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      "callSetName": "HG00099",
      "callSetId": "HG00099",
      "phaseset": "",
      "genotypeLikelihood": [],
      "genotype": ["0", "0"]
    }, {
  
100  512k    0  512k  100   208   375k    152  0:00:01  0:00:01 --:--:--  375k
    "callSetName": "HG00100",
      "callSetId": "HG00100",
      "phaseset": "",
      "genotypeLikelihood": [],
      "genotype": ["0", "0"]
    }, {
      "callSetName": "HG00101",
      "callSetId": "HG00101",
      "phaseset": "",
      "genotypeLikelihood": [],
      "genotype": ["0", "0"]
    }],
    "filtersApplied": false,
    "filtersPassed": true,
    "filtersFailed": [],
    "variantType": "",
    "svlen": "0",
    "cipos": [],
    "ciend": []
  }],
  "nextPageToken": ""
}+ PROCESSES=($(ps aux | grep -F 'browser-scripts/run-example.sh' | grep -v -F 'grep' | awk '{ print $2 }'))
ps aux | grep -F 'browser-scripts/run-example.sh' | grep -v -F 'grep' | awk '{ print $2 }'
++ ps aux
++ grep -F browser-scripts/run-example.sh
++ grep -v -F grep
++ awk '{ print $2 }'
+ '[' 1 -gt 0 ']'
+ echo 'Mango Browser Succeeded'
Mango Browser Succeeded
+ kill 127302
+ TEST_GENOME=anoGam1
+ bash -xv /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/scripts/../bin/make_genome anoGam1 /tmp/mangoTestomLifRb/deleteMePleaseThisIsNoLongerNeeded
#!/usr/bin/env bash
#
# Licensed to Big Data Genomics (BDG) under one
# or more contributor license agreements.  See the NOTICE file
# distributed with this work for additional information
# regarding copyright ownership.  The BDG licenses this file
# to you under the Apache License, Version 2.0 (the
# "License"); you may not use this file except in compliance
# with the License.  You may obtain a copy of the License at
#
#     http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
#

# Runs MakeGenome, which generates a .genome file containing reference, genes, cytoband, and chromsizes.
# Requires 2 arguments: genome name and output file to save .genome file to.

SOURCE_DIR=$(dirname ${BASH_SOURCE[0]})
dirname ${BASH_SOURCE[0]}
++ dirname /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/scripts/../bin/make_genome
+ SOURCE_DIR=/home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/scripts/../bin

# get Mango jar
MANGO_CLI_JAR=$(${SOURCE_DIR}/find-mango-assembly.sh)
${SOURCE_DIR}/find-mango-assembly.sh
++ /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/scripts/../bin/find-mango-assembly.sh
+ MANGO_CLI_JAR=/home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-assembly/target/mango-assembly-0.0.3-SNAPSHOT.jar

SPARK_SUBMIT=$(${SOURCE_DIR}/find-spark.sh)
${SOURCE_DIR}/find-spark.sh
++ /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/scripts/../bin/find-spark.sh
+ SPARK_SUBMIT=/tmp/mangoTestomLifRb/deleteMePleaseThisIsNoLongerNeeded/spark-2.3.3-bin-hadoop2.7/bin/spark-submit

# submit the job to Spark
"$SPARK_SUBMIT" \
  --class "org.bdgenomics.adam.cli.MangoMain" \
  --conf spark.serializer=org.apache.spark.serializer.KryoSerializer \
  --conf spark.kryo.registrator=org.bdgenomics.mango.serialization.MangoKryoRegistrator \
  $MANGO_CLI_JAR \
  "MakeGenome" "$@" \

