FailedConsole Output

Started by upstream project "cannoli" build number 2122
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/2.12/SPARK_VERSION/3.0.1/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 a6388e24c69eecbed2bd84d67d345889f82ee14a (refs/remotes/origin/master)
 > git config core.sparsecheckout # timeout=10
 > git checkout -f a6388e24c69eecbed2bd84d67d345889f82ee14a
 > git rev-list a6388e24c69eecbed2bd84d67d345889f82ee14a # 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/hudson314255049902308113.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/2.12/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/cannoliTestMvn5o5M6vS

# 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/cannoliTestMvn5o5M6vS: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 ${BASH_SOURCE[0]} 
+++ dirname /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/scripts/jenkins-test
++ cd /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/scripts
++ pwd
+ DIR=/home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/scripts
PROJECT_ROOT=${DIR}/..
+ PROJECT_ROOT=/home/jenkins/workspace/cannoli/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/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=0.11.0-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 2.12 ]]

# 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 0.11.0-SNAPSHOT on Spark 3.0.1 Scala 2.12 and Hadoop 2.7.5'
Testing Cannoli version 0.11.0-SNAPSHOT on Spark 3.0.1 Scala 2.12 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
+ '[' 2.12 == 2.11 ']'

# 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
+ '[' 2.12 == 2.12 ']'
+ set +e
+ ./scripts/move_to_scala_2.12.sh
Scala version is already set to 2.12 (Scala artifacts have _2.12 version suffix in artifact name).
Cowardly refusing to move to Scala 2.12 a second time...
+ set -e

# move to Spark 2.x if requested
if [ ${SPARK_VERSION} == 2.4.7 ];
then
    set +e
    ./scripts/move_to_spark_2.sh
    set -e
fi
+ '[' 3.0.1 == 2.4.7 ']'

# 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
+ '[' 3.0.1 == 3.0.1 ']'
+ set +e
+ ./scripts/move_to_spark_3.sh
POM is already set up for Spark 3 (Spark 3 artifacts have -spark3 suffix in artifact names).
Cowardly refusing to move to Spark 3 a second time...
+ set -e

