FailedConsole Output

Started by upstream project "cannoli" build number 2108
originally caused by:
 Started by timer
[EnvInject] - Loading node environment variables.
Building remotely on ubuntu-testing (ubuntu ubuntu-testing-gpu) in workspace /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu
 > git rev-parse --is-inside-work-tree # timeout=10
Fetching changes from the remote Git repository
 > git config remote.origin.url https://github.com/bigdatagenomics/cannoli.git # timeout=10
Fetching upstream changes from https://github.com/bigdatagenomics/cannoli.git
 > git --version # timeout=10
 > git fetch --tags --progress https://github.com/bigdatagenomics/cannoli.git +refs/heads/*:refs/remotes/origin/*
Checking out Revision e85bd292f66b0a078c34ef3d7a56a2ca351fd658 (refs/remotes/origin/master)
 > git config core.sparsecheckout # timeout=10
 > git checkout -f e85bd292f66b0a078c34ef3d7a56a2ca351fd658
 > git rev-list e85bd292f66b0a078c34ef3d7a56a2ca351fd658 # timeout=10
Cleaning workspace
 > git rev-parse --verify HEAD # timeout=10
Resetting working tree
 > git reset --hard # timeout=10
 > git clean -fdx # timeout=10
[ubuntu] $ /bin/bash /tmp/hudson5896728748674295228.sh
+ set -e
+ export JAVA_HOME=/usr/lib/jvm/java-8-oracle
+ JAVA_HOME=/usr/lib/jvm/java-8-oracle
+ export CONDA_BIN=/home/anaconda/bin/
+ CONDA_BIN=/home/anaconda/bin/
+ export PATH=/usr/lib/jvm/java-8-oracle/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:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games
+ PATH=/usr/lib/jvm/java-8-oracle/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:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games
+ set +x
+ /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/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/cannoliTestMvnUw1mjQa

# 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/cannoliTestMvnUw1mjQa:g' '{}' ';'
find . -name "*.bak" -exec rm -f {} \;
+ find . -name '*.bak' -exec rm -f '{}' ';'

# variable declarations
export PATH=${JAVA_HOME}/bin/:${PATH}
+ export PATH=/usr/lib/jvm/java-8-oracle/bin/:/usr/lib/jvm/java-8-oracle/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:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games
+ PATH=/usr/lib/jvm/java-8-oracle/bin/:/usr/lib/jvm/java-8-oracle/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:/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 ${BASH_SOURCE[0]} 
+++ dirname /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/scripts/jenkins-test
++ cd /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/scripts
++ pwd
+ DIR=/home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/scripts
PROJECT_ROOT=${DIR}/..
+ PROJECT_ROOT=/home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/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/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/scripts/../pom.xml
++ head -2
++ tail -1
++ sed 's/ *<version>//g'
++ sed 's/<\/version>//g'
+ VERSION=0.11.0-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 2.11 ]]

# 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 2.4.6 ]]

# print versions
echo "Testing Cannoli version ${VERSION} on Spark ${SPARK_VERSION} Scala ${SCALA_VERSION} and Hadoop ${HADOOP_VERSION}"
+ echo 'Testing Cannoli version 0.11.0-SNAPSHOT on Spark 2.4.6 Scala 2.11 and Hadoop 2.7.5'
Testing Cannoli version 0.11.0-SNAPSHOT on Spark 2.4.6 Scala 2.11 and Hadoop 2.7.5

# move to Scala 2.11 if requested
if [ ${SCALA_VERSION} == 2.11 ];
then
    set +e
    ./scripts/move_to_scala_2.11.sh
    set -e
fi
+ '[' 2.11 == 2.11 ']'
+ set +e
+ ./scripts/move_to_scala_2.11.sh
+ set -e

# move to Scala 2.12 if requested
if [ ${SCALA_VERSION} == 2.12 ];
then
    set +e
    ./scripts/move_to_scala_2.12.sh
    set -e
fi
+ '[' 2.11 == 2.12 ']'

# move to Spark 2.x if requested
if [ ${SPARK_VERSION} == 2.4.6 ];
then
    set +e
    ./scripts/move_to_spark_2.sh
    set -e
fi
+ '[' 2.4.6 == 2.4.6 ']'
+ set +e
+ ./scripts/move_to_spark_2.sh
+ set -e

# move to Spark 3.x if requested
if [ ${SPARK_VERSION} == 3.0.1 ];
then
    set +e
    ./scripts/move_to_spark_3.sh
    set -e
fi
+ '[' 2.4.6 == 3.0.1 ']'

# first, build the sources, run the unit tests, and generate a coverage report
mvn clean \
    -Dhadoop.version=${HADOOP_VERSION}
+ mvn clean -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_2.11                                                       [pom]
[INFO] Cannoli_2.11: Builder                                              [jar]
[INFO] Cannoli_2.11: Core                                                 [jar]
[INFO] Cannoli_2.11: CLI                                                  [jar]
[INFO] Cannoli_2.11: Assembly                                             [jar]
[INFO] 
[INFO] ---------< org.bdgenomics.cannoli:cannoli-parent-spark2_2.11 >----------
[INFO] Building Cannoli_2.11 0.11.0-SNAPSHOT                              [1/5]
[INFO] --------------------------------[ pom ]---------------------------------
[INFO] 
[INFO] --- maven-clean-plugin:3.1.0:clean (default-clean) @ cannoli-parent-spark2_2.11 ---
[INFO] 
[INFO] ---------< org.bdgenomics.cannoli:cannoli-builder-spark2_2.11 >---------
[INFO] Building Cannoli_2.11: Builder 0.11.0-SNAPSHOT                     [2/5]
[INFO] --------------------------------[ jar ]---------------------------------
[INFO] 
[INFO] --- maven-clean-plugin:3.1.0:clean (default-clean) @ cannoli-builder-spark2_2.11 ---
[INFO] 
[INFO] ----------< org.bdgenomics.cannoli:cannoli-core-spark2_2.11 >-----------
[INFO] Building Cannoli_2.11: Core 0.11.0-SNAPSHOT                        [3/5]
[INFO] --------------------------------[ jar ]---------------------------------
[INFO] 
[INFO] --- maven-clean-plugin:3.1.0:clean (default-clean) @ cannoli-core-spark2_2.11 ---
[INFO] 
[INFO] -----------< org.bdgenomics.cannoli:cannoli-cli-spark2_2.11 >-----------
[INFO] Building Cannoli_2.11: CLI 0.11.0-SNAPSHOT                         [4/5]
[INFO] --------------------------------[ jar ]---------------------------------
[INFO] 
[INFO] --- maven-clean-plugin:3.1.0:clean (default-clean) @ cannoli-cli-spark2_2.11 ---
[INFO] 
[INFO] --------< org.bdgenomics.cannoli:cannoli-assembly-spark2_2.11 >---------
[INFO] Building Cannoli_2.11: Assembly 0.11.0-SNAPSHOT                    [5/5]
[INFO] --------------------------------[ jar ]---------------------------------
[INFO] 
[INFO] --- maven-clean-plugin:3.1.0:clean (default-clean) @ cannoli-assembly-spark2_2.11 ---
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary for Cannoli_2.11 0.11.0-SNAPSHOT:
[INFO] 
[INFO] Cannoli_2.11 ....................................... SUCCESS [  0.243 s]
[INFO] Cannoli_2.11: Builder .............................. SUCCESS [  0.003 s]
[INFO] Cannoli_2.11: Core ................................. SUCCESS [  0.007 s]
[INFO] Cannoli_2.11: CLI .................................. SUCCESS [  0.023 s]
[INFO] Cannoli_2.11: Assembly ............................. SUCCESS [  0.003 s]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time:  0.419 s
[INFO] Finished at: 2020-10-08T05:52:01-07:00
[INFO] ------------------------------------------------------------------------

# if this is a pull request, we need to set the coveralls pr id
if [[ ! -z $ghprbPullId ]];
then
    COVERALLS_PRB_OPTION="-DpullRequest=${ghprbPullId}"
fi
+ [[ ! -z '' ]]

# coveralls token should not be visible
set +x +v
+ set +x +v
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_2.11                                                       [pom]
[INFO] Cannoli_2.11: Builder                                              [jar]
[INFO] Cannoli_2.11: Core                                                 [jar]
[INFO] Cannoli_2.11: CLI                                                  [jar]
[INFO] Cannoli_2.11: Assembly                                             [jar]
[INFO] 
[INFO] ---------< org.bdgenomics.cannoli:cannoli-parent-spark2_2.11 >----------
[INFO] Building Cannoli_2.11 0.11.0-SNAPSHOT                              [1/5]
[INFO] --------------------------------[ pom ]---------------------------------
[INFO] 
[INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-maven) @ cannoli-parent-spark2_2.11 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-java) @ cannoli-parent-spark2_2.11 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ cannoli-parent-spark2_2.11 ---
[INFO] Source directory: /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/src/main/scala added.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ cannoli-parent-spark2_2.11 ---
[INFO] Modified 0 of 54 .scala files
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ cannoli-parent-spark2_2.11 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ cannoli-parent-spark2_2.11 ---
[INFO] Test Source directory: /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/src/test/scala added.
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ cannoli-parent-spark2_2.11 ---
[INFO] No sources to compile
[INFO] 
[INFO] >>> scoverage-maven-plugin:1.1.1:report (default-cli) > [scoverage]test @ cannoli-parent-spark2_2.11 >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-maven) @ cannoli-parent-spark2_2.11 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-java) @ cannoli-parent-spark2_2.11 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ cannoli-parent-spark2_2.11 ---
[INFO] Source directory: /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/src/main/scala added.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ cannoli-parent-spark2_2.11 ---
[INFO] Modified 0 of 54 .scala files
[INFO] 
[INFO] --- scoverage-maven-plugin:1.1.1:pre-compile (default-cli) @ cannoli-parent-spark2_2.11 ---
[INFO] Skipping SCoverage execution for project with packaging type 'pom'
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ cannoli-parent-spark2_2.11 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- scoverage-maven-plugin:1.1.1:post-compile (default-cli) @ cannoli-parent-spark2_2.11 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ cannoli-parent-spark2_2.11 ---
[INFO] Test Source directory: /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/src/test/scala added.
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ cannoli-parent-spark2_2.11 ---
[INFO] No sources to compile
[INFO] 
[INFO] <<< scoverage-maven-plugin:1.1.1:report (default-cli) < [scoverage]test @ cannoli-parent-spark2_2.11 <<<
[INFO] 
[INFO] 
[INFO] --- scoverage-maven-plugin:1.1.1:report (default-cli) @ cannoli-parent-spark2_2.11 ---
[INFO] 
[INFO] ---------< org.bdgenomics.cannoli:cannoli-builder-spark2_2.11 >---------
[INFO] Building Cannoli_2.11: Builder 0.11.0-SNAPSHOT                     [2/5]
[INFO] --------------------------------[ jar ]---------------------------------
[INFO] 
[INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-maven) @ cannoli-builder-spark2_2.11 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-java) @ cannoli-builder-spark2_2.11 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ cannoli-builder-spark2_2.11 ---
[INFO] Source directory: /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/builder/src/main/scala added.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ cannoli-builder-spark2_2.11 ---
[INFO] Modified 0 of 0 .scala files
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ cannoli-builder-spark2_2.11 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/builder/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ cannoli-builder-spark2_2.11 ---
[INFO] /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/builder/src/main/java:-1: info: compiling
[INFO] Compiling 7 source files to /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/builder/target/scala-2.11.12/classes at 1602161527094
[INFO] prepare-compile in 0 s
[INFO] compile in 1 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ cannoli-builder-spark2_2.11 ---
[INFO] Changes detected - recompiling the module!
[INFO] Compiling 7 source files to /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/builder/target/scala-2.11.12/classes
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ cannoli-builder-spark2_2.11 ---
[INFO] Test Source directory: /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/builder/src/test/scala added.
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ cannoli-builder-spark2_2.11 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/builder/src/test/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ cannoli-builder-spark2_2.11 ---
[INFO] /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/builder/src/test/java:-1: info: compiling
[INFO] Compiling 4 source files to /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/builder/target/scala-2.11.12/test-classes at 1602161529088
[INFO] prepare-compile in 0 s
[INFO] compile in 1 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ cannoli-builder-spark2_2.11 ---
[INFO] Changes detected - recompiling the module!
[INFO] Compiling 4 source files to /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/builder/target/scala-2.11.12/test-classes
[INFO] 
[INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ cannoli-builder-spark2_2.11 ---
[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: 0.067 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: 0.001 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 s - in org.bdgenomics.cannoli.builder.CommandBuildersTest
[INFO] 
[INFO] Results:
[INFO] 
[INFO] Tests run: 40, Failures: 0, Errors: 0, Skipped: 0
[INFO] 
[INFO] 
[INFO] >>> scoverage-maven-plugin:1.1.1:report (default-cli) > [scoverage]test @ cannoli-builder-spark2_2.11 >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-maven) @ cannoli-builder-spark2_2.11 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-java) @ cannoli-builder-spark2_2.11 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ cannoli-builder-spark2_2.11 ---
[INFO] Source directory: /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/builder/src/main/scala added.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ cannoli-builder-spark2_2.11 ---
[INFO] Modified 0 of 0 .scala files
[INFO] 
[INFO] --- scoverage-maven-plugin:1.1.1:pre-compile (default-cli) @ cannoli-builder-spark2_2.11 ---
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ cannoli-builder-spark2_2.11 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/builder/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ cannoli-builder-spark2_2.11 ---
[WARNING]  Expected all dependencies to require Scala version: 2.11.12
[WARNING]  org.bdgenomics.utils:utils-misc-spark2_2.11:0.3.0 requires scala version: 2.11.7
[WARNING] Multiple versions of scala libraries detected!
[INFO] /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/builder/src/main/java:-1: info: compiling
[INFO] /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/builder/target/generated-sources/annotations:-1: info: compiling
[INFO] Compiling 7 source files to /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/builder/target/scala-2.11.12/scoverage-classes at 1602161531541
[INFO] [info] Cleaning datadir [/home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/builder/target/scoverage-data]
[INFO] [info] Beginning coverage instrumentation
[INFO] [info] Instrumentation completed [0 statements]
[INFO] [info] Wrote instrumentation file [/home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/builder/target/scoverage-data/scoverage.coverage.xml]
[INFO] [info] Will write measurement data to [/home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/builder/target/scoverage-data]
[INFO] prepare-compile in 0 s
[INFO] compile in 1 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ cannoli-builder-spark2_2.11 ---
[INFO] Changes detected - recompiling the module!
[INFO] Compiling 7 source files to /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/builder/target/scala-2.11.12/scoverage-classes
[INFO] 
[INFO] --- scoverage-maven-plugin:1.1.1:post-compile (default-cli) @ cannoli-builder-spark2_2.11 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ cannoli-builder-spark2_2.11 ---
[INFO] Test Source directory: /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/builder/src/test/scala added.
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ cannoli-builder-spark2_2.11 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/builder/src/test/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ cannoli-builder-spark2_2.11 ---
[WARNING]  Expected all dependencies to require Scala version: 2.11.12
[WARNING]  org.bdgenomics.utils:utils-misc-spark2_2.11:0.3.0 requires scala version: 2.11.7
[WARNING] Multiple versions of scala libraries detected!
[INFO] /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/builder/src/test/java:-1: info: compiling
[INFO] /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/builder/target/generated-test-sources/test-annotations:-1: info: compiling
[INFO] Compiling 4 source files to /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/builder/target/scala-2.11.12/test-classes at 1602161532981
[INFO] prepare-compile in 0 s
[INFO] compile in 1 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ cannoli-builder-spark2_2.11 ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ cannoli-builder-spark2_2.11 ---
[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: 0.074 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: 0.006 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: 0.001 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 s - in org.bdgenomics.cannoli.builder.CommandBuildersTest
[INFO] 
[INFO] Results:
[INFO] 
[INFO] Tests run: 40, Failures: 0, Errors: 0, Skipped: 0
[INFO] 
[INFO] 
[INFO] <<< scoverage-maven-plugin:1.1.1:report (default-cli) < [scoverage]test @ cannoli-builder-spark2_2.11 <<<
[INFO] 
[INFO] 
[INFO] --- scoverage-maven-plugin:1.1.1:report (default-cli) @ cannoli-builder-spark2_2.11 ---
[INFO] [scoverage] Generating cobertura XML report...
[INFO] [scoverage] Generating scoverage XML report...
[INFO] [scoverage] Generating scoverage HTML report...
[INFO] 
[INFO] ----------< org.bdgenomics.cannoli:cannoli-core-spark2_2.11 >-----------
[INFO] Building Cannoli_2.11: Core 0.11.0-SNAPSHOT                        [3/5]
[INFO] --------------------------------[ jar ]---------------------------------
[INFO] 
[INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-maven) @ cannoli-core-spark2_2.11 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-java) @ cannoli-core-spark2_2.11 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ cannoli-core-spark2_2.11 ---
[INFO] Source directory: /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/core/src/main/scala added.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ cannoli-core-spark2_2.11 ---
[INFO] Modified 0 of 27 .scala files
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ cannoli-core-spark2_2.11 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/core/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ cannoli-core-spark2_2.11 ---
[WARNING]  Expected all dependencies to require Scala version: 2.11.12
[WARNING]  com.twitter:chill_2.11:0.9.3 requires scala version: 2.11.12
[WARNING]  org.apache.spark:spark-core_2.11:2.4.6 requires scala version: 2.11.12
