Started by upstream project "ADAM-prb" build number 2989 originally caused by: GitHub pull request #2149 of commit c074a30f0cca50fcb0be7d514f927e6e2d9f0baf automatically merged. [EnvInject] - Loading node environment variables. Building remotely on research-jenkins-worker-07 (research-07 ubuntu) in workspace /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu Wiping out workspace first. Cloning the remote Git repository Cloning repository https://github.com/bigdatagenomics/adam.git > git init /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu # timeout=10 Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git --version # timeout=10 > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/heads/*:refs/remotes/origin/* # timeout=15 > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10 > git config --add remote.origin.fetch +refs/heads/*:refs/remotes/origin/* # timeout=10 > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10 Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/*:refs/remotes/origin/pr/* # timeout=15 Checking out Revision 6ee9ab951e276e23f45f21deb458d206f12d3d36 (origin/pr/2149/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f 6ee9ab951e276e23f45f21deb458d206f12d3d36 > git rev-list 08944b44bddbba2bea95b14b8e9631eb95c0205a # timeout=10 First time build. Skipping changelog. [ubuntu] $ /bin/bash /tmp/hudson3517339808103490652.sh + set -e + unset SPARK_TESTING + export JAVA_HOME=/usr/lib/jvm/java-8-oracle + JAVA_HOME=/usr/lib/jvm/java-8-oracle + export CONDA_BIN=/home/anaconda/bin/ + CONDA_BIN=/home/anaconda/bin/ + export PATH=/usr/lib/jvm/java-8-oracle/bin/:/home/anaconda/bin/:/home/jenkins/gems/bin:/usr/local/go/bin:/home/jenkins/go-projects/bin:/home/jenkins/anaconda2/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games + PATH=/usr/lib/jvm/java-8-oracle/bin/:/home/anaconda/bin/:/home/jenkins/gems/bin:/usr/local/go/bin:/home/jenkins/go-projects/bin:/home/jenkins/anaconda2/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games + set +x + /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/scripts/jenkins-test # make a tempdir for writing maven cruft to ADAM_MVN_TMP_DIR=$(mktemp -d -t adamTestMvnXXXXXXX) mktemp -d -t adamTestMvnXXXXXXX ++ mktemp -d -t adamTestMvnXXXXXXX + ADAM_MVN_TMP_DIR=/tmp/adamTestMvnpjenoa0 # add this tempdir to the poms... find . -name pom.xml \ -exec sed -i.bak \ -e "s:sun.io.serialization.extendedDebugInfo=true:sun.io.serialization.extendedDebugInfo=true -Djava.io.tmpdir=${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/adamTestMvnpjenoa0:g' '{}' ';' find . -name "*.bak" -exec rm -f {} \; + find . -name '*.bak' -exec rm -f '{}' ';' # variable declarations export PATH=${JAVA_HOME}/bin/:${PATH} + export PATH=/usr/lib/jvm/java-8-oracle/bin/:/usr/lib/jvm/java-8-oracle/bin/:/home/anaconda/bin/:/home/jenkins/gems/bin:/usr/local/go/bin:/home/jenkins/go-projects/bin:/home/jenkins/anaconda2/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games + PATH=/usr/lib/jvm/java-8-oracle/bin/:/usr/lib/jvm/java-8-oracle/bin/:/home/anaconda/bin/:/home/jenkins/gems/bin:/usr/local/go/bin:/home/jenkins/go-projects/bin:/home/jenkins/anaconda2/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games export MAVEN_OPTS="-Xmx1536m -XX:MaxPermSize=1g -Dfile.encoding=utf-8" + export 'MAVEN_OPTS=-Xmx1536m -XX:MaxPermSize=1g -Dfile.encoding=utf-8' + MAVEN_OPTS='-Xmx1536m -XX:MaxPermSize=1g -Dfile.encoding=utf-8' DIR=$( cd $( dirname ${BASH_SOURCE[0]} ) && pwd ) cd $( dirname ${BASH_SOURCE[0]} ) && pwd dirname ${BASH_SOURCE[0]} +++ dirname /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/scripts/jenkins-test ++ cd /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/scripts ++ pwd + DIR=/home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/scripts PROJECT_ROOT=${DIR}/.. + PROJECT_ROOT=/home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/scripts/.. VERSION=$(grep "<version>" ${PROJECT_ROOT}/pom.xml | head -2 | tail -1 | sed 's/ *<version>//g' | sed 's/<\/version>//g') grep "<version>" ${PROJECT_ROOT}/pom.xml | head -2 | tail -1 | sed 's/ *<version>//g' | sed 's/<\/version>//g' ++ grep '<version>' /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/scripts/../pom.xml ++ head -2 ++ tail -1 ++ sed 's/ *<version>//g' ++ sed 's/<\/version>//g' + VERSION=0.27.0-SNAPSHOT # is the hadoop version set? if ! [[ ${HADOOP_VERSION} ]]; then echo "HADOOP_VERSION environment variable is not set." echo "Please set this variable before running." exit 1 fi + [[ -n 2.7.5 ]] # is the spark version set? if ! [[ ${SPARK_VERSION} ]]; then echo "SPARK_VERSION environment variable is not set." echo "Please set this variable before running." exit 1 fi + [[ -n 2.4.3 ]] set -e + set -e # build defaults to Scala 2.11 if [ ${SCALAVER} == 2.11 ]; then # shouldn't be able to move to scala 2.11 twice set +e ./scripts/move_to_scala_2.11.sh if [[ $? == 0 ]]; then echo "We have already moved to Scala 2.11, so running move_to_scala_2.11.sh a second time should fail, but error code was 0 (success)." exit 1 fi set -e fi + '[' 2.12 == 2.11 ']' # move to Scala 2.12 if requested if [ ${SCALAVER} == 2.12 ]; then set +e ./scripts/move_to_scala_2.12.sh set -e fi + '[' 2.12 == 2.12 ']' + set +e + ./scripts/move_to_scala_2.12.sh + set -e # print versions echo "Testing ADAM version ${VERSION} on Spark ${SPARK_VERSION} and Hadoop ${HADOOP_VERSION}" + echo 'Testing ADAM version 0.27.0-SNAPSHOT on Spark 2.4.3 and Hadoop 2.7.5' Testing ADAM version 0.27.0-SNAPSHOT on Spark 2.4.3 and Hadoop 2.7.5 # first, build the sources, run the unit tests, and generate a coverage report mvn clean \ -Dhadoop.version=${HADOOP_VERSION} + mvn clean -Dhadoop.version=2.7.5 Java HotSpot(TM) 64-Bit Server VM warning: ignoring option MaxPermSize=1g; support was removed in 8.0 [INFO] Scanning for projects... [INFO] ------------------------------------------------------------------------ [INFO] Reactor Build Order: [INFO] [INFO] ADAM_2.12 [INFO] ADAM_2.12: Shader workaround [INFO] ADAM_2.12: Avro-to-Dataset codegen utils [INFO] ADAM_2.12: Core [INFO] ADAM_2.12: APIs for Java, Python [INFO] ADAM_2.12: CLI [INFO] ADAM_2.12: Assembly [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building ADAM_2.12 0.27.0-SNAPSHOT [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-clean-plugin:3.1.0:clean (default-clean) @ adam-parent-spark2_2.12 --- [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building ADAM_2.12: Shader workaround 0.27.0-SNAPSHOT [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-clean-plugin:3.1.0:clean (default-clean) @ adam-shade-spark2_2.12 --- [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building ADAM_2.12: Avro-to-Dataset codegen utils 0.27.0-SNAPSHOT [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-clean-plugin:3.1.0:clean (default-clean) @ adam-codegen-spark2_2.12 --- [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building ADAM_2.12: Core 0.27.0-SNAPSHOT [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-clean-plugin:3.1.0:clean (default-clean) @ adam-core-spark2_2.12 --- [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building ADAM_2.12: APIs for Java, Python 0.27.0-SNAPSHOT [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-clean-plugin:3.1.0:clean (default-clean) @ adam-apis-spark2_2.12 --- [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building ADAM_2.12: CLI 0.27.0-SNAPSHOT [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-clean-plugin:3.1.0:clean (default-clean) @ adam-cli-spark2_2.12 --- [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building ADAM_2.12: Assembly 0.27.0-SNAPSHOT [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-clean-plugin:3.1.0:clean (default-clean) @ adam-assembly-spark2_2.12 --- [INFO] ------------------------------------------------------------------------ [INFO] Reactor Summary: [INFO] [INFO] ADAM_2.12 .......................................... SUCCESS [ 0.188 s] [INFO] ADAM_2.12: Shader workaround ....................... SUCCESS [ 0.009 s] [INFO] ADAM_2.12: Avro-to-Dataset codegen utils ........... SUCCESS [ 0.006 s] [INFO] ADAM_2.12: Core .................................... SUCCESS [ 0.011 s] [INFO] ADAM_2.12: APIs for Java, Python ................... SUCCESS [ 0.001 s] [INFO] ADAM_2.12: CLI ..................................... SUCCESS [ 0.019 s] [INFO] ADAM_2.12: Assembly ................................ SUCCESS [ 0.002 s] [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ [INFO] Total time: 0.448 s [INFO] Finished at: 2019-05-15T09:53:28-07:00 [INFO] Final Memory: 23M/1472M [INFO] ------------------------------------------------------------------------ # if this is a pull request, we need to set the coveralls pr id if [[ ! -z $ghprbPullId ]]; then COVERALLS_PRB_OPTION="-DpullRequest=${ghprbPullId}" fi + [[ ! -z 2149 ]] + COVERALLS_PRB_OPTION=-DpullRequest=2149 # coveralls token should not be visible set +x +v + set +x +v Java HotSpot(TM) 64-Bit Server VM warning: ignoring option MaxPermSize=1g; support was removed in 8.0 [INFO] Scanning for projects... [INFO] ------------------------------------------------------------------------ [INFO] Reactor Build Order: [INFO] [INFO] ADAM_2.12 [INFO] ADAM_2.12: Shader workaround [INFO] ADAM_2.12: Avro-to-Dataset codegen utils [INFO] ADAM_2.12: Core [INFO] ADAM_2.12: APIs for Java, Python [INFO] ADAM_2.12: CLI [INFO] ADAM_2.12: Assembly [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building ADAM_2.12 0.27.0-SNAPSHOT [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-parent-spark2_2.12 --- [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-parent-spark2_2.12 --- [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ adam-parent-spark2_2.12 --- [INFO] Modified 0 of 239 .scala files [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ adam-parent-spark2_2.12 --- [INFO] No sources to compile [INFO] [INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ adam-parent-spark2_2.12 --- [INFO] No sources to compile [INFO] [INFO] >>> scoverage-maven-plugin:1.1.1:report (default-cli) > [scoverage]test @ adam-parent-spark2_2.12 >>> [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-parent-spark2_2.12 --- [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-parent-spark2_2.12 --- [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ adam-parent-spark2_2.12 --- [INFO] Modified 0 of 239 .scala files [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:pre-compile (default-cli) @ adam-parent-spark2_2.12 --- [INFO] Skipping SCoverage execution for project with packaging type 'pom' [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ adam-parent-spark2_2.12 --- [INFO] No sources to compile [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:post-compile (default-cli) @ adam-parent-spark2_2.12 --- [INFO] [INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ adam-parent-spark2_2.12 --- [INFO] No sources to compile [INFO] [INFO] <<< scoverage-maven-plugin:1.1.1:report (default-cli) < [scoverage]test @ adam-parent-spark2_2.12 <<< [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:report (default-cli) @ adam-parent-spark2_2.12 --- [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building ADAM_2.12: Shader workaround 0.27.0-SNAPSHOT [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-shade-spark2_2.12 --- [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-shade-spark2_2.12 --- [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ adam-shade-spark2_2.12 --- [INFO] Modified 0 of 0 .scala files [INFO] [INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ adam-shade-spark2_2.12 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-shade/src/main/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ adam-shade-spark2_2.12 --- [INFO] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-shade/src/main/java:-1: info: compiling [INFO] Compiling 1 source files to /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-shade/target/2.12.8/classes at 1557939222156 [INFO] prepare-compile in 0 s [INFO] compile in 2 s [INFO] [INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ adam-shade-spark2_2.12 --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 1 source file to /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-shade/target/2.12.8/classes [INFO] [INFO] --- plexus-component-metadata:1.5.5:generate-metadata (default) @ adam-shade-spark2_2.12 --- [INFO] Discovered 1 component descriptors(s) [INFO] [INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ adam-shade-spark2_2.12 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-shade/src/test/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ adam-shade-spark2_2.12 --- [INFO] No sources to compile [INFO] [INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ adam-shade-spark2_2.12 --- [INFO] No sources to compile [INFO] [INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ adam-shade-spark2_2.12 --- [INFO] No tests to run. [INFO] [INFO] >>> scoverage-maven-plugin:1.1.1:report (default-cli) > [scoverage]test @ adam-shade-spark2_2.12 >>> [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-shade-spark2_2.12 --- [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-shade-spark2_2.12 --- [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ adam-shade-spark2_2.12 --- [INFO] Modified 0 of 0 .scala files [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:pre-compile (default-cli) @ adam-shade-spark2_2.12 --- [WARNING] Skipping SCoverage execution - unsupported Scala version "2.12.8" [INFO] [INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ adam-shade-spark2_2.12 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-shade/src/main/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ adam-shade-spark2_2.12 --- [INFO] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-shade/src/main/java:-1: info: compiling [INFO] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-shade/target/generated-sources/annotations:-1: info: compiling [INFO] Compiling 1 source files to /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-shade/target/2.12.8/classes at 1557939225242 [INFO] prepare-compile in 0 s [INFO] compile in 1 s [INFO] [INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ adam-shade-spark2_2.12 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- plexus-component-metadata:1.5.5:generate-metadata (default) @ adam-shade-spark2_2.12 --- [INFO] Discovered 1 component descriptors(s) [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:post-compile (default-cli) @ adam-shade-spark2_2.12 --- [INFO] [INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ adam-shade-spark2_2.12 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-shade/src/test/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ adam-shade-spark2_2.12 --- [INFO] No sources to compile [INFO] [INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ adam-shade-spark2_2.12 --- [INFO] No sources to compile [INFO] [INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ adam-shade-spark2_2.12 --- [INFO] No tests to run. [INFO] Skipping execution of surefire because it has already been run for this configuration [INFO] [INFO] <<< scoverage-maven-plugin:1.1.1:report (default-cli) < [scoverage]test @ adam-shade-spark2_2.12 <<< [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:report (default-cli) @ adam-shade-spark2_2.12 --- [INFO] Skipping SCoverage report generation [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building ADAM_2.12: Avro-to-Dataset codegen utils 0.27.0-SNAPSHOT [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-codegen-spark2_2.12 --- [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-codegen-spark2_2.12 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ adam-codegen-spark2_2.12 --- [INFO] Source directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-codegen/src/main/scala added. [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ adam-codegen-spark2_2.12 --- [INFO] Modified 0 of 4 .scala files [INFO] [INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ adam-codegen-spark2_2.12 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-codegen/src/main/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ adam-codegen-spark2_2.12 --- [INFO] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-codegen/src/main/scala:-1: info: compiling [INFO] Compiling 4 source files to /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-codegen/target/2.12.8/classes at 1557939227514 [WARNING] warning: there were 5 deprecation warnings (since 2.12.0); re-run with -deprecation for details [WARNING] one warning found [INFO] prepare-compile in 0 s [INFO] compile in 4 s [INFO] [INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ adam-codegen-spark2_2.12 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ adam-codegen-spark2_2.12 --- [INFO] Test Source directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-codegen/src/test/scala added. [INFO] [INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ adam-codegen-spark2_2.12 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-codegen/src/test/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ adam-codegen-spark2_2.12 --- [INFO] No sources to compile [INFO] [INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ adam-codegen-spark2_2.12 --- [INFO] No sources to compile [INFO] [INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ adam-codegen-spark2_2.12 --- [INFO] Tests are skipped. [INFO] [INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ adam-codegen-spark2_2.12 --- Discovery starting. Discovery completed in 80 milliseconds. Run starting. Expected test count is: 0 DiscoverySuite: Run completed in 126 milliseconds. Total number of tests run: 0 Suites: completed 1, aborted 0 Tests: succeeded 0, failed 0, canceled 0, ignored 0, pending 0 No tests were executed. [INFO] [INFO] >>> scoverage-maven-plugin:1.1.1:report (default-cli) > [scoverage]test @ adam-codegen-spark2_2.12 >>> [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-codegen-spark2_2.12 --- [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-codegen-spark2_2.12 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ adam-codegen-spark2_2.12 --- [INFO] Source directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-codegen/src/main/scala added. [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ adam-codegen-spark2_2.12 --- [INFO] Modified 0 of 4 .scala files [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:pre-compile (default-cli) @ adam-codegen-spark2_2.12 --- [WARNING] Skipping SCoverage execution - unsupported Scala version "2.12.8" [INFO] [INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ adam-codegen-spark2_2.12 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-codegen/src/main/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ adam-codegen-spark2_2.12 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ adam-codegen-spark2_2.12 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:post-compile (default-cli) @ adam-codegen-spark2_2.12 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ adam-codegen-spark2_2.12 --- [INFO] Test Source directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-codegen/src/test/scala added. [INFO] [INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ adam-codegen-spark2_2.12 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-codegen/src/test/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ adam-codegen-spark2_2.12 --- [INFO] No sources to compile [INFO] [INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ adam-codegen-spark2_2.12 --- [INFO] No sources to compile [INFO] [INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ adam-codegen-spark2_2.12 --- [INFO] Tests are skipped. [INFO] [INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ adam-codegen-spark2_2.12 --- Discovery starting. Discovery completed in 79 milliseconds. Run starting. Expected test count is: 0 DiscoverySuite: Run completed in 121 milliseconds. Total number of tests run: 0 Suites: completed 1, aborted 0 Tests: succeeded 0, failed 0, canceled 0, ignored 0, pending 0 No tests were executed. [INFO] [INFO] <<< scoverage-maven-plugin:1.1.1:report (default-cli) < [scoverage]test @ adam-codegen-spark2_2.12 <<< [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:report (default-cli) @ adam-codegen-spark2_2.12 --- [INFO] Skipping SCoverage report generation [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building ADAM_2.12: Core 0.27.0-SNAPSHOT [INFO] ------------------------------------------------------------------------ Downloading: https://repo.maven.apache.org/maven2/org/bdgenomics/utils/utils-misc-spark2_2.12/0.2.15/utils-misc-spark2_2.12-0.2.15.pom 3/4 KB 4/4 KB Downloaded: https://repo.maven.apache.org/maven2/org/bdgenomics/utils/utils-misc-spark2_2.12/0.2.15/utils-misc-spark2_2.12-0.2.15.pom (4 KB at 18.8 KB/sec) Downloading: https://repo.maven.apache.org/maven2/org/bdgenomics/utils/utils-parent-spark2_2.12/0.2.15/utils-parent-spark2_2.12-0.2.15.pom 3/18 KB 5/18 KB 8/18 KB 11/18 KB 13/18 KB 16/18 KB 18/18 KB Downloaded: https://repo.maven.apache.org/maven2/org/bdgenomics/utils/utils-parent-spark2_2.12/0.2.15/utils-parent-spark2_2.12-0.2.15.pom (18 KB at 1057.4 KB/sec) Downloading: https://repo.maven.apache.org/maven2/org/bdgenomics/utils/utils-metrics-spark2_2.12/0.2.15/utils-metrics-spark2_2.12-0.2.15.pom 3/5 KB 5/5 KB Downloaded: https://repo.maven.apache.org/maven2/org/bdgenomics/utils/utils-metrics-spark2_2.12/0.2.15/utils-metrics-spark2_2.12-0.2.15.pom (5 KB at 410.6 KB/sec) Downloading: https://repo.maven.apache.org/maven2/org/bdgenomics/utils/utils-io-spark2_2.12/0.2.15/utils-io-spark2_2.12-0.2.15.pom 3/5 KB 5/5 KB Downloaded: https://repo.maven.apache.org/maven2/org/bdgenomics/utils/utils-io-spark2_2.12/0.2.15/utils-io-spark2_2.12-0.2.15.pom (5 KB at 370.7 KB/sec) Downloading: https://repo.maven.apache.org/maven2/org/bdgenomics/utils/utils-cli-spark2_2.12/0.2.15/utils-cli-spark2_2.12-0.2.15.pom 3/3 KB 3/3 KB Downloaded: https://repo.maven.apache.org/maven2/org/bdgenomics/utils/utils-cli-spark2_2.12/0.2.15/utils-cli-spark2_2.12-0.2.15.pom (3 KB at 260.9 KB/sec) Downloading: https://repo.maven.apache.org/maven2/org/bdgenomics/utils/utils-intervalrdd-spark2_2.12/0.2.15/utils-intervalrdd-spark2_2.12-0.2.15.pom 3/4 KB 4/4 KB Downloaded: https://repo.maven.apache.org/maven2/org/bdgenomics/utils/utils-intervalrdd-spark2_2.12/0.2.15/utils-intervalrdd-spark2_2.12-0.2.15.pom (4 KB at 345.8 KB/sec) Downloading: https://repo.maven.apache.org/maven2/org/bdgenomics/utils/utils-misc-spark2_2.12/0.2.15/utils-misc-spark2_2.12-0.2.15-tests.jar Downloading: https://repo.maven.apache.org/maven2/org/bdgenomics/utils/utils-misc-spark2_2.12/0.2.15/utils-misc-spark2_2.12-0.2.15.jar Downloading: https://repo.maven.apache.org/maven2/org/bdgenomics/utils/utils-metrics-spark2_2.12/0.2.15/utils-metrics-spark2_2.12-0.2.15.jar Downloading: https://repo.maven.apache.org/maven2/org/bdgenomics/utils/utils-io-spark2_2.12/0.2.15/utils-io-spark2_2.12-0.2.15.jar Downloading: https://repo.maven.apache.org/maven2/org/bdgenomics/utils/utils-cli-spark2_2.12/0.2.15/utils-cli-spark2_2.12-0.2.15.jar 3/29 KB 5/29 KB 8/29 KB 11/29 KB 13/29 KB 16/29 KB 19/29 KB 21/29 KB 24/29 KB 27/29 KB 29/29 KB Downloaded: https://repo.maven.apache.org/maven2/org/bdgenomics/utils/utils-misc-spark2_2.12/0.2.15/utils-misc-spark2_2.12-0.2.15-tests.jar (29 KB at 1506.7 KB/sec) Downloading: https://repo.maven.apache.org/maven2/org/bdgenomics/utils/utils-intervalrdd-spark2_2.12/0.2.15/utils-intervalrdd-spark2_2.12-0.2.15.jar 3/20 KB 6/20 KB 3/15 KB 6/20 KB 5/15 KB 6/20 KB 5/15 KB 9/20 KB 8/15 KB 9/20 KB 3/23 KB 8/15 KB 9/20 KB 3/23 KB 8/15 KB 11/20 KB 3/23 KB 11/15 KB 11/20 KB 5/23 KB 11/15 KB 11/20 KB 5/23 KB 13/15 KB 11/20 KB 5/23 KB 15/15 KB 11/20 KB 8/23 KB 15/15 KB 11/20 KB 8/23 KB 15/15 KB 14/20 KB 11/23 KB 15/15 KB 14/20 KB 11/23 KB 15/15 KB 16/20 KB 13/23 KB 15/15 KB 16/20 KB 16/23 KB 15/15 KB 16/20 KB 16/23 KB 15/15 KB 19/20 KB 19/23 KB 15/15 KB 19/20 KB 19/23 KB 15/15 KB 20/20 KB 21/23 KB 15/15 KB 20/20 KB 23/23 KB 15/15 KB 20/20 KB 3/49 KB 23/23 KB 15/15 KB 20/20 KB 5/49 KB 23/23 KB 15/15 KB 20/20 KB 5/49 KB 23/23 KB 15/15 KB 20/20 KB 3/213 KB 8/49 KB 23/23 KB 15/15 KB 20/20 KB 3/213 KB 8/49 KB 23/23 KB 15/15 KB 20/20 KB 5/213 KB 11/49 KB 23/23 KB 15/15 KB 20/20 KB 5/213 KB 11/49 KB 23/23 KB 15/15 KB 20/20 KB 8/213 KB 13/49 KB 23/23 KB 15/15 KB 20/20 KB 8/213 KB 13/49 KB 23/23 KB 15/15 KB 20/20 KB 11/213 KB 16/49 KB 23/23 KB 20/20 KB 11/213 KB Downloaded: https://repo.maven.apache.org/maven2/org/bdgenomics/utils/utils-misc-spark2_2.12/0.2.15/utils-misc-spark2_2.12-0.2.15.jar (15 KB at 507.1 KB/sec) 16/49 KB 23/23 KB 20/20 KB 13/213 KB 19/49 KB 23/23 KB 20/20 KB 13/213 KB 19/49 KB 23/23 KB 20/20 KB 16/213 KB 21/49 KB 23/23 KB 20/20 KB 16/213 KB 21/49 KB 23/23 KB 20/20 KB 19/213 KB 24/49 KB 23/23 KB 20/20 KB 19/213 KB 24/49 KB 23/23 KB 20/20 KB 21/213 KB 27/49 KB 23/23 KB 20/20 KB 21/213 KB 27/49 KB 23/23 KB 20/20 KB 24/213 KB 29/49 KB 23/23 KB 20/20 KB 24/213 KB 29/49 KB 23/23 KB 20/20 KB 27/213 KB 32/49 KB 23/23 KB 20/20 KB 27/213 KB Downloaded: https://repo.maven.apache.org/maven2/org/bdgenomics/utils/utils-cli-spark2_2.12/0.2.15/utils-cli-spark2_2.12-0.2.15.jar (20 KB at 668.9 KB/sec) 32/49 KB 23/23 KB 29/213 KB 32/49 KB 23/23 KB 32/213 KB 36/49 KB 23/23 KB 32/213 KB 40/49 KB 23/23 KB 32/213 KB 44/49 KB 23/23 KB 32/213 KB 48/49 KB 23/23 KB 32/213 KB 49/49 KB 23/23 KB 32/213 KB 49/49 KB 23/23 KB 36/213 KB 49/49 KB 23/23 KB 40/213 KB 49/49 KB 23/23 KB 44/213 KB 49/49 KB 48/213 KB Downloaded: https://repo.maven.apache.org/maven2/org/bdgenomics/utils/utils-io-spark2_2.12/0.2.15/utils-io-spark2_2.12-0.2.15.jar (23 KB at 740.2 KB/sec) 49/49 KB 52/213 KB 49/49 KB 56/213 KB 49/49 KB 60/213 KB 49/49 KB 64/213 KB 49/49 KB 68/213 KB 49/49 KB 72/213 KB 49/49 KB 76/213 KB 49/49 KB 80/213 KB 49/49 KB 84/213 KB 49/49 KB 88/213 KB 49/49 KB 92/213 KB 96/213 KB Downloaded: https://repo.maven.apache.org/maven2/org/bdgenomics/utils/utils-intervalrdd-spark2_2.12/0.2.15/utils-intervalrdd-spark2_2.12-0.2.15.jar (49 KB at 1414.1 KB/sec) 100/213 KB 104/213 KB 108/213 KB 112/213 KB 116/213 KB 120/213 KB 124/213 KB 128/213 KB 132/213 KB 136/213 KB 140/213 KB 144/213 KB 148/213 KB 152/213 KB 156/213 KB 160/213 KB 164/213 KB 168/213 KB 172/213 KB 176/213 KB 180/213 KB 184/213 KB 188/213 KB 192/213 KB 196/213 KB 200/213 KB 204/213 KB 208/213 KB 212/213 KB 213/213 KB Downloaded: https://repo.maven.apache.org/maven2/org/bdgenomics/utils/utils-metrics-spark2_2.12/0.2.15/utils-metrics-spark2_2.12-0.2.15.jar (213 KB at 4163.8 KB/sec) [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-core-spark2_2.12 --- [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-core-spark2_2.12 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ adam-core-spark2_2.12 --- [INFO] Source directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/main/scala added. [INFO] Source directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/target/generated-sources/src/main/scala added. [INFO] [INFO] --- exec-maven-plugin:1.5.0:java (generate-scala-products) @ adam-core-spark2_2.12 --- SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] [INFO] --- exec-maven-plugin:1.5.0:java (generate-scala-projection-fields) @ adam-core-spark2_2.12 --- SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ adam-core-spark2_2.12 --- [INFO] Modified 2 of 199 .scala files [INFO] [INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ adam-core-spark2_2.12 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/main/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ adam-core-spark2_2.12 --- [INFO] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/main/java:-1: info: compiling [INFO] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/main/scala:-1: info: compiling [INFO] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/target/generated-sources/src/main/scala:-1: info: compiling [INFO] Compiling 136 source files to /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/target/2.12.8/classes at 1557939242835 [WARNING] warning: there were 21 deprecation warnings [WARNING] warning: there were 31 deprecation warnings (since 0.21.0) [WARNING] warning: there was one deprecation warning (since 1.0.6) [WARNING] warning: there were 31 deprecation warnings (since 2.0.0) [WARNING] warning: there was one deprecation warning (since 2.11.0) [WARNING] warning: there were 170 deprecation warnings (since 2.12.0) [WARNING] warning: there was one deprecation warning (since 2.12.7) [WARNING] warning: there were 256 deprecation warnings in total; re-run with -deprecation for details [WARNING] warning: there were 5 feature warnings; re-run with -feature for details [WARNING] 9 warnings found [INFO] prepare-compile in 0 s [INFO] compile in 25 s [INFO] [INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ adam-core-spark2_2.12 --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 6 source files to /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/target/2.12.8/classes [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ adam-core-spark2_2.12 --- [INFO] Test Source directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala added. [INFO] [INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ adam-core-spark2_2.12 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 150 resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ adam-core-spark2_2.12 --- [INFO] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala:-1: info: compiling [INFO] Compiling 69 source files to /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/target/2.12.8/test-classes at 1557939270116 [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/algorithms/consensus/NormalizationUtilsSuite.scala:59: warning: method recordToRichRecord in object RichAlignmentRecord is deprecated (since 0.21.0): Use explicit conversion wherever possible in new development. [WARNING] .build() [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/algorithms/consensus/NormalizationUtilsSuite.scala:61: warning: method richRecordToRecord in object RichAlignmentRecord is deprecated (since 0.21.0): Use explicit conversion wherever possible in new development. [WARNING] val new_cigar = NormalizationUtils.leftAlignIndel(read) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/algorithms/consensus/NormalizationUtilsSuite.scala:66: warning: method richRecordToRecord in object RichAlignmentRecord is deprecated (since 0.21.0): Use explicit conversion wherever possible in new development. [WARNING] assert(RichAlignmentRecord(read).samtoolsCigar.getReadLength === new_cigar.getReadLength) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/AlignmentRecordConverterSuite.scala:171: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] val newSAMRecord = newSAMReader.iterator().dropWhile(r => r.getReadName != readName) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/AlignmentRecordConverterSuite.scala:274: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] .setAlignments(seqAsJavaList(alignments)) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/AlignmentRecordConverterSuite.scala:311: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] .setAlignments(seqAsJavaList(alignments)) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/AlignmentRecordConverterSuite.scala:335: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] val fragment = Fragment.newBuilder().setAlignments(List(record)).build() [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/SAMRecordConverterSuite.scala:54: warning: method getNotPrimaryAlignmentFlag in class SAMRecord is deprecated: see corresponding Javadoc for more information. [WARNING] assert(!testAlignmentRecord.getPrimaryAlignment === testSAMRecord.getNotPrimaryAlignmentFlag) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/SAMRecordConverterSuite.scala:89: warning: method getNotPrimaryAlignmentFlag in class SAMRecord is deprecated: see corresponding Javadoc for more information. [WARNING] assert(!testAlignmentRecord.getPrimaryAlignment === testSAMRecord.getNotPrimaryAlignmentFlag) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/SAMRecordConverterSuite.scala:106: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] val samIter = asScalaIterator(newSAMReader.iterator()) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:53: warning: method extractDictionary in class SAMSequenceDictionaryExtractor is deprecated: see corresponding Javadoc for more information. [WARNING] SequenceDictionary(SAMSequenceDictionaryExtractor.extractDictionary(new File(path))) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:63: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] .alleles(List(Allele.create("A", true), Allele.create("T"))) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:69: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] .alleles(List(Allele.create("A", true), Allele.create("T"), Allele.create("G"))) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:75: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] .alleles(List(Allele.create("A", true), Allele.create("<NON_REF>", false))) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:81: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] .alleles(List(Allele.create("A", true), Allele.create("<CN0>", false))) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:109: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] .alleles(List(Allele.create("A", true), Allele.create("T"))) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:143: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] GenotypeBuilder.create("NA12878", vcb.getAlleles(), genotypeAttributes)) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:154: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] assert(adamGT.getAlleles.sameElements(List(GenotypeAllele.REF, GenotypeAllele.ALT))) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:184: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] assert(adamVariant.variant.getFiltersFailed.sameElements(List("LowMQ"))) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:219: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] assert(adamGT.getVariantCallingAnnotations.getFiltersFailed.sameElements(List("LowMQ"))) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:234: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] assert(htsjdkVC.getAlternateAlleles.sameElements(List(Allele.create("T")))) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:245: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] .setStrandBiasComponents(List(0, 2, 4, 6).map(i => i: java.lang.Integer)) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:246: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] .setAlleles(List(GenotypeAllele.REF, GenotypeAllele.ALT)) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:279: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] .setStrandBiasComponents(List(0, 2).map(i => i: java.lang.Integer)) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:280: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] .setAlleles(List(GenotypeAllele.REF, GenotypeAllele.ALT)) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:298: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] .setStrandBiasComponents(List(0, 2).map(i => i: java.lang.Integer)) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:299: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] .setAlleles(List(GenotypeAllele.REF, GenotypeAllele.ALT)) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:320: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] for ((allele, idx) <- vc.getAlternateAlleles.zipWithIndex) { [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:328: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] val gb = new GenotypeBuilder("NA12878", List(Allele.create("T"), Allele.create("G"))) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:347: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] assert(adamGT1.getAlleles.sameElements(List(GenotypeAllele.ALT, GenotypeAllele.OTHER_ALT))) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:349: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] assert(adamGT1.getGenotypeLikelihoods [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:354: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] assert(adamGT2.getAlleles.sameElements(List(GenotypeAllele.OTHER_ALT, GenotypeAllele.ALT))) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:356: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] assert(adamGT2.getGenotypeLikelihoods [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:380: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] val gb = new GenotypeBuilder("NA12878", List(Allele.create("A", true), Allele.create("A", true))) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:393: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] assert(adamGT.getAlleles.sameElements(List(GenotypeAllele.REF, GenotypeAllele.REF))) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:396: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] assert(adamGT.getNonReferenceLikelihoods [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:421: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] assert(variant.variant.getNames.length === 1) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:433: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] assert(variant.variant.getNames.length === 2) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:543: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] genotypeAttributes)))((bldr, fn) => { [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:693: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] assert(gls(0) < -0.99e-1 && gls(0) > -1.1e-1) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:693: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] assert(gls(0) < -0.99e-1 && gls(0) > -1.1e-1) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:694: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] assert(gls(1) < -0.99e-3 && gls(1) > -1.1e-3) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:694: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] assert(gls(1) < -0.99e-3 && gls(1) > -1.1e-3) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:695: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] assert(gls(2) < -0.99e-6 && gls(2) > -1.1e-6) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:695: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] assert(gls(2) < -0.99e-6 && gls(2) > -1.1e-6) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:714: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] assert(sb(0) === 10) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:715: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] assert(sb(1) === 12) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:716: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] assert(sb(2) === 14) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:717: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] assert(sb(3) === 16) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:762: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] assert(failedFilters(0) === "FAILED_FILTER") [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:776: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] assert(failedFilters(0) === "FAILED_FILTER1") [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:777: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] assert(failedFilters(1) === "FAILED_FILTER2") [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:778: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] assert(failedFilters(2) === "FAILED_FILTER3") [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:930: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] .map(d => d: java.lang.Double)) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:954: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] .map(i => i: java.lang.Integer)) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:962: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] .map(i => i: java.lang.Integer)) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1089: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] .setFiltersFailed(Seq("lowmq")) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1101: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] .setFiltersFailed(Seq("lowmq", "lowdp")) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1195: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] assert(v.getNames.length === 1) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1205: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] assert(v.getNames.length === 2) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1262: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] vcb.filters(Set("FAILED1", "FAILED2", "FAILED3")) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1267: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] val failedSet = v.getFiltersFailed.toSet [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1285: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] .setNames(Seq("name")) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1295: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] .setNames(Seq("name1", "name2")) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1364: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] .setFiltersFailed(Seq("FAILED")) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1378: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] .setFiltersFailed(Seq("FAILED1", "FAILED2")) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1493: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] 10).map(i => i: java.lang.Integer) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1501: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] 10, 13, 16).map(i => i: java.lang.Integer) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1516: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] 0.1f).map(i => i: java.lang.Float) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1523: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] val acList: java.util.List[String] = List("+Inf") [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1530: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] val acList: java.util.List[String] = List("-Inf") [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1538: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] 0.1f, 0.01f, 0.001f).map(i => i: java.lang.Float) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1552: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] val acList: java.util.List[String] = List("10D90M") [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1559: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] val acList: java.util.List[String] = List("10D90M", "100M", "90M10D") [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1575: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] 5, 10).map(i => i: java.lang.Integer) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1584: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] 5, 10, 13, 16).map(i => i: java.lang.Integer) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1601: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] 5, 10).map(i => i: java.lang.Integer) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1610: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] 5, 10, 13, 16).map(i => i: java.lang.Integer) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1627: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] 5, 10).map(i => i: java.lang.Integer) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1636: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] 5, 10, 13, 16).map(i => i: java.lang.Integer) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:2436: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] Map[String, java.lang.Object](("ONE_INT", "42"))) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:2459: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] Map[String, java.lang.Object](("FOUR_INTS", "5,10,15,20"))) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:2482: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] Map[String, java.lang.Object](("FOUR_FLOATS", "5.0,10.1,15.2,20.3"))) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:2505: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] Map[String, java.lang.Object](("A_INT", "10,15,20"))) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:2528: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] Map[String, java.lang.Object](("R_INT", "5,10,15,20"))) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:2551: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] Map[String, java.lang.Object](("R_STRING", "foo,bar,baz"))) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:2574: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] Map[String, java.lang.Object](("STRING_G", "foo,bar,baz"))) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/models/CoverageSuite.scala:37: warning: variable start in class Feature is deprecated: see corresponding Javadoc for more information. [WARNING] assert(coverageAfterConversion.start == featureToConvert.start) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/models/CoverageSuite.scala:38: warning: variable end in class Feature is deprecated: see corresponding Javadoc for more information. [WARNING] assert(coverageAfterConversion.end == featureToConvert.end) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/models/CoverageSuite.scala:40: warning: variable score in class Feature is deprecated: see corresponding Javadoc for more information. [WARNING] assert(coverageAfterConversion.count == featureToConvert.score) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/models/CoverageSuite.scala:57: warning: variable start in class Feature is deprecated: see corresponding Javadoc for more information. [WARNING] assert(coverageAfterConversion.start == featureToConvert.start) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/models/CoverageSuite.scala:58: warning: variable end in class Feature is deprecated: see corresponding Javadoc for more information. [WARNING] assert(coverageAfterConversion.end == featureToConvert.end) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/models/CoverageSuite.scala:60: warning: variable score in class Feature is deprecated: see corresponding Javadoc for more information. [WARNING] assert(coverageAfterConversion.count == featureToConvert.score) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/models/CoverageSuite.scala:61: warning: variable sampleId in class Feature is deprecated: see corresponding Javadoc for more information. [WARNING] assert(coverageAfterConversion.optSampleId == Some(featureToConvert.sampleId)) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/models/MdTagSuite.scala:194: warning: method recordToRichRecord in object RichAlignmentRecord is deprecated (since 0.21.0): Use explicit conversion wherever possible in new development. [WARNING] assert(read.mdTag.get.end === read.getEnd) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/models/MdTagSuite.scala:475: warning: method recordToRichRecord in object RichAlignmentRecord is deprecated (since 0.21.0): Use explicit conversion wherever possible in new development. [WARNING] val tag = read.mdTag.get [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/models/MdTagSuite.scala:482: warning: method recordToRichRecord in object RichAlignmentRecord is deprecated (since 0.21.0): Use explicit conversion wherever possible in new development. [WARNING] assert(tag.getReference(read) === "AAAAAAAAAAAAAAAAAAAAAAAAAAAAAGGGGGGGGGGAAAAAAAAAAGGGGGGGGGGAAAAAAAAAAA") [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/models/MdTagSuite.scala:495: warning: method recordToRichRecord in object RichAlignmentRecord is deprecated (since 0.21.0): Use explicit conversion wherever possible in new development. [WARNING] val tag = read.mdTag.get [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/models/MdTagSuite.scala:496: warning: method recordToRichRecord in object RichAlignmentRecord is deprecated (since 0.21.0): Use explicit conversion wherever possible in new development. [WARNING] assert(tag.getReference(read, withGaps = true) === "AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGGGGGGGGGGAAAAAAAAAAA") [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/models/MdTagSuite.scala:510: warning: method recordToRichRecord in object RichAlignmentRecord is deprecated (since 0.21.0): Use explicit conversion wherever possible in new development. [WARNING] val newTag = MdTag.moveAlignment(read, newCigar) [WARNING] ^ [WARNING] 211 warnings found [INFO] prepare-compile in 0 s [INFO] compile in 27 s [INFO] [INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ adam-core-spark2_2.12 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ adam-core-spark2_2.12 --- [INFO] Tests are skipped. [INFO] [INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ adam-core-spark2_2.12 --- Discovery starting. Discovery completed in 1 second, 568 milliseconds. Run starting. Expected test count is: 1146 RepairPartitionsSuite: - don't pull from the first partition - properly handle pulling from an empty iterator - gets a single read from the partition if there are no other reads in the pair - gets all the reads from a pair from the start of a partition - properly handle dropping from an empty iterator - don't drop from the first partition - drop a single read from the partition if there are no other reads in the pair - drops all the reads from a pair from the start of a partition - only append to the first partition - drop a single read from the partition and append read when in the middle - drop reads from the start and don't append when in the last partition - can't have more records than number of partitions - unroll array for broadcast 2019-05-15 09:55:00 WARN Utils:66 - Your hostname, research-jenkins-worker-07 resolves to a loopback address: 127.0.1.1; using 192.168.10.27 instead (on interface eth0) 2019-05-15 09:55:00 WARN Utils:66 - Set SPARK_LOCAL_IP if you need to bind to another address 2019-05-15 09:55:00 WARN NativeCodeLoader:62 - Unable to load native-hadoop library for your platform... using builtin-java classes where applicable - move pairs around an rdd FlagStatSuite: - Standard FlagStat test ModPartitionerSuite: - report number of partitions correctly - partition a number that is lower than the number of partitions and positive - partition a number that is greater than the number of partitions and positive - partition a number that is lower than the number of partitions and negative - partition a number that is greater than the number of partitions and negative - fire an exception if input is not an integer TwoBitFileSuite: - correctly read sequence from .2bit file - correctly return masked sequences from .2bit file - correctly return Ns from .2bit file - correctly calculates sequence dictionary NonoverlappingRegionsSuite: - alternating returns an alternating seq of items - Single region returns itself - Two adjacent regions will be merged - Nonoverlapping regions will all be returned - Many overlapping regions will all be merged - ADAMRecords return proper references FlankReferenceFragmentsSuite: - don't put flanks on non-adjacent fragments - put flanks on adjacent fragments ReferencePositionSuite: - create reference position from mapped read - create reference position from variant - create reference position from genotype - create reference position from variant starting at vcf 0 - create reference position from genotype starting at vcf 0 ConsensusGeneratorFromReadsSuite: - checking search for consensus list for artificial reads FragmentConverterSuite: - build a fragment collector and convert to a read - if a fragment isn't associated with a contig, don't get a fragment collector - convert an rdd of discontinuous fragments, all from the same contig - convert an rdd of contiguous fragments, all from the same contig - convert an rdd of varied fragments from multiple contigs FileMergerSuite: - cannot write both empty gzip block and cram eof - buffer size must be non-negative AlignmentRecordDatasetSuite: - sorting reads - unmapped reads go at the end when sorting - coverage does not fail on unmapped reads 2019-05-15 09:55:13 WARN Utils:66 - Truncated the string representation of a plan since it was too large. This behavior can be adjusted by setting 'spark.debug.maxToStringFields' in SparkEnv.conf. - computes coverage - computes coverage with multiple samples - merges adjacent records with equal coverage values - sorting reads by reference index - round trip from ADAM to SAM and back to ADAM produces equivalent Read values - round trip with single CRAM file produces equivalent Read values - round trip with sharded CRAM file produces equivalent Read values - SAM conversion sets read mapped flag properly - load long FASTQ reads - load FASTQ with no bases - convert malformed FASTQ (no quality scores) => SAM => well-formed FASTQ => SAM - round trip from ADAM to FASTQ and back to ADAM produces equivalent Read values - round trip from ADAM to paired-FASTQ and back to ADAM produces equivalent Read values - writing a small file with tags should produce the expected result - writing a small sorted file as SAM should produce the expected result - writing unordered sam from unordered sam - writing ordered sam from unordered sam - write single sam file back - write single bam file back - saveAsParquet with save args, sequence dictionary, and read group dictionary - load parquet to sql, save, re-read from avro - load from sam, save as partitioned parquet, and re-read from partitioned parquet - save as SAM format - save as sorted SAM format - save as BAM format - save as sorted BAM format - save as FASTQ format - save as ADAM parquet format - saveAsSam SAM format - saveAsSam SAM format single file - saveAsSam sorted SAM format single file - saveAsSam BAM format - saveAsSam BAM format single file - saveAsSam sorted BAM format single file - saveAsFastq - saveAsFastq as single file - saveAsFastq with original base qualities - saveAsFastq sorted by read name - saveAsFastq sorted by read name with original base qualities 2019-05-15 09:55:38 WARN RDDBoundAlignmentRecordDataset:190 - Found 20 read names that don't occur exactly twice: 1x: 20 Samples: simread:1:237728409:true simread:1:195211965:false simread:1:163841413:false simread:1:231911906:false simread:1:26472783:false simread:1:165341382:true simread:1:240344442:true simread:1:50683371:false simread:1:240997787:true simread:1:14397233:false simread:1:207027738:true simread:1:20101800:true simread:1:101556378:false simread:1:37577445:false simread:1:189606653:true simread:1:5469106:true simread:1:186794283:true simread:1:89554252:false simread:1:153978724:false simread:1:169801933:true - saveAsFastq paired FASTQ 2019-05-15 09:55:39 WARN RDDBoundAlignmentRecordDataset:190 - Found 20 read names that don't occur exactly twice: 1x: 20 Samples: simread:1:237728409:true simread:1:195211965:false simread:1:163841413:false simread:1:231911906:false simread:1:26472783:false simread:1:165341382:true simread:1:240344442:true simread:1:50683371:false simread:1:240997787:true simread:1:14397233:false simread:1:207027738:true simread:1:20101800:true simread:1:101556378:false simread:1:37577445:false simread:1:189606653:true simread:1:5469106:true simread:1:186794283:true simread:1:89554252:false simread:1:153978724:false simread:1:169801933:true - saveAsPairedFastq 2019-05-15 09:55:41 WARN RDDBoundAlignmentRecordDataset:190 - Found 20 read names that don't occur exactly twice: 1x: 20 Samples: simread:1:237728409:true simread:1:195211965:false simread:1:163841413:false simread:1:231911906:false simread:1:26472783:false simread:1:165341382:true simread:1:240344442:true simread:1:50683371:false simread:1:240997787:true simread:1:14397233:false simread:1:207027738:true simread:1:20101800:true simread:1:101556378:false simread:1:37577445:false simread:1:189606653:true simread:1:5469106:true simread:1:186794283:true simread:1:89554252:false simread:1:153978724:false simread:1:169801933:true - saveAsPairedFastq as single files - don't lose any reads when piping as SAM 2019-05-15 09:55:52 WARN OutFormatterRunner:190 - Piped command List(sleep, 10) timed out after 5 seconds. 2019-05-15 09:55:52 WARN OutFormatterRunner:190 - Piped command List(sleep, 10) timed out after 5 seconds. - lose all records when a command times out - lose no records without a timeout 2019-05-15 09:56:13 WARN OutFormatterRunner:190 - Piped command List(python, /tmp/adamTestMvnpjenoa0/spark-94cb1988-868f-475e-8306-fd0b0259d0a9/userFiles-7392759b-4293-447a-bd2e-941284862e81/timeout.py) timed out after 5 seconds. 2019-05-15 09:56:13 WARN OutFormatterRunner:190 - Piped command List(python, /tmp/adamTestMvnpjenoa0/spark-94cb1988-868f-475e-8306-fd0b0259d0a9/userFiles-7392759b-4293-447a-bd2e-941284862e81/timeout.py) timed out after 5 seconds. - lose some records when a command times out - don't lose any reads when piping as SAM using java pipe - don't lose any reads when piping as BAM - don't lose any reads when piping fastq to sam - can properly set environment variables inside of a pipe - read vcf from alignment record pipe !!! IGNORED !!! - use broadcast join to pull down reads mapped to targets - use broadcast join against to pull down reads mapped to targets - use right outer broadcast join to pull down reads mapped to targets - use right outer broadcast join against to pull down reads mapped to targets - use shuffle join with feature spanning partitions - use shuffle join to pull down reads mapped to targets - use shuffle join with flankSize to pull down reads mapped close to targets - use right outer shuffle join to pull down reads mapped to targets - use left outer shuffle join to pull down reads mapped to targets - use full outer shuffle join to pull down reads mapped to targets - use shuffle join with group by to pull down reads mapped to targets - use right outer shuffle join with group by to pull down reads mapped to targets - cannot provide empty quality score bins - cannot provide bins with a gap - cannot provide overlapping bins - binning quality scores in reads succeeds even if reads have no quality scores - bin quality scores in reads - union two read files together - test k-mer counter - test dataset based k-mer counter - transform reads to contig genomic dataset - transform reads to coverage genomic dataset - transform reads to feature genomic dataset - transform reads to fragment genomic dataset - transform reads to genotype genomic dataset loading /tmp/adamTestMvnpjenoa0/TempSuite477488884395722689.adam as parquet into RDD... loading /tmp/adamTestMvnpjenoa0/TempSuite415673015835628979.adam as parquet into RDD... - transform reads to variant genomic dataset - cannot have a null processing step ID - convert a processing description to htsjdk - GenomicDataset.sort does not fail on unmapped reads - GenomicDataset.sortLexicographically does not fail on unmapped reads - left normalize indels - running base recalibration with downsampling doesn't drop reads - filter RDD bound alignments by MAPQ - filter dataset bound alignments by MAPQ - filter RDD bound unaligned alignments - filter dataset bound unaligned alignments - filter RDD bound unpaired alignments - filter dataset bound unpaired alignments - filter RDD bound duplicate alignments - filter dataset bound duplicate alignments - filter RDD bound alignments to primary alignments - filter dataset bound alignments to primary alignments - filter RDD bound alignments to read group - filter dataset bound alignments to read group - filter RDD bound alignments to read groups - filter dataset bound alignments to read groups - filter RDD bound alignments to sample - filter dataset bound alignments to sample - filter RDD bound alignments to samples - filter dataset bound alignments to samples - sort by read name - transform dataset via java API SingleReadBucketSuite: - convert unmapped pair to fragment - convert proper pair to fragment - convert read pair to fragment with first of pair chimeric read RecalibrationTableSuite: - look up quality scores in table InterleavedFastqInputFormatSuite: - interleaved FASTQ hadoop reader: interleaved_fastq_sample1.ifq->interleaved_fastq_sample1.ifq.output - interleaved FASTQ hadoop reader: interleaved_fastq_sample2.ifq->interleaved_fastq_sample2.ifq.output - interleaved FASTQ hadoop reader: interleaved_fastq_sample3.ifq->interleaved_fastq_sample3.ifq.output - interleaved FASTQ hadoop reader: interleaved_fastq_sample4.ifq->interleaved_fastq_sample4.ifq.output - interleaved FASTQ hadoop reader: interleaved_fastq_sample5.ifq->interleaved_fastq_sample5.ifq.output TreeRegionJoinSuite: - run a join between data on a single contig ReferenceRegionSuite: - cannot create an empty predicate - parse empty string throws IllegalArgumentException - parse contigName only string into reference regions - parse to end strings into reference regions - parse string into reference regions - contains(: ReferenceRegion) - contains(: ReferencePosition) - merge - overlaps and covers - overlapsBy and coversBy - distance(: ReferenceRegion) - distance(: ReferencePosition) - unstrandedDistance - subtract fails on non-overlapping and non-covering regions - subtract - create region from unmapped read fails - create region from read with null alignment positions fails - create stranded region from unmapped read fails - create stranded region from read with null alignment positions fails - create stranded region from read with null alignment strand fails - create stranded region from read on forward strand - create stranded region from read on reverse strand - create region from mapped read contains read start and end - validate that adjacent regions can be merged - validate that non-adjacent regions cannot be merged - validate that nearby regions can be merged - validate that non-nearby regions cannot be merged - compute convex hull of two sets - region name is sanitized when creating region from read - intersection fails on non-overlapping regions - intersection fails when minOverlap is not met - compute intersection - overlap tests for oriented reference region - check the width of a reference region - make a reference region for a variant or genotype - make a reference region for a variant or genotype starting at VCF 0 - uniformly pad a reference region - uniformly pad a reference region into negative coordinate space, ensure non negative start - unevenly pad a reference region - unevenly pad a reference region into negative coordinate space, ensure non negative start - can build an open ended reference region - can build an open ended reference region with strand - can build a reference region with an open start position - can build a reference region with an open start position with strand - can build a reference region that covers the entirety of a contig - can build a reference region that covers the entirety of a contig with strand - convert a genotype and then get the reference region - create region from feature with null alignment positions fails - create stranded region from feature with null alignment positions fails - create stranded region from feature with null alignment strand fails - create stranded region from feature on forward strand - create stranded region from feature on reverse strand AlignmentRecordConverterSuite: - testing the fields in a converted ADAM Read - converting a read with null quality is OK - convert a read to fastq - reverse complement reads when converting to fastq - converting to fastq with unmapped reads where read reverse complemented flag (Ox10) was NOT set - converting to fastq with unmapped reads where reverse complemented flag (0x10) was set - converting a fragment with no alignments should yield unaligned reads - converting a fragment with alignments should restore the alignments - read negative strand is propagated even when not mapped CoverageDatasetSuite: - correctly saves coverage - can read a bed file to coverage - correctly filters coverage with predicate - keeps sample metadata - can read a bed file with multiple samples to coverage - correctly flatmaps coverage without aggregated bins - correctly flatmaps coverage with aggregated bins - collapses coverage records in one partition - approximately collapses coverage records in multiple partitions - transform coverage to contig rdd - transform coverage to feature rdd - transform coverage to fragment rdd - transform coverage to read rdd - transform coverage to genotype rdd - transform coverage to variant rdd - transform coverage to variant context rdd - copy coverage rdd - copy coverage dataset - copy coverage rdd without sequence dictionary - copy coverage dataset without sequence dictionary - transform dataset via java API RecalibratorSuite: - don't replace quality if quality was null - if no covariates, return alignment - skip recalibration if base is below quality threshold - recalibrate changed bases above quality threshold GenotypeDatasetSuite: - union two genotype genomic datasets together - round trip to parquet - round trip to partitioned parquet - use broadcast join to pull down genotypes mapped to targets - use right outer broadcast join to pull down genotypes mapped to targets - use shuffle join to pull down genotypes mapped to targets - use right outer shuffle join to pull down genotypes mapped to targets - use left outer shuffle join to pull down genotypes mapped to targets - use full outer shuffle join to pull down genotypes mapped to targets - use shuffle join with group by to pull down genotypes mapped to targets - use right outer shuffle join with group by to pull down genotypes mapped to targets - convert back to variant contexts - load parquet to sql, save, re-read from avro - transform genotypes to contig genomic dataset - transform genotypes to coverage genomic dataset - transform genotypes to feature genomic dataset - transform genotypes to fragment genomic dataset - transform genotypes to read genomic dataset - transform genotypes to variant genomic dataset - transform genotypes to variant context genomic dataset - loading genotypes then converting to variants yields same output as loading variants - filter RDD bound genotypes to genotype filters passed - filter dataset bound genotypes to genotype filters passed - filter RDD bound genotypes by genotype quality - filter dataset bound genotypes by genotype quality - filter RDD bound genotypes by read depth - filter dataset bound genotypes by read depth - filter RDD bound genotypes by alternate read depth - filter dataset bound genotypes by alternate read depth - filter RDD bound genotypes by reference read depth - filter dataset bound genotypes by reference read depth - filter RDD bound genotypes by sample - filter dataset bound genotypes by sample - filter RDD bound genotypes by samples - filter dataset bound genotypes by samples - filter RDD bound no call genotypes - filter dataset no call genotypes - round trip gVCF END attribute without nested variant annotations rdd bound - round trip gVCF END attribute without nested variant annotations dataset bound - round trip gVCF END attribute with nested variant annotations rdd bound - round trip gVCF END attribute with nested variant annotations dataset bound - transform dataset via java API FragmentDatasetSuite: - don't lose any reads when piping interleaved fastq to sam - don't lose any reads when piping tab5 to sam - don't lose any reads when piping tab6 to sam - use broadcast join to pull down fragments mapped to targets - use right outer broadcast join to pull down fragments mapped to targets - use shuffle join to pull down fragments mapped to targets - use right outer shuffle join to pull down fragments mapped to targets - use left outer shuffle join to pull down fragments mapped to targets - use full outer shuffle join to pull down fragments mapped to targets - use shuffle join with group by to pull down fragments mapped to targets - use right outer shuffle join with group by to pull down fragments mapped to targets - bin quality scores in fragments - union two genomic datasets of fragments together - load parquet to sql, save, re-read from avro - transform fragments to contig genomic dataset - transform fragments to coverage genomic dataset - transform fragments to feature genomic dataset - transform fragments to read genomic dataset - transform fragments to genotype genomic dataset - transform fragments to variant genomic dataset - transform fragments to variant context genomic dataset - paired read names with index sequences in read names can group into fragments - interleaved paired read names with index sequences in read names can group into fragments - interleaved paired read names with index sequences in read names as fragments - transform dataset via java API SingleFastqInputFormatSuite: - FASTQ hadoop reader: fastq_sample1.fq->single_fastq_sample1.fq.output - FASTQ hadoop reader: fastq_sample2.fq->single_fastq_sample2.fq.output - FASTQ hadoop reader: fastq_sample3.fq->single_fastq_sample3.fq.output - FASTQ hadoop reader: fastq_sample4.fq->single_fastq_sample4.fq.output VariantContextDatasetSuite: - load a gvcf with a missing info field set to . - union two variant context genomic datasets together - can write, then read in .vcf file - can write as a single file via simple saveAsVcf method, then read in .vcf file - can write as a single file via full saveAsVcf method, then read in .vcf file - transform a vcf file with bad header - read a vcf file with multi-allelic variants to split - support VCFs with +Inf/-Inf float values - support VCFs with `nan` instead of `NaN` float values - don't lose any variants when piping as VCF - pipe works with empty partitions - don't lose any non-default VCF header lines or attributes when piping as VCF - save a file sorted by contig index - save a lexicographically sorted file - save a multiallelic gvcf !!! IGNORED !!! - test metadata - save sharded bgzip vcf - save bgzip vcf as single file - can't save file with non-vcf extension - transform variant contexts to contig genomic dataset - transform variant contexts to coverage genomic dataset - transform variant contexts to feature genomic dataset - transform variant contexts to fragment genomic dataset - transform variant contexts to read genomic dataset - transform variant contexts to genotype genomic dataset - transform variant contexts to variant genomic dataset - save and reload from partitioned parquet - transform dataset via java API ConsensusSuite: - test the insertion of a consensus insertion into a reference - test the insertion of a consensus deletion into a reference - inserting empty consensus returns the reference AttributeUtilsSuite: - parseTags returns a reasonable set of tagStrings - parseTags works with NumericSequence tagType - empty string is parsed as zero tagStrings - incorrectly formatted tag throws an exception - string tag with a ':' in it is correctly parsed - oq string tag with many ':' in it is correctly parsed - oq string tag with a ',' in it is correctly parsed - if a tag is an array but doesn't define it's format, throw MarkDuplicatesSuite: - single read - reads at different positions - reads at the same position - reads at the same position with clipping - reads on reverse strand - unmapped reads - read pairs - read pairs with fragments - quality scores - read pairs that cross chromosomes - single fragment - fragments at different positions - fragments at the same position - fragments at the same position with clipping - fragments on reverse strand - unmapped fragments - read pairs as fragments - read pairs with fragments as fragments - chimeric fragments - inverse pairs - supplemental reads TranscriptEffectConverterSuite: - parse empty transcript effect - parse empty transcript effect strict validation stringency - parse invalid transcript effect - parse invalid transcript effect strict validation stringency - parse transcript effect - parse empty list VCF ANN attribute - parse empty list VCF ANN attribute strict validation stringency - parse empty string VCF ANN attribute - parse empty string VCF ANN attribute strict validation stringency - parse invalid VCF ANN attribute - parse invalid VCF ANN attribute strict validation stringency - parse VCF ANN attribute with one transcript effect - parse VCF ANN attribute with multiple transcript effects - convert to transcript effect from null VCF ANN attribute in variant context - convert to transcript effect from empty list VCF ANN attribute in variant context - convert to transcript effect from empty list VCF ANN attribute in variant context strict validation stringency - convert to transcript effect from empty string VCF ANN attribute in variant context - convert to transcript effect from empty string VCF ANN attribute in variant context strict validation stringency - convert to transcript effect from invalid VCF ANN attribute in variant context - convert to transcript effect from invalid VCF ANN attribute in variant context strict validation stringency 2019-05-15 09:58:36 WARN TranscriptEffectConverter$:190 - Could not convert VCF INFO reserved key ANN value to TranscriptEffect, caught java.lang.NumberFormatException: For input string: "not a number". - convert to transcript effect from VCF ANN attribute with invalid number in variant context lenient validation stringency 2019-05-15 09:58:36 WARN TranscriptEffectConverter$:190 - Could not convert VCF INFO reserved key ANN value to TranscriptEffect, caught java.lang.NumberFormatException: For input string: "not a number". - convert to transcript effect from VCF ANN attribute with invalid fraction in variant context lenient validation stringency - convert to transcript effect from VCF ANN attribute with invalid number in variant context strict validation stringency - convert to transcript effect from VCF ANN attribute with invalid fraction in variant context strict validation stringency - convert to transcript effect from VCF ANN attribute in variant context different alt allele - convert to transcript effect from VCF ANN attribute in variant context same alt allele - convert to transcript effect from VCF ANN attribute in variant context multiple effects same alt allele - convert transcript effect to VCF ANN attribute value - convert transcript effect with null fields to VCF ANN attribute value 2019-05-15 09:58:36 WARN TranscriptEffectConverter$:190 - Incorrect fractional value ?/2, missing numerator - convert transcript effect with incorrect fractional value to VCF ANN attribute value IndelRealignmentTargetSuite: - checking simple realignment target - creating simple target from read with deletion - creating simple target from read with insertion - joining simple realignment targets on same chr - joining simple realignment targets on different chr throws exception - creating targets from three intersecting reads, same indel - creating targets from three intersecting reads, two different indel - creating targets from two disjoint reads - creating targets for artificial reads: one-by-one - creating targets for artificial reads: all-at-once (merged) - creating indel targets for mason reads - additional indel targets taken from consensus generator NormalizationUtilsSuite: - cannot move an indel left if there are no bases to it's left - move a simple indel to farthest position left until bases run out - move a simple indel to farthest position left, past length of indel - cannot move a left normalized indel in a short tandem repeat - move an indel in a short tandem repeat - move an indel in a short tandem repeat of more than 2 bases, where shift is not an integer multiple of repeated sequence length - moving a simple read with single deletion that cannot shift - shift an indel left by 0 in a cigar - shift an indel left by 1 in a cigar - do not left align a complex read which is already left aligned ReadGroupDictionarySuite: - simple conversion to and from sam read group - sample name must be set - simple equality checks - get samples from read group dictionary - empty read group is empty - merging a dictionary with itself should work - round trip a record with all attributes set NucleotideContigFragmentDatasetSuite: - union two ncf genomic datasets together - round trip a ncf to parquet - round trip a ncf to partitioned parquet - save fasta back as a single file - generate sequence dict from fasta - recover reference string from a single contig fragment - recover trimmed reference string from a single contig fragment - recover reference string from multiple contig fragments - extract sequences based on the list of reference regions - recover trimmed reference string from multiple contig fragments - testing nondeterminism from reduce when recovering referencestring - save single contig fragment as FASTA text file - save single contig fragment with description as FASTA text file - save single contig fragment with null fields as FASTA text file - save single contig fragment with null fragment number as FASTA text file - save single contig fragment with null number of fragments in contig as FASTA text file - save multiple contig fragments from same contig as FASTA text file - save multiple contig fragments with description from same contig as FASTA text file - merge single contig fragment null fragment number - merge single contig fragment number zero - merge multiple contig fragments - save as parquet and apply predicate pushdown - load fasta sequences from GFF3 file - transform contigs to coverage genomic dataset - transform contigs to feature genomic dataset - transform contigs to fragment genomic dataset - transform contigs to read genomic dataset - transform contigs to genotype genomic dataset - transform contigs to variant genomic dataset - transform contigs to variant context genomic dataset RightOuterTreeRegionJoinSuite: - Ensure same reference regions get passed together - Overlapping reference regions InnerShuffleRegionJoinSuite: - Overlapping reference regions - Multiple reference regions do not throw exception FeatureDatasetSuite: - round trip GTF format - save GTF as GFF3 format - save GTF as BED format - save GTF as IntervalList format - save GTF as NarrowPeak format - save GFF3 as GTF format - save GFF3 as BED format - save GFF3 as IntervalList format - save GFF3 as NarrowPeak format - round trip GFF3 format - ignore FASTA sequence in GFF3 file - save BED as GTF format - save BED as GFF3 format - save BED as IntervalList format - save BED as NarrowPeak format - round trip BED6 format - keeps sample metadata - round trip BED12 format - save to UCSC BED format - save IntervalList as GTF format - save IntervalList as GFF3 format - save IntervalList as BED format - save IntervalList as IntervalList format - save IntervalList as NarrowPeak format - round trip IntervalList format - save NarrowPeak as GTF format - save NarrowPeak as GFF3 format - save NarrowPeak as BED format - save NarrowPeak as IntervalList format - save NarrowPeak as NarrowPeak format - round trip NarrowPeak format - sort by reference - sort by reference and feature fields - sort gene features by reference and gene structure - sort transcript features by reference and gene structure - sort exon features by reference and gene structure - sort intron features by reference and gene structure - correctly flatmaps CoverageDataset from FeatureDataset - use broadcast join to pull down features mapped to targets - use right outer broadcast join to pull down features mapped to targets - use shuffle join to pull down features mapped to targets - use right outer shuffle join to pull down features mapped to targets - use left outer shuffle join to pull down features mapped to targets - use full outer shuffle join to pull down features mapped to targets - use shuffle join with group by to pull down features mapped to targets - use right outer shuffle join with group by to pull down features mapped to targets - union two feature rdds together - obtain sequence dictionary contig lengths from header in IntervalList format - don't lose any features when piping as BED format - don't lose any features when piping as GTF format - don't lose any features when piping as GFF3 format - don't lose any features when piping as NarrowPeak format - load parquet to sql, save, re-read from avro - load partitioned parquet to sql, save, re-read from avro - transform features to contig rdd - transform features to coverage rdd - transform features to fragment rdd - transform features to read rdd - transform features to genotype rdd - transform features to variant rdd - transform features to variant context rdd - filter RDD bound features by feature type - filter dataset bound features by feature type - filter RDD bound features by feature types - filter dataset bound features by feature types - filter RDD bound features by gene - filter dataset bound features by gene - filter RDD bound features by genes - filter dataset bound features by genes - filter RDD bound features by transcript - filter dataset bound features by transcript - filter RDD bound features by transcripts - filter dataset bound features by transcripts - filter RDD bound features by exon - filter dataset bound features by exon - filter RDD bound features by exons - filter dataset bound features by exons - filter RDD bound features by score - filter dataset bound features by score - filter RDD bound features by parent - filter dataset bound features by parent - filter RDD bound features by parents - filter dataset bound features by parents - filter RDD bound features by attribute - filter dataset bound features by attribute - transform dataset via java API AlphabetSuite: - test size of a case-sensitive alphabet - test apply of a case-sensitive alphabet - test reverse complement of a case-sensitive alphabet - test exact reverse complement of a case-sensitive alphabet - test size of a case-insensitive alphabet - test apply of a case-insensitive alphabet - test reverse complement of a case-insensitive alphabet - test exact reverse complement of a case-insensitive alphabet - DNA alphabet - map unknown bases to N SortedGenomicDatasetSuite: - testing that partition and sort provide correct outputs - testing copartition maintains or adds sort - testing that we don't drop any data on the right side even though it doesn't map to a partition on the left - testing that sorted shuffleRegionJoin matches unsorted - testing that sorted fullOuterShuffleRegionJoin matches unsorted - testing that sorted rightOuterShuffleRegionJoin matches unsorted - testing that sorted leftOuterShuffleRegionJoin matches unsorted - testing that we can persist the sorted knowledge VariantContextConverterSuite: - Convert htsjdk site-only SNV to ADAM - Convert somatic htsjdk site-only SNV to ADAM - Convert htsjdk site-only CNV to ADAM - Convert htsjdk SNV w/ genotypes w/ phase information to ADAM - Convert htsjdk SNV with different variant filters to ADAM - Convert htsjdk SNV with different genotype filters to ADAM - Convert ADAM site-only SNV to htsjdk - Convert ADAM SNV w/ genotypes to htsjdk - Convert ADAM SNV w/ genotypes but bad SB to htsjdk with strict validation 2019-05-15 09:59:48 WARN VariantContextConverter:2300 - Applying annotation extraction function org.bdgenomics.adam.converters.VariantContextConverter$$Lambda$803/87060781@6e01e259 to {"variant": {"referenceName": "1", "start": 0, "end": 1, "names": [], "splitFromMultiAllelic": false, "referenceAllele": "A", "alternateAllele": "T", "quality": null, "filtersApplied": null, "filtersPassed": null, "filtersFailed": [], "annotation": null}, "referenceName": null, "start": null, "end": null, "variantCallingAnnotations": {"filtersApplied": null, "filtersPassed": null, "filtersFailed": [], "downsampled": null, "baseQRankSum": null, "fisherStrandBiasPValue": 3.0, "rmsMapQ": 0.0, "mapq0Reads": 5, "mqRankSum": null, "readPositionRankSum": null, "genotypePriors": [], "genotypePosteriors": [], "vqslod": null, "culprit": null, "attributes": {}}, "sampleId": "NA12878", "sampleDescription": null, "processingDescription": null, "alleles": ["REF", "ALT"], "expectedAlleleDosage": null, "referenceReadDepth": null, "alternateReadDepth": null, "readDepth": null, "minReadDepth": null, "genotypeQuality": null, "genotypeLikelihoods": [], "nonReferenceLikelihoods": [], "strandBiasComponents": [0, 2], "splitFromMultiAllelic": false, "phased": false, "phaseSetId": null, "phaseQuality": null} failed with java.lang.IllegalArgumentException: requirement failed: Illegal strand bias components length. Must be empty or 4. In: {"variant": {"referenceName": "1", "start": 0, "end": 1, "names": [], "splitFromMultiAllelic": false, "referenceAllele": "A", "alternateAllele": "T", "quality": null, "filtersApplied": null, "filtersPassed": null, "filtersFailed": [], "annotation": null}, "referenceName": null, "start": null, "end": null, "variantCallingAnnotations": {"filtersApplied": null, "filtersPassed": null, "filtersFailed": [], "downsampled": null, "baseQRankSum": null, "fisherStrandBiasPValue": 3.0, "rmsMapQ": 0.0, "mapq0Reads": 5, "mqRankSum": null, "readPositionRankSum": null, "genotypePriors": [], "genotypePosteriors": [], "vqslod": null, "culprit": null, "attributes": {}}, "sampleId": "NA12878", "sampleDescription": null, "processingDescription": null, "alleles": ["REF", "ALT"], "expectedAlleleDosage": null, "referenceReadDepth": null, "alternateReadDepth": null, "readDepth": null, "minReadDepth": null, "genotypeQuality": null, "genotypeLikelihoods": [], "nonReferenceLikelihoods": [], "strandBiasComponents": [0, 2], "splitFromMultiAllelic": false, "phased": false, "phaseSetId": null, "phaseQuality": null}. - Convert ADAM SNV w/ genotypes but bad SB to htsjdk with lenient validation - Convert htsjdk multi-allelic sites-only SNVs to ADAM - Convert htsjdk multi-allelic SNVs to ADAM and back to htsjdk - Convert gVCF reference records to ADAM - Convert htsjdk variant context with no IDs to ADAM - Convert htsjdk variant context with one ID to ADAM - Convert htsjdk variant context with multiple IDs to ADAM - Convert ADAM variant context with no names to htsjdk - Convert ADAM variant context with one name to htsjdk - Convert ADAM variant context with multiple names to htsjdk - Convert ADAM variant context with null filters applied to htsjdk - Convert ADAM variant context with no filters applied to htsjdk - Convert ADAM variant context with passing filters to htsjdk - Convert ADAM variant context with failing filters to htsjdk - no phasing set going htsjdk->adam - phased but no phase set info going htsjdk->adam - set phase set and extract going htsjdk->adam - no allelic depth going htsjdk->adam - set allelic depth going htsjdk->adam - no gt read depth going htsjdk->adam - extract gt read depth going htsjdk->adam - no min gt read depth going htsjdk->adam - extract min gt read depth going htsjdk->adam - no genotype quality going htsjdk->adam - extract genotype quality going htsjdk->adam - no phred likelihood going htsjdk->adam - extract phred likelihoods going htsjdk->adam - no strand bias info going htsjdk->adam - extract strand bias info going htsjdk->adam - no filters going htsjdk->adam - filters passed going htsjdk->adam - extract single filter going htsjdk->adam - extract multiple filters going htsjdk->adam - no fisher strand bias going htsjdk->adam - extract fisher strand bias going htsjdk->adam - no rms mapping quality going htsjdk->adam - extract rms mapping quality going htsjdk->adam - no mq0 going htsjdk->adam - extract mq0 going htsjdk->adam - no gt read depth going adam->htsjdk - extract gt read depth going adam->htsjdk - throw iae if missing one component of gt read depth going adam->htsjdk - no depth going adam->htsjdk - extract depth going adam->htsjdk - no min depth going adam->htsjdk - extract min depth going adam->htsjdk - no quality going adam->htsjdk - extract quality going adam->htsjdk - no genotype likelihoods going adam->htsjdk - extract genotype likelihoods going adam->htsjdk - no strand bias going adam->htsjdk - malformed strand bias going adam->htsjdk - extract strand bias going adam->htsjdk - no phasing info going adam->htsjdk - unphased going adam->htsjdk - phased but no ps/pq going adam->htsjdk - phased but no pq going adam->htsjdk - phased but no ps going adam->htsjdk - phased going adam->htsjdk - no filter info going adam->htsjdk - if filters applied, must set passed/failed going adam->htsjdk - filters passed going adam->htsjdk - if filters failed, must set filters failed going adam->htsjdk - single filter failed going adam->htsjdk - multiple filters failed going adam->htsjdk - no fisher strand bias going adam->htsjdk - extract fisher strand bias going adam->htsjdk - no rms mapping quality going adam->htsjdk - extract rms mapping quality going adam->htsjdk - no mapping quality 0 reads going adam->htsjdk - extract mapping quality 0 reads going adam->htsjdk - no names set going htsjdk->adam - single name set going htsjdk->adam - multiple names set going htsjdk->adam - no quality going htsjdk->adam - quality set going htsjdk->adam - no filters applied going htsjdk->adam - filters applied and passed going htsjdk->adam - single filter applied and failed going htsjdk->adam - multiple filters applied and failed going htsjdk->adam - no names set adam->htsjdk - set a single name adam->htsjdk - set multiple names adam->htsjdk - no qual set adam->htsjdk - qual is set adam->htsjdk - no filters applied adam->htsjdk - null filters applied adam->htsjdk - filters passed adam->htsjdk - if filter failed, must have filters adam->htsjdk - single filter failed adam->htsjdk - multiple filters failed adam->htsjdk - no ancestral allele set going htsjdk->adam - ancestral allele set going htsjdk->adam - no dbsnp membership set going htsjdk->adam - dbsnp membership set going htsjdk->adam - no hapmap2 membership set going htsjdk->adam - hapmap2 membership set going htsjdk->adam - no hapmap3 membership set going htsjdk->adam - hapmap3 membership set going htsjdk->adam - no validated set going htsjdk->adam - validated set going htsjdk->adam - no 1000G membership set going htsjdk->adam - 1000G membership set going htsjdk->adam - not somatic going htsjdk->adam - somatic going htsjdk->adam - no allele count going htsjdk->adam - single allele count going htsjdk->adam - multiple allele counts going htsjdk->adam - no allele frequency going htsjdk->adam - single allele frequency going htsjdk->adam - single allele frequency is +Inf going htsjdk->adam - single allele frequency is -Inf going htsjdk->adam - multiple allele frequencies going htsjdk->adam - no CIGAR going htsjdk->adam - single CIGAR going htsjdk->adam - multiple CIGARs going htsjdk->adam - no read depth going htsjdk->adam - single read depth going htsjdk->adam - multiple read depths going htsjdk->adam - no forward read depth going htsjdk->adam - single forward read depth going htsjdk->adam - multiple forward read depths going htsjdk->adam - no reverse read depth going htsjdk->adam - single reverse read depth going htsjdk->adam - multiple reverse read depths going htsjdk->adam - no ancestral allele set adam->htsjdk - ancestral allele set adam->htsjdk - no dbsnp membership set adam->htsjdk - dbsnp membership set adam->htsjdk - no hapmap2 membership set adam->htsjdk - hapmap2 membership set adam->htsjdk - no hapmap3 membership set adam->htsjdk - hapmap3 membership set adam->htsjdk - no validated set adam->htsjdk - validated set adam->htsjdk - no 1000G membership set adam->htsjdk - 1000G membership set adam->htsjdk - no allele count set adam->htsjdk - allele count set adam->htsjdk - no allele frequency set adam->htsjdk - allele frequency set adam->htsjdk - no cigar set adam->htsjdk - cigar set adam->htsjdk - no read depth set adam->htsjdk - read depth set adam->htsjdk - read depth without reference read depth - reference read depth without read depth - no forward read depth set adam->htsjdk - forward read depth set adam->htsjdk - reference forward read depth without forward read depth - forward read depth without reference forward read depth - no reverse read depth set adam->htsjdk - reverse read depth set adam->htsjdk - reference reverse read depth without reverse read depth - reverse read depth without reference reverse read depth - VCF INFO attribute Number=0 Type=Flag adam->htsjdk - VCF INFO attribute Number=4 Type=Flag adam->htsjdk unsupported, strict !!! IGNORED !!! - VCF INFO attribute Number=1 Type=Integer adam->htsjdk - VCF INFO attribute Number=4 Type=Integer adam->htsjdk - VCF INFO attribute Number=A Type=Integer adam->htsjdk - VCF INFO attribute Number=R Type=Integer adam->htsjdk - VCF INFO attribute Number=R Type=String adam->htsjdk - VCF INFO attribute Number=G Type=String adam->htsjdk not supported - VCF INFO attribute Number=0 Type=Flag htsjdk->adam - VCF INFO attribute Number=1 Type=Integer htsjdk->adam - VCF INFO attribute Number=4 Type=Integer htsjdk->adam - VCF INFO attribute Number=4 Type=Float htsjdk->adam - VCF INFO attribute Number=A Type=Integer htsjdk->adam - VCF INFO attribute Number=R Type=Integer htsjdk->adam - VCF INFO attribute Number=R Type=String htsjdk->adam - VCF INFO attribute Number=G Type=String htsjdk->adam not supported - VCF FORMAT attribute Number=0 Type=Flag adam->htsjdk not supported - VCF FORMAT attribute Number=1 Type=Integer adam->htsjdk - VCF FORMAT attribute Number=4 Type=Integer adam->htsjdk - VCF FORMAT attribute Number=A Type=Integer adam->htsjdk - VCF FORMAT attribute Number=R Type=Integer adam->htsjdk - VCF FORMAT attribute Number=R Type=String adam->htsjdk - VCF FORMAT attribute Number=0 Type=Flag htsjdk->adam is not supported - VCF FORMAT attribute Number=1 Type=Integer htsjdk->adam - VCF FORMAT attribute Number=4 Type=Integer htsjdk->adam - VCF FORMAT attribute Number=4 Type=Float htsjdk->adam - VCF FORMAT attribute Number=A Type=Integer htsjdk->adam - VCF FORMAT attribute Number=R Type=Integer htsjdk->adam - VCF FORMAT attribute Number=R Type=String htsjdk->adam - VCF FORMAT attribute Number=G Type=String htsjdk->adam - respect end position for symbolic alts FastqRecordConverterSuite: - test read name suffix and index of pair must match - test parseReadInFastq, read suffix removal - test parseReadInFastq, read metadata removal - test parseReadInFastq, read quality shorter than read length, padded with B - test parseReadInFastq, read quality longer than read length - test parseReadInFastq, no read quality - testing FastqRecordConverter.convertPair with valid input - testing FastqRecordConverter.convertPair with 7-line invalid input - testing FastqRecordConverter.convertPair with invalid input: first read length and qual don't match - testing FastqRecordConverter.convertPair with invalid input: second read length and qual don't match - testing FastqRecordConverter.convertFragment with valid input - testing FastqRecordConverter.convertFragment with another valid input having /1, /2 suffixes - testing FastqRecordConverter.convertFragment with invalid input: different read names - testing FastqRecordConverter.convertRead with valid input - testing FastqRecordConverter.convertRead with valid input: setFirstOfPair set to true - testing FastqRecordConverter.convertRead with valid input: setSecondOfPair set to true - testing FastqRecordConverter.convertRead with valid input: setFirstOfPair and setSecondOfPair both true - testing FastqRecordConverter.convertRead with valid input, no qual, strict - testing FastqRecordConverter.convertRead with valid input, no qual, not strict AttributeSuite: - test SAMTagAndValue parsing - Attributes can be correctly re-encoded as text SAM tags GFF3HeaderWriterSuite: - write gff3 header pragma BinQualitiesSuite: - make a quality score bin - can't have a quality score bin with negative score - can't have a quality score bin with high score below low - can't have a quality score bin with high score above 255 - can't have a quality score bin with score outside - make a quality score bin from a string - quality score bin must have exactly 3 elements - quality score bin must be integers - must define at least one bin - build multiple bins - rewrite quality scores for a read - rewriting quality scores fails if bins overlap - rewriting quality scores fails if base is out of bounds - skip read if qualities are null - rewrite a read IndexedFastaFileSuite: - correctly generates sequence dictionary from .dict file - correctly gets sequence - fails when fai index is not provided 2019-05-15 09:59:48 WARN IndexedFastaFile:190 - Caught exception java.lang.NullPointerException when loading FASTA sequence dictionary. Using empty dictionary instead. - passes when dict is not provided and ValidationStringency = LENIENT SAMRecordConverterSuite: - testing the fields in an alignmentRecord obtained from a mapped samRecord conversion - testing the fields in an alignmentRecord obtained from an unmapped samRecord conversion - '*' quality gets nulled out - don't keep denormalized fields ADAMContextSuite: - ctr is accessible - load from an empty directory - sc.loadParquet should not fail on unmapped reads - sc.loadParquet should not load a file without a type specified - can read a small .SAM file - can read a small .SAM file with a bad header with lenient validation - loading a sam file with a bad header and strict stringency should fail - can read a small .CRAM file - can read a small .SAM with all attribute tag types - can filter a .SAM file based on quality - Can convert to phred - Can convert from phred - Can read a .gtf file - Can read a .bed file - Can read a BED 12 file - Can read a .narrowPeak file - Can read a .interval_list file 2019-05-15 09:59:52 WARN VariantContextConverter:1662 - Saw invalid info field java.lang.IllegalArgumentException: Multivalued flags are not supported for INFO lines: INFO=<ID=ABADFLAG,Number=.,Type=Flag,Description="A no good, very bad flag.">. Ignoring... 2019-05-15 09:59:52 WARN VariantContextConverter:2169 - Generating field extractor from header line INFO=<ID=ABADFLAG,Number=.,Type=Flag,Description="A no good, very bad flag."> failed: java.lang.IllegalArgumentException: Multivalue flags are not supported for INFO lines: INFO=<ID=ABADFLAG,Number=.,Type=Flag,Description="A no good, very bad flag."> - can read a small .vcf file with a validation issue - can read a small .vcf file 2019-05-15 09:59:52 WARN VCFInputFormat:218 - file:/home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/target/2.12.8/test-classes/test.vcf.gz is not splittable, consider using block-compressed gzip (BGZF) - can read a gzipped .vcf file - can read a vcf file with an empty alt - can read a BGZF gzipped .vcf file with .gz file extension - can read a BGZF gzipped .vcf file with .bgz file extension - can read a vcf file with a projection - can read an uncompressed BCFv2.2 file !!! IGNORED !!! - can read a BGZF compressed BCFv2.2 file !!! IGNORED !!! - loadIndexedVcf with 1 ReferenceRegion - loadIndexedVcf with multiple ReferenceRegions - load block compressed interleaved fastq - import records from interleaved FASTQ: 1 - import records from interleaved FASTQ: 2 - import records from interleaved FASTQ: 3 - import records from interleaved FASTQ: 4 - import block compressed single fastq - import records from single ended FASTQ: 1 - import records from single ended FASTQ: 2 - import records from single ended FASTQ: 3 - import records from single ended FASTQ: 4 - filter on load using the filter2 API - saveAsParquet with file path - saveAsParquet with file path, block size, page size - saveAsParquet with save args - read a HLA fasta from GRCh38 - read a gzipped fasta file - loadIndexedBam with 1 ReferenceRegion - loadIndexedBam with multiple ReferenceRegions - loadIndexedBam with multiple ReferenceRegions and indexed bams - loadIndexedBam with multiple ReferenceRegions and a directory of indexed bams - loadIndexedBam should throw exception without an index file - loadIndexedBam should work with indexed file with index naming format <filename>.bai - loadIndexedBam glob should throw exception without an index file - loadBam with a glob - loadBam with a directory - load vcf with a glob - load vcf from a directory - load gvcf which contains a multi-allelic row from a directory - load and save gvcf which contains rows without likelihoods - parse annotations for multi-allelic rows - load parquet with globs - bad glob should fail - empty directory should fail - can read a SnpEff-annotated .vcf file - loadAlignments should not fail on single-end and paired-end fastq reads - load queryname sorted sam as fragments - load query grouped sam as fragments - load paired fastq - load paired fastq without cache - load paired fastq as fragments - load paired fastq as fragments without cache - load HTSJDK sequence dictionary - load Bedtools .genome file as sequence dictionary - load Bedtools .genome.txt file as sequence dictionary - load UCSC Genome Browser chromInfo.txt file as sequence dictionary - load unrecognized file extension as sequence dictionary fails - load BED features with Bedtools .genome file as sequence dictionary - load BED features with Bedtools .genome file as sequence dictionary, no matching features - convert program record - load program record from sam file CycleCovariateSuite: - compute covariates for an unpaired read on the negative strand - compute covariates for a first-of-pair read on the negative strand - compute covariates for a second-of-pair read on the negative strand - compute covariates for an unpaired read on the positive strand - compute covariates for a first-of-pair read on the positive strand - compute covariates for a second-of-pair read on the positive strand ConsensusGeneratorFromKnownsSuite: - no consensuses for empty target - no consensuses for reads that don't overlap a target - return a consensus for read overlapping a single target RichCigarSuite: - moving 2 bp from a deletion to a match operator - moving 2 bp from a insertion to a match operator - moving 1 base in a two element cigar - move to start of read - process right clipped cigar - process left clipped cigar - process cigar clipped on both ends MDTaggingSuite: - test adding MDTags over boundary - test adding MDTags; reads span full contig - test adding MDTags; reads start inside first fragment - test adding MDTags; reads end inside last fragment - test adding MDTags; reads start inside first fragment and end inside last fragment - test adding MDTags; reads start and end in middle fragements 2019-05-15 10:00:13 WARN BlockManager:66 - Putting block rdd_5_3 failed due to exception java.lang.Exception: Contig chr2 not found in reference map with keys: chr1. 2019-05-15 10:00:13 WARN BlockManager:66 - Block rdd_5_3 could not be removed as it was not found on disk or in memory 2019-05-15 10:00:13 ERROR Executor:91 - Exception in task 3.0 in stage 2.0 (TID 11) java.lang.Exception: Contig chr2 not found in reference map with keys: chr1 at org.bdgenomics.adam.util.ReferenceContigMap.