Started by upstream project "avocado-prb" build number 213 originally caused by: GitHub pull request #250 of commit 6234a49a85794509a5f250329c5172e320b790df automatically merged. [EnvInject] - Loading node environment variables. Building remotely on amp-jenkins-worker-01 (spark-packaging spark-compile spark-experimental-docker spark-release spark-docs centos) in workspace /home/jenkins/workspace/avocado-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos > git rev-parse --is-inside-work-tree # timeout=10 Fetching changes from the remote Git repository > git config remote.origin.url https://github.com/bigdatagenomics/avocado.git # timeout=10 Fetching upstream changes from https://github.com/bigdatagenomics/avocado.git > git --version # timeout=10 > git fetch --tags --progress https://github.com/bigdatagenomics/avocado.git +refs/pull/*:refs/remotes/origin/pr/* Checking out Revision 417f88eac88514c4864bac92b8aad89368784402 (origin/pr/250/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f 417f88eac88514c4864bac92b8aad89368784402 > git rev-list f07e918345ca6edd9088dd5e8c6e8c859cd0c18e # timeout=10 First time build. Skipping changelog. [centos] $ /bin/bash /tmp/hudson1060648124192992435.sh + set -e + export JAVA_HOME=/usr/java/jdk1.8.0_60 + JAVA_HOME=/usr/java/jdk1.8.0_60 + export CONDA_BIN=/home/anaconda/bin/ + CONDA_BIN=/home/anaconda/bin/ + export MVN_BIN=/home/jenkins/tools/hudson.tasks.Maven_MavenInstallation/Maven_3.1.1/bin/ + MVN_BIN=/home/jenkins/tools/hudson.tasks.Maven_MavenInstallation/Maven_3.1.1/bin/ + export PATH=/usr/java/jdk1.8.0_60/bin/:/home/jenkins/tools/hudson.tasks.Maven_MavenInstallation/Maven_3.1.1/bin/:/home/anaconda/bin/:/usr/sbin:/home/jenkins/.cargo/bin:/home/anaconda/bin:/home/jenkins/tools/hudson.tasks.Maven_MavenInstallation/Maven_3.1.1/bin/:/home/android-sdk/:/usr/local/bin:/bin:/usr/bin + PATH=/usr/java/jdk1.8.0_60/bin/:/home/jenkins/tools/hudson.tasks.Maven_MavenInstallation/Maven_3.1.1/bin/:/home/anaconda/bin/:/usr/sbin:/home/jenkins/.cargo/bin:/home/anaconda/bin:/home/jenkins/tools/hudson.tasks.Maven_MavenInstallation/Maven_3.1.1/bin/:/home/android-sdk/:/usr/local/bin:/bin:/usr/bin + set +x + /home/jenkins/workspace/avocado-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/scripts/jenkins-test # make a tempdir for writing maven cruft to AVOCADO_MVN_TMP_DIR=$(mktemp -d -t avocadoTestMvnXXXXXXX) ++ mktemp -d -t avocadoTestMvnXXXXXXX + AVOCADO_MVN_TMP_DIR=/tmp/avocadoTestMvn1AeakLO # add this tempdir to the poms... find . -name pom.xml \ -exec sed -i.bak \ -e "s:sun.io.serialization.extendedDebugInfo=true:sun.io.serialization.extendedDebugInfo=true -Djava.io.tmpdir=${AVOCADO_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/avocadoTestMvn1AeakLO: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/jdk1.8.0_60/bin/:/usr/java/jdk1.8.0_60/bin/:/home/jenkins/tools/hudson.tasks.Maven_MavenInstallation/Maven_3.1.1/bin/:/home/anaconda/bin/:/usr/sbin:/home/jenkins/.cargo/bin:/home/anaconda/bin:/home/jenkins/tools/hudson.tasks.Maven_MavenInstallation/Maven_3.1.1/bin/:/home/android-sdk/:/usr/local/bin:/bin:/usr/bin + PATH=/usr/java/jdk1.8.0_60/bin/:/usr/java/jdk1.8.0_60/bin/:/home/jenkins/tools/hudson.tasks.Maven_MavenInstallation/Maven_3.1.1/bin/:/home/anaconda/bin/:/usr/sbin:/home/jenkins/.cargo/bin:/home/anaconda/bin:/home/jenkins/tools/hudson.tasks.Maven_MavenInstallation/Maven_3.1.1/bin/:/home/android-sdk/:/usr/local/bin:/bin:/usr/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 ${BASH_SOURCE[0]} ) && pwd ) +++ dirname /home/jenkins/workspace/avocado-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/scripts/jenkins-test ++ cd /home/jenkins/workspace/avocado-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/scripts ++ pwd + DIR=/home/jenkins/workspace/avocado-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/scripts PROJECT_ROOT=${DIR}/.. + PROJECT_ROOT=/home/jenkins/workspace/avocado-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/scripts/.. VERSION=$(grep "<version>" ${PROJECT_ROOT}/pom.xml | head -2 | tail -1 | sed 's/ *<version>//g' | sed 's/<\/version>//g') ++ grep '<version>' /home/jenkins/workspace/avocado-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/scripts/../pom.xml ++ head -2 ++ tail -1 ++ sed 's/ *<version>//g' ++ sed 's/<\/version>//g' + VERSION=0.0.3-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 2.6.0 ]] # is the spark version set? if ! [[ ${SPARK_VERSION} ]]; then echo "SPARK_VERSION environment variable is not set." echo "Please set this variable before running." exit 1 fi + [[ -n 2.0.0 ]] # this next line is supposed to fail set +e + set +e echo "Rewriting POM.xml files to Scala 2.10 and Spark 1 should error..." + echo 'Rewriting POM.xml files to Scala 2.10 and Spark 1 should error...' Rewriting POM.xml files to Scala 2.10 and Spark 1 should error... ./scripts/move_to_spark_1.sh + ./scripts/move_to_spark_1.sh POM is already set up for Spark 1 (Spark 1/2 artifacts are missing -spark2 suffix in artifact names). Cowardly refusing to move to Spark 1 a second time... if [[ $? == 0 ]]; then echo "Running move_to_spark_1.sh when POMs are set up for Spark 1 should fail, but error code was 0 (success)." exit 1 fi + [[ 1 == 0 ]] ./scripts/move_to_scala_2.10.sh + ./scripts/move_to_scala_2.10.sh Scala version is already set to 2.10 (Scala artifacts have _2.10 version suffix in artifact name). Cowardly refusing to move to Scala 2.10 a second time... if [[ $? == 0 ]]; then echo "Running move_to_scala_2.10.sh when POMs are set up for Scala 2.10 should fail, but error code was 0 (success)." exit 1 fi + [[ 1 == 0 ]] set -e + set -e # are we testing for spark 2.0.0? if so, we need to rewrite our poms first if [ ${SPARK_VERSION} == 2.0.0 ]; then echo "Rewriting POM.xml files for Spark 2." ./scripts/move_to_spark_2.sh # shouldn't be able to move to spark 2 twice set +e ./scripts/move_to_spark_2.sh if [[ $? == 0 ]]; then echo "We have already moved to Spark 2, so running move_to_spark_2.sh a second time should fail, but error code was 0 (success)." exit 1 fi set -e fi + '[' 2.0.0 == 2.0.0 ']' + echo 'Rewriting POM.xml files for Spark 2.' Rewriting POM.xml files for Spark 2. + ./scripts/move_to_spark_2.sh + set +e + ./scripts/move_to_spark_2.sh POM is already set up for Spark 2 (Spark 1/2 artifacts have -spark2 suffix in artifact names). Cowardly refusing to move to Spark 2 a second time... + [[ 1 == 0 ]] + set -e # are we testing for scala 2.11? if so, we need to rewrite our poms to 2.11 first if [ ${SCALAVER} == 2.11 ]; then echo "Rewriting POM.xml files for Scala 2.11." ./scripts/move_to_scala_2.11.sh # shouldn't be able to move to scala 2.11 twice set +e ./scripts/move_to_scala_2.11.sh if [[ $? == 0 ]]; then echo "We have already moved to Scala 2.11, so running move_to_scala_2.11.sh a second time should fail, but error code was 0 (success)." exit 1 fi set -e fi + '[' 2.11 == 2.11 ']' + echo 'Rewriting POM.xml files for Scala 2.11.' Rewriting POM.xml files for Scala 2.11. + ./scripts/move_to_scala_2.11.sh + set +e + ./scripts/move_to_scala_2.11.sh Scala version is already set to 2.11 (Scala artifacts have _2.11 version suffix in artifact name). Cowardly refusing to move to Scala 2.11 a second time... + [[ 1 == 0 ]] + set -e # print versions echo "Testing AVOCADO version ${VERSION} on Spark ${SPARK_VERSION} and Hadoop ${HADOOP_VERSION}" + echo 'Testing AVOCADO version 0.0.3-SNAPSHOT on Spark 2.0.0 and Hadoop 2.6.0' Testing AVOCADO version 0.0.3-SNAPSHOT on Spark 2.0.0 and Hadoop 2.6.0 # first, build the sources, run the unit tests, and generate a coverage report mvn clean \ -Dhadoop.version=${HADOOP_VERSION} \ -Dspark.version=${SPARK_VERSION} + mvn clean -Dhadoop.version=2.6.0 -Dspark.version=2.0.0 Java HotSpot(TM) 64-Bit Server VM warning: ignoring option MaxPermSize=1g; support was removed in 8.0 [INFO] Scanning for projects... [WARNING] [WARNING] Some problems were encountered while building the effective model for org.bdgenomics.avocado:avocado-core-spark2_2.11:jar:0.0.3-SNAPSHOT [WARNING] 'build.plugins.plugin.version' for org.apache.maven.plugins:maven-jar-plugin is missing. @ line 66, column 15 [WARNING] 'dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '*' does