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[WARNING] Entry: adam-distribution-spark3_2.12-0.33.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/AlignmentsToVariantsDatasetConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark3_2.12-0.33.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/SequencesToFragmentsDatasetConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark3_2.12-0.33.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/FragmentsToVariantsConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark3_2.12-0.33.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/FragmentsToFragmentsConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark3_2.12-0.33.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/FeaturesToGenotypesDatasetConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark3_2.12-0.33.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/VariantsToFeaturesConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark3_2.12-0.33.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/AlignmentsToReadsDatasetConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark3_2.12-0.33.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/ReadsToGenotypesConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark3_2.12-0.33.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/SlicesToFragmentsConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark3_2.12-0.33.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/GenotypesToAlignmentsConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark3_2.12-0.33.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/FragmentsToReadsConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark3_2.12-0.33.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/ReadsToFeaturesDatasetConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark3_2.12-0.33.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/VariantsToAlignmentsDatasetConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark3_2.12-0.33.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/ReadsToFragmentsConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark3_2.12-0.33.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/ReadsToGenotypesDatasetConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark3_2.12-0.33.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/FeaturesToFragmentsConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark3_2.12-0.33.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/SequencesToReadsConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark3_2.12-0.33.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/ReadsToAlignmentsDatasetConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark3_2.12-0.33.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/FragmentsToCoverageDatasetConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark3_2.12-0.33.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/VariantsToReadsConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark3_2.12-0.33.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/SequencesToGenotypesDatasetConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark3_2.12-0.33.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/GenotypesToSlicesDatasetConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark3_2.12-0.33.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/SequencesToAlignmentsDatasetConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark3_2.12-0.33.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/ReadsToSequencesConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark3_2.12-0.33.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/VariantContextsToVariantsConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark3_2.12-0.33.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/SlicesToVariantsConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark3_2.12-0.33.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/SlicesToAlignmentsDatasetConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark3_2.12-0.33.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/VariantContextsToFragmentsConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark3_2.12-0.33.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/JavaADAMContext$.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark3_2.12-0.33.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/SlicesToReadsConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark3_2.12-0.33.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/SlicesToFragmentsDatasetConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark3_2.12-0.33.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/ToAlignmentDatasetConversion.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark3_2.12-0.33.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/ReadsToSlicesDatasetConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark3_2.12-0.33.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/AlignmentsToReadsConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark3_2.12-0.33.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/VariantContextsToReadsConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark3_2.12-0.33.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/SequencesToGenotypesConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark3_2.12-0.33.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/cli/MergeShardsArgs.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark3_2.12-0.33.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/cli/TransformSequences$.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark3_2.12-0.33.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/cli/TransformVariants.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark3_2.12-0.33.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/cli/TransformGenotypesArgs.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark3_2.12-0.33.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/cli/TransformAlignments$.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark3_2.12-0.33.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/cli/CountSliceKmers$.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark3_2.12-0.33.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/cli/TransformFragments.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark3_2.12-0.33.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/cli/TransformAlignmentsArgs.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark3_2.12-0.33.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/cli/TransformFragmentsArgs.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark3_2.12-0.33.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/cli/TransformSlicesArgs.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark3_2.12-0.33.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/cli/TransformFeatures$.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark3_2.12-0.33.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/cli/CountSliceKmers.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark3_2.12-0.33.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/cli/TransformFeaturesArgs.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark3_2.12-0.33.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/cli/TransformSlices.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark3_2.12-0.33.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/cli/TransformFragments$.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark3_2.12-0.33.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/cli/TransformSequences.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark3_2.12-0.33.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/cli/TransformAlignments.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark3_2.12-0.33.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/cli/TransformGenotypes$.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark3_2.12-0.33.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/cli/TransformGenotypes.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark3_2.12-0.33.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/cli/CountSliceKmersArgs.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark3_2.12-0.33.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/cli/TransformVariants$.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark3_2.12-0.33.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/cli/CountReadKmers$.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark3_2.12-0.33.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/cli/TransformSequencesArgs.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark3_2.12-0.33.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/cli/TransformFeatures.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark3_2.12-0.33.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/cli/CountReadKmersArgs.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark3_2.12-0.33.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/cli/TransformSlices$.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark3_2.12-0.33.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/cli/TransformVariantsArgs.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark3_2.12-0.33.0-SNAPSHOT/repo/adam-assembly-spark3_2.12-0.33.0-SNAPSHOT-sources.jar longer than 100 characters.
[WARNING] Entry: adam-distribution-spark3_2.12-0.33.0-SNAPSHOT/repo/adam-assembly-spark3_2.12-0.33.0-SNAPSHOT-javadoc.jar longer than 100 characters.
[INFO] Building zip: /tmp/adamTestIb4eRTC/deleteMePleaseThisIsNoLongerNeeded/adam-distribution/target/adam-distribution-spark3_2.12-0.33.0-SNAPSHOT-bin.zip
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary for ADAM_2.12 0.33.0-SNAPSHOT:
[INFO] 
[INFO] ADAM_2.12 .......................................... SUCCESS [  8.594 s]
[INFO] ADAM_2.12: Shader workaround ....................... SUCCESS [  7.377 s]
[INFO] ADAM_2.12: Avro-to-Dataset codegen utils ........... SUCCESS [  9.066 s]
[INFO] ADAM_2.12: Core .................................... SUCCESS [01:27 min]
[INFO] ADAM_2.12: APIs for Java, Python ................... SUCCESS [ 21.545 s]
[INFO] ADAM_2.12: CLI ..................................... SUCCESS [ 26.457 s]
[INFO] ADAM_2.12: Assembly ................................ SUCCESS [ 13.742 s]
[INFO] ADAM_2.12: Python APIs ............................. SUCCESS [01:14 min]
[INFO] ADAM_2.12: Distribution ............................ SUCCESS [ 39.931 s]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time:  04:49 min
[INFO] Finished at: 2020-08-06T14:39:35-07:00
[INFO] ------------------------------------------------------------------------
+ grep bdgenomics.adam
+ tar tzvf adam-distribution/target/adam-distribution-spark3_2.12-0.33.0-SNAPSHOT-bin.tar.gz
+ grep egg
drwxrwxr-x jenkins/jenkins        0 2020-08-06 14:37 adam-distribution-spark3_2.12-0.33.0-SNAPSHOT/r/bdgenomics.adam.egg-info/
-rw-r--r-- jenkins/jenkins 36237861 2020-08-06 14:37 adam-distribution-spark3_2.12-0.33.0-SNAPSHOT/repo/bdgenomics.adam-0.32.0a0-py3.6.egg
+ ./bin/pyadam
Using PYSPARK=/tmp/adamTestIb4eRTC/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.0-bin-hadoop2.7/bin/pyspark
2020-08-06 14:39:38 WARN  Utils:69 - Your hostname, ubuntu-testing resolves to a loopback address: 127.0.1.1; using 192.168.10.30 instead (on interface eno1)
2020-08-06 14:39:38 WARN  Utils:69 - Set SPARK_LOCAL_IP if you need to bind to another address
2020-08-06 14:39:39 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).
2020-08-06 14:39:45 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/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-b49499fa-a639-4807-8d98-d51a10ef8724) '
+++ /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/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'\'''
++ 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/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_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/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'
+++ export PATH=/usr/lib/jvm/java-8-oracle/bin/:/usr/lib/jvm/java-8-oracle/bin/:/home/anaconda/bin/:/home/jenkins/tools/hudson.tasks.Maven_MavenInstallation/Maven_3.6.3/bin/:/home/jenkins/gems/bin:/usr/local/go/bin:/home/jenkins/go-projects/bin:/home/jenkins/anaconda2/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games
+++ PATH=/usr/lib/jvm/java-8-oracle/bin/:/usr/lib/jvm/java-8-oracle/bin/:/home/anaconda/bin/:/home/jenkins/tools/hudson.tasks.Maven_MavenInstallation/Maven_3.6.3/bin/:/home/jenkins/gems/bin:/usr/local/go/bin:/home/jenkins/go-projects/bin:/home/jenkins/anaconda2/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games
++ _conda_hashr
++ case "$_CONDA_SHELL_FLAVOR" in
++ hash -r
+ conda remove -y -n adam-build-b49499fa-a639-4807-8d98-d51a10ef8724 --all
+ '[' 5 -lt 1 ']'
+ local cmd=remove
+ shift
+ case "$cmd" in
+ /home/jenkins/anaconda2/bin/conda remove -y -n adam-build-b49499fa-a639-4807-8d98-d51a10ef8724 --all

