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[INFO] Building zip: /tmp/adamTest2Mw865Z/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 [  9.792 s]
[INFO] ADAM_2.11: Shader workaround ....................... SUCCESS [  5.591 s]
[INFO] ADAM_2.11: Avro-to-Dataset codegen utils ........... SUCCESS [  7.227 s]
[INFO] ADAM_2.11: Core .................................... SUCCESS [01:52 min]
[INFO] ADAM_2.11: APIs for Java, Python ................... SUCCESS [ 18.188 s]
[INFO] ADAM_2.11: CLI ..................................... SUCCESS [ 23.528 s]
[INFO] ADAM_2.11: Assembly ................................ SUCCESS [ 13.645 s]
[INFO] ADAM_2.11: Python APIs ............................. SUCCESS [01:25 min]
[INFO] ADAM_2.11: R APIs .................................. SUCCESS [ 53.109 s]
[INFO] ADAM_2.11: Distribution ............................ SUCCESS [ 38.802 s]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 06:07 min
[INFO] Finished at: 2020-01-03T23:28:50-08:00
[INFO] Final Memory: 93M/1462M
[INFO] ------------------------------------------------------------------------
+ grep bdgenomics.adam
+ grep egg
+ tar tzvf adam-distribution/target/adam-distribution-spark2_2.11-0.31.0-SNAPSHOT-bin.tar.gz
drwxrwxr-x jenkins/jenkins        0 2020-01-03 23:25 adam-distribution-spark2_2.11-0.31.0-SNAPSHOT/r/bdgenomics.adam.egg-info/
-rw-r--r-- jenkins/jenkins 39602138 2020-01-03 23:25 adam-distribution-spark2_2.11-0.31.0-SNAPSHOT/repo/bdgenomics.adam-0.31.0a0-py3.6.egg
+ ./bin/pyadam
Using PYSPARK=/tmp/adamTest2Mw865Z/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.4-bin-hadoop2.7/bin/pyspark
2020-01-03 23:28:53 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)
2020-01-03 23:28:53 WARN  Utils:66 - Set SPARK_LOCAL_IP if you need to bind to another address
2020-01-03 23:28:53 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).
2020-01-03 23:28:58 WARN  Utils:66 - Truncated the string representation of a plan since it was too large. This behavior can be adjusted by setting 'spark.debug.maxToStringFields' in SparkEnv.conf.
+ source deactivate
#!/bin/bash

# Determine the directory containing this script
if [[ -n $BASH_VERSION ]]; then
    _SCRIPT_LOCATION=${BASH_SOURCE[0]}
    _SHELL="bash"
elif [[ -n $ZSH_VERSION ]]; then
    _SCRIPT_LOCATION=${funcstack[1]}
    _SHELL="zsh"
else
    echo "Only bash and zsh are supported"
    return 1
fi
++ [[ -n 4.3.48(1)-release ]]
++ _SCRIPT_LOCATION=/home/jenkins/anaconda2/envs/adam-build-df4bb903-1e3d-4790-9b9a-f9be226b47cd/bin/deactivate
++ _SHELL=bash
_CONDA_DIR=$(dirname "$_SCRIPT_LOCATION")
dirname "$_SCRIPT_LOCATION"
+++ dirname /home/jenkins/anaconda2/envs/adam-build-df4bb903-1e3d-4790-9b9a-f9be226b47cd/bin/deactivate
++ _CONDA_DIR=/home/jenkins/anaconda2/envs/adam-build-df4bb903-1e3d-4790-9b9a-f9be226b47cd/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 $?
fi
++ ((  0 == 0  ))
++ _CONDA_D=/home/jenkins/anaconda2/envs/adam-build-df4bb903-1e3d-4790-9b9a-f9be226b47cd/etc/conda/deactivate.d
++ [[ -d /home/jenkins/anaconda2/envs/adam-build-df4bb903-1e3d-4790-9b9a-f9be226b47cd/etc/conda/deactivate.d ]]
"$_CONDA_DIR/conda" ..deactivate.path $_SHELL$EXT "$CONDA_PREFIX"
+++ /home/jenkins/anaconda2/envs/adam-build-df4bb903-1e3d-4790-9b9a-f9be226b47cd/bin/conda ..deactivate.path bash /home/jenkins/anaconda2/envs/adam-build-df4bb903-1e3d-4790-9b9a-f9be226b47cd
++ 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-df4bb903-1e3d-4790-9b9a-f9be226b47cd --all

Package plan for package removal in environment /home/jenkins/anaconda2/envs/adam-build-df4bb903-1e3d-4790-9b9a-f9be226b47cd:

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/adamTest2Mw865Z/deleteMePleaseThisIsNoLongerNeeded/adam-python /tmp/adamTest2Mw865Z/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/adamTest2Mw865Z/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/adamTest2Mw865Z/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.4-bin-hadoop2.7/bin/spark-submit
20/01/03 23:29:06 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)
20/01/03 23:29:06 WARN Utils: Set SPARK_LOCAL_IP if you need to bind to another address
20/01/03 23:29:06 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
20/01/03 23:29:06 INFO SparkContext: Running Spark version 2.4.4
20/01/03 23:29:06 INFO SparkContext: Submitted application: transformAlignments
20/01/03 23:29:07 INFO SecurityManager: Changing view acls to: jenkins
20/01/03 23:29:07 INFO SecurityManager: Changing modify acls to: jenkins
20/01/03 23:29:07 INFO SecurityManager: Changing view acls groups to: 
20/01/03 23:29:07 INFO SecurityManager: Changing modify acls groups to: 
20/01/03 23:29:07 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()
20/01/03 23:29:07 INFO Utils: Successfully started service 'sparkDriver' on port 33715.
20/01/03 23:29:07 INFO SparkEnv: Registering MapOutputTracker
20/01/03 23:29:07 INFO SparkEnv: Registering BlockManagerMaster
20/01/03 23:29:07 INFO BlockManagerMasterEndpoint: Using org.apache.spark.storage.DefaultTopologyMapper for getting topology information
20/01/03 23:29:07 INFO BlockManagerMasterEndpoint: BlockManagerMasterEndpoint up
20/01/03 23:29:07 INFO DiskBlockManager: Created local directory at /tmp/blockmgr-2689c858-d179-4b7b-8f93-dc619f7245e1
20/01/03 23:29:07 INFO MemoryStore: MemoryStore started with capacity 366.3 MB
20/01/03 23:29:07 INFO SparkEnv: Registering OutputCommitCoordinator
20/01/03 23:29:07 INFO Utils: Successfully started service 'SparkUI' on port 4040.
20/01/03 23:29:07 INFO SparkUI: Bound SparkUI to 0.0.0.0, and started at http://192.168.10.27:4040
20/01/03 23:29:07 INFO SparkContext: Added JAR file:/tmp/adamTest2Mw865Z/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/target/adam-assembly-spark2_2.11-0.31.0-SNAPSHOT.jar at spark://192.168.10.27:33715/jars/adam-assembly-spark2_2.11-0.31.0-SNAPSHOT.jar with timestamp 1578122947693
20/01/03 23:29:07 INFO Executor: Starting executor ID driver on host localhost
20/01/03 23:29:07 INFO Utils: Successfully started service 'org.apache.spark.network.netty.NettyBlockTransferService' on port 37151.
20/01/03 23:29:07 INFO NettyBlockTransferService: Server created on 192.168.10.27:37151
20/01/03 23:29:07 INFO BlockManager: Using org.apache.spark.storage.RandomBlockReplicationPolicy for block replication policy
20/01/03 23:29:07 INFO BlockManagerMaster: Registering BlockManager BlockManagerId(driver, 192.168.10.27, 37151, None)
20/01/03 23:29:07 INFO BlockManagerMasterEndpoint: Registering block manager 192.168.10.27:37151 with 366.3 MB RAM, BlockManagerId(driver, 192.168.10.27, 37151, None)
20/01/03 23:29:07 INFO BlockManagerMaster: Registered BlockManager BlockManagerId(driver, 192.168.10.27, 37151, None)
20/01/03 23:29:07 INFO BlockManager: Initialized BlockManager: BlockManagerId(driver, 192.168.10.27, 37151, None)
20/01/03 23:29:08 INFO ADAMContext: Loading mouse_chrM.bam as BAM/CRAM/SAM and converting to Alignments.
