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[WARNING] Entry: adam-distribution-spark2_2.11-0.32.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/FragmentsToReadsConverter.html longer than 100 characters.
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[WARNING] Entry: adam-distribution-spark2_2.11-0.32.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/VariantsToAlignmentsDatasetConverter.html longer than 100 characters.
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[WARNING] Entry: adam-distribution-spark2_2.11-0.32.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/ReadsToGenotypesDatasetConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.32.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/FeaturesToFragmentsConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.32.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/SequencesToReadsConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.32.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/ReadsToAlignmentsDatasetConverter.html longer than 100 characters.
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[WARNING] Entry: adam-distribution-spark2_2.11-0.32.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/VariantsToReadsConverter.html longer than 100 characters.
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[WARNING] Entry: adam-distribution-spark2_2.11-0.32.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/GenotypesToSlicesDatasetConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.32.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/SequencesToAlignmentsDatasetConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.32.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/ReadsToSequencesConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.32.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/VariantContextsToVariantsConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.32.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/SlicesToVariantsConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.32.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/SlicesToAlignmentsDatasetConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.32.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/VariantContextsToFragmentsConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.32.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/JavaADAMContext$.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.32.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/SlicesToReadsConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.32.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/SlicesToFragmentsDatasetConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.32.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/ToAlignmentDatasetConversion.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.32.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/ReadsToSlicesDatasetConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.32.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/AlignmentsToReadsConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.32.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/VariantContextsToReadsConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.32.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/SequencesToGenotypesConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.32.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/cli/MergeShardsArgs.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.32.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/cli/TransformSequences$.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.32.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/cli/TransformVariants.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.32.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/cli/TransformGenotypesArgs.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.32.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/cli/TransformAlignments$.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.32.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/cli/CountSliceKmers$.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.32.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/cli/TransformFragments.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.32.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/cli/TransformAlignmentsArgs.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.32.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/cli/TransformFragmentsArgs.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.32.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/cli/TransformSlicesArgs.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.32.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/cli/TransformFeatures$.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.32.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/cli/CountSliceKmers.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.32.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/cli/TransformFeaturesArgs.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.32.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/cli/TransformSlices.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.32.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/cli/TransformFragments$.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.32.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/cli/TransformSequences.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.32.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/cli/TransformAlignments.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.32.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/cli/TransformGenotypes$.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.32.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/cli/TransformGenotypes.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.32.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/cli/CountSliceKmersArgs.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.32.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/cli/TransformVariants$.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.32.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/cli/CountReadKmers$.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.32.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/cli/TransformSequencesArgs.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.32.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/cli/TransformFeatures.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.32.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/cli/CountReadKmersArgs.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.32.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/cli/TransformSlices$.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.32.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/cli/TransformVariantsArgs.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.32.0-SNAPSHOT/repo/adam-assembly-spark2_2.11-0.32.0-SNAPSHOT-sources.jar longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.32.0-SNAPSHOT/repo/adam-assembly-spark2_2.11-0.32.0-SNAPSHOT-javadoc.jar longer than 100 characters.
[INFO] Building zip: /tmp/adamTesttnQQnB7/deleteMePleaseThisIsNoLongerNeeded/adam-distribution/target/adam-distribution-spark2_2.11-0.32.0-SNAPSHOT-bin.zip
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary:
[INFO] 
[INFO] ADAM_2.11 .......................................... SUCCESS [  8.917 s]
[INFO] ADAM_2.11: Shader workaround ....................... SUCCESS [  4.404 s]
[INFO] ADAM_2.11: Avro-to-Dataset codegen utils ........... SUCCESS [  3.994 s]
[INFO] ADAM_2.11: Core .................................... SUCCESS [01:16 min]
[INFO] ADAM_2.11: APIs for Java, Python ................... SUCCESS [  8.140 s]
[INFO] ADAM_2.11: CLI ..................................... SUCCESS [ 10.205 s]
[INFO] ADAM_2.11: Assembly ................................ SUCCESS [ 17.921 s]
[INFO] ADAM_2.11: Python APIs ............................. SUCCESS [01:16 min]
[INFO] ADAM_2.11: R APIs .................................. SUCCESS [01:01 min]
[INFO] ADAM_2.11: Distribution ............................ SUCCESS [ 38.746 s]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 05:07 min
[INFO] Finished at: 2020-03-04T13:28:05-08:00
[INFO] Final Memory: 61M/1494M
[INFO] ------------------------------------------------------------------------
+ grep bdgenomics.adam
+ tar tzvf adam-distribution/target/adam-distribution-spark2_2.11-0.32.0-SNAPSHOT-bin.tar.gz
+ grep egg
drwxrwxr-x jenkins/jenkins        0 2020-03-04 13:25 adam-distribution-spark2_2.11-0.32.0-SNAPSHOT/r/bdgenomics.adam.egg-info/
-rw-r--r-- jenkins/jenkins 39613807 2020-03-04 13:25 adam-distribution-spark2_2.11-0.32.0-SNAPSHOT/repo/bdgenomics.adam-0.32.0a0-py3.6.egg
+ ./bin/pyadam
Using PYSPARK=/tmp/adamTesttnQQnB7/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.5-bin-hadoop2.7/bin/pyspark
2020-03-04 13:28:08 WARN  Utils:66 - Your hostname, ubuntu-testing resolves to a loopback address: 127.0.1.1; using 192.168.10.30 instead (on interface eno1)
2020-03-04 13:28:08 WARN  Utils:66 - Set SPARK_LOCAL_IP if you need to bind to another address
2020-03-04 13:28:08 WARN  NativeCodeLoader:62 - 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).
2020-03-04 13:28:14 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.

[Stage 0:>                                                          (0 + 1) / 1]
                                                                                
+ source deactivate
#!/bin/sh
_CONDA_ROOT="/home/jenkins/anaconda2"
++ _CONDA_ROOT=/home/jenkins/anaconda2
\. "$_CONDA_ROOT/etc/profile.d/conda.sh" || return $?
++ . /home/jenkins/anaconda2/etc/profile.d/conda.sh
_CONDA_EXE="/home/jenkins/anaconda2/bin/conda"
+++ _CONDA_EXE=/home/jenkins/anaconda2/bin/conda
_CONDA_ROOT="/home/jenkins/anaconda2"
+++ _CONDA_ROOT=/home/jenkins/anaconda2
_conda_set_vars() {
    # set _CONDA_SHELL_FLAVOR
    if [ -n "${BASH_VERSION:+x}" ]; then
        _CONDA_SHELL_FLAVOR=bash
    elif [ -n "${ZSH_VERSION:+x}" ]; then
        _CONDA_SHELL_FLAVOR=zsh
    elif [ -n "${KSH_VERSION:+x}" ]; then
        _CONDA_SHELL_FLAVOR=ksh
    elif [ -n "${POSH_VERSION:+x}" ]; then
        _CONDA_SHELL_FLAVOR=posh
    else
        # default to dash; if we run into a problem here, please raise an issue
        _CONDA_SHELL_FLAVOR=dash
    fi

    if [ -z "${_CONDA_EXE+x}" ]; then
        if [ -n "${_CONDA_ROOT:+x}" ]; then
            # typically this should be for dev only; _CONDA_EXE should be written at top of file
            # for normal installs
            _CONDA_EXE="$_CONDA_ROOT/conda/shell/bin/conda"
        fi
        if ! [ -f "${_CONDA_EXE-x}" ]; then
            _CONDA_EXE="$PWD/conda/shell/bin/conda"
        fi
    fi

    # We're not allowing PS1 to be unbound. It must at least be set.
    # However, we're not exporting it, which can cause problems when starting a second shell
    # via a first shell (i.e. starting zsh from bash).
    if [ -z "${PS1+x}" ]; then
        PS1=
    fi

}


_conda_hashr() {
    case "$_CONDA_SHELL_FLAVOR" in
        zsh) \rehash;;
        posh) ;;
        *) \hash -r;;
    esac
}


_conda_activate() {
    if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then
        # Handle transition from shell activated with conda <= 4.3 to a subsequent activation
        # after conda updated to >= 4.4. See issue #6173.
        PS1="$CONDA_PS1_BACKUP"
        \unset CONDA_PS1_BACKUP
    fi

    \local ask_conda
    ask_conda="$(PS1="$PS1" $_CONDA_EXE shell.posix activate "$@")" || \return $?
    \eval "$ask_conda"

    _conda_hashr
}

_conda_deactivate() {
    \local ask_conda
    ask_conda="$(PS1="$PS1" $_CONDA_EXE shell.posix deactivate "$@")" || \return $?
    \eval "$ask_conda"

    _conda_hashr
}

_conda_reactivate() {
    \local ask_conda
    ask_conda="$(PS1="$PS1" $_CONDA_EXE shell.posix reactivate)" || \return $?
    \eval "$ask_conda"

    _conda_hashr
}


conda() {
    if [ "$#" -lt 1 ]; then
        $_CONDA_EXE
    else
        \local cmd="$1"
        shift
        case "$cmd" in
            activate)
                _conda_activate "$@"
                ;;
            deactivate)
                _conda_deactivate "$@"
                ;;
            install|update|uninstall|remove)
                $_CONDA_EXE "$cmd" "$@" && _conda_reactivate
                ;;
            *)
                $_CONDA_EXE "$cmd" "$@"
                ;;
        esac
    fi
}


_conda_set_vars
+++ _conda_set_vars
+++ '[' -n x ']'
+++ _CONDA_SHELL_FLAVOR=bash
+++ '[' -z x ']'
+++ '[' -z x ']'

if [ -z "${CONDA_SHLVL+x}" ]; then
    \export CONDA_SHLVL=0
fi
+++ '[' -z x ']'

