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[WARNING] Entry: adam-distribution-spark2_2.12-0.29.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/CoverageToGenotypesConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.29.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/FeaturesToReadsDatasetConverter.html longer than 100 characters.
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[WARNING] Entry: adam-distribution-spark2_2.12-0.29.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/ReadsToSlicesConverter.html longer than 100 characters.
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[WARNING] Entry: adam-distribution-spark2_2.12-0.29.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/VariantContextsToSequencesConverter.html longer than 100 characters.
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[WARNING] Entry: adam-distribution-spark2_2.12-0.29.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/cli/TransformSequences.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.29.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/cli/TransformFeatures.html longer than 100 characters.
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[INFO] Building zip: /tmp/adamTestMP40nkE/deleteMePleaseThisIsNoLongerNeeded/adam-distribution/target/adam-distribution-spark2_2.12-0.29.0-SNAPSHOT-bin.zip
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary:
[INFO] 
[INFO] ADAM_2.12 .......................................... SUCCESS [  9.100 s]
[INFO] ADAM_2.12: Shader workaround ....................... SUCCESS [  5.828 s]
[INFO] ADAM_2.12: Avro-to-Dataset codegen utils ........... SUCCESS [  6.170 s]
[INFO] ADAM_2.12: Core .................................... SUCCESS [01:19 min]
[INFO] ADAM_2.12: APIs for Java, Python ................... SUCCESS [ 11.661 s]
[INFO] ADAM_2.12: CLI ..................................... SUCCESS [ 13.713 s]
[INFO] ADAM_2.12: Assembly ................................ SUCCESS [ 18.740 s]
[INFO] ADAM_2.12: Python APIs ............................. SUCCESS [01:40 min]
[INFO] ADAM_2.12: R APIs .................................. SUCCESS [01:08 min]
[INFO] ADAM_2.12: Distribution ............................ SUCCESS [ 41.100 s]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 05:54 min
[INFO] Finished at: 2019-08-10T12:17:40-07:00
[INFO] Final Memory: 69M/1515M
[INFO] ------------------------------------------------------------------------
+ grep bdgenomics.adam
+ tar tzvf adam-distribution/target/adam-distribution-spark2_2.12-0.29.0-SNAPSHOT-bin.tar.gz
+ grep egg
drwxrwxr-x jenkins/jenkins        0 2019-08-10 12:14 adam-distribution-spark2_2.12-0.29.0-SNAPSHOT/r/bdgenomics.adam.egg-info/
-rw-r--r-- jenkins/jenkins 36823483 2019-08-10 12:14 adam-distribution-spark2_2.12-0.29.0-SNAPSHOT/repo/bdgenomics.adam-0.28.0a0-py3.6.egg
+ ./bin/pyadam
Using PYSPARK=/tmp/adamTestMP40nkE/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.3-bin-without-hadoop-scala-2.12/bin/pyspark
2019-08-10 12:17:44 WARN  Utils:66 - Your hostname, amp-jenkins-staging-worker-02 resolves to a loopback address: 127.0.1.1; using 192.168.10.32 instead (on interface eno1)
2019-08-10 12:17:44 WARN  Utils:66 - Set SPARK_LOCAL_IP if you need to bind to another address
2019-08-10 12:17:44 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).
2019-08-10 12:17:52 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/bash

# Determine the directory containing this script
if [[ -n $BASH_VERSION ]]; then
    _SCRIPT_LOCATION=${BASH_SOURCE[0]}
    _SHELL="bash"
elif [[ -n $ZSH_VERSION ]]; then
    _SCRIPT_LOCATION=${funcstack[1]}
    _SHELL="zsh"
else
    echo "Only bash and zsh are supported"
    return 1
fi
++ [[ -n 4.3.48(1)-release ]]
++ _SCRIPT_LOCATION=/home/jenkins/anaconda2/envs/adam-build-918cef9f-6899-440a-87ac-accc424cb516/bin/deactivate
++ _SHELL=bash
_CONDA_DIR=$(dirname "$_SCRIPT_LOCATION")
dirname "$_SCRIPT_LOCATION"
+++ dirname /home/jenkins/anaconda2/envs/adam-build-918cef9f-6899-440a-87ac-accc424cb516/bin/deactivate
++ _CONDA_DIR=/home/jenkins/anaconda2/envs/adam-build-918cef9f-6899-440a-87ac-accc424cb516/bin

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

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

# Ensure that this script is sourced, not executed
# Note that if the script was executed, we're running inside bash!
# Also note that errors are ignored as `activate foo` doesn't generate a bad
# value for $0 which would cause errors.
if [[ -n $BASH_VERSION ]] && [[ "$(basename "$0" 2> /dev/null)" == "deactivate" ]]; then
    (>&2 echo "Error: deactivate must be sourced. Run 'source deactivate'
instead of 'deactivate'.
")
    "$_CONDA_DIR/conda" ..deactivate $_SHELL$EXT -h
    exit 1
fi
++ [[ -n 4.3.48(1)-release ]]
basename "$0" 2> /dev/null
+++ basename /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/scripts/jenkins-test
++ [[ jenkins-test == \d\e\a\c\t\i\v\a\t\e ]]

if [[ -z "$CONDA_PATH_BACKUP" ]]; then
    if [[ -n $BASH_VERSION ]] && [[ "$(basename "$0" 2> /dev/null)" == "deactivate" ]]; then
        exit 0
    else
        return 0
    fi
fi
++ [[ -z /usr/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 ]]

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

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

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

    unset CONDA_DEFAULT_ENV
    unset CONDA_PREFIX
    unset CONDA_PATH_BACKUP
    export PS1="$CONDA_PS1_BACKUP"
    unset CONDA_PS1_BACKUP
    unset _CONDA_PYTHON2
else
    unset _CONDA_PYTHON2
    return $?
fi
++ ((  0 == 0  ))
++ _CONDA_D=/home/jenkins/anaconda2/envs/adam-build-918cef9f-6899-440a-87ac-accc424cb516/etc/conda/deactivate.d
++ [[ -d /home/jenkins/anaconda2/envs/adam-build-918cef9f-6899-440a-87ac-accc424cb516/etc/conda/deactivate.d ]]
"$_CONDA_DIR/conda" ..deactivate.path $_SHELL$EXT "$CONDA_PREFIX"
+++ /home/jenkins/anaconda2/envs/adam-build-918cef9f-6899-440a-87ac-accc424cb516/bin/conda ..deactivate.path bash /home/jenkins/anaconda2/envs/adam-build-918cef9f-6899-440a-87ac-accc424cb516
++ 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
++ unset CONDA_DEFAULT_ENV
++ unset CONDA_PREFIX
++ unset CONDA_PATH_BACKUP
++ export PS1=
++ PS1=
++ unset CONDA_PS1_BACKUP
++ unset _CONDA_PYTHON2

if [[ -n $BASH_VERSION ]]; then
    hash -r
elif [[ -n $ZSH_VERSION ]]; then
    rehash
fi
++ [[ -n 4.3.48(1)-release ]]
++ hash -r
+ conda remove -y -n adam-build-918cef9f-6899-440a-87ac-accc424cb516 --all

Package plan for package removal in environment /home/jenkins/anaconda2/envs/adam-build-918cef9f-6899-440a-87ac-accc424cb516:

The following packages will be REMOVED:

    _libgcc_mutex:   0.1-main               
    ca-certificates: 2019.5.15-1            
    certifi:         2019.6.16-py36_1       
    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:         6.1-he6710b0_1         
    openssl:         1.1.1c-h7b6447c_1      
    pip:             19.1.1-py36_0          
    python:          3.6.9-h265db76_0       
    readline:        7.0-h7b6447c_5         
    setuptools:      41.0.1-py36_0          
    sqlite:          3.29.0-h7b6447c_0      
    tk:              8.6.8-hbc83047_0       
    wheel:           0.33.4-py36_0          
    xz:              5.2.4-h14c3975_4       
    zlib:            1.2.11-h7b6447c_3      

