-misc-spark3_2.12:jar:0.3.0 in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-intervalrdd-spark3_2.12:jar:0.3.0 in the shaded jar.
[INFO] Including org.eclipse.jetty:jetty-server:jar:9.4.17.v20190418 in the shaded jar.
[INFO] Including javax.servlet:javax.servlet-api:jar:3.1.0 in the shaded jar.
[INFO] Including org.eclipse.jetty:jetty-http:jar:9.4.17.v20190418 in the shaded jar.
[INFO] Including org.eclipse.jetty:jetty-util:jar:9.4.17.v20190418 in the shaded jar.
[INFO] Including org.eclipse.jetty:jetty-io:jar:9.4.17.v20190418 in the shaded jar.
[INFO] Including org.eclipse.jetty:jetty-webapp:jar:9.4.17.v20190418 in the shaded jar.
[INFO] Including org.eclipse.jetty:jetty-xml:jar:9.4.17.v20190418 in the shaded jar.
[INFO] Including org.eclipse.jetty:jetty-servlet:jar:9.4.17.v20190418 in the shaded jar.
[INFO] Including org.eclipse.jetty:jetty-security:jar:9.4.17.v20190418 in the shaded jar.
[INFO] Including org.scalatra:scalatra_2.12:jar:2.5.0 in the shaded jar.
[INFO] Including org.scalatra:scalatra-common_2.12:jar:2.5.0 in the shaded jar.
[INFO] Including com.googlecode.juniversalchardet:juniversalchardet:jar:1.0.3 in the shaded jar.
[INFO] Including eu.medsea.mimeutil:mime-util:jar:2.1.3 in the shaded jar.
[INFO] Including org.apache.commons:commons-lang3:jar:3.5 in the shaded jar.
[INFO] Including org.scala-lang.modules:scala-parser-combinators_2.12:jar:1.0.4 in the shaded jar.
[INFO] Including org.scala-lang.modules:scala-xml_2.12:jar:1.0.6 in the shaded jar.
[INFO] Including org.scalatra.scalate:scalate-core_2.12:jar:1.9.1 in the shaded jar.
[INFO] Including org.scala-lang:scala-compiler:jar:2.12.8 in the shaded jar.
[INFO] Including org.scalatra.scalate:scalate-util_2.12:jar:1.9.1 in the shaded jar.
[INFO] Including org.bdgenomics.mango:mango-core-spark3_2.12:jar:0.0.6-SNAPSHOT in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-io-spark3_2.12:jar:0.3.0 in the shaded jar.
[INFO] Including com.google.protobuf:protobuf-java:jar:3.0.0-beta-3 in the shaded jar.
[INFO] Including com.google.protobuf:protobuf-java-util:jar:3.0.0-beta-3 in the shaded jar.
[INFO] Including com.google.code.gson:gson:jar:2.3 in the shaded jar.
[INFO] Including org.ga4gh:ga4gh-schemas:jar:0.6.0a10 in the shaded jar.
[INFO] Including org.bdgenomics.convert:convert-ga4gh:jar:0.9.0 in the shaded jar.
[INFO] Including org.bdgenomics.convert:convert-htsjdk:jar:0.9.0 in the shaded jar.
[INFO] Including com.google.inject.extensions:guice-assistedinject:jar:4.2.2 in the shaded jar.
[INFO] Including org.bdgenomics.convert:convert:jar:0.9.0 in the shaded jar.