not match a valid id pattern. @ line 134, column 23 [WARNING] 'dependencyManagement.dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '*' does not match a valid id pattern. @ org.bdgenomics.avocado:avocado-parent-spark2_2.11:0.0.3-SNAPSHOT, /home/jenkins/workspace/avocado-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/pom.xml, line 336, column 25 [WARNING] 'dependencyManagement.dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '*' does not match a valid id pattern. @ org.bdgenomics.avocado:avocado-parent-spark2_2.11:0.0.3-SNAPSHOT, /home/jenkins/workspace/avocado-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/pom.xml, line 340, column 25 [WARNING] 'dependencyManagement.dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '*' does not match a valid id pattern. @ org.bdgenomics.avocado:avocado-parent-spark2_2.11:0.0.3-SNAPSHOT, /home/jenkins/workspace/avocado-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/pom.xml, line 344, column 25 [WARNING] [WARNING] Some problems were encountered while building the effective model for org.bdgenomics.avocado:avocado-cli-spark2_2.11:jar:0.0.3-SNAPSHOT [WARNING] 'dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '*' does not match a valid id pattern. @ line 176, column 23 [WARNING] 'dependencyManagement.dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '*' does not match a valid id pattern. @ org.bdgenomics.avocado:avocado-parent-spark2_2.11:0.0.3-SNAPSHOT, /home/jenkins/workspace/avocado-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/pom.xml, line 336, column 25 [WARNING] 'dependencyManagement.dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '*' does not match a valid id pattern. @ org.bdgenomics.avocado:avocado-parent-spark2_2.11:0.0.3-SNAPSHOT, /home/jenkins/workspace/avocado-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/pom.xml, line 340, column 25 [WARNING] 'dependencyManagement.dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '*' does not match a valid id pattern. @ org.bdgenomics.avocado:avocado-parent-spark2_2.11:0.0.3-SNAPSHOT, /home/jenkins/workspace/avocado-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/pom.xml, line 344, column 25 [WARNING] [WARNING] Some problems were encountered while building the effective model for org.bdgenomics.avocado:avocado-parent-spark2_2.11:pom:0.0.3-SNAPSHOT [WARNING] 'dependencyManagement.dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '*' does not match a valid id pattern. @ line 336, column 25 [WARNING] 'dependencyManagement.dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '*' does not match a valid id pattern. @ line 340, column 25 [WARNING] 'dependencyManagement.dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '*' does not match a valid id pattern. @ line 344, column 25 [WARNING] [WARNING] It is highly recommended to fix these problems because they threaten the stability of your build. [WARNING] [WARNING] For this reason, future Maven versions might no longer support building such malformed projects. [WARNING] [INFO] ------------------------------------------------------------------------ [INFO] Reactor Build Order: [INFO] [INFO] avocado: A Variant Caller, Distributed [INFO] avocado-core: Core variant calling algorithms [INFO] avocado-cli: Command line interface for a distributed variant caller [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building avocado: A Variant Caller, Distributed 0.0.3-SNAPSHOT [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-clean-plugin:2.5:clean (default-clean) @ avocado-parent-spark2_2.11 --- [INFO] Deleting /home/jenkins/workspace/avocado-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/target [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building avocado-core: Core variant calling algorithms 0.0.3-SNAPSHOT [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-clean-plugin:2.5:clean (default-clean) @ avocado-core-spark2_2.11 --- [INFO] Deleting /home/jenkins/workspace/avocado-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/avocado-core/target [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building avocado-cli: Command line interface for a distributed variant caller 0.0.3-SNAPSHOT [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-clean-plugin:2.5:clean (default-clean) @ avocado-cli-spark2_2.11 --- [INFO] Deleting /home/jenkins/workspace/avocado-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/avocado-cli/target [INFO] ------------------------------------------------------------------------ [INFO] Reactor Summary: [INFO] [INFO] avocado: A Variant Caller, Distributed ............ SUCCESS [0.119s] [INFO] avocado-core: Core variant calling algorithms ..... SUCCESS [0.089s] [INFO] avocado-cli: Command line interface for a distributed variant caller SUCCESS [0.040s] [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ [INFO] Total time: 0.408s [INFO] Finished at: Thu Oct 12 09:07:33 PDT 2017 [INFO] Final Memory: 19M/1472M [INFO] ------------------------------------------------------------------------ # if this is a pull request, we need to set the coveralls pr id if [[ ! -z $ghprbPullId ]]; then COVERALLS_PRB_OPTION="-DpullRequest=${ghprbPullId}" fi + [[ ! -z 250 ]] + COVERALLS_PRB_OPTION=-DpullRequest=250 # coveralls token should not be visible set +x +v + set +x +v Java HotSpot(TM) 64-Bit Server VM warning: ignoring option MaxPermSize=1g; support was removed in 8.0 [INFO] Scanning for projects... [WARNING] [WARNING] Some problems were encountered while building the effective model for org.bdgenomics.avocado:avocado-core-spark2_2.11:jar:0.0.3-SNAPSHOT [WARNING] 'build.plugins.plugin.version' for org.apache.maven.plugins:maven-jar-plugin is missing. @ line 66, column 15 [WARNING] 'dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '*' does not match a valid id pattern. @ line 134, column 23 [WARNING] 'dependencyManagement.dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '*' does not match a valid id pattern. @ org.bdgenomics.avocado:avocado-parent-spark2_2.11:0.0.3-SNAPSHOT, /home/jenkins/workspace/avocado-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/pom.xml, line 336, column 25 [WARNING] 'dependencyManagement.dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '*' does not match a valid id pattern. @ org.bdgenomics.avocado:avocado-parent-spark2_2.11:0.0.3-SNAPSHOT, /home/jenkins/workspace/avocado-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/pom.xml, line 340, column 25 [WARNING] 'dependencyManagement.dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '*' does not match a valid id pattern. @ org.bdgenomics.avocado:avocado-parent-spark2_2.11:0.0.3-SNAPSHOT, /home/jenkins/workspace/avocado-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/pom.xml, line 344, column 25 [WARNING] [WARNING] Some problems were encountered while building the effective model for org.bdgenomics.avocado:avocado-cli-spark2_2.11:jar:0.0.3-SNAPSHOT [WARNING] 'dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '*' does not match a valid id pattern. @ line 176, column 23 [WARNING] 'dependencyManagement.dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '*' does not match a valid id pattern. @ org.bdgenomics.avocado:avocado-parent-spark2_2.11:0.0.3-SNAPSHOT, /home/jenkins/workspace/avocado-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/pom.xml, line 336, column 25 [WARNING] 'dependencyManagement.dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '*' does not match a valid id pattern. @ org.bdgenomics.avocado:avocado-parent-spark2_2.11:0.0.3-SNAPSHOT, /home/jenkins/workspace/avocado-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/pom.xml, line 340, column 25 [WARNING] 'dependencyManagement.dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '*' does not match a valid id pattern. @ org.bdgenomics.avocado:avocado-parent-spark2_2.11:0.0.3-SNAPSHOT, /home/jenkins/workspace/avocado-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/pom.xml, line 344, column 25 [WARNING] [WARNING] Some problems were encountered while building the effective model for org.bdgenomics.avocado:avocado-parent-spark2_2.11:pom:0.0.3-SNAPSHOT [WARNING] 'dependencyManagement.dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '*' does