$anonfun$extract$1(ReferenceContigMap.scala:64) at scala.collection.immutable.Map$Map1.getOrElse(Map.scala:119) at org.bdgenomics.adam.util.ReferenceContigMap.extract(ReferenceContigMap.scala:63) at org.bdgenomics.adam.rdd.read.MDTagging.$anonfun$addMDTagsBroadcast$3(MDTagging.scala:76) at scala.Option$WithFilter.map(Option.scala:163) at org.bdgenomics.adam.rdd.read.MDTagging.$anonfun$addMDTagsBroadcast$1(MDTagging.scala:71) at scala.collection.Iterator$$anon$10.next(Iterator.scala:459) at org.apache.spark.storage.memory.MemoryStore.putIterator(MemoryStore.scala:222) at org.apache.spark.storage.memory.MemoryStore.putIteratorAsValues(MemoryStore.scala:299) at org.apache.spark.storage.BlockManager.$anonfun$doPutIterator$1(BlockManager.scala:1165) at org.apache.spark.storage.BlockManager.doPut(BlockManager.scala:1091) at org.apache.spark.storage.BlockManager.doPutIterator(BlockManager.scala:1156) at org.apache.spark.storage.BlockManager.getOrElseUpdate(BlockManager.scala:882) at org.apache.spark.rdd.RDD.getOrCompute(RDD.scala:335) at org.apache.spark.rdd.RDD.iterator(RDD.scala:286) at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:90) at org.apache.spark.scheduler.Task.run(Task.scala:121) at org.apache.spark.executor.Executor$TaskRunner.$anonfun$run$3(Executor.scala:411) at org.apache.spark.util.Utils$.tryWithSafeFinally(Utils.scala:1360) at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:414) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624) at java.lang.Thread.run(Thread.java:748) 2019-05-15 10:00:13 WARN TaskSetManager:66 - Lost task 3.0 in stage 2.0 (TID 11, localhost, executor driver): java.lang.Exception: Contig chr2 not found in reference map with keys: chr1 at org.bdgenomics.adam.util.ReferenceContigMap.$anonfun$extract$1(ReferenceContigMap.scala:64) at scala.collection.immutable.Map$Map1.getOrElse(Map.scala:119) at org.bdgenomics.adam.util.ReferenceContigMap.extract(ReferenceContigMap.scala:63) at org.bdgenomics.adam.rdd.read.MDTagging.$anonfun$addMDTagsBroadcast$3(MDTagging.scala:76) at scala.Option$WithFilter.map(Option.scala:163) at org.bdgenomics.adam.rdd.read.MDTagging.$anonfun$addMDTagsBroadcast$1(MDTagging.scala:71) at scala.collection.Iterator$$anon$10.next(Iterator.scala:459) at org.apache.spark.storage.memory.MemoryStore.putIterator(MemoryStore.scala:222) at org.apache.spark.storage.memory.MemoryStore.putIteratorAsValues(MemoryStore.scala:299) at org.apache.spark.storage.BlockManager.$anonfun$doPutIterator$1(BlockManager.scala:1165) at org.apache.spark.storage.BlockManager.doPut(BlockManager.scala:1091) at org.apache.spark.storage.BlockManager.doPutIterator(BlockManager.scala:1156) at org.apache.spark.storage.BlockManager.getOrElseUpdate(BlockManager.scala:882) at org.apache.spark.rdd.RDD.getOrCompute(RDD.scala:335) at org.apache.spark.rdd.RDD.iterator(RDD.scala:286) at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:90) at org.apache.spark.scheduler.Task.run(Task.scala:121) at org.apache.spark.executor.Executor$TaskRunner.$anonfun$run$3(Executor.scala:411) at org.apache.spark.util.Utils$.tryWithSafeFinally(Utils.scala:1360) at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:414) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624) at java.lang.Thread.run(Thread.java:748) 2019-05-15 10:00:13 ERROR TaskSetManager:70 - Task 3 in stage 2.0 failed 1 times; aborting job - try realigning a read on a missing contig, stringency == STRICT 2019-05-15 10:00:13 WARN MDTagging:190 - Caught exception when processing read chr2: java.lang.Exception: Contig chr2 not found in reference map with keys: chr1 - try realigning a read on a missing contig, stringency == LENIENT FileExtensionsSuite: - ends in gzip extension - is a vcf extension PhredUtilsSuite: - convert low phred score to log and back - convert high phred score to log and back - convert overflowing phred score to log and back and clip - convert negative zero log probability to phred and clip - round trip log probabilities SmithWatermanSuite: - gather max position from simple scoring matrix - gather max position from irregular scoring matrix - gather max position from irregular scoring matrix with deletions - score simple alignment with constant gap - score irregular scoring matrix - score irregular scoring matrix with indel - can unroll cigars correctly - execute simple trackback - execute trackback with indel - run end to end smith waterman for simple reads - run end to end smith waterman for short sequences with indel - run end to end smith waterman for longer sequences with snp - run end to end smith waterman for longer sequences with short indel - run end to end smith waterman for shorter sequence in longer sequence - run end to end smith waterman for shorter sequence in longer sequence, with indel - smithWaterman - simple alignment FastaConverterSuite: - find contig index - convert a single record without naming information - convert a single record with naming information - convert single fasta sequence - convert fasta with multiple sequences - convert fasta with multiple sequences; short fragment - convert reference fasta file MdTagSuite: - null md tag - zero length md tag - md tag with non-digit initial value - md tag invalid base - md tag, pure insertion - md tag, pure insertion, test 2 - md tag pure insertion equality - md tag equality and hashcode - valid md tags - get start of read with no mismatches or deletions - get start of read with no mismatches, but with a deletion at the start - get start of read with mismatches at the start - get end of read with no mismatches or deletions - check that mdtag and rich record return same end - get end of read with no mismatches, but a deletion at end - CIGAR with N operator - CIGAR with multiple N operators - CIGAR with P operators - Get correct matches for mdtag with insertion - Get correct matches for mdtag with mismatches and insertion - Get correct matches for mdtag with insertion between mismatches - Get correct matches for mdtag with intron between mismatches - Get correct matches for mdtag with intron and deletion between mismatches - Throw exception when number of deleted bases in mdtag disagrees with CIGAR - Get correct matches for mdtag with mismatch, insertion and deletion - Get correct matches for mdtag with mismatches, insertion and deletion - Get correct matches for MDTag with mismatches and deletions - Get correct matches base from MDTag and CIGAR with N - get end of read with mismatches and a deletion at end - get correct string out of mdtag with no mismatches - get correct string out of mdtag with mismatches at start - get correct string out of mdtag with deletion at end - get correct string out of mdtag with mismatches at end - get correct string out of complex mdtag - check complex mdtag - get gapped reference - move a cigar alignment by two for a read - rewrite alignment to all matches - rewrite alignment to two mismatches followed by all matches - rewrite alignment to include a deletion but otherwise all matches - rewrite alignment to include an insertion at the start of the read but otherwise all matches - create new md tag from read vs. reference, perfect match - create new md tag from read vs. reference, perfect alignment match, 1 mismatch - create new md tag from read vs. reference, alignment with deletion - create new md tag from read vs. reference, alignment with insert - handle '=' and 'X' operators - CIGAR/MD tag mismatch should cause errors GenomicDatasetSuite: - processing a command that is the spark root directory should return an absolute path - processing a command that is just a single word should do nothing - processing a command should handle arguments that include spaces - processing a command that is a single substitution should succeed - processing a command that is multiple words should split the string - process a command that is multiple words with a replacement - process a command that is multiple words with multiple replacements ParallelFileMergerSuite: - cannot write both empty gzip block and cram eof - buffer size must be non-negative - get the size of several files - block size must be positive and non-zero when trying to merge files - must provide files to merge - if two files are both below the block size, they should merge into one shard - merge two files where one is greater than the block size - merge a sharded sam file - merge a sharded bam file - merge a sharded cram file - can't turn a negative index into a path - generate a path from an index IndelTableSuite: - check for indels in a region with known indels - check for indels in a contig that doesn't exist - check for indels in a region without known indels - build indel table from rdd of variants SnpTableSuite: - create an empty snp table - create a snp table from variants on multiple contigs - create a snp table from a larger set of variants - perform lookups on multi-contig snp table - perform lookups on larger snp table RealignIndelsSuite: - map reads to targets - checking mapping to targets for artificial reads - checking alternative consensus for artificial reads - checking extraction of reference from reads - checking realigned reads for artificial input - checking realigned reads for artificial input with reference file - checking realigned reads for artificial input using knowns - checking realigned reads for artificial input using knowns and reads - skip realigning reads if target is highly covered - skip realignment if target is an insufficient LOD improvement - realign reads to an insertion - test mismatch quality scoring - test mismatch quality scoring for no mismatches - test mismatch quality scoring for offset - test mismatch quality scoring with early exit - test mismatch quality scoring after unpacking read - we shouldn't try to realign a region with no target - we shouldn't try to realign reads with no indel evidence - test OP and OC tags - realign a read with an insertion that goes off the end of the read - if realigning a target doesn't improve the LOD, don't drop reads - extract seq/qual from a read with no clipped bases - extract seq/qual from a read with clipped bases at start - extract seq/qual from a read with clipped bases at end - if unclip is selected, don't drop base when extracting from a read with clipped bases - get cigar and coordinates for read that spans indel, no clipped bases - get cigar and coordinates for read that spans deletion, clipped bases at start - get cigar and coordinates for read that falls wholly before insertion - get cigar and coordinates for read that falls wholly after insertion - get cigar and coordinates for read that falls wholly after deletion - get cigar and coordinates for read that partially spans insertion, no clipped bases - get cigar and coordinates for read that partially spans insertion, clipped bases at end - get cigar and coordinates for read that partially spans insertion, clipped bases both ends BaseQualityRecalibrationSuite: - BQSR Test Input #1 w/ VCF Sites without caching - BQSR Test Input #1 w/ VCF Sites with caching - BQSR Test Input #1 w/ VCF Sites with serialized caching DinucCovariateSuite: - computing dinucleotide pairs for a single base sequence should return (N,N) - compute dinucleotide pairs for a string of all valid bases - compute dinucleotide pairs for a string with an N - compute covariates for a read on the negative strand - compute covariates for a read on the positive strand SequenceDictionarySuite: - Convert from sam sequence record and back - Convert from SAM sequence dictionary file (with extra fields) - merge into existing dictionary - Convert from SAM sequence dictionary and back - Can retrieve sequence by name - SequenceDictionary's with same single element are equal - SequenceDictionary's with same two elements are equals - SequenceDictionary's with different elements are unequal - SequenceDictionaries with same elements in different order are compatible - isCompatible tests equality on overlap - The addition + works correctly - The append operation ++ works correctly - ContainsRefName works correctly for different string types - Apply on name works correctly for different String types - convert from sam sequence record and back - convert from sam sequence dictionary and back - conversion to sam sequence dictionary has correct sort order - load sequence dictionary from VCF file - empty sequence dictionary must be empty - test filter to reference name - test filter to reference names - test filter to reference name by function GenomicPositionPartitionerSuite: - partitions the UNMAPPED ReferencePosition into the top partition - if we do not have a contig for a record, we throw an IAE - partitioning into N pieces on M total sequence length, where N > M, results in M partitions - correctly partitions a single dummy sequence into two pieces - correctly counts cumulative lengths - correctly partitions positions across two dummy sequences - test that we can range partition ADAMRecords - test that we can range partition ADAMRecords indexed by sample - test that simple partitioning works okay on a reasonable set of ADAMRecords - test indexed ReferencePosition partitioning works on a set of indexed ADAMRecords CoverageSuite: - Convert to coverage from valid Feature - Convert to coverage from valid Feature with sampleId - Convert to coverage from Feature with null/empty contigName fails with correct error - Convert to coverage from Feature with no start/end position fails with correct error - Convert to coverage from Feature with no score fails with correct error InnerTreeRegionJoinSuite: - Ensure same reference regions get passed together - Overlapping reference regions - Multiple reference regions do not throw exception RichAlignmentRecordSuite: - Unclipped Start - Unclipped End - tags contains optional fields - read overlap unmapped read - read overlap reference position - read overlap same position different contig VariantDatasetSuite: - union two variant genomic datasets together - round trip to parquet - save and reload from partitioned parquet - use broadcast join to pull down variants mapped to targets - use right outer broadcast join to pull down variants mapped to targets - use shuffle join to pull down variants mapped to targets - use right outer shuffle join to pull down variants mapped to targets - use left outer shuffle join to pull down variants mapped to targets - use full outer shuffle join to pull down variants mapped to targets - use shuffle join with group by to pull down variants mapped to targets - use right outer shuffle join with group by to pull down variants mapped to targets - convert back to variant contexts - load parquet to sql, save, re-read from avro - transform variants to contig genomic dataset - transform variants to coverage genomic dataset - transform variants to feature genomic dataset - transform variants to fragment genomic dataset - transform variants to read genomic dataset - transform variants to genotype genomic dataset - transform variants to variant context genomic dataset - filter RDD bound variants to filters passed - filter dataset bound variants to filters passed - filter RDD bound variants by quality - filter dataset bound variants by quality - filter RDD bound variants by read depth - filter dataset bound variants by read depth - filter RDD bound variants by reference read depth - filter dataset bound variants by reference read depth - filter RDD bound single nucleotide variants - filter dataset bound single nucleotide variants - filter RDD bound multiple nucleotide variants - filter dataset bound multiple nucleotide variants - filter RDD bound indel variants - filter dataset bound indel variants - filter RDD bound variants to single nucleotide variants - filter dataset bound variants to single nucleotide variants - filter RDD bound variants to multiple nucleotide variants - filter dataset bound variants to multiple nucleotide variants - filter RDD bound variants to indel variants - filter dataset bound variants to indel variants - transform dataset via java API Run completed in 6 minutes, 20 seconds. Total number of tests run: 1146 Suites: completed 67, aborted 0 Tests: succeeded 1146, failed 0, canceled 0, ignored 5, pending 0 All tests passed. [INFO] [INFO] >>> scoverage-maven-plugin:1.1.1:report (default-cli) > [scoverage]test @ adam-core-spark2_2.12 >>> [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-core-spark2_2.12 --- [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-core-spark2_2.12 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ adam-core-spark2_2.12 --- [INFO] Source directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/main/scala added. [INFO] Source directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/target/generated-sources/src/main/scala added. [INFO] [INFO] --- exec-maven-plugin:1.5.0:java (generate-scala-products) @ adam-core-spark2_2.12 --- SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] [INFO] --- exec-maven-plugin:1.5.0:java (generate-scala-projection-fields) @ adam-core-spark2_2.12 --- SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ adam-core-spark2_2.12 --- [INFO] Modified 2 of 199 .scala files [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:pre-compile (default-cli) @ adam-core-spark2_2.12 --- [WARNING] Skipping SCoverage execution - unsupported Scala version "2.12.8" [INFO] [INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ adam-core-spark2_2.12 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/main/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ adam-core-spark2_2.12 --- [INFO] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/main/java:-1: info: compiling [INFO] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/main/scala:-1: info: compiling [INFO] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/target/generated-sources/src/main/scala:-1: info: compiling [INFO] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/target/generated-sources/annotations:-1: info: compiling [INFO] Compiling 136 source files to /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/target/2.12.8/classes at 1557939685917 [WARNING] warning: there were 21 deprecation warnings [WARNING] warning: there were 31 deprecation warnings (since 0.21.0) [WARNING] warning: there was one deprecation warning (since 1.0.6) [WARNING] warning: there were 31 deprecation warnings (since 2.0.0) [WARNING] warning: there was one deprecation warning (since 2.11.0) [WARNING] warning: there were 170 deprecation warnings (since 2.12.0) [WARNING] warning: there was one deprecation warning (since 2.12.7) [WARNING] warning: there were 256 deprecation warnings in total; re-run with -deprecation for details [WARNING] warning: there were 5 feature warnings; re-run with -feature for details [WARNING] 9 warnings found [INFO] prepare-compile in 0 s [INFO] compile in 25 s [INFO] [INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ adam-core-spark2_2.12 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:post-compile (default-cli) @ adam-core-spark2_2.12 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ adam-core-spark2_2.12 --- [INFO] Test Source directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala added. [INFO] [INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ adam-core-spark2_2.12 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 150 resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ adam-core-spark2_2.12 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ adam-core-spark2_2.12 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ adam-core-spark2_2.12 --- [INFO] Tests are skipped. [INFO] [INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ adam-core-spark2_2.12 --- Discovery starting. Discovery completed in 1 second, 586 milliseconds. Run starting. Expected test count is: 1146 RepairPartitionsSuite: - don't pull from the first partition - properly handle pulling from an empty iterator - gets a single read from the partition if there are no other reads in the pair - gets all the reads from a pair from the start of a partition - properly handle dropping from an empty iterator - don't drop from the first partition - drop a single read from the partition if there are no other reads in the pair - drops all the reads from a pair from the start of a partition - only append to the first partition - drop a single read from the partition and append read when in the middle - drop reads from the start and don't append when in the last partition - can't have more records than number of partitions - unroll array for broadcast 2019-05-15 10:01:55 WARN Utils:66 - Your hostname, research-jenkins-worker-07 resolves to a loopback address: 127.0.1.1; using 192.168.10.27 instead (on interface eth0) 2019-05-15 10:01:55 WARN Utils:66 - Set SPARK_LOCAL_IP if you need to bind to another address 2019-05-15 10:01:55 WARN NativeCodeLoader:62 - Unable to load native-hadoop library for your platform... using builtin-java classes where applicable - move pairs around an rdd FlagStatSuite: - Standard FlagStat test ModPartitionerSuite: - report number of partitions correctly - partition a number that is lower than the number of partitions and positive - partition a number that is greater than the number of partitions and positive - partition a number that is lower than the number of partitions and negative - partition a number that is greater than the number of partitions and negative - fire an exception if input is not an integer TwoBitFileSuite: - correctly read sequence from .2bit file - correctly return masked sequences from .2bit file - correctly return Ns from .2bit file - correctly calculates sequence dictionary NonoverlappingRegionsSuite: - alternating returns an alternating seq of items - Single region returns itself - Two adjacent regions will be merged - Nonoverlapping regions will all be returned - Many overlapping regions will all be merged - ADAMRecords return proper references FlankReferenceFragmentsSuite: - don't put flanks on non-adjacent fragments - put flanks on adjacent fragments ReferencePositionSuite: - create reference position from mapped read - create reference position from variant - create reference position from genotype - create reference position from variant starting at vcf 0 - create reference position from genotype starting at vcf 0 ConsensusGeneratorFromReadsSuite: - checking search for consensus list for artificial reads FragmentConverterSuite: - build a fragment collector and convert to a read - if a fragment isn't associated with a contig, don't get a fragment collector - convert an rdd of discontinuous fragments, all from the same contig - convert an rdd of contiguous fragments, all from the same contig - convert an rdd of varied fragments from multiple contigs FileMergerSuite: - cannot write both empty gzip block and cram eof - buffer size must be non-negative AlignmentRecordDatasetSuite: - sorting reads - unmapped reads go at the end when sorting - coverage does not fail on unmapped reads 2019-05-15 10:02:06 WARN Utils:66 - Truncated the string representation of a plan since it was too large. This behavior can be adjusted by setting 'spark.debug.maxToStringFields' in SparkEnv.conf. - computes coverage - computes coverage with multiple samples - merges adjacent records with equal coverage values - sorting reads by reference index - round trip from ADAM to SAM and back to ADAM produces equivalent Read values - round trip with single CRAM file produces equivalent Read values - round trip with sharded CRAM file produces equivalent Read values - SAM conversion sets read mapped flag properly - load long FASTQ reads - load FASTQ with no bases - convert malformed FASTQ (no quality scores) => SAM => well-formed FASTQ => SAM - round trip from ADAM to FASTQ and back to ADAM produces equivalent Read values - round trip from ADAM to paired-FASTQ and back to ADAM produces equivalent Read values - writing a small file with tags should produce the expected result - writing a small sorted file as SAM should produce the expected result - writing unordered sam from unordered sam - writing ordered sam from unordered sam - write single sam file back - write single bam file back - saveAsParquet with save args, sequence dictionary, and read group dictionary - load parquet to sql, save, re-read from avro - load from sam, save as partitioned parquet, and re-read from partitioned parquet - save as SAM format - save as sorted SAM format - save as BAM format - save as sorted BAM format - save as FASTQ format - save as ADAM parquet format - saveAsSam SAM format - saveAsSam SAM format single file - saveAsSam sorted SAM format single file - saveAsSam BAM format - saveAsSam BAM format single file - saveAsSam sorted BAM format single file - saveAsFastq - saveAsFastq as single file - saveAsFastq with original base qualities - saveAsFastq sorted by read name - saveAsFastq sorted by read name with original base qualities 2019-05-15 10:02:32 WARN RDDBoundAlignmentRecordDataset:190 - Found 20 read names that don't occur exactly twice: 1x: 20 Samples: simread:1:237728409:true simread:1:195211965:false simread:1:163841413:false simread:1:231911906:false simread:1:26472783:false simread:1:165341382:true simread:1:240344442:true simread:1:50683371:false simread:1:240997787:true simread:1:14397233:false simread:1:207027738:true simread:1:20101800:true simread:1:101556378:false simread:1:37577445:false simread:1:189606653:true simread:1:5469106:true simread:1:186794283:true simread:1:89554252:false simread:1:153978724:false simread:1:169801933:true - saveAsFastq paired FASTQ 2019-05-15 10:02:33 WARN RDDBoundAlignmentRecordDataset:190 - Found 20 read names that don't occur exactly twice: 1x: 20 Samples: simread:1:237728409:true simread:1:195211965:false simread:1:163841413:false simread:1:231911906:false simread:1:26472783:false simread:1:165341382:true simread:1:240344442:true simread:1:50683371:false simread:1:240997787:true simread:1:14397233:false simread:1:207027738:true simread:1:20101800:true simread:1:101556378:false simread:1:37577445:false simread:1:189606653:true simread:1:5469106:true simread:1:186794283:true simread:1:89554252:false simread:1:153978724:false simread:1:169801933:true - saveAsPairedFastq 2019-05-15 10:02:34 WARN RDDBoundAlignmentRecordDataset:190 - Found 20 read names that don't occur exactly twice: 1x: 20 Samples: simread:1:237728409:true simread:1:195211965:false simread:1:163841413:false simread:1:231911906:false simread:1:26472783:false simread:1:165341382:true simread:1:240344442:true simread:1:50683371:false simread:1:240997787:true simread:1:14397233:false simread:1:207027738:true simread:1:20101800:true simread:1:101556378:false simread:1:37577445:false simread:1:189606653:true simread:1:5469106:true simread:1:186794283:true simread:1:89554252:false simread:1:153978724:false simread:1:169801933:true - saveAsPairedFastq as single files - don't lose any reads when piping as SAM 2019-05-15 10:02:45 WARN OutFormatterRunner:190 - Piped command List(sleep, 10) timed out after 5 seconds. 2019-05-15 10:02:45 WARN OutFormatterRunner:190 - Piped command List(sleep, 10) timed out after 5 seconds. - lose all records when a command times out - lose no records without a timeout 2019-05-15 10:03:06 WARN OutFormatterRunner:190 - Piped command List(python, /tmp/adamTestMvnpjenoa0/spark-9545e254-1b9c-462f-80c0-4e8160a68f34/userFiles-832f7c25-cf20-4752-88e5-0aab5ca52177/timeout.py) timed out after 5 seconds. 2019-05-15 10:03:06 WARN OutFormatterRunner:190 - Piped command List(python, /tmp/adamTestMvnpjenoa0/spark-9545e254-1b9c-462f-80c0-4e8160a68f34/userFiles-832f7c25-cf20-4752-88e5-0aab5ca52177/timeout.py) timed out after 5 seconds. - lose some records when a command times out - don't lose any reads when piping as SAM using java pipe - don't lose any reads when piping as BAM - don't lose any reads when piping fastq to sam - can properly set environment variables inside of a pipe - read vcf from alignment record pipe !!! IGNORED !!! - use broadcast join to pull down reads mapped to targets - use broadcast join against to pull down reads mapped to targets - use right outer broadcast join to pull down reads mapped to targets - use right outer broadcast join against to pull down reads mapped to targets - use shuffle join with feature spanning partitions - use shuffle join to pull down reads mapped to targets - use shuffle join with flankSize to pull down reads mapped close to targets - use right outer shuffle join to pull down reads mapped to targets - use left outer shuffle join to pull down reads mapped to targets - use full outer shuffle join to pull down reads mapped to targets - use shuffle join with group by to pull down reads mapped to targets - use right outer shuffle join with group by to pull down reads mapped to targets - cannot provide empty quality score bins - cannot provide bins with a gap - cannot provide overlapping bins - binning quality scores in reads succeeds even if reads have no quality scores - bin quality scores in reads - union two read files together - test k-mer counter - test dataset based k-mer counter - transform reads to contig genomic dataset - transform reads to coverage genomic dataset - transform reads to feature genomic dataset - transform reads to fragment genomic dataset - transform reads to genotype genomic dataset loading /tmp/adamTestMvnpjenoa0/TempSuite2092003803646348106.adam as parquet into RDD... loading /tmp/adamTestMvnpjenoa0/TempSuite7790111402099210763.adam as parquet into RDD... - transform reads to variant genomic dataset - cannot have a null processing step ID - convert a processing description to htsjdk - GenomicDataset.sort does not fail on unmapped reads - GenomicDataset.sortLexicographically does not fail on unmapped reads - left normalize indels - running base recalibration with downsampling doesn't drop reads - filter RDD bound alignments by MAPQ - filter dataset bound alignments by MAPQ - filter RDD bound unaligned alignments - filter dataset bound unaligned alignments - filter RDD bound unpaired alignments - filter dataset bound unpaired alignments - filter RDD bound duplicate alignments - filter dataset bound duplicate alignments - filter RDD bound alignments to primary alignments - filter dataset bound alignments to primary alignments - filter RDD bound alignments to read group - filter dataset bound alignments to read group - filter RDD bound alignments to read groups - filter dataset bound alignments to read groups - filter RDD bound alignments to sample - filter dataset bound alignments to sample - filter RDD bound alignments to samples - filter dataset bound alignments to samples - sort by read name - transform dataset via java API SingleReadBucketSuite: - convert unmapped pair to fragment - convert proper pair to fragment - convert read pair to fragment with first of pair chimeric read RecalibrationTableSuite: - look up quality scores in table InterleavedFastqInputFormatSuite: - interleaved FASTQ hadoop reader: interleaved_fastq_sample1.ifq->interleaved_fastq_sample1.ifq.output - interleaved FASTQ hadoop reader: interleaved_fastq_sample2.ifq->interleaved_fastq_sample2.ifq.output - interleaved FASTQ hadoop reader: interleaved_fastq_sample3.ifq->interleaved_fastq_sample3.ifq.output - interleaved FASTQ hadoop reader: interleaved_fastq_sample4.ifq->interleaved_fastq_sample4.ifq.output - interleaved FASTQ hadoop reader: interleaved_fastq_sample5.ifq->interleaved_fastq_sample5.ifq.output TreeRegionJoinSuite: - run a join between data on a single contig ReferenceRegionSuite: - cannot create an empty predicate - parse empty string throws IllegalArgumentException - parse contigName only string into reference regions - parse to end strings into reference regions - parse string into reference regions - contains(: ReferenceRegion) - contains(: ReferencePosition) - merge - overlaps and covers - overlapsBy and coversBy - distance(: ReferenceRegion) - distance(: ReferencePosition) - unstrandedDistance - subtract fails on non-overlapping and non-covering regions - subtract - create region from unmapped read fails - create region from read with null alignment positions fails - create stranded region from unmapped read fails - create stranded region from read with null alignment positions fails - create stranded region from read with null alignment strand fails - create stranded region from read on forward strand - create stranded region from read on reverse strand - create region from mapped read contains read start and end - validate that adjacent regions can be merged - validate that non-adjacent regions cannot be merged - validate that nearby regions can be merged - validate that non-nearby regions cannot be merged - compute convex hull of two sets - region name is sanitized when creating region from read - intersection fails on non-overlapping regions - intersection fails when minOverlap is not met - compute intersection - overlap tests for oriented reference region - check the width of a reference region - make a reference region for a variant or genotype - make a reference region for a variant or genotype starting at VCF 0 - uniformly pad a reference region - uniformly pad a reference region into negative coordinate space, ensure non negative start - unevenly pad a reference region - unevenly pad a reference region into negative coordinate space, ensure non negative start - can build an open ended reference region - can build an open ended reference region with strand - can build a reference region with an open start position - can build a reference region with an open start position with strand - can build a reference region that covers the entirety of a contig - can build a reference region that covers the entirety of a contig with strand - convert a genotype and then get the reference region - create region from feature with null alignment positions fails - create stranded region from feature with null alignment positions fails - create stranded region from feature with null alignment strand fails - create stranded region from feature on forward strand - create stranded region from feature on reverse strand AlignmentRecordConverterSuite: - testing the fields in a converted ADAM Read - converting a read with null quality is OK - convert a read to fastq - reverse complement reads when converting to fastq - converting to fastq with unmapped reads where read reverse complemented flag (Ox10) was NOT set - converting to fastq with unmapped reads where reverse complemented flag (0x10) was set - converting a fragment with no alignments should yield unaligned reads - converting a fragment with alignments should restore the alignments - read negative strand is propagated even when not mapped CoverageDatasetSuite: - correctly saves coverage - can read a bed file to coverage - correctly filters coverage with predicate - keeps sample metadata - can read a bed file with multiple samples to coverage - correctly flatmaps coverage without aggregated bins - correctly flatmaps coverage with aggregated bins - collapses coverage records in one partition - approximately collapses coverage records in multiple partitions - transform coverage to contig rdd - transform coverage to feature rdd - transform coverage to fragment rdd - transform coverage to read rdd - transform coverage to genotype rdd - transform coverage to variant rdd - transform coverage to variant context rdd - copy coverage rdd - copy coverage dataset - copy coverage rdd without sequence dictionary - copy coverage dataset without sequence dictionary - transform dataset via java API RecalibratorSuite: - don't replace quality if quality was null - if no covariates, return alignment - skip recalibration if base is below quality threshold - recalibrate changed bases above quality threshold GenotypeDatasetSuite: - union two genotype genomic datasets together - round trip to parquet - round trip to partitioned parquet - use broadcast join to pull down genotypes mapped to targets - use right outer broadcast join to pull down genotypes mapped to targets - use shuffle join to pull down genotypes mapped to targets - use right outer shuffle join to pull down genotypes mapped to targets - use left outer shuffle join to pull down genotypes mapped to targets - use full outer shuffle join to pull down genotypes mapped to targets - use shuffle join with group by to pull down genotypes mapped to targets - use right outer shuffle join with group by to pull down genotypes mapped to targets - convert back to variant contexts - load parquet to sql, save, re-read from avro - transform genotypes to contig genomic dataset - transform genotypes to coverage genomic dataset - transform genotypes to feature genomic dataset - transform genotypes to fragment genomic dataset - transform genotypes to read genomic dataset - transform genotypes to variant genomic dataset - transform genotypes to variant context genomic dataset - loading genotypes then converting to variants yields same output as loading variants - filter RDD bound genotypes to genotype filters passed - filter dataset bound genotypes to genotype filters passed - filter RDD bound genotypes by genotype quality - filter dataset bound genotypes by genotype quality - filter RDD bound genotypes by read depth - filter dataset bound genotypes by read depth - filter RDD bound genotypes by alternate read depth - filter dataset bound genotypes by alternate read depth - filter RDD bound genotypes by reference read depth - filter dataset bound genotypes by reference read depth - filter RDD bound genotypes by sample - filter dataset bound genotypes by sample - filter RDD bound genotypes by samples - filter dataset bound genotypes by samples - filter RDD bound no call genotypes - filter dataset no call genotypes - round trip gVCF END attribute without nested variant annotations rdd bound - round trip gVCF END attribute without nested variant annotations dataset bound - round trip gVCF END attribute with nested variant annotations rdd bound - round trip gVCF END attribute with nested variant annotations dataset bound - transform dataset via java API FragmentDatasetSuite: - don't lose any reads when piping interleaved fastq to sam - don't lose any reads when piping tab5 to sam - don't lose any reads when piping tab6 to sam - use broadcast join to pull down fragments mapped to targets - use right outer broadcast join to pull down fragments mapped to targets - use shuffle join to pull down fragments mapped to targets - use right outer shuffle join to pull down fragments mapped to targets - use left outer shuffle join to pull down fragments mapped to targets - use full outer shuffle join to pull down fragments mapped to targets - use shuffle join with group by to pull down fragments mapped to targets - use right outer shuffle join with group by to pull down fragments mapped to targets - bin quality scores in fragments - union two genomic datasets of fragments together - load parquet to sql, save, re-read from avro - transform fragments to contig genomic dataset - transform fragments to coverage genomic dataset - transform fragments to feature genomic dataset - transform fragments to read genomic dataset - transform fragments to genotype genomic dataset - transform fragments to variant genomic dataset - transform fragments to variant context genomic dataset - paired read names with index sequences in read names can group into fragments - interleaved paired read names with index sequences in read names can group into fragments - interleaved paired read names with index sequences in read names as fragments - transform dataset via java API SingleFastqInputFormatSuite: - FASTQ hadoop reader: fastq_sample1.fq->single_fastq_sample1.fq.output - FASTQ hadoop reader: fastq_sample2.fq->single_fastq_sample2.fq.output - FASTQ hadoop reader: fastq_sample3.fq->single_fastq_sample3.fq.output - FASTQ hadoop reader: fastq_sample4.fq->single_fastq_sample4.fq.output VariantContextDatasetSuite: - load a gvcf with a missing info field set to . - union two variant context genomic datasets together - can write, then read in .vcf file - can write as a single file via simple saveAsVcf method, then read in .vcf file - can write as a single file via full saveAsVcf method, then read in .vcf file - transform a vcf file with bad header - read a vcf file with multi-allelic variants to split - support VCFs with +Inf/-Inf float values - support VCFs with `nan` instead of `NaN` float values - don't lose any variants when piping as VCF - pipe works with empty partitions - don't lose any non-default VCF header lines or attributes when piping as VCF - save a file sorted by contig index - save a lexicographically sorted file - save a multiallelic gvcf !!! IGNORED !!! - test metadata - save sharded bgzip vcf - save bgzip vcf as single file - can't save file with non-vcf extension - transform variant contexts to contig genomic dataset - transform variant contexts to coverage genomic dataset - transform variant contexts to feature genomic dataset - transform variant contexts to fragment genomic dataset - transform variant contexts to read genomic dataset - transform variant contexts to genotype genomic dataset - transform variant contexts to variant genomic dataset - save and reload from partitioned parquet - transform dataset via java API ConsensusSuite: - test the insertion of a consensus insertion into a reference - test the insertion of a consensus deletion into a reference - inserting empty consensus returns the reference AttributeUtilsSuite: - parseTags returns a reasonable set of tagStrings - parseTags works with NumericSequence tagType - empty string is parsed as zero tagStrings - incorrectly formatted tag throws an exception - string tag with a ':' in it is correctly parsed - oq string tag with many ':' in it is correctly parsed - oq string tag with a ',' in it is correctly parsed - if a tag is an array but doesn't define it's format, throw MarkDuplicatesSuite: - single read - reads at different positions - reads at the same position - reads at the same position with clipping - reads on reverse strand - unmapped reads - read pairs - read pairs with fragments - quality scores - read pairs that cross chromosomes - single fragment - fragments at different positions - fragments at the same position - fragments at the same position with clipping - fragments on reverse strand - unmapped fragments - read pairs as fragments - read pairs with fragments as fragments - chimeric fragments - inverse pairs - supplemental reads TranscriptEffectConverterSuite: - parse empty transcript effect - parse empty transcript effect strict validation stringency - parse invalid transcript effect - parse invalid transcript effect strict validation stringency - parse transcript effect - parse empty list VCF ANN attribute - parse empty list VCF ANN attribute strict validation stringency - parse empty string VCF ANN attribute - parse empty string VCF ANN attribute strict validation stringency - parse invalid VCF ANN attribute - parse invalid VCF ANN attribute strict validation stringency - parse VCF ANN attribute with one transcript effect - parse VCF ANN attribute with multiple transcript effects - convert to transcript effect from null VCF ANN attribute in variant context - convert to transcript effect from empty list VCF ANN attribute in variant context - convert to transcript effect from empty list VCF ANN attribute in variant context strict validation stringency - convert to transcript effect from empty string VCF ANN attribute in variant context - convert to transcript effect from empty string VCF ANN attribute in variant context strict validation stringency - convert to transcript effect from invalid VCF ANN attribute in variant context - convert to transcript effect from invalid VCF ANN attribute in variant context strict validation stringency 2019-05-15 10:05:29 WARN TranscriptEffectConverter$:190 - Could not convert VCF INFO reserved key ANN value to TranscriptEffect, caught java.lang.NumberFormatException: For input string: "not a number". - convert to transcript effect from VCF ANN attribute with invalid number in variant context lenient validation stringency 2019-05-15 10:05:29 WARN TranscriptEffectConverter$:190 - Could not convert VCF INFO reserved key ANN value to TranscriptEffect, caught java.lang.NumberFormatException: For input string: "not a number". - convert to transcript effect from VCF ANN attribute with invalid fraction in variant context lenient validation stringency - convert to transcript effect from VCF ANN attribute with invalid number in variant context strict validation stringency - convert to transcript effect from VCF ANN attribute with invalid fraction in variant context strict validation stringency - convert to transcript effect from VCF ANN attribute in variant context different alt allele - convert to transcript effect from VCF ANN attribute in variant context same alt allele - convert to transcript effect from VCF ANN attribute in variant context multiple effects same alt allele - convert transcript effect to VCF ANN attribute value - convert transcript effect with null fields to VCF ANN attribute value 2019-05-15 10:05:29 WARN TranscriptEffectConverter$:190 - Incorrect fractional value ?/2, missing numerator - convert transcript effect with incorrect fractional value to VCF ANN attribute value IndelRealignmentTargetSuite: - checking simple realignment target - creating simple target from read with deletion - creating simple target from read with insertion - joining simple realignment targets on same chr - joining simple realignment targets on different chr throws exception - creating targets from three intersecting reads, same indel - creating targets from three intersecting reads, two different indel - creating targets from two disjoint reads - creating targets for artificial reads: one-by-one - creating targets for artificial reads: all-at-once (merged) - creating indel targets for mason reads - additional indel targets taken from consensus generator NormalizationUtilsSuite: - cannot move an indel left if there are no bases to it's left - move a simple indel to farthest position left until bases run out - move a simple indel to farthest position left, past length of indel - cannot move a left normalized indel in a short tandem repeat - move an indel in a short tandem repeat - move an indel in a short tandem repeat of more than 2 bases, where shift is not an integer multiple of repeated sequence length - moving a simple read with single deletion that cannot shift - shift an indel left by 0 in a cigar - shift an indel left by 1 in a cigar - do not left align a complex read which is already left aligned ReadGroupDictionarySuite: - simple conversion to and from sam read group - sample name must be set - simple equality checks - get samples from read group dictionary - empty read group is empty - merging a dictionary with itself should work - round trip a record with all attributes set NucleotideContigFragmentDatasetSuite: - union two ncf genomic datasets together - round trip a ncf to parquet - round trip a ncf to partitioned parquet - save fasta back as a single file - generate sequence dict from fasta - recover reference string from a single contig fragment - recover trimmed reference string from a single contig fragment - recover reference string from multiple contig fragments - extract sequences based on the list of reference regions - recover trimmed reference string from multiple contig fragments - testing nondeterminism from reduce when recovering referencestring - save single contig fragment as FASTA text file - save single contig fragment with description as FASTA text file - save single contig fragment with null fields as FASTA text file - save single contig fragment with null fragment number as FASTA text file - save single contig fragment with null number of fragments in contig as FASTA text file - save multiple contig fragments from same contig as FASTA text file - save multiple contig fragments with description from same contig as FASTA text file - merge single contig fragment null fragment number - merge single contig fragment number zero - merge multiple contig fragments - save as parquet and apply predicate pushdown - load fasta sequences from GFF3 file - transform contigs to coverage genomic dataset - transform contigs to feature genomic dataset - transform contigs to fragment genomic dataset - transform contigs to read genomic dataset - transform contigs to genotype genomic dataset - transform contigs to variant genomic dataset - transform contigs to variant context genomic dataset RightOuterTreeRegionJoinSuite: - Ensure same reference regions get passed together - Overlapping reference regions InnerShuffleRegionJoinSuite: - Overlapping reference regions - Multiple reference regions do not throw exception FeatureDatasetSuite: - round trip GTF format - save GTF as GFF3 format - save GTF as BED format - save GTF as IntervalList format - save GTF as NarrowPeak format - save GFF3 as GTF format - save GFF3 as BED format - save GFF3 as IntervalList format - save GFF3 as NarrowPeak format - round trip GFF3 format - ignore FASTA sequence in GFF3 file - save BED as GTF format - save BED as GFF3 format - save BED as IntervalList format - save BED as NarrowPeak format - round trip BED6 format - keeps sample metadata - round trip BED12 format - save to UCSC BED format - save IntervalList as GTF format - save IntervalList as GFF3 format - save IntervalList as BED format - save IntervalList as IntervalList format - save IntervalList as NarrowPeak format - round trip IntervalList format - save NarrowPeak as GTF format - save NarrowPeak as GFF3 format - save NarrowPeak as BED format - save NarrowPeak as IntervalList format - save NarrowPeak as NarrowPeak format - round trip NarrowPeak format - sort by reference - sort by reference and feature fields - sort gene features by reference and gene structure - sort transcript features by reference and gene structure - sort exon features by reference and gene structure - sort intron features by reference and gene structure - correctly flatmaps CoverageDataset from FeatureDataset - use broadcast join to pull down features mapped to targets - use right outer broadcast join to pull down features mapped to targets - use shuffle join to pull down features mapped to targets - use right outer shuffle join to pull down features mapped to targets - use left outer shuffle join to pull down features mapped to targets - use full outer shuffle join to pull down features mapped to targets - use shuffle join with group by to pull down features mapped to targets - use right outer shuffle join with group by to pull down features mapped to targets - union two feature rdds together - obtain sequence dictionary contig lengths from header in IntervalList format - don't lose any features when piping as BED format - don't lose any features when piping as GTF format - don't lose any features when piping as GFF3 format - don't lose any features when piping as NarrowPeak format - load parquet to sql, save, re-read from avro - load partitioned parquet to sql, save, re-read from avro - transform features to contig rdd - transform features to coverage rdd - transform features to fragment rdd - transform features to read rdd - transform features to genotype rdd - transform features to variant rdd - transform features to variant context rdd - filter RDD bound features by feature type - filter dataset bound features by feature type - filter RDD bound features by feature types - filter dataset bound features by feature types - filter RDD bound features by gene - filter dataset bound features by gene - filter RDD bound features by genes - filter dataset bound features by genes - filter RDD bound features by transcript - filter dataset bound features by transcript - filter RDD bound features by transcripts - filter dataset bound features by transcripts - filter RDD bound features by exon - filter dataset bound features by exon - filter RDD bound features by exons - filter dataset bound features by exons - filter RDD bound features by score - filter dataset bound features by score - filter RDD bound features by parent - filter dataset bound features by parent - filter RDD bound features by parents - filter dataset bound features by parents - filter RDD bound features by attribute - filter dataset bound features by attribute - transform dataset via java API AlphabetSuite: - test size of a case-sensitive alphabet - test apply of a case-sensitive alphabet - test reverse complement of a case-sensitive alphabet - test exact reverse complement of a case-sensitive alphabet - test size of a case-insensitive alphabet - test apply of a case-insensitive alphabet - test reverse complement of a case-insensitive alphabet - test exact reverse complement of a case-insensitive alphabet - DNA alphabet - map unknown bases to N SortedGenomicDatasetSuite: - testing that partition and sort provide correct outputs - testing copartition maintains or adds sort - testing that we don't drop any data on the right side even though it doesn't map to a partition on the left - testing that sorted shuffleRegionJoin matches unsorted - testing that sorted fullOuterShuffleRegionJoin matches unsorted - testing that sorted rightOuterShuffleRegionJoin matches unsorted - testing that sorted leftOuterShuffleRegionJoin matches unsorted - testing that we can persist the sorted knowledge VariantContextConverterSuite: - Convert htsjdk site-only SNV to ADAM - Convert somatic htsjdk site-only SNV to ADAM - Convert htsjdk site-only CNV to ADAM - Convert htsjdk SNV w/ genotypes w/ phase information to ADAM - Convert htsjdk SNV with different variant filters to ADAM - Convert htsjdk SNV with different genotype filters to ADAM - Convert ADAM site-only SNV to htsjdk - Convert ADAM SNV w/ genotypes to htsjdk - Convert ADAM SNV w/ genotypes but bad SB to htsjdk with strict validation 2019-05-15 10:06:40 WARN VariantContextConverter:2300 - Applying annotation extraction function org.bdgenomics.adam.converters.VariantContextConverter$$Lambda$803/87060781@52ff0e02 to {"variant": {"referenceName": "1", "start": 0, "end": 1, "names": [], "splitFromMultiAllelic": false, "referenceAllele": "A", "alternateAllele": "T", "quality": null, "filtersApplied": null, "filtersPassed": null, "filtersFailed": [], "annotation": null}, "referenceName": null, "start": null, "end": null, "variantCallingAnnotations": {"filtersApplied": null, "filtersPassed": null, "filtersFailed": [], "downsampled": null, "baseQRankSum": null, "fisherStrandBiasPValue": 3.0, "rmsMapQ": 0.0, "mapq0Reads": 5, "mqRankSum": null, "readPositionRankSum": null, "genotypePriors": [], "genotypePosteriors": [], "vqslod": null, "culprit": null, "attributes": {}}, "sampleId": "NA12878", "sampleDescription": null, "processingDescription": null, "alleles": ["REF", "ALT"], "expectedAlleleDosage": null, "referenceReadDepth": null, "alternateReadDepth": null, "readDepth": null, "minReadDepth": null, "genotypeQuality": null, "genotypeLikelihoods": [], "nonReferenceLikelihoods": [], "strandBiasComponents": [0, 2], "splitFromMultiAllelic": false, "phased": false, "phaseSetId": null, "phaseQuality": null} failed with java.lang.IllegalArgumentException: requirement failed: Illegal strand bias components length. Must be empty or 4. In: {"variant": {"referenceName": "1", "start": 0, "end": 1, "names": [], "splitFromMultiAllelic": false, "referenceAllele": "A", "alternateAllele": "T", "quality": null, "filtersApplied": null, "filtersPassed": null, "filtersFailed": [], "annotation": null}, "referenceName": null, "start": null, "end": null, "variantCallingAnnotations": {"filtersApplied": null, "filtersPassed": null, "filtersFailed": [], "downsampled": null, "baseQRankSum": null, "fisherStrandBiasPValue": 3.0, "rmsMapQ": 0.0, "mapq0Reads": 5, "mqRankSum": null, "readPositionRankSum": null, "genotypePriors": [], "genotypePosteriors": [], "vqslod": null, "culprit": null, "attributes": {}}, "sampleId": "NA12878", "sampleDescription": null, "processingDescription": null, "alleles": ["REF", "ALT"], "expectedAlleleDosage": null, "referenceReadDepth": null, "alternateReadDepth": null, "readDepth": null, "minReadDepth": null, "genotypeQuality": null, "genotypeLikelihoods": [], "nonReferenceLikelihoods": [], "strandBiasComponents": [0, 2], "splitFromMultiAllelic": false, "phased": false, "phaseSetId": null, "phaseQuality": null}. - Convert ADAM SNV w/ genotypes but bad SB to htsjdk with lenient validation - Convert htsjdk multi-allelic sites-only SNVs to ADAM - Convert htsjdk multi-allelic SNVs to ADAM and back to htsjdk - Convert gVCF reference records to ADAM - Convert htsjdk variant context with no IDs to ADAM - Convert htsjdk variant context with one ID to ADAM - Convert htsjdk variant context with multiple IDs to ADAM - Convert ADAM variant context with no names to htsjdk - Convert ADAM variant context with one name to htsjdk - Convert ADAM variant context with multiple names to htsjdk - Convert ADAM variant context with null filters applied to htsjdk - Convert ADAM variant context with no filters applied to htsjdk - Convert ADAM variant context with passing filters to htsjdk - Convert ADAM variant context with failing filters to htsjdk - no phasing set going htsjdk->adam - phased but no phase set info going htsjdk->adam - set phase set and extract going htsjdk->adam - no allelic depth going htsjdk->adam - set allelic depth going htsjdk->adam - no gt read depth going htsjdk->adam - extract gt read depth going htsjdk->adam - no min gt read depth going htsjdk->adam - extract min gt read depth going htsjdk->adam - no genotype quality going htsjdk->adam - extract genotype quality going htsjdk->adam - no phred likelihood going htsjdk->adam - extract phred likelihoods going htsjdk->adam - no strand bias info going htsjdk->adam - extract strand bias info going htsjdk->adam - no filters going htsjdk->adam - filters passed going htsjdk->adam - extract single filter going htsjdk->adam - extract multiple filters going htsjdk->adam - no fisher strand bias going htsjdk->adam - extract fisher strand bias going htsjdk->adam - no rms mapping quality going htsjdk->adam - extract rms mapping quality going htsjdk->adam - no mq0 going htsjdk->adam - extract mq0 going htsjdk->adam - no gt read depth going adam->htsjdk - extract gt read depth going adam->htsjdk - throw iae if missing one component of gt read depth going adam->htsjdk - no depth going adam->htsjdk - extract depth going adam->htsjdk - no min depth going adam->htsjdk - extract min depth going adam->htsjdk - no quality going adam->htsjdk - extract quality going adam->htsjdk - no genotype likelihoods going adam->htsjdk - extract genotype likelihoods going adam->htsjdk - no strand bias going adam->htsjdk - malformed strand bias going adam->htsjdk - extract strand bias going adam->htsjdk - no phasing info going adam->htsjdk - unphased going adam->htsjdk - phased but no ps/pq going adam->htsjdk - phased but no pq going adam->htsjdk - phased but no ps going adam->htsjdk - phased going adam->htsjdk - no filter info going adam->htsjdk - if filters applied, must set passed/failed going adam->htsjdk - filters passed going adam->htsjdk - if filters failed, must set filters failed going adam->htsjdk - single filter failed going adam->htsjdk - multiple filters failed going adam->htsjdk - no fisher strand bias going adam->htsjdk - extract fisher strand bias going adam->htsjdk - no rms mapping quality going adam->htsjdk - extract rms mapping quality going adam->htsjdk - no mapping quality 0 reads going adam->htsjdk - extract mapping quality 0 reads going adam->htsjdk - no names set going htsjdk->adam - single name set going htsjdk->adam - multiple names set going htsjdk->adam - no quality going htsjdk->adam - quality set going htsjdk->adam - no filters applied going htsjdk->adam - filters applied and passed going htsjdk->adam - single filter applied and failed going htsjdk->adam - multiple filters applied and failed going htsjdk->adam - no names set adam->htsjdk - set a single name adam->htsjdk - set multiple names adam->htsjdk - no qual set adam->htsjdk - qual is set adam->htsjdk - no filters applied adam->htsjdk - null filters applied adam->htsjdk - filters passed adam->htsjdk - if filter failed, must have filters adam->htsjdk - single filter failed adam->htsjdk - multiple filters failed adam->htsjdk - no ancestral allele set going htsjdk->adam - ancestral allele set going htsjdk->adam - no dbsnp membership set going htsjdk->adam - dbsnp membership set going htsjdk->adam - no hapmap2 membership set going htsjdk->adam - hapmap2 membership set going htsjdk->adam - no hapmap3 membership set going htsjdk->adam - hapmap3 membership set going htsjdk->adam - no validated set going htsjdk->adam - validated set going htsjdk->adam - no 1000G membership set going htsjdk->adam - 1000G membership set going htsjdk->adam - not somatic going htsjdk->adam - somatic going htsjdk->adam - no allele count going htsjdk->adam - single allele count going htsjdk->adam - multiple allele counts going htsjdk->adam - no allele frequency going htsjdk->adam - single allele frequency going htsjdk->adam - single allele frequency is +Inf going htsjdk->adam - single allele frequency is -Inf going htsjdk->adam - multiple allele frequencies going htsjdk->adam - no CIGAR going htsjdk->adam - single CIGAR going htsjdk->adam - multiple CIGARs going htsjdk->adam - no read depth going htsjdk->adam - single read depth going htsjdk->adam - multiple read depths going htsjdk->adam - no forward read depth going htsjdk->adam - single forward read depth going htsjdk->adam - multiple forward read depths going htsjdk->adam - no reverse read depth going htsjdk->adam - single reverse read depth going htsjdk->adam - multiple reverse read depths going htsjdk->adam - no ancestral allele set adam->htsjdk - ancestral allele set adam->htsjdk - no dbsnp membership set adam->htsjdk - dbsnp membership set adam->htsjdk - no hapmap2 membership set adam->htsjdk - hapmap2 membership set adam->htsjdk - no hapmap3 membership set adam->htsjdk - hapmap3 membership set adam->htsjdk - no validated set adam->htsjdk - validated set adam->htsjdk - no 1000G membership set adam->htsjdk - 1000G membership set adam->htsjdk - no allele count set adam->htsjdk - allele count set adam->htsjdk - no allele frequency set adam->htsjdk - allele frequency set adam->htsjdk - no cigar set adam->htsjdk - cigar set adam->htsjdk - no read depth set adam->htsjdk - read depth set adam->htsjdk - read depth without reference read depth - reference read depth without read depth - no forward read depth set adam->htsjdk - forward read depth set adam->htsjdk - reference forward read depth without forward read depth - forward read depth without reference forward read depth - no reverse read depth set adam->htsjdk - reverse read depth set adam->htsjdk - reference reverse read depth without reverse read depth - reverse read depth without reference reverse read depth - VCF INFO attribute Number=0 Type=Flag adam->htsjdk - VCF INFO attribute Number=4 Type=Flag adam->htsjdk unsupported, strict !!! IGNORED !!! - VCF INFO attribute Number=1 Type=Integer adam->htsjdk - VCF INFO attribute Number=4 Type=Integer adam->htsjdk - VCF INFO attribute Number=A Type=Integer adam->htsjdk - VCF INFO attribute Number=R Type=Integer adam->htsjdk - VCF INFO attribute Number=R Type=String adam->htsjdk - VCF INFO attribute Number=G Type=String adam->htsjdk not supported - VCF INFO attribute Number=0 Type=Flag htsjdk->adam - VCF INFO attribute Number=1 Type=Integer htsjdk->adam - VCF INFO attribute Number=4 Type=Integer htsjdk->adam - VCF INFO attribute Number=4 Type=Float htsjdk->adam - VCF INFO attribute Number=A Type=Integer htsjdk->adam - VCF INFO attribute Number=R Type=Integer htsjdk->adam - VCF INFO attribute Number=R Type=String htsjdk->adam - VCF INFO attribute Number=G Type=String htsjdk->adam not supported - VCF FORMAT attribute Number=0 Type=Flag adam->htsjdk not supported - VCF FORMAT attribute Number=1 Type=Integer adam->htsjdk - VCF FORMAT attribute Number=4 Type=Integer adam->htsjdk - VCF FORMAT attribute Number=A Type=Integer adam->htsjdk - VCF FORMAT attribute Number=R Type=Integer adam->htsjdk - VCF FORMAT attribute Number=R Type=String adam->htsjdk - VCF FORMAT attribute Number=0 Type=Flag htsjdk->adam is not supported - VCF FORMAT attribute Number=1 Type=Integer htsjdk->adam - VCF FORMAT attribute Number=4 Type=Integer htsjdk->adam - VCF FORMAT attribute Number=4 Type=Float htsjdk->adam - VCF FORMAT attribute Number=A Type=Integer htsjdk->adam - VCF FORMAT attribute Number=R Type=Integer htsjdk->adam - VCF FORMAT attribute Number=R Type=String htsjdk->adam - VCF FORMAT attribute Number=G Type=String htsjdk->adam - respect end position for symbolic alts FastqRecordConverterSuite: - test read name suffix and index of pair must match - test parseReadInFastq, read suffix removal - test parseReadInFastq, read metadata removal - test parseReadInFastq, read quality shorter than read length, padded with B - test parseReadInFastq, read quality longer than read length - test parseReadInFastq, no read quality - testing FastqRecordConverter.convertPair with valid input - testing FastqRecordConverter.convertPair with 7-line invalid input - testing FastqRecordConverter.convertPair with invalid input: first read length and qual don't match - testing FastqRecordConverter.convertPair with invalid input: second read length and qual don't match - testing FastqRecordConverter.convertFragment with valid input - testing FastqRecordConverter.convertFragment with another valid input having /1, /2 suffixes - testing FastqRecordConverter.convertFragment with invalid input: different read names - testing FastqRecordConverter.convertRead with valid input - testing FastqRecordConverter.convertRead with valid input: setFirstOfPair set to true - testing FastqRecordConverter.convertRead with valid input: setSecondOfPair set to true - testing FastqRecordConverter.convertRead with valid input: setFirstOfPair and setSecondOfPair both true - testing FastqRecordConverter.convertRead with valid input, no qual, strict - testing FastqRecordConverter.convertRead with valid input, no qual, not strict AttributeSuite: - test SAMTagAndValue parsing - Attributes can be correctly re-encoded as text SAM tags GFF3HeaderWriterSuite: - write gff3 header pragma BinQualitiesSuite: - make a quality score bin - can't have a quality score bin with negative score - can't have a quality score bin with high score below low - can't have a quality score bin with high score above 255 - can't have a quality score bin with score outside - make a quality score bin from a string - quality score bin must have exactly 3 elements - quality score bin must be integers - must define at least one bin - build multiple bins - rewrite quality scores for a read - rewriting quality scores fails if bins overlap - rewriting quality scores fails if base is out of bounds - skip read if qualities are null - rewrite a read IndexedFastaFileSuite: - correctly generates sequence dictionary from .dict file - correctly gets sequence - fails when fai index is not provided 2019-05-15 10:06:41 WARN IndexedFastaFile:190 - Caught exception java.lang.NullPointerException when loading FASTA sequence dictionary. Using empty dictionary instead. - passes when dict is not provided and ValidationStringency = LENIENT SAMRecordConverterSuite: - testing the fields in an alignmentRecord obtained from a mapped samRecord conversion - testing the fields in an alignmentRecord obtained from an unmapped samRecord conversion - '*' quality gets nulled out - don't keep denormalized fields ADAMContextSuite: - ctr is accessible - load from an empty directory - sc.loadParquet should not fail on unmapped reads - sc.loadParquet should not load a file without a type specified - can read a small .SAM file - can read a small .SAM file with a bad header with lenient validation - loading a sam file with a bad header and strict stringency should fail - can read a small .CRAM file - can read a small .SAM with all attribute tag types - can filter a .SAM file based on quality - Can convert to phred - Can convert from phred - Can read a .gtf file - Can read a .bed file - Can read a BED 12 file - Can read a .narrowPeak file - Can read a .interval_list file 2019-05-15 10:06:44 WARN VariantContextConverter:1662 - Saw invalid info field java.lang.IllegalArgumentException: Multivalued flags are not supported for INFO lines: INFO=<ID=ABADFLAG,Number=.,Type=Flag,Description="A no good, very bad flag.">. Ignoring... 2019-05-15 10:06:44 WARN VariantContextConverter:2169 - Generating field extractor from header line INFO=<ID=ABADFLAG,Number=.,Type=Flag,Description="A no good, very bad flag."> failed: java.lang.IllegalArgumentException: Multivalue flags are not supported for INFO lines: INFO=<ID=ABADFLAG,Number=.,Type=Flag,Description="A no good, very bad flag."> - can read a small .vcf file with a validation issue - can read a small .vcf file 2019-05-15 10:06:45 WARN VCFInputFormat:218 - file:/home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/target/2.12.8/test-classes/test.vcf.gz is not splittable, consider using block-compressed gzip (BGZF) - can read a gzipped .vcf file - can read a vcf file with an empty alt - can read a BGZF gzipped .vcf file with .gz file extension - can read a BGZF gzipped .vcf file with .bgz file extension - can read a vcf file with a projection - can read an uncompressed BCFv2.2 file !!! IGNORED !!! - can read a BGZF compressed BCFv2.2 file !!! IGNORED !!! - loadIndexedVcf with 1 ReferenceRegion - loadIndexedVcf with multiple ReferenceRegions - load block compressed interleaved fastq - import records from interleaved FASTQ: 1 - import records from interleaved FASTQ: 2 - import records from interleaved FASTQ: 3 - import records from interleaved FASTQ: 4 - import block compressed single fastq - import records from single ended FASTQ: 1 - import records from single ended FASTQ: 2 - import records from single ended FASTQ: 3 - import records from single ended FASTQ: 4 - filter on load using the filter2 API - saveAsParquet with file path - saveAsParquet with file path, block size, page size - saveAsParquet with save args - read a HLA fasta from GRCh38 - read a gzipped fasta file - loadIndexedBam with 1 ReferenceRegion - loadIndexedBam with multiple ReferenceRegions - loadIndexedBam with multiple ReferenceRegions and indexed bams - loadIndexedBam with multiple ReferenceRegions and a directory of indexed bams - loadIndexedBam should throw exception without an index file - loadIndexedBam should work with indexed file with index naming format <filename>.bai - loadIndexedBam glob should throw exception without an index file - loadBam with a glob - loadBam with a directory - load vcf with a glob - load vcf from a directory - load gvcf which contains a multi-allelic row from a directory - load and save gvcf which contains rows without likelihoods - parse annotations for multi-allelic rows - load parquet with globs - bad glob should fail - empty directory should fail - can read a SnpEff-annotated .vcf file - loadAlignments should not fail on single-end and paired-end fastq reads - load queryname sorted sam as fragments - load query grouped sam as fragments - load paired fastq - load paired fastq without cache - load paired fastq as fragments - load paired fastq as fragments without cache - load HTSJDK sequence dictionary - load Bedtools .genome file as sequence dictionary - load Bedtools .genome.txt file as sequence dictionary - load UCSC Genome Browser chromInfo.txt file as sequence dictionary - load unrecognized file extension as sequence dictionary fails - load BED features with Bedtools .genome file as sequence dictionary - load BED features with Bedtools .genome file as sequence dictionary, no matching features - convert program record - load program record from sam file CycleCovariateSuite: - compute covariates for an unpaired read on the negative strand - compute covariates for a first-of-pair read on the negative strand - compute covariates for a second-of-pair read on the negative strand - compute covariates for an unpaired read on the positive strand - compute covariates for a first-of-pair read on the positive strand - compute covariates for a second-of-pair read on the positive strand ConsensusGeneratorFromKnownsSuite: - no consensuses for empty target - no consensuses for reads that don't overlap a target - return a consensus for read overlapping a single target RichCigarSuite: - moving 2 bp from a deletion to a match operator - moving 2 bp from a insertion to a match operator - moving 1 base in a two element cigar - move to start of read - process right clipped cigar - process left clipped cigar - process cigar clipped on both ends MDTaggingSuite: - test adding MDTags over boundary - test adding MDTags; reads span full contig - test adding MDTags; reads start inside first fragment - test adding MDTags; reads end inside last fragment - test adding MDTags; reads start inside first fragment and end inside last fragment - test adding MDTags; reads start and end in middle fragements 2019-05-15 10:07:06 WARN BlockManager:66 - Putting block rdd_5_3 failed due to exception java.lang.Exception: Contig chr2 not found in reference map with keys: chr1. 2019-05-15 10:07:06 WARN BlockManager:66 - Block rdd_5_3 could not be removed as it was not found on disk or in memory 2019-05-15 10:07:06 ERROR Executor:91 - Exception in task 3.0 in stage 2.0 (TID 11) java.lang.Exception: Contig chr2 not found in reference map with keys: chr1 at org.bdgenomics.adam.util.ReferenceContigMap.$anonfun$extract$1(ReferenceContigMap.scala:64) at scala.collection.immutable.Map$Map1.getOrElse(Map.scala:119) at org.bdgenomics.adam.util.ReferenceContigMap.extract(ReferenceContigMap.scala:63) at org.bdgenomics.adam.rdd.read.MDTagging.$anonfun$addMDTagsBroadcast$3(MDTagging.scala:76) at scala.Option$WithFilter.map(Option.scala:163) at org.bdgenomics.adam.rdd.read.MDTagging.$anonfun$addMDTagsBroadcast$1(MDTagging.scala:71) at scala.collection.Iterator$$anon$10.next(Iterator.scala:459) at org.apache.spark.storage.memory.MemoryStore.putIterator(MemoryStore.scala:222) at org.apache.spark.storage.memory.MemoryStore.putIteratorAsValues(MemoryStore.scala:299) at org.apache.spark.storage.BlockManager.$anonfun$doPutIterator$1(BlockManager.scala:1165) at org.apache.spark.storage.BlockManager.doPut(BlockManager.scala:1091) at org.apache.spark.storage.BlockManager.doPutIterator(BlockManager.scala:1156) at org.apache.spark.storage.BlockManager.getOrElseUpdate(BlockManager.scala:882) at org.apache.spark.rdd.RDD.getOrCompute(RDD.scala:335) at org.apache.spark.rdd.RDD.iterator(RDD.scala:286) at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:90) at org.apache.spark.scheduler.Task.run(Task.scala:121) at org.apache.spark.executor.Executor$TaskRunner.$anonfun$run$3(Executor.scala:411) at org.apache.spark.util.Utils$.tryWithSafeFinally(Utils.scala:1360) at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:414) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624) at java.lang.Thread.run(Thread.java:748) 2019-05-15 10:07:06 WARN TaskSetManager:66 - Lost task 3.0 in stage 2.0 (TID 11, localhost, executor driver): java.lang.Exception: Contig chr2 not found in reference map with keys: chr1 at org.bdgenomics.adam.util.ReferenceContigMap.$anonfun$extract$1(ReferenceContigMap.scala:64) at scala.collection.immutable.Map$Map1.getOrElse(Map.scala:119) at org.bdgenomics.adam.util.ReferenceContigMap.extract(ReferenceContigMap.scala:63) at org.bdgenomics.adam.rdd.read.MDTagging.$anonfun$addMDTagsBroadcast$3(MDTagging.scala:76) at scala.Option$WithFilter.map(Option.scala:163) at org.bdgenomics.adam.rdd.read.MDTagging.$anonfun$addMDTagsBroadcast$1(MDTagging.scala:71) at scala.collection.Iterator$$anon$10.next(Iterator.scala:459) at org.apache.spark.storage.memory.MemoryStore.putIterator(MemoryStore.scala:222) at org.apache.spark.storage.memory.MemoryStore.putIteratorAsValues(MemoryStore.scala:299) at org.apache.spark.storage.BlockManager.$anonfun$doPutIterator$1(BlockManager.scala:1165) at org.apache.spark.storage.BlockManager.doPut(BlockManager.scala:1091) at org.apache.spark.storage.BlockManager.doPutIterator(BlockManager.scala:1156) at org.apache.spark.storage.BlockManager.getOrElseUpdate(BlockManager.scala:882) at org.apache.spark.rdd.RDD.getOrCompute(RDD.scala:335) at org.apache.spark.rdd.RDD.iterator(RDD.scala:286) at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:90) at org.apache.spark.scheduler.Task.run(Task.scala:121) at org.apache.spark.executor.Executor$TaskRunner.$anonfun$run$3(Executor.scala:411) at org.apache.spark.util.Utils$.tryWithSafeFinally(Utils.scala:1360) at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:414) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624) at java.lang.Thread.run(Thread.java:748) 2019-05-15 10:07:06 ERROR TaskSetManager:70 - Task 3 in stage 2.0 failed 1 times; aborting job - try realigning a read on a missing contig, stringency == STRICT 2019-05-15 10:07:06 WARN MDTagging:190 - Caught exception when processing read chr2: java.lang.Exception: Contig chr2 not found in reference map with keys: chr1 - try realigning a read on a missing contig, stringency == LENIENT FileExtensionsSuite: - ends in gzip extension - is a vcf extension PhredUtilsSuite: - convert low phred score to log and back - convert high phred score to log and back - convert overflowing phred score to log and back and clip - convert negative zero log probability to phred and clip - round trip log probabilities SmithWatermanSuite: - gather max position from simple scoring matrix - gather max position from irregular scoring matrix - gather max position from irregular scoring matrix with deletions - score simple alignment with constant gap - score irregular scoring matrix - score irregular scoring matrix with indel - can unroll cigars correctly - execute simple trackback - execute trackback with indel - run end to end smith waterman for simple reads - run end to end smith waterman for short sequences with indel - run end to end smith waterman for longer sequences with snp - run end to end smith waterman for longer sequences with short indel - run end to end smith waterman for shorter sequence in longer sequence - run end to end smith waterman for shorter sequence in longer sequence, with indel - smithWaterman - simple alignment FastaConverterSuite: - find contig index - convert a single record without naming information - convert a single record with naming information - convert single fasta sequence - convert fasta with multiple sequences - convert fasta with multiple sequences; short fragment - convert reference fasta file MdTagSuite: - null md tag - zero length md tag - md tag with non-digit initial value - md tag invalid base - md tag, pure insertion - md tag, pure insertion, test 2 - md tag pure insertion equality - md tag equality and hashcode - valid md tags - get start of read with no mismatches or deletions - get start of read with no mismatches, but with a deletion at the start - get start of read with mismatches at the start - get end of read with no mismatches or deletions - check that mdtag and rich record return same end - get end of read with no mismatches, but a deletion at end - CIGAR with N operator - CIGAR with multiple N operators - CIGAR with P operators - Get correct matches for mdtag with insertion - Get correct matches for mdtag with mismatches and insertion - Get correct matches for mdtag with insertion between mismatches - Get correct matches for mdtag with intron between mismatches - Get correct matches for mdtag with intron and deletion between mismatches - Throw exception when number of deleted bases in mdtag disagrees with CIGAR - Get correct matches for mdtag with mismatch, insertion and deletion - Get correct matches for mdtag with mismatches, insertion and deletion - Get correct matches for MDTag with mismatches and deletions - Get correct matches base from MDTag and CIGAR with N - get end of read with mismatches and a deletion at end - get correct string out of mdtag with no mismatches - get correct string out of mdtag with mismatches at start - get correct string out of mdtag with deletion at end - get correct string out of mdtag with mismatches at end - get correct string out of complex mdtag - check complex mdtag - get gapped reference - move a cigar alignment by two for a read - rewrite alignment to all matches - rewrite alignment to two mismatches followed by all matches - rewrite alignment to include a deletion but otherwise all matches - rewrite alignment to include an insertion at the start of the read but otherwise all matches - create new md tag from read vs. reference, perfect match - create new md tag from read vs. reference, perfect alignment match, 1 mismatch - create new md tag from read vs. reference, alignment with deletion - create new md tag from read vs. reference, alignment with insert - handle '=' and 'X' operators - CIGAR/MD tag mismatch should cause errors GenomicDatasetSuite: - processing a command that is the spark root directory should return an absolute path - processing a command that is just a single word should do nothing - processing a command should handle arguments that include spaces - processing a command that is a single substitution should succeed - processing a command that is multiple words should split the string - process a command that is multiple words with a replacement - process a command that is multiple words with multiple replacements ParallelFileMergerSuite: - cannot write both empty gzip block and cram eof - buffer size must be non-negative - get the size of several files - block size must be positive and non-zero when trying to merge files - must provide files to merge - if two files are both below the block size, they should merge into one shard - merge two files where one is greater than the block size - merge a sharded sam file - merge a sharded bam file - merge a sharded cram file - can't turn a negative index into a path - generate a path from an index IndelTableSuite: - check for indels in a region with known indels - check for indels in a contig that doesn't exist - check for indels in a region without known indels - build indel table from rdd of variants SnpTableSuite: - create an empty snp table - create a snp table from variants on multiple contigs - create a snp table from a larger set of variants - perform lookups on multi-contig snp table - perform lookups on larger snp table RealignIndelsSuite: - map reads to targets - checking mapping to targets for artificial reads - checking alternative consensus for artificial reads - checking extraction of reference from reads - checking realigned reads for artificial input - checking realigned reads for artificial input with reference file - checking realigned reads for artificial input using knowns - checking realigned reads for artificial input using knowns and reads - skip realigning reads if target is highly covered - skip realignment if target is an insufficient LOD improvement - realign reads to an insertion - test mismatch quality scoring - test mismatch quality scoring for no mismatches - test mismatch quality scoring for offset - test mismatch quality scoring with early exit - test mismatch quality scoring after unpacking read - we shouldn't try to realign a region with no target - we shouldn't try to realign reads with no indel evidence - test OP and OC tags - realign a read with an insertion that goes off the end of the read - if realigning a target doesn't improve the LOD, don't drop reads - extract seq/qual from a read with no clipped bases - extract seq/qual from a read with clipped bases at start - extract seq/qual from a read with clipped bases at end - if unclip is selected, don't drop base when extracting from a read with clipped bases - get cigar and coordinates for read that spans indel, no clipped bases - get cigar and coordinates for read that spans deletion, clipped bases at start - get cigar and coordinates for read that falls wholly before insertion - get cigar and coordinates for read that falls wholly after insertion - get cigar and coordinates for read that falls wholly after deletion - get cigar and coordinates for read that partially spans insertion, no clipped bases - get cigar and coordinates for read that partially spans insertion, clipped bases at end - get cigar and coordinates for read that partially spans insertion, clipped bases both ends BaseQualityRecalibrationSuite: - BQSR Test Input #1 w/ VCF Sites without caching - BQSR Test Input #1 w/ VCF Sites with caching - BQSR Test Input #1 w/ VCF Sites with serialized caching DinucCovariateSuite: - computing dinucleotide pairs for a single base sequence should return (N,N) - compute dinucleotide pairs for a string of all valid bases - compute dinucleotide pairs for a string with an N - compute covariates for a read on the negative strand - compute covariates for a read on the positive strand SequenceDictionarySuite: - Convert from sam sequence record and back - Convert from SAM sequence dictionary file (with extra fields) - merge into existing dictionary - Convert from SAM sequence dictionary and back - Can retrieve sequence by name - SequenceDictionary's with same single element are equal - SequenceDictionary's with same two elements are equals - SequenceDictionary's with different elements are unequal - SequenceDictionaries with same elements in different order are compatible - isCompatible tests equality on overlap - The addition + works correctly - The append operation ++ works correctly - ContainsRefName works correctly for different string types - Apply on name works correctly for different String types - convert from sam sequence record and back - convert from sam sequence dictionary and back - conversion to sam sequence dictionary has correct sort order - load sequence dictionary from VCF file - empty sequence dictionary must be empty - test filter to reference name - test filter to reference names - test filter to reference name by function GenomicPositionPartitionerSuite: - partitions the UNMAPPED ReferencePosition into the top partition - if we do not have a contig for a record, we throw an IAE - partitioning into N pieces on M total sequence length, where N > M, results in M partitions - correctly partitions a single dummy sequence into two pieces - correctly counts cumulative lengths - correctly partitions positions across two dummy sequences - test that we can range partition ADAMRecords - test that we can range partition ADAMRecords indexed by sample - test that simple partitioning works okay on a reasonable set of ADAMRecords - test indexed ReferencePosition partitioning works on a set of indexed ADAMRecords CoverageSuite: - Convert to coverage from valid Feature - Convert to coverage from valid Feature with sampleId - Convert to coverage from Feature with null/empty contigName fails with correct error - Convert to coverage from Feature with no start/end position fails with correct error - Convert to coverage from Feature with no score fails with correct error InnerTreeRegionJoinSuite: - Ensure same reference regions get passed together - Overlapping reference regions - Multiple reference regions do not throw exception RichAlignmentRecordSuite: - Unclipped Start - Unclipped End - tags contains optional fields - read overlap unmapped read - read overlap reference position - read overlap same position different contig VariantDatasetSuite: - union two variant genomic datasets together - round trip to parquet - save and reload from partitioned parquet - use broadcast join to pull down variants mapped to targets - use right outer broadcast join to pull down variants mapped to targets - use shuffle join to pull down variants mapped to targets - use right outer shuffle join to pull down variants mapped to targets - use left outer shuffle join to pull down variants mapped to targets - use full outer shuffle join to pull down variants mapped to targets - use shuffle join with group by to pull down variants mapped to targets - use right outer shuffle join with group by to pull down variants mapped to targets - convert back to variant contexts - load parquet to sql, save, re-read from avro - transform variants to contig genomic dataset - transform variants to coverage genomic dataset - transform variants to feature genomic dataset - transform variants to fragment genomic dataset - transform variants to read genomic dataset - transform variants to genotype genomic dataset - transform variants to variant context genomic dataset - filter RDD bound variants to filters passed - filter dataset bound variants to filters passed - filter RDD bound variants by quality - filter dataset bound variants by quality - filter RDD bound variants by read depth - filter dataset bound variants by read depth - filter RDD bound variants by reference read depth - filter dataset bound variants by reference read depth - filter RDD bound single nucleotide variants - filter dataset bound single nucleotide variants - filter RDD bound multiple nucleotide variants - filter dataset bound multiple nucleotide variants - filter RDD bound indel variants - filter dataset bound indel variants - filter RDD bound variants to single nucleotide variants - filter dataset bound variants to single nucleotide variants - filter RDD bound variants to multiple nucleotide variants - filter dataset bound variants to multiple nucleotide variants - filter RDD bound variants to indel variants - filter dataset bound variants to indel variants - transform dataset via java API Run completed in 6 minutes, 18 seconds. Total number of tests run: 1146 Suites: completed 67, aborted 0 Tests: succeeded 1146, failed 0, canceled 0, ignored 5, pending 0 All tests passed. [INFO] [INFO] <<< scoverage-maven-plugin:1.1.1:report (default-cli) < [scoverage]test @ adam-core-spark2_2.12 <<< [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:report (default-cli) @ adam-core-spark2_2.12 --- [INFO] Skipping SCoverage report generation [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building ADAM_2.12: APIs for Java, Python 0.27.0-SNAPSHOT [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-apis-spark2_2.12 --- [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-apis-spark2_2.12 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ adam-apis-spark2_2.12 --- [INFO] Source directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-apis/src/main/scala added. [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ adam-apis-spark2_2.12 --- [INFO] Modified 0 of 5 .scala files [INFO] [INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ adam-apis-spark2_2.12 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-apis/src/main/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ adam-apis-spark2_2.12 --- [INFO] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-apis/src/main/scala:-1: info: compiling [INFO] Compiling 4 source files to /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-apis/target/2.12.8/classes at 1557940092579 [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 5 s [INFO] [INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ adam-apis-spark2_2.12 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ adam-apis-spark2_2.12 --- [INFO] Test Source directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-apis/src/test/scala added. [INFO] [INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ adam-apis-spark2_2.12 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 2 resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ adam-apis-spark2_2.12 --- [INFO] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-apis/src/test/java:-1: info: compiling [INFO] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-apis/src/test/scala:-1: info: compiling [INFO] Compiling 8 source files to /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-apis/target/2.12.8/test-classes at 1557940098223 [INFO] prepare-compile in 0 s [INFO] compile in 4 s [INFO] [INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ adam-apis-spark2_2.12 --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 7 source files to /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-apis/target/2.12.8/test-classes [INFO] [INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ adam-apis-spark2_2.12 --- [INFO] Tests are skipped. [INFO] [INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ adam-apis-spark2_2.12 --- Discovery starting. Discovery completed in 188 milliseconds. Run starting. Expected test count is: 9 JavaADAMContextSuite: 2019-05-15 10:08:23 WARN Utils:66 - Your hostname, research-jenkins-worker-07 resolves to a loopback address: 127.0.1.1; using 192.168.10.27 instead (on interface eth0) 2019-05-15 10:08:23 WARN Utils:66 - Set SPARK_LOCAL_IP if you need to bind to another address 2019-05-15 10:08:24 WARN NativeCodeLoader:62 - Unable to load native-hadoop library for your platform... using builtin-java classes where applicable - can read and write a small .SAM file - loadIndexedBam with multiple ReferenceRegions - can read and write a small FASTA file - can read and write a small .SAM file as fragments - can read and write a small .bed file as features - can read and write a small .bed file as coverage - can read and write a small .vcf as genotypes - can read and write a small .vcf as variants - can read a two bit file Run completed in 11 seconds, 431 milliseconds. Total number of tests run: 9 Suites: completed 2, aborted 0 Tests: succeeded 9, failed 0, canceled 0, ignored 0, pending 0 All tests passed. [INFO] [INFO] >>> scoverage-maven-plugin:1.1.1:report (default-cli) > [scoverage]test @ adam-apis-spark2_2.12 >>> [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-apis-spark2_2.12 --- [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-apis-spark2_2.12 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ adam-apis-spark2_2.12 --- [INFO] Source directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-apis/src/main/scala added. [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ adam-apis-spark2_2.12 --- [INFO] Modified 0 of 5 .scala files [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:pre-compile (default-cli) @ adam-apis-spark2_2.12 --- [WARNING] Skipping SCoverage execution - unsupported Scala version "2.12.8" [INFO] [INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ adam-apis-spark2_2.12 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-apis/src/main/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ adam-apis-spark2_2.12 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ adam-apis-spark2_2.12 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:post-compile (default-cli) @ adam-apis-spark2_2.12 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ adam-apis-spark2_2.12 --- [INFO] Test Source directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-apis/src/test/scala added. [INFO] [INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ adam-apis-spark2_2.12 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 2 resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ adam-apis-spark2_2.12 --- [INFO] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-apis/src/test/java:-1: info: compiling [INFO] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-apis/src/test/scala:-1: info: compiling [INFO] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-apis/target/generated-test-sources/test-annotations:-1: info: compiling [INFO] Compiling 8 source files to /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-apis/target/2.12.8/test-classes at 1557940115529 [INFO] prepare-compile in 0 s [INFO] compile in 4 s [INFO] [INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ adam-apis-spark2_2.12 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ adam-apis-spark2_2.12 --- [INFO] Tests are skipped. [INFO] [INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ adam-apis-spark2_2.12 --- Discovery starting. Discovery completed in 200 milliseconds. Run starting. Expected test count is: 9 JavaADAMContextSuite: 2019-05-15 10:08:40 WARN Utils:66 - Your hostname, research-jenkins-worker-07 resolves to a loopback address: 127.0.1.1; using 192.168.10.27 instead (on interface eth0) 2019-05-15 10:08:40 WARN Utils:66 - Set SPARK_LOCAL_IP if you need to bind to another address 2019-05-15 10:08:41 WARN NativeCodeLoader:62 - Unable to load native-hadoop library for your platform... using builtin-java classes where applicable - can read and write a small .SAM file - loadIndexedBam with multiple ReferenceRegions - can read and write a small FASTA file - can read and write a small .SAM file as fragments - can read and write a small .bed file as features - can read and write a small .bed file as coverage - can read and write a small .vcf as genotypes - can read and write a small .vcf as variants - can read a two bit file Run completed in 11 seconds, 391 milliseconds. Total number of tests run: 9 Suites: completed 2, aborted 0 Tests: succeeded 9, failed 0, canceled 0, ignored 0, pending 0 All tests passed. [INFO] [INFO] <<< scoverage-maven-plugin:1.1.1:report (default-cli) < [scoverage]test @ adam-apis-spark2_2.12 <<< [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:report (default-cli) @ adam-apis-spark2_2.12 --- [INFO] Skipping SCoverage report generation [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building ADAM_2.12: CLI 0.27.0-SNAPSHOT [INFO] ------------------------------------------------------------------------ Downloading: https://repo.maven.apache.org/maven2/net/codingwell/scala-guice_2.12/4.2.1/scala-guice_2.12-4.2.1.pom 3/3 KB 3/3 KB Downloaded: https://repo.maven.apache.org/maven2/net/codingwell/scala-guice_2.12/4.2.1/scala-guice_2.12-4.2.1.pom (3 KB at 64.5 KB/sec) Downloading: https://repo.maven.apache.org/maven2/net/codingwell/scala-guice_2.12/4.2.1/scala-guice_2.12-4.2.1.jar 3/136 KB 5/136 KB 8/136 KB 11/136 KB 13/136 KB 16/136 KB 19/136 KB 21/136 KB 24/136 KB 27/136 KB 29/136 KB 32/136 KB 36/136 KB 40/136 KB 44/136 KB 48/136 KB 52/136 KB 56/136 KB 60/136 KB 64/136 KB 68/136 KB 72/136 KB 76/136 KB 80/136 KB 84/136 KB 88/136 KB 92/136 KB 96/136 KB 100/136 KB 104/136 KB 108/136 KB 112/136 KB 116/136 KB 120/136 KB 124/136 KB 128/136 KB 132/136 KB 136/136 KB 136/136 KB Downloaded: https://repo.maven.apache.org/maven2/net/codingwell/scala-guice_2.12/4.2.1/scala-guice_2.12-4.2.1.jar (136 KB at 5229.5 KB/sec) [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-cli-spark2_2.12 --- [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-cli-spark2_2.12 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:timestamp-property (timestamp-property) @ adam-cli-spark2_2.12 --- [INFO] [INFO] --- git-commit-id-plugin:2.2.2:revision (default) @ adam-cli-spark2_2.12 --- [INFO] [INFO] --- templating-maven-plugin:1.0.0:filter-sources (filter-src) @ adam-cli-spark2_2.12 --- [INFO] Coping files with filtering to temporary directory. [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 1 resource [INFO] Copied 1 files to output directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-cli/target/generated-sources/java-templates [INFO] Source directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-cli/target/generated-sources/java-templates added. [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ adam-cli-spark2_2.12 --- [INFO] Source directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-cli/src/main/scala added. [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ adam-cli-spark2_2.12 --- [INFO] Modified 0 of 31 .scala files [INFO] [INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ adam-cli-spark2_2.12 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-cli/src/main/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ adam-cli-spark2_2.12 --- [INFO] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-cli/target/generated-sources/java-templates:-1: info: compiling [INFO] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-cli/src/main/scala:-1: info: compiling [INFO] Compiling 18 source files to /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-cli/target/2.12.8/classes at 1557940133703 [WARNING] warning: there was one deprecation warning [WARNING] warning: there was one deprecation warning (since 2.12.0) [WARNING] warning: there were two deprecation warnings in total; re-run with -deprecation for details [WARNING] three warnings found [INFO] prepare-compile in 0 s [INFO] compile in 7 s [INFO] [INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ adam-cli-spark2_2.12 --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 1 source file to /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-cli/target/2.12.8/classes [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ adam-cli-spark2_2.12 --- [INFO] Test Source directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-cli/src/test/scala added. [INFO] [INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ adam-cli-spark2_2.12 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 15 resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ adam-cli-spark2_2.12 --- [INFO] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-cli/src/test/scala:-1: info: compiling [INFO] Compiling 14 source files to /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-cli/target/2.12.8/test-classes at 1557940141784 [INFO] prepare-compile in 0 s [INFO] compile in 6 s [INFO] [INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ adam-cli-spark2_2.12 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ adam-cli-spark2_2.12 --- [INFO] Tests are skipped. [INFO] [INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ adam-cli-spark2_2.12 --- Discovery starting. Discovery completed in 213 milliseconds. Run starting. Expected test count is: 46 TransformFeaturesSuite: 2019-05-15 10:09:09 WARN Utils:66 - Your hostname, research-jenkins-worker-07 resolves to a loopback address: 127.0.1.1; using 192.168.10.27 instead (on interface eth0) 2019-05-15 10:09:09 WARN Utils:66 - Set SPARK_LOCAL_IP if you need to bind to another address 2019-05-15 10:09:10 WARN NativeCodeLoader:62 - Unable to load native-hadoop library for your platform... using builtin-java classes where applicable - can convert a simple BED file TransformVariantsSuite: - save a file sorted by contig index - save a lexicographically sorted file ViewSuite: - -f 0 -F 0 is a no-op - no -f or -F args is a no-op - -f 4: only unmapped reads - -F 4: only mapped reads - -f 4 -F 8: unmapped reads with mapped mates - -f 12: unmapped reads with unmapped mates - -g 12: reads that are unmapped or whose mate is unmapped - -F 12: mapped reads with mapped mates - -g 36: unmapped reads or reads with mate on negative strand - -F 36: unmapped reads or