_conda_deactivate
++ _conda_deactivate
++ local ask_conda
PS1="$PS1" $_CONDA_EXE shell.posix deactivate "$@"
+++ PS1='(adam-build-78a991a0-5e9a-4ce2-bd0a-0ba640282a00) '
+++ /home/jenkins/anaconda2/bin/conda shell.posix deactivate
++ ask_conda='\unset CONDA_DEFAULT_ENV
\unset CONDA_EXE
\unset CONDA_PREFIX
\unset CONDA_PROMPT_MODIFIER
\unset CONDA_PYTHON_EXE
PS1='\'''\''
\export CONDA_SHLVL='\''0'\''
\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'\'''
++ eval '\unset CONDA_DEFAULT_ENV
\unset CONDA_EXE
\unset CONDA_PREFIX
\unset CONDA_PROMPT_MODIFIER
\unset CONDA_PYTHON_EXE
PS1='\'''\''
\export CONDA_SHLVL='\''0'\''
\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'\'''
\unset CONDA_DEFAULT_ENV
+++ unset CONDA_DEFAULT_ENV
\unset CONDA_EXE
+++ unset CONDA_EXE
\unset CONDA_PREFIX
+++ unset CONDA_PREFIX
\unset CONDA_PROMPT_MODIFIER
+++ unset CONDA_PROMPT_MODIFIER
\unset CONDA_PYTHON_EXE
+++ unset CONDA_PYTHON_EXE
PS1=''
+++ PS1=
\export CONDA_SHLVL='0'
+++ export CONDA_SHLVL=0
+++ CONDA_SHLVL=0
\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'
+++ 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
++ _conda_hashr
++ case "$_CONDA_SHELL_FLAVOR" in
++ hash -r
+ conda remove -y -n adam-build-78a991a0-5e9a-4ce2-bd0a-0ba640282a00 --all
+ '[' 5 -lt 1 ']'
+ local cmd=remove
+ shift
+ case "$cmd" in
+ /home/jenkins/anaconda2/bin/conda remove -y -n adam-build-78a991a0-5e9a-4ce2-bd0a-0ba640282a00 --all

Remove all packages in environment /home/jenkins/anaconda2/envs/adam-build-78a991a0-5e9a-4ce2-bd0a-0ba640282a00:


## Package Plan ##

  environment location: /home/jenkins/anaconda2/envs/adam-build-78a991a0-5e9a-4ce2-bd0a-0ba640282a00


The following packages will be REMOVED:

    _libgcc_mutex:    0.1-main               
    ca-certificates:  2020.1.1-0             
    certifi:          2019.11.28-py36_0      
    ld_impl_linux-64: 2.33.1-h53a641e_7      
    libedit:          3.1.20181209-hc058e9b_0
    libffi:           3.2.1-hd88cf55_4       
    libgcc-ng:        9.1.0-hdf63c60_0       
    libstdcxx-ng:     9.1.0-hdf63c60_0       
    ncurses:          6.2-he6710b0_0         
    openssl:          1.1.1d-h7b6447c_4      
    pip:              20.0.2-py36_1          
    python:           3.6.10-h0371630_0      
    readline:         7.0-h7b6447c_5         
    setuptools:       45.2.0-py36_0          
    sqlite:           3.31.1-h7b6447c_0      
    tk:               8.6.8-hbc83047_0       
    wheel:            0.34.2-py36_0          
    xz:               5.2.4-h14c3975_4       
    zlib:             1.2.11-h7b6447c_3      

+ _conda_reactivate
+ local ask_conda
PS1="$PS1" $_CONDA_EXE shell.posix reactivate
++ PS1=
++ /home/jenkins/anaconda2/bin/conda shell.posix reactivate
+ ask_conda=
+ eval ''
+ _conda_hashr
+ case "$_CONDA_SHELL_FLAVOR" in
+ hash -r
+ cp -r adam-python/target /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.5/label/ubuntu/scripts/../adam-python/
+ pushd adam-python
/tmp/adamTesttnQQnB7/deleteMePleaseThisIsNoLongerNeeded/adam-python /tmp/adamTesttnQQnB7/deleteMePleaseThisIsNoLongerNeeded ~/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.5/label/ubuntu
+ make clean
pip uninstall -y adam
DEPRECATION: Python 2.7 reached the end of its life on January 1st, 2020. Please upgrade your Python as Python 2.7 is no longer maintained. A future version of pip will drop support for Python 2.7. More details about Python 2 support in pip, can be found at https://pip.pypa.io/en/latest/development/release-process/#python-2-support
WARNING: Skipping adam as it is not installed.
rm -rf bdgenomics/*.egg*
rm -rf build/
rm -rf dist/
+ make clean_sdist
rm -rf dist
+ popd
/tmp/adamTesttnQQnB7/deleteMePleaseThisIsNoLongerNeeded ~/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.5/label/ubuntu
	