not match a valid id pattern. @ line 336, column 25 [WARNING] 'dependencyManagement.dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '*' does not match a valid id pattern. @ line 340, column 25 [WARNING] 'dependencyManagement.dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '*' does not match a valid id pattern. @ line 344, column 25 [WARNING] [WARNING] It is highly recommended to fix these problems because they threaten the stability of your build. [WARNING] [WARNING] For this reason, future Maven versions might no longer support building such malformed projects. [WARNING] [INFO] ------------------------------------------------------------------------ [INFO] Reactor Build Order: [INFO] [INFO] avocado: A Variant Caller, Distributed [INFO] avocado-core: Core variant calling algorithms [INFO] avocado-cli: Command line interface for a distributed variant caller [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building avocado: A Variant Caller, Distributed 0.0.3-SNAPSHOT [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ avocado-parent-spark2_2.11 --- [INFO] [INFO] --- build-helper-maven-plugin:1.10:add-source (add-source) @ avocado-parent-spark2_2.11 --- [INFO] Source directory: /home/jenkins/workspace/avocado-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/src/main/scala added. [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ avocado-parent-spark2_2.11 --- [INFO] Modified 0 of 54 .scala files [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ avocado-parent-spark2_2.11 --- [INFO] No sources to compile [INFO] [INFO] --- build-helper-maven-plugin:1.10:add-test-source (add-test-source) @ avocado-parent-spark2_2.11 --- [INFO] Test Source directory: /home/jenkins/workspace/avocado-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/src/test/scala added. [INFO] [INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ avocado-parent-spark2_2.11 --- [INFO] No sources to compile [INFO] [INFO] >>> scoverage-maven-plugin:1.1.1:report (default-cli) @ avocado-parent-spark2_2.11 >>> [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ avocado-parent-spark2_2.11 --- [INFO] [INFO] --- build-helper-maven-plugin:1.10:add-source (add-source) @ avocado-parent-spark2_2.11 --- [INFO] Source directory: /home/jenkins/workspace/avocado-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/src/main/scala added. [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ avocado-parent-spark2_2.11 --- [INFO] Modified 0 of 54 .scala files [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:pre-compile (default-cli) @ avocado-parent-spark2_2.11 --- [INFO] Skipping SCoverage execution for project with packaging type 'pom' [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ avocado-parent-spark2_2.11 --- [INFO] No sources to compile [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:post-compile (default-cli) @ avocado-parent-spark2_2.11 --- [INFO] [INFO] --- build-helper-maven-plugin:1.10:add-test-source (add-test-source) @ avocado-parent-spark2_2.11 --- [INFO] Test Source directory: /home/jenkins/workspace/avocado-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/src/test/scala added. [INFO] [INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ avocado-parent-spark2_2.11 --- [INFO] No sources to compile [INFO] [INFO] <<< scoverage-maven-plugin:1.1.1:report (default-cli) @ avocado-parent-spark2_2.11 <<< [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:report (default-cli) @ avocado-parent-spark2_2.11 --- [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building avocado-core: Core variant calling algorithms 0.0.3-SNAPSHOT [INFO] ------------------------------------------------------------------------ Downloading: http://people.apache.org/repo/m2-snapshot-repository/org/bdgenomics/adam/adam-core-spark2_2.11/0.23.0-SNAPSHOT/maven-metadata.xml Downloading: http://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/adam/adam-core-spark2_2.11/0.23.0-SNAPSHOT/maven-metadata.xml Downloading: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/adam/adam-core-spark2_2.11/0.23.0-SNAPSHOT/maven-metadata.xml 2/2 KB 2/2 KB 2/2 KB Downloaded: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/adam/adam-core-spark2_2.11/0.23.0-SNAPSHOT/maven-metadata.xml (2 KB at 1.9 KB/sec) Downloaded: http://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/adam/adam-core-spark2_2.11/0.23.0-SNAPSHOT/maven-metadata.xml (2 KB at 1.8 KB/sec) Downloading: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/adam/adam-parent-spark2_2.11/0.23.0-SNAPSHOT/maven-metadata.xml Downloading: http://people.apache.org/repo/m2-snapshot-repository/org/bdgenomics/adam/adam-parent-spark2_2.11/0.23.0-SNAPSHOT/maven-metadata.xml Downloading: http://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/adam/adam-parent-spark2_2.11/0.23.0-SNAPSHOT/maven-metadata.xml 625/625 B 625/625 B 625/625 B Downloaded: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/adam/adam-parent-spark2_2.11/0.23.0-SNAPSHOT/maven-metadata.xml (625 B at 3.4 KB/sec) Downloaded: http://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/adam/adam-parent-spark2_2.11/0.23.0-SNAPSHOT/maven-metadata.xml (625 B at 2.0 KB/sec) Downloading: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/adam/adam-codegen-spark2_2.11/0.23.0-SNAPSHOT/maven-metadata.xml Downloading: http://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/adam/adam-codegen-spark2_2.11/0.23.0-SNAPSHOT/maven-metadata.xml Downloading: http://people.apache.org/repo/m2-snapshot-repository/org/bdgenomics/adam/adam-codegen-spark2_2.11/0.23.0-SNAPSHOT/maven-metadata.xml 2/2 KB 2/2 KB 2/2 KB Downloaded: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/adam/adam-codegen-spark2_2.11/0.23.0-SNAPSHOT/maven-metadata.xml (2 KB at 6.0 KB/sec) Downloaded: http://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/adam/adam-codegen-spark2_2.11/0.23.0-SNAPSHOT/maven-metadata.xml (2 KB at 4.0 KB/sec) [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ avocado-core-spark2_2.11 --- [INFO] [INFO] --- build-helper-maven-plugin:1.10:add-source (add-source) @ avocado-core-spark2_2.11 --- [INFO] Source directory: /home/jenkins/workspace/avocado-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/avocado-core/src/main/scala added. [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ avocado-core-spark2_2.11 --- [INFO] Modified 0 of 45 .scala files [INFO] [INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ avocado-core-spark2_2.11 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/avocado-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/avocado-core/src/main/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ avocado-core-spark2_2.11 --- [WARNING] Expected all dependencies to require Scala version: 2.11.4 [WARNING] org.bdgenomics.utils:utils-misc-spark2_2.11:0.2.11 requires scala version: 2.11.4 [WARNING] org.bdgenomics.utils:utils-metrics-spark2_2.11:0.2.11 requires scala version: 2.11.4 [WARNING] org.bdgenomics.utils:utils-serialization-spark2_2.11:0.2.11 requires scala version: 2.11.4 [WARNING] org.bdgenomics.utils:utils-misc-spark2_2.11:0.2.11 requires scala version: 2.11.4 [WARNING] org.bdgenomics.utils:utils-io-spark2_2.11:0.2.13 requires scala version: 2.11.8 [WARNING] Multiple versions of scala libraries detected! [INFO] /home/jenkins/workspace/avocado-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/avocado-core/src/main/scala:-1: info: compiling [INFO] Compiling 24 source files to /home/jenkins/workspace/avocado-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/avocado-core/target/scala-2.11.4/classes at 1507824462561 [WARNING] warning: there were three deprecation warnings; re-run with -deprecation for details [WARNING] one warning found [INFO] prepare-compile in 0 s [INFO] compile in 10 s [INFO] [INFO] --- maven-compiler-plugin:3.5.1:compile (default-compile) @ avocado-core-spark2_2.11 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- build-helper-maven-plugin:1.10:add-test-source (add-test-source) @ avocado-core-spark2_2.11 --- [INFO] Test Source directory: /home/jenkins/workspace/avocado-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/avocado-core/src/test/scala