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[INFO] Building zip: /tmp/adamTestesvklDQ/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 [ 12.699 s]
[INFO] ADAM_2.12: Shader workaround ....................... SUCCESS [  6.274 s]
[INFO] ADAM_2.12: Avro-to-Dataset codegen utils ........... SUCCESS [  6.526 s]
[INFO] ADAM_2.12: Core .................................... SUCCESS [01:36 min]
[INFO] ADAM_2.12: APIs for Java, Python ................... SUCCESS [ 12.617 s]
[INFO] ADAM_2.12: CLI ..................................... SUCCESS [ 15.805 s]
[INFO] ADAM_2.12: Assembly ................................ SUCCESS [ 22.653 s]
[INFO] ADAM_2.12: Python APIs ............................. SUCCESS [01:45 min]
[INFO] ADAM_2.12: R APIs .................................. SUCCESS [ 56.306 s]
[INFO] ADAM_2.12: Distribution ............................ SUCCESS [ 45.816 s]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 06:20 min
[INFO] Finished at: 2019-09-03T13:55:11-07:00
[INFO] Final Memory: 64M/1500M
[INFO] ------------------------------------------------------------------------
+ grep bdgenomics.adam
+ grep egg
+ tar tzvf adam-distribution/target/adam-distribution-spark2_2.12-0.29.0-SNAPSHOT-bin.tar.gz
drwxrwxr-x jenkins/jenkins        0 2019-09-03 13:51 adam-distribution-spark2_2.12-0.29.0-SNAPSHOT/r/bdgenomics.adam.egg-info/
-rw-r--r-- jenkins/jenkins 36822300 2019-09-03 13:51 adam-distribution-spark2_2.12-0.29.0-SNAPSHOT/repo/bdgenomics.adam-0.28.0a0-py3.6.egg
+ ./bin/pyadam
Using PYSPARK=/tmp/adamTestesvklDQ/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.3-bin-without-hadoop-scala-2.12/bin/pyspark
2019-09-03 13:55:14 WARN  Utils:66 - Your hostname, research-jenkins-worker-07 resolves to a loopback address: 127.0.1.1; using 192.168.10.27 instead (on interface eth0)
2019-09-03 13:55:14 WARN  Utils:66 - Set SPARK_LOCAL_IP if you need to bind to another address
2019-09-03 13:55:14 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).
2019-09-03 13:55:20 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-b0f6ce25-15ee-4155-846e-22be0805d330/bin/deactivate
++ _SHELL=bash
_CONDA_DIR=$(dirname "$_SCRIPT_LOCATION")
dirname "$_SCRIPT_LOCATION"
+++ dirname /home/jenkins/anaconda2/envs/adam-build-b0f6ce25-15ee-4155-846e-22be0805d330/bin/deactivate
++ _CONDA_DIR=/home/jenkins/anaconda2/envs/adam-build-b0f6ce25-15ee-4155-846e-22be0805d330/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 $?
fi
++ ((  0 == 0  ))
++ _CONDA_D=/home/jenkins/anaconda2/envs/adam-build-b0f6ce25-15ee-4155-846e-22be0805d330/etc/conda/deactivate.d
++ [[ -d /home/jenkins/anaconda2/envs/adam-build-b0f6ce25-15ee-4155-846e-22be0805d330/etc/conda/deactivate.d ]]
"$_CONDA_DIR/conda" ..deactivate.path $_SHELL$EXT "$CONDA_PREFIX"
+++ /home/jenkins/anaconda2/envs/adam-build-b0f6ce25-15ee-4155-846e-22be0805d330/bin/conda ..deactivate.path bash /home/jenkins/anaconda2/envs/adam-build-b0f6ce25-15ee-4155-846e-22be0805d330
++ 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-b0f6ce25-15ee-4155-846e-22be0805d330 --all

Package plan for package removal in environment /home/jenkins/anaconda2/envs/adam-build-b0f6ce25-15ee-4155-846e-22be0805d330:

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:             19.2.2-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/adamTestesvklDQ/deleteMePleaseThisIsNoLongerNeeded/adam-python /tmp/adamTestesvklDQ/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/adamTestesvklDQ/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/adamTestesvklDQ/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.3-bin-without-hadoop-scala-2.12/bin/spark-submit
19/09/03 13:55:35 WARN util.Utils: Your hostname, research-jenkins-worker-07 resolves to a loopback address: 127.0.1.1; using 192.168.10.27 instead (on interface eth0)
19/09/03 13:55:35 WARN util.Utils: Set SPARK_LOCAL_IP if you need to bind to another address
19/09/03 13:55:36 WARN util.NativeCodeLoader: Unable to load native-hadoop library for your platform... using builtin-java classes where applicable
19/09/03 13:55:36 INFO cli.ADAMMain: ADAM invoked with args: "transformAlignments" "mouse_chrM.bam" "mouse_chrM.bam.reads.adam"
19/09/03 13:55:36 INFO spark.SparkContext: Running Spark version 2.4.3
19/09/03 13:55:36 INFO spark.SparkContext: Submitted application: transformAlignments
19/09/03 13:55:36 INFO spark.SecurityManager: Changing view acls to: jenkins
19/09/03 13:55:36 INFO spark.SecurityManager: Changing modify acls to: jenkins
19/09/03 13:55:36 INFO spark.SecurityManager: Changing view acls groups to: 
19/09/03 13:55:36 INFO spark.SecurityManager: Changing modify acls groups to: 
19/09/03 13:55:36 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()
19/09/03 13:55:36 INFO util.Utils: Successfully started service 'sparkDriver' on port 45915.
19/09/03 13:55:36 INFO spark.SparkEnv: Registering MapOutputTracker
19/09/03 13:55:36 INFO spark.SparkEnv: Registering BlockManagerMaster
19/09/03 13:55:36 INFO storage.BlockManagerMasterEndpoint: Using org.apache.spark.storage.DefaultTopologyMapper for getting topology information
19/09/03 13:55:36 INFO storage.BlockManagerMasterEndpoint: BlockManagerMasterEndpoint up
19/09/03 13:55:36 INFO storage.DiskBlockManager: Created local directory at /tmp/blockmgr-23ffb400-1adf-4e3f-9bbb-1157a91e9b78
19/09/03 13:55:36 INFO memory.MemoryStore: MemoryStore started with capacity 366.3 MB
19/09/03 13:55:36 INFO spark.SparkEnv: Registering OutputCommitCoordinator
19/09/03 13:55:37 INFO util.log: Logging initialized @2331ms
19/09/03 13:55:37 INFO server.Server: jetty-9.3.z-SNAPSHOT, build timestamp: unknown, git hash: unknown
19/09/03 13:55:37 INFO server.Server: Started @2414ms
19/09/03 13:55:37 INFO server.AbstractConnector: Started ServerConnector@1af7f54a{HTTP/1.1,[http/1.1]}{0.0.0.0:4040}
19/09/03 13:55:37 INFO util.Utils: Successfully started service 'SparkUI' on port 4040.
19/09/03 13:55:37 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@6f0628de{/jobs,null,AVAILABLE,@Spark}
19/09/03 13:55:37 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@2b27cc70{/jobs/json,null,AVAILABLE,@Spark}
19/09/03 13:55:37 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@6f6a7463{/jobs/job,null,AVAILABLE,@Spark}
19/09/03 13:55:37 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@79f227a9{/jobs/job/json,null,AVAILABLE,@Spark}
19/09/03 13:55:37 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@6ca320ab{/stages,null,AVAILABLE,@Spark}
19/09/03 13:55:37 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@50d68830{/stages/json,null,AVAILABLE,@Spark}
19/09/03 13:55:37 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@1e53135d{/stages/stage,null,AVAILABLE,@Spark}
19/09/03 13:55:37 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@6754ef00{/stages/stage/json,null,AVAILABLE,@Spark}
19/09/03 13:55:37 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@619bd14c{/stages/pool,null,AVAILABLE,@Spark}
19/09/03 13:55:37 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@323e8306{/stages/pool/json,null,AVAILABLE,@Spark}
19/09/03 13:55:37 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@a23a01d{/storage,null,AVAILABLE,@Spark}
19/09/03 13:55:37 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@4acf72b6{/storage/json,null,AVAILABLE,@Spark}
19/09/03 13:55:37 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@7561db12{/storage/rdd,null,AVAILABLE,@Spark}
19/09/03 13:55:37 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@3301500b{/storage/rdd/json,null,AVAILABLE,@Spark}
19/09/03 13:55:37 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@24b52d3e{/environment,null,AVAILABLE,@Spark}
19/09/03 13:55:37 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@15deb1dc{/environment/json,null,AVAILABLE,@Spark}
19/09/03 13:55:37 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@6e9c413e{/executors,null,AVAILABLE,@Spark}
19/09/03 13:55:37 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@57a4d5ee{/executors/json,null,AVAILABLE,@Spark}
19/09/03 13:55:37 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@5af5def9{/executors/threadDump,null,AVAILABLE,@Spark}
19/09/03 13:55:37 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@3a45c42a{/executors/threadDump/json,null,AVAILABLE,@Spark}
19/09/03 13:55:37 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@36dce7ed{/static,null,AVAILABLE,@Spark}
19/09/03 13:55:37 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@4b770e40{/,null,AVAILABLE,@Spark}
19/09/03 13:55:37 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@78e16155{/api,null,AVAILABLE,@Spark}
19/09/03 13:55:37 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@19868320{/jobs/job/kill,null,AVAILABLE,@Spark}
19/09/03 13:55:37 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@50b0bc4c{/stages/stage/kill,null,AVAILABLE,@Spark}
19/09/03 13:55:37 INFO ui.SparkUI: Bound SparkUI to 0.0.0.0, and started at http://192.168.10.27:4040
19/09/03 13:55:37 INFO spark.SparkContext: Added JAR file:/tmp/adamTestesvklDQ/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/target/adam-assembly-spark2_2.12-0.29.0-SNAPSHOT.jar at spark://192.168.10.27:45915/jars/adam-assembly-spark2_2.12-0.29.0-SNAPSHOT.jar with timestamp 1567544137214
19/09/03 13:55:37 INFO executor.Executor: Starting executor ID driver on host localhost
19/09/03 13:55:37 INFO util.Utils: Successfully started service 'org.apache.spark.network.netty.NettyBlockTransferService' on port 36729.
