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[WARNING] Entry: adam-distribution-spark2_2.12-0.32.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/VariantContextsToVariantContextConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.32.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/ReadsToVariantContextsConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.32.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/GenotypesToReadsDatasetConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.32.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/SlicesToFeaturesConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.32.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/AlignmentsToSlicesDatasetConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.32.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/GenotypesToReadsConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.32.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/ToFeatureDatasetConversion.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.32.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/ToSequenceDatasetConversion.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.32.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/ToReadDatasetConversion.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.32.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/GenotypesToFragmentsConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.32.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/SlicesToFeaturesDatasetConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.32.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/FeaturesToReadsConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.32.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/FragmentsToFeaturesConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.32.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/SequencesToSlicesConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.32.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/CoverageToVariantsDatasetConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.32.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/FeaturesToGenotypesConverter.html longer than 100 characters.
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[WARNING] Entry: adam-distribution-spark2_2.12-0.32.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/AlignmentsToVariantsDatasetConverter.html longer than 100 characters.
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[WARNING] Entry: adam-distribution-spark2_2.12-0.32.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/AlignmentsToReadsDatasetConverter.html longer than 100 characters.
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[WARNING] Entry: adam-distribution-spark2_2.12-0.32.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/FragmentsToReadsConverter.html longer than 100 characters.
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[WARNING] Entry: adam-distribution-spark2_2.12-0.32.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/VariantContextsToVariantsConverter.html longer than 100 characters.
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[WARNING] Entry: adam-distribution-spark2_2.12-0.32.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/ReadsToSlicesDatasetConverter.html longer than 100 characters.
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[WARNING] Entry: adam-distribution-spark2_2.12-0.32.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/cli/TransformSequences$.html longer than 100 characters.
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[WARNING] Entry: adam-distribution-spark2_2.12-0.32.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/cli/TransformGenotypesArgs.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.32.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/cli/TransformAlignments$.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.32.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/cli/CountSliceKmers$.html longer than 100 characters.
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[WARNING] Entry: adam-distribution-spark2_2.12-0.32.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/cli/TransformAlignmentsArgs.html longer than 100 characters.
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[WARNING] Entry: adam-distribution-spark2_2.12-0.32.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/cli/TransformFeatures$.html longer than 100 characters.
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[WARNING] Entry: adam-distribution-spark2_2.12-0.32.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/cli/TransformFeaturesArgs.html longer than 100 characters.
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[WARNING] Entry: adam-distribution-spark2_2.12-0.32.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/cli/TransformSequences.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.32.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/cli/TransformAlignments.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.32.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/cli/TransformGenotypes$.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.32.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/cli/TransformGenotypes.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.32.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/cli/CountSliceKmersArgs.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.32.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/cli/TransformVariants$.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.32.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/cli/CountReadKmers$.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.32.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/cli/TransformSequencesArgs.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.32.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/cli/TransformFeatures.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.32.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/cli/CountReadKmersArgs.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.32.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/cli/TransformSlices$.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.32.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/cli/TransformVariantsArgs.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.32.0-SNAPSHOT/repo/adam-assembly-spark2_2.12-0.32.0-SNAPSHOT-javadoc.jar longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.32.0-SNAPSHOT/repo/adam-assembly-spark2_2.12-0.32.0-SNAPSHOT-sources.jar longer than 100 characters.
[INFO] Building zip: /tmp/adamTestZP7FAWz/deleteMePleaseThisIsNoLongerNeeded/adam-distribution/target/adam-distribution-spark2_2.12-0.32.0-SNAPSHOT-bin.zip
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary:
[INFO] 
[INFO] ADAM_2.12 .......................................... SUCCESS [  7.437 s]
[INFO] ADAM_2.12: Shader workaround ....................... SUCCESS [  4.822 s]
[INFO] ADAM_2.12: Avro-to-Dataset codegen utils ........... SUCCESS [  4.751 s]
[INFO] ADAM_2.12: Core .................................... SUCCESS [01:02 min]
[INFO] ADAM_2.12: APIs for Java, Python ................... SUCCESS [  9.288 s]
[INFO] ADAM_2.12: CLI ..................................... SUCCESS [ 11.065 s]
[INFO] ADAM_2.12: Assembly ................................ SUCCESS [ 17.030 s]
[INFO] ADAM_2.12: Python APIs ............................. SUCCESS [01:20 min]
[INFO] ADAM_2.12: R APIs .................................. SUCCESS [ 55.819 s]
[INFO] ADAM_2.12: Distribution ............................ SUCCESS [ 40.885 s]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 04:54 min
[INFO] Finished at: 2020-04-28T08:45:49-07:00
[INFO] Final Memory: 64M/1498M
[INFO] ------------------------------------------------------------------------
+ grep bdgenomics.adam
+ tar tzvf adam-distribution/target/adam-distribution-spark2_2.12-0.32.0-SNAPSHOT-bin.tar.gz
+ grep egg
drwxrwxr-x jenkins/jenkins        0 2020-04-28 08:42 adam-distribution-spark2_2.12-0.32.0-SNAPSHOT/r/bdgenomics.adam.egg-info/
-rw-r--r-- jenkins/jenkins 36836455 2020-04-28 08:43 adam-distribution-spark2_2.12-0.32.0-SNAPSHOT/repo/bdgenomics.adam-0.32.0a0-py3.6.egg
+ ./bin/pyadam
Using PYSPARK=/tmp/adamTestZP7FAWz/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.5-bin-without-hadoop-scala-2.12/bin/pyspark
2020-04-28 08:45:52 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)
2020-04-28 08:45:52 WARN  Utils:66 - Set SPARK_LOCAL_IP if you need to bind to another address
2020-04-28 08:45:52 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).
2020-04-28 08:45:58 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-36cb9965-e642-4b6a-a678-bcb5b9001e34) '
+++ /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 "$_CONDA_SHELL_FLAVOR" in
++ hash -r
+ conda remove -y -n adam-build-36cb9965-e642-4b6a-a678-bcb5b9001e34 --all
+ '[' 5 -lt 1 ']'
+ local cmd=remove
+ shift
+ case "$cmd" in
+ /home/jenkins/anaconda2/bin/conda remove -y -n adam-build-36cb9965-e642-4b6a-a678-bcb5b9001e34 --all

Remove all packages in environment /home/jenkins/anaconda2/envs/adam-build-36cb9965-e642-4b6a-a678-bcb5b9001e34:


## Package Plan ##

  environment location: /home/jenkins/anaconda2/envs/adam-build-36cb9965-e642-4b6a-a678-bcb5b9001e34


The following packages will be REMOVED:

    _libgcc_mutex:    0.1-main               
    ca-certificates:  2020.1.1-0             
    certifi:          2020.4.5.1-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:          1.1.1g-h7b6447c_0      
    pip:              20.0.2-py36_1          
    python:           3.6.10-hcf32534_1      
    readline:         8.0-h7b6447c_0         
    setuptools:       46.1.3-py36_0          
    sqlite:           3.31.1-h62c20be_1      
    tk:               8.6.8-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/SCALAVER/2.12/SPARK_VERSION/2.4.5/label/ubuntu/scripts/../adam-python/
+ pushd adam-python
/tmp/adamTestZP7FAWz/deleteMePleaseThisIsNoLongerNeeded/adam-python /tmp/adamTestZP7FAWz/deleteMePleaseThisIsNoLongerNeeded ~/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/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/adamTestZP7FAWz/deleteMePleaseThisIsNoLongerNeeded ~/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/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/adamTestZP7FAWz/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.5-bin-without-hadoop-scala-2.12/bin/spark-submit
20/04/28 08:46:06 WARN util.Utils: Your hostname, ubuntu-testing resolves to a loopback address: 127.0.1.1; using 192.168.10.30 instead (on interface eno1)
20/04/28 08:46:06 WARN util.Utils: Set SPARK_LOCAL_IP if you need to bind to another address
20/04/28 08:46:07 WARN util.NativeCodeLoader: Unable to load native-hadoop library for your platform... using builtin-java classes where applicable
20/04/28 08:46:07 INFO cli.ADAMMain: ADAM invoked with args: "transformAlignments" "mouse_chrM.bam" "mouse_chrM.bam.reads.adam"
20/04/28 08:46:07 INFO spark.SparkContext: Running Spark version 2.4.5
20/04/28 08:46:07 INFO spark.SparkContext: Submitted application: transformAlignments
20/04/28 08:46:07 INFO spark.SecurityManager: Changing view acls to: jenkins
20/04/28 08:46:07 INFO spark.SecurityManager: Changing modify acls to: jenkins
20/04/28 08:46:07 INFO spark.SecurityManager: Changing view acls groups to: 
20/04/28 08:46:07 INFO spark.SecurityManager: Changing modify acls groups to: 
20/04/28 08:46:07 INFO spark.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()
20/04/28 08:46:08 INFO util.Utils: Successfully started service 'sparkDriver' on port 42849.
20/04/28 08:46:08 INFO spark.SparkEnv: Registering MapOutputTracker
20/04/28 08:46:08 INFO spark.SparkEnv: Registering BlockManagerMaster
20/04/28 08:46:08 INFO storage.BlockManagerMasterEndpoint: Using org.apache.spark.storage.DefaultTopologyMapper for getting topology information
20/04/28 08:46:08 INFO storage.BlockManagerMasterEndpoint: BlockManagerMasterEndpoint up
20/04/28 08:46:08 INFO storage.DiskBlockManager: Created local directory at /tmp/blockmgr-77c5ff7e-6125-4f22-83b6-e38fc0b7da3e
20/04/28 08:46:08 INFO memory.MemoryStore: MemoryStore started with capacity 366.3 MB
20/04/28 08:46:08 INFO spark.SparkEnv: Registering OutputCommitCoordinator
20/04/28 08:46:08 INFO util.log: Logging initialized @2272ms
20/04/28 08:46:08 INFO server.Server: jetty-9.3.z-SNAPSHOT, build timestamp: unknown, git hash: unknown
20/04/28 08:46:08 INFO server.Server: Started @2341ms
20/04/28 08:46:08 INFO server.AbstractConnector: Started ServerConnector@1e53135d{HTTP/1.1,[http/1.1]}{0.0.0.0:4040}
20/04/28 08:46:08 INFO util.Utils: Successfully started service 'SparkUI' on port 4040.
20/04/28 08:46:08 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@6b739528{/jobs,null,AVAILABLE,@Spark}
20/04/28 08:46:08 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@61e3a1fd{/jobs/json,null,AVAILABLE,@Spark}
20/04/28 08:46:08 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@51abf713{/jobs/job,null,AVAILABLE,@Spark}
20/04/28 08:46:08 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@4d4d48a6{/jobs/job/json,null,AVAILABLE,@Spark}
20/04/28 08:46:08 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@315df4bb{/stages,null,AVAILABLE,@Spark}
20/04/28 08:46:08 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@3fc08eec{/stages/json,null,AVAILABLE,@Spark}
20/04/28 08:46:08 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@5cad8b7d{/stages/stage,null,AVAILABLE,@Spark}
20/04/28 08:46:08 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@1e287667{/stages/stage/json,null,AVAILABLE,@Spark}
20/04/28 08:46:08 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@2e6ee0bc{/stages/pool,null,AVAILABLE,@Spark}
20/04/28 08:46:08 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@4201a617{/stages/pool/json,null,AVAILABLE,@Spark}
20/04/28 08:46:08 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@467f77a5{/storage,null,AVAILABLE,@Spark}
20/04/28 08:46:08 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@1bb9aa43{/storage/json,null,AVAILABLE,@Spark}
20/04/28 08:46:08 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@420bc288{/storage/rdd,null,AVAILABLE,@Spark}
20/04/28 08:46:08 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@df5f5c0{/storage/rdd/json,null,AVAILABLE,@Spark}
20/04/28 08:46:08 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@308a6984{/environment,null,AVAILABLE,@Spark}
20/04/28 08:46:08 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@66b72664{/environment/json,null,AVAILABLE,@Spark}
20/04/28 08:46:08 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@7a34b7b8{/executors,null,AVAILABLE,@Spark}
20/04/28 08:46:08 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@58cd06cb{/executors/json,null,AVAILABLE,@Spark}
20/04/28 08:46:08 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@3be8821f{/executors/threadDump,null,AVAILABLE,@Spark}
20/04/28 08:46:08 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@64b31700{/executors/threadDump/json,null,AVAILABLE,@Spark}
20/04/28 08:46:08 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@3b65e559{/static,null,AVAILABLE,@Spark}
20/04/28 08:46:08 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@49bd54f7{/,null,AVAILABLE,@Spark}
20/04/28 08:46:08 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@6b5f8707{/api,null,AVAILABLE,@Spark}
20/04/28 08:46:08 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@6e5bfdfc{/jobs/job/kill,null,AVAILABLE,@Spark}
20/04/28 08:46:08 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@3d829787{/stages/stage/kill,null,AVAILABLE,@Spark}
20/04/28 08:46:08 INFO ui.SparkUI: Bound SparkUI to 0.0.0.0, and started at http://192.168.10.30:4040
20/04/28 08:46:08 INFO spark.SparkContext: Added JAR file:/tmp/adamTestZP7FAWz/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/target/adam-assembly-spark2_2.12-0.32.0-SNAPSHOT.jar at spark://192.168.10.30:42849/jars/adam-assembly-spark2_2.12-0.32.0-SNAPSHOT.jar with timestamp 1588088768332
20/04/28 08:46:08 INFO executor.Executor: Starting executor ID driver on host localhost
20/04/28 08:46:08 INFO util.Utils: Successfully started service 'org.apache.spark.network.netty.NettyBlockTransferService' on port 42281.
20/04/28 08:46:08 INFO netty.NettyBlockTransferService: Server created on 192.168.10.30:42281
20/04/28 08:46:08 INFO storage.BlockManager: Using org.apache.spark.storage.RandomBlockReplicationPolicy for block replication policy
20/04/28 08:46:08 INFO storage.BlockManagerMaster: Registering BlockManager BlockManagerId(driver, 192.168.10.30, 42281, None)
20/04/28 08:46:08 INFO storage.BlockManagerMasterEndpoint: Registering block manager 192.168.10.30:42281 with 366.3 MB RAM, BlockManagerId(driver, 192.168.10.30, 42281, None)
20/04/28 08:46:08 INFO storage.BlockManagerMaster: Registered BlockManager BlockManagerId(driver, 192.168.10.30, 42281, None)
20/04/28 08:46:08 INFO storage.BlockManager: Initialized BlockManager: BlockManagerId(driver, 192.168.10.30, 42281, None)
20/04/28 08:46:08 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@79a1728c{/metrics/json,null,AVAILABLE,@Spark}
20/04/28 08:46:09 INFO rdd.ADAMContext: Loading mouse_chrM.bam as BAM/CRAM/SAM and converting to Alignments.
20/04/28 08:46:09 INFO rdd.ADAMContext: Loaded header from file:/tmp/adamTestZP7FAWz/deleteMePleaseThisIsNoLongerNeeded/mouse_chrM.bam
20/04/28 08:46:09 INFO memory.MemoryStore: Block broadcast_0 stored as values in memory (estimated size 295.6 KB, free 366.0 MB)
20/04/28 08:46:10 INFO memory.MemoryStore: Block broadcast_0_piece0 stored as bytes in memory (estimated size 24.0 KB, free 366.0 MB)
20/04/28 08:46:10 INFO storage.BlockManagerInfo: Added broadcast_0_piece0 in memory on 192.168.10.30:42281 (size: 24.0 KB, free: 366.3 MB)
20/04/28 08:46:10 INFO spark.SparkContext: Created broadcast 0 from newAPIHadoopFile at ADAMContext.scala:2059
20/04/28 08:46:11 INFO read.RDDBoundAlignmentDataset: Saving data in ADAM format
20/04/28 08:46:11 INFO output.FileOutputCommitter: File Output Committer Algorithm version is 1
20/04/28 08:46:11 INFO input.FileInputFormat: Total input paths to process : 1
20/04/28 08:46:11 INFO spark.SparkContext: Starting job: runJob at SparkHadoopWriter.scala:78
20/04/28 08:46:11 INFO scheduler.DAGScheduler: Got job 0 (runJob at SparkHadoopWriter.scala:78) with 1 output partitions
20/04/28 08:46:11 INFO scheduler.DAGScheduler: Final stage: ResultStage 0 (runJob at SparkHadoopWriter.scala:78)
20/04/28 08:46:11 INFO scheduler.DAGScheduler: Parents of final stage: List()
20/04/28 08:46:11 INFO scheduler.DAGScheduler: Missing parents: List()
20/04/28 08:46:11 INFO scheduler.DAGScheduler: Submitting ResultStage 0 (MapPartitionsRDD[2] at map at GenomicDataset.scala:3814), which has no missing parents
20/04/28 08:46:11 INFO memory.MemoryStore: Block broadcast_1 stored as values in memory (estimated size 85.6 KB, free 365.9 MB)
20/04/28 08:46:11 INFO memory.MemoryStore: Block broadcast_1_piece0 stored as bytes in memory (estimated size 31.6 KB, free 365.9 MB)
20/04/28 08:46:11 INFO storage.BlockManagerInfo: Added broadcast_1_piece0 in memory on 192.168.10.30:42281 (size: 31.6 KB, free: 366.2 MB)
20/04/28 08:46:11 INFO spark.SparkContext: Created broadcast 1 from broadcast at DAGScheduler.scala:1163
20/04/28 08:46:11 INFO scheduler.DAGScheduler: Submitting 1 missing tasks from ResultStage 0 (MapPartitionsRDD[2] at map at GenomicDataset.scala:3814) (first 15 tasks are for partitions Vector(0))
20/04/28 08:46:11 INFO scheduler.TaskSchedulerImpl: Adding task set 0.0 with 1 tasks
20/04/28 08:46:11 INFO scheduler.TaskSetManager: Starting task 0.0 in stage 0.0 (TID 0, localhost, executor driver, partition 0, PROCESS_LOCAL, 7441 bytes)
20/04/28 08:46:11 INFO executor.Executor: Running task 0.0 in stage 0.0 (TID 0)
20/04/28 08:46:11 INFO executor.Executor: Fetching spark://192.168.10.30:42849/jars/adam-assembly-spark2_2.12-0.32.0-SNAPSHOT.jar with timestamp 1588088768332
20/04/28 08:46:11 INFO client.TransportClientFactory: Successfully created connection to /192.168.10.30:42849 after 36 ms (0 ms spent in bootstraps)
20/04/28 08:46:11 INFO util.Utils: Fetching spark://192.168.10.30:42849/jars/adam-assembly-spark2_2.12-0.32.0-SNAPSHOT.jar to /tmp/spark-acf772ef-e536-4d40-814f-3f9012f0f946/userFiles-7c4394f0-3927-4ac1-a17a-bd9eb2e04917/fetchFileTemp3605040721392360538.tmp
20/04/28 08:46:11 INFO executor.Executor: Adding file:/tmp/spark-acf772ef-e536-4d40-814f-3f9012f0f946/userFiles-7c4394f0-3927-4ac1-a17a-bd9eb2e04917/adam-assembly-spark2_2.12-0.32.0-SNAPSHOT.jar to class loader
20/04/28 08:46:12 INFO rdd.NewHadoopRDD: Input split: file:/tmp/adamTestZP7FAWz/deleteMePleaseThisIsNoLongerNeeded/mouse_chrM.bam:83361792-833134657535
20/04/28 08:46:12 INFO output.FileOutputCommitter: File Output Committer Algorithm version is 1
20/04/28 08:46:12 INFO codec.CodecConfig: Compression: GZIP
20/04/28 08:46:12 INFO output.FileOutputCommitter: File Output Committer Algorithm version is 1
20/04/28 08:46:12 INFO hadoop.ParquetOutputFormat: Parquet block size to 134217728
20/04/28 08:46:12 INFO hadoop.ParquetOutputFormat: Parquet page size to 1048576
20/04/28 08:46:12 INFO hadoop.ParquetOutputFormat: Parquet dictionary page size to 1048576
20/04/28 08:46:12 INFO hadoop.ParquetOutputFormat: Dictionary is on
20/04/28 08:46:12 INFO hadoop.ParquetOutputFormat: Validation is off
20/04/28 08:46:12 INFO hadoop.ParquetOutputFormat: Writer version is: PARQUET_1_0
20/04/28 08:46:12 INFO hadoop.ParquetOutputFormat: Maximum row group padding size is 8388608 bytes
20/04/28 08:46:12 INFO hadoop.ParquetOutputFormat: Page size checking is: estimated
20/04/28 08:46:12 INFO hadoop.ParquetOutputFormat: Min row count for page size check is: 100
20/04/28 08:46:12 INFO hadoop.ParquetOutputFormat: Max row count for page size check is: 10000
20/04/28 08:46:12 INFO compress.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.
20/04/28 08:46:20 INFO hadoop.InternalParquetRecordWriter: Flushing mem columnStore to file. allocated memory: 16043959
20/04/28 08:46:21 INFO output.FileOutputCommitter: Saved output of task 'attempt_20200428084611_0002_r_000000_0' to file:/tmp/adamTestZP7FAWz/deleteMePleaseThisIsNoLongerNeeded/mouse_chrM.bam.reads.adam/_temporary/0/task_20200428084611_0002_r_000000
20/04/28 08:46:21 INFO mapred.SparkHadoopMapRedUtil: attempt_20200428084611_0002_r_000000_0: Committed
20/04/28 08:46:21 INFO executor.Executor: Finished task 0.0 in stage 0.0 (TID 0). 856 bytes result sent to driver
20/04/28 08:46:21 INFO scheduler.TaskSetManager: Finished task 0.0 in stage 0.0 (TID 0) in 9660 ms on localhost (executor driver) (1/1)
20/04/28 08:46:21 INFO scheduler.TaskSchedulerImpl: Removed TaskSet 0.0, whose tasks have all completed, from pool 
20/04/28 08:46:21 INFO scheduler.DAGScheduler: ResultStage 0 (runJob at SparkHadoopWriter.scala:78) finished in 9.784 s
20/04/28 08:46:21 INFO scheduler.DAGScheduler: Job 0 finished: runJob at SparkHadoopWriter.scala:78, took 9.845650 s
20/04/28 08:46:21 INFO hadoop.ParquetFileReader: Initiating action with parallelism: 5
20/04/28 08:46:21 INFO io.SparkHadoopWriter: Job job_20200428084611_0002 committed.
20/04/28 08:46:21 INFO cli.TransformAlignments: Overall Duration: 13.69 secs
20/04/28 08:46:21 INFO spark.SparkContext: Invoking stop() from shutdown hook
20/04/28 08:46:21 INFO server.AbstractConnector: Stopped Spark@1e53135d{HTTP/1.1,[http/1.1]}{0.0.0.0:4040}
20/04/28 08:46:21 INFO ui.SparkUI: Stopped Spark web UI at http://192.168.10.30:4040
20/04/28 08:46:21 INFO spark.MapOutputTrackerMasterEndpoint: MapOutputTrackerMasterEndpoint stopped!
20/04/28 08:46:21 INFO memory.MemoryStore: MemoryStore cleared
20/04/28 08:46:21 INFO storage.BlockManager: BlockManager stopped
20/04/28 08:46:21 INFO storage.BlockManagerMaster: BlockManagerMaster stopped
20/04/28 08:46:21 INFO scheduler.OutputCommitCoordinator$OutputCommitCoordinatorEndpoint: OutputCommitCoordinator stopped!
20/04/28 08:46:21 INFO spark.SparkContext: Successfully stopped SparkContext
20/04/28 08:46:21 INFO util.ShutdownHookManager: Shutdown hook called
20/04/28 08:46:21 INFO util.ShutdownHookManager: Deleting directory /tmp/spark-ac0d1d17-0e39-4feb-904b-2d574710243d
20/04/28 08:46:21 INFO util.ShutdownHookManager: Deleting directory /tmp/spark-acf772ef-e536-4d40-814f-3f9012f0f946

