Started by upstream project "ADAM-prb" build number 3139 originally caused by: GitHub pull request #2282 of commit e6332ef5bac0dc6ce37cb840631c62f3e67a8351, no merge conflicts. Running as SYSTEM [EnvInject] - Loading node environment variables. Building remotely on research-jenkins-worker-01 (ubuntu) in workspace /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu The recommended git tool is: NONE No credentials specified 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/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu # timeout=10 Using reference repository: /home/jenkins/gitcaches/adam.reference Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git --version # timeout=10 > git --version # 'git version 2.25.1' > git fetch --tags --force --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 --force --progress -- https://github.com/bigdatagenomics/adam.git +refs/pull/*:refs/remotes/origin/pr/* # timeout=15 Checking out Revision e6332ef5bac0dc6ce37cb840631c62f3e67a8351 (detached) > git config core.sparsecheckout # timeout=10 > git checkout -f e6332ef5bac0dc6ce37cb840631c62f3e67a8351 # timeout=10 Commit message: "code format fix" > git rev-list --no-walk e6332ef5bac0dc6ce37cb840631c62f3e67a8351 # timeout=10 [ubuntu] $ /bin/bash /tmp/jenkins7631094594909921273.sh + set -e + unset SPARK_TESTING + export JAVA_HOME=/usr/java/latest + JAVA_HOME=/usr/java/latest + export CONDA_BIN=/home/anaconda/bin/ + CONDA_BIN=/home/anaconda/bin/ + export PATH=/usr/java/latest/bin/:/home/anaconda/bin/:/home/jenkins/tools/hudson.tasks.Maven_MavenInstallation/Maven_3.6.3/bin/:/home/jenkins/gems/bin:/usr/local/go/bin:/home/jenkins/go-projects/bin:/home/jenkins/anaconda2/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin + PATH=/usr/java/latest/bin/:/home/anaconda/bin/:/home/jenkins/tools/hudson.tasks.Maven_MavenInstallation/Maven_3.6.3/bin/:/home/jenkins/gems/bin:/usr/local/go/bin:/home/jenkins/go-projects/bin:/home/jenkins/anaconda2/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin + set +x + /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/scripts/jenkins-test # make a tempdir for writing maven cruft to ADAM_MVN_TMP_DIR=$(mktemp -d -t adamTestMvnXXXXXXX) ++ mktemp -d -t adamTestMvnXXXXXXX + ADAM_MVN_TMP_DIR=/tmp/adamTestMvncIb5npe # add this tempdir to the poms... find . -name pom.xml \ -exec sed -i.bak \ -e "s:sun.io.serialization.extendedDebugInfo=true:sun.io.serialization.extendedDebugInfo=true -Djava.io.tmpdir=${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/adamTestMvncIb5npe:g' '{}' ';' find . -name "*.bak" -exec rm -f {} \; + find . -name '*.bak' -exec rm -f '{}' ';' # variable declarations export PATH=${JAVA_HOME}/bin/:${PATH} + export PATH=/usr/java/latest/bin/:/usr/java/latest/bin/:/home/anaconda/bin/:/home/jenkins/tools/hudson.tasks.Maven_MavenInstallation/Maven_3.6.3/bin/:/home/jenkins/gems/bin:/usr/local/go/bin:/home/jenkins/go-projects/bin:/home/jenkins/anaconda2/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin + PATH=/usr/java/latest/bin/:/usr/java/latest/bin/:/home/anaconda/bin/:/home/jenkins/tools/hudson.tasks.Maven_MavenInstallation/Maven_3.6.3/bin/:/home/jenkins/gems/bin:/usr/local/go/bin:/home/jenkins/go-projects/bin:/home/jenkins/anaconda2/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin export MAVEN_OPTS="-Xmx1536m -XX:MaxPermSize=1g -Dfile.encoding=utf-8" + export 'MAVEN_OPTS=-Xmx1536m -XX:MaxPermSize=1g -Dfile.encoding=utf-8' + MAVEN_OPTS='-Xmx1536m -XX:MaxPermSize=1g -Dfile.encoding=utf-8' DIR=$( cd $( dirname ${BASH_SOURCE[0]} ) && pwd ) +++ dirname /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/scripts/jenkins-test ++ cd /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/scripts ++ pwd + DIR=/home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/scripts PROJECT_ROOT=${DIR}/.. + PROJECT_ROOT=/home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/scripts/.. VERSION=$(grep "" ${PROJECT_ROOT}/pom.xml | head -2 | tail -1 | sed 's/ *//g' | sed 's/<\/version>//g') ++ grep '' /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/scripts/../pom.xml ++ head -2 ++ tail -1 ++ sed 's/ *//g' ++ sed 's/<\/version>//g' + VERSION=0.33.0-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 3.0.1 ]] set -e + set -e # move to Scala 2.11 if requested if [ ${SCALA_VERSION} == 2.11 ]; then set +e ./scripts/move_to_scala_2.11.sh set -e fi + '[' 2.12 == 2.11 ']' # move to Scala 2.12 if requested if [ ${SCALA_VERSION} == 2.12 ]; then set +e ./scripts/move_to_scala_2.12.sh set -e fi + '[' 2.12 == 2.12 ']' + set +e + ./scripts/move_to_scala_2.12.sh Scala version is already set to 2.12 (Scala artifacts have _2.12 version suffix in artifact name). Cowardly refusing to move to Scala 2.12 a second time... + set -e # move to Spark 2.x if requested if [ ${SPARK_VERSION} == 2.4.7 ]; then set +e ./scripts/move_to_spark_2.sh set -e fi + '[' 3.0.1 == 2.4.7 ']' # move to Spark 3.x if requested if [ ${SPARK_VERSION} == 3.0.1 ]; then set +e ./scripts/move_to_spark_3.sh set -e fi + '[' 3.0.1 == 3.0.1 ']' + set +e + ./scripts/move_to_spark_3.sh POM is already set up for Spark 3 (Spark 3 artifacts have -spark3 suffix in artifact names). Cowardly refusing to move to Spark 3 a second time... + set -e # print versions echo "Testing ADAM version ${VERSION} on Spark ${SPARK_VERSION} and Hadoop ${HADOOP_VERSION}" + echo 'Testing ADAM version 0.33.0-SNAPSHOT on Spark 3.0.1 and Hadoop 2.7.5' Testing ADAM version 0.33.0-SNAPSHOT on Spark 3.0.1 and Hadoop 2.7.5 # first, build the sources, run the unit tests, and generate a coverage report mvn clean \ -Dhadoop.version=${HADOOP_VERSION} + mvn clean -Dhadoop.version=2.7.5 OpenJDK 64-Bit Server VM warning: ignoring option MaxPermSize=1g; support was removed in 8.0 [INFO] Scanning for projects... 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.......................................... SUCCESS [ 0.588 s] [INFO] ADAM_2.12: Shader workaround ....................... SUCCESS [ 0.066 s] [INFO] ADAM_2.12: Avro-to-Dataset codegen utils ........... SUCCESS [ 0.023 s] [INFO] ADAM_2.12: Core .................................... SUCCESS [ 0.054 s] [INFO] ADAM_2.12: APIs for Java, Python ................... SUCCESS [ 0.002 s] [INFO] ADAM_2.12: CLI ..................................... SUCCESS [ 0.197 s] [INFO] ADAM_2.12: Assembly ................................ SUCCESS [ 0.002 s] [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ [INFO] Total time: 1.666 s [INFO] Finished at: 2020-12-02T19:17:47-08:00 [INFO] ------------------------------------------------------------------------ # if this is a pull request, we need to set the coveralls pr id if [[ ! -z $ghprbPullId ]]; then COVERALLS_PRB_OPTION="-DpullRequest=${ghprbPullId}" fi + [[ ! -z 2282 ]] + COVERALLS_PRB_OPTION=-DpullRequest=2282 # coveralls token should not be visible set +x +v + set +x +v OpenJDK 64-Bit Server VM warning: ignoring option MaxPermSize=1g; support was removed in 8.0 [INFO] Scanning for projects... [INFO] ------------------------------------------------------------------------ [INFO] Reactor Build Order: [INFO] [INFO] ADAM_2.12 [pom] [INFO] ADAM_2.12: Shader workaround [jar] [INFO] ADAM_2.12: Avro-to-Dataset codegen utils [jar] [INFO] ADAM_2.12: Core [jar] [INFO] ADAM_2.12: APIs for Java, Python [jar] [INFO] ADAM_2.12: CLI [jar] [INFO] ADAM_2.12: Assembly [jar] Downloading from central: https://repo.maven.apache.org/maven2/net/alchim31/maven/scala-maven-plugin/3.2.2/scala-maven-plugin-3.2.2.pom Downloaded from central: https://repo.maven.apache.org/maven2/net/alchim31/maven/scala-maven-plugin/3.2.2/scala-maven-plugin-3.2.2.pom (0 B at 0 B/s) Downloading from central: https://repo.maven.apache.org/maven2/net/alchim31/maven/scala-maven-plugin/3.2.2/scala-maven-plugin-3.2.2.jar Downloaded from central: https://repo.maven.apache.org/maven2/net/alchim31/maven/scala-maven-plugin/3.2.2/scala-maven-plugin-3.2.2.jar (0 B at 0 B/s) Downloading from central: 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2.7/37 kB Progress (4): 30/160 kB | 14 kB | 27/30 kB | 2.7/37 kB Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/maven/maven-error-diagnostics/2.0.9/maven-error-diagnostics-2.0.9.jar (14 kB at 300 kB/s) Progress (3): 30/160 kB | 30 kB | 2.7/37 kB Progress (3): 33/160 kB | 30 kB | 2.7/37 kB Progress (3): 33/160 kB | 30 kB | 5.5/37 kB Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/maven-monitor/2.0.9/maven-monitor-2.0.9.jar Progress (3): 33/160 kB | 30 kB | 8.2/37 kB Progress (3): 36/160 kB | 30 kB | 8.2/37 kB Downloaded from central: https://repo.maven.apache.org/maven2/org/codehaus/plexus/plexus-interactivity-api/1.0-alpha-4/plexus-interactivity-api-1.0-alpha-4.jar (0 B at 0 B/s) Progress (3): 38/160 kB | 30 kB | 8.2/37 kB Progress (3): 38/160 kB | 30 kB | 11/37 kB Downloading from central: https://repo.maven.apache.org/maven2/classworlds/classworlds/1.1/classworlds-1.1.jar Progress (3): 38/160 kB | 30 kB | 14/37 kB Progress (3): 41/160 kB | 30 kB | 14/37 kB Progress (3): 41/160 kB | 30 kB | 16/37 kB Progress (3): 44/160 kB | 30 kB | 16/37 kB Progress (3): 44/160 kB | 30 kB | 19/37 kB Progress (3): 47/160 kB | 30 kB | 19/37 kB Progress (3): 47/160 kB | 30 kB | 22/37 kB Progress (3): 49/160 kB | 30 kB | 22/37 kB Progress (3): 49/160 kB | 30 kB | 25/37 kB Progress (3): 52/160 kB | 30 kB | 25/37 kB Downloaded from central: https://repo.maven.apache.org/maven2/classworlds/classworlds/1.1/classworlds-1.1.jar (0 B at 0 B/s) Downloaded from central: https://repo.maven.apache.org/maven2/commons-cli/commons-cli/1.0/commons-cli-1.0.jar (30 kB at 568 kB/s) Progress (2): 55/160 kB | 25/37 kB Downloading from central: https://repo.maven.apache.org/maven2/org/codehaus/plexus/plexus-utils/1.5.8/plexus-utils-1.5.8.jar Progress (3): 55/160 kB | 25/37 kB | 2.7/10 kB Progress (3): 55/160 kB | 27/37 kB | 2.7/10 kB Progress (3): 58/160 kB | 27/37 kB | 2.7/10 kB Downloading from central: 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kB | 2.7/268 kB Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/enforcer/enforcer-api/1.0/enforcer-api-1.0.jar Progress (3): 85/160 kB | 37 kB | 5.5/268 kB Progress (3): 88/160 kB | 37 kB | 5.5/268 kB Progress (4): 88/160 kB | 37 kB | 5.5/268 kB | 4.1/245 kB Progress (4): 90/160 kB | 37 kB | 5.5/268 kB | 4.1/245 kB Progress (4): 90/160 kB | 37 kB | 8.2/268 kB | 4.1/245 kB Progress (4): 90/160 kB | 37 kB | 8.2/268 kB | 8.2/245 kB Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/maven/maven-plugin-descriptor/2.0.9/maven-plugin-descriptor-2.0.9.jar (37 kB at 597 kB/s) Progress (3): 90/160 kB | 11/268 kB | 8.2/245 kB Progress (3): 90/160 kB | 11/268 kB | 12/245 kB Progress (3): 93/160 kB | 11/268 kB | 12/245 kB Progress (3): 93/160 kB | 14/268 kB | 12/245 kB Progress (3): 93/160 kB | 14/268 kB | 16/245 kB Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/enforcer/enforcer-rules/1.0/enforcer-rules-1.0.jar Progress (3): 93/160 kB | 16/268 kB | 16/245 kB Progress (3): 96/160 kB | 16/268 kB | 16/245 kB Progress (3): 96/160 kB | 16/268 kB | 20/245 kB Progress (3): 96/160 kB | 16/268 kB | 25/245 kB Progress (3): 99/160 kB | 16/268 kB | 25/245 kB Progress (3): 99/160 kB | 19/268 kB | 25/245 kB Progress (3): 99/160 kB | 19/268 kB | 29/245 kB Progress (4): 99/160 kB | 19/268 kB | 29/245 kB | 2.7/9.8 kB Progress (4): 99/160 kB | 22/268 kB | 29/245 kB | 2.7/9.8 kB Progress (4): 99/160 kB | 22/268 kB | 33/245 kB | 2.7/9.8 kB Progress (4): 101/160 kB | 22/268 kB | 33/245 kB | 2.7/9.8 kB Progress (4): 101/160 kB | 25/268 kB | 33/245 kB | 2.7/9.8 kB Progress (4): 101/160 kB | 25/268 kB | 33/245 kB | 5.5/9.8 kB Progress (4): 101/160 kB | 25/268 kB | 37/245 kB | 5.5/9.8 kB Progress (4): 104/160 kB | 25/268 kB | 37/245 kB | 5.5/9.8 kB Progress (4): 104/160 kB | 25/268 kB | 41/245 kB | 5.5/9.8 kB Progress (4): 104/160 kB | 25/268 kB | 41/245 kB | 8.2/9.8 kB Progress (4): 104/160 kB | 27/268 kB | 41/245 kB | 8.2/9.8 kB Progress (4): 104/160 kB | 27/268 kB | 41/245 kB | 9.8 kB Progress (4): 107/160 kB | 27/268 kB | 41/245 kB | 9.8 kB Progress (4): 107/160 kB | 27/268 kB | 45/245 kB | 9.8 kB Progress (4): 107/160 kB | 30/268 kB | 45/245 kB | 9.8 kB Progress (4): 107/160 kB | 30/268 kB | 49/245 kB | 9.8 kB Progress (4): 110/160 kB | 30/268 kB | 49/245 kB | 9.8 kB Progress (4): 110/160 kB | 33/268 kB | 49/245 kB | 9.8 kB Progress (5): 110/160 kB | 33/268 kB | 49/245 kB | 9.8 kB | 2.7/61 kB Progress (5): 112/160 kB | 33/268 kB | 49/245 kB | 9.8 kB | 2.7/61 kB Progress (5): 112/160 kB | 33/268 kB | 53/245 kB | 9.8 kB | 2.7/61 kB Progress (5): 112/160 kB | 36/268 kB | 53/245 kB | 9.8 kB | 2.7/61 kB Progress (5): 112/160 kB | 36/268 kB | 57/245 kB | 9.8 kB | 2.7/61 kB Progress (5): 115/160 kB | 36/268 kB | 57/245 kB | 9.8 kB | 2.7/61 kB Progress (5): 115/160 kB | 36/268 kB | 57/245 kB | 9.8 kB | 5.5/61 kB Progress (5): 115/160 kB | 36/268 kB | 61/245 kB | 9.8 kB | 5.5/61 kB Progress (5): 115/160 kB | 38/268 kB | 61/245 kB | 9.8 kB | 5.5/61 kB Progress (5): 115/160 kB | 38/268 kB | 66/245 kB | 9.8 kB | 5.5/61 kB Progress (5): 115/160 kB | 38/268 kB | 66/245 kB | 9.8 kB | 8.2/61 kB Progress (5): 118/160 kB | 38/268 kB | 66/245 kB | 9.8 kB | 8.2/61 kB Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/maven/enforcer/enforcer-api/1.0/enforcer-api-1.0.jar (9.8 kB at 132 kB/s) Progress (4): 118/160 kB | 41/268 kB | 66/245 kB | 8.2/61 kB Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/shared/maven-common-artifact-filters/1.2/maven-common-artifact-filters-1.2.jar Progress (4): 121/160 kB | 41/268 kB | 66/245 kB | 8.2/61 kB Progress (4): 121/160 kB | 41/268 kB | 70/245 kB | 8.2/61 kB Progress (4): 121/160 kB | 41/268 kB | 70/245 kB | 11/61 kB Progress (4): 121/160 kB | 41/268 kB | 74/245 kB | 11/61 kB Progress (4): 123/160 kB | 41/268 kB | 74/245 kB | 11/61 kB Progress (4): 123/160 kB | 44/268 kB | 74/245 kB | 11/61 kB Progress (4): 123/160 kB | 44/268 kB | 78/245 kB | 11/61 kB Progress (4): 123/160 kB | 44/268 kB | 78/245 kB | 14/61 kB Progress (4): 123/160 kB | 47/268 kB | 78/245 kB | 14/61 kB Progress (4): 123/160 kB | 47/268 kB | 82/245 kB | 14/61 kB Progress (4): 126/160 kB | 47/268 kB | 82/245 kB | 14/61 kB Progress (4): 126/160 kB | 49/268 kB | 82/245 kB | 14/61 kB Progress (4): 129/160 kB | 49/268 kB | 82/245 kB | 14/61 kB Progress (4): 129/160 kB | 49/268 kB | 82/245 kB | 16/61 kB Progress (4): 129/160 kB | 52/268 kB | 82/245 kB | 16/61 kB Progress (4): 129/160 kB | 52/268 kB | 86/245 kB | 16/61 kB Progress (4): 129/160 kB | 52/268 kB | 86/245 kB | 19/61 kB Progress (4): 132/160 kB | 52/268 kB | 86/245 kB | 19/61 kB Progress (4): 132/160 kB | 55/268 kB | 86/245 kB | 19/61 kB Progress (4): 132/160 kB | 55/268 kB | 86/245 kB | 22/61 kB Progress (4): 132/160 kB | 55/268 kB | 90/245 kB | 22/61 kB Progress (4): 134/160 kB | 55/268 kB | 90/245 kB | 22/61 kB Progress (5): 134/160 kB | 55/268 kB | 90/245 kB | 22/61 kB | 2.7/32 kB Progress (5): 134/160 kB | 55/268 kB | 94/245 kB | 22/61 kB | 2.7/32 kB Progress (5): 134/160 kB | 55/268 kB | 94/245 kB | 25/61 kB | 2.7/32 kB Progress (5): 134/160 kB | 58/268 kB | 94/245 kB | 25/61 kB | 2.7/32 kB Progress (5): 134/160 kB | 58/268 kB | 94/245 kB | 27/61 kB | 2.7/32 kB Progress (5): 134/160 kB | 58/268 kB | 94/245 kB | 27/61 kB | 5.5/32 kB Progress (5): 134/160 kB | 58/268 kB | 98/245 kB | 27/61 kB | 5.5/32 kB Progress (5): 137/160 kB | 58/268 kB | 98/245 kB | 27/61 kB | 5.5/32 kB Progress (5): 137/160 kB | 58/268 kB | 98/245 kB | 27/61 kB | 8.2/32 kB Progress (5): 137/160 kB | 58/268 kB | 98/245 kB | 30/61 kB | 8.2/32 kB Progress (5): 137/160 kB | 60/268 kB | 98/245 kB | 30/61 kB | 8.2/32 kB Progress (5): 137/160 kB | 60/268 kB | 102/245 kB | 30/61 kB | 8.2/32 kB Progress (5): 137/160 kB | 60/268 kB | 102/245 kB | 30/61 kB | 11/32 kB Progress (5): 140/160 kB | 60/268 kB | 102/245 kB | 30/61 kB | 11/32 kB Progress (5): 140/160 kB | 60/268 kB | 106/245 kB | 30/61 kB | 11/32 kB Progress (5): 140/160 kB | 63/268 kB | 106/245 kB | 30/61 kB | 11/32 kB Progress (5): 140/160 kB | 63/268 kB | 106/245 kB | 33/61 kB | 11/32 kB Progress (5): 140/160 kB | 63/268 kB | 111/245 kB | 33/61 kB | 11/32 kB Progress (5): 143/160 kB | 63/268 kB | 111/245 kB | 33/61 kB | 11/32 kB Progress (5): 143/160 kB | 63/268 kB | 111/245 kB | 33/61 kB | 14/32 kB Progress (5): 143/160 kB | 63/268 kB | 115/245 kB | 33/61 kB | 14/32 kB Progress (5): 143/160 kB | 63/268 kB | 115/245 kB | 36/61 kB | 14/32 kB Progress (5): 143/160 kB | 66/268 kB | 115/245 kB | 36/61 kB | 14/32 kB Progress (5): 143/160 kB | 66/268 kB | 115/245 kB | 36/61 kB | 16/32 kB Progress (5): 145/160 kB | 66/268 kB | 115/245 kB | 36/61 kB | 16/32 kB Progress (5): 145/160 kB | 66/268 kB | 115/245 kB | 36/61 kB | 19/32 kB Progress (5): 145/160 kB | 66/268 kB | 119/245 kB | 36/61 kB | 19/32 kB Progress (5): 145/160 kB | 69/268 kB | 119/245 kB | 36/61 kB | 19/32 kB Progress (5): 145/160 kB | 69/268 kB | 119/245 kB | 38/61 kB | 19/32 kB Progress (5): 145/160 kB | 69/268 kB | 123/245 kB | 38/61 kB | 19/32 kB Progress (5): 145/160 kB | 69/268 kB | 123/245 kB | 41/61 kB | 19/32 kB Progress (5): 145/160 kB | 69/268 kB | 123/245 kB | 41/61 kB | 22/32 kB Progress (5): 148/160 kB | 69/268 kB | 123/245 kB | 41/61 kB | 22/32 kB Progress (5): 148/160 kB | 69/268 kB | 123/245 kB | 41/61 kB | 25/32 kB Progress (5): 148/160 kB | 69/268 kB | 123/245 kB | 44/61 kB | 25/32 kB Progress (5): 148/160 kB | 69/268 kB | 127/245 kB | 44/61 kB | 25/32 kB Progress (5): 148/160 kB | 71/268 kB | 127/245 kB | 44/61 kB | 25/32 kB Progress (5): 148/160 kB | 71/268 kB | 131/245 kB | 44/61 kB | 25/32 kB Progress (5): 148/160 kB | 71/268 kB | 131/245 kB | 47/61 kB | 25/32 kB Progress (5): 148/160 kB | 71/268 kB | 131/245 kB | 47/61 kB | 27/32 kB Progress (5): 151/160 kB | 71/268 kB | 131/245 kB | 47/61 kB | 27/32 kB Progress (5): 151/160 kB | 71/268 kB | 131/245 kB | 47/61 kB | 30/32 kB Progress (5): 151/160 kB | 71/268 kB | 135/245 kB | 47/61 kB | 30/32 kB Progress (5): 151/160 kB | 71/268 kB | 135/245 kB | 49/61 kB | 30/32 kB Progress (5): 151/160 kB | 74/268 kB | 135/245 kB | 49/61 kB | 30/32 kB Progress (5): 151/160 kB | 74/268 kB | 135/245 kB | 52/61 kB | 30/32 kB Progress (5): 151/160 kB | 74/268 kB | 139/245 kB | 52/61 kB | 30/32 kB Progress (5): 151/160 kB | 74/268 kB | 139/245 kB | 55/61 kB | 30/32 kB Progress (5): 151/160 kB | 74/268 kB | 139/245 kB | 55/61 kB | 32 kB Progress (5): 154/160 kB | 74/268 kB | 139/245 kB | 55/61 kB | 32 kB Progress (5): 154/160 kB | 74/268 kB | 139/245 kB | 58/61 kB | 32 kB Progress (5): 154/160 kB | 74/268 kB | 143/245 kB | 58/61 kB | 32 kB Progress (5): 154/160 kB | 77/268 kB | 143/245 kB | 58/61 kB | 32 kB Progress (5): 154/160 kB | 77/268 kB | 147/245 kB | 58/61 kB | 32 kB Progress (5): 154/160 kB | 77/268 kB | 147/245 kB | 60/61 kB | 32 kB Progress (5): 156/160 kB | 77/268 kB | 147/245 kB | 60/61 kB | 32 kB Progress (5): 156/160 kB | 77/268 kB | 147/245 kB | 61 kB | 32 kB Progress (5): 156/160 kB | 77/268 kB | 152/245 kB | 61 kB | 32 kB Progress (5): 156/160 kB | 80/268 kB | 152/245 kB | 61 kB | 32 kB Progress (5): 156/160 kB | 80/268 kB | 156/245 kB | 61 kB | 32 kB Progress (5): 159/160 kB | 80/268 kB | 156/245 kB | 61 kB | 32 kB Progress (5): 159/160 kB | 80/268 kB | 160/245 kB | 61 kB | 32 kB Progress (5): 159/160 kB | 82/268 kB | 160/245 kB | 61 kB | 32 kB Progress (5): 159/160 kB | 82/268 kB | 164/245 kB | 61 kB | 32 kB Progress (5): 160 kB | 82/268 kB | 164/245 kB | 61 kB | 32 kB Progress (5): 160 kB | 85/268 kB | 164/245 kB | 61 kB | 32 kB Progress (5): 160 kB | 85/268 kB | 168/245 kB | 61 kB | 32 kB Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/maven/shared/maven-common-artifact-filters/1.2/maven-common-artifact-filters-1.2.jar (32 kB at 316 kB/s) Progress (4): 160 kB | 88/268 kB | 168/245 kB | 61 kB Downloading from central: https://repo.maven.apache.org/maven2/org/beanshell/bsh/2.0b4/bsh-2.0b4.jar Progress (4): 160 kB | 88/268 kB | 172/245 kB | 61 kB Progress (4): 160 kB | 90/268 kB | 172/245 kB | 61 kB Progress (4): 160 kB | 90/268 kB | 176/245 kB | 61 kB Progress (4): 160 kB | 90/268 kB | 180/245 kB | 61 kB Progress (4): 160 kB | 93/268 kB | 180/245 kB | 61 kB Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/maven/enforcer/enforcer-rules/1.0/enforcer-rules-1.0.jar (61 kB at 598 kB/s) Progress (3): 160 kB | 96/268 kB | 180/245 kB Progress (3): 160 kB | 96/268 kB | 184/245 kB Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/shared/maven-dependency-tree/1.2/maven-dependency-tree-1.2.jar Progress (3): 160 kB | 99/268 kB | 184/245 kB Progress (3): 160 kB | 99/268 kB | 188/245 kB Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/maven/maven-core/2.0.9/maven-core-2.0.9.jar (160 kB at 1.5 MB/s) Progress (2): 101/268 kB | 188/245 kB 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[INFO] skip non existing resourceDirectory /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/adam-shade/src/main/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ adam-shade-spark3_2.12 --- [INFO] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/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/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/adam-shade/target/2.12.8/classes at 1606965484704 Downloading from central: https://repo.maven.apache.org/maven2/org/scala-lang/scala-compiler/2.12.8/scala-compiler-2.12.8.jar Downloaded from central: https://repo.maven.apache.org/maven2/org/scala-lang/scala-compiler/2.12.8/scala-compiler-2.12.8.jar (0 B at 0 B/s) Downloading from central: 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| 49/217 kB | 20/45 kB | 25/358 kB Progress (5): 33/46 kB | 45/134 kB | 49/217 kB | 20/45 kB | 25/358 kB Progress (5): 33/46 kB | 45/134 kB | 49/217 kB | 20/45 kB | 29/358 kB Progress (5): 33/46 kB | 45/134 kB | 49/217 kB | 25/45 kB | 29/358 kB Progress (5): 33/46 kB | 45/134 kB | 49/217 kB | 25/45 kB | 33/358 kB Progress (5): 33/46 kB | 49/134 kB | 49/217 kB | 25/45 kB | 33/358 kB Progress (5): 33/46 kB | 49/134 kB | 53/217 kB | 25/45 kB | 33/358 kB Progress (5): 37/46 kB | 49/134 kB | 53/217 kB | 25/45 kB | 33/358 kB Progress (5): 37/46 kB | 53/134 kB | 53/217 kB | 25/45 kB | 33/358 kB Progress (5): 37/46 kB | 53/134 kB | 57/217 kB | 25/45 kB | 33/358 kB Progress (5): 37/46 kB | 53/134 kB | 57/217 kB | 25/45 kB | 37/358 kB Progress (5): 37/46 kB | 53/134 kB | 57/217 kB | 29/45 kB | 37/358 kB Progress (5): 37/46 kB | 53/134 kB | 57/217 kB | 29/45 kB | 41/358 kB Progress (5): 37/46 kB | 53/134 kB | 61/217 kB | 29/45 kB | 41/358 kB Progress (5): 37/46 kB | 57/134 kB | 61/217 kB | 29/45 kB | 41/358 kB Progress (5): 41/46 kB | 57/134 kB | 61/217 kB | 29/45 kB | 41/358 kB Progress (5): 41/46 kB | 61/134 kB | 61/217 kB | 29/45 kB | 41/358 kB Progress (5): 41/46 kB | 61/134 kB | 66/217 kB | 29/45 kB | 41/358 kB Progress (5): 41/46 kB | 61/134 kB | 66/217 kB | 29/45 kB | 45/358 kB Progress (5): 41/46 kB | 61/134 kB | 66/217 kB | 33/45 kB | 45/358 kB Progress (5): 41/46 kB | 61/134 kB | 66/217 kB | 33/45 kB | 49/358 kB Progress (5): 41/46 kB | 61/134 kB | 66/217 kB | 37/45 kB | 49/358 kB Progress (5): 41/46 kB | 61/134 kB | 70/217 kB | 37/45 kB | 49/358 kB Progress (5): 41/46 kB | 61/134 kB | 70/217 kB | 37/45 kB | 53/358 kB Progress (5): 41/46 kB | 66/134 kB | 70/217 kB | 37/45 kB | 53/358 kB Progress (5): 45/46 kB | 66/134 kB | 70/217 kB | 37/45 kB | 53/358 kB Progress (5): 45/46 kB | 66/134 kB | 70/217 kB | 37/45 kB | 57/358 kB Progress (5): 45/46 kB | 66/134 kB | 74/217 kB | 37/45 kB | 57/358 kB Progress (5): 45/46 kB | 66/134 kB | 74/217 kB | 41/45 kB | 57/358 kB Progress (5): 45/46 kB | 66/134 kB | 78/217 kB | 41/45 kB | 57/358 kB Progress (5): 45/46 kB | 66/134 kB | 78/217 kB | 41/45 kB | 61/358 kB Progress (5): 45/46 kB | 70/134 kB | 78/217 kB | 41/45 kB | 61/358 kB Progress (5): 46 kB | 70/134 kB | 78/217 kB | 41/45 kB | 61/358 kB Progress (5): 46 kB | 74/134 kB | 78/217 kB | 41/45 kB | 61/358 kB Progress (5): 46 kB | 74/134 kB | 78/217 kB | 41/45 kB | 66/358 kB Progress (5): 46 kB | 74/134 kB | 82/217 kB | 41/45 kB | 66/358 kB Progress (5): 46 kB | 74/134 kB | 82/217 kB | 45 kB | 66/358 kB Progress (5): 46 kB | 78/134 kB | 82/217 kB | 45 kB | 66/358 kB Progress (5): 46 kB | 78/134 kB | 86/217 kB | 45 kB | 66/358 kB Progress (5): 46 kB | 78/134 kB | 86/217 kB | 45 kB | 70/358 kB Progress (5): 46 kB | 78/134 kB | 90/217 kB | 45 kB | 70/358 kB Progress (5): 46 kB | 82/134 kB | 90/217 kB | 45 kB | 70/358 kB Progress (5): 46 kB | 82/134 kB | 94/217 kB | 45 kB | 70/358 kB Progress (5): 46 kB | 82/134 kB | 94/217 kB | 45 kB | 74/358 kB Progress (5): 46 kB | 86/134 kB | 94/217 kB | 45 kB | 74/358 kB Progress (5): 46 kB | 86/134 kB | 98/217 kB | 45 kB | 74/358 kB Progress (5): 46 kB | 90/134 kB | 98/217 kB | 45 kB | 74/358 kB Progress (5): 46 kB | 90/134 kB | 98/217 kB | 45 kB | 78/358 kB Progress (5): 46 kB | 90/134 kB | 102/217 kB | 45 kB | 78/358 kB Progress (5): 46 kB | 94/134 kB | 102/217 kB | 45 kB | 78/358 kB Progress (5): 46 kB | 94/134 kB | 106/217 kB | 45 kB | 78/358 kB Progress (5): 46 kB | 94/134 kB | 106/217 kB | 45 kB | 82/358 kB Progress (5): 46 kB | 94/134 kB | 111/217 kB | 45 kB | 82/358 kB Progress (5): 46 kB | 98/134 kB | 111/217 kB | 45 kB | 82/358 kB Progress (5): 46 kB | 98/134 kB | 115/217 kB | 45 kB | 82/358 kB Progress (5): 46 kB | 98/134 kB | 115/217 kB | 45 kB | 86/358 kB Progress (5): 46 kB | 102/134 kB | 115/217 kB | 45 kB | 86/358 kB Progress (5): 46 kB | 102/134 kB | 115/217 kB | 45 kB | 90/358 kB Downloaded from central: 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131/217 kB | 45 kB | 106/358 kB Progress (4): 123/134 kB | 131/217 kB | 45 kB | 111/358 kB Progress (4): 127/134 kB | 131/217 kB | 45 kB | 111/358 kB Progress (4): 127/134 kB | 131/217 kB | 45 kB | 115/358 kB Progress (4): 127/134 kB | 135/217 kB | 45 kB | 115/358 kB Progress (4): 131/134 kB | 135/217 kB | 45 kB | 115/358 kB Progress (4): 131/134 kB | 139/217 kB | 45 kB | 115/358 kB Progress (4): 134 kB | 139/217 kB | 45 kB | 115/358 kB Progress (4): 134 kB | 139/217 kB | 45 kB | 119/358 kB Downloaded from central: https://repo.maven.apache.org/maven2/commons-logging/commons-logging-api/1.1/commons-logging-api-1.1.jar (45 kB at 1.4 MB/s) Progress (3): 134 kB | 143/217 kB | 119/358 kB Downloading from central: https://repo.maven.apache.org/maven2/junit/junit/3.8.2/junit-3.8.2.jar Progress (3): 134 kB | 143/217 kB | 123/358 kB Progress (3): 134 kB | 147/217 kB | 123/358 kB Progress (3): 134 kB | 147/217 kB | 127/358 kB Progress (3): 134 kB | 147/217 kB | 131/358 kB Progress (3): 134 kB | 152/217 kB | 131/358 kB Progress (3): 134 kB | 156/217 kB | 131/358 kB Progress (3): 134 kB | 156/217 kB | 135/358 kB Downloaded from central: https://repo.maven.apache.org/maven2/com/google/collections/google-collections/1.0/google-collections-1.0.jar (0 B at 0 B/s) Progress (3): 134 kB | 160/217 kB | 135/358 kB Downloading from central: https://repo.maven.apache.org/maven2/org/codehaus/plexus/plexus-utils/1.4.5/plexus-utils-1.4.5.jar Progress (3): 134 kB | 160/217 kB | 139/358 kB Progress (3): 134 kB | 164/217 kB | 139/358 kB Progress (3): 134 kB | 164/217 kB | 143/358 kB Progress (3): 134 kB | 164/217 kB | 147/358 kB Progress (3): 134 kB | 168/217 kB | 147/358 kB Progress (3): 134 kB | 172/217 kB | 147/358 kB Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/xbean/xbean-reflect/3.4/xbean-reflect-3.4.jar (134 kB at 3.7 MB/s) Progress (2): 172/217 kB | 152/358 kB Downloading from central: https://repo.maven.apache.org/maven2/com/thoughtworks/qdox/qdox/1.9.2/qdox-1.9.2.jar Progress (2): 176/217 kB | 152/358 kB Progress (2): 176/217 kB | 156/358 kB Progress (2): 180/217 kB | 156/358 kB Progress (2): 180/217 kB | 160/358 kB Progress (2): 180/217 kB | 164/358 kB Progress (2): 184/217 kB | 164/358 kB Progress (3): 184/217 kB | 164/358 kB | 4.1/121 kB Progress (3): 188/217 kB | 164/358 kB | 4.1/121 kB Progress (3): 188/217 kB | 164/358 kB | 8.2/121 kB Progress (3): 188/217 kB | 168/358 kB | 8.2/121 kB Progress (3): 188/217 kB | 168/358 kB | 12/121 kB Progress (3): 193/217 kB | 168/358 kB | 12/121 kB Progress (3): 193/217 kB | 168/358 kB | 16/121 kB Progress (3): 193/217 kB | 172/358 kB | 16/121 kB Progress (3): 197/217 kB | 172/358 kB | 16/121 kB Progress (3): 197/217 kB | 176/358 kB | 16/121 kB Progress (3): 197/217 kB | 176/358 kB | 20/121 kB Progress (3): 197/217 kB | 180/358 kB | 20/121 kB Progress (3): 197/217 kB | 180/358 kB | 25/121 kB Progress (3): 201/217 kB | 180/358 kB | 25/121 kB Progress (3): 201/217 kB | 180/358 kB | 29/121 kB Progress (3): 205/217 kB | 180/358 kB | 29/121 kB Progress (3): 205/217 kB | 184/358 kB | 29/121 kB Progress (3): 209/217 kB | 184/358 kB | 29/121 kB Progress (3): 209/217 kB | 184/358 kB | 33/121 kB Progress (3): 213/217 kB | 184/358 kB | 33/121 kB Progress (3): 213/217 kB | 188/358 kB | 33/121 kB Progress (3): 213/217 kB | 188/358 kB | 37/121 kB Progress (3): 213/217 kB | 193/358 kB | 37/121 kB Progress (3): 217 kB | 193/358 kB | 37/121 kB Progress (3): 217 kB | 197/358 kB | 37/121 kB Progress (3): 217 kB | 197/358 kB | 41/121 kB Progress (3): 217 kB | 197/358 kB | 45/121 kB Progress (3): 217 kB | 201/358 kB | 45/121 kB Progress (3): 217 kB | 201/358 kB | 49/121 kB Progress (3): 217 kB | 205/358 kB | 49/121 kB Progress (3): 217 kB | 209/358 kB | 49/121 kB Progress (3): 217 kB | 209/358 kB | 53/121 kB Progress (3): 217 kB | 213/358 kB | 53/121 kB Progress (3): 217 kB | 213/358 kB | 57/121 kB Progress (3): 217 kB | 213/358 kB | 61/121 kB Progress (3): 217 kB | 217/358 kB | 61/121 kB Progress (3): 217 kB | 217/358 kB | 66/121 kB Progress (3): 217 kB | 221/358 kB | 66/121 kB Progress (3): 217 kB | 225/358 kB | 66/121 kB Progress (3): 217 kB | 225/358 kB | 70/121 kB Progress (3): 217 kB | 229/358 kB | 70/121 kB Progress (3): 217 kB | 229/358 kB | 74/121 kB Progress (3): 217 kB | 229/358 kB | 78/121 kB Progress (3): 217 kB | 233/358 kB | 78/121 kB Progress (3): 217 kB | 233/358 kB | 82/121 kB Progress (3): 217 kB | 238/358 kB | 82/121 kB Progress (3): 217 kB | 242/358 kB | 82/121 kB Progress (3): 217 kB | 242/358 kB | 86/121 kB Progress (3): 217 kB | 246/358 kB | 86/121 kB Progress (3): 217 kB | 246/358 kB | 90/121 kB Progress (3): 217 kB | 246/358 kB | 94/121 kB Progress (3): 217 kB | 250/358 kB | 94/121 kB Progress (3): 217 kB | 250/358 kB | 98/121 kB Progress (3): 217 kB | 254/358 kB | 98/121 kB Progress (4): 217 kB | 254/358 kB | 98/121 kB | 4.1/170 kB Progress (4): 217 kB | 254/358 kB | 102/121 kB | 4.1/170 kB Progress (4): 217 kB | 258/358 kB | 102/121 kB | 4.1/170 kB Progress (4): 217 kB | 258/358 kB | 106/121 kB | 4.1/170 kB Progress (4): 217 kB | 258/358 kB | 106/121 kB | 8.2/170 kB Downloaded from central: https://repo.maven.apache.org/maven2/org/codehaus/plexus/plexus-container-default/1.5.5/plexus-container-default-1.5.5.jar (217 kB at 4.8 MB/s) Progress (3): 258/358 kB | 106/121 kB | 12/170 kB Progress (3): 258/358 kB | 111/121 kB | 12/170 kB Progress (3): 262/358 kB | 111/121 kB | 12/170 kB Progress (3): 262/358 kB | 115/121 kB | 12/170 kB Progress (3): 262/358 kB | 115/121 kB | 16/170 kB Downloading from central: https://repo.maven.apache.org/maven2/jdom/jdom/1.0/jdom-1.0.jar Progress (3): 262/358 kB | 119/121 kB | 16/170 kB Progress (3): 266/358 kB | 119/121 kB | 16/170 kB Progress (3): 266/358 kB | 121 kB | 16/170 kB Progress (3): 266/358 kB | 121 kB | 20/170 kB Progress (3): 270/358 kB | 121 kB | 20/170 kB Progress (3): 270/358 kB | 121 kB | 25/170 kB Progress (3): 274/358 kB | 121 kB | 25/170 kB Progress (3): 274/358 kB | 121 kB | 29/170 kB Progress (3): 279/358 kB | 121 kB | 29/170 kB Progress (3): 279/358 kB | 121 kB | 33/170 kB Progress (3): 283/358 kB | 121 kB | 33/170 kB Progress (3): 283/358 kB | 121 kB | 37/170 kB Progress (3): 287/358 kB | 121 kB | 37/170 kB Progress (3): 287/358 kB | 121 kB | 41/170 kB Progress (3): 291/358 kB | 121 kB | 41/170 kB Progress (3): 291/358 kB | 121 kB | 45/170 kB Progress (3): 295/358 kB | 121 kB | 45/170 kB Progress (3): 295/358 kB | 121 kB | 49/170 kB Progress (3): 299/358 kB | 121 kB | 49/170 kB Progress (3): 299/358 kB | 121 kB | 53/170 kB Progress (3): 303/358 kB | 121 kB | 53/170 kB Progress (3): 303/358 kB | 121 kB | 57/170 kB Progress (3): 307/358 kB | 121 kB | 57/170 kB Progress (3): 307/358 kB | 121 kB | 61/170 kB Progress (3): 311/358 kB | 121 kB | 61/170 kB Progress (3): 311/358 kB | 121 kB | 66/170 kB Progress (3): 315/358 kB | 121 kB | 66/170 kB Progress (3): 315/358 kB | 121 kB | 70/170 kB Progress (3): 319/358 kB | 121 kB | 70/170 kB Progress (3): 319/358 kB | 121 kB | 74/170 kB Progress (3): 324/358 kB | 121 kB | 74/170 kB Progress (3): 324/358 kB | 121 kB | 78/170 kB Progress (3): 328/358 kB | 121 kB | 78/170 kB Progress (3): 328/358 kB | 121 kB | 82/170 kB Progress (3): 332/358 kB | 121 kB | 82/170 kB Downloaded from central: https://repo.maven.apache.org/maven2/junit/junit/3.8.2/junit-3.8.2.jar (121 kB at 2.5 MB/s) Progress (2): 336/358 kB | 82/170 kB Progress (2): 336/358 kB | 86/170 kB Progress (2): 340/358 kB | 86/170 kB Downloading from central: https://repo.maven.apache.org/maven2/org/codehaus/plexus/plexus-cli/1.2/plexus-cli-1.2.jar Progress (2): 344/358 kB | 86/170 kB Progress (2): 344/358 kB | 90/170 kB Progress (2): 344/358 kB | 94/170 kB Progress (2): 348/358 kB | 94/170 kB Progress (2): 348/358 kB | 98/170 kB Progress (2): 352/358 kB | 98/170 kB Progress (3): 352/358 kB | 98/170 kB | 4.1/153 kB Progress (3): 356/358 kB | 98/170 kB | 4.1/153 kB Progress (3): 356/358 kB | 102/170 kB | 4.1/153 kB Progress (3): 358 kB | 102/170 kB | 4.1/153 kB Progress (3): 358 kB | 102/170 kB | 8.2/153 kB Progress (3): 358 kB | 106/170 kB | 8.2/153 kB Progress (3): 358 kB | 106/170 kB | 12/153 kB Progress (3): 358 kB | 111/170 kB | 12/153 kB Progress (3): 358 kB | 111/170 kB | 16/153 kB Progress (3): 358 kB | 115/170 kB | 16/153 kB Progress (3): 358 kB | 119/170 kB | 16/153 kB Progress (3): 358 kB | 123/170 kB | 16/153 kB Progress (3): 358 kB | 127/170 kB | 16/153 kB Progress (3): 358 kB | 131/170 kB | 16/153 kB Progress (3): 358 kB | 131/170 kB | 20/153 kB Progress (3): 358 kB | 131/170 kB | 25/153 kB Progress (3): 358 kB | 135/170 kB | 25/153 kB Progress (3): 358 kB | 135/170 kB | 29/153 kB Progress (3): 358 kB | 139/170 kB | 29/153 kB Progress (3): 358 kB | 139/170 kB | 33/153 kB Progress (3): 358 kB | 143/170 kB | 33/153 kB Progress (3): 358 kB | 147/170 kB | 33/153 kB Progress (3): 358 kB | 147/170 kB | 37/153 kB Progress (3): 358 kB | 147/170 kB | 41/153 kB Progress (3): 358 kB | 152/170 kB | 41/153 kB Progress (3): 358 kB | 152/170 kB | 45/153 kB Progress (3): 358 kB | 156/170 kB | 45/153 kB Progress (3): 358 kB | 156/170 kB | 49/153 kB Progress (3): 358 kB | 160/170 kB | 49/153 kB Progress (3): 358 kB | 164/170 kB | 49/153 kB Progress (3): 358 kB | 164/170 kB | 53/153 kB Progress (3): 358 kB | 168/170 kB | 53/153 kB Progress (3): 358 kB | 168/170 kB | 57/153 kB Progress (3): 358 kB | 170 kB | 57/153 kB Progress (3): 358 kB | 170 kB | 61/153 kB Downloaded from central: https://repo.maven.apache.org/maven2/log4j/log4j/1.2.12/log4j-1.2.12.jar (358 kB at 6.4 MB/s) Progress (2): 170 kB | 66/153 kB Progress (3): 170 kB | 66/153 kB | 4.1/7.7 kB Downloading from central: https://repo.maven.apache.org/maven2/commons-logging/commons-logging/1.0/commons-logging-1.0.jar Progress (3): 170 kB | 70/153 kB | 4.1/7.7 kB Progress (3): 170 kB | 70/153 kB | 7.7 kB Progress (3): 170 kB | 74/153 kB | 7.7 kB Progress (3): 170 kB | 78/153 kB | 7.7 kB Progress (3): 170 kB | 82/153 kB | 7.7 kB Progress (3): 170 kB | 86/153 kB | 7.7 kB Progress (3): 170 kB | 90/153 kB | 7.7 kB Progress (3): 170 kB | 94/153 kB | 7.7 kB Progress (3): 170 kB | 98/153 kB | 7.7 kB Progress (3): 170 kB | 102/153 kB | 7.7 kB Progress (3): 170 kB | 106/153 kB | 7.7 kB Progress (3): 170 kB | 111/153 kB | 7.7 kB Progress (3): 170 kB | 115/153 kB | 7.7 kB Progress (3): 170 kB | 119/153 kB | 7.7 kB Progress (3): 170 kB | 123/153 kB | 7.7 kB Progress (3): 170 kB | 127/153 kB | 7.7 kB Progress (3): 170 kB | 131/153 kB | 7.7 kB Progress (3): 170 kB | 135/153 kB | 7.7 kB Progress (3): 170 kB | 139/153 kB | 7.7 kB Progress (3): 170 kB | 143/153 kB | 7.7 kB Progress (3): 170 kB | 147/153 kB | 7.7 kB Progress (3): 170 kB | 152/153 kB | 7.7 kB Progress (3): 170 kB | 153 kB | 7.7 kB Progress (4): 170 kB | 153 kB | 7.7 kB | 4.1/22 kB Downloaded from central: https://repo.maven.apache.org/maven2/org/codehaus/plexus/plexus-cli/1.2/plexus-cli-1.2.jar (7.7 kB at 126 kB/s) Progress (3): 170 kB | 153 kB | 8.2/22 kB Downloading from central: https://repo.maven.apache.org/maven2/commons-lang/commons-lang/1.0/commons-lang-1.0.jar Progress (3): 170 kB | 153 kB | 12/22 kB Progress (3): 170 kB | 153 kB | 16/22 kB Progress (3): 170 kB | 153 kB | 20/22 kB Progress (3): 170 kB | 153 kB | 22 kB Downloaded from central: https://repo.maven.apache.org/maven2/jdom/jdom/1.0/jdom-1.0.jar (153 kB at 2.4 MB/s) Downloading from central: https://repo.maven.apache.org/maven2/asm/asm/3.1/asm-3.1.jar Downloaded from central: https://repo.maven.apache.org/maven2/commons-logging/commons-logging/1.0/commons-logging-1.0.jar (22 kB at 333 kB/s) Progress (2): 170 kB | 4.1/64 kB Progress (2): 170 kB | 8.2/64 kB Progress (2): 170 kB | 12/64 kB Progress (2): 170 kB | 16/64 kB Progress (2): 170 kB | 20/64 kB Progress (2): 170 kB | 25/64 kB Progress (2): 170 kB | 29/64 kB Progress (2): 170 kB | 33/64 kB Progress (2): 170 kB | 37/64 kB Progress (2): 170 kB | 41/64 kB Progress (2): 170 kB | 45/64 kB Progress (2): 170 kB | 49/64 kB Downloaded from central: https://repo.maven.apache.org/maven2/asm/asm/3.1/asm-3.1.jar (0 B at 0 B/s) Progress (2): 170 kB | 53/64 kB Progress (2): 170 kB | 57/64 kB Progress (2): 170 kB | 61/64 kB Progress (2): 170 kB | 64 kB Downloaded from central: https://repo.maven.apache.org/maven2/commons-lang/commons-lang/1.0/commons-lang-1.0.jar (64 kB at 851 kB/s) Downloaded from central: https://repo.maven.apache.org/maven2/com/thoughtworks/qdox/qdox/1.9.2/qdox-1.9.2.jar (170 kB at 966 kB/s) Progress (1): 4.1/205 kB Progress (1): 8.2/205 kB Progress (1): 12/205 kB Progress (1): 16/205 kB Progress (1): 20/205 kB Progress (1): 25/205 kB Progress (1): 29/205 kB Progress (1): 33/205 kB Progress (1): 37/205 kB Progress (1): 41/205 kB Progress (1): 45/205 kB Progress (1): 49/205 kB Progress (1): 53/205 kB Progress (1): 57/205 kB Progress (1): 61/205 kB Progress (1): 66/205 kB Progress (1): 70/205 kB Progress (1): 74/205 kB Progress (1): 78/205 kB Progress (1): 82/205 kB Progress (1): 86/205 kB Progress (1): 90/205 kB Progress (1): 94/205 kB Progress (1): 98/205 kB Progress (1): 102/205 kB Progress (1): 106/205 kB Progress (1): 111/205 kB Progress (1): 115/205 kB Progress (1): 119/205 kB Progress (1): 123/205 kB Progress (1): 127/205 kB Progress (1): 131/205 kB Progress (1): 135/205 kB Progress (1): 139/205 kB Progress (1): 143/205 kB Progress (1): 147/205 kB Progress (1): 152/205 kB Progress (1): 156/205 kB Progress (1): 160/205 kB Progress (1): 164/205 kB Progress (1): 168/205 kB Progress (1): 172/205 kB Progress (1): 176/205 kB Progress (1): 180/205 kB Progress (1): 184/205 kB Progress (1): 188/205 kB Progress (1): 193/205 kB Progress (1): 197/205 kB Progress (1): 201/205 kB Progress (1): 205/205 kB Progress (1): 205 kB Downloaded from central: https://repo.maven.apache.org/maven2/org/codehaus/plexus/plexus-utils/1.4.5/plexus-utils-1.4.5.jar (205 kB at 820 kB/s) [INFO] Discovered 1 component descriptors(s) [INFO] [INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ adam-shade-spark3_2.12 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/adam-shade/src/test/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ adam-shade-spark3_2.12 --- [INFO] No sources to compile [INFO] [INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ adam-shade-spark3_2.12 --- [INFO] No sources to compile [INFO] [INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ adam-shade-spark3_2.12 --- Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/surefire/maven-surefire-common/3.0.0-M3/maven-surefire-common-3.0.0-M3.pom Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/maven/surefire/maven-surefire-common/3.0.0-M3/maven-surefire-common-3.0.0-M3.pom (0 B at 0 B/s) Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/surefire/surefire-api/3.0.0-M3/surefire-api-3.0.0-M3.pom Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/maven/surefire/surefire-api/3.0.0-M3/surefire-api-3.0.0-M3.pom (0 B at 0 