19/09/03 13:55:37 INFO netty.NettyBlockTransferService: Server created on 192.168.10.27:36729
19/09/03 13:55:37 INFO storage.BlockManager: Using org.apache.spark.storage.RandomBlockReplicationPolicy for block replication policy
19/09/03 13:55:37 INFO storage.BlockManagerMaster: Registering BlockManager BlockManagerId(driver, 192.168.10.27, 36729, None)
19/09/03 13:55:37 INFO storage.BlockManagerMasterEndpoint: Registering block manager 192.168.10.27:36729 with 366.3 MB RAM, BlockManagerId(driver, 192.168.10.27, 36729, None)
19/09/03 13:55:37 INFO storage.BlockManagerMaster: Registered BlockManager BlockManagerId(driver, 192.168.10.27, 36729, None)
19/09/03 13:55:37 INFO storage.BlockManager: Initialized BlockManager: BlockManagerId(driver, 192.168.10.27, 36729, None)
19/09/03 13:55:37 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@4c9e38{/metrics/json,null,AVAILABLE,@Spark}
19/09/03 13:55:37 INFO rdd.ADAMContext: Loading mouse_chrM.bam as BAM/CRAM/SAM and converting to AlignmentRecords.
19/09/03 13:55:38 INFO rdd.ADAMContext: Loaded header from file:/tmp/adamTestesvklDQ/deleteMePleaseThisIsNoLongerNeeded/mouse_chrM.bam
19/09/03 13:55:38 INFO memory.MemoryStore: Block broadcast_0 stored as values in memory (estimated size 295.6 KB, free 366.0 MB)
19/09/03 13:55:39 INFO memory.MemoryStore: Block broadcast_0_piece0 stored as bytes in memory (estimated size 24.0 KB, free 366.0 MB)
19/09/03 13:55:39 INFO storage.BlockManagerInfo: Added broadcast_0_piece0 in memory on 192.168.10.27:36729 (size: 24.0 KB, free: 366.3 MB)
19/09/03 13:55:39 INFO spark.SparkContext: Created broadcast 0 from newAPIHadoopFile at ADAMContext.scala:2059
19/09/03 13:55:40 INFO read.RDDBoundAlignmentRecordDataset: Saving data in ADAM format
19/09/03 13:55:40 INFO output.FileOutputCommitter: File Output Committer Algorithm version is 1
19/09/03 13:55:40 INFO input.FileInputFormat: Total input paths to process : 1
19/09/03 13:55:40 INFO spark.SparkContext: Starting job: runJob at SparkHadoopWriter.scala:78
19/09/03 13:55:40 INFO scheduler.DAGScheduler: Got job 0 (runJob at SparkHadoopWriter.scala:78) with 1 output partitions
19/09/03 13:55:40 INFO scheduler.DAGScheduler: Final stage: ResultStage 0 (runJob at SparkHadoopWriter.scala:78)
19/09/03 13:55:40 INFO scheduler.DAGScheduler: Parents of final stage: List()
19/09/03 13:55:40 INFO scheduler.DAGScheduler: Missing parents: List()
19/09/03 13:55:40 INFO scheduler.DAGScheduler: Submitting ResultStage 0 (MapPartitionsRDD[2] at map at GenomicDataset.scala:3814), which has no missing parents
19/09/03 13:55:40 INFO memory.MemoryStore: Block broadcast_1 stored as values in memory (estimated size 85.6 KB, free 365.9 MB)
19/09/03 13:55:40 INFO memory.MemoryStore: Block broadcast_1_piece0 stored as bytes in memory (estimated size 31.6 KB, free 365.9 MB)
19/09/03 13:55:40 INFO storage.BlockManagerInfo: Added broadcast_1_piece0 in memory on 192.168.10.27:36729 (size: 31.6 KB, free: 366.2 MB)
19/09/03 13:55:40 INFO spark.SparkContext: Created broadcast 1 from broadcast at DAGScheduler.scala:1161
19/09/03 13:55:40 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))
19/09/03 13:55:40 INFO scheduler.TaskSchedulerImpl: Adding task set 0.0 with 1 tasks
19/09/03 13:55:40 INFO scheduler.TaskSetManager: Starting task 0.0 in stage 0.0 (TID 0, localhost, executor driver, partition 0, PROCESS_LOCAL, 7441 bytes)
19/09/03 13:55:40 INFO executor.Executor: Running task 0.0 in stage 0.0 (TID 0)
19/09/03 13:55:40 INFO executor.Executor: Fetching spark://192.168.10.27:45915/jars/adam-assembly-spark2_2.12-0.29.0-SNAPSHOT.jar with timestamp 1567544137214
19/09/03 13:55:40 INFO client.TransportClientFactory: Successfully created connection to /192.168.10.27:45915 after 28 ms (0 ms spent in bootstraps)
19/09/03 13:55:40 INFO util.Utils: Fetching spark://192.168.10.27:45915/jars/adam-assembly-spark2_2.12-0.29.0-SNAPSHOT.jar to /tmp/spark-156f484b-330f-4056-a81e-90682c494abe/userFiles-7cce35d9-33e0-44dd-8d4e-c2d6361d1b1c/fetchFileTemp8951337911283809970.tmp
19/09/03 13:55:40 INFO executor.Executor: Adding file:/tmp/spark-156f484b-330f-4056-a81e-90682c494abe/userFiles-7cce35d9-33e0-44dd-8d4e-c2d6361d1b1c/adam-assembly-spark2_2.12-0.29.0-SNAPSHOT.jar to class loader
19/09/03 13:55:41 INFO rdd.NewHadoopRDD: Input split: file:/tmp/adamTestesvklDQ/deleteMePleaseThisIsNoLongerNeeded/mouse_chrM.bam:83361792-833134657535
19/09/03 13:55:41 INFO output.FileOutputCommitter: File Output Committer Algorithm version is 1
19/09/03 13:55:41 INFO codec.CodecConfig: Compression: GZIP
19/09/03 13:55:41 INFO output.FileOutputCommitter: File Output Committer Algorithm version is 1
19/09/03 13:55:41 INFO hadoop.ParquetOutputFormat: Parquet block size to 134217728
19/09/03 13:55:41 INFO hadoop.ParquetOutputFormat: Parquet page size to 1048576
19/09/03 13:55:41 INFO hadoop.ParquetOutputFormat: Parquet dictionary page size to 1048576
19/09/03 13:55:41 INFO hadoop.ParquetOutputFormat: Dictionary is on
19/09/03 13:55:41 INFO hadoop.ParquetOutputFormat: Validation is off
19/09/03 13:55:41 INFO hadoop.ParquetOutputFormat: Writer version is: PARQUET_1_0
19/09/03 13:55:41 INFO hadoop.ParquetOutputFormat: Maximum row group padding size is 8388608 bytes
19/09/03 13:55:41 INFO hadoop.ParquetOutputFormat: Page size checking is: estimated
19/09/03 13:55:41 INFO hadoop.ParquetOutputFormat: Min row count for page size check is: 100
19/09/03 13:55:41 INFO hadoop.ParquetOutputFormat: Max row count for page size check is: 10000
19/09/03 13:55:41 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.
19/09/03 13:55:51 INFO hadoop.InternalParquetRecordWriter: Flushing mem columnStore to file. allocated memory: 16043959
19/09/03 13:55:51 INFO output.FileOutputCommitter: Saved output of task 'attempt_20190903135540_0002_r_000000_0' to file:/tmp/adamTestesvklDQ/deleteMePleaseThisIsNoLongerNeeded/mouse_chrM.bam.reads.adam/_temporary/0/task_20190903135540_0002_r_000000
19/09/03 13:55:51 INFO mapred.SparkHadoopMapRedUtil: attempt_20190903135540_0002_r_000000_0: Committed
19/09/03 13:55:51 INFO executor.Executor: Finished task 0.0 in stage 0.0 (TID 0). 856 bytes result sent to driver
19/09/03 13:55:51 INFO scheduler.TaskSetManager: Finished task 0.0 in stage 0.0 (TID 0) in 10832 ms on localhost (executor driver) (1/1)
19/09/03 13:55:51 INFO scheduler.TaskSchedulerImpl: Removed TaskSet 0.0, whose tasks have all completed, from pool 
19/09/03 13:55:51 INFO scheduler.DAGScheduler: ResultStage 0 (runJob at SparkHadoopWriter.scala:78) finished in 10.973 s
19/09/03 13:55:51 INFO scheduler.DAGScheduler: Job 0 finished: runJob at SparkHadoopWriter.scala:78, took 11.041953 s
19/09/03 13:55:51 INFO hadoop.ParquetFileReader: Initiating action with parallelism: 5
19/09/03 13:55:51 INFO io.SparkHadoopWriter: Job job_20190903135540_0002 committed.
19/09/03 13:55:51 INFO cli.TransformAlignments: Overall Duration: 15.35 secs
19/09/03 13:55:51 INFO spark.SparkContext: Invoking stop() from shutdown hook
19/09/03 13:55:51 INFO server.AbstractConnector: Stopped Spark@1af7f54a{HTTP/1.1,[http/1.1]}{0.0.0.0:4040}
19/09/03 13:55:51 INFO ui.SparkUI: Stopped Spark web UI at http://192.168.10.27:4040
19/09/03 13:55:51 INFO spark.MapOutputTrackerMasterEndpoint: MapOutputTrackerMasterEndpoint stopped!
19/09/03 13:55:51 INFO memory.MemoryStore: MemoryStore cleared
19/09/03 13:55:51 INFO storage.BlockManager: BlockManager stopped
19/09/03 13:55:51 INFO storage.BlockManagerMaster: BlockManagerMaster stopped
19/09/03 13:55:51 INFO scheduler.OutputCommitCoordinator$OutputCommitCoordinatorEndpoint: OutputCommitCoordinator stopped!
