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[INFO] Building zip: /tmp/adamTestmyXyrYL/deleteMePleaseThisIsNoLongerNeeded/adam-distribution/target/adam-distribution-spark2_2.11-0.31.0-SNAPSHOT-bin.zip
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary:
[INFO] 
[INFO] ADAM_2.11 .......................................... SUCCESS [  9.455 s]
[INFO] ADAM_2.11: Shader workaround ....................... SUCCESS [  6.594 s]
[INFO] ADAM_2.11: Avro-to-Dataset codegen utils ........... SUCCESS [  7.471 s]
[INFO] ADAM_2.11: Core .................................... SUCCESS [01:54 min]
[INFO] ADAM_2.11: APIs for Java, Python ................... SUCCESS [ 18.165 s]
[INFO] ADAM_2.11: CLI ..................................... SUCCESS [ 24.588 s]
[INFO] ADAM_2.11: Assembly ................................ SUCCESS [ 14.497 s]
[INFO] ADAM_2.11: Python APIs ............................. SUCCESS [01:13 min]
[INFO] ADAM_2.11: R APIs .................................. SUCCESS [ 56.612 s]
[INFO] ADAM_2.11: Distribution ............................ SUCCESS [ 38.511 s]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 06:03 min
[INFO] Finished at: 2020-01-08T13:42:15-08:00
[INFO] Final Memory: 94M/1480M
[INFO] ------------------------------------------------------------------------
+ grep bdgenomics.adam
+ tar tzvf adam-distribution/target/adam-distribution-spark2_2.11-0.31.0-SNAPSHOT-bin.tar.gz
+ grep egg
drwxrwxr-x jenkins/jenkins        0 2020-01-08 13:39 adam-distribution-spark2_2.11-0.31.0-SNAPSHOT/r/bdgenomics.adam.egg-info/
-rw-r--r-- jenkins/jenkins 39603100 2020-01-08 13:39 adam-distribution-spark2_2.11-0.31.0-SNAPSHOT/repo/bdgenomics.adam-0.31.0a0-py3.6.egg
+ ./bin/pyadam
Using PYSPARK=/tmp/adamTestmyXyrYL/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.4-bin-hadoop2.7/bin/pyspark
2020-01-08 13:42:18 WARN  Utils:66 - Your hostname, amp-jenkins-staging-worker-02 resolves to a loopback address: 127.0.1.1; using 192.168.10.32 instead (on interface eno1)
2020-01-08 13:42:18 WARN  Utils:66 - Set SPARK_LOCAL_IP if you need to bind to another address
2020-01-08 13:42:18 WARN  NativeCodeLoader:62 - Unable to load native-hadoop library for your platform... using builtin-java classes where applicable
Setting default log level to "WARN".
To adjust logging level use sc.setLogLevel(newLevel). For SparkR, use setLogLevel(newLevel).
2020-01-08 13:42:20 WARN  Utils:66 - Service 'SparkUI' could not bind on port 4040. Attempting port 4041.
2020-01-08 13:42:24 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]
[Stage 0:===========================================================(1 + 0) / 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-7b390948-1fe6-401b-a868-701d75d88f8f/bin/deactivate
++ _SHELL=bash
_CONDA_DIR=$(dirname "$_SCRIPT_LOCATION")
dirname "$_SCRIPT_LOCATION"
+++ dirname /home/jenkins/anaconda2/envs/adam-build-7b390948-1fe6-401b-a868-701d75d88f8f/bin/deactivate
++ _CONDA_DIR=/home/jenkins/anaconda2/envs/adam-build-7b390948-1fe6-401b-a868-701d75d88f8f/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 $?
fi
++ ((  0 == 0  ))
++ _CONDA_D=/home/jenkins/anaconda2/envs/adam-build-7b390948-1fe6-401b-a868-701d75d88f8f/etc/conda/deactivate.d
++ [[ -d /home/jenkins/anaconda2/envs/adam-build-7b390948-1fe6-401b-a868-701d75d88f8f/etc/conda/deactivate.d ]]
"$_CONDA_DIR/conda" ..deactivate.path $_SHELL$EXT "$CONDA_PREFIX"
+++ /home/jenkins/anaconda2/envs/adam-build-7b390948-1fe6-401b-a868-701d75d88f8f/bin/conda ..deactivate.path bash /home/jenkins/anaconda2/envs/adam-build-7b390948-1fe6-401b-a868-701d75d88f8f
++ 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-7b390948-1fe6-401b-a868-701d75d88f8f --all

Package plan for package removal in environment /home/jenkins/anaconda2/envs/adam-build-7b390948-1fe6-401b-a868-701d75d88f8f:

The following packages will be REMOVED:

    _libgcc_mutex:   0.1-main               
    ca-certificates: 2019.11.27-0           
    certifi:         2019.11.28-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:      42.0.2-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/adamTestmyXyrYL/deleteMePleaseThisIsNoLongerNeeded/adam-python /tmp/adamTestmyXyrYL/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/adamTestmyXyrYL/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/adamTestmyXyrYL/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.4-bin-hadoop2.7/bin/spark-submit
20/01/08 13:42:39 WARN Utils: Your hostname, amp-jenkins-staging-worker-02 resolves to a loopback address: 127.0.1.1; using 192.168.10.32 instead (on interface eno1)
20/01/08 13:42:39 WARN Utils: Set SPARK_LOCAL_IP if you need to bind to another address
20/01/08 13:42:40 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
20/01/08 13:42:40 INFO SparkContext: Running Spark version 2.4.4
20/01/08 13:42:40 INFO SparkContext: Submitted application: transformAlignments
20/01/08 13:42:40 INFO SecurityManager: Changing view acls to: jenkins
20/01/08 13:42:40 INFO SecurityManager: Changing modify acls to: jenkins
20/01/08 13:42:40 INFO SecurityManager: Changing view acls groups to: 
20/01/08 13:42:40 INFO SecurityManager: Changing modify acls groups to: 
20/01/08 13:42:40 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()
20/01/08 13:42:41 INFO Utils: Successfully started service 'sparkDriver' on port 36307.
20/01/08 13:42:41 INFO SparkEnv: Registering MapOutputTracker
20/01/08 13:42:41 INFO SparkEnv: Registering BlockManagerMaster
20/01/08 13:42:41 INFO BlockManagerMasterEndpoint: Using org.apache.spark.storage.DefaultTopologyMapper for getting topology information
20/01/08 13:42:41 INFO BlockManagerMasterEndpoint: BlockManagerMasterEndpoint up
20/01/08 13:42:41 INFO DiskBlockManager: Created local directory at /tmp/blockmgr-4a33e5e9-f7b5-474a-b330-96bacd297001
20/01/08 13:42:41 INFO MemoryStore: MemoryStore started with capacity 366.3 MB
20/01/08 13:42:41 INFO SparkEnv: Registering OutputCommitCoordinator
20/01/08 13:42:41 WARN Utils: Service 'SparkUI' could not bind on port 4040. Attempting port 4041.
20/01/08 13:42:41 INFO Utils: Successfully started service 'SparkUI' on port 4041.
20/01/08 13:42:41 INFO SparkUI: Bound SparkUI to 0.0.0.0, and started at http://192.168.10.32:4041
20/01/08 13:42:41 INFO SparkContext: Added JAR file:/tmp/adamTestmyXyrYL/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/target/adam-assembly-spark2_2.11-0.31.0-SNAPSHOT.jar at spark://192.168.10.32:36307/jars/adam-assembly-spark2_2.11-0.31.0-SNAPSHOT.jar with timestamp 1578519761568
20/01/08 13:42:41 INFO Executor: Starting executor ID driver on host localhost
20/01/08 13:42:41 INFO Utils: Successfully started service 'org.apache.spark.network.netty.NettyBlockTransferService' on port 36978.