20/01/03 23:29:08 INFO ADAMContext: Loaded header from file:/tmp/adamTest2Mw865Z/deleteMePleaseThisIsNoLongerNeeded/mouse_chrM.bam
20/01/03 23:29:08 INFO MemoryStore: Block broadcast_0 stored as values in memory (estimated size 284.3 KB, free 366.0 MB)
20/01/03 23:29:09 INFO MemoryStore: Block broadcast_0_piece0 stored as bytes in memory (estimated size 23.1 KB, free 366.0 MB)
20/01/03 23:29:09 INFO BlockManagerInfo: Added broadcast_0_piece0 in memory on 192.168.10.27:37151 (size: 23.1 KB, free: 366.3 MB)
20/01/03 23:29:09 INFO SparkContext: Created broadcast 0 from newAPIHadoopFile at ADAMContext.scala:2058
20/01/03 23:29:10 INFO RDDBoundAlignmentDataset: Saving data in ADAM format
20/01/03 23:29:10 INFO FileOutputCommitter: File Output Committer Algorithm version is 1
20/01/03 23:29:10 INFO FileInputFormat: Total input paths to process : 1
20/01/03 23:29:10 INFO SparkContext: Starting job: runJob at SparkHadoopWriter.scala:78
20/01/03 23:29:10 INFO DAGScheduler: Got job 0 (runJob at SparkHadoopWriter.scala:78) with 1 output partitions
20/01/03 23:29:10 INFO DAGScheduler: Final stage: ResultStage 0 (runJob at SparkHadoopWriter.scala:78)
20/01/03 23:29:10 INFO DAGScheduler: Parents of final stage: List()
20/01/03 23:29:10 INFO DAGScheduler: Missing parents: List()
20/01/03 23:29:10 INFO DAGScheduler: Submitting ResultStage 0 (MapPartitionsRDD[2] at map at GenomicDataset.scala:3814), which has no missing parents
20/01/03 23:29:10 INFO MemoryStore: Block broadcast_1 stored as values in memory (estimated size 82.0 KB, free 365.9 MB)
20/01/03 23:29:10 INFO MemoryStore: Block broadcast_1_piece0 stored as bytes in memory (estimated size 30.2 KB, free 365.9 MB)
20/01/03 23:29:10 INFO BlockManagerInfo: Added broadcast_1_piece0 in memory on 192.168.10.27:37151 (size: 30.2 KB, free: 366.2 MB)
20/01/03 23:29:10 INFO SparkContext: Created broadcast 1 from broadcast at DAGScheduler.scala:1161
20/01/03 23:29:10 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))
20/01/03 23:29:10 INFO TaskSchedulerImpl: Adding task set 0.0 with 1 tasks
20/01/03 23:29:10 INFO TaskSetManager: Starting task 0.0 in stage 0.0 (TID 0, localhost, executor driver, partition 0, PROCESS_LOCAL, 7962 bytes)
20/01/03 23:29:10 INFO Executor: Running task 0.0 in stage 0.0 (TID 0)
20/01/03 23:29:10 INFO Executor: Fetching spark://192.168.10.27:33715/jars/adam-assembly-spark2_2.11-0.31.0-SNAPSHOT.jar with timestamp 1578122947693
20/01/03 23:29:11 INFO TransportClientFactory: Successfully created connection to /192.168.10.27:33715 after 177 ms (0 ms spent in bootstraps)
20/01/03 23:29:11 INFO Utils: Fetching spark://192.168.10.27:33715/jars/adam-assembly-spark2_2.11-0.31.0-SNAPSHOT.jar to /tmp/spark-a81ede16-1810-45ae-883d-0264c5d9559d/userFiles-dc40ed85-d6d5-4174-87a6-8d3abadb6017/fetchFileTemp9113019598540960598.tmp
20/01/03 23:29:11 INFO Executor: Adding file:/tmp/spark-a81ede16-1810-45ae-883d-0264c5d9559d/userFiles-dc40ed85-d6d5-4174-87a6-8d3abadb6017/adam-assembly-spark2_2.11-0.31.0-SNAPSHOT.jar to class loader
20/01/03 23:29:11 INFO NewHadoopRDD: Input split: file:/tmp/adamTest2Mw865Z/deleteMePleaseThisIsNoLongerNeeded/mouse_chrM.bam:83361792-833134657535
20/01/03 23:29:11 INFO FileOutputCommitter: File Output Committer Algorithm version is 1
20/01/03 23:29:11 INFO CodecConfig: Compression: GZIP
20/01/03 23:29:11 INFO FileOutputCommitter: File Output Committer Algorithm version is 1
20/01/03 23:29:11 INFO ParquetOutputFormat: Parquet block size to 134217728
20/01/03 23:29:11 INFO ParquetOutputFormat: Parquet page size to 1048576
20/01/03 23:29:11 INFO ParquetOutputFormat: Parquet dictionary page size to 1048576
20/01/03 23:29:11 INFO ParquetOutputFormat: Dictionary is on
20/01/03 23:29:11 INFO ParquetOutputFormat: Validation is off
20/01/03 23:29:11 INFO ParquetOutputFormat: Writer version is: PARQUET_1_0
20/01/03 23:29:11 INFO ParquetOutputFormat: Maximum row group padding size is 8388608 bytes
20/01/03 23:29:11 INFO ParquetOutputFormat: Page size checking is: estimated
20/01/03 23:29:11 INFO ParquetOutputFormat: Min row count for page size check is: 100
20/01/03 23:29:11 INFO ParquetOutputFormat: Max row count for page size check is: 10000
20/01/03 23:29:11 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.
20/01/03 23:29:21 INFO InternalParquetRecordWriter: Flushing mem columnStore to file. allocated memory: 16043959
20/01/03 23:29:21 INFO FileOutputCommitter: Saved output of task 'attempt_20200103232910_0002_r_000000_0' to file:/tmp/adamTest2Mw865Z/deleteMePleaseThisIsNoLongerNeeded/mouse_chrM.bam.reads.adam/_temporary/0/task_20200103232910_0002_r_000000
20/01/03 23:29:21 INFO SparkHadoopMapRedUtil: attempt_20200103232910_0002_r_000000_0: Committed
20/01/03 23:29:21 INFO Executor: Finished task 0.0 in stage 0.0 (TID 0). 893 bytes result sent to driver
20/01/03 23:29:21 INFO TaskSetManager: Finished task 0.0 in stage 0.0 (TID 0) in 10664 ms on localhost (executor driver) (1/1)
20/01/03 23:29:21 INFO TaskSchedulerImpl: Removed TaskSet 0.0, whose tasks have all completed, from pool 
20/01/03 23:29:21 INFO DAGScheduler: ResultStage 0 (runJob at SparkHadoopWriter.scala:78) finished in 10.778 s
20/01/03 23:29:21 INFO DAGScheduler: Job 0 finished: runJob at SparkHadoopWriter.scala:78, took 10.837831 s
20/01/03 23:29:21 INFO ParquetFileReader: Initiating action with parallelism: 5
20/01/03 23:29:21 INFO SparkHadoopWriter: Job job_20200103232910_0002 committed.
20/01/03 23:29:21 INFO TransformAlignments: Overall Duration: 14.7 secs
20/01/03 23:29:21 INFO SparkContext: Invoking stop() from shutdown hook
20/01/03 23:29:21 INFO SparkUI: Stopped Spark web UI at http://192.168.10.27:4040
20/01/03 23:29:21 INFO MapOutputTrackerMasterEndpoint: MapOutputTrackerMasterEndpoint stopped!