19/09/03 13:55:51 INFO spark.SparkContext: Successfully stopped SparkContext
19/09/03 13:55:51 INFO util.ShutdownHookManager: Shutdown hook called
19/09/03 13:55:51 INFO util.ShutdownHookManager: Deleting directory /tmp/spark-1784f788-78e0-47bd-8afc-23ea86e01459
19/09/03 13:55:51 INFO util.ShutdownHookManager: Deleting directory /tmp/spark-156f484b-330f-4056-a81e-90682c494abe

# 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/adamTestesvklDQ/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.3-bin-without-hadoop-scala-2.12/bin/spark-submit
19/09/03 13:55:53 WARN util.Utils: Your hostname, research-jenkins-worker-07 resolves to a loopback address: 127.0.1.1; using 192.168.10.27 instead (on interface eth0)
19/09/03 13:55:53 WARN util.Utils: Set SPARK_LOCAL_IP if you need to bind to another address
19/09/03 13:55:53 WARN util.NativeCodeLoader: Unable to load native-hadoop library for your platform... using builtin-java classes where applicable
19/09/03 13:55:54 INFO cli.ADAMMain: ADAM invoked with args: "transformAlignments" "-sort_by_reference_position" "mouse_chrM.bam.reads.adam" "mouse_chrM.bam.reads.sorted.adam"
19/09/03 13:55:54 INFO spark.SparkContext: Running Spark version 2.4.3
19/09/03 13:55:54 INFO spark.SparkContext: Submitted application: transformAlignments
19/09/03 13:55:54 INFO spark.SecurityManager: Changing view acls to: jenkins
19/09/03 13:55:54 INFO spark.SecurityManager: Changing modify acls to: jenkins
19/09/03 13:55:54 INFO spark.SecurityManager: Changing view acls groups to: 
19/09/03 13:55:54 INFO spark.SecurityManager: Changing modify acls groups to: 
19/09/03 13:55:54 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()
19/09/03 13:55:54 INFO util.Utils: Successfully started service 'sparkDriver' on port 35141.
19/09/03 13:55:54 INFO spark.SparkEnv: Registering MapOutputTracker
19/09/03 13:55:54 INFO spark.SparkEnv: Registering BlockManagerMaster
19/09/03 13:55:54 INFO storage.BlockManagerMasterEndpoint: Using org.apache.spark.storage.DefaultTopologyMapper for getting topology information
19/09/03 13:55:54 INFO storage.BlockManagerMasterEndpoint: BlockManagerMasterEndpoint up
19/09/03 13:55:54 INFO storage.DiskBlockManager: Created local directory at /tmp/blockmgr-19286ed2-0a98-483b-9534-96f70dd71510
19/09/03 13:55:54 INFO memory.MemoryStore: MemoryStore started with capacity 366.3 MB
19/09/03 13:55:54 INFO spark.SparkEnv: Registering OutputCommitCoordinator
19/09/03 13:55:54 INFO util.log: Logging initialized @2279ms
19/09/03 13:55:54 INFO server.Server: jetty-9.3.z-SNAPSHOT, build timestamp: unknown, git hash: unknown
19/09/03 13:55:54 INFO server.Server: Started @2354ms
19/09/03 13:55:54 INFO server.AbstractConnector: Started ServerConnector@6ebd78d1{HTTP/1.1,[http/1.1]}{0.0.0.0:4040}
19/09/03 13:55:54 INFO util.Utils: Successfully started service 'SparkUI' on port 4040.
19/09/03 13:55:54 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@3fabf088{/jobs,null,AVAILABLE,@Spark}
19/09/03 13:55:54 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@6f6a7463{/jobs/json,null,AVAILABLE,@Spark}
19/09/03 13:55:54 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@1bdaa23d{/jobs/job,null,AVAILABLE,@Spark}
19/09/03 13:55:54 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@6ca320ab{/jobs/job/json,null,AVAILABLE,@Spark}
19/09/03 13:55:54 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@50d68830{/stages,null,AVAILABLE,@Spark}
19/09/03 13:55:54 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@1e53135d{/stages/json,null,AVAILABLE,@Spark}
19/09/03 13:55:54 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@7674a051{/stages/stage,null,AVAILABLE,@Spark}
19/09/03 13:55:54 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@619bd14c{/stages/stage/json,null,AVAILABLE,@Spark}
19/09/03 13:55:54 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@323e8306{/stages/pool,null,AVAILABLE,@Spark}
19/09/03 13:55:54 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@a23a01d{/stages/pool/json,null,AVAILABLE,@Spark}
19/09/03 13:55:54 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@4acf72b6{/storage,null,AVAILABLE,@Spark}
19/09/03 13:55:54 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@7561db12{/storage/json,null,AVAILABLE,@Spark}
19/09/03 13:55:54 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@3301500b{/storage/rdd,null,AVAILABLE,@Spark}
19/09/03 13:55:54 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@24b52d3e{/storage/rdd/json,null,AVAILABLE,@Spark}
19/09/03 13:55:54 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@15deb1dc{/environment,null,AVAILABLE,@Spark}
19/09/03 13:55:54 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@6e9c413e{/environment/json,null,AVAILABLE,@Spark}
19/09/03 13:55:54 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@57a4d5ee{/executors,null,AVAILABLE,@Spark}
19/09/03 13:55:54 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@5af5def9{/executors/json,null,AVAILABLE,@Spark}
19/09/03 13:55:54 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@3a45c42a{/executors/threadDump,null,AVAILABLE,@Spark}
19/09/03 13:55:54 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@36dce7ed{/executors/threadDump/json,null,AVAILABLE,@Spark}
19/09/03 13:55:54 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@47a64f7d{/static,null,AVAILABLE,@Spark}
19/09/03 13:55:54 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@78e16155{/,null,AVAILABLE,@Spark}
19/09/03 13:55:54 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@54a3ab8f{/api,null,AVAILABLE,@Spark}
19/09/03 13:55:54 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@50b0bc4c{/jobs/job/kill,null,AVAILABLE,@Spark}
19/09/03 13:55:54 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@c20be82{/stages/stage/kill,null,AVAILABLE,@Spark}
19/09/03 13:55:54 INFO ui.SparkUI: Bound SparkUI to 0.0.0.0, and started at http://192.168.10.27:4040
19/09/03 13:55:54 INFO spark.SparkContext: Added JAR file:/tmp/adamTestesvklDQ/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/target/adam-assembly-spark2_2.12-0.29.0-SNAPSHOT.jar at spark://192.168.10.27:35141/jars/adam-assembly-spark2_2.12-0.29.0-SNAPSHOT.jar with timestamp 1567544154849
19/09/03 13:55:54 INFO executor.Executor: Starting executor ID driver on host localhost
19/09/03 13:55:54 INFO util.Utils: Successfully started service 'org.apache.spark.network.netty.NettyBlockTransferService' on port 39985.
19/09/03 13:55:54 INFO netty.NettyBlockTransferService: Server created on 192.168.10.27:39985
19/09/03 13:55:54 INFO storage.BlockManager: Using org.apache.spark.storage.RandomBlockReplicationPolicy for block replication policy
19/09/03 13:55:55 INFO storage.BlockManagerMaster: Registering BlockManager BlockManagerId(driver, 192.168.10.27, 39985, None)
19/09/03 13:55:55 INFO storage.BlockManagerMasterEndpoint: Registering block manager 192.168.10.27:39985 with 366.3 MB RAM, BlockManagerId(driver, 192.168.10.27, 39985, None)
19/09/03 13:55:55 INFO storage.BlockManagerMaster: Registered BlockManager BlockManagerId(driver, 192.168.10.27, 39985, None)
19/09/03 13:55:55 INFO storage.BlockManager: Initialized BlockManager: BlockManagerId(driver, 192.168.10.27, 39985, None)
19/09/03 13:55:55 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@5d1e09bc{/metrics/json,null,AVAILABLE,@Spark}
19/09/03 13:55:55 INFO rdd.ADAMContext: Loading mouse_chrM.bam.reads.adam as Parquet of AlignmentRecords.
