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[WARNING] Entry: adam-distribution-spark2_2.11-0.26.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/cli/TransformAlignments$.html longer than 100 characters.
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[WARNING] Entry: adam-distribution-spark2_2.11-0.26.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/cli/TransformVariants.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.26.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/cli/CountReadKmers$.html longer than 100 characters.
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[INFO] Building zip: /tmp/adamTestqsWBwl7/deleteMePleaseThisIsNoLongerNeeded/adam-distribution/target/adam-distribution-spark2_2.11-0.26.0-SNAPSHOT-bin.zip
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary:
[INFO] 
[INFO] ADAM_2.11 .......................................... SUCCESS [  8.576 s]
[INFO] ADAM_2.11: Avro-to-Dataset codegen utils ........... SUCCESS [  4.986 s]
[INFO] ADAM_2.11: Core .................................... SUCCESS [01:18 min]
[INFO] ADAM_2.11: APIs for Java, Python ................... SUCCESS [  8.138 s]
[INFO] ADAM_2.11: CLI ..................................... SUCCESS [ 18.946 s]
[INFO] ADAM_2.11: Assembly ................................ SUCCESS [  8.945 s]
[INFO] ADAM_2.11: Python APIs ............................. SUCCESS [01:08 min]
[INFO] ADAM_2.11: R APIs .................................. SUCCESS [01:08 min]
[INFO] ADAM_2.11: Distribution ............................ SUCCESS [ 49.512 s]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 05:15 min
[INFO] Finished at: 2019-02-13T16:08:52-08:00
[INFO] Final Memory: 91M/1421M
[INFO] ------------------------------------------------------------------------
+ grep bdgenomics.adam
+ tar tzvf adam-distribution/target/adam-distribution-spark2_2.11-0.26.0-SNAPSHOT-bin.tar.gz
+ grep egg
drwxrwxr-x jenkins/jenkins        0 2019-02-13 16:05 adam-distribution-spark2_2.11-0.26.0-SNAPSHOT/r/bdgenomics.adam.egg-info/
-rw-r--r-- jenkins/jenkins 36268341 2019-02-13 16:05 adam-distribution-spark2_2.11-0.26.0-SNAPSHOT/repo/bdgenomics.adam-0.25.0a0-py3.6.egg
+ ./bin/pyadam
Using PYSPARK=/tmp/adamTestqsWBwl7/deleteMePleaseThisIsNoLongerNeeded/spark-2.2.3-bin-hadoop2.7/bin/pyspark
Setting default log level to "WARN".
To adjust logging level use sc.setLogLevel(newLevel). For SparkR, use setLogLevel(newLevel).
2019-02-13 16:08:56 WARN  Utils:66 - Your hostname, amp-jenkins-staging-worker-01 resolves to a loopback address: 127.0.1.1; using 192.168.10.31 instead (on interface eno1)
2019-02-13 16:08:56 WARN  Utils:66 - Set SPARK_LOCAL_IP if you need to bind to another address
2019-02-13 16:08:56 WARN  NativeCodeLoader:62 - Unable to load native-hadoop library for your platform... using builtin-java classes where applicable
2019-02-13 16:09:03 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.
+ 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-2f811c44-f012-424e-9171-2d81b126372b/bin/deactivate
++ _SHELL=bash
_CONDA_DIR=$(dirname "$_SCRIPT_LOCATION")
dirname "$_SCRIPT_LOCATION"
+++ dirname /home/jenkins/anaconda2/envs/adam-build-2f811c44-f012-424e-9171-2d81b126372b/bin/deactivate
++ _CONDA_DIR=/home/jenkins/anaconda2/envs/adam-build-2f811c44-f012-424e-9171-2d81b126372b/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/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.2.3/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 $?
fi
++ ((  0 == 0  ))
++ _CONDA_D=/home/jenkins/anaconda2/envs/adam-build-2f811c44-f012-424e-9171-2d81b126372b/etc/conda/deactivate.d
++ [[ -d /home/jenkins/anaconda2/envs/adam-build-2f811c44-f012-424e-9171-2d81b126372b/etc/conda/deactivate.d ]]
"$_CONDA_DIR/conda" ..deactivate.path $_SHELL$EXT "$CONDA_PREFIX"
+++ /home/jenkins/anaconda2/envs/adam-build-2f811c44-f012-424e-9171-2d81b126372b/bin/conda ..deactivate.path bash /home/jenkins/anaconda2/envs/adam-build-2f811c44-f012-424e-9171-2d81b126372b
++ 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 -n adam-build-2f811c44-f012-424e-9171-2d81b126372b --all

Package plan for package removal in environment /home/jenkins/anaconda2/envs/adam-build-2f811c44-f012-424e-9171-2d81b126372b:

The following packages will be REMOVED:

    ca-certificates: 2019.1.23-0            
    certifi:         2018.11.29-py36_0      
    libedit:         3.1.20181209-hc058e9b_0
    libffi:          3.2.1-hd88cf55_4       
    libgcc-ng:       8.2.0-hdf63c60_1       
    libstdcxx-ng:    8.2.0-hdf63c60_1       
    ncurses:         6.1-he6710b0_1         
    openssl:         1.1.1a-h7b6447c_0      
    pip:             19.0.1-py36_0          
    python:          3.6.8-h0371630_0       
    readline:        7.0-h7b6447c_5         
    setuptools:      40.7.3-py36_0          
    sqlite:          3.26.0-h7b6447c_0      
    tk:              8.6.8-hbc83047_0       
    wheel:           0.32.3-py36_0          
    xz:              5.2.4-h14c3975_4       
    zlib:            1.2.11-h7b6447c_3      

Proceed ([y]/n)? 
+ cp -r adam-python/target /home/jenkins/workspace/ADAM/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.2.3/label/ubuntu/scripts/../adam-python/
+ pushd adam-python
/tmp/adamTestqsWBwl7/deleteMePleaseThisIsNoLongerNeeded/adam-python /tmp/adamTestqsWBwl7/deleteMePleaseThisIsNoLongerNeeded ~/workspace/ADAM/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.2.3/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/adamTestqsWBwl7/deleteMePleaseThisIsNoLongerNeeded ~/workspace/ADAM/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.2.3/label/ubuntu
+ BAM=mouse_chrM.bam
+ READS=mouse_chrM.bam.reads.adam
+ SORTED_READS=mouse_chrM.bam.reads.sorted.adam
+ FRAGMENTS=mouse_chrM.bam.fragments.adam
+ echo 'Fetching BAM file'
Fetching BAM file
+ rm -rf mouse_chrM.bam
+ wget -q https://s3.amazonaws.com/bdgenomics-test/mouse_chrM.bam
+ echo 'Converting BAM to ADAM read format'
Converting BAM to ADAM read format
+ rm -rf mouse_chrM.bam.reads.adam
+ ./bin/adam-submit transformAlignments mouse_chrM.bam mouse_chrM.bam.reads.adam
Using ADAM_MAIN=org.bdgenomics.adam.cli.ADAMMain
Using spark-submit=/tmp/adamTestqsWBwl7/deleteMePleaseThisIsNoLongerNeeded/spark-2.2.3-bin-hadoop2.7/bin/spark-submit
log4j:WARN No appenders could be found for logger (org.bdgenomics.adam.cli.ADAMMain).
log4j:WARN Please initialize the log4j system properly.
log4j:WARN See http://logging.apache.org/log4j/1.2/faq.html#noconfig for more info.
Using Spark's default log4j profile: org/apache/spark/log4j-defaults.properties
19/02/13 16:09:48 INFO SparkContext: Running Spark version 2.2.3
19/02/13 16:09:49 WARN NativeCodeLoader: Unable to load native-hadoop library for your platform... using builtin-java classes where applicable
19/02/13 16:09:49 WARN Utils: Your hostname, amp-jenkins-staging-worker-01 resolves to a loopback address: 127.0.1.1; using 192.168.10.31 instead (on interface eno1)
19/02/13 16:09:49 WARN Utils: Set SPARK_LOCAL_IP if you need to bind to another address
19/02/13 16:09:49 INFO SparkContext: Submitted application: transformAlignments
19/02/13 16:09:49 INFO SecurityManager: Changing view acls to: jenkins
19/02/13 16:09:49 INFO SecurityManager: Changing modify acls to: jenkins
19/02/13 16:09:49 INFO SecurityManager: Changing view acls groups to: 
19/02/13 16:09:49 INFO SecurityManager: Changing modify acls groups to: 
19/02/13 16:09:49 INFO SecurityManager: SecurityManager: authentication disabled; ui acls disabled; users  with view permissions: Set(jenkins); groups with view permissions: Set(); users  with modify permissions: Set(jenkins); groups with modify permissions: Set()
19/02/13 16:09:49 INFO Utils: Successfully started service 'sparkDriver' on port 38037.
19/02/13 16:09:49 INFO SparkEnv: Registering MapOutputTracker
19/02/13 16:09:49 INFO SparkEnv: Registering BlockManagerMaster
19/02/13 16:09:49 INFO BlockManagerMasterEndpoint: Using org.apache.spark.storage.DefaultTopologyMapper for getting topology information
19/02/13 16:09:49 INFO BlockManagerMasterEndpoint: BlockManagerMasterEndpoint up
19/02/13 16:09:49 INFO DiskBlockManager: Created local directory at /tmp/blockmgr-9ecf3b83-efb2-40c0-b8b8-f7ccaaaaac0f
19/02/13 16:09:49 INFO MemoryStore: MemoryStore started with capacity 366.3 MB
19/02/13 16:09:49 INFO SparkEnv: Registering OutputCommitCoordinator
19/02/13 16:09:50 INFO Utils: Successfully started service 'SparkUI' on port 4040.
