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[WARNING] Entry: adam-distribution-spark2_2.11-0.30.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/CoverageToFragmentsConverter.html longer than 100 characters.
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[WARNING] Entry: adam-distribution-spark2_2.11-0.30.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/cli/TransformSequencesArgs.html longer than 100 characters.
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[WARNING] Entry: adam-distribution-spark2_2.11-0.30.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/cli/TransformVariantsArgs.html longer than 100 characters.
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[WARNING] Entry: adam-distribution-spark2_2.11-0.30.0-SNAPSHOT/repo/adam-assembly-spark2_2.11-0.30.0-SNAPSHOT-javadoc.jar longer than 100 characters.
[INFO] Building zip: /tmp/adamTestxbwUJbj/deleteMePleaseThisIsNoLongerNeeded/adam-distribution/target/adam-distribution-spark2_2.11-0.30.0-SNAPSHOT-bin.zip
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary:
[INFO] 
[INFO] ADAM_2.11 .......................................... SUCCESS [  9.195 s]
[INFO] ADAM_2.11: Shader workaround ....................... SUCCESS [  3.979 s]
[INFO] ADAM_2.11: Avro-to-Dataset codegen utils ........... SUCCESS [  3.525 s]
[INFO] ADAM_2.11: Core .................................... SUCCESS [01:15 min]
[INFO] ADAM_2.11: APIs for Java, Python ................... SUCCESS [  7.993 s]
[INFO] ADAM_2.11: CLI ..................................... SUCCESS [ 17.451 s]
[INFO] ADAM_2.11: Assembly ................................ SUCCESS [ 16.996 s]
[INFO] ADAM_2.11: Python APIs ............................. SUCCESS [01:25 min]
[INFO] ADAM_2.11: R APIs .................................. SUCCESS [ 52.514 s]
[INFO] ADAM_2.11: Distribution ............................ SUCCESS [ 41.462 s]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 05:14 min
[INFO] Finished at: 2019-10-28T17:05:12-07:00
[INFO] Final Memory: 88M/1482M
[INFO] ------------------------------------------------------------------------
+ tar tzvf adam-distribution/target/adam-distribution-spark2_2.11-0.30.0-SNAPSHOT-bin.tar.gz
+ grep bdgenomics.adam
+ grep egg
drwxrwxr-x jenkins/jenkins        0 2019-10-28 17:02 adam-distribution-spark2_2.11-0.30.0-SNAPSHOT/r/bdgenomics.adam.egg-info/
-rw-r--r-- jenkins/jenkins 39644910 2019-10-28 17:02 adam-distribution-spark2_2.11-0.30.0-SNAPSHOT/repo/bdgenomics.adam-0.30.0a0-py3.6.egg
+ ./bin/pyadam
Using PYSPARK=/tmp/adamTestxbwUJbj/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.4-bin-hadoop2.7/bin/pyspark
2019-10-28 17:05:14 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)
2019-10-28 17:05:14 WARN  Utils:66 - Set SPARK_LOCAL_IP if you need to bind to another address
2019-10-28 17:05:15 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).
2019-10-28 17:05:20 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-5f3b2f2f-f233-4640-a1d9-1d097aeb3d24/bin/deactivate
++ _SHELL=bash
_CONDA_DIR=$(dirname "$_SCRIPT_LOCATION")
dirname "$_SCRIPT_LOCATION"
+++ dirname /home/jenkins/anaconda2/envs/adam-build-5f3b2f2f-f233-4640-a1d9-1d097aeb3d24/bin/deactivate
++ _CONDA_DIR=/home/jenkins/anaconda2/envs/adam-build-5f3b2f2f-f233-4640-a1d9-1d097aeb3d24/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/2.11/SPARK_VERSION/2.4.4/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 $?
fi
++ ((  0 == 0  ))
++ _CONDA_D=/home/jenkins/anaconda2/envs/adam-build-5f3b2f2f-f233-4640-a1d9-1d097aeb3d24/etc/conda/deactivate.d
++ [[ -d /home/jenkins/anaconda2/envs/adam-build-5f3b2f2f-f233-4640-a1d9-1d097aeb3d24/etc/conda/deactivate.d ]]
"$_CONDA_DIR/conda" ..deactivate.path $_SHELL$EXT "$CONDA_PREFIX"
+++ /home/jenkins/anaconda2/envs/adam-build-5f3b2f2f-f233-4640-a1d9-1d097aeb3d24/bin/conda ..deactivate.path bash /home/jenkins/anaconda2/envs/adam-build-5f3b2f2f-f233-4640-a1d9-1d097aeb3d24
++ 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-5f3b2f2f-f233-4640-a1d9-1d097aeb3d24 --all

Package plan for package removal in environment /home/jenkins/anaconda2/envs/adam-build-5f3b2f2f-f233-4640-a1d9-1d097aeb3d24:

The following packages will be REMOVED:

    _libgcc_mutex:   0.1-main               
    ca-certificates: 2019.10.16-0           
    certifi:         2019.9.11-py36_0       
    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:         1.1.1d-h7b6447c_3      
    pip:             19.3.1-py36_0          
    python:          3.6.9-h265db76_0       
    readline:        7.0-h7b6447c_5         
    setuptools:      41.4.0-py36_0          
    sqlite:          3.30.1-h7b6447c_0      
    tk:              8.6.8-hbc83047_0       
    wheel:           0.33.6-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/2.11/SPARK_VERSION/2.4.4/label/ubuntu/scripts/../adam-python/
+ pushd adam-python
/tmp/adamTestxbwUJbj/deleteMePleaseThisIsNoLongerNeeded/adam-python /tmp/adamTestxbwUJbj/deleteMePleaseThisIsNoLongerNeeded ~/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu
+ make clean
pip uninstall -y adam
Skipping adam as it is not installed.
rm -rf bdgenomics/*.egg*
rm -rf build/
rm -rf dist/
+ make clean_sdist
rm -rf dist
+ popd
/tmp/adamTestxbwUJbj/deleteMePleaseThisIsNoLongerNeeded ~/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/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/adamTestxbwUJbj/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.4-bin-hadoop2.7/bin/spark-submit
19/10/28 17:05:26 WARN 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)
19/10/28 17:05:26 WARN Utils: Set SPARK_LOCAL_IP if you need to bind to another address
19/10/28 17:05:27 WARN NativeCodeLoader: Unable to load native-hadoop library for your platform... using builtin-java classes where applicable
log4j:WARN No appenders could be found for logger (org.bdgenomics.adam.cli.ADAMMain).
log4j:WARN Please initialize the log4j system properly.
log4j:WARN See http://logging.apache.org/log4j/1.2/faq.html#noconfig for more info.
Using Spark's default log4j profile: org/apache/spark/log4j-defaults.properties
19/10/28 17:05:27 INFO SparkContext: Running Spark version 2.4.4
19/10/28 17:05:27 INFO SparkContext: Submitted application: transformAlignments
19/10/28 17:05:27 INFO SecurityManager: Changing view acls to: jenkins
19/10/28 17:05:27 INFO SecurityManager: Changing modify acls to: jenkins
19/10/28 17:05:27 INFO SecurityManager: Changing view acls groups to: 
19/10/28 17:05:27 INFO SecurityManager: Changing modify acls groups to: 
19/10/28 17:05:27 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()
19/10/28 17:05:27 INFO Utils: Successfully started service 'sparkDriver' on port 38025.
19/10/28 17:05:27 INFO SparkEnv: Registering MapOutputTracker
19/10/28 17:05:27 INFO SparkEnv: Registering BlockManagerMaster
19/10/28 17:05:27 INFO BlockManagerMasterEndpoint: Using org.apache.spark.storage.DefaultTopologyMapper for getting topology information
19/10/28 17:05:27 INFO BlockManagerMasterEndpoint: BlockManagerMasterEndpoint up
19/10/28 17:05:27 INFO DiskBlockManager: Created local directory at /tmp/blockmgr-297de7c2-13db-4412-bd0a-1fca3a0746a0
19/10/28 17:05:27 INFO MemoryStore: MemoryStore started with capacity 366.3 MB
19/10/28 17:05:27 INFO SparkEnv: Registering OutputCommitCoordinator
19/10/28 17:05:27 INFO Utils: Successfully started service 'SparkUI' on port 4040.