[WARNING] WORKAROUND:  refusing to add class org/apache/parquet/avro/AvroSchemaConverter$2.class from jar /home/jenkins/.m2/repository/org/apache/parquet/parquet-avro/1.10.1/parquet-avro-1.10.1.jar
[WARNING] WORKAROUND:  refusing to add class org/apache/parquet/avro/AvroSchemaConverter.class from jar /home/jenkins/.m2/repository/org/apache/parquet/parquet-avro/1.10.1/parquet-avro-1.10.1.jar
[WARNING] WORKAROUND:  refusing to add class org/apache/parquet/avro/AvroSchemaConverter$1.class from jar /home/jenkins/.m2/repository/org/apache/parquet/parquet-avro/1.10.1/parquet-avro-1.10.1.jar
[WARNING] mango-cli-spark3_2.12-0.0.6-SNAPSHOT.jar, adam-cli-spark3_2.12-0.32.0.jar define 3 overlapping classes: 
[WARNING]   - org.bdgenomics.adam.cli.CommandGroup
[WARNING]   - org.bdgenomics.adam.cli.InitArgs
[WARNING]   - org.bdgenomics.adam.cli.CommandGroup$
[WARNING] guava-27.0-jre.jar, failureaccess-1.0.jar define 2 overlapping classes: 
[WARNING]   - com.google.common.util.concurrent.internal.InternalFutureFailureAccess
[WARNING]   - com.google.common.util.concurrent.internal.InternalFutures
[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 /tmp/mangoTestpODQhLH/deleteMePleaseThisIsNoLongerNeeded/mango-assembly/target/mango-assembly-spark3_2.12-0.0.6-SNAPSHOT.jar with /tmp/mangoTestpODQhLH/deleteMePleaseThisIsNoLongerNeeded/mango-assembly/target/mango-assembly-spark3_2.12-0.0.6-SNAPSHOT-shaded.jar
[INFO] 
[INFO] --------< org.bdgenomics.mango:mango-distribution-spark3_2.12 >---------
[INFO] Building mango_2.12: Distribution 0.0.6-SNAPSHOT                   [4/5]
[INFO] --------------------------------[ pom ]---------------------------------
Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/plugins/maven-assembly-plugin/2.2-beta-5/maven-assembly-plugin-2.2-beta-5.pom
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Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/plugins/maven-assembly-plugin/2.2-beta-5/maven-assembly-plugin-2.2-beta-5.jar
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Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/maven/plugins/maven-assembly-plugin/2.2-beta-5/maven-assembly-plugin-2.2-beta-5.jar (209 kB at 7.0 MB/s)
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ mango-distribution-spark3_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ mango-distribution-spark3_2.12 ---
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default) @ mango-distribution-spark3_2.12 ---
[INFO] Modified 0 of 0 .scala files
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ mango-distribution-spark3_2.12 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ mango-distribution-spark3_2.12 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ mango-distribution-spark3_2.12 ---
[INFO] 
[INFO] --- maven-javadoc-plugin:3.1.0:jar (attach-javadocs) @ mango-distribution-spark3_2.12 ---
[INFO] 
[INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) > generate-sources @ mango-distribution-spark3_2.12 >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ mango-distribution-spark3_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ mango-distribution-spark3_2.12 ---
[INFO] 
[INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) < generate-sources @ mango-distribution-spark3_2.12 <<<
[INFO] 
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ mango-distribution-spark3_2.12 ---
[INFO] No source files found
[INFO] 
[INFO] --- maven-assembly-plugin:2.2-beta-5:single (default) @ mango-distribution-spark3_2.12 ---
Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/shared/maven-common-artifact-filters/1.1/maven-common-artifact-filters-1.1.pom
Progress (1): 2.8 kB
                    
Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/maven/shared/maven-common-artifact-filters/1.1/maven-common-artifact-filters-1.1.pom (2.8 kB at 277 kB/s)
Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/shared/maven-shared-components/10/maven-shared-components-10.pom
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[INFO] Reading assembly descriptor: src/main/assembly/assembly.xml
[INFO] Building tar : /tmp/mangoTestpODQhLH/deleteMePleaseThisIsNoLongerNeeded/mango-distribution/target/mango-distribution-spark3_2.12-0.0.6-SNAPSHOT-bin.tar.gz
[WARNING] Entry: mango-distribution-spark3_2.12-0.0.6-SNAPSHOT/repo/mango-assembly-spark3_2.12-0.0.6-SNAPSHOT-javadoc.jar longer than 100 characters.
[WARNING] Resulting tar file can only be processed successfully by GNU compatible tar commands
[WARNING] Entry: mango-distribution-spark3_2.12-0.0.6-SNAPSHOT/repo/mango-assembly-spark3_2.12-0.0.6-SNAPSHOT-sources.jar longer than 100 characters.
[INFO] Building tar : /tmp/mangoTestpODQhLH/deleteMePleaseThisIsNoLongerNeeded/mango-distribution/target/mango-distribution-spark3_2.12-0.0.6-SNAPSHOT-bin.tar.bz2
[WARNING] Entry: mango-distribution-spark3_2.12-0.0.6-SNAPSHOT/repo/mango-assembly-spark3_2.12-0.0.6-SNAPSHOT-javadoc.jar longer than 100 characters.