20/01/03 23:29:21 INFO MemoryStore: MemoryStore cleared
20/01/03 23:29:21 INFO BlockManager: BlockManager stopped
20/01/03 23:29:21 INFO BlockManagerMaster: BlockManagerMaster stopped
20/01/03 23:29:21 INFO OutputCommitCoordinator$OutputCommitCoordinatorEndpoint: OutputCommitCoordinator stopped!
20/01/03 23:29:21 INFO SparkContext: Successfully stopped SparkContext
20/01/03 23:29:21 INFO ShutdownHookManager: Shutdown hook called
20/01/03 23:29:21 INFO ShutdownHookManager: Deleting directory /tmp/spark-a81ede16-1810-45ae-883d-0264c5d9559d
20/01/03 23:29:21 INFO ShutdownHookManager: Deleting directory /tmp/spark-45ebc835-56dd-47a3-9951-d822ac80b153

# 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/adamTest2Mw865Z/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.4-bin-hadoop2.7/bin/spark-submit
20/01/03 23:29:23 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)
20/01/03 23:29:23 WARN Utils: Set SPARK_LOCAL_IP if you need to bind to another address
20/01/03 23:29:23 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
20/01/03 23:29:23 INFO SparkContext: Running Spark version 2.4.4
20/01/03 23:29:23 INFO SparkContext: Submitted application: transformAlignments
20/01/03 23:29:23 INFO SecurityManager: Changing view acls to: jenkins
20/01/03 23:29:23 INFO SecurityManager: Changing modify acls to: jenkins
20/01/03 23:29:23 INFO SecurityManager: Changing view acls groups to: 
20/01/03 23:29:23 INFO SecurityManager: Changing modify acls groups to: 
20/01/03 23:29:23 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()
20/01/03 23:29:24 INFO Utils: Successfully started service 'sparkDriver' on port 39865.
20/01/03 23:29:24 INFO SparkEnv: Registering MapOutputTracker
20/01/03 23:29:24 INFO SparkEnv: Registering BlockManagerMaster
20/01/03 23:29:24 INFO BlockManagerMasterEndpoint: Using org.apache.spark.storage.DefaultTopologyMapper for getting topology information
20/01/03 23:29:24 INFO BlockManagerMasterEndpoint: BlockManagerMasterEndpoint up
20/01/03 23:29:24 INFO DiskBlockManager: Created local directory at /tmp/blockmgr-450ec469-b4e3-4ad4-8829-e30f9fc75813
20/01/03 23:29:24 INFO MemoryStore: MemoryStore started with capacity 366.3 MB
20/01/03 23:29:24 INFO SparkEnv: Registering OutputCommitCoordinator
20/01/03 23:29:24 INFO Utils: Successfully started service 'SparkUI' on port 4040.
20/01/03 23:29:24 INFO SparkUI: Bound SparkUI to 0.0.0.0, and started at http://192.168.10.27:4040
20/01/03 23:29:24 INFO SparkContext: Added JAR file:/tmp/adamTest2Mw865Z/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/target/adam-assembly-spark2_2.11-0.31.0-SNAPSHOT.jar at spark://192.168.10.27:39865/jars/adam-assembly-spark2_2.11-0.31.0-SNAPSHOT.jar with timestamp 1578122964342
20/01/03 23:29:24 INFO Executor: Starting executor ID driver on host localhost
20/01/03 23:29:24 INFO Utils: Successfully started service 'org.apache.spark.network.netty.NettyBlockTransferService' on port 34197.
20/01/03 23:29:24 INFO NettyBlockTransferService: Server created on 192.168.10.27:34197
20/01/03 23:29:24 INFO BlockManager: Using org.apache.spark.storage.RandomBlockReplicationPolicy for block replication policy
20/01/03 23:29:24 INFO BlockManagerMaster: Registering BlockManager BlockManagerId(driver, 192.168.10.27, 34197, None)
20/01/03 23:29:24 INFO BlockManagerMasterEndpoint: Registering block manager 192.168.10.27:34197 with 366.3 MB RAM, BlockManagerId(driver, 192.168.10.27, 34197, None)
20/01/03 23:29:24 INFO BlockManagerMaster: Registered BlockManager BlockManagerId(driver, 192.168.10.27, 34197, None)
20/01/03 23:29:24 INFO BlockManager: Initialized BlockManager: BlockManagerId(driver, 192.168.10.27, 34197, None)
20/01/03 23:29:25 INFO ADAMContext: Loading mouse_chrM.bam.reads.adam as Parquet of Alignments.
20/01/03 23:29:26 INFO ADAMContext: Reading the ADAM file at mouse_chrM.bam.reads.adam to create RDD
20/01/03 23:29:26 INFO MemoryStore: Block broadcast_0 stored as values in memory (estimated size 303.7 KB, free 366.0 MB)
20/01/03 23:29:26 INFO MemoryStore: Block broadcast_0_piece0 stored as bytes in memory (estimated size 27.4 KB, free 366.0 MB)
20/01/03 23:29:26 INFO BlockManagerInfo: Added broadcast_0_piece0 in memory on 192.168.10.27:34197 (size: 27.4 KB, free: 366.3 MB)
20/01/03 23:29:26 INFO SparkContext: Created broadcast 0 from newAPIHadoopFile at ADAMContext.scala:1796
20/01/03 23:29:26 INFO TransformAlignments: Sorting alignments by reference position, with references ordered by name
20/01/03 23:29:26 INFO RDDBoundAlignmentDataset: Sorting alignments by reference position
20/01/03 23:29:27 INFO FileInputFormat: Total input paths to process : 1
20/01/03 23:29:27 INFO ParquetInputFormat: Total input paths to process : 1
20/01/03 23:29:27 INFO RDDBoundAlignmentDataset: Saving data in ADAM format
20/01/03 23:29:27 INFO FileOutputCommitter: File Output Committer Algorithm version is 1
20/01/03 23:29:27 INFO SparkContext: Starting job: runJob at SparkHadoopWriter.scala:78
20/01/03 23:29:27 INFO DAGScheduler: Registering RDD 2 (sortBy at AlignmentDataset.scala:1008)
20/01/03 23:29:27 INFO DAGScheduler: Got job 0 (runJob at SparkHadoopWriter.scala:78) with 1 output partitions
20/01/03 23:29:27 INFO DAGScheduler: Final stage: ResultStage 1 (runJob at SparkHadoopWriter.scala:78)
20/01/03 23:29:27 INFO DAGScheduler: Parents of final stage: List(ShuffleMapStage 0)
20/01/03 23:29:27 INFO DAGScheduler: Missing parents: List(ShuffleMapStage 0)
20/01/03 23:29:27 INFO DAGScheduler: Submitting ShuffleMapStage 0 (MapPartitionsRDD[2] at sortBy at AlignmentDataset.scala:1008), which has no missing parents
20/01/03 23:29:27 INFO MemoryStore: Block broadcast_1 stored as values in memory (estimated size 5.0 KB, free 366.0 MB)
20/01/03 23:29:27 INFO MemoryStore: Block broadcast_1_piece0 stored as bytes in memory (estimated size 2.9 KB, free 366.0 MB)
20/01/03 23:29:27 INFO BlockManagerInfo: Added broadcast_1_piece0 in memory on 192.168.10.27:34197 (size: 2.9 KB, free: 366.3 MB)
20/01/03 23:29:27 INFO SparkContext: Created broadcast 1 from broadcast at DAGScheduler.scala:1161
20/01/03 23:29:27 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))
20/01/03 23:29:27 INFO TaskSchedulerImpl: Adding task set 0.0 with 1 tasks
20/01/03 23:29:27 INFO TaskSetManager: Starting task 0.0 in stage 0.0 (TID 0, localhost, executor driver, partition 0, PROCESS_LOCAL, 8001 bytes)
20/01/03 23:29:27 INFO Executor: Running task 0.0 in stage 0.0 (TID 0)
20/01/03 23:29:27 INFO Executor: Fetching spark://192.168.10.27:39865/jars/adam-assembly-spark2_2.11-0.31.0-SNAPSHOT.jar with timestamp 1578122964342
20/01/03 23:29:27 INFO TransportClientFactory: Successfully created connection to /192.168.10.27:39865 after 30 ms (0 ms spent in bootstraps)
20/01/03 23:29:27 INFO Utils: Fetching spark://192.168.10.27:39865/jars/adam-assembly-spark2_2.11-0.31.0-SNAPSHOT.jar to /tmp/spark-75977e42-3306-4cc2-bec3-a8f8204d877b/userFiles-7498a9d2-01ec-4fda-bf2e-63587c81ac9a/fetchFileTemp7446136570257134261.tmp
20/01/03 23:29:27 INFO Executor: Adding file:/tmp/spark-75977e42-3306-4cc2-bec3-a8f8204d877b/userFiles-7498a9d2-01ec-4fda-bf2e-63587c81ac9a/adam-assembly-spark2_2.11-0.31.0-SNAPSHOT.jar to class loader
20/01/03 23:29:27 INFO NewHadoopRDD: Input split: file:/tmp/adamTest2Mw865Z/deleteMePleaseThisIsNoLongerNeeded/mouse_chrM.bam.reads.adam/part-r-00000.gz.parquet:0+10132211
20/01/03 23:29:27 INFO InternalParquetRecordReader: RecordReader initialized will read a total of 163064 records.
