Console Output

Started by upstream project "cannoli" build number 2219
originally caused by:
 Started by timer
Running as SYSTEM
[EnvInject] - Loading node environment variables.
Building remotely on research-jenkins-worker-02 (ubuntu20 worker-02 ubuntu) in workspace /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu
The recommended git tool is: NONE
No credentials specified
Cloning the remote Git repository
Cloning repository https://github.com/bigdatagenomics/cannoli.git
 > git init /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu # timeout=10
Fetching upstream changes from https://github.com/bigdatagenomics/cannoli.git
 > git --version # timeout=10
 > git --version # 'git version 2.25.1'
 > git fetch --tags --force --progress -- https://github.com/bigdatagenomics/cannoli.git +refs/heads/*:refs/remotes/origin/* # timeout=10
 > git config remote.origin.url https://github.com/bigdatagenomics/cannoli.git # timeout=10
 > git config --add remote.origin.fetch +refs/heads/*:refs/remotes/origin/* # timeout=10
Avoid second fetch
Checking out Revision 211e500289ff9ec1f6fe07f7f56c4857406df505 (refs/remotes/origin/master)
 > git config core.sparsecheckout # timeout=10
 > git checkout -f 211e500289ff9ec1f6fe07f7f56c4857406df505 # timeout=10
Commit message: "Update default container images for bcftools and samtools to 1.12."
 > git rev-list --no-walk 211e500289ff9ec1f6fe07f7f56c4857406df505 # 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/jenkins8375013758003086055.sh
+ set -e
+ unset SPARK_TESTING
+ export JAVA_HOME=/usr/java/latest
+ JAVA_HOME=/usr/java/latest
+ export CONDA_BIN=/home/anaconda/bin/
+ CONDA_BIN=/home/anaconda/bin/
+ export PATH=/usr/java/latest/bin/:/home/anaconda/bin/:/home/jenkins/tools/hudson.tasks.Maven_MavenInstallation/Maven_3.6.3/bin/:/home/jenkins/gems/bin:/usr/local/go/bin:/home/jenkins/go-projects/bin:/home/jenkins/anaconda2/bin:/home/jenkins/tools/hudson.tasks.Maven_MavenInstallation/Maven_3.6.3/bin/:/home/jenkins/gems/bin:/usr/local/go/bin:/home/jenkins/go-projects/bin:/home/jenkins/anaconda2/bin:/home/jenkins/tools/hudson.tasks.Maven_MavenInstallation/Maven_3.6.3/bin/:/home/jenkins/gems/bin:/usr/local/go/bin:/home/jenkins/go-projects/bin:/home/jenkins/anaconda2/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin
+ PATH=/usr/java/latest/bin/:/home/anaconda/bin/:/home/jenkins/tools/hudson.tasks.Maven_MavenInstallation/Maven_3.6.3/bin/:/home/jenkins/gems/bin:/usr/local/go/bin:/home/jenkins/go-projects/bin:/home/jenkins/anaconda2/bin:/home/jenkins/tools/hudson.tasks.Maven_MavenInstallation/Maven_3.6.3/bin/:/home/jenkins/gems/bin:/usr/local/go/bin:/home/jenkins/go-projects/bin:/home/jenkins/anaconda2/bin:/home/jenkins/tools/hudson.tasks.Maven_MavenInstallation/Maven_3.6.3/bin/:/home/jenkins/gems/bin:/usr/local/go/bin:/home/jenkins/go-projects/bin:/home/jenkins/anaconda2/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin
+ /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/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
+ CANNOLI_MVN_TMP_DIR=/tmp/cannoliTestMvnJHnfimN

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

# variable declarations
export PATH=${JAVA_HOME}/bin/:${PATH}
+ export PATH=/usr/java/latest/bin/:/usr/java/latest/bin/:/home/anaconda/bin/:/home/jenkins/tools/hudson.tasks.Maven_MavenInstallation/Maven_3.6.3/bin/:/home/jenkins/gems/bin:/usr/local/go/bin:/home/jenkins/go-projects/bin:/home/jenkins/anaconda2/bin:/home/jenkins/tools/hudson.tasks.Maven_MavenInstallation/Maven_3.6.3/bin/:/home/jenkins/gems/bin:/usr/local/go/bin:/home/jenkins/go-projects/bin:/home/jenkins/anaconda2/bin:/home/jenkins/tools/hudson.tasks.Maven_MavenInstallation/Maven_3.6.3/bin/:/home/jenkins/gems/bin:/usr/local/go/bin:/home/jenkins/go-projects/bin:/home/jenkins/anaconda2/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin
+ PATH=/usr/java/latest/bin/:/usr/java/latest/bin/:/home/anaconda/bin/:/home/jenkins/tools/hudson.tasks.Maven_MavenInstallation/Maven_3.6.3/bin/:/home/jenkins/gems/bin:/usr/local/go/bin:/home/jenkins/go-projects/bin:/home/jenkins/anaconda2/bin:/home/jenkins/tools/hudson.tasks.Maven_MavenInstallation/Maven_3.6.3/bin/:/home/jenkins/gems/bin:/usr/local/go/bin:/home/jenkins/go-projects/bin:/home/jenkins/anaconda2/bin:/home/jenkins/tools/hudson.tasks.Maven_MavenInstallation/Maven_3.6.3/bin/:/home/jenkins/gems/bin:/usr/local/go/bin:/home/jenkins/go-projects/bin:/home/jenkins/anaconda2/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin
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 ${BASH_SOURCE[0]} ) && pwd )
+++ dirname /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/scripts/jenkins-test
++ cd /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/scripts
++ pwd
+ DIR=/home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/scripts
PROJECT_ROOT=${DIR}/..
+ PROJECT_ROOT=/home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/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>' /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/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=0.13.0-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 3.2.1 ]]

# 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 0.13.0-SNAPSHOT on Spark 3.0.1 Scala 2.12 and Hadoop 3.2.1'
Testing Cannoli version 0.13.0-SNAPSHOT on Spark 3.0.1 Scala 2.12 and Hadoop 3.2.1

