Started by upstream project "ADAM-prb" build number 3030 originally caused by: GitHub pull request #2176 of commit 536e12a15e75359c02fad33787c890fc8234a8ec automatically merged. [EnvInject] - Loading node environment variables. Building remotely on research-jenkins-worker-07 (research-07 ubuntu) in workspace /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu Wiping out workspace first. Cloning the remote Git repository Cloning repository https://github.com/bigdatagenomics/adam.git > git init /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu # timeout=10 Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git --version # timeout=10 > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/heads/*:refs/remotes/origin/* # timeout=15 > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10 > git config --add remote.origin.fetch +refs/heads/*:refs/remotes/origin/* # timeout=10 > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10 Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/*:refs/remotes/origin/pr/* # timeout=15 Checking out Revision dfd674d33e931eca91ff5ebc8a55c88e1478fba5 (origin/pr/2176/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f dfd674d33e931eca91ff5ebc8a55c88e1478fba5 > git rev-list 308d76fe1ef79bd21d7fde4e2e5bb07ee20da913 # timeout=10 First time build. Skipping changelog. [ubuntu] $ /bin/bash /tmp/hudson6753747137758555496.sh + set -e + unset SPARK_TESTING + 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/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/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/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/scripts/jenkins-test # make a tempdir for writing maven cruft to ADAM_MVN_TMP_DIR=$(mktemp -d -t adamTestMvnXXXXXXX) mktemp -d -t adamTestMvnXXXXXXX ++ mktemp -d -t adamTestMvnXXXXXXX + ADAM_MVN_TMP_DIR=/tmp/adamTestMvnJlGqi5R # add this tempdir to the poms... find . -name pom.xml \ -exec sed -i.bak \ -e "s:sun.io.serialization.extendedDebugInfo=true:sun.io.serialization.extendedDebugInfo=true -Djava.io.tmpdir=${ADAM_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/adamTestMvnJlGqi5R: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/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/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 ${BASH_SOURCE[0]} +++ dirname /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/scripts/jenkins-test ++ cd /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/scripts ++ pwd + DIR=/home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/scripts PROJECT_ROOT=${DIR}/.. + PROJECT_ROOT=/home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/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/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/scripts/../pom.xml ++ head -2 ++ tail -1 ++ sed 's/ *<version>//g' ++ sed 's/<\/version>//g' + VERSION=0.28.0-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 spark version set? if ! [[ ${SPARK_VERSION} ]]; then echo "SPARK_VERSION environment variable is not set." echo "Please set this variable before running." exit 1 fi + [[ -n 2.4.3 ]] set -e + set -e # build defaults to Scala 2.11 if [ ${SCALAVER} == 2.11 ]; then # shouldn't be able to move to scala 2.11 twice set +e ./scripts/move_to_scala_2.11.sh if [[ $? == 0 ]]; then echo "We have already moved to Scala 2.11, so running move_to_scala_2.11.sh a second time should fail, but error code was 0 (success)." exit 1 fi set -e fi + '[' 2.12 == 2.11 ']' # move to Scala 2.12 if requested if [ ${SCALAVER} == 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 + set -e # print versions echo "Testing ADAM version ${VERSION} on Spark ${SPARK_VERSION} and Hadoop ${HADOOP_VERSION}" + echo 'Testing ADAM version 0.28.0-SNAPSHOT on Spark 2.4.3 and Hadoop 2.7.5' Testing ADAM version 0.28.0-SNAPSHOT on Spark 2.4.3 and Hadoop 2.7.5 # first, build the sources, run the unit tests, and generate a coverage report mvn clean \ -Dhadoop.version=${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] ADAM_2.12 [INFO] ADAM_2.12: Shader workaround [INFO] ADAM_2.12: Avro-to-Dataset codegen utils [INFO] ADAM_2.12: Core [INFO] ADAM_2.12: APIs for Java, Python [INFO] ADAM_2.12: CLI [INFO] ADAM_2.12: Assembly [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building ADAM_2.12 0.28.0-SNAPSHOT [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-clean-plugin:3.1.0:clean (default-clean) @ adam-parent-spark2_2.12 --- [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building ADAM_2.12: Shader workaround 0.28.0-SNAPSHOT [INFO] ------------------------------------------------------------------------ Downloading: https://repo.maven.apache.org/maven2/org/codehaus/plexus/plexus-component-metadata/1.5.5/plexus-component-metadata-1.5.5.pom 3/4 KB 4/4 KB Downloaded: https://repo.maven.apache.org/maven2/org/codehaus/plexus/plexus-component-metadata/1.5.5/plexus-component-metadata-1.5.5.pom (4 KB at 19.3 KB/sec) Downloading: https://repo.maven.apache.org/maven2/org/codehaus/plexus/plexus-component-metadata/1.5.5/plexus-component-metadata-1.5.5.jar 3/108 KB 5/108 KB 8/108 KB 11/108 KB 13/108 KB 16/108 KB 19/108 KB 21/108 KB 24/108 KB 27/108 KB 29/108 KB 32/108 KB 36/108 KB 40/108 KB 44/108 KB 48/108 KB 52/108 KB 56/108 KB 60/108 KB 64/108 KB 68/108 KB 72/108 KB 76/108 KB 80/108 KB 84/108 KB 88/108 KB 92/108 KB 96/108 KB 100/108 KB 104/108 KB 108/108 KB 108/108 KB Downloaded: https://repo.maven.apache.org/maven2/org/codehaus/plexus/plexus-component-metadata/1.5.5/plexus-component-metadata-1.5.5.jar (108 KB at 1007.4 KB/sec) [INFO] [INFO] --- maven-clean-plugin:3.1.0:clean (default-clean) @ adam-shade-spark2_2.12 --- [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building ADAM_2.12: Avro-to-Dataset codegen utils 0.28.0-SNAPSHOT [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-clean-plugin:3.1.0:clean (default-clean) @ adam-codegen-spark2_2.12 --- [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building ADAM_2.12: Core 0.28.0-SNAPSHOT [INFO] ------------------------------------------------------------------------ Downloading: https://repo.maven.apache.org/maven2/org/apache/maven/plugins/maven-jar-plugin/3.1.2/maven-jar-plugin-3.1.2.pom 3/8 KB 6/8 KB 8/8 KB Downloaded: https://repo.maven.apache.org/maven2/org/apache/maven/plugins/maven-jar-plugin/3.1.2/maven-jar-plugin-3.1.2.pom (8 KB at 648.6 KB/sec) Downloading: https://repo.maven.apache.org/maven2/org/apache/maven/plugins/maven-jar-plugin/3.1.2/maven-jar-plugin-3.1.2.jar 3/28 KB 5/28 KB 8/28 KB 11/28 KB 13/28 KB 16/28 KB 19/28 KB 21/28 KB 24/28 KB 27/28 KB 28/28 KB Downloaded: https://repo.maven.apache.org/maven2/org/apache/maven/plugins/maven-jar-plugin/3.1.2/maven-jar-plugin-3.1.2.jar (28 KB at 2274.3 KB/sec) [INFO] [INFO] --- maven-clean-plugin:3.1.0:clean (default-clean) @ adam-core-spark2_2.12 --- [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building ADAM_2.12: APIs for Java, Python 0.28.0-SNAPSHOT [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-clean-plugin:3.1.0:clean (default-clean) @ adam-apis-spark2_2.12 --- [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building ADAM_2.12: CLI 0.28.0-SNAPSHOT [INFO] ------------------------------------------------------------------------ Downloading: https://repo.maven.apache.org/maven2/pl/project13/maven/git-commit-id-plugin/2.2.2/git-commit-id-plugin-2.2.2.pom 3/13 KB 5/13 KB 8/13 KB 11/13 KB 13/13 KB Downloaded: https://repo.maven.apache.org/maven2/pl/project13/maven/git-commit-id-plugin/2.2.2/git-commit-id-plugin-2.2.2.pom (13 KB at 1063.2 KB/sec) Downloading: https://repo.maven.apache.org/maven2/pl/project13/maven/git-commit-id-plugin/2.2.2/git-commit-id-plugin-2.2.2.jar 3/82 KB 5/82 KB 8/82 KB 11/82 KB 13/82 KB 16/82 KB 19/82 KB 21/82 KB 24/82 KB 27/82 KB 29/82 KB 32/82 KB 36/82 KB 40/82 KB 44/82 KB 48/82 KB 52/82 KB 56/82 KB 60/82 KB 64/82 KB 68/82 KB 72/82 KB 76/82 KB 80/82 KB 82/82 KB Downloaded: https://repo.maven.apache.org/maven2/pl/project13/maven/git-commit-id-plugin/2.2.2/git-commit-id-plugin-2.2.2.jar (82 KB at 4509.3 KB/sec) [INFO] [INFO] --- maven-clean-plugin:3.1.0:clean (default-clean) @ adam-cli-spark2_2.12 --- [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building ADAM_2.12: Assembly 0.28.0-SNAPSHOT [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-clean-plugin:3.1.0:clean (default-clean) @ adam-assembly-spark2_2.12 --- [INFO] ------------------------------------------------------------------------ [INFO] Reactor Summary: [INFO] [INFO] ADAM_2.12 .......................................... SUCCESS [ 0.194 s] [INFO] ADAM_2.12: Shader workaround ....................... SUCCESS [ 0.706 s] [INFO] ADAM_2.12: Avro-to-Dataset codegen utils ........... SUCCESS [ 0.007 s] [INFO] ADAM_2.12: Core .................................... SUCCESS [ 0.038 s] [INFO] ADAM_2.12: APIs for Java, Python ................... SUCCESS [ 0.002 s] [INFO] ADAM_2.12: CLI ..................................... SUCCESS [ 0.055 s] [INFO] ADAM_2.12: Assembly ................................ SUCCESS [ 0.001 s] [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ [INFO] Total time: 1.235 s [INFO] Finished at: 2019-06-28T14:00:33-07:00 [INFO] Final Memory: 19M/1092M [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 2176 ]] + COVERALLS_PRB_OPTION=-DpullRequest=2176 # 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] ADAM_2.12 [INFO] ADAM_2.12: Shader workaround [INFO] ADAM_2.12: Avro-to-Dataset codegen utils [INFO] ADAM_2.12: Core [INFO] ADAM_2.12: APIs for Java, Python [INFO] ADAM_2.12: CLI [INFO] ADAM_2.12: Assembly [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building ADAM_2.12 0.28.0-SNAPSHOT [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-parent-spark2_2.12 --- [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-parent-spark2_2.12 --- [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ adam-parent-spark2_2.12 --- [INFO] Modified 0 of 240 .scala files [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ adam-parent-spark2_2.12 --- [INFO] No sources to compile [INFO] [INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ adam-parent-spark2_2.12 --- [INFO] No sources to compile [INFO] [INFO] >>> scoverage-maven-plugin:1.1.1:report (default-cli) > [scoverage]test @ adam-parent-spark2_2.12 >>> [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-parent-spark2_2.12 --- [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-parent-spark2_2.12 --- [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ adam-parent-spark2_2.12 --- [INFO] Modified 0 of 240 .scala files [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:pre-compile (default-cli) @ adam-parent-spark2_2.12 --- [INFO] Skipping SCoverage execution for project with packaging type 'pom' [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ adam-parent-spark2_2.12 --- [INFO] No sources to compile [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:post-compile (default-cli) @ adam-parent-spark2_2.12 --- [INFO] [INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ adam-parent-spark2_2.12 --- [INFO] No sources to compile [INFO] [INFO] <<< scoverage-maven-plugin:1.1.1:report (default-cli) < [scoverage]test @ adam-parent-spark2_2.12 <<< [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:report (default-cli) @ adam-parent-spark2_2.12 --- [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building ADAM_2.12: Shader workaround 0.28.0-SNAPSHOT [INFO] ------------------------------------------------------------------------ Downloading: https://repo.maven.apache.org/maven2/org/apache/maven/plugins/maven-resources-plugin/3.1.0/maven-resources-plugin-3.1.0.pom 3/7 KB 6/7 KB 7/7 KB Downloaded: https://repo.maven.apache.org/maven2/org/apache/maven/plugins/maven-resources-plugin/3.1.0/maven-resources-plugin-3.1.0.pom (7 KB at 26.2 KB/sec) Downloading: https://repo.maven.apache.org/maven2/org/apache/maven/plugins/maven-resources-plugin/3.1.0/maven-resources-plugin-3.1.0.jar 3/31 KB 5/31 KB 8/31 KB 11/31 KB 13/31 KB 16/31 KB 19/31 KB 21/31 KB 24/31 KB 27/31 KB 29/31 KB 31/31 KB Downloaded: https://repo.maven.apache.org/maven2/org/apache/maven/plugins/maven-resources-plugin/3.1.0/maven-resources-plugin-3.1.0.jar (31 KB at 1541.1 KB/sec) [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-shade-spark2_2.12 --- [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-shade-spark2_2.12 --- [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ adam-shade-spark2_2.12 --- [INFO] Modified 0 of 0 .scala files [INFO] [INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ adam-shade-spark2_2.12 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-shade/src/main/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ adam-shade-spark2_2.12 --- [INFO] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-shade/src/main/java:-1: info: compiling [INFO] Compiling 1 source files to /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-shade/target/2.12.8/classes at 1561755648877 [INFO] prepare-compile in 0 s [INFO] compile in 2 s [INFO] [INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ adam-shade-spark2_2.12 --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 1 source file to /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-shade/target/2.12.8/classes [INFO] [INFO] --- plexus-component-metadata:1.5.5:generate-metadata (default) @ adam-shade-spark2_2.12 --- Downloading: https://repo.maven.apache.org/maven2/com/thoughtworks/qdox/qdox/1.9.2/qdox-1.9.2.pom 3/17 KB 5/17 KB 8/17 KB 11/17 KB 13/17 KB 16/17 KB 17/17 KB Downloaded: https://repo.maven.apache.org/maven2/com/thoughtworks/qdox/qdox/1.9.2/qdox-1.9.2.pom (17 KB at 1116.5 KB/sec) Downloading: https://repo.maven.apache.org/maven2/jdom/jdom/1.0/jdom-1.0.pom 2/2 KB Downloaded: https://repo.maven.apache.org/maven2/jdom/jdom/1.0/jdom-1.0.pom (2 KB at 127.0 KB/sec) Downloading: https://repo.maven.apache.org/maven2/org/codehaus/plexus/plexus-cli/1.2/plexus-cli-1.2.pom 2/2 KB Downloaded: https://repo.maven.apache.org/maven2/org/codehaus/plexus/plexus-cli/1.2/plexus-cli-1.2.pom (2 KB at 218.5 KB/sec) Downloading: 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8/8 KB 22/22 KB 44/150 KB 201/201 KB 48/167 KB 8/8 KB 22/22 KB 48/150 KB 201/201 KB 48/167 KB Downloaded: https://repo.maven.apache.org/maven2/org/codehaus/plexus/plexus-cli/1.2/plexus-cli-1.2.jar (8 KB at 277.2 KB/sec) Downloading: https://repo.maven.apache.org/maven2/commons-lang/commons-lang/1.0/commons-lang-1.0.jar 22/22 KB 48/150 KB 201/201 KB 52/167 KB Downloaded: https://repo.maven.apache.org/maven2/commons-logging/commons-logging/1.0/commons-logging-1.0.jar (22 KB at 793.9 KB/sec) 48/150 KB 201/201 KB 56/167 KB 52/150 KB 201/201 KB 56/167 KB 52/150 KB 201/201 KB 60/167 KB 56/150 KB 201/201 KB 60/167 KB 56/150 KB 201/201 KB 64/167 KB 60/150 KB 201/201 KB 64/167 KB 64/150 KB 201/201 KB 64/167 KB 68/150 KB 201/201 KB 64/167 KB 72/150 KB 201/201 KB 64/167 KB 72/150 KB 201/201 KB 68/167 KB 76/150 KB 201/201 KB 68/167 KB Downloaded: https://repo.maven.apache.org/maven2/org/codehaus/plexus/plexus-utils/1.4.5/plexus-utils-1.4.5.jar (201 KB at 6257.4 KB/sec) 80/150 KB 68/167 KB 80/150 KB 72/167 KB 80/150 KB 76/167 KB 80/150 KB 80/167 KB 84/150 KB 80/167 KB 88/150 KB 80/167 KB 92/150 KB 80/167 KB 96/150 KB 80/167 KB 96/150 KB 84/167 KB 96/150 KB 88/167 KB 96/150 KB 92/167 KB 96/150 KB 3/63 KB 92/167 KB 96/150 KB 3/63 KB 96/167 KB 96/150 KB 5/63 KB 96/167 KB 100/150 KB 5/63 KB 96/167 KB 104/150 KB 5/63 KB 96/167 KB 108/150 KB 5/63 KB 96/167 KB 108/150 KB 8/63 KB 96/167 KB 112/150 KB 8/63 KB 96/167 KB 112/150 KB 11/63 KB 100/167 KB 112/150 KB 11/63 KB 100/167 KB 112/150 KB 11/63 KB 104/167 KB 112/150 KB 11/63 KB 108/167 KB 112/150 KB 13/63 KB 108/167 KB 112/150 KB 13/63 KB 112/167 KB 116/150 KB 13/63 KB 112/167 KB 116/150 KB 16/63 KB 112/167 KB 120/150 KB 16/63 KB 112/167 KB 124/150 KB 16/63 KB 112/167 KB 128/150 KB 16/63 KB 112/167 KB 128/150 KB 19/63 KB 112/167 KB 128/150 KB 21/63 KB 112/167 KB 128/150 KB 24/63 KB 112/167 KB 128/150 KB 27/63 KB 112/167 KB 128/150 KB 29/63 KB 112/167 KB 132/150 KB 29/63 KB 112/167 KB 132/150 KB 32/63 KB 112/167 KB 136/150 KB 32/63 KB 112/167 KB 140/150 KB 32/63 KB 112/167 KB 140/150 KB 32/63 KB 116/167 KB 144/150 KB 32/63 KB 116/167 KB 144/150 KB 32/63 KB 120/167 KB 144/150 KB 32/63 KB 124/167 KB 144/150 KB 32/63 KB 128/167 KB 148/150 KB 32/63 KB 128/167 KB 148/150 KB 36/63 KB 128/167 KB 150/150 KB 36/63 KB 128/167 KB 150/150 KB 40/63 KB 128/167 KB 150/150 KB 44/63 KB 128/167 KB 150/150 KB 48/63 KB 128/167 KB 150/150 KB 48/63 KB 132/167 KB 150/150 KB 48/63 KB 136/167 KB 150/150 KB 48/63 KB 140/167 KB 150/150 KB 48/63 KB 144/167 KB 150/150 KB 52/63 KB 144/167 KB 150/150 KB 56/63 KB 144/167 KB 150/150 KB 60/63 KB 144/167 KB 150/150 KB 63/63 KB 144/167 KB 150/150 KB 63/63 KB 148/167 KB 150/150 KB 63/63 KB 152/167 KB 150/150 KB 63/63 KB 156/167 KB 150/150 KB 63/63 KB 160/167 KB 150/150 KB 63/63 KB 164/167 KB 150/150 KB 63/63 KB 167/167 KB Downloaded: https://repo.maven.apache.org/maven2/jdom/jdom/1.0/jdom-1.0.jar (150 KB at 3563.4 KB/sec) Downloaded: https://repo.maven.apache.org/maven2/commons-lang/commons-lang/1.0/commons-lang-1.0.jar (63 KB at 1521.1 KB/sec) Downloaded: https://repo.maven.apache.org/maven2/com/thoughtworks/qdox/qdox/1.9.2/qdox-1.9.2.jar (167 KB at 3690.6 KB/sec) [INFO] Discovered 1 component descriptors(s) [INFO] [INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ adam-shade-spark2_2.12 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-shade/src/test/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ adam-shade-spark2_2.12 --- [INFO] No sources to compile [INFO] [INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ adam-shade-spark2_2.12 --- [INFO] No sources to compile [INFO] [INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ adam-shade-spark2_2.12 --- [INFO] No tests to run. [INFO] [INFO] >>> scoverage-maven-plugin:1.1.1:report (default-cli) > [scoverage]test @ adam-shade-spark2_2.12 >>> [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-shade-spark2_2.12 --- [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-shade-spark2_2.12 --- [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ adam-shade-spark2_2.12 --- [INFO] Modified 0 of 0 .scala files [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:pre-compile (default-cli) @ adam-shade-spark2_2.12 --- [WARNING] Skipping SCoverage execution - unsupported Scala version "2.12.8" [INFO] [INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ adam-shade-spark2_2.12 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-shade/src/main/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ adam-shade-spark2_2.12 --- [INFO] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-shade/src/main/java:-1: info: compiling [INFO] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-shade/target/generated-sources/annotations:-1: info: compiling [INFO] Compiling 1 source files to /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-shade/target/2.12.8/classes at 1561755652107 [INFO] prepare-compile in 0 s [INFO] compile in 1 s [INFO] [INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ adam-shade-spark2_2.12 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- plexus-component-metadata:1.5.5:generate-metadata (default) @ adam-shade-spark2_2.12 --- [INFO] Discovered 1 component descriptors(s) [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:post-compile (default-cli) @ adam-shade-spark2_2.12 --- [INFO] [INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ adam-shade-spark2_2.12 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-shade/src/test/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ adam-shade-spark2_2.12 --- [INFO] No sources to compile [INFO] [INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ adam-shade-spark2_2.12 --- [INFO] No sources to compile [INFO] [INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ adam-shade-spark2_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 @ adam-shade-spark2_2.12 <<< [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:report (default-cli) @ adam-shade-spark2_2.12 --- [INFO] Skipping SCoverage report generation [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building ADAM_2.12: Avro-to-Dataset codegen utils 0.28.0-SNAPSHOT [INFO] ------------------------------------------------------------------------ Downloading: https://repo.maven.apache.org/maven2/org/scalatest/scalatest_2.12/3.0.7/scalatest_2.12-3.0.7.pom 3/5 KB 5/5 KB 5/5 KB Downloaded: https://repo.maven.apache.org/maven2/org/scalatest/scalatest_2.12/3.0.7/scalatest_2.12-3.0.7.pom (5 KB at 217.3 KB/sec) Downloading: https://repo.maven.apache.org/maven2/org/scalactic/scalactic_2.12/3.0.7/scalactic_2.12-3.0.7.pom 3/3 KB 3/3 KB Downloaded: https://repo.maven.apache.org/maven2/org/scalactic/scalactic_2.12/3.0.7/scalactic_2.12-3.0.7.pom (3 KB at 236.5 KB/sec) Downloading: https://repo.maven.apache.org/maven2/org/scala-lang/modules/scala-xml_2.12/1.1.0/scala-xml_2.12-1.1.0.pom 3/3 KB Downloaded: https://repo.maven.apache.org/maven2/org/scala-lang/modules/scala-xml_2.12/1.1.0/scala-xml_2.12-1.1.0.pom (3 KB at 298.7 KB/sec) Downloading: https://repo.maven.apache.org/maven2/org/xerial/snappy/snappy-java/1.1.1.3/snappy-java-1.1.1.3.jar Downloading: https://repo.maven.apache.org/maven2/org/scalatest/scalatest_2.12/3.0.7/scalatest_2.12-3.0.7.jar Downloading: https://repo.maven.apache.org/maven2/org/scalactic/scalactic_2.12/3.0.7/scalactic_2.12-3.0.7.jar Downloading: https://repo.maven.apache.org/maven2/org/scala-lang/modules/scala-xml_2.12/1.1.0/scala-xml_2.12-1.1.0.jar 3/576 KB 5/576 KB 8/576 KB 11/576 KB 13/576 KB 16/576 KB 19/576 KB 19/576 KB 3/702 KB 21/576 KB 3/702 KB 21/576 KB 5/702 KB 24/576 KB 5/702 KB 24/576 KB 8/702 KB 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https://repo.maven.apache.org/maven2/org/scalatest/scalatest_2.12/3.0.7/scalatest_2.12-3.0.7.jar (6935 KB at 21143.2 KB/sec) [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-codegen-spark2_2.12 --- [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-codegen-spark2_2.12 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ adam-codegen-spark2_2.12 --- [INFO] Source directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-codegen/src/main/scala added. [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ adam-codegen-spark2_2.12 --- [INFO] Modified 0 of 4 .scala files [INFO] [INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ adam-codegen-spark2_2.12 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-codegen/src/main/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ adam-codegen-spark2_2.12 --- [INFO] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-codegen/src/main/scala:-1: info: compiling [INFO] Compiling 4 source files to /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-codegen/target/2.12.8/classes at 1561755654704 [WARNING] warning: there were 5 deprecation warnings (since 2.12.0); re-run with -deprecation for details [WARNING] one warning found [INFO] prepare-compile in 0 s [INFO] compile in 4 s [INFO] [INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ adam-codegen-spark2_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) @ adam-codegen-spark2_2.12 --- [INFO] Test Source directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-codegen/src/test/scala added. [INFO] [INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ adam-codegen-spark2_2.12 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-codegen/src/test/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ adam-codegen-spark2_2.12 --- [INFO] No sources to compile [INFO] [INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ adam-codegen-spark2_2.12 --- [INFO] No sources to compile [INFO] [INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ adam-codegen-spark2_2.12 --- [INFO] Tests are skipped. [INFO] [INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ adam-codegen-spark2_2.12 --- Discovery starting. Discovery completed in 85 milliseconds. Run starting. Expected test count is: 0 DiscoverySuite: Run completed in 130 milliseconds. Total number of tests run: 0 Suites: completed 1, aborted 0 Tests: succeeded 0, failed 0, canceled 0, ignored 0, pending 0 No tests were executed. [INFO] [INFO] >>> scoverage-maven-plugin:1.1.1:report (default-cli) > [scoverage]test @ adam-codegen-spark2_2.12 >>> [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-codegen-spark2_2.12 --- [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-codegen-spark2_2.12 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ adam-codegen-spark2_2.12 --- [INFO] Source directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-codegen/src/main/scala added. [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ adam-codegen-spark2_2.12 --- [INFO] Modified 0 of 4 .scala files [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:pre-compile (default-cli) @ adam-codegen-spark2_2.12 --- [WARNING] Skipping SCoverage execution - unsupported Scala version "2.12.8" [INFO] [INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ adam-codegen-spark2_2.12 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-codegen/src/main/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ adam-codegen-spark2_2.12 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ adam-codegen-spark2_2.12 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:post-compile (default-cli) @ adam-codegen-spark2_2.12 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ adam-codegen-spark2_2.12 --- [INFO] Test Source directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-codegen/src/test/scala added. [INFO] [INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ adam-codegen-spark2_2.12 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-codegen/src/test/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ adam-codegen-spark2_2.12 --- [INFO] No sources to compile [INFO] [INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ adam-codegen-spark2_2.12 --- [INFO] No sources to compile [INFO] [INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ adam-codegen-spark2_2.12 --- [INFO] Tests are skipped. [INFO] [INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ adam-codegen-spark2_2.12 --- Discovery starting. Discovery completed in 83 milliseconds. Run starting. Expected test count is: 0 DiscoverySuite: Run completed in 125 milliseconds. Total number of tests run: 0 Suites: completed 1, aborted 0 Tests: succeeded 0, failed 0, canceled 0, ignored 0, pending 0 No tests were executed. [INFO] [INFO] <<< scoverage-maven-plugin:1.1.1:report (default-cli) < [scoverage]test @ adam-codegen-spark2_2.12 <<< [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:report (default-cli) @ adam-codegen-spark2_2.12 --- [INFO] Skipping SCoverage report generation [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building ADAM_2.12: Core 0.28.0-SNAPSHOT [INFO] ------------------------------------------------------------------------ Downloading: https://repo.maven.apache.org/maven2/org/codehaus/mojo/exec-maven-plugin/1.5.0/exec-maven-plugin-1.5.0.pom 3/13 KB 6/13 KB 9/13 KB 11/13 KB 13/13 KB Downloaded: https://repo.maven.apache.org/maven2/org/codehaus/mojo/exec-maven-plugin/1.5.0/exec-maven-plugin-1.5.0.pom (13 KB at 752.2 KB/sec) Downloading: https://repo.maven.apache.org/maven2/org/codehaus/mojo/exec-maven-plugin/1.5.0/exec-maven-plugin-1.5.0.jar 3/53 KB 5/53 KB 8/53 KB 11/53 KB 13/53 KB 16/53 KB 19/53 KB 21/53 KB 24/53 KB 27/53 KB 29/53 KB 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maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-core-spark2_2.12 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ adam-core-spark2_2.12 --- [INFO] Source directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/main/scala added. [INFO] Source directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/target/generated-sources/src/main/scala added. [INFO] [INFO] --- exec-maven-plugin:1.5.0:java (generate-scala-products) @ adam-core-spark2_2.12 --- SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] [INFO] --- exec-maven-plugin:1.5.0:java (generate-scala-projection-fields) @ adam-core-spark2_2.12 --- SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ adam-core-spark2_2.12 --- [INFO] Modified 2 of 202 .scala files [INFO] [INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ adam-core-spark2_2.12 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/main/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ adam-core-spark2_2.12 --- [INFO] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/main/java:-1: info: compiling [INFO] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/main/scala:-1: info: compiling [INFO] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/target/generated-sources/src/main/scala:-1: info: compiling [INFO] Compiling 138 source files to /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/target/2.12.8/classes at 1561755672418 [WARNING] warning: there were 21 deprecation warnings [WARNING] warning: there were 31 deprecation warnings (since 0.21.0) [WARNING] warning: there was one deprecation warning (since 1.0.6) [WARNING] warning: there were 36 deprecation warnings (since 2.0.0) [WARNING] warning: there was one deprecation warning (since 2.11.0) [WARNING] warning: there were 173 deprecation warnings (since 2.12.0) [WARNING] warning: there was one deprecation warning (since 2.12.7) [WARNING] warning: there were 264 deprecation warnings in total; re-run with -deprecation for details [WARNING] warning: there were 5 feature warnings; re-run with -feature for details [WARNING] 9 warnings found [INFO] prepare-compile in 0 s [INFO] compile in 26 s [INFO] [INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ adam-core-spark2_2.12 --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 6 source files to /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/target/2.12.8/classes [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ adam-core-spark2_2.12 --- [INFO] Test Source directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala added. [INFO] [INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ adam-core-spark2_2.12 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 152 resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ adam-core-spark2_2.12 --- [INFO] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala:-1: info: compiling [INFO] Compiling 70 source files to /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/target/2.12.8/test-classes at 1561755700408 [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/algorithms/consensus/NormalizationUtilsSuite.scala:59: warning: method recordToRichRecord in object RichAlignmentRecord is deprecated (since 0.21.0): Use explicit conversion wherever possible in new development. [WARNING] .build() [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/algorithms/consensus/NormalizationUtilsSuite.scala:61: warning: method richRecordToRecord in object RichAlignmentRecord is deprecated (since 0.21.0): Use explicit conversion wherever possible in new development. [WARNING] val new_cigar = NormalizationUtils.leftAlignIndel(read) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/algorithms/consensus/NormalizationUtilsSuite.scala:66: warning: method richRecordToRecord in object RichAlignmentRecord is deprecated (since 0.21.0): Use explicit conversion wherever possible in new development. [WARNING] assert(RichAlignmentRecord(read).samtoolsCigar.getReadLength === new_cigar.getReadLength) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/AlignmentRecordConverterSuite.scala:171: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] val newSAMRecord = newSAMReader.iterator().dropWhile(r => r.getReadName != readName) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/AlignmentRecordConverterSuite.scala:274: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] .setAlignments(seqAsJavaList(alignments)) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/AlignmentRecordConverterSuite.scala:311: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] .setAlignments(seqAsJavaList(alignments)) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/AlignmentRecordConverterSuite.scala:335: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] val fragment = Fragment.newBuilder().setAlignments(List(record)).build() [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/SAMRecordConverterSuite.scala:54: warning: method getNotPrimaryAlignmentFlag in class SAMRecord is deprecated: see corresponding Javadoc for more information. [WARNING] assert(!testAlignmentRecord.getPrimaryAlignment === testSAMRecord.getNotPrimaryAlignmentFlag) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/SAMRecordConverterSuite.scala:89: warning: method getNotPrimaryAlignmentFlag in class SAMRecord is deprecated: see corresponding Javadoc for more information. [WARNING] assert(!testAlignmentRecord.getPrimaryAlignment === testSAMRecord.getNotPrimaryAlignmentFlag) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/SAMRecordConverterSuite.scala:106: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] val samIter = asScalaIterator(newSAMReader.iterator()) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:53: warning: method extractDictionary in class SAMSequenceDictionaryExtractor is deprecated: see corresponding Javadoc for more information. [WARNING] SequenceDictionary(SAMSequenceDictionaryExtractor.extractDictionary(new