19/10/28 17:05:28 INFO SparkUI: Bound SparkUI to 0.0.0.0, and started at http://192.168.10.27:4040
19/10/28 17:05:28 INFO SparkContext: Added JAR file:/tmp/adamTestxbwUJbj/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/target/adam-assembly-spark2_2.11-0.30.0-SNAPSHOT.jar at spark://192.168.10.27:38025/jars/adam-assembly-spark2_2.11-0.30.0-SNAPSHOT.jar with timestamp 1572307528033
19/10/28 17:05:28 INFO Executor: Starting executor ID driver on host localhost
19/10/28 17:05:28 INFO Utils: Successfully started service 'org.apache.spark.network.netty.NettyBlockTransferService' on port 45869.
19/10/28 17:05:28 INFO NettyBlockTransferService: Server created on 192.168.10.27:45869
19/10/28 17:05:28 INFO BlockManager: Using org.apache.spark.storage.RandomBlockReplicationPolicy for block replication policy
19/10/28 17:05:28 INFO BlockManagerMaster: Registering BlockManager BlockManagerId(driver, 192.168.10.27, 45869, None)
19/10/28 17:05:28 INFO BlockManagerMasterEndpoint: Registering block manager 192.168.10.27:45869 with 366.3 MB RAM, BlockManagerId(driver, 192.168.10.27, 45869, None)
19/10/28 17:05:28 INFO BlockManagerMaster: Registered BlockManager BlockManagerId(driver, 192.168.10.27, 45869, None)
19/10/28 17:05:28 INFO BlockManager: Initialized BlockManager: BlockManagerId(driver, 192.168.10.27, 45869, None)
19/10/28 17:05:28 INFO ADAMContext: Loading mouse_chrM.bam as BAM/CRAM/SAM and converting to Alignments.
19/10/28 17:05:28 INFO ADAMContext: Loaded header from file:/tmp/adamTestxbwUJbj/deleteMePleaseThisIsNoLongerNeeded/mouse_chrM.bam
19/10/28 17:05:29 INFO MemoryStore: Block broadcast_0 stored as values in memory (estimated size 284.3 KB, free 366.0 MB)
19/10/28 17:05:29 INFO MemoryStore: Block broadcast_0_piece0 stored as bytes in memory (estimated size 23.1 KB, free 366.0 MB)
19/10/28 17:05:29 INFO BlockManagerInfo: Added broadcast_0_piece0 in memory on 192.168.10.27:45869 (size: 23.1 KB, free: 366.3 MB)
19/10/28 17:05:29 INFO SparkContext: Created broadcast 0 from newAPIHadoopFile at ADAMContext.scala:2058
19/10/28 17:05:30 INFO RDDBoundAlignmentDataset: Saving data in ADAM format
19/10/28 17:05:30 INFO FileOutputCommitter: File Output Committer Algorithm version is 1
19/10/28 17:05:30 INFO FileInputFormat: Total input paths to process : 1
19/10/28 17:05:30 INFO SparkContext: Starting job: runJob at SparkHadoopWriter.scala:78
19/10/28 17:05:30 INFO DAGScheduler: Got job 0 (runJob at SparkHadoopWriter.scala:78) with 1 output partitions
19/10/28 17:05:30 INFO DAGScheduler: Final stage: ResultStage 0 (runJob at SparkHadoopWriter.scala:78)
19/10/28 17:05:30 INFO DAGScheduler: Parents of final stage: List()
19/10/28 17:05:30 INFO DAGScheduler: Missing parents: List()
19/10/28 17:05:30 INFO DAGScheduler: Submitting ResultStage 0 (MapPartitionsRDD[2] at map at GenomicDataset.scala:3814), which has no missing parents
19/10/28 17:05:30 INFO MemoryStore: Block broadcast_1 stored as values in memory (estimated size 82.0 KB, free 365.9 MB)
19/10/28 17:05:30 INFO MemoryStore: Block broadcast_1_piece0 stored as bytes in memory (estimated size 30.2 KB, free 365.9 MB)
19/10/28 17:05:30 INFO BlockManagerInfo: Added broadcast_1_piece0 in memory on 192.168.10.27:45869 (size: 30.2 KB, free: 366.2 MB)
19/10/28 17:05:30 INFO SparkContext: Created broadcast 1 from broadcast at DAGScheduler.scala:1161
19/10/28 17:05:31 INFO DAGScheduler: Submitting 1 missing tasks from ResultStage 0 (MapPartitionsRDD[2] at map at GenomicDataset.scala:3814) (first 15 tasks are for partitions Vector(0))
19/10/28 17:05:31 INFO TaskSchedulerImpl: Adding task set 0.0 with 1 tasks
19/10/28 17:05:31 INFO TaskSetManager: Starting task 0.0 in stage 0.0 (TID 0, localhost, executor driver, partition 0, PROCESS_LOCAL, 7962 bytes)
19/10/28 17:05:31 INFO Executor: Running task 0.0 in stage 0.0 (TID 0)
19/10/28 17:05:31 INFO Executor: Fetching spark://192.168.10.27:38025/jars/adam-assembly-spark2_2.11-0.30.0-SNAPSHOT.jar with timestamp 1572307528033
19/10/28 17:05:31 INFO TransportClientFactory: Successfully created connection to /192.168.10.27:38025 after 141 ms (0 ms spent in bootstraps)
19/10/28 17:05:31 INFO Utils: Fetching spark://192.168.10.27:38025/jars/adam-assembly-spark2_2.11-0.30.0-SNAPSHOT.jar to /tmp/spark-1b4fa86f-35af-4811-9561-37407ca0b854/userFiles-fb68e5f5-d177-4170-96ee-23a0f900fcd8/fetchFileTemp9019245134523870358.tmp
19/10/28 17:05:31 INFO Executor: Adding file:/tmp/spark-1b4fa86f-35af-4811-9561-37407ca0b854/userFiles-fb68e5f5-d177-4170-96ee-23a0f900fcd8/adam-assembly-spark2_2.11-0.30.0-SNAPSHOT.jar to class loader
19/10/28 17:05:31 INFO NewHadoopRDD: Input split: file:/tmp/adamTestxbwUJbj/deleteMePleaseThisIsNoLongerNeeded/mouse_chrM.bam:83361792-833134657535
19/10/28 17:05:31 INFO FileOutputCommitter: File Output Committer Algorithm version is 1
19/10/28 17:05:31 INFO CodecConfig: Compression: GZIP
19/10/28 17:05:31 INFO FileOutputCommitter: File Output Committer Algorithm version is 1
19/10/28 17:05:31 INFO ParquetOutputFormat: Parquet block size to 134217728
19/10/28 17:05:31 INFO ParquetOutputFormat: Parquet page size to 1048576
19/10/28 17:05:31 INFO ParquetOutputFormat: Parquet dictionary page size to 1048576
19/10/28 17:05:31 INFO ParquetOutputFormat: Dictionary is on
19/10/28 17:05:31 INFO ParquetOutputFormat: Validation is off
19/10/28 17:05:31 INFO ParquetOutputFormat: Writer version is: PARQUET_1_0
19/10/28 17:05:31 INFO ParquetOutputFormat: Maximum row group padding size is 8388608 bytes
19/10/28 17:05:31 INFO ParquetOutputFormat: Page size checking is: estimated
19/10/28 17:05:31 INFO ParquetOutputFormat: Min row count for page size check is: 100
19/10/28 17:05:31 INFO ParquetOutputFormat: Max row count for page size check is: 10000
19/10/28 17:05:31 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.
19/10/28 17:05:41 INFO InternalParquetRecordWriter: Flushing mem columnStore to file. allocated memory: 16043959
19/10/28 17:05:42 INFO FileOutputCommitter: Saved output of task 'attempt_20191028170530_0002_r_000000_0' to file:/tmp/adamTestxbwUJbj/deleteMePleaseThisIsNoLongerNeeded/mouse_chrM.bam.reads.adam/_temporary/0/task_20191028170530_0002_r_000000
19/10/28 17:05:42 INFO SparkHadoopMapRedUtil: attempt_20191028170530_0002_r_000000_0: Committed
19/10/28 17:05:42 INFO Executor: Finished task 0.0 in stage 0.0 (TID 0). 893 bytes result sent to driver
19/10/28 17:05:42 INFO TaskSetManager: Finished task 0.0 in stage 0.0 (TID 0) in 11117 ms on localhost (executor driver) (1/1)
19/10/28 17:05:42 INFO TaskSchedulerImpl: Removed TaskSet 0.0, whose tasks have all completed, from pool 
19/10/28 17:05:42 INFO DAGScheduler: ResultStage 0 (runJob at SparkHadoopWriter.scala:78) finished in 11.230 s
19/10/28 17:05:42 INFO DAGScheduler: Job 0 finished: runJob at SparkHadoopWriter.scala:78, took 11.287854 s
19/10/28 17:05:42 INFO ParquetFileReader: Initiating action with parallelism: 5
19/10/28 17:05:42 INFO SparkHadoopWriter: Job job_20191028170530_0002 committed.