# 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/adamTesttnQQnB7/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.5-bin-hadoop2.7/bin/spark-submit
20/03/04 13:28:20 WARN Utils: Your hostname, ubuntu-testing resolves to a loopback address: 127.0.1.1; using 192.168.10.30 instead (on interface eno1)
20/03/04 13:28:20 WARN Utils: Set SPARK_LOCAL_IP if you need to bind to another address
20/03/04 13:28:21 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
20/03/04 13:28:21 INFO SparkContext: Running Spark version 2.4.5
20/03/04 13:28:21 INFO SparkContext: Submitted application: transformAlignments
20/03/04 13:28:21 INFO SecurityManager: Changing view acls to: jenkins
20/03/04 13:28:21 INFO SecurityManager: Changing modify acls to: jenkins
20/03/04 13:28:21 INFO SecurityManager: Changing view acls groups to: 
20/03/04 13:28:21 INFO SecurityManager: Changing modify acls groups to: 
20/03/04 13:28:21 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()
20/03/04 13:28:21 INFO Utils: Successfully started service 'sparkDriver' on port 40569.
20/03/04 13:28:21 INFO SparkEnv: Registering MapOutputTracker
20/03/04 13:28:21 INFO SparkEnv: Registering BlockManagerMaster
20/03/04 13:28:21 INFO BlockManagerMasterEndpoint: Using org.apache.spark.storage.DefaultTopologyMapper for getting topology information
20/03/04 13:28:21 INFO BlockManagerMasterEndpoint: BlockManagerMasterEndpoint up
20/03/04 13:28:21 INFO DiskBlockManager: Created local directory at /tmp/blockmgr-c664e552-c398-4350-929f-cb5c0ad4e5a4
20/03/04 13:28:21 INFO MemoryStore: MemoryStore started with capacity 366.3 MB
20/03/04 13:28:21 INFO SparkEnv: Registering OutputCommitCoordinator
20/03/04 13:28:22 INFO Utils: Successfully started service 'SparkUI' on port 4040.
20/03/04 13:28:22 INFO SparkUI: Bound SparkUI to 0.0.0.0, and started at http://192.168.10.30:4040
20/03/04 13:28:22 INFO SparkContext: Added JAR file:/tmp/adamTesttnQQnB7/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/target/adam-assembly-spark2_2.11-0.32.0-SNAPSHOT.jar at spark://192.168.10.30:40569/jars/adam-assembly-spark2_2.11-0.32.0-SNAPSHOT.jar with timestamp 1583357302206
20/03/04 13:28:22 INFO Executor: Starting executor ID driver on host localhost
20/03/04 13:28:22 INFO Utils: Successfully started service 'org.apache.spark.network.netty.NettyBlockTransferService' on port 34831.
20/03/04 13:28:22 INFO NettyBlockTransferService: Server created on 192.168.10.30:34831
20/03/04 13:28:22 INFO BlockManager: Using org.apache.spark.storage.RandomBlockReplicationPolicy for block replication policy
20/03/04 13:28:22 INFO BlockManagerMaster: Registering BlockManager BlockManagerId(driver, 192.168.10.30, 34831, None)
20/03/04 13:28:22 INFO BlockManagerMasterEndpoint: Registering block manager 192.168.10.30:34831 with 366.3 MB RAM, BlockManagerId(driver, 192.168.10.30, 34831, None)
20/03/04 13:28:22 INFO BlockManagerMaster: Registered BlockManager BlockManagerId(driver, 192.168.10.30, 34831, None)
20/03/04 13:28:22 INFO BlockManager: Initialized BlockManager: BlockManagerId(driver, 192.168.10.30, 34831, None)
20/03/04 13:28:22 INFO ADAMContext: Loading mouse_chrM.bam as BAM/CRAM/SAM and converting to Alignments.
20/03/04 13:28:22 INFO ADAMContext: Loaded header from file:/tmp/adamTesttnQQnB7/deleteMePleaseThisIsNoLongerNeeded/mouse_chrM.bam
20/03/04 13:28:23 INFO MemoryStore: Block broadcast_0 stored as values in memory (estimated size 284.3 KB, free 366.0 MB)
20/03/04 13:28:23 INFO MemoryStore: Block broadcast_0_piece0 stored as bytes in memory (estimated size 23.1 KB, free 366.0 MB)
20/03/04 13:28:23 INFO BlockManagerInfo: Added broadcast_0_piece0 in memory on 192.168.10.30:34831 (size: 23.1 KB, free: 366.3 MB)
20/03/04 13:28:23 INFO SparkContext: Created broadcast 0 from newAPIHadoopFile at ADAMContext.scala:2058
20/03/04 13:28:24 INFO RDDBoundAlignmentDataset: Saving data in ADAM format
20/03/04 13:28:25 INFO FileOutputCommitter: File Output Committer Algorithm version is 1
20/03/04 13:28:25 INFO FileInputFormat: Total input paths to process : 1
20/03/04 13:28:25 INFO SparkContext: Starting job: runJob at SparkHadoopWriter.scala:78
20/03/04 13:28:25 INFO DAGScheduler: Got job 0 (runJob at SparkHadoopWriter.scala:78) with 1 output partitions
20/03/04 13:28:25 INFO DAGScheduler: Final stage: ResultStage 0 (runJob at SparkHadoopWriter.scala:78)
20/03/04 13:28:25 INFO DAGScheduler: Parents of final stage: List()
20/03/04 13:28:25 INFO DAGScheduler: Missing parents: List()
20/03/04 13:28:25 INFO DAGScheduler: Submitting ResultStage 0 (MapPartitionsRDD[2] at map at GenomicDataset.scala:3814), which has no missing parents
20/03/04 13:28:25 INFO MemoryStore: Block broadcast_1 stored as values in memory (estimated size 82.2 KB, free 365.9 MB)
20/03/04 13:28:25 INFO MemoryStore: Block broadcast_1_piece0 stored as bytes in memory (estimated size 30.3 KB, free 365.9 MB)
20/03/04 13:28:25 INFO BlockManagerInfo: Added broadcast_1_piece0 in memory on 192.168.10.30:34831 (size: 30.3 KB, free: 366.2 MB)
20/03/04 13:28:25 INFO SparkContext: Created broadcast 1 from broadcast at DAGScheduler.scala:1163
20/03/04 13:28:25 INFO DAGScheduler: Submitting 1 missing tasks from ResultStage 0 (MapPartitionsRDD[2] at map at GenomicDataset.scala:3814) (first 15 tasks are for partitions Vector(0))
20/03/04 13:28:25 INFO TaskSchedulerImpl: Adding task set 0.0 with 1 tasks
20/03/04 13:28:25 INFO TaskSetManager: Starting task 0.0 in stage 0.0 (TID 0, localhost, executor driver, partition 0, PROCESS_LOCAL, 7962 bytes)
20/03/04 13:28:25 INFO Executor: Running task 0.0 in stage 0.0 (TID 0)
20/03/04 13:28:25 INFO Executor: Fetching spark://192.168.10.30:40569/jars/adam-assembly-spark2_2.11-0.32.0-SNAPSHOT.jar with timestamp 1583357302206
20/03/04 13:28:25 INFO TransportClientFactory: Successfully created connection to /192.168.10.30:40569 after 180 ms (0 ms spent in bootstraps)
20/03/04 13:28:25 INFO Utils: Fetching spark://192.168.10.30:40569/jars/adam-assembly-spark2_2.11-0.32.0-SNAPSHOT.jar to /tmp/spark-1d180e62-9b9d-42d6-9f42-ed4f9fa5d232/userFiles-e90a4a8d-7840-4930-b22b-17a7dc0a6ea9/fetchFileTemp4542790450018289869.tmp
20/03/04 13:28:25 INFO Executor: Adding file:/tmp/spark-1d180e62-9b9d-42d6-9f42-ed4f9fa5d232/userFiles-e90a4a8d-7840-4930-b22b-17a7dc0a6ea9/adam-assembly-spark2_2.11-0.32.0-SNAPSHOT.jar to class loader
20/03/04 13:28:25 INFO NewHadoopRDD: Input split: file:/tmp/adamTesttnQQnB7/deleteMePleaseThisIsNoLongerNeeded/mouse_chrM.bam:83361792-833134657535
20/03/04 13:28:25 INFO FileOutputCommitter: File Output Committer Algorithm version is 1
20/03/04 13:28:25 INFO CodecConfig: Compression: GZIP
20/03/04 13:28:25 INFO FileOutputCommitter: File Output Committer Algorithm version is 1
20/03/04 13:28:25 INFO ParquetOutputFormat: Parquet block size to 134217728
20/03/04 13:28:25 INFO ParquetOutputFormat: Parquet page size to 1048576
20/03/04 13:28:25 INFO ParquetOutputFormat: Parquet dictionary page size to 1048576
20/03/04 13:28:25 INFO ParquetOutputFormat: Dictionary is on
20/03/04 13:28:25 INFO ParquetOutputFormat: Validation is off
20/03/04 13:28:25 INFO ParquetOutputFormat: Writer version is: PARQUET_1_0
20/03/04 13:28:25 INFO ParquetOutputFormat: Maximum row group padding size is 8388608 bytes
20/03/04 13:28:25 INFO ParquetOutputFormat: Page size checking is: estimated
20/03/04 13:28:25 INFO ParquetOutputFormat: Min row count for page size check is: 100
20/03/04 13:28:25 INFO ParquetOutputFormat: Max row count for page size check is: 10000
20/03/04 13:28:25 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.
20/03/04 13:28:36 INFO InternalParquetRecordWriter: Flushing mem columnStore to file. allocated memory: 16043959
20/03/04 13:28:36 INFO FileOutputCommitter: Saved output of task 'attempt_20200304132824_0002_r_000000_0' to file:/tmp/adamTesttnQQnB7/deleteMePleaseThisIsNoLongerNeeded/mouse_chrM.bam.reads.adam/_temporary/0/task_20200304132824_0002_r_000000
20/03/04 13:28:36 INFO SparkHadoopMapRedUtil: attempt_20200304132824_0002_r_000000_0: Committed
20/03/04 13:28:36 INFO Executor: Finished task 0.0 in stage 0.0 (TID 0). 850 bytes result sent to driver
20/03/04 13:28:36 INFO TaskSetManager: Finished task 0.0 in stage 0.0 (TID 0) in 11189 ms on localhost (executor driver) (1/1)
20/03/04 13:28:36 INFO TaskSchedulerImpl: Removed TaskSet 0.0, whose tasks have all completed, from pool 
20/03/04 13:28:36 INFO DAGScheduler: ResultStage 0 (runJob at SparkHadoopWriter.scala:78) finished in 11.323 s
20/03/04 13:28:36 INFO DAGScheduler: Job 0 finished: runJob at SparkHadoopWriter.scala:78, took 11.394443 s
20/03/04 13:28:36 INFO ParquetFileReader: Initiating action with parallelism: 5
20/03/04 13:28:36 INFO SparkHadoopWriter: Job job_20200304132824_0002 committed.
20/03/04 13:28:36 INFO TransformAlignments: Overall Duration: 15.25 secs
20/03/04 13:28:36 INFO SparkContext: Invoking stop() from shutdown hook
20/03/04 13:28:36 INFO SparkUI: Stopped Spark web UI at http://192.168.10.30:4040
20/03/04 13:28:36 INFO MapOutputTrackerMasterEndpoint: MapOutputTrackerMasterEndpoint stopped!
20/03/04 13:28:36 INFO MemoryStore: MemoryStore cleared
20/03/04 13:28:36 INFO BlockManager: BlockManager stopped
20/03/04 13:28:36 INFO BlockManagerMaster: BlockManagerMaster stopped
20/03/04 13:28:36 INFO OutputCommitCoordinator$OutputCommitCoordinatorEndpoint: OutputCommitCoordinator stopped!
20/03/04 13:28:36 INFO SparkContext: Successfully stopped SparkContext
20/03/04 13:28:36 INFO ShutdownHookManager: Shutdown hook called
20/03/04 13:28:36 INFO ShutdownHookManager: Deleting directory /tmp/spark-8ea42852-b515-44db-8f0b-4eef9a5ca456
20/03/04 13:28:36 INFO ShutdownHookManager: Deleting directory /tmp/spark-1d180e62-9b9d-42d6-9f42-ed4f9fa5d232

