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/tmp/adamTestMvnrdsg3D6/TempSuite6685890660586981504.bam
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/tmp/adamTestMvnrdsg3D6/TempSuite6685890660586981504.bam/_SUCCESS
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/tmp/adamTestMvnrdsg3D6/TempSuite2118565568315330746.adam/_readGroups.avro
/tmp/adamTestMvnrdsg3D6/TempSuite2118565568315330746.adam/.part-00000-8f397423-97ab-4089-b9d0-9933ac623b8f-c000.snappy.parquet.crc
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/tmp/adamTestMvnrdsg3D6/TempSuite2118565568315330746.adam/_processingSteps.avro
/tmp/adamTestMvnrdsg3D6/TempSuite2118565568315330746.adam/._readGroups.avro.crc
/tmp/adamTestMvnrdsg3D6/TempSuite2118565568315330746.adam/_SUCCESS
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/tmp/adamTestMvnrdsg3D6/TempSuite2118565568315330746.adam/._references.avro.crc
/tmp/adamTestMvnrdsg3D6/TempSuite2118565568315330746.adam/_references.avro
/tmp/adamTestMvnrdsg3D6/TempSuite2128316450182925450
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/tmp/adamTestMvnrdsg3D6/4211853318334010469/genotypes.adam
/tmp/adamTestMvnrdsg3D6/4211853318334010469/genotypes.adam/._common_metadata.crc
/tmp/adamTestMvnrdsg3D6/4211853318334010469/genotypes.adam/_common_metadata
/tmp/adamTestMvnrdsg3D6/4211853318334010469/genotypes.adam/._samples.avro.crc
/tmp/adamTestMvnrdsg3D6/4211853318334010469/genotypes.adam/._metadata.crc
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/tmp/adamTestMvnrdsg3D6/4211853318334010469/genotypes.adam/._references.avro.crc
/tmp/adamTestMvnrdsg3D6/4211853318334010469/genotypes.adam/_metadata
/tmp/adamTestMvnrdsg3D6/4211853318334010469/genotypes.adam/.part-r-00000.gz.parquet.crc
/tmp/adamTestMvnrdsg3D6/4211853318334010469/genotypes.adam/_references.avro
/tmp/adamTestMvnrdsg3D6/TempSuite5833776313583579215.adam
/tmp/adamTestMvnrdsg3D6/TempSuite5833776313583579215.adam/._common_metadata.crc
/tmp/adamTestMvnrdsg3D6/TempSuite5833776313583579215.adam/_common_metadata
/tmp/adamTestMvnrdsg3D6/TempSuite5833776313583579215.adam/._metadata.crc
/tmp/adamTestMvnrdsg3D6/TempSuite5833776313583579215.adam/._header.crc
/tmp/adamTestMvnrdsg3D6/TempSuite5833776313583579215.adam/part-r-00000.gz.parquet
/tmp/adamTestMvnrdsg3D6/TempSuite5833776313583579215.adam/_header
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/tmp/adamTestMvnrdsg3D6/TempSuite5833776313583579215.adam/._references.avro.crc
/tmp/adamTestMvnrdsg3D6/TempSuite5833776313583579215.adam/_metadata
/tmp/adamTestMvnrdsg3D6/TempSuite5833776313583579215.adam/.part-r-00000.gz.parquet.crc
/tmp/adamTestMvnrdsg3D6/TempSuite5833776313583579215.adam/_references.avro
/tmp/adamTestMvnrdsg3D6/TempSuite4150871716568644620
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/tmp/adamTestMvnrdsg3D6/TempSuite8023511389841390660.adam/._common_metadata.crc
/tmp/adamTestMvnrdsg3D6/TempSuite8023511389841390660.adam/_common_metadata
/tmp/adamTestMvnrdsg3D6/TempSuite8023511389841390660.adam/._metadata.crc
/tmp/adamTestMvnrdsg3D6/TempSuite8023511389841390660.adam/part-r-00000.gz.parquet
/tmp/adamTestMvnrdsg3D6/TempSuite8023511389841390660.adam/_SUCCESS
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/tmp/adamTestMvnrdsg3D6/TempSuite8023511389841390660.adam/_metadata
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/tmp/adamTestMvnrdsg3D6/TempSuite8023511389841390660.adam/_references.avro
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/tmp/adamTestMvnrdsg3D6/TempSuite4048793090657134865.bed/._SUCCESS.crc
/tmp/adamTestMvnrdsg3D6/unordered.sam2421670338032837821.sam
/tmp/adamTestMvnrdsg3D6/TempSuite9174390436163876013
/tmp/adamTestMvnrdsg3D6/TempSuite3196169748385784035
/tmp/adamTestMvnrdsg3D6/4053569315470625306
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/tmp/adamTestMvnrdsg3D6/4053569315470625306/binned.adam/._common_metadata.crc
/tmp/adamTestMvnrdsg3D6/4053569315470625306/binned.adam/_readGroups.avro
/tmp/adamTestMvnrdsg3D6/4053569315470625306/binned.adam/_common_metadata
/tmp/adamTestMvnrdsg3D6/4053569315470625306/binned.adam/._metadata.crc
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/tmp/adamTestMvnrdsg3D6/4053569315470625306/binned.adam/_processingSteps.avro
/tmp/adamTestMvnrdsg3D6/4053569315470625306/binned.adam/._readGroups.avro.crc
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/tmp/adamTestMvnrdsg3D6/sample1.queryname.sam2202753825883237237.queryname.sam
/tmp/adamTestMvnrdsg3D6/FeatureDatasetFunctionsSuite3297810926456383367
/tmp/adamTestMvnrdsg3D6/TempSuite5446944208291227594
/tmp/adamTestMvnrdsg3D6/TempSuite1910935521289489435
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/tmp/adamTestMvnrdsg3D6/TempSuite6697154490044552294.adam/_header
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/tmp/adamTestMvnrdsg3D6/TempSuite6697154490044552294.adam/_metadata
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/tmp/adamTestMvnrdsg3D6/FeatureDatasetFunctionsSuite1328788067610973737
/tmp/adamTestMvnrdsg3D6/SequenceDatasetSuite5821458604502117680
/tmp/adamTestMvnrdsg3D6/TempSuite5446944208291227594.fq
/tmp/adamTestMvnrdsg3D6/TempSuite5446944208291227594.fq/part-00000
/tmp/adamTestMvnrdsg3D6/TempSuite5446944208291227594.fq/_SUCCESS
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/tmp/adamTestMvnrdsg3D6/TempSuite5446944208291227594.fq/._SUCCESS.crc
rm -rf ${ADAM_MVN_TMP_DIR}
+ rm -rf /tmp/adamTestMvnrdsg3D6