reads with mate on negative strand ADAM2FastaSuite: - round trip FASTA to nucleotide contig fragments in ADAM format to FASTA TransformFragmentsSuite: - load queryname sorted sam and save as parquet - cannot sort if not saving as sam 2019-05-15 10:09:24 WARN TransformFragments:190 - If loading and saving as reads, consider using TransformAlignments instead. - load reads as sam and save them sorted - bin quality scores on reads TransformGenotypesSuite: - save a file sorted by contig index - save a lexicographically sorted file - transform VCF without nested annotations - transform VCF with nested annotations Reads2CoverageSuite: - correctly calculates coverage from small sam file AboutSuite: - template variables have been replaced - templated values are not empty MergeShardsSuite: - merge shards from unordered sam to unordered sam - unordered sam to ordered sam - merge sharded bam - merge sharded cram Fasta2ADAMSuite: - can load fasta records after conversion TransformAlignmentsSuite: - unordered sam to unordered sam - unordered sam to ordered sam - unordered sam, to adam, to sam - unordered sam, to adam, to ordered sam - put quality scores into bins - run region predicate ADAMMainSuite: - default command groups is non empty - module provides default command groups - inject default command groups when called via main - command groups is empty when called via apply - single command group - add new command group to default command groups - module restores default command groups when called via apply - custom module with single command group - custom module with new command group added to default command groups Adam2FastqSuite: 2019-05-15 10:09:36 WARN RDDBoundAlignmentRecordDataset:190 - Found 16 read names that don't occur exactly twice: 1x: 16 Samples: SRR062634.16445865 SRR062634.9119161 SRR062634.17190076 SRR062634.17969132 SRR062634.7301099 SRR062634.2087100 SRR062634.20911784 SRR062634.16769670 SRR062634.18958430 SRR062634.12099057 SRR062634.12606172 SRR062634.14985224 SRR062634.10448889 SRR062634.4789722 SRR062634.3203184 SRR062634.17698657 - convert SAM to paired FASTQ Run completed in 28 seconds, 167 milliseconds. Total number of tests run: 46 Suites: completed 14, aborted 0 Tests: succeeded 46, failed 0, canceled 0, ignored 0, pending 0 All tests passed. [INFO] [INFO] >>> scoverage-maven-plugin:1.1.1:report (default-cli) > [scoverage]test @ adam-cli-spark2_2.12 >>> [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-cli-spark2_2.12 --- [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-cli-spark2_2.12 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:timestamp-property (timestamp-property) @ adam-cli-spark2_2.12 --- [INFO] [INFO] --- git-commit-id-plugin:2.2.2:revision (default) @ adam-cli-spark2_2.12 --- [INFO] [INFO] --- templating-maven-plugin:1.0.0:filter-sources (filter-src) @ adam-cli-spark2_2.12 --- [INFO] Coping files with filtering to temporary directory. [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 1 resource [INFO] No files needs to be copied to output directory. Up to date: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-cli/target/generated-sources/java-templates [INFO] Source directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-cli/target/generated-sources/java-templates added. [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ adam-cli-spark2_2.12 --- [INFO] Source directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-cli/src/main/scala added. [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ adam-cli-spark2_2.12 --- [INFO] Modified 0 of 31 .scala files [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:pre-compile (default-cli) @ adam-cli-spark2_2.12 --- [WARNING] Skipping SCoverage execution - unsupported Scala version "2.12.8" [INFO] [INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ adam-cli-spark2_2.12 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-cli/src/main/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ adam-cli-spark2_2.12 --- [INFO] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-cli/target/generated-sources/java-templates:-1: info: compiling [INFO] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-cli/src/main/scala:-1: info: compiling [INFO] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-cli/target/generated-sources/annotations:-1: info: compiling [INFO] Compiling 18 source files to /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-cli/target/2.12.8/classes at 1557940178448 [WARNING] warning: there was one deprecation warning [WARNING] warning: there was one deprecation warning (since 2.12.0) [WARNING] warning: there were two deprecation warnings in total; re-run with -deprecation for details [WARNING] three warnings found [INFO] prepare-compile in 0 s [INFO] compile in 7 s [INFO] [INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ adam-cli-spark2_2.12 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:post-compile (default-cli) @ adam-cli-spark2_2.12 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ adam-cli-spark2_2.12 --- [INFO] Test Source directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-cli/src/test/scala added. [INFO] [INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ adam-cli-spark2_2.12 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 15 resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ adam-cli-spark2_2.12 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ adam-cli-spark2_2.12 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ adam-cli-spark2_2.12 --- [INFO] Tests are skipped. [INFO] [INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ adam-cli-spark2_2.12 --- Discovery starting. Discovery completed in 211 milliseconds. Run starting. Expected test count is: 46 TransformFeaturesSuite: 2019-05-15 10:09:47 WARN Utils:66 - Your hostname, research-jenkins-worker-07 resolves to a loopback address: 127.0.1.1; using 192.168.10.27 instead (on interface eth0) 2019-05-15 10:09:47 WARN Utils:66 - Set SPARK_LOCAL_IP if you need to bind to another address 2019-05-15 10:09:48 WARN NativeCodeLoader:62 - Unable to load native-hadoop library for your platform... using builtin-java classes where applicable - can convert a simple BED file TransformVariantsSuite: - save a file sorted by contig index - save a lexicographically sorted file ViewSuite: - -f 0 -F 0 is a no-op - no -f or -F args is a no-op - -f 4: only unmapped reads - -F 4: only mapped reads - -f 4 -F 8: unmapped reads with mapped mates - -f 12: unmapped reads with unmapped mates - -g 12: reads that are unmapped or whose mate is unmapped - -F 12: mapped reads with mapped mates - -g 36: unmapped reads or reads with mate on negative strand - -F 36: unmapped reads or reads with mate on negative strand ADAM2FastaSuite: - round trip FASTA to nucleotide contig fragments in ADAM format to FASTA TransformFragmentsSuite: - load queryname sorted sam and save as parquet - cannot sort if not saving as sam 2019-05-15 10:10:02 WARN TransformFragments:190 - If loading and saving as reads, consider using TransformAlignments instead. - load reads as sam and save them sorted - bin quality scores on reads TransformGenotypesSuite: - save a file sorted by contig index - save a lexicographically sorted file - transform VCF without nested annotations - transform VCF with nested annotations Reads2CoverageSuite: - correctly calculates coverage from small sam file AboutSuite: - template variables have been replaced - templated values are not empty MergeShardsSuite: - merge shards from unordered sam to unordered sam - unordered sam to ordered sam - merge sharded bam - merge sharded cram Fasta2ADAMSuite: - can load fasta records after conversion TransformAlignmentsSuite: - unordered sam to unordered sam - unordered sam to ordered sam - unordered sam, to adam, to sam - unordered sam, to adam, to ordered sam - put quality scores into bins - run region predicate ADAMMainSuite: - default command groups is non empty - module provides default command groups - inject default command groups when called via main - command groups is empty when called via apply - single command group - add new command group to default command groups - module restores default command groups when called via apply - custom module with single command group - custom module with new command group added to default command groups Adam2FastqSuite: 2019-05-15 10:10:14 WARN RDDBoundAlignmentRecordDataset:190 - Found 16 read names that don't occur exactly twice: 1x: 16 Samples: SRR062634.16445865 SRR062634.9119161 SRR062634.17190076 SRR062634.17969132 SRR062634.7301099 SRR062634.2087100 SRR062634.20911784 SRR062634.16769670 SRR062634.18958430 SRR062634.12099057 SRR062634.12606172 SRR062634.14985224 SRR062634.10448889 SRR062634.4789722 SRR062634.3203184 SRR062634.17698657 - convert SAM to paired FASTQ Run completed in 28 seconds, 240 milliseconds. Total number of tests run: 46 Suites: completed 14, aborted 0 Tests: succeeded 46, failed 0, canceled 0, ignored 0, pending 0 All tests passed. [INFO] [INFO] <<< scoverage-maven-plugin:1.1.1:report (default-cli) < [scoverage]test @ adam-cli-spark2_2.12 <<< [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:report (default-cli) @ adam-cli-spark2_2.12 --- [INFO] Skipping SCoverage report generation [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building ADAM_2.12: Assembly 0.27.0-SNAPSHOT [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-assembly-spark2_2.12 --- [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-assembly-spark2_2.12 --- [INFO] [INFO] --- git-commit-id-plugin:2.2.2:revision (default) @ adam-assembly-spark2_2.12 --- [INFO] [INFO] --- templating-maven-plugin:1.0.0:filter-sources (filter-src) @ adam-assembly-spark2_2.12 --- [INFO] Request to add '/home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-assembly/src/main/java-templates' folder. Not added since it does not exist. [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ adam-assembly-spark2_2.12 --- [INFO] Source directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-assembly/src/main/scala added. [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ adam-assembly-spark2_2.12 --- [INFO] Modified 0 of 1 .scala files [INFO] [INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ adam-assembly-spark2_2.12 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-assembly/src/main/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ adam-assembly-spark2_2.12 --- [INFO] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-assembly/src/main/scala:-1: info: compiling [INFO] Compiling 1 source files to /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-assembly/target/2.12.8/classes at 1557940216606 [INFO] prepare-compile in 0 s [INFO] compile in 2 s [INFO] [INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ adam-assembly-spark2_2.12 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ adam-assembly-spark2_2.12 --- [INFO] Test Source directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-assembly/src/test/scala added. [INFO] [INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ adam-assembly-spark2_2.12 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-assembly/src/test/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ adam-assembly-spark2_2.12 --- [INFO] No sources to compile [INFO] [INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ adam-assembly-spark2_2.12 --- [INFO] No sources to compile [INFO] [INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ adam-assembly-spark2_2.12 --- [INFO] Tests are skipped. [INFO] [INFO] >>> scoverage-maven-plugin:1.1.1:report (default-cli) > [scoverage]test @ adam-assembly-spark2_2.12 >>> [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-assembly-spark2_2.12 --- [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-assembly-spark2_2.12 --- [INFO] [INFO] --- git-commit-id-plugin:2.2.2:revision (default) @ adam-assembly-spark2_2.12 --- [INFO] [INFO] --- templating-maven-plugin:1.0.0:filter-sources (filter-src) @ adam-assembly-spark2_2.12 --- [INFO] Request to add '/home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-assembly/src/main/java-templates' folder. Not added since it does not exist. [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ adam-assembly-spark2_2.12 --- [INFO] Source directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-assembly/src/main/scala added. [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ adam-assembly-spark2_2.12 --- [INFO] Modified 0 of 1 .scala files [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:pre-compile (default-cli) @ adam-assembly-spark2_2.12 --- [WARNING] Skipping SCoverage execution - unsupported Scala version "2.12.8" [INFO] [INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ adam-assembly-spark2_2.12 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-assembly/src/main/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ adam-assembly-spark2_2.12 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ adam-assembly-spark2_2.12 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:post-compile (default-cli) @ adam-assembly-spark2_2.12 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ adam-assembly-spark2_2.12 --- [INFO] Test Source directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-assembly/src/test/scala added. [INFO] [INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ adam-assembly-spark2_2.12 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-assembly/src/test/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ adam-assembly-spark2_2.12 --- [INFO] No sources to compile [INFO] [INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ adam-assembly-spark2_2.12 --- [INFO] No sources to compile [INFO] [INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ adam-assembly-spark2_2.12 --- [INFO] Tests are skipped. [INFO] [INFO] <<< scoverage-maven-plugin:1.1.1:report (default-cli) < [scoverage]test @ adam-assembly-spark2_2.12 <<< [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:report (default-cli) @ adam-assembly-spark2_2.12 --- [INFO] [scoverage] Generating aggregated cobertura XML report... [INFO] [scoverage] Generating aggregated scoverage XML report... [INFO] [scoverage] Generating aggregated scoverage HTML report... [INFO] Skipping SCoverage report generation [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building ADAM_2.12 0.27.0-SNAPSHOT [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- coveralls-maven-plugin:4.3.0:report (default-cli) @ adam-parent-spark2_2.12 --- [INFO] Starting Coveralls job for jenkins (2989 / https://amplab.cs.berkeley.edu/jenkins/job/ADAM-prb/HADOOP_VERSION=2.7.5,SCALAVER=2.12,SPARK_VERSION=2.4.3,label=ubuntu/2989/) [INFO] Using repository token <secret> [INFO] Git commit 6ee9ab9 in travis-spark-2.4-scala-2.12 [INFO] Writing Coveralls data to /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/target/coveralls.json... [INFO] Processing coverage report from /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/target/cobertura.xml [INFO] Successfully wrote Coveralls data in 53ms [INFO] Gathered code coverage metrics for 0 source files with 0 lines of code: [INFO] - 0 relevant lines [INFO] - 0 covered lines [INFO] - 0 missed lines [INFO] Submitting Coveralls data to API [INFO] Successfully submitted Coveralls data in 744ms for Job #2989.1 [INFO] https://coveralls.io/jobs/48532114 [INFO] *** It might take hours for Coveralls to update the actual coverage numbers for a job [INFO] If you see question marks in the report, please be patient [INFO] ------------------------------------------------------------------------ [INFO] Reactor Summary: [INFO] [INFO] ADAM_2.12 .......................................... SUCCESS [ 1.134 s] [INFO] ADAM_2.12: Shader workaround ....................... SUCCESS [ 5.772 s] [INFO] ADAM_2.12: Avro-to-Dataset codegen utils ........... SUCCESS [ 6.817 s] [INFO] ADAM_2.12: Core .................................... SUCCESS [14:18 min] [INFO] ADAM_2.12: APIs for Java, Python ................... SUCCESS [ 40.072 s] [INFO] ADAM_2.12: CLI ..................................... SUCCESS [01:23 min] [INFO] ADAM_2.12: Assembly ................................ SUCCESS [ 3.722 s] [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ [INFO] Total time: 16:50 min [INFO] Finished at: 2019-05-15T10:10:20-07:00 [INFO] Final Memory: 95M/1482M [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/adamTestMvnpjenoa0 Java HotSpot(TM) 64-Bit Server VM warning: ignoring option MaxPermSize=1g; support was removed in 8.0 [INFO] Scanning for projects... [INFO] ------------------------------------------------------------------------ [INFO] Reactor Build Order: [INFO] [INFO] ADAM_2.12 [INFO] ADAM_2.12: Shader workaround [INFO] ADAM_2.12: Avro-to-Dataset codegen utils [INFO] ADAM_2.12: Core [INFO] ADAM_2.12: APIs for Java, Python [INFO] ADAM_2.12: CLI [INFO] ADAM_2.12: Assembly [INFO] ADAM_2.12: Distribution [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building ADAM_2.12 0.27.0-SNAPSHOT [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-parent-spark2_2.12 --- [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-parent-spark2_2.12 --- [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ adam-parent-spark2_2.12 --- [INFO] Modified 0 of 241 .scala files [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ adam-parent-spark2_2.12 --- [INFO] No sources to compile [INFO] [INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ adam-parent-spark2_2.12 --- [INFO] No sources to compile [INFO] [INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ adam-parent-spark2_2.12 --- [INFO] [INFO] --- maven-javadoc-plugin:3.1.0:jar (attach-javadoc) @ adam-parent-spark2_2.12 --- [INFO] [INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) > generate-sources @ adam-parent-spark2_2.12 >>> [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-parent-spark2_2.12 --- [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-parent-spark2_2.12 --- [INFO] [INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) < generate-sources @ adam-parent-spark2_2.12 <<< [INFO] [INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ adam-parent-spark2_2.12 --- [INFO] No source files found [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building ADAM_2.12: Shader workaround 0.27.0-SNAPSHOT [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-shade-spark2_2.12 --- [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-shade-spark2_2.12 --- [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ adam-shade-spark2_2.12 --- [INFO] Modified 0 of 0 .scala files [INFO] [INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ adam-shade-spark2_2.12 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-shade/src/main/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ adam-shade-spark2_2.12 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ adam-shade-spark2_2.12 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- plexus-component-metadata:1.5.5:generate-metadata (default) @ adam-shade-spark2_2.12 --- [INFO] Discovered 1 component descriptors(s) [INFO] [INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ adam-shade-spark2_2.12 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-shade/src/test/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ adam-shade-spark2_2.12 --- [INFO] No sources to compile [INFO] [INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ adam-shade-spark2_2.12 --- [INFO] No sources to compile [INFO] [INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ adam-shade-spark2_2.12 --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:3.1.2:jar (default-jar) @ adam-shade-spark2_2.12 --- [INFO] Building jar: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-shade/target/adam-shade-spark2_2.12-0.27.0-SNAPSHOT.jar [INFO] [INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ adam-shade-spark2_2.12 --- [INFO] Building jar: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-shade/target/adam-shade-spark2_2.12-0.27.0-SNAPSHOT-sources.jar [INFO] [INFO] --- maven-javadoc-plugin:3.1.0:jar (attach-javadoc) @ adam-shade-spark2_2.12 --- [INFO] Loading source files for package org.bdgenomics.adam.shade... Constructing Javadoc information... Standard Doclet version 1.8.0_191 Building tree for all the packages and classes... Generating /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-shade/target/apidocs/org/bdgenomics/adam/shade/ParquetAvroWorkaroundShader.html... Generating /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-shade/target/apidocs/org/bdgenomics/adam/shade/package-frame.html... Generating /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-shade/target/apidocs/org/bdgenomics/adam/shade/package-summary.html... Generating /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-shade/target/apidocs/org/bdgenomics/adam/shade/package-tree.html... Generating /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-shade/target/apidocs/constant-values.html... Generating /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-shade/target/apidocs/org/bdgenomics/adam/shade/class-use/ParquetAvroWorkaroundShader.html... Generating /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-shade/target/apidocs/org/bdgenomics/adam/shade/package-use.html... Building index for all the packages and classes... Generating /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-shade/target/apidocs/overview-tree.html... Generating /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-shade/target/apidocs/index-all.html... Generating /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-shade/target/apidocs/deprecated-list.html... Building index for all classes... Generating /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-shade/target/apidocs/allclasses-frame.html... Generating /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-shade/target/apidocs/allclasses-noframe.html... Generating /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-shade/target/apidocs/index.html... Generating /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-shade/target/apidocs/help-doc.html... [INFO] Building jar: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-shade/target/adam-shade-spark2_2.12-0.27.0-SNAPSHOT-javadoc.jar [INFO] [INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) > generate-sources @ adam-shade-spark2_2.12 >>> [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-shade-spark2_2.12 --- [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-shade-spark2_2.12 --- [INFO] [INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) < generate-sources @ adam-shade-spark2_2.12 <<< [INFO] [INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ adam-shade-spark2_2.12 --- model contains 6 documentable templates [INFO] Building jar: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-shade/target/adam-shade-spark2_2.12-0.27.0-SNAPSHOT-javadoc.jar [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building ADAM_2.12: Avro-to-Dataset codegen utils 0.27.0-SNAPSHOT [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-codegen-spark2_2.12 --- [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-codegen-spark2_2.12 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ adam-codegen-spark2_2.12 --- [INFO] Source directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-codegen/src/main/scala added. [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ adam-codegen-spark2_2.12 --- [INFO] Modified 0 of 4 .scala files [INFO] [INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ adam-codegen-spark2_2.12 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-codegen/src/main/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ adam-codegen-spark2_2.12 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ adam-codegen-spark2_2.12 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ adam-codegen-spark2_2.12 --- [INFO] Test Source directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-codegen/src/test/scala added. [INFO] [INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ adam-codegen-spark2_2.12 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-codegen/src/test/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ adam-codegen-spark2_2.12 --- [INFO] No sources to compile [INFO] [INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ adam-codegen-spark2_2.12 --- [INFO] No sources to compile [INFO] [INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ adam-codegen-spark2_2.12 --- [INFO] Tests are skipped. [INFO] [INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ adam-codegen-spark2_2.12 --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:3.1.2:jar (default-jar) @ adam-codegen-spark2_2.12 --- [INFO] Building jar: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-codegen/target/adam-codegen-spark2_2.12-0.27.0-SNAPSHOT.jar [INFO] [INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ adam-codegen-spark2_2.12 --- [INFO] Building jar: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-codegen/target/adam-codegen-spark2_2.12-0.27.0-SNAPSHOT-sources.jar [INFO] [INFO] --- maven-javadoc-plugin:3.1.0:jar (attach-javadoc) @ adam-codegen-spark2_2.12 --- [INFO] [INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) > generate-sources @ adam-codegen-spark2_2.12 >>> [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-codegen-spark2_2.12 --- [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-codegen-spark2_2.12 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ adam-codegen-spark2_2.12 --- [INFO] Source directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-codegen/src/main/scala added. [INFO] [INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) < generate-sources @ adam-codegen-spark2_2.12 <<< [INFO] [INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ adam-codegen-spark2_2.12 --- model contains 11 documentable templates [INFO] Building jar: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-codegen/target/adam-codegen-spark2_2.12-0.27.0-SNAPSHOT-javadoc.jar [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building ADAM_2.12: Core 0.27.0-SNAPSHOT [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-core-spark2_2.12 --- [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-core-spark2_2.12 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ adam-core-spark2_2.12 --- [INFO] Source directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/main/scala added. [INFO] Source directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/target/generated-sources/src/main/scala added. [INFO] [INFO] --- exec-maven-plugin:1.5.0:java (generate-scala-products) @ adam-core-spark2_2.12 --- SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] [INFO] --- exec-maven-plugin:1.5.0:java (generate-scala-projection-fields) @ adam-core-spark2_2.12 --- SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ adam-core-spark2_2.12 --- [INFO] Modified 2 of 199 .scala files [INFO] [INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ adam-core-spark2_2.12 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/main/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ adam-core-spark2_2.12 --- [INFO] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/main/java:-1: info: compiling [INFO] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/main/scala:-1: info: compiling [INFO] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/target/generated-sources/src/main/scala:-1: info: compiling [INFO] Compiling 136 source files to /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/target/2.12.8/classes at 1557940247247 [WARNING] warning: there were 21 deprecation warnings [WARNING] warning: there were 31 deprecation warnings (since 0.21.0) [WARNING] warning: there was one deprecation warning (since 1.0.6) [WARNING] warning: there were 31 deprecation warnings (since 2.0.0) [WARNING] warning: there was one deprecation warning (since 2.11.0) [WARNING] warning: there were 170 deprecation warnings (since 2.12.0) [WARNING] warning: there was one deprecation warning (since 2.12.7) [WARNING] warning: there were 256 deprecation warnings in total; re-run with -deprecation for details [WARNING] warning: there were 5 feature warnings; re-run with -feature for details [WARNING] 9 warnings found [INFO] prepare-compile in 0 s [INFO] compile in 24 s [INFO] [INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ adam-core-spark2_2.12 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ adam-core-spark2_2.12 --- [INFO] Test Source directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/test/scala added. [INFO] [INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ adam-core-spark2_2.12 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 150 resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ adam-core-spark2_2.12 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ adam-core-spark2_2.12 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ adam-core-spark2_2.12 --- [INFO] Tests are skipped. [INFO] [INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ adam-core-spark2_2.12 --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:3.1.2:jar (default-jar) @ adam-core-spark2_2.12 --- [INFO] Building jar: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/target/adam-core-spark2_2.12-0.27.0-SNAPSHOT.jar [INFO] [INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ adam-core-spark2_2.12 --- [INFO] Building jar: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/target/adam-core-spark2_2.12-0.27.0-SNAPSHOT-sources.jar [INFO] [INFO] --- maven-javadoc-plugin:3.1.0:jar (attach-javadoc) @ adam-core-spark2_2.12 --- [INFO] The goal 'org.apache.maven.plugins:maven-javadoc-plugin:3.1.0:javadoc' has not been previously called for the module: 'org.bdgenomics.adam:adam-codegen-spark2_2.12:jar:0.27.0-SNAPSHOT'. Trying to invoke it... Java HotSpot(TM) 64-Bit Server VM warning: ignoring option MaxPermSize=1g; support was removed in 8.0 [WARNING] Creating fake javadoc directory to prevent repeated invocations: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-codegen/target/apidocs [ERROR] Error fetching link: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-codegen/target/apidocs. Ignored it. [INFO] Loading source files for package org.apache.parquet.avro... Loading source files for package org.bdgenomics.adam.io... Constructing Javadoc information... Standard Doclet version 1.8.0_191 Building tree for all the packages and classes... Generating /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/target/apidocs/org/apache/parquet/avro/AvroSchemaConverter.html... Generating /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/target/apidocs/org/bdgenomics/adam/io/FastqInputFormat.html... Generating /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/target/apidocs/org/bdgenomics/adam/io/FastqRecordReader.html... Generating /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/target/apidocs/org/bdgenomics/adam/io/InterleavedFastqInputFormat.html... Generating /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/target/apidocs/org/bdgenomics/adam/io/SingleFastqInputFormat.html... Generating /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/target/apidocs/overview-frame.html... Generating /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/target/apidocs/org/apache/parquet/avro/package-frame.html... Generating /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/target/apidocs/org/apache/parquet/avro/package-summary.html... Generating /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/target/apidocs/org/apache/parquet/avro/package-tree.html... Generating /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/target/apidocs/org/bdgenomics/adam/io/package-frame.html... Generating /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/target/apidocs/org/bdgenomics/adam/io/package-summary.html... Generating /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/target/apidocs/org/bdgenomics/adam/io/package-tree.html... Generating /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/target/apidocs/constant-values.html... Generating /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/target/apidocs/org/apache/parquet/avro/class-use/AvroSchemaConverter.html... Generating /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/target/apidocs/org/bdgenomics/adam/io/class-use/InterleavedFastqInputFormat.html... Generating /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/target/apidocs/org/bdgenomics/adam/io/class-use/SingleFastqInputFormat.html... Generating /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/target/apidocs/org/bdgenomics/adam/io/class-use/FastqInputFormat.html... Generating /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/target/apidocs/org/bdgenomics/adam/io/class-use/FastqRecordReader.html... Generating /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/target/apidocs/org/apache/parquet/avro/package-use.html... Generating /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/target/apidocs/org/bdgenomics/adam/io/package-use.html... Building index for all the packages and classes... Generating /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/target/apidocs/overview-tree.html... Generating /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/target/apidocs/index-all.html... Generating /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/target/apidocs/deprecated-list.html... Building index for all classes... Generating /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/target/apidocs/allclasses-frame.html... Generating /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/target/apidocs/allclasses-noframe.html... Generating /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/target/apidocs/index.html... Generating /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/target/apidocs/overview-summary.html... Generating /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/target/apidocs/help-doc.html... 6 warnings [WARNING] Javadoc Warnings [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/main/java/org/bdgenomics/adam/io/FastqRecordReader.java:235: warning: no @param for codec [WARNING] protected final int positionAtFirstRecord(final FSDataInputStream stream, [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/main/java/org/bdgenomics/adam/io/FastqRecordReader.java:235: warning: no @return [WARNING] protected final int positionAtFirstRecord(final FSDataInputStream stream, [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/main/java/org/bdgenomics/adam/io/FastqRecordReader.java:235: warning: no @throws for java.io.IOException [WARNING] protected final int positionAtFirstRecord(final FSDataInputStream stream, [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/main/java/org/bdgenomics/adam/io/FastqRecordReader.java:389: warning: no @throws for java.io.IOException [WARNING] protected final boolean lowLevelFastqRead(final Text readName, final Text value) [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/main/java/org/bdgenomics/adam/io/FastqRecordReader.java:431: warning: no @throws for java.io.IOException [WARNING] abstract protected boolean next(Text value) throws IOException; [WARNING] ^ [WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/main/java/org/bdgenomics/adam/io/FastqRecordReader.java:154: warning: no @throws for java.io.IOException [WARNING] protected FastqRecordReader(final Configuration conf, [WARNING] ^ [INFO] Building jar: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/target/adam-core-spark2_2.12-0.27.0-SNAPSHOT-javadoc.jar [INFO] [INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) > generate-sources @ adam-core-spark2_2.12 >>> [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-core-spark2_2.12 --- [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-core-spark2_2.12 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ adam-core-spark2_2.12 --- [INFO] Source directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/main/scala added. [INFO] Source directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/target/generated-sources/src/main/scala added. [INFO] [INFO] --- exec-maven-plugin:1.5.0:java (generate-scala-products) @ adam-core-spark2_2.12 --- SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] [INFO] --- exec-maven-plugin:1.5.0:java (generate-scala-projection-fields) @ adam-core-spark2_2.12 --- SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] [INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) < generate-sources @ adam-core-spark2_2.12 <<< [INFO] [INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ adam-core-spark2_2.12 --- /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/main/scala/org/bdgenomics/adam/converters/FastaConverter.scala:230: warning: discarding unmoored doc comment /** ^ /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/main/scala/org/bdgenomics/adam/rdd/read/AlignmentRecordDataset.scala:803: warning: Octal escape literals are deprecated, use \u0001 instead. binaryCodec.writeBytes("BAM\001".getBytes()) ^ /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/main/scala/org/bdgenomics/adam/rich/RichCigar.scala:43: warning: discarding unmoored doc comment /** ^ warning: there were 5 feature warnings; re-run with -feature for details model contains 276 documentable templates /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/main/scala/org/bdgenomics/adam/models/ReadGroupDictionary.scala:47: warning: Could not find any member to link for "IllegalArgumentException". /** ^ /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/main/scala/org/bdgenomics/adam/util/AttributeUtils.scala:70: warning: Could not find any member to link for "IllegalArgumentException". /** ^ /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/main/scala/org/bdgenomics/adam/rdd/GenomicDataset.scala:755: warning: Variable x undefined in comment for method pipe in trait GenomicDataset * Files are substituted in to the command with a $x syntax. E.g., to invoke ^ /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/main/scala/org/bdgenomics/adam/rdd/GenomicDataset.scala:756: warning: Variable 0 undefined in comment for method pipe in trait GenomicDataset * a command that uses the first file from the files Seq, use $0. To access ^ /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/main/scala/org/bdgenomics/adam/rdd/GenomicDataset.scala:757: warning: Variable root undefined in comment for method pipe in trait GenomicDataset * the path to the directory where the files are copied, use $root. ^ /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/main/scala/org/bdgenomics/adam/rdd/contig/NucleotideContigFragmentDataset.scala:365: warning: Could not find any member to link for "UnsupportedOperationException". /** ^ /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/main/scala/org/bdgenomics/adam/rdd/GenomicPartitioners.scala:178: warning: Could not find any member to link for "IllegalArgumentException". /** ^ /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/main/scala/org/bdgenomics/adam/rdd/GenomicPartitioners.scala:75: warning: Could not find any member to link for "IllegalArgumentException". /** ^ /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/main/scala/org/bdgenomics/adam/rdd/ADAMContext.scala:3085: warning: Could not find any member to link for "IllegalArgumentException". /** ^ /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/main/scala/org/bdgenomics/adam/rdd/ADAMContext.scala:1388: warning: Could not find any member to link for "FileNotFoundException". /** ^ /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/main/scala/org/bdgenomics/adam/rdd/ADAMContext.scala:1368: warning: Could not find any member to link for "FileNotFoundException". /** ^ /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/main/scala/org/bdgenomics/adam/rdd/ADAMContext.scala:1339: warning: Could not find any member to link for "FileNotFoundException". /** ^ /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/main/scala/org/bdgenomics/adam/projections/Projection.scala:45: warning: Could not find any member to link for "IllegalArgumentException". /** ^ /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/main/scala/org/bdgenomics/adam/models/ReferenceRegion.scala:456: warning: Could not find any member to link for "IllegalArgumentException". /** ^ /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/main/scala/org/bdgenomics/adam/models/ReferenceRegion.scala:426: warning: Could not find any member to link for "IllegalArgumentException". /** ^ /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/main/scala/org/bdgenomics/adam/models/ReferenceRegion.scala:411: warning: Could not find any member to link for "IllegalArgumentException". /** ^ /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/main/scala/org/bdgenomics/adam/models/ReferenceRegion.scala:336: warning: Could not find any member to link for "IllegalArgumentException". /** ^ /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/main/scala/org/bdgenomics/adam/models/ReferenceRegion.scala:258: warning: Could not find any member to link for "IllegalArgumentException". /** ^ /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/main/scala/org/bdgenomics/adam/models/ReferenceRegion.scala:242: warning: Could not find any member to link for "IllegalArgumentException". /** ^ /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/main/scala/org/bdgenomics/adam/models/Alphabet.scala:44: warning: Could not find any member to link for "IllegalArgumentException". /** ^ /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/src/main/java/org/bdgenomics/adam/io/FastqRecordReader.java:377: warning: Could not find any member to link for "RuntimeException". /** ^ 25 warnings found [INFO] Building jar: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/target/adam-core-spark2_2.12-0.27.0-SNAPSHOT-javadoc.jar [INFO] [INFO] --- maven-jar-plugin:3.1.2:test-jar (default) @ adam-core-spark2_2.12 --- [INFO] Building jar: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-core/target/adam-core-spark2_2.12-0.27.0-SNAPSHOT-tests.jar [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building ADAM_2.12: APIs for Java, Python 0.27.0-SNAPSHOT [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-apis-spark2_2.12 --- [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-apis-spark2_2.12 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ adam-apis-spark2_2.12 --- [INFO] Source directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-apis/src/main/scala added. [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ adam-apis-spark2_2.12 --- [INFO] Modified 0 of 5 .scala files [INFO] [INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ adam-apis-spark2_2.12 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-apis/src/main/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ adam-apis-spark2_2.12 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ adam-apis-spark2_2.12 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ adam-apis-spark2_2.12 --- [INFO] Test Source directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-apis/src/test/scala added. [INFO] [INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ adam-apis-spark2_2.12 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 2 resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ adam-apis-spark2_2.12 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ adam-apis-spark2_2.12 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ adam-apis-spark2_2.12 --- [INFO] Tests are skipped. [INFO] [INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ adam-apis-spark2_2.12 --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:3.1.2:jar (default-jar) @ adam-apis-spark2_2.12 --- [INFO] Building jar: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-apis/target/adam-apis-spark2_2.12-0.27.0-SNAPSHOT.jar [INFO] [INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ adam-apis-spark2_2.12 --- [INFO] Building jar: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-apis/target/adam-apis-spark2_2.12-0.27.0-SNAPSHOT-sources.jar [INFO] [INFO] --- maven-javadoc-plugin:3.1.0:jar (attach-javadoc) @ adam-apis-spark2_2.12 --- [INFO] [INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) > generate-sources @ adam-apis-spark2_2.12 >>> [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-apis-spark2_2.12 --- [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-apis-spark2_2.12 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ adam-apis-spark2_2.12 --- [INFO] Source directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-apis/src/main/scala added. [INFO] [INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) < generate-sources @ adam-apis-spark2_2.12 <<< [INFO] [INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ adam-apis-spark2_2.12 --- warning: there were two feature warnings; re-run with -feature for details model contains 124 documentable templates one warning found [INFO] Building jar: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-apis/target/adam-apis-spark2_2.12-0.27.0-SNAPSHOT-javadoc.jar [INFO] [INFO] --- maven-jar-plugin:3.1.2:test-jar (default) @ adam-apis-spark2_2.12 --- [INFO] Building jar: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-apis/target/adam-apis-spark2_2.12-0.27.0-SNAPSHOT-tests.jar [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building ADAM_2.12: CLI 0.27.0-SNAPSHOT [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-cli-spark2_2.12 --- [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-cli-spark2_2.12 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:timestamp-property (timestamp-property) @ adam-cli-spark2_2.12 --- [INFO] [INFO] --- git-commit-id-plugin:2.2.2:revision (default) @ adam-cli-spark2_2.12 --- [INFO] [INFO] --- templating-maven-plugin:1.0.0:filter-sources (filter-src) @ adam-cli-spark2_2.12 --- [INFO] Coping files with filtering to temporary directory. [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 1 resource [INFO] No files needs to be copied to output directory. Up to date: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-cli/target/generated-sources/java-templates [INFO] Source directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-cli/target/generated-sources/java-templates added. [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ adam-cli-spark2_2.12 --- [INFO] Source directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-cli/src/main/scala added. [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ adam-cli-spark2_2.12 --- [INFO] Modified 0 of 31 .scala files [INFO] [INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ adam-cli-spark2_2.12 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-cli/src/main/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ adam-cli-spark2_2.12 --- [INFO] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-cli/target/generated-sources/java-templates:-1: info: compiling [INFO] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-cli/src/main/scala:-1: info: compiling [INFO] Compiling 18 source files to /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-cli/target/2.12.8/classes at 1557940318316 [WARNING] warning: there was one deprecation warning [WARNING] warning: there was one deprecation warning (since 2.12.0) [WARNING] warning: there were two deprecation warnings in total; re-run with -deprecation for details [WARNING] three warnings found [INFO] prepare-compile in 0 s [INFO] compile in 7 s [INFO] [INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ adam-cli-spark2_2.12 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ adam-cli-spark2_2.12 --- [INFO] Test Source directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-cli/src/test/scala added. [INFO] [INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ adam-cli-spark2_2.12 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 15 resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ adam-cli-spark2_2.12 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ adam-cli-spark2_2.12 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ adam-cli-spark2_2.12 --- [INFO] Tests are skipped. [INFO] [INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ adam-cli-spark2_2.12 --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:3.1.2:jar (default-jar) @ adam-cli-spark2_2.12 --- [INFO] Building jar: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-cli/target/adam-cli-spark2_2.12-0.27.0-SNAPSHOT.jar [INFO] [INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ adam-cli-spark2_2.12 --- [INFO] Building jar: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-cli/target/adam-cli-spark2_2.12-0.27.0-SNAPSHOT-sources.jar [INFO] [INFO] --- maven-javadoc-plugin:3.1.0:jar (attach-javadoc) @ adam-cli-spark2_2.12 --- [INFO] The goal 'org.apache.maven.plugins:maven-javadoc-plugin:3.1.0:javadoc' has not been previously called for the module: 'org.bdgenomics.adam:adam-apis-spark2_2.12:jar:0.27.0-SNAPSHOT'. Trying to invoke it... Java HotSpot(TM) 64-Bit Server VM warning: ignoring option MaxPermSize=1g; support was removed in 8.0 [ERROR] MavenInvocationException: Error when invoking Maven, consult the invoker log file: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-cli/target/invoker/maven-javadoc-plugin2145684977.txt [WARNING] Creating fake javadoc directory to prevent repeated invocations: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-apis/target/apidocs [ERROR] Error fetching link: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-apis/target/apidocs. Ignored it. [INFO] Loading source files for package org.bdgenomics.adam.cli... Constructing Javadoc information... Standard Doclet version 1.8.0_191 Building tree for all the packages and classes... Generating /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-cli/target/apidocs/org/bdgenomics/adam/cli/About.html... Generating /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-cli/target/apidocs/org/bdgenomics/adam/cli/package-frame.html... Generating /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-cli/target/apidocs/org/bdgenomics/adam/cli/package-summary.html... Generating /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-cli/target/apidocs/org/bdgenomics/adam/cli/package-tree.html... Generating /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-cli/target/apidocs/constant-values.html... Generating /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-cli/target/apidocs/org/bdgenomics/adam/cli/class-use/About.html... Generating /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-cli/target/apidocs/org/bdgenomics/adam/cli/package-use.html... Building index for all the packages and classes... Generating /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-cli/target/apidocs/overview-tree.html... Generating /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-cli/target/apidocs/index-all.html... Generating /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-cli/target/apidocs/deprecated-list.html... Building index for all classes... Generating /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-cli/target/apidocs/allclasses-frame.html... Generating /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-cli/target/apidocs/allclasses-noframe.html... Generating /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-cli/target/apidocs/index.html... Generating /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-cli/target/apidocs/help-doc.html... [INFO] Building jar: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-cli/target/adam-cli-spark2_2.12-0.27.0-SNAPSHOT-javadoc.jar [INFO] [INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) > generate-sources @ adam-cli-spark2_2.12 >>> [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-cli-spark2_2.12 --- [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-cli-spark2_2.12 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:timestamp-property (timestamp-property) @ adam-cli-spark2_2.12 --- [INFO] [INFO] --- git-commit-id-plugin:2.2.2:revision (default) @ adam-cli-spark2_2.12 --- [INFO] [INFO] --- templating-maven-plugin:1.0.0:filter-sources (filter-src) @ adam-cli-spark2_2.12 --- [INFO] Coping files with filtering to temporary directory. [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 1 resource [INFO] No files needs to be copied to output directory. Up to date: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-cli/target/generated-sources/java-templates [INFO] Source directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-cli/target/generated-sources/java-templates added. [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ adam-cli-spark2_2.12 --- [INFO] Source directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-cli/src/main/scala added. [INFO] [INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) < generate-sources @ adam-cli-spark2_2.12 <<< [INFO] [INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ adam-cli-spark2_2.12 --- model contains 55 documentable templates [INFO] Building jar: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-cli/target/adam-cli-spark2_2.12-0.27.0-SNAPSHOT-javadoc.jar [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building ADAM_2.12: Assembly 0.27.0-SNAPSHOT [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-assembly-spark2_2.12 --- [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-assembly-spark2_2.12 --- [INFO] [INFO] --- git-commit-id-plugin:2.2.2:revision (default) @ adam-assembly-spark2_2.12 --- [INFO] [INFO] --- templating-maven-plugin:1.0.0:filter-sources (filter-src) @ adam-assembly-spark2_2.12 --- [INFO] Request to add '/home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-assembly/src/main/java-templates' folder. Not added since it does not exist. [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ adam-assembly-spark2_2.12 --- [INFO] Source directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-assembly/src/main/scala added. [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ adam-assembly-spark2_2.12 --- [INFO] Modified 0 of 1 .scala files [INFO] [INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ adam-assembly-spark2_2.12 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-assembly/src/main/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ adam-assembly-spark2_2.12 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ adam-assembly-spark2_2.12 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ adam-assembly-spark2_2.12 --- [INFO] Test Source directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-assembly/src/test/scala added. [INFO] [INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ adam-assembly-spark2_2.12 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-assembly/src/test/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ adam-assembly-spark2_2.12 --- [INFO] No sources to compile [INFO] [INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ adam-assembly-spark2_2.12 --- [INFO] No sources to compile [INFO] [INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ adam-assembly-spark2_2.12 --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:3.1.2:jar (default-jar) @ adam-assembly-spark2_2.12 --- [INFO] Building jar: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-assembly/target/adam-assembly-spark2_2.12-0.27.0-SNAPSHOT.jar [INFO] [INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ adam-assembly-spark2_2.12 --- [INFO] Building jar: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-assembly/target/adam-assembly-spark2_2.12-0.27.0-SNAPSHOT-sources.jar [INFO] [INFO] --- maven-javadoc-plugin:3.1.0:jar (attach-javadoc) @ adam-assembly-spark2_2.12 --- [INFO] [INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) > generate-sources @ adam-assembly-spark2_2.12 >>> [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-assembly-spark2_2.12 --- [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-assembly-spark2_2.12 --- [INFO] [INFO] --- git-commit-id-plugin:2.2.2:revision (default) @ adam-assembly-spark2_2.12 --- [INFO] [INFO] --- templating-maven-plugin:1.0.0:filter-sources (filter-src) @ adam-assembly-spark2_2.12 --- [INFO] Request to add '/home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-assembly/src/main/java-templates' folder. Not added since it does not exist. [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ adam-assembly-spark2_2.12 --- [INFO] Source directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-assembly/src/main/scala added. [INFO] [INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) < generate-sources @ adam-assembly-spark2_2.12 <<< [INFO] [INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ adam-assembly-spark2_2.12 --- model contains 6 documentable templates [INFO] Building jar: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-assembly/target/adam-assembly-spark2_2.12-0.27.0-SNAPSHOT-javadoc.jar [INFO] [INFO] --- maven-shade-plugin:3.2.0:shade (default) @ adam-assembly-spark2_2.12 --- [INFO] Including org.bdgenomics.adam:adam-cli-spark2_2.12:jar:0.27.0-SNAPSHOT in the shaded jar. [INFO] Including org.bdgenomics.utils:utils-misc-spark2_2.12:jar:0.2.15 in the shaded jar. [INFO] Including org.bdgenomics.utils:utils-io-spark2_2.12:jar:0.2.15 in the shaded jar. [INFO] Including org.apache.httpcomponents:httpclient:jar:4.5.7 in the shaded jar. [INFO] Including org.apache.httpcomponents:httpcore:jar:4.4.11 in the shaded jar. [INFO] Including commons-logging:commons-logging:jar:1.2 in the shaded jar. [INFO] Including commons-codec:commons-codec:jar:1.11 in the shaded jar. [INFO] Including org.bdgenomics.utils:utils-cli-spark2_2.12:jar:0.2.15 in the shaded jar. [INFO] Including org.clapper:grizzled-slf4j_2.12:jar:1.3.3 in the shaded jar. [INFO] Including org.apache.parquet:parquet-avro:jar:1.10.1 in the shaded jar. [INFO] Including org.apache.parquet:parquet-column:jar:1.10.1 in the shaded jar. [INFO] Including org.apache.parquet:parquet-common:jar:1.10.1 in the shaded jar. [INFO] Including org.apache.parquet:parquet-encoding:jar:1.10.1 in the shaded jar. [INFO] Including org.apache.parquet:parquet-hadoop:jar:1.10.1 in the shaded jar. [INFO] Including org.apache.parquet:parquet-jackson:jar:1.10.1 in the shaded jar. [INFO] Including commons-pool:commons-pool:jar:1.6 in the shaded jar. [INFO] Including org.apache.parquet:parquet-format:jar:2.4.0 in the shaded jar. [INFO] Including org.bdgenomics.utils:utils-metrics-spark2_2.12:jar:0.2.15 in the shaded jar. [INFO] Including com.netflix.servo:servo-core:jar:0.12.25 in the shaded jar. [INFO] Including com.netflix.spectator:spectator-api:jar:0.67.0 in the shaded jar. [INFO] Including org.slf4j:slf4j-api:jar:1.7.25 in the shaded jar. [INFO] Including org.bdgenomics.bdg-formats:bdg-formats:jar:0.12.0 in the shaded jar. [INFO] Including org.apache.avro:avro:jar:1.8.2 in the shaded jar. [INFO] Including org.codehaus.jackson:jackson-core-asl:jar:1.9.13 in the shaded jar. [INFO] Including org.codehaus.jackson:jackson-mapper-asl:jar:1.9.13 in the shaded jar. [INFO] Including com.thoughtworks.paranamer:paranamer:jar:2.7 in the shaded jar. [INFO] Including org.xerial.snappy:snappy-java:jar:1.1.1.3 in the shaded jar. [INFO] Including org.apache.commons:commons-compress:jar:1.8.1 in the shaded jar. [INFO] Including org.tukaani:xz:jar:1.5 in the shaded jar. [INFO] Including org.bdgenomics.adam:adam-core-spark2_2.12:jar:0.27.0-SNAPSHOT in the shaded jar. [INFO] Including org.bdgenomics.utils:utils-intervalrdd-spark2_2.12:jar:0.2.15 in the shaded jar. [INFO] Including com.esotericsoftware.kryo:kryo:jar:2.24.0 in the shaded jar. [INFO] Including com.esotericsoftware.minlog:minlog:jar:1.2 in the shaded jar. [INFO] Including org.objenesis:objenesis:jar:2.1 in the shaded jar. [INFO] Including commons-io:commons-io:jar:2.6 in the shaded jar. [INFO] Including it.unimi.dsi:fastutil:jar:6.6.5 in the shaded jar. [INFO] Including org.seqdoop:hadoop-bam:jar:7.9.2 in the shaded jar. [INFO] Including com.github.jsr203hadoop:jsr203hadoop:jar:1.0.3 in the shaded jar. [INFO] Including com.github.samtools:htsjdk:jar:2.18.2 in the shaded jar. [INFO] Including org.apache.commons:commons-jexl:jar:2.1.1 in the shaded jar. [INFO] Including gov.nih.nlm.ncbi:ngs-java:jar:2.9.0 in the shaded jar. [INFO] Including com.google.guava:guava:jar:27.0-jre in the shaded jar. [INFO] Including com.google.guava:failureaccess:jar:1.0 in the shaded jar. [INFO] Including com.google.guava:listenablefuture:jar:9999.0-empty-to-avoid-conflict-with-guava in the shaded jar. [INFO] Including org.checkerframework:checker-qual:jar:2.5.2 in the shaded jar. [INFO] Including com.google.errorprone:error_prone_annotations:jar:2.2.0 in the shaded jar. [INFO] Including com.google.j2objc:j2objc-annotations:jar:1.1 in the shaded jar. [INFO] Including org.codehaus.mojo:animal-sniffer-annotations:jar:1.17 in the shaded jar. [INFO] Including org.bdgenomics.adam:adam-codegen-spark2_2.12:jar:0.27.0-SNAPSHOT in the shaded jar. [INFO] Including org.bdgenomics.adam:adam-apis-spark2_2.12:jar:0.27.0-SNAPSHOT in the shaded jar. [INFO] Including args4j:args4j:jar:2.33 in the shaded jar. [INFO] Including net.codingwell:scala-guice_2.12:jar:4.2.1 in the shaded jar. [INFO] Including com.google.inject:guice:jar:4.2.0 in the shaded jar. [INFO] Including javax.inject:javax.inject:jar:1 in the shaded jar. [INFO] Including aopalliance:aopalliance:jar:1.0 in the shaded jar. [INFO] Including org.scala-lang:scala-reflect:jar:2.12.6 in the shaded jar. [INFO] Including com.google.code.findbugs:jsr305:jar:1.3.9 in the shaded jar. [WARNING] WORKAROUND: refusing to add class org/apache/parquet/avro/AvroSchemaConverter$2.class from jar /home/jenkins/.m2/repository/org/apache/parquet/parquet-avro/1.10.1/parquet-avro-1.10.1.jar [WARNING] WORKAROUND: refusing to add class org/apache/parquet/avro/AvroSchemaConverter.class from jar /home/jenkins/.m2/repository/org/apache/parquet/parquet-avro/1.10.1/parquet-avro-1.10.1.jar [WARNING] WORKAROUND: refusing to add class org/apache/parquet/avro/AvroSchemaConverter$1.class from jar /home/jenkins/.m2/repository/org/apache/parquet/parquet-avro/1.10.1/parquet-avro-1.10.1.jar [WARNING] guava-27.0-jre.jar, failureaccess-1.0.jar define 2 overlapping classes: [WARNING] - com.google.common.util.concurrent.internal.InternalFutureFailureAccess [WARNING] - com.google.common.util.concurrent.internal.InternalFutures [WARNING] maven-shade-plugin has detected that some class files are [WARNING] present in two or more JARs. When this happens, only one [WARNING] single version of the class is copied to the uber jar. [WARNING] Usually this is not harmful and you can skip these warnings, [WARNING] otherwise try to manually exclude artifacts based on [WARNING] mvn dependency:tree -Ddetail=true and the above output. [WARNING] See http://maven.apache.org/plugins/maven-shade-plugin/ [INFO] Replacing original artifact with shaded artifact. [INFO] Replacing /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-assembly/target/adam-assembly-spark2_2.12-0.27.0-SNAPSHOT.jar with /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-assembly/target/adam-assembly-spark2_2.12-0.27.0-SNAPSHOT-shaded.jar [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building ADAM_2.12: Distribution 0.27.0-SNAPSHOT [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-distribution-spark2_2.12 --- [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-distribution-spark2_2.12 --- [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ adam-distribution-spark2_2.12 --- [INFO] Modified 0 of 0 .scala files [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ adam-distribution-spark2_2.12 --- [INFO] No sources to compile [INFO] [INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ adam-distribution-spark2_2.12 --- [INFO] No sources to compile [INFO] [INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ adam-distribution-spark2_2.12 --- [INFO] [INFO] --- maven-javadoc-plugin:3.1.0:jar (attach-javadoc) @ adam-distribution-spark2_2.12 --- [INFO] [INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) > generate-sources @ adam-distribution-spark2_2.12 >>> [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-distribution-spark2_2.12 --- [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-distribution-spark2_2.12 --- [INFO] [INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) < generate-sources @ adam-distribution-spark2_2.12 <<< [INFO] [INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ adam-distribution-spark2_2.12 --- [INFO] No source files found [INFO] [INFO] --- maven-assembly-plugin:3.1.0:single (default) @ adam-distribution-spark2_2.12 --- [INFO] Reading assembly descriptor: src/main/assembly/assembly.xml [INFO] Building tar: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-distribution/target/adam-distribution-spark2_2.12-0.27.0-SNAPSHOT-bin.tar.gz [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/algorithms/smithwaterman/ longer than 100 characters. [WARNING] Resulting tar file can only be processed successfully by GNU compatible tar commands [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/apache/parquet/avro/AvroSchemaConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/models/OptionalPositionOrdering$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/models/OptionalRegionOrdering$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/models/ReadGroupDictionary$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/models/OptionalReferenceOrdering.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/models/ReferencePosition.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/models/VariantContext.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/models/VariantContext$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/models/ReferencePosition$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/models/ReferenceRegionSerializer.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/models/ReferenceOrdering.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/models/ReadGroupDictionary.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/models/SequenceDictionary$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/models/PositionOrdering$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/models/ReferenceRegion$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/models/RegionOrdering$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/models/SequenceDictionary.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/models/SequenceRecord.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/models/ReferenceRegion.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/models/SequenceRecord$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/models/ReferencePositionSerializer.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/models/VariantContextSerializer.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/models/TagType$$TypeVal.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/projections/GenotypeField$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/projections/ReadField$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/projections/ReadGroupField$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/projections/Projection$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/projections/ReferenceField$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/projections/Filter$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/projections/DbxrefField$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/projections/SliceField$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/projections/FeatureField$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/projections/FieldValue.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/projections/OntologyTermField$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/projections/SampleField$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/projections/VariantAnnotationField$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/projections/SequenceField$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/projections/FieldEnumeration$SchemaVal.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/projections/VariantField$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/projections/VariantCallingAnnotationsField$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/projections/FragmentField$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/projections/NucleotideContigFragmentField$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/projections/TranscriptEffectField$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/projections/AlignmentRecordField$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/projections/FieldEnumeration.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rich/RichAlignmentRecord.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rich/RichAlignmentRecord$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/sql/NucleotideContigFragment$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/sql/VariantContext$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/sql/VariantCallingAnnotations$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/sql/TranscriptEffect.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/sql/AlignmentRecord.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/sql/VariantAnnotation$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/sql/TranscriptEffect$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/sql/ProcessingStep$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/sql/VariantCallingAnnotations.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/sql/VariantAnnotation.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/sql/NucleotideContigFragment.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/sql/AlignmentRecord$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/serialization/ADAMKryoRegistrator.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/serialization/AvroSerializer.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/serialization/InputStreamWithDecoder.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/serialization/index.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/serialization/WritableSerializer.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/instrumentation/Timers$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/instrumentation/index.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/io/SingleFastqInputFormat.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/io/FastqInputFormat.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/io/FastqRecordReader.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/io/InterleavedFastqInputFormat.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/algorithms/smithwaterman/SmithWaterman.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/algorithms/smithwaterman/SmithWatermanConstantGapScoring.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/algorithms/smithwaterman/index.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/algorithms/consensus/ConsensusGenerator$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/algorithms/consensus/index.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/algorithms/consensus/ConsensusGenerator.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/util/FileExtensions$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/util/AttributeUtils$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/util/ParquetFileTraversable.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/util/TextRddWriter$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/util/SequenceDictionaryReader$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/util/TwoBitFileSerializer.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/util/GenomeFileReader$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/util/ReferenceContigMapSerializer.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/util/ReferenceContigMap$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/util/ParquetLogger$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/util/IndexedFastaFile.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/util/ReferenceContigMap.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/RDDBoundGenericGenomicDataset.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/GenomicDatasetWithLineage.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/LeftOuterShuffleRegionJoin.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/GenomicDatasetConversion.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/RightOuterTreeRegionJoinAndGroupByRight.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/read/AlignmentRecordDataset.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/read/ADAMSAMOutputFormat.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/read/AlignmentRecordDataset$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/read/SAMInFormatter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/read/FASTQInFormatter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/read/ADAMCRAMOutputFormat.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/read/BAMInFormatter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/read/ADAMCRAMOutputFormatHeaderLess.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/read/InstrumentedADAMBAMOutputFormatHeaderLess.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/read/DatasetBoundAlignmentRecordDataset.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/read/AnySAMOutFormatter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/read/InstrumentedADAMSAMOutputFormat.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/read/ADAMBAMOutputFormatHeaderLess.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/read/QualityScoreBin.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/read/ReferencePositionPairSerializer.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/read/InstrumentedADAMCRAMOutputFormatHeaderLess.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/read/AnySAMInFormatter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/read/BAMInFormatter$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/read/FASTQInFormatter$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/read/RDDBoundAlignmentRecordDataset.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/read/ADAMBAMOutputFormat.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/read/QualityScoreBin$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/read/InstrumentedADAMSAMOutputFormatHeaderLess.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/read/SingleReadBucketSerializer.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/read/IncorrectMDTagException.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/read/ADAMSAMOutputFormatHeaderLess.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/read/SAMInFormatter$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/read/AnySAMInFormatterCompanion.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/read/InstrumentedADAMBAMOutputFormat.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/read/InstrumentedADAMCRAMOutputFormat.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/read/ParquetUnboundAlignmentRecordDataset.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/GenericGenomicDataset.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/AvroGenomicDataset.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/InnerTreeRegionJoin.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/MultisampleGenomicDataset.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/GenomicRegionPartitioner$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/GenomicPositionPartitioner.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/VictimlessSortedIntervalPartitionJoin.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/LeftOuterShuffleRegionJoinAndGroupByLeft.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/InFormatterCompanion.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/feature/NarrowPeakInFormatter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/feature/RDDBoundCoverageDataset.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/feature/ParquetUnboundFeatureDataset.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/feature/DatasetBoundCoverageDataset.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/feature/GTFInFormatter$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/feature/BEDInFormatter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/feature/BEDOutFormatter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/feature/GFF3InFormatter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/feature/GTFInFormatter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/feature/NarrowPeakInFormatter$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/feature/CoverageDataset$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/feature/GFF3InFormatter$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/feature/GFF3OutFormatter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/feature/CoverageDataset.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/feature/FeatureDataset$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/feature/RDDBoundFeatureDataset.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/feature/GTFOutFormatter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/feature/BEDInFormatter$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/feature/ParquetUnboundCoverageDataset.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/feature/FeatureDataset.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/feature/NarrowPeakOutFormatter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/feature/DatasetBoundFeatureDataset.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/variant/RDDBoundVariantContextDataset.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/variant/VariantDataset.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/variant/VariantContextDataset.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/variant/VariantDataset$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/variant/RDDBoundVariantDataset.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/variant/VCFOutFormatter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/variant/ADAMVCFOutputFormat.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/variant/DatasetBoundVariantContextDataset.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/variant/RDDBoundGenotypeDataset.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/variant/VCFInFormatter$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/variant/DatasetBoundGenotypeDataset.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/variant/DatasetBoundVariantDataset.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/variant/ParquetUnboundGenotypeDataset.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/variant/VCFInFormatter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/variant/GenotypeDataset$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/variant/ParquetUnboundVariantDataset.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/variant/VariantContextDataset$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/variant/GenotypeDataset.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/InnerShuffleRegionJoin.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/GenomicRegionPartitioner.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/MultisampleAvroGenomicDataset.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/AvroReadGroupGenomicDataset.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/ShuffleRegionJoin.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/ReferencePartitioner.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/InnerTreeRegionJoinAndGroupByRight.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/GenomicBroadcast.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/GenericConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/fragment/ParquetUnboundFragmentDataset.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/fragment/Tab6InFormatter$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/fragment/FragmentDataset.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/fragment/Tab6InFormatter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/fragment/FragmentDataset$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/fragment/InterleavedFASTQInFormatter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/fragment/DatasetBoundFragmentDataset.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/fragment/RDDBoundFragmentDataset.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/fragment/InterleavedFASTQInFormatter$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/fragment/Tab5InFormatter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/fragment/Tab5InFormatter$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/DatasetBoundGenericGenomicDataset.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/ADAMSaveAnyArgs.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/FullOuterShuffleRegionJoin.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/SortedIntervalPartitionJoinWithVictims.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/RightOuterTreeRegionJoin.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/contig/DatasetBoundNucleotideContigFragmentDataset.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/contig/NucleotideContigFragmentDataset$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/contig/RDDBoundNucleotideContigFragmentDataset.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/contig/ParquetUnboundNucleotideContigFragmentDataset.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/contig/NucleotideContigFragmentDataset.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/InnerShuffleRegionJoinAndGroupByLeft.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/DatasetBoundGenomicDataset.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/GenomicPositionPartitioner$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/RightOuterShuffleRegionJoinAndGroupByLeft.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/converters/AlignmentRecordConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/converters/VariantContextConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/converters/DefaultHeaderLines$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/converters/VariantContextConverter$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/javadocs/org/apache/parquet/avro/class-use/AvroSchemaConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/javadocs/org/apache/parquet/avro/AvroSchemaConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/javadocs/org/bdgenomics/adam/io/class-use/SingleFastqInputFormat.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/javadocs/org/bdgenomics/adam/io/class-use/FastqInputFormat.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/javadocs/org/bdgenomics/adam/io/class-use/FastqRecordReader.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/javadocs/org/bdgenomics/adam/io/class-use/InterleavedFastqInputFormat.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/javadocs/org/bdgenomics/adam/io/SingleFastqInputFormat.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/javadocs/org/bdgenomics/adam/io/FastqRecordReader.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/javadocs/org/bdgenomics/adam/io/InterleavedFastqInputFormat.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/python/DataFrameConversionWrapper.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/VariantsToFeaturesConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/VariantsToContigsConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/FragmentsToVariantsConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/VariantsToVariantsConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/ToCoverageDatasetConversion.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/FeaturesToGenotypesConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/ContigsToFragmentsConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/JavaADAMContext$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/FragmentsToAlignmentRecordsDatasetConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/GenotypesToCoverageDatasetConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/VariantContextsToVariantContextConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/CoverageToVariantsConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/ContigsToContigsConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/FragmentsToFragmentsConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/FeaturesToFragmentsConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/FeaturesToContigsDatasetConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/AlignmentRecordsToVariantsDatasetConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/AlignmentRecordsToFragmentsDatasetConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/ContigsToVariantsDatasetConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/AlignmentRecordsToAlignmentRecordsConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/ContigsToAlignmentRecordsDatasetConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/VariantsToCoverageDatasetConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/GenotypesToContigsDatasetConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/CoverageToContigsDatasetConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/FragmentsToVariantsDatasetConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/CoverageToFragmentsDatasetConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/CoverageToGenotypesDatasetConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/FeaturesToVariantsConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/FragmentsToGenotypesConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/GenotypesToVariantsDatasetConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/ContigsToGenotypesConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/CoverageToVariantsDatasetConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/CoverageToFeaturesDatasetConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/ToAlignmentRecordDatasetConversion.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/FeaturesToContigsConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/GenotypesToFragmentsConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/FeaturesToCoverageDatasetConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/CoverageToAlignmentRecordsDatasetConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/FragmentsToContigsDatasetConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/ContigsToVariantsConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/CoverageToContigsConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/GenotypesToVariantContextConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/FragmentsToCoverageConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/ContigsToAlignmentRecordsConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/VariantContextsToGenotypesConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/VariantContextsToVariantsConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/GenotypesToCoverageConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/FragmentsToContigsConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/GenotypesToFeaturesDatasetConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/ContigsToFragmentsDatasetConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/VariantContextsToFragmentsConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/AlignmentRecordsToVariantContextConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/AlignmentRecordsToContigsDatasetConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/FeaturesToVariantsDatasetConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/CoverageToGenotypesConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/AlignmentRecordsToGenotypesDatasetConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/CoverageToFeaturesConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/ToContigDatasetConversion.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/ToGenotypeDatasetConversion.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/VariantsToVariantContextConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/FeaturesToCoverageConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/FragmentsToFeaturesDatasetConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/FeaturesToFragmentsDatasetConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/AlignmentRecordsToFeaturesDatasetConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/VariantsToAlignmentRecordsConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/ToFragmentDatasetConversion.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/GenotypesToFragmentsDatasetConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/FragmentsToFeaturesConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/AlignmentRecordsToFeaturesConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/GenotypesToAlignmentRecordsDatasetConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/CoverageToAlignmentRecordsConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/ContigsToCoverageDatasetConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/VariantsToGenotypesDatasetConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/VariantsToCoverageConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/AlignmentRecordsToGenotypesConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/VariantsToFeaturesDatasetConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/AlignmentRecordsToCoverageDatasetConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/FeaturesToVariantContextConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/FeaturesToGenotypesDatasetConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/ContigsToFeaturesConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/CoverageToCoverageConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/FeaturesToFeatureConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/FragmentsToGenotypesDatasetConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/AlignmentRecordsToFragmentsConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/CoverageToVariantContextConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/FragmentsToCoverageDatasetConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/VariantsToFragmentsDatasetConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/GenotypesToVariantsConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/ContigsToVariantContextsConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/GenotypesToAlignmentRecordsConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/VariantsToFragmentsConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/FragmentsToVariantContextConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/CoverageToFragmentsConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/ToVariantDatasetConversion.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/VariantContextsToCoverageConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/VariantsToGenotypesConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/AlignmentRecordsToCoverageConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/VariantContextsToContigsConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/VariantsToContigsDatasetConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/ContigsToGenotypesDatasetConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/AlignmentRecordsToVariantsConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/FragmentsToAlignmentRecordsConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/GenotypesToContigsConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/AlignmentRecordsToContigsConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/JavaADAMContext.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/ToFeatureDatasetConversion.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/VariantsToAlignmentRecordsDatasetConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/FeaturesToAlignmentRecordsConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/ContigsToCoverageConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/VariantContextsToFeaturesConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/GenotypesToFeaturesConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/ToVariantContextDatasetConversion.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/ContigsToFeaturesDatasetConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/GenotypesToGenotypesConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/VariantContextsToAlignmentRecordsConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/FeaturesToAlignmentRecordsDatasetConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/cli/Reads2Coverage$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/cli/TransformFragments$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/cli/Reads2CoverageArgs.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/cli/TransformFeaturesArgs.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/cli/CountContigKmers.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/cli/MergeShardsArgs.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/cli/TransformGenotypes.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/cli/TransformVariantsArgs.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/cli/CountContigKmers$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/cli/TransformAlignments.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/cli/CountReadKmers$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/cli/TransformGenotypes$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/cli/TransformFragments.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/cli/TransformFeatures$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/cli/TransformFragmentsArgs.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/cli/TransformVariants.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/cli/CountContigKmersArgs.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/cli/TransformVariants$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/cli/TransformFeatures.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/cli/CountReadKmersArgs.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/cli/TransformAlignmentsArgs.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/cli/TransformGenotypesArgs.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/cli/TransformAlignments$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/repo/adam-assembly-spark2_2.12-0.27.0-SNAPSHOT-sources.jar longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/repo/adam-assembly-spark2_2.12-0.27.0-SNAPSHOT-javadoc.jar longer than 100 characters. [INFO] Building tar: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-distribution/target/adam-distribution-spark2_2.12-0.27.0-SNAPSHOT-bin.tar.bz2 [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/algorithms/smithwaterman/ longer than 100 characters. [WARNING] Resulting tar file can only be processed successfully by GNU compatible tar commands [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/apache/parquet/avro/AvroSchemaConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/models/OptionalPositionOrdering$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/models/OptionalRegionOrdering$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/models/ReadGroupDictionary$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/models/OptionalReferenceOrdering.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/models/ReferencePosition.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/models/VariantContext.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/models/VariantContext$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/models/ReferencePosition$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/models/ReferenceRegionSerializer.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/models/ReferenceOrdering.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/models/ReadGroupDictionary.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/models/SequenceDictionary$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/models/PositionOrdering$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/models/ReferenceRegion$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/models/RegionOrdering$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/models/SequenceDictionary.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/models/SequenceRecord.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/models/ReferenceRegion.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/models/SequenceRecord$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/models/ReferencePositionSerializer.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/models/VariantContextSerializer.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/models/TagType$$TypeVal.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/projections/GenotypeField$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/projections/ReadField$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/projections/ReadGroupField$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/projections/Projection$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/projections/ReferenceField$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/projections/Filter$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/projections/DbxrefField$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/projections/SliceField$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/projections/FeatureField$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/projections/FieldValue.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/projections/OntologyTermField$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/projections/SampleField$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/projections/VariantAnnotationField$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/projections/SequenceField$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/projections/FieldEnumeration$SchemaVal.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/projections/VariantField$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/projections/VariantCallingAnnotationsField$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/projections/FragmentField$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/projections/NucleotideContigFragmentField$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/projections/TranscriptEffectField$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/projections/AlignmentRecordField$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/projections/FieldEnumeration.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rich/RichAlignmentRecord.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rich/RichAlignmentRecord$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/sql/NucleotideContigFragment$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/sql/VariantContext$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/sql/VariantCallingAnnotations$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/sql/TranscriptEffect.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/sql/AlignmentRecord.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/sql/VariantAnnotation$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/sql/TranscriptEffect$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/sql/ProcessingStep$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/sql/VariantCallingAnnotations.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/sql/VariantAnnotation.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/sql/NucleotideContigFragment.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/sql/AlignmentRecord$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/serialization/ADAMKryoRegistrator.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/serialization/AvroSerializer.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/serialization/InputStreamWithDecoder.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/serialization/index.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/serialization/WritableSerializer.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/instrumentation/Timers$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/instrumentation/index.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/io/SingleFastqInputFormat.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/io/FastqInputFormat.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/io/FastqRecordReader.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/io/InterleavedFastqInputFormat.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/algorithms/smithwaterman/SmithWaterman.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/algorithms/smithwaterman/SmithWatermanConstantGapScoring.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/algorithms/smithwaterman/index.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/algorithms/consensus/ConsensusGenerator$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/algorithms/consensus/index.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/algorithms/consensus/ConsensusGenerator.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/util/FileExtensions$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/util/AttributeUtils$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/util/ParquetFileTraversable.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/util/TextRddWriter$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/util/SequenceDictionaryReader$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/util/TwoBitFileSerializer.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/util/GenomeFileReader$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/util/ReferenceContigMapSerializer.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/util/ReferenceContigMap$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/util/ParquetLogger$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/util/IndexedFastaFile.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/util/ReferenceContigMap.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/RDDBoundGenericGenomicDataset.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/GenomicDatasetWithLineage.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/LeftOuterShuffleRegionJoin.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/GenomicDatasetConversion.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/RightOuterTreeRegionJoinAndGroupByRight.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/read/AlignmentRecordDataset.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/read/ADAMSAMOutputFormat.