20/01/08 13:42:41 INFO NettyBlockTransferService: Server created on 192.168.10.32:36978
20/01/08 13:42:41 INFO BlockManager: Using org.apache.spark.storage.RandomBlockReplicationPolicy for block replication policy
20/01/08 13:42:41 INFO BlockManagerMaster: Registering BlockManager BlockManagerId(driver, 192.168.10.32, 36978, None)
20/01/08 13:42:41 INFO BlockManagerMasterEndpoint: Registering block manager 192.168.10.32:36978 with 366.3 MB RAM, BlockManagerId(driver, 192.168.10.32, 36978, None)
20/01/08 13:42:41 INFO BlockManagerMaster: Registered BlockManager BlockManagerId(driver, 192.168.10.32, 36978, None)
20/01/08 13:42:41 INFO BlockManager: Initialized BlockManager: BlockManagerId(driver, 192.168.10.32, 36978, None)
20/01/08 13:42:42 INFO ADAMContext: Loading mouse_chrM.bam as BAM/CRAM/SAM and converting to Alignments.
20/01/08 13:42:42 INFO ADAMContext: Loaded header from file:/tmp/adamTestmyXyrYL/deleteMePleaseThisIsNoLongerNeeded/mouse_chrM.bam
20/01/08 13:42:43 INFO MemoryStore: Block broadcast_0 stored as values in memory (estimated size 284.3 KB, free 366.0 MB)
20/01/08 13:42:43 INFO MemoryStore: Block broadcast_0_piece0 stored as bytes in memory (estimated size 23.1 KB, free 366.0 MB)
20/01/08 13:42:43 INFO BlockManagerInfo: Added broadcast_0_piece0 in memory on 192.168.10.32:36978 (size: 23.1 KB, free: 366.3 MB)
20/01/08 13:42:43 INFO SparkContext: Created broadcast 0 from newAPIHadoopFile at ADAMContext.scala:2058
20/01/08 13:42:44 INFO RDDBoundAlignmentDataset: Saving data in ADAM format
20/01/08 13:42:44 INFO FileOutputCommitter: File Output Committer Algorithm version is 1
20/01/08 13:42:44 INFO FileInputFormat: Total input paths to process : 1
20/01/08 13:42:44 INFO SparkContext: Starting job: runJob at SparkHadoopWriter.scala:78
20/01/08 13:42:44 INFO DAGScheduler: Got job 0 (runJob at SparkHadoopWriter.scala:78) with 1 output partitions
20/01/08 13:42:44 INFO DAGScheduler: Final stage: ResultStage 0 (runJob at SparkHadoopWriter.scala:78)
20/01/08 13:42:44 INFO DAGScheduler: Parents of final stage: List()
20/01/08 13:42:44 INFO DAGScheduler: Missing parents: List()
20/01/08 13:42:44 INFO DAGScheduler: Submitting ResultStage 0 (MapPartitionsRDD[2] at map at GenomicDataset.scala:3814), which has no missing parents
20/01/08 13:42:44 INFO MemoryStore: Block broadcast_1 stored as values in memory (estimated size 82.0 KB, free 365.9 MB)
20/01/08 13:42:44 INFO MemoryStore: Block broadcast_1_piece0 stored as bytes in memory (estimated size 30.2 KB, free 365.9 MB)
20/01/08 13:42:44 INFO BlockManagerInfo: Added broadcast_1_piece0 in memory on 192.168.10.32:36978 (size: 30.2 KB, free: 366.2 MB)
20/01/08 13:42:44 INFO SparkContext: Created broadcast 1 from broadcast at DAGScheduler.scala:1161
20/01/08 13:42:44 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))
20/01/08 13:42:45 INFO TaskSchedulerImpl: Adding task set 0.0 with 1 tasks
20/01/08 13:42:45 INFO TaskSetManager: Starting task 0.0 in stage 0.0 (TID 0, localhost, executor driver, partition 0, PROCESS_LOCAL, 7962 bytes)
20/01/08 13:42:45 INFO Executor: Running task 0.0 in stage 0.0 (TID 0)
20/01/08 13:42:45 INFO Executor: Fetching spark://192.168.10.32:36307/jars/adam-assembly-spark2_2.11-0.31.0-SNAPSHOT.jar with timestamp 1578519761568
20/01/08 13:42:45 INFO TransportClientFactory: Successfully created connection to /192.168.10.32:36307 after 187 ms (0 ms spent in bootstraps)
20/01/08 13:42:45 INFO Utils: Fetching spark://192.168.10.32:36307/jars/adam-assembly-spark2_2.11-0.31.0-SNAPSHOT.jar to /tmp/spark-39871051-1234-4155-84a9-2a4e2279353d/userFiles-f86635e7-d8c5-4e8d-89f3-2b879d8d3e53/fetchFileTemp3530601320598535478.tmp
20/01/08 13:42:45 INFO Executor: Adding file:/tmp/spark-39871051-1234-4155-84a9-2a4e2279353d/userFiles-f86635e7-d8c5-4e8d-89f3-2b879d8d3e53/adam-assembly-spark2_2.11-0.31.0-SNAPSHOT.jar to class loader
20/01/08 13:42:45 INFO NewHadoopRDD: Input split: file:/tmp/adamTestmyXyrYL/deleteMePleaseThisIsNoLongerNeeded/mouse_chrM.bam:83361792-833134657535
20/01/08 13:42:45 INFO FileOutputCommitter: File Output Committer Algorithm version is 1
20/01/08 13:42:45 INFO CodecConfig: Compression: GZIP
20/01/08 13:42:45 INFO FileOutputCommitter: File Output Committer Algorithm version is 1
20/01/08 13:42:45 INFO ParquetOutputFormat: Parquet block size to 134217728
20/01/08 13:42:45 INFO ParquetOutputFormat: Parquet page size to 1048576
20/01/08 13:42:45 INFO ParquetOutputFormat: Parquet dictionary page size to 1048576
20/01/08 13:42:45 INFO ParquetOutputFormat: Dictionary is on
20/01/08 13:42:45 INFO ParquetOutputFormat: Validation is off
20/01/08 13:42:45 INFO ParquetOutputFormat: Writer version is: PARQUET_1_0
20/01/08 13:42:45 INFO ParquetOutputFormat: Maximum row group padding size is 8388608 bytes
20/01/08 13:42:45 INFO ParquetOutputFormat: Page size checking is: estimated
20/01/08 13:42:45 INFO ParquetOutputFormat: Min row count for page size check is: 100
20/01/08 13:42:45 INFO ParquetOutputFormat: Max row count for page size check is: 10000
20/01/08 13:42:45 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.
20/01/08 13:42:56 INFO InternalParquetRecordWriter: Flushing mem columnStore to file. allocated memory: 16043959
20/01/08 13:42:56 INFO FileOutputCommitter: Saved output of task 'attempt_20200108134244_0002_r_000000_0' to file:/tmp/adamTestmyXyrYL/deleteMePleaseThisIsNoLongerNeeded/mouse_chrM.bam.reads.adam/_temporary/0/task_20200108134244_0002_r_000000
20/01/08 13:42:56 INFO SparkHadoopMapRedUtil: attempt_20200108134244_0002_r_000000_0: Committed
20/01/08 13:42:56 INFO Executor: Finished task 0.0 in stage 0.0 (TID 0). 850 bytes result sent to driver
20/01/08 13:42:56 INFO TaskSetManager: Finished task 0.0 in stage 0.0 (TID 0) in 11649 ms on localhost (executor driver) (1/1)
20/01/08 13:42:56 INFO TaskSchedulerImpl: Removed TaskSet 0.0, whose tasks have all completed, from pool 
20/01/08 13:42:56 INFO DAGScheduler: ResultStage 0 (runJob at SparkHadoopWriter.scala:78) finished in 11.810 s
20/01/08 13:42:56 INFO DAGScheduler: Job 0 finished: runJob at SparkHadoopWriter.scala:78, took 11.890146 s
20/01/08 13:42:56 INFO ParquetFileReader: Initiating action with parallelism: 5
20/01/08 13:42:56 INFO SparkHadoopWriter: Job job_20200108134244_0002 committed.
20/01/08 13:42:56 INFO TransformAlignments: Overall Duration: 16.2 secs
20/01/08 13:42:56 INFO SparkContext: Invoking stop() from shutdown hook
20/01/08 13:42:56 INFO SparkUI: Stopped Spark web UI at http://192.168.10.32:4041
20/01/08 13:42:56 INFO MapOutputTrackerMasterEndpoint: MapOutputTrackerMasterEndpoint stopped!