19/02/13 16:09:50 INFO SparkUI: Bound SparkUI to 0.0.0.0, and started at http://192.168.10.31:4040
19/02/13 16:09:50 INFO SparkContext: Added JAR file:/tmp/adamTestqsWBwl7/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/target/adam-assembly-spark2_2.11-0.26.0-SNAPSHOT.jar at spark://192.168.10.31:38037/jars/adam-assembly-spark2_2.11-0.26.0-SNAPSHOT.jar with timestamp 1550102990304
19/02/13 16:09:50 INFO Executor: Starting executor ID driver on host localhost
19/02/13 16:09:50 INFO Utils: Successfully started service 'org.apache.spark.network.netty.NettyBlockTransferService' on port 33617.
19/02/13 16:09:50 INFO NettyBlockTransferService: Server created on 192.168.10.31:33617
19/02/13 16:09:50 INFO BlockManager: Using org.apache.spark.storage.RandomBlockReplicationPolicy for block replication policy
19/02/13 16:09:50 INFO BlockManagerMaster: Registering BlockManager BlockManagerId(driver, 192.168.10.31, 33617, None)
19/02/13 16:09:50 INFO BlockManagerMasterEndpoint: Registering block manager 192.168.10.31:33617 with 366.3 MB RAM, BlockManagerId(driver, 192.168.10.31, 33617, None)
19/02/13 16:09:50 INFO BlockManagerMaster: Registered BlockManager BlockManagerId(driver, 192.168.10.31, 33617, None)
19/02/13 16:09:50 INFO BlockManager: Initialized BlockManager: BlockManagerId(driver, 192.168.10.31, 33617, None)
19/02/13 16:09:50 INFO ADAMContext: Loading mouse_chrM.bam as BAM/CRAM/SAM and converting to AlignmentRecords.
19/02/13 16:09:51 INFO ADAMContext: Loaded header from file:/tmp/adamTestqsWBwl7/deleteMePleaseThisIsNoLongerNeeded/mouse_chrM.bam
19/02/13 16:09:51 INFO MemoryStore: Block broadcast_0 stored as values in memory (estimated size 284.1 KB, free 366.0 MB)
19/02/13 16:09:51 INFO MemoryStore: Block broadcast_0_piece0 stored as bytes in memory (estimated size 23.1 KB, free 366.0 MB)
19/02/13 16:09:51 INFO BlockManagerInfo: Added broadcast_0_piece0 in memory on 192.168.10.31:33617 (size: 23.1 KB, free: 366.3 MB)
19/02/13 16:09:52 INFO SparkContext: Created broadcast 0 from newAPIHadoopFile at ADAMContext.scala:1579
19/02/13 16:09:53 INFO RDDBoundAlignmentRecordDataset: Saving data in ADAM format
19/02/13 16:09:53 INFO FileOutputCommitter: File Output Committer Algorithm version is 1
19/02/13 16:09:53 INFO FileInputFormat: Total input paths to process : 1
19/02/13 16:09:53 INFO SparkContext: Starting job: runJob at SparkHadoopMapReduceWriter.scala:88
19/02/13 16:09:53 INFO DAGScheduler: Got job 0 (runJob at SparkHadoopMapReduceWriter.scala:88) with 1 output partitions
19/02/13 16:09:53 INFO DAGScheduler: Final stage: ResultStage 0 (runJob at SparkHadoopMapReduceWriter.scala:88)
19/02/13 16:09:53 INFO DAGScheduler: Parents of final stage: List()
19/02/13 16:09:53 INFO DAGScheduler: Missing parents: List()
19/02/13 16:09:53 INFO DAGScheduler: Submitting ResultStage 0 (MapPartitionsRDD[2] at map at GenomicDataset.scala:3813), which has no missing parents
19/02/13 16:09:53 INFO MemoryStore: Block broadcast_1 stored as values in memory (estimated size 81.6 KB, free 365.9 MB)
19/02/13 16:09:53 INFO MemoryStore: Block broadcast_1_piece0 stored as bytes in memory (estimated size 29.9 KB, free 365.9 MB)
19/02/13 16:09:53 INFO BlockManagerInfo: Added broadcast_1_piece0 in memory on 192.168.10.31:33617 (size: 29.9 KB, free: 366.2 MB)
19/02/13 16:09:53 INFO SparkContext: Created broadcast 1 from broadcast at DAGScheduler.scala:1004
19/02/13 16:09:53 INFO DAGScheduler: Submitting 1 missing tasks from ResultStage 0 (MapPartitionsRDD[2] at map at GenomicDataset.scala:3813) (first 15 tasks are for partitions Vector(0))
19/02/13 16:09:53 INFO TaskSchedulerImpl: Adding task set 0.0 with 1 tasks
19/02/13 16:09:53 INFO TaskSetManager: Starting task 0.0 in stage 0.0 (TID 0, localhost, executor driver, partition 0, PROCESS_LOCAL, 4921 bytes)
19/02/13 16:09:53 INFO Executor: Running task 0.0 in stage 0.0 (TID 0)
19/02/13 16:09:53 INFO Executor: Fetching spark://192.168.10.31:38037/jars/adam-assembly-spark2_2.11-0.26.0-SNAPSHOT.jar with timestamp 1550102990304
19/02/13 16:09:53 INFO TransportClientFactory: Successfully created connection to /192.168.10.31:38037 after 35 ms (0 ms spent in bootstraps)
19/02/13 16:09:53 INFO Utils: Fetching spark://192.168.10.31:38037/jars/adam-assembly-spark2_2.11-0.26.0-SNAPSHOT.jar to /tmp/spark-7976aca1-fc76-46b6-ae00-66fce3d4cac2/userFiles-ae80e465-0d0c-49fc-8910-e388be50a52e/fetchFileTemp5247717320207479560.tmp
19/02/13 16:09:53 INFO Executor: Adding file:/tmp/spark-7976aca1-fc76-46b6-ae00-66fce3d4cac2/userFiles-ae80e465-0d0c-49fc-8910-e388be50a52e/adam-assembly-spark2_2.11-0.26.0-SNAPSHOT.jar to class loader
19/02/13 16:09:53 INFO NewHadoopRDD: Input split: file:/tmp/adamTestqsWBwl7/deleteMePleaseThisIsNoLongerNeeded/mouse_chrM.bam:83361792-833134657535
19/02/13 16:09:53 INFO FileOutputCommitter: File Output Committer Algorithm version is 1
19/02/13 16:09:53 INFO CodecConfig: Compression: GZIP
19/02/13 16:09:53 INFO FileOutputCommitter: File Output Committer Algorithm version is 1
19/02/13 16:09:53 INFO ParquetOutputFormat: Parquet block size to 134217728
19/02/13 16:09:53 INFO ParquetOutputFormat: Parquet page size to 1048576
19/02/13 16:09:53 INFO ParquetOutputFormat: Parquet dictionary page size to 1048576
19/02/13 16:09:53 INFO ParquetOutputFormat: Dictionary is on
19/02/13 16:09:53 INFO ParquetOutputFormat: Validation is off
19/02/13 16:09:53 INFO ParquetOutputFormat: Writer version is: PARQUET_1_0
19/02/13 16:09:53 INFO ParquetOutputFormat: Maximum row group padding size is 0 bytes
19/02/13 16:09:53 INFO ParquetOutputFormat: Page size checking is: estimated
19/02/13 16:09:53 INFO ParquetOutputFormat: Min row count for page size check is: 100
19/02/13 16:09:53 INFO ParquetOutputFormat: Max row count for page size check is: 10000
19/02/13 16:09:53 INFO CodecPool: Got brand-new compressor [.gz]
Ignoring SAM validation error: ERROR: Record 162622, Read name 613F0AAXX100423:3:58:9979:16082, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162624, Read name 613F0AAXX100423:6:13:3141:11793, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162625, Read name 613F0AAXX100423:8:39:18592:13552, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162635, Read name 613F1AAXX100423:7:2:13114:10698, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162637, Read name 613F1AAXX100423:6:100:8840:11167, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162639, Read name 613F1AAXX100423:8:15:10944:11181, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162640, Read name 613F1AAXX100423:8:17:5740:10104, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162651, Read name 613F1AAXX100423:1:53:11097:8261, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162654, Read name 613F1AAXX100423:2:112:16779:19612, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162657, Read name 613F0AAXX100423:8:28:7084:17683, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162659, Read name 613F0AAXX100423:8:39:19796:12794, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162662, Read name 613F1AAXX100423:5:116:9339:3264, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162667, Read name 613F0AAXX100423:4:67:2015:3054, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162669, Read name 613F0AAXX100423:7:7:11297:11738, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162674, Read name 613F0AAXX100423:6:59:10490:20829, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162678, Read name 613F1AAXX100423:8:11:17603:4766, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162682, Read name 613F0AAXX100423:5:86:10814:10257, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162683, Read name 613F0AAXX100423:5:117:14178:6111, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162685, Read name 613F0AAXX100423:2:3:13563:6720, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162689, Read name 613F0AAXX100423:7:59:16009:15799, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162696, Read name 613F0AAXX100423:5:31:9663:18252, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162698, Read name 613F1AAXX100423:2:27:12264:14626, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162699, Read name 613F0AAXX100423:1:120:19003:6647, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162702, Read name 613F1AAXX100423:3:37:6972:18407, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162704, Read name 613F1AAXX100423:3:77:6946:3880, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162706, Read name 613F0AAXX100423:7:48:2692:3492, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162708, Read name 613F1AAXX100423:7:80:8790:1648, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162710, Read name 6141AAAXX100423:5:30:15036:17610, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162712, Read name 613F1AAXX100423:8:80:6261:4465, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162713, Read name 6141AAAXX100423:5:74:5542:6195, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162715, Read name 613F1AAXX100423:5:14:14844:13639, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162718, Read name 613F1AAXX100423:7:112:14569:8480, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162725, Read name 613F1AAXX100423:4:56:10160:9879, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162727, Read name 6141AAAXX100423:7:89:12209:9221, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162731, Read name 6141AAAXX100423:6:55:1590:19793, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162732, Read name 6141AAAXX100423:7:102:16679:12368, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162734, Read name 613F1AAXX100423:2:7:4909:18472, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162737, Read name 6141AAAXX100423:4:73:6574:10572, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162741, Read name 6141AAAXX100423:1:8:14113:12655, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162743, Read name 6141AAAXX100423:3:40:7990:5056, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162744, Read name 6141AAAXX100423:4:36:15793:3411, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162745, Read name 6141AAAXX100423:8:83:1139:18985, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162746, Read name 6141AAAXX100423:5:7:18196:13562, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162748, Read name 6141AAAXX100423:3:114:5639:7123, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162751, Read name 6141AAAXX100423:7:47:4898:8640, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162753, Read name 6141AAAXX100423:3:64:8064:8165, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162756, Read name 613F1AAXX100423:1:105:14386:1684, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162757, Read name 613F1AAXX100423:6:98:1237:19470, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162761, Read name 613F1AAXX100423:7:106:19658:9261, MAPQ should be 0 for unmapped read.