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/read/AlignmentRecordDataset$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/read/SAMInFormatter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/read/FASTQInFormatter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/read/ADAMCRAMOutputFormat.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/read/BAMInFormatter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/read/ADAMCRAMOutputFormatHeaderLess.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/read/InstrumentedADAMBAMOutputFormatHeaderLess.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/read/DatasetBoundAlignmentRecordDataset.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/read/AnySAMOutFormatter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/read/InstrumentedADAMSAMOutputFormat.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/read/ADAMBAMOutputFormatHeaderLess.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/read/QualityScoreBin.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/read/ReferencePositionPairSerializer.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/read/InstrumentedADAMCRAMOutputFormatHeaderLess.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/read/AnySAMInFormatter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/read/BAMInFormatter$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/read/FASTQInFormatter$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/read/RDDBoundAlignmentRecordDataset.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/read/ADAMBAMOutputFormat.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/read/QualityScoreBin$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/read/InstrumentedADAMSAMOutputFormatHeaderLess.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/read/SingleReadBucketSerializer.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/read/IncorrectMDTagException.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/read/ADAMSAMOutputFormatHeaderLess.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/read/SAMInFormatter$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/read/AnySAMInFormatterCompanion.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/read/InstrumentedADAMBAMOutputFormat.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/read/InstrumentedADAMCRAMOutputFormat.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/read/ParquetUnboundAlignmentRecordDataset.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/GenericGenomicDataset.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/AvroGenomicDataset.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/InnerTreeRegionJoin.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/MultisampleGenomicDataset.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/GenomicRegionPartitioner$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/GenomicPositionPartitioner.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/VictimlessSortedIntervalPartitionJoin.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/LeftOuterShuffleRegionJoinAndGroupByLeft.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/InFormatterCompanion.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/feature/NarrowPeakInFormatter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/feature/RDDBoundCoverageDataset.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/feature/ParquetUnboundFeatureDataset.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/feature/DatasetBoundCoverageDataset.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/feature/GTFInFormatter$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/feature/BEDInFormatter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/feature/BEDOutFormatter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/feature/GFF3InFormatter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/feature/GTFInFormatter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/feature/NarrowPeakInFormatter$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/feature/CoverageDataset$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/feature/GFF3InFormatter$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/feature/GFF3OutFormatter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/feature/CoverageDataset.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/feature/FeatureDataset$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/feature/RDDBoundFeatureDataset.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/feature/GTFOutFormatter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/feature/BEDInFormatter$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/feature/ParquetUnboundCoverageDataset.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/feature/FeatureDataset.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/feature/NarrowPeakOutFormatter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/feature/DatasetBoundFeatureDataset.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/variant/RDDBoundVariantContextDataset.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/variant/VariantDataset.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/variant/VariantContextDataset.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/variant/VariantDataset$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/variant/RDDBoundVariantDataset.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/variant/VCFOutFormatter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/variant/ADAMVCFOutputFormat.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/variant/DatasetBoundVariantContextDataset.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/variant/RDDBoundGenotypeDataset.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/variant/VCFInFormatter$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/variant/DatasetBoundGenotypeDataset.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/variant/DatasetBoundVariantDataset.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/variant/ParquetUnboundGenotypeDataset.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/variant/VCFInFormatter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/variant/GenotypeDataset$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/variant/ParquetUnboundVariantDataset.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/variant/VariantContextDataset$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/variant/GenotypeDataset.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/InnerShuffleRegionJoin.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/GenomicRegionPartitioner.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/MultisampleAvroGenomicDataset.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/AvroReadGroupGenomicDataset.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/ShuffleRegionJoin.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/ReferencePartitioner.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/InnerTreeRegionJoinAndGroupByRight.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/GenomicBroadcast.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/GenericConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/fragment/ParquetUnboundFragmentDataset.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/fragment/Tab6InFormatter$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/fragment/FragmentDataset.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/fragment/Tab6InFormatter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/fragment/FragmentDataset$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/fragment/InterleavedFASTQInFormatter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/fragment/DatasetBoundFragmentDataset.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/fragment/RDDBoundFragmentDataset.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/fragment/InterleavedFASTQInFormatter$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/fragment/Tab5InFormatter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/fragment/Tab5InFormatter$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/DatasetBoundGenericGenomicDataset.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/ADAMSaveAnyArgs.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/FullOuterShuffleRegionJoin.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/SortedIntervalPartitionJoinWithVictims.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/RightOuterTreeRegionJoin.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/contig/DatasetBoundNucleotideContigFragmentDataset.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/contig/NucleotideContigFragmentDataset$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/contig/RDDBoundNucleotideContigFragmentDataset.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/contig/ParquetUnboundNucleotideContigFragmentDataset.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/contig/NucleotideContigFragmentDataset.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/InnerShuffleRegionJoinAndGroupByLeft.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/DatasetBoundGenomicDataset.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/GenomicPositionPartitioner$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/RightOuterShuffleRegionJoinAndGroupByLeft.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/converters/AlignmentRecordConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/converters/VariantContextConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/converters/DefaultHeaderLines$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/converters/VariantContextConverter$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/javadocs/org/apache/parquet/avro/class-use/AvroSchemaConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/javadocs/org/apache/parquet/avro/AvroSchemaConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/javadocs/org/bdgenomics/adam/io/class-use/SingleFastqInputFormat.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/javadocs/org/bdgenomics/adam/io/class-use/FastqInputFormat.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/javadocs/org/bdgenomics/adam/io/class-use/FastqRecordReader.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/javadocs/org/bdgenomics/adam/io/class-use/InterleavedFastqInputFormat.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/javadocs/org/bdgenomics/adam/io/SingleFastqInputFormat.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/javadocs/org/bdgenomics/adam/io/FastqRecordReader.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/javadocs/org/bdgenomics/adam/io/InterleavedFastqInputFormat.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/python/DataFrameConversionWrapper.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/VariantsToFeaturesConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/VariantsToContigsConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/FragmentsToVariantsConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/VariantsToVariantsConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/ToCoverageDatasetConversion.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/FeaturesToGenotypesConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/ContigsToFragmentsConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/JavaADAMContext$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/FragmentsToAlignmentRecordsDatasetConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/GenotypesToCoverageDatasetConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/VariantContextsToVariantContextConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/CoverageToVariantsConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/ContigsToContigsConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/FragmentsToFragmentsConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/FeaturesToFragmentsConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/FeaturesToContigsDatasetConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/AlignmentRecordsToVariantsDatasetConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/AlignmentRecordsToFragmentsDatasetConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/ContigsToVariantsDatasetConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/AlignmentRecordsToAlignmentRecordsConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/ContigsToAlignmentRecordsDatasetConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/VariantsToCoverageDatasetConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/GenotypesToContigsDatasetConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/CoverageToContigsDatasetConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/FragmentsToVariantsDatasetConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/CoverageToFragmentsDatasetConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/CoverageToGenotypesDatasetConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/FeaturesToVariantsConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/FragmentsToGenotypesConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/GenotypesToVariantsDatasetConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/ContigsToGenotypesConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/CoverageToVariantsDatasetConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/CoverageToFeaturesDatasetConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/ToAlignmentRecordDatasetConversion.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/FeaturesToContigsConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/GenotypesToFragmentsConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/FeaturesToCoverageDatasetConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/CoverageToAlignmentRecordsDatasetConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/FragmentsToContigsDatasetConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/ContigsToVariantsConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/CoverageToContigsConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/GenotypesToVariantContextConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/FragmentsToCoverageConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/ContigsToAlignmentRecordsConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/VariantContextsToGenotypesConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/VariantContextsToVariantsConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/GenotypesToCoverageConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/FragmentsToContigsConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/GenotypesToFeaturesDatasetConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/ContigsToFragmentsDatasetConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/VariantContextsToFragmentsConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/AlignmentRecordsToVariantContextConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/AlignmentRecordsToContigsDatasetConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/FeaturesToVariantsDatasetConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/CoverageToGenotypesConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/AlignmentRecordsToGenotypesDatasetConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/CoverageToFeaturesConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/ToContigDatasetConversion.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/ToGenotypeDatasetConversion.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/VariantsToVariantContextConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/FeaturesToCoverageConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/FragmentsToFeaturesDatasetConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/FeaturesToFragmentsDatasetConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/AlignmentRecordsToFeaturesDatasetConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/VariantsToAlignmentRecordsConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/ToFragmentDatasetConversion.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/GenotypesToFragmentsDatasetConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/FragmentsToFeaturesConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/AlignmentRecordsToFeaturesConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/GenotypesToAlignmentRecordsDatasetConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/CoverageToAlignmentRecordsConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/ContigsToCoverageDatasetConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/VariantsToGenotypesDatasetConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/VariantsToCoverageConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/AlignmentRecordsToGenotypesConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/VariantsToFeaturesDatasetConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/AlignmentRecordsToCoverageDatasetConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/FeaturesToVariantContextConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/FeaturesToGenotypesDatasetConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/ContigsToFeaturesConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/CoverageToCoverageConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/FeaturesToFeatureConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/FragmentsToGenotypesDatasetConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/AlignmentRecordsToFragmentsConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/CoverageToVariantContextConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/FragmentsToCoverageDatasetConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/VariantsToFragmentsDatasetConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/GenotypesToVariantsConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/ContigsToVariantContextsConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/GenotypesToAlignmentRecordsConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/VariantsToFragmentsConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/FragmentsToVariantContextConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/CoverageToFragmentsConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/ToVariantDatasetConversion.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/VariantContextsToCoverageConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/VariantsToGenotypesConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/AlignmentRecordsToCoverageConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/VariantContextsToContigsConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/VariantsToContigsDatasetConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/ContigsToGenotypesDatasetConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/AlignmentRecordsToVariantsConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/FragmentsToAlignmentRecordsConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/GenotypesToContigsConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/AlignmentRecordsToContigsConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/JavaADAMContext.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/ToFeatureDatasetConversion.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/VariantsToAlignmentRecordsDatasetConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/FeaturesToAlignmentRecordsConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/ContigsToCoverageConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/VariantContextsToFeaturesConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/GenotypesToFeaturesConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/ToVariantContextDatasetConversion.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/ContigsToFeaturesDatasetConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/GenotypesToGenotypesConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/VariantContextsToAlignmentRecordsConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/FeaturesToAlignmentRecordsDatasetConverter.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/cli/Reads2Coverage$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/cli/TransformFragments$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/cli/Reads2CoverageArgs.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/cli/TransformFeaturesArgs.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/cli/CountContigKmers.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/cli/MergeShardsArgs.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/cli/TransformGenotypes.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/cli/TransformVariantsArgs.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/cli/CountContigKmers$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/cli/TransformAlignments.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/cli/CountReadKmers$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/cli/TransformGenotypes$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/cli/TransformFragments.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/cli/TransformFeatures$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/cli/TransformFragmentsArgs.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/cli/TransformVariants.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/cli/CountContigKmersArgs.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/cli/TransformVariants$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/cli/TransformFeatures.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/cli/CountReadKmersArgs.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/cli/TransformAlignmentsArgs.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/cli/TransformGenotypesArgs.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/cli/TransformAlignments$.html longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/repo/adam-assembly-spark2_2.12-0.27.0-SNAPSHOT-sources.jar longer than 100 characters. [WARNING] Entry: adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/repo/adam-assembly-spark2_2.12-0.27.0-SNAPSHOT-javadoc.jar longer than 100 characters. [INFO] Building zip: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/adam-distribution/target/adam-distribution-spark2_2.12-0.27.0-SNAPSHOT-bin.zip [INFO] ------------------------------------------------------------------------ [INFO] Reactor Summary: [INFO] [INFO] ADAM_2.12 .......................................... SUCCESS [ 8.052 s] [INFO] ADAM_2.12: Shader workaround ....................... SUCCESS [ 4.797 s] [INFO] ADAM_2.12: Avro-to-Dataset codegen utils ........... SUCCESS [ 4.234 s] [INFO] ADAM_2.12: Core .................................... SUCCESS [01:09 min] [INFO] ADAM_2.12: APIs for Java, Python ................... SUCCESS [ 7.904 s] [INFO] ADAM_2.12: CLI ..................................... SUCCESS [ 22.322 s] [INFO] ADAM_2.12: Assembly ................................ SUCCESS [ 12.290 s] [INFO] ADAM_2.12: Distribution ............................ SUCCESS [ 28.393 s] [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ [INFO] Total time: 02:37 min [INFO] Finished at: 2019-05-15T10:13:00-07:00 [INFO] Final Memory: 63M/1481M [INFO] ------------------------------------------------------------------------ # make sure that the distribution package contains an assembly jar # if no assembly jar is found, this will exit with code 1 and fail the build tar tzvf adam-distribution/target/adam-distribution*-bin.tar.gz | \ grep adam-assembly | \ grep jar | \ grep -v -e sources -e javadoc + grep adam-assembly + grep jar + tar tzvf adam-distribution/target/adam-distribution-spark2_2.12-0.27.0-SNAPSHOT-bin.tar.gz + grep -v -e sources -e javadoc -rw-r--r-- jenkins/jenkins 40587928 2019-05-15 10:12 adam-distribution-spark2_2.12-0.27.0-SNAPSHOT/repo/adam-assembly-spark2_2.12-0.27.0-SNAPSHOT.jar # we are done with maven, so clean up the maven temp dir find ${ADAM_MVN_TMP_DIR} + find /tmp/adamTestMvnpjenoa0 /tmp/adamTestMvnpjenoa0 /tmp/adamTestMvnpjenoa0/TempSuite7790111402099210763.adam /tmp/adamTestMvnpjenoa0/TempSuite7790111402099210763.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite7790111402099210763.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite7790111402099210763.adam/part-00000-57e1c7c6-85fb-4db5-ac9f-44c4cdef8d49-c000.snappy.parquet /tmp/adamTestMvnpjenoa0/TempSuite7790111402099210763.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite7790111402099210763.adam/._header.crc /tmp/adamTestMvnpjenoa0/TempSuite7790111402099210763.adam/.part-00000-57e1c7c6-85fb-4db5-ac9f-44c4cdef8d49-c000.snappy.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite7790111402099210763.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite7790111402099210763.adam/_header /tmp/adamTestMvnpjenoa0/TempSuite5656143053371088087 /tmp/adamTestMvnpjenoa0/TempSuite7629081788710742136 /tmp/adamTestMvnpjenoa0/TempSuite7081652395279320996_2.fq /tmp/adamTestMvnpjenoa0/small.vcf8661770162562869134.vcf /tmp/adamTestMvnpjenoa0/TempSuite7961983911993998754.adam /tmp/adamTestMvnpjenoa0/TempSuite7961983911993998754.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite7961983911993998754.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite7961983911993998754.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite7961983911993998754.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite7961983911993998754.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite7961983911993998754.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite7961983911993998754.adam/_common_metadata /tmp/adamTestMvnpjenoa0/TempSuite7961983911993998754.adam/._header.crc /tmp/adamTestMvnpjenoa0/TempSuite7961983911993998754.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite7961983911993998754.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite7961983911993998754.adam/_metadata /tmp/adamTestMvnpjenoa0/TempSuite7961983911993998754.adam/_header /tmp/adamTestMvnpjenoa0/TempSuite5599628095909759302.adam /tmp/adamTestMvnpjenoa0/TempSuite5599628095909759302.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite5599628095909759302.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite5599628095909759302.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite5599628095909759302.adam/.part-r-00003.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite5599628095909759302.adam/part-r-00001.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite5599628095909759302.adam/_readGroups.avro /tmp/adamTestMvnpjenoa0/TempSuite5599628095909759302.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite5599628095909759302.adam/_partitionMap.avro /tmp/adamTestMvnpjenoa0/TempSuite5599628095909759302.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite5599628095909759302.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite5599628095909759302.adam/.part-r-00001.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite5599628095909759302.adam/part-r-00002.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite5599628095909759302.adam/._processingSteps.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite5599628095909759302.adam/.part-r-00002.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite5599628095909759302.adam/_common_metadata /tmp/adamTestMvnpjenoa0/TempSuite5599628095909759302.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite5599628095909759302.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite5599628095909759302.adam/._readGroups.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite5599628095909759302.adam/._partitionMap.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite5599628095909759302.adam/_metadata /tmp/adamTestMvnpjenoa0/TempSuite5599628095909759302.adam/part-r-00003.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite5599628095909759302.adam/_processingSteps.avro /tmp/adamTestMvnpjenoa0/TempSuite531660189808326994 /tmp/adamTestMvnpjenoa0/random.vcf4808875699905324248.vcf /tmp/adamTestMvnpjenoa0/TempSuite2073119608557682301.fq /tmp/adamTestMvnpjenoa0/TempSuite2073119608557682301.fq/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite2073119608557682301.fq/part-00000 /tmp/adamTestMvnpjenoa0/TempSuite2073119608557682301.fq/.part-00000.crc /tmp/adamTestMvnpjenoa0/TempSuite2073119608557682301.fq/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/4462186568819299832 /tmp/adamTestMvnpjenoa0/4462186568819299832/sorted-variants.lex.vcf /tmp/adamTestMvnpjenoa0/4462186568819299832/.sorted-variants.lex.vcf.crc /tmp/adamTestMvnpjenoa0/TempSuite1034882394398341639 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite1557351998696526247 /tmp/adamTestMvnpjenoa0/TempSuite2221067587595277651 /tmp/adamTestMvnpjenoa0/reads123179788556845215157 /tmp/adamTestMvnpjenoa0/reads123179788556845215157/reads12.sam /tmp/adamTestMvnpjenoa0/reads123179788556845215157/reads12.sam/_SUCCESS /tmp/adamTestMvnpjenoa0/reads123179788556845215157/reads12.sam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/reads123179788556845215157/reads12.sam/.part-r-00000.sam.crc /tmp/adamTestMvnpjenoa0/reads123179788556845215157/reads12.sam/part-r-00000.sam /tmp/adamTestMvnpjenoa0/TempSuite1056021066846908985 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite4284140672707150483 /tmp/adamTestMvnpjenoa0/TempSuite7472332666443096298.adam /tmp/adamTestMvnpjenoa0/TempSuite7472332666443096298.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite7472332666443096298.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite7472332666443096298.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite7472332666443096298.adam/.part-00000-da366158-ef16-4bb8-a73f-3516b6dd540c-c000.snappy.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite7472332666443096298.adam/part-00000-da366158-ef16-4bb8-a73f-3516b6dd540c-c000.snappy.parquet /tmp/adamTestMvnpjenoa0/TempSuite7472332666443096298.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite1062702206035455186 /tmp/adamTestMvnpjenoa0/TempSuite3498858269218556215.adam /tmp/adamTestMvnpjenoa0/TempSuite3498858269218556215.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite3498858269218556215.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite3498858269218556215.adam/._samples.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite3498858269218556215.adam/part-00000-dd932d66-3d3e-4288-b66b-2c43b3c5d8aa-c000.snappy.parquet /tmp/adamTestMvnpjenoa0/TempSuite3498858269218556215.adam/.part-00001-dd932d66-3d3e-4288-b66b-2c43b3c5d8aa-c000.snappy.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite3498858269218556215.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite3498858269218556215.adam/._header.crc /tmp/adamTestMvnpjenoa0/TempSuite3498858269218556215.adam/part-00001-dd932d66-3d3e-4288-b66b-2c43b3c5d8aa-c000.snappy.parquet /tmp/adamTestMvnpjenoa0/TempSuite3498858269218556215.adam/.part-00002-dd932d66-3d3e-4288-b66b-2c43b3c5d8aa-c000.snappy.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite3498858269218556215.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite3498858269218556215.adam/.part-00000-dd932d66-3d3e-4288-b66b-2c43b3c5d8aa-c000.snappy.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite3498858269218556215.adam/_samples.avro /tmp/adamTestMvnpjenoa0/TempSuite3498858269218556215.adam/part-00002-dd932d66-3d3e-4288-b66b-2c43b3c5d8aa-c000.snappy.parquet /tmp/adamTestMvnpjenoa0/TempSuite3498858269218556215.adam/_header /tmp/adamTestMvnpjenoa0/TempSuite5823670682827686736.adam /tmp/adamTestMvnpjenoa0/TempSuite5823670682827686736.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite5823670682827686736.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite5823670682827686736.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite5823670682827686736.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite5823670682827686736.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite5823670682827686736.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite5823670682827686736.adam/_common_metadata /tmp/adamTestMvnpjenoa0/TempSuite5823670682827686736.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite5823670682827686736.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite5823670682827686736.adam/_metadata /tmp/adamTestMvnpjenoa0/TempSuite9169091240049456396 /tmp/adamTestMvnpjenoa0/TempSuite5950386164177715206 /tmp/adamTestMvnpjenoa0/TempSuite3955910051511586392_1.fq /tmp/adamTestMvnpjenoa0/TempSuite3955910051511586392_1.fq/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite3955910051511586392_1.fq/part-00000 /tmp/adamTestMvnpjenoa0/TempSuite3955910051511586392_1.fq/.part-00000.crc /tmp/adamTestMvnpjenoa0/TempSuite3955910051511586392_1.fq/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite7368695202327364990 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite4627558136253177920 /tmp/adamTestMvnpjenoa0/TempSuite8396237150087203606fragments.adam /tmp/adamTestMvnpjenoa0/TempSuite8396237150087203606fragments.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite8396237150087203606fragments.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite8396237150087203606fragments.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite8396237150087203606fragments.adam/_readGroups.avro /tmp/adamTestMvnpjenoa0/TempSuite8396237150087203606fragments.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite8396237150087203606fragments.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite8396237150087203606fragments.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite8396237150087203606fragments.adam/._processingSteps.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite8396237150087203606fragments.adam/_common_metadata /tmp/adamTestMvnpjenoa0/TempSuite8396237150087203606fragments.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite8396237150087203606fragments.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite8396237150087203606fragments.adam/._readGroups.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite8396237150087203606fragments.adam/_metadata /tmp/adamTestMvnpjenoa0/TempSuite8396237150087203606fragments.adam/_processingSteps.avro /tmp/adamTestMvnpjenoa0/TempSuite3230692174078317538 /tmp/adamTestMvnpjenoa0/TempSuite7847523129585802179 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite4645048015409656528 /tmp/adamTestMvnpjenoa0/TempSuite3498858269218556215 /tmp/adamTestMvnpjenoa0/TempSuite8523171384202153600 /tmp/adamTestMvnpjenoa0/bqsr14866815435896616084 /tmp/adamTestMvnpjenoa0/bqsr14866815435896616084/.bqsr1.sam.crc /tmp/adamTestMvnpjenoa0/bqsr14866815435896616084/bqsr1.sam /tmp/adamTestMvnpjenoa0/TempSuite2221783522305252815.adam /tmp/adamTestMvnpjenoa0/TempSuite2221783522305252815.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite2221783522305252815.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite2221783522305252815.adam/._samples.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite2221783522305252815.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite2221783522305252815.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite2221783522305252815.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite2221783522305252815.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite2221783522305252815.adam/_common_metadata /tmp/adamTestMvnpjenoa0/TempSuite2221783522305252815.adam/._header.crc /tmp/adamTestMvnpjenoa0/TempSuite2221783522305252815.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite2221783522305252815.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite2221783522305252815.adam/_samples.avro /tmp/adamTestMvnpjenoa0/TempSuite2221783522305252815.adam/_metadata /tmp/adamTestMvnpjenoa0/TempSuite2221783522305252815.adam/_header /tmp/adamTestMvnpjenoa0/TempSuite871135829501858286 /tmp/adamTestMvnpjenoa0/javaAC1691709686454799805 /tmp/adamTestMvnpjenoa0/javaAC1691709686454799805/testRdd.variant.adam /tmp/adamTestMvnpjenoa0/javaAC1691709686454799805/testRdd.variant.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/javaAC1691709686454799805/testRdd.variant.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/javaAC1691709686454799805/testRdd.variant.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/javaAC1691709686454799805/testRdd.variant.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/javaAC1691709686454799805/testRdd.variant.adam/_references.avro /tmp/adamTestMvnpjenoa0/javaAC1691709686454799805/testRdd.variant.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/javaAC1691709686454799805/testRdd.variant.adam/_common_metadata /tmp/adamTestMvnpjenoa0/javaAC1691709686454799805/testRdd.variant.adam/._header.crc /tmp/adamTestMvnpjenoa0/javaAC1691709686454799805/testRdd.variant.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/javaAC1691709686454799805/testRdd.variant.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/javaAC1691709686454799805/testRdd.variant.adam/_metadata /tmp/adamTestMvnpjenoa0/javaAC1691709686454799805/testRdd.variant.adam/_header /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite8844978334613793167.bed /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite8844978334613793167.bed/_SUCCESS /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite8844978334613793167.bed/part-00001 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite8844978334613793167.bed/.part-00003.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite8844978334613793167.bed/part-00000 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite8844978334613793167.bed/part-00003 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite8844978334613793167.bed/.part-00000.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite8844978334613793167.bed/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite8844978334613793167.bed/part-00002 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite8844978334613793167.bed/.part-00002.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite8844978334613793167.bed/.part-00001.crc /tmp/adamTestMvnpjenoa0/TempSuite8821205413415988154 /tmp/adamTestMvnpjenoa0/TempSuite8066014653926878091.sam /tmp/adamTestMvnpjenoa0/TempSuite5109285308672328680 /tmp/adamTestMvnpjenoa0/TempSuite3767086643913756235 /tmp/adamTestMvnpjenoa0/1953265549210010201 /tmp/adamTestMvnpjenoa0/1953265549210010201/genotypes.nested-annotations.adam /tmp/adamTestMvnpjenoa0/1953265549210010201/genotypes.nested-annotations.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/1953265549210010201/genotypes.nested-annotations.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/1953265549210010201/genotypes.nested-annotations.adam/._samples.avro.crc /tmp/adamTestMvnpjenoa0/1953265549210010201/genotypes.nested-annotations.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/1953265549210010201/genotypes.nested-annotations.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/1953265549210010201/genotypes.nested-annotations.adam/_references.avro /tmp/adamTestMvnpjenoa0/1953265549210010201/genotypes.nested-annotations.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/1953265549210010201/genotypes.nested-annotations.adam/_common_metadata /tmp/adamTestMvnpjenoa0/1953265549210010201/genotypes.nested-annotations.adam/._header.crc /tmp/adamTestMvnpjenoa0/1953265549210010201/genotypes.nested-annotations.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/1953265549210010201/genotypes.nested-annotations.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/1953265549210010201/genotypes.nested-annotations.adam/_samples.avro /tmp/adamTestMvnpjenoa0/1953265549210010201/genotypes.nested-annotations.adam/_metadata /tmp/adamTestMvnpjenoa0/1953265549210010201/genotypes.nested-annotations.adam/_header /tmp/adamTestMvnpjenoa0/TempSuite8066014653926878091 /tmp/adamTestMvnpjenoa0/TempSuite1134365893929950796.fq /tmp/adamTestMvnpjenoa0/TempSuite1134365893929950796.fq/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite1134365893929950796.fq/part-00000 /tmp/adamTestMvnpjenoa0/TempSuite1134365893929950796.fq/.part-00000.crc /tmp/adamTestMvnpjenoa0/TempSuite1134365893929950796.fq/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite787098745758403258_1.fq /tmp/adamTestMvnpjenoa0/TempSuite7284403123459791885 /tmp/adamTestMvnpjenoa0/TempSuite4879366274265961749.adam /tmp/adamTestMvnpjenoa0/TempSuite4879366274265961749.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite4879366274265961749.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite4879366274265961749.adam/._samples.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite4879366274265961749.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite4879366274265961749.adam/.part-r-00003.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite4879366274265961749.adam/part-r-00001.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite4879366274265961749.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite4879366274265961749.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite4879366274265961749.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite4879366274265961749.adam/.part-r-00001.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite4879366274265961749.adam/part-r-00002.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite4879366274265961749.adam/.part-r-00002.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite4879366274265961749.adam/_common_metadata /tmp/adamTestMvnpjenoa0/TempSuite4879366274265961749.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite4879366274265961749.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite4879366274265961749.adam/_samples.avro /tmp/adamTestMvnpjenoa0/TempSuite4879366274265961749.adam/_metadata /tmp/adamTestMvnpjenoa0/TempSuite4879366274265961749.adam/part-r-00003.gz.parquet /tmp/adamTestMvnpjenoa0/2297065091497550676 /tmp/adamTestMvnpjenoa0/2297065091497550676/chr20.contig.adam /tmp/adamTestMvnpjenoa0/2297065091497550676/chr20.contig.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/2297065091497550676/chr20.contig.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/2297065091497550676/chr20.contig.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/2297065091497550676/chr20.contig.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/2297065091497550676/chr20.contig.adam/_references.avro /tmp/adamTestMvnpjenoa0/2297065091497550676/chr20.contig.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/2297065091497550676/chr20.contig.adam/_common_metadata /tmp/adamTestMvnpjenoa0/2297065091497550676/chr20.contig.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/2297065091497550676/chr20.contig.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/2297065091497550676/chr20.contig.adam/_metadata /tmp/adamTestMvnpjenoa0/bqsr1.sam6768740195546547860.sam /tmp/adamTestMvnpjenoa0/291194691562892310 /tmp/adamTestMvnpjenoa0/291194691562892310/sorted.vcf /tmp/adamTestMvnpjenoa0/291194691562892310/.sorted.vcf.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite8374151915469850813 /tmp/adamTestMvnpjenoa0/.FeatureDatasetFunctionsSuite2796341201094247953.narrowPeak.crc /tmp/adamTestMvnpjenoa0/TempSuite3731831443337525137.adam /tmp/adamTestMvnpjenoa0/TempSuite3731831443337525137.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite3731831443337525137.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite3731831443337525137.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite3731831443337525137.adam/part-00000-efa3e365-a3a9-4b07-834f-641a4ec0bf64-c000.snappy.parquet /tmp/adamTestMvnpjenoa0/TempSuite3731831443337525137.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite3731831443337525137.adam/.part-00000-efa3e365-a3a9-4b07-834f-641a4ec0bf64-c000.snappy.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite8729714883702295667.adam /tmp/adamTestMvnpjenoa0/TempSuite8729714883702295667.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite8729714883702295667.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite8729714883702295667.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite8729714883702295667.adam/_readGroups.avro /tmp/adamTestMvnpjenoa0/TempSuite8729714883702295667.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite8729714883702295667.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite8729714883702295667.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite8729714883702295667.adam/._processingSteps.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite8729714883702295667.adam/_common_metadata /tmp/adamTestMvnpjenoa0/TempSuite8729714883702295667.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite8729714883702295667.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite8729714883702295667.adam/._readGroups.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite8729714883702295667.adam/_metadata /tmp/adamTestMvnpjenoa0/TempSuite8729714883702295667.adam/_processingSteps.avro /tmp/adamTestMvnpjenoa0/TempSuite4003557705590353492.adam /tmp/adamTestMvnpjenoa0/TempSuite4003557705590353492.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite4003557705590353492.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite4003557705590353492.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite4003557705590353492.adam/_readGroups.avro /tmp/adamTestMvnpjenoa0/TempSuite4003557705590353492.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite4003557705590353492.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite4003557705590353492.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite4003557705590353492.adam/._processingSteps.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite4003557705590353492.adam/_common_metadata /tmp/adamTestMvnpjenoa0/TempSuite4003557705590353492.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite4003557705590353492.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite4003557705590353492.adam/._readGroups.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite4003557705590353492.adam/_metadata /tmp/adamTestMvnpjenoa0/TempSuite4003557705590353492.adam/_processingSteps.avro /tmp/adamTestMvnpjenoa0/random.vcf165528468219191207.vcf /tmp/adamTestMvnpjenoa0/TempSuite4907055810381785358.bed /tmp/adamTestMvnpjenoa0/TempSuite4907055810381785358.bed/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite4907055810381785358.bed/part-00000 /tmp/adamTestMvnpjenoa0/TempSuite4907055810381785358.bed/.part-00000.crc /tmp/adamTestMvnpjenoa0/TempSuite4907055810381785358.bed/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/903877333580977377 /tmp/adamTestMvnpjenoa0/903877333580977377/out.cram /tmp/adamTestMvnpjenoa0/903877333580977377/.out.cram.crc /tmp/adamTestMvnpjenoa0/903877333580977377/out.cram_head /tmp/adamTestMvnpjenoa0/903877333580977377/out.cram_tail /tmp/adamTestMvnpjenoa0/903877333580977377/out.cram_tail/_SUCCESS /tmp/adamTestMvnpjenoa0/903877333580977377/out.cram_tail/part-r-00001.cram /tmp/adamTestMvnpjenoa0/903877333580977377/out.cram_tail/.part-r-00003.cram.crc /tmp/adamTestMvnpjenoa0/903877333580977377/out.cram_tail/part-r-00000.cram /tmp/adamTestMvnpjenoa0/903877333580977377/out.cram_tail/.part-r-00002.cram.crc /tmp/adamTestMvnpjenoa0/903877333580977377/out.cram_tail/part-r-00003.cram /tmp/adamTestMvnpjenoa0/903877333580977377/out.cram_tail/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/903877333580977377/out.cram_tail/.part-r-00001.cram.crc /tmp/adamTestMvnpjenoa0/903877333580977377/out.cram_tail/part-r-00002.cram /tmp/adamTestMvnpjenoa0/903877333580977377/out.cram_tail/.part-r-00000.cram.crc /tmp/adamTestMvnpjenoa0/903877333580977377/.out.cram_head.crc /tmp/adamTestMvnpjenoa0/TempSuite8039972552865898985.bed /tmp/adamTestMvnpjenoa0/TempSuite8039972552865898985.bed/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite8039972552865898985.bed/part-00000 /tmp/adamTestMvnpjenoa0/TempSuite8039972552865898985.bed/.part-00000.crc /tmp/adamTestMvnpjenoa0/TempSuite8039972552865898985.bed/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite6797992931226841804 /tmp/adamTestMvnpjenoa0/TempSuite6626342383813690462 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite8066613744102904888 /tmp/adamTestMvnpjenoa0/TempSuite7600051512605092301 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite9049085739336270777 /tmp/adamTestMvnpjenoa0/1557939528099-0 /tmp/adamTestMvnpjenoa0/1557939528099-0/test.fa /tmp/adamTestMvnpjenoa0/1557939528099-0/test.fa/_SUCCESS /tmp/adamTestMvnpjenoa0/1557939528099-0/test.fa/part-00000 /tmp/adamTestMvnpjenoa0/1557939528099-0/test.fa/.part-00000.crc /tmp/adamTestMvnpjenoa0/1557939528099-0/test.fa/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite6372047981977032559.adam /tmp/adamTestMvnpjenoa0/TempSuite6372047981977032559.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite6372047981977032559.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite6372047981977032559.adam/_readGroups.avro /tmp/adamTestMvnpjenoa0/TempSuite6372047981977032559.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite6372047981977032559.adam/._processingSteps.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite6372047981977032559.adam/part-00000-d8256573-f9c0-4c0e-9fc4-f03654b0e457-c000.snappy.parquet /tmp/adamTestMvnpjenoa0/TempSuite6372047981977032559.adam/.part-00000-d8256573-f9c0-4c0e-9fc4-f03654b0e457-c000.snappy.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite6372047981977032559.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite6372047981977032559.adam/._readGroups.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite6372047981977032559.adam/_processingSteps.avro /tmp/adamTestMvnpjenoa0/TempSuite5928571840237724678 /tmp/adamTestMvnpjenoa0/TempSuite4930684203949131432.adam /tmp/adamTestMvnpjenoa0/TempSuite4930684203949131432.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite4930684203949131432.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite4930684203949131432.adam/part-00000-50d9fc81-79a7-41aa-bce3-80d84589f735-c000.snappy.parquet /tmp/adamTestMvnpjenoa0/TempSuite4930684203949131432.adam/_readGroups.avro /tmp/adamTestMvnpjenoa0/TempSuite4930684203949131432.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite4930684203949131432.adam/.part-00000-50d9fc81-79a7-41aa-bce3-80d84589f735-c000.snappy.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite4930684203949131432.adam/._processingSteps.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite4930684203949131432.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite4930684203949131432.adam/._readGroups.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite4930684203949131432.adam/_processingSteps.avro /tmp/adamTestMvnpjenoa0/TempSuite9012567376839610898.sam /tmp/adamTestMvnpjenoa0/TempSuite9012567376839610898.sam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite9012567376839610898.sam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite9012567376839610898.sam/.part-r-00000.sam.crc /tmp/adamTestMvnpjenoa0/TempSuite9012567376839610898.sam/part-r-00000.sam /tmp/adamTestMvnpjenoa0/TempSuite9032794718835850390 /tmp/adamTestMvnpjenoa0/unordered.sam7638727031512405156.sam /tmp/adamTestMvnpjenoa0/unordered.sam6106420750227935556.sam /tmp/adamTestMvnpjenoa0/TempSuite4467856944529846887.adam /tmp/adamTestMvnpjenoa0/TempSuite4467856944529846887.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite4467856944529846887.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite4467856944529846887.adam/_readGroups.avro /tmp/adamTestMvnpjenoa0/TempSuite4467856944529846887.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite4467856944529846887.adam/._processingSteps.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite4467856944529846887.adam/part-00000-52cdc77a-d436-43b8-9c76-b9b273857cc7-c000.snappy.parquet /tmp/adamTestMvnpjenoa0/TempSuite4467856944529846887.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite4467856944529846887.adam/._readGroups.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite4467856944529846887.adam/.part-00000-52cdc77a-d436-43b8-9c76-b9b273857cc7-c000.snappy.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite4467856944529846887.adam/_processingSteps.avro /tmp/adamTestMvnpjenoa0/TempSuite1334836826716448281 /tmp/adamTestMvnpjenoa0/artificial.sam5691077438943749171.sam /tmp/adamTestMvnpjenoa0/TempSuite2706637733824238589 /tmp/adamTestMvnpjenoa0/TempSuite2225237885301104863 /tmp/adamTestMvnpjenoa0/4693288757460910960 /tmp/adamTestMvnpjenoa0/4693288757460910960/variants.lex.adam /tmp/adamTestMvnpjenoa0/4693288757460910960/variants.lex.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/4693288757460910960/variants.lex.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/4693288757460910960/variants.lex.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/4693288757460910960/variants.lex.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/4693288757460910960/variants.lex.adam/_references.avro /tmp/adamTestMvnpjenoa0/4693288757460910960/variants.lex.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/4693288757460910960/variants.lex.adam/_common_metadata /tmp/adamTestMvnpjenoa0/4693288757460910960/variants.lex.adam/._header.crc /tmp/adamTestMvnpjenoa0/4693288757460910960/variants.lex.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/4693288757460910960/variants.lex.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/4693288757460910960/variants.lex.adam/_metadata /tmp/adamTestMvnpjenoa0/4693288757460910960/variants.lex.adam/_header /tmp/adamTestMvnpjenoa0/TempSuite7616973969459567191 /tmp/adamTestMvnpjenoa0/TempSuite9165048014138494986.adam /tmp/adamTestMvnpjenoa0/TempSuite9165048014138494986.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite9165048014138494986.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite9165048014138494986.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite9165048014138494986.adam/_readGroups.avro /tmp/adamTestMvnpjenoa0/TempSuite9165048014138494986.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite9165048014138494986.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite9165048014138494986.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite9165048014138494986.adam/._processingSteps.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite9165048014138494986.adam/_common_metadata /tmp/adamTestMvnpjenoa0/TempSuite9165048014138494986.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite9165048014138494986.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite9165048014138494986.adam/._readGroups.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite9165048014138494986.adam/_metadata /tmp/adamTestMvnpjenoa0/TempSuite9165048014138494986.adam/_processingSteps.avro /tmp/adamTestMvnpjenoa0/TempSuite6323293992388568571.adam /tmp/adamTestMvnpjenoa0/TempSuite6323293992388568571.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite6323293992388568571.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite6323293992388568571.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite6323293992388568571.adam/_readGroups.avro /tmp/adamTestMvnpjenoa0/TempSuite6323293992388568571.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite6323293992388568571.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite6323293992388568571.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite6323293992388568571.adam/._processingSteps.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite6323293992388568571.adam/_common_metadata /tmp/adamTestMvnpjenoa0/TempSuite6323293992388568571.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite6323293992388568571.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite6323293992388568571.adam/._readGroups.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite6323293992388568571.adam/_metadata /tmp/adamTestMvnpjenoa0/TempSuite6323293992388568571.adam/_processingSteps.avro /tmp/adamTestMvnpjenoa0/8258077457700413390 /tmp/adamTestMvnpjenoa0/8258077457700413390/variants.adam /tmp/adamTestMvnpjenoa0/8258077457700413390/variants.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/8258077457700413390/variants.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/8258077457700413390/variants.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/8258077457700413390/variants.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/8258077457700413390/variants.adam/_references.avro /tmp/adamTestMvnpjenoa0/8258077457700413390/variants.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/8258077457700413390/variants.adam/_common_metadata /tmp/adamTestMvnpjenoa0/8258077457700413390/variants.adam/._header.crc /tmp/adamTestMvnpjenoa0/8258077457700413390/variants.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/8258077457700413390/variants.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/8258077457700413390/variants.adam/_metadata /tmp/adamTestMvnpjenoa0/8258077457700413390/variants.adam/_header /tmp/adamTestMvnpjenoa0/TempSuite7109671856500759762.adam /tmp/adamTestMvnpjenoa0/TempSuite7109671856500759762.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite7109671856500759762.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite7109671856500759762.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite7109671856500759762.adam/part-00000-94e3b1a6-eb49-4862-8e63-b4a9c0901616-c000.snappy.parquet /tmp/adamTestMvnpjenoa0/TempSuite7109671856500759762.adam/._header.crc /tmp/adamTestMvnpjenoa0/TempSuite7109671856500759762.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite7109671856500759762.adam/_header /tmp/adamTestMvnpjenoa0/TempSuite7109671856500759762.adam/.part-00000-94e3b1a6-eb49-4862-8e63-b4a9c0901616-c000.snappy.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite5226740842708597039 /tmp/adamTestMvnpjenoa0/TempSuite5166272876013598357.adam /tmp/adamTestMvnpjenoa0/TempSuite5166272876013598357.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite5166272876013598357.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite5166272876013598357.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite5166272876013598357.adam/_readGroups.avro /tmp/adamTestMvnpjenoa0/TempSuite5166272876013598357.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite5166272876013598357.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite5166272876013598357.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite5166272876013598357.adam/._processingSteps.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite5166272876013598357.adam/_common_metadata /tmp/adamTestMvnpjenoa0/TempSuite5166272876013598357.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite5166272876013598357.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite5166272876013598357.adam/._readGroups.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite5166272876013598357.adam/_metadata /tmp/adamTestMvnpjenoa0/TempSuite5166272876013598357.adam/_processingSteps.avro /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite6336583279887222371.interval_list /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite6336583279887222371.interval_list/_SUCCESS /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite6336583279887222371.interval_list/part-00001 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite6336583279887222371.interval_list/.part-00003.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite6336583279887222371.interval_list/part-00000 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite6336583279887222371.interval_list/part-00003 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite6336583279887222371.interval_list/.part-00000.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite6336583279887222371.interval_list/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite6336583279887222371.interval_list/part-00002 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite6336583279887222371.interval_list/.part-00002.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite6336583279887222371.interval_list/.part-00001.crc /tmp/adamTestMvnpjenoa0/unsorted.sam7594992943098551837.sam /tmp/adamTestMvnpjenoa0/TempSuite1644617014410985988 /tmp/adamTestMvnpjenoa0/299363141779675788 /tmp/adamTestMvnpjenoa0/299363141779675788/binned.adam /tmp/adamTestMvnpjenoa0/299363141779675788/binned.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/299363141779675788/binned.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/299363141779675788/binned.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/299363141779675788/binned.adam/_readGroups.avro /tmp/adamTestMvnpjenoa0/299363141779675788/binned.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/299363141779675788/binned.adam/_references.avro /tmp/adamTestMvnpjenoa0/299363141779675788/binned.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/299363141779675788/binned.adam/._processingSteps.avro.crc /tmp/adamTestMvnpjenoa0/299363141779675788/binned.adam/_common_metadata /tmp/adamTestMvnpjenoa0/299363141779675788/binned.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/299363141779675788/binned.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/299363141779675788/binned.adam/._readGroups.avro.crc /tmp/adamTestMvnpjenoa0/299363141779675788/binned.adam/_metadata /tmp/adamTestMvnpjenoa0/299363141779675788/binned.adam/_processingSteps.avro /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite5941898558128187081 /tmp/adamTestMvnpjenoa0/TempSuite6916189427966453141 /tmp/adamTestMvnpjenoa0/TempSuite1334836826716448281.adam /tmp/adamTestMvnpjenoa0/TempSuite1334836826716448281.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite1334836826716448281.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite1334836826716448281.adam/._samples.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite1334836826716448281.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite1334836826716448281.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite1334836826716448281.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite1334836826716448281.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite1334836826716448281.adam/_common_metadata /tmp/adamTestMvnpjenoa0/TempSuite1334836826716448281.adam/._header.crc /tmp/adamTestMvnpjenoa0/TempSuite1334836826716448281.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite1334836826716448281.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite1334836826716448281.adam/_samples.avro /tmp/adamTestMvnpjenoa0/TempSuite1334836826716448281.adam/_metadata /tmp/adamTestMvnpjenoa0/TempSuite1334836826716448281.adam/_header /tmp/adamTestMvnpjenoa0/TempSuite3469418622014128494 /tmp/adamTestMvnpjenoa0/TempSuite1590136513995882366 /tmp/adamTestMvnpjenoa0/TempSuite1944360032336399887 /tmp/adamTestMvnpjenoa0/TempSuite5384485631917827852 /tmp/adamTestMvnpjenoa0/reads7690411326988464362 /tmp/adamTestMvnpjenoa0/reads7690411326988464362/reads2.fq /tmp/adamTestMvnpjenoa0/reads7690411326988464362/reads2.fq/_SUCCESS /tmp/adamTestMvnpjenoa0/reads7690411326988464362/reads2.fq/part-00000 /tmp/adamTestMvnpjenoa0/reads7690411326988464362/reads2.fq/.part-00000.crc /tmp/adamTestMvnpjenoa0/reads7690411326988464362/reads2.fq/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/reads7690411326988464362/reads1.fq /tmp/adamTestMvnpjenoa0/reads7690411326988464362/reads1.fq/_SUCCESS /tmp/adamTestMvnpjenoa0/reads7690411326988464362/reads1.fq/part-00000 /tmp/adamTestMvnpjenoa0/reads7690411326988464362/reads1.fq/.part-00000.crc /tmp/adamTestMvnpjenoa0/reads7690411326988464362/reads1.fq/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite4782027620194032085.bed /tmp/adamTestMvnpjenoa0/TempSuite4782027620194032085.bed/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite4782027620194032085.bed/part-00000 /tmp/adamTestMvnpjenoa0/TempSuite4782027620194032085.bed/.part-00000.crc /tmp/adamTestMvnpjenoa0/TempSuite4782027620194032085.bed/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/1738183090893754021 /tmp/adamTestMvnpjenoa0/1738183090893754021/unordered.sam /tmp/adamTestMvnpjenoa0/1738183090893754021/.unordered.sam.crc /tmp/adamTestMvnpjenoa0/TempSuite7109671856500759762 /tmp/adamTestMvnpjenoa0/TempSuite7785230418672949898 /tmp/adamTestMvnpjenoa0/.FeatureDatasetFunctionsSuite1491887521662331166.gff3.crc /tmp/adamTestMvnpjenoa0/TempSuite5455883223414912677 /tmp/adamTestMvnpjenoa0/TempSuite4078849357887539435.bed /tmp/adamTestMvnpjenoa0/TempSuite4078849357887539435.bed/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite4078849357887539435.bed/part-00001 /tmp/adamTestMvnpjenoa0/TempSuite4078849357887539435.bed/.part-00003.crc /tmp/adamTestMvnpjenoa0/TempSuite4078849357887539435.bed/part-00000 /tmp/adamTestMvnpjenoa0/TempSuite4078849357887539435.bed/part-00003 /tmp/adamTestMvnpjenoa0/TempSuite4078849357887539435.bed/.part-00000.crc /tmp/adamTestMvnpjenoa0/TempSuite4078849357887539435.bed/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite4078849357887539435.bed/part-00002 /tmp/adamTestMvnpjenoa0/TempSuite4078849357887539435.bed/.part-00002.crc /tmp/adamTestMvnpjenoa0/TempSuite4078849357887539435.bed/.part-00001.crc /tmp/adamTestMvnpjenoa0/TempSuite2904458924458676828 /tmp/adamTestMvnpjenoa0/TempSuite1921283225866147775.adam /tmp/adamTestMvnpjenoa0/TempSuite1921283225866147775.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite1921283225866147775.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite1921283225866147775.adam/._samples.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite1921283225866147775.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite1921283225866147775.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite1921283225866147775.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite1921283225866147775.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite1921283225866147775.adam/_common_metadata /tmp/adamTestMvnpjenoa0/TempSuite1921283225866147775.adam/._header.crc /tmp/adamTestMvnpjenoa0/TempSuite1921283225866147775.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite1921283225866147775.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite1921283225866147775.adam/_samples.avro /tmp/adamTestMvnpjenoa0/TempSuite1921283225866147775.adam/_metadata /tmp/adamTestMvnpjenoa0/TempSuite1921283225866147775.adam/_header /tmp/adamTestMvnpjenoa0/TempSuite3854446984732693819reads12.sam_2 /tmp/adamTestMvnpjenoa0/TempSuite4736184015014702030.adam /tmp/adamTestMvnpjenoa0/TempSuite4736184015014702030.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite4736184015014702030.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite4736184015014702030.adam/._samples.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite4736184015014702030.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite4736184015014702030.adam/.part-r-00003.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite4736184015014702030.adam/part-r-00001.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite4736184015014702030.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite4736184015014702030.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite4736184015014702030.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite4736184015014702030.adam/.part-r-00001.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite4736184015014702030.adam/part-r-00002.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite4736184015014702030.adam/.part-r-00002.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite4736184015014702030.adam/_common_metadata /tmp/adamTestMvnpjenoa0/TempSuite4736184015014702030.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite4736184015014702030.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite4736184015014702030.adam/_samples.avro /tmp/adamTestMvnpjenoa0/TempSuite4736184015014702030.adam/_metadata /tmp/adamTestMvnpjenoa0/TempSuite4736184015014702030.adam/part-r-00003.gz.parquet /tmp/adamTestMvnpjenoa0/artificial.sam5035843674256532019.sam /tmp/adamTestMvnpjenoa0/TempSuite6511645711249290561 /tmp/adamTestMvnpjenoa0/TempSuite6074061586347408026 /tmp/adamTestMvnpjenoa0/.TempSuite2791217825696054455.sam.crc /tmp/adamTestMvnpjenoa0/TempSuite8605394601149688532 /tmp/adamTestMvnpjenoa0/TempSuite5384485631917827852.adam /tmp/adamTestMvnpjenoa0/TempSuite5384485631917827852.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite5384485631917827852.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite5384485631917827852.adam/._samples.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite5384485631917827852.adam/.part-00000-41a5dcb5-7861-4548-a3f4-0ecb32e9f557-c000.snappy.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite5384485631917827852.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite5384485631917827852.adam/._header.crc /tmp/adamTestMvnpjenoa0/TempSuite5384485631917827852.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite5384485631917827852.adam/_samples.avro /tmp/adamTestMvnpjenoa0/TempSuite5384485631917827852.adam/part-00000-41a5dcb5-7861-4548-a3f4-0ecb32e9f557-c000.snappy.parquet /tmp/adamTestMvnpjenoa0/TempSuite5384485631917827852.adam/_header /tmp/adamTestMvnpjenoa0/1973450039425872050 /tmp/adamTestMvnpjenoa0/1973450039425872050/predicate.3.adam /tmp/adamTestMvnpjenoa0/1973450039425872050/predicate.3.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/1973450039425872050/predicate.3.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/1973450039425872050/predicate.3.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/1973450039425872050/predicate.3.adam/_readGroups.avro /tmp/adamTestMvnpjenoa0/1973450039425872050/predicate.3.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/1973450039425872050/predicate.3.adam/_references.avro /tmp/adamTestMvnpjenoa0/1973450039425872050/predicate.3.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/1973450039425872050/predicate.3.adam/._processingSteps.avro.crc /tmp/adamTestMvnpjenoa0/1973450039425872050/predicate.3.adam/_common_metadata /tmp/adamTestMvnpjenoa0/1973450039425872050/predicate.3.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/1973450039425872050/predicate.3.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/1973450039425872050/predicate.3.adam/._readGroups.avro.crc /tmp/adamTestMvnpjenoa0/1973450039425872050/predicate.3.adam/_metadata /tmp/adamTestMvnpjenoa0/1973450039425872050/predicate.3.adam/_processingSteps.avro /tmp/adamTestMvnpjenoa0/TempSuite1163457635644320715.adam /tmp/adamTestMvnpjenoa0/TempSuite1163457635644320715.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite1163457635644320715.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite1163457635644320715.adam/._samples.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite1163457635644320715.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite1163457635644320715.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite1163457635644320715.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite1163457635644320715.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite1163457635644320715.adam/_common_metadata /tmp/adamTestMvnpjenoa0/TempSuite1163457635644320715.adam/._header.crc /tmp/adamTestMvnpjenoa0/TempSuite1163457635644320715.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite1163457635644320715.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite1163457635644320715.adam/_samples.avro /tmp/adamTestMvnpjenoa0/TempSuite1163457635644320715.adam/_metadata /tmp/adamTestMvnpjenoa0/TempSuite1163457635644320715.adam/_header /tmp/adamTestMvnpjenoa0/TempSuite6770366044267204747 /tmp/adamTestMvnpjenoa0/9007799149014160750 /tmp/adamTestMvnpjenoa0/9007799149014160750/out.bam /tmp/adamTestMvnpjenoa0/9007799149014160750/out.bam_head /tmp/adamTestMvnpjenoa0/9007799149014160750/.out.bam.crc /tmp/adamTestMvnpjenoa0/9007799149014160750/out.bam_tail /tmp/adamTestMvnpjenoa0/9007799149014160750/out.bam_tail/_SUCCESS /tmp/adamTestMvnpjenoa0/9007799149014160750/out.bam_tail/.part-r-00001.bam.crc /tmp/adamTestMvnpjenoa0/9007799149014160750/out.bam_tail/part-r-00000.bam /tmp/adamTestMvnpjenoa0/9007799149014160750/out.bam_tail/part-r-00001.bam /tmp/adamTestMvnpjenoa0/9007799149014160750/out.bam_tail/.part-r-00002.bam.crc /tmp/adamTestMvnpjenoa0/9007799149014160750/out.bam_tail/part-r-00003.bam /tmp/adamTestMvnpjenoa0/9007799149014160750/out.bam_tail/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/9007799149014160750/out.bam_tail/.part-r-00003.bam.crc /tmp/adamTestMvnpjenoa0/9007799149014160750/out.bam_tail/part-r-00002.bam /tmp/adamTestMvnpjenoa0/9007799149014160750/out.bam_tail/.part-r-00000.bam.crc /tmp/adamTestMvnpjenoa0/9007799149014160750/.out.bam_head.crc /tmp/adamTestMvnpjenoa0/TempSuite6561990423157415865.bed /tmp/adamTestMvnpjenoa0/TempSuite6561990423157415865.bed/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite6561990423157415865.bed/part-00000 /tmp/adamTestMvnpjenoa0/TempSuite6561990423157415865.bed/.part-00000.crc /tmp/adamTestMvnpjenoa0/TempSuite6561990423157415865.bed/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite8610345334512584837.adam /tmp/adamTestMvnpjenoa0/TempSuite8610345334512584837.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite8610345334512584837.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite8610345334512584837.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite8610345334512584837.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite8610345334512584837.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite8610345334512584837.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite8610345334512584837.adam/_common_metadata /tmp/adamTestMvnpjenoa0/TempSuite8610345334512584837.adam/._header.crc /tmp/adamTestMvnpjenoa0/TempSuite8610345334512584837.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite8610345334512584837.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite8610345334512584837.adam/_metadata /tmp/adamTestMvnpjenoa0/TempSuite8610345334512584837.adam/_header /tmp/adamTestMvnpjenoa0/TempSuite3703439285256403523.fq /tmp/adamTestMvnpjenoa0/TempSuite3788564896957749131 /tmp/adamTestMvnpjenoa0/TempSuite3886084837997019277.sam /tmp/adamTestMvnpjenoa0/TempSuite3886084837997019277.sam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite3886084837997019277.sam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite3886084837997019277.sam/.part-r-00000.sam.crc /tmp/adamTestMvnpjenoa0/TempSuite3886084837997019277.sam/part-r-00000.sam /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite1149986837268046739 /tmp/adamTestMvnpjenoa0/3903216039418587959 /tmp/adamTestMvnpjenoa0/3903216039418587959/predicate.2.adam /tmp/adamTestMvnpjenoa0/3903216039418587959/predicate.2.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/3903216039418587959/predicate.2.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/3903216039418587959/predicate.2.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/3903216039418587959/predicate.2.adam/_readGroups.avro /tmp/adamTestMvnpjenoa0/3903216039418587959/predicate.2.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/3903216039418587959/predicate.2.adam/_references.avro /tmp/adamTestMvnpjenoa0/3903216039418587959/predicate.2.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/3903216039418587959/predicate.2.adam/._processingSteps.avro.crc /tmp/adamTestMvnpjenoa0/3903216039418587959/predicate.2.adam/_common_metadata /tmp/adamTestMvnpjenoa0/3903216039418587959/predicate.2.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/3903216039418587959/predicate.2.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/3903216039418587959/predicate.2.adam/._readGroups.avro.crc /tmp/adamTestMvnpjenoa0/3903216039418587959/predicate.2.adam/_metadata /tmp/adamTestMvnpjenoa0/3903216039418587959/predicate.2.adam/_processingSteps.avro /tmp/adamTestMvnpjenoa0/6329074804922629456 /tmp/adamTestMvnpjenoa0/6329074804922629456/sorted.vcf /tmp/adamTestMvnpjenoa0/6329074804922629456/.sorted.vcf.crc /tmp/adamTestMvnpjenoa0/TempSuite6626342383813690462.adam /tmp/adamTestMvnpjenoa0/TempSuite6626342383813690462.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite6626342383813690462.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite6626342383813690462.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite6626342383813690462.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite6626342383813690462.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite6626342383813690462.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite6626342383813690462.adam/_common_metadata /tmp/adamTestMvnpjenoa0/TempSuite6626342383813690462.adam/._header.crc /tmp/adamTestMvnpjenoa0/TempSuite6626342383813690462.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite6626342383813690462.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite6626342383813690462.adam/_metadata /tmp/adamTestMvnpjenoa0/TempSuite6626342383813690462.adam/_header /tmp/adamTestMvnpjenoa0/.FeatureDatasetFunctionsSuite3348708032767544682.gff3.crc /tmp/adamTestMvnpjenoa0/8124025791687974986 /tmp/adamTestMvnpjenoa0/8124025791687974986/predicate.3.adam /tmp/adamTestMvnpjenoa0/8124025791687974986/predicate.3.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/8124025791687974986/predicate.3.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/8124025791687974986/predicate.3.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/8124025791687974986/predicate.3.adam/_readGroups.avro /tmp/adamTestMvnpjenoa0/8124025791687974986/predicate.3.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/8124025791687974986/predicate.3.adam/_references.avro /tmp/adamTestMvnpjenoa0/8124025791687974986/predicate.3.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/8124025791687974986/predicate.3.adam/._processingSteps.avro.crc /tmp/adamTestMvnpjenoa0/8124025791687974986/predicate.3.adam/_common_metadata /tmp/adamTestMvnpjenoa0/8124025791687974986/predicate.3.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/8124025791687974986/predicate.3.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/8124025791687974986/predicate.3.adam/._readGroups.avro.crc /tmp/adamTestMvnpjenoa0/8124025791687974986/predicate.3.adam/_metadata /tmp/adamTestMvnpjenoa0/8124025791687974986/predicate.3.adam/_processingSteps.avro /tmp/adamTestMvnpjenoa0/bqsr18110879552340226286 /tmp/adamTestMvnpjenoa0/bqsr18110879552340226286/bqsr1.bam /tmp/adamTestMvnpjenoa0/bqsr18110879552340226286/.bqsr1.bam.crc /tmp/adamTestMvnpjenoa0/TempSuite3788564896957749131.2.adam /tmp/adamTestMvnpjenoa0/TempSuite3788564896957749131.2.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite3788564896957749131.2.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite3788564896957749131.2.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite3788564896957749131.2.adam/_readGroups.avro /tmp/adamTestMvnpjenoa0/TempSuite3788564896957749131.2.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite3788564896957749131.2.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite3788564896957749131.2.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite3788564896957749131.2.adam/._processingSteps.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite3788564896957749131.2.adam/_common_metadata /tmp/adamTestMvnpjenoa0/TempSuite3788564896957749131.2.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite3788564896957749131.2.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite3788564896957749131.2.adam/._readGroups.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite3788564896957749131.2.adam/_metadata /tmp/adamTestMvnpjenoa0/TempSuite3788564896957749131.2.adam/_processingSteps.avro /tmp/adamTestMvnpjenoa0/TempSuite6765689595171322898 /tmp/adamTestMvnpjenoa0/7965101757692030473 /tmp/adamTestMvnpjenoa0/7965101757692030473/.gff3 /tmp/adamTestMvnpjenoa0/7965101757692030473/..gff3.crc /tmp/adamTestMvnpjenoa0/TempSuite3972207146601449166.sam /tmp/adamTestMvnpjenoa0/1557939714374-0 /tmp/adamTestMvnpjenoa0/1557939714374-0/test.gvcf.vcf /tmp/adamTestMvnpjenoa0/1557939714374-0/.test.gvcf.vcf.crc /tmp/adamTestMvnpjenoa0/TempSuite8798149563532951202 /tmp/adamTestMvnpjenoa0/random.vcf4974322201213609282.vcf /tmp/adamTestMvnpjenoa0/TempSuite7179151447783901112.fa /tmp/adamTestMvnpjenoa0/TempSuite7179151447783901112.fa/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite7179151447783901112.fa/part-00000 /tmp/adamTestMvnpjenoa0/TempSuite7179151447783901112.fa/.part-00000.crc /tmp/adamTestMvnpjenoa0/TempSuite7179151447783901112.fa/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite7774792650731328615 /tmp/adamTestMvnpjenoa0/TempSuite2049374544996348903 /tmp/adamTestMvnpjenoa0/TempSuite2238341828894551124 /tmp/adamTestMvnpjenoa0/sample_coverage.bed3905954095565400226.bed /tmp/adamTestMvnpjenoa0/TempSuite8039972552865898985 /tmp/adamTestMvnpjenoa0/TempSuite6213403521807431518 /tmp/adamTestMvnpjenoa0/9083774054702731562 /tmp/adamTestMvnpjenoa0/9083774054702731562/unordered.sam /tmp/adamTestMvnpjenoa0/9083774054702731562/.unordered.sam.crc /tmp/adamTestMvnpjenoa0/TempSuite2092003803646348106 /tmp/adamTestMvnpjenoa0/TempSuite6916189427966453141.adam /tmp/adamTestMvnpjenoa0/TempSuite6916189427966453141.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite6916189427966453141.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite6916189427966453141.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite6916189427966453141.adam/.part-r-00003.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite6916189427966453141.adam/part-r-00001.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite6916189427966453141.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite6916189427966453141.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite6916189427966453141.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite6916189427966453141.adam/.part-r-00001.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite6916189427966453141.adam/part-r-00002.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite6916189427966453141.adam/.part-r-00002.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite6916189427966453141.adam/_common_metadata /tmp/adamTestMvnpjenoa0/TempSuite6916189427966453141.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite6916189427966453141.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite6916189427966453141.adam/_metadata /tmp/adamTestMvnpjenoa0/TempSuite6916189427966453141.adam/part-r-00003.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite5768045921574454351.adam /tmp/adamTestMvnpjenoa0/TempSuite5768045921574454351.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite5768045921574454351.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite5768045921574454351.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite5768045921574454351.adam/_readGroups.avro /tmp/adamTestMvnpjenoa0/TempSuite5768045921574454351.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite5768045921574454351.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite5768045921574454351.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite5768045921574454351.adam/._processingSteps.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite5768045921574454351.adam/_common_metadata /tmp/adamTestMvnpjenoa0/TempSuite5768045921574454351.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite5768045921574454351.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite5768045921574454351.adam/._readGroups.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite5768045921574454351.adam/_metadata /tmp/adamTestMvnpjenoa0/TempSuite5768045921574454351.adam/_processingSteps.avro /tmp/adamTestMvnpjenoa0/TempSuite1811472737585393713 /tmp/adamTestMvnpjenoa0/TempSuite7114444225650152302.adam /tmp/adamTestMvnpjenoa0/TempSuite7114444225650152302.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite7114444225650152302.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite7114444225650152302.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite7114444225650152302.adam/_readGroups.avro /tmp/adamTestMvnpjenoa0/TempSuite7114444225650152302.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite7114444225650152302.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite7114444225650152302.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite7114444225650152302.adam/._processingSteps.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite7114444225650152302.adam/_common_metadata /tmp/adamTestMvnpjenoa0/TempSuite7114444225650152302.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite7114444225650152302.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite7114444225650152302.adam/._readGroups.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite7114444225650152302.adam/_metadata /tmp/adamTestMvnpjenoa0/TempSuite7114444225650152302.adam/_processingSteps.avro /tmp/adamTestMvnpjenoa0/1450724944966030661 /tmp/adamTestMvnpjenoa0/1450724944966030661/bqsr1.vcf.bgz /tmp/adamTestMvnpjenoa0/1450724944966030661/bqsr1.vcf.bgz/_SUCCESS /tmp/adamTestMvnpjenoa0/1450724944966030661/bqsr1.vcf.bgz/part-r-00000.bgz /tmp/adamTestMvnpjenoa0/1450724944966030661/bqsr1.vcf.bgz/part-r-00003.bgz /tmp/adamTestMvnpjenoa0/1450724944966030661/bqsr1.vcf.bgz/.part-r-00001.bgz.crc /tmp/adamTestMvnpjenoa0/1450724944966030661/bqsr1.vcf.bgz/part-r-00001.bgz /tmp/adamTestMvnpjenoa0/1450724944966030661/bqsr1.vcf.bgz/.part-r-00003.bgz.crc /tmp/adamTestMvnpjenoa0/1450724944966030661/bqsr1.vcf.bgz/.part-r-00002.bgz.crc /tmp/adamTestMvnpjenoa0/1450724944966030661/bqsr1.vcf.bgz/part-r-00002.bgz /tmp/adamTestMvnpjenoa0/1450724944966030661/bqsr1.vcf.bgz/.part-r-00000.bgz.crc /tmp/adamTestMvnpjenoa0/1450724944966030661/bqsr1.vcf.bgz/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite5744315304893091712.sam /tmp/adamTestMvnpjenoa0/TempSuite5744315304893091712.sam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite5744315304893091712.sam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite5744315304893091712.sam/.part-r-00000.sam.crc /tmp/adamTestMvnpjenoa0/TempSuite5744315304893091712.sam/part-r-00000.sam /tmp/adamTestMvnpjenoa0/TempSuite2653598405119108961.adam /tmp/adamTestMvnpjenoa0/TempSuite2653598405119108961.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite2653598405119108961.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite2653598405119108961.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite2653598405119108961.adam/_readGroups.avro /tmp/adamTestMvnpjenoa0/TempSuite2653598405119108961.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite2653598405119108961.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite2653598405119108961.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite2653598405119108961.adam/._processingSteps.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite2653598405119108961.adam/_common_metadata /tmp/adamTestMvnpjenoa0/TempSuite2653598405119108961.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite2653598405119108961.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite2653598405119108961.adam/._readGroups.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite2653598405119108961.adam/_metadata /tmp/adamTestMvnpjenoa0/TempSuite2653598405119108961.adam/_processingSteps.avro /tmp/adamTestMvnpjenoa0/TempSuite2221783522305252815 /tmp/adamTestMvnpjenoa0/unordered.sam7185231963840657226.sam /tmp/adamTestMvnpjenoa0/TempSuite5636692660280034715 /tmp/adamTestMvnpjenoa0/5027207176048475419 /tmp/adamTestMvnpjenoa0/5027207176048475419/ordered.sam /tmp/adamTestMvnpjenoa0/5027207176048475419/.ordered.sam.crc /tmp/adamTestMvnpjenoa0/TempSuite1475724770962317356.adam /tmp/adamTestMvnpjenoa0/TempSuite1475724770962317356.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite1475724770962317356.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite1475724770962317356.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite1475724770962317356.adam/.part-r-00003.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite1475724770962317356.adam/part-r-00001.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite1475724770962317356.adam/_readGroups.avro /tmp/adamTestMvnpjenoa0/TempSuite1475724770962317356.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite1475724770962317356.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite1475724770962317356.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite1475724770962317356.adam/.part-r-00001.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite1475724770962317356.adam/part-r-00002.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite1475724770962317356.adam/._processingSteps.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite1475724770962317356.adam/.part-r-00002.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite1475724770962317356.adam/_common_metadata /tmp/adamTestMvnpjenoa0/TempSuite1475724770962317356.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite1475724770962317356.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite1475724770962317356.adam/._readGroups.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite1475724770962317356.adam/_metadata /tmp/adamTestMvnpjenoa0/TempSuite1475724770962317356.adam/part-r-00003.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite1475724770962317356.adam/_processingSteps.avro /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite4558689597353408251.gff3 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite4558689597353408251.gff3/_SUCCESS /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite4558689597353408251.gff3/part-00001 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite4558689597353408251.gff3/.part-00003.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite4558689597353408251.gff3/part-00000 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite4558689597353408251.gff3/part-00003 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite4558689597353408251.gff3/.part-00000.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite4558689597353408251.gff3/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite4558689597353408251.gff3/part-00002 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite4558689597353408251.gff3/.part-00002.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite4558689597353408251.gff3/.part-00001.crc /tmp/adamTestMvnpjenoa0/TempSuite599532972129454608.adam /tmp/adamTestMvnpjenoa0/TempSuite599532972129454608.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite599532972129454608.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite599532972129454608.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite599532972129454608.adam/_readGroups.avro /tmp/adamTestMvnpjenoa0/TempSuite599532972129454608.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite599532972129454608.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite599532972129454608.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite599532972129454608.adam/._processingSteps.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite599532972129454608.adam/_common_metadata /tmp/adamTestMvnpjenoa0/TempSuite599532972129454608.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite599532972129454608.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite599532972129454608.adam/._readGroups.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite599532972129454608.adam/_metadata /tmp/adamTestMvnpjenoa0/TempSuite599532972129454608.adam/_processingSteps.avro /tmp/adamTestMvnpjenoa0/TempSuite3476488343346340560 /tmp/adamTestMvnpjenoa0/TempSuite9057847475247381088.bed /tmp/adamTestMvnpjenoa0/TempSuite9057847475247381088.bed/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite9057847475247381088.bed/part-00000 /tmp/adamTestMvnpjenoa0/TempSuite9057847475247381088.bed/.part-00000.crc /tmp/adamTestMvnpjenoa0/TempSuite9057847475247381088.bed/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/.TempSuite3703439285256403523.fq.crc /tmp/adamTestMvnpjenoa0/TempSuite8382378137815932429 /tmp/adamTestMvnpjenoa0/TempSuite1226413419164272962 /tmp/adamTestMvnpjenoa0/TempSuite4749479781037507784 /tmp/adamTestMvnpjenoa0/javaAC4189707145559413005 /tmp/adamTestMvnpjenoa0/javaAC4189707145559413005/testRdd.read.adam /tmp/adamTestMvnpjenoa0/javaAC4189707145559413005/testRdd.read.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/javaAC4189707145559413005/testRdd.read.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/javaAC4189707145559413005/testRdd.read.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/javaAC4189707145559413005/testRdd.read.adam/_readGroups.avro /tmp/adamTestMvnpjenoa0/javaAC4189707145559413005/testRdd.read.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/javaAC4189707145559413005/testRdd.read.adam/_references.avro /tmp/adamTestMvnpjenoa0/javaAC4189707145559413005/testRdd.read.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/javaAC4189707145559413005/testRdd.read.adam/._processingSteps.avro.crc /tmp/adamTestMvnpjenoa0/javaAC4189707145559413005/testRdd.read.adam/_common_metadata /tmp/adamTestMvnpjenoa0/javaAC4189707145559413005/testRdd.read.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/javaAC4189707145559413005/testRdd.read.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/javaAC4189707145559413005/testRdd.read.adam/._readGroups.avro.crc /tmp/adamTestMvnpjenoa0/javaAC4189707145559413005/testRdd.read.adam/_metadata /tmp/adamTestMvnpjenoa0/javaAC4189707145559413005/testRdd.read.adam/_processingSteps.avro /tmp/adamTestMvnpjenoa0/TempSuite3469418622014128494.adam /tmp/adamTestMvnpjenoa0/TempSuite3469418622014128494.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite3469418622014128494.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite3469418622014128494.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite3469418622014128494.adam/_readGroups.avro /tmp/adamTestMvnpjenoa0/TempSuite3469418622014128494.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite3469418622014128494.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite3469418622014128494.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite3469418622014128494.adam/._processingSteps.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite3469418622014128494.adam/_common_metadata /tmp/adamTestMvnpjenoa0/TempSuite3469418622014128494.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite3469418622014128494.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite3469418622014128494.adam/._readGroups.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite3469418622014128494.adam/_metadata /tmp/adamTestMvnpjenoa0/TempSuite3469418622014128494.adam/_processingSteps.avro /tmp/adamTestMvnpjenoa0/TempSuite5488680254576040254.adam /tmp/adamTestMvnpjenoa0/TempSuite5488680254576040254.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite5488680254576040254.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite5488680254576040254.adam/._samples.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite5488680254576040254.adam/.part-00000-3e0a9d7e-50b4-4a86-ae31-991914803a0d-c000.snappy.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite5488680254576040254.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite5488680254576040254.adam/._header.crc /tmp/adamTestMvnpjenoa0/TempSuite5488680254576040254.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite5488680254576040254.adam/_samples.avro /tmp/adamTestMvnpjenoa0/TempSuite5488680254576040254.adam/part-00000-3e0a9d7e-50b4-4a86-ae31-991914803a0d-c000.snappy.parquet /tmp/adamTestMvnpjenoa0/TempSuite5488680254576040254.adam/_header /tmp/adamTestMvnpjenoa0/TempSuite8737981847127160617 /tmp/adamTestMvnpjenoa0/TempSuite7616904499627491412 /tmp/adamTestMvnpjenoa0/reads126634809151662283459 /tmp/adamTestMvnpjenoa0/reads126634809151662283459/reads12.sam /tmp/adamTestMvnpjenoa0/reads126634809151662283459/reads12.sam/_SUCCESS /tmp/adamTestMvnpjenoa0/reads126634809151662283459/reads12.sam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/reads126634809151662283459/reads12.sam/.part-r-00000.sam.crc /tmp/adamTestMvnpjenoa0/reads126634809151662283459/reads12.sam/part-r-00000.sam /tmp/adamTestMvnpjenoa0/ordered.sam667978404274563379.sam /tmp/adamTestMvnpjenoa0/TempSuite5370826037317384489 /tmp/adamTestMvnpjenoa0/TempSuite4631402722900267245.adam /tmp/adamTestMvnpjenoa0/TempSuite4631402722900267245.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite4631402722900267245.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite4631402722900267245.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite4631402722900267245.adam/_readGroups.avro /tmp/adamTestMvnpjenoa0/TempSuite4631402722900267245.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite4631402722900267245.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite4631402722900267245.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite4631402722900267245.adam/._processingSteps.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite4631402722900267245.adam/_common_metadata /tmp/adamTestMvnpjenoa0/TempSuite4631402722900267245.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite4631402722900267245.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite4631402722900267245.adam/._readGroups.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite4631402722900267245.adam/_metadata /tmp/adamTestMvnpjenoa0/TempSuite4631402722900267245.adam/_processingSteps.avro /tmp/adamTestMvnpjenoa0/TempSuite8286440147751900879 /tmp/adamTestMvnpjenoa0/TempSuite4927734975449021992 /tmp/adamTestMvnpjenoa0/TempSuite3567792921892032226.sam /tmp/adamTestMvnpjenoa0/TempSuite3567792921892032226.sam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite3567792921892032226.sam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite3567792921892032226.sam/.part-r-00000.sam.crc /tmp/adamTestMvnpjenoa0/TempSuite3567792921892032226.sam/part-r-00000.sam /tmp/adamTestMvnpjenoa0/TempSuite7179151447783901112 /tmp/adamTestMvnpjenoa0/sample1.queryname.sam2314397711105765326.queryname.sam /tmp/adamTestMvnpjenoa0/TempSuite5841261163310104463 /tmp/adamTestMvnpjenoa0/javaAC4104969254328047884 /tmp/adamTestMvnpjenoa0/javaAC4104969254328047884/testRdd.variant.adam /tmp/adamTestMvnpjenoa0/javaAC4104969254328047884/testRdd.variant.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/javaAC4104969254328047884/testRdd.variant.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/javaAC4104969254328047884/testRdd.variant.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/javaAC4104969254328047884/testRdd.variant.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/javaAC4104969254328047884/testRdd.variant.adam/_references.avro /tmp/adamTestMvnpjenoa0/javaAC4104969254328047884/testRdd.variant.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/javaAC4104969254328047884/testRdd.variant.adam/_common_metadata /tmp/adamTestMvnpjenoa0/javaAC4104969254328047884/testRdd.variant.adam/._header.crc /tmp/adamTestMvnpjenoa0/javaAC4104969254328047884/testRdd.variant.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/javaAC4104969254328047884/testRdd.variant.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/javaAC4104969254328047884/testRdd.variant.adam/_metadata /tmp/adamTestMvnpjenoa0/javaAC4104969254328047884/testRdd.variant.adam/_header /tmp/adamTestMvnpjenoa0/4068059490149931408 /tmp/adamTestMvnpjenoa0/4068059490149931408/ctg.adam /tmp/adamTestMvnpjenoa0/4068059490149931408/ctg.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/4068059490149931408/ctg.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/4068059490149931408/ctg.adam/_partitionedByStartPos /tmp/adamTestMvnpjenoa0/4068059490149931408/ctg.adam/_references.avro /tmp/adamTestMvnpjenoa0/4068059490149931408/ctg.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/4068059490149931408/ctg.adam/._partitionedByStartPos.crc /tmp/adamTestMvnpjenoa0/4068059490149931408/ctg.adam/referenceName=HLA-DQB1%2A05%3A01%3A01%3A02 /tmp/adamTestMvnpjenoa0/4068059490149931408/ctg.adam/referenceName=HLA-DQB1%2A05%3A01%3A01%3A02/positionBin=0 /tmp/adamTestMvnpjenoa0/4068059490149931408/ctg.adam/referenceName=HLA-DQB1%2A05%3A01%3A01%3A02/positionBin=0/.part-00000-71e1687a-50c8-4c5b-9c6b-6a16f0ff0be6.c000.snappy.parquet.crc /tmp/adamTestMvnpjenoa0/4068059490149931408/ctg.adam/referenceName=HLA-DQB1%2A05%3A01%3A01%3A02/positionBin=0/part-00000-71e1687a-50c8-4c5b-9c6b-6a16f0ff0be6.c000.snappy.parquet /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite6336583279887222371 /tmp/adamTestMvnpjenoa0/7856465324297879686 /tmp/adamTestMvnpjenoa0/7856465324297879686/sorted-variants.lex.vcf /tmp/adamTestMvnpjenoa0/7856465324297879686/.sorted-variants.lex.vcf.crc /tmp/adamTestMvnpjenoa0/TempSuite1475466858704024357 /tmp/adamTestMvnpjenoa0/TempSuite8356449429863811796.bed /tmp/adamTestMvnpjenoa0/TempSuite8356449429863811796.bed/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite8356449429863811796.bed/part-00000 /tmp/adamTestMvnpjenoa0/TempSuite8356449429863811796.bed/.part-00000.crc /tmp/adamTestMvnpjenoa0/TempSuite8356449429863811796.bed/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite8335755103731210972 /tmp/adamTestMvnpjenoa0/TempSuite8514477946221416938 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite4460167511342863621 /tmp/adamTestMvnpjenoa0/TempSuite862125649864846177 /tmp/adamTestMvnpjenoa0/3372210225197092189 /tmp/adamTestMvnpjenoa0/3372210225197092189/variants.lex.adam /tmp/adamTestMvnpjenoa0/3372210225197092189/variants.lex.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/3372210225197092189/variants.lex.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/3372210225197092189/variants.lex.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/3372210225197092189/variants.lex.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/3372210225197092189/variants.lex.adam/_references.avro /tmp/adamTestMvnpjenoa0/3372210225197092189/variants.lex.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/3372210225197092189/variants.lex.adam/_common_metadata /tmp/adamTestMvnpjenoa0/3372210225197092189/variants.lex.adam/._header.crc /tmp/adamTestMvnpjenoa0/3372210225197092189/variants.lex.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/3372210225197092189/variants.lex.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/3372210225197092189/variants.lex.adam/_metadata /tmp/adamTestMvnpjenoa0/3372210225197092189/variants.lex.adam/_header /tmp/adamTestMvnpjenoa0/TempSuite3972207146601449166 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite7975308750151627586.interval_list /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite7975308750151627586.interval_list/_SUCCESS /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite7975308750151627586.interval_list/part-00001 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite7975308750151627586.interval_list/.part-00003.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite7975308750151627586.interval_list/part-00000 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite7975308750151627586.interval_list/part-00003 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite7975308750151627586.interval_list/.part-00000.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite7975308750151627586.interval_list/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite7975308750151627586.interval_list/part-00002 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite7975308750151627586.interval_list/.part-00002.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite7975308750151627586.interval_list/.part-00001.