B/s) Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/surefire/surefire-logger-api/3.0.0-M3/surefire-logger-api-3.0.0-M3.pom Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/maven/surefire/surefire-logger-api/3.0.0-M3/surefire-logger-api-3.0.0-M3.pom (0 B at 0 B/s) Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/surefire/surefire-booter/3.0.0-M3/surefire-booter-3.0.0-M3.pom Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/maven/surefire/surefire-booter/3.0.0-M3/surefire-booter-3.0.0-M3.pom (0 B at 0 B/s) Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/maven-toolchain/3.0-alpha-2/maven-toolchain-3.0-alpha-2.pom Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/maven/maven-toolchain/3.0-alpha-2/maven-toolchain-3.0-alpha-2.pom (0 B at 0 B/s) Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/maven/3.0-alpha-2/maven-3.0-alpha-2.pom Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/maven/maven/3.0-alpha-2/maven-3.0-alpha-2.pom (0 B at 0 B/s) Downloading from central: https://repo.maven.apache.org/maven2/org/codehaus/plexus/plexus-java/1.0.1/plexus-java-1.0.1.pom Downloaded from central: https://repo.maven.apache.org/maven2/org/codehaus/plexus/plexus-java/1.0.1/plexus-java-1.0.1.pom (0 B at 0 B/s) Downloading from central: https://repo.maven.apache.org/maven2/org/codehaus/plexus/plexus-languages/1.0.1/plexus-languages-1.0.1.pom Downloaded from central: https://repo.maven.apache.org/maven2/org/codehaus/plexus/plexus-languages/1.0.1/plexus-languages-1.0.1.pom (0 B at 0 B/s) Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/surefire/maven-surefire-common/3.0.0-M3/maven-surefire-common-3.0.0-M3.jar Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/surefire/surefire-logger-api/3.0.0-M3/surefire-logger-api-3.0.0-M3.jar Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/maven-toolchain/3.0-alpha-2/maven-toolchain-3.0-alpha-2.jar Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/surefire/surefire-booter/3.0.0-M3/surefire-booter-3.0.0-M3.jar Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/surefire/surefire-api/3.0.0-M3/surefire-api-3.0.0-M3.jar Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/maven/maven-toolchain/3.0-alpha-2/maven-toolchain-3.0-alpha-2.jar (0 B at 0 B/s) Downloading from central: https://repo.maven.apache.org/maven2/org/codehaus/plexus/plexus-java/1.0.1/plexus-java-1.0.1.jar Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/maven/surefire/surefire-logger-api/3.0.0-M3/surefire-logger-api-3.0.0-M3.jar (0 B at 0 B/s) Downloading from central: https://repo.maven.apache.org/maven2/org/ow2/asm/asm/7.0-beta/asm-7.0-beta.jar Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/maven/surefire/surefire-api/3.0.0-M3/surefire-api-3.0.0-M3.jar (0 B at 0 B/s) Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/maven/surefire/surefire-booter/3.0.0-M3/surefire-booter-3.0.0-M3.jar (0 B at 0 B/s) Downloaded from central: https://repo.maven.apache.org/maven2/org/codehaus/plexus/plexus-java/1.0.1/plexus-java-1.0.1.jar (0 B at 0 B/s) Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/maven/surefire/maven-surefire-common/3.0.0-M3/maven-surefire-common-3.0.0-M3.jar (0 B at 0 B/s) Downloaded from central: https://repo.maven.apache.org/maven2/org/ow2/asm/asm/7.0-beta/asm-7.0-beta.jar (0 B at 0 B/s) [INFO] No tests to run. [INFO] [INFO] >>> scoverage-maven-plugin:1.1.1:report (default-cli) > [scoverage]test @ adam-shade-spark3_2.12 >>> [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-shade-spark3_2.12 --- [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-shade-spark3_2.12 --- [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ adam-shade-spark3_2.12 --- [INFO] Modified 0 of 0 .scala files [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:pre-compile (default-cli) @ adam-shade-spark3_2.12 --- [WARNING] Skipping SCoverage execution - unsupported Scala version "2.12.8" [INFO] [INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ adam-shade-spark3_2.12 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/adam-shade/src/main/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ adam-shade-spark3_2.12 --- [INFO] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/adam-shade/src/main/java:-1: info: compiling [INFO] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/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/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/adam-shade/target/2.12.8/classes at 1606965488425 [INFO] prepare-compile in 0 s [INFO] compile in 1 s [INFO] [INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ adam-shade-spark3_2.12 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- plexus-component-metadata:1.5.5:generate-metadata (default) @ adam-shade-spark3_2.12 --- [INFO] Discovered 1 component descriptors(s) [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:post-compile (default-cli) @ adam-shade-spark3_2.12 --- [INFO] [INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ adam-shade-spark3_2.12 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/adam-shade/src/test/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ adam-shade-spark3_2.12 --- [INFO] No sources to compile [INFO] [INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ adam-shade-spark3_2.12 --- [INFO] No sources to compile [INFO] [INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ adam-shade-spark3_2.12 --- [INFO] No tests to run. [INFO] Skipping execution of surefire because it has already been run for this configuration [INFO] [INFO] <<< scoverage-maven-plugin:1.1.1:report (default-cli) < [scoverage]test @ adam-shade-spark3_2.12 <<< [INFO] [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:report (default-cli) @ adam-shade-spark3_2.12 --- [INFO] Skipping SCoverage report generation [INFO] [INFO] ------------< org.bdgenomics.adam:adam-codegen-spark3_2.12 >------------ [INFO] Building ADAM_2.12: Avro-to-Dataset codegen utils 0.33.0-SNAPSHOT [3/7] [INFO] --------------------------------[ jar ]--------------------------------- Downloading from central: https://repo.maven.apache.org/maven2/org/apache/avro/avro/1.8.2/avro-1.8.2.pom Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/avro/avro/1.8.2/avro-1.8.2.pom (0 B at 0 B/s) Downloading from central: https://repo.maven.apache.org/maven2/org/apache/avro/avro-parent/1.8.2/avro-parent-1.8.2.pom Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/avro/avro-parent/1.8.2/avro-parent-1.8.2.pom (0 B at 0 B/s) Downloading from central: https://repo.maven.apache.org/maven2/org/apache/avro/avro-toplevel/1.8.2/avro-toplevel-1.8.2.pom Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/avro/avro-toplevel/1.8.2/avro-toplevel-1.8.2.pom (0 B at 0 B/s) Downloading from central: https://repo.maven.apache.org/maven2/org/codehaus/jackson/jackson-core-asl/1.9.13/jackson-core-asl-1.9.13.pom Downloaded from central: https://repo.maven.apache.org/maven2/org/codehaus/jackson/jackson-core-asl/1.9.13/jackson-core-asl-1.9.13.pom (0 B at 0 B/s) Downloading from central: https://repo.maven.apache.org/maven2/org/codehaus/jackson/jackson-mapper-asl/1.9.13/jackson-mapper-asl-1.9.13.pom Downloaded from central: https://repo.maven.apache.org/maven2/org/codehaus/jackson/jackson-mapper-asl/1.9.13/jackson-mapper-asl-1.9.13.pom (0 B at 0 B/s) Downloading from central: https://repo.maven.apache.org/maven2/com/thoughtworks/paranamer/paranamer/2.8/paranamer-2.8.pom Downloaded from central: https://repo.maven.apache.org/maven2/com/thoughtworks/paranamer/paranamer/2.8/paranamer-2.8.pom (0 B at 0 B/s) Downloading from central: https://repo.maven.apache.org/maven2/com/thoughtworks/paranamer/paranamer-parent/2.8/paranamer-parent-2.8.pom Downloaded from central: https://repo.maven.apache.org/maven2/com/thoughtworks/paranamer/paranamer-parent/2.8/paranamer-parent-2.8.pom (0 B at 0 B/s) Downloading from central: https://repo.maven.apache.org/maven2/org/xerial/snappy/snappy-java/1.1.1.3/snappy-java-1.1.1.3.pom Progress (1): 3.3 kB Downloaded from central: https://repo.maven.apache.org/maven2/org/xerial/snappy/snappy-java/1.1.1.3/snappy-java-1.1.1.3.pom (3.3 kB at 253 kB/s) Downloading from central: https://repo.maven.apache.org/maven2/org/apache/commons/commons-compress/1.8.1/commons-compress-1.8.1.pom Progress (1): 4.1/11 kB Progress (1): 8.2/11 kB Progress (1): 11 kB Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/commons/commons-compress/1.8.1/commons-compress-1.8.1.pom (11 kB at 1.0 MB/s) Downloading from central: https://repo.maven.apache.org/maven2/org/apache/commons/commons-parent/33/commons-parent-33.pom Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/commons/commons-parent/33/commons-parent-33.pom (0 B at 0 B/s) Downloading from central: https://repo.maven.apache.org/maven2/org/tukaani/xz/1.5/xz-1.5.pom Downloaded from central: https://repo.maven.apache.org/maven2/org/tukaani/xz/1.5/xz-1.5.pom (0 B at 0 B/s) Downloading from central: https://repo.maven.apache.org/maven2/org/scalatest/scalatest_2.12/3.0.7/scalatest_2.12-3.0.7.pom Progress (1): 4.1/5.1 kB Progress (1): 5.1 kB Downloaded from central: https://repo.maven.apache.org/maven2/org/scalatest/scalatest_2.12/3.0.7/scalatest_2.12-3.0.7.pom (5.1 kB at 38 kB/s) Downloading from central: 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Progress (5): 188/366 kB | 201/589 kB | 0.9/7.1 MB | 147/718 kB | 98/549 kB Progress (5): 188/366 kB | 205/589 kB | 0.9/7.1 MB | 147/718 kB | 98/549 kB Progress (5): 193/366 kB | 205/589 kB | 0.9/7.1 MB | 147/718 kB | 98/549 kB Progress (5): 193/366 kB | 205/589 kB | 0.9/7.1 MB | 152/718 kB | 98/549 kB Progress (5): 193/366 kB | 205/589 kB | 0.9/7.1 MB | 152/718 kB | 102/549 kB Progress (5): 193/366 kB | 205/589 kB | 0.9/7.1 MB | 156/718 kB | 102/549 kB Progress (5): 197/366 kB | 205/589 kB | 0.9/7.1 MB | 156/718 kB | 102/549 kB Progress (5): 197/366 kB | 209/589 kB | 0.9/7.1 MB | 156/718 kB | 102/549 kB Progress (5): 197/366 kB | 209/589 kB | 1.0/7.1 MB | 156/718 kB | 102/549 kB Progress (5): 197/366 kB | 209/589 kB | 1.0/7.1 MB | 160/718 kB | 102/549 kB Progress (5): 197/366 kB | 209/589 kB | 1.0/7.1 MB | 160/718 kB | 106/549 kB Progress (5): 197/366 kB | 209/589 kB | 1.0/7.1 MB | 164/718 kB | 106/549 kB Progress (5): 197/366 kB | 209/589 kB | 1.0/7.1 MB | 164/718 kB | 111/549 kB Progress (5): 201/366 kB | 209/589 kB | 1.0/7.1 MB | 164/718 kB | 111/549 kB Progress (5): 201/366 kB | 213/589 kB | 1.0/7.1 MB | 164/718 kB | 111/549 kB Progress (5): 205/366 kB | 213/589 kB | 1.0/7.1 MB | 164/718 kB | 111/549 kB Progress (5): 205/366 kB | 213/589 kB | 1.0/7.1 MB | 164/718 kB | 115/549 kB Progress (5): 205/366 kB | 213/589 kB | 1.0/7.1 MB | 168/718 kB | 115/549 kB Progress (5): 205/366 kB | 213/589 kB | 1.0/7.1 MB | 168/718 kB | 115/549 kB Progress (5): 205/366 kB | 213/589 kB | 1.0/7.1 MB | 172/718 kB | 115/549 kB Progress (5): 209/366 kB | 213/589 kB | 1.0/7.1 MB | 172/718 kB | 115/549 kB Progress (5): 209/366 kB | 217/589 kB | 1.0/7.1 MB | 172/718 kB | 115/549 kB Progress (5): 213/366 kB | 217/589 kB | 1.0/7.1 MB | 172/718 kB | 115/549 kB Progress (5): 213/366 kB | 217/589 kB | 1.0/7.1 MB | 176/718 kB | 115/549 kB Progress (5): 213/366 kB | 217/589 kB | 1.0/7.1 MB | 176/718 kB | 119/549 kB Progress (5): 213/366 kB | 217/589 kB | 1.0/7.1 MB | 180/718 kB | 119/549 kB Progress (5): 217/366 kB | 217/589 kB | 1.0/7.1 MB | 180/718 kB | 119/549 kB Progress (5): 217/366 kB | 221/589 kB | 1.0/7.1 MB | 180/718 kB | 119/549 kB Progress (5): 221/366 kB | 221/589 kB | 1.0/7.1 MB | 180/718 kB | 119/549 kB Progress (5): 221/366 kB | 221/589 kB | 1.0/7.1 MB | 180/718 kB | 123/549 kB Progress (5): 221/366 kB | 221/589 kB | 1.1/7.1 MB | 180/718 kB | 123/549 kB Progress (5): 221/366 kB | 221/589 kB | 1.1/7.1 MB | 180/718 kB | 127/549 kB Progress (5): 225/366 kB | 221/589 kB | 1.1/7.1 MB | 180/718 kB | 127/549 kB Progress (5): 225/366 kB | 225/589 kB | 1.1/7.1 MB | 180/718 kB | 127/549 kB Progress (5): 225/366 kB | 225/589 kB | 1.1/7.1 MB | 184/718 kB | 127/549 kB Progress (5): 225/366 kB | 229/589 kB | 1.1/7.1 MB | 184/718 kB | 127/549 kB Progress (5): 229/366 kB | 229/589 kB | 1.1/7.1 MB | 184/718 kB | 127/549 kB Progress (5): 229/366 kB | 229/589 kB | 1.1/7.1 MB | 184/718 kB | 131/549 kB Progress (5): 233/366 kB | 229/589 kB | 1.1/7.1 MB | 184/718 kB | 131/549 kB Progress (5): 233/366 kB | 233/589 kB | 1.1/7.1 MB | 184/718 kB | 131/549 kB Progress (5): 233/366 kB | 233/589 kB | 1.1/7.1 MB | 184/718 kB | 131/549 kB Progress (5): 233/366 kB | 233/589 kB | 1.1/7.1 MB | 188/718 kB | 131/549 kB Progress (5): 233/366 kB | 233/589 kB | 1.1/7.1 MB | 188/718 kB | 135/549 kB Progress (5): 233/366 kB | 238/589 kB | 1.1/7.1 MB | 188/718 kB | 135/549 kB Progress (5): 238/366 kB | 238/589 kB | 1.1/7.1 MB | 188/718 kB | 135/549 kB Progress (5): 238/366 kB | 242/589 kB | 1.1/7.1 MB | 188/718 kB | 135/549 kB Progress (5): 238/366 kB | 242/589 kB | 1.1/7.1 MB | 188/718 kB | 139/549 kB Progress (5): 238/366 kB | 242/589 kB | 1.1/7.1 MB | 193/718 kB | 139/549 kB Progress (5): 238/366 kB | 242/589 kB | 1.1/7.1 MB | 193/718 kB | 143/549 kB Progress (5): 238/366 kB | 246/589 kB | 1.1/7.1 MB | 193/718 kB | 143/549 kB Progress (5): 238/366 kB | 246/589 kB | 1.1/7.1 MB | 193/718 kB | 143/549 kB Progress (5): 242/366 kB | 246/589 kB | 1.1/7.1 MB | 193/718 kB | 143/549 kB Progress (5): 242/366 kB | 250/589 kB | 1.1/7.1 MB | 193/718 kB | 143/549 kB Progress (5): 242/366 kB | 250/589 kB | 1.1/7.1 MB | 193/718 kB | 147/549 kB Progress (5): 242/366 kB | 250/589 kB | 1.1/7.1 MB | 197/718 kB | 147/549 kB Progress (5): 242/366 kB | 254/589 kB | 1.1/7.1 MB | 197/718 kB | 147/549 kB Progress (5): 246/366 kB | 254/589 kB | 1.1/7.1 MB | 197/718 kB | 147/549 kB Progress (5): 246/366 kB | 254/589 kB | 1.1/7.1 MB | 201/718 kB | 147/549 kB Progress (5): 246/366 kB | 258/589 kB | 1.1/7.1 MB | 201/718 kB | 147/549 kB Progress (5): 246/366 kB | 258/589 kB | 1.2/7.1 MB | 201/718 kB | 147/549 kB Progress (5): 246/366 kB | 262/589 kB | 1.2/7.1 MB | 201/718 kB | 147/549 kB Progress (5): 250/366 kB | 262/589 kB | 1.2/7.1 MB | 201/718 kB | 147/549 kB Progress (5): 250/366 kB | 262/589 kB | 1.2/7.1 MB | 205/718 kB | 147/549 kB Progress (5): 250/366 kB | 262/589 kB | 1.2/7.1 MB | 205/718 kB | 152/549 kB Progress (5): 250/366 kB | 262/589 kB | 1.2/7.1 MB | 209/718 kB | 152/549 kB Progress (5): 254/366 kB | 262/589 kB | 1.2/7.1 MB | 209/718 kB | 152/549 kB Progress (5): 254/366 kB | 266/589 kB | 1.2/7.1 MB | 209/718 kB | 152/549 kB Progress (5): 258/366 kB | 266/589 kB | 1.2/7.1 MB | 209/718 kB | 152/549 kB Progress (5): 258/366 kB | 266/589 kB | 1.2/7.1 MB | 213/718 kB | 152/549 kB Progress (5): 258/366 kB | 266/589 kB | 1.2/7.1 MB | 213/718 kB | 152/549 kB Progress (5): 258/366 kB | 266/589 kB | 1.2/7.1 MB | 213/718 kB | 156/549 kB Progress (5): 258/366 kB | 266/589 kB | 1.2/7.1 MB | 217/718 kB | 156/549 kB Progress (5): 258/366 kB | 270/589 kB | 1.2/7.1 MB | 217/718 kB | 156/549 kB Progress (5): 262/366 kB | 270/589 kB | 1.2/7.1 MB | 217/718 kB | 156/549 kB Progress (5): 262/366 kB | 270/589 kB | 1.3/7.1 MB | 217/718 kB | 156/549 kB Progress (5): 262/366 kB | 274/589 kB | 1.3/7.1 MB | 217/718 kB | 156/549 kB Progress (5): 262/366 kB | 274/589 kB | 1.3/7.1 MB | 221/718 kB | 156/549 kB Progress (5): 262/366 kB | 274/589 kB | 1.3/7.1 MB | 221/718 kB | 160/549 kB Progress (5): 262/366 kB | 274/589 kB | 1.3/7.1 MB | 225/718 kB | 160/549 kB Progress (5): 262/366 kB | 274/589 kB | 1.3/7.1 MB | 225/718 kB | 160/549 kB Progress (5): 262/366 kB | 279/589 kB | 1.3/7.1 MB | 225/718 kB | 160/549 kB Progress (5): 266/366 kB | 279/589 kB | 1.3/7.1 MB | 225/718 kB | 160/549 kB Progress (5): 266/366 kB | 283/589 kB | 1.3/7.1 MB | 225/718 kB | 160/549 kB Progress (5): 266/366 kB | 283/589 kB | 1.3/7.1 MB | 229/718 kB | 160/549 kB Progress (5): 266/366 kB | 283/589 kB | 1.3/7.1 MB | 229/718 kB | 164/549 kB Progress (5): 266/366 kB | 283/589 kB | 1.3/7.1 MB | 229/718 kB | 164/549 kB Progress (5): 266/366 kB | 287/589 kB | 1.3/7.1 MB | 229/718 kB | 164/549 kB Progress (5): 270/366 kB | 287/589 kB | 1.3/7.1 MB | 229/718 kB | 164/549 kB Progress (5): 270/366 kB | 291/589 kB | 1.3/7.1 MB | 229/718 kB | 164/549 kB Progress (5): 270/366 kB | 291/589 kB | 1.3/7.1 MB | 233/718 kB | 164/549 kB Progress (5): 270/366 kB | 295/589 kB | 1.3/7.1 MB | 233/718 kB | 164/549 kB Progress (5): 274/366 kB | 295/589 kB | 1.3/7.1 MB | 233/718 kB | 164/549 kB Progress (5): 274/366 kB | 295/589 kB | 1.3/7.1 MB | 233/718 kB | 168/549 kB Progress (5): 279/366 kB | 295/589 kB | 1.3/7.1 MB | 233/718 kB | 168/549 kB Progress (5): 279/366 kB | 295/589 kB | 1.4/7.1 MB | 233/718 kB | 168/549 kB Progress (5): 279/366 kB | 299/589 kB | 1.4/7.1 MB | 233/718 kB | 168/549 kB Progress (5): 279/366 kB | 299/589 kB | 1.4/7.1 MB | 238/718 kB | 168/549 kB Progress (5): 283/366 kB | 299/589 kB | 1.4/7.1 MB | 238/718 kB | 168/549 kB Progress (5): 283/366 kB | 299/589 kB | 1.4/7.1 MB | 238/718 kB | 172/549 kB Progress (5): 283/366 kB | 299/589 kB | 1.4/7.1 MB | 238/718 kB | 172/549 kB Progress (5): 287/366 kB | 299/589 kB | 1.4/7.1 MB | 238/718 kB | 172/549 kB Progress (5): 287/366 kB | 299/589 kB | 1.4/7.1 MB | 242/718 kB | 172/549 kB Progress (5): 287/366 kB | 303/589 kB | 1.4/7.1 MB | 242/718 kB | 172/549 kB Progress (5): 287/366 kB | 303/589 kB | 1.4/7.1 MB | 246/718 kB | 172/549 kB Progress (5): 291/366 kB | 303/589 kB | 1.4/7.1 MB | 246/718 kB | 172/549 kB Progress (5): 291/366 kB | 303/589 kB | 1.4/7.1 MB | 246/718 kB | 176/549 kB Progress (5): 295/366 kB | 303/589 kB | 1.4/7.1 MB | 246/718 kB | 176/549 kB Progress (5): 295/366 kB | 303/589 kB | 1.5/7.1 MB | 246/718 kB | 176/549 kB Progress (5): 295/366 kB | 303/589 kB | 1.5/7.1 MB | 250/718 kB | 176/549 kB Progress (5): 295/366 kB | 307/589 kB | 1.5/7.1 MB | 250/718 kB | 176/549 kB Progress (5): 295/366 kB | 307/589 kB | 1.5/7.1 MB | 254/718 kB | 176/549 kB Progress (5): 299/366 kB | 307/589 kB | 1.5/7.1 MB | 254/718 kB | 176/549 kB Progress (5): 299/366 kB | 307/589 kB | 1.5/7.1 MB | 254/718 kB | 180/549 kB Progress (5): 299/366 kB | 307/589 kB | 1.5/7.1 MB | 254/718 kB | 180/549 kB Progress (5): 303/366 kB | 307/589 kB | 1.5/7.1 MB | 254/718 kB | 180/549 kB Progress (5): 303/366 kB | 307/589 kB | 1.5/7.1 MB | 258/718 kB | 180/549 kB Progress (5): 303/366 kB | 311/589 kB | 1.5/7.1 MB | 258/718 kB | 180/549 kB Progress (5): 303/366 kB | 311/589 kB | 1.5/7.1 MB | 262/718 kB | 180/549 kB Progress (5): 307/366 kB | 311/589 kB | 1.5/7.1 MB | 262/718 kB | 180/549 kB Progress (5): 307/366 kB | 311/589 kB | 1.5/7.1 MB | 262/718 kB | 180/549 kB Progress (5): 307/366 kB | 311/589 kB | 1.5/7.1 MB | 262/718 kB | 184/549 kB Progress (5): 307/366 kB | 311/589 kB | 1.5/7.1 MB | 266/718 kB | 184/549 kB Progress (5): 311/366 kB | 311/589 kB | 1.5/7.1 MB | 266/718 kB | 184/549 kB Progress (5): 311/366 kB | 315/589 kB | 1.5/7.1 MB | 266/718 kB | 184/549 kB Progress (5): 311/366 kB | 315/589 kB | 1.5/7.1 MB | 270/718 kB | 184/549 kB Progress (5): 311/366 kB | 315/589 kB | 1.5/7.1 MB | 270/718 kB | 188/549 kB Progress (5): 311/366 kB | 319/589 kB | 1.5/7.1 MB | 270/718 kB | 188/549 kB Progress (5): 311/366 kB | 319/589 kB | 1.5/7.1 MB | 274/718 kB | 188/549 kB Progress (5): 315/366 kB | 319/589 kB | 1.5/7.1 MB | 274/718 kB | 188/549 kB Progress (5): 315/366 kB | 319/589 kB | 1.6/7.1 MB | 274/718 kB | 188/549 kB Progress (5): 319/366 kB | 319/589 kB | 1.6/7.1 MB | 274/718 kB | 188/549 kB Progress (5): 319/366 kB | 319/589 kB | 1.6/7.1 MB | 279/718 kB | 188/549 kB Progress (5): 319/366 kB | 324/589 kB | 1.6/7.1 MB | 279/718 kB | 188/549 kB Progress (5): 319/366 kB | 324/589 kB | 1.6/7.1 MB | 279/718 kB | 193/549 kB Progress (5): 319/366 kB | 324/589 kB | 1.6/7.1 MB | 283/718 kB | 193/549 kB Progress (5): 319/366 kB | 328/589 kB | 1.6/7.1 MB | 283/718 kB | 193/549 kB Progress (5): 324/366 kB | 328/589 kB | 1.6/7.1 MB | 283/718 kB | 193/549 kB Progress (5): 324/366 kB | 332/589 kB | 1.6/7.1 MB | 283/718 kB | 193/549 kB Progress (5): 324/366 kB | 332/589 kB | 1.6/7.1 MB | 283/718 kB | 193/549 kB Progress (5): 324/366 kB | 332/589 kB | 1.6/7.1 MB | 287/718 kB | 193/549 kB Progress (5): 324/366 kB | 332/589 kB | 1.6/7.1 MB | 287/718 kB | 197/549 kB Progress (5): 324/366 kB | 332/589 kB | 1.6/7.1 MB | 291/718 kB | 197/549 kB Progress (5): 324/366 kB | 336/589 kB | 1.6/7.1 MB | 291/718 kB | 197/549 kB Progress (5): 328/366 kB | 336/589 kB | 1.6/7.1 MB | 291/718 kB | 197/549 kB Progress (5): 328/366 kB | 336/589 kB | 1.7/7.1 MB | 291/718 kB | 197/549 kB Progress (5): 328/366 kB | 340/589 kB | 1.7/7.1 MB | 291/718 kB | 197/549 kB Progress (5): 328/366 kB | 340/589 kB | 1.7/7.1 MB | 295/718 kB | 197/549 kB Progress (5): 328/366 kB | 340/589 kB | 1.7/7.1 MB | 295/718 kB | 201/549 kB Progress (5): 328/366 kB | 344/589 kB | 1.7/7.1 MB | 295/718 kB | 201/549 kB Progress (5): 328/366 kB | 344/589 kB | 1.7/7.1 MB | 299/718 kB | 201/549 kB Progress (5): 332/366 kB | 344/589 kB | 1.7/7.1 MB | 299/718 kB | 201/549 kB Progress (5): 332/366 kB | 344/589 kB | 1.7/7.1 MB | 303/718 kB | 201/549 kB Progress (5): 332/366 kB | 344/589 kB | 1.7/7.1 MB | 303/718 kB | 201/549 kB Progress (5): 332/366 kB | 348/589 kB | 1.7/7.1 MB | 303/718 kB | 201/549 kB Progress (5): 332/366 kB | 348/589 kB | 1.7/7.1 MB | 303/718 kB | 205/549 kB Progress (5): 332/366 kB | 352/589 kB | 1.7/7.1 MB | 303/718 kB | 205/549 kB Progress (5): 332/366 kB | 352/589 kB | 1.7/7.1 MB | 307/718 kB | 205/549 kB Progress (5): 336/366 kB | 352/589 kB | 1.7/7.1 MB | 307/718 kB | 205/549 kB Progress (5): 336/366 kB | 352/589 kB | 1.7/7.1 MB | 311/718 kB | 205/549 kB Progress (5): 336/366 kB | 356/589 kB | 1.7/7.1 MB | 311/718 kB | 205/549 kB Progress (5): 336/366 kB | 356/589 kB | 1.7/7.1 MB | 311/718 kB | 209/549 kB Progress (5): 336/366 kB | 356/589 kB | 1.7/7.1 MB | 315/718 kB | 209/549 kB Progress (5): 336/366 kB | 360/589 kB | 1.7/7.1 MB | 315/718 kB | 209/549 kB Progress (5): 336/366 kB | 360/589 kB | 1.7/7.1 MB | 315/718 kB | 209/549 kB Progress (5): 340/366 kB | 360/589 kB | 1.7/7.1 MB | 315/718 kB | 209/549 kB Progress (5): 340/366 kB | 365/589 kB | 1.7/7.1 MB | 315/718 kB | 209/549 kB Progress (5): 340/366 kB | 365/589 kB | 1.7/7.1 MB | 319/718 kB | 209/549 kB Progress (5): 340/366 kB | 365/589 kB | 1.7/7.1 MB | 319/718 kB | 213/549 kB Progress (5): 340/366 kB | 365/589 kB | 1.7/7.1 MB | 324/718 kB | 213/549 kB Progress (5): 340/366 kB | 369/589 kB | 1.7/7.1 MB | 324/718 kB | 213/549 kB Progress (5): 344/366 kB | 369/589 kB | 1.7/7.1 MB | 324/718 kB | 213/549 kB Progress (5): 344/366 kB | 373/589 kB | 1.7/7.1 MB | 324/718 kB | 213/549 kB Progress (5): 344/366 kB | 373/589 kB | 1.7/7.1 MB | 328/718 kB | 213/549 kB Progress (5): 344/366 kB | 373/589 kB | 1.7/7.1 MB | 328/718 kB | 217/549 kB Progress (5): 344/366 kB | 373/589 kB | 1.8/7.1 MB | 328/718 kB | 217/549 kB Progress (5): 344/366 kB | 373/589 kB | 1.8/7.1 MB | 328/718 kB | 221/549 kB Progress (5): 348/366 kB | 373/589 kB | 1.8/7.1 MB | 328/718 kB | 221/549 kB Progress (5): 348/366 kB | 377/589 kB | 1.8/7.1 MB | 328/718 kB | 221/549 kB Progress (5): 352/366 kB | 377/589 kB | 1.8/7.1 MB | 328/718 kB | 221/549 kB Progress (5): 352/366 kB | 377/589 kB | 1.8/7.1 MB | 328/718 kB | 225/549 kB Progress (5): 352/366 kB | 377/589 kB | 1.8/7.1 MB | 332/718 kB | 225/549 kB Progress (5): 352/366 kB | 377/589 kB | 1.8/7.1 MB | 332/718 kB | 225/549 kB Progress (5): 352/366 kB | 377/589 kB | 1.8/7.1 MB | 332/718 kB | 229/549 kB Progress (5): 356/366 kB | 377/589 kB | 1.8/7.1 MB | 332/718 kB | 229/549 kB Progress (5): 356/366 kB | 381/589 kB | 1.8/7.1 MB | 332/718 kB | 229/549 kB Progress (5): 356/366 kB | 381/589 kB | 1.8/7.1 MB | 332/718 kB | 233/549 kB Progress (5): 360/366 kB | 381/589 kB | 1.8/7.1 MB | 332/718 kB | 233/549 kB Progress (5): 360/366 kB | 381/589 kB | 1.8/7.1 MB | 336/718 kB | 233/549 kB Progress (5): 365/366 kB | 381/589 kB | 1.8/7.1 MB | 336/718 kB | 233/549 kB Progress (5): 365/366 kB | 385/589 kB | 1.8/7.1 MB | 336/718 kB | 233/549 kB Progress (5): 365/366 kB | 385/589 kB | 1.8/7.1 MB | 336/718 kB | 238/549 kB Progress (5): 365/366 kB | 389/589 kB | 1.8/7.1 MB | 336/718 kB | 238/549 kB Progress (5): 366 kB | 389/589 kB | 1.8/7.1 MB | 336/718 kB | 238/549 kB Progress (5): 366 kB | 389/589 kB | 1.9/7.1 MB | 336/718 kB | 238/549 kB Progress (5): 366 kB | 389/589 kB | 1.9/7.1 MB | 340/718 kB | 238/549 kB Progress (5): 366 kB | 393/589 kB | 1.9/7.1 MB | 340/718 kB | 238/549 kB Progress (5): 366 kB | 393/589 kB | 1.9/7.1 MB | 340/718 kB | 242/549 kB Progress (5): 366 kB | 397/589 kB | 1.9/7.1 MB | 340/718 kB | 242/549 kB Progress (5): 366 kB | 397/589 kB | 1.9/7.1 MB | 344/718 kB | 242/549 kB Progress (5): 366 kB | 397/589 kB | 1.9/7.1 MB | 344/718 kB | 246/549 kB Progress (5): 366 kB | 401/589 kB | 1.9/7.1 MB | 344/718 kB | 246/549 kB Progress (5): 366 kB | 401/589 kB | 1.9/7.1 MB | 344/718 kB | 246/549 kB Progress (5): 366 kB | 401/589 kB | 1.9/7.1 MB | 344/718 kB | 250/549 kB Progress (5): 366 kB | 406/589 kB | 1.9/7.1 MB | 344/718 kB | 250/549 kB Progress (5): 366 kB | 406/589 kB | 1.9/7.1 MB | 348/718 kB | 250/549 kB Progress (5): 366 kB | 410/589 kB | 1.9/7.1 MB | 348/718 kB | 250/549 kB Progress (5): 366 kB | 410/589 kB | 1.9/7.1 MB | 348/718 kB | 254/549 kB Progress (5): 366 kB | 414/589 kB | 1.9/7.1 MB | 348/718 kB | 254/549 kB Progress (5): 366 kB | 414/589 kB | 1.9/7.1 MB | 352/718 kB | 254/549 kB Progress (5): 366 kB | 414/589 kB | 2.0/7.1 MB | 352/718 kB | 254/549 kB Progress (5): 366 kB | 414/589 kB | 2.0/7.1 MB | 352/718 kB | 258/549 kB Progress (5): 366 kB | 414/589 kB | 2.0/7.1 MB | 356/718 kB | 258/549 kB Progress (5): 366 kB | 418/589 kB | 2.0/7.1 MB | 356/718 kB | 258/549 kB Progress (5): 366 kB | 418/589 kB | 2.0/7.1 MB | 360/718 kB | 258/549 kB Progress (5): 366 kB | 418/589 kB | 2.0/7.1 MB | 360/718 kB | 262/549 kB Progress (5): 366 kB | 418/589 kB | 2.0/7.1 MB | 360/718 kB | 262/549 kB Progress (5): 366 kB | 422/589 kB | 2.0/7.1 MB | 360/718 kB | 262/549 kB Progress (5): 366 kB | 422/589 kB | 2.0/7.1 MB | 360/718 kB | 266/549 kB Progress (5): 366 kB | 422/589 kB | 2.0/7.1 MB | 365/718 kB | 266/549 kB Progress (5): 366 kB | 422/589 kB | 2.0/7.1 MB | 365/718 kB | 270/549 kB Progress (5): 366 kB | 426/589 kB | 2.0/7.1 MB | 365/718 kB | 270/549 kB Downloaded from central: 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(enforce-versions) @ adam-codegen-spark3_2.12 --- [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-codegen-spark3_2.12 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ adam-codegen-spark3_2.12 --- Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/shared/file-management/3.0.0/file-management-3.0.0.pom Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/maven/shared/file-management/3.0.0/file-management-3.0.0.pom (0 B at 0 B/s) Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/shared/maven-shared-components/22/maven-shared-components-22.pom Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/maven/shared/maven-shared-components/22/maven-shared-components-22.pom (0 B at 0 B/s) Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/maven-parent/27/maven-parent-27.pom Downloaded from central: 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[INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ adam-codegen-spark3_2.12 --- [INFO] Modified 0 of 4 .scala files [INFO] [INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ adam-codegen-spark3_2.12 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/adam-codegen/src/main/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ adam-codegen-spark3_2.12 --- [INFO] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/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/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/adam-codegen/target/2.12.8/classes at 1606965491162 [WARNING] warning: there were 5 deprecation warnings (since 2.12.0); re-run with -deprecation for details [WARNING] one warning found [INFO] prepare-compile in 0 s [INFO] compile in 4 s [INFO] [INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ adam-codegen-spark3_2.12 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ adam-codegen-spark3_2.12 --- [INFO] Test Source directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/adam-codegen/src/test/scala added. [INFO] [INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ adam-codegen-spark3_2.12 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/adam-codegen/src/test/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ adam-codegen-spark3_2.12 --- [INFO] No sources to compile [INFO] [INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ adam-codegen-spark3_2.12 --- [INFO] No sources to compile [INFO] [INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ adam-codegen-spark3_2.12 --- [INFO] Tests are skipped. 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Discovery completed in 85 milliseconds. Run starting. Expected test count is: 0 DiscoverySuite: Run completed in 130 milliseconds. Total number of tests run: 0 Suites: completed 1, aborted 0 Tests: succeeded 0, failed 0, canceled 0, ignored 0, pending 0 No tests were executed. [INFO] [INFO] >>> scoverage-maven-plugin:1.1.1:report (default-cli) > [scoverage]test @ adam-codegen-spark3_2.12 >>> [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-codegen-spark3_2.12 --- [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-codegen-spark3_2.12 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ adam-codegen-spark3_2.12 --- [INFO] Source directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/adam-codegen/src/main/scala added. [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ adam-codegen-spark3_2.12 --- [INFO] Modified 0 of 4 .scala files [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:pre-compile (default-cli) @ adam-codegen-spark3_2.12 --- [WARNING] Skipping SCoverage execution - unsupported Scala version "2.12.8" [INFO] [INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ adam-codegen-spark3_2.12 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/adam-codegen/src/main/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ adam-codegen-spark3_2.12 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ adam-codegen-spark3_2.12 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:post-compile (default-cli) @ adam-codegen-spark3_2.12 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ adam-codegen-spark3_2.12 --- [INFO] Test Source directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/adam-codegen/src/test/scala added. [INFO] [INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ adam-codegen-spark3_2.12 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/adam-codegen/src/test/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ adam-codegen-spark3_2.12 --- [INFO] No sources to compile [INFO] [INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ adam-codegen-spark3_2.12 --- [INFO] No sources to compile [INFO] [INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ adam-codegen-spark3_2.12 --- [INFO] Tests are skipped. [INFO] [INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ adam-codegen-spark3_2.12 --- Discovery starting. Discovery completed in 82 milliseconds. Run starting. Expected test count is: 0 DiscoverySuite: Run completed in 127 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-spark3_2.12 <<< [INFO] [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:report (default-cli) @ adam-codegen-spark3_2.12 --- [INFO] Skipping SCoverage report generation [INFO] [INFO] -------------< org.bdgenomics.adam:adam-core-spark3_2.12 >-------------- [INFO] Building ADAM_2.12: Core 0.33.0-SNAPSHOT [4/7] [INFO] --------------------------------[ jar ]--------------------------------- Downloading from central: https://repo.maven.apache.org/maven2/org/codehaus/mojo/exec-maven-plugin/1.5.0/exec-maven-plugin-1.5.0.pom Progress (1): 4.1/12 kB Progress (1): 8.2/12 kB Progress (1): 12/12 kB Progress (1): 12 kB Downloaded from central: https://repo.maven.apache.org/maven2/org/codehaus/mojo/exec-maven-plugin/1.5.0/exec-maven-plugin-1.5.0.pom (12 kB at 196 kB/s) Downloading from central: https://repo.maven.apache.org/maven2/org/codehaus/mojo/exec-maven-plugin/1.5.0/exec-maven-plugin-1.5.0.jar 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| 0.4/1.2 MB | 143/544 kB | 25/777 kB Progress (4): 2.7/3.5 MB | 0.4/1.2 MB | 143/544 kB | 29/777 kB Progress (4): 2.7/3.5 MB | 0.4/1.2 MB | 147/544 kB | 29/777 kB Progress (4): 2.7/3.5 MB | 0.4/1.2 MB | 147/544 kB | 33/777 kB Progress (4): 2.7/3.5 MB | 0.4/1.2 MB | 147/544 kB | 33/777 kB Progress (4): 2.7/3.5 MB | 0.4/1.2 MB | 147/544 kB | 37/777 kB Progress (4): 2.7/3.5 MB | 0.4/1.2 MB | 147/544 kB | 37/777 kB Progress (4): 2.7/3.5 MB | 0.4/1.2 MB | 152/544 kB | 37/777 kB Progress (4): 2.7/3.5 MB | 0.4/1.2 MB | 152/544 kB | 41/777 kB Progress (4): 2.7/3.5 MB | 0.4/1.2 MB | 152/544 kB | 41/777 kB Progress (4): 2.7/3.5 MB | 0.4/1.2 MB | 152/544 kB | 41/777 kB Progress (4): 2.7/3.5 MB | 0.4/1.2 MB | 152/544 kB | 45/777 kB Progress (4): 2.7/3.5 MB | 0.4/1.2 MB | 156/544 kB | 45/777 kB Progress (4): 2.7/3.5 MB | 0.4/1.2 MB | 156/544 kB | 49/777 kB Progress (4): 2.7/3.5 MB | 0.4/1.2 MB | 156/544 kB | 49/777 kB Progress (4): 2.7/3.5 MB | 0.4/1.2 MB | 160/544 kB | 49/777 kB Progress (4): 2.7/3.5 MB | 0.4/1.2 MB | 160/544 kB | 49/777 kB Progress (4): 2.7/3.5 MB | 0.4/1.2 MB | 164/544 kB | 49/777 kB Progress (4): 2.7/3.5 MB | 0.4/1.2 MB | 164/544 kB | 53/777 kB Progress (4): 2.7/3.5 MB | 0.4/1.2 MB | 164/544 kB | 53/777 kB Progress (4): 2.8/3.5 MB | 0.4/1.2 MB | 164/544 kB | 53/777 kB Progress (4): 2.8/3.5 MB | 0.4/1.2 MB | 168/544 kB | 53/777 kB Progress (4): 2.8/3.5 MB | 0.4/1.2 MB | 168/544 kB | 57/777 kB Progress (4): 2.8/3.5 MB | 0.4/1.2 MB | 168/544 kB | 57/777 kB Progress (4): 2.8/3.5 MB | 0.4/1.2 MB | 168/544 kB | 57/777 kB Progress (4): 2.8/3.5 MB | 0.4/1.2 MB | 172/544 kB | 57/777 kB Progress (4): 2.8/3.5 MB | 0.4/1.2 MB | 172/544 kB | 57/777 kB Progress (4): 2.8/3.5 MB | 0.4/1.2 MB | 172/544 kB | 61/777 kB Progress (4): 2.8/3.5 MB | 0.4/1.2 MB | 172/544 kB | 61/777 kB Progress (4): 2.8/3.5 MB | 0.4/1.2 MB | 176/544 kB | 61/777 kB Progress (4): 2.8/3.5 MB | 0.4/1.2 MB | 176/544 kB | 61/777 kB Progress (4): 2.8/3.5 MB | 0.4/1.2 MB | 176/544 kB | 66/777 kB Progress (4): 2.8/3.5 MB | 0.4/1.2 MB | 176/544 kB | 66/777 kB Progress (4): 2.8/3.5 MB | 0.4/1.2 MB | 180/544 kB | 66/777 kB Progress (4): 2.8/3.5 MB | 0.4/1.2 MB | 180/544 kB | 66/777 kB Progress (4): 2.8/3.5 MB | 0.4/1.2 MB | 180/544 kB | 70/777 kB Progress (4): 2.8/3.5 MB | 0.4/1.2 MB | 184/544 kB | 70/777 kB Progress (4): 2.8/3.5 MB | 0.4/1.2 MB | 184/544 kB | 70/777 kB Progress (4): 2.8/3.5 MB | 0.4/1.2 MB | 188/544 kB | 70/777 kB Progress (4): 2.8/3.5 MB | 0.4/1.2 MB | 188/544 kB | 74/777 kB Progress (4): 2.8/3.5 MB | 0.5/1.2 MB | 188/544 kB | 74/777 kB Progress (4): 2.8/3.5 MB | 0.5/1.2 MB | 188/544 kB | 78/777 kB Progress (4): 2.8/3.5 MB | 0.5/1.2 MB | 188/544 kB | 78/777 kB Progress (4): 2.8/3.5 MB | 0.5/1.2 MB | 193/544 kB | 78/777 kB Progress (4): 2.8/3.5 MB | 0.5/1.2 MB | 193/544 kB | 78/777 kB Progress (4): 2.8/3.5 MB | 0.5/1.2 MB | 193/544 kB | 82/777 kB Progress (4): 2.9/3.5 MB | 0.5/1.2 MB | 193/544 kB | 82/777 kB Progress (4): 2.9/3.5 MB | 0.5/1.2 MB | 197/544 kB | 82/777 kB Progress (4): 2.9/3.5 MB | 0.5/1.2 MB | 197/544 kB | 82/777 kB Progress (4): 2.9/3.5 MB | 0.5/1.2 MB | 197/544 kB | 86/777 kB Progress (4): 2.9/3.5 MB | 0.5/1.2 MB | 197/544 kB | 86/777 kB Progress (4): 2.9/3.5 MB | 0.5/1.2 MB | 201/544 kB | 86/777 kB Progress (4): 2.9/3.5 MB | 0.5/1.2 MB | 201/544 kB | 86/777 kB Progress (4): 2.9/3.5 MB | 0.5/1.2 MB | 201/544 kB | 90/777 kB Progress (4): 2.9/3.5 MB | 0.5/1.2 MB | 201/544 kB | 90/777 kB Progress (4): 2.9/3.5 MB | 0.5/1.2 MB | 205/544 kB | 90/777 kB Progress (4): 2.9/3.5 MB | 0.5/1.2 MB | 205/544 kB | 94/777 kB Progress (4): 2.9/3.5 MB | 0.5/1.2 MB | 205/544 kB | 94/777 kB Progress (4): 2.9/3.5 MB | 0.5/1.2 MB | 205/544 kB | 98/777 kB Progress (4): 2.9/3.5 MB | 0.5/1.2 MB | 209/544 kB | 98/777 kB Progress (4): 2.9/3.5 MB | 0.5/1.2 MB | 209/544 kB | 98/777 kB Progress (4): 2.9/3.5 MB | 0.5/1.2 MB | 209/544 kB | 98/777 kB Progress (4): 2.9/3.5 MB | 0.5/1.2 MB | 213/544 kB | 98/777 kB Progress (4): 2.9/3.5 MB | 0.5/1.2 MB | 213/544 kB | 102/777 kB Progress (4): 2.9/3.5 MB | 0.5/1.2 MB | 213/544 kB | 102/777 kB Progress (4): 2.9/3.5 MB | 0.5/1.2 MB | 213/544 kB | 106/777 kB Progress (4): 2.9/3.5 MB | 0.5/1.2 MB | 213/544 kB | 106/777 kB Progress (4): 2.9/3.5 MB | 0.5/1.2 MB | 217/544 kB | 106/777 kB Progress (4): 2.9/3.5 MB | 0.5/1.2 MB | 217/544 kB | 106/777 kB Progress (4): 2.9/3.5 MB | 0.5/1.2 MB | 217/544 kB | 111/777 kB Progress (4): 2.9/3.5 MB | 0.5/1.2 MB | 221/544 kB | 111/777 kB Progress (4): 2.9/3.5 MB | 0.5/1.2 MB | 221/544 kB | 111/777 kB Progress (4): 2.9/3.5 MB | 0.5/1.2 MB | 225/544 kB | 111/777 kB Progress (4): 2.9/3.5 MB | 0.5/1.2 MB | 225/544 kB | 115/777 kB Progress (4): 2.9/3.5 MB | 0.5/1.2 MB | 225/544 kB | 115/777 kB Progress (4): 3.0/3.5 MB | 0.5/1.2 MB | 225/544 kB | 115/777 kB Progress (4): 3.0/3.5 MB | 0.5/1.2 MB | 229/544 kB | 115/777 kB Progress (4): 3.0/3.5 MB | 0.5/1.2 MB | 229/544 kB | 119/777 kB Progress (4): 3.0/3.5 MB | 0.5/1.2 MB | 229/544 kB | 119/777 kB Progress (4): 3.0/3.5 MB | 0.5/1.2 MB | 233/544 kB | 119/777 kB Progress (4): 3.0/3.5 MB | 0.5/1.2 MB | 233/544 kB | 123/777 kB Progress (4): 3.0/3.5 MB | 0.5/1.2 MB | 233/544 kB | 123/777 kB Progress (4): 3.0/3.5 MB | 0.5/1.2 MB | 233/544 kB | 123/777 kB Progress (4): 3.0/3.5 MB | 0.5/1.2 MB | 233/544 kB | 127/777 kB Progress (4): 3.0/3.5 MB | 0.5/1.2 MB | 238/544 kB | 127/777 kB Progress (4): 3.0/3.5 MB | 0.5/1.2 MB | 238/544 kB | 127/777 kB Progress (4): 3.0/3.5 MB | 0.5/1.2 MB | 238/544 kB | 131/777 kB Progress (4): 3.0/3.5 MB | 0.5/1.2 MB | 238/544 kB | 131/777 kB Progress (4): 3.0/3.5 MB | 0.5/1.2 MB | 242/544 kB | 131/777 kB Progress (4): 3.0/3.5 MB | 0.6/1.2 MB | 242/544 kB | 131/777 kB Progress (4): 3.0/3.5 MB | 0.6/1.2 MB | 246/544 kB | 131/777 kB Progress (4): 3.0/3.5 MB | 0.6/1.2 MB | 246/544 kB | 135/777 kB Progress (4): 3.0/3.5 MB | 0.6/1.2 MB | 250/544 kB | 135/777 kB Progress (4): 3.0/3.5 MB | 0.6/1.2 MB | 250/544 kB | 135/777 kB Progress (4): 3.0/3.5 MB | 0.6/1.2 MB | 250/544 kB | 139/777 kB Progress (4): 3.0/3.5 MB | 0.6/1.2 MB | 250/544 kB | 139/777 kB Progress (4): 3.0/3.5 MB | 0.6/1.2 MB | 250/544 kB | 143/777 kB Progress (4): 3.0/3.5 MB | 0.6/1.2 MB | 254/544 kB | 143/777 kB Progress (4): 3.0/3.5 MB | 0.6/1.2 MB | 254/544 kB | 147/777 kB Progress (4): 3.0/3.5 MB | 0.6/1.2 MB | 254/544 kB | 147/777 kB Progress (4): 3.0/3.5 MB | 0.6/1.2 MB | 254/544 kB | 147/777 kB Progress (4): 3.0/3.5 MB | 0.6/1.2 MB | 254/544 kB | 152/777 kB Progress (4): 3.0/3.5 MB | 0.6/1.2 MB | 258/544 kB | 152/777 kB Progress (4): 3.0/3.5 MB | 0.6/1.2 MB | 258/544 kB | 152/777 kB Progress (4): 3.0/3.5 MB | 0.6/1.2 MB | 258/544 kB | 156/777 kB Progress (4): 3.0/3.5 MB | 0.6/1.2 MB | 258/544 kB | 156/777 kB Progress (4): 3.0/3.5 MB | 0.6/1.2 MB | 262/544 kB | 156/777 kB Progress (4): 3.0/3.5 MB | 0.6/1.2 MB | 262/544 kB | 160/777 kB Progress (4): 3.0/3.5 MB | 0.6/1.2 MB | 262/544 kB | 160/777 kB Progress (4): 3.1/3.5 MB | 0.6/1.2 MB | 262/544 kB | 160/777 kB Progress (4): 3.1/3.5 MB | 0.6/1.2 MB | 262/544 kB | 164/777 kB Progress (4): 3.1/3.5 MB | 0.6/1.2 MB | 266/544 kB | 164/777 kB Progress (4): 3.1/3.5 MB | 0.6/1.2 MB | 266/544 kB | 164/777 kB Progress (4): 3.1/3.5 MB | 0.6/1.2 MB | 266/544 kB | 168/777 kB Progress (4): 3.1/3.5 MB | 0.6/1.2 MB | 266/544 kB | 168/777 kB Progress (4): 3.1/3.5 MB | 0.6/1.2 MB | 266/544 kB | 172/777 kB Progress (4): 3.1/3.5 MB | 0.6/1.2 MB | 270/544 kB | 172/777 kB Progress (4): 3.1/3.5 MB | 0.6/1.2 MB | 270/544 kB | 172/777 kB Progress (4): 3.1/3.5 MB | 0.6/1.2 MB | 270/544 kB | 172/777 kB Progress (4): 3.1/3.5 MB | 0.6/1.2 MB | 274/544 kB | 172/777 kB Progress (4): 3.1/3.5 MB | 0.6/1.2 MB | 274/544 kB | 176/777 kB Progress (4): 3.1/3.5 MB | 0.6/1.2 MB | 274/544 kB | 176/777 kB Progress (4): 3.1/3.5 MB | 0.6/1.2 MB | 279/544 kB | 176/777 kB Progress (4): 3.1/3.5 MB | 0.6/1.2 MB | 279/544 kB | 176/777 kB Progress (4): 3.1/3.5 MB | 0.6/1.2 MB | 279/544 kB | 176/777 kB Progress (4): 3.1/3.5 MB | 0.6/1.2 MB | 279/544 kB | 180/777 kB Progress (4): 3.1/3.5 MB | 0.6/1.2 MB | 283/544 kB | 180/777 kB Progress (4): 3.1/3.5 MB | 0.6/1.2 MB | 283/544 kB | 180/777 kB Progress (4): 3.1/3.5 MB | 0.6/1.2 MB | 283/544 kB | 184/777 kB Progress (4): 