[WARNING] Resulting tar file can only be processed successfully by GNU compatible tar commands
[WARNING] Entry: mango-distribution-spark3_2.12-0.0.6-SNAPSHOT/repo/mango-assembly-spark3_2.12-0.0.6-SNAPSHOT-sources.jar longer than 100 characters.
[INFO] Building zip: /tmp/mangoTestpODQhLH/deleteMePleaseThisIsNoLongerNeeded/mango-distribution/target/mango-distribution-spark3_2.12-0.0.6-SNAPSHOT-bin.zip
[INFO] 
[INFO] -----------< org.bdgenomics.mango:mango-parent-spark3_2.12 >------------
[INFO] Building mango_2.12 0.0.6-SNAPSHOT                                 [5/5]
[INFO] --------------------------------[ pom ]---------------------------------
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ mango-parent-spark3_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ mango-parent-spark3_2.12 ---
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default) @ mango-parent-spark3_2.12 ---
[INFO] Modified 0 of 41 .scala files
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ mango-parent-spark3_2.12 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ mango-parent-spark3_2.12 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ mango-parent-spark3_2.12 ---
[INFO] 
[INFO] --- maven-javadoc-plugin:3.1.0:jar (attach-javadocs) @ mango-parent-spark3_2.12 ---
[INFO] 
[INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) > generate-sources @ mango-parent-spark3_2.12 >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ mango-parent-spark3_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ mango-parent-spark3_2.12 ---
[INFO] 
[INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) < generate-sources @ mango-parent-spark3_2.12 <<<
[INFO] 
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ mango-parent-spark3_2.12 ---
[INFO] No source files found
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary for mango_2.12 0.0.6-SNAPSHOT:
[INFO] 
[INFO] mango_2.12: CORE ................................... SUCCESS [01:12 min]
[INFO] mango_2.12: CLI .................................... SUCCESS [ 49.511 s]
[INFO] Mango_2.12: Assembly ............................... SUCCESS [ 29.090 s]
[INFO] mango_2.12: Distribution ........................... SUCCESS [01:46 min]
[INFO] mango_2.12 ......................................... SUCCESS [  2.369 s]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time:  04:20 min
[INFO] Finished at: 2021-02-04T18:24:23Z
[INFO] ------------------------------------------------------------------------

# make sure that the distribution package contains an assembly jar
# if no assembly jar is found, this will exit with code 1 and fail the build
tar tzf mango-distribution/target/mango-distribution*-bin.tar.gz | \
    grep mango-assembly | \
    grep jar | \
    grep -v -e sources -e javadoc
+ grep mango-assembly
+ tar tzf mango-distribution/target/mango-distribution-spark3_2.12-0.0.6-SNAPSHOT-bin.tar.gz
+ grep jar
+ grep -v -e sources -e javadoc
mango-distribution-spark3_2.12-0.0.6-SNAPSHOT/repo/mango-assembly-spark3_2.12-0.0.6-SNAPSHOT.jar

# we are done with maven, so clean up the maven temp dir
find ${MANGO_MVN_TMP_DIR}
