FailedConsole Output

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.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/read/ADAMCRAMOutputFormatHeaderLess.html longer than 100 characters.
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[WARNING] Entry: adam-distribution-spark2_2.12-0.29.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/read/QualityScoreBin.html longer than 100 characters.
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[WARNING] Entry: adam-distribution-spark2_2.12-0.29.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/read/RDDBoundAlignmentRecordDataset.html longer than 100 characters.
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[WARNING] Entry: adam-distribution-spark2_2.12-0.29.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/read/SAMInFormatter$.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.29.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/FullOuterShuffleRegionJoin.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.29.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/RDDBoundGenericGenomicDataset.html longer than 100 characters.
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[WARNING] Entry: adam-distribution-spark2_2.12-0.29.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/feature/BEDInFormatter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.29.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/feature/NarrowPeakOutFormatter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.29.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/feature/GFF3InFormatter$.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.29.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/feature/GFF3InFormatter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.29.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/feature/DatasetBoundCoverageDataset.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.29.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/feature/GTFInFormatter$.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.29.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/feature/ParquetUnboundCoverageDataset.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.29.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/feature/BEDInFormatter$.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.29.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/feature/DatasetBoundFeatureDataset.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.29.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/feature/GTFInFormatter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.29.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/feature/GTFOutFormatter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.29.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/feature/NarrowPeakInFormatter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.29.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/feature/ParquetUnboundFeatureDataset.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.29.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/feature/RDDBoundFeatureDataset.html longer than 100 characters.
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[WARNING] Entry: adam-distribution-spark2_2.12-0.29.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/feature/RDDBoundCoverageDataset.html longer than 100 characters.
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[WARNING] Entry: adam-distribution-spark2_2.12-0.29.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/SortedIntervalPartitionJoinWithVictims.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.29.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/InnerShuffleRegionJoinAndGroupByLeft.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.29.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/rdd/AvroReadGroupGenomicDataset.html longer than 100 characters.
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[INFO] Building zip: /tmp/adamTestwqqoBb3/deleteMePleaseThisIsNoLongerNeeded/adam-distribution/target/adam-distribution-spark2_2.12-0.29.0-SNAPSHOT-bin.zip
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary:
[INFO] 
[INFO] ADAM_2.12 .......................................... SUCCESS [  7.489 s]
[INFO] ADAM_2.12: Shader workaround ....................... SUCCESS [  5.142 s]
[INFO] ADAM_2.12: Avro-to-Dataset codegen utils ........... SUCCESS [  5.005 s]
[INFO] ADAM_2.12: Core .................................... SUCCESS [01:07 min]
[INFO] ADAM_2.12: APIs for Java, Python ................... SUCCESS [ 10.508 s]
[INFO] ADAM_2.12: CLI ..................................... SUCCESS [ 12.188 s]
[INFO] ADAM_2.12: Assembly ................................ SUCCESS [ 18.002 s]
[INFO] ADAM_2.12: Python APIs ............................. SUCCESS [01:17 min]
[INFO] ADAM_2.12: R APIs .................................. SUCCESS [01:01 min]
[INFO] ADAM_2.12: Distribution ............................ SUCCESS [ 43.471 s]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 05:09 min
[INFO] Finished at: 2019-09-03T12:47:43-07:00
[INFO] Final Memory: 63M/1498M
[INFO] ------------------------------------------------------------------------
+ grep bdgenomics.adam
+ tar tzvf adam-distribution/target/adam-distribution-spark2_2.12-0.29.0-SNAPSHOT-bin.tar.gz
+ grep egg
drwxrwxr-x jenkins/jenkins        0 2019-09-03 12:44 adam-distribution-spark2_2.12-0.29.0-SNAPSHOT/r/bdgenomics.adam.egg-info/
-rw-r--r-- jenkins/jenkins 36825250 2019-09-03 12:44 adam-distribution-spark2_2.12-0.29.0-SNAPSHOT/repo/bdgenomics.adam-0.28.0a0-py3.6.egg
+ ./bin/pyadam
Using PYSPARK=/tmp/adamTestwqqoBb3/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.3-bin-without-hadoop-scala-2.12/bin/pyspark
2019-09-03 12:47:48 WARN  Utils:66 - Your hostname, research-jenkins-worker-09 resolves to a loopback address: 127.0.1.1; using 192.168.10.31 instead (on interface enp4s0f0)
2019-09-03 12:47:48 WARN  Utils:66 - Set SPARK_LOCAL_IP if you need to bind to another address
2019-09-03 12:47:49 WARN  NativeCodeLoader:62 - Unable to load native-hadoop library for your platform... using builtin-java classes where applicable
Setting default log level to "WARN".
To adjust logging level use sc.setLogLevel(newLevel). For SparkR, use setLogLevel(newLevel).
2019-09-03 12:47:56 WARN  Utils:66 - Truncated the string representation of a plan since it was too large. This behavior can be adjusted by setting 'spark.debug.maxToStringFields' in SparkEnv.conf.