3.1/3.5 MB | 0.6/1.2 MB | 283/544 kB | 184/777 kB Progress (4): 3.1/3.5 MB | 0.6/1.2 MB | 283/544 kB | 184/777 kB Progress (4): 3.1/3.5 MB | 0.6/1.2 MB | 283/544 kB | 188/777 kB Progress (4): 3.1/3.5 MB | 0.6/1.2 MB | 287/544 kB | 188/777 kB Progress (4): 3.1/3.5 MB | 0.6/1.2 MB | 287/544 kB | 188/777 kB Progress (4): 3.1/3.5 MB | 0.6/1.2 MB | 287/544 kB | 193/777 kB Progress (4): 3.1/3.5 MB | 0.6/1.2 MB | 287/544 kB | 193/777 kB Progress (4): 3.1/3.5 MB | 0.6/1.2 MB | 291/544 kB | 193/777 kB Progress (4): 3.1/3.5 MB | 0.6/1.2 MB | 291/544 kB | 197/777 kB Progress (4): 3.1/3.5 MB | 0.7/1.2 MB | 291/544 kB | 197/777 kB Progress (4): 3.2/3.5 MB | 0.7/1.2 MB | 291/544 kB | 197/777 kB Progress (4): 3.2/3.5 MB | 0.7/1.2 MB | 295/544 kB | 197/777 kB Progress (4): 3.2/3.5 MB | 0.7/1.2 MB | 295/544 kB | 197/777 kB Progress (4): 3.2/3.5 MB | 0.7/1.2 MB | 295/544 kB | 201/777 kB Progress (4): 3.2/3.5 MB | 0.7/1.2 MB | 295/544 kB | 201/777 kB Progress (4): 3.2/3.5 MB | 0.7/1.2 MB | 299/544 kB | 201/777 kB Progress (4): 3.2/3.5 MB | 0.7/1.2 MB | 299/544 kB | 205/777 kB Progress (4): 3.2/3.5 MB | 0.7/1.2 MB | 299/544 kB | 205/777 kB Progress (4): 3.2/3.5 MB | 0.7/1.2 MB | 303/544 kB | 205/777 kB Progress (4): 3.2/3.5 MB | 0.7/1.2 MB | 303/544 kB | 205/777 kB Progress (4): 3.2/3.5 MB | 0.7/1.2 MB | 303/544 kB | 209/777 kB Progress (4): 3.2/3.5 MB | 0.7/1.2 MB | 307/544 kB | 209/777 kB Progress (4): 3.2/3.5 MB | 0.7/1.2 MB | 307/544 kB | 209/777 kB Progress (4): 3.2/3.5 MB | 0.7/1.2 MB | 307/544 kB | 209/777 kB Progress (4): 3.2/3.5 MB | 0.7/1.2 MB | 311/544 kB | 209/777 kB Progress (4): 3.2/3.5 MB | 0.7/1.2 MB | 311/544 kB | 213/777 kB Progress (4): 3.2/3.5 MB | 0.7/1.2 MB | 311/544 kB | 213/777 kB Progress (4): 3.2/3.5 MB | 0.7/1.2 MB | 315/544 kB | 213/777 kB Progress (4): 3.2/3.5 MB | 0.7/1.2 MB | 315/544 kB | 217/777 kB Progress (4): 3.2/3.5 MB | 0.7/1.2 MB | 315/544 kB | 217/777 kB Progress (4): 3.2/3.5 MB | 0.7/1.2 MB | 319/544 kB | 217/777 kB Progress (4): 3.2/3.5 MB | 0.7/1.2 MB | 319/544 kB | 221/777 kB Progress (4): 3.2/3.5 MB | 0.7/1.2 MB | 319/544 kB | 221/777 kB Progress (4): 3.2/3.5 MB | 0.7/1.2 MB | 319/544 kB | 221/777 kB Progress (4): 3.2/3.5 MB | 0.7/1.2 MB | 319/544 kB | 225/777 kB Progress (4): 3.2/3.5 MB | 0.7/1.2 MB | 324/544 kB | 225/777 kB Progress (4): 3.2/3.5 MB | 0.7/1.2 MB | 324/544 kB | 225/777 kB Progress (4): 3.2/3.5 MB | 0.7/1.2 MB | 324/544 kB | 229/777 kB Progress (4): 3.3/3.5 MB | 0.7/1.2 MB | 324/544 kB | 229/777 kB Progress (4): 3.3/3.5 MB | 0.7/1.2 MB | 328/544 kB | 229/777 kB Progress (4): 3.3/3.5 MB | 0.7/1.2 MB | 328/544 kB | 233/777 kB Progress (4): 3.3/3.5 MB | 0.7/1.2 MB | 328/544 kB | 233/777 kB Progress (4): 3.3/3.5 MB | 0.7/1.2 MB | 328/544 kB | 233/777 kB Progress (4): 3.3/3.5 MB | 0.7/1.2 MB | 328/544 kB | 238/777 kB Progress (4): 3.3/3.5 MB | 0.7/1.2 MB | 332/544 kB | 238/777 kB Progress (4): 3.3/3.5 MB | 0.7/1.2 MB | 332/544 kB | 238/777 kB Progress (4): 3.3/3.5 MB | 0.7/1.2 MB | 332/544 kB | 242/777 kB Progress (4): 3.3/3.5 MB | 0.7/1.2 MB | 336/544 kB | 242/777 kB Progress (4): 3.3/3.5 MB | 0.7/1.2 MB | 336/544 kB | 242/777 kB Progress (4): 3.3/3.5 MB | 0.7/1.2 MB | 340/544 kB | 242/777 kB Progress (4): 3.3/3.5 MB | 0.7/1.2 MB | 340/544 kB | 246/777 kB Progress (4): 3.3/3.5 MB | 0.7/1.2 MB | 340/544 kB | 246/777 kB Progress (4): 3.3/3.5 MB | 0.7/1.2 MB | 340/544 kB | 246/777 kB Progress (4): 3.3/3.5 MB | 0.7/1.2 MB | 344/544 kB | 246/777 kB Progress (4): 3.3/3.5 MB | 0.7/1.2 MB | 344/544 kB | 250/777 kB Progress (4): 3.3/3.5 MB | 0.7/1.2 MB | 344/544 kB | 250/777 kB Progress (4): 3.3/3.5 MB | 0.7/1.2 MB | 348/544 kB | 250/777 kB Progress (4): 3.3/3.5 MB | 0.7/1.2 MB | 348/544 kB | 250/777 kB Progress (4): 3.3/3.5 MB | 0.7/1.2 MB | 348/544 kB | 250/777 kB Progress (4): 3.3/3.5 MB | 0.7/1.2 MB | 348/544 kB | 254/777 kB Progress (4): 3.3/3.5 MB | 0.7/1.2 MB | 352/544 kB | 254/777 kB Progress (4): 3.3/3.5 MB | 0.7/1.2 MB | 352/544 kB | 254/777 kB Progress (4): 3.3/3.5 MB | 0.7/1.2 MB | 352/544 kB | 258/777 kB Progress (4): 3.3/3.5 MB | 0.7/1.2 MB | 352/544 kB | 258/777 kB Progress (4): 3.3/3.5 MB | 0.7/1.2 MB | 356/544 kB | 258/777 kB Progress (4): 3.3/3.5 MB | 0.7/1.2 MB | 356/544 kB | 262/777 kB Progress (4): 3.3/3.5 MB | 0.8/1.2 MB | 356/544 kB | 262/777 kB Progress (4): 3.4/3.5 MB | 0.8/1.2 MB | 356/544 kB | 262/777 kB Progress (4): 3.4/3.5 MB | 0.8/1.2 MB | 360/544 kB | 262/777 kB Progress (4): 3.4/3.5 MB | 0.8/1.2 MB | 360/544 kB | 266/777 kB Progress (4): 3.4/3.5 MB | 0.8/1.2 MB | 360/544 kB | 266/777 kB Progress (4): 3.4/3.5 MB | 0.8/1.2 MB | 365/544 kB | 266/777 kB Progress (4): 3.4/3.5 MB | 0.8/1.2 MB | 365/544 kB | 270/777 kB Progress (4): 3.4/3.5 MB | 0.8/1.2 MB | 365/544 kB | 270/777 kB Progress (4): 3.4/3.5 MB | 0.8/1.2 MB | 369/544 kB | 270/777 kB Progress (4): 3.4/3.5 MB | 0.8/1.2 MB | 369/544 kB | 274/777 kB Progress (4): 3.4/3.5 MB | 0.8/1.2 MB | 369/544 kB | 274/777 kB Progress (4): 3.4/3.5 MB | 0.8/1.2 MB | 369/544 kB | 274/777 kB Progress (4): 3.4/3.5 MB | 0.8/1.2 MB | 369/544 kB | 279/777 kB Progress (4): 3.4/3.5 MB | 0.8/1.2 MB | 373/544 kB | 279/777 kB Progress (4): 3.4/3.5 MB | 0.8/1.2 MB | 373/544 kB | 279/777 kB Progress (4): 3.4/3.5 MB | 0.8/1.2 MB | 373/544 kB | 283/777 kB Progress (4): 3.4/3.5 MB | 0.8/1.2 MB | 373/544 kB | 283/777 kB Progress (4): 3.4/3.5 MB | 0.8/1.2 MB | 377/544 kB | 283/777 kB Progress (4): 3.4/3.5 MB | 0.8/1.2 MB | 377/544 kB | 287/777 kB Progress (4): 3.4/3.5 MB | 0.8/1.2 MB | 377/544 kB | 287/777 kB Progress (4): 3.4/3.5 MB | 0.8/1.2 MB | 377/544 kB | 287/777 kB Progress (4): 3.4/3.5 MB | 0.8/1.2 MB | 377/544 kB | 291/777 kB Progress (4): 3.4/3.5 MB | 0.8/1.2 MB | 381/544 kB | 291/777 kB Progress (4): 3.4/3.5 MB | 0.8/1.2 MB | 381/544 kB | 295/777 kB Progress (4): 3.4/3.5 MB | 0.8/1.2 MB | 381/544 kB | 295/777 kB Progress (4): 3.4/3.5 MB | 0.8/1.2 MB | 385/544 kB | 295/777 kB Progress (4): 3.4/3.5 MB | 0.8/1.2 MB | 385/544 kB | 295/777 kB Progress (4): 3.4/3.5 MB | 0.8/1.2 MB | 385/544 kB | 295/777 kB Progress (4): 3.4/3.5 MB | 0.8/1.2 MB | 389/544 kB | 295/777 kB Progress (4): 3.4/3.5 MB | 0.8/1.2 MB | 389/544 kB | 299/777 kB Progress (4): 3.4/3.5 MB | 0.8/1.2 MB | 389/544 kB | 299/777 kB Progress (4): 3.4/3.5 MB | 0.8/1.2 MB | 393/544 kB | 299/777 kB Progress (4): 3.5/3.5 MB | 0.8/1.2 MB | 393/544 kB | 299/777 kB Progress (4): 3.5/3.5 MB | 0.8/1.2 MB | 393/544 kB | 303/777 kB Progress (4): 3.5/3.5 MB | 0.8/1.2 MB | 397/544 kB | 303/777 kB Progress (4): 3.5/3.5 MB | 0.8/1.2 MB | 397/544 kB | 303/777 kB Progress (4): 3.5/3.5 MB | 0.8/1.2 MB | 397/544 kB | 303/777 kB Progress (4): 3.5/3.5 MB | 0.8/1.2 MB | 397/544 kB | 307/777 kB Progress (4): 3.5/3.5 MB | 0.8/1.2 MB | 401/544 kB | 307/777 kB Progress (4): 3.5/3.5 MB | 0.8/1.2 MB | 401/544 kB | 311/777 kB Progress (4): 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| 463/544 kB | 373/777 kB Progress (3): 0.9/1.2 MB | 463/544 kB | 377/777 kB Progress (3): 0.9/1.2 MB | 467/544 kB | 377/777 kB Progress (3): 0.9/1.2 MB | 467/544 kB | 377/777 kB Progress (3): 0.9/1.2 MB | 471/544 kB | 377/777 kB Progress (3): 0.9/1.2 MB | 471/544 kB | 381/777 kB Progress (3): 1.0/1.2 MB | 471/544 kB | 381/777 kB Progress (3): 1.0/1.2 MB | 471/544 kB | 385/777 kB Progress (3): 1.0/1.2 MB | 471/544 kB | 385/777 kB Progress (3): 1.0/1.2 MB | 475/544 kB | 385/777 kB Progress (3): 1.0/1.2 MB | 475/544 kB | 389/777 kB Progress (3): 1.0/1.2 MB | 479/544 kB | 389/777 kB Progress (3): 1.0/1.2 MB | 479/544 kB | 393/777 kB Progress (3): 1.0/1.2 MB | 479/544 kB | 393/777 kB Progress (3): 1.0/1.2 MB | 483/544 kB | 393/777 kB Progress (3): 1.0/1.2 MB | 483/544 kB | 393/777 kB Progress (3): 1.0/1.2 MB | 487/544 kB | 393/777 kB Progress (3): 1.0/1.2 MB | 487/544 kB | 397/777 kB Progress (3): 1.0/1.2 MB | 487/544 kB | 397/777 kB Progress (3): 1.0/1.2 MB | 491/544 kB | 397/777 kB Progress (3): 1.0/1.2 MB | 491/544 kB | 397/777 kB Progress (3): 1.0/1.2 MB | 491/544 kB | 401/777 kB Progress (3): 1.0/1.2 MB | 495/544 kB | 401/777 kB Progress (3): 1.0/1.2 MB | 495/544 kB | 406/777 kB Progress (3): 1.0/1.2 MB | 499/544 kB | 406/777 kB Progress (3): 1.0/1.2 MB | 499/544 kB | 406/777 kB Progress (3): 1.0/1.2 MB | 504/544 kB | 406/777 kB Progress (3): 1.0/1.2 MB | 504/544 kB | 410/777 kB Progress (3): 1.0/1.2 MB | 504/544 kB | 410/777 kB Progress (3): 1.0/1.2 MB | 508/544 kB | 410/777 kB Progress (3): 1.0/1.2 MB | 508/544 kB | 414/777 kB Progress (3): 1.0/1.2 MB | 512/544 kB | 414/777 kB Progress (3): 1.0/1.2 MB | 512/544 kB | 414/777 kB Progress (3): 1.0/1.2 MB | 516/544 kB | 414/777 kB Progress (3): 1.0/1.2 MB | 516/544 kB | 418/777 kB Progress (3): 1.0/1.2 MB | 520/544 kB | 418/777 kB Progress (3): 1.0/1.2 MB | 520/544 kB | 418/777 kB Progress (3): 1.0/1.2 MB | 520/544 kB | 422/777 kB Progress (3): 1.0/1.2 MB | 524/544 kB | 422/777 kB Progress (3): 1.0/1.2 MB | 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| 442/777 kB | 12/166 kB Progress (4): 1.1/1.2 MB | 544 kB | 446/777 kB | 12/166 kB Progress (4): 1.1/1.2 MB | 544 kB | 446/777 kB | 16/166 kB Progress (4): 1.1/1.2 MB | 544 kB | 451/777 kB | 16/166 kB Progress (4): 1.1/1.2 MB | 544 kB | 451/777 kB | 16/166 kB Progress (4): 1.1/1.2 MB | 544 kB | 451/777 kB | 20/166 kB Progress (4): 1.1/1.2 MB | 544 kB | 455/777 kB | 20/166 kB Progress (4): 1.1/1.2 MB | 544 kB | 455/777 kB | 25/166 kB Progress (4): 1.1/1.2 MB | 544 kB | 455/777 kB | 25/166 kB Progress (4): 1.1/1.2 MB | 544 kB | 455/777 kB | 29/166 kB Progress (4): 1.1/1.2 MB | 544 kB | 459/777 kB | 29/166 kB Progress (4): 1.1/1.2 MB | 544 kB | 459/777 kB | 33/166 kB Progress (4): 1.1/1.2 MB | 544 kB | 459/777 kB | 33/166 kB Progress (4): 1.1/1.2 MB | 544 kB | 463/777 kB | 33/166 kB Progress (4): 1.1/1.2 MB | 544 kB | 463/777 kB | 37/166 kB Progress (4): 1.1/1.2 MB | 544 kB | 467/777 kB | 37/166 kB Progress (4): 1.1/1.2 MB | 544 kB | 467/777 kB | 41/166 kB Progress (4): 1.1/1.2 MB | 544 kB | 467/777 kB | 41/166 kB Progress (4): 1.1/1.2 MB | 544 kB | 467/777 kB | 45/166 kB Progress (4): 1.1/1.2 MB | 544 kB | 471/777 kB | 45/166 kB Progress (4): 1.1/1.2 MB | 544 kB | 471/777 kB | 49/166 kB Progress (4): 1.1/1.2 MB | 544 kB | 471/777 kB | 49/166 kB Progress (4): 1.1/1.2 MB | 544 kB | 475/777 kB | 49/166 kB Progress (4): 1.1/1.2 MB | 544 kB | 475/777 kB | 53/166 kB Progress (4): 1.1/1.2 MB | 544 kB | 475/777 kB | 53/166 kB Progress (4): 1.1/1.2 MB | 544 kB | 479/777 kB | 53/166 kB Progress (4): 1.1/1.2 MB | 544 kB | 479/777 kB | 57/166 kB Progress (4): 1.1/1.2 MB | 544 kB | 483/777 kB | 57/166 kB Progress (4): 1.1/1.2 MB | 544 kB | 483/777 kB | 57/166 kB Progress (4): 1.1/1.2 MB | 544 kB | 487/777 kB | 57/166 kB Progress (4): 1.1/1.2 MB | 544 kB | 487/777 kB | 61/166 kB Progress (4): 1.1/1.2 MB | 544 kB | 492/777 kB | 61/166 kB Progress (4): 1.1/1.2 MB | 544 kB | 492/777 kB | 66/166 kB Progress (4): 1.1/1.2 MB | 544 kB | 492/777 kB | 66/166 kB Progress (4): 1.1/1.2 MB | 544 kB | 496/777 kB | 66/166 kB Progress (4): 1.1/1.2 MB | 544 kB | 496/777 kB | 66/166 kB Progress (4): 1.1/1.2 MB | 544 kB | 500/777 kB | 66/166 kB Progress (4): 1.1/1.2 MB | 544 kB | 500/777 kB | 70/166 kB Progress (4): 1.2/1.2 MB | 544 kB | 500/777 kB | 70/166 kB Progress (4): 1.2/1.2 MB | 544 kB | 504/777 kB | 70/166 kB Progress (4): 1.2/1.2 MB | 544 kB | 504/777 kB | 70/166 kB Progress (4): 1.2/1.2 MB | 544 kB | 504/777 kB | 74/166 kB Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/hadoop/hadoop-mapreduce-client-app/2.7.5/hadoop-mapreduce-client-app-2.7.5.jar (544 kB at 3.2 MB/s) Progress (3): 1.2/1.2 MB | 508/777 kB | 74/166 kB Downloading from central: https://repo.maven.apache.org/maven2/org/apache/hadoop/hadoop-yarn-server-common/2.7.5/hadoop-yarn-server-common-2.7.5.jar Progress (3): 1.2/1.2 MB | 508/777 kB | 74/166 kB Progress (3): 1.2/1.2 MB | 508/777 kB | 78/166 kB Progress (3): 1.2/1.2 MB | 512/777 kB | 78/166 kB Progress (3): 1.2/1.2 MB | 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Progress (3): 1.2 MB | 545/777 kB | 119/166 kB Progress (3): 1.2 MB | 549/777 kB | 119/166 kB Progress (3): 1.2 MB | 549/777 kB | 123/166 kB Progress (3): 1.2 MB | 553/777 kB | 123/166 kB Progress (3): 1.2 MB | 553/777 kB | 127/166 kB Progress (3): 1.2 MB | 557/777 kB | 127/166 kB Progress (3): 1.2 MB | 557/777 kB | 131/166 kB Progress (3): 1.2 MB | 561/777 kB | 131/166 kB Progress (3): 1.2 MB | 561/777 kB | 135/166 kB Progress (3): 1.2 MB | 565/777 kB | 135/166 kB Progress (3): 1.2 MB | 565/777 kB | 139/166 kB Progress (3): 1.2 MB | 569/777 kB | 139/166 kB Progress (3): 1.2 MB | 569/777 kB | 143/166 kB Progress (3): 1.2 MB | 573/777 kB | 143/166 kB Progress (3): 1.2 MB | 573/777 kB | 147/166 kB Progress (3): 1.2 MB | 578/777 kB | 147/166 kB Progress (3): 1.2 MB | 578/777 kB | 152/166 kB Progress (3): 1.2 MB | 582/777 kB | 152/166 kB Progress (3): 1.2 MB | 582/777 kB | 156/166 kB Progress (3): 1.2 MB | 586/777 kB | 156/166 kB Progress (3): 1.2 MB | 586/777 kB | 160/166 kB Progress (3): 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Progress (3): 2.4/9.7 MB | 1.8/2.4 MB | 1.2/7.1 MB Progress (3): 2.4/9.7 MB | 1.8/2.4 MB | 1.2/7.1 MB Progress (3): 2.4/9.7 MB | 1.9/2.4 MB | 1.2/7.1 MB Progress (3): 2.4/9.7 MB | 1.9/2.4 MB | 1.2/7.1 MB Progress (3): 2.4/9.7 MB | 1.9/2.4 MB | 1.2/7.1 MB Progress (3): 2.4/9.7 MB | 1.9/2.4 MB | 1.3/7.1 MB Progress (3): 2.4/9.7 MB | 1.9/2.4 MB | 1.3/7.1 MB Progress (3): 2.5/9.7 MB | 1.9/2.4 MB | 1.3/7.1 MB Progress (3): 2.5/9.7 MB | 1.9/2.4 MB | 1.3/7.1 MB Progress (3): 2.5/9.7 MB | 1.9/2.4 MB | 1.3/7.1 MB Progress (3): 2.5/9.7 MB | 1.9/2.4 MB | 1.3/7.1 MB Progress (3): 2.5/9.7 MB | 1.9/2.4 MB | 1.3/7.1 MB Progress (3): 2.5/9.7 MB | 1.9/2.4 MB | 1.3/7.1 MB Progress (3): 2.5/9.7 MB | 1.9/2.4 MB | 1.4/7.1 MB Progress (3): 2.5/9.7 MB | 2.0/2.4 MB | 1.4/7.1 MB Progress (3): 2.5/9.7 MB | 2.0/2.4 MB | 1.4/7.1 MB Progress (3): 2.5/9.7 MB | 2.0/2.4 MB | 1.4/7.1 MB Progress (3): 2.6/9.7 MB | 2.0/2.4 MB | 1.4/7.1 MB Progress (3): 2.6/9.7 MB | 2.0/2.4 MB | 1.4/7.1 MB Progress (3): 2.6/9.7 MB | 2.0/2.4 MB | 1.4/7.1 MB Progress (3): 2.6/9.7 MB | 2.0/2.4 MB | 1.4/7.1 MB Progress (3): 2.6/9.7 MB | 2.0/2.4 MB | 1.4/7.1 MB Progress (3): 2.6/9.7 MB | 2.0/2.4 MB | 1.4/7.1 MB Progress (3): 2.6/9.7 MB | 2.0/2.4 MB | 1.5/7.1 MB Progress (3): 2.6/9.7 MB | 2.0/2.4 MB | 1.5/7.1 MB Progress (3): 2.6/9.7 MB | 2.1/2.4 MB | 1.5/7.1 MB Progress (3): 2.6/9.7 MB | 2.1/2.4 MB | 1.5/7.1 MB Progress (3): 2.6/9.7 MB | 2.1/2.4 MB | 1.5/7.1 MB Progress (3): 2.6/9.7 MB | 2.1/2.4 MB | 1.5/7.1 MB Progress (3): 2.7/9.7 MB | 2.1/2.4 MB | 1.5/7.1 MB Progress (3): 2.7/9.7 MB | 2.1/2.4 MB | 1.5/7.1 MB Progress (3): 2.7/9.7 MB | 2.1/2.4 MB | 1.6/7.1 MB Progress (3): 2.7/9.7 MB | 2.1/2.4 MB | 1.6/7.1 MB Progress (3): 2.7/9.7 MB | 2.1/2.4 MB | 1.6/7.1 MB Progress (3): 2.7/9.7 MB | 2.1/2.4 MB | 1.6/7.1 MB Progress (3): 2.7/9.7 MB | 2.1/2.4 MB | 1.6/7.1 MB Progress (3): 2.7/9.7 MB | 2.1/2.4 MB | 1.6/7.1 MB Progress (3): 2.7/9.7 MB | 2.2/2.4 MB | 1.6/7.1 MB Progress (3): 2.7/9.7 MB | 2.2/2.4 MB | 1.6/7.1 MB Progress (3): 2.7/9.7 MB | 2.2/2.4 MB | 1.6/7.1 MB Progress (3): 2.8/9.7 MB | 2.2/2.4 MB | 1.6/7.1 MB Progress (3): 2.8/9.7 MB | 2.2/2.4 MB | 1.6/7.1 MB Progress (3): 2.8/9.7 MB | 2.2/2.4 MB | 1.7/7.1 MB Progress (3): 2.8/9.7 MB | 2.2/2.4 MB | 1.7/7.1 MB Progress (3): 2.8/9.7 MB | 2.2/2.4 MB | 1.7/7.1 MB Progress (3): 2.8/9.7 MB | 2.2/2.4 MB | 1.7/7.1 MB Progress (3): 2.8/9.7 MB | 2.2/2.4 MB | 1.7/7.1 MB Progress (3): 2.8/9.7 MB | 2.2/2.4 MB | 1.7/7.1 MB Progress (3): 2.9/9.7 MB | 2.2/2.4 MB | 1.7/7.1 MB Progress (3): 2.9/9.7 MB | 2.3/2.4 MB | 1.7/7.1 MB Progress (3): 2.9/9.7 MB | 2.3/2.4 MB | 1.8/7.1 MB Progress (3): 2.9/9.7 MB | 2.3/2.4 MB | 1.8/7.1 MB Progress (3): 2.9/9.7 MB | 2.3/2.4 MB | 1.8/7.1 MB Progress (3): 2.9/9.7 MB | 2.3/2.4 MB | 1.8/7.1 MB Progress (3): 2.9/9.7 MB | 2.3/2.4 MB | 1.8/7.1 MB Progress (3): 2.9/9.7 MB | 2.3/2.4 MB | 1.8/7.1 MB Progress (3): 2.9/9.7 MB | 2.3/2.4 MB | 1.8/7.1 MB Progress (3): 3.0/9.7 MB | 2.3/2.4 MB | 1.8/7.1 MB Progress (3): 3.0/9.7 MB | 2.3/2.4 MB | 1.8/7.1 MB Progress (3): 3.0/9.7 MB | 2.3/2.4 MB | 1.8/7.1 MB Progress (3): 3.0/9.7 MB | 2.4/2.4 MB | 1.8/7.1 MB Progress (3): 3.0/9.7 MB | 2.4/2.4 MB | 1.9/7.1 MB Progress (3): 3.0/9.7 MB | 2.4/2.4 MB | 1.9/7.1 MB Progress (3): 3.0/9.7 MB | 2.4/2.4 MB | 1.9/7.1 MB Progress (3): 3.0/9.7 MB | 2.4/2.4 MB | 1.9/7.1 MB Progress (3): 3.0/9.7 MB | 2.4/2.4 MB | 1.9/7.1 MB Progress (3): 3.0/9.7 MB | 2.4 MB | 1.9/7.1 MB Progress (3): 3.1/9.7 MB | 2.4 MB | 1.9/7.1 MB Progress (3): 3.1/9.7 MB | 2.4 MB | 2.0/7.1 MB Progress (3): 3.1/9.7 MB | 2.4 MB | 2.0/7.1 MB Progress (3): 3.1/9.7 MB | 2.4 MB | 2.0/7.1 MB Progress (3): 3.1/9.7 MB | 2.4 MB | 2.0/7.1 MB Progress (3): 3.1/9.7 MB | 2.4 MB | 2.0/7.1 MB Progress (3): 3.2/9.7 MB | 2.4 MB | 2.0/7.1 MB Progress (3): 3.2/9.7 MB | 2.4 MB | 2.1/7.1 MB Progress (3): 3.2/9.7 MB | 2.4 MB | 2.1/7.1 MB Progress (3): 3.2/9.7 MB | 2.4 MB | 2.1/7.1 MB Progress (3): 3.3/9.7 MB | 2.4 MB | 2.1/7.1 MB Progress (3): 3.3/9.7 MB | 2.4 MB | 2.2/7.1 MB Progress (3): 3.3/9.7 MB | 2.4 MB | 2.2/7.1 MB Progress (3): 3.3/9.7 MB | 2.4 MB | 2.2/7.1 MB Progress (3): 3.3/9.7 MB | 2.4 MB | 2.2/7.1 MB Progress (3): 3.4/9.7 MB | 2.4 MB | 2.2/7.1 MB Progress (3): 3.4/9.7 MB | 2.4 MB | 2.3/7.1 MB Progress (3): 3.4/9.7 MB | 2.4 MB | 2.3/7.1 MB Progress (3): 3.4/9.7 MB | 2.4 MB | 2.3/7.1 MB Progress (3): 3.5/9.7 MB | 2.4 MB | 2.3/7.1 MB Progress (3): 3.5/9.7 MB | 2.4 MB | 2.4/7.1 MB Progress (3): 3.5/9.7 MB | 2.4 MB | 2.4/7.1 MB Progress (3): 3.5/9.7 MB | 2.4 MB | 2.4/7.1 MB Progress (3): 3.6/9.7 MB | 2.4 MB | 2.4/7.1 MB Progress (3): 3.6/9.7 MB | 2.4 MB | 2.5/7.1 MB Progress (3): 3.6/9.7 MB | 2.4 MB | 2.5/7.1 MB Progress (3): 3.6/9.7 MB | 2.4 MB | 2.5/7.1 MB Progress (3): 3.6/9.7 MB | 2.4 MB | 2.5/7.1 MB Progress (3): 3.7/9.7 MB | 2.4 MB | 2.5/7.1 MB Progress (3): 3.7/9.7 MB | 2.4 MB | 2.6/7.1 MB Progress (3): 3.7/9.7 MB | 2.4 MB | 2.6/7.1 MB Progress (3): 3.7/9.7 MB | 2.4 MB | 2.6/7.1 MB Progress (3): 3.8/9.7 MB | 2.4 MB | 2.6/7.1 MB Progress (3): 3.8/9.7 MB | 2.4 MB | 2.7/7.1 MB Progress (3): 3.8/9.7 MB | 2.4 MB | 2.7/7.1 MB Progress (3): 3.8/9.7 MB | 2.4 MB | 2.7/7.1 MB Progress (3): 3.9/9.7 MB | 2.4 MB | 2.7/7.1 MB Progress (3): 3.9/9.7 MB | 2.4 MB | 2.7/7.1 MB Progress (3): 3.9/9.7 MB | 2.4 MB | 2.7/7.1 MB Progress (3): 3.9/9.7 MB | 2.4 MB | 2.8/7.1 MB Progress (3): 4.0/9.7 MB | 2.4 MB | 2.8/7.1 MB Progress (3): 4.0/9.7 MB | 2.4 MB | 2.8/7.1 MB Progress (3): 4.0/9.7 MB | 2.4 MB | 2.9/7.1 MB Progress (3): 4.0/9.7 MB | 2.4 MB | 2.9/7.1 MB Progress (3): 4.0/9.7 MB | 2.4 MB | 2.9/7.1 MB Progress (3): 4.1/9.7 MB | 2.4 MB | 2.9/7.1 MB Progress (3): 4.1/9.7 MB | 2.4 MB | 2.9/7.1 MB Progress (3): 4.1/9.7 MB | 2.4 MB | 2.9/7.1 MB Progress (3): 4.1/9.7 MB | 2.4 MB | 3.0/7.1 MB Progress (3): 4.2/9.7 MB | 2.4 MB | 3.0/7.1 MB Progress (3): 4.2/9.7 MB | 2.4 MB | 3.0/7.1 MB Progress (3): 4.2/9.7 MB | 2.4 MB | 3.0/7.1 MB Progress (3): 4.2/9.7 MB | 2.4 MB | 3.1/7.1 MB Progress (3): 4.3/9.7 MB | 2.4 MB | 3.1/7.1 MB Progress (3): 4.3/9.7 MB | 2.4 MB | 3.1/7.1 MB Progress (3): 4.3/9.7 MB | 2.4 MB | 3.1/7.1 MB Progress (3): 4.3/9.7 MB | 2.4 MB | 3.2/7.1 MB Progress (3): 4.3/9.7 MB | 2.4 MB | 3.2/7.1 MB Progress (3): 4.4/9.7 MB | 2.4 MB | 3.2/7.1 MB Progress (3): 4.4/9.7 MB | 2.4 MB | 3.2/7.1 MB Progress (3): 4.4/9.7 MB | 2.4 MB | 3.2/7.1 MB Progress (3): 4.4/9.7 MB | 2.4 MB | 3.3/7.1 MB Progress (3): 4.5/9.7 MB | 2.4 MB | 3.3/7.1 MB Progress (3): 4.5/9.7 MB | 2.4 MB | 3.3/7.1 MB Progress (3): 4.5/9.7 MB | 2.4 MB | 3.3/7.1 MB Progress (3): 4.5/9.7 MB | 2.4 MB | 3.4/7.1 MB Progress (3): 4.6/9.7 MB | 2.4 MB | 3.4/7.1 MB Progress (3): 4.6/9.7 MB | 2.4 MB | 3.4/7.1 MB Progress (3): 4.6/9.7 MB | 2.4 MB | 3.4/7.1 MB Progress (3): 4.6/9.7 MB | 2.4 MB | 3.4/7.1 MB Progress (3): 4.7/9.7 MB | 2.4 MB | 3.4/7.1 MB Progress (3): 4.7/9.7 MB | 2.4 MB | 3.5/7.1 MB Progress (3): 4.7/9.7 MB | 2.4 MB | 3.5/7.1 MB Progress (3): 4.7/9.7 MB | 2.4 MB | 3.5/7.1 MB Progress (3): 4.7/9.7 MB | 2.4 MB | 3.6/7.1 MB Progress (3): 4.8/9.7 MB | 2.4 MB | 3.6/7.1 MB Progress (4): 4.8/9.7 MB | 2.4 MB | 3.6/7.1 MB | 0/1.6 MB Progress (4): 4.8/9.7 MB | 2.4 MB | 3.6/7.1 MB | 0/1.6 MB Progress (4): 4.8/9.7 MB | 2.4 MB | 3.6/7.1 MB | 0/1.6 MB Progress (4): 4.8/9.7 MB | 2.4 MB | 3.6/7.1 MB | 0/1.6 MB Progress (4): 4.8/9.7 MB | 2.4 MB | 3.6/7.1 MB | 0/1.6 MB Progress (4): 4.8/9.7 MB | 2.4 MB | 3.6/7.1 MB | 0/1.6 MB Progress (4): 4.8/9.7 MB | 2.4 MB | 3.6/7.1 MB | 0/1.6 MB Progress (4): 4.8/9.7 MB | 2.4 MB | 3.6/7.1 MB | 0/1.6 MB Progress (4): 4.9/9.7 MB | 2.4 MB | 3.6/7.1 MB | 0/1.6 MB Progress (4): 4.9/9.7 MB | 2.4 MB | 3.6/7.1 MB | 0/1.6 MB Progress (4): 4.9/9.7 MB | 2.4 MB | 3.6/7.1 MB | 0.1/1.6 MB Progress (4): 4.9/9.7 MB | 2.4 MB | 3.7/7.1 MB | 0.1/1.6 MB Progress (4): 4.9/9.7 MB | 2.4 MB | 3.7/7.1 MB | 0.1/1.6 MB Progress (4): 4.9/9.7 MB | 2.4 MB | 3.7/7.1 MB | 0.1/1.6 MB Progress (4): 4.9/9.7 MB | 2.4 MB | 3.7/7.1 MB | 0.1/1.6 MB Progress (4): 4.9/9.7 MB | 2.4 MB | 3.7/7.1 MB | 0.1/1.6 MB Progress (4): 4.9/9.7 MB | 2.4 MB | 3.7/7.1 MB | 0.1/1.6 MB Progress (4): 4.9/9.7 MB | 2.4 MB | 3.7/7.1 MB | 0.1/1.6 MB Progress (4): 4.9/9.7 MB | 2.4 MB | 3.7/7.1 MB | 0.1/1.6 MB Progress (4): 5.0/9.7 MB | 2.4 MB | 3.7/7.1 MB | 0.1/1.6 MB Progress (4): 5.0/9.7 MB | 2.4 MB | 3.7/7.1 MB | 0.1/1.6 MB Progress (4): 5.0/9.7 MB | 2.4 MB | 3.8/7.1 MB | 0.1/1.6 MB Progress (4): 5.0/9.7 MB | 2.4 MB | 3.8/7.1 MB | 0.1/1.6 MB Progress (4): 5.0/9.7 MB | 2.4 MB | 3.8/7.1 MB | 0.1/1.6 MB Progress (4): 5.0/9.7 MB | 2.4 MB | 3.8/7.1 MB | 0.1/1.6 MB Progress (4): 5.0/9.7 MB | 2.4 MB | 3.8/7.1 MB | 0.1/1.6 MB Progress (4): 5.0/9.7 MB | 2.4 MB | 3.8/7.1 MB | 0.1/1.6 MB Progress (4): 5.0/9.7 MB | 2.4 MB | 3.8/7.1 MB | 0.1/1.6 MB Progress (4): 5.0/9.7 MB | 2.4 MB | 3.8/7.1 MB | 0.1/1.6 MB Progress (4): 5.0/9.7 MB | 2.4 MB | 3.8/7.1 MB | 0.2/1.6 MB Progress (4): 5.0/9.7 MB | 2.4 MB | 3.8/7.1 MB | 0.2/1.6 MB Progress (4): 5.1/9.7 MB | 2.4 MB | 3.8/7.1 MB | 0.2/1.6 MB Progress (4): 5.1/9.7 MB | 2.4 MB | 3.8/7.1 MB | 0.2/1.6 MB Progress (4): 5.1/9.7 MB | 2.4 MB | 3.8/7.1 MB | 0.2/1.6 MB Progress (4): 5.1/9.7 MB | 2.4 MB | 3.8/7.1 MB | 0.2/1.6 MB Progress (4): 5.1/9.7 MB | 2.4 MB | 3.9/7.1 MB | 0.2/1.6 MB Progress (4): 5.1/9.7 MB | 2.4 MB | 3.9/7.1 MB | 0.2/1.6 MB Progress (4): 5.1/9.7 MB | 2.4 MB | 3.9/7.1 MB | 0.2/1.6 MB Progress (4): 5.1/9.7 MB | 2.4 MB | 3.9/7.1 MB | 0.2/1.6 MB Progress (4): 5.1/9.7 MB | 2.4 MB | 3.9/7.1 MB | 0.2/1.6 MB Progress (4): 5.1/9.7 MB | 2.4 MB | 3.9/7.1 MB | 0.2/1.6 MB Progress (4): 5.1/9.7 MB | 2.4 MB | 3.9/7.1 MB | 0.2/1.6 MB Progress (4): 5.1/9.7 MB | 2.4 MB | 3.9/7.1 MB | 0.2/1.6 MB Progress (4): 5.2/9.7 MB | 2.4 MB | 3.9/7.1 MB | 0.2/1.6 MB Progress (4): 5.2/9.7 MB | 2.4 MB | 3.9/7.1 MB | 0.2/1.6 MB Progress (4): 5.2/9.7 MB | 2.4 MB | 3.9/7.1 MB | 0.2/1.6 MB Progress (4): 5.2/9.7 MB | 2.4 MB | 4.0/7.1 MB | 0.2/1.6 MB Progress (4): 5.2/9.7 MB | 2.4 MB | 4.0/7.1 MB | 0.2/1.6 MB Progress (4): 5.2/9.7 MB | 2.4 MB | 4.0/7.1 MB | 0.3/1.6 MB Progress (4): 5.2/9.7 MB | 2.4 MB | 4.0/7.1 MB | 0.3/1.6 MB Progress (4): 5.2/9.7 MB | 2.4 MB | 4.0/7.1 MB | 0.3/1.6 MB Progress (4): 5.2/9.7 MB | 2.4 MB | 4.0/7.1 MB | 0.3/1.6 MB Progress (4): 5.2/9.7 MB | 2.4 MB | 4.0/7.1 MB | 0.3/1.6 MB Progress (4): 5.2/9.7 MB | 2.4 MB | 4.0/7.1 MB | 0.3/1.6 MB Progress (4): 5.3/9.7 MB | 2.4 MB | 4.0/7.1 MB | 0.3/1.6 MB Progress (4): 5.3/9.7 MB | 2.4 MB | 4.0/7.1 MB | 0.3/1.6 MB Progress (4): 5.3/9.7 MB | 2.4 MB | 4.0/7.1 MB | 0.3/1.6 MB Progress (4): 5.3/9.7 MB | 2.4 MB | 4.1/7.1 MB | 0.3/1.6 MB Progress (4): 5.3/9.7 MB | 2.4 MB | 4.1/7.1 MB | 0.3/1.6 MB Progress (4): 5.3/9.7 MB | 2.4 MB | 4.1/7.1 MB | 0.3/1.6 MB Progress (4): 5.3/9.7 MB | 2.4 MB | 4.1/7.1 MB | 0.3/1.6 MB Progress (4): 5.3/9.7 MB | 2.4 MB | 4.1/7.1 MB | 0.3/1.6 MB Progress (4): 5.3/9.7 MB | 2.4 MB | 4.1/7.1 MB | 0.3/1.6 MB Progress (4): 5.3/9.7 MB | 2.4 MB | 4.1/7.1 MB | 0.3/1.6 MB Progress (4): 5.3/9.7 MB | 2.4 MB | 4.1/7.1 MB | 0.3/1.6 MB Progress (4): 5.3/9.7 MB | 2.4 MB | 4.1/7.1 MB | 0.3/1.6 MB Progress (4): 5.4/9.7 MB | 2.4 MB | 4.1/7.1 MB | 0.3/1.6 MB Progress (4): 5.4/9.7 MB | 2.4 MB | 4.1/7.1 MB | 0.4/1.6 MB Progress (4): 5.4/9.7 MB | 2.4 MB | 4.1/7.1 MB | 0.4/1.6 MB Progress (4): 5.4/9.7 MB | 2.4 MB | 4.1/7.1 MB | 0.4/1.6 MB Progress (4): 5.4/9.7 MB | 2.4 MB | 4.1/7.1 MB | 0.4/1.6 MB Progress (4): 5.4/9.7 MB | 2.4 MB | 4.1/7.1 MB | 0.4/1.6 MB Progress (4): 5.4/9.7 MB | 2.4 MB | 4.1/7.1 MB | 0.4/1.6 MB Progress (4): 5.4/9.7 MB | 2.4 MB | 4.2/7.1 MB | 0.4/1.6 MB Progress (4): 5.4/9.7 MB | 2.4 MB | 4.2/7.1 MB | 0.4/1.6 MB Progress (4): 5.4/9.7 MB | 2.4 MB | 4.2/7.1 MB | 0.4/1.6 MB Progress (4): 5.4/9.7 MB | 2.4 MB | 4.2/7.1 MB | 0.4/1.6 MB Progress (4): 5.4/9.7 MB | 2.4 MB | 4.2/7.1 MB | 0.4/1.6 MB Progress (4): 5.4/9.7 MB | 2.4 MB | 4.2/7.1 MB | 0.4/1.6 MB Progress (4): 5.5/9.7 MB | 2.4 MB | 4.2/7.1 MB | 0.4/1.6 MB Progress (4): 5.5/9.7 MB | 2.4 MB | 4.2/7.1 MB | 0.4/1.6 MB Progress (4): 5.5/9.7 MB | 2.4 MB | 4.2/7.1 MB | 0.4/1.6 MB Progress (4): 5.5/9.7 MB | 2.4 MB | 4.2/7.1 MB | 0.4/1.6 MB Progress (4): 5.5/9.7 MB | 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Progress (4): 5.6/9.7 MB | 2.4 MB | 4.4/7.1 MB | 0.5/1.6 MB Progress (4): 5.6/9.7 MB | 2.4 MB | 4.4/7.1 MB | 0.5/1.6 MB Progress (4): 5.6/9.7 MB | 2.4 MB | 4.4/7.1 MB | 0.5/1.6 MB Progress (4): 5.7/9.7 MB | 2.4 MB | 4.4/7.1 MB | 0.5/1.6 MB Progress (4): 5.7/9.7 MB | 2.4 MB | 4.4/7.1 MB | 0.5/1.6 MB Progress (4): 5.7/9.7 MB | 2.4 MB | 4.4/7.1 MB | 0.5/1.6 MB Progress (4): 5.7/9.7 MB | 2.4 MB | 4.5/7.1 MB | 0.5/1.6 MB Progress (4): 5.7/9.7 MB | 2.4 MB | 4.5/7.1 MB | 0.6/1.6 MB Progress (4): 5.7/9.7 MB | 2.4 MB | 4.5/7.1 MB | 0.6/1.6 MB Progress (4): 5.7/9.7 MB | 2.4 MB | 4.5/7.1 MB | 0.6/1.6 MB Progress (4): 5.7/9.7 MB | 2.4 MB | 4.5/7.1 MB | 0.6/1.6 MB Progress (4): 5.7/9.7 MB | 2.4 MB | 4.5/7.1 MB | 0.6/1.6 MB Progress (4): 5.7/9.7 MB | 2.4 MB | 4.5/7.1 MB | 0.6/1.6 MB Progress (4): 5.7/9.7 MB | 2.4 MB | 4.5/7.1 MB | 0.6/1.6 MB Progress (4): 5.7/9.7 MB | 2.4 MB | 4.5/7.1 MB | 0.6/1.6 MB Progress (4): 5.7/9.7 MB | 2.4 MB | 4.5/7.1 MB | 0.6/1.6 MB Progress (4): 5.7/9.7 MB | 2.4 MB | 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Progress (4): 6.3/9.7 MB | 5.1/7.1 MB | 1.0/1.6 MB | 30 kB Progress (4): 6.3/9.7 MB | 5.1/7.1 MB | 1.0/1.6 MB | 30 kB Progress (4): 6.4/9.7 MB | 5.1/7.1 MB | 1.0/1.6 MB | 30 kB Progress (4): 6.4/9.7 MB | 5.1/7.1 MB | 1.1/1.6 MB | 30 kB Progress (4): 6.4/9.7 MB | 5.1/7.1 MB | 1.1/1.6 MB | 30 kB Progress (4): 6.4/9.7 MB | 5.1/7.1 MB | 1.1/1.6 MB | 30 kB Progress (4): 6.4/9.7 MB | 5.1/7.1 MB | 1.1/1.6 MB | 30 kB Progress (4): 6.4/9.7 MB | 5.1/7.1 MB | 1.1/1.6 MB | 30 kB Progress (4): 6.4/9.7 MB | 5.1/7.1 MB | 1.1/1.6 MB | 30 kB Progress (4): 6.4/9.7 MB | 5.1/7.1 MB | 1.1/1.6 MB | 30 kB Progress (4): 6.4/9.7 MB | 5.2/7.1 MB | 1.1/1.6 MB | 30 kB Progress (4): 6.4/9.7 MB | 5.2/7.1 MB | 1.1/1.6 MB | 30 kB Progress (4): 6.5/9.7 MB | 5.2/7.1 MB | 1.1/1.6 MB | 30 kB Progress (4): 6.5/9.7 MB | 5.2/7.1 MB | 1.1/1.6 MB | 30 kB Progress (4): 6.5/9.7 MB | 5.2/7.1 MB | 1.1/1.6 MB | 30 kB Progress (4): 6.5/9.7 MB | 5.2/7.1 MB | 1.1/1.6 MB | 30 kB Progress (4): 6.5/9.7 MB | 5.2/7.1 MB | 1.1/1.6 MB | 30 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30 kB Progress (4): 6.7/9.7 MB | 5.3/7.1 MB | 1.2/1.6 MB | 30 kB Progress (4): 6.7/9.7 MB | 5.3/7.1 MB | 1.2/1.6 MB | 30 kB Progress (4): 6.7/9.7 MB | 5.3/7.1 MB | 1.2/1.6 MB | 30 kB Progress (4): 6.7/9.7 MB | 5.4/7.1 MB | 1.2/1.6 MB | 30 kB Progress (4): 6.7/9.7 MB | 5.4/7.1 MB | 1.2/1.6 MB | 30 kB Progress (4): 6.7/9.7 MB | 5.4/7.1 MB | 1.2/1.6 MB | 30 kB Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/spark/spark-sketch_2.12/3.0.1/spark-sketch_2.12-3.0.1.jar (30 kB at 40 kB/s) Progress (3): 6.7/9.7 MB | 5.4/7.1 MB | 1.2/1.6 MB Progress (3): 6.8/9.7 MB | 5.4/7.1 MB | 1.2/1.6 MB Progress (3): 6.8/9.7 MB | 5.4/7.1 MB | 1.3/1.6 MB Progress (3): 6.8/9.7 MB | 5.4/7.1 MB | 1.3/1.6 MB Downloading from central: https://repo.maven.apache.org/maven2/org/apache/spark/spark-catalyst_2.12/3.0.1/spark-catalyst_2.12-3.0.1.jar Progress (3): 6.8/9.7 MB | 5.4/7.1 MB | 1.3/1.6 MB Progress (3): 6.8/9.7 MB | 5.4/7.1 MB | 1.3/1.6 MB Progress (3): 6.8/9.7 MB | 5.4/7.1 MB | 1.3/1.6 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3.0/8.4 MB | 0.8/1.7 MB | 268 kB Progress (4): 5.4/9.4 MB | 3.0/8.4 MB | 0.8/1.7 MB | 268 kB Progress (4): 5.4/9.4 MB | 3.0/8.4 MB | 0.8/1.7 MB | 268 kB Progress (4): 5.4/9.4 MB | 3.1/8.4 MB | 0.8/1.7 MB | 268 kB Progress (4): 5.4/9.4 MB | 3.1/8.4 MB | 0.8/1.7 MB | 268 kB Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/commons/commons-jexl/2.1.1/commons-jexl-2.1.1.jar (268 kB at 291 kB/s) Progress (3): 5.5/9.4 MB | 3.1/8.4 MB | 0.8/1.7 MB Progress (3): 5.5/9.4 MB | 3.1/8.4 MB | 0.8/1.7 MB Progress (3): 5.5/9.4 MB | 3.1/8.4 MB | 0.8/1.7 MB Downloading from central: https://repo.maven.apache.org/maven2/commons-logging/commons-logging/1.1.1/commons-logging-1.1.1.jar Progress (3): 5.5/9.4 MB | 3.1/8.4 MB | 0.8/1.7 MB Progress (3): 5.5/9.4 MB | 3.1/8.4 MB | 0.8/1.7 MB Progress (3): 5.5/9.4 MB | 3.1/8.4 MB | 0.8/1.7 MB Progress (3): 5.5/9.4 MB | 3.1/8.4 MB | 0.8/1.7 MB Progress (3): 5.5/9.4 MB | 3.2/8.4 MB | 0.8/1.7 MB Progress (3): 5.5/9.4 MB | 3.2/8.4 MB | 0.9/1.7 MB Progress (3): 5.5/9.4 MB | 3.2/8.4 MB | 0.9/1.7 MB Progress (3): 5.5/9.4 MB | 3.2/8.4 MB | 0.9/1.7 MB Progress (3): 5.6/9.4 MB | 3.2/8.4 MB | 0.9/1.7 MB Progress (3): 5.6/9.4 MB | 3.2/8.4 MB | 0.9/1.7 MB Progress (3): 5.6/9.4 MB | 3.2/8.4 MB | 0.9/1.7 MB Progress (3): 5.6/9.4 MB | 3.2/8.4 MB | 0.9/1.7 MB Progress (3): 5.6/9.4 MB | 3.2/8.4 MB | 0.9/1.7 MB Progress (3): 5.6/9.4 MB | 3.2/8.4 MB | 0.9/1.7 MB Progress (3): 5.6/9.4 MB | 3.2/8.4 MB | 0.9/1.7 MB Progress (3): 5.6/9.4 MB | 3.2/8.4 MB | 0.9/1.7 MB Progress (3): 5.6/9.4 MB | 3.2/8.4 MB | 0.9/1.7 MB Progress (3): 5.6/9.4 MB | 3.2/8.4 MB | 0.9/1.7 MB Progress (3): 5.6/9.4 MB | 3.2/8.4 MB | 0.9/1.7 MB Progress (3): 5.7/9.4 MB | 3.2/8.4 MB | 0.9/1.7 MB Progress (3): 5.7/9.4 MB | 3.3/8.4 MB | 0.9/1.7 MB Progress (3): 5.7/9.4 MB | 3.3/8.4 MB | 0.9/1.7 MB Progress (3): 5.7/9.4 MB | 3.3/8.4 MB | 0.9/1.7 MB Progress (3): 5.7/9.4 MB | 3.3/8.4 MB | 1.0/1.7 MB Progress (3): 5.7/9.4 MB | 3.3/8.4 MB | 1.0/1.7 MB Progress (4): 5.7/9.4 MB | 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Progress (3): 7.0/9.4 MB | 4.5/8.4 MB | 1.7 MB Progress (3): 7.1/9.4 MB | 4.5/8.4 MB | 1.7 MB Progress (3): 7.1/9.4 MB | 4.6/8.4 MB | 1.7 MB Progress (3): 7.1/9.4 MB | 4.6/8.4 MB | 1.7 MB Progress (3): 7.1/9.4 MB | 4.6/8.4 MB | 1.7 MB Progress (3): 7.1/9.4 MB | 4.6/8.4 MB | 1.7 MB Progress (3): 7.2/9.4 MB | 4.6/8.4 MB | 1.7 MB Progress (3): 7.2/9.4 MB | 4.7/8.4 MB | 1.7 MB Progress (3): 7.2/9.4 MB | 4.7/8.4 MB | 1.7 MB Progress (3): 7.2/9.4 MB | 4.7/8.4 MB | 1.7 MB Downloaded from central: https://repo.maven.apache.org/maven2/com/github/samtools/htsjdk/2.19.0/htsjdk-2.19.0.jar (1.7 MB at 1.7 MB/s) Downloading from central: https://repo.maven.apache.org/maven2/org/apache/httpcomponents/httpclient/4.5.7/httpclient-4.5.7.jar Progress (2): 7.3/9.4 MB | 4.7/8.4 MB Progress (2): 7.3/9.4 MB | 4.8/8.4 MB Progress (2): 7.3/9.4 MB | 4.8/8.4 MB Progress (2): 7.3/9.4 MB | 4.8/8.4 MB Progress (2): 7.4/9.4 MB | 4.8/8.4 MB Progress (2): 7.4/9.4 MB | 4.8/8.4 MB Progress (2): 7.4/9.4 MB | 4.9/8.4 MB 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Progress (3): 8.7/9.4 MB | 5.8/8.4 MB | 385/768 kB Progress (3): 8.7/9.4 MB | 5.8/8.4 MB | 389/768 kB Progress (3): 8.7/9.4 MB | 5.8/8.4 MB | 393/768 kB Progress (3): 8.7/9.4 MB | 5.8/8.4 MB | 397/768 kB Progress (3): 8.7/9.4 MB | 5.8/8.4 MB | 401/768 kB Progress (3): 8.7/9.4 MB | 5.8/8.4 MB | 401/768 kB Progress (3): 8.7/9.4 MB | 5.8/8.4 MB | 406/768 kB Progress (3): 8.7/9.4 MB | 5.8/8.4 MB | 406/768 kB Progress (3): 8.7/9.4 MB | 5.8/8.4 MB | 410/768 kB Progress (3): 8.7/9.4 MB | 5.8/8.4 MB | 414/768 kB Progress (3): 8.7/9.4 MB | 5.8/8.4 MB | 418/768 kB Progress (3): 8.7/9.4 MB | 5.8/8.4 MB | 422/768 kB Progress (3): 8.7/9.4 MB | 5.9/8.4 MB | 422/768 kB Progress (3): 8.7/9.4 MB | 5.9/8.4 MB | 426/768 kB Progress (3): 8.8/9.4 MB | 5.9/8.4 MB | 426/768 kB Progress (3): 8.8/9.4 MB | 5.9/8.4 MB | 430/768 kB Progress (4): 8.8/9.4 MB | 5.9/8.4 MB | 430/768 kB | 4.1/74 kB Progress (4): 8.8/9.4 MB | 5.9/8.4 MB | 434/768 kB | 4.1/74 kB Progress (4): 8.8/9.4 MB | 5.9/8.4 MB | 434/768 kB | 8.2/74 kB Progress (4): 8.8/9.4 MB | 5.9/8.4 MB | 434/768 kB | 8.2/74 kB Progress (4): 8.8/9.4 MB | 5.9/8.4 MB | 438/768 kB | 8.2/74 kB Progress (4): 8.8/9.4 MB | 5.9/8.4 MB | 438/768 kB | 12/74 kB Progress (4): 8.8/9.4 MB | 5.9/8.4 MB | 438/768 kB | 12/74 kB Progress (4): 8.8/9.4 MB | 5.9/8.4 MB | 438/768 kB | 16/74 kB Progress (4): 8.8/9.4 MB | 5.9/8.4 MB | 442/768 kB | 16/74 kB Progress (4): 8.8/9.4 MB | 5.9/8.4 MB | 446/768 kB | 16/74 kB Progress (4): 8.8/9.4 MB | 5.9/8.4 MB | 446/768 kB | 20/74 kB Progress (4): 8.8/9.4 MB | 5.9/8.4 MB | 451/768 kB | 20/74 kB Progress (4): 8.8/9.4 MB | 5.9/8.4 MB | 451/768 kB | 25/74 kB Progress (4): 8.8/9.4 MB | 5.9/8.4 MB | 451/768 kB | 25/74 kB Progress (4): 8.9/9.4 MB | 5.9/8.4 MB | 451/768 kB | 25/74 kB Progress (4): 8.9/9.4 MB | 5.9/8.4 MB | 451/768 kB | 29/74 kB Progress (4): 8.9/9.4 MB | 5.9/8.4 MB | 455/768 kB | 29/74 kB Progress (4): 8.9/9.4 MB | 5.9/8.4 MB | 455/768 kB | 33/74 kB Progress (4): 8.9/9.4 MB | 5.9/8.4 MB | 459/768 kB | 33/74 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9.1/9.4 MB | 6.3/8.4 MB | 561/768 kB | 74 kB Progress (4): 9.2/9.4 MB | 6.3/8.4 MB | 561/768 kB | 74 kB Progress (4): 9.2/9.4 MB | 6.3/8.4 MB | 565/768 kB | 74 kB Progress (4): 9.2/9.4 MB | 6.3/8.4 MB | 569/768 kB | 74 kB Progress (4): 9.2/9.4 MB | 6.3/8.4 MB | 569/768 kB | 74 kB Progress (4): 9.2/9.4 MB | 6.3/8.4 MB | 573/768 kB | 74 kB Progress (4): 9.2/9.4 MB | 6.3/8.4 MB | 578/768 kB | 74 kB Progress (4): 9.2/9.4 MB | 6.3/8.4 MB | 582/768 kB | 74 kB Progress (4): 9.2/9.4 MB | 6.3/8.4 MB | 586/768 kB | 74 kB Progress (4): 9.2/9.4 MB | 6.3/8.4 MB | 586/768 kB | 74 kB Downloaded from central: https://repo.maven.apache.org/maven2/gov/nih/nlm/ncbi/ngs-java/2.9.0/ngs-java-2.9.0.jar (74 kB at 74 kB/s) Downloading from central: https://repo.maven.apache.org/maven2/org/apache/httpcomponents/httpcore/4.4.11/httpcore-4.4.11.jar Progress (3): 9.2/9.4 MB | 6.4/8.4 MB | 586/768 kB Progress (3): 9.2/9.4 MB | 6.4/8.4 MB | 590/768 kB Progress (3): 9.3/9.4 MB | 6.4/8.4 MB | 590/768 kB Progress (3): 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MB | 6.5/8.4 MB | 655/768 kB Progress (3): 9.4 MB | 6.5/8.4 MB | 659/768 kB Progress (3): 9.4 MB | 6.5/8.4 MB | 664/768 kB Progress (3): 9.4 MB | 6.5/8.4 MB | 664/768 kB Progress (3): 9.4 MB | 6.5/8.4 MB | 668/768 kB Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/httpcomponents/httpcore/4.4.11/httpcore-4.4.11.jar (0 B at 0 B/s) Progress (3): 9.4 MB | 6.5/8.4 MB | 672/768 kB Progress (3): 9.4 MB | 6.6/8.4 MB | 672/768 kB Downloading from central: https://repo.maven.apache.org/maven2/org/mockito/mockito-core/2.25.1/mockito-core-2.25.1.jar Progress (3): 9.4 MB | 6.6/8.4 MB | 676/768 kB Progress (3): 9.4 MB | 6.6/8.4 MB | 680/768 kB Progress (3): 9.4 MB | 6.6/8.4 MB | 684/768 kB Progress (3): 9.4 MB | 6.6/8.4 MB | 688/768 kB Progress (3): 9.4 MB | 6.6/8.4 MB | 688/768 kB Progress (3): 9.4 MB | 6.6/8.4 MB | 692/768 kB Progress (3): 9.4 MB | 6.6/8.4 MB | 696/768 kB Progress (3): 9.4 MB | 6.6/8.4 MB | 700/768 kB Progress (3): 9.4 MB | 6.6/8.4 MB | 705/768 kB Progress (3): 9.4 MB | 6.6/8.4 MB | 709/768 kB Progress (3): 9.4 MB | 6.6/8.4 MB | 709/768 kB Progress (3): 9.4 MB | 6.6/8.4 MB | 713/768 kB Progress (3): 9.4 MB | 6.6/8.4 MB | 717/768 kB Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/spark/spark-catalyst_2.12/3.0.1/spark-catalyst_2.12-3.0.1.jar (9.4 MB at 9.3 MB/s) Progress (2): 6.6/8.4 MB | 721/768 kB Downloading from central: https://repo.maven.apache.org/maven2/net/bytebuddy/byte-buddy/1.9.7/byte-buddy-1.9.7.jar Progress (2): 6.6/8.4 MB | 725/768 kB Progress (2): 6.7/8.4 MB | 725/768 kB Progress (2): 6.7/8.4 MB | 729/768 kB Progress (2): 6.7/8.4 MB | 733/768 kB Progress (2): 6.7/8.4 MB | 737/768 kB Progress (2): 6.7/8.4 MB | 741/768 kB Progress (2): 6.7/8.4 MB | 745/768 kB Progress (2): 6.7/8.4 MB | 745/768 kB Progress (2): 6.7/8.4 MB | 750/768 kB Progress (2): 6.7/8.4 MB | 754/768 kB Progress (2): 6.7/8.4 MB | 758/768 kB Progress (2): 6.7/8.4 MB | 762/768 kB Progress (2): 6.7/8.4 MB | 766/768 kB Progress (2): 6.7/8.4 MB | 768 kB Progress (2): 6.8/8.4 MB | 768 kB Progress (2): 6.8/8.4 MB | 768 kB Progress (2): 6.8/8.4 MB | 768 kB Progress (2): 6.9/8.4 MB | 768 kB Progress (2): 6.9/8.4 MB | 768 kB Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/httpcomponents/httpclient/4.5.7/httpclient-4.5.7.jar (768 kB at 755 kB/s) Downloading from central: https://repo.maven.apache.org/maven2/net/bytebuddy/byte-buddy-agent/1.9.7/byte-buddy-agent-1.9.7.jar Progress (1): 7.0/8.4 MB Progress (1): 7.0/8.4 MB Progress (1): 7.1/8.4 MB Progress (1): 7.1/8.4 MB Progress (1): 7.1/8.4 MB Progress (2): 7.1/8.4 MB | 4.1/43 kB Progress (2): 7.1/8.4 MB | 8.2/43 kB Progress (2): 7.1/8.4 MB | 12/43 kB Progress (2): 7.2/8.4 MB | 12/43 kB Progress (2): 7.2/8.4 MB | 16/43 kB Progress (2): 7.2/8.4 MB | 20/43 kB Progress (2): 7.2/8.4 MB | 25/43 kB Progress (2): 7.2/8.4 MB | 29/43 kB Progress (2): 7.2/8.4 MB | 33/43 kB Progress (2): 7.2/8.4 MB | 33/43 kB Progress (2): 7.2/8.4 MB | 37/43 kB Progress (2): 7.2/8.4 MB | 41/43 kB Progress (2): 7.2/8.4 MB | 43 kB Progress (2): 7.3/8.4 MB | 43 kB Progress (2): 7.3/8.4 MB | 43 kB Progress (2): 7.3/8.4 MB | 43 kB Progress (3): 7.3/8.4 MB | 43 kB | 0/3.3 MB Progress (3): 7.4/8.4 MB | 43 kB | 0/3.3 MB Progress (3): 7.4/8.4 MB | 43 kB | 0/3.3 MB Progress (3): 7.4/8.4 MB | 43 kB | 0/3.3 MB Progress (3): 7.4/8.4 MB | 43 kB | 0/3.3 MB Progress (3): 7.4/8.4 MB | 43 kB | 0.1/3.3 MB Progress (3): 7.4/8.4 MB | 43 kB | 0.1/3.3 MB Downloaded from central: https://repo.maven.apache.org/maven2/net/bytebuddy/byte-buddy-agent/1.9.7/byte-buddy-agent-1.9.7.jar (43 kB at 42 kB/s) Progress (2): 7.5/8.4 MB | 0.1/3.3 MB Progress (2): 7.5/8.4 MB | 0.1/3.3 MB Progress (2): 7.5/8.4 MB | 0.1/3.3 MB Progress (2): 7.5/8.4 MB | 0.1/3.3 MB Progress (2): 7.5/8.4 MB | 0.1/3.3 MB Progress (2): 7.5/8.4 MB | 0.1/3.3 MB Progress (2): 7.5/8.4 MB | 0.1/3.3 MB Progress (2): 7.5/8.4 MB | 0.2/3.3 MB Progress (2): 7.5/8.4 MB | 0.2/3.3 MB Progress (3): 7.5/8.4 MB | 0.2/3.3 MB | 4.1/581 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| 0.5/3.3 MB | 139/581 kB Progress (3): 8.0/8.4 MB | 0.5/3.3 MB | 139/581 kB Progress (3): 8.0/8.4 MB | 0.5/3.3 MB | 143/581 kB Progress (3): 8.0/8.4 MB | 0.5/3.3 MB | 143/581 kB Progress (3): 8.0/8.4 MB | 0.5/3.3 MB | 147/581 kB Progress (3): 8.0/8.4 MB | 0.5/3.3 MB | 152/581 kB Progress (3): 8.0/8.4 MB | 0.5/3.3 MB | 152/581 kB Progress (3): 8.0/8.4 MB | 0.5/3.3 MB | 156/581 kB Progress (3): 8.0/8.4 MB | 0.5/3.3 MB | 160/581 kB Progress (3): 8.0/8.4 MB | 0.5/3.3 MB | 164/581 kB Progress (3): 8.0/8.4 MB | 0.5/3.3 MB | 164/581 kB Progress (3): 8.0/8.4 MB | 0.5/3.3 MB | 168/581 kB Progress (3): 8.0/8.4 MB | 0.5/3.3 MB | 172/581 kB Progress (3): 8.0/8.4 MB | 0.5/3.3 MB | 176/581 kB Progress (3): 8.0/8.4 MB | 0.5/3.3 MB | 176/581 kB Progress (3): 8.0/8.4 MB | 0.5/3.3 MB | 180/581 kB Progress (3): 8.0/8.4 MB | 0.5/3.3 MB | 184/581 kB Progress (3): 8.0/8.4 MB | 0.6/3.3 MB | 184/581 kB Progress (3): 8.0/8.4 MB | 0.6/3.3 MB | 188/581 kB Progress (3): 8.0/8.4 MB | 0.6/3.3 MB | 193/581 kB Progress (3): 8.0/8.4 MB | 0.6/3.3 MB | 197/581 kB Progress (3): 8.0/8.4 MB | 0.6/3.3 MB | 197/581 kB Progress (3): 8.0/8.4 MB | 0.6/3.3 MB | 201/581 kB Progress (3): 8.0/8.4 MB | 0.6/3.3 MB | 201/581 kB Progress (3): 8.0/8.4 MB | 0.6/3.3 MB | 205/581 kB Progress (3): 8.0/8.4 MB | 0.6/3.3 MB | 205/581 kB Progress (3): 8.0/8.4 MB | 0.6/3.3 MB | 209/581 kB Progress (3): 8.0/8.4 MB | 0.6/3.3 MB | 213/581 kB Progress (3): 8.0/8.4 MB | 0.6/3.3 MB | 213/581 kB Progress (3): 8.0/8.4 MB | 0.6/3.3 MB | 217/581 kB Progress (3): 8.0/8.4 MB | 0.6/3.3 MB | 221/581 kB Progress (3): 8.0/8.4 MB | 0.6/3.3 MB | 221/581 kB Progress (3): 8.0/8.4 MB | 0.6/3.3 MB | 225/581 kB Progress (3): 8.0/8.4 MB | 0.6/3.3 MB | 225/581 kB Progress (3): 8.0/8.4 MB | 0.6/3.3 MB | 229/581 kB Progress (3): 8.0/8.4 MB | 0.6/3.3 MB | 229/581 kB Progress (3): 8.0/8.4 MB | 0.6/3.3 MB | 233/581 kB Progress (3): 8.0/8.4 MB | 0.7/3.3 MB | 233/581 kB Progress (3): 8.0/8.4 MB | 0.7/3.3 MB | 238/581 kB Progress (3): 8.0/8.4 MB | 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Progress (3): 8.1/8.4 MB | 0.8/3.3 MB | 291/581 kB Progress (3): 8.1/8.4 MB | 0.8/3.3 MB | 295/581 kB Progress (3): 8.1/8.4 MB | 0.8/3.3 MB | 295/581 kB Progress (3): 8.1/8.4 MB | 0.8/3.3 MB | 299/581 kB Progress (3): 8.1/8.4 MB | 0.8/3.3 MB | 303/581 kB Progress (3): 8.1/8.4 MB | 0.8/3.3 MB | 303/581 kB Progress (3): 8.1/8.4 MB | 0.8/3.3 MB | 307/581 kB Progress (3): 8.1/8.4 MB | 0.8/3.3 MB | 311/581 kB Progress (3): 8.1/8.4 MB | 0.8/3.3 MB | 315/581 kB Progress (3): 8.1/8.4 MB | 0.8/3.3 MB | 315/581 kB Progress (3): 8.2/8.4 MB | 0.8/3.3 MB | 315/581 kB Progress (3): 8.2/8.4 MB | 0.8/3.3 MB | 319/581 kB Progress (3): 8.2/8.4 MB | 0.8/3.3 MB | 319/581 kB Progress (3): 8.2/8.4 MB | 0.8/3.3 MB | 324/581 kB Progress (3): 8.2/8.4 MB | 0.8/3.3 MB | 328/581 kB Progress (3): 8.2/8.4 MB | 0.8/3.3 MB | 332/581 kB Progress (3): 8.2/8.4 MB | 0.8/3.3 MB | 332/581 kB Progress (3): 8.2/8.4 MB | 0.8/3.3 MB | 336/581 kB Progress (3): 8.2/8.4 MB | 0.8/3.3 MB | 336/581 kB Progress (3): 8.2/8.4 MB | 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Progress (3): 8.2/8.4 MB | 0.9/3.3 MB | 393/581 kB Progress (3): 8.2/8.4 MB | 0.9/3.3 MB | 397/581 kB Progress (3): 8.3/8.4 MB | 0.9/3.3 MB | 397/581 kB Progress (3): 8.3/8.4 MB | 1.0/3.3 MB | 397/581 kB Progress (3): 8.3/8.4 MB | 1.0/3.3 MB | 401/581 kB Progress (3): 8.3/8.4 MB | 1.0/3.3 MB | 406/581 kB Progress (3): 8.3/8.4 MB | 1.0/3.3 MB | 410/581 kB Progress (3): 8.3/8.4 MB | 1.0/3.3 MB | 410/581 kB Progress (3): 8.3/8.4 MB | 1.0/3.3 MB | 414/581 kB Progress (3): 8.3/8.4 MB | 1.0/3.3 MB | 418/581 kB Progress (3): 8.3/8.4 MB | 1.0/3.3 MB | 418/581 kB Progress (3): 8.3/8.4 MB | 1.0/3.3 MB | 422/581 kB Progress (3): 8.3/8.4 MB | 1.0/3.3 MB | 426/581 kB Progress (3): 8.3/8.4 MB | 1.0/3.3 MB | 430/581 kB Progress (3): 8.3/8.4 MB | 1.0/3.3 MB | 430/581 kB Progress (3): 8.3/8.4 MB | 1.0/3.3 MB | 434/581 kB Progress (3): 8.3/8.4 MB | 1.0/3.3 MB | 434/581 kB Progress (3): 8.3/8.4 MB | 1.0/3.3 MB | 438/581 kB Progress (3): 8.3/8.4 MB | 1.0/3.3 MB | 438/581 kB Progress (3): 8.3/8.4 MB | 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557/581 kB Progress (3): 8.4 MB | 1.2/3.3 MB | 561/581 kB Progress (3): 8.4 MB | 1.2/3.3 MB | 565/581 kB Progress (3): 8.4 MB | 1.2/3.3 MB | 569/581 kB Progress (3): 8.4 MB | 1.2/3.3 MB | 569/581 kB Progress (3): 8.4 MB | 1.2/3.3 MB | 573/581 kB Progress (3): 8.4 MB | 1.2/3.3 MB | 577/581 kB Progress (3): 8.4 MB | 1.3/3.3 MB | 577/581 kB Progress (3): 8.4 MB | 1.3/3.3 MB | 581 kB Progress (3): 8.4 MB | 1.3/3.3 MB | 581 kB Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/hadoop/hadoop-hdfs/2.7.5/hadoop-hdfs-2.7.5.jar (8.4 MB at 7.9 MB/s) Progress (2): 1.3/3.3 MB | 581 kB Progress (2): 1.3/3.3 MB | 581 kB Progress (2): 1.3/3.3 MB | 581 kB Progress (2): 1.3/3.3 MB | 581 kB Progress (2): 1.4/3.3 MB | 581 kB Progress (2): 1.4/3.3 MB | 581 kB Progress (2): 1.4/3.3 MB | 581 kB Progress (2): 1.4/3.3 MB | 581 kB Progress (2): 1.4/3.3 MB | 581 kB Downloaded from central: https://repo.maven.apache.org/maven2/org/mockito/mockito-core/2.25.1/mockito-core-2.25.1.jar (581 kB 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(1): 15/17 MB Progress (1): 15/17 MB Progress (1): 15/17 MB Progress (1): 16/17 MB Progress (1): 16/17 MB Progress (1): 16/17 MB Progress (1): 16/17 MB Progress (1): 16/17 MB Progress (1): 16/17 MB Progress (1): 16/17 MB Progress (1): 16/17 MB Progress (1): 16/17 MB Progress (1): 16/17 MB Progress (1): 16/17 MB Progress (1): 17/17 MB Progress (1): 17/17 MB Progress (1): 17/17 MB Progress (1): 17/17 MB Progress (1): 17/17 MB Progress (1): 17/17 MB Progress (1): 17/17 MB Progress (1): 17 MB Downloaded from central: https://repo.maven.apache.org/maven2/it/unimi/dsi/fastutil/6.6.5/fastutil-6.6.5.jar (17 MB at 6.7 MB/s) [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-core-spark3_2.12 --- [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-core-spark3_2.12 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ adam-core-spark3_2.12 --- [INFO] Source directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/adam-core/src/main/scala added. [INFO] Source directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/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-spark3_2.12 --- Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/maven-toolchain/1.0/maven-toolchain-1.0.pom Progress (1): 3.4 kB Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/maven/maven-toolchain/1.0/maven-toolchain-1.0.pom (3.4 kB at 427 kB/s) Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/reporting/maven-reporting-api/2.2.1/maven-reporting-api-2.2.1.pom Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/maven/reporting/maven-reporting-api/2.2.1/maven-reporting-api-2.2.1.pom (0 B at 0 B/s) Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/reporting/maven-reporting/2.2.1/maven-reporting-2.2.1.pom Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/maven/reporting/maven-reporting/2.2.1/maven-reporting-2.2.1.pom (0 B at 0 B/s) Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/doxia/doxia-sink-api/1.1/doxia-sink-api-1.1.pom Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/maven/doxia/doxia-sink-api/1.1/doxia-sink-api-1.1.pom (0 B at 0 B/s) Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/doxia/doxia/1.1/doxia-1.1.pom Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/maven/doxia/doxia/1.1/doxia-1.1.pom (0 B at 0 B/s) Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/doxia/doxia-logging-api/1.1/doxia-logging-api-1.1.pom Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/maven/doxia/doxia-logging-api/1.1/doxia-logging-api-1.1.pom (0 B at 0 B/s) Downloading from central: https://repo.maven.apache.org/maven2/org/codehaus/plexus/plexus-utils/3.0.20/plexus-utils-3.0.20.pom Downloaded from central: 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https://repo.maven.apache.org/maven2/org/apache/maven/maven-settings/2.2.1/maven-settings-2.2.1.jar Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/maven-project/2.2.1/maven-project-2.2.1.jar Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/maven-plugin-registry/2.2.1/maven-plugin-registry-2.2.1.jar Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/maven/maven-profile/2.2.1/maven-profile-2.2.1.jar (0 B at 0 B/s) Downloading from central: https://repo.maven.apache.org/maven2/org/codehaus/plexus/plexus-interpolation/1.11/plexus-interpolation-1.11.jar Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/maven/maven-plugin-registry/2.2.1/maven-plugin-registry-2.2.1.jar (0 B at 0 B/s) Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/maven/maven-project/2.2.1/maven-project-2.2.1.jar (0 B at 0 B/s) Downloading from central: 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https://repo.maven.apache.org/maven2/org/apache/maven/doxia/doxia-sink-api/1.1/doxia-sink-api-1.1.jar Downloaded from central: https://repo.maven.apache.org/maven2/org/slf4j/slf4j-jdk14/1.5.6/slf4j-jdk14-1.5.6.jar (0 B at 0 B/s) Downloaded from central: https://repo.maven.apache.org/maven2/org/slf4j/slf4j-api/1.5.6/slf4j-api-1.5.6.jar (0 B at 0 B/s) Downloaded from central: https://repo.maven.apache.org/maven2/org/slf4j/jcl-over-slf4j/1.5.6/jcl-over-slf4j-1.5.6.jar (0 B at 0 B/s) Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/doxia/doxia-logging-api/1.1/doxia-logging-api-1.1.jar Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/maven-plugin-descriptor/2.2.1/maven-plugin-descriptor-2.2.1.jar Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/maven-error-diagnostics/2.2.1/maven-error-diagnostics-2.2.1.jar Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/maven/reporting/maven-reporting-api/2.2.1/maven-reporting-api-2.2.1.jar (0 B at 0 B/s) Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/maven-monitor/2.2.1/maven-monitor-2.2.1.jar Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/maven/doxia/doxia-sink-api/1.1/doxia-sink-api-1.1.jar (0 B at 0 B/s) Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/maven/maven-plugin-descriptor/2.2.1/maven-plugin-descriptor-2.2.1.jar (0 B at 0 B/s) Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/maven-plugin-api/2.2.1/maven-plugin-api-2.2.1.jar Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/maven/doxia/doxia-logging-api/1.1/doxia-logging-api-1.1.jar (0 B at 0 B/s) Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/maven/maven-error-diagnostics/2.2.1/maven-error-diagnostics-2.2.1.jar (0 B at 0 B/s) Downloading from central: https://repo.maven.apache.org/maven2/org/codehaus/plexus/plexus-utils/3.0.20/plexus-utils-3.0.20.jar Downloading from central: https://repo.maven.apache.org/maven2/org/apache/commons/commons-exec/1.3/commons-exec-1.3.jar Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/maven/maven-monitor/2.2.1/maven-monitor-2.2.1.jar (0 B at 0 B/s) Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/commons/commons-exec/1.3/commons-exec-1.3.jar (0 B at 0 B/s) Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/maven/maven-plugin-api/2.2.1/maven-plugin-api-2.2.1.jar (0 B at 0 B/s) Downloaded from central: https://repo.maven.apache.org/maven2/org/codehaus/plexus/plexus-utils/3.0.20/plexus-utils-3.0.20.jar (0 B at 0 B/s) 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-spark3_2.12 --- SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ adam-core-spark3_2.12 --- [INFO] Modified 2 of 204 .scala files [INFO] [INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ adam-core-spark3_2.12 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/adam-core/src/main/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ adam-core-spark3_2.12 --- [INFO] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/adam-core/src/main/java:-1: info: compiling [INFO] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/adam-core/src/main/scala:-1: info: compiling [INFO] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/adam-core/target/generated-sources/src/main/scala:-1: info: compiling [INFO] Compiling 140 source files to /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/adam-core/target/2.12.8/classes at 1606965509951 [WARNING] warning: there were 21 deprecation warnings [WARNING] warning: there were 31 deprecation warnings (since 0.21.0) [WARNING] warning: there was one deprecation warning (since 1.0.6) [WARNING] warning: there was one deprecation warning (since 2.11.0) [WARNING] warning: there were 174 deprecation warnings (since 2.12.0) [WARNING] warning: there was one deprecation warning (since 2.12.7) [WARNING] warning: there were 229 deprecation warnings in total; re-run with -deprecation for details [WARNING] warning: there were 5 feature warnings; re-run with -feature for details [WARNING] 8 warnings found [INFO] prepare-compile in 0 s [INFO] compile in 27 s [INFO] [INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ adam-core-spark3_2.12 --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 6 source files to /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/adam-core/target/2.12.8/classes [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ adam-core-spark3_2.12 --- [INFO] Test Source directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/adam-core/src/test/scala added. [INFO] [INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ adam-core-spark3_2.12 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 153 resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ adam-core-spark3_2.12 --- [INFO] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/adam-core/src/test/scala:-1: info: compiling [INFO] Compiling 70 source files to /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/adam-core/target/2.12.8/test-classes at 1606965538969 [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/algorithms/consensus/NormalizationUtilsSuite.scala:59: warning: method recordToRichRecord in object RichAlignment is deprecated (since 0.21.0): Use explicit conversion wherever possible in new development. [WARNING] .build() [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/algorithms/consensus/NormalizationUtilsSuite.scala:61: warning: method richRecordToRecord in object RichAlignment is deprecated (since 0.21.0): Use explicit conversion wherever possible in new development. [WARNING] val new_cigar = NormalizationUtils.leftAlignIndel(read) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/algorithms/consensus/NormalizationUtilsSuite.scala:66: warning: method richRecordToRecord in object RichAlignment is deprecated (since 0.21.0): Use explicit conversion wherever possible in new development. [WARNING] assert(RichAlignment(read).samtoolsCigar.getReadLength === new_cigar.getReadLength) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/AlignmentConverterSuite.scala:171: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] val newSAMRecord = newSAMReader.iterator().dropWhile(r => r.getReadName != readName) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/AlignmentConverterSuite.scala:274: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] .setAlignments(seqAsJavaList(alignments)) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/AlignmentConverterSuite.scala:311: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] .setAlignments(seqAsJavaList(alignments)) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/AlignmentConverterSuite.scala:335: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] val fragment = Fragment.newBuilder().setAlignments(List(record)).build() [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/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(!testAlignment.getPrimaryAlignment === testSAMRecord.getNotPrimaryAlignmentFlag) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/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(!testAlignment.getPrimaryAlignment === testSAMRecord.getNotPrimaryAlignmentFlag) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/SAMRecordConverterSuite.scala:106: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] val samIter = asScalaIterator(newSAMReader.iterator()) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:53: warning: method extractDictionary in class SAMSequenceDictionaryExtractor is deprecated: see corresponding Javadoc for more information. [WARNING] SequenceDictionary(SAMSequenceDictionaryExtractor.extractDictionary(new File(path))) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:63: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] .alleles(List(Allele.create("A", true), Allele.create("T"))) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:69: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] .alleles(List(Allele.create("A", true), Allele.create("T"), Allele.create("G"))) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:75: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] .alleles(List(Allele.create("A", true), Allele.create("", false))) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:81: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] .alleles(List(Allele.create("A", true), Allele.create("", false))) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:109: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] .alleles(List(Allele.create("A", true), Allele.create("T"))) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:143: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] GenotypeBuilder.create("NA12878", vcb.getAlleles(), genotypeAttributes)) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:154: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] assert(adamGT.getAlleles.sameElements(List(GenotypeAllele.REF, GenotypeAllele.ALT))) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:184: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] assert(adamVariant.variant.getFiltersFailed.sameElements(List("LowMQ"))) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:219: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] assert(adamGT.getVariantCallingAnnotations.getFiltersFailed.sameElements(List("LowMQ"))) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:234: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] assert(htsjdkVC.getAlternateAlleles.sameElements(List(Allele.create("T")))) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:245: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] .setStrandBiasComponents(List(0, 2, 4, 6).map(i => i: java.lang.Integer)) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:246: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] .setAlleles(List(GenotypeAllele.REF, GenotypeAllele.ALT)) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:279: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] .setStrandBiasComponents(List(0, 2).map(i => i: java.lang.Integer)) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:280: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] .setAlleles(List(GenotypeAllele.REF, GenotypeAllele.ALT)) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:298: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] .setStrandBiasComponents(List(0, 2).map(i => i: java.lang.Integer)) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:299: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] .setAlleles(List(GenotypeAllele.REF, GenotypeAllele.ALT)) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:320: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] for ((allele, idx) <- vc.getAlternateAlleles.zipWithIndex) { [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:328: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] val gb = new GenotypeBuilder("NA12878", List(Allele.create("T"), Allele.create("G"))) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:347: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] assert(adamGT1.getAlleles.sameElements(List(GenotypeAllele.ALT, GenotypeAllele.OTHER_ALT))) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:349: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] assert(adamGT1.getGenotypeLikelihoods [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:354: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] assert(adamGT2.getAlleles.sameElements(List(GenotypeAllele.OTHER_ALT, GenotypeAllele.ALT))) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:356: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] assert(adamGT2.getGenotypeLikelihoods [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:380: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] val gb = new GenotypeBuilder("NA12878", List(Allele.create("A", true), Allele.create("A", true))) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:393: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] assert(adamGT.getAlleles.sameElements(List(GenotypeAllele.REF, GenotypeAllele.REF))) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:396: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] assert(adamGT.getNonReferenceLikelihoods [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:421: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] assert(variant.variant.getNames.length === 1) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:433: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] assert(variant.variant.getNames.length === 2) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:543: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] genotypeAttributes)))((bldr, fn) => { [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:693: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] assert(gls(0) < -0.99e-1 && gls(0) > -1.1e-1) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:693: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] assert(gls(0) < -0.99e-1 && gls(0) > -1.1e-1) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:694: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] assert(gls(1) < -0.99e-3 && gls(1) > -1.1e-3) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:694: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] assert(gls(1) < -0.99e-3 && gls(1) > -1.1e-3) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:695: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] assert(gls(2) < -0.99e-6 && gls(2) > -1.1e-6) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:695: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] assert(gls(2) < -0.99e-6 && gls(2) > -1.1e-6) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:714: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] assert(sb(0) === 10) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:715: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] assert(sb(1) === 12) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:716: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] assert(sb(2) === 14) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:717: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] assert(sb(3) === 16) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:762: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] assert(failedFilters(0) === "FAILED_FILTER") [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:776: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] assert(failedFilters(0) === "FAILED_FILTER1") [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:777: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] assert(failedFilters(1) === "FAILED_FILTER2") [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:778: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] assert(failedFilters(2) === "FAILED_FILTER3") [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:930: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] .map(d => d: java.lang.Double)) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:954: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] .map(i => i: java.lang.Integer)) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:962: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] .map(i => i: java.lang.Integer)) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1089: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] .setFiltersFailed(Seq("lowmq")) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1101: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] .setFiltersFailed(Seq("lowmq", "lowdp")) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1195: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] assert(v.getNames.length === 1) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1205: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] assert(v.getNames.length === 2) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1262: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] vcb.filters(Set("FAILED1", "FAILED2", "FAILED3")) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1267: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] val failedSet = v.getFiltersFailed.toSet [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1285: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] .setNames(Seq("name")) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1295: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] .setNames(Seq("name1", "name2")) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1364: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] .setFiltersFailed(Seq("FAILED")) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1378: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] .setFiltersFailed(Seq("FAILED1", "FAILED2")) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1493: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] 10).map(i => i: java.lang.Integer) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1501: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] 10, 13, 16).map(i => i: java.lang.Integer) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1516: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] 0.1f).map(i => i: java.lang.Float) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1523: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] val acList: java.util.List[String] = List("+Inf") [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1530: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] val acList: java.util.List[String] = List("-Inf") [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1538: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] 0.1f, 0.01f, 0.001f).map(i => i: java.lang.Float) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1552: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] val acList: java.util.List[String] = List("10D90M") [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1559: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] val acList: java.util.List[String] = List("10D90M", "100M", "90M10D") [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1575: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] 5, 10).map(i => i: java.lang.Integer) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1584: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] 5, 10, 13, 16).map(i => i: java.lang.Integer) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1601: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] 5, 10).map(i => i: java.lang.Integer) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1610: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] 5, 10, 13, 16).map(i => i: java.lang.Integer) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1627: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] 5, 10).map(i => i: java.lang.Integer) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1636: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] 5, 10, 13, 16).map(i => i: java.lang.Integer) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:2436: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] Map[String, java.lang.Object](("ONE_INT", "42"))) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:2459: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] Map[String, java.lang.Object](("FOUR_INTS", "5,10,15,20"))) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:2482: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] Map[String, java.lang.Object](("FOUR_FLOATS", "5.0,10.1,15.2,20.3"))) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:2505: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] Map[String, java.lang.Object](("A_INT", "10,15,20"))) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:2528: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] Map[String, java.lang.Object](("R_INT", "5,10,15,20"))) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:2551: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] Map[String, java.lang.Object](("R_STRING", "foo,bar,baz"))) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:2574: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] Map[String, java.lang.Object](("STRING_G", "foo,bar,baz"))) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/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/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/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/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/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/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/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/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/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/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/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/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/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/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/models/MdTagSuite.scala:194: warning: method recordToRichRecord in object RichAlignment is deprecated (since 0.21.0): Use explicit conversion wherever possible in new development. [WARNING] assert(read.mdTag.get.end === read.getEnd) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/models/MdTagSuite.scala:475: warning: method recordToRichRecord in object RichAlignment is deprecated (since 0.21.0): Use explicit conversion wherever possible in new development. [WARNING] val tag = read.mdTag.get [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/models/MdTagSuite.scala:482: warning: method recordToRichRecord in object RichAlignment is deprecated (since 0.21.0): Use explicit conversion wherever possible in new development. [WARNING] assert(tag.getReference(read) === "AAAAAAAAAAAAAAAAAAAAAAAAAAAAAGGGGGGGGGGAAAAAAAAAAGGGGGGGGGGAAAAAAAAAAA") [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/models/MdTagSuite.scala:495: warning: method recordToRichRecord in object RichAlignment is deprecated (since 0.21.0): Use explicit conversion wherever possible in new development. [WARNING] val tag = read.mdTag.get [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/models/MdTagSuite.scala:496: warning: method recordToRichRecord in object RichAlignment is deprecated (since 0.21.0): Use explicit conversion wherever possible in new development. [WARNING] assert(tag.getReference(read, withGaps = true) === "AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGGGGGGGGGGAAAAAAAAAAA") [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/models/MdTagSuite.scala:510: warning: method recordToRichRecord in object RichAlignment is deprecated (since 0.21.0): Use explicit conversion wherever possible in new development. [WARNING] val newTag = MdTag.moveAlignment(read, newCigar) [WARNING] ^ [WARNING] 168 warnings found [INFO] prepare-compile in 0 s [INFO] compile in 29 s [INFO] [INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ adam-core-spark3_2.12 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ adam-core-spark3_2.12 --- [INFO] Tests are skipped. [INFO] [INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ adam-core-spark3_2.12 --- Discovery starting. Discovery completed in 1 second, 625 milliseconds. Run starting. Expected test count is: 1177 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 2020-12-02 19:19:31 WARN Utils:69 - Your hostname, research-jenkins-worker-01 resolves to a loopback address: 127.0.1.1; using 192.168.122.1 instead (on interface virbr0) 2020-12-02 19:19:31 WARN Utils:69 - Set SPARK_LOCAL_IP if you need to bind to another address 2020-12-02 19:19:31 WARN NativeCodeLoader:62 - Unable to load native-hadoop library for your platform... using builtin-java classes where applicable - move pairs around an rdd FlagStatSuite: - Standard FlagStat test ModPartitionerSuite: - report number of partitions correctly - partition a number that is lower than the number of partitions and positive - partition a number that is greater than the number of partitions and positive - partition a number that is lower than the number of partitions and negative - partition a number that is greater than the number of partitions and negative - fire an exception if input is not an integer TwoBitFileSuite: - correctly read sequence from .2bit file - correctly return masked sequences from .2bit file - correctly return Ns from .2bit file - correctly calculates sequence dictionary NonoverlappingRegionsSuite: - alternating returns an alternating seq of items - Single region returns itself - Two adjacent regions will be merged - Nonoverlapping regions will all be returned - Many overlapping regions will all be merged - ADAMRecords return proper references ReferencePositionSuite: - create reference position from mapped read - create reference position from variant - create reference position from genotype - create reference position from variant starting at vcf 0 - create reference position from genotype starting at vcf 0 ConsensusGeneratorFromReadsSuite: - checking search for consensus list for artificial reads FragmentConverterSuite: - build a fragment collector and convert to a read - if a fragment isn't associated with a contig, don't get a fragment collector - convert an rdd of discontinuous fragments, all from the same contig - convert an rdd of contiguous fragments, all from the same contig - convert an rdd of varied fragments from multiple contigs FileMergerSuite: - cannot write both empty gzip block and cram eof - buffer size must be non-negative RichAlignmentSuite: - Unclipped Start - Unclipped End - tags contains optional fields - read overlap unmapped read - read overlap reference position - read overlap same position different contig SingleReadBucketSuite: - convert unmapped pair to fragment - convert proper pair to fragment - convert read pair to fragment with first of pair chimeric read RecalibrationTableSuite: - look up quality scores in table FlankSlicesSuite: - don't put flanks on non-adjacent slices - put flanks on adjacent slices InterleavedFastqInputFormatSuite: - interleaved FASTQ hadoop reader: interleaved_fastq_sample1.ifq->interleaved_fastq_sample1.ifq.output - interleaved FASTQ hadoop reader: interleaved_fastq_sample2.ifq->interleaved_fastq_sample2.ifq.output - interleaved FASTQ hadoop reader: interleaved_fastq_sample3.ifq->interleaved_fastq_sample3.ifq.output - interleaved FASTQ hadoop reader: interleaved_fastq_sample4.ifq->interleaved_fastq_sample4.ifq.output - interleaved FASTQ hadoop reader: interleaved_fastq_sample5.ifq->interleaved_fastq_sample5.ifq.output TreeRegionJoinSuite: - run a join between data on a single contig ReferenceRegionSuite: - cannot create an empty predicate - parse empty string throws IllegalArgumentException - parse contigName only string into reference regions - parse to end strings into reference regions - parse string into reference regions - contains(: ReferenceRegion) - contains(: ReferencePosition) - merge - overlaps and covers - overlapsBy and coversBy - distance(: ReferenceRegion) - distance(: ReferencePosition) - unstrandedDistance - subtract fails on non-overlapping and non-covering regions - subtract - create region from unmapped read fails - create region from read with null alignment positions fails - create stranded region from unmapped read fails - create stranded region from read with null alignment positions fails - create stranded region from read with null alignment strand fails - create stranded region from read on forward strand - create stranded region from read on reverse strand - create region from mapped read contains read start and end - validate that adjacent regions can be merged - validate that non-adjacent regions cannot be merged - validate that nearby regions can be merged - validate that non-nearby regions cannot be merged - compute convex hull of two sets - region name is sanitized when creating region from read - intersection fails on non-overlapping regions - intersection fails when minOverlap is not met - compute intersection - overlap tests for oriented reference region - check the width of a reference region - make a reference region for a variant or genotype - make a reference region for a variant or genotype starting at VCF 0 - uniformly pad a reference region - uniformly pad a reference region into negative coordinate space, ensure non negative start - unevenly pad a reference region - unevenly pad a reference region into negative coordinate space, ensure non negative start - can build an open ended reference region - can build an open ended reference region with strand - can build a reference region with an open start position - can build a reference region with an open start position with strand - can build a reference region that covers the entirety of a contig - can build a reference region that covers the entirety of a contig with strand - convert a genotype and then get the reference region - create region from feature with null alignment positions fails - create stranded region from feature with null alignment positions fails - create stranded region from feature with null alignment strand fails - create stranded region from feature on forward strand - create stranded region from feature on reverse strand 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 2020-12-02 19:19:49 WARN DatasetBoundSliceDataset:190 - Saving directly as Parquet from SQL. Options other than compression codec are ignored. - transform coverage to slice genomic dataset - transform coverage to feature genomic dataset 2020-12-02 19:19:51 WARN package:69 - Truncated the string representation of a plan since it was too large. This behavior can be adjusted by setting 'spark.sql.debug.maxToStringFields'. - transform coverage to fragment genomic dataset - transform coverage to read genomic dataset - transform coverage to genotype genomic dataset - transform coverage to variant genomic dataset - transform coverage to variant context genomic dataset - copy coverage rdd - copy coverage dataset - copy coverage rdd without sequence dictionary - copy coverage dataset without sequence dictionary - transform dataset via java API RecalibratorSuite: - don't replace quality if quality was null - if no covariates, return alignment - skip recalibration if base is below quality threshold - recalibrate changed bases above quality threshold SliceDatasetSuite: - create a new slice genomic dataset - create a new slice genomic dataset with sequence dictionary - merge slices into a sequence genomic dataset - save as parquet - round trip as parquet - save as fasta - save as single file fasta - convert slices to reads - convert slices to sequences GenotypeDatasetSuite: - union two genotype genomic datasets together - round trip to parquet - round trip to partitioned parquet - use broadcast join to pull down genotypes mapped to targets - use right outer broadcast join to pull down genotypes mapped to targets - use shuffle join to pull down genotypes mapped to targets - use right outer shuffle join to pull down genotypes mapped to targets - use left outer shuffle join to pull down genotypes mapped to targets - use full outer shuffle join to pull down genotypes mapped to targets - use shuffle join with group by to pull down genotypes mapped to targets - use right outer shuffle join with group by to pull down genotypes mapped to targets - convert back to variant contexts - load parquet to sql, save, re-read from avro 2020-12-02 19:20:07 WARN DatasetBoundSliceDataset:190 - Saving directly as Parquet from SQL. Options other than compression codec are ignored. - transform genotypes to slice genomic dataset - transform genotypes to coverage genomic dataset - transform genotypes to feature genomic dataset - transform genotypes to fragment genomic dataset - transform genotypes to read genomic dataset - transform genotypes to variant genomic dataset - transform genotypes to variant context genomic dataset - loading genotypes then converting to variants yields same output as loading variants - filter RDD bound genotypes to genotype filters passed - filter dataset bound genotypes to genotype filters passed - filter RDD bound genotypes by genotype quality - filter dataset bound genotypes by genotype quality - filter RDD bound genotypes by read depth - filter dataset bound genotypes by read depth - filter RDD bound genotypes by alternate read depth - filter dataset bound genotypes by alternate read depth - filter RDD bound genotypes by reference read depth - filter dataset bound genotypes by reference read depth - filter RDD bound genotypes by sample - filter dataset bound genotypes by sample - filter RDD bound genotypes by samples - filter dataset bound genotypes by samples - filter RDD bound no call genotypes - filter dataset no call genotypes - round trip gVCF END attribute without nested variant annotations rdd bound - round trip gVCF END attribute without nested variant annotations dataset bound - round trip gVCF END attribute with nested variant annotations rdd bound - round trip gVCF END attribute with nested variant annotations dataset bound - transform dataset via java API FragmentDatasetSuite: - don't lose any reads when piping interleaved fastq to sam - don't lose any reads when piping tab5 to sam - don't lose any reads when piping tab6 to sam - use broadcast join to pull down fragments mapped to targets - use right outer broadcast join to pull down fragments mapped to targets - use shuffle join to pull down fragments mapped to targets - use right outer shuffle join to pull down fragments mapped to targets - use left outer shuffle join to pull down fragments mapped to targets - use full outer shuffle join to pull down fragments mapped to targets - use shuffle join with group by to pull down fragments mapped to targets - use right outer shuffle join with group by to pull down fragments mapped to targets - bin quality scores in fragments - union two genomic datasets of fragments together - load parquet to sql, save, re-read from avro - transform fragments to slice genomic dataset - transform fragments to coverage genomic dataset - transform fragments to feature genomic dataset - transform fragments to read genomic dataset - transform fragments to genotype genomic dataset - transform fragments to variant genomic dataset - transform fragments to variant context genomic dataset - paired read names with index sequences in read names can group into fragments - interleaved paired read names with index sequences in read names can group into fragments - interleaved paired read names with index sequences in read names as fragments - transform dataset via java API - dataset and rdd conversion to alignments are equivalent - Compare unpaired FragmentDataset with optimisation to non-optimised SingleFastqInputFormatSuite: - FASTQ hadoop reader: fastq_sample1.fq->single_fastq_sample1.fq.output - FASTQ hadoop reader: fastq_sample2.fq->single_fastq_sample2.fq.output - FASTQ hadoop reader: fastq_sample3.fq->single_fastq_sample3.fq.output - FASTQ hadoop reader: fastq_sample4.fq->single_fastq_sample4.fq.output VariantContextDatasetSuite: - load a gvcf with a missing info field set to . - union two variant context genomic datasets together - can write, then read in .vcf file - can write as a single file via simple saveAsVcf method, then read in .vcf file - can write as a single file via full saveAsVcf method, then read in .vcf file - transform a vcf file with bad header - read a vcf file with multi-allelic variants to split - support VCFs with +Inf/-Inf float values - support VCFs with `nan` instead of `NaN` float values - don't lose any variants when piping as VCF - pipe works with empty partitions - don't lose any non-default VCF header lines or attributes when piping as VCF - save a file sorted by contig index - save a lexicographically sorted file - save a multiallelic gvcf !!! IGNORED !!! - test metadata - save sharded bgzip vcf - save bgzip vcf as single file - can't save file with non-vcf extension - transform variant contexts to slice genomic dataset - transform variant contexts to coverage genomic dataset - transform variant contexts to feature genomic dataset - transform variant contexts to fragment genomic dataset - transform variant contexts to read genomic dataset - transform variant contexts to genotype genomic dataset - transform variant contexts to variant genomic dataset - save and reload from partitioned parquet - transform dataset via java API ConsensusSuite: - test the insertion of a consensus insertion into a reference - test the insertion of a consensus deletion into a reference - inserting empty consensus returns the reference SequenceDatasetSuite: - create a new sequence genomic dataset - create a new sequence genomic dataset with sequence dictionary - save as parquet - round trip as parquet - save as fasta - save as single file fasta - convert sequences to reads - convert sequences to slices - slice sequences to a maximum length - slice sequences shorter than maximum length - filter sequences by overlapping region - filter sequences failing to overlap region - filter sequences by overlapping regions - filter sequences failing to overlap regions - slice sequences overlapping a smaller region - slice sequences overlapping a larger region - slice sequences failing to overlap a region - slice sequences overlapping smaller regions - slice sequences overlapping larger regions - slice sequences failing to overlap regions AttributeUtilsSuite: - parseTags returns a reasonable set of tagStrings - parseTags works with NumericSequence tagType - empty string is parsed as zero tagStrings - incorrectly formatted tag throws an exception - string tag with a ':' in it is correctly parsed - oq string tag with many ':' in it is correctly parsed - oq string tag with a ',' in it is correctly parsed - if a tag is an array but doesn't define it's format, throw MarkDuplicatesSuite: - single read - reads at different positions - reads at the same position - reads at the same position with clipping - reads on reverse strand - unmapped reads - read pairs - read pairs with fragments - quality scores - read pairs that cross chromosomes - single fragment - fragments at different positions - fragments at the same position - fragments at the same position with clipping - fragments on reverse strand - unmapped fragments - read pairs as fragments - read pairs with fragments as fragments - chimeric fragments - inverse pairs - supplemental reads TranscriptEffectConverterSuite: - parse empty transcript effect - parse empty transcript effect strict validation stringency - parse invalid transcript effect - parse invalid transcript effect strict validation stringency - parse transcript effect - parse empty list VCF ANN attribute - parse empty list VCF ANN attribute strict validation stringency - parse empty string VCF ANN attribute - parse empty string VCF ANN attribute strict validation stringency - parse invalid VCF ANN attribute - parse invalid VCF ANN attribute strict validation stringency - parse VCF ANN attribute with one transcript effect - parse VCF ANN attribute with multiple transcript effects - parse VCF ANN attribute with Ensembl VEP position attribute - 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 2020-12-02 19:21:03 WARN TranscriptEffectConverter$:190 - Could not convert VCF INFO reserved key ANN value to TranscriptEffect, caught java.lang.NumberFormatException: For input string: "not a number". - convert to transcript effect from VCF ANN attribute with invalid number in variant context lenient validation stringency 2020-12-02 19:21:03 WARN TranscriptEffectConverter$: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 2020-12-02 19:21:03 WARN TranscriptEffectConverter$:190 - Incorrect fractional value ?