20/01/08 13:42:56 INFO MemoryStore: MemoryStore cleared
20/01/08 13:42:56 INFO BlockManager: BlockManager stopped
20/01/08 13:42:56 INFO BlockManagerMaster: BlockManagerMaster stopped
20/01/08 13:42:56 INFO OutputCommitCoordinator$OutputCommitCoordinatorEndpoint: OutputCommitCoordinator stopped!
20/01/08 13:42:56 INFO SparkContext: Successfully stopped SparkContext
20/01/08 13:42:56 INFO ShutdownHookManager: Shutdown hook called
20/01/08 13:42:56 INFO ShutdownHookManager: Deleting directory /tmp/spark-a1249cf0-f632-47a7-91e5-4c43e3e0c35f
20/01/08 13:42:56 INFO ShutdownHookManager: Deleting directory /tmp/spark-39871051-1234-4155-84a9-2a4e2279353d

# 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/adamTestmyXyrYL/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.4-bin-hadoop2.7/bin/spark-submit
20/01/08 13:42:58 WARN Utils: Your hostname, amp-jenkins-staging-worker-02 resolves to a loopback address: 127.0.1.1; using 192.168.10.32 instead (on interface eno1)
20/01/08 13:42:58 WARN Utils: Set SPARK_LOCAL_IP if you need to bind to another address
20/01/08 13:42:58 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
20/01/08 13:42:59 INFO SparkContext: Running Spark version 2.4.4
20/01/08 13:42:59 INFO SparkContext: Submitted application: transformAlignments
20/01/08 13:42:59 INFO SecurityManager: Changing view acls to: jenkins
20/01/08 13:42:59 INFO SecurityManager: Changing modify acls to: jenkins
20/01/08 13:42:59 INFO SecurityManager: Changing view acls groups to: 
20/01/08 13:42:59 INFO SecurityManager: Changing modify acls groups to: 
20/01/08 13:42:59 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()
20/01/08 13:42:59 INFO Utils: Successfully started service 'sparkDriver' on port 45945.
20/01/08 13:42:59 INFO SparkEnv: Registering MapOutputTracker
20/01/08 13:42:59 INFO SparkEnv: Registering BlockManagerMaster
20/01/08 13:42:59 INFO BlockManagerMasterEndpoint: Using org.apache.spark.storage.DefaultTopologyMapper for getting topology information
20/01/08 13:42:59 INFO BlockManagerMasterEndpoint: BlockManagerMasterEndpoint up
20/01/08 13:42:59 INFO DiskBlockManager: Created local directory at /tmp/blockmgr-7bd913e8-e72b-4848-a7d5-596ea60b4546
20/01/08 13:42:59 INFO MemoryStore: MemoryStore started with capacity 366.3 MB
20/01/08 13:42:59 INFO SparkEnv: Registering OutputCommitCoordinator
20/01/08 13:43:00 WARN Utils: Service 'SparkUI' could not bind on port 4040. Attempting port 4041.
20/01/08 13:43:00 INFO Utils: Successfully started service 'SparkUI' on port 4041.
20/01/08 13:43:00 INFO SparkUI: Bound SparkUI to 0.0.0.0, and started at http://192.168.10.32:4041
20/01/08 13:43:00 INFO SparkContext: Added JAR file:/tmp/adamTestmyXyrYL/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/target/adam-assembly-spark2_2.11-0.31.0-SNAPSHOT.jar at spark://192.168.10.32:45945/jars/adam-assembly-spark2_2.11-0.31.0-SNAPSHOT.jar with timestamp 1578519780125
20/01/08 13:43:00 INFO Executor: Starting executor ID driver on host localhost
20/01/08 13:43:00 INFO Utils: Successfully started service 'org.apache.spark.network.netty.NettyBlockTransferService' on port 32800.
20/01/08 13:43:00 INFO NettyBlockTransferService: Server created on 192.168.10.32:32800
20/01/08 13:43:00 INFO BlockManager: Using org.apache.spark.storage.RandomBlockReplicationPolicy for block replication policy
20/01/08 13:43:00 INFO BlockManagerMaster: Registering BlockManager BlockManagerId(driver, 192.168.10.32, 32800, None)
20/01/08 13:43:00 INFO BlockManagerMasterEndpoint: Registering block manager 192.168.10.32:32800 with 366.3 MB RAM, BlockManagerId(driver, 192.168.10.32, 32800, None)
20/01/08 13:43:00 INFO BlockManagerMaster: Registered BlockManager BlockManagerId(driver, 192.168.10.32, 32800, None)
20/01/08 13:43:00 INFO BlockManager: Initialized BlockManager: BlockManagerId(driver, 192.168.10.32, 32800, None)
20/01/08 13:43:00 INFO ADAMContext: Loading mouse_chrM.bam.reads.adam as Parquet of Alignments.
20/01/08 13:43:02 INFO ADAMContext: Reading the ADAM file at mouse_chrM.bam.reads.adam to create RDD
20/01/08 13:43:02 INFO MemoryStore: Block broadcast_0 stored as values in memory (estimated size 303.7 KB, free 366.0 MB)
20/01/08 13:43:03 INFO MemoryStore: Block broadcast_0_piece0 stored as bytes in memory (estimated size 27.4 KB, free 366.0 MB)
20/01/08 13:43:03 INFO BlockManagerInfo: Added broadcast_0_piece0 in memory on 192.168.10.32:32800 (size: 27.4 KB, free: 366.3 MB)
20/01/08 13:43:03 INFO SparkContext: Created broadcast 0 from newAPIHadoopFile at ADAMContext.scala:1796
20/01/08 13:43:03 INFO TransformAlignments: Sorting alignments by reference position, with references ordered by name
20/01/08 13:43:03 INFO RDDBoundAlignmentDataset: Sorting alignments by reference position
20/01/08 13:43:03 INFO FileInputFormat: Total input paths to process : 1
20/01/08 13:43:03 INFO ParquetInputFormat: Total input paths to process : 1
20/01/08 13:43:03 INFO RDDBoundAlignmentDataset: Saving data in ADAM format
20/01/08 13:43:03 INFO FileOutputCommitter: File Output Committer Algorithm version is 1
20/01/08 13:43:03 INFO SparkContext: Starting job: runJob at SparkHadoopWriter.scala:78
20/01/08 13:43:03 INFO DAGScheduler: Registering RDD 2 (sortBy at AlignmentDataset.scala:1008)
20/01/08 13:43:03 INFO DAGScheduler: Got job 0 (runJob at SparkHadoopWriter.scala:78) with 1 output partitions
20/01/08 13:43:03 INFO DAGScheduler: Final stage: ResultStage 1 (runJob at SparkHadoopWriter.scala:78)
20/01/08 13:43:03 INFO DAGScheduler: Parents of final stage: List(ShuffleMapStage 0)
20/01/08 13:43:03 INFO DAGScheduler: Missing parents: List(ShuffleMapStage 0)
20/01/08 13:43:03 INFO DAGScheduler: Submitting ShuffleMapStage 0 (MapPartitionsRDD[2] at sortBy at AlignmentDataset.scala:1008), which has no missing parents
20/01/08 13:43:03 INFO MemoryStore: Block broadcast_1 stored as values in memory (estimated size 5.0 KB, free 366.0 MB)
20/01/08 13:43:03 INFO MemoryStore: Block broadcast_1_piece0 stored as bytes in memory (estimated size 2.9 KB, free 366.0 MB)
20/01/08 13:43:03 INFO BlockManagerInfo: Added broadcast_1_piece0 in memory on 192.168.10.32:32800 (size: 2.9 KB, free: 366.3 MB)
20/01/08 13:43:03 INFO SparkContext: Created broadcast 1 from broadcast at DAGScheduler.scala:1161
20/01/08 13:43:03 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))
20/01/08 13:43:03 INFO TaskSchedulerImpl: Adding task set 0.0 with 1 tasks
20/01/08 13:43:03 INFO TaskSetManager: Starting task 0.0 in stage 0.0 (TID 0, localhost, executor driver, partition 0, PROCESS_LOCAL, 8001 bytes)
20/01/08 13:43:03 INFO Executor: Running task 0.0 in stage 0.0 (TID 0)
20/01/08 13:43:03 INFO Executor: Fetching spark://192.168.10.32:45945/jars/adam-assembly-spark2_2.11-0.31.0-SNAPSHOT.jar with timestamp 1578519780125
20/01/08 13:43:03 INFO TransportClientFactory: Successfully created connection to /192.168.10.32:45945 after 56 ms (0 ms spent in bootstraps)
20/01/08 13:43:03 INFO Utils: Fetching spark://192.168.10.32:45945/jars/adam-assembly-spark2_2.11-0.31.0-SNAPSHOT.jar to /tmp/spark-ba5577cd-1342-4a10-bd9e-5db0e8bd29a7/userFiles-e8d1586f-5470-43e5-a9ff-3d43d1e4dfc4/fetchFileTemp7594376500411628668.tmp
20/01/08 13:43:03 INFO Executor: Adding file:/tmp/spark-ba5577cd-1342-4a10-bd9e-5db0e8bd29a7/userFiles-e8d1586f-5470-43e5-a9ff-3d43d1e4dfc4/adam-assembly-spark2_2.11-0.31.0-SNAPSHOT.jar to class loader
20/01/08 13:43:04 INFO NewHadoopRDD: Input split: file:/tmp/adamTestmyXyrYL/deleteMePleaseThisIsNoLongerNeeded/mouse_chrM.bam.reads.adam/part-r-00000.gz.parquet:0+10132211
20/01/08 13:43:04 INFO InternalParquetRecordReader: RecordReader initialized will read a total of 163064 records.