[Stage 0:>                                                          (0 + 1) / 1]
                                                                                
+ source deactivate
#!/bin/bash

# Determine the directory containing this script
if [[ -n $BASH_VERSION ]]; then
    _SCRIPT_LOCATION=${BASH_SOURCE[0]}
    _SHELL="bash"
elif [[ -n $ZSH_VERSION ]]; then
    _SCRIPT_LOCATION=${funcstack[1]}
    _SHELL="zsh"
else
    echo "Only bash and zsh are supported"
    return 1
fi
++ [[ -n 4.3.48(1)-release ]]
++ _SCRIPT_LOCATION=/home/jenkins/anaconda2/envs/adam-build-b5986841-5ed2-4b33-8a97-5dd1b9461fd2/bin/deactivate
++ _SHELL=bash
_CONDA_DIR=$(dirname "$_SCRIPT_LOCATION")
dirname "$_SCRIPT_LOCATION"
+++ dirname /home/jenkins/anaconda2/envs/adam-build-b5986841-5ed2-4b33-8a97-5dd1b9461fd2/bin/deactivate
++ _CONDA_DIR=/home/jenkins/anaconda2/envs/adam-build-b5986841-5ed2-4b33-8a97-5dd1b9461fd2/bin

case "$(uname -s)" in
    CYGWIN*|MINGW*|MSYS*)
        EXT=".exe"
        export MSYS2_ENV_CONV_EXCL=CONDA_PATH
        ;;
    *)
        EXT=""
        ;;
esac
++ case "$(uname -s)" in
uname -s
+++ uname -s
++ EXT=

# shift over all args.  We don't accept any, so it's OK that we ignore them all here.
while [[ $# > 0 ]]
do
    key="$1"
    case $key in
        -h|--help)
            "$_CONDA_DIR/conda" ..deactivate $_SHELL$EXT -h
            if [[ -n $BASH_VERSION ]] && [[ "$(basename "$0" 2> /dev/null)" == "deactivate" ]]; then
                exit 0
            else
                return 0
            fi
            ;;
    esac
    shift # past argument or value
done
++ [[ 0 > 0 ]]

# Ensure that this script is sourced, not executed
# Note that if the script was executed, we're running inside bash!
# Also note that errors are ignored as `activate foo` doesn't generate a bad
# value for $0 which would cause errors.
if [[ -n $BASH_VERSION ]] && [[ "$(basename "$0" 2> /dev/null)" == "deactivate" ]]; then
    (>&2 echo "Error: deactivate must be sourced. Run 'source deactivate'
instead of 'deactivate'.
")
    "$_CONDA_DIR/conda" ..deactivate $_SHELL$EXT -h
    exit 1
fi
++ [[ -n 4.3.48(1)-release ]]
basename "$0" 2> /dev/null
+++ basename /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/scripts/jenkins-test
++ [[ jenkins-test == \d\e\a\c\t\i\v\a\t\e ]]

if [[ -z "$CONDA_PATH_BACKUP" ]]; then
    if [[ -n $BASH_VERSION ]] && [[ "$(basename "$0" 2> /dev/null)" == "deactivate" ]]; then
        exit 0
    else
        return 0
    fi
fi
++ [[ -z /usr/lib/jvm/java-8-oracle/bin/:/usr/lib/jvm/java-8-oracle/bin/:/home/anaconda/bin/:/home/jenkins/gems/bin:/usr/local/go/bin:/home/jenkins/go-projects/bin:/home/jenkins/anaconda2/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games ]]

if (( $? == 0 )); then
    # Inverse of activation: run deactivate scripts prior to deactivating env
    _CONDA_D="${CONDA_PREFIX}/etc/conda/deactivate.d"
    if [[ -d $_CONDA_D ]]; then
        eval $(find "$_CONDA_D" -iname "*.sh" -exec echo source \'{}\'';' \;)
    fi