19/10/28 17:05:42 INFO TransformAlignments: Overall Duration: 15.03 secs
19/10/28 17:05:42 INFO SparkContext: Invoking stop() from shutdown hook
19/10/28 17:05:42 INFO SparkUI: Stopped Spark web UI at http://192.168.10.27:4040
19/10/28 17:05:42 INFO MapOutputTrackerMasterEndpoint: MapOutputTrackerMasterEndpoint stopped!
19/10/28 17:05:42 INFO MemoryStore: MemoryStore cleared
19/10/28 17:05:42 INFO BlockManager: BlockManager stopped
19/10/28 17:05:42 INFO BlockManagerMaster: BlockManagerMaster stopped
19/10/28 17:05:42 INFO OutputCommitCoordinator$OutputCommitCoordinatorEndpoint: OutputCommitCoordinator stopped!
19/10/28 17:05:42 INFO SparkContext: Successfully stopped SparkContext
19/10/28 17:05:42 INFO ShutdownHookManager: Shutdown hook called
19/10/28 17:05:42 INFO ShutdownHookManager: Deleting directory /tmp/spark-1b4fa86f-35af-4811-9561-37407ca0b854
19/10/28 17:05:42 INFO ShutdownHookManager: Deleting directory /tmp/spark-f2c1cbfe-0ea1-44f5-93a1-796095200b8d

# 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/adamTestxbwUJbj/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.4-bin-hadoop2.7/bin/spark-submit
19/10/28 17:05:43 WARN 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)
19/10/28 17:05:43 WARN Utils: Set SPARK_LOCAL_IP if you need to bind to another address
19/10/28 17:05:44 WARN NativeCodeLoader: Unable to load native-hadoop library for your platform... using builtin-java classes where applicable
log4j:WARN No appenders could be found for logger (org.bdgenomics.adam.cli.ADAMMain).
log4j:WARN Please initialize the log4j system properly.
log4j:WARN See http://logging.apache.org/log4j/1.2/faq.html#noconfig for more info.
Using Spark's default log4j profile: org/apache/spark/log4j-defaults.properties
19/10/28 17:05:44 INFO SparkContext: Running Spark version 2.4.4
19/10/28 17:05:44 INFO SparkContext: Submitted application: transformAlignments
19/10/28 17:05:44 INFO SecurityManager: Changing view acls to: jenkins
19/10/28 17:05:44 INFO SecurityManager: Changing modify acls to: jenkins
19/10/28 17:05:44 INFO SecurityManager: Changing view acls groups to: 
19/10/28 17:05:44 INFO SecurityManager: Changing modify acls groups to: 
19/10/28 17:05:44 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()
19/10/28 17:05:44 INFO Utils: Successfully started service 'sparkDriver' on port 42027.
19/10/28 17:05:44 INFO SparkEnv: Registering MapOutputTracker
19/10/28 17:05:44 INFO SparkEnv: Registering BlockManagerMaster
19/10/28 17:05:44 INFO BlockManagerMasterEndpoint: Using org.apache.spark.storage.DefaultTopologyMapper for getting topology information
19/10/28 17:05:44 INFO BlockManagerMasterEndpoint: BlockManagerMasterEndpoint up
19/10/28 17:05:44 INFO DiskBlockManager: Created local directory at /tmp/blockmgr-afe04f17-bdf1-4f3f-b1f0-bf70b2ae3b90
19/10/28 17:05:44 INFO MemoryStore: MemoryStore started with capacity 366.3 MB
19/10/28 17:05:44 INFO SparkEnv: Registering OutputCommitCoordinator
19/10/28 17:05:44 INFO Utils: Successfully started service 'SparkUI' on port 4040.
19/10/28 17:05:44 INFO SparkUI: Bound SparkUI to 0.0.0.0, and started at http://192.168.10.27:4040
19/10/28 17:05:45 INFO SparkContext: Added JAR file:/tmp/adamTestxbwUJbj/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/target/adam-assembly-spark2_2.11-0.30.0-SNAPSHOT.jar at spark://192.168.10.27:42027/jars/adam-assembly-spark2_2.11-0.30.0-SNAPSHOT.jar with timestamp 1572307545005
19/10/28 17:05:45 INFO Executor: Starting executor ID driver on host localhost
19/10/28 17:05:45 INFO Utils: Successfully started service 'org.apache.spark.network.netty.NettyBlockTransferService' on port 45243.
19/10/28 17:05:45 INFO NettyBlockTransferService: Server created on 192.168.10.27:45243
19/10/28 17:05:45 INFO BlockManager: Using org.apache.spark.storage.RandomBlockReplicationPolicy for block replication policy
19/10/28 17:05:45 INFO BlockManagerMaster: Registering BlockManager BlockManagerId(driver, 192.168.10.27, 45243, None)
19/10/28 17:05:45 INFO BlockManagerMasterEndpoint: Registering block manager 192.168.10.27:45243 with 366.3 MB RAM, BlockManagerId(driver, 192.168.10.27, 45243, None)
19/10/28 17:05:45 INFO BlockManagerMaster: Registered BlockManager BlockManagerId(driver, 192.168.10.27, 45243, None)
19/10/28 17:05:45 INFO BlockManager: Initialized BlockManager: BlockManagerId(driver, 192.168.10.27, 45243, None)
19/10/28 17:05:45 INFO ADAMContext: Loading mouse_chrM.bam.reads.adam as Parquet of Alignments.
19/10/28 17:05:46 INFO ADAMContext: Reading the ADAM file at mouse_chrM.bam.reads.adam to create RDD
19/10/28 17:05:47 INFO MemoryStore: Block broadcast_0 stored as values in memory (estimated size 303.7 KB, free 366.0 MB)
19/10/28 17:05:47 INFO MemoryStore: Block broadcast_0_piece0 stored as bytes in memory (estimated size 27.4 KB, free 366.0 MB)
19/10/28 17:05:47 INFO BlockManagerInfo: Added broadcast_0_piece0 in memory on 192.168.10.27:45243 (size: 27.4 KB, free: 366.3 MB)
19/10/28 17:05:47 INFO SparkContext: Created broadcast 0 from newAPIHadoopFile at ADAMContext.scala:1796
19/10/28 17:05:47 INFO TransformAlignments: Sorting alignments by reference position, with references ordered by name
19/10/28 17:05:47 INFO RDDBoundAlignmentDataset: Sorting alignments by reference position
19/10/28 17:05:47 INFO FileInputFormat: Total input paths to process : 1
19/10/28 17:05:47 INFO ParquetInputFormat: Total input paths to process : 1
19/10/28 17:05:47 INFO RDDBoundAlignmentDataset: Saving data in ADAM format
19/10/28 17:05:47 INFO FileOutputCommitter: File Output Committer Algorithm version is 1
19/10/28 17:05:47 INFO SparkContext: Starting job: runJob at SparkHadoopWriter.scala:78
19/10/28 17:05:47 INFO DAGScheduler: Registering RDD 2 (sortBy at AlignmentDataset.scala:1008)
19/10/28 17:05:47 INFO DAGScheduler: Got job 0 (runJob at SparkHadoopWriter.scala:78) with 1 output partitions
19/10/28 17:05:47 INFO DAGScheduler: Final stage: ResultStage 1 (runJob at SparkHadoopWriter.scala:78)
19/10/28 17:05:47 INFO DAGScheduler: Parents of final stage: List(ShuffleMapStage 0)
19/10/28 17:05:47 INFO DAGScheduler: Missing parents: List(ShuffleMapStage 0)
19/10/28 17:05:47 INFO DAGScheduler: Submitting ShuffleMapStage 0 (MapPartitionsRDD[2] at sortBy at AlignmentDataset.scala:1008), which has no missing parents
19/10/28 17:05:47 INFO MemoryStore: Block broadcast_1 stored as values in memory (estimated size 5.0 KB, free 366.0 MB)
19/10/28 17:05:47 INFO MemoryStore: Block broadcast_1_piece0 stored as bytes in memory (estimated size 2.9 KB, free 366.0 MB)
19/10/28 17:05:47 INFO BlockManagerInfo: Added broadcast_1_piece0 in memory on 192.168.10.27:45243 (size: 2.9 KB, free: 366.3 MB)
19/10/28 17:05:47 INFO SparkContext: Created broadcast 1 from broadcast at DAGScheduler.scala:1161
19/10/28 17:05:47 INFO DAGScheduler: Submitting 1 missing tasks from ShuffleMapStage 0 (MapPartitionsRDD[2] at sortBy at AlignmentDataset.scala:1008) (first 15 tasks are for partitions Vector(0))
19/10/28 17:05:47 INFO TaskSchedulerImpl: Adding task set 0.0 with 1 tasks
19/10/28 17:05:47 INFO TaskSetManager: Starting task 0.0 in stage 0.0 (TID 0, localhost, executor driver, partition 0, PROCESS_LOCAL, 8001 bytes)
19/10/28 17:05:47 INFO Executor: Running task 0.0 in stage 0.0 (TID 0)
19/10/28 17:05:48 INFO Executor: Fetching spark://192.168.10.27:42027/jars/adam-assembly-spark2_2.11-0.30.0-SNAPSHOT.jar with timestamp 1572307545005
19/10/28 17:05:48 INFO TransportClientFactory: Successfully created connection to /192.168.10.27:42027 after 36 ms (0 ms spent in bootstraps)
19/10/28 17:05:48 INFO Utils: Fetching spark://192.168.10.27:42027/jars/adam-assembly-spark2_2.11-0.30.0-SNAPSHOT.jar to /tmp/spark-d5010c5a-11ac-45ab-9ab5-c644bc3d1f52/userFiles-3e2342c6-37c6-4820-89aa-b5207793f89b/fetchFileTemp1163045513780038378.tmp
19/10/28 17:05:48 INFO Executor: Adding file:/tmp/spark-d5010c5a-11ac-45ab-9ab5-c644bc3d1f52/userFiles-3e2342c6-37c6-4820-89aa-b5207793f89b/adam-assembly-spark2_2.11-0.30.0-SNAPSHOT.jar to class loader
19/10/28 17:05:48 INFO NewHadoopRDD: Input split: file:/tmp/adamTestxbwUJbj/deleteMePleaseThisIsNoLongerNeeded/mouse_chrM.bam.reads.adam/part-r-00000.gz.parquet:0+10132211
19/10/28 17:05:48 INFO InternalParquetRecordReader: RecordReader initialized will read a total of 163064 records.