# 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/adamTestZP7FAWz/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.5-bin-without-hadoop-scala-2.12/bin/spark-submit
20/04/28 08:46:22 WARN util.Utils: Your hostname, ubuntu-testing resolves to a loopback address: 127.0.1.1; using 192.168.10.30 instead (on interface eno1)
20/04/28 08:46:22 WARN util.Utils: Set SPARK_LOCAL_IP if you need to bind to another address
20/04/28 08:46:23 WARN util.NativeCodeLoader: Unable to load native-hadoop library for your platform... using builtin-java classes where applicable
20/04/28 08:46:23 INFO cli.ADAMMain: ADAM invoked with args: "transformAlignments" "-sort_by_reference_position" "mouse_chrM.bam.reads.adam" "mouse_chrM.bam.reads.sorted.adam"
20/04/28 08:46:23 INFO spark.SparkContext: Running Spark version 2.4.5
20/04/28 08:46:23 INFO spark.SparkContext: Submitted application: transformAlignments
20/04/28 08:46:23 INFO spark.SecurityManager: Changing view acls to: jenkins
20/04/28 08:46:23 INFO spark.SecurityManager: Changing modify acls to: jenkins
20/04/28 08:46:23 INFO spark.SecurityManager: Changing view acls groups to: 
20/04/28 08:46:23 INFO spark.SecurityManager: Changing modify acls groups to: 
20/04/28 08:46:23 INFO spark.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()
20/04/28 08:46:24 INFO util.Utils: Successfully started service 'sparkDriver' on port 45317.
20/04/28 08:46:24 INFO spark.SparkEnv: Registering MapOutputTracker
20/04/28 08:46:24 INFO spark.SparkEnv: Registering BlockManagerMaster
20/04/28 08:46:24 INFO storage.BlockManagerMasterEndpoint: Using org.apache.spark.storage.DefaultTopologyMapper for getting topology information
20/04/28 08:46:24 INFO storage.BlockManagerMasterEndpoint: BlockManagerMasterEndpoint up
20/04/28 08:46:24 INFO storage.DiskBlockManager: Created local directory at /tmp/blockmgr-679ff1a0-cfe7-4ab0-a220-77b9af639e0d
20/04/28 08:46:24 INFO memory.MemoryStore: MemoryStore started with capacity 366.3 MB
20/04/28 08:46:24 INFO spark.SparkEnv: Registering OutputCommitCoordinator
20/04/28 08:46:24 INFO util.log: Logging initialized @2319ms
20/04/28 08:46:24 INFO server.Server: jetty-9.3.z-SNAPSHOT, build timestamp: unknown, git hash: unknown
20/04/28 08:46:24 INFO server.Server: Started @2383ms
20/04/28 08:46:24 INFO server.AbstractConnector: Started ServerConnector@7674a051{HTTP/1.1,[http/1.1]}{0.0.0.0:4040}
20/04/28 08:46:24 INFO util.Utils: Successfully started service 'SparkUI' on port 4040.
20/04/28 08:46:24 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@622ef26a{/jobs,null,AVAILABLE,@Spark}
20/04/28 08:46:24 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@51abf713{/jobs/json,null,AVAILABLE,@Spark}
20/04/28 08:46:24 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@eadb475{/jobs/job,null,AVAILABLE,@Spark}
20/04/28 08:46:24 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@315df4bb{/jobs/job/json,null,AVAILABLE,@Spark}
20/04/28 08:46:24 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@3fc08eec{/stages,null,AVAILABLE,@Spark}
20/04/28 08:46:24 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@5cad8b7d{/stages/json,null,AVAILABLE,@Spark}
20/04/28 08:46:24 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@7b02e036{/stages/stage,null,AVAILABLE,@Spark}
20/04/28 08:46:24 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@2e6ee0bc{/stages/stage/json,null,AVAILABLE,@Spark}
20/04/28 08:46:24 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@4201a617{/stages/pool,null,AVAILABLE,@Spark}
20/04/28 08:46:24 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@467f77a5{/stages/pool/json,null,AVAILABLE,@Spark}
20/04/28 08:46:24 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@1bb9aa43{/storage,null,AVAILABLE,@Spark}
20/04/28 08:46:24 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@420bc288{/storage/json,null,AVAILABLE,@Spark}
20/04/28 08:46:24 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@df5f5c0{/storage/rdd,null,AVAILABLE,@Spark}
20/04/28 08:46:24 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@308a6984{/storage/rdd/json,null,AVAILABLE,@Spark}
20/04/28 08:46:24 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@66b72664{/environment,null,AVAILABLE,@Spark}
20/04/28 08:46:24 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@7a34b7b8{/environment/json,null,AVAILABLE,@Spark}
20/04/28 08:46:24 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@58cd06cb{/executors,null,AVAILABLE,@Spark}
20/04/28 08:46:24 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@3be8821f{/executors/json,null,AVAILABLE,@Spark}
20/04/28 08:46:24 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@64b31700{/executors/threadDump,null,AVAILABLE,@Spark}
20/04/28 08:46:24 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@3b65e559{/executors/threadDump/json,null,AVAILABLE,@Spark}
20/04/28 08:46:24 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@bae47a0{/static,null,AVAILABLE,@Spark}
20/04/28 08:46:24 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@6b5f8707{/,null,AVAILABLE,@Spark}
20/04/28 08:46:24 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@772485dd{/api,null,AVAILABLE,@Spark}
20/04/28 08:46:24 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@3d829787{/jobs/job/kill,null,AVAILABLE,@Spark}
20/04/28 08:46:24 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@71652c98{/stages/stage/kill,null,AVAILABLE,@Spark}
20/04/28 08:46:24 INFO ui.SparkUI: Bound SparkUI to 0.0.0.0, and started at http://192.168.10.30:4040
20/04/28 08:46:24 INFO spark.SparkContext: Added JAR file:/tmp/adamTestZP7FAWz/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/target/adam-assembly-spark2_2.12-0.32.0-SNAPSHOT.jar at spark://192.168.10.30:45317/jars/adam-assembly-spark2_2.12-0.32.0-SNAPSHOT.jar with timestamp 1588088784412
20/04/28 08:46:24 INFO executor.Executor: Starting executor ID driver on host localhost
20/04/28 08:46:24 INFO util.Utils: Successfully started service 'org.apache.spark.network.netty.NettyBlockTransferService' on port 39719.
20/04/28 08:46:24 INFO netty.NettyBlockTransferService: Server created on 192.168.10.30:39719
20/04/28 08:46:24 INFO storage.BlockManager: Using org.apache.spark.storage.RandomBlockReplicationPolicy for block replication policy
20/04/28 08:46:24 INFO storage.BlockManagerMaster: Registering BlockManager BlockManagerId(driver, 192.168.10.30, 39719, None)
20/04/28 08:46:24 INFO storage.BlockManagerMasterEndpoint: Registering block manager 192.168.10.30:39719 with 366.3 MB RAM, BlockManagerId(driver, 192.168.10.30, 39719, None)
20/04/28 08:46:24 INFO storage.BlockManagerMaster: Registered BlockManager BlockManagerId(driver, 192.168.10.30, 39719, None)
20/04/28 08:46:24 INFO storage.BlockManager: Initialized BlockManager: BlockManagerId(driver, 192.168.10.30, 39719, None)
20/04/28 08:46:24 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@a7f0ab6{/metrics/json,null,AVAILABLE,@Spark}
20/04/28 08:46:25 INFO rdd.ADAMContext: Loading mouse_chrM.bam.reads.adam as Parquet of Alignments.
20/04/28 08:46:26 INFO rdd.ADAMContext: Reading the ADAM file at mouse_chrM.bam.reads.adam to create RDD
20/04/28 08:46:26 INFO memory.MemoryStore: Block broadcast_0 stored as values in memory (estimated size 315.0 KB, free 366.0 MB)
20/04/28 08:46:27 INFO memory.MemoryStore: Block broadcast_0_piece0 stored as bytes in memory (estimated size 28.1 KB, free 366.0 MB)
20/04/28 08:46:27 INFO storage.BlockManagerInfo: Added broadcast_0_piece0 in memory on 192.168.10.30:39719 (size: 28.1 KB, free: 366.3 MB)
20/04/28 08:46:27 INFO spark.SparkContext: Created broadcast 0 from newAPIHadoopFile at ADAMContext.scala:1801
20/04/28 08:46:27 INFO cli.TransformAlignments: Sorting alignments by reference position, with references ordered by name
20/04/28 08:46:27 INFO read.RDDBoundAlignmentDataset: Sorting alignments by reference position
20/04/28 08:46:27 INFO input.FileInputFormat: Total input paths to process : 1
20/04/28 08:46:27 INFO hadoop.ParquetInputFormat: Total input paths to process : 1
20/04/28 08:46:27 INFO read.RDDBoundAlignmentDataset: Saving data in ADAM format
20/04/28 08:46:27 INFO output.FileOutputCommitter: File Output Committer Algorithm version is 1
20/04/28 08:46:27 INFO spark.SparkContext: Starting job: runJob at SparkHadoopWriter.scala:78
20/04/28 08:46:27 INFO scheduler.DAGScheduler: Registering RDD 2 (sortBy at AlignmentDataset.scala:1008) as input to shuffle 0
20/04/28 08:46:27 INFO scheduler.DAGScheduler: Got job 0 (runJob at SparkHadoopWriter.scala:78) with 1 output partitions
20/04/28 08:46:27 INFO scheduler.DAGScheduler: Final stage: ResultStage 1 (runJob at SparkHadoopWriter.scala:78)