20/01/08 13:43:04 INFO InternalParquetRecordReader: at row 0. reading next block
20/01/08 13:43:04 INFO CodecPool: Got brand-new decompressor [.gz]
20/01/08 13:43:04 INFO InternalParquetRecordReader: block read in memory in 45 ms. row count = 163064
20/01/08 13:43:07 INFO Executor: Finished task 0.0 in stage 0.0 (TID 0). 999 bytes result sent to driver
20/01/08 13:43:07 INFO TaskSetManager: Finished task 0.0 in stage 0.0 (TID 0) in 4151 ms on localhost (executor driver) (1/1)
20/01/08 13:43:07 INFO TaskSchedulerImpl: Removed TaskSet 0.0, whose tasks have all completed, from pool 
20/01/08 13:43:07 INFO DAGScheduler: ShuffleMapStage 0 (sortBy at AlignmentDataset.scala:1008) finished in 4.296 s
20/01/08 13:43:07 INFO DAGScheduler: looking for newly runnable stages
20/01/08 13:43:07 INFO DAGScheduler: running: Set()
20/01/08 13:43:07 INFO DAGScheduler: waiting: Set(ResultStage 1)
20/01/08 13:43:07 INFO DAGScheduler: failed: Set()
20/01/08 13:43:07 INFO DAGScheduler: Submitting ResultStage 1 (MapPartitionsRDD[5] at map at GenomicDataset.scala:3814), which has no missing parents
20/01/08 13:43:07 INFO MemoryStore: Block broadcast_2 stored as values in memory (estimated size 83.3 KB, free 365.9 MB)
20/01/08 13:43:07 INFO MemoryStore: Block broadcast_2_piece0 stored as bytes in memory (estimated size 30.9 KB, free 365.9 MB)
20/01/08 13:43:07 INFO BlockManagerInfo: Added broadcast_2_piece0 in memory on 192.168.10.32:32800 (size: 30.9 KB, free: 366.2 MB)
20/01/08 13:43:07 INFO SparkContext: Created broadcast 2 from broadcast at DAGScheduler.scala:1161
20/01/08 13:43:07 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))
20/01/08 13:43:07 INFO TaskSchedulerImpl: Adding task set 1.0 with 1 tasks
20/01/08 13:43:07 INFO TaskSetManager: Starting task 0.0 in stage 1.0 (TID 1, localhost, executor driver, partition 0, ANY, 7662 bytes)
20/01/08 13:43:07 INFO Executor: Running task 0.0 in stage 1.0 (TID 1)
20/01/08 13:43:07 INFO ShuffleBlockFetcherIterator: Getting 1 non-empty blocks including 1 local blocks and 0 remote blocks
20/01/08 13:43:07 INFO ShuffleBlockFetcherIterator: Started 0 remote fetches in 11 ms
20/01/08 13:43:09 INFO FileOutputCommitter: File Output Committer Algorithm version is 1
20/01/08 13:43:09 INFO CodecConfig: Compression: GZIP
20/01/08 13:43:09 INFO FileOutputCommitter: File Output Committer Algorithm version is 1
20/01/08 13:43:09 INFO ParquetOutputFormat: Parquet block size to 134217728
20/01/08 13:43:09 INFO ParquetOutputFormat: Parquet page size to 1048576
20/01/08 13:43:09 INFO ParquetOutputFormat: Parquet dictionary page size to 1048576
20/01/08 13:43:09 INFO ParquetOutputFormat: Dictionary is on
20/01/08 13:43:09 INFO ParquetOutputFormat: Validation is off
20/01/08 13:43:09 INFO ParquetOutputFormat: Writer version is: PARQUET_1_0
20/01/08 13:43:09 INFO ParquetOutputFormat: Maximum row group padding size is 8388608 bytes
20/01/08 13:43:09 INFO ParquetOutputFormat: Page size checking is: estimated
20/01/08 13:43:09 INFO ParquetOutputFormat: Min row count for page size check is: 100
20/01/08 13:43:09 INFO ParquetOutputFormat: Max row count for page size check is: 10000
20/01/08 13:43:09 INFO CodecPool: Got brand-new compressor [.gz]
20/01/08 13:43:12 INFO BlockManagerInfo: Removed broadcast_1_piece0 on 192.168.10.32:32800 in memory (size: 2.9 KB, free: 366.2 MB)
20/01/08 13:43:15 INFO InternalParquetRecordWriter: Flushing mem columnStore to file. allocated memory: 16004474
20/01/08 13:43:15 INFO FileOutputCommitter: Saved output of task 'attempt_20200108134303_0005_r_000000_0' to file:/tmp/adamTestmyXyrYL/deleteMePleaseThisIsNoLongerNeeded/mouse_chrM.bam.reads.sorted.adam/_temporary/0/task_20200108134303_0005_r_000000
20/01/08 13:43:15 INFO SparkHadoopMapRedUtil: attempt_20200108134303_0005_r_000000_0: Committed
20/01/08 13:43:15 INFO Executor: Finished task 0.0 in stage 1.0 (TID 1). 1280 bytes result sent to driver
20/01/08 13:43:15 INFO TaskSetManager: Finished task 0.0 in stage 1.0 (TID 1) in 7904 ms on localhost (executor driver) (1/1)
20/01/08 13:43:15 INFO TaskSchedulerImpl: Removed TaskSet 1.0, whose tasks have all completed, from pool 
20/01/08 13:43:15 INFO DAGScheduler: ResultStage 1 (runJob at SparkHadoopWriter.scala:78) finished in 7.971 s
20/01/08 13:43:15 INFO DAGScheduler: Job 0 finished: runJob at SparkHadoopWriter.scala:78, took 12.365229 s
20/01/08 13:43:15 INFO ParquetFileReader: Initiating action with parallelism: 5
20/01/08 13:43:15 INFO SparkHadoopWriter: Job job_20200108134303_0005 committed.
20/01/08 13:43:15 INFO TransformAlignments: Overall Duration: 16.54 secs
20/01/08 13:43:15 INFO SparkContext: Invoking stop() from shutdown hook
20/01/08 13:43:15 INFO SparkUI: Stopped Spark web UI at http://192.168.10.32:4041
20/01/08 13:43:15 INFO MapOutputTrackerMasterEndpoint: MapOutputTrackerMasterEndpoint stopped!
20/01/08 13:43:15 INFO MemoryStore: MemoryStore cleared
20/01/08 13:43:15 INFO BlockManager: BlockManager stopped
20/01/08 13:43:15 INFO BlockManagerMaster: BlockManagerMaster stopped
20/01/08 13:43:15 INFO OutputCommitCoordinator$OutputCommitCoordinatorEndpoint: OutputCommitCoordinator stopped!