19/10/28 17:05:48 INFO InternalParquetRecordReader: at row 0. reading next block
19/10/28 17:05:48 INFO CodecPool: Got brand-new decompressor [.gz]
19/10/28 17:05:48 INFO InternalParquetRecordReader: block read in memory in 45 ms. row count = 163064
19/10/28 17:05:51 INFO Executor: Finished task 0.0 in stage 0.0 (TID 0). 999 bytes result sent to driver
19/10/28 17:05:51 INFO TaskSetManager: Finished task 0.0 in stage 0.0 (TID 0) in 3416 ms on localhost (executor driver) (1/1)
19/10/28 17:05:51 INFO TaskSchedulerImpl: Removed TaskSet 0.0, whose tasks have all completed, from pool 
19/10/28 17:05:51 INFO DAGScheduler: ShuffleMapStage 0 (sortBy at AlignmentDataset.scala:1008) finished in 3.552 s
19/10/28 17:05:51 INFO DAGScheduler: looking for newly runnable stages
19/10/28 17:05:51 INFO DAGScheduler: running: Set()
19/10/28 17:05:51 INFO DAGScheduler: waiting: Set(ResultStage 1)
19/10/28 17:05:51 INFO DAGScheduler: failed: Set()
19/10/28 17:05:51 INFO DAGScheduler: Submitting ResultStage 1 (MapPartitionsRDD[5] at map at GenomicDataset.scala:3814), which has no missing parents
19/10/28 17:05:51 INFO MemoryStore: Block broadcast_2 stored as values in memory (estimated size 83.3 KB, free 365.9 MB)
19/10/28 17:05:51 INFO MemoryStore: Block broadcast_2_piece0 stored as bytes in memory (estimated size 30.9 KB, free 365.9 MB)
19/10/28 17:05:51 INFO BlockManagerInfo: Added broadcast_2_piece0 in memory on 192.168.10.27:45243 (size: 30.9 KB, free: 366.2 MB)
19/10/28 17:05:51 INFO SparkContext: Created broadcast 2 from broadcast at DAGScheduler.scala:1161
19/10/28 17:05:51 INFO DAGScheduler: Submitting 1 missing tasks from ResultStage 1 (MapPartitionsRDD[5] at map at GenomicDataset.scala:3814) (first 15 tasks are for partitions Vector(0))
19/10/28 17:05:51 INFO TaskSchedulerImpl: Adding task set 1.0 with 1 tasks
19/10/28 17:05:51 INFO TaskSetManager: Starting task 0.0 in stage 1.0 (TID 1, localhost, executor driver, partition 0, ANY, 7662 bytes)
19/10/28 17:05:51 INFO Executor: Running task 0.0 in stage 1.0 (TID 1)
19/10/28 17:05:51 INFO ShuffleBlockFetcherIterator: Getting 1 non-empty blocks including 1 local blocks and 0 remote blocks
19/10/28 17:05:51 INFO ShuffleBlockFetcherIterator: Started 0 remote fetches in 7 ms
19/10/28 17:05:53 INFO FileOutputCommitter: File Output Committer Algorithm version is 1
19/10/28 17:05:53 INFO CodecConfig: Compression: GZIP
19/10/28 17:05:53 INFO FileOutputCommitter: File Output Committer Algorithm version is 1
19/10/28 17:05:53 INFO ParquetOutputFormat: Parquet block size to 134217728
19/10/28 17:05:53 INFO ParquetOutputFormat: Parquet page size to 1048576
19/10/28 17:05:53 INFO ParquetOutputFormat: Parquet dictionary page size to 1048576
19/10/28 17:05:53 INFO ParquetOutputFormat: Dictionary is on
19/10/28 17:05:53 INFO ParquetOutputFormat: Validation is off
19/10/28 17:05:53 INFO ParquetOutputFormat: Writer version is: PARQUET_1_0
19/10/28 17:05:53 INFO ParquetOutputFormat: Maximum row group padding size is 8388608 bytes
19/10/28 17:05:53 INFO ParquetOutputFormat: Page size checking is: estimated
19/10/28 17:05:53 INFO ParquetOutputFormat: Min row count for page size check is: 100
19/10/28 17:05:53 INFO ParquetOutputFormat: Max row count for page size check is: 10000
19/10/28 17:05:53 INFO CodecPool: Got brand-new compressor [.gz]
19/10/28 17:05:57 INFO InternalParquetRecordWriter: Flushing mem columnStore to file. allocated memory: 16004474
19/10/28 17:05:57 INFO FileOutputCommitter: Saved output of task 'attempt_20191028170547_0005_r_000000_0' to file:/tmp/adamTestxbwUJbj/deleteMePleaseThisIsNoLongerNeeded/mouse_chrM.bam.reads.sorted.adam/_temporary/0/task_20191028170547_0005_r_000000
19/10/28 17:05:57 INFO SparkHadoopMapRedUtil: attempt_20191028170547_0005_r_000000_0: Committed
19/10/28 17:05:57 INFO Executor: Finished task 0.0 in stage 1.0 (TID 1). 1280 bytes result sent to driver
19/10/28 17:05:57 INFO TaskSetManager: Finished task 0.0 in stage 1.0 (TID 1) in 6233 ms on localhost (executor driver) (1/1)
19/10/28 17:05:57 INFO TaskSchedulerImpl: Removed TaskSet 1.0, whose tasks have all completed, from pool 
19/10/28 17:05:57 INFO DAGScheduler: ResultStage 1 (runJob at SparkHadoopWriter.scala:78) finished in 6.289 s
19/10/28 17:05:57 INFO DAGScheduler: Job 0 finished: runJob at SparkHadoopWriter.scala:78, took 9.930483 s
19/10/28 17:05:57 INFO ParquetFileReader: Initiating action with parallelism: 5
19/10/28 17:05:57 INFO SparkHadoopWriter: Job job_20191028170547_0005 committed.
19/10/28 17:05:57 INFO TransformAlignments: Overall Duration: 13.55 secs
19/10/28 17:05:57 INFO SparkContext: Invoking stop() from shutdown hook
19/10/28 17:05:57 INFO SparkUI: Stopped Spark web UI at http://192.168.10.27:4040
19/10/28 17:05:57 INFO MapOutputTrackerMasterEndpoint: MapOutputTrackerMasterEndpoint stopped!