/2, missing numerator - convert transcript effect with incorrect fractional value to VCF ANN attribute value IndelRealignmentTargetSuite: - checking simple realignment target - creating simple target from read with deletion - creating simple target from read with insertion - joining simple realignment targets on same chr - joining simple realignment targets on different chr throws exception - creating targets from three intersecting reads, same indel - creating targets from three intersecting reads, two different indel - creating targets from two disjoint reads - creating targets for artificial reads: one-by-one - creating targets for artificial reads: all-at-once (merged) - creating indel targets for mason reads - additional indel targets taken from consensus generator NormalizationUtilsSuite: - cannot move an indel left if there are no bases to it's left - move a simple indel to farthest position left until bases run out - move a simple indel to farthest position left, past length of indel - cannot move a left normalized indel in a short tandem repeat - move an indel in a short tandem repeat - move an indel in a short tandem repeat of more than 2 bases, where shift is not an integer multiple of repeated sequence length - moving a simple read with single deletion that cannot shift - shift an indel left by 0 in a cigar - shift an indel left by 1 in a cigar - do not left align a complex read which is already left aligned ReadGroupDictionarySuite: - simple conversion to and from sam read group - sample name must be set - simple equality checks - get samples from read group dictionary - empty read group is empty - merging a dictionary with itself should work - round trip a record with all attributes set RightOuterTreeRegionJoinSuite: - Ensure same reference regions get passed together - Overlapping reference regions InnerShuffleRegionJoinSuite: - Overlapping reference regions - Multiple reference regions do not throw exception FeatureDatasetSuite: - round trip GTF format - save GTF as GFF3 format - save GTF as BED format - save GTF as IntervalList format - save GTF as NarrowPeak format - save GFF3 as GTF format - save GFF3 as BED format - save GFF3 as IntervalList format - save GFF3 as NarrowPeak format - round trip GFF3 format - ignore FASTA sequence in GFF3 file - save BED as GTF format - save BED as GFF3 format - save BED as IntervalList format - save BED as NarrowPeak format - round trip BED6 format - keeps sample metadata - round trip BED12 format - save to UCSC BED format - save IntervalList as GTF format - save IntervalList as GFF3 format - save IntervalList as BED format - save IntervalList as IntervalList format - save IntervalList as NarrowPeak format - round trip IntervalList format - save NarrowPeak as GTF format - save NarrowPeak as GFF3 format - save NarrowPeak as BED format - save NarrowPeak as IntervalList format - save NarrowPeak as NarrowPeak format - round trip NarrowPeak format - sort by reference - sort by reference and feature fields - sort gene features by reference and gene structure - sort transcript features by reference and gene structure - sort exon features by reference and gene structure - sort intron features by reference and gene structure - correctly flatmaps CoverageDataset from FeatureDataset - use broadcast join to pull down features mapped to targets - use right outer broadcast join to pull down features mapped to targets - use shuffle join to pull down features mapped to targets - use right outer shuffle join to pull down features mapped to targets - use left outer shuffle join to pull down features mapped to targets - use full outer shuffle join to pull down features mapped to targets - use shuffle join with group by to pull down features mapped to targets - use right outer shuffle join with group by to pull down features mapped to targets - union two feature rdds together - obtain sequence dictionary contig lengths from header in IntervalList format - don't lose any features when piping as BED format - don't lose any features when piping as GTF format - don't lose any features when piping as GFF3 format - don't lose any features when piping as NarrowPeak format - load parquet to sql, save, re-read from avro - load partitioned parquet to sql, save, re-read from avro 2020-12-02 19:21:23 WARN DatasetBoundSliceDataset:190 - Saving directly as Parquet from SQL. Options other than compression codec are ignored. - transform features to slice genomic dataset - transform features to coverage genomic dataset - transform features to fragment genomic dataset - transform features to read genomic dataset - transform features to genotype genomic dataset - transform features to variant genomic dataset - transform features to variant context genomic dataset - filter RDD bound features by feature type - filter dataset bound features by feature type - filter RDD bound features by feature types - filter dataset bound features by feature types - filter RDD bound features by gene - filter dataset bound features by gene - filter RDD bound features by genes - filter dataset bound features by genes - filter RDD bound features by transcript - filter dataset bound features by transcript - filter RDD bound features by transcripts - filter dataset bound features by transcripts - filter RDD bound features by exon - filter dataset bound features by exon - filter RDD bound features by exons - filter dataset bound features by exons - filter RDD bound features by score - filter dataset bound features by score - filter RDD bound features by parent - filter dataset bound features by parent - filter RDD bound features by parents - filter dataset bound features by parents - filter RDD bound features by attribute - filter dataset bound features by attribute - transform dataset via java API AlphabetSuite: - test size of a case-sensitive alphabet - test apply of a case-sensitive alphabet - test reverse complement of a case-sensitive alphabet - test exact reverse complement of a case-sensitive alphabet - test size of a case-insensitive alphabet - test apply of a case-insensitive alphabet - test reverse complement of a case-insensitive alphabet - test exact reverse complement of a case-insensitive alphabet - DNA alphabet - map unknown bases to N SortedGenomicDatasetSuite: - testing that partition and sort provide correct outputs - testing copartition maintains or adds sort - testing that we don't drop any data on the right side even though it doesn't map to a partition on the left - testing that sorted shuffleRegionJoin matches unsorted - testing that sorted fullOuterShuffleRegionJoin matches unsorted - testing that sorted rightOuterShuffleRegionJoin matches unsorted - testing that sorted leftOuterShuffleRegionJoin matches unsorted - testing that we can persist the sorted knowledge VariantContextConverterSuite: - Convert htsjdk site-only SNV to ADAM - Convert somatic htsjdk site-only SNV to ADAM - Convert htsjdk site-only CNV to ADAM - Convert htsjdk SNV w/ genotypes w/ phase information to ADAM - Convert htsjdk SNV with different variant filters to ADAM - Convert htsjdk SNV with different genotype filters to ADAM - Convert ADAM site-only SNV to htsjdk - Convert ADAM SNV w/ genotypes to htsjdk - Convert ADAM SNV w/ genotypes but bad SB to htsjdk with strict validation 2020-12-02 19:21:37 WARN VariantContextConverter:190 - Applying annotation extraction function org.bdgenomics.adam.converters.VariantContextConverter$$Lambda$696/605101809@3e4afddc 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 2020-12-02 19:21:38 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 Alignment obtained from a mapped samRecord conversion - testing the fields in an Alignment 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 2020-12-02 19:21:41 WARN VariantContextConverter:190 - Saw invalid info field java.lang.IllegalArgumentException: Multivalued flags are not supported for INFO lines: INFO=. Ignoring... 2020-12-02 19:21:41 WARN VariantContextConverter:190 - Generating field extractor from header line INFO= failed: java.lang.IllegalArgumentException: Multivalue flags are not supported for INFO lines: INFO= - can read a small .vcf file with a validation issue - can read a small .vcf file 2020-12-02 19:21:41 WARN VCFInputFormat:218 - file:/home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/adam-core/target/2.12.8/test-classes/test.vcf.gz is not splittable, consider using block-compressed gzip (BGZF) - can read a gzipped .vcf file - can read a vcf file with an empty alt - can read a BGZF gzipped .vcf file with .gz file extension - can read a BGZF gzipped .vcf file with .bgz file extension - can read a vcf file with a projection - can read an uncompressed BCFv2.2 file !!! IGNORED !!! - can read a BGZF compressed BCFv2.2 file !!! IGNORED !!! - loadIndexedVcf with 1 ReferenceRegion - loadIndexedVcf with multiple ReferenceRegions - load block compressed interleaved fastq - import records from interleaved FASTQ: 1 - import records from interleaved FASTQ: 2 - import records from interleaved FASTQ: 3 - import records from interleaved FASTQ: 4 - import block compressed single fastq - import records from single ended FASTQ: 1 - import records from single ended FASTQ: 2 - import records from single ended FASTQ: 3 - import records from single ended FASTQ: 4 - filter on load using the filter2 API - saveAsParquet with file path - saveAsParquet with file path, block size, page size - saveAsParquet with save args - read a HLA fasta from GRCh38 - read a gzipped fasta file - read a fasta file with comments, gaps, and translation stops - loadIndexedBam with 1 ReferenceRegion - loadIndexedBam with multiple ReferenceRegions - loadIndexedBam with multiple ReferenceRegions and indexed bams - loadIndexedBam with multiple ReferenceRegions and a directory of indexed bams - loadIndexedBam should throw exception without an index file - loadIndexedBam should work with indexed file with index naming format .bai - loadIndexedBam glob should throw exception without an index file - loadBam with a glob - loadBam with a directory - load vcf with a glob - load vcf from a directory - load gvcf which contains a multi-allelic row from a directory - load and save gvcf which contains rows without likelihoods - parse annotations for multi-allelic rows - load parquet with globs - bad glob should fail - empty directory should fail - can read a SnpEff-annotated .vcf file - loadAlignments should not fail on single-end and paired-end fastq reads - load queryname sorted sam as fragments - load query grouped sam as fragments - load paired fastq - load paired fastq without cache - load paired fastq as fragments - load paired fastq as fragments without cache - load HTSJDK sequence dictionary - load Bedtools .genome file as sequence dictionary - load Bedtools .genome.txt file as sequence dictionary - load UCSC Genome Browser chromInfo.txt file as sequence dictionary - load unrecognized file extension as sequence dictionary fails - load BED features with Bedtools .genome file as sequence dictionary - load BED features with Bedtools .genome file as sequence dictionary, no matching features - convert program record - load program record from sam file - load alignments from data frame - load features from data frame - load fragments from data frame - load genotypes from data frame with default header lines - load genotypes from data frame with empty header lines - load reads from data frame - load sequences from data frame - load slices from data frame - load variant contexts from data frame with default header lines - load variant contexts from data frame with empty header lines - load variants from data frame with default header lines - load variants from data frame with empty header lines - load alignments with metadata from data frame - load features with metadata from data frame - load fragments with metadata from data frame - load genotypes with metadata from data frame - load variant contexts with metadata from data frame - load variants with metadata from data frame - read a fasta file with short sequences as sequences - read a fasta file with long sequences as sequences - read a fasta file with short sequences as slices - read a fasta file with long sequences as slices CycleCovariateSuite: - compute covariates for an unpaired read on the negative strand - compute covariates for a first-of-pair read on the negative strand - compute covariates for a second-of-pair read on the negative strand - compute covariates for an unpaired read on the positive strand - compute covariates for a first-of-pair read on the positive strand - compute covariates for a second-of-pair read on the positive strand AlignmentConverterSuite: - 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 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 2020-12-02 19:22:49 WARN BlockManager:69 - Putting block rdd_5_3 failed due to exception java.lang.Exception: Contig chr2 not found in reference map with keys: chr1. 2020-12-02 19:22:49 WARN BlockManager:69 - Block rdd_5_3 could not be removed as it was not found on disk or in memory 2020-12-02 19:22:49 ERROR Executor:94 - Exception in task 3.0 in stage 2.0 (TID 11) java.lang.Exception: Contig chr2 not found in reference map with keys: chr1 at org.bdgenomics.adam.util.ReferenceContigMap.$anonfun$extract$1(ReferenceContigMap.scala:64) at scala.collection.immutable.Map$Map1.getOrElse(Map.scala:119) at org.bdgenomics.adam.util.ReferenceContigMap.extract(ReferenceContigMap.scala:63) at org.bdgenomics.adam.rdd.read.MDTagging.$anonfun$addMDTagsBroadcast$3(MDTagging.scala:76) at scala.Option$WithFilter.map(Option.scala:163) at org.bdgenomics.adam.rdd.read.MDTagging.$anonfun$addMDTagsBroadcast$1(MDTagging.scala:71) at scala.collection.Iterator$$anon$10.next(Iterator.scala:459) at org.apache.spark.storage.memory.MemoryStore.putIterator(MemoryStore.scala:222) at org.apache.spark.storage.memory.MemoryStore.putIteratorAsValues(MemoryStore.scala:299) at org.apache.spark.storage.BlockManager.$anonfun$doPutIterator$1(BlockManager.scala:1371) at org.apache.spark.storage.BlockManager.org$apache$spark$storage$BlockManager$$doPut(BlockManager.scala:1298) at org.apache.spark.storage.BlockManager.doPutIterator(BlockManager.scala:1362) at org.apache.spark.storage.BlockManager.getOrElseUpdate(BlockManager.scala:1186) at org.apache.spark.rdd.RDD.getOrCompute(RDD.scala:360) at org.apache.spark.rdd.RDD.iterator(RDD.scala:311) at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:90) at org.apache.spark.scheduler.Task.run(Task.scala:127) at org.apache.spark.executor.Executor$TaskRunner.$anonfun$run$3(Executor.scala:446) at org.apache.spark.util.Utils$.tryWithSafeFinally(Utils.scala:1377) at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:449) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624) at java.lang.Thread.run(Thread.java:748) 2020-12-02 19:22:49 WARN TaskSetManager:69 - Lost task 3.0 in stage 2.0 (TID 11, 192.168.122.1, executor driver): java.lang.Exception: Contig chr2 not found in reference map with keys: chr1 at org.bdgenomics.adam.util.ReferenceContigMap.$anonfun$extract$1(ReferenceContigMap.scala:64) at scala.collection.immutable.Map$Map1.getOrElse(Map.scala:119) at org.bdgenomics.adam.util.ReferenceContigMap.extract(ReferenceContigMap.scala:63) at org.bdgenomics.adam.rdd.read.MDTagging.$anonfun$addMDTagsBroadcast$3(MDTagging.scala:76) at scala.Option$WithFilter.map(Option.scala:163) at org.bdgenomics.adam.rdd.read.MDTagging.$anonfun$addMDTagsBroadcast$1(MDTagging.scala:71) at scala.collection.Iterator$$anon$10.next(Iterator.scala:459) at org.apache.spark.storage.memory.MemoryStore.putIterator(MemoryStore.scala:222) at org.apache.spark.storage.memory.MemoryStore.putIteratorAsValues(MemoryStore.scala:299) at org.apache.spark.storage.BlockManager.$anonfun$doPutIterator$1(BlockManager.scala:1371) at org.apache.spark.storage.BlockManager.org$apache$spark$storage$BlockManager$$doPut(BlockManager.scala:1298) at org.apache.spark.storage.BlockManager.doPutIterator(BlockManager.scala:1362) at org.apache.spark.storage.BlockManager.getOrElseUpdate(BlockManager.scala:1186) at org.apache.spark.rdd.RDD.getOrCompute(RDD.scala:360) at org.apache.spark.rdd.RDD.iterator(RDD.scala:311) at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:90) at org.apache.spark.scheduler.Task.run(Task.scala:127) at org.apache.spark.executor.Executor$TaskRunner.$anonfun$run$3(Executor.scala:446) at org.apache.spark.util.Utils$.tryWithSafeFinally(Utils.scala:1377) at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:449) 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) 2020-12-02 19:22:49 ERROR TaskSetManager:73 - Task 3 in stage 2.0 failed 1 times; aborting job - try realigning a read on a missing contig, stringency == STRICT 2020-12-02 19:22:50 WARN MDTagging:190 - Caught exception when processing read chr2: java.lang.Exception: Contig chr2 not found in reference map with keys: chr1 - try realigning a read on a missing contig, stringency == LENIENT FileExtensionsSuite: - ends in gzip extension - is a vcf extension PhredUtilsSuite: - convert low phred score to log and back - convert high phred score to log and back - convert overflowing phred score to log and back and clip - convert negative zero log probability to phred and clip - round trip log probabilities ReadDatasetSuite: - create a new read genomic dataset - create a new read genomic dataset with sequence dictionary - save as parquet - round trip as parquet - save as fastq - save as single file fastq - filter read genomic dataset by reference region - broadcast region join reads and features - shuffle region join reads and features - convert reads to alignments - convert reads to sequences - convert reads to slices AlignmentDatasetSuite: - sorting reads - unmapped reads go at the end when sorting - coverage does not fail on unmapped reads - 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 2020-12-02 19:23:51 WARN RDDBoundAlignmentDataset: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 2020-12-02 19:23:52 WARN RDDBoundAlignmentDataset: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 2020-12-02 19:23:54 WARN RDDBoundAlignmentDataset: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 2020-12-02 19:24:07 WARN OutFormatterRunner:190 - Piped command List(sleep, 10) timed out after 5 seconds. 2020-12-02 19:24:07 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 2020-12-02 19:24:28 WARN OutFormatterRunner:190 - Piped command List(python, /tmp/adamTestMvncIb5npe/spark-353efc6f-5458-46d7-85b5-5c87d3ab9ca0/userFiles-6814db8c-50c6-4575-97d3-92106d04e6df/timeout.py) timed out after 5 seconds. 2020-12-02 19:24:28 WARN OutFormatterRunner:190 - Piped command List(python, /tmp/adamTestMvncIb5npe/spark-353efc6f-5458-46d7-85b5-5c87d3ab9ca0/userFiles-6814db8c-50c6-4575-97d3-92106d04e6df/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 pipe !!! IGNORED !!! - use broadcast join to pull down reads mapped to targets - use broadcast join against to pull down reads mapped to targets - use right outer broadcast join to pull down reads mapped to targets - use right outer broadcast join against to pull down reads mapped to targets - use shuffle join with feature spanning partitions - use shuffle join to pull down reads mapped to targets - use shuffle join with flankSize to pull down reads mapped close to targets - use right outer shuffle join to pull down reads mapped to targets - use left outer shuffle join to pull down reads mapped to targets - use full outer shuffle join to pull down reads mapped to targets - use shuffle join with group by to pull down reads mapped to targets - use right outer shuffle join with group by to pull down reads mapped to targets - cannot provide empty quality score bins - cannot provide bins with a gap - cannot provide overlapping bins - binning quality scores in reads succeeds even if reads have no quality scores - bin quality scores in reads - union two read files together - test k-mer counter - test dataset based k-mer counter - transform reads to slice genomic dataset - transform reads to coverage genomic dataset - transform reads to feature genomic dataset - transform reads to fragment genomic dataset - transform reads to genotype genomic dataset loading /tmp/adamTestMvncIb5npe/TempSuite9049463449289134766.adam as parquet into RDD... loading /tmp/adamTestMvncIb5npe/TempSuite3988564967045884044.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 2020-12-02 19:25:34 WARN DAGScheduler:69 - Broadcasting large task binary with size 1134.2 KiB - running base recalibration with downsampling doesn't drop reads - filter RDD bound alignments by MAPQ - filter dataset bound alignments by MAPQ - filter RDD bound unaligned alignments - filter dataset bound unaligned alignments - filter RDD bound unpaired alignments - filter dataset bound unpaired alignments - filter RDD bound duplicate alignments - filter dataset bound duplicate alignments - filter RDD bound alignments to primary alignments - filter dataset bound alignments to primary alignments - filter RDD bound alignments to read group - filter dataset bound alignments to read group - filter RDD bound alignments to read groups - filter dataset bound alignments to read groups - filter RDD bound alignments to sample - filter dataset bound alignments to sample - filter RDD bound alignments to samples - filter dataset bound alignments to samples - sort by read name - transform dataset via java API - convert alignments to reads SmithWatermanSuite: - gather max position from simple scoring matrix - gather max position from irregular scoring matrix - gather max position from irregular scoring matrix with deletions - score simple alignment with constant gap - score irregular scoring matrix - score irregular scoring matrix with indel - can unroll cigars correctly - execute simple trackback - execute trackback with indel - run end to end smith waterman for simple reads - run end to end smith waterman for short sequences with indel - run end to end smith waterman for longer sequences with snp - run end to end smith waterman for longer sequences with short indel - run end to end smith waterman for shorter sequence in longer sequence - run end to end smith waterman for shorter sequence in longer sequence, with indel - smithWaterman - simple alignment MdTagSuite: - null md tag - zero length md tag - md tag with non-digit initial value - md tag invalid base - md tag, pure insertion - md tag, pure insertion, test 2 - md tag pure insertion equality - md tag equality and hashcode - valid md tags - get start of read with no mismatches or deletions - get start of read with no mismatches, but with a deletion at the start - get start of read with mismatches at the start - get end of read with no mismatches or deletions - check that mdtag and rich record return same end - get end of read with no mismatches, but a deletion at end - CIGAR with N operator - CIGAR with multiple N operators - CIGAR with P operators - Get correct matches for mdtag with insertion - Get correct matches for mdtag with mismatches and insertion - Get correct matches for mdtag with insertion between mismatches - Get correct matches for mdtag with intron between mismatches - Get correct matches for mdtag with intron and deletion between mismatches - Throw exception when number of deleted bases in mdtag disagrees with CIGAR - Get correct matches for mdtag with mismatch, insertion and deletion - Get correct matches for mdtag with mismatches, insertion and deletion - Get correct matches for MDTag with mismatches and deletions - Get correct matches base from MDTag and CIGAR with N - get end of read with mismatches and a deletion at end - get correct string out of mdtag with no mismatches - get correct string out of mdtag with mismatches at start - get correct string out of mdtag with deletion at end - get correct string out of mdtag with mismatches at end - get correct string out of complex mdtag - check complex mdtag - get gapped reference - move a cigar alignment by two for a read - rewrite alignment to all matches - rewrite alignment to two mismatches followed by all matches - rewrite alignment to include a deletion but otherwise all matches - rewrite alignment to include an insertion at the start of the read but otherwise all matches - create new md tag from read vs. reference, perfect match - create new md tag from read vs. reference, perfect alignment match, 1 mismatch - create new md tag from read vs. reference, alignment with deletion - create new md tag from read vs. reference, alignment with insert - handle '=' and 'X' operators - CIGAR/MD tag mismatch should cause errors GenomicDatasetSuite: - processing a command that is the spark root directory should return an absolute path - processing a command that is just a single word should do nothing - processing a command should handle arguments that include spaces - processing a command that is a single substitution should succeed - processing a command that is multiple words should split the string - process a command that is multiple words with a replacement - process a command that is multiple words with multiple replacements ParallelFileMergerSuite: - cannot write both empty gzip block and cram eof - buffer size must be non-negative - get the size of several files - block size must be positive and non-zero when trying to merge files - must provide files to merge - if two files are both below the block size, they should merge into one shard - merge two files where one is greater than the block size - merge a sharded sam file - merge a sharded bam file - merge a sharded cram file - can't turn a negative index into a path - generate a path from an index IndelTableSuite: - check for indels in a region with known indels - check for indels in a contig that doesn't exist - check for indels in a region without known indels - build indel table from rdd of variants SnpTableSuite: - create an empty snp table - create a snp table from variants on multiple contigs - create a snp table from a larger set of variants - perform lookups on multi-contig snp table - perform lookups on larger snp table RealignIndelsSuite: - map reads to targets - checking mapping to targets for artificial reads - checking alternative consensus for artificial reads - checking extraction of reference from reads - checking realigned reads for artificial input - checking realigned reads for artificial input with reference file - checking realigned reads for artificial input using knowns - checking realigned reads for artificial input using knowns and reads - skip realigning reads if target is highly covered - skip realignment if target is an insufficient LOD improvement - realign reads to an insertion - test mismatch quality scoring - test mismatch quality scoring for no mismatches - test mismatch quality scoring for offset - test mismatch quality scoring with early exit - test mismatch quality scoring after unpacking read - we shouldn't try to realign a region with no target - we shouldn't try to realign reads with no indel evidence - test OP and OC tags - realign a read with an insertion that goes off the end of the read - if realigning a target doesn't improve the LOD, don't drop reads - extract seq/qual from a read with no clipped bases - extract seq/qual from a read with clipped bases at start - extract seq/qual from a read with clipped bases at end - if unclip is selected, don't drop base when extracting from a read with clipped bases - get cigar and coordinates for read that spans indel, no clipped bases - get cigar and coordinates for read that spans deletion, clipped bases at start - get cigar and coordinates for read that falls wholly before insertion - get cigar and coordinates for read that falls wholly after insertion - get cigar and coordinates for read that falls wholly after deletion - get cigar and coordinates for read that partially spans insertion, no clipped bases - get cigar and coordinates for read that partially spans insertion, clipped bases at end - get cigar and coordinates for read that partially spans insertion, clipped bases both ends BaseQualityRecalibrationSuite: 2020-12-02 19:26:20 WARN DAGScheduler:69 - Broadcasting large task binary with size 1134.2 KiB - BQSR Test Input #1 w/ VCF Sites without caching 2020-12-02 19:26:27 WARN DAGScheduler:69 - Broadcasting large task binary with size 1134.2 KiB - BQSR Test Input #1 w/ VCF Sites with caching 2020-12-02 19:26:32 WARN DAGScheduler:69 - Broadcasting large task binary with size 1134.2 KiB - 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 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 2020-12-02 19:27:08 WARN DatasetBoundSliceDataset:190 - Saving directly as Parquet from SQL. Options other than compression codec are ignored. - transform variants to slice genomic dataset - transform variants to coverage genomic dataset - transform variants to feature genomic dataset - transform variants to fragment genomic dataset - transform variants to read genomic dataset - transform variants to genotype genomic dataset - transform variants to variant context genomic dataset - filter RDD bound variants to filters passed - filter dataset bound variants to filters passed - filter RDD bound variants by quality - filter dataset bound variants by quality - filter RDD bound variants by read depth - filter dataset bound variants by read depth - filter RDD bound variants by reference read depth - filter dataset bound variants by reference read depth - filter RDD bound single nucleotide variants - filter dataset bound single nucleotide variants - filter RDD bound multiple nucleotide variants - filter dataset bound multiple nucleotide variants - filter RDD bound indel variants - filter dataset bound indel variants - filter RDD bound variants to single nucleotide variants - filter dataset bound variants to single nucleotide variants - filter RDD bound variants to multiple nucleotide variants - filter dataset bound variants to multiple nucleotide variants - filter RDD bound variants to indel variants - filter dataset bound variants to indel variants - transform dataset via java API Run completed in 8 minutes, 6 seconds. Total number of tests run: 1177 Suites: completed 68, aborted 0 Tests: succeeded 1177, 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-spark3_2.12 >>> [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-core-spark3_2.12 --- [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-core-spark3_2.12 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ adam-core-spark3_2.12 --- [INFO] Source directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/adam-core/src/main/scala added. [INFO] Source directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/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-spark3_2.12 --- SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] [INFO] --- exec-maven-plugin:1.5.0:java (generate-scala-projection-fields) @ adam-core-spark3_2.12 --- SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ adam-core-spark3_2.12 --- [INFO] Modified 2 of 204 .scala files [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:pre-compile (default-cli) @ adam-core-spark3_2.12 --- [WARNING] Skipping SCoverage execution - unsupported Scala version "2.12.8" [INFO] [INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ adam-core-spark3_2.12 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/adam-core/src/main/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ adam-core-spark3_2.12 --- [INFO] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/adam-core/src/main/java:-1: info: compiling [INFO] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/adam-core/src/main/scala:-1: info: compiling [INFO] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/adam-core/target/generated-sources/src/main/scala:-1: info: compiling [INFO] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/adam-core/target/generated-sources/annotations:-1: info: compiling [INFO] Compiling 140 source files to /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/adam-core/target/2.12.8/classes at 1606966061316 [WARNING] warning: there were 21 deprecation warnings [WARNING] warning: there were 31 deprecation warnings (since 0.21.0) [WARNING] warning: there was one deprecation warning (since 1.0.6) [WARNING] warning: there was one deprecation warning (since 2.11.0) [WARNING] warning: there were 174 deprecation warnings (since 2.12.0) [WARNING] warning: there was one deprecation warning (since 2.12.7) [WARNING] warning: there were 229 deprecation warnings in total; re-run with -deprecation for details [WARNING] warning: there were 5 feature warnings; re-run with -feature for details [WARNING] 8 warnings found [INFO] prepare-compile in 0 s [INFO] compile in 27 s [INFO] [INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ adam-core-spark3_2.12 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:post-compile (default-cli) @ adam-core-spark3_2.12 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ adam-core-spark3_2.12 --- [INFO] Test Source directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/adam-core/src/test/scala added. [INFO] [INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ adam-core-spark3_2.12 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 153 resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ adam-core-spark3_2.12 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ adam-core-spark3_2.12 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ adam-core-spark3_2.12 --- [INFO] Tests are skipped. [INFO] [INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ adam-core-spark3_2.12 --- Discovery starting. Discovery completed in 1 second, 674 milliseconds. Run starting. Expected test count is: 1177 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 2020-12-02 19:28:12 WARN Utils:69 - Your hostname, research-jenkins-worker-01 resolves to a loopback address: 127.0.1.1; using 192.168.122.1 instead (on interface virbr0) 2020-12-02 19:28:12 WARN Utils:69 - Set SPARK_LOCAL_IP if you need to bind to another address 2020-12-02 19:28:12 WARN NativeCodeLoader:62 - Unable to load native-hadoop library for your platform... using builtin-java classes where applicable - move pairs around an rdd FlagStatSuite: - Standard FlagStat test