Console Output

Started by upstream project "cannoli-prb" build number 265
originally caused by:
 GitHub pull request #286 of commit 394186256718cff9b7189adecdaac5bfd47b404a, no merge conflicts.
Running as SYSTEM
[EnvInject] - Loading node environment variables.
Building remotely on ubuntu-testing (ubuntu ubuntu-testing-gpu) in workspace /home/jenkins/workspace/cannoli-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu
The recommended git tool is: NONE
No credentials specified
Wiping out workspace first.
Cloning the remote Git repository
Cloning repository https://github.com/bigdatagenomics/cannoli.git
 > git init /home/jenkins/workspace/cannoli-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu # timeout=10
Using reference repository: /home/jenkins/gitcaches/adam.reference
Fetching upstream changes from https://github.com/bigdatagenomics/cannoli.git
 > git --version # timeout=10
 > git --version # 'git version 2.7.4'
 > git fetch --tags --progress https://github.com/bigdatagenomics/cannoli.git +refs/heads/*:refs/remotes/origin/* # timeout=15
 > git config remote.origin.url https://github.com/bigdatagenomics/cannoli.git # timeout=10
 > git config --add remote.origin.fetch +refs/heads/*:refs/remotes/origin/* # timeout=10
 > git config remote.origin.url https://github.com/bigdatagenomics/cannoli.git # timeout=10
Fetching upstream changes from https://github.com/bigdatagenomics/cannoli.git
 > git fetch --tags --progress https://github.com/bigdatagenomics/cannoli.git +refs/pull/*:refs/remotes/origin/pr/* # timeout=15
Checking out Revision 394186256718cff9b7189adecdaac5bfd47b404a (detached)
 > git config core.sparsecheckout # timeout=10
 > git checkout -f 394186256718cff9b7189adecdaac5bfd47b404a # timeout=10
Commit message: "Update ADAM dependency version to 0.34.0-SNAPSHOT."
 > git rev-list --no-walk 68f9e162ae85f29b4e0d6cb0816f9b080128a1e3 # timeout=10
[ubuntu] $ /bin/bash /tmp/jenkins3276541611674085928.sh
+ set -e
+ unset SPARK_TESTING
+ export JAVA_HOME=/usr/java/latest
+ JAVA_HOME=/usr/java/latest
+ export CONDA_BIN=/home/anaconda/bin/
+ CONDA_BIN=/home/anaconda/bin/
+ export PATH=/usr/java/latest/bin/:/home/anaconda/bin/:/home/jenkins/tools/hudson.tasks.Maven_MavenInstallation/Maven_3.6.3/bin/:/home/jenkins/gems/bin:/usr/local/go/bin:/home/jenkins/go-projects/bin:/home/jenkins/anaconda2/bin:/home/jenkins/tools/hudson.tasks.Maven_MavenInstallation/Maven_3.6.3/bin/:/home/jenkins/gems/bin:/usr/local/go/bin:/home/jenkins/go-projects/bin:/home/jenkins/anaconda2/bin:/home/jenkins/tools/hudson.tasks.Maven_MavenInstallation/Maven_3.6.3/bin/:/home/jenkins/gems/bin:/usr/local/go/bin:/home/jenkins/go-projects/bin:/home/jenkins/anaconda2/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games
+ PATH=/usr/java/latest/bin/:/home/anaconda/bin/:/home/jenkins/tools/hudson.tasks.Maven_MavenInstallation/Maven_3.6.3/bin/:/home/jenkins/gems/bin:/usr/local/go/bin:/home/jenkins/go-projects/bin:/home/jenkins/anaconda2/bin:/home/jenkins/tools/hudson.tasks.Maven_MavenInstallation/Maven_3.6.3/bin/:/home/jenkins/gems/bin:/usr/local/go/bin:/home/jenkins/go-projects/bin:/home/jenkins/anaconda2/bin:/home/jenkins/tools/hudson.tasks.Maven_MavenInstallation/Maven_3.6.3/bin/:/home/jenkins/gems/bin:/usr/local/go/bin:/home/jenkins/go-projects/bin:/home/jenkins/anaconda2/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games
+ /home/jenkins/workspace/cannoli-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/scripts/jenkins-test

# make a tempdir for writing maven cruft to
CANNOLI_MVN_TMP_DIR=$(mktemp -d -t cannoliTestMvnXXXXXXX)
mktemp -d -t cannoliTestMvnXXXXXXX
++ mktemp -d -t cannoliTestMvnXXXXXXX
+ CANNOLI_MVN_TMP_DIR=/tmp/cannoliTestMvnc3lYIyG

# add this tempdir to the poms...
find . -name pom.xml \
    -exec sed -i.bak \
    -e "s:sun.io.serialization.extendedDebugInfo=true:sun.io.serialization.extendedDebugInfo=true -Djava.io.tmpdir=${CANNOLI_MVN_TMP_DIR}:g" \
    {} \;
+ find . -name pom.xml -exec sed -i.bak -e 's:sun.io.serialization.extendedDebugInfo=true:sun.io.serialization.extendedDebugInfo=true -Djava.io.tmpdir=/tmp/cannoliTestMvnc3lYIyG:g' '{}' ';'
find . -name "*.bak" -exec rm -f {} \;
+ find . -name '*.bak' -exec rm -f '{}' ';'

# variable declarations
export PATH=${JAVA_HOME}/bin/:${PATH}
+ export PATH=/usr/java/latest/bin/:/usr/java/latest/bin/:/home/anaconda/bin/:/home/jenkins/tools/hudson.tasks.Maven_MavenInstallation/Maven_3.6.3/bin/:/home/jenkins/gems/bin:/usr/local/go/bin:/home/jenkins/go-projects/bin:/home/jenkins/anaconda2/bin:/home/jenkins/tools/hudson.tasks.Maven_MavenInstallation/Maven_3.6.3/bin/:/home/jenkins/gems/bin:/usr/local/go/bin:/home/jenkins/go-projects/bin:/home/jenkins/anaconda2/bin:/home/jenkins/tools/hudson.tasks.Maven_MavenInstallation/Maven_3.6.3/bin/:/home/jenkins/gems/bin:/usr/local/go/bin:/home/jenkins/go-projects/bin:/home/jenkins/anaconda2/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games
+ PATH=/usr/java/latest/bin/:/usr/java/latest/bin/:/home/anaconda/bin/:/home/jenkins/tools/hudson.tasks.Maven_MavenInstallation/Maven_3.6.3/bin/:/home/jenkins/gems/bin:/usr/local/go/bin:/home/jenkins/go-projects/bin:/home/jenkins/anaconda2/bin:/home/jenkins/tools/hudson.tasks.Maven_MavenInstallation/Maven_3.6.3/bin/:/home/jenkins/gems/bin:/usr/local/go/bin:/home/jenkins/go-projects/bin:/home/jenkins/anaconda2/bin:/home/jenkins/tools/hudson.tasks.Maven_MavenInstallation/Maven_3.6.3/bin/:/home/jenkins/gems/bin:/usr/local/go/bin:/home/jenkins/go-projects/bin:/home/jenkins/anaconda2/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games
export MAVEN_OPTS="-Xmx1536m -XX:MaxPermSize=1g -Dfile.encoding=utf-8"
+ export 'MAVEN_OPTS=-Xmx1536m -XX:MaxPermSize=1g -Dfile.encoding=utf-8'
+ MAVEN_OPTS='-Xmx1536m -XX:MaxPermSize=1g -Dfile.encoding=utf-8'
DIR=$( cd $( dirname ${BASH_SOURCE[0]} ) && pwd )
 cd $( dirname ${BASH_SOURCE[0]} ) && pwd 
 dirname ${BASH_SOURCE[0]} 
+++ dirname /home/jenkins/workspace/cannoli-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/scripts/jenkins-test
++ cd /home/jenkins/workspace/cannoli-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/scripts
++ pwd
+ DIR=/home/jenkins/workspace/cannoli-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/scripts
PROJECT_ROOT=${DIR}/..
+ PROJECT_ROOT=/home/jenkins/workspace/cannoli-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/scripts/..
VERSION=$(grep "<version>" ${PROJECT_ROOT}/pom.xml  | head -2 | tail -1 | sed 's/ *<version>//g' | sed 's/<\/version>//g')
grep "<version>" ${PROJECT_ROOT}/pom.xml  | head -2 | tail -1 | sed 's/ *<version>//g' | sed 's/<\/version>//g'
++ grep '<version>' /home/jenkins/workspace/cannoli-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/scripts/../pom.xml
++ head -2
++ tail -1
++ sed 's/ *<version>//g'
++ sed 's/<\/version>//g'
+ VERSION=0.12.0-SNAPSHOT

# is the hadoop version set?
if ! [[ ${HADOOP_VERSION} ]];
then
    echo "HADOOP_VERSION environment variable is not set."
    echo "Please set this variable before running."
    exit 1
fi
+ [[ -n 2.7.5 ]]

# is the scala version set?
if ! [[ ${SCALA_VERSION} ]];
then
    echo "SCALA_VERSION environment variable is not set."
    echo "Please set this variable before running."
    exit 1
fi
+ [[ -n 2.12 ]]

# is the spark version set?
if ! [[ ${SPARK_VERSION} ]];
then
    echo "SPARK_VERSION environment variable is not set."
    echo "Please set this variable before running."
    exit 1
fi
+ [[ -n 3.0.1 ]]

# print versions
echo "Testing Cannoli version ${VERSION} on Spark ${SPARK_VERSION} Scala ${SCALA_VERSION} and Hadoop ${HADOOP_VERSION}"
+ echo 'Testing Cannoli version 0.12.0-SNAPSHOT on Spark 3.0.1 Scala 2.12 and Hadoop 2.7.5'
Testing Cannoli version 0.12.0-SNAPSHOT on Spark 3.0.1 Scala 2.12 and Hadoop 2.7.5

# build the distribution package and the integration tests
mvn -U \
    clean \
    package \
    -Dhadoop.version=${HADOOP_VERSION}
+ mvn -U clean package -Dhadoop.version=2.7.5
Java HotSpot(TM) 64-Bit Server VM warning: ignoring option MaxPermSize=1g; support was removed in 8.0
[INFO] Scanning for projects...
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Build Order:
[INFO] 
[INFO] Cannoli_2.12                                                       [pom]
[INFO] Cannoli_2.12: Builder                                              [jar]
[INFO] Cannoli_2.12: Core                                                 [jar]
[INFO] Cannoli_2.12: CLI                                                  [jar]
[INFO] Cannoli_2.12: Assembly                                             [jar]
[INFO] 
[INFO] ---------< org.bdgenomics.cannoli:cannoli-parent-spark3_2.12 >----------
[INFO] Building Cannoli_2.12 0.12.0-SNAPSHOT                              [1/5]
[INFO] --------------------------------[ pom ]---------------------------------
[INFO] 
[INFO] --- maven-clean-plugin:3.1.0:clean (default-clean) @ cannoli-parent-spark3_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-maven) @ cannoli-parent-spark3_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-java) @ cannoli-parent-spark3_2.12 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ cannoli-parent-spark3_2.12 ---
[INFO] Source directory: /home/jenkins/workspace/cannoli-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/src/main/scala added.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ cannoli-parent-spark3_2.12 ---
[INFO] Modified 0 of 55 .scala files
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ cannoli-parent-spark3_2.12 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ cannoli-parent-spark3_2.12 ---
[INFO] Test Source directory: /home/jenkins/workspace/cannoli-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/src/test/scala added.
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ cannoli-parent-spark3_2.12 ---
[INFO] No sources to compile
[INFO] 
[INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-javadocs) > generate-sources @ cannoli-parent-spark3_2.12 >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-maven) @ cannoli-parent-spark3_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-java) @ cannoli-parent-spark3_2.12 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ cannoli-parent-spark3_2.12 ---
[INFO] Source directory: /home/jenkins/workspace/cannoli-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/src/main/scala added.
[INFO] 
[INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-javadocs) < generate-sources @ cannoli-parent-spark3_2.12 <<<
[INFO] 
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-javadocs) @ cannoli-parent-spark3_2.12 ---
[INFO] No source files found
[INFO] 
[INFO] ---------< org.bdgenomics.cannoli:cannoli-builder-spark3_2.12 >---------
[INFO] Building Cannoli_2.12: Builder 0.12.0-SNAPSHOT                     [2/5]
[INFO] --------------------------------[ jar ]---------------------------------
Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/plugins/maven-jar-plugin/3.1.2/maven-jar-plugin-3.1.2.pom
Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/maven/plugins/maven-jar-plugin/3.1.2/maven-jar-plugin-3.1.2.pom (0 B at 0 B/s)
Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/plugins/maven-jar-plugin/3.1.2/maven-jar-plugin-3.1.2.jar
Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/maven/plugins/maven-jar-plugin/3.1.2/maven-jar-plugin-3.1.2.jar (0 B at 0 B/s)
Downloading from sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/adam/adam-core-spark3_2.12/0.34.0-SNAPSHOT/maven-metadata.xml
Progress (1): 1.4 kB
                    
Downloaded from sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/adam/adam-core-spark3_2.12/0.34.0-SNAPSHOT/maven-metadata.xml (1.4 kB at 3.5 kB/s)
Downloading from sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/adam/adam-parent-spark3_2.12/0.34.0-SNAPSHOT/maven-metadata.xml
Progress (1): 623 B
                   
Downloaded from sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/adam/adam-parent-spark3_2.12/0.34.0-SNAPSHOT/maven-metadata.xml (623 B at 4.3 kB/s)
Downloading from sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/adam/adam-codegen-spark3_2.12/0.34.0-SNAPSHOT/maven-metadata.xml
Progress (1): 1.2 kB
                    
Downloaded from sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/adam/adam-codegen-spark3_2.12/0.34.0-SNAPSHOT/maven-metadata.xml (1.2 kB at 4.0 kB/s)
[INFO] 
[INFO] --- maven-clean-plugin:3.1.0:clean (default-clean) @ cannoli-builder-spark3_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-maven) @ cannoli-builder-spark3_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-java) @ cannoli-builder-spark3_2.12 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ cannoli-builder-spark3_2.12 ---
[INFO] Source directory: /home/jenkins/workspace/cannoli-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/builder/src/main/scala added.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ cannoli-builder-spark3_2.12 ---
[INFO] Modified 0 of 0 .scala files
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ cannoli-builder-spark3_2.12 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/cannoli-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/builder/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ cannoli-builder-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] /home/jenkins/workspace/cannoli-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/builder/src/main/java:-1: info: compiling
[INFO] Compiling 7 source files to /home/jenkins/workspace/cannoli-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/builder/target/scala-2.12.10/classes at 1611162300803
[INFO] prepare-compile in 0 s
[INFO] compile in 2 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ cannoli-builder-spark3_2.12 ---
[INFO] Changes detected - recompiling the module!
[INFO] Compiling 7 source files to /home/jenkins/workspace/cannoli-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/builder/target/scala-2.12.10/classes
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ cannoli-builder-spark3_2.12 ---
[INFO] Test Source directory: /home/jenkins/workspace/cannoli-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/builder/src/test/scala added.
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ cannoli-builder-spark3_2.12 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/cannoli-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/builder/src/test/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ cannoli-builder-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] /home/jenkins/workspace/cannoli-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/builder/src/test/java:-1: info: compiling
[INFO] Compiling 4 source files to /home/jenkins/workspace/cannoli-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/builder/target/scala-2.12.10/test-classes at 1611162304005
[INFO] prepare-compile in 0 s
[INFO] compile in 2 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ cannoli-builder-spark3_2.12 ---
[INFO] Changes detected - recompiling the module!
[INFO] Compiling 4 source files to /home/jenkins/workspace/cannoli-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/builder/target/scala-2.12.10/test-classes
[INFO] 
[INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ cannoli-builder-spark3_2.12 ---
[INFO] 
[INFO] -------------------------------------------------------
[INFO]  T E S T S
[INFO] -------------------------------------------------------
[INFO] Running org.bdgenomics.cannoli.builder.LocalBuilderTest
[INFO] Tests run: 18, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.089 s - in org.bdgenomics.cannoli.builder.LocalBuilderTest
[INFO] Running org.bdgenomics.cannoli.builder.DockerBuilderTest
[INFO] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.bdgenomics.cannoli.builder.DockerBuilderTest
[INFO] Running org.bdgenomics.cannoli.builder.SingularityBuilderTest
[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.bdgenomics.cannoli.builder.SingularityBuilderTest
[INFO] Running org.bdgenomics.cannoli.builder.CommandBuildersTest
[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.bdgenomics.cannoli.builder.CommandBuildersTest
[INFO] 
[INFO] Results:
[INFO] 
[INFO] Tests run: 40, Failures: 0, Errors: 0, Skipped: 0
[INFO] 
[INFO] 
[INFO] --- maven-jar-plugin:3.1.2:jar (default-jar) @ cannoli-builder-spark3_2.12 ---
Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/maven-archiver/3.4.0/maven-archiver-3.4.0.pom
Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/maven/maven-archiver/3.4.0/maven-archiver-3.4.0.pom (0 B at 0 B/s)
Downloading from central: https://repo.maven.apache.org/maven2/org/codehaus/plexus/plexus-archiver/4.1.0/plexus-archiver-4.1.0.pom
Downloaded from central: https://repo.maven.apache.org/maven2/org/codehaus/plexus/plexus-archiver/4.1.0/plexus-archiver-4.1.0.pom (0 B at 0 B/s)
Downloading from central: https://repo.maven.apache.org/maven2/org/codehaus/plexus/plexus-utils/3.2.0/plexus-utils-3.2.0.pom
Downloaded from central: https://repo.maven.apache.org/maven2/org/codehaus/plexus/plexus-utils/3.2.0/plexus-utils-3.2.0.pom (0 B at 0 B/s)
Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/maven-archiver/3.4.0/maven-archiver-3.4.0.jar
Downloading from central: https://repo.maven.apache.org/maven2/org/codehaus/plexus/plexus-archiver/4.1.0/plexus-archiver-4.1.0.jar
Downloading from central: https://repo.maven.apache.org/maven2/org/codehaus/plexus/plexus-utils/3.2.0/plexus-utils-3.2.0.jar
Downloaded from central: https://repo.maven.apache.org/maven2/org/codehaus/plexus/plexus-archiver/4.1.0/plexus-archiver-4.1.0.jar (0 B at 0 B/s)
Downloaded from central: https://repo.maven.apache.org/maven2/org/codehaus/plexus/plexus-utils/3.2.0/plexus-utils-3.2.0.jar (0 B at 0 B/s)
Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/maven/maven-archiver/3.4.0/maven-archiver-3.4.0.jar (0 B at 0 B/s)
[INFO] Building jar: /home/jenkins/workspace/cannoli-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/builder/target/cannoli-builder-spark3_2.12-0.12.0-SNAPSHOT.jar
[INFO] 
[INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-javadocs) > generate-sources @ cannoli-builder-spark3_2.12 >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-maven) @ cannoli-builder-spark3_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-java) @ cannoli-builder-spark3_2.12 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ cannoli-builder-spark3_2.12 ---
[INFO] Source directory: /home/jenkins/workspace/cannoli-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/builder/src/main/scala added.
[INFO] 
[INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-javadocs) < generate-sources @ cannoli-builder-spark3_2.12 <<<
[INFO] 
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-javadocs) @ cannoli-builder-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 10 documentable templates
/home/jenkins/workspace/cannoli-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/builder/src/main/java/org/bdgenomics/cannoli/builder/CommandBuilder.java:449: warning: Could not find any member to link for "IllegalStateException".
    /**
    ^
one warning found
[INFO] Building jar: /home/jenkins/workspace/cannoli-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/builder/target/cannoli-builder-spark3_2.12-0.12.0-SNAPSHOT-javadoc.jar
[INFO] 
[INFO] ----------< org.bdgenomics.cannoli:cannoli-core-spark3_2.12 >-----------
[INFO] Building Cannoli_2.12: Core 0.12.0-SNAPSHOT                        [3/5]
[INFO] --------------------------------[ jar ]---------------------------------
Downloading from central: https://repo.maven.apache.org/maven2/org/slf4j/slf4j-api/1.7.28/slf4j-api-1.7.28.pom
Progress (1): 2.7/3.8 kB
Progress (1): 3.8 kB    
                    
Downloaded from central: https://repo.maven.apache.org/maven2/org/slf4j/slf4j-api/1.7.28/slf4j-api-1.7.28.pom (3.8 kB at 202 kB/s)
Downloading from central: https://repo.maven.apache.org/maven2/org/slf4j/slf4j-parent/1.7.28/slf4j-parent-1.7.28.pom
Progress (1): 2.7/14 kB
Progress (1): 5.5/14 kB
Progress (1): 8.2/14 kB
Progress (1): 11/14 kB 
Progress (1): 14/14 kB
Progress (1): 14 kB   
                   
Downloaded from central: https://repo.maven.apache.org/maven2/org/slf4j/slf4j-parent/1.7.28/slf4j-parent-1.7.28.pom (14 kB at 863 kB/s)
Downloading from central: https://repo.maven.apache.org/maven2/org/slf4j/slf4j-log4j12/1.7.25/slf4j-log4j12-1.7.25.pom
Progress (1): 1.1 kB
                    
Downloaded from central: https://repo.maven.apache.org/maven2/org/slf4j/slf4j-log4j12/1.7.25/slf4j-log4j12-1.7.25.pom (1.1 kB at 103 kB/s)
[INFO] 
[INFO] --- maven-clean-plugin:3.1.0:clean (default-clean) @ cannoli-core-spark3_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-maven) @ cannoli-core-spark3_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-java) @ cannoli-core-spark3_2.12 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ cannoli-core-spark3_2.12 ---
[INFO] Source directory: /home/jenkins/workspace/cannoli-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/core/src/main/scala added.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ cannoli-core-spark3_2.12 ---
[INFO] Modified 0 of 28 .scala files
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ cannoli-core-spark3_2.12 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/cannoli-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/core/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ cannoli-core-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_2.12:3.0.1 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] /home/jenkins/workspace/cannoli-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/core/src/main/scala:-1: info: compiling
[INFO] Compiling 27 source files to /home/jenkins/workspace/cannoli-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/core/target/scala-2.12.10/classes at 1611162313175
[WARNING] /home/jenkins/workspace/cannoli-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/core/src/main/scala/org/bdgenomics/cannoli/BcftoolsCall.scala:93: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       cmd = builder.build(),
[WARNING]                          ^
[WARNING] /home/jenkins/workspace/cannoli-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/core/src/main/scala/org/bdgenomics/cannoli/BcftoolsCall.scala:94: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       files = builder.getFiles()
[WARNING]                               ^
[WARNING] /home/jenkins/workspace/cannoli-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/core/src/main/scala/org/bdgenomics/cannoli/BcftoolsMpileup.scala:106: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       cmd = builder.build(),
[WARNING]                          ^
[WARNING] /home/jenkins/workspace/cannoli-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/core/src/main/scala/org/bdgenomics/cannoli/BcftoolsMpileup.scala:107: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       files = builder.getFiles()
[WARNING]                               ^
[WARNING] /home/jenkins/workspace/cannoli-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/core/src/main/scala/org/bdgenomics/cannoli/BcftoolsNorm.scala:101: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       cmd = builder.build(),
[WARNING]                          ^
[WARNING] /home/jenkins/workspace/cannoli-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/core/src/main/scala/org/bdgenomics/cannoli/BcftoolsNorm.scala:102: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       files = builder.getFiles()
[WARNING]                               ^
[WARNING] /home/jenkins/workspace/cannoli-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/core/src/main/scala/org/bdgenomics/cannoli/BedtoolsIntersect.scala:91: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     val file = List(optA, optB).flatten.get(0)
[WARNING]                                 ^
[WARNING] /home/jenkins/workspace/cannoli-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/core/src/main/scala/org/bdgenomics/cannoli/BedtoolsIntersect.scala:118: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       cmd = builder.build(),
[WARNING]                          ^
[WARNING] /home/jenkins/workspace/cannoli-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/core/src/main/scala/org/bdgenomics/cannoli/BedtoolsIntersect.scala:119: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       files = builder.getFiles()
[WARNING]                               ^
[WARNING] /home/jenkins/workspace/cannoli-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/core/src/main/scala/org/bdgenomics/cannoli/Blastn.scala:134: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       builder.addFiles(files(args.db + "*"))
[WARNING]                             ^
[WARNING] /home/jenkins/workspace/cannoli-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/core/src/main/scala/org/bdgenomics/cannoli/Blastn.scala:151: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       cmd = builder.build(),
[WARNING]                          ^
[WARNING] /home/jenkins/workspace/cannoli-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/core/src/main/scala/org/bdgenomics/cannoli/Blastn.scala:152: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       files = builder.getFiles()
[WARNING]                               ^
[WARNING] /home/jenkins/workspace/cannoli-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/core/src/main/scala/org/bdgenomics/cannoli/Bowtie.scala:81: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       builder.addFiles(files(args.indexPath + "*.ebwt"))
[WARNING]                             ^
[WARNING] /home/jenkins/workspace/cannoli-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/core/src/main/scala/org/bdgenomics/cannoli/Bowtie.scala:98: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       cmd = builder.build(),
[WARNING]                          ^
[WARNING] /home/jenkins/workspace/cannoli-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/core/src/main/scala/org/bdgenomics/cannoli/Bowtie.scala:99: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       files = builder.getFiles()
[WARNING]                               ^
[WARNING] /home/jenkins/workspace/cannoli-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/core/src/main/scala/org/bdgenomics/cannoli/Bowtie2.scala:97: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       builder.addFiles(files(args.indexPath + "*.bt2"))
[WARNING]                             ^
[WARNING] /home/jenkins/workspace/cannoli-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/core/src/main/scala/org/bdgenomics/cannoli/Bowtie2.scala:114: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       cmd = builder.build(),
[WARNING]                          ^
[WARNING] /home/jenkins/workspace/cannoli-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/core/src/main/scala/org/bdgenomics/cannoli/Bowtie2.scala:115: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       files = builder.getFiles()
[WARNING]                               ^
[WARNING] /home/jenkins/workspace/cannoli-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/core/src/main/scala/org/bdgenomics/cannoli/BwaMem.scala:140: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       cmd = builder.build(),
[WARNING]                          ^
[WARNING] /home/jenkins/workspace/cannoli-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/core/src/main/scala/org/bdgenomics/cannoli/BwaMem.scala:141: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       files = builder.getFiles()
[WARNING]                               ^
[WARNING] /home/jenkins/workspace/cannoli-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/core/src/main/scala/org/bdgenomics/cannoli/BwaMem2.scala:140: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       cmd = builder.build(),
[WARNING]                          ^
[WARNING] /home/jenkins/workspace/cannoli-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/core/src/main/scala/org/bdgenomics/cannoli/BwaMem2.scala:141: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       files = builder.getFiles()
[WARNING]                               ^
[WARNING] /home/jenkins/workspace/cannoli-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/core/src/main/scala/org/bdgenomics/cannoli/Freebayes.scala:115: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       cmd = builder.build(),
[WARNING]                          ^
[WARNING] /home/jenkins/workspace/cannoli-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/core/src/main/scala/org/bdgenomics/cannoli/Freebayes.scala:116: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       files = builder.getFiles()
[WARNING]                               ^
[WARNING] /home/jenkins/workspace/cannoli-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/core/src/main/scala/org/bdgenomics/cannoli/Gem.scala:94: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       cmd = builder.build(),
[WARNING]                          ^
[WARNING] /home/jenkins/workspace/cannoli-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/core/src/main/scala/org/bdgenomics/cannoli/Gem.scala:95: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       files = builder.getFiles()
[WARNING]                               ^
[WARNING] /home/jenkins/workspace/cannoli-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/core/src/main/scala/org/bdgenomics/cannoli/MagicBlast.scala:135: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       builder.addFiles(files(args.db + "*"))
[WARNING]                             ^
[WARNING] /home/jenkins/workspace/cannoli-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/core/src/main/scala/org/bdgenomics/cannoli/MagicBlast.scala:152: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       cmd = builder.build(),
[WARNING]                          ^
[WARNING] /home/jenkins/workspace/cannoli-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/core/src/main/scala/org/bdgenomics/cannoli/MagicBlast.scala:153: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       files = builder.getFiles()
[WARNING]                               ^
[WARNING] /home/jenkins/workspace/cannoli-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/core/src/main/scala/org/bdgenomics/cannoli/Minimap2.scala:109: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       cmd = builder.build(),