# 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_2.12                                                       [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] --- maven-clean-plugin:3.1.0:clean (default-clean) @ cannoli-parent-spark3_2.12 ---
[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] --- maven-clean-plugin:3.1.0:clean (default-clean) @ cannoli-builder-spark3_2.12 ---
[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] --- maven-clean-plugin:3.1.0:clean (default-clean) @ cannoli-core-spark3_2.12 ---
[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] --- maven-clean-plugin:3.1.0:clean (default-clean) @ cannoli-cli-spark3_2.12 ---
[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] --- maven-clean-plugin:3.1.0:clean (default-clean) @ cannoli-assembly-spark3_2.12 ---
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary for Cannoli_2.12 0.11.0-SNAPSHOT:
[INFO] 
[INFO] Cannoli_2.12 ....................................... SUCCESS [  0.208 s]
[INFO] Cannoli_2.12: Builder .............................. SUCCESS [  0.003 s]
[INFO] Cannoli_2.12: Core ................................. SUCCESS [  0.006 s]
[INFO] Cannoli_2.12: CLI .................................. SUCCESS [  0.021 s]
[INFO] Cannoli_2.12: Assembly ............................. SUCCESS [  0.002 s]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time:  0.378 s
[INFO] Finished at: 2020-10-25T13:14:32-07:00
[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_2.12                                                       [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] --- 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/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 54 .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/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] >>> scoverage-maven-plugin:1.1.1:report (default-cli) > [scoverage]test @ 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/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 54 .scala files
[INFO] 
[INFO] --- scoverage-maven-plugin:1.1.1:pre-compile (default-cli) @ cannoli-parent-spark3_2.12 ---
[INFO] Skipping SCoverage execution for project with packaging type 'pom'
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ cannoli-parent-spark3_2.12 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- scoverage-maven-plugin:1.1.1:post-compile (default-cli) @ cannoli-parent-spark3_2.12 ---
[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/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] <<< scoverage-maven-plugin:1.1.1:report (default-cli) < [scoverage]test @ cannoli-parent-spark3_2.12 <<<
[INFO] 
[INFO] 
[INFO] --- scoverage-maven-plugin:1.1.1:report (default-cli) @ cannoli-parent-spark3_2.12 ---
[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] --- 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/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/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 ---
[INFO] /home/jenkins/workspace/cannoli/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/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/builder/target/scala-2.12.8/classes at 1603656877396
[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/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/builder/target/scala-2.12.8/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/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/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 ---
[INFO] /home/jenkins/workspace/cannoli/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/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/builder/target/scala-2.12.8/test-classes at 1603656880556
[INFO] prepare-compile in 0 s
[INFO] compile in 1 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/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/builder/target/scala-2.12.8/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: 0.069 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: 0.001 s - in org.bdgenomics.cannoli.builder.CommandBuildersTest
[INFO] 
[INFO] Results:
[INFO] 
[INFO] Tests run: 40, Failures: 0, Errors: 0, Skipped: 0
[INFO] 
[INFO] 
[INFO] >>> scoverage-maven-plugin:1.1.1:report (default-cli) > [scoverage]test @ 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/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] --- scoverage-maven-plugin:1.1.1:pre-compile (default-cli) @ cannoli-builder-spark3_2.12 ---
[WARNING] Skipping SCoverage execution - unsupported Scala version "2.12.8"
[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/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 ---
[INFO] /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/builder/src/main/java:-1: info: compiling
[INFO] /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/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/2.12/SPARK_VERSION/3.0.1/label/ubuntu/builder/target/scala-2.12.8/classes at 1603656883728
[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/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/builder/target/scala-2.12.8/classes
[INFO] 
[INFO] --- scoverage-maven-plugin:1.1.1:post-compile (default-cli) @ cannoli-builder-spark3_2.12 ---
[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/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/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 ---
[INFO] /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/builder/src/test/java:-1: info: compiling
[INFO] /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/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/2.12/SPARK_VERSION/3.0.1/label/ubuntu/builder/target/scala-2.12.8/test-classes at 1603656885957
[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] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ cannoli-builder-spark3_2.12 ---
[INFO] Skipping execution of surefire because it has already been run for this configuration
[INFO] 
[INFO] <<< scoverage-maven-plugin:1.1.1:report (default-cli) < [scoverage]test @ cannoli-builder-spark3_2.12 <<<
[INFO] 
[INFO] 
[INFO] --- scoverage-maven-plugin:1.1.1:report (default-cli) @ cannoli-builder-spark3_2.12 ---
[INFO] Skipping SCoverage report generation
[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] --- 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/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 27 .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/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: 2.12.8
[WARNING]  com.twitter:chill_2.12:0.9.5 requires scala version: 2.12.10
[WARNING] Multiple versions of scala libraries detected!
[INFO] /home/jenkins/workspace/cannoli/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 26 source files to /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/core/target/scala-2.12.8/classes at 1603656889241
[WARNING] /home/jenkins/workspace/cannoli/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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: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/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]       files = builder.getFiles()
[WARNING]                               ^
[WARNING] /home/jenkins/workspace/cannoli/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:118: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     val headerLines = accumulator.value.distinct
[WARNING]                                   ^