# 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/adamTesttnQQnB7/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.5-bin-hadoop2.7/bin/spark-submit
20/03/04 13:28:38 WARN Utils: Your hostname, ubuntu-testing resolves to a loopback address: 127.0.1.1; using 192.168.10.30 instead (on interface eno1)
20/03/04 13:28:38 WARN Utils: Set SPARK_LOCAL_IP if you need to bind to another address
20/03/04 13:28:38 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
20/03/04 13:28:38 INFO SparkContext: Running Spark version 2.4.5
20/03/04 13:28:38 INFO SparkContext: Submitted application: transformAlignments
20/03/04 13:28:38 INFO SecurityManager: Changing view acls to: jenkins
20/03/04 13:28:38 INFO SecurityManager: Changing modify acls to: jenkins
20/03/04 13:28:38 INFO SecurityManager: Changing view acls groups to: 
20/03/04 13:28:38 INFO SecurityManager: Changing modify acls groups to: 
20/03/04 13:28:38 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()
20/03/04 13:28:39 INFO Utils: Successfully started service 'sparkDriver' on port 43965.
20/03/04 13:28:39 INFO SparkEnv: Registering MapOutputTracker
20/03/04 13:28:39 INFO SparkEnv: Registering BlockManagerMaster
20/03/04 13:28:39 INFO BlockManagerMasterEndpoint: Using org.apache.spark.storage.DefaultTopologyMapper for getting topology information
20/03/04 13:28:39 INFO BlockManagerMasterEndpoint: BlockManagerMasterEndpoint up
20/03/04 13:28:39 INFO DiskBlockManager: Created local directory at /tmp/blockmgr-f74f3688-75f5-4a97-9f97-04f1d33e1c41
20/03/04 13:28:39 INFO MemoryStore: MemoryStore started with capacity 366.3 MB
20/03/04 13:28:39 INFO SparkEnv: Registering OutputCommitCoordinator
20/03/04 13:28:39 INFO Utils: Successfully started service 'SparkUI' on port 4040.
20/03/04 13:28:39 INFO SparkUI: Bound SparkUI to 0.0.0.0, and started at http://192.168.10.30:4040
20/03/04 13:28:39 INFO SparkContext: Added JAR file:/tmp/adamTesttnQQnB7/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/target/adam-assembly-spark2_2.11-0.32.0-SNAPSHOT.jar at spark://192.168.10.30:43965/jars/adam-assembly-spark2_2.11-0.32.0-SNAPSHOT.jar with timestamp 1583357319595
20/03/04 13:28:39 INFO Executor: Starting executor ID driver on host localhost
20/03/04 13:28:39 INFO Utils: Successfully started service 'org.apache.spark.network.netty.NettyBlockTransferService' on port 45587.
20/03/04 13:28:39 INFO NettyBlockTransferService: Server created on 192.168.10.30:45587
20/03/04 13:28:39 INFO BlockManager: Using org.apache.spark.storage.RandomBlockReplicationPolicy for block replication policy
20/03/04 13:28:39 INFO BlockManagerMaster: Registering BlockManager BlockManagerId(driver, 192.168.10.30, 45587, None)
20/03/04 13:28:39 INFO BlockManagerMasterEndpoint: Registering block manager 192.168.10.30:45587 with 366.3 MB RAM, BlockManagerId(driver, 192.168.10.30, 45587, None)
20/03/04 13:28:39 INFO BlockManagerMaster: Registered BlockManager BlockManagerId(driver, 192.168.10.30, 45587, None)
20/03/04 13:28:39 INFO BlockManager: Initialized BlockManager: BlockManagerId(driver, 192.168.10.30, 45587, None)
20/03/04 13:28:40 INFO ADAMContext: Loading mouse_chrM.bam.reads.adam as Parquet of Alignments.
20/03/04 13:28:41 INFO ADAMContext: Reading the ADAM file at mouse_chrM.bam.reads.adam to create RDD
20/03/04 13:28:41 INFO MemoryStore: Block broadcast_0 stored as values in memory (estimated size 303.7 KB, free 366.0 MB)
20/03/04 13:28:42 INFO MemoryStore: Block broadcast_0_piece0 stored as bytes in memory (estimated size 27.4 KB, free 366.0 MB)
20/03/04 13:28:42 INFO BlockManagerInfo: Added broadcast_0_piece0 in memory on 192.168.10.30:45587 (size: 27.4 KB, free: 366.3 MB)
20/03/04 13:28:42 INFO SparkContext: Created broadcast 0 from newAPIHadoopFile at ADAMContext.scala:1796
20/03/04 13:28:42 INFO TransformAlignments: Sorting alignments by reference position, with references ordered by name
20/03/04 13:28:42 INFO RDDBoundAlignmentDataset: Sorting alignments by reference position
20/03/04 13:28:42 INFO FileInputFormat: Total input paths to process : 1
20/03/04 13:28:42 INFO ParquetInputFormat: Total input paths to process : 1
20/03/04 13:28:42 INFO RDDBoundAlignmentDataset: Saving data in ADAM format
20/03/04 13:28:42 INFO FileOutputCommitter: File Output Committer Algorithm version is 1
20/03/04 13:28:42 INFO SparkContext: Starting job: runJob at SparkHadoopWriter.scala:78
20/03/04 13:28:42 INFO DAGScheduler: Registering RDD 2 (sortBy at AlignmentDataset.scala:1008) as input to shuffle 0
20/03/04 13:28:42 INFO DAGScheduler: Got job 0 (runJob at SparkHadoopWriter.scala:78) with 1 output partitions
20/03/04 13:28:42 INFO DAGScheduler: Final stage: ResultStage 1 (runJob at SparkHadoopWriter.scala:78)
20/03/04 13:28:42 INFO DAGScheduler: Parents of final stage: List(ShuffleMapStage 0)
20/03/04 13:28:42 INFO DAGScheduler: Missing parents: List(ShuffleMapStage 0)
20/03/04 13:28:42 INFO DAGScheduler: Submitting ShuffleMapStage 0 (MapPartitionsRDD[2] at sortBy at AlignmentDataset.scala:1008), which has no missing parents
20/03/04 13:28:42 INFO MemoryStore: Block broadcast_1 stored as values in memory (estimated size 5.1 KB, free 366.0 MB)
20/03/04 13:28:42 INFO MemoryStore: Block broadcast_1_piece0 stored as bytes in memory (estimated size 3.0 KB, free 366.0 MB)
20/03/04 13:28:42 INFO BlockManagerInfo: Added broadcast_1_piece0 in memory on 192.168.10.30:45587 (size: 3.0 KB, free: 366.3 MB)
20/03/04 13:28:42 INFO SparkContext: Created broadcast 1 from broadcast at DAGScheduler.scala:1163
20/03/04 13:28:42 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))
20/03/04 13:28:42 INFO TaskSchedulerImpl: Adding task set 0.0 with 1 tasks
20/03/04 13:28:42 INFO TaskSetManager: Starting task 0.0 in stage 0.0 (TID 0, localhost, executor driver, partition 0, PROCESS_LOCAL, 8001 bytes)
20/03/04 13:28:42 INFO Executor: Running task 0.0 in stage 0.0 (TID 0)
20/03/04 13:28:42 INFO Executor: Fetching spark://192.168.10.30:43965/jars/adam-assembly-spark2_2.11-0.32.0-SNAPSHOT.jar with timestamp 1583357319595
20/03/04 13:28:42 INFO TransportClientFactory: Successfully created connection to /192.168.10.30:43965 after 46 ms (0 ms spent in bootstraps)
20/03/04 13:28:42 INFO Utils: Fetching spark://192.168.10.30:43965/jars/adam-assembly-spark2_2.11-0.32.0-SNAPSHOT.jar to /tmp/spark-a5413a43-33b8-430a-8211-f0c01a9244e5/userFiles-de006786-f5e9-4a66-9b7d-ac5c517a6b18/fetchFileTemp3664860847928701022.tmp
20/03/04 13:28:43 INFO Executor: Adding file:/tmp/spark-a5413a43-33b8-430a-8211-f0c01a9244e5/userFiles-de006786-f5e9-4a66-9b7d-ac5c517a6b18/adam-assembly-spark2_2.11-0.32.0-SNAPSHOT.jar to class loader
20/03/04 13:28:43 INFO NewHadoopRDD: Input split: file:/tmp/adamTesttnQQnB7/deleteMePleaseThisIsNoLongerNeeded/mouse_chrM.bam.reads.adam/part-r-00000.gz.parquet:0+10132211
20/03/04 13:28:43 INFO InternalParquetRecordReader: RecordReader initialized will read a total of 163064 records.
20/03/04 13:28:43 INFO InternalParquetRecordReader: at row 0. reading next block
20/03/04 13:28:43 INFO CodecPool: Got brand-new decompressor [.gz]
20/03/04 13:28:43 INFO InternalParquetRecordReader: block read in memory in 40 ms. row count = 163064
20/03/04 13:28:46 INFO Executor: Finished task 0.0 in stage 0.0 (TID 0). 956 bytes result sent to driver
20/03/04 13:28:46 INFO TaskSetManager: Finished task 0.0 in stage 0.0 (TID 0) in 3658 ms on localhost (executor driver) (1/1)
20/03/04 13:28:46 INFO TaskSchedulerImpl: Removed TaskSet 0.0, whose tasks have all completed, from pool 
20/03/04 13:28:46 INFO DAGScheduler: ShuffleMapStage 0 (sortBy at AlignmentDataset.scala:1008) finished in 3.803 s
20/03/04 13:28:46 INFO DAGScheduler: looking for newly runnable stages
20/03/04 13:28:46 INFO DAGScheduler: running: Set()
20/03/04 13:28:46 INFO DAGScheduler: waiting: Set(ResultStage 1)
20/03/04 13:28:46 INFO DAGScheduler: failed: Set()
20/03/04 13:28:46 INFO DAGScheduler: Submitting ResultStage 1 (MapPartitionsRDD[5] at map at GenomicDataset.scala:3814), which has no missing parents
20/03/04 13:28:46 INFO MemoryStore: Block broadcast_2 stored as values in memory (estimated size 83.4 KB, free 365.9 MB)
20/03/04 13:28:46 INFO MemoryStore: Block broadcast_2_piece0 stored as bytes in memory (estimated size 31.0 KB, free 365.9 MB)
20/03/04 13:28:46 INFO BlockManagerInfo: Added broadcast_2_piece0 in memory on 192.168.10.30:45587 (size: 31.0 KB, free: 366.2 MB)
20/03/04 13:28:46 INFO SparkContext: Created broadcast 2 from broadcast at DAGScheduler.scala:1163
20/03/04 13:28:46 INFO DAGScheduler: Submitting 1 missing tasks from ResultStage 1 (MapPartitionsRDD[5] at map at GenomicDataset.scala:3814) (first 15 tasks are for partitions Vector(0))
20/03/04 13:28:46 INFO TaskSchedulerImpl: Adding task set 1.0 with 1 tasks
20/03/04 13:28:46 INFO TaskSetManager: Starting task 0.0 in stage 1.0 (TID 1, localhost, executor driver, partition 0, ANY, 7662 bytes)
20/03/04 13:28:46 INFO Executor: Running task 0.0 in stage 1.0 (TID 1)
20/03/04 13:28:46 INFO ShuffleBlockFetcherIterator: Getting 1 non-empty blocks including 1 local blocks and 0 remote blocks
20/03/04 13:28:46 INFO ShuffleBlockFetcherIterator: Started 0 remote fetches in 32 ms
20/03/04 13:28:48 INFO FileOutputCommitter: File Output Committer Algorithm version is 1
20/03/04 13:28:48 INFO CodecConfig: Compression: GZIP
20/03/04 13:28:48 INFO FileOutputCommitter: File Output Committer Algorithm version is 1
20/03/04 13:28:48 INFO ParquetOutputFormat: Parquet block size to 134217728
20/03/04 13:28:48 INFO ParquetOutputFormat: Parquet page size to 1048576
20/03/04 13:28:48 INFO ParquetOutputFormat: Parquet dictionary page size to 1048576
20/03/04 13:28:48 INFO ParquetOutputFormat: Dictionary is on
20/03/04 13:28:48 INFO ParquetOutputFormat: Validation is off
20/03/04 13:28:48 INFO ParquetOutputFormat: Writer version is: PARQUET_1_0
20/03/04 13:28:48 INFO ParquetOutputFormat: Maximum row group padding size is 8388608 bytes
20/03/04 13:28:48 INFO ParquetOutputFormat: Page size checking is: estimated
20/03/04 13:28:48 INFO ParquetOutputFormat: Min row count for page size check is: 100
20/03/04 13:28:48 INFO ParquetOutputFormat: Max row count for page size check is: 10000
20/03/04 13:28:48 INFO CodecPool: Got brand-new compressor [.gz]
20/03/04 13:28:49 INFO BlockManagerInfo: Removed broadcast_1_piece0 on 192.168.10.30:45587 in memory (size: 3.0 KB, free: 366.2 MB)
20/03/04 13:28:53 INFO InternalParquetRecordWriter: Flushing mem columnStore to file. allocated memory: 16004474
20/03/04 13:28:54 INFO FileOutputCommitter: Saved output of task 'attempt_20200304132842_0005_r_000000_0' to file:/tmp/adamTesttnQQnB7/deleteMePleaseThisIsNoLongerNeeded/mouse_chrM.bam.reads.sorted.adam/_temporary/0/task_20200304132842_0005_r_000000
20/03/04 13:28:54 INFO SparkHadoopMapRedUtil: attempt_20200304132842_0005_r_000000_0: Committed
20/03/04 13:28:54 INFO Executor: Finished task 0.0 in stage 1.0 (TID 1). 1280 bytes result sent to driver
20/03/04 13:28:54 INFO TaskSetManager: Finished task 0.0 in stage 1.0 (TID 1) in 7756 ms on localhost (executor driver) (1/1)
20/03/04 13:28:54 INFO TaskSchedulerImpl: Removed TaskSet 1.0, whose tasks have all completed, from pool 
20/03/04 13:28:54 INFO DAGScheduler: ResultStage 1 (runJob at SparkHadoopWriter.scala:78) finished in 7.815 s
20/03/04 13:28:54 INFO DAGScheduler: Job 0 finished: runJob at SparkHadoopWriter.scala:78, took 11.710722 s
20/03/04 13:28:54 INFO ParquetFileReader: Initiating action with parallelism: 5
20/03/04 13:28:54 INFO SparkHadoopWriter: Job job_20200304132842_0005 committed.
20/03/04 13:28:54 INFO TransformAlignments: Overall Duration: 15.58 secs
20/03/04 13:28:54 INFO SparkContext: Invoking stop() from shutdown hook
20/03/04 13:28:54 INFO SparkUI: Stopped Spark web UI at http://192.168.10.30:4040
20/03/04 13:28:54 INFO MapOutputTrackerMasterEndpoint: MapOutputTrackerMasterEndpoint stopped!
20/03/04 13:28:54 INFO MemoryStore: MemoryStore cleared
20/03/04 13:28:54 INFO BlockManager: BlockManager stopped
20/03/04 13:28:54 INFO BlockManagerMaster: BlockManagerMaster stopped
20/03/04 13:28:54 INFO OutputCommitCoordinator$OutputCommitCoordinatorEndpoint: OutputCommitCoordinator stopped!
20/03/04 13:28:54 INFO SparkContext: Successfully stopped SparkContext
20/03/04 13:28:54 INFO ShutdownHookManager: Shutdown hook called
20/03/04 13:28:54 INFO ShutdownHookManager: Deleting directory /tmp/spark-a5413a43-33b8-430a-8211-f0c01a9244e5
20/03/04 13:28:54 INFO ShutdownHookManager: Deleting directory /tmp/spark-ebc407c6-cdc0-4a67-ae3c-b5104a5bb339