20/01/03 23:29:27 INFO InternalParquetRecordReader: at row 0. reading next block
20/01/03 23:29:27 INFO CodecPool: Got brand-new decompressor [.gz]
20/01/03 23:29:27 INFO InternalParquetRecordReader: block read in memory in 44 ms. row count = 163064
20/01/03 23:29:30 INFO Executor: Finished task 0.0 in stage 0.0 (TID 0). 956 bytes result sent to driver
20/01/03 23:29:30 INFO TaskSetManager: Finished task 0.0 in stage 0.0 (TID 0) in 3339 ms on localhost (executor driver) (1/1)
20/01/03 23:29:30 INFO TaskSchedulerImpl: Removed TaskSet 0.0, whose tasks have all completed, from pool 
20/01/03 23:29:30 INFO DAGScheduler: ShuffleMapStage 0 (sortBy at AlignmentDataset.scala:1008) finished in 3.482 s
20/01/03 23:29:30 INFO DAGScheduler: looking for newly runnable stages
20/01/03 23:29:30 INFO DAGScheduler: running: Set()
20/01/03 23:29:30 INFO DAGScheduler: waiting: Set(ResultStage 1)
20/01/03 23:29:30 INFO DAGScheduler: failed: Set()
20/01/03 23:29:30 INFO DAGScheduler: Submitting ResultStage 1 (MapPartitionsRDD[5] at map at GenomicDataset.scala:3814), which has no missing parents
20/01/03 23:29:30 INFO MemoryStore: Block broadcast_2 stored as values in memory (estimated size 83.3 KB, free 365.9 MB)
20/01/03 23:29:30 INFO MemoryStore: Block broadcast_2_piece0 stored as bytes in memory (estimated size 30.9 KB, free 365.9 MB)
20/01/03 23:29:30 INFO BlockManagerInfo: Added broadcast_2_piece0 in memory on 192.168.10.27:34197 (size: 30.9 KB, free: 366.2 MB)
20/01/03 23:29:30 INFO SparkContext: Created broadcast 2 from broadcast at DAGScheduler.scala:1161
20/01/03 23:29:30 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))
20/01/03 23:29:30 INFO TaskSchedulerImpl: Adding task set 1.0 with 1 tasks
20/01/03 23:29:30 INFO TaskSetManager: Starting task 0.0 in stage 1.0 (TID 1, localhost, executor driver, partition 0, ANY, 7662 bytes)
20/01/03 23:29:30 INFO Executor: Running task 0.0 in stage 1.0 (TID 1)
20/01/03 23:29:30 INFO ShuffleBlockFetcherIterator: Getting 1 non-empty blocks including 1 local blocks and 0 remote blocks
20/01/03 23:29:30 INFO ShuffleBlockFetcherIterator: Started 0 remote fetches in 7 ms
20/01/03 23:29:32 INFO FileOutputCommitter: File Output Committer Algorithm version is 1
20/01/03 23:29:32 INFO CodecConfig: Compression: GZIP
20/01/03 23:29:32 INFO FileOutputCommitter: File Output Committer Algorithm version is 1
20/01/03 23:29:32 INFO ParquetOutputFormat: Parquet block size to 134217728
20/01/03 23:29:32 INFO ParquetOutputFormat: Parquet page size to 1048576
20/01/03 23:29:32 INFO ParquetOutputFormat: Parquet dictionary page size to 1048576
20/01/03 23:29:32 INFO ParquetOutputFormat: Dictionary is on
20/01/03 23:29:32 INFO ParquetOutputFormat: Validation is off
20/01/03 23:29:32 INFO ParquetOutputFormat: Writer version is: PARQUET_1_0
20/01/03 23:29:32 INFO ParquetOutputFormat: Maximum row group padding size is 8388608 bytes
20/01/03 23:29:32 INFO ParquetOutputFormat: Page size checking is: estimated
20/01/03 23:29:32 INFO ParquetOutputFormat: Min row count for page size check is: 100
20/01/03 23:29:32 INFO ParquetOutputFormat: Max row count for page size check is: 10000
20/01/03 23:29:32 INFO CodecPool: Got brand-new compressor [.gz]
20/01/03 23:29:36 INFO InternalParquetRecordWriter: Flushing mem columnStore to file. allocated memory: 16004474
20/01/03 23:29:36 INFO FileOutputCommitter: Saved output of task 'attempt_20200103232927_0005_r_000000_0' to file:/tmp/adamTest2Mw865Z/deleteMePleaseThisIsNoLongerNeeded/mouse_chrM.bam.reads.sorted.adam/_temporary/0/task_20200103232927_0005_r_000000
20/01/03 23:29:36 INFO SparkHadoopMapRedUtil: attempt_20200103232927_0005_r_000000_0: Committed
20/01/03 23:29:36 INFO Executor: Finished task 0.0 in stage 1.0 (TID 1). 1237 bytes result sent to driver
20/01/03 23:29:36 INFO TaskSetManager: Finished task 0.0 in stage 1.0 (TID 1) in 5999 ms on localhost (executor driver) (1/1)
20/01/03 23:29:36 INFO TaskSchedulerImpl: Removed TaskSet 1.0, whose tasks have all completed, from pool 
20/01/03 23:29:36 INFO DAGScheduler: ResultStage 1 (runJob at SparkHadoopWriter.scala:78) finished in 6.050 s
20/01/03 23:29:36 INFO DAGScheduler: Job 0 finished: runJob at SparkHadoopWriter.scala:78, took 9.609053 s
20/01/03 23:29:36 INFO ParquetFileReader: Initiating action with parallelism: 5
20/01/03 23:29:36 INFO SparkHadoopWriter: Job job_20200103232927_0005 committed.
20/01/03 23:29:36 INFO TransformAlignments: Overall Duration: 13.2 secs
20/01/03 23:29:36 INFO SparkContext: Invoking stop() from shutdown hook
20/01/03 23:29:36 INFO SparkUI: Stopped Spark web UI at http://192.168.10.27:4040
20/01/03 23:29:36 INFO MapOutputTrackerMasterEndpoint: MapOutputTrackerMasterEndpoint stopped!