find . -name pom.xml \
    -exec sed -i.bak \
    -e "s:sun.io.serialization.extendedDebugInfo=true -Djava.io.tmpdir=${ADAM_MVN_TMP_DIR}:sun.io.serialization.extendedDebugInfo=true:g" \
    {} \;
+ find . -name pom.xml -exec sed -i.bak -e 's:sun.io.serialization.extendedDebugInfo=true -Djava.io.tmpdir=/tmp/adamTestMvnrdsg3D6:sun.io.serialization.extendedDebugInfo=true:g' '{}' ';'
find . -name "*.bak" -exec rm -f {} \;
+ find . -name '*.bak' -exec rm -f '{}' ';'

# run integration tests

# make a temp directory
ADAM_TMP_DIR=$(mktemp -d -t adamTestXXXXXXX)
mktemp -d -t adamTestXXXXXXX
++ mktemp -d -t adamTestXXXXXXX
+ ADAM_TMP_DIR=/tmp/adamTestTsIwWXl

# Just to be paranoid.. use a directory internal to the ADAM_TMP_DIR
ADAM_TMP_DIR=$ADAM_TMP_DIR/deleteMePleaseThisIsNoLongerNeeded
+ ADAM_TMP_DIR=/tmp/adamTestTsIwWXl/deleteMePleaseThisIsNoLongerNeeded
mkdir $ADAM_TMP_DIR
+ mkdir /tmp/adamTestTsIwWXl/deleteMePleaseThisIsNoLongerNeeded