19/09/03 13:55:56 INFO rdd.ADAMContext: Reading the ADAM file at mouse_chrM.bam.reads.adam to create RDD
19/09/03 13:55:57 INFO memory.MemoryStore: Block broadcast_0 stored as values in memory (estimated size 315.0 KB, free 366.0 MB)
19/09/03 13:55:57 INFO memory.MemoryStore: Block broadcast_0_piece0 stored as bytes in memory (estimated size 28.2 KB, free 366.0 MB)
19/09/03 13:55:57 INFO storage.BlockManagerInfo: Added broadcast_0_piece0 in memory on 192.168.10.27:39985 (size: 28.2 KB, free: 366.3 MB)
19/09/03 13:55:57 INFO spark.SparkContext: Created broadcast 0 from newAPIHadoopFile at ADAMContext.scala:1801
19/09/03 13:55:57 INFO cli.TransformAlignments: Sorting alignments by reference position, with references ordered by name
19/09/03 13:55:57 INFO read.RDDBoundAlignmentRecordDataset: Sorting alignments by reference position
19/09/03 13:55:57 INFO input.FileInputFormat: Total input paths to process : 1
19/09/03 13:55:57 INFO hadoop.ParquetInputFormat: Total input paths to process : 1
19/09/03 13:55:58 INFO read.RDDBoundAlignmentRecordDataset: Saving data in ADAM format
19/09/03 13:55:58 INFO output.FileOutputCommitter: File Output Committer Algorithm version is 1
19/09/03 13:55:58 INFO spark.SparkContext: Starting job: runJob at SparkHadoopWriter.scala:78
19/09/03 13:55:58 INFO scheduler.DAGScheduler: Registering RDD 2 (sortBy at AlignmentRecordDataset.scala:1001)
19/09/03 13:55:58 INFO scheduler.DAGScheduler: Got job 0 (runJob at SparkHadoopWriter.scala:78) with 1 output partitions
19/09/03 13:55:58 INFO scheduler.DAGScheduler: Final stage: ResultStage 1 (runJob at SparkHadoopWriter.scala:78)
19/09/03 13:55:58 INFO scheduler.DAGScheduler: Parents of final stage: List(ShuffleMapStage 0)
19/09/03 13:55:58 INFO scheduler.DAGScheduler: Missing parents: List(ShuffleMapStage 0)
19/09/03 13:55:58 INFO scheduler.DAGScheduler: Submitting ShuffleMapStage 0 (MapPartitionsRDD[2] at sortBy at AlignmentRecordDataset.scala:1001), which has no missing parents
19/09/03 13:55:58 INFO memory.MemoryStore: Block broadcast_1 stored as values in memory (estimated size 5.8 KB, free 366.0 MB)
19/09/03 13:55:58 INFO memory.MemoryStore: Block broadcast_1_piece0 stored as bytes in memory (estimated size 3.4 KB, free 366.0 MB)
19/09/03 13:55:58 INFO storage.BlockManagerInfo: Added broadcast_1_piece0 in memory on 192.168.10.27:39985 (size: 3.4 KB, free: 366.3 MB)
19/09/03 13:55:58 INFO spark.SparkContext: Created broadcast 1 from broadcast at DAGScheduler.scala:1161
19/09/03 13:55:58 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))
19/09/03 13:55:58 INFO scheduler.TaskSchedulerImpl: Adding task set 0.0 with 1 tasks
19/09/03 13:55:58 INFO scheduler.TaskSetManager: Starting task 0.0 in stage 0.0 (TID 0, localhost, executor driver, partition 0, PROCESS_LOCAL, 7480 bytes)
19/09/03 13:55:58 INFO executor.Executor: Running task 0.0 in stage 0.0 (TID 0)
19/09/03 13:55:58 INFO executor.Executor: Fetching spark://192.168.10.27:35141/jars/adam-assembly-spark2_2.12-0.29.0-SNAPSHOT.jar with timestamp 1567544154849
19/09/03 13:55:58 INFO client.TransportClientFactory: Successfully created connection to /192.168.10.27:35141 after 26 ms (0 ms spent in bootstraps)
19/09/03 13:55:58 INFO util.Utils: Fetching spark://192.168.10.27:35141/jars/adam-assembly-spark2_2.12-0.29.0-SNAPSHOT.jar to /tmp/spark-7cb9291c-1f1b-4e54-8978-ecaf470d974c/userFiles-7a6e68ca-3e7b-4706-9d6e-7522a5791547/fetchFileTemp3351945076155965723.tmp
19/09/03 13:55:58 INFO executor.Executor: Adding file:/tmp/spark-7cb9291c-1f1b-4e54-8978-ecaf470d974c/userFiles-7a6e68ca-3e7b-4706-9d6e-7522a5791547/adam-assembly-spark2_2.12-0.29.0-SNAPSHOT.jar to class loader
19/09/03 13:55:58 INFO rdd.NewHadoopRDD: Input split: file:/tmp/adamTestesvklDQ/deleteMePleaseThisIsNoLongerNeeded/mouse_chrM.bam.reads.adam/part-r-00000.gz.parquet:0+10132194
19/09/03 13:55:58 INFO hadoop.InternalParquetRecordReader: RecordReader initialized will read a total of 163064 records.
19/09/03 13:55:58 INFO hadoop.InternalParquetRecordReader: at row 0. reading next block
19/09/03 13:55:58 INFO compress.CodecPool: Got brand-new decompressor [.gz]
19/09/03 13:55:58 INFO hadoop.InternalParquetRecordReader: block read in memory in 42 ms. row count = 163064
19/09/03 13:56:01 INFO executor.Executor: Finished task 0.0 in stage 0.0 (TID 0). 919 bytes result sent to driver
19/09/03 13:56:01 INFO scheduler.TaskSetManager: Finished task 0.0 in stage 0.0 (TID 0) in 3448 ms on localhost (executor driver) (1/1)
19/09/03 13:56:01 INFO scheduler.TaskSchedulerImpl: Removed TaskSet 0.0, whose tasks have all completed, from pool 
19/09/03 13:56:01 INFO scheduler.DAGScheduler: ShuffleMapStage 0 (sortBy at AlignmentRecordDataset.scala:1001) finished in 3.583 s
19/09/03 13:56:01 INFO scheduler.DAGScheduler: looking for newly runnable stages
19/09/03 13:56:01 INFO scheduler.DAGScheduler: running: Set()
19/09/03 13:56:01 INFO scheduler.DAGScheduler: waiting: Set(ResultStage 1)
19/09/03 13:56:01 INFO scheduler.DAGScheduler: failed: Set()
19/09/03 13:56:01 INFO scheduler.DAGScheduler: Submitting ResultStage 1 (MapPartitionsRDD[5] at map at GenomicDataset.scala:3814), which has no missing parents
19/09/03 13:56:01 INFO memory.MemoryStore: Block broadcast_2 stored as values in memory (estimated size 86.8 KB, free 365.9 MB)
19/09/03 13:56:01 INFO memory.MemoryStore: Block broadcast_2_piece0 stored as bytes in memory (estimated size 32.3 KB, free 365.8 MB)
19/09/03 13:56:01 INFO storage.BlockManagerInfo: Added broadcast_2_piece0 in memory on 192.168.10.27:39985 (size: 32.3 KB, free: 366.2 MB)
19/09/03 13:56:01 INFO spark.SparkContext: Created broadcast 2 from broadcast at DAGScheduler.scala:1161
19/09/03 13:56:01 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))
19/09/03 13:56:01 INFO scheduler.TaskSchedulerImpl: Adding task set 1.0 with 1 tasks
19/09/03 13:56:01 INFO scheduler.TaskSetManager: Starting task 0.0 in stage 1.0 (TID 1, localhost, executor driver, partition 0, ANY, 7141 bytes)
19/09/03 13:56:01 INFO executor.Executor: Running task 0.0 in stage 1.0 (TID 1)
19/09/03 13:56:01 INFO storage.ShuffleBlockFetcherIterator: Getting 1 non-empty blocks including 1 local blocks and 0 remote blocks
19/09/03 13:56:01 INFO storage.ShuffleBlockFetcherIterator: Started 0 remote fetches in 6 ms
19/09/03 13:56:03 INFO output.FileOutputCommitter: File Output Committer Algorithm version is 1
19/09/03 13:56:03 INFO codec.CodecConfig: Compression: GZIP
19/09/03 13:56:03 INFO output.FileOutputCommitter: File Output Committer Algorithm version is 1
19/09/03 13:56:03 INFO hadoop.ParquetOutputFormat: Parquet block size to 134217728
19/09/03 13:56:03 INFO hadoop.ParquetOutputFormat: Parquet page size to 1048576
19/09/03 13:56:03 INFO hadoop.ParquetOutputFormat: Parquet dictionary page size to 1048576
19/09/03 13:56:03 INFO hadoop.ParquetOutputFormat: Dictionary is on
19/09/03 13:56:03 INFO hadoop.ParquetOutputFormat: Validation is off
19/09/03 13:56:03 INFO hadoop.ParquetOutputFormat: Writer version is: PARQUET_1_0
19/09/03 13:56:03 INFO hadoop.ParquetOutputFormat: Maximum row group padding size is 8388608 bytes
19/09/03 13:56:03 INFO hadoop.ParquetOutputFormat: Page size checking is: estimated
19/09/03 13:56:03 INFO hadoop.ParquetOutputFormat: Min row count for page size check is: 100
19/09/03 13:56:03 INFO hadoop.ParquetOutputFormat: Max row count for page size check is: 10000
19/09/03 13:56:03 INFO compress.CodecPool: Got brand-new compressor [.gz]
19/09/03 13:56:07 INFO hadoop.InternalParquetRecordWriter: Flushing mem columnStore to file. allocated memory: 16004474
19/09/03 13:56:07 INFO output.FileOutputCommitter: Saved output of task 'attempt_20190903135558_0005_r_000000_0' to file:/tmp/adamTestesvklDQ/deleteMePleaseThisIsNoLongerNeeded/mouse_chrM.bam.reads.sorted.adam/_temporary/0/task_20190903135558_0005_r_000000
19/09/03 13:56:07 INFO mapred.SparkHadoopMapRedUtil: attempt_20190903135558_0005_r_000000_0: Committed
19/09/03 13:56:07 INFO executor.Executor: Finished task 0.0 in stage 1.0 (TID 1). 1243 bytes result sent to driver
19/09/03 13:56:07 INFO scheduler.TaskSetManager: Finished task 0.0 in stage 1.0 (TID 1) in 6096 ms on localhost (executor driver) (1/1)
19/09/03 13:56:07 INFO scheduler.TaskSchedulerImpl: Removed TaskSet 1.0, whose tasks have all completed, from pool 
19/09/03 13:56:07 INFO scheduler.DAGScheduler: ResultStage 1 (runJob at SparkHadoopWriter.scala:78) finished in 6.153 s
19/09/03 13:56:07 INFO scheduler.DAGScheduler: Job 0 finished: runJob at SparkHadoopWriter.scala:78, took 9.825001 s
19/09/03 13:56:07 INFO hadoop.ParquetFileReader: Initiating action with parallelism: 5
19/09/03 13:56:07 INFO io.SparkHadoopWriter: Job job_20190903135558_0005 committed.
19/09/03 13:56:08 INFO cli.TransformAlignments: Overall Duration: 13.96 secs
19/09/03 13:56:08 INFO spark.SparkContext: Invoking stop() from shutdown hook
19/09/03 13:56:08 INFO server.AbstractConnector: Stopped Spark@6ebd78d1{HTTP/1.1,[http/1.1]}{0.0.0.0:4040}
19/09/03 13:56:08 INFO ui.SparkUI: Stopped Spark web UI at http://192.168.10.27:4040
19/09/03 13:56:08 INFO spark.MapOutputTrackerMasterEndpoint: MapOutputTrackerMasterEndpoint stopped!
19/09/03 13:56:08 INFO memory.MemoryStore: MemoryStore cleared
19/09/03 13:56:08 INFO storage.BlockManager: BlockManager stopped
19/09/03 13:56:08 INFO storage.BlockManagerMaster: BlockManagerMaster stopped
19/09/03 13:56:08 INFO scheduler.OutputCommitCoordinator$OutputCommitCoordinatorEndpoint: OutputCommitCoordinator stopped!