+ find /tmp/mangoTestMvnYgWKmeh
/tmp/mangoTestMvnYgWKmeh
/tmp/mangoTestMvnYgWKmeh/invalidBuild.genome4523523445541114800
/tmp/mangoTestMvnYgWKmeh/invalidBuild.genome4523523445541114800/properties.txt
/tmp/mangoTestMvnYgWKmeh/invalidBuild.genome2002285554147594158
/tmp/mangoTestMvnYgWKmeh/invalidBuild.genome2002285554147594158/properties.txt
/tmp/mangoTestMvnYgWKmeh/3099032127463781458
/tmp/mangoTestMvnYgWKmeh/fake-7033825325594895653.txt
/tmp/mangoTestMvnYgWKmeh/6949661014348384306
/tmp/mangoTestMvnYgWKmeh/6949661014348384306/anoGam1.genome
/tmp/mangoTestMvnYgWKmeh/TempSuite815019620652935549
/tmp/mangoTestMvnYgWKmeh/genomes1665191934920852072
/tmp/mangoTestMvnYgWKmeh/genomes1665191934920852072/hg19.genome
/tmp/mangoTestMvnYgWKmeh/612762542175822901
/tmp/mangoTestMvnYgWKmeh/fake-4279764451219387958.sh
/tmp/mangoTestMvnYgWKmeh/8480258437373648814
/tmp/mangoTestMvnYgWKmeh/8480258437373648814/anoGam1.genome
/tmp/mangoTestMvnYgWKmeh/TempSuite73419205880212186.adam
/tmp/mangoTestMvnYgWKmeh/TempSuite73419205880212186.adam/._references.avro.crc
/tmp/mangoTestMvnYgWKmeh/TempSuite73419205880212186.adam/_SUCCESS
/tmp/mangoTestMvnYgWKmeh/TempSuite73419205880212186.adam/_partitionedByStartPos
/tmp/mangoTestMvnYgWKmeh/TempSuite73419205880212186.adam/referenceName=1
/tmp/mangoTestMvnYgWKmeh/TempSuite73419205880212186.adam/referenceName=1/positionBin=0
/tmp/mangoTestMvnYgWKmeh/TempSuite73419205880212186.adam/referenceName=1/positionBin=0/.part-00000-bd36b054-7c43-4125-979c-d6c1b2fa307b.c000.snappy.parquet.crc
/tmp/mangoTestMvnYgWKmeh/TempSuite73419205880212186.adam/referenceName=1/positionBin=0/part-00000-bd36b054-7c43-4125-979c-d6c1b2fa307b.c000.snappy.parquet
/tmp/mangoTestMvnYgWKmeh/TempSuite73419205880212186.adam/._partitionedByStartPos.crc
/tmp/mangoTestMvnYgWKmeh/TempSuite73419205880212186.adam/_references.avro
/tmp/mangoTestMvnYgWKmeh/TempSuite73419205880212186.adam/_samples.avro
/tmp/mangoTestMvnYgWKmeh/TempSuite73419205880212186.adam/._SUCCESS.crc
/tmp/mangoTestMvnYgWKmeh/TempSuite73419205880212186.adam/._samples.avro.crc
/tmp/mangoTestMvnYgWKmeh/TempSuite73419205880212186.adam/._header.crc
/tmp/mangoTestMvnYgWKmeh/TempSuite73419205880212186.adam/_header
/tmp/mangoTestMvnYgWKmeh/mmbroken2829695636561992531.genome
/tmp/mangoTestMvnYgWKmeh/TempSuite73419205880212186
/tmp/mangoTestMvnYgWKmeh/TempSuite4960643451781323276
/tmp/mangoTestMvnYgWKmeh/TempSuite4886209003650286683
/tmp/mangoTestMvnYgWKmeh/TempSuite4886209003650286683.adam
/tmp/mangoTestMvnYgWKmeh/TempSuite4886209003650286683.adam/._references.avro.crc
/tmp/mangoTestMvnYgWKmeh/TempSuite4886209003650286683.adam/_SUCCESS
/tmp/mangoTestMvnYgWKmeh/TempSuite4886209003650286683.adam/_partitionedByStartPos
/tmp/mangoTestMvnYgWKmeh/TempSuite4886209003650286683.adam/referenceName=1
/tmp/mangoTestMvnYgWKmeh/TempSuite4886209003650286683.adam/referenceName=1/positionBin=0
/tmp/mangoTestMvnYgWKmeh/TempSuite4886209003650286683.adam/referenceName=1/positionBin=0/part-00000-4298ea55-8ff5-449b-baf4-3d5ba86b7a3d.c000.snappy.parquet