+ /tmp/mangoTestomLifRb/deleteMePleaseThisIsNoLongerNeeded/spark-2.3.3-bin-hadoop2.7/bin/spark-submit --class org.bdgenomics.adam.cli.MangoMain --conf spark.serializer=org.apache.spark.serializer.KryoSerializer --conf spark.kryo.registrator=org.bdgenomics.mango.serialization.MangoKryoRegistrator /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-assembly/target/mango-assembly-0.0.3-SNAPSHOT.jar MakeGenome anoGam1 /tmp/mangoTestomLifRb/deleteMePleaseThisIsNoLongerNeeded
2019-05-22 15:18:08 WARN  Utils:66 - Your hostname, amp-jenkins-staging-worker-02 resolves to a loopback address: 127.0.1.1; using 192.168.10.32 instead (on interface eno1)
2019-05-22 15:18:08 WARN  Utils:66 - Set SPARK_LOCAL_IP if you need to bind to another address
2019-05-22 15:18:08 WARN  NativeCodeLoader:62 - Unable to load native-hadoop library for your platform... using builtin-java classes where applicable
2019-05-22 15:18:08 INFO  MangoMain:87 - Mango invoked with args: "MakeGenome" "anoGam1" "/tmp/mangoTestomLifRb/deleteMePleaseThisIsNoLongerNeeded"
2019-05-22 15:18:08 INFO  SparkContext:54 - Running Spark version 2.3.3
2019-05-22 15:18:09 INFO  SparkContext:54 - Submitted application: MakeGenome
2019-05-22 15:18:09 INFO  SecurityManager:54 - Changing view acls to: jenkins
2019-05-22 15:18:09 INFO  SecurityManager:54 - Changing modify acls to: jenkins
2019-05-22 15:18:09 INFO  SecurityManager:54 - Changing view acls groups to: 
2019-05-22 15:18:09 INFO  SecurityManager:54 - Changing modify acls groups to: 
2019-05-22 15:18:09 INFO  SecurityManager:54 - 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()
2019-05-22 15:18:09 INFO  Utils:54 - Successfully started service 'sparkDriver' on port 34877.
2019-05-22 15:18:09 INFO  SparkEnv:54 - Registering MapOutputTracker
2019-05-22 15:18:09 INFO  SparkEnv:54 - Registering BlockManagerMaster
2019-05-22 15:18:09 INFO  BlockManagerMasterEndpoint:54 - Using org.apache.spark.storage.DefaultTopologyMapper for getting topology information
2019-05-22 15:18:09 INFO  BlockManagerMasterEndpoint:54 - BlockManagerMasterEndpoint up
2019-05-22 15:18:09 INFO  DiskBlockManager:54 - Created local directory at /tmp/blockmgr-cb2afcaa-0fdd-49fc-836c-a52699fffe96
2019-05-22 15:18:09 INFO  MemoryStore:54 - MemoryStore started with capacity 366.3 MB
2019-05-22 15:18:09 INFO  SparkEnv:54 - Registering OutputCommitCoordinator
2019-05-22 15:18:09 INFO  log:192 - Logging initialized @1977ms
2019-05-22 15:18:09 INFO  Server:351 - jetty-9.3.z-SNAPSHOT, build timestamp: unknown, git hash: unknown
2019-05-22 15:18:09 INFO  Server:419 - Started @2061ms
2019-05-22 15:18:09 WARN  Utils:66 - Service 'SparkUI' could not bind on port 4040. Attempting port 4041.
2019-05-22 15:18:09 INFO  AbstractConnector:278 - Started ServerConnector@547e29a4{HTTP/1.1,[http/1.1]}{0.0.0.0:4041}
2019-05-22 15:18:09 INFO  Utils:54 - Successfully started service 'SparkUI' on port 4041.
2019-05-22 15:18:09 INFO  ContextHandler:781 - Started o.s.j.s.ServletContextHandler@47d93e0d{/jobs,null,AVAILABLE,@Spark}
2019-05-22 15:18:09 INFO  ContextHandler:781 - Started o.s.j.s.ServletContextHandler@610db97e{/jobs/json,null,AVAILABLE,@Spark}
2019-05-22 15:18:09 INFO  ContextHandler:781 - Started o.s.j.s.ServletContextHandler@6f0628de{/jobs/job,null,AVAILABLE,@Spark}
2019-05-22 15:18:09 INFO  ContextHandler:781 - Started o.s.j.s.ServletContextHandler@1e392345{/jobs/job/json,null,AVAILABLE,@Spark}