# 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/adamTesttnQQnB7/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.5-bin-hadoop2.7/bin/spark-submit
20/03/04 13:28:55 WARN Utils: Your hostname, ubuntu-testing resolves to a loopback address: 127.0.1.1; using 192.168.10.30 instead (on interface eno1)
20/03/04 13:28:55 WARN Utils: Set SPARK_LOCAL_IP if you need to bind to another address
20/03/04 13:28:56 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
20/03/04 13:28:56 INFO SparkContext: Running Spark version 2.4.5
20/03/04 13:28:56 INFO SparkContext: Submitted application: transformFragments
20/03/04 13:28:56 INFO SecurityManager: Changing view acls to: jenkins
20/03/04 13:28:56 INFO SecurityManager: Changing modify acls to: jenkins
20/03/04 13:28:56 INFO SecurityManager: Changing view acls groups to: 
20/03/04 13:28:56 INFO SecurityManager: Changing modify acls groups to: 
20/03/04 13:28:56 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()
20/03/04 13:28:57 INFO Utils: Successfully started service 'sparkDriver' on port 36753.
20/03/04 13:28:57 INFO SparkEnv: Registering MapOutputTracker
20/03/04 13:28:57 INFO SparkEnv: Registering BlockManagerMaster
20/03/04 13:28:57 INFO BlockManagerMasterEndpoint: Using org.apache.spark.storage.DefaultTopologyMapper for getting topology information
20/03/04 13:28:57 INFO BlockManagerMasterEndpoint: BlockManagerMasterEndpoint up
20/03/04 13:28:57 INFO DiskBlockManager: Created local directory at /tmp/blockmgr-f8272a00-1c12-42d3-8608-23eede2d4bfb
20/03/04 13:28:57 INFO MemoryStore: MemoryStore started with capacity 366.3 MB
20/03/04 13:28:57 INFO SparkEnv: Registering OutputCommitCoordinator
20/03/04 13:28:57 INFO Utils: Successfully started service 'SparkUI' on port 4040.
20/03/04 13:28:57 INFO SparkUI: Bound SparkUI to 0.0.0.0, and started at http://192.168.10.30:4040
20/03/04 13:28:57 INFO SparkContext: Added JAR file:/tmp/adamTesttnQQnB7/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/target/adam-assembly-spark2_2.11-0.32.0-SNAPSHOT.jar at spark://192.168.10.30:36753/jars/adam-assembly-spark2_2.11-0.32.0-SNAPSHOT.jar with timestamp 1583357337354
20/03/04 13:28:57 INFO Executor: Starting executor ID driver on host localhost
20/03/04 13:28:57 INFO Utils: Successfully started service 'org.apache.spark.network.netty.NettyBlockTransferService' on port 46213.
20/03/04 13:28:57 INFO NettyBlockTransferService: Server created on 192.168.10.30:46213
20/03/04 13:28:57 INFO BlockManager: Using org.apache.spark.storage.RandomBlockReplicationPolicy for block replication policy
20/03/04 13:28:57 INFO BlockManagerMaster: Registering BlockManager BlockManagerId(driver, 192.168.10.30, 46213, None)
20/03/04 13:28:57 INFO BlockManagerMasterEndpoint: Registering block manager 192.168.10.30:46213 with 366.3 MB RAM, BlockManagerId(driver, 192.168.10.30, 46213, None)
20/03/04 13:28:57 INFO BlockManagerMaster: Registered BlockManager BlockManagerId(driver, 192.168.10.30, 46213, None)
20/03/04 13:28:57 INFO BlockManager: Initialized BlockManager: BlockManagerId(driver, 192.168.10.30, 46213, None)
20/03/04 13:28:58 INFO ADAMContext: Loading mouse_chrM.bam.reads.adam as Parquet of Alignments.
20/03/04 13:28:59 INFO ADAMContext: Reading the ADAM file at mouse_chrM.bam.reads.adam to create RDD
20/03/04 13:28:59 INFO MemoryStore: Block broadcast_0 stored as values in memory (estimated size 303.7 KB, free 366.0 MB)
20/03/04 13:29:00 INFO MemoryStore: Block broadcast_0_piece0 stored as bytes in memory (estimated size 27.4 KB, free 366.0 MB)
20/03/04 13:29:00 INFO BlockManagerInfo: Added broadcast_0_piece0 in memory on 192.168.10.30:46213 (size: 27.4 KB, free: 366.3 MB)
20/03/04 13:29:00 INFO SparkContext: Created broadcast 0 from newAPIHadoopFile at ADAMContext.scala:1796
20/03/04 13:29:00 INFO FileInputFormat: Total input paths to process : 1
20/03/04 13:29:00 INFO ParquetInputFormat: Total input paths to process : 1
20/03/04 13:29:00 INFO RDDBoundFragmentDataset: Saving data in ADAM format
20/03/04 13:29:00 INFO FileOutputCommitter: File Output Committer Algorithm version is 1
20/03/04 13:29:00 INFO SparkContext: Starting job: runJob at SparkHadoopWriter.scala:78
20/03/04 13:29:00 INFO DAGScheduler: Registering RDD 2 (groupBy at SingleReadBucket.scala:97) as input to shuffle 0
20/03/04 13:29:00 INFO DAGScheduler: Got job 0 (runJob at SparkHadoopWriter.scala:78) with 1 output partitions
20/03/04 13:29:00 INFO DAGScheduler: Final stage: ResultStage 1 (runJob at SparkHadoopWriter.scala:78)
20/03/04 13:29:00 INFO DAGScheduler: Parents of final stage: List(ShuffleMapStage 0)
20/03/04 13:29:00 INFO DAGScheduler: Missing parents: List(ShuffleMapStage 0)
20/03/04 13:29:00 INFO DAGScheduler: Submitting ShuffleMapStage 0 (MapPartitionsRDD[2] at groupBy at SingleReadBucket.scala:97), which has no missing parents
20/03/04 13:29:00 INFO MemoryStore: Block broadcast_1 stored as values in memory (estimated size 5.5 KB, free 366.0 MB)
20/03/04 13:29:00 INFO MemoryStore: Block broadcast_1_piece0 stored as bytes in memory (estimated size 3.1 KB, free 366.0 MB)
20/03/04 13:29:00 INFO BlockManagerInfo: Added broadcast_1_piece0 in memory on 192.168.10.30:46213 (size: 3.1 KB, free: 366.3 MB)
20/03/04 13:29:00 INFO SparkContext: Created broadcast 1 from broadcast at DAGScheduler.scala:1163
20/03/04 13:29:00 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))
20/03/04 13:29:00 INFO TaskSchedulerImpl: Adding task set 0.0 with 1 tasks
20/03/04 13:29:00 INFO TaskSetManager: Starting task 0.0 in stage 0.0 (TID 0, localhost, executor driver, partition 0, PROCESS_LOCAL, 8001 bytes)
20/03/04 13:29:00 INFO Executor: Running task 0.0 in stage 0.0 (TID 0)
20/03/04 13:29:00 INFO Executor: Fetching spark://192.168.10.30:36753/jars/adam-assembly-spark2_2.11-0.32.0-SNAPSHOT.jar with timestamp 1583357337354
20/03/04 13:29:00 INFO TransportClientFactory: Successfully created connection to /192.168.10.30:36753 after 195 ms (0 ms spent in bootstraps)
20/03/04 13:29:00 INFO Utils: Fetching spark://192.168.10.30:36753/jars/adam-assembly-spark2_2.11-0.32.0-SNAPSHOT.jar to /tmp/spark-20958648-f6f6-42d4-97f6-eed6165f66c9/userFiles-31c02ad3-9f36-432c-a505-7938a08a3ae2/fetchFileTemp803051308068535464.tmp
20/03/04 13:29:01 INFO Executor: Adding file:/tmp/spark-20958648-f6f6-42d4-97f6-eed6165f66c9/userFiles-31c02ad3-9f36-432c-a505-7938a08a3ae2/adam-assembly-spark2_2.11-0.32.0-SNAPSHOT.jar to class loader
20/03/04 13:29:01 INFO NewHadoopRDD: Input split: file:/tmp/adamTesttnQQnB7/deleteMePleaseThisIsNoLongerNeeded/mouse_chrM.bam.reads.adam/part-r-00000.gz.parquet:0+10132211
20/03/04 13:29:01 INFO InternalParquetRecordReader: RecordReader initialized will read a total of 163064 records.
20/03/04 13:29:01 INFO InternalParquetRecordReader: at row 0. reading next block
20/03/04 13:29:01 INFO CodecPool: Got brand-new decompressor [.gz]
20/03/04 13:29:01 INFO InternalParquetRecordReader: block read in memory in 49 ms. row count = 163064
20/03/04 13:29:04 INFO Executor: Finished task 0.0 in stage 0.0 (TID 0). 956 bytes result sent to driver
20/03/04 13:29:04 INFO TaskSetManager: Finished task 0.0 in stage 0.0 (TID 0) in 3780 ms on localhost (executor driver) (1/1)
20/03/04 13:29:04 INFO TaskSchedulerImpl: Removed TaskSet 0.0, whose tasks have all completed, from pool 
20/03/04 13:29:04 INFO DAGScheduler: ShuffleMapStage 0 (groupBy at SingleReadBucket.scala:97) finished in 3.891 s
20/03/04 13:29:04 INFO DAGScheduler: looking for newly runnable stages
20/03/04 13:29:04 INFO DAGScheduler: running: Set()
20/03/04 13:29:04 INFO DAGScheduler: waiting: Set(ResultStage 1)
20/03/04 13:29:04 INFO DAGScheduler: failed: Set()
20/03/04 13:29:04 INFO DAGScheduler: Submitting ResultStage 1 (MapPartitionsRDD[6] at map at GenomicDataset.scala:3814), which has no missing parents
20/03/04 13:29:04 INFO MemoryStore: Block broadcast_2 stored as values in memory (estimated size 86.4 KB, free 365.9 MB)
20/03/04 13:29:04 INFO MemoryStore: Block broadcast_2_piece0 stored as bytes in memory (estimated size 32.3 KB, free 365.9 MB)
20/03/04 13:29:04 INFO BlockManagerInfo: Added broadcast_2_piece0 in memory on 192.168.10.30:46213 (size: 32.3 KB, free: 366.2 MB)
20/03/04 13:29:04 INFO SparkContext: Created broadcast 2 from broadcast at DAGScheduler.scala:1163
20/03/04 13:29:04 INFO DAGScheduler: Submitting 1 missing tasks from ResultStage 1 (MapPartitionsRDD[6] at map at GenomicDataset.scala:3814) (first 15 tasks are for partitions Vector(0))
20/03/04 13:29:04 INFO TaskSchedulerImpl: Adding task set 1.0 with 1 tasks
20/03/04 13:29:04 INFO TaskSetManager: Starting task 0.0 in stage 1.0 (TID 1, localhost, executor driver, partition 0, ANY, 7662 bytes)
20/03/04 13:29:04 INFO Executor: Running task 0.0 in stage 1.0 (TID 1)
20/03/04 13:29:04 INFO ShuffleBlockFetcherIterator: Getting 1 non-empty blocks including 1 local blocks and 0 remote blocks
20/03/04 13:29:04 INFO ShuffleBlockFetcherIterator: Started 0 remote fetches in 8 ms
20/03/04 13:29:06 INFO FileOutputCommitter: File Output Committer Algorithm version is 1
20/03/04 13:29:06 INFO CodecConfig: Compression: GZIP
20/03/04 13:29:06 INFO FileOutputCommitter: File Output Committer Algorithm version is 1
20/03/04 13:29:06 INFO ParquetOutputFormat: Parquet block size to 134217728
20/03/04 13:29:06 INFO ParquetOutputFormat: Parquet page size to 1048576
20/03/04 13:29:06 INFO ParquetOutputFormat: Parquet dictionary page size to 1048576
20/03/04 13:29:06 INFO ParquetOutputFormat: Dictionary is on
20/03/04 13:29:06 INFO ParquetOutputFormat: Validation is off
20/03/04 13:29:06 INFO ParquetOutputFormat: Writer version is: PARQUET_1_0
20/03/04 13:29:06 INFO ParquetOutputFormat: Maximum row group padding size is 8388608 bytes
20/03/04 13:29:06 INFO ParquetOutputFormat: Page size checking is: estimated
20/03/04 13:29:06 INFO ParquetOutputFormat: Min row count for page size check is: 100
20/03/04 13:29:06 INFO ParquetOutputFormat: Max row count for page size check is: 10000
20/03/04 13:29:06 INFO CodecPool: Got brand-new compressor [.gz]
20/03/04 13:29:08 INFO BlockManagerInfo: Removed broadcast_1_piece0 on 192.168.10.30:46213 in memory (size: 3.1 KB, free: 366.2 MB)
20/03/04 13:29:14 INFO InternalParquetRecordWriter: Flushing mem columnStore to file. allocated memory: 21417928
20/03/04 13:29:14 INFO FileOutputCommitter: Saved output of task 'attempt_20200304132900_0006_r_000000_0' to file:/tmp/adamTesttnQQnB7/deleteMePleaseThisIsNoLongerNeeded/mouse_chrM.bam.fragments.adam/_temporary/0/task_20200304132900_0006_r_000000
20/03/04 13:29:14 INFO SparkHadoopMapRedUtil: attempt_20200304132900_0006_r_000000_0: Committed
20/03/04 13:29:14 INFO Executor: Finished task 0.0 in stage 1.0 (TID 1). 1237 bytes result sent to driver
20/03/04 13:29:14 INFO TaskSetManager: Finished task 0.0 in stage 1.0 (TID 1) in 10324 ms on localhost (executor driver) (1/1)
20/03/04 13:29:14 INFO TaskSchedulerImpl: Removed TaskSet 1.0, whose tasks have all completed, from pool 
20/03/04 13:29:14 INFO DAGScheduler: ResultStage 1 (runJob at SparkHadoopWriter.scala:78) finished in 10.361 s
20/03/04 13:29:14 INFO DAGScheduler: Job 0 finished: runJob at SparkHadoopWriter.scala:78, took 14.331706 s
20/03/04 13:29:14 INFO ParquetFileReader: Initiating action with parallelism: 5
20/03/04 13:29:14 INFO SparkHadoopWriter: Job job_20200304132900_0006 committed.
20/03/04 13:29:14 INFO TransformFragments: Overall Duration: 18.38 secs
20/03/04 13:29:14 INFO SparkContext: Invoking stop() from shutdown hook
20/03/04 13:29:14 INFO SparkUI: Stopped Spark web UI at http://192.168.10.30:4040
20/03/04 13:29:14 INFO MapOutputTrackerMasterEndpoint: MapOutputTrackerMasterEndpoint stopped!
20/03/04 13:29:14 INFO MemoryStore: MemoryStore cleared
20/03/04 13:29:14 INFO BlockManager: BlockManager stopped
20/03/04 13:29:14 INFO BlockManagerMaster: BlockManagerMaster stopped
20/03/04 13:29:14 INFO OutputCommitCoordinator$OutputCommitCoordinatorEndpoint: OutputCommitCoordinator stopped!
20/03/04 13:29:14 INFO SparkContext: Successfully stopped SparkContext
20/03/04 13:29:14 INFO ShutdownHookManager: Shutdown hook called
20/03/04 13:29:15 INFO ShutdownHookManager: Deleting directory /tmp/spark-679145bd-da02-4382-9e05-5bedbdad05dc
20/03/04 13:29:15 INFO ShutdownHookManager: Deleting directory /tmp/spark-20958648-f6f6-42d4-97f6-eed6165f66c9