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite4174236648008664065.narrowPeak /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite4174236648008664065.narrowPeak/_SUCCESS /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite4174236648008664065.narrowPeak/part-00001 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite4174236648008664065.narrowPeak/.part-00003.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite4174236648008664065.narrowPeak/part-00000 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite4174236648008664065.narrowPeak/part-00003 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite4174236648008664065.narrowPeak/.part-00000.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite4174236648008664065.narrowPeak/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite4174236648008664065.narrowPeak/part-00002 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite4174236648008664065.narrowPeak/.part-00002.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite4174236648008664065.narrowPeak/.part-00001.crc /tmp/adamTestMvnpjenoa0/TempSuite5432434921240934593.bed /tmp/adamTestMvnpjenoa0/TempSuite5432434921240934593.bed/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite5432434921240934593.bed/part-00000 /tmp/adamTestMvnpjenoa0/TempSuite5432434921240934593.bed/.part-00000.crc /tmp/adamTestMvnpjenoa0/TempSuite5432434921240934593.bed/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/1557940001828-0 /tmp/adamTestMvnpjenoa0/1557940001828-0/bamReads.adam /tmp/adamTestMvnpjenoa0/1557940001828-0/bamReads.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/1557940001828-0/bamReads.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/1557940001828-0/bamReads.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/1557940001828-0/bamReads.adam/_readGroups.avro /tmp/adamTestMvnpjenoa0/1557940001828-0/bamReads.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/1557940001828-0/bamReads.adam/_references.avro /tmp/adamTestMvnpjenoa0/1557940001828-0/bamReads.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/1557940001828-0/bamReads.adam/._processingSteps.avro.crc /tmp/adamTestMvnpjenoa0/1557940001828-0/bamReads.adam/_common_metadata /tmp/adamTestMvnpjenoa0/1557940001828-0/bamReads.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/1557940001828-0/bamReads.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/1557940001828-0/bamReads.adam/._readGroups.avro.crc /tmp/adamTestMvnpjenoa0/1557940001828-0/bamReads.adam/_metadata /tmp/adamTestMvnpjenoa0/1557940001828-0/bamReads.adam/_processingSteps.avro /tmp/adamTestMvnpjenoa0/TempSuite423983098930022445.adam /tmp/adamTestMvnpjenoa0/TempSuite423983098930022445.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite423983098930022445.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite423983098930022445.adam/._samples.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite423983098930022445.adam/.part-00005-9ec99176-46af-4036-8cfc-ef502349becf-c000.snappy.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite423983098930022445.adam/.part-00003-9ec99176-46af-4036-8cfc-ef502349becf-c000.snappy.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite423983098930022445.adam/part-00005-9ec99176-46af-4036-8cfc-ef502349becf-c000.snappy.parquet /tmp/adamTestMvnpjenoa0/TempSuite423983098930022445.adam/part-00000-9ec99176-46af-4036-8cfc-ef502349becf-c000.snappy.parquet /tmp/adamTestMvnpjenoa0/TempSuite423983098930022445.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite423983098930022445.adam/.part-00000-9ec99176-46af-4036-8cfc-ef502349becf-c000.snappy.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite423983098930022445.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite423983098930022445.adam/_samples.avro /tmp/adamTestMvnpjenoa0/TempSuite423983098930022445.adam/part-00003-9ec99176-46af-4036-8cfc-ef502349becf-c000.snappy.parquet /tmp/adamTestMvnpjenoa0/TempSuite1171417020645719520.adam /tmp/adamTestMvnpjenoa0/TempSuite1171417020645719520.adam/part-00002-5a6b80b0-4e0e-4ee5-bbeb-6098ae5b60bf-c000.snappy.parquet /tmp/adamTestMvnpjenoa0/TempSuite1171417020645719520.adam/.part-00002-5a6b80b0-4e0e-4ee5-bbeb-6098ae5b60bf-c000.snappy.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite1171417020645719520.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite1171417020645719520.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite1171417020645719520.adam/.part-00001-5a6b80b0-4e0e-4ee5-bbeb-6098ae5b60bf-c000.snappy.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite1171417020645719520.adam/part-00000-5a6b80b0-4e0e-4ee5-bbeb-6098ae5b60bf-c000.snappy.parquet /tmp/adamTestMvnpjenoa0/TempSuite1171417020645719520.adam/part-00001-5a6b80b0-4e0e-4ee5-bbeb-6098ae5b60bf-c000.snappy.parquet /tmp/adamTestMvnpjenoa0/TempSuite1171417020645719520.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite1171417020645719520.adam/._header.crc /tmp/adamTestMvnpjenoa0/TempSuite1171417020645719520.adam/.part-00000-5a6b80b0-4e0e-4ee5-bbeb-6098ae5b60bf-c000.snappy.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite1171417020645719520.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite1171417020645719520.adam/_header /tmp/adamTestMvnpjenoa0/.TempSuite8737981847127160617.bam.crc /tmp/adamTestMvnpjenoa0/TempSuite7768261566229609624.adam /tmp/adamTestMvnpjenoa0/TempSuite7768261566229609624.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite7768261566229609624.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite7768261566229609624.adam/part-00000-3927b2f2-92dc-46c8-bb6a-4ebbca5281b2-c000.snappy.parquet /tmp/adamTestMvnpjenoa0/TempSuite7768261566229609624.adam/_readGroups.avro /tmp/adamTestMvnpjenoa0/TempSuite7768261566229609624.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite7768261566229609624.adam/._processingSteps.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite7768261566229609624.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite7768261566229609624.adam/._readGroups.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite7768261566229609624.adam/.part-00000-3927b2f2-92dc-46c8-bb6a-4ebbca5281b2-c000.snappy.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite7768261566229609624.adam/_processingSteps.avro /tmp/adamTestMvnpjenoa0/TempSuite7989129825859549658.bam /tmp/adamTestMvnpjenoa0/TempSuite7989129825859549658.bam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite7989129825859549658.bam/part-r-00000.bam /tmp/adamTestMvnpjenoa0/TempSuite7989129825859549658.bam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite7989129825859549658.bam/.part-r-00000.bam.crc /tmp/adamTestMvnpjenoa0/sorted-variants.lex.vcf1285700455101330745.lex.vcf /tmp/adamTestMvnpjenoa0/TempSuite8798149563532951202.adam /tmp/adamTestMvnpjenoa0/TempSuite8798149563532951202.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite8798149563532951202.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite8798149563532951202.adam/._samples.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite8798149563532951202.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite8798149563532951202.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite8798149563532951202.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite8798149563532951202.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite8798149563532951202.adam/_common_metadata /tmp/adamTestMvnpjenoa0/TempSuite8798149563532951202.adam/._header.crc /tmp/adamTestMvnpjenoa0/TempSuite8798149563532951202.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite8798149563532951202.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite8798149563532951202.adam/_samples.avro /tmp/adamTestMvnpjenoa0/TempSuite8798149563532951202.adam/_metadata /tmp/adamTestMvnpjenoa0/TempSuite8798149563532951202.adam/_header /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite5752425844141218720 /tmp/adamTestMvnpjenoa0/TempSuite7413174118720940431.sam /tmp/adamTestMvnpjenoa0/TempSuite7413174118720940431.sam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite7413174118720940431.sam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite7413174118720940431.sam/.part-r-00000.sam.crc /tmp/adamTestMvnpjenoa0/TempSuite7413174118720940431.sam/part-r-00000.sam /tmp/adamTestMvnpjenoa0/TempSuite8901349017941121010.bam /tmp/adamTestMvnpjenoa0/unordered.sam9106290784056006384.sam /tmp/adamTestMvnpjenoa0/TempSuite2238341828894551124.adam /tmp/adamTestMvnpjenoa0/TempSuite2238341828894551124.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite2238341828894551124.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite2238341828894551124.adam/._samples.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite2238341828894551124.adam/part-00000-daf1f82f-9b84-490c-839c-b9a9a829d5d0-c000.snappy.parquet /tmp/adamTestMvnpjenoa0/TempSuite2238341828894551124.adam/.part-00001-daf1f82f-9b84-490c-839c-b9a9a829d5d0-c000.snappy.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite2238341828894551124.adam/.part-00002-daf1f82f-9b84-490c-839c-b9a9a829d5d0-c000.snappy.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite2238341828894551124.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite2238341828894551124.adam/part-00001-daf1f82f-9b84-490c-839c-b9a9a829d5d0-c000.snappy.parquet /tmp/adamTestMvnpjenoa0/TempSuite2238341828894551124.adam/._header.crc /tmp/adamTestMvnpjenoa0/TempSuite2238341828894551124.adam/.part-00000-daf1f82f-9b84-490c-839c-b9a9a829d5d0-c000.snappy.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite2238341828894551124.adam/part-00002-daf1f82f-9b84-490c-839c-b9a9a829d5d0-c000.snappy.parquet /tmp/adamTestMvnpjenoa0/TempSuite2238341828894551124.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite2238341828894551124.adam/_samples.avro /tmp/adamTestMvnpjenoa0/TempSuite2238341828894551124.adam/_header /tmp/adamTestMvnpjenoa0/TempSuite3854446984732693819 /tmp/adamTestMvnpjenoa0/TempSuite4930684203949131432 /tmp/adamTestMvnpjenoa0/TempSuite1475724770962317356 /tmp/adamTestMvnpjenoa0/TempSuite879753549103032827 /tmp/adamTestMvnpjenoa0/8042592185166754165 /tmp/adamTestMvnpjenoa0/8042592185166754165/.unordered.bam.crc /tmp/adamTestMvnpjenoa0/8042592185166754165/unordered.bam /tmp/adamTestMvnpjenoa0/noqual8899780874434281648 /tmp/adamTestMvnpjenoa0/noqual8899780874434281648/noqualA.sam /tmp/adamTestMvnpjenoa0/noqual8899780874434281648/noqualA.sam/_SUCCESS /tmp/adamTestMvnpjenoa0/noqual8899780874434281648/noqualA.sam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/noqual8899780874434281648/noqualA.sam/.part-r-00000.sam.crc /tmp/adamTestMvnpjenoa0/noqual8899780874434281648/noqualA.sam/part-r-00000.sam /tmp/adamTestMvnpjenoa0/noqual8899780874434281648/noqualB.fastq /tmp/adamTestMvnpjenoa0/noqual8899780874434281648/noqualB.fastq/_SUCCESS /tmp/adamTestMvnpjenoa0/noqual8899780874434281648/noqualB.fastq/part-00000 /tmp/adamTestMvnpjenoa0/noqual8899780874434281648/noqualB.fastq/.part-00000.crc /tmp/adamTestMvnpjenoa0/noqual8899780874434281648/noqualB.fastq/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite7252950499310565687.adam /tmp/adamTestMvnpjenoa0/TempSuite7252950499310565687.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite7252950499310565687.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite7252950499310565687.adam/referenceName=1 /tmp/adamTestMvnpjenoa0/TempSuite7252950499310565687.adam/referenceName=1/positionBin=169 /tmp/adamTestMvnpjenoa0/TempSuite7252950499310565687.adam/referenceName=1/positionBin=169/.part-00001-fa268d4d-3b98-4750-92f2-9996404b650e.c000.snappy.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite7252950499310565687.adam/referenceName=1/positionBin=169/part-00001-fa268d4d-3b98-4750-92f2-9996404b650e.c000.snappy.parquet /tmp/adamTestMvnpjenoa0/TempSuite7252950499310565687.adam/referenceName=1/positionBin=14 /tmp/adamTestMvnpjenoa0/TempSuite7252950499310565687.adam/referenceName=1/positionBin=14/part-00000-fa268d4d-3b98-4750-92f2-9996404b650e.c000.snappy.parquet /tmp/adamTestMvnpjenoa0/TempSuite7252950499310565687.adam/referenceName=1/positionBin=14/.part-00000-fa268d4d-3b98-4750-92f2-9996404b650e.c000.snappy.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite7252950499310565687.adam/referenceName=1/positionBin=240 /tmp/adamTestMvnpjenoa0/TempSuite7252950499310565687.adam/referenceName=1/positionBin=240/.part-00002-fa268d4d-3b98-4750-92f2-9996404b650e.c000.snappy.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite7252950499310565687.adam/referenceName=1/positionBin=240/part-00002-fa268d4d-3b98-4750-92f2-9996404b650e.c000.snappy.parquet /tmp/adamTestMvnpjenoa0/TempSuite7252950499310565687.adam/referenceName=1/positionBin=0 /tmp/adamTestMvnpjenoa0/TempSuite7252950499310565687.adam/referenceName=1/positionBin=0/part-00000-fa268d4d-3b98-4750-92f2-9996404b650e.c000.snappy.parquet /tmp/adamTestMvnpjenoa0/TempSuite7252950499310565687.adam/referenceName=1/positionBin=0/.part-00000-fa268d4d-3b98-4750-92f2-9996404b650e.c000.snappy.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite7252950499310565687.adam/._samples.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite7252950499310565687.adam/_partitionedByStartPos /tmp/adamTestMvnpjenoa0/TempSuite7252950499310565687.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite7252950499310565687.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite7252950499310565687.adam/._partitionedByStartPos.crc /tmp/adamTestMvnpjenoa0/TempSuite7252950499310565687.adam/_samples.avro /tmp/adamTestMvnpjenoa0/TempSuite9169091240049456396.adam /tmp/adamTestMvnpjenoa0/TempSuite9169091240049456396.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite9169091240049456396.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite9169091240049456396.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite9169091240049456396.adam/_readGroups.avro /tmp/adamTestMvnpjenoa0/TempSuite9169091240049456396.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite9169091240049456396.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite9169091240049456396.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite9169091240049456396.adam/._processingSteps.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite9169091240049456396.adam/_common_metadata /tmp/adamTestMvnpjenoa0/TempSuite9169091240049456396.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite9169091240049456396.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite9169091240049456396.adam/._readGroups.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite9169091240049456396.adam/_metadata /tmp/adamTestMvnpjenoa0/TempSuite9169091240049456396.adam/_processingSteps.avro /tmp/adamTestMvnpjenoa0/chr20.250k.fa.gz550691534870684812.250k.fa.gz /tmp/adamTestMvnpjenoa0/sorted.sam5214077032241004767.sam /tmp/adamTestMvnpjenoa0/2307050274216410204 /tmp/adamTestMvnpjenoa0/2307050274216410204/chr20.contig.adam /tmp/adamTestMvnpjenoa0/2307050274216410204/chr20.contig.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/2307050274216410204/chr20.contig.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/2307050274216410204/chr20.contig.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/2307050274216410204/chr20.contig.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/2307050274216410204/chr20.contig.adam/_references.avro /tmp/adamTestMvnpjenoa0/2307050274216410204/chr20.contig.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/2307050274216410204/chr20.contig.adam/_common_metadata /tmp/adamTestMvnpjenoa0/2307050274216410204/chr20.contig.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/2307050274216410204/chr20.contig.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/2307050274216410204/chr20.contig.adam/_metadata /tmp/adamTestMvnpjenoa0/TempSuite3182899383636188767.bed /tmp/adamTestMvnpjenoa0/TempSuite3182899383636188767.bed/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite3182899383636188767.bed/part-00000 /tmp/adamTestMvnpjenoa0/TempSuite3182899383636188767.bed/.part-00000.crc /tmp/adamTestMvnpjenoa0/TempSuite3182899383636188767.bed/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/635077786754766973 /tmp/adamTestMvnpjenoa0/635077786754766973/.artificial.cram.crc /tmp/adamTestMvnpjenoa0/635077786754766973/artificial.cram /tmp/adamTestMvnpjenoa0/hg19.chrM.2bit4726177438321439164.chrM.2bit /tmp/adamTestMvnpjenoa0/TempSuite3731831443337525137 /tmp/adamTestMvnpjenoa0/TempSuite8629576419337217000.bed /tmp/adamTestMvnpjenoa0/TempSuite8629576419337217000.bed/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite8629576419337217000.bed/part-00001 /tmp/adamTestMvnpjenoa0/TempSuite8629576419337217000.bed/.part-00003.crc /tmp/adamTestMvnpjenoa0/TempSuite8629576419337217000.bed/part-00000 /tmp/adamTestMvnpjenoa0/TempSuite8629576419337217000.bed/part-00003 /tmp/adamTestMvnpjenoa0/TempSuite8629576419337217000.bed/.part-00000.crc /tmp/adamTestMvnpjenoa0/TempSuite8629576419337217000.bed/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite8629576419337217000.bed/part-00002 /tmp/adamTestMvnpjenoa0/TempSuite8629576419337217000.bed/.part-00002.crc /tmp/adamTestMvnpjenoa0/TempSuite8629576419337217000.bed/.part-00001.crc /tmp/adamTestMvnpjenoa0/TempSuite1921283225866147775 /tmp/adamTestMvnpjenoa0/TempSuite6581687445591240826.bed /tmp/adamTestMvnpjenoa0/TempSuite6581687445591240826.bed/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite6581687445591240826.bed/part-00001 /tmp/adamTestMvnpjenoa0/TempSuite6581687445591240826.bed/.part-00003.crc /tmp/adamTestMvnpjenoa0/TempSuite6581687445591240826.bed/part-00000 /tmp/adamTestMvnpjenoa0/TempSuite6581687445591240826.bed/part-00003 /tmp/adamTestMvnpjenoa0/TempSuite6581687445591240826.bed/.part-00000.crc /tmp/adamTestMvnpjenoa0/TempSuite6581687445591240826.bed/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite6581687445591240826.bed/part-00002 /tmp/adamTestMvnpjenoa0/TempSuite6581687445591240826.bed/.part-00002.crc /tmp/adamTestMvnpjenoa0/TempSuite6581687445591240826.bed/.part-00001.crc /tmp/adamTestMvnpjenoa0/TempSuite209877206283105131 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite4460167511342863621.narrowPeak /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite4460167511342863621.narrowPeak/_SUCCESS /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite4460167511342863621.narrowPeak/part-00001 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite4460167511342863621.narrowPeak/.part-00003.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite4460167511342863621.narrowPeak/part-00000 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite4460167511342863621.narrowPeak/part-00003 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite4460167511342863621.narrowPeak/.part-00000.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite4460167511342863621.narrowPeak/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite4460167511342863621.narrowPeak/part-00002 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite4460167511342863621.narrowPeak/.part-00002.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite4460167511342863621.narrowPeak/.part-00001.crc /tmp/adamTestMvnpjenoa0/TempSuite3595158599837711064 /tmp/adamTestMvnpjenoa0/TempSuite181986275264734832.sam /tmp/adamTestMvnpjenoa0/TempSuite181986275264734832.sam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite181986275264734832.sam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite181986275264734832.sam/.part-r-00000.sam.crc /tmp/adamTestMvnpjenoa0/TempSuite181986275264734832.sam/part-r-00000.sam /tmp/adamTestMvnpjenoa0/4968086367794820352 /tmp/adamTestMvnpjenoa0/4968086367794820352/.out.sam_head.crc /tmp/adamTestMvnpjenoa0/4968086367794820352/out.sam_head /tmp/adamTestMvnpjenoa0/4968086367794820352/.out.sam.crc /tmp/adamTestMvnpjenoa0/4968086367794820352/out.sam /tmp/adamTestMvnpjenoa0/4968086367794820352/out.sam_tail /tmp/adamTestMvnpjenoa0/4968086367794820352/out.sam_tail/_SUCCESS /tmp/adamTestMvnpjenoa0/4968086367794820352/out.sam_tail/part-r-00001.sam /tmp/adamTestMvnpjenoa0/4968086367794820352/out.sam_tail/part-r-00002.sam /tmp/adamTestMvnpjenoa0/4968086367794820352/out.sam_tail/.part-r-00001.sam.crc /tmp/adamTestMvnpjenoa0/4968086367794820352/out.sam_tail/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/4968086367794820352/out.sam_tail/part-r-00003.sam /tmp/adamTestMvnpjenoa0/4968086367794820352/out.sam_tail/.part-r-00000.sam.crc /tmp/adamTestMvnpjenoa0/4968086367794820352/out.sam_tail/.part-r-00003.sam.crc /tmp/adamTestMvnpjenoa0/4968086367794820352/out.sam_tail/part-r-00000.sam /tmp/adamTestMvnpjenoa0/4968086367794820352/out.sam_tail/.part-r-00002.sam.crc /tmp/adamTestMvnpjenoa0/random.vcf2394178611383650627.vcf /tmp/adamTestMvnpjenoa0/TempSuite4907055810381785358 /tmp/adamTestMvnpjenoa0/88839796722533341 /tmp/adamTestMvnpjenoa0/88839796722533341/ctg.adam /tmp/adamTestMvnpjenoa0/88839796722533341/ctg.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/88839796722533341/ctg.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/88839796722533341/ctg.adam/part-00000-85d45805-0bff-4c17-b572-74cc330b2880-c000.snappy.parquet /tmp/adamTestMvnpjenoa0/88839796722533341/ctg.adam/_references.avro /tmp/adamTestMvnpjenoa0/88839796722533341/ctg.adam/.part-00000-85d45805-0bff-4c17-b572-74cc330b2880-c000.snappy.parquet.crc /tmp/adamTestMvnpjenoa0/88839796722533341/ctg.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite7697049635245201364.adam /tmp/adamTestMvnpjenoa0/TempSuite7697049635245201364.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite7697049635245201364.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite7697049635245201364.adam/.part-00000-ea3f5ff7-6b9c-46a5-bfc8-68f72b251ad6-c000.snappy.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite7697049635245201364.adam/_readGroups.avro /tmp/adamTestMvnpjenoa0/TempSuite7697049635245201364.adam/part-00000-ea3f5ff7-6b9c-46a5-bfc8-68f72b251ad6-c000.snappy.parquet /tmp/adamTestMvnpjenoa0/TempSuite7697049635245201364.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite7697049635245201364.adam/._processingSteps.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite7697049635245201364.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite7697049635245201364.adam/._readGroups.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite7697049635245201364.adam/_processingSteps.avro /tmp/adamTestMvnpjenoa0/TempSuite8523171384202153600.adam /tmp/adamTestMvnpjenoa0/TempSuite8523171384202153600.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite8523171384202153600.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite8523171384202153600.adam/part-00000-dc6ac387-076a-4ca4-98e4-fdb4ebb24e8e-c000.snappy.parquet /tmp/adamTestMvnpjenoa0/TempSuite8523171384202153600.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite8523171384202153600.adam/._header.crc /tmp/adamTestMvnpjenoa0/TempSuite8523171384202153600.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite8523171384202153600.adam/.part-00000-dc6ac387-076a-4ca4-98e4-fdb4ebb24e8e-c000.snappy.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite8523171384202153600.adam/_header /tmp/adamTestMvnpjenoa0/TempSuite458648407072348352 /tmp/adamTestMvnpjenoa0/TempSuite8843902435803302365 /tmp/adamTestMvnpjenoa0/5688563773953523480 /tmp/adamTestMvnpjenoa0/5688563773953523480/sorted.vcf /tmp/adamTestMvnpjenoa0/5688563773953523480/.sorted.vcf.crc /tmp/adamTestMvnpjenoa0/5413461452096534510 /tmp/adamTestMvnpjenoa0/5413461452096534510/coverage.adam /tmp/adamTestMvnpjenoa0/5413461452096534510/coverage.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/5413461452096534510/coverage.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/5413461452096534510/coverage.adam/._samples.avro.crc /tmp/adamTestMvnpjenoa0/5413461452096534510/coverage.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/5413461452096534510/coverage.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/5413461452096534510/coverage.adam/_references.avro /tmp/adamTestMvnpjenoa0/5413461452096534510/coverage.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/5413461452096534510/coverage.adam/_common_metadata /tmp/adamTestMvnpjenoa0/5413461452096534510/coverage.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/5413461452096534510/coverage.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/5413461452096534510/coverage.adam/_samples.avro /tmp/adamTestMvnpjenoa0/5413461452096534510/coverage.adam/_metadata /tmp/adamTestMvnpjenoa0/TempSuite4248693576641947554.bed /tmp/adamTestMvnpjenoa0/TempSuite4248693576641947554.bed/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite4248693576641947554.bed/part-00000 /tmp/adamTestMvnpjenoa0/TempSuite4248693576641947554.bed/.part-00000.crc /tmp/adamTestMvnpjenoa0/TempSuite4248693576641947554.bed/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite7600585556506155801 /tmp/adamTestMvnpjenoa0/TempSuite246166508477427213 /tmp/adamTestMvnpjenoa0/TempSuite6331633504217711598.adam /tmp/adamTestMvnpjenoa0/TempSuite6331633504217711598.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite6331633504217711598.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite6331633504217711598.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite6331633504217711598.adam/.part-r-00003.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite6331633504217711598.adam/part-r-00001.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite6331633504217711598.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite6331633504217711598.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite6331633504217711598.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite6331633504217711598.adam/.part-r-00001.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite6331633504217711598.adam/part-r-00002.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite6331633504217711598.adam/.part-r-00002.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite6331633504217711598.adam/_common_metadata /tmp/adamTestMvnpjenoa0/TempSuite6331633504217711598.adam/._header.crc /tmp/adamTestMvnpjenoa0/TempSuite6331633504217711598.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite6331633504217711598.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite6331633504217711598.adam/_metadata /tmp/adamTestMvnpjenoa0/TempSuite6331633504217711598.adam/part-r-00003.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite6331633504217711598.adam/_header /tmp/adamTestMvnpjenoa0/artificial.cram8286084648242947040.cram /tmp/adamTestMvnpjenoa0/TempSuite1931648927121224698.adam /tmp/adamTestMvnpjenoa0/TempSuite1931648927121224698.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite1931648927121224698.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite1931648927121224698.adam/.part-00000-9a326266-f21b-49b9-b96b-c115162181fc-c000.snappy.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite1931648927121224698.adam/_readGroups.avro /tmp/adamTestMvnpjenoa0/TempSuite1931648927121224698.adam/part-00000-9a326266-f21b-49b9-b96b-c115162181fc-c000.snappy.parquet /tmp/adamTestMvnpjenoa0/TempSuite1931648927121224698.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite1931648927121224698.adam/._processingSteps.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite1931648927121224698.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite1931648927121224698.adam/._readGroups.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite1931648927121224698.adam/_processingSteps.avro /tmp/adamTestMvnpjenoa0/TempSuite5432434921240934593 /tmp/adamTestMvnpjenoa0/TempSuite6713588017199396936 /tmp/adamTestMvnpjenoa0/6032496378044176968 /tmp/adamTestMvnpjenoa0/6032496378044176968/genotypes.adam /tmp/adamTestMvnpjenoa0/6032496378044176968/genotypes.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/6032496378044176968/genotypes.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/6032496378044176968/genotypes.adam/._samples.avro.crc /tmp/adamTestMvnpjenoa0/6032496378044176968/genotypes.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/6032496378044176968/genotypes.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/6032496378044176968/genotypes.adam/_references.avro /tmp/adamTestMvnpjenoa0/6032496378044176968/genotypes.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/6032496378044176968/genotypes.adam/_common_metadata /tmp/adamTestMvnpjenoa0/6032496378044176968/genotypes.adam/._header.crc /tmp/adamTestMvnpjenoa0/6032496378044176968/genotypes.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/6032496378044176968/genotypes.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/6032496378044176968/genotypes.adam/_samples.avro /tmp/adamTestMvnpjenoa0/6032496378044176968/genotypes.adam/_metadata /tmp/adamTestMvnpjenoa0/6032496378044176968/genotypes.adam/_header /tmp/adamTestMvnpjenoa0/1557939530378-0 /tmp/adamTestMvnpjenoa0/1557939530378-0/test.fa /tmp/adamTestMvnpjenoa0/1557939530378-0/test.fa/_SUCCESS /tmp/adamTestMvnpjenoa0/1557939530378-0/test.fa/part-00000 /tmp/adamTestMvnpjenoa0/1557939530378-0/test.fa/.part-00000.crc /tmp/adamTestMvnpjenoa0/1557939530378-0/test.fa/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite6848185083882174587.adam /tmp/adamTestMvnpjenoa0/TempSuite6848185083882174587.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite6848185083882174587.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite6848185083882174587.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite6848185083882174587.adam/_readGroups.avro /tmp/adamTestMvnpjenoa0/TempSuite6848185083882174587.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite6848185083882174587.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite6848185083882174587.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite6848185083882174587.adam/._processingSteps.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite6848185083882174587.adam/_common_metadata /tmp/adamTestMvnpjenoa0/TempSuite6848185083882174587.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite6848185083882174587.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite6848185083882174587.adam/._readGroups.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite6848185083882174587.adam/_metadata /tmp/adamTestMvnpjenoa0/TempSuite6848185083882174587.adam/_processingSteps.avro /tmp/adamTestMvnpjenoa0/TempSuite5146695925444329026.adam /tmp/adamTestMvnpjenoa0/TempSuite5146695925444329026.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite5146695925444329026.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite5146695925444329026.adam/part-00000-300b4a87-799a-4e6c-afab-2c9922234c19-c000.snappy.parquet /tmp/adamTestMvnpjenoa0/TempSuite5146695925444329026.adam/.part-00000-300b4a87-799a-4e6c-afab-2c9922234c19-c000.snappy.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite5146695925444329026.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite5146695925444329026.adam/.part-00002-300b4a87-799a-4e6c-afab-2c9922234c19-c000.snappy.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite5146695925444329026.adam/part-00002-300b4a87-799a-4e6c-afab-2c9922234c19-c000.snappy.parquet /tmp/adamTestMvnpjenoa0/TempSuite5146695925444329026.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite5146695925444329026.adam/.part-00001-300b4a87-799a-4e6c-afab-2c9922234c19-c000.snappy.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite5146695925444329026.adam/part-00001-300b4a87-799a-4e6c-afab-2c9922234c19-c000.snappy.parquet /tmp/adamTestMvnpjenoa0/TempSuite5226740842708597039.adam /tmp/adamTestMvnpjenoa0/TempSuite5226740842708597039.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite5226740842708597039.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite5226740842708597039.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite5226740842708597039.adam/_readGroups.avro /tmp/adamTestMvnpjenoa0/TempSuite5226740842708597039.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite5226740842708597039.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite5226740842708597039.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite5226740842708597039.adam/._processingSteps.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite5226740842708597039.adam/_common_metadata /tmp/adamTestMvnpjenoa0/TempSuite5226740842708597039.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite5226740842708597039.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite5226740842708597039.adam/._readGroups.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite5226740842708597039.adam/_metadata /tmp/adamTestMvnpjenoa0/TempSuite5226740842708597039.adam/_processingSteps.avro /tmp/adamTestMvnpjenoa0/TempSuite6948893285446280395.adam /tmp/adamTestMvnpjenoa0/TempSuite6948893285446280395.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite6948893285446280395.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite6948893285446280395.adam/._samples.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite6948893285446280395.adam/part-00000-83971d66-2a16-43bc-918a-88b49f972ea6-c000.snappy.parquet /tmp/adamTestMvnpjenoa0/TempSuite6948893285446280395.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite6948893285446280395.adam/.part-00000-83971d66-2a16-43bc-918a-88b49f972ea6-c000.snappy.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite6948893285446280395.adam/._header.crc /tmp/adamTestMvnpjenoa0/TempSuite6948893285446280395.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite6948893285446280395.adam/_samples.avro /tmp/adamTestMvnpjenoa0/TempSuite6948893285446280395.adam/_header /tmp/adamTestMvnpjenoa0/4780882591807545762 /tmp/adamTestMvnpjenoa0/4780882591807545762/test.fa /tmp/adamTestMvnpjenoa0/4780882591807545762/.test.fa.crc /tmp/adamTestMvnpjenoa0/TempSuite6372047981977032559 /tmp/adamTestMvnpjenoa0/TempSuite7252950499310565687 /tmp/adamTestMvnpjenoa0/TempSuite5755290255175389970 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite5234029325846072790 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite6832653214527920584.gff3 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite6832653214527920584.gff3/_SUCCESS /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite6832653214527920584.gff3/part-00001 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite6832653214527920584.gff3/.part-00003.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite6832653214527920584.gff3/part-00000 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite6832653214527920584.gff3/part-00003 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite6832653214527920584.gff3/.part-00000.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite6832653214527920584.gff3/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite6832653214527920584.gff3/part-00002 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite6832653214527920584.gff3/.part-00002.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite6832653214527920584.gff3/.part-00001.crc /tmp/adamTestMvnpjenoa0/TempSuite1033833905333125913.adam /tmp/adamTestMvnpjenoa0/TempSuite1033833905333125913.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite1033833905333125913.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite1033833905333125913.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite1033833905333125913.adam/_readGroups.avro /tmp/adamTestMvnpjenoa0/TempSuite1033833905333125913.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite1033833905333125913.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite1033833905333125913.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite1033833905333125913.adam/._processingSteps.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite1033833905333125913.adam/_common_metadata /tmp/adamTestMvnpjenoa0/TempSuite1033833905333125913.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite1033833905333125913.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite1033833905333125913.adam/._readGroups.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite1033833905333125913.adam/_metadata /tmp/adamTestMvnpjenoa0/TempSuite1033833905333125913.adam/_processingSteps.avro /tmp/adamTestMvnpjenoa0/TempSuite5247604677884151520.adam /tmp/adamTestMvnpjenoa0/TempSuite5247604677884151520.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite5247604677884151520.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite5247604677884151520.adam/._samples.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite5247604677884151520.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite5247604677884151520.adam/.part-r-00003.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite5247604677884151520.adam/part-r-00001.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite5247604677884151520.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite5247604677884151520.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite5247604677884151520.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite5247604677884151520.adam/.part-r-00001.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite5247604677884151520.adam/part-r-00002.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite5247604677884151520.adam/.part-r-00002.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite5247604677884151520.adam/_common_metadata /tmp/adamTestMvnpjenoa0/TempSuite5247604677884151520.adam/._header.crc /tmp/adamTestMvnpjenoa0/TempSuite5247604677884151520.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite5247604677884151520.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite5247604677884151520.adam/_samples.avro /tmp/adamTestMvnpjenoa0/TempSuite5247604677884151520.adam/_metadata /tmp/adamTestMvnpjenoa0/TempSuite5247604677884151520.adam/part-r-00003.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite5247604677884151520.adam/_header /tmp/adamTestMvnpjenoa0/1557940162885-0 /tmp/adamTestMvnpjenoa0/1557940162885-0/contigs.fa /tmp/adamTestMvnpjenoa0/1557940162885-0/contigs.fa/_SUCCESS /tmp/adamTestMvnpjenoa0/1557940162885-0/contigs.fa/part-00000 /tmp/adamTestMvnpjenoa0/1557940162885-0/contigs.fa/.part-00000.crc /tmp/adamTestMvnpjenoa0/1557940162885-0/contigs.fa/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/1557940162885-0/contigs.adam /tmp/adamTestMvnpjenoa0/1557940162885-0/contigs.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/1557940162885-0/contigs.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/1557940162885-0/contigs.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/1557940162885-0/contigs.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/1557940162885-0/contigs.adam/_references.avro /tmp/adamTestMvnpjenoa0/1557940162885-0/contigs.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/1557940162885-0/contigs.adam/_common_metadata /tmp/adamTestMvnpjenoa0/1557940162885-0/contigs.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/1557940162885-0/contigs.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/1557940162885-0/contigs.adam/_metadata /tmp/adamTestMvnpjenoa0/TempSuite5320512173435773115 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite1986997657229897457 /tmp/adamTestMvnpjenoa0/TempSuite5166090571668865461 /tmp/adamTestMvnpjenoa0/reads6120150628625141864 /tmp/adamTestMvnpjenoa0/reads6120150628625141864/reads2.fq /tmp/adamTestMvnpjenoa0/reads6120150628625141864/reads2.fq/_SUCCESS /tmp/adamTestMvnpjenoa0/reads6120150628625141864/reads2.fq/part-00000 /tmp/adamTestMvnpjenoa0/reads6120150628625141864/reads2.fq/.part-00000.crc /tmp/adamTestMvnpjenoa0/reads6120150628625141864/reads2.fq/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/reads6120150628625141864/reads1.fq /tmp/adamTestMvnpjenoa0/reads6120150628625141864/reads1.fq/_SUCCESS /tmp/adamTestMvnpjenoa0/reads6120150628625141864/reads1.fq/part-00000 /tmp/adamTestMvnpjenoa0/reads6120150628625141864/reads1.fq/.part-00000.crc /tmp/adamTestMvnpjenoa0/reads6120150628625141864/reads1.fq/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite8604832664310408528.adam /tmp/adamTestMvnpjenoa0/TempSuite8604832664310408528.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite8604832664310408528.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite8604832664310408528.adam/._samples.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite8604832664310408528.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite8604832664310408528.adam/.part-r-00003.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite8604832664310408528.adam/part-r-00001.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite8604832664310408528.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite8604832664310408528.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite8604832664310408528.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite8604832664310408528.adam/.part-r-00001.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite8604832664310408528.adam/part-r-00002.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite8604832664310408528.adam/.part-r-00002.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite8604832664310408528.adam/_common_metadata /tmp/adamTestMvnpjenoa0/TempSuite8604832664310408528.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite8604832664310408528.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite8604832664310408528.adam/_samples.avro /tmp/adamTestMvnpjenoa0/TempSuite8604832664310408528.adam/_metadata /tmp/adamTestMvnpjenoa0/TempSuite8604832664310408528.adam/part-r-00003.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite5656143053371088087.fq /tmp/adamTestMvnpjenoa0/TempSuite5656143053371088087.fq/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite5656143053371088087.fq/part-00000 /tmp/adamTestMvnpjenoa0/TempSuite5656143053371088087.fq/.part-00000.crc /tmp/adamTestMvnpjenoa0/TempSuite5656143053371088087.fq/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite9159592525869374102 /tmp/adamTestMvnpjenoa0/TempSuite7611216962712174691 /tmp/adamTestMvnpjenoa0/TempSuite6563902507541632662 /tmp/adamTestMvnpjenoa0/TempSuite924780161293674120 /tmp/adamTestMvnpjenoa0/5971446530890809358 /tmp/adamTestMvnpjenoa0/5971446530890809358/ordered.sam /tmp/adamTestMvnpjenoa0/5971446530890809358/.ordered.sam.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite1986997657229897457.bed /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite1986997657229897457.bed/_SUCCESS /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite1986997657229897457.bed/part-00001 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite1986997657229897457.bed/.part-00003.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite1986997657229897457.bed/part-00000 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite1986997657229897457.bed/part-00003 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite1986997657229897457.bed/.part-00000.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite1986997657229897457.bed/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite1986997657229897457.bed/part-00002 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite1986997657229897457.bed/.part-00002.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite1986997657229897457.bed/.part-00001.crc /tmp/adamTestMvnpjenoa0/.FeatureDatasetFunctionsSuite4645048015409656528.interval_list.crc /tmp/adamTestMvnpjenoa0/6391317255092409276 /tmp/adamTestMvnpjenoa0/6391317255092409276/unordered.sam /tmp/adamTestMvnpjenoa0/6391317255092409276/.unordered.sam.crc /tmp/adamTestMvnpjenoa0/TempSuite8262798602615562595 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite5268671011899402358.narrowPeak /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite5268671011899402358.narrowPeak/_SUCCESS /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite5268671011899402358.narrowPeak/part-00001 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite5268671011899402358.narrowPeak/.part-00003.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite5268671011899402358.narrowPeak/part-00000 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite5268671011899402358.narrowPeak/part-00003 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite5268671011899402358.narrowPeak/.part-00000.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite5268671011899402358.narrowPeak/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite5268671011899402358.narrowPeak/part-00002 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite5268671011899402358.narrowPeak/.part-00002.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite5268671011899402358.narrowPeak/.part-00001.crc /tmp/adamTestMvnpjenoa0/TempSuite316669657898728846 /tmp/adamTestMvnpjenoa0/TempSuite8306103485182329665.adam /tmp/adamTestMvnpjenoa0/TempSuite8306103485182329665.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite8306103485182329665.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite8306103485182329665.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite8306103485182329665.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite8306103485182329665.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite8306103485182329665.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite8306103485182329665.adam/_common_metadata /tmp/adamTestMvnpjenoa0/TempSuite8306103485182329665.adam/._header.crc /tmp/adamTestMvnpjenoa0/TempSuite8306103485182329665.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite8306103485182329665.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite8306103485182329665.adam/_metadata /tmp/adamTestMvnpjenoa0/TempSuite8306103485182329665.adam/_header /tmp/adamTestMvnpjenoa0/2683756946103785665 /tmp/adamTestMvnpjenoa0/2683756946103785665/.sorted.lex.vcf.crc /tmp/adamTestMvnpjenoa0/2683756946103785665/sorted.lex.vcf /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite3222945418650442634 /tmp/adamTestMvnpjenoa0/.TempSuite3972207146601449166.sam.crc /tmp/adamTestMvnpjenoa0/TempSuite8306103485182329665 /tmp/adamTestMvnpjenoa0/TempSuite8964895141311071451 /tmp/adamTestMvnpjenoa0/reads121407362399203856089 /tmp/adamTestMvnpjenoa0/reads121407362399203856089/reads12.fq /tmp/adamTestMvnpjenoa0/reads121407362399203856089/reads12.fq/_SUCCESS /tmp/adamTestMvnpjenoa0/reads121407362399203856089/reads12.fq/part-00000 /tmp/adamTestMvnpjenoa0/reads121407362399203856089/reads12.fq/.part-00000.crc /tmp/adamTestMvnpjenoa0/reads121407362399203856089/reads12.fq/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite8676583558860388852 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite9117836399178227118 /tmp/adamTestMvnpjenoa0/TempSuite8396237150087203606 /tmp/adamTestMvnpjenoa0/TempSuite3915827702697355578.adam /tmp/adamTestMvnpjenoa0/TempSuite3915827702697355578.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite3915827702697355578.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite3915827702697355578.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite3915827702697355578.adam/_readGroups.avro /tmp/adamTestMvnpjenoa0/TempSuite3915827702697355578.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite3915827702697355578.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite3915827702697355578.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite3915827702697355578.adam/._processingSteps.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite3915827702697355578.adam/_common_metadata /tmp/adamTestMvnpjenoa0/TempSuite3915827702697355578.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite3915827702697355578.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite3915827702697355578.adam/._readGroups.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite3915827702697355578.adam/_metadata /tmp/adamTestMvnpjenoa0/TempSuite3915827702697355578.adam/_processingSteps.avro /tmp/adamTestMvnpjenoa0/TempSuite4743729739127654238.adam /tmp/adamTestMvnpjenoa0/TempSuite4743729739127654238.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite4743729739127654238.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite4743729739127654238.adam/referenceName=1 /tmp/adamTestMvnpjenoa0/TempSuite4743729739127654238.adam/referenceName=1/positionBin=0 /tmp/adamTestMvnpjenoa0/TempSuite4743729739127654238.adam/referenceName=1/positionBin=0/.part-00000-efb52dfa-b8aa-4aef-969a-d6505c5325a1.c000.snappy.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite4743729739127654238.adam/referenceName=1/positionBin=0/part-00000-efb52dfa-b8aa-4aef-969a-d6505c5325a1.c000.snappy.parquet /tmp/adamTestMvnpjenoa0/TempSuite4743729739127654238.adam/referenceName=13 /tmp/adamTestMvnpjenoa0/TempSuite4743729739127654238.adam/referenceName=13/positionBin=0 /tmp/adamTestMvnpjenoa0/TempSuite4743729739127654238.adam/referenceName=13/positionBin=0/.part-00000-efb52dfa-b8aa-4aef-969a-d6505c5325a1.c000.snappy.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite4743729739127654238.adam/referenceName=13/positionBin=0/part-00000-efb52dfa-b8aa-4aef-969a-d6505c5325a1.c000.snappy.parquet /tmp/adamTestMvnpjenoa0/TempSuite4743729739127654238.adam/_partitionedByStartPos /tmp/adamTestMvnpjenoa0/TempSuite4743729739127654238.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite4743729739127654238.adam/._header.crc /tmp/adamTestMvnpjenoa0/TempSuite4743729739127654238.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite4743729739127654238.adam/._partitionedByStartPos.crc /tmp/adamTestMvnpjenoa0/TempSuite4743729739127654238.adam/referenceName=2 /tmp/adamTestMvnpjenoa0/TempSuite4743729739127654238.adam/referenceName=2/positionBin=0 /tmp/adamTestMvnpjenoa0/TempSuite4743729739127654238.adam/referenceName=2/positionBin=0/.part-00000-efb52dfa-b8aa-4aef-969a-d6505c5325a1.c000.snappy.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite4743729739127654238.adam/referenceName=2/positionBin=0/part-00000-efb52dfa-b8aa-4aef-969a-d6505c5325a1.c000.snappy.parquet /tmp/adamTestMvnpjenoa0/TempSuite4743729739127654238.adam/_header /tmp/adamTestMvnpjenoa0/TempSuite3760846456780411430.bed /tmp/adamTestMvnpjenoa0/TempSuite3760846456780411430.bed/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite3760846456780411430.bed/part-00001 /tmp/adamTestMvnpjenoa0/TempSuite3760846456780411430.bed/.part-00003.crc /tmp/adamTestMvnpjenoa0/TempSuite3760846456780411430.bed/part-00000 /tmp/adamTestMvnpjenoa0/TempSuite3760846456780411430.bed/part-00003 /tmp/adamTestMvnpjenoa0/TempSuite3760846456780411430.bed/.part-00000.crc /tmp/adamTestMvnpjenoa0/TempSuite3760846456780411430.bed/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite3760846456780411430.bed/part-00002 /tmp/adamTestMvnpjenoa0/TempSuite3760846456780411430.bed/.part-00002.crc /tmp/adamTestMvnpjenoa0/TempSuite3760846456780411430.bed/.part-00001.crc /tmp/adamTestMvnpjenoa0/3713901472569816225 /tmp/adamTestMvnpjenoa0/3713901472569816225/sorted.vcf /tmp/adamTestMvnpjenoa0/3713901472569816225/.sorted.vcf.crc /tmp/adamTestMvnpjenoa0/TempSuite8592915387563865048 /tmp/adamTestMvnpjenoa0/TempSuite9092770215249166335 /tmp/adamTestMvnpjenoa0/TempSuite1251284635878575359 /tmp/adamTestMvnpjenoa0/TempSuite1875973419751237668 /tmp/adamTestMvnpjenoa0/small.sam835715224185812472.sam /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite2796341201094247953.narrowPeak /tmp/adamTestMvnpjenoa0/7007878758325526405 /tmp/adamTestMvnpjenoa0/7007878758325526405/bqsr1.vcf.bgz /tmp/adamTestMvnpjenoa0/7007878758325526405/bqsr1.vcf.bgz/_SUCCESS /tmp/adamTestMvnpjenoa0/7007878758325526405/bqsr1.vcf.bgz/part-r-00000.bgz /tmp/adamTestMvnpjenoa0/7007878758325526405/bqsr1.vcf.bgz/part-r-00003.bgz /tmp/adamTestMvnpjenoa0/7007878758325526405/bqsr1.vcf.bgz/.part-r-00001.bgz.crc /tmp/adamTestMvnpjenoa0/7007878758325526405/bqsr1.vcf.bgz/part-r-00001.bgz /tmp/adamTestMvnpjenoa0/7007878758325526405/bqsr1.vcf.bgz/.part-r-00003.bgz.crc /tmp/adamTestMvnpjenoa0/7007878758325526405/bqsr1.vcf.bgz/.part-r-00002.bgz.crc /tmp/adamTestMvnpjenoa0/7007878758325526405/bqsr1.vcf.bgz/part-r-00002.bgz /tmp/adamTestMvnpjenoa0/7007878758325526405/bqsr1.vcf.bgz/.part-r-00000.bgz.crc /tmp/adamTestMvnpjenoa0/7007878758325526405/bqsr1.vcf.bgz/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite4274165549462923049 /tmp/adamTestMvnpjenoa0/TempSuite8986117090025058793 /tmp/adamTestMvnpjenoa0/.TempSuite8901349017941121010.bam.crc /tmp/adamTestMvnpjenoa0/TempSuite9165048014138494986 /tmp/adamTestMvnpjenoa0/TempSuite7958740948188535183 /tmp/adamTestMvnpjenoa0/TempSuite6524376824309086566 /tmp/adamTestMvnpjenoa0/hg19.chrM.2bit8789586472880859955.chrM.2bit /tmp/adamTestMvnpjenoa0/TempSuite7687617383536916886 /tmp/adamTestMvnpjenoa0/TempSuite2225237885301104863.fa /tmp/adamTestMvnpjenoa0/TempSuite2225237885301104863.fa/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite2225237885301104863.fa/part-00000 /tmp/adamTestMvnpjenoa0/TempSuite2225237885301104863.fa/.part-00000.crc /tmp/adamTestMvnpjenoa0/TempSuite2225237885301104863.fa/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite5154624431810492890 /tmp/adamTestMvnpjenoa0/TempSuite2791217825696054455 /tmp/adamTestMvnpjenoa0/TempSuite9057218356735794271 /tmp/adamTestMvnpjenoa0/TempSuite531660189808326994.adam /tmp/adamTestMvnpjenoa0/TempSuite531660189808326994.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite531660189808326994.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite531660189808326994.adam/referenceName=1 /tmp/adamTestMvnpjenoa0/TempSuite531660189808326994.adam/referenceName=1/positionBin=0 /tmp/adamTestMvnpjenoa0/TempSuite531660189808326994.adam/referenceName=1/positionBin=0/.part-00000-5cebfe09-6ee9-4f53-bdea-929d2e722e81.c000.snappy.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite531660189808326994.adam/referenceName=1/positionBin=0/part-00000-5cebfe09-6ee9-4f53-bdea-929d2e722e81.c000.snappy.parquet /tmp/adamTestMvnpjenoa0/TempSuite531660189808326994.adam/._samples.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite531660189808326994.adam/referenceName=13 /tmp/adamTestMvnpjenoa0/TempSuite531660189808326994.adam/referenceName=13/positionBin=0 /tmp/adamTestMvnpjenoa0/TempSuite531660189808326994.adam/referenceName=13/positionBin=0/.part-00000-5cebfe09-6ee9-4f53-bdea-929d2e722e81.c000.snappy.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite531660189808326994.adam/referenceName=13/positionBin=0/part-00000-5cebfe09-6ee9-4f53-bdea-929d2e722e81.c000.snappy.parquet /tmp/adamTestMvnpjenoa0/TempSuite531660189808326994.adam/_partitionedByStartPos /tmp/adamTestMvnpjenoa0/TempSuite531660189808326994.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite531660189808326994.adam/._header.crc /tmp/adamTestMvnpjenoa0/TempSuite531660189808326994.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite531660189808326994.adam/._partitionedByStartPos.crc /tmp/adamTestMvnpjenoa0/TempSuite531660189808326994.adam/_samples.avro /tmp/adamTestMvnpjenoa0/TempSuite531660189808326994.adam/referenceName=2 /tmp/adamTestMvnpjenoa0/TempSuite531660189808326994.adam/referenceName=2/positionBin=0 /tmp/adamTestMvnpjenoa0/TempSuite531660189808326994.adam/referenceName=2/positionBin=0/.part-00000-5cebfe09-6ee9-4f53-bdea-929d2e722e81.c000.snappy.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite531660189808326994.adam/referenceName=2/positionBin=0/part-00000-5cebfe09-6ee9-4f53-bdea-929d2e722e81.c000.snappy.parquet /tmp/adamTestMvnpjenoa0/TempSuite531660189808326994.adam/_header /tmp/adamTestMvnpjenoa0/.FeatureDatasetFunctionsSuite1149986837268046739.bed.crc /tmp/adamTestMvnpjenoa0/TempSuite6323293992388568571 /tmp/adamTestMvnpjenoa0/TempSuite4085734275694747234.sam /tmp/adamTestMvnpjenoa0/TempSuite4085734275694747234.sam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite4085734275694747234.sam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite4085734275694747234.sam/.part-r-00000.sam.crc /tmp/adamTestMvnpjenoa0/TempSuite4085734275694747234.sam/part-r-00000.sam /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite2309174855776508211.gtf /tmp/adamTestMvnpjenoa0/TempSuite6036072080182044767.adam /tmp/adamTestMvnpjenoa0/TempSuite6036072080182044767.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite6036072080182044767.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite6036072080182044767.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite6036072080182044767.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite6036072080182044767.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite6036072080182044767.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite6036072080182044767.adam/_common_metadata /tmp/adamTestMvnpjenoa0/TempSuite6036072080182044767.adam/._header.crc /tmp/adamTestMvnpjenoa0/TempSuite6036072080182044767.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite6036072080182044767.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite6036072080182044767.adam/_metadata /tmp/adamTestMvnpjenoa0/TempSuite6036072080182044767.adam/_header /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite5895798626854010945 /tmp/adamTestMvnpjenoa0/TempSuite7110799967104893760 /tmp/adamTestMvnpjenoa0/437170524037750317 /tmp/adamTestMvnpjenoa0/437170524037750317/contigs.adam /tmp/adamTestMvnpjenoa0/437170524037750317/contigs.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/437170524037750317/contigs.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/437170524037750317/contigs.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/437170524037750317/contigs.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/437170524037750317/contigs.adam/_references.avro /tmp/adamTestMvnpjenoa0/437170524037750317/contigs.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/437170524037750317/contigs.adam/_common_metadata /tmp/adamTestMvnpjenoa0/437170524037750317/contigs.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/437170524037750317/contigs.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/437170524037750317/contigs.adam/_metadata /tmp/adamTestMvnpjenoa0/TempSuite262166617179322680 /tmp/adamTestMvnpjenoa0/TempSuite2266416622975484073 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite3348708032767544682 /tmp/adamTestMvnpjenoa0/TempSuite4408182672842833830 /tmp/adamTestMvnpjenoa0/TempSuite1900933834625183911.fa /tmp/adamTestMvnpjenoa0/TempSuite1900933834625183911.fa/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite1900933834625183911.fa/part-00000 /tmp/adamTestMvnpjenoa0/TempSuite1900933834625183911.fa/.part-00000.crc /tmp/adamTestMvnpjenoa0/TempSuite1900933834625183911.fa/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite7600585556506155801.bed /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite361418958970110841.narrowPeak /tmp/adamTestMvnpjenoa0/TempSuite974830346482781115 /tmp/adamTestMvnpjenoa0/TempSuite4083522371559257358.adam /tmp/adamTestMvnpjenoa0/TempSuite4083522371559257358.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite4083522371559257358.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite4083522371559257358.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite4083522371559257358.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite4083522371559257358.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite4083522371559257358.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite4083522371559257358.adam/_common_metadata /tmp/adamTestMvnpjenoa0/TempSuite4083522371559257358.adam/._header.crc /tmp/adamTestMvnpjenoa0/TempSuite4083522371559257358.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite4083522371559257358.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite4083522371559257358.adam/_metadata /tmp/adamTestMvnpjenoa0/TempSuite4083522371559257358.adam/_header /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite4937555853815722038.gtf /tmp/adamTestMvnpjenoa0/1557939299664-0 /tmp/adamTestMvnpjenoa0/1557939299664-0/test.gvcf.vcf /tmp/adamTestMvnpjenoa0/1557939299664-0/.test.gvcf.vcf.crc /tmp/adamTestMvnpjenoa0/4841355691105794010 /tmp/adamTestMvnpjenoa0/4841355691105794010/unordered.adam /tmp/adamTestMvnpjenoa0/4841355691105794010/unordered.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/4841355691105794010/unordered.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/4841355691105794010/unordered.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/4841355691105794010/unordered.adam/_readGroups.avro /tmp/adamTestMvnpjenoa0/4841355691105794010/unordered.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/4841355691105794010/unordered.adam/_references.avro /tmp/adamTestMvnpjenoa0/4841355691105794010/unordered.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/4841355691105794010/unordered.adam/._processingSteps.avro.crc /tmp/adamTestMvnpjenoa0/4841355691105794010/unordered.adam/_common_metadata /tmp/adamTestMvnpjenoa0/4841355691105794010/unordered.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/4841355691105794010/unordered.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/4841355691105794010/unordered.adam/._readGroups.avro.crc /tmp/adamTestMvnpjenoa0/4841355691105794010/unordered.adam/_metadata /tmp/adamTestMvnpjenoa0/4841355691105794010/unordered.adam/_processingSteps.avro /tmp/adamTestMvnpjenoa0/7096700665159500678 /tmp/adamTestMvnpjenoa0/7096700665159500678/unordered.adam /tmp/adamTestMvnpjenoa0/7096700665159500678/unordered.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/7096700665159500678/unordered.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/7096700665159500678/unordered.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/7096700665159500678/unordered.adam/_readGroups.avro /tmp/adamTestMvnpjenoa0/7096700665159500678/unordered.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/7096700665159500678/unordered.adam/_references.avro /tmp/adamTestMvnpjenoa0/7096700665159500678/unordered.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/7096700665159500678/unordered.adam/._processingSteps.avro.crc /tmp/adamTestMvnpjenoa0/7096700665159500678/unordered.adam/_common_metadata /tmp/adamTestMvnpjenoa0/7096700665159500678/unordered.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/7096700665159500678/unordered.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/7096700665159500678/unordered.adam/._readGroups.avro.crc /tmp/adamTestMvnpjenoa0/7096700665159500678/unordered.adam/_metadata /tmp/adamTestMvnpjenoa0/7096700665159500678/unordered.adam/_processingSteps.avro /tmp/adamTestMvnpjenoa0/TempSuite5950386164177715206.adam /tmp/adamTestMvnpjenoa0/TempSuite5950386164177715206.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite5950386164177715206.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite5950386164177715206.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite5950386164177715206.adam/.part-00000-3aa218fd-bacb-4290-8c8e-3bf67bbd9647-c000.snappy.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite5950386164177715206.adam/._header.crc /tmp/adamTestMvnpjenoa0/TempSuite5950386164177715206.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite5950386164177715206.adam/part-00000-3aa218fd-bacb-4290-8c8e-3bf67bbd9647-c000.snappy.parquet /tmp/adamTestMvnpjenoa0/TempSuite5950386164177715206.adam/_header /tmp/adamTestMvnpjenoa0/TempSuite4455342517077777381.adam /tmp/adamTestMvnpjenoa0/TempSuite4455342517077777381.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite4455342517077777381.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite4455342517077777381.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite4455342517077777381.adam/_readGroups.avro /tmp/adamTestMvnpjenoa0/TempSuite4455342517077777381.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite4455342517077777381.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite4455342517077777381.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite4455342517077777381.adam/._processingSteps.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite4455342517077777381.adam/_common_metadata /tmp/adamTestMvnpjenoa0/TempSuite4455342517077777381.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite4455342517077777381.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite4455342517077777381.adam/._readGroups.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite4455342517077777381.adam/_metadata /tmp/adamTestMvnpjenoa0/TempSuite4455342517077777381.adam/_processingSteps.avro /tmp/adamTestMvnpjenoa0/TempSuite8755731092838480176 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite2449717568714814113 /tmp/adamTestMvnpjenoa0/TempSuite5455883223414912677.adam /tmp/adamTestMvnpjenoa0/TempSuite5455883223414912677.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite5455883223414912677.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite5455883223414912677.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite5455883223414912677.adam/.part-r-00003.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite5455883223414912677.adam/part-r-00001.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite5455883223414912677.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite5455883223414912677.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite5455883223414912677.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite5455883223414912677.adam/.part-r-00001.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite5455883223414912677.adam/part-r-00002.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite5455883223414912677.adam/.part-r-00002.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite5455883223414912677.adam/_common_metadata /tmp/adamTestMvnpjenoa0/TempSuite5455883223414912677.adam/._header.crc /tmp/adamTestMvnpjenoa0/TempSuite5455883223414912677.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite5455883223414912677.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite5455883223414912677.adam/_metadata /tmp/adamTestMvnpjenoa0/TempSuite5455883223414912677.adam/part-r-00003.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite5455883223414912677.adam/_header /tmp/adamTestMvnpjenoa0/TempSuite7284403123459791885.adam /tmp/adamTestMvnpjenoa0/TempSuite7284403123459791885.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite7284403123459791885.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite7284403123459791885.adam/part-00000-25f3ee94-6d58-4f77-a6d3-2c14831b8846-c000.snappy.parquet /tmp/adamTestMvnpjenoa0/TempSuite7284403123459791885.adam/._samples.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite7284403123459791885.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite7284403123459791885.adam/._header.crc /tmp/adamTestMvnpjenoa0/TempSuite7284403123459791885.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite7284403123459791885.adam/_samples.avro /tmp/adamTestMvnpjenoa0/TempSuite7284403123459791885.adam/.part-00000-25f3ee94-6d58-4f77-a6d3-2c14831b8846-c000.snappy.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite7284403123459791885.adam/_header /tmp/adamTestMvnpjenoa0/TempSuite209877206283105131.sam /tmp/adamTestMvnpjenoa0/TempSuite209877206283105131.sam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite209877206283105131.sam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite209877206283105131.sam/.part-r-00000.sam.crc /tmp/adamTestMvnpjenoa0/TempSuite209877206283105131.sam/part-r-00000.sam /tmp/adamTestMvnpjenoa0/TempSuite1811472737585393713.bed /tmp/adamTestMvnpjenoa0/TempSuite1811472737585393713.bed/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite1811472737585393713.bed/part-00000 /tmp/adamTestMvnpjenoa0/TempSuite1811472737585393713.bed/.part-00000.crc /tmp/adamTestMvnpjenoa0/TempSuite1811472737585393713.bed/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite6561990423157415865 /tmp/adamTestMvnpjenoa0/TempSuite6848185083882174587 /tmp/adamTestMvnpjenoa0/TempSuite8737981847127160617.bam /tmp/adamTestMvnpjenoa0/TempSuite2269854606739391836.adam /tmp/adamTestMvnpjenoa0/TempSuite2269854606739391836.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite2269854606739391836.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite2269854606739391836.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite2269854606739391836.adam/.part-r-00003.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite2269854606739391836.adam/part-r-00001.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite2269854606739391836.adam/_readGroups.avro /tmp/adamTestMvnpjenoa0/TempSuite2269854606739391836.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite2269854606739391836.adam/_partitionMap.avro /tmp/adamTestMvnpjenoa0/TempSuite2269854606739391836.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite2269854606739391836.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite2269854606739391836.adam/.part-r-00001.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite2269854606739391836.adam/part-r-00002.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite2269854606739391836.adam/._processingSteps.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite2269854606739391836.adam/.part-r-00002.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite2269854606739391836.adam/_common_metadata /tmp/adamTestMvnpjenoa0/TempSuite2269854606739391836.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite2269854606739391836.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite2269854606739391836.adam/._readGroups.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite2269854606739391836.adam/._partitionMap.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite2269854606739391836.adam/_metadata /tmp/adamTestMvnpjenoa0/TempSuite2269854606739391836.adam/part-r-00003.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite2269854606739391836.adam/_processingSteps.avro /tmp/adamTestMvnpjenoa0/2109860853132808270 /tmp/adamTestMvnpjenoa0/2109860853132808270/sorted-variants.vcf /tmp/adamTestMvnpjenoa0/2109860853132808270/.sorted-variants.vcf.crc /tmp/adamTestMvnpjenoa0/TempSuite4749479781037507784_1.fq /tmp/adamTestMvnpjenoa0/TempSuite4749479781037507784_1.fq/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite4749479781037507784_1.fq/part-00000 /tmp/adamTestMvnpjenoa0/TempSuite4749479781037507784_1.fq/.part-00000.crc /tmp/adamTestMvnpjenoa0/TempSuite4749479781037507784_1.fq/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/javaAC6486671121136201120 /tmp/adamTestMvnpjenoa0/javaAC6486671121136201120/testRdd.read.adam /tmp/adamTestMvnpjenoa0/javaAC6486671121136201120/testRdd.read.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/javaAC6486671121136201120/testRdd.read.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/javaAC6486671121136201120/testRdd.read.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/javaAC6486671121136201120/testRdd.read.adam/_readGroups.avro /tmp/adamTestMvnpjenoa0/javaAC6486671121136201120/testRdd.read.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/javaAC6486671121136201120/testRdd.read.adam/_references.avro /tmp/adamTestMvnpjenoa0/javaAC6486671121136201120/testRdd.read.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/javaAC6486671121136201120/testRdd.read.adam/._processingSteps.avro.crc /tmp/adamTestMvnpjenoa0/javaAC6486671121136201120/testRdd.read.adam/_common_metadata /tmp/adamTestMvnpjenoa0/javaAC6486671121136201120/testRdd.read.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/javaAC6486671121136201120/testRdd.read.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/javaAC6486671121136201120/testRdd.read.adam/._readGroups.avro.crc /tmp/adamTestMvnpjenoa0/javaAC6486671121136201120/testRdd.read.adam/_metadata /tmp/adamTestMvnpjenoa0/javaAC6486671121136201120/testRdd.read.adam/_processingSteps.avro /tmp/adamTestMvnpjenoa0/TempSuite7038626970299123759.adam /tmp/adamTestMvnpjenoa0/TempSuite7038626970299123759.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite7038626970299123759.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite7038626970299123759.adam/.part-00000-74767d1a-f216-42e9-805d-f622fd8e4575-c000.snappy.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite7038626970299123759.adam/_readGroups.avro /tmp/adamTestMvnpjenoa0/TempSuite7038626970299123759.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite7038626970299123759.adam/._processingSteps.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite7038626970299123759.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite7038626970299123759.adam/._readGroups.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite7038626970299123759.adam/part-00000-74767d1a-f216-42e9-805d-f622fd8e4575-c000.snappy.parquet /tmp/adamTestMvnpjenoa0/TempSuite7038626970299123759.adam/_processingSteps.avro /tmp/adamTestMvnpjenoa0/TempSuite8451402568221737471.sam /tmp/adamTestMvnpjenoa0/TempSuite5370826037317384489.adam /tmp/adamTestMvnpjenoa0/TempSuite5370826037317384489.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite5370826037317384489.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite5370826037317384489.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite5370826037317384489.adam/_readGroups.avro /tmp/adamTestMvnpjenoa0/TempSuite5370826037317384489.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite5370826037317384489.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite5370826037317384489.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite5370826037317384489.adam/._processingSteps.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite5370826037317384489.adam/_common_metadata /tmp/adamTestMvnpjenoa0/TempSuite5370826037317384489.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite5370826037317384489.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite5370826037317384489.adam/._readGroups.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite5370826037317384489.adam/_metadata /tmp/adamTestMvnpjenoa0/TempSuite5370826037317384489.adam/_processingSteps.avro /tmp/adamTestMvnpjenoa0/javaAC3109684135038436330 /tmp/adamTestMvnpjenoa0/javaAC3109684135038436330/testRdd.genotype.adam /tmp/adamTestMvnpjenoa0/javaAC3109684135038436330/testRdd.genotype.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/javaAC3109684135038436330/testRdd.genotype.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/javaAC3109684135038436330/testRdd.genotype.adam/._samples.avro.crc /tmp/adamTestMvnpjenoa0/javaAC3109684135038436330/testRdd.genotype.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/javaAC3109684135038436330/testRdd.genotype.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/javaAC3109684135038436330/testRdd.genotype.adam/_references.avro /tmp/adamTestMvnpjenoa0/javaAC3109684135038436330/testRdd.genotype.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/javaAC3109684135038436330/testRdd.genotype.adam/_common_metadata /tmp/adamTestMvnpjenoa0/javaAC3109684135038436330/testRdd.genotype.adam/._header.crc /tmp/adamTestMvnpjenoa0/javaAC3109684135038436330/testRdd.genotype.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/javaAC3109684135038436330/testRdd.genotype.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/javaAC3109684135038436330/testRdd.genotype.adam/_samples.avro /tmp/adamTestMvnpjenoa0/javaAC3109684135038436330/testRdd.genotype.adam/_metadata /tmp/adamTestMvnpjenoa0/javaAC3109684135038436330/testRdd.genotype.adam/_header /tmp/adamTestMvnpjenoa0/TempSuite6511645711249290561.adam /tmp/adamTestMvnpjenoa0/TempSuite6511645711249290561.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite6511645711249290561.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite6511645711249290561.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite6511645711249290561.adam/_readGroups.avro /tmp/adamTestMvnpjenoa0/TempSuite6511645711249290561.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite6511645711249290561.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite6511645711249290561.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite6511645711249290561.adam/._processingSteps.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite6511645711249290561.adam/_common_metadata /tmp/adamTestMvnpjenoa0/TempSuite6511645711249290561.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite6511645711249290561.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite6511645711249290561.adam/._readGroups.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite6511645711249290561.adam/_metadata /tmp/adamTestMvnpjenoa0/TempSuite6511645711249290561.adam/_processingSteps.avro /tmp/adamTestMvnpjenoa0/TempSuite7989129825859549658 /tmp/adamTestMvnpjenoa0/.TempSuite7368695202327364990.fq.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite359129980305290861 /tmp/adamTestMvnpjenoa0/TempSuite5823670682827686736 /tmp/adamTestMvnpjenoa0/1940896131086448128 /tmp/adamTestMvnpjenoa0/1940896131086448128/ordered.sam /tmp/adamTestMvnpjenoa0/1940896131086448128/.ordered.sam.crc /tmp/adamTestMvnpjenoa0/TempSuite4299727146294675061.bed /tmp/adamTestMvnpjenoa0/TempSuite4299727146294675061.bed/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite4299727146294675061.bed/part-00000 /tmp/adamTestMvnpjenoa0/TempSuite4299727146294675061.bed/.part-00000.crc /tmp/adamTestMvnpjenoa0/TempSuite4299727146294675061.bed/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite8629576419337217000 /tmp/adamTestMvnpjenoa0/reads121776906792077113320 /tmp/adamTestMvnpjenoa0/reads121776906792077113320/reads12.fq /tmp/adamTestMvnpjenoa0/reads121776906792077113320/reads12.fq/_SUCCESS /tmp/adamTestMvnpjenoa0/reads121776906792077113320/reads12.fq/part-00000 /tmp/adamTestMvnpjenoa0/reads121776906792077113320/reads12.fq/.part-00000.crc /tmp/adamTestMvnpjenoa0/reads121776906792077113320/reads12.fq/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite7361981565445851203 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite5754122912166156516.narrowPeak /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite5754122912166156516.narrowPeak/_SUCCESS /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite5754122912166156516.narrowPeak/part-00001 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite5754122912166156516.narrowPeak/.part-00003.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite5754122912166156516.narrowPeak/part-00000 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite5754122912166156516.narrowPeak/part-00003 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite5754122912166156516.narrowPeak/.part-00000.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite5754122912166156516.narrowPeak/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite5754122912166156516.narrowPeak/part-00002 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite5754122912166156516.narrowPeak/.part-00002.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite5754122912166156516.narrowPeak/.part-00001.crc /tmp/adamTestMvnpjenoa0/TempSuite1768585581212685977.adam /tmp/adamTestMvnpjenoa0/TempSuite1768585581212685977.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite1768585581212685977.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite1768585581212685977.adam/part-00000-955e0163-23b0-44de-8876-d795d0e22c52-c000.snappy.parquet /tmp/adamTestMvnpjenoa0/TempSuite1768585581212685977.adam/_readGroups.avro /tmp/adamTestMvnpjenoa0/TempSuite1768585581212685977.adam/.part-00000-955e0163-23b0-44de-8876-d795d0e22c52-c000.snappy.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite1768585581212685977.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite1768585581212685977.adam/._processingSteps.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite1768585581212685977.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite1768585581212685977.adam/._readGroups.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite1768585581212685977.adam/_processingSteps.avro /tmp/adamTestMvnpjenoa0/TempSuite5893508920392847756 /tmp/adamTestMvnpjenoa0/TempSuite3017277336060454342 /tmp/adamTestMvnpjenoa0/TempSuite8947341446828070501 /tmp/adamTestMvnpjenoa0/TempSuite8947341446828070501.adam /tmp/adamTestMvnpjenoa0/TempSuite8947341446828070501.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite8947341446828070501.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite8947341446828070501.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite8947341446828070501.adam/_readGroups.avro /tmp/adamTestMvnpjenoa0/TempSuite8947341446828070501.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite8947341446828070501.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite8947341446828070501.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite8947341446828070501.adam/._processingSteps.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite8947341446828070501.adam/_common_metadata /tmp/adamTestMvnpjenoa0/TempSuite8947341446828070501.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite8947341446828070501.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite8947341446828070501.adam/._readGroups.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite8947341446828070501.adam/_metadata /tmp/adamTestMvnpjenoa0/TempSuite8947341446828070501.adam/_processingSteps.avro /tmp/adamTestMvnpjenoa0/TempSuite2198978203599306232 /tmp/adamTestMvnpjenoa0/sorted.sam3417117590366271042.sam /tmp/adamTestMvnpjenoa0/1557939528509-0 /tmp/adamTestMvnpjenoa0/1557939528509-0/test.fa /tmp/adamTestMvnpjenoa0/1557939528509-0/test.fa/_SUCCESS /tmp/adamTestMvnpjenoa0/1557939528509-0/test.fa/part-00000 /tmp/adamTestMvnpjenoa0/1557939528509-0/test.fa/.part-00000.crc /tmp/adamTestMvnpjenoa0/1557939528509-0/test.fa/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite3521924285109635108.adam /tmp/adamTestMvnpjenoa0/TempSuite3521924285109635108.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite3521924285109635108.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite3521924285109635108.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite3521924285109635108.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite3521924285109635108.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite3521924285109635108.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite3521924285109635108.adam/_common_metadata /tmp/adamTestMvnpjenoa0/TempSuite3521924285109635108.adam/._header.crc /tmp/adamTestMvnpjenoa0/TempSuite3521924285109635108.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite3521924285109635108.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite3521924285109635108.adam/_metadata /tmp/adamTestMvnpjenoa0/TempSuite3521924285109635108.adam/_header /tmp/adamTestMvnpjenoa0/TempSuite8803344612487790304 /tmp/adamTestMvnpjenoa0/TempSuite1816874181471195783 /tmp/adamTestMvnpjenoa0/TempSuite8964895141311071451.adam /tmp/adamTestMvnpjenoa0/TempSuite8964895141311071451.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite8964895141311071451.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite8964895141311071451.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite8964895141311071451.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite8964895141311071451.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite8964895141311071451.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite8964895141311071451.adam/_common_metadata /tmp/adamTestMvnpjenoa0/TempSuite8964895141311071451.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite8964895141311071451.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite8964895141311071451.adam/_metadata /tmp/adamTestMvnpjenoa0/TempSuite6681591804528478661_1.fq /tmp/adamTestMvnpjenoa0/TempSuite4395382513521882609 /tmp/adamTestMvnpjenoa0/TempSuite4083522371559257358 /tmp/adamTestMvnpjenoa0/TempSuite4408182672842833830.adam /tmp/adamTestMvnpjenoa0/TempSuite4408182672842833830.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite4408182672842833830.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite4408182672842833830.adam/._samples.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite4408182672842833830.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite4408182672842833830.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite4408182672842833830.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite4408182672842833830.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite4408182672842833830.adam/_common_metadata /tmp/adamTestMvnpjenoa0/TempSuite4408182672842833830.adam/._header.crc /tmp/adamTestMvnpjenoa0/TempSuite4408182672842833830.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite4408182672842833830.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite4408182672842833830.adam/_samples.avro /tmp/adamTestMvnpjenoa0/TempSuite4408182672842833830.adam/_metadata /tmp/adamTestMvnpjenoa0/TempSuite4408182672842833830.adam/_header /tmp/adamTestMvnpjenoa0/TempSuite1768585581212685977 /tmp/adamTestMvnpjenoa0/TempSuite2501700038666840262.adam /tmp/adamTestMvnpjenoa0/TempSuite2501700038666840262.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite2501700038666840262.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite2501700038666840262.adam/._samples.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite2501700038666840262.adam/part-00000-f1666f61-aa96-43a5-8d4b-0e20473c03fe-c000.snappy.parquet /tmp/adamTestMvnpjenoa0/TempSuite2501700038666840262.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite2501700038666840262.adam/._header.crc /tmp/adamTestMvnpjenoa0/TempSuite2501700038666840262.adam/.part-00000-f1666f61-aa96-43a5-8d4b-0e20473c03fe-c000.snappy.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite2501700038666840262.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite2501700038666840262.adam/_samples.avro /tmp/adamTestMvnpjenoa0/TempSuite2501700038666840262.adam/_header /tmp/adamTestMvnpjenoa0/.FeatureDatasetFunctionsSuite3490034250567771633.bed.crc /tmp/adamTestMvnpjenoa0/TempSuite4165278431039046691 /tmp/adamTestMvnpjenoa0/TempSuite3879360464944867174 /tmp/adamTestMvnpjenoa0/1557939941679-0 /tmp/adamTestMvnpjenoa0/1557939941679-0/test.fa /tmp/adamTestMvnpjenoa0/1557939941679-0/test.fa/_SUCCESS /tmp/adamTestMvnpjenoa0/1557939941679-0/test.fa/part-00000 /tmp/adamTestMvnpjenoa0/1557939941679-0/test.fa/.part-00000.crc /tmp/adamTestMvnpjenoa0/1557939941679-0/test.fa/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite5754122912166156516 /tmp/adamTestMvnpjenoa0/4001818615424836241 /tmp/adamTestMvnpjenoa0/4001818615424836241/out.cram /tmp/adamTestMvnpjenoa0/4001818615424836241/.out.cram.crc /tmp/adamTestMvnpjenoa0/4001818615424836241/out.cram_head /tmp/adamTestMvnpjenoa0/4001818615424836241/out.cram_tail /tmp/adamTestMvnpjenoa0/4001818615424836241/out.cram_tail/_SUCCESS /tmp/adamTestMvnpjenoa0/4001818615424836241/out.cram_tail/part-r-00001.cram /tmp/adamTestMvnpjenoa0/4001818615424836241/out.cram_tail/.part-r-00003.cram.crc /tmp/adamTestMvnpjenoa0/4001818615424836241/out.cram_tail/part-r-00000.cram /tmp/adamTestMvnpjenoa0/4001818615424836241/out.cram_tail/.part-r-00002.cram.crc /tmp/adamTestMvnpjenoa0/4001818615424836241/out.cram_tail/part-r-00003.cram /tmp/adamTestMvnpjenoa0/4001818615424836241/out.cram_tail/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/4001818615424836241/out.cram_tail/.part-r-00001.cram.crc /tmp/adamTestMvnpjenoa0/4001818615424836241/out.cram_tail/part-r-00002.cram /tmp/adamTestMvnpjenoa0/4001818615424836241/out.cram_tail/.part-r-00000.cram.crc /tmp/adamTestMvnpjenoa0/4001818615424836241/.out.cram_head.crc /tmp/adamTestMvnpjenoa0/TempSuite1944360032336399887.adam /tmp/adamTestMvnpjenoa0/TempSuite1944360032336399887.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite1944360032336399887.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite1944360032336399887.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite1944360032336399887.adam/.part-00000-339a7658-8799-43b1-8c1e-0a9722083766-c000.snappy.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite1944360032336399887.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite1944360032336399887.adam/part-00000-339a7658-8799-43b1-8c1e-0a9722083766-c000.snappy.parquet /tmp/adamTestMvnpjenoa0/TempSuite6397240184609528647.sam /tmp/adamTestMvnpjenoa0/TempSuite6397240184609528647.sam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite6397240184609528647.sam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite6397240184609528647.sam/.part-r-00000.sam.crc /tmp/adamTestMvnpjenoa0/TempSuite6397240184609528647.sam/part-r-00000.sam /tmp/adamTestMvnpjenoa0/TempSuite757360818588446018.adam /tmp/adamTestMvnpjenoa0/TempSuite757360818588446018.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite757360818588446018.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite757360818588446018.adam/.part-00000-1a3c85c9-7fa6-49c8-8339-6591f2f40af5-c000.snappy.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite757360818588446018.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite757360818588446018.adam/part-00000-1a3c85c9-7fa6-49c8-8339-6591f2f40af5-c000.snappy.parquet /tmp/adamTestMvnpjenoa0/TempSuite757360818588446018.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite7687617383536916886.adam /tmp/adamTestMvnpjenoa0/TempSuite7687617383536916886.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite7687617383536916886.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite7687617383536916886.adam/._samples.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite7687617383536916886.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite7687617383536916886.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite7687617383536916886.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite7687617383536916886.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite7687617383536916886.adam/_common_metadata /tmp/adamTestMvnpjenoa0/TempSuite7687617383536916886.adam/._header.crc /tmp/adamTestMvnpjenoa0/TempSuite7687617383536916886.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite7687617383536916886.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite7687617383536916886.adam/_samples.avro /tmp/adamTestMvnpjenoa0/TempSuite7687617383536916886.adam/_metadata /tmp/adamTestMvnpjenoa0/TempSuite7687617383536916886.adam/_header /tmp/adamTestMvnpjenoa0/TempSuite4743729739127654238 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite3490034250567771633.bed /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite2624089682562548137.interval_list /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite2624089682562548137.interval_list/_SUCCESS /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite2624089682562548137.interval_list/part-00001 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite2624089682562548137.interval_list/.part-00003.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite2624089682562548137.interval_list/part-00000 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite2624089682562548137.interval_list/part-00003 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite2624089682562548137.interval_list/.part-00000.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite2624089682562548137.interval_list/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite2624089682562548137.interval_list/part-00002 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite2624089682562548137.interval_list/.part-00002.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite2624089682562548137.interval_list/.part-00001.crc /tmp/adamTestMvnpjenoa0/TempSuite4248693576641947554 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite3738128330690294641.gtf /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite3738128330690294641.gtf/_SUCCESS /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite3738128330690294641.gtf/part-00001 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite3738128330690294641.gtf/.part-00003.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite3738128330690294641.gtf/part-00000 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite3738128330690294641.gtf/part-00003 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite3738128330690294641.gtf/.part-00000.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite3738128330690294641.gtf/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite3738128330690294641.gtf/part-00002 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite3738128330690294641.gtf/.part-00002.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite3738128330690294641.gtf/.part-00001.crc /tmp/adamTestMvnpjenoa0/TempSuite298446164686410486.adam /tmp/adamTestMvnpjenoa0/TempSuite298446164686410486.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite298446164686410486.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite298446164686410486.adam/._samples.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite298446164686410486.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite298446164686410486.adam/.part-r-00003.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite298446164686410486.adam/part-r-00001.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite298446164686410486.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite298446164686410486.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite298446164686410486.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite298446164686410486.adam/.part-r-00001.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite298446164686410486.adam/part-r-00002.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite298446164686410486.adam/.part-r-00002.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite298446164686410486.adam/_common_metadata /tmp/adamTestMvnpjenoa0/TempSuite298446164686410486.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite298446164686410486.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite298446164686410486.adam/_samples.avro /tmp/adamTestMvnpjenoa0/TempSuite298446164686410486.adam/_metadata /tmp/adamTestMvnpjenoa0/TempSuite298446164686410486.adam/part-r-00003.gz.parquet /tmp/adamTestMvnpjenoa0/unordered.sam8585527819730520660.sam /tmp/adamTestMvnpjenoa0/random.vcf1410091108010900093.vcf /tmp/adamTestMvnpjenoa0/TempSuite5146695925444329026 /tmp/adamTestMvnpjenoa0/6886877276094723843 /tmp/adamTestMvnpjenoa0/6886877276094723843/genotypes.lex.adam /tmp/adamTestMvnpjenoa0/6886877276094723843/genotypes.lex.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/6886877276094723843/genotypes.lex.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/6886877276094723843/genotypes.lex.adam/._samples.avro.crc /tmp/adamTestMvnpjenoa0/6886877276094723843/genotypes.lex.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/6886877276094723843/genotypes.lex.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/6886877276094723843/genotypes.lex.adam/_references.avro /tmp/adamTestMvnpjenoa0/6886877276094723843/genotypes.lex.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/6886877276094723843/genotypes.lex.adam/_common_metadata /tmp/adamTestMvnpjenoa0/6886877276094723843/genotypes.lex.adam/._header.crc /tmp/adamTestMvnpjenoa0/6886877276094723843/genotypes.lex.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/6886877276094723843/genotypes.lex.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/6886877276094723843/genotypes.lex.adam/_samples.avro /tmp/adamTestMvnpjenoa0/6886877276094723843/genotypes.lex.adam/_metadata /tmp/adamTestMvnpjenoa0/6886877276094723843/genotypes.lex.adam/_header /tmp/adamTestMvnpjenoa0/2743084094189656142 /tmp/adamTestMvnpjenoa0/2743084094189656142/genotypes.adam /tmp/adamTestMvnpjenoa0/2743084094189656142/genotypes.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/2743084094189656142/genotypes.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/2743084094189656142/genotypes.adam/._samples.avro.crc /tmp/adamTestMvnpjenoa0/2743084094189656142/genotypes.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/2743084094189656142/genotypes.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/2743084094189656142/genotypes.adam/_references.avro /tmp/adamTestMvnpjenoa0/2743084094189656142/genotypes.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/2743084094189656142/genotypes.adam/_common_metadata /tmp/adamTestMvnpjenoa0/2743084094189656142/genotypes.adam/._header.crc /tmp/adamTestMvnpjenoa0/2743084094189656142/genotypes.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/2743084094189656142/genotypes.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/2743084094189656142/genotypes.adam/_samples.avro /tmp/adamTestMvnpjenoa0/2743084094189656142/genotypes.adam/_metadata /tmp/adamTestMvnpjenoa0/2743084094189656142/genotypes.adam/_header /tmp/adamTestMvnpjenoa0/TempSuite458648407072348352.adam /tmp/adamTestMvnpjenoa0/TempSuite458648407072348352.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite458648407072348352.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite458648407072348352.adam/part-00000-d8584035-4c0f-42c2-871f-d8ddca39c23a-c000.snappy.parquet /tmp/adamTestMvnpjenoa0/TempSuite458648407072348352.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite458648407072348352.adam/.part-00000-d8584035-4c0f-42c2-871f-d8ddca39c23a-c000.snappy.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite458648407072348352.adam/._header.crc /tmp/adamTestMvnpjenoa0/TempSuite458648407072348352.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite458648407072348352.adam/_header /tmp/adamTestMvnpjenoa0/TempSuite6833882510255996642.fa /tmp/adamTestMvnpjenoa0/TempSuite6833882510255996642.fa/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite6833882510255996642.fa/part-00000 /tmp/adamTestMvnpjenoa0/TempSuite6833882510255996642.fa/.part-00000.crc /tmp/adamTestMvnpjenoa0/TempSuite6833882510255996642.fa/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite7794953380181836051.adam /tmp/adamTestMvnpjenoa0/TempSuite7794953380181836051.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite7794953380181836051.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite7794953380181836051.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite7794953380181836051.adam/_readGroups.avro /tmp/adamTestMvnpjenoa0/TempSuite7794953380181836051.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite7794953380181836051.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite7794953380181836051.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite7794953380181836051.adam/._processingSteps.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite7794953380181836051.adam/_common_metadata /tmp/adamTestMvnpjenoa0/TempSuite7794953380181836051.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite7794953380181836051.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite7794953380181836051.adam/._readGroups.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite7794953380181836051.adam/_metadata /tmp/adamTestMvnpjenoa0/TempSuite7794953380181836051.adam/_processingSteps.avro /tmp/adamTestMvnpjenoa0/TempSuite3087847937306202517 /tmp/adamTestMvnpjenoa0/7362080193179349827 /tmp/adamTestMvnpjenoa0/7362080193179349827/variants.adam /tmp/adamTestMvnpjenoa0/7362080193179349827/variants.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/7362080193179349827/variants.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/7362080193179349827/variants.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/7362080193179349827/variants.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/7362080193179349827/variants.adam/_references.avro /tmp/adamTestMvnpjenoa0/7362080193179349827/variants.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/7362080193179349827/variants.adam/_common_metadata /tmp/adamTestMvnpjenoa0/7362080193179349827/variants.adam/._header.crc /tmp/adamTestMvnpjenoa0/7362080193179349827/variants.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/7362080193179349827/variants.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/7362080193179349827/variants.adam/_metadata /tmp/adamTestMvnpjenoa0/7362080193179349827/variants.adam/_header /tmp/adamTestMvnpjenoa0/TempSuite2151836679811834185.adam /tmp/adamTestMvnpjenoa0/TempSuite2151836679811834185.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite2151836679811834185.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite2151836679811834185.adam/._samples.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite2151836679811834185.adam/part-r-00004.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite2151836679811834185.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite2151836679811834185.adam/.part-r-00003.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite2151836679811834185.adam/part-r-00001.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite2151836679811834185.adam/.part-r-00004.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite2151836679811834185.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite2151836679811834185.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite2151836679811834185.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite2151836679811834185.adam/.part-r-00001.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite2151836679811834185.adam/part-r-00002.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite2151836679811834185.adam/.part-r-00002.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite2151836679811834185.adam/_common_metadata /tmp/adamTestMvnpjenoa0/TempSuite2151836679811834185.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite2151836679811834185.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite2151836679811834185.adam/_samples.avro /tmp/adamTestMvnpjenoa0/TempSuite2151836679811834185.adam/_metadata /tmp/adamTestMvnpjenoa0/TempSuite2151836679811834185.adam/part-r-00003.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite7361981565445851203.adam /tmp/adamTestMvnpjenoa0/TempSuite7361981565445851203.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite7361981565445851203.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite7361981565445851203.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite7361981565445851203.adam/_readGroups.avro /tmp/adamTestMvnpjenoa0/TempSuite7361981565445851203.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite7361981565445851203.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite7361981565445851203.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite7361981565445851203.adam/._processingSteps.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite7361981565445851203.adam/_common_metadata /tmp/adamTestMvnpjenoa0/TempSuite7361981565445851203.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite7361981565445851203.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite7361981565445851203.adam/._readGroups.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite7361981565445851203.adam/_metadata /tmp/adamTestMvnpjenoa0/TempSuite7361981565445851203.adam/_processingSteps.avro /tmp/adamTestMvnpjenoa0/TempSuite1939925426745959041 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite1579150911363265296.narrowPeak /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite1579150911363265296.narrowPeak/_SUCCESS /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite1579150911363265296.narrowPeak/part-00001 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite1579150911363265296.narrowPeak/.part-00003.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite1579150911363265296.narrowPeak/part-00000 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite1579150911363265296.narrowPeak/part-00003 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite1579150911363265296.narrowPeak/.part-00000.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite1579150911363265296.narrowPeak/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite1579150911363265296.narrowPeak/part-00002 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite1579150911363265296.narrowPeak/.part-00002.