20/01/03 23:29:36 INFO MemoryStore: MemoryStore cleared
20/01/03 23:29:36 INFO BlockManager: BlockManager stopped
20/01/03 23:29:36 INFO BlockManagerMaster: BlockManagerMaster stopped
20/01/03 23:29:36 INFO OutputCommitCoordinator$OutputCommitCoordinatorEndpoint: OutputCommitCoordinator stopped!
20/01/03 23:29:36 INFO SparkContext: Successfully stopped SparkContext
20/01/03 23:29:36 INFO ShutdownHookManager: Shutdown hook called
20/01/03 23:29:36 INFO ShutdownHookManager: Deleting directory /tmp/spark-75977e42-3306-4cc2-bec3-a8f8204d877b
20/01/03 23:29:36 INFO ShutdownHookManager: Deleting directory /tmp/spark-16afbe29-b122-46dc-9d69-a2884ae10094

# 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/adamTest2Mw865Z/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.4-bin-hadoop2.7/bin/spark-submit
20/01/03 23:29:38 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)
20/01/03 23:29:38 WARN Utils: Set SPARK_LOCAL_IP if you need to bind to another address
20/01/03 23:29:38 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
20/01/03 23:29:38 INFO SparkContext: Running Spark version 2.4.4
20/01/03 23:29:38 INFO SparkContext: Submitted application: transformFragments
20/01/03 23:29:38 INFO SecurityManager: Changing view acls to: jenkins
20/01/03 23:29:38 INFO SecurityManager: Changing modify acls to: jenkins
20/01/03 23:29:38 INFO SecurityManager: Changing view acls groups to: 
20/01/03 23:29:38 INFO SecurityManager: Changing modify acls groups to: 
20/01/03 23:29:38 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()
20/01/03 23:29:39 INFO Utils: Successfully started service 'sparkDriver' on port 39563.
20/01/03 23:29:39 INFO SparkEnv: Registering MapOutputTracker
20/01/03 23:29:39 INFO SparkEnv: Registering BlockManagerMaster
20/01/03 23:29:39 INFO BlockManagerMasterEndpoint: Using org.apache.spark.storage.DefaultTopologyMapper for getting topology information
20/01/03 23:29:39 INFO BlockManagerMasterEndpoint: BlockManagerMasterEndpoint up
20/01/03 23:29:39 INFO DiskBlockManager: Created local directory at /tmp/blockmgr-72d76a62-a807-4f85-b60f-2a11737fd603
20/01/03 23:29:39 INFO MemoryStore: MemoryStore started with capacity 366.3 MB
20/01/03 23:29:39 INFO SparkEnv: Registering OutputCommitCoordinator
20/01/03 23:29:39 INFO Utils: Successfully started service 'SparkUI' on port 4040.
20/01/03 23:29:39 INFO SparkUI: Bound SparkUI to 0.0.0.0, and started at http://192.168.10.27:4040
20/01/03 23:29:39 INFO SparkContext: Added JAR file:/tmp/adamTest2Mw865Z/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/target/adam-assembly-spark2_2.11-0.31.0-SNAPSHOT.jar at spark://192.168.10.27:39563/jars/adam-assembly-spark2_2.11-0.31.0-SNAPSHOT.jar with timestamp 1578122979569
20/01/03 23:29:39 INFO Executor: Starting executor ID driver on host localhost
20/01/03 23:29:39 INFO Utils: Successfully started service 'org.apache.spark.network.netty.NettyBlockTransferService' on port 34235.
20/01/03 23:29:39 INFO NettyBlockTransferService: Server created on 192.168.10.27:34235
20/01/03 23:29:39 INFO BlockManager: Using org.apache.spark.storage.RandomBlockReplicationPolicy for block replication policy
20/01/03 23:29:39 INFO BlockManagerMaster: Registering BlockManager BlockManagerId(driver, 192.168.10.27, 34235, None)
20/01/03 23:29:39 INFO BlockManagerMasterEndpoint: Registering block manager 192.168.10.27:34235 with 366.3 MB RAM, BlockManagerId(driver, 192.168.10.27, 34235, None)
20/01/03 23:29:39 INFO BlockManagerMaster: Registered BlockManager BlockManagerId(driver, 192.168.10.27, 34235, None)
20/01/03 23:29:39 INFO BlockManager: Initialized BlockManager: BlockManagerId(driver, 192.168.10.27, 34235, None)
20/01/03 23:29:40 INFO ADAMContext: Loading mouse_chrM.bam.reads.adam as Parquet of Alignments.
20/01/03 23:29:41 INFO ADAMContext: Reading the ADAM file at mouse_chrM.bam.reads.adam to create RDD
20/01/03 23:29:41 INFO MemoryStore: Block broadcast_0 stored as values in memory (estimated size 303.7 KB, free 366.0 MB)
20/01/03 23:29:42 INFO MemoryStore: Block broadcast_0_piece0 stored as bytes in memory (estimated size 27.4 KB, free 366.0 MB)
20/01/03 23:29:42 INFO BlockManagerInfo: Added broadcast_0_piece0 in memory on 192.168.10.27:34235 (size: 27.4 KB, free: 366.3 MB)
20/01/03 23:29:42 INFO SparkContext: Created broadcast 0 from newAPIHadoopFile at ADAMContext.scala:1796
20/01/03 23:29:42 INFO FileInputFormat: Total input paths to process : 1
20/01/03 23:29:42 INFO ParquetInputFormat: Total input paths to process : 1
20/01/03 23:29:42 INFO RDDBoundFragmentDataset: Saving data in ADAM format
20/01/03 23:29:42 INFO FileOutputCommitter: File Output Committer Algorithm version is 1
20/01/03 23:29:42 INFO SparkContext: Starting job: runJob at SparkHadoopWriter.scala:78
20/01/03 23:29:42 INFO DAGScheduler: Registering RDD 2 (groupBy at SingleReadBucket.scala:97)
20/01/03 23:29:42 INFO DAGScheduler: Got job 0 (runJob at SparkHadoopWriter.scala:78) with 1 output partitions
20/01/03 23:29:42 INFO DAGScheduler: Final stage: ResultStage 1 (runJob at SparkHadoopWriter.scala:78)
20/01/03 23:29:42 INFO DAGScheduler: Parents of final stage: List(ShuffleMapStage 0)
20/01/03 23:29:42 INFO DAGScheduler: Missing parents: List(ShuffleMapStage 0)
20/01/03 23:29:42 INFO DAGScheduler: Submitting ShuffleMapStage 0 (MapPartitionsRDD[2] at groupBy at SingleReadBucket.scala:97), which has no missing parents
20/01/03 23:29:42 INFO MemoryStore: Block broadcast_1 stored as values in memory (estimated size 5.3 KB, free 366.0 MB)
20/01/03 23:29:42 INFO MemoryStore: Block broadcast_1_piece0 stored as bytes in memory (estimated size 3.0 KB, free 366.0 MB)
20/01/03 23:29:42 INFO BlockManagerInfo: Added broadcast_1_piece0 in memory on 192.168.10.27:34235 (size: 3.0 KB, free: 366.3 MB)
20/01/03 23:29:42 INFO SparkContext: Created broadcast 1 from broadcast at DAGScheduler.scala:1161
20/01/03 23:29:42 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))
20/01/03 23:29:42 INFO TaskSchedulerImpl: Adding task set 0.0 with 1 tasks
20/01/03 23:29:42 INFO TaskSetManager: Starting task 0.0 in stage 0.0 (TID 0, localhost, executor driver, partition 0, PROCESS_LOCAL, 8001 bytes)
20/01/03 23:29:42 INFO Executor: Running task 0.0 in stage 0.0 (TID 0)
20/01/03 23:29:42 INFO Executor: Fetching spark://192.168.10.27:39563/jars/adam-assembly-spark2_2.11-0.31.0-SNAPSHOT.jar with timestamp 1578122979569
20/01/03 23:29:42 INFO TransportClientFactory: Successfully created connection to /192.168.10.27:39563 after 33 ms (0 ms spent in bootstraps)
20/01/03 23:29:42 INFO Utils: Fetching spark://192.168.10.27:39563/jars/adam-assembly-spark2_2.11-0.31.0-SNAPSHOT.jar to /tmp/spark-2bdf3ecd-7560-4a4f-9891-bc72425e8fa1/userFiles-e9e2b47b-9376-4c4e-b87b-e347d7878c28/fetchFileTemp3902149446501294402.tmp
20/01/03 23:29:42 INFO Executor: Adding file:/tmp/spark-2bdf3ecd-7560-4a4f-9891-bc72425e8fa1/userFiles-e9e2b47b-9376-4c4e-b87b-e347d7878c28/adam-assembly-spark2_2.11-0.31.0-SNAPSHOT.jar to class loader
20/01/03 23:29:42 INFO NewHadoopRDD: Input split: file:/tmp/adamTest2Mw865Z/deleteMePleaseThisIsNoLongerNeeded/mouse_chrM.bam.reads.adam/part-r-00000.gz.parquet:0+10132211
20/01/03 23:29:43 INFO InternalParquetRecordReader: RecordReader initialized will read a total of 163064 records.