# build the distribution package and the integration tests
mvn -U \
    clean \
    package \
    -Dhadoop.version=${HADOOP_VERSION}
+ mvn -U clean package -Dhadoop.version=3.2.1
OpenJDK 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 0.13.0-SNAPSHOT                              [1/5]
[INFO] --------------------------------[ pom ]---------------------------------
[INFO] 
[INFO] --- maven-clean-plugin:3.1.0:clean (default-clean) @ cannoli-parent-spark3_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-maven) @ cannoli-parent-spark3_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-java) @ cannoli-parent-spark3_2.12 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ cannoli-parent-spark3_2.12 ---
[INFO] Source directory: /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/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 56 .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/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/src/test/scala added.
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ cannoli-parent-spark3_2.12 ---
[INFO] No sources to compile
[INFO] 
[INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-javadocs) > generate-sources @ cannoli-parent-spark3_2.12 >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-maven) @ cannoli-parent-spark3_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-java) @ cannoli-parent-spark3_2.12 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ cannoli-parent-spark3_2.12 ---
[INFO] Source directory: /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/src/main/scala added.
[INFO] 
[INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-javadocs) < generate-sources @ cannoli-parent-spark3_2.12 <<<
[INFO] 
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-javadocs) @ cannoli-parent-spark3_2.12 ---
[INFO] No source files found
[INFO] 
[INFO] ---------< org.bdgenomics.cannoli:cannoli-builder-spark3_2.12 >---------
[INFO] Building Cannoli_2.12: Builder 0.13.0-SNAPSHOT                     [2/5]
[INFO] --------------------------------[ jar ]---------------------------------
Downloading from central: https://repo.maven.apache.org/maven2/com/google/guava/guava/27.0.1-jre/guava-27.0.1-jre.pom
Progress (1): 2.7/8.3 kB
Progress (1): 5.5/8.3 kB
Progress (1): 8.2/8.3 kB
Progress (1): 8.3 kB    
                    
Downloaded from central: https://repo.maven.apache.org/maven2/com/google/guava/guava/27.0.1-jre/guava-27.0.1-jre.pom (8.3 kB at 21 kB/s)
Downloading from central: https://repo.maven.apache.org/maven2/com/google/guava/guava-parent/27.0.1-jre/guava-parent-27.0.1-jre.pom
Progress (1): 2.7/10 kB
Progress (1): 5.5/10 kB
Progress (1): 8.2/10 kB
Progress (1): 10 kB    
                   