19/09/03 13:56:08 INFO spark.SparkContext: Successfully stopped SparkContext
19/09/03 13:56:08 INFO util.ShutdownHookManager: Shutdown hook called
19/09/03 13:56:08 INFO util.ShutdownHookManager: Deleting directory /tmp/spark-7cb9291c-1f1b-4e54-8978-ecaf470d974c
19/09/03 13:56:08 INFO util.ShutdownHookManager: Deleting directory /tmp/spark-c2b741e5-cbd4-4f68-9924-a5d08f802747

# 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/adamTestesvklDQ/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.3-bin-without-hadoop-scala-2.12/bin/spark-submit
19/09/03 13:56:09 WARN util.Utils: Your hostname, research-jenkins-worker-07 resolves to a loopback address: 127.0.1.1; using 192.168.10.27 instead (on interface eth0)
19/09/03 13:56:09 WARN util.Utils: Set SPARK_LOCAL_IP if you need to bind to another address
19/09/03 13:56:10 WARN util.NativeCodeLoader: Unable to load native-hadoop library for your platform... using builtin-java classes where applicable
19/09/03 13:56:10 INFO cli.ADAMMain: ADAM invoked with args: "transformFragments" "-load_as_alignments" "mouse_chrM.bam.reads.adam" "mouse_chrM.bam.fragments.adam"
19/09/03 13:56:10 INFO spark.SparkContext: Running Spark version 2.4.3
19/09/03 13:56:10 INFO spark.SparkContext: Submitted application: transformFragments
19/09/03 13:56:10 INFO spark.SecurityManager: Changing view acls to: jenkins
19/09/03 13:56:10 INFO spark.SecurityManager: Changing modify acls to: jenkins
19/09/03 13:56:10 INFO spark.SecurityManager: Changing view acls groups to: 
19/09/03 13:56:10 INFO spark.SecurityManager: Changing modify acls groups to: 
19/09/03 13:56:10 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()
19/09/03 13:56:10 INFO util.Utils: Successfully started service 'sparkDriver' on port 41119.
19/09/03 13:56:10 INFO spark.SparkEnv: Registering MapOutputTracker
19/09/03 13:56:10 INFO spark.SparkEnv: Registering BlockManagerMaster
19/09/03 13:56:10 INFO storage.BlockManagerMasterEndpoint: Using org.apache.spark.storage.DefaultTopologyMapper for getting topology information
19/09/03 13:56:10 INFO storage.BlockManagerMasterEndpoint: BlockManagerMasterEndpoint up
19/09/03 13:56:10 INFO storage.DiskBlockManager: Created local directory at /tmp/blockmgr-49e56161-38c0-4a2f-bd12-0021da66d699
19/09/03 13:56:10 INFO memory.MemoryStore: MemoryStore started with capacity 366.3 MB
19/09/03 13:56:10 INFO spark.SparkEnv: Registering OutputCommitCoordinator
19/09/03 13:56:11 INFO util.log: Logging initialized @2300ms
19/09/03 13:56:11 INFO server.Server: jetty-9.3.z-SNAPSHOT, build timestamp: unknown, git hash: unknown
19/09/03 13:56:11 INFO server.Server: Started @2375ms
19/09/03 13:56:11 INFO server.AbstractConnector: Started ServerConnector@6e0ff644{HTTP/1.1,[http/1.1]}{0.0.0.0:4040}
19/09/03 13:56:11 INFO util.Utils: Successfully started service 'SparkUI' on port 4040.
19/09/03 13:56:11 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@3f2049b6{/jobs,null,AVAILABLE,@Spark}
19/09/03 13:56:11 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@6b85300e{/jobs/json,null,AVAILABLE,@Spark}
19/09/03 13:56:11 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@3aaf4f07{/jobs/job,null,AVAILABLE,@Spark}
19/09/03 13:56:11 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@18e8473e{/jobs/job/json,null,AVAILABLE,@Spark}
19/09/03 13:56:11 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@5a2f016d{/stages,null,AVAILABLE,@Spark}
19/09/03 13:56:11 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@1a38ba58{/stages/json,null,AVAILABLE,@Spark}
19/09/03 13:56:11 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@3ad394e6{/stages/stage,null,AVAILABLE,@Spark}
19/09/03 13:56:11 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@1deb2c43{/stages/stage/json,null,AVAILABLE,@Spark}
19/09/03 13:56:11 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@3bb9efbc{/stages/pool,null,AVAILABLE,@Spark}
19/09/03 13:56:11 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@1cefc4b3{/stages/pool/json,null,AVAILABLE,@Spark}
19/09/03 13:56:11 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@2b27cc70{/storage,null,AVAILABLE,@Spark}
19/09/03 13:56:11 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@6f6a7463{/storage/json,null,AVAILABLE,@Spark}
19/09/03 13:56:11 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@1bdaa23d{/storage/rdd,null,AVAILABLE,@Spark}
19/09/03 13:56:11 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@79f227a9{/storage/rdd/json,null,AVAILABLE,@Spark}
19/09/03 13:56:11 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@6ca320ab{/environment,null,AVAILABLE,@Spark}
19/09/03 13:56:11 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@50d68830{/environment/json,null,AVAILABLE,@Spark}
19/09/03 13:56:11 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@1e53135d{/executors,null,AVAILABLE,@Spark}
19/09/03 13:56:11 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@7674a051{/executors/json,null,AVAILABLE,@Spark}
19/09/03 13:56:11 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@3a7704c{/executors/threadDump,null,AVAILABLE,@Spark}
19/09/03 13:56:11 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@6754ef00{/executors/threadDump/json,null,AVAILABLE,@Spark}
19/09/03 13:56:11 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@619bd14c{/static,null,AVAILABLE,@Spark}
19/09/03 13:56:11 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@106faf11{/,null,AVAILABLE,@Spark}
19/09/03 13:56:11 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@70f43b45{/api,null,AVAILABLE,@Spark}
19/09/03 13:56:11 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@2c282004{/jobs/job/kill,null,AVAILABLE,@Spark}
19/09/03 13:56:11 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@22ee2d0{/stages/stage/kill,null,AVAILABLE,@Spark}
19/09/03 13:56:11 INFO ui.SparkUI: Bound SparkUI to 0.0.0.0, and started at http://192.168.10.27:4040
19/09/03 13:56:11 INFO spark.SparkContext: Added JAR file:/tmp/adamTestesvklDQ/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/target/adam-assembly-spark2_2.12-0.29.0-SNAPSHOT.jar at spark://192.168.10.27:41119/jars/adam-assembly-spark2_2.12-0.29.0-SNAPSHOT.jar with timestamp 1567544171158
19/09/03 13:56:11 INFO executor.Executor: Starting executor ID driver on host localhost
19/09/03 13:56:11 INFO util.Utils: Successfully started service 'org.apache.spark.network.netty.NettyBlockTransferService' on port 36059.
19/09/03 13:56:11 INFO netty.NettyBlockTransferService: Server created on 192.168.10.27:36059
19/09/03 13:56:11 INFO storage.BlockManager: Using org.apache.spark.storage.RandomBlockReplicationPolicy for block replication policy
19/09/03 13:56:11 INFO storage.BlockManagerMaster: Registering BlockManager BlockManagerId(driver, 192.168.10.27, 36059, None)
19/09/03 13:56:11 INFO storage.BlockManagerMasterEndpoint: Registering block manager 192.168.10.27:36059 with 366.3 MB RAM, BlockManagerId(driver, 192.168.10.27, 36059, None)
19/09/03 13:56:11 INFO storage.BlockManagerMaster: Registered BlockManager BlockManagerId(driver, 192.168.10.27, 36059, None)
19/09/03 13:56:11 INFO storage.BlockManager: Initialized BlockManager: BlockManagerId(driver, 192.168.10.27, 36059, None)
19/09/03 13:56:11 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@6075b2d3{/metrics/json,null,AVAILABLE,@Spark}
19/09/03 13:56:11 INFO rdd.ADAMContext: Loading mouse_chrM.bam.reads.adam as Parquet of AlignmentRecords.