File(path))) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:63: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] .alleles(List(Allele.create("A", true), Allele.create("T"))) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:69: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] .alleles(List(Allele.create("A", true), Allele.create("T"), Allele.create("G"))) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:75: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] .alleles(List(Allele.create("A", true), Allele.create("<NON_REF>", false))) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:81: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] .alleles(List(Allele.create("A", true), Allele.create("<CN0>", false))) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:109: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] .alleles(List(Allele.create("A", true), Allele.create("T"))) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:143: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] GenotypeBuilder.create("NA12878", vcb.getAlleles(), genotypeAttributes)) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:154: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] assert(adamGT.getAlleles.sameElements(List(GenotypeAllele.REF, GenotypeAllele.ALT))) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:184: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] assert(adamVariant.variant.getFiltersFailed.sameElements(List("LowMQ"))) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:219: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] assert(adamGT.getVariantCallingAnnotations.getFiltersFailed.sameElements(List("LowMQ"))) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:234: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] assert(htsjdkVC.getAlternateAlleles.sameElements(List(Allele.create("T")))) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:245: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] .setStrandBiasComponents(List(0, 2, 4, 6).map(i => i: java.lang.Integer)) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:246: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] .setAlleles(List(GenotypeAllele.REF, GenotypeAllele.ALT)) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:279: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] .setStrandBiasComponents(List(0, 2).map(i => i: java.lang.Integer)) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:280: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] .setAlleles(List(GenotypeAllele.REF, GenotypeAllele.ALT)) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:298: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] .setStrandBiasComponents(List(0, 2).map(i => i: java.lang.Integer)) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:299: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] .setAlleles(List(GenotypeAllele.REF, GenotypeAllele.ALT)) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:320: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] for ((allele, idx) <- vc.getAlternateAlleles.zipWithIndex) { [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:328: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] val gb = new GenotypeBuilder("NA12878", List(Allele.create("T"), Allele.create("G"))) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:347: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] assert(adamGT1.getAlleles.sameElements(List(GenotypeAllele.ALT, GenotypeAllele.OTHER_ALT))) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:349: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] assert(adamGT1.getGenotypeLikelihoods [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:354: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] assert(adamGT2.getAlleles.sameElements(List(GenotypeAllele.OTHER_ALT, GenotypeAllele.ALT))) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:356: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] assert(adamGT2.getGenotypeLikelihoods [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:380: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] val gb = new GenotypeBuilder("NA12878", List(Allele.create("A", true), Allele.create("A", true))) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:393: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] assert(adamGT.getAlleles.sameElements(List(GenotypeAllele.REF, GenotypeAllele.REF))) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:396: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] assert(adamGT.getNonReferenceLikelihoods [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:421: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] assert(variant.variant.getNames.length === 1) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:433: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] assert(variant.variant.getNames.length === 2) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:543: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] genotypeAttributes)))((bldr, fn) => { [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:693: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] assert(gls(0) < -0.99e-1 && gls(0) > -1.1e-1) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:693: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] assert(gls(0) < -0.99e-1 && gls(0) > -1.1e-1) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:694: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] assert(gls(1) < -0.99e-3 && gls(1) > -1.1e-3) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:694: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] assert(gls(1) < -0.99e-3 && gls(1) > -1.1e-3) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:695: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] assert(gls(2) < -0.99e-6 && gls(2) > -1.1e-6) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:695: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] assert(gls(2) < -0.99e-6 && gls(2) > -1.1e-6) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:714: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] assert(sb(0) === 10) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:715: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] assert(sb(1) === 12) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:716: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] assert(sb(2) === 14) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:717: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] assert(sb(3) === 16) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:762: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] assert(failedFilters(0) === "FAILED_FILTER") [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:776: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] assert(failedFilters(0) === "FAILED_FILTER1") [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:777: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] assert(failedFilters(1) === "FAILED_FILTER2") [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:778: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] assert(failedFilters(2) === "FAILED_FILTER3") [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:930: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] .map(d => d: java.lang.Double)) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:954: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] .map(i => i: java.lang.Integer)) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:962: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] .map(i => i: java.lang.Integer)) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1089: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] .setFiltersFailed(Seq("lowmq")) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1101: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] .setFiltersFailed(Seq("lowmq", "lowdp")) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1195: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] assert(v.getNames.length === 1) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1205: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] assert(v.getNames.length === 2) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1262: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] vcb.filters(Set("FAILED1", "FAILED2", "FAILED3")) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1267: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] val failedSet = v.getFiltersFailed.toSet [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1285: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] .setNames(Seq("name")) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1295: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] .setNames(Seq("name1", "name2")) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1364: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] .setFiltersFailed(Seq("FAILED")) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1378: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] .setFiltersFailed(Seq("FAILED1", "FAILED2")) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1493: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] 10).map(i => i: java.lang.Integer) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1501: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] 10, 13, 16).map(i => i: java.lang.Integer) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1516: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] 0.1f).map(i => i: java.lang.Float) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1523: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] val acList: java.util.List[String] = List("+Inf") [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1530: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] val acList: java.util.List[String] = List("-Inf") [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1538: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] 0.1f, 0.01f, 0.001f).map(i => i: java.lang.Float) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1552: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] val acList: java.util.List[String] = List("10D90M") [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1559: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] val acList: java.util.List[String] = List("10D90M", "100M", "90M10D") [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1575: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] 5, 10).map(i => i: java.lang.Integer) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1584: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] 5, 10, 13, 16).map(i => i: java.lang.Integer) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1601: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] 5, 10).map(i => i: java.lang.Integer) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1610: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] 5, 10, 13, 16).map(i => i: java.lang.Integer) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1627: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] 5, 10).map(i => i: java.lang.Integer) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1636: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] 5, 10, 13, 16).map(i => i: java.lang.Integer) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:2436: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] Map[String, java.lang.Object](("ONE_INT", "42"))) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:2459: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] Map[String, java.lang.Object](("FOUR_INTS", "5,10,15,20"))) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:2482: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] Map[String, java.lang.Object](("FOUR_FLOATS", "5.0,10.1,15.2,20.3"))) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:2505: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] Map[String, java.lang.Object](("A_INT", "10,15,20"))) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:2528: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] Map[String, java.lang.Object](("R_INT", "5,10,15,20"))) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:2551: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] Map[String, java.lang.Object](("R_STRING", "foo,bar,baz"))) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:2574: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] Map[String, java.lang.Object](("STRING_G", "foo,bar,baz"))) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/models/CoverageSuite.scala:37: warning: variable start in class Feature is deprecated: see corresponding Javadoc for more information. [WARNING] assert(coverageAfterConversion.start == featureToConvert.start) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/models/CoverageSuite.scala:38: warning: variable end in class Feature is deprecated: see corresponding Javadoc for more information. [WARNING] assert(coverageAfterConversion.end == featureToConvert.end) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/models/CoverageSuite.scala:40: warning: variable score in class Feature is deprecated: see corresponding Javadoc for more information. [WARNING] assert(coverageAfterConversion.count == featureToConvert.score) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/models/CoverageSuite.scala:57: warning: variable start in class Feature is deprecated: see corresponding Javadoc for more information. [WARNING] assert(coverageAfterConversion.start == featureToConvert.start) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/models/CoverageSuite.scala:58: warning: variable end in class Feature is deprecated: see corresponding Javadoc for more information. [WARNING] assert(coverageAfterConversion.end == featureToConvert.end) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/models/CoverageSuite.scala:60: warning: variable score in class Feature is deprecated: see corresponding Javadoc for more information. [WARNING] assert(coverageAfterConversion.count == featureToConvert.score) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/models/CoverageSuite.scala:61: warning: variable sampleId in class Feature is deprecated: see corresponding Javadoc for more information. [WARNING] assert(coverageAfterConversion.optSampleId == Some(featureToConvert.sampleId)) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/models/MdTagSuite.scala:194: warning: method recordToRichRecord in object RichAlignmentRecord is deprecated (since 0.21.0): Use explicit conversion wherever possible in new development. [WARNING] assert(read.mdTag.get.end === read.getEnd) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/models/MdTagSuite.scala:475: warning: method recordToRichRecord in object RichAlignmentRecord is deprecated (since 0.21.0): Use explicit conversion wherever possible in new development. [WARNING] val tag = read.mdTag.get [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/models/MdTagSuite.scala:482: warning: method recordToRichRecord in object RichAlignmentRecord is deprecated (since 0.21.0): Use explicit conversion wherever possible in new development. [WARNING] assert(tag.getReference(read) === "AAAAAAAAAAAAAAAAAAAAAAAAAAAAAGGGGGGGGGGAAAAAAAAAAGGGGGGGGGGAAAAAAAAAAA") [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/models/MdTagSuite.scala:495: warning: method recordToRichRecord in object RichAlignmentRecord is deprecated (since 0.21.0): Use explicit conversion wherever possible in new development. [WARNING] val tag = read.mdTag.get [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/models/MdTagSuite.scala:496: warning: method recordToRichRecord in object RichAlignmentRecord is deprecated (since 0.21.0): Use explicit conversion wherever possible in new development. [WARNING] assert(tag.getReference(read, withGaps = true) === "AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGGGGGGGGGGAAAAAAAAAAA") [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/models/MdTagSuite.scala:510: warning: method recordToRichRecord in object RichAlignmentRecord is deprecated (since 0.21.0): Use explicit conversion wherever possible in new development. [WARNING] val newTag = MdTag.moveAlignment(read, newCigar) [WARNING] ^ [WARNING] 223 warnings found [INFO] prepare-compile in 0 s [INFO] compile in 28 s [INFO] [INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ adam-core-spark2_2.12 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ adam-core-spark2_2.12 --- [INFO] Tests are skipped. [INFO] [INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ adam-core-spark2_2.12 --- Discovery starting. Discovery completed in 1 second, 578 milliseconds. Run starting. Expected test count is: 1175 RepairPartitionsSuite: - don't pull from the first partition - properly handle pulling from an empty iterator - gets a single read from the partition if there are no other reads in the pair - gets all the reads from a pair from the start of a partition - properly handle dropping from an empty iterator - don't drop from the first partition - drop a single read from the partition if there are no other reads in the pair - drops all the reads from a pair from the start of a partition - only append to the first partition - drop a single read from the partition and append read when in the middle - drop reads from the start and don't append when in the last partition - can't have more records than number of partitions - unroll array for broadcast 2019-06-28 14:02:11 WARN Utils:66 - Your hostname, research-jenkins-worker-07 resolves to a loopback address: 127.0.1.1; using 192.168.10.27 instead (on interface eth0) 2019-06-28 14:02:11 WARN Utils:66 - Set SPARK_LOCAL_IP if you need to bind to another address 2019-06-28 14:02:11 WARN NativeCodeLoader:62 - Unable to load native-hadoop library for your platform... using builtin-java classes where applicable - move pairs around an rdd FlagStatSuite: - Standard FlagStat test ModPartitionerSuite: - report number of partitions correctly - partition a number that is lower than the number of partitions and positive - partition a number that is greater than the number of partitions and positive - partition a number that is lower than the number of partitions and negative - partition a number that is greater than the number of partitions and negative - fire an exception if input is not an integer TwoBitFileSuite: - correctly read sequence from .2bit file - correctly return masked sequences from .2bit file - correctly return Ns from .2bit file - correctly calculates sequence dictionary NonoverlappingRegionsSuite: - alternating returns an alternating seq of items - Single region returns itself - Two adjacent regions will be merged - Nonoverlapping regions will all be returned - Many overlapping regions will all be merged - ADAMRecords return proper references ReferencePositionSuite: - create reference position from mapped read - create reference position from variant - create reference position from genotype - create reference position from variant starting at vcf 0 - create reference position from genotype starting at vcf 0 ConsensusGeneratorFromReadsSuite: - checking search for consensus list for artificial reads FragmentConverterSuite: - build a fragment collector and convert to a read - if a fragment isn't associated with a contig, don't get a fragment collector - convert an rdd of discontinuous fragments, all from the same contig - convert an rdd of contiguous fragments, all from the same contig - convert an rdd of varied fragments from multiple contigs FileMergerSuite: - cannot write both empty gzip block and cram eof - buffer size must be non-negative AlignmentRecordDatasetSuite: - sorting reads - unmapped reads go at the end when sorting - coverage does not fail on unmapped reads 2019-06-28 14:02:22 WARN Utils:66 - Truncated the string representation of a plan since it was too large. This behavior can be adjusted by setting 'spark.debug.maxToStringFields' in SparkEnv.conf. - computes coverage - computes coverage with multiple samples - merges adjacent records with equal coverage values - sorting reads by reference index - round trip from ADAM to SAM and back to ADAM produces equivalent Read values - round trip with single CRAM file produces equivalent Read values - round trip with sharded CRAM file produces equivalent Read values - SAM conversion sets read mapped flag properly - load long FASTQ reads - load FASTQ with no bases - convert malformed FASTQ (no quality scores) => SAM => well-formed FASTQ => SAM - round trip from ADAM to FASTQ and back to ADAM produces equivalent Read values - round trip from ADAM to paired-FASTQ and back to ADAM produces equivalent Read values - writing a small file with tags should produce the expected result - writing a small sorted file as SAM should produce the expected result - writing unordered sam from unordered sam - writing ordered sam from unordered sam - write single sam file back - write single bam file back - saveAsParquet with save args, sequence dictionary, and read group dictionary - load parquet to sql, save, re-read from avro - load from sam, save as partitioned parquet, and re-read from partitioned parquet - save as SAM format - save as sorted SAM format - save as BAM format - save as sorted BAM format - save as FASTQ format - save as ADAM parquet format - saveAsSam SAM format - saveAsSam SAM format single file - saveAsSam sorted SAM format single file - saveAsSam BAM format - saveAsSam BAM format single file - saveAsSam sorted BAM format single file - saveAsFastq - saveAsFastq as single file - saveAsFastq with original base qualities - saveAsFastq sorted by read name - saveAsFastq sorted by read name with original base qualities 2019-06-28 14:02:48 WARN RDDBoundAlignmentRecordDataset:190 - Found 20 read names that don't occur exactly twice: 1x: 20 Samples: simread:1:237728409:true simread:1:195211965:false simread:1:163841413:false simread:1:231911906:false simread:1:26472783:false simread:1:165341382:true simread:1:240344442:true simread:1:50683371:false simread:1:240997787:true simread:1:14397233:false simread:1:207027738:true simread:1:20101800:true simread:1:101556378:false simread:1:37577445:false simread:1:189606653:true simread:1:5469106:true simread:1:186794283:true simread:1:89554252:false simread:1:153978724:false simread:1:169801933:true - saveAsFastq paired FASTQ 2019-06-28 14:02:49 WARN RDDBoundAlignmentRecordDataset:190 - Found 20 read names that don't occur exactly twice: 1x: 20 Samples: simread:1:237728409:true simread:1:195211965:false simread:1:163841413:false simread:1:231911906:false simread:1:26472783:false simread:1:165341382:true simread:1:240344442:true simread:1:50683371:false simread:1:240997787:true simread:1:14397233:false simread:1:207027738:true simread:1:20101800:true simread:1:101556378:false simread:1:37577445:false simread:1:189606653:true simread:1:5469106:true simread:1:186794283:true simread:1:89554252:false simread:1:153978724:false simread:1:169801933:true - saveAsPairedFastq 2019-06-28 14:02:50 WARN RDDBoundAlignmentRecordDataset:190 - Found 20 read names that don't occur exactly twice: 1x: 20 Samples: simread:1:237728409:true simread:1:195211965:false simread:1:163841413:false simread:1:231911906:false simread:1:26472783:false simread:1:165341382:true simread:1:240344442:true simread:1:50683371:false simread:1:240997787:true simread:1:14397233:false simread:1:207027738:true simread:1:20101800:true simread:1:101556378:false simread:1:37577445:false simread:1:189606653:true simread:1:5469106:true simread:1:186794283:true simread:1:89554252:false simread:1:153978724:false simread:1:169801933:true - saveAsPairedFastq as single files - don't lose any reads when piping as SAM 2019-06-28 14:03:02 WARN OutFormatterRunner:190 - Piped command List(sleep, 10) timed out after 5 seconds. 2019-06-28 14:03:02 WARN OutFormatterRunner:190 - Piped command List(sleep, 10) timed out after 5 seconds. - lose all records when a command times out - lose no records without a timeout 2019-06-28 14:03:22 WARN OutFormatterRunner:190 - Piped command List(python, /tmp/adamTestMvnJlGqi5R/spark-6b3f4574-6abb-442c-b538-411274870ac0/userFiles-63be99eb-664e-46a2-908f-5539c2aed9e2/timeout.py) timed out after 5 seconds. 2019-06-28 14:03:22 WARN OutFormatterRunner:190 - Piped command List(python, /tmp/adamTestMvnJlGqi5R/spark-6b3f4574-6abb-442c-b538-411274870ac0/userFiles-63be99eb-664e-46a2-908f-5539c2aed9e2/timeout.py) timed out after 5 seconds. - lose some records when a command times out - don't lose any reads when piping as SAM using java pipe - don't lose any reads when piping as BAM - don't lose any reads when piping fastq to sam - can properly set environment variables inside of a pipe - read vcf from alignment record pipe !!! IGNORED !!! - use broadcast join to pull down reads mapped to targets - use broadcast join against to pull down reads mapped to targets - use right outer broadcast join to pull down reads mapped to targets - use right outer broadcast join against to pull down reads mapped to targets - use shuffle join with feature spanning partitions - use shuffle join to pull down reads mapped to targets - use shuffle join with flankSize to pull down reads mapped close to targets - use right outer shuffle join to pull down reads mapped to targets - use left outer shuffle join to pull down reads mapped to targets - use full outer shuffle join to pull down reads mapped to targets - use shuffle join with group by to pull down reads mapped to targets - use right outer shuffle join with group by to pull down reads mapped to targets - cannot provide empty quality score bins - cannot provide bins with a gap - cannot provide overlapping bins - binning quality scores in reads succeeds even if reads have no quality scores - bin quality scores in reads - union two read files together - test k-mer counter - test dataset based k-mer counter - transform reads to slice genomic dataset - transform reads to coverage genomic dataset - transform reads to feature genomic dataset - transform reads to fragment genomic dataset - transform reads to genotype genomic dataset loading /tmp/adamTestMvnJlGqi5R/TempSuite4768414873732522867.adam as parquet into RDD... loading /tmp/adamTestMvnJlGqi5R/TempSuite8376180470130683297.adam as parquet into RDD... - transform reads to variant genomic dataset - cannot have a null processing step ID - convert a processing description to htsjdk - GenomicDataset.sort does not fail on unmapped reads - GenomicDataset.sortLexicographically does not fail on unmapped reads - left normalize indels - running base recalibration with downsampling doesn't drop reads - filter RDD bound alignments by MAPQ - filter dataset bound alignments by MAPQ - filter RDD bound unaligned alignments - filter dataset bound unaligned alignments - filter RDD bound unpaired alignments - filter dataset bound unpaired alignments - filter RDD bound duplicate alignments - filter dataset bound duplicate alignments - filter RDD bound alignments to primary alignments - filter dataset bound alignments to primary alignments - filter RDD bound alignments to read group - filter dataset bound alignments to read group - filter RDD bound alignments to read groups - filter dataset bound alignments to read groups - filter RDD bound alignments to sample - filter dataset bound alignments to sample - filter RDD bound alignments to samples - filter dataset bound alignments to samples - sort by read name - transform dataset via java API - convert alignments to reads SingleReadBucketSuite: - convert unmapped pair to fragment - convert proper pair to fragment - convert read pair to fragment with first of pair chimeric read RecalibrationTableSuite: - look up quality scores in table FlankSlicesSuite: - don't put flanks on non-adjacent slices - put flanks on adjacent slices InterleavedFastqInputFormatSuite: - interleaved FASTQ hadoop reader: interleaved_fastq_sample1.ifq->interleaved_fastq_sample1.ifq.output - interleaved FASTQ hadoop reader: interleaved_fastq_sample2.ifq->interleaved_fastq_sample2.ifq.output - interleaved FASTQ hadoop reader: interleaved_fastq_sample3.ifq->interleaved_fastq_sample3.ifq.output - interleaved FASTQ hadoop reader: interleaved_fastq_sample4.ifq->interleaved_fastq_sample4.ifq.output - interleaved FASTQ hadoop reader: interleaved_fastq_sample5.ifq->interleaved_fastq_sample5.ifq.output TreeRegionJoinSuite: - run a join between data on a single contig ReferenceRegionSuite: - cannot create an empty predicate - parse empty string throws IllegalArgumentException - parse contigName only string into reference regions - parse to end strings into reference regions - parse string into reference regions - contains(: ReferenceRegion) - contains(: ReferencePosition) - merge - overlaps and covers - overlapsBy and coversBy - distance(: ReferenceRegion) - distance(: ReferencePosition) - unstrandedDistance - subtract fails on non-overlapping and non-covering regions - subtract - create region from unmapped read fails - create region from read with null alignment positions fails - create stranded region from unmapped read fails - create stranded region from read with null alignment positions fails - create stranded region from read with null alignment strand fails - create stranded region from read on forward strand - create stranded region from read on reverse strand - create region from mapped read contains read start and end - validate that adjacent regions can be merged - validate that non-adjacent regions cannot be merged - validate that nearby regions can be merged - validate that non-nearby regions cannot be merged - compute convex hull of two sets - region name is sanitized when creating region from read - intersection fails on non-overlapping regions - intersection fails when minOverlap is not met - compute intersection - overlap tests for oriented reference region - check the width of a reference region - make a reference region for a variant or genotype - make a reference region for a variant or genotype starting at VCF 0 - uniformly pad a reference region - uniformly pad a reference region into negative coordinate space, ensure non negative start - unevenly pad a reference region - unevenly pad a reference region into negative coordinate space, ensure non negative start - can build an open ended reference region - can build an open ended reference region with strand - can build a reference region with an open start position - can build a reference region with an open start position with strand - can build a reference region that covers the entirety of a contig - can build a reference region that covers the entirety of a contig with strand - convert a genotype and then get the reference region - create region from feature with null alignment positions fails - create stranded region from feature with null alignment positions fails - create stranded region from feature with null alignment strand fails - create stranded region from feature on forward strand - create stranded region from feature on reverse strand AlignmentRecordConverterSuite: - testing the fields in a converted ADAM Read - converting a read with null quality is OK - convert a read to fastq - reverse complement reads when converting to fastq - converting to fastq with unmapped reads where read reverse complemented flag (Ox10) was NOT set - converting to fastq with unmapped reads where reverse complemented flag (0x10) was set - converting a fragment with no alignments should yield unaligned reads - converting a fragment with alignments should restore the alignments - read negative strand is propagated even when not mapped CoverageDatasetSuite: - correctly saves coverage - can read a bed file to coverage - correctly filters coverage with predicate - keeps sample metadata - can read a bed file with multiple samples to coverage - correctly flatmaps coverage without aggregated bins - correctly flatmaps coverage with aggregated bins - collapses coverage records in one partition - approximately collapses coverage records in multiple partitions 2019-06-28 14:04:10 WARN DatasetBoundSliceDataset:190 - Saving directly as Parquet from SQL. Options other than compression codec are ignored. - transform coverage to slice genomic dataset - transform coverage to feature genomic dataset - transform coverage to fragment genomic dataset - transform coverage to read genomic dataset - transform coverage to genotype genomic dataset - transform coverage to variant genomic dataset - transform coverage to variant context genomic dataset - copy coverage rdd - copy coverage dataset - copy coverage rdd without sequence dictionary - copy coverage dataset without sequence dictionary - transform dataset via java API RecalibratorSuite: - don't replace quality if quality was null - if no covariates, return alignment - skip recalibration if base is below quality threshold - recalibrate changed bases above quality threshold SliceDatasetSuite: - create a new slice genomic dataset - create a new slice genomic dataset with sequence dictionary - merge slices into a sequence genomic dataset - save as parquet - round trip as parquet - save as fasta - save as single file fasta - convert slices to reads - convert slices to sequences GenotypeDatasetSuite: - union two genotype genomic datasets together - round trip to parquet - round trip to partitioned parquet - use broadcast join to pull down genotypes mapped to targets - use right outer broadcast join to pull down genotypes mapped to targets - use shuffle join to pull down genotypes mapped to targets - use right outer shuffle join to pull down genotypes mapped to targets - use left outer shuffle join to pull down genotypes mapped to targets - use full outer shuffle join to pull down genotypes mapped to targets - use shuffle join with group by to pull down genotypes mapped to targets - use right outer shuffle join with group by to pull down genotypes mapped to targets - convert back to variant contexts - load parquet to sql, save, re-read from avro 2019-06-28 14:04:35 WARN DatasetBoundSliceDataset:190 - Saving directly as Parquet from SQL. Options other than compression codec are ignored. - transform genotypes to slice genomic dataset - transform genotypes to coverage genomic dataset - transform genotypes to feature genomic dataset - transform genotypes to fragment genomic dataset - transform genotypes to read genomic dataset - transform genotypes to variant genomic dataset - transform genotypes to variant context genomic dataset - loading genotypes then converting to variants yields same output as loading variants - filter RDD bound genotypes to genotype filters passed - filter dataset bound genotypes to genotype filters passed - filter RDD bound genotypes by genotype quality - filter dataset bound genotypes by genotype quality - filter RDD bound genotypes by read depth - filter dataset bound genotypes by read depth - filter RDD bound genotypes by alternate read depth - filter dataset bound genotypes by alternate read depth - filter RDD bound