added. [INFO] [INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ avocado-core-spark2_2.11 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 25 resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ avocado-core-spark2_2.11 --- [WARNING] Expected all dependencies to require Scala version: 2.11.4 [WARNING] org.bdgenomics.utils:utils-misc-spark2_2.11:0.2.11 requires scala version: 2.11.4 [WARNING] org.bdgenomics.utils:utils-metrics-spark2_2.11:0.2.11 requires scala version: 2.11.4 [WARNING] org.bdgenomics.utils:utils-serialization-spark2_2.11:0.2.11 requires scala version: 2.11.4 [WARNING] org.bdgenomics.utils:utils-misc-spark2_2.11:0.2.11 requires scala version: 2.11.4 [WARNING] org.bdgenomics.utils:utils-io-spark2_2.11:0.2.13 requires scala version: 2.11.8 [WARNING] Multiple versions of scala libraries detected! [INFO] /home/jenkins/workspace/avocado-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/avocado-core/src/test/scala:-1: info: compiling [INFO] Compiling 21 source files to /home/jenkins/workspace/avocado-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/avocado-core/target/scala-2.11.4/test-classes at 1507824473038 [INFO] prepare-compile in 0 s [INFO] compile in 15 s [INFO] [INFO] --- maven-compiler-plugin:3.5.1:testCompile (default-testCompile) @ avocado-core-spark2_2.11 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-surefire-plugin:2.7:test (default-test) @ avocado-core-spark2_2.11 --- [INFO] Tests are skipped. [INFO] [INFO] --- scalatest-maven-plugin:1.0:test (test) @ avocado-core-spark2_2.11 --- Discovery starting. Discovery completed in 653 milliseconds. Run starting. Expected test count is: 267 LogPhredSuite: - convert log error probabilities to phred scores TreeRegionJoinSuite: - build a forest with a single item and retrieve data - build a forest with data from a single contig and retrieve data - build a forest with data from multiple contigs and retrieve data 2017-10-12 09:08:10 WARN NativeCodeLoader:62 - Unable to load native-hadoop library for your platform... using builtin-java classes where applicable - build a forest out of data on a single contig and retrieve data - run a join between data on a single contig HardLimiterSuite: - add a read to an empty buffer - add a read to a non-empty buffer, without moving forward - add a read to a non-empty buffer, and move forward - trying to add a read to a full buffer?without moving forward?drops the read - add a read to a full buffer, while moving forward and keeping buffer full - add a read to a full buffer, while moving forward and emptying buffer - adding an out of order read should fire an assert - adding a read that is on the wrong contig should fire an assert - apply hard limiting to an iterator that is wholly under the coverage limit - apply hard limiting to an iterator that is partially under the coverage limit - apply hard limiting to an iterator that is wholly over the coverage limit - apply hard limiting on a file that is wholly under the coverage limit - apply hard limiting on a file with sections over the coverage limit VariantSummarySuite: - create from genotype without strand bias components - create from genotype with strand bias components - invalid strand bias causes exception - merge two fully populated summaries - merge two partially populated summaries - populating an annotation should carry old fields RewriteHetsSuite: - should rewrite a bad het snp - should not rewrite het snp if snp filtering is disabled - should rewrite a bad het indel - should not rewrite het indel if indel filtering is disabled - don't rewrite good het calls - don't rewrite homozygous calls - rewrite a het call as a hom alt snp - processing a valid call should not change the call - if processing is disabled, don't rewrite bad calls - process a bad het snp call - process a bad het indel call - disable processing for a whole rdd - process a whole rdd RealignerSuite: - realignment candidate code needs at least one block - read is not a realignment candidate if it is canonical - read is not a realignment candidate if it is canonical and clipped - read is a realignment candidate if there is at least one non-canonical block - realign an indel that is not left normalized - realign a mnp expressed as a complex indel - realign two snps expressed as a complex indel - align sequence with a complex deletion - realign a read with a complex deletion - realign a read with a snp and deletion separated by a flank - realigning a repetative read will fire an assert - realign a set of reads around an insert - realign a set of reads around a deletion 2017-10-12 09:08:15 WARN Realigner:101 - Realigning A_READ failed with exception java.lang.AssertionError: assertion failed: Input sequence contains a repeat.. - realigning a read with a repeat will return the original read - one sample read should fail due to a repeat, all others should realign HardFilterGenotypesSuite: - filter out reference calls - filter out low quality calls - filter out genotypes for emission - filter out genotypes with a low quality per depth - filter out genotypes with a low depth - filter out genotypes with a high depth - filter out genotypes with a low RMS mapping quality - filter out genotypes with a high strand bias - update genotype where no filters were applied - update genotype where filters were applied and passed - update genotype where filters were applied and failed - discard a ref genotype call - keep a ref genotype call - discard a genotype whose quality is too low *** FAILED *** java.lang.NullPointerException: at org.bdgenomics.avocado.util.HardFilterGenotypes$.filterGenotype(HardFilterGenotypes.scala:642) at org.bdgenomics.avocado.util.HardFilterGenotypesSuite$$anonfun$14.apply$mcV$sp(HardFilterGenotypesSuite.scala:289) at org.bdgenomics.avocado.util.HardFilterGenotypesSuite$$anonfun$14.apply(HardFilterGenotypesSuite.scala:287) at org.bdgenomics.avocado.util.HardFilterGenotypesSuite$$anonfun$14.apply(HardFilterGenotypesSuite.scala:287) at org.scalatest.Transformer$$anonfun$apply$1.apply$mcV$sp(Transformer.scala:22) at org.scalatest.OutcomeOf$class.outcomeOf(OutcomeOf.scala:85) at org.scalatest.OutcomeOf$.outcomeOf(OutcomeOf.scala:104) at org.scalatest.Transformer.apply(Transformer.scala:22) at org.scalatest.Transformer.apply(Transformer.scala:20) at org.scalatest.FunSuiteLike$$anon$1.apply(FunSuiteLike.scala:166) at org.scalatest.Suite$class.withFixture(Suite.scala:1122) at org.scalatest.FunSuite.withFixture(FunSuite.scala:1555) at org.scalatest.FunSuiteLike$class.invokeWithFixture$1(FunSuiteLike.scala:163) at org.scalatest.FunSuiteLike$$anonfun$runTest$1.apply(FunSuiteLike.scala:175) at org.scalatest.FunSuiteLike$$anonfun$runTest$1.apply(FunSuiteLike.scala:175) at org.scalatest.SuperEngine.runTestImpl(Engine.scala:306) at org.scalatest.FunSuiteLike$class.runTest(FunSuiteLike.scala:175) at org.bdgenomics.avocado.util.HardFilterGenotypesSuite.org$scalatest$BeforeAndAfter$$super$runTest(HardFilterGenotypesSuite.scala:52) at org.scalatest.BeforeAndAfter$class.runTest(BeforeAndAfter.scala:200) at org.bdgenomics.avocado.util.HardFilterGenotypesSuite.runTest(HardFilterGenotypesSuite.scala:52) at org.scalatest.FunSuiteLike$$anonfun$runTests$1.apply(FunSuiteLike.scala:208) at org.scalatest.FunSuiteLike$$anonfun$runTests$1.apply(FunSuiteLike.scala:208) at org.scalatest.SuperEngine$$anonfun$traverseSubNodes$1$1.apply(Engine.scala:413) at org.scalatest.SuperEngine$$anonfun$traverseSubNodes$1$1.apply(Engine.scala:401) at scala.collection.immutable.List.foreach(List.scala:381) at org.scalatest.SuperEngine.traverseSubNodes$1(Engine.scala:401) at org.scalatest.SuperEngine.org$scalatest$SuperEngine$$runTestsInBranch(Engine.scala:396) at org.scalatest.SuperEngine.runTestsImpl(Engine.scala:483) at org.scalatest.FunSuiteLike$class.runTests(FunSuiteLike.scala:208) at org.scalatest.FunSuite.runTests(FunSuite.scala:1555) at org.scalatest.Suite$class.run(Suite.scala:1424) at org.scalatest.FunSuite.org$scalatest$FunSuiteLike$$super$run(FunSuite.scala:1555) at org.scalatest.FunSuiteLike$$anonfun$run$1.apply(FunSuiteLike.scala:212) at org.scalatest.FunSuiteLike$$anonfun$run$1.apply(FunSuiteLike.scala:212) at