+ cp -r adam-python/target /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/scripts/../adam-python/
+ pushd adam-python
/tmp/adamTestMP40nkE/deleteMePleaseThisIsNoLongerNeeded/adam-python /tmp/adamTestMP40nkE/deleteMePleaseThisIsNoLongerNeeded ~/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu
+ make clean
pip uninstall -y adam
Skipping adam as it is not installed.
rm -rf bdgenomics/*.egg*
rm -rf build/
+ make clean_sdist
rm -rf dist
+ popd
/tmp/adamTestMP40nkE/deleteMePleaseThisIsNoLongerNeeded ~/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/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/adamTestMP40nkE/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.3-bin-without-hadoop-scala-2.12/bin/spark-submit
19/08/10 12:18:08 WARN util.Utils: Your hostname, amp-jenkins-staging-worker-02 resolves to a loopback address: 127.0.1.1; using 192.168.10.32 instead (on interface eno1)
19/08/10 12:18:08 WARN util.Utils: Set SPARK_LOCAL_IP if you need to bind to another address
19/08/10 12:18:09 WARN util.NativeCodeLoader: Unable to load native-hadoop library for your platform... using builtin-java classes where applicable
19/08/10 12:18:09 INFO cli.ADAMMain: ADAM invoked with args: "transformAlignments" "mouse_chrM.bam" "mouse_chrM.bam.reads.adam"
19/08/10 12:18:09 INFO spark.SparkContext: Running Spark version 2.4.3
19/08/10 12:18:09 INFO spark.SparkContext: Submitted application: transformAlignments
19/08/10 12:18:10 INFO spark.SecurityManager: Changing view acls to: jenkins
19/08/10 12:18:10 INFO spark.SecurityManager: Changing modify acls to: jenkins
19/08/10 12:18:10 INFO spark.SecurityManager: Changing view acls groups to: 
19/08/10 12:18:10 INFO spark.SecurityManager: Changing modify acls groups to: 
19/08/10 12:18:10 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()
19/08/10 12:18:10 INFO util.Utils: Successfully started service 'sparkDriver' on port 39783.
19/08/10 12:18:10 INFO spark.SparkEnv: Registering MapOutputTracker
19/08/10 12:18:10 INFO spark.SparkEnv: Registering BlockManagerMaster
19/08/10 12:18:10 INFO storage.BlockManagerMasterEndpoint: Using org.apache.spark.storage.DefaultTopologyMapper for getting topology information
19/08/10 12:18:10 INFO storage.BlockManagerMasterEndpoint: BlockManagerMasterEndpoint up
19/08/10 12:18:10 INFO storage.DiskBlockManager: Created local directory at /tmp/blockmgr-e02ed5ed-f203-442b-bbb3-a6fc57cbecc4
19/08/10 12:18:10 INFO memory.MemoryStore: MemoryStore started with capacity 366.3 MB
19/08/10 12:18:10 INFO spark.SparkEnv: Registering OutputCommitCoordinator
19/08/10 12:18:10 INFO util.log: Logging initialized @3081ms
19/08/10 12:18:10 INFO server.Server: jetty-9.3.z-SNAPSHOT, build timestamp: unknown, git hash: unknown
19/08/10 12:18:10 INFO server.Server: Started @3166ms
19/08/10 12:18:10 INFO server.AbstractConnector: Started ServerConnector@512d92b{HTTP/1.1,[http/1.1]}{0.0.0.0:4040}
19/08/10 12:18:10 INFO util.Utils: Successfully started service 'SparkUI' on port 4040.
19/08/10 12:18:10 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@1a38ba58{/jobs,null,AVAILABLE,@Spark}
19/08/10 12:18:10 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@24b52d3e{/jobs/json,null,AVAILABLE,@Spark}
19/08/10 12:18:10 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@15deb1dc{/jobs/job,null,AVAILABLE,@Spark}
19/08/10 12:18:10 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@57a4d5ee{/jobs/job/json,null,AVAILABLE,@Spark}
19/08/10 12:18:10 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@5af5def9{/stages,null,AVAILABLE,@Spark}
19/08/10 12:18:10 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@3a45c42a{/stages/json,null,AVAILABLE,@Spark}
19/08/10 12:18:10 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@36dce7ed{/stages/stage,null,AVAILABLE,@Spark}
19/08/10 12:18:10 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@27a0a5a2{/stages/stage/json,null,AVAILABLE,@Spark}
19/08/10 12:18:10 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@7692cd34{/stages/pool,null,AVAILABLE,@Spark}
19/08/10 12:18:10 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@33aa93c{/stages/pool/json,null,AVAILABLE,@Spark}
19/08/10 12:18:10 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@32c0915e{/storage,null,AVAILABLE,@Spark}
19/08/10 12:18:10 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@106faf11{/storage/json,null,AVAILABLE,@Spark}
19/08/10 12:18:10 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@70f43b45{/storage/rdd,null,AVAILABLE,@Spark}
19/08/10 12:18:10 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@26d10f2e{/storage/rdd/json,null,AVAILABLE,@Spark}
19/08/10 12:18:10 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@10ad20cb{/environment,null,AVAILABLE,@Spark}
19/08/10 12:18:10 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@7dd712e8{/environment/json,null,AVAILABLE,@Spark}
19/08/10 12:18:10 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@2c282004{/executors,null,AVAILABLE,@Spark}
19/08/10 12:18:10 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@22ee2d0{/executors/json,null,AVAILABLE,@Spark}
19/08/10 12:18:10 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@7bfc3126{/executors/threadDump,null,AVAILABLE,@Spark}
19/08/10 12:18:10 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@3e792ce3{/executors/threadDump/json,null,AVAILABLE,@Spark}
19/08/10 12:18:10 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@53bc1328{/static,null,AVAILABLE,@Spark}
19/08/10 12:18:10 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@e041f0c{/,null,AVAILABLE,@Spark}
19/08/10 12:18:10 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@6a175569{/api,null,AVAILABLE,@Spark}
19/08/10 12:18:10 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@4102b1b1{/jobs/job/kill,null,AVAILABLE,@Spark}
19/08/10 12:18:11 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@61a5b4ae{/stages/stage/kill,null,AVAILABLE,@Spark}
19/08/10 12:18:11 INFO ui.SparkUI: Bound SparkUI to 0.0.0.0, and started at http://192.168.10.32:4040
19/08/10 12:18:11 INFO spark.SparkContext: Added JAR file:/tmp/adamTestMP40nkE/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/target/adam-assembly-spark2_2.12-0.29.0-SNAPSHOT.jar at spark://192.168.10.32:39783/jars/adam-assembly-spark2_2.12-0.29.0-SNAPSHOT.jar with timestamp 1565464691043
19/08/10 12:18:11 INFO executor.Executor: Starting executor ID driver on host localhost
19/08/10 12:18:11 INFO util.Utils: Successfully started service 'org.apache.spark.network.netty.NettyBlockTransferService' on port 45267.
19/08/10 12:18:11 INFO netty.NettyBlockTransferService: Server created on 192.168.10.32:45267
19/08/10 12:18:11 INFO storage.BlockManager: Using org.apache.spark.storage.RandomBlockReplicationPolicy for block replication policy
19/08/10 12:18:11 INFO storage.BlockManagerMaster: Registering BlockManager BlockManagerId(driver, 192.168.10.32, 45267, None)
19/08/10 12:18:11 INFO storage.BlockManagerMasterEndpoint: Registering block manager 192.168.10.32:45267 with 366.3 MB RAM, BlockManagerId(driver, 192.168.10.32, 45267, None)
19/08/10 12:18:11 INFO storage.BlockManagerMaster: Registered BlockManager BlockManagerId(driver, 192.168.10.32, 45267, None)
19/08/10 12:18:11 INFO storage.BlockManager: Initialized BlockManager: BlockManagerId(driver, 192.168.10.32, 45267, None)
19/08/10 12:18:11 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@21719a0{/metrics/json,null,AVAILABLE,@Spark}
19/08/10 12:18:12 INFO rdd.ADAMContext: Loading mouse_chrM.bam as BAM/CRAM/SAM and converting to AlignmentRecords.
19/08/10 12:18:12 INFO rdd.ADAMContext: Loaded header from file:/tmp/adamTestMP40nkE/deleteMePleaseThisIsNoLongerNeeded/mouse_chrM.bam
19/08/10 12:18:12 INFO memory.MemoryStore: Block broadcast_0 stored as values in memory (estimated size 295.6 KB, free 366.0 MB)
19/08/10 12:18:13 INFO memory.MemoryStore: Block broadcast_0_piece0 stored as bytes in memory (estimated size 24.0 KB, free 366.0 MB)
19/08/10 12:18:13 INFO storage.BlockManagerInfo: Added broadcast_0_piece0 in memory on 192.168.10.32:45267 (size: 24.0 KB, free: 366.3 MB)
19/08/10 12:18:13 INFO spark.SparkContext: Created broadcast 0 from newAPIHadoopFile at ADAMContext.scala:2059
19/08/10 12:18:15 INFO read.RDDBoundAlignmentRecordDataset: Saving data in ADAM format
19/08/10 12:18:15 INFO output.FileOutputCommitter: File Output Committer Algorithm version is 1
19/08/10 12:18:15 INFO input.FileInputFormat: Total input paths to process : 1
19/08/10 12:18:15 INFO spark.SparkContext: Starting job: runJob at SparkHadoopWriter.scala:78
19/08/10 12:18:15 INFO scheduler.DAGScheduler: Got job 0 (runJob at SparkHadoopWriter.scala:78) with 1 output partitions
19/08/10 12:18:15 INFO scheduler.DAGScheduler: Final stage: ResultStage 0 (runJob at SparkHadoopWriter.scala:78)
19/08/10 12:18:15 INFO scheduler.DAGScheduler: Parents of final stage: List()
19/08/10 12:18:15 INFO scheduler.DAGScheduler: Missing parents: List()
19/08/10 12:18:15 INFO scheduler.DAGScheduler: Submitting ResultStage 0 (MapPartitionsRDD[2] at map at GenomicDataset.scala:3814), which has no missing parents
19/08/10 12:18:15 INFO memory.MemoryStore: Block broadcast_1 stored as values in memory (estimated size 85.6 KB, free 365.9 MB)
19/08/10 12:18:15 INFO memory.MemoryStore: Block broadcast_1_piece0 stored as bytes in memory (estimated size 31.6 KB, free 365.9 MB)
19/08/10 12:18:15 INFO storage.BlockManagerInfo: Added broadcast_1_piece0 in memory on 192.168.10.32:45267 (size: 31.6 KB, free: 366.2 MB)
19/08/10 12:18:15 INFO spark.SparkContext: Created broadcast 1 from broadcast at DAGScheduler.scala:1161
19/08/10 12:18:15 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))
19/08/10 12:18:15 INFO scheduler.TaskSchedulerImpl: Adding task set 0.0 with 1 tasks
19/08/10 12:18:16 INFO scheduler.TaskSetManager: Starting task 0.0 in stage 0.0 (TID 0, localhost, executor driver, partition 0, PROCESS_LOCAL, 7441 bytes)
19/08/10 12:18:16 INFO executor.Executor: Running task 0.0 in stage 0.0 (TID 0)
19/08/10 12:18:16 INFO executor.Executor: Fetching spark://192.168.10.32:39783/jars/adam-assembly-spark2_2.12-0.29.0-SNAPSHOT.jar with timestamp 1565464691043
19/08/10 12:18:16 INFO client.TransportClientFactory: Successfully created connection to /192.168.10.32:39783 after 55 ms (0 ms spent in bootstraps)
19/08/10 12:18:16 INFO util.Utils: Fetching spark://192.168.10.32:39783/jars/adam-assembly-spark2_2.12-0.29.0-SNAPSHOT.jar to /tmp/spark-acb963f4-ab1a-4766-8cb1-16a49757ee58/userFiles-49fc496a-aeb2-4e7d-91cb-98ae8e958855/fetchFileTemp5407456118382929037.tmp
19/08/10 12:18:16 INFO executor.Executor: Adding file:/tmp/spark-acb963f4-ab1a-4766-8cb1-16a49757ee58/userFiles-49fc496a-aeb2-4e7d-91cb-98ae8e958855/adam-assembly-spark2_2.12-0.29.0-SNAPSHOT.jar to class loader
19/08/10 12:18:16 INFO rdd.NewHadoopRDD: Input split: file:/tmp/adamTestMP40nkE/deleteMePleaseThisIsNoLongerNeeded/mouse_chrM.bam:83361792-833134657535
19/08/10 12:18:16 INFO output.FileOutputCommitter: File Output Committer Algorithm version is 1
19/08/10 12:18:16 INFO codec.CodecConfig: Compression: GZIP
19/08/10 12:18:16 INFO output.FileOutputCommitter: File Output Committer Algorithm version is 1
19/08/10 12:18:16 INFO hadoop.ParquetOutputFormat: Parquet block size to 134217728
19/08/10 12:18:16 INFO hadoop.ParquetOutputFormat: Parquet page size to 1048576
19/08/10 12:18:16 INFO hadoop.ParquetOutputFormat: Parquet dictionary page size to 1048576
19/08/10 12:18:16 INFO hadoop.ParquetOutputFormat: Dictionary is on
19/08/10 12:18:16 INFO hadoop.ParquetOutputFormat: Validation is off
19/08/10 12:18:16 INFO hadoop.ParquetOutputFormat: Writer version is: PARQUET_1_0
19/08/10 12:18:16 INFO hadoop.ParquetOutputFormat: Maximum row group padding size is 8388608 bytes
19/08/10 12:18:16 INFO hadoop.ParquetOutputFormat: Page size checking is: estimated
19/08/10 12:18:16 INFO hadoop.ParquetOutputFormat: Min row count for page size check is: 100
19/08/10 12:18:16 INFO hadoop.ParquetOutputFormat: Max row count for page size check is: 10000
19/08/10 12:18:16 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.
19/08/10 12:18:26 INFO hadoop.InternalParquetRecordWriter: Flushing mem columnStore to file. allocated memory: 16043959
19/08/10 12:18:27 INFO output.FileOutputCommitter: Saved output of task 'attempt_20190810121815_0002_r_000000_0' to file:/tmp/adamTestMP40nkE/deleteMePleaseThisIsNoLongerNeeded/mouse_chrM.bam.reads.adam/_temporary/0/task_20190810121815_0002_r_000000
19/08/10 12:18:27 INFO mapred.SparkHadoopMapRedUtil: attempt_20190810121815_0002_r_000000_0: Committed
19/08/10 12:18:27 INFO executor.Executor: Finished task 0.0 in stage 0.0 (TID 0). 856 bytes result sent to driver
19/08/10 12:18:27 INFO scheduler.TaskSetManager: Finished task 0.0 in stage 0.0 (TID 0) in 11334 ms on localhost (executor driver) (1/1)
19/08/10 12:18:27 INFO scheduler.TaskSchedulerImpl: Removed TaskSet 0.0, whose tasks have all completed, from pool 
19/08/10 12:18:27 INFO scheduler.DAGScheduler: ResultStage 0 (runJob at SparkHadoopWriter.scala:78) finished in 11.494 s
19/08/10 12:18:27 INFO scheduler.DAGScheduler: Job 0 finished: runJob at SparkHadoopWriter.scala:78, took 11.579136 s
19/08/10 12:18:27 INFO hadoop.ParquetFileReader: Initiating action with parallelism: 5
19/08/10 12:18:27 INFO io.SparkHadoopWriter: Job job_20190810121815_0002 committed.
19/08/10 12:18:27 INFO cli.TransformAlignments: Overall Duration: 17.75 secs
19/08/10 12:18:27 INFO spark.SparkContext: Invoking stop() from shutdown hook
19/08/10 12:18:27 INFO server.AbstractConnector: Stopped Spark@512d92b{HTTP/1.1,[http/1.1]}{0.0.0.0:4040}
19/08/10 12:18:27 INFO ui.SparkUI: Stopped Spark web UI at http://192.168.10.32:4040
19/08/10 12:18:27 INFO spark.MapOutputTrackerMasterEndpoint: MapOutputTrackerMasterEndpoint stopped!
19/08/10 12:18:27 INFO memory.MemoryStore: MemoryStore cleared
19/08/10 12:18:27 INFO storage.BlockManager: BlockManager stopped
19/08/10 12:18:27 INFO storage.BlockManagerMaster: BlockManagerMaster stopped
19/08/10 12:18:27 INFO scheduler.OutputCommitCoordinator$OutputCommitCoordinatorEndpoint: OutputCommitCoordinator stopped!
19/08/10 12:18:27 INFO spark.SparkContext: Successfully stopped SparkContext
19/08/10 12:18:27 INFO util.ShutdownHookManager: Shutdown hook called
19/08/10 12:18:27 INFO util.ShutdownHookManager: Deleting directory /tmp/spark-43929e82-4d0a-4f2f-9aec-52768428cf35
19/08/10 12:18:27 INFO util.ShutdownHookManager: Deleting directory /tmp/spark-acb963f4-ab1a-4766-8cb1-16a49757ee58