Remove all packages in environment /home/jenkins/anaconda2/envs/adam-build-b49499fa-a639-4807-8d98-d51a10ef8724:


## Package Plan ##

  environment location: /home/jenkins/anaconda2/envs/adam-build-b49499fa-a639-4807-8d98-d51a10ef8724


The following packages will be REMOVED:

    _libgcc_mutex:    0.1-main               
    ca-certificates:  2020.6.24-0            
    certifi:          2020.6.20-py36_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:          1.1.1g-h7b6447c_0      
    pip:              20.1.1-py36_1          
    python:           3.6.10-h7579374_2      
    readline:         8.0-h7b6447c_0         
    setuptools:       49.2.0-py36_0          
    sqlite:           3.32.3-h62c20be_0      
    tk:               8.6.10-hbc83047_0      
    wheel:            0.34.2-py36_0          
    xz:               5.2.5-h7b6447c_0       
    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/SCALA_VERSION/2.12/SPARK_VERSION/3.0.0/label/ubuntu/scripts/../adam-python/
+ pushd adam-python
/tmp/adamTestIb4eRTC/deleteMePleaseThisIsNoLongerNeeded/adam-python /tmp/adamTestIb4eRTC/deleteMePleaseThisIsNoLongerNeeded ~/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.0/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/adamTestIb4eRTC/deleteMePleaseThisIsNoLongerNeeded ~/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.0/label/ubuntu

if [ ${SPARK_VERSION} == 3.0.0 ]
then
    echo "Unable to build R support for Spark 3.0.0, SparkR is not available"
else
    # make a directory to install SparkR into, and set the R user libs path
    export R_LIBS_USER=${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
+ '[' 3.0.0 == 3.0.0 ']'
+ echo 'Unable to build R support for Spark 3.0.0, SparkR is not available'
Unable to build R support for Spark 3.0.0, 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/adamTestIb4eRTC/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.0-bin-hadoop2.7/bin/spark-submit
20/08/06 14:40:00 WARN Utils: Your hostname, ubuntu-testing resolves to a loopback address: 127.0.1.1; using 192.168.10.30 instead (on interface eno1)
20/08/06 14:40:00 WARN Utils: Set SPARK_LOCAL_IP if you need to bind to another address
20/08/06 14:40:01 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
20/08/06 14:40:01 INFO SparkContext: Running Spark version 3.0.0
20/08/06 14:40:01 INFO ResourceUtils: ==============================================================
20/08/06 14:40:01 INFO ResourceUtils: Resources for spark.driver:

20/08/06 14:40:01 INFO ResourceUtils: ==============================================================
20/08/06 14:40:01 INFO SparkContext: Submitted application: transformAlignments
20/08/06 14:40:01 INFO SecurityManager: Changing view acls to: jenkins
20/08/06 14:40:01 INFO SecurityManager: Changing modify acls to: jenkins
20/08/06 14:40:01 INFO SecurityManager: Changing view acls groups to: 
20/08/06 14:40:01 INFO SecurityManager: Changing modify acls groups to: 
20/08/06 14:40:01 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()
20/08/06 14:40:02 INFO Utils: Successfully started service 'sparkDriver' on port 45191.
20/08/06 14:40:02 INFO SparkEnv: Registering MapOutputTracker
20/08/06 14:40:02 INFO SparkEnv: Registering BlockManagerMaster
20/08/06 14:40:02 INFO BlockManagerMasterEndpoint: Using org.apache.spark.storage.DefaultTopologyMapper for getting topology information
20/08/06 14:40:02 INFO BlockManagerMasterEndpoint: BlockManagerMasterEndpoint up
20/08/06 14:40:02 INFO SparkEnv: Registering BlockManagerMasterHeartbeat
20/08/06 14:40:02 INFO DiskBlockManager: Created local directory at /tmp/blockmgr-55d4ed9f-0204-4d55-8cfb-5aa33b3ac618
20/08/06 14:40:02 INFO MemoryStore: MemoryStore started with capacity 408.9 MiB
20/08/06 14:40:02 INFO SparkEnv: Registering OutputCommitCoordinator
20/08/06 14:40:02 INFO Utils: Successfully started service 'SparkUI' on port 4040.
20/08/06 14:40:02 INFO SparkUI: Bound SparkUI to 0.0.0.0, and started at http://192.168.10.30:4040
20/08/06 14:40:02 INFO SparkContext: Added JAR file:/tmp/adamTestIb4eRTC/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/target/adam-assembly-spark3_2.12-0.33.0-SNAPSHOT.jar at spark://192.168.10.30:45191/jars/adam-assembly-spark3_2.12-0.33.0-SNAPSHOT.jar with timestamp 1596750002739
20/08/06 14:40:02 INFO Executor: Starting executor ID driver on host 192.168.10.30
20/08/06 14:40:02 INFO Utils: Successfully started service 'org.apache.spark.network.netty.NettyBlockTransferService' on port 38135.
20/08/06 14:40:02 INFO NettyBlockTransferService: Server created on 192.168.10.30:38135
20/08/06 14:40:02 INFO BlockManager: Using org.apache.spark.storage.RandomBlockReplicationPolicy for block replication policy
20/08/06 14:40:02 INFO BlockManagerMaster: Registering BlockManager BlockManagerId(driver, 192.168.10.30, 38135, None)
20/08/06 14:40:02 INFO BlockManagerMasterEndpoint: Registering block manager 192.168.10.30:38135 with 408.9 MiB RAM, BlockManagerId(driver, 192.168.10.30, 38135, None)
20/08/06 14:40:02 INFO BlockManagerMaster: Registered BlockManager BlockManagerId(driver, 192.168.10.30, 38135, None)
20/08/06 14:40:02 INFO BlockManager: Initialized BlockManager: BlockManagerId(driver, 192.168.10.30, 38135, None)
20/08/06 14:40:03 INFO ADAMContext: Loading mouse_chrM.bam as BAM/CRAM/SAM and converting to Alignments.
20/08/06 14:40:03 INFO ADAMContext: Loaded header from file:/tmp/adamTestIb4eRTC/deleteMePleaseThisIsNoLongerNeeded/mouse_chrM.bam
20/08/06 14:40:04 INFO MemoryStore: Block broadcast_0 stored as values in memory (estimated size 289.9 KiB, free 408.6 MiB)
20/08/06 14:40:04 INFO MemoryStore: Block broadcast_0_piece0 stored as bytes in memory (estimated size 23.6 KiB, free 408.6 MiB)
20/08/06 14:40:04 INFO BlockManagerInfo: Added broadcast_0_piece0 in memory on 192.168.10.30:38135 (size: 23.6 KiB, free: 408.9 MiB)
20/08/06 14:40:04 INFO SparkContext: Created broadcast 0 from newAPIHadoopFile at ADAMContext.scala:2054
