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/tmp/adamTestMvnjWyR1bF/FeatureDatasetFunctionsSuite4333406816956198306.narrowPeak/.part-00000.crc
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/tmp/adamTestMvnjWyR1bF/FeatureDatasetFunctionsSuite7275854540793202916
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/tmp/adamTestMvnjWyR1bF/TempSuite1167219571730764231.adam/_readGroups.avro
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/tmp/adamTestMvnjWyR1bF/TempSuite1167219571730764231.adam/_references.avro
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/tmp/adamTestMvnjWyR1bF/TempSuite1167219571730764231.adam/._readGroups.avro.crc
/tmp/adamTestMvnjWyR1bF/.SequenceDatasetSuite5422146486485714623.fasta.crc
rm -rf ${ADAM_MVN_TMP_DIR}
+ rm -rf /tmp/adamTestMvnjWyR1bF

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/adamTestMvnjWyR1bF: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/adamTestyuCl6HX

# Just to be paranoid.. use a directory internal to the ADAM_TMP_DIR
ADAM_TMP_DIR=$ADAM_TMP_DIR/deleteMePleaseThisIsNoLongerNeeded
+ ADAM_TMP_DIR=/tmp/adamTestyuCl6HX/deleteMePleaseThisIsNoLongerNeeded
mkdir $ADAM_TMP_DIR
+ mkdir /tmp/adamTestyuCl6HX/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/adamTestyuCl6HX/deleteMePleaseThisIsNoLongerNeeded
+ TMPDIR=/tmp/adamTestyuCl6HX/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/adamTestyuCl6HX/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/adamTestyuCl6HX/deleteMePleaseThisIsNoLongerNeeded
/tmp/adamTestyuCl6HX/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+ needs special case for Scala 2.12
if [[ ${SCALA_VERSION} == 2.12 ] && [ ${SPARK_VERSION} == 2.4.6 ]]
/home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.6/label/ubuntu/scripts/jenkins-test: line 153: syntax error in conditional expression
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/449de64516d9dd4adf566a32305e75f2c2441cd0
Finished: FAILURE