# 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/adamTestMP40nkE/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.3-bin-without-hadoop-scala-2.12/bin/spark-submit
19/08/10 12:18:29 WARN util.Utils: Your hostname, amp-jenkins-staging-worker-02 resolves to a loopback address: 127.0.1.1; using 192.168.10.32 instead (on interface eno1)
19/08/10 12:18:29 WARN util.Utils: Set SPARK_LOCAL_IP if you need to bind to another address
19/08/10 12:18:30 WARN util.NativeCodeLoader: Unable to load native-hadoop library for your platform... using builtin-java classes where applicable
19/08/10 12:18:30 INFO cli.ADAMMain: ADAM invoked with args: "transformAlignments" "-sort_by_reference_position" "mouse_chrM.bam.reads.adam" "mouse_chrM.bam.reads.sorted.adam"
19/08/10 12:18:30 INFO spark.SparkContext: Running Spark version 2.4.3
19/08/10 12:18:30 INFO spark.SparkContext: Submitted application: transformAlignments
19/08/10 12:18:30 INFO spark.SecurityManager: Changing view acls to: jenkins
19/08/10 12:18:30 INFO spark.SecurityManager: Changing modify acls to: jenkins
19/08/10 12:18:30 INFO spark.SecurityManager: Changing view acls groups to: 
19/08/10 12:18:30 INFO spark.SecurityManager: Changing modify acls groups to: 
19/08/10 12:18:30 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()
19/08/10 12:18:31 INFO util.Utils: Successfully started service 'sparkDriver' on port 36315.
19/08/10 12:18:31 INFO spark.SparkEnv: Registering MapOutputTracker
19/08/10 12:18:31 INFO spark.SparkEnv: Registering BlockManagerMaster
19/08/10 12:18:31 INFO storage.BlockManagerMasterEndpoint: Using org.apache.spark.storage.DefaultTopologyMapper for getting topology information
19/08/10 12:18:31 INFO storage.BlockManagerMasterEndpoint: BlockManagerMasterEndpoint up
19/08/10 12:18:31 INFO storage.DiskBlockManager: Created local directory at /tmp/blockmgr-85a9ffc6-d957-4bbd-8204-3bcd7cc1709d
19/08/10 12:18:31 INFO memory.MemoryStore: MemoryStore started with capacity 366.3 MB
19/08/10 12:18:31 INFO spark.SparkEnv: Registering OutputCommitCoordinator
19/08/10 12:18:31 INFO util.log: Logging initialized @3136ms
19/08/10 12:18:31 INFO server.Server: jetty-9.3.z-SNAPSHOT, build timestamp: unknown, git hash: unknown
19/08/10 12:18:31 INFO server.Server: Started @3231ms
19/08/10 12:18:31 INFO server.AbstractConnector: Started ServerConnector@62c5bbdc{HTTP/1.1,[http/1.1]}{0.0.0.0:4040}
19/08/10 12:18:31 INFO util.Utils: Successfully started service 'SparkUI' on port 4040.
19/08/10 12:18:31 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@3ad394e6{/jobs,null,AVAILABLE,@Spark}
19/08/10 12:18:31 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@15deb1dc{/jobs/json,null,AVAILABLE,@Spark}
19/08/10 12:18:31 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@6e9c413e{/jobs/job,null,AVAILABLE,@Spark}
19/08/10 12:18:31 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@5af5def9{/jobs/job/json,null,AVAILABLE,@Spark}
19/08/10 12:18:31 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@3a45c42a{/stages,null,AVAILABLE,@Spark}
19/08/10 12:18:31 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@36dce7ed{/stages/json,null,AVAILABLE,@Spark}
19/08/10 12:18:31 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@47a64f7d{/stages/stage,null,AVAILABLE,@Spark}
19/08/10 12:18:31 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@7692cd34{/stages/stage/json,null,AVAILABLE,@Spark}
19/08/10 12:18:31 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@33aa93c{/stages/pool,null,AVAILABLE,@Spark}
19/08/10 12:18:31 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@32c0915e{/stages/pool/json,null,AVAILABLE,@Spark}
19/08/10 12:18:31 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@106faf11{/storage,null,AVAILABLE,@Spark}
19/08/10 12:18:31 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@70f43b45{/storage/json,null,AVAILABLE,@Spark}
19/08/10 12:18:31 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@26d10f2e{/storage/rdd,null,AVAILABLE,@Spark}
19/08/10 12:18:31 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@10ad20cb{/storage/rdd/json,null,AVAILABLE,@Spark}
19/08/10 12:18:31 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@7dd712e8{/environment,null,AVAILABLE,@Spark}
19/08/10 12:18:31 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@2c282004{/environment/json,null,AVAILABLE,@Spark}
19/08/10 12:18:31 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@22ee2d0{/executors,null,AVAILABLE,@Spark}
19/08/10 12:18:31 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@7bfc3126{/executors/json,null,AVAILABLE,@Spark}
19/08/10 12:18:31 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@3e792ce3{/executors/threadDump,null,AVAILABLE,@Spark}
19/08/10 12:18:31 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@53bc1328{/executors/threadDump/json,null,AVAILABLE,@Spark}
19/08/10 12:18:31 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@26f143ed{/static,null,AVAILABLE,@Spark}
19/08/10 12:18:31 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@6a175569{/,null,AVAILABLE,@Spark}
19/08/10 12:18:31 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@11963225{/api,null,AVAILABLE,@Spark}
19/08/10 12:18:31 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@61a5b4ae{/jobs/job/kill,null,AVAILABLE,@Spark}
19/08/10 12:18:31 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@3a71c100{/stages/stage/kill,null,AVAILABLE,@Spark}
19/08/10 12:18:31 INFO ui.SparkUI: Bound SparkUI to 0.0.0.0, and started at http://192.168.10.32:4040
19/08/10 12:18:31 INFO spark.SparkContext: Added JAR file:/tmp/adamTestMP40nkE/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/target/adam-assembly-spark2_2.12-0.29.0-SNAPSHOT.jar at spark://192.168.10.32:36315/jars/adam-assembly-spark2_2.12-0.29.0-SNAPSHOT.jar with timestamp 1565464711706
19/08/10 12:18:31 INFO executor.Executor: Starting executor ID driver on host localhost
19/08/10 12:18:31 INFO util.Utils: Successfully started service 'org.apache.spark.network.netty.NettyBlockTransferService' on port 37994.
19/08/10 12:18:31 INFO netty.NettyBlockTransferService: Server created on 192.168.10.32:37994
19/08/10 12:18:31 INFO storage.BlockManager: Using org.apache.spark.storage.RandomBlockReplicationPolicy for block replication policy
19/08/10 12:18:32 INFO storage.BlockManagerMaster: Registering BlockManager BlockManagerId(driver, 192.168.10.32, 37994, None)
19/08/10 12:18:32 INFO storage.BlockManagerMasterEndpoint: Registering block manager 192.168.10.32:37994 with 366.3 MB RAM, BlockManagerId(driver, 192.168.10.32, 37994, None)
19/08/10 12:18:32 INFO storage.BlockManagerMaster: Registered BlockManager BlockManagerId(driver, 192.168.10.32, 37994, None)
19/08/10 12:18:32 INFO storage.BlockManager: Initialized BlockManager: BlockManagerId(driver, 192.168.10.32, 37994, None)
19/08/10 12:18:32 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@76b224cd{/metrics/json,null,AVAILABLE,@Spark}
19/08/10 12:18:32 INFO rdd.ADAMContext: Loading mouse_chrM.bam.reads.adam as Parquet of AlignmentRecords.
19/08/10 12:18:34 INFO rdd.ADAMContext: Reading the ADAM file at mouse_chrM.bam.reads.adam to create RDD
19/08/10 12:18:35 INFO memory.MemoryStore: Block broadcast_0 stored as values in memory (estimated size 315.0 KB, free 366.0 MB)
19/08/10 12:18:35 INFO memory.MemoryStore: Block broadcast_0_piece0 stored as bytes in memory (estimated size 28.2 KB, free 366.0 MB)
19/08/10 12:18:35 INFO storage.BlockManagerInfo: Added broadcast_0_piece0 in memory on 192.168.10.32:37994 (size: 28.2 KB, free: 366.3 MB)
19/08/10 12:18:35 INFO spark.SparkContext: Created broadcast 0 from newAPIHadoopFile at ADAMContext.scala:1801
19/08/10 12:18:36 INFO cli.TransformAlignments: Sorting alignments by reference position, with references ordered by name
19/08/10 12:18:36 INFO read.RDDBoundAlignmentRecordDataset: Sorting alignments by reference position
19/08/10 12:18:36 INFO input.FileInputFormat: Total input paths to process : 1
19/08/10 12:18:36 INFO hadoop.ParquetInputFormat: Total input paths to process : 1
19/08/10 12:18:36 INFO read.RDDBoundAlignmentRecordDataset: Saving data in ADAM format
19/08/10 12:18:36 INFO output.FileOutputCommitter: File Output Committer Algorithm version is 1
19/08/10 12:18:36 INFO spark.SparkContext: Starting job: runJob at SparkHadoopWriter.scala:78
19/08/10 12:18:36 INFO scheduler.DAGScheduler: Registering RDD 2 (sortBy at AlignmentRecordDataset.scala:1001)
19/08/10 12:18:36 INFO scheduler.DAGScheduler: Got job 0 (runJob at SparkHadoopWriter.scala:78) with 1 output partitions