org.scalatest.SuperEngine.runImpl(Engine.scala:545) at org.scalatest.FunSuiteLike$class.run(FunSuiteLike.scala:212) at org.bdgenomics.avocado.util.HardFilterGenotypesSuite.org$scalatest$BeforeAndAfter$$super$run(HardFilterGenotypesSuite.scala:52) at org.scalatest.BeforeAndAfter$class.run(BeforeAndAfter.scala:241) at org.bdgenomics.avocado.util.HardFilterGenotypesSuite.run(HardFilterGenotypesSuite.scala:52) at org.scalatest.Suite$class.callExecuteOnSuite$1(Suite.scala:1492) at org.scalatest.Suite$$anonfun$runNestedSuites$1.apply(Suite.scala:1528) at org.scalatest.Suite$$anonfun$runNestedSuites$1.apply(Suite.scala:1526) at scala.collection.IndexedSeqOptimized$class.foreach(IndexedSeqOptimized.scala:33) at scala.collection.mutable.ArrayOps$ofRef.foreach(ArrayOps.scala:186) at org.scalatest.Suite$class.runNestedSuites(Suite.scala:1526) at org.scalatest.tools.DiscoverySuite.runNestedSuites(DiscoverySuite.scala:29) at org.scalatest.Suite$class.run(Suite.scala:1421) at org.scalatest.tools.DiscoverySuite.run(DiscoverySuite.scala:29) at org.scalatest.tools.SuiteRunner.run(SuiteRunner.scala:55) at org.scalatest.tools.Runner$$anonfun$doRunRunRunDaDoRunRun$3.apply(Runner.scala:2563) at org.scalatest.tools.Runner$$anonfun$doRunRunRunDaDoRunRun$3.apply(Runner.scala:2557) at scala.collection.immutable.List.foreach(List.scala:381) at org.scalatest.tools.Runner$.doRunRunRunDaDoRunRun(Runner.scala:2557) at org.scalatest.tools.Runner$$anonfun$runOptionallyWithPassFailReporter$2.apply(Runner.scala:1044) at org.scalatest.tools.Runner$$anonfun$runOptionallyWithPassFailReporter$2.apply(Runner.scala:1043) at org.scalatest.tools.Runner$.withClassLoaderAndDispatchReporter(Runner.scala:2722) at org.scalatest.tools.Runner$.runOptionallyWithPassFailReporter(Runner.scala:1043) at org.scalatest.tools.Runner$.main(Runner.scala:860) at org.scalatest.tools.Runner.main(Runner.scala) - build filters and apply to snp - build filters and apply to indel - test adding filters - filter out genotypes with a low allelic fraction - filter out genotypes with a high allelic fraction TrioCallerSuite: - cannot have a sample with no record groups - cannot have a sample with discordant sample ids - extract id from a single read group - extract id from multiple read groups - filter an empty site - filter a site with only ref calls - keep a site with a non-ref call - fill in no-calls for site with missing parents - pass through site with odd copy number - confirm call at site where proband and parents are consistent and phase - confirm call at site where proband and parents are consistent but cannot phase - invalidate call at site where proband and parents are inconsistent - end-to-end trio call test BlockSuite: - folding over a match block returns a match operator - an unknown block must have mismatching input sequences - folding over an unknown block returns our function's result AlignerSuite: - aligning a repetative sequence will fire an assert - align a minimally flanked sequence with a snp - align a minimally flanked sequence with a 3 bp mnp - align a minimally flanked sequence with 2 snps separated by 1bp - align a minimally flanked sequence with 2 snps separated by 3bp - align a minimally flanked sequence with a simple insert - align a minimally flanked sequence with a complex insert - align a minimally flanked sequence with a simple deletion - align a minimally flanked sequence that contains a discordant k-mer pair - align a minimally flanked sequence with a complex deletion - align a minimally flanked sequence with 2 snps separated by two matching k-mers - align a minimally flanked sequence with a snp and an indel separated by one matching k-mer - zip and trim short insert - zip and trim short deletion - cut up a sequence that is longer than the k-mer length - cutting up a sequence that is shorter than the k-mer length yields an empty map - cutting up a repeated sequence throws an assert - get no indices if we have no intersection - get correct index for a single intersection - get correct indices for two k-mers in a row - get correct indices for two k-mers separated by a snp - get correct indices for two k-mers separated by an indel - get correct indices for two k-mers whose positions are flipped - fire assert when cutting up repeatitive reads - fire assert when checking negative index pair - a set of a single index pair is concordant - a set with a pair of index pairs is concordant - a set with multiple good index pairs is concordant - a set with a pair of swapped index pairs is discordant - a set with a pair of both con/discordant index pairs is discordant - making blocks from no indices returns a single unknown block - make blocks from a single match between two snps - make blocks from three matches between two snps - make blocks from three matches between two indels, opposite events - make blocks from three matches between two indels, same events - make blocks from matches between snp/indel/snp BiallelicGenotyperSuite: - properly handle haploid genotype state - properly handle diploid genotype state with het call - properly handle triploid genotype state with hom alt call - scoring read that overlaps no variants should return empty observations in variant only mode - score snp in a read with no evidence of the snp - score snp in a read with evidence of the snp - score snp in a read with evidence of the snp, and non-variant bases *** FAILED *** org.bdgenomics.utils.misc.MathUtils.fpEquals(nonRefObservation.alleleLogLikelihoods.apply(0), BiallelicGenotyperSuite.this.os.logL(2, 2, 0.9999, 0.9999), org.bdgenomics.utils.misc.MathUtils.fpEquals$default$3) was false (BiallelicGenotyperSuite.scala:182) org.scalatest.exceptions.TestFailedException: at org.scalatest.Assertions$class.newAssertionFailedException(Assertions.scala:500) at org.scalatest.FunSuite.newAssertionFailedException(FunSuite.scala:1555) at org.scalatest.Assertions$AssertionsHelper.macroAssert(Assertions.scala:466) at org.bdgenomics.avocado.genotyping.BiallelicGenotyperSuite$$anonfun$7$$anonfun$apply$mcV$sp$1.apply(BiallelicGenotyperSuite.scala:182) at org.bdgenomics.avocado.genotyping.BiallelicGenotyperSuite$$anonfun$7$$anonfun$apply$mcV$sp$1.apply(BiallelicGenotyperSuite.scala:171) at scala.collection.immutable.List.foreach(List.scala:381) at org.bdgenomics.avocado.genotyping.BiallelicGenotyperSuite$$anonfun$7.apply$mcV$sp(BiallelicGenotyperSuite.scala:171) at org.bdgenomics.utils.misc.SparkFunSuite$$anonfun$sparkTest$1.apply$mcV$sp(SparkFunSuite.scala:102) at org.bdgenomics.utils.misc.SparkFunSuite$$anonfun$sparkTest$1.apply(SparkFunSuite.scala:98) at org.bdgenomics.utils.misc.SparkFunSuite$$anonfun$sparkTest$1.apply(SparkFunSuite.scala:98) at org.scalatest.Transformer$$anonfun$apply$1.apply$mcV$sp(Transformer.scala:22) at org.scalatest.OutcomeOf$class.outcomeOf(OutcomeOf.scala:85) at org.scalatest.OutcomeOf$.outcomeOf(OutcomeOf.scala:104) at org.scalatest.Transformer.apply(Transformer.scala:22) at org.scalatest.Transformer.apply(Transformer.scala:20) at org.scalatest.FunSuiteLike$$anon$1.apply(FunSuiteLike.scala:166) at org.scalatest.Suite$class.withFixture(Suite.scala:1122) at org.scalatest.FunSuite.withFixture(FunSuite.scala:1555) at org.scalatest.FunSuiteLike$class.invokeWithFixture$1(FunSuiteLike.scala:163) at org.scalatest.FunSuiteLike$$anonfun$runTest$1.apply(FunSuiteLike.scala:175) at org.scalatest.FunSuiteLike$$anonfun$runTest$1.apply(FunSuiteLike.scala:175) at org.scalatest.SuperEngine.runTestImpl(Engine.scala:306) at org.scalatest.FunSuiteLike$class.runTest(FunSuiteLike.scala:175) at org.bdgenomics.avocado.genotyping.BiallelicGenotyperSuite.org$scalatest$BeforeAndAfter$$super$runTest(BiallelicGenotyperSuite.scala:43) at org.scalatest.BeforeAndAfter$class.runTest(BeforeAndAfter.scala:200) at org.bdgenomics.avocado.genotyping.BiallelicGenotyperSuite.runTest(BiallelicGenotyperSuite.scala:43) at org.scalatest.FunSuiteLike$$anonfun$runTests$1.apply(FunSuiteLike.scala:208) at org.scalatest.FunSuiteLike$$anonfun$runTests$1.apply(FunSuiteLike.scala:208) at org.scalatest.SuperEngine$$anonfun$traverseSubNodes$1$1.apply(Engine.scala:413) at org.scalatest.SuperEngine$$anonfun$traverseSubNodes$1$1.apply(Engine.scala:401) at