genotypes by reference read depth - filter dataset bound genotypes by reference read depth - filter RDD bound genotypes by sample - filter dataset bound genotypes by sample - filter RDD bound genotypes by samples - filter dataset bound genotypes by samples - filter RDD bound no call genotypes - filter dataset no call genotypes - round trip gVCF END attribute without nested variant annotations rdd bound - round trip gVCF END attribute without nested variant annotations dataset bound - round trip gVCF END attribute with nested variant annotations rdd bound - round trip gVCF END attribute with nested variant annotations dataset bound - transform dataset via java API FragmentDatasetSuite: - don't lose any reads when piping interleaved fastq to sam - don't lose any reads when piping tab5 to sam - don't lose any reads when piping tab6 to sam - use broadcast join to pull down fragments mapped to targets - use right outer broadcast join to pull down fragments mapped to targets - use shuffle join to pull down fragments mapped to targets - use right outer shuffle join to pull down fragments mapped to targets - use left outer shuffle join to pull down fragments mapped to targets - use full outer shuffle join to pull down fragments mapped to targets - use shuffle join with group by to pull down fragments mapped to targets - use right outer shuffle join with group by to pull down fragments mapped to targets - bin quality scores in fragments - union two genomic datasets of fragments together - load parquet to sql, save, re-read from avro - transform fragments to slice genomic dataset - transform fragments to coverage genomic dataset - transform fragments to feature genomic dataset - transform fragments to read genomic dataset - transform fragments to genotype genomic dataset - transform fragments to variant genomic dataset - transform fragments to variant context genomic dataset - paired read names with index sequences in read names can group into fragments - interleaved paired read names with index sequences in read names can group into fragments - interleaved paired read names with index sequences in read names as fragments - transform dataset via java API - dataset and rdd conversion to alignments are equivalent SingleFastqInputFormatSuite: - FASTQ hadoop reader: fastq_sample1.fq->single_fastq_sample1.fq.output - FASTQ hadoop reader: fastq_sample2.fq->single_fastq_sample2.fq.output - FASTQ hadoop reader: fastq_sample3.fq->single_fastq_sample3.fq.output - FASTQ hadoop reader: fastq_sample4.fq->single_fastq_sample4.fq.output VariantContextDatasetSuite: - load a gvcf with a missing info field set to . - union two variant context genomic datasets together - can write, then read in .vcf file - can write as a single file via simple saveAsVcf method, then read in .vcf file - can write as a single file via full saveAsVcf method, then read in .vcf file - transform a vcf file with bad header - read a vcf file with multi-allelic variants to split - support VCFs with +Inf/-Inf float values - support VCFs with `nan` instead of `NaN` float values - don't lose any variants when piping as VCF - pipe works with empty partitions - don't lose any non-default VCF header lines or attributes when piping as VCF - save a file sorted by contig index - save a lexicographically sorted file - save a multiallelic gvcf !!! IGNORED !!! - test metadata - save sharded bgzip vcf - save bgzip vcf as single file - can't save file with non-vcf extension - transform variant contexts to slice genomic dataset - transform variant contexts to coverage genomic dataset - transform variant contexts to feature genomic dataset - transform variant contexts to fragment genomic dataset - transform variant contexts to read genomic dataset - transform variant contexts to genotype genomic dataset - transform variant contexts to variant genomic dataset - save and reload from partitioned parquet - transform dataset via java API ConsensusSuite: - test the insertion of a consensus insertion into a reference - test the insertion of a consensus deletion into a reference - inserting empty consensus returns the reference SequenceDatasetSuite: - create a new sequence genomic dataset - create a new sequence genomic dataset with sequence dictionary - save as parquet - round trip as parquet - save as fasta - save as single file fasta - convert sequences to reads - convert sequences to slices - slice sequences to a maximum length - slice sequences shorter than maximum length - filter sequences by overlapping region - filter sequences failing to overlap region - filter sequences by overlapping regions - filter sequences failing to overlap regions - slice sequences overlapping a smaller region - slice sequences overlapping a larger region - slice sequences failing to overlap a region - slice sequences overlapping smaller regions - slice sequences overlapping larger regions - slice sequences failing to overlap regions AttributeUtilsSuite: - parseTags returns a reasonable set of tagStrings - parseTags works with NumericSequence tagType - empty string is parsed as zero tagStrings - incorrectly formatted tag throws an exception - string tag with a ':' in it is correctly parsed - oq string tag with many ':' in it is correctly parsed - oq string tag with a ',' in it is correctly parsed - if a tag is an array but doesn't define it's format, throw MarkDuplicatesSuite: - single read - reads at different positions - reads at the same position - reads at the same position with clipping - reads on reverse strand - unmapped reads - read pairs - read pairs with fragments - quality scores - read pairs that cross chromosomes - single fragment - fragments at different positions - fragments at the same position - fragments at the same position with clipping - fragments on reverse strand - unmapped fragments - read pairs as fragments - read pairs with fragments as fragments - chimeric fragments - inverse pairs - supplemental reads TranscriptEffectConverterSuite: - parse empty transcript effect - parse empty transcript effect strict validation stringency - parse invalid transcript effect - parse invalid transcript effect strict validation stringency - parse transcript effect - parse empty list VCF ANN attribute - parse empty list VCF ANN attribute strict validation stringency - parse empty string VCF ANN attribute - parse empty string VCF ANN attribute strict validation stringency - parse invalid VCF ANN attribute - parse invalid VCF ANN attribute strict validation stringency - parse VCF ANN attribute with one transcript effect - parse VCF ANN attribute with multiple transcript effects - convert to transcript effect from null VCF ANN attribute in variant context - convert to transcript effect from empty list VCF ANN attribute in variant context - convert to transcript effect from empty list VCF ANN attribute in variant context strict validation stringency - convert to transcript effect from empty string VCF ANN attribute in variant context - convert to transcript effect from empty string VCF ANN attribute in variant context strict validation stringency - convert to transcript effect from invalid VCF ANN attribute in variant context - convert to transcript effect from invalid VCF ANN attribute in variant context strict validation stringency 2019-06-28 14:05:53 WARN TranscriptEffectConverter$:190 - Could not convert VCF INFO reserved key ANN value to TranscriptEffect, caught java.lang.NumberFormatException: For input string: "not a number". - convert to transcript effect from VCF ANN attribute with invalid number in variant context lenient validation stringency 2019-06-28 14:05:53 WARN TranscriptEffectConverter$:190 - Could not convert VCF INFO reserved key ANN value to TranscriptEffect, caught java.lang.NumberFormatException: For input string: "not a number". - convert to transcript effect from VCF ANN attribute with invalid fraction in variant context lenient validation stringency - convert to transcript effect from VCF ANN attribute with invalid number in variant context strict validation stringency - convert to transcript effect from VCF ANN attribute with invalid fraction in variant context strict validation stringency - convert to transcript effect from VCF ANN attribute in variant context different alt allele - convert to transcript effect from VCF ANN attribute in variant context same alt allele - convert to transcript effect from VCF ANN attribute in variant context multiple effects same alt allele - convert transcript effect to VCF ANN attribute value - convert transcript effect with null fields to VCF ANN attribute value 2019-06-28 14:05:53 WARN TranscriptEffectConverter$:190 - Incorrect fractional value ?/2, missing numerator - convert transcript effect with incorrect fractional value to VCF ANN attribute value IndelRealignmentTargetSuite: - checking simple realignment target - creating simple target from read with deletion - creating simple target from read with insertion - joining simple realignment targets on same chr - joining simple realignment targets on different chr throws exception - creating targets from three intersecting reads, same indel - creating targets from three intersecting reads, two different indel - creating targets from two disjoint reads - creating targets for artificial reads: one-by-one - creating targets for artificial reads: all-at-once (merged) - creating indel targets for mason reads - additional indel targets taken from consensus generator NormalizationUtilsSuite: - cannot move an indel left if there are no bases to it's left - move a simple indel to farthest position left until bases run out - move a simple indel to farthest position left, past length of indel - cannot move a left normalized indel in a short tandem repeat - move an indel in a short tandem repeat - move an indel in a short tandem repeat of more than 2 bases, where shift is not an integer multiple of repeated sequence length - moving a simple read with single deletion that cannot shift - shift an indel left by 0 in a cigar - shift an indel left by 1 in a cigar - do not left align a complex read which is already left aligned ReadGroupDictionarySuite: - simple conversion to and from sam read group - sample name must be set - simple equality checks - get samples from read group dictionary - empty read group is empty - merging a dictionary with itself should work - round trip a record with all attributes set RightOuterTreeRegionJoinSuite: - Ensure same reference regions get passed together - Overlapping reference regions InnerShuffleRegionJoinSuite: - Overlapping reference regions - Multiple reference regions do not throw exception FeatureDatasetSuite: - round trip GTF format - save GTF as GFF3 format - save GTF as BED format - save GTF as IntervalList format - save GTF as NarrowPeak format - save GFF3 as GTF format - save GFF3 as BED format - save GFF3 as IntervalList format - save GFF3 as NarrowPeak format - round trip GFF3 format - ignore FASTA sequence in GFF3 file - save BED as GTF format - save BED as GFF3 format - save BED as IntervalList format - save BED as NarrowPeak format - round trip BED6 format - keeps sample metadata - round trip BED12 format - save to UCSC BED format - save IntervalList as GTF format - save IntervalList as GFF3 format - save IntervalList as BED format - save IntervalList as IntervalList format - save IntervalList as NarrowPeak format - round trip IntervalList format - save NarrowPeak as GTF format - save NarrowPeak as GFF3 format - save NarrowPeak as BED format - save NarrowPeak as IntervalList format - save NarrowPeak as NarrowPeak format - round trip NarrowPeak format - sort by reference - sort by reference and feature fields - sort gene features by reference and gene structure - sort transcript features by reference and gene structure - sort exon features by reference and gene structure - sort intron features by reference and gene structure - correctly flatmaps CoverageDataset from FeatureDataset - use broadcast join to pull down features mapped to targets - use right outer broadcast join to pull down features mapped to targets - use shuffle join to pull down features mapped to targets - use right outer shuffle join to pull down features mapped to targets - use left outer shuffle join to pull down features mapped to targets - use full outer shuffle join to pull down features mapped to targets - use shuffle join with group by to pull down features mapped to targets - use right outer shuffle join with group by to pull down features mapped to targets - union two feature rdds together - obtain sequence dictionary contig lengths from header in IntervalList format - don't lose any features when piping as BED format - don't lose any features when piping as GTF format - don't lose any features when piping as GFF3 format - don't lose any features when piping as NarrowPeak format - load parquet to sql, save, re-read from avro - load partitioned parquet to sql, save, re-read from avro 2019-06-28 14:06:26 WARN DatasetBoundSliceDataset:190 - Saving directly as Parquet from SQL. Options other than compression codec are ignored. - transform features to slice genomic dataset - transform features to coverage genomic dataset - transform features to fragment genomic dataset - transform features to read genomic dataset - transform features to genotype genomic dataset - transform features to variant genomic dataset - transform features to variant context genomic dataset - filter RDD bound features by feature type - filter dataset bound features by feature type - filter RDD bound features by feature types - filter dataset bound features by feature types - filter RDD bound features by gene - filter dataset bound features by gene - filter RDD bound features by genes - filter dataset bound features by genes - filter RDD bound features by transcript - filter dataset bound features by transcript - filter RDD bound features by transcripts - filter dataset bound features by transcripts - filter RDD bound features by exon - filter dataset bound features by exon - filter RDD bound features by exons - filter dataset bound features by exons - filter RDD bound features by score - filter dataset bound features by score - filter RDD bound features by parent - filter dataset bound features by parent - filter RDD bound features by parents - filter dataset bound features by parents - filter RDD bound features by attribute - filter dataset bound features by attribute - transform dataset via java API AlphabetSuite: - test size of a case-sensitive alphabet - test apply of a case-sensitive alphabet - test reverse complement of a case-sensitive alphabet - test exact reverse complement of a case-sensitive alphabet - test size of a case-insensitive alphabet - test apply of a case-insensitive alphabet - test reverse complement of a case-insensitive alphabet - test exact reverse complement of a case-insensitive alphabet - DNA alphabet - map unknown bases to N SortedGenomicDatasetSuite: - testing that partition and sort provide correct outputs - testing copartition maintains or adds sort - testing that we don't drop any data on the right side even though it doesn't map to a partition on the left - testing that sorted shuffleRegionJoin matches unsorted - testing that sorted fullOuterShuffleRegionJoin matches unsorted - testing that sorted rightOuterShuffleRegionJoin matches unsorted - testing that sorted leftOuterShuffleRegionJoin matches unsorted - testing that we can persist the sorted knowledge VariantContextConverterSuite: - Convert htsjdk site-only SNV to ADAM - Convert somatic htsjdk site-only SNV to ADAM - Convert htsjdk site-only CNV to ADAM - Convert htsjdk SNV w/ genotypes w/ phase information to ADAM - Convert htsjdk SNV with different variant filters to ADAM - Convert htsjdk SNV with different genotype filters to ADAM - Convert ADAM site-only SNV to htsjdk - Convert ADAM SNV w/ genotypes to htsjdk - Convert ADAM SNV w/ genotypes but bad SB to htsjdk with strict validation 2019-06-28 14:06:42 WARN VariantContextConverter:2300 - Applying annotation extraction function org.bdgenomics.adam.converters.VariantContextConverter$$Lambda$804/1770437551@14b3659c to {"variant": {"referenceName": "1", "start": 0, "end": 1, "names": [], "splitFromMultiAllelic": false, "referenceAllele": "A", "alternateAllele": "T", "quality": null, "filtersApplied": null, "filtersPassed": null, "filtersFailed": [], "annotation": null}, "referenceName": null, "start": null, "end": null, "variantCallingAnnotations": {"filtersApplied": null, "filtersPassed": null, "filtersFailed": [], "downsampled": null, "baseQRankSum": null, "fisherStrandBiasPValue": 3.0, "rmsMapQ": 0.0, "mapq0Reads": 5, "mqRankSum": null, "readPositionRankSum": null, "genotypePriors": [], "genotypePosteriors": [], "vqslod": null, "culprit": null, "attributes": {}}, "sampleId": "NA12878", "sampleDescription": null, "processingDescription": null, "alleles": ["REF", "ALT"], "expectedAlleleDosage": null, "referenceReadDepth": null, "alternateReadDepth": null, "readDepth": null, "minReadDepth": null, "genotypeQuality": null, "genotypeLikelihoods": [], "nonReferenceLikelihoods": [], "strandBiasComponents": [0, 2], "splitFromMultiAllelic": false, "phased": false, "phaseSetId": null, "phaseQuality": null} failed with java.lang.IllegalArgumentException: requirement failed: Illegal strand bias components length. Must be empty or 4. In: {"variant": {"referenceName": "1", "start": 0, "end": 1, "names": [], "splitFromMultiAllelic": false, "referenceAllele": "A", "alternateAllele": "T", "quality": null, "filtersApplied": null, "filtersPassed": null, "filtersFailed": [], "annotation": null}, "referenceName": null, "start": null, "end": null, "variantCallingAnnotations": {"filtersApplied": null, "filtersPassed": null, "filtersFailed": [], "downsampled": null, "baseQRankSum": null, "fisherStrandBiasPValue": 3.0, "rmsMapQ": 0.0, "mapq0Reads": 5, "mqRankSum": null, "readPositionRankSum": null, "genotypePriors": [], "genotypePosteriors": [], "vqslod": null, "culprit": null, "attributes": {}}, "sampleId": "NA12878", "sampleDescription": null, "processingDescription": null, "alleles": ["REF", "ALT"], "expectedAlleleDosage": null, "referenceReadDepth": null, "alternateReadDepth": null, "readDepth": null, "minReadDepth": null, "genotypeQuality": null, "genotypeLikelihoods": [], "nonReferenceLikelihoods": [], "strandBiasComponents": [0, 2], "splitFromMultiAllelic": false, "phased": false, "phaseSetId": null, "phaseQuality": null}. - Convert ADAM SNV w/ genotypes but bad SB to htsjdk with lenient validation - Convert htsjdk multi-allelic sites-only SNVs to ADAM - Convert htsjdk multi-allelic SNVs to ADAM and back to htsjdk - Convert gVCF reference records to ADAM - Convert htsjdk variant context with no IDs to ADAM - Convert htsjdk variant context with one ID to ADAM - Convert htsjdk variant context with multiple IDs to ADAM - Convert ADAM variant context with no names to htsjdk - Convert ADAM variant context with one name to htsjdk - Convert ADAM variant context with multiple names to htsjdk - Convert ADAM variant context with null filters applied to htsjdk - Convert ADAM variant context with no filters applied to htsjdk - Convert ADAM variant context with passing filters to htsjdk - Convert ADAM variant context with failing filters to htsjdk - no phasing set going htsjdk->adam - phased but no phase set info going htsjdk->adam - set phase set and extract going htsjdk->adam - no allelic depth going htsjdk->adam - set allelic depth going htsjdk->adam - no gt read depth going htsjdk->adam - extract gt read depth going htsjdk->adam - no min gt read depth going htsjdk->adam - extract min gt read depth going htsjdk->adam - no genotype quality going htsjdk->adam - extract genotype quality going htsjdk->adam - no phred likelihood going htsjdk->adam - extract phred likelihoods going htsjdk->adam - no strand bias info going htsjdk->adam - extract strand bias info going htsjdk->adam - no filters going htsjdk->adam - filters passed going htsjdk->adam - extract single filter going htsjdk->adam - extract multiple filters going htsjdk->adam - no fisher strand bias going htsjdk->adam - extract fisher strand bias going htsjdk->adam - no rms mapping quality going htsjdk->adam - extract rms mapping quality going htsjdk->adam - no mq0 going htsjdk->adam - extract mq0 going htsjdk->adam - no gt read depth going adam->htsjdk - extract gt read depth going adam->htsjdk - throw iae if missing one component of gt read depth going adam->htsjdk - no depth going adam->htsjdk - extract depth going adam->htsjdk - no min depth going adam->htsjdk - extract min depth going adam->htsjdk - no quality going adam->htsjdk - extract quality going adam->htsjdk - no genotype likelihoods going adam->htsjdk - extract genotype likelihoods going adam->htsjdk - no strand bias going adam->htsjdk - malformed strand bias going adam->htsjdk - extract strand bias going adam->htsjdk - no phasing info going adam->htsjdk - unphased going adam->htsjdk - phased but no ps/pq going adam->htsjdk - phased but no pq going adam->htsjdk - phased but no ps going adam->htsjdk - phased going adam->htsjdk - no filter info going adam->htsjdk - if filters applied, must set passed/failed going adam->htsjdk - filters passed going adam->htsjdk - if filters failed, must set filters failed going adam->htsjdk - single filter failed going adam->htsjdk - multiple filters failed going adam->htsjdk - no fisher strand bias going adam->htsjdk - extract fisher strand bias going adam->htsjdk - no rms mapping quality going adam->htsjdk - extract rms mapping quality going adam->htsjdk - no mapping quality 0 reads going adam->htsjdk - extract mapping quality 0 reads going adam->htsjdk - no names set going htsjdk->adam - single name set going htsjdk->adam - multiple names set going htsjdk->adam - no quality going htsjdk->adam - quality set going htsjdk->adam - no filters applied going htsjdk->adam - filters applied and passed going htsjdk->adam - single filter applied and failed going htsjdk->adam - multiple filters applied and failed going htsjdk->adam - no names set adam->htsjdk - set a single name adam->htsjdk - set multiple names adam->htsjdk - no qual set adam->htsjdk - qual is set adam->htsjdk - no filters applied adam->htsjdk - null filters applied adam->htsjdk - filters passed adam->htsjdk - if filter failed, must have filters adam->htsjdk - single filter failed adam->htsjdk - multiple filters failed adam->htsjdk - no ancestral allele set going htsjdk->adam - ancestral allele set going htsjdk->adam - no dbsnp membership set going htsjdk->adam - dbsnp membership set going htsjdk->adam - no hapmap2 membership set going htsjdk->adam - hapmap2 membership set going htsjdk->adam - no hapmap3 membership set going htsjdk->adam - hapmap3 membership set going htsjdk->adam - no validated set going htsjdk->adam - validated set going htsjdk->adam - no 1000G membership set going htsjdk->adam - 1000G membership set going htsjdk->adam - not somatic going htsjdk->adam - somatic going htsjdk->adam - no allele count going htsjdk->adam - single allele count going htsjdk->adam - multiple allele counts going htsjdk->adam - no allele frequency going htsjdk->adam - single allele frequency going htsjdk->adam - single allele frequency is +Inf going htsjdk->adam - single allele frequency is -Inf going htsjdk->adam - multiple allele frequencies going htsjdk->adam - no CIGAR going htsjdk->adam - single CIGAR going htsjdk->adam - multiple CIGARs going htsjdk->adam - no read depth going htsjdk->adam - single read depth going htsjdk->adam - multiple read depths going htsjdk->adam - no forward read depth going htsjdk->adam - single forward read depth going htsjdk->adam - multiple forward read depths going htsjdk->adam - no reverse read depth going htsjdk->adam - single reverse read depth going htsjdk->adam - multiple reverse read depths going htsjdk->adam - no ancestral allele set adam->htsjdk - ancestral allele set adam->htsjdk - no dbsnp membership set adam->htsjdk - dbsnp membership set adam->htsjdk - no hapmap2 membership set adam->htsjdk - hapmap2 membership set adam->htsjdk - no hapmap3 membership set adam->htsjdk - hapmap3 membership set adam->htsjdk - no validated set adam->htsjdk - validated set adam->htsjdk - no 1000G membership set adam->htsjdk - 1000G membership set adam->htsjdk - no allele count set adam->htsjdk - allele count set adam->htsjdk - no allele frequency set adam->htsjdk - allele frequency set adam->htsjdk - no cigar set adam->htsjdk - cigar set adam->htsjdk - no read depth set adam->htsjdk - read depth set adam->htsjdk - read depth without reference read depth - reference read depth without read depth - no forward read depth set adam->htsjdk - forward read depth set adam->htsjdk - reference forward read depth without forward read depth - forward read depth without reference forward read depth - no reverse read depth set adam->htsjdk - reverse read depth set adam->htsjdk - reference reverse read depth without reverse read depth - reverse read depth without reference reverse read depth - VCF INFO attribute Number=0 Type=Flag adam->htsjdk - VCF INFO attribute Number=4 Type=Flag adam->htsjdk unsupported, strict !!! IGNORED !!! - VCF INFO attribute Number=1 Type=Integer adam->htsjdk - VCF INFO attribute Number=4 Type=Integer adam->htsjdk - VCF INFO attribute Number=A Type=Integer adam->htsjdk - VCF INFO attribute Number=R Type=Integer adam->htsjdk - VCF INFO attribute Number=R Type=String adam->htsjdk - VCF INFO attribute Number=G Type=String adam->htsjdk not supported - VCF INFO attribute Number=0 Type=Flag htsjdk->adam - VCF INFO attribute Number=1 Type=Integer htsjdk->adam - VCF INFO attribute Number=4 Type=Integer htsjdk->adam - VCF INFO attribute Number=4 Type=Float htsjdk->adam - VCF INFO attribute Number=A Type=Integer htsjdk->adam - VCF INFO attribute Number=R Type=Integer htsjdk->adam - VCF INFO attribute Number=R Type=String htsjdk->adam - VCF INFO attribute Number=G Type=String htsjdk->adam not supported - VCF FORMAT attribute Number=0 Type=Flag adam->htsjdk not supported - VCF FORMAT attribute Number=1 Type=Integer adam->htsjdk - VCF FORMAT attribute Number=4 Type=Integer adam->htsjdk - VCF FORMAT attribute Number=A Type=Integer adam->htsjdk - VCF FORMAT attribute Number=R Type=Integer adam->htsjdk - VCF FORMAT attribute Number=R Type=String adam->htsjdk - VCF FORMAT attribute Number=0 Type=Flag htsjdk->adam is not supported - VCF FORMAT attribute Number=1 Type=Integer htsjdk->adam - VCF FORMAT attribute Number=4 Type=Integer htsjdk->adam - VCF FORMAT attribute Number=4 Type=Float htsjdk->adam - VCF FORMAT attribute Number=A Type=Integer htsjdk->adam - VCF FORMAT attribute Number=R Type=Integer htsjdk->adam - VCF FORMAT attribute Number=R Type=String htsjdk->adam - VCF FORMAT attribute Number=G Type=String htsjdk->adam - respect end position for symbolic alts FastqRecordConverterSuite: - test read name suffix and index of pair must match - test parseReadInFastq, read suffix removal - test parseReadInFastq, read metadata removal - test parseReadInFastq, read quality shorter than read length, padded with B - test parseReadInFastq, read quality longer than read length - test parseReadInFastq, no read quality - testing FastqRecordConverter.convertPair with valid input - testing FastqRecordConverter.convertPair with 7-line invalid input - testing FastqRecordConverter.convertPair with invalid input: first read length and qual don't match - testing FastqRecordConverter.convertPair with invalid input: second read length and qual don't match - testing FastqRecordConverter.convertFragment with valid input - testing FastqRecordConverter.convertFragment with another valid input having /1, /2 suffixes - testing FastqRecordConverter.convertFragment with invalid input: different read names - testing FastqRecordConverter.convertRead with valid input - testing FastqRecordConverter.convertRead with valid input: setFirstOfPair set to true - testing FastqRecordConverter.convertRead with valid input: setSecondOfPair set to true - testing FastqRecordConverter.convertRead with valid input: setFirstOfPair and setSecondOfPair both true - testing FastqRecordConverter.convertRead with valid input, no qual, strict - testing FastqRecordConverter.convertRead with valid input, no qual, not strict AttributeSuite: - test SAMTagAndValue parsing - Attributes can be correctly re-encoded as text SAM tags GFF3HeaderWriterSuite: - write gff3 header pragma BinQualitiesSuite: - make a quality score bin - can't have a quality score bin with negative score - can't have a quality score bin with high score below low - can't have a quality score bin with high score above 255 - can't have a quality score bin with score outside - make a quality score bin from a string - quality score bin must have exactly 3 elements - quality score bin must be integers - must define at least one bin - build multiple bins - rewrite quality scores for a read - rewriting quality scores fails if bins overlap - rewriting quality scores fails if base is out of bounds - skip read if qualities are null - rewrite a read IndexedFastaFileSuite: - correctly generates sequence dictionary from .dict file - correctly gets sequence - fails when fai index is not provided 2019-06-28 14:06:43 WARN IndexedFastaFile:190 - Caught exception java.lang.NullPointerException when loading FASTA sequence dictionary. Using empty dictionary instead. - passes when dict is not provided and ValidationStringency = LENIENT SAMRecordConverterSuite: - testing the fields in an alignmentRecord obtained from a mapped samRecord conversion - testing the fields in an alignmentRecord obtained from an unmapped samRecord conversion - '*' quality gets nulled out - don't keep denormalized fields ADAMContextSuite: - ctr is accessible - load from an empty directory - sc.loadParquet should not fail on unmapped reads - sc.loadParquet should not load a file without a type specified - can read a small .SAM file - can read a small .SAM file with a bad header with lenient validation - loading a sam file with a bad header and strict stringency should fail - can read a small .CRAM file - can read a small .SAM with all attribute tag types - can filter a .SAM file based on quality - Can convert to phred - Can convert from phred - Can read a .gtf file - Can read a .bed file - Can read a BED 12 file - Can read a .narrowPeak file - Can read a .interval_list file 2019-06-28 14:06:46 WARN VariantContextConverter:1662 - Saw invalid info field java.lang.IllegalArgumentException: Multivalued flags are not supported for INFO lines: INFO=<ID=ABADFLAG,Number=.,Type=Flag,Description="A no good, very bad flag.">. Ignoring... 2019-06-28 14:06:46 WARN VariantContextConverter:2169 - Generating field extractor from header line INFO=<ID=ABADFLAG,Number=.,Type=Flag,Description="A no good, very bad flag."> failed: java.lang.IllegalArgumentException: Multivalue flags are not supported for INFO lines: INFO=<ID=ABADFLAG,Number=.,Type=Flag,Description="A no good, very bad flag."> - can read a small .vcf file with a validation issue - can read a small .vcf file 2019-06-28 14:06:47 WARN VCFInputFormat:218 - file:/home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/target/2.12.8/test-classes/test.vcf.gz is not splittable, consider using block-compressed gzip (BGZF) - can read a gzipped .vcf file - can read a vcf file with an empty alt - can read a BGZF gzipped .vcf file with .gz file extension - can read a BGZF gzipped .vcf file with .bgz file extension - can read a vcf file with a projection - can read an uncompressed BCFv2.2 file !!! IGNORED !!! - can read a BGZF compressed BCFv2.2 file !!! IGNORED !!! - loadIndexedVcf with 1 ReferenceRegion - loadIndexedVcf with multiple ReferenceRegions - load block compressed interleaved fastq - import records from interleaved FASTQ: 1 - import records from interleaved FASTQ: 2 - import records from interleaved FASTQ: 3 - import records from interleaved FASTQ: 4 - import block compressed single fastq - import records from single ended FASTQ: 1 - import records from single ended FASTQ: 2 - import records from single ended FASTQ: 3 - import records from single ended FASTQ: 4 - filter on load using the filter2 API - saveAsParquet with file path - saveAsParquet with file path, block size, page size - saveAsParquet with save args - read a HLA fasta from GRCh38 - read a gzipped fasta file - read a fasta file with comments, gaps, and translation stops - loadIndexedBam with 1 ReferenceRegion - loadIndexedBam with multiple ReferenceRegions - loadIndexedBam with multiple ReferenceRegions and indexed bams - loadIndexedBam with multiple ReferenceRegions and a directory of indexed bams - loadIndexedBam should throw exception without an index file - loadIndexedBam should work with indexed file with index naming format <filename>.bai - loadIndexedBam glob should throw exception without an index file - loadBam with a glob - loadBam with a directory - load vcf with a glob - load vcf from a directory - load gvcf which contains a multi-allelic row from a directory - load and save gvcf which contains rows without likelihoods - parse annotations for multi-allelic rows - load parquet with globs - bad glob should fail - empty directory should fail - can read a SnpEff-annotated .vcf file - loadAlignments should not fail on single-end and paired-end fastq reads - load queryname sorted sam as fragments - load query grouped sam as fragments - load paired fastq - load paired fastq without cache - load paired fastq as fragments - load paired fastq as fragments without cache - load HTSJDK sequence dictionary - load Bedtools .genome file as sequence dictionary - load Bedtools .genome.txt file as sequence dictionary - load UCSC Genome Browser chromInfo.txt file as sequence dictionary - load unrecognized file extension as sequence dictionary fails - load BED features with Bedtools .genome file as sequence dictionary - load BED features with Bedtools .genome file as sequence dictionary, no matching features - convert program record - load program record from sam file - load alignments from data frame - load features from data frame - load fragments from data frame - load genotypes from data frame with default header lines - load genotypes from data frame with empty header lines - load reads from data frame - load sequences from data frame - load slices from data frame - load variant contexts from data frame with default header lines - load variant contexts from data frame with empty header lines - load variants from data frame with default header lines - load variants from data frame with empty header lines - load alignments with metadata from data frame - load features with metadata from data frame - load fragments with metadata from data frame - load genotypes with metadata from data frame - load variant contexts with metadata from data frame - load variants with metadata from data frame - read a fasta file with short sequences as sequences - read a fasta file with long sequences as sequences - read a fasta file with short sequences as slices - read a fasta file with long sequences as slices CycleCovariateSuite: - compute covariates for an unpaired read on the negative strand - compute covariates for a first-of-pair read on the negative strand - compute covariates for a second-of-pair read on the negative strand - compute covariates for an unpaired read on the positive strand - compute covariates for a first-of-pair read on the positive strand - compute covariates for a second-of-pair read on the positive strand ConsensusGeneratorFromKnownsSuite: - no consensuses for empty target - no consensuses for reads that don't overlap a target - return a consensus for read overlapping a single target RichCigarSuite: - moving 2 bp from a deletion to a match operator - moving 2 bp from a insertion to a match operator - moving 1 base in a two element cigar - move to start of read - process right clipped cigar - process left clipped cigar - process cigar clipped on both ends MDTaggingSuite: - test adding MDTags over boundary - test adding MDTags; reads span full contig - test adding MDTags; reads start inside first fragment - test adding MDTags; reads end inside last fragment - test adding MDTags; reads start inside first fragment and end inside last fragment - test adding MDTags; reads start and end in middle fragements 2019-06-28 14:07:32 WARN BlockManager:66 - Putting block rdd_5_3 failed due to exception java.lang.Exception: Contig chr2 not found in reference map with keys: chr1. 