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite1579150911363265296.narrowPeak/.part-00001.crc /tmp/adamTestMvnpjenoa0/TempSuite6982542365057987604 /tmp/adamTestMvnpjenoa0/TempSuite9133417666675141967.bed /tmp/adamTestMvnpjenoa0/TempSuite9133417666675141967.bed/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite9133417666675141967.bed/part-00000 /tmp/adamTestMvnpjenoa0/TempSuite9133417666675141967.bed/.part-00000.crc /tmp/adamTestMvnpjenoa0/TempSuite9133417666675141967.bed/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite277214127024262540.bed /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite277214127024262540.bed/_SUCCESS /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite277214127024262540.bed/part-00001 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite277214127024262540.bed/.part-00003.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite277214127024262540.bed/part-00000 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite277214127024262540.bed/part-00003 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite277214127024262540.bed/.part-00000.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite277214127024262540.bed/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite277214127024262540.bed/part-00002 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite277214127024262540.bed/.part-00002.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite277214127024262540.bed/.part-00001.crc /tmp/adamTestMvnpjenoa0/TempSuite5755290255175389970.adam /tmp/adamTestMvnpjenoa0/TempSuite5755290255175389970.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite5755290255175389970.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite5755290255175389970.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite5755290255175389970.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite5755290255175389970.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite5755290255175389970.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite5755290255175389970.adam/_common_metadata /tmp/adamTestMvnpjenoa0/TempSuite5755290255175389970.adam/._header.crc /tmp/adamTestMvnpjenoa0/TempSuite5755290255175389970.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite5755290255175389970.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite5755290255175389970.adam/_metadata /tmp/adamTestMvnpjenoa0/TempSuite5755290255175389970.adam/_header /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite2977519491974886712.gtf /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite2977519491974886712.gtf/_SUCCESS /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite2977519491974886712.gtf/part-00001 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite2977519491974886712.gtf/.part-00003.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite2977519491974886712.gtf/part-00000 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite2977519491974886712.gtf/part-00003 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite2977519491974886712.gtf/.part-00000.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite2977519491974886712.gtf/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite2977519491974886712.gtf/part-00002 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite2977519491974886712.gtf/.part-00002.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite2977519491974886712.gtf/.part-00001.crc /tmp/adamTestMvnpjenoa0/1557939942107-0 /tmp/adamTestMvnpjenoa0/1557939942107-0/test.fa /tmp/adamTestMvnpjenoa0/1557939942107-0/test.fa/_SUCCESS /tmp/adamTestMvnpjenoa0/1557939942107-0/test.fa/part-00000 /tmp/adamTestMvnpjenoa0/1557939942107-0/test.fa/.part-00000.crc /tmp/adamTestMvnpjenoa0/1557939942107-0/test.fa/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite749629422878677306.gff3 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite749629422878677306.gff3/_SUCCESS /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite749629422878677306.gff3/part-00001 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite749629422878677306.gff3/.part-00003.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite749629422878677306.gff3/part-00000 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite749629422878677306.gff3/part-00003 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite749629422878677306.gff3/.part-00000.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite749629422878677306.gff3/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite749629422878677306.gff3/part-00002 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite749629422878677306.gff3/.part-00002.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite749629422878677306.gff3/.part-00001.crc /tmp/adamTestMvnpjenoa0/TempSuite8654128942180173260.adam /tmp/adamTestMvnpjenoa0/TempSuite8654128942180173260.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite8654128942180173260.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite8654128942180173260.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite8654128942180173260.adam/.part-r-00003.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite8654128942180173260.adam/part-r-00001.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite8654128942180173260.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite8654128942180173260.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite8654128942180173260.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite8654128942180173260.adam/.part-r-00001.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite8654128942180173260.adam/part-r-00002.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite8654128942180173260.adam/.part-r-00002.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite8654128942180173260.adam/_common_metadata /tmp/adamTestMvnpjenoa0/TempSuite8654128942180173260.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite8654128942180173260.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite8654128942180173260.adam/_metadata /tmp/adamTestMvnpjenoa0/TempSuite8654128942180173260.adam/part-r-00003.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite2718680204873500417.adam /tmp/adamTestMvnpjenoa0/TempSuite2718680204873500417.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite2718680204873500417.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite2718680204873500417.adam/.part-00000-5608894f-f034-47dc-acb4-aa058bc1e2da-c000.snappy.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite2718680204873500417.adam/part-00000-5608894f-f034-47dc-acb4-aa058bc1e2da-c000.snappy.parquet /tmp/adamTestMvnpjenoa0/TempSuite2718680204873500417.adam/._samples.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite2718680204873500417.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite2718680204873500417.adam/.part-00005-5608894f-f034-47dc-acb4-aa058bc1e2da-c000.snappy.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite2718680204873500417.adam/.part-00003-5608894f-f034-47dc-acb4-aa058bc1e2da-c000.snappy.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite2718680204873500417.adam/part-00003-5608894f-f034-47dc-acb4-aa058bc1e2da-c000.snappy.parquet /tmp/adamTestMvnpjenoa0/TempSuite2718680204873500417.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite2718680204873500417.adam/part-00005-5608894f-f034-47dc-acb4-aa058bc1e2da-c000.snappy.parquet /tmp/adamTestMvnpjenoa0/TempSuite2718680204873500417.adam/_samples.avro /tmp/adamTestMvnpjenoa0/TempSuite4003557705590353492 /tmp/adamTestMvnpjenoa0/TempSuite8681581463592444244 /tmp/adamTestMvnpjenoa0/TempSuite8901349017941121010 /tmp/adamTestMvnpjenoa0/TempSuite5803476424088697544 /tmp/adamTestMvnpjenoa0/gencode.v7.annotation.trunc10.bed7381195683803461527.v7.annotation.trunc10.bed /tmp/adamTestMvnpjenoa0/TempSuite6765689595171322898.sam /tmp/adamTestMvnpjenoa0/TempSuite6765689595171322898.sam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite6765689595171322898.sam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite6765689595171322898.sam/.part-r-00000.sam.crc /tmp/adamTestMvnpjenoa0/TempSuite6765689595171322898.sam/part-r-00000.sam /tmp/adamTestMvnpjenoa0/unordered.sam4797327559086489905.sam /tmp/adamTestMvnpjenoa0/125134546734241861 /tmp/adamTestMvnpjenoa0/125134546734241861/unordered.sam /tmp/adamTestMvnpjenoa0/125134546734241861/.unordered.sam.crc /tmp/adamTestMvnpjenoa0/TempSuite477488884395722689 /tmp/adamTestMvnpjenoa0/TempSuite5636692660280034715.adam /tmp/adamTestMvnpjenoa0/TempSuite5636692660280034715.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite5636692660280034715.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite5636692660280034715.adam/_readGroups.avro /tmp/adamTestMvnpjenoa0/TempSuite5636692660280034715.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite5636692660280034715.adam/part-00000-dff6ea58-db85-4ae4-8ac4-1a49a6e9ab4a-c000.snappy.parquet /tmp/adamTestMvnpjenoa0/TempSuite5636692660280034715.adam/._processingSteps.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite5636692660280034715.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite5636692660280034715.adam/.part-00000-dff6ea58-db85-4ae4-8ac4-1a49a6e9ab4a-c000.snappy.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite5636692660280034715.adam/._readGroups.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite5636692660280034715.adam/_processingSteps.avro /tmp/adamTestMvnpjenoa0/TempSuite6982542365057987604.adam /tmp/adamTestMvnpjenoa0/TempSuite6982542365057987604.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite6982542365057987604.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite6982542365057987604.adam/.part-00000-4bd0d987-5f01-4e75-8be2-cd06d9b692c6-c000.snappy.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite6982542365057987604.adam/_readGroups.avro /tmp/adamTestMvnpjenoa0/TempSuite6982542365057987604.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite6982542365057987604.adam/part-00000-4bd0d987-5f01-4e75-8be2-cd06d9b692c6-c000.snappy.parquet /tmp/adamTestMvnpjenoa0/TempSuite6982542365057987604.adam/._processingSteps.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite6982542365057987604.adam/part-00001-4bd0d987-5f01-4e75-8be2-cd06d9b692c6-c000.snappy.parquet /tmp/adamTestMvnpjenoa0/TempSuite6982542365057987604.adam/.part-00002-4bd0d987-5f01-4e75-8be2-cd06d9b692c6-c000.snappy.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite6982542365057987604.adam/.part-00001-4bd0d987-5f01-4e75-8be2-cd06d9b692c6-c000.snappy.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite6982542365057987604.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite6982542365057987604.adam/._readGroups.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite6982542365057987604.adam/part-00002-4bd0d987-5f01-4e75-8be2-cd06d9b692c6-c000.snappy.parquet /tmp/adamTestMvnpjenoa0/TempSuite6982542365057987604.adam/_processingSteps.avro /tmp/adamTestMvnpjenoa0/TempSuite2511598494164752768 /tmp/adamTestMvnpjenoa0/3873028271278329613 /tmp/adamTestMvnpjenoa0/3873028271278329613/binned.adam /tmp/adamTestMvnpjenoa0/3873028271278329613/binned.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/3873028271278329613/binned.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/3873028271278329613/binned.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/3873028271278329613/binned.adam/_readGroups.avro /tmp/adamTestMvnpjenoa0/3873028271278329613/binned.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/3873028271278329613/binned.adam/_references.avro /tmp/adamTestMvnpjenoa0/3873028271278329613/binned.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/3873028271278329613/binned.adam/._processingSteps.avro.crc /tmp/adamTestMvnpjenoa0/3873028271278329613/binned.adam/_common_metadata /tmp/adamTestMvnpjenoa0/3873028271278329613/binned.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/3873028271278329613/binned.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/3873028271278329613/binned.adam/._readGroups.avro.crc /tmp/adamTestMvnpjenoa0/3873028271278329613/binned.adam/_metadata /tmp/adamTestMvnpjenoa0/3873028271278329613/binned.adam/_processingSteps.avro /tmp/adamTestMvnpjenoa0/TempSuite976231192151270081_2.fq /tmp/adamTestMvnpjenoa0/TempSuite976231192151270081_2.fq/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite976231192151270081_2.fq/part-00000 /tmp/adamTestMvnpjenoa0/TempSuite976231192151270081_2.fq/.part-00000.crc /tmp/adamTestMvnpjenoa0/TempSuite976231192151270081_2.fq/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/bqsr1.sam311077498221612659.sam /tmp/adamTestMvnpjenoa0/TempSuite1816874181471195783.adam /tmp/adamTestMvnpjenoa0/TempSuite1816874181471195783.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite1816874181471195783.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite1816874181471195783.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite1816874181471195783.adam/.part-r-00003.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite1816874181471195783.adam/part-r-00001.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite1816874181471195783.adam/_readGroups.avro /tmp/adamTestMvnpjenoa0/TempSuite1816874181471195783.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite1816874181471195783.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite1816874181471195783.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite1816874181471195783.adam/.part-r-00001.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite1816874181471195783.adam/part-r-00002.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite1816874181471195783.adam/._processingSteps.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite1816874181471195783.adam/.part-r-00002.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite1816874181471195783.adam/_common_metadata /tmp/adamTestMvnpjenoa0/TempSuite1816874181471195783.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite1816874181471195783.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite1816874181471195783.adam/._readGroups.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite1816874181471195783.adam/_metadata /tmp/adamTestMvnpjenoa0/TempSuite1816874181471195783.adam/part-r-00003.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite1816874181471195783.adam/_processingSteps.avro /tmp/adamTestMvnpjenoa0/unordered.sam6031907505248746238.sam /tmp/adamTestMvnpjenoa0/TempSuite6036072080182044767 /tmp/adamTestMvnpjenoa0/TempSuite3182899383636188767 /tmp/adamTestMvnpjenoa0/TempSuite5810990179749433916 /tmp/adamTestMvnpjenoa0/4501651052748875147 /tmp/adamTestMvnpjenoa0/4501651052748875147/unordered.sam /tmp/adamTestMvnpjenoa0/4501651052748875147/.unordered.sam.crc /tmp/adamTestMvnpjenoa0/3634930680698397674 /tmp/adamTestMvnpjenoa0/3634930680698397674/ctg.adam /tmp/adamTestMvnpjenoa0/3634930680698397674/ctg.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/3634930680698397674/ctg.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/3634930680698397674/ctg.adam/_references.avro /tmp/adamTestMvnpjenoa0/3634930680698397674/ctg.adam/.part-00000-e08b5b89-6852-4c64-b708-17cc003c15c0-c000.snappy.parquet.crc /tmp/adamTestMvnpjenoa0/3634930680698397674/ctg.adam/part-00000-e08b5b89-6852-4c64-b708-17cc003c15c0-c000.snappy.parquet /tmp/adamTestMvnpjenoa0/3634930680698397674/ctg.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite7368695202327364990.fq /tmp/adamTestMvnpjenoa0/8800280216725752187 /tmp/adamTestMvnpjenoa0/8800280216725752187/genotypes.nested-annotations.adam /tmp/adamTestMvnpjenoa0/8800280216725752187/genotypes.nested-annotations.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/8800280216725752187/genotypes.nested-annotations.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/8800280216725752187/genotypes.nested-annotations.adam/._samples.avro.crc /tmp/adamTestMvnpjenoa0/8800280216725752187/genotypes.nested-annotations.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/8800280216725752187/genotypes.nested-annotations.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/8800280216725752187/genotypes.nested-annotations.adam/_references.avro /tmp/adamTestMvnpjenoa0/8800280216725752187/genotypes.nested-annotations.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/8800280216725752187/genotypes.nested-annotations.adam/_common_metadata /tmp/adamTestMvnpjenoa0/8800280216725752187/genotypes.nested-annotations.adam/._header.crc /tmp/adamTestMvnpjenoa0/8800280216725752187/genotypes.nested-annotations.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/8800280216725752187/genotypes.nested-annotations.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/8800280216725752187/genotypes.nested-annotations.adam/_samples.avro /tmp/adamTestMvnpjenoa0/8800280216725752187/genotypes.nested-annotations.adam/_metadata /tmp/adamTestMvnpjenoa0/8800280216725752187/genotypes.nested-annotations.adam/_header /tmp/adamTestMvnpjenoa0/TempSuite6337087559168697621 /tmp/adamTestMvnpjenoa0/unsorted.sam5161979003755449883.sam /tmp/adamTestMvnpjenoa0/small.sam8707308900148981815.sam /tmp/adamTestMvnpjenoa0/1937429235913914858 /tmp/adamTestMvnpjenoa0/1937429235913914858/artificial.cram /tmp/adamTestMvnpjenoa0/1937429235913914858/artificial.cram/_SUCCESS /tmp/adamTestMvnpjenoa0/1937429235913914858/artificial.cram/part-r-00000.cram /tmp/adamTestMvnpjenoa0/1937429235913914858/artificial.cram/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/1937429235913914858/artificial.cram/.part-r-00000.cram.crc /tmp/adamTestMvnpjenoa0/ordered.sam1904573720616233573.sam /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite4081021514912266843 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite1491887521662331166.gff3 /tmp/adamTestMvnpjenoa0/.FeatureDatasetFunctionsSuite9015503689203818919.bed.crc /tmp/adamTestMvnpjenoa0/1163747818264402171 /tmp/adamTestMvnpjenoa0/1163747818264402171/genotypes.adam /tmp/adamTestMvnpjenoa0/1163747818264402171/genotypes.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/1163747818264402171/genotypes.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/1163747818264402171/genotypes.adam/._samples.avro.crc /tmp/adamTestMvnpjenoa0/1163747818264402171/genotypes.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/1163747818264402171/genotypes.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/1163747818264402171/genotypes.adam/_references.avro /tmp/adamTestMvnpjenoa0/1163747818264402171/genotypes.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/1163747818264402171/genotypes.adam/_common_metadata /tmp/adamTestMvnpjenoa0/1163747818264402171/genotypes.adam/._header.crc /tmp/adamTestMvnpjenoa0/1163747818264402171/genotypes.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/1163747818264402171/genotypes.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/1163747818264402171/genotypes.adam/_samples.avro /tmp/adamTestMvnpjenoa0/1163747818264402171/genotypes.adam/_metadata /tmp/adamTestMvnpjenoa0/1163747818264402171/genotypes.adam/_header /tmp/adamTestMvnpjenoa0/TempSuite409310598779627053 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite2449717568714814113.narrowPeak /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite2449717568714814113.narrowPeak/_SUCCESS /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite2449717568714814113.narrowPeak/part-00001 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite2449717568714814113.narrowPeak/.part-00003.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite2449717568714814113.narrowPeak/part-00000 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite2449717568714814113.narrowPeak/part-00003 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite2449717568714814113.narrowPeak/.part-00000.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite2449717568714814113.narrowPeak/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite2449717568714814113.narrowPeak/part-00002 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite2449717568714814113.narrowPeak/.part-00002.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite2449717568714814113.narrowPeak/.part-00001.crc /tmp/adamTestMvnpjenoa0/TempSuite7785230418672949898.adam /tmp/adamTestMvnpjenoa0/TempSuite7785230418672949898.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite7785230418672949898.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite7785230418672949898.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite7785230418672949898.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite7785230418672949898.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite7785230418672949898.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite7785230418672949898.adam/_common_metadata /tmp/adamTestMvnpjenoa0/TempSuite7785230418672949898.adam/._header.crc /tmp/adamTestMvnpjenoa0/TempSuite7785230418672949898.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite7785230418672949898.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite7785230418672949898.adam/_metadata /tmp/adamTestMvnpjenoa0/TempSuite7785230418672949898.adam/_header /tmp/adamTestMvnpjenoa0/TempSuite3297386314051980773 /tmp/adamTestMvnpjenoa0/TempSuite9032794718835850390_1.fq /tmp/adamTestMvnpjenoa0/TempSuite9032794718835850390_1.fq/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite9032794718835850390_1.fq/part-00000 /tmp/adamTestMvnpjenoa0/TempSuite9032794718835850390_1.fq/.part-00000.crc /tmp/adamTestMvnpjenoa0/TempSuite9032794718835850390_1.fq/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite4274291447532204628 /tmp/adamTestMvnpjenoa0/adam-cli.TransformFeaturesSuite6112311238351725464.adam /tmp/adamTestMvnpjenoa0/adam-cli.TransformFeaturesSuite6112311238351725464.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/adam-cli.TransformFeaturesSuite6112311238351725464.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/adam-cli.TransformFeaturesSuite6112311238351725464.adam/._samples.avro.crc /tmp/adamTestMvnpjenoa0/adam-cli.TransformFeaturesSuite6112311238351725464.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/adam-cli.TransformFeaturesSuite6112311238351725464.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/adam-cli.TransformFeaturesSuite6112311238351725464.adam/_references.avro /tmp/adamTestMvnpjenoa0/adam-cli.TransformFeaturesSuite6112311238351725464.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/adam-cli.TransformFeaturesSuite6112311238351725464.adam/_common_metadata /tmp/adamTestMvnpjenoa0/adam-cli.TransformFeaturesSuite6112311238351725464.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/adam-cli.TransformFeaturesSuite6112311238351725464.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/adam-cli.TransformFeaturesSuite6112311238351725464.adam/_samples.avro /tmp/adamTestMvnpjenoa0/adam-cli.TransformFeaturesSuite6112311238351725464.adam/_metadata /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite2815515414849352137.narrowPeak /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite2815515414849352137.narrowPeak/_SUCCESS /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite2815515414849352137.narrowPeak/part-00001 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite2815515414849352137.narrowPeak/.part-00003.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite2815515414849352137.narrowPeak/part-00000 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite2815515414849352137.narrowPeak/part-00003 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite2815515414849352137.narrowPeak/.part-00000.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite2815515414849352137.narrowPeak/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite2815515414849352137.narrowPeak/part-00002 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite2815515414849352137.narrowPeak/.part-00002.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite2815515414849352137.narrowPeak/.part-00001.crc /tmp/adamTestMvnpjenoa0/TempSuite941656443948141376 /tmp/adamTestMvnpjenoa0/TempSuite533243511128917849.adam /tmp/adamTestMvnpjenoa0/TempSuite533243511128917849.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite533243511128917849.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite533243511128917849.adam/part-00000-485da5a8-45cb-46e7-a668-e30dfc8da7d5-c000.snappy.parquet /tmp/adamTestMvnpjenoa0/TempSuite533243511128917849.adam/part-00001-485da5a8-45cb-46e7-a668-e30dfc8da7d5-c000.snappy.parquet /tmp/adamTestMvnpjenoa0/TempSuite533243511128917849.adam/.part-00002-485da5a8-45cb-46e7-a668-e30dfc8da7d5-c000.snappy.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite533243511128917849.adam/.part-00001-485da5a8-45cb-46e7-a668-e30dfc8da7d5-c000.snappy.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite533243511128917849.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite533243511128917849.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite533243511128917849.adam/.part-00000-485da5a8-45cb-46e7-a668-e30dfc8da7d5-c000.snappy.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite533243511128917849.adam/part-00002-485da5a8-45cb-46e7-a668-e30dfc8da7d5-c000.snappy.parquet /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite4605734144246192556 /tmp/adamTestMvnpjenoa0/2801858347048529460 /tmp/adamTestMvnpjenoa0/2801858347048529460/test.fa /tmp/adamTestMvnpjenoa0/2801858347048529460/test.fa/_SUCCESS /tmp/adamTestMvnpjenoa0/2801858347048529460/test.fa/part-00000 /tmp/adamTestMvnpjenoa0/2801858347048529460/test.fa/.part-00000.crc /tmp/adamTestMvnpjenoa0/2801858347048529460/test.fa/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite7710545530433433082.bed /tmp/adamTestMvnpjenoa0/TempSuite7710545530433433082.bed/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite7710545530433433082.bed/part-00000 /tmp/adamTestMvnpjenoa0/TempSuite7710545530433433082.bed/.part-00000.crc /tmp/adamTestMvnpjenoa0/TempSuite7710545530433433082.bed/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite3506079618954841859.adam /tmp/adamTestMvnpjenoa0/TempSuite3506079618954841859.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite3506079618954841859.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite3506079618954841859.adam/._samples.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite3506079618954841859.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite3506079618954841859.adam/._header.crc /tmp/adamTestMvnpjenoa0/TempSuite3506079618954841859.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite3506079618954841859.adam/part-00000-98be82f1-8808-4daf-a9a3-b97b90c31b33-c000.snappy.parquet /tmp/adamTestMvnpjenoa0/TempSuite3506079618954841859.adam/_samples.avro /tmp/adamTestMvnpjenoa0/TempSuite3506079618954841859.adam/.part-00000-98be82f1-8808-4daf-a9a3-b97b90c31b33-c000.snappy.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite3506079618954841859.adam/_header /tmp/adamTestMvnpjenoa0/TempSuite5413678912049287670 /tmp/adamTestMvnpjenoa0/3575951363376454873 /tmp/adamTestMvnpjenoa0/3575951363376454873/.artificial.cram.crc /tmp/adamTestMvnpjenoa0/3575951363376454873/artificial.cram /tmp/adamTestMvnpjenoa0/TempSuite1136416851151774814.bed /tmp/adamTestMvnpjenoa0/TempSuite1136416851151774814.bed/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite1136416851151774814.bed/part-00000 /tmp/adamTestMvnpjenoa0/TempSuite1136416851151774814.bed/.part-00000.crc /tmp/adamTestMvnpjenoa0/TempSuite1136416851151774814.bed/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite4205365562331058664.bed /tmp/adamTestMvnpjenoa0/TempSuite4205365562331058664.bed/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite4205365562331058664.bed/part-00000 /tmp/adamTestMvnpjenoa0/TempSuite4205365562331058664.bed/.part-00000.crc /tmp/adamTestMvnpjenoa0/TempSuite4205365562331058664.bed/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite4103715118168983188.adam /tmp/adamTestMvnpjenoa0/TempSuite4103715118168983188.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite4103715118168983188.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite4103715118168983188.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite4103715118168983188.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite4103715118168983188.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite4103715118168983188.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite4103715118168983188.adam/_common_metadata /tmp/adamTestMvnpjenoa0/TempSuite4103715118168983188.adam/._header.crc /tmp/adamTestMvnpjenoa0/TempSuite4103715118168983188.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite4103715118168983188.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite4103715118168983188.adam/_metadata /tmp/adamTestMvnpjenoa0/TempSuite4103715118168983188.adam/_header /tmp/adamTestMvnpjenoa0/1557939943114-0 /tmp/adamTestMvnpjenoa0/1557939943114-0/test.fa /tmp/adamTestMvnpjenoa0/1557939943114-0/test.fa/_SUCCESS /tmp/adamTestMvnpjenoa0/1557939943114-0/test.fa/part-00000 /tmp/adamTestMvnpjenoa0/1557939943114-0/test.fa/.part-00000.crc /tmp/adamTestMvnpjenoa0/1557939943114-0/test.fa/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/bqsr1.sam1536533420125703832.sam /tmp/adamTestMvnpjenoa0/4394732250219833613 /tmp/adamTestMvnpjenoa0/4394732250219833613/genotypes.adam /tmp/adamTestMvnpjenoa0/4394732250219833613/genotypes.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/4394732250219833613/genotypes.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/4394732250219833613/genotypes.adam/._samples.avro.crc /tmp/adamTestMvnpjenoa0/4394732250219833613/genotypes.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/4394732250219833613/genotypes.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/4394732250219833613/genotypes.adam/_references.avro /tmp/adamTestMvnpjenoa0/4394732250219833613/genotypes.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/4394732250219833613/genotypes.adam/_common_metadata /tmp/adamTestMvnpjenoa0/4394732250219833613/genotypes.adam/._header.crc /tmp/adamTestMvnpjenoa0/4394732250219833613/genotypes.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/4394732250219833613/genotypes.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/4394732250219833613/genotypes.adam/_samples.avro /tmp/adamTestMvnpjenoa0/4394732250219833613/genotypes.adam/_metadata /tmp/adamTestMvnpjenoa0/4394732250219833613/genotypes.adam/_header /tmp/adamTestMvnpjenoa0/TempSuite9092770215249166335.bed /tmp/adamTestMvnpjenoa0/TempSuite9092770215249166335.bed/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite9092770215249166335.bed/part-00000 /tmp/adamTestMvnpjenoa0/TempSuite9092770215249166335.bed/.part-00000.crc /tmp/adamTestMvnpjenoa0/TempSuite9092770215249166335.bed/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite5941898558128187081.bed /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite5941898558128187081.bed/_SUCCESS /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite5941898558128187081.bed/part-00001 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite5941898558128187081.bed/.part-00003.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite5941898558128187081.bed/part-00000 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite5941898558128187081.bed/part-00003 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite5941898558128187081.bed/.part-00000.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite5941898558128187081.bed/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite5941898558128187081.bed/part-00002 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite5941898558128187081.bed/.part-00002.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite5941898558128187081.bed/.part-00001.crc /tmp/adamTestMvnpjenoa0/random.vcf2055091855952770787.vcf /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite5268671011899402358 /tmp/adamTestMvnpjenoa0/TempSuite2073119608557682301 /tmp/adamTestMvnpjenoa0/TempSuite2151836679811834185 /tmp/adamTestMvnpjenoa0/TempSuite871135829501858286.adam /tmp/adamTestMvnpjenoa0/TempSuite871135829501858286.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite871135829501858286.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite871135829501858286.adam/._samples.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite871135829501858286.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite871135829501858286.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite871135829501858286.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite871135829501858286.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite871135829501858286.adam/_common_metadata /tmp/adamTestMvnpjenoa0/TempSuite871135829501858286.adam/._header.crc /tmp/adamTestMvnpjenoa0/TempSuite871135829501858286.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite871135829501858286.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite871135829501858286.adam/_samples.avro /tmp/adamTestMvnpjenoa0/TempSuite871135829501858286.adam/_metadata /tmp/adamTestMvnpjenoa0/TempSuite871135829501858286.adam/_header /tmp/adamTestMvnpjenoa0/unordered.sam3139405270899529862.sam /tmp/adamTestMvnpjenoa0/TempSuite5744315304893091712 /tmp/adamTestMvnpjenoa0/TempSuite8262798602615562595.adam /tmp/adamTestMvnpjenoa0/TempSuite8262798602615562595.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite8262798602615562595.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite8262798602615562595.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite8262798602615562595.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite8262798602615562595.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite8262798602615562595.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite8262798602615562595.adam/_common_metadata /tmp/adamTestMvnpjenoa0/TempSuite8262798602615562595.adam/._header.crc /tmp/adamTestMvnpjenoa0/TempSuite8262798602615562595.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite8262798602615562595.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite8262798602615562595.adam/_metadata /tmp/adamTestMvnpjenoa0/TempSuite8262798602615562595.adam/_header /tmp/adamTestMvnpjenoa0/TempSuite7357984471275857528 /tmp/adamTestMvnpjenoa0/random.vcf2190263365567315010.vcf /tmp/adamTestMvnpjenoa0/TempSuite346986507046483108.adam /tmp/adamTestMvnpjenoa0/TempSuite346986507046483108.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite346986507046483108.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite346986507046483108.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite346986507046483108.adam/_readGroups.avro /tmp/adamTestMvnpjenoa0/TempSuite346986507046483108.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite346986507046483108.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite346986507046483108.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite346986507046483108.adam/._processingSteps.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite346986507046483108.adam/_common_metadata /tmp/adamTestMvnpjenoa0/TempSuite346986507046483108.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite346986507046483108.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite346986507046483108.adam/._readGroups.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite346986507046483108.adam/_metadata /tmp/adamTestMvnpjenoa0/TempSuite346986507046483108.adam/_processingSteps.avro /tmp/adamTestMvnpjenoa0/TempSuite7362627036234776380 /tmp/adamTestMvnpjenoa0/TempSuite6797992931226841804.adam /tmp/adamTestMvnpjenoa0/TempSuite6797992931226841804.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite6797992931226841804.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite6797992931226841804.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite6797992931226841804.adam/_readGroups.avro /tmp/adamTestMvnpjenoa0/TempSuite6797992931226841804.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite6797992931226841804.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite6797992931226841804.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite6797992931226841804.adam/._processingSteps.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite6797992931226841804.adam/_common_metadata /tmp/adamTestMvnpjenoa0/TempSuite6797992931226841804.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite6797992931226841804.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite6797992931226841804.adam/._readGroups.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite6797992931226841804.adam/_metadata /tmp/adamTestMvnpjenoa0/TempSuite6797992931226841804.adam/_processingSteps.avro /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite7979139564226981697 /tmp/adamTestMvnpjenoa0/8536582828456124018 /tmp/adamTestMvnpjenoa0/8536582828456124018/small.vcf.bgz /tmp/adamTestMvnpjenoa0/8536582828456124018/.small.vcf.bgz.crc /tmp/adamTestMvnpjenoa0/TempSuite1939925426745959041.adam /tmp/adamTestMvnpjenoa0/TempSuite1939925426745959041.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite1939925426745959041.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite1939925426745959041.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite1939925426745959041.adam/_readGroups.avro /tmp/adamTestMvnpjenoa0/TempSuite1939925426745959041.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite1939925426745959041.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite1939925426745959041.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite1939925426745959041.adam/._processingSteps.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite1939925426745959041.adam/_common_metadata /tmp/adamTestMvnpjenoa0/TempSuite1939925426745959041.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite1939925426745959041.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite1939925426745959041.adam/._readGroups.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite1939925426745959041.adam/_metadata /tmp/adamTestMvnpjenoa0/TempSuite1939925426745959041.adam/_processingSteps.avro /tmp/adamTestMvnpjenoa0/TempSuite3567792921892032226 /tmp/adamTestMvnpjenoa0/TempSuite3923037089729063325.adam /tmp/adamTestMvnpjenoa0/TempSuite3923037089729063325.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite3923037089729063325.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite3923037089729063325.adam/._samples.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite3923037089729063325.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite3923037089729063325.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite3923037089729063325.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite3923037089729063325.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite3923037089729063325.adam/_common_metadata /tmp/adamTestMvnpjenoa0/TempSuite3923037089729063325.adam/._header.crc /tmp/adamTestMvnpjenoa0/TempSuite3923037089729063325.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite3923037089729063325.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite3923037089729063325.adam/_samples.avro /tmp/adamTestMvnpjenoa0/TempSuite3923037089729063325.adam/_metadata /tmp/adamTestMvnpjenoa0/TempSuite3923037089729063325.adam/_header /tmp/adamTestMvnpjenoa0/TempSuite4299727146294675061 /tmp/adamTestMvnpjenoa0/TempSuite6713588017199396936.adam /tmp/adamTestMvnpjenoa0/TempSuite6713588017199396936.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite6713588017199396936.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite6713588017199396936.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite6713588017199396936.adam/_readGroups.avro /tmp/adamTestMvnpjenoa0/TempSuite6713588017199396936.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite6713588017199396936.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite6713588017199396936.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite6713588017199396936.adam/._processingSteps.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite6713588017199396936.adam/_common_metadata /tmp/adamTestMvnpjenoa0/TempSuite6713588017199396936.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite6713588017199396936.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite6713588017199396936.adam/._readGroups.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite6713588017199396936.adam/_metadata /tmp/adamTestMvnpjenoa0/TempSuite6713588017199396936.adam/_processingSteps.avro /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite4126011776911139231 /tmp/adamTestMvnpjenoa0/TempSuite4205365562331058664 /tmp/adamTestMvnpjenoa0/noqual5486261296273039930 /tmp/adamTestMvnpjenoa0/noqual5486261296273039930/noqualA.sam /tmp/adamTestMvnpjenoa0/noqual5486261296273039930/noqualA.sam/_SUCCESS /tmp/adamTestMvnpjenoa0/noqual5486261296273039930/noqualA.sam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/noqual5486261296273039930/noqualA.sam/.part-r-00000.sam.crc /tmp/adamTestMvnpjenoa0/noqual5486261296273039930/noqualA.sam/part-r-00000.sam /tmp/adamTestMvnpjenoa0/noqual5486261296273039930/noqualB.fastq /tmp/adamTestMvnpjenoa0/noqual5486261296273039930/noqualB.fastq/_SUCCESS /tmp/adamTestMvnpjenoa0/noqual5486261296273039930/noqualB.fastq/part-00000 /tmp/adamTestMvnpjenoa0/noqual5486261296273039930/noqualB.fastq/.part-00000.crc /tmp/adamTestMvnpjenoa0/noqual5486261296273039930/noqualB.fastq/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite545004467142402362.bed /tmp/adamTestMvnpjenoa0/TempSuite545004467142402362.bed/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite545004467142402362.bed/part-00000 /tmp/adamTestMvnpjenoa0/TempSuite545004467142402362.bed/.part-00000.crc /tmp/adamTestMvnpjenoa0/TempSuite545004467142402362.bed/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/4949771716965102650 /tmp/adamTestMvnpjenoa0/4949771716965102650/ctg.adam /tmp/adamTestMvnpjenoa0/4949771716965102650/ctg.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/4949771716965102650/ctg.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/4949771716965102650/ctg.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/4949771716965102650/ctg.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/4949771716965102650/ctg.adam/_references.avro /tmp/adamTestMvnpjenoa0/4949771716965102650/ctg.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/4949771716965102650/ctg.adam/_common_metadata /tmp/adamTestMvnpjenoa0/4949771716965102650/ctg.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/4949771716965102650/ctg.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/4949771716965102650/ctg.adam/_metadata /tmp/adamTestMvnpjenoa0/TempSuite5217560609831811643 /tmp/adamTestMvnpjenoa0/TempSuite7413174118720940431 /tmp/adamTestMvnpjenoa0/.FeatureDatasetFunctionsSuite4627558136253177920.bed.crc /tmp/adamTestMvnpjenoa0/TempSuite7007716153721705864.adam /tmp/adamTestMvnpjenoa0/TempSuite7007716153721705864.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite7007716153721705864.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite7007716153721705864.adam/_readGroups.avro /tmp/adamTestMvnpjenoa0/TempSuite7007716153721705864.adam/.part-00001-ab341db4-1ba4-4ded-806f-fd152aa7ec39-c000.snappy.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite7007716153721705864.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite7007716153721705864.adam/.part-00000-ab341db4-1ba4-4ded-806f-fd152aa7ec39-c000.snappy.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite7007716153721705864.adam/.part-00002-ab341db4-1ba4-4ded-806f-fd152aa7ec39-c000.snappy.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite7007716153721705864.adam/._processingSteps.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite7007716153721705864.adam/part-00000-ab341db4-1ba4-4ded-806f-fd152aa7ec39-c000.snappy.parquet /tmp/adamTestMvnpjenoa0/TempSuite7007716153721705864.adam/part-00002-ab341db4-1ba4-4ded-806f-fd152aa7ec39-c000.snappy.parquet /tmp/adamTestMvnpjenoa0/TempSuite7007716153721705864.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite7007716153721705864.adam/._readGroups.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite7007716153721705864.adam/_processingSteps.avro /tmp/adamTestMvnpjenoa0/TempSuite7007716153721705864.adam/part-00001-ab341db4-1ba4-4ded-806f-fd152aa7ec39-c000.snappy.parquet /tmp/adamTestMvnpjenoa0/TempSuite7472332666443096298 /tmp/adamTestMvnpjenoa0/TempSuite477488884395722689.adam /tmp/adamTestMvnpjenoa0/TempSuite477488884395722689.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite477488884395722689.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite477488884395722689.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite477488884395722689.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite477488884395722689.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite477488884395722689.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite477488884395722689.adam/_common_metadata /tmp/adamTestMvnpjenoa0/TempSuite477488884395722689.adam/._header.crc /tmp/adamTestMvnpjenoa0/TempSuite477488884395722689.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite477488884395722689.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite477488884395722689.adam/_metadata /tmp/adamTestMvnpjenoa0/TempSuite477488884395722689.adam/_header /tmp/adamTestMvnpjenoa0/TempSuite8604832664310408528 /tmp/adamTestMvnpjenoa0/TempSuite531641688329952021.adam /tmp/adamTestMvnpjenoa0/TempSuite531641688329952021.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite531641688329952021.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite531641688329952021.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite531641688329952021.adam/.part-r-00003.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite531641688329952021.adam/part-r-00001.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite531641688329952021.adam/_readGroups.avro /tmp/adamTestMvnpjenoa0/TempSuite531641688329952021.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite531641688329952021.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite531641688329952021.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite531641688329952021.adam/.part-r-00001.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite531641688329952021.adam/part-r-00002.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite531641688329952021.adam/._processingSteps.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite531641688329952021.adam/.part-r-00002.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite531641688329952021.adam/_common_metadata /tmp/adamTestMvnpjenoa0/TempSuite531641688329952021.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite531641688329952021.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite531641688329952021.adam/._readGroups.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite531641688329952021.adam/_metadata /tmp/adamTestMvnpjenoa0/TempSuite531641688329952021.adam/part-r-00003.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite531641688329952021.adam/_processingSteps.avro /tmp/adamTestMvnpjenoa0/TempSuite8140406761761149070.adam /tmp/adamTestMvnpjenoa0/TempSuite8140406761761149070.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite8140406761761149070.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite8140406761761149070.adam/._samples.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite8140406761761149070.adam/part-r-00004.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite8140406761761149070.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite8140406761761149070.adam/.part-r-00003.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite8140406761761149070.adam/part-r-00001.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite8140406761761149070.adam/.part-r-00004.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite8140406761761149070.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite8140406761761149070.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite8140406761761149070.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite8140406761761149070.adam/.part-r-00001.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite8140406761761149070.adam/part-r-00002.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite8140406761761149070.adam/.part-r-00002.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite8140406761761149070.adam/_common_metadata /tmp/adamTestMvnpjenoa0/TempSuite8140406761761149070.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite8140406761761149070.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite8140406761761149070.adam/_samples.avro /tmp/adamTestMvnpjenoa0/TempSuite8140406761761149070.adam/_metadata /tmp/adamTestMvnpjenoa0/TempSuite8140406761761149070.adam/part-r-00003.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite6331633504217711598 /tmp/adamTestMvnpjenoa0/javaAC1147751634394524153 /tmp/adamTestMvnpjenoa0/javaAC1147751634394524153/testRdd.feature.adam /tmp/adamTestMvnpjenoa0/javaAC1147751634394524153/testRdd.feature.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/javaAC1147751634394524153/testRdd.feature.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/javaAC1147751634394524153/testRdd.feature.adam/._samples.avro.crc /tmp/adamTestMvnpjenoa0/javaAC1147751634394524153/testRdd.feature.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/javaAC1147751634394524153/testRdd.feature.adam/.part-r-00003.gz.parquet.crc /tmp/adamTestMvnpjenoa0/javaAC1147751634394524153/testRdd.feature.adam/part-r-00001.gz.parquet /tmp/adamTestMvnpjenoa0/javaAC1147751634394524153/testRdd.feature.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/javaAC1147751634394524153/testRdd.feature.adam/_references.avro /tmp/adamTestMvnpjenoa0/javaAC1147751634394524153/testRdd.feature.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/javaAC1147751634394524153/testRdd.feature.adam/.part-r-00001.gz.parquet.crc /tmp/adamTestMvnpjenoa0/javaAC1147751634394524153/testRdd.feature.adam/part-r-00002.gz.parquet /tmp/adamTestMvnpjenoa0/javaAC1147751634394524153/testRdd.feature.adam/.part-r-00002.gz.parquet.crc /tmp/adamTestMvnpjenoa0/javaAC1147751634394524153/testRdd.feature.adam/_common_metadata /tmp/adamTestMvnpjenoa0/javaAC1147751634394524153/testRdd.feature.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/javaAC1147751634394524153/testRdd.feature.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/javaAC1147751634394524153/testRdd.feature.adam/_samples.avro /tmp/adamTestMvnpjenoa0/javaAC1147751634394524153/testRdd.feature.adam/_metadata /tmp/adamTestMvnpjenoa0/javaAC1147751634394524153/testRdd.feature.adam/part-r-00003.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite6564694594282219992.bed /tmp/adamTestMvnpjenoa0/TempSuite6564694594282219992.bed/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite6564694594282219992.bed/part-00000 /tmp/adamTestMvnpjenoa0/TempSuite6564694594282219992.bed/.part-00000.crc /tmp/adamTestMvnpjenoa0/TempSuite6564694594282219992.bed/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite2115713021301080792.bed /tmp/adamTestMvnpjenoa0/TempSuite2115713021301080792.bed/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite2115713021301080792.bed/part-00000 /tmp/adamTestMvnpjenoa0/TempSuite2115713021301080792.bed/.part-00000.crc /tmp/adamTestMvnpjenoa0/TempSuite2115713021301080792.bed/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite4841127484515976577.adam /tmp/adamTestMvnpjenoa0/TempSuite4841127484515976577.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite4841127484515976577.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite4841127484515976577.adam/._samples.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite4841127484515976577.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite4841127484515976577.adam/._header.crc /tmp/adamTestMvnpjenoa0/TempSuite4841127484515976577.adam/part-00000-d2489ef5-a96a-483b-a19c-bfb6cdca4526-c000.snappy.parquet /tmp/adamTestMvnpjenoa0/TempSuite4841127484515976577.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite4841127484515976577.adam/_samples.avro /tmp/adamTestMvnpjenoa0/TempSuite4841127484515976577.adam/.part-00000-d2489ef5-a96a-483b-a19c-bfb6cdca4526-c000.snappy.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite4841127484515976577.adam/_header /tmp/adamTestMvnpjenoa0/TempSuite3926589950473106911 /tmp/adamTestMvnpjenoa0/TempSuite1875973419751237668.bed /tmp/adamTestMvnpjenoa0/TempSuite1875973419751237668.bed/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite1875973419751237668.bed/part-00000 /tmp/adamTestMvnpjenoa0/TempSuite1875973419751237668.bed/.part-00000.crc /tmp/adamTestMvnpjenoa0/TempSuite1875973419751237668.bed/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/ordered.sam7628463934844341241.sam /tmp/adamTestMvnpjenoa0/3220812849624722466 /tmp/adamTestMvnpjenoa0/3220812849624722466/ordered.sam /tmp/adamTestMvnpjenoa0/3220812849624722466/.ordered.sam.crc /tmp/adamTestMvnpjenoa0/TempSuite3509450891392034332.adam /tmp/adamTestMvnpjenoa0/TempSuite3509450891392034332.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite3509450891392034332.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite3509450891392034332.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite3509450891392034332.adam/.part-r-00003.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite3509450891392034332.adam/part-r-00001.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite3509450891392034332.adam/_readGroups.avro /tmp/adamTestMvnpjenoa0/TempSuite3509450891392034332.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite3509450891392034332.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite3509450891392034332.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite3509450891392034332.adam/.part-r-00001.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite3509450891392034332.adam/part-r-00002.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite3509450891392034332.adam/._processingSteps.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite3509450891392034332.adam/.part-r-00002.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite3509450891392034332.adam/_common_metadata /tmp/adamTestMvnpjenoa0/TempSuite3509450891392034332.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite3509450891392034332.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite3509450891392034332.adam/._readGroups.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite3509450891392034332.adam/_metadata /tmp/adamTestMvnpjenoa0/TempSuite3509450891392034332.adam/part-r-00003.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite3509450891392034332.adam/_processingSteps.avro /tmp/adamTestMvnpjenoa0/TempSuite879753549103032827.bed /tmp/adamTestMvnpjenoa0/TempSuite879753549103032827.bed/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite879753549103032827.bed/part-00001 /tmp/adamTestMvnpjenoa0/TempSuite879753549103032827.bed/.part-00003.crc /tmp/adamTestMvnpjenoa0/TempSuite879753549103032827.bed/part-00000 /tmp/adamTestMvnpjenoa0/TempSuite879753549103032827.bed/part-00003 /tmp/adamTestMvnpjenoa0/TempSuite879753549103032827.bed/.part-00000.crc /tmp/adamTestMvnpjenoa0/TempSuite879753549103032827.bed/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite879753549103032827.bed/part-00002 /tmp/adamTestMvnpjenoa0/TempSuite879753549103032827.bed/.part-00002.crc /tmp/adamTestMvnpjenoa0/TempSuite879753549103032827.bed/.part-00001.crc /tmp/adamTestMvnpjenoa0/TempSuite8165895894338538824.adam /tmp/adamTestMvnpjenoa0/TempSuite8165895894338538824.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite8165895894338538824.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite8165895894338538824.adam/._samples.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite8165895894338538824.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite8165895894338538824.adam/._header.crc /tmp/adamTestMvnpjenoa0/TempSuite8165895894338538824.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite8165895894338538824.adam/_samples.avro /tmp/adamTestMvnpjenoa0/TempSuite8165895894338538824.adam/part-00000-2ea29bc3-08f4-4b74-932d-ce5ff754fc32-c000.snappy.parquet /tmp/adamTestMvnpjenoa0/TempSuite8165895894338538824.adam/_header /tmp/adamTestMvnpjenoa0/TempSuite8165895894338538824.adam/.part-00000-2ea29bc3-08f4-4b74-932d-ce5ff754fc32-c000.snappy.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite1033833905333125913 /tmp/adamTestMvnpjenoa0/TempSuite1931648927121224698 /tmp/adamTestMvnpjenoa0/TempSuite6820875629505030184 /tmp/adamTestMvnpjenoa0/7185716133135071496 /tmp/adamTestMvnpjenoa0/7185716133135071496/.tag.sam.crc /tmp/adamTestMvnpjenoa0/7185716133135071496/tag.sam /tmp/adamTestMvnpjenoa0/TempSuite3506079618954841859 /tmp/adamTestMvnpjenoa0/TempSuite7357984471275857528.fq /tmp/adamTestMvnpjenoa0/TempSuite7357984471275857528.fq/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite7357984471275857528.fq/part-00000 /tmp/adamTestMvnpjenoa0/TempSuite7357984471275857528.fq/.part-00000.crc /tmp/adamTestMvnpjenoa0/TempSuite7357984471275857528.fq/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/small.sam3967703123059361902.sam /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite5516135037215301637 /tmp/adamTestMvnpjenoa0/6473678100030263515 /tmp/adamTestMvnpjenoa0/6473678100030263515/test2.fa /tmp/adamTestMvnpjenoa0/6473678100030263515/test2.fa/_SUCCESS /tmp/adamTestMvnpjenoa0/6473678100030263515/test2.fa/part-00000 /tmp/adamTestMvnpjenoa0/6473678100030263515/test2.fa/.part-00000.crc /tmp/adamTestMvnpjenoa0/6473678100030263515/test2.fa/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite3183325159833493769.adam /tmp/adamTestMvnpjenoa0/TempSuite3183325159833493769.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite3183325159833493769.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite3183325159833493769.adam/._samples.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite3183325159833493769.adam/part-00000-e3514513-3cfb-495a-ba63-06a51dd33760-c000.snappy.parquet /tmp/adamTestMvnpjenoa0/TempSuite3183325159833493769.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite3183325159833493769.adam/._header.crc /tmp/adamTestMvnpjenoa0/TempSuite3183325159833493769.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite3183325159833493769.adam/_samples.avro /tmp/adamTestMvnpjenoa0/TempSuite3183325159833493769.adam/_header /tmp/adamTestMvnpjenoa0/TempSuite3183325159833493769.adam/.part-00000-e3514513-3cfb-495a-ba63-06a51dd33760-c000.snappy.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite4078849357887539435 /tmp/adamTestMvnpjenoa0/TempSuite1768097519194226507 /tmp/adamTestMvnpjenoa0/TempSuite9012567376839610898 /tmp/adamTestMvnpjenoa0/TempSuite477657437665447946.adam /tmp/adamTestMvnpjenoa0/TempSuite477657437665447946.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite477657437665447946.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite477657437665447946.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite477657437665447946.adam/_readGroups.avro /tmp/adamTestMvnpjenoa0/TempSuite477657437665447946.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite477657437665447946.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite477657437665447946.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite477657437665447946.adam/._processingSteps.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite477657437665447946.adam/_common_metadata /tmp/adamTestMvnpjenoa0/TempSuite477657437665447946.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite477657437665447946.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite477657437665447946.adam/._readGroups.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite477657437665447946.adam/_metadata /tmp/adamTestMvnpjenoa0/TempSuite477657437665447946.adam/_processingSteps.avro /tmp/adamTestMvnpjenoa0/TempSuite1226413419164272962.adam /tmp/adamTestMvnpjenoa0/TempSuite1226413419164272962.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite1226413419164272962.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite1226413419164272962.adam/._samples.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite1226413419164272962.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite1226413419164272962.adam/part-00000-936f66e5-4a78-46ba-a41d-76776495539a-c000.snappy.parquet /tmp/adamTestMvnpjenoa0/TempSuite1226413419164272962.adam/.part-00001-936f66e5-4a78-46ba-a41d-76776495539a-c000.snappy.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite1226413419164272962.adam/._header.crc /tmp/adamTestMvnpjenoa0/TempSuite1226413419164272962.adam/.part-00000-936f66e5-4a78-46ba-a41d-76776495539a-c000.snappy.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite1226413419164272962.adam/part-00002-936f66e5-4a78-46ba-a41d-76776495539a-c000.snappy.parquet /tmp/adamTestMvnpjenoa0/TempSuite1226413419164272962.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite1226413419164272962.adam/_samples.avro /tmp/adamTestMvnpjenoa0/TempSuite1226413419164272962.adam/part-00001-936f66e5-4a78-46ba-a41d-76776495539a-c000.snappy.parquet /tmp/adamTestMvnpjenoa0/TempSuite1226413419164272962.adam/.part-00002-936f66e5-4a78-46ba-a41d-76776495539a-c000.snappy.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite1226413419164272962.adam/_header /tmp/adamTestMvnpjenoa0/TempSuite3183325159833493769 /tmp/adamTestMvnpjenoa0/TempSuite7958740948188535183.bed /tmp/adamTestMvnpjenoa0/TempSuite7958740948188535183.bed/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite7958740948188535183.bed/part-00000 /tmp/adamTestMvnpjenoa0/TempSuite7958740948188535183.bed/.part-00000.crc /tmp/adamTestMvnpjenoa0/TempSuite7958740948188535183.bed/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite5166272876013598357 /tmp/adamTestMvnpjenoa0/.TempSuite8451402568221737471.sam.crc /tmp/adamTestMvnpjenoa0/TempSuite3087847937306202517.bed /tmp/adamTestMvnpjenoa0/TempSuite3087847937306202517.bed/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite3087847937306202517.bed/part-00000 /tmp/adamTestMvnpjenoa0/TempSuite3087847937306202517.bed/.part-00000.crc /tmp/adamTestMvnpjenoa0/TempSuite3087847937306202517.bed/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite4547726345774740187 /tmp/adamTestMvnpjenoa0/TempSuite2871722268671373585 /tmp/adamTestMvnpjenoa0/2031145770482056166 /tmp/adamTestMvnpjenoa0/gencode.v7.annotation.trunc10.bed6514302060342347775.v7.annotation.trunc10.bed /tmp/adamTestMvnpjenoa0/TempSuite3886084837997019277 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite9117836399178227118.interval_list /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite9117836399178227118.interval_list/_SUCCESS /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite9117836399178227118.interval_list/part-00001 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite9117836399178227118.interval_list/.part-00003.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite9117836399178227118.interval_list/part-00000 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite9117836399178227118.interval_list/part-00003 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite9117836399178227118.interval_list/.part-00000.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite9117836399178227118.interval_list/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite9117836399178227118.interval_list/part-00002 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite9117836399178227118.interval_list/.part-00002.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite9117836399178227118.interval_list/.part-00001.crc /tmp/adamTestMvnpjenoa0/TempSuite862125649864846177.adam /tmp/adamTestMvnpjenoa0/TempSuite862125649864846177.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite862125649864846177.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite862125649864846177.adam/referenceName=1 /tmp/adamTestMvnpjenoa0/TempSuite862125649864846177.adam/referenceName=1/positionBin=0 /tmp/adamTestMvnpjenoa0/TempSuite862125649864846177.adam/referenceName=1/positionBin=0/part-00000-49751919-4d88-4dcd-a091-ca0808fcbd0f.c000.snappy.parquet /tmp/adamTestMvnpjenoa0/TempSuite862125649864846177.adam/referenceName=1/positionBin=0/.part-00000-49751919-4d88-4dcd-a091-ca0808fcbd0f.c000.snappy.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite862125649864846177.adam/._samples.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite862125649864846177.adam/_partitionedByStartPos /tmp/adamTestMvnpjenoa0/TempSuite862125649864846177.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite862125649864846177.adam/._header.crc /tmp/adamTestMvnpjenoa0/TempSuite862125649864846177.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite862125649864846177.adam/._partitionedByStartPos.crc /tmp/adamTestMvnpjenoa0/TempSuite862125649864846177.adam/_samples.avro /tmp/adamTestMvnpjenoa0/TempSuite862125649864846177.adam/_header /tmp/adamTestMvnpjenoa0/TempSuite3019155058482802182 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite4284140672707150483.bed /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite4284140672707150483.bed/_SUCCESS /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite4284140672707150483.bed/part-00001 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite4284140672707150483.bed/.part-00003.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite4284140672707150483.bed/part-00000 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite4284140672707150483.bed/part-00003 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite4284140672707150483.bed/.part-00000.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite4284140672707150483.bed/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite4284140672707150483.bed/part-00002 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite4284140672707150483.bed/.part-00002.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite4284140672707150483.bed/.part-00001.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite5516135037215301637.gff3 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite5516135037215301637.gff3/_SUCCESS /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite5516135037215301637.gff3/part-00001 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite5516135037215301637.gff3/.part-00003.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite5516135037215301637.gff3/part-00000 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite5516135037215301637.gff3/part-00003 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite5516135037215301637.gff3/.part-00000.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite5516135037215301637.gff3/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite5516135037215301637.gff3/part-00002 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite5516135037215301637.gff3/.part-00002.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite5516135037215301637.gff3/.part-00001.crc /tmp/adamTestMvnpjenoa0/TempSuite7114444225650152302 /tmp/adamTestMvnpjenoa0/random.vcf6332757757641874602.vcf /tmp/adamTestMvnpjenoa0/TempSuite6367271564930924635.adam /tmp/adamTestMvnpjenoa0/TempSuite6367271564930924635.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite6367271564930924635.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite6367271564930924635.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite6367271564930924635.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite6367271564930924635.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite6367271564930924635.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite6367271564930924635.adam/_common_metadata /tmp/adamTestMvnpjenoa0/TempSuite6367271564930924635.adam/._header.crc /tmp/adamTestMvnpjenoa0/TempSuite6367271564930924635.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite6367271564930924635.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite6367271564930924635.adam/_metadata /tmp/adamTestMvnpjenoa0/TempSuite6367271564930924635.adam/_header /tmp/adamTestMvnpjenoa0/TempSuite6770366044267204747.fq /tmp/adamTestMvnpjenoa0/TempSuite6770366044267204747.fq/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite6770366044267204747.fq/part-00000 /tmp/adamTestMvnpjenoa0/TempSuite6770366044267204747.fq/.part-00000.crc /tmp/adamTestMvnpjenoa0/TempSuite6770366044267204747.fq/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/unordered.sam1842185956189826717.sam /tmp/adamTestMvnpjenoa0/sorted-variants.vcf683521472125302717.vcf /tmp/adamTestMvnpjenoa0/TempSuite5488680254576040254 /tmp/adamTestMvnpjenoa0/1418250867435273939 /tmp/adamTestMvnpjenoa0/1418250867435273939/.sorted.lex.vcf.crc /tmp/adamTestMvnpjenoa0/1418250867435273939/sorted.lex.vcf /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite9015503689203818919.bed /tmp/adamTestMvnpjenoa0/TempSuite5166272876013598357.2.adam /tmp/adamTestMvnpjenoa0/TempSuite5166272876013598357.2.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite5166272876013598357.2.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite5166272876013598357.2.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite5166272876013598357.2.adam/_readGroups.avro /tmp/adamTestMvnpjenoa0/TempSuite5166272876013598357.2.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite5166272876013598357.2.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite5166272876013598357.2.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite5166272876013598357.2.adam/._processingSteps.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite5166272876013598357.2.adam/_common_metadata /tmp/adamTestMvnpjenoa0/TempSuite5166272876013598357.2.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite5166272876013598357.2.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite5166272876013598357.2.adam/._readGroups.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite5166272876013598357.2.adam/_metadata /tmp/adamTestMvnpjenoa0/TempSuite5166272876013598357.2.adam/_processingSteps.avro /tmp/adamTestMvnpjenoa0/TempSuite7007716153721705864 /tmp/adamTestMvnpjenoa0/TempSuite6499955018995365844 /tmp/adamTestMvnpjenoa0/TempSuite3003661673355067845 /tmp/adamTestMvnpjenoa0/TempSuite4103715118168983188 /tmp/adamTestMvnpjenoa0/1362161480505857741 /tmp/adamTestMvnpjenoa0/1362161480505857741/test.fa /tmp/adamTestMvnpjenoa0/1362161480505857741/.test.fa.crc /tmp/adamTestMvnpjenoa0/TempSuite1475466858704024357fragments.adam /tmp/adamTestMvnpjenoa0/TempSuite1475466858704024357fragments.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite1475466858704024357fragments.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite1475466858704024357fragments.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite1475466858704024357fragments.adam/_readGroups.avro /tmp/adamTestMvnpjenoa0/TempSuite1475466858704024357fragments.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite1475466858704024357fragments.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite1475466858704024357fragments.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite1475466858704024357fragments.adam/._processingSteps.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite1475466858704024357fragments.adam/_common_metadata /tmp/adamTestMvnpjenoa0/TempSuite1475466858704024357fragments.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite1475466858704024357fragments.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite1475466858704024357fragments.adam/._readGroups.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite1475466858704024357fragments.adam/_metadata /tmp/adamTestMvnpjenoa0/TempSuite1475466858704024357fragments.adam/_processingSteps.avro /tmp/adamTestMvnpjenoa0/TempSuite5934219242757433895.bed /tmp/adamTestMvnpjenoa0/TempSuite5934219242757433895.bed/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite5934219242757433895.bed/part-00000 /tmp/adamTestMvnpjenoa0/TempSuite5934219242757433895.bed/.part-00000.crc /tmp/adamTestMvnpjenoa0/TempSuite5934219242757433895.bed/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite545004467142402362 /tmp/adamTestMvnpjenoa0/javaAC4677320901851021339 /tmp/adamTestMvnpjenoa0/javaAC4677320901851021339/testRdd.coverage.adam /tmp/adamTestMvnpjenoa0/javaAC4677320901851021339/testRdd.coverage.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/javaAC4677320901851021339/testRdd.coverage.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/javaAC4677320901851021339/testRdd.coverage.adam/._samples.avro.crc /tmp/adamTestMvnpjenoa0/javaAC4677320901851021339/testRdd.coverage.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/javaAC4677320901851021339/testRdd.coverage.adam/.part-r-00003.gz.parquet.crc /tmp/adamTestMvnpjenoa0/javaAC4677320901851021339/testRdd.coverage.adam/part-r-00001.gz.parquet /tmp/adamTestMvnpjenoa0/javaAC4677320901851021339/testRdd.coverage.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/javaAC4677320901851021339/testRdd.coverage.adam/_references.avro /tmp/adamTestMvnpjenoa0/javaAC4677320901851021339/testRdd.coverage.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/javaAC4677320901851021339/testRdd.coverage.adam/.part-r-00001.gz.parquet.crc /tmp/adamTestMvnpjenoa0/javaAC4677320901851021339/testRdd.coverage.adam/part-r-00002.gz.parquet /tmp/adamTestMvnpjenoa0/javaAC4677320901851021339/testRdd.coverage.adam/.part-r-00002.gz.parquet.crc /tmp/adamTestMvnpjenoa0/javaAC4677320901851021339/testRdd.coverage.adam/_common_metadata /tmp/adamTestMvnpjenoa0/javaAC4677320901851021339/testRdd.coverage.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/javaAC4677320901851021339/testRdd.coverage.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/javaAC4677320901851021339/testRdd.coverage.adam/_samples.avro /tmp/adamTestMvnpjenoa0/javaAC4677320901851021339/testRdd.coverage.adam/_metadata /tmp/adamTestMvnpjenoa0/javaAC4677320901851021339/testRdd.coverage.adam/part-r-00003.gz.parquet /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite2624089682562548137 /tmp/adamTestMvnpjenoa0/TempSuite3509450891392034332 /tmp/adamTestMvnpjenoa0/TempSuite3424450956843792997 /tmp/adamTestMvnpjenoa0/TempSuite4395382513521882609.adam /tmp/adamTestMvnpjenoa0/TempSuite4395382513521882609.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite4395382513521882609.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite4395382513521882609.adam/._samples.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite4395382513521882609.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite4395382513521882609.adam/.part-r-00003.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite4395382513521882609.adam/part-r-00001.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite4395382513521882609.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite4395382513521882609.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite4395382513521882609.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite4395382513521882609.adam/.part-r-00001.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite4395382513521882609.adam/part-r-00002.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite4395382513521882609.adam/.part-r-00002.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite4395382513521882609.adam/_common_metadata /tmp/adamTestMvnpjenoa0/TempSuite4395382513521882609.adam/._header.crc /tmp/adamTestMvnpjenoa0/TempSuite4395382513521882609.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite4395382513521882609.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite4395382513521882609.adam/_samples.avro /tmp/adamTestMvnpjenoa0/TempSuite4395382513521882609.adam/_metadata /tmp/adamTestMvnpjenoa0/TempSuite4395382513521882609.adam/part-r-00003.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite4395382513521882609.adam/_header /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite4605734144246192556.gtf /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite4605734144246192556.gtf/_SUCCESS /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite4605734144246192556.gtf/part-00001 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite4605734144246192556.gtf/.part-00003.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite4605734144246192556.gtf/part-00000 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite4605734144246192556.gtf/part-00003 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite4605734144246192556.gtf/.part-00000.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite4605734144246192556.gtf/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite4605734144246192556.gtf/part-00002 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite4605734144246192556.gtf/.part-00002.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite4605734144246192556.gtf/.part-00001.crc /tmp/adamTestMvnpjenoa0/TempSuite1713443263698808030.bed /tmp/adamTestMvnpjenoa0/TempSuite1713443263698808030.bed/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite1713443263698808030.bed/part-00000 /tmp/adamTestMvnpjenoa0/TempSuite1713443263698808030.bed/.part-00000.crc /tmp/adamTestMvnpjenoa0/TempSuite1713443263698808030.bed/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite4455342517077777381 /tmp/adamTestMvnpjenoa0/TempSuite2511598494164752768.adam /tmp/adamTestMvnpjenoa0/TempSuite2511598494164752768.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite2511598494164752768.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite2511598494164752768.adam/referenceName=1 /tmp/adamTestMvnpjenoa0/TempSuite2511598494164752768.adam/referenceName=1/positionBin=169 /tmp/adamTestMvnpjenoa0/TempSuite2511598494164752768.adam/referenceName=1/positionBin=169/part-00001-ec9d38f1-b175-4f82-b0dc-98e1069bce2a.c000.snappy.parquet /tmp/adamTestMvnpjenoa0/TempSuite2511598494164752768.adam/referenceName=1/positionBin=169/.part-00001-ec9d38f1-b175-4f82-b0dc-98e1069bce2a.c000.snappy.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite2511598494164752768.adam/referenceName=1/positionBin=14 /tmp/adamTestMvnpjenoa0/TempSuite2511598494164752768.adam/referenceName=1/positionBin=14/.part-00000-ec9d38f1-b175-4f82-b0dc-98e1069bce2a.c000.snappy.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite2511598494164752768.adam/referenceName=1/positionBin=14/part-00000-ec9d38f1-b175-4f82-b0dc-98e1069bce2a.c000.snappy.parquet /tmp/adamTestMvnpjenoa0/TempSuite2511598494164752768.adam/referenceName=1/positionBin=240 /tmp/adamTestMvnpjenoa0/TempSuite2511598494164752768.adam/referenceName=1/positionBin=240/.part-00002-ec9d38f1-b175-4f82-b0dc-98e1069bce2a.c000.snappy.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite2511598494164752768.adam/referenceName=1/positionBin=240/part-00002-ec9d38f1-b175-4f82-b0dc-98e1069bce2a.c000.snappy.parquet /tmp/adamTestMvnpjenoa0/TempSuite2511598494164752768.adam/referenceName=1/positionBin=0 /tmp/adamTestMvnpjenoa0/TempSuite2511598494164752768.adam/referenceName=1/positionBin=0/.part-00000-ec9d38f1-b175-4f82-b0dc-98e1069bce2a.c000.snappy.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite2511598494164752768.adam/referenceName=1/positionBin=0/part-00000-ec9d38f1-b175-4f82-b0dc-98e1069bce2a.c000.snappy.parquet /tmp/adamTestMvnpjenoa0/TempSuite2511598494164752768.adam/._samples.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite2511598494164752768.adam/_partitionedByStartPos /tmp/adamTestMvnpjenoa0/TempSuite2511598494164752768.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite2511598494164752768.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite2511598494164752768.adam/._partitionedByStartPos.crc /tmp/adamTestMvnpjenoa0/TempSuite2511598494164752768.adam/_samples.avro /tmp/adamTestMvnpjenoa0/TempSuite3760846456780411430 /tmp/adamTestMvnpjenoa0/TempSuite6499955018995365844.adam /tmp/adamTestMvnpjenoa0/TempSuite6499955018995365844.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite6499955018995365844.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite6499955018995365844.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite6499955018995365844.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite6499955018995365844.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite6499955018995365844.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite6499955018995365844.adam/_common_metadata /tmp/adamTestMvnpjenoa0/TempSuite6499955018995365844.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite6499955018995365844.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite6499955018995365844.adam/_metadata /tmp/adamTestMvnpjenoa0/TempSuite7412582376594988878 /tmp/adamTestMvnpjenoa0/TempSuite3313501648601678200.adam /tmp/adamTestMvnpjenoa0/TempSuite3313501648601678200.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite3313501648601678200.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite3313501648601678200.adam/part-00000-9f31ef81-ec40-453c-b947-2d599e219452-c000.snappy.parquet /tmp/adamTestMvnpjenoa0/TempSuite3313501648601678200.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite3313501648601678200.adam/._header.crc /tmp/adamTestMvnpjenoa0/TempSuite3313501648601678200.adam/.part-00000-9f31ef81-ec40-453c-b947-2d599e219452-c000.snappy.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite3313501648601678200.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite3313501648601678200.adam/_header /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite5261417657002336405.bed /tmp/adamTestMvnpjenoa0/unordered.sam2718679690801149712.sam /tmp/adamTestMvnpjenoa0/6719859710367928086 /tmp/adamTestMvnpjenoa0/6719859710367928086/readname_sorted.sam /tmp/adamTestMvnpjenoa0/6719859710367928086/.readname_sorted.sam.crc /tmp/adamTestMvnpjenoa0/TempSuite5810990179749433916.adam /tmp/adamTestMvnpjenoa0/TempSuite5810990179749433916.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite5810990179749433916.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite5810990179749433916.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite5810990179749433916.adam/.part-r-00003.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite5810990179749433916.adam/part-r-00001.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite5810990179749433916.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite5810990179749433916.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite5810990179749433916.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite5810990179749433916.adam/.part-r-00001.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite5810990179749433916.adam/part-r-00002.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite5810990179749433916.adam/.part-r-00002.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite5810990179749433916.adam/_common_metadata /tmp/adamTestMvnpjenoa0/TempSuite5810990179749433916.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite5810990179749433916.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite5810990179749433916.adam/_metadata /tmp/adamTestMvnpjenoa0/TempSuite5810990179749433916.adam/part-r-00003.gz.parquet /tmp/adamTestMvnpjenoa0/88719451628226859 /tmp/adamTestMvnpjenoa0/88719451628226859/.tag.sam.crc /tmp/adamTestMvnpjenoa0/88719451628226859/tag.sam /tmp/adamTestMvnpjenoa0/2595588446105756227 /tmp/adamTestMvnpjenoa0/2595588446105756227/ordered.sam /tmp/adamTestMvnpjenoa0/2595588446105756227/.ordered.sam.crc /tmp/adamTestMvnpjenoa0/sample_coverage.bed456145507497352402.bed /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite5631867145567236052 /tmp/adamTestMvnpjenoa0/TempSuite2137169130426970700.adam /tmp/adamTestMvnpjenoa0/TempSuite2137169130426970700.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite2137169130426970700.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite2137169130426970700.adam/.part-00001-cf132dca-2c9a-487b-af1d-057ed1a35102-c000.snappy.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite2137169130426970700.adam/part-00002-cf132dca-2c9a-487b-af1d-057ed1a35102-c000.snappy.parquet /tmp/adamTestMvnpjenoa0/TempSuite2137169130426970700.adam/.part-00002-cf132dca-2c9a-487b-af1d-057ed1a35102-c000.snappy.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite2137169130426970700.adam/_readGroups.avro /tmp/adamTestMvnpjenoa0/TempSuite2137169130426970700.adam/part-00000-cf132dca-2c9a-487b-af1d-057ed1a35102-c000.snappy.parquet /tmp/adamTestMvnpjenoa0/TempSuite2137169130426970700.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite2137169130426970700.adam/._processingSteps.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite2137169130426970700.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite2137169130426970700.adam/._readGroups.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite2137169130426970700.adam/.part-00000-cf132dca-2c9a-487b-af1d-057ed1a35102-c000.snappy.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite2137169130426970700.adam/part-00001-cf132dca-2c9a-487b-af1d-057ed1a35102-c000.snappy.parquet /tmp/adamTestMvnpjenoa0/TempSuite2137169130426970700.adam/_processingSteps.avro /tmp/adamTestMvnpjenoa0/5166541273791006374 /tmp/adamTestMvnpjenoa0/5166541273791006374/ordered.sam /tmp/adamTestMvnpjenoa0/5166541273791006374/.ordered.sam.crc /tmp/adamTestMvnpjenoa0/4601703092693422496 /tmp/adamTestMvnpjenoa0/4601703092693422496/binned.adam /tmp/adamTestMvnpjenoa0/4601703092693422496/binned.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/4601703092693422496/binned.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/4601703092693422496/binned.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/4601703092693422496/binned.adam/_readGroups.avro /tmp/adamTestMvnpjenoa0/4601703092693422496/binned.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/4601703092693422496/binned.adam/_references.avro /tmp/adamTestMvnpjenoa0/4601703092693422496/binned.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/4601703092693422496/binned.adam/._processingSteps.avro.crc /tmp/adamTestMvnpjenoa0/4601703092693422496/binned.adam/_common_metadata /tmp/adamTestMvnpjenoa0/4601703092693422496/binned.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/4601703092693422496/binned.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/4601703092693422496/binned.adam/._readGroups.avro.crc /tmp/adamTestMvnpjenoa0/4601703092693422496/binned.adam/_metadata /tmp/adamTestMvnpjenoa0/4601703092693422496/binned.adam/_processingSteps.avro /tmp/adamTestMvnpjenoa0/TempSuite1136416851151774814 /tmp/adamTestMvnpjenoa0/TempSuite7081652395279320996 /tmp/adamTestMvnpjenoa0/TempSuite4841127484515976577 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite5895798626854010945.gff3 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite5895798626854010945.gff3/_SUCCESS /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite5895798626854010945.gff3/part-00001 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite5895798626854010945.gff3/.part-00003.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite5895798626854010945.gff3/part-00000 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite5895798626854010945.gff3/part-00003 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite5895798626854010945.gff3/.part-00000.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite5895798626854010945.gff3/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite5895798626854010945.gff3/part-00002 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite5895798626854010945.gff3/.part-00002.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite5895798626854010945.gff3/.part-00001.crc /tmp/adamTestMvnpjenoa0/1557939528952-0 /tmp/adamTestMvnpjenoa0/1557939528952-0/test.fa /tmp/adamTestMvnpjenoa0/1557939528952-0/test.fa/_SUCCESS /tmp/adamTestMvnpjenoa0/1557939528952-0/test.fa/part-00000 /tmp/adamTestMvnpjenoa0/1557939528952-0/test.fa/.part-00000.crc /tmp/adamTestMvnpjenoa0/1557939528952-0/test.fa/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite4933303931400674710.adam /tmp/adamTestMvnpjenoa0/TempSuite4933303931400674710.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite4933303931400674710.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite4933303931400674710.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite4933303931400674710.adam/_readGroups.avro /tmp/adamTestMvnpjenoa0/TempSuite4933303931400674710.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite4933303931400674710.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite4933303931400674710.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite4933303931400674710.adam/._processingSteps.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite4933303931400674710.adam/_common_metadata /tmp/adamTestMvnpjenoa0/TempSuite4933303931400674710.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite4933303931400674710.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite4933303931400674710.adam/._readGroups.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite4933303931400674710.adam/_metadata /tmp/adamTestMvnpjenoa0/TempSuite4933303931400674710.adam/_processingSteps.avro /tmp/adamTestMvnpjenoa0/8949606722468305458 /tmp/adamTestMvnpjenoa0/8949606722468305458/unordered.sam /tmp/adamTestMvnpjenoa0/8949606722468305458/.unordered.sam.crc /tmp/adamTestMvnpjenoa0/TempSuite2718680204873500417 /tmp/adamTestMvnpjenoa0/4237148987481988102 /tmp/adamTestMvnpjenoa0/4237148987481988102/.artificial.cram.crc /tmp/adamTestMvnpjenoa0/4237148987481988102/artificial.cram /tmp/adamTestMvnpjenoa0/TempSuite7629081788710742136.adam /tmp/adamTestMvnpjenoa0/TempSuite7629081788710742136.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite7629081788710742136.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite7629081788710742136.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite7629081788710742136.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite7629081788710742136.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite7629081788710742136.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite7629081788710742136.adam/_common_metadata /tmp/adamTestMvnpjenoa0/TempSuite7629081788710742136.adam/._header.crc /tmp/adamTestMvnpjenoa0/TempSuite7629081788710742136.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite7629081788710742136.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite7629081788710742136.adam/_metadata /tmp/adamTestMvnpjenoa0/TempSuite7629081788710742136.adam/_header /tmp/adamTestMvnpjenoa0/TempSuite869153603301233793.fq /tmp/adamTestMvnpjenoa0/TempSuite869153603301233793.fq/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite869153603301233793.fq/part-00000 /tmp/adamTestMvnpjenoa0/TempSuite869153603301233793.fq/.part-00000.crc /tmp/adamTestMvnpjenoa0/TempSuite869153603301233793.fq/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite7613213390210882074 /tmp/adamTestMvnpjenoa0/TempSuite1163457635644320715 /tmp/adamTestMvnpjenoa0/TempSuite6763088628571796715 /tmp/adamTestMvnpjenoa0/TempSuite8770139105033904741.adam /tmp/adamTestMvnpjenoa0/TempSuite8770139105033904741.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite8770139105033904741.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite8770139105033904741.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite8770139105033904741.adam/.part-r-00003.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite8770139105033904741.adam/part-r-00001.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite8770139105033904741.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite8770139105033904741.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite8770139105033904741.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite8770139105033904741.adam/.part-r-00001.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite8770139105033904741.adam/part-r-00002.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite8770139105033904741.adam/.part-r-00002.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite8770139105033904741.adam/_common_metadata /tmp/adamTestMvnpjenoa0/TempSuite8770139105033904741.adam/._header.crc /tmp/adamTestMvnpjenoa0/TempSuite8770139105033904741.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite8770139105033904741.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite8770139105033904741.adam/_metadata /tmp/adamTestMvnpjenoa0/TempSuite8770139105033904741.adam/part-r-00003.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite8770139105033904741.adam/_header /tmp/adamTestMvnpjenoa0/TempSuite4933303931400674710 /tmp/adamTestMvnpjenoa0/1506573926629616275 /tmp/adamTestMvnpjenoa0/1506573926629616275/predicate.2.adam /tmp/adamTestMvnpjenoa0/1506573926629616275/predicate.2.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/1506573926629616275/predicate.2.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/1506573926629616275/predicate.2.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/1506573926629616275/predicate.2.adam/_readGroups.avro /tmp/adamTestMvnpjenoa0/1506573926629616275/predicate.2.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/1506573926629616275/predicate.2.adam/_references.avro /tmp/adamTestMvnpjenoa0/1506573926629616275/predicate.2.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/1506573926629616275/predicate.2.adam/._processingSteps.avro.crc /tmp/adamTestMvnpjenoa0/1506573926629616275/predicate.2.adam/_common_metadata /tmp/adamTestMvnpjenoa0/1506573926629616275/predicate.2.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/1506573926629616275/predicate.2.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/1506573926629616275/predicate.2.adam/._readGroups.avro.crc /tmp/adamTestMvnpjenoa0/1506573926629616275/predicate.2.adam/_metadata /tmp/adamTestMvnpjenoa0/1506573926629616275/predicate.2.adam/_processingSteps.avro /tmp/adamTestMvnpjenoa0/TempSuite3788564896957749131.adam /tmp/adamTestMvnpjenoa0/TempSuite3788564896957749131.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite3788564896957749131.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite3788564896957749131.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite3788564896957749131.adam/_readGroups.avro /tmp/adamTestMvnpjenoa0/TempSuite3788564896957749131.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite3788564896957749131.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite3788564896957749131.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite3788564896957749131.adam/._processingSteps.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite3788564896957749131.adam/_common_metadata /tmp/adamTestMvnpjenoa0/TempSuite3788564896957749131.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite3788564896957749131.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite3788564896957749131.adam/._readGroups.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite3788564896957749131.adam/_metadata /tmp/adamTestMvnpjenoa0/TempSuite3788564896957749131.adam/_processingSteps.avro /tmp/adamTestMvnpjenoa0/TempSuite8286440147751900879.bam /tmp/adamTestMvnpjenoa0/3950114897756828080 /tmp/adamTestMvnpjenoa0/3950114897756828080/.out.sam_head.crc /tmp/adamTestMvnpjenoa0/3950114897756828080/out.sam_head /tmp/adamTestMvnpjenoa0/3950114897756828080/.out.sam.crc /tmp/adamTestMvnpjenoa0/3950114897756828080/out.sam /tmp/adamTestMvnpjenoa0/3950114897756828080/out.sam_tail /tmp/adamTestMvnpjenoa0/3950114897756828080/out.sam_tail/_SUCCESS /tmp/adamTestMvnpjenoa0/3950114897756828080/out.sam_tail/part-r-00001.sam /tmp/adamTestMvnpjenoa0/3950114897756828080/out.sam_tail/part-r-00002.sam /tmp/adamTestMvnpjenoa0/3950114897756828080/out.sam_tail/.part-r-00001.sam.crc /tmp/adamTestMvnpjenoa0/3950114897756828080/out.sam_tail/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/3950114897756828080/out.sam_tail/part-r-00003.sam /tmp/adamTestMvnpjenoa0/3950114897756828080/out.sam_tail/.part-r-00000.sam.crc /tmp/adamTestMvnpjenoa0/3950114897756828080/out.sam_tail/.part-r-00003.sam.crc /tmp/adamTestMvnpjenoa0/3950114897756828080/out.sam_tail/part-r-00000.sam /tmp/adamTestMvnpjenoa0/3950114897756828080/out.sam_tail/.part-r-00002.sam.crc /tmp/adamTestMvnpjenoa0/TempSuite5320512173435773115.adam /tmp/adamTestMvnpjenoa0/TempSuite5320512173435773115.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite5320512173435773115.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite5320512173435773115.adam/part-00000-1994493b-5ec5-4b54-adba-90f1177479e6-c000.snappy.parquet /tmp/adamTestMvnpjenoa0/TempSuite5320512173435773115.adam/_readGroups.avro /tmp/adamTestMvnpjenoa0/TempSuite5320512173435773115.adam/.part-00000-1994493b-5ec5-4b54-adba-90f1177479e6-c000.snappy.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite5320512173435773115.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite5320512173435773115.adam/._processingSteps.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite5320512173435773115.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite5320512173435773115.adam/._readGroups.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite5320512173435773115.adam/_processingSteps.avro /tmp/adamTestMvnpjenoa0/1445974471327150299 /tmp/adamTestMvnpjenoa0/1445974471327150299/unordered.adam /tmp/adamTestMvnpjenoa0/1445974471327150299/unordered.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/1445974471327150299/unordered.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/1445974471327150299/unordered.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/1445974471327150299/unordered.adam/_readGroups.avro /tmp/adamTestMvnpjenoa0/1445974471327150299/unordered.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/1445974471327150299/unordered.adam/_references.avro /tmp/adamTestMvnpjenoa0/1445974471327150299/unordered.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/1445974471327150299/unordered.adam/._processingSteps.avro.crc /tmp/adamTestMvnpjenoa0/1445974471327150299/unordered.adam/_common_metadata /tmp/adamTestMvnpjenoa0/1445974471327150299/unordered.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/1445974471327150299/unordered.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/1445974471327150299/unordered.adam/._readGroups.avro.crc /tmp/adamTestMvnpjenoa0/1445974471327150299/unordered.adam/_metadata /tmp/adamTestMvnpjenoa0/1445974471327150299/unordered.adam/_processingSteps.avro /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite2815515414849352137 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite3477891220341065232 /tmp/adamTestMvnpjenoa0/TempSuite6763088628571796715.adam /tmp/adamTestMvnpjenoa0/TempSuite6763088628571796715.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite6763088628571796715.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite6763088628571796715.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite6763088628571796715.adam/_readGroups.avro /tmp/adamTestMvnpjenoa0/TempSuite6763088628571796715.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite6763088628571796715.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite6763088628571796715.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite6763088628571796715.adam/._processingSteps.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite6763088628571796715.adam/_common_metadata /tmp/adamTestMvnpjenoa0/TempSuite6763088628571796715.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite6763088628571796715.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite6763088628571796715.adam/._readGroups.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite6763088628571796715.adam/_metadata /tmp/adamTestMvnpjenoa0/TempSuite6763088628571796715.adam/_processingSteps.avro /tmp/adamTestMvnpjenoa0/TempSuite8280402691048794791.adam /tmp/adamTestMvnpjenoa0/TempSuite8280402691048794791.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite8280402691048794791.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite8280402691048794791.adam/._samples.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite8280402691048794791.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite8280402691048794791.adam/.part-r-00003.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite8280402691048794791.adam/part-r-00001.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite8280402691048794791.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite8280402691048794791.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite8280402691048794791.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite8280402691048794791.adam/.part-r-00001.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite8280402691048794791.adam/part-r-00002.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite8280402691048794791.adam/.part-r-00002.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite8280402691048794791.adam/_common_metadata /tmp/adamTestMvnpjenoa0/TempSuite8280402691048794791.adam/._header.crc /tmp/adamTestMvnpjenoa0/TempSuite8280402691048794791.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite8280402691048794791.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite8280402691048794791.adam/_samples.avro /tmp/adamTestMvnpjenoa0/TempSuite8280402691048794791.adam/_metadata /tmp/adamTestMvnpjenoa0/TempSuite8280402691048794791.adam/part-r-00003.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite8280402691048794791.adam/_header /tmp/adamTestMvnpjenoa0/TempSuite4648806516878885886 /tmp/adamTestMvnpjenoa0/TempSuite6583163745404908914 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite8844978334613793167 /tmp/adamTestMvnpjenoa0/TempSuite2115713021301080792 /tmp/adamTestMvnpjenoa0/.TempSuite5154624431810492890.bam.crc /tmp/adamTestMvnpjenoa0/.TempSuite4274165549462923049_2.fq.crc /tmp/adamTestMvnpjenoa0/TempSuite5154624431810492890.bam /tmp/adamTestMvnpjenoa0/8282638904425513081 /tmp/adamTestMvnpjenoa0/8282638904425513081/unordered.sam /tmp/adamTestMvnpjenoa0/8282638904425513081/.unordered.sam.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite5261417657002336405 /tmp/adamTestMvnpjenoa0/TempSuite7710545530433433082 /tmp/adamTestMvnpjenoa0/TempSuite8231743441889909402.bam /tmp/adamTestMvnpjenoa0/TempSuite8231743441889909402.bam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite8231743441889909402.bam/part-r-00000.bam /tmp/adamTestMvnpjenoa0/TempSuite8231743441889909402.bam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite8231743441889909402.bam/.part-r-00000.bam.crc /tmp/adamTestMvnpjenoa0/TempSuite3313501648601678200 /tmp/adamTestMvnpjenoa0/TempSuite5928571840237724678.fq /tmp/adamTestMvnpjenoa0/TempSuite5928571840237724678.fq/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite5928571840237724678.fq/part-00000 /tmp/adamTestMvnpjenoa0/TempSuite5928571840237724678.fq/.part-00000.crc /tmp/adamTestMvnpjenoa0/TempSuite5928571840237724678.fq/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite6397240184609528647 /tmp/adamTestMvnpjenoa0/unordered.sam5279413378568617854.sam /tmp/adamTestMvnpjenoa0/TempSuite4547726345774740187.sam /tmp/adamTestMvnpjenoa0/TempSuite4547726345774740187.sam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite4547726345774740187.sam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite4547726345774740187.sam/.part-r-00000.sam.crc /tmp/adamTestMvnpjenoa0/TempSuite4547726345774740187.sam/part-r-00000.sam /tmp/adamTestMvnpjenoa0/TempSuite4097811632542236011.adam /tmp/adamTestMvnpjenoa0/TempSuite4097811632542236011.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite4097811632542236011.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite4097811632542236011.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite4097811632542236011.