#    # get the activation path that would have been provided for this prefix
#    _LAST_ACTIVATE_PATH=$("$_CONDA_DIR/conda" ..activate $_SHELL$EXT "$CONDA_PREFIX")
#
#    # in activate, we replace a placeholder so that conda keeps its place in the PATH order
#    # The activate script sets _CONDA_HOLD here to activate that behavior.
#    #   Otherwise, PATH is simply removed.
#    if [ -n "$_CONDA_HOLD" ]; then
#        export PATH="$($_CONDA_PYTHON2 -c "import re; print(re.sub(r'$_LAST_ACTIVATE_PATH(:?)', r'CONDA_PATH_PLACEHOLDER\1', '$PATH', 1))")"
#    else
#        export PATH="$($_CONDA_PYTHON2 -c "import re; print(re.sub(r'$_LAST_ACTIVATE_PATH(:?)', r'', '$PATH', 1))")"
#    fi
#
#    unset _LAST_ACTIVATE_PATH

    export PATH=$("$_CONDA_DIR/conda" ..deactivate.path $_SHELL$EXT "$CONDA_PREFIX")

    unset CONDA_DEFAULT_ENV
    unset CONDA_PREFIX
    unset CONDA_PATH_BACKUP
    export PS1="$CONDA_PS1_BACKUP"
    unset CONDA_PS1_BACKUP
    unset _CONDA_PYTHON2
else
    unset _CONDA_PYTHON2
    return $?
fi
++ ((  0 == 0  ))
++ _CONDA_D=/home/jenkins/anaconda2/envs/adam-build-b5986841-5ed2-4b33-8a97-5dd1b9461fd2/etc/conda/deactivate.d
++ [[ -d /home/jenkins/anaconda2/envs/adam-build-b5986841-5ed2-4b33-8a97-5dd1b9461fd2/etc/conda/deactivate.d ]]
"$_CONDA_DIR/conda" ..deactivate.path $_SHELL$EXT "$CONDA_PREFIX"
+++ /home/jenkins/anaconda2/envs/adam-build-b5986841-5ed2-4b33-8a97-5dd1b9461fd2/bin/conda ..deactivate.path bash /home/jenkins/anaconda2/envs/adam-build-b5986841-5ed2-4b33-8a97-5dd1b9461fd2
++ 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-b5986841-5ed2-4b33-8a97-5dd1b9461fd2 --all

Package plan for package removal in environment /home/jenkins/anaconda2/envs/adam-build-b5986841-5ed2-4b33-8a97-5dd1b9461fd2:

The following packages will be REMOVED:

    _libgcc_mutex:   0.1-main               
    ca-certificates: 2019.5.15-1            
    certifi:         2019.6.16-py36_1       
    libedit:         3.1.20181209-hc058e9b_0
    libffi:          3.2.1-hd88cf55_4       
    libgcc-ng:       9.1.0-hdf63c60_0       
    libstdcxx-ng:    9.1.0-hdf63c60_0       
    ncurses:         6.1-he6710b0_1         
    openssl:         1.1.1c-h7b6447c_1      
    pip:             19.2.2-py36_0          
    python:          3.6.9-h265db76_0       
    readline:        7.0-h7b6447c_5         
    setuptools:      41.0.1-py36_0          
    sqlite:          3.29.0-h7b6447c_0      
    tk:              8.6.8-hbc83047_0       
    wheel:           0.33.4-py36_0          
    xz:              5.2.4-h14c3975_4       
    zlib:            1.2.11-h7b6447c_3      