20/01/03 23:29:43 INFO InternalParquetRecordReader: at row 0. reading next block
20/01/03 23:29:43 INFO CodecPool: Got brand-new decompressor [.gz]
20/01/03 23:29:43 INFO InternalParquetRecordReader: block read in memory in 46 ms. row count = 163064
20/01/03 23:29:45 INFO Executor: Finished task 0.0 in stage 0.0 (TID 0). 956 bytes result sent to driver
20/01/03 23:29:45 INFO TaskSetManager: Finished task 0.0 in stage 0.0 (TID 0) in 3458 ms on localhost (executor driver) (1/1)
20/01/03 23:29:45 INFO TaskSchedulerImpl: Removed TaskSet 0.0, whose tasks have all completed, from pool 
20/01/03 23:29:45 INFO DAGScheduler: ShuffleMapStage 0 (groupBy at SingleReadBucket.scala:97) finished in 3.570 s
20/01/03 23:29:45 INFO DAGScheduler: looking for newly runnable stages
20/01/03 23:29:45 INFO DAGScheduler: running: Set()
20/01/03 23:29:45 INFO DAGScheduler: waiting: Set(ResultStage 1)
20/01/03 23:29:45 INFO DAGScheduler: failed: Set()
20/01/03 23:29:45 INFO DAGScheduler: Submitting ResultStage 1 (MapPartitionsRDD[6] at map at GenomicDataset.scala:3814), which has no missing parents
20/01/03 23:29:45 INFO MemoryStore: Block broadcast_2 stored as values in memory (estimated size 86.2 KB, free 365.9 MB)
20/01/03 23:29:45 INFO MemoryStore: Block broadcast_2_piece0 stored as bytes in memory (estimated size 32.2 KB, free 365.9 MB)
20/01/03 23:29:45 INFO BlockManagerInfo: Added broadcast_2_piece0 in memory on 192.168.10.27:34235 (size: 32.2 KB, free: 366.2 MB)
20/01/03 23:29:45 INFO SparkContext: Created broadcast 2 from broadcast at DAGScheduler.scala:1161
20/01/03 23:29:45 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))
20/01/03 23:29:45 INFO TaskSchedulerImpl: Adding task set 1.0 with 1 tasks
20/01/03 23:29:45 INFO TaskSetManager: Starting task 0.0 in stage 1.0 (TID 1, localhost, executor driver, partition 0, ANY, 7662 bytes)
20/01/03 23:29:45 INFO Executor: Running task 0.0 in stage 1.0 (TID 1)
20/01/03 23:29:46 INFO ShuffleBlockFetcherIterator: Getting 1 non-empty blocks including 1 local blocks and 0 remote blocks
20/01/03 23:29:46 INFO ShuffleBlockFetcherIterator: Started 0 remote fetches in 7 ms
20/01/03 23:29:47 INFO FileOutputCommitter: File Output Committer Algorithm version is 1
20/01/03 23:29:47 INFO CodecConfig: Compression: GZIP
20/01/03 23:29:47 INFO FileOutputCommitter: File Output Committer Algorithm version is 1
20/01/03 23:29:47 INFO ParquetOutputFormat: Parquet block size to 134217728
20/01/03 23:29:47 INFO ParquetOutputFormat: Parquet page size to 1048576
20/01/03 23:29:47 INFO ParquetOutputFormat: Parquet dictionary page size to 1048576
20/01/03 23:29:47 INFO ParquetOutputFormat: Dictionary is on
20/01/03 23:29:47 INFO ParquetOutputFormat: Validation is off
20/01/03 23:29:47 INFO ParquetOutputFormat: Writer version is: PARQUET_1_0
20/01/03 23:29:47 INFO ParquetOutputFormat: Maximum row group padding size is 8388608 bytes
20/01/03 23:29:47 INFO ParquetOutputFormat: Page size checking is: estimated
20/01/03 23:29:47 INFO ParquetOutputFormat: Min row count for page size check is: 100
20/01/03 23:29:47 INFO ParquetOutputFormat: Max row count for page size check is: 10000
20/01/03 23:29:47 INFO CodecPool: Got brand-new compressor [.gz]
20/01/03 23:29:53 INFO InternalParquetRecordWriter: Flushing mem columnStore to file. allocated memory: 21417928
20/01/03 23:29:54 INFO FileOutputCommitter: Saved output of task 'attempt_20200103232942_0006_r_000000_0' to file:/tmp/adamTest2Mw865Z/deleteMePleaseThisIsNoLongerNeeded/mouse_chrM.bam.fragments.adam/_temporary/0/task_20200103232942_0006_r_000000
20/01/03 23:29:54 INFO SparkHadoopMapRedUtil: attempt_20200103232942_0006_r_000000_0: Committed
20/01/03 23:29:54 INFO Executor: Finished task 0.0 in stage 1.0 (TID 1). 1237 bytes result sent to driver
20/01/03 23:29:54 INFO TaskSetManager: Finished task 0.0 in stage 1.0 (TID 1) in 8332 ms on localhost (executor driver) (1/1)
20/01/03 23:29:54 INFO TaskSchedulerImpl: Removed TaskSet 1.0, whose tasks have all completed, from pool 
20/01/03 23:29:54 INFO DAGScheduler: ResultStage 1 (runJob at SparkHadoopWriter.scala:78) finished in 8.370 s
20/01/03 23:29:54 INFO DAGScheduler: Job 0 finished: runJob at SparkHadoopWriter.scala:78, took 12.018296 s
20/01/03 23:29:54 INFO ParquetFileReader: Initiating action with parallelism: 5
20/01/03 23:29:54 INFO SparkHadoopWriter: Job job_20200103232942_0006 committed.
20/01/03 23:29:54 INFO TransformFragments: Overall Duration: 15.49 secs
20/01/03 23:29:54 INFO SparkContext: Invoking stop() from shutdown hook
20/01/03 23:29:54 INFO SparkUI: Stopped Spark web UI at http://192.168.10.27:4040
20/01/03 23:29:54 INFO MapOutputTrackerMasterEndpoint: MapOutputTrackerMasterEndpoint stopped!
20/01/03 23:29:54 INFO MemoryStore: MemoryStore cleared
20/01/03 23:29:54 INFO BlockManager: BlockManager stopped
20/01/03 23:29:54 INFO BlockManagerMaster: BlockManagerMaster stopped
20/01/03 23:29:54 INFO OutputCommitCoordinator$OutputCommitCoordinatorEndpoint: OutputCommitCoordinator stopped!