19/02/13 16:10:05 INFO InternalParquetRecordWriter: Flushing mem columnStore to file. allocated memory: 16415387
19/02/13 16:10:06 INFO FileOutputCommitter: Saved output of task 'attempt_20190213160953_0002_r_000000_0' to file:/tmp/adamTestqsWBwl7/deleteMePleaseThisIsNoLongerNeeded/mouse_chrM.bam.reads.adam/_temporary/0/task_20190213160953_0002_r_000000
19/02/13 16:10:06 INFO SparkHadoopMapRedUtil: attempt_20190213160953_0002_r_000000_0: Committed
19/02/13 16:10:06 INFO Executor: Finished task 0.0 in stage 0.0 (TID 0). 842 bytes result sent to driver
19/02/13 16:10:06 INFO TaskSetManager: Finished task 0.0 in stage 0.0 (TID 0) in 12956 ms on localhost (executor driver) (1/1)
19/02/13 16:10:06 INFO TaskSchedulerImpl: Removed TaskSet 0.0, whose tasks have all completed, from pool 
19/02/13 16:10:06 INFO DAGScheduler: ResultStage 0 (runJob at SparkHadoopMapReduceWriter.scala:88) finished in 12.978 s
19/02/13 16:10:06 INFO DAGScheduler: Job 0 finished: runJob at SparkHadoopMapReduceWriter.scala:88, took 13.135724 s
19/02/13 16:10:06 INFO ParquetFileReader: Initiating action with parallelism: 5
19/02/13 16:10:06 INFO SparkHadoopMapReduceWriter: Job job_20190213160953_0002 committed.
19/02/13 16:10:06 INFO TransformAlignments: Overall Duration: 18.04 secs
19/02/13 16:10:06 INFO SparkContext: Invoking stop() from shutdown hook
19/02/13 16:10:06 INFO SparkUI: Stopped Spark web UI at http://192.168.10.31:4040
19/02/13 16:10:06 INFO MapOutputTrackerMasterEndpoint: MapOutputTrackerMasterEndpoint stopped!
19/02/13 16:10:06 INFO MemoryStore: MemoryStore cleared
19/02/13 16:10:06 INFO BlockManager: BlockManager stopped
19/02/13 16:10:06 INFO BlockManagerMaster: BlockManagerMaster stopped
19/02/13 16:10:06 INFO OutputCommitCoordinator$OutputCommitCoordinatorEndpoint: OutputCommitCoordinator stopped!
19/02/13 16:10:06 INFO SparkContext: Successfully stopped SparkContext
19/02/13 16:10:06 INFO ShutdownHookManager: Shutdown hook called
19/02/13 16:10:06 INFO ShutdownHookManager: Deleting directory /tmp/spark-7976aca1-fc76-46b6-ae00-66fce3d4cac2
+ echo 'Converting BAM to ADAM read format with sorting'
Converting BAM to ADAM read format with sorting
+ rm -rf mouse_chrM.bam.reads.sorted.adam
+ ./bin/adam-submit transformAlignments -sort_reads mouse_chrM.bam.reads.adam mouse_chrM.bam.reads.sorted.adam
Using ADAM_MAIN=org.bdgenomics.adam.cli.ADAMMain
Using spark-submit=/tmp/adamTestqsWBwl7/deleteMePleaseThisIsNoLongerNeeded/spark-2.2.3-bin-hadoop2.7/bin/spark-submit
log4j:WARN No appenders could be found for logger (org.bdgenomics.adam.cli.ADAMMain).
log4j:WARN Please initialize the log4j system properly.
log4j:WARN See http://logging.apache.org/log4j/1.2/faq.html#noconfig for more info.
Using Spark's default log4j profile: org/apache/spark/log4j-defaults.properties
19/02/13 16:10:08 INFO SparkContext: Running Spark version 2.2.3
19/02/13 16:10:08 WARN NativeCodeLoader: Unable to load native-hadoop library for your platform... using builtin-java classes where applicable
19/02/13 16:10:08 WARN Utils: Your hostname, amp-jenkins-staging-worker-01 resolves to a loopback address: 127.0.1.1; using 192.168.10.31 instead (on interface eno1)
19/02/13 16:10:08 WARN Utils: Set SPARK_LOCAL_IP if you need to bind to another address
19/02/13 16:10:09 INFO SparkContext: Submitted application: transformAlignments
19/02/13 16:10:09 INFO SecurityManager: Changing view acls to: jenkins
19/02/13 16:10:09 INFO SecurityManager: Changing modify acls to: jenkins
19/02/13 16:10:09 INFO SecurityManager: Changing view acls groups to: 
19/02/13 16:10:09 INFO SecurityManager: Changing modify acls groups to: 
19/02/13 16:10:09 INFO SecurityManager: SecurityManager: authentication disabled; ui acls disabled; users  with view permissions: Set(jenkins); groups with view permissions: Set(); users  with modify permissions: Set(jenkins); groups with modify permissions: Set()
19/02/13 16:10:09 INFO Utils: Successfully started service 'sparkDriver' on port 40947.
19/02/13 16:10:09 INFO SparkEnv: Registering MapOutputTracker
19/02/13 16:10:09 INFO SparkEnv: Registering BlockManagerMaster
19/02/13 16:10:09 INFO BlockManagerMasterEndpoint: Using org.apache.spark.storage.DefaultTopologyMapper for getting topology information
19/02/13 16:10:09 INFO BlockManagerMasterEndpoint: BlockManagerMasterEndpoint up
19/02/13 16:10:09 INFO DiskBlockManager: Created local directory at /tmp/blockmgr-36dc0da3-5202-4a93-bad4-7ca3f9c3bcac
19/02/13 16:10:09 INFO MemoryStore: MemoryStore started with capacity 366.3 MB
19/02/13 16:10:09 INFO SparkEnv: Registering OutputCommitCoordinator
19/02/13 16:10:09 INFO Utils: Successfully started service 'SparkUI' on port 4040.
19/02/13 16:10:09 INFO SparkUI: Bound SparkUI to 0.0.0.0, and started at http://192.168.10.31:4040
19/02/13 16:10:10 INFO SparkContext: Added JAR file:/tmp/adamTestqsWBwl7/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/target/adam-assembly-spark2_2.11-0.26.0-SNAPSHOT.jar at spark://192.168.10.31:40947/jars/adam-assembly-spark2_2.11-0.26.0-SNAPSHOT.jar with timestamp 1550103010013
19/02/13 16:10:10 INFO Executor: Starting executor ID driver on host localhost
19/02/13 16:10:10 INFO Utils: Successfully started service 'org.apache.spark.network.netty.NettyBlockTransferService' on port 40003.
19/02/13 16:10:10 INFO NettyBlockTransferService: Server created on 192.168.10.31:40003
19/02/13 16:10:10 INFO BlockManager: Using org.apache.spark.storage.RandomBlockReplicationPolicy for block replication policy
19/02/13 16:10:10 INFO BlockManagerMaster: Registering BlockManager BlockManagerId(driver, 192.168.10.31, 40003, None)
19/02/13 16:10:10 INFO BlockManagerMasterEndpoint: Registering block manager 192.168.10.31:40003 with 366.3 MB RAM, BlockManagerId(driver, 192.168.10.31, 40003, None)
19/02/13 16:10:10 INFO BlockManagerMaster: Registered BlockManager BlockManagerId(driver, 192.168.10.31, 40003, None)
19/02/13 16:10:10 INFO BlockManager: Initialized BlockManager: BlockManagerId(driver, 192.168.10.31, 40003, None)
19/02/13 16:10:10 INFO ADAMContext: Loading mouse_chrM.bam.reads.adam as Parquet of AlignmentRecords.