+ cp -r adam-python/target /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/scripts/../adam-python/
+ pushd adam-python
/tmp/adamTestwqqoBb3/deleteMePleaseThisIsNoLongerNeeded/adam-python /tmp/adamTestwqqoBb3/deleteMePleaseThisIsNoLongerNeeded ~/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu
+ make clean
pip uninstall -y adam
Cannot uninstall requirement adam, not installed
You are using pip version 19.1.1, however version 19.2.3 is available.
You should consider upgrading via the 'pip install --upgrade pip' command.
Makefile:65: recipe for target 'clean_develop' failed
make: [clean_develop] Error 1 (ignored)
rm -rf bdgenomics/*.egg*
rm -rf build/
+ make clean_sdist
rm -rf dist
+ popd
/tmp/adamTestwqqoBb3/deleteMePleaseThisIsNoLongerNeeded ~/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu
	
# define filenames
BAM=mouse_chrM.bam
+ BAM=mouse_chrM.bam
READS=${BAM}.reads.adam
+ READS=mouse_chrM.bam.reads.adam
SORTED_READS=${BAM}.reads.sorted.adam
+ SORTED_READS=mouse_chrM.bam.reads.sorted.adam
FRAGMENTS=${BAM}.fragments.adam
+ FRAGMENTS=mouse_chrM.bam.fragments.adam
    
# fetch our input dataset
echo "Fetching BAM file"
+ echo 'Fetching BAM file'
Fetching BAM file
rm -rf ${BAM}
+ rm -rf mouse_chrM.bam
wget -q https://s3.amazonaws.com/bdgenomics-test/${BAM}
+ wget -q https://s3.amazonaws.com/bdgenomics-test/mouse_chrM.bam