ModPartitionerSuite: - report number of partitions correctly - partition a number that is lower than the number of partitions and positive - partition a number that is greater than the number of partitions and positive - partition a number that is lower than the number of partitions and negative - partition a number that is greater than the number of partitions and negative - fire an exception if input is not an integer TwoBitFileSuite: - correctly read sequence from .2bit file - correctly return masked sequences from .2bit file - correctly return Ns from .2bit file - correctly calculates sequence dictionary NonoverlappingRegionsSuite: - alternating returns an alternating seq of items - Single region returns itself - Two adjacent regions will be merged - Nonoverlapping regions will all be returned - Many overlapping regions will all be merged - ADAMRecords return proper references ReferencePositionSuite: - create reference position from mapped read - create reference position from variant - create reference position from genotype - create reference position from variant starting at vcf 0 - create reference position from genotype starting at vcf 0 ConsensusGeneratorFromReadsSuite: - checking search for consensus list for artificial reads FragmentConverterSuite: - build a fragment collector and convert to a read - if a fragment isn't associated with a contig, don't get a fragment collector - convert an rdd of discontinuous fragments, all from the same contig - convert an rdd of contiguous fragments, all from the same contig - convert an rdd of varied fragments from multiple contigs FileMergerSuite: - cannot write both empty gzip block and cram eof - buffer size must be non-negative RichAlignmentSuite: - Unclipped Start - Unclipped End - tags contains optional fields - read overlap unmapped read - read overlap reference position - read overlap same position different contig SingleReadBucketSuite: - convert unmapped pair to fragment - convert proper pair to fragment - convert read pair to fragment with first of pair chimeric read RecalibrationTableSuite: - look up quality scores in table FlankSlicesSuite: - don't put flanks on non-adjacent slices - put flanks on adjacent slices InterleavedFastqInputFormatSuite: - interleaved FASTQ hadoop reader: interleaved_fastq_sample1.ifq->interleaved_fastq_sample1.ifq.output - interleaved FASTQ hadoop reader: interleaved_fastq_sample2.ifq->interleaved_fastq_sample2.ifq.output - interleaved FASTQ hadoop reader: interleaved_fastq_sample3.ifq->interleaved_fastq_sample3.ifq.output - interleaved FASTQ hadoop reader: interleaved_fastq_sample4.ifq->interleaved_fastq_sample4.ifq.output - interleaved FASTQ hadoop reader: interleaved_fastq_sample5.ifq->interleaved_fastq_sample5.ifq.output TreeRegionJoinSuite: - run a join between data on a single contig ReferenceRegionSuite: - cannot create an empty predicate - parse empty string throws IllegalArgumentException - parse contigName only string into reference regions - parse to end strings into reference regions - parse string into reference regions - contains(: ReferenceRegion) - contains(: ReferencePosition) - merge - overlaps and covers - overlapsBy and coversBy - distance(: ReferenceRegion) - distance(: ReferencePosition) - unstrandedDistance - subtract fails on non-overlapping and non-covering regions - subtract - create region from unmapped read fails - create region from read with null alignment positions fails - create stranded region from unmapped read fails - create stranded region from read with null alignment positions fails - create stranded region from read with null alignment strand fails - create stranded region from read on forward strand - create stranded region from read on reverse strand - create region from mapped read contains read start and end - validate that adjacent regions can be merged - validate that non-adjacent regions cannot be merged - validate that nearby regions can be merged - validate that non-nearby regions cannot be merged - compute convex hull of two sets - region name is sanitized when creating region from read - intersection fails on non-overlapping regions - intersection fails when minOverlap is not met - compute intersection - overlap tests for oriented reference region - check the width of a reference region - make a reference region for a variant or genotype - make a reference region for a variant or genotype starting at VCF 0 - uniformly pad a reference region - uniformly pad a reference region into negative coordinate space, ensure non negative start - unevenly pad a reference region - unevenly pad a reference region into negative coordinate space, ensure non negative start - can build an open ended reference region - can build an open ended reference region with strand - can build a reference region with an open start position - can build a reference region with an open start position with strand - can build a reference region that covers the entirety of a contig - can build a reference region that covers the entirety of a contig with strand - convert a genotype and then get the reference region - create region from feature with null alignment positions fails - create stranded region from feature with null alignment positions fails - create stranded region from feature with null alignment strand fails - create stranded region from feature on forward strand - create stranded region from feature on reverse strand 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 2020-12-02 19:28:30 WARN DatasetBoundSliceDataset:190 - Saving directly as Parquet from SQL. Options other than compression codec are ignored. - transform coverage to slice genomic dataset - transform coverage to feature genomic dataset 2020-12-02 19:28:31 WARN package:69 - Truncated the string representation of a plan since it was too large. This behavior can be adjusted by setting 'spark.sql.debug.maxToStringFields'. - transform coverage to fragment genomic dataset - transform coverage to read genomic dataset - transform coverage to genotype genomic dataset - transform coverage to variant genomic dataset - transform coverage to variant context genomic dataset - copy coverage rdd - copy coverage dataset - copy coverage rdd without sequence dictionary - copy coverage dataset without sequence dictionary - transform dataset via java API RecalibratorSuite: - don't replace quality if quality was null - if no covariates, return alignment - skip recalibration if base is below quality threshold - recalibrate changed bases above quality threshold SliceDatasetSuite: - create a new slice genomic dataset - create a new slice genomic dataset with sequence dictionary - merge slices into a sequence genomic dataset - save as parquet - round trip as parquet - save as fasta - save as single file fasta - convert slices to reads - convert slices to sequences GenotypeDatasetSuite: - union two genotype genomic datasets together - round trip to parquet - round trip to partitioned parquet - use broadcast join to pull down genotypes mapped to targets - use right outer broadcast join to pull down genotypes mapped to targets - use shuffle join to pull down genotypes mapped to targets - use right outer shuffle join to pull down genotypes mapped to targets - use left outer shuffle join to pull down genotypes mapped to targets - use full outer shuffle join to pull down genotypes mapped to targets - use shuffle join with group by to pull down genotypes mapped to targets - use right outer shuffle join with group by to pull down genotypes mapped to targets - convert back to variant contexts - load parquet to sql, save, re-read from avro 2020-12-02 19:28:49 WARN DatasetBoundSliceDataset:190 - Saving directly as Parquet from SQL. Options other than compression codec are ignored. - transform genotypes to slice genomic dataset - transform genotypes to coverage genomic dataset - transform genotypes to feature genomic dataset - transform genotypes to fragment genomic dataset - transform genotypes to read genomic dataset - transform genotypes to variant genomic dataset - transform genotypes to variant context genomic dataset - loading genotypes then converting to variants yields same output as loading variants - filter RDD bound genotypes to genotype filters passed - filter dataset bound genotypes to genotype filters passed - filter RDD bound genotypes by genotype quality - filter dataset bound genotypes by genotype quality - filter RDD bound genotypes by read depth - filter dataset bound genotypes by read depth - filter RDD bound genotypes by alternate read depth - filter dataset bound genotypes by alternate read depth - filter RDD bound genotypes by reference read depth - filter dataset bound genotypes by reference read depth - filter RDD bound genotypes by sample - filter dataset bound genotypes by sample - filter RDD bound genotypes by samples - filter dataset bound genotypes by samples - filter RDD bound no call genotypes - filter dataset no call genotypes - round trip gVCF END attribute without nested variant annotations rdd bound - round trip gVCF END attribute without nested variant annotations dataset bound - round trip gVCF END attribute with nested variant annotations rdd bound - round trip gVCF END attribute with nested variant annotations dataset bound - transform dataset via java API FragmentDatasetSuite: - don't lose any reads when piping interleaved fastq to sam - don't lose any reads when piping tab5 to sam - don't lose any reads when piping tab6 to sam - use broadcast join to pull down fragments mapped to targets - use right outer broadcast join to pull down fragments mapped to targets - use shuffle join to pull down fragments mapped to targets - use right outer shuffle join to pull down fragments mapped to targets - use left outer shuffle join to pull down fragments mapped to targets - use full outer shuffle join to pull down fragments mapped to targets - use shuffle join with group by to pull down fragments mapped to targets - use right outer shuffle join with group by to pull down fragments mapped to targets - bin quality scores in fragments - union two genomic datasets of fragments together - load parquet to sql, save, re-read from avro - transform fragments to slice genomic dataset - transform fragments to coverage genomic dataset - transform fragments to feature genomic dataset - transform fragments to read genomic dataset - transform fragments to genotype genomic dataset - transform fragments to variant genomic dataset - transform fragments to variant context genomic dataset - paired read names with index sequences in read names can group into fragments - interleaved paired read names with index sequences in read names can group into fragments - interleaved paired read names with index sequences in read names as fragments - transform dataset via java API - dataset and rdd conversion to alignments are equivalent - Compare unpaired FragmentDataset with optimisation to non-optimised SingleFastqInputFormatSuite: - FASTQ hadoop reader: fastq_sample1.fq->single_fastq_sample1.fq.output - FASTQ hadoop reader: fastq_sample2.fq->single_fastq_sample2.fq.output - FASTQ hadoop reader: fastq_sample3.fq->single_fastq_sample3.fq.output - FASTQ hadoop reader: fastq_sample4.fq->single_fastq_sample4.fq.output VariantContextDatasetSuite: - load a gvcf with a missing info field set to . - union two variant context genomic datasets together - can write, then read in .vcf file - can write as a single file via simple saveAsVcf method, then read in .vcf file - can write as a single file via full saveAsVcf method, then read in .vcf file - transform a vcf file with bad header - read a vcf file with multi-allelic variants to split - support VCFs with +Inf/-Inf float values - support VCFs with `nan` instead of `NaN` float values - don't lose any variants when piping as VCF - pipe works with empty partitions - don't lose any non-default VCF header lines or attributes when piping as VCF - save a file sorted by contig index - save a lexicographically sorted file - save a multiallelic gvcf !!! IGNORED !!! - test metadata - save sharded bgzip vcf - save bgzip vcf as single file - can't save file with non-vcf extension - transform variant contexts to slice genomic dataset - transform variant contexts to coverage genomic dataset - transform variant contexts to feature genomic dataset - transform variant contexts to fragment genomic dataset - transform variant contexts to read genomic dataset - transform variant contexts to genotype genomic dataset - transform variant contexts to variant genomic dataset - save and reload from partitioned parquet - transform dataset via java API ConsensusSuite: - test the insertion of a consensus insertion into a reference - test the insertion of a consensus deletion into a reference - inserting empty consensus returns the reference SequenceDatasetSuite: - create a new sequence genomic dataset - create a new sequence genomic dataset with sequence dictionary - save as parquet - round trip as parquet - save as fasta - save as single file fasta - convert sequences to reads - convert sequences to slices - slice sequences to a maximum length - slice sequences shorter than maximum length - filter sequences by overlapping region - filter sequences failing to overlap region - filter sequences by overlapping regions - filter sequences failing to overlap regions - slice sequences overlapping a smaller region - slice sequences overlapping a larger region - slice sequences failing to overlap a region - slice sequences overlapping smaller regions - slice sequences overlapping larger regions - slice sequences failing to overlap regions AttributeUtilsSuite: - parseTags returns a reasonable set of tagStrings - parseTags works with NumericSequence tagType - empty string is parsed as zero tagStrings - incorrectly formatted tag throws an exception - string tag with a ':' in it is correctly parsed - oq string tag with many ':' in it is correctly parsed - oq string tag with a ',' in it is correctly parsed - if a tag is an array but doesn't define it's format, throw MarkDuplicatesSuite: - single read - reads at different positions - reads at the same position - reads at the same position with clipping - reads on reverse strand - unmapped reads - read pairs - read pairs with fragments - quality scores - read pairs that cross chromosomes - single fragment - fragments at different positions - fragments at the same position - fragments at the same position with clipping - fragments on reverse strand - unmapped fragments - read pairs as fragments - read pairs with fragments as fragments - chimeric fragments - inverse pairs - supplemental reads TranscriptEffectConverterSuite: - parse empty transcript effect - parse empty transcript effect strict validation stringency - parse invalid transcript effect - parse invalid transcript effect strict validation stringency - parse transcript effect - parse empty list VCF ANN attribute - parse empty list VCF ANN attribute strict validation stringency - parse empty string VCF ANN attribute - parse empty string VCF ANN attribute strict validation stringency - parse invalid VCF ANN attribute - parse invalid VCF ANN attribute strict validation stringency - parse VCF ANN attribute with one transcript effect - parse VCF ANN attribute with multiple transcript effects - parse VCF ANN attribute with Ensembl VEP position attribute - 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 2020-12-02 19:29:42 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 2020-12-02 19:29:42 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 2020-12-02 19:29:42 WARN TranscriptEffectConverter$:190 - Incorrect fractional value ?/2, missing numerator - convert transcript effect with incorrect fractional value to VCF ANN attribute value IndelRealignmentTargetSuite: - checking simple realignment target - creating simple target from read with deletion - creating simple target from read with insertion - joining simple realignment targets on same chr - joining simple realignment targets on different chr throws exception - creating targets from three intersecting reads, same indel - creating targets from three intersecting reads, two different indel - creating targets from two disjoint reads - creating targets for artificial reads: one-by-one - creating targets for artificial reads: all-at-once (merged) - creating indel targets for mason reads - additional indel targets taken from consensus generator NormalizationUtilsSuite: - cannot move an indel left if there are no bases to it's left - move a simple indel to farthest position left until bases run out - move a simple indel to farthest position left, past length of indel - cannot move a left normalized indel in a short tandem repeat - move an indel in a short tandem repeat - move an indel in a short tandem repeat of more than 2 bases, where shift is not an integer multiple of repeated sequence length - moving a simple read with single deletion that cannot shift - shift an indel left by 0 in a cigar - shift an indel left by 1 in a cigar - do not left align a complex read which is already left aligned ReadGroupDictionarySuite: - simple conversion to and from sam read group - sample name must be set - simple equality checks - get samples from read group dictionary - empty read group is empty - merging a dictionary with itself should work - round trip a record with all attributes set RightOuterTreeRegionJoinSuite: - Ensure same reference regions get passed together - Overlapping reference regions InnerShuffleRegionJoinSuite: - Overlapping reference regions - Multiple reference regions do not throw exception FeatureDatasetSuite: - round trip GTF format - save GTF as GFF3 format - save GTF as BED format - save GTF as IntervalList format - save GTF as NarrowPeak format - save GFF3 as GTF format - save GFF3 as BED format - save GFF3 as IntervalList format - save GFF3 as NarrowPeak format - round trip GFF3 format - ignore FASTA sequence in GFF3 file - save BED as GTF format - save BED as GFF3 format - save BED as IntervalList format - save BED as NarrowPeak format - round trip BED6 format - keeps sample metadata - round trip BED12 format - save to UCSC BED format - save IntervalList as GTF format - save IntervalList as GFF3 format - save IntervalList as BED format - save IntervalList as IntervalList format - save IntervalList as NarrowPeak format - round trip IntervalList format - save NarrowPeak as GTF format - save NarrowPeak as GFF3 format - save NarrowPeak as BED format - save NarrowPeak as IntervalList format - save NarrowPeak as NarrowPeak format - round trip NarrowPeak format - sort by reference - sort by reference and feature fields - sort gene features by reference and gene structure - sort transcript features by reference and gene structure - sort exon features by reference and gene structure - sort intron features by reference and gene structure - correctly flatmaps CoverageDataset from FeatureDataset - use broadcast join to pull down features mapped to targets - use right outer broadcast join to pull down features mapped to targets - use shuffle join to pull down features mapped to targets - use right outer shuffle join to pull down features mapped to targets - use left outer shuffle join to pull down features mapped to targets - use full outer shuffle join to pull down features mapped to targets - use shuffle join with group by to pull down features mapped to targets - use right outer shuffle join with group by to pull down features mapped to targets - union two feature rdds together - obtain sequence dictionary contig lengths from header in IntervalList format - don't lose any features when piping as BED format - don't lose any features when piping as GTF format - don't lose any features when piping as GFF3 format - don't lose any features when piping as NarrowPeak format - load parquet to sql, save, re-read from avro - load partitioned parquet to sql, save, re-read from avro 2020-12-02 19:30:02 WARN DatasetBoundSliceDataset:190 - Saving directly as Parquet from SQL. Options other than compression codec are ignored. - transform features to slice genomic dataset - transform features to coverage genomic dataset - transform features to fragment genomic dataset - transform features to read genomic dataset - transform features to genotype genomic dataset - transform features to variant genomic dataset - transform features to variant context genomic dataset - filter RDD bound features by feature type - filter dataset bound features by feature type - filter RDD bound features by feature types - filter dataset bound features by feature types - filter RDD bound features by gene - filter dataset bound features by gene - filter RDD bound features by genes - filter dataset bound features by genes - filter RDD bound features by transcript - filter dataset bound features by transcript - filter RDD bound features by transcripts - filter dataset bound features by transcripts - filter RDD bound features by exon - filter dataset bound features by exon - filter RDD bound features by exons - filter dataset bound features by exons - filter RDD bound features by score - filter dataset bound features by score - filter RDD bound features by parent - filter dataset bound features by parent - filter RDD bound features by parents - filter dataset bound features by parents - filter RDD bound features by attribute - filter dataset bound features by attribute - transform dataset via java API AlphabetSuite: - test size of a case-sensitive alphabet - test apply of a case-sensitive alphabet - test reverse complement of a case-sensitive alphabet - test exact reverse complement of a case-sensitive alphabet - test size of a case-insensitive alphabet - test apply of a case-insensitive alphabet - test reverse complement of a case-insensitive alphabet - test exact reverse complement of a case-insensitive alphabet - DNA alphabet - map unknown bases to N SortedGenomicDatasetSuite: - testing that partition and sort provide correct outputs - testing copartition maintains or adds sort - testing that we don't drop any data on the right side even though it doesn't map to a partition on the left - testing that sorted shuffleRegionJoin matches unsorted - testing that sorted fullOuterShuffleRegionJoin matches unsorted - testing that sorted rightOuterShuffleRegionJoin matches unsorted - testing that sorted leftOuterShuffleRegionJoin matches unsorted - testing that we can persist the sorted knowledge VariantContextConverterSuite: - Convert htsjdk site-only SNV to ADAM - Convert somatic htsjdk site-only SNV to ADAM - Convert htsjdk site-only CNV to ADAM - Convert htsjdk SNV w/ genotypes w/ phase information to ADAM - Convert htsjdk SNV with different variant filters to ADAM - Convert htsjdk SNV with different genotype filters to ADAM - Convert ADAM site-only SNV to htsjdk - Convert ADAM SNV w/ genotypes to htsjdk - Convert ADAM SNV w/ genotypes but bad SB to htsjdk with strict validation 2020-12-02 19:30:16 WARN VariantContextConverter:190 - Applying annotation extraction function org.bdgenomics.adam.converters.VariantContextConverter$$Lambda$696/605101809@122ef650 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 2020-12-02 19:30:16 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 Alignment obtained from a mapped samRecord conversion - testing the fields in an Alignment 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 2020-12-02 19:30:19 WARN VariantContextConverter:190 - Saw invalid info field java.lang.IllegalArgumentException: Multivalued flags are not supported for INFO lines: INFO=. Ignoring... 2020-12-02 19:30:19 WARN VariantContextConverter:190 - Generating field extractor from header line INFO= failed: java.lang.IllegalArgumentException: Multivalue flags are not supported for INFO lines: INFO= - can read a small .vcf file with a validation issue - can read a small .vcf file 2020-12-02 19:30:19 WARN VCFInputFormat:218 - file:/home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/adam-core/target/2.12.8/test-classes/test.vcf.gz is not splittable, consider using block-compressed gzip (BGZF) - can read a gzipped .vcf file - can read a vcf file with an empty alt - can read a BGZF gzipped .vcf file with .gz file extension - can read a BGZF gzipped .vcf file with .bgz file extension - can read a vcf file with a projection - can read an uncompressed BCFv2.2 file !!! IGNORED !!! - can read a BGZF compressed BCFv2.2 file !!! IGNORED !!! - loadIndexedVcf with 1 ReferenceRegion - loadIndexedVcf with multiple ReferenceRegions - load block compressed interleaved fastq - import records from interleaved FASTQ: 1 - import records from interleaved FASTQ: 2 - import records from interleaved FASTQ: 3 - import records from interleaved FASTQ: 4 - import block compressed single fastq - import records from single ended FASTQ: 1 - import records from single ended FASTQ: 2 - import records from single ended FASTQ: 3 - import records from single ended FASTQ: 4 - filter on load using the filter2 API - saveAsParquet with file path - saveAsParquet with file path, block size, page size - saveAsParquet with save args - read a HLA fasta from GRCh38 - read a gzipped fasta file - read a fasta file with comments, gaps, and translation stops - loadIndexedBam with 1 ReferenceRegion - loadIndexedBam with multiple ReferenceRegions - loadIndexedBam with multiple ReferenceRegions and indexed bams - loadIndexedBam with multiple ReferenceRegions and a directory of indexed bams - loadIndexedBam should throw exception without an index file - loadIndexedBam should work with indexed file with index naming format .bai - loadIndexedBam glob should throw exception without an index file - loadBam with a glob - loadBam with a directory - load vcf with a glob - load vcf from a directory - load gvcf which contains a multi-allelic row from a directory - load and save gvcf which contains rows without likelihoods - parse annotations for multi-allelic rows - load parquet with globs - bad glob should fail - empty directory should fail - can read a SnpEff-annotated .vcf file - loadAlignments should not fail on single-end and paired-end fastq reads - load queryname sorted sam as fragments - load query grouped sam as fragments - load paired fastq - load paired fastq without cache - load paired fastq as fragments - load paired fastq as fragments without cache - load HTSJDK sequence dictionary - load Bedtools .genome file as sequence dictionary - load Bedtools .genome.txt file as sequence dictionary - load UCSC Genome Browser chromInfo.txt file as sequence dictionary - load unrecognized file extension as sequence dictionary fails - load BED features with Bedtools .genome file as sequence dictionary - load BED features with Bedtools .genome file as sequence dictionary, no matching features - convert program record - load program record from sam file - load alignments from data frame - load features from data frame - load fragments from data frame - load genotypes from data frame with default header lines - load genotypes from data frame with empty header lines - load reads from data frame - load sequences from data frame - load slices from data frame - load variant contexts from data frame with default header lines - load variant contexts from data frame with empty header lines - load variants from data frame with default header lines - load variants from data frame with empty header lines - load alignments with metadata from data frame - load features with metadata from data frame - load fragments with metadata from data frame - load genotypes with metadata from data frame - load variant contexts with metadata from data frame - load variants with metadata from data frame - read a fasta file with short sequences as sequences - read a fasta file with long sequences as sequences - read a fasta file with short sequences as slices - read a fasta file with long sequences as slices CycleCovariateSuite: - compute covariates for an unpaired read on the negative strand - compute covariates for a first-of-pair read on the negative strand - compute covariates for a second-of-pair read on the negative strand - compute covariates for an unpaired read on the positive strand - compute covariates for a first-of-pair read on the positive strand - compute covariates for a second-of-pair read on the positive strand AlignmentConverterSuite: - 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 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 2020-12-02 19:31:33 WARN BlockManager:69 - Putting block rdd_5_3 failed due to exception java.lang.Exception: Contig chr2 not found in reference map with keys: chr1. 2020-12-02 19:31:33 WARN BlockManager:69 - Block rdd_5_3 could not be removed as it was not found on disk or in memory 2020-12-02 19:31:33 ERROR Executor:94 - Exception in task 3.0 in stage 2.0 (TID 11) java.lang.Exception: Contig chr2 not found in reference map with keys: chr1 at org.bdgenomics.adam.util.ReferenceContigMap.$anonfun$extract$1(ReferenceContigMap.scala:64) at scala.collection.immutable.Map$Map1.getOrElse(Map.scala:119) at org.bdgenomics.adam.util.ReferenceContigMap.extract(ReferenceContigMap.scala:63) at org.bdgenomics.adam.rdd.read.MDTagging.$anonfun$addMDTagsBroadcast$3(MDTagging.scala:76) at scala.Option$WithFilter.map(Option.scala:163) at org.bdgenomics.adam.rdd.read.MDTagging.$anonfun$addMDTagsBroadcast$1(MDTagging.scala:71) at scala.collection.Iterator$$anon$10.next(Iterator.scala:459) at org.apache.spark.storage.memory.MemoryStore.putIterator(MemoryStore.scala:222) at org.apache.spark.storage.memory.MemoryStore.putIteratorAsValues(MemoryStore.scala:299) at org.apache.spark.storage.BlockManager.$anonfun$doPutIterator$1(BlockManager.scala:1371) at org.apache.spark.storage.BlockManager.org$apache$spark$storage$BlockManager$$doPut(BlockManager.scala:1298) at org.apache.spark.storage.BlockManager.doPutIterator(BlockManager.scala:1362) at org.apache.spark.storage.BlockManager.getOrElseUpdate(BlockManager.scala:1186) at org.apache.spark.rdd.RDD.getOrCompute(RDD.scala:360) at org.apache.spark.rdd.RDD.iterator(RDD.scala:311) at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:90) at org.apache.spark.scheduler.Task.run(Task.scala:127) at org.apache.spark.executor.Executor$TaskRunner.$anonfun$run$3(Executor.scala:446) at org.apache.spark.util.Utils$.tryWithSafeFinally(Utils.scala:1377) at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:449) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624) at java.lang.Thread.run(Thread.java:748) 2020-12-02 19:31:33 WARN TaskSetManager:69 - Lost task 3.0 in stage 2.0 (TID 11, 192.168.122.1, executor driver): java.lang.Exception: Contig chr2 not found in reference map with keys: chr1 at org.bdgenomics.adam.util.ReferenceContigMap.$anonfun$extract$1(ReferenceContigMap.scala:64) at scala.collection.immutable.Map$Map1.getOrElse(Map.scala:119) at org.bdgenomics.adam.util.ReferenceContigMap.extract(ReferenceContigMap.scala:63) at org.bdgenomics.adam.rdd.read.MDTagging.$anonfun$addMDTagsBroadcast$3(MDTagging.scala:76) at scala.Option$WithFilter.map(Option.scala:163) at org.bdgenomics.adam.rdd.read.MDTagging.$anonfun$addMDTagsBroadcast$1(MDTagging.scala:71) at scala.collection.Iterator$$anon$10.next(Iterator.scala:459) at org.apache.spark.storage.memory.MemoryStore.putIterator(MemoryStore.scala:222) at org.apache.spark.storage.memory.MemoryStore.putIteratorAsValues(MemoryStore.scala:299) at org.apache.spark.storage.BlockManager.$anonfun$doPutIterator$1(BlockManager.scala:1371) at org.apache.spark.storage.BlockManager.org$apache$spark$storage$BlockManager$$doPut(BlockManager.scala:1298) at org.apache.spark.storage.BlockManager.doPutIterator(BlockManager.scala:1362) at org.apache.spark.storage.BlockManager.getOrElseUpdate(BlockManager.scala:1186) at org.apache.spark.rdd.RDD.getOrCompute(RDD.scala:360) at org.apache.spark.rdd.RDD.iterator(RDD.scala:311) at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:90) at org.apache.spark.scheduler.Task.run(Task.scala:127) at org.apache.spark.executor.Executor$TaskRunner.$anonfun$run$3(Executor.scala:446) at org.apache.spark.util.Utils$.tryWithSafeFinally(Utils.scala:1377) at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:449) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624) at java.lang.Thread.run(Thread.java:748) 2020-12-02 19:31:33 ERROR TaskSetManager:73 - Task 3 in stage 2.0 failed 1 times; aborting job - try realigning a read on a missing contig, stringency == STRICT 2020-12-02 19:31:35 WARN MDTagging:190 - Caught exception when processing read chr2: java.lang.Exception: Contig chr2 not found in reference map with keys: chr1 - try realigning a read on a missing contig, stringency == LENIENT FileExtensionsSuite: - ends in gzip extension - is a vcf extension PhredUtilsSuite: - convert low phred score to log and back - convert high phred score to log and back - convert overflowing phred score to log and back and clip - convert negative zero log probability to phred and clip - round trip log probabilities ReadDatasetSuite: - create a new read genomic dataset - create a new read genomic dataset with sequence dictionary - save as parquet - round trip as parquet - save as fastq - save as single file fastq - filter read genomic dataset by reference region - broadcast region join reads and features - shuffle region join reads and features - convert reads to alignments - convert reads to sequences - convert reads to slices AlignmentDatasetSuite: - sorting reads - unmapped reads go at the end when sorting - coverage does not fail on unmapped reads - 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 2020-12-02 19:33:05 WARN RDDBoundAlignmentDataset: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 2020-12-02 19:33:07 WARN RDDBoundAlignmentDataset: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 2020-12-02 19:33:09 WARN RDDBoundAlignmentDataset: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 2020-12-02 19:33:23 WARN OutFormatterRunner:190 - Piped command List(sleep, 10) timed out after 5 seconds. 2020-12-02 19:33:23 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 2020-12-02 19:33:46 WARN OutFormatterRunner:190 - Piped command List(python, /tmp/adamTestMvncIb5npe/spark-cae6a06e-1cf8-4877-8ccb-88040b954995/userFiles-7c49da95-8e36-4bc4-b1c6-0bd539041afb/timeout.py) timed out after 5 seconds. 2020-12-02 19:33:46 WARN OutFormatterRunner:190 - Piped command List(python, /tmp/adamTestMvncIb5npe/spark-cae6a06e-1cf8-4877-8ccb-88040b954995/userFiles-7c49da95-8e36-4bc4-b1c6-0bd539041afb/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 pipe !!! IGNORED !!! - use broadcast join to pull down reads mapped to targets - use broadcast join against to pull down reads mapped to targets - use right outer broadcast join to pull down reads mapped to targets - use right outer broadcast join against to pull down reads mapped to targets - use shuffle join with feature spanning partitions - use shuffle join to pull down reads mapped to targets - use shuffle join with flankSize to pull down reads mapped close to targets - use right outer shuffle join to pull down reads mapped to targets - use left outer shuffle join to pull down reads mapped to targets - use full outer shuffle join to pull down reads mapped to targets - use shuffle join with group by to pull down reads mapped to targets - use right outer shuffle join with group by to pull down reads mapped to targets - cannot provide empty quality score bins - cannot provide bins with a gap - cannot provide overlapping bins - binning quality scores in reads succeeds even if reads have no quality scores - bin quality scores in reads - union two read files together - test k-mer counter - test dataset based k-mer counter - transform reads to slice genomic dataset - transform reads to coverage genomic dataset - transform reads to feature genomic dataset - transform reads to fragment genomic dataset - transform reads to genotype genomic dataset loading /tmp/adamTestMvncIb5npe/TempSuite4058564826757187275.adam as parquet into RDD... loading /tmp/adamTestMvncIb5npe/TempSuite865467443419020903.