19/08/10 12:18:36 INFO scheduler.DAGScheduler: Final stage: ResultStage 1 (runJob at SparkHadoopWriter.scala:78)
19/08/10 12:18:36 INFO scheduler.DAGScheduler: Parents of final stage: List(ShuffleMapStage 0)
19/08/10 12:18:36 INFO scheduler.DAGScheduler: Missing parents: List(ShuffleMapStage 0)
19/08/10 12:18:36 INFO scheduler.DAGScheduler: Submitting ShuffleMapStage 0 (MapPartitionsRDD[2] at sortBy at AlignmentRecordDataset.scala:1001), which has no missing parents
19/08/10 12:18:36 INFO memory.MemoryStore: Block broadcast_1 stored as values in memory (estimated size 5.8 KB, free 366.0 MB)
19/08/10 12:18:36 INFO memory.MemoryStore: Block broadcast_1_piece0 stored as bytes in memory (estimated size 3.4 KB, free 366.0 MB)
19/08/10 12:18:36 INFO storage.BlockManagerInfo: Added broadcast_1_piece0 in memory on 192.168.10.32:37994 (size: 3.4 KB, free: 366.3 MB)
19/08/10 12:18:36 INFO spark.SparkContext: Created broadcast 1 from broadcast at DAGScheduler.scala:1161
19/08/10 12:18:36 INFO scheduler.DAGScheduler: Submitting 1 missing tasks from ShuffleMapStage 0 (MapPartitionsRDD[2] at sortBy at AlignmentRecordDataset.scala:1001) (first 15 tasks are for partitions Vector(0))
19/08/10 12:18:36 INFO scheduler.TaskSchedulerImpl: Adding task set 0.0 with 1 tasks
19/08/10 12:18:36 INFO scheduler.TaskSetManager: Starting task 0.0 in stage 0.0 (TID 0, localhost, executor driver, partition 0, PROCESS_LOCAL, 7480 bytes)
19/08/10 12:18:36 INFO executor.Executor: Running task 0.0 in stage 0.0 (TID 0)
19/08/10 12:18:36 INFO executor.Executor: Fetching spark://192.168.10.32:36315/jars/adam-assembly-spark2_2.12-0.29.0-SNAPSHOT.jar with timestamp 1565464711706
19/08/10 12:18:36 INFO client.TransportClientFactory: Successfully created connection to /192.168.10.32:36315 after 43 ms (0 ms spent in bootstraps)
19/08/10 12:18:36 INFO util.Utils: Fetching spark://192.168.10.32:36315/jars/adam-assembly-spark2_2.12-0.29.0-SNAPSHOT.jar to /tmp/spark-8a1517ec-2ca0-47d6-a868-db840b642f8a/userFiles-6ba7e900-3d96-4bd1-8dba-0de4abe27ec8/fetchFileTemp8447800107364490465.tmp
19/08/10 12:18:36 INFO executor.Executor: Adding file:/tmp/spark-8a1517ec-2ca0-47d6-a868-db840b642f8a/userFiles-6ba7e900-3d96-4bd1-8dba-0de4abe27ec8/adam-assembly-spark2_2.12-0.29.0-SNAPSHOT.jar to class loader
19/08/10 12:18:37 INFO rdd.NewHadoopRDD: Input split: file:/tmp/adamTestMP40nkE/deleteMePleaseThisIsNoLongerNeeded/mouse_chrM.bam.reads.adam/part-r-00000.gz.parquet:0+10132194
19/08/10 12:18:37 INFO hadoop.InternalParquetRecordReader: RecordReader initialized will read a total of 163064 records.
19/08/10 12:18:37 INFO hadoop.InternalParquetRecordReader: at row 0. reading next block
19/08/10 12:18:37 INFO compress.CodecPool: Got brand-new decompressor [.gz]
19/08/10 12:18:37 INFO hadoop.InternalParquetRecordReader: block read in memory in 64 ms. row count = 163064
19/08/10 12:18:40 INFO executor.Executor: Finished task 0.0 in stage 0.0 (TID 0). 919 bytes result sent to driver
19/08/10 12:18:40 INFO scheduler.TaskSetManager: Finished task 0.0 in stage 0.0 (TID 0) in 4373 ms on localhost (executor driver) (1/1)
19/08/10 12:18:40 INFO scheduler.TaskSchedulerImpl: Removed TaskSet 0.0, whose tasks have all completed, from pool 
19/08/10 12:18:40 INFO scheduler.DAGScheduler: ShuffleMapStage 0 (sortBy at AlignmentRecordDataset.scala:1001) finished in 4.560 s
19/08/10 12:18:40 INFO scheduler.DAGScheduler: looking for newly runnable stages
19/08/10 12:18:40 INFO scheduler.DAGScheduler: running: Set()
19/08/10 12:18:40 INFO scheduler.DAGScheduler: waiting: Set(ResultStage 1)
19/08/10 12:18:40 INFO scheduler.DAGScheduler: failed: Set()
19/08/10 12:18:40 INFO scheduler.DAGScheduler: Submitting ResultStage 1 (MapPartitionsRDD[5] at map at GenomicDataset.scala:3814), which has no missing parents
19/08/10 12:18:40 INFO memory.MemoryStore: Block broadcast_2 stored as values in memory (estimated size 86.8 KB, free 365.9 MB)
19/08/10 12:18:40 INFO memory.MemoryStore: Block broadcast_2_piece0 stored as bytes in memory (estimated size 32.3 KB, free 365.8 MB)
19/08/10 12:18:40 INFO storage.BlockManagerInfo: Added broadcast_2_piece0 in memory on 192.168.10.32:37994 (size: 32.3 KB, free: 366.2 MB)
19/08/10 12:18:40 INFO spark.SparkContext: Created broadcast 2 from broadcast at DAGScheduler.scala:1161
19/08/10 12:18:40 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))
19/08/10 12:18:40 INFO scheduler.TaskSchedulerImpl: Adding task set 1.0 with 1 tasks
19/08/10 12:18:40 INFO scheduler.TaskSetManager: Starting task 0.0 in stage 1.0 (TID 1, localhost, executor driver, partition 0, ANY, 7141 bytes)
19/08/10 12:18:40 INFO executor.Executor: Running task 0.0 in stage 1.0 (TID 1)
19/08/10 12:18:41 INFO storage.ShuffleBlockFetcherIterator: Getting 1 non-empty blocks including 1 local blocks and 0 remote blocks
19/08/10 12:18:41 INFO storage.ShuffleBlockFetcherIterator: Started 0 remote fetches in 10 ms
19/08/10 12:18:42 INFO output.FileOutputCommitter: File Output Committer Algorithm version is 1
19/08/10 12:18:42 INFO codec.CodecConfig: Compression: GZIP
19/08/10 12:18:42 INFO output.FileOutputCommitter: File Output Committer Algorithm version is 1
19/08/10 12:18:42 INFO hadoop.ParquetOutputFormat: Parquet block size to 134217728
19/08/10 12:18:42 INFO hadoop.ParquetOutputFormat: Parquet page size to 1048576
19/08/10 12:18:42 INFO hadoop.ParquetOutputFormat: Parquet dictionary page size to 1048576
19/08/10 12:18:42 INFO hadoop.ParquetOutputFormat: Dictionary is on
19/08/10 12:18:42 INFO hadoop.ParquetOutputFormat: Validation is off
19/08/10 12:18:42 INFO hadoop.ParquetOutputFormat: Writer version is: PARQUET_1_0
19/08/10 12:18:42 INFO hadoop.ParquetOutputFormat: Maximum row group padding size is 8388608 bytes
19/08/10 12:18:42 INFO hadoop.ParquetOutputFormat: Page size checking is: estimated
19/08/10 12:18:42 INFO hadoop.ParquetOutputFormat: Min row count for page size check is: 100
19/08/10 12:18:42 INFO hadoop.ParquetOutputFormat: Max row count for page size check is: 10000
19/08/10 12:18:42 INFO compress.CodecPool: Got brand-new compressor [.gz]
19/08/10 12:18:44 INFO storage.BlockManagerInfo: Removed broadcast_1_piece0 on 192.168.10.32:37994 in memory (size: 3.4 KB, free: 366.2 MB)
19/08/10 12:18:48 INFO hadoop.InternalParquetRecordWriter: Flushing mem columnStore to file. allocated memory: 16004474
19/08/10 12:18:49 INFO output.FileOutputCommitter: Saved output of task 'attempt_20190810121836_0005_r_000000_0' to file:/tmp/adamTestMP40nkE/deleteMePleaseThisIsNoLongerNeeded/mouse_chrM.bam.reads.sorted.adam/_temporary/0/task_20190810121836_0005_r_000000
19/08/10 12:18:49 INFO mapred.SparkHadoopMapRedUtil: attempt_20190810121836_0005_r_000000_0: Committed
19/08/10 12:18:49 INFO executor.Executor: Finished task 0.0 in stage 1.0 (TID 1). 1200 bytes result sent to driver
19/08/10 12:18:49 INFO scheduler.TaskSetManager: Finished task 0.0 in stage 1.0 (TID 1) in 8393 ms on localhost (executor driver) (1/1)
19/08/10 12:18:49 INFO scheduler.TaskSchedulerImpl: Removed TaskSet 1.0, whose tasks have all completed, from pool 
19/08/10 12:18:49 INFO scheduler.DAGScheduler: ResultStage 1 (runJob at SparkHadoopWriter.scala:78) finished in 8.457 s
19/08/10 12:18:49 INFO scheduler.DAGScheduler: Job 0 finished: runJob at SparkHadoopWriter.scala:78, took 13.157415 s
19/08/10 12:18:49 INFO hadoop.ParquetFileReader: Initiating action with parallelism: 5
19/08/10 12:18:49 INFO io.SparkHadoopWriter: Job job_20190810121836_0005 committed.
19/08/10 12:18:49 INFO cli.TransformAlignments: Overall Duration: 19.06 secs
19/08/10 12:18:49 INFO spark.SparkContext: Invoking stop() from shutdown hook
19/08/10 12:18:49 INFO server.AbstractConnector: Stopped Spark@62c5bbdc{HTTP/1.1,[http/1.1]}{0.0.0.0:4040}
19/08/10 12:18:49 INFO ui.SparkUI: Stopped Spark web UI at http://192.168.10.32:4040
19/08/10 12:18:49 INFO spark.MapOutputTrackerMasterEndpoint: MapOutputTrackerMasterEndpoint stopped!
19/08/10 12:18:49 INFO memory.MemoryStore: MemoryStore cleared
19/08/10 12:18:49 INFO storage.BlockManager: BlockManager stopped
19/08/10 12:18:49 INFO storage.BlockManagerMaster: BlockManagerMaster stopped
19/08/10 12:18:49 INFO scheduler.OutputCommitCoordinator$OutputCommitCoordinatorEndpoint: OutputCommitCoordinator stopped!
19/08/10 12:18:49 INFO spark.SparkContext: Successfully stopped SparkContext
19/08/10 12:18:49 INFO util.ShutdownHookManager: Shutdown hook called
19/08/10 12:18:49 INFO util.ShutdownHookManager: Deleting directory /tmp/spark-eec64c5a-a2c3-4a93-9da0-ed55ef52f969
19/08/10 12:18:49 INFO util.ShutdownHookManager: Deleting directory /tmp/spark-8a1517ec-2ca0-47d6-a868-db840b642f8a