19/02/13 16:10:12 INFO ADAMContext: Reading the ADAM file at mouse_chrM.bam.reads.adam to create RDD
19/02/13 16:10:12 INFO MemoryStore: Block broadcast_0 stored as values in memory (estimated size 303.5 KB, free 366.0 MB)
19/02/13 16:10:13 INFO MemoryStore: Block broadcast_0_piece0 stored as bytes in memory (estimated size 27.3 KB, free 366.0 MB)
19/02/13 16:10:13 INFO BlockManagerInfo: Added broadcast_0_piece0 in memory on 192.168.10.31:40003 (size: 27.3 KB, free: 366.3 MB)
19/02/13 16:10:13 INFO SparkContext: Created broadcast 0 from newAPIHadoopFile at ADAMContext.scala:1319
19/02/13 16:10:13 INFO TransformAlignments: Sorting reads
19/02/13 16:10:13 INFO RDDBoundAlignmentRecordDataset: Sorting reads by reference index, using SequenceDictionary{
chrM->16299, 0
chr1->194532772, 1
chr2->181993374, 2
chr3->159377569, 3
chr4->155544171, 4
chr5->151694555, 5
chr6->149307077, 6
chr7->142600211, 7
chr8->129558836, 8
chr9->124827824, 9
chr10->130854437, 10
chr11->122260198, 11
chr12->119596406, 12
chr13->120421117, 13
chr14->124162362, 14
chr15->104036045, 15
chr16->98095624, 16
chr17->95052499, 17
chr18->90827538, 18
chr19->61533103, 19
chrX->170682864, 20
chrY->91744698, 21
chr1_GL456210_random->169725, 22
chr1_GL456211_random->241735, 23
chr1_GL456212_random->153618, 24
chr1_GL456213_random->39340, 25
chr1_GL456221_random->206961, 26
chr4_GL456216_random->66673, 27
chr4_GL456350_random->227966, 28
chr4_JH584292_random->14945, 29
chr4_JH584293_random->207968, 30
chr4_JH584294_random->191905, 31
chr4_JH584295_random->1976, 32
chr5_GL456354_random->195993, 33
chr5_JH584296_random->199368, 34
chr5_JH584297_random->205776, 35
chr5_JH584298_random->184189, 36
chr5_JH584299_random->953012, 37
chr7_GL456219_random->175968, 38
chrUn_GL456239->40056, 39
chrUn_GL456359->22974, 40
chrUn_GL456360->31704, 41
chrUn_GL456366->47073, 42
chrUn_GL456367->42057, 43
chrUn_GL456368->20208, 44
chrUn_GL456370->26764, 45
chrUn_GL456372->28664, 46
chrUn_GL456378->31602, 47
chrUn_GL456379->72385, 48
chrUn_GL456381->25871, 49
chrUn_GL456382->23158, 50
chrUn_GL456383->38659, 51
chrUn_GL456385->35240, 52
chrUn_GL456387->24685, 53
chrUn_GL456389->28772, 54
chrUn_GL456390->24668, 55
chrUn_GL456392->23629, 56
chrUn_GL456393->55711, 57
chrUn_GL456394->24323, 58
chrUn_GL456396->21240, 59
chrUn_JH584304->114452, 60
chrX_GL456233_random->336933, 61
chrY_JH584300_random->182347, 62
chrY_JH584301_random->259875, 63
chrY_JH584302_random->155838, 64
chrY_JH584303_random->158099, 65}.
19/02/13 16:10:13 INFO FileInputFormat: Total input paths to process : 1
19/02/13 16:10:13 INFO ParquetInputFormat: Total input paths to process : 1
19/02/13 16:10:13 INFO RDDBoundAlignmentRecordDataset: Saving data in ADAM format
19/02/13 16:10:13 INFO FileOutputCommitter: File Output Committer Algorithm version is 1
19/02/13 16:10:13 INFO SparkContext: Starting job: runJob at SparkHadoopMapReduceWriter.scala:88
19/02/13 16:10:13 INFO DAGScheduler: Registering RDD 2 (sortBy at AlignmentRecordDataset.scala:997)
19/02/13 16:10:13 INFO DAGScheduler: Got job 0 (runJob at SparkHadoopMapReduceWriter.scala:88) with 1 output partitions
19/02/13 16:10:13 INFO DAGScheduler: Final stage: ResultStage 1 (runJob at SparkHadoopMapReduceWriter.scala:88)
19/02/13 16:10:13 INFO DAGScheduler: Parents of final stage: List(ShuffleMapStage 0)
19/02/13 16:10:13 INFO DAGScheduler: Missing parents: List(ShuffleMapStage 0)
19/02/13 16:10:13 INFO DAGScheduler: Submitting ShuffleMapStage 0 (MapPartitionsRDD[2] at sortBy at AlignmentRecordDataset.scala:997), which has no missing parents
19/02/13 16:10:13 INFO MemoryStore: Block broadcast_1 stored as values in memory (estimated size 15.1 KB, free 366.0 MB)
19/02/13 16:10:13 INFO MemoryStore: Block broadcast_1_piece0 stored as bytes in memory (estimated size 6.8 KB, free 366.0 MB)
19/02/13 16:10:13 INFO BlockManagerInfo: Added broadcast_1_piece0 in memory on 192.168.10.31:40003 (size: 6.8 KB, free: 366.3 MB)
19/02/13 16:10:13 INFO SparkContext: Created broadcast 1 from broadcast at DAGScheduler.scala:1004
19/02/13 16:10:13 INFO DAGScheduler: Submitting 1 missing tasks from ShuffleMapStage 0 (MapPartitionsRDD[2] at sortBy at AlignmentRecordDataset.scala:997) (first 15 tasks are for partitions Vector(0))
19/02/13 16:10:13 INFO TaskSchedulerImpl: Adding task set 0.0 with 1 tasks
19/02/13 16:10:13 INFO TaskSetManager: Starting task 0.0 in stage 0.0 (TID 0, localhost, executor driver, partition 0, PROCESS_LOCAL, 4960 bytes)
19/02/13 16:10:13 INFO Executor: Running task 0.0 in stage 0.0 (TID 0)
19/02/13 16:10:13 INFO Executor: Fetching spark://192.168.10.31:40947/jars/adam-assembly-spark2_2.11-0.26.0-SNAPSHOT.jar with timestamp 1550103010013
19/02/13 16:10:13 INFO TransportClientFactory: Successfully created connection to /192.168.10.31:40947 after 31 ms (0 ms spent in bootstraps)
19/02/13 16:10:13 INFO Utils: Fetching spark://192.168.10.31:40947/jars/adam-assembly-spark2_2.11-0.26.0-SNAPSHOT.jar to /tmp/spark-093b5e7f-77b9-45e0-b46d-d2d760818233/userFiles-b4727445-4052-4586-a4ea-cb98b57542fc/fetchFileTemp5788733949708269740.tmp
19/02/13 16:10:13 INFO Executor: Adding file:/tmp/spark-093b5e7f-77b9-45e0-b46d-d2d760818233/userFiles-b4727445-4052-4586-a4ea-cb98b57542fc/adam-assembly-spark2_2.11-0.26.0-SNAPSHOT.jar to class loader
19/02/13 16:10:13 INFO NewHadoopRDD: Input split: file:/tmp/adamTestqsWBwl7/deleteMePleaseThisIsNoLongerNeeded/mouse_chrM.bam.reads.adam/part-r-00000.gz.parquet:0+10131504
19/02/13 16:10:13 INFO InternalParquetRecordReader: RecordReader initialized will read a total of 163064 records.