20/04/28 08:46:27 INFO scheduler.DAGScheduler: Parents of final stage: List(ShuffleMapStage 0)
20/04/28 08:46:27 INFO scheduler.DAGScheduler: Missing parents: List(ShuffleMapStage 0)
20/04/28 08:46:27 INFO scheduler.DAGScheduler: Submitting ShuffleMapStage 0 (MapPartitionsRDD[2] at sortBy at AlignmentDataset.scala:1008), which has no missing parents
20/04/28 08:46:27 INFO memory.MemoryStore: Block broadcast_1 stored as values in memory (estimated size 5.9 KB, free 366.0 MB)
20/04/28 08:46:27 INFO memory.MemoryStore: Block broadcast_1_piece0 stored as bytes in memory (estimated size 3.4 KB, free 366.0 MB)
20/04/28 08:46:27 INFO storage.BlockManagerInfo: Added broadcast_1_piece0 in memory on 192.168.10.30:39719 (size: 3.4 KB, free: 366.3 MB)
20/04/28 08:46:27 INFO spark.SparkContext: Created broadcast 1 from broadcast at DAGScheduler.scala:1163
20/04/28 08:46:27 INFO scheduler.DAGScheduler: Submitting 1 missing tasks from ShuffleMapStage 0 (MapPartitionsRDD[2] at sortBy at AlignmentDataset.scala:1008) (first 15 tasks are for partitions Vector(0))
20/04/28 08:46:27 INFO scheduler.TaskSchedulerImpl: Adding task set 0.0 with 1 tasks
20/04/28 08:46:27 INFO scheduler.TaskSetManager: Starting task 0.0 in stage 0.0 (TID 0, localhost, executor driver, partition 0, PROCESS_LOCAL, 7480 bytes)
20/04/28 08:46:27 INFO executor.Executor: Running task 0.0 in stage 0.0 (TID 0)
20/04/28 08:46:27 INFO executor.Executor: Fetching spark://192.168.10.30:45317/jars/adam-assembly-spark2_2.12-0.32.0-SNAPSHOT.jar with timestamp 1588088784412
20/04/28 08:46:27 INFO client.TransportClientFactory: Successfully created connection to /192.168.10.30:45317 after 37 ms (0 ms spent in bootstraps)
20/04/28 08:46:27 INFO util.Utils: Fetching spark://192.168.10.30:45317/jars/adam-assembly-spark2_2.12-0.32.0-SNAPSHOT.jar to /tmp/spark-b01b6db5-2c17-4fe2-91e0-a895275e1516/userFiles-87f63086-688e-4b4d-9795-28220c862ac2/fetchFileTemp1311572846069397147.tmp
20/04/28 08:46:27 INFO executor.Executor: Adding file:/tmp/spark-b01b6db5-2c17-4fe2-91e0-a895275e1516/userFiles-87f63086-688e-4b4d-9795-28220c862ac2/adam-assembly-spark2_2.12-0.32.0-SNAPSHOT.jar to class loader
20/04/28 08:46:28 INFO rdd.NewHadoopRDD: Input split: file:/tmp/adamTestZP7FAWz/deleteMePleaseThisIsNoLongerNeeded/mouse_chrM.bam.reads.adam/part-r-00000.gz.parquet:0+10132211
20/04/28 08:46:28 INFO hadoop.InternalParquetRecordReader: RecordReader initialized will read a total of 163064 records.
20/04/28 08:46:28 INFO hadoop.InternalParquetRecordReader: at row 0. reading next block
20/04/28 08:46:28 INFO compress.CodecPool: Got brand-new decompressor [.gz]
20/04/28 08:46:28 INFO hadoop.InternalParquetRecordReader: block read in memory in 35 ms. row count = 163064
20/04/28 08:46:30 INFO executor.Executor: Finished task 0.0 in stage 0.0 (TID 0). 919 bytes result sent to driver
20/04/28 08:46:30 INFO scheduler.TaskSetManager: Finished task 0.0 in stage 0.0 (TID 0) in 3451 ms on localhost (executor driver) (1/1)
20/04/28 08:46:30 INFO scheduler.TaskSchedulerImpl: Removed TaskSet 0.0, whose tasks have all completed, from pool 
20/04/28 08:46:31 INFO scheduler.DAGScheduler: ShuffleMapStage 0 (sortBy at AlignmentDataset.scala:1008) finished in 3.581 s
20/04/28 08:46:31 INFO scheduler.DAGScheduler: looking for newly runnable stages
20/04/28 08:46:31 INFO scheduler.DAGScheduler: running: Set()
20/04/28 08:46:31 INFO scheduler.DAGScheduler: waiting: Set(ResultStage 1)
20/04/28 08:46:31 INFO scheduler.DAGScheduler: failed: Set()
20/04/28 08:46:31 INFO scheduler.DAGScheduler: Submitting ResultStage 1 (MapPartitionsRDD[5] at map at GenomicDataset.scala:3814), which has no missing parents
20/04/28 08:46:31 INFO memory.MemoryStore: Block broadcast_2 stored as values in memory (estimated size 86.8 KB, free 365.9 MB)
20/04/28 08:46:31 INFO memory.MemoryStore: Block broadcast_2_piece0 stored as bytes in memory (estimated size 32.4 KB, free 365.8 MB)
20/04/28 08:46:31 INFO storage.BlockManagerInfo: Added broadcast_2_piece0 in memory on 192.168.10.30:39719 (size: 32.4 KB, free: 366.2 MB)
20/04/28 08:46:31 INFO spark.SparkContext: Created broadcast 2 from broadcast at DAGScheduler.scala:1163
20/04/28 08:46:31 INFO scheduler.DAGScheduler: Submitting 1 missing tasks from ResultStage 1 (MapPartitionsRDD[5] at map at GenomicDataset.scala:3814) (first 15 tasks are for partitions Vector(0))
20/04/28 08:46:31 INFO scheduler.TaskSchedulerImpl: Adding task set 1.0 with 1 tasks
20/04/28 08:46:31 INFO scheduler.TaskSetManager: Starting task 0.0 in stage 1.0 (TID 1, localhost, executor driver, partition 0, ANY, 7141 bytes)
20/04/28 08:46:31 INFO executor.Executor: Running task 0.0 in stage 1.0 (TID 1)
20/04/28 08:46:31 INFO storage.ShuffleBlockFetcherIterator: Getting 1 non-empty blocks including 1 local blocks and 0 remote blocks
20/04/28 08:46:31 INFO storage.ShuffleBlockFetcherIterator: Started 0 remote fetches in 7 ms
20/04/28 08:46:33 INFO storage.BlockManagerInfo: Removed broadcast_1_piece0 on 192.168.10.30:39719 in memory (size: 3.4 KB, free: 366.2 MB)
20/04/28 08:46:33 INFO output.FileOutputCommitter: File Output Committer Algorithm version is 1
20/04/28 08:46:33 INFO codec.CodecConfig: Compression: GZIP
20/04/28 08:46:33 INFO output.FileOutputCommitter: File Output Committer Algorithm version is 1
20/04/28 08:46:33 INFO hadoop.ParquetOutputFormat: Parquet block size to 134217728
20/04/28 08:46:33 INFO hadoop.ParquetOutputFormat: Parquet page size to 1048576
20/04/28 08:46:33 INFO hadoop.ParquetOutputFormat: Parquet dictionary page size to 1048576
20/04/28 08:46:33 INFO hadoop.ParquetOutputFormat: Dictionary is on
20/04/28 08:46:33 INFO hadoop.ParquetOutputFormat: Validation is off
20/04/28 08:46:33 INFO hadoop.ParquetOutputFormat: Writer version is: PARQUET_1_0
20/04/28 08:46:33 INFO hadoop.ParquetOutputFormat: Maximum row group padding size is 8388608 bytes
20/04/28 08:46:33 INFO hadoop.ParquetOutputFormat: Page size checking is: estimated
20/04/28 08:46:33 INFO hadoop.ParquetOutputFormat: Min row count for page size check is: 100
20/04/28 08:46:33 INFO hadoop.ParquetOutputFormat: Max row count for page size check is: 10000
20/04/28 08:46:33 INFO compress.CodecPool: Got brand-new compressor [.gz]
20/04/28 08:46:37 INFO hadoop.InternalParquetRecordWriter: Flushing mem columnStore to file. allocated memory: 16004474
20/04/28 08:46:37 INFO output.FileOutputCommitter: Saved output of task 'attempt_20200428084627_0005_r_000000_0' to file:/tmp/adamTestZP7FAWz/deleteMePleaseThisIsNoLongerNeeded/mouse_chrM.bam.reads.sorted.adam/_temporary/0/task_20200428084627_0005_r_000000
20/04/28 08:46:37 INFO mapred.SparkHadoopMapRedUtil: attempt_20200428084627_0005_r_000000_0: Committed
20/04/28 08:46:37 INFO executor.Executor: Finished task 0.0 in stage 1.0 (TID 1). 1200 bytes result sent to driver
20/04/28 08:46:37 INFO scheduler.TaskSetManager: Finished task 0.0 in stage 1.0 (TID 1) in 6719 ms on localhost (executor driver) (1/1)
20/04/28 08:46:37 INFO scheduler.TaskSchedulerImpl: Removed TaskSet 1.0, whose tasks have all completed, from pool 
20/04/28 08:46:37 INFO scheduler.DAGScheduler: ResultStage 1 (runJob at SparkHadoopWriter.scala:78) finished in 6.766 s
20/04/28 08:46:37 INFO scheduler.DAGScheduler: Job 0 finished: runJob at SparkHadoopWriter.scala:78, took 10.439737 s
20/04/28 08:46:37 INFO hadoop.ParquetFileReader: Initiating action with parallelism: 5
20/04/28 08:46:37 INFO io.SparkHadoopWriter: Job job_20200428084627_0005 committed.
20/04/28 08:46:37 INFO cli.TransformAlignments: Overall Duration: 14.28 secs
20/04/28 08:46:37 INFO spark.SparkContext: Invoking stop() from shutdown hook
20/04/28 08:46:37 INFO server.AbstractConnector: Stopped Spark@7674a051{HTTP/1.1,[http/1.1]}{0.0.0.0:4040}
20/04/28 08:46:37 INFO ui.SparkUI: Stopped Spark web UI at http://192.168.10.30:4040
20/04/28 08:46:37 INFO spark.MapOutputTrackerMasterEndpoint: MapOutputTrackerMasterEndpoint stopped!
20/04/28 08:46:37 INFO memory.MemoryStore: MemoryStore cleared
20/04/28 08:46:37 INFO storage.BlockManager: BlockManager stopped
20/04/28 08:46:37 INFO storage.BlockManagerMaster: BlockManagerMaster stopped
20/04/28 08:46:37 INFO scheduler.OutputCommitCoordinator$OutputCommitCoordinatorEndpoint: OutputCommitCoordinator stopped!
20/04/28 08:46:37 INFO spark.SparkContext: Successfully stopped SparkContext
20/04/28 08:46:37 INFO util.ShutdownHookManager: Shutdown hook called
20/04/28 08:46:37 INFO util.ShutdownHookManager: Deleting directory /tmp/spark-d25195f5-a4a1-412b-9ac2-21e918e85cb3
20/04/28 08:46:37 INFO util.ShutdownHookManager: Deleting directory /tmp/spark-b01b6db5-2c17-4fe2-91e0-a895275e1516