scala.collection.immutable.List.foreach(List.scala:381) at org.scalatest.SuperEngine.traverseSubNodes$1(Engine.scala:401) at org.scalatest.SuperEngine.org$scalatest$SuperEngine$$runTestsInBranch(Engine.scala:396) at org.scalatest.SuperEngine.runTestsImpl(Engine.scala:483) at org.scalatest.FunSuiteLike$class.runTests(FunSuiteLike.scala:208) at org.scalatest.FunSuite.runTests(FunSuite.scala:1555) at org.scalatest.Suite$class.run(Suite.scala:1424) at org.scalatest.FunSuite.org$scalatest$FunSuiteLike$$super$run(FunSuite.scala:1555) at org.scalatest.FunSuiteLike$$anonfun$run$1.apply(FunSuiteLike.scala:212) at org.scalatest.FunSuiteLike$$anonfun$run$1.apply(FunSuiteLike.scala:212) at org.scalatest.SuperEngine.runImpl(Engine.scala:545) at org.scalatest.FunSuiteLike$class.run(FunSuiteLike.scala:212) at org.bdgenomics.avocado.genotyping.BiallelicGenotyperSuite.org$scalatest$BeforeAndAfter$$super$run(BiallelicGenotyperSuite.scala:43) at org.scalatest.BeforeAndAfter$class.run(BeforeAndAfter.scala:241) at org.bdgenomics.avocado.genotyping.BiallelicGenotyperSuite.run(BiallelicGenotyperSuite.scala:43) at org.scalatest.Suite$class.callExecuteOnSuite$1(Suite.scala:1492) at org.scalatest.Suite$$anonfun$runNestedSuites$1.apply(Suite.scala:1528) at org.scalatest.Suite$$anonfun$runNestedSuites$1.apply(Suite.scala:1526) at scala.collection.IndexedSeqOptimized$class.foreach(IndexedSeqOptimized.scala:33) at scala.collection.mutable.ArrayOps$ofRef.foreach(ArrayOps.scala:186) at org.scalatest.Suite$class.runNestedSuites(Suite.scala:1526) at org.scalatest.tools.DiscoverySuite.runNestedSuites(DiscoverySuite.scala:29) at org.scalatest.Suite$class.run(Suite.scala:1421) at org.scalatest.tools.DiscoverySuite.run(DiscoverySuite.scala:29) at org.scalatest.tools.SuiteRunner.run(SuiteRunner.scala:55) at org.scalatest.tools.Runner$$anonfun$doRunRunRunDaDoRunRun$3.apply(Runner.scala:2563) at org.scalatest.tools.Runner$$anonfun$doRunRunRunDaDoRunRun$3.apply(Runner.scala:2557) at scala.collection.immutable.List.foreach(List.scala:381) at org.scalatest.tools.Runner$.doRunRunRunDaDoRunRun(Runner.scala:2557) at org.scalatest.tools.Runner$$anonfun$runOptionallyWithPassFailReporter$2.apply(Runner.scala:1044) at org.scalatest.tools.Runner$$anonfun$runOptionallyWithPassFailReporter$2.apply(Runner.scala:1043) at org.scalatest.tools.Runner$.withClassLoaderAndDispatchReporter(Runner.scala:2722) at org.scalatest.tools.Runner$.runOptionallyWithPassFailReporter(Runner.scala:1043) at org.scalatest.tools.Runner$.main(Runner.scala:860) at org.scalatest.tools.Runner.main(Runner.scala) - build genotype for het snp - force call possible STR/indel !!! IGNORED !!! - log space factorial - fisher test for strand bias 2017-10-12 09:08:21 WARN BiallelicGenotyper:157 - Input RDD is not persisted. Performance may be degraded. 2017-10-12 09:08:28 WARN TaskSetManager:66 - Stage 5 contains a task of very large size (10540 KB). The maximum recommended task size is 100 KB. - discover and call simple SNP 2017-10-12 09:09:37 WARN BiallelicGenotyper:157 - Input RDD is not persisted. Performance may be degraded. 2017-10-12 09:09:43 WARN TaskSetManager:66 - Stage 5 contains a task of very large size (10540 KB). The maximum recommended task size is 100 KB. - discover and call simple SNP and score all sites 2017-10-12 09:10:53 WARN BiallelicGenotyper:157 - Input RDD is not persisted. Performance may be degraded. 2017-10-12 09:11:00 WARN TaskSetManager:66 - Stage 5 contains a task of very large size (10540 KB). The maximum recommended task size is 100 KB. - discover and call short indel 2017-10-12 09:12:10 WARN BiallelicGenotyper:157 - Input RDD is not persisted. Performance may be degraded. 2017-10-12 09:12:18 WARN TaskSetManager:66 - Stage 5 contains a task of very large size (10540 KB). The maximum recommended task size is 100 KB. 2017-10-12 09:12:30 ERROR BiallelicGenotyper:358 - Processing read H06JUADXX130110:1:1109:10925:52628 failed with exception java.lang.StringIndexOutOfBoundsException: String index out of range: 0. Skipping... 2017-10-12 09:12:30 ERROR BiallelicGenotyper:358 - Processing read H06JUADXX130110:1:1116:7369:15293 failed with exception java.lang.StringIndexOutOfBoundsException: String index out of range: 0. Skipping... 2017-10-12 09:12:30 ERROR BiallelicGenotyper:358 - Processing read H06HDADXX130110:2:1115:12347:40533 failed with exception java.lang.StringIndexOutOfBoundsException: String index out of range: 0. Skipping... 2017-10-12 09:12:30 ERROR BiallelicGenotyper:358 - Processing read H06HDADXX130110:1:2110:7844:95190 failed with exception java.lang.StringIndexOutOfBoundsException: String index out of range: 0. Skipping... 2017-10-12 09:12:30 ERROR BiallelicGenotyper:358 - Processing read H06HDADXX130110:1:2203:13041:33390 failed with exception java.lang.StringIndexOutOfBoundsException: String index out of range: 0. Skipping... - discover and call het and hom snps 2017-10-12 09:13:30 WARN Executor:66 - 1 block locks were not released by TID = 202: [rdd_2_0] - score a single read covering a deletion 2017-10-12 09:13:37 WARN TaskSetManager:66 - Stage 7 contains a task of very large size (10540 KB). The maximum recommended task size is 100 KB. - discover and force call hom alt deletion 2017-10-12 09:14:53 WARN TaskSetManager:66 - Stage 7 contains a task of very large size (10540 KB). The maximum recommended task size is 100 KB. - call hom alt AGCCAGTGGACGCCGACCT->A deletion at 1/875159 2017-10-12 09:16:01 WARN BiallelicGenotyper:157 - Input RDD is not persisted. Performance may be degraded. 2017-10-12 09:16:08 WARN TaskSetManager:66 - Stage 5 contains a task of very large size (10540 KB). The maximum recommended task size is 100 KB. - call hom alt TACACACACACACACACACACACACACACAC->T deletion at 1/1777263 2017-10-12 09:17:16 WARN BiallelicGenotyper:157 - Input RDD is not persisted. Performance may be degraded. 2017-10-12 09:17:23 WARN TaskSetManager:66 - Stage 5 contains a task of very large size (10540 KB). The maximum recommended task size is 100 KB. - call hom alt CAG->C deletion at 1/1067596 2017-10-12 09:18:33 WARN BiallelicGenotyper:157 - Input RDD is not persisted. Performance may be degraded. 2017-10-12 09:18:39 WARN TaskSetManager:66 - Stage 5 contains a task of very large size (10540 KB). The maximum recommended task size is 100 KB. - call hom alt C->G snp at 1/877715 2017-10-12 09:19:48 WARN BiallelicGenotyper:157 - Input RDD is not persisted. Performance may be degraded. 2017-10-12 09:19:55 WARN TaskSetManager:66 - Stage 5 contains a task of very large size (10540 KB). The maximum recommended task size is 100 KB. - call hom alt ACAG->A deletion at 1/886049 2017-10-12 09:21:07 WARN BiallelicGenotyper:157 - Input RDD is not persisted. Performance may be degraded. 2017-10-12 09:21:14 WARN TaskSetManager:66 - Stage 5 contains a task of very large size (10540 KB). The maximum recommended task size is 100 KB. - call hom alt GA->CC mnp at 1/889158?9 2017-10-12 09:22:24 WARN BiallelicGenotyper:157 - Input RDD is not persisted. Performance may be degraded. 2017-10-12 09:22:32 WARN TaskSetManager:66 - Stage 14 contains a task of very large size (10540 KB). The maximum recommended task size is 100 KB. - call hom alt C->CCCCT insertion at 1/866511 2017-10-12 09:22:37 WARN BiallelicGenotyper:157 - Input RDD is not persisted. Performance may be degraded. 2017-10-12 09:22:43 WARN TaskSetManager:66 - Stage 5 contains a task of very large size (10540 KB). The maximum recommended task size is 100 KB. - call het ATG->A deletion at 1/905130 2017-10-12 09:23:53 WARN BiallelicGenotyper:157 - Input RDD is not persisted. Performance may be degraded. 2017-10-12 09:24:00 WARN TaskSetManager:66 - Stage 5 contains a task of very large size (10540 KB). The maximum recommended task size is 100 KB. - call het ATG->A deletion at 1/905130 while scoring all sites 2017-10-12 09:25:13 WARN BiallelicGenotyper:157 - Input RDD is not persisted. Performance may be degraded. 2017-10-12 09:25:20 WARN TaskSetManager:66 - Stage 5 contains a task of very large size (10540 KB). The maximum recommended task size is 100 KB. - call het AG->A deletion at 1/907170 2017-10-12 09:26:28 WARN BiallelicGenotyper:157 - Input RDD is not persisted. Performance may be degraded. 