# 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 -print_metrics ${READS}
+ ./bin/adam-submit flagstat -print_metrics mouse_chrM.bam.reads.adam
Using ADAM_MAIN=org.bdgenomics.adam.cli.ADAMMain
Using spark-submit=/tmp/adamTesttnQQnB7/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.5-bin-hadoop2.7/bin/spark-submit
20/03/04 13:29:32 WARN Utils: Your hostname, ubuntu-testing resolves to a loopback address: 127.0.1.1; using 192.168.10.30 instead (on interface eno1)
20/03/04 13:29:32 WARN Utils: Set SPARK_LOCAL_IP if you need to bind to another address
20/03/04 13:29:33 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
20/03/04 13:29:33 INFO SparkContext: Running Spark version 2.4.5
20/03/04 13:29:33 INFO SparkContext: Submitted application: flagstat
20/03/04 13:29:33 INFO SecurityManager: Changing view acls to: jenkins
20/03/04 13:29:33 INFO SecurityManager: Changing modify acls to: jenkins
20/03/04 13:29:33 INFO SecurityManager: Changing view acls groups to: 
20/03/04 13:29:33 INFO SecurityManager: Changing modify acls groups to: 
20/03/04 13:29:33 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()
20/03/04 13:29:33 INFO Utils: Successfully started service 'sparkDriver' on port 41301.
20/03/04 13:29:33 INFO SparkEnv: Registering MapOutputTracker
20/03/04 13:29:33 INFO SparkEnv: Registering BlockManagerMaster
20/03/04 13:29:33 INFO BlockManagerMasterEndpoint: Using org.apache.spark.storage.DefaultTopologyMapper for getting topology information
20/03/04 13:29:33 INFO BlockManagerMasterEndpoint: BlockManagerMasterEndpoint up
20/03/04 13:29:33 INFO DiskBlockManager: Created local directory at /tmp/blockmgr-0ffeaaf4-9695-449e-b57f-48a750b71880
20/03/04 13:29:33 INFO MemoryStore: MemoryStore started with capacity 366.3 MB
20/03/04 13:29:33 INFO SparkEnv: Registering OutputCommitCoordinator
20/03/04 13:29:34 INFO Utils: Successfully started service 'SparkUI' on port 4040.
20/03/04 13:29:34 INFO SparkUI: Bound SparkUI to 0.0.0.0, and started at http://192.168.10.30:4040
20/03/04 13:29:34 INFO SparkContext: Added JAR file:/tmp/adamTesttnQQnB7/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/target/adam-assembly-spark2_2.11-0.32.0-SNAPSHOT.jar at spark://192.168.10.30:41301/jars/adam-assembly-spark2_2.11-0.32.0-SNAPSHOT.jar with timestamp 1583357374223
20/03/04 13:29:34 INFO Executor: Starting executor ID driver on host localhost
20/03/04 13:29:34 INFO Utils: Successfully started service 'org.apache.spark.network.netty.NettyBlockTransferService' on port 46199.
20/03/04 13:29:34 INFO NettyBlockTransferService: Server created on 192.168.10.30:46199
20/03/04 13:29:34 INFO BlockManager: Using org.apache.spark.storage.RandomBlockReplicationPolicy for block replication policy
20/03/04 13:29:34 INFO BlockManagerMaster: Registering BlockManager BlockManagerId(driver, 192.168.10.30, 46199, None)
20/03/04 13:29:34 INFO BlockManagerMasterEndpoint: Registering block manager 192.168.10.30:46199 with 366.3 MB RAM, BlockManagerId(driver, 192.168.10.30, 46199, None)
20/03/04 13:29:34 INFO BlockManagerMaster: Registered BlockManager BlockManagerId(driver, 192.168.10.30, 46199, None)
20/03/04 13:29:34 INFO BlockManager: Initialized BlockManager: BlockManagerId(driver, 192.168.10.30, 46199, None)
20/03/04 13:29:35 INFO ADAMContext: Loading mouse_chrM.bam.reads.adam as Parquet of Alignments.
20/03/04 13:29:35 INFO ADAMContext: Reading the ADAM file at mouse_chrM.bam.reads.adam to create RDD
20/03/04 13:29:35 INFO ADAMContext: Using the specified projection schema
20/03/04 13:29:35 INFO MemoryStore: Block broadcast_0 stored as values in memory (estimated size 313.1 KB, free 366.0 MB)
20/03/04 13:29:35 INFO MemoryStore: Block broadcast_0_piece0 stored as bytes in memory (estimated size 28.4 KB, free 366.0 MB)
20/03/04 13:29:35 INFO BlockManagerInfo: Added broadcast_0_piece0 in memory on 192.168.10.30:46199 (size: 28.4 KB, free: 366.3 MB)
20/03/04 13:29:35 INFO SparkContext: Created broadcast 0 from newAPIHadoopFile at ADAMContext.scala:1796
20/03/04 13:29:37 INFO FileInputFormat: Total input paths to process : 1
20/03/04 13:29:37 INFO ParquetInputFormat: Total input paths to process : 1
20/03/04 13:29:37 INFO SparkContext: Starting job: aggregate at FlagStat.scala:115
20/03/04 13:29:37 INFO DAGScheduler: Got job 0 (aggregate at FlagStat.scala:115) with 1 output partitions
20/03/04 13:29:37 INFO DAGScheduler: Final stage: ResultStage 0 (aggregate at FlagStat.scala:115)
20/03/04 13:29:37 INFO DAGScheduler: Parents of final stage: List()
20/03/04 13:29:37 INFO DAGScheduler: Missing parents: List()
20/03/04 13:29:37 INFO DAGScheduler: Submitting ResultStage 0 (MapPartitionsRDD[4] at map at FlagStat.scala:96), which has no missing parents
20/03/04 13:29:37 INFO MemoryStore: Block broadcast_1 stored as values in memory (estimated size 12.7 KB, free 366.0 MB)
20/03/04 13:29:37 INFO MemoryStore: Block broadcast_1_piece0 stored as bytes in memory (estimated size 5.5 KB, free 365.9 MB)
20/03/04 13:29:37 INFO BlockManagerInfo: Added broadcast_1_piece0 in memory on 192.168.10.30:46199 (size: 5.5 KB, free: 366.3 MB)
20/03/04 13:29:37 INFO SparkContext: Created broadcast 1 from broadcast at DAGScheduler.scala:1163
20/03/04 13:29:37 INFO DAGScheduler: Submitting 1 missing tasks from ResultStage 0 (MapPartitionsRDD[4] at map at FlagStat.scala:96) (first 15 tasks are for partitions Vector(0))
20/03/04 13:29:37 INFO TaskSchedulerImpl: Adding task set 0.0 with 1 tasks
20/03/04 13:29:37 INFO TaskSetManager: Starting task 0.0 in stage 0.0 (TID 0, localhost, executor driver, partition 0, PROCESS_LOCAL, 8012 bytes)
20/03/04 13:29:37 INFO Executor: Running task 0.0 in stage 0.0 (TID 0)
20/03/04 13:29:37 INFO Executor: Fetching spark://192.168.10.30:41301/jars/adam-assembly-spark2_2.11-0.32.0-SNAPSHOT.jar with timestamp 1583357374223
20/03/04 13:29:37 INFO TransportClientFactory: Successfully created connection to /192.168.10.30:41301 after 165 ms (0 ms spent in bootstraps)
20/03/04 13:29:37 INFO Utils: Fetching spark://192.168.10.30:41301/jars/adam-assembly-spark2_2.11-0.32.0-SNAPSHOT.jar to /tmp/spark-11161eaf-8339-487b-b7c3-5e89e5ccd371/userFiles-11764201-050a-4e38-b321-65f62091395a/fetchFileTemp7481861371726908807.tmp
20/03/04 13:29:37 INFO Executor: Adding file:/tmp/spark-11161eaf-8339-487b-b7c3-5e89e5ccd371/userFiles-11764201-050a-4e38-b321-65f62091395a/adam-assembly-spark2_2.11-0.32.0-SNAPSHOT.jar to class loader
20/03/04 13:29:37 INFO NewHadoopRDD: Input split: file:/tmp/adamTesttnQQnB7/deleteMePleaseThisIsNoLongerNeeded/mouse_chrM.bam.reads.adam/part-r-00000.gz.parquet:0+10132211
20/03/04 13:29:38 INFO InternalParquetRecordReader: RecordReader initialized will read a total of 163064 records.
20/03/04 13:29:38 INFO InternalParquetRecordReader: at row 0. reading next block
20/03/04 13:29:38 INFO CodecPool: Got brand-new decompressor [.gz]
20/03/04 13:29:38 INFO InternalParquetRecordReader: block read in memory in 27 ms. row count = 163064
20/03/04 13:29:38 INFO Executor: Finished task 0.0 in stage 0.0 (TID 0). 8196 bytes result sent to driver
20/03/04 13:29:38 INFO TaskSetManager: Finished task 0.0 in stage 0.0 (TID 0) in 1633 ms on localhost (executor driver) (1/1)
20/03/04 13:29:38 INFO TaskSchedulerImpl: Removed TaskSet 0.0, whose tasks have all completed, from pool 
20/03/04 13:29:38 INFO DAGScheduler: ResultStage 0 (aggregate at FlagStat.scala:115) finished in 1.712 s
20/03/04 13:29:39 INFO DAGScheduler: Job 0 finished: aggregate at FlagStat.scala:115, took 1.766354 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)
20/03/04 13:29:39 INFO FlagStat: Overall Duration: 5.61 secs
20/03/04 13:29:39 INFO FlagStat: Metrics:

Timings
+--------------------------------------+--------------+--------------+-------------+--------+-----------+-----------+-----------+
|                Metric                | Worker Total | Driver Total | Driver Only | Count  |   Mean    |    Min    |    Max    |
+--------------------------------------+--------------+--------------+-------------+--------+-----------+-----------+-----------+
| └─ Load Alignments                   |            - |    2.04 secs |   1.97 secs |      1 | 2.04 secs | 2.04 secs | 2.04 secs |
|     └─ map at ADAMContext.scala:1805 |            - |     60.95 ms |           - |      1 |  60.95 ms |  60.95 ms |  60.95 ms |
|         └─ function call             |     18.64 ms |            - |           - | 163064 |    114 ns |     62 ns |  86.71 µs |
| └─ map at FlagStat.scala:96          |            - |     23.36 ms |           - |      1 |  23.36 ms |  23.36 ms |  23.36 ms |
|     └─ function call                 |    171.09 ms |            - |           - | 163064 |   1.05 µs |    177 ns |  20.43 ms |
| └─ aggregate at FlagStat.scala:115   |            - |    1.92 secs |           - |      1 | 1.92 secs | 1.92 secs | 1.92 secs |
|     └─ function call                 |     31.17 ms |            - |           - | 163065 |    191 ns |     89 ns | 431.58 µs |
+--------------------------------------+--------------+--------------+-------------+--------+-----------+-----------+-----------+