# 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/adamTestZP7FAWz/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.5-bin-without-hadoop-scala-2.12/bin/spark-submit
20/04/28 08:46:39 WARN util.Utils: Your hostname, ubuntu-testing resolves to a loopback address: 127.0.1.1; using 192.168.10.30 instead (on interface eno1)
20/04/28 08:46:39 WARN util.Utils: Set SPARK_LOCAL_IP if you need to bind to another address
20/04/28 08:46:39 WARN util.NativeCodeLoader: Unable to load native-hadoop library for your platform... using builtin-java classes where applicable
20/04/28 08:46:40 INFO cli.ADAMMain: ADAM invoked with args: "transformFragments" "-load_as_alignments" "mouse_chrM.bam.reads.adam" "mouse_chrM.bam.fragments.adam"
20/04/28 08:46:40 INFO spark.SparkContext: Running Spark version 2.4.5
20/04/28 08:46:40 INFO spark.SparkContext: Submitted application: transformFragments
20/04/28 08:46:40 INFO spark.SecurityManager: Changing view acls to: jenkins
20/04/28 08:46:40 INFO spark.SecurityManager: Changing modify acls to: jenkins
20/04/28 08:46:40 INFO spark.SecurityManager: Changing view acls groups to: 
20/04/28 08:46:40 INFO spark.SecurityManager: Changing modify acls groups to: 
20/04/28 08:46:40 INFO spark.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()
20/04/28 08:46:40 INFO util.Utils: Successfully started service 'sparkDriver' on port 40901.
20/04/28 08:46:40 INFO spark.SparkEnv: Registering MapOutputTracker
20/04/28 08:46:40 INFO spark.SparkEnv: Registering BlockManagerMaster
20/04/28 08:46:40 INFO storage.BlockManagerMasterEndpoint: Using org.apache.spark.storage.DefaultTopologyMapper for getting topology information
20/04/28 08:46:40 INFO storage.BlockManagerMasterEndpoint: BlockManagerMasterEndpoint up
20/04/28 08:46:40 INFO storage.DiskBlockManager: Created local directory at /tmp/blockmgr-65033d22-804b-4273-aa60-cb5abb1f82c3
20/04/28 08:46:40 INFO memory.MemoryStore: MemoryStore started with capacity 366.3 MB
20/04/28 08:46:40 INFO spark.SparkEnv: Registering OutputCommitCoordinator
20/04/28 08:46:40 INFO util.log: Logging initialized @2189ms
20/04/28 08:46:40 INFO server.Server: jetty-9.3.z-SNAPSHOT, build timestamp: unknown, git hash: unknown
20/04/28 08:46:40 INFO server.Server: Started @2265ms
20/04/28 08:46:40 INFO server.AbstractConnector: Started ServerConnector@3ad394e6{HTTP/1.1,[http/1.1]}{0.0.0.0:4040}
20/04/28 08:46:40 INFO util.Utils: Successfully started service 'SparkUI' on port 4040.
20/04/28 08:46:40 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@26f143ed{/jobs,null,AVAILABLE,@Spark}
20/04/28 08:46:40 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@4102b1b1{/jobs/json,null,AVAILABLE,@Spark}
20/04/28 08:46:40 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@61a5b4ae{/jobs/job,null,AVAILABLE,@Spark}
20/04/28 08:46:40 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@5b69fd74{/jobs/job/json,null,AVAILABLE,@Spark}
20/04/28 08:46:40 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@f325091{/stages,null,AVAILABLE,@Spark}
20/04/28 08:46:40 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@437e951d{/stages/json,null,AVAILABLE,@Spark}
20/04/28 08:46:40 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@77b325b3{/stages/stage,null,AVAILABLE,@Spark}
20/04/28 08:46:40 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@49ef32e0{/stages/stage/json,null,AVAILABLE,@Spark}
20/04/28 08:46:40 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@271f18d3{/stages/pool,null,AVAILABLE,@Spark}
20/04/28 08:46:40 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@6bd51ed8{/stages/pool/json,null,AVAILABLE,@Spark}
20/04/28 08:46:40 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@61e3a1fd{/storage,null,AVAILABLE,@Spark}
20/04/28 08:46:40 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@51abf713{/storage/json,null,AVAILABLE,@Spark}
20/04/28 08:46:40 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@eadb475{/storage/rdd,null,AVAILABLE,@Spark}
20/04/28 08:46:40 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@4d4d48a6{/storage/rdd/json,null,AVAILABLE,@Spark}
20/04/28 08:46:40 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@315df4bb{/environment,null,AVAILABLE,@Spark}
20/04/28 08:46:40 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@3fc08eec{/environment/json,null,AVAILABLE,@Spark}
20/04/28 08:46:40 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@5cad8b7d{/executors,null,AVAILABLE,@Spark}
20/04/28 08:46:40 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@7b02e036{/executors/json,null,AVAILABLE,@Spark}
20/04/28 08:46:40 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@25243bc1{/executors/threadDump,null,AVAILABLE,@Spark}
20/04/28 08:46:40 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@1e287667{/executors/threadDump/json,null,AVAILABLE,@Spark}
20/04/28 08:46:40 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@2e6ee0bc{/static,null,AVAILABLE,@Spark}
20/04/28 08:46:40 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@214894fc{/,null,AVAILABLE,@Spark}
20/04/28 08:46:40 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@10567255{/api,null,AVAILABLE,@Spark}
20/04/28 08:46:40 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@5aa360ea{/jobs/job/kill,null,AVAILABLE,@Spark}
20/04/28 08:46:40 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@6548bb7d{/stages/stage/kill,null,AVAILABLE,@Spark}
20/04/28 08:46:40 INFO ui.SparkUI: Bound SparkUI to 0.0.0.0, and started at http://192.168.10.30:4040
20/04/28 08:46:41 INFO spark.SparkContext: Added JAR file:/tmp/adamTestZP7FAWz/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/target/adam-assembly-spark2_2.12-0.32.0-SNAPSHOT.jar at spark://192.168.10.30:40901/jars/adam-assembly-spark2_2.12-0.32.0-SNAPSHOT.jar with timestamp 1588088801003
20/04/28 08:46:41 INFO executor.Executor: Starting executor ID driver on host localhost
20/04/28 08:46:41 INFO util.Utils: Successfully started service 'org.apache.spark.network.netty.NettyBlockTransferService' on port 38609.
20/04/28 08:46:41 INFO netty.NettyBlockTransferService: Server created on 192.168.10.30:38609
20/04/28 08:46:41 INFO storage.BlockManager: Using org.apache.spark.storage.RandomBlockReplicationPolicy for block replication policy
20/04/28 08:46:41 INFO storage.BlockManagerMaster: Registering BlockManager BlockManagerId(driver, 192.168.10.30, 38609, None)
20/04/28 08:46:41 INFO storage.BlockManagerMasterEndpoint: Registering block manager 192.168.10.30:38609 with 366.3 MB RAM, BlockManagerId(driver, 192.168.10.30, 38609, None)
20/04/28 08:46:41 INFO storage.BlockManagerMaster: Registered BlockManager BlockManagerId(driver, 192.168.10.30, 38609, None)
20/04/28 08:46:41 INFO storage.BlockManager: Initialized BlockManager: BlockManagerId(driver, 192.168.10.30, 38609, None)
20/04/28 08:46:41 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@38548b19{/metrics/json,null,AVAILABLE,@Spark}
20/04/28 08:46:41 INFO rdd.ADAMContext: Loading mouse_chrM.bam.reads.adam as Parquet of Alignments.
20/04/28 08:46:42 INFO rdd.ADAMContext: Reading the ADAM file at mouse_chrM.bam.reads.adam to create RDD
20/04/28 08:46:43 INFO memory.MemoryStore: Block broadcast_0 stored as values in memory (estimated size 315.0 KB, free 366.0 MB)
20/04/28 08:46:43 INFO memory.MemoryStore: Block broadcast_0_piece0 stored as bytes in memory (estimated size 28.1 KB, free 366.0 MB)
20/04/28 08:46:43 INFO storage.BlockManagerInfo: Added broadcast_0_piece0 in memory on 192.168.10.30:38609 (size: 28.1 KB, free: 366.3 MB)
20/04/28 08:46:43 INFO spark.SparkContext: Created broadcast 0 from newAPIHadoopFile at ADAMContext.scala:1801
20/04/28 08:46:43 INFO input.FileInputFormat: Total input paths to process : 1
20/04/28 08:46:43 INFO hadoop.ParquetInputFormat: Total input paths to process : 1
20/04/28 08:46:44 INFO fragment.RDDBoundFragmentDataset: Saving data in ADAM format
20/04/28 08:46:44 INFO output.FileOutputCommitter: File Output Committer Algorithm version is 1
20/04/28 08:46:44 INFO spark.SparkContext: Starting job: runJob at SparkHadoopWriter.scala:78
20/04/28 08:46:44 INFO scheduler.DAGScheduler: Registering RDD 2 (groupBy at SingleReadBucket.scala:97) as input to shuffle 0
20/04/28 08:46:44 INFO scheduler.DAGScheduler: Got job 0 (runJob at SparkHadoopWriter.scala:78) with 1 output partitions
20/04/28 08:46:44 INFO scheduler.DAGScheduler: Final stage: ResultStage 1 (runJob at SparkHadoopWriter.scala:78)
20/04/28 08:46:44 INFO scheduler.DAGScheduler: Parents of final stage: List(ShuffleMapStage 0)
20/04/28 08:46:44 INFO scheduler.DAGScheduler: Missing parents: List(ShuffleMapStage 0)
20/04/28 08:46:44 INFO scheduler.DAGScheduler: Submitting ShuffleMapStage 0 (MapPartitionsRDD[2] at groupBy at SingleReadBucket.scala:97), which has no missing parents
20/04/28 08:46:44 INFO memory.MemoryStore: Block broadcast_1 stored as values in memory (estimated size 6.4 KB, free 366.0 MB)
20/04/28 08:46:44 INFO memory.MemoryStore: Block broadcast_1_piece0 stored as bytes in memory (estimated size 3.5 KB, free 366.0 MB)
20/04/28 08:46:44 INFO storage.BlockManagerInfo: Added broadcast_1_piece0 in memory on 192.168.10.30:38609 (size: 3.5 KB, free: 366.3 MB)
20/04/28 08:46:44 INFO spark.SparkContext: Created broadcast 1 from broadcast at DAGScheduler.scala:1163
20/04/28 08:46:44 INFO scheduler.DAGScheduler: Submitting 1 missing tasks from ShuffleMapStage 0 (MapPartitionsRDD[2] at groupBy at SingleReadBucket.scala:97) (first 15 tasks are for partitions Vector(0))
20/04/28 08:46:44 INFO scheduler.TaskSchedulerImpl: Adding task set 0.0 with 1 tasks
20/04/28 08:46:44 INFO scheduler.TaskSetManager: Starting task 0.0 in stage 0.0 (TID 0, localhost, executor driver, partition 0, PROCESS_LOCAL, 7480 bytes)
20/04/28 08:46:44 INFO executor.Executor: Running task 0.0 in stage 0.0 (TID 0)
20/04/28 08:46:44 INFO executor.Executor: Fetching spark://192.168.10.30:40901/jars/adam-assembly-spark2_2.12-0.32.0-SNAPSHOT.jar with timestamp 1588088801003
20/04/28 08:46:44 INFO client.TransportClientFactory: Successfully created connection to /192.168.10.30:40901 after 35 ms (0 ms spent in bootstraps)
20/04/28 08:46:44 INFO util.Utils: Fetching spark://192.168.10.30:40901/jars/adam-assembly-spark2_2.12-0.32.0-SNAPSHOT.jar to /tmp/spark-da5c7ac8-b71e-4ccc-ac5d-d32417725942/userFiles-578ea954-1471-4853-ada6-d08d32b064b3/fetchFileTemp1439739640471445746.tmp
20/04/28 08:46:44 INFO executor.Executor: Adding file:/tmp/spark-da5c7ac8-b71e-4ccc-ac5d-d32417725942/userFiles-578ea954-1471-4853-ada6-d08d32b064b3/adam-assembly-spark2_2.12-0.32.0-SNAPSHOT.jar to class loader
20/04/28 08:46:44 INFO rdd.NewHadoopRDD: Input split: file:/tmp/adamTestZP7FAWz/deleteMePleaseThisIsNoLongerNeeded/mouse_chrM.bam.reads.adam/part-r-00000.gz.parquet:0+10132211
20/04/28 08:46:45 INFO hadoop.InternalParquetRecordReader: RecordReader initialized will read a total of 163064 records.
20/04/28 08:46:45 INFO hadoop.InternalParquetRecordReader: at row 0. reading next block
20/04/28 08:46:45 INFO compress.CodecPool: Got brand-new decompressor [.gz]
20/04/28 08:46:45 INFO hadoop.InternalParquetRecordReader: block read in memory in 40 ms. row count = 163064
20/04/28 08:46:47 INFO executor.Executor: Finished task 0.0 in stage 0.0 (TID 0). 919 bytes result sent to driver
20/04/28 08:46:47 INFO scheduler.TaskSetManager: Finished task 0.0 in stage 0.0 (TID 0) in 3354 ms on localhost (executor driver) (1/1)
20/04/28 08:46:47 INFO scheduler.TaskSchedulerImpl: Removed TaskSet 0.0, whose tasks have all completed, from pool 
20/04/28 08:46:47 INFO scheduler.DAGScheduler: ShuffleMapStage 0 (groupBy at SingleReadBucket.scala:97) finished in 3.466 s
20/04/28 08:46:47 INFO scheduler.DAGScheduler: looking for newly runnable stages
20/04/28 08:46:47 INFO scheduler.DAGScheduler: running: Set()
20/04/28 08:46:47 INFO scheduler.DAGScheduler: waiting: Set(ResultStage 1)
20/04/28 08:46:47 INFO scheduler.DAGScheduler: failed: Set()
20/04/28 08:46:47 INFO scheduler.DAGScheduler: Submitting ResultStage 1 (MapPartitionsRDD[6] at map at GenomicDataset.scala:3814), which has no missing parents
20/04/28 08:46:47 INFO memory.MemoryStore: Block broadcast_2 stored as values in memory (estimated size 90.2 KB, free 365.9 MB)
20/04/28 08:46:47 INFO memory.MemoryStore: Block broadcast_2_piece0 stored as bytes in memory (estimated size 33.5 KB, free 365.8 MB)
20/04/28 08:46:47 INFO storage.BlockManagerInfo: Added broadcast_2_piece0 in memory on 192.168.10.30:38609 (size: 33.5 KB, free: 366.2 MB)
20/04/28 08:46:47 INFO spark.SparkContext: Created broadcast 2 from broadcast at DAGScheduler.scala:1163
20/04/28 08:46:47 INFO scheduler.DAGScheduler: Submitting 1 missing tasks from ResultStage 1 (MapPartitionsRDD[6] at map at GenomicDataset.scala:3814) (first 15 tasks are for partitions Vector(0))
20/04/28 08:46:47 INFO scheduler.TaskSchedulerImpl: Adding task set 1.0 with 1 tasks
20/04/28 08:46:47 INFO scheduler.TaskSetManager: Starting task 0.0 in stage 1.0 (TID 1, localhost, executor driver, partition 0, ANY, 7141 bytes)
20/04/28 08:46:47 INFO executor.Executor: Running task 0.0 in stage 1.0 (TID 1)
20/04/28 08:46:47 INFO storage.ShuffleBlockFetcherIterator: Getting 1 non-empty blocks including 1 local blocks and 0 remote blocks
20/04/28 08:46:47 INFO storage.ShuffleBlockFetcherIterator: Started 0 remote fetches in 5 ms
20/04/28 08:46:49 INFO output.FileOutputCommitter: File Output Committer Algorithm version is 1
20/04/28 08:46:49 INFO codec.CodecConfig: Compression: GZIP
20/04/28 08:46:49 INFO output.FileOutputCommitter: File Output Committer Algorithm version is 1
20/04/28 08:46:49 INFO hadoop.ParquetOutputFormat: Parquet block size to 134217728
20/04/28 08:46:49 INFO hadoop.ParquetOutputFormat: Parquet page size to 1048576
20/04/28 08:46:49 INFO hadoop.ParquetOutputFormat: Parquet dictionary page size to 1048576
20/04/28 08:46:49 INFO hadoop.ParquetOutputFormat: Dictionary is on
20/04/28 08:46:49 INFO hadoop.ParquetOutputFormat: Validation is off
20/04/28 08:46:49 INFO hadoop.ParquetOutputFormat: Writer version is: PARQUET_1_0
20/04/28 08:46:49 INFO hadoop.ParquetOutputFormat: Maximum row group padding size is 8388608 bytes
20/04/28 08:46:49 INFO hadoop.ParquetOutputFormat: Page size checking is: estimated
20/04/28 08:46:49 INFO hadoop.ParquetOutputFormat: Min row count for page size check is: 100
20/04/28 08:46:49 INFO hadoop.ParquetOutputFormat: Max row count for page size check is: 10000
20/04/28 08:46:49 INFO compress.CodecPool: Got brand-new compressor [.gz]
20/04/28 08:46:50 INFO storage.BlockManagerInfo: Removed broadcast_1_piece0 on 192.168.10.30:38609 in memory (size: 3.5 KB, free: 366.2 MB)
20/04/28 08:46:56 INFO hadoop.InternalParquetRecordWriter: Flushing mem columnStore to file. allocated memory: 21417928
20/04/28 08:46:56 INFO output.FileOutputCommitter: Saved output of task 'attempt_20200428084644_0006_r_000000_0' to file:/tmp/adamTestZP7FAWz/deleteMePleaseThisIsNoLongerNeeded/mouse_chrM.bam.fragments.adam/_temporary/0/task_20200428084644_0006_r_000000
20/04/28 08:46:56 INFO mapred.SparkHadoopMapRedUtil: attempt_20200428084644_0006_r_000000_0: Committed
20/04/28 08:46:56 INFO executor.Executor: Finished task 0.0 in stage 1.0 (TID 1). 1200 bytes result sent to driver
20/04/28 08:46:56 INFO scheduler.TaskSetManager: Finished task 0.0 in stage 1.0 (TID 1) in 8938 ms on localhost (executor driver) (1/1)
20/04/28 08:46:56 INFO scheduler.TaskSchedulerImpl: Removed TaskSet 1.0, whose tasks have all completed, from pool 
20/04/28 08:46:56 INFO scheduler.DAGScheduler: ResultStage 1 (runJob at SparkHadoopWriter.scala:78) finished in 8.978 s
20/04/28 08:46:56 INFO scheduler.DAGScheduler: Job 0 finished: runJob at SparkHadoopWriter.scala:78, took 12.533694 s
20/04/28 08:46:56 INFO hadoop.ParquetFileReader: Initiating action with parallelism: 5
20/04/28 08:46:56 INFO io.SparkHadoopWriter: Job job_20200428084644_0006 committed.
20/04/28 08:46:56 INFO cli.TransformFragments: Overall Duration: 16.53 secs
20/04/28 08:46:56 INFO spark.SparkContext: Invoking stop() from shutdown hook
20/04/28 08:46:56 INFO server.AbstractConnector: Stopped Spark@3ad394e6{HTTP/1.1,[http/1.1]}{0.0.0.0:4040}
20/04/28 08:46:56 INFO ui.SparkUI: Stopped Spark web UI at http://192.168.10.30:4040
20/04/28 08:46:56 INFO spark.MapOutputTrackerMasterEndpoint: MapOutputTrackerMasterEndpoint stopped!
20/04/28 08:46:56 INFO memory.MemoryStore: MemoryStore cleared
20/04/28 08:46:56 INFO storage.BlockManager: BlockManager stopped
20/04/28 08:46:56 INFO storage.BlockManagerMaster: BlockManagerMaster stopped
20/04/28 08:46:56 INFO scheduler.OutputCommitCoordinator$OutputCommitCoordinatorEndpoint: OutputCommitCoordinator stopped!
20/04/28 08:46:56 INFO spark.SparkContext: Successfully stopped SparkContext
20/04/28 08:46:56 INFO util.ShutdownHookManager: Shutdown hook called
20/04/28 08:46:56 INFO util.ShutdownHookManager: Deleting directory /tmp/spark-da5c7ac8-b71e-4ccc-ac5d-d32417725942
20/04/28 08:46:56 INFO util.ShutdownHookManager: Deleting directory /tmp/spark-46bf661d-71dd-403c-aaf8-4e0ac2026ee5