19/02/13 16:10:13 INFO InternalParquetRecordReader: at row 0. reading next block
19/02/13 16:10:13 INFO CodecPool: Got brand-new decompressor [.gz]
19/02/13 16:10:13 INFO InternalParquetRecordReader: block read in memory in 42 ms. row count = 163064
19/02/13 16:10:17 INFO Executor: Finished task 0.0 in stage 0.0 (TID 0). 956 bytes result sent to driver
19/02/13 16:10:17 INFO TaskSetManager: Finished task 0.0 in stage 0.0 (TID 0) in 3558 ms on localhost (executor driver) (1/1)
19/02/13 16:10:17 INFO TaskSchedulerImpl: Removed TaskSet 0.0, whose tasks have all completed, from pool 
19/02/13 16:10:17 INFO DAGScheduler: ShuffleMapStage 0 (sortBy at AlignmentRecordDataset.scala:997) finished in 3.583 s
19/02/13 16:10:17 INFO DAGScheduler: looking for newly runnable stages
19/02/13 16:10:17 INFO DAGScheduler: running: Set()
19/02/13 16:10:17 INFO DAGScheduler: waiting: Set(ResultStage 1)
19/02/13 16:10:17 INFO DAGScheduler: failed: Set()
19/02/13 16:10:17 INFO DAGScheduler: Submitting ResultStage 1 (MapPartitionsRDD[5] at map at GenomicDataset.scala:3813), which has no missing parents
19/02/13 16:10:17 INFO MemoryStore: Block broadcast_2 stored as values in memory (estimated size 82.8 KB, free 365.9 MB)
19/02/13 16:10:17 INFO MemoryStore: Block broadcast_2_piece0 stored as bytes in memory (estimated size 30.6 KB, free 365.8 MB)
19/02/13 16:10:17 INFO BlockManagerInfo: Added broadcast_2_piece0 in memory on 192.168.10.31:40003 (size: 30.6 KB, free: 366.2 MB)
19/02/13 16:10:17 INFO SparkContext: Created broadcast 2 from broadcast at DAGScheduler.scala:1004
19/02/13 16:10:17 INFO DAGScheduler: Submitting 1 missing tasks from ResultStage 1 (MapPartitionsRDD[5] at map at GenomicDataset.scala:3813) (first 15 tasks are for partitions Vector(0))
19/02/13 16:10:17 INFO TaskSchedulerImpl: Adding task set 1.0 with 1 tasks
19/02/13 16:10:17 INFO TaskSetManager: Starting task 0.0 in stage 1.0 (TID 1, localhost, executor driver, partition 0, ANY, 4621 bytes)
19/02/13 16:10:17 INFO Executor: Running task 0.0 in stage 1.0 (TID 1)
19/02/13 16:10:17 INFO ShuffleBlockFetcherIterator: Getting 1 non-empty blocks out of 1 blocks
19/02/13 16:10:17 INFO ShuffleBlockFetcherIterator: Started 0 remote fetches in 4 ms
19/02/13 16:10:19 INFO FileOutputCommitter: File Output Committer Algorithm version is 1
19/02/13 16:10:19 INFO CodecConfig: Compression: GZIP
19/02/13 16:10:19 INFO FileOutputCommitter: File Output Committer Algorithm version is 1
19/02/13 16:10:19 INFO ParquetOutputFormat: Parquet block size to 134217728
19/02/13 16:10:19 INFO ParquetOutputFormat: Parquet page size to 1048576
19/02/13 16:10:19 INFO ParquetOutputFormat: Parquet dictionary page size to 1048576
19/02/13 16:10:19 INFO ParquetOutputFormat: Dictionary is on
19/02/13 16:10:19 INFO ParquetOutputFormat: Validation is off
19/02/13 16:10:19 INFO ParquetOutputFormat: Writer version is: PARQUET_1_0
19/02/13 16:10:19 INFO ParquetOutputFormat: Maximum row group padding size is 0 bytes
19/02/13 16:10:19 INFO ParquetOutputFormat: Page size checking is: estimated
19/02/13 16:10:19 INFO ParquetOutputFormat: Min row count for page size check is: 100
19/02/13 16:10:19 INFO ParquetOutputFormat: Max row count for page size check is: 10000
19/02/13 16:10:19 INFO CodecPool: Got brand-new compressor [.gz]
19/02/13 16:10:24 INFO InternalParquetRecordWriter: Flushing mem columnStore to file. allocated memory: 16375919
19/02/13 16:10:25 INFO FileOutputCommitter: Saved output of task 'attempt_20190213161013_0005_r_000000_0' to file:/tmp/adamTestqsWBwl7/deleteMePleaseThisIsNoLongerNeeded/mouse_chrM.bam.reads.sorted.adam/_temporary/0/task_20190213161013_0005_r_000000
19/02/13 16:10:25 INFO SparkHadoopMapRedUtil: attempt_20190213161013_0005_r_000000_0: Committed
19/02/13 16:10:25 INFO Executor: Finished task 0.0 in stage 1.0 (TID 1). 1186 bytes result sent to driver
19/02/13 16:10:25 INFO TaskSetManager: Finished task 0.0 in stage 1.0 (TID 1) in 8201 ms on localhost (executor driver) (1/1)
19/02/13 16:10:25 INFO TaskSchedulerImpl: Removed TaskSet 1.0, whose tasks have all completed, from pool 
19/02/13 16:10:25 INFO DAGScheduler: ResultStage 1 (runJob at SparkHadoopMapReduceWriter.scala:88) finished in 8.203 s
19/02/13 16:10:25 INFO DAGScheduler: Job 0 finished: runJob at SparkHadoopMapReduceWriter.scala:88, took 12.073804 s
19/02/13 16:10:25 INFO ParquetFileReader: Initiating action with parallelism: 5
19/02/13 16:10:25 INFO SparkHadoopMapReduceWriter: Job job_20190213161013_0005 committed.
19/02/13 16:10:25 INFO TransformAlignments: Overall Duration: 17.11 secs
19/02/13 16:10:25 INFO SparkContext: Invoking stop() from shutdown hook
19/02/13 16:10:25 INFO SparkUI: Stopped Spark web UI at http://192.168.10.31:4040
19/02/13 16:10:25 INFO MapOutputTrackerMasterEndpoint: MapOutputTrackerMasterEndpoint stopped!
19/02/13 16:10:25 INFO MemoryStore: MemoryStore cleared
19/02/13 16:10:25 INFO BlockManager: BlockManager stopped
19/02/13 16:10:25 INFO BlockManagerMaster: BlockManagerMaster stopped
19/02/13 16:10:25 INFO OutputCommitCoordinator$OutputCommitCoordinatorEndpoint: OutputCommitCoordinator stopped!
19/02/13 16:10:25 INFO SparkContext: Successfully stopped SparkContext
19/02/13 16:10:25 INFO ShutdownHookManager: Shutdown hook called
19/02/13 16:10:25 INFO ShutdownHookManager: Deleting directory /tmp/spark-093b5e7f-77b9-45e0-b46d-d2d760818233
+ echo 'Converting read file to fragments'
Converting read file to fragments
+ rm -rf mouse_chrM.bam.fragments.adam
+ ./bin/adam-submit transformFragments -load_as_reads mouse_chrM.bam.reads.adam mouse_chrM.bam.fragments.adam
Using ADAM_MAIN=org.bdgenomics.adam.cli.ADAMMain
Using spark-submit=/tmp/adamTestqsWBwl7/deleteMePleaseThisIsNoLongerNeeded/spark-2.2.3-bin-hadoop2.7/bin/spark-submit
log4j:WARN No appenders could be found for logger (org.bdgenomics.adam.cli.ADAMMain).
log4j:WARN Please initialize the log4j system properly.
log4j:WARN See http://logging.apache.org/log4j/1.2/faq.html#noconfig for more info.
Using Spark's default log4j profile: org/apache/spark/log4j-defaults.properties
19/02/13 16:10:27 INFO SparkContext: Running Spark version 2.2.3
19/02/13 16:10:27 WARN NativeCodeLoader: Unable to load native-hadoop library for your platform... using builtin-java classes where applicable
19/02/13 16:10:27 WARN Utils: Your hostname, amp-jenkins-staging-worker-01 resolves to a loopback address: 127.0.1.1; using 192.168.10.31 instead (on interface eno1)
19/02/13 16:10:27 WARN Utils: Set SPARK_LOCAL_IP if you need to bind to another address
19/02/13 16:10:27 INFO SparkContext: Submitted application: transformFragments
19/02/13 16:10:27 INFO SecurityManager: Changing view acls to: jenkins
19/02/13 16:10:27 INFO SecurityManager: Changing modify acls to: jenkins
19/02/13 16:10:27 INFO SecurityManager: Changing view acls groups to: 
19/02/13 16:10:27 INFO SecurityManager: Changing modify acls groups to: 
19/02/13 16:10:27 INFO SecurityManager: SecurityManager: authentication disabled; ui acls disabled; users  with view permissions: Set(jenkins); groups with view permissions: Set(); users  with modify permissions: Set(jenkins); groups with modify permissions: Set()
19/02/13 16:10:28 INFO Utils: Successfully started service 'sparkDriver' on port 46767.
19/02/13 16:10:28 INFO SparkEnv: Registering MapOutputTracker
19/02/13 16:10:28 INFO SparkEnv: Registering BlockManagerMaster
19/02/13 16:10:28 INFO BlockManagerMasterEndpoint: Using org.apache.spark.storage.DefaultTopologyMapper for getting topology information
19/02/13 16:10:28 INFO BlockManagerMasterEndpoint: BlockManagerMasterEndpoint up
19/02/13 16:10:28 INFO DiskBlockManager: Created local directory at /tmp/blockmgr-60d1146c-b3da-42a6-80f4-ad13a925b1c0
19/02/13 16:10:28 INFO MemoryStore: MemoryStore started with capacity 366.3 MB
19/02/13 16:10:28 INFO SparkEnv: Registering OutputCommitCoordinator
19/02/13 16:10:28 INFO Utils: Successfully started service 'SparkUI' on port 4040.
19/02/13 16:10:28 INFO SparkUI: Bound SparkUI to 0.0.0.0, and started at http://192.168.10.31:4040
19/02/13 16:10:28 INFO SparkContext: Added JAR file:/tmp/adamTestqsWBwl7/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/target/adam-assembly-spark2_2.11-0.26.0-SNAPSHOT.jar at spark://192.168.10.31:46767/jars/adam-assembly-spark2_2.11-0.26.0-SNAPSHOT.jar with timestamp 1550103028567
19/02/13 16:10:28 INFO Executor: Starting executor ID driver on host localhost
19/02/13 16:10:28 INFO Utils: Successfully started service 'org.apache.spark.network.netty.NettyBlockTransferService' on port 36913.
19/02/13 16:10:28 INFO NettyBlockTransferService: Server created on 192.168.10.31:36913
19/02/13 16:10:28 INFO BlockManager: Using org.apache.spark.storage.RandomBlockReplicationPolicy for block replication policy
19/02/13 16:10:28 INFO BlockManagerMaster: Registering BlockManager BlockManagerId(driver, 192.168.10.31, 36913, None)
19/02/13 16:10:28 INFO BlockManagerMasterEndpoint: Registering block manager 192.168.10.31:36913 with 366.3 MB RAM, BlockManagerId(driver, 192.168.10.31, 36913, None)
19/02/13 16:10:28 INFO BlockManagerMaster: Registered BlockManager BlockManagerId(driver, 192.168.10.31, 36913, None)
19/02/13 16:10:28 INFO BlockManager: Initialized BlockManager: BlockManagerId(driver, 192.168.10.31, 36913, None)
19/02/13 16:10:28 INFO ADAMContext: Loading mouse_chrM.bam.reads.adam as Parquet of AlignmentRecords.