20/01/08 13:43:15 INFO SparkContext: Successfully stopped SparkContext
20/01/08 13:43:15 INFO ShutdownHookManager: Shutdown hook called
20/01/08 13:43:15 INFO ShutdownHookManager: Deleting directory /tmp/spark-6aa6aa66-8a2d-45f2-a65b-381ec17dd692
20/01/08 13:43:15 INFO ShutdownHookManager: Deleting directory /tmp/spark-ba5577cd-1342-4a10-bd9e-5db0e8bd29a7

# 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/adamTestmyXyrYL/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.4-bin-hadoop2.7/bin/spark-submit
20/01/08 13:43:17 WARN Utils: Your hostname, amp-jenkins-staging-worker-02 resolves to a loopback address: 127.0.1.1; using 192.168.10.32 instead (on interface eno1)
20/01/08 13:43:17 WARN Utils: Set SPARK_LOCAL_IP if you need to bind to another address
20/01/08 13:43:17 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
20/01/08 13:43:18 INFO SparkContext: Running Spark version 2.4.4
20/01/08 13:43:18 INFO SparkContext: Submitted application: transformFragments
20/01/08 13:43:18 INFO SecurityManager: Changing view acls to: jenkins
20/01/08 13:43:18 INFO SecurityManager: Changing modify acls to: jenkins
20/01/08 13:43:18 INFO SecurityManager: Changing view acls groups to: 
20/01/08 13:43:18 INFO SecurityManager: Changing modify acls groups to: 
20/01/08 13:43:18 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()
20/01/08 13:43:18 INFO Utils: Successfully started service 'sparkDriver' on port 42608.
20/01/08 13:43:18 INFO SparkEnv: Registering MapOutputTracker
20/01/08 13:43:18 INFO SparkEnv: Registering BlockManagerMaster
20/01/08 13:43:18 INFO BlockManagerMasterEndpoint: Using org.apache.spark.storage.DefaultTopologyMapper for getting topology information
20/01/08 13:43:18 INFO BlockManagerMasterEndpoint: BlockManagerMasterEndpoint up
20/01/08 13:43:18 INFO DiskBlockManager: Created local directory at /tmp/blockmgr-5a80f52a-ccf1-4564-9ad4-30d24590eae1
20/01/08 13:43:18 INFO MemoryStore: MemoryStore started with capacity 366.3 MB
20/01/08 13:43:18 INFO SparkEnv: Registering OutputCommitCoordinator
20/01/08 13:43:18 INFO Utils: Successfully started service 'SparkUI' on port 4040.
20/01/08 13:43:18 INFO SparkUI: Bound SparkUI to 0.0.0.0, and started at http://192.168.10.32:4040
20/01/08 13:43:19 INFO SparkContext: Added JAR file:/tmp/adamTestmyXyrYL/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/target/adam-assembly-spark2_2.11-0.31.0-SNAPSHOT.jar at spark://192.168.10.32:42608/jars/adam-assembly-spark2_2.11-0.31.0-SNAPSHOT.jar with timestamp 1578519799021
20/01/08 13:43:19 INFO Executor: Starting executor ID driver on host localhost
20/01/08 13:43:19 INFO Utils: Successfully started service 'org.apache.spark.network.netty.NettyBlockTransferService' on port 34430.
20/01/08 13:43:19 INFO NettyBlockTransferService: Server created on 192.168.10.32:34430
20/01/08 13:43:19 INFO BlockManager: Using org.apache.spark.storage.RandomBlockReplicationPolicy for block replication policy
20/01/08 13:43:19 INFO BlockManagerMaster: Registering BlockManager BlockManagerId(driver, 192.168.10.32, 34430, None)
20/01/08 13:43:19 INFO BlockManagerMasterEndpoint: Registering block manager 192.168.10.32:34430 with 366.3 MB RAM, BlockManagerId(driver, 192.168.10.32, 34430, None)
20/01/08 13:43:19 INFO BlockManagerMaster: Registered BlockManager BlockManagerId(driver, 192.168.10.32, 34430, None)
20/01/08 13:43:19 INFO BlockManager: Initialized BlockManager: BlockManagerId(driver, 192.168.10.32, 34430, None)
20/01/08 13:43:19 INFO ADAMContext: Loading mouse_chrM.bam.reads.adam as Parquet of Alignments.
20/01/08 13:43:21 INFO ADAMContext: Reading the ADAM file at mouse_chrM.bam.reads.adam to create RDD
20/01/08 13:43:21 INFO MemoryStore: Block broadcast_0 stored as values in memory (estimated size 303.7 KB, free 366.0 MB)
20/01/08 13:43:21 INFO MemoryStore: Block broadcast_0_piece0 stored as bytes in memory (estimated size 27.4 KB, free 366.0 MB)
20/01/08 13:43:21 INFO BlockManagerInfo: Added broadcast_0_piece0 in memory on 192.168.10.32:34430 (size: 27.4 KB, free: 366.3 MB)
20/01/08 13:43:21 INFO SparkContext: Created broadcast 0 from newAPIHadoopFile at ADAMContext.scala:1796
20/01/08 13:43:22 INFO FileInputFormat: Total input paths to process : 1
20/01/08 13:43:22 INFO ParquetInputFormat: Total input paths to process : 1
20/01/08 13:43:22 INFO RDDBoundFragmentDataset: Saving data in ADAM format
20/01/08 13:43:22 INFO FileOutputCommitter: File Output Committer Algorithm version is 1
20/01/08 13:43:22 INFO SparkContext: Starting job: runJob at SparkHadoopWriter.scala:78
20/01/08 13:43:22 INFO DAGScheduler: Registering RDD 2 (groupBy at SingleReadBucket.scala:97)
20/01/08 13:43:22 INFO DAGScheduler: Got job 0 (runJob at SparkHadoopWriter.scala:78) with 1 output partitions
20/01/08 13:43:22 INFO DAGScheduler: Final stage: ResultStage 1 (runJob at SparkHadoopWriter.scala:78)
20/01/08 13:43:22 INFO DAGScheduler: Parents of final stage: List(ShuffleMapStage 0)
20/01/08 13:43:22 INFO DAGScheduler: Missing parents: List(ShuffleMapStage 0)
20/01/08 13:43:22 INFO DAGScheduler: Submitting ShuffleMapStage 0 (MapPartitionsRDD[2] at groupBy at SingleReadBucket.scala:97), which has no missing parents
20/01/08 13:43:22 INFO MemoryStore: Block broadcast_1 stored as values in memory (estimated size 5.3 KB, free 366.0 MB)
20/01/08 13:43:22 INFO MemoryStore: Block broadcast_1_piece0 stored as bytes in memory (estimated size 3.0 KB, free 366.0 MB)
20/01/08 13:43:22 INFO BlockManagerInfo: Added broadcast_1_piece0 in memory on 192.168.10.32:34430 (size: 3.0 KB, free: 366.3 MB)
20/01/08 13:43:22 INFO SparkContext: Created broadcast 1 from broadcast at DAGScheduler.scala:1161
20/01/08 13:43:22 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))
20/01/08 13:43:22 INFO TaskSchedulerImpl: Adding task set 0.0 with 1 tasks
20/01/08 13:43:22 INFO TaskSetManager: Starting task 0.0 in stage 0.0 (TID 0, localhost, executor driver, partition 0, PROCESS_LOCAL, 8001 bytes)
20/01/08 13:43:22 INFO Executor: Running task 0.0 in stage 0.0 (TID 0)
20/01/08 13:43:22 INFO Executor: Fetching spark://192.168.10.32:42608/jars/adam-assembly-spark2_2.11-0.31.0-SNAPSHOT.jar with timestamp 1578519799021
20/01/08 13:43:22 INFO TransportClientFactory: Successfully created connection to /192.168.10.32:42608 after 40 ms (0 ms spent in bootstraps)
20/01/08 13:43:22 INFO Utils: Fetching spark://192.168.10.32:42608/jars/adam-assembly-spark2_2.11-0.31.0-SNAPSHOT.jar to /tmp/spark-e077192a-5363-493e-abd3-047bb50e280c/userFiles-47fb9901-9b81-4562-bd8c-069f44875fe3/fetchFileTemp4104958371050988076.tmp
20/01/08 13:43:22 INFO Executor: Adding file:/tmp/spark-e077192a-5363-493e-abd3-047bb50e280c/userFiles-47fb9901-9b81-4562-bd8c-069f44875fe3/adam-assembly-spark2_2.11-0.31.0-SNAPSHOT.jar to class loader
20/01/08 13:43:22 INFO NewHadoopRDD: Input split: file:/tmp/adamTestmyXyrYL/deleteMePleaseThisIsNoLongerNeeded/mouse_chrM.bam.reads.adam/part-r-00000.gz.parquet:0+10132211
20/01/08 13:43:23 INFO InternalParquetRecordReader: RecordReader initialized will read a total of 163064 records.