# once fetched, convert BAM to ADAM
echo "Converting BAM to ADAM read format"
+ echo 'Converting BAM to ADAM read format'
Converting BAM to ADAM read format
rm -rf ${READS}
+ rm -rf mouse_chrM.bam.reads.adam
${ADAM} transformAlignments ${BAM} ${READS}
+ ./bin/adam-submit transformAlignments mouse_chrM.bam mouse_chrM.bam.reads.adam
Using ADAM_MAIN=org.bdgenomics.adam.cli.ADAMMain
Using spark-submit=/tmp/adamTestwqqoBb3/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.3-bin-without-hadoop-scala-2.12/bin/spark-submit
19/09/03 12:48:12 WARN util.Utils: Your hostname, research-jenkins-worker-09 resolves to a loopback address: 127.0.1.1; using 192.168.10.31 instead (on interface enp4s0f0)
19/09/03 12:48:12 WARN util.Utils: Set SPARK_LOCAL_IP if you need to bind to another address
19/09/03 12:48:12 WARN util.NativeCodeLoader: Unable to load native-hadoop library for your platform... using builtin-java classes where applicable
19/09/03 12:48:12 INFO cli.ADAMMain: ADAM invoked with args: "transformAlignments" "mouse_chrM.bam" "mouse_chrM.bam.reads.adam"
19/09/03 12:48:12 INFO spark.SparkContext: Running Spark version 2.4.3
19/09/03 12:48:12 INFO spark.SparkContext: Submitted application: transformAlignments
19/09/03 12:48:12 INFO spark.SecurityManager: Changing view acls to: jenkins
19/09/03 12:48:12 INFO spark.SecurityManager: Changing modify acls to: jenkins
19/09/03 12:48:12 INFO spark.SecurityManager: Changing view acls groups to: 
19/09/03 12:48:12 INFO spark.SecurityManager: Changing modify acls groups to: 
19/09/03 12:48:12 INFO spark.SecurityManager: SecurityManager: authentication disabled; ui acls disabled; users  with view permissions: Set(jenkins); groups with view permissions: Set(); users  with modify permissions: Set(jenkins); groups with modify permissions: Set()
19/09/03 12:48:13 INFO util.Utils: Successfully started service 'sparkDriver' on port 33529.
19/09/03 12:48:13 INFO spark.SparkEnv: Registering MapOutputTracker
19/09/03 12:48:13 INFO spark.SparkEnv: Registering BlockManagerMaster
19/09/03 12:48:13 INFO storage.BlockManagerMasterEndpoint: Using org.apache.spark.storage.DefaultTopologyMapper for getting topology information
19/09/03 12:48:13 INFO storage.BlockManagerMasterEndpoint: BlockManagerMasterEndpoint up
19/09/03 12:48:13 INFO storage.DiskBlockManager: Created local directory at /tmp/blockmgr-513966da-8492-43ad-9e3d-0e1db641da49
19/09/03 12:48:13 INFO memory.MemoryStore: MemoryStore started with capacity 366.3 MB
19/09/03 12:48:13 INFO spark.SparkEnv: Registering OutputCommitCoordinator
19/09/03 12:48:13 INFO util.log: Logging initialized @2517ms
19/09/03 12:48:13 INFO server.Server: jetty-9.3.z-SNAPSHOT, build timestamp: unknown, git hash: unknown
19/09/03 12:48:13 INFO server.Server: Started @2623ms
19/09/03 12:48:13 INFO server.AbstractConnector: Started ServerConnector@4d0402b{HTTP/1.1,[http/1.1]}{0.0.0.0:4040}
19/09/03 12:48:13 INFO util.Utils: Successfully started service 'SparkUI' on port 4040.
19/09/03 12:48:13 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@79f227a9{/jobs,null,AVAILABLE,@Spark}
19/09/03 12:48:13 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@7692cd34{/jobs/json,null,AVAILABLE,@Spark}
19/09/03 12:48:13 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@33aa93c{/jobs/job,null,AVAILABLE,@Spark}
19/09/03 12:48:13 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@106faf11{/jobs/job/json,null,AVAILABLE,@Spark}
19/09/03 12:48:13 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@70f43b45{/stages,null,AVAILABLE,@Spark}
19/09/03 12:48:13 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@26d10f2e{/stages/json,null,AVAILABLE,@Spark}
19/09/03 12:48:13 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@10ad20cb{/stages/stage,null,AVAILABLE,@Spark}
19/09/03 12:48:13 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@22ee2d0{/stages/stage/json,null,AVAILABLE,@Spark}
19/09/03 12:48:13 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@7bfc3126{/stages/pool,null,AVAILABLE,@Spark}
19/09/03 12:48:13 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@3e792ce3{/stages/pool/json,null,AVAILABLE,@Spark}
19/09/03 12:48:13 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@53bc1328{/storage,null,AVAILABLE,@Spark}