20/08/06 14:40:05 INFO RDDBoundAlignmentDataset: Saving data in ADAM format
20/08/06 14:40:05 INFO FileOutputCommitter: File Output Committer Algorithm version is 1
20/08/06 14:40:05 INFO FileInputFormat: Total input paths to process : 1
20/08/06 14:40:05 INFO SparkContext: Starting job: runJob at SparkHadoopWriter.scala:78
20/08/06 14:40:05 INFO DAGScheduler: Got job 0 (runJob at SparkHadoopWriter.scala:78) with 1 output partitions
20/08/06 14:40:05 INFO DAGScheduler: Final stage: ResultStage 0 (runJob at SparkHadoopWriter.scala:78)
20/08/06 14:40:05 INFO DAGScheduler: Parents of final stage: List()
20/08/06 14:40:05 INFO DAGScheduler: Missing parents: List()
20/08/06 14:40:05 INFO DAGScheduler: Submitting ResultStage 0 (MapPartitionsRDD[2] at map at GenomicDataset.scala:3805), which has no missing parents
20/08/06 14:40:05 INFO MemoryStore: Block broadcast_1 stored as values in memory (estimated size 84.5 KiB, free 408.5 MiB)
20/08/06 14:40:05 INFO MemoryStore: Block broadcast_1_piece0 stored as bytes in memory (estimated size 31.3 KiB, free 408.5 MiB)
20/08/06 14:40:05 INFO BlockManagerInfo: Added broadcast_1_piece0 in memory on 192.168.10.30:38135 (size: 31.3 KiB, free: 408.8 MiB)
20/08/06 14:40:05 INFO SparkContext: Created broadcast 1 from broadcast at DAGScheduler.scala:1200
20/08/06 14:40:05 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))
20/08/06 14:40:05 INFO TaskSchedulerImpl: Adding task set 0.0 with 1 tasks
20/08/06 14:40:06 INFO TaskSetManager: Starting task 0.0 in stage 0.0 (TID 0, 192.168.10.30, executor driver, partition 0, PROCESS_LOCAL, 7443 bytes)
20/08/06 14:40:06 INFO Executor: Running task 0.0 in stage 0.0 (TID 0)
20/08/06 14:40:06 INFO Executor: Fetching spark://192.168.10.30:45191/jars/adam-assembly-spark3_2.12-0.33.0-SNAPSHOT.jar with timestamp 1596750002739
20/08/06 14:40:06 INFO TransportClientFactory: Successfully created connection to /192.168.10.30:45191 after 44 ms (0 ms spent in bootstraps)
20/08/06 14:40:06 INFO Utils: Fetching spark://192.168.10.30:45191/jars/adam-assembly-spark3_2.12-0.33.0-SNAPSHOT.jar to /tmp/spark-3edfcccb-b410-49e2-a30f-f3f190255530/userFiles-b276c39a-f864-4cce-a680-656418f43063/fetchFileTemp6183108441981642608.tmp
20/08/06 14:40:06 INFO Executor: Adding file:/tmp/spark-3edfcccb-b410-49e2-a30f-f3f190255530/userFiles-b276c39a-f864-4cce-a680-656418f43063/adam-assembly-spark3_2.12-0.33.0-SNAPSHOT.jar to class loader
20/08/06 14:40:06 INFO NewHadoopRDD: Input split: file:/tmp/adamTestIb4eRTC/deleteMePleaseThisIsNoLongerNeeded/mouse_chrM.bam:83361792-833134657535
20/08/06 14:40:06 INFO FileOutputCommitter: File Output Committer Algorithm version is 1
20/08/06 14:40:06 INFO CodecConfig: Compression: GZIP
20/08/06 14:40:06 INFO FileOutputCommitter: File Output Committer Algorithm version is 1
20/08/06 14:40:06 INFO ParquetOutputFormat: Parquet block size to 134217728
20/08/06 14:40:06 INFO ParquetOutputFormat: Parquet page size to 1048576
20/08/06 14:40:06 INFO ParquetOutputFormat: Parquet dictionary page size to 1048576
20/08/06 14:40:06 INFO ParquetOutputFormat: Dictionary is on
20/08/06 14:40:06 INFO ParquetOutputFormat: Validation is off
20/08/06 14:40:06 INFO ParquetOutputFormat: Writer version is: PARQUET_1_0
20/08/06 14:40:06 INFO ParquetOutputFormat: Maximum row group padding size is 8388608 bytes
20/08/06 14:40:06 INFO ParquetOutputFormat: Page size checking is: estimated
20/08/06 14:40:06 INFO ParquetOutputFormat: Min row count for page size check is: 100
20/08/06 14:40:06 INFO ParquetOutputFormat: Max row count for page size check is: 10000
20/08/06 14:40:06 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.
20/08/06 14:40:15 INFO InternalParquetRecordWriter: Flushing mem columnStore to file. allocated memory: 16043959
20/08/06 14:40:16 INFO FileOutputCommitter: Saved output of task 'attempt_20200806144005_0002_r_000000_0' to file:/tmp/adamTestIb4eRTC/deleteMePleaseThisIsNoLongerNeeded/mouse_chrM.bam.reads.adam/_temporary/0/task_20200806144005_0002_r_000000
20/08/06 14:40:16 INFO SparkHadoopMapRedUtil: attempt_20200806144005_0002_r_000000_0: Committed
20/08/06 14:40:16 INFO Executor: Finished task 0.0 in stage 0.0 (TID 0). 978 bytes result sent to driver
20/08/06 14:40:16 INFO TaskSetManager: Finished task 0.0 in stage 0.0 (TID 0) in 10297 ms on 192.168.10.30 (executor driver) (1/1)
20/08/06 14:40:16 INFO TaskSchedulerImpl: Removed TaskSet 0.0, whose tasks have all completed, from pool 
20/08/06 14:40:16 INFO DAGScheduler: ResultStage 0 (runJob at SparkHadoopWriter.scala:78) finished in 10.427 s
20/08/06 14:40:16 INFO DAGScheduler: Job 0 is finished. Cancelling potential speculative or zombie tasks for this job
20/08/06 14:40:16 INFO TaskSchedulerImpl: Killing all running tasks in stage 0: Stage finished
20/08/06 14:40:16 INFO DAGScheduler: Job 0 finished: runJob at SparkHadoopWriter.scala:78, took 10.482377 s
20/08/06 14:40:16 INFO ParquetFileReader: Initiating action with parallelism: 5
20/08/06 14:40:16 INFO SparkHadoopWriter: Job job_20200806144005_0002 committed.
20/08/06 14:40:16 INFO SparkContext: Invoking stop() from shutdown hook
20/08/06 14:40:16 INFO SparkUI: Stopped Spark web UI at http://192.168.10.30:4040
20/08/06 14:40:16 INFO MapOutputTrackerMasterEndpoint: MapOutputTrackerMasterEndpoint stopped!
20/08/06 14:40:16 INFO MemoryStore: MemoryStore cleared
20/08/06 14:40:16 INFO BlockManager: BlockManager stopped
20/08/06 14:40:16 INFO BlockManagerMaster: BlockManagerMaster stopped
20/08/06 14:40:16 INFO OutputCommitCoordinator$OutputCommitCoordinatorEndpoint: OutputCommitCoordinator stopped!
20/08/06 14:40:16 INFO SparkContext: Successfully stopped SparkContext
20/08/06 14:40:16 INFO ShutdownHookManager: Shutdown hook called
20/08/06 14:40:16 INFO ShutdownHookManager: Deleting directory /tmp/spark-7241f96c-b2d7-47f5-9652-9cea649fc7e6
20/08/06 14:40:16 INFO ShutdownHookManager: Deleting directory /tmp/spark-3edfcccb-b410-49e2-a30f-f3f190255530