20/01/08 13:43:23 INFO InternalParquetRecordReader: at row 0. reading next block
20/01/08 13:43:23 INFO CodecPool: Got brand-new decompressor [.gz]
20/01/08 13:43:23 INFO InternalParquetRecordReader: block read in memory in 47 ms. row count = 163064
20/01/08 13:43:26 INFO Executor: Finished task 0.0 in stage 0.0 (TID 0). 999 bytes result sent to driver
20/01/08 13:43:26 INFO TaskSetManager: Finished task 0.0 in stage 0.0 (TID 0) in 4082 ms on localhost (executor driver) (1/1)
20/01/08 13:43:26 INFO TaskSchedulerImpl: Removed TaskSet 0.0, whose tasks have all completed, from pool 
20/01/08 13:43:26 INFO DAGScheduler: ShuffleMapStage 0 (groupBy at SingleReadBucket.scala:97) finished in 4.220 s
20/01/08 13:43:26 INFO DAGScheduler: looking for newly runnable stages
20/01/08 13:43:26 INFO DAGScheduler: running: Set()
20/01/08 13:43:26 INFO DAGScheduler: waiting: Set(ResultStage 1)
20/01/08 13:43:26 INFO DAGScheduler: failed: Set()
20/01/08 13:43:26 INFO DAGScheduler: Submitting ResultStage 1 (MapPartitionsRDD[6] at map at GenomicDataset.scala:3814), which has no missing parents
20/01/08 13:43:26 INFO MemoryStore: Block broadcast_2 stored as values in memory (estimated size 86.2 KB, free 365.9 MB)
20/01/08 13:43:26 INFO MemoryStore: Block broadcast_2_piece0 stored as bytes in memory (estimated size 32.2 KB, free 365.9 MB)
20/01/08 13:43:26 INFO BlockManagerInfo: Added broadcast_2_piece0 in memory on 192.168.10.32:34430 (size: 32.2 KB, free: 366.2 MB)
20/01/08 13:43:26 INFO SparkContext: Created broadcast 2 from broadcast at DAGScheduler.scala:1161
20/01/08 13:43:26 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))
20/01/08 13:43:26 INFO TaskSchedulerImpl: Adding task set 1.0 with 1 tasks
20/01/08 13:43:26 INFO TaskSetManager: Starting task 0.0 in stage 1.0 (TID 1, localhost, executor driver, partition 0, ANY, 7662 bytes)
20/01/08 13:43:26 INFO Executor: Running task 0.0 in stage 1.0 (TID 1)
20/01/08 13:43:26 INFO ShuffleBlockFetcherIterator: Getting 1 non-empty blocks including 1 local blocks and 0 remote blocks
20/01/08 13:43:26 INFO ShuffleBlockFetcherIterator: Started 0 remote fetches in 8 ms
20/01/08 13:43:28 INFO FileOutputCommitter: File Output Committer Algorithm version is 1
20/01/08 13:43:28 INFO CodecConfig: Compression: GZIP
20/01/08 13:43:28 INFO FileOutputCommitter: File Output Committer Algorithm version is 1
20/01/08 13:43:28 INFO ParquetOutputFormat: Parquet block size to 134217728
20/01/08 13:43:28 INFO ParquetOutputFormat: Parquet page size to 1048576
20/01/08 13:43:28 INFO ParquetOutputFormat: Parquet dictionary page size to 1048576
20/01/08 13:43:28 INFO ParquetOutputFormat: Dictionary is on
20/01/08 13:43:28 INFO ParquetOutputFormat: Validation is off
20/01/08 13:43:28 INFO ParquetOutputFormat: Writer version is: PARQUET_1_0
20/01/08 13:43:28 INFO ParquetOutputFormat: Maximum row group padding size is 8388608 bytes
20/01/08 13:43:28 INFO ParquetOutputFormat: Page size checking is: estimated
20/01/08 13:43:28 INFO ParquetOutputFormat: Min row count for page size check is: 100
20/01/08 13:43:28 INFO ParquetOutputFormat: Max row count for page size check is: 10000
20/01/08 13:43:28 INFO CodecPool: Got brand-new compressor [.gz]
20/01/08 13:43:35 INFO InternalParquetRecordWriter: Flushing mem columnStore to file. allocated memory: 21417928
20/01/08 13:43:35 INFO FileOutputCommitter: Saved output of task 'attempt_20200108134322_0006_r_000000_0' to file:/tmp/adamTestmyXyrYL/deleteMePleaseThisIsNoLongerNeeded/mouse_chrM.bam.fragments.adam/_temporary/0/task_20200108134322_0006_r_000000
20/01/08 13:43:35 INFO SparkHadoopMapRedUtil: attempt_20200108134322_0006_r_000000_0: Committed
20/01/08 13:43:35 INFO Executor: Finished task 0.0 in stage 1.0 (TID 1). 1280 bytes result sent to driver
20/01/08 13:43:35 INFO TaskSetManager: Finished task 0.0 in stage 1.0 (TID 1) in 9410 ms on localhost (executor driver) (1/1)
20/01/08 13:43:35 INFO TaskSchedulerImpl: Removed TaskSet 1.0, whose tasks have all completed, from pool 
20/01/08 13:43:35 INFO DAGScheduler: ResultStage 1 (runJob at SparkHadoopWriter.scala:78) finished in 9.451 s
20/01/08 13:43:35 INFO DAGScheduler: Job 0 finished: runJob at SparkHadoopWriter.scala:78, took 13.778645 s
20/01/08 13:43:35 INFO ParquetFileReader: Initiating action with parallelism: 5
20/01/08 13:43:36 INFO SparkHadoopWriter: Job job_20200108134322_0006 committed.
20/01/08 13:43:36 INFO TransformFragments: Overall Duration: 17.99 secs
20/01/08 13:43:36 INFO SparkContext: Invoking stop() from shutdown hook
20/01/08 13:43:36 INFO SparkUI: Stopped Spark web UI at http://192.168.10.32:4040
20/01/08 13:43:36 INFO MapOutputTrackerMasterEndpoint: MapOutputTrackerMasterEndpoint stopped!
20/01/08 13:43:36 INFO MemoryStore: MemoryStore cleared
20/01/08 13:43:36 INFO BlockManager: BlockManager stopped
20/01/08 13:43:36 INFO BlockManagerMaster: BlockManagerMaster stopped
20/01/08 13:43:36 INFO OutputCommitCoordinator$OutputCommitCoordinatorEndpoint: OutputCommitCoordinator stopped!
20/01/08 13:43:36 INFO SparkContext: Successfully stopped SparkContext
20/01/08 13:43:36 INFO ShutdownHookManager: Shutdown hook called
20/01/08 13:43:36 INFO ShutdownHookManager: Deleting directory /tmp/spark-e077192a-5363-493e-abd3-047bb50e280c
20/01/08 13:43:36 INFO ShutdownHookManager: Deleting directory /tmp/spark-0d5f3759-c59f-4076-bbb7-9114bf568d2c

# 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/adamTestmyXyrYL/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.4-bin-hadoop2.7/bin/spark-submit
20/01/08 13:43:57 WARN Utils: Your hostname, amp-jenkins-staging-worker-02 resolves to a loopback address: 127.0.1.1; using 192.168.10.32 instead (on interface eno1)
20/01/08 13:43:57 WARN Utils: Set SPARK_LOCAL_IP if you need to bind to another address
20/01/08 13:43:57 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
20/01/08 13:43:57 INFO SparkContext: Running Spark version 2.4.4
20/01/08 13:43:57 INFO SparkContext: Submitted application: flagstat
20/01/08 13:43:57 INFO SecurityManager: Changing view acls to: jenkins
20/01/08 13:43:57 INFO SecurityManager: Changing modify acls to: jenkins
20/01/08 13:43:57 INFO SecurityManager: Changing view acls groups to: 
20/01/08 13:43:57 INFO SecurityManager: Changing modify acls groups to: 
20/01/08 13:43:57 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()
20/01/08 13:43:58 INFO Utils: Successfully started service 'sparkDriver' on port 41881.