Downloaded from central: https://repo.maven.apache.org/maven2/com/google/guava/guava-parent/27.0.1-jre/guava-parent-27.0.1-jre.pom (10 kB at 650 kB/s)
Downloading from central: https://repo.maven.apache.org/maven2/com/google/guava/guava/27.0.1-jre/guava-27.0.1-jre.jar
Progress (1): 0/2.7 MB
Progress (1): 0/2.7 MB
Progress (1): 0/2.7 MB
Progress (1): 0/2.7 MB
Progress (1): 0.1/2.7 MB
Progress (1): 0.1/2.7 MB
Progress (1): 0.1/2.7 MB
Progress (1): 0.1/2.7 MB
Progress (1): 0.1/2.7 MB
Progress (1): 0.1/2.7 MB
Progress (1): 0.1/2.7 MB
Progress (1): 0.1/2.7 MB
Progress (1): 0.2/2.7 MB
Progress (1): 0.2/2.7 MB
Progress (1): 0.2/2.7 MB
Progress (1): 0.2/2.7 MB
Progress (1): 0.2/2.7 MB
Progress (1): 0.2/2.7 MB
Progress (1): 0.2/2.7 MB
Progress (1): 0.2/2.7 MB
Progress (1): 0.3/2.7 MB
Progress (1): 0.3/2.7 MB
Progress (1): 0.3/2.7 MB
Progress (1): 0.3/2.7 MB
Progress (1): 0.3/2.7 MB
Progress (1): 0.3/2.7 MB
Progress (1): 0.3/2.7 MB
Progress (1): 0.3/2.7 MB
Progress (1): 0.4/2.7 MB
Progress (1): 0.4/2.7 MB
Progress (1): 0.4/2.7 MB
Progress (1): 0.4/2.7 MB
Progress (1): 0.4/2.7 MB
Progress (1): 0.4/2.7 MB
Progress (1): 0.4/2.7 MB
Progress (1): 0.4/2.7 MB
Progress (1): 0.5/2.7 MB
Progress (1): 0.5/2.7 MB
Progress (1): 0.5/2.7 MB
Progress (1): 0.5/2.7 MB
Progress (1): 0.5/2.7 MB
Progress (1): 0.5/2.7 MB
Progress (1): 0.5/2.7 MB
Progress (1): 0.5/2.7 MB
Progress (1): 0.6/2.7 MB
Progress (1): 0.6/2.7 MB
Progress (1): 0.6/2.7 MB
Progress (1): 0.6/2.7 MB
Progress (1): 0.6/2.7 MB
Progress (1): 0.6/2.7 MB
Progress (1): 0.6/2.7 MB
Progress (1): 0.6/2.7 MB
Progress (1): 0.7/2.7 MB
Progress (1): 0.7/2.7 MB
Progress (1): 0.7/2.7 MB
Progress (1): 0.7/2.7 MB
Progress (1): 0.7/2.7 MB
Progress (1): 0.7/2.7 MB
Progress (1): 0.7/2.7 MB
Progress (1): 0.7/2.7 MB
Progress (1): 0.8/2.7 MB
Progress (1): 0.8/2.7 MB
Progress (1): 0.8/2.7 MB
Progress (1): 0.8/2.7 MB
Progress (1): 0.8/2.7 MB
Progress (1): 0.8/2.7 MB
Progress (1): 0.9/2.7 MB
Progress (1): 0.9/2.7 MB
Progress (1): 0.9/2.7 MB
Progress (1): 0.9/2.7 MB
Progress (1): 0.9/2.7 MB
Progress (1): 0.9/2.7 MB
Progress (1): 1.0/2.7 MB
Progress (1): 1.0/2.7 MB
Progress (1): 1.0/2.7 MB
Progress (1): 1.0/2.7 MB
Progress (1): 1.0/2.7 MB
Progress (1): 1.0/2.7 MB
Progress (1): 1.1/2.7 MB
Progress (1): 1.1/2.7 MB
Progress (1): 1.1/2.7 MB
Progress (1): 1.1/2.7 MB
Progress (1): 1.1/2.7 MB
Progress (1): 1.1/2.7 MB
Progress (1): 1.2/2.7 MB
Progress (1): 1.2/2.7 MB
Progress (1): 1.2/2.7 MB
Progress (1): 1.2/2.7 MB
Progress (1): 1.2/2.7 MB
Progress (1): 1.2/2.7 MB
Progress (1): 1.3/2.7 MB
Progress (1): 1.3/2.7 MB
Progress (1): 1.3/2.7 MB
Progress (1): 1.3/2.7 MB
Progress (1): 1.3/2.7 MB
Progress (1): 1.3/2.7 MB
Progress (1): 1.3/2.7 MB
Progress (1): 1.4/2.7 MB
Progress (1): 1.4/2.7 MB
Progress (1): 1.4/2.7 MB
Progress (1): 1.4/2.7 MB
Progress (1): 1.4/2.7 MB
Progress (1): 1.4/2.7 MB
Progress (1): 1.5/2.7 MB
Progress (1): 1.5/2.7 MB
Progress (1): 1.5/2.7 MB
Progress (1): 1.5/2.7 MB
Progress (1): 1.5/2.7 MB
Progress (1): 1.5/2.7 MB
Progress (1): 1.6/2.7 MB
Progress (1): 1.6/2.7 MB
Progress (1): 1.6/2.7 MB
Progress (1): 1.6/2.7 MB
Progress (1): 1.6/2.7 MB
Progress (1): 1.6/2.7 MB
Progress (1): 1.7/2.7 MB
Progress (1): 1.7/2.7 MB
Progress (1): 1.7/2.7 MB
Progress (1): 1.7/2.7 MB
Progress (1): 1.7/2.7 MB
Progress (1): 1.7/2.7 MB
Progress (1): 1.8/2.7 MB
Progress (1): 1.8/2.7 MB
Progress (1): 1.8/2.7 MB
Progress (1): 1.8/2.7 MB
Progress (1): 1.8/2.7 MB
Progress (1): 1.8/2.7 MB
Progress (1): 1.9/2.7 MB
Progress (1): 1.9/2.7 MB
Progress (1): 1.9/2.7 MB
Progress (1): 1.9/2.7 MB
Progress (1): 1.9/2.7 MB
Progress (1): 1.9/2.7 MB
Progress (1): 1.9/2.7 MB
Progress (1): 2.0/2.7 MB
Progress (1): 2.0/2.7 MB
Progress (1): 2.0/2.7 MB
Progress (1): 2.0/2.7 MB
Progress (1): 2.0/2.7 MB
Progress (1): 2.0/2.7 MB
Progress (1): 2.1/2.7 MB
Progress (1): 2.1/2.7 MB
Progress (1): 2.1/2.7 MB
Progress (1): 2.1/2.7 MB
Progress (1): 2.1/2.7 MB
Progress (1): 2.1/2.7 MB
Progress (1): 2.2/2.7 MB
Progress (1): 2.2/2.7 MB
Progress (1): 2.2/2.7 MB
Progress (1): 2.2/2.7 MB
Progress (1): 2.2/2.7 MB
Progress (1): 2.2/2.7 MB
Progress (1): 2.3/2.7 MB
Progress (1): 2.3/2.7 MB
Progress (1): 2.3/2.7 MB
Progress (1): 2.3/2.7 MB
Progress (1): 2.3/2.7 MB
Progress (1): 2.3/2.7 MB
Progress (1): 2.4/2.7 MB
Progress (1): 2.4/2.7 MB
Progress (1): 2.4/2.7 MB
Progress (1): 2.4/2.7 MB
Progress (1): 2.4/2.7 MB
Progress (1): 2.4/2.7 MB
Progress (1): 2.5/2.7 MB
Progress (1): 2.5/2.7 MB
Progress (1): 2.5/2.7 MB
Progress (1): 2.5/2.7 MB
Progress (1): 2.5/2.7 MB
Progress (1): 2.5/2.7 MB
Progress (1): 2.5/2.7 MB
Progress (1): 2.6/2.7 MB
Progress (1): 2.6/2.7 MB
Progress (1): 2.6/2.7 MB
Progress (1): 2.6/2.7 MB
Progress (1): 2.6/2.7 MB
Progress (1): 2.6/2.7 MB
Progress (1): 2.7/2.7 MB
Progress (1): 2.7/2.7 MB
Progress (1): 2.7/2.7 MB
Progress (1): 2.7/2.7 MB
Progress (1): 2.7/2.7 MB
Progress (1): 2.7/2.7 MB
Progress (1): 2.7 MB    
                    