19/10/28 17:05:57 INFO MemoryStore: MemoryStore cleared
19/10/28 17:05:57 INFO BlockManager: BlockManager stopped
19/10/28 17:05:57 INFO BlockManagerMaster: BlockManagerMaster stopped
19/10/28 17:05:57 INFO OutputCommitCoordinator$OutputCommitCoordinatorEndpoint: OutputCommitCoordinator stopped!
19/10/28 17:05:57 INFO SparkContext: Successfully stopped SparkContext
19/10/28 17:05:57 INFO ShutdownHookManager: Shutdown hook called
19/10/28 17:05:57 INFO ShutdownHookManager: Deleting directory /tmp/spark-0bb5b832-d90d-4552-a3a3-b311b102b30b
19/10/28 17:05:57 INFO ShutdownHookManager: Deleting directory /tmp/spark-d5010c5a-11ac-45ab-9ab5-c644bc3d1f52

# 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/adamTestxbwUJbj/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.4-bin-hadoop2.7/bin/spark-submit
19/10/28 17:05:59 WARN 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)
19/10/28 17:05:59 WARN Utils: Set SPARK_LOCAL_IP if you need to bind to another address
19/10/28 17:05:59 WARN NativeCodeLoader: Unable to load native-hadoop library for your platform... using builtin-java classes where applicable
log4j:WARN No appenders could be found for logger (org.bdgenomics.adam.cli.ADAMMain).
log4j:WARN Please initialize the log4j system properly.
log4j:WARN See http://logging.apache.org/log4j/1.2/faq.html#noconfig for more info.
Using Spark's default log4j profile: org/apache/spark/log4j-defaults.properties
19/10/28 17:05:59 INFO SparkContext: Running Spark version 2.4.4
19/10/28 17:05:59 INFO SparkContext: Submitted application: transformFragments
19/10/28 17:05:59 INFO SecurityManager: Changing view acls to: jenkins
19/10/28 17:05:59 INFO SecurityManager: Changing modify acls to: jenkins
19/10/28 17:05:59 INFO SecurityManager: Changing view acls groups to: 
19/10/28 17:05:59 INFO SecurityManager: Changing modify acls groups to: 
19/10/28 17:05:59 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()
19/10/28 17:06:00 INFO Utils: Successfully started service 'sparkDriver' on port 38881.
19/10/28 17:06:00 INFO SparkEnv: Registering MapOutputTracker
19/10/28 17:06:00 INFO SparkEnv: Registering BlockManagerMaster
19/10/28 17:06:00 INFO BlockManagerMasterEndpoint: Using org.apache.spark.storage.DefaultTopologyMapper for getting topology information
19/10/28 17:06:00 INFO BlockManagerMasterEndpoint: BlockManagerMasterEndpoint up
19/10/28 17:06:00 INFO DiskBlockManager: Created local directory at /tmp/blockmgr-e855f904-3ef3-42db-8b2b-6d30d2eae821
19/10/28 17:06:00 INFO MemoryStore: MemoryStore started with capacity 366.3 MB
19/10/28 17:06:00 INFO SparkEnv: Registering OutputCommitCoordinator
19/10/28 17:06:00 INFO Utils: Successfully started service 'SparkUI' on port 4040.
19/10/28 17:06:00 INFO SparkUI: Bound SparkUI to 0.0.0.0, and started at http://192.168.10.27:4040
19/10/28 17:06:00 INFO SparkContext: Added JAR file:/tmp/adamTestxbwUJbj/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/target/adam-assembly-spark2_2.11-0.30.0-SNAPSHOT.jar at spark://192.168.10.27:38881/jars/adam-assembly-spark2_2.11-0.30.0-SNAPSHOT.jar with timestamp 1572307560662
19/10/28 17:06:00 INFO Executor: Starting executor ID driver on host localhost
19/10/28 17:06:00 INFO Utils: Successfully started service 'org.apache.spark.network.netty.NettyBlockTransferService' on port 36269.
19/10/28 17:06:00 INFO NettyBlockTransferService: Server created on 192.168.10.27:36269
19/10/28 17:06:00 INFO BlockManager: Using org.apache.spark.storage.RandomBlockReplicationPolicy for block replication policy
19/10/28 17:06:00 INFO BlockManagerMaster: Registering BlockManager BlockManagerId(driver, 192.168.10.27, 36269, None)
19/10/28 17:06:00 INFO BlockManagerMasterEndpoint: Registering block manager 192.168.10.27:36269 with 366.3 MB RAM, BlockManagerId(driver, 192.168.10.27, 36269, None)
19/10/28 17:06:00 INFO BlockManagerMaster: Registered BlockManager BlockManagerId(driver, 192.168.10.27, 36269, None)
19/10/28 17:06:00 INFO BlockManager: Initialized BlockManager: BlockManagerId(driver, 192.168.10.27, 36269, None)
19/10/28 17:06:01 INFO ADAMContext: Loading mouse_chrM.bam.reads.adam as Parquet of Alignments.
19/10/28 17:06:02 INFO ADAMContext: Reading the ADAM file at mouse_chrM.bam.reads.adam to create RDD
19/10/28 17:06:02 INFO MemoryStore: Block broadcast_0 stored as values in memory (estimated size 303.7 KB, free 366.0 MB)
19/10/28 17:06:03 INFO MemoryStore: Block broadcast_0_piece0 stored as bytes in memory (estimated size 27.4 KB, free 366.0 MB)
19/10/28 17:06:03 INFO BlockManagerInfo: Added broadcast_0_piece0 in memory on 192.168.10.27:36269 (size: 27.4 KB, free: 366.3 MB)
19/10/28 17:06:03 INFO SparkContext: Created broadcast 0 from newAPIHadoopFile at ADAMContext.scala:1796
19/10/28 17:06:03 INFO FileInputFormat: Total input paths to process : 1
19/10/28 17:06:03 INFO ParquetInputFormat: Total input paths to process : 1
19/10/28 17:06:03 INFO RDDBoundFragmentDataset: Saving data in ADAM format
19/10/28 17:06:03 INFO FileOutputCommitter: File Output Committer Algorithm version is 1
19/10/28 17:06:03 INFO SparkContext: Starting job: runJob at SparkHadoopWriter.scala:78
19/10/28 17:06:03 INFO DAGScheduler: Registering RDD 2 (groupBy at SingleReadBucket.scala:97)
19/10/28 17:06:03 INFO DAGScheduler: Got job 0 (runJob at SparkHadoopWriter.scala:78) with 1 output partitions
19/10/28 17:06:03 INFO DAGScheduler: Final stage: ResultStage 1 (runJob at SparkHadoopWriter.scala:78)
19/10/28 17:06:03 INFO DAGScheduler: Parents of final stage: List(ShuffleMapStage 0)
19/10/28 17:06:03 INFO DAGScheduler: Missing parents: List(ShuffleMapStage 0)
19/10/28 17:06:03 INFO DAGScheduler: Submitting ShuffleMapStage 0 (MapPartitionsRDD[2] at groupBy at SingleReadBucket.scala:97), which has no missing parents
19/10/28 17:06:03 INFO MemoryStore: Block broadcast_1 stored as values in memory (estimated size 5.3 KB, free 366.0 MB)
19/10/28 17:06:03 INFO MemoryStore: Block broadcast_1_piece0 stored as bytes in memory (estimated size 3.0 KB, free 366.0 MB)
19/10/28 17:06:03 INFO BlockManagerInfo: Added broadcast_1_piece0 in memory on 192.168.10.27:36269 (size: 3.0 KB, free: 366.3 MB)
19/10/28 17:06:03 INFO SparkContext: Created broadcast 1 from broadcast at DAGScheduler.scala:1161
19/10/28 17:06:03 INFO DAGScheduler: Submitting 1 missing tasks from ShuffleMapStage 0 (MapPartitionsRDD[2] at groupBy at SingleReadBucket.scala:97) (first 15 tasks are for partitions Vector(0))
19/10/28 17:06:03 INFO TaskSchedulerImpl: Adding task set 0.0 with 1 tasks
19/10/28 17:06:03 INFO TaskSetManager: Starting task 0.0 in stage 0.0 (TID 0, localhost, executor driver, partition 0, PROCESS_LOCAL, 8001 bytes)
19/10/28 17:06:03 INFO Executor: Running task 0.0 in stage 0.0 (TID 0)
19/10/28 17:06:03 INFO Executor: Fetching spark://192.168.10.27:38881/jars/adam-assembly-spark2_2.11-0.30.0-SNAPSHOT.jar with timestamp 1572307560662
19/10/28 17:06:03 INFO TransportClientFactory: Successfully created connection to /192.168.10.27:38881 after 31 ms (0 ms spent in bootstraps)
19/10/28 17:06:03 INFO Utils: Fetching spark://192.168.10.27:38881/jars/adam-assembly-spark2_2.11-0.30.0-SNAPSHOT.jar to /tmp/spark-90da5fa1-e974-420a-a535-3552c4765728/userFiles-beea6e13-2337-4242-b05c-51cd1a7940bf/fetchFileTemp7659381037043078224.tmp
19/10/28 17:06:04 INFO Executor: Adding file:/tmp/spark-90da5fa1-e974-420a-a535-3552c4765728/userFiles-beea6e13-2337-4242-b05c-51cd1a7940bf/adam-assembly-spark2_2.11-0.30.0-SNAPSHOT.jar to class loader
19/10/28 17:06:04 INFO NewHadoopRDD: Input split: file:/tmp/adamTestxbwUJbj/deleteMePleaseThisIsNoLongerNeeded/mouse_chrM.bam.reads.adam/part-r-00000.gz.parquet:0+10132211
19/10/28 17:06:04 INFO InternalParquetRecordReader: RecordReader initialized will read a total of 163064 records.