19/09/03 13:56:13 INFO rdd.ADAMContext: Reading the ADAM file at mouse_chrM.bam.reads.adam to create RDD
19/09/03 13:56:13 INFO memory.MemoryStore: Block broadcast_0 stored as values in memory (estimated size 315.0 KB, free 366.0 MB)
19/09/03 13:56:14 INFO memory.MemoryStore: Block broadcast_0_piece0 stored as bytes in memory (estimated size 28.2 KB, free 366.0 MB)
19/09/03 13:56:14 INFO storage.BlockManagerInfo: Added broadcast_0_piece0 in memory on 192.168.10.27:36059 (size: 28.2 KB, free: 366.3 MB)
19/09/03 13:56:14 INFO spark.SparkContext: Created broadcast 0 from newAPIHadoopFile at ADAMContext.scala:1801
19/09/03 13:56:14 INFO input.FileInputFormat: Total input paths to process : 1
19/09/03 13:56:14 INFO hadoop.ParquetInputFormat: Total input paths to process : 1
19/09/03 13:56:14 INFO fragment.RDDBoundFragmentDataset: Saving data in ADAM format
19/09/03 13:56:14 INFO output.FileOutputCommitter: File Output Committer Algorithm version is 1
19/09/03 13:56:14 INFO spark.SparkContext: Starting job: runJob at SparkHadoopWriter.scala:78
19/09/03 13:56:14 INFO scheduler.DAGScheduler: Registering RDD 2 (groupBy at SingleReadBucket.scala:97)
19/09/03 13:56:14 INFO scheduler.DAGScheduler: Got job 0 (runJob at SparkHadoopWriter.scala:78) with 1 output partitions
19/09/03 13:56:14 INFO scheduler.DAGScheduler: Final stage: ResultStage 1 (runJob at SparkHadoopWriter.scala:78)
19/09/03 13:56:14 INFO scheduler.DAGScheduler: Parents of final stage: List(ShuffleMapStage 0)
19/09/03 13:56:14 INFO scheduler.DAGScheduler: Missing parents: List(ShuffleMapStage 0)
19/09/03 13:56:14 INFO scheduler.DAGScheduler: Submitting ShuffleMapStage 0 (MapPartitionsRDD[2] at groupBy at SingleReadBucket.scala:97), which has no missing parents
19/09/03 13:56:14 INFO memory.MemoryStore: Block broadcast_1 stored as values in memory (estimated size 6.3 KB, free 366.0 MB)
19/09/03 13:56:14 INFO memory.MemoryStore: Block broadcast_1_piece0 stored as bytes in memory (estimated size 3.4 KB, free 366.0 MB)
19/09/03 13:56:14 INFO storage.BlockManagerInfo: Added broadcast_1_piece0 in memory on 192.168.10.27:36059 (size: 3.4 KB, free: 366.3 MB)
19/09/03 13:56:14 INFO spark.SparkContext: Created broadcast 1 from broadcast at DAGScheduler.scala:1161
19/09/03 13:56:14 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))
19/09/03 13:56:14 INFO scheduler.TaskSchedulerImpl: Adding task set 0.0 with 1 tasks
19/09/03 13:56:14 INFO scheduler.TaskSetManager: Starting task 0.0 in stage 0.0 (TID 0, localhost, executor driver, partition 0, PROCESS_LOCAL, 7480 bytes)
19/09/03 13:56:14 INFO executor.Executor: Running task 0.0 in stage 0.0 (TID 0)
19/09/03 13:56:14 INFO executor.Executor: Fetching spark://192.168.10.27:41119/jars/adam-assembly-spark2_2.12-0.29.0-SNAPSHOT.jar with timestamp 1567544171158
19/09/03 13:56:14 INFO client.TransportClientFactory: Successfully created connection to /192.168.10.27:41119 after 29 ms (0 ms spent in bootstraps)
19/09/03 13:56:14 INFO util.Utils: Fetching spark://192.168.10.27:41119/jars/adam-assembly-spark2_2.12-0.29.0-SNAPSHOT.jar to /tmp/spark-c775e253-165d-464e-8f44-c00bb209ecb6/userFiles-ad08914d-ece4-4bab-b36b-b68f2b41a607/fetchFileTemp4388739466021990536.tmp
19/09/03 13:56:14 INFO executor.Executor: Adding file:/tmp/spark-c775e253-165d-464e-8f44-c00bb209ecb6/userFiles-ad08914d-ece4-4bab-b36b-b68f2b41a607/adam-assembly-spark2_2.12-0.29.0-SNAPSHOT.jar to class loader
19/09/03 13:56:15 INFO rdd.NewHadoopRDD: Input split: file:/tmp/adamTestesvklDQ/deleteMePleaseThisIsNoLongerNeeded/mouse_chrM.bam.reads.adam/part-r-00000.gz.parquet:0+10132194
19/09/03 13:56:15 INFO hadoop.InternalParquetRecordReader: RecordReader initialized will read a total of 163064 records.
19/09/03 13:56:15 INFO hadoop.InternalParquetRecordReader: at row 0. reading next block
19/09/03 13:56:15 INFO compress.CodecPool: Got brand-new decompressor [.gz]
19/09/03 13:56:15 INFO hadoop.InternalParquetRecordReader: block read in memory in 40 ms. row count = 163064
19/09/03 13:56:18 INFO executor.Executor: Finished task 0.0 in stage 0.0 (TID 0). 919 bytes result sent to driver
19/09/03 13:56:18 INFO scheduler.TaskSetManager: Finished task 0.0 in stage 0.0 (TID 0) in 3578 ms on localhost (executor driver) (1/1)
19/09/03 13:56:18 INFO scheduler.TaskSchedulerImpl: Removed TaskSet 0.0, whose tasks have all completed, from pool 
19/09/03 13:56:18 INFO scheduler.DAGScheduler: ShuffleMapStage 0 (groupBy at SingleReadBucket.scala:97) finished in 3.686 s
19/09/03 13:56:18 INFO scheduler.DAGScheduler: looking for newly runnable stages
19/09/03 13:56:18 INFO scheduler.DAGScheduler: running: Set()
19/09/03 13:56:18 INFO scheduler.DAGScheduler: waiting: Set(ResultStage 1)
19/09/03 13:56:18 INFO scheduler.DAGScheduler: failed: Set()
19/09/03 13:56:18 INFO scheduler.DAGScheduler: Submitting ResultStage 1 (MapPartitionsRDD[6] at map at GenomicDataset.scala:3814), which has no missing parents
19/09/03 13:56:18 INFO memory.MemoryStore: Block broadcast_2 stored as values in memory (estimated size 90.2 KB, free 365.9 MB)
19/09/03 13:56:18 INFO memory.MemoryStore: Block broadcast_2_piece0 stored as bytes in memory (estimated size 33.5 KB, free 365.8 MB)
19/09/03 13:56:18 INFO storage.BlockManagerInfo: Added broadcast_2_piece0 in memory on 192.168.10.27:36059 (size: 33.5 KB, free: 366.2 MB)
19/09/03 13:56:18 INFO spark.SparkContext: Created broadcast 2 from broadcast at DAGScheduler.scala:1161
19/09/03 13:56:18 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))
19/09/03 13:56:18 INFO scheduler.TaskSchedulerImpl: Adding task set 1.0 with 1 tasks
19/09/03 13:56:18 INFO scheduler.TaskSetManager: Starting task 0.0 in stage 1.0 (TID 1, localhost, executor driver, partition 0, ANY, 7141 bytes)
19/09/03 13:56:18 INFO executor.Executor: Running task 0.0 in stage 1.0 (TID 1)
19/09/03 13:56:18 INFO storage.ShuffleBlockFetcherIterator: Getting 1 non-empty blocks including 1 local blocks and 0 remote blocks
19/09/03 13:56:18 INFO storage.ShuffleBlockFetcherIterator: Started 0 remote fetches in 7 ms
19/09/03 13:56:19 INFO output.FileOutputCommitter: File Output Committer Algorithm version is 1
19/09/03 13:56:19 INFO codec.CodecConfig: Compression: GZIP
19/09/03 13:56:19 INFO output.FileOutputCommitter: File Output Committer Algorithm version is 1
19/09/03 13:56:19 INFO hadoop.ParquetOutputFormat: Parquet block size to 134217728
19/09/03 13:56:19 INFO hadoop.ParquetOutputFormat: Parquet page size to 1048576
19/09/03 13:56:19 INFO hadoop.ParquetOutputFormat: Parquet dictionary page size to 1048576
19/09/03 13:56:19 INFO hadoop.ParquetOutputFormat: Dictionary is on
19/09/03 13:56:19 INFO hadoop.ParquetOutputFormat: Validation is off
19/09/03 13:56:19 INFO hadoop.ParquetOutputFormat: Writer version is: PARQUET_1_0
19/09/03 13:56:19 INFO hadoop.ParquetOutputFormat: Maximum row group padding size is 8388608 bytes
19/09/03 13:56:19 INFO hadoop.ParquetOutputFormat: Page size checking is: estimated
19/09/03 13:56:19 INFO hadoop.ParquetOutputFormat: Min row count for page size check is: 100
19/09/03 13:56:19 INFO hadoop.ParquetOutputFormat: Max row count for page size check is: 10000
19/09/03 13:56:19 INFO compress.CodecPool: Got brand-new compressor [.gz]
19/09/03 13:56:26 INFO hadoop.InternalParquetRecordWriter: Flushing mem columnStore to file. allocated memory: 21417928
19/09/03 13:56:26 INFO output.FileOutputCommitter: Saved output of task 'attempt_20190903135614_0006_r_000000_0' to file:/tmp/adamTestesvklDQ/deleteMePleaseThisIsNoLongerNeeded/mouse_chrM.bam.fragments.adam/_temporary/0/task_20190903135614_0006_r_000000
19/09/03 13:56:26 INFO mapred.SparkHadoopMapRedUtil: attempt_20190903135614_0006_r_000000_0: Committed
19/09/03 13:56:26 INFO executor.Executor: Finished task 0.0 in stage 1.0 (TID 1). 1200 bytes result sent to driver
19/09/03 13:56:26 INFO scheduler.TaskSetManager: Finished task 0.0 in stage 1.0 (TID 1) in 8523 ms on localhost (executor driver) (1/1)
19/09/03 13:56:26 INFO scheduler.TaskSchedulerImpl: Removed TaskSet 1.0, whose tasks have all completed, from pool 
19/09/03 13:56:26 INFO scheduler.DAGScheduler: ResultStage 1 (runJob at SparkHadoopWriter.scala:78) finished in 8.572 s
19/09/03 13:56:26 INFO scheduler.DAGScheduler: Job 0 finished: runJob at SparkHadoopWriter.scala:78, took 12.349461 s
19/09/03 13:56:26 INFO hadoop.ParquetFileReader: Initiating action with parallelism: 5
19/09/03 13:56:26 INFO io.SparkHadoopWriter: Job job_20190903135614_0006 committed.
19/09/03 13:56:27 INFO cli.TransformFragments: Overall Duration: 16.63 secs
19/09/03 13:56:27 INFO spark.SparkContext: Invoking stop() from shutdown hook
19/09/03 13:56:27 INFO server.AbstractConnector: Stopped Spark@6e0ff644{HTTP/1.1,[http/1.1]}{0.0.0.0:4040}
19/09/03 13:56:27 INFO ui.SparkUI: Stopped Spark web UI at http://192.168.10.27:4040
19/09/03 13:56:27 INFO spark.MapOutputTrackerMasterEndpoint: MapOutputTrackerMasterEndpoint stopped!
19/09/03 13:56:27 INFO memory.MemoryStore: MemoryStore cleared
19/09/03 13:56:27 INFO storage.BlockManager: BlockManager stopped
19/09/03 13:56:27 INFO storage.BlockManagerMaster: BlockManagerMaster stopped
19/09/03 13:56:27 INFO scheduler.OutputCommitCoordinator$OutputCommitCoordinatorEndpoint: OutputCommitCoordinator stopped!