20/01/03 23:29:54 INFO SparkContext: Successfully stopped SparkContext
20/01/03 23:29:54 INFO ShutdownHookManager: Shutdown hook called
20/01/03 23:29:54 INFO ShutdownHookManager: Deleting directory /tmp/spark-2bdf3ecd-7560-4a4f-9891-bc72425e8fa1
20/01/03 23:29:54 INFO ShutdownHookManager: Deleting directory /tmp/spark-e7bedf26-dd28-4892-8838-d529786512e4

# 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/adamTest2Mw865Z/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.4-bin-hadoop2.7/bin/spark-submit
20/01/03 23:30:11 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)
20/01/03 23:30:11 WARN Utils: Set SPARK_LOCAL_IP if you need to bind to another address
20/01/03 23:30:11 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
20/01/03 23:30:12 INFO SparkContext: Running Spark version 2.4.4
20/01/03 23:30:12 INFO SparkContext: Submitted application: flagstat
20/01/03 23:30:12 INFO SecurityManager: Changing view acls to: jenkins
20/01/03 23:30:12 INFO SecurityManager: Changing modify acls to: jenkins
20/01/03 23:30:12 INFO SecurityManager: Changing view acls groups to: 
20/01/03 23:30:12 INFO SecurityManager: Changing modify acls groups to: 
20/01/03 23:30:12 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()
20/01/03 23:30:12 INFO Utils: Successfully started service 'sparkDriver' on port 45213.
20/01/03 23:30:12 INFO SparkEnv: Registering MapOutputTracker
20/01/03 23:30:12 INFO SparkEnv: Registering BlockManagerMaster
20/01/03 23:30:12 INFO BlockManagerMasterEndpoint: Using org.apache.spark.storage.DefaultTopologyMapper for getting topology information
20/01/03 23:30:12 INFO BlockManagerMasterEndpoint: BlockManagerMasterEndpoint up
20/01/03 23:30:12 INFO DiskBlockManager: Created local directory at /tmp/blockmgr-18deb864-89da-4eea-ace3-6db987ffb074
20/01/03 23:30:12 INFO MemoryStore: MemoryStore started with capacity 366.3 MB
20/01/03 23:30:12 INFO SparkEnv: Registering OutputCommitCoordinator
20/01/03 23:30:12 INFO Utils: Successfully started service 'SparkUI' on port 4040.
20/01/03 23:30:12 INFO SparkUI: Bound SparkUI to 0.0.0.0, and started at http://192.168.10.27:4040
20/01/03 23:30:12 INFO SparkContext: Added JAR file:/tmp/adamTest2Mw865Z/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/target/adam-assembly-spark2_2.11-0.31.0-SNAPSHOT.jar at spark://192.168.10.27:45213/jars/adam-assembly-spark2_2.11-0.31.0-SNAPSHOT.jar with timestamp 1578123012865
20/01/03 23:30:12 INFO Executor: Starting executor ID driver on host localhost
20/01/03 23:30:13 INFO Utils: Successfully started service 'org.apache.spark.network.netty.NettyBlockTransferService' on port 39613.
20/01/03 23:30:13 INFO NettyBlockTransferService: Server created on 192.168.10.27:39613
20/01/03 23:30:13 INFO BlockManager: Using org.apache.spark.storage.RandomBlockReplicationPolicy for block replication policy
20/01/03 23:30:13 INFO BlockManagerMaster: Registering BlockManager BlockManagerId(driver, 192.168.10.27, 39613, None)
20/01/03 23:30:13 INFO BlockManagerMasterEndpoint: Registering block manager 192.168.10.27:39613 with 366.3 MB RAM, BlockManagerId(driver, 192.168.10.27, 39613, None)
20/01/03 23:30:13 INFO BlockManagerMaster: Registered BlockManager BlockManagerId(driver, 192.168.10.27, 39613, None)
20/01/03 23:30:13 INFO BlockManager: Initialized BlockManager: BlockManagerId(driver, 192.168.10.27, 39613, None)
20/01/03 23:30:13 INFO ADAMContext: Loading mouse_chrM.bam.reads.adam as Parquet of Alignments.
20/01/03 23:30:13 INFO ADAMContext: Reading the ADAM file at mouse_chrM.bam.reads.adam to create RDD
20/01/03 23:30:13 INFO ADAMContext: Using the specified projection schema
20/01/03 23:30:14 INFO MemoryStore: Block broadcast_0 stored as values in memory (estimated size 313.1 KB, free 366.0 MB)
20/01/03 23:30:14 INFO MemoryStore: Block broadcast_0_piece0 stored as bytes in memory (estimated size 28.4 KB, free 366.0 MB)
20/01/03 23:30:14 INFO BlockManagerInfo: Added broadcast_0_piece0 in memory on 192.168.10.27:39613 (size: 28.4 KB, free: 366.3 MB)
20/01/03 23:30:14 INFO SparkContext: Created broadcast 0 from newAPIHadoopFile at ADAMContext.scala:1796
20/01/03 23:30:15 INFO FileInputFormat: Total input paths to process : 1
20/01/03 23:30:15 INFO ParquetInputFormat: Total input paths to process : 1
20/01/03 23:30:15 INFO SparkContext: Starting job: aggregate at FlagStat.scala:115
20/01/03 23:30:15 INFO DAGScheduler: Got job 0 (aggregate at FlagStat.scala:115) with 1 output partitions
20/01/03 23:30:15 INFO DAGScheduler: Final stage: ResultStage 0 (aggregate at FlagStat.scala:115)
20/01/03 23:30:15 INFO DAGScheduler: Parents of final stage: List()
20/01/03 23:30:15 INFO DAGScheduler: Missing parents: List()
20/01/03 23:30:15 INFO DAGScheduler: Submitting ResultStage 0 (MapPartitionsRDD[4] at map at FlagStat.scala:96), which has no missing parents
20/01/03 23:30:15 INFO MemoryStore: Block broadcast_1 stored as values in memory (estimated size 12.5 KB, free 366.0 MB)
20/01/03 23:30:15 INFO MemoryStore: Block broadcast_1_piece0 stored as bytes in memory (estimated size 5.5 KB, free 365.9 MB)
20/01/03 23:30:15 INFO BlockManagerInfo: Added broadcast_1_piece0 in memory on 192.168.10.27:39613 (size: 5.5 KB, free: 366.3 MB)
20/01/03 23:30:15 INFO SparkContext: Created broadcast 1 from broadcast at DAGScheduler.scala:1161
20/01/03 23:30:15 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))
20/01/03 23:30:15 INFO TaskSchedulerImpl: Adding task set 0.0 with 1 tasks
20/01/03 23:30:15 INFO TaskSetManager: Starting task 0.0 in stage 0.0 (TID 0, localhost, executor driver, partition 0, PROCESS_LOCAL, 8012 bytes)
20/01/03 23:30:15 INFO Executor: Running task 0.0 in stage 0.0 (TID 0)
20/01/03 23:30:15 INFO Executor: Fetching spark://192.168.10.27:45213/jars/adam-assembly-spark2_2.11-0.31.0-SNAPSHOT.jar with timestamp 1578123012865
20/01/03 23:30:16 INFO TransportClientFactory: Successfully created connection to /192.168.10.27:45213 after 157 ms (0 ms spent in bootstraps)
20/01/03 23:30:16 INFO Utils: Fetching spark://192.168.10.27:45213/jars/adam-assembly-spark2_2.11-0.31.0-SNAPSHOT.jar to /tmp/spark-a5c6b0c4-dd47-4259-8db5-bc511d3c60f1/userFiles-931cd32b-96c8-45d1-b0b3-91e7da3fb74e/fetchFileTemp8408035001803915809.tmp
20/01/03 23:30:16 INFO Executor: Adding file:/tmp/spark-a5c6b0c4-dd47-4259-8db5-bc511d3c60f1/userFiles-931cd32b-96c8-45d1-b0b3-91e7da3fb74e/adam-assembly-spark2_2.11-0.31.0-SNAPSHOT.jar to class loader
20/01/03 23:30:16 INFO NewHadoopRDD: Input split: file:/tmp/adamTest2Mw865Z/deleteMePleaseThisIsNoLongerNeeded/mouse_chrM.bam.reads.adam/part-r-00000.gz.parquet:0+10132211
20/01/03 23:30:16 INFO InternalParquetRecordReader: RecordReader initialized will read a total of 163064 records.