Spark Operations
+----------+---------------------------------+---------------+----------------+--------------+----------+
| Sequence |            Operation            | Is New Stage? | Stage Duration | Driver Total | Stage ID |
+----------+---------------------------------+---------------+----------------+--------------+----------+
| 1        | map at ADAMContext.scala:1805   | false         |              - |     60.95 ms | -        |
| 2        | map at FlagStat.scala:96        | false         |              - |     23.36 ms | -        |
| 3        | aggregate at FlagStat.scala:115 | true          |     -1.71 secs |    1.92 secs | 0        |
+----------+---------------------------------+---------------+----------------+--------------+----------+

Task Timings
+-------------------------------+------------+-------+-----------+-----------+-----------+
|            Metric             | Total Time | Count |   Mean    |    Min    |    Max    |
+-------------------------------+------------+-------+-----------+-----------+-----------+
| Task Duration                 |  1.63 secs |     1 | 1.63 secs | 1.63 secs | 1.63 secs |
| Executor Run Time             |  1.14 secs |     1 | 1.14 secs | 1.14 secs | 1.14 secs |
| Executor Deserialization Time |     432 ms |     1 |    432 ms |    432 ms |    432 ms |
| Result Serialization Time     |          0 |     1 |         0 |         0 |         0 |
+-------------------------------+------------+-------+-----------+-----------+-----------+

Task Timings By Host
+-------------------------------+--------+------------+-------+-----------+-----------+-----------+
|            Metric             |  Host  | Total Time | Count |   Mean    |    Min    |    Max    |
+-------------------------------+--------+------------+-------+-----------+-----------+-----------+
| Task Duration                 | driver |  1.63 secs |     1 | 1.63 secs | 1.63 secs | 1.63 secs |
| Executor Run Time             | driver |  1.14 secs |     1 | 1.14 secs | 1.14 secs | 1.14 secs |
| Executor Deserialization Time | driver |     432 ms |     1 |    432 ms |    432 ms |    432 ms |
| Result Serialization Time     | driver |          0 |     1 |         0 |         0 |         0 |
+-------------------------------+--------+------------+-------+-----------+-----------+-----------+

Task Timings By Stage
+-------------------------------+------------------------------------+------------+-------+-----------+-----------+-----------+
|            Metric             |          Stage ID & Name           | Total Time | Count |   Mean    |    Min    |    Max    |
+-------------------------------+------------------------------------+------------+-------+-----------+-----------+-----------+
| Task Duration                 | 0: aggregate at FlagStat.scala:115 |  1.63 secs |     1 | 1.63 secs | 1.63 secs | 1.63 secs |
| Executor Run Time             | 0: aggregate at FlagStat.scala:115 |  1.14 secs |     1 | 1.14 secs | 1.14 secs | 1.14 secs |
| Executor Deserialization Time | 0: aggregate at FlagStat.scala:115 |     432 ms |     1 |    432 ms |    432 ms |    432 ms |
| Result Serialization Time     | 0: aggregate at FlagStat.scala:115 |          0 |     1 |         0 |         0 |         0 |
+-------------------------------+------------------------------------+------------+-------+-----------+-----------+-----------+

20/03/04 13:29:39 INFO SparkContext: Invoking stop() from shutdown hook
20/03/04 13:29:39 INFO SparkUI: Stopped Spark web UI at http://192.168.10.30:4040
20/03/04 13:29:39 INFO MapOutputTrackerMasterEndpoint: MapOutputTrackerMasterEndpoint stopped!
20/03/04 13:29:39 INFO MemoryStore: MemoryStore cleared
20/03/04 13:29:39 INFO BlockManager: BlockManager stopped
20/03/04 13:29:39 INFO BlockManagerMaster: BlockManagerMaster stopped
20/03/04 13:29:39 INFO OutputCommitCoordinator$OutputCommitCoordinatorEndpoint: OutputCommitCoordinator stopped!
20/03/04 13:29:39 INFO SparkContext: Successfully stopped SparkContext
20/03/04 13:29:39 INFO ShutdownHookManager: Shutdown hook called
20/03/04 13:29:39 INFO ShutdownHookManager: Deleting directory /tmp/spark-fdc36109-afa7-402a-ad9a-9fb8d01980a5
20/03/04 13:29:39 INFO ShutdownHookManager: Deleting directory /tmp/spark-11161eaf-8339-487b-b7c3-5e89e5ccd371
rm -rf ${ADAM_TMP_DIR}
+ rm -rf /tmp/adamTesttnQQnB7/deleteMePleaseThisIsNoLongerNeeded
popd
+ popd
~/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.5/label/ubuntu

pushd ${PROJECT_ROOT}
+ pushd /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.5/label/ubuntu/scripts/..
~/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.5/label/ubuntu ~/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.5/label/ubuntu
# move back to Scala 2.11 as default
if [ ${SCALAVER} == 2.12 ];
then
    set +e
    ./scripts/move_to_scala_2.11.sh
    set -e
fi
+ '[' 2.11 == 2.12 ']'

# 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/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.5/label/ubuntu/scripts
+ pushd /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.5/label/ubuntu/scripts/..
~/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.5/label/ubuntu ~/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.5/label/ubuntu
+ mvn org.scalariform:scalariform-maven-plugin:format license:format
Java HotSpot(TM) 64-Bit Server VM warning: ignoring option MaxPermSize=1g; support was removed in 8.0
[INFO] Scanning for projects...
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Build Order:
[INFO] 
[INFO] ADAM_2.11
[INFO] ADAM_2.11: Shader workaround
[INFO] ADAM_2.11: Avro-to-Dataset codegen utils
[INFO] ADAM_2.11: Core
[INFO] ADAM_2.11: APIs for Java, Python
[INFO] ADAM_2.11: CLI
[INFO] ADAM_2.11: Assembly
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building ADAM_2.11 0.32.0-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ adam-parent-spark2_2.11 ---
[INFO] Modified 2 of 243 .scala files
[INFO] 
[INFO] --- maven-license-plugin:1.10.b1:format (default-cli) @ adam-parent-spark2_2.11 ---
[INFO] Updating license headers...
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building ADAM_2.11: Shader workaround 0.32.0-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ adam-shade-spark2_2.11 ---
[INFO] Modified 0 of 0 .scala files
[INFO] 
[INFO] --- maven-license-plugin:1.10.b1:format (default-cli) @ adam-shade-spark2_2.11 ---
[INFO] Updating license headers...
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building ADAM_2.11: Avro-to-Dataset codegen utils 0.32.0-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ adam-codegen-spark2_2.11 ---
[INFO] Modified 0 of 4 .scala files
[INFO] 
[INFO] --- maven-license-plugin:1.10.b1:format (default-cli) @ adam-codegen-spark2_2.11 ---
[INFO] Updating license headers...
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building ADAM_2.11: Core 0.32.0-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ adam-core-spark2_2.11 ---
[INFO] Modified 0 of 203 .scala files
[INFO] 
[INFO] --- maven-license-plugin:1.10.b1:format (default-cli) @ adam-core-spark2_2.11 ---
[INFO] Updating license headers...
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building ADAM_2.11: APIs for Java, Python 0.32.0-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ adam-apis-spark2_2.11 ---
[INFO] Modified 0 of 5 .scala files
[INFO] 
[INFO] --- maven-license-plugin:1.10.b1:format (default-cli) @ adam-apis-spark2_2.11 ---
[INFO] Updating license headers...
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building ADAM_2.11: CLI 0.32.0-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ adam-cli-spark2_2.11 ---
[INFO] Modified 0 of 29 .scala files
[INFO] 
[INFO] --- maven-license-plugin:1.10.b1:format (default-cli) @ adam-cli-spark2_2.11 ---
[INFO] Updating license headers...
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building ADAM_2.11: Assembly 0.32.0-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ adam-assembly-spark2_2.11 ---
[INFO] Modified 0 of 1 .scala files
[INFO] 
[INFO] --- maven-license-plugin:1.10.b1:format (default-cli) @ adam-assembly-spark2_2.11 ---
[INFO] Updating license headers...
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary:
[INFO] 
[INFO] ADAM_2.11 .......................................... SUCCESS [  7.248 s]
[INFO] ADAM_2.11: Shader workaround ....................... SUCCESS [  0.029 s]
[INFO] ADAM_2.11: Avro-to-Dataset codegen utils ........... SUCCESS [  0.062 s]
[INFO] ADAM_2.11: Core .................................... SUCCESS [  4.203 s]
[INFO] ADAM_2.11: APIs for Java, Python ................... SUCCESS [  0.168 s]
[INFO] ADAM_2.11: CLI ..................................... SUCCESS [  0.250 s]
[INFO] ADAM_2.11: Assembly ................................ SUCCESS [  0.013 s]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 12.450 s
[INFO] Finished at: 2020-03-04T13:29:53-08:00
[INFO] Final Memory: 20M/1117M
[INFO] ------------------------------------------------------------------------
+ popd
~/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.5/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/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.5/label/ubuntu

echo
+ echo

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

Recording test results
Publishing Scoverage XML and HTML report...
Setting commit status on GitHub for https://github.com/bigdatagenomics/adam/commit/0e54b0d0d18b883f04a60bc0e506ff68c5cf5b9f
Finished: SUCCESS