Started by upstream project "ADAM-prb" build number 2986 originally caused by: GitHub pull request #2149 of commit 0babacdce2e155e2853a8bd1da7b9f1264f9b305 automatically merged. [EnvInject] - Loading node environment variables. Building remotely on research-jenkins-worker-08 (ubuntu research-08) in workspace /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/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/2.11/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 3718c8d21eb71b332d4cb15a65a62054d27f210f (origin/pr/2149/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f 3718c8d21eb71b332d4cb15a65a62054d27f210f > git rev-list 0d6565b036217e99af3454b3fcb49a90c1ff6ee0 # timeout=10 First time build. Skipping changelog. [ubuntu] $ /bin/bash /tmp/hudson7732777577888538762.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/2.11/SPARK_VERSION/2.4.3/label/ubuntu/scripts/jenkins-test # make a tempdir for writing maven cruft to ADAM_MVN_TMP_DIR=$(mktemp -d -t adamTestMvnXXXXXXX) mktemp -d -t adamTestMvnXXXXXXX ++ mktemp -d -t adamTestMvnXXXXXXX + ADAM_MVN_TMP_DIR=/tmp/adamTestMvnQbVzgrO # add this tempdir to the poms... find . -name pom.xml \ -exec sed -i.bak \ -e "s:sun.io.serialization.extendedDebugInfo=true:sun.io.serialization.extendedDebugInfo=true -Djava.io.tmpdir=${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/adamTestMvnQbVzgrO: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 ${BASH_SOURCE[0]} +++ dirname /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/scripts/jenkins-test ++ cd /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/scripts ++ pwd + DIR=/home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/scripts PROJECT_ROOT=${DIR}/.. + PROJECT_ROOT=/home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/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/2.11/SPARK_VERSION/2.4.3/label/ubuntu/scripts/../pom.xml ++ head -2 ++ tail -1 ++ sed 's/ *<version>//g' ++ sed 's/<\/version>//g' + VERSION=0.27.0-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 + '[' 2.11 == 2.11 ']' + set +e + ./scripts/move_to_scala_2.11.sh Scala version is already set to 2.11 (Scala artifacts have _2.11 version suffix in artifact name). Cowardly refusing to move to Scala 2.11 a second time... + [[ 1 == 0 ]] + set -e # move to Scala 2.12 if requested if [ ${SCALAVER} == 2.12 ]; then set +e ./scripts/move_to_scala_2.12.sh set -e fi + '[' 2.11 == 2.12 ']' # print versions echo "Testing ADAM version ${VERSION} on Spark ${SPARK_VERSION} and Hadoop ${HADOOP_VERSION}" + echo 'Testing ADAM version 0.27.0-SNAPSHOT on Spark 2.4.3 and Hadoop 2.7.5' Testing ADAM version 0.27.0-SNAPSHOT on Spark 2.4.3 and Hadoop 2.7.5 # first, build the sources, run the unit tests, and generate a coverage report mvn clean \ -Dhadoop.version=${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_2.11 [INFO] ADAM_2.11: Shader workaround [INFO] ADAM_2.11: Avro-to-Dataset codegen utils [INFO] ADAM_2.11: Core [INFO] ADAM_2.11: APIs for Java, Python [INFO] ADAM_2.11: CLI [INFO] ADAM_2.11: Assembly [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building ADAM_2.11 0.27.0-SNAPSHOT [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-clean-plugin:3.1.0:clean (default-clean) @ adam-parent-spark2_2.11 --- [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building ADAM_2.11: Shader workaround 0.27.0-SNAPSHOT [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-clean-plugin:3.1.0:clean (default-clean) @ adam-shade-spark2_2.11 --- [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building ADAM_2.11: Avro-to-Dataset codegen utils 0.27.0-SNAPSHOT [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-clean-plugin:3.1.0:clean (default-clean) @ adam-codegen-spark2_2.11 --- [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building ADAM_2.11: Core 0.27.0-SNAPSHOT [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-clean-plugin:3.1.0:clean (default-clean) @ adam-core-spark2_2.11 --- [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building ADAM_2.11: APIs for Java, Python 0.27.0-SNAPSHOT [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-clean-plugin:3.1.0:clean (default-clean) @ adam-apis-spark2_2.11 --- [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building ADAM_2.11: CLI 0.27.0-SNAPSHOT [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-clean-plugin:3.1.0:clean (default-clean) @ adam-cli-spark2_2.11 --- [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building ADAM_2.11: Assembly 0.27.0-SNAPSHOT [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-clean-plugin:3.1.0:clean (default-clean) @ adam-assembly-spark2_2.11 --- [INFO] ------------------------------------------------------------------------ [INFO] Reactor Summary: [INFO] [INFO] ADAM_2.11 .......................................... SUCCESS [ 0.192 s] [INFO] ADAM_2.11: Shader workaround ....................... SUCCESS [ 0.009 s] [INFO] ADAM_2.11: Avro-to-Dataset codegen utils ........... SUCCESS [ 0.008 s] [INFO] ADAM_2.11: Core .................................... SUCCESS [ 0.011 s] [INFO] ADAM_2.11: APIs for Java, Python ................... SUCCESS [ 0.002 s] [INFO] ADAM_2.11: CLI ..................................... SUCCESS [ 0.024 s] [INFO] ADAM_2.11: Assembly ................................ SUCCESS [ 0.002 s] [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ [INFO] Total time: 0.464 s [INFO] Finished at: 2019-05-14T11:37:07-07:00 [INFO] Final Memory: 23M/1472M [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 2149 ]] + COVERALLS_PRB_OPTION=-DpullRequest=2149 # 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_2.11 [INFO] ADAM_2.11: Shader workaround [INFO] ADAM_2.11: Avro-to-Dataset codegen utils [INFO] ADAM_2.11: Core [INFO] ADAM_2.11: APIs for Java, Python [INFO] ADAM_2.11: CLI [INFO] ADAM_2.11: Assembly [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building ADAM_2.11 0.27.0-SNAPSHOT [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-parent-spark2_2.11 --- [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-parent-spark2_2.11 --- [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ adam-parent-spark2_2.11 --- [INFO] Modified 0 of 239 .scala files [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ adam-parent-spark2_2.11 --- [INFO] No sources to compile [INFO] [INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ adam-parent-spark2_2.11 --- [INFO] No sources to compile [INFO] [INFO] >>> scoverage-maven-plugin:1.1.1:report (default-cli) > [scoverage]test @ adam-parent-spark2_2.11 >>> [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-parent-spark2_2.11 --- [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-parent-spark2_2.11 --- [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ adam-parent-spark2_2.11 --- [INFO] Modified 0 of 239 .scala files [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:pre-compile (default-cli) @ adam-parent-spark2_2.11 --- [INFO] Skipping SCoverage execution for project with packaging type 'pom' [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ adam-parent-spark2_2.11 --- [INFO] No sources to compile [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:post-compile (default-cli) @ adam-parent-spark2_2.11 --- [INFO] [INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ adam-parent-spark2_2.11 --- [INFO] No sources to compile [INFO] [INFO] <<< scoverage-maven-plugin:1.1.1:report (default-cli) < [scoverage]test @ adam-parent-spark2_2.11 <<< [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:report (default-cli) @ adam-parent-spark2_2.11 --- [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building ADAM_2.11: Shader workaround 0.27.0-SNAPSHOT [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-shade-spark2_2.11 --- [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-shade-spark2_2.11 --- [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ adam-shade-spark2_2.11 --- [INFO] Modified 0 of 0 .scala files [INFO] [INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ adam-shade-spark2_2.11 --- [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/2.11/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_2.11 --- [INFO] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/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/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-shade/target/2.11.12/classes at 1557859041056 [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_2.11 --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 1 source file to /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-shade/target/2.11.12/classes [INFO] [INFO] --- plexus-component-metadata:1.5.5:generate-metadata (default) @ adam-shade-spark2_2.11 --- [INFO] Discovered 1 component descriptors(s) [INFO] [INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ adam-shade-spark2_2.11 --- [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/2.11/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_2.11 --- [INFO] No sources to compile [INFO] [INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ adam-shade-spark2_2.11 --- [INFO] No sources to compile [INFO] [INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ adam-shade-spark2_2.11 --- [INFO] No tests to run. [INFO] [INFO] >>> scoverage-maven-plugin:1.1.1:report (default-cli) > [scoverage]test @ adam-shade-spark2_2.11 >>> [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-shade-spark2_2.11 --- [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-shade-spark2_2.11 --- [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ adam-shade-spark2_2.11 --- [INFO] Modified 0 of 0 .scala files [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:pre-compile (default-cli) @ adam-shade-spark2_2.11 --- [INFO] [INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ adam-shade-spark2_2.11 --- [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/2.11/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_2.11 --- [INFO] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/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/2.11/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/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-shade/target/2.11.12/scoverage-classes at 1557859043200 [INFO] [info] Cleaning datadir [/home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-shade/target/scoverage-data] [INFO] [info] Beginning coverage instrumentation [INFO] [info] Instrumentation completed [0 statements] [INFO] [info] Wrote instrumentation file [/home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-shade/target/scoverage-data/scoverage.coverage.xml] [INFO] [info] Will write measurement data to [/home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-shade/target/scoverage-data] [INFO] prepare-compile in 0 s [INFO] compile in 1 s [INFO] [INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ adam-shade-spark2_2.11 --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 1 source file to /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-shade/target/2.11.12/scoverage-classes [INFO] [INFO] --- plexus-component-metadata:1.5.5:generate-metadata (default) @ adam-shade-spark2_2.11 --- [INFO] Discovered 1 component descriptors(s) [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:post-compile (default-cli) @ adam-shade-spark2_2.11 --- [INFO] [INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ adam-shade-spark2_2.11 --- [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/2.11/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_2.11 --- [INFO] No sources to compile [INFO] [INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ adam-shade-spark2_2.11 --- [INFO] No sources to compile [INFO] [INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ adam-shade-spark2_2.11 --- [INFO] No tests to run. [INFO] [INFO] <<< scoverage-maven-plugin:1.1.1:report (default-cli) < [scoverage]test @ adam-shade-spark2_2.11 <<< [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:report (default-cli) @ adam-shade-spark2_2.11 --- [INFO] [scoverage] Generating cobertura XML report... [INFO] [scoverage] Generating scoverage XML report... [INFO] [scoverage] Generating scoverage HTML report... [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building ADAM_2.11: Avro-to-Dataset codegen utils 0.27.0-SNAPSHOT [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-codegen-spark2_2.11 --- [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-codegen-spark2_2.11 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ adam-codegen-spark2_2.11 --- [INFO] Source directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/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_2.11 --- [INFO] Modified 0 of 4 .scala files [INFO] [INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ adam-codegen-spark2_2.11 --- [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/2.11/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_2.11 --- [INFO] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/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/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-codegen/target/2.11.12/classes at 1557859045002 [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_2.11 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ adam-codegen-spark2_2.11 --- [INFO] Test Source directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/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_2.11 --- [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/2.11/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_2.11 --- [INFO] No sources to compile [INFO] [INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ adam-codegen-spark2_2.11 --- [INFO] No sources to compile [INFO] [INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ adam-codegen-spark2_2.11 --- [INFO] Tests are skipped. [INFO] [INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ adam-codegen-spark2_2.11 --- Discovery starting. Discovery completed in 56 milliseconds. Run starting. Expected test count is: 0 DiscoverySuite: Run completed in 81 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_2.11 >>> [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-codegen-spark2_2.11 --- [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-codegen-spark2_2.11 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ adam-codegen-spark2_2.11 --- [INFO] Source directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/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_2.11 --- [INFO] Modified 0 of 4 .scala files [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:pre-compile (default-cli) @ adam-codegen-spark2_2.11 --- [INFO] [INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ adam-codegen-spark2_2.11 --- [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/2.11/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_2.11 --- [INFO] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/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/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-codegen/target/2.11.12/scoverage-classes at 1557859049674 [INFO] [info] Cleaning datadir [/home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-codegen/target/scoverage-data] [INFO] [info] Beginning coverage instrumentation [INFO] [info] Instrumentation completed [0 statements] [INFO] [info] Wrote instrumentation file [/home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-codegen/target/scoverage-data/scoverage.coverage.xml] [INFO] [info] Will write measurement data to [/home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-codegen/target/scoverage-data] [INFO] prepare-compile in 0 s [INFO] compile in 3 s [INFO] [INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ adam-codegen-spark2_2.11 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:post-compile (default-cli) @ adam-codegen-spark2_2.11 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ adam-codegen-spark2_2.11 --- [INFO] Test Source directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/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_2.11 --- [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/2.11/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_2.11 --- [INFO] No sources to compile [INFO] [INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ adam-codegen-spark2_2.11 --- [INFO] No sources to compile [INFO] [INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ adam-codegen-spark2_2.11 --- [INFO] Tests are skipped. [INFO] [INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ adam-codegen-spark2_2.11 --- Discovery starting. Discovery completed in 56 milliseconds. Run starting. Expected test count is: 0 DiscoverySuite: Run completed in 82 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_2.11 <<< [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:report (default-cli) @ adam-codegen-spark2_2.11 --- [INFO] [scoverage] Generating cobertura XML report... [INFO] [scoverage] Generating scoverage XML report... [INFO] [scoverage] Generating scoverage HTML report... [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building ADAM_2.11: Core 0.27.0-SNAPSHOT [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-core-spark2_2.11 --- [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-core-spark2_2.11 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ adam-core-spark2_2.11 --- [INFO] Source directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/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/2.11/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_2.11 --- 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_2.11 --- 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_2.11 --- [INFO] Modified 2 of 199 .scala files [INFO] [INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ adam-core-spark2_2.11 --- [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/2.11/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_2.11 --- [INFO] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/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/2.11/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/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/target/generated-sources/src/main/scala:-1: info: compiling [INFO] Compiling 136 source files to /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/target/2.11.12/classes at 1557859060990 [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/main/scala/org/bdgenomics/adam/rdd/GenomicDataset.scala:3099: warning: no valid targets for annotation on value uTag - it is discarded unused. You may specify targets with meta-annotations, e.g. @(transient @getter) [WARNING] @transient val uTag: TypeTag[U] [WARNING] ^ [WARNING] warning: there were 84 deprecation warnings; re-run with -deprecation for details [WARNING] warning: there were 5 feature warnings; re-run with -feature for details [WARNING] three warnings found [INFO] prepare-compile in 0 s [INFO] compile in 29 s [INFO] [INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ adam-core-spark2_2.11 --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 6 source files to /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/target/2.11.12/classes [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ adam-core-spark2_2.11 --- [INFO] Test Source directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/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_2.11 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 150 resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ adam-core-spark2_2.11 --- [INFO] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala:-1: info: compiling [INFO] Compiling 69 source files to /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/target/2.11.12/test-classes at 1557859092696 [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/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: Use explicit conversion wherever possible in new development. [WARNING] .build() [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/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: 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/2.11/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: 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/2.11/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/2.11/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/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:53: warning: method extractDictionary in object 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/2.11/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/2.11/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/2.11/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/2.11/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/2.11/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/2.11/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/2.11/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/2.11/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: 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/2.11/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: 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/2.11/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: 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/2.11/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: 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/2.11/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: 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/2.11/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: Use explicit conversion wherever possible in new development. [WARNING] val newTag = MdTag.moveAlignment(read, newCigar) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/models/MdTagSuite.scala:526: warning: method recordToRichRecord in object RichAlignmentRecord is deprecated: Use explicit conversion wherever possible in new development. [WARNING] val newTag = MdTag.moveAlignment(read, newCigar, "AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA", 100L) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/models/MdTagSuite.scala:544: warning: method recordToRichRecord in object RichAlignmentRecord is deprecated: Use explicit conversion wherever possible in new development. [WARNING] val newTag = MdTag.moveAlignment(read, newCigar, "GGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA", 100L) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/models/MdTagSuite.scala:562: warning: method recordToRichRecord in object RichAlignmentRecord is deprecated: Use explicit conversion wherever possible in new development. [WARNING] val newTag = MdTag.moveAlignment(read, newCigar, "AAAAAAAAAAGGGGGGGGGGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA", 100L) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/models/MdTagSuite.scala:580: warning: method recordToRichRecord in object RichAlignmentRecord is deprecated: Use explicit conversion wherever possible in new development. [WARNING] val newTag = MdTag.moveAlignment(read, newCigar, "AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA", 100L) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/models/SequenceDictionarySuite.scala:48: warning: method extractDictionary in object SAMSequenceDictionaryExtractor is deprecated: see corresponding Javadoc for more information. [WARNING] val ssd = SAMSequenceDictionaryExtractor.extractDictionary(new File(path)) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/models/SequenceDictionarySuite.scala:62: warning: method extractDictionary in object SAMSequenceDictionaryExtractor is deprecated: see corresponding Javadoc for more information. [WARNING] val ssd = SAMSequenceDictionaryExtractor.extractDictionary(new File(path)) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/models/SequenceDictionarySuite.scala:75: warning: method extractDictionary in object SAMSequenceDictionaryExtractor is deprecated: see corresponding Javadoc for more information. [WARNING] val ssd = SAMSequenceDictionaryExtractor.extractDictionary(new File(path)) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/rdd/contig/NucleotideContigFragmentDatasetSuite.scala:742: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead [WARNING] val sqlContext = SQLContext.getOrCreate(sc) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/rdd/contig/NucleotideContigFragmentDatasetSuite.scala:770: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead [WARNING] val sqlContext = SQLContext.getOrCreate(sc) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/rdd/contig/NucleotideContigFragmentDatasetSuite.scala:801: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead [WARNING] val sqlContext = SQLContext.getOrCreate(sc) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/rdd/contig/NucleotideContigFragmentDatasetSuite.scala:832: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead [WARNING] val sqlContext = SQLContext.getOrCreate(sc) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/rdd/contig/NucleotideContigFragmentDatasetSuite.scala:863: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead [WARNING] val sqlContext = SQLContext.getOrCreate(sc) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/rdd/contig/NucleotideContigFragmentDatasetSuite.scala:894: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead [WARNING] val sqlContext = SQLContext.getOrCreate(sc) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/rdd/feature/CoverageDatasetSuite.scala:309: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead [WARNING] val sqlContext = SQLContext.getOrCreate(sc) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/rdd/feature/CoverageDatasetSuite.scala:340: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead [WARNING] val sqlContext = SQLContext.getOrCreate(sc) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/rdd/feature/CoverageDatasetSuite.scala:371: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead [WARNING] val sqlContext = SQLContext.getOrCreate(sc) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/rdd/feature/CoverageDatasetSuite.scala:402: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead [WARNING] val sqlContext = SQLContext.getOrCreate(sc) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/rdd/feature/CoverageDatasetSuite.scala:433: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead [WARNING] val sqlContext = SQLContext.getOrCreate(sc) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/rdd/feature/CoverageDatasetSuite.scala:464: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead [WARNING] val sqlContext = SQLContext.getOrCreate(sc) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/rdd/feature/FeatureDatasetSuite.scala:1022: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead [WARNING] val sqlContext = SQLContext.getOrCreate(sc) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/rdd/feature/FeatureDatasetSuite.scala:1053: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead [WARNING] val sqlContext = SQLContext.getOrCreate(sc) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/rdd/feature/FeatureDatasetSuite.scala:1081: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead [WARNING] val sqlContext = SQLContext.getOrCreate(sc) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/rdd/feature/FeatureDatasetSuite.scala:1112: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead [WARNING] val sqlContext = SQLContext.getOrCreate(sc) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/rdd/feature/FeatureDatasetSuite.scala:1143: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead [WARNING] val sqlContext = SQLContext.getOrCreate(sc) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/rdd/feature/FeatureDatasetSuite.scala:1174: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead [WARNING] val sqlContext = SQLContext.getOrCreate(sc) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/rdd/fragment/FragmentDatasetSuite.scala:400: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead [WARNING] val sqlContext = SQLContext.getOrCreate(sc) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/rdd/fragment/FragmentDatasetSuite.scala:431: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead [WARNING] val sqlContext = SQLContext.getOrCreate(sc) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/rdd/fragment/FragmentDatasetSuite.scala:459: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead [WARNING] val sqlContext = SQLContext.getOrCreate(sc) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/rdd/fragment/FragmentDatasetSuite.scala:490: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead [WARNING] val sqlContext = SQLContext.getOrCreate(sc) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/rdd/fragment/FragmentDatasetSuite.scala:521: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead [WARNING] val sqlContext = SQLContext.getOrCreate(sc) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/rdd/fragment/FragmentDatasetSuite.scala:552: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead [WARNING] val sqlContext = SQLContext.getOrCreate(sc) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/rdd/read/AlignmentRecordDatasetSuite.scala:1438: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead [WARNING] val sqlContext = SQLContext.getOrCreate(sc) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/rdd/read/AlignmentRecordDatasetSuite.scala:1460: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead [WARNING] val sqlContext = SQLContext.getOrCreate(sc) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/rdd/read/AlignmentRecordDatasetSuite.scala:1491: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead [WARNING] val sqlContext = SQLContext.getOrCreate(sc) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/rdd/read/AlignmentRecordDatasetSuite.scala:1519: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead [WARNING] val sqlContext = SQLContext.getOrCreate(sc) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/rdd/read/AlignmentRecordDatasetSuite.scala:1550: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead [WARNING] val sqlContext = SQLContext.getOrCreate(sc) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/rdd/read/AlignmentRecordDatasetSuite.scala:1581: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead [WARNING] val sqlContext = SQLContext.getOrCreate(sc) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/rdd/read/AlignmentRecordDatasetSuite.scala:1613: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead [WARNING] val sqlContext = SQLContext.getOrCreate(sc) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/rdd/read/realignment/IndelRealignmentTargetSuite.scala:83: warning: method richRecordToRecord in object RichAlignmentRecord is deprecated: Use explicit conversion wherever possible in new development. [WARNING] assert(TargetOrdering.contains(targets.head, read)) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/rdd/read/realignment/IndelRealignmentTargetSuite.scala:191: warning: method richRecordToRecord in object RichAlignmentRecord is deprecated: Use explicit conversion wherever possible in new development. [WARNING] if (read.getStart < 105) { [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/rdd/read/realignment/IndelRealignmentTargetSuite.scala:194: warning: method richRecordToRecord in object RichAlignmentRecord is deprecated: Use explicit conversion wherever possible in new development. [WARNING] assert(targets.head.readRange.start === read.getStart) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/rdd/read/realignment/IndelRealignmentTargetSuite.scala:195: warning: method richRecordToRecord in object RichAlignmentRecord is deprecated: Use explicit conversion wherever possible in new development. [WARNING] assert(targets.head.readRange.end === read.getEnd) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/rdd/read/realignment/IndelRealignmentTargetSuite.scala:196: warning: method richRecordToRecord in object RichAlignmentRecord is deprecated: Use explicit conversion wherever possible in new development. [WARNING] assert(check_indel(targets.head, read)) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/rdd/variant/GenotypeDatasetSuite.scala:406: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead [WARNING] val sqlContext = SQLContext.getOrCreate(sc) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/rdd/variant/GenotypeDatasetSuite.scala:437: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead [WARNING] val sqlContext = SQLContext.getOrCreate(sc) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/rdd/variant/GenotypeDatasetSuite.scala:465: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead [WARNING] val sqlContext = SQLContext.getOrCreate(sc) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/rdd/variant/GenotypeDatasetSuite.scala:496: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead [WARNING] val sqlContext = SQLContext.getOrCreate(sc) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/rdd/variant/GenotypeDatasetSuite.scala:527: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead [WARNING] val sqlContext = SQLContext.getOrCreate(sc) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/rdd/variant/GenotypeDatasetSuite.scala:558: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead [WARNING] val sqlContext = SQLContext.getOrCreate(sc) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/rdd/variant/GenotypeDatasetSuite.scala:697: warning: variable end in class Genotype is deprecated: see corresponding Javadoc for more information. [WARNING] assert(first.end === 16157602L) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/rdd/variant/GenotypeDatasetSuite.scala:698: warning: variable end in class Variant is deprecated: see corresponding Javadoc for more information. [WARNING] assert(first.variant.end === 16157602L) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/rdd/variant/GenotypeDatasetSuite.scala:698: warning: variable variant in class Genotype is deprecated: see corresponding Javadoc for more information. [WARNING] assert(first.variant.end === 16157602L) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/rdd/variant/GenotypeDatasetSuite.scala:699: warning: variable annotation in class Variant is deprecated: see corresponding Javadoc for more information. [WARNING] assert(first.variant.annotation === null) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/rdd/variant/GenotypeDatasetSuite.scala:699: warning: variable variant in class Genotype is deprecated: see corresponding Javadoc for more information. [WARNING] assert(first.variant.annotation === null) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/rdd/variant/GenotypeDatasetSuite.scala:710: warning: variable end in class Genotype is deprecated: see corresponding Javadoc for more information. [WARNING] assert(firstVcfGenotype.end === 16157602L) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/rdd/variant/GenotypeDatasetSuite.scala:712: warning: variable end in class Variant is deprecated: see corresponding Javadoc for more information. [WARNING] assert(firstVcfGenotype.variant.end === 16157602L) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/rdd/variant/GenotypeDatasetSuite.scala:712: warning: variable variant in class Genotype is deprecated: see corresponding Javadoc for more information. [WARNING] assert(firstVcfGenotype.variant.end === 16157602L) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/rdd/variant/GenotypeDatasetSuite.scala:714: warning: variable annotation in class Variant is deprecated: see corresponding Javadoc for more information. [WARNING] assert(firstVcfGenotype.variant.annotation === null) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/rdd/variant/GenotypeDatasetSuite.scala:714: warning: variable variant in class Genotype is deprecated: see corresponding Javadoc for more information. [WARNING] assert(firstVcfGenotype.variant.annotation === null) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/rdd/variant/GenotypeDatasetSuite.scala:745: warning: variable end in class Genotype is deprecated: see corresponding Javadoc for more information. [WARNING] assert(first.end === 16157602L) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/rdd/variant/GenotypeDatasetSuite.scala:746: warning: variable end in class Variant is deprecated: see corresponding Javadoc for more information. [WARNING] assert(first.variant.end === 16157602L) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/rdd/variant/GenotypeDatasetSuite.scala:746: warning: variable variant in class Genotype is deprecated: see corresponding Javadoc for more information. [WARNING] assert(first.variant.end === 16157602L) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/rdd/variant/GenotypeDatasetSuite.scala:747: warning: variable attributes in class VariantAnnotation is deprecated: see corresponding Javadoc for more information. [WARNING] assert(first.variant.annotation.attributes.get("END") === "16157602") [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/rdd/variant/GenotypeDatasetSuite.scala:747: warning: variable annotation in class Variant is deprecated: see corresponding Javadoc for more information. [WARNING] assert(first.variant.annotation.attributes.get("END") === "16157602") [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/rdd/variant/GenotypeDatasetSuite.scala:747: warning: variable variant in class Genotype is deprecated: see corresponding Javadoc for more information. [WARNING] assert(first.variant.annotation.attributes.get("END") === "16157602") [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/rdd/variant/GenotypeDatasetSuite.scala:758: warning: variable end in class Genotype is deprecated: see corresponding Javadoc for more information. [WARNING] assert(firstVcfGenotype.end === 16157602L) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/rdd/variant/GenotypeDatasetSuite.scala:759: warning: variable end in class Variant is deprecated: see corresponding Javadoc for more information. [WARNING] assert(firstVcfGenotype.variant.end === 16157602L) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/rdd/variant/GenotypeDatasetSuite.scala:759: warning: variable variant in class Genotype is deprecated: see corresponding Javadoc for more information. [WARNING] assert(firstVcfGenotype.variant.end === 16157602L) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/rdd/variant/GenotypeDatasetSuite.scala:760: warning: variable attributes in class VariantAnnotation is deprecated: see corresponding Javadoc for more