# 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/adamTestIb4eRTC/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.0-bin-hadoop2.7/bin/spark-submit
20/08/06 14:40:17 WARN Utils: Your hostname, ubuntu-testing resolves to a loopback address: 127.0.1.1; using 192.168.10.30 instead (on interface eno1)
20/08/06 14:40:17 WARN Utils: Set SPARK_LOCAL_IP if you need to bind to another address
20/08/06 14:40:18 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
20/08/06 14:40:18 INFO SparkContext: Running Spark version 3.0.0
20/08/06 14:40:19 INFO ResourceUtils: ==============================================================
20/08/06 14:40:19 INFO ResourceUtils: Resources for spark.driver:

20/08/06 14:40:19 INFO ResourceUtils: ==============================================================
20/08/06 14:40:19 INFO SparkContext: Submitted application: transformAlignments
20/08/06 14:40:19 INFO SecurityManager: Changing view acls to: jenkins
20/08/06 14:40:19 INFO SecurityManager: Changing modify acls to: jenkins
20/08/06 14:40:19 INFO SecurityManager: Changing view acls groups to: 
20/08/06 14:40:19 INFO SecurityManager: Changing modify acls groups to: 
20/08/06 14:40:19 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()
20/08/06 14:40:19 INFO Utils: Successfully started service 'sparkDriver' on port 38005.
20/08/06 14:40:19 INFO SparkEnv: Registering MapOutputTracker
20/08/06 14:40:19 INFO SparkEnv: Registering BlockManagerMaster
20/08/06 14:40:19 INFO BlockManagerMasterEndpoint: Using org.apache.spark.storage.DefaultTopologyMapper for getting topology information
20/08/06 14:40:19 INFO BlockManagerMasterEndpoint: BlockManagerMasterEndpoint up
20/08/06 14:40:19 INFO SparkEnv: Registering BlockManagerMasterHeartbeat
20/08/06 14:40:19 INFO DiskBlockManager: Created local directory at /tmp/blockmgr-a59ea330-165f-4785-98c3-42bd3842c471
20/08/06 14:40:19 INFO MemoryStore: MemoryStore started with capacity 408.9 MiB
20/08/06 14:40:19 INFO SparkEnv: Registering OutputCommitCoordinator
20/08/06 14:40:19 INFO Utils: Successfully started service 'SparkUI' on port 4040.
20/08/06 14:40:19 INFO SparkUI: Bound SparkUI to 0.0.0.0, and started at http://192.168.10.30:4040
20/08/06 14:40:19 INFO SparkContext: Added JAR file:/tmp/adamTestIb4eRTC/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/target/adam-assembly-spark3_2.12-0.33.0-SNAPSHOT.jar at spark://192.168.10.30:38005/jars/adam-assembly-spark3_2.12-0.33.0-SNAPSHOT.jar with timestamp 1596750019884
20/08/06 14:40:20 INFO Executor: Starting executor ID driver on host 192.168.10.30
20/08/06 14:40:20 INFO Utils: Successfully started service 'org.apache.spark.network.netty.NettyBlockTransferService' on port 35397.
20/08/06 14:40:20 INFO NettyBlockTransferService: Server created on 192.168.10.30:35397
20/08/06 14:40:20 INFO BlockManager: Using org.apache.spark.storage.RandomBlockReplicationPolicy for block replication policy
20/08/06 14:40:20 INFO BlockManagerMaster: Registering BlockManager BlockManagerId(driver, 192.168.10.30, 35397, None)
20/08/06 14:40:20 INFO BlockManagerMasterEndpoint: Registering block manager 192.168.10.30:35397 with 408.9 MiB RAM, BlockManagerId(driver, 192.168.10.30, 35397, None)
20/08/06 14:40:20 INFO BlockManagerMaster: Registered BlockManager BlockManagerId(driver, 192.168.10.30, 35397, None)
20/08/06 14:40:20 INFO BlockManager: Initialized BlockManager: BlockManagerId(driver, 192.168.10.30, 35397, None)
20/08/06 14:40:20 INFO ADAMContext: Loading mouse_chrM.bam.reads.adam as Parquet of Alignments.
20/08/06 14:40:22 INFO ADAMContext: Reading the ADAM file at mouse_chrM.bam.reads.adam to create RDD
20/08/06 14:40:22 INFO MemoryStore: Block broadcast_0 stored as values in memory (estimated size 309.3 KiB, free 408.6 MiB)
20/08/06 14:40:22 INFO MemoryStore: Block broadcast_0_piece0 stored as bytes in memory (estimated size 27.9 KiB, free 408.6 MiB)
20/08/06 14:40:22 INFO BlockManagerInfo: Added broadcast_0_piece0 in memory on 192.168.10.30:35397 (size: 27.9 KiB, free: 408.9 MiB)
20/08/06 14:40:22 INFO SparkContext: Created broadcast 0 from newAPIHadoopFile at ADAMContext.scala:1797
20/08/06 14:40:22 INFO TransformAlignments: Sorting alignments by reference position, with references ordered by name
20/08/06 14:40:22 INFO RDDBoundAlignmentDataset: Sorting alignments by reference position
20/08/06 14:40:22 INFO FileInputFormat: Total input paths to process : 1
20/08/06 14:40:22 INFO ParquetInputFormat: Total input paths to process : 1
20/08/06 14:40:22 INFO RDDBoundAlignmentDataset: Saving data in ADAM format
20/08/06 14:40:23 INFO FileOutputCommitter: File Output Committer Algorithm version is 1
20/08/06 14:40:23 INFO SparkContext: Starting job: runJob at SparkHadoopWriter.scala:78
20/08/06 14:40:23 INFO DAGScheduler: Registering RDD 2 (sortBy at AlignmentDataset.scala:1004) as input to shuffle 0
20/08/06 14:40:23 INFO DAGScheduler: Got job 0 (runJob at SparkHadoopWriter.scala:78) with 1 output partitions
20/08/06 14:40:23 INFO DAGScheduler: Final stage: ResultStage 1 (runJob at SparkHadoopWriter.scala:78)
20/08/06 14:40:23 INFO DAGScheduler: Parents of final stage: List(ShuffleMapStage 0)
20/08/06 14:40:23 INFO DAGScheduler: Missing parents: List(ShuffleMapStage 0)
20/08/06 14:40:23 INFO DAGScheduler: Submitting ShuffleMapStage 0 (MapPartitionsRDD[2] at sortBy at AlignmentDataset.scala:1004), which has no missing parents
20/08/06 14:40:23 INFO MemoryStore: Block broadcast_1 stored as values in memory (estimated size 6.9 KiB, free 408.6 MiB)
20/08/06 14:40:23 INFO MemoryStore: Block broadcast_1_piece0 stored as bytes in memory (estimated size 4.0 KiB, free 408.6 MiB)
20/08/06 14:40:23 INFO BlockManagerInfo: Added broadcast_1_piece0 in memory on 192.168.10.30:35397 (size: 4.0 KiB, free: 408.9 MiB)
20/08/06 14:40:23 INFO SparkContext: Created broadcast 1 from broadcast at DAGScheduler.scala:1200
20/08/06 14:40:23 INFO DAGScheduler: Submitting 1 missing tasks from ShuffleMapStage 0 (MapPartitionsRDD[2] at sortBy at AlignmentDataset.scala:1004) (first 15 tasks are for partitions Vector(0))
20/08/06 14:40:23 INFO TaskSchedulerImpl: Adding task set 0.0 with 1 tasks
20/08/06 14:40:23 INFO TaskSetManager: Starting task 0.0 in stage 0.0 (TID 0, 192.168.10.30, executor driver, partition 0, PROCESS_LOCAL, 7482 bytes)
20/08/06 14:40:23 INFO Executor: Running task 0.0 in stage 0.0 (TID 0)
20/08/06 14:40:23 INFO Executor: Fetching spark://192.168.10.30:38005/jars/adam-assembly-spark3_2.12-0.33.0-SNAPSHOT.jar with timestamp 1596750019884