2019-05-22 15:18:09 INFO  ContextHandler:781 - Started o.s.j.s.ServletContextHandler@12f3afb5{/stages,null,AVAILABLE,@Spark}
2019-05-22 15:18:09 INFO  ContextHandler:781 - Started o.s.j.s.ServletContextHandler@4ced35ed{/stages/json,null,AVAILABLE,@Spark}
2019-05-22 15:18:09 INFO  ContextHandler:781 - Started o.s.j.s.ServletContextHandler@2c22a348{/stages/stage,null,AVAILABLE,@Spark}
2019-05-22 15:18:09 INFO  ContextHandler:781 - Started o.s.j.s.ServletContextHandler@51b01960{/stages/stage/json,null,AVAILABLE,@Spark}
2019-05-22 15:18:09 INFO  ContextHandler:781 - Started o.s.j.s.ServletContextHandler@6831d8fd{/stages/pool,null,AVAILABLE,@Spark}
2019-05-22 15:18:09 INFO  ContextHandler:781 - Started o.s.j.s.ServletContextHandler@27dc79f7{/stages/pool/json,null,AVAILABLE,@Spark}
2019-05-22 15:18:09 INFO  ContextHandler:781 - Started o.s.j.s.ServletContextHandler@6b85300e{/storage,null,AVAILABLE,@Spark}
2019-05-22 15:18:09 INFO  ContextHandler:781 - Started o.s.j.s.ServletContextHandler@3aaf4f07{/storage/json,null,AVAILABLE,@Spark}
2019-05-22 15:18:09 INFO  ContextHandler:781 - Started o.s.j.s.ServletContextHandler@5cbf9e9f{/storage/rdd,null,AVAILABLE,@Spark}
2019-05-22 15:18:09 INFO  ContextHandler:781 - Started o.s.j.s.ServletContextHandler@18e8473e{/storage/rdd/json,null,AVAILABLE,@Spark}
2019-05-22 15:18:09 INFO  ContextHandler:781 - Started o.s.j.s.ServletContextHandler@5a2f016d{/environment,null,AVAILABLE,@Spark}
2019-05-22 15:18:09 INFO  ContextHandler:781 - Started o.s.j.s.ServletContextHandler@1a38ba58{/environment/json,null,AVAILABLE,@Spark}
2019-05-22 15:18:09 INFO  ContextHandler:781 - Started o.s.j.s.ServletContextHandler@3ad394e6{/executors,null,AVAILABLE,@Spark}
2019-05-22 15:18:09 INFO  ContextHandler:781 - Started o.s.j.s.ServletContextHandler@6058e535{/executors/json,null,AVAILABLE,@Spark}
2019-05-22 15:18:09 INFO  ContextHandler:781 - Started o.s.j.s.ServletContextHandler@42deb43a{/executors/threadDump,null,AVAILABLE,@Spark}
2019-05-22 15:18:09 INFO  ContextHandler:781 - Started o.s.j.s.ServletContextHandler@1deb2c43{/executors/threadDump/json,null,AVAILABLE,@Spark}
2019-05-22 15:18:09 INFO  ContextHandler:781 - Started o.s.j.s.ServletContextHandler@3bb9efbc{/static,null,AVAILABLE,@Spark}
2019-05-22 15:18:09 INFO  ContextHandler:781 - Started o.s.j.s.ServletContextHandler@15deb1dc{/,null,AVAILABLE,@Spark}
2019-05-22 15:18:09 INFO  ContextHandler:781 - Started o.s.j.s.ServletContextHandler@6e9c413e{/api,null,AVAILABLE,@Spark}
2019-05-22 15:18:09 INFO  ContextHandler:781 - Started o.s.j.s.ServletContextHandler@36dce7ed{/jobs/job/kill,null,AVAILABLE,@Spark}
2019-05-22 15:18:09 INFO  ContextHandler:781 - Started o.s.j.s.ServletContextHandler@47a64f7d{/stages/stage/kill,null,AVAILABLE,@Spark}
2019-05-22 15:18:09 INFO  SparkUI:54 - Bound SparkUI to 0.0.0.0, and started at http://192.168.10.32:4041
2019-05-22 15:18:09 INFO  SparkContext:54 - Added JAR file:/home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-assembly/target/mango-assembly-0.0.3-SNAPSHOT.jar at spark://192.168.10.32:34877/jars/mango-assembly-0.0.3-SNAPSHOT.jar with timestamp 1558563489867
2019-05-22 15:18:09 INFO  Executor:54 - Starting executor ID driver on host localhost
2019-05-22 15:18:10 INFO  Utils:54 - Successfully started service 'org.apache.spark.network.netty.NettyBlockTransferService' on port 37552.