[WARNING]  org.json4s:json4s-jackson_2.11:3.5.3 requires scala version: 2.11.11
[WARNING] Multiple versions of scala libraries detected!
[INFO] /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/core/src/main/scala:-1: info: compiling
[INFO] Compiling 26 source files to /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/core/target/scala-2.11.12/classes at 1602161536536
[INFO] prepare-compile in 0 s
[INFO] compile in 6 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ cannoli-core-spark2_2.11 ---
[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-spark2_2.11 ---
[INFO] Test Source directory: /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/core/src/test/scala added.
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ cannoli-core-spark2_2.11 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/core/src/test/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ cannoli-core-spark2_2.11 ---
[WARNING]  Expected all dependencies to require Scala version: 2.11.12
[WARNING]  com.twitter:chill_2.11:0.9.3 requires scala version: 2.11.12
[WARNING]  org.apache.spark:spark-core_2.11:2.4.6 requires scala version: 2.11.12
[WARNING]  org.json4s:json4s-jackson_2.11:3.5.3 requires scala version: 2.11.11
[WARNING] Multiple versions of scala libraries detected!
[INFO] /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/core/src/test/scala:-1: info: compiling
[INFO] Compiling 1 source files to /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/core/target/scala-2.11.12/test-classes at 1602161543613
[INFO] prepare-compile in 0 s
[INFO] compile in 3 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ cannoli-core-spark2_2.11 ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ cannoli-core-spark2_2.11 ---
[INFO] 
[INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ cannoli-core-spark2_2.11 ---
Discovery starting.
Discovery completed in 140 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 500 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] >>> scoverage-maven-plugin:1.1.1:report (default-cli) > [scoverage]test @ cannoli-core-spark2_2.11 >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-maven) @ cannoli-core-spark2_2.11 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-java) @ cannoli-core-spark2_2.11 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ cannoli-core-spark2_2.11 ---
[INFO] Source directory: /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/core/src/main/scala added.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ cannoli-core-spark2_2.11 ---
[INFO] Modified 0 of 27 .scala files
[INFO] 
[INFO] --- scoverage-maven-plugin:1.1.1:pre-compile (default-cli) @ cannoli-core-spark2_2.11 ---
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ cannoli-core-spark2_2.11 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/core/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ cannoli-core-spark2_2.11 ---
[WARNING]  Expected all dependencies to require Scala version: 2.11.12
[WARNING]  com.twitter:chill_2.11:0.9.3 requires scala version: 2.11.12
[WARNING]  org.apache.spark:spark-core_2.11:2.4.6 requires scala version: 2.11.12
[WARNING]  org.json4s:json4s-jackson_2.11:3.5.3 requires scala version: 2.11.11
[WARNING] Multiple versions of scala libraries detected!
[INFO] /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/core/src/main/scala:-1: info: compiling
[INFO] Compiling 26 source files to /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/core/target/scala-2.11.12/scoverage-classes at 1602161548872
[INFO] [info] Cleaning datadir [/home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/core/target/scoverage-data]
[INFO] [info] Beginning coverage instrumentation
[WARNING] [warn] Could not instrument [EmptyTree$/null]. No pos.
[WARNING] [warn] Could not instrument [EmptyTree$/null]. No pos.
[WARNING] [warn] Could not instrument [EmptyTree$/null]. No pos.
[WARNING] [warn] Could not instrument [EmptyTree$/null]. No pos.
[INFO] [info] Instrumentation completed [1598 statements]
[INFO] [info] Wrote instrumentation file [/home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/core/target/scoverage-data/scoverage.coverage.xml]
[INFO] [info] Will write measurement data to [/home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/core/target/scoverage-data]
[INFO] prepare-compile in 0 s
[INFO] compile in 7 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ cannoli-core-spark2_2.11 ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- scoverage-maven-plugin:1.1.1:post-compile (default-cli) @ cannoli-core-spark2_2.11 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ cannoli-core-spark2_2.11 ---
[INFO] Test Source directory: /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/core/src/test/scala added.
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ cannoli-core-spark2_2.11 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/core/src/test/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ cannoli-core-spark2_2.11 ---
[WARNING]  Expected all dependencies to require Scala version: 2.11.12
[WARNING]  com.twitter:chill_2.11:0.9.3 requires scala version: 2.11.12
[WARNING]  org.apache.spark:spark-core_2.11:2.4.6 requires scala version: 2.11.12
[WARNING]  org.json4s:json4s-jackson_2.11:3.5.3 requires scala version: 2.11.11
[WARNING] Multiple versions of scala libraries detected!
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ cannoli-core-spark2_2.11 ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ cannoli-core-spark2_2.11 ---
[INFO] 
[INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ cannoli-core-spark2_2.11 ---
Discovery starting.
Discovery completed in 136 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 523 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] <<< scoverage-maven-plugin:1.1.1:report (default-cli) < [scoverage]test @ cannoli-core-spark2_2.11 <<<
[INFO] 
[INFO] 
[INFO] --- scoverage-maven-plugin:1.1.1:report (default-cli) @ cannoli-core-spark2_2.11 ---
[INFO] [scoverage] Generating cobertura XML report...
[INFO] [scoverage] Generating scoverage XML report...
[INFO] [scoverage] Generating scoverage HTML report...
[INFO] 
[INFO] -----------< org.bdgenomics.cannoli:cannoli-cli-spark2_2.11 >-----------
[INFO] Building Cannoli_2.11: CLI 0.11.0-SNAPSHOT                         [4/5]
[INFO] --------------------------------[ jar ]---------------------------------
[INFO] 
[INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-maven) @ cannoli-cli-spark2_2.11 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-java) @ cannoli-cli-spark2_2.11 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:timestamp-property (timestamp-property) @ cannoli-cli-spark2_2.11 ---
[INFO] 
[INFO] --- git-commit-id-plugin:2.2.2:revision (default) @ cannoli-cli-spark2_2.11 ---
[INFO] 
[INFO] --- templating-maven-plugin:1.0.0:filter-sources (filter-src) @ cannoli-cli-spark2_2.11 ---
[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/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/cli/target/generated-sources/java-templates
[INFO] Source directory: /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/cli/target/generated-sources/java-templates added.
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ cannoli-cli-spark2_2.11 ---
[INFO] Source directory: /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/cli/src/main/scala added.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ cannoli-cli-spark2_2.11 ---
[INFO] Modified 0 of 26 .scala files
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ cannoli-cli-spark2_2.11 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/cli/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ cannoli-cli-spark2_2.11 ---
[WARNING]  Expected all dependencies to require Scala version: 2.11.12
[WARNING]  com.twitter:chill_2.11:0.9.3 requires scala version: 2.11.12
[WARNING]  org.apache.spark:spark-core_2.11:2.4.6 requires scala version: 2.11.12
[WARNING]  org.json4s:json4s-jackson_2.11:3.5.3 requires scala version: 2.11.11
[WARNING] Multiple versions of scala libraries detected!
[INFO] /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/cli/target/generated-sources/java-templates:-1: info: compiling
[INFO] /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/cli/src/main/scala:-1: info: compiling
[INFO] Compiling 25 source files to /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/cli/target/scala-2.11.12/classes at 1602161559911
[WARNING] /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/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/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/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-spark2_2.11 ---
[INFO] Changes detected - recompiling the module!
[INFO] Compiling 1 source file to /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/cli/target/scala-2.11.12/classes
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ cannoli-cli-spark2_2.11 ---
[INFO] Test Source directory: /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/cli/src/test/scala added.
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ cannoli-cli-spark2_2.11 ---
[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-spark2_2.11 ---
[WARNING]  Expected all dependencies to require Scala version: 2.11.12
[WARNING]  com.twitter:chill_2.11:0.9.3 requires scala version: 2.11.12
[WARNING]  org.apache.spark:spark-core_2.11:2.4.6 requires scala version: 2.11.12
[WARNING]  org.json4s:json4s-jackson_2.11:3.5.3 requires scala version: 2.11.11
[WARNING] Multiple versions of scala libraries detected!
[INFO] /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/cli/src/test/scala:-1: info: compiling
[INFO] Compiling 2 source files to /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/cli/target/scala-2.11.12/test-classes at 1602161566623
[WARNING] /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/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 3 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ cannoli-cli-spark2_2.11 ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ cannoli-cli-spark2_2.11 ---
[INFO] 
[INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ cannoli-cli-spark2_2.11 ---
Discovery starting.
Discovery completed in 153 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
2020-10-08 05:52:52 WARN  Utils:66 - Your hostname, ubuntu-testing resolves to a loopback address: 127.0.1.1; using 192.168.10.30 instead (on interface eno1)
2020-10-08 05:52:52 WARN  Utils:66 - Set SPARK_LOCAL_IP if you need to bind to another address
InterleaveFastqSuite:
2020-10-08 05:52:52 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 4 seconds, 753 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] >>> scoverage-maven-plugin:1.1.1:report (default-cli) > [scoverage]test @ cannoli-cli-spark2_2.11 >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-maven) @ cannoli-cli-spark2_2.11 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-java) @ cannoli-cli-spark2_2.11 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:timestamp-property (timestamp-property) @ cannoli-cli-spark2_2.11 ---
[INFO] 
[INFO] --- git-commit-id-plugin:2.2.2:revision (default) @ cannoli-cli-spark2_2.11 ---
[INFO] 
[INFO] --- templating-maven-plugin:1.0.0:filter-sources (filter-src) @ cannoli-cli-spark2_2.11 ---
[INFO] Coping files with filtering to temporary directory.
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 1 resource
[INFO] No files needs to be copied to output directory. Up to date: /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/cli/target/generated-sources/java-templates
[INFO] Source directory: /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/cli/target/generated-sources/java-templates added.
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ cannoli-cli-spark2_2.11 ---