# 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/adamTestZP7FAWz/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.5-bin-without-hadoop-scala-2.12/bin/spark-submit
20/04/28 08:47:13 WARN util.Utils: Your hostname, ubuntu-testing resolves to a loopback address: 127.0.1.1; using 192.168.10.30 instead (on interface eno1)
20/04/28 08:47:13 WARN util.Utils: Set SPARK_LOCAL_IP if you need to bind to another address
20/04/28 08:47:13 WARN util.NativeCodeLoader: Unable to load native-hadoop library for your platform... using builtin-java classes where applicable
20/04/28 08:47:14 INFO cli.ADAMMain: ADAM invoked with args: "flagstat" "-print_metrics" "mouse_chrM.bam.reads.adam"
20/04/28 08:47:14 INFO spark.SparkContext: Running Spark version 2.4.5
20/04/28 08:47:14 INFO spark.SparkContext: Submitted application: flagstat
20/04/28 08:47:14 INFO spark.SecurityManager: Changing view acls to: jenkins
20/04/28 08:47:14 INFO spark.SecurityManager: Changing modify acls to: jenkins
20/04/28 08:47:14 INFO spark.SecurityManager: Changing view acls groups to: 
20/04/28 08:47:14 INFO spark.SecurityManager: Changing modify acls groups to: 
20/04/28 08:47:14 INFO spark.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()
20/04/28 08:47:14 INFO util.Utils: Successfully started service 'sparkDriver' on port 46217.
20/04/28 08:47:14 INFO spark.SparkEnv: Registering MapOutputTracker
20/04/28 08:47:14 INFO spark.SparkEnv: Registering BlockManagerMaster
20/04/28 08:47:14 INFO storage.BlockManagerMasterEndpoint: Using org.apache.spark.storage.DefaultTopologyMapper for getting topology information
20/04/28 08:47:14 INFO storage.BlockManagerMasterEndpoint: BlockManagerMasterEndpoint up
20/04/28 08:47:14 INFO storage.DiskBlockManager: Created local directory at /tmp/blockmgr-e3f22d43-f673-474d-9115-4e61a5620441
20/04/28 08:47:14 INFO memory.MemoryStore: MemoryStore started with capacity 366.3 MB
20/04/28 08:47:14 INFO spark.SparkEnv: Registering OutputCommitCoordinator
20/04/28 08:47:14 INFO util.log: Logging initialized @2258ms
20/04/28 08:47:14 INFO server.Server: jetty-9.3.z-SNAPSHOT, build timestamp: unknown, git hash: unknown
20/04/28 08:47:14 INFO server.Server: Started @2329ms
20/04/28 08:47:14 INFO server.AbstractConnector: Started ServerConnector@3aaf4f07{HTTP/1.1,[http/1.1]}{0.0.0.0:4040}
20/04/28 08:47:14 INFO util.Utils: Successfully started service 'SparkUI' on port 4040.
20/04/28 08:47:14 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@2c282004{/jobs,null,AVAILABLE,@Spark}
20/04/28 08:47:14 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@e041f0c{/jobs/json,null,AVAILABLE,@Spark}
20/04/28 08:47:14 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@6a175569{/jobs/job,null,AVAILABLE,@Spark}
20/04/28 08:47:14 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@3f3c966c{/jobs/job/json,null,AVAILABLE,@Spark}
20/04/28 08:47:14 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@11ee02f8{/stages,null,AVAILABLE,@Spark}
20/04/28 08:47:14 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@4102b1b1{/stages/json,null,AVAILABLE,@Spark}
20/04/28 08:47:14 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@61a5b4ae{/stages/stage,null,AVAILABLE,@Spark}
20/04/28 08:47:14 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@f325091{/stages/stage/json,null,AVAILABLE,@Spark}
20/04/28 08:47:14 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@437e951d{/stages/pool,null,AVAILABLE,@Spark}
20/04/28 08:47:14 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@77b325b3{/stages/pool/json,null,AVAILABLE,@Spark}
20/04/28 08:47:14 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@63a5e46c{/storage,null,AVAILABLE,@Spark}
20/04/28 08:47:14 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@7e8e8651{/storage/json,null,AVAILABLE,@Spark}
20/04/28 08:47:14 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@49ef32e0{/storage/rdd,null,AVAILABLE,@Spark}
20/04/28 08:47:14 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@271f18d3{/storage/rdd/json,null,AVAILABLE,@Spark}
20/04/28 08:47:14 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@6bd51ed8{/environment,null,AVAILABLE,@Spark}
20/04/28 08:47:14 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@61e3a1fd{/environment/json,null,AVAILABLE,@Spark}
20/04/28 08:47:14 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@51abf713{/executors,null,AVAILABLE,@Spark}
20/04/28 08:47:14 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@eadb475{/executors/json,null,AVAILABLE,@Spark}
20/04/28 08:47:14 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@4d4d48a6{/executors/threadDump,null,AVAILABLE,@Spark}
20/04/28 08:47:14 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@315df4bb{/executors/threadDump/json,null,AVAILABLE,@Spark}
20/04/28 08:47:14 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@3fc08eec{/static,null,AVAILABLE,@Spark}
20/04/28 08:47:14 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@74a9c4b0{/,null,AVAILABLE,@Spark}
20/04/28 08:47:14 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@85ec632{/api,null,AVAILABLE,@Spark}
20/04/28 08:47:14 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@214894fc{/jobs/job/kill,null,AVAILABLE,@Spark}
20/04/28 08:47:14 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@10567255{/stages/stage/kill,null,AVAILABLE,@Spark}
20/04/28 08:47:14 INFO ui.SparkUI: Bound SparkUI to 0.0.0.0, and started at http://192.168.10.30:4040
20/04/28 08:47:15 INFO spark.SparkContext: Added JAR file:/tmp/adamTestZP7FAWz/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/target/adam-assembly-spark2_2.12-0.32.0-SNAPSHOT.jar at spark://192.168.10.30:46217/jars/adam-assembly-spark2_2.12-0.32.0-SNAPSHOT.jar with timestamp 1588088835015
20/04/28 08:47:15 INFO executor.Executor: Starting executor ID driver on host localhost
20/04/28 08:47:15 INFO util.Utils: Successfully started service 'org.apache.spark.network.netty.NettyBlockTransferService' on port 36969.
20/04/28 08:47:15 INFO netty.NettyBlockTransferService: Server created on 192.168.10.30:36969
20/04/28 08:47:15 INFO storage.BlockManager: Using org.apache.spark.storage.RandomBlockReplicationPolicy for block replication policy
20/04/28 08:47:15 INFO storage.BlockManagerMaster: Registering BlockManager BlockManagerId(driver, 192.168.10.30, 36969, None)
20/04/28 08:47:15 INFO storage.BlockManagerMasterEndpoint: Registering block manager 192.168.10.30:36969 with 366.3 MB RAM, BlockManagerId(driver, 192.168.10.30, 36969, None)
20/04/28 08:47:15 INFO storage.BlockManagerMaster: Registered BlockManager BlockManagerId(driver, 192.168.10.30, 36969, None)
20/04/28 08:47:15 INFO storage.BlockManager: Initialized BlockManager: BlockManagerId(driver, 192.168.10.30, 36969, None)
20/04/28 08:47:15 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@4443ef6f{/metrics/json,null,AVAILABLE,@Spark}
20/04/28 08:47:15 INFO rdd.ADAMContext: Loading mouse_chrM.bam.reads.adam as Parquet of Alignments.
20/04/28 08:47:15 INFO rdd.ADAMContext: Reading the ADAM file at mouse_chrM.bam.reads.adam to create RDD
20/04/28 08:47:16 INFO rdd.ADAMContext: Using the specified projection schema
20/04/28 08:47:16 INFO memory.MemoryStore: Block broadcast_0 stored as values in memory (estimated size 322.5 KB, free 366.0 MB)
20/04/28 08:47:16 INFO memory.MemoryStore: Block broadcast_0_piece0 stored as bytes in memory (estimated size 29.1 KB, free 366.0 MB)
20/04/28 08:47:16 INFO storage.BlockManagerInfo: Added broadcast_0_piece0 in memory on 192.168.10.30:36969 (size: 29.1 KB, free: 366.3 MB)
20/04/28 08:47:16 INFO spark.SparkContext: Created broadcast 0 from newAPIHadoopFile at ADAMContext.scala:1801
20/04/28 08:47:18 INFO input.FileInputFormat: Total input paths to process : 1
20/04/28 08:47:18 INFO hadoop.ParquetInputFormat: Total input paths to process : 1
20/04/28 08:47:18 INFO spark.SparkContext: Starting job: aggregate at FlagStat.scala:115
20/04/28 08:47:18 INFO scheduler.DAGScheduler: Got job 0 (aggregate at FlagStat.scala:115) with 1 output partitions
20/04/28 08:47:18 INFO scheduler.DAGScheduler: Final stage: ResultStage 0 (aggregate at FlagStat.scala:115)
20/04/28 08:47:18 INFO scheduler.DAGScheduler: Parents of final stage: List()
20/04/28 08:47:18 INFO scheduler.DAGScheduler: Missing parents: List()
20/04/28 08:47:18 INFO scheduler.DAGScheduler: Submitting ResultStage 0 (MapPartitionsRDD[4] at map at FlagStat.scala:96), which has no missing parents
20/04/28 08:47:18 INFO memory.MemoryStore: Block broadcast_1 stored as values in memory (estimated size 13.6 KB, free 365.9 MB)
20/04/28 08:47:18 INFO memory.MemoryStore: Block broadcast_1_piece0 stored as bytes in memory (estimated size 6.0 KB, free 365.9 MB)
20/04/28 08:47:18 INFO storage.BlockManagerInfo: Added broadcast_1_piece0 in memory on 192.168.10.30:36969 (size: 6.0 KB, free: 366.3 MB)
20/04/28 08:47:18 INFO spark.SparkContext: Created broadcast 1 from broadcast at DAGScheduler.scala:1163
20/04/28 08:47:18 INFO scheduler.DAGScheduler: Submitting 1 missing tasks from ResultStage 0 (MapPartitionsRDD[4] at map at FlagStat.scala:96) (first 15 tasks are for partitions Vector(0))
20/04/28 08:47:18 INFO scheduler.TaskSchedulerImpl: Adding task set 0.0 with 1 tasks
20/04/28 08:47:18 INFO scheduler.TaskSetManager: Starting task 0.0 in stage 0.0 (TID 0, localhost, executor driver, partition 0, PROCESS_LOCAL, 7491 bytes)
20/04/28 08:47:18 INFO executor.Executor: Running task 0.0 in stage 0.0 (TID 0)
20/04/28 08:47:18 INFO executor.Executor: Fetching spark://192.168.10.30:46217/jars/adam-assembly-spark2_2.12-0.32.0-SNAPSHOT.jar with timestamp 1588088835015
20/04/28 08:47:18 INFO client.TransportClientFactory: Successfully created connection to /192.168.10.30:46217 after 35 ms (0 ms spent in bootstraps)
20/04/28 08:47:18 INFO util.Utils: Fetching spark://192.168.10.30:46217/jars/adam-assembly-spark2_2.12-0.32.0-SNAPSHOT.jar to /tmp/spark-f18880c8-b3c0-48f5-b09c-2fe4798b45b1/userFiles-6c874c30-4a8a-4b6f-9aa9-e3419353f873/fetchFileTemp6513387956108119604.tmp
20/04/28 08:47:18 INFO executor.Executor: Adding file:/tmp/spark-f18880c8-b3c0-48f5-b09c-2fe4798b45b1/userFiles-6c874c30-4a8a-4b6f-9aa9-e3419353f873/adam-assembly-spark2_2.12-0.32.0-SNAPSHOT.jar to class loader
20/04/28 08:47:18 INFO rdd.NewHadoopRDD: Input split: file:/tmp/adamTestZP7FAWz/deleteMePleaseThisIsNoLongerNeeded/mouse_chrM.bam.reads.adam/part-r-00000.gz.parquet:0+10132211
20/04/28 08:47:19 INFO hadoop.InternalParquetRecordReader: RecordReader initialized will read a total of 163064 records.
20/04/28 08:47:19 INFO hadoop.InternalParquetRecordReader: at row 0. reading next block
20/04/28 08:47:19 INFO compress.CodecPool: Got brand-new decompressor [.gz]
20/04/28 08:47:19 INFO hadoop.InternalParquetRecordReader: block read in memory in 19 ms. row count = 163064
20/04/28 08:47:20 INFO executor.Executor: Finished task 0.0 in stage 0.0 (TID 0). 9641 bytes result sent to driver
20/04/28 08:47:20 INFO scheduler.TaskSetManager: Finished task 0.0 in stage 0.0 (TID 0) in 1791 ms on localhost (executor driver) (1/1)
20/04/28 08:47:20 INFO scheduler.TaskSchedulerImpl: Removed TaskSet 0.0, whose tasks have all completed, from pool 
20/04/28 08:47:20 INFO scheduler.DAGScheduler: ResultStage 0 (aggregate at FlagStat.scala:115) finished in 1.898 s
20/04/28 08:47:20 INFO scheduler.DAGScheduler: Job 0 finished: aggregate at FlagStat.scala:115, took 1.958870 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)
20/04/28 08:47:20 INFO cli.FlagStat: Overall Duration: 5.82 secs
20/04/28 08:47:20 INFO cli.FlagStat: Metrics:

Timings
+--------------------------------------+--------------+--------------+-------------+--------+-----------+-----------+-----------+
|                Metric                | Worker Total | Driver Total | Driver Only | Count  |   Mean    |    Min    |    Max    |
+--------------------------------------+--------------+--------------+-------------+--------+-----------+-----------+-----------+
| └─ Load Alignments                   |            - |    2.21 secs |   2.11 secs |      1 | 2.21 secs | 2.21 secs | 2.21 secs |
|     └─ map at ADAMContext.scala:1805 |            - |     94.72 ms |           - |      1 |  94.72 ms |  94.72 ms |  94.72 ms |
|         └─ function call             |     19.74 ms |            - |           - | 163064 |    121 ns |     48 ns |   86.4 µs |
| └─ map at FlagStat.scala:96          |            - |     26.64 ms |           - |      1 |  26.64 ms |  26.64 ms |  26.64 ms |
|     └─ function call                 |    207.05 ms |            - |           - | 163064 |   1.27 µs |    161 ns |  23.93 ms |
| └─ aggregate at FlagStat.scala:115   |            - |    2.06 secs |           - |      1 | 2.06 secs | 2.06 secs | 2.06 secs |
|     └─ function call                 |     32.13 ms |            - |           - | 163065 |    197 ns |     61 ns | 372.34 µs |
+--------------------------------------+--------------+--------------+-------------+--------+-----------+-----------+-----------+

Spark Operations
+----------+---------------------------------+---------------+----------------+--------------+----------+
| Sequence |            Operation            | Is New Stage? | Stage Duration | Driver Total | Stage ID |
+----------+---------------------------------+---------------+----------------+--------------+----------+
| 1        | map at ADAMContext.scala:1805   | false         |              - |     94.72 ms | -        |
| 2        | map at FlagStat.scala:96        | false         |              - |     26.64 ms | -        |
| 3        | aggregate at FlagStat.scala:115 | true          |      -1.9 secs |    2.06 secs | 0        |
+----------+---------------------------------+---------------+----------------+--------------+----------+

Task Timings
+-------------------------------+------------+-------+-----------+-----------+-----------+
|            Metric             | Total Time | Count |   Mean    |    Min    |    Max    |
+-------------------------------+------------+-------+-----------+-----------+-----------+
| Task Duration                 |  1.79 secs |     1 | 1.79 secs | 1.79 secs | 1.79 secs |
| Executor Run Time             |   1.1 secs |     1 |  1.1 secs |  1.1 secs |  1.1 secs |
| Executor Deserialization Time |     610 ms |     1 |    610 ms |    610 ms |    610 ms |
| Result Serialization Time     |          0 |     1 |         0 |         0 |         0 |
+-------------------------------+------------+-------+-----------+-----------+-----------+

Task Timings By Host
+-------------------------------+--------+------------+-------+-----------+-----------+-----------+
|            Metric             |  Host  | Total Time | Count |   Mean    |    Min    |    Max    |
+-------------------------------+--------+------------+-------+-----------+-----------+-----------+
| Task Duration                 | driver |  1.79 secs |     1 | 1.79 secs | 1.79 secs | 1.79 secs |
| Executor Run Time             | driver |   1.1 secs |     1 |  1.1 secs |  1.1 secs |  1.1 secs |
| Executor Deserialization Time | driver |     610 ms |     1 |    610 ms |    610 ms |    610 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 |  1.79 secs |     1 | 1.79 secs | 1.79 secs | 1.79 secs |
| Executor Run Time             | 0: aggregate at FlagStat.scala:115 |   1.1 secs |     1 |  1.1 secs |  1.1 secs |  1.1 secs |
| Executor Deserialization Time | 0: aggregate at FlagStat.scala:115 |     610 ms |     1 |    610 ms |    610 ms |    610 ms |
| Result Serialization Time     | 0: aggregate at FlagStat.scala:115 |          0 |     1 |         0 |         0 |         0 |
+-------------------------------+------------------------------------+------------+-------+-----------+-----------+-----------+

20/04/28 08:47:20 INFO spark.SparkContext: Invoking stop() from shutdown hook
20/04/28 08:47:20 INFO server.AbstractConnector: Stopped Spark@3aaf4f07{HTTP/1.1,[http/1.1]}{0.0.0.0:4040}
20/04/28 08:47:20 INFO ui.SparkUI: Stopped Spark web UI at http://192.168.10.30:4040
20/04/28 08:47:20 INFO spark.MapOutputTrackerMasterEndpoint: MapOutputTrackerMasterEndpoint stopped!
20/04/28 08:47:20 INFO memory.MemoryStore: MemoryStore cleared
20/04/28 08:47:20 INFO storage.BlockManager: BlockManager stopped
20/04/28 08:47:20 INFO storage.BlockManagerMaster: BlockManagerMaster stopped
20/04/28 08:47:20 INFO scheduler.OutputCommitCoordinator$OutputCommitCoordinatorEndpoint: OutputCommitCoordinator stopped!
20/04/28 08:47:20 INFO spark.SparkContext: Successfully stopped SparkContext
20/04/28 08:47:20 INFO util.ShutdownHookManager: Shutdown hook called
20/04/28 08:47:20 INFO util.ShutdownHookManager: Deleting directory /tmp/spark-f18880c8-b3c0-48f5-b09c-2fe4798b45b1
20/04/28 08:47:20 INFO util.ShutdownHookManager: Deleting directory /tmp/spark-391e4e8a-9137-42a2-a75e-9979670adde7
rm -rf ${ADAM_TMP_DIR}
+ rm -rf /tmp/adamTestZP7FAWz/deleteMePleaseThisIsNoLongerNeeded
popd
+ popd
~/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.5/label/ubuntu

pushd ${PROJECT_ROOT}
+ pushd /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.5/label/ubuntu/scripts/..
~/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.5/label/ubuntu ~/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/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
+ '[' 2.12 == 2.12 ']'
+ set +e
+ ./scripts/move_to_scala_2.11.sh
+ set -e

# 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/2.12/SPARK_VERSION/2.4.5/label/ubuntu/scripts
+ pushd /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.5/label/ubuntu/scripts/..
~/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.5/label/ubuntu ~/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/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 [  6.521 s]
[INFO] ADAM_2.11: Shader workaround ....................... SUCCESS [  0.028 s]
[INFO] ADAM_2.11: Avro-to-Dataset codegen utils ........... SUCCESS [  0.062 s]
[INFO] ADAM_2.11: Core .................................... SUCCESS [  3.381 s]
[INFO] ADAM_2.11: APIs for Java, Python ................... SUCCESS [  0.138 s]
[INFO] ADAM_2.11: CLI ..................................... SUCCESS [  0.222 s]
[INFO] ADAM_2.11: Assembly ................................ SUCCESS [  0.013 s]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 10.836 s
[INFO] Finished at: 2020-04-28T08:47:33-07:00
[INFO] Final Memory: 21M/1104M
[INFO] ------------------------------------------------------------------------
+ popd
~/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/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/2.12/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...
null
Setting commit status on GitHub for https://github.com/bigdatagenomics/adam/commit/96ff1cfdcce4df82483d3a0de5dc254b20ea1448
Finished: SUCCESS