[WARNING]                          ^
[WARNING] /home/jenkins/workspace/cannoli-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/core/src/main/scala/org/bdgenomics/cannoli/Minimap2.scala:110: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       files = builder.getFiles()
[WARNING]                               ^
[WARNING] /home/jenkins/workspace/cannoli-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/core/src/main/scala/org/bdgenomics/cannoli/SamtoolsMpileup.scala:101: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       cmd = builder.build(),
[WARNING]                          ^
[WARNING] /home/jenkins/workspace/cannoli-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/core/src/main/scala/org/bdgenomics/cannoli/SamtoolsMpileup.scala:102: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       files = builder.getFiles()
[WARNING]                               ^
[WARNING] /home/jenkins/workspace/cannoli-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/core/src/main/scala/org/bdgenomics/cannoli/SingleEndBowtie2.scala:101: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       builder.addFiles(files(args.indexPath + "*.bt2"))
[WARNING]                             ^
[WARNING] /home/jenkins/workspace/cannoli-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/core/src/main/scala/org/bdgenomics/cannoli/SingleEndBowtie2.scala:118: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       cmd = builder.build(),
[WARNING]                          ^
[WARNING] /home/jenkins/workspace/cannoli-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/core/src/main/scala/org/bdgenomics/cannoli/SingleEndBowtie2.scala:119: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       files = builder.getFiles()
[WARNING]                               ^
[WARNING] /home/jenkins/workspace/cannoli-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/core/src/main/scala/org/bdgenomics/cannoli/SingleEndStar.scala:102: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       builder.addFiles(files(args.genomePath + "**"))
[WARNING]                             ^
[WARNING] /home/jenkins/workspace/cannoli-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/core/src/main/scala/org/bdgenomics/cannoli/SingleEndStar.scala:120: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]         cmd = builder.build(),
[WARNING]                            ^
[WARNING] /home/jenkins/workspace/cannoli-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/core/src/main/scala/org/bdgenomics/cannoli/SingleEndStar.scala:121: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]         files = builder.getFiles()
[WARNING]                                 ^
[WARNING] /home/jenkins/workspace/cannoli-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/core/src/main/scala/org/bdgenomics/cannoli/Snap.scala:124: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       cmd = builder.build(),
[WARNING]                          ^
[WARNING] /home/jenkins/workspace/cannoli-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/core/src/main/scala/org/bdgenomics/cannoli/Snap.scala:125: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       files = builder.getFiles()
[WARNING]                               ^
[WARNING] /home/jenkins/workspace/cannoli-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/core/src/main/scala/org/bdgenomics/cannoli/SnpEff.scala:91: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       cmd = builder.build(),
[WARNING]                          ^
[WARNING] /home/jenkins/workspace/cannoli-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/core/src/main/scala/org/bdgenomics/cannoli/SnpEff.scala:92: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       files = builder.getFiles()
[WARNING]                               ^
[WARNING] /home/jenkins/workspace/cannoli-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/core/src/main/scala/org/bdgenomics/cannoli/Star.scala:103: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       builder.addFiles(files(args.genomePath + "**"))
[WARNING]                             ^
[WARNING] /home/jenkins/workspace/cannoli-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/core/src/main/scala/org/bdgenomics/cannoli/Star.scala:122: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]         cmd = builder.build(),
[WARNING]                            ^
[WARNING] /home/jenkins/workspace/cannoli-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/core/src/main/scala/org/bdgenomics/cannoli/Star.scala:123: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]         files = builder.getFiles()
[WARNING]                                 ^
[WARNING] /home/jenkins/workspace/cannoli-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/core/src/main/scala/org/bdgenomics/cannoli/Vep.scala:119: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       cmd = builder.build(),
[WARNING]                          ^
[WARNING] /home/jenkins/workspace/cannoli-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/core/src/main/scala/org/bdgenomics/cannoli/Vep.scala:120: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       files = builder.getFiles()
[WARNING]                               ^
[WARNING] /home/jenkins/workspace/cannoli-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/core/src/main/scala/org/bdgenomics/cannoli/VtNormalize.scala:104: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       cmd = builder.build(),
[WARNING]                          ^
[WARNING] /home/jenkins/workspace/cannoli-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/core/src/main/scala/org/bdgenomics/cannoli/VtNormalize.scala:105: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       files = builder.getFiles()
[WARNING]                               ^
[WARNING] /home/jenkins/workspace/cannoli-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/core/src/main/scala/org/bdgenomics/cannoli/util/QuerynameGroupingIterator.scala:58: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       .setAlignments(readsInFragment)
[WARNING]                      ^
[WARNING] 51 warnings found
[INFO] prepare-compile in 0 s
[INFO] compile in 7 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ cannoli-core-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-core-spark3_2.12 ---
[INFO] Test Source directory: /home/jenkins/workspace/cannoli-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/core/src/test/scala added.
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ cannoli-core-spark3_2.12 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/cannoli-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/core/src/test/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ cannoli-core-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_2.12:3.0.1 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] /home/jenkins/workspace/cannoli-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/core/src/test/scala:-1: info: compiling
[INFO] Compiling 1 source files to /home/jenkins/workspace/cannoli-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/core/target/scala-2.12.10/test-classes at 1611162321054
[WARNING] /home/jenkins/workspace/cannoli-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/core/src/test/scala/org/bdgenomics/cannoli/util/QuerynameGroupingIteratorSuite.scala:41: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     val readNames = fragments.flatMap(_.getAlignments.map(r => r.getReadName))
[WARNING]                                         ^
[WARNING] /home/jenkins/workspace/cannoli-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/core/src/test/scala/org/bdgenomics/cannoli/util/QuerynameGroupingIteratorSuite.scala:71: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     val readNames = fragments.flatMap(_.getAlignments.map(r => r.getReadName))
[WARNING]                                         ^
[WARNING] two warnings found
[INFO] prepare-compile in 0 s
[INFO] compile in 3 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ cannoli-core-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-core-spark3_2.12 ---
[INFO] 
[INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ cannoli-core-spark3_2.12 ---
Discovery starting.
Discovery completed in 157 milliseconds.
Run starting. Expected test count is: 3
QuerynameGroupingIteratorSuite:
- can't call next when empty
- if no paired reads, return fragments of single reads
- return fragments on iterator with paired reads
Run completed in 666 milliseconds.
Total number of tests run: 3
Suites: completed 2, aborted 0
Tests: succeeded 3, failed 0, canceled 0, ignored 0, pending 0
All tests passed.
[INFO] 
[INFO] --- maven-jar-plugin:3.1.2:jar (default-jar) @ cannoli-core-spark3_2.12 ---
[INFO] Building jar: /home/jenkins/workspace/cannoli-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/core/target/cannoli-core-spark3_2.12-0.12.0-SNAPSHOT.jar
[INFO] 
[INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-javadocs) > generate-sources @ cannoli-core-spark3_2.12 >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-maven) @ cannoli-core-spark3_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-java) @ cannoli-core-spark3_2.12 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ cannoli-core-spark3_2.12 ---
[INFO] Source directory: /home/jenkins/workspace/cannoli-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/core/src/main/scala added.
[INFO] 
[INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-javadocs) < generate-sources @ cannoli-core-spark3_2.12 <<<
[INFO] 
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-javadocs) @ cannoli-core-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_2.12:3.0.1 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_2.12:3.0.1 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 54 documentable templates
[INFO] Building jar: /home/jenkins/workspace/cannoli-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/core/target/cannoli-core-spark3_2.12-0.12.0-SNAPSHOT-javadoc.jar
[INFO] 
[INFO] -----------< org.bdgenomics.cannoli:cannoli-cli-spark3_2.12 >-----------
[INFO] Building Cannoli_2.12: CLI 0.12.0-SNAPSHOT                         [4/5]
[INFO] --------------------------------[ jar ]---------------------------------
Downloading from sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/adam/adam-cli-spark3_2.12/0.34.0-SNAPSHOT/maven-metadata.xml
Progress (1): 1.2 kB
                    