# set the TMPDIR envar, which is used by python to choose where to make temp directories
export TMPDIR=${ADAM_TMP_DIR}
+ export TMPDIR=/tmp/adamTestTsIwWXl/deleteMePleaseThisIsNoLongerNeeded
+ TMPDIR=/tmp/adamTestTsIwWXl/deleteMePleaseThisIsNoLongerNeeded

pushd $PROJECT_ROOT
+ pushd /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.6/label/ubuntu/scripts/..
~/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.6/label/ubuntu ~/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.6/label/ubuntu

# Copy the jar into our temp space for testing
cp -r . $ADAM_TMP_DIR
+ cp -r . /tmp/adamTestTsIwWXl/deleteMePleaseThisIsNoLongerNeeded
popd
+ popd
~/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.6/label/ubuntu

pushd $ADAM_TMP_DIR
+ pushd /tmp/adamTestTsIwWXl/deleteMePleaseThisIsNoLongerNeeded
/tmp/adamTestTsIwWXl/deleteMePleaseThisIsNoLongerNeeded ~/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.6/label/ubuntu

# what hadoop version are we on? format string for downloading spark assembly
if [[ $HADOOP_VERSION =~ ^2\.7 ]]; then
    HADOOP=hadoop2.7
else
    echo "Unknown Hadoop version."
    exit 1
fi
+ [[ 2.7.5 =~ ^2\.7 ]]
+ HADOOP=hadoop2.7

# set spark artifact string for downloading assembly
SPARK=spark-${SPARK_VERSION}
+ SPARK=spark-2.4.6
    
# download prepackaged spark assembly

# Spark 2.4.3+ and less than 3.0.0 needs special case for Scala 2.12
if [ ${SCALA_VERSION} == 2.12 ] && [ ${SPARK_VERSION} == 2.4.6 ]
then
    curl \
        -L "https://www.apache.org/dyn/mirrors/mirrors.cgi?action=download&filename=spark/${SPARK}/${SPARK}-bin-without-hadoop-scala-2.12.tgz" \
        -o ${SPARK}-bin-without-hadoop-scala-2.12.tgz

    tar xzvf ${SPARK}-bin-without-hadoop-scala-2.12.tgz
    export SPARK_HOME=${ADAM_TMP_DIR}/${SPARK}-bin-without-hadoop-scala-2.12

    curl \
        -L "https://www.apache.org/dyn/mirrors/mirrors.cgi?action=download&filename=hadoop/core/hadoop-2.7.7/hadoop-2.7.7.tar.gz" \
        -o hadoop-2.7.7.tar.gz

    tar xzvf hadoop-2.7.7.tar.gz

    # remove references to avro 1.7.x
    find hadoop-2.7.7 -name *.jar | grep avro | xargs rm

    # download avro 1.8.x
    #curl \
    #    -L "https://repo1.maven.org/maven2/org/apache/avro/avro/1.8.2/avro-1.8.2.jar" \
    #    -o hadoop-2.7.7/share/hadoop/common/avro-1.8.2.jar

    export SPARK_DIST_CLASSPATH=$(hadoop-2.7.7/bin/hadoop classpath)
else
    curl \
        -v \
        -L "https://www.apache.org/dyn/mirrors/mirrors.cgi?action=download&filename=spark/${SPARK}/${SPARK}-bin-${HADOOP}.tgz" \
        -o ${SPARK}-bin-${HADOOP}.tgz

    tar xzvf ${SPARK}-bin-${HADOOP}.tgz
    export SPARK_HOME=${ADAM_TMP_DIR}/${SPARK}-bin-${HADOOP}
fi
+ '[' 2.12 == 2.12 ']'
+ '[' 2.4.6 == 2.4.6 ']'
+ curl -L 'https://www.apache.org/dyn/mirrors/mirrors.cgi?action=download&filename=spark/spark-2.4.6/spark-2.4.6-bin-without-hadoop-scala-2.12.tgz' -o spark-2.4.6-bin-without-hadoop-scala-2.12.tgz
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0

100   196  100   196    0     0    192      0  0:00:01  0:00:01 --:--:--   192
+ tar xzvf spark-2.4.6-bin-without-hadoop-scala-2.12.tgz

gzip: stdin: not in gzip format
tar: Child returned status 1
tar: Error is not recoverable: exiting now
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/19acc911f2995a8df016c4a624f383deded47f6a
Finished: FAILURE