Downloaded from central: https://repo.maven.apache.org/maven2/com/google/guava/guava/27.0.1-jre/guava-27.0.1-jre.jar (2.7 MB at 13 MB/s)
[INFO] 
[INFO] --- maven-clean-plugin:3.1.0:clean (default-clean) @ cannoli-builder-spark3_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-maven) @ cannoli-builder-spark3_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-java) @ cannoli-builder-spark3_2.12 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ cannoli-builder-spark3_2.12 ---
[INFO] Source directory: /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/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/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/builder/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ cannoli-builder-spark3_2.12 ---
[WARNING]  Expected all dependencies to require Scala version: 2.12.10
[WARNING]  org.bdgenomics.utils:utils-misc-spark3_2.12:0.3.0 requires scala version: 2.12.8
[WARNING] Multiple versions of scala libraries detected!
[INFO] /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/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/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/builder/target/scala-2.12.10/classes at 1617332203264
[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/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/builder/target/scala-2.12.10/classes
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ cannoli-builder-spark3_2.12 ---
[INFO] Test Source directory: /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/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/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/builder/src/test/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ cannoli-builder-spark3_2.12 ---
[WARNING]  Expected all dependencies to require Scala version: 2.12.10
[WARNING]  org.bdgenomics.utils:utils-misc-spark3_2.12:0.3.0 requires scala version: 2.12.8
[WARNING] Multiple versions of scala libraries detected!
[INFO] /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/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/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/builder/target/scala-2.12.10/test-classes at 1617332206628
[INFO] prepare-compile in 0 s
[INFO] compile in 2 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ cannoli-builder-spark3_2.12 ---
[INFO] Changes detected - recompiling the module!
[INFO] Compiling 4 source files to /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/builder/target/scala-2.12.10/test-classes
[INFO] 
[INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ cannoli-builder-spark3_2.12 ---
[INFO] 
[INFO] -------------------------------------------------------
[INFO]  T E S T S
[INFO] -------------------------------------------------------
[INFO] Running org.bdgenomics.cannoli.builder.CommandBuildersTest
[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.062 s - in org.bdgenomics.cannoli.builder.CommandBuildersTest
[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.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.LocalBuilderTest
[INFO] Tests run: 18, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.bdgenomics.cannoli.builder.LocalBuilderTest
[INFO] 
[INFO] Results:
[INFO] 
[INFO] Tests run: 40, Failures: 0, Errors: 0, Skipped: 0
[INFO] 
[INFO] 
[INFO] --- maven-jar-plugin:3.1.2:jar (default-jar) @ cannoli-builder-spark3_2.12 ---
[INFO] Building jar: /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/builder/target/cannoli-builder-spark3_2.12-0.13.0-SNAPSHOT.jar
[INFO] 
[INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-javadocs) > generate-sources @ cannoli-builder-spark3_2.12 >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-maven) @ cannoli-builder-spark3_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-java) @ cannoli-builder-spark3_2.12 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ cannoli-builder-spark3_2.12 ---
[INFO] Source directory: /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/builder/src/main/scala added.
[INFO] 
[INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-javadocs) < generate-sources @ cannoli-builder-spark3_2.12 <<<
[INFO] 
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-javadocs) @ cannoli-builder-spark3_2.12 ---
[WARNING]  Expected all dependencies to require Scala version: 2.12.10
[WARNING]  org.bdgenomics.utils:utils-misc-spark3_2.12:0.3.0 requires scala version: 2.12.8
[WARNING] Multiple versions of scala libraries detected!
[WARNING]  Expected all dependencies to require Scala version: 2.12.10
[WARNING]  org.bdgenomics.utils:utils-misc-spark3_2.12:0.3.0 requires scala version: 2.12.8
[WARNING] Multiple versions of scala libraries detected!
model contains 10 documentable templates
/home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/builder/src/main/java/org/bdgenomics/cannoli/builder/CommandBuilder.java:449: warning: Could not find any member to link for "IllegalStateException".
    /**
    ^
one warning found
[INFO] Building jar: /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/builder/target/cannoli-builder-spark3_2.12-0.13.0-SNAPSHOT-javadoc.jar
[INFO] 
[INFO] ----------< org.bdgenomics.cannoli:cannoli-core-spark3_2.12 >-----------
[INFO] Building Cannoli_2.12: Core 0.13.0-SNAPSHOT                        [3/5]
[INFO] --------------------------------[ jar ]---------------------------------
[INFO] 
[INFO] --- maven-clean-plugin:3.1.0:clean (default-clean) @ cannoli-core-spark3_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-maven) @ cannoli-core-spark3_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-java) @ cannoli-core-spark3_2.12 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ cannoli-core-spark3_2.12 ---
[INFO] Source directory: /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/core/src/main/scala added.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ cannoli-core-spark3_2.12 ---
[INFO] Modified 0 of 28 .scala files
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ cannoli-core-spark3_2.12 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/core/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ cannoli-core-spark3_2.12 ---
[WARNING]  Expected all dependencies to require Scala version: 2.12.10
[WARNING]  com.twitter:chill_2.12:0.9.5 requires scala version: 2.12.10
[WARNING]  org.apache.spark:spark-network-common_2.12:3.0.2 requires scala version: 2.12.10
[WARNING]  org.scala-lang.modules:scala-xml_2.12:1.2.0 requires scala version: 2.12.8
[WARNING] Multiple versions of scala libraries detected!
[INFO] /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/core/src/main/scala:-1: info: compiling
[INFO] Compiling 27 source files to /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/core/target/scala-2.12.10/classes at 1617332216444
[WARNING] /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/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/3.2.1/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/3.2.1/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/3.2.1/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/3.2.1/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/3.2.1/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/3.2.1/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/3.2.1/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/3.2.1/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/3.2.1/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/3.2.1/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/3.2.1/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/3.2.1/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/3.2.1/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/3.2.1/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/3.2.1/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/3.2.1/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/3.2.1/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/3.2.1/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/3.2.1/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/3.2.1/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/3.2.1/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/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/core/src/main/scala/org/bdgenomics/cannoli/CannoliFn.scala:76: warning: method isDirectory in class FileSystem is deprecated: see corresponding Javadoc for more information.