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite4097811632542236011.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite4097811632542236011.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite4097811632542236011.adam/_common_metadata /tmp/adamTestMvnpjenoa0/TempSuite4097811632542236011.adam/._header.crc /tmp/adamTestMvnpjenoa0/TempSuite4097811632542236011.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite4097811632542236011.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite4097811632542236011.adam/_metadata /tmp/adamTestMvnpjenoa0/TempSuite4097811632542236011.adam/_header /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite4645048015409656528.interval_list /tmp/adamTestMvnpjenoa0/TempSuite6524376824309086566.adam /tmp/adamTestMvnpjenoa0/TempSuite6524376824309086566.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite6524376824309086566.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite6524376824309086566.adam/part-00000-d988bdcf-68cf-4d7d-aa2f-94c2fa6fa70a-c000.snappy.parquet /tmp/adamTestMvnpjenoa0/TempSuite6524376824309086566.adam/part-00001-d988bdcf-68cf-4d7d-aa2f-94c2fa6fa70a-c000.snappy.parquet /tmp/adamTestMvnpjenoa0/TempSuite6524376824309086566.adam/.part-00001-d988bdcf-68cf-4d7d-aa2f-94c2fa6fa70a-c000.snappy.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite6524376824309086566.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite6524376824309086566.adam/.part-00002-d988bdcf-68cf-4d7d-aa2f-94c2fa6fa70a-c000.snappy.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite6524376824309086566.adam/part-00002-d988bdcf-68cf-4d7d-aa2f-94c2fa6fa70a-c000.snappy.parquet /tmp/adamTestMvnpjenoa0/TempSuite6524376824309086566.adam/._header.crc /tmp/adamTestMvnpjenoa0/TempSuite6524376824309086566.adam/.part-00000-d988bdcf-68cf-4d7d-aa2f-94c2fa6fa70a-c000.snappy.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite6524376824309086566.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite6524376824309086566.adam/_header /tmp/adamTestMvnpjenoa0/TempSuite1895162954070760589.bed /tmp/adamTestMvnpjenoa0/TempSuite1895162954070760589.bed/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite1895162954070760589.bed/part-00000 /tmp/adamTestMvnpjenoa0/TempSuite1895162954070760589.bed/.part-00000.crc /tmp/adamTestMvnpjenoa0/TempSuite1895162954070760589.bed/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite3617875519498963883.adam /tmp/adamTestMvnpjenoa0/TempSuite3617875519498963883.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite3617875519498963883.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite3617875519498963883.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite3617875519498963883.adam/_readGroups.avro /tmp/adamTestMvnpjenoa0/TempSuite3617875519498963883.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite3617875519498963883.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite3617875519498963883.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite3617875519498963883.adam/._processingSteps.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite3617875519498963883.adam/_common_metadata /tmp/adamTestMvnpjenoa0/TempSuite3617875519498963883.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite3617875519498963883.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite3617875519498963883.adam/._readGroups.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite3617875519498963883.adam/_metadata /tmp/adamTestMvnpjenoa0/TempSuite3617875519498963883.adam/_processingSteps.avro /tmp/adamTestMvnpjenoa0/TempSuite2866337395919035423.adam /tmp/adamTestMvnpjenoa0/TempSuite2866337395919035423.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite2866337395919035423.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite2866337395919035423.adam/._samples.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite2866337395919035423.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite2866337395919035423.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite2866337395919035423.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite2866337395919035423.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite2866337395919035423.adam/_common_metadata /tmp/adamTestMvnpjenoa0/TempSuite2866337395919035423.adam/._header.crc /tmp/adamTestMvnpjenoa0/TempSuite2866337395919035423.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite2866337395919035423.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite2866337395919035423.adam/_samples.avro /tmp/adamTestMvnpjenoa0/TempSuite2866337395919035423.adam/_metadata /tmp/adamTestMvnpjenoa0/TempSuite2866337395919035423.adam/_header /tmp/adamTestMvnpjenoa0/.TempSuite8286440147751900879.bam.crc /tmp/adamTestMvnpjenoa0/TempSuite7350422981194583357.fa /tmp/adamTestMvnpjenoa0/TempSuite7350422981194583357.fa/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite7350422981194583357.fa/part-00000 /tmp/adamTestMvnpjenoa0/TempSuite7350422981194583357.fa/.part-00000.crc /tmp/adamTestMvnpjenoa0/TempSuite7350422981194583357.fa/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite6367271564930924635 /tmp/adamTestMvnpjenoa0/TempSuite2221067587595277651.adam /tmp/adamTestMvnpjenoa0/TempSuite2221067587595277651.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite2221067587595277651.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite2221067587595277651.adam/.part-00000-de782abf-dbcc-4a6d-b26c-8235f38cf7cd-c000.snappy.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite2221067587595277651.adam/_readGroups.avro /tmp/adamTestMvnpjenoa0/TempSuite2221067587595277651.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite2221067587595277651.adam/part-00000-de782abf-dbcc-4a6d-b26c-8235f38cf7cd-c000.snappy.parquet /tmp/adamTestMvnpjenoa0/TempSuite2221067587595277651.adam/._processingSteps.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite2221067587595277651.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite2221067587595277651.adam/._readGroups.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite2221067587595277651.adam/_processingSteps.avro /tmp/adamTestMvnpjenoa0/TempSuite1062702206035455186.bed /tmp/adamTestMvnpjenoa0/TempSuite1062702206035455186.bed/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite1062702206035455186.bed/part-00000 /tmp/adamTestMvnpjenoa0/TempSuite1062702206035455186.bed/.part-00000.crc /tmp/adamTestMvnpjenoa0/TempSuite1062702206035455186.bed/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/3401985812670272937 /tmp/adamTestMvnpjenoa0/3401985812670272937/ordered.sam /tmp/adamTestMvnpjenoa0/3401985812670272937/.ordered.sam.crc /tmp/adamTestMvnpjenoa0/TempSuite8654128942180173260 /tmp/adamTestMvnpjenoa0/TempSuite4631402722900267245 /tmp/adamTestMvnpjenoa0/TempSuite1768097519194226507.adam /tmp/adamTestMvnpjenoa0/TempSuite1768097519194226507.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite1768097519194226507.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite1768097519194226507.adam/.part-00000-f88cacfd-d2db-4de3-a4bd-9742992b9cac-c000.snappy.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite1768097519194226507.adam/part-00000-f88cacfd-d2db-4de3-a4bd-9742992b9cac-c000.snappy.parquet /tmp/adamTestMvnpjenoa0/TempSuite1768097519194226507.adam/_readGroups.avro /tmp/adamTestMvnpjenoa0/TempSuite1768097519194226507.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite1768097519194226507.adam/._processingSteps.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite1768097519194226507.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite1768097519194226507.adam/._readGroups.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite1768097519194226507.adam/_processingSteps.avro /tmp/adamTestMvnpjenoa0/5017660525002300051 /tmp/adamTestMvnpjenoa0/5017660525002300051/ctg.adam /tmp/adamTestMvnpjenoa0/5017660525002300051/ctg.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/5017660525002300051/ctg.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/5017660525002300051/ctg.adam/_partitionedByStartPos /tmp/adamTestMvnpjenoa0/5017660525002300051/ctg.adam/_references.avro /tmp/adamTestMvnpjenoa0/5017660525002300051/ctg.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/5017660525002300051/ctg.adam/._partitionedByStartPos.crc /tmp/adamTestMvnpjenoa0/5017660525002300051/ctg.adam/referenceName=HLA-DQB1%2A05%3A01%3A01%3A02 /tmp/adamTestMvnpjenoa0/5017660525002300051/ctg.adam/referenceName=HLA-DQB1%2A05%3A01%3A01%3A02/positionBin=0 /tmp/adamTestMvnpjenoa0/5017660525002300051/ctg.adam/referenceName=HLA-DQB1%2A05%3A01%3A01%3A02/positionBin=0/.part-00000-4a3f89a3-b23b-4616-aa71-14c8346b5f58.c000.snappy.parquet.crc /tmp/adamTestMvnpjenoa0/5017660525002300051/ctg.adam/referenceName=HLA-DQB1%2A05%3A01%3A01%3A02/positionBin=0/part-00000-4a3f89a3-b23b-4616-aa71-14c8346b5f58.c000.snappy.parquet /tmp/adamTestMvnpjenoa0/TempSuite4085734275694747234 /tmp/adamTestMvnpjenoa0/TempSuite2791217825696054455.sam /tmp/adamTestMvnpjenoa0/1720137235407179251 /tmp/adamTestMvnpjenoa0/1720137235407179251/.unordered.bam.crc /tmp/adamTestMvnpjenoa0/1720137235407179251/unordered.bam /tmp/adamTestMvnpjenoa0/TempSuite6948893285446280395 /tmp/adamTestMvnpjenoa0/1557939940822-0 /tmp/adamTestMvnpjenoa0/1557939940822-0/test.fa /tmp/adamTestMvnpjenoa0/1557939940822-0/test.fa/_SUCCESS /tmp/adamTestMvnpjenoa0/1557939940822-0/test.fa/part-00000 /tmp/adamTestMvnpjenoa0/1557939940822-0/test.fa/.part-00000.crc /tmp/adamTestMvnpjenoa0/1557939940822-0/test.fa/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite3017277336060454342.adam /tmp/adamTestMvnpjenoa0/TempSuite3017277336060454342.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite3017277336060454342.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite3017277336060454342.adam/._samples.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite3017277336060454342.adam/part-00000-41a35085-2b5f-4d15-8de6-d29f6108a71c-c000.snappy.parquet /tmp/adamTestMvnpjenoa0/TempSuite3017277336060454342.adam/part-00001-41a35085-2b5f-4d15-8de6-d29f6108a71c-c000.snappy.parquet /tmp/adamTestMvnpjenoa0/TempSuite3017277336060454342.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite3017277336060454342.adam/part-00002-41a35085-2b5f-4d15-8de6-d29f6108a71c-c000.snappy.parquet /tmp/adamTestMvnpjenoa0/TempSuite3017277336060454342.adam/.part-00000-41a35085-2b5f-4d15-8de6-d29f6108a71c-c000.snappy.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite3017277336060454342.adam/.part-00001-41a35085-2b5f-4d15-8de6-d29f6108a71c-c000.snappy.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite3017277336060454342.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite3017277336060454342.adam/_samples.avro /tmp/adamTestMvnpjenoa0/TempSuite3017277336060454342.adam/.part-00002-41a35085-2b5f-4d15-8de6-d29f6108a71c-c000.snappy.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite4930003273437140418 /tmp/adamTestMvnpjenoa0/TempSuite3767086643913756235.bed /tmp/adamTestMvnpjenoa0/TempSuite3767086643913756235.bed/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite3767086643913756235.bed/part-00000 /tmp/adamTestMvnpjenoa0/TempSuite3767086643913756235.bed/.part-00000.crc /tmp/adamTestMvnpjenoa0/TempSuite3767086643913756235.bed/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/small.sam6663343500791366240.sam /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite4081021514912266843.interval_list /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite4081021514912266843.interval_list/_SUCCESS /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite4081021514912266843.interval_list/part-00001 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite4081021514912266843.interval_list/.part-00003.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite4081021514912266843.interval_list/part-00000 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite4081021514912266843.interval_list/part-00003 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite4081021514912266843.interval_list/.part-00000.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite4081021514912266843.interval_list/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite4081021514912266843.interval_list/part-00002 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite4081021514912266843.interval_list/.part-00002.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite4081021514912266843.interval_list/.part-00001.crc /tmp/adamTestMvnpjenoa0/TempSuite599532972129454608 /tmp/adamTestMvnpjenoa0/TempSuite8729714883702295667 /tmp/adamTestMvnpjenoa0/TempSuite974830346482781115.fq /tmp/adamTestMvnpjenoa0/TempSuite974830346482781115.fq/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite974830346482781115.fq/part-00000 /tmp/adamTestMvnpjenoa0/TempSuite974830346482781115.fq/.part-00000.crc /tmp/adamTestMvnpjenoa0/TempSuite974830346482781115.fq/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite7961983911993998754 /tmp/adamTestMvnpjenoa0/bqsr1.sam3274671169059188742.sam /tmp/adamTestMvnpjenoa0/TempSuite181986275264734832 /tmp/adamTestMvnpjenoa0/TempSuite4142813558507540852.adam /tmp/adamTestMvnpjenoa0/TempSuite4142813558507540852.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite4142813558507540852.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite4142813558507540852.adam/referenceName=1 /tmp/adamTestMvnpjenoa0/TempSuite4142813558507540852.adam/referenceName=1/positionBin=169 /tmp/adamTestMvnpjenoa0/TempSuite4142813558507540852.adam/referenceName=1/positionBin=169/part-00001-45326dfa-f2f2-4c92-a21a-342aea259c0c.c000.snappy.parquet /tmp/adamTestMvnpjenoa0/TempSuite4142813558507540852.adam/referenceName=1/positionBin=169/.part-00001-45326dfa-f2f2-4c92-a21a-342aea259c0c.c000.snappy.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite4142813558507540852.adam/referenceName=1/positionBin=14 /tmp/adamTestMvnpjenoa0/TempSuite4142813558507540852.adam/referenceName=1/positionBin=14/.part-00000-45326dfa-f2f2-4c92-a21a-342aea259c0c.c000.snappy.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite4142813558507540852.adam/referenceName=1/positionBin=14/part-00000-45326dfa-f2f2-4c92-a21a-342aea259c0c.c000.snappy.parquet /tmp/adamTestMvnpjenoa0/TempSuite4142813558507540852.adam/referenceName=1/positionBin=240 /tmp/adamTestMvnpjenoa0/TempSuite4142813558507540852.adam/referenceName=1/positionBin=240/part-00002-45326dfa-f2f2-4c92-a21a-342aea259c0c.c000.snappy.parquet /tmp/adamTestMvnpjenoa0/TempSuite4142813558507540852.adam/referenceName=1/positionBin=240/.part-00002-45326dfa-f2f2-4c92-a21a-342aea259c0c.c000.snappy.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite4142813558507540852.adam/referenceName=1/positionBin=0 /tmp/adamTestMvnpjenoa0/TempSuite4142813558507540852.adam/referenceName=1/positionBin=0/.part-00000-45326dfa-f2f2-4c92-a21a-342aea259c0c.c000.snappy.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite4142813558507540852.adam/referenceName=1/positionBin=0/part-00000-45326dfa-f2f2-4c92-a21a-342aea259c0c.c000.snappy.parquet /tmp/adamTestMvnpjenoa0/TempSuite4142813558507540852.adam/._samples.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite4142813558507540852.adam/_partitionedByStartPos /tmp/adamTestMvnpjenoa0/TempSuite4142813558507540852.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite4142813558507540852.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite4142813558507540852.adam/._partitionedByStartPos.crc /tmp/adamTestMvnpjenoa0/TempSuite4142813558507540852.adam/_samples.avro /tmp/adamTestMvnpjenoa0/.FeatureDatasetFunctionsSuite7600585556506155801.bed.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite749629422878677306 /tmp/adamTestMvnpjenoa0/5467107404021500752 /tmp/adamTestMvnpjenoa0/5467107404021500752/.sorted.sam.crc /tmp/adamTestMvnpjenoa0/5467107404021500752/sorted.sam /tmp/adamTestMvnpjenoa0/TempSuite5968469603544640016 /tmp/adamTestMvnpjenoa0/TempSuite409310598779627053.bed /tmp/adamTestMvnpjenoa0/TempSuite409310598779627053.bed/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite409310598779627053.bed/part-00000 /tmp/adamTestMvnpjenoa0/TempSuite409310598779627053.bed/.part-00000.crc /tmp/adamTestMvnpjenoa0/TempSuite409310598779627053.bed/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/bqsr1465354583197822486 /tmp/adamTestMvnpjenoa0/bqsr1465354583197822486/bqsr1.bam /tmp/adamTestMvnpjenoa0/bqsr1465354583197822486/.bqsr1.bam.crc /tmp/adamTestMvnpjenoa0/TempSuite477657437665447946 /tmp/adamTestMvnpjenoa0/TempSuite1171417020645719520 /tmp/adamTestMvnpjenoa0/TempSuite4930003273437140418.adam /tmp/adamTestMvnpjenoa0/TempSuite4930003273437140418.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite4930003273437140418.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite4930003273437140418.adam/part-00000-af357078-ad16-4ee6-98b2-7c1052a3c793-c000.snappy.parquet /tmp/adamTestMvnpjenoa0/TempSuite4930003273437140418.adam/.part-00000-af357078-ad16-4ee6-98b2-7c1052a3c793-c000.snappy.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite4930003273437140418.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite4930003273437140418.adam/._header.crc /tmp/adamTestMvnpjenoa0/TempSuite4930003273437140418.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite4930003273437140418.adam/_header /tmp/adamTestMvnpjenoa0/TempSuite5841261163310104463.fa /tmp/adamTestMvnpjenoa0/TempSuite5841261163310104463.fa/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite5841261163310104463.fa/part-00000 /tmp/adamTestMvnpjenoa0/TempSuite5841261163310104463.fa/.part-00000.crc /tmp/adamTestMvnpjenoa0/TempSuite5841261163310104463.fa/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite1202817804488828426 /tmp/adamTestMvnpjenoa0/TempSuite3003661673355067845.adam /tmp/adamTestMvnpjenoa0/TempSuite3003661673355067845.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite3003661673355067845.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite3003661673355067845.adam/referenceName=1 /tmp/adamTestMvnpjenoa0/TempSuite3003661673355067845.adam/referenceName=1/positionBin=26 /tmp/adamTestMvnpjenoa0/TempSuite3003661673355067845.adam/referenceName=1/positionBin=26/part-00000-7f0a24dd-3f49-46e7-b753-6507d66b5fe9.c000.snappy.parquet /tmp/adamTestMvnpjenoa0/TempSuite3003661673355067845.adam/referenceName=1/positionBin=26/.part-00000-7f0a24dd-3f49-46e7-b753-6507d66b5fe9.c000.snappy.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite3003661673355067845.adam/referenceName=1/positionBin=240 /tmp/adamTestMvnpjenoa0/TempSuite3003661673355067845.adam/referenceName=1/positionBin=240/part-00000-7f0a24dd-3f49-46e7-b753-6507d66b5fe9.c000.snappy.parquet /tmp/adamTestMvnpjenoa0/TempSuite3003661673355067845.adam/referenceName=1/positionBin=240/.part-00000-7f0a24dd-3f49-46e7-b753-6507d66b5fe9.c000.snappy.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite3003661673355067845.adam/_readGroups.avro /tmp/adamTestMvnpjenoa0/TempSuite3003661673355067845.adam/_partitionedByStartPos /tmp/adamTestMvnpjenoa0/TempSuite3003661673355067845.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite3003661673355067845.adam/._processingSteps.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite3003661673355067845.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite3003661673355067845.adam/._readGroups.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite3003661673355067845.adam/._partitionedByStartPos.crc /tmp/adamTestMvnpjenoa0/TempSuite3003661673355067845.adam/referenceName=2 /tmp/adamTestMvnpjenoa0/TempSuite3003661673355067845.adam/referenceName=2/positionBin=189 /tmp/adamTestMvnpjenoa0/TempSuite3003661673355067845.adam/referenceName=2/positionBin=189/part-00000-7f0a24dd-3f49-46e7-b753-6507d66b5fe9.c000.snappy.parquet /tmp/adamTestMvnpjenoa0/TempSuite3003661673355067845.adam/referenceName=2/positionBin=189/.part-00000-7f0a24dd-3f49-46e7-b753-6507d66b5fe9.c000.snappy.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite3003661673355067845.adam/_processingSteps.avro /tmp/adamTestMvnpjenoa0/TempSuite7350422981194583357 /tmp/adamTestMvnpjenoa0/.FeatureDatasetFunctionsSuite3222945418650442634.interval_list.crc /tmp/adamTestMvnpjenoa0/TempSuite262166617179322680reads12.sam /tmp/adamTestMvnpjenoa0/TempSuite401858085426789011 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite2796341201094247953 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite2611305893602536323 /tmp/adamTestMvnpjenoa0/TempSuite4319920536613111518.adam /tmp/adamTestMvnpjenoa0/TempSuite4319920536613111518.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite4319920536613111518.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite4319920536613111518.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite4319920536613111518.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite4319920536613111518.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite4319920536613111518.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite4319920536613111518.adam/_common_metadata /tmp/adamTestMvnpjenoa0/TempSuite4319920536613111518.adam/._header.crc /tmp/adamTestMvnpjenoa0/TempSuite4319920536613111518.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite4319920536613111518.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite4319920536613111518.adam/_metadata /tmp/adamTestMvnpjenoa0/TempSuite4319920536613111518.adam/_header /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite8066613744102904888.interval_list /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite8066613744102904888.interval_list/_SUCCESS /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite8066613744102904888.interval_list/part-00001 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite8066613744102904888.interval_list/.part-00003.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite8066613744102904888.interval_list/part-00000 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite8066613744102904888.interval_list/part-00003 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite8066613744102904888.interval_list/.part-00000.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite8066613744102904888.interval_list/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite8066613744102904888.interval_list/part-00002 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite8066613744102904888.interval_list/.part-00002.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite8066613744102904888.interval_list/.part-00001.crc /tmp/adamTestMvnpjenoa0/TempSuite1004286049073876191.adam /tmp/adamTestMvnpjenoa0/TempSuite1004286049073876191.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite1004286049073876191.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite1004286049073876191.adam/.part-00000-36cecc58-fd55-4473-8a8b-960eb806e462-c000.snappy.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite1004286049073876191.adam/part-00001-36cecc58-fd55-4473-8a8b-960eb806e462-c000.snappy.parquet /tmp/adamTestMvnpjenoa0/TempSuite1004286049073876191.adam/_readGroups.avro /tmp/adamTestMvnpjenoa0/TempSuite1004286049073876191.adam/part-00000-36cecc58-fd55-4473-8a8b-960eb806e462-c000.snappy.parquet /tmp/adamTestMvnpjenoa0/TempSuite1004286049073876191.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite1004286049073876191.adam/part-00002-36cecc58-fd55-4473-8a8b-960eb806e462-c000.snappy.parquet /tmp/adamTestMvnpjenoa0/TempSuite1004286049073876191.adam/.part-00001-36cecc58-fd55-4473-8a8b-960eb806e462-c000.snappy.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite1004286049073876191.adam/._processingSteps.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite1004286049073876191.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite1004286049073876191.adam/._readGroups.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite1004286049073876191.adam/.part-00002-36cecc58-fd55-4473-8a8b-960eb806e462-c000.snappy.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite1004286049073876191.adam/_processingSteps.avro /tmp/adamTestMvnpjenoa0/TempSuite246166508477427213.sam /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite4558689597353408251 /tmp/adamTestMvnpjenoa0/TempSuite7306932562337019922 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite5889890028593780031.interval_list /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite5889890028593780031.interval_list/_SUCCESS /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite5889890028593780031.interval_list/part-00001 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite5889890028593780031.interval_list/.part-00003.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite5889890028593780031.interval_list/part-00000 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite5889890028593780031.interval_list/part-00003 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite5889890028593780031.interval_list/.part-00000.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite5889890028593780031.interval_list/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite5889890028593780031.interval_list/part-00002 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite5889890028593780031.interval_list/.part-00002.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite5889890028593780031.interval_list/.part-00001.crc /tmp/adamTestMvnpjenoa0/TempSuite6213403521807431518.adam /tmp/adamTestMvnpjenoa0/TempSuite6213403521807431518.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite6213403521807431518.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite6213403521807431518.adam/._samples.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite6213403521807431518.adam/.part-00002-10488d9f-03ed-433e-9a45-3b01d4a1b275-c000.snappy.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite6213403521807431518.adam/part-00001-10488d9f-03ed-433e-9a45-3b01d4a1b275-c000.snappy.parquet /tmp/adamTestMvnpjenoa0/TempSuite6213403521807431518.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite6213403521807431518.adam/part-00000-10488d9f-03ed-433e-9a45-3b01d4a1b275-c000.snappy.parquet /tmp/adamTestMvnpjenoa0/TempSuite6213403521807431518.adam/._header.crc /tmp/adamTestMvnpjenoa0/TempSuite6213403521807431518.adam/.part-00001-10488d9f-03ed-433e-9a45-3b01d4a1b275-c000.snappy.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite6213403521807431518.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite6213403521807431518.adam/_samples.avro /tmp/adamTestMvnpjenoa0/TempSuite6213403521807431518.adam/part-00002-10488d9f-03ed-433e-9a45-3b01d4a1b275-c000.snappy.parquet /tmp/adamTestMvnpjenoa0/TempSuite6213403521807431518.adam/_header /tmp/adamTestMvnpjenoa0/TempSuite6213403521807431518.adam/.part-00000-10488d9f-03ed-433e-9a45-3b01d4a1b275-c000.snappy.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite2823063181070911277.vcf /tmp/adamTestMvnpjenoa0/TempSuite2823063181070911277.vcf/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite2823063181070911277.vcf/part-r-00000 /tmp/adamTestMvnpjenoa0/TempSuite2823063181070911277.vcf/.part-r-00000.crc /tmp/adamTestMvnpjenoa0/TempSuite2823063181070911277.vcf/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite4274291447532204628.bed /tmp/adamTestMvnpjenoa0/TempSuite4274291447532204628.bed/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite4274291447532204628.bed/part-00000 /tmp/adamTestMvnpjenoa0/TempSuite4274291447532204628.bed/.part-00000.crc /tmp/adamTestMvnpjenoa0/TempSuite4274291447532204628.bed/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite2473079845127639752 /tmp/adamTestMvnpjenoa0/TempSuite8356449429863811796 /tmp/adamTestMvnpjenoa0/TempSuite8231743441889909402 /tmp/adamTestMvnpjenoa0/TempSuite2269854606739391836 /tmp/adamTestMvnpjenoa0/1557939589287-0 /tmp/adamTestMvnpjenoa0/1557939589287-0/bamReads.adam /tmp/adamTestMvnpjenoa0/1557939589287-0/bamReads.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/1557939589287-0/bamReads.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/1557939589287-0/bamReads.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/1557939589287-0/bamReads.adam/_readGroups.avro /tmp/adamTestMvnpjenoa0/1557939589287-0/bamReads.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/1557939589287-0/bamReads.adam/_references.avro /tmp/adamTestMvnpjenoa0/1557939589287-0/bamReads.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/1557939589287-0/bamReads.adam/._processingSteps.avro.crc /tmp/adamTestMvnpjenoa0/1557939589287-0/bamReads.adam/_common_metadata /tmp/adamTestMvnpjenoa0/1557939589287-0/bamReads.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/1557939589287-0/bamReads.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/1557939589287-0/bamReads.adam/._readGroups.avro.crc /tmp/adamTestMvnpjenoa0/1557939589287-0/bamReads.adam/_metadata /tmp/adamTestMvnpjenoa0/1557939589287-0/bamReads.adam/_processingSteps.avro /tmp/adamTestMvnpjenoa0/TempSuite6124671484567629296.bed /tmp/adamTestMvnpjenoa0/TempSuite6124671484567629296.bed/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite6124671484567629296.bed/part-00000 /tmp/adamTestMvnpjenoa0/TempSuite6124671484567629296.bed/.part-00000.crc /tmp/adamTestMvnpjenoa0/TempSuite6124671484567629296.bed/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite1644617014410985988.bed /tmp/adamTestMvnpjenoa0/TempSuite1644617014410985988.bed/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite1644617014410985988.bed/part-00000 /tmp/adamTestMvnpjenoa0/TempSuite1644617014410985988.bed/.part-00000.crc /tmp/adamTestMvnpjenoa0/TempSuite1644617014410985988.bed/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite316669657898728846.adam /tmp/adamTestMvnpjenoa0/TempSuite316669657898728846.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite316669657898728846.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite316669657898728846.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite316669657898728846.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite316669657898728846.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite316669657898728846.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite316669657898728846.adam/_common_metadata /tmp/adamTestMvnpjenoa0/TempSuite316669657898728846.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite316669657898728846.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite316669657898728846.adam/_metadata /tmp/adamTestMvnpjenoa0/TempSuite5109285308672328680.bed /tmp/adamTestMvnpjenoa0/TempSuite5109285308672328680.bed/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite5109285308672328680.bed/part-00000 /tmp/adamTestMvnpjenoa0/TempSuite5109285308672328680.bed/.part-00000.crc /tmp/adamTestMvnpjenoa0/TempSuite5109285308672328680.bed/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite4927734975449021992.bed /tmp/adamTestMvnpjenoa0/TempSuite4927734975449021992.bed/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite4927734975449021992.bed/part-00001 /tmp/adamTestMvnpjenoa0/TempSuite4927734975449021992.bed/.part-00003.crc /tmp/adamTestMvnpjenoa0/TempSuite4927734975449021992.bed/part-00000 /tmp/adamTestMvnpjenoa0/TempSuite4927734975449021992.bed/part-00003 /tmp/adamTestMvnpjenoa0/TempSuite4927734975449021992.bed/.part-00000.crc /tmp/adamTestMvnpjenoa0/TempSuite4927734975449021992.bed/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite4927734975449021992.bed/part-00002 /tmp/adamTestMvnpjenoa0/TempSuite4927734975449021992.bed/.part-00002.crc /tmp/adamTestMvnpjenoa0/TempSuite4927734975449021992.bed/.part-00001.crc /tmp/adamTestMvnpjenoa0/TempSuite7126587291281374998.adam /tmp/adamTestMvnpjenoa0/TempSuite7126587291281374998.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite7126587291281374998.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite7126587291281374998.adam/_readGroups.avro /tmp/adamTestMvnpjenoa0/TempSuite7126587291281374998.adam/.part-00000-a8485f4c-f93c-400e-a170-01d95ef2d13d-c000.snappy.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite7126587291281374998.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite7126587291281374998.adam/._processingSteps.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite7126587291281374998.adam/part-00000-a8485f4c-f93c-400e-a170-01d95ef2d13d-c000.snappy.parquet /tmp/adamTestMvnpjenoa0/TempSuite7126587291281374998.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite7126587291281374998.adam/._readGroups.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite7126587291281374998.adam/_processingSteps.avro /tmp/adamTestMvnpjenoa0/TempSuite4660722870795249047 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite2977519491974886712 /tmp/adamTestMvnpjenoa0/TempSuite1713443263698808030 /tmp/adamTestMvnpjenoa0/TempSuite1202817804488828426.bed /tmp/adamTestMvnpjenoa0/TempSuite1202817804488828426.bed/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite1202817804488828426.bed/part-00000 /tmp/adamTestMvnpjenoa0/TempSuite1202817804488828426.bed/.part-00000.crc /tmp/adamTestMvnpjenoa0/TempSuite1202817804488828426.bed/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/1472562767134176217 /tmp/adamTestMvnpjenoa0/1472562767134176217/sorted-variants.vcf /tmp/adamTestMvnpjenoa0/1472562767134176217/.sorted-variants.vcf.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite3284951755692471043.bed /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite3284951755692471043.bed/_SUCCESS /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite3284951755692471043.bed/part-00001 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite3284951755692471043.bed/.part-00003.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite3284951755692471043.bed/part-00000 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite3284951755692471043.bed/part-00003 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite3284951755692471043.bed/.part-00000.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite3284951755692471043.bed/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite3284951755692471043.bed/part-00002 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite3284951755692471043.bed/.part-00002.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite3284951755692471043.bed/.part-00001.crc /tmp/adamTestMvnpjenoa0/TempSuite9057847475247381088 /tmp/adamTestMvnpjenoa0/TempSuite2866337395919035423 /tmp/adamTestMvnpjenoa0/TempSuite6820875629505030184.sam /tmp/adamTestMvnpjenoa0/ordered.sam5128802125097480764.sam /tmp/adamTestMvnpjenoa0/TempSuite480595958702862540.adam /tmp/adamTestMvnpjenoa0/TempSuite480595958702862540.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite480595958702862540.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite480595958702862540.adam/_readGroups.avro /tmp/adamTestMvnpjenoa0/TempSuite480595958702862540.adam/part-00000-86026f7b-9537-49c8-b558-64e016b2e373-c000.snappy.parquet /tmp/adamTestMvnpjenoa0/TempSuite480595958702862540.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite480595958702862540.adam/.part-00000-86026f7b-9537-49c8-b558-64e016b2e373-c000.snappy.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite480595958702862540.adam/._processingSteps.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite480595958702862540.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite480595958702862540.adam/._readGroups.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite480595958702862540.adam/_processingSteps.avro /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite7975308750151627586 /tmp/adamTestMvnpjenoa0/TempSuite5681689456063823319.bed /tmp/adamTestMvnpjenoa0/TempSuite5681689456063823319.bed/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite5681689456063823319.bed/part-00001 /tmp/adamTestMvnpjenoa0/TempSuite5681689456063823319.bed/.part-00003.crc /tmp/adamTestMvnpjenoa0/TempSuite5681689456063823319.bed/part-00000 /tmp/adamTestMvnpjenoa0/TempSuite5681689456063823319.bed/part-00003 /tmp/adamTestMvnpjenoa0/TempSuite5681689456063823319.bed/.part-00000.crc /tmp/adamTestMvnpjenoa0/TempSuite5681689456063823319.bed/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite5681689456063823319.bed/part-00002 /tmp/adamTestMvnpjenoa0/TempSuite5681689456063823319.bed/.part-00002.crc /tmp/adamTestMvnpjenoa0/TempSuite5681689456063823319.bed/.part-00001.crc /tmp/adamTestMvnpjenoa0/TempSuite1398970179786229198 /tmp/adamTestMvnpjenoa0/sorted-variants.vcf2466917594149069690.vcf /tmp/adamTestMvnpjenoa0/TempSuite4660722870795249047.adam /tmp/adamTestMvnpjenoa0/TempSuite4660722870795249047.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite4660722870795249047.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite4660722870795249047.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite4660722870795249047.adam/_readGroups.avro /tmp/adamTestMvnpjenoa0/TempSuite4660722870795249047.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite4660722870795249047.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite4660722870795249047.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite4660722870795249047.adam/._processingSteps.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite4660722870795249047.adam/_common_metadata /tmp/adamTestMvnpjenoa0/TempSuite4660722870795249047.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite4660722870795249047.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite4660722870795249047.adam/._readGroups.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite4660722870795249047.adam/_metadata /tmp/adamTestMvnpjenoa0/TempSuite4660722870795249047.adam/_processingSteps.avro /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite5821732757281570214.narrowPeak /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite5821732757281570214.narrowPeak/_SUCCESS /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite5821732757281570214.narrowPeak/part-00001 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite5821732757281570214.narrowPeak/.part-00003.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite5821732757281570214.narrowPeak/part-00000 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite5821732757281570214.narrowPeak/part-00003 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite5821732757281570214.narrowPeak/.part-00000.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite5821732757281570214.narrowPeak/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite5821732757281570214.narrowPeak/part-00002 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite5821732757281570214.narrowPeak/.part-00002.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite5821732757281570214.narrowPeak/.part-00001.crc /tmp/adamTestMvnpjenoa0/TempSuite6563902507541632662.adam /tmp/adamTestMvnpjenoa0/TempSuite6563902507541632662.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite6563902507541632662.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite6563902507541632662.adam/._samples.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite6563902507541632662.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite6563902507541632662.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite6563902507541632662.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite6563902507541632662.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite6563902507541632662.adam/_common_metadata /tmp/adamTestMvnpjenoa0/TempSuite6563902507541632662.adam/._header.crc /tmp/adamTestMvnpjenoa0/TempSuite6563902507541632662.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite6563902507541632662.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite6563902507541632662.adam/_samples.avro /tmp/adamTestMvnpjenoa0/TempSuite6563902507541632662.adam/_metadata /tmp/adamTestMvnpjenoa0/TempSuite6563902507541632662.adam/_header /tmp/adamTestMvnpjenoa0/TempSuite1004286049073876191 /tmp/adamTestMvnpjenoa0/TempSuite5228295354935105937.adam /tmp/adamTestMvnpjenoa0/TempSuite5228295354935105937.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite5228295354935105937.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite5228295354935105937.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite5228295354935105937.adam/_readGroups.avro /tmp/adamTestMvnpjenoa0/TempSuite5228295354935105937.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite5228295354935105937.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite5228295354935105937.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite5228295354935105937.adam/._processingSteps.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite5228295354935105937.adam/_common_metadata /tmp/adamTestMvnpjenoa0/TempSuite5228295354935105937.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite5228295354935105937.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite5228295354935105937.adam/._readGroups.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite5228295354935105937.adam/_metadata /tmp/adamTestMvnpjenoa0/TempSuite5228295354935105937.adam/_processingSteps.avro /tmp/adamTestMvnpjenoa0/7228446162899603462 /tmp/adamTestMvnpjenoa0/7228446162899603462/ctg.adam /tmp/adamTestMvnpjenoa0/7228446162899603462/ctg.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/7228446162899603462/ctg.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/7228446162899603462/ctg.adam/_partitionedByStartPos /tmp/adamTestMvnpjenoa0/7228446162899603462/ctg.adam/_references.avro /tmp/adamTestMvnpjenoa0/7228446162899603462/ctg.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/7228446162899603462/ctg.adam/._partitionedByStartPos.crc /tmp/adamTestMvnpjenoa0/7228446162899603462/ctg.adam/referenceName=HLA-DQB1%2A05%3A01%3A01%3A02 /tmp/adamTestMvnpjenoa0/7228446162899603462/ctg.adam/referenceName=HLA-DQB1%2A05%3A01%3A01%3A02/positionBin=0 /tmp/adamTestMvnpjenoa0/7228446162899603462/ctg.adam/referenceName=HLA-DQB1%2A05%3A01%3A01%3A02/positionBin=0/part-00000-a979e8cf-b286-4722-bbc2-c0883d8afb88.c000.snappy.parquet /tmp/adamTestMvnpjenoa0/7228446162899603462/ctg.adam/referenceName=HLA-DQB1%2A05%3A01%3A01%3A02/positionBin=0/.part-00000-a979e8cf-b286-4722-bbc2-c0883d8afb88.c000.snappy.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite8605394601149688532.adam /tmp/adamTestMvnpjenoa0/TempSuite8605394601149688532.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite8605394601149688532.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite8605394601149688532.adam/.part-00000-ae9e62d0-0295-48e5-91e2-5baaef4ca0f0-c000.snappy.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite8605394601149688532.adam/part-00000-ae9e62d0-0295-48e5-91e2-5baaef4ca0f0-c000.snappy.parquet /tmp/adamTestMvnpjenoa0/TempSuite8605394601149688532.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite8605394601149688532.adam/.part-00002-ae9e62d0-0295-48e5-91e2-5baaef4ca0f0-c000.snappy.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite8605394601149688532.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite8605394601149688532.adam/part-00001-ae9e62d0-0295-48e5-91e2-5baaef4ca0f0-c000.snappy.parquet /tmp/adamTestMvnpjenoa0/TempSuite8605394601149688532.adam/part-00002-ae9e62d0-0295-48e5-91e2-5baaef4ca0f0-c000.snappy.parquet /tmp/adamTestMvnpjenoa0/TempSuite8605394601149688532.adam/.part-00001-ae9e62d0-0295-48e5-91e2-5baaef4ca0f0-c000.snappy.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite5934219242757433895 /tmp/adamTestMvnpjenoa0/TempSuite4142813558507540852 /tmp/adamTestMvnpjenoa0/unordered.sam1086684960515358259.sam /tmp/adamTestMvnpjenoa0/TempSuite8165895894338538824 /tmp/adamTestMvnpjenoa0/TempSuite415673015835628979.adam /tmp/adamTestMvnpjenoa0/TempSuite415673015835628979.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite415673015835628979.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite415673015835628979.adam/.part-00000-343e529d-6e3e-43b9-92b8-2af4405d0e30-c000.snappy.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite415673015835628979.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite415673015835628979.adam/part-00000-343e529d-6e3e-43b9-92b8-2af4405d0e30-c000.snappy.parquet /tmp/adamTestMvnpjenoa0/TempSuite415673015835628979.adam/._header.crc /tmp/adamTestMvnpjenoa0/TempSuite415673015835628979.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite415673015835628979.adam/_header /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite3222945418650442634.interval_list /tmp/adamTestMvnpjenoa0/TempSuite7774792650731328615.adam /tmp/adamTestMvnpjenoa0/TempSuite7774792650731328615.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite7774792650731328615.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite7774792650731328615.adam/._samples.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite7774792650731328615.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite7774792650731328615.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite7774792650731328615.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite7774792650731328615.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite7774792650731328615.adam/_common_metadata /tmp/adamTestMvnpjenoa0/TempSuite7774792650731328615.adam/._header.crc /tmp/adamTestMvnpjenoa0/TempSuite7774792650731328615.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite7774792650731328615.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite7774792650731328615.adam/_samples.avro /tmp/adamTestMvnpjenoa0/TempSuite7774792650731328615.adam/_metadata /tmp/adamTestMvnpjenoa0/TempSuite7774792650731328615.adam/_header /tmp/adamTestMvnpjenoa0/.FeatureDatasetFunctionsSuite361418958970110841.narrowPeak.crc /tmp/adamTestMvnpjenoa0/TempSuite3854446984732693819reads12.sam /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite3490034250567771633 /tmp/adamTestMvnpjenoa0/adam-cli.TransformFeaturesSuite3809618386616708636.adam /tmp/adamTestMvnpjenoa0/adam-cli.TransformFeaturesSuite3809618386616708636.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/adam-cli.TransformFeaturesSuite3809618386616708636.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/adam-cli.TransformFeaturesSuite3809618386616708636.adam/._samples.avro.crc /tmp/adamTestMvnpjenoa0/adam-cli.TransformFeaturesSuite3809618386616708636.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/adam-cli.TransformFeaturesSuite3809618386616708636.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/adam-cli.TransformFeaturesSuite3809618386616708636.adam/_references.avro /tmp/adamTestMvnpjenoa0/adam-cli.TransformFeaturesSuite3809618386616708636.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/adam-cli.TransformFeaturesSuite3809618386616708636.adam/_common_metadata /tmp/adamTestMvnpjenoa0/adam-cli.TransformFeaturesSuite3809618386616708636.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/adam-cli.TransformFeaturesSuite3809618386616708636.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/adam-cli.TransformFeaturesSuite3809618386616708636.adam/_samples.avro /tmp/adamTestMvnpjenoa0/adam-cli.TransformFeaturesSuite3809618386616708636.adam/_metadata /tmp/adamTestMvnpjenoa0/2515019442109072873 /tmp/adamTestMvnpjenoa0/2515019442109072873/out.bam /tmp/adamTestMvnpjenoa0/2515019442109072873/out.bam_head /tmp/adamTestMvnpjenoa0/2515019442109072873/.out.bam.crc /tmp/adamTestMvnpjenoa0/2515019442109072873/out.bam_tail /tmp/adamTestMvnpjenoa0/2515019442109072873/out.bam_tail/_SUCCESS /tmp/adamTestMvnpjenoa0/2515019442109072873/out.bam_tail/.part-r-00001.bam.crc /tmp/adamTestMvnpjenoa0/2515019442109072873/out.bam_tail/part-r-00000.bam /tmp/adamTestMvnpjenoa0/2515019442109072873/out.bam_tail/part-r-00001.bam /tmp/adamTestMvnpjenoa0/2515019442109072873/out.bam_tail/.part-r-00002.bam.crc /tmp/adamTestMvnpjenoa0/2515019442109072873/out.bam_tail/part-r-00003.bam /tmp/adamTestMvnpjenoa0/2515019442109072873/out.bam_tail/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/2515019442109072873/out.bam_tail/.part-r-00003.bam.crc /tmp/adamTestMvnpjenoa0/2515019442109072873/out.bam_tail/part-r-00002.bam /tmp/adamTestMvnpjenoa0/2515019442109072873/out.bam_tail/.part-r-00000.bam.crc /tmp/adamTestMvnpjenoa0/2515019442109072873/.out.bam_head.crc /tmp/adamTestMvnpjenoa0/TempSuite6583163745404908914.bed /tmp/adamTestMvnpjenoa0/TempSuite6583163745404908914.bed/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite6583163745404908914.bed/part-00000 /tmp/adamTestMvnpjenoa0/TempSuite6583163745404908914.bed/.part-00000.crc /tmp/adamTestMvnpjenoa0/TempSuite6583163745404908914.bed/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/.FeatureDatasetFunctionsSuite5261417657002336405.bed.crc /tmp/adamTestMvnpjenoa0/.TempSuite246166508477427213.sam.crc /tmp/adamTestMvnpjenoa0/TempSuite7768261566229609624 /tmp/adamTestMvnpjenoa0/.TempSuite787098745758403258_1.fq.crc /tmp/adamTestMvnpjenoa0/TempSuite1900933834625183911 /tmp/adamTestMvnpjenoa0/TempSuite4165278431039046691.adam /tmp/adamTestMvnpjenoa0/TempSuite4165278431039046691.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite4165278431039046691.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite4165278431039046691.adam/.part-00000-43bd2ab2-c813-4bcd-9d6e-d1ab68def107-c000.snappy.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite4165278431039046691.adam/_readGroups.avro /tmp/adamTestMvnpjenoa0/TempSuite4165278431039046691.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite4165278431039046691.adam/.part-00001-43bd2ab2-c813-4bcd-9d6e-d1ab68def107-c000.snappy.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite4165278431039046691.adam/part-00002-43bd2ab2-c813-4bcd-9d6e-d1ab68def107-c000.snappy.parquet /tmp/adamTestMvnpjenoa0/TempSuite4165278431039046691.adam/._processingSteps.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite4165278431039046691.adam/part-00001-43bd2ab2-c813-4bcd-9d6e-d1ab68def107-c000.snappy.parquet /tmp/adamTestMvnpjenoa0/TempSuite4165278431039046691.adam/.part-00002-43bd2ab2-c813-4bcd-9d6e-d1ab68def107-c000.snappy.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite4165278431039046691.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite4165278431039046691.adam/._readGroups.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite4165278431039046691.adam/part-00000-43bd2ab2-c813-4bcd-9d6e-d1ab68def107-c000.snappy.parquet /tmp/adamTestMvnpjenoa0/TempSuite4165278431039046691.adam/_processingSteps.avro /tmp/adamTestMvnpjenoa0/TempSuite4358674517477618490.bam /tmp/adamTestMvnpjenoa0/TempSuite4358674517477618490.bam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite4358674517477618490.bam/part-r-00000.bam /tmp/adamTestMvnpjenoa0/TempSuite4358674517477618490.bam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite4358674517477618490.bam/.part-r-00000.bam.crc /tmp/adamTestMvnpjenoa0/TempSuite8610345334512584837 /tmp/adamTestMvnpjenoa0/6126392146347460276 /tmp/adamTestMvnpjenoa0/6126392146347460276/unordered.adam /tmp/adamTestMvnpjenoa0/6126392146347460276/unordered.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/6126392146347460276/unordered.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/6126392146347460276/unordered.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/6126392146347460276/unordered.adam/_readGroups.avro /tmp/adamTestMvnpjenoa0/6126392146347460276/unordered.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/6126392146347460276/unordered.adam/_references.avro /tmp/adamTestMvnpjenoa0/6126392146347460276/unordered.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/6126392146347460276/unordered.adam/._processingSteps.avro.crc /tmp/adamTestMvnpjenoa0/6126392146347460276/unordered.adam/_common_metadata /tmp/adamTestMvnpjenoa0/6126392146347460276/unordered.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/6126392146347460276/unordered.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/6126392146347460276/unordered.adam/._readGroups.avro.crc /tmp/adamTestMvnpjenoa0/6126392146347460276/unordered.adam/_metadata /tmp/adamTestMvnpjenoa0/6126392146347460276/unordered.adam/_processingSteps.avro /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite8676583558860388852.gff3 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite8676583558860388852.gff3/_SUCCESS /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite8676583558860388852.gff3/part-00001 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite8676583558860388852.gff3/.part-00003.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite8676583558860388852.gff3/part-00000 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite8676583558860388852.gff3/part-00003 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite8676583558860388852.gff3/.part-00000.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite8676583558860388852.gff3/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite8676583558860388852.gff3/part-00002 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite8676583558860388852.gff3/.part-00002.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite8676583558860388852.gff3/.part-00001.crc /tmp/adamTestMvnpjenoa0/sample1.queryname.sam8292472699012842631.queryname.sam /tmp/adamTestMvnpjenoa0/2942142225627878812 /tmp/adamTestMvnpjenoa0/2942142225627878812/predicate.1.adam /tmp/adamTestMvnpjenoa0/2942142225627878812/predicate.1.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/2942142225627878812/predicate.1.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/2942142225627878812/predicate.1.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/2942142225627878812/predicate.1.adam/_readGroups.avro /tmp/adamTestMvnpjenoa0/2942142225627878812/predicate.1.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/2942142225627878812/predicate.1.adam/_references.avro /tmp/adamTestMvnpjenoa0/2942142225627878812/predicate.1.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/2942142225627878812/predicate.1.adam/._processingSteps.avro.crc /tmp/adamTestMvnpjenoa0/2942142225627878812/predicate.1.adam/_common_metadata /tmp/adamTestMvnpjenoa0/2942142225627878812/predicate.1.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/2942142225627878812/predicate.1.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/2942142225627878812/predicate.1.adam/._readGroups.avro.crc /tmp/adamTestMvnpjenoa0/2942142225627878812/predicate.1.adam/_metadata /tmp/adamTestMvnpjenoa0/2942142225627878812/predicate.1.adam/_processingSteps.avro /tmp/adamTestMvnpjenoa0/TempSuite8592915387563865048.adam /tmp/adamTestMvnpjenoa0/TempSuite8592915387563865048.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite8592915387563865048.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite8592915387563865048.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite8592915387563865048.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite8592915387563865048.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite8592915387563865048.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite8592915387563865048.adam/_common_metadata /tmp/adamTestMvnpjenoa0/TempSuite8592915387563865048.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite8592915387563865048.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite8592915387563865048.adam/_metadata /tmp/adamTestMvnpjenoa0/TempSuite8335755103731210972.adam /tmp/adamTestMvnpjenoa0/TempSuite8335755103731210972.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite8335755103731210972.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite8335755103731210972.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite8335755103731210972.adam/.part-r-00003.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite8335755103731210972.adam/part-r-00001.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite8335755103731210972.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite8335755103731210972.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite8335755103731210972.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite8335755103731210972.adam/.part-r-00001.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite8335755103731210972.adam/part-r-00002.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite8335755103731210972.adam/.part-r-00002.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite8335755103731210972.adam/_common_metadata /tmp/adamTestMvnpjenoa0/TempSuite8335755103731210972.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite8335755103731210972.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite8335755103731210972.adam/_metadata /tmp/adamTestMvnpjenoa0/TempSuite8335755103731210972.adam/part-r-00003.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite5681689456063823319 /tmp/adamTestMvnpjenoa0/ordered.sam476881862253689092.sam /tmp/adamTestMvnpjenoa0/TempSuite3476488343346340560.adam /tmp/adamTestMvnpjenoa0/TempSuite3476488343346340560.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite3476488343346340560.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite3476488343346340560.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite3476488343346340560.adam/_readGroups.avro /tmp/adamTestMvnpjenoa0/TempSuite3476488343346340560.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite3476488343346340560.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite3476488343346340560.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite3476488343346340560.adam/._processingSteps.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite3476488343346340560.adam/_common_metadata /tmp/adamTestMvnpjenoa0/TempSuite3476488343346340560.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite3476488343346340560.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite3476488343346340560.adam/._readGroups.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite3476488343346340560.adam/_metadata /tmp/adamTestMvnpjenoa0/TempSuite3476488343346340560.adam/_processingSteps.avro /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite5234029325846072790.gtf /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite5234029325846072790.gtf/_SUCCESS /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite5234029325846072790.gtf/part-00001 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite5234029325846072790.gtf/.part-00003.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite5234029325846072790.gtf/part-00000 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite5234029325846072790.gtf/part-00003 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite5234029325846072790.gtf/.part-00000.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite5234029325846072790.gtf/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite5234029325846072790.gtf/part-00002 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite5234029325846072790.gtf/.part-00002.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite5234029325846072790.gtf/.part-00001.crc /tmp/adamTestMvnpjenoa0/TempSuite8792683224090933900.adam /tmp/adamTestMvnpjenoa0/TempSuite8792683224090933900.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite8792683224090933900.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite8792683224090933900.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite8792683224090933900.adam/.part-r-00003.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite8792683224090933900.adam/part-r-00001.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite8792683224090933900.adam/_readGroups.avro /tmp/adamTestMvnpjenoa0/TempSuite8792683224090933900.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite8792683224090933900.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite8792683224090933900.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite8792683224090933900.adam/.part-r-00001.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite8792683224090933900.adam/part-r-00002.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite8792683224090933900.adam/._processingSteps.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite8792683224090933900.adam/.part-r-00002.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite8792683224090933900.adam/_common_metadata /tmp/adamTestMvnpjenoa0/TempSuite8792683224090933900.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite8792683224090933900.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite8792683224090933900.adam/._readGroups.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite8792683224090933900.adam/_metadata /tmp/adamTestMvnpjenoa0/TempSuite8792683224090933900.adam/part-r-00003.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite8792683224090933900.adam/_processingSteps.avro /tmp/adamTestMvnpjenoa0/TempSuite3915827702697355578 /tmp/adamTestMvnpjenoa0/TempSuite8681581463592444244_1.fq /tmp/adamTestMvnpjenoa0/TempSuite8681581463592444244_1.fq/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite8681581463592444244_1.fq/part-00000 /tmp/adamTestMvnpjenoa0/TempSuite8681581463592444244_1.fq/.part-00000.crc /tmp/adamTestMvnpjenoa0/TempSuite8681581463592444244_1.fq/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite4274165549462923049_2.fq /tmp/adamTestMvnpjenoa0/TempSuite3595158599837711064.fa /tmp/adamTestMvnpjenoa0/TempSuite3595158599837711064.fa/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite3595158599837711064.fa/part-00000 /tmp/adamTestMvnpjenoa0/TempSuite3595158599837711064.fa/.part-00000.crc /tmp/adamTestMvnpjenoa0/TempSuite3595158599837711064.fa/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite3141056714993409856.narrowPeak /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite3141056714993409856.narrowPeak/_SUCCESS /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite3141056714993409856.narrowPeak/part-00001 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite3141056714993409856.narrowPeak/.part-00003.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite3141056714993409856.narrowPeak/part-00000 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite3141056714993409856.narrowPeak/part-00003 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite3141056714993409856.narrowPeak/.part-00000.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite3141056714993409856.narrowPeak/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite3141056714993409856.narrowPeak/part-00002 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite3141056714993409856.narrowPeak/.part-00002.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite3141056714993409856.narrowPeak/.part-00001.crc /tmp/adamTestMvnpjenoa0/TempSuite924780161293674120.adam /tmp/adamTestMvnpjenoa0/TempSuite924780161293674120.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite924780161293674120.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite924780161293674120.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite924780161293674120.adam/_readGroups.avro /tmp/adamTestMvnpjenoa0/TempSuite924780161293674120.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite924780161293674120.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite924780161293674120.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite924780161293674120.adam/._processingSteps.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite924780161293674120.adam/_common_metadata /tmp/adamTestMvnpjenoa0/TempSuite924780161293674120.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite924780161293674120.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite924780161293674120.adam/._readGroups.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite924780161293674120.adam/_metadata /tmp/adamTestMvnpjenoa0/TempSuite924780161293674120.adam/_processingSteps.avro /tmp/adamTestMvnpjenoa0/TempSuite7306932562337019922.adam /tmp/adamTestMvnpjenoa0/TempSuite7306932562337019922.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite7306932562337019922.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite7306932562337019922.adam/._samples.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite7306932562337019922.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite7306932562337019922.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite7306932562337019922.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite7306932562337019922.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite7306932562337019922.adam/_common_metadata /tmp/adamTestMvnpjenoa0/TempSuite7306932562337019922.adam/._header.crc /tmp/adamTestMvnpjenoa0/TempSuite7306932562337019922.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite7306932562337019922.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite7306932562337019922.adam/_samples.avro /tmp/adamTestMvnpjenoa0/TempSuite7306932562337019922.adam/_metadata /tmp/adamTestMvnpjenoa0/TempSuite7306932562337019922.adam/_header /tmp/adamTestMvnpjenoa0/javaAC937407777658364077 /tmp/adamTestMvnpjenoa0/javaAC937407777658364077/testRdd.feature.adam /tmp/adamTestMvnpjenoa0/javaAC937407777658364077/testRdd.feature.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/javaAC937407777658364077/testRdd.feature.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/javaAC937407777658364077/testRdd.feature.adam/._samples.avro.crc /tmp/adamTestMvnpjenoa0/javaAC937407777658364077/testRdd.feature.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/javaAC937407777658364077/testRdd.feature.adam/.part-r-00003.gz.parquet.crc /tmp/adamTestMvnpjenoa0/javaAC937407777658364077/testRdd.feature.adam/part-r-00001.gz.parquet /tmp/adamTestMvnpjenoa0/javaAC937407777658364077/testRdd.feature.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/javaAC937407777658364077/testRdd.feature.adam/_references.avro /tmp/adamTestMvnpjenoa0/javaAC937407777658364077/testRdd.feature.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/javaAC937407777658364077/testRdd.feature.adam/.part-r-00001.gz.parquet.crc /tmp/adamTestMvnpjenoa0/javaAC937407777658364077/testRdd.feature.adam/part-r-00002.gz.parquet /tmp/adamTestMvnpjenoa0/javaAC937407777658364077/testRdd.feature.adam/.part-r-00002.gz.parquet.crc /tmp/adamTestMvnpjenoa0/javaAC937407777658364077/testRdd.feature.adam/_common_metadata /tmp/adamTestMvnpjenoa0/javaAC937407777658364077/testRdd.feature.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/javaAC937407777658364077/testRdd.feature.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/javaAC937407777658364077/testRdd.feature.adam/_samples.avro /tmp/adamTestMvnpjenoa0/javaAC937407777658364077/testRdd.feature.adam/_metadata /tmp/adamTestMvnpjenoa0/javaAC937407777658364077/testRdd.feature.adam/part-r-00003.gz.parquet /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite7057506912432072166 /tmp/adamTestMvnpjenoa0/TempSuite7520680222865061927.bed /tmp/adamTestMvnpjenoa0/TempSuite7520680222865061927.bed/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite7520680222865061927.bed/part-00000 /tmp/adamTestMvnpjenoa0/TempSuite7520680222865061927.bed/.part-00000.crc /tmp/adamTestMvnpjenoa0/TempSuite7520680222865061927.bed/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite8374151915469850813.gtf /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite8374151915469850813.gtf/_SUCCESS /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite8374151915469850813.gtf/part-00001 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite8374151915469850813.gtf/.part-00003.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite8374151915469850813.gtf/part-00000 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite8374151915469850813.gtf/part-00003 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite8374151915469850813.gtf/.part-00000.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite8374151915469850813.gtf/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite8374151915469850813.gtf/part-00002 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite8374151915469850813.gtf/.part-00002.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite8374151915469850813.gtf/.part-00001.crc /tmp/adamTestMvnpjenoa0/sorted-variants.lex.vcf7107085885001799021.lex.vcf /tmp/adamTestMvnpjenoa0/2991859857638692561 /tmp/adamTestMvnpjenoa0/2991859857638692561/predicate.1.adam /tmp/adamTestMvnpjenoa0/2991859857638692561/predicate.1.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/2991859857638692561/predicate.1.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/2991859857638692561/predicate.1.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/2991859857638692561/predicate.1.adam/_readGroups.avro /tmp/adamTestMvnpjenoa0/2991859857638692561/predicate.1.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/2991859857638692561/predicate.1.adam/_references.avro /tmp/adamTestMvnpjenoa0/2991859857638692561/predicate.1.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/2991859857638692561/predicate.1.adam/._processingSteps.avro.crc /tmp/adamTestMvnpjenoa0/2991859857638692561/predicate.1.adam/_common_metadata /tmp/adamTestMvnpjenoa0/2991859857638692561/predicate.1.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/2991859857638692561/predicate.1.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/2991859857638692561/predicate.1.adam/._readGroups.avro.crc /tmp/adamTestMvnpjenoa0/2991859857638692561/predicate.1.adam/_metadata /tmp/adamTestMvnpjenoa0/2991859857638692561/predicate.1.adam/_processingSteps.avro /tmp/adamTestMvnpjenoa0/TempSuite346986507046483108 /tmp/adamTestMvnpjenoa0/TempSuite3297386314051980773.adam /tmp/adamTestMvnpjenoa0/TempSuite3297386314051980773.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite3297386314051980773.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite3297386314051980773.adam/._samples.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite3297386314051980773.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite3297386314051980773.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite3297386314051980773.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite3297386314051980773.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite3297386314051980773.adam/_common_metadata /tmp/adamTestMvnpjenoa0/TempSuite3297386314051980773.adam/._header.crc /tmp/adamTestMvnpjenoa0/TempSuite3297386314051980773.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite3297386314051980773.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite3297386314051980773.adam/_samples.avro /tmp/adamTestMvnpjenoa0/TempSuite3297386314051980773.adam/_metadata /tmp/adamTestMvnpjenoa0/TempSuite3297386314051980773.adam/_header /tmp/adamTestMvnpjenoa0/artificial.cram8445281605555165204.cram /tmp/adamTestMvnpjenoa0/TempSuite2930306370869346516 /tmp/adamTestMvnpjenoa0/1557940175781-0 /tmp/adamTestMvnpjenoa0/1557940175781-0/bqsr1-r1.fq /tmp/adamTestMvnpjenoa0/1557940175781-0/bqsr1-r1.fq/_SUCCESS /tmp/adamTestMvnpjenoa0/1557940175781-0/bqsr1-r1.fq/part-00000 /tmp/adamTestMvnpjenoa0/1557940175781-0/bqsr1-r1.fq/.part-00000.crc /tmp/adamTestMvnpjenoa0/1557940175781-0/bqsr1-r1.fq/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/1557940175781-0/bqsr1-r2.fq /tmp/adamTestMvnpjenoa0/1557940175781-0/bqsr1-r2.fq/_SUCCESS /tmp/adamTestMvnpjenoa0/1557940175781-0/bqsr1-r2.fq/part-00000 /tmp/adamTestMvnpjenoa0/1557940175781-0/bqsr1-r2.fq/.part-00000.crc /tmp/adamTestMvnpjenoa0/1557940175781-0/bqsr1-r2.fq/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite3617875519498963883 /tmp/adamTestMvnpjenoa0/5365139363809872538 /tmp/adamTestMvnpjenoa0/TempSuite2266416622975484073.adam /tmp/adamTestMvnpjenoa0/TempSuite2266416622975484073.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite2266416622975484073.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite2266416622975484073.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite2266416622975484073.adam/_readGroups.avro /tmp/adamTestMvnpjenoa0/TempSuite2266416622975484073.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite2266416622975484073.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite2266416622975484073.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite2266416622975484073.adam/._processingSteps.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite2266416622975484073.adam/_common_metadata /tmp/adamTestMvnpjenoa0/TempSuite2266416622975484073.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite2266416622975484073.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite2266416622975484073.adam/._readGroups.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite2266416622975484073.adam/_metadata /tmp/adamTestMvnpjenoa0/TempSuite2266416622975484073.adam/_processingSteps.avro /tmp/adamTestMvnpjenoa0/TempSuite4648806516878885886.fq /tmp/adamTestMvnpjenoa0/TempSuite4648806516878885886.fq/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite4648806516878885886.fq/part-00000 /tmp/adamTestMvnpjenoa0/TempSuite4648806516878885886.fq/.part-00000.crc /tmp/adamTestMvnpjenoa0/TempSuite4648806516878885886.fq/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/1557939527656-0 /tmp/adamTestMvnpjenoa0/1557939527656-0/test.fa /tmp/adamTestMvnpjenoa0/1557939527656-0/test.fa/_SUCCESS /tmp/adamTestMvnpjenoa0/1557939527656-0/test.fa/part-00000 /tmp/adamTestMvnpjenoa0/1557939527656-0/test.fa/.part-00000.crc /tmp/adamTestMvnpjenoa0/1557939527656-0/test.fa/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite7697049635245201364 /tmp/adamTestMvnpjenoa0/1557940200725-0 /tmp/adamTestMvnpjenoa0/1557940200725-0/contigs.fa /tmp/adamTestMvnpjenoa0/1557940200725-0/contigs.fa/_SUCCESS /tmp/adamTestMvnpjenoa0/1557940200725-0/contigs.fa/part-00000 /tmp/adamTestMvnpjenoa0/1557940200725-0/contigs.fa/.part-00000.crc /tmp/adamTestMvnpjenoa0/1557940200725-0/contigs.fa/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/1557940200725-0/contigs.adam /tmp/adamTestMvnpjenoa0/1557940200725-0/contigs.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/1557940200725-0/contigs.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/1557940200725-0/contigs.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/1557940200725-0/contigs.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/1557940200725-0/contigs.adam/_references.avro /tmp/adamTestMvnpjenoa0/1557940200725-0/contigs.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/1557940200725-0/contigs.adam/_common_metadata /tmp/adamTestMvnpjenoa0/1557940200725-0/contigs.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/1557940200725-0/contigs.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/1557940200725-0/contigs.adam/_metadata /tmp/adamTestMvnpjenoa0/javaAC3150150697231059924 /tmp/adamTestMvnpjenoa0/javaAC3150150697231059924/testRdd.fragment.adam /tmp/adamTestMvnpjenoa0/javaAC3150150697231059924/testRdd.fragment.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/javaAC3150150697231059924/testRdd.fragment.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/javaAC3150150697231059924/testRdd.fragment.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/javaAC3150150697231059924/testRdd.fragment.adam/_readGroups.avro /tmp/adamTestMvnpjenoa0/javaAC3150150697231059924/testRdd.fragment.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/javaAC3150150697231059924/testRdd.fragment.adam/_references.avro /tmp/adamTestMvnpjenoa0/javaAC3150150697231059924/testRdd.fragment.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/javaAC3150150697231059924/testRdd.fragment.adam/._processingSteps.avro.crc /tmp/adamTestMvnpjenoa0/javaAC3150150697231059924/testRdd.fragment.adam/_common_metadata /tmp/adamTestMvnpjenoa0/javaAC3150150697231059924/testRdd.fragment.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/javaAC3150150697231059924/testRdd.fragment.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/javaAC3150150697231059924/testRdd.fragment.adam/._readGroups.avro.crc /tmp/adamTestMvnpjenoa0/javaAC3150150697231059924/testRdd.fragment.adam/_metadata /tmp/adamTestMvnpjenoa0/javaAC3150150697231059924/testRdd.fragment.adam/_processingSteps.avro /tmp/adamTestMvnpjenoa0/bqsr11548393029216240637 /tmp/adamTestMvnpjenoa0/bqsr11548393029216240637/.bqsr1.sam.crc /tmp/adamTestMvnpjenoa0/bqsr11548393029216240637/bqsr1.sam /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite3738128330690294641 /tmp/adamTestMvnpjenoa0/TempSuite415673015835628979 /tmp/adamTestMvnpjenoa0/chr20.250k.fa.gz584999154461107684.250k.fa.gz /tmp/adamTestMvnpjenoa0/TempSuite3326500691268380368.adam /tmp/adamTestMvnpjenoa0/TempSuite3326500691268380368.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite3326500691268380368.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite3326500691268380368.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite3326500691268380368.adam/_readGroups.avro /tmp/adamTestMvnpjenoa0/TempSuite3326500691268380368.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite3326500691268380368.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite3326500691268380368.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite3326500691268380368.adam/._processingSteps.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite3326500691268380368.adam/_common_metadata /tmp/adamTestMvnpjenoa0/TempSuite3326500691268380368.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite3326500691268380368.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite3326500691268380368.adam/._readGroups.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite3326500691268380368.adam/_metadata /tmp/adamTestMvnpjenoa0/TempSuite3326500691268380368.adam/_processingSteps.avro /tmp/adamTestMvnpjenoa0/TempSuite3926589950473106911.adam /tmp/adamTestMvnpjenoa0/TempSuite3926589950473106911.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite3926589950473106911.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite3926589950473106911.adam/._samples.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite3926589950473106911.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite3926589950473106911.adam/.part-r-00003.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite3926589950473106911.adam/part-r-00001.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite3926589950473106911.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite3926589950473106911.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite3926589950473106911.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite3926589950473106911.adam/.part-r-00001.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite3926589950473106911.adam/part-r-00002.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite3926589950473106911.adam/.part-r-00002.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite3926589950473106911.adam/_common_metadata /tmp/adamTestMvnpjenoa0/TempSuite3926589950473106911.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite3926589950473106911.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite3926589950473106911.adam/_samples.avro /tmp/adamTestMvnpjenoa0/TempSuite3926589950473106911.adam/_metadata /tmp/adamTestMvnpjenoa0/TempSuite3926589950473106911.adam/part-r-00003.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite2433004316762971474 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite277214127024262540 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite7057506912432072166.gff3 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite7057506912432072166.gff3/_SUCCESS /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite7057506912432072166.gff3/part-00001 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite7057506912432072166.gff3/.part-00003.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite7057506912432072166.gff3/part-00000 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite7057506912432072166.gff3/part-00003 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite7057506912432072166.gff3/.part-00000.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite7057506912432072166.gff3/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite7057506912432072166.gff3/part-00002 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite7057506912432072166.gff3/.part-00002.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite7057506912432072166.gff3/.part-00001.crc /tmp/adamTestMvnpjenoa0/unordered.sam1891561647807715981.sam /tmp/adamTestMvnpjenoa0/TempSuite7110799967104893760.adam /tmp/adamTestMvnpjenoa0/TempSuite7110799967104893760.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite7110799967104893760.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite7110799967104893760.adam/._samples.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite7110799967104893760.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite7110799967104893760.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite7110799967104893760.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite7110799967104893760.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite7110799967104893760.adam/_common_metadata /tmp/adamTestMvnpjenoa0/TempSuite7110799967104893760.adam/._header.crc /tmp/adamTestMvnpjenoa0/TempSuite7110799967104893760.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite7110799967104893760.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite7110799967104893760.adam/_samples.avro /tmp/adamTestMvnpjenoa0/TempSuite7110799967104893760.adam/_metadata /tmp/adamTestMvnpjenoa0/TempSuite7110799967104893760.adam/_header /tmp/adamTestMvnpjenoa0/TempSuite5875114460019877737.adam /tmp/adamTestMvnpjenoa0/TempSuite5875114460019877737.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite5875114460019877737.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite5875114460019877737.adam/.part-00002-3a353d44-45e8-402d-8576-d446572a9dba-c000.snappy.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite5875114460019877737.adam/_readGroups.avro /tmp/adamTestMvnpjenoa0/TempSuite5875114460019877737.adam/part-00000-3a353d44-45e8-402d-8576-d446572a9dba-c000.snappy.parquet /tmp/adamTestMvnpjenoa0/TempSuite5875114460019877737.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite5875114460019877737.adam/part-00002-3a353d44-45e8-402d-8576-d446572a9dba-c000.snappy.parquet /tmp/adamTestMvnpjenoa0/TempSuite5875114460019877737.adam/._processingSteps.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite5875114460019877737.adam/.part-00000-3a353d44-45e8-402d-8576-d446572a9dba-c000.snappy.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite5875114460019877737.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite5875114460019877737.adam/._readGroups.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite5875114460019877737.adam/.part-00001-3a353d44-45e8-402d-8576-d446572a9dba-c000.snappy.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite5875114460019877737.adam/_processingSteps.avro /tmp/adamTestMvnpjenoa0/TempSuite5875114460019877737.adam/part-00001-3a353d44-45e8-402d-8576-d446572a9dba-c000.snappy.parquet /tmp/adamTestMvnpjenoa0/.TempSuite7081652395279320996_2.fq.crc /tmp/adamTestMvnpjenoa0/TempSuite6501048191494208824 /tmp/adamTestMvnpjenoa0/TempSuite3230692174078317538.bed /tmp/adamTestMvnpjenoa0/TempSuite3230692174078317538.bed/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite3230692174078317538.bed/part-00000 /tmp/adamTestMvnpjenoa0/TempSuite3230692174078317538.bed/.part-00000.crc /tmp/adamTestMvnpjenoa0/TempSuite3230692174078317538.bed/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite2706637733824238589.bed /tmp/adamTestMvnpjenoa0/TempSuite2706637733824238589.bed/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite2706637733824238589.bed/part-00000 /tmp/adamTestMvnpjenoa0/TempSuite2706637733824238589.bed/.part-00000.crc /tmp/adamTestMvnpjenoa0/TempSuite2706637733824238589.bed/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite480595958702862540 /tmp/adamTestMvnpjenoa0/TempSuite8140406761761149070 /tmp/adamTestMvnpjenoa0/TempSuite56850008582945515.adam /tmp/adamTestMvnpjenoa0/TempSuite56850008582945515.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite56850008582945515.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite56850008582945515.adam/.part-00001-d1bf77c0-88c7-447c-be47-d85e59df982f-c000.snappy.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite56850008582945515.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite56850008582945515.adam/part-00000-d1bf77c0-88c7-447c-be47-d85e59df982f-c000.snappy.parquet /tmp/adamTestMvnpjenoa0/TempSuite56850008582945515.adam/.part-00002-d1bf77c0-88c7-447c-be47-d85e59df982f-c000.snappy.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite56850008582945515.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite56850008582945515.adam/part-00001-d1bf77c0-88c7-447c-be47-d85e59df982f-c000.snappy.parquet /tmp/adamTestMvnpjenoa0/TempSuite56850008582945515.adam/part-00002-d1bf77c0-88c7-447c-be47-d85e59df982f-c000.snappy.parquet /tmp/adamTestMvnpjenoa0/TempSuite56850008582945515.adam/.part-00000-d1bf77c0-88c7-447c-be47-d85e59df982f-c000.snappy.parquet.crc /tmp/adamTestMvnpjenoa0/4043403519671264523 /tmp/adamTestMvnpjenoa0/4043403519671264523/test2.fa /tmp/adamTestMvnpjenoa0/4043403519671264523/test2.fa/_SUCCESS /tmp/adamTestMvnpjenoa0/4043403519671264523/test2.fa/part-00000 /tmp/adamTestMvnpjenoa0/4043403519671264523/test2.fa/.part-00000.crc /tmp/adamTestMvnpjenoa0/4043403519671264523/test2.fa/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite3430088968831191375 /tmp/adamTestMvnpjenoa0/9152381028753718192 /tmp/adamTestMvnpjenoa0/9152381028753718192/.gff3 /tmp/adamTestMvnpjenoa0/9152381028753718192/..gff3.crc /tmp/adamTestMvnpjenoa0/2233122457580770911 /tmp/adamTestMvnpjenoa0/2233122457580770911/unordered.sam /tmp/adamTestMvnpjenoa0/2233122457580770911/.unordered.sam.crc /tmp/adamTestMvnpjenoa0/TempSuite2049374544996348903.bam /tmp/adamTestMvnpjenoa0/TempSuite2049374544996348903.bam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite2049374544996348903.bam/part-r-00000.bam /tmp/adamTestMvnpjenoa0/TempSuite2049374544996348903.bam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite2049374544996348903.bam/.part-r-00000.bam.crc /tmp/adamTestMvnpjenoa0/TempSuite6681591804528478661 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite5889890028593780031 /tmp/adamTestMvnpjenoa0/ordered.sam5414698954195205520.sam /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite7979139564226981697.gff3 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite7979139564226981697.gff3/_SUCCESS /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite7979139564226981697.gff3/part-00001 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite7979139564226981697.gff3/.part-00003.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite7979139564226981697.gff3/part-00000 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite7979139564226981697.gff3/part-00003 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite7979139564226981697.gff3/.part-00000.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite7979139564226981697.gff3/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite7979139564226981697.gff3/part-00002 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite7979139564226981697.gff3/.part-00002.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite7979139564226981697.gff3/.part-00001.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite5821732757281570214 /tmp/adamTestMvnpjenoa0/TempSuite7794953380181836051 /tmp/adamTestMvnpjenoa0/TempSuite8821205413415988154.adam /tmp/adamTestMvnpjenoa0/TempSuite8821205413415988154.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite8821205413415988154.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite8821205413415988154.adam/.part-00000-ee8e9136-2943-4fdd-8b24-29218e984041-c000.snappy.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite8821205413415988154.adam/_readGroups.avro /tmp/adamTestMvnpjenoa0/TempSuite8821205413415988154.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite8821205413415988154.adam/._processingSteps.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite8821205413415988154.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite8821205413415988154.adam/._readGroups.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite8821205413415988154.adam/part-00000-ee8e9136-2943-4fdd-8b24-29218e984041-c000.snappy.parquet /tmp/adamTestMvnpjenoa0/TempSuite8821205413415988154.adam/_processingSteps.avro /tmp/adamTestMvnpjenoa0/TempSuite1134365893929950796 /tmp/adamTestMvnpjenoa0/TempSuite4358674517477618490 /tmp/adamTestMvnpjenoa0/TempSuite4782027620194032085 /tmp/adamTestMvnpjenoa0/TempSuite5893508920392847756.adam /tmp/adamTestMvnpjenoa0/TempSuite5893508920392847756.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite5893508920392847756.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite5893508920392847756.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite5893508920392847756.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite5893508920392847756.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite5893508920392847756.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite5893508920392847756.adam/_common_metadata /tmp/adamTestMvnpjenoa0/TempSuite5893508920392847756.adam/._header.crc /tmp/adamTestMvnpjenoa0/TempSuite5893508920392847756.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite5893508920392847756.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite5893508920392847756.adam/_metadata /tmp/adamTestMvnpjenoa0/TempSuite5893508920392847756.adam/_header /tmp/adamTestMvnpjenoa0/TempSuite8803344612487790304.adam /tmp/adamTestMvnpjenoa0/TempSuite8803344612487790304.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite8803344612487790304.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite8803344612487790304.adam/._samples.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite8803344612487790304.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite8803344612487790304.adam/.part-r-00003.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite8803344612487790304.adam/part-r-00001.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite8803344612487790304.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite8803344612487790304.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite8803344612487790304.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite8803344612487790304.adam/.part-r-00001.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite8803344612487790304.adam/part-r-00002.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite8803344612487790304.adam/.part-r-00002.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite8803344612487790304.adam/_common_metadata /tmp/adamTestMvnpjenoa0/TempSuite8803344612487790304.adam/._header.crc /tmp/adamTestMvnpjenoa0/TempSuite8803344612487790304.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite8803344612487790304.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite8803344612487790304.adam/_samples.avro /tmp/adamTestMvnpjenoa0/TempSuite8803344612487790304.adam/_metadata /tmp/adamTestMvnpjenoa0/TempSuite8803344612487790304.adam/part-r-00003.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite8803344612487790304.adam/_header /tmp/adamTestMvnpjenoa0/unordered.sam4003183493134393423.sam /tmp/adamTestMvnpjenoa0/TempSuite7611216962712174691.bed /tmp/adamTestMvnpjenoa0/TempSuite7611216962712174691.bed/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite7611216962712174691.bed/part-00000 /tmp/adamTestMvnpjenoa0/TempSuite7611216962712174691.bed/.part-00000.crc /tmp/adamTestMvnpjenoa0/TempSuite7611216962712174691.bed/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite359129980305290861.narrowPeak /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite359129980305290861.narrowPeak/_SUCCESS /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite359129980305290861.narrowPeak/part-00001 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite359129980305290861.narrowPeak/.part-00003.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite359129980305290861.narrowPeak/part-00000 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite359129980305290861.narrowPeak/part-00003 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite359129980305290861.narrowPeak/.part-00000.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite359129980305290861.narrowPeak/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite359129980305290861.narrowPeak/part-00002 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite359129980305290861.narrowPeak/.part-00002.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite359129980305290861.narrowPeak/.part-00001.crc /tmp/adamTestMvnpjenoa0/TempSuite5247604677884151520 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite2473079845127639752.gtf /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite2473079845127639752.gtf/_SUCCESS /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite2473079845127639752.gtf/part-00001 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite2473079845127639752.gtf/.part-00003.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite2473079845127639752.gtf/part-00000 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite2473079845127639752.gtf/part-00003 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite2473079845127639752.gtf/.part-00000.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite2473079845127639752.gtf/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite2473079845127639752.gtf/part-00002 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite2473079845127639752.gtf/.part-00002.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite2473079845127639752.gtf/.part-00001.crc /tmp/adamTestMvnpjenoa0/TempSuite1895162954070760589 /tmp/adamTestMvnpjenoa0/TempSuite3564918522804962223 /tmp/adamTestMvnpjenoa0/small.vcf3192377525589105732.vcf /tmp/adamTestMvnpjenoa0/TempSuite6074061586347408026.adam /tmp/adamTestMvnpjenoa0/TempSuite6074061586347408026.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite6074061586347408026.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite6074061586347408026.adam/_readGroups.avro /tmp/adamTestMvnpjenoa0/TempSuite6074061586347408026.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite6074061586347408026.adam/._processingSteps.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite6074061586347408026.adam/.part-00000-25cf9081-2345-4237-95b8-0036f7c22f40-c000.snappy.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite6074061586347408026.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite6074061586347408026.adam/._readGroups.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite6074061586347408026.adam/part-00000-25cf9081-2345-4237-95b8-0036f7c22f40-c000.snappy.parquet /tmp/adamTestMvnpjenoa0/TempSuite6074061586347408026.adam/_processingSteps.avro /tmp/adamTestMvnpjenoa0/TempSuite5413678912049287670.adam /tmp/adamTestMvnpjenoa0/TempSuite5413678912049287670.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite5413678912049287670.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite5413678912049287670.adam/referenceName=1 /tmp/adamTestMvnpjenoa0/TempSuite5413678912049287670.adam/referenceName=1/positionBin=0 /tmp/adamTestMvnpjenoa0/TempSuite5413678912049287670.adam/referenceName=1/positionBin=0/part-00000-8452e751-147e-46d0-9a24-e40705921e93.c000.snappy.parquet /tmp/adamTestMvnpjenoa0/TempSuite5413678912049287670.adam/referenceName=1/positionBin=0/.part-00000-8452e751-147e-46d0-9a24-e40705921e93.c000.snappy.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite5413678912049287670.adam/._samples.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite5413678912049287670.adam/referenceName=13 /tmp/adamTestMvnpjenoa0/TempSuite5413678912049287670.adam/referenceName=13/positionBin=0 /tmp/adamTestMvnpjenoa0/TempSuite5413678912049287670.adam/referenceName=13/positionBin=0/part-00000-8452e751-147e-46d0-9a24-e40705921e93.c000.snappy.parquet /tmp/adamTestMvnpjenoa0/TempSuite5413678912049287670.adam/referenceName=13/positionBin=0/.part-00000-8452e751-147e-46d0-9a24-e40705921e93.c000.snappy.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite5413678912049287670.adam/_partitionedByStartPos /tmp/adamTestMvnpjenoa0/TempSuite5413678912049287670.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite5413678912049287670.adam/._header.crc /tmp/adamTestMvnpjenoa0/TempSuite5413678912049287670.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite5413678912049287670.adam/._partitionedByStartPos.crc /tmp/adamTestMvnpjenoa0/TempSuite5413678912049287670.adam/_samples.avro /tmp/adamTestMvnpjenoa0/TempSuite5413678912049287670.adam/referenceName=2 /tmp/adamTestMvnpjenoa0/TempSuite5413678912049287670.adam/referenceName=2/positionBin=0 /tmp/adamTestMvnpjenoa0/TempSuite5413678912049287670.adam/referenceName=2/positionBin=0/part-00000-8452e751-147e-46d0-9a24-e40705921e93.c000.snappy.parquet /tmp/adamTestMvnpjenoa0/TempSuite5413678912049287670.adam/referenceName=2/positionBin=0/.part-00000-8452e751-147e-46d0-9a24-e40705921e93.c000.snappy.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite5413678912049287670.adam/_header /tmp/adamTestMvnpjenoa0/TempSuite423983098930022445 /tmp/adamTestMvnpjenoa0/9063627738360062306 /tmp/adamTestMvnpjenoa0/9063627738360062306/.artificial.cram.crc /tmp/adamTestMvnpjenoa0/9063627738360062306/artificial.cram /tmp/adamTestMvnpjenoa0/TempSuite2092003803646348106.adam /tmp/adamTestMvnpjenoa0/TempSuite2092003803646348106.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite2092003803646348106.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite2092003803646348106.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite2092003803646348106.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite2092003803646348106.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite2092003803646348106.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite2092003803646348106.adam/_common_metadata /tmp/adamTestMvnpjenoa0/TempSuite2092003803646348106.adam/._header.crc /tmp/adamTestMvnpjenoa0/TempSuite2092003803646348106.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite2092003803646348106.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite2092003803646348106.adam/_metadata /tmp/adamTestMvnpjenoa0/TempSuite2092003803646348106.adam/_header /tmp/adamTestMvnpjenoa0/TempSuite8770139105033904741 /tmp/adamTestMvnpjenoa0/TempSuite415318838795345129 /tmp/adamTestMvnpjenoa0/TempSuite976231192151270081 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite4937555853815722038 /tmp/adamTestMvnpjenoa0/4486444693578176285 /tmp/adamTestMvnpjenoa0/4486444693578176285/genotypes.lex.adam /tmp/adamTestMvnpjenoa0/4486444693578176285/genotypes.lex.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/4486444693578176285/genotypes.lex.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/4486444693578176285/genotypes.lex.adam/._samples.avro.crc /tmp/adamTestMvnpjenoa0/4486444693578176285/genotypes.lex.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/4486444693578176285/genotypes.lex.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/4486444693578176285/genotypes.lex.adam/_references.avro /tmp/adamTestMvnpjenoa0/4486444693578176285/genotypes.lex.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/4486444693578176285/genotypes.lex.adam/_common_metadata /tmp/adamTestMvnpjenoa0/4486444693578176285/genotypes.lex.adam/._header.crc /tmp/adamTestMvnpjenoa0/4486444693578176285/genotypes.lex.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/4486444693578176285/genotypes.lex.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/4486444693578176285/genotypes.lex.adam/_samples.avro /tmp/adamTestMvnpjenoa0/4486444693578176285/genotypes.lex.adam/_metadata /tmp/adamTestMvnpjenoa0/4486444693578176285/genotypes.lex.adam/_header /tmp/adamTestMvnpjenoa0/TempSuite3923037089729063325 /tmp/adamTestMvnpjenoa0/small.vcf328876925634947912.vcf /tmp/adamTestMvnpjenoa0/6501399050445710111 /tmp/adamTestMvnpjenoa0/6501399050445710111/readname_sorted.sam /tmp/adamTestMvnpjenoa0/6501399050445710111/.readname_sorted.sam.crc /tmp/adamTestMvnpjenoa0/TempSuite896480339816517436 /tmp/adamTestMvnpjenoa0/TempSuite7643753394919033254.bed /tmp/adamTestMvnpjenoa0/TempSuite7643753394919033254.bed/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite7643753394919033254.bed/part-00000 /tmp/adamTestMvnpjenoa0/TempSuite7643753394919033254.bed/.part-00000.crc /tmp/adamTestMvnpjenoa0/TempSuite7643753394919033254.bed/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite7616904499627491412.adam /tmp/adamTestMvnpjenoa0/TempSuite7616904499627491412.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite7616904499627491412.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite7616904499627491412.adam/_readGroups.avro /tmp/adamTestMvnpjenoa0/TempSuite7616904499627491412.adam/part-00000-fc39c4f3-e336-4970-9ce8-7862077946b2-c000.snappy.parquet /tmp/adamTestMvnpjenoa0/TempSuite7616904499627491412.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite7616904499627491412.adam/._processingSteps.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite7616904499627491412.adam/.part-00000-fc39c4f3-e336-4970-9ce8-7862077946b2-c000.snappy.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite7616904499627491412.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite7616904499627491412.adam/._readGroups.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite7616904499627491412.adam/_processingSteps.avro /tmp/adamTestMvnpjenoa0/TempSuite2930306370869346516.bam /tmp/adamTestMvnpjenoa0/TempSuite2930306370869346516.bam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite2930306370869346516.bam/part-r-00000.bam /tmp/adamTestMvnpjenoa0/TempSuite2930306370869346516.bam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite2930306370869346516.bam/.part-r-00000.bam.crc /tmp/adamTestMvnpjenoa0/TempSuite2198978203599306232.bed /tmp/adamTestMvnpjenoa0/TempSuite2198978203599306232.bed/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite2198978203599306232.bed/part-00000 /tmp/adamTestMvnpjenoa0/TempSuite2198978203599306232.bed/.part-00000.crc /tmp/adamTestMvnpjenoa0/TempSuite2198978203599306232.bed/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite4879366274265961749 /tmp/adamTestMvnpjenoa0/TempSuite401858085426789011.bed /tmp/adamTestMvnpjenoa0/TempSuite401858085426789011.bed/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite401858085426789011.bed/part-00001 /tmp/adamTestMvnpjenoa0/TempSuite401858085426789011.bed/.part-00003.crc /tmp/adamTestMvnpjenoa0/TempSuite401858085426789011.bed/part-00000 /tmp/adamTestMvnpjenoa0/TempSuite401858085426789011.bed/part-00003 /tmp/adamTestMvnpjenoa0/TempSuite401858085426789011.bed/.part-00000.crc /tmp/adamTestMvnpjenoa0/TempSuite401858085426789011.bed/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite401858085426789011.bed/part-00002 /tmp/adamTestMvnpjenoa0/TempSuite401858085426789011.bed/.part-00002.crc /tmp/adamTestMvnpjenoa0/TempSuite401858085426789011.bed/.part-00001.crc /tmp/adamTestMvnpjenoa0/TempSuite1034882394398341639.adam /tmp/adamTestMvnpjenoa0/TempSuite1034882394398341639.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite1034882394398341639.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite1034882394398341639.adam/._samples.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite1034882394398341639.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite1034882394398341639.adam/.part-r-00003.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite1034882394398341639.adam/part-r-00001.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite1034882394398341639.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite1034882394398341639.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite1034882394398341639.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite1034882394398341639.adam/.part-r-00001.