/tmp/mangoTestMvnYgWKmeh/TempSuite4886209003650286683.adam/referenceName=1/positionBin=0/.part-00000-4298ea55-8ff5-449b-baf4-3d5ba86b7a3d.c000.snappy.parquet.crc
/tmp/mangoTestMvnYgWKmeh/TempSuite4886209003650286683.adam/._partitionedByStartPos.crc
/tmp/mangoTestMvnYgWKmeh/TempSuite4886209003650286683.adam/_references.avro
/tmp/mangoTestMvnYgWKmeh/TempSuite4886209003650286683.adam/_samples.avro
/tmp/mangoTestMvnYgWKmeh/TempSuite4886209003650286683.adam/._SUCCESS.crc
/tmp/mangoTestMvnYgWKmeh/TempSuite4886209003650286683.adam/._samples.avro.crc
/tmp/mangoTestMvnYgWKmeh/TempSuite4886209003650286683.adam/._header.crc
/tmp/mangoTestMvnYgWKmeh/TempSuite4886209003650286683.adam/_header
/tmp/mangoTestMvnYgWKmeh/mmbroken9059079083307479963.genome
/tmp/mangoTestMvnYgWKmeh/snappy-1.0.5-libsnappyjava.so
/tmp/mangoTestMvnYgWKmeh/TempSuite815019620652935549.adam
/tmp/mangoTestMvnYgWKmeh/TempSuite815019620652935549.adam/._references.avro.crc
/tmp/mangoTestMvnYgWKmeh/TempSuite815019620652935549.adam/._processingSteps.avro.crc
/tmp/mangoTestMvnYgWKmeh/TempSuite815019620652935549.adam/_readGroups.avro
/tmp/mangoTestMvnYgWKmeh/TempSuite815019620652935549.adam/_processingSteps.avro
/tmp/mangoTestMvnYgWKmeh/TempSuite815019620652935549.adam/_SUCCESS
/tmp/mangoTestMvnYgWKmeh/TempSuite815019620652935549.adam/_partitionedByStartPos
/tmp/mangoTestMvnYgWKmeh/TempSuite815019620652935549.adam/referenceName=1
/tmp/mangoTestMvnYgWKmeh/TempSuite815019620652935549.adam/referenceName=1/positionBin=26
/tmp/mangoTestMvnYgWKmeh/TempSuite815019620652935549.adam/referenceName=1/positionBin=26/part-00000-81dce21f-edc3-46d6-8ce7-b032873a9dcf.c000.snappy.parquet
/tmp/mangoTestMvnYgWKmeh/TempSuite815019620652935549.adam/referenceName=1/positionBin=26/.part-00000-81dce21f-edc3-46d6-8ce7-b032873a9dcf.c000.snappy.parquet.crc
/tmp/mangoTestMvnYgWKmeh/TempSuite815019620652935549.adam/referenceName=1/positionBin=240
/tmp/mangoTestMvnYgWKmeh/TempSuite815019620652935549.adam/referenceName=1/positionBin=240/part-00000-81dce21f-edc3-46d6-8ce7-b032873a9dcf.c000.snappy.parquet
/tmp/mangoTestMvnYgWKmeh/TempSuite815019620652935549.adam/referenceName=1/positionBin=240/.part-00000-81dce21f-edc3-46d6-8ce7-b032873a9dcf.c000.snappy.parquet.crc
/tmp/mangoTestMvnYgWKmeh/TempSuite815019620652935549.adam/._partitionedByStartPos.crc
/tmp/mangoTestMvnYgWKmeh/TempSuite815019620652935549.adam/_references.avro
/tmp/mangoTestMvnYgWKmeh/TempSuite815019620652935549.adam/referenceName=2
/tmp/mangoTestMvnYgWKmeh/TempSuite815019620652935549.adam/referenceName=2/positionBin=189
/tmp/mangoTestMvnYgWKmeh/TempSuite815019620652935549.adam/referenceName=2/positionBin=189/part-00000-81dce21f-edc3-46d6-8ce7-b032873a9dcf.c000.snappy.parquet
/tmp/mangoTestMvnYgWKmeh/TempSuite815019620652935549.adam/referenceName=2/positionBin=189/.part-00000-81dce21f-edc3-46d6-8ce7-b032873a9dcf.c000.snappy.parquet.crc
/tmp/mangoTestMvnYgWKmeh/TempSuite815019620652935549.adam/._SUCCESS.crc
/tmp/mangoTestMvnYgWKmeh/TempSuite815019620652935549.adam/._readGroups.avro.crc
/tmp/mangoTestMvnYgWKmeh/genomes8115801472524600423