19/02/13 16:10:30 INFO ADAMContext: Reading the ADAM file at mouse_chrM.bam.reads.adam to create RDD
19/02/13 16:10:31 INFO MemoryStore: Block broadcast_0 stored as values in memory (estimated size 303.5 KB, free 366.0 MB)
19/02/13 16:10:31 INFO MemoryStore: Block broadcast_0_piece0 stored as bytes in memory (estimated size 27.3 KB, free 366.0 MB)
19/02/13 16:10:31 INFO BlockManagerInfo: Added broadcast_0_piece0 in memory on 192.168.10.31:36913 (size: 27.3 KB, free: 366.3 MB)
19/02/13 16:10:31 INFO SparkContext: Created broadcast 0 from newAPIHadoopFile at ADAMContext.scala:1319
19/02/13 16:10:31 INFO FileInputFormat: Total input paths to process : 1
19/02/13 16:10:31 INFO ParquetInputFormat: Total input paths to process : 1
19/02/13 16:10:31 INFO RDDBoundFragmentDataset: Saving data in ADAM format
19/02/13 16:10:31 INFO FileOutputCommitter: File Output Committer Algorithm version is 1
19/02/13 16:10:31 INFO SparkContext: Starting job: runJob at SparkHadoopMapReduceWriter.scala:88
19/02/13 16:10:31 INFO DAGScheduler: Registering RDD 2 (groupBy at SingleReadBucket.scala:98)
19/02/13 16:10:31 INFO DAGScheduler: Got job 0 (runJob at SparkHadoopMapReduceWriter.scala:88) with 1 output partitions
19/02/13 16:10:31 INFO DAGScheduler: Final stage: ResultStage 1 (runJob at SparkHadoopMapReduceWriter.scala:88)
19/02/13 16:10:31 INFO DAGScheduler: Parents of final stage: List(ShuffleMapStage 0)
19/02/13 16:10:31 INFO DAGScheduler: Missing parents: List(ShuffleMapStage 0)
19/02/13 16:10:31 INFO DAGScheduler: Submitting ShuffleMapStage 0 (MapPartitionsRDD[2] at groupBy at SingleReadBucket.scala:98), which has no missing parents
19/02/13 16:10:31 INFO MemoryStore: Block broadcast_1 stored as values in memory (estimated size 5.2 KB, free 366.0 MB)
19/02/13 16:10:32 INFO MemoryStore: Block broadcast_1_piece0 stored as bytes in memory (estimated size 2.9 KB, free 366.0 MB)
19/02/13 16:10:32 INFO BlockManagerInfo: Added broadcast_1_piece0 in memory on 192.168.10.31:36913 (size: 2.9 KB, free: 366.3 MB)
19/02/13 16:10:32 INFO SparkContext: Created broadcast 1 from broadcast at DAGScheduler.scala:1004
19/02/13 16:10:32 INFO DAGScheduler: Submitting 1 missing tasks from ShuffleMapStage 0 (MapPartitionsRDD[2] at groupBy at SingleReadBucket.scala:98) (first 15 tasks are for partitions Vector(0))
19/02/13 16:10:32 INFO TaskSchedulerImpl: Adding task set 0.0 with 1 tasks
19/02/13 16:10:32 INFO TaskSetManager: Starting task 0.0 in stage 0.0 (TID 0, localhost, executor driver, partition 0, PROCESS_LOCAL, 4960 bytes)
19/02/13 16:10:32 INFO Executor: Running task 0.0 in stage 0.0 (TID 0)
19/02/13 16:10:32 INFO Executor: Fetching spark://192.168.10.31:46767/jars/adam-assembly-spark2_2.11-0.26.0-SNAPSHOT.jar with timestamp 1550103028567
19/02/13 16:10:32 INFO TransportClientFactory: Successfully created connection to /192.168.10.31:46767 after 31 ms (0 ms spent in bootstraps)
19/02/13 16:10:32 INFO Utils: Fetching spark://192.168.10.31:46767/jars/adam-assembly-spark2_2.11-0.26.0-SNAPSHOT.jar to /tmp/spark-f06bbdb7-4c24-4efb-aead-ebe093ca6756/userFiles-8843a86c-66e3-4e50-af90-8d4444a4222b/fetchFileTemp6471496194403723926.tmp
19/02/13 16:10:32 INFO Executor: Adding file:/tmp/spark-f06bbdb7-4c24-4efb-aead-ebe093ca6756/userFiles-8843a86c-66e3-4e50-af90-8d4444a4222b/adam-assembly-spark2_2.11-0.26.0-SNAPSHOT.jar to class loader
19/02/13 16:10:32 INFO NewHadoopRDD: Input split: file:/tmp/adamTestqsWBwl7/deleteMePleaseThisIsNoLongerNeeded/mouse_chrM.bam.reads.adam/part-r-00000.gz.parquet:0+10131504
19/02/13 16:10:32 INFO InternalParquetRecordReader: RecordReader initialized will read a total of 163064 records.
19/02/13 16:10:32 INFO InternalParquetRecordReader: at row 0. reading next block
19/02/13 16:10:32 INFO CodecPool: Got brand-new decompressor [.gz]
19/02/13 16:10:32 INFO InternalParquetRecordReader: block read in memory in 49 ms. row count = 163064
19/02/13 16:10:36 INFO Executor: Finished task 0.0 in stage 0.0 (TID 0). 956 bytes result sent to driver
19/02/13 16:10:36 INFO TaskSetManager: Finished task 0.0 in stage 0.0 (TID 0) in 4257 ms on localhost (executor driver) (1/1)
19/02/13 16:10:36 INFO TaskSchedulerImpl: Removed TaskSet 0.0, whose tasks have all completed, from pool 
19/02/13 16:10:36 INFO DAGScheduler: ShuffleMapStage 0 (groupBy at SingleReadBucket.scala:98) finished in 4.327 s
19/02/13 16:10:36 INFO DAGScheduler: looking for newly runnable stages
19/02/13 16:10:36 INFO DAGScheduler: running: Set()
19/02/13 16:10:36 INFO DAGScheduler: waiting: Set(ResultStage 1)
19/02/13 16:10:36 INFO DAGScheduler: failed: Set()
19/02/13 16:10:36 INFO DAGScheduler: Submitting ResultStage 1 (MapPartitionsRDD[6] at map at GenomicDataset.scala:3813), which has no missing parents
19/02/13 16:10:36 INFO MemoryStore: Block broadcast_2 stored as values in memory (estimated size 85.8 KB, free 365.9 MB)
19/02/13 16:10:36 INFO MemoryStore: Block broadcast_2_piece0 stored as bytes in memory (estimated size 31.9 KB, free 365.9 MB)
19/02/13 16:10:36 INFO BlockManagerInfo: Added broadcast_2_piece0 in memory on 192.168.10.31:36913 (size: 31.9 KB, free: 366.2 MB)
19/02/13 16:10:36 INFO SparkContext: Created broadcast 2 from broadcast at DAGScheduler.scala:1004
19/02/13 16:10:36 INFO DAGScheduler: Submitting 1 missing tasks from ResultStage 1 (MapPartitionsRDD[6] at map at GenomicDataset.scala:3813) (first 15 tasks are for partitions Vector(0))
19/02/13 16:10:36 INFO TaskSchedulerImpl: Adding task set 1.0 with 1 tasks
19/02/13 16:10:36 INFO TaskSetManager: Starting task 0.0 in stage 1.0 (TID 1, localhost, executor driver, partition 0, ANY, 4621 bytes)
19/02/13 16:10:36 INFO Executor: Running task 0.0 in stage 1.0 (TID 1)
19/02/13 16:10:36 INFO ShuffleBlockFetcherIterator: Getting 1 non-empty blocks out of 1 blocks
19/02/13 16:10:36 INFO ShuffleBlockFetcherIterator: Started 0 remote fetches in 5 ms
19/02/13 16:10:38 INFO FileOutputCommitter: File Output Committer Algorithm version is 1
19/02/13 16:10:38 INFO CodecConfig: Compression: GZIP
19/02/13 16:10:38 INFO FileOutputCommitter: File Output Committer Algorithm version is 1
19/02/13 16:10:38 INFO ParquetOutputFormat: Parquet block size to 134217728
19/02/13 16:10:38 INFO ParquetOutputFormat: Parquet page size to 1048576
19/02/13 16:10:38 INFO ParquetOutputFormat: Parquet dictionary page size to 1048576
19/02/13 16:10:38 INFO ParquetOutputFormat: Dictionary is on
19/02/13 16:10:38 INFO ParquetOutputFormat: Validation is off
19/02/13 16:10:38 INFO ParquetOutputFormat: Writer version is: PARQUET_1_0
19/02/13 16:10:38 INFO ParquetOutputFormat: Maximum row group padding size is 0 bytes
19/02/13 16:10:38 INFO ParquetOutputFormat: Page size checking is: estimated
19/02/13 16:10:38 INFO ParquetOutputFormat: Min row count for page size check is: 100
19/02/13 16:10:38 INFO ParquetOutputFormat: Max row count for page size check is: 10000
19/02/13 16:10:38 INFO CodecPool: Got brand-new compressor [.gz]
19/02/13 16:10:46 INFO InternalParquetRecordWriter: Flushing mem columnStore to file. allocated memory: 21780002
19/02/13 16:10:46 INFO FileOutputCommitter: Saved output of task 'attempt_20190213161031_0006_r_000000_0' to file:/tmp/adamTestqsWBwl7/deleteMePleaseThisIsNoLongerNeeded/mouse_chrM.bam.fragments.adam/_temporary/0/task_20190213161031_0006_r_000000
19/02/13 16:10:46 INFO SparkHadoopMapRedUtil: attempt_20190213161031_0006_r_000000_0: Committed
19/02/13 16:10:46 INFO Executor: Finished task 0.0 in stage 1.0 (TID 1). 1186 bytes result sent to driver
19/02/13 16:10:46 INFO TaskSetManager: Finished task 0.0 in stage 1.0 (TID 1) in 10556 ms on localhost (executor driver) (1/1)
19/02/13 16:10:46 INFO TaskSchedulerImpl: Removed TaskSet 1.0, whose tasks have all completed, from pool 
19/02/13 16:10:46 INFO DAGScheduler: ResultStage 1 (runJob at SparkHadoopMapReduceWriter.scala:88) finished in 10.558 s
19/02/13 16:10:47 INFO DAGScheduler: Job 0 finished: runJob at SparkHadoopMapReduceWriter.scala:88, took 15.074032 s
19/02/13 16:10:47 INFO ParquetFileReader: Initiating action with parallelism: 5
19/02/13 16:10:47 INFO SparkHadoopMapReduceWriter: Job job_20190213161031_0006 committed.