[INFO] Source directory: /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/cli/src/main/scala added.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ cannoli-cli-spark2_2.11 ---
[INFO] Modified 0 of 26 .scala files
[INFO] 
[INFO] --- scoverage-maven-plugin:1.1.1:pre-compile (default-cli) @ cannoli-cli-spark2_2.11 ---
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ cannoli-cli-spark2_2.11 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/cli/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ cannoli-cli-spark2_2.11 ---
[WARNING]  Expected all dependencies to require Scala version: 2.11.12
[WARNING]  com.twitter:chill_2.11:0.9.3 requires scala version: 2.11.12
[WARNING]  org.apache.spark:spark-core_2.11:2.4.6 requires scala version: 2.11.12
[WARNING]  org.json4s:json4s-jackson_2.11:3.5.3 requires scala version: 2.11.11
[WARNING] Multiple versions of scala libraries detected!
[INFO] /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/cli/target/generated-sources/java-templates:-1: info: compiling
[INFO] /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/cli/src/main/scala:-1: info: compiling
[INFO] /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/cli/target/generated-sources/annotations:-1: info: compiling
[INFO] Compiling 25 source files to /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/cli/target/scala-2.11.12/scoverage-classes at 1602161576471
[INFO] [info] Cleaning datadir [/home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/cli/target/scoverage-data]
[INFO] [info] Beginning coverage instrumentation
[INFO] [info] Instrumentation completed [945 statements]
[INFO] [info] Wrote instrumentation file [/home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/cli/target/scoverage-data/scoverage.coverage.xml]
[INFO] [info] Will write measurement data to [/home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/cli/target/scoverage-data]
[WARNING] /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/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/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/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-spark2_2.11 ---
[INFO] Changes detected - recompiling the module!
[INFO] Compiling 1 source file to /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/cli/target/scala-2.11.12/scoverage-classes
[INFO] 
[INFO] --- scoverage-maven-plugin:1.1.1:post-compile (default-cli) @ cannoli-cli-spark2_2.11 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ cannoli-cli-spark2_2.11 ---
[INFO] Test Source directory: /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/cli/src/test/scala added.
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ cannoli-cli-spark2_2.11 ---
[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-spark2_2.11 ---
[WARNING]  Expected all dependencies to require Scala version: 2.11.12
[WARNING]  com.twitter:chill_2.11:0.9.3 requires scala version: 2.11.12
[WARNING]  org.apache.spark:spark-core_2.11:2.4.6 requires scala version: 2.11.12
[WARNING]  org.json4s:json4s-jackson_2.11:3.5.3 requires scala version: 2.11.11
[WARNING] Multiple versions of scala libraries detected!
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ cannoli-cli-spark2_2.11 ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ cannoli-cli-spark2_2.11 ---
[INFO] 
[INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ cannoli-cli-spark2_2.11 ---
Discovery starting.
Discovery completed in 149 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
2020-10-08 05:53:05 WARN  Utils:66 - Your hostname, ubuntu-testing resolves to a loopback address: 127.0.1.1; using 192.168.10.30 instead (on interface eno1)
2020-10-08 05:53:05 WARN  Utils:66 - Set SPARK_LOCAL_IP if you need to bind to another address
InterleaveFastqSuite:
2020-10-08 05:53:05 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 4 seconds, 455 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] <<< scoverage-maven-plugin:1.1.1:report (default-cli) < [scoverage]test @ cannoli-cli-spark2_2.11 <<<
[INFO] 
[INFO] 
[INFO] --- scoverage-maven-plugin:1.1.1:report (default-cli) @ cannoli-cli-spark2_2.11 ---
[INFO] [scoverage] Generating cobertura XML report...
[INFO] [scoverage] Generating scoverage XML report...
[INFO] [scoverage] Generating scoverage HTML report...
[INFO] 
[INFO] --------< org.bdgenomics.cannoli:cannoli-assembly-spark2_2.11 >---------
[INFO] Building Cannoli_2.11: Assembly 0.11.0-SNAPSHOT                    [5/5]
[INFO] --------------------------------[ jar ]---------------------------------
[INFO] 
[INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-maven) @ cannoli-assembly-spark2_2.11 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-java) @ cannoli-assembly-spark2_2.11 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ cannoli-assembly-spark2_2.11 ---
[INFO] Source directory: /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/assembly/src/main/scala added.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ cannoli-assembly-spark2_2.11 ---
[INFO] Modified 0 of 1 .scala files
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ cannoli-assembly-spark2_2.11 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/assembly/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ cannoli-assembly-spark2_2.11 ---
[INFO] /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/assembly/src/main/scala:-1: info: compiling
[INFO] Compiling 1 source files to /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/assembly/target/scala-2.11.12/classes at 1602161589296
[INFO] prepare-compile in 0 s
[INFO] compile in 1 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ cannoli-assembly-spark2_2.11 ---
[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-spark2_2.11 ---
[INFO] Test Source directory: /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/assembly/src/test/scala added.
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ cannoli-assembly-spark2_2.11 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/assembly/src/test/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ cannoli-assembly-spark2_2.11 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ cannoli-assembly-spark2_2.11 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ cannoli-assembly-spark2_2.11 ---
[INFO] No tests to run.
[INFO] 
[INFO] >>> scoverage-maven-plugin:1.1.1:report (default-cli) > [scoverage]test @ cannoli-assembly-spark2_2.11 >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-maven) @ cannoli-assembly-spark2_2.11 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-java) @ cannoli-assembly-spark2_2.11 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ cannoli-assembly-spark2_2.11 ---
[INFO] Source directory: /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/assembly/src/main/scala added.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ cannoli-assembly-spark2_2.11 ---
[INFO] Modified 0 of 1 .scala files
[INFO] 
[INFO] --- scoverage-maven-plugin:1.1.1:pre-compile (default-cli) @ cannoli-assembly-spark2_2.11 ---
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ cannoli-assembly-spark2_2.11 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/assembly/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ cannoli-assembly-spark2_2.11 ---
[WARNING]  Expected all dependencies to require Scala version: 2.11.12
[WARNING]  org.bdgenomics.utils:utils-misc-spark2_2.11:0.3.0 requires scala version: 2.11.7
[WARNING] Multiple versions of scala libraries detected!
[INFO] /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/assembly/src/main/scala:-1: info: compiling
[INFO] Compiling 1 source files to /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/assembly/target/scala-2.11.12/scoverage-classes at 1602161590891
[INFO] [info] Cleaning datadir [/home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/assembly/target/scoverage-data]
[INFO] [info] Beginning coverage instrumentation
[INFO] [info] Instrumentation completed [0 statements]
[INFO] [info] Wrote instrumentation file [/home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/assembly/target/scoverage-data/scoverage.coverage.xml]
[INFO] [info] Will write measurement data to [/home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/assembly/target/scoverage-data]
[INFO] prepare-compile in 0 s
[INFO] compile in 1 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ cannoli-assembly-spark2_2.11 ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- scoverage-maven-plugin:1.1.1:post-compile (default-cli) @ cannoli-assembly-spark2_2.11 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ cannoli-assembly-spark2_2.11 ---
[INFO] Test Source directory: /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/assembly/src/test/scala added.
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ cannoli-assembly-spark2_2.11 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/assembly/src/test/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ cannoli-assembly-spark2_2.11 ---
[WARNING]  Expected all dependencies to require Scala version: 2.11.12
[WARNING]  org.bdgenomics.utils:utils-misc-spark2_2.11:0.3.0 requires scala version: 2.11.7
[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-spark2_2.11 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ cannoli-assembly-spark2_2.11 ---
[INFO] No tests to run.
[INFO] 
[INFO] <<< scoverage-maven-plugin:1.1.1:report (default-cli) < [scoverage]test @ cannoli-assembly-spark2_2.11 <<<
[INFO] 
[INFO] 
[INFO] --- scoverage-maven-plugin:1.1.1:report (default-cli) @ cannoli-assembly-spark2_2.11 ---
[INFO] [scoverage] Generating cobertura XML report...
[INFO] [scoverage] Generating scoverage XML report...
[INFO] [scoverage] Generating scoverage HTML report...
[INFO] [scoverage] Generating aggregated cobertura XML report...
[INFO] [scoverage] Generating aggregated scoverage XML report...
[INFO] [scoverage] Generating aggregated scoverage HTML report...
[INFO] 
[INFO] ---------< org.bdgenomics.cannoli:cannoli-parent-spark2_2.11 >----------
[INFO] Building Cannoli_2.11 0.11.0-SNAPSHOT                              [6/5]
[INFO] --------------------------------[ pom ]---------------------------------
[INFO] 
[INFO] --- coveralls-maven-plugin:4.3.0:report (default-cli) @ cannoli-parent-spark2_2.11 ---
[INFO] Starting Coveralls job for jenkins (2108 / https://amplab.cs.berkeley.edu/jenkins/job/cannoli/HADOOP_VERSION=2.7.5,SCALA_VERSION=2.11,SPARK_VERSION=2.4.6,label=ubuntu/2108/)
[INFO] Using repository token <secret>
[INFO] Git commit e85bd29 in master
[INFO] Writing Coveralls data to /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/target/coveralls.json...
[INFO] Processing coverage report from /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/target/cobertura.xml
[INFO] Successfully wrote Coveralls data in 482ms
[INFO] Gathered code coverage metrics for 50 source files with 5421 lines of code:
[INFO] - 1279 relevant lines
[INFO] - 153 covered lines
[INFO] - 1126 missed lines
[INFO] Submitting Coveralls data to API
[INFO] Successfully submitted Coveralls data in 925ms for Job #2108.1
[INFO] https://coveralls.io/jobs/68828659
[INFO] *** It might take hours for Coveralls to update the actual coverage numbers for a job
[INFO]     If you see question marks in the report, please be patient
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary for Cannoli_2.11 0.11.0-SNAPSHOT:
[INFO] 
[INFO] Cannoli_2.11 ....................................... SUCCESS [  1.798 s]
[INFO] Cannoli_2.11: Builder .............................. SUCCESS [  9.090 s]
[INFO] Cannoli_2.11: Core ................................. SUCCESS [ 23.549 s]
[INFO] Cannoli_2.11: CLI .................................. SUCCESS [ 30.167 s]
[INFO] Cannoli_2.11: Assembly ............................. SUCCESS [  4.915 s]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time:  01:12 min
[INFO] Finished at: 2020-10-08T05:53:15-07:00
[INFO] ------------------------------------------------------------------------