20/01/08 13:43:58 INFO SparkEnv: Registering MapOutputTracker
20/01/08 13:43:58 INFO SparkEnv: Registering BlockManagerMaster
20/01/08 13:43:58 INFO BlockManagerMasterEndpoint: Using org.apache.spark.storage.DefaultTopologyMapper for getting topology information
20/01/08 13:43:58 INFO BlockManagerMasterEndpoint: BlockManagerMasterEndpoint up
20/01/08 13:43:58 INFO DiskBlockManager: Created local directory at /tmp/blockmgr-36b537b4-fe53-4af7-9780-6ea540e8872d
20/01/08 13:43:58 INFO MemoryStore: MemoryStore started with capacity 366.3 MB
20/01/08 13:43:58 INFO SparkEnv: Registering OutputCommitCoordinator
20/01/08 13:43:58 INFO Utils: Successfully started service 'SparkUI' on port 4040.
20/01/08 13:43:58 INFO SparkUI: Bound SparkUI to 0.0.0.0, and started at http://192.168.10.32:4040
20/01/08 13:43:58 INFO SparkContext: Added JAR file:/tmp/adamTestmyXyrYL/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/target/adam-assembly-spark2_2.11-0.31.0-SNAPSHOT.jar at spark://192.168.10.32:41881/jars/adam-assembly-spark2_2.11-0.31.0-SNAPSHOT.jar with timestamp 1578519838710
20/01/08 13:43:58 INFO Executor: Starting executor ID driver on host localhost
20/01/08 13:43:58 INFO Utils: Successfully started service 'org.apache.spark.network.netty.NettyBlockTransferService' on port 42955.
20/01/08 13:43:58 INFO NettyBlockTransferService: Server created on 192.168.10.32:42955
20/01/08 13:43:58 INFO BlockManager: Using org.apache.spark.storage.RandomBlockReplicationPolicy for block replication policy
20/01/08 13:43:58 INFO BlockManagerMaster: Registering BlockManager BlockManagerId(driver, 192.168.10.32, 42955, None)
20/01/08 13:43:58 INFO BlockManagerMasterEndpoint: Registering block manager 192.168.10.32:42955 with 366.3 MB RAM, BlockManagerId(driver, 192.168.10.32, 42955, None)
20/01/08 13:43:58 INFO BlockManagerMaster: Registered BlockManager BlockManagerId(driver, 192.168.10.32, 42955, None)
20/01/08 13:43:58 INFO BlockManager: Initialized BlockManager: BlockManagerId(driver, 192.168.10.32, 42955, None)
20/01/08 13:43:59 INFO ADAMContext: Loading mouse_chrM.bam.reads.adam as Parquet of Alignments.
20/01/08 13:43:59 INFO ADAMContext: Reading the ADAM file at mouse_chrM.bam.reads.adam to create RDD
20/01/08 13:43:59 INFO ADAMContext: Using the specified projection schema
20/01/08 13:44:00 INFO MemoryStore: Block broadcast_0 stored as values in memory (estimated size 313.1 KB, free 366.0 MB)
20/01/08 13:44:00 INFO MemoryStore: Block broadcast_0_piece0 stored as bytes in memory (estimated size 28.4 KB, free 366.0 MB)
20/01/08 13:44:00 INFO BlockManagerInfo: Added broadcast_0_piece0 in memory on 192.168.10.32:42955 (size: 28.4 KB, free: 366.3 MB)
20/01/08 13:44:00 INFO SparkContext: Created broadcast 0 from newAPIHadoopFile at ADAMContext.scala:1796
20/01/08 13:44:02 INFO FileInputFormat: Total input paths to process : 1
20/01/08 13:44:02 INFO ParquetInputFormat: Total input paths to process : 1
20/01/08 13:44:02 INFO SparkContext: Starting job: aggregate at FlagStat.scala:115
20/01/08 13:44:02 INFO DAGScheduler: Got job 0 (aggregate at FlagStat.scala:115) with 1 output partitions
20/01/08 13:44:02 INFO DAGScheduler: Final stage: ResultStage 0 (aggregate at FlagStat.scala:115)
20/01/08 13:44:02 INFO DAGScheduler: Parents of final stage: List()
20/01/08 13:44:02 INFO DAGScheduler: Missing parents: List()
20/01/08 13:44:02 INFO DAGScheduler: Submitting ResultStage 0 (MapPartitionsRDD[4] at map at FlagStat.scala:96), which has no missing parents
20/01/08 13:44:02 INFO MemoryStore: Block broadcast_1 stored as values in memory (estimated size 12.5 KB, free 366.0 MB)
20/01/08 13:44:02 INFO MemoryStore: Block broadcast_1_piece0 stored as bytes in memory (estimated size 5.5 KB, free 365.9 MB)
20/01/08 13:44:02 INFO BlockManagerInfo: Added broadcast_1_piece0 in memory on 192.168.10.32:42955 (size: 5.5 KB, free: 366.3 MB)
20/01/08 13:44:02 INFO SparkContext: Created broadcast 1 from broadcast at DAGScheduler.scala:1161
20/01/08 13:44:02 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))
20/01/08 13:44:02 INFO TaskSchedulerImpl: Adding task set 0.0 with 1 tasks
20/01/08 13:44:02 INFO TaskSetManager: Starting task 0.0 in stage 0.0 (TID 0, localhost, executor driver, partition 0, PROCESS_LOCAL, 8012 bytes)
20/01/08 13:44:02 INFO Executor: Running task 0.0 in stage 0.0 (TID 0)
20/01/08 13:44:02 INFO Executor: Fetching spark://192.168.10.32:41881/jars/adam-assembly-spark2_2.11-0.31.0-SNAPSHOT.jar with timestamp 1578519838710
20/01/08 13:44:02 INFO TransportClientFactory: Successfully created connection to /192.168.10.32:41881 after 281 ms (0 ms spent in bootstraps)
20/01/08 13:44:02 INFO Utils: Fetching spark://192.168.10.32:41881/jars/adam-assembly-spark2_2.11-0.31.0-SNAPSHOT.jar to /tmp/spark-6998eafa-f03b-4ece-a308-7be2bdfeb38e/userFiles-8333e238-9b4f-4ed9-9eb9-46feae8dc0e2/fetchFileTemp3160489841295143685.tmp
20/01/08 13:44:02 INFO Executor: Adding file:/tmp/spark-6998eafa-f03b-4ece-a308-7be2bdfeb38e/userFiles-8333e238-9b4f-4ed9-9eb9-46feae8dc0e2/adam-assembly-spark2_2.11-0.31.0-SNAPSHOT.jar to class loader
20/01/08 13:44:03 INFO NewHadoopRDD: Input split: file:/tmp/adamTestmyXyrYL/deleteMePleaseThisIsNoLongerNeeded/mouse_chrM.bam.reads.adam/part-r-00000.gz.parquet:0+10132211
20/01/08 13:44:03 INFO InternalParquetRecordReader: RecordReader initialized will read a total of 163064 records.