Downloaded from sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/adam/adam-cli-spark3_2.12/0.34.0-SNAPSHOT/maven-metadata.xml (1.2 kB at 6.5 kB/s)
Downloading from sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/adam/adam-cli-spark3_2.12/0.34.0-SNAPSHOT/adam-cli-spark3_2.12-0.34.0-20210115.132340-10.pom
Progress (1): 4.1/6.8 kB
Progress (1): 6.8 kB    
                    
Downloaded from sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/adam/adam-cli-spark3_2.12/0.34.0-SNAPSHOT/adam-cli-spark3_2.12-0.34.0-20210115.132340-10.pom (6.8 kB at 36 kB/s)
Downloading from sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/adam/adam-apis-spark3_2.12/0.34.0-SNAPSHOT/maven-metadata.xml
Progress (1): 1.4 kB
                    
Downloaded from sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/adam/adam-apis-spark3_2.12/0.34.0-SNAPSHOT/maven-metadata.xml (1.4 kB at 8.3 kB/s)
Downloading from sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/adam/adam-apis-spark3_2.12/0.34.0-SNAPSHOT/adam-apis-spark3_2.12-0.34.0-20210115.132307-10.pom
Progress (1): 4.1/5.0 kB
Progress (1): 5.0 kB    
                    
Downloaded from sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/adam/adam-apis-spark3_2.12/0.34.0-SNAPSHOT/adam-apis-spark3_2.12-0.34.0-20210115.132307-10.pom (5.0 kB at 8.7 kB/s)
Downloading from sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/adam/adam-cli-spark3_2.12/0.34.0-SNAPSHOT/adam-cli-spark3_2.12-0.34.0-20210115.132340-10.jar
Downloading from sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/adam/adam-apis-spark3_2.12/0.34.0-SNAPSHOT/adam-apis-spark3_2.12-0.34.0-20210115.132307-10.jar
Progress (1): 4.1/193 kB
Progress (1): 7.8/193 kB
Progress (1): 12/193 kB 
Progress (1): 16/193 kB
Progress (1): 20/193 kB
Progress (1): 24/193 kB
Progress (1): 28/193 kB
Progress (1): 32/193 kB
Progress (1): 37/193 kB
Progress (1): 41/193 kB
Progress (1): 45/193 kB
Progress (1): 49/193 kB
Progress (1): 53/193 kB
Progress (1): 57/193 kB
Progress (1): 61/193 kB
Progress (1): 65/193 kB
Progress (1): 69/193 kB
Progress (1): 73/193 kB
Progress (1): 77/193 kB
Progress (1): 82/193 kB
Progress (1): 86/193 kB
Progress (1): 90/193 kB
Progress (1): 94/193 kB
Progress (1): 98/193 kB
Progress (1): 102/193 kB
Progress (1): 106/193 kB
Progress (1): 110/193 kB
Progress (1): 114/193 kB
Progress (1): 118/193 kB
Progress (1): 123/193 kB
Progress (1): 127/193 kB
Progress (1): 131/193 kB
Progress (1): 135/193 kB
Progress (1): 139/193 kB
Progress (1): 143/193 kB
Progress (1): 147/193 kB
Progress (1): 151/193 kB
Progress (1): 155/193 kB
Progress (1): 159/193 kB
Progress (1): 163/193 kB
Progress (1): 168/193 kB
Progress (1): 172/193 kB
Progress (1): 176/193 kB
Progress (1): 180/193 kB
Progress (1): 184/193 kB
Progress (1): 188/193 kB
Progress (1): 192/193 kB
Progress (1): 193 kB    
                    