# we are done with maven, so clean up the maven temp dir
find ${CANNOLI_MVN_TMP_DIR}
+ find /tmp/cannoliTestMvnUw1mjQa
/tmp/cannoliTestMvnUw1mjQa
/tmp/cannoliTestMvnUw1mjQa/8367128752813066133
/tmp/cannoliTestMvnUw1mjQa/8367128752813066133/test.ifq
/tmp/cannoliTestMvnUw1mjQa/8367128752813066133/.test.ifq.crc
/tmp/cannoliTestMvnUw1mjQa/1671118907193016597
/tmp/cannoliTestMvnUw1mjQa/1671118907193016597/.test.ifq.gz.crc
/tmp/cannoliTestMvnUw1mjQa/1671118907193016597/test.ifq.gz
/tmp/cannoliTestMvnUw1mjQa/5643367200882206553
/tmp/cannoliTestMvnUw1mjQa/5643367200882206553/test.bam
/tmp/cannoliTestMvnUw1mjQa/5643367200882206553/.test.bam.crc
/tmp/cannoliTestMvnUw1mjQa/3205882306889336161
/tmp/cannoliTestMvnUw1mjQa/3205882306889336161/.test.ifq.bz2.crc
/tmp/cannoliTestMvnUw1mjQa/3205882306889336161/test.ifq.bz2
/tmp/cannoliTestMvnUw1mjQa/8623513528588836725
/tmp/cannoliTestMvnUw1mjQa/8623513528588836725/.double.ifq.crc
/tmp/cannoliTestMvnUw1mjQa/8623513528588836725/double.ifq
/tmp/cannoliTestMvnUw1mjQa/8031099961944774837
/tmp/cannoliTestMvnUw1mjQa/8031099961944774837/test.ifq
/tmp/cannoliTestMvnUw1mjQa/8031099961944774837/.test.ifq.crc
/tmp/cannoliTestMvnUw1mjQa/5932654031217726548
/tmp/cannoliTestMvnUw1mjQa/5932654031217726548/.test.ifq.gz.crc
/tmp/cannoliTestMvnUw1mjQa/5932654031217726548/test.ifq.gz
/tmp/cannoliTestMvnUw1mjQa/745672247421613075
/tmp/cannoliTestMvnUw1mjQa/745672247421613075/.test.ifq.bz2.crc
/tmp/cannoliTestMvnUw1mjQa/745672247421613075/test.ifq.bz2
/tmp/cannoliTestMvnUw1mjQa/3602413488781219842
/tmp/cannoliTestMvnUw1mjQa/3602413488781219842/test.bam
/tmp/cannoliTestMvnUw1mjQa/3602413488781219842/.test.bam.crc
/tmp/cannoliTestMvnUw1mjQa/4456209773097074011
/tmp/cannoliTestMvnUw1mjQa/4456209773097074011/.double.ifq.crc
/tmp/cannoliTestMvnUw1mjQa/4456209773097074011/double.ifq
rm -rf ${CANNOLI_MVN_TMP_DIR}
+ rm -rf /tmp/cannoliTestMvnUw1mjQa