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 2020-12-02 19:35:03 WARN DAGScheduler:69 - Broadcasting large task binary with size 1134.2 KiB - running base recalibration with downsampling doesn't drop reads - filter RDD bound alignments by MAPQ - filter dataset bound alignments by MAPQ - filter RDD bound unaligned alignments - filter dataset bound unaligned alignments - filter RDD bound unpaired alignments - filter dataset bound unpaired alignments - filter RDD bound duplicate alignments - filter dataset bound duplicate alignments - filter RDD bound alignments to primary alignments - filter dataset bound alignments to primary alignments - filter RDD bound alignments to read group - filter dataset bound alignments to read group - filter RDD bound alignments to read groups - filter dataset bound alignments to read groups - filter RDD bound alignments to sample - filter dataset bound alignments to sample - filter RDD bound alignments to samples - filter dataset bound alignments to samples - sort by read name - transform dataset via java API - convert alignments to reads SmithWatermanSuite: - gather max position from simple scoring matrix - gather max position from irregular scoring matrix - gather max position from irregular scoring matrix with deletions - score simple alignment with constant gap - score irregular scoring matrix - score irregular scoring matrix with indel - can unroll cigars correctly - execute simple trackback - execute trackback with indel - run end to end smith waterman for simple reads - run end to end smith waterman for short sequences with indel - run end to end smith waterman for longer sequences with snp - run end to end smith waterman for longer sequences with short indel - run end to end smith waterman for shorter sequence in longer sequence - run end to end smith waterman for shorter sequence in longer sequence, with indel - smithWaterman - simple alignment MdTagSuite: - null md tag - zero length md tag - md tag with non-digit initial value - md tag invalid base - md tag, pure insertion - md tag, pure insertion, test 2 - md tag pure insertion equality - md tag equality and hashcode - valid md tags - get start of read with no mismatches or deletions - get start of read with no mismatches, but with a deletion at the start - get start of read with mismatches at the start - get end of read with no mismatches or deletions - check that mdtag and rich record return same end - get end of read with no mismatches, but a deletion at end - CIGAR with N operator - CIGAR with multiple N operators - CIGAR with P operators - Get correct matches for mdtag with insertion - Get correct matches for mdtag with mismatches and insertion - Get correct matches for mdtag with insertion between mismatches - Get correct matches for mdtag with intron between mismatches - Get correct matches for mdtag with intron and deletion between mismatches - Throw exception when number of deleted bases in mdtag disagrees with CIGAR - Get correct matches for mdtag with mismatch, insertion and deletion - Get correct matches for mdtag with mismatches, insertion and deletion - Get correct matches for MDTag with mismatches and deletions - Get correct matches base from MDTag and CIGAR with N - get end of read with mismatches and a deletion at end - get correct string out of mdtag with no mismatches - get correct string out of mdtag with mismatches at start - get correct string out of mdtag with deletion at end - get correct string out of mdtag with mismatches at end - get correct string out of complex mdtag - check complex mdtag - get gapped reference - move a cigar alignment by two for a read - rewrite alignment to all matches - rewrite alignment to two mismatches followed by all matches - rewrite alignment to include a deletion but otherwise all matches - rewrite alignment to include an insertion at the start of the read but otherwise all matches - create new md tag from read vs. reference, perfect match - create new md tag from read vs. reference, perfect alignment match, 1 mismatch - create new md tag from read vs. reference, alignment with deletion - create new md tag from read vs. reference, alignment with insert - handle '=' and 'X' operators - CIGAR/MD tag mismatch should cause errors GenomicDatasetSuite: - processing a command that is the spark root directory should return an absolute path - processing a command that is just a single word should do nothing - processing a command should handle arguments that include spaces - processing a command that is a single substitution should succeed - processing a command that is multiple words should split the string - process a command that is multiple words with a replacement - process a command that is multiple words with multiple replacements ParallelFileMergerSuite: - cannot write both empty gzip block and cram eof - buffer size must be non-negative - get the size of several files - block size must be positive and non-zero when trying to merge files - must provide files to merge - if two files are both below the block size, they should merge into one shard - merge two files where one is greater than the block size - merge a sharded sam file - merge a sharded bam file - merge a sharded cram file - can't turn a negative index into a path - generate a path from an index IndelTableSuite: - check for indels in a region with known indels - check for indels in a contig that doesn't exist - check for indels in a region without known indels - build indel table from rdd of variants SnpTableSuite: - create an empty snp table - create a snp table from variants on multiple contigs - create a snp table from a larger set of variants - perform lookups on multi-contig snp table - perform lookups on larger snp table RealignIndelsSuite: - map reads to targets - checking mapping to targets for artificial reads - checking alternative consensus for artificial reads - checking extraction of reference from reads - checking realigned reads for artificial input - checking realigned reads for artificial input with reference file - checking realigned reads for artificial input using knowns - checking realigned reads for artificial input using knowns and reads - skip realigning reads if target is highly covered - skip realignment if target is an insufficient LOD improvement - realign reads to an insertion - test mismatch quality scoring - test mismatch quality scoring for no mismatches - test mismatch quality scoring for offset - test mismatch quality scoring with early exit - test mismatch quality scoring after unpacking read - we shouldn't try to realign a region with no target - we shouldn't try to realign reads with no indel evidence - test OP and OC tags - realign a read with an insertion that goes off the end of the read - if realigning a target doesn't improve the LOD, don't drop reads - extract seq/qual from a read with no clipped bases - extract seq/qual from a read with clipped bases at start - extract seq/qual from a read with clipped bases at end - if unclip is selected, don't drop base when extracting from a read with clipped bases - get cigar and coordinates for read that spans indel, no clipped bases - get cigar and coordinates for read that spans deletion, clipped bases at start - get cigar and coordinates for read that falls wholly before insertion - get cigar and coordinates for read that falls wholly after insertion - get cigar and coordinates for read that falls wholly after deletion - get cigar and coordinates for read that partially spans insertion, no clipped bases - get cigar and coordinates for read that partially spans insertion, clipped bases at end - get cigar and coordinates for read that partially spans insertion, clipped bases both ends BaseQualityRecalibrationSuite: 2020-12-02 19:35:56 WARN DAGScheduler:69 - Broadcasting large task binary with size 1134.2 KiB - BQSR Test Input #1 w/ VCF Sites without caching 2020-12-02 19:36:03 WARN DAGScheduler:69 - Broadcasting large task binary with size 1134.2 KiB - BQSR Test Input #1 w/ VCF Sites with caching 2020-12-02 19:36:12 WARN DAGScheduler:69 - Broadcasting large task binary with size 1134.2 KiB - 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 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 2020-12-02 19:36:55 WARN DatasetBoundSliceDataset:190 - Saving directly as Parquet from SQL. Options other than compression codec are ignored. - transform variants to slice genomic dataset - transform variants to coverage genomic dataset - transform variants to feature genomic dataset - transform variants to fragment genomic dataset - transform variants to read genomic dataset - transform variants to genotype genomic dataset - transform variants to variant context genomic dataset - filter RDD bound variants to filters passed - filter dataset bound variants to filters passed - filter RDD bound variants by quality - filter dataset bound variants by quality - filter RDD bound variants by read depth - filter dataset bound variants by read depth - filter RDD bound variants by reference read depth - filter dataset bound variants by reference read depth - filter RDD bound single nucleotide variants - filter dataset bound single nucleotide variants - filter RDD bound multiple nucleotide variants - filter dataset bound multiple nucleotide variants - filter RDD bound indel variants - filter dataset bound indel variants - filter RDD bound variants to single nucleotide variants - filter dataset bound variants to single nucleotide variants - filter RDD bound variants to multiple nucleotide variants - filter dataset bound variants to multiple nucleotide variants - filter RDD bound variants to indel variants - filter dataset bound variants to indel variants - transform dataset via java API Run completed in 9 minutes, 18 seconds. Total number of tests run: 1177 Suites: completed 68, aborted 0 Tests: succeeded 1177, 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-spark3_2.12 <<< [INFO] [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:report (default-cli) @ adam-core-spark3_2.12 --- [INFO] Skipping SCoverage report generation [INFO] [INFO] -------------< org.bdgenomics.adam:adam-apis-spark3_2.12 >-------------- [INFO] Building ADAM_2.12: APIs for Java, Python 0.33.0-SNAPSHOT [5/7] [INFO] --------------------------------[ jar ]--------------------------------- Downloading from central: https://repo.maven.apache.org/maven2/commons-logging/commons-logging/1.1.3/commons-logging-1.1.3.jar Downloading from central: https://repo.maven.apache.org/maven2/org/apache/commons/commons-compress/1.4.1/commons-compress-1.4.1.jar Downloaded from central: https://repo.maven.apache.org/maven2/commons-logging/commons-logging/1.1.3/commons-logging-1.1.3.jar (0 B at 0 B/s) Progress (1): 2.7/241 kB Progress (1): 5.5/241 kB Progress (1): 8.2/241 kB Progress (1): 11/241 kB Progress (1): 14/241 kB Progress (1): 16/241 kB Progress (1): 19/241 kB Progress (1): 22/241 kB Progress (1): 25/241 kB Progress (1): 27/241 kB Progress (1): 30/241 kB Progress (1): 33/241 kB Progress (1): 36/241 kB Progress (1): 38/241 kB Progress (1): 41/241 kB Progress (1): 44/241 kB Progress (1): 47/241 kB Progress (1): 49/241 kB Progress (1): 52/241 kB Progress (1): 55/241 kB Progress (1): 58/241 kB Progress (1): 60/241 kB Progress (1): 63/241 kB Progress (1): 66/241 kB Progress (1): 69/241 kB Progress (1): 71/241 kB Progress (1): 74/241 kB Progress (1): 77/241 kB Progress (1): 80/241 kB Progress (1): 82/241 kB Progress (1): 85/241 kB Progress (1): 88/241 kB Progress (1): 90/241 kB Progress (1): 93/241 kB Progress (1): 96/241 kB Progress (1): 99/241 kB Progress (1): 101/241 kB Progress (1): 104/241 kB Progress (1): 107/241 kB Progress (1): 110/241 kB Progress (1): 112/241 kB Progress (1): 115/241 kB Progress (1): 118/241 kB Progress (1): 121/241 kB Progress (1): 123/241 kB Progress (1): 126/241 kB Progress (1): 129/241 kB Progress (1): 132/241 kB Progress (1): 134/241 kB Progress (1): 137/241 kB Progress (1): 140/241 kB Progress (1): 143/241 kB Progress (1): 145/241 kB Progress (1): 148/241 kB Progress (1): 151/241 kB Progress (1): 154/241 kB Progress (1): 156/241 kB Progress (1): 159/241 kB Progress (1): 162/241 kB Progress (1): 165/241 kB Progress (1): 167/241 kB Progress (1): 170/241 kB Progress (1): 173/241 kB Progress (1): 175/241 kB Progress (1): 178/241 kB Progress (1): 181/241 kB Progress (1): 184/241 kB Progress (1): 186/241 kB Progress (1): 189/241 kB Progress (1): 192/241 kB Progress (1): 195/241 kB Progress (1): 197/241 kB Progress (1): 200/241 kB Progress (1): 203/241 kB Progress (1): 206/241 kB Progress (1): 208/241 kB Progress (1): 211/241 kB Progress (1): 214/241 kB Progress (1): 217/241 kB Progress (1): 219/241 kB Progress (1): 222/241 kB Progress (1): 225/241 kB Progress (1): 228/241 kB Progress (1): 230/241 kB Progress (1): 233/241 kB Progress (1): 236/241 kB Progress (1): 239/241 kB Progress (1): 241/241 kB Progress (1): 241 kB Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/commons/commons-compress/1.4.1/commons-compress-1.4.1.jar (241 kB at 3.3 MB/s) [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-apis-spark3_2.12 --- [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-apis-spark3_2.12 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ adam-apis-spark3_2.12 --- [INFO] Source directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/adam-apis/src/main/scala added. [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ adam-apis-spark3_2.12 --- [INFO] Modified 0 of 5 .scala files [INFO] [INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ adam-apis-spark3_2.12 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/adam-apis/src/main/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ adam-apis-spark3_2.12 --- [INFO] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/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/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/adam-apis/target/2.12.8/classes at 1606966651638 [WARNING] warning: there was one deprecation warning (since 2.12.0); re-run with -deprecation for details [WARNING] warning: there were two feature warnings; re-run with -feature for details [WARNING] two warnings found [INFO] prepare-compile in 0 s [INFO] compile in 6 s [INFO] [INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ adam-apis-spark3_2.12 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ adam-apis-spark3_2.12 --- [INFO] Test Source directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/adam-apis/src/test/scala added. [INFO] [INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ adam-apis-spark3_2.12 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 2 resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ adam-apis-spark3_2.12 --- [INFO] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/adam-apis/src/test/java:-1: info: compiling [INFO] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/adam-apis/src/test/scala:-1: info: compiling [INFO] Compiling 9 source files to /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/adam-apis/target/2.12.8/test-classes at 1606966658486 [INFO] prepare-compile in 0 s [INFO] compile in 4 s [INFO] [INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ adam-apis-spark3_2.12 --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 8 source files to /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/adam-apis/target/2.12.8/test-classes [INFO] [INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ adam-apis-spark3_2.12 --- [INFO] Tests are skipped. [INFO] [INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ adam-apis-spark3_2.12 --- Discovery starting. Discovery completed in 202 milliseconds. Run starting. Expected test count is: 10 JavaADAMContextSuite: 2020-12-02 19:37:44 WARN Utils:69 - Your hostname, research-jenkins-worker-01 resolves to a loopback address: 127.0.1.1; using 192.168.122.1 instead (on interface virbr0) 2020-12-02 19:37:44 WARN Utils:69 - Set SPARK_LOCAL_IP if you need to bind to another address 2020-12-02 19:37:44 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 .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 2020-12-02 19:37:54 WARN RDDBoundSequenceDataset:190 - asSingleFile = true ignored when saving as Parquet. - can read and write .fa as sequences 2020-12-02 19:37:54 WARN RDDBoundSliceDataset:190 - asSingleFile = true ignored when saving as Parquet. - can read and write .fa as slices Run completed in 11 seconds, 141 milliseconds. Total number of tests run: 10 Suites: completed 2, aborted 0 Tests: succeeded 10, failed 0, canceled 0, ignored 0, pending 0 All tests passed. [INFO] [INFO] >>> scoverage-maven-plugin:1.1.1:report (default-cli) > [scoverage]test @ adam-apis-spark3_2.12 >>> [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-apis-spark3_2.12 --- [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-apis-spark3_2.12 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ adam-apis-spark3_2.12 --- [INFO] Source directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/adam-apis/src/main/scala added. [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ adam-apis-spark3_2.12 --- [INFO] Modified 0 of 5 .scala files [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:pre-compile (default-cli) @ adam-apis-spark3_2.12 --- [WARNING] Skipping SCoverage execution - unsupported Scala version "2.12.8" [INFO] [INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ adam-apis-spark3_2.12 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/adam-apis/src/main/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ adam-apis-spark3_2.12 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ adam-apis-spark3_2.12 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:post-compile (default-cli) @ adam-apis-spark3_2.12 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ adam-apis-spark3_2.12 --- [INFO] Test Source directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/adam-apis/src/test/scala added. [INFO] [INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ adam-apis-spark3_2.12 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 2 resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ adam-apis-spark3_2.12 --- [INFO] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/adam-apis/src/test/java:-1: info: compiling [INFO] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/adam-apis/src/test/scala:-1: info: compiling [INFO] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/adam-apis/target/generated-test-sources/test-annotations:-1: info: compiling [INFO] Compiling 9 source files to /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/adam-apis/target/2.12.8/test-classes at 1606966676645 [INFO] prepare-compile in 0 s [INFO] compile in 4 s [INFO] [INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ adam-apis-spark3_2.12 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ adam-apis-spark3_2.12 --- [INFO] Tests are skipped. [INFO] [INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ adam-apis-spark3_2.12 --- Discovery starting. Discovery completed in 219 milliseconds. Run starting. Expected test count is: 10 JavaADAMContextSuite: 2020-12-02 19:38:02 WARN Utils:69 - Your hostname, research-jenkins-worker-01 resolves to a loopback address: 127.0.1.1; using 192.168.122.1 instead (on interface virbr0) 2020-12-02 19:38:02 WARN Utils:69 - Set SPARK_LOCAL_IP if you need to bind to another address 2020-12-02 19:38:02 WARN NativeCodeLoader:62 - Unable to load native-hadoop library for your platform... using builtin-java classes where applicable - can read and write a small .SAM file - loadIndexedBam with multiple ReferenceRegions - can read and write a small .SAM file as fragments - can read and write a small .bed file as features - can read and write a small .bed file as coverage - can read and write a small .vcf as genotypes - can read and write a small .vcf as variants - can read a two bit file 2020-12-02 19:38:11 WARN RDDBoundSequenceDataset:190 - asSingleFile = true ignored when saving as Parquet. - can read and write .fa as sequences 2020-12-02 19:38:12 WARN RDDBoundSliceDataset:190 - asSingleFile = true ignored when saving as Parquet. - can read and write .fa as slices Run completed in 10 seconds, 832 milliseconds. Total number of tests run: 10 Suites: completed 2, aborted 0 Tests: succeeded 10, failed 0, canceled 0, ignored 0, pending 0 All tests passed. [INFO] [INFO] <<< scoverage-maven-plugin:1.1.1:report (default-cli) < [scoverage]test @ adam-apis-spark3_2.12 <<< [INFO] [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:report (default-cli) @ adam-apis-spark3_2.12 --- [INFO] Skipping SCoverage report generation [INFO] [INFO] --------------< org.bdgenomics.adam:adam-cli-spark3_2.12 >-------------- [INFO] Building ADAM_2.12: CLI 0.33.0-SNAPSHOT [6/7] [INFO] --------------------------------[ jar ]--------------------------------- Downloading from central: https://repo.maven.apache.org/maven2/net/codingwell/scala-guice_2.12/4.2.1/scala-guice_2.12-4.2.1.pom Progress (1): 3.0 kB Downloaded from central: https://repo.maven.apache.org/maven2/net/codingwell/scala-guice_2.12/4.2.1/scala-guice_2.12-4.2.1.pom (3.0 kB at 248 kB/s) Downloading from central: https://repo.maven.apache.org/maven2/com/google/inject/guice/4.2.0/guice-4.2.0.pom Progress (1): 4.1/11 kB Progress (1): 8.2/11 kB Progress (1): 11 kB Downloaded from central: 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(2): 74/557 kB | 5.5/52 kB Progress (3): 74/557 kB | 5.5/52 kB | 2.7/197 kB Progress (3): 78/557 kB | 5.5/52 kB | 2.7/197 kB Progress (3): 78/557 kB | 8.2/52 kB | 2.7/197 kB Progress (3): 82/557 kB | 8.2/52 kB | 2.7/197 kB Progress (3): 82/557 kB | 8.2/52 kB | 5.5/197 kB Progress (4): 82/557 kB | 8.2/52 kB | 5.5/197 kB | 4.1/42 kB Progress (4): 86/557 kB | 8.2/52 kB | 5.5/197 kB | 4.1/42 kB Progress (4): 86/557 kB | 8.2/52 kB | 8.2/197 kB | 4.1/42 kB Progress (4): 86/557 kB | 11/52 kB | 8.2/197 kB | 4.1/42 kB Progress (4): 86/557 kB | 11/52 kB | 11/197 kB | 4.1/42 kB Progress (4): 90/557 kB | 11/52 kB | 11/197 kB | 4.1/42 kB Progress (4): 90/557 kB | 11/52 kB | 11/197 kB | 8.2/42 kB Progress (4): 94/557 kB | 11/52 kB | 11/197 kB | 8.2/42 kB Progress (4): 94/557 kB | 11/52 kB | 11/197 kB | 12/42 kB Progress (4): 94/557 kB | 11/52 kB | 14/197 kB | 12/42 kB Progress (4): 94/557 kB | 14/52 kB | 14/197 kB | 12/42 kB Progress (4): 94/557 kB | 14/52 kB | 16/197 kB | 12/42 kB Progress (4): 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36/197 kB | 25/42 kB | 8.2/291 kB Progress (5): 115/557 kB | 44/52 kB | 36/197 kB | 25/42 kB | 11/291 kB Progress (5): 115/557 kB | 47/52 kB | 36/197 kB | 25/42 kB | 11/291 kB Progress (5): 119/557 kB | 47/52 kB | 36/197 kB | 25/42 kB | 11/291 kB Progress (5): 119/557 kB | 49/52 kB | 36/197 kB | 25/42 kB | 11/291 kB Progress (5): 119/557 kB | 49/52 kB | 36/197 kB | 29/42 kB | 11/291 kB Progress (5): 119/557 kB | 52/52 kB | 36/197 kB | 29/42 kB | 11/291 kB Progress (5): 123/557 kB | 52/52 kB | 36/197 kB | 29/42 kB | 11/291 kB Progress (5): 123/557 kB | 52/52 kB | 36/197 kB | 29/42 kB | 14/291 kB Progress (5): 123/557 kB | 52/52 kB | 38/197 kB | 29/42 kB | 14/291 kB Progress (5): 123/557 kB | 52/52 kB | 38/197 kB | 29/42 kB | 16/291 kB Progress (5): 127/557 kB | 52/52 kB | 38/197 kB | 29/42 kB | 16/291 kB Progress (5): 127/557 kB | 52 kB | 38/197 kB | 29/42 kB | 16/291 kB Progress (5): 127/557 kB | 52 kB | 38/197 kB | 33/42 kB | 16/291 kB Progress (5): 131/557 kB | 52 kB | 38/197 kB | 33/42 kB | 16/291 kB Progress (5): 131/557 kB | 52 kB | 38/197 kB | 33/42 kB | 19/291 kB Progress (5): 131/557 kB | 52 kB | 41/197 kB | 33/42 kB | 19/291 kB Progress (5): 131/557 kB | 52 kB | 41/197 kB | 33/42 kB | 22/291 kB Progress (5): 131/557 kB | 52 kB | 41/197 kB | 37/42 kB | 22/291 kB Progress (5): 131/557 kB | 52 kB | 41/197 kB | 37/42 kB | 25/291 kB Progress (5): 131/557 kB | 52 kB | 44/197 kB | 37/42 kB | 25/291 kB Progress (5): 131/557 kB | 52 kB | 44/197 kB | 37/42 kB | 27/291 kB Progress (5): 135/557 kB | 52 kB | 44/197 kB | 37/42 kB | 27/291 kB Progress (5): 135/557 kB | 52 kB | 44/197 kB | 37/42 kB | 30/291 kB Progress (5): 135/557 kB | 52 kB | 47/197 kB | 37/42 kB | 30/291 kB Progress (5): 135/557 kB | 52 kB | 47/197 kB | 41/42 kB | 30/291 kB Progress (5): 135/557 kB | 52 kB | 47/197 kB | 41/42 kB | 33/291 kB Progress (5): 139/557 kB | 52 kB | 47/197 kB | 41/42 kB | 33/291 kB Progress (5): 139/557 kB | 52 kB | 47/197 kB | 41/42 kB | 36/291 kB Progress (5): 139/557 kB | 52 kB | 47/197 kB | 42 kB | 36/291 kB Progress (5): 139/557 kB | 52 kB | 49/197 kB | 42 kB | 36/291 kB Progress (5): 139/557 kB | 52 kB | 49/197 kB | 42 kB | 38/291 kB Progress (5): 143/557 kB | 52 kB | 49/197 kB | 42 kB | 38/291 kB Progress (5): 143/557 kB | 52 kB | 52/197 kB | 42 kB | 38/291 kB Progress (5): 147/557 kB | 52 kB | 52/197 kB | 42 kB | 38/291 kB Progress (5): 147/557 kB | 52 kB | 52/197 kB | 42 kB | 41/291 kB Progress (5): 147/557 kB | 52 kB | 55/197 kB | 42 kB | 41/291 kB Progress (5): 152/557 kB | 52 kB | 55/197 kB | 42 kB | 41/291 kB Progress (5): 152/557 kB | 52 kB | 58/197 kB | 42 kB | 41/291 kB Progress (5): 152/557 kB | 52 kB | 58/197 kB | 42 kB | 44/291 kB Progress (5): 156/557 kB | 52 kB | 58/197 kB | 42 kB | 44/291 kB Progress (5): 156/557 kB | 52 kB | 60/197 kB | 42 kB | 44/291 kB Progress (5): 160/557 kB | 52 kB | 60/197 kB | 42 kB | 44/291 kB Progress (5): 160/557 kB | 52 kB | 60/197 kB | 42 kB | 47/291 kB Progress (5): 164/557 kB | 52 kB | 60/197 kB | 42 kB | 47/291 kB Progress (5): 164/557 kB | 52 kB | 60/197 kB | 42 kB | 49/291 kB Progress (5): 164/557 kB | 52 kB | 63/197 kB | 42 kB | 49/291 kB Progress (5): 164/557 kB | 52 kB | 63/197 kB | 42 kB | 52/291 kB Progress (5): 168/557 kB | 52 kB | 63/197 kB | 42 kB | 52/291 kB Progress (5): 168/557 kB | 52 kB | 63/197 kB | 42 kB | 55/291 kB Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/maven/maven-artifact/3.1.1/maven-artifact-3.1.1.jar (52 kB at 1.3 MB/s) Progress (4): 168/557 kB | 63/197 kB | 42 kB | 58/291 kB Progress (4): 172/557 kB | 63/197 kB | 42 kB | 58/291 kB Progress (4): 172/557 kB | 66/197 kB | 42 kB | 58/291 kB Progress (4): 176/557 kB | 66/197 kB | 42 kB | 58/291 kB Progress (4): 176/557 kB | 66/197 kB | 42 kB | 60/291 kB Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/maven-settings-builder/3.1.1/maven-settings-builder-3.1.1.jar Progress (4): 176/557 kB | 66/197 kB | 42 kB | 63/291 kB Progress (4): 180/557 kB | 66/197 kB | 42 kB | 63/291 kB Progress (4): 180/557 kB | 69/197 kB | 42 kB | 63/291 kB Progress (4): 180/557 kB | 69/197 kB | 42 kB | 66/291 kB Progress (4): 184/557 kB | 69/197 kB | 42 kB | 66/291 kB Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/maven/maven-settings/3.1.1/maven-settings-3.1.1.jar (42 kB at 1.0 MB/s) Progress (3): 188/557 kB | 69/197 kB | 66/291 kB Progress (3): 188/557 kB | 69/197 kB | 69/291 kB Progress (3): 188/557 kB | 71/197 kB | 69/291 kB Progress (3): 193/557 kB | 71/197 kB | 69/291 kB Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/maven-repository-metadata/3.1.1/maven-repository-metadata-3.1.1.jar Progress (3): 193/557 kB | 74/197 kB | 69/291 kB Progress (3): 197/557 kB | 74/197 kB | 69/291 kB Progress (3): 197/557 kB | 74/197 kB | 71/291 kB Progress (3): 197/557 kB | 77/197 kB | 71/291 kB Progress (3): 197/557 kB | 77/197 kB | 74/291 kB Progress (3): 201/557 kB | 77/197 kB | 74/291 kB Progress (3): 201/557 kB | 80/197 kB | 74/291 kB Progress (3): 205/557 kB | 80/197 kB | 74/291 kB Progress (3): 205/557 kB | 80/197 kB | 77/291 kB Progress (3): 205/557 kB | 82/197 kB | 77/291 kB Progress (3): 209/557 kB | 82/197 kB | 77/291 kB Progress (3): 209/557 kB | 82/197 kB | 80/291 kB Progress (3): 209/557 kB | 85/197 kB | 80/291 kB Progress (3): 209/557 kB | 85/197 kB | 82/291 kB Progress (3): 213/557 kB | 85/197 kB | 82/291 kB Progress (3): 213/557 kB | 88/197 kB | 82/291 kB Progress (3): 213/557 kB | 88/197 kB | 85/291 kB Progress (4): 213/557 kB | 88/197 kB | 85/291 kB | 4.1/42 kB Progress (4): 213/557 kB | 88/197 kB | 88/291 kB | 4.1/42 kB Progress (4): 213/557 kB | 90/197 kB | 88/291 kB | 4.1/42 kB Progress (4): 213/557 kB | 90/197 kB | 90/291 kB | 4.1/42 kB Progress (4): 217/557 kB | 90/197 kB | 90/291 kB | 4.1/42 kB Progress (4): 217/557 kB | 93/197 kB | 90/291 kB | 4.1/42 kB Progress (4): 217/557 kB | 93/197 kB | 90/291 kB | 8.2/42 kB Progress (4): 221/557 kB | 93/197 kB | 90/291 kB | 8.2/42 kB Progress (4): 221/557 kB | 93/197 kB | 93/291 kB | 8.2/42 kB Progress (4): 225/557 kB | 93/197 kB | 93/291 kB | 8.2/42 kB Progress (4): 225/557 kB | 93/197 kB | 93/291 kB | 12/42 kB Progress (4): 225/557 kB | 96/197 kB | 93/291 kB | 12/42 kB Progress (4): 225/557 kB | 96/197 kB | 93/291 kB | 16/42 kB Progress (4): 229/557 kB | 96/197 kB | 93/291 kB | 16/42 kB Progress (4): 229/557 kB | 96/197 kB | 96/291 kB | 16/42 kB Progress (5): 229/557 kB | 96/197 kB | 96/291 kB | 16/42 kB | 2.7/25 kB Progress (5): 229/557 kB | 96/197 kB | 99/291 kB | 16/42 kB | 2.7/25 kB Progress (5): 233/557 kB | 96/197 kB | 99/291 kB | 16/42 kB | 2.7/25 kB Progress (5): 233/557 kB | 96/197 kB | 99/291 kB | 20/42 kB | 2.7/25 kB Progress (5): 233/557 kB | 99/197 kB | 99/291 kB | 20/42 kB | 2.7/25 kB Progress (5): 233/557 kB | 99/197 kB | 99/291 kB | 25/42 kB | 2.7/25 kB Progress (5): 238/557 kB | 99/197 kB | 99/291 kB | 25/42 kB | 2.7/25 kB Progress (5): 238/557 kB | 99/197 kB | 101/291 kB | 25/42 kB | 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| 107/291 kB | 37/42 kB | 14/25 kB Progress (5): 250/557 kB | 104/197 kB | 107/291 kB | 41/42 kB | 14/25 kB Progress (5): 254/557 kB | 104/197 kB | 107/291 kB | 41/42 kB | 14/25 kB Progress (5): 254/557 kB | 104/197 kB | 107/291 kB | 41/42 kB | 16/25 kB Progress (5): 254/557 kB | 104/197 kB | 110/291 kB | 41/42 kB | 16/25 kB Progress (5): 254/557 kB | 104/197 kB | 110/291 kB | 41/42 kB | 19/25 kB Progress (5): 254/557 kB | 104/197 kB | 112/291 kB | 41/42 kB | 19/25 kB Progress (5): 258/557 kB | 104/197 kB | 112/291 kB | 41/42 kB | 19/25 kB Progress (5): 258/557 kB | 104/197 kB | 112/291 kB | 42 kB | 19/25 kB Progress (5): 258/557 kB | 107/197 kB | 112/291 kB | 42 kB | 19/25 kB Progress (5): 262/557 kB | 107/197 kB | 112/291 kB | 42 kB | 19/25 kB Progress (5): 262/557 kB | 107/197 kB | 115/291 kB | 42 kB | 19/25 kB Progress (5): 262/557 kB | 107/197 kB | 115/291 kB | 42 kB | 22/25 kB Progress (5): 266/557 kB | 107/197 kB | 115/291 kB | 42 kB | 22/25 kB Progress (5): 266/557 kB | 110/197 kB | 115/291 kB | 42 kB | 22/25 kB Progress (5): 270/557 kB | 110/197 kB | 115/291 kB | 42 kB | 22/25 kB Progress (5): 270/557 kB | 110/197 kB | 115/291 kB | 42 kB | 25/25 kB Progress (5): 270/557 kB | 110/197 kB | 118/291 kB | 42 kB | 25/25 kB Progress (5): 270/557 kB | 110/197 kB | 118/291 kB | 42 kB | 25 kB Progress (5): 274/557 kB | 110/197 kB | 118/291 kB | 42 kB | 25 kB Progress (5): 274/557 kB | 112/197 kB | 118/291 kB | 42 kB | 25 kB Progress (5): 279/557 kB | 112/197 kB | 118/291 kB | 42 kB | 25 kB Progress (5): 279/557 kB | 112/197 kB | 121/291 kB | 42 kB | 25 kB Progress (5): 279/557 kB | 115/197 kB | 121/291 kB | 42 kB | 25 kB Progress (5): 279/557 kB | 115/197 kB | 123/291 kB | 42 kB | 25 kB Progress (5): 283/557 kB | 115/197 kB | 123/291 kB | 42 kB | 25 kB Progress (5): 283/557 kB | 118/197 kB | 123/291 kB | 42 kB | 25 kB Progress (5): 287/557 kB | 118/197 kB | 123/291 kB | 42 kB | 25 kB Progress (5): 287/557 kB | 118/197 kB | 126/291 kB | 42 kB | 25 kB Progress (5): 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(5): 311/557 kB | 132/197 kB | 140/291 kB | 42 kB | 25 kB Progress (5): 315/557 kB | 132/197 kB | 140/291 kB | 42 kB | 25 kB Progress (5): 315/557 kB | 132/197 kB | 143/291 kB | 42 kB | 25 kB Progress (5): 315/557 kB | 134/197 kB | 143/291 kB | 42 kB | 25 kB Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/maven/maven-settings-builder/3.1.1/maven-settings-builder-3.1.1.jar (42 kB at 784 kB/s) Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/maven/maven-repository-metadata/3.1.1/maven-repository-metadata-3.1.1.jar (25 kB at 475 kB/s) Progress (3): 315/557 kB | 137/197 kB | 143/291 kB Progress (3): 315/557 kB | 137/197 kB | 145/291 kB Progress (3): 319/557 kB | 137/197 kB | 145/291 kB Progress (3): 319/557 kB | 137/197 kB | 148/291 kB Progress (3): 319/557 kB | 140/197 kB | 148/291 kB Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/maven-aether-provider/3.1.1/maven-aether-provider-3.1.1.jar Downloading from 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340/557 kB | 154/197 kB | 170/291 kB Progress (3): 340/557 kB | 156/197 kB | 170/291 kB Progress (3): 340/557 kB | 156/197 kB | 173/291 kB Progress (3): 344/557 kB | 156/197 kB | 173/291 kB Progress (3): 344/557 kB | 156/197 kB | 175/291 kB Progress (3): 344/557 kB | 159/197 kB | 175/291 kB Progress (3): 344/557 kB | 159/197 kB | 178/291 kB Progress (3): 348/557 kB | 159/197 kB | 178/291 kB Progress (3): 348/557 kB | 159/197 kB | 181/291 kB Progress (3): 348/557 kB | 162/197 kB | 181/291 kB Progress (3): 348/557 kB | 162/197 kB | 184/291 kB Progress (3): 352/557 kB | 162/197 kB | 184/291 kB Progress (3): 352/557 kB | 162/197 kB | 186/291 kB Progress (3): 352/557 kB | 165/197 kB | 186/291 kB Progress (3): 352/557 kB | 165/197 kB | 189/291 kB Progress (3): 356/557 kB | 165/197 kB | 189/291 kB Progress (3): 356/557 kB | 165/197 kB | 192/291 kB Progress (3): 356/557 kB | 167/197 kB | 192/291 kB Progress (3): 356/557 kB | 167/197 kB | 195/291 kB Progress (3): 360/557 kB | 167/197 kB | 195/291 kB Progress (3): 360/557 kB | 170/197 kB | 195/291 kB Progress (4): 360/557 kB | 170/197 kB | 195/291 kB | 4.1/160 kB Progress (4): 360/557 kB | 170/197 kB | 197/291 kB | 4.1/160 kB Progress (4): 360/557 kB | 173/197 kB | 197/291 kB | 4.1/160 kB Progress (4): 365/557 kB | 173/197 kB | 197/291 kB | 4.1/160 kB Progress (5): 365/557 kB | 173/197 kB | 197/291 kB | 4.1/160 kB | 2.7/60 kB Progress (5): 369/557 kB | 173/197 kB | 197/291 kB | 4.1/160 kB | 2.7/60 kB Progress (5): 369/557 kB | 175/197 kB | 197/291 kB | 4.1/160 kB | 2.7/60 kB Progress (5): 369/557 kB | 175/197 kB | 200/291 kB | 4.1/160 kB | 2.7/60 kB Progress (5): 369/557 kB | 175/197 kB | 200/291 kB | 8.2/160 kB | 2.7/60 kB Progress (5): 369/557 kB | 175/197 kB | 203/291 kB | 8.2/160 kB | 2.7/60 kB Progress (5): 369/557 kB | 178/197 kB | 203/291 kB | 8.2/160 kB | 2.7/60 kB Progress (5): 373/557 kB | 178/197 kB | 203/291 kB | 8.2/160 kB | 2.7/60 kB Progress (5): 373/557 kB | 178/197 kB | 203/291 kB | 8.2/160 kB | 5.5/60 kB Progress (5): 377/557 kB | 178/197 kB | 203/291 kB | 8.2/160 kB | 5.5/60 kB Progress (5): 377/557 kB | 181/197 kB | 203/291 kB | 8.2/160 kB | 5.5/60 kB Progress (5): 377/557 kB | 181/197 kB | 206/291 kB | 8.2/160 kB | 5.5/60 kB Progress (5): 377/557 kB | 181/197 kB | 206/291 kB | 12/160 kB | 5.5/60 kB Progress (5): 377/557 kB | 181/197 kB | 208/291 kB | 12/160 kB | 5.5/60 kB Progress (5): 377/557 kB | 184/197 kB | 208/291 kB | 12/160 kB | 5.5/60 kB Progress (5): 381/557 kB | 184/197 kB | 208/291 kB | 12/160 kB | 5.5/60 kB Progress (5): 381/557 kB | 184/197 kB | 208/291 kB | 12/160 kB | 8.2/60 kB Progress (5): 385/557 kB | 184/197 kB | 208/291 kB | 12/160 kB | 8.2/60 kB Progress (5): 385/557 kB | 186/197 kB | 208/291 kB | 12/160 kB | 8.2/60 kB Progress (5): 385/557 kB | 186/197 kB | 211/291 kB | 12/160 kB | 8.2/60 kB Progress (5): 385/557 kB | 186/197 kB | 211/291 kB | 16/160 kB | 8.2/60 kB Progress (5): 385/557 kB | 186/197 kB | 214/291 kB | 16/160 kB | 8.2/60 kB Progress (5): 385/557 kB | 189/197 kB | 214/291 kB | 16/160 kB | 8.2/60 kB Progress (5): 389/557 kB | 189/197 kB | 214/291 kB | 16/160 kB | 8.2/60 kB Progress (5): 389/557 kB | 189/197 kB | 214/291 kB | 16/160 kB | 11/60 kB Progress (5): 393/557 kB | 189/197 kB | 214/291 kB | 16/160 kB | 11/60 kB Progress (5): 393/557 kB | 192/197 kB | 214/291 kB | 16/160 kB | 11/60 kB Progress (5): 393/557 kB | 192/197 kB | 214/291 kB | 20/160 kB | 11/60 kB Progress (5): 393/557 kB | 192/197 kB | 217/291 kB | 20/160 kB | 11/60 kB Progress (5): 393/557 kB | 192/197 kB | 217/291 kB | 25/160 kB | 11/60 kB Progress (5): 393/557 kB | 195/197 kB | 217/291 kB | 25/160 kB | 11/60 kB Progress (5): 397/557 kB | 195/197 kB | 217/291 kB | 25/160 kB | 11/60 kB Progress (5): 397/557 kB | 195/197 kB | 217/291 kB | 25/160 kB | 14/60 kB Progress (5): 397/557 kB | 197 kB | 217/291 kB | 25/160 kB | 14/60 kB Progress (5): 397/557 kB | 197 kB | 217/291 kB | 29/160 kB | 14/60 kB Progress (5): 397/557 kB | 197 kB | 219/291 kB | 29/160 kB | 14/60 kB Progress (5): 397/557 kB | 197 kB | 219/291 kB | 33/160 kB | 14/60 kB Progress (5): 397/557 kB | 197 kB | 219/291 kB | 33/160 kB | 16/60 kB Progress (5): 401/557 kB | 197 kB | 219/291 kB | 33/160 kB | 16/60 kB Progress (5): 401/557 kB | 197 kB | 219/291 kB | 33/160 kB | 19/60 kB Progress (5): 401/557 kB | 197 kB | 223/291 kB | 33/160 kB | 19/60 kB Progress (5): 401/557 kB | 197 kB | 223/291 kB | 33/160 kB | 22/60 kB Progress (5): 401/557 kB | 197 kB | 223/291 kB | 37/160 kB | 22/60 kB Progress (5): 406/557 kB | 197 kB | 223/291 kB | 37/160 kB | 22/60 kB Progress (5): 406/557 kB | 197 kB | 223/291 kB | 41/160 kB | 22/60 kB Progress (5): 406/557 kB | 197 kB | 223/291 kB | 41/160 kB | 25/60 kB Progress (5): 406/557 kB | 197 kB | 227/291 kB | 41/160 kB | 25/60 kB Progress (5): 406/557 kB | 197 kB | 227/291 kB | 41/160 kB | 27/60 kB Progress (5): 406/557 kB | 197 kB | 227/291 kB | 45/160 kB | 27/60 kB Progress (5): 410/557 kB | 197 kB | 227/291 kB | 45/160 kB | 27/60 kB Progress (5): 410/557 kB | 197 kB | 227/291 kB | 49/160 kB | 27/60 kB Progress (5): 410/557 kB | 197 kB | 227/291 kB | 49/160 kB | 30/60 kB Progress (5): 410/557 kB | 197 kB | 231/291 kB | 49/160 kB | 30/60 kB Progress (5): 410/557 kB | 197 kB | 231/291 kB | 49/160 kB | 33/60 kB Progress (5): 414/557 kB | 197 kB | 231/291 kB | 49/160 kB | 33/60 kB Progress (5): 414/557 kB | 197 kB | 231/291 kB | 49/160 kB | 36/60 kB Progress (5): 414/557 kB | 197 kB | 231/291 kB | 53/160 kB | 36/60 kB Progress (5): 414/557 kB | 197 kB | 235/291 kB | 53/160 kB | 36/60 kB Progress (5): 414/557 kB | 197 kB | 235/291 kB | 57/160 kB | 36/60 kB Progress (5): 414/557 kB | 197 kB | 235/291 kB | 57/160 kB | 38/60 kB Progress (5): 418/557 kB | 197 kB | 235/291 kB | 57/160 kB | 38/60 kB Progress (5): 418/557 kB | 197 kB | 235/291 kB | 57/160 kB | 41/60 kB Progress (5): 418/557 kB | 197 kB | 235/291 kB | 61/160 kB | 41/60 kB Progress (5): 418/557 kB | 197 kB | 239/291 kB | 61/160 kB | 41/60 kB Progress (5): 418/557 kB | 197 kB | 239/291 kB | 66/160 kB | 41/60 kB Downloaded from central: https://repo.maven.apache.org/maven2/org/eclipse/sisu/org.eclipse.sisu.plexus/0.0.0.M5/org.eclipse.sisu.plexus-0.0.0.M5.jar (197 kB at 2.9 MB/s) Progress (4): 418/557 kB | 239/291 kB | 66/160 kB | 44/60 kB Progress (4): 422/557 kB | 239/291 kB | 66/160 kB | 44/60 kB Downloading from central: https://repo.maven.apache.org/maven2/org/eclipse/aether/aether-spi/0.9.0.M2/aether-spi-0.9.0.M2.jar Progress (4): 422/557 kB | 239/291 kB | 70/160 kB | 44/60 kB Progress (4): 422/557 kB | 243/291 kB | 70/160 kB | 44/60 kB Progress (4): 426/557 kB | 243/291 kB | 70/160 kB | 44/60 kB Progress (4): 426/557 kB | 243/291 kB | 70/160 kB | 47/60 kB Progress (4): 426/557 kB | 247/291 kB | 70/160 kB | 47/60 kB Progress (4): 426/557 kB | 247/291 kB | 70/160 kB | 49/60 kB Progress (4): 426/557 kB | 247/291 kB | 74/160 kB | 49/60 kB Progress (4): 426/557 kB | 247/291 kB | 74/160 kB | 52/60 kB Progress (4): 426/557 kB | 251/291 kB | 74/160 kB | 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kB | 60 kB | 8.2/18 kB Progress (5): 467/557 kB | 291 kB | 106/160 kB | 60 kB | 8.2/18 kB Progress (5): 471/557 kB | 291 kB | 106/160 kB | 60 kB | 8.2/18 kB Progress (5): 471/557 kB | 291 kB | 106/160 kB | 60 kB | 11/18 kB Progress (5): 475/557 kB | 291 kB | 106/160 kB | 60 kB | 11/18 kB Progress (5): 475/557 kB | 291 kB | 106/160 kB | 60 kB | 14/18 kB Progress (5): 475/557 kB | 291 kB | 111/160 kB | 60 kB | 14/18 kB Progress (5): 475/557 kB | 291 kB | 111/160 kB | 60 kB | 16/18 kB Progress (5): 479/557 kB | 291 kB | 111/160 kB | 60 kB | 16/18 kB Progress (5): 479/557 kB | 291 kB | 111/160 kB | 60 kB | 18 kB Progress (5): 479/557 kB | 291 kB | 115/160 kB | 60 kB | 18 kB Progress (5): 483/557 kB | 291 kB | 115/160 kB | 60 kB | 18 kB Progress (5): 487/557 kB | 291 kB | 115/160 kB | 60 kB | 18 kB Progress (5): 492/557 kB | 291 kB | 115/160 kB | 60 kB | 18 kB Downloaded from central: 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(2): 557 kB | 160 kB Progress (3): 557 kB | 160 kB | 4.1/145 kB Downloaded from central: https://repo.maven.apache.org/maven2/org/codehaus/plexus/plexus-interpolation/1.19/plexus-interpolation-1.19.jar (0 B at 0 B/s) Downloading from central: https://repo.maven.apache.org/maven2/org/codehaus/plexus/plexus-utils/3.0.15/plexus-utils-3.0.15.jar Progress (3): 557 kB | 160 kB | 8.2/145 kB Progress (4): 557 kB | 160 kB | 8.2/145 kB | 2.7/134 kB Progress (4): 557 kB | 160 kB | 12/145 kB | 2.7/134 kB Progress (4): 557 kB | 160 kB | 12/145 kB | 5.5/134 kB Progress (4): 557 kB | 160 kB | 16/145 kB | 5.5/134 kB Progress (4): 557 kB | 160 kB | 16/145 kB | 8.2/134 kB Progress (4): 557 kB | 160 kB | 16/145 kB | 11/134 kB Progress (4): 557 kB | 160 kB | 20/145 kB | 11/134 kB Progress (4): 557 kB | 160 kB | 20/145 kB | 14/134 kB Progress (4): 557 kB | 160 kB | 25/145 kB | 14/134 kB Progress (4): 557 kB | 160 kB | 25/145 kB | 16/134 kB Progress (4): 557 kB | 160 kB | 29/145 kB | 16/134 kB Progress (4): 557 kB | 160 kB | 29/145 kB | 19/134 kB Progress (4): 557 kB | 160 kB | 33/145 kB | 19/134 kB Progress (4): 557 kB | 160 kB | 33/145 kB | 22/134 kB Progress (4): 557 kB | 160 kB | 33/145 kB | 25/134 kB Progress (4): 557 kB | 160 kB | 37/145 kB | 25/134 kB Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/maven/maven-model-builder/3.1.1/maven-model-builder-3.1.1.jar (160 kB at 1.9 MB/s) Progress (3): 557 kB | 37/145 kB | 27/134 kB Downloading from central: https://repo.maven.apache.org/maven2/org/codehaus/plexus/plexus-classworlds/2.5.1/plexus-classworlds-2.5.1.jar Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/maven/maven-core/3.1.1/maven-core-3.1.1.jar (557 kB at 6.6 MB/s) Progress (2): 41/145 kB | 27/134 kB Downloading from central: https://repo.maven.apache.org/maven2/com/fasterxml/jackson/core/jackson-databind/2.6.4/jackson-databind-2.6.4.jar Downloaded from central: 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85/134 kB | 25/50 kB | 4.1/47 kB Progress (4): 102/145 kB | 85/134 kB | 25/50 kB | 4.1/47 kB Progress (4): 102/145 kB | 85/134 kB | 25/50 kB | 8.2/47 kB Progress (4): 102/145 kB | 88/134 kB | 25/50 kB | 8.2/47 kB Progress (4): 102/145 kB | 88/134 kB | 25/50 kB | 12/47 kB Progress (4): 106/145 kB | 88/134 kB | 25/50 kB | 12/47 kB Progress (4): 106/145 kB | 88/134 kB | 29/50 kB | 12/47 kB Progress (4): 111/145 kB | 88/134 kB | 29/50 kB | 12/47 kB Progress (4): 111/145 kB | 88/134 kB | 29/50 kB | 16/47 kB Progress (4): 111/145 kB | 90/134 kB | 29/50 kB | 16/47 kB Progress (5): 111/145 kB | 90/134 kB | 29/50 kB | 16/47 kB | 0/1.2 MB Progress (5): 111/145 kB | 90/134 kB | 29/50 kB | 20/47 kB | 0/1.2 MB Progress (5): 111/145 kB | 93/134 kB | 29/50 kB | 20/47 kB | 0/1.2 MB Progress (5): 115/145 kB | 93/134 kB | 29/50 kB | 20/47 kB | 0/1.2 MB Progress (5): 115/145 kB | 93/134 kB | 33/50 kB | 20/47 kB | 0/1.2 MB Progress (5): 115/145 kB | 96/134 kB | 33/50 kB | 20/47 kB | 0/1.2 MB Progress (5): 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107/134 kB | 45/50 kB | 33/47 kB | 0/1.2 MB Progress (5): 123/145 kB | 107/134 kB | 49/50 kB | 33/47 kB | 0/1.2 MB Progress (5): 123/145 kB | 107/134 kB | 49/50 kB | 33/47 kB | 0/1.2 MB Progress (5): 123/145 kB | 107/134 kB | 50 kB | 33/47 kB | 0/1.2 MB Progress (5): 123/145 kB | 107/134 kB | 50 kB | 37/47 kB | 0/1.2 MB Progress (5): 123/145 kB | 107/134 kB | 50 kB | 37/47 kB | 0/1.2 MB Progress (5): 123/145 kB | 109/134 kB | 50 kB | 37/47 kB | 0/1.2 MB Progress (5): 127/145 kB | 109/134 kB | 50 kB | 37/47 kB | 0/1.2 MB Progress (5): 127/145 kB | 109/134 kB | 50 kB | 37/47 kB | 0.1/1.2 MB Progress (5): 127/145 kB | 109/134 kB | 50 kB | 41/47 kB | 0.1/1.2 MB Progress (5): 127/145 kB | 109/134 kB | 50 kB | 41/47 kB | 0.1/1.2 MB Progress (5): 131/145 kB | 109/134 kB | 50 kB | 41/47 kB | 0.1/1.2 MB Progress (5): 131/145 kB | 113/134 kB | 50 kB | 41/47 kB | 0.1/1.2 MB Progress (5): 131/145 kB | 113/134 kB | 50 kB | 41/47 kB | 0.1/1.2 MB Progress (5): 131/145 kB | 113/134 kB | 50 kB | 45/47 kB | 0.1/1.2 MB Progress (5): 131/145 kB | 113/134 kB | 50 kB | 45/47 kB | 0.1/1.2 MB Progress (5): 135/145 kB | 