19/09/03 12:48:13 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@26f143ed{/storage/json,null,AVAILABLE,@Spark}
19/09/03 12:48:13 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@3c1e3314{/storage/rdd,null,AVAILABLE,@Spark}
19/09/03 12:48:13 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@4b770e40{/storage/rdd/json,null,AVAILABLE,@Spark}
19/09/03 12:48:13 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@78e16155{/environment,null,AVAILABLE,@Spark}
19/09/03 12:48:13 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@54a3ab8f{/environment/json,null,AVAILABLE,@Spark}
19/09/03 12:48:13 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@1968a49c{/executors,null,AVAILABLE,@Spark}
19/09/03 12:48:13 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@6a1ebcff{/executors/json,null,AVAILABLE,@Spark}
19/09/03 12:48:13 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@19868320{/executors/threadDump,null,AVAILABLE,@Spark}
19/09/03 12:48:13 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@50b0bc4c{/executors/threadDump/json,null,AVAILABLE,@Spark}
19/09/03 12:48:13 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@c20be82{/static,null,AVAILABLE,@Spark}
19/09/03 12:48:13 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@437e951d{/,null,AVAILABLE,@Spark}
19/09/03 12:48:13 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@77b325b3{/api,null,AVAILABLE,@Spark}
19/09/03 12:48:13 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@271f18d3{/jobs/job/kill,null,AVAILABLE,@Spark}
19/09/03 12:48:13 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@6bd51ed8{/stages/stage/kill,null,AVAILABLE,@Spark}
19/09/03 12:48:13 INFO ui.SparkUI: Bound SparkUI to 0.0.0.0, and started at http://192.168.10.31:4040
19/09/03 12:48:13 INFO spark.SparkContext: Added JAR file:/tmp/adamTestwqqoBb3/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/target/adam-assembly-spark2_2.12-0.29.0-SNAPSHOT.jar at spark://192.168.10.31:33529/jars/adam-assembly-spark2_2.12-0.29.0-SNAPSHOT.jar with timestamp 1567540093788
19/09/03 12:48:13 INFO executor.Executor: Starting executor ID driver on host localhost
19/09/03 12:48:13 INFO util.Utils: Successfully started service 'org.apache.spark.network.netty.NettyBlockTransferService' on port 33545.
19/09/03 12:48:13 INFO netty.NettyBlockTransferService: Server created on 192.168.10.31:33545
19/09/03 12:48:13 INFO storage.BlockManager: Using org.apache.spark.storage.RandomBlockReplicationPolicy for block replication policy
19/09/03 12:48:13 INFO storage.BlockManagerMaster: Registering BlockManager BlockManagerId(driver, 192.168.10.31, 33545, None)
19/09/03 12:48:13 INFO storage.BlockManagerMasterEndpoint: Registering block manager 192.168.10.31:33545 with 366.3 MB RAM, BlockManagerId(driver, 192.168.10.31, 33545, None)
19/09/03 12:48:13 INFO storage.BlockManagerMaster: Registered BlockManager BlockManagerId(driver, 192.168.10.31, 33545, None)
19/09/03 12:48:13 INFO storage.BlockManager: Initialized BlockManager: BlockManagerId(driver, 192.168.10.31, 33545, None)
19/09/03 12:48:14 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@37095ded{/metrics/json,null,AVAILABLE,@Spark}
19/09/03 12:48:14 INFO rdd.ADAMContext: Loading mouse_chrM.bam as BAM/CRAM/SAM and converting to AlignmentRecords.
19/09/03 12:48:14 INFO rdd.ADAMContext: Loaded header from file:/tmp/adamTestwqqoBb3/deleteMePleaseThisIsNoLongerNeeded/mouse_chrM.bam
19/09/03 12:48:15 INFO memory.MemoryStore: Block broadcast_0 stored as values in memory (estimated size 295.6 KB, free 366.0 MB)
Command body threw exception:
java.lang.NoClassDefFoundError: org/apache/avro/generic/GenericRecord
19/09/03 12:48:15 INFO cli.TransformAlignments: Overall Duration: 2.5 secs
Exception in thread "main" java.lang.NoClassDefFoundError: org/apache/avro/generic/GenericRecord
	at org.apache.spark.serializer.KryoSerializer.newKryo(KryoSerializer.scala:123)
	at org.apache.spark.serializer.KryoSerializerInstance.borrowKryo(KryoSerializer.scala:324)
	at org.apache.spark.serializer.KryoSerializerInstance.<init>(KryoSerializer.scala:309)
	at org.apache.spark.serializer.KryoSerializer.newInstance(KryoSerializer.scala:218)