19/09/03 13:56:27 INFO spark.SparkContext: Successfully stopped SparkContext
19/09/03 13:56:27 INFO util.ShutdownHookManager: Shutdown hook called
19/09/03 13:56:27 INFO util.ShutdownHookManager: Deleting directory /tmp/spark-3cb092c3-a228-4711-963a-e809616833f8
19/09/03 13:56:27 INFO util.ShutdownHookManager: Deleting directory /tmp/spark-c775e253-165d-464e-8f44-c00bb209ecb6

# 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/adamTestesvklDQ/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.3-bin-without-hadoop-scala-2.12/bin/spark-submit
19/09/03 13:56:45 WARN util.Utils: Your hostname, research-jenkins-worker-07 resolves to a loopback address: 127.0.1.1; using 192.168.10.27 instead (on interface eth0)
19/09/03 13:56:45 WARN util.Utils: Set SPARK_LOCAL_IP if you need to bind to another address
19/09/03 13:56:45 WARN util.NativeCodeLoader: Unable to load native-hadoop library for your platform... using builtin-java classes where applicable
19/09/03 13:56:45 INFO cli.ADAMMain: ADAM invoked with args: "flagstat" "-print_metrics" "mouse_chrM.bam.reads.adam"
19/09/03 13:56:45 INFO spark.SparkContext: Running Spark version 2.4.3
19/09/03 13:56:46 INFO spark.SparkContext: Submitted application: flagstat
19/09/03 13:56:46 INFO spark.SecurityManager: Changing view acls to: jenkins
19/09/03 13:56:46 INFO spark.SecurityManager: Changing modify acls to: jenkins
19/09/03 13:56:46 INFO spark.SecurityManager: Changing view acls groups to: 
19/09/03 13:56:46 INFO spark.SecurityManager: Changing modify acls groups to: 
19/09/03 13:56:46 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()
19/09/03 13:56:46 INFO util.Utils: Successfully started service 'sparkDriver' on port 41843.
19/09/03 13:56:46 INFO spark.SparkEnv: Registering MapOutputTracker
19/09/03 13:56:46 INFO spark.SparkEnv: Registering BlockManagerMaster
19/09/03 13:56:46 INFO storage.BlockManagerMasterEndpoint: Using org.apache.spark.storage.DefaultTopologyMapper for getting topology information
19/09/03 13:56:46 INFO storage.BlockManagerMasterEndpoint: BlockManagerMasterEndpoint up
19/09/03 13:56:46 INFO storage.DiskBlockManager: Created local directory at /tmp/blockmgr-e9319e78-e45d-4a6d-8fb9-de9a4ec2cb74
19/09/03 13:56:46 INFO memory.MemoryStore: MemoryStore started with capacity 366.3 MB
19/09/03 13:56:46 INFO spark.SparkEnv: Registering OutputCommitCoordinator
19/09/03 13:56:46 INFO util.log: Logging initialized @2328ms
19/09/03 13:56:46 INFO server.Server: jetty-9.3.z-SNAPSHOT, build timestamp: unknown, git hash: unknown
19/09/03 13:56:46 INFO server.Server: Started @2411ms
19/09/03 13:56:46 INFO server.AbstractConnector: Started ServerConnector@2024293c{HTTP/1.1,[http/1.1]}{0.0.0.0:4040}
19/09/03 13:56:46 INFO util.Utils: Successfully started service 'SparkUI' on port 4040.
19/09/03 13:56:46 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@7577b641{/jobs,null,AVAILABLE,@Spark}
19/09/03 13:56:46 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@7bd69e82{/jobs/json,null,AVAILABLE,@Spark}
19/09/03 13:56:46 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@74d7184a{/jobs/job,null,AVAILABLE,@Spark}
19/09/03 13:56:46 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@6831d8fd{/jobs/job/json,null,AVAILABLE,@Spark}
19/09/03 13:56:46 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@27dc79f7{/stages,null,AVAILABLE,@Spark}
19/09/03 13:56:46 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@6b85300e{/stages/json,null,AVAILABLE,@Spark}
19/09/03 13:56:46 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@3aaf4f07{/stages/stage,null,AVAILABLE,@Spark}
19/09/03 13:56:46 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@5a2f016d{/stages/stage/json,null,AVAILABLE,@Spark}
19/09/03 13:56:46 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@1a38ba58{/stages/pool,null,AVAILABLE,@Spark}
19/09/03 13:56:46 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@3ad394e6{/stages/pool/json,null,AVAILABLE,@Spark}
19/09/03 13:56:46 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@6058e535{/storage,null,AVAILABLE,@Spark}
19/09/03 13:56:46 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@42deb43a{/storage/json,null,AVAILABLE,@Spark}
19/09/03 13:56:46 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@1deb2c43{/storage/rdd,null,AVAILABLE,@Spark}
19/09/03 13:56:46 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@3bb9efbc{/storage/rdd/json,null,AVAILABLE,@Spark}
19/09/03 13:56:46 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@1cefc4b3{/environment,null,AVAILABLE,@Spark}
19/09/03 13:56:46 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@2b27cc70{/environment/json,null,AVAILABLE,@Spark}
19/09/03 13:56:46 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@6f6a7463{/executors,null,AVAILABLE,@Spark}
19/09/03 13:56:46 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@1bdaa23d{/executors/json,null,AVAILABLE,@Spark}
19/09/03 13:56:46 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@79f227a9{/executors/threadDump,null,AVAILABLE,@Spark}
19/09/03 13:56:46 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@6ca320ab{/executors/threadDump/json,null,AVAILABLE,@Spark}
19/09/03 13:56:46 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@50d68830{/static,null,AVAILABLE,@Spark}
19/09/03 13:56:46 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@33d05366{/,null,AVAILABLE,@Spark}
19/09/03 13:56:46 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@27a0a5a2{/api,null,AVAILABLE,@Spark}
19/09/03 13:56:46 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@106faf11{/jobs/job/kill,null,AVAILABLE,@Spark}
19/09/03 13:56:46 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@70f43b45{/stages/stage/kill,null,AVAILABLE,@Spark}
19/09/03 13:56:46 INFO ui.SparkUI: Bound SparkUI to 0.0.0.0, and started at http://192.168.10.27:4040
19/09/03 13:56:46 INFO spark.SparkContext: Added JAR file:/tmp/adamTestesvklDQ/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/target/adam-assembly-spark2_2.12-0.29.0-SNAPSHOT.jar at spark://192.168.10.27:41843/jars/adam-assembly-spark2_2.12-0.29.0-SNAPSHOT.jar with timestamp 1567544206710
19/09/03 13:56:46 INFO executor.Executor: Starting executor ID driver on host localhost
19/09/03 13:56:46 INFO util.Utils: Successfully started service 'org.apache.spark.network.netty.NettyBlockTransferService' on port 35121.
19/09/03 13:56:46 INFO netty.NettyBlockTransferService: Server created on 192.168.10.27:35121
19/09/03 13:56:46 INFO storage.BlockManager: Using org.apache.spark.storage.RandomBlockReplicationPolicy for block replication policy
19/09/03 13:56:46 INFO storage.BlockManagerMaster: Registering BlockManager BlockManagerId(driver, 192.168.10.27, 35121, None)
19/09/03 13:56:46 INFO storage.BlockManagerMasterEndpoint: Registering block manager 192.168.10.27:35121 with 366.3 MB RAM, BlockManagerId(driver, 192.168.10.27, 35121, None)
19/09/03 13:56:46 INFO storage.BlockManagerMaster: Registered BlockManager BlockManagerId(driver, 192.168.10.27, 35121, None)
19/09/03 13:56:46 INFO storage.BlockManager: Initialized BlockManager: BlockManagerId(driver, 192.168.10.27, 35121, None)
19/09/03 13:56:47 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@5b5c0057{/metrics/json,null,AVAILABLE,@Spark}
19/09/03 13:56:47 INFO rdd.ADAMContext: Loading mouse_chrM.bam.reads.adam as Parquet of AlignmentRecords.
19/09/03 13:56:47 INFO rdd.ADAMContext: Reading the ADAM file at mouse_chrM.bam.reads.adam to create RDD
19/09/03 13:56:47 INFO rdd.ADAMContext: Using the specified projection schema
19/09/03 13:56:48 INFO memory.MemoryStore: Block broadcast_0 stored as values in memory (estimated size 322.5 KB, free 366.0 MB)
19/09/03 13:56:48 INFO memory.MemoryStore: Block broadcast_0_piece0 stored as bytes in memory (estimated size 29.1 KB, free 366.0 MB)
19/09/03 13:56:48 INFO storage.BlockManagerInfo: Added broadcast_0_piece0 in memory on 192.168.10.27:35121 (size: 29.1 KB, free: 366.3 MB)
19/09/03 13:56:48 INFO spark.SparkContext: Created broadcast 0 from newAPIHadoopFile at ADAMContext.scala:1801
19/09/03 13:56:49 INFO input.FileInputFormat: Total input paths to process : 1
19/09/03 13:56:49 INFO hadoop.ParquetInputFormat: Total input paths to process : 1
19/09/03 13:56:49 INFO spark.SparkContext: Starting job: aggregate at FlagStat.scala:115
19/09/03 13:56:49 INFO scheduler.DAGScheduler: Got job 0 (aggregate at FlagStat.scala:115) with 1 output partitions
19/09/03 13:56:49 INFO scheduler.DAGScheduler: Final stage: ResultStage 0 (aggregate at FlagStat.scala:115)
19/09/03 13:56:49 INFO scheduler.DAGScheduler: Parents of final stage: List()
19/09/03 13:56:49 INFO scheduler.DAGScheduler: Missing parents: List()
19/09/03 13:56:49 INFO scheduler.DAGScheduler: Submitting ResultStage 0 (MapPartitionsRDD[4] at map at FlagStat.scala:96), which has no missing parents
19/09/03 13:56:50 INFO memory.MemoryStore: Block broadcast_1 stored as values in memory (estimated size 13.5 KB, free 365.9 MB)
19/09/03 13:56:50 INFO memory.MemoryStore: Block broadcast_1_piece0 stored as bytes in memory (estimated size 5.9 KB, free 365.9 MB)
19/09/03 13:56:50 INFO storage.BlockManagerInfo: Added broadcast_1_piece0 in memory on 192.168.10.27:35121 (size: 5.9 KB, free: 366.3 MB)
19/09/03 13:56:50 INFO spark.SparkContext: Created broadcast 1 from broadcast at DAGScheduler.scala:1161
19/09/03 13:56:50 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))
19/09/03 13:56:50 INFO scheduler.TaskSchedulerImpl: Adding task set 0.0 with 1 tasks
19/09/03 13:56:50 INFO scheduler.TaskSetManager: Starting task 0.0 in stage 0.0 (TID 0, localhost, executor driver, partition 0, PROCESS_LOCAL, 7491 bytes)
19/09/03 13:56:50 INFO executor.Executor: Running task 0.0 in stage 0.0 (TID 0)
19/09/03 13:56:50 INFO executor.Executor: Fetching spark://192.168.10.27:41843/jars/adam-assembly-spark2_2.12-0.29.0-SNAPSHOT.jar with timestamp 1567544206710
19/09/03 13:56:50 INFO client.TransportClientFactory: Successfully created connection to /192.168.10.27:41843 after 32 ms (0 ms spent in bootstraps)
19/09/03 13:56:50 INFO util.Utils: Fetching spark://192.168.10.27:41843/jars/adam-assembly-spark2_2.12-0.29.0-SNAPSHOT.jar to /tmp/spark-a49fcac5-aba7-4f64-9547-7b09a9a6cf24/userFiles-42356c1f-8b9f-4ee5-965b-fc7d9d631adc/fetchFileTemp6665039597218514784.tmp
19/09/03 13:56:50 INFO executor.Executor: Adding file:/tmp/spark-a49fcac5-aba7-4f64-9547-7b09a9a6cf24/userFiles-42356c1f-8b9f-4ee5-965b-fc7d9d631adc/adam-assembly-spark2_2.12-0.29.0-SNAPSHOT.jar to class loader
19/09/03 13:56:50 INFO rdd.NewHadoopRDD: Input split: file:/tmp/adamTestesvklDQ/deleteMePleaseThisIsNoLongerNeeded/mouse_chrM.bam.reads.adam/part-r-00000.gz.parquet:0+10132194
19/09/03 13:56:50 INFO hadoop.InternalParquetRecordReader: RecordReader initialized will read a total of 163064 records.