2019-06-28 14:07:32 WARN BlockManager:66 - Block rdd_5_3 could not be removed as it was not found on disk or in memory 2019-06-28 14:07:32 ERROR Executor:91 - Exception in task 3.0 in stage 2.0 (TID 11) java.lang.Exception: Contig chr2 not found in reference map with keys: chr1 at org.bdgenomics.adam.util.ReferenceContigMap.$anonfun$extract$1(ReferenceContigMap.scala:64) at scala.collection.immutable.Map$Map1.getOrElse(Map.scala:119) at org.bdgenomics.adam.util.ReferenceContigMap.extract(ReferenceContigMap.scala:63) at org.bdgenomics.adam.rdd.read.MDTagging.$anonfun$addMDTagsBroadcast$3(MDTagging.scala:76) at scala.Option$WithFilter.map(Option.scala:163) at org.bdgenomics.adam.rdd.read.MDTagging.$anonfun$addMDTagsBroadcast$1(MDTagging.scala:71) at scala.collection.Iterator$$anon$10.next(Iterator.scala:459) at org.apache.spark.storage.memory.MemoryStore.putIterator(MemoryStore.scala:222) at org.apache.spark.storage.memory.MemoryStore.putIteratorAsValues(MemoryStore.scala:299) at org.apache.spark.storage.BlockManager.$anonfun$doPutIterator$1(BlockManager.scala:1165) at org.apache.spark.storage.BlockManager.doPut(BlockManager.scala:1091) at org.apache.spark.storage.BlockManager.doPutIterator(BlockManager.scala:1156) at org.apache.spark.storage.BlockManager.getOrElseUpdate(BlockManager.scala:882) at org.apache.spark.rdd.RDD.getOrCompute(RDD.scala:335) at org.apache.spark.rdd.RDD.iterator(RDD.scala:286) at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:90) at org.apache.spark.scheduler.Task.run(Task.scala:121) at org.apache.spark.executor.Executor$TaskRunner.$anonfun$run$3(Executor.scala:411) at org.apache.spark.util.Utils$.tryWithSafeFinally(Utils.scala:1360) at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:414) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624) at java.lang.Thread.run(Thread.java:748) 2019-06-28 14:07:32 WARN TaskSetManager:66 - Lost task 3.0 in stage 2.0 (TID 11, localhost, executor driver): java.lang.Exception: Contig chr2 not found in reference map with keys: chr1 at org.bdgenomics.adam.util.ReferenceContigMap.$anonfun$extract$1(ReferenceContigMap.scala:64) at scala.collection.immutable.Map$Map1.getOrElse(Map.scala:119) at org.bdgenomics.adam.util.ReferenceContigMap.extract(ReferenceContigMap.scala:63) at org.bdgenomics.adam.rdd.read.MDTagging.$anonfun$addMDTagsBroadcast$3(MDTagging.scala:76) at scala.Option$WithFilter.map(Option.scala:163) at org.bdgenomics.adam.rdd.read.MDTagging.$anonfun$addMDTagsBroadcast$1(MDTagging.scala:71) at scala.collection.Iterator$$anon$10.next(Iterator.scala:459) at org.apache.spark.storage.memory.MemoryStore.putIterator(MemoryStore.scala:222) at org.apache.spark.storage.memory.MemoryStore.putIteratorAsValues(MemoryStore.scala:299) at org.apache.spark.storage.BlockManager.$anonfun$doPutIterator$1(BlockManager.scala:1165) at org.apache.spark.storage.BlockManager.doPut(BlockManager.scala:1091) at org.apache.spark.storage.BlockManager.doPutIterator(BlockManager.scala:1156) at org.apache.spark.storage.BlockManager.getOrElseUpdate(BlockManager.scala:882) at org.apache.spark.rdd.RDD.getOrCompute(RDD.scala:335) at org.apache.spark.rdd.RDD.iterator(RDD.scala:286) at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:90) at org.apache.spark.scheduler.Task.run(Task.scala:121) at org.apache.spark.executor.Executor$TaskRunner.$anonfun$run$3(Executor.scala:411) at org.apache.spark.util.Utils$.tryWithSafeFinally(Utils.scala:1360) at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:414) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624) at java.lang.Thread.run(Thread.java:748) 2019-06-28 14:07:32 ERROR TaskSetManager:70 - Task 3 in stage 2.0 failed 1 times; aborting job - try realigning a read on a missing contig, stringency == STRICT 2019-06-28 14:07:33 WARN MDTagging:190 - Caught exception when processing read chr2: java.lang.Exception: Contig chr2 not found in reference map with keys: chr1 - try realigning a read on a missing contig, stringency == LENIENT FileExtensionsSuite: - ends in gzip extension - is a vcf extension PhredUtilsSuite: - convert low phred score to log and back - convert high phred score to log and back - convert overflowing phred score to log and back and clip - convert negative zero log probability to phred and clip - round trip log probabilities ReadDatasetSuite: - create a new read genomic dataset - create a new read genomic dataset with sequence dictionary - save as parquet - round trip as parquet - save as fastq - save as single file fastq - filter read genomic dataset by reference region - broadcast region join reads and features - shuffle region join reads and features - convert reads to alignments - convert reads to sequences - convert reads to slices SmithWatermanSuite: - gather max position from simple scoring matrix - gather max position from irregular scoring matrix - gather max position from irregular scoring matrix with deletions - score simple alignment with constant gap - score irregular scoring matrix - score irregular scoring matrix with indel - can unroll cigars correctly - execute simple trackback - execute trackback with indel - run end to end smith waterman for simple reads - run end to end smith waterman for short sequences with indel - run end to end smith waterman for longer sequences with snp - run end to end smith waterman for longer sequences with short indel - run end to end smith waterman for shorter sequence in longer sequence - run end to end smith waterman for shorter sequence in longer sequence, with indel - smithWaterman - simple alignment MdTagSuite: - null md tag - zero length md tag - md tag with non-digit initial value - md tag invalid base - md tag, pure insertion - md tag, pure insertion, test 2 - md tag pure insertion equality - md tag equality and hashcode - valid md tags - get start of read with no mismatches or deletions - get start of read with no mismatches, but with a deletion at the start - get start of read with mismatches at the start - get end of read with no mismatches or deletions - check that mdtag and rich record return same end - get end of read with no mismatches, but a deletion at end - CIGAR with N operator - CIGAR with multiple N operators - CIGAR with P operators - Get correct matches for mdtag with insertion - Get correct matches for mdtag with mismatches and insertion - Get correct matches for mdtag with insertion between mismatches - Get correct matches for mdtag with intron between mismatches - Get correct matches for mdtag with intron and deletion between mismatches - Throw exception when number of deleted bases in mdtag disagrees with CIGAR - Get correct matches for mdtag with mismatch, insertion and deletion - Get correct matches for mdtag with mismatches, insertion and deletion - Get correct matches for MDTag with mismatches and deletions - Get correct matches base from MDTag and CIGAR with N - get end of read with mismatches and a deletion at end - get correct string out of mdtag with no mismatches - get correct string out of mdtag with mismatches at start - get correct string out of mdtag with deletion at end - get correct string out of mdtag with mismatches at end - get correct string out of complex mdtag - check complex mdtag - get gapped reference - move a cigar alignment by two for a read - rewrite alignment to all matches - rewrite alignment to two mismatches followed by all matches - rewrite alignment to include a deletion but otherwise all matches - rewrite alignment to include an insertion at the start of the read but otherwise all matches - create new md tag from read vs. reference, perfect match - create new md tag from read vs. reference, perfect alignment match, 1 mismatch - create new md tag from read vs. reference, alignment with deletion - create new md tag from read vs. reference, alignment with insert - handle '=' and 'X' operators - CIGAR/MD tag mismatch should cause errors GenomicDatasetSuite: - processing a command that is the spark root directory should return an absolute path - processing a command that is just a single word should do nothing - processing a command should handle arguments that include spaces - processing a command that is a single substitution should succeed - processing a command that is multiple words should split the string - process a command that is multiple words with a replacement - process a command that is multiple words with multiple replacements ParallelFileMergerSuite: - cannot write both empty gzip block and cram eof - buffer size must be non-negative - get the size of several files - block size must be positive and non-zero when trying to merge files - must provide files to merge - if two files are both below the block size, they should merge into one shard - merge two files where one is greater than the block size - merge a sharded sam file - merge a sharded bam file - merge a sharded cram file - can't turn a negative index into a path - generate a path from an index IndelTableSuite: - check for indels in a region with known indels - check for indels in a contig that doesn't exist - check for indels in a region without known indels - build indel table from rdd of variants SnpTableSuite: - create an empty snp table - create a snp table from variants on multiple contigs - create a snp table from a larger set of variants - perform lookups on multi-contig snp table - perform lookups on larger snp table RealignIndelsSuite: - map reads to targets - checking mapping to targets for artificial reads - checking alternative consensus for artificial reads - checking extraction of reference from reads - checking realigned reads for artificial input - checking realigned reads for artificial input with reference file - checking realigned reads for artificial input using knowns - checking realigned reads for artificial input using knowns and reads - skip realigning reads if target is highly covered - skip realignment if target is an insufficient LOD improvement - realign reads to an insertion - test mismatch quality scoring - test mismatch quality scoring for no mismatches - test mismatch quality scoring for offset - test mismatch quality scoring with early exit - test mismatch quality scoring after unpacking read - we shouldn't try to realign a region with no target - we shouldn't try to realign reads with no indel evidence - test OP and OC tags - realign a read with an insertion that goes off the end of the read - if realigning a target doesn't improve the LOD, don't drop reads - extract seq/qual from a read with no clipped bases - extract seq/qual from a read with clipped bases at start - extract seq/qual from a read with clipped bases at end - if unclip is selected, don't drop base when extracting from a read with clipped bases - get cigar and coordinates for read that spans indel, no clipped bases - get cigar and coordinates for read that spans deletion, clipped bases at start - get cigar and coordinates for read that falls wholly before insertion - get cigar and coordinates for read that falls wholly after insertion - get cigar and coordinates for read that falls wholly after deletion - get cigar and coordinates for read that partially spans insertion, no clipped bases - get cigar and coordinates for read that partially spans insertion, clipped bases at end - get cigar and coordinates for read that partially spans insertion, clipped bases both ends BaseQualityRecalibrationSuite: - BQSR Test Input #1 w/ VCF Sites without caching - BQSR Test Input #1 w/ VCF Sites with caching - BQSR Test Input #1 w/ VCF Sites with serialized caching DinucCovariateSuite: - computing dinucleotide pairs for a single base sequence should return (N,N) - compute dinucleotide pairs for a string of all valid bases - compute dinucleotide pairs for a string with an N - compute covariates for a read on the negative strand - compute covariates for a read on the positive strand SequenceDictionarySuite: - Convert from sam sequence record and back - Convert from SAM sequence dictionary file (with extra fields) - merge into existing dictionary - Convert from SAM sequence dictionary and back - Can retrieve sequence by name - SequenceDictionary's with same single element are equal - SequenceDictionary's with same two elements are equals - SequenceDictionary's with different elements are unequal - SequenceDictionaries with same elements in different order are compatible - isCompatible tests equality on overlap - The addition + works correctly - The append operation ++ works correctly - ContainsRefName works correctly for different string types - Apply on name works correctly for different String types - convert from sam sequence record and back - convert from sam sequence dictionary and back - conversion to sam sequence dictionary has correct sort order - load sequence dictionary from VCF file - empty sequence dictionary must be empty - test filter to reference name - test filter to reference names - test filter to reference name by function GenomicPositionPartitionerSuite: - partitions the UNMAPPED ReferencePosition into the top partition - if we do not have a contig for a record, we throw an IAE - partitioning into N pieces on M total sequence length, where N > M, results in M partitions - correctly partitions a single dummy sequence into two pieces - correctly counts cumulative lengths - correctly partitions positions across two dummy sequences - test that we can range partition ADAMRecords - test that we can range partition ADAMRecords indexed by sample - test that simple partitioning works okay on a reasonable set of ADAMRecords - test indexed ReferencePosition partitioning works on a set of indexed ADAMRecords CoverageSuite: - Convert to coverage from valid Feature - Convert to coverage from valid Feature with sampleId - Convert to coverage from Feature with null/empty contigName fails with correct error - Convert to coverage from Feature with no start/end position fails with correct error - Convert to coverage from Feature with no score fails with correct error InnerTreeRegionJoinSuite: - Ensure same reference regions get passed together - Overlapping reference regions - Multiple reference regions do not throw exception RichAlignmentRecordSuite: - Unclipped Start - Unclipped End - tags contains optional fields - read overlap unmapped read - read overlap reference position - read overlap same position different contig VariantDatasetSuite: - union two variant genomic datasets together - round trip to parquet - save and reload from partitioned parquet - use broadcast join to pull down variants mapped to targets - use right outer broadcast join to pull down variants mapped to targets - use shuffle join to pull down variants mapped to targets - use right outer shuffle join to pull down variants mapped to targets - use left outer shuffle join to pull down variants mapped to targets - use full outer shuffle join to pull down variants mapped to targets - use shuffle join with group by to pull down variants mapped to targets - use right outer shuffle join with group by to pull down variants mapped to targets - convert back to variant contexts - load parquet to sql, save, re-read from avro 2019-06-28 14:08:25 WARN DatasetBoundSliceDataset:190 - Saving directly as Parquet from SQL. Options other than compression codec are ignored. - transform variants to slice genomic dataset - transform variants to coverage genomic dataset - transform variants to feature genomic dataset - transform variants to fragment genomic dataset - transform variants to read genomic dataset - transform variants to genotype genomic dataset - transform variants to variant context genomic dataset - filter RDD bound variants to filters passed - filter dataset bound variants to filters passed - filter RDD bound variants by quality - filter dataset bound variants by quality - filter RDD bound variants by read depth - filter dataset bound variants by read depth - filter RDD bound variants by reference read depth - filter dataset bound variants by reference read depth - filter RDD bound single nucleotide variants - filter dataset bound single nucleotide variants - filter RDD bound multiple nucleotide variants - filter dataset bound multiple nucleotide variants - filter RDD bound indel variants - filter dataset bound indel variants - filter RDD bound variants to single nucleotide variants - filter dataset bound variants to single nucleotide variants - filter RDD bound variants to multiple nucleotide variants - filter dataset bound variants to multiple nucleotide variants - filter RDD bound variants to indel variants - filter dataset bound variants to indel variants - transform dataset via java API Run completed in 6 minutes, 30 seconds. Total number of tests run: 1175 Suites: completed 68, aborted 0 Tests: succeeded 1175, failed 0, canceled 0, ignored 5, pending 0 All tests passed. [INFO] [INFO] >>> scoverage-maven-plugin:1.1.1:report (default-cli) > [scoverage]test @ adam-core-spark2_2.12 >>> [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-core-spark2_2.12 --- [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-core-spark2_2.12 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ adam-core-spark2_2.12 --- [INFO] Source directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/main/scala added. [INFO] Source directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/target/generated-sources/src/main/scala added. [INFO] [INFO] --- exec-maven-plugin:1.5.0:java (generate-scala-products) @ adam-core-spark2_2.12 --- SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] [INFO] --- exec-maven-plugin:1.5.0:java (generate-scala-projection-fields) @ adam-core-spark2_2.12 --- SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ adam-core-spark2_2.12 --- [INFO] Modified 2 of 202 .scala files [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:pre-compile (default-cli) @ adam-core-spark2_2.12 --- [WARNING] Skipping SCoverage execution - unsupported Scala version "2.12.8" [INFO] [INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ adam-core-spark2_2.12 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/main/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ adam-core-spark2_2.12 --- [INFO] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/main/java:-1: info: compiling [INFO] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/main/scala:-1: info: compiling [INFO] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/target/generated-sources/src/main/scala:-1: info: compiling [INFO] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/target/generated-sources/annotations:-1: info: compiling [INFO] Compiling 138 source files to /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/target/2.12.8/classes at 1561756127362 [WARNING] warning: there were 21 deprecation warnings [WARNING] warning: there were 31 deprecation warnings (since 0.21.0) [WARNING] warning: there was one deprecation warning (since 1.0.6) [WARNING] warning: there were 36 deprecation warnings (since 2.0.0) [WARNING] warning: there was one deprecation warning (since 2.11.0) [WARNING] warning: there were 173 deprecation warnings (since 2.12.0) [WARNING] warning: there was one deprecation warning (since 2.12.7) [WARNING] warning: there were 264 deprecation warnings in total; re-run with -deprecation for details [WARNING] warning: there were 5 feature warnings; re-run with -feature for details [WARNING] 9 warnings found [INFO] prepare-compile in 0 s [INFO] compile in 25 s [INFO] [INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ adam-core-spark2_2.12 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:post-compile (default-cli) @ adam-core-spark2_2.12 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ adam-core-spark2_2.12 --- [INFO] Test Source directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala added. [INFO] [INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ adam-core-spark2_2.12 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 152 resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ adam-core-spark2_2.12 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ adam-core-spark2_2.12 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ adam-core-spark2_2.12 --- [INFO] Tests are skipped. [INFO] [INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ adam-core-spark2_2.12 --- Discovery starting. Discovery completed in 1 second, 560 milliseconds. Run starting. Expected test count is: 1175 RepairPartitionsSuite: - don't pull from the first partition - properly handle pulling from an empty iterator - gets a single read from the partition if there are no other reads in the pair - gets all the reads from a pair from the start of a partition - properly handle dropping from an empty iterator - don't drop from the first partition - drop a single read from the partition if there are no other reads in the pair - drops all the reads from a pair from the start of a partition - only append to the first partition - drop a single read from the partition and append read when in the middle - drop reads from the start and don't append when in the last partition - can't have more records than number of partitions - unroll array for broadcast 2019-06-28 14:09:17 WARN Utils:66 - Your hostname, research-jenkins-worker-07 resolves to a loopback address: 127.0.1.1; using 192.168.10.27 instead (on interface eth0) 2019-06-28 14:09:17 WARN Utils:66 - Set SPARK_LOCAL_IP if you need to bind to another address 2019-06-28 14:09:17 WARN NativeCodeLoader:62 - Unable to load native-hadoop library for your platform... using builtin-java classes where applicable - move pairs around an rdd FlagStatSuite: - Standard FlagStat test ModPartitionerSuite: - report number of partitions correctly - partition a number that is lower than the number of partitions and positive - partition a number that is greater than the number of partitions and positive - partition a number that is lower than the number of partitions and negative - partition a number that is greater than the number of partitions and negative - fire an exception if input is not an integer TwoBitFileSuite: - correctly read sequence from .2bit file - correctly return masked sequences from .2bit file - correctly return Ns from .2bit file - correctly calculates sequence dictionary NonoverlappingRegionsSuite: - alternating returns an alternating seq of items - Single region returns itself - Two adjacent regions will be merged - Nonoverlapping regions will all be returned - Many overlapping regions will all be merged - ADAMRecords return proper references ReferencePositionSuite: - create reference position from mapped read - create reference position from variant - create reference position from genotype - create reference position from variant starting at vcf 0 - create reference position from genotype starting at vcf 0 ConsensusGeneratorFromReadsSuite: - checking search for consensus list for artificial reads FragmentConverterSuite: - build a fragment collector and convert to a read - if a fragment isn't associated with a contig, don't get a fragment collector - convert an rdd of discontinuous fragments, all from the same contig - convert an rdd of contiguous fragments, all from the same contig - convert an rdd of varied fragments from multiple contigs FileMergerSuite: - cannot write both empty gzip block and cram eof - buffer size must be non-negative AlignmentRecordDatasetSuite: - sorting reads - unmapped reads go at the end when sorting - coverage does not fail on unmapped reads 2019-06-28 14:09:28 WARN Utils:66 - Truncated the string representation of a plan since it was too large. This behavior can be adjusted by setting 'spark.debug.maxToStringFields' in SparkEnv.conf. - computes coverage - computes coverage with multiple samples - merges adjacent records with equal coverage values - sorting reads by reference index - round trip from ADAM to SAM and back to ADAM produces equivalent Read values - round trip with single CRAM file produces equivalent Read values - round trip with sharded CRAM file produces equivalent Read values - SAM conversion sets read mapped flag properly - load long FASTQ reads - load FASTQ with no bases - convert malformed FASTQ (no quality scores) => SAM => well-formed FASTQ => SAM - round trip from ADAM to FASTQ and back to ADAM produces equivalent Read values - round trip from ADAM to paired-FASTQ and back to ADAM produces equivalent Read values - writing a small file with tags should produce the expected result - writing a small sorted file as SAM should produce the expected result - writing unordered sam from unordered sam - writing ordered sam from unordered sam - write single sam file back - write single bam file back - saveAsParquet with save args, sequence dictionary, and read group dictionary - load parquet to sql, save, re-read from avro - load from sam, save as partitioned parquet, and re-read from partitioned parquet - save as SAM format - save as sorted SAM format - save as BAM format - save as sorted BAM format - save as FASTQ format - save as ADAM parquet format - saveAsSam SAM format - saveAsSam SAM format single file - saveAsSam sorted SAM format single file - saveAsSam BAM format - saveAsSam BAM format single file - saveAsSam sorted BAM format single file - saveAsFastq - saveAsFastq as single file - saveAsFastq with original base qualities - saveAsFastq sorted by read name - saveAsFastq sorted by read name with original base qualities 2019-06-28 14:09:54 WARN RDDBoundAlignmentRecordDataset:190 - Found 20 read names that don't occur exactly twice: 1x: 20 Samples: simread:1:237728409:true simread:1:195211965:false simread:1:163841413:false simread:1:231911906:false simread:1:26472783:false simread:1:165341382:true simread:1:240344442:true simread:1:50683371:false simread:1:240997787:true simread:1:14397233:false simread:1:207027738:true simread:1:20101800:true simread:1:101556378:false simread:1:37577445:false simread:1:189606653:true simread:1:5469106:true simread:1:186794283:true simread:1:89554252:false simread:1:153978724:false simread:1:169801933:true - saveAsFastq paired FASTQ 2019-06-28 14:09:56 WARN RDDBoundAlignmentRecordDataset:190 - Found 20 read names that don't occur exactly twice: 1x: 20 Samples: simread:1:237728409:true simread:1:195211965:false simread:1:163841413:false simread:1:231911906:false simread:1:26472783:false simread:1:165341382:true simread:1:240344442:true simread:1:50683371:false simread:1:240997787:true simread:1:14397233:false simread:1:207027738:true simread:1:20101800:true simread:1:101556378:false simread:1:37577445:false simread:1:189606653:true simread:1:5469106:true simread:1:186794283:true simread:1:89554252:false simread:1:153978724:false simread:1:169801933:true - saveAsPairedFastq 2019-06-28 14:09:57 WARN RDDBoundAlignmentRecordDataset:190 - Found 20 read names that don't occur exactly twice: 1x: 20 Samples: simread:1:237728409:true simread:1:195211965:false simread:1:163841413:false simread:1:231911906:false simread:1:26472783:false simread:1:165341382:true simread:1:240344442:true simread:1:50683371:false simread:1:240997787:true simread:1:14397233:false simread:1:207027738:true simread:1:20101800:true simread:1:101556378:false simread:1:37577445:false simread:1:189606653:true simread:1:5469106:true simread:1:186794283:true simread:1:89554252:false simread:1:153978724:false simread:1:169801933:true - saveAsPairedFastq as single files - don't lose any reads when piping as SAM 2019-06-28 14:10:08 WARN OutFormatterRunner:190 - Piped command List(sleep, 10) timed out after 5 seconds. 2019-06-28 14:10:08 WARN OutFormatterRunner:190 - Piped command List(sleep, 10) timed out after 5 seconds. - lose all records when a command times out - lose no records without a timeout 2019-06-28 14:10:29 WARN OutFormatterRunner:190 - Piped command List(python, /tmp/adamTestMvnJlGqi5R/spark-86c13da1-fe35-441e-a02d-d4a40ed6707b/userFiles-dddb2e57-8356-49aa-b20e-6efbb4b802cc/timeout.py) timed out after 5 seconds. 