Downloaded from sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/adam/adam-cli-spark3_2.12/0.34.0-SNAPSHOT/adam-cli-spark3_2.12-0.34.0-20210115.132340-10.jar (193 kB at 31 kB/s)
Progress (1): 4.1/292 kB
Progress (1): 7.8/292 kB
Progress (1): 12/292 kB 
Progress (1): 16/292 kB
Progress (1): 20/292 kB
Progress (1): 24/292 kB
Progress (1): 28/292 kB
Progress (1): 32/292 kB
Progress (1): 37/292 kB
Progress (1): 41/292 kB
Progress (1): 45/292 kB
Progress (1): 49/292 kB
Progress (1): 53/292 kB
Progress (1): 57/292 kB
Progress (1): 61/292 kB
Progress (1): 65/292 kB
Progress (1): 69/292 kB
Progress (1): 73/292 kB
Progress (1): 77/292 kB
Progress (1): 82/292 kB
Progress (1): 86/292 kB
Progress (1): 90/292 kB
Progress (1): 94/292 kB
Progress (1): 98/292 kB
Progress (1): 102/292 kB
Progress (1): 106/292 kB
Progress (1): 110/292 kB
Progress (1): 114/292 kB
Progress (1): 118/292 kB
Progress (1): 123/292 kB
Progress (1): 127/292 kB
Progress (1): 131/292 kB
Progress (1): 135/292 kB
Progress (1): 139/292 kB
Progress (1): 143/292 kB
Progress (1): 147/292 kB
Progress (1): 151/292 kB
Progress (1): 155/292 kB
Progress (1): 159/292 kB
Progress (1): 163/292 kB
Progress (1): 168/292 kB
Progress (1): 172/292 kB
Progress (1): 176/292 kB
Progress (1): 180/292 kB
Progress (1): 184/292 kB
Progress (1): 188/292 kB
Progress (1): 192/292 kB
Progress (1): 196/292 kB
Progress (1): 200/292 kB
Progress (1): 204/292 kB
Progress (1): 209/292 kB
Progress (1): 213/292 kB
Progress (1): 217/292 kB
Progress (1): 221/292 kB
Progress (1): 225/292 kB
Progress (1): 229/292 kB
Progress (1): 233/292 kB
Progress (1): 237/292 kB
Progress (1): 241/292 kB
Progress (1): 245/292 kB
Progress (1): 249/292 kB
Progress (1): 254/292 kB
Progress (1): 258/292 kB
Progress (1): 262/292 kB
Progress (1): 266/292 kB
Progress (1): 270/292 kB
Progress (1): 274/292 kB
Progress (1): 278/292 kB
Progress (1): 282/292 kB
Progress (1): 286/292 kB
Progress (1): 290/292 kB
Progress (1): 292 kB    
                    