# 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/adamTestMP40nkE/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.3-bin-without-hadoop-scala-2.12/bin/spark-submit
19/08/10 12:18:51 WARN util.Utils: Your hostname, amp-jenkins-staging-worker-02 resolves to a loopback address: 127.0.1.1; using 192.168.10.32 instead (on interface eno1)
19/08/10 12:18:51 WARN util.Utils: Set SPARK_LOCAL_IP if you need to bind to another address
19/08/10 12:18:51 WARN util.NativeCodeLoader: Unable to load native-hadoop library for your platform... using builtin-java classes where applicable
19/08/10 12:18:52 INFO cli.ADAMMain: ADAM invoked with args: "transformFragments" "-load_as_alignments" "mouse_chrM.bam.reads.adam" "mouse_chrM.bam.fragments.adam"
19/08/10 12:18:52 INFO spark.SparkContext: Running Spark version 2.4.3
19/08/10 12:18:52 INFO spark.SparkContext: Submitted application: transformFragments
19/08/10 12:18:52 INFO spark.SecurityManager: Changing view acls to: jenkins
19/08/10 12:18:52 INFO spark.SecurityManager: Changing modify acls to: jenkins
19/08/10 12:18:52 INFO spark.SecurityManager: Changing view acls groups to: 
19/08/10 12:18:52 INFO spark.SecurityManager: Changing modify acls groups to: 
19/08/10 12:18:52 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()
19/08/10 12:18:53 INFO util.Utils: Successfully started service 'sparkDriver' on port 37312.
19/08/10 12:18:53 INFO spark.SparkEnv: Registering MapOutputTracker
19/08/10 12:18:53 INFO spark.SparkEnv: Registering BlockManagerMaster
19/08/10 12:18:53 INFO storage.BlockManagerMasterEndpoint: Using org.apache.spark.storage.DefaultTopologyMapper for getting topology information
19/08/10 12:18:53 INFO storage.BlockManagerMasterEndpoint: BlockManagerMasterEndpoint up
19/08/10 12:18:53 INFO storage.DiskBlockManager: Created local directory at /tmp/blockmgr-cefc6bea-267c-4c57-852a-23b7ee199bce
19/08/10 12:18:53 INFO memory.MemoryStore: MemoryStore started with capacity 366.3 MB
19/08/10 12:18:53 INFO spark.SparkEnv: Registering OutputCommitCoordinator
19/08/10 12:18:53 INFO util.log: Logging initialized @3073ms
19/08/10 12:18:53 INFO server.Server: jetty-9.3.z-SNAPSHOT, build timestamp: unknown, git hash: unknown
19/08/10 12:18:53 INFO server.Server: Started @3184ms
19/08/10 12:18:53 INFO server.AbstractConnector: Started ServerConnector@68ed96ca{HTTP/1.1,[http/1.1]}{0.0.0.0:4040}
19/08/10 12:18:53 INFO util.Utils: Successfully started service 'SparkUI' on port 4040.
19/08/10 12:18:53 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@4ced35ed{/jobs,null,AVAILABLE,@Spark}
19/08/10 12:18:53 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@6ca320ab{/jobs/json,null,AVAILABLE,@Spark}
19/08/10 12:18:53 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@50d68830{/jobs/job,null,AVAILABLE,@Spark}
19/08/10 12:18:53 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@7674a051{/jobs/job/json,null,AVAILABLE,@Spark}
19/08/10 12:18:53 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@3a7704c{/stages,null,AVAILABLE,@Spark}
19/08/10 12:18:53 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@6754ef00{/stages/json,null,AVAILABLE,@Spark}
19/08/10 12:18:53 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@619bd14c{/stages/stage,null,AVAILABLE,@Spark}
19/08/10 12:18:53 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@4acf72b6{/stages/stage/json,null,AVAILABLE,@Spark}
19/08/10 12:18:53 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@7561db12{/stages/pool,null,AVAILABLE,@Spark}
19/08/10 12:18:53 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@3301500b{/stages/pool/json,null,AVAILABLE,@Spark}
19/08/10 12:18:53 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@24b52d3e{/storage,null,AVAILABLE,@Spark}
19/08/10 12:18:53 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@15deb1dc{/storage/json,null,AVAILABLE,@Spark}
19/08/10 12:18:53 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@6e9c413e{/storage/rdd,null,AVAILABLE,@Spark}
19/08/10 12:18:53 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@57a4d5ee{/storage/rdd/json,null,AVAILABLE,@Spark}
19/08/10 12:18:53 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@5af5def9{/environment,null,AVAILABLE,@Spark}
19/08/10 12:18:53 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@3a45c42a{/environment/json,null,AVAILABLE,@Spark}
19/08/10 12:18:53 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@36dce7ed{/executors,null,AVAILABLE,@Spark}
19/08/10 12:18:53 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@47a64f7d{/executors/json,null,AVAILABLE,@Spark}
19/08/10 12:18:53 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@33d05366{/executors/threadDump,null,AVAILABLE,@Spark}
19/08/10 12:18:53 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@27a0a5a2{/executors/threadDump/json,null,AVAILABLE,@Spark}
19/08/10 12:18:53 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@7692cd34{/static,null,AVAILABLE,@Spark}
19/08/10 12:18:53 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@6a1ebcff{/,null,AVAILABLE,@Spark}
19/08/10 12:18:53 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@19868320{/api,null,AVAILABLE,@Spark}
19/08/10 12:18:53 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@3ef41c66{/jobs/job/kill,null,AVAILABLE,@Spark}
19/08/10 12:18:53 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@6b739528{/stages/stage/kill,null,AVAILABLE,@Spark}
19/08/10 12:18:53 INFO ui.SparkUI: Bound SparkUI to 0.0.0.0, and started at http://192.168.10.32:4040
19/08/10 12:18:53 INFO spark.SparkContext: Added JAR file:/tmp/adamTestMP40nkE/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/target/adam-assembly-spark2_2.12-0.29.0-SNAPSHOT.jar at spark://192.168.10.32:37312/jars/adam-assembly-spark2_2.12-0.29.0-SNAPSHOT.jar with timestamp 1565464733678
19/08/10 12:18:53 INFO executor.Executor: Starting executor ID driver on host localhost
19/08/10 12:18:53 INFO util.Utils: Successfully started service 'org.apache.spark.network.netty.NettyBlockTransferService' on port 34467.
19/08/10 12:18:53 INFO netty.NettyBlockTransferService: Server created on 192.168.10.32:34467
19/08/10 12:18:53 INFO storage.BlockManager: Using org.apache.spark.storage.RandomBlockReplicationPolicy for block replication policy
19/08/10 12:18:54 INFO storage.BlockManagerMaster: Registering BlockManager BlockManagerId(driver, 192.168.10.32, 34467, None)
19/08/10 12:18:54 INFO storage.BlockManagerMasterEndpoint: Registering block manager 192.168.10.32:34467 with 366.3 MB RAM, BlockManagerId(driver, 192.168.10.32, 34467, None)
19/08/10 12:18:54 INFO storage.BlockManagerMaster: Registered BlockManager BlockManagerId(driver, 192.168.10.32, 34467, None)
19/08/10 12:18:54 INFO storage.BlockManager: Initialized BlockManager: BlockManagerId(driver, 192.168.10.32, 34467, None)
19/08/10 12:18:54 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@5f14a673{/metrics/json,null,AVAILABLE,@Spark}
19/08/10 12:18:54 INFO rdd.ADAMContext: Loading mouse_chrM.bam.reads.adam as Parquet of AlignmentRecords.
19/08/10 12:18:56 INFO rdd.ADAMContext: Reading the ADAM file at mouse_chrM.bam.reads.adam to create RDD
19/08/10 12:18:57 INFO memory.MemoryStore: Block broadcast_0 stored as values in memory (estimated size 315.0 KB, free 366.0 MB)
19/08/10 12:18:58 INFO memory.MemoryStore: Block broadcast_0_piece0 stored as bytes in memory (estimated size 28.2 KB, free 366.0 MB)
19/08/10 12:18:58 INFO storage.BlockManagerInfo: Added broadcast_0_piece0 in memory on 192.168.10.32:34467 (size: 28.2 KB, free: 366.3 MB)
19/08/10 12:18:58 INFO spark.SparkContext: Created broadcast 0 from newAPIHadoopFile at ADAMContext.scala:1801
19/08/10 12:18:58 INFO input.FileInputFormat: Total input paths to process : 1
19/08/10 12:18:58 INFO hadoop.ParquetInputFormat: Total input paths to process : 1
19/08/10 12:18:58 INFO fragment.RDDBoundFragmentDataset: Saving data in ADAM format
19/08/10 12:18:58 INFO output.FileOutputCommitter: File Output Committer Algorithm version is 1
19/08/10 12:18:58 INFO spark.SparkContext: Starting job: runJob at SparkHadoopWriter.scala:78
19/08/10 12:18:58 INFO scheduler.DAGScheduler: Registering RDD 2 (groupBy at SingleReadBucket.scala:97)
19/08/10 12:18:58 INFO scheduler.DAGScheduler: Got job 0 (runJob at SparkHadoopWriter.scala:78) with 1 output partitions
19/08/10 12:18:58 INFO scheduler.DAGScheduler: Final stage: ResultStage 1 (runJob at SparkHadoopWriter.scala:78)
19/08/10 12:18:58 INFO scheduler.DAGScheduler: Parents of final stage: List(ShuffleMapStage 0)
19/08/10 12:18:58 INFO scheduler.DAGScheduler: Missing parents: List(ShuffleMapStage 0)
19/08/10 12:18:58 INFO scheduler.DAGScheduler: Submitting ShuffleMapStage 0 (MapPartitionsRDD[2] at groupBy at SingleReadBucket.scala:97), which has no missing parents
19/08/10 12:18:58 INFO memory.MemoryStore: Block broadcast_1 stored as values in memory (estimated size 6.3 KB, free 366.0 MB)
19/08/10 12:18:58 INFO memory.MemoryStore: Block broadcast_1_piece0 stored as bytes in memory (estimated size 3.4 KB, free 366.0 MB)
19/08/10 12:18:58 INFO storage.BlockManagerInfo: Added broadcast_1_piece0 in memory on 192.168.10.32:34467 (size: 3.4 KB, free: 366.3 MB)
19/08/10 12:18:58 INFO spark.SparkContext: Created broadcast 1 from broadcast at DAGScheduler.scala:1161
19/08/10 12:18:58 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))
19/08/10 12:18:58 INFO scheduler.TaskSchedulerImpl: Adding task set 0.0 with 1 tasks
19/08/10 12:18:58 INFO scheduler.TaskSetManager: Starting task 0.0 in stage 0.0 (TID 0, localhost, executor driver, partition 0, PROCESS_LOCAL, 7480 bytes)
19/08/10 12:18:58 INFO executor.Executor: Running task 0.0 in stage 0.0 (TID 0)
19/08/10 12:18:58 INFO executor.Executor: Fetching spark://192.168.10.32:37312/jars/adam-assembly-spark2_2.12-0.29.0-SNAPSHOT.jar with timestamp 1565464733678
19/08/10 12:18:58 INFO client.TransportClientFactory: Successfully created connection to /192.168.10.32:37312 after 51 ms (0 ms spent in bootstraps)
19/08/10 12:18:58 INFO util.Utils: Fetching spark://192.168.10.32:37312/jars/adam-assembly-spark2_2.12-0.29.0-SNAPSHOT.jar to /tmp/spark-53985a96-0f00-4070-ad59-3b3f220fdbf2/userFiles-ff22e9cb-0c7c-40bc-b2ff-e569d79f24e7/fetchFileTemp7807655624623361856.tmp
19/08/10 12:18:58 INFO executor.Executor: Adding file:/tmp/spark-53985a96-0f00-4070-ad59-3b3f220fdbf2/userFiles-ff22e9cb-0c7c-40bc-b2ff-e569d79f24e7/adam-assembly-spark2_2.12-0.29.0-SNAPSHOT.jar to class loader
19/08/10 12:18:59 INFO rdd.NewHadoopRDD: Input split: file:/tmp/adamTestMP40nkE/deleteMePleaseThisIsNoLongerNeeded/mouse_chrM.bam.reads.adam/part-r-00000.gz.parquet:0+10132194
19/08/10 12:18:59 INFO hadoop.InternalParquetRecordReader: RecordReader initialized will read a total of 163064 records.
19/08/10 12:18:59 INFO hadoop.InternalParquetRecordReader: at row 0. reading next block
19/08/10 12:18:59 INFO compress.CodecPool: Got brand-new decompressor [.gz]
19/08/10 12:18:59 INFO hadoop.InternalParquetRecordReader: block read in memory in 45 ms. row count = 163064
19/08/10 12:19:02 INFO executor.Executor: Finished task 0.0 in stage 0.0 (TID 0). 962 bytes result sent to driver
19/08/10 12:19:02 INFO scheduler.TaskSetManager: Finished task 0.0 in stage 0.0 (TID 0) in 4196 ms on localhost (executor driver) (1/1)
19/08/10 12:19:02 INFO scheduler.TaskSchedulerImpl: Removed TaskSet 0.0, whose tasks have all completed, from pool 
19/08/10 12:19:02 INFO scheduler.DAGScheduler: ShuffleMapStage 0 (groupBy at SingleReadBucket.scala:97) finished in 4.328 s
19/08/10 12:19:02 INFO scheduler.DAGScheduler: looking for newly runnable stages
19/08/10 12:19:02 INFO scheduler.DAGScheduler: running: Set()
19/08/10 12:19:02 INFO scheduler.DAGScheduler: waiting: Set(ResultStage 1)
19/08/10 12:19:02 INFO scheduler.DAGScheduler: failed: Set()
19/08/10 12:19:02 INFO scheduler.DAGScheduler: Submitting ResultStage 1 (MapPartitionsRDD[6] at map at GenomicDataset.scala:3814), which has no missing parents
19/08/10 12:19:02 INFO memory.MemoryStore: Block broadcast_2 stored as values in memory (estimated size 90.2 KB, free 365.9 MB)
19/08/10 12:19:02 INFO memory.MemoryStore: Block broadcast_2_piece0 stored as bytes in memory (estimated size 33.5 KB, free 365.8 MB)
19/08/10 12:19:02 INFO storage.BlockManagerInfo: Added broadcast_2_piece0 in memory on 192.168.10.32:34467 (size: 33.5 KB, free: 366.2 MB)
19/08/10 12:19:02 INFO spark.SparkContext: Created broadcast 2 from broadcast at DAGScheduler.scala:1161
19/08/10 12:19:02 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))
19/08/10 12:19:02 INFO scheduler.TaskSchedulerImpl: Adding task set 1.0 with 1 tasks
19/08/10 12:19:02 INFO scheduler.TaskSetManager: Starting task 0.0 in stage 1.0 (TID 1, localhost, executor driver, partition 0, ANY, 7141 bytes)
19/08/10 12:19:02 INFO executor.Executor: Running task 0.0 in stage 1.0 (TID 1)
19/08/10 12:19:03 INFO storage.ShuffleBlockFetcherIterator: Getting 1 non-empty blocks including 1 local blocks and 0 remote blocks
19/08/10 12:19:03 INFO storage.ShuffleBlockFetcherIterator: Started 0 remote fetches in 8 ms
19/08/10 12:19:04 INFO output.FileOutputCommitter: File Output Committer Algorithm version is 1
19/08/10 12:19:04 INFO codec.CodecConfig: Compression: GZIP
19/08/10 12:19:04 INFO output.FileOutputCommitter: File Output Committer Algorithm version is 1
19/08/10 12:19:04 INFO hadoop.ParquetOutputFormat: Parquet block size to 134217728
19/08/10 12:19:04 INFO hadoop.ParquetOutputFormat: Parquet page size to 1048576
19/08/10 12:19:04 INFO hadoop.ParquetOutputFormat: Parquet dictionary page size to 1048576
19/08/10 12:19:04 INFO hadoop.ParquetOutputFormat: Dictionary is on
19/08/10 12:19:04 INFO hadoop.ParquetOutputFormat: Validation is off
19/08/10 12:19:04 INFO hadoop.ParquetOutputFormat: Writer version is: PARQUET_1_0
19/08/10 12:19:04 INFO hadoop.ParquetOutputFormat: Maximum row group padding size is 8388608 bytes
19/08/10 12:19:04 INFO hadoop.ParquetOutputFormat: Page size checking is: estimated
19/08/10 12:19:04 INFO hadoop.ParquetOutputFormat: Min row count for page size check is: 100
19/08/10 12:19:04 INFO hadoop.ParquetOutputFormat: Max row count for page size check is: 10000
19/08/10 12:19:04 INFO compress.CodecPool: Got brand-new compressor [.gz]
19/08/10 12:19:09 INFO storage.BlockManagerInfo: Removed broadcast_1_piece0 on 192.168.10.32:34467 in memory (size: 3.4 KB, free: 366.2 MB)
19/08/10 12:19:12 INFO hadoop.InternalParquetRecordWriter: Flushing mem columnStore to file. allocated memory: 21417928
19/08/10 12:19:12 INFO output.FileOutputCommitter: Saved output of task 'attempt_20190810121858_0006_r_000000_0' to file:/tmp/adamTestMP40nkE/deleteMePleaseThisIsNoLongerNeeded/mouse_chrM.bam.fragments.adam/_temporary/0/task_20190810121858_0006_r_000000
19/08/10 12:19:12 INFO mapred.SparkHadoopMapRedUtil: attempt_20190810121858_0006_r_000000_0: Committed
19/08/10 12:19:12 INFO executor.Executor: Finished task 0.0 in stage 1.0 (TID 1). 1243 bytes result sent to driver
19/08/10 12:19:12 INFO scheduler.TaskSetManager: Finished task 0.0 in stage 1.0 (TID 1) in 9762 ms on localhost (executor driver) (1/1)
19/08/10 12:19:12 INFO scheduler.TaskSchedulerImpl: Removed TaskSet 1.0, whose tasks have all completed, from pool 
19/08/10 12:19:12 INFO scheduler.DAGScheduler: ResultStage 1 (runJob at SparkHadoopWriter.scala:78) finished in 9.815 s
19/08/10 12:19:12 INFO scheduler.DAGScheduler: Job 0 finished: runJob at SparkHadoopWriter.scala:78, took 14.277962 s
19/08/10 12:19:12 INFO hadoop.ParquetFileReader: Initiating action with parallelism: 5
19/08/10 12:19:12 INFO io.SparkHadoopWriter: Job job_20190810121858_0006 committed.
19/08/10 12:19:12 INFO cli.TransformFragments: Overall Duration: 20.45 secs
19/08/10 12:19:12 INFO spark.SparkContext: Invoking stop() from shutdown hook
19/08/10 12:19:12 INFO server.AbstractConnector: Stopped Spark@68ed96ca{HTTP/1.1,[http/1.1]}{0.0.0.0:4040}
19/08/10 12:19:12 INFO ui.SparkUI: Stopped Spark web UI at http://192.168.10.32:4040
19/08/10 12:19:12 INFO spark.MapOutputTrackerMasterEndpoint: MapOutputTrackerMasterEndpoint stopped!
19/08/10 12:19:12 INFO memory.MemoryStore: MemoryStore cleared
19/08/10 12:19:12 INFO storage.BlockManager: BlockManager stopped
19/08/10 12:19:12 INFO storage.BlockManagerMaster: BlockManagerMaster stopped
19/08/10 12:19:12 INFO scheduler.OutputCommitCoordinator$OutputCommitCoordinatorEndpoint: OutputCommitCoordinator stopped!
19/08/10 12:19:12 INFO spark.SparkContext: Successfully stopped SparkContext
19/08/10 12:19:12 INFO util.ShutdownHookManager: Shutdown hook called
19/08/10 12:19:12 INFO util.ShutdownHookManager: Deleting directory /tmp/spark-53985a96-0f00-4070-ad59-3b3f220fdbf2
19/08/10 12:19:12 INFO util.ShutdownHookManager: Deleting directory /tmp/spark-f6c3a6c4-9f49-48a7-9107-a6bc1e284d43