[WARNING] /home/jenkins/workspace/cannoli/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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: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/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]       files = builder.getFiles()
[WARNING]                               ^
[WARNING] /home/jenkins/workspace/cannoli/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/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/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] 52 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-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/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/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: 2.12.8
[WARNING]  com.twitter:chill_2.12:0.9.5 requires scala version: 2.12.10
[WARNING] Multiple versions of scala libraries detected!
[INFO] /home/jenkins/workspace/cannoli/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/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/core/target/scala-2.12.8/test-classes at 1603656896368
[WARNING] /home/jenkins/workspace/cannoli/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/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 137 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 550 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-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/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 27 .scala files
[INFO] 
[INFO] --- scoverage-maven-plugin:1.1.1:pre-compile (default-cli) @ cannoli-core-spark3_2.12 ---
[WARNING] Skipping SCoverage execution - unsupported Scala version "2.12.8"
[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/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: 2.12.8
[WARNING]  com.twitter:chill_2.12:0.9.5 requires scala version: 2.12.10
[WARNING] Multiple versions of scala libraries detected!
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ cannoli-core-spark3_2.12 ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- scoverage-maven-plugin:1.1.1:post-compile (default-cli) @ cannoli-core-spark3_2.12 ---
[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/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/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: 2.12.8
[WARNING]  com.twitter:chill_2.12:0.9.5 requires scala version: 2.12.10
[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-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] Skipping execution of surefire because it has already been run for this configuration
[INFO] 
[INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ cannoli-core-spark3_2.12 ---
Discovery starting.
Discovery completed in 128 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 530 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-spark3_2.12 <<<
[INFO] 
[INFO] 
[INFO] --- scoverage-maven-plugin:1.1.1:report (default-cli) @ cannoli-core-spark3_2.12 ---
[INFO] Skipping SCoverage report generation
[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] --- 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/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/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/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/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: 2.12.8
[WARNING]  com.twitter:chill_2.12:0.9.5 requires scala version: 2.12.10
[WARNING] Multiple versions of scala libraries detected!
[INFO] /home/jenkins/workspace/cannoli/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/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/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/cli/target/scala-2.12.8/classes at 1603656905482
[WARNING] /home/jenkins/workspace/cannoli/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/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/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/cli/target/scala-2.12.8/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/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: 2.12.8
[WARNING]  com.twitter:chill_2.12:0.9.5 requires scala version: 2.12.10
[WARNING] Multiple versions of scala libraries detected!
[INFO] /home/jenkins/workspace/cannoli/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/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/cli/target/scala-2.12.8/test-classes at 1603656912696
[WARNING] /home/jenkins/workspace/cannoli/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 175 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
2020-10-25 13:15:19 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)
2020-10-25 13:15:19 WARN  Utils:69 - Set SPARK_LOCAL_IP if you need to bind to another address
InterleaveFastqSuite:
2020-10-25 13:15:20 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 5 seconds, 639 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-spark3_2.12 >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-maven) @ cannoli-cli-spark3_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-java) @ cannoli-cli-spark3_2.12 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:timestamp-property (timestamp-property) @ cannoli-cli-spark3_2.12 ---
[INFO] 
[INFO] --- git-commit-id-plugin:2.2.2:revision (default) @ cannoli-cli-spark3_2.12 ---
[INFO] 
[INFO] --- templating-maven-plugin:1.0.0:filter-sources (filter-src) @ cannoli-cli-spark3_2.12 ---
[INFO] Coping files with filtering to temporary directory.
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 1 resource
[INFO] No files needs to be copied to output directory. Up to date: /home/jenkins/workspace/cannoli/HADOOP_VERSION/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/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/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] --- scoverage-maven-plugin:1.1.1:pre-compile (default-cli) @ cannoli-cli-spark3_2.12 ---
[WARNING] Skipping SCoverage execution - unsupported Scala version "2.12.8"
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ cannoli-cli-spark3_2.12 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/cannoli/HADOOP_VERSION/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: 2.12.8
[WARNING]  com.twitter:chill_2.12:0.9.5 requires scala version: 2.12.10
[WARNING] Multiple versions of scala libraries detected!
[INFO] /home/jenkins/workspace/cannoli/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/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/cli/src/main/scala:-1: info: compiling
[INFO] /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/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/2.12/SPARK_VERSION/3.0.1/label/ubuntu/cli/target/scala-2.12.8/classes at 1603656924613
[WARNING] /home/jenkins/workspace/cannoli/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/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] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- scoverage-maven-plugin:1.1.1:post-compile (default-cli) @ cannoli-cli-spark3_2.12 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ cannoli-cli-spark3_2.12 ---
[INFO] Test Source directory: /home/jenkins/workspace/cannoli/HADOOP_VERSION/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: 2.12.8
[WARNING]  com.twitter:chill_2.12:0.9.5 requires scala version: 2.12.10
[WARNING] Multiple versions of scala libraries detected!
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ cannoli-cli-spark3_2.12 ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ cannoli-cli-spark3_2.12 ---
[INFO] Skipping execution of surefire because it has already been run for this configuration
[INFO] 
[INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ cannoli-cli-spark3_2.12 ---