2019-05-22 15:18:10 INFO  NettyBlockTransferService:54 - Server created on 192.168.10.32:37552
2019-05-22 15:18:10 INFO  BlockManager:54 - Using org.apache.spark.storage.RandomBlockReplicationPolicy for block replication policy
2019-05-22 15:18:10 INFO  BlockManagerMaster:54 - Registering BlockManager BlockManagerId(driver, 192.168.10.32, 37552, None)
2019-05-22 15:18:10 INFO  BlockManagerMasterEndpoint:54 - Registering block manager 192.168.10.32:37552 with 366.3 MB RAM, BlockManagerId(driver, 192.168.10.32, 37552, None)
2019-05-22 15:18:10 INFO  BlockManagerMaster:54 - Registered BlockManager BlockManagerId(driver, 192.168.10.32, 37552, None)
2019-05-22 15:18:10 INFO  BlockManager:54 - Initialized BlockManager: BlockManagerId(driver, 192.168.10.32, 37552, None)
2019-05-22 15:18:10 INFO  ContextHandler:781 - Started o.s.j.s.ServletContextHandler@11841b15{/metrics/json,null,AVAILABLE,@Spark}
Exception in thread "Thread-27" java.io.FileNotFoundException: http://hgdownload.soe.ucsc.edu/goldenPath/anoGam1/database/refGene.txt.gz
	at sun.net.www.protocol.http.HttpURLConnection.getInputStream0(HttpURLConnection.java:1890)
	at sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1492)
	at java.net.URL.openStream(URL.java:1045)
	at scala.sys.process.ProcessBuilderImpl$URLInput$$anonfun$$lessinit$greater$1.apply(ProcessBuilderImpl.scala:31)
	at scala.sys.process.ProcessBuilderImpl$URLInput$$anonfun$$lessinit$greater$1.apply(ProcessBuilderImpl.scala:31)
	at scala.sys.process.ProcessBuilderImpl$IStreamBuilder$$anonfun$$lessinit$greater$5.apply(ProcessBuilderImpl.scala:45)
	at scala.sys.process.ProcessBuilderImpl$IStreamBuilder$$anonfun$$lessinit$greater$5.apply(ProcessBuilderImpl.scala:45)
	at scala.sys.process.ProcessBuilderImpl$ThreadBuilder$$anonfun$1.apply$mcV$sp(ProcessBuilderImpl.scala:58)
	at scala.sys.process.ProcessImpl$Spawn$$anon$1.run(ProcessImpl.scala:23)
Exception in thread "Thread-39" java.io.FileNotFoundException: http://hgdownload.cse.ucsc.edu/goldenpath/anoGam1/database/cytoBand.txt.gz
	at sun.net.www.protocol.http.HttpURLConnection.getInputStream0(HttpURLConnection.java:1890)
	at sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1492)
	at java.net.URL.openStream(URL.java:1045)
	at scala.sys.process.ProcessBuilderImpl$URLInput$$anonfun$$lessinit$greater$1.apply(ProcessBuilderImpl.scala:31)
	at scala.sys.process.ProcessBuilderImpl$URLInput$$anonfun$$lessinit$greater$1.apply(ProcessBuilderImpl.scala:31)
	at scala.sys.process.ProcessBuilderImpl$IStreamBuilder$$anonfun$$lessinit$greater$5.apply(ProcessBuilderImpl.scala:45)
	at scala.sys.process.ProcessBuilderImpl$IStreamBuilder$$anonfun$$lessinit$greater$5.apply(ProcessBuilderImpl.scala:45)
	at scala.sys.process.ProcessBuilderImpl$ThreadBuilder$$anonfun$1.apply$mcV$sp(ProcessBuilderImpl.scala:58)
	at scala.sys.process.ProcessImpl$Spawn$$anon$1.run(ProcessImpl.scala:23)
2019-05-22 15:18:12 WARN  GenomeConfig:141 - No refGene file found at http://hgdownload.cse.ucsc.edu/goldenpath/anoGam1/database/cytoBand.txt.gz for genome anoGam1
2019-05-22 15:18:12 INFO  MakeGenome:54 - Saved genome anoGam1 to /tmp/mangoTestomLifRb/deleteMePleaseThisIsNoLongerNeeded
2019-05-22 15:18:12 INFO  MakeGenome:44 - Overall Duration: 3.77 secs
2019-05-22 15:18:12 INFO  SparkContext:54 - Invoking stop() from shutdown hook
2019-05-22 15:18:12 INFO  AbstractConnector:318 - Stopped Spark@547e29a4{HTTