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/tmp/adamTestMvnFJdRuV3/1599678444192-0/bamReads.adam/_common_metadata
/tmp/adamTestMvnFJdRuV3/1599678444192-0/bamReads.adam/._metadata.crc
/tmp/adamTestMvnFJdRuV3/1599678444192-0/bamReads.adam/._SUCCESS.crc
/tmp/adamTestMvnFJdRuV3/1599678444192-0/bamReads.adam/._readGroups.avro.crc
/tmp/adamTestMvnFJdRuV3/1599678444192-0/bamReads.adam/_metadata
/tmp/adamTestMvnFJdRuV3/1599678444192-0/bamReads.adam/_processingSteps.avro
/tmp/adamTestMvnFJdRuV3/TempSuite1049024630879925047.adam
/tmp/adamTestMvnFJdRuV3/TempSuite1049024630879925047.adam/_SUCCESS
/tmp/adamTestMvnFJdRuV3/TempSuite1049024630879925047.adam/._references.avro.crc
/tmp/adamTestMvnFJdRuV3/TempSuite1049024630879925047.adam/._samples.avro.crc
/tmp/adamTestMvnFJdRuV3/TempSuite1049024630879925047.adam/part-r-00000.gz.parquet
/tmp/adamTestMvnFJdRuV3/TempSuite1049024630879925047.adam/.part-r-00003.gz.parquet.crc
/tmp/adamTestMvnFJdRuV3/TempSuite1049024630879925047.adam/part-r-00001.gz.parquet
/tmp/adamTestMvnFJdRuV3/TempSuite1049024630879925047.adam/._common_metadata.crc
/tmp/adamTestMvnFJdRuV3/TempSuite1049024630879925047.adam/_references.avro
/tmp/adamTestMvnFJdRuV3/TempSuite1049024630879925047.adam/.part-r-00000.gz.parquet.crc
/tmp/adamTestMvnFJdRuV3/TempSuite1049024630879925047.adam/.part-r-00001.gz.parquet.crc
/tmp/adamTestMvnFJdRuV3/TempSuite1049024630879925047.adam/part-r-00002.gz.parquet
/tmp/adamTestMvnFJdRuV3/TempSuite1049024630879925047.adam/.part-r-00002.gz.parquet.crc
/tmp/adamTestMvnFJdRuV3/TempSuite1049024630879925047.adam/_common_metadata
/tmp/adamTestMvnFJdRuV3/TempSuite1049024630879925047.adam/._metadata.crc
/tmp/adamTestMvnFJdRuV3/TempSuite1049024630879925047.adam/._SUCCESS.crc
/tmp/adamTestMvnFJdRuV3/TempSuite1049024630879925047.adam/_samples.avro
/tmp/adamTestMvnFJdRuV3/TempSuite1049024630879925047.adam/_metadata
/tmp/adamTestMvnFJdRuV3/TempSuite1049024630879925047.adam/part-r-00003.gz.parquet
/tmp/adamTestMvnFJdRuV3/TempSuite2267616016608143555.adam
/tmp/adamTestMvnFJdRuV3/TempSuite2267616016608143555.adam/_SUCCESS
/tmp/adamTestMvnFJdRuV3/TempSuite2267616016608143555.adam/._references.avro.crc
/tmp/adamTestMvnFJdRuV3/TempSuite2267616016608143555.adam/part-r-00000.gz.parquet
/tmp/adamTestMvnFJdRuV3/TempSuite2267616016608143555.adam/._common_metadata.crc
/tmp/adamTestMvnFJdRuV3/TempSuite2267616016608143555.adam/_references.avro
/tmp/adamTestMvnFJdRuV3/TempSuite2267616016608143555.adam/.part-r-00000.gz.parquet.crc
/tmp/adamTestMvnFJdRuV3/TempSuite2267616016608143555.adam/_common_metadata
/tmp/adamTestMvnFJdRuV3/TempSuite2267616016608143555.adam/._metadata.crc
/tmp/adamTestMvnFJdRuV3/TempSuite2267616016608143555.adam/._SUCCESS.crc
/tmp/adamTestMvnFJdRuV3/TempSuite2267616016608143555.adam/_metadata
/tmp/adamTestMvnFJdRuV3/small.vcf5749239957936170733.vcf
/tmp/adamTestMvnFJdRuV3/TempSuite14085009300287244
/tmp/adamTestMvnFJdRuV3/ReadDatasetSuite3293108480769442682.fastq
/tmp/adamTestMvnFJdRuV3/ReadDatasetSuite3293108480769442682.fastq/_SUCCESS
/tmp/adamTestMvnFJdRuV3/ReadDatasetSuite3293108480769442682.fastq/part-00001
/tmp/adamTestMvnFJdRuV3/ReadDatasetSuite3293108480769442682.fastq/.part-00003.crc
/tmp/adamTestMvnFJdRuV3/ReadDatasetSuite3293108480769442682.fastq/part-00000
/tmp/adamTestMvnFJdRuV3/ReadDatasetSuite3293108480769442682.fastq/part-00003
/tmp/adamTestMvnFJdRuV3/ReadDatasetSuite3293108480769442682.fastq/.part-00000.crc
/tmp/adamTestMvnFJdRuV3/ReadDatasetSuite3293108480769442682.fastq/._SUCCESS.crc
/tmp/adamTestMvnFJdRuV3/ReadDatasetSuite3293108480769442682.fastq/part-00002
/tmp/adamTestMvnFJdRuV3/ReadDatasetSuite3293108480769442682.fastq/.part-00002.crc
/tmp/adamTestMvnFJdRuV3/ReadDatasetSuite3293108480769442682.fastq/.part-00001.crc
/tmp/adamTestMvnFJdRuV3/TempSuite4262460684449933744
/tmp/adamTestMvnFJdRuV3/FeatureDatasetFunctionsSuite4175744934550297537.gtf
/tmp/adamTestMvnFJdRuV3/FeatureDatasetFunctionsSuite4175744934550297537.gtf/_SUCCESS
/tmp/adamTestMvnFJdRuV3/FeatureDatasetFunctionsSuite4175744934550297537.gtf/part-00001
/tmp/adamTestMvnFJdRuV3/FeatureDatasetFunctionsSuite4175744934550297537.gtf/.part-00003.crc
/tmp/adamTestMvnFJdRuV3/FeatureDatasetFunctionsSuite4175744934550297537.gtf/part-00000
/tmp/adamTestMvnFJdRuV3/FeatureDatasetFunctionsSuite4175744934550297537.gtf/part-00003
/tmp/adamTestMvnFJdRuV3/FeatureDatasetFunctionsSuite4175744934550297537.gtf/.part-00000.crc
/tmp/adamTestMvnFJdRuV3/FeatureDatasetFunctionsSuite4175744934550297537.gtf/._SUCCESS.crc
/tmp/adamTestMvnFJdRuV3/FeatureDatasetFunctionsSuite4175744934550297537.gtf/part-00002
/tmp/adamTestMvnFJdRuV3/FeatureDatasetFunctionsSuite4175744934550297537.gtf/.part-00002.crc
/tmp/adamTestMvnFJdRuV3/FeatureDatasetFunctionsSuite4175744934550297537.gtf/.part-00001.crc
/tmp/adamTestMvnFJdRuV3/TempSuite4063634326602876162.bed
/tmp/adamTestMvnFJdRuV3/TempSuite4063634326602876162.bed/_SUCCESS
/tmp/adamTestMvnFJdRuV3/TempSuite4063634326602876162.bed/part-00000
/tmp/adamTestMvnFJdRuV3/TempSuite4063634326602876162.bed/.part-00000.crc
/tmp/adamTestMvnFJdRuV3/TempSuite4063634326602876162.bed/._SUCCESS.crc
/tmp/adamTestMvnFJdRuV3/8916385041373081451
/tmp/adamTestMvnFJdRuV3/8916385041373081451/.sorted.sam.crc
/tmp/adamTestMvnFJdRuV3/8916385041373081451/sorted.sam
/tmp/adamTestMvnFJdRuV3/TempSuite6375762109368032305.adam
/tmp/adamTestMvnFJdRuV3/TempSuite6375762109368032305.adam/_SUCCESS
/tmp/adamTestMvnFJdRuV3/TempSuite6375762109368032305.adam/._references.avro.crc
/tmp/adamTestMvnFJdRuV3/TempSuite6375762109368032305.adam/part-r-00000.gz.parquet
/tmp/adamTestMvnFJdRuV3/TempSuite6375762109368032305.adam/_readGroups.avro
/tmp/adamTestMvnFJdRuV3/TempSuite6375762109368032305.adam/._common_metadata.crc
/tmp/adamTestMvnFJdRuV3/TempSuite6375762109368032305.adam/_references.avro
/tmp/adamTestMvnFJdRuV3/TempSuite6375762109368032305.adam/.part-r-00000.gz.parquet.crc
/tmp/adamTestMvnFJdRuV3/TempSuite6375762109368032305.adam/._processingSteps.avro.crc
/tmp/adamTestMvnFJdRuV3/TempSuite6375762109368032305.adam/_common_metadata
/tmp/adamTestMvnFJdRuV3/TempSuite6375762109368032305.adam/._metadata.crc
/tmp/adamTestMvnFJdRuV3/TempSuite6375762109368032305.adam/._SUCCESS.crc
/tmp/adamTestMvnFJdRuV3/TempSuite6375762109368032305.adam/._readGroups.avro.crc
/tmp/adamTestMvnFJdRuV3/TempSuite6375762109368032305.adam/_metadata
/tmp/adamTestMvnFJdRuV3/TempSuite6375762109368032305.adam/_processingSteps.avro
rm -rf ${ADAM_MVN_TMP_DIR}
+ rm -rf /tmp/adamTestMvnFJdRuV3

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/adamTestMvnFJdRuV3: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/adamTestyG4njcn

# Just to be paranoid.. use a directory internal to the ADAM_TMP_DIR
ADAM_TMP_DIR=$ADAM_TMP_DIR/deleteMePleaseThisIsNoLongerNeeded
+ ADAM_TMP_DIR=/tmp/adamTestyG4njcn/deleteMePleaseThisIsNoLongerNeeded
mkdir $ADAM_TMP_DIR
+ mkdir /tmp/adamTestyG4njcn/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/adamTestyG4njcn/deleteMePleaseThisIsNoLongerNeeded
+ TMPDIR=/tmp/adamTestyG4njcn/deleteMePleaseThisIsNoLongerNeeded

pushd $PROJECT_ROOT
+ pushd /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.0/label/ubuntu/scripts/..
~/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.0/label/ubuntu ~/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.0/label/ubuntu

# Copy the jar into our temp space for testing
cp -r . $ADAM_TMP_DIR
+ cp -r . /tmp/adamTestyG4njcn/deleteMePleaseThisIsNoLongerNeeded
popd
+ popd
~/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.0/label/ubuntu

pushd $ADAM_TMP_DIR
+ pushd /tmp/adamTestyG4njcn/deleteMePleaseThisIsNoLongerNeeded
/tmp/adamTestyG4njcn/deleteMePleaseThisIsNoLongerNeeded ~/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.0/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-3.0.0
    
# 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 ']'
+ '[' 3.0.0 == 2.4.6 ']'
+ curl -v -L 'https://www.apache.org/dyn/mirrors/mirrors.cgi?action=download&filename=spark/spark-3.0.0/spark-3.0.0-bin-hadoop2.7.tgz' -o spark-3.0.0-bin-hadoop2.7.tgz
*   Trying 40.79.78.1...
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0* Connected to www.apache.org (40.79.78.1) port 443 (#0)
* ALPN, offering http/1.1
* Cipher selection: ALL:!EXPORT:!EXPORT40:!EXPORT56:!aNULL:!LOW:!RC4:@STRENGTH
* successfully set certificate verify locations:
*   CAfile: /home/jenkins/anaconda2/ssl/cacert.pem
  CApath: none
* TLSv1.2 (OUT), TLS header, Certificate Status (22):
} [5 bytes data]
* TLSv1.2 (OUT), TLS handshake, Client hello (1):
} [512 bytes data]
* TLSv1.2 (IN), TLS handshake, Server hello (2):
{ [113 bytes data]
* TLSv1.2 (IN), TLS handshake, Certificate (11):
{ [4639 bytes data]
* TLSv1.2 (IN), TLS handshake, Server key exchange (12):
{ [333 bytes data]
* TLSv1.2 (IN), TLS handshake, Server finished (14):
{ [4 bytes data]
* TLSv1.2 (OUT), TLS handshake, Client key exchange (16):
} [70 bytes data]
* TLSv1.2 (OUT), TLS change cipher, Client hello (1):
} [1 bytes data]
* TLSv1.2 (OUT), TLS handshake, Finished (20):
} [16 bytes data]
* TLSv1.2 (IN), TLS change cipher, Client hello (1):
{ [1 bytes data]
* TLSv1.2 (IN), TLS handshake, Finished (20):
{ [16 bytes data]
* SSL connection using TLSv1.2 / ECDHE-RSA-AES256-GCM-SHA384
* ALPN, server accepted to use http/1.1
* Server certificate:
*  subject: OU=Domain Control Validated; OU=PositiveSSL Wildcard; CN=*.apache.org
*  start date: Jul  1 00:00:00 2019 GMT
*  expire date: Jun 30 23:59:59 2021 GMT
*  subjectAltName: host "www.apache.org" matched cert's "*.apache.org"
*  issuer: C=GB; ST=Greater Manchester; L=Salford; O=Sectigo Limited; CN=Sectigo RSA Domain Validation Secure Server CA
*  SSL certificate verify ok.
} [5 bytes data]
> GET /dyn/mirrors/mirrors.cgi?action=download&filename=spark/spark-3.0.0/spark-3.0.0-bin-hadoop2.7.tgz HTTP/1.1
> Host: www.apache.org
> User-Agent: curl/7.49.0
> Accept: */*
> 
{ [5 bytes data]
< HTTP/1.1 302 Found
< Date: Wed, 09 Sep 2020 19:19:51 GMT
< Server: Apache/2.4.18 (Ubuntu)
< Location: https://mirrors.sonic.net/apache/spark/spark-3.0.0/spark-3.0.0-bin-hadoop2.7.tgz
< Cache-Control: max-age=3600
< Expires: Wed, 09 Sep 2020 20:19:51 GMT
< Content-Length: 0
< 