19/02/13 16:10:47 INFO TransformFragments: Overall Duration: 20.11 secs
19/02/13 16:10:47 INFO SparkContext: Invoking stop() from shutdown hook
19/02/13 16:10:47 INFO SparkUI: Stopped Spark web UI at http://192.168.10.31:4040
19/02/13 16:10:47 INFO MapOutputTrackerMasterEndpoint: MapOutputTrackerMasterEndpoint stopped!
19/02/13 16:10:47 INFO MemoryStore: MemoryStore cleared
19/02/13 16:10:47 INFO BlockManager: BlockManager stopped
19/02/13 16:10:47 INFO BlockManagerMaster: BlockManagerMaster stopped
19/02/13 16:10:47 INFO OutputCommitCoordinator$OutputCommitCoordinatorEndpoint: OutputCommitCoordinator stopped!
19/02/13 16:10:47 INFO SparkContext: Successfully stopped SparkContext
19/02/13 16:10:47 INFO ShutdownHookManager: Shutdown hook called
19/02/13 16:10:47 INFO ShutdownHookManager: Deleting directory /tmp/spark-f06bbdb7-4c24-4efb-aead-ebe093ca6756
+ echo 'Printing reads and fragments'
Printing reads and fragments
+ ./bin/adam-submit print mouse_chrM.bam.reads.adam
+ ./bin/adam-submit print mouse_chrM.bam.fragments.adam
+ echo 'Printing read statistics'
Printing read statistics
+ ./bin/adam-submit flagstat -print_metrics mouse_chrM.bam.reads.adam
Using ADAM_MAIN=org.bdgenomics.adam.cli.ADAMMain
Using spark-submit=/tmp/adamTestqsWBwl7/deleteMePleaseThisIsNoLongerNeeded/spark-2.2.3-bin-hadoop2.7/bin/spark-submit
log4j:WARN No appenders could be found for logger (org.bdgenomics.adam.cli.ADAMMain).
log4j:WARN Please initialize the log4j system properly.
log4j:WARN See http://logging.apache.org/log4j/1.2/faq.html#noconfig for more info.
Using Spark's default log4j profile: org/apache/spark/log4j-defaults.properties
19/02/13 16:11:06 INFO SparkContext: Running Spark version 2.2.3
19/02/13 16:11:06 WARN NativeCodeLoader: Unable to load native-hadoop library for your platform... using builtin-java classes where applicable
19/02/13 16:11:06 WARN Utils: Your hostname, amp-jenkins-staging-worker-01 resolves to a loopback address: 127.0.1.1; using 192.168.10.31 instead (on interface eno1)
19/02/13 16:11:06 WARN Utils: Set SPARK_LOCAL_IP if you need to bind to another address
19/02/13 16:11:06 INFO SparkContext: Submitted application: flagstat
19/02/13 16:11:06 INFO SecurityManager: Changing view acls to: jenkins
19/02/13 16:11:06 INFO SecurityManager: Changing modify acls to: jenkins
19/02/13 16:11:06 INFO SecurityManager: Changing view acls groups to: 
19/02/13 16:11:06 INFO SecurityManager: Changing modify acls groups to: 
19/02/13 16:11:06 INFO SecurityManager: SecurityManager: authentication disabled; ui acls disabled; users  with view permissions: Set(jenkins); groups with view permissions: Set(); users  with modify permissions: Set(jenkins); groups with modify permissions: Set()
19/02/13 16:11:07 INFO Utils: Successfully started service 'sparkDriver' on port 33078.
19/02/13 16:11:07 INFO SparkEnv: Registering MapOutputTracker
19/02/13 16:11:07 INFO SparkEnv: Registering BlockManagerMaster
19/02/13 16:11:07 INFO BlockManagerMasterEndpoint: Using org.apache.spark.storage.DefaultTopologyMapper for getting topology information
19/02/13 16:11:07 INFO BlockManagerMasterEndpoint: BlockManagerMasterEndpoint up
19/02/13 16:11:07 INFO DiskBlockManager: Created local directory at /tmp/blockmgr-612e446f-eba9-48ca-83b9-09b94ca07bf0
19/02/13 16:11:07 INFO MemoryStore: MemoryStore started with capacity 366.3 MB
19/02/13 16:11:07 INFO SparkEnv: Registering OutputCommitCoordinator
19/02/13 16:11:07 INFO Utils: Successfully started service 'SparkUI' on port 4040.
19/02/13 16:11:07 INFO SparkUI: Bound SparkUI to 0.0.0.0, and started at http://192.168.10.31:4040
19/02/13 16:11:07 INFO SparkContext: Added JAR file:/tmp/adamTestqsWBwl7/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/target/adam-assembly-spark2_2.11-0.26.0-SNAPSHOT.jar at spark://192.168.10.31:33078/jars/adam-assembly-spark2_2.11-0.26.0-SNAPSHOT.jar with timestamp 1550103067758
19/02/13 16:11:07 INFO Executor: Starting executor ID driver on host localhost
19/02/13 16:11:07 INFO Utils: Successfully started service 'org.apache.spark.network.netty.NettyBlockTransferService' on port 36747.
19/02/13 16:11:07 INFO NettyBlockTransferService: Server created on 192.168.10.31:36747
19/02/13 16:11:07 INFO BlockManager: Using org.apache.spark.storage.RandomBlockReplicationPolicy for block replication policy
19/02/13 16:11:07 INFO BlockManagerMaster: Registering BlockManager BlockManagerId(driver, 192.168.10.31, 36747, None)
19/02/13 16:11:07 INFO BlockManagerMasterEndpoint: Registering block manager 192.168.10.31:36747 with 366.3 MB RAM, BlockManagerId(driver, 192.168.10.31, 36747, None)
19/02/13 16:11:07 INFO BlockManagerMaster: Registered BlockManager BlockManagerId(driver, 192.168.10.31, 36747, None)
19/02/13 16:11:07 INFO BlockManager: Initialized BlockManager: BlockManagerId(driver, 192.168.10.31, 36747, None)
19/02/13 16:11:08 INFO ADAMContext: Loading mouse_chrM.bam.reads.adam as Parquet of AlignmentRecords.
19/02/13 16:11:08 INFO ADAMContext: Reading the ADAM file at mouse_chrM.bam.reads.adam to create RDD
19/02/13 16:11:08 INFO ADAMContext: Using the specified projection schema
19/02/13 16:11:09 INFO MemoryStore: Block broadcast_0 stored as values in memory (estimated size 313.0 KB, free 366.0 MB)
19/02/13 16:11:09 INFO MemoryStore: Block broadcast_0_piece0 stored as bytes in memory (estimated size 28.3 KB, free 366.0 MB)
19/02/13 16:11:09 INFO BlockManagerInfo: Added broadcast_0_piece0 in memory on 192.168.10.31:36747 (size: 28.3 KB, free: 366.3 MB)
19/02/13 16:11:09 INFO SparkContext: Created broadcast 0 from newAPIHadoopFile at ADAMContext.scala:1319
19/02/13 16:11:11 INFO FileInputFormat: Total input paths to process : 1
19/02/13 16:11:11 INFO ParquetInputFormat: Total input paths to process : 1
19/02/13 16:11:11 INFO SparkContext: Starting job: aggregate at FlagStat.scala:115
19/02/13 16:11:11 INFO DAGScheduler: Got job 0 (aggregate at FlagStat.scala:115) with 1 output partitions
19/02/13 16:11:11 INFO DAGScheduler: Final stage: ResultStage 0 (aggregate at FlagStat.scala:115)
19/02/13 16:11:11 INFO DAGScheduler: Parents of final stage: List()
19/02/13 16:11:11 INFO DAGScheduler: Missing parents: List()
19/02/13 16:11:11 INFO DAGScheduler: Submitting ResultStage 0 (MapPartitionsRDD[4] at map at FlagStat.scala:96), which has no missing parents
19/02/13 16:11:11 INFO MemoryStore: Block broadcast_1 stored as values in memory (estimated size 12.4 KB, free 366.0 MB)
19/02/13 16:11:11 INFO MemoryStore: Block broadcast_1_piece0 stored as bytes in memory (estimated size 5.4 KB, free 365.9 MB)
19/02/13 16:11:11 INFO BlockManagerInfo: Added broadcast_1_piece0 in memory on 192.168.10.31:36747 (size: 5.4 KB, free: 366.3 MB)
19/02/13 16:11:11 INFO SparkContext: Created broadcast 1 from broadcast at DAGScheduler.scala:1004
19/02/13 16:11:11 INFO DAGScheduler: Submitting 1 missing tasks from ResultStage 0 (MapPartitionsRDD[4] at map at FlagStat.scala:96) (first 15 tasks are for partitions Vector(0))
19/02/13 16:11:11 INFO TaskSchedulerImpl: Adding task set 0.0 with 1 tasks
19/02/13 16:11:11 INFO TaskSetManager: Starting task 0.0 in stage 0.0 (TID 0, localhost, executor driver, partition 0, PROCESS_LOCAL, 4971 bytes)
19/02/13 16:11:11 INFO Executor: Running task 0.0 in stage 0.0 (TID 0)
19/02/13 16:11:11 INFO Executor: Fetching spark://192.168.10.31:33078/jars/adam-assembly-spark2_2.11-0.26.0-SNAPSHOT.jar with timestamp 1550103067758
19/02/13 16:11:11 INFO TransportClientFactory: Successfully created connection to /192.168.10.31:33078 after 45 ms (0 ms spent in bootstraps)
19/02/13 16:11:11 INFO Utils: Fetching spark://192.168.10.31:33078/jars/adam-assembly-spark2_2.11-0.26.0-SNAPSHOT.jar to /tmp/spark-d0c9aa1f-504c-43b2-a837-032c2d120e05/userFiles-7f3e94d5-a198-4fbf-a8c4-226bfbf5fdb5/fetchFileTemp1111009340182290049.tmp
19/02/13 16:11:11 INFO Executor: Adding file:/tmp/spark-d0c9aa1f-504c-43b2-a837-032c2d120e05/userFiles-7f3e94d5-a198-4fbf-a8c4-226bfbf5fdb5/adam-assembly-spark2_2.11-0.26.0-SNAPSHOT.jar to class loader
19/02/13 16:11:11 INFO NewHadoopRDD: Input split: file:/tmp/adamTestqsWBwl7/deleteMePleaseThisIsNoLongerNeeded/mouse_chrM.bam.reads.adam/part-r-00000.gz.parquet:0+10131504
19/02/13 16:11:11 INFO InternalParquetRecordReader: RecordReader initialized will read a total of 163064 records.