[WARNING]     val paths = if (fs.isDirectory(path)) {
[WARNING]                        ^
[WARNING] /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/core/src/main/scala/org/bdgenomics/cannoli/Freebayes.scala:115: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       cmd = builder.build(),
[WARNING]                          ^
[WARNING] /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/core/src/main/scala/org/bdgenomics/cannoli/Freebayes.scala:116: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       files = builder.getFiles()
[WARNING]                               ^
[WARNING] /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/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/3.2.1/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/3.2.1/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/3.2.1/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/3.2.1/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/3.2.1/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/3.2.1/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/3.2.1/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/3.2.1/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/3.2.1/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/3.2.1/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/3.2.1/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/3.2.1/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/3.2.1/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/3.2.1/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/3.2.1/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/3.2.1/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/3.2.1/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/3.2.1/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/3.2.1/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/3.2.1/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/3.2.1/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/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/core/src/main/scala/org/bdgenomics/cannoli/Vep.scala:119: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       cmd = builder.build(),
[WARNING]                          ^
[WARNING] /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/core/src/main/scala/org/bdgenomics/cannoli/Vep.scala:120: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       files = builder.getFiles()
[WARNING]                               ^
[WARNING] /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/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/3.2.1/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/3.2.1/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 10 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/3.2.1/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/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/core/src/test/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ cannoli-core-spark3_2.12 ---
[WARNING]  Expected all dependencies to require Scala version: 2.12.10
[WARNING]  com.twitter:chill_2.12:0.9.5 requires scala version: 2.12.10
[WARNING]  org.apache.spark:spark-network-common_2.12:3.0.2 requires scala version: 2.12.10
[WARNING]  org.scala-lang.modules:scala-xml_2.12:1.2.0 requires scala version: 2.12.8
[WARNING] Multiple versions of scala libraries detected!
[INFO] /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/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/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/core/target/scala-2.12.10/test-classes at 1617332227143
[WARNING] /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/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/3.2.1/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 4 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 215 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 824 milliseconds.
Total number of tests run: 3
Suites: completed 2, aborted 0
Tests: succeeded 3, failed 0, canceled 0, ignored 0, pending 0
All tests passed.
[INFO] 
[INFO] --- maven-jar-plugin:3.1.2:jar (default-jar) @ cannoli-core-spark3_2.12 ---
[INFO] Building jar: /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/core/target/cannoli-core-spark3_2.12-0.13.0-SNAPSHOT.jar
[INFO] 
[INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-javadocs) > generate-sources @ cannoli-core-spark3_2.12 >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-maven) @ cannoli-core-spark3_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-java) @ cannoli-core-spark3_2.12 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ cannoli-core-spark3_2.12 ---
[INFO] Source directory: /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/core/src/main/scala added.
[INFO] 
[INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-javadocs) < generate-sources @ cannoli-core-spark3_2.12 <<<
[INFO] 
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-javadocs) @ cannoli-core-spark3_2.12 ---
[WARNING]  Expected all dependencies to require Scala version: 2.12.10
[WARNING]  com.twitter:chill_2.12:0.9.5 requires scala version: 2.12.10
[WARNING]  org.apache.spark:spark-network-common_2.12:3.0.2 requires scala version: 2.12.10
[WARNING]  org.scala-lang.modules:scala-xml_2.12:1.2.0 requires scala version: 2.12.8
[WARNING] Multiple versions of scala libraries detected!
[WARNING]  Expected all dependencies to require Scala version: 2.12.10
[WARNING]  com.twitter:chill_2.12:0.9.5 requires scala version: 2.12.10
[WARNING]  org.apache.spark:spark-network-common_2.12:3.0.2 requires scala version: 2.12.10
[WARNING]  org.scala-lang.modules:scala-xml_2.12:1.2.0 requires scala version: 2.12.8
[WARNING] Multiple versions of scala libraries detected!
model contains 54 documentable templates
[INFO] Building jar: /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/core/target/cannoli-core-spark3_2.12-0.13.0-SNAPSHOT-javadoc.jar
[INFO] 
[INFO] -----------< org.bdgenomics.cannoli:cannoli-cli-spark3_2.12 >-----------
[INFO] Building Cannoli_2.12: CLI 0.13.0-SNAPSHOT                         [4/5]
[INFO] --------------------------------[ jar ]---------------------------------
[INFO] 
[INFO] --- maven-clean-plugin:3.1.0:clean (default-clean) @ cannoli-cli-spark3_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-maven) @ cannoli-cli-spark3_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-java) @ cannoli-cli-spark3_2.12 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:timestamp-property (timestamp-property) @ cannoli-cli-spark3_2.12 ---
[INFO] 
[INFO] --- git-commit-id-plugin:2.2.2:revision (default) @ cannoli-cli-spark3_2.12 ---
[INFO] 
[INFO] --- templating-maven-plugin:1.0.0:filter-sources (filter-src) @ cannoli-cli-spark3_2.12 ---
[INFO] Coping files with filtering to temporary directory.
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 1 resource
[INFO] Copied 1 files to output directory: /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/cli/target/generated-sources/java-templates
[INFO] Source directory: /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/cli/target/generated-sources/java-templates added.
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ cannoli-cli-spark3_2.12 ---
[INFO] Source directory: /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/cli/src/main/scala added.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ cannoli-cli-spark3_2.12 ---
[INFO] Modified 0 of 27 .scala files
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ cannoli-cli-spark3_2.12 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/cli/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ cannoli-cli-spark3_2.12 ---