2017-10-12 09:26:35 WARN TaskSetManager:66 - Stage 5 contains a task of very large size (10540 KB). The maximum recommended task size is 100 KB. - call het T->G snp at 1/240898 2017-10-12 09:27:45 WARN BiallelicGenotyper:157 - Input RDD is not persisted. Performance may be degraded. 2017-10-12 09:27:51 WARN TaskSetManager:66 - Stage 5 contains a task of very large size (10540 KB). The maximum recommended task size is 100 KB. - make het alt calls at biallelic snp locus 2017-10-12 09:29:01 WARN BiallelicGenotyper:157 - Input RDD is not persisted. Performance may be degraded. 2017-10-12 09:29:07 WARN TaskSetManager:66 - Stage 5 contains a task of very large size (10540 KB). The maximum recommended task size is 100 KB. - call hom alt T->TAAA insertion at 1/4120185 2017-10-12 09:30:17 WARN BiallelicGenotyper:157 - Input RDD is not persisted. Performance may be degraded. 2017-10-12 09:30:22 WARN TaskSetManager:66 - Stage 5 contains a task of very large size (10540 KB). The maximum recommended task size is 100 KB. {"variant": {"contigName": "1", "start": 5274546, "end": 5274551, "names": [], "splitFromMultiAllelic": false, "referenceAllele": "TTATA", "alternateAllele": "T", "quality": null, "filtersApplied": null, "filtersPassed": null, "filtersFailed": [], "annotation": null}, "contigName": "1", "start": 5274546, "end": 5274551, "variantCallingAnnotations": {"filtersApplied": null, "filtersPassed": null, "filtersFailed": [], "downsampled": null, "baseQRankSum": null, "fisherStrandBiasPValue": -0.0, "rmsMapQ": 97.46794, "mapq0Reads": null, "mqRankSum": null, "readPositionRankSum": null, "genotypePriors": [], "genotypePosteriors": [], "vqslod": null, "culprit": null, "attributes": {}}, "sampleId": "NA12878", "sampleDescription": null, "processingDescription": null, "alleles": ["ALT", "OTHER_ALT"], "expectedAlleleDosage": null, "referenceReadDepth": 0, "alternateReadDepth": 17, "readDepth": 38, "minReadDepth": null, "genotypeQuality": 249, "genotypeLikelihoods": [-70.87324901033372, 0.0, 9.157569518503912], "nonReferenceLikelihoods": [0.46526149370831527, 0.0, -0.6073937268968032], "strandBiasComponents": [0, 0, 8, 9], "splitFromMultiAllelic": false, "phased": false, "phaseSetId": null, "phaseQuality": null} {"variant": {"contigName": "1", "start": 5274546, "end": 5274549, "names": [], "splitFromMultiAllelic": false, "referenceAllele": "TTA", "alternateAllele": "T", "quality": null, "filtersApplied": null, "filtersPassed": null, "filtersFailed": [], "annotation": null}, "contigName": "1", "start": 5274546, "end": 5274549, "variantCallingAnnotations": {"filtersApplied": null, "filtersPassed": null, "filtersFailed": [], "downsampled": null, "baseQRankSum": null, "fisherStrandBiasPValue": -0.0, "rmsMapQ": 83.795815, "mapq0Reads": null, "mqRankSum": null, "readPositionRankSum": null, "genotypePriors": [], "genotypePosteriors": [], "vqslod": null, "culprit": null, "attributes": {}}, "sampleId": "NA12878", "sampleDescription": null, "processingDescription": null, "alleles": ["ALT", "OTHER_ALT"], "expectedAlleleDosage": null, "referenceReadDepth": 0, "alternateReadDepth": 23, "readDepth": 38, "minReadDepth": null, "genotypeQuality": 249, "genotypeLikelihoods": [-126.58664682399018, 0.0, 13.440146510587008], "nonReferenceLikelihoods": [0.46526149370831527, 0.0, -0.6073937268968032], "strandBiasComponents": [0, 0, 11, 12], "splitFromMultiAllelic": false, "phased": false, "phaseSetId": null, "phaseQuality": null} - call het alt TTATA,TTA->T insertion at 1/5274547 ObserverSuite: - a fully clipped read will not generate any observations - generate observations for a sequence match under diploid model - generate observations for a read with an insertion under diploid model - generate observations for a read with a deletion under diploid model DiscoveredVariantSuite: - round trip conversion to/from variant DiscoverVariantsSuite: - no variants in unaligned read - no variants in rdd with unaligned read - no variants in read that is a perfect sequence match - no variants in rdd with sequence match reads - find snp in read with a 1bp sequence mismatch - find one snp in reads with 1bp sequence mismatch - find insertion in read - find insertion in reads - find deletion in read - find deletion in reads - find variants in alignment record rdd - break TT->CA mnp into two snps *** FAILED *** optC.isDefined was false (DiscoverVariantsSuite.scala:256) org.scalatest.exceptions.TestFailedException: at org.scalatest.Assertions$class.newAssertionFailedException(Assertions.scala:500) at org.scalatest.FunSuite.newAssertionFailedException(FunSuite.scala:1555) at org.scalatest.Assertions$AssertionsHelper.macroAssert(Assertions.scala:466) at org.bdgenomics.avocado.genotyping.DiscoverVariantsSuite$$anonfun$12.apply$mcV$sp(DiscoverVariantsSuite.scala:256) at org.bdgenomics.avocado.genotyping.DiscoverVariantsSuite$$anonfun$12.apply(DiscoverVariantsSuite.scala:250) at org.bdgenomics.avocado.genotyping.DiscoverVariantsSuite$$anonfun$12.apply(DiscoverVariantsSuite.scala:250) at org.scalatest.Transformer$$anonfun$apply$1.apply$mcV$sp(Transformer.scala:22) at org.scalatest.OutcomeOf$class.outcomeOf(OutcomeOf.scala:85) at org.scalatest.OutcomeOf$.outcomeOf(OutcomeOf.scala:104) at org.scalatest.Transformer.apply(Transformer.scala:22) at org.scalatest.Transformer.apply(Transformer.scala:20) at org.scalatest.FunSuiteLike$$anon$1.apply(FunSuiteLike.scala:166) at org.scalatest.Suite$class.withFixture(Suite.scala:1122) at org.scalatest.FunSuite.withFixture(FunSuite.scala:1555) at org.scalatest.FunSuiteLike$class.invokeWithFixture$1(FunSuiteLike.scala:163) at org.scalatest.FunSuiteLike$$anonfun$runTest$1.apply(FunSuiteLike.scala:175) at org.scalatest.FunSuiteLike$$anonfun$runTest$1.apply(FunSuiteLike.scala:175) at org.scalatest.SuperEngine.runTestImpl(Engine.scala:306) at org.scalatest.FunSuiteLike$class.runTest(FunSuiteLike.scala:175) at org.bdgenomics.avocado.genotyping.DiscoverVariantsSuite.org$scalatest$BeforeAndAfter$$super$runTest(DiscoverVariantsSuite.scala:29) at org.scalatest.BeforeAndAfter$class.runTest(BeforeAndAfter.scala:200) at org.bdgenomics.avocado.genotyping.DiscoverVariantsSuite.runTest(DiscoverVariantsSuite.scala:29) at org.scalatest.FunSuiteLike$$anonfun$runTests$1.apply(FunSuiteLike.scala:208) at org.scalatest.FunSuiteLike$$anonfun$runTests$1.apply(FunSuiteLike.scala:208) at org.scalatest.SuperEngine$$anonfun$traverseSubNodes$1$1.apply(Engine.scala:413) at org.scalatest.SuperEngine$$anonfun$traverseSubNodes$1$1.apply(Engine.scala:401) at scala.collection.immutable.List.foreach(List.scala:381) at org.scalatest.SuperEngine.traverseSubNodes$1(Engine.scala:401) at org.scalatest.SuperEngine.org$scalatest$SuperEngine$$runTestsInBranch(Engine.scala:396) at org.scalatest.SuperEngine.runTestsImpl(Engine.scala:483) at org.scalatest.FunSuiteLike$class.runTests(FunSuiteLike.scala:208) at org.scalatest.FunSuite.runTests(FunSuite.scala:1555) at org.scalatest.Suite$class.run(Suite.scala:1424) at org.scalatest.FunSuite.org$scalatest$FunSuiteLike$$super$run(FunSuite.scala:1555) at org.scalatest.FunSuiteLike$$anonfun$run$1.apply(FunSuiteLike.scala:212) at org.scalatest.FunSuiteLike$$anonfun$run$1.apply(FunSuiteLike.scala:212) at org.scalatest.SuperEngine.runImpl(Engine.scala:545) at org.scalatest.FunSuiteLike$class.run(FunSuiteLike.scala:212) at org.bdgenomics.avocado.genotyping.DiscoverVariantsSuite.org$scalatest$BeforeAndAfter$$super$run(DiscoverVariantsSuite.scala:29) at org.scalatest.BeforeAndAfter$class.run(BeforeAndAfter.scala:241) at org.bdgenomics.avocado.genotyping.DiscoverVariantsSuite.run(DiscoverVariantsSuite.scala:29) at org.scalatest.Suite$class.callExecuteOnSuite$1(Suite.scala:1492) at org.scalatest.Suite$$anonfun$runNestedSuites$1.apply(Suite.scala:1528) at org.scalatest.Suite$$anonfun$runNestedSuites$1.apply(Suite.scala:1526) at scala.collection.IndexedSeqOptimized$class.foreach(IndexedSeqOptimized.scala:33) at scala.collection.mutable.ArrayOps$ofRef.foreach(ArrayOps.scala:186) at org.scalatest.Suite$class.runNestedSuites(Suite.scala:1526) at org.scalatest.tools.DiscoverySuite.runNestedSuites(DiscoverySuite.scala:29) at org.scalatest.Suite$class.run(Suite.scala:1421) at