/tmp/mangoTestMvnYgWKmeh/genomes8115801472524600423/hg19.genome
/tmp/mangoTestMvnYgWKmeh/fake-9210030305124907697.sh
/tmp/mangoTestMvnYgWKmeh/fake-7745591128512640538.txt
/tmp/mangoTestMvnYgWKmeh/TempSuite4960643451781323276.adam
/tmp/mangoTestMvnYgWKmeh/TempSuite4960643451781323276.adam/._references.avro.crc
/tmp/mangoTestMvnYgWKmeh/TempSuite4960643451781323276.adam/._processingSteps.avro.crc
/tmp/mangoTestMvnYgWKmeh/TempSuite4960643451781323276.adam/_readGroups.avro
/tmp/mangoTestMvnYgWKmeh/TempSuite4960643451781323276.adam/_processingSteps.avro
/tmp/mangoTestMvnYgWKmeh/TempSuite4960643451781323276.adam/_SUCCESS
/tmp/mangoTestMvnYgWKmeh/TempSuite4960643451781323276.adam/_partitionedByStartPos
/tmp/mangoTestMvnYgWKmeh/TempSuite4960643451781323276.adam/referenceName=1
/tmp/mangoTestMvnYgWKmeh/TempSuite4960643451781323276.adam/referenceName=1/positionBin=26
/tmp/mangoTestMvnYgWKmeh/TempSuite4960643451781323276.adam/referenceName=1/positionBin=26/part-00000-ce667bd3-2a49-4fbf-a06a-f429a4f3fb7f.c000.snappy.parquet
/tmp/mangoTestMvnYgWKmeh/TempSuite4960643451781323276.adam/referenceName=1/positionBin=26/.part-00000-ce667bd3-2a49-4fbf-a06a-f429a4f3fb7f.c000.snappy.parquet.crc
/tmp/mangoTestMvnYgWKmeh/TempSuite4960643451781323276.adam/referenceName=1/positionBin=240
/tmp/mangoTestMvnYgWKmeh/TempSuite4960643451781323276.adam/referenceName=1/positionBin=240/part-00000-ce667bd3-2a49-4fbf-a06a-f429a4f3fb7f.c000.snappy.parquet
/tmp/mangoTestMvnYgWKmeh/TempSuite4960643451781323276.adam/referenceName=1/positionBin=240/.part-00000-ce667bd3-2a49-4fbf-a06a-f429a4f3fb7f.c000.snappy.parquet.crc
/tmp/mangoTestMvnYgWKmeh/TempSuite4960643451781323276.adam/._partitionedByStartPos.crc
/tmp/mangoTestMvnYgWKmeh/TempSuite4960643451781323276.adam/_references.avro
/tmp/mangoTestMvnYgWKmeh/TempSuite4960643451781323276.adam/referenceName=2
/tmp/mangoTestMvnYgWKmeh/TempSuite4960643451781323276.adam/referenceName=2/positionBin=189
/tmp/mangoTestMvnYgWKmeh/TempSuite4960643451781323276.adam/referenceName=2/positionBin=189/part-00000-ce667bd3-2a49-4fbf-a06a-f429a4f3fb7f.c000.snappy.parquet
/tmp/mangoTestMvnYgWKmeh/TempSuite4960643451781323276.adam/referenceName=2/positionBin=189/.part-00000-ce667bd3-2a49-4fbf-a06a-f429a4f3fb7f.c000.snappy.parquet.crc
/tmp/mangoTestMvnYgWKmeh/TempSuite4960643451781323276.adam/._SUCCESS.crc
/tmp/mangoTestMvnYgWKmeh/TempSuite4960643451781323276.adam/._readGroups.avro.crc
rm -rf ${MANGO_MVN_TMP_DIR}
+ rm -rf /tmp/mangoTestMvnYgWKmeh

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

# set spark artifact string for downloading assembly
SPARK=spark-${SPARK_VERSION}
+ SPARK=spark-3.0.1

# what hadoop version are we on? format string for downloading spark assembly
if [[ $HADOOP_VERSION =~ ^2\.7 ]]; then
    HADOOP=hadoop2.7
else
    echo "Unknown Hadoop version."
    exit 1
fi
+ [[ 3.2.1 =~ ^2\.7 ]]
+ echo 'Unknown Hadoop version.'
+ exit 1
clean_up
+ clean_up
Unknown Hadoop version.
+ set +x +v
DeprecationWarning: 'source deactivate' is deprecated. Use 'conda deactivate'.
Build step 'Execute shell' marked build as failure
Finished: FAILURE