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[WARNING] Entry: adam-distribution-spark3_2.12-0.34.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/SequencesToCoverageDatasetConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark3_2.12-0.34.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/FragmentsToReadsDatasetConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark3_2.12-0.34.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/GenotypesToCoverageDatasetConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark3_2.12-0.34.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/SlicesToSequencesConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark3_2.12-0.34.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/CoverageToGenotypesConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark3_2.12-0.34.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/JavaADAMContext$.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark3_2.12-0.34.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/ReadsToVariantsDatasetConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark3_2.12-0.34.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/ReadsToFragmentsConverter.html longer than 100 characters.
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[WARNING] Entry: adam-distribution-spark3_2.12-0.34.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/SequencesToSlicesConverter.html longer than 100 characters.
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[WARNING] Entry: adam-distribution-spark3_2.12-0.34.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/FragmentsToVariantsDatasetConverter.html longer than 100 characters.
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[WARNING] Entry: adam-distribution-spark3_2.12-0.34.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/ToVariantDatasetConversion.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark3_2.12-0.34.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/FragmentsToCoverageConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark3_2.12-0.34.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/FeaturesToSequencesDatasetConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark3_2.12-0.34.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/ReadsToVariantContextsConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark3_2.12-0.34.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/AlignmentsToGenotypesDatasetConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark3_2.12-0.34.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/FragmentsToFeaturesDatasetConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark3_2.12-0.34.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/CoverageToFragmentsConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark3_2.12-0.34.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/ToSliceDatasetConversion.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark3_2.12-0.34.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/cli/CountReadKmersArgs.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark3_2.12-0.34.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/cli/TransformVariantsArgs.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark3_2.12-0.34.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/cli/TransformSequences$.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark3_2.12-0.34.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/cli/TransformGenotypes.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark3_2.12-0.34.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/cli/TransformGenotypes$.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark3_2.12-0.34.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/cli/TransformAlignments$.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark3_2.12-0.34.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/cli/CountSliceKmersArgs.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark3_2.12-0.34.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/cli/TransformFeaturesArgs.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark3_2.12-0.34.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/cli/TransformFeatures$.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark3_2.12-0.34.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/cli/TransformAlignmentsArgs.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark3_2.12-0.34.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/cli/TransformGenotypesArgs.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark3_2.12-0.34.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/cli/TransformFragmentsArgs.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark3_2.12-0.34.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/cli/TransformSequencesArgs.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark3_2.12-0.34.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/cli/CountSliceKmers.html longer than 100 characters.
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[WARNING] Entry: adam-distribution-spark3_2.12-0.34.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/cli/TransformSlicesArgs.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark3_2.12-0.34.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/cli/TransformFragments.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark3_2.12-0.34.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/cli/TransformSequences.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark3_2.12-0.34.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/cli/TransformFeatures.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark3_2.12-0.34.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/cli/TransformVariants.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark3_2.12-0.34.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/cli/TransformAlignments.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark3_2.12-0.34.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/cli/TransformFragments$.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark3_2.12-0.34.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/cli/MergeShardsArgs.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark3_2.12-0.34.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/cli/TransformVariants$.html longer than 100 characters.
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[WARNING] Entry: adam-distribution-spark3_2.12-0.34.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/cli/CountReadKmers$.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark3_2.12-0.34.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/cli/TransformSlices$.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark3_2.12-0.34.0-SNAPSHOT/repo/adam-assembly-spark3_2.12-0.34.0-SNAPSHOT-javadoc.jar longer than 100 characters.
[WARNING] Entry: adam-distribution-spark3_2.12-0.34.0-SNAPSHOT/repo/adam-assembly-spark3_2.12-0.34.0-SNAPSHOT-sources.jar longer than 100 characters.
[INFO] Building zip: /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-distribution/target/adam-distribution-spark3_2.12-0.34.0-SNAPSHOT-bin.zip
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary for ADAM_2.12 0.34.0-SNAPSHOT:
[INFO] 
[INFO] ADAM_2.12 .......................................... SUCCESS [  7.871 s]
[INFO] ADAM_2.12: Shader workaround ....................... SUCCESS [  7.136 s]
[INFO] ADAM_2.12: Avro-to-Dataset codegen utils ........... SUCCESS [  8.663 s]
[INFO] ADAM_2.12: Core .................................... SUCCESS [01:22 min]
[INFO] ADAM_2.12: APIs for Java, Python ................... SUCCESS [ 21.184 s]
[INFO] ADAM_2.12: CLI ..................................... SUCCESS [ 24.552 s]
[INFO] ADAM_2.12: Assembly ................................ SUCCESS [ 13.810 s]
[INFO] ADAM_2.12: Python APIs ............................. SUCCESS [01:31 min]
[INFO] ADAM_2.12: Distribution ............................ SUCCESS [ 41.482 s]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time:  04:58 min
[INFO] Finished at: 2021-02-20T18:35:05-08:00
[INFO] ------------------------------------------------------------------------
+ grep bdgenomics.adam
+ tar tzvf adam-distribution/target/adam-distribution-spark3_2.12-0.34.0-SNAPSHOT-bin.tar.gz
+ grep egg
drwxrwxr-x jenkins/jenkins        0 2021-02-20 18:33 adam-distribution-spark3_2.12-0.34.0-SNAPSHOT/r/bdgenomics.adam.egg-info/
-rw-r--r-- jenkins/jenkins 41136268 2021-02-20 18:33 adam-distribution-spark3_2.12-0.34.0-SNAPSHOT/repo/bdgenomics.adam-0.34.0a0-py3.6.egg
+ ./bin/pyadam
Using PYSPARK=/tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.2-bin-hadoop3.2/bin/pyspark
2021-02-20 18:35:08 WARN  Utils:69 - Your hostname, research-jenkins-worker-09 resolves to a loopback address: 127.0.1.1; using 192.168.10.31 instead (on interface enp4s0f0)
2021-02-20 18:35:08 WARN  Utils:69 - Set SPARK_LOCAL_IP if you need to bind to another address
2021-02-20 18:35:09 WARN  NativeCodeLoader:60 - Unable to load native-hadoop library for your platform... using builtin-java classes where applicable
Setting default log level to "WARN".
To adjust logging level use sc.setLogLevel(newLevel). For SparkR, use setLogLevel(newLevel).
2021-02-20 18:35:15 WARN  package:69 - Truncated the string representation of a plan since it was too large. This behavior can be adjusted by setting 'spark.sql.debug.maxToStringFields'.

[Stage 0:>                                                          (0 + 1) / 1]

                                                                                
+ source deactivate
#!/bin/bash

# Determine the directory containing this script
if [[ -n $BASH_VERSION ]]; then
    _SCRIPT_LOCATION=${BASH_SOURCE[0]}
    _SHELL="bash"
elif [[ -n $ZSH_VERSION ]]; then
    _SCRIPT_LOCATION=${funcstack[1]}
    _SHELL="zsh"
else
    echo "Only bash and zsh are supported"
    return 1
fi
++ [[ -n 4.3.48(1)-release ]]
++ _SCRIPT_LOCATION=/home/jenkins/anaconda2/envs/adam-build-fcd2223c-a4e5-4f5c-a966-121bc529034f/bin/deactivate
++ _SHELL=bash
_CONDA_DIR=$(dirname "$_SCRIPT_LOCATION")
dirname "$_SCRIPT_LOCATION"
+++ dirname /home/jenkins/anaconda2/envs/adam-build-fcd2223c-a4e5-4f5c-a966-121bc529034f/bin/deactivate
++ _CONDA_DIR=/home/jenkins/anaconda2/envs/adam-build-fcd2223c-a4e5-4f5c-a966-121bc529034f/bin

case "$(uname -s)" in
    CYGWIN*|MINGW*|MSYS*)
        EXT=".exe"
        export MSYS2_ENV_CONV_EXCL=CONDA_PATH
        ;;
    *)
        EXT=""
        ;;
esac
++ case "$(uname -s)" in
uname -s
+++ uname -s
++ EXT=

# shift over all args.  We don't accept any, so it's OK that we ignore them all here.
while [[ $# > 0 ]]
do
    key="$1"
    case $key in
        -h|--help)
            "$_CONDA_DIR/conda" ..deactivate $_SHELL$EXT -h
            if [[ -n $BASH_VERSION ]] && [[ "$(basename "$0" 2> /dev/null)" == "deactivate" ]]; then
                exit 0
            else
                return 0
            fi
            ;;
    esac
    shift # past argument or value
done
++ [[ 0 > 0 ]]

# Ensure that this script is sourced, not executed
# Note that if the script was executed, we're running inside bash!
# Also note that errors are ignored as `activate foo` doesn't generate a bad
# value for $0 which would cause errors.
if [[ -n $BASH_VERSION ]] && [[ "$(basename "$0" 2> /dev/null)" == "deactivate" ]]; then
    (>&2 echo "Error: deactivate must be sourced. Run 'source deactivate'
instead of 'deactivate'.
")
    "$_CONDA_DIR/conda" ..deactivate $_SHELL$EXT -h
    exit 1
fi
++ [[ -n 4.3.48(1)-release ]]
basename "$0" 2> /dev/null
+++ basename /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/scripts/jenkins-test
++ [[ jenkins-test == \d\e\a\c\t\i\v\a\t\e ]]

if [[ -z "$CONDA_PATH_BACKUP" ]]; then
    if [[ -n $BASH_VERSION ]] && [[ "$(basename "$0" 2> /dev/null)" == "deactivate" ]]; then
        exit 0
    else
        return 0
    fi
fi
++ [[ -z /usr/java/latest/bin/:/usr/java/latest/bin/:/home/anaconda/bin/:/home/jenkins/tools/hudson.tasks.Maven_MavenInstallation/Maven_3.6.3/bin/:/home/jenkins/gems/bin:/usr/local/go/bin:/home/jenkins/go-projects/bin:/home/jenkins/anaconda2/bin:/home/jenkins/tools/hudson.tasks.Maven_MavenInstallation/Maven_3.6.3/bin/:/home/jenkins/gems/bin:/usr/local/go/bin:/home/jenkins/go-projects/bin:/home/jenkins/anaconda2/bin:/home/jenkins/tools/hudson.tasks.Maven_MavenInstallation/Maven_3.6.3/bin/:/home/jenkins/gems/bin:/usr/local/go/bin:/home/jenkins/go-projects/bin:/home/jenkins/anaconda2/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games ]]

if (( $? == 0 )); then
    # Inverse of activation: run deactivate scripts prior to deactivating env
    _CONDA_D="${CONDA_PREFIX}/etc/conda/deactivate.d"
    if [[ -d $_CONDA_D ]]; then
        eval $(find "$_CONDA_D" -iname "*.sh" -exec echo source \'{}\'';' \;)
    fi