2019-06-28 14:10:29 WARN OutFormatterRunner:190 - Piped command List(python, /tmp/adamTestMvnJlGqi5R/spark-86c13da1-fe35-441e-a02d-d4a40ed6707b/userFiles-dddb2e57-8356-49aa-b20e-6efbb4b802cc/timeout.py) timed out after 5 seconds. - lose some records when a command times out - don't lose any reads when piping as SAM using java pipe - don't lose any reads when piping as BAM - don't lose any reads when piping fastq to sam - can properly set environment variables inside of a pipe - read vcf from alignment record pipe !!! IGNORED !!! - use broadcast join to pull down reads mapped to targets - use broadcast join against to pull down reads mapped to targets - use right outer broadcast join to pull down reads mapped to targets - use right outer broadcast join against to pull down reads mapped to targets - use shuffle join with feature spanning partitions - use shuffle join to pull down reads mapped to targets - use shuffle join with flankSize to pull down reads mapped close to targets - use right outer shuffle join to pull down reads mapped to targets - use left outer shuffle join to pull down reads mapped to targets - use full outer shuffle join to pull down reads mapped to targets - use shuffle join with group by to pull down reads mapped to targets - use right outer shuffle join with group by to pull down reads mapped to targets - cannot provide empty quality score bins - cannot provide bins with a gap - cannot provide overlapping bins - binning quality scores in reads succeeds even if reads have no quality scores - bin quality scores in reads - union two read files together - test k-mer counter - test dataset based k-mer counter - transform reads to slice genomic dataset - transform reads to coverage genomic dataset - transform reads to feature genomic dataset - transform reads to fragment genomic dataset - transform reads to genotype genomic dataset loading /tmp/adamTestMvnJlGqi5R/TempSuite2961412746439740806.adam as parquet into RDD... loading /tmp/adamTestMvnJlGqi5R/TempSuite8751909781715580249.adam as parquet into RDD... - transform reads to variant genomic dataset - cannot have a null processing step ID - convert a processing description to htsjdk - GenomicDataset.sort does not fail on unmapped reads - GenomicDataset.sortLexicographically does not fail on unmapped reads - left normalize indels - running base recalibration with downsampling doesn't drop reads - filter RDD bound alignments by MAPQ - filter dataset bound alignments by MAPQ - filter RDD bound unaligned alignments - filter dataset bound unaligned alignments - filter RDD bound unpaired alignments - filter dataset bound unpaired alignments - filter RDD bound duplicate alignments - filter dataset bound duplicate alignments - filter RDD bound alignments to primary alignments - filter dataset bound alignments to primary alignments - filter RDD bound alignments to read group - filter dataset bound alignments to read group - filter RDD bound alignments to read groups - filter dataset bound alignments to read groups - filter RDD bound alignments to sample - filter dataset bound alignments to sample - filter RDD bound alignments to samples - filter dataset bound alignments to samples - sort by read name - transform dataset via java API - convert alignments to reads SingleReadBucketSuite: - convert unmapped pair to fragment - convert proper pair to fragment - convert read pair to fragment with first of pair chimeric read RecalibrationTableSuite: - look up quality scores in table FlankSlicesSuite: - don't put flanks on non-adjacent slices - put flanks on adjacent slices InterleavedFastqInputFormatSuite: - interleaved FASTQ hadoop reader: interleaved_fastq_sample1.ifq->interleaved_fastq_sample1.ifq.output - interleaved FASTQ hadoop reader: interleaved_fastq_sample2.ifq->interleaved_fastq_sample2.ifq.output - interleaved FASTQ hadoop reader: interleaved_fastq_sample3.ifq->interleaved_fastq_sample3.ifq.output - interleaved FASTQ hadoop reader: interleaved_fastq_sample4.ifq->interleaved_fastq_sample4.ifq.output - interleaved FASTQ hadoop reader: interleaved_fastq_sample5.ifq->interleaved_fastq_sample5.ifq.output TreeRegionJoinSuite: - run a join between data on a single contig ReferenceRegionSuite: - cannot create an empty predicate - parse empty string throws IllegalArgumentException - parse contigName only string into reference regions - parse to end strings into reference regions - parse string into reference regions - contains(: ReferenceRegion) - contains(: ReferencePosition) - merge - overlaps and covers - overlapsBy and coversBy - distance(: ReferenceRegion) - distance(: ReferencePosition) - unstrandedDistance - subtract fails on non-overlapping and non-covering regions - subtract - create region from unmapped read fails - create region from read with null alignment positions fails - create stranded region from unmapped read fails - create stranded region from read with null alignment positions fails - create stranded region from read with null alignment strand fails - create stranded region from read on forward strand - create stranded region from read on reverse strand - create region from mapped read contains read start and end - validate that adjacent regions can be merged - validate that non-adjacent regions cannot be merged - validate that nearby regions can be merged - validate that non-nearby regions cannot be merged - compute convex hull of two sets - region name is sanitized when creating region from read - intersection fails on non-overlapping regions - intersection fails when minOverlap is not met - compute intersection - overlap tests for oriented reference region - check the width of a reference region - make a reference region for a variant or genotype - make a reference region for a variant or genotype starting at VCF 0 - uniformly pad a reference region - uniformly pad a reference region into negative coordinate space, ensure non negative start - unevenly pad a reference region - unevenly pad a reference region into negative coordinate space, ensure non negative start - can build an open ended reference region - can build an open ended reference region with strand - can build a reference region with an open start position - can build a reference region with an open start position with strand - can build a reference region that covers the entirety of a contig - can build a reference region that covers the entirety of a contig with strand - convert a genotype and then get the reference region - create region from feature with null alignment positions fails - create stranded region from feature with null alignment positions fails - create stranded region from feature with null alignment strand fails - create stranded region from feature on forward strand - create stranded region from feature on reverse strand AlignmentRecordConverterSuite: - testing the fields in a converted ADAM Read - converting a read with null quality is OK - convert a read to fastq - reverse complement reads when converting to fastq - converting to fastq with unmapped reads where read reverse complemented flag (Ox10) was NOT set - converting to fastq with unmapped reads where reverse complemented flag (0x10) was set - converting a fragment with no alignments should yield unaligned reads - converting a fragment with alignments should restore the alignments - read negative strand is propagated even when not mapped CoverageDatasetSuite: - correctly saves coverage - can read a bed file to coverage - correctly filters coverage with predicate - keeps sample metadata - can read a bed file with multiple samples to coverage - correctly flatmaps coverage without aggregated bins - correctly flatmaps coverage with aggregated bins - collapses coverage records in one partition - approximately collapses coverage records in multiple partitions 2019-06-28 14:11:17 WARN DatasetBoundSliceDataset:190 - Saving directly as Parquet from SQL. Options other than compression codec are ignored. - transform coverage to slice genomic dataset - transform coverage to feature genomic dataset - transform coverage to fragment genomic dataset - transform coverage to read genomic dataset - transform coverage to genotype genomic dataset - transform coverage to variant genomic dataset - transform coverage to variant context genomic dataset - copy coverage rdd - copy coverage dataset - copy coverage rdd without sequence dictionary - copy coverage dataset without sequence dictionary - transform dataset via java API RecalibratorSuite: - don't replace quality if quality was null - if no covariates, return alignment - skip recalibration if base is below quality threshold - recalibrate changed bases above quality threshold SliceDatasetSuite: - create a new slice genomic dataset - create a new slice genomic dataset with sequence dictionary - merge slices into a sequence genomic dataset - save as parquet - round trip as parquet - save as fasta - save as single file fasta - convert slices to reads - convert slices to sequences GenotypeDatasetSuite: - union two genotype genomic datasets together - round trip to parquet - round trip to partitioned parquet - use broadcast join to pull down genotypes mapped to targets - use right outer broadcast join to pull down genotypes mapped to targets - use shuffle join to pull down genotypes mapped to targets - use right outer shuffle join to pull down genotypes mapped to targets - use left outer shuffle join to pull down genotypes mapped to targets - use full outer shuffle join to pull down genotypes mapped to targets - use shuffle join with group by to pull down genotypes mapped to targets - use right outer shuffle join with group by to pull down genotypes mapped to targets - convert back to variant contexts - load parquet to sql, save, re-read from avro 2019-06-28 14:11:42 WARN DatasetBoundSliceDataset:190 - Saving directly as Parquet from SQL. Options other than compression codec are ignored. - transform genotypes to slice genomic dataset - transform genotypes to coverage genomic dataset - transform genotypes to feature genomic dataset - transform genotypes to fragment genomic dataset - transform genotypes to read genomic dataset - transform genotypes to variant genomic dataset - transform genotypes to variant context genomic dataset - loading genotypes then converting to variants yields same output as loading variants - filter RDD bound genotypes to genotype filters passed - filter dataset bound genotypes to genotype filters passed - filter RDD bound genotypes by genotype quality - filter dataset bound genotypes by genotype quality - filter RDD bound genotypes by read depth - filter dataset bound genotypes by read depth - filter RDD bound genotypes by alternate read depth - filter dataset bound genotypes by alternate read depth - filter RDD bound genotypes by reference read depth - filter dataset bound genotypes by reference read depth - filter RDD bound genotypes by sample - filter dataset bound genotypes by sample - filter RDD bound genotypes by samples - filter dataset bound genotypes by samples - filter RDD bound no call genotypes - filter dataset no call genotypes - round trip gVCF END attribute without nested variant annotations rdd bound - round trip gVCF END attribute without nested variant annotations dataset bound - round trip gVCF END attribute with nested variant annotations rdd bound - round trip gVCF END attribute with nested variant annotations dataset bound - transform dataset via java API FragmentDatasetSuite: - don't lose any reads when piping interleaved fastq to sam - don't lose any reads when piping tab5 to sam - don't lose any reads when piping tab6 to sam - use broadcast join to pull down fragments mapped to targets - use right outer broadcast join to pull down fragments mapped to targets - use shuffle join to pull down fragments mapped to targets - use right outer shuffle join to pull down fragments mapped to targets - use left outer shuffle join to pull down fragments mapped to targets - use full outer shuffle join to pull down fragments mapped to targets - use shuffle join with group by to pull down fragments mapped to targets - use right outer shuffle join with group by to pull down fragments mapped to targets - bin quality scores in fragments - union two genomic datasets of fragments together - load parquet to sql, save, re-read from avro - transform fragments to slice genomic dataset - transform fragments to coverage genomic dataset - transform fragments to feature genomic dataset - transform fragments to read genomic dataset - transform fragments to genotype genomic dataset - transform fragments to variant genomic dataset - transform fragments to variant context genomic dataset - paired read names with index sequences in read names can group into fragments - interleaved paired read names with index sequences in read names can group into fragments - interleaved paired read names with index sequences in read names as fragments - transform dataset via java API - dataset and rdd conversion to alignments are equivalent SingleFastqInputFormatSuite: - FASTQ hadoop reader: fastq_sample1.fq->single_fastq_sample1.fq.output - FASTQ hadoop reader: fastq_sample2.fq->single_fastq_sample2.fq.output - FASTQ hadoop reader: fastq_sample3.fq->single_fastq_sample3.fq.output - FASTQ hadoop reader: fastq_sample4.fq->single_fastq_sample4.fq.output VariantContextDatasetSuite: - load a gvcf with a missing info field set to . - union two variant context genomic datasets together - can write, then read in .vcf file - can write as a single file via simple saveAsVcf method, then read in .vcf file - can write as a single file via full saveAsVcf method, then read in .vcf file - transform a vcf file with bad header - read a vcf file with multi-allelic variants to split - support VCFs with +Inf/-Inf float values - support VCFs with `nan` instead of `NaN` float values - don't lose any variants when piping as VCF - pipe works with empty partitions - don't lose any non-default VCF header lines or attributes when piping as VCF - save a file sorted by contig index - save a lexicographically sorted file - save a multiallelic gvcf !!! IGNORED !!! - test metadata - save sharded bgzip vcf - save bgzip vcf as single file - can't save file with non-vcf extension - transform variant contexts to slice genomic dataset - transform variant contexts to coverage genomic dataset - transform variant contexts to feature genomic dataset - transform variant contexts to fragment genomic dataset - transform variant contexts to read genomic dataset - transform variant contexts to genotype genomic dataset - transform variant contexts to variant genomic dataset - save and reload from partitioned parquet - transform dataset via java API ConsensusSuite: - test the insertion of a consensus insertion into a reference - test the insertion of a consensus deletion into a reference - inserting empty consensus returns the reference SequenceDatasetSuite: - create a new sequence genomic dataset - create a new sequence genomic dataset with sequence dictionary - save as parquet - round trip as parquet - save as fasta - save as single file fasta - convert sequences to reads - convert sequences to slices - slice sequences to a maximum length - slice sequences shorter than maximum length - filter sequences by overlapping region - filter sequences failing to overlap region - filter sequences by overlapping regions - filter sequences failing to overlap regions - slice sequences overlapping a smaller region - slice sequences overlapping a larger region - slice sequences failing to overlap a region - slice sequences overlapping smaller regions - slice sequences overlapping larger regions - slice sequences failing to overlap regions AttributeUtilsSuite: - parseTags returns a reasonable set of tagStrings - parseTags works with NumericSequence tagType - empty string is parsed as zero tagStrings - incorrectly formatted tag throws an exception - string tag with a ':' in it is correctly parsed - oq string tag with many ':' in it is correctly parsed - oq string tag with a ',' in it is correctly parsed - if a tag is an array but doesn't define it's format, throw MarkDuplicatesSuite: - single read - reads at different positions - reads at the same position - reads at the same position with clipping - reads on reverse strand - unmapped reads - read pairs - read pairs with fragments - quality scores - read pairs that cross chromosomes - single fragment - fragments at different positions - fragments at the same position - fragments at the same position with clipping - fragments on reverse strand - unmapped fragments - read pairs as fragments - read pairs with fragments as fragments - chimeric fragments - inverse pairs - supplemental reads TranscriptEffectConverterSuite: - parse empty transcript effect - parse empty transcript effect strict validation stringency - parse invalid transcript effect - parse invalid transcript effect strict validation stringency - parse transcript effect - parse empty list VCF ANN attribute - parse empty list VCF ANN attribute strict validation stringency - parse empty string VCF ANN attribute - parse empty string VCF ANN attribute strict validation stringency - parse invalid VCF ANN attribute - parse invalid VCF ANN attribute strict validation stringency - parse VCF ANN attribute with one transcript effect - parse VCF ANN attribute with multiple transcript effects - convert to transcript effect from null VCF ANN attribute in variant context - convert to transcript effect from empty list VCF ANN attribute in variant context - convert to transcript effect from empty list VCF ANN attribute in variant context strict validation stringency - convert to transcript effect from empty string VCF ANN attribute in variant context - convert to transcript effect from empty string VCF ANN attribute in variant context strict validation stringency - convert to transcript effect from invalid VCF ANN attribute in variant context - convert to transcript effect from invalid VCF ANN attribute in variant context strict validation stringency 2019-06-28 14:13:02 WARN TranscriptEffectConverter$:190 - Could not convert VCF INFO reserved key ANN value to TranscriptEffect, caught java.lang.NumberFormatException: For input string: "not a number". - convert to transcript effect from VCF ANN attribute with invalid number in variant context lenient validation stringency 2019-06-28 14:13:02 WARN TranscriptEffectConverter$:190 - Could not convert VCF INFO reserved key ANN value to TranscriptEffect, caught java.lang.NumberFormatException: For input string: "not a number". - convert to transcript effect from VCF ANN attribute with invalid fraction in variant context lenient validation stringency - convert to transcript effect from VCF ANN attribute with invalid number in variant context strict validation stringency - convert to transcript effect from VCF ANN attribute with invalid fraction in variant context strict validation stringency - convert to transcript effect from VCF ANN attribute in variant context different alt allele - convert to transcript effect from VCF ANN attribute in variant context same alt allele - convert to transcript effect from VCF ANN attribute in variant context multiple effects same alt allele - convert transcript effect to VCF ANN attribute value - convert transcript effect with null fields to VCF ANN attribute value 2019-06-28 14:13:02 WARN TranscriptEffectConverter$:190 - Incorrect fractional value ?/2, missing numerator - convert transcript effect with incorrect fractional value to VCF ANN attribute value IndelRealignmentTargetSuite: - checking simple realignment target - creating simple target from read with deletion - creating simple target from read with insertion - joining simple realignment targets on same chr - joining simple realignment targets on different chr throws exception - creating targets from three intersecting reads, same indel - creating targets from three intersecting reads, two different indel - creating targets from two disjoint reads - creating targets for artificial reads: one-by-one - creating targets for artificial reads: all-at-once (merged) - creating indel targets for mason reads - additional indel targets taken from consensus generator NormalizationUtilsSuite: - cannot move an indel left if there are no bases to it's left - move a simple indel to farthest position left until bases run out - move a simple indel to farthest position left, past length of indel - cannot move a left normalized indel in a short tandem repeat - move an indel in a short tandem repeat - move an indel in a short tandem repeat of more than 2 bases, where shift is not an integer multiple of repeated sequence length - moving a simple read with single deletion that cannot shift - shift an indel left by 0 in a cigar - shift an indel left by 1 in a cigar - do not left align a complex read which is already left aligned ReadGroupDictionarySuite: - simple conversion to and from sam read group - sample name must be set - simple equality checks - get samples from read group dictionary - empty read group is empty - merging a dictionary with itself should work - round trip a record with all attributes set RightOuterTreeRegionJoinSuite: - Ensure same reference regions get passed together - Overlapping reference regions InnerShuffleRegionJoinSuite: - Overlapping reference regions - Multiple reference regions do not throw exception FeatureDatasetSuite: - round trip GTF format - save GTF as GFF3 format - save GTF as BED format - save GTF as IntervalList format - save GTF as NarrowPeak format - save GFF3 as GTF format - save GFF3 as BED format - save GFF3 as IntervalList format - save GFF3 as NarrowPeak format - round trip GFF3 format - ignore FASTA sequence in GFF3 file - save BED as GTF format - save BED as GFF3 format - save BED as IntervalList format - save BED as NarrowPeak format - round trip BED6 format - keeps sample metadata - round trip BED12 format - save to UCSC BED format - save IntervalList as GTF format - save IntervalList as GFF3 format - save IntervalList as BED format - save IntervalList as IntervalList format - save IntervalList as NarrowPeak format - round trip IntervalList format - save NarrowPeak as GTF format - save NarrowPeak as GFF3 format - save NarrowPeak as BED format - save NarrowPeak as IntervalList format - save NarrowPeak as NarrowPeak format - round trip NarrowPeak format - sort by reference - sort by reference and feature fields - sort gene features by reference and gene structure - sort transcript features by reference and gene structure - sort exon features by reference and gene structure - sort intron features by reference and gene structure - correctly flatmaps CoverageDataset from FeatureDataset - use broadcast join to pull down features mapped to targets - use right outer broadcast join to pull down features mapped to targets - use shuffle join to pull down features mapped to targets - use right outer shuffle join to pull down features mapped to targets - use left outer shuffle join to pull down features mapped to targets - use full outer shuffle join to pull down features mapped to targets - use shuffle join with group by to pull down features mapped to targets - use right outer shuffle join with group by to pull down features mapped to targets - union two feature rdds together - obtain sequence dictionary contig lengths from header in IntervalList format - don't lose any features when piping as BED format - don't lose any features when piping as GTF format - don't lose any features when piping as GFF3 format - don't lose any features when piping as NarrowPeak format - load parquet to sql, save, re-read from avro - load partitioned parquet to sql, save, re-read from avro 2019-06-28 14:13:35 WARN DatasetBoundSliceDataset:190 - Saving directly as Parquet from SQL. Options other than compression codec are ignored. - transform features to slice genomic dataset - transform features to coverage genomic dataset - transform features to fragment genomic dataset - transform features to read genomic dataset - transform features to genotype genomic dataset - transform features to variant genomic dataset - transform features to variant context genomic dataset - filter RDD bound features by feature type - filter dataset bound features by feature type - filter RDD bound features by feature types - filter dataset bound features by feature types - filter RDD bound features by gene - filter dataset bound features by gene - filter RDD bound features by genes - filter dataset bound features by genes - filter RDD bound features by transcript - filter dataset bound features by transcript - filter RDD bound features by transcripts - filter dataset bound features by transcripts - filter RDD bound features by exon - filter dataset bound features by exon - filter RDD bound features by exons - filter dataset bound features by exons - filter RDD bound features by score - filter dataset bound features by score - filter RDD bound features by parent - filter dataset bound features by parent - filter RDD bound features by parents - filter dataset bound features by parents - filter RDD bound features by attribute - filter dataset bound features by attribute - transform dataset via java API AlphabetSuite: - test size of a case-sensitive alphabet - test apply of a case-sensitive alphabet - test reverse complement of a case-sensitive alphabet - test exact reverse complement of a case-sensitive alphabet - test size of a case-insensitive alphabet - test apply of a case-insensitive alphabet - test reverse complement of a case-insensitive alphabet - test exact reverse complement of a case-insensitive alphabet - DNA alphabet - map unknown bases to N SortedGenomicDatasetSuite: - testing that partition and sort provide correct outputs - testing copartition maintains or adds sort - testing that we don't drop any data on the right side even though it doesn't map to a partition on the left - testing that sorted shuffleRegionJoin matches unsorted - testing that sorted fullOuterShuffleRegionJoin matches unsorted - testing that sorted rightOuterShuffleRegionJoin matches unsorted - testing that sorted leftOuterShuffleRegionJoin matches unsorted - testing that we can persist the sorted knowledge VariantContextConverterSuite: - Convert htsjdk site-only SNV to ADAM - Convert somatic htsjdk site-only SNV to ADAM - Convert htsjdk site-only CNV to ADAM - Convert htsjdk SNV w/ genotypes w/ phase information to ADAM - Convert htsjdk SNV with different variant filters to ADAM - Convert htsjdk SNV with different genotype filters to ADAM - Convert ADAM site-only SNV to htsjdk - Convert ADAM SNV w/ genotypes to htsjdk - Convert ADAM SNV w/ genotypes but bad SB to htsjdk with strict validation 2019-06-28 14:13:52 WARN VariantContextConverter:2300 - Applying annotation extraction function org.bdgenomics.adam.converters.VariantContextConverter$$Lambda$804/1770437551@79f62f12 to {"variant": {"referenceName": "1", "start": 0, "end": 1, "names": [], "splitFromMultiAllelic": false, "referenceAllele": "A", "alternateAllele": "T", "quality": null, "filtersApplied": null, "filtersPassed": null, "filtersFailed": [], "annotation": null}, "referenceName": null, "start": null, "end": null, "variantCallingAnnotations": {"filtersApplied": null, "filtersPassed": null, "filtersFailed": [], "downsampled": null, "baseQRankSum": null, "fisherStrandBiasPValue": 3.0, "rmsMapQ": 0.0, "mapq0Reads": 5, "mqRankSum": null, "readPositionRankSum": null, "genotypePriors": [], "genotypePosteriors": [], "vqslod": null, "culprit": null, "attributes": {}}, "sampleId": "NA12878", "sampleDescription": null, "processingDescription": null, "alleles": ["REF", "ALT"], "expectedAlleleDosage": null, "referenceReadDepth": null, "alternateReadDepth": null, "readDepth": null, "minReadDepth": null, "genotypeQuality": null, "genotypeLikelihoods": [], "nonReferenceLikelihoods": [], "strandBiasComponents": [0, 2], "splitFromMultiAllelic": false, "phased": false, "phaseSetId": null, "phaseQuality": null} failed with java.lang.IllegalArgumentException: requirement failed: Illegal strand bias components length. Must be empty or 4. In: {"variant": {"referenceName": "1", "start": 0, "end": 1, "names": [], "splitFromMultiAllelic": false, "referenceAllele": "A", "alternateAllele": "T", "quality": null, "filtersApplied": null, "filtersPassed": null, "filtersFailed": [], "annotation": null}, "referenceName": null, "start": null, "end": null, "variantCallingAnnotations": {"filtersApplied": null, "filtersPassed": null, "filtersFailed": [], "downsampled": null, "baseQRankSum": null, "fisherStrandBiasPValue": 3.0, "rmsMapQ": 0.0, "mapq0Reads": 5, "mqRankSum": null, "readPositionRankSum": null, "genotypePriors": [], "genotypePosteriors": [], "vqslod": null, "culprit": null, "attributes": {}}, "sampleId": "NA12878", "sampleDescription": null, "processingDescription": null, "alleles": ["REF", "ALT"], "expectedAlleleDosage": null, "referenceReadDepth": null, "alternateReadDepth": null, "readDepth": null, "minReadDepth": null, "genotypeQuality": null, "genotypeLikelihoods": [], "nonReferenceLikelihoods": [], "strandBiasComponents": [0, 2], "splitFromMultiAllelic": false, "phased": false, "phaseSetId": null, "phaseQuality": null}. - Convert ADAM SNV w/ genotypes but bad SB to htsjdk with lenient validation - Convert htsjdk multi-allelic sites-only SNVs to ADAM - Convert htsjdk multi-allelic SNVs to ADAM and back to htsjdk - Convert gVCF reference records to ADAM - Convert htsjdk variant context with no IDs to ADAM - Convert htsjdk variant context with one ID to ADAM - Convert htsjdk variant context with multiple IDs to ADAM - Convert ADAM variant context with no names to htsjdk - Convert ADAM variant context with one name to htsjdk - Convert ADAM variant context with multiple names to htsjdk - Convert ADAM variant context with null filters applied to htsjdk - Convert ADAM variant context with no filters applied to htsjdk - Convert ADAM variant context with passing filters to htsjdk - Convert ADAM variant context with failing filters to htsjdk - no phasing set going htsjdk->adam - phased but no phase set info going htsjdk->adam - set phase set and extract going htsjdk->adam - no allelic depth going htsjdk->adam - set allelic depth going htsjdk->adam - no gt read depth going htsjdk->adam - extract gt read depth going htsjdk->adam - no min gt read depth going htsjdk->adam - extract min gt read depth going htsjdk->adam - no genotype quality going htsjdk->adam - extract genotype quality going htsjdk->adam - no phred likelihood going htsjdk->adam - extract phred likelihoods going htsjdk->adam - no strand bias info going htsjdk->adam - extract strand bias info going htsjdk->adam - no filters going htsjdk->adam - filters passed going htsjdk->adam - extract single filter going htsjdk->adam - extract multiple filters going htsjdk->adam - no fisher strand bias going htsjdk->adam - extract fisher strand bias going htsjdk->adam - no rms mapping quality going htsjdk->adam - extract rms mapping quality going htsjdk->adam - no mq0 going htsjdk->adam - extract mq0 going htsjdk->adam - no gt read depth going adam->htsjdk - extract gt read depth going adam->htsjdk - throw iae if missing one component of gt read depth going adam->htsjdk - no depth going adam->htsjdk - extract depth going adam->htsjdk - no min depth going adam->htsjdk - extract min depth going adam->htsjdk - no quality going adam->htsjdk - extract quality going adam->htsjdk - no genotype likelihoods going adam->htsjdk - extract genotype likelihoods going adam->htsjdk - no strand bias going adam->htsjdk - malformed strand bias going adam->htsjdk - extract strand bias going adam->htsjdk - no phasing info going adam->htsjdk - unphased going adam->htsjdk - phased but no ps/pq going adam->htsjdk - phased but no pq going adam->htsjdk - phased but no ps going adam->htsjdk - phased going adam->htsjdk - no filter info going adam->htsjdk - if filters applied, must set passed/failed going adam->htsjdk - filters passed going adam->htsjdk - if filters failed, must set filters failed going adam->htsjdk - single filter failed going adam->htsjdk - multiple filters failed going adam->htsjdk - no fisher strand bias going adam->htsjdk - extract fisher strand bias going adam->htsjdk - no rms mapping quality going adam->htsjdk - extract rms mapping quality going adam->htsjdk - no mapping quality 0 reads going adam->htsjdk - extract mapping quality 0 reads going adam->htsjdk - no names set going htsjdk->adam - single name set going htsjdk->adam - multiple names set going htsjdk->adam - no quality going htsjdk->adam - quality set going htsjdk->adam - no filters applied going htsjdk->adam - filters applied and passed going htsjdk->adam - single filter applied and failed going htsjdk->adam - multiple filters applied and failed going htsjdk->adam - no names set adam->htsjdk - set a single name adam->htsjdk - set multiple names adam->htsjdk - no qual set adam->htsjdk - qual is set adam->htsjdk - no filters applied adam->htsjdk - null filters applied adam->htsjdk - filters passed adam->htsjdk - if filter failed, must have filters adam->htsjdk - single filter failed adam->htsjdk - multiple filters failed adam->htsjdk - no ancestral allele set going htsjdk->adam - ancestral allele set going htsjdk->adam - no dbsnp membership set going htsjdk->adam - dbsnp membership set going htsjdk->adam - no hapmap2 membership set going htsjdk->adam - hapmap2 membership set going htsjdk->adam - no hapmap3 membership set going htsjdk->adam - hapmap3 membership set going htsjdk->adam - no validated set going htsjdk->adam - validated set going htsjdk->adam - no 1000G membership set going htsjdk->adam - 1000G membership set going htsjdk->adam - not somatic going htsjdk->adam - somatic going htsjdk->adam - no allele count going htsjdk->adam - single allele count going htsjdk->adam - multiple allele counts going htsjdk->adam - no allele frequency going htsjdk->adam - single allele frequency going htsjdk->adam - single allele frequency is +Inf going htsjdk->adam - single allele frequency is -Inf going htsjdk->adam - multiple allele frequencies going htsjdk->adam - no CIGAR going htsjdk->adam - single CIGAR going htsjdk->adam - multiple CIGARs going htsjdk->adam - no read depth going htsjdk->adam - single read depth going htsjdk->adam - multiple read depths going htsjdk->adam - no forward read depth going htsjdk->adam - single forward read depth going htsjdk->adam - multiple forward read depths going htsjdk->adam - no reverse read depth going htsjdk->adam - single reverse read depth going htsjdk->adam - multiple reverse read depths going htsjdk->adam - no ancestral allele set adam->htsjdk - ancestral allele set adam->htsjdk - no dbsnp membership set adam->htsjdk - dbsnp membership set adam->htsjdk - no hapmap2 membership set adam->htsjdk - hapmap2 membership set adam->htsjdk - no hapmap3 membership set adam->htsjdk - hapmap3 membership set adam->htsjdk - no validated set adam->htsjdk - validated set adam->htsjdk - no 1000G membership set adam->htsjdk - 1000G membership set adam->htsjdk - no allele count set adam->htsjdk - allele count set adam->htsjdk - no allele frequency set adam->htsjdk - allele frequency set adam->htsjdk - no cigar set adam->htsjdk - cigar set adam->htsjdk - no read depth set adam->htsjdk - read depth set adam->htsjdk - read depth without reference read depth - reference read depth without read depth - no forward read depth set adam->htsjdk - forward read depth set adam->htsjdk - reference forward read depth without forward read depth - forward read depth without reference forward read depth - no reverse read depth set adam->htsjdk - reverse read depth set adam->htsjdk - reference reverse read depth without reverse read depth - reverse read depth without reference reverse read depth - VCF INFO attribute Number=0 Type=Flag adam->htsjdk - VCF INFO attribute Number=4 Type=Flag adam->htsjdk unsupported, strict !!! IGNORED !!! - VCF INFO attribute Number=1 Type=Integer adam->htsjdk - VCF INFO attribute Number=4 Type=Integer adam->htsjdk - VCF INFO attribute Number=A Type=Integer adam->htsjdk - VCF INFO attribute Number=R Type=Integer adam->htsjdk - VCF INFO attribute Number=R Type=String adam->htsjdk - VCF INFO attribute Number=G Type=String adam->htsjdk not supported - VCF INFO attribute Number=0 Type=Flag htsjdk->adam - VCF INFO attribute Number=1 Type=Integer htsjdk->adam - VCF INFO attribute Number=4 Type=Integer htsjdk->adam - VCF INFO attribute Number=4 Type=Float htsjdk->adam - VCF INFO attribute Number=A Type=Integer htsjdk->adam - VCF INFO attribute Number=R Type=Integer htsjdk->adam - VCF INFO attribute Number=R Type=String htsjdk->adam - VCF INFO attribute Number=G Type=String htsjdk->adam not supported - VCF FORMAT attribute Number=0 Type=Flag adam->htsjdk not supported - VCF FORMAT attribute Number=1 Type=Integer adam->htsjdk - VCF FORMAT attribute Number=4 Type=Integer adam->htsjdk - VCF FORMAT attribute Number=A Type=Integer adam->htsjdk - VCF FORMAT attribute Number=R Type=Integer adam->htsjdk - VCF FORMAT attribute Number=R Type=String adam->htsjdk - VCF FORMAT attribute Number=0 Type=Flag htsjdk->adam is not supported - VCF FORMAT attribute Number=1 Type=Integer htsjdk->adam - VCF FORMAT attribute Number=4 Type=Integer htsjdk->adam - VCF FORMAT attribute Number=4 Type=Float htsjdk->adam - VCF FORMAT attribute Number=A Type=Integer htsjdk->adam - VCF FORMAT attribute Number=R Type=Integer htsjdk->adam - VCF FORMAT attribute Number=R Type=String htsjdk->adam - VCF FORMAT attribute Number=G Type=String htsjdk->adam - respect end position for symbolic alts FastqRecordConverterSuite: - test read name suffix and index of pair must match - test parseReadInFastq, read suffix removal - test parseReadInFastq, read metadata removal - test parseReadInFastq, read quality shorter than read length, padded with B - test parseReadInFastq, read quality longer than read length - test parseReadInFastq, no read quality - testing FastqRecordConverter.convertPair with valid input - testing FastqRecordConverter.convertPair with 7-line invalid input - testing FastqRecordConverter.convertPair with invalid input: first read length and qual don't match - testing FastqRecordConverter.convertPair with invalid input: second read length and qual don't match - testing FastqRecordConverter.convertFragment with valid input - testing FastqRecordConverter.convertFragment with another valid input having /1, /2 suffixes - testing FastqRecordConverter.convertFragment with invalid input: different read names - testing FastqRecordConverter.convertRead with valid input - testing FastqRecordConverter.convertRead with valid input: setFirstOfPair set to true - testing FastqRecordConverter.convertRead with valid input: setSecondOfPair set to true - testing FastqRecordConverter.convertRead with valid input: setFirstOfPair and setSecondOfPair both true - testing FastqRecordConverter.convertRead with valid input, no qual, strict - testing FastqRecordConverter.convertRead with valid input, no qual, not strict AttributeSuite: - test SAMTagAndValue parsing - Attributes can be correctly re-encoded as text SAM tags GFF3HeaderWriterSuite: - write gff3 header pragma BinQualitiesSuite: - make a quality score bin - can't have a quality score bin with negative score - can't have a quality score bin with high score below low - can't have a quality score bin with high score above 255 - can't have a quality score bin with score outside - make a quality score bin from a string - quality score bin must have exactly 3 elements - quality score bin must be integers - must define at least one bin - build multiple bins - rewrite quality scores for a read - rewriting quality scores fails if bins overlap - rewriting quality scores fails if base is out of bounds - skip read if qualities are null - rewrite a read IndexedFastaFileSuite: - correctly generates sequence dictionary from .dict file - correctly gets sequence - fails when fai index is not provided 2019-06-28 14:13:52 WARN IndexedFastaFile:190 - Caught exception java.lang.NullPointerException when loading FASTA sequence dictionary. Using empty dictionary instead. - passes when dict is not provided and ValidationStringency = LENIENT SAMRecordConverterSuite: - testing the fields in an alignmentRecord obtained from a mapped samRecord conversion - testing the fields in an alignmentRecord obtained from an unmapped samRecord conversion - '*' quality gets nulled out - don't keep denormalized fields ADAMContextSuite: - ctr is accessible - load from an empty directory - sc.loadParquet should not fail on unmapped reads - sc.loadParquet should not load a file without a type specified - can read a small .SAM file - can read a small .SAM file with a bad header with lenient validation - loading a sam file with a bad header and strict stringency should fail - can read a small .CRAM file - can read a small .SAM with all attribute tag types - can filter a .SAM file based on quality - Can convert to phred - Can convert from phred - Can read a .gtf file - Can read a .bed file - Can read a BED 12 file - Can read a .narrowPeak file - Can read a .interval_list file 2019-06-28 14:13:56 WARN VariantContextConverter:1662 - Saw invalid info field java.lang.IllegalArgumentException: Multivalued flags are not supported for INFO lines: INFO=<ID=ABADFLAG,Number=.,Type=Flag,Description="A no good, very bad flag.">. Ignoring... 