19/02/13 16:11:11 INFO InternalParquetRecordReader: at row 0. reading next block
19/02/13 16:11:11 INFO CodecPool: Got brand-new decompressor [.gz]
19/02/13 16:11:11 INFO InternalParquetRecordReader: block read in memory in 31 ms. row count = 163064
19/02/13 16:11:12 INFO Executor: Finished task 0.0 in stage 0.0 (TID 0). 8196 bytes result sent to driver
19/02/13 16:11:13 INFO TaskSetManager: Finished task 0.0 in stage 0.0 (TID 0) in 1690 ms on localhost (executor driver) (1/1)
19/02/13 16:11:13 INFO TaskSchedulerImpl: Removed TaskSet 0.0, whose tasks have all completed, from pool 
19/02/13 16:11:13 INFO DAGScheduler: ResultStage 0 (aggregate at FlagStat.scala:115) finished in 1.917 s
19/02/13 16:11:13 INFO DAGScheduler: Job 0 finished: aggregate at FlagStat.scala:115, took 2.106684 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)
19/02/13 16:11:13 INFO FlagStat: Overall Duration: 6.96 secs
19/02/13 16:11:13 INFO FlagStat: Metrics:

Timings
+--------------------------------------+--------------+--------------+-------------+--------+-----------+-----------+-----------+
|                Metric                | Worker Total | Driver Total | Driver Only | Count  |   Mean    |    Min    |    Max    |
+--------------------------------------+--------------+--------------+-------------+--------+-----------+-----------+-----------+
| └─ Load Alignments                   |            - |    2.47 secs |    2.4 secs |      1 | 2.47 secs | 2.47 secs | 2.47 secs |
|     └─ map at ADAMContext.scala:1328 |            - |     77.27 ms |           - |      1 |  77.27 ms |  77.27 ms |  77.27 ms |
|         └─ function call             |     26.41 ms |            - |           - | 163064 |    161 ns |     62 ns | 112.83 µs |
| └─ map at FlagStat.scala:96          |            - |     42.72 ms |           - |      1 |  42.72 ms |  42.72 ms |  42.72 ms |
|     └─ function call                 |     254.6 ms |            - |           - | 163064 |   1.56 µs |    178 ns |   1.66 ms |
| └─ aggregate at FlagStat.scala:115   |            - |    2.28 secs |           - |      1 | 2.28 secs | 2.28 secs | 2.28 secs |
|     └─ function call                 |     85.68 ms |            - |           - | 163065 |    525 ns |     93 ns |  39.34 ms |
+--------------------------------------+--------------+--------------+-------------+--------+-----------+-----------+-----------+

Spark Operations
+----------+---------------------------------+---------------+----------------+--------------+----------+
| Sequence |            Operation            | Is New Stage? | Stage Duration | Driver Total | Stage ID |
+----------+---------------------------------+---------------+----------------+--------------+----------+
| 1        | map at ADAMContext.scala:1328   | false         |              - |     77.27 ms | -        |
| 2        | map at FlagStat.scala:96        | false         |              - |     42.72 ms | -        |
| 3        | aggregate at FlagStat.scala:115 | true          |     -1.92 secs |    2.28 secs | 0        |
+----------+---------------------------------+---------------+----------------+--------------+----------+

Task Timings
+-------------------------------+------------+-------+-----------+-----------+-----------+
|            Metric             | Total Time | Count |   Mean    |    Min    |    Max    |
+-------------------------------+------------+-------+-----------+-----------+-----------+
| Task Duration                 |  1.69 secs |     1 | 1.69 secs | 1.69 secs | 1.69 secs |
| Executor Run Time             |  1.32 secs |     1 | 1.32 secs | 1.32 secs | 1.32 secs |
| Executor Deserialization Time |     299 ms |     1 |    299 ms |    299 ms |    299 ms |
| Result Serialization Time     |          0 |     1 |         0 |         0 |         0 |
+-------------------------------+------------+-------+-----------+-----------+-----------+

Task Timings By Host
+-------------------------------+--------+------------+-------+-----------+-----------+-----------+
|            Metric             |  Host  | Total Time | Count |   Mean    |    Min    |    Max    |
+-------------------------------+--------+------------+-------+-----------+-----------+-----------+
| Task Duration                 | driver |  1.69 secs |     1 | 1.69 secs | 1.69 secs | 1.69 secs |
| Executor Run Time             | driver |  1.32 secs |     1 | 1.32 secs | 1.32 secs | 1.32 secs |
| Executor Deserialization Time | driver |     299 ms |     1 |    299 ms |    299 ms |    299 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 |  1.69 secs |     1 | 1.69 secs | 1.69 secs | 1.69 secs |
| Executor Run Time             | 0: aggregate at FlagStat.scala:115 |  1.32 secs |     1 | 1.32 secs | 1.32 secs | 1.32 secs |
| Executor Deserialization Time | 0: aggregate at FlagStat.scala:115 |     299 ms |     1 |    299 ms |    299 ms |    299 ms |
| Result Serialization Time     | 0: aggregate at FlagStat.scala:115 |          0 |     1 |         0 |         0 |         0 |
+-------------------------------+------------------------------------+------------+-------+-----------+-----------+-----------+

19/02/13 16:11:13 INFO SparkContext: Invoking stop() from shutdown hook
19/02/13 16:11:13 INFO SparkUI: Stopped Spark web UI at http://192.168.10.31:4040
19/02/13 16:11:13 INFO MapOutputTrackerMasterEndpoint: MapOutputTrackerMasterEndpoint stopped!
19/02/13 16:11:13 INFO MemoryStore: MemoryStore cleared
19/02/13 16:11:13 INFO BlockManager: BlockManager stopped
19/02/13 16:11:13 INFO BlockManagerMaster: BlockManagerMaster stopped
19/02/13 16:11:13 INFO OutputCommitCoordinator$OutputCommitCoordinatorEndpoint: OutputCommitCoordinator stopped!
19/02/13 16:11:13 INFO SparkContext: Successfully stopped SparkContext
19/02/13 16:11:13 INFO ShutdownHookManager: Shutdown hook called
19/02/13 16:11:13 INFO ShutdownHookManager: Deleting directory /tmp/spark-d0c9aa1f-504c-43b2-a837-032c2d120e05
+ rm -rf /tmp/adamTestqsWBwl7/deleteMePleaseThisIsNoLongerNeeded
+ popd
~/workspace/ADAM/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.2.3/label/ubuntu
+ pushd /home/jenkins/workspace/ADAM/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.2.3/label/ubuntu/scripts/..
~/workspace/ADAM/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.2.3/label/ubuntu ~/workspace/ADAM/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.2.3/label/ubuntu
+ ./scripts/format-source
+++ dirname ./scripts/format-source
++ cd ./scripts
++ pwd
+ DIR=/home/jenkins/workspace/ADAM/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.2.3/label/ubuntu/scripts
+ pushd /home/jenkins/workspace/ADAM/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.2.3/label/ubuntu/scripts/..
~/workspace/ADAM/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.2.3/label/ubuntu ~/workspace/ADAM/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.2.3/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: 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 0.26.0-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ adam-parent-spark2_2.11 ---
[INFO] Modified 2 of 240 .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: Avro-to-Dataset codegen utils 0.26.0-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 0.26.0-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ adam-core-spark2_2.11 ---
[INFO] Modified 0 of 199 .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 0.26.0-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 0.26.0-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ adam-cli-spark2_2.11 ---
[INFO] Modified 0 of 30 .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 0.26.0-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 [  8.285 s]
[INFO] ADAM_2.11: Avro-to-Dataset codegen utils ........... SUCCESS [  0.096 s]
[INFO] ADAM_2.11: Core .................................... SUCCESS [  4.077 s]
[INFO] ADAM_2.11: APIs for Java, Python ................... SUCCESS [  0.117 s]
[INFO] ADAM_2.11: CLI ..................................... SUCCESS [  0.245 s]
[INFO] ADAM_2.11: Assembly ................................ SUCCESS [  0.024 s]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 13.594 s
[INFO] Finished at: 2019-02-13T16:11:29-08:00
[INFO] Final Memory: 21M/1133M
[INFO] ------------------------------------------------------------------------
+ popd
~/workspace/ADAM/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.2.3/label/ubuntu
git status --porcelain
++ git status --porcelain
+ test -n ''
+ popd
~/workspace/ADAM/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.2.3/label/ubuntu

echo
+ echo

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

+ '[' 2.2.3 == 2.2.2 ']'
Recording test results
Publishing Scoverage XML and HTML report...
Finished: SUCCESS