19/09/03 13:56:50 INFO hadoop.InternalParquetRecordReader: at row 0. reading next block
19/09/03 13:56:50 INFO compress.CodecPool: Got brand-new decompressor [.gz]
19/09/03 13:56:50 INFO hadoop.InternalParquetRecordReader: block read in memory in 20 ms. row count = 163064
19/09/03 13:56:51 INFO executor.Executor: Finished task 0.0 in stage 0.0 (TID 0). 9641 bytes result sent to driver
19/09/03 13:56:51 INFO scheduler.TaskSetManager: Finished task 0.0 in stage 0.0 (TID 0) in 1795 ms on localhost (executor driver) (1/1)
19/09/03 13:56:51 INFO scheduler.TaskSchedulerImpl: Removed TaskSet 0.0, whose tasks have all completed, from pool 
19/09/03 13:56:51 INFO scheduler.DAGScheduler: ResultStage 0 (aggregate at FlagStat.scala:115) finished in 1.920 s
19/09/03 13:56:51 INFO scheduler.DAGScheduler: Job 0 finished: aggregate at FlagStat.scala:115, took 1.989861 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)
19/09/03 13:56:51 INFO cli.FlagStat: Overall Duration: 6.07 secs
19/09/03 13:56:52 INFO cli.FlagStat: Metrics:

Timings
+--------------------------------------+--------------+--------------+-------------+--------+-----------+-----------+-----------+
|                Metric                | Worker Total | Driver Total | Driver Only | Count  |   Mean    |    Min    |    Max    |
+--------------------------------------+--------------+--------------+-------------+--------+-----------+-----------+-----------+
| └─ Load Alignments                   |            - |    2.33 secs |   2.23 secs |      1 | 2.33 secs | 2.33 secs | 2.33 secs |
|     └─ map at ADAMContext.scala:1805 |            - |     97.92 ms |           - |      1 |  97.92 ms |  97.92 ms |  97.92 ms |
|         └─ function call             |     21.73 ms |            - |           - | 163064 |    133 ns |     56 ns | 139.77 µs |
| └─ map at FlagStat.scala:96          |            - |     29.18 ms |           - |      1 |  29.18 ms |  29.18 ms |  29.18 ms |
|     └─ function call                 |    207.69 ms |            - |           - | 163064 |   1.27 µs |    198 ns |   1.09 ms |
| └─ aggregate at FlagStat.scala:115   |            - |     2.1 secs |           - |      1 |  2.1 secs |  2.1 secs |  2.1 secs |
|     └─ function call                 |     56.67 ms |            - |           - | 163065 |    347 ns |     83 ns |  23.88 ms |
+--------------------------------------+--------------+--------------+-------------+--------+-----------+-----------+-----------+

Spark Operations
+----------+---------------------------------+---------------+----------------+--------------+----------+
| Sequence |            Operation            | Is New Stage? | Stage Duration | Driver Total | Stage ID |
+----------+---------------------------------+---------------+----------------+--------------+----------+
| 1        | map at ADAMContext.scala:1805   | false         |              - |     97.92 ms | -        |
| 2        | map at FlagStat.scala:96        | false         |              - |     29.18 ms | -        |
| 3        | aggregate at FlagStat.scala:115 | true          |     -1.92 secs |     2.1 secs | 0        |
+----------+---------------------------------+---------------+----------------+--------------+----------+

Task Timings
+-------------------------------+------------+-------+-----------+-----------+-----------+
|            Metric             | Total Time | Count |   Mean    |    Min    |    Max    |
+-------------------------------+------------+-------+-----------+-----------+-----------+
| Task Duration                 |  1.79 secs |     1 | 1.79 secs | 1.79 secs | 1.79 secs |
| Executor Run Time             |  1.17 secs |     1 | 1.17 secs | 1.17 secs | 1.17 secs |
| Executor Deserialization Time |     523 ms |     1 |    523 ms |    523 ms |    523 ms |
| Result Serialization Time     |          0 |     1 |         0 |         0 |         0 |
+-------------------------------+------------+-------+-----------+-----------+-----------+

Task Timings By Host
+-------------------------------+--------+------------+-------+-----------+-----------+-----------+
|            Metric             |  Host  | Total Time | Count |   Mean    |    Min    |    Max    |
+-------------------------------+--------+------------+-------+-----------+-----------+-----------+
| Task Duration                 | driver |  1.79 secs |     1 | 1.79 secs | 1.79 secs | 1.79 secs |
| Executor Run Time             | driver |  1.17 secs |     1 | 1.17 secs | 1.17 secs | 1.17 secs |
| Executor Deserialization Time | driver |     523 ms |     1 |    523 ms |    523 ms |    523 ms |
| Result Serialization Time     | driver |          0 |     1 |         0 |         0 |         0 |
+-------------------------------+--------+------------+-------+-----------+-----------+-----------+

Task Timings By Stage
+-------------------------------+------------------------------------+------------+-------+-----------+-----------+-----------+
|            Metric             |          Stage ID & Name           | Total Time | Count |   Mean    |    Min    |    Max    |
+-------------------------------+------------------------------------+------------+-------+-----------+-----------+-----------+
| Task Duration                 | 0: aggregate at FlagStat.scala:115 |  1.79 secs |     1 | 1.79 secs | 1.79 secs | 1.79 secs |
| Executor Run Time             | 0: aggregate at FlagStat.scala:115 |  1.17 secs |     1 | 1.17 secs | 1.17 secs | 1.17 secs |
| Executor Deserialization Time | 0: aggregate at FlagStat.scala:115 |     523 ms |     1 |    523 ms |    523 ms |    523 ms |
| Result Serialization Time     | 0: aggregate at FlagStat.scala:115 |          0 |     1 |         0 |         0 |         0 |
+-------------------------------+------------------------------------+------------+-------+-----------+-----------+-----------+

19/09/03 13:56:52 INFO spark.SparkContext: Invoking stop() from shutdown hook
19/09/03 13:56:52 INFO server.AbstractConnector: Stopped Spark@2024293c{HTTP/1.1,[http/1.1]}{0.0.0.0:4040}
19/09/03 13:56:52 INFO ui.SparkUI: Stopped Spark web UI at http://192.168.10.27:4040
19/09/03 13:56:52 INFO spark.MapOutputTrackerMasterEndpoint: MapOutputTrackerMasterEndpoint stopped!
19/09/03 13:56:52 INFO memory.MemoryStore: MemoryStore cleared
19/09/03 13:56:52 INFO storage.BlockManager: BlockManager stopped
19/09/03 13:56:52 INFO storage.BlockManagerMaster: BlockManagerMaster stopped
19/09/03 13:56:52 INFO scheduler.OutputCommitCoordinator$OutputCommitCoordinatorEndpoint: OutputCommitCoordinator stopped!
19/09/03 13:56:52 INFO spark.SparkContext: Successfully stopped SparkContext
19/09/03 13:56:52 INFO util.ShutdownHookManager: Shutdown hook called
19/09/03 13:56:52 INFO util.ShutdownHookManager: Deleting directory /tmp/spark-19cf796d-bf13-4045-b2fe-f36202d391cc
19/09/03 13:56:52 INFO util.ShutdownHookManager: Deleting directory /tmp/spark-a49fcac5-aba7-4f64-9547-7b09a9a6cf24
rm -rf ${ADAM_TMP_DIR}
+ rm -rf /tmp/adamTestesvklDQ/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 [  7.636 s]
[INFO] ADAM_2.11: Shader workaround ....................... SUCCESS [  0.023 s]
[INFO] ADAM_2.11: Avro-to-Dataset codegen utils ........... SUCCESS [  0.060 s]
[INFO] ADAM_2.11: Core .................................... SUCCESS [  4.204 s]
[INFO] ADAM_2.11: APIs for Java, Python ................... SUCCESS [  0.172 s]
[INFO] ADAM_2.11: CLI ..................................... SUCCESS [  0.269 s]
[INFO] ADAM_2.11: Assembly ................................ SUCCESS [  0.015 s]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 12.887 s
[INFO] Finished at: 2019-09-03T13:57:07-07:00
[INFO] Final Memory: 22M/1137M
[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/5804048c1591b549c54410828ad47df186fa1db5
Finished: SUCCESS