[WARNING]  Expected all dependencies to require Scala version: 2.12.10
[WARNING]  com.twitter:chill_2.12:0.9.5 requires scala version: 2.12.10
[WARNING]  org.apache.spark:spark-network-common_2.12:3.0.2 requires scala version: 2.12.10
[WARNING]  org.scala-lang.modules:scala-xml_2.12:1.2.0 requires scala version: 2.12.8
[WARNING] Multiple versions of scala libraries detected!
[INFO] /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/cli/target/generated-sources/java-templates:-1: info: compiling
[INFO] /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/cli/src/main/scala:-1: info: compiling
[INFO] Compiling 26 source files to /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/cli/target/scala-2.12.10/classes at 1617332247243
[WARNING] /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/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/3.2.1/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 8 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/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/cli/target/scala-2.12.10/classes
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ cannoli-cli-spark3_2.12 ---
[INFO] Test Source directory: /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/cli/src/test/scala added.
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ cannoli-cli-spark3_2.12 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 5 resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ cannoli-cli-spark3_2.12 ---
[WARNING]  Expected all dependencies to require Scala version: 2.12.10
[WARNING]  com.twitter:chill_2.12:0.9.5 requires scala version: 2.12.10
[WARNING]  org.apache.spark:spark-network-common_2.12:3.0.2 requires scala version: 2.12.10
[WARNING]  org.scala-lang.modules:scala-xml_2.12:1.2.0 requires scala version: 2.12.8
[WARNING] Multiple versions of scala libraries detected!
[INFO] /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/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/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/cli/target/scala-2.12.10/test-classes at 1617332256788
[WARNING] /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/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 7 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 284 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
InterleaveFastqSuite:
2021-04-01 19:57:48 WARN  Utils:69 - Your hostname, research-jenkins-worker-02 resolves to a loopback address: 127.0.1.1; using 192.168.122.1 instead (on interface virbr0)
2021-04-01 19:57:48 WARN  Utils:69 - Set SPARK_LOCAL_IP if you need to bind to another address
2021-04-01 19:57:48 WARN  NativeCodeLoader:60 - 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 8 seconds, 877 milliseconds.
Total number of tests run: 12
Suites: completed 3, aborted 0
Tests: succeeded 12, failed 0, canceled 0, ignored 0, pending 0
All tests passed.
[INFO] 
[INFO] --- maven-jar-plugin:3.1.2:jar (default-jar) @ cannoli-cli-spark3_2.12 ---
[INFO] Building jar: /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/cli/target/cannoli-cli-spark3_2.12-0.13.0-SNAPSHOT.jar
[INFO] 
[INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-javadocs) > generate-sources @ cannoli-cli-spark3_2.12 >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-maven) @ cannoli-cli-spark3_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-java) @ cannoli-cli-spark3_2.12 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:timestamp-property (timestamp-property) @ cannoli-cli-spark3_2.12 ---
[INFO] 
[INFO] --- git-commit-id-plugin:2.2.2:revision (default) @ cannoli-cli-spark3_2.12 ---
[INFO] 
[INFO] --- templating-maven-plugin:1.0.0:filter-sources (filter-src) @ cannoli-cli-spark3_2.12 ---
[INFO] Coping files with filtering to temporary directory.
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 1 resource
[INFO] No files needs to be copied to output directory. Up to date: /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/cli/target/generated-sources/java-templates
[INFO] Source directory: /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/cli/target/generated-sources/java-templates added.
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ cannoli-cli-spark3_2.12 ---
[INFO] Source directory: /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/cli/src/main/scala added.
[INFO] 
[INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-javadocs) < generate-sources @ cannoli-cli-spark3_2.12 <<<
[INFO] 
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-javadocs) @ cannoli-cli-spark3_2.12 ---
[WARNING]  Expected all dependencies to require Scala version: 2.12.10
[WARNING]  com.twitter:chill_2.12:0.9.5 requires scala version: 2.12.10
[WARNING]  org.apache.spark:spark-network-common_2.12:3.0.2 requires scala version: 2.12.10
[WARNING]  org.scala-lang.modules:scala-xml_2.12:1.2.0 requires scala version: 2.12.8
[WARNING] Multiple versions of scala libraries detected!
[WARNING]  Expected all dependencies to require Scala version: 2.12.10
[WARNING]  com.twitter:chill_2.12:0.9.5 requires scala version: 2.12.10
[WARNING]  org.apache.spark:spark-network-common_2.12:3.0.2 requires scala version: 2.12.10
[WARNING]  org.scala-lang.modules:scala-xml_2.12:1.2.0 requires scala version: 2.12.8
[WARNING] Multiple versions of scala libraries detected!
model contains 78 documentable templates
[INFO] Building jar: /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/cli/target/cannoli-cli-spark3_2.12-0.13.0-SNAPSHOT-javadoc.jar
[INFO] 
[INFO] --------< org.bdgenomics.cannoli:cannoli-assembly-spark3_2.12 >---------
[INFO] Building Cannoli_2.12: Assembly 0.13.0-SNAPSHOT                    [5/5]
[INFO] --------------------------------[ jar ]---------------------------------
[INFO] 
[INFO] --- maven-clean-plugin:3.1.0:clean (default-clean) @ cannoli-assembly-spark3_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-maven) @ cannoli-assembly-spark3_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-java) @ cannoli-assembly-spark3_2.12 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ cannoli-assembly-spark3_2.12 ---
[INFO] Source directory: /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/assembly/src/main/scala added.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ cannoli-assembly-spark3_2.12 ---
[INFO] Modified 0 of 1 .scala files
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ cannoli-assembly-spark3_2.12 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/assembly/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ cannoli-assembly-spark3_2.12 ---
[WARNING]  Expected all dependencies to require Scala version: 2.12.10
[WARNING]  org.bdgenomics.utils:utils-misc-spark3_2.12:0.3.0 requires scala version: 2.12.8
[WARNING] Multiple versions of scala libraries detected!
[INFO] /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/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/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/assembly/target/scala-2.12.10/classes at 1617332286324
[INFO] prepare-compile in 0 s
[INFO] compile in 3 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/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/assembly/src/test/scala added.
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ cannoli-assembly-spark3_2.12 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/assembly/src/test/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ cannoli-assembly-spark3_2.12 ---
[WARNING]  Expected all dependencies to require Scala version: 2.12.10
[WARNING]  org.bdgenomics.utils:utils-misc-spark3_2.12:0.3.0 requires scala version: 2.12.8
[WARNING] Multiple versions of scala libraries detected!
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ cannoli-assembly-spark3_2.12 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ cannoli-assembly-spark3_2.12 ---
[INFO] No tests to run.
[INFO] 
[INFO] --- maven-jar-plugin:3.1.2:jar (default-jar) @ cannoli-assembly-spark3_2.12 ---
[INFO] Building jar: /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/assembly/target/cannoli-assembly-spark3_2.12-0.13.0-SNAPSHOT.jar
[INFO] 
[INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-javadocs) > generate-sources @ cannoli-assembly-spark3_2.12 >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-maven) @ cannoli-assembly-spark3_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-java) @ cannoli-assembly-spark3_2.12 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ cannoli-assembly-spark3_2.12 ---
[INFO] Source directory: /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/assembly/src/main/scala added.
[INFO] 
[INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-javadocs) < generate-sources @ cannoli-assembly-spark3_2.12 <<<
[INFO] 
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-javadocs) @ cannoli-assembly-spark3_2.12 ---
[WARNING]  Expected all dependencies to require Scala version: 2.12.10
[WARNING]  org.bdgenomics.utils:utils-misc-spark3_2.12:0.3.0 requires scala version: 2.12.8
[WARNING] Multiple versions of scala libraries detected!
[WARNING]  Expected all dependencies to require Scala version: 2.12.10
[WARNING]  org.bdgenomics.utils:utils-misc-spark3_2.12:0.3.0 requires scala version: 2.12.8
[WARNING] Multiple versions of scala libraries detected!
model contains 6 documentable templates
[INFO] Building jar: /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/assembly/target/cannoli-assembly-spark3_2.12-0.13.0-SNAPSHOT-javadoc.jar
[INFO] 
[INFO] --- maven-shade-plugin:3.2.0:shade (default) @ cannoli-assembly-spark3_2.12 ---
[INFO] Including org.bdgenomics.cannoli:cannoli-cli-spark3_2.12:jar:0.13.0-SNAPSHOT in the shaded jar.
[INFO] Including org.bdgenomics.adam:adam-cli-spark3_2.12:jar:0.34.0 in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-misc-spark3_2.12:jar:0.3.0 in the shaded jar.
[INFO] Including org.scala-lang:scala-library:jar:2.12.8 in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-io-spark3_2.12:jar:0.3.0 in the shaded jar.
[INFO] Including org.apache.httpcomponents:httpclient:jar:4.5.7 in the shaded jar.
[INFO] Including org.apache.httpcomponents:httpcore:jar:4.4.11 in the shaded jar.
[INFO] Including commons-logging:commons-logging:jar:1.2 in the shaded jar.
[INFO] Including commons-codec:commons-codec:jar:1.11 in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-cli-spark3_2.12:jar:0.3.0 in the shaded jar.
[INFO] Including org.clapper:grizzled-slf4j_2.12:jar:1.3.4 in the shaded jar.
[INFO] Including org.slf4j:slf4j-api:jar:1.7.9 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-avro:jar:1.10.1 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-column:jar:1.10.1 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-common:jar:1.10.1 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-encoding:jar:1.10.1 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-hadoop:jar:1.10.1 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-jackson:jar:1.10.1 in the shaded jar.
[INFO] Including commons-pool:commons-pool:jar:1.6 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-format:jar:2.4.0 in the shaded jar.
[INFO] Including org.bdgenomics.bdg-formats:bdg-formats:jar:0.15.0 in the shaded jar.
[INFO] Including org.apache.avro:avro:jar:1.8.2 in the shaded jar.
[INFO] Including org.codehaus.jackson:jackson-core-asl:jar:1.9.13 in the shaded jar.
[INFO] Including org.codehaus.jackson:jackson-mapper-asl:jar:1.9.13 in the shaded jar.
[INFO] Including com.thoughtworks.paranamer:paranamer:jar:2.7 in the shaded jar.
[INFO] Including org.xerial.snappy:snappy-java:jar:1.1.1.3 in the shaded jar.
[INFO] Including org.apache.commons:commons-compress:jar:1.8.1 in the shaded jar.
[INFO] Including org.tukaani:xz:jar:1.5 in the shaded jar.
[INFO] Including org.bdgenomics.adam:adam-core-spark3_2.12:jar:0.34.0 in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-intervalrdd-spark3_2.12:jar:0.3.0 in the shaded jar.
[INFO] Including com.esotericsoftware.kryo:kryo:jar:2.24.0 in the shaded jar.
[INFO] Including com.esotericsoftware.minlog:minlog:jar:1.2 in the shaded jar.
[INFO] Including org.objenesis:objenesis:jar:2.1 in the shaded jar.
[INFO] Including commons-io:commons-io:jar:2.6 in the shaded jar.
[INFO] Including it.unimi.dsi:fastutil:jar:6.6.5 in the shaded jar.
[INFO] Including org.seqdoop:hadoop-bam:jar:7.9.2 in the shaded jar.
[INFO] Including com.github.jsr203hadoop:jsr203hadoop:jar:1.0.3 in the shaded jar.
[INFO] Including com.github.samtools:htsjdk:jar:2.19.0 in the shaded jar.
[INFO] Including org.apache.commons:commons-jexl:jar:2.1.1 in the shaded jar.
[INFO] Including gov.nih.nlm.ncbi:ngs-java:jar:2.9.0 in the shaded jar.
[INFO] Including com.google.guava:guava:jar:27.0.1-jre in the shaded jar.
[INFO] Including com.google.guava:failureaccess:jar:1.0.1 in the shaded jar.
[INFO] Including com.google.guava:listenablefuture:jar:9999.0-empty-to-avoid-conflict-with-guava in the shaded jar.
[INFO] Including org.checkerframework:checker-qual:jar:2.5.2 in the shaded jar.
[INFO] Including com.google.errorprone:error_prone_annotations:jar:2.2.0 in the shaded jar.
[INFO] Including com.google.j2objc:j2objc-annotations:jar:1.1 in the shaded jar.
[INFO] Including org.codehaus.mojo:animal-sniffer-annotations:jar:1.17 in the shaded jar.
[INFO] Including org.bdgenomics.adam:adam-codegen-spark3_2.12:jar:0.34.0 in the shaded jar.
[INFO] Including org.bdgenomics.adam:adam-apis-spark3_2.12:jar:0.34.0 in the shaded jar.
[INFO] Including args4j:args4j:jar:2.33 in the shaded jar.
[INFO] Including net.codingwell:scala-guice_2.12:jar:4.2.1 in the shaded jar.
[INFO] Including com.google.inject:guice:jar:4.2.0 in the shaded jar.
[INFO] Including javax.inject:javax.inject:jar:1 in the shaded jar.
[INFO] Including aopalliance:aopalliance:jar:1.0 in the shaded jar.
[INFO] Including org.scala-lang:scala-reflect:jar:2.12.6 in the shaded jar.
[INFO] Including com.google.code.findbugs:jsr305:jar:1.3.9 in the shaded jar.
[INFO] Including org.bdgenomics.cannoli:cannoli-core-spark3_2.12:jar:0.13.0-SNAPSHOT in the shaded jar.
[INFO] Including org.bdgenomics.cannoli:cannoli-builder-spark3_2.12:jar:0.13.0-SNAPSHOT in the shaded jar.
[WARNING] parquet-avro-1.10.1.jar, adam-core-spark3_2.12-0.34.0.jar define 3 overlapping classes: 
[WARNING]   - org.apache.parquet.avro.AvroSchemaConverter$2
[WARNING]   - org.apache.parquet.avro.AvroSchemaConverter
[WARNING]   - org.apache.parquet.avro.AvroSchemaConverter$1
[WARNING] maven-shade-plugin has detected that some class files are
[WARNING] present in two or more JARs. When this happens, only one
[WARNING] single version of the class is copied to the uber jar.
[WARNING] Usually this is not harmful and you can skip these warnings,
[WARNING] otherwise try to manually exclude artifacts based on
[WARNING] mvn dependency:tree -Ddetail=true and the above output.
[WARNING] See http://maven.apache.org/plugins/maven-shade-plugin/
[INFO] Replacing original artifact with shaded artifact.
[INFO] Replacing /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/assembly/target/cannoli-assembly-spark3_2.12-0.13.0-SNAPSHOT.jar with /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/assembly/target/cannoli-assembly-spark3_2.12-0.13.0-SNAPSHOT-shaded.jar
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary for Cannoli_2.12 0.13.0-SNAPSHOT:
[INFO] 
[INFO] Cannoli_2.12 ....................................... SUCCESS [  3.200 s]
[INFO] Cannoli_2.12: Builder .............................. SUCCESS [ 14.179 s]
[INFO] Cannoli_2.12: Core ................................. SUCCESS [ 30.660 s]
[INFO] Cannoli_2.12: CLI .................................. SUCCESS [ 40.541 s]
[INFO] Cannoli_2.12: Assembly ............................. SUCCESS [ 13.374 s]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time:  01:42 min
[INFO] Finished at: 2021-04-01T19:58:19-07:00
[INFO] ------------------------------------------------------------------------