20/08/06 14:40:23 INFO TransportClientFactory: Successfully created connection to /192.168.10.30:38005 after 43 ms (0 ms spent in bootstraps)
20/08/06 14:40:23 INFO Utils: Fetching spark://192.168.10.30:38005/jars/adam-assembly-spark3_2.12-0.33.0-SNAPSHOT.jar to /tmp/spark-8b62e2c0-b93a-413a-9429-b62e759a5ded/userFiles-ee2935c4-3904-40a2-a902-968598244fe9/fetchFileTemp8649725337383957680.tmp
20/08/06 14:40:23 INFO Executor: Adding file:/tmp/spark-8b62e2c0-b93a-413a-9429-b62e759a5ded/userFiles-ee2935c4-3904-40a2-a902-968598244fe9/adam-assembly-spark3_2.12-0.33.0-SNAPSHOT.jar to class loader
20/08/06 14:40:23 INFO NewHadoopRDD: Input split: file:/tmp/adamTestIb4eRTC/deleteMePleaseThisIsNoLongerNeeded/mouse_chrM.bam.reads.adam/part-r-00000.gz.parquet:0+10132211
20/08/06 14:40:23 INFO InternalParquetRecordReader: RecordReader initialized will read a total of 163064 records.
20/08/06 14:40:23 INFO InternalParquetRecordReader: at row 0. reading next block
20/08/06 14:40:24 INFO CodecPool: Got brand-new decompressor [.gz]
20/08/06 14:40:24 INFO InternalParquetRecordReader: block read in memory in 39 ms. row count = 163064
20/08/06 14:40:26 INFO Executor: Finished task 0.0 in stage 0.0 (TID 0). 1086 bytes result sent to driver
20/08/06 14:40:26 INFO TaskSetManager: Finished task 0.0 in stage 0.0 (TID 0) in 3551 ms on 192.168.10.30 (executor driver) (1/1)
20/08/06 14:40:26 INFO TaskSchedulerImpl: Removed TaskSet 0.0, whose tasks have all completed, from pool 
20/08/06 14:40:26 INFO DAGScheduler: ShuffleMapStage 0 (sortBy at AlignmentDataset.scala:1004) finished in 3.698 s
20/08/06 14:40:26 INFO DAGScheduler: looking for newly runnable stages
20/08/06 14:40:26 INFO DAGScheduler: running: Set()
20/08/06 14:40:26 INFO DAGScheduler: waiting: Set(ResultStage 1)
20/08/06 14:40:26 INFO DAGScheduler: failed: Set()
20/08/06 14:40:26 INFO DAGScheduler: Submitting ResultStage 1 (MapPartitionsRDD[5] at map at GenomicDataset.scala:3805), which has no missing parents
20/08/06 14:40:26 INFO MemoryStore: Block broadcast_2 stored as values in memory (estimated size 85.9 KiB, free 408.5 MiB)
20/08/06 14:40:26 INFO MemoryStore: Block broadcast_2_piece0 stored as bytes in memory (estimated size 32.2 KiB, free 408.4 MiB)
20/08/06 14:40:26 INFO BlockManagerInfo: Added broadcast_2_piece0 in memory on 192.168.10.30:35397 (size: 32.2 KiB, free: 408.8 MiB)
20/08/06 14:40:26 INFO SparkContext: Created broadcast 2 from broadcast at DAGScheduler.scala:1200
20/08/06 14:40:26 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))
20/08/06 14:40:26 INFO TaskSchedulerImpl: Adding task set 1.0 with 1 tasks
20/08/06 14:40:26 INFO TaskSetManager: Starting task 0.0 in stage 1.0 (TID 1, 192.168.10.30, executor driver, partition 0, NODE_LOCAL, 7143 bytes)
20/08/06 14:40:26 INFO Executor: Running task 0.0 in stage 1.0 (TID 1)
20/08/06 14:40:26 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
20/08/06 14:40:26 INFO ShuffleBlockFetcherIterator: Started 0 remote fetches in 10 ms
20/08/06 14:40:27 INFO BlockManagerInfo: Removed broadcast_1_piece0 on 192.168.10.30:35397 in memory (size: 4.0 KiB, free: 408.8 MiB)
20/08/06 14:40:28 INFO FileOutputCommitter: File Output Committer Algorithm version is 1
20/08/06 14:40:28 INFO CodecConfig: Compression: GZIP
20/08/06 14:40:28 INFO FileOutputCommitter: File Output Committer Algorithm version is 1
20/08/06 14:40:28 INFO ParquetOutputFormat: Parquet block size to 134217728
20/08/06 14:40:28 INFO ParquetOutputFormat: Parquet page size to 1048576
20/08/06 14:40:28 INFO ParquetOutputFormat: Parquet dictionary page size to 1048576
20/08/06 14:40:28 INFO ParquetOutputFormat: Dictionary is on
20/08/06 14:40:28 INFO ParquetOutputFormat: Validation is off
20/08/06 14:40:28 INFO ParquetOutputFormat: Writer version is: PARQUET_1_0
20/08/06 14:40:28 INFO ParquetOutputFormat: Maximum row group padding size is 8388608 bytes
20/08/06 14:40:28 INFO ParquetOutputFormat: Page size checking is: estimated
20/08/06 14:40:28 INFO ParquetOutputFormat: Min row count for page size check is: 100
20/08/06 14:40:28 INFO ParquetOutputFormat: Max row count for page size check is: 10000
20/08/06 14:40:28 INFO CodecPool: Got brand-new compressor [.gz]
20/08/06 14:40:32 INFO InternalParquetRecordWriter: Flushing mem columnStore to file. allocated memory: 16004474
20/08/06 14:40:32 INFO FileOutputCommitter: Saved output of task 'attempt_20200806144022_0005_r_000000_0' to file:/tmp/adamTestIb4eRTC/deleteMePleaseThisIsNoLongerNeeded/mouse_chrM.bam.reads.sorted.adam/_temporary/0/task_20200806144022_0005_r_000000
20/08/06 14:40:32 INFO SparkHadoopMapRedUtil: attempt_20200806144022_0005_r_000000_0: Committed
20/08/06 14:40:32 INFO Executor: Finished task 0.0 in stage 1.0 (TID 1). 1365 bytes result sent to driver
20/08/06 14:40:32 INFO TaskSetManager: Finished task 0.0 in stage 1.0 (TID 1) in 6113 ms on 192.168.10.30 (executor driver) (1/1)
20/08/06 14:40:32 INFO TaskSchedulerImpl: Removed TaskSet 1.0, whose tasks have all completed, from pool 
20/08/06 14:40:32 INFO DAGScheduler: ResultStage 1 (runJob at SparkHadoopWriter.scala:78) finished in 6.145 s
20/08/06 14:40:32 INFO DAGScheduler: Job 0 is finished. Cancelling potential speculative or zombie tasks for this job
20/08/06 14:40:32 INFO TaskSchedulerImpl: Killing all running tasks in stage 1: Stage finished
20/08/06 14:40:32 INFO DAGScheduler: Job 0 finished: runJob at SparkHadoopWriter.scala:78, took 9.936456 s
20/08/06 14:40:32 INFO ParquetFileReader: Initiating action with parallelism: 5
20/08/06 14:40:33 INFO SparkHadoopWriter: Job job_20200806144022_0005 committed.
20/08/06 14:40:33 INFO SparkContext: Invoking stop() from shutdown hook
20/08/06 14:40:33 INFO SparkUI: Stopped Spark web UI at http://192.168.10.30:4040
20/08/06 14:40:33 INFO MapOutputTrackerMasterEndpoint: MapOutputTrackerMasterEndpoint stopped!
20/08/06 14:40:33 INFO MemoryStore: MemoryStore cleared
20/08/06 14:40:33 INFO BlockManager: BlockManager stopped
20/08/06 14:40:33 INFO BlockManagerMaster: BlockManagerMaster stopped
20/08/06 14:40:33 INFO OutputCommitCoordinator$OutputCommitCoordinatorEndpoint: OutputCommitCoordinator stopped!
20/08/06 14:40:33 INFO SparkContext: Successfully stopped SparkContext
20/08/06 14:40:33 INFO ShutdownHookManager: Shutdown hook called
20/08/06 14:40:33 INFO ShutdownHookManager: Deleting directory /tmp/spark-44586c3c-eb6a-4760-9c46-ef466be38d54
20/08/06 14:40:33 INFO ShutdownHookManager: Deleting directory /tmp/spark-8b62e2c0-b93a-413a-9429-b62e759a5ded