19/10/28 17:06:04 INFO InternalParquetRecordReader: at row 0. reading next block
19/10/28 17:06:04 INFO CodecPool: Got brand-new decompressor [.gz]
19/10/28 17:06:04 INFO InternalParquetRecordReader: block read in memory in 49 ms. row count = 163064
19/10/28 17:06:07 INFO Executor: Finished task 0.0 in stage 0.0 (TID 0). 956 bytes result sent to driver
19/10/28 17:06:07 INFO TaskSetManager: Finished task 0.0 in stage 0.0 (TID 0) in 3482 ms on localhost (executor driver) (1/1)
19/10/28 17:06:07 INFO TaskSchedulerImpl: Removed TaskSet 0.0, whose tasks have all completed, from pool 
19/10/28 17:06:07 INFO DAGScheduler: ShuffleMapStage 0 (groupBy at SingleReadBucket.scala:97) finished in 3.590 s
19/10/28 17:06:07 INFO DAGScheduler: looking for newly runnable stages
19/10/28 17:06:07 INFO DAGScheduler: running: Set()
19/10/28 17:06:07 INFO DAGScheduler: waiting: Set(ResultStage 1)
19/10/28 17:06:07 INFO DAGScheduler: failed: Set()
19/10/28 17:06:07 INFO DAGScheduler: Submitting ResultStage 1 (MapPartitionsRDD[6] at map at GenomicDataset.scala:3814), which has no missing parents
19/10/28 17:06:07 INFO MemoryStore: Block broadcast_2 stored as values in memory (estimated size 86.2 KB, free 365.9 MB)
19/10/28 17:06:07 INFO MemoryStore: Block broadcast_2_piece0 stored as bytes in memory (estimated size 32.1 KB, free 365.9 MB)
19/10/28 17:06:07 INFO BlockManagerInfo: Added broadcast_2_piece0 in memory on 192.168.10.27:36269 (size: 32.1 KB, free: 366.2 MB)
19/10/28 17:06:07 INFO SparkContext: Created broadcast 2 from broadcast at DAGScheduler.scala:1161
19/10/28 17:06:07 INFO DAGScheduler: Submitting 1 missing tasks from ResultStage 1 (MapPartitionsRDD[6] at map at GenomicDataset.scala:3814) (first 15 tasks are for partitions Vector(0))
19/10/28 17:06:07 INFO TaskSchedulerImpl: Adding task set 1.0 with 1 tasks
19/10/28 17:06:07 INFO TaskSetManager: Starting task 0.0 in stage 1.0 (TID 1, localhost, executor driver, partition 0, ANY, 7662 bytes)
19/10/28 17:06:07 INFO Executor: Running task 0.0 in stage 1.0 (TID 1)
19/10/28 17:06:07 INFO ShuffleBlockFetcherIterator: Getting 1 non-empty blocks including 1 local blocks and 0 remote blocks
19/10/28 17:06:07 INFO ShuffleBlockFetcherIterator: Started 0 remote fetches in 7 ms
19/10/28 17:06:08 INFO BlockManagerInfo: Removed broadcast_1_piece0 on 192.168.10.27:36269 in memory (size: 3.0 KB, free: 366.2 MB)
19/10/28 17:06:09 INFO FileOutputCommitter: File Output Committer Algorithm version is 1
19/10/28 17:06:09 INFO CodecConfig: Compression: GZIP
19/10/28 17:06:09 INFO FileOutputCommitter: File Output Committer Algorithm version is 1
19/10/28 17:06:09 INFO ParquetOutputFormat: Parquet block size to 134217728
19/10/28 17:06:09 INFO ParquetOutputFormat: Parquet page size to 1048576
19/10/28 17:06:09 INFO ParquetOutputFormat: Parquet dictionary page size to 1048576
19/10/28 17:06:09 INFO ParquetOutputFormat: Dictionary is on
19/10/28 17:06:09 INFO ParquetOutputFormat: Validation is off
19/10/28 17:06:09 INFO ParquetOutputFormat: Writer version is: PARQUET_1_0
19/10/28 17:06:09 INFO ParquetOutputFormat: Maximum row group padding size is 8388608 bytes
19/10/28 17:06:09 INFO ParquetOutputFormat: Page size checking is: estimated
19/10/28 17:06:09 INFO ParquetOutputFormat: Min row count for page size check is: 100
19/10/28 17:06:09 INFO ParquetOutputFormat: Max row count for page size check is: 10000
19/10/28 17:06:09 INFO CodecPool: Got brand-new compressor [.gz]
19/10/28 17:06:15 INFO InternalParquetRecordWriter: Flushing mem columnStore to file. allocated memory: 21417928
19/10/28 17:06:15 INFO FileOutputCommitter: Saved output of task 'attempt_20191028170603_0006_r_000000_0' to file:/tmp/adamTestxbwUJbj/deleteMePleaseThisIsNoLongerNeeded/mouse_chrM.bam.fragments.adam/_temporary/0/task_20191028170603_0006_r_000000
19/10/28 17:06:15 INFO SparkHadoopMapRedUtil: attempt_20191028170603_0006_r_000000_0: Committed
19/10/28 17:06:15 INFO Executor: Finished task 0.0 in stage 1.0 (TID 1). 1237 bytes result sent to driver
19/10/28 17:06:15 INFO TaskSetManager: Finished task 0.0 in stage 1.0 (TID 1) in 8700 ms on localhost (executor driver) (1/1)
19/10/28 17:06:15 INFO TaskSchedulerImpl: Removed TaskSet 1.0, whose tasks have all completed, from pool 
19/10/28 17:06:15 INFO DAGScheduler: ResultStage 1 (runJob at SparkHadoopWriter.scala:78) finished in 8.741 s
19/10/28 17:06:15 INFO DAGScheduler: Job 0 finished: runJob at SparkHadoopWriter.scala:78, took 12.403478 s
19/10/28 17:06:16 INFO ParquetFileReader: Initiating action with parallelism: 5
19/10/28 17:06:16 INFO SparkHadoopWriter: Job job_20191028170603_0006 committed.
19/10/28 17:06:16 INFO TransformFragments: Overall Duration: 16.22 secs
19/10/28 17:06:16 INFO SparkContext: Invoking stop() from shutdown hook
19/10/28 17:06:16 INFO SparkUI: Stopped Spark web UI at http://192.168.10.27:4040
19/10/28 17:06:16 INFO MapOutputTrackerMasterEndpoint: MapOutputTrackerMasterEndpoint stopped!
19/10/28 17:06:16 INFO MemoryStore: MemoryStore cleared
19/10/28 17:06:16 INFO BlockManager: BlockManager stopped
19/10/28 17:06:16 INFO BlockManagerMaster: BlockManagerMaster stopped
19/10/28 17:06:16 INFO OutputCommitCoordinator$OutputCommitCoordinatorEndpoint: OutputCommitCoordinator stopped!