113/134 kB | 50 kB | 45/47 kB | 0.1/1.2 MB Progress (5): 135/145 kB | 117/134 kB | 50 kB | 45/47 kB | 0.1/1.2 MB Progress (5): 135/145 kB | 117/134 kB | 50 kB | 45/47 kB | 0.1/1.2 MB Progress (5): 135/145 kB | 117/134 kB | 50 kB | 47 kB | 0.1/1.2 MB Progress (5): 135/145 kB | 121/134 kB | 50 kB | 47 kB | 0.1/1.2 MB Progress (5): 139/145 kB | 121/134 kB | 50 kB | 47 kB | 0.1/1.2 MB Progress (5): 139/145 kB | 125/134 kB | 50 kB | 47 kB | 0.1/1.2 MB Progress (5): 139/145 kB | 125/134 kB | 50 kB | 47 kB | 0.1/1.2 MB Progress (5): 139/145 kB | 130/134 kB | 50 kB | 47 kB | 0.1/1.2 MB Progress (5): 143/145 kB | 130/134 kB | 50 kB | 47 kB | 0.1/1.2 MB Progress (5): 143/145 kB | 130/134 kB | 50 kB | 47 kB | 0.1/1.2 MB Progress (5): 143/145 kB | 134/134 kB | 50 kB | 47 kB | 0.1/1.2 MB Progress (5): 145 kB | 134/134 kB | 50 kB | 47 kB | 0.1/1.2 MB Progress (5): 145 kB | 134 kB | 50 kB | 47 kB | 0.1/1.2 MB Progress (5): 145 kB | 134 kB | 50 kB | 47 kB | 0.1/1.2 MB Progress (5): 145 kB | 134 kB | 50 kB | 47 kB | 0.1/1.2 MB Progress (5): 145 kB | 134 kB | 50 kB | 47 kB | 0.1/1.2 MB Progress (5): 145 kB | 134 kB | 50 kB | 47 kB | 0.1/1.2 MB Downloaded from central: https://repo.maven.apache.org/maven2/org/codehaus/plexus/plexus-classworlds/2.5.1/plexus-classworlds-2.5.1.jar (50 kB at 493 kB/s) Progress (4): 145 kB | 134 kB | 47 kB | 0.1/1.2 MB Downloaded from central: https://repo.maven.apache.org/maven2/com/fasterxml/jackson/core/jackson-annotations/2.6.0/jackson-annotations-2.6.0.jar (47 kB at 465 kB/s) Downloading from central: https://repo.maven.apache.org/maven2/com/fasterxml/jackson/core/jackson-core/2.6.4/jackson-core-2.6.4.jar Downloading from central: https://repo.maven.apache.org/maven2/joda-time/joda-time/2.9.1/joda-time-2.9.1.jar Progress (3): 145 kB | 134 kB | 0.2/1.2 MB Progress (3): 145 kB | 134 kB | 0.2/1.2 MB Progress (3): 145 kB | 134 kB | 0.2/1.2 MB Progress (3): 145 kB | 134 kB | 0.2/1.2 MB Progress (3): 145 kB | 134 kB | 0.2/1.2 MB Downloaded from central: https://repo.maven.apache.org/maven2/org/eclipse/aether/aether-api/0.9.0.M2/aether-api-0.9.0.M2.jar (134 kB at 1.3 MB/s) Progress (2): 145 kB | 0.2/1.2 MB Downloaded from central: https://repo.maven.apache.org/maven2/org/eclipse/aether/aether-impl/0.9.0.M2/aether-impl-0.9.0.M2.jar (145 kB at 1.4 MB/s) Progress (1): 0.2/1.2 MB Downloading from central: https://repo.maven.apache.org/maven2/com/google/guava/guava/19.0/guava-19.0.jar Downloading from central: https://repo.maven.apache.org/maven2/com/intellij/annotations/12.0/annotations-12.0.jar Progress (1): 0.2/1.2 MB Progress (1): 0.2/1.2 MB Progress (1): 0.2/1.2 MB Progress (1): 0.2/1.2 MB Progress (1): 0.2/1.2 MB Progress (1): 0.3/1.2 MB Progress (1): 0.3/1.2 MB Progress (1): 0.3/1.2 MB Progress (2): 0.3/1.2 MB | 4.1/626 kB Progress (2): 0.3/1.2 MB | 8.2/626 kB Progress (2): 0.3/1.2 MB | 8.2/626 kB Progress (2): 0.3/1.2 MB | 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kB | 49/259 kB | 8.2/20 kB Progress (4): 0.4/1.2 MB | 70/626 kB | 49/259 kB | 8.2/20 kB Progress (4): 0.4/1.2 MB | 70/626 kB | 49/259 kB | 12/20 kB Progress (4): 0.4/1.2 MB | 70/626 kB | 49/259 kB | 12/20 kB Progress (4): 0.4/1.2 MB | 74/626 kB | 49/259 kB | 12/20 kB Progress (4): 0.4/1.2 MB | 74/626 kB | 53/259 kB | 12/20 kB Downloaded from central: https://repo.maven.apache.org/maven2/com/google/guava/guava/19.0/guava-19.0.jar (0 B at 0 B/s) Progress (4): 0.4/1.2 MB | 74/626 kB | 57/259 kB | 12/20 kB Progress (4): 0.4/1.2 MB | 78/626 kB | 57/259 kB | 12/20 kB Progress (4): 0.4/1.2 MB | 78/626 kB | 57/259 kB | 12/20 kB Progress (4): 0.4/1.2 MB | 78/626 kB | 57/259 kB | 16/20 kB Progress (4): 0.4/1.2 MB | 82/626 kB | 57/259 kB | 16/20 kB Progress (4): 0.4/1.2 MB | 82/626 kB | 61/259 kB | 16/20 kB Downloading from central: https://repo.maven.apache.org/maven2/org/eclipse/jgit/org.eclipse.jgit/4.3.1.201605051710-r/org.eclipse.jgit-4.3.1.201605051710-r.jar Progress (4): 0.4/1.2 MB | 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| 20 kB Progress (4): 0.4/1.2 MB | 106/626 kB | 90/259 kB | 20 kB Progress (4): 0.4/1.2 MB | 106/626 kB | 94/259 kB | 20 kB Progress (4): 0.4/1.2 MB | 111/626 kB | 94/259 kB | 20 kB Progress (4): 0.4/1.2 MB | 111/626 kB | 98/259 kB | 20 kB Progress (4): 0.4/1.2 MB | 111/626 kB | 98/259 kB | 20 kB Progress (4): 0.4/1.2 MB | 115/626 kB | 98/259 kB | 20 kB Progress (4): 0.4/1.2 MB | 115/626 kB | 102/259 kB | 20 kB Progress (4): 0.5/1.2 MB | 115/626 kB | 102/259 kB | 20 kB Progress (4): 0.5/1.2 MB | 119/626 kB | 102/259 kB | 20 kB Progress (4): 0.5/1.2 MB | 119/626 kB | 106/259 kB | 20 kB Progress (4): 0.5/1.2 MB | 119/626 kB | 106/259 kB | 20 kB Progress (4): 0.5/1.2 MB | 119/626 kB | 111/259 kB | 20 kB Progress (4): 0.5/1.2 MB | 123/626 kB | 111/259 kB | 20 kB Progress (4): 0.5/1.2 MB | 123/626 kB | 115/259 kB | 20 kB Progress (4): 0.5/1.2 MB | 127/626 kB | 115/259 kB | 20 kB Progress (4): 0.5/1.2 MB | 127/626 kB | 115/259 kB | 20 kB Progress (4): 0.5/1.2 MB | 131/626 kB | 115/259 kB | 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kB | 201/259 kB | 0/2.4 MB Progress (4): 0.6/1.2 MB | 238/626 kB | 205/259 kB | 0/2.4 MB Progress (4): 0.6/1.2 MB | 238/626 kB | 205/259 kB | 0.1/2.4 MB Progress (4): 0.6/1.2 MB | 238/626 kB | 205/259 kB | 0.1/2.4 MB Progress (4): 0.6/1.2 MB | 238/626 kB | 209/259 kB | 0.1/2.4 MB Progress (4): 0.6/1.2 MB | 242/626 kB | 209/259 kB | 0.1/2.4 MB Progress (4): 0.6/1.2 MB | 242/626 kB | 213/259 kB | 0.1/2.4 MB Progress (4): 0.6/1.2 MB | 246/626 kB | 213/259 kB | 0.1/2.4 MB Progress (4): 0.6/1.2 MB | 246/626 kB | 217/259 kB | 0.1/2.4 MB Progress (4): 0.6/1.2 MB | 246/626 kB | 217/259 kB | 0.1/2.4 MB Progress (4): 0.6/1.2 MB | 250/626 kB | 217/259 kB | 0.1/2.4 MB Progress (4): 0.6/1.2 MB | 250/626 kB | 217/259 kB | 0.1/2.4 MB Progress (4): 0.6/1.2 MB | 250/626 kB | 221/259 kB | 0.1/2.4 MB Progress (4): 0.6/1.2 MB | 250/626 kB | 221/259 kB | 0.1/2.4 MB Progress (4): 0.6/1.2 MB | 254/626 kB | 221/259 kB | 0.1/2.4 MB Progress (4): 0.6/1.2 MB | 254/626 kB | 221/259 kB | 0.1/2.4 MB Progress (4): 0.6/1.2 MB | 254/626 kB | 225/259 kB | 0.1/2.4 MB Progress (4): 0.6/1.2 MB | 254/626 kB | 225/259 kB | 0.1/2.4 MB Progress (4): 0.6/1.2 MB | 258/626 kB | 225/259 kB | 0.1/2.4 MB Progress (4): 0.6/1.2 MB | 258/626 kB | 229/259 kB | 0.1/2.4 MB Progress (4): 0.6/1.2 MB | 258/626 kB | 229/259 kB | 0.1/2.4 MB Progress (5): 0.6/1.2 MB | 258/626 kB | 229/259 kB | 0.1/2.4 MB | 4.1/280 kB Progress (5): 0.7/1.2 MB | 258/626 kB | 229/259 kB | 0.1/2.4 MB | 4.1/280 kB Progress (5): 0.7/1.2 MB | 258/626 kB | 233/259 kB | 0.1/2.4 MB | 4.1/280 kB Progress (5): 0.7/1.2 MB | 258/626 kB | 233/259 kB | 0.1/2.4 MB | 4.1/280 kB Progress (5): 0.7/1.2 MB | 262/626 kB | 233/259 kB | 0.1/2.4 MB | 4.1/280 kB Progress (5): 0.7/1.2 MB | 262/626 kB | 238/259 kB | 0.1/2.4 MB | 4.1/280 kB Progress (5): 0.7/1.2 MB | 262/626 kB | 238/259 kB | 0.1/2.4 MB | 4.1/280 kB Progress (5): 0.7/1.2 MB | 262/626 kB | 238/259 kB | 0.1/2.4 MB | 8.2/280 kB Progress (5): 0.7/1.2 MB | 266/626 kB | 238/259 kB | 0.1/2.4 MB | 8.2/280 kB Progress (5): 0.7/1.2 MB | 266/626 kB | 238/259 kB | 0.1/2.4 MB | 8.2/280 kB Progress (5): 0.7/1.2 MB | 266/626 kB | 242/259 kB | 0.1/2.4 MB | 8.2/280 kB Progress (5): 0.7/1.2 MB | 270/626 kB | 242/259 kB | 0.1/2.4 MB | 8.2/280 kB Progress (5): 0.7/1.2 MB | 270/626 kB | 242/259 kB | 0.1/2.4 MB | 8.2/280 kB Progress (5): 0.7/1.2 MB | 270/626 kB | 242/259 kB | 0.1/2.4 MB | 12/280 kB Progress (5): 0.7/1.2 MB | 270/626 kB | 242/259 kB | 0.1/2.4 MB | 12/280 kB Progress (5): 0.7/1.2 MB | 270/626 kB | 242/259 kB | 0.1/2.4 MB | 12/280 kB Progress (5): 0.7/1.2 MB | 274/626 kB | 242/259 kB | 0.1/2.4 MB | 12/280 kB Progress (5): 0.7/1.2 MB | 274/626 kB | 246/259 kB | 0.1/2.4 MB | 12/280 kB Progress (5): 0.7/1.2 MB | 279/626 kB | 246/259 kB | 0.1/2.4 MB | 12/280 kB Progress (5): 0.7/1.2 MB | 279/626 kB | 246/259 kB | 0.1/2.4 MB | 12/280 kB Progress (5): 0.7/1.2 MB | 279/626 kB | 246/259 kB | 0.1/2.4 MB | 16/280 kB Progress (5): 0.7/1.2 MB | 279/626 kB | 246/259 kB | 0.1/2.4 MB | 16/280 kB Progress (5): 0.7/1.2 MB | 283/626 kB | 246/259 kB | 0.1/2.4 MB | 16/280 kB Progress (5): 0.7/1.2 MB | 283/626 kB | 246/259 kB | 0.2/2.4 MB | 16/280 kB Progress (5): 0.7/1.2 MB | 283/626 kB | 250/259 kB | 0.2/2.4 MB | 16/280 kB Progress (5): 0.7/1.2 MB | 283/626 kB | 250/259 kB | 0.2/2.4 MB | 16/280 kB Progress (5): 0.7/1.2 MB | 283/626 kB | 254/259 kB | 0.2/2.4 MB | 16/280 kB Progress (5): 0.7/1.2 MB | 283/626 kB | 254/259 kB | 0.2/2.4 MB | 20/280 kB Progress (5): 0.7/1.2 MB | 287/626 kB | 254/259 kB | 0.2/2.4 MB | 20/280 kB Progress (5): 0.7/1.2 MB | 287/626 kB | 258/259 kB | 0.2/2.4 MB | 20/280 kB Progress (5): 0.7/1.2 MB | 287/626 kB | 258/259 kB | 0.2/2.4 MB | 20/280 kB Progress (5): 0.7/1.2 MB | 287/626 kB | 258/259 kB | 0.2/2.4 MB | 20/280 kB Progress (5): 0.7/1.2 MB | 287/626 kB | 259 kB | 0.2/2.4 MB | 20/280 kB Progress (5): 0.7/1.2 MB | 287/626 kB | 259 kB | 0.2/2.4 MB | 20/280 kB Progress (5): 0.7/1.2 MB | 291/626 kB | 259 kB | 0.2/2.4 MB | 20/280 kB Progress (5): 0.7/1.2 MB | 291/626 kB | 259 kB | 0.2/2.4 MB | 25/280 kB Progress (5): 0.7/1.2 MB | 295/626 kB | 259 kB | 0.2/2.4 MB | 25/280 kB Progress (5): 0.7/1.2 MB | 295/626 kB | 259 kB | 0.2/2.4 MB | 25/280 kB Progress (5): 0.7/1.2 MB | 295/626 kB | 259 kB | 0.2/2.4 MB | 25/280 kB Progress (5): 0.7/1.2 MB | 299/626 kB | 259 kB | 0.2/2.4 MB | 25/280 kB Progress (5): 0.7/1.2 MB | 299/626 kB | 259 kB | 0.2/2.4 MB | 29/280 kB Progress (5): 0.7/1.2 MB | 299/626 kB | 259 kB | 0.2/2.4 MB | 29/280 kB Progress (5): 0.7/1.2 MB | 303/626 kB | 259 kB | 0.2/2.4 MB | 29/280 kB Progress (5): 0.7/1.2 MB | 303/626 kB | 259 kB | 0.2/2.4 MB | 29/280 kB Progress (5): 0.7/1.2 MB | 307/626 kB | 259 kB | 0.2/2.4 MB | 29/280 kB Progress (5): 0.7/1.2 MB | 307/626 kB | 259 kB | 0.2/2.4 MB | 33/280 kB Progress (5): 0.7/1.2 MB | 311/626 kB | 259 kB | 0.2/2.4 MB | 33/280 kB Progress (5): 0.7/1.2 MB | 311/626 kB | 259 kB | 0.2/2.4 MB | 33/280 kB Progress (5): 0.7/1.2 MB | 311/626 kB | 259 kB | 0.2/2.4 MB | 33/280 kB Progress (5): 0.7/1.2 MB | 311/626 kB | 259 kB | 0.2/2.4 MB | 37/280 kB Progress (5): 0.7/1.2 MB | 315/626 kB | 259 kB | 0.2/2.4 MB | 37/280 kB Progress (5): 0.7/1.2 MB | 315/626 kB | 259 kB | 0.2/2.4 MB | 37/280 kB Progress (5): 0.8/1.2 MB | 315/626 kB | 259 kB | 0.2/2.4 MB | 37/280 kB Progress (5): 0.8/1.2 MB | 319/626 kB | 259 kB | 0.2/2.4 MB | 37/280 kB Progress (5): 0.8/1.2 MB | 319/626 kB | 259 kB | 0.2/2.4 MB | 41/280 kB Progress (5): 0.8/1.2 MB | 319/626 kB | 259 kB | 0.3/2.4 MB | 41/280 kB Progress (5): 0.8/1.2 MB | 319/626 kB | 259 kB | 0.3/2.4 MB | 45/280 kB Progress (5): 0.8/1.2 MB | 324/626 kB | 259 kB | 0.3/2.4 MB | 45/280 kB Progress (5): 0.8/1.2 MB | 324/626 kB | 259 kB | 0.3/2.4 MB | 45/280 kB Progress (5): 0.8/1.2 MB | 328/626 kB | 259 kB | 0.3/2.4 MB | 45/280 kB Progress (5): 0.8/1.2 MB | 328/626 kB | 259 kB | 0.3/2.4 MB | 45/280 kB Progress (5): 0.8/1.2 MB | 328/626 kB | 259 kB | 0.3/2.4 MB | 49/280 kB Progress (5): 0.8/1.2 MB | 332/626 kB | 259 kB | 0.3/2.4 MB | 49/280 kB Progress (5): 0.8/1.2 MB | 332/626 kB | 259 kB | 0.3/2.4 MB | 49/280 kB Progress (5): 0.8/1.2 MB | 332/626 kB | 259 kB | 0.3/2.4 MB | 49/280 kB Progress (5): 0.8/1.2 MB | 336/626 kB | 259 kB | 0.3/2.4 MB | 49/280 kB Progress (5): 0.8/1.2 MB | 336/626 kB | 259 kB | 0.3/2.4 MB | 49/280 kB Progress (5): 0.8/1.2 MB | 336/626 kB | 259 kB | 0.3/2.4 MB | 53/280 kB Downloaded from central: https://repo.maven.apache.org/maven2/com/fasterxml/jackson/core/jackson-core/2.6.4/jackson-core-2.6.4.jar (259 kB at 1.9 MB/s) Progress (4): 0.8/1.2 MB | 336/626 kB | 0.3/2.4 MB | 53/280 kB Progress (4): 0.8/1.2 MB | 340/626 kB | 0.3/2.4 MB | 53/280 kB Downloading from central: https://repo.maven.apache.org/maven2/com/googlecode/javaewah/JavaEWAH/0.7.9/JavaEWAH-0.7.9.jar Progress (4): 0.8/1.2 MB | 340/626 kB | 0.3/2.4 MB | 57/280 kB Progress (4): 0.8/1.2 MB | 340/626 kB | 0.3/2.4 MB | 57/280 kB Progress (4): 0.8/1.2 MB | 340/626 kB | 0.3/2.4 MB | 57/280 kB Progress (4): 0.8/1.2 MB | 340/626 kB | 0.3/2.4 MB | 57/280 kB Progress (4): 0.8/1.2 MB | 344/626 kB | 0.3/2.4 MB | 57/280 kB Progress (4): 0.8/1.2 MB | 344/626 kB | 0.3/2.4 MB | 61/280 kB Progress (4): 0.8/1.2 MB | 344/626 kB | 0.3/2.4 MB | 61/280 kB Progress (4): 0.8/1.2 MB | 344/626 kB | 0.3/2.4 MB | 61/280 kB Progress (4): 0.8/1.2 MB | 348/626 kB | 0.3/2.4 MB | 61/280 kB Progress (4): 0.8/1.2 MB | 348/626 kB | 0.3/2.4 MB | 61/280 kB Progress (4): 0.8/1.2 MB | 348/626 kB | 0.3/2.4 MB | 66/280 kB Progress (4): 0.8/1.2 MB | 348/626 kB | 0.4/2.4 MB | 66/280 kB Progress (4): 0.8/1.2 MB | 352/626 kB | 0.4/2.4 MB | 66/280 kB Progress (4): 0.8/1.2 MB | 352/626 kB | 0.4/2.4 MB | 66/280 kB Progress (4): 0.8/1.2 MB | 356/626 kB | 0.4/2.4 MB | 66/280 kB Progress (4): 0.8/1.2 MB | 356/626 kB | 0.4/2.4 MB | 66/280 kB Progress (4): 0.8/1.2 MB | 356/626 kB | 0.4/2.4 MB | 66/280 kB Progress (4): 0.8/1.2 MB | 356/626 kB | 0.4/2.4 MB | 70/280 kB Progress (4): 0.8/1.2 MB | 360/626 kB | 0.4/2.4 MB | 70/280 kB Progress (4): 0.8/1.2 MB | 360/626 kB | 0.4/2.4 MB | 70/280 kB Progress (4): 0.8/1.2 MB | 360/626 kB | 0.4/2.4 MB | 70/280 kB Progress (4): 0.8/1.2 MB | 365/626 kB | 0.4/2.4 MB | 70/280 kB Progress (4): 0.8/1.2 MB | 365/626 kB | 0.4/2.4 MB | 70/280 kB Progress (4): 0.8/1.2 MB | 365/626 kB | 0.4/2.4 MB | 74/280 kB Progress (4): 0.8/1.2 MB | 365/626 kB | 0.4/2.4 MB | 74/280 kB Progress (4): 0.8/1.2 MB | 369/626 kB | 0.4/2.4 MB | 74/280 kB Progress (4): 0.8/1.2 MB | 369/626 kB | 0.4/2.4 MB | 78/280 kB Progress (4): 0.9/1.2 MB | 369/626 kB | 0.4/2.4 MB | 78/280 kB Progress (4): 0.9/1.2 MB | 373/626 kB | 0.4/2.4 MB | 78/280 kB Progress (4): 0.9/1.2 MB | 373/626 kB | 0.4/2.4 MB | 78/280 kB Progress (4): 0.9/1.2 MB | 373/626 kB | 0.4/2.4 MB | 78/280 kB Progress (4): 0.9/1.2 MB | 373/626 kB | 0.4/2.4 MB | 82/280 kB Progress (4): 0.9/1.2 MB | 373/626 kB | 0.4/2.4 MB | 82/280 kB Progress (4): 0.9/1.2 MB | 377/626 kB | 0.4/2.4 MB | 82/280 kB Progress (4): 0.9/1.2 MB | 377/626 kB | 0.4/2.4 MB | 82/280 kB Progress (4): 0.9/1.2 MB | 377/626 kB | 0.4/2.4 MB | 82/280 kB Progress (4): 0.9/1.2 MB | 381/626 kB | 0.4/2.4 MB | 82/280 kB Progress (5): 0.9/1.2 MB | 381/626 kB | 0.4/2.4 MB | 82/280 kB | 4.1/125 kB Progress (5): 0.9/1.2 MB | 381/626 kB | 0.4/2.4 MB | 86/280 kB | 4.1/125 kB Progress (5): 0.9/1.2 MB | 381/626 kB | 0.4/2.4 MB | 86/280 kB | 8.2/125 kB Progress (5): 0.9/1.2 MB | 381/626 kB | 0.5/2.4 MB | 86/280 kB | 8.2/125 kB Progress (5): 0.9/1.2 MB | 385/626 kB | 0.5/2.4 MB | 86/280 kB | 8.2/125 kB Progress (5): 0.9/1.2 MB | 385/626 kB | 0.5/2.4 MB | 86/280 kB | 8.2/125 kB Progress (5): 0.9/1.2 MB | 389/626 kB | 0.5/2.4 MB | 86/280 kB | 8.2/125 kB Progress (5): 0.9/1.2 MB | 389/626 kB | 0.5/2.4 MB | 86/280 kB | 12/125 kB Progress (5): 0.9/1.2 MB | 389/626 kB | 0.5/2.4 MB | 90/280 kB | 12/125 kB Progress (5): 0.9/1.2 MB | 389/626 kB | 0.5/2.4 MB | 90/280 kB | 16/125 kB Progress (5): 0.9/1.2 MB | 393/626 kB | 0.5/2.4 MB | 90/280 kB | 16/125 kB Progress (5): 0.9/1.2 MB | 393/626 kB | 0.5/2.4 MB | 90/280 kB | 16/125 kB Progress (5): 0.9/1.2 MB | 393/626 kB | 0.5/2.4 MB | 90/280 kB | 16/125 kB Progress (5): 0.9/1.2 MB | 397/626 kB | 0.5/2.4 MB | 90/280 kB | 16/125 kB Progress (5): 0.9/1.2 MB | 397/626 kB | 0.5/2.4 MB | 90/280 kB | 20/125 kB Progress (5): 0.9/1.2 MB | 397/626 kB | 0.5/2.4 MB | 94/280 kB | 20/125 kB Progress (5): 0.9/1.2 MB | 397/626 kB | 0.5/2.4 MB | 94/280 kB | 25/125 kB Progress (5): 0.9/1.2 MB | 397/626 kB | 0.5/2.4 MB | 98/280 kB | 25/125 kB Progress (5): 0.9/1.2 MB | 397/626 kB | 0.5/2.4 MB | 98/280 kB | 25/125 kB Progress (5): 0.9/1.2 MB | 401/626 kB | 0.5/2.4 MB | 98/280 kB | 25/125 kB Progress (5): 0.9/1.2 MB | 401/626 kB | 0.5/2.4 MB | 98/280 kB | 25/125 kB Progress (5): 0.9/1.2 MB | 406/626 kB | 0.5/2.4 MB | 98/280 kB | 25/125 kB Progress (5): 0.9/1.2 MB | 406/626 kB | 0.5/2.4 MB | 102/280 kB | 25/125 kB Progress (5): 0.9/1.2 MB | 406/626 kB | 0.5/2.4 MB | 102/280 kB | 29/125 kB Progress (5): 0.9/1.2 MB | 406/626 kB | 0.5/2.4 MB | 106/280 kB | 29/125 kB Progress (5): 0.9/1.2 MB | 410/626 kB | 0.5/2.4 MB | 106/280 kB | 29/125 kB Progress (5): 0.9/1.2 MB | 410/626 kB | 0.5/2.4 MB | 106/280 kB | 29/125 kB Progress (5): 0.9/1.2 MB | 410/626 kB | 0.5/2.4 MB | 106/280 kB | 29/125 kB Progress (5): 0.9/1.2 MB | 414/626 kB | 0.5/2.4 MB | 106/280 kB | 29/125 kB Progress (5): 0.9/1.2 MB | 414/626 kB | 0.5/2.4 MB | 111/280 kB | 29/125 kB Progress (5): 0.9/1.2 MB | 414/626 kB | 0.5/2.4 MB | 111/280 kB | 33/125 kB Progress (5): 0.9/1.2 MB | 414/626 kB | 0.5/2.4 MB | 115/280 kB | 33/125 kB Progress (5): 0.9/1.2 MB | 414/626 kB | 0.5/2.4 MB | 115/280 kB | 33/125 kB Progress (5): 0.9/1.2 MB | 418/626 kB | 0.5/2.4 MB | 115/280 kB | 33/125 kB Progress (5): 0.9/1.2 MB | 418/626 kB | 0.5/2.4 MB | 115/280 kB | 33/125 kB Progress (5): 0.9/1.2 MB | 422/626 kB | 0.5/2.4 MB | 115/280 kB | 33/125 kB Progress (5): 0.9/1.2 MB | 422/626 kB | 0.5/2.4 MB | 119/280 kB | 33/125 kB Progress (5): 0.9/1.2 MB | 422/626 kB | 0.5/2.4 MB | 119/280 kB | 37/125 kB Progress (5): 0.9/1.2 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Progress (3): 626 kB | 1.2/2.4 MB | 33/592 kB Progress (3): 626 kB | 1.2/2.4 MB | 37/592 kB Downloading from central: https://repo.maven.apache.org/maven2/commons-codec/commons-codec/1.6/commons-codec-1.6.jar Progress (3): 626 kB | 1.2/2.4 MB | 37/592 kB Progress (3): 626 kB | 1.2/2.4 MB | 41/592 kB Progress (3): 626 kB | 1.2/2.4 MB | 45/592 kB Progress (3): 626 kB | 1.2/2.4 MB | 49/592 kB Progress (3): 626 kB | 1.2/2.4 MB | 49/592 kB Progress (3): 626 kB | 1.2/2.4 MB | 53/592 kB Progress (3): 626 kB | 1.2/2.4 MB | 57/592 kB Progress (3): 626 kB | 1.2/2.4 MB | 57/592 kB Progress (3): 626 kB | 1.2/2.4 MB | 61/592 kB Progress (3): 626 kB | 1.2/2.4 MB | 66/592 kB Progress (3): 626 kB | 1.2/2.4 MB | 66/592 kB Progress (3): 626 kB | 1.2/2.4 MB | 70/592 kB Progress (3): 626 kB | 1.2/2.4 MB | 74/592 kB Progress (3): 626 kB | 1.2/2.4 MB | 74/592 kB Progress (3): 626 kB | 1.2/2.4 MB | 78/592 kB Progress (3): 626 kB | 1.2/2.4 MB | 82/592 kB Downloaded from central: 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20/26 kB Progress (4): 1.5/2.4 MB | 176/592 kB | 102/283 kB | 25/26 kB Progress (4): 1.5/2.4 MB | 180/592 kB | 102/283 kB | 25/26 kB Progress (4): 1.5/2.4 MB | 180/592 kB | 102/283 kB | 26 kB Progress (4): 1.5/2.4 MB | 180/592 kB | 102/283 kB | 26 kB Progress (4): 1.5/2.4 MB | 180/592 kB | 106/283 kB | 26 kB Progress (4): 1.5/2.4 MB | 184/592 kB | 106/283 kB | 26 kB Progress (4): 1.5/2.4 MB | 184/592 kB | 111/283 kB | 26 kB Progress (4): 1.5/2.4 MB | 188/592 kB | 111/283 kB | 26 kB Progress (4): 1.5/2.4 MB | 188/592 kB | 115/283 kB | 26 kB Progress (4): 1.5/2.4 MB | 188/592 kB | 115/283 kB | 26 kB Progress (4): 1.5/2.4 MB | 193/592 kB | 115/283 kB | 26 kB Progress (4): 1.5/2.4 MB | 193/592 kB | 119/283 kB | 26 kB Progress (4): 1.5/2.4 MB | 197/592 kB | 119/283 kB | 26 kB Progress (4): 1.5/2.4 MB | 197/592 kB | 123/283 kB | 26 kB Progress (4): 1.5/2.4 MB | 197/592 kB | 123/283 kB | 26 kB Progress (4): 1.5/2.4 MB | 197/592 kB | 127/283 kB | 26 kB Progress (4): 1.5/2.4 MB | 201/592 kB | 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| 160/283 kB | 26 kB Progress (4): 1.6/2.4 MB | 225/592 kB | 160/283 kB | 26 kB Progress (4): 1.6/2.4 MB | 225/592 kB | 164/283 kB | 26 kB Progress (4): 1.6/2.4 MB | 229/592 kB | 164/283 kB | 26 kB Progress (4): 1.6/2.4 MB | 233/592 kB | 164/283 kB | 26 kB Progress (4): 1.6/2.4 MB | 233/592 kB | 164/283 kB | 26 kB Progress (4): 1.6/2.4 MB | 233/592 kB | 168/283 kB | 26 kB Progress (4): 1.6/2.4 MB | 238/592 kB | 168/283 kB | 26 kB Downloaded from central: https://repo.maven.apache.org/maven2/org/slf4j/slf4j-api/1.7.2/slf4j-api-1.7.2.jar (26 kB at 137 kB/s) Progress (3): 1.6/2.4 MB | 238/592 kB | 168/283 kB Progress (3): 1.6/2.4 MB | 242/592 kB | 168/283 kB Progress (3): 1.6/2.4 MB | 242/592 kB | 172/283 kB Progress (3): 1.6/2.4 MB | 246/592 kB | 172/283 kB Progress (3): 1.6/2.4 MB | 246/592 kB | 176/283 kB Progress (3): 1.7/2.4 MB | 246/592 kB | 176/283 kB Progress (3): 1.7/2.4 MB | 250/592 kB | 176/283 kB Progress (3): 1.7/2.4 MB | 250/592 kB | 180/283 kB Progress (3): 1.7/2.4 MB | 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(2): 2.2/2.4 MB | 536/592 kB Progress (2): 2.2/2.4 MB | 540/592 kB Progress (2): 2.2/2.4 MB | 544/592 kB Progress (2): 2.2/2.4 MB | 549/592 kB Progress (2): 2.2/2.4 MB | 549/592 kB Progress (2): 2.2/2.4 MB | 553/592 kB Progress (2): 2.2/2.4 MB | 557/592 kB Progress (2): 2.2/2.4 MB | 557/592 kB Progress (2): 2.2/2.4 MB | 561/592 kB Progress (2): 2.2/2.4 MB | 565/592 kB Progress (2): 2.2/2.4 MB | 569/592 kB Progress (2): 2.2/2.4 MB | 569/592 kB Progress (2): 2.2/2.4 MB | 573/592 kB Progress (2): 2.2/2.4 MB | 577/592 kB Progress (2): 2.2/2.4 MB | 577/592 kB Progress (2): 2.2/2.4 MB | 581/592 kB Progress (2): 2.2/2.4 MB | 585/592 kB Progress (2): 2.2/2.4 MB | 590/592 kB Progress (2): 2.2/2.4 MB | 590/592 kB Progress (2): 2.2/2.4 MB | 592 kB Progress (2): 2.3/2.4 MB | 592 kB Progress (2): 2.3/2.4 MB | 592 kB Progress (2): 2.3/2.4 MB | 592 kB Progress (2): 2.3/2.4 MB | 592 kB Progress (2): 2.3/2.4 MB | 592 kB Progress (2): 2.3/2.4 MB | 592 kB Progress (2): 2.4 MB | 592 kB Downloaded from 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[INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 1 resource [INFO] Copied 1 files to output directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/adam-cli/target/generated-sources/java-templates [INFO] Source directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/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-spark3_2.12 --- [INFO] Source directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/adam-cli/src/main/scala added. [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ adam-cli-spark3_2.12 --- [INFO] Modified 0 of 29 .scala files [INFO] [INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ adam-cli-spark3_2.12 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/adam-cli/src/main/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ adam-cli-spark3_2.12 --- [INFO] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/adam-cli/target/generated-sources/java-templates:-1: info: compiling [INFO] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/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/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/adam-cli/target/2.12.8/classes at 1606966695625 [WARNING] warning: there was one deprecation warning [WARNING] warning: there was one deprecation warning (since 2.12.0) [WARNING] warning: there were two deprecation warnings in total; re-run with -deprecation for details [WARNING] three warnings found [INFO] prepare-compile in 0 s [INFO] compile in 8 s [INFO] [INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ adam-cli-spark3_2.12 --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 1 source file to /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/adam-cli/target/2.12.8/classes [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ adam-cli-spark3_2.12 --- [INFO] Test Source directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/adam-cli/src/test/scala added. [INFO] [INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ adam-cli-spark3_2.12 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 15 resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ adam-cli-spark3_2.12 --- [INFO] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/adam-cli/src/test/scala:-1: info: compiling [INFO] Compiling 12 source files to /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/adam-cli/target/2.12.8/test-classes at 1606966704429 [INFO] prepare-compile in 0 s [INFO] compile in 7 s [INFO] [INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ adam-cli-spark3_2.12 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ adam-cli-spark3_2.12 --- [INFO] Tests are skipped. [INFO] [INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ adam-cli-spark3_2.12 --- Discovery starting. Discovery completed in 228 milliseconds. Run starting. Expected test count is: 44 TransformFeaturesSuite: 2020-12-02 19:38:32 WARN Utils:69 - Your hostname, research-jenkins-worker-01 resolves to a loopback address: 127.0.1.1; using 192.168.122.1 instead (on interface virbr0) 2020-12-02 19:38:32 WARN Utils:69 - Set SPARK_LOCAL_IP if you need to bind to another address 2020-12-02 19:38:33 WARN NativeCodeLoader:62 - Unable to load native-hadoop library for your platform... using builtin-java classes where applicable - can convert a simple BED file TransformVariantsSuite: - save a file sorted by contig index - save a lexicographically sorted file ViewSuite: - -f 0 -F 0 is a no-op - no -f or -F args is a no-op - -f 4: only unmapped reads - -F 4: only mapped reads - -f 4 -F 8: unmapped reads with mapped mates - -f 12: unmapped reads with unmapped mates - -g 12: reads that are unmapped or whose mate is unmapped - -F 12: mapped reads with mapped mates - -g 36: unmapped reads or reads with mate on negative strand - -F 36: unmapped reads or reads with mate on negative strand TransformFragmentsSuite: - load queryname sorted sam and save as parquet - cannot sort if not saving as sam 2020-12-02 19:38:45 WARN TransformFragments:190 - If loading and saving as alignments, 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 AboutSuite: - template variables have been replaced - templated values are not empty CoverageSuite: - correctly calculates coverage from small sam file MergeShardsSuite: - merge shards from unordered sam to unordered sam - unordered sam to ordered sam - merge sharded bam - merge sharded cram TransformAlignmentsSuite: - unordered sam to unordered sam - unordered sam to ordered sam - unordered sam, to adam, to sam - unordered sam, to adam, to ordered sam - put quality scores into bins - run region predicate ADAMMainSuite: - default command groups is non empty - module provides default command groups - inject default command groups when called via main - command groups is empty when called via apply - single command group - add new command group to default command groups - module restores default command groups when called via apply - custom module with single command group - custom module with new command group added to default command groups Adam2FastqSuite: 2020-12-02 19:38:54 WARN RDDBoundAlignmentDataset: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 22 seconds, 555 milliseconds. Total number of tests run: 44 Suites: completed 12, aborted 0 Tests: succeeded 44, failed 0, canceled 0, ignored 0, pending 0 All tests passed. [INFO] [INFO] >>> scoverage-maven-plugin:1.1.1:report (default-cli) > [scoverage]test @ adam-cli-spark3_2.12 >>> [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-cli-spark3_2.12 --- [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-cli-spark3_2.12 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:timestamp-property (timestamp-property) @ adam-cli-spark3_2.12 --- [INFO] [INFO] --- git-commit-id-plugin:2.2.2:revision (default) @ adam-cli-spark3_2.12 --- [INFO] [INFO] --- templating-maven-plugin:1.0.0:filter-sources (filter-src) @ adam-cli-spark3_2.12 --- [INFO] Coping files with filtering to temporary directory. [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 1 resource [INFO] No files needs to be copied to output directory. Up to date: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/adam-cli/target/generated-sources/java-templates [INFO] Source directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/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-spark3_2.12 --- [INFO] Source directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/adam-cli/src/main/scala added. [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ adam-cli-spark3_2.12 --- [INFO] Modified 0 of 29 .scala files [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:pre-compile (default-cli) @ adam-cli-spark3_2.12 --- [WARNING] Skipping SCoverage execution - unsupported Scala version "2.12.8" [INFO] [INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ adam-cli-spark3_2.12 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/adam-cli/src/main/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ adam-cli-spark3_2.12 --- [INFO] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/adam-cli/target/generated-sources/java-templates:-1: info: compiling [INFO] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/adam-cli/src/main/scala:-1: info: compiling [INFO] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/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/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/adam-cli/target/2.12.8/classes at 1606966736257 [WARNING] warning: there was one deprecation warning [WARNING] warning: there was one deprecation warning (since 2.12.0) [WARNING] warning: there were two deprecation warnings in total; re-run with -deprecation for details [WARNING] three warnings found [INFO] prepare-compile in 0 s [INFO] compile in 8 s [INFO] [INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ adam-cli-spark3_2.12 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:post-compile (default-cli) @ adam-cli-spark3_2.12 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ adam-cli-spark3_2.12 --- [INFO] Test Source directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/adam-cli/src/test/scala added. [INFO] [INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ adam-cli-spark3_2.12 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 15 resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ adam-cli-spark3_2.12 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ adam-cli-spark3_2.12 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ adam-cli-spark3_2.12 --- [INFO] Tests are skipped. [INFO] [INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ adam-cli-spark3_2.12 --- Discovery starting. Discovery completed in 213 milliseconds. Run starting. Expected test count is: 44 TransformFeaturesSuite: 2020-12-02 19:39:06 WARN Utils:69 - Your hostname, research-jenkins-worker-01 resolves to a loopback address: 127.0.1.1; using 192.168.122.1 instead (on interface virbr0) 2020-12-02 19:39:06 WARN Utils:69 - Set SPARK_LOCAL_IP if you need to bind to another address 2020-12-02 19:39:07 WARN NativeCodeLoader:62 - Unable to load native-hadoop library for your platform... using builtin-java classes where applicable - can convert a simple BED file TransformVariantsSuite: - save a file sorted by contig index - save a lexicographically sorted file ViewSuite: - -f 0 -F 0 is a no-op - no -f or -F args is a no-op - -f 4: only unmapped reads - -F 4: only mapped reads - -f 4 -F 8: unmapped reads with mapped mates - -f 12: unmapped reads with unmapped mates - -g 12: reads that are unmapped or whose mate is unmapped - -F 12: mapped reads with mapped mates - -g 36: unmapped reads or reads with mate on negative strand - -F 36: unmapped reads or reads with mate on negative strand TransformFragmentsSuite: - load queryname sorted sam and save as parquet - cannot sort if not saving as sam 2020-12-02 19:39:19 WARN TransformFragments:190 - If loading and saving as alignments, 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 AboutSuite: - template variables have been replaced - templated values are not empty CoverageSuite: - correctly calculates coverage from small sam file MergeShardsSuite: - merge shards from unordered sam to unordered sam - unordered sam to ordered sam - merge sharded bam - merge sharded cram TransformAlignmentsSuite: - unordered sam to unordered sam - unordered sam to ordered sam - unordered sam, to adam, to sam - unordered sam, to adam, to ordered sam - put quality scores into bins - run region predicate ADAMMainSuite: - default command groups is non empty - module provides default command groups - inject default command groups when called via main - command groups is empty when called via apply - single command group - add new command group to default command groups - module restores default command groups when called via apply - custom module with single command group - custom module with new command group added to default command groups Adam2FastqSuite: 2020-12-02 19:39:28 WARN RDDBoundAlignmentDataset: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 22 seconds, 728 milliseconds. Total number of tests run: 44 Suites: completed 12, aborted 0 Tests: succeeded 44, failed 0, canceled 0, ignored 0, pending 0 All tests passed. [INFO] [INFO] <<< scoverage-maven-plugin:1.1.1:report (default-cli) < [scoverage]test @ adam-cli-spark3_2.12 <<< [INFO] [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:report (default-cli) @ adam-cli-spark3_2.12 --- [INFO] Skipping SCoverage report generation [INFO] [INFO] -----------< org.bdgenomics.adam:adam-assembly-spark3_2.12 >------------ [INFO] Building ADAM_2.12: Assembly 0.33.0-SNAPSHOT [7/7] [INFO] --------------------------------[ jar ]--------------------------------- Downloading from central: https://repo.maven.apache.org/maven2/commons-logging/commons-logging/1.2/commons-logging-1.2.jar Downloading from central: https://repo.maven.apache.org/maven2/org/apache/parquet/parquet-common/1.10.1/parquet-common-1.10.1.jar Downloading from central: https://repo.maven.apache.org/maven2/org/apache/parquet/parquet-column/1.10.1/parquet-column-1.10.1.jar Downloading from central: https://repo.maven.apache.org/maven2/org/apache/parquet/parquet-hadoop/1.10.1/parquet-hadoop-1.10.1.jar 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https://repo.maven.apache.org/maven2/org/scala-lang/scala-reflect/2.12.6/scala-reflect-2.12.6.jar (3.6 MB at 29 MB/s) [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-assembly-spark3_2.12 --- [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-assembly-spark3_2.12 --- [INFO] [INFO] --- git-commit-id-plugin:2.2.2:revision (default) @ adam-assembly-spark3_2.12 --- [INFO] [INFO] --- templating-maven-plugin:1.0.0:filter-sources (filter-src) @ adam-assembly-spark3_2.12 --- [INFO] Request to add '/home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/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-spark3_2.12 --- [INFO] Source directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/adam-assembly/src/main/scala added. [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ adam-assembly-spark3_2.12 --- [INFO] Modified 0 of 1 .scala files [INFO] [INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ adam-assembly-spark3_2.12 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/adam-assembly/src/main/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ adam-assembly-spark3_2.12 --- [INFO] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/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/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/adam-assembly/target/2.12.8/classes at 1606966770178 [INFO] prepare-compile in 0 s [INFO] compile in 2 s [INFO] [INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ adam-assembly-spark3_2.12 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ adam-assembly-spark3_2.12 --- [INFO] Test Source directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/adam-assembly/src/test/scala added. [INFO] [INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ adam-assembly-spark3_2.12 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/adam-assembly/src/test/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ adam-assembly-spark3_2.12 --- [INFO] No sources to compile [INFO] [INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ adam-assembly-spark3_2.12 --- [INFO] No sources to compile [INFO] [INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ adam-assembly-spark3_2.12 --- [INFO] Tests are skipped. [INFO] [INFO] >>> scoverage-maven-plugin:1.1.1:report (default-cli) > [scoverage]test @ adam-assembly-spark3_2.12 >>> [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-assembly-spark3_2.12 --- [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-assembly-spark3_2.12 --- [INFO] [INFO] --- git-commit-id-plugin:2.2.2:revision (default) @ adam-assembly-spark3_2.12 --- [INFO] [INFO] --- templating-maven-plugin:1.0.0:filter-sources (filter-src) @ adam-assembly-spark3_2.12 --- [INFO] Request to add '/home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/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-spark3_2.12 --- [INFO] Source directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/adam-assembly/src/main/scala added. [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ adam-assembly-spark3_2.12 --- [INFO] Modified 0 of 1 .scala files [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:pre-compile (default-cli) @ adam-assembly-spark3_2.12 --- [WARNING] Skipping SCoverage execution - unsupported Scala version "2.12.8" [INFO] [INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ adam-assembly-spark3_2.12 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/adam-assembly/src/main/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ adam-assembly-spark3_2.12 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ adam-assembly-spark3_2.12 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:post-compile (default-cli) @ adam-assembly-spark3_2.12 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ adam-assembly-spark3_2.12 --- [INFO] Test Source directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/adam-assembly/src/test/scala added. [INFO] [INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ adam-assembly-spark3_2.12 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/adam-assembly/src/test/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ adam-assembly-spark3_2.12 --- [INFO] No sources to compile [INFO] [INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ adam-assembly-spark3_2.12 --- [INFO] No sources to compile [INFO] [INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ adam-assembly-spark3_2.12 --- [INFO] Tests are skipped. [INFO] [INFO] <<< scoverage-maven-plugin:1.1.1:report (default-cli) < [scoverage]test @ adam-assembly-spark3_2.12 <<< [INFO] [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:report (default-cli) @ adam-assembly-spark3_2.12 --- [INFO] [scoverage] Generating aggregated cobertura XML report... [INFO] [scoverage] Generating aggregated scoverage XML report... [INFO] [scoverage] Generating aggregated scoverage HTML report... [INFO] Skipping SCoverage report generation [INFO] ------------------------------------------------------------------------ [INFO] Reactor Summary for ADAM_2.12 0.33.0-SNAPSHOT: [INFO] [INFO] ADAM_2.12 .......................................... SUCCESS [ 13.705 s] [INFO] ADAM_2.12: Shader workaround ....................... SUCCESS [ 7.496 s] [INFO] ADAM_2.12: Avro-to-Dataset codegen utils ........... SUCCESS [ 7.707 s] [INFO] ADAM_2.12: Core .................................... SUCCESS [19:12 min] [INFO] ADAM_2.12: APIs for Java, Python ................... SUCCESS [ 42.129 s] [INFO] ADAM_2.12: CLI ..................................... SUCCESS [01:16 min] [INFO] ADAM_2.12: Assembly ................................ SUCCESS [ 3.899 s] [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ [INFO] Total time: 21:44 min [INFO] Finished at: 2020-12-02T19:39:33-08:00 [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/adamTestMvncIb5npe OpenJDK 64-Bit Server VM warning: ignoring option MaxPermSize=1g; support was removed in 8.0 [INFO] Scanning for projects... [INFO] ------------------------------------------------------------------------ [INFO] Reactor Build Order: [INFO] [INFO] ADAM_2.12 [pom] [INFO] ADAM_2.12: Shader workaround [jar] [INFO] ADAM_2.12: Avro-to-Dataset codegen utils [jar] [INFO] ADAM_2.12: Core [jar] [INFO] ADAM_2.12: APIs for Java, Python [jar] [INFO] ADAM_2.12: CLI [jar] [INFO] ADAM_2.12: Assembly [jar] [INFO] ADAM_2.12: Distribution [pom] [INFO] [INFO] ------------< org.bdgenomics.adam:adam-parent-spark3_2.12 >------------- [INFO] Building ADAM_2.12 0.33.0-SNAPSHOT [1/8] [INFO] --------------------------------[ pom ]--------------------------------- Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/plugins/maven-source-plugin/3.0.1/maven-source-plugin-3.0.1.pom Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/maven/plugins/maven-source-plugin/3.0.1/maven-source-plugin-3.0.1.pom (0 B at 0 B/s) Downloading from central: 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