Discovery starting.
Discovery completed in 171 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
2020-10-25 13:15:33 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)
2020-10-25 13:15:33 WARN  Utils:69 - Set SPARK_LOCAL_IP if you need to bind to another address
InterleaveFastqSuite:
2020-10-25 13:15:34 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 5 seconds, 666 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-spark3_2.12 <<<
[INFO] 
[INFO] 
[INFO] --- scoverage-maven-plugin:1.1.1:report (default-cli) @ cannoli-cli-spark3_2.12 ---
[INFO] Skipping SCoverage report generation
[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] --- maven-enforcer-plugin:1.2:enforce (enforce-maven) @ cannoli-assembly-spark3_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-java) @ cannoli-assembly-spark3_2.12 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ cannoli-assembly-spark3_2.12 ---
[INFO] Source directory: /home/jenkins/workspace/cannoli/HADOOP_VERSION/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/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: 2.12.8
[WARNING]  org.bdgenomics.utils:utils-misc-spark3_2.12:0.3.0 requires scala version: 2.12.8
[WARNING]  org.bdgenomics.utils:utils-io-spark3_2.12:0.3.0 requires scala version: 2.12.8
[WARNING]  org.clapper:grizzled-slf4j_2.12:1.3.4 requires scala version: 2.12.8
[WARNING]  org.bdgenomics.utils:utils-cli-spark3_2.12:0.3.0 requires scala version: 2.12.8
[WARNING]  net.codingwell:scala-guice_2.12:4.2.1 requires scala version: 2.12.6
[WARNING] Multiple versions of scala libraries detected!
[INFO] /home/jenkins/workspace/cannoli/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/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/assembly/target/scala-2.12.8/classes at 1603656938222
[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/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/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: 2.12.8
[WARNING]  org.bdgenomics.utils:utils-misc-spark3_2.12:0.3.0 requires scala version: 2.12.8
[WARNING]  org.bdgenomics.utils:utils-io-spark3_2.12:0.3.0 requires scala version: 2.12.8
[WARNING]  org.clapper:grizzled-slf4j_2.12:1.3.4 requires scala version: 2.12.8
[WARNING]  org.bdgenomics.utils:utils-cli-spark3_2.12:0.3.0 requires scala version: 2.12.8
[WARNING]  net.codingwell:scala-guice_2.12:4.2.1 requires scala version: 2.12.6
[WARNING] Multiple versions of scala libraries detected!
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ 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] >>> scoverage-maven-plugin:1.1.1:report (default-cli) > [scoverage]test @ cannoli-assembly-spark3_2.12 >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-maven) @ cannoli-assembly-spark3_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-java) @ cannoli-assembly-spark3_2.12 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ cannoli-assembly-spark3_2.12 ---
[INFO] Source directory: /home/jenkins/workspace/cannoli/HADOOP_VERSION/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] --- scoverage-maven-plugin:1.1.1:pre-compile (default-cli) @ cannoli-assembly-spark3_2.12 ---
[WARNING] Skipping SCoverage execution - unsupported Scala version "2.12.8"
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ cannoli-assembly-spark3_2.12 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/cannoli/HADOOP_VERSION/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: 2.12.8
[WARNING]  org.bdgenomics.utils:utils-misc-spark3_2.12:0.3.0 requires scala version: 2.12.8
[WARNING]  org.bdgenomics.utils:utils-io-spark3_2.12:0.3.0 requires scala version: 2.12.8
[WARNING]  org.clapper:grizzled-slf4j_2.12:1.3.4 requires scala version: 2.12.8
[WARNING]  org.bdgenomics.utils:utils-cli-spark3_2.12:0.3.0 requires scala version: 2.12.8
[WARNING]  net.codingwell:scala-guice_2.12:4.2.1 requires scala version: 2.12.6
[WARNING] Multiple versions of scala libraries detected!
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ cannoli-assembly-spark3_2.12 ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- scoverage-maven-plugin:1.1.1:post-compile (default-cli) @ cannoli-assembly-spark3_2.12 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ cannoli-assembly-spark3_2.12 ---
[INFO] Test Source directory: /home/jenkins/workspace/cannoli/HADOOP_VERSION/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/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: 2.12.8
[WARNING]  org.bdgenomics.utils:utils-misc-spark3_2.12:0.3.0 requires scala version: 2.12.8
[WARNING]  org.bdgenomics.utils:utils-io-spark3_2.12:0.3.0 requires scala version: 2.12.8
[WARNING]  org.clapper:grizzled-slf4j_2.12:1.3.4 requires scala version: 2.12.8
[WARNING]  org.bdgenomics.utils:utils-cli-spark3_2.12:0.3.0 requires scala version: 2.12.8
[WARNING]  net.codingwell:scala-guice_2.12:4.2.1 requires scala version: 2.12.6
[WARNING] Multiple versions of scala libraries detected!
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ 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] Skipping execution of surefire because it has already been run for this configuration
[INFO] 
[INFO] <<< scoverage-maven-plugin:1.1.1:report (default-cli) < [scoverage]test @ cannoli-assembly-spark3_2.12 <<<
[INFO] 
[INFO] 
[INFO] --- scoverage-maven-plugin:1.1.1:report (default-cli) @ cannoli-assembly-spark3_2.12 ---
[INFO] [scoverage] Generating aggregated cobertura XML report...
[INFO] [scoverage] Generating aggregated scoverage XML report...
[INFO] [scoverage] Generating aggregated scoverage HTML report...
[INFO] Skipping SCoverage report generation
[INFO] 
[INFO] ---------< org.bdgenomics.cannoli:cannoli-parent-spark3_2.12 >----------
[INFO] Building Cannoli_2.12 0.11.0-SNAPSHOT                              [6/5]
[INFO] --------------------------------[ pom ]---------------------------------
[INFO] 
[INFO] --- coveralls-maven-plugin:4.3.0:report (default-cli) @ cannoli-parent-spark3_2.12 ---
[INFO] Starting Coveralls job for jenkins (2122 / https://amplab.cs.berkeley.edu/jenkins/job/cannoli/HADOOP_VERSION=2.7.5,SCALA_VERSION=2.12,SPARK_VERSION=3.0.1,label=ubuntu/2122/)
[INFO] Using repository token <secret>
[INFO] Git commit a6388e2 in master
[INFO] Writing Coveralls data to /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/target/coveralls.json...
[INFO] Processing coverage report from /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/target/cobertura.xml
[INFO] Successfully wrote Coveralls data in 52ms
[INFO] Gathered code coverage metrics for 0 source files with 0 lines of code:
[INFO] - 0 relevant lines
[INFO] - 0 covered lines
[INFO] - 0 missed lines
[INFO] Submitting Coveralls data to API
[INFO] Successfully submitted Coveralls data in 929ms for Job #2122.1
[INFO] https://coveralls.io/jobs/69667723
[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_2.12 0.11.0-SNAPSHOT:
[INFO] 
[INFO] Cannoli_2.12 ....................................... SUCCESS [  1.421 s]
[INFO] Cannoli_2.12: Builder .............................. SUCCESS [ 11.624 s]
[INFO] Cannoli_2.12: Core ................................. SUCCESS [ 16.203 s]
[INFO] Cannoli_2.12: CLI .................................. SUCCESS [ 33.642 s]
[INFO] Cannoli_2.12: Assembly ............................. SUCCESS [  2.878 s]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time:  01:08 min
[INFO] Finished at: 2020-10-25T13:15:42-07:00
[INFO] ------------------------------------------------------------------------