information. [WARNING] assert(firstVcfGenotype.variant.annotation.attributes.get("END") === "16157602") [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/rdd/variant/GenotypeDatasetSuite.scala:760: warning: variable annotation in class Variant is deprecated: see corresponding Javadoc for more information. [WARNING] assert(firstVcfGenotype.variant.annotation.attributes.get("END") === "16157602") [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/rdd/variant/GenotypeDatasetSuite.scala:760: warning: variable variant in class Genotype is deprecated: see corresponding Javadoc for more information. [WARNING] assert(firstVcfGenotype.variant.annotation.attributes.get("END") === "16157602") [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/rdd/variant/VariantContextDatasetSuite.scala:181: warning: variable start in class Genotype is deprecated: see corresponding Javadoc for more information. [WARNING] val filtered = vcs.toGenotypes().rdd.filter(_.start == 66631043) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/rdd/variant/VariantDatasetSuite.scala:422: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead [WARNING] val sqlContext = SQLContext.getOrCreate(sc) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/rdd/variant/VariantDatasetSuite.scala:453: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead [WARNING] val sqlContext = SQLContext.getOrCreate(sc) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/rdd/variant/VariantDatasetSuite.scala:481: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead [WARNING] val sqlContext = SQLContext.getOrCreate(sc) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/rdd/variant/VariantDatasetSuite.scala:512: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead [WARNING] val sqlContext = SQLContext.getOrCreate(sc) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/rdd/variant/VariantDatasetSuite.scala:543: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead [WARNING] val sqlContext = SQLContext.getOrCreate(sc) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/rdd/variant/VariantDatasetSuite.scala:574: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead [WARNING] val sqlContext = SQLContext.getOrCreate(sc) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/rich/RichAlignmentRecordSuite.scala:31: warning: method recordToRichRecord in object RichAlignmentRecord is deprecated: Use explicit conversion wherever possible in new development. [WARNING] assert(recordWithoutClipping.unclippedStart == 42L) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/rich/RichAlignmentRecordSuite.scala:32: warning: method recordToRichRecord in object RichAlignmentRecord is deprecated: Use explicit conversion wherever possible in new development. [WARNING] assert(recordWithClipping.unclippedStart == 40L) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/rich/RichAlignmentRecordSuite.scala:33: warning: method recordToRichRecord in object RichAlignmentRecord is deprecated: Use explicit conversion wherever possible in new development. [WARNING] assert(recordWithHardClipping.unclippedStart == 37L) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/rich/RichAlignmentRecordSuite.scala:41: warning: method recordToRichRecord in object RichAlignmentRecord is deprecated: Use explicit conversion wherever possible in new development. [WARNING] assert(recordWithoutClipping.unclippedEnd == 20L) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/rich/RichAlignmentRecordSuite.scala:42: warning: method recordToRichRecord in object RichAlignmentRecord is deprecated: Use explicit conversion wherever possible in new development. [WARNING] assert(recordWithClipping.unclippedEnd == 20L) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/rich/RichAlignmentRecordSuite.scala:43: warning: method recordToRichRecord in object RichAlignmentRecord is deprecated: Use explicit conversion wherever possible in new development. [WARNING] assert(recordWithHardClipping.unclippedEnd == 20L) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/rich/RichAlignmentRecordSuite.scala:49: warning: method recordToRichRecord in object RichAlignmentRecord is deprecated: Use explicit conversion wherever possible in new development. [WARNING] assert(rec.tags.size === 2) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/rich/RichAlignmentRecordSuite.scala:50: warning: method recordToRichRecord in object RichAlignmentRecord is deprecated: Use explicit conversion wherever possible in new development. [WARNING] assert(rec.tags(0) === Attribute("XX", TagType.Integer, 3)) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/rich/RichAlignmentRecordSuite.scala:51: warning: method recordToRichRecord in object RichAlignmentRecord is deprecated: Use explicit conversion wherever possible in new development. [WARNING] assert(rec.tags(1) === Attribute("YY", TagType.String, "foo")) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/rich/RichAlignmentRecordSuite.scala:57: warning: method recordToRichRecord in object RichAlignmentRecord is deprecated: Use explicit conversion wherever possible in new development. [WARNING] val overlaps = unmappedRead.overlapsReferencePosition(ReferencePosition("chr1", 10)) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/rich/RichCigarSuite.scala:34: warning: method recordToRichRecord in object RichAlignmentRecord is deprecated: Use explicit conversion wherever possible in new development. [WARNING] val newCigar = RichCigar(new Cigar(read.samtoolsCigar.getCigarElements)).moveLeft(1) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/rich/RichCigarSuite.scala:37: warning: method recordToRichRecord in object RichAlignmentRecord is deprecated: Use explicit conversion wherever possible in new development. [WARNING] assert(newCigar2.cigar.getReadLength == read.samtoolsCigar.getReadLength) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/rich/RichCigarSuite.scala:49: warning: method recordToRichRecord in object RichAlignmentRecord is deprecated: Use explicit conversion wherever possible in new development. [WARNING] val newCigar = RichCigar(new Cigar(read.samtoolsCigar.getCigarElements)).moveLeft(1) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/rich/RichCigarSuite.scala:52: warning: method recordToRichRecord in object RichAlignmentRecord is deprecated: Use explicit conversion wherever possible in new development. [WARNING] assert(newCigar2.cigar.getReadLength == read.samtoolsCigar.getReadLength) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/rich/RichCigarSuite.scala:64: warning: method recordToRichRecord in object RichAlignmentRecord is deprecated: Use explicit conversion wherever possible in new development. [WARNING] val newCigar = RichCigar(new Cigar(read.samtoolsCigar.getCigarElements)).moveLeft(1) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/rich/RichCigarSuite.scala:66: warning: method recordToRichRecord in object RichAlignmentRecord is deprecated: Use explicit conversion wherever possible in new development. [WARNING] assert(newCigar.cigar.getReadLength == read.samtoolsCigar.getReadLength) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/rich/RichCigarSuite.scala:78: warning: method recordToRichRecord in object RichAlignmentRecord is deprecated: Use explicit conversion wherever possible in new development. [WARNING] val newCigar = RichCigar(new Cigar(read.samtoolsCigar.getCigarElements)).moveLeft(1) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/rich/RichCigarSuite.scala:80: warning: method recordToRichRecord in object RichAlignmentRecord is deprecated: Use explicit conversion wherever possible in new development. [WARNING] assert(newCigar.cigar.getReadLength == read.samtoolsCigar.getReadLength) [WARNING] ^ [WARNING] 115 warnings found [INFO] prepare-compile in 0 s [INFO] compile in 35 s [INFO] [INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ adam-core-spark2_2.11 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ adam-core-spark2_2.11 --- [INFO] Tests are skipped. [INFO] [INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ adam-core-spark2_2.11 --- Discovery starting. Discovery completed in 2 seconds, 33 milliseconds. Run starting. Expected test count is: 1146 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 2019-05-14 11:38:51 WARN Utils:66 - Your hostname, research-jenkins-worker-08 resolves to a loopback address: 127.0.1.1; using 192.168.10.28 instead (on interface eth0) 2019-05-14 11:38:51 WARN Utils:66 - Set SPARK_LOCAL_IP if you need to bind to another address 2019-05-14 11:38:51 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 FlankReferenceFragmentsSuite: - don't put flanks on non-adjacent fragments - put flanks on adjacent fragments 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 2019-05-14 11:39:01 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 2019-05-14 11:39:25 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 2019-05-14 11:39:26 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 2019-05-14 11:39:27 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 2019-05-14 11:39:39 WARN OutFormatterRunner:190 - Piped command List(sleep, 10) timed out after 5 seconds. 2019-05-14 11:39:39 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 2019-05-14 11:39:59 WARN OutFormatterRunner:190 - Piped command List(python, /tmp/adamTestMvnQbVzgrO/spark-169c822d-000c-46ca-85b6-3d7454bc21a7/userFiles-35444c59-3b36-4ea1-87e3-123d753f4ad6/timeout.py) timed out after 5 seconds. 2019-05-14 11:39:59 WARN OutFormatterRunner:190 - Piped command List(python, /tmp/adamTestMvnQbVzgrO/spark-169c822d-000c-46ca-85b6-3d7454bc21a7/userFiles-35444c59-3b36-4ea1-87e3-123d753f4ad6/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 contig 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/adamTestMvnQbVzgrO/TempSuite6381356567852089834.adam as parquet into RDD... loading /tmp/adamTestMvnQbVzgrO/TempSuite1150882431221983223.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 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 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 - transform coverage to contig rdd - transform coverage to feature rdd - transform coverage to fragment rdd - transform coverage to read rdd - transform coverage to genotype rdd - transform coverage to variant rdd - transform coverage to variant context rdd - 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 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 - transform genotypes to contig 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 contig 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 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 contig 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 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 2019-05-14 11:42:20 WARN TranscriptEffectConverter$:190 - Could not convert VCF INFO reserved key ANN value to TranscriptEffect, caught java.lang.NumberFormatException: For input string: "not a number". - convert to transcript effect from VCF ANN attribute with invalid number in variant context lenient validation stringency 2019-05-14 11:42:20 WARN TranscriptEffectConverter$: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 2019-05-14 11:42:20 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 NucleotideContigFragmentDatasetSuite: - union two ncf genomic datasets together - round trip a ncf to parquet - round trip a ncf to partitioned parquet - save fasta back as a single file - generate sequence dict from fasta - recover reference string from a single contig fragment - recover trimmed reference string from a single contig fragment - recover reference string from multiple contig fragments - extract sequences based on the list of reference regions - recover trimmed reference string from multiple contig fragments - testing nondeterminism from reduce when recovering referencestring - save single contig fragment as FASTA text file - save single contig fragment with description as FASTA text file - save single contig fragment with null fields as FASTA text file - save single contig fragment with null fragment number as FASTA text file - save single contig fragment with null number of fragments in contig as FASTA text file - save multiple contig fragments from same contig as FASTA text file - save multiple contig fragments with description from same contig as FASTA text file - merge single contig fragment null fragment number - merge single contig fragment number zero - merge multiple contig fragments - save as parquet and apply predicate pushdown - load fasta sequences from GFF3 file - transform contigs to coverage genomic dataset - transform contigs to feature genomic dataset - transform contigs to fragment genomic dataset - transform contigs to read genomic dataset - transform contigs to genotype genomic dataset - transform contigs to variant genomic dataset - transform contigs to variant context genomic dataset 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 - transform features to contig rdd - transform features to coverage rdd - transform features to fragment rdd - transform features to read rdd - transform features to genotype rdd - transform features to variant rdd - transform features to variant context rdd - 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 2019-05-14 11:43:30 WARN VariantContextConverter:2300 - Applying annotation extraction function <function2> 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: - Convert ADAM SNV w/ genotypes but bad SB to htsjdk with lenient validation {"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 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 2019-05-14 11:43:30 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 2019-05-14 11:43:34 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... 2019-05-14 11:43:34 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 2019-05-14 11:43:34 WARN VCFInputFormat:218 - file:/home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/target/2.11.12/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 - 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 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 2019-05-14 11:43:54 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. 2019-05-14 11:43:54 WARN BlockManager:66 - Block rdd_5_3 could not be removed as it was not found on disk or in memory 2019-05-14 11:43:54 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$$anonfun$extract$1.apply(ReferenceContigMap.scala:63) at org.bdgenomics.adam.util.ReferenceContigMap$$anonfun$extract$1.apply(ReferenceContigMap.scala:63) at scala.collection.MapLike$class.getOrElse(MapLike.scala:128) at scala.collection.AbstractMap.getOrElse(Map.scala:59) at org.bdgenomics.adam.util.ReferenceContigMap.extract(ReferenceContigMap.scala:61) at org.bdgenomics.adam.rdd.read.MDTagging$$anonfun$addMDTagsBroadcast$1$$anonfun$apply$2.apply(MDTagging.scala:76) at org.bdgenomics.adam.rdd.read.MDTagging$$anonfun$addMDTagsBroadcast$1$$anonfun$apply$2.apply(MDTagging.scala:71) at scala.Option$WithFilter.map(Option.scala:207) at org.bdgenomics.adam.rdd.read.MDTagging$$anonfun$addMDTagsBroadcast$1.apply(MDTagging.scala:71) at org.bdgenomics.adam.rdd.read.MDTagging$$anonfun$addMDTagsBroadcast$1.apply(MDTagging.scala:69) at scala.collection.Iterator$$anon$11.next(Iterator.scala:410) at org.apache.spark.storage.memory.MemoryStore.putIterator(MemoryStore.scala:222) at org.apache.spark.storage.memory.MemoryStore.putIteratorAsValues(MemoryStore.scala:299) at org.apache.spark.storage.BlockManager$$anonfun$doPutIterator$1.apply(BlockManager.scala:1165) at org.apache.spark.storage.BlockManager$$anonfun$doPutIterator$1.apply(BlockManager.scala:1156) at org.apache.spark.storage.BlockManager.doPut(BlockManager.scala:1091) at org.apache.spark.storage.BlockManager.doPutIterator(BlockManager.scala:1156) at org.apache.spark.storage.BlockManager.getOrElseUpdate(BlockManager.scala:882) at org.apache.spark.rdd.RDD.getOrCompute(RDD.scala:335) at org.apache.spark.rdd.RDD.iterator(RDD.scala:286) at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:90) at org.apache.spark.scheduler.Task.run(Task.scala:121) at org.apache.spark.executor.Executor$TaskRunner$$anonfun$10.apply(Executor.scala:408) at org.apache.spark.util.Utils$.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) 2019-05-14 11:43:54 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$$anonfun$extract$1.apply(ReferenceContigMap.scala:63) at org.bdgenomics.adam.util.ReferenceContigMap$$anonfun$extract$1.apply(ReferenceContigMap.scala:63) at scala.collection.MapLike$class.getOrElse(MapLike.scala:128) at scala.collection.AbstractMap.getOrElse(Map.scala:59) at org.bdgenomics.adam.util.ReferenceContigMap.extract(ReferenceContigMap.scala:61) at org.bdgenomics.adam.rdd.read.MDTagging$$anonfun$addMDTagsBroadcast$1$$anonfun$apply$2.apply(MDTagging.scala:76) at org.bdgenomics.adam.rdd.read.MDTagging$$anonfun$addMDTagsBroadcast$1$$anonfun$apply$2.apply(MDTagging.scala:71) at scala.Option$WithFilter.map(Option.scala:207) at org.bdgenomics.adam.rdd.read.MDTagging$$anonfun$addMDTagsBroadcast$1.apply(MDTagging.scala:71) at org.bdgenomics.adam.rdd.read.MDTagging$$anonfun$addMDTagsBroadcast$1.apply(MDTagging.scala:69) at scala.collection.Iterator$$anon$11.next(Iterator.scala:410) at org.apache.spark.storage.memory.MemoryStore.putIterator(MemoryStore.scala:222) at org.apache.spark.storage.memory.MemoryStore.putIteratorAsValues(MemoryStore.scala:299) at org.apache.spark.storage.BlockManager$$anonfun$doPutIterator$1.apply(BlockManager.scala:1165) at org.apache.spark.storage.BlockManager$$anonfun$doPutIterator$1.apply(BlockManager.scala:1156) at org.apache.spark.storage.BlockManager.doPut(BlockManager.scala:1091) at org.apache.spark.storage.BlockManager.doPutIterator(BlockManager.scala:1156) at org.apache.spark.storage.BlockManager.getOrElseUpdate(BlockManager.scala:882) at org.apache.spark.rdd.RDD.getOrCompute(RDD.scala:335) at org.apache.spark.rdd.RDD.iterator(RDD.scala:286) at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:90) at org.apache.spark.scheduler.Task.run(Task.scala:121) at org.apache.spark.executor.Executor$TaskRunner$$anonfun$10.apply(Executor.scala:408) at org.apache.spark.util.Utils$.