	at org.apache.spark.broadcast.TorrentBroadcast$.blockifyObject(TorrentBroadcast.scala:288)
	at org.apache.spark.broadcast.TorrentBroadcast.writeBlocks(TorrentBroadcast.scala:127)
	at org.apache.spark.broadcast.TorrentBroadcast.<init>(TorrentBroadcast.scala:88)
	at org.apache.spark.broadcast.TorrentBroadcastFactory.newBroadcast(TorrentBroadcastFactory.scala:34)
	at org.apache.spark.broadcast.BroadcastManager.newBroadcast(BroadcastManager.scala:62)
	at org.apache.spark.SparkContext.broadcast(SparkContext.scala:1489)
	at org.apache.spark.rdd.NewHadoopRDD.<init>(NewHadoopRDD.scala:79)
	at org.apache.spark.SparkContext.$anonfun$newAPIHadoopFile$2(SparkContext.scala:1160)
	at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:151)
	at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:112)
	at org.apache.spark.SparkContext.withScope(SparkContext.scala:699)
	at org.apache.spark.SparkContext.newAPIHadoopFile(SparkContext.scala:1146)
	at org.bdgenomics.adam.rdd.ADAMContext.$anonfun$loadBam$1(ADAMContext.scala:2059)
	at scala.Option.fold(Option.scala:175)
	at org.apache.spark.rdd.Timer.time(Timer.scala:48)
	at org.bdgenomics.adam.rdd.ADAMContext.loadBam(ADAMContext.scala:1999)
	at org.bdgenomics.adam.rdd.ADAMContext.$anonfun$loadAlignments$1(ADAMContext.scala:3646)
	at scala.Option.fold(Option.scala:175)
	at org.apache.spark.rdd.Timer.time(Timer.scala:48)
	at org.bdgenomics.adam.rdd.ADAMContext.loadAlignments(ADAMContext.scala:3637)
	at org.bdgenomics.adam.cli.TransformAlignments.run(TransformAlignments.scala:567)
	at org.bdgenomics.utils.cli.BDGSparkCommand.run(BDGCommand.scala:55)
	at org.bdgenomics.utils.cli.BDGSparkCommand.run$(BDGCommand.scala:46)
	at org.bdgenomics.adam.cli.TransformAlignments.run(TransformAlignments.scala:204)
	at org.bdgenomics.adam.cli.ADAMMain.apply(ADAMMain.scala:126)
	at org.bdgenomics.adam.cli.ADAMMain$.main(ADAMMain.scala:65)
	at org.bdgenomics.adam.cli.ADAMMain.main(ADAMMain.scala)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at org.apache.spark.deploy.JavaMainApplication.start(SparkApplication.scala:52)
	at org.apache.spark.deploy.SparkSubmit.org$apache$spark$deploy$SparkSubmit$$runMain(SparkSubmit.scala:849)
	at org.apache.spark.deploy.SparkSubmit.doRunMain$1(SparkSubmit.scala:167)
	at org.apache.spark.deploy.SparkSubmit.submit(SparkSubmit.scala:195)
	at org.apache.spark.deploy.SparkSubmit.doSubmit(SparkSubmit.scala:86)
	at org.apache.spark.deploy.SparkSubmit$$anon$2.doSubmit(SparkSubmit.scala:924)
	at org.apache.spark.deploy.SparkSubmit$.main(SparkSubmit.scala:933)
	at org.apache.spark.deploy.SparkSubmit.main(SparkSubmit.scala)
Caused by: java.lang.ClassNotFoundException: org.apache.avro.generic.GenericRecord
	at java.net.URLClassLoader.findClass(URLClassLoader.java:382)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
	at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:349)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
	... 43 more
19/09/03 12:48:15 INFO spark.SparkContext: Invoking stop() from shutdown hook
19/09/03 12:48:15 INFO server.AbstractConnector: Stopped Spark@4d0402b{HTTP/1.1,[http/1.1]}{0.0.0.0:4040}
19/09/03 12:48:15 INFO ui.SparkUI: Stopped Spark web UI at http://192.168.10.31:4040
19/09/03 12:48:15 INFO spark.MapOutputTrackerMasterEndpoint: MapOutputTrackerMasterEndpoint stopped!
19/09/03 12:48:15 INFO memory.MemoryStore: MemoryStore cleared
19/09/03 12:48:15 INFO storage.BlockManager: BlockManager stopped
19/09/03 12:48:15 INFO storage.BlockManagerMaster: BlockManagerMaster stopped
19/09/03 12:48:15 INFO scheduler.OutputCommitCoordinator$OutputCommitCoordinatorEndpoint: OutputCommitCoordinator stopped!
19/09/03 12:48:15 INFO spark.SparkContext: Successfully stopped SparkContext
19/09/03 12:48:15 INFO util.ShutdownHookManager: Shutdown hook called
19/09/03 12:48:15 INFO util.ShutdownHookManager: Deleting directory /tmp/spark-067eccaf-c0e8-4a6a-b5df-5aab347e420b
19/09/03 12:48:15 INFO util.ShutdownHookManager: Deleting directory /tmp/spark-d6e16e02-b003-4e62-a201-411f6c85a697
Build step 'Execute shell' marked build as failure
Recording test results
Publishing Scoverage XML and HTML report...
null
Setting commit status on GitHub for https://github.com/bigdatagenomics/adam/commit/69ab9662497816fdd1f378f9a914f2f8a3f72391
Finished: FAILURE