#    # get the activation path that would have been provided for this prefix
#    _LAST_ACTIVATE_PATH=$("$_CONDA_DIR/conda" ..activate $_SHELL$EXT "$CONDA_PREFIX")
#
#    # in activate, we replace a placeholder so that conda keeps its place in the PATH order
#    # The activate script sets _CONDA_HOLD here to activate that behavior.
#    #   Otherwise, PATH is simply removed.
#    if [ -n "$_CONDA_HOLD" ]; then
#        export PATH="$($_CONDA_PYTHON2 -c "import re; print(re.sub(r'$_LAST_ACTIVATE_PATH(:?)', r'CONDA_PATH_PLACEHOLDER\1', '$PATH', 1))")"
#    else
#        export PATH="$($_CONDA_PYTHON2 -c "import re; print(re.sub(r'$_LAST_ACTIVATE_PATH(:?)', r'', '$PATH', 1))")"
#    fi
#
#    unset _LAST_ACTIVATE_PATH

    export PATH=$("$_CONDA_DIR/conda" ..deactivate.path $_SHELL$EXT "$CONDA_PREFIX")

    unset CONDA_DEFAULT_ENV
    unset CONDA_PREFIX
    unset CONDA_PATH_BACKUP
    export PS1="$CONDA_PS1_BACKUP"
    unset CONDA_PS1_BACKUP
    unset _CONDA_PYTHON2
else
    unset _CONDA_PYTHON2
    return $?
fi
++ ((  0 == 0  ))
++ _CONDA_D=/home/jenkins/anaconda2/envs/adam-build-fcd2223c-a4e5-4f5c-a966-121bc529034f/etc/conda/deactivate.d
++ [[ -d /home/jenkins/anaconda2/envs/adam-build-fcd2223c-a4e5-4f5c-a966-121bc529034f/etc/conda/deactivate.d ]]
"$_CONDA_DIR/conda" ..deactivate.path $_SHELL$EXT "$CONDA_PREFIX"
+++ /home/jenkins/anaconda2/envs/adam-build-fcd2223c-a4e5-4f5c-a966-121bc529034f/bin/conda ..deactivate.path bash /home/jenkins/anaconda2/envs/adam-build-fcd2223c-a4e5-4f5c-a966-121bc529034f
++ export PATH=/usr/java/latest/bin/:/usr/java/latest/bin/:/home/anaconda/bin/:/home/jenkins/tools/hudson.tasks.Maven_MavenInstallation/Maven_3.6.3/bin/:/home/jenkins/gems/bin:/usr/local/go/bin:/home/jenkins/go-projects/bin:/home/jenkins/anaconda2/bin:/home/jenkins/tools/hudson.tasks.Maven_MavenInstallation/Maven_3.6.3/bin/:/home/jenkins/gems/bin:/usr/local/go/bin:/home/jenkins/go-projects/bin:/home/jenkins/anaconda2/bin:/home/jenkins/tools/hudson.tasks.Maven_MavenInstallation/Maven_3.6.3/bin/:/home/jenkins/gems/bin:/usr/local/go/bin:/home/jenkins/go-projects/bin:/home/jenkins/anaconda2/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games
++ PATH=/usr/java/latest/bin/:/usr/java/latest/bin/:/home/anaconda/bin/:/home/jenkins/tools/hudson.tasks.Maven_MavenInstallation/Maven_3.6.3/bin/:/home/jenkins/gems/bin:/usr/local/go/bin:/home/jenkins/go-projects/bin:/home/jenkins/anaconda2/bin:/home/jenkins/tools/hudson.tasks.Maven_MavenInstallation/Maven_3.6.3/bin/:/home/jenkins/gems/bin:/usr/local/go/bin:/home/jenkins/go-projects/bin:/home/jenkins/anaconda2/bin:/home/jenkins/tools/hudson.tasks.Maven_MavenInstallation/Maven_3.6.3/bin/:/home/jenkins/gems/bin:/usr/local/go/bin:/home/jenkins/go-projects/bin:/home/jenkins/anaconda2/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games
++ unset CONDA_DEFAULT_ENV
++ unset CONDA_PREFIX
++ unset CONDA_PATH_BACKUP
++ export PS1=
++ PS1=
++ unset CONDA_PS1_BACKUP
++ unset _CONDA_PYTHON2

if [[ -n $BASH_VERSION ]]; then
    hash -r
elif [[ -n $ZSH_VERSION ]]; then
    rehash
fi
++ [[ -n 4.3.48(1)-release ]]
++ hash -r
+ conda remove -y -n adam-build-fcd2223c-a4e5-4f5c-a966-121bc529034f --all

Package plan for package removal in environment /home/jenkins/anaconda2/envs/adam-build-fcd2223c-a4e5-4f5c-a966-121bc529034f:

The following packages will be REMOVED:

    _libgcc_mutex:    0.1-main                
    ca-certificates:  2021.1.19-h06a4308_0    
    certifi:          2020.12.5-py36h06a4308_0
    ld_impl_linux-64: 2.33.1-h53a641e_7       
    libedit:          3.1.20191231-h14c3975_1 
    libffi:           3.3-he6710b0_2          
    libgcc-ng:        9.1.0-hdf63c60_0        
    libstdcxx-ng:     9.1.0-hdf63c60_0        
    ncurses:          6.2-he6710b0_1          
    openssl:          1.1.1j-h27cfd23_0       
    pip:              21.0.1-py36h06a4308_0   
    python:           3.6.12-hcff3b4d_2       
    readline:         8.1-h27cfd23_0          
    setuptools:       52.0.0-py36h06a4308_0   
    sqlite:           3.33.0-h62c20be_0       
    tk:               8.6.10-hbc83047_0       
    wheel:            0.36.2-pyhd3eb1b0_0     
    xz:               5.2.5-h7b6447c_0        
    zlib:             1.2.11-h7b6447c_3       

+ cp -r adam-python/target /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/scripts/../adam-python/
+ pushd adam-python
/tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-python /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded ~/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu
+ make clean
pip uninstall -y adam
Cannot uninstall requirement adam, not installed
You are using pip version 19.1.1, however version 21.0.1 is available.
You should consider upgrading via the 'pip install --upgrade pip' command.
Makefile:65: recipe for target 'clean_develop' failed
make: [clean_develop] Error 1 (ignored)
rm -rf bdgenomics/*.egg*
rm -rf build/
rm -rf dist/
+ make clean_sdist
rm -rf dist
+ popd
/tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded ~/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu

if [ ${SPARK_VERSION} == 3.0.2 ]
then
    echo "Unable to build R support for Spark 3.0.2, SparkR is not available"
else
    # make a directory to install SparkR into, and set the R user libs path
    export R_LIBS_USER=${SPARK_HOME}/local_R_libs
    mkdir -p ${R_LIBS_USER}
    R CMD INSTALL \
      -l ${R_LIBS_USER} \
      ${SPARK_HOME}/R/lib/SparkR/

    export SPARKR_SUBMIT_ARGS="--jars ${ASSEMBLY_DIR}/${ASSEMBLY_JAR} --driver-class-path ${ASSEMBLY_DIR}/${ASSEMBLY_JAR} sparkr-shell"

    mvn -U \
    	-P r \
    	package \
    	-Dsuites=select.no.suites\* \
    	-Dhadoop.version=${HADOOP_VERSION}
fi
+ '[' 3.0.2 == 3.0.2 ']'
+ echo 'Unable to build R support for Spark 3.0.2, SparkR is not available'
Unable to build R support for Spark 3.0.2, SparkR is not available

# define filenames
BAM=mouse_chrM.bam
+ BAM=mouse_chrM.bam
READS=${BAM}.reads.adam
+ READS=mouse_chrM.bam.reads.adam
SORTED_READS=${BAM}.reads.sorted.adam
+ SORTED_READS=mouse_chrM.bam.reads.sorted.adam
FRAGMENTS=${BAM}.fragments.adam
+ FRAGMENTS=mouse_chrM.bam.fragments.adam
    
# fetch our input dataset
echo "Fetching BAM file"
+ echo 'Fetching BAM file'
Fetching BAM file
rm -rf ${BAM}
+ rm -rf mouse_chrM.bam
wget -q https://s3.amazonaws.com/bdgenomics-test/${BAM}
+ wget -q https://s3.amazonaws.com/bdgenomics-test/mouse_chrM.bam

# once fetched, convert BAM to ADAM
echo "Converting BAM to ADAM read format"
+ echo 'Converting BAM to ADAM read format'
Converting BAM to ADAM read format
rm -rf ${READS}
+ rm -rf mouse_chrM.bam.reads.adam
${ADAM} transformAlignments ${BAM} ${READS}
+ ./bin/adam-submit transformAlignments mouse_chrM.bam mouse_chrM.bam.reads.adam
Using ADAM_MAIN=org.bdgenomics.adam.cli.ADAMMain
Using spark-submit=/tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.2-bin-hadoop3.2/bin/spark-submit
21/02/20 18:35:30 WARN Utils: Your hostname, research-jenkins-worker-09 resolves to a loopback address: 127.0.1.1; using 192.168.10.31 instead (on interface enp4s0f0)
21/02/20 18:35:30 WARN Utils: Set SPARK_LOCAL_IP if you need to bind to another address
21/02/20 18:35:30 WARN NativeCodeLoader: Unable to load native-hadoop library for your platform... using builtin-java classes where applicable
log4j:WARN No appenders could be found for logger (org.bdgenomics.adam.cli.ADAMMain).
log4j:WARN Please initialize the log4j system properly.
log4j:WARN See http://logging.apache.org/log4j/1.2/faq.html#noconfig for more info.
Using Spark's default log4j profile: org/apache/spark/log4j-defaults.properties
21/02/20 18:35:31 INFO SparkContext: Running Spark version 3.0.2
21/02/20 18:35:31 INFO ResourceUtils: ==============================================================
21/02/20 18:35:31 INFO ResourceUtils: Resources for spark.driver:

21/02/20 18:35:31 INFO ResourceUtils: ==============================================================
21/02/20 18:35:31 INFO SparkContext: Submitted application: transformAlignments
21/02/20 18:35:31 INFO SecurityManager: Changing view acls to: jenkins
21/02/20 18:35:31 INFO SecurityManager: Changing modify acls to: jenkins
21/02/20 18:35:31 INFO SecurityManager: Changing view acls groups to: 
21/02/20 18:35:31 INFO SecurityManager: Changing modify acls groups to: 
21/02/20 18:35:31 INFO SecurityManager: SecurityManager: authentication disabled; ui acls disabled; users  with view permissions: Set(jenkins); groups with view permissions: Set(); users  with modify permissions: Set(jenkins); groups with modify permissions: Set()
21/02/20 18:35:31 INFO Utils: Successfully started service 'sparkDriver' on port 45759.
21/02/20 18:35:31 INFO SparkEnv: Registering MapOutputTracker
21/02/20 18:35:31 INFO SparkEnv: Registering BlockManagerMaster
21/02/20 18:35:31 INFO BlockManagerMasterEndpoint: Using org.apache.spark.storage.DefaultTopologyMapper for getting topology information
21/02/20 18:35:31 INFO BlockManagerMasterEndpoint: BlockManagerMasterEndpoint up
21/02/20 18:35:31 INFO SparkEnv: Registering BlockManagerMasterHeartbeat
21/02/20 18:35:31 INFO DiskBlockManager: Created local directory at /tmp/blockmgr-ff22c2a3-88dd-44cf-9354-9218b77c28ef
21/02/20 18:35:31 INFO MemoryStore: MemoryStore started with capacity 408.9 MiB
21/02/20 18:35:31 INFO SparkEnv: Registering OutputCommitCoordinator
21/02/20 18:35:32 INFO Utils: Successfully started service 'SparkUI' on port 4040.
21/02/20 18:35:32 INFO SparkUI: Bound SparkUI to 0.0.0.0, and started at http://192.168.10.31:4040
21/02/20 18:35:32 INFO SparkContext: Added JAR file:/tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/target/adam-assembly-spark3_2.12-0.34.0-SNAPSHOT.jar at spark://192.168.10.31:45759/jars/adam-assembly-spark3_2.12-0.34.0-SNAPSHOT.jar with timestamp 1613874931205
21/02/20 18:35:32 INFO Executor: Starting executor ID driver on host 192.168.10.31
21/02/20 18:35:32 INFO Executor: Fetching spark://192.168.10.31:45759/jars/adam-assembly-spark3_2.12-0.34.0-SNAPSHOT.jar with timestamp 1613874931205
21/02/20 18:35:32 INFO TransportClientFactory: Successfully created connection to /192.168.10.31:45759 after 43 ms (0 ms spent in bootstraps)
21/02/20 18:35:32 INFO Utils: Fetching spark://192.168.10.31:45759/jars/adam-assembly-spark3_2.12-0.34.0-SNAPSHOT.jar to /tmp/spark-b194cb34-4c20-41b8-bf7d-45d8251b6cc4/userFiles-24202530-334a-43aa-a67a-7b8a9c944796/fetchFileTemp8776877959480517314.tmp
21/02/20 18:35:32 INFO Executor: Adding file:/tmp/spark-b194cb34-4c20-41b8-bf7d-45d8251b6cc4/userFiles-24202530-334a-43aa-a67a-7b8a9c944796/adam-assembly-spark3_2.12-0.34.0-SNAPSHOT.jar to class loader
21/02/20 18:35:32 INFO Utils: Successfully started service 'org.apache.spark.network.netty.NettyBlockTransferService' on port 44709.
21/02/20 18:35:32 INFO NettyBlockTransferService: Server created on 192.168.10.31:44709
21/02/20 18:35:32 INFO BlockManager: Using org.apache.spark.storage.RandomBlockReplicationPolicy for block replication policy
21/02/20 18:35:32 INFO BlockManagerMaster: Registering BlockManager BlockManagerId(driver, 192.168.10.31, 44709, None)
21/02/20 18:35:32 INFO BlockManagerMasterEndpoint: Registering block manager 192.168.10.31:44709 with 408.9 MiB RAM, BlockManagerId(driver, 192.168.10.31, 44709, None)
21/02/20 18:35:32 INFO BlockManagerMaster: Registered BlockManager BlockManagerId(driver, 192.168.10.31, 44709, None)
21/02/20 18:35:32 INFO BlockManager: Initialized BlockManager: BlockManagerId(driver, 192.168.10.31, 44709, None)
21/02/20 18:35:32 INFO ADAMContext: Loading mouse_chrM.bam as BAM/CRAM/SAM and converting to Alignments.
21/02/20 18:35:33 INFO ADAMContext: Loaded header from file:/tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/mouse_chrM.bam
21/02/20 18:35:33 INFO MemoryStore: Block broadcast_0 stored as values in memory (estimated size 314.0 KiB, free 408.6 MiB)
21/02/20 18:35:34 INFO MemoryStore: Block broadcast_0_piece0 stored as bytes in memory (estimated size 27.3 KiB, free 408.6 MiB)
21/02/20 18:35:34 INFO BlockManagerInfo: Added broadcast_0_piece0 in memory on 192.168.10.31:44709 (size: 27.3 KiB, free: 408.9 MiB)
21/02/20 18:35:34 INFO SparkContext: Created broadcast 0 from newAPIHadoopFile at ADAMContext.scala:2054
21/02/20 18:35:35 INFO RDDBoundAlignmentDataset: Saving data in ADAM format
21/02/20 18:35:35 INFO FileOutputCommitter: File Output Committer Algorithm version is 1
21/02/20 18:35:35 INFO FileOutputCommitter: FileOutputCommitter skip cleanup _temporary folders under output directory:false, ignore cleanup failures: false
21/02/20 18:35:35 INFO FileInputFormat: Total input files to process : 1
21/02/20 18:35:35 INFO SparkContext: Starting job: runJob at SparkHadoopWriter.scala:83
21/02/20 18:35:35 INFO DAGScheduler: Got job 0 (runJob at SparkHadoopWriter.scala:83) with 1 output partitions
21/02/20 18:35:35 INFO DAGScheduler: Final stage: ResultStage 0 (runJob at SparkHadoopWriter.scala:83)
21/02/20 18:35:35 INFO DAGScheduler: Parents of final stage: List()
21/02/20 18:35:35 INFO DAGScheduler: Missing parents: List()
21/02/20 18:35:35 INFO DAGScheduler: Submitting ResultStage 0 (MapPartitionsRDD[2] at map at GenomicDataset.scala:3805), which has no missing parents
21/02/20 18:35:35 INFO MemoryStore: Block broadcast_1 stored as values in memory (estimated size 95.2 KiB, free 408.5 MiB)
21/02/20 18:35:35 INFO MemoryStore: Block broadcast_1_piece0 stored as bytes in memory (estimated size 34.6 KiB, free 408.4 MiB)
21/02/20 18:35:35 INFO BlockManagerInfo: Added broadcast_1_piece0 in memory on 192.168.10.31:44709 (size: 34.6 KiB, free: 408.8 MiB)
21/02/20 18:35:35 INFO SparkContext: Created broadcast 1 from broadcast at DAGScheduler.scala:1223
21/02/20 18:35:35 INFO DAGScheduler: Submitting 1 missing tasks from ResultStage 0 (MapPartitionsRDD[2] at map at GenomicDataset.scala:3805) (first 15 tasks are for partitions Vector(0))
21/02/20 18:35:35 INFO TaskSchedulerImpl: Adding task set 0.0 with 1 tasks
21/02/20 18:35:35 INFO TaskSetManager: Starting task 0.0 in stage 0.0 (TID 0, 192.168.10.31, executor driver, partition 0, PROCESS_LOCAL, 7443 bytes)
21/02/20 18:35:35 INFO Executor: Running task 0.0 in stage 0.0 (TID 0)
21/02/20 18:35:36 INFO NewHadoopRDD: Input split: file:/tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/mouse_chrM.bam:83361792-833134657535
21/02/20 18:35:36 INFO FileOutputCommitter: File Output Committer Algorithm version is 1
21/02/20 18:35:36 INFO FileOutputCommitter: FileOutputCommitter skip cleanup _temporary folders under output directory:false, ignore cleanup failures: false
21/02/20 18:35:36 INFO CodecConfig: Compression: GZIP
21/02/20 18:35:36 INFO FileOutputCommitter: File Output Committer Algorithm version is 1
21/02/20 18:35:36 INFO FileOutputCommitter: FileOutputCommitter skip cleanup _temporary folders under output directory:false, ignore cleanup failures: false
21/02/20 18:35:36 INFO ParquetOutputFormat: Parquet block size to 134217728
21/02/20 18:35:36 INFO ParquetOutputFormat: Parquet page size to 1048576
21/02/20 18:35:36 INFO ParquetOutputFormat: Parquet dictionary page size to 1048576
21/02/20 18:35:36 INFO ParquetOutputFormat: Dictionary is on
21/02/20 18:35:36 INFO ParquetOutputFormat: Validation is off
21/02/20 18:35:36 INFO ParquetOutputFormat: Writer version is: PARQUET_1_0
21/02/20 18:35:36 INFO ParquetOutputFormat: Maximum row group padding size is 8388608 bytes
21/02/20 18:35:36 INFO ParquetOutputFormat: Page size checking is: estimated
21/02/20 18:35:36 INFO ParquetOutputFormat: Min row count for page size check is: 100
21/02/20 18:35:36 INFO ParquetOutputFormat: Max row count for page size check is: 10000
21/02/20 18:35:36 INFO CodecPool: Got brand-new compressor [.gz]
Ignoring SAM validation error: ERROR: Record 162622, Read name 613F0AAXX100423:3:58:9979:16082, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162624, Read name 613F0AAXX100423:6:13:3141:11793, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162625, Read name 613F0AAXX100423:8:39:18592:13552, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162635, Read name 613F1AAXX100423:7:2:13114:10698, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162637, Read name 613F1AAXX100423:6:100:8840:11167, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162639, Read name 613F1AAXX100423:8:15:10944:11181, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162640, Read name 613F1AAXX100423:8:17:5740:10104, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162651, Read name 613F1AAXX100423:1:53:11097:8261, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162654, Read name 613F1AAXX100423:2:112:16779:19612, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162657, Read name 613F0AAXX100423:8:28:7084:17683, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162659, Read name 613F0AAXX100423:8:39:19796:12794, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162662, Read name 613F1AAXX100423:5:116:9339:3264, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162667, Read name 613F0AAXX100423:4:67:2015:3054, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162669, Read name 613F0AAXX100423:7:7:11297:11738, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162674, Read name 613F0AAXX100423:6:59:10490:20829, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162678, Read name 613F1AAXX100423:8:11:17603:4766, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162682, Read name 613F0AAXX100423:5:86:10814:10257, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162683, Read name 613F0AAXX100423:5:117:14178:6111, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162685, Read name 613F0AAXX100423:2:3:13563:6720, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162689, Read name 613F0AAXX100423:7:59:16009:15799, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162696, Read name 613F0AAXX100423:5:31:9663:18252, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162698, Read name 613F1AAXX100423:2:27:12264:14626, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162699, Read name 613F0AAXX100423:1:120:19003:6647, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162702, Read name 613F1AAXX100423:3:37:6972:18407, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162704, Read name 613F1AAXX100423:3:77:6946:3880, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162706, Read name 613F0AAXX100423:7:48:2692:3492, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162708, Read name 613F1AAXX100423:7:80:8790:1648, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162710, Read name 6141AAAXX100423:5:30:15036:17610, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162712, Read name 613F1AAXX100423:8:80:6261:4465, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162713, Read name 6141AAAXX100423:5:74:5542:6195, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162715, Read name 613F1AAXX100423:5:14:14844:13639, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162718, Read name 613F1AAXX100423:7:112:14569:8480, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162725, Read name 613F1AAXX100423:4:56:10160:9879, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162727, Read name 6141AAAXX100423:7:89:12209:9221, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162731, Read name 6141AAAXX100423:6:55:1590:19793, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162732, Read name 6141AAAXX100423:7:102:16679:12368, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162734, Read name 613F1AAXX100423:2:7:4909:18472, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162737, Read name 6141AAAXX100423:4:73:6574:10572, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162741, Read name 6141AAAXX100423:1:8:14113:12655, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162743, Read name 6141AAAXX100423:3:40:7990:5056, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162744, Read name 6141AAAXX100423:4:36:15793:3411, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162745, Read name 6141AAAXX100423:8:83:1139:18985, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162746, Read name 6141AAAXX100423:5:7:18196:13562, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162748, Read name 6141AAAXX100423:3:114:5639:7123, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162751, Read name 6141AAAXX100423:7:47:4898:8640, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162753, Read name 6141AAAXX100423:3:64:8064:8165, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162756, Read name 613F1AAXX100423:1:105:14386:1684, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162757, Read name 613F1AAXX100423:6:98:1237:19470, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162761, Read name 613F1AAXX100423:7:106:19658:9261, MAPQ should be 0 for unmapped read.
21/02/20 18:35:42 INFO InternalParquetRecordWriter: Flushing mem columnStore to file. allocated memory: 16043959
21/02/20 18:35:42 INFO FileOutputCommitter: Saved output of task 'attempt_202102201835351295297715269229863_0002_r_000000_0' to file:/tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/mouse_chrM.bam.reads.adam/_temporary/0/task_202102201835351295297715269229863_0002_r_000000
21/02/20 18:35:42 INFO SparkHadoopMapRedUtil: attempt_202102201835351295297715269229863_0002_r_000000_0: Committed
21/02/20 18:35:42 INFO Executor: Finished task 0.0 in stage 0.0 (TID 0). 1021 bytes result sent to driver
21/02/20 18:35:42 INFO TaskSetManager: Finished task 0.0 in stage 0.0 (TID 0) in 6413 ms on 192.168.10.31 (executor driver) (1/1)
21/02/20 18:35:42 INFO TaskSchedulerImpl: Removed TaskSet 0.0, whose tasks have all completed, from pool 
21/02/20 18:35:42 INFO DAGScheduler: ResultStage 0 (runJob at SparkHadoopWriter.scala:83) finished in 6.545 s
21/02/20 18:35:42 INFO DAGScheduler: Job 0 is finished. Cancelling potential speculative or zombie tasks for this job
21/02/20 18:35:42 INFO TaskSchedulerImpl: Killing all running tasks in stage 0: Stage finished
21/02/20 18:35:42 INFO DAGScheduler: Job 0 finished: runJob at SparkHadoopWriter.scala:83, took 6.597073 s
21/02/20 18:35:42 INFO ParquetFileReader: Initiating action with parallelism: 5
21/02/20 18:35:42 INFO SparkHadoopWriter: Job job_202102201835351295297715269229863_0002 committed.
21/02/20 18:35:42 INFO SparkContext: Invoking stop() from shutdown hook
21/02/20 18:35:42 INFO SparkUI: Stopped Spark web UI at http://192.168.10.31:4040
21/02/20 18:35:42 INFO MapOutputTrackerMasterEndpoint: MapOutputTrackerMasterEndpoint stopped!
21/02/20 18:35:42 INFO MemoryStore: MemoryStore cleared
21/02/20 18:35:42 INFO BlockManager: BlockManager stopped
21/02/20 18:35:42 INFO BlockManagerMaster: BlockManagerMaster stopped
21/02/20 18:35:42 INFO OutputCommitCoordinator$OutputCommitCoordinatorEndpoint: OutputCommitCoordinator stopped!
21/02/20 18:35:42 INFO SparkContext: Successfully stopped SparkContext
21/02/20 18:35:42 INFO ShutdownHookManager: Shutdown hook called
21/02/20 18:35:42 INFO ShutdownHookManager: Deleting directory /tmp/spark-b194cb34-4c20-41b8-bf7d-45d8251b6cc4
21/02/20 18:35:42 INFO ShutdownHookManager: Deleting directory /tmp/spark-2f7afb16-2498-415e-ab39-ae5407e935e9