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) 2019-05-14 11:43:54 ERROR TaskSetManager:70 - Task 3 in stage 2.0 failed 1 times; aborting job - try realigning a read on a missing contig, stringency == STRICT 2019-05-14 11:43:54 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 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 FastaConverterSuite: - find contig index - convert a single record without naming information - convert a single record with naming information - convert single fasta sequence - convert fasta with multiple sequences - convert fasta with multiple sequences; short fragment - convert reference fasta file 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 - transform variants to contig 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, 11 seconds. Total number of tests run: 1146 Suites: completed 67, aborted 0 Tests: succeeded 1146, 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_2.11 >>> [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-core-spark2_2.11 --- [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-core-spark2_2.11 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ adam-core-spark2_2.11 --- [INFO] Source directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/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/2.11/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_2.11 --- 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_2.11 --- 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_2.11 --- [INFO] Modified 2 of 199 .scala files [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:pre-compile (default-cli) @ adam-core-spark2_2.11 --- [INFO] [INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ adam-core-spark2_2.11 --- [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/2.11/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_2.11 --- [INFO] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/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/2.11/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/2.11/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/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/target/generated-sources/annotations:-1: info: compiling [INFO] Compiling 136 source files to /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/target/2.11.12/scoverage-classes at 1557859506288 [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/main/scala/org/bdgenomics/adam/rdd/GenomicDataset.scala:3099: warning: no valid targets for annotation on value uTag - it is discarded unused. You may specify targets with meta-annotations, e.g. @(transient @getter) [WARNING] @transient val uTag: TypeTag[U] [WARNING] ^ [INFO] [info] Cleaning datadir [/home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/target/scoverage-data] [INFO] [info] Beginning coverage instrumentation [WARNING] [warn] Could not instrument [EmptyTree$/null]. No pos. [WARNING] [warn] Could not instrument [EmptyTree$/null]. No pos. [WARNING] [warn] Could not instrument [EmptyTree$/null]. No pos. [WARNING] [warn] Could not instrument [EmptyTree$/null]. No pos. [WARNING] [warn] Could not instrument [EmptyTree$/null]. No pos. [WARNING] [warn] Could not instrument [EmptyTree$/null]. No pos. [WARNING] [warn] Could not instrument [EmptyTree$/null]. No pos. [WARNING] [warn] Could not instrument [EmptyTree$/null]. No pos. [WARNING] [warn] Could not instrument [EmptyTree$/null]. No pos. [WARNING] [warn] Could not instrument [EmptyTree$/null]. No pos. 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[WARNING] [warn] Could not instrument [EmptyTree$/null]. No pos. [WARNING] [warn] Could not instrument [EmptyTree$/null]. No pos. [WARNING] [warn] Could not instrument [EmptyTree$/null]. No pos. [WARNING] [warn] Could not instrument [EmptyTree$/null]. No pos. [WARNING] [warn] Could not instrument [EmptyTree$/null]. No pos. [WARNING] [warn] Could not instrument [EmptyTree$/null]. No pos. [WARNING] [warn] Could not instrument [EmptyTree$/null]. No pos. [INFO] [info] Instrumentation completed [16156 statements] [INFO] [info] Wrote instrumentation file [/home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/target/scoverage-data/scoverage.coverage.xml] [INFO] [info] Will write measurement data to [/home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/target/scoverage-data] [WARNING] warning: there were 84 deprecation warnings; re-run with -deprecation for details [WARNING] warning: there were 5 feature warnings; re-run with -feature for details [WARNING] three warnings found [INFO] prepare-compile in 0 s [INFO] compile in 33 s [INFO] [INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ adam-core-spark2_2.11 --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 6 source files to /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/target/2.11.12/scoverage-classes [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:post-compile (default-cli) @ adam-core-spark2_2.11 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ adam-core-spark2_2.11 --- [INFO] Test Source directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/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_2.11 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 150 resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ adam-core-spark2_2.11 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ adam-core-spark2_2.11 --- [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_2.11 --- [INFO] Tests are skipped. [INFO] [INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ adam-core-spark2_2.11 --- Discovery starting. Discovery completed in 1 second, 911 milliseconds. Run starting. Expected test count is: 1146 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 2019-05-14 11:45:43 WARN Utils:66 - Your hostname, research-jenkins-worker-08 resolves to a loopback address: 127.0.1.1; using 192.168.10.28 instead (on interface eth0) 2019-05-14 11:45:43 WARN Utils:66 - Set SPARK_LOCAL_IP if you need to bind to another address 2019-05-14 11:45:44 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 FlankReferenceFragmentsSuite: - don't put flanks on non-adjacent fragments - put flanks on adjacent fragments 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 2019-05-14 11:45:54 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 2019-05-14 11:46:21 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 2019-05-14 11:46:22 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 2019-05-14 11:46:23 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 2019-05-14 11:46:34 WARN OutFormatterRunner:190 - Piped command List(sleep, 10) timed out after 5 seconds. 2019-05-14 11:46:34 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 2019-05-14 11:46:55 WARN OutFormatterRunner:190 - Piped command List(python, /tmp/adamTestMvnQbVzgrO/spark-312e02ed-2b53-4b55-a47a-a2cf984475b0/userFiles-c30a661d-2b4f-43d5-be91-6c94e62a8d77/timeout.py) timed out after 5 seconds. 2019-05-14 11:46:55 WARN OutFormatterRunner:190 - Piped command List(python, /tmp/adamTestMvnQbVzgrO/spark-312e02ed-2b53-4b55-a47a-a2cf984475b0/userFiles-c30a661d-2b4f-43d5-be91-6c94e62a8d77/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 contig 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/adamTestMvnQbVzgrO/TempSuite376824572653490318.adam as parquet into RDD... loading /tmp/adamTestMvnQbVzgrO/TempSuite7974541461782367693.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 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 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 - transform coverage to contig rdd - transform coverage to feature rdd - transform coverage to fragment rdd - transform coverage to read rdd - transform coverage to genotype rdd - transform coverage to variant rdd - transform coverage to variant context rdd - 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 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 - transform genotypes to contig 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 contig 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 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 contig 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 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 2019-05-14 11:49:20 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 2019-05-14 11:49:20 WARN TranscriptEffectConverter$:190 - Could not convert VCF INFO reserved key ANN value to TranscriptEffect, caught java.lang.NumberFormatException: For input string: "not a number". - convert to transcript effect from VCF ANN attribute with invalid fraction in variant context lenient validation stringency - convert to transcript effect from VCF ANN attribute with invalid number in variant context strict validation stringency - convert to transcript effect from VCF ANN attribute with invalid fraction in variant context strict validation stringency - convert to transcript effect from VCF ANN attribute in variant context different alt allele - convert to transcript effect from VCF ANN attribute in variant context same alt allele - convert to transcript effect from VCF ANN attribute in variant context multiple effects same alt allele - convert transcript effect to VCF ANN attribute value - convert transcript effect with null fields to VCF ANN attribute value 2019-05-14 11:49:20 WARN TranscriptEffectConverter$: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 NucleotideContigFragmentDatasetSuite: - union two ncf genomic datasets together - round trip a ncf to parquet - round trip a ncf to partitioned parquet - save fasta back as a single file - generate sequence dict from fasta - recover reference string from a single contig fragment - recover trimmed reference string from a single contig fragment - recover reference string from multiple contig fragments - extract sequences based on the list of reference regions - recover trimmed reference string from multiple contig fragments - testing nondeterminism from reduce when recovering referencestring - save single contig fragment as FASTA text file - save single contig fragment with description as FASTA text file - save single contig fragment with null fields as FASTA text file - save single contig fragment with null fragment number as FASTA text file - save single contig fragment with null number of fragments in contig as FASTA text file - save multiple contig fragments from same contig as FASTA text file - save multiple contig fragments with description from same contig as FASTA text file - merge single contig fragment null fragment number - merge single contig fragment number zero - merge multiple contig fragments - save as parquet and apply predicate pushdown - load fasta sequences from GFF3 file - transform contigs to coverage genomic dataset - transform contigs to feature genomic dataset - transform contigs to fragment genomic dataset - transform contigs to read genomic dataset - transform contigs to genotype genomic dataset - transform contigs to variant genomic dataset - transform contigs to variant context genomic dataset 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 - transform features to contig rdd - transform features to coverage rdd - transform features to fragment rdd - transform features to read rdd - transform features to genotype rdd - transform features to variant rdd - transform features to variant context rdd - 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 2019-05-14 11:50:30 WARN VariantContextConverter:2300 - Applying annotation extraction function <function2> 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 2019-05-14 11:50:30 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 2019-05-14 11:50:34 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... 2019-05-14 11:50:34 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 2019-05-14 11:50:34 WARN VCFInputFormat:218 - file:/home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/target/2.11.12/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 - 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 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 2019-05-14 11:50:54 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. 2019-05-14 11:50:54 WARN BlockManager:66 - Block rdd_5_3 could not be removed as it was not found on disk or in memory 2019-05-14 11:50:54 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$$anonfun$extract$1.apply(ReferenceContigMap.scala:63) at org.bdgenomics.adam.util.ReferenceContigMap$$anonfun$extract$1.apply(ReferenceContigMap.scala:63) at scala.collection.MapLike$class.getOrElse(MapLike.scala:128) at scala.collection.AbstractMap.getOrElse(Map.scala:59) at org.bdgenomics.adam.util.ReferenceContigMap.extract(ReferenceContigMap.scala:61) at org.bdgenomics.adam.rdd.read.MDTagging$$anonfun$addMDTagsBroadcast$1$$anonfun$apply$2.apply(MDTagging.scala:76) at org.bdgenomics.adam.rdd.read.MDTagging$$anonfun$addMDTagsBroadcast$1$$anonfun$apply$2.apply(MDTagging.scala:71) at scala.Option$WithFilter.map(Option.scala:207) at org.bdgenomics.adam.rdd.read.MDTagging$$anonfun$addMDTagsBroadcast$1.apply(MDTagging.scala:71) at org.bdgenomics.adam.rdd.read.MDTagging$$anonfun$addMDTagsBroadcast$1.apply(MDTagging.scala:69) at scala.collection.Iterator$$anon$11.next(Iterator.scala:410) at org.apache.spark.storage.memory.MemoryStore.putIterator(MemoryStore.scala:222) at org.apache.spark.storage.memory.MemoryStore.putIteratorAsValues(MemoryStore.scala:299) at org.apache.spark.storage.BlockManager$$anonfun$doPutIterator$1.apply(BlockManager.scala:1165) at org.apache.spark.storage.BlockManager$$anonfun$doPutIterator$1.apply(BlockManager.scala:1156) at org.apache.spark.storage.BlockManager.doPut(BlockManager.scala:1091) at org.apache.spark.storage.BlockManager.doPutIterator(BlockManager.scala:1156) at org.apache.spark.storage.BlockManager.getOrElseUpdate(BlockManager.scala:882) at org.apache.spark.rdd.RDD.getOrCompute(RDD.scala:335) at org.apache.spark.rdd.RDD.iterator(RDD.scala:286) at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:90) at org.apache.spark.scheduler.Task.run(Task.scala:121) at org.apache.spark.executor.Executor$TaskRunner$$anonfun$10.apply(Executor.scala:408) at org.apache.spark.util.Utils$.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) 2019-05-14 11:50:54 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$$anonfun$extract$1.apply(ReferenceContigMap.scala:63) at org.bdgenomics.adam.util.ReferenceContigMap$$anonfun$extract$1.apply(ReferenceContigMap.scala:63) at scala.collection.MapLike$class.getOrElse(MapLike.scala:128) at scala.collection.AbstractMap.getOrElse(Map.scala:59) at org.bdgenomics.adam.util.ReferenceContigMap.extract(ReferenceContigMap.scala:61) at org.bdgenomics.adam.rdd.read.MDTagging$$anonfun$addMDTagsBroadcast$1$$anonfun$apply$2.apply(MDTagging.scala:76) at org.bdgenomics.adam.rdd.read.MDTagging$$anonfun$addMDTagsBroadcast$1$$anonfun$apply$2.apply(MDTagging.scala:71) at scala.Option$WithFilter.map(Option.scala:207) at org.bdgenomics.adam.rdd.read.MDTagging$$anonfun$addMDTagsBroadcast$1.apply(MDTagging.scala:71) at org.bdgenomics.adam.rdd.read.MDTagging$$anonfun$addMDTagsBroadcast$1.apply(MDTagging.scala:69) at scala.collection.Iterator$$anon$11.next(Iterator.scala:410) at org.apache.spark.storage.memory.MemoryStore.putIterator(MemoryStore.scala:222) at org.apache.spark.storage.memory.MemoryStore.putIteratorAsValues(MemoryStore.scala:299) at org.apache.spark.storage.BlockManager$$anonfun$doPutIterator$1.apply(BlockManager.scala:1165) at org.apache.spark.storage.BlockManager$$anonfun$doPutIterator$1.apply(BlockManager.scala:1156) at org.apache.spark.storage.BlockManager.doPut(BlockManager.scala:1091) at org.apache.spark.storage.BlockManager.doPutIterator(BlockManager.scala:1156) at org.apache.spark.storage.BlockManager.getOrElseUpdate(BlockManager.scala:882) at org.apache.spark.rdd.RDD.getOrCompute(RDD.scala:335) at org.apache.spark.rdd.RDD.iterator(RDD.scala:286) at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:90) at org.apache.spark.scheduler.Task.run(Task.scala:121) at org.apache.spark.executor.Executor$TaskRunner$$anonfun$10.apply(Executor.scala:408) at org.apache.spark.util.Utils$.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) 2019-05-14 11:50:54 ERROR TaskSetManager:70 - Task 3 in stage 2.0 failed 1 times; aborting job - try realigning a read on a missing contig, stringency == STRICT 2019-05-14 11:50:54 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 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 FastaConverterSuite: - find contig index - convert a single record without naming information - convert a single record with naming information - convert single fasta sequence - convert fasta with multiple sequences - convert fasta with multiple sequences; short fragment - convert reference fasta file 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 - transform variants to contig 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, 24 seconds. Total number of tests run: 1146 Suites: completed 67, aborted 0 Tests: succeeded 1146, 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_2.11 <<< [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:report (default-cli) @ adam-core-spark2_2.11 --- [INFO] [scoverage] Generating cobertura XML report... [INFO] [scoverage] Generating scoverage XML report... [INFO] [scoverage] Generating scoverage HTML report... [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building ADAM_2.11: APIs for Java, Python 0.27.0-SNAPSHOT [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-apis-spark2_2.11 --- [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-apis-spark2_2.11 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ adam-apis-spark2_2.11 --- [INFO] Source directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/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_2.11 --- [INFO] Modified 0 of 5 .scala files [INFO] [INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ adam-apis-spark2_2.11 --- [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/2.11/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_2.11 --- [INFO] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/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/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-apis/target/2.11.12/classes at 1557859933466 [WARNING] warning: there were two feature warnings; re-run with -feature 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-apis-spark2_2.11 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ adam-apis-spark2_2.11 --- [INFO] Test Source directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/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_2.11 --- [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_2.11 --- [INFO] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/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/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-apis/src/test/scala:-1: info: compiling [INFO] Compiling 8 source files to /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-apis/target/2.11.12/test-classes at 1557859938370 [INFO] prepare-compile in 0 s [INFO] compile in 3 s [INFO] [INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ adam-apis-spark2_2.11 --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 7 source files to /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-apis/target/2.11.12/test-classes [INFO] [INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ adam-apis-spark2_2.11 --- [INFO] Tests are skipped. [INFO] [INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ adam-apis-spark2_2.11 --- Discovery starting. Discovery completed in 153 milliseconds. Run starting. Expected test count is: 9 JavaADAMContextSuite: 2019-05-14 11:52:23 WARN Utils:66 - Your hostname, research-jenkins-worker-08 resolves to a loopback address: 127.0.1.1; using 192.168.10.28 instead (on interface eth0) 2019-05-14 11:52:23 WARN Utils:66 - Set SPARK_LOCAL_IP if you need to bind to another address 2019-05-14 11:52:23 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 FASTA file - 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 Run completed in 9 seconds, 875 milliseconds. Total number of tests run: 9 Suites: completed 2, aborted 0 Tests: succeeded 9, 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_2.11 >>> [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-apis-spark2_2.11 --- [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-apis-spark2_2.11 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ adam-apis-spark2_2.11 --- [INFO] Source directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/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_2.11 --- [INFO] Modified 0 of 5 .scala files [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:pre-compile (default-cli) @ adam-apis-spark2_2.11 --- [INFO] [INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ adam-apis-spark2_2.11 --- [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/2.11/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_2.11 --- [INFO] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/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/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-apis/target/2.11.12/scoverage-classes at 1557859953712 [INFO] [info] Cleaning datadir [/home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-apis/target/scoverage-data] [INFO] [info] Beginning coverage instrumentation [INFO] [info] Instrumentation completed [184 statements] [INFO] [info] Wrote instrumentation file [/home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-apis/target/scoverage-data/scoverage.coverage.xml] [INFO] [info] Will write measurement data to [/home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-apis/target/scoverage-data] [WARNING] warning: there were two feature warnings; re-run with -feature for details [WARNING] one warning found [INFO] prepare-compile in 0 s [INFO] compile in 5 s [INFO] [INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ adam-apis-spark2_2.11 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:post-compile (default-cli) @ adam-apis-spark2_2.11 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ adam-apis-spark2_2.11 --- [INFO] Test Source directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/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_2.11 --- [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_2.11 --- [INFO] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/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/2.11/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/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-apis/target/generated-test-sources/test-annotations:-1: info: compiling [INFO] Compiling 8 source files to /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-apis/target/2.11.12/test-classes at 1557859959215 [INFO] prepare-compile in 0 s [INFO] compile in 3 s [INFO] [INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ adam-apis-spark2_2.11 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ adam-apis-spark2_2.11 --- [INFO] Tests are skipped. [INFO] [INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ adam-apis-spark2_2.11 --- Discovery starting. Discovery completed in 152 milliseconds. Run starting. Expected test count is: 9 JavaADAMContextSuite: 2019-05-14 11:52:44 WARN Utils:66 - Your hostname, research-jenkins-worker-08 resolves to a loopback address: 127.0.1.1; using 192.168.10.28 instead (on interface eth0) 2019-05-14 11:52:44 WARN Utils:66 - Set SPARK_LOCAL_IP if you need to bind to another address 2019-05-14 11:52:44 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 FASTA file - 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 Run completed in 10 seconds, 278 milliseconds. Total number of tests run: 9 Suites: completed 2, aborted 0 Tests: succeeded 9, 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_2.11 <<< [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:report (default-cli) @ adam-apis-spark2_2.11 --- [INFO] [scoverage] Generating cobertura XML report... [INFO] [scoverage] Generating scoverage XML report... [INFO] [scoverage] Generating scoverage HTML report... [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building ADAM_2.11: CLI 0.27.0-SNAPSHOT [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-cli-spark2_2.11 --- [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-cli-spark2_2.11 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:timestamp-property (timestamp-property) @ adam-cli-spark2_2.11 --- [INFO] [INFO] --- git-commit-id-plugin:2.2.2:revision (default) @ adam-cli-spark2_2.11 --- [INFO] [INFO] --- templating-maven-plugin:1.0.0:filter-sources (filter-src) @ adam-cli-spark2_2.11 --- [INFO] Coping files with filtering to temporary directory. [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 1 resource [INFO] Copied 1 files to output directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/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/2.11/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_2.11 --- [INFO] Source directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/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_2.11 --- [INFO] Modified 0 of 31 .scala files [INFO] [INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ adam-cli-spark2_2.11 --- [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/2.11/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_2.11 --- [INFO] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/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/2.11/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/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-cli/target/2.11.12/classes at 1557859975876 [WARNING] warning: there was one deprecation warning; re-run with -deprecation for details [WARNING] one warning 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_2.11 --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 1 source file to /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-cli/target/2.11.12/classes [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ adam-cli-spark2_2.11 --- [INFO] Test Source directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/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_2.11 --- [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_2.11 --- [INFO] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-cli/src/test/scala:-1: info: compiling [INFO] Compiling 14 source files to /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-cli/target/2.11.12/test-classes at 1557859983083 [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_2.11 --- [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_2.11 --- [INFO] Tests are skipped. [INFO] [INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ adam-cli-spark2_2.11 --- Discovery starting. Discovery completed in 209 milliseconds. Run starting. Expected test count is: 46 TransformFeaturesSuite: 2019-05-14 11:53:10 WARN Utils:66 - Your hostname, research-jenkins-worker-08 resolves to a loopback address: 127.0.1.1; using 192.168.10.28 instead (on interface eth0) 2019-05-14 11:53:10 WARN Utils:66 - Set SPARK_LOCAL_IP if you need to bind to another address 2019-05-14 11:53:10 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 ADAM2FastaSuite: - round trip FASTA to nucleotide contig fragments in ADAM format to FASTA TransformFragmentsSuite: - load queryname sorted sam and save as parquet - cannot sort if not saving as sam 2019-05-14 11:53:23 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 Fasta2ADAMSuite: - can load fasta records after conversion 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: 2019-05-14 11:53:34 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 25 seconds, 708 milliseconds. Total number of tests run: 46 Suites: completed 14, aborted 0 Tests: succeeded 46, 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_2.11 >>> [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-cli-spark2_2.11 --- [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-cli-spark2_2.11 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:timestamp-property (timestamp-property) @ adam-cli-spark2_2.11 --- [INFO] [INFO] --- git-commit-id-plugin:2.2.2:revision (default) @ adam-cli-spark2_2.11 --- [INFO] [INFO] --- templating-maven-plugin:1.0.0:filter-sources (filter-src) @ adam-cli-spark2_2.11 --- [INFO] Coping files with filtering to temporary directory. [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 1 resource [INFO] No files needs to be copied to output directory. Up to date: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/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/2.11/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_2.11 --- [INFO] Source directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/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_2.11 --- [INFO] Modified 0 of 31 .scala files [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:pre-compile (default-cli) @ adam-cli-spark2_2.11 --- [INFO] [INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ adam-cli-spark2_2.11 --- [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/2.11/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_2.11 --- [INFO] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/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/2.11/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/2.11/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/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-cli/target/2.11.12/scoverage-classes at 1557860016809 [INFO] [info] Cleaning datadir [/home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-cli/target/scoverage-data] [INFO] [info] Beginning coverage instrumentation [INFO] [info] Instrumentation completed [1439 statements] [INFO] [info] Wrote instrumentation file [/home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-cli/target/scoverage-data/scoverage.coverage.xml] [INFO] [info] Will write measurement data to [/home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-cli/target/scoverage-data] [WARNING] warning: there was one deprecation warning; re-run with -deprecation for details [WARNING] one warning found [INFO] prepare-compile in 0 s [INFO] compile in 8 s [INFO] [INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ adam-cli-spark2_2.11 --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 1 source file to /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-cli/target/2.11.12/scoverage-classes [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:post-compile (default-cli) @ adam-cli-spark2_2.11 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ adam-cli-spark2_2.11 --- [INFO] Test Source directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/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_2.11 --- [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_2.11 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ adam-cli-spark2_2.11 --- [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_2.11 --- [INFO] Tests are skipped. [INFO] [INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ adam-cli-spark2_2.11 --- Discovery starting. Discovery completed in 206 milliseconds. Run starting. Expected test count is: 46 TransformFeaturesSuite: 2019-05-14 11:53:46 WARN Utils:66 - Your hostname, research-jenkins-worker-08 resolves to a loopback address: 127.0.1.1; using 192.168.10.28 instead (on interface eth0) 2019-05-14 11:53:46 WARN Utils:66 - Set SPARK_LOCAL_IP if you need to bind to another address 2019-05-14 11:53:46 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 ADAM2FastaSuite: - round trip FASTA to nucleotide contig fragments in ADAM format to FASTA TransformFragmentsSuite: - load queryname sorted sam and save as parquet - cannot sort if not saving as sam 2019-05-14 11:54:00 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 Fasta2ADAMSuite: - can load fasta records after conversion 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: 2019-05-14 11:54:12 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 27 seconds, 521 milliseconds. Total number of tests run: 46 Suites: completed 14, aborted 0 Tests: succeeded 46, 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_2.11 <<< [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:report (default-cli) @ adam-cli-spark2_2.11 --- [INFO] [scoverage] Generating cobertura XML report... [INFO] [scoverage] Generating scoverage XML report... [INFO] [scoverage] Generating scoverage HTML report... [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building ADAM_2.11: Assembly 0.27.0-SNAPSHOT [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-assembly-spark2_2.11 --- [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-assembly-spark2_2.11 --- [INFO] [INFO] --- git-commit-id-plugin:2.2.2:revision (default) @ adam-assembly-spark2_2.11 --- [INFO] [INFO] --- templating-maven-plugin:1.0.0:filter-sources (filter-src) @ adam-assembly-spark2_2.11 --- [INFO] Request to add '/home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/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_2.11 --- [INFO] Source directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/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_2.11 --- [INFO] Modified 0 of 1 .scala files [INFO] [INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ adam-assembly-spark2_2.11 --- [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/2.11/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_2.11 --- [INFO] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/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/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-assembly/target/2.11.12/classes at 1557860054978 [INFO] prepare-compile in 0 s [INFO] compile in 1 s [INFO] [INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ adam-assembly-spark2_2.11 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ adam-assembly-spark2_2.11 --- [INFO] Test Source directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/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_2.11 --- [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/2.11/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_2.11 --- [INFO] No sources to compile [INFO] [INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ adam-assembly-spark2_2.11 --- [INFO] No sources to compile [INFO] [INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ adam-assembly-spark2_2.11 --- [INFO] Tests are skipped. [INFO] [INFO] >>> scoverage-maven-plugin:1.1.1:report (default-cli) > [scoverage]test @ adam-assembly-spark2_2.11 >>> [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-assembly-spark2_2.11 --- [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-assembly-spark2_2.11 --- [INFO] [INFO] --- git-commit-id-plugin:2.2.2:revision (default) @ adam-assembly-spark2_2.11 --- [INFO] [INFO] --- templating-maven-plugin:1.0.0:filter-sources (filter-src) @ adam-assembly-spark2_2.11 --- [INFO] Request to add '/home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/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_2.11 --- [INFO] Source directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/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_2.11 --- [INFO] Modified 0 of 1 .scala files [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:pre-compile (default-cli) @ adam-assembly-spark2_2.11 --- [INFO] [INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ adam-assembly-spark2_2.11 --- [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/2.11/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_2.11 --- [INFO] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/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/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-assembly/target/2.11.12/scoverage-classes at 1557860056925 [INFO] [info] Cleaning datadir [/home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-assembly/target/scoverage-data] [INFO] [info] Beginning coverage instrumentation [INFO] [info] Instrumentation completed [0 statements] [INFO] [info] Wrote instrumentation file [/home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-assembly/target/scoverage-data/scoverage.coverage.xml] [INFO] [info] Will write measurement data to [/home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-assembly/target/scoverage-data] [INFO] prepare-compile in 0 s [INFO] compile in 1 s [INFO] [INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ adam-assembly-spark2_2.11 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:post-compile (default-cli) @ adam-assembly-spark2_2.11 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ adam-assembly-spark2_2.11 --- [INFO] Test Source directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/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_2.11 --- [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/2.11/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_2.11 --- [INFO] No sources to compile [INFO] [INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ adam-assembly-spark2_2.11 --- [INFO] No sources to compile [INFO] [INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ adam-assembly-spark2_2.11 --- [INFO] Tests are skipped. [INFO] [INFO] <<< scoverage-maven-plugin:1.1.1:report (default-cli) < [scoverage]test @ adam-assembly-spark2_2.11 <<< [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:report (default-cli) @ adam-assembly-spark2_2.11 --- [INFO] [scoverage] Generating cobertura XML report... [INFO] [scoverage] Generating scoverage XML report... [INFO] [scoverage] Generating scoverage HTML report... [INFO] [scoverage] Generating aggregated cobertura XML report... [INFO] [scoverage] Generating aggregated scoverage XML report... [INFO] [scoverage] Generating aggregated scoverage HTML report... [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building ADAM_2.11 0.27.0-SNAPSHOT [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- coveralls-maven-plugin:4.3.0:report (default-cli) @ adam-parent-spark2_2.11 --- [INFO] Starting Coveralls job for jenkins (2986 / https://amplab.cs.berkeley.edu/jenkins/job/ADAM-prb/HADOOP_VERSION=2.7.5,SCALAVER=2.11,SPARK_VERSION=2.4.3,label=ubuntu/2986/) [INFO] Using repository token <secret> [INFO] Git commit 3718c8d in travis-spark-2.4-scala-2.12 [INFO] Writing Coveralls data to /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/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/2.11/SPARK_VERSION/2.4.3/label/ubuntu/target/cobertura.xml [INFO] Successfully wrote Coveralls data in 467ms [INFO] Gathered code coverage metrics for 143 source files with 36840 lines of code: [INFO] - 8546 relevant lines [INFO] - 6741 covered lines [INFO] - 1805 missed lines [INFO] Submitting Coveralls data to API [INFO] Successfully submitted Coveralls data in 1336ms for Job #2986.1 [INFO] https://coveralls.io/jobs/48485560 [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_2.11 .......................................... SUCCESS [ 2.163 s] [INFO] ADAM_2.11: Shader workaround ....................... SUCCESS [ 4.380 s] [INFO] ADAM_2.11: Avro-to-Dataset codegen utils ........... SUCCESS [ 9.235 s] [INFO] ADAM_2.11: Core .................................... SUCCESS [14:39 min] [INFO] ADAM_2.11: APIs for Java, Python ................... SUCCESS [ 41.440 s] [INFO] ADAM_2.11: CLI ..................................... SUCCESS [01:19 min] [INFO] ADAM_2.11: Assembly ................................ SUCCESS [ 9.240 s] [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ [INFO] Total time: 17:16 min [INFO] Finished at: 2019-05-14T11:54:25-07:00 [INFO] Final Memory: 95M/1478M [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/adamTestMvnQbVzgrO 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_2.11 [INFO] ADAM_2.11: Shader workaround [INFO] ADAM_2.11: Avro-to-Dataset codegen utils [INFO] ADAM_2.11: Core [INFO] ADAM_2.11: APIs for Java, Python [INFO] ADAM_2.11: CLI [INFO] ADAM_2.11: Assembly [INFO] ADAM_2.11: Distribution [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building ADAM_2.11 0.27.0-SNAPSHOT [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-parent-spark2_2.11 --- [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-parent-spark2_2.11 --- [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ adam-parent-spark2_2.11 --- [INFO] Modified 0 of 241 .scala files [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ adam-parent-spark2_2.11 --- [INFO] No sources to compile [INFO] [INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ adam-parent-spark2_2.11 --- [INFO] No sources to compile [INFO] [INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ adam-parent-spark2_2.11 --- [INFO] [INFO] --- maven-javadoc-plugin:3.1.0:jar (attach-javadoc) @ adam-parent-spark2_2.11 --- [INFO] [INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) > generate-sources @ adam-parent-spark2_2.11 >>> [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-parent-spark2_2.11 --- [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-parent-spark2_2.11 --- [INFO] [INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) < generate-sources @ adam-parent-spark2_2.11 <<< [INFO] [INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ adam-parent-spark2_2.11 --- [INFO] No source files found [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building ADAM_2.11: Shader workaround 0.27.0-SNAPSHOT [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-shade-spark2_2.11 --- [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-shade-spark2_2.11 --- [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ adam-shade-spark2_2.11 --- [INFO] Modified 0 of 0 .scala files [INFO] [INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ adam-shade-spark2_2.11 --- [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/2.11/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_2.11 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ adam-shade-spark2_2.11 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- plexus-component-metadata:1.5.5:generate-metadata (default) @ adam-shade-spark2_2.11 --- [INFO] Discovered 1 component descriptors(s) [INFO] [INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ adam-shade-spark2_2.11 --- [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/2.11/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_2.11 --- [INFO] No sources to compile [INFO] [INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ adam-shade-spark2_2.11 --- [INFO] No sources to compile [INFO] [INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ adam-shade-spark2_2.11 --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:3.1.2:jar (default-jar) @ adam-shade-spark2_2.11 --- [INFO] Building jar: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-shade/target/adam-shade-spark2_2.11-0.27.0-SNAPSHOT.jar [INFO] [INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ adam-shade-spark2_2.11 --- [INFO] Building jar: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-shade/target/adam-shade-spark2_2.11-0.27.0-SNAPSHOT-sources.jar [INFO] [INFO] --- maven-javadoc-plugin:3.1.0:jar (attach-javadoc) @ adam-shade-spark2_2.11 --- [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/2.11/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/2.11/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/2.11/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/2.11/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/2.11/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/2.11/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/2.11/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/2.11/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/2.11/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/2.11/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/2.11/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/2.11/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/2.11/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/2.11/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/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-shade/target/adam-shade-spark2_2.11-0.27.0-SNAPSHOT-javadoc.jar [INFO] [INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) > generate-sources @ adam-shade-spark2_2.11 >>> [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-shade-spark2_2.11 --- [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-shade-spark2_2.11 --- [INFO] [INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) < generate-sources @ adam-shade-spark2_2.11 <<< [INFO] [INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ adam-shade-spark2_2.11 --- model contains 6 documentable templates [INFO] Building jar: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-shade/target/adam-shade-spark2_2.11-0.27.0-SNAPSHOT-javadoc.jar [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building ADAM_2.11: Avro-to-Dataset codegen utils 0.27.0-SNAPSHOT [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-codegen-spark2_2.11 --- [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-codegen-spark2_2.11 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ adam-codegen-spark2_2.11 --- [INFO] Source directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/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_2.11 --- [INFO] Modified 0 of 4 .scala files [INFO] [INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ adam-codegen-spark2_2.11 --- [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/2.11/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_2.11 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ adam-codegen-spark2_2.11 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ adam-codegen-spark2_2.11 --- [INFO] Test Source directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/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_2.11 --- [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/2.11/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_2.11 --- [INFO] No sources to compile [INFO] [INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ adam-codegen-spark2_2.11 --- [INFO] No sources to compile [INFO] [INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ adam-codegen-spark2_2.11 --- [INFO] Tests are skipped. [INFO] [INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ adam-codegen-spark2_2.11 --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:3.1.2:jar (default-jar) @ adam-codegen-spark2_2.11 --- [INFO] Building jar: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-codegen/target/adam-codegen-spark2_2.11-0.27.0-SNAPSHOT.jar [INFO] [INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ adam-codegen-spark2_2.11 --- [INFO] Building jar: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-codegen/target/adam-codegen-spark2_2.11-0.27.0-SNAPSHOT-sources.jar [INFO] [INFO] --- maven-javadoc-plugin:3.1.0:jar (attach-javadoc) @ adam-codegen-spark2_2.11 --- [INFO] [INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) > generate-sources @ adam-codegen-spark2_2.11 >>> [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-codegen-spark2_2.11 --- [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-codegen-spark2_2.11 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ adam-codegen-spark2_2.11 --- [INFO] Source directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/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_2.11 <<< [INFO] [INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ adam-codegen-spark2_2.11 --- model contains 11 documentable templates [INFO] Building jar: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-codegen/target/adam-codegen-spark2_2.11-0.27.0-SNAPSHOT-javadoc.jar [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building ADAM_2.11: Core 0.27.0-SNAPSHOT [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-core-spark2_2.11 --- [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-core-spark2_2.11 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ adam-core-spark2_2.11 --- [INFO] Source directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/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/2.11/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_2.11 --- 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_2.11 --- 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_2.11 --- [INFO] Modified 2 of 199 .scala files [INFO] [INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ adam-core-spark2_2.11 --- [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/2.11/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_2.11 --- [INFO] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/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/2.11/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/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/target/generated-sources/src/main/scala:-1: info: compiling [INFO] Compiling 136 source files to /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/target/2.11.12/classes at 1557860090047 [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/main/scala/org/bdgenomics/adam/rdd/GenomicDataset.scala:3099: warning: no valid targets for annotation on value uTag - it is discarded unused. You may specify targets with meta-annotations, e.g. @(transient @getter) [WARNING] @transient val uTag: TypeTag[U] [WARNING] ^ [WARNING] warning: there were 84 deprecation warnings; re-run with -deprecation for details [WARNING] warning: there were 5 feature warnings; re-run with -feature for details [WARNING] three warnings found [INFO] prepare-compile in 0 s [INFO] compile in 28 s [INFO] [INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ adam-core-spark2_2.11 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ adam-core-spark2_2.11 --- [INFO] Test Source directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/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_2.11 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 150 resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ adam-core-spark2_2.11 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ adam-core-spark2_2.11 --- [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_2.11 --- [INFO] Tests are skipped. [INFO] [INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ adam-core-spark2_2.11 --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:3.1.2:jar (default-jar) @ adam-core-spark2_2.11 --- [INFO] Building jar: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/target/adam-core-spark2_2.11-0.27.0-SNAPSHOT.jar [INFO] [INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ adam-core-spark2_2.11 --- [INFO] Building jar: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/target/adam-core-spark2_2.11-0.27.0-SNAPSHOT-sources.jar [INFO] [INFO] --- maven-javadoc-plugin:3.1.0:jar (attach-javadoc) @ adam-core-spark2_2.11 --- [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_2.11:jar:0.27.0-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/2.11/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/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-codegen/target/apidocs. Ignored it. [INFO] Loading source files for package org.bdgenomics.adam.io... Loading source files for package org.apache.parquet.avro... 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/2.11/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/2.11/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/2.11/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/2.11/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/2.11/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/2.11/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/2.11/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/2.11/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/2.11/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/2.11/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/2.11/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/2.11/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/2.11/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/2.11/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/2.11/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/2.11/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/2.11/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/2.11/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/2.11/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/2.11/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/2.11/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/2.11/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/2.11/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/2.11/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/2.11/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/2.11/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/2.11/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/2.11/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/2.11/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/2.11/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/2.11/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/2.11/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/2.11/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/2.11/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/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/target/adam-core-spark2_2.11-0.27.0-SNAPSHOT-javadoc.jar [INFO] [INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) > generate-sources @ adam-core-spark2_2.11 >>> [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-core-spark2_2.11 --- [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-core-spark2_2.11 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ adam-core-spark2_2.11 --- [INFO] Source directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/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/2.11/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_2.11 --- 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_2.11 --- 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_2.11 <<< [INFO] [INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ adam-core-spark2_2.11 --- /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/main/scala/org/bdgenomics/adam/converters/FastaConverter.scala:230: warning: discarding unmoored doc comment /** ^ /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/main/scala/org/bdgenomics/adam/rdd/read/AlignmentRecordDataset.scala:803: 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/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/main/scala/org/bdgenomics/adam/rich/RichCigar.scala:43: warning: discarding unmoored doc comment /** ^ /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/main/scala/org/bdgenomics/adam/rdd/GenomicDataset.scala:3099: warning: no valid targets for annotation on value uTag - it is discarded unused. You may specify targets with meta-annotations, e.g. @(transient @getter) @transient val uTag: TypeTag[U] ^ warning: there were 5 feature warnings; re-run with -feature for details model contains 276 documentable templates /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/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/2.11/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/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/main/scala/org/bdgenomics/adam/rdd/contig/NucleotideContigFragmentDataset.scala:365: warning: Could not find any member to link for "UnsupportedOperationException". /** ^ /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/main/scala/org/bdgenomics/adam/rdd/ADAMContext.scala:1339: warning: Could not find any member to link for "FileNotFoundException". /** ^ /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/main/scala/org/bdgenomics/adam/rdd/ADAMContext.scala:1368: warning: Could not find any member to link for "FileNotFoundException". /** ^ /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/main/scala/org/bdgenomics/adam/rdd/ADAMContext.scala:1388: warning: Could not find any member to link for "FileNotFoundException". /** ^ /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/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/2.11/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/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/main/scala/org/bdgenomics/adam/models/ReferenceRegion.scala:456: warning: Could not find any member to link for "IllegalArgumentException". /** ^ /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/main/scala/org/bdgenomics/adam/rdd/ADAMContext.scala:3085: warning: Could not find any member to link for "IllegalArgumentException". /** ^ /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/main/scala/org/bdgenomics/adam/models/ReferenceRegion.scala:411: warning: Could not find any member to link for "IllegalArgumentException". /** ^ /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/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/2.11/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/2.11/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/2.11/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/2.11/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/2.11/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/2.11/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/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/main/scala/org/bdgenomics/adam/models/ReferenceRegion.scala:426: warning: Could not find any member to link for "IllegalArgumentException". /** ^ /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/main/scala/org/bdgenomics/adam/models/ReferenceRegion.scala:336: warning: Could not find any member to link for "IllegalArgumentException". /** ^ 25 warnings found [INFO] Building jar: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/target/adam-core-spark2_2.11-0.27.0-SNAPSHOT-javadoc.jar [INFO] [INFO] --- maven-jar-plugin:3.1.2:test-jar (default) @ adam-core-spark2_2.11 --- [INFO] Building jar: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/target/adam-core-spark2_2.11-0.27.0-SNAPSHOT-tests.jar [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building ADAM_2.11: APIs for Java, Python 0.27.0-SNAPSHOT [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-apis-spark2_2.11 --- [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-apis-spark2_2.11 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ adam-apis-spark2_2.11 --- [INFO] Source directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/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_2.11 --- [INFO] Modified 0 of 5 .scala files [INFO] [INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ adam-apis-spark2_2.11 --- [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/2.11/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_2.11 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ adam-apis-spark2_2.11 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ adam-apis-spark2_2.11 --- [INFO] Test Source directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/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_2.11 --- [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_2.11 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ adam-apis-spark2_2.11 --- [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_2.11 --- [INFO] Tests are skipped. [INFO] [INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ adam-apis-spark2_2.11 --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:3.1.2:jar (default-jar) @ adam-apis-spark2_2.11 --- [INFO] Building jar: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-apis/target/adam-apis-spark2_2.11-0.27.0-SNAPSHOT.jar [INFO] [INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ adam-apis-spark2_2.11 --- [INFO] Building jar: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-apis/target/adam-apis-spark2_2.11-0.27.0-SNAPSHOT-sources.jar [INFO] [INFO] --- maven-javadoc-plugin:3.1.0:jar (attach-javadoc) @ adam-apis-spark2_2.11 --- [INFO] [INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) > generate-sources @ adam-apis-spark2_2.11 >>> [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-apis-spark2_2.11 --- [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-apis-spark2_2.11 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ adam-apis-spark2_2.11 --- [INFO] Source directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/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_2.11 <<< [INFO] [INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ adam-apis-spark2_2.11 --- warning: there were two feature warnings; re-run with -feature for details model contains 124 documentable templates one warning found [INFO] Building jar: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-apis/target/adam-apis-spark2_2.11-0.27.0-SNAPSHOT-javadoc.jar [INFO] [INFO] --- maven-jar-plugin:3.1.2:test-jar (default) @ adam-apis-spark2_2.11 --- [INFO] Building jar: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-apis/target/adam-apis-spark2_2.11-0.27.0-SNAPSHOT-tests.jar [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building ADAM_2.11: CLI 0.27.0-SNAPSHOT [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-cli-spark2_2.11 --- [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-cli-spark2_2.11 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:timestamp-property (timestamp-property) @ adam-cli-spark2_2.11 --- [INFO] [INFO] --- git-commit-id-plugin:2.2.2:revision (default) @ adam-cli-spark2_2.11 --- [INFO] [INFO] --- templating-maven-plugin:1.0.0:filter-sources (filter-src) @ adam-cli-spark2_2.11 --- [INFO] Coping files with filtering to temporary directory. [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 1 resource [INFO] No files needs to be copied to output directory. Up to date: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/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/2.11/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_2.11 --- [INFO] Source directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/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_2.11 --- [INFO] Modified 0 of 31 .scala files [INFO] [INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ adam-cli-spark2_2.11 --- [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/2.11/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_2.11 --- [INFO] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/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/2.11/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/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-cli/target/2.11.12/classes at 1557860162159 [WARNING] warning: there was one deprecation warning; re-run with -deprecation for details [WARNING] one warning 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_2.11 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ adam-cli-spark2_2.11 --- [INFO] Test Source directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/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_2.11 --- [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_2.11 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ adam-cli-spark2_2.11 --- [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_2.11 --- [INFO] Tests are skipped. [INFO] [INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ adam-cli-spark2_2.11 --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:3.1.2:jar (default-jar) @ adam-cli-spark2_2.11 --- [INFO] Building jar: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-cli/target/adam-cli-spark2_2.11-0.27.0-SNAPSHOT.jar [INFO] [INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ adam-cli-spark2_2.11 --- [INFO] Building jar: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-cli/target/adam-cli-spark2_2.11-0.27.0-SNAPSHOT-sources.jar [INFO] [INFO] --- maven-javadoc-plugin:3.1.0:jar (attach-javadoc) @ adam-cli-spark2_2.11 --- [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_2.11:jar:0.27.0-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/2.11/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/2.11/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/2.11/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/2.11/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/2.11/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/2.11/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/2.11/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/2.11/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/2.11/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/2.11/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/2.11/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/2.11/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/2.11/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/2.11/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/2.11/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/2.11/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/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-cli/target/adam-cli-spark2_2.11-0.27.0-SNAPSHOT-javadoc.jar [INFO] [INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) > generate-sources @ adam-cli-spark2_2.11 >>> [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-cli-spark2_2.11 --- [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-cli-spark2_2.11 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:timestamp-property (timestamp-property) @ adam-cli-spark2_2.11 --- [INFO] [INFO] --- git-commit-id-plugin:2.2.2:revision (default) @ adam-cli-spark2_2.11 --- [INFO] [INFO] --- templating-maven-plugin:1.0.0:filter-sources (filter-src) @ adam-cli-spark2_2.11 --- [INFO] Coping files with filtering to temporary directory. [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 1 resource [INFO] No files needs to be copied to output directory. Up to date: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/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/2.11/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_2.11 --- [INFO] Source directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/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_2.11 <<< [INFO] [INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ adam-cli-spark2_2.11 --- model contains 55 documentable templates [INFO] Building jar: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-cli/target/adam-cli-spark2_2.11-0.27.0-SNAPSHOT-javadoc.jar [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building ADAM_2.11: Assembly 0.27.0-SNAPSHOT [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-assembly-spark2_2.11 --- [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-assembly-spark2_2.11 --- [INFO] [INFO] --- git-commit-id-plugin:2.2.2:revision (default) @ adam-assembly-spark2_2.11 --- [INFO] [INFO] --- templating-maven-plugin:1.0.0:filter-sources (filter-src) @ adam-assembly-spark2_2.11 --- [INFO] Request to add '/home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/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_2.11 --- [INFO] Source directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/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_2.11 --- [INFO] Modified 0 of 1 .scala files [INFO] [INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ adam-assembly-spark2_2.11 --- [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/2.11/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_2.11 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ adam-assembly-spark2_2.11 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ adam-assembly-spark2_2.11 --- [INFO] Test Source directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/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_2.11 --- [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/2.11/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_2.11 --- [INFO] No sources to compile [INFO] [INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ adam-assembly-spark2_2.11 --- [INFO] No sources to compile [INFO] [INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ adam-assembly-spark2_2.11 --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:3.1.2:jar (default-jar) @ adam-assembly-spark2_2.11 --- [INFO] Building jar: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-assembly/target/adam-assembly-spark2_2.11-0.27.0-SNAPSHOT.jar [INFO] [INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ adam-assembly-spark2_2.11 --- [INFO] Building jar: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-assembly/target/adam-assembly-spark2_2.11-0.27.0-SNAPSHOT-sources.jar [INFO] [INFO] --- maven-javadoc-plugin:3.1.0:jar (attach-javadoc) @ adam-assembly-spark2_2.11 --- [INFO] [INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) > generate-sources @ adam-assembly-spark2_2.11 >>> [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-assembly-spark2_2.11 --- [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-assembly-spark2_2.11 --- [INFO] [INFO] --- git-commit-id-plugin:2.2.2:revision (default) @ adam-assembly-spark2_2.11 --- [INFO] [INFO] --- templating-maven-plugin:1.0.0:filter-sources (filter-src) @ adam-assembly-spark2_2.11 --- [INFO] Request to add '/home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/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_2.11 --- [INFO] Source directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/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_2.11 <<< [INFO] [INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ adam-assembly-spark2_2.11 --- model contains 6 documentable templates [INFO] Building jar: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-assembly/target/adam-assembly-spark2_2.11-0.27.0-SNAPSHOT-javadoc.jar [INFO] [INFO] --- maven-shade-plugin:3.2.0:shade (default) @ adam-assembly-spark2_2.11 --- [INFO] Including org.bdgenomics.adam:adam-cli-spark2_2.11:jar:0.27.0-SNAPSHOT in the shaded jar. [INFO] Including org.bdgenomics.utils:utils-misc-spark2_2.11:jar:0.2.15 in the shaded jar. [INFO] Including org.bdgenomics.utils:utils-io-spark2_2.11: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_2.11:jar:0.2.15 in the shaded jar. [INFO] Including org.clapper:grizzled-slf4j_2.11: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_2.11: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:2.7 in the shaded jar. [INFO] Including org.xerial.snappy:snappy-java:jar:1.1.1.3 in the shaded jar. [INFO] Including org.apache.commons:commons-compress:jar:1.8.1 in the shaded jar. [INFO] Including org.tukaani:xz:jar:1.5 in the shaded jar. [INFO] Including org.bdgenomics.adam:adam-core-spark2_2.11:jar:0.27.0-SNAPSHOT in the shaded jar. [INFO] Including org.bdgenomics.utils:utils-intervalrdd-spark2_2.11: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_2.11:jar:0.27.0-SNAPSHOT in the shaded jar. [INFO] Including org.bdgenomics.adam:adam-apis-spark2_2.11:jar:0.27.0-SNAPSHOT in the shaded jar. [INFO] Including args4j:args4j:jar:2.33 in the shaded jar. [INFO] Including net.codingwell:scala-guice_2.11: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:2.11.12 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/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-assembly/target/adam-assembly-spark2_2.11-0.27.0-SNAPSHOT.jar with /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-assembly/target/adam-assembly-spark2_2.11-0.27.0-SNAPSHOT-shaded.jar [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building ADAM_2.11: Distribution 0.27.0-SNAPSHOT [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-distribution-spark2_2.11 --- [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-distribution-spark2_2.11 --- [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ adam-distribution-spark2_2.11 --- [INFO] Modified 0 of 0 .scala files [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ adam-distribution-spark2_2.11 --- [INFO] No sources to compile [INFO] [INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ adam-distribution-spark2_2.11 --- [INFO] No sources to compile [INFO] [INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ adam-distribution-spark2_2.11 --- [INFO] [INFO] --- maven-javadoc-plugin:3.1.0:jar (attach-javadoc) @ adam-distribution-spark2_2.11 --- [INFO] [INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) > generate-sources @ adam-distribution-spark2_2.11 >>> [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-distribution-spark2_2.11 --- [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-distribution-spark2_2.11 --- [INFO] [INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) < generate-sources @ adam-distribution-spark2_2.11 <<< [INFO] [INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ adam-distribution-spark2_2.11 --- [INFO] No source files found [INFO] [INFO] --- maven-assembly-plugin:3.1.0:single (default) @ adam-distribution-spark2_2.11 --- [INFO] Reading assembly descriptor: src/main/assembly/assembly.xml [INFO] Building tar: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-distribution/target/adam-distribution-spark2_2.11-0.27.0-SNAPSHOT-bin.tar.gz [WARNING] Entry: adam-distribution-spark2_2.11-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/algorithms/smithwaterman/ longer than 100 characters. [WARNING] Resulting tar file can only be processed successfully by GNU compatible tar commands [WARNING] Entry: adam-distribution-spark2_2.11-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/projections/VariantField$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.11-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/projections/Filter$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.11-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/projections/package.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.11-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/projections/SampleField$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.11-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/projections/VariantAnnotationField$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.11-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/projections/ReferenceField$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.11-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/projections/ReadGroupField$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.11-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/projections/OntologyTermField$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.11-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/projections/AlignmentRecordField$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.11-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/projections/SequenceField$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.11-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/projections/TranscriptEffectField$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.11-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/projections/FragmentField$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.11-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/projections/ReadField$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.11-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/projections/GenotypeField$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.11-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/projections/FieldValue.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.11-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/projections/NucleotideContigFragmentField$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.11-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/projections/FeatureField$.html longer than 100 characters. 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[WARNING] Entry: adam-distribution-spark2_2.11-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/cli/TransformGenotypes.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.11-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/cli/Reads2CoverageArgs.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.11-0.27.0-SNAPSHOT/repo/adam-assembly-spark2_2.11-0.27.0-SNAPSHOT-sources.jar longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.11-0.27.0-SNAPSHOT/repo/adam-assembly-spark2_2.11-0.27.0-SNAPSHOT-javadoc.jar longer than 100 characters. [INFO] Building zip: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/adam-distribution/target/adam-distribution-spark2_2.11-0.27.0-SNAPSHOT-bin.zip [INFO] ------------------------------------------------------------------------ [INFO] Reactor Summary: [INFO] [INFO] ADAM_2.11 .......................................... SUCCESS [ 8.249 s] [INFO] ADAM_2.11: Shader workaround ....................... SUCCESS [ 3.947 s] [INFO] ADAM_2.11: Avro-to-Dataset codegen utils ........... SUCCESS [ 3.058 s] [INFO] ADAM_2.11: Core .................................... SUCCESS [01:12 min] [INFO] ADAM_2.11: APIs for Java, Python ................... SUCCESS [ 6.035 s] [INFO] ADAM_2.11: CLI ..................................... SUCCESS [ 20.002 s] [INFO] ADAM_2.11: Assembly ................................ SUCCESS [ 11.743 s] [INFO] ADAM_2.11: Distribution ............................ SUCCESS [ 25.759 s] [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ [INFO] Total time: 02:31 min [INFO] Finished at: 2019-05-14T11:56:58-07:00 [INFO] Final Memory: 63M/1468M [INFO] ------------------------------------------------------------------------ # make sure that the distribution package contains an assembly jar # if no assembly jar is found, this will exit with code 1 and fail the build tar tzvf adam-distribution/target/adam-distribution*-bin.tar.gz | \ grep adam-assembly | \ grep jar | \ grep -v -e sources -e javadoc + grep adam-assembly + grep jar + grep -v -e sources -e javadoc + tar tzvf adam-distribution/target/adam-distribution-spark2_2.11-0.27.0-SNAPSHOT-bin.tar.gz -rw-r--r-- jenkins/jenkins 44167656 2019-05-14 11:56 adam-distribution-spark2_2.11-0.27.0-SNAPSHOT/repo/adam-assembly-spark2_2.11-0.27.0-SNAPSHOT.jar # we are done with maven, so clean up the maven temp dir find ${ADAM_MVN_TMP_DIR} + find /tmp/adamTestMvnQbVzgrO /tmp/adamTestMvnQbVzgrO /tmp/adamTestMvnQbVzgrO/TempSuite5358356180860747514 /tmp/adamTestMvnQbVzgrO/TempSuite6320869559847645522 /tmp/adamTestMvnQbVzgrO/TempSuite8585495011247415923.adam /tmp/adamTestMvnQbVzgrO/TempSuite8585495011247415923.adam/part-00000-6b6518bc-882b-42b0-ba33-c00bbb9b5ea1-c000.snappy.parquet /tmp/adamTestMvnQbVzgrO/TempSuite8585495011247415923.adam/.part-00000-6b6518bc-882b-42b0-ba33-c00bbb9b5ea1-c000.snappy.parquet.crc /tmp/adamTestMvnQbVzgrO/TempSuite8585495011247415923.adam/_SUCCESS /tmp/adamTestMvnQbVzgrO/TempSuite8585495011247415923.adam/._SUCCESS.crc /tmp/adamTestMvnQbVzgrO/TempSuite8585495011247415923.adam/._references.avro.crc /tmp/adamTestMvnQbVzgrO/TempSuite8585495011247415923.adam/_references.avro /tmp/adamTestMvnQbVzgrO/FeatureDatasetFunctionsSuite4644967907528429146 /tmp/adamTestMvnQbVzgrO/TempSuite7106800478240110402 /tmp/adamTestMvnQbVzgrO/unordered.sam578033407149890561.sam /tmp/adamTestMvnQbVzgrO/TempSuite5714373589508743171_1.fq /tmp/adamTestMvnQbVzgrO/FeatureDatasetFunctionsSuite6584297791875846127 /tmp/adamTestMvnQbVzgrO/.FeatureDatasetFunctionsSuite4156659047445714912.gff3.crc /tmp/adamTestMvnQbVzgrO/random.vcf1048025916554839274.vcf /tmp/adamTestMvnQbVzgrO/FeatureDatasetFunctionsSuite4723251313709398414 /tmp/adamTestMvnQbVzgrO/TempSuite770941537254012369.adam /tmp/adamTestMvnQbVzgrO/TempSuite770941537254012369.adam/_readGroups.avro /tmp/adamTestMvnQbVzgrO/TempSuite770941537254012369.adam/._partitionedByStartPos.crc /tmp/adamTestMvnQbVzgrO/TempSuite770941537254012369.adam/_processingSteps.avro /tmp/adamTestMvnQbVzgrO/TempSuite770941537254012369.adam/._readGroups.avro.crc /tmp/adamTestMvnQbVzgrO/TempSuite770941537254012369.adam/_partitionedByStartPos /tmp/adamTestMvnQbVzgrO/TempSuite770941537254012369.adam/_SUCCESS /tmp/adamTestMvnQbVzgrO/TempSuite770941537254012369.adam/referenceName=2 /tmp/adamTestMvnQbVzgrO/TempSuite770941537254012369.adam/referenceName=2/positionBin=189 /tmp/adamTestMvnQbVzgrO/TempSuite770941537254012369.adam/referenceName=2/positionBin=189/part-00000-3c2d7c20-5cb5-4926-81a4-bc1fcc41ca35.c000.snappy.parquet /tmp/adamTestMvnQbVzgrO/TempSuite770941537254012369.adam/referenceName=2/positionBin=189/.part-00000-3c2d7c20-5cb5-4926-81a4-bc1fcc41ca35.c000.snappy.parquet.crc /tmp/adamTestMvnQbVzgrO/TempSuite770941537254012369.adam/._SUCCESS.crc /tmp/adamTestMvnQbVzgrO/TempSuite770941537254012369.adam/referenceName=1 /tmp/adamTestMvnQbVzgrO/TempSuite770941537254012369.adam/referenceName=1/positionBin=240 /tmp/adamTestMvnQbVzgrO/TempSuite770941537254012369.adam/referenceName=1/positionBin=240/part-00000-3c2d7c20-5cb5-4926-81a4-bc1fcc41ca35.c000.snappy.parquet /tmp/adamTestMvnQbVzgrO/TempSuite770941537254012369.adam/referenceName=1/positionBin=240/.part-00000-3c2d7c20-5cb5-4926-81a4-bc1fcc41ca35.c000.snappy.parquet.crc /tmp/adamTestMvnQbVzgrO/TempSuite770941537254012369.adam/referenceName=1/positionBin=26 /tmp/adamTestMvnQbVzgrO/TempSuite770941537254012369.adam/referenceName=1/positionBin=26/part-00000-3c2d7c20-5cb5-4926-81a4-bc1fcc41ca35.c000.snappy.parquet /tmp/adamTestMvnQbVzgrO/TempSuite770941537254012369.adam/referenceName=1/positionBin=26/.part-00000-3c2d7c20-5cb5-4926-81a4-bc1fcc41ca35.c000.snappy.parquet.crc /tmp/adamTestMvnQbVzgrO/TempSuite770941537254012369.adam/._processingSteps.avro.crc /tmp/adamTestMvnQbVzgrO/TempSuite770941537254012369.adam/._references.avro.crc /tmp/adamTestMvnQbVzgrO/TempSuite770941537254012369.adam/_references.avro /tmp/adamTestMvnQbVzgrO/TempSuite1476035104325550448.bed /tmp/adamTestMvnQbVzgrO/TempSuite1476035104325550448.bed/part-00000 /tmp/adamTestMvnQbVzgrO/TempSuite1476035104325550448.bed/_SUCCESS /tmp/adamTestMvnQbVzgrO/TempSuite1476035104325550448.bed/.part-00000.crc /tmp/adamTestMvnQbVzgrO/TempSuite1476035104325550448.bed/._SUCCESS.crc /tmp/adamTestMvnQbVzgrO/sample_coverage.bed3207650689984412012.bed /tmp/adamTestMvnQbVzgrO/FeatureDatasetFunctionsSuite6834444474436284625.bed /tmp/adamTestMvnQbVzgrO/FeatureDatasetFunctionsSuite6834444474436284625.bed/part-00002 /tmp/adamTestMvnQbVzgrO/FeatureDatasetFunctionsSuite6834444474436284625.bed/.part-00003.crc /tmp/adamTestMvnQbVzgrO/FeatureDatasetFunctionsSuite6834444474436284625.bed/part-00000 /tmp/adamTestMvnQbVzgrO/FeatureDatasetFunctionsSuite6834444474436284625.bed/part-00003 /tmp/adamTestMvnQbVzgrO/FeatureDatasetFunctionsSuite6834444474436284625.bed/.part-00002.crc /tmp/adamTestMvnQbVzgrO/FeatureDatasetFunctionsSuite6834444474436284625.bed/_SUCCESS /tmp/adamTestMvnQbVzgrO/FeatureDatasetFunctionsSuite6834444474436284625.bed/part-00001 /tmp/adamTestMvnQbVzgrO/FeatureDatasetFunctionsSuite6834444474436284625.bed/.part-00000.crc /tmp/adamTestMvnQbVzgrO/FeatureDatasetFunctionsSuite6834444474436284625.bed/._SUCCESS.crc /tmp/adamTestMvnQbVzgrO/FeatureDatasetFunctionsSuite6834444474436284625.bed/.part-00001.crc /tmp/adamTestMvnQbVzgrO/3820911679929040629 /tmp/adamTestMvnQbVzgrO/3820911679929040629/.ordered.sam.crc /tmp/adamTestMvnQbVzgrO/3820911679929040629/ordered.sam /tmp/adamTestMvnQbVzgrO/TempSuite6300031002677451127.adam /tmp/adamTestMvnQbVzgrO/TempSuite6300031002677451127.adam/_readGroups.avro /tmp/adamTestMvnQbVzgrO/TempSuite6300031002677451127.adam/_processingSteps.avro /tmp/adamTestMvnQbVzgrO/TempSuite6300031002677451127.adam/._readGroups.avro.crc /tmp/adamTestMvnQbVzgrO/TempSuite6300031002677451127.adam/_SUCCESS /tmp/adamTestMvnQbVzgrO/TempSuite6300031002677451127.adam/.part-00000-e7e44d3a-6391-4224-aca9-f3a273cb85f0-c000.snappy.parquet.crc /tmp/adamTestMvnQbVzgrO/TempSuite6300031002677451127.adam/._SUCCESS.crc /tmp/adamTestMvnQbVzgrO/TempSuite6300031002677451127.adam/part-00000-e7e44d3a-6391-4224-aca9-f3a273cb85f0-c000.snappy.parquet /tmp/adamTestMvnQbVzgrO/TempSuite6300031002677451127.adam/._processingSteps.avro.crc /tmp/adamTestMvnQbVzgrO/TempSuite6300031002677451127.adam/._references.avro.crc /tmp/adamTestMvnQbVzgrO/TempSuite6300031002677451127.adam/_references.avro /tmp/adamTestMvnQbVzgrO/TempSuite7182782788744585369 /tmp/adamTestMvnQbVzgrO/FeatureDatasetFunctionsSuite3035275374773859525 /tmp/adamTestMvnQbVzgrO/TempSuite6785585371244686151.sam /tmp/adamTestMvnQbVzgrO/TempSuite6785585371244686151.sam/part-r-00000.sam /tmp/adamTestMvnQbVzgrO/TempSuite6785585371244686151.sam/_SUCCESS /tmp/adamTestMvnQbVzgrO/TempSuite6785585371244686151.sam/._SUCCESS.crc /tmp/adamTestMvnQbVzgrO/TempSuite6785585371244686151.sam/.part-r-00000.sam.crc /tmp/adamTestMvnQbVzgrO/TempSuite5478182647121096823 /tmp/adamTestMvnQbVzgrO/TempSuite7017420737392587110.sam /tmp/adamTestMvnQbVzgrO/TempSuite7017420737392587110.sam/part-r-00000.sam /tmp/adamTestMvnQbVzgrO/TempSuite7017420737392587110.sam/_SUCCESS 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/tmp/adamTestMvnQbVzgrO/1767586396612596504/out.cram_tail/part-r-00001.cram /tmp/adamTestMvnQbVzgrO/1767586396612596504/out.cram_tail/part-r-00000.cram /tmp/adamTestMvnQbVzgrO/1767586396612596504/out.cram_tail/._SUCCESS.crc /tmp/adamTestMvnQbVzgrO/1767586396612596504/out.cram_tail/.part-r-00003.cram.crc /tmp/adamTestMvnQbVzgrO/1767586396612596504/out.cram_tail/part-r-00002.cram /tmp/adamTestMvnQbVzgrO/1767586396612596504/out.cram_head /tmp/adamTestMvnQbVzgrO/1767586396612596504/.out.cram.crc rm -rf ${ADAM_MVN_TMP_DIR} + rm -rf /tmp/adamTestMvnQbVzgrO find . -name pom.xml \ -exec sed -i.bak \ -e "s:sun.io.serialization.extendedDebugInfo=true -Djava.io.tmpdir=${ADAM_MVN_TMP_DIR}:sun.io.serialization.extendedDebugInfo=true:g" \ {} \; + find . -name pom.xml -exec sed -i.bak -e 's:sun.io.serialization.extendedDebugInfo=true -Djava.io.tmpdir=/tmp/adamTestMvnQbVzgrO:sun.io.serialization.extendedDebugInfo=true:g' '{}' ';' find . -name "*.bak" -exec rm -f {} \; + find . -name '*.bak' -exec rm -f '{}' ';' if test -n "$(git status --porcelain)" then echo "Applying move_to_xyz script marred a pom.xml file." echo "Exiting..." exit 1 fi git status --porcelain ++ git status --porcelain + test -n '' # run integration tests # make a temp directory ADAM_TMP_DIR=$(mktemp -d -t adamTestXXXXXXX) mktemp -d -t adamTestXXXXXXX ++ mktemp -d -t adamTestXXXXXXX + ADAM_TMP_DIR=/tmp/adamTestyHk1zRx # Just to be paranoid.. use a directory internal to the ADAM_TMP_DIR ADAM_TMP_DIR=$ADAM_TMP_DIR/deleteMePleaseThisIsNoLongerNeeded + ADAM_TMP_DIR=/tmp/adamTestyHk1zRx/deleteMePleaseThisIsNoLongerNeeded mkdir $ADAM_TMP_DIR + mkdir /tmp/adamTestyHk1zRx/deleteMePleaseThisIsNoLongerNeeded # set the TMPDIR envar, which is used by python to choose where to make temp directories export TMPDIR=${ADAM_TMP_DIR} + export TMPDIR=/tmp/adamTestyHk1zRx/deleteMePleaseThisIsNoLongerNeeded + TMPDIR=/tmp/adamTestyHk1zRx/deleteMePleaseThisIsNoLongerNeeded pushd $PROJECT_ROOT + pushd /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu/scripts/.. ~/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu ~/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu # Copy the jar into our temp space for testing cp -r . $ADAM_TMP_DIR + cp -r . /tmp/adamTestyHk1zRx/deleteMePleaseThisIsNoLongerNeeded popd + popd ~/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu pushd $ADAM_TMP_DIR + pushd /tmp/adamTestyHk1zRx/deleteMePleaseThisIsNoLongerNeeded /tmp/adamTestyHk1zRx/deleteMePleaseThisIsNoLongerNeeded ~/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.3/label/ubuntu # what hadoop version are we on? format string for downloading spark assembly if [[ $HADOOP_VERSION =~ ^2\.6 ]]; then HADOOP=hadoop2.6 elif [[ $HADOOP_VERSION =~ ^2\.7 ]]; then HADOOP=hadoop2.7 else echo "Unknown Hadoop version." exit 1 fi + [[ 2.7.5 =~ ^2\.6 ]] + [[ 2.7.5 =~ ^2\.7 ]] + HADOOP=hadoop2.7 # set spark artifact string for downloading assembly SPARK=spark-${SPARK_VERSION} + SPARK=spark-2.4.3 # download prepackaged spark assembly curl \ -L "https://www.apache.org/dyn/mirrors/mirrors.cgi?action=download&filename=spark/${SPARK}/${SPARK}-bin-${HADOOP}.tgz" \ -o ${SPARK}-bin-${HADOOP}.tgz + curl -L 'https://www.apache.org/dyn/mirrors/mirrors.cgi?action=download&filename=spark/spark-2.4.3/spark-2.4.3-bin-hadoop2.7.tgz' -o spark-2.4.3-bin-hadoop2.7.tgz % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 0 219M 0 14213 0 0 14544 0 4:23:33 --:--:-- 4:23:33 14544 0 219M 0 1096k 0 0 566k 0 0:06:36 0:00:01 0:06:35 1127k 1 219M 1 2686k 0 0 914k 0 0:04:05 0:00:02 0:04:03 1362k 1 219M 1 4298k 0 0 1090k 0 0:03:25 0:00:03 0:03:22 1445k 2 219M 2 5918k 0 0 1198k 0 0:03:07 0:00:04 0:03:03 1489k 3 219M 3 7514k 0 0 1265k 0 0:02:57 0:00:05 0:02:52 1511k 4 219M 4 9125k 0 0 1315k 0 0:02:50 0:00:06 0:02:44 1605k 4 219M 4 10.4M 0 0 1352k 0 0:02:46 0:00:07 0:02:39 1610k 5 219M 5 12.0M 0 0 1377k 0 0:02:43 0:00:08 0:02:35 1604k 6 219M 6 13.6M 0 0 1402k 0 0:02:40 0:00:09 0:02:31 1604k 6 219M 6 15.1M 0 0 1421k 0 0:02:37 0:00:10 0:02:27 1608k 7 219M 7 16.7M 0 0 1438k 0 0:02:36 0:00:11 0:02:25 1608k 8 219M 8 18.3M 0 0 1451k 0 0:02:34 0:00:12 0:02:22 1609k 9 219M 9 19.9M 0 0 1462k 0 0:02:33 0:00:13 0:02:20 1613k 9 219M 9 21.4M 0 0 1471k 0 0:02:32 0:00:14 0:02:18 1607k 10 219M 10 23.0M 0 0 1480k 0 0:02:31 0:00:15 0:02:16 1608k 11 219M 11 24.4M 0 0 1476k 0 0:02:32 0:00:16 0:02:16 1567k 11 219M 11 25.8M 0 0 1478k 0 0:02:31 0:00:17 0:02:14 1545k 12 219M 12 27.1M 0 0 1468k 0 0:02:32 0:00:18 0:02:14 1486k 12 219M 12 27.9M 0 0 1397k 0 0:02:40 0:00:20 0:02:20 1198k 13 219M 13 29.1M 0 0 1423k 0 0:02:37 0:00:20 0:02:17 1242k 13 219M 13 30.4M 0 0 1422k 0 0:02:37 0:00:21 0:02:16 1240k 14 219M 14 31.9M 0 0 1424k 0 0:02:37 0:00:22 0:02:15 1231k 15 219M 15 33.2M 0 0 1423k 0 0:02:37 0:00:23 0:02:14 1251k 15 219M 15 34.6M 0 0 1422k 0 0:02:37 0:00:24 0:02:13 1540k 16 219M 16 36.0M 0 0 1421k 0 0:02:38 0:00:25 0:02:13 1411k 17 219M 17 37.4M 0 0 1421k 0 0:02:37 0:00:26 0:02:11 1418k 17 219M 17 38.7M 0 0 1421k 0 0:02:37 0:00:27 0:02:10 1410k 18 219M 18 40.1M 0 0 1422k 0 0:02:37 0:00:28 0:02:09 1415k 18 219M 18 41.5M 0 0 1422k 0 0:02:37 0:00:29 0:02:08 1419k 19 219M 19 42.9M 0 0 1422k 0 0:02:37 0:00:30 0:02:07 1430k 20 219M 20 44.4M 0 0 1425k 0 0:02:37 0:00:31 0:02:06 1445k 20 219M 20 45.8M 0 0 1426k 0 0:02:37 0:00:32 0:02:05 1453k 21 219M 21 47.2M 0 0 1425k 0 0:02:37 0:00:33 0:02:04 1446k 22 219M 22 48.8M 0 0 1431k 0 0:02:36 0:00:34 0:02:02 1487k 22 219M 22 50.4M 0 0 1436k 0 0:02:36 0:00:35 0:02:01 1519k 23 219M 23 51.8M 0 0 1438k 0 0:02:36 0:00:36 0:02:00 1522k 24 219M 24 53.2M 0 0 1437k 0 0:02:36 0:00:37 0:01:59 1506k 24 219M 24 54.6M 0 0 1436k 0 0:02:36 0:00:38 0:01:58 1507k 25 219M 25 56.1M 0 0 1440k 0 0:02:35 0:00:39 0:01:56 1499k 26 219M 26 57.7M 0 0 1444k 0 0:02:35 0:00:40 0:01:55 1503k 27 219M 27 59.2M 0 0 1447k 0 0:02:35 0:00:41 0:01:54 1510k 27 219M 27 60.8M 0 0 1451k 0 0:02:34 0:00:42 0:01:52 1557k 28 219M 28 62.4M 0 0 1455k 0 0:02:34 0:00:43 0:01:51 1603k 29 219M 29 64.0M 0 0 1458k 0 0:02:33 0:00:44 0:01:49 1608k 29 219M 29 65.5M 0 0 1460k 0 0:02:33 0:00:45 0:01:48 1593k 30 219M 30 66.8M 0 0 1458k 0 0:02:33 0:00:46 0:01:47 1558k 31 219M 31 68.0M 0 0 1453k 0 0:02:34 0:00:47 0:01:47 1471k 31 219M 31 69.4M 0 0 1451k 0 0:02:34 0:00:48 0:01:46 1422k 32 219M 32 70.7M 0 0 1450k 0 0:02:34 0:00:49 0:01:45 1377k 32 219M 32 71.9M 0 0 1445k 0 0:02:35 0:00:50 0:01:45 1306k 33 219M 33 73.1M 0 0 1442k 0 0:02:35 0:00:51 0:01:44 1289k 33 219M 33 74.5M 0 0 1441k 0 0:02:35 0:00:52 0:01:43 1323k 34 219M 34 75.5M 0 0 1434k 0 0:02:36 0:00:53 0:01:43 1268k 35 219M 35 77.1M 0 0 1437k 0 0:02:36 0:00:54 0:01:42 1311k 35 219M 35 78.7M 0 0 1440k 0 0:02:35 0:00:55 0:01:40 1392k 36 219M 36 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spark-2.4.3-bin-hadoop2.7/ spark-2.4.3-bin-hadoop2.7/python/ spark-2.4.3-bin-hadoop2.7/python/setup.cfg spark-2.4.3-bin-hadoop2.7/python/pyspark/ spark-2.4.3-bin-hadoop2.7/python/pyspark/resultiterable.py spark-2.4.3-bin-hadoop2.7/python/pyspark/python/ spark-2.4.3-bin-hadoop2.7/python/pyspark/python/pyspark/ spark-2.4.3-bin-hadoop2.7/python/pyspark/python/pyspark/shell.py spark-2.4.3-bin-hadoop2.7/python/pyspark/heapq3.py spark-2.4.3-bin-hadoop2.7/python/pyspark/join.py spark-2.4.3-bin-hadoop2.7/python/pyspark/version.py spark-2.4.3-bin-hadoop2.7/python/pyspark/rdd.py spark-2.4.3-bin-hadoop2.7/python/pyspark/java_gateway.py spark-2.4.3-bin-hadoop2.7/python/pyspark/find_spark_home.py spark-2.4.3-bin-hadoop2.7/python/pyspark/_globals.py spark-2.4.3-bin-hadoop2.7/python/pyspark/worker.py spark-2.4.3-bin-hadoop2.7/python/pyspark/accumulators.py spark-2.4.3-bin-hadoop2.7/python/pyspark/mllib/ spark-2.4.3-bin-hadoop2.7/python/pyspark/mllib/feature.py spark-2.4.3-bin-hadoop2.7/python/pyspark/mllib/random.py spark-2.4.3-bin-hadoop2.7/python/pyspark/mllib/recommendation.py spark-2.4.3-bin-hadoop2.7/python/pyspark/mllib/fpm.py spark-2.4.3-bin-hadoop2.7/python/pyspark/mllib/classification.py spark-2.4.3-bin-hadoop2.7/python/pyspark/mllib/stat/ spark-2.4.3-bin-hadoop2.7/python/pyspark/mllib/stat/KernelDensity.py spark-2.4.3-bin-hadoop2.7/python/pyspark/mllib/stat/distribution.py spark-2.4.3-bin-hadoop2.7/python/pyspark/mllib/stat/test.py spark-2.4.3-bin-hadoop2.7/python/pyspark/mllib/stat/_statistics.py spark-2.4.3-bin-hadoop2.7/python/pyspark/mllib/stat/__init__.py spark-2.4.3-bin-hadoop2.7/python/pyspark/mllib/util.py spark-2.4.3-bin-hadoop2.7/python/pyspark/mllib/regression.py spark-2.4.3-bin-hadoop2.7/python/pyspark/mllib/clustering.py spark-2.4.3-bin-hadoop2.7/python/pyspark/mllib/linalg/ spark-2.4.3-bin-hadoop2.7/python/pyspark/mllib/linalg/distributed.py spark-2.4.3-bin-hadoop2.7/python/pyspark/mllib/linalg/__init__.py spark-2.4.3-bin-hadoop2.7/python/pyspark/mllib/tree.py spark-2.4.3-bin-hadoop2.7/python/pyspark/mllib/__init__.py spark-2.4.3-bin-hadoop2.7/python/pyspark/mllib/evaluation.py spark-2.4.3-bin-hadoop2.7/python/pyspark/mllib/common.py spark-2.4.3-bin-hadoop2.7/python/pyspark/mllib/tests.py spark-2.4.3-bin-hadoop2.7/python/pyspark/util.py spark-2.4.3-bin-hadoop2.7/python/pyspark/test_broadcast.py spark-2.4.3-bin-hadoop2.7/python/pyspark/shell.py spark-2.4.3-bin-hadoop2.7/python/pyspark/ml/ spark-2.4.3-bin-hadoop2.7/python/pyspark/ml/feature.py spark-2.4.3-bin-hadoop2.7/python/pyspark/ml/recommendation.py spark-2.4.3-bin-hadoop2.7/python/pyspark/ml/fpm.py spark-2.4.3-bin-hadoop2.7/python/pyspark/ml/classification.py spark-2.4.3-bin-hadoop2.7/python/pyspark/ml/stat.py spark-2.4.3-bin-hadoop2.7/python/pyspark/ml/util.py spark-2.4.3-bin-hadoop2.7/python/pyspark/ml/tuning.py spark-2.4.3-bin-hadoop2.7/python/pyspark/ml/regression.py spark-2.4.3-bin-hadoop2.7/python/pyspark/ml/base.py spark-2.4.3-bin-hadoop2.7/python/pyspark/ml/clustering.py spark-2.4.3-bin-hadoop2.7/python/pyspark/ml/wrapper.py spark-2.4.3-bin-hadoop2.7/python/pyspark/ml/pipeline.py spark-2.4.3-bin-hadoop2.7/python/pyspark/ml/linalg/ spark-2.4.3-bin-hadoop2.7/python/pyspark/ml/linalg/__init__.py spark-2.4.3-bin-hadoop2.7/python/pyspark/ml/param/ spark-2.4.3-bin-hadoop2.7/python/pyspark/ml/param/_shared_params_code_gen.py spark-2.4.3-bin-hadoop2.7/python/pyspark/ml/param/shared.py spark-2.4.3-bin-hadoop2.7/python/pyspark/ml/param/__init__.py spark-2.4.3-bin-hadoop2.7/python/pyspark/ml/__init__.py spark-2.4.3-bin-hadoop2.7/python/pyspark/ml/evaluation.py spark-2.4.3-bin-hadoop2.7/python/pyspark/ml/common.py spark-2.4.3-bin-hadoop2.7/python/pyspark/ml/tests.py spark-2.4.3-bin-hadoop2.7/python/pyspark/ml/image.py spark-2.4.3-bin-hadoop2.7/python/pyspark/test_serializers.py spark-2.4.3-bin-hadoop2.7/python/pyspark/cloudpickle.py spark-2.4.3-bin-hadoop2.7/python/pyspark/serializers.py spark-2.4.3-bin-hadoop2.7/python/pyspark/daemon.py spark-2.4.3-bin-hadoop2.7/python/pyspark/files.py spark-2.4.3-bin-hadoop2.7/python/pyspark/rddsampler.py spark-2.4.3-bin-hadoop2.7/python/pyspark/statcounter.py spark-2.4.3-bin-hadoop2.7/python/pyspark/streaming/ spark-2.4.3-bin-hadoop2.7/python/pyspark/streaming/kafka.py spark-2.4.3-bin-hadoop2.7/python/pyspark/streaming/util.py spark-2.4.3-bin-hadoop2.7/python/pyspark/streaming/kinesis.py spark-2.4.3-bin-hadoop2.7/python/pyspark/streaming/flume.py spark-2.4.3-bin-hadoop2.7/python/pyspark/streaming/__init__.py spark-2.4.3-bin-hadoop2.7/python/pyspark/streaming/context.py spark-2.4.3-bin-hadoop2.7/python/pyspark/streaming/tests.py spark-2.4.3-bin-hadoop2.7/python/pyspark/streaming/dstream.py spark-2.4.3-bin-hadoop2.7/python/pyspark/streaming/listener.py spark-2.4.3-bin-hadoop2.7/python/pyspark/taskcontext.py spark-2.4.3-bin-hadoop2.7/python/pyspark/__init__.py spark-2.4.3-bin-hadoop2.7/python/pyspark/storagelevel.py spark-2.4.3-bin-hadoop2.7/python/pyspark/broadcast.py spark-2.4.3-bin-hadoop2.7/python/pyspark/profiler.py spark-2.4.3-bin-hadoop2.7/python/pyspark/traceback_utils.py spark-2.4.3-bin-hadoop2.7/python/pyspark/context.py spark-2.4.3-bin-hadoop2.7/python/pyspark/status.py spark-2.4.3-bin-hadoop2.7/python/pyspark/sql/ spark-2.4.3-bin-hadoop2.7/python/pyspark/sql/streaming.py spark-2.4.3-bin-hadoop2.7/python/pyspark/sql/readwriter.py spark-2.4.3-bin-hadoop2.7/python/pyspark/sql/catalog.py spark-2.4.3-bin-hadoop2.7/python/pyspark/sql/session.py spark-2.4.3-bin-hadoop2.7/python/pyspark/sql/column.py spark-2.4.3-bin-hadoop2.7/python/pyspark/sql/functions.py spark-2.4.3-bin-hadoop2.7/python/pyspark/sql/dataframe.py spark-2.4.3-bin-hadoop2.7/python/pyspark/sql/window.py spark-2.4.3-bin-hadoop2.7/python/pyspark/sql/udf.py spark-2.4.3-bin-hadoop2.7/python/pyspark/sql/__init__.py spark-2.4.3-bin-hadoop2.7/python/pyspark/sql/utils.py spark-2.4.3-bin-hadoop2.7/python/pyspark/sql/group.py 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