19/10/28 17:06:16 INFO SparkContext: Successfully stopped SparkContext
19/10/28 17:06:16 INFO ShutdownHookManager: Shutdown hook called
19/10/28 17:06:16 INFO ShutdownHookManager: Deleting directory /tmp/spark-a7a728ef-f784-42cd-821d-af81eed5ccb6
19/10/28 17:06:16 INFO ShutdownHookManager: Deleting directory /tmp/spark-90da5fa1-e974-420a-a535-3552c4765728

# 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/adamTestxbwUJbj/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.4-bin-hadoop2.7/bin/spark-submit
19/10/28 17:06:33 WARN 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)
19/10/28 17:06:33 WARN Utils: Set SPARK_LOCAL_IP if you need to bind to another address
19/10/28 17:06:33 WARN NativeCodeLoader: Unable to load native-hadoop library for your platform... using builtin-java classes where applicable
log4j:WARN No appenders could be found for logger (org.bdgenomics.adam.cli.ADAMMain).
log4j:WARN Please initialize the log4j system properly.
log4j:WARN See http://logging.apache.org/log4j/1.2/faq.html#noconfig for more info.
Using Spark's default log4j profile: org/apache/spark/log4j-defaults.properties
19/10/28 17:06:33 INFO SparkContext: Running Spark version 2.4.4
19/10/28 17:06:33 INFO SparkContext: Submitted application: flagstat
19/10/28 17:06:33 INFO SecurityManager: Changing view acls to: jenkins
19/10/28 17:06:33 INFO SecurityManager: Changing modify acls to: jenkins
19/10/28 17:06:33 INFO SecurityManager: Changing view acls groups to: 
19/10/28 17:06:33 INFO SecurityManager: Changing modify acls groups to: 
19/10/28 17:06:33 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()
19/10/28 17:06:34 INFO Utils: Successfully started service 'sparkDriver' on port 34437.
19/10/28 17:06:34 INFO SparkEnv: Registering MapOutputTracker
19/10/28 17:06:34 INFO SparkEnv: Registering BlockManagerMaster
19/10/28 17:06:34 INFO BlockManagerMasterEndpoint: Using org.apache.spark.storage.DefaultTopologyMapper for getting topology information
19/10/28 17:06:34 INFO BlockManagerMasterEndpoint: BlockManagerMasterEndpoint up
19/10/28 17:06:34 INFO DiskBlockManager: Created local directory at /tmp/blockmgr-cb635a5b-d80c-443d-9490-bc903e7b23f3
19/10/28 17:06:34 INFO MemoryStore: MemoryStore started with capacity 366.3 MB
19/10/28 17:06:34 INFO SparkEnv: Registering OutputCommitCoordinator
19/10/28 17:06:34 INFO Utils: Successfully started service 'SparkUI' on port 4040.
19/10/28 17:06:34 INFO SparkUI: Bound SparkUI to 0.0.0.0, and started at http://192.168.10.27:4040
19/10/28 17:06:34 INFO SparkContext: Added JAR file:/tmp/adamTestxbwUJbj/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/target/adam-assembly-spark2_2.11-0.30.0-SNAPSHOT.jar at spark://192.168.10.27:34437/jars/adam-assembly-spark2_2.11-0.30.0-SNAPSHOT.jar with timestamp 1572307594352
19/10/28 17:06:34 INFO Executor: Starting executor ID driver on host localhost
19/10/28 17:06:34 INFO Utils: Successfully started service 'org.apache.spark.network.netty.NettyBlockTransferService' on port 43305.
19/10/28 17:06:34 INFO NettyBlockTransferService: Server created on 192.168.10.27:43305
19/10/28 17:06:34 INFO BlockManager: Using org.apache.spark.storage.RandomBlockReplicationPolicy for block replication policy
19/10/28 17:06:34 INFO BlockManagerMaster: Registering BlockManager BlockManagerId(driver, 192.168.10.27, 43305, None)
19/10/28 17:06:34 INFO BlockManagerMasterEndpoint: Registering block manager 192.168.10.27:43305 with 366.3 MB RAM, BlockManagerId(driver, 192.168.10.27, 43305, None)
19/10/28 17:06:34 INFO BlockManagerMaster: Registered BlockManager BlockManagerId(driver, 192.168.10.27, 43305, None)
19/10/28 17:06:34 INFO BlockManager: Initialized BlockManager: BlockManagerId(driver, 192.168.10.27, 43305, None)
19/10/28 17:06:35 INFO ADAMContext: Loading mouse_chrM.bam.reads.adam as Parquet of Alignments.
19/10/28 17:06:35 INFO ADAMContext: Reading the ADAM file at mouse_chrM.bam.reads.adam to create RDD
19/10/28 17:06:35 INFO ADAMContext: Using the specified projection schema
19/10/28 17:06:35 INFO MemoryStore: Block broadcast_0 stored as values in memory (estimated size 313.1 KB, free 366.0 MB)
19/10/28 17:06:35 INFO MemoryStore: Block broadcast_0_piece0 stored as bytes in memory (estimated size 28.4 KB, free 366.0 MB)
19/10/28 17:06:35 INFO BlockManagerInfo: Added broadcast_0_piece0 in memory on 192.168.10.27:43305 (size: 28.4 KB, free: 366.3 MB)
19/10/28 17:06:35 INFO SparkContext: Created broadcast 0 from newAPIHadoopFile at ADAMContext.scala:1796
19/10/28 17:06:37 INFO FileInputFormat: Total input paths to process : 1
19/10/28 17:06:37 INFO ParquetInputFormat: Total input paths to process : 1
19/10/28 17:06:37 INFO SparkContext: Starting job: aggregate at FlagStat.scala:115
19/10/28 17:06:37 INFO DAGScheduler: Got job 0 (aggregate at FlagStat.scala:115) with 1 output partitions
19/10/28 17:06:37 INFO DAGScheduler: Final stage: ResultStage 0 (aggregate at FlagStat.scala:115)
19/10/28 17:06:37 INFO DAGScheduler: Parents of final stage: List()
19/10/28 17:06:37 INFO DAGScheduler: Missing parents: List()
19/10/28 17:06:37 INFO DAGScheduler: Submitting ResultStage 0 (MapPartitionsRDD[4] at map at FlagStat.scala:96), which has no missing parents
19/10/28 17:06:37 INFO MemoryStore: Block broadcast_1 stored as values in memory (estimated size 12.5 KB, free 366.0 MB)
19/10/28 17:06:37 INFO MemoryStore: Block broadcast_1_piece0 stored as bytes in memory (estimated size 5.5 KB, free 365.9 MB)
19/10/28 17:06:37 INFO BlockManagerInfo: Added broadcast_1_piece0 in memory on 192.168.10.27:43305 (size: 5.5 KB, free: 366.3 MB)
19/10/28 17:06:37 INFO SparkContext: Created broadcast 1 from broadcast at DAGScheduler.scala:1161
19/10/28 17:06:37 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))
19/10/28 17:06:37 INFO TaskSchedulerImpl: Adding task set 0.0 with 1 tasks
19/10/28 17:06:37 INFO TaskSetManager: Starting task 0.0 in stage 0.0 (TID 0, localhost, executor driver, partition 0, PROCESS_LOCAL, 8012 bytes)
19/10/28 17:06:37 INFO Executor: Running task 0.0 in stage 0.0 (TID 0)
19/10/28 17:06:37 INFO Executor: Fetching spark://192.168.10.27:34437/jars/adam-assembly-spark2_2.11-0.30.0-SNAPSHOT.jar with timestamp 1572307594352
19/10/28 17:06:37 INFO TransportClientFactory: Successfully created connection to /192.168.10.27:34437 after 135 ms (0 ms spent in bootstraps)
19/10/28 17:06:37 INFO Utils: Fetching spark://192.168.10.27:34437/jars/adam-assembly-spark2_2.11-0.30.0-SNAPSHOT.jar to /tmp/spark-8bb75efb-8254-4df2-b445-4c05651d93ae/userFiles-02f7a924-92c8-451b-9f82-07e8ef93206f/fetchFileTemp2897288344783541211.tmp
19/10/28 17:06:37 INFO Executor: Adding file:/tmp/spark-8bb75efb-8254-4df2-b445-4c05651d93ae/userFiles-02f7a924-92c8-451b-9f82-07e8ef93206f/adam-assembly-spark2_2.11-0.30.0-SNAPSHOT.jar to class loader
19/10/28 17:06:37 INFO NewHadoopRDD: Input split: file:/tmp/adamTestxbwUJbj/deleteMePleaseThisIsNoLongerNeeded/mouse_chrM.bam.reads.adam/part-r-00000.gz.parquet:0+10132211
19/10/28 17:06:37 INFO InternalParquetRecordReader: RecordReader initialized will read a total of 163064 records.