# we are done with maven, so clean up the maven temp dir
find ${CANNOLI_MVN_TMP_DIR}
+ find /tmp/cannoliTestMvn5o5M6vS
/tmp/cannoliTestMvn5o5M6vS
/tmp/cannoliTestMvn5o5M6vS/4748863245561157640
/tmp/cannoliTestMvn5o5M6vS/4748863245561157640/.test.ifq.gz.crc
/tmp/cannoliTestMvn5o5M6vS/4748863245561157640/test.ifq.gz
/tmp/cannoliTestMvn5o5M6vS/5810773866295493098
/tmp/cannoliTestMvn5o5M6vS/5810773866295493098/.double.ifq.crc
/tmp/cannoliTestMvn5o5M6vS/5810773866295493098/double.ifq
/tmp/cannoliTestMvn5o5M6vS/5326665751553889746
/tmp/cannoliTestMvn5o5M6vS/5326665751553889746/.test.ifq.bz2.crc
/tmp/cannoliTestMvn5o5M6vS/5326665751553889746/test.ifq.bz2
/tmp/cannoliTestMvn5o5M6vS/3824712580317439089
/tmp/cannoliTestMvn5o5M6vS/3824712580317439089/test.ifq
/tmp/cannoliTestMvn5o5M6vS/3824712580317439089/.test.ifq.crc
/tmp/cannoliTestMvn5o5M6vS/55580443976007732
/tmp/cannoliTestMvn5o5M6vS/55580443976007732/test.bam
/tmp/cannoliTestMvn5o5M6vS/55580443976007732/.test.bam.crc
/tmp/cannoliTestMvn5o5M6vS/526146806936619860
/tmp/cannoliTestMvn5o5M6vS/526146806936619860/.double.ifq.crc
/tmp/cannoliTestMvn5o5M6vS/526146806936619860/double.ifq
/tmp/cannoliTestMvn5o5M6vS/64297429057037194
/tmp/cannoliTestMvn5o5M6vS/64297429057037194/.test.ifq.gz.crc
/tmp/cannoliTestMvn5o5M6vS/64297429057037194/test.ifq.gz
/tmp/cannoliTestMvn5o5M6vS/8675198879896573884
/tmp/cannoliTestMvn5o5M6vS/8675198879896573884/.test.ifq.bz2.crc
/tmp/cannoliTestMvn5o5M6vS/8675198879896573884/test.ifq.bz2
/tmp/cannoliTestMvn5o5M6vS/4189722107487256916
/tmp/cannoliTestMvn5o5M6vS/4189722107487256916/test.ifq
/tmp/cannoliTestMvn5o5M6vS/4189722107487256916/.test.ifq.crc
/tmp/cannoliTestMvn5o5M6vS/2000298754922131579
/tmp/cannoliTestMvn5o5M6vS/2000298754922131579/test.bam
/tmp/cannoliTestMvn5o5M6vS/2000298754922131579/.test.bam.crc
rm -rf ${CANNOLI_MVN_TMP_DIR}
+ rm -rf /tmp/cannoliTestMvn5o5M6vS