# 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/adamTestMP40nkE/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.3-bin-without-hadoop-scala-2.12/bin/spark-submit
19/08/10 12:19:35 WARN util.Utils: Your hostname, amp-jenkins-staging-worker-02 resolves to a loopback address: 127.0.1.1; using 192.168.10.32 instead (on interface eno1)
19/08/10 12:19:35 WARN util.Utils: Set SPARK_LOCAL_IP if you need to bind to another address
19/08/10 12:19:36 WARN util.NativeCodeLoader: Unable to load native-hadoop library for your platform... using builtin-java classes where applicable
19/08/10 12:19:36 INFO cli.ADAMMain: ADAM invoked with args: "flagstat" "-print_metrics" "mouse_chrM.bam.reads.adam"
19/08/10 12:19:36 INFO spark.SparkContext: Running Spark version 2.4.3
19/08/10 12:19:36 INFO spark.SparkContext: Submitted application: flagstat
19/08/10 12:19:36 INFO spark.SecurityManager: Changing view acls to: jenkins
19/08/10 12:19:36 INFO spark.SecurityManager: Changing modify acls to: jenkins
19/08/10 12:19:36 INFO spark.SecurityManager: Changing view acls groups to: 
19/08/10 12:19:36 INFO spark.SecurityManager: Changing modify acls groups to: 
19/08/10 12:19:36 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()
19/08/10 12:19:37 INFO util.Utils: Successfully started service 'sparkDriver' on port 40211.
19/08/10 12:19:37 INFO spark.SparkEnv: Registering MapOutputTracker
19/08/10 12:19:37 INFO spark.SparkEnv: Registering BlockManagerMaster
19/08/10 12:19:37 INFO storage.BlockManagerMasterEndpoint: Using org.apache.spark.storage.DefaultTopologyMapper for getting topology information
19/08/10 12:19:37 INFO storage.BlockManagerMasterEndpoint: BlockManagerMasterEndpoint up
19/08/10 12:19:37 INFO storage.DiskBlockManager: Created local directory at /tmp/blockmgr-799f14e3-0335-4b17-95fc-f2582727b7fd
19/08/10 12:19:37 INFO memory.MemoryStore: MemoryStore started with capacity 366.3 MB
19/08/10 12:19:37 INFO spark.SparkEnv: Registering OutputCommitCoordinator
19/08/10 12:19:37 INFO util.log: Logging initialized @3149ms
19/08/10 12:19:37 INFO server.Server: jetty-9.3.z-SNAPSHOT, build timestamp: unknown, git hash: unknown
19/08/10 12:19:37 INFO server.Server: Started @3282ms
19/08/10 12:19:37 INFO server.AbstractConnector: Started ServerConnector@2c444798{HTTP/1.1,[http/1.1]}{0.0.0.0:4040}
19/08/10 12:19:37 INFO util.Utils: Successfully started service 'SparkUI' on port 4040.
19/08/10 12:19:37 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@610db97e{/jobs,null,AVAILABLE,@Spark}
19/08/10 12:19:37 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@1cefc4b3{/jobs/json,null,AVAILABLE,@Spark}
19/08/10 12:19:37 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@2b27cc70{/jobs/job,null,AVAILABLE,@Spark}
19/08/10 12:19:37 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@1bdaa23d{/jobs/job/json,null,AVAILABLE,@Spark}
19/08/10 12:19:37 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@79f227a9{/stages,null,AVAILABLE,@Spark}
19/08/10 12:19:37 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@6ca320ab{/stages/json,null,AVAILABLE,@Spark}
19/08/10 12:19:37 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@50d68830{/stages/stage,null,AVAILABLE,@Spark}
19/08/10 12:19:37 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@3a7704c{/stages/stage/json,null,AVAILABLE,@Spark}
19/08/10 12:19:37 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@6754ef00{/stages/pool,null,AVAILABLE,@Spark}
19/08/10 12:19:37 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@619bd14c{/stages/pool/json,null,AVAILABLE,@Spark}
19/08/10 12:19:37 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@323e8306{/storage,null,AVAILABLE,@Spark}
19/08/10 12:19:37 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@a23a01d{/storage/json,null,AVAILABLE,@Spark}
19/08/10 12:19:37 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@4acf72b6{/storage/rdd,null,AVAILABLE,@Spark}
19/08/10 12:19:37 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@7561db12{/storage/rdd/json,null,AVAILABLE,@Spark}
19/08/10 12:19:37 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@3301500b{/environment,null,AVAILABLE,@Spark}
19/08/10 12:19:37 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@24b52d3e{/environment/json,null,AVAILABLE,@Spark}
19/08/10 12:19:37 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@15deb1dc{/executors,null,AVAILABLE,@Spark}
19/08/10 12:19:37 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@6e9c413e{/executors/json,null,AVAILABLE,@Spark}
19/08/10 12:19:37 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@57a4d5ee{/executors/threadDump,null,AVAILABLE,@Spark}
19/08/10 12:19:37 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@5af5def9{/executors/threadDump/json,null,AVAILABLE,@Spark}
19/08/10 12:19:37 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@3a45c42a{/static,null,AVAILABLE,@Spark}
19/08/10 12:19:37 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@3c1e3314{/,null,AVAILABLE,@Spark}
19/08/10 12:19:37 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@4b770e40{/api,null,AVAILABLE,@Spark}
19/08/10 12:19:37 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@6a1ebcff{/jobs/job/kill,null,AVAILABLE,@Spark}
19/08/10 12:19:37 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@19868320{/stages/stage/kill,null,AVAILABLE,@Spark}
19/08/10 12:19:37 INFO ui.SparkUI: Bound SparkUI to 0.0.0.0, and started at http://192.168.10.32:4040
19/08/10 12:19:37 INFO spark.SparkContext: Added JAR file:/tmp/adamTestMP40nkE/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/target/adam-assembly-spark2_2.12-0.29.0-SNAPSHOT.jar at spark://192.168.10.32:40211/jars/adam-assembly-spark2_2.12-0.29.0-SNAPSHOT.jar with timestamp 1565464777677
19/08/10 12:19:37 INFO executor.Executor: Starting executor ID driver on host localhost
19/08/10 12:19:37 INFO util.Utils: Successfully started service 'org.apache.spark.network.netty.NettyBlockTransferService' on port 33321.
19/08/10 12:19:37 INFO netty.NettyBlockTransferService: Server created on 192.168.10.32:33321
19/08/10 12:19:37 INFO storage.BlockManager: Using org.apache.spark.storage.RandomBlockReplicationPolicy for block replication policy
19/08/10 12:19:37 INFO storage.BlockManagerMaster: Registering BlockManager BlockManagerId(driver, 192.168.10.32, 33321, None)
19/08/10 12:19:37 INFO storage.BlockManagerMasterEndpoint: Registering block manager 192.168.10.32:33321 with 366.3 MB RAM, BlockManagerId(driver, 192.168.10.32, 33321, None)
19/08/10 12:19:37 INFO storage.BlockManagerMaster: Registered BlockManager BlockManagerId(driver, 192.168.10.32, 33321, None)
19/08/10 12:19:37 INFO storage.BlockManager: Initialized BlockManager: BlockManagerId(driver, 192.168.10.32, 33321, None)
19/08/10 12:19:38 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@27aae97b{/metrics/json,null,AVAILABLE,@Spark}
19/08/10 12:19:38 INFO rdd.ADAMContext: Loading mouse_chrM.bam.reads.adam as Parquet of AlignmentRecords.
19/08/10 12:19:39 INFO rdd.ADAMContext: Reading the ADAM file at mouse_chrM.bam.reads.adam to create RDD
19/08/10 12:19:39 INFO rdd.ADAMContext: Using the specified projection schema
19/08/10 12:19:39 INFO memory.MemoryStore: Block broadcast_0 stored as values in memory (estimated size 322.5 KB, free 366.0 MB)
19/08/10 12:19:40 INFO memory.MemoryStore: Block broadcast_0_piece0 stored as bytes in memory (estimated size 29.1 KB, free 366.0 MB)
19/08/10 12:19:40 INFO storage.BlockManagerInfo: Added broadcast_0_piece0 in memory on 192.168.10.32:33321 (size: 29.1 KB, free: 366.3 MB)
19/08/10 12:19:40 INFO spark.SparkContext: Created broadcast 0 from newAPIHadoopFile at ADAMContext.scala:1801
19/08/10 12:19:42 INFO input.FileInputFormat: Total input paths to process : 1
19/08/10 12:19:42 INFO hadoop.ParquetInputFormat: Total input paths to process : 1
19/08/10 12:19:42 INFO spark.SparkContext: Starting job: aggregate at FlagStat.scala:115
19/08/10 12:19:42 INFO scheduler.DAGScheduler: Got job 0 (aggregate at FlagStat.scala:115) with 1 output partitions
19/08/10 12:19:42 INFO scheduler.DAGScheduler: Final stage: ResultStage 0 (aggregate at FlagStat.scala:115)
19/08/10 12:19:42 INFO scheduler.DAGScheduler: Parents of final stage: List()
19/08/10 12:19:42 INFO scheduler.DAGScheduler: Missing parents: List()
19/08/10 12:19:42 INFO scheduler.DAGScheduler: Submitting ResultStage 0 (MapPartitionsRDD[4] at map at FlagStat.scala:96), which has no missing parents
19/08/10 12:19:42 INFO memory.MemoryStore: Block broadcast_1 stored as values in memory (estimated size 13.5 KB, free 365.9 MB)
19/08/10 12:19:42 INFO memory.MemoryStore: Block broadcast_1_piece0 stored as bytes in memory (estimated size 5.9 KB, free 365.9 MB)
19/08/10 12:19:42 INFO storage.BlockManagerInfo: Added broadcast_1_piece0 in memory on 192.168.10.32:33321 (size: 5.9 KB, free: 366.3 MB)
19/08/10 12:19:42 INFO spark.SparkContext: Created broadcast 1 from broadcast at DAGScheduler.scala:1161
19/08/10 12:19:42 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))
19/08/10 12:19:42 INFO scheduler.TaskSchedulerImpl: Adding task set 0.0 with 1 tasks
19/08/10 12:19:42 INFO scheduler.TaskSetManager: Starting task 0.0 in stage 0.0 (TID 0, localhost, executor driver, partition 0, PROCESS_LOCAL, 7491 bytes)
19/08/10 12:19:42 INFO executor.Executor: Running task 0.0 in stage 0.0 (TID 0)
19/08/10 12:19:42 INFO executor.Executor: Fetching spark://192.168.10.32:40211/jars/adam-assembly-spark2_2.12-0.29.0-SNAPSHOT.jar with timestamp 1565464777677
19/08/10 12:19:42 INFO client.TransportClientFactory: Successfully created connection to /192.168.10.32:40211 after 49 ms (0 ms spent in bootstraps)
19/08/10 12:19:42 INFO util.Utils: Fetching spark://192.168.10.32:40211/jars/adam-assembly-spark2_2.12-0.29.0-SNAPSHOT.jar to /tmp/spark-fd95e5bb-b5c6-4083-bced-ff395f4dc544/userFiles-c5414ad1-4869-4a9d-94ff-99594e2ce7b5/fetchFileTemp2175240321469338358.tmp
19/08/10 12:19:42 INFO executor.Executor: Adding file:/tmp/spark-fd95e5bb-b5c6-4083-bced-ff395f4dc544/userFiles-c5414ad1-4869-4a9d-94ff-99594e2ce7b5/adam-assembly-spark2_2.12-0.29.0-SNAPSHOT.jar to class loader
19/08/10 12:19:43 INFO rdd.NewHadoopRDD: Input split: file:/tmp/adamTestMP40nkE/deleteMePleaseThisIsNoLongerNeeded/mouse_chrM.bam.reads.adam/part-r-00000.gz.parquet:0+10132194
19/08/10 12:19:43 INFO hadoop.InternalParquetRecordReader: RecordReader initialized will read a total of 163064 records.
19/08/10 12:19:43 INFO hadoop.InternalParquetRecordReader: at row 0. reading next block
19/08/10 12:19:43 INFO compress.CodecPool: Got brand-new decompressor [.gz]
19/08/10 12:19:43 INFO hadoop.InternalParquetRecordReader: block read in memory in 33 ms. row count = 163064
19/08/10 12:19:44 INFO executor.Executor: Finished task 0.0 in stage 0.0 (TID 0). 9641 bytes result sent to driver
19/08/10 12:19:44 INFO scheduler.TaskSetManager: Finished task 0.0 in stage 0.0 (TID 0) in 2168 ms on localhost (executor driver) (1/1)
19/08/10 12:19:44 INFO scheduler.TaskSchedulerImpl: Removed TaskSet 0.0, whose tasks have all completed, from pool 
19/08/10 12:19:44 INFO scheduler.DAGScheduler: ResultStage 0 (aggregate at FlagStat.scala:115) finished in 2.328 s
19/08/10 12:19:44 INFO scheduler.DAGScheduler: Job 0 finished: aggregate at FlagStat.scala:115, took 2.414093 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)
19/08/10 12:19:44 INFO cli.FlagStat: Overall Duration: 8.07 secs
19/08/10 12:19:44 INFO cli.FlagStat: Metrics:

Timings
+--------------------------------------+--------------+--------------+-------------+--------+-----------+-----------+-----------+
|                Metric                | Worker Total | Driver Total | Driver Only | Count  |   Mean    |    Min    |    Max    |
+--------------------------------------+--------------+--------------+-------------+--------+-----------+-----------+-----------+
| └─ Load Alignments                   |            - |    3.03 secs |   2.85 secs |      1 | 3.03 secs | 3.03 secs | 3.03 secs |
|     └─ map at ADAMContext.scala:1805 |            - |    185.36 ms |           - |      1 | 185.36 ms | 185.36 ms | 185.36 ms |
|         └─ function call             |     22.49 ms |            - |           - | 163064 |    137 ns |     64 ns | 187.62 µs |
| └─ map at FlagStat.scala:96          |            - |     30.84 ms |           - |      1 |  30.84 ms |  30.84 ms |  30.84 ms |
|     └─ function call                 |    145.34 ms |            - |           - | 163064 |    891 ns |    218 ns |   2.08 ms |
| └─ aggregate at FlagStat.scala:115   |            - |    2.52 secs |           - |      1 | 2.52 secs | 2.52 secs | 2.52 secs |
|     └─ function call                 |      38.9 ms |            - |           - | 163065 |    238 ns |     97 ns | 735.48 µs |
+--------------------------------------+--------------+--------------+-------------+--------+-----------+-----------+-----------+