# then, sort the BAM
echo "Converting BAM to ADAM read format with sorting"
+ echo 'Converting BAM to ADAM read format with sorting'
Converting BAM to ADAM read format with sorting
rm -rf ${SORTED_READS}
+ rm -rf mouse_chrM.bam.reads.sorted.adam
${ADAM} transformAlignments -sort_by_reference_position ${READS} ${SORTED_READS}
+ ./bin/adam-submit transformAlignments -sort_by_reference_position mouse_chrM.bam.reads.adam mouse_chrM.bam.reads.sorted.adam
Using ADAM_MAIN=org.bdgenomics.adam.cli.ADAMMain
Using spark-submit=/tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.2-bin-hadoop3.2/bin/spark-submit
21/02/20 18:35:44 WARN Utils: Your hostname, research-jenkins-worker-09 resolves to a loopback address: 127.0.1.1; using 192.168.10.31 instead (on interface enp4s0f0)
21/02/20 18:35:44 WARN Utils: Set SPARK_LOCAL_IP if you need to bind to another address
21/02/20 18:35:44 WARN NativeCodeLoader: Unable to load native-hadoop library for your platform... using builtin-java classes where applicable
log4j:WARN No appenders could be found for logger (org.bdgenomics.adam.cli.ADAMMain).
log4j:WARN Please initialize the log4j system properly.
log4j:WARN See http://logging.apache.org/log4j/1.2/faq.html#noconfig for more info.
Using Spark's default log4j profile: org/apache/spark/log4j-defaults.properties
21/02/20 18:35:44 INFO SparkContext: Running Spark version 3.0.2
21/02/20 18:35:44 INFO ResourceUtils: ==============================================================
21/02/20 18:35:44 INFO ResourceUtils: Resources for spark.driver:

21/02/20 18:35:44 INFO ResourceUtils: ==============================================================
21/02/20 18:35:44 INFO SparkContext: Submitted application: transformAlignments
21/02/20 18:35:44 INFO SecurityManager: Changing view acls to: jenkins
21/02/20 18:35:44 INFO SecurityManager: Changing modify acls to: jenkins
21/02/20 18:35:44 INFO SecurityManager: Changing view acls groups to: 
21/02/20 18:35:44 INFO SecurityManager: Changing modify acls groups to: 
21/02/20 18:35:44 INFO SecurityManager: SecurityManager: authentication disabled; ui acls disabled; users  with view permissions: Set(jenkins); groups with view permissions: Set(); users  with modify permissions: Set(jenkins); groups with modify permissions: Set()
21/02/20 18:35:45 INFO Utils: Successfully started service 'sparkDriver' on port 39309.
21/02/20 18:35:45 INFO SparkEnv: Registering MapOutputTracker
21/02/20 18:35:45 INFO SparkEnv: Registering BlockManagerMaster
21/02/20 18:35:45 INFO BlockManagerMasterEndpoint: Using org.apache.spark.storage.DefaultTopologyMapper for getting topology information
21/02/20 18:35:45 INFO BlockManagerMasterEndpoint: BlockManagerMasterEndpoint up
21/02/20 18:35:45 INFO SparkEnv: Registering BlockManagerMasterHeartbeat
21/02/20 18:35:45 INFO DiskBlockManager: Created local directory at /tmp/blockmgr-484dd3fa-0555-4563-b4b8-6797c6315287
21/02/20 18:35:45 INFO MemoryStore: MemoryStore started with capacity 408.9 MiB
21/02/20 18:35:45 INFO SparkEnv: Registering OutputCommitCoordinator
21/02/20 18:35:45 INFO Utils: Successfully started service 'SparkUI' on port 4040.
21/02/20 18:35:45 INFO SparkUI: Bound SparkUI to 0.0.0.0, and started at http://192.168.10.31:4040
21/02/20 18:35:45 INFO SparkContext: Added JAR file:/tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/target/adam-assembly-spark3_2.12-0.34.0-SNAPSHOT.jar at spark://192.168.10.31:39309/jars/adam-assembly-spark3_2.12-0.34.0-SNAPSHOT.jar with timestamp 1613874944676
21/02/20 18:35:45 INFO Executor: Starting executor ID driver on host 192.168.10.31
21/02/20 18:35:45 INFO Executor: Fetching spark://192.168.10.31:39309/jars/adam-assembly-spark3_2.12-0.34.0-SNAPSHOT.jar with timestamp 1613874944676
21/02/20 18:35:46 INFO TransportClientFactory: Successfully created connection to /192.168.10.31:39309 after 42 ms (0 ms spent in bootstraps)
21/02/20 18:35:46 INFO Utils: Fetching spark://192.168.10.31:39309/jars/adam-assembly-spark3_2.12-0.34.0-SNAPSHOT.jar to /tmp/spark-65736c6a-9276-4599-8966-1d417ea919d3/userFiles-dc8c30d0-5f1a-4d80-86bb-5aff63be2fa4/fetchFileTemp7937285126915278403.tmp
21/02/20 18:35:46 INFO Executor: Adding file:/tmp/spark-65736c6a-9276-4599-8966-1d417ea919d3/userFiles-dc8c30d0-5f1a-4d80-86bb-5aff63be2fa4/adam-assembly-spark3_2.12-0.34.0-SNAPSHOT.jar to class loader
21/02/20 18:35:46 INFO Utils: Successfully started service 'org.apache.spark.network.netty.NettyBlockTransferService' on port 44165.
21/02/20 18:35:46 INFO NettyBlockTransferService: Server created on 192.168.10.31:44165
21/02/20 18:35:46 INFO BlockManager: Using org.apache.spark.storage.RandomBlockReplicationPolicy for block replication policy
21/02/20 18:35:46 INFO BlockManagerMaster: Registering BlockManager BlockManagerId(driver, 192.168.10.31, 44165, None)
21/02/20 18:35:46 INFO BlockManagerMasterEndpoint: Registering block manager 192.168.10.31:44165 with 408.9 MiB RAM, BlockManagerId(driver, 192.168.10.31, 44165, None)
21/02/20 18:35:46 INFO BlockManagerMaster: Registered BlockManager BlockManagerId(driver, 192.168.10.31, 44165, None)
21/02/20 18:35:46 INFO BlockManager: Initialized BlockManager: BlockManagerId(driver, 192.168.10.31, 44165, None)
21/02/20 18:35:46 INFO ADAMContext: Loading mouse_chrM.bam.reads.adam as Parquet of Alignments.
21/02/20 18:35:48 INFO ADAMContext: Reading the ADAM file at mouse_chrM.bam.reads.adam to create RDD
21/02/20 18:35:48 INFO MemoryStore: Block broadcast_0 stored as values in memory (estimated size 333.7 KiB, free 408.6 MiB)
21/02/20 18:35:49 INFO MemoryStore: Block broadcast_0_piece0 stored as bytes in memory (estimated size 31.0 KiB, free 408.5 MiB)
21/02/20 18:35:49 INFO BlockManagerInfo: Added broadcast_0_piece0 in memory on 192.168.10.31:44165 (size: 31.0 KiB, free: 408.9 MiB)
21/02/20 18:35:49 INFO SparkContext: Created broadcast 0 from newAPIHadoopFile at ADAMContext.scala:1797
21/02/20 18:35:49 INFO TransformAlignments: Sorting alignments by reference position, with references ordered by name
21/02/20 18:35:49 INFO RDDBoundAlignmentDataset: Sorting alignments by reference position
21/02/20 18:35:49 INFO FileInputFormat: Total input files to process : 1
21/02/20 18:35:49 INFO ParquetInputFormat: Total input paths to process : 1
21/02/20 18:35:49 INFO RDDBoundAlignmentDataset: Saving data in ADAM format
21/02/20 18:35:49 INFO FileOutputCommitter: File Output Committer Algorithm version is 1
21/02/20 18:35:49 INFO FileOutputCommitter: FileOutputCommitter skip cleanup _temporary folders under output directory:false, ignore cleanup failures: false
21/02/20 18:35:49 INFO SparkContext: Starting job: runJob at SparkHadoopWriter.scala:83
21/02/20 18:35:49 INFO DAGScheduler: Registering RDD 2 (sortBy at AlignmentDataset.scala:1008) as input to shuffle 0
21/02/20 18:35:49 INFO DAGScheduler: Got job 0 (runJob at SparkHadoopWriter.scala:83) with 1 output partitions
21/02/20 18:35:49 INFO DAGScheduler: Final stage: ResultStage 1 (runJob at SparkHadoopWriter.scala:83)
21/02/20 18:35:49 INFO DAGScheduler: Parents of final stage: List(ShuffleMapStage 0)
21/02/20 18:35:49 INFO DAGScheduler: Missing parents: List(ShuffleMapStage 0)
21/02/20 18:35:49 INFO DAGScheduler: Submitting ShuffleMapStage 0 (MapPartitionsRDD[2] at sortBy at AlignmentDataset.scala:1008), which has no missing parents
21/02/20 18:35:49 INFO MemoryStore: Block broadcast_1 stored as values in memory (estimated size 6.9 KiB, free 408.5 MiB)
21/02/20 18:35:49 INFO MemoryStore: Block broadcast_1_piece0 stored as bytes in memory (estimated size 4.0 KiB, free 408.5 MiB)
21/02/20 18:35:49 INFO BlockManagerInfo: Added broadcast_1_piece0 in memory on 192.168.10.31:44165 (size: 4.0 KiB, free: 408.9 MiB)
21/02/20 18:35:49 INFO SparkContext: Created broadcast 1 from broadcast at DAGScheduler.scala:1223
21/02/20 18:35:50 INFO DAGScheduler: Submitting 1 missing tasks from ShuffleMapStage 0 (MapPartitionsRDD[2] at sortBy at AlignmentDataset.scala:1008) (first 15 tasks are for partitions Vector(0))
21/02/20 18:35:50 INFO TaskSchedulerImpl: Adding task set 0.0 with 1 tasks
21/02/20 18:35:50 INFO TaskSetManager: Starting task 0.0 in stage 0.0 (TID 0, 192.168.10.31, executor driver, partition 0, PROCESS_LOCAL, 7482 bytes)
21/02/20 18:35:50 INFO Executor: Running task 0.0 in stage 0.0 (TID 0)
21/02/20 18:35:50 INFO NewHadoopRDD: Input split: file:/tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/mouse_chrM.bam.reads.adam/part-r-00000.gz.parquet:0+10132211
21/02/20 18:35:50 INFO InternalParquetRecordReader: RecordReader initialized will read a total of 163064 records.
21/02/20 18:35:50 INFO InternalParquetRecordReader: at row 0. reading next block
21/02/20 18:35:50 INFO CodecPool: Got brand-new decompressor [.gz]
21/02/20 18:35:50 INFO InternalParquetRecordReader: block read in memory in 49 ms. row count = 163064
21/02/20 18:35:53 INFO Executor: Finished task 0.0 in stage 0.0 (TID 0). 1086 bytes result sent to driver
21/02/20 18:35:53 INFO TaskSetManager: Finished task 0.0 in stage 0.0 (TID 0) in 3296 ms on 192.168.10.31 (executor driver) (1/1)
21/02/20 18:35:53 INFO TaskSchedulerImpl: Removed TaskSet 0.0, whose tasks have all completed, from pool 
21/02/20 18:35:53 INFO DAGScheduler: ShuffleMapStage 0 (sortBy at AlignmentDataset.scala:1008) finished in 3.439 s
21/02/20 18:35:53 INFO DAGScheduler: looking for newly runnable stages
21/02/20 18:35:53 INFO DAGScheduler: running: Set()
21/02/20 18:35:53 INFO DAGScheduler: waiting: Set(ResultStage 1)
21/02/20 18:35:53 INFO DAGScheduler: failed: Set()
21/02/20 18:35:53 INFO DAGScheduler: Submitting ResultStage 1 (MapPartitionsRDD[5] at map at GenomicDataset.scala:3805), which has no missing parents
21/02/20 18:35:53 INFO MemoryStore: Block broadcast_2 stored as values in memory (estimated size 96.7 KiB, free 408.4 MiB)
21/02/20 18:35:53 INFO MemoryStore: Block broadcast_2_piece0 stored as bytes in memory (estimated size 35.5 KiB, free 408.4 MiB)
21/02/20 18:35:53 INFO BlockManagerInfo: Added broadcast_2_piece0 in memory on 192.168.10.31:44165 (size: 35.5 KiB, free: 408.8 MiB)
21/02/20 18:35:53 INFO SparkContext: Created broadcast 2 from broadcast at DAGScheduler.scala:1223
21/02/20 18:35:53 INFO DAGScheduler: Submitting 1 missing tasks from ResultStage 1 (MapPartitionsRDD[5] at map at GenomicDataset.scala:3805) (first 15 tasks are for partitions Vector(0))
21/02/20 18:35:53 INFO TaskSchedulerImpl: Adding task set 1.0 with 1 tasks
21/02/20 18:35:53 INFO TaskSetManager: Starting task 0.0 in stage 1.0 (TID 1, 192.168.10.31, executor driver, partition 0, NODE_LOCAL, 7143 bytes)
21/02/20 18:35:53 INFO Executor: Running task 0.0 in stage 1.0 (TID 1)
21/02/20 18:35:53 INFO ShuffleBlockFetcherIterator: Getting 1 (24.5 MiB) non-empty blocks including 1 (24.5 MiB) local and 0 (0.0 B) host-local and 0 (0.0 B) remote blocks
21/02/20 18:35:53 INFO ShuffleBlockFetcherIterator: Started 0 remote fetches in 9 ms
21/02/20 18:35:54 INFO FileOutputCommitter: File Output Committer Algorithm version is 1
21/02/20 18:35:54 INFO FileOutputCommitter: FileOutputCommitter skip cleanup _temporary folders under output directory:false, ignore cleanup failures: false
21/02/20 18:35:54 INFO CodecConfig: Compression: GZIP
21/02/20 18:35:54 INFO FileOutputCommitter: File Output Committer Algorithm version is 1
21/02/20 18:35:54 INFO FileOutputCommitter: FileOutputCommitter skip cleanup _temporary folders under output directory:false, ignore cleanup failures: false
21/02/20 18:35:54 INFO ParquetOutputFormat: Parquet block size to 134217728
21/02/20 18:35:54 INFO ParquetOutputFormat: Parquet page size to 1048576
21/02/20 18:35:54 INFO ParquetOutputFormat: Parquet dictionary page size to 1048576
21/02/20 18:35:54 INFO ParquetOutputFormat: Dictionary is on
21/02/20 18:35:54 INFO ParquetOutputFormat: Validation is off
21/02/20 18:35:54 INFO ParquetOutputFormat: Writer version is: PARQUET_1_0
21/02/20 18:35:54 INFO ParquetOutputFormat: Maximum row group padding size is 8388608 bytes
21/02/20 18:35:54 INFO ParquetOutputFormat: Page size checking is: estimated
21/02/20 18:35:54 INFO ParquetOutputFormat: Min row count for page size check is: 100
21/02/20 18:35:54 INFO ParquetOutputFormat: Max row count for page size check is: 10000
21/02/20 18:35:54 INFO CodecPool: Got brand-new compressor [.gz]
21/02/20 18:35:57 INFO BlockManagerInfo: Removed broadcast_1_piece0 on 192.168.10.31:44165 in memory (size: 4.0 KiB, free: 408.8 MiB)
21/02/20 18:35:59 INFO InternalParquetRecordWriter: Flushing mem columnStore to file. allocated memory: 16004474
21/02/20 18:35:59 INFO FileOutputCommitter: Saved output of task 'attempt_202102201835494688667745398004674_0005_r_000000_0' to file:/tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/mouse_chrM.bam.reads.sorted.adam/_temporary/0/task_202102201835494688667745398004674_0005_r_000000
21/02/20 18:35:59 INFO SparkHadoopMapRedUtil: attempt_202102201835494688667745398004674_0005_r_000000_0: Committed
21/02/20 18:35:59 INFO Executor: Finished task 0.0 in stage 1.0 (TID 1). 1365 bytes result sent to driver
21/02/20 18:35:59 INFO TaskSetManager: Finished task 0.0 in stage 1.0 (TID 1) in 6384 ms on 192.168.10.31 (executor driver) (1/1)
21/02/20 18:35:59 INFO TaskSchedulerImpl: Removed TaskSet 1.0, whose tasks have all completed, from pool 
21/02/20 18:35:59 INFO DAGScheduler: ResultStage 1 (runJob at SparkHadoopWriter.scala:83) finished in 6.417 s
21/02/20 18:35:59 INFO DAGScheduler: Job 0 is finished. Cancelling potential speculative or zombie tasks for this job
21/02/20 18:35:59 INFO TaskSchedulerImpl: Killing all running tasks in stage 1: Stage finished
21/02/20 18:35:59 INFO DAGScheduler: Job 0 finished: runJob at SparkHadoopWriter.scala:83, took 9.942168 s
21/02/20 18:35:59 INFO ParquetFileReader: Initiating action with parallelism: 5
21/02/20 18:35:59 INFO SparkHadoopWriter: Job job_202102201835494688667745398004674_0005 committed.
21/02/20 18:35:59 INFO SparkContext: Invoking stop() from shutdown hook
21/02/20 18:35:59 INFO SparkUI: Stopped Spark web UI at http://192.168.10.31:4040
21/02/20 18:35:59 INFO MapOutputTrackerMasterEndpoint: MapOutputTrackerMasterEndpoint stopped!
21/02/20 18:36:00 INFO MemoryStore: MemoryStore cleared
21/02/20 18:36:00 INFO BlockManager: BlockManager stopped
21/02/20 18:36:00 INFO BlockManagerMaster: BlockManagerMaster stopped
21/02/20 18:36:00 INFO OutputCommitCoordinator$OutputCommitCoordinatorEndpoint: OutputCommitCoordinator stopped!
21/02/20 18:36:00 INFO SparkContext: Successfully stopped SparkContext
21/02/20 18:36:00 INFO ShutdownHookManager: Shutdown hook called
21/02/20 18:36:00 INFO ShutdownHookManager: Deleting directory /tmp/spark-220ac829-b73e-4446-b6d4-0a69e002b7c5
21/02/20 18:36:00 INFO ShutdownHookManager: Deleting directory /tmp/spark-65736c6a-9276-4599-8966-1d417ea919d3

# convert the reads to fragments to re-pair the reads
echo "Converting read file to fragments"
+ echo 'Converting read file to fragments'
Converting read file to fragments
rm -rf ${FRAGMENTS}
+ rm -rf mouse_chrM.bam.fragments.adam
${ADAM} transformFragments -load_as_alignments ${READS} ${FRAGMENTS}
+ ./bin/adam-submit transformFragments -load_as_alignments mouse_chrM.bam.reads.adam mouse_chrM.bam.fragments.adam
Using ADAM_MAIN=org.bdgenomics.adam.cli.ADAMMain
Using spark-submit=/tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.2-bin-hadoop3.2/bin/spark-submit
21/02/20 18:36:01 WARN Utils: Your hostname, research-jenkins-worker-09 resolves to a loopback address: 127.0.1.1; using 192.168.10.31 instead (on interface enp4s0f0)
21/02/20 18:36:01 WARN Utils: Set SPARK_LOCAL_IP if you need to bind to another address
21/02/20 18:36:01 WARN NativeCodeLoader: Unable to load native-hadoop library for your platform... using builtin-java classes where applicable
log4j:WARN No appenders could be found for logger (org.bdgenomics.adam.cli.ADAMMain).
log4j:WARN Please initialize the log4j system properly.
log4j:WARN See http://logging.apache.org/log4j/1.2/faq.html#noconfig for more info.
Using Spark's default log4j profile: org/apache/spark/log4j-defaults.properties
21/02/20 18:36:02 INFO SparkContext: Running Spark version 3.0.2
21/02/20 18:36:02 INFO ResourceUtils: ==============================================================
21/02/20 18:36:02 INFO ResourceUtils: Resources for spark.driver:

21/02/20 18:36:02 INFO ResourceUtils: ==============================================================
21/02/20 18:36:02 INFO SparkContext: Submitted application: transformFragments
21/02/20 18:36:02 INFO SecurityManager: Changing view acls to: jenkins
21/02/20 18:36:02 INFO SecurityManager: Changing modify acls to: jenkins
21/02/20 18:36:02 INFO SecurityManager: Changing view acls groups to: 
21/02/20 18:36:02 INFO SecurityManager: Changing modify acls groups to: 
21/02/20 18:36:02 INFO SecurityManager: SecurityManager: authentication disabled; ui acls disabled; users  with view permissions: Set(jenkins); groups with view permissions: Set(); users  with modify permissions: Set(jenkins); groups with modify permissions: Set()
21/02/20 18:36:02 INFO Utils: Successfully started service 'sparkDriver' on port 46675.
21/02/20 18:36:02 INFO SparkEnv: Registering MapOutputTracker
21/02/20 18:36:02 INFO SparkEnv: Registering BlockManagerMaster
21/02/20 18:36:02 INFO BlockManagerMasterEndpoint: Using org.apache.spark.storage.DefaultTopologyMapper for getting topology information
21/02/20 18:36:02 INFO BlockManagerMasterEndpoint: BlockManagerMasterEndpoint up
21/02/20 18:36:02 INFO SparkEnv: Registering BlockManagerMasterHeartbeat
21/02/20 18:36:02 INFO DiskBlockManager: Created local directory at /tmp/blockmgr-3d8a30f6-c751-4ca5-8cf5-92882add8fca
21/02/20 18:36:02 INFO MemoryStore: MemoryStore started with capacity 408.9 MiB
21/02/20 18:36:02 INFO SparkEnv: Registering OutputCommitCoordinator
21/02/20 18:36:02 INFO Utils: Successfully started service 'SparkUI' on port 4040.
21/02/20 18:36:03 INFO SparkUI: Bound SparkUI to 0.0.0.0, and started at http://192.168.10.31:4040
21/02/20 18:36:03 INFO SparkContext: Added JAR file:/tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/target/adam-assembly-spark3_2.12-0.34.0-SNAPSHOT.jar at spark://192.168.10.31:46675/jars/adam-assembly-spark3_2.12-0.34.0-SNAPSHOT.jar with timestamp 1613874962165
21/02/20 18:36:03 INFO Executor: Starting executor ID driver on host 192.168.10.31
21/02/20 18:36:03 INFO Executor: Fetching spark://192.168.10.31:46675/jars/adam-assembly-spark3_2.12-0.34.0-SNAPSHOT.jar with timestamp 1613874962165
21/02/20 18:36:03 INFO TransportClientFactory: Successfully created connection to /192.168.10.31:46675 after 35 ms (0 ms spent in bootstraps)
21/02/20 18:36:03 INFO Utils: Fetching spark://192.168.10.31:46675/jars/adam-assembly-spark3_2.12-0.34.0-SNAPSHOT.jar to /tmp/spark-9aeeb1aa-f85a-465a-a1cd-66b40236342a/userFiles-5f5c96fc-ba84-4bf5-9528-741227f6fae2/fetchFileTemp5154628536218476703.tmp
21/02/20 18:36:03 INFO Executor: Adding file:/tmp/spark-9aeeb1aa-f85a-465a-a1cd-66b40236342a/userFiles-5f5c96fc-ba84-4bf5-9528-741227f6fae2/adam-assembly-spark3_2.12-0.34.0-SNAPSHOT.jar to class loader
21/02/20 18:36:03 INFO Utils: Successfully started service 'org.apache.spark.network.netty.NettyBlockTransferService' on port 34729.
21/02/20 18:36:03 INFO NettyBlockTransferService: Server created on 192.168.10.31:34729
21/02/20 18:36:03 INFO BlockManager: Using org.apache.spark.storage.RandomBlockReplicationPolicy for block replication policy
21/02/20 18:36:03 INFO BlockManagerMaster: Registering BlockManager BlockManagerId(driver, 192.168.10.31, 34729, None)
21/02/20 18:36:03 INFO BlockManagerMasterEndpoint: Registering block manager 192.168.10.31:34729 with 408.9 MiB RAM, BlockManagerId(driver, 192.168.10.31, 34729, None)
21/02/20 18:36:03 INFO BlockManagerMaster: Registered BlockManager BlockManagerId(driver, 192.168.10.31, 34729, None)
21/02/20 18:36:03 INFO BlockManager: Initialized BlockManager: BlockManagerId(driver, 192.168.10.31, 34729, None)
21/02/20 18:36:03 INFO ADAMContext: Loading mouse_chrM.bam.reads.adam as Parquet of Alignments.
21/02/20 18:36:05 INFO ADAMContext: Reading the ADAM file at mouse_chrM.bam.reads.adam to create RDD
21/02/20 18:36:05 INFO MemoryStore: Block broadcast_0 stored as values in memory (estimated size 333.7 KiB, free 408.6 MiB)
21/02/20 18:36:06 INFO MemoryStore: Block broadcast_0_piece0 stored as bytes in memory (estimated size 31.0 KiB, free 408.5 MiB)
21/02/20 18:36:06 INFO BlockManagerInfo: Added broadcast_0_piece0 in memory on 192.168.10.31:34729 (size: 31.0 KiB, free: 408.9 MiB)
21/02/20 18:36:06 INFO SparkContext: Created broadcast 0 from newAPIHadoopFile at ADAMContext.scala:1797
21/02/20 18:36:06 INFO FileInputFormat: Total input files to process : 1
21/02/20 18:36:06 INFO ParquetInputFormat: Total input paths to process : 1
21/02/20 18:36:06 INFO RDDBoundFragmentDataset: Saving data in ADAM format
21/02/20 18:36:06 INFO FileOutputCommitter: File Output Committer Algorithm version is 1
21/02/20 18:36:06 INFO FileOutputCommitter: FileOutputCommitter skip cleanup _temporary folders under output directory:false, ignore cleanup failures: false
21/02/20 18:36:06 INFO SparkContext: Starting job: runJob at SparkHadoopWriter.scala:83
21/02/20 18:36:06 INFO DAGScheduler: Registering RDD 2 (groupBy at SingleReadBucket.scala:97) as input to shuffle 0
21/02/20 18:36:06 INFO DAGScheduler: Got job 0 (runJob at SparkHadoopWriter.scala:83) with 1 output partitions
21/02/20 18:36:06 INFO DAGScheduler: Final stage: ResultStage 1 (runJob at SparkHadoopWriter.scala:83)
21/02/20 18:36:06 INFO DAGScheduler: Parents of final stage: List(ShuffleMapStage 0)
21/02/20 18:36:06 INFO DAGScheduler: Missing parents: List(ShuffleMapStage 0)
21/02/20 18:36:06 INFO DAGScheduler: Submitting ShuffleMapStage 0 (MapPartitionsRDD[2] at groupBy at SingleReadBucket.scala:97), which has no missing parents
21/02/20 18:36:06 INFO MemoryStore: Block broadcast_1 stored as values in memory (estimated size 7.4 KiB, free 408.5 MiB)
21/02/20 18:36:06 INFO MemoryStore: Block broadcast_1_piece0 stored as bytes in memory (estimated size 4.0 KiB, free 408.5 MiB)
21/02/20 18:36:06 INFO BlockManagerInfo: Added broadcast_1_piece0 in memory on 192.168.10.31:34729 (size: 4.0 KiB, free: 408.9 MiB)
21/02/20 18:36:06 INFO SparkContext: Created broadcast 1 from broadcast at DAGScheduler.scala:1223
21/02/20 18:36:06 INFO DAGScheduler: Submitting 1 missing tasks from ShuffleMapStage 0 (MapPartitionsRDD[2] at groupBy at SingleReadBucket.scala:97) (first 15 tasks are for partitions Vector(0))
21/02/20 18:36:06 INFO TaskSchedulerImpl: Adding task set 0.0 with 1 tasks
21/02/20 18:36:06 INFO TaskSetManager: Starting task 0.0 in stage 0.0 (TID 0, 192.168.10.31, executor driver, partition 0, PROCESS_LOCAL, 7482 bytes)
21/02/20 18:36:06 INFO Executor: Running task 0.0 in stage 0.0 (TID 0)
21/02/20 18:36:07 INFO NewHadoopRDD: Input split: file:/tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/mouse_chrM.bam.reads.adam/part-r-00000.gz.parquet:0+10132211
21/02/20 18:36:07 INFO InternalParquetRecordReader: RecordReader initialized will read a total of 163064 records.
21/02/20 18:36:07 INFO InternalParquetRecordReader: at row 0. reading next block
21/02/20 18:36:07 INFO CodecPool: Got brand-new decompressor [.gz]
21/02/20 18:36:07 INFO InternalParquetRecordReader: block read in memory in 45 ms. row count = 163064
21/02/20 18:36:10 INFO Executor: Finished task 0.0 in stage 0.0 (TID 0). 1086 bytes result sent to driver
21/02/20 18:36:10 INFO TaskSetManager: Finished task 0.0 in stage 0.0 (TID 0) in 3316 ms on 192.168.10.31 (executor driver) (1/1)
21/02/20 18:36:10 INFO TaskSchedulerImpl: Removed TaskSet 0.0, whose tasks have all completed, from pool 
21/02/20 18:36:10 INFO DAGScheduler: ShuffleMapStage 0 (groupBy at SingleReadBucket.scala:97) finished in 3.437 s
21/02/20 18:36:10 INFO DAGScheduler: looking for newly runnable stages
21/02/20 18:36:10 INFO DAGScheduler: running: Set()
21/02/20 18:36:10 INFO DAGScheduler: waiting: Set(ResultStage 1)
21/02/20 18:36:10 INFO DAGScheduler: failed: Set()
21/02/20 18:36:10 INFO DAGScheduler: Submitting ResultStage 1 (MapPartitionsRDD[6] at map at GenomicDataset.scala:3805), which has no missing parents
21/02/20 18:36:10 INFO MemoryStore: Block broadcast_2 stored as values in memory (estimated size 100.8 KiB, free 408.4 MiB)
21/02/20 18:36:10 INFO MemoryStore: Block broadcast_2_piece0 stored as bytes in memory (estimated size 37.8 KiB, free 408.4 MiB)
21/02/20 18:36:10 INFO BlockManagerInfo: Added broadcast_2_piece0 in memory on 192.168.10.31:34729 (size: 37.8 KiB, free: 408.8 MiB)
21/02/20 18:36:10 INFO SparkContext: Created broadcast 2 from broadcast at DAGScheduler.scala:1223
21/02/20 18:36:10 INFO DAGScheduler: Submitting 1 missing tasks from ResultStage 1 (MapPartitionsRDD[6] at map at GenomicDataset.scala:3805) (first 15 tasks are for partitions Vector(0))
21/02/20 18:36:10 INFO TaskSchedulerImpl: Adding task set 1.0 with 1 tasks
21/02/20 18:36:10 INFO TaskSetManager: Starting task 0.0 in stage 1.0 (TID 1, 192.168.10.31, executor driver, partition 0, NODE_LOCAL, 7143 bytes)
21/02/20 18:36:10 INFO Executor: Running task 0.0 in stage 1.0 (TID 1)
21/02/20 18:36:10 INFO ShuffleBlockFetcherIterator: Getting 1 (26.9 MiB) non-empty blocks including 1 (26.9 MiB) local and 0 (0.0 B) host-local and 0 (0.0 B) remote blocks
21/02/20 18:36:10 INFO ShuffleBlockFetcherIterator: Started 0 remote fetches in 10 ms
21/02/20 18:36:11 INFO FileOutputCommitter: File Output Committer Algorithm version is 1
21/02/20 18:36:11 INFO FileOutputCommitter: FileOutputCommitter skip cleanup _temporary folders under output directory:false, ignore cleanup failures: false
21/02/20 18:36:11 INFO CodecConfig: Compression: GZIP
21/02/20 18:36:11 INFO FileOutputCommitter: File Output Committer Algorithm version is 1
21/02/20 18:36:11 INFO FileOutputCommitter: FileOutputCommitter skip cleanup _temporary folders under output directory:false, ignore cleanup failures: false
21/02/20 18:36:11 INFO ParquetOutputFormat: Parquet block size to 134217728
21/02/20 18:36:11 INFO ParquetOutputFormat: Parquet page size to 1048576
21/02/20 18:36:11 INFO ParquetOutputFormat: Parquet dictionary page size to 1048576
21/02/20 18:36:11 INFO ParquetOutputFormat: Dictionary is on
21/02/20 18:36:11 INFO ParquetOutputFormat: Validation is off
21/02/20 18:36:11 INFO ParquetOutputFormat: Writer version is: PARQUET_1_0
21/02/20 18:36:11 INFO ParquetOutputFormat: Maximum row group padding size is 8388608 bytes
21/02/20 18:36:11 INFO ParquetOutputFormat: Page size checking is: estimated
21/02/20 18:36:11 INFO ParquetOutputFormat: Min row count for page size check is: 100
21/02/20 18:36:11 INFO ParquetOutputFormat: Max row count for page size check is: 10000
21/02/20 18:36:11 INFO CodecPool: Got brand-new compressor [.gz]
21/02/20 18:36:14 INFO BlockManagerInfo: Removed broadcast_1_piece0 on 192.168.10.31:34729 in memory (size: 4.0 KiB, free: 408.8 MiB)
21/02/20 18:36:17 INFO InternalParquetRecordWriter: Flushing mem columnStore to file. allocated memory: 21417928
21/02/20 18:36:17 INFO FileOutputCommitter: Saved output of task 'attempt_202102201836064201166533631868665_0006_r_000000_0' to file:/tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/mouse_chrM.bam.fragments.adam/_temporary/0/task_202102201836064201166533631868665_0006_r_000000
21/02/20 18:36:17 INFO SparkHadoopMapRedUtil: attempt_202102201836064201166533631868665_0006_r_000000_0: Committed
21/02/20 18:36:17 INFO Executor: Finished task 0.0 in stage 1.0 (TID 1). 1365 bytes result sent to driver
21/02/20 18:36:17 INFO TaskSetManager: Finished task 0.0 in stage 1.0 (TID 1) in 7311 ms on 192.168.10.31 (executor driver) (1/1)
21/02/20 18:36:17 INFO TaskSchedulerImpl: Removed TaskSet 1.0, whose tasks have all completed, from pool 
21/02/20 18:36:17 INFO DAGScheduler: ResultStage 1 (runJob at SparkHadoopWriter.scala:83) finished in 7.345 s
21/02/20 18:36:17 INFO DAGScheduler: Job 0 is finished. Cancelling potential speculative or zombie tasks for this job
21/02/20 18:36:17 INFO TaskSchedulerImpl: Killing all running tasks in stage 1: Stage finished
21/02/20 18:36:17 INFO DAGScheduler: Job 0 finished: runJob at SparkHadoopWriter.scala:83, took 10.859016 s
21/02/20 18:36:17 INFO ParquetFileReader: Initiating action with parallelism: 5
21/02/20 18:36:17 INFO SparkHadoopWriter: Job job_202102201836064201166533631868665_0006 committed.
21/02/20 18:36:17 INFO SparkContext: Invoking stop() from shutdown hook
21/02/20 18:36:17 INFO SparkUI: Stopped Spark web UI at http://192.168.10.31:4040
21/02/20 18:36:17 INFO MapOutputTrackerMasterEndpoint: MapOutputTrackerMasterEndpoint stopped!
21/02/20 18:36:17 INFO MemoryStore: MemoryStore cleared
21/02/20 18:36:17 INFO BlockManager: BlockManager stopped
21/02/20 18:36:17 INFO BlockManagerMaster: BlockManagerMaster stopped
21/02/20 18:36:17 INFO OutputCommitCoordinator$OutputCommitCoordinatorEndpoint: OutputCommitCoordinator stopped!
21/02/20 18:36:17 INFO SparkContext: Successfully stopped SparkContext
21/02/20 18:36:17 INFO ShutdownHookManager: Shutdown hook called
21/02/20 18:36:17 INFO ShutdownHookManager: Deleting directory /tmp/spark-9aeeb1aa-f85a-465a-a1cd-66b40236342a
21/02/20 18:36:17 INFO ShutdownHookManager: Deleting directory /tmp/spark-7e3b0650-c08c-44bb-82fb-33ed4be4a77e