# 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
+ '[' 2.12 == 2.11 ']'
if [ ${SPARK_VERSION} == 2.4.7 ];
then
    echo "Rewriting POM.xml files back to Spark 3."
    ./scripts/move_to_spark_3.sh
fi
+ '[' 3.0.1 == 2.4.7 ']'

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/cannoliTestMvn5o5M6vS: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/2.12/SPARK_VERSION/3.0.1/label/ubuntu/scripts
+ pushd /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/scripts/..
~/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu ~/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/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 [  1.799 s]
[INFO] Cannoli_2.12: Builder .............................. SUCCESS [  0.008 s]
[INFO] Cannoli_2.12: Core ................................. SUCCESS [  0.438 s]
[INFO] Cannoli_2.12: CLI .................................. SUCCESS [  0.255 s]
[INFO] Cannoli_2.12: Assembly ............................. SUCCESS [  0.008 s]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time:  2.680 s
[INFO] Finished at: 2020-10-25T13:15:46-07:00
[INFO] ------------------------------------------------------------------------
+ popd
~/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/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

+ '[' 2.12 == 2.11 ']'
+ '[' 2.12 == 2.12 ']'
+ echo 'Moving build to Scala 2.12...'
Moving build to Scala 2.12...
+ set +e
+ /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/scripts/move_to_scala_2.12.sh
Scala version is already set to 2.12 (Scala artifacts have _2.12 version suffix in artifact name).
Cowardly refusing to move to Scala 2.12 a second time...
+ set -e
+ '[' 3.0.1 == 2.4.7 ']'
+ '[' 3.0.1 == 3.0.1 ']'
+ echo 'Moving build to Spark 3.x...'
Moving build to Spark 3.x...
+ set +e
+ /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/scripts/move_to_spark_3.sh
POM is already set up for Spark 3 (Spark 3 artifacts have -spark3 suffix in artifact names).
Cowardly refusing to move to Spark 3 a second time...
+ set -e
+ 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