# 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/adamTestIb4eRTC/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.0-bin-hadoop2.7/bin/spark-submit
20/08/06 14:40:34 WARN Utils: Your hostname, ubuntu-testing resolves to a loopback address: 127.0.1.1; using 192.168.10.30 instead (on interface eno1)
20/08/06 14:40:34 WARN Utils: Set SPARK_LOCAL_IP if you need to bind to another address
20/08/06 14:40:35 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
20/08/06 14:40:35 INFO SparkContext: Running Spark version 3.0.0
20/08/06 14:40:35 INFO ResourceUtils: ==============================================================
20/08/06 14:40:35 INFO ResourceUtils: Resources for spark.driver:

20/08/06 14:40:35 INFO ResourceUtils: ==============================================================
20/08/06 14:40:35 INFO SparkContext: Submitted application: transformFragments
20/08/06 14:40:35 INFO SecurityManager: Changing view acls to: jenkins
20/08/06 14:40:35 INFO SecurityManager: Changing modify acls to: jenkins
20/08/06 14:40:35 INFO SecurityManager: Changing view acls groups to: 
20/08/06 14:40:35 INFO SecurityManager: Changing modify acls groups to: 
20/08/06 14:40:35 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()
20/08/06 14:40:35 INFO Utils: Successfully started service 'sparkDriver' on port 40457.
20/08/06 14:40:36 INFO SparkEnv: Registering MapOutputTracker
20/08/06 14:40:36 INFO SparkEnv: Registering BlockManagerMaster
20/08/06 14:40:36 INFO BlockManagerMasterEndpoint: Using org.apache.spark.storage.DefaultTopologyMapper for getting topology information
20/08/06 14:40:36 INFO BlockManagerMasterEndpoint: BlockManagerMasterEndpoint up
20/08/06 14:40:36 INFO SparkEnv: Registering BlockManagerMasterHeartbeat
20/08/06 14:40:36 INFO DiskBlockManager: Created local directory at /tmp/blockmgr-160c1f32-259c-4231-8bac-940eb4ffdd31
20/08/06 14:40:36 INFO MemoryStore: MemoryStore started with capacity 408.9 MiB
20/08/06 14:40:36 INFO SparkEnv: Registering OutputCommitCoordinator
20/08/06 14:40:36 INFO Utils: Successfully started service 'SparkUI' on port 4040.
20/08/06 14:40:36 INFO SparkUI: Bound SparkUI to 0.0.0.0, and started at http://192.168.10.30:4040
20/08/06 14:40:36 INFO SparkContext: Added JAR file:/tmp/adamTestIb4eRTC/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/target/adam-assembly-spark3_2.12-0.33.0-SNAPSHOT.jar at spark://192.168.10.30:40457/jars/adam-assembly-spark3_2.12-0.33.0-SNAPSHOT.jar with timestamp 1596750036489
20/08/06 14:40:36 INFO Executor: Starting executor ID driver on host 192.168.10.30
20/08/06 14:40:36 INFO Utils: Successfully started service 'org.apache.spark.network.netty.NettyBlockTransferService' on port 44169.
20/08/06 14:40:36 INFO NettyBlockTransferService: Server created on 192.168.10.30:44169
20/08/06 14:40:36 INFO BlockManager: Using org.apache.spark.storage.RandomBlockReplicationPolicy for block replication policy
20/08/06 14:40:36 INFO BlockManagerMaster: Registering BlockManager BlockManagerId(driver, 192.168.10.30, 44169, None)
20/08/06 14:40:36 INFO BlockManagerMasterEndpoint: Registering block manager 192.168.10.30:44169 with 408.9 MiB RAM, BlockManagerId(driver, 192.168.10.30, 44169, None)
20/08/06 14:40:36 INFO BlockManagerMaster: Registered BlockManager BlockManagerId(driver, 192.168.10.30, 44169, None)
20/08/06 14:40:36 INFO BlockManager: Initialized BlockManager: BlockManagerId(driver, 192.168.10.30, 44169, None)
20/08/06 14:40:37 INFO ADAMContext: Loading mouse_chrM.bam.reads.adam as Parquet of Alignments.
20/08/06 14:40:38 INFO ADAMContext: Reading the ADAM file at mouse_chrM.bam.reads.adam to create RDD
20/08/06 14:40:38 INFO MemoryStore: Block broadcast_0 stored as values in memory (estimated size 309.3 KiB, free 408.6 MiB)
20/08/06 14:40:39 INFO MemoryStore: Block broadcast_0_piece0 stored as bytes in memory (estimated size 27.9 KiB, free 408.6 MiB)
20/08/06 14:40:39 INFO BlockManagerInfo: Added broadcast_0_piece0 in memory on 192.168.10.30:44169 (size: 27.9 KiB, free: 408.9 MiB)
20/08/06 14:40:39 INFO SparkContext: Created broadcast 0 from newAPIHadoopFile at ADAMContext.scala:1797
20/08/06 14:40:39 INFO FileInputFormat: Total input paths to process : 1
20/08/06 14:40:39 INFO ParquetInputFormat: Total input paths to process : 1
20/08/06 14:40:39 INFO RDDBoundFragmentDataset: Saving data in ADAM format
20/08/06 14:40:39 INFO FileOutputCommitter: File Output Committer Algorithm version is 1
20/08/06 14:40:39 INFO SparkContext: Starting job: runJob at SparkHadoopWriter.scala:78
20/08/06 14:40:39 INFO DAGScheduler: Registering RDD 2 (groupBy at SingleReadBucket.scala:97) as input to shuffle 0
20/08/06 14:40:39 INFO DAGScheduler: Got job 0 (runJob at SparkHadoopWriter.scala:78) with 1 output partitions
20/08/06 14:40:39 INFO DAGScheduler: Final stage: ResultStage 1 (runJob at SparkHadoopWriter.scala:78)
20/08/06 14:40:39 INFO DAGScheduler: Parents of final stage: List(ShuffleMapStage 0)
20/08/06 14:40:39 INFO DAGScheduler: Missing parents: List(ShuffleMapStage 0)
20/08/06 14:40:39 INFO DAGScheduler: Submitting ShuffleMapStage 0 (MapPartitionsRDD[2] at groupBy at SingleReadBucket.scala:97), which has no missing parents
20/08/06 14:40:39 INFO MemoryStore: Block broadcast_1 stored as values in memory (estimated size 7.3 KiB, free 408.6 MiB)
20/08/06 14:40:39 INFO MemoryStore: Block broadcast_1_piece0 stored as bytes in memory (estimated size 4.0 KiB, free 408.6 MiB)
20/08/06 14:40:39 INFO BlockManagerInfo: Added broadcast_1_piece0 in memory on 192.168.10.30:44169 (size: 4.0 KiB, free: 408.9 MiB)
20/08/06 14:40:39 INFO SparkContext: Created broadcast 1 from broadcast at DAGScheduler.scala:1200
20/08/06 14:40:39 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))
20/08/06 14:40:39 INFO TaskSchedulerImpl: Adding task set 0.0 with 1 tasks
20/08/06 14:40:39 INFO TaskSetManager: Starting task 0.0 in stage 0.0 (TID 0, 192.168.10.30, executor driver, partition 0, PROCESS_LOCAL, 7482 bytes)
20/08/06 14:40:39 INFO Executor: Running task 0.0 in stage 0.0 (TID 0)
20/08/06 14:40:39 INFO Executor: Fetching spark://192.168.10.30:40457/jars/adam-assembly-spark3_2.12-0.33.0-SNAPSHOT.jar with timestamp 1596750036489
20/08/06 14:40:39 INFO TransportClientFactory: Successfully created connection to /192.168.10.30:40457 after 42 ms (0 ms spent in bootstraps)