19/10/28 17:06:37 INFO InternalParquetRecordReader: at row 0. reading next block
19/10/28 17:06:37 INFO CodecPool: Got brand-new decompressor [.gz]
19/10/28 17:06:37 INFO InternalParquetRecordReader: block read in memory in 24 ms. row count = 163064
19/10/28 17:06:38 INFO Executor: Finished task 0.0 in stage 0.0 (TID 0). 8196 bytes result sent to driver
19/10/28 17:06:38 INFO TaskSetManager: Finished task 0.0 in stage 0.0 (TID 0) in 1535 ms on localhost (executor driver) (1/1)
19/10/28 17:06:38 INFO TaskSchedulerImpl: Removed TaskSet 0.0, whose tasks have all completed, from pool 
19/10/28 17:06:38 INFO DAGScheduler: ResultStage 0 (aggregate at FlagStat.scala:115) finished in 1.618 s
19/10/28 17:06:38 INFO DAGScheduler: Job 0 finished: aggregate at FlagStat.scala:115, took 1.673264 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)
19/10/28 17:06:38 INFO FlagStat: Overall Duration: 5.19 secs
19/10/28 17:06:38 INFO FlagStat: Metrics:

Timings
+--------------------------------------+--------------+--------------+-------------+--------+-----------+-----------+-----------+
|                Metric                | Worker Total | Driver Total | Driver Only | Count  |   Mean    |    Min    |    Max    |
+--------------------------------------+--------------+--------------+-------------+--------+-----------+-----------+-----------+
| └─ Load Alignments                   |            - |    1.94 secs |   1.88 secs |      1 | 1.94 secs | 1.94 secs | 1.94 secs |
|     └─ map at ADAMContext.scala:1805 |            - |     60.95 ms |           - |      1 |  60.95 ms |  60.95 ms |  60.95 ms |
|         └─ function call             |     19.41 ms |            - |           - | 163064 |    119 ns |     56 ns | 121.77 µs |
| └─ map at FlagStat.scala:96          |            - |     24.16 ms |           - |      1 |  24.16 ms |  24.16 ms |  24.16 ms |
|     └─ function call                 |    184.35 ms |            - |           - | 163064 |   1.13 µs |    155 ns |  18.74 ms |
| └─ aggregate at FlagStat.scala:115   |            - |    1.79 secs |           - |      1 | 1.79 secs | 1.79 secs | 1.79 secs |
|     └─ function call                 |     36.65 ms |            - |           - | 163065 |    224 ns |     85 ns | 427.28 µs |
+--------------------------------------+--------------+--------------+-------------+--------+-----------+-----------+-----------+

Spark Operations
+----------+---------------------------------+---------------+----------------+--------------+----------+
| Sequence |            Operation            | Is New Stage? | Stage Duration | Driver Total | Stage ID |
+----------+---------------------------------+---------------+----------------+--------------+----------+
| 1        | map at ADAMContext.scala:1805   | false         |              - |     60.95 ms | -        |
| 2        | map at FlagStat.scala:96        | false         |              - |     24.16 ms | -        |
| 3        | aggregate at FlagStat.scala:115 | true          |     -1.62 secs |    1.79 secs | 0        |
+----------+---------------------------------+---------------+----------------+--------------+----------+

Task Timings
+-------------------------------+------------+-------+-----------+-----------+-----------+
|            Metric             | Total Time | Count |   Mean    |    Min    |    Max    |
+-------------------------------+------------+-------+-----------+-----------+-----------+
| Task Duration                 |  1.54 secs |     1 | 1.54 secs | 1.54 secs | 1.54 secs |
| Executor Run Time             |  1.12 secs |     1 | 1.12 secs | 1.12 secs | 1.12 secs |
| Executor Deserialization Time |     353 ms |     1 |    353 ms |    353 ms |    353 ms |
| Result Serialization Time     |          0 |     1 |         0 |         0 |         0 |
+-------------------------------+------------+-------+-----------+-----------+-----------+

Task Timings By Host
+-------------------------------+--------+------------+-------+-----------+-----------+-----------+
|            Metric             |  Host  | Total Time | Count |   Mean    |    Min    |    Max    |
+-------------------------------+--------+------------+-------+-----------+-----------+-----------+
| Task Duration                 | driver |  1.54 secs |     1 | 1.54 secs | 1.54 secs | 1.54 secs |
| Executor Run Time             | driver |  1.12 secs |     1 | 1.12 secs | 1.12 secs | 1.12 secs |
| Executor Deserialization Time | driver |     353 ms |     1 |    353 ms |    353 ms |    353 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 |  1.54 secs |     1 | 1.54 secs | 1.54 secs | 1.54 secs |
| Executor Run Time             | 0: aggregate at FlagStat.scala:115 |  1.12 secs |     1 | 1.12 secs | 1.12 secs | 1.12 secs |
| Executor Deserialization Time | 0: aggregate at FlagStat.scala:115 |     353 ms |     1 |    353 ms |    353 ms |    353 ms |
| Result Serialization Time     | 0: aggregate at FlagStat.scala:115 |          0 |     1 |         0 |         0 |         0 |
+-------------------------------+------------------------------------+------------+-------+-----------+-----------+-----------+

19/10/28 17:06:38 INFO SparkContext: Invoking stop() from shutdown hook
19/10/28 17:06:38 INFO SparkUI: Stopped Spark web UI at http://192.168.10.27:4040
19/10/28 17:06:38 INFO MapOutputTrackerMasterEndpoint: MapOutputTrackerMasterEndpoint stopped!
19/10/28 17:06:38 INFO MemoryStore: MemoryStore cleared
19/10/28 17:06:38 INFO BlockManager: BlockManager stopped
19/10/28 17:06:38 INFO BlockManagerMaster: BlockManagerMaster stopped
19/10/28 17:06:38 INFO OutputCommitCoordinator$OutputCommitCoordinatorEndpoint: OutputCommitCoordinator stopped!
19/10/28 17:06:38 INFO SparkContext: Successfully stopped SparkContext
19/10/28 17:06:38 INFO ShutdownHookManager: Shutdown hook called
19/10/28 17:06:38 INFO ShutdownHookManager: Deleting directory /tmp/spark-2638e9be-1746-4e1e-b318-8f4d312736b7
19/10/28 17:06:38 INFO ShutdownHookManager: Deleting directory /tmp/spark-8bb75efb-8254-4df2-b445-4c05651d93ae
rm -rf ${ADAM_TMP_DIR}
+ rm -rf /tmp/adamTestxbwUJbj/deleteMePleaseThisIsNoLongerNeeded
popd
+ popd
~/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu

pushd ${PROJECT_ROOT}
+ pushd /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/scripts/..
~/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu ~/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/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
+ '[' 2.11 == 2.12 ']'

# 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/2.11/SPARK_VERSION/2.4.4/label/ubuntu/scripts
+ pushd /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/scripts/..
~/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu ~/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/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 0.30.0-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ adam-parent-spark2_2.11 ---
[INFO] Modified 2 of 243 .scala files
[INFO] 
[INFO] --- maven-license-plugin:1.10.b1:format (default-cli) @ adam-parent-spark2_2.11 ---
[INFO] Updating license headers...
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building ADAM_2.11: Shader workaround 0.30.0-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 0.30.0-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 0.30.0-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ adam-core-spark2_2.11 ---
[INFO] Modified 0 of 203 .scala files
[INFO] 
[INFO] --- maven-license-plugin:1.10.b1:format (default-cli) @ adam-core-spark2_2.11 ---
[INFO] Updating license headers...
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building ADAM_2.11: APIs for Java, Python 0.30.0-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 0.30.0-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 0.30.0-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 [  8.398 s]
[INFO] ADAM_2.11: Shader workaround ....................... SUCCESS [  0.026 s]
[INFO] ADAM_2.11: Avro-to-Dataset codegen utils ........... SUCCESS [  0.060 s]
[INFO] ADAM_2.11: Core .................................... SUCCESS [  4.609 s]
[INFO] ADAM_2.11: APIs for Java, Python ................... SUCCESS [  0.149 s]
[INFO] ADAM_2.11: CLI ..................................... SUCCESS [  0.238 s]
[INFO] ADAM_2.11: Assembly ................................ SUCCESS [  0.019 s]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 14.324 s
[INFO] Finished at: 2019-10-28T17:06:55-07:00
[INFO] Final Memory: 22M/1128M
[INFO] ------------------------------------------------------------------------
+ popd
~/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/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/2.11/SPARK_VERSION/2.4.4/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...
Setting commit status on GitHub for https://github.com/bigdatagenomics/adam/commit/25d27ee3528becbdcaf260551788b0475609b19c
Finished: SUCCESS