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite1034882394398341639.adam/part-r-00002.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite1034882394398341639.adam/.part-r-00002.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite1034882394398341639.adam/_common_metadata /tmp/adamTestMvnpjenoa0/TempSuite1034882394398341639.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite1034882394398341639.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite1034882394398341639.adam/_samples.avro /tmp/adamTestMvnpjenoa0/TempSuite1034882394398341639.adam/_metadata /tmp/adamTestMvnpjenoa0/TempSuite1034882394398341639.adam/part-r-00003.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite2137169130426970700 /tmp/adamTestMvnpjenoa0/TempSuite2823063181070911277 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite3348708032767544682.gff3 /tmp/adamTestMvnpjenoa0/TempSuite7600051512605092301.adam /tmp/adamTestMvnpjenoa0/TempSuite7600051512605092301.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite7600051512605092301.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite7600051512605092301.adam/._samples.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite7600051512605092301.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite7600051512605092301.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite7600051512605092301.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite7600051512605092301.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite7600051512605092301.adam/_common_metadata /tmp/adamTestMvnpjenoa0/TempSuite7600051512605092301.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite7600051512605092301.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite7600051512605092301.adam/_samples.avro /tmp/adamTestMvnpjenoa0/TempSuite7600051512605092301.adam/_metadata /tmp/adamTestMvnpjenoa0/TempSuite533243511128917849 /tmp/adamTestMvnpjenoa0/TempSuite3326500691268380368 /tmp/adamTestMvnpjenoa0/TempSuite5029742658528610165 /tmp/adamTestMvnpjenoa0/TempSuite6337087559168697621.adam /tmp/adamTestMvnpjenoa0/TempSuite6337087559168697621.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite6337087559168697621.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite6337087559168697621.adam/part-00001-d4269a59-15e2-4ff3-acd6-c181db8c6b42-c000.snappy.parquet /tmp/adamTestMvnpjenoa0/TempSuite6337087559168697621.adam/.part-00000-d4269a59-15e2-4ff3-acd6-c181db8c6b42-c000.snappy.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite6337087559168697621.adam/.part-00002-d4269a59-15e2-4ff3-acd6-c181db8c6b42-c000.snappy.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite6337087559168697621.adam/part-00002-d4269a59-15e2-4ff3-acd6-c181db8c6b42-c000.snappy.parquet /tmp/adamTestMvnpjenoa0/TempSuite6337087559168697621.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite6337087559168697621.adam/._header.crc /tmp/adamTestMvnpjenoa0/TempSuite6337087559168697621.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite6337087559168697621.adam/.part-00001-d4269a59-15e2-4ff3-acd6-c181db8c6b42-c000.snappy.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite6337087559168697621.adam/_header /tmp/adamTestMvnpjenoa0/TempSuite6337087559168697621.adam/part-00000-d4269a59-15e2-4ff3-acd6-c181db8c6b42-c000.snappy.parquet /tmp/adamTestMvnpjenoa0/.FeatureDatasetFunctionsSuite4937555853815722038.gtf.crc /tmp/adamTestMvnpjenoa0/TempSuite896480339816517436.adam /tmp/adamTestMvnpjenoa0/TempSuite896480339816517436.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite896480339816517436.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite896480339816517436.adam/part-00000-febff1cf-e96f-4e62-9764-ce561988ba2d-c000.snappy.parquet /tmp/adamTestMvnpjenoa0/TempSuite896480339816517436.adam/.part-00000-febff1cf-e96f-4e62-9764-ce561988ba2d-c000.snappy.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite896480339816517436.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite896480339816517436.adam/._header.crc /tmp/adamTestMvnpjenoa0/TempSuite896480339816517436.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite896480339816517436.adam/_header /tmp/adamTestMvnpjenoa0/TempSuite8843902435803302365.bed /tmp/adamTestMvnpjenoa0/TempSuite8843902435803302365.bed/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite8843902435803302365.bed/part-00000 /tmp/adamTestMvnpjenoa0/TempSuite8843902435803302365.bed/.part-00000.crc /tmp/adamTestMvnpjenoa0/TempSuite8843902435803302365.bed/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/1557939529955-0 /tmp/adamTestMvnpjenoa0/1557939529955-0/test.fa /tmp/adamTestMvnpjenoa0/1557939529955-0/test.fa/_SUCCESS /tmp/adamTestMvnpjenoa0/1557939529955-0/test.fa/part-00000 /tmp/adamTestMvnpjenoa0/1557939529955-0/test.fa/.part-00000.crc /tmp/adamTestMvnpjenoa0/1557939529955-0/test.fa/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite7126587291281374998 /tmp/adamTestMvnpjenoa0/TempSuite7643753394919033254 /tmp/adamTestMvnpjenoa0/TempSuite6876003813360252754.adam /tmp/adamTestMvnpjenoa0/TempSuite6876003813360252754.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite6876003813360252754.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite6876003813360252754.adam/._samples.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite6876003813360252754.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite6876003813360252754.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite6876003813360252754.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite6876003813360252754.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite6876003813360252754.adam/_common_metadata /tmp/adamTestMvnpjenoa0/TempSuite6876003813360252754.adam/._header.crc /tmp/adamTestMvnpjenoa0/TempSuite6876003813360252754.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite6876003813360252754.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite6876003813360252754.adam/_samples.avro /tmp/adamTestMvnpjenoa0/TempSuite6876003813360252754.adam/_metadata /tmp/adamTestMvnpjenoa0/TempSuite6876003813360252754.adam/_header /tmp/adamTestMvnpjenoa0/TempSuite1251284635878575359.adam /tmp/adamTestMvnpjenoa0/TempSuite1251284635878575359.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite1251284635878575359.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite1251284635878575359.adam/referenceName=1 /tmp/adamTestMvnpjenoa0/TempSuite1251284635878575359.adam/referenceName=1/positionBin=0 /tmp/adamTestMvnpjenoa0/TempSuite1251284635878575359.adam/referenceName=1/positionBin=0/.part-00000-68b9de53-7704-4f20-9195-e57b2332fad6.c000.snappy.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite1251284635878575359.adam/referenceName=1/positionBin=0/part-00000-68b9de53-7704-4f20-9195-e57b2332fad6.c000.snappy.parquet /tmp/adamTestMvnpjenoa0/TempSuite1251284635878575359.adam/referenceName=13 /tmp/adamTestMvnpjenoa0/TempSuite1251284635878575359.adam/referenceName=13/positionBin=0 /tmp/adamTestMvnpjenoa0/TempSuite1251284635878575359.adam/referenceName=13/positionBin=0/.part-00000-68b9de53-7704-4f20-9195-e57b2332fad6.c000.snappy.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite1251284635878575359.adam/referenceName=13/positionBin=0/part-00000-68b9de53-7704-4f20-9195-e57b2332fad6.c000.snappy.parquet /tmp/adamTestMvnpjenoa0/TempSuite1251284635878575359.adam/_partitionedByStartPos /tmp/adamTestMvnpjenoa0/TempSuite1251284635878575359.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite1251284635878575359.adam/._header.crc /tmp/adamTestMvnpjenoa0/TempSuite1251284635878575359.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite1251284635878575359.adam/._partitionedByStartPos.crc /tmp/adamTestMvnpjenoa0/TempSuite1251284635878575359.adam/referenceName=2 /tmp/adamTestMvnpjenoa0/TempSuite1251284635878575359.adam/referenceName=2/positionBin=0 /tmp/adamTestMvnpjenoa0/TempSuite1251284635878575359.adam/referenceName=2/positionBin=0/.part-00000-68b9de53-7704-4f20-9195-e57b2332fad6.c000.snappy.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite1251284635878575359.adam/referenceName=2/positionBin=0/part-00000-68b9de53-7704-4f20-9195-e57b2332fad6.c000.snappy.parquet /tmp/adamTestMvnpjenoa0/TempSuite1251284635878575359.adam/_header /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite9049085739336270777.interval_list /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite9049085739336270777.interval_list/_SUCCESS /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite9049085739336270777.interval_list/part-00001 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite9049085739336270777.interval_list/.part-00003.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite9049085739336270777.interval_list/part-00000 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite9049085739336270777.interval_list/part-00003 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite9049085739336270777.interval_list/.part-00000.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite9049085739336270777.interval_list/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite9049085739336270777.interval_list/part-00002 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite9049085739336270777.interval_list/.part-00002.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite9049085739336270777.interval_list/.part-00001.crc /tmp/adamTestMvnpjenoa0/TempSuite787098745758403258 /tmp/adamTestMvnpjenoa0/TempSuite869153603301233793 /tmp/adamTestMvnpjenoa0/TempSuite7652450895275188384.adam /tmp/adamTestMvnpjenoa0/TempSuite7652450895275188384.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite7652450895275188384.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite7652450895275188384.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite7652450895275188384.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite7652450895275188384.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite7652450895275188384.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite7652450895275188384.adam/_common_metadata /tmp/adamTestMvnpjenoa0/TempSuite7652450895275188384.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite7652450895275188384.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite7652450895275188384.adam/_metadata /tmp/adamTestMvnpjenoa0/random.vcf6571996351066822272.vcf /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite2611305893602536323.gtf /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite2611305893602536323.gtf/_SUCCESS /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite2611305893602536323.gtf/part-00001 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite2611305893602536323.gtf/.part-00003.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite2611305893602536323.gtf/part-00000 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite2611305893602536323.gtf/part-00003 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite2611305893602536323.gtf/.part-00000.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite2611305893602536323.gtf/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite2611305893602536323.gtf/part-00002 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite2611305893602536323.gtf/.part-00002.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite2611305893602536323.gtf/.part-00001.crc /tmp/adamTestMvnpjenoa0/TempSuite3424450956843792997.adam /tmp/adamTestMvnpjenoa0/TempSuite3424450956843792997.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite3424450956843792997.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite3424450956843792997.adam/referenceName=1 /tmp/adamTestMvnpjenoa0/TempSuite3424450956843792997.adam/referenceName=1/positionBin=169 /tmp/adamTestMvnpjenoa0/TempSuite3424450956843792997.adam/referenceName=1/positionBin=169/.part-00001-3ee28f64-487b-4ae9-b3ca-0dcbba87a065.c000.snappy.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite3424450956843792997.adam/referenceName=1/positionBin=169/part-00001-3ee28f64-487b-4ae9-b3ca-0dcbba87a065.c000.snappy.parquet /tmp/adamTestMvnpjenoa0/TempSuite3424450956843792997.adam/referenceName=1/positionBin=14 /tmp/adamTestMvnpjenoa0/TempSuite3424450956843792997.adam/referenceName=1/positionBin=14/.part-00000-3ee28f64-487b-4ae9-b3ca-0dcbba87a065.c000.snappy.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite3424450956843792997.adam/referenceName=1/positionBin=14/part-00000-3ee28f64-487b-4ae9-b3ca-0dcbba87a065.c000.snappy.parquet /tmp/adamTestMvnpjenoa0/TempSuite3424450956843792997.adam/referenceName=1/positionBin=240 /tmp/adamTestMvnpjenoa0/TempSuite3424450956843792997.adam/referenceName=1/positionBin=240/part-00002-3ee28f64-487b-4ae9-b3ca-0dcbba87a065.c000.snappy.parquet /tmp/adamTestMvnpjenoa0/TempSuite3424450956843792997.adam/referenceName=1/positionBin=240/.part-00002-3ee28f64-487b-4ae9-b3ca-0dcbba87a065.c000.snappy.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite3424450956843792997.adam/referenceName=1/positionBin=0 /tmp/adamTestMvnpjenoa0/TempSuite3424450956843792997.adam/referenceName=1/positionBin=0/.part-00000-3ee28f64-487b-4ae9-b3ca-0dcbba87a065.c000.snappy.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite3424450956843792997.adam/referenceName=1/positionBin=0/part-00000-3ee28f64-487b-4ae9-b3ca-0dcbba87a065.c000.snappy.parquet /tmp/adamTestMvnpjenoa0/TempSuite3424450956843792997.adam/._samples.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite3424450956843792997.adam/_partitionedByStartPos /tmp/adamTestMvnpjenoa0/TempSuite3424450956843792997.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite3424450956843792997.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite3424450956843792997.adam/._partitionedByStartPos.crc /tmp/adamTestMvnpjenoa0/TempSuite3424450956843792997.adam/_samples.avro /tmp/adamTestMvnpjenoa0/TempSuite1398970179786229198.adam /tmp/adamTestMvnpjenoa0/TempSuite1398970179786229198.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite1398970179786229198.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite1398970179786229198.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite1398970179786229198.adam/.part-r-00003.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite1398970179786229198.adam/part-r-00001.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite1398970179786229198.adam/_readGroups.avro /tmp/adamTestMvnpjenoa0/TempSuite1398970179786229198.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite1398970179786229198.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite1398970179786229198.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite1398970179786229198.adam/.part-r-00001.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite1398970179786229198.adam/part-r-00002.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite1398970179786229198.adam/._processingSteps.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite1398970179786229198.adam/.part-r-00002.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite1398970179786229198.adam/_common_metadata /tmp/adamTestMvnpjenoa0/TempSuite1398970179786229198.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite1398970179786229198.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite1398970179786229198.adam/._readGroups.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite1398970179786229198.adam/_metadata /tmp/adamTestMvnpjenoa0/TempSuite1398970179786229198.adam/part-r-00003.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite1398970179786229198.adam/_processingSteps.avro /tmp/adamTestMvnpjenoa0/TempSuite7616973969459567191.adam /tmp/adamTestMvnpjenoa0/TempSuite7616973969459567191.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite7616973969459567191.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite7616973969459567191.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite7616973969459567191.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite7616973969459567191.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite7616973969459567191.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite7616973969459567191.adam/_common_metadata /tmp/adamTestMvnpjenoa0/TempSuite7616973969459567191.adam/._header.crc /tmp/adamTestMvnpjenoa0/TempSuite7616973969459567191.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite7616973969459567191.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite7616973969459567191.adam/_metadata /tmp/adamTestMvnpjenoa0/TempSuite7616973969459567191.adam/_header /tmp/adamTestMvnpjenoa0/TempSuite6581687445591240826 /tmp/adamTestMvnpjenoa0/TempSuite5599628095909759302 /tmp/adamTestMvnpjenoa0/TempSuite8514477946221416938.adam /tmp/adamTestMvnpjenoa0/TempSuite8514477946221416938.adam/part-00001-aa6d653f-65e5-4734-839b-0581a23c2f53-c000.snappy.parquet /tmp/adamTestMvnpjenoa0/TempSuite8514477946221416938.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite8514477946221416938.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite8514477946221416938.adam/_readGroups.avro /tmp/adamTestMvnpjenoa0/TempSuite8514477946221416938.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite8514477946221416938.adam/.part-00002-aa6d653f-65e5-4734-839b-0581a23c2f53-c000.snappy.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite8514477946221416938.adam/._processingSteps.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite8514477946221416938.adam/.part-00000-aa6d653f-65e5-4734-839b-0581a23c2f53-c000.snappy.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite8514477946221416938.adam/.part-00001-aa6d653f-65e5-4734-839b-0581a23c2f53-c000.snappy.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite8514477946221416938.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite8514477946221416938.adam/._readGroups.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite8514477946221416938.adam/part-00002-aa6d653f-65e5-4734-839b-0581a23c2f53-c000.snappy.parquet /tmp/adamTestMvnpjenoa0/TempSuite8514477946221416938.adam/_processingSteps.avro /tmp/adamTestMvnpjenoa0/TempSuite8514477946221416938.adam/part-00000-aa6d653f-65e5-4734-839b-0581a23c2f53-c000.snappy.parquet /tmp/adamTestMvnpjenoa0/TempSuite5989210529891535695 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite1557351998696526247.interval_list /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite1557351998696526247.interval_list/_SUCCESS /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite1557351998696526247.interval_list/part-00001 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite1557351998696526247.interval_list/.part-00003.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite1557351998696526247.interval_list/part-00000 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite1557351998696526247.interval_list/part-00003 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite1557351998696526247.interval_list/.part-00000.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite1557351998696526247.interval_list/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite1557351998696526247.interval_list/part-00002 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite1557351998696526247.interval_list/.part-00002.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite1557351998696526247.interval_list/.part-00001.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite3141056714993409856 /tmp/adamTestMvnpjenoa0/TempSuite2433004316762971474.adam /tmp/adamTestMvnpjenoa0/TempSuite2433004316762971474.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite2433004316762971474.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite2433004316762971474.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite2433004316762971474.adam/._header.crc /tmp/adamTestMvnpjenoa0/TempSuite2433004316762971474.adam/part-00000-860395a4-c274-4b90-8f09-ace582ebe08d-c000.snappy.parquet /tmp/adamTestMvnpjenoa0/TempSuite2433004316762971474.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite2433004316762971474.adam/.part-00000-860395a4-c274-4b90-8f09-ace582ebe08d-c000.snappy.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite2433004316762971474.adam/_header /tmp/adamTestMvnpjenoa0/7759236574517264590 /tmp/adamTestMvnpjenoa0/7759236574517264590/coverage.adam /tmp/adamTestMvnpjenoa0/7759236574517264590/coverage.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/7759236574517264590/coverage.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/7759236574517264590/coverage.adam/._samples.avro.crc /tmp/adamTestMvnpjenoa0/7759236574517264590/coverage.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/7759236574517264590/coverage.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/7759236574517264590/coverage.adam/_references.avro /tmp/adamTestMvnpjenoa0/7759236574517264590/coverage.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/7759236574517264590/coverage.adam/_common_metadata /tmp/adamTestMvnpjenoa0/7759236574517264590/coverage.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/7759236574517264590/coverage.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/7759236574517264590/coverage.adam/_samples.avro /tmp/adamTestMvnpjenoa0/7759236574517264590/coverage.adam/_metadata /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite1491887521662331166 /tmp/adamTestMvnpjenoa0/TempSuite5166090571668865461.bam /tmp/adamTestMvnpjenoa0/TempSuite5166090571668865461.bam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite5166090571668865461.bam/part-r-00000.bam /tmp/adamTestMvnpjenoa0/TempSuite5166090571668865461.bam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite5166090571668865461.bam/.part-r-00000.bam.crc /tmp/adamTestMvnpjenoa0/TempSuite531641688329952021 /tmp/adamTestMvnpjenoa0/6623719113417974218 /tmp/adamTestMvnpjenoa0/6623719113417974218/contigs.adam /tmp/adamTestMvnpjenoa0/6623719113417974218/contigs.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/6623719113417974218/contigs.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/6623719113417974218/contigs.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/6623719113417974218/contigs.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/6623719113417974218/contigs.adam/_references.avro /tmp/adamTestMvnpjenoa0/6623719113417974218/contigs.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/6623719113417974218/contigs.adam/_common_metadata /tmp/adamTestMvnpjenoa0/6623719113417974218/contigs.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/6623719113417974218/contigs.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/6623719113417974218/contigs.adam/_metadata /tmp/adamTestMvnpjenoa0/TempSuite3521924285109635108 /tmp/adamTestMvnpjenoa0/TempSuite3703439285256403523 /tmp/adamTestMvnpjenoa0/TempSuite8986117090025058793.adam /tmp/adamTestMvnpjenoa0/TempSuite8986117090025058793.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite8986117090025058793.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite8986117090025058793.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite8986117090025058793.adam/_readGroups.avro /tmp/adamTestMvnpjenoa0/TempSuite8986117090025058793.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite8986117090025058793.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite8986117090025058793.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite8986117090025058793.adam/._processingSteps.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite8986117090025058793.adam/_common_metadata /tmp/adamTestMvnpjenoa0/TempSuite8986117090025058793.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite8986117090025058793.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite8986117090025058793.adam/._readGroups.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite8986117090025058793.adam/_metadata /tmp/adamTestMvnpjenoa0/TempSuite8986117090025058793.adam/_processingSteps.avro /tmp/adamTestMvnpjenoa0/TempSuite1099724985131552573.adam /tmp/adamTestMvnpjenoa0/TempSuite1099724985131552573.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite1099724985131552573.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite1099724985131552573.adam/._samples.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite1099724985131552573.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite1099724985131552573.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite1099724985131552573.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite1099724985131552573.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite1099724985131552573.adam/_common_metadata /tmp/adamTestMvnpjenoa0/TempSuite1099724985131552573.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite1099724985131552573.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite1099724985131552573.adam/_samples.avro /tmp/adamTestMvnpjenoa0/TempSuite1099724985131552573.adam/_metadata /tmp/adamTestMvnpjenoa0/1583915414992024315 /tmp/adamTestMvnpjenoa0/1583915414992024315/artificial.cram /tmp/adamTestMvnpjenoa0/1583915414992024315/artificial.cram/_SUCCESS /tmp/adamTestMvnpjenoa0/1583915414992024315/artificial.cram/part-r-00000.cram /tmp/adamTestMvnpjenoa0/1583915414992024315/artificial.cram/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/1583915414992024315/artificial.cram/.part-r-00000.cram.crc /tmp/adamTestMvnpjenoa0/.FeatureDatasetFunctionsSuite2309174855776508211.gtf.crc /tmp/adamTestMvnpjenoa0/TempSuite415318838795345129.vcf /tmp/adamTestMvnpjenoa0/TempSuite415318838795345129.vcf/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite415318838795345129.vcf/part-r-00000 /tmp/adamTestMvnpjenoa0/TempSuite415318838795345129.vcf/.part-r-00000.crc /tmp/adamTestMvnpjenoa0/TempSuite415318838795345129.vcf/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite5029742658528610165.adam /tmp/adamTestMvnpjenoa0/TempSuite5029742658528610165.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite5029742658528610165.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite5029742658528610165.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite5029742658528610165.adam/.part-r-00003.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite5029742658528610165.adam/part-r-00001.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite5029742658528610165.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite5029742658528610165.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite5029742658528610165.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite5029742658528610165.adam/.part-r-00001.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite5029742658528610165.adam/part-r-00002.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite5029742658528610165.adam/.part-r-00002.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite5029742658528610165.adam/_common_metadata /tmp/adamTestMvnpjenoa0/TempSuite5029742658528610165.adam/._header.crc /tmp/adamTestMvnpjenoa0/TempSuite5029742658528610165.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite5029742658528610165.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite5029742658528610165.adam/_metadata /tmp/adamTestMvnpjenoa0/TempSuite5029742658528610165.adam/part-r-00003.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite5029742658528610165.adam/_header /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite4627558136253177920.bed /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite9015503689203818919 /tmp/adamTestMvnpjenoa0/TempSuite262166617179322680reads12.sam_2 /tmp/adamTestMvnpjenoa0/javaAC8905830533948263803 /tmp/adamTestMvnpjenoa0/javaAC8905830533948263803/testRdd.genotype.adam /tmp/adamTestMvnpjenoa0/javaAC8905830533948263803/testRdd.genotype.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/javaAC8905830533948263803/testRdd.genotype.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/javaAC8905830533948263803/testRdd.genotype.adam/._samples.avro.crc /tmp/adamTestMvnpjenoa0/javaAC8905830533948263803/testRdd.genotype.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/javaAC8905830533948263803/testRdd.genotype.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/javaAC8905830533948263803/testRdd.genotype.adam/_references.avro /tmp/adamTestMvnpjenoa0/javaAC8905830533948263803/testRdd.genotype.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/javaAC8905830533948263803/testRdd.genotype.adam/_common_metadata /tmp/adamTestMvnpjenoa0/javaAC8905830533948263803/testRdd.genotype.adam/._header.crc /tmp/adamTestMvnpjenoa0/javaAC8905830533948263803/testRdd.genotype.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/javaAC8905830533948263803/testRdd.genotype.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/javaAC8905830533948263803/testRdd.genotype.adam/_samples.avro /tmp/adamTestMvnpjenoa0/javaAC8905830533948263803/testRdd.genotype.adam/_metadata /tmp/adamTestMvnpjenoa0/javaAC8905830533948263803/testRdd.genotype.adam/_header /tmp/adamTestMvnpjenoa0/TempSuite5217560609831811643.bed /tmp/adamTestMvnpjenoa0/TempSuite5217560609831811643.bed/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite5217560609831811643.bed/part-00001 /tmp/adamTestMvnpjenoa0/TempSuite5217560609831811643.bed/.part-00003.crc /tmp/adamTestMvnpjenoa0/TempSuite5217560609831811643.bed/part-00000 /tmp/adamTestMvnpjenoa0/TempSuite5217560609831811643.bed/part-00003 /tmp/adamTestMvnpjenoa0/TempSuite5217560609831811643.bed/.part-00000.crc /tmp/adamTestMvnpjenoa0/TempSuite5217560609831811643.bed/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite5217560609831811643.bed/part-00002 /tmp/adamTestMvnpjenoa0/TempSuite5217560609831811643.bed/.part-00002.crc /tmp/adamTestMvnpjenoa0/TempSuite5217560609831811643.bed/.part-00001.crc /tmp/adamTestMvnpjenoa0/7537189900063719960 /tmp/adamTestMvnpjenoa0/7537189900063719960/.sorted.lex.vcf.crc /tmp/adamTestMvnpjenoa0/7537189900063719960/sorted.lex.vcf /tmp/adamTestMvnpjenoa0/TempSuite1590136513995882366.bed /tmp/adamTestMvnpjenoa0/TempSuite1590136513995882366.bed/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite1590136513995882366.bed/part-00000 /tmp/adamTestMvnpjenoa0/TempSuite1590136513995882366.bed/.part-00000.crc /tmp/adamTestMvnpjenoa0/TempSuite1590136513995882366.bed/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite4126011776911139231.bed /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite4126011776911139231.bed/_SUCCESS /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite4126011776911139231.bed/part-00001 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite4126011776911139231.bed/.part-00003.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite4126011776911139231.bed/part-00000 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite4126011776911139231.bed/part-00003 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite4126011776911139231.bed/.part-00000.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite4126011776911139231.bed/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite4126011776911139231.bed/part-00002 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite4126011776911139231.bed/.part-00002.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite4126011776911139231.bed/.part-00001.crc /tmp/adamTestMvnpjenoa0/1557939299692-0 /tmp/adamTestMvnpjenoa0/1557939299692-0/.test_single.vcf.crc /tmp/adamTestMvnpjenoa0/1557939299692-0/test.vcf /tmp/adamTestMvnpjenoa0/1557939299692-0/test.vcf/_SUCCESS /tmp/adamTestMvnpjenoa0/1557939299692-0/test.vcf/part-r-00000 /tmp/adamTestMvnpjenoa0/1557939299692-0/test.vcf/.part-r-00000.crc /tmp/adamTestMvnpjenoa0/1557939299692-0/test.vcf/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/1557939299692-0/test_single.vcf /tmp/adamTestMvnpjenoa0/TempSuite4319920536613111518 /tmp/adamTestMvnpjenoa0/.TempSuite8066014653926878091.sam.crc /tmp/adamTestMvnpjenoa0/TempSuite2871722268671373585.adam /tmp/adamTestMvnpjenoa0/TempSuite2871722268671373585.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite2871722268671373585.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite2871722268671373585.adam/._samples.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite2871722268671373585.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite2871722268671373585.adam/._header.crc /tmp/adamTestMvnpjenoa0/TempSuite2871722268671373585.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite2871722268671373585.adam/_samples.avro /tmp/adamTestMvnpjenoa0/TempSuite2871722268671373585.adam/part-00000-674ecd30-e5c5-4e87-a4b1-52f3efa4a0bd-c000.snappy.parquet /tmp/adamTestMvnpjenoa0/TempSuite2871722268671373585.adam/.part-00000-674ecd30-e5c5-4e87-a4b1-52f3efa4a0bd-c000.snappy.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite2871722268671373585.adam/_header /tmp/adamTestMvnpjenoa0/2921339138517380508 /tmp/adamTestMvnpjenoa0/2921339138517380508/.sorted.sam.crc /tmp/adamTestMvnpjenoa0/2921339138517380508/sorted.sam /tmp/adamTestMvnpjenoa0/TempSuite5803476424088697544.bed /tmp/adamTestMvnpjenoa0/TempSuite5803476424088697544.bed/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite5803476424088697544.bed/part-00000 /tmp/adamTestMvnpjenoa0/TempSuite5803476424088697544.bed/.part-00000.crc /tmp/adamTestMvnpjenoa0/TempSuite5803476424088697544.bed/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite7847523129585802179.fa /tmp/adamTestMvnpjenoa0/TempSuite7847523129585802179.fa/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite7847523129585802179.fa/part-00000 /tmp/adamTestMvnpjenoa0/TempSuite7847523129585802179.fa/.part-00000.crc /tmp/adamTestMvnpjenoa0/TempSuite7847523129585802179.fa/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite941656443948141376.sam /tmp/adamTestMvnpjenoa0/TempSuite941656443948141376.sam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite941656443948141376.sam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite941656443948141376.sam/.part-r-00000.sam.crc /tmp/adamTestMvnpjenoa0/TempSuite941656443948141376.sam/part-r-00000.sam /tmp/adamTestMvnpjenoa0/TempSuite757360818588446018 /tmp/adamTestMvnpjenoa0/TempSuite6833882510255996642 /tmp/adamTestMvnpjenoa0/random.vcf4897282965072623007.vcf /tmp/adamTestMvnpjenoa0/chr20.250k.fa.gz602631028121669504.250k.fa.gz /tmp/adamTestMvnpjenoa0/TempSuite4736184015014702030 /tmp/adamTestMvnpjenoa0/1557939714402-0 /tmp/adamTestMvnpjenoa0/1557939714402-0/.test_single.vcf.crc /tmp/adamTestMvnpjenoa0/1557939714402-0/test.vcf /tmp/adamTestMvnpjenoa0/1557939714402-0/test.vcf/_SUCCESS /tmp/adamTestMvnpjenoa0/1557939714402-0/test.vcf/part-r-00000 /tmp/adamTestMvnpjenoa0/1557939714402-0/test.vcf/.part-r-00000.crc /tmp/adamTestMvnpjenoa0/1557939714402-0/test.vcf/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/1557939714402-0/test_single.vcf /tmp/adamTestMvnpjenoa0/TempSuite56850008582945515 /tmp/adamTestMvnpjenoa0/TempSuite2406635389262883420.adam /tmp/adamTestMvnpjenoa0/TempSuite2406635389262883420.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite2406635389262883420.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite2406635389262883420.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite2406635389262883420.adam/.part-r-00003.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite2406635389262883420.adam/part-r-00001.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite2406635389262883420.adam/_readGroups.avro /tmp/adamTestMvnpjenoa0/TempSuite2406635389262883420.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite2406635389262883420.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite2406635389262883420.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite2406635389262883420.adam/.part-r-00001.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite2406635389262883420.adam/part-r-00002.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite2406635389262883420.adam/._processingSteps.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite2406635389262883420.adam/.part-r-00002.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite2406635389262883420.adam/_common_metadata /tmp/adamTestMvnpjenoa0/TempSuite2406635389262883420.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite2406635389262883420.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite2406635389262883420.adam/._readGroups.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite2406635389262883420.adam/_metadata /tmp/adamTestMvnpjenoa0/TempSuite2406635389262883420.adam/part-r-00003.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite2406635389262883420.adam/_processingSteps.avro /tmp/adamTestMvnpjenoa0/7000435320103032144 /tmp/adamTestMvnpjenoa0/7000435320103032144/ordered.sam /tmp/adamTestMvnpjenoa0/7000435320103032144/.ordered.sam.crc /tmp/adamTestMvnpjenoa0/TempSuite3955910051511586392 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite361418958970110841 /tmp/adamTestMvnpjenoa0/TempSuite6564694594282219992 /tmp/adamTestMvnpjenoa0/small.vcf5984477939855011836.vcf /tmp/adamTestMvnpjenoa0/2197289476803366129 /tmp/adamTestMvnpjenoa0/2197289476803366129/.sorted.lex.vcf.crc /tmp/adamTestMvnpjenoa0/2197289476803366129/sorted.lex.vcf /tmp/adamTestMvnpjenoa0/TempSuite5989210529891535695.adam /tmp/adamTestMvnpjenoa0/TempSuite5989210529891535695.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite5989210529891535695.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite5989210529891535695.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite5989210529891535695.adam/.part-r-00003.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite5989210529891535695.adam/part-r-00001.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite5989210529891535695.adam/_readGroups.avro /tmp/adamTestMvnpjenoa0/TempSuite5989210529891535695.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite5989210529891535695.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite5989210529891535695.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite5989210529891535695.adam/.part-r-00001.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite5989210529891535695.adam/part-r-00002.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite5989210529891535695.adam/._processingSteps.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite5989210529891535695.adam/.part-r-00002.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite5989210529891535695.adam/_common_metadata /tmp/adamTestMvnpjenoa0/TempSuite5989210529891535695.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite5989210529891535695.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite5989210529891535695.adam/._readGroups.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite5989210529891535695.adam/_metadata /tmp/adamTestMvnpjenoa0/TempSuite5989210529891535695.adam/part-r-00003.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite5989210529891535695.adam/_processingSteps.avro /tmp/adamTestMvnpjenoa0/TempSuite7613213390210882074.bed /tmp/adamTestMvnpjenoa0/TempSuite7613213390210882074.bed/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite7613213390210882074.bed/part-00000 /tmp/adamTestMvnpjenoa0/TempSuite7613213390210882074.bed/.part-00000.crc /tmp/adamTestMvnpjenoa0/TempSuite7613213390210882074.bed/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/3119668115935453517 /tmp/adamTestMvnpjenoa0/3119668115935453517/binned.adam /tmp/adamTestMvnpjenoa0/3119668115935453517/binned.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/3119668115935453517/binned.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/3119668115935453517/binned.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/3119668115935453517/binned.adam/_readGroups.avro /tmp/adamTestMvnpjenoa0/3119668115935453517/binned.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/3119668115935453517/binned.adam/_references.avro /tmp/adamTestMvnpjenoa0/3119668115935453517/binned.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/3119668115935453517/binned.adam/._processingSteps.avro.crc /tmp/adamTestMvnpjenoa0/3119668115935453517/binned.adam/_common_metadata /tmp/adamTestMvnpjenoa0/3119668115935453517/binned.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/3119668115935453517/binned.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/3119668115935453517/binned.adam/._readGroups.avro.crc /tmp/adamTestMvnpjenoa0/3119668115935453517/binned.adam/_metadata /tmp/adamTestMvnpjenoa0/3119668115935453517/binned.adam/_processingSteps.avro /tmp/adamTestMvnpjenoa0/TempSuite9133417666675141967 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite2309174855776508211 /tmp/adamTestMvnpjenoa0/chr20.250k.fa.gz4519218887623554079.250k.fa.gz /tmp/adamTestMvnpjenoa0/TempSuite6876003813360252754 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite1149986837268046739.bed /tmp/adamTestMvnpjenoa0/TempSuite4097811632542236011 /tmp/adamTestMvnpjenoa0/javaAC6100880595763102756 /tmp/adamTestMvnpjenoa0/javaAC6100880595763102756/testRdd.coverage.adam /tmp/adamTestMvnpjenoa0/javaAC6100880595763102756/testRdd.coverage.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/javaAC6100880595763102756/testRdd.coverage.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/javaAC6100880595763102756/testRdd.coverage.adam/._samples.avro.crc /tmp/adamTestMvnpjenoa0/javaAC6100880595763102756/testRdd.coverage.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/javaAC6100880595763102756/testRdd.coverage.adam/.part-r-00003.gz.parquet.crc /tmp/adamTestMvnpjenoa0/javaAC6100880595763102756/testRdd.coverage.adam/part-r-00001.gz.parquet /tmp/adamTestMvnpjenoa0/javaAC6100880595763102756/testRdd.coverage.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/javaAC6100880595763102756/testRdd.coverage.adam/_references.avro /tmp/adamTestMvnpjenoa0/javaAC6100880595763102756/testRdd.coverage.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/javaAC6100880595763102756/testRdd.coverage.adam/.part-r-00001.gz.parquet.crc /tmp/adamTestMvnpjenoa0/javaAC6100880595763102756/testRdd.coverage.adam/part-r-00002.gz.parquet /tmp/adamTestMvnpjenoa0/javaAC6100880595763102756/testRdd.coverage.adam/.part-r-00002.gz.parquet.crc /tmp/adamTestMvnpjenoa0/javaAC6100880595763102756/testRdd.coverage.adam/_common_metadata /tmp/adamTestMvnpjenoa0/javaAC6100880595763102756/testRdd.coverage.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/javaAC6100880595763102756/testRdd.coverage.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/javaAC6100880595763102756/testRdd.coverage.adam/_samples.avro /tmp/adamTestMvnpjenoa0/javaAC6100880595763102756/testRdd.coverage.adam/_metadata /tmp/adamTestMvnpjenoa0/javaAC6100880595763102756/testRdd.coverage.adam/part-r-00003.gz.parquet /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite6832653214527920584 /tmp/adamTestMvnpjenoa0/TempSuite5228295354935105937 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite1579150911363265296 /tmp/adamTestMvnpjenoa0/random.vcf679941606982649524.vcf /tmp/adamTestMvnpjenoa0/TempSuite6124671484567629296 /tmp/adamTestMvnpjenoa0/javaAC6696002864333652488 /tmp/adamTestMvnpjenoa0/javaAC6696002864333652488/testRdd.contig.adam /tmp/adamTestMvnpjenoa0/javaAC6696002864333652488/testRdd.contig.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/javaAC6696002864333652488/testRdd.contig.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/javaAC6696002864333652488/testRdd.contig.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/javaAC6696002864333652488/testRdd.contig.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/javaAC6696002864333652488/testRdd.contig.adam/_references.avro /tmp/adamTestMvnpjenoa0/javaAC6696002864333652488/testRdd.contig.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/javaAC6696002864333652488/testRdd.contig.adam/_common_metadata /tmp/adamTestMvnpjenoa0/javaAC6696002864333652488/testRdd.contig.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/javaAC6696002864333652488/testRdd.contig.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/javaAC6696002864333652488/testRdd.contig.adam/_metadata /tmp/adamTestMvnpjenoa0/TempSuite7038626970299123759 /tmp/adamTestMvnpjenoa0/TempSuite6501048191494208824.adam /tmp/adamTestMvnpjenoa0/TempSuite6501048191494208824.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite6501048191494208824.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite6501048191494208824.adam/.part-00000-9294d77f-ff21-4faf-9693-96b104a31c5f-c000.snappy.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite6501048191494208824.adam/_readGroups.avro /tmp/adamTestMvnpjenoa0/TempSuite6501048191494208824.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite6501048191494208824.adam/._processingSteps.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite6501048191494208824.adam/part-00000-9294d77f-ff21-4faf-9693-96b104a31c5f-c000.snappy.parquet /tmp/adamTestMvnpjenoa0/TempSuite6501048191494208824.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite6501048191494208824.adam/._readGroups.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite6501048191494208824.adam/_processingSteps.avro /tmp/adamTestMvnpjenoa0/TempSuite2653598405119108961 /tmp/adamTestMvnpjenoa0/TempSuite1056021066846908985_2.fq /tmp/adamTestMvnpjenoa0/TempSuite1056021066846908985_2.fq/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite1056021066846908985_2.fq/part-00000 /tmp/adamTestMvnpjenoa0/TempSuite1056021066846908985_2.fq/.part-00000.crc /tmp/adamTestMvnpjenoa0/TempSuite1056021066846908985_2.fq/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite8451402568221737471 /tmp/adamTestMvnpjenoa0/TempSuite2703227874603062832 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite5631867145567236052.bed /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite5631867145567236052.bed/_SUCCESS /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite5631867145567236052.bed/part-00001 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite5631867145567236052.bed/.part-00003.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite5631867145567236052.bed/part-00000 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite5631867145567236052.bed/part-00003 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite5631867145567236052.bed/.part-00000.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite5631867145567236052.bed/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite5631867145567236052.bed/part-00002 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite5631867145567236052.bed/.part-00002.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite5631867145567236052.bed/.part-00001.crc /tmp/adamTestMvnpjenoa0/TempSuite7412582376594988878.adam /tmp/adamTestMvnpjenoa0/TempSuite7412582376594988878.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite7412582376594988878.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite7412582376594988878.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/TempSuite7412582376594988878.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite7412582376594988878.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite7412582376594988878.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite7412582376594988878.adam/_common_metadata /tmp/adamTestMvnpjenoa0/TempSuite7412582376594988878.adam/._header.crc /tmp/adamTestMvnpjenoa0/TempSuite7412582376594988878.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/TempSuite7412582376594988878.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite7412582376594988878.adam/_metadata /tmp/adamTestMvnpjenoa0/TempSuite7412582376594988878.adam/_header /tmp/adamTestMvnpjenoa0/javaAC3602304177871431200 /tmp/adamTestMvnpjenoa0/javaAC3602304177871431200/testRdd.contig.adam /tmp/adamTestMvnpjenoa0/javaAC3602304177871431200/testRdd.contig.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/javaAC3602304177871431200/testRdd.contig.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/javaAC3602304177871431200/testRdd.contig.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/javaAC3602304177871431200/testRdd.contig.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/javaAC3602304177871431200/testRdd.contig.adam/_references.avro /tmp/adamTestMvnpjenoa0/javaAC3602304177871431200/testRdd.contig.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/javaAC3602304177871431200/testRdd.contig.adam/_common_metadata /tmp/adamTestMvnpjenoa0/javaAC3602304177871431200/testRdd.contig.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/javaAC3602304177871431200/testRdd.contig.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/javaAC3602304177871431200/testRdd.contig.adam/_metadata /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite5752425844141218720.gtf /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite5752425844141218720.gtf/_SUCCESS /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite5752425844141218720.gtf/part-00001 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite5752425844141218720.gtf/.part-00003.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite5752425844141218720.gtf/part-00000 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite5752425844141218720.gtf/part-00003 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite5752425844141218720.gtf/.part-00000.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite5752425844141218720.gtf/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite5752425844141218720.gtf/part-00002 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite5752425844141218720.gtf/.part-00002.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite5752425844141218720.gtf/.part-00001.crc /tmp/adamTestMvnpjenoa0/TempSuite298446164686410486 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite3477891220341065232.interval_list /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite3477891220341065232.interval_list/_SUCCESS /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite3477891220341065232.interval_list/part-00001 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite3477891220341065232.interval_list/.part-00003.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite3477891220341065232.interval_list/part-00000 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite3477891220341065232.interval_list/part-00003 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite3477891220341065232.interval_list/.part-00000.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite3477891220341065232.interval_list/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite3477891220341065232.interval_list/part-00002 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite3477891220341065232.interval_list/.part-00002.crc /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite3477891220341065232.interval_list/.part-00001.crc /tmp/adamTestMvnpjenoa0/3724691874941840468 /tmp/adamTestMvnpjenoa0/3724691874941840468/small.vcf.bgz /tmp/adamTestMvnpjenoa0/3724691874941840468/.small.vcf.bgz.crc /tmp/adamTestMvnpjenoa0/TempSuite5968469603544640016_2.fq /tmp/adamTestMvnpjenoa0/TempSuite5968469603544640016_2.fq/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite5968469603544640016_2.fq/part-00000 /tmp/adamTestMvnpjenoa0/TempSuite5968469603544640016_2.fq/.part-00000.crc /tmp/adamTestMvnpjenoa0/TempSuite5968469603544640016_2.fq/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite3430088968831191375.adam /tmp/adamTestMvnpjenoa0/TempSuite3430088968831191375.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite3430088968831191375.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite3430088968831191375.adam/referenceName=1 /tmp/adamTestMvnpjenoa0/TempSuite3430088968831191375.adam/referenceName=1/positionBin=0 /tmp/adamTestMvnpjenoa0/TempSuite3430088968831191375.adam/referenceName=1/positionBin=0/.part-00000-d0836af7-df46-4602-9725-2b06452a1681.c000.snappy.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite3430088968831191375.adam/referenceName=1/positionBin=0/part-00000-d0836af7-df46-4602-9725-2b06452a1681.c000.snappy.parquet /tmp/adamTestMvnpjenoa0/TempSuite3430088968831191375.adam/._samples.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite3430088968831191375.adam/_partitionedByStartPos /tmp/adamTestMvnpjenoa0/TempSuite3430088968831191375.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite3430088968831191375.adam/._header.crc /tmp/adamTestMvnpjenoa0/TempSuite3430088968831191375.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite3430088968831191375.adam/._partitionedByStartPos.crc /tmp/adamTestMvnpjenoa0/TempSuite3430088968831191375.adam/_samples.avro /tmp/adamTestMvnpjenoa0/TempSuite3430088968831191375.adam/_header /tmp/adamTestMvnpjenoa0/TempSuite6584657516960874689.bed /tmp/adamTestMvnpjenoa0/TempSuite6584657516960874689.bed/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite6584657516960874689.bed/part-00001 /tmp/adamTestMvnpjenoa0/TempSuite6584657516960874689.bed/.part-00003.crc /tmp/adamTestMvnpjenoa0/TempSuite6584657516960874689.bed/part-00000 /tmp/adamTestMvnpjenoa0/TempSuite6584657516960874689.bed/part-00003 /tmp/adamTestMvnpjenoa0/TempSuite6584657516960874689.bed/.part-00000.crc /tmp/adamTestMvnpjenoa0/TempSuite6584657516960874689.bed/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite6584657516960874689.bed/part-00002 /tmp/adamTestMvnpjenoa0/TempSuite6584657516960874689.bed/.part-00002.crc /tmp/adamTestMvnpjenoa0/TempSuite6584657516960874689.bed/.part-00001.crc /tmp/adamTestMvnpjenoa0/TempSuite2904458924458676828.adam /tmp/adamTestMvnpjenoa0/TempSuite2904458924458676828.adam/.part-00002-84fdc13c-5fd2-4fc2-958f-9cad9a812e99-c000.snappy.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite2904458924458676828.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite2904458924458676828.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite2904458924458676828.adam/._samples.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite2904458924458676828.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite2904458924458676828.adam/part-00000-84fdc13c-5fd2-4fc2-958f-9cad9a812e99-c000.snappy.parquet /tmp/adamTestMvnpjenoa0/TempSuite2904458924458676828.adam/part-00002-84fdc13c-5fd2-4fc2-958f-9cad9a812e99-c000.snappy.parquet /tmp/adamTestMvnpjenoa0/TempSuite2904458924458676828.adam/.part-00001-84fdc13c-5fd2-4fc2-958f-9cad9a812e99-c000.snappy.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite2904458924458676828.adam/.part-00000-84fdc13c-5fd2-4fc2-958f-9cad9a812e99-c000.snappy.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite2904458924458676828.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite2904458924458676828.adam/_samples.avro /tmp/adamTestMvnpjenoa0/TempSuite2904458924458676828.adam/part-00001-84fdc13c-5fd2-4fc2-958f-9cad9a812e99-c000.snappy.parquet /tmp/adamTestMvnpjenoa0/TempSuite1099724985131552573 /tmp/adamTestMvnpjenoa0/TempSuite7520680222865061927 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite3284951755692471043 /tmp/adamTestMvnpjenoa0/TempSuite8792683224090933900 /tmp/adamTestMvnpjenoa0/TempSuite8280402691048794791 /tmp/adamTestMvnpjenoa0/2020505558618987790 /tmp/adamTestMvnpjenoa0/2020505558618987790/ctg.adam /tmp/adamTestMvnpjenoa0/2020505558618987790/ctg.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/2020505558618987790/ctg.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/2020505558618987790/ctg.adam/_partitionedByStartPos /tmp/adamTestMvnpjenoa0/2020505558618987790/ctg.adam/_references.avro /tmp/adamTestMvnpjenoa0/2020505558618987790/ctg.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/2020505558618987790/ctg.adam/._partitionedByStartPos.crc /tmp/adamTestMvnpjenoa0/2020505558618987790/ctg.adam/referenceName=HLA-DQB1%2A05%3A01%3A01%3A02 /tmp/adamTestMvnpjenoa0/2020505558618987790/ctg.adam/referenceName=HLA-DQB1%2A05%3A01%3A01%3A02/positionBin=0 /tmp/adamTestMvnpjenoa0/2020505558618987790/ctg.adam/referenceName=HLA-DQB1%2A05%3A01%3A01%3A02/positionBin=0/part-00000-04094056-9279-43b2-a29b-44d6c3d217f9.c000.snappy.parquet /tmp/adamTestMvnpjenoa0/2020505558618987790/ctg.adam/referenceName=HLA-DQB1%2A05%3A01%3A01%3A02/positionBin=0/.part-00000-04094056-9279-43b2-a29b-44d6c3d217f9.c000.snappy.parquet.crc /tmp/adamTestMvnpjenoa0/1557940213730-0 /tmp/adamTestMvnpjenoa0/1557940213730-0/bqsr1-r1.fq /tmp/adamTestMvnpjenoa0/1557940213730-0/bqsr1-r1.fq/_SUCCESS /tmp/adamTestMvnpjenoa0/1557940213730-0/bqsr1-r1.fq/part-00000 /tmp/adamTestMvnpjenoa0/1557940213730-0/bqsr1-r1.fq/.part-00000.crc /tmp/adamTestMvnpjenoa0/1557940213730-0/bqsr1-r1.fq/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/1557940213730-0/bqsr1-r2.fq /tmp/adamTestMvnpjenoa0/1557940213730-0/bqsr1-r2.fq/_SUCCESS /tmp/adamTestMvnpjenoa0/1557940213730-0/bqsr1-r2.fq/part-00000 /tmp/adamTestMvnpjenoa0/1557940213730-0/bqsr1-r2.fq/.part-00000.crc /tmp/adamTestMvnpjenoa0/1557940213730-0/bqsr1-r2.fq/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite5875114460019877737 /tmp/adamTestMvnpjenoa0/TempSuite5768045921574454351 /tmp/adamTestMvnpjenoa0/TempSuite2406635389262883420 /tmp/adamTestMvnpjenoa0/1557939943545-0 /tmp/adamTestMvnpjenoa0/1557939943545-0/test.fa /tmp/adamTestMvnpjenoa0/1557939943545-0/test.fa/_SUCCESS /tmp/adamTestMvnpjenoa0/1557939943545-0/test.fa/part-00000 /tmp/adamTestMvnpjenoa0/1557939943545-0/test.fa/.part-00000.crc /tmp/adamTestMvnpjenoa0/1557939943545-0/test.fa/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite8755731092838480176_2.fq /tmp/adamTestMvnpjenoa0/TempSuite8755731092838480176_2.fq/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite8755731092838480176_2.fq/part-00000 /tmp/adamTestMvnpjenoa0/TempSuite8755731092838480176_2.fq/.part-00000.crc /tmp/adamTestMvnpjenoa0/TempSuite8755731092838480176_2.fq/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/.TempSuite6820875629505030184.sam.crc /tmp/adamTestMvnpjenoa0/TempSuite6584657516960874689 /tmp/adamTestMvnpjenoa0/.TempSuite6681591804528478661_1.fq.crc /tmp/adamTestMvnpjenoa0/TempSuite8382378137815932429.adam /tmp/adamTestMvnpjenoa0/TempSuite8382378137815932429.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite8382378137815932429.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite8382378137815932429.adam/part-00002-6e677ba1-7287-44aa-a2d0-82dec6f09bae-c000.snappy.parquet /tmp/adamTestMvnpjenoa0/TempSuite8382378137815932429.adam/.part-00001-6e677ba1-7287-44aa-a2d0-82dec6f09bae-c000.snappy.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite8382378137815932429.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite8382378137815932429.adam/.part-00002-6e677ba1-7287-44aa-a2d0-82dec6f09bae-c000.snappy.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite8382378137815932429.adam/.part-00000-6e677ba1-7287-44aa-a2d0-82dec6f09bae-c000.snappy.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite8382378137815932429.adam/._header.crc /tmp/adamTestMvnpjenoa0/TempSuite8382378137815932429.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite8382378137815932429.adam/part-00001-6e677ba1-7287-44aa-a2d0-82dec6f09bae-c000.snappy.parquet /tmp/adamTestMvnpjenoa0/TempSuite8382378137815932429.adam/part-00000-6e677ba1-7287-44aa-a2d0-82dec6f09bae-c000.snappy.parquet /tmp/adamTestMvnpjenoa0/TempSuite8382378137815932429.adam/_header /tmp/adamTestMvnpjenoa0/TempSuite3879360464944867174.adam /tmp/adamTestMvnpjenoa0/TempSuite3879360464944867174.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite3879360464944867174.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite3879360464944867174.adam/referenceName=1 /tmp/adamTestMvnpjenoa0/TempSuite3879360464944867174.adam/referenceName=1/positionBin=26 /tmp/adamTestMvnpjenoa0/TempSuite3879360464944867174.adam/referenceName=1/positionBin=26/.part-00000-7e40c18e-9e5f-4949-837b-c768911c58fa.c000.snappy.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite3879360464944867174.adam/referenceName=1/positionBin=26/part-00000-7e40c18e-9e5f-4949-837b-c768911c58fa.c000.snappy.parquet /tmp/adamTestMvnpjenoa0/TempSuite3879360464944867174.adam/referenceName=1/positionBin=240 /tmp/adamTestMvnpjenoa0/TempSuite3879360464944867174.adam/referenceName=1/positionBin=240/.part-00000-7e40c18e-9e5f-4949-837b-c768911c58fa.c000.snappy.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite3879360464944867174.adam/referenceName=1/positionBin=240/part-00000-7e40c18e-9e5f-4949-837b-c768911c58fa.c000.snappy.parquet /tmp/adamTestMvnpjenoa0/TempSuite3879360464944867174.adam/_readGroups.avro /tmp/adamTestMvnpjenoa0/TempSuite3879360464944867174.adam/_partitionedByStartPos /tmp/adamTestMvnpjenoa0/TempSuite3879360464944867174.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite3879360464944867174.adam/._processingSteps.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite3879360464944867174.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite3879360464944867174.adam/._readGroups.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite3879360464944867174.adam/._partitionedByStartPos.crc /tmp/adamTestMvnpjenoa0/TempSuite3879360464944867174.adam/referenceName=2 /tmp/adamTestMvnpjenoa0/TempSuite3879360464944867174.adam/referenceName=2/positionBin=189 /tmp/adamTestMvnpjenoa0/TempSuite3879360464944867174.adam/referenceName=2/positionBin=189/.part-00000-7e40c18e-9e5f-4949-837b-c768911c58fa.c000.snappy.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite3879360464944867174.adam/referenceName=2/positionBin=189/part-00000-7e40c18e-9e5f-4949-837b-c768911c58fa.c000.snappy.parquet /tmp/adamTestMvnpjenoa0/TempSuite3879360464944867174.adam/_processingSteps.avro /tmp/adamTestMvnpjenoa0/TempSuite7652450895275188384 /tmp/adamTestMvnpjenoa0/FeatureDatasetFunctionsSuite4174236648008664065 /tmp/adamTestMvnpjenoa0/random.vcf2116042941607263790.vcf /tmp/adamTestMvnpjenoa0/4225534459004049612 /tmp/adamTestMvnpjenoa0/4225534459004049612/ctg.adam /tmp/adamTestMvnpjenoa0/4225534459004049612/ctg.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/4225534459004049612/ctg.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/4225534459004049612/ctg.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/4225534459004049612/ctg.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/4225534459004049612/ctg.adam/_references.avro /tmp/adamTestMvnpjenoa0/4225534459004049612/ctg.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/4225534459004049612/ctg.adam/_common_metadata /tmp/adamTestMvnpjenoa0/4225534459004049612/ctg.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/4225534459004049612/ctg.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/4225534459004049612/ctg.adam/_metadata /tmp/adamTestMvnpjenoa0/TempSuite3564918522804962223.adam /tmp/adamTestMvnpjenoa0/TempSuite3564918522804962223.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite3564918522804962223.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite3564918522804962223.adam/.part-00002-7b5c489f-8e47-4de6-a516-132843f8c90d-c000.snappy.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite3564918522804962223.adam/part-00002-7b5c489f-8e47-4de6-a516-132843f8c90d-c000.snappy.parquet /tmp/adamTestMvnpjenoa0/TempSuite3564918522804962223.adam/_readGroups.avro /tmp/adamTestMvnpjenoa0/TempSuite3564918522804962223.adam/_references.avro /tmp/adamTestMvnpjenoa0/TempSuite3564918522804962223.adam/part-00000-7b5c489f-8e47-4de6-a516-132843f8c90d-c000.snappy.parquet /tmp/adamTestMvnpjenoa0/TempSuite3564918522804962223.adam/._processingSteps.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite3564918522804962223.adam/.part-00001-7b5c489f-8e47-4de6-a516-132843f8c90d-c000.snappy.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite3564918522804962223.adam/.part-00000-7b5c489f-8e47-4de6-a516-132843f8c90d-c000.snappy.parquet.crc /tmp/adamTestMvnpjenoa0/TempSuite3564918522804962223.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite3564918522804962223.adam/._readGroups.avro.crc /tmp/adamTestMvnpjenoa0/TempSuite3564918522804962223.adam/part-00001-7b5c489f-8e47-4de6-a516-132843f8c90d-c000.snappy.parquet /tmp/adamTestMvnpjenoa0/TempSuite3564918522804962223.adam/_processingSteps.avro /tmp/adamTestMvnpjenoa0/javaAC6152499516160315547 /tmp/adamTestMvnpjenoa0/javaAC6152499516160315547/testRdd.fragment.adam /tmp/adamTestMvnpjenoa0/javaAC6152499516160315547/testRdd.fragment.adam/_SUCCESS /tmp/adamTestMvnpjenoa0/javaAC6152499516160315547/testRdd.fragment.adam/._references.avro.crc /tmp/adamTestMvnpjenoa0/javaAC6152499516160315547/testRdd.fragment.adam/part-r-00000.gz.parquet /tmp/adamTestMvnpjenoa0/javaAC6152499516160315547/testRdd.fragment.adam/_readGroups.avro /tmp/adamTestMvnpjenoa0/javaAC6152499516160315547/testRdd.fragment.adam/._common_metadata.crc /tmp/adamTestMvnpjenoa0/javaAC6152499516160315547/testRdd.fragment.adam/_references.avro /tmp/adamTestMvnpjenoa0/javaAC6152499516160315547/testRdd.fragment.adam/.part-r-00000.gz.parquet.crc /tmp/adamTestMvnpjenoa0/javaAC6152499516160315547/testRdd.fragment.adam/._processingSteps.avro.crc /tmp/adamTestMvnpjenoa0/javaAC6152499516160315547/testRdd.fragment.adam/_common_metadata /tmp/adamTestMvnpjenoa0/javaAC6152499516160315547/testRdd.fragment.adam/._metadata.crc /tmp/adamTestMvnpjenoa0/javaAC6152499516160315547/testRdd.fragment.adam/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/javaAC6152499516160315547/testRdd.fragment.adam/._readGroups.avro.crc /tmp/adamTestMvnpjenoa0/javaAC6152499516160315547/testRdd.fragment.adam/_metadata /tmp/adamTestMvnpjenoa0/javaAC6152499516160315547/testRdd.fragment.adam/_processingSteps.avro /tmp/adamTestMvnpjenoa0/TempSuite4467856944529846887 /tmp/adamTestMvnpjenoa0/TempSuite2501700038666840262 /tmp/adamTestMvnpjenoa0/7889844968169383716 /tmp/adamTestMvnpjenoa0/7889844968169383716/test.fa /tmp/adamTestMvnpjenoa0/7889844968169383716/test.fa/_SUCCESS /tmp/adamTestMvnpjenoa0/7889844968169383716/test.fa/part-00000 /tmp/adamTestMvnpjenoa0/7889844968169383716/test.fa/.part-00000.crc /tmp/adamTestMvnpjenoa0/7889844968169383716/test.fa/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite7790111402099210763 /tmp/adamTestMvnpjenoa0/1557939941258-0 /tmp/adamTestMvnpjenoa0/1557939941258-0/test.fa /tmp/adamTestMvnpjenoa0/1557939941258-0/test.fa/_SUCCESS /tmp/adamTestMvnpjenoa0/1557939941258-0/test.fa/part-00000 /tmp/adamTestMvnpjenoa0/1557939941258-0/test.fa/.part-00000.crc /tmp/adamTestMvnpjenoa0/1557939941258-0/test.fa/._SUCCESS.crc /tmp/adamTestMvnpjenoa0/TempSuite9159592525869374102.fq /tmp/adamTestMvnpjenoa0/TempSuite9159592525869374102.fq/_SUCCESS /tmp/adamTestMvnpjenoa0/TempSuite9159592525869374102.fq/part-00000 /tmp/adamTestMvnpjenoa0/TempSuite9159592525869374102.fq/.part-00000.crc /tmp/adamTestMvnpjenoa0/TempSuite9159592525869374102.fq/._SUCCESS.crc rm -rf ${ADAM_MVN_TMP_DIR} + rm -rf /tmp/adamTestMvnpjenoa0 find . -name pom.xml \ -exec sed -i.bak \ -e "s:sun.io.serialization.extendedDebugInfo=true -Djava.io.tmpdir=${ADAM_MVN_TMP_DIR}:sun.io.serialization.extendedDebugInfo=true:g" \ {} \; + find . -name pom.xml -exec sed -i.bak -e 's:sun.io.serialization.extendedDebugInfo=true -Djava.io.tmpdir=/tmp/adamTestMvnpjenoa0:sun.io.serialization.extendedDebugInfo=true:g' '{}' ';' find . -name "*.bak" -exec rm -f {} \; + find . -name '*.bak' -exec rm -f '{}' ';' # run integration tests # make a temp directory ADAM_TMP_DIR=$(mktemp -d -t adamTestXXXXXXX) mktemp -d -t adamTestXXXXXXX ++ mktemp -d -t adamTestXXXXXXX + ADAM_TMP_DIR=/tmp/adamTestqfLQDtM # Just to be paranoid.. use a directory internal to the ADAM_TMP_DIR ADAM_TMP_DIR=$ADAM_TMP_DIR/deleteMePleaseThisIsNoLongerNeeded + ADAM_TMP_DIR=/tmp/adamTestqfLQDtM/deleteMePleaseThisIsNoLongerNeeded mkdir $ADAM_TMP_DIR + mkdir /tmp/adamTestqfLQDtM/deleteMePleaseThisIsNoLongerNeeded # set the TMPDIR envar, which is used by python to choose where to make temp directories export TMPDIR=${ADAM_TMP_DIR} + export TMPDIR=/tmp/adamTestqfLQDtM/deleteMePleaseThisIsNoLongerNeeded + TMPDIR=/tmp/adamTestqfLQDtM/deleteMePleaseThisIsNoLongerNeeded pushd $PROJECT_ROOT + pushd /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/scripts/.. ~/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu ~/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu # Copy the jar into our temp space for testing cp -r . $ADAM_TMP_DIR + cp -r . /tmp/adamTestqfLQDtM/deleteMePleaseThisIsNoLongerNeeded popd + popd ~/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu pushd $ADAM_TMP_DIR + pushd /tmp/adamTestqfLQDtM/deleteMePleaseThisIsNoLongerNeeded /tmp/adamTestqfLQDtM/deleteMePleaseThisIsNoLongerNeeded ~/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu # what hadoop version are we on? format string for downloading spark assembly if [[ $HADOOP_VERSION =~ ^2\.6 ]]; then HADOOP=hadoop2.6 elif [[ $HADOOP_VERSION =~ ^2\.7 ]]; then HADOOP=hadoop2.7 else echo "Unknown Hadoop version." exit 1 fi + [[ 2.7.5 =~ ^2\.6 ]] + [[ 2.7.5 =~ ^2\.7 ]] + HADOOP=hadoop2.7 # set spark artifact string for downloading assembly SPARK=spark-${SPARK_VERSION} + SPARK=spark-2.4.3 # download prepackaged spark assembly # Spark 2.4.3 needs special case for Scala 2.12 if [ ${SCALAVER} == 2.12 ]; then curl \ -L "https://www.apache.org/dyn/mirrors/mirrors.cgi?action=download&filename=spark/${SPARK}/${SPARK}-bin-without-hadoop-scala-2.12.tgz" \ -o ${SPARK}-bin-${HADOOP}.tgz else curl \ -L "https://www.apache.org/dyn/mirrors/mirrors.cgi?action=download&filename=spark/${SPARK}/${SPARK}-bin-${HADOOP}.tgz" \ -o ${SPARK}-bin-${HADOOP}.tgz fi + '[' 2.12 == 2.12 ']' + curl -L 'https://www.apache.org/dyn/mirrors/mirrors.cgi?action=download&filename=spark/spark-2.4.3/spark-2.4.3-bin-without-hadoop-scala-2.12.tgz' -o spark-2.4.3-bin-hadoop2.7.tgz % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 0 134M 0 207k 0 0 116k 0 0:19:46 0:00:01 0:19:45 116k 0 134M 0 331k 0 0 118k 0 0:19:23 0:00:02 0:19:21 122k 0 134M 0 524k 0 0 138k 0 0:16:34 0:00:03 0:16:31 159k 0 134M 0 884k 0 0 186k 0 0:12:20 0:00:04 0:12:16 228k 1 134M 1 1618k 0 0 281k 0 0:08:11 0:00:05 0:08:06 354k 1 134M 1 2711k 0 0 401k 0 0:05:43 0:00:06 0:05:37 504k 3 134M 3 4299k 0 0 555k 0 0:04:08 0:00:07 0:04:01 801k 3 134M 3 4937k 0 0 562k 0 0:04:05 0:00:08 0:03:57 882k 3 134M 3 5298k 0 0 543k 0 0:04:14 0:00:09 0:04:05 880k 4 134M 4 6073k 0 0 564k 0 0:04:04 0:00:10 0:03:54 890k 5 134M 5 7267k 0 0 618k 0 0:03:43 0:00:11 0:03:32 909k 6 134M 6 8932k 0 0 689k 0 0:03:20 0:00:12 0:03:08 888k 6 134M 6 9193k 0 0 668k 0 0:03:26 0:00:13 0:03:13 855k 7 134M 7 10.2M 0 0 714k 0 0:03:13 0:00:14 0:02:59 1049k 7 134M 7 10.5M 0 0 683k 0 0:03:22 0:00:15 0:03:07 940k 8 134M 8 11.0M 0 0 678k 0 0:03:23 0:00:16 0:03:07 820k 8 134M 8 12.0M 0 0 697k 0 0:03:18 0:00:17 0:03:01 719k 10 134M 10 13.5M 0 0 738k 0 0:03:07 0:00:18 0:02:49 929k 10 134M 10 14.6M 0 0 760k 0 0:03:01 0:00:19 0:02:42 893k 11 134M 11 15.4M 0 0 762k 0 0:03:01 0:00:20 0:02:41 1007k 12 134M 12 16.4M 0 0 772k 0 0:02:58 0:00:21 0:02:37 1084k 13 134M 13 17.6M 0 0 793k 0 0:02:54 0:00:22 0:02:32 1129k 14 134M 14 19.2M 0 0 830k 0 0:02:46 0:00:23 0:02:23 1176k 14 134M 14 19.5M 0 0 807k 0 0:02:51 0:00:24 0:02:27 997k 14 134M 14 19.9M 0 0 792k 0 0:02:54 0:00:25 0:02:29 920k 15 134M 15 20.7M 0 0 794k 0 0:02:53 0:00:26 0:02:27 888k 16 134M 16 22.0M 0 0 812k 0 0:02:49 0:00:27 0:02:22 901k 17 134M 17 23.4M 0 0 832k 0 0:02:45 0:00:28 0:02:17 840k 17 134M 17 23.6M 0 0 812k 0 0:02:49 0:00:29 0:02:20 839k 17 134M 17 24.1M 0 0 804k 0 0:02:51 0:00:30 0:02:21 866k 18 134M 18 25.0M 0 0 807k 0 0:02:51 0:00:31 0:02:20 879k 19 134M 19 26.3M 0 0 823k 0 0:02:47 0:00:32 0:02:15 884k 20 134M 20 27.6M 0 0 832k 0 0:02:45 0:00:34 0:02:11 833k 20 134M 20 28.2M 0 0 826k 0 0:02:47 0:00:35 0:02:12 903k 21 134M 21 28.4M 0 0 814k 0 0:02:49 0:00:35 0:02:14 876k 22 134M 22 29.9M 0 0 834k 0 0:02:45 0:00:36 0:02:09 1003k 22 134M 22 30.6M 0 0 831k 0 0:02:46 0:00:37 0:02:09 880k 22 134M 22 30.9M 0 0 818k 0 0:02:48 0:00:38 0:02:10 718k 23 134M 23 31.6M 0 0 815k 0 0:02:49 0:00:39 0:02:10 734k 24 134M 24 32.7M 0 0 822k 0 0:02:48 0:00:40 0:02:08 875k 25 134M 25 34.2M 0 0 840k 0 0:02:44 0:00:41 0:02:03 887k 25 134M 25 34.7M 0 0 832k 0 0:02:45 0:00:42 0:02:03 843k 26 134M 26 35.1M 0 0 823k 0 0:02:47 0:00:43 0:02:04 860k 26 134M 26 35.9M 0 0 822k 0 0:02:47 0:00:44 0:02:03 879k 27 134M 27 37.2M 0 0 833k 0 0:02:45 0:00:45 0:02:00 927k 28 134M 28 38.5M 0 0 844k 0 0:02:43 0:00:46 0:01:57 877k 28 134M 28 38.7M 0 0 831k 0 0:02:46 0:00:47 0:01:59 822k 29 134M 29 39.3M 0 0 826k 0 0:02:47 0:00:48 0:01:59 851k 29 134M 29 40.1M 0 0 827k 0 0:02:46 0:00:49 0:01:57 872k 30 134M 30 41.5M 0 0 839k 0 0:02:44 0:00:50 0:01:54 888k 31 134M 31 42.6M 0 0 840k 0 0:02:44 0:00:51 0:01:53 807k 31 134M 31 42.8M 0 0 832k 0 0:02:45 0:00:52 0:01:53 838k 32 134M 32 43.4M 0 0 828k 0 0:02:46 0:00:53 0:01:53 852k 32 134M 32 44.4M 0 0 832k 0 0:02:45 0:00:54 0:01:51 877k 34 134M 34 46.0M 0 0 845k 0 0:02:43 0:00:55 0:01:48 914k 34 134M 34 47.0M 0 0 848k 0 0:02:42 0:00:56 0:01:46 935k 36 134M 36 48.6M 0 0 861k 0 0:02:40 0:00:57 0:01:43 1167k 36 134M 36 49.5M 0 0 863k 0 0:02:40 0:00:58 0:01:42 1230k 37 134M 37 50.9M 0 0 872k 0 0:02:38 0:00:59 0:01:39 1302k 37 134M 37 51.1M 0 0 862k 0 0:02:40 0:01:00 0:01:40 1046k 38 134M 38 51.7M 0 0 857k 0 0:02:41 0:01:01 0:01:40 950k 38 134M 38 52.6M 0 0 858k 0 0:02:40 0:01:02 0:01:38 821k 40 134M 40 54.0M 0 0 867k 0 0:02:39 0:01:03 0:01:36 923k 40 134M 40 54.7M 0 0 866k 0 0:02:39 0:01:04 0:01:35 790k 40 134M 40 55.0M 0 0 857k 0 0:02:41 0:01:05 0:01:36 803k 41 134M 41 55.6M 0 0 853k 0 0:02:41 0:01:06 0:01:35 805k 41 134M 41 56.4M 0 0 854k 0 0:02:41 0:01:07 0:01:34 799k 42 134M 42 57.8M 0 0 861k 0 0:02:40 0:01:08 0:01:32 786k 43 134M 43 59.0M 0 0 864k 0 0:02:39 0:01:09 0:01:30 851k 44 134M 44 59.7M 0 0 865k 0 0:02:39 0:01:10 0:01:29 967k 45 134M 45 60.8M 0 0 866k 0 0:02:39 0:01:11 0:01:28 1043k 45 134M 45 61.1M 0 0 860k 0 0:02:40 0:01:12 0:01:28 946k 45 134M 45 61.7M 0 0 857k 0 0:02:41 0:01:13 0:01:28 799k 46 134M 46 62.8M 0 0 860k 0 0:02:40 0:01:14 0:01:26 793k 47 134M 47 64.3M 0 0 870k 0 0:02:38 0:01:15 0:01:23 934k 48 134M 48 65.5M 0 0 873k 0 0:02:38 0:01:16 0:01:22 978k 49 134M 49 66.6M 0 0 875k 0 0:02:37 0:01:17 0:01:20 1083k 49 134M 49 66.9M 0 0 869k 0 0:02:38 0:01:18 0:01:20 1048k 50 134M 50 67.4M 0 0 866k 0 0:02:39 0:01:19 0:01:20 957k 50 134M 50 68.4M 0 0 867k 0 0:02:39 0:01:20 0:01:19 832k 51 134M 51 69.8M 0 0 874k 0 0:02:37 0:01:21 0:01:16 889k 52 134M 52 70.8M 0 0 875k 0 0:02:37 0:01:22 0:01:15 882k 53 134M 53 71.8M 0 0 878k 0 0:02:37 0:01:23 0:01:14 1015k 53 134M 53 72.4M 0 0 875k 0 0:02:37 0:01:24 0:01:13 1013k 53 134M 53 72.8M 0 0 869k 0 0:02:38 0:01:25 0:01:13 901k 54 134M 54 73.5M 0 0 868k 0 0:02:39 0:01:26 0:01:13 759k 55 134M 55 74.7M 0 0 871k 0 0:02:38 0:01:27 0:01:11 806k 56 134M 56 76.3M 0 0 878k 0 0:02:37 0:01:28 0:01:09 876k 56 134M 56 76.4M 0 0 871k 0 0:02:38 0:01:29 0:01:09 818k 57 134M 57 76.9M 0 0 867k 0 0:02:39 0:01:30 0:01:09 834k 57 134M 57 77.7M 0 0 867k 0 0:02:39 0:01:31 0:01:08 850k 58 134M 58 78.9M 0 0 871k 0 0:02:38 0:01:32 0:01:06 868k 59 134M 59 80.5M 0 0 877k 0 0:02:37 0:01:34 0:01:03 855k 60 134M 60 81.7M 0 0 883k 0 0:02:36 0:01:34 0:01:02 1095k 60 134M 60 82.1M 0 0 878k 0 0:02:37 0:01:35 0:01:02 1075k 61 134M 61 82.5M 0 0 873k 0 0:02:38 0:01:36 0:01:02 995k 61 134M 61 83.3M 0 0 873k 0 0:02:38 0:01:37 0:01:01 905k 62 134M 62 84.6M 0 0 877k 0 0:02:37 0:01:38 0:00:59 894k 63 134M 63 86.1M 0 0 883k 0 0:02:36 0:01:39 0:00:57 880k 64 134M 64 86.5M 0 0 880k 0 0:02:36 0:01:40 0:00:56 911k 65 134M 65 87.9M 0 0 885k 0 0:02:36 0:01:41 0:00:55 1101k 65 134M 65 88.1M 0 0 878k 0 0:02:37 0:01:42 0:00:55 977k 65 134M 65 88.6M 0 0 875k 0 0:02:37 0:01:43 0:00:54 820k 66 134M 66 89.5M 0 0 875k 0 0:02:37 0:01:44 0:00:53 715k 67 134M 67 90.8M 0 0 880k 0 0:02:36 0:01:45 0:00:51 880k 68 134M 68 92.0M 0 0 882k 0 0:02:36 0:01:46 0:00:50 839k 69 134M 69 93.7M 0 0 890k 0 0:02:35 0:01:47 0:00:48 1134k 70 134M 70 94.7M 0 0 892k 0 0:02:34 0:01:48 0:00:46 1251k 70 134M 70 95.4M 0 0 890k 0 0:02:35 0:01:49 0:00:46 1202k 70 134M 70 95.5M 0 0 883k 0 0:02:36 0:01:50 0:00:46 960k 71 134M 71 95.9M 0 0 879k 0 0:02:37 0:01:51 0:00:46 798k 71 134M 71 96.6M 0 0 877k 0 0:02:37 0:01:52 0:00:45 603k 72 134M 72 97.7M 0 0 879k 0 0:02:37 0:01:53 0:00:44 601k 73 134M 73 99.3M 0 0 886k 0 0:02:35 0:01:54 0:00:41 803k 74 134M 74 99.8M 0 0 883k 0 0:02:36 0:01:55 0:00:41 869k 74 134M 74 100M 0 0 878k 0 0:02:37 0:01:56 0:00:41 866k 74 134M 74 100M 0 0 877k 0 0:02:37 0:01:57 0:00:40 873k 75 134M 75 102M 0 0 879k 0 0:02:37 0:01:58 0:00:39 884k 76 134M 76 103M 0 0 885k 0 0:02:36 0:02:00 0:00:36 853k 77 134M 77 103M 0 0 881k 0 0:02:36 0:02:00 0:00:36 834k 78 134M 78 105M 0 0 887k 0 0:02:35 0:02:01 0:00:34 1091k 79 134M 79 106M 0 0 889k 0 0:02:35 0:02:02 0:00:33 1180k 79 134M 79 107M 0 0 887k 0 0:02:35 0:02:03 0:00:32 1074k 80 134M 80 108M 0 0 891k 0 0:02:34 0:02:04 0:00:30 1053k 80 134M 80 108M 0 0 887k 0 0:02:35 0:02:05 0:00:30 1036k 81 134M 81 109M 0 0 883k 0 0:02:36 0:02:06 0:00:30 781k 81 134M 81 110M 0 0 882k 0 0:02:36 0:02:07 0:00:29 701k 82 134M 82 111M 0 0 884k 0 0:02:36 0:02:08 0:00:28 801k 83 134M 83 112M 0 0 890k 0 0:02:35 0:02:09 0:00:26 860k 83 134M 83 113M 0 0 886k 0 0:02:35 0:02:10 0:00:25 862k 84 134M 84 113M 0 0 882k 0 0:02:36 0:02:11 0:00:25 866k 84 134M 84 114M 0 0 881k 0 0:02:36 0:02:12 0:00:24 859k 85 134M 85 115M 0 0 883k 0 0:02:36 0:02:13 0:00:23 858k 86 134M 86 117M 0 0 889k 0 0:02:35 0:02:14 0:00:21 868k 87 134M 87 117M 0 0 885k 0 0:02:35 0:02:15 0:00:20 866k 87 134M 87 118M 0 0 887k 0 0:02:35 0:02:16 0:00:19 1017k 88 134M 88 118M 0 0 882k 0 0:02:36 0:02:17 0:00:19 916k 88 134M 88 119M 0 0 880k 0 0:02:36 0:02:18 0:00:18 790k 89 134M 89 120M 0 0 880k 0 0:02:36 0:02:19 0:00:17 628k 89 134M 89 121M 0 0 882k 0 0:02:36 0:02:20 0:00:16 806k 90 134M 90 122M 0 0 886k 0 0:02:35 0:02:21 0:00:14 854k 91 134M 91 122M 0 0 881k 0 0:02:36 0:02:22 0:00:14 854k 91 134M 91 123M 0 0 879k 0 0:02:37 0:02:23 0:00:14 865k 92 134M 92 124M 0 0 880k 0 0:02:36 0:02:24 0:00:12 890k 93 134M 93 125M 0 0 884k 0 0:02:36 0:02:25 0:00:11 944k 93 134M 93 126M 0 0 883k 0 0:02:36 0:02:26 0:00:10 807k 94 134M 94 127M 0 0 880k 0 0:02:36 0:02:27 0:00:09 834k 94 134M 94 127M 0 0 878k 0 0:02:37 0:02:28 0:00:09 864k 95 134M 95 128M 0 0 880k 0 0:02:36 0:02:29 0:00:07 886k 96 134M 96 130M 0 0 884k 0 0:02:36 0:02:30 0:00:06 880k 96 134M 96 130M 0 0 881k 0 0:02:36 0:02:31 0:00:05 831k 97 134M 97 132M 0 0 885k 0 0:02:36 0:02:32 0:00:04 1036k 98 134M 98 132M 0 0 881k 0 0:02:36 0:02:33 0:00:03 952k 98 134M 98 132M 0 0 878k 0 0:02:37 0:02:34 0:00:03 825k 99 134M 99 133M 0 0 878k 0 0:02:37 0:02:35 0:00:02 687k 99 134M 99 134M 0 0 880k 0 0:02:36 0:02:36 --:--:-- 832k 100 134M 100 134M 0 0 880k 0 0:02:36 0:02:36 --:--:-- 711k tar xzvf ${SPARK}-bin-${HADOOP}.tgz + tar xzvf spark-2.4.3-bin-hadoop2.7.tgz spark-2.4.3-bin-without-hadoop-scala-2.12/ spark-2.4.3-bin-without-hadoop-scala-2.12/python/ spark-2.4.3-bin-without-hadoop-scala-2.12/python/setup.cfg spark-2.4.3-bin-without-hadoop-scala-2.12/python/pyspark/ spark-2.4.3-bin-without-hadoop-scala-2.12/python/pyspark/resultiterable.py spark-2.4.3-bin-without-hadoop-scala-2.12/python/pyspark/heapq3.py spark-2.4.3-bin-without-hadoop-scala-2.12/python/pyspark/join.py spark-2.4.3-bin-without-hadoop-scala-2.12/python/pyspark/version.py spark-2.4.3-bin-without-hadoop-scala-2.12/python/pyspark/rdd.py spark-2.4.3-bin-without-hadoop-scala-2.12/python/pyspark/java_gateway.py spark-2.4.3-bin-without-hadoop-scala-2.12/python/pyspark/find_spark_home.py spark-2.4.3-bin-without-hadoop-scala-2.12/python/pyspark/_globals.py spark-2.4.3-bin-without-hadoop-scala-2.12/python/pyspark/worker.py spark-2.4.3-bin-without-hadoop-scala-2.12/python/pyspark/accumulators.py spark-2.4.3-bin-without-hadoop-scala-2.12/python/pyspark/mllib/ spark-2.4.3-bin-without-hadoop-scala-2.12/python/pyspark/mllib/feature.py spark-2.4.3-bin-without-hadoop-scala-2.12/python/pyspark/mllib/random.py spark-2.4.3-bin-without-hadoop-scala-2.12/python/pyspark/mllib/recommendation.py spark-2.4.3-bin-without-hadoop-scala-2.12/python/pyspark/mllib/fpm.py spark-2.4.3-bin-without-hadoop-scala-2.12/python/pyspark/mllib/classification.py spark-2.4.3-bin-without-hadoop-scala-2.12/python/pyspark/mllib/stat/ spark-2.4.3-bin-without-hadoop-scala-2.12/python/pyspark/mllib/stat/KernelDensity.py spark-2.4.3-bin-without-hadoop-scala-2.12/python/pyspark/mllib/stat/distribution.py spark-2.4.3-bin-without-hadoop-scala-2.12/python/pyspark/mllib/stat/test.py spark-2.4.3-bin-without-hadoop-scala-2.12/python/pyspark/mllib/stat/_statistics.py spark-2.4.3-bin-without-hadoop-scala-2.12/python/pyspark/mllib/stat/__init__.py spark-2.4.3-bin-without-hadoop-scala-2.12/python/pyspark/mllib/util.py spark-2.4.3-bin-without-hadoop-scala-2.12/python/pyspark/mllib/regression.py spark-2.4.3-bin-without-hadoop-scala-2.12/python/pyspark/mllib/clustering.py spark-2.4.3-bin-without-hadoop-scala-2.12/python/pyspark/mllib/linalg/ spark-2.4.3-bin-without-hadoop-scala-2.12/python/pyspark/mllib/linalg/distributed.py spark-2.4.3-bin-without-hadoop-scala-2.12/python/pyspark/mllib/linalg/__init__.py spark-2.4.3-bin-without-hadoop-scala-2.12/python/pyspark/mllib/tree.py spark-2.4.3-bin-without-hadoop-scala-2.12/python/pyspark/mllib/__init__.py spark-2.4.3-bin-without-hadoop-scala-2.12/python/pyspark/mllib/evaluation.py spark-2.4.3-bin-without-hadoop-scala-2.12/python/pyspark/mllib/common.py spark-2.4.3-bin-without-hadoop-scala-2.12/python/pyspark/mllib/tests.py spark-2.4.3-bin-without-hadoop-scala-2.12/python/pyspark/util.py spark-2.4.3-bin-without-hadoop-scala-2.12/python/pyspark/test_broadcast.py spark-2.4.3-bin-without-hadoop-scala-2.12/python/pyspark/shell.py spark-2.4.3-bin-without-hadoop-scala-2.12/python/pyspark/ml/ spark-2.4.3-bin-without-hadoop-scala-2.12/python/pyspark/ml/feature.py spark-2.4.3-bin-without-hadoop-scala-2.12/python/pyspark/ml/recommendation.py spark-2.4.3-bin-without-hadoop-scala-2.12/python/pyspark/ml/fpm.py spark-2.4.3-bin-without-hadoop-scala-2.12/python/pyspark/ml/classification.py spark-2.4.3-bin-without-hadoop-scala-2.12/python/pyspark/ml/stat.py spark-2.4.3-bin-without-hadoop-scala-2.12/python/pyspark/ml/util.py spark-2.4.3-bin-without-hadoop-scala-2.12/python/pyspark/ml/tuning.py spark-2.4.3-bin-without-hadoop-scala-2.12/python/pyspark/ml/regression.py spark-2.4.3-bin-without-hadoop-scala-2.12/python/pyspark/ml/base.py spark-2.4.3-bin-without-hadoop-scala-2.12/python/pyspark/ml/clustering.py spark-2.4.3-bin-without-hadoop-scala-2.12/python/pyspark/ml/wrapper.py spark-2.4.3-bin-without-hadoop-scala-2.12/python/pyspark/ml/pipeline.py spark-2.4.3-bin-without-hadoop-scala-2.12/python/pyspark/ml/linalg/ spark-2.4.3-bin-without-hadoop-scala-2.12/python/pyspark/ml/linalg/__init__.py spark-2.4.3-bin-without-hadoop-scala-2.12/python/pyspark/ml/param/ spark-2.4.3-bin-without-hadoop-scala-2.12/python/pyspark/ml/param/_shared_params_code_gen.py spark-2.4.3-bin-without-hadoop-scala-2.12/python/pyspark/ml/param/shared.py spark-2.4.3-bin-without-hadoop-scala-2.12/python/pyspark/ml/param/__init__.py spark-2.4.3-bin-without-hadoop-scala-2.12/python/pyspark/ml/__init__.py spark-2.4.3-bin-without-hadoop-scala-2.12/python/pyspark/ml/evaluation.py spark-2.4.3-bin-without-hadoop-scala-2.12/python/pyspark/ml/common.py spark-2.4.3-bin-without-hadoop-scala-2.12/python/pyspark/ml/tests.py spark-2.4.3-bin-without-hadoop-scala-2.12/python/pyspark/ml/image.py spark-2.4.3-bin-without-hadoop-scala-2.12/python/pyspark/test_serializers.py spark-2.4.3-bin-without-hadoop-scala-2.12/python/pyspark/cloudpickle.py spark-2.4.3-bin-without-hadoop-scala-2.12/python/pyspark/serializers.py spark-2.4.3-bin-without-hadoop-scala-2.12/python/pyspark/daemon.py spark-2.4.3-bin-without-hadoop-scala-2.12/python/pyspark/files.py spark-2.4.3-bin-without-hadoop-scala-2.12/python/pyspark/rddsampler.py spark-2.4.3-bin-without-hadoop-scala-2.12/python/pyspark/statcounter.py spark-2.4.3-bin-without-hadoop-scala-2.12/python/pyspark/streaming/ spark-2.4.3-bin-without-hadoop-scala-2.12/python/pyspark/streaming/kafka.py spark-2.4.3-bin-without-hadoop-scala-2.12/python/pyspark/streaming/util.py spark-2.4.3-bin-without-hadoop-scala-2.12/python/pyspark/streaming/kinesis.py spark-2.4.3-bin-without-hadoop-scala-2.12/python/pyspark/streaming/flume.py spark-2.4.3-bin-without-hadoop-scala-2.12/python/pyspark/streaming/__init__.py spark-2.4.3-bin-without-hadoop-scala-2.12/python/pyspark/streaming/context.py spark-2.4.3-bin-without-hadoop-scala-2.12/python/pyspark/streaming/tests.py spark-2.4.3-bin-without-hadoop-scala-2.12/python/pyspark/streaming/dstream.py spark-2.4.3-bin-without-hadoop-scala-2.12/python/pyspark/streaming/listener.py spark-2.4.3-bin-without-hadoop-scala-2.12/python/pyspark/taskcontext.py spark-2.4.3-bin-without-hadoop-scala-2.12/python/pyspark/__init__.py spark-2.4.3-bin-without-hadoop-scala-2.12/python/pyspark/storagelevel.py spark-2.4.3-bin-without-hadoop-scala-2.12/python/pyspark/broadcast.py spark-2.4.3-bin-without-hadoop-scala-2.12/python/pyspark/profiler.py spark-2.4.3-bin-without-hadoop-scala-2.12/python/pyspark/traceback_utils.py spark-2.4.3-bin-without-hadoop-scala-2.12/python/pyspark/context.py spark-2.4.3-bin-without-hadoop-scala-2.12/python/pyspark/status.py spark-2.4.3-bin-without-hadoop-scala-2.12/python/pyspark/sql/ spark-2.4.3-bin-without-hadoop-scala-2.12/python/pyspark/sql/streaming.py spark-2.4.3-bin-without-hadoop-scala-2.12/python/pyspark/sql/readwriter.py spark-2.4.3-bin-without-hadoop-scala-2.12/python/pyspark/sql/catalog.py spark-2.4.3-bin-without-hadoop-scala-2.12/python/pyspark/sql/session.py spark-2.4.3-bin-without-hadoop-scala-2.12/python/pyspark/sql/column.py spark-2.4.3-bin-without-hadoop-scala-2.12/python/pyspark/sql/functions.py spark-2.4.3-bin-without-hadoop-scala-2.12/python/pyspark/sql/dataframe.py spark-2.4.3-bin-without-hadoop-scala-2.12/python/pyspark/sql/window.py spark-2.4.3-bin-without-hadoop-scala-2.12/python/pyspark/sql/udf.py spark-2.4.3-bin-without-hadoop-scala-2.12/python/pyspark/sql/__init__.py spark-2.4.3-bin-without-hadoop-scala-2.12/python/pyspark/sql/utils.py spark-2.4.3-bin-without-hadoop-scala-2.12/python/pyspark/sql/group.py spark-2.4.3-bin-without-hadoop-scala-2.12/python/pyspark/sql/context.py spark-2.4.3-bin-without-hadoop-scala-2.12/python/pyspark/sql/tests.py spark-2.4.3-bin-without-hadoop-scala-2.12/python/pyspark/sql/conf.py spark-2.4.3-bin-without-hadoop-scala-2.12/python/pyspark/sql/types.py spark-2.4.3-bin-without-hadoop-scala-2.12/python/pyspark/tests.py spark-2.4.3-bin-without-hadoop-scala-2.12/python/pyspark/conf.py spark-2.4.3-bin-without-hadoop-scala-2.12/python/pyspark/shuffle.py spark-2.4.3-bin-without-hadoop-scala-2.12/python/.gitignore spark-2.4.3-bin-without-hadoop-scala-2.12/python/docs/ spark-2.4.3-bin-without-hadoop-scala-2.12/python/docs/epytext.py spark-2.4.3-bin-without-hadoop-scala-2.12/python/docs/make2.bat spark-2.4.3-bin-without-hadoop-scala-2.12/python/docs/pyspark.sql.rst spark-2.4.3-bin-without-hadoop-scala-2.12/python/docs/make.bat spark-2.4.3-bin-without-hadoop-scala-2.12/python/docs/index.rst spark-2.4.3-bin-without-hadoop-scala-2.12/python/docs/_templates/ spark-2.4.3-bin-without-hadoop-scala-2.12/python/docs/_templates/layout.html spark-2.4.3-bin-without-hadoop-scala-2.12/python/docs/_static/ spark-2.4.3-bin-without-hadoop-scala-2.12/python/docs/_static/pyspark.js spark-2.4.3-bin-without-hadoop-scala-2.12/python/docs/_static/pyspark.css spark-2.4.3-bin-without-hadoop-scala-2.12/python/docs/pyspark.ml.rst spark-2.4.3-bin-without-hadoop-scala-2.12/python/docs/pyspark.streaming.rst spark-2.4.3-bin-without-hadoop-scala-2.12/python/docs/conf.py spark-2.4.3-bin-without-hadoop-scala-2.12/python/docs/pyspark.mllib.rst spark-2.4.3-bin-without-hadoop-scala-2.12/python/docs/pyspark.rst spark-2.4.3-bin-without-hadoop-scala-2.12/python/docs/Makefile spark-2.4.3-bin-without-hadoop-scala-2.12/python/test_coverage/ spark-2.4.3-bin-without-hadoop-scala-2.12/python/test_coverage/conf/ spark-2.4.3-bin-without-hadoop-scala-2.12/python/test_coverage/conf/spark-defaults.conf spark-2.4.3-bin-without-hadoop-scala-2.12/python/test_coverage/sitecustomize.py spark-2.4.3-bin-without-hadoop-scala-2.12/python/test_coverage/coverage_daemon.py spark-2.4.3-bin-without-hadoop-scala-2.12/python/run-tests-with-coverage spark-2.4.3-bin-without-hadoop-scala-2.12/python/MANIFEST.in spark-2.4.3-bin-without-hadoop-scala-2.12/python/test_support/ spark-2.4.3-bin-without-hadoop-scala-2.12/python/test_support/userlibrary.py spark-2.4.3-bin-without-hadoop-scala-2.12/python/test_support/userlib-0.1.zip spark-2.4.3-bin-without-hadoop-scala-2.12/python/test_support/SimpleHTTPServer.py spark-2.4.3-bin-without-hadoop-scala-2.12/python/test_support/hello/ spark-2.4.3-bin-without-hadoop-scala-2.12/python/test_support/hello/sub_hello/ spark-2.4.3-bin-without-hadoop-scala-2.12/python/test_support/hello/sub_hello/sub_hello.txt spark-2.4.3-bin-without-hadoop-scala-2.12/python/test_support/hello/hello.txt spark-2.4.3-bin-without-hadoop-scala-2.12/python/test_support/sql/ spark-2.4.3-bin-without-hadoop-scala-2.12/python/test_support/sql/people_array.json spark-2.4.3-bin-without-hadoop-scala-2.12/python/test_support/sql/text-test.txt spark-2.4.3-bin-without-hadoop-scala-2.12/python/test_support/sql/ages_newlines.csv spark-2.4.3-bin-without-hadoop-scala-2.12/python/test_support/sql/people.json spark-2.4.3-bin-without-hadoop-scala-2.12/python/test_support/sql/parquet_partitioned/ spark-2.4.3-bin-without-hadoop-scala-2.12/python/test_support/sql/parquet_partitioned/year=2014/ spark-2.4.3-bin-without-hadoop-scala-2.12/python/test_support/sql/parquet_partitioned/year=2014/month=9/ spark-2.4.3-bin-without-hadoop-scala-2.12/python/test_support/sql/parquet_partitioned/year=2014/month=9/day=1/ spark-2.4.3-bin-without-hadoop-scala-2.12/python/test_support/sql/parquet_partitioned/year=2014/month=9/day=1/part-r-00008.gz.parquet spark-2.4.3-bin-without-hadoop-scala-2.12/python/test_support/sql/parquet_partitioned/year=2014/month=9/day=1/.part-r-00008.gz.parquet.crc spark-2.4.3-bin-without-hadoop-scala-2.12/python/test_support/sql/parquet_partitioned/year=2015/ spark-2.4.3-bin-without-hadoop-scala-2.12/python/test_support/sql/parquet_partitioned/year=2015/month=10/ spark-2.4.3-bin-without-hadoop-scala-2.12/python/test_support/sql/parquet_partitioned/year=2015/month=10/day=26/ spark-2.4.3-bin-without-hadoop-scala-2.12/python/test_support/sql/parquet_partitioned/year=2015/month=10/day=26/part-r-00005.gz.parquet spark-2.4.3-bin-without-hadoop-scala-2.12/python/test_support/sql/parquet_partitioned/year=2015/month=10/day=26/.part-r-00005.gz.parquet.crc spark-2.4.3-bin-without-hadoop-scala-2.12/python/test_support/sql/parquet_partitioned/year=2015/month=10/day=25/ spark-2.4.3-bin-without-hadoop-scala-2.12/python/test_support/sql/parquet_partitioned/year=2015/month=10/day=25/.part-r-00002.gz.parquet.crc spark-2.4.3-bin-without-hadoop-scala-2.12/python/test_support/sql/parquet_partitioned/year=2015/month=10/day=25/part-r-00002.gz.parquet spark-2.4.3-bin-without-hadoop-scala-2.12/python/test_support/sql/parquet_partitioned/year=2015/month=10/day=25/part-r-00004.gz.parquet spark-2.4.3-bin-without-hadoop-scala-2.12/python/test_support/sql/parquet_partitioned/year=2015/month=10/day=25/.part-r-00004.gz.parquet.crc spark-2.4.3-bin-without-hadoop-scala-2.12/python/test_support/sql/parquet_partitioned/year=2015/month=9/ spark-2.4.3-bin-without-hadoop-scala-2.12/python/test_support/sql/parquet_partitioned/year=2015/month=9/day=1/ spark-2.4.3-bin-without-hadoop-scala-2.12/python/test_support/sql/parquet_partitioned/year=2015/month=9/day=1/.part-r-00007.gz.parquet.crc spark-2.4.3-bin-without-hadoop-scala-2.12/python/test_support/sql/parquet_partitioned/year=2015/month=9/day=1/part-r-00007.gz.parquet spark-2.4.3-bin-without-hadoop-scala-2.12/python/test_support/sql/parquet_partitioned/_common_metadata spark-2.4.3-bin-without-hadoop-scala-2.12/python/test_support/sql/parquet_partitioned/_metadata spark-2.4.3-bin-without-hadoop-scala-2.12/python/test_support/sql/parquet_partitioned/_SUCCESS spark-2.4.3-bin-without-hadoop-scala-2.12/python/test_support/sql/streaming/ spark-2.4.3-bin-without-hadoop-scala-2.12/python/test_support/sql/streaming/text-test.txt spark-2.4.3-bin-without-hadoop-scala-2.12/python/test_support/sql/ages.csv spark-2.4.3-bin-without-hadoop-scala-2.12/python/test_support/sql/people1.json spark-2.4.3-bin-without-hadoop-scala-2.12/python/test_support/sql/orc_partitioned/ spark-2.4.3-bin-without-hadoop-scala-2.12/python/test_support/sql/orc_partitioned/b=0/ spark-2.4.3-bin-without-hadoop-scala-2.12/python/test_support/sql/orc_partitioned/b=0/c=0/ spark-2.4.3-bin-without-hadoop-scala-2.12/python/test_support/sql/orc_partitioned/b=0/c=0/part-r-00000-829af031-b970-49d6-ad39-30460a0be2c8.orc spark-2.4.3-bin-without-hadoop-scala-2.12/python/test_support/sql/orc_partitioned/b=0/c=0/.part-r-00000-829af031-b970-49d6-ad39-30460a0be2c8.orc.crc spark-2.4.3-bin-without-hadoop-scala-2.12/python/test_support/sql/orc_partitioned/_SUCCESS spark-2.4.3-bin-without-hadoop-scala-2.12/python/test_support/sql/orc_partitioned/b=1/ spark-2.4.3-bin-without-hadoop-scala-2.12/python/test_support/sql/orc_partitioned/b=1/c=1/ spark-2.4.3-bin-without-hadoop-scala-2.12/python/test_support/sql/orc_partitioned/b=1/c=1/part-r-00000-829af031-b970-49d6-ad39-30460a0be2c8.orc spark-2.4.3-bin-without-hadoop-scala-2.12/python/test_support/sql/orc_partitioned/b=1/c=1/.part-r-00000-829af031-b970-49d6-ad39-30460a0be2c8.orc.crc spark-2.4.3-bin-without-hadoop-scala-2.12/python/test_support/sql/people_array_utf16le.json spark-2.4.3-bin-without-hadoop-scala-2.12/python/run-tests.py spark-2.4.3-bin-without-hadoop-scala-2.12/python/run-tests spark-2.4.3-bin-without-hadoop-scala-2.12/python/.coveragerc spark-2.4.3-bin-without-hadoop-scala-2.12/python/lib/ spark-2.4.3-bin-without-hadoop-scala-2.12/python/lib/pyspark.zip spark-2.4.3-bin-without-hadoop-scala-2.12/python/lib/PY4J_LICENSE.txt spark-2.4.3-bin-without-hadoop-scala-2.12/python/lib/py4j-0.10.7-src.zip spark-2.4.3-bin-without-hadoop-scala-2.12/python/setup.py spark-2.4.3-bin-without-hadoop-scala-2.12/python/README.md spark-2.4.3-bin-without-hadoop-scala-2.12/python/pylintrc spark-2.4.3-bin-without-hadoop-scala-2.12/conf/ spark-2.4.3-bin-without-hadoop-scala-2.12/conf/fairscheduler.xml.template spark-2.4.3-bin-without-hadoop-scala-2.12/conf/spark-defaults.conf.template spark-2.4.3-bin-without-hadoop-scala-2.12/conf/docker.properties.template spark-2.4.3-bin-without-hadoop-scala-2.12/conf/log4j.properties.template spark-2.4.3-bin-without-hadoop-scala-2.12/conf/metrics.properties.template spark-2.4.3-bin-without-hadoop-scala-2.12/conf/slaves.template spark-2.4.3-bin-without-hadoop-scala-2.12/conf/spark-env.sh.template spark-2.4.3-bin-without-hadoop-scala-2.12/licenses/ spark-2.4.3-bin-without-hadoop-scala-2.12/licenses/LICENSE-heapq.txt spark-2.4.3-bin-without-hadoop-scala-2.12/licenses/LICENSE-paranamer.txt spark-2.4.3-bin-without-hadoop-scala-2.12/licenses/LICENSE-graphlib-dot.txt spark-2.4.3-bin-without-hadoop-scala-2.12/licenses/LICENSE-minlog.txt spark-2.4.3-bin-without-hadoop-scala-2.12/licenses/LICENSE-slf4j.txt spark-2.4.3-bin-without-hadoop-scala-2.12/licenses/LICENSE-jquery.txt spark-2.4.3-bin-without-hadoop-scala-2.12/licenses/LICENSE-scopt.txt spark-2.4.3-bin-without-hadoop-scala-2.12/licenses/LICENSE-vis.txt spark-2.4.3-bin-without-hadoop-scala-2.12/licenses/LICENSE-sbt-launch-lib.txt spark-2.4.3-bin-without-hadoop-scala-2.12/licenses/LICENSE-spire.txt spark-2.4.3-bin-without-hadoop-scala-2.12/licenses/LICENSE-matchMedia-polyfill.txt spark-2.4.3-bin-without-hadoop-scala-2.12/licenses/LICENSE-kryo.txt spark-2.4.3-bin-without-hadoop-scala-2.12/licenses/LICENSE-mustache.txt spark-2.4.3-bin-without-hadoop-scala-2.12/licenses/LICENSE-arpack.txt spark-2.4.3-bin-without-hadoop-scala-2.12/licenses/LICENSE-scala.txt spark-2.4.3-bin-without-hadoop-scala-2.12/licenses/LICENSE-javassist.html spark-2.4.3-bin-without-hadoop-scala-2.12/licenses/LICENSE-json-formatter.txt spark-2.4.3-bin-without-hadoop-scala-2.12/licenses/LICENSE-jodd.txt spark-2.4.3-bin-without-hadoop-scala-2.12/licenses/LICENSE-automaton.txt spark-2.4.3-bin-without-hadoop-scala-2.12/licenses/LICENSE-janino.txt spark-2.4.3-bin-without-hadoop-scala-2.12/licenses/LICENSE-dagre-d3.txt spark-2.4.3-bin-without-hadoop-scala-2.12/licenses/LICENSE-sorttable.js.txt spark-2.4.3-bin-without-hadoop-scala-2.12/licenses/LICENSE-py4j.txt spark-2.4.3-bin-without-hadoop-scala-2.12/licenses/LICENSE-d3.min.js.txt spark-2.4.3-bin-without-hadoop-scala-2.12/licenses/LICENSE-respond.txt spark-2.4.3-bin-without-hadoop-scala-2.12/licenses/LICENSE-CC0.txt spark-2.4.3-bin-without-hadoop-scala-2.12/licenses/LICENSE-zstd.txt spark-2.4.3-bin-without-hadoop-scala-2.12/licenses/LICENSE-cloudpickle.txt spark-2.4.3-bin-without-hadoop-scala-2.12/licenses/LICENSE-pmml-model.txt spark-2.4.3-bin-without-hadoop-scala-2.12/licenses/LICENSE-pyrolite.txt spark-2.4.3-bin-without-hadoop-scala-2.12/licenses/LICENSE-netlib.txt spark-2.4.3-bin-without-hadoop-scala-2.12/licenses/LICENSE-AnchorJS.txt spark-2.4.3-bin-without-hadoop-scala-2.12/licenses/LICENSE-modernizr.txt spark-2.4.3-bin-without-hadoop-scala-2.12/licenses/LICENSE-machinist.txt spark-2.4.3-bin-without-hadoop-scala-2.12/licenses/LICENSE-javolution.txt spark-2.4.3-bin-without-hadoop-scala-2.12/licenses/LICENSE-xmlenc.txt spark-2.4.3-bin-without-hadoop-scala-2.12/licenses/LICENSE-join.txt spark-2.4.3-bin-without-hadoop-scala-2.12/licenses/LICENSE-jline.txt spark-2.4.3-bin-without-hadoop-scala-2.12/licenses/LICENSE-antlr.txt spark-2.4.3-bin-without-hadoop-scala-2.12/licenses/LICENSE-jtransforms.html spark-2.4.3-bin-without-hadoop-scala-2.12/licenses/LICENSE-leveldbjni.txt spark-2.4.3-bin-without-hadoop-scala-2.12/licenses/LICENSE-protobuf.txt spark-2.4.3-bin-without-hadoop-scala-2.12/licenses/LICENSE-bootstrap.txt spark-2.4.3-bin-without-hadoop-scala-2.12/licenses/LICENSE-zstd-jni.txt spark-2.4.3-bin-without-hadoop-scala-2.12/licenses/LICENSE-datatables.txt spark-2.4.3-bin-without-hadoop-scala-2.12/licenses/LICENSE-f2j.txt spark-2.4.3-bin-without-hadoop-scala-2.12/licenses/LICENSE-reflectasm.txt spark-2.4.3-bin-without-hadoop-scala-2.12/sbin/ spark-2.4.3-bin-without-hadoop-scala-2.12/sbin/start-slave.sh spark-2.4.3-bin-without-hadoop-scala-2.12/sbin/stop-history-server.sh spark-2.4.3-bin-without-hadoop-scala-2.12/sbin/stop-slave.sh spark-2.4.3-bin-without-hadoop-scala-2.12/sbin/stop-mesos-dispatcher.sh spark-2.4.3-bin-without-hadoop-scala-2.12/sbin/start-all.sh spark-2.4.3-bin-without-hadoop-scala-2.12/sbin/spark-daemon.sh spark-2.4.3-bin-without-hadoop-scala-2.12/sbin/start-master.sh spark-2.4.3-bin-without-hadoop-scala-2.12/sbin/spark-daemons.sh spark-2.4.3-bin-without-hadoop-scala-2.12/sbin/spark-config.sh spark-2.4.3-bin-without-hadoop-scala-2.12/sbin/start-slaves.sh spark-2.4.3-bin-without-hadoop-scala-2.12/sbin/start-mesos-shuffle-service.sh spark-2.4.3-bin-without-hadoop-scala-2.12/sbin/start-history-server.sh spark-2.4.3-bin-without-hadoop-scala-2.12/sbin/start-shuffle-service.sh spark-2.4.3-bin-without-hadoop-scala-2.12/sbin/slaves.sh spark-2.4.3-bin-without-hadoop-scala-2.12/sbin/stop-slaves.sh spark-2.4.3-bin-without-hadoop-scala-2.12/sbin/stop-thriftserver.sh spark-2.4.3-bin-without-hadoop-scala-2.12/sbin/stop-master.sh spark-2.4.3-bin-without-hadoop-scala-2.12/sbin/stop-shuffle-service.sh spark-2.4.3-bin-without-hadoop-scala-2.12/sbin/start-mesos-dispatcher.sh spark-2.4.3-bin-without-hadoop-scala-2.12/sbin/stop-mesos-shuffle-service.sh spark-2.4.3-bin-without-hadoop-scala-2.12/sbin/start-thriftserver.sh spark-2.4.3-bin-without-hadoop-scala-2.12/sbin/stop-all.sh spark-2.4.3-bin-without-hadoop-scala-2.12/kubernetes/ spark-2.4.3-bin-without-hadoop-scala-2.12/kubernetes/tests/ spark-2.4.3-bin-without-hadoop-scala-2.12/kubernetes/tests/pyfiles.py spark-2.4.3-bin-without-hadoop-scala-2.12/kubernetes/tests/worker_memory_check.py spark-2.4.3-bin-without-hadoop-scala-2.12/kubernetes/tests/py_container_checks.py spark-2.4.3-bin-without-hadoop-scala-2.12/kubernetes/dockerfiles/ spark-2.4.3-bin-without-hadoop-scala-2.12/kubernetes/dockerfiles/spark/ spark-2.4.3-bin-without-hadoop-scala-2.12/kubernetes/dockerfiles/spark/Dockerfile spark-2.4.3-bin-without-hadoop-scala-2.12/kubernetes/dockerfiles/spark/bindings/ spark-2.4.3-bin-without-hadoop-scala-2.12/kubernetes/dockerfiles/spark/bindings/python/ spark-2.4.3-bin-without-hadoop-scala-2.12/kubernetes/dockerfiles/spark/bindings/python/Dockerfile spark-2.4.3-bin-without-hadoop-scala-2.12/kubernetes/dockerfiles/spark/bindings/R/ spark-2.4.3-bin-without-hadoop-scala-2.12/kubernetes/dockerfiles/spark/bindings/R/Dockerfile spark-2.4.3-bin-without-hadoop-scala-2.12/kubernetes/dockerfiles/spark/entrypoint.sh spark-2.4.3-bin-without-hadoop-scala-2.12/jars/ spark-2.4.3-bin-without-hadoop-scala-2.12/jars/spark-network-shuffle_2.12-2.4.3.jar spark-2.4.3-bin-without-hadoop-scala-2.12/jars/commons-lang3-3.5.jar spark-2.4.3-bin-without-hadoop-scala-2.12/jars/spire-macros_2.12-0.13.0.jar spark-2.4.3-bin-without-hadoop-scala-2.12/jars/arrow-format-0.10.0.jar spark-2.4.3-bin-without-hadoop-scala-2.12/jars/scala-xml_2.12-1.0.5.jar spark-2.4.3-bin-without-hadoop-scala-2.12/jars/jersey-container-servlet-2.22.2.jar spark-2.4.3-bin-without-hadoop-scala-2.12/jars/pyrolite-4.13.jar spark-2.4.3-bin-without-hadoop-scala-2.12/jars/hppc-0.7.2.jar spark-2.4.3-bin-without-hadoop-scala-2.12/jars/chill_2.12-0.9.3.jar spark-2.4.3-bin-without-hadoop-scala-2.12/jars/metrics-jvm-3.1.5.jar spark-2.4.3-bin-without-hadoop-scala-2.12/jars/jersey-guava-2.22.2.jar spark-2.4.3-bin-without-hadoop-scala-2.12/jars/breeze-macros_2.12-0.13.2.jar spark-2.4.3-bin-without-hadoop-scala-2.12/jars/commons-net-3.1.jar spark-2.4.3-bin-without-hadoop-scala-2.12/jars/validation-api-1.1.0.Final.jar spark-2.4.3-bin-without-hadoop-scala-2.12/jars/spark-yarn_2.12-2.4.3.jar spark-2.4.3-bin-without-hadoop-scala-2.12/jars/orc-mapreduce-1.5.5-nohive.jar spark-2.4.3-bin-without-hadoop-scala-2.12/jars/parquet-encoding-1.10.1.jar spark-2.4.3-bin-without-hadoop-scala-2.12/jars/jersey-container-servlet-core-2.22.2.jar spark-2.4.3-bin-without-hadoop-scala-2.12/jars/zjsonpatch-0.3.0.jar spark-2.4.3-bin-without-hadoop-scala-2.12/jars/spark-kubernetes_2.12-2.4.3.jar spark-2.4.3-bin-without-hadoop-scala-2.12/jars/jersey-media-jaxb-2.22.2.jar spark-2.4.3-bin-without-hadoop-scala-2.12/jars/avro-mapred-1.8.2-hadoop2.jar spark-2.4.3-bin-without-hadoop-scala-2.12/jars/antlr4-runtime-4.7.jar spark-2.4.3-bin-without-hadoop-scala-2.12/jars/jackson-module-jaxb-annotations-2.6.7.jar spark-2.4.3-bin-without-hadoop-scala-2.12/jars/json4s-scalap_2.12-3.5.3.jar spark-2.4.3-bin-without-hadoop-scala-2.12/jars/okhttp-3.8.1.jar spark-2.4.3-bin-without-hadoop-scala-2.12/jars/leveldbjni-all-1.8.jar spark-2.4.3-bin-without-hadoop-scala-2.12/jars/spark-sketch_2.12-2.4.3.jar spark-2.4.3-bin-without-hadoop-scala-2.12/jars/scala-library-2.12.8.jar spark-2.4.3-bin-without-hadoop-scala-2.12/jars/jackson-module-scala_2.12-2.6.7.1.jar spark-2.4.3-bin-without-hadoop-scala-2.12/jars/jackson-annotations-2.6.7.jar spark-2.4.3-bin-without-hadoop-scala-2.12/jars/jackson-module-paranamer-2.7.9.jar spark-2.4.3-bin-without-hadoop-scala-2.12/jars/jersey-server-2.22.2.jar spark-2.4.3-bin-without-hadoop-scala-2.12/jars/arrow-memory-0.10.0.jar spark-2.4.3-bin-without-hadoop-scala-2.12/jars/hk2-utils-2.4.0-b34.jar spark-2.4.3-bin-without-hadoop-scala-2.12/jars/joda-time-2.9.3.jar spark-2.4.3-bin-without-hadoop-scala-2.12/jars/commons-crypto-1.0.0.jar spark-2.4.3-bin-without-hadoop-scala-2.12/jars/logging-interceptor-3.12.0.jar spark-2.4.3-bin-without-hadoop-scala-2.12/jars/parquet-common-1.10.1.jar spark-2.4.3-bin-without-hadoop-scala-2.12/jars/json4s-jackson_2.12-3.5.3.jar spark-2.4.3-bin-without-hadoop-scala-2.12/jars/hk2-locator-2.4.0-