20/08/06 14:40:39 INFO Utils: Fetching spark://192.168.10.30:40457/jars/adam-assembly-spark3_2.12-0.33.0-SNAPSHOT.jar to /tmp/spark-adb1aac4-ff49-4fdf-af2f-69e923eb8235/userFiles-07c7e69c-e0fd-4dae-9493-8ba4565aa186/fetchFileTemp5305626427569488784.tmp
20/08/06 14:40:40 INFO Executor: Adding file:/tmp/spark-adb1aac4-ff49-4fdf-af2f-69e923eb8235/userFiles-07c7e69c-e0fd-4dae-9493-8ba4565aa186/adam-assembly-spark3_2.12-0.33.0-SNAPSHOT.jar to class loader
20/08/06 14:40:40 INFO NewHadoopRDD: Input split: file:/tmp/adamTestIb4eRTC/deleteMePleaseThisIsNoLongerNeeded/mouse_chrM.bam.reads.adam/part-r-00000.gz.parquet:0+10132211
20/08/06 14:40:40 INFO InternalParquetRecordReader: RecordReader initialized will read a total of 163064 records.
20/08/06 14:40:40 INFO InternalParquetRecordReader: at row 0. reading next block
20/08/06 14:40:40 INFO CodecPool: Got brand-new decompressor [.gz]
20/08/06 14:40:40 INFO InternalParquetRecordReader: block read in memory in 36 ms. row count = 163064
20/08/06 14:40:43 INFO Executor: Finished task 0.0 in stage 0.0 (TID 0). 1086 bytes result sent to driver
20/08/06 14:40:43 INFO TaskSetManager: Finished task 0.0 in stage 0.0 (TID 0) in 3657 ms on 192.168.10.30 (executor driver) (1/1)
20/08/06 14:40:43 INFO TaskSchedulerImpl: Removed TaskSet 0.0, whose tasks have all completed, from pool 
20/08/06 14:40:43 INFO DAGScheduler: ShuffleMapStage 0 (groupBy at SingleReadBucket.scala:97) finished in 3.791 s
20/08/06 14:40:43 INFO DAGScheduler: looking for newly runnable stages
20/08/06 14:40:43 INFO DAGScheduler: running: Set()
20/08/06 14:40:43 INFO DAGScheduler: waiting: Set(ResultStage 1)
20/08/06 14:40:43 INFO DAGScheduler: failed: Set()
20/08/06 14:40:43 INFO DAGScheduler: Submitting ResultStage 1 (MapPartitionsRDD[6] at map at GenomicDataset.scala:3805), which has no missing parents
20/08/06 14:40:43 INFO MemoryStore: Block broadcast_2 stored as values in memory (estimated size 90.1 KiB, free 408.5 MiB)
20/08/06 14:40:43 INFO MemoryStore: Block broadcast_2_piece0 stored as bytes in memory (estimated size 33.7 KiB, free 408.4 MiB)
20/08/06 14:40:43 INFO BlockManagerInfo: Added broadcast_2_piece0 in memory on 192.168.10.30:44169 (size: 33.7 KiB, free: 408.8 MiB)
20/08/06 14:40:43 INFO SparkContext: Created broadcast 2 from broadcast at DAGScheduler.scala:1200
20/08/06 14:40:43 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))
20/08/06 14:40:43 INFO TaskSchedulerImpl: Adding task set 1.0 with 1 tasks
20/08/06 14:40:43 INFO TaskSetManager: Starting task 0.0 in stage 1.0 (TID 1, 192.168.10.30, executor driver, partition 0, NODE_LOCAL, 7143 bytes)
20/08/06 14:40:43 INFO Executor: Running task 0.0 in stage 1.0 (TID 1)
20/08/06 14:40:43 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
20/08/06 14:40:43 INFO ShuffleBlockFetcherIterator: Started 0 remote fetches in 7 ms
20/08/06 14:40:44 INFO BlockManagerInfo: Removed broadcast_1_piece0 on 192.168.10.30:44169 in memory (size: 4.0 KiB, free: 408.8 MiB)
20/08/06 14:40:45 INFO FileOutputCommitter: File Output Committer Algorithm version is 1
20/08/06 14:40:45 INFO CodecConfig: Compression: GZIP
20/08/06 14:40:45 INFO FileOutputCommitter: File Output Committer Algorithm version is 1
20/08/06 14:40:45 INFO ParquetOutputFormat: Parquet block size to 134217728
20/08/06 14:40:45 INFO ParquetOutputFormat: Parquet page size to 1048576
20/08/06 14:40:45 INFO ParquetOutputFormat: Parquet dictionary page size to 1048576
20/08/06 14:40:45 INFO ParquetOutputFormat: Dictionary is on
20/08/06 14:40:45 INFO ParquetOutputFormat: Validation is off
20/08/06 14:40:45 INFO ParquetOutputFormat: Writer version is: PARQUET_1_0
20/08/06 14:40:45 INFO ParquetOutputFormat: Maximum row group padding size is 8388608 bytes
20/08/06 14:40:45 INFO ParquetOutputFormat: Page size checking is: estimated
20/08/06 14:40:45 INFO ParquetOutputFormat: Min row count for page size check is: 100
20/08/06 14:40:45 INFO ParquetOutputFormat: Max row count for page size check is: 10000
20/08/06 14:40:45 INFO CodecPool: Got brand-new compressor [.gz]
20/08/06 14:40:52 INFO InternalParquetRecordWriter: Flushing mem columnStore to file. allocated memory: 21417928
20/08/06 14:40:52 INFO FileOutputCommitter: Saved output of task 'attempt_20200806144039_0006_r_000000_0' to file:/tmp/adamTestIb4eRTC/deleteMePleaseThisIsNoLongerNeeded/mouse_chrM.bam.fragments.adam/_temporary/0/task_20200806144039_0006_r_000000
20/08/06 14:40:52 INFO SparkHadoopMapRedUtil: attempt_20200806144039_0006_r_000000_0: Committed
20/08/06 14:40:52 INFO Executor: Finished task 0.0 in stage 1.0 (TID 1). 1365 bytes result sent to driver
20/08/06 14:40:52 INFO TaskSetManager: Finished task 0.0 in stage 1.0 (TID 1) in 9175 ms on 192.168.10.30 (executor driver) (1/1)
20/08/06 14:40:52 INFO TaskSchedulerImpl: Removed TaskSet 1.0, whose tasks have all completed, from pool 
20/08/06 14:40:52 INFO DAGScheduler: ResultStage 1 (runJob at SparkHadoopWriter.scala:78) finished in 9.201 s
20/08/06 14:40:52 INFO DAGScheduler: Job 0 is finished. Cancelling potential speculative or zombie tasks for this job
20/08/06 14:40:52 INFO TaskSchedulerImpl: Killing all running tasks in stage 1: Stage finished
20/08/06 14:40:52 INFO DAGScheduler: Job 0 finished: runJob at SparkHadoopWriter.scala:78, took 13.074170 s
20/08/06 14:40:52 INFO ParquetFileReader: Initiating action with parallelism: 5
20/08/06 14:40:52 INFO SparkHadoopWriter: Job job_20200806144039_0006 committed.
20/08/06 14:40:52 INFO SparkContext: Invoking stop() from shutdown hook
20/08/06 14:40:52 INFO SparkUI: Stopped Spark web UI at http://192.168.10.30:4040
20/08/06 14:40:52 INFO MapOutputTrackerMasterEndpoint: MapOutputTrackerMasterEndpoint stopped!
20/08/06 14:40:52 INFO MemoryStore: MemoryStore cleared
20/08/06 14:40:52 INFO BlockManager: BlockManager stopped
20/08/06 14:40:52 INFO BlockManagerMaster: BlockManagerMaster stopped
20/08/06 14:40:52 INFO OutputCommitCoordinator$OutputCommitCoordinatorEndpoint: OutputCommitCoordinator stopped!
20/08/06 14:40:52 INFO SparkContext: Successfully stopped SparkContext
20/08/06 14:40:52 INFO ShutdownHookManager: Shutdown hook called
20/08/06 14:40:52 INFO ShutdownHookManager: Deleting directory /tmp/spark-d63908d1-de1c-43a4-8e2e-37786de63c46
20/08/06 14:40:52 INFO ShutdownHookManager: Deleting directory /tmp/spark-adb1aac4-ff49-4fdf-af2f-69e923eb8235