2019-06-28 14:13:56 WARN VariantContextConverter:2169 - Generating field extractor from header line INFO=<ID=ABADFLAG,Number=.,Type=Flag,Description="A no good, very bad flag."> failed: java.lang.IllegalArgumentException: Multivalue flags are not supported for INFO lines: INFO=<ID=ABADFLAG,Number=.,Type=Flag,Description="A no good, very bad flag."> - can read a small .vcf file with a validation issue - can read a small .vcf file 2019-06-28 14:13:56 WARN VCFInputFormat:218 - file:/home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/target/2.12.8/test-classes/test.vcf.gz is not splittable, consider using block-compressed gzip (BGZF) - can read a gzipped .vcf file - can read a vcf file with an empty alt - can read a BGZF gzipped .vcf file with .gz file extension - can read a BGZF gzipped .vcf file with .bgz file extension - can read a vcf file with a projection - can read an uncompressed BCFv2.2 file !!! IGNORED !!! - can read a BGZF compressed BCFv2.2 file !!! IGNORED !!! - loadIndexedVcf with 1 ReferenceRegion - loadIndexedVcf with multiple ReferenceRegions - load block compressed interleaved fastq - import records from interleaved FASTQ: 1 - import records from interleaved FASTQ: 2 - import records from interleaved FASTQ: 3 - import records from interleaved FASTQ: 4 - import block compressed single fastq - import records from single ended FASTQ: 1 - import records from single ended FASTQ: 2 - import records from single ended FASTQ: 3 - import records from single ended FASTQ: 4 - filter on load using the filter2 API - saveAsParquet with file path - saveAsParquet with file path, block size, page size - saveAsParquet with save args - read a HLA fasta from GRCh38 - read a gzipped fasta file - read a fasta file with comments, gaps, and translation stops - loadIndexedBam with 1 ReferenceRegion - loadIndexedBam with multiple ReferenceRegions - loadIndexedBam with multiple ReferenceRegions and indexed bams - loadIndexedBam with multiple ReferenceRegions and a directory of indexed bams - loadIndexedBam should throw exception without an index file - loadIndexedBam should work with indexed file with index naming format <filename>.bai - loadIndexedBam glob should throw exception without an index file - loadBam with a glob - loadBam with a directory - load vcf with a glob - load vcf from a directory - load gvcf which contains a multi-allelic row from a directory - load and save gvcf which contains rows without likelihoods - parse annotations for multi-allelic rows - load parquet with globs - bad glob should fail - empty directory should fail - can read a SnpEff-annotated .vcf file - loadAlignments should not fail on single-end and paired-end fastq reads - load queryname sorted sam as fragments - load query grouped sam as fragments - load paired fastq - load paired fastq without cache - load paired fastq as fragments - load paired fastq as fragments without cache - load HTSJDK sequence dictionary - load Bedtools .genome file as sequence dictionary - load Bedtools .genome.txt file as sequence dictionary - load UCSC Genome Browser chromInfo.txt file as sequence dictionary - load unrecognized file extension as sequence dictionary fails - load BED features with Bedtools .genome file as sequence dictionary - load BED features with Bedtools .genome file as sequence dictionary, no matching features - convert program record - load program record from sam file - load alignments from data frame - load features from data frame - load fragments from data frame - load genotypes from data frame with default header lines - load genotypes from data frame with empty header lines - load reads from data frame - load sequences from data frame - load slices from data frame - load variant contexts from data frame with default header lines - load variant contexts from data frame with empty header lines - load variants from data frame with default header lines - load variants from data frame with empty header lines - load alignments with metadata from data frame - load features with metadata from data frame - load fragments with metadata from data frame - load genotypes with metadata from data frame - load variant contexts with metadata from data frame - load variants with metadata from data frame - read a fasta file with short sequences as sequences - read a fasta file with long sequences as sequences - read a fasta file with short sequences as slices - read a fasta file with long sequences as slices CycleCovariateSuite: - compute covariates for an unpaired read on the negative strand - compute covariates for a first-of-pair read on the negative strand - compute covariates for a second-of-pair read on the negative strand - compute covariates for an unpaired read on the positive strand - compute covariates for a first-of-pair read on the positive strand - compute covariates for a second-of-pair read on the positive strand ConsensusGeneratorFromKnownsSuite: - no consensuses for empty target - no consensuses for reads that don't overlap a target - return a consensus for read overlapping a single target RichCigarSuite: - moving 2 bp from a deletion to a match operator - moving 2 bp from a insertion to a match operator - moving 1 base in a two element cigar - move to start of read - process right clipped cigar - process left clipped cigar - process cigar clipped on both ends MDTaggingSuite: - test adding MDTags over boundary - test adding MDTags; reads span full contig - test adding MDTags; reads start inside first fragment - test adding MDTags; reads end inside last fragment - test adding MDTags; reads start inside first fragment and end inside last fragment - test adding MDTags; reads start and end in middle fragements 2019-06-28 14:14:43 WARN BlockManager:66 - Putting block rdd_5_3 failed due to exception java.lang.Exception: Contig chr2 not found in reference map with keys: chr1. 2019-06-28 14:14:43 WARN BlockManager:66 - Block rdd_5_3 could not be removed as it was not found on disk or in memory 2019-06-28 14:14:43 ERROR Executor:91 - Exception in task 3.0 in stage 2.0 (TID 11) java.lang.Exception: Contig chr2 not found in reference map with keys: chr1 at org.bdgenomics.adam.util.ReferenceContigMap.$anonfun$extract$1(ReferenceContigMap.scala:64) at scala.collection.immutable.Map$Map1.getOrElse(Map.scala:119) at org.bdgenomics.adam.util.ReferenceContigMap.extract(ReferenceContigMap.scala:63) at org.bdgenomics.adam.rdd.read.MDTagging.$anonfun$addMDTagsBroadcast$3(MDTagging.scala:76) at scala.Option$WithFilter.map(Option.scala:163) at org.bdgenomics.adam.rdd.read.MDTagging.$anonfun$addMDTagsBroadcast$1(MDTagging.scala:71) at scala.collection.Iterator$$anon$10.next(Iterator.scala:459) at org.apache.spark.storage.memory.MemoryStore.putIterator(MemoryStore.scala:222) at org.apache.spark.storage.memory.MemoryStore.putIteratorAsValues(MemoryStore.scala:299) at org.apache.spark.storage.BlockManager.$anonfun$doPutIterator$1(BlockManager.scala:1165) at org.apache.spark.storage.BlockManager.doPut(BlockManager.scala:1091) at org.apache.spark.storage.BlockManager.doPutIterator(BlockManager.scala:1156) at org.apache.spark.storage.BlockManager.getOrElseUpdate(BlockManager.scala:882) at org.apache.spark.rdd.RDD.getOrCompute(RDD.scala:335) at org.apache.spark.rdd.RDD.iterator(RDD.scala:286) at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:90) at org.apache.spark.scheduler.Task.run(Task.scala:121) at org.apache.spark.executor.Executor$TaskRunner.$anonfun$run$3(Executor.scala:411) at org.apache.spark.util.Utils$.tryWithSafeFinally(Utils.scala:1360) at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:414) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624) at java.lang.Thread.run(Thread.java:748) 2019-06-28 14:14:43 WARN TaskSetManager:66 - Lost task 3.0 in stage 2.0 (TID 11, localhost, executor driver): java.lang.Exception: Contig chr2 not found in reference map with keys: chr1 at org.bdgenomics.adam.util.ReferenceContigMap.$anonfun$extract$1(ReferenceContigMap.scala:64) at scala.collection.immutable.Map$Map1.getOrElse(Map.scala:119) at org.bdgenomics.adam.util.ReferenceContigMap.extract(ReferenceContigMap.scala:63) at org.bdgenomics.adam.rdd.read.MDTagging.$anonfun$addMDTagsBroadcast$3(MDTagging.scala:76) at scala.Option$WithFilter.map(Option.scala:163) at org.bdgenomics.adam.rdd.read.MDTagging.$anonfun$addMDTagsBroadcast$1(MDTagging.scala:71) at scala.collection.Iterator$$anon$10.next(Iterator.scala:459) at org.apache.spark.storage.memory.MemoryStore.putIterator(MemoryStore.scala:222) at org.apache.spark.storage.memory.MemoryStore.putIteratorAsValues(MemoryStore.scala:299) at org.apache.spark.storage.BlockManager.$anonfun$doPutIterator$1(BlockManager.scala:1165) at org.apache.spark.storage.BlockManager.doPut(BlockManager.scala:1091) at org.apache.spark.storage.BlockManager.doPutIterator(BlockManager.scala:1156) at org.apache.spark.storage.BlockManager.getOrElseUpdate(BlockManager.scala:882) at org.apache.spark.rdd.RDD.getOrCompute(RDD.scala:335) at org.apache.spark.rdd.RDD.iterator(RDD.scala:286) at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:90) at org.apache.spark.scheduler.Task.run(Task.scala:121) at org.apache.spark.executor.Executor$TaskRunner.$anonfun$run$3(Executor.scala:411) at org.apache.spark.util.Utils$.tryWithSafeFinally(Utils.scala:1360) at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:414) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624) at java.lang.Thread.run(Thread.java:748) 2019-06-28 14:14:43 ERROR TaskSetManager:70 - Task 3 in stage 2.0 failed 1 times; aborting job - try realigning a read on a missing contig, stringency == STRICT 2019-06-28 14:14:44 WARN MDTagging:190 - Caught exception when processing read chr2: java.lang.Exception: Contig chr2 not found in reference map with keys: chr1 - try realigning a read on a missing contig, stringency == LENIENT FileExtensionsSuite: - ends in gzip extension - is a vcf extension PhredUtilsSuite: - convert low phred score to log and back - convert high phred score to log and back - convert overflowing phred score to log and back and clip - convert negative zero log probability to phred and clip - round trip log probabilities ReadDatasetSuite: - create a new read genomic dataset - create a new read genomic dataset with sequence dictionary - save as parquet - round trip as parquet - save as fastq - save as single file fastq - filter read genomic dataset by reference region - broadcast region join reads and features - shuffle region join reads and features - convert reads to alignments - convert reads to sequences - convert reads to slices SmithWatermanSuite: - gather max position from simple scoring matrix - gather max position from irregular scoring matrix - gather max position from irregular scoring matrix with deletions - score simple alignment with constant gap - score irregular scoring matrix - score irregular scoring matrix with indel - can unroll cigars correctly - execute simple trackback - execute trackback with indel - run end to end smith waterman for simple reads - run end to end smith waterman for short sequences with indel - run end to end smith waterman for longer sequences with snp - run end to end smith waterman for longer sequences with short indel - run end to end smith waterman for shorter sequence in longer sequence - run end to end smith waterman for shorter sequence in longer sequence, with indel - smithWaterman - simple alignment MdTagSuite: - null md tag - zero length md tag - md tag with non-digit initial value - md tag invalid base - md tag, pure insertion - md tag, pure insertion, test 2 - md tag pure insertion equality - md tag equality and hashcode - valid md tags - get start of read with no mismatches or deletions - get start of read with no mismatches, but with a deletion at the start - get start of read with mismatches at the start - get end of read with no mismatches or deletions - check that mdtag and rich record return same end - get end of read with no mismatches, but a deletion at end - CIGAR with N operator - CIGAR with multiple N operators - CIGAR with P operators - Get correct matches for mdtag with insertion - Get correct matches for mdtag with mismatches and insertion - Get correct matches for mdtag with insertion between mismatches - Get correct matches for mdtag with intron between mismatches - Get correct matches for mdtag with intron and deletion between mismatches - Throw exception when number of deleted bases in mdtag disagrees with CIGAR - Get correct matches for mdtag with mismatch, insertion and deletion - Get correct matches for mdtag with mismatches, insertion and deletion - Get correct matches for MDTag with mismatches and deletions - Get correct matches base from MDTag and CIGAR with N - get end of read with mismatches and a deletion at end - get correct string out of mdtag with no mismatches - get correct string out of mdtag with mismatches at start - get correct string out of mdtag with deletion at end - get correct string out of mdtag with mismatches at end - get correct string out of complex mdtag - check complex mdtag - get gapped reference - move a cigar alignment by two for a read - rewrite alignment to all matches - rewrite alignment to two mismatches followed by all matches - rewrite alignment to include a deletion but otherwise all matches - rewrite alignment to include an insertion at the start of the read but otherwise all matches - create new md tag from read vs. reference, perfect match - create new md tag from read vs. reference, perfect alignment match, 1 mismatch - create new md tag from read vs. reference, alignment with deletion - create new md tag from read vs. reference, alignment with insert - handle '=' and 'X' operators - CIGAR/MD tag mismatch should cause errors GenomicDatasetSuite: - processing a command that is the spark root directory should return an absolute path - processing a command that is just a single word should do nothing - processing a command should handle arguments that include spaces - processing a command that is a single substitution should succeed - processing a command that is multiple words should split the string - process a command that is multiple words with a replacement - process a command that is multiple words with multiple replacements ParallelFileMergerSuite: - cannot write both empty gzip block and cram eof - buffer size must be non-negative - get the size of several files - block size must be positive and non-zero when trying to merge files - must provide files to merge - if two files are both below the block size, they should merge into one shard - merge two files where one is greater than the block size - merge a sharded sam file - merge a sharded bam file - merge a sharded cram file - can't turn a negative index into a path - generate a path from an index IndelTableSuite: - check for indels in a region with known indels - check for indels in a contig that doesn't exist - check for indels in a region without known indels - build indel table from rdd of variants SnpTableSuite: - create an empty snp table - create a snp table from variants on multiple contigs - create a snp table from a larger set of variants - perform lookups on multi-contig snp table - perform lookups on larger snp table RealignIndelsSuite: - map reads to targets - checking mapping to targets for artificial reads - checking alternative consensus for artificial reads - checking extraction of reference from reads - checking realigned reads for artificial input - checking realigned reads for artificial input with reference file - checking realigned reads for artificial input using knowns - checking realigned reads for artificial input using knowns and reads - skip realigning reads if target is highly covered - skip realignment if target is an insufficient LOD improvement - realign reads to an insertion - test mismatch quality scoring - test mismatch quality scoring for no mismatches - test mismatch quality scoring for offset - test mismatch quality scoring with early exit - test mismatch quality scoring after unpacking read - we shouldn't try to realign a region with no target - we shouldn't try to realign reads with no indel evidence - test OP and OC tags - realign a read with an insertion that goes off the end of the read - if realigning a target doesn't improve the LOD, don't drop reads - extract seq/qual from a read with no clipped bases - extract seq/qual from a read with clipped bases at start - extract seq/qual from a read with clipped bases at end - if unclip is selected, don't drop base when extracting from a read with clipped bases - get cigar and coordinates for read that spans indel, no clipped bases - get cigar and coordinates for read that spans deletion, clipped bases at start - get cigar and coordinates for read that falls wholly before insertion - get cigar and coordinates for read that falls wholly after insertion - get cigar and coordinates for read that falls wholly after deletion - get cigar and coordinates for read that partially spans insertion, no clipped bases - get cigar and coordinates for read that partially spans insertion, clipped bases at end - get cigar and coordinates for read that partially spans insertion, clipped bases both ends BaseQualityRecalibrationSuite: - BQSR Test Input #1 w/ VCF Sites without caching - BQSR Test Input #1 w/ VCF Sites with caching - BQSR Test Input #1 w/ VCF Sites with serialized caching DinucCovariateSuite: - computing dinucleotide pairs for a single base sequence should return (N,N) - compute dinucleotide pairs for a string of all valid bases - compute dinucleotide pairs for a string with an N - compute covariates for a read on the negative strand - compute covariates for a read on the positive strand SequenceDictionarySuite: - Convert from sam sequence record and back - Convert from SAM sequence dictionary file (with extra fields) - merge into existing dictionary - Convert from SAM sequence dictionary and back - Can retrieve sequence by name - SequenceDictionary's with same single element are equal - SequenceDictionary's with same two elements are equals - SequenceDictionary's with different elements are unequal - SequenceDictionaries with same elements in different order are compatible - isCompatible tests equality on overlap - The addition + works correctly - The append operation ++ works correctly - ContainsRefName works correctly for different string types - Apply on name works correctly for different String types - convert from sam sequence record and back - convert from sam sequence dictionary and back - conversion to sam sequence dictionary has correct sort order - load sequence dictionary from VCF file - empty sequence dictionary must be empty - test filter to reference name - test filter to reference names - test filter to reference name by function GenomicPositionPartitionerSuite: - partitions the UNMAPPED ReferencePosition into the top partition - if we do not have a contig for a record, we throw an IAE - partitioning into N pieces on M total sequence length, where N > M, results in M partitions - correctly partitions a single dummy sequence into two pieces - correctly counts cumulative lengths - correctly partitions positions across two dummy sequences - test that we can range partition ADAMRecords - test that we can range partition ADAMRecords indexed by sample - test that simple partitioning works okay on a reasonable set of ADAMRecords - test indexed ReferencePosition partitioning works on a set of indexed ADAMRecords CoverageSuite: - Convert to coverage from valid Feature - Convert to coverage from valid Feature with sampleId - Convert to coverage from Feature with null/empty contigName fails with correct error - Convert to coverage from Feature with no start/end position fails with correct error - Convert to coverage from Feature with no score fails with correct error InnerTreeRegionJoinSuite: - Ensure same reference regions get passed together - Overlapping reference regions - Multiple reference regions do not throw exception RichAlignmentRecordSuite: - Unclipped Start - Unclipped End - tags contains optional fields - read overlap unmapped read - read overlap reference position - read overlap same position different contig VariantDatasetSuite: - union two variant genomic datasets together - round trip to parquet - save and reload from partitioned parquet - use broadcast join to pull down variants mapped to targets - use right outer broadcast join to pull down variants mapped to targets - use shuffle join to pull down variants mapped to targets - use right outer shuffle join to pull down variants mapped to targets - use left outer shuffle join to pull down variants mapped to targets - use full outer shuffle join to pull down variants mapped to targets - use shuffle join with group by to pull down variants mapped to targets - use right outer shuffle join with group by to pull down variants mapped to targets - convert back to variant contexts - load parquet to sql, save, re-read from avro 2019-06-28 14:15:36 WARN DatasetBoundSliceDataset:190 - Saving directly as Parquet from SQL. Options other than compression codec are ignored. - transform variants to slice genomic dataset - transform variants to coverage genomic dataset - transform variants to feature genomic dataset - transform variants to fragment genomic dataset - transform variants to read genomic dataset - transform variants to genotype genomic dataset - transform variants to variant context genomic dataset - filter RDD bound variants to filters passed - filter dataset bound variants to filters passed - filter RDD bound variants by quality - filter dataset bound variants by quality - filter RDD bound variants by read depth - filter dataset bound variants by read depth - filter RDD bound variants by reference read depth - filter dataset bound variants by reference read depth - filter RDD bound single nucleotide variants - filter dataset bound single nucleotide variants - filter RDD bound multiple nucleotide variants - filter dataset bound multiple nucleotide variants - filter RDD bound indel variants - filter dataset bound indel variants - filter RDD bound variants to single nucleotide variants - filter dataset bound variants to single nucleotide variants - filter RDD bound variants to multiple nucleotide variants - filter dataset bound variants to multiple nucleotide variants - filter RDD bound variants to indel variants - filter dataset bound variants to indel variants - transform dataset via java API Run completed in 6 minutes, 36 seconds. Total number of tests run: 1175 Suites: completed 68, aborted 0 Tests: succeeded 1175, failed 0, canceled 0, ignored 5, pending 0 All tests passed. [INFO] [INFO] <<< scoverage-maven-plugin:1.1.1:report (default-cli) < [scoverage]test @ adam-core-spark2_2.12 <<< [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:report (default-cli) @ adam-core-spark2_2.12 --- [INFO] Skipping SCoverage report generation [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building ADAM_2.12: APIs for Java, Python 0.28.0-SNAPSHOT [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-apis-spark2_2.12 --- [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-apis-spark2_2.12 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ adam-apis-spark2_2.12 --- [INFO] Source directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-apis/src/main/scala added. [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ adam-apis-spark2_2.12 --- [INFO] Modified 0 of 5 .scala files [INFO] [INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ adam-apis-spark2_2.12 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-apis/src/main/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ adam-apis-spark2_2.12 --- [INFO] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-apis/src/main/scala:-1: info: compiling [INFO] Compiling 4 source files to /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-apis/target/2.12.8/classes at 1561756552883 [WARNING] warning: there was one deprecation warning (since 2.12.0); re-run with -deprecation for details [WARNING] warning: there were two feature warnings; re-run with -feature for details [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) @ adam-apis-spark2_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) @ adam-apis-spark2_2.12 --- [INFO] Test Source directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-apis/src/test/scala added. [INFO] [INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ adam-apis-spark2_2.12 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 2 resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ adam-apis-spark2_2.12 --- [INFO] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-apis/src/test/java:-1: info: compiling [INFO] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-apis/src/test/scala:-1: info: compiling [INFO] Compiling 9 source files to /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-apis/target/2.12.8/test-classes at 1561756559268 [INFO] prepare-compile in 0 s [INFO] compile in 4 s [INFO] [INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ adam-apis-spark2_2.12 --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 8 source files to /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-apis/target/2.12.8/test-classes [INFO] [INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ adam-apis-spark2_2.12 --- [INFO] Tests are skipped. [INFO] [INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ adam-apis-spark2_2.12 --- Discovery starting. Discovery completed in 216 milliseconds. Run starting. Expected test count is: 10 JavaADAMContextSuite: 2019-06-28 14:16:05 WARN Utils:66 - Your hostname, research-jenkins-worker-07 resolves to a loopback address: 127.0.1.1; using 192.168.10.27 instead (on interface eth0) 2019-06-28 14:16:05 WARN Utils:66 - Set SPARK_LOCAL_IP if you need to bind to another address 2019-06-28 14:16:05 WARN NativeCodeLoader:62 - Unable to load native-hadoop library for your platform... using builtin-java classes where applicable - can read and write a small .SAM file - loadIndexedBam with multiple ReferenceRegions - can read and write a small .SAM file as fragments - can read and write a small .bed file as features - can read and write a small .bed file as coverage - can read and write a small .vcf as genotypes - can read and write a small .vcf as variants - can read a two bit file 2019-06-28 14:16:15 WARN RDDBoundSequenceDataset:190 - asSingleFile = true ignored when saving as Parquet. - can read and write .fa as sequences 2019-06-28 14:16:16 WARN RDDBoundSliceDataset:190 - asSingleFile = true ignored when saving as Parquet. - can read and write .fa as slices Run completed in 12 seconds, 186 milliseconds. Total number of tests run: 10 Suites: completed 2, aborted 0 Tests: succeeded 10, failed 0, canceled 0, ignored 0, pending 0 All tests passed. [INFO] [INFO] >>> scoverage-maven-plugin:1.1.1:report (default-cli) > [scoverage]test @ adam-apis-spark2_2.12 >>> [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-apis-spark2_2.12 --- [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-apis-spark2_2.12 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ adam-apis-spark2_2.12 --- [INFO] Source directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-apis/src/main/scala added. [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ adam-apis-spark2_2.12 --- [INFO] Modified 0 of 5 .scala files [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:pre-compile (default-cli) @ adam-apis-spark2_2.12 --- [WARNING] Skipping SCoverage execution - unsupported Scala version "2.12.8" [INFO] [INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ adam-apis-spark2_2.12 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-apis/src/main/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ adam-apis-spark2_2.12 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ adam-apis-spark2_2.12 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:post-compile (default-cli) @ adam-apis-spark2_2.12 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ adam-apis-spark2_2.12 --- [INFO] Test Source directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-apis/src/test/scala added. [INFO] [INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ adam-apis-spark2_2.12 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 2 resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ adam-apis-spark2_2.12 --- [INFO] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-apis/src/test/java:-1: info: compiling [INFO] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-apis/src/test/scala:-1: info: compiling [INFO] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-apis/target/generated-test-sources/test-annotations:-1: info: compiling [INFO] Compiling 9 source files to /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-apis/target/2.12.8/test-classes at 1561756577660 [INFO] prepare-compile in 0 s [INFO] compile in 4 s [INFO] [INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ adam-apis-spark2_2.12 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ adam-apis-spark2_2.12 --- [INFO] Tests are skipped. [INFO] [INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ adam-apis-spark2_2.12 --- Discovery starting. Discovery completed in 214 milliseconds. Run starting. Expected test count is: 10 JavaADAMContextSuite: 2019-06-28 14:16:23 WARN Utils:66 - Your hostname, research-jenkins-worker-07 resolves to a loopback address: 127.0.1.1; using 192.168.10.27 instead (on interface eth0) 2019-06-28 14:16:23 WARN Utils:66 - Set SPARK_LOCAL_IP if you need to bind to another address 2019-06-28 14:16:23 WARN NativeCodeLoader:62 - Unable to load native-hadoop library for your platform... using builtin-java classes where applicable - can read and write a small .SAM file - loadIndexedBam with multiple ReferenceRegions - can read and write a small .SAM file as fragments - can read and write a small .bed file as features - can read and write a small .bed file as coverage - can read and write a small .vcf as genotypes - can read and write a small .vcf as variants - can read a two bit file 2019-06-28 14:16:33 WARN RDDBoundSequenceDataset:190 - asSingleFile = true ignored when saving as Parquet. - can read and write .fa as sequences 2019-06-28 14:16:34 WARN RDDBoundSliceDataset:190 - asSingleFile = true ignored when saving as Parquet. - can read and write .fa as slices Run completed in 11 seconds, 980 milliseconds. Total number of tests run: 10 Suites: completed 2, aborted 0 Tests: succeeded 10, failed 0, canceled 0, ignored 0, pending 0 All tests passed. 