20/01/03 23:30:16 INFO InternalParquetRecordReader: at row 0. reading next block
20/01/03 23:30:16 INFO CodecPool: Got brand-new decompressor [.gz]
20/01/03 23:30:16 INFO InternalParquetRecordReader: block read in memory in 25 ms. row count = 163064
20/01/03 23:30:17 INFO Executor: Finished task 0.0 in stage 0.0 (TID 0). 8196 bytes result sent to driver
20/01/03 23:30:17 INFO TaskSetManager: Finished task 0.0 in stage 0.0 (TID 0) in 1663 ms on localhost (executor driver) (1/1)
20/01/03 23:30:17 INFO TaskSchedulerImpl: Removed TaskSet 0.0, whose tasks have all completed, from pool 
20/01/03 23:30:17 INFO DAGScheduler: ResultStage 0 (aggregate at FlagStat.scala:115) finished in 1.745 s
20/01/03 23:30:17 INFO DAGScheduler: Job 0 finished: aggregate at FlagStat.scala:115, took 1.797855 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)
20/01/03 23:30:17 INFO FlagStat: Overall Duration: 5.47 secs
20/01/03 23:30:17 INFO FlagStat: Metrics:

Timings
+--------------------------------------+--------------+--------------+-------------+--------+-----------+-----------+-----------+
|                Metric                | Worker Total | Driver Total | Driver Only | Count  |   Mean    |    Min    |    Max    |
+--------------------------------------+--------------+--------------+-------------+--------+-----------+-----------+-----------+
| └─ Load Alignments                   |            - |       2 secs |   1.94 secs |      1 |    2 secs |    2 secs |    2 secs |
|     └─ map at ADAMContext.scala:1805 |            - |     58.21 ms |           - |      1 |  58.21 ms |  58.21 ms |  58.21 ms |
|         └─ function call             |     20.64 ms |            - |           - | 163064 |    126 ns |     57 ns | 138.09 µs |
| └─ map at FlagStat.scala:96          |            - |      23.4 ms |           - |      1 |   23.4 ms |   23.4 ms |   23.4 ms |
|     └─ function call                 |    236.98 ms |            - |           - | 163064 |   1.45 µs |    154 ns |   1.37 ms |
| └─ aggregate at FlagStat.scala:115   |            - |    1.93 secs |           - |      1 | 1.93 secs | 1.93 secs | 1.93 secs |
|     └─ function call                 |     36.51 ms |            - |           - | 163065 |    223 ns |     84 ns | 604.19 µs |
+--------------------------------------+--------------+--------------+-------------+--------+-----------+-----------+-----------+

Spark Operations
+----------+---------------------------------+---------------+----------------+--------------+----------+
| Sequence |            Operation            | Is New Stage? | Stage Duration | Driver Total | Stage ID |
+----------+---------------------------------+---------------+----------------+--------------+----------+
| 1        | map at ADAMContext.scala:1805   | false         |              - |     58.21 ms | -        |
| 2        | map at FlagStat.scala:96        | false         |              - |      23.4 ms | -        |
| 3        | aggregate at FlagStat.scala:115 | true          |     -1.75 secs |    1.93 secs | 0        |
+----------+---------------------------------+---------------+----------------+--------------+----------+

Task Timings
+-------------------------------+------------+-------+-----------+-----------+-----------+
|            Metric             | Total Time | Count |   Mean    |    Min    |    Max    |
+-------------------------------+------------+-------+-----------+-----------+-----------+
| Task Duration                 |  1.66 secs |     1 | 1.66 secs | 1.66 secs | 1.66 secs |
| Executor Run Time             |  1.19 secs |     1 | 1.19 secs | 1.19 secs | 1.19 secs |
| Executor Deserialization Time |     390 ms |     1 |    390 ms |    390 ms |    390 ms |
| Result Serialization Time     |          0 |     1 |         0 |         0 |         0 |
+-------------------------------+------------+-------+-----------+-----------+-----------+

Task Timings By Host
+-------------------------------+--------+------------+-------+-----------+-----------+-----------+
|            Metric             |  Host  | Total Time | Count |   Mean    |    Min    |    Max    |
+-------------------------------+--------+------------+-------+-----------+-----------+-----------+
| Task Duration                 | driver |  1.66 secs |     1 | 1.66 secs | 1.66 secs | 1.66 secs |
| Executor Run Time             | driver |  1.19 secs |     1 | 1.19 secs | 1.19 secs | 1.19 secs |
| Executor Deserialization Time | driver |     390 ms |     1 |    390 ms |    390 ms |    390 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 |  1.66 secs |     1 | 1.66 secs | 1.66 secs | 1.66 secs |
| Executor Run Time             | 0: aggregate at FlagStat.scala:115 |  1.19 secs |     1 | 1.19 secs | 1.19 secs | 1.19 secs |
| Executor Deserialization Time | 0: aggregate at FlagStat.scala:115 |     390 ms |     1 |    390 ms |    390 ms |    390 ms |
| Result Serialization Time     | 0: aggregate at FlagStat.scala:115 |          0 |     1 |         0 |         0 |         0 |
+-------------------------------+------------------------------------+------------+-------+-----------+-----------+-----------+

20/01/03 23:30:17 INFO SparkContext: Invoking stop() from shutdown hook
20/01/03 23:30:17 INFO SparkUI: Stopped Spark web UI at http://192.168.10.27:4040
20/01/03 23:30:17 INFO MapOutputTrackerMasterEndpoint: MapOutputTrackerMasterEndpoint stopped!
20/01/03 23:30:17 INFO MemoryStore: MemoryStore cleared
20/01/03 23:30:17 INFO BlockManager: BlockManager stopped
20/01/03 23:30:17 INFO BlockManagerMaster: BlockManagerMaster stopped
20/01/03 23:30:17 INFO OutputCommitCoordinator$OutputCommitCoordinatorEndpoint: OutputCommitCoordinator stopped!
20/01/03 23:30:17 INFO SparkContext: Successfully stopped SparkContext
20/01/03 23:30:17 INFO ShutdownHookManager: Shutdown hook called
20/01/03 23:30:17 INFO ShutdownHookManager: Deleting directory /tmp/spark-96d698a7-8a6f-4d5f-b7e5-3c043dc61677
20/01/03 23:30:17 INFO ShutdownHookManager: Deleting directory /tmp/spark-a5c6b0c4-dd47-4259-8db5-bc511d3c60f1
rm -rf ${ADAM_TMP_DIR}
+ rm -rf /tmp/adamTest2Mw865Z/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 [  7.762 s]
[INFO] ADAM_2.11: Shader workaround ....................... SUCCESS [  0.030 s]
[INFO] ADAM_2.11: Avro-to-Dataset codegen utils ........... SUCCESS [  0.060 s]
[INFO] ADAM_2.11: Core .................................... SUCCESS [  4.167 s]
[INFO] ADAM_2.11: APIs for Java, Python ................... SUCCESS [  0.148 s]
[INFO] ADAM_2.11: CLI ..................................... SUCCESS [  0.258 s]
[INFO] ADAM_2.11: Assembly ................................ SUCCESS [  0.019 s]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 13.271 s
[INFO] Finished at: 2020-01-03T23:30:33-08:00
[INFO] Final Memory: 21M/1082M
[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/9180708da37ae5716ed12c0cce504d51468a81db
Finished: SUCCESS