# 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/adamTestIb4eRTC/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.0-bin-hadoop2.7/bin/spark-submit
20/08/06 14:41:10 WARN Utils: Your hostname, ubuntu-testing resolves to a loopback address: 127.0.1.1; using 192.168.10.30 instead (on interface eno1)
20/08/06 14:41:10 WARN Utils: Set SPARK_LOCAL_IP if you need to bind to another address
20/08/06 14:41:10 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
20/08/06 14:41:11 INFO SparkContext: Running Spark version 3.0.0
20/08/06 14:41:11 INFO ResourceUtils: ==============================================================
20/08/06 14:41:11 INFO ResourceUtils: Resources for spark.driver:

20/08/06 14:41:11 INFO ResourceUtils: ==============================================================
20/08/06 14:41:11 INFO SparkContext: Submitted application: flagstat
20/08/06 14:41:11 INFO SecurityManager: Changing view acls to: jenkins
20/08/06 14:41:11 INFO SecurityManager: Changing modify acls to: jenkins
20/08/06 14:41:11 INFO SecurityManager: Changing view acls groups to: 
20/08/06 14:41:11 INFO SecurityManager: Changing modify acls groups to: 
20/08/06 14:41:11 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()
20/08/06 14:41:11 INFO Utils: Successfully started service 'sparkDriver' on port 37771.
20/08/06 14:41:11 INFO SparkEnv: Registering MapOutputTracker
20/08/06 14:41:11 INFO SparkEnv: Registering BlockManagerMaster
20/08/06 14:41:11 INFO BlockManagerMasterEndpoint: Using org.apache.spark.storage.DefaultTopologyMapper for getting topology information
20/08/06 14:41:11 INFO BlockManagerMasterEndpoint: BlockManagerMasterEndpoint up
20/08/06 14:41:11 INFO SparkEnv: Registering BlockManagerMasterHeartbeat
20/08/06 14:41:11 INFO DiskBlockManager: Created local directory at /tmp/blockmgr-a40ef068-a8e0-4ac1-aff3-e6355ecefdb0
20/08/06 14:41:11 INFO MemoryStore: MemoryStore started with capacity 408.9 MiB
20/08/06 14:41:11 INFO SparkEnv: Registering OutputCommitCoordinator
20/08/06 14:41:12 INFO Utils: Successfully started service 'SparkUI' on port 4040.
20/08/06 14:41:12 INFO SparkUI: Bound SparkUI to 0.0.0.0, and started at http://192.168.10.30:4040
20/08/06 14:41:12 INFO SparkContext: Added JAR file:/tmp/adamTestIb4eRTC/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/target/adam-assembly-spark3_2.12-0.33.0-SNAPSHOT.jar at spark://192.168.10.30:37771/jars/adam-assembly-spark3_2.12-0.33.0-SNAPSHOT.jar with timestamp 1596750072225
20/08/06 14:41:12 INFO Executor: Starting executor ID driver on host 192.168.10.30
20/08/06 14:41:12 INFO Utils: Successfully started service 'org.apache.spark.network.netty.NettyBlockTransferService' on port 34889.
20/08/06 14:41:12 INFO NettyBlockTransferService: Server created on 192.168.10.30:34889
20/08/06 14:41:12 INFO BlockManager: Using org.apache.spark.storage.RandomBlockReplicationPolicy for block replication policy
20/08/06 14:41:12 INFO BlockManagerMaster: Registering BlockManager BlockManagerId(driver, 192.168.10.30, 34889, None)
20/08/06 14:41:12 INFO BlockManagerMasterEndpoint: Registering block manager 192.168.10.30:34889 with 408.9 MiB RAM, BlockManagerId(driver, 192.168.10.30, 34889, None)
20/08/06 14:41:12 INFO BlockManagerMaster: Registered BlockManager BlockManagerId(driver, 192.168.10.30, 34889, None)
20/08/06 14:41:12 INFO BlockManager: Initialized BlockManager: BlockManagerId(driver, 192.168.10.30, 34889, None)
20/08/06 14:41:13 INFO ADAMContext: Loading mouse_chrM.bam.reads.adam as Parquet of Alignments.
20/08/06 14:41:13 INFO ADAMContext: Reading the ADAM file at mouse_chrM.bam.reads.adam to create RDD
20/08/06 14:41:13 INFO ADAMContext: Using the specified projection schema
20/08/06 14:41:13 INFO MemoryStore: Block broadcast_0 stored as values in memory (estimated size 320.5 KiB, free 408.6 MiB)
20/08/06 14:41:14 INFO MemoryStore: Block broadcast_0_piece0 stored as bytes in memory (estimated size 28.8 KiB, free 408.6 MiB)
20/08/06 14:41:14 INFO BlockManagerInfo: Added broadcast_0_piece0 in memory on 192.168.10.30:34889 (size: 28.8 KiB, free: 408.9 MiB)
20/08/06 14:41:14 INFO SparkContext: Created broadcast 0 from newAPIHadoopFile at ADAMContext.scala:1797
20/08/06 14:41:15 INFO FileInputFormat: Total input paths to process : 1
20/08/06 14:41:15 INFO ParquetInputFormat: Total input paths to process : 1
20/08/06 14:41:15 INFO SparkContext: Starting job: aggregate at FlagStat.scala:115
20/08/06 14:41:15 INFO DAGScheduler: Got job 0 (aggregate at FlagStat.scala:115) with 1 output partitions
20/08/06 14:41:15 INFO DAGScheduler: Final stage: ResultStage 0 (aggregate at FlagStat.scala:115)
20/08/06 14:41:15 INFO DAGScheduler: Parents of final stage: List()
20/08/06 14:41:15 INFO DAGScheduler: Missing parents: List()
20/08/06 14:41:15 INFO DAGScheduler: Submitting ResultStage 0 (MapPartitionsRDD[2] at map at FlagStat.scala:96), which has no missing parents
20/08/06 14:41:15 INFO MemoryStore: Block broadcast_1 stored as values in memory (estimated size 5.3 KiB, free 408.6 MiB)
20/08/06 14:41:15 INFO MemoryStore: Block broadcast_1_piece0 stored as bytes in memory (estimated size 2.9 KiB, free 408.6 MiB)
20/08/06 14:41:15 INFO BlockManagerInfo: Added broadcast_1_piece0 in memory on 192.168.10.30:34889 (size: 2.9 KiB, free: 408.9 MiB)
20/08/06 14:41:15 INFO SparkContext: Created broadcast 1 from broadcast at DAGScheduler.scala:1200
20/08/06 14:41:15 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))
20/08/06 14:41:15 INFO TaskSchedulerImpl: Adding task set 0.0 with 1 tasks
20/08/06 14:41:15 INFO TaskSetManager: Starting task 0.0 in stage 0.0 (TID 0, 192.168.10.30, executor driver, partition 0, PROCESS_LOCAL, 7493 bytes)
20/08/06 14:41:15 INFO Executor: Running task 0.0 in stage 0.0 (TID 0)
20/08/06 14:41:15 INFO Executor: Fetching spark://192.168.10.30:37771/jars/adam-assembly-spark3_2.12-0.33.0-SNAPSHOT.jar with timestamp 1596750072225
20/08/06 14:41:15 INFO TransportClientFactory: Successfully created connection to /192.168.10.30:37771 after 44 ms (0 ms spent in bootstraps)
20/08/06 14:41:15 INFO Utils: Fetching spark://192.168.10.30:37771/jars/adam-assembly-spark3_2.12-0.33.0-SNAPSHOT.jar to /tmp/spark-0b4ce629-1570-4fc6-a7d5-b807091182bf/userFiles-14af2011-fd13-4c1e-981f-d06cc8ca572c/fetchFileTemp5767572903385437181.tmp
20/08/06 14:41:16 INFO Executor: Adding file:/tmp/spark-0b4ce629-1570-4fc6-a7d5-b807091182bf/userFiles-14af2011-fd13-4c1e-981f-d06cc8ca572c/adam-assembly-spark3_2.12-0.33.0-SNAPSHOT.jar to class loader
20/08/06 14:41:16 INFO NewHadoopRDD: Input split: file:/tmp/adamTestIb4eRTC/deleteMePleaseThisIsNoLongerNeeded/mouse_chrM.bam.reads.adam/part-r-00000.gz.parquet:0+10132211
20/08/06 14:41:16 INFO InternalParquetRecordReader: RecordReader initialized will read a total of 163064 records.
20/08/06 14:41:16 INFO InternalParquetRecordReader: at row 0. reading next block
20/08/06 14:41:16 INFO CodecPool: Got brand-new decompressor [.gz]
20/08/06 14:41:16 INFO InternalParquetRecordReader: block read in memory in 20 ms. row count = 163064
20/08/06 14:41:17 INFO Executor: Finished task 0.0 in stage 0.0 (TID 0). 988 bytes result sent to driver
20/08/06 14:41:17 INFO TaskSetManager: Finished task 0.0 in stage 0.0 (TID 0) in 1399 ms on 192.168.10.30 (executor driver) (1/1)
20/08/06 14:41:17 INFO TaskSchedulerImpl: Removed TaskSet 0.0, whose tasks have all completed, from pool 
20/08/06 14:41:17 INFO DAGScheduler: ResultStage 0 (aggregate at FlagStat.scala:115) finished in 1.502 s
20/08/06 14:41:17 INFO DAGScheduler: Job 0 is finished. Cancelling potential speculative or zombie tasks for this job
20/08/06 14:41:17 INFO TaskSchedulerImpl: Killing all running tasks in stage 0: Stage finished
20/08/06 14:41:17 INFO DAGScheduler: Job 0 finished: aggregate at FlagStat.scala:115, took 1.562692 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)
20/08/06 14:41:17 INFO SparkContext: Invoking stop() from shutdown hook
20/08/06 14:41:17 INFO SparkUI: Stopped Spark web UI at http://192.168.10.30:4040
20/08/06 14:41:17 INFO MapOutputTrackerMasterEndpoint: MapOutputTrackerMasterEndpoint stopped!
20/08/06 14:41:17 INFO MemoryStore: MemoryStore cleared
20/08/06 14:41:17 INFO BlockManager: BlockManager stopped
20/08/06 14:41:17 INFO BlockManagerMaster: BlockManagerMaster stopped
20/08/06 14:41:17 INFO OutputCommitCoordinator$OutputCommitCoordinatorEndpoint: OutputCommitCoordinator stopped!
20/08/06 14:41:17 INFO SparkContext: Successfully stopped SparkContext
20/08/06 14:41:17 INFO ShutdownHookManager: Shutdown hook called
20/08/06 14:41:17 INFO ShutdownHookManager: Deleting directory /tmp/spark-0b4ce629-1570-4fc6-a7d5-b807091182bf
20/08/06 14:41:17 INFO ShutdownHookManager: Deleting directory /tmp/spark-fcd15618-0a87-486d-a7be-97603e39cdce
rm -rf ${ADAM_TMP_DIR}
+ rm -rf /tmp/adamTestIb4eRTC/deleteMePleaseThisIsNoLongerNeeded
popd
+ popd
~/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.0/label/ubuntu

pushd ${PROJECT_ROOT}
+ pushd /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.0/label/ubuntu/scripts/..
~/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.0/label/ubuntu ~/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.0/label/ubuntu

# move back to Scala 2.12 as default
if [ ${SCALA_VERSION} == 2.11 ];
then
    set +e
    ./scripts/move_to_scala_2.12.sh
    set -e
fi
+ '[' 2.12 == 2.11 ']'
# move back to Spark 3.x as default
if [ ${SPARK_VERSION} == 2.4.6 ];
then
    set +e
    ./scripts/move_to_spark_3.sh
    set -e
fi
+ '[' 3.0.0 == 2.4.6 ']'

# 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/SCALA_VERSION/2.12/SPARK_VERSION/3.0.0/label/ubuntu/scripts
+ pushd /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.0/label/ubuntu/scripts/..
~/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.0/label/ubuntu ~/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.0/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_2.12                                                          [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 0.33.0-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 244 .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 0.33.0-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 0.33.0-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 0.33.0-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 0.33.0-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 0.33.0-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 29 .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 0.33.0-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 0.33.0-SNAPSHOT:
[INFO] 
[INFO] ADAM_2.12 .......................................... SUCCESS [  6.873 s]
[INFO] ADAM_2.12: Shader workaround ....................... SUCCESS [  0.029 s]
[INFO] ADAM_2.12: Avro-to-Dataset codegen utils ........... SUCCESS [  0.049 s]
[INFO] ADAM_2.12: Core .................................... SUCCESS [  3.435 s]
[INFO] ADAM_2.12: APIs for Java, Python ................... SUCCESS [  0.138 s]
[INFO] ADAM_2.12: CLI ..................................... SUCCESS [  0.225 s]
[INFO] ADAM_2.12: Assembly ................................ SUCCESS [  0.012 s]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time:  11.212 s
[INFO] Finished at: 2020-08-06T14:41:30-07:00
[INFO] ------------------------------------------------------------------------
+ popd
~/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.0/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/SCALA_VERSION/2.12/SPARK_VERSION/3.0.0/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...
null
Setting commit status on GitHub for https://github.com/bigdatagenomics/adam/commit/e784e3f9c54a2759017edf39e0e26a2e7c346470
Finished: SUCCESS