# test that printing works
echo "Printing reads and fragments"
+ echo 'Printing reads and fragments'
Printing reads and fragments
${ADAM} print ${READS} 1>/dev/null 2>/dev/null
+ ./bin/adam-submit print mouse_chrM.bam.reads.adam
${ADAM} print ${FRAGMENTS} 1>/dev/null 2>/dev/null
+ ./bin/adam-submit print mouse_chrM.bam.fragments.adam

# run flagstat to verify that flagstat runs OK
echo "Printing read statistics"
+ echo 'Printing read statistics'
Printing read statistics
${ADAM} flagstat ${READS}
+ ./bin/adam-submit flagstat mouse_chrM.bam.reads.adam
Using ADAM_MAIN=org.bdgenomics.adam.cli.ADAMMain
Using spark-submit=/tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.2-bin-hadoop3.2/bin/spark-submit
21/02/20 18:36:36 WARN Utils: Your hostname, research-jenkins-worker-09 resolves to a loopback address: 127.0.1.1; using 192.168.10.31 instead (on interface enp4s0f0)
21/02/20 18:36:36 WARN Utils: Set SPARK_LOCAL_IP if you need to bind to another address
21/02/20 18:36:36 WARN NativeCodeLoader: Unable to load native-hadoop library for your platform... using builtin-java classes where applicable
log4j:WARN No appenders could be found for logger (org.bdgenomics.adam.cli.ADAMMain).
log4j:WARN Please initialize the log4j system properly.
log4j:WARN See http://logging.apache.org/log4j/1.2/faq.html#noconfig for more info.
Using Spark's default log4j profile: org/apache/spark/log4j-defaults.properties
21/02/20 18:36:36 INFO SparkContext: Running Spark version 3.0.2
21/02/20 18:36:37 INFO ResourceUtils: ==============================================================
21/02/20 18:36:37 INFO ResourceUtils: Resources for spark.driver:

21/02/20 18:36:37 INFO ResourceUtils: ==============================================================
21/02/20 18:36:37 INFO SparkContext: Submitted application: flagstat
21/02/20 18:36:37 INFO SecurityManager: Changing view acls to: jenkins
21/02/20 18:36:37 INFO SecurityManager: Changing modify acls to: jenkins
21/02/20 18:36:37 INFO SecurityManager: Changing view acls groups to: 
21/02/20 18:36:37 INFO SecurityManager: Changing modify acls groups to: 
21/02/20 18:36:37 INFO SecurityManager: SecurityManager: authentication disabled; ui acls disabled; users  with view permissions: Set(jenkins); groups with view permissions: Set(); users  with modify permissions: Set(jenkins); groups with modify permissions: Set()
21/02/20 18:36:37 INFO Utils: Successfully started service 'sparkDriver' on port 38563.
21/02/20 18:36:37 INFO SparkEnv: Registering MapOutputTracker
21/02/20 18:36:37 INFO SparkEnv: Registering BlockManagerMaster
21/02/20 18:36:37 INFO BlockManagerMasterEndpoint: Using org.apache.spark.storage.DefaultTopologyMapper for getting topology information
21/02/20 18:36:37 INFO BlockManagerMasterEndpoint: BlockManagerMasterEndpoint up
21/02/20 18:36:37 INFO SparkEnv: Registering BlockManagerMasterHeartbeat
21/02/20 18:36:37 INFO DiskBlockManager: Created local directory at /tmp/blockmgr-d62970a7-2fec-49b3-9c85-52a643008ce3
21/02/20 18:36:37 INFO MemoryStore: MemoryStore started with capacity 408.9 MiB
21/02/20 18:36:37 INFO SparkEnv: Registering OutputCommitCoordinator
21/02/20 18:36:37 INFO Utils: Successfully started service 'SparkUI' on port 4040.
21/02/20 18:36:37 INFO SparkUI: Bound SparkUI to 0.0.0.0, and started at http://192.168.10.31:4040
21/02/20 18:36:37 INFO SparkContext: Added JAR file:/tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/target/adam-assembly-spark3_2.12-0.34.0-SNAPSHOT.jar at spark://192.168.10.31:38563/jars/adam-assembly-spark3_2.12-0.34.0-SNAPSHOT.jar with timestamp 1613874996946
21/02/20 18:36:37 INFO Executor: Starting executor ID driver on host 192.168.10.31
21/02/20 18:36:37 INFO Executor: Fetching spark://192.168.10.31:38563/jars/adam-assembly-spark3_2.12-0.34.0-SNAPSHOT.jar with timestamp 1613874996946
21/02/20 18:36:38 INFO TransportClientFactory: Successfully created connection to /192.168.10.31:38563 after 42 ms (0 ms spent in bootstraps)
21/02/20 18:36:38 INFO Utils: Fetching spark://192.168.10.31:38563/jars/adam-assembly-spark3_2.12-0.34.0-SNAPSHOT.jar to /tmp/spark-37ea932d-58dc-43e8-9c87-9e318ef8d473/userFiles-ead5dd42-95b6-4ca4-84c1-53fc229ceec4/fetchFileTemp4804108476542870706.tmp
21/02/20 18:36:38 INFO Executor: Adding file:/tmp/spark-37ea932d-58dc-43e8-9c87-9e318ef8d473/userFiles-ead5dd42-95b6-4ca4-84c1-53fc229ceec4/adam-assembly-spark3_2.12-0.34.0-SNAPSHOT.jar to class loader
21/02/20 18:36:38 INFO Utils: Successfully started service 'org.apache.spark.network.netty.NettyBlockTransferService' on port 34019.
21/02/20 18:36:38 INFO NettyBlockTransferService: Server created on 192.168.10.31:34019
21/02/20 18:36:38 INFO BlockManager: Using org.apache.spark.storage.RandomBlockReplicationPolicy for block replication policy
21/02/20 18:36:38 INFO BlockManagerMaster: Registering BlockManager BlockManagerId(driver, 192.168.10.31, 34019, None)
21/02/20 18:36:38 INFO BlockManagerMasterEndpoint: Registering block manager 192.168.10.31:34019 with 408.9 MiB RAM, BlockManagerId(driver, 192.168.10.31, 34019, None)
21/02/20 18:36:38 INFO BlockManagerMaster: Registered BlockManager BlockManagerId(driver, 192.168.10.31, 34019, None)
21/02/20 18:36:38 INFO BlockManager: Initialized BlockManager: BlockManagerId(driver, 192.168.10.31, 34019, None)
21/02/20 18:36:38 INFO ADAMContext: Loading mouse_chrM.bam.reads.adam as Parquet of Alignments.
21/02/20 18:36:39 INFO ADAMContext: Reading the ADAM file at mouse_chrM.bam.reads.adam to create RDD
21/02/20 18:36:39 INFO ADAMContext: Using the specified projection schema
21/02/20 18:36:39 INFO MemoryStore: Block broadcast_0 stored as values in memory (estimated size 338.3 KiB, free 408.6 MiB)
21/02/20 18:36:40 INFO MemoryStore: Block broadcast_0_piece0 stored as bytes in memory (estimated size 31.8 KiB, free 408.5 MiB)
21/02/20 18:36:40 INFO BlockManagerInfo: Added broadcast_0_piece0 in memory on 192.168.10.31:34019 (size: 31.8 KiB, free: 408.9 MiB)
21/02/20 18:36:40 INFO SparkContext: Created broadcast 0 from newAPIHadoopFile at ADAMContext.scala:1797
21/02/20 18:36:41 INFO FileInputFormat: Total input files to process : 1
21/02/20 18:36:41 INFO ParquetInputFormat: Total input paths to process : 1
21/02/20 18:36:41 INFO SparkContext: Starting job: aggregate at FlagStat.scala:115
21/02/20 18:36:41 INFO DAGScheduler: Got job 0 (aggregate at FlagStat.scala:115) with 1 output partitions
21/02/20 18:36:41 INFO DAGScheduler: Final stage: ResultStage 0 (aggregate at FlagStat.scala:115)
21/02/20 18:36:41 INFO DAGScheduler: Parents of final stage: List()
21/02/20 18:36:41 INFO DAGScheduler: Missing parents: List()
21/02/20 18:36:41 INFO DAGScheduler: Submitting ResultStage 0 (MapPartitionsRDD[2] at map at FlagStat.scala:96), which has no missing parents
21/02/20 18:36:41 INFO MemoryStore: Block broadcast_1 stored as values in memory (estimated size 5.3 KiB, free 408.5 MiB)
21/02/20 18:36:41 INFO MemoryStore: Block broadcast_1_piece0 stored as bytes in memory (estimated size 2.9 KiB, free 408.5 MiB)
21/02/20 18:36:41 INFO BlockManagerInfo: Added broadcast_1_piece0 in memory on 192.168.10.31:34019 (size: 2.9 KiB, free: 408.9 MiB)
21/02/20 18:36:41 INFO SparkContext: Created broadcast 1 from broadcast at DAGScheduler.scala:1223
21/02/20 18:36:41 INFO DAGScheduler: Submitting 1 missing tasks from ResultStage 0 (MapPartitionsRDD[2] at map at FlagStat.scala:96) (first 15 tasks are for partitions Vector(0))
21/02/20 18:36:41 INFO TaskSchedulerImpl: Adding task set 0.0 with 1 tasks
21/02/20 18:36:41 INFO TaskSetManager: Starting task 0.0 in stage 0.0 (TID 0, 192.168.10.31, executor driver, partition 0, PROCESS_LOCAL, 7493 bytes)
21/02/20 18:36:41 INFO Executor: Running task 0.0 in stage 0.0 (TID 0)
21/02/20 18:36:41 INFO NewHadoopRDD: Input split: file:/tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/mouse_chrM.bam.reads.adam/part-r-00000.gz.parquet:0+10132211
21/02/20 18:36:41 INFO InternalParquetRecordReader: RecordReader initialized will read a total of 163064 records.
21/02/20 18:36:41 INFO InternalParquetRecordReader: at row 0. reading next block
21/02/20 18:36:41 INFO CodecPool: Got brand-new decompressor [.gz]
21/02/20 18:36:41 INFO InternalParquetRecordReader: block read in memory in 21 ms. row count = 163064
21/02/20 18:36:42 INFO Executor: Finished task 0.0 in stage 0.0 (TID 0). 988 bytes result sent to driver
21/02/20 18:36:42 INFO TaskSetManager: Finished task 0.0 in stage 0.0 (TID 0) in 1166 ms on 192.168.10.31 (executor driver) (1/1)
21/02/20 18:36:42 INFO TaskSchedulerImpl: Removed TaskSet 0.0, whose tasks have all completed, from pool 
21/02/20 18:36:42 INFO DAGScheduler: ResultStage 0 (aggregate at FlagStat.scala:115) finished in 1.272 s
21/02/20 18:36:42 INFO DAGScheduler: Job 0 is finished. Cancelling potential speculative or zombie tasks for this job
21/02/20 18:36:42 INFO TaskSchedulerImpl: Killing all running tasks in stage 0: Stage finished
21/02/20 18:36:42 INFO DAGScheduler: Job 0 finished: aggregate at FlagStat.scala:115, took 1.327746 s
163064 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 primary duplicates
0 + 0 primary duplicates - both read and mate mapped
0 + 0 primary duplicates - only read mapped
0 + 0 primary duplicates - cross chromosome
0 + 0 secondary duplicates
0 + 0 secondary duplicates - both read and mate mapped
0 + 0 secondary duplicates - only read mapped
0 + 0 secondary duplicates - cross chromosome
160512 + 0 mapped (98.43%:0.00%)
163064 + 0 paired in sequencing
81524 + 0 read1
81540 + 0 read2
154982 + 0 properly paired (95.04%:0.00%)
158044 + 0 with itself and mate mapped
2468 + 0 singletons (1.51%:0.00%)
418 + 0 with mate mapped to a different chr
120 + 0 with mate mapped to a different chr (mapQ>=5)
21/02/20 18:36:42 INFO SparkContext: Invoking stop() from shutdown hook
21/02/20 18:36:42 INFO SparkUI: Stopped Spark web UI at http://192.168.10.31:4040
21/02/20 18:36:42 INFO BlockManagerInfo: Removed broadcast_1_piece0 on 192.168.10.31:34019 in memory (size: 2.9 KiB, free: 408.9 MiB)
21/02/20 18:36:42 INFO MapOutputTrackerMasterEndpoint: MapOutputTrackerMasterEndpoint stopped!
21/02/20 18:36:42 INFO MemoryStore: MemoryStore cleared
21/02/20 18:36:42 INFO BlockManager: BlockManager stopped
21/02/20 18:36:42 INFO BlockManagerMaster: BlockManagerMaster stopped
21/02/20 18:36:42 INFO OutputCommitCoordinator$OutputCommitCoordinatorEndpoint: OutputCommitCoordinator stopped!
21/02/20 18:36:42 INFO SparkContext: Successfully stopped SparkContext
21/02/20 18:36:42 INFO ShutdownHookManager: Shutdown hook called
21/02/20 18:36:42 INFO ShutdownHookManager: Deleting directory /tmp/spark-37ea932d-58dc-43e8-9c87-9e318ef8d473
21/02/20 18:36:42 INFO ShutdownHookManager: Deleting directory /tmp/spark-c4e70078-ca6f-49b0-b72e-54b063fae2a6
rm -rf ${ADAM_TMP_DIR}
+ rm -rf /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded
popd
+ popd
~/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu

pushd ${PROJECT_ROOT}
+ pushd /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/scripts/..
~/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu ~/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu

# test that the source is formatted correctly
./scripts/format-source
+ ./scripts/format-source
+++ dirname ./scripts/format-source
++ cd ./scripts
++ pwd
+ DIR=/home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/scripts
+ pushd /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/scripts/..
~/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu ~/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu
+ mvn org.scalariform:scalariform-maven-plugin:format license:format
OpenJDK 64-Bit Server VM warning: ignoring option MaxPermSize=1g; support was removed in 8.0
[INFO] Scanning for projects...
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Build Order:
[INFO] 
[INFO] ADAM_2.12                                                          [pom]
[INFO] ADAM_2.12: Shader workaround                                       [jar]
[INFO] ADAM_2.12: Avro-to-Dataset codegen utils                           [jar]
[INFO] ADAM_2.12: Core                                                    [jar]
[INFO] ADAM_2.12: APIs for Java, Python                                   [jar]
[INFO] ADAM_2.12: CLI                                                     [jar]
[INFO] ADAM_2.12: Assembly                                                [jar]
[INFO] 
[INFO] ------------< org.bdgenomics.adam:adam-parent-spark3_2.12 >-------------
[INFO] Building ADAM_2.12 0.34.0-SNAPSHOT                                 [1/7]
[INFO] --------------------------------[ pom ]---------------------------------
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ adam-parent-spark3_2.12 ---
[INFO] Modified 2 of 245 .scala files
[INFO] 
[INFO] --- maven-license-plugin:1.10.b1:format (default-cli) @ adam-parent-spark3_2.12 ---
[INFO] Updating license headers...
[INFO] 
[INFO] -------------< org.bdgenomics.adam:adam-shade-spark3_2.12 >-------------
[INFO] Building ADAM_2.12: Shader workaround 0.34.0-SNAPSHOT              [2/7]
[INFO] --------------------------------[ jar ]---------------------------------
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ adam-shade-spark3_2.12 ---
[INFO] Modified 0 of 0 .scala files
[INFO] 
[INFO] --- maven-license-plugin:1.10.b1:format (default-cli) @ adam-shade-spark3_2.12 ---
[INFO] Updating license headers...
[INFO] 
[INFO] ------------< org.bdgenomics.adam:adam-codegen-spark3_2.12 >------------
[INFO] Building ADAM_2.12: Avro-to-Dataset codegen utils 0.34.0-SNAPSHOT  [3/7]
[INFO] --------------------------------[ jar ]---------------------------------
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ adam-codegen-spark3_2.12 ---
[INFO] Modified 0 of 4 .scala files
[INFO] 
[INFO] --- maven-license-plugin:1.10.b1:format (default-cli) @ adam-codegen-spark3_2.12 ---
[INFO] Updating license headers...
[INFO] 
[INFO] -------------< org.bdgenomics.adam:adam-core-spark3_2.12 >--------------
[INFO] Building ADAM_2.12: Core 0.34.0-SNAPSHOT                           [4/7]
[INFO] --------------------------------[ jar ]---------------------------------
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ adam-core-spark3_2.12 ---
[INFO] Modified 0 of 204 .scala files
[INFO] 
[INFO] --- maven-license-plugin:1.10.b1:format (default-cli) @ adam-core-spark3_2.12 ---
[INFO] Updating license headers...
[INFO] 
[INFO] -------------< org.bdgenomics.adam:adam-apis-spark3_2.12 >--------------
[INFO] Building ADAM_2.12: APIs for Java, Python 0.34.0-SNAPSHOT          [5/7]
[INFO] --------------------------------[ jar ]---------------------------------
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ adam-apis-spark3_2.12 ---
[INFO] Modified 0 of 5 .scala files
[INFO] 
[INFO] --- maven-license-plugin:1.10.b1:format (default-cli) @ adam-apis-spark3_2.12 ---
[INFO] Updating license headers...
[INFO] 
[INFO] --------------< org.bdgenomics.adam:adam-cli-spark3_2.12 >--------------
[INFO] Building ADAM_2.12: CLI 0.34.0-SNAPSHOT                            [6/7]
[INFO] --------------------------------[ jar ]---------------------------------
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ adam-cli-spark3_2.12 ---
[INFO] Modified 0 of 30 .scala files
[INFO] 
[INFO] --- maven-license-plugin:1.10.b1:format (default-cli) @ adam-cli-spark3_2.12 ---
[INFO] Updating license headers...
[INFO] 
[INFO] -----------< org.bdgenomics.adam:adam-assembly-spark3_2.12 >------------
[INFO] Building ADAM_2.12: Assembly 0.34.0-SNAPSHOT                       [7/7]
[INFO] --------------------------------[ jar ]---------------------------------
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ adam-assembly-spark3_2.12 ---
[INFO] Modified 0 of 1 .scala files
[INFO] 
[INFO] --- maven-license-plugin:1.10.b1:format (default-cli) @ adam-assembly-spark3_2.12 ---
[INFO] Updating license headers...
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary for ADAM_2.12 0.34.0-SNAPSHOT:
[INFO] 
[INFO] ADAM_2.12 .......................................... SUCCESS [  5.598 s]
[INFO] ADAM_2.12: Shader workaround ....................... SUCCESS [  0.030 s]
[INFO] ADAM_2.12: Avro-to-Dataset codegen utils ........... SUCCESS [  0.045 s]
[INFO] ADAM_2.12: Core .................................... SUCCESS [  2.678 s]
[INFO] ADAM_2.12: APIs for Java, Python ................... SUCCESS [  0.138 s]
[INFO] ADAM_2.12: CLI ..................................... SUCCESS [  0.215 s]
[INFO] ADAM_2.12: Assembly ................................ SUCCESS [  0.017 s]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time:  9.207 s
[INFO] Finished at: 2021-02-20T18:36:53-08:00
[INFO] ------------------------------------------------------------------------
+ popd
~/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu
if test -n "$(git status --porcelain)"
then
    echo "Please run './scripts/format-source'"
    exit 1
fi
git status --porcelain
++ git status --porcelain
+ test -n ''
popd    
+ popd
~/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu

echo
+ echo

echo "All the tests passed"
+ echo 'All the tests passed'
All the tests passed
echo
+ echo

Recording test results
[Checks API] No suitable checks publisher found.
[Set GitHub commit status (universal)] SUCCESS on repos [] (sha:fc9b1cf) with context:ADAM-prb/HADOOP_VERSION=3.2.1,SCALA_VERSION=2.12,SPARK_VERSION=3.0.2,label=ubuntu
Finished: SUCCESS