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
* Connection #0 to host www.apache.org left intact
* Issue another request to this URL: 'https://mirrors.sonic.net/apache/spark/spark-3.0.0/spark-3.0.0-bin-hadoop2.7.tgz'
*   Trying 157.131.0.16...
* Connected to mirrors.sonic.net (157.131.0.16) port 443 (#1)
* ALPN, offering http/1.1
* Cipher selection: ALL:!EXPORT:!EXPORT40:!EXPORT56:!aNULL:!LOW:!RC4:@STRENGTH
* successfully set certificate verify locations:
*   CAfile: /home/jenkins/anaconda2/ssl/cacert.pem
  CApath: none
* TLSv1.2 (OUT), TLS header, Certificate Status (22):
} [5 bytes data]
* TLSv1.2 (OUT), TLS handshake, Client hello (1):
} [512 bytes data]
* TLSv1.2 (IN), TLS handshake, Server hello (2):
{ [94 bytes data]
* TLSv1.2 (IN), TLS handshake, Certificate (11):
{ [4849 bytes data]
* TLSv1.2 (IN), TLS handshake, Server key exchange (12):
{ [589 bytes data]
* TLSv1.2 (IN), TLS handshake, Server finished (14):
{ [4 bytes data]
* TLSv1.2 (OUT), TLS handshake, Client key exchange (16):
} [70 bytes data]
* TLSv1.2 (OUT), TLS change cipher, Client hello (1):
} [1 bytes data]
* TLSv1.2 (OUT), TLS handshake, Finished (20):
} [16 bytes data]
* TLSv1.2 (IN), TLS change cipher, Client hello (1):
{ [1 bytes data]
* TLSv1.2 (IN), TLS handshake, Finished (20):
{ [16 bytes data]
* SSL connection using TLSv1.2 / ECDHE-RSA-AES128-GCM-SHA256
* ALPN, server did not agree to a protocol
* Server certificate:
*  subject: CN=mirrors.sonic.net
*  start date: Jan 23 00:00:00 2020 GMT
*  expire date: Jan 22 23:59:59 2022 GMT
*  subjectAltName: host "mirrors.sonic.net" matched cert's "mirrors.sonic.net"
*  issuer: C=GB; ST=Greater Manchester; L=Salford; O=Sectigo Limited; CN=Sectigo RSA Domain Validation Secure Server CA
*  SSL certificate verify ok.
} [5 bytes data]
> GET /apache/spark/spark-3.0.0/spark-3.0.0-bin-hadoop2.7.tgz HTTP/1.1
> Host: mirrors.sonic.net
> User-Agent: curl/7.49.0
> Accept: */*
> 
{ [5 bytes data]
< HTTP/1.1 404 Not Found
< Date: Wed, 09 Sep 2020 19:19:51 GMT
< Server: Apache/2.4.6 (CentOS)
< Content-Length: 335
< Content-Type: text/html; charset=iso-8859-1
< 
{ [5 bytes data]

100   335  100   335    0     0   1061      0 --:--:-- --:--:-- --:--:--  1061
* Connection #1 to host mirrors.sonic.net left intact
+ tar xzvf spark-3.0.0-bin-hadoop2.7.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/a30a822f2f1fae4c474b307d1f73ba8b63ce8f37
Finished: FAILURE