org.scalatest.tools.DiscoverySuite.run(DiscoverySuite.scala:29) at org.scalatest.tools.SuiteRunner.run(SuiteRunner.scala:55) at org.scalatest.tools.Runner$$anonfun$doRunRunRunDaDoRunRun$3.apply(Runner.scala:2563) at org.scalatest.tools.Runner$$anonfun$doRunRunRunDaDoRunRun$3.apply(Runner.scala:2557) at scala.collection.immutable.List.foreach(List.scala:381) at org.scalatest.tools.Runner$.doRunRunRunDaDoRunRun(Runner.scala:2557) at org.scalatest.tools.Runner$$anonfun$runOptionallyWithPassFailReporter$2.apply(Runner.scala:1044) at org.scalatest.tools.Runner$$anonfun$runOptionallyWithPassFailReporter$2.apply(Runner.scala:1043) at org.scalatest.tools.Runner$.withClassLoaderAndDispatchReporter(Runner.scala:2722) at org.scalatest.tools.Runner$.runOptionallyWithPassFailReporter(Runner.scala:1043) at org.scalatest.tools.Runner$.main(Runner.scala:860) at org.scalatest.tools.Runner.main(Runner.scala) ObservationOperatorSuite: - zero operators are empty - non-zero operators are non-empty - cannot build mismatch with wrong ref length - collapsing a non repeated set of operators should eliminate 0 ops - collapsing a repeated set of operators with mixed match/mismatch - collapse a set of operators with repeats - collapse a set of operators with repeats and clips - make a cigar and md tag from a single sequence match - make a cigar and md tag from a single sequence mismatch - make a cigar and md tag from a single multi-base sequence match - make a cigar and md tag from a single deletion - make a cigar and md tag from a single insertion - make a cigar for a match followed by a deletion - make a cigar for an insertion flanked by matches - make a cigar for a match followed by a mismatch - make a cigar for a multi-base mismatch flanked by matches - make a cigar for a match after a clip - make a cigar for a mismatch after a clip - extract reference from a single snp - extract reference from a single deletion - extract reference from a single insertion - extract reference from a soft clipped sequence - extract reference from a hard clipped sequence - extract reference from a match flanked deletion - extract reference from a match flanked insertion - read must be mapped to extract alignment operators - extracting alignment operators will fail if cigar is unset - extracting alignment operators will fail if cigar is * - extracting alignment operators will fail if MD tag is unset - extract alignment operators from a perfect read - extract alignment operators from a read with a single mismatch - extract alignment operators from a read with a single deletion - extract alignment operators from a read with a single insertion LogUtilsSuite: - test our nifty log summer - can we compute the sum of logs correctly? - can we compute the additive inverse of logs correctly? ObservationSuite: - cannot create an observation with empty likelihoods - cannot create an observation with 1-length likelihoods - cannot create an observation with mismatching likelihood lengths - forward strand must be >= 0 - forward strand cannot exceed coverage - square map-q must be >= 0 - coverage is strictly positive - invert an observation - null an observation RealignmentBlockSuite: - folding over a clip returns the clip operator, soft clip - folding over a clip returns the clip operator, hard clip - folding over a canonical block returns the original alignment - violate an invariant of the fold function, part 1 - violate an invariant of the fold function, part 2 - apply the fold function on a realignable block - having a clip in the middle of a read is illegal - can't have two soft clips back to back - a read that is an exact sequence match is canonical - hard clip before soft clip is ok at start of read - hard clip after soft clip is ok at end of read - a read with a single snp is canonical - a read containing an indel with exact flanks is wholly realignable - a read containing an indel with exact flanks is wholly realignable, with soft clipped bases - a read containing an indel with longer flanks can be split into multiple blocks - a read containing an indel with longer flanks on both sides can be split into multiple blocks - properly handle a read that starts with a long soft clip JointAnnotatorCallerSuite: - discard reference site - calculate MAF for all called genotypes - calculate MAF ignoring uncalled genotypes - roll up variant annotations from a single genotype - roll up variant annotations across multiple genotypes - recalling genotypes is a no-op for no calls and complex hets - recall a genotype so that the state changes - allele frequency being outside of (0.0, 1.0) just computes posteriors - compute variant quality from a single genotype - compute variant quality from multiple genotypes PrefilterReadsSuite: - filter on read uniqueness - filter unmapped reads - filter autosomal chromosomes with grc names - filter sex chromosomes with grc names - filter mitochondrial chromosome with a grc names - filter autosomal chromosomes with hg names - filter sex chromosomes with hg names - filter mitochondrial chromosome with a hg names - filter autosomal chromosomes from generator - filter autosomal + sex chromosomes from generator - filter all chromosomes from generator - update a read whose mate is mapped to a filtered contig - filter reads mapped to autosomal chromosomes from generator - filter reads mapped to autosomal + sex chromosomes from generator - filter reads mapped to all chromosomes from generator - filter reads uniquely mapped to autosomal chromosomes from generator - filter reads uniquely mapped to autosomal + sex chromosomes from generator - filter reads uniquely mapped to all chromosomes from generator - filter rdd of reads mapped to autosomal chromosomes from generator - filter rdd of reads mapped to autosomal + sex chromosomes from generator - filter rdd of reads mapped to all chromosomes from generator - filter rdd of reads uniquely mapped to autosomal chromosomes from generator - filter rdd of reads uniquely mapped to autosomal + sex chromosomes from generator - filter rdd of reads uniquely mapped to all chromosomes from generator Run completed in 23 minutes, 30 seconds. Total number of tests run: 267 Suites: completed 21, aborted 0 Tests: succeeded 264, failed 3, canceled 0, ignored 1, pending 0 *** 3 TESTS FAILED *** [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Skipping avocado: A Variant Caller, Distributed [INFO] This project has been banned from the build due to previous failures. [INFO] ------------------------------------------------------------------------ [INFO] ------------------------------------------------------------------------ [INFO] Reactor Summary: [INFO] [INFO] avocado: A Variant Caller, Distributed ............ SUCCESS [3.647s] [INFO] avocado-core: Core variant calling algorithms ..... FAILURE [24:01.235s] [INFO] avocado-cli: Command line interface for a distributed variant caller SKIPPED [INFO] ------------------------------------------------------------------------ [INFO] BUILD FAILURE [INFO] ------------------------------------------------------------------------ [INFO] Total time: 24:05.115s [INFO] Finished at: Thu Oct 12 09:31:40 PDT 2017 [INFO] Final Memory: 34M/1080M [INFO] ------------------------------------------------------------------------ [ERROR] Failed to execute goal org.scalatest:scalatest-maven-plugin:1.0:test (test) on project avocado-core-spark2_2.11: There are test failures -> [Help 1] [ERROR] [ERROR] To see the full stack trace of the errors, re-run Maven with the -e switch. [ERROR] Re-run Maven using the -X switch to enable full debug logging. [ERROR] [ERROR] For more information about the errors and possible solutions, please read the following articles: [ERROR] [Help 1] http://cwiki.apache.org/confluence/display/MAVEN/MojoFailureException [ERROR] [ERROR] After correcting the problems, you can resume the build with the command [ERROR] mvn <goals> -rf :avocado-core-spark2_2.11 Build step 'Execute shell' marked build as failure Recording test results Publishing Scoverage XML and HTML report... null Setting commit status on GitHub for https://github.com/bigdatagenomics/avocado/commit/417f88eac88514c4864bac92b8aad89368784402 Finished: FAILURE