20/01/08 13:44:03 INFO InternalParquetRecordReader: at row 0. reading next block
20/01/08 13:44:03 INFO CodecPool: Got brand-new decompressor [.gz]
20/01/08 13:44:03 INFO InternalParquetRecordReader: block read in memory in 29 ms. row count = 163064
20/01/08 13:44:04 INFO Executor: Finished task 0.0 in stage 0.0 (TID 0). 8196 bytes result sent to driver
20/01/08 13:44:04 INFO TaskSetManager: Finished task 0.0 in stage 0.0 (TID 0) in 1751 ms on localhost (executor driver) (1/1)
20/01/08 13:44:04 INFO TaskSchedulerImpl: Removed TaskSet 0.0, whose tasks have all completed, from pool 
20/01/08 13:44:04 INFO DAGScheduler: ResultStage 0 (aggregate at FlagStat.scala:115) finished in 1.883 s
20/01/08 13:44:04 INFO DAGScheduler: Job 0 finished: aggregate at FlagStat.scala:115, took 1.970726 s
163064 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 primary duplicates
0 + 0 primary duplicates - both read and mate mapped
0 + 0 primary duplicates - only read mapped
0 + 0 primary duplicates - cross chromosome
0 + 0 secondary duplicates
0 + 0 secondary duplicates - both read and mate mapped
0 + 0 secondary duplicates - only read mapped
0 + 0 secondary duplicates - cross chromosome
160512 + 0 mapped (98.43%:0.00%)
163064 + 0 paired in sequencing
81524 + 0 read1
81540 + 0 read2
154982 + 0 properly paired (95.04%:0.00%)
158044 + 0 with itself and mate mapped
2468 + 0 singletons (1.51%:0.00%)
418 + 0 with mate mapped to a different chr
120 + 0 with mate mapped to a different chr (mapQ>=5)
20/01/08 13:44:04 INFO FlagStat: Overall Duration: 6.43 secs
20/01/08 13:44:04 INFO FlagStat: Metrics:

Timings
+--------------------------------------+--------------+--------------+-------------+--------+-----------+-----------+-----------+
|                Metric                | Worker Total | Driver Total | Driver Only | Count  |   Mean    |    Min    |    Max    |
+--------------------------------------+--------------+--------------+-------------+--------+-----------+-----------+-----------+
| └─ Load Alignments                   |            - |    2.43 secs |   2.34 secs |      1 | 2.43 secs | 2.43 secs | 2.43 secs |
|     └─ map at ADAMContext.scala:1805 |            - |     85.55 ms |           - |      1 |  85.55 ms |  85.55 ms |  85.55 ms |
|         └─ function call             |     17.48 ms |            - |           - | 163064 |    107 ns |     49 ns | 117.71 µs |
| └─ map at FlagStat.scala:96          |            - |     30.94 ms |           - |      1 |  30.94 ms |  30.94 ms |  30.94 ms |
|     └─ function call                 |    149.81 ms |            - |           - | 163064 |    918 ns |    137 ns |   1.39 ms |
| └─ aggregate at FlagStat.scala:115   |            - |    2.16 secs |           - |      1 | 2.16 secs | 2.16 secs | 2.16 secs |
|     └─ function call                 |     30.46 ms |            - |           - | 163065 |    186 ns |     64 ns | 697.01 µs |
+--------------------------------------+--------------+--------------+-------------+--------+-----------+-----------+-----------+

Spark Operations
+----------+---------------------------------+---------------+----------------+--------------+----------+
| Sequence |            Operation            | Is New Stage? | Stage Duration | Driver Total | Stage ID |
+----------+---------------------------------+---------------+----------------+--------------+----------+
| 1        | map at ADAMContext.scala:1805   | false         |              - |     85.55 ms | -        |
| 2        | map at FlagStat.scala:96        | false         |              - |     30.94 ms | -        |
| 3        | aggregate at FlagStat.scala:115 | true          |     -1.89 secs |    2.16 secs | 0        |
+----------+---------------------------------+---------------+----------------+--------------+----------+

Task Timings
+-------------------------------+------------+-------+-----------+-----------+-----------+
|            Metric             | Total Time | Count |   Mean    |    Min    |    Max    |
+-------------------------------+------------+-------+-----------+-----------+-----------+
| Task Duration                 |  1.75 secs |     1 | 1.75 secs | 1.75 secs | 1.75 secs |
| Executor Run Time             |  1.11 secs |     1 | 1.11 secs | 1.11 secs | 1.11 secs |
| Executor Deserialization Time |     548 ms |     1 |    548 ms |    548 ms |    548 ms |
| Result Serialization Time     |          0 |     1 |         0 |         0 |         0 |
+-------------------------------+------------+-------+-----------+-----------+-----------+

Task Timings By Host
+-------------------------------+--------+------------+-------+-----------+-----------+-----------+
|            Metric             |  Host  | Total Time | Count |   Mean    |    Min    |    Max    |
+-------------------------------+--------+------------+-------+-----------+-----------+-----------+
| Task Duration                 | driver |  1.75 secs |     1 | 1.75 secs | 1.75 secs | 1.75 secs |
| Executor Run Time             | driver |  1.11 secs |     1 | 1.11 secs | 1.11 secs | 1.11 secs |
| Executor Deserialization Time | driver |     548 ms |     1 |    548 ms |    548 ms |    548 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 |  1.75 secs |     1 | 1.75 secs | 1.75 secs | 1.75 secs |
| Executor Run Time             | 0: aggregate at FlagStat.scala:115 |  1.11 secs |     1 | 1.11 secs | 1.11 secs | 1.11 secs |
| Executor Deserialization Time | 0: aggregate at FlagStat.scala:115 |     548 ms |     1 |    548 ms |    548 ms |    548 ms |
| Result Serialization Time     | 0: aggregate at FlagStat.scala:115 |          0 |     1 |         0 |         0 |         0 |
+-------------------------------+------------------------------------+------------+-------+-----------+-----------+-----------+

20/01/08 13:44:04 INFO SparkContext: Invoking stop() from shutdown hook
20/01/08 13:44:04 INFO SparkUI: Stopped Spark web UI at http://192.168.10.32:4040
20/01/08 13:44:04 INFO MapOutputTrackerMasterEndpoint: MapOutputTrackerMasterEndpoint stopped!
20/01/08 13:44:04 INFO MemoryStore: MemoryStore cleared
20/01/08 13:44:04 INFO BlockManager: BlockManager stopped
20/01/08 13:44:04 INFO BlockManagerMaster: BlockManagerMaster stopped
20/01/08 13:44:04 INFO OutputCommitCoordinator$OutputCommitCoordinatorEndpoint: OutputCommitCoordinator stopped!
20/01/08 13:44:04 INFO SparkContext: Successfully stopped SparkContext
20/01/08 13:44:04 INFO ShutdownHookManager: Shutdown hook called
20/01/08 13:44:04 INFO ShutdownHookManager: Deleting directory /tmp/spark-1a529d3a-dac6-409b-9c11-3db06a18e281
20/01/08 13:44:04 INFO ShutdownHookManager: Deleting directory /tmp/spark-6998eafa-f03b-4ece-a308-7be2bdfeb38e
rm -rf ${ADAM_TMP_DIR}
+ rm -rf /tmp/adamTestmyXyrYL/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 0.31.0-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 0.31.0-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 0.31.0-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 0.31.0-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 0.31.0-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 0.31.0-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 0.31.0-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ adam-assembly-spark2_2.11 ---
[INFO] Modified 0 of 1 .scala files
[INFO] 
[INFO] --- maven-license-plugin:1.10.b1:format (default-cli) @ adam-assembly-spark2_2.11 ---
[INFO] Updating license headers...
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary:
[INFO] 
[INFO] ADAM_2.11 .......................................... SUCCESS [  6.897 s]
[INFO] ADAM_2.11: Shader workaround ....................... SUCCESS [  0.026 s]
[INFO] ADAM_2.11: Avro-to-Dataset codegen utils ........... SUCCESS [  0.051 s]
[INFO] ADAM_2.11: Core .................................... SUCCESS [  3.453 s]
[INFO] ADAM_2.11: APIs for Java, Python ................... SUCCESS [  0.170 s]
[INFO] ADAM_2.11: CLI ..................................... SUCCESS [  0.208 s]
[INFO] ADAM_2.11: Assembly ................................ SUCCESS [  0.019 s]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 11.456 s
[INFO] Finished at: 2020-01-08T13:44:18-08:00
[INFO] Final Memory: 20M/1110M
[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/ca9a15b8ea71dcd714059ec68929015943e0b550
Finished: SUCCESS