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git-commit-id-plugin:2.2.2:revision (default) @ adam-cli-spark2_2.12 --- Downloading: https://repo.maven.apache.org/maven2/org/eclipse/jgit/org.eclipse.jgit/4.3.1.201605051710-r/org.eclipse.jgit-4.3.1.201605051710-r.pom 4/10 KB 8/10 KB 10/10 KB Downloaded: https://repo.maven.apache.org/maven2/org/eclipse/jgit/org.eclipse.jgit/4.3.1.201605051710-r/org.eclipse.jgit-4.3.1.201605051710-r.pom (10 KB at 913.0 KB/sec) Downloading: https://repo.maven.apache.org/maven2/org/eclipse/jgit/org.eclipse.jgit-parent/4.3.1.201605051710-r/org.eclipse.jgit-parent-4.3.1.201605051710-r.pom 4/26 KB 8/26 KB 12/26 KB 16/26 KB 20/26 KB 24/26 KB 26/26 KB Downloaded: https://repo.maven.apache.org/maven2/org/eclipse/jgit/org.eclipse.jgit-parent/4.3.1.201605051710-r/org.eclipse.jgit-parent-4.3.1.201605051710-r.pom (26 KB at 2582.9 KB/sec) Downloading: https://repo.maven.apache.org/maven2/org/eclipse/jgit/org.eclipse.jgit/4.3.1.201605051710-r/org.eclipse.jgit-4.3.1.201605051710-r.jar 4/2296 KB 8/2296 KB 12/2296 KB 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[INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 1 resource [INFO] Copied 1 files to output directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-cli/target/generated-sources/java-templates [INFO] Source directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-cli/target/generated-sources/java-templates added. [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ adam-cli-spark2_2.12 --- [INFO] Source directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-cli/src/main/scala added. [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ adam-cli-spark2_2.12 --- [INFO] Modified 0 of 29 .scala files [INFO] [INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ adam-cli-spark2_2.12 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-cli/src/main/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ adam-cli-spark2_2.12 --- [INFO] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-cli/target/generated-sources/java-templates:-1: info: compiling [INFO] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-cli/src/main/scala:-1: info: compiling [INFO] Compiling 18 source files to /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-cli/target/2.12.8/classes at 1561756596723 [WARNING] warning: there was one deprecation warning [WARNING] warning: there was one deprecation warning (since 2.12.0) [WARNING] warning: there were two deprecation warnings in total; re-run with -deprecation for details [WARNING] three warnings found [INFO] prepare-compile in 0 s [INFO] compile in 7 s [INFO] [INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ adam-cli-spark2_2.12 --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 1 source file to /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-cli/target/2.12.8/classes [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ adam-cli-spark2_2.12 --- [INFO] Test Source directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-cli/src/test/scala added. [INFO] [INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ adam-cli-spark2_2.12 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 15 resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ adam-cli-spark2_2.12 --- [INFO] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-cli/src/test/scala:-1: info: compiling [INFO] Compiling 12 source files to /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-cli/target/2.12.8/test-classes at 1561756604604 [INFO] prepare-compile in 0 s [INFO] compile in 6 s [INFO] [INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ adam-cli-spark2_2.12 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ adam-cli-spark2_2.12 --- [INFO] Tests are skipped. [INFO] [INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ adam-cli-spark2_2.12 --- Discovery starting. Discovery completed in 213 milliseconds. Run starting. Expected test count is: 44 TransformFeaturesSuite: 2019-06-28 14:16:52 WARN Utils:66 - Your hostname, research-jenkins-worker-07 resolves to a loopback address: 127.0.1.1; using 192.168.10.27 instead (on interface eth0) 2019-06-28 14:16:52 WARN Utils:66 - Set SPARK_LOCAL_IP if you need to bind to another address 2019-06-28 14:16:52 WARN NativeCodeLoader:62 - Unable to load native-hadoop library for your platform... using builtin-java classes where applicable - can convert a simple BED file TransformVariantsSuite: - save a file sorted by contig index - save a lexicographically sorted file ViewSuite: - -f 0 -F 0 is a no-op - no -f or -F args is a no-op - -f 4: only unmapped reads - -F 4: only mapped reads - -f 4 -F 8: unmapped reads with mapped mates - -f 12: unmapped reads with unmapped mates - -g 12: reads that are unmapped or whose mate is unmapped - -F 12: mapped reads with mapped mates - -g 36: unmapped reads or reads with mate on negative strand - -F 36: unmapped reads or reads with mate on negative strand TransformFragmentsSuite: - load queryname sorted sam and save as parquet - cannot sort if not saving as sam 2019-06-28 14:17:06 WARN TransformFragments:190 - If loading and saving as reads, consider using TransformAlignments instead. - load reads as sam and save them sorted - bin quality scores on reads TransformGenotypesSuite: - save a file sorted by contig index - save a lexicographically sorted file - transform VCF without nested annotations - transform VCF with nested annotations Reads2CoverageSuite: - correctly calculates coverage from small sam file AboutSuite: - template variables have been replaced - templated values are not empty MergeShardsSuite: - merge shards from unordered sam to unordered sam - unordered sam to ordered sam - merge sharded bam - merge sharded cram TransformAlignmentsSuite: - unordered sam to unordered sam - unordered sam to ordered sam - unordered sam, to adam, to sam - unordered sam, to adam, to ordered sam - put quality scores into bins - run region predicate ADAMMainSuite: - 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 Adam2FastqSuite: 2019-06-28 14:17:17 WARN RDDBoundAlignmentRecordDataset:190 - Found 16 read names that don't occur exactly twice: 1x: 16 Samples: SRR062634.16445865 SRR062634.9119161 SRR062634.17190076 SRR062634.17969132 SRR062634.7301099 SRR062634.2087100 SRR062634.20911784 SRR062634.16769670 SRR062634.18958430 SRR062634.12099057 SRR062634.12606172 SRR062634.14985224 SRR062634.10448889 SRR062634.4789722 SRR062634.3203184 SRR062634.17698657 - convert SAM to paired FASTQ Run completed in 26 seconds, 172 milliseconds. Total number of tests run: 44 Suites: completed 12, aborted 0 Tests: succeeded 44, failed 0, canceled 0, ignored 0, pending 0 All tests passed. [INFO] [INFO] >>> scoverage-maven-plugin:1.1.1:report (default-cli) > [scoverage]test @ adam-cli-spark2_2.12 >>> [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-cli-spark2_2.12 --- [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-cli-spark2_2.12 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:timestamp-property (timestamp-property) @ adam-cli-spark2_2.12 --- [INFO] [INFO] --- git-commit-id-plugin:2.2.2:revision (default) @ adam-cli-spark2_2.12 --- [INFO] [INFO] --- templating-maven-plugin:1.0.0:filter-sources (filter-src) @ adam-cli-spark2_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/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-cli/target/generated-sources/java-templates [INFO] Source directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-cli/target/generated-sources/java-templates added. [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ adam-cli-spark2_2.12 --- [INFO] Source directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-cli/src/main/scala added. [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ adam-cli-spark2_2.12 --- [INFO] Modified 0 of 29 .scala files [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:pre-compile (default-cli) @ adam-cli-spark2_2.12 --- [WARNING] Skipping SCoverage execution - unsupported Scala version "2.12.8" [INFO] [INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ adam-cli-spark2_2.12 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-cli/src/main/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ adam-cli-spark2_2.12 --- [INFO] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-cli/target/generated-sources/java-templates:-1: info: compiling [INFO] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-cli/src/main/scala:-1: info: compiling [INFO] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-cli/target/generated-sources/annotations:-1: info: compiling [INFO] Compiling 18 source files to /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-cli/target/2.12.8/classes at 1561756639132 [WARNING] warning: there was one deprecation warning [WARNING] warning: there was one deprecation warning (since 2.12.0) [WARNING] warning: there were two deprecation warnings in total; re-run with -deprecation for details [WARNING] three warnings found [INFO] prepare-compile in 0 s [INFO] compile in 7 s [INFO] [INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ adam-cli-spark2_2.12 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:post-compile (default-cli) @ adam-cli-spark2_2.12 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ adam-cli-spark2_2.12 --- [INFO] Test Source directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-cli/src/test/scala added. [INFO] [INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ adam-cli-spark2_2.12 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 15 resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ adam-cli-spark2_2.12 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ adam-cli-spark2_2.12 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ adam-cli-spark2_2.12 --- [INFO] Tests are skipped. [INFO] [INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ adam-cli-spark2_2.12 --- Discovery starting. Discovery completed in 210 milliseconds. Run starting. Expected test count is: 44 TransformFeaturesSuite: 2019-06-28 14:17:28 WARN Utils:66 - Your hostname, research-jenkins-worker-07 resolves to a loopback address: 127.0.1.1; using 192.168.10.27 instead (on interface eth0) 2019-06-28 14:17:28 WARN Utils:66 - Set SPARK_LOCAL_IP if you need to bind to another address 2019-06-28 14:17:28 WARN NativeCodeLoader:62 - Unable to load native-hadoop library for your platform... using builtin-java classes where applicable - can convert a simple BED file TransformVariantsSuite: - save a file sorted by contig index - save a lexicographically sorted file ViewSuite: - -f 0 -F 0 is a no-op - no -f or -F args is a no-op - -f 4: only unmapped reads - -F 4: only mapped reads - -f 4 -F 8: unmapped reads with mapped mates - -f 12: unmapped reads with unmapped mates - -g 12: reads that are unmapped or whose mate is unmapped - -F 12: mapped reads with mapped mates - -g 36: unmapped reads or reads with mate on negative strand - -F 36: unmapped reads or reads with mate on negative strand TransformFragmentsSuite: - load queryname sorted sam and save as parquet - cannot sort if not saving as sam 2019-06-28 14:17:41 WARN TransformFragments:190 - If loading and saving as reads, consider using TransformAlignments instead. - load reads as sam and save them sorted - bin quality scores on reads TransformGenotypesSuite: - save a file sorted by contig index - save a lexicographically sorted file - transform VCF without nested annotations - transform VCF with nested annotations Reads2CoverageSuite: - correctly calculates coverage from small sam file AboutSuite: - template variables have been replaced - templated values are not empty MergeShardsSuite: - merge shards from unordered sam to unordered sam - unordered sam to ordered sam - merge sharded bam - merge sharded cram TransformAlignmentsSuite: - unordered sam to unordered sam - unordered sam to ordered sam - unordered sam, to adam, to sam - unordered sam, to adam, to ordered sam - put quality scores into bins - run region predicate ADAMMainSuite: - 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 Adam2FastqSuite: 2019-06-28 14:17:52 WARN RDDBoundAlignmentRecordDataset:190 - Found 16 read names that don't occur exactly twice: 1x: 16 Samples: SRR062634.16445865 SRR062634.9119161 SRR062634.17190076 SRR062634.17969132 SRR062634.7301099 SRR062634.2087100 SRR062634.20911784 SRR062634.16769670 SRR062634.18958430 SRR062634.12099057 SRR062634.12606172 SRR062634.14985224 SRR062634.10448889 SRR062634.4789722 SRR062634.3203184 SRR062634.17698657 - convert SAM to paired FASTQ Run completed in 26 seconds, 277 milliseconds. Total number of tests run: 44 Suites: completed 12, aborted 0 Tests: succeeded 44, failed 0, canceled 0, ignored 0, pending 0 All tests passed. [INFO] [INFO] <<< scoverage-maven-plugin:1.1.1:report (default-cli) < [scoverage]test @ adam-cli-spark2_2.12 <<< [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:report (default-cli) @ adam-cli-spark2_2.12 --- [INFO] Skipping SCoverage report generation [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building ADAM_2.12: Assembly 0.28.0-SNAPSHOT [INFO] ------------------------------------------------------------------------ Downloading: https://repo.maven.apache.org/maven2/commons-pool/commons-pool/1.6/commons-pool-1.6.jar Downloading: https://repo.maven.apache.org/maven2/org/scala-lang/scala-reflect/2.12.6/scala-reflect-2.12.6.jar 3/3523 KB 5/3523 KB 8/3523 KB 11/3523 KB 13/3523 KB 16/3523 KB 19/3523 KB 21/3523 KB 24/3523 KB 27/3523 KB 29/3523 KB 32/3523 KB 36/3523 KB 40/3523 KB 44/3523 KB 48/3523 KB 52/3523 KB 56/3523 KB 60/3523 KB 64/3523 KB 68/3523 KB 72/3523 KB 76/3523 KB 80/3523 KB 84/3523 KB 88/3523 KB 92/3523 KB 96/3523 KB 100/3523 KB 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(enforce-versions) @ adam-assembly-spark2_2.12 --- [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-assembly-spark2_2.12 --- [INFO] [INFO] --- git-commit-id-plugin:2.2.2:revision (default) @ adam-assembly-spark2_2.12 --- [INFO] [INFO] --- templating-maven-plugin:1.0.0:filter-sources (filter-src) @ adam-assembly-spark2_2.12 --- [INFO] Request to add '/home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-assembly/src/main/java-templates' folder. Not added since it does not exist. [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ adam-assembly-spark2_2.12 --- [INFO] Source directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-assembly/src/main/scala added. [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ adam-assembly-spark2_2.12 --- [INFO] Modified 0 of 1 .scala files [INFO] [INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ adam-assembly-spark2_2.12 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-assembly/src/main/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ adam-assembly-spark2_2.12 --- [INFO] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-assembly/src/main/scala:-1: info: compiling [INFO] Compiling 1 source files to /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-assembly/target/2.12.8/classes at 1561756675330 [INFO] prepare-compile in 0 s [INFO] compile in 2 s [INFO] [INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ adam-assembly-spark2_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) @ adam-assembly-spark2_2.12 --- [INFO] Test Source directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-assembly/src/test/scala added. [INFO] [INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ adam-assembly-spark2_2.12 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-assembly/src/test/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ adam-assembly-spark2_2.12 --- [INFO] No sources to compile [INFO] [INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ adam-assembly-spark2_2.12 --- [INFO] No sources to compile [INFO] [INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ adam-assembly-spark2_2.12 --- [INFO] Tests are skipped. [INFO] [INFO] >>> scoverage-maven-plugin:1.1.1:report (default-cli) > [scoverage]test @ adam-assembly-spark2_2.12 >>> [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-assembly-spark2_2.12 --- [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-assembly-spark2_2.12 --- [INFO] [INFO] --- git-commit-id-plugin:2.2.2:revision (default) @ adam-assembly-spark2_2.12 --- [INFO] [INFO] --- templating-maven-plugin:1.0.0:filter-sources (filter-src) @ adam-assembly-spark2_2.12 --- [INFO] Request to add '/home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-assembly/src/main/java-templates' folder. Not added since it does not exist. [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ adam-assembly-spark2_2.12 --- [INFO] Source directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-assembly/src/main/scala added. [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ adam-assembly-spark2_2.12 --- [INFO] Modified 0 of 1 .scala files [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:pre-compile (default-cli) @ adam-assembly-spark2_2.12 --- [WARNING] Skipping SCoverage execution - unsupported Scala version "2.12.8" [INFO] [INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ adam-assembly-spark2_2.12 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-assembly/src/main/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ adam-assembly-spark2_2.12 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ adam-assembly-spark2_2.12 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:post-compile (default-cli) @ adam-assembly-spark2_2.12 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ adam-assembly-spark2_2.12 --- [INFO] Test Source directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-assembly/src/test/scala added. [INFO] [INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ adam-assembly-spark2_2.12 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-assembly/src/test/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ adam-assembly-spark2_2.12 --- [INFO] No sources to compile [INFO] [INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ adam-assembly-spark2_2.12 --- [INFO] No sources to compile [INFO] [INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ adam-assembly-spark2_2.12 --- [INFO] Tests are skipped. [INFO] [INFO] <<< scoverage-maven-plugin:1.1.1:report (default-cli) < [scoverage]test @ adam-assembly-spark2_2.12 <<< [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:report (default-cli) @ adam-assembly-spark2_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] ------------------------------------------------------------------------ [INFO] Building ADAM_2.12 0.28.0-SNAPSHOT [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- coveralls-maven-plugin:4.3.0:report (default-cli) @ adam-parent-spark2_2.12 --- [INFO] Starting Coveralls job for jenkins (3030 / https://amplab.cs.berkeley.edu/jenkins/job/ADAM-prb/HADOOP_VERSION=2.7.5,SCALAVER=2.12,SPARK_VERSION=2.4.3,label=ubuntu/3030/) [INFO] Using repository token <secret> [INFO] Git commit dfd674d in issue-2172 [INFO] Writing Coveralls data to /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/target/coveralls.json... [INFO] Processing coverage report from /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/target/cobertura.xml [INFO] Successfully wrote Coveralls data in 54ms [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 6361ms for Job #3030.1 [INFO] https://coveralls.io/jobs/50221746 [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: [INFO] [INFO] ADAM_2.12 .......................................... SUCCESS [ 6.752 s] [INFO] ADAM_2.12: Shader workaround ....................... SUCCESS [ 6.583 s] [INFO] ADAM_2.12: Avro-to-Dataset codegen utils ........... SUCCESS [ 7.379 s] [INFO] ADAM_2.12: Core .................................... SUCCESS [14:51 min] [INFO] ADAM_2.12: APIs for Java, Python ................... SUCCESS [ 42.749 s] [INFO] ADAM_2.12: CLI ..................................... SUCCESS [01:18 min] [INFO] ADAM_2.12: Assembly ................................ SUCCESS [ 3.971 s] [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ [INFO] Total time: 17:29 min [INFO] Finished at: 2019-06-28T14:18:04-07:00 [INFO] Final Memory: 97M/1472M [INFO] ------------------------------------------------------------------------ # if those pass, build the distribution package mvn -U \ -P distribution \ package \ -DskipTests \ -Dhadoop.version=${HADOOP_VERSION} \ -DargLine=${ADAM_MVN_TMP_DIR} + mvn -U -P distribution package -DskipTests -Dhadoop.version=2.7.5 -DargLine=/tmp/adamTestMvnJlGqi5R 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] ADAM_2.12 [INFO] ADAM_2.12: Shader workaround [INFO] ADAM_2.12: Avro-to-Dataset codegen utils [INFO] ADAM_2.12: Core [INFO] ADAM_2.12: APIs for Java, Python [INFO] ADAM_2.12: CLI [INFO] ADAM_2.12: Assembly [INFO] ADAM_2.12: Distribution [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building ADAM_2.12 0.28.0-SNAPSHOT [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-parent-spark2_2.12 --- [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-parent-spark2_2.12 --- [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ adam-parent-spark2_2.12 --- [INFO] Modified 0 of 242 .scala files [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ adam-parent-spark2_2.12 --- [INFO] No sources to compile [INFO] [INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ adam-parent-spark2_2.12 --- [INFO] No sources to compile [INFO] [INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ adam-parent-spark2_2.12 --- [INFO] [INFO] --- maven-javadoc-plugin:3.1.0:jar (attach-javadoc) @ adam-parent-spark2_2.12 --- [INFO] [INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) > generate-sources @ adam-parent-spark2_2.12 >>> [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-parent-spark2_2.12 --- [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-parent-spark2_2.12 --- [INFO] [INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) < generate-sources @ adam-parent-spark2_2.12 <<< [INFO] [INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ adam-parent-spark2_2.12 --- [INFO] No source files found [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building ADAM_2.12: Shader workaround 0.28.0-SNAPSHOT [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-shade-spark2_2.12 --- [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-shade-spark2_2.12 --- [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ adam-shade-spark2_2.12 --- [INFO] Modified 0 of 0 .scala files [INFO] [INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ adam-shade-spark2_2.12 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-shade/src/main/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ adam-shade-spark2_2.12 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ adam-shade-spark2_2.12 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- plexus-component-metadata:1.5.5:generate-metadata (default) @ adam-shade-spark2_2.12 --- [INFO] Discovered 1 component descriptors(s) [INFO] [INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ adam-shade-spark2_2.12 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-shade/src/test/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ adam-shade-spark2_2.12 --- [INFO] No sources to compile [INFO] [INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ adam-shade-spark2_2.12 --- [INFO] No sources to compile [INFO] [INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ adam-shade-spark2_2.12 --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:3.1.2:jar (default-jar) @ adam-shade-spark2_2.12 --- Downloading: https://repo.maven.apache.org/maven2/org/apache/maven/maven-archiver/3.4.0/maven-archiver-3.4.0.pom 3/5 KB 5/5 KB Downloaded: https://repo.maven.apache.org/maven2/org/apache/maven/maven-archiver/3.4.0/maven-archiver-3.4.0.pom (5 KB at 22.7 KB/sec) Downloading: https://repo.maven.apache.org/maven2/org/codehaus/plexus/plexus-archiver/4.1.0/plexus-archiver-4.1.0.pom 3/5 KB 5/5 KB Downloaded: https://repo.maven.apache.org/maven2/org/codehaus/plexus/plexus-archiver/4.1.0/plexus-archiver-4.1.0.pom (5 KB at 429.3 KB/sec) Downloading: https://repo.maven.apache.org/maven2/org/codehaus/plexus/plexus-utils/3.1.1/plexus-utils-3.1.1.pom 3/5 KB 5/5 KB 5/5 KB Downloaded: https://repo.maven.apache.org/maven2/org/codehaus/plexus/plexus-utils/3.1.1/plexus-utils-3.1.1.pom (5 KB at 450.0 KB/sec) Downloading: https://repo.maven.apache.org/maven2/org/apache/maven/maven-archiver/3.4.0/maven-archiver-3.4.0.jar Downloading: https://repo.maven.apache.org/maven2/org/codehaus/plexus/plexus-archiver/4.1.0/plexus-archiver-4.1.0.jar 3/188 KB 5/188 KB 8/188 KB 11/188 KB 13/188 KB 16/188 KB 19/188 KB 21/188 KB 24/188 KB 27/188 KB 29/188 KB 32/188 KB 3/24 KB 32/188 KB 3/24 KB 36/188 KB 6/24 KB 36/188 KB 6/24 KB 40/188 KB 6/24 KB 44/188 KB 6/24 KB 48/188 KB 9/24 KB 48/188 KB 11/24 KB 48/188 KB 11/24 KB 52/188 KB 11/24 KB 56/188 KB 11/24 KB 60/188 KB 11/24 KB 64/188 KB 14/24 KB 64/188 KB 16/24 KB 64/188 KB 16/24 KB 68/188 KB 19/24 KB 68/188 KB 19/24 KB 72/188 KB 19/24 KB 76/188 KB 19/24 KB 80/188 KB 22/24 KB 80/188 KB 24/24 KB 80/188 KB 24/24 KB 84/188 KB 24/24 KB 88/188 KB 24/24 KB 92/188 KB 24/24 KB 96/188 KB 24/24 KB 100/188 KB 24/24 KB 104/188 KB 24/24 KB 108/188 KB 24/24 KB 112/188 KB 24/24 KB 116/188 KB 24/24 KB 120/188 KB 24/24 KB 124/188 KB 24/24 KB 128/188 KB 24/24 KB 132/188 KB 24/24 KB 136/188 KB 24/24 KB 140/188 KB 24/24 KB 144/188 KB Downloaded: https://repo.maven.apache.org/maven2/org/apache/maven/maven-archiver/3.4.0/maven-archiver-3.4.0.jar (24 KB at 849.5 KB/sec) 148/188 KB 152/188 KB 156/188 KB 160/188 KB 164/188 KB 168/188 KB 172/188 KB 176/188 KB 180/188 KB 184/188 KB 188/188 KB Downloaded: https://repo.maven.apache.org/maven2/org/codehaus/plexus/plexus-archiver/4.1.0/plexus-archiver-4.1.0.jar (188 KB at 5206.0 KB/sec) [INFO] Building jar: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-shade/target/adam-shade-spark2_2.12-0.28.0-SNAPSHOT.jar [INFO] [INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ adam-shade-spark2_2.12 --- [INFO] Building jar: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-shade/target/adam-shade-spark2_2.12-0.28.0-SNAPSHOT-sources.jar [INFO] [INFO] --- maven-javadoc-plugin:3.1.0:jar (attach-javadoc) @ adam-shade-spark2_2.12 --- [INFO] Loading source files for package org.bdgenomics.adam.shade... Constructing Javadoc information... Standard Doclet version 1.8.0_191 Building tree for all the packages and classes... Generating /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-shade/target/apidocs/org/bdgenomics/adam/shade/ParquetAvroWorkaroundShader.html... Generating /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-shade/target/apidocs/org/bdgenomics/adam/shade/package-frame.html... Generating /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-shade/target/apidocs/org/bdgenomics/adam/shade/package-summary.html... Generating /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-shade/target/apidocs/org/bdgenomics/adam/shade/package-tree.html... Generating /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-shade/target/apidocs/constant-values.html... Generating /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-shade/target/apidocs/org/bdgenomics/adam/shade/class-use/ParquetAvroWorkaroundShader.html... Generating /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-shade/target/apidocs/org/bdgenomics/adam/shade/package-use.html... Building index for all the packages and classes... Generating /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-shade/target/apidocs/overview-tree.html... Generating /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-shade/target/apidocs/index-all.html... Generating /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-shade/target/apidocs/deprecated-list.html... Building index for all classes... Generating /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-shade/target/apidocs/allclasses-frame.html... Generating /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-shade/target/apidocs/allclasses-noframe.html... Generating /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-shade/target/apidocs/index.html... Generating /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-shade/target/apidocs/help-doc.html... [INFO] Building jar: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-shade/target/adam-shade-spark2_2.12-0.28.0-SNAPSHOT-javadoc.jar [INFO] [INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) > generate-sources @ adam-shade-spark2_2.12 >>> [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-shade-spark2_2.12 --- [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-shade-spark2_2.12 --- [INFO] [INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) < generate-sources @ adam-shade-spark2_2.12 <<< [INFO] [INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ adam-shade-spark2_2.12 --- model contains 6 documentable templates [INFO] Building jar: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-shade/target/adam-shade-spark2_2.12-0.28.0-SNAPSHOT-javadoc.jar [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building ADAM_2.12: Avro-to-Dataset codegen utils 0.28.0-SNAPSHOT [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-codegen-spark2_2.12 --- [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-codegen-spark2_2.12 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ adam-codegen-spark2_2.12 --- [INFO] Source directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-codegen/src/main/scala added. [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ adam-codegen-spark2_2.12 --- [INFO] Modified 0 of 4 .scala files [INFO] [INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ adam-codegen-spark2_2.12 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-codegen/src/main/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ adam-codegen-spark2_2.12 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ adam-codegen-spark2_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) @ adam-codegen-spark2_2.12 --- [INFO] Test Source directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-codegen/src/test/scala added. [INFO] [INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ adam-codegen-spark2_2.12 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-codegen/src/test/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ adam-codegen-spark2_2.12 --- [INFO] No sources to compile [INFO] [INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ adam-codegen-spark2_2.12 --- [INFO] No sources to compile [INFO] [INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ adam-codegen-spark2_2.12 --- [INFO] Tests are skipped. [INFO] [INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ adam-codegen-spark2_2.12 --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:3.1.2:jar (default-jar) @ adam-codegen-spark2_2.12 --- [INFO] Building jar: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-codegen/target/adam-codegen-spark2_2.12-0.28.0-SNAPSHOT.jar [INFO] [INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ adam-codegen-spark2_2.12 --- [INFO] Building jar: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-codegen/target/adam-codegen-spark2_2.12-0.28.0-SNAPSHOT-sources.jar [INFO] [INFO] --- maven-javadoc-plugin:3.1.0:jar (attach-javadoc) @ adam-codegen-spark2_2.12 --- [INFO] [INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) > generate-sources @ adam-codegen-spark2_2.12 >>> [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-codegen-spark2_2.12 --- [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-codegen-spark2_2.12 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ adam-codegen-spark2_2.12 --- [INFO] Source directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-codegen/src/main/scala added. [INFO] [INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) < generate-sources @ adam-codegen-spark2_2.12 <<< [INFO] [INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ adam-codegen-spark2_2.12 --- model contains 11 documentable templates [INFO] Building jar: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-codegen/target/adam-codegen-spark2_2.12-0.28.0-SNAPSHOT-javadoc.jar [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building ADAM_2.12: Core 0.28.0-SNAPSHOT [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-core-spark2_2.12 --- [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-core-spark2_2.12 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ adam-core-spark2_2.12 --- [INFO] Source directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/main/scala added. [INFO] Source directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/target/generated-sources/src/main/scala added. [INFO] [INFO] --- exec-maven-plugin:1.5.0:java (generate-scala-products) @ adam-core-spark2_2.12 --- SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] [INFO] --- exec-maven-plugin:1.5.0:java (generate-scala-projection-fields) @ adam-core-spark2_2.12 --- SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ adam-core-spark2_2.12 --- [INFO] Modified 2 of 202 .scala files [INFO] [INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ adam-core-spark2_2.12 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/main/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ adam-core-spark2_2.12 --- [INFO] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/main/java:-1: info: compiling [INFO] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/main/scala:-1: info: compiling [INFO] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/target/generated-sources/src/main/scala:-1: info: compiling [INFO] Compiling 138 source files to /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/target/2.12.8/classes at 1561756713327 [WARNING] warning: there were 21 deprecation warnings [WARNING] warning: there were 31 deprecation warnings (since 0.21.0) [WARNING] warning: there was one deprecation warning (since 1.0.6) [WARNING] warning: there were 36 deprecation warnings (since 2.0.0) [WARNING] warning: there was one deprecation warning (since 2.11.0) [WARNING] warning: there were 173 deprecation warnings (since 2.12.0) [WARNING] warning: there was one deprecation warning (since 2.12.7) [WARNING] warning: there were 264 deprecation warnings in total; re-run with -deprecation for details [WARNING] warning: there were 5 feature warnings; re-run with -feature for details [WARNING] 9 warnings found [INFO] prepare-compile in 0 s [INFO] compile in 25 s [INFO] [INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ adam-core-spark2_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) @ adam-core-spark2_2.12 --- [INFO] Test Source directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala added. [INFO] [INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ adam-core-spark2_2.12 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 152 resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ adam-core-spark2_2.12 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ adam-core-spark2_2.12 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ adam-core-spark2_2.12 --- [INFO] Tests are skipped. [INFO] [INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ adam-core-spark2_2.12 --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:3.1.2:jar (default-jar) @ adam-core-spark2_2.12 --- [INFO] Building jar: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/target/adam-core-spark2_2.12-0.28.0-SNAPSHOT.jar [INFO] [INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ adam-core-spark2_2.12 --- [INFO] Building jar: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/target/adam-core-spark2_2.12-0.28.0-SNAPSHOT-sources.jar [INFO] [INFO] --- maven-javadoc-plugin:3.1.0:jar (attach-javadoc) @ adam-core-spark2_2.12 --- [INFO] The goal 'org.apache.maven.plugins:maven-javadoc-plugin:3.1.0:javadoc' has not been previously called for the module: 'org.bdgenomics.adam:adam-codegen-spark2_2.12:jar:0.28.0-SNAPSHOT'. Trying to invoke it... Java HotSpot(TM) 64-Bit Server VM warning: ignoring option MaxPermSize=1g; support was removed in 8.0 [WARNING] Creating fake javadoc directory to prevent repeated invocations: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-codegen/target/apidocs [ERROR] Error fetching link: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-codegen/target/apidocs. Ignored it. [INFO] Loading source files for package org.apache.parquet.avro... Loading source files for package org.bdgenomics.adam.io... Constructing Javadoc information... Standard Doclet version 1.8.0_191 Building tree for all the packages and classes... Generating /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/target/apidocs/org/apache/parquet/avro/AvroSchemaConverter.html... Generating /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/target/apidocs/org/bdgenomics/adam/io/FastqInputFormat.html... Generating /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/target/apidocs/org/bdgenomics/adam/io/FastqRecordReader.html... Generating /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/target/apidocs/org/bdgenomics/adam/io/InterleavedFastqInputFormat.html... Generating /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/target/apidocs/org/bdgenomics/adam/io/SingleFastqInputFormat.html... Generating /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/target/apidocs/overview-frame.html... Generating /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/target/apidocs/org/apache/parquet/avro/package-frame.html... Generating /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/target/apidocs/org/apache/parquet/avro/package-summary.html... Generating /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/target/apidocs/org/apache/parquet/avro/package-tree.html... Generating /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/target/apidocs/org/bdgenomics/adam/io/package-frame.html... Generating /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/target/apidocs/org/bdgenomics/adam/io/package-summary.html... Generating /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/target/apidocs/org/bdgenomics/adam/io/package-tree.html... Generating /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/target/apidocs/constant-values.html... Generating /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/target/apidocs/org/apache/parquet/avro/class-use/AvroSchemaConverter.html... Generating /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/target/apidocs/org/bdgenomics/adam/io/class-use/InterleavedFastqInputFormat.html... Generating /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/target/apidocs/org/bdgenomics/adam/io/class-use/SingleFastqInputFormat.html... Generating /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/target/apidocs/org/bdgenomics/adam/io/class-use/FastqInputFormat.html... Generating /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/target/apidocs/org/bdgenomics/adam/io/class-use/FastqRecordReader.html... Generating /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/target/apidocs/org/apache/parquet/avro/package-use.html... Generating /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/target/apidocs/org/bdgenomics/adam/io/package-use.html... Building index for all the packages and classes... Generating /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/target/apidocs/overview-tree.html... Generating /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/target/apidocs/index-all.html... Generating /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/target/apidocs/deprecated-list.html... Building index for all classes... Generating /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/target/apidocs/allclasses-frame.html... Generating /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/target/apidocs/allclasses-noframe.html... Generating /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/target/apidocs/index.html... Generating /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/target/apidocs/overview-summary.html... Generating /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/target/apidocs/help-doc.html... 6 warnings [WARNING] Javadoc Warnings [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/main/java/org/bdgenomics/adam/io/FastqRecordReader.java:235: warning: no @param for codec [WARNING] protected final int positionAtFirstRecord(final FSDataInputStream stream, [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/main/java/org/bdgenomics/adam/io/FastqRecordReader.java:235: warning: no @return [WARNING] protected final int positionAtFirstRecord(final FSDataInputStream stream, [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/main/java/org/bdgenomics/adam/io/FastqRecordReader.java:235: warning: no @throws for java.io.IOException [WARNING] protected final int positionAtFirstRecord(final FSDataInputStream stream, [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/main/java/org/bdgenomics/adam/io/FastqRecordReader.java:389: warning: no @throws for java.io.IOException [WARNING] protected final boolean lowLevelFastqRead(final Text readName, final Text value) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/main/java/org/bdgenomics/adam/io/FastqRecordReader.java:431: warning: no @throws for java.io.IOException [WARNING] abstract protected boolean next(Text value) throws IOException; [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/main/java/org/bdgenomics/adam/io/FastqRecordReader.java:154: warning: no @throws for java.io.IOException [WARNING] protected FastqRecordReader(final Configuration conf, [WARNING] ^ [INFO] Building jar: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/target/adam-core-spark2_2.12-0.28.0-SNAPSHOT-javadoc.jar [INFO] [INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) > generate-sources @ adam-core-spark2_2.12 >>> [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-core-spark2_2.12 --- [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-core-spark2_2.12 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ adam-core-spark2_2.12 --- [INFO] Source directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/main/scala added. [INFO] Source directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/target/generated-sources/src/main/scala added. [INFO] [INFO] --- exec-maven-plugin:1.5.0:java (generate-scala-products) @ adam-core-spark2_2.12 --- SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] [INFO] --- exec-maven-plugin:1.5.0:java (generate-scala-projection-fields) @ adam-core-spark2_2.12 --- SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] [INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) < generate-sources @ adam-core-spark2_2.12 <<< [INFO] [INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ adam-core-spark2_2.12 --- /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/main/scala/org/bdgenomics/adam/converters/FastaConverters.scala:274: warning: discarding unmoored doc comment /** ^ /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/main/scala/org/bdgenomics/adam/rdd/read/AlignmentRecordDataset.scala:837: warning: Octal escape literals are deprecated, use \u0001 instead. binaryCodec.writeBytes("BAM\001".getBytes()) ^ /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/main/scala/org/bdgenomics/adam/rich/RichCigar.scala:43: warning: discarding unmoored doc comment /** ^ warning: there were 5 feature warnings; re-run with -feature for details model contains 289 documentable templates /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/main/scala/org/bdgenomics/adam/models/ReadGroupDictionary.scala:47: warning: Could not find any member to link for "IllegalArgumentException". /** ^ /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/main/scala/org/bdgenomics/adam/util/AttributeUtils.scala:70: warning: Could not find any member to link for "IllegalArgumentException". /** ^ /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/main/scala/org/bdgenomics/adam/rdd/GenomicDataset.scala:755: warning: Variable x undefined in comment for method pipe in trait GenomicDataset * Files are substituted in to the command with a $x syntax. E.g., to invoke ^ /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/main/scala/org/bdgenomics/adam/rdd/GenomicDataset.scala:756: warning: Variable 0 undefined in comment for method pipe in trait GenomicDataset * a command that uses the first file from the files Seq, use $0. To access ^ /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/main/scala/org/bdgenomics/adam/rdd/GenomicDataset.scala:757: warning: Variable root undefined in comment for method pipe in trait GenomicDataset * the path to the directory where the files are copied, use $root. ^ /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/main/scala/org/bdgenomics/adam/rdd/GenomicPartitioners.scala:178: warning: Could not find any member to link for "IllegalArgumentException". /** ^ /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/main/scala/org/bdgenomics/adam/rdd/GenomicPartitioners.scala:75: warning: Could not find any member to link for "IllegalArgumentException". /** ^ /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/main/scala/org/bdgenomics/adam/rdd/ADAMContext.scala:3472: warning: Could not find any member to link for "IllegalArgumentException". /** ^ /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/main/scala/org/bdgenomics/adam/rdd/ADAMContext.scala:1864: warning: Could not find any member to link for "FileNotFoundException". /** ^ /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/main/scala/org/bdgenomics/adam/rdd/ADAMContext.scala:1844: warning: Could not find any member to link for "FileNotFoundException". /** ^ /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/main/scala/org/bdgenomics/adam/rdd/ADAMContext.scala:1815: warning: Could not find any member to link for "FileNotFoundException". /** ^ /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/main/scala/org/bdgenomics/adam/projections/Projection.scala:45: warning: Could not find any member to link for "IllegalArgumentException". /** ^ /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/main/scala/org/bdgenomics/adam/models/ReferenceRegion.scala:474: warning: Could not find any member to link for "IllegalArgumentException". /** ^ /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/main/scala/org/bdgenomics/adam/models/ReferenceRegion.scala:444: warning: Could not find any member to link for "IllegalArgumentException". /** ^ /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/main/scala/org/bdgenomics/adam/models/ReferenceRegion.scala:429: warning: Could not find any member to link for "IllegalArgumentException". /** ^ /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/main/scala/org/bdgenomics/adam/models/ReferenceRegion.scala:354: warning: Could not find any member to link for "IllegalArgumentException". /** ^ /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/main/scala/org/bdgenomics/adam/models/ReferenceRegion.scala:258: warning: Could not find any member to link for "IllegalArgumentException". /** ^ /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/main/scala/org/bdgenomics/adam/models/ReferenceRegion.scala:242: warning: Could not find any member to link for "IllegalArgumentException". /** ^ /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/main/scala/org/bdgenomics/adam/models/Alphabet.scala:44: warning: Could not find any member to link for "IllegalArgumentException". /** ^ /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/main/java/org/bdgenomics/adam/io/FastqRecordReader.java:377: warning: Could not find any member to link for "RuntimeException". /** ^ 24 warnings found [INFO] Building jar: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/target/adam-core-spark2_2.12-0.28.0-SNAPSHOT-javadoc.jar [INFO] [INFO] --- maven-jar-plugin:3.1.2:test-jar (default) @ adam-core-spark2_2.12 --- [INFO] Building jar: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/target/adam-core-spark2_2.12-0.28.0-SNAPSHOT-tests.jar [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building ADAM_2.12: APIs for Java, Python 0.28.0-SNAPSHOT [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-apis-spark2_2.12 --- [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-apis-spark2_2.12 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ adam-apis-spark2_2.12 --- [INFO] Source directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-apis/src/main/scala added. [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ adam-apis-spark2_2.12 --- [INFO] Modified 0 of 5 .scala files [INFO] [INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ adam-apis-spark2_2.12 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-apis/src/main/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ adam-apis-spark2_2.12 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ adam-apis-spark2_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) @ adam-apis-spark2_2.12 --- [INFO] Test Source directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-apis/src/test/scala added. [INFO] [INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ adam-apis-spark2_2.12 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 2 resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ adam-apis-spark2_2.12 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ adam-apis-spark2_2.12 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ adam-apis-spark2_2.12 --- [INFO] Tests are skipped. [INFO] [INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ adam-apis-spark2_2.12 --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:3.1.2:jar (default-jar) @ adam-apis-spark2_2.12 --- [INFO] Building jar: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-apis/target/adam-apis-spark2_2.12-0.28.0-SNAPSHOT.jar [INFO] [INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ adam-apis-spark2_2.12 --- [INFO] Building jar: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-apis/target/adam-apis-spark2_2.12-0.28.0-SNAPSHOT-sources.jar [INFO] [INFO] --- maven-javadoc-plugin:3.1.0:jar (attach-javadoc) @ adam-apis-spark2_2.12 --- [INFO] [INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) > generate-sources @ adam-apis-spark2_2.12 >>> [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-apis-spark2_2.12 --- [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-apis-spark2_2.12 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ adam-apis-spark2_2.12 --- [INFO] Source directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-apis/src/main/scala added. [INFO] [INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) < generate-sources @ adam-apis-spark2_2.12 <<< [INFO] [INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ adam-apis-spark2_2.12 --- warning: there were two feature warnings; re-run with -feature for details model contains 192 documentable templates one warning found [INFO] Building jar: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-apis/target/adam-apis-spark2_2.12-0.28.0-SNAPSHOT-javadoc.jar [INFO] [INFO] --- maven-jar-plugin:3.1.2:test-jar (default) @ adam-apis-spark2_2.12 --- [INFO] Building jar: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-apis/target/adam-apis-spark2_2.12-0.28.0-SNAPSHOT-tests.jar [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building ADAM_2.12: CLI 0.28.0-SNAPSHOT [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-cli-spark2_2.12 --- [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-cli-spark2_2.12 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:timestamp-property (timestamp-property) @ adam-cli-spark2_2.12 --- [INFO] [INFO] --- git-commit-id-plugin:2.2.2:revision (default) @ adam-cli-spark2_2.12 --- [INFO] [INFO] --- templating-maven-plugin:1.0.0:filter-sources (filter-src) @ adam-cli-spark2_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/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-cli/target/generated-sources/java-templates [INFO] Source directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-cli/target/generated-sources/java-templates added. [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ adam-cli-spark2_2.12 --- [INFO] Source directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-cli/src/main/scala added. [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ adam-cli-spark2_2.12 --- [INFO] Modified 0 of 29 .scala files [INFO] [INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ adam-cli-spark2_2.12 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-cli/src/main/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ adam-cli-spark2_2.12 --- [INFO] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-cli/target/generated-sources/java-templates:-1: info: compiling [INFO] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-cli/src/main/scala:-1: info: compiling [INFO] Compiling 18 source files to /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-cli/target/2.12.8/classes at 1561756788126 [WARNING] warning: there was one deprecation warning [WARNING] warning: there was one deprecation warning (since 2.12.0) [WARNING] warning: there were two deprecation warnings in total; re-run with -deprecation for details [WARNING] three warnings found [INFO] prepare-compile in 0 s [INFO] compile in 7 s [INFO] [INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ adam-cli-spark2_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) @ adam-cli-spark2_2.12 --- [INFO] Test Source directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-cli/src/test/scala added. [INFO] [INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ adam-cli-spark2_2.12 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 15 resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ adam-cli-spark2_2.12 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ adam-cli-spark2_2.12 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ adam-cli-spark2_2.12 --- [INFO] Tests are skipped. [INFO] [INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ adam-cli-spark2_2.12 --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:3.1.2:jar (default-jar) @ adam-cli-spark2_2.12 --- [INFO] Building jar: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-cli/target/adam-cli-spark2_2.12-0.28.0-SNAPSHOT.jar [INFO] [INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ adam-cli-spark2_2.12 --- [INFO] Building jar: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-cli/target/adam-cli-spark2_2.12-0.28.0-SNAPSHOT-sources.jar [INFO] [INFO] --- maven-javadoc-plugin:3.1.0:jar (attach-javadoc) @ adam-cli-spark2_2.12 --- [INFO] The goal 'org.apache.maven.plugins:maven-javadoc-plugin:3.1.0:javadoc' has not been previously called for the module: 'org.bdgenomics.adam:adam-apis-spark2_2.12:jar:0.28.0-SNAPSHOT'. Trying to invoke it... Java HotSpot(TM) 64-Bit Server VM warning: ignoring option MaxPermSize=1g; support was removed in 8.0 [WARNING] Creating fake javadoc directory to prevent repeated invocations: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-apis/target/apidocs [ERROR] Error fetching link: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-apis/target/apidocs. Ignored it. [INFO] Loading source files for package org.bdgenomics.adam.cli... Constructing Javadoc information... Standard Doclet version 1.8.0_191 Building tree for all the packages and classes... Generating /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-cli/target/apidocs/org/bdgenomics/adam/cli/About.html... Generating /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-cli/target/apidocs/org/bdgenomics/adam/cli/package-frame.html... Generating /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-cli/target/apidocs/org/bdgenomics/adam/cli/package-summary.html... Generating /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-cli/target/apidocs/org/bdgenomics/adam/cli/package-tree.html... Generating /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-cli/target/apidocs/constant-values.html... Generating /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-cli/target/apidocs/org/bdgenomics/adam/cli/class-use/About.html... Generating /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-cli/target/apidocs/org/bdgenomics/adam/cli/package-use.html... Building index for all the packages and classes... Generating /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-cli/target/apidocs/overview-tree.html... Generating /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-cli/target/apidocs/index-all.html... Generating /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-cli/target/apidocs/deprecated-list.html... Building index for all classes... Generating /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-cli/target/apidocs/allclasses-frame.html... Generating /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-cli/target/apidocs/allclasses-noframe.html... Generating /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-cli/target/apidocs/index.html... Generating /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-cli/target/apidocs/help-doc.html... [INFO] Building jar: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-cli/target/adam-cli-spark2_2.12-0.28.0-SNAPSHOT-javadoc.jar [INFO] [INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) > generate-sources @ adam-cli-spark2_2.12 >>> [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-cli-spark2_2.12 --- [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-cli-spark2_2.12 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:timestamp-property (timestamp-property) @ adam-cli-spark2_2.12 --- [INFO] [INFO] --- git-commit-id-plugin:2.2.2:revision (default) @ adam-cli-spark2_2.12 --- [INFO] [INFO] --- templating-maven-plugin:1.0.0:filter-sources (filter-src) @ adam-cli-spark2_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/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-cli/target/generated-sources/java-templates [INFO] Source directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-cli/target/generated-sources/java-templates added. [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ adam-cli-spark2_2.12 --- [INFO] Source directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-cli/src/main/scala added. [INFO] [INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) < generate-sources @ adam-cli-spark2_2.12 <<< [INFO] [INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ adam-cli-spark2_2.12 --- model contains 55 documentable templates [INFO] Building jar: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-cli/target/adam-cli-spark2_2.12-0.28.0-SNAPSHOT-javadoc.jar [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building ADAM_2.12: Assembly 0.28.0-SNAPSHOT [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-assembly-spark2_2.12 --- [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-assembly-spark2_2.12 --- [INFO] [INFO] --- git-commit-id-plugin:2.2.2:revision (default) @ adam-assembly-spark2_2.12 --- [INFO] [INFO] --- templating-maven-plugin:1.0.0:filter-sources (filter-src) @ adam-assembly-spark2_2.12 --- [INFO] Request to add '/home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-assembly/src/main/java-templates' folder. Not added since it does not exist. [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ adam-assembly-spark2_2.12 --- [INFO] Source directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-assembly/src/main/scala added. [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ adam-assembly-spark2_2.12 --- [INFO] Modified 0 of 1 .scala files [INFO] [INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ adam-assembly-spark2_2.12 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-assembly/src/main/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ adam-assembly-spark2_2.12 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ adam-assembly-spark2_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) @ adam-assembly-spark2_2.12 --- [INFO] Test Source directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-assembly/src/test/scala added. [INFO] [INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ adam-assembly-spark2_2.12 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-assembly/src/test/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ adam-assembly-spark2_2.12 --- [INFO] No sources to compile [INFO] [INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ adam-assembly-spark2_2.12 --- [INFO] No sources to compile [INFO] [INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ adam-assembly-spark2_2.12 --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:3.1.2:jar (default-jar) @ adam-assembly-spark2_2.12 --- [INFO] Building jar: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-assembly/target/adam-assembly-spark2_2.12-0.28.0-SNAPSHOT.jar [INFO] [INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ adam-assembly-spark2_2.12 --- [INFO] Building jar: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-assembly/target/adam-assembly-spark2_2.12-0.28.0-SNAPSHOT-sources.jar [INFO] [INFO] --- maven-javadoc-plugin:3.1.0:jar (attach-javadoc) @ adam-assembly-spark2_2.12 --- [INFO] [INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) > generate-sources @ adam-assembly-spark2_2.12 >>> [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-assembly-spark2_2.12 --- [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-assembly-spark2_2.12 --- [INFO] [INFO] --- git-commit-id-plugin:2.2.2:revision (default) @ adam-assembly-spark2_2.12 --- [INFO] [INFO] --- templating-maven-plugin:1.0.0:filter-sources (filter-src) @ adam-assembly-spark2_2.12 --- [INFO] Request to add '/home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-assembly/src/main/java-templates' folder. Not added since it does not exist. [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ adam-assembly-spark2_2.12 --- [INFO] Source directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-assembly/src/main/scala added. [INFO] [INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) < generate-sources @ adam-assembly-spark2_2.12 <<< [INFO] [INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ adam-assembly-spark2_2.12 --- model contains 6 documentable templates [INFO] Building jar: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-assembly/target/adam-assembly-spark2_2.12-0.28.0-SNAPSHOT-javadoc.jar [INFO] [INFO] --- maven-shade-plugin:3.2.0:shade (default) @ adam-assembly-spark2_2.12 --- [INFO] Including org.bdgenomics.adam:adam-cli-spark2_2.12:jar:0.28.0-SNAPSHOT in the shaded jar. [INFO] Including org.bdgenomics.utils:utils-misc-spark2_2.12:jar:0.2.15 in the shaded jar. [INFO] Including org.bdgenomics.utils:utils-io-spark2_2.12:jar:0.2.15 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-spark2_2.12:jar:0.2.15 in the shaded jar. [INFO] Including org.clapper:grizzled-slf4j_2.12:jar:1.3.3 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.utils:utils-metrics-spark2_2.12:jar:0.2.15 in the shaded jar. [INFO] Including com.netflix.servo:servo-core:jar:0.12.25 in the shaded jar. [INFO] Including com.netflix.spectator:spectator-api:jar:0.67.0 in the shaded jar. [INFO] Including org.slf4j:slf4j-api:jar:1.7.25 in the shaded jar. [INFO] Including org.bdgenomics.bdg-formats:bdg-formats:jar:0.12.0 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:2.8 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-spark2_2.12:jar:0.28.0-SNAPSHOT in the shaded jar. [INFO] Including org.bdgenomics.utils:utils-intervalrdd-spark2_2.12:jar:0.2.15 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:2.18.2 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-jre in the shaded jar. [INFO] Including com.google.guava:failureaccess:jar:1.0 in the shaded jar. [INFO] Including com.google.guava:listenablefuture:jar:9999.0-empty-to-avoid-conflict-with-guava in the shaded jar. [INFO] Including org.checkerframework:checker-qual:jar:2.5.2 in the shaded jar. [INFO] Including com.google.errorprone:error_prone_annotations:jar:2.2.0 in the shaded jar. [INFO] Including com.google.j2objc:j2objc-annotations:jar:1.1 in the shaded jar. [INFO] Including org.codehaus.mojo:animal-sniffer-annotations:jar:1.17 in the shaded jar. [INFO] Including org.bdgenomics.adam:adam-codegen-spark2_2.12:jar:0.28.0-SNAPSHOT in the shaded jar. [INFO] Including org.bdgenomics.adam:adam-apis-spark2_2.12:jar:0.28.0-SNAPSHOT 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. [WARNING] WORKAROUND: refusing to add class org/apache/parquet/avro/AvroSchemaConverter$2.class from jar /home/jenkins/.m2/repository/org/apache/parquet/parquet-avro/1.10.1/parquet-avro-1.10.1.jar [WARNING] WORKAROUND: refusing to add class org/apache/parquet/avro/AvroSchemaConverter.class from jar /home/jenkins/.m2/repository/org/apache/parquet/parquet-avro/1.10.1/parquet-avro-1.10.1.jar [WARNING] WORKAROUND: refusing to add class org/apache/parquet/avro/AvroSchemaConverter$1.class from jar /home/jenkins/.m2/repository/org/apache/parquet/parquet-avro/1.10.1/parquet-avro-1.10.1.jar [WARNING] guava-27.0-jre.jar, failureaccess-1.0.jar define 2 overlapping classes: [WARNING] - com.google.common.util.concurrent.internal.InternalFutureFailureAccess [WARNING] - com.google.common.util.concurrent.internal.InternalFutures [WARNING] maven-shade-plugin has detected that some class files are [WARNING] present in two or more JARs. When this happens, only one [WARNING] single version of the class is copied to the uber jar. [WARNING] Usually this is not harmful and you can skip these warnings, [WARNING] otherwise try to manually exclude artifacts based on [WARNING] mvn dependency:tree -Ddetail=true and the above output. [WARNING] See http://maven.apache.org/plugins/maven-shade-plugin/ [INFO] Replacing original artifact with shaded artifact. [INFO] Replacing /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-assembly/target/adam-assembly-spark2_2.12-0.28.0-SNAPSHOT.jar with /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-assembly/target/adam-assembly-spark2_2.12-0.28.0-SNAPSHOT-shaded.jar [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building ADAM_2.12: Distribution 0.28.0-SNAPSHOT [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-distribution-spark2_2.12 --- [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-distribution-spark2_2.12 --- [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ adam-distribution-spark2_2.12 --- [INFO] Modified 0 of 0 .scala files [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ adam-distribution-spark2_2.12 --- [INFO] No sources to compile [INFO] [INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ adam-distribution-spark2_2.12 --- [INFO] No sources to compile [INFO] [INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ adam-distribution-spark2_2.12 --- [INFO] [INFO] --- maven-javadoc-plugin:3.1.0:jar (attach-javadoc) @ adam-distribution-spark2_2.12 --- [INFO] [INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) > generate-sources @ adam-distribution-spark2_2.12 >>> [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-distribution-spark2_2.12 --- [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-distribution-spark2_2.12 --- [INFO] [INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) < generate-sources @ adam-distribution-spark2_2.12 <<< [INFO] [INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ adam-distribution-spark2_2.12 --- [INFO] No source files found [INFO] [INFO] --- maven-assembly-plugin:3.1.0:single (default) @ adam-distribution-spark2_2.12 --- Downloading: https://repo.maven.apache.org/maven2/org/apache/maven/shared/maven-artifact-transfer/0.9.0/maven-artifact-transfer-0.9.0.pom 3/8 KB 5/8 KB 8/8 KB Downloaded: https://repo.maven.apache.org/maven2/org/apache/maven/shared/maven-artifact-transfer/0.9.0/maven-artifact-transfer-0.9.0.pom (8 KB at 618.8 KB/sec) Downloading: https://repo.maven.apache.org/maven2/org/apache/maven/shared/maven-artifact-transfer/0.9.0/maven-artifact-transfer-0.9.0.jar 3/121 KB 5/121 KB 8/121 KB 11/121 KB 13/121 KB 16/121 KB 19/121 KB 21/121 KB 24/121 KB 27/121 KB 29/121 KB 32/121 KB 36/121 KB 40/121 KB 44/121 KB 48/121 KB 52/121 KB 56/121 KB 60/121 KB 64/121 KB 68/121 KB 72/121 KB 76/121 KB 80/121 KB 84/121 KB 88/121 KB 92/121 KB 96/121 KB 100/121 KB 104/121 KB 108/121 KB 112/121 KB 116/121 KB 120/121 KB 121/121 KB Downloaded: https://repo.maven.apache.org/maven2/org/apache/maven/shared/maven-artifact-transfer/0.9.0/maven-artifact-transfer-0.9.0.jar (121 KB at 6006.3 KB/sec) [INFO] Reading assembly descriptor: src/main/assembly/assembly.xml [INFO] Building tar: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-distribution/target/adam-distribution-spark2_2.12-0.28.0-SNAPSHOT-bin.tar.gz [WARNING] Entry: adam-distribution-spark2_2.12-0.28.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/algorithms/smithwaterman/ longer than 100 characters. 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