# and move our poms back to their original values
# this will allow us to pass our porcelain test at the end
if [ ${SCALA_VERSION} == 2.11 ];
then
    echo "Rewriting POM.xml files back to Scala 2.12."
    ./scripts/move_to_scala_2.12.sh
fi
+ '[' 2.11 == 2.11 ']'
+ echo 'Rewriting POM.xml files back to Scala 2.12.'
Rewriting POM.xml files back to Scala 2.12.
+ ./scripts/move_to_scala_2.12.sh
if [ ${SPARK_VERSION} == 2.4.6 ];
then
    echo "Rewriting POM.xml files back to Spark 3."
    ./scripts/move_to_spark_3.sh
fi
+ '[' 2.4.6 == 2.4.6 ']'
+ echo 'Rewriting POM.xml files back to Spark 3.'
Rewriting POM.xml files back to Spark 3.
+ ./scripts/move_to_spark_3.sh

find . -name pom.xml \
    -exec sed -i.bak \
    -e "s:sun.io.serialization.extendedDebugInfo=true -Djava.io.tmpdir=${CANNOLI_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/cannoliTestMvnUw1mjQa:sun.io.serialization.extendedDebugInfo=true:g' '{}' ';'
find . -name "*.bak" -exec rm -f {} \;
+ find . -name '*.bak' -exec rm -f '{}' ';'