Downloaded from sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/adam/adam-apis-spark3_2.12/0.34.0-SNAPSHOT/adam-apis-spark3_2.12-0.34.0-20210115.132307-10.jar (292 kB at 41 kB/s)
[INFO] 
[INFO] --- maven-clean-plugin:3.1.0:clean (default-clean) @ 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] Copied 1 files to output directory: /home/jenkins/workspace/cannoli-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/cli/target/generated-sources/java-templates
[INFO] Source directory: /home/jenkins/workspace/cannoli-prb/HADOOP_VERSION/2.7.5/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-prb/HADOOP_VERSION/2.7.5/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 26 .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-prb/HADOOP_VERSION/2.7.5/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_2.12:3.0.1 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] /home/jenkins/workspace/cannoli-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/cli/target/generated-sources/java-templates:-1: info: compiling
[INFO] /home/jenkins/workspace/cannoli-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/cli/src/main/scala:-1: info: compiling
[INFO] Compiling 25 source files to /home/jenkins/workspace/cannoli-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/cli/target/scala-2.12.10/classes at 1611162345324
[WARNING] /home/jenkins/workspace/cannoli-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/cli/src/main/scala/org/bdgenomics/cannoli/cli/InterleaveFastq.scala:108: warning: constructor AsciiLineReader in class AsciiLineReader is deprecated: see corresponding Javadoc for more information.
[WARNING]     val pair1Reader = new AsciiLineReaderIterator(new AsciiLineReader(cIs1))
[WARNING]                                                   ^
[WARNING] /home/jenkins/workspace/cannoli-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/cli/src/main/scala/org/bdgenomics/cannoli/cli/InterleaveFastq.scala:109: warning: constructor AsciiLineReader in class AsciiLineReader is deprecated: see corresponding Javadoc for more information.
[WARNING]     val pair2Reader = new AsciiLineReaderIterator(new AsciiLineReader(cIs2))
[WARNING]                                                   ^
[WARNING] two warnings found
[INFO] prepare-compile in 0 s
[INFO] compile in 6 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ cannoli-cli-spark3_2.12 ---
[INFO] Changes detected - recompiling the module!
[INFO] Compiling 1 source file to /home/jenkins/workspace/cannoli-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/cli/target/scala-2.12.10/classes
[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-prb/HADOOP_VERSION/2.7.5/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_2.12:3.0.1 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] /home/jenkins/workspace/cannoli-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/cli/src/test/scala:-1: info: compiling
[INFO] Compiling 2 source files to /home/jenkins/workspace/cannoli-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/cli/target/scala-2.12.10/test-classes at 1611162352395
[WARNING] /home/jenkins/workspace/cannoli-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/cli/src/test/scala/org/bdgenomics/cannoli/cli/InterleaveFastqSuite.scala:69: warning: constructor AsciiLineReader in class AsciiLineReader is deprecated: see corresponding Javadoc for more information.
[WARNING]     val iter = new AsciiLineReaderIterator(new AsciiLineReader(cIs))
[WARNING]                                            ^
[WARNING] one warning found
[INFO] prepare-compile in 0 s
[INFO] compile in 4 s
[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] 
[INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ cannoli-cli-spark3_2.12 ---
Discovery starting.
Discovery completed in 180 milliseconds.
Run starting. Expected test count is: 12
CannoliSuite:
- default command groups is non empty
- module provides default command groups
- inject default command groups when called via main
- command groups is empty when called via apply
- single command group
- add new command group to default command groups
- module restores default command groups when called via apply
- custom module with single command group
- custom module with new command group added to default command groups
2021-01-20 09:05:59 WARN  Utils:69 - Your hostname, ubuntu-testing resolves to a loopback address: 127.0.1.1; using 192.168.10.30 instead (on interface eno1)
2021-01-20 09:05:59 WARN  Utils:69 - Set SPARK_LOCAL_IP if you need to bind to another address
InterleaveFastqSuite:
2021-01-20 09:05:59 WARN  NativeCodeLoader:62 - Unable to load native-hadoop library for your platform... using builtin-java classes where applicable
- interleave two paired FASTQ files
- interleave two paired FASTQ files and save as BAM
- interleave gzipped and bzipped files
Run completed in 6 seconds, 161 milliseconds.
Total number of tests run: 12
Suites: completed 3, aborted 0
Tests: succeeded 12, failed 0, canceled 0, ignored 0, pending 0
All tests passed.
[INFO] 
[INFO] --- maven-jar-plugin:3.1.2:jar (default-jar) @ cannoli-cli-spark3_2.12 ---
[INFO] Building jar: /home/jenkins/workspace/cannoli-prb/HADOOP_VERSION/2.7.5/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] >>> 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-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/cli/target/generated-sources/java-templates
[INFO] Source directory: /home/jenkins/workspace/cannoli-prb/HADOOP_VERSION/2.7.5/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-prb/HADOOP_VERSION/2.7.5/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_2.12:3.0.1 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_2.12:3.0.1 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-prb/HADOOP_VERSION/2.7.5/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] --------< org.bdgenomics.cannoli:cannoli-assembly-spark3_2.12 >---------
[INFO] Building Cannoli_2.12: Assembly 0.12.0-SNAPSHOT                    [5/5]
[INFO] --------------------------------[ jar ]---------------------------------
[INFO] 
[INFO] --- maven-clean-plugin:3.1.0:clean (default-clean) @ 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-prb/HADOOP_VERSION/2.7.5/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-prb/HADOOP_VERSION/2.7.5/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] /home/jenkins/workspace/cannoli-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/assembly/src/main/scala:-1: info: compiling
[INFO] Compiling 1 source files to /home/jenkins/workspace/cannoli-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/assembly/target/scala-2.12.10/classes at 1611162372331
[INFO] prepare-compile in 0 s
[INFO] compile in 2 s
[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-prb/HADOOP_VERSION/2.7.5/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-prb/HADOOP_VERSION/2.7.5/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] No tests to run.
[INFO] 
[INFO] --- maven-jar-plugin:3.1.2:jar (default-jar) @ cannoli-assembly-spark3_2.12 ---
[INFO] Building jar: /home/jenkins/workspace/cannoli-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/assembly/target/cannoli-assembly-spark3_2.12-0.12.0-SNAPSHOT.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-prb/HADOOP_VERSION/2.7.5/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-prb/HADOOP_VERSION/2.7.5/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 ---
Downloading from apache.snapshots: https://repository.apache.org/snapshots/org/bdgenomics/adam/adam-shade-spark3_2.12/0.34.0-SNAPSHOT/maven-metadata.xml
Downloading from apache.snapshots: https://repository.apache.org/snapshots/org/bdgenomics/adam/adam-shade-spark3_2.12/0.34.0-SNAPSHOT/adam-shade-spark3_2.12-0.34.0-SNAPSHOT.pom
[WARNING] The POM for org.bdgenomics.adam:adam-shade-spark3_2.12:jar:0.34.0-SNAPSHOT is missing, no dependency information available
Downloading from apache.snapshots: https://repository.apache.org/snapshots/org/bdgenomics/adam/adam-shade-spark3_2.12/0.34.0-SNAPSHOT/adam-shade-spark3_2.12-0.34.0-SNAPSHOT.jar
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary for Cannoli_2.12 0.12.0-SNAPSHOT:
[INFO] 
[INFO] Cannoli_2.12 ....................................... SUCCESS [  2.686 s]
[INFO] Cannoli_2.12: Builder .............................. SUCCESS [ 13.414 s]
[INFO] Cannoli_2.12: Core ................................. SUCCESS [ 23.962 s]
[INFO] Cannoli_2.12: CLI .................................. SUCCESS [ 36.548 s]
[INFO] Cannoli_2.12: Assembly ............................. FAILURE [  6.881 s]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time:  01:23 min
[INFO] Finished at: 2021-01-20T09:06:18-08:00
[INFO] ------------------------------------------------------------------------
[ERROR] Failed to execute goal org.apache.maven.plugins:maven-shade-plugin:3.2.0:shade (default) on project cannoli-assembly-spark3_2.12: Execution default of goal org.apache.maven.plugins:maven-shade-plugin:3.2.0:shade failed: Plugin org.apache.maven.plugins:maven-shade-plugin:3.2.0 or one of its dependencies could not be resolved: Could not find artifact org.bdgenomics.adam:adam-shade-spark3_2.12:jar:0.34.0-SNAPSHOT in apache.snapshots (https://repository.apache.org/snapshots) -> [Help 1]
[ERROR] 
[ERROR] To see the full stack trace of the errors, re-run Maven with the -e switch.
[ERROR] Re-run Maven using the -X switch to enable full debug logging.
[ERROR] 
[ERROR] For more information about the errors and possible solutions, please read the following articles:
[ERROR] [Help 1] http://cwiki.apache.org/confluence/display/MAVEN/PluginResolutionException
[ERROR] 
[ERROR] After correcting the problems, you can resume the build with the command
[ERROR]   mvn <args> -rf :cannoli-assembly-spark3_2.12
Build step 'Execute shell' marked build as failure
Recording test results
[Checks API] No suitable checks publisher found.
[Set GitHub commit status (universal)] ERROR on repos [GHRepository@197aebba[nodeId=MDEwOlJlcG9zaXRvcnk3ODQ3MzA5OA==,description=Distributed execution of bioinformatics tools on Apache Spark. Apache 2 licensed.,homepage=,name=cannoli,fork=false,archived=false,size=525,milestones={},language=Scala,commits={},source=<null>,parent=<null>,isTemplate=<null>,url=https://api.github.com/repos/bigdatagenomics/cannoli,id=78473098,nodeId=<null>,createdAt=2017-01-09T22:02:42Z,updatedAt=2021-01-05T14:09:18Z]] (sha:3941862) with context:cannoli-prb/HADOOP_VERSION=2.7.5,SCALA_VERSION=2.12,SPARK_VERSION=3.0.1,label=ubuntu
Setting commit status on GitHub for https://github.com/bigdatagenomics/cannoli/commit/394186256718cff9b7189adecdaac5bfd47b404a
Finished: FAILURE