# make verbose again
set -x -v
+ set -x -v

# we are done with maven, so clean up the maven temp dir
find ${CANNOLI_MVN_TMP_DIR}
+ find /tmp/cannoliTestMvnJHnfimN
/tmp/cannoliTestMvnJHnfimN
/tmp/cannoliTestMvnJHnfimN/4832683409755566892
/tmp/cannoliTestMvnJHnfimN/4832683409755566892/.test.ifq.bz2.crc
/tmp/cannoliTestMvnJHnfimN/4832683409755566892/test.ifq.bz2
/tmp/cannoliTestMvnJHnfimN/8399304836192438210
/tmp/cannoliTestMvnJHnfimN/8399304836192438210/.double.ifq.crc
/tmp/cannoliTestMvnJHnfimN/8399304836192438210/double.ifq
/tmp/cannoliTestMvnJHnfimN/8446446006951946579
/tmp/cannoliTestMvnJHnfimN/8446446006951946579/test.ifq
/tmp/cannoliTestMvnJHnfimN/8446446006951946579/.test.ifq.crc
/tmp/cannoliTestMvnJHnfimN/8619261125197707263
/tmp/cannoliTestMvnJHnfimN/8619261125197707263/test.ifq.gz
/tmp/cannoliTestMvnJHnfimN/8619261125197707263/.test.ifq.gz.crc
/tmp/cannoliTestMvnJHnfimN/7654316279718161788
/tmp/cannoliTestMvnJHnfimN/7654316279718161788/test.bam
/tmp/cannoliTestMvnJHnfimN/7654316279718161788/.test.bam.crc
rm -rf ${CANNOLI_MVN_TMP_DIR}
+ rm -rf /tmp/cannoliTestMvnJHnfimN

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/cannoliTestMvnJHnfimN:sun.io.serialization.extendedDebugInfo=true:g' '{}' ';'
find . -name "*.bak" -exec rm -f {} \;
+ find . -name '*.bak' -exec rm -f '{}' ';'

./scripts/format-source
+ ./scripts/format-source
+++ dirname ./scripts/format-source
++ cd ./scripts
++ pwd
+ DIR=/home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/scripts
+ pushd /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/scripts/..
~/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu ~/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu
+ mvn org.scalariform:scalariform-maven-plugin:format license:format
OpenJDK 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 0.13.0-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 56 .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 0.13.0-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 0.13.0-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 28 .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 0.13.0-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 27 .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 0.13.0-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 0.13.0-SNAPSHOT:
[INFO] 
[INFO] Cannoli_2.12 ....................................... SUCCESS [  2.789 s]
[INFO] Cannoli_2.12: Builder .............................. SUCCESS [  0.024 s]
[INFO] Cannoli_2.12: Core ................................. SUCCESS [  0.558 s]
[INFO] Cannoli_2.12: CLI .................................. SUCCESS [  0.364 s]
[INFO] Cannoli_2.12: Assembly ............................. SUCCESS [  0.021 s]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time:  4.018 s
[INFO] Finished at: 2021-04-01T19:58:24-07:00
[INFO] ------------------------------------------------------------------------
+ popd
~/workspace/cannoli/HADOOP_VERSION/3.2.1/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
+ test -n ''

echo
+ echo

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

+ 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
[Checks API] No suitable checks publisher found.
Sending e-mails to: heuermh@gmail.com fnothaft@berkeley.edu
ERROR: Couldn't connect to host, port: 127.0.0.1, 25; timeout 60000
com.sun.mail.util.MailConnectException: Couldn't connect to host, port: 127.0.0.1, 25; timeout 60000;
  nested exception is:
	java.net.ConnectException: Connection refused (Connection refused)
	at com.sun.mail.smtp.SMTPTransport.openServer(SMTPTransport.java:2210)
	at com.sun.mail.smtp.SMTPTransport.protocolConnect(SMTPTransport.java:722)
	at javax.mail.Service.connect(Service.java:342)
	at javax.mail.Service.connect(Service.java:222)
	at javax.mail.Service.connect(Service.java:171)
	at javax.mail.Transport.send0(Transport.java:230)
	at javax.mail.Transport.send(Transport.java:100)
	at hudson.tasks.MailSender.run(MailSender.java:130)
	at hudson.tasks.Mailer.perform(Mailer.java:176)
	at hudson.tasks.Mailer.perform(Mailer.java:139)
	at hudson.tasks.BuildStepMonitor$1.perform(BuildStepMonitor.java:20)
	at hudson.model.AbstractBuild$AbstractBuildExecution.perform(AbstractBuild.java:803)
	at hudson.model.AbstractBuild$AbstractBuildExecution.performAllBuildSteps(AbstractBuild.java:752)
	at hudson.model.Build$BuildExecution.post2(Build.java:177)
	at hudson.model.AbstractBuild$AbstractBuildExecution.post(AbstractBuild.java:697)
	at hudson.model.Run.execute(Run.java:1932)
	at hudson.matrix.MatrixRun.run(MatrixRun.java:153)
	at hudson.model.ResourceController.execute(ResourceController.java:97)
	at hudson.model.Executor.run(Executor.java:429)
Caused by: java.net.ConnectException: Connection refused (Connection refused)
	at java.net.PlainSocketImpl.socketConnect(Native Method)
	at java.net.AbstractPlainSocketImpl.doConnect(AbstractPlainSocketImpl.java:350)
	at java.net.AbstractPlainSocketImpl.connectToAddress(AbstractPlainSocketImpl.java:206)
	at java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:188)
	at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:392)
	at java.net.Socket.connect(Socket.java:607)
	at com.sun.mail.util.SocketFetcher.createSocket(SocketFetcher.java:333)
	at com.sun.mail.util.SocketFetcher.getSocket(SocketFetcher.java:214)
	at com.sun.mail.smtp.SMTPTransport.openServer(SMTPTransport.java:2160)
	... 18 more
Finished: FAILURE