if test -n "$(git status --porcelain)"
then
    echo "Applying move_to_xyz script marred a pom.xml file."
    echo "Exiting..."
    exit 1
fi
git status --porcelain
++ git status --porcelain
+ test -n ''

./scripts/format-source
+ ./scripts/format-source
+++ dirname ./scripts/format-source
++ cd ./scripts
++ pwd
+ DIR=/home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/scripts
+ pushd /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/scripts/..
~/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu ~/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu
+ mvn org.scalariform:scalariform-maven-plugin:format license:format
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 0.11.0-SNAPSHOT                              [1/5]
[INFO] --------------------------------[ pom ]---------------------------------
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ cannoli-parent-spark3_2.12 ---
[INFO] Modified 0 of 54 .scala files
[INFO] 
[INFO] --- maven-license-plugin:1.10.b1:format (default-cli) @ cannoli-parent-spark3_2.12 ---
[INFO] Updating license headers...
[INFO] 
[INFO] ---------< org.bdgenomics.cannoli:cannoli-builder-spark3_2.12 >---------
[INFO] Building Cannoli_2.12: Builder 0.11.0-SNAPSHOT                     [2/5]
[INFO] --------------------------------[ jar ]---------------------------------
[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-license-plugin:1.10.b1:format (default-cli) @ cannoli-builder-spark3_2.12 ---
[INFO] Updating license headers...
[INFO] 
[INFO] ----------< org.bdgenomics.cannoli:cannoli-core-spark3_2.12 >-----------
[INFO] Building Cannoli_2.12: Core 0.11.0-SNAPSHOT                        [3/5]
[INFO] --------------------------------[ jar ]---------------------------------
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ cannoli-core-spark3_2.12 ---
[INFO] Modified 0 of 27 .scala files
[INFO] 
[INFO] --- maven-license-plugin:1.10.b1:format (default-cli) @ cannoli-core-spark3_2.12 ---
[INFO] Updating license headers...
[INFO] 
[INFO] -----------< org.bdgenomics.cannoli:cannoli-cli-spark3_2.12 >-----------
[INFO] Building Cannoli_2.12: CLI 0.11.0-SNAPSHOT                         [4/5]
[INFO] --------------------------------[ jar ]---------------------------------
[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-license-plugin:1.10.b1:format (default-cli) @ cannoli-cli-spark3_2.12 ---
[INFO] Updating license headers...
[INFO] 
[INFO] --------< org.bdgenomics.cannoli:cannoli-assembly-spark3_2.12 >---------
[INFO] Building Cannoli_2.12: Assembly 0.11.0-SNAPSHOT                    [5/5]
[INFO] --------------------------------[ jar ]---------------------------------
[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-license-plugin:1.10.b1:format (default-cli) @ cannoli-assembly-spark3_2.12 ---
[INFO] Updating license headers...
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary for Cannoli_2.12 0.11.0-SNAPSHOT:
[INFO] 
[INFO] Cannoli_2.12 ....................................... SUCCESS [  1.632 s]
[INFO] Cannoli_2.12: Builder .............................. SUCCESS [  0.008 s]
[INFO] Cannoli_2.12: Core ................................. SUCCESS [  0.374 s]
[INFO] Cannoli_2.12: CLI .................................. SUCCESS [  0.269 s]
[INFO] Cannoli_2.12: Assembly ............................. SUCCESS [  0.009 s]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time:  2.458 s
[INFO] Finished at: 2020-10-08T05:53:19-07:00
[INFO] ------------------------------------------------------------------------
+ popd
~/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu
if test -n "$(git status --porcelain)"
then
    echo "Please run './scripts/format-source'"
    exit 1
fi
git status --porcelain
++ git status --porcelain
+ test -n ''

echo
+ echo

echo "All the tests passed"
+ echo 'All the tests passed'
All the tests passed
echo
+ echo

+ '[' 2.11 == 2.11 ']'
+ echo 'Moving build to Scala 2.11...'
Moving build to Scala 2.11...
+ set +e
+ /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/scripts/move_to_scala_2.11.sh
+ set -e
+ '[' 2.11 == 2.12 ']'
+ '[' 2.4.6 == 2.4.6 ']'
+ echo 'Moving build to Spark 2.x...'
Moving build to Spark 2.x...
+ set +e
+ /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/scripts/move_to_spark_2.sh
+ set -e
+ '[' 2.4.6 == 3.0.1 ']'
+ mvn --settings=/home/jenkins/workspace/settings.xml deploy -DskipTests -Pdistribution
[ERROR] Error executing Maven.
[ERROR] The specified user settings file does not exist: /home/jenkins/workspace/settings.xml
Build step 'Execute shell' marked build as failure
Recording test results
Publishing Scoverage XML and HTML report...
Sending e-mails to: heuermh@gmail.com fnothaft@berkeley.edu
Finished: FAILURE