Spark Operations
+----------+---------------------------------+---------------+----------------+--------------+----------+
| Sequence |            Operation            | Is New Stage? | Stage Duration | Driver Total | Stage ID |
+----------+---------------------------------+---------------+----------------+--------------+----------+
| 1        | map at ADAMContext.scala:1805   | false         |              - |    185.36 ms | -        |
| 2        | map at FlagStat.scala:96        | false         |              - |     30.84 ms | -        |
| 3        | aggregate at FlagStat.scala:115 | true          |     -2.33 secs |    2.52 secs | 0        |
+----------+---------------------------------+---------------+----------------+--------------+----------+

Task Timings
+-------------------------------+------------+-------+-----------+-----------+-----------+
|            Metric             | Total Time | Count |   Mean    |    Min    |    Max    |
+-------------------------------+------------+-------+-----------+-----------+-----------+
| Task Duration                 |  2.17 secs |     1 | 2.17 secs | 2.17 secs | 2.17 secs |
| Executor Run Time             |  1.39 secs |     1 | 1.39 secs | 1.39 secs | 1.39 secs |
| Executor Deserialization Time |     658 ms |     1 |    658 ms |    658 ms |    658 ms |
| Result Serialization Time     |          0 |     1 |         0 |         0 |         0 |
+-------------------------------+------------+-------+-----------+-----------+-----------+

Task Timings By Host
+-------------------------------+--------+------------+-------+-----------+-----------+-----------+
|            Metric             |  Host  | Total Time | Count |   Mean    |    Min    |    Max    |
+-------------------------------+--------+------------+-------+-----------+-----------+-----------+
| Task Duration                 | driver |  2.17 secs |     1 | 2.17 secs | 2.17 secs | 2.17 secs |
| Executor Run Time             | driver |  1.39 secs |     1 | 1.39 secs | 1.39 secs | 1.39 secs |
| Executor Deserialization Time | driver |     658 ms |     1 |    658 ms |    658 ms |    658 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 |  2.17 secs |     1 | 2.17 secs | 2.17 secs | 2.17 secs |
| Executor Run Time             | 0: aggregate at FlagStat.scala:115 |  1.39 secs |     1 | 1.39 secs | 1.39 secs | 1.39 secs |
| Executor Deserialization Time | 0: aggregate at FlagStat.scala:115 |     658 ms |     1 |    658 ms |    658 ms |    658 ms |
| Result Serialization Time     | 0: aggregate at FlagStat.scala:115 |          0 |     1 |         0 |         0 |         0 |
+-------------------------------+------------------------------------+------------+-------+-----------+-----------+-----------+

19/08/10 12:19:44 INFO spark.SparkContext: Invoking stop() from shutdown hook
19/08/10 12:19:44 INFO server.AbstractConnector: Stopped Spark@2c444798{HTTP/1.1,[http/1.1]}{0.0.0.0:4040}
19/08/10 12:19:44 INFO ui.SparkUI: Stopped Spark web UI at http://192.168.10.32:4040
19/08/10 12:19:44 INFO spark.MapOutputTrackerMasterEndpoint: MapOutputTrackerMasterEndpoint stopped!
19/08/10 12:19:44 INFO memory.MemoryStore: MemoryStore cleared
19/08/10 12:19:44 INFO storage.BlockManager: BlockManager stopped
19/08/10 12:19:44 INFO storage.BlockManagerMaster: BlockManagerMaster stopped
19/08/10 12:19:44 INFO scheduler.OutputCommitCoordinator$OutputCommitCoordinatorEndpoint: OutputCommitCoordinator stopped!
19/08/10 12:19:44 INFO spark.SparkContext: Successfully stopped SparkContext
19/08/10 12:19:44 INFO util.ShutdownHookManager: Shutdown hook called
19/08/10 12:19:44 INFO util.ShutdownHookManager: Deleting directory /tmp/spark-fd95e5bb-b5c6-4083-bced-ff395f4dc544
19/08/10 12:19:44 INFO util.ShutdownHookManager: Deleting directory /tmp/spark-a567fba2-62ee-4906-9430-29c3c017952b
rm -rf ${ADAM_TMP_DIR}
+ rm -rf /tmp/adamTestMP40nkE/deleteMePleaseThisIsNoLongerNeeded
popd
+ popd
~/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu

pushd ${PROJECT_ROOT}
+ pushd /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/scripts/..
~/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu ~/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu
# 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/2.4.3/label/ubuntu/scripts
+ pushd /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/scripts/..
~/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu ~/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu
+ 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 0.29.0-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ adam-parent-spark2_2.11 ---
[INFO] Modified 2 of 242 .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 0.29.0-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 0.29.0-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 0.29.0-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ adam-core-spark2_2.11 ---
[INFO] Modified 0 of 202 .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 0.29.0-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 0.29.0-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 0.29.0-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 [  6.882 s]
[INFO] ADAM_2.11: Shader workaround ....................... SUCCESS [  0.027 s]
[INFO] ADAM_2.11: Avro-to-Dataset codegen utils ........... SUCCESS [  0.069 s]
[INFO] ADAM_2.11: Core .................................... SUCCESS [  3.329 s]
[INFO] ADAM_2.11: APIs for Java, Python ................... SUCCESS [  0.129 s]
[INFO] ADAM_2.11: CLI ..................................... SUCCESS [  0.224 s]
[INFO] ADAM_2.11: Assembly ................................ SUCCESS [  0.020 s]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 11.334 s
[INFO] Finished at: 2019-08-10T12:19:58-07:00
[INFO] Final Memory: 22M/1180M
[INFO] ------------------------------------------------------------------------
+ popd
~/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/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/2.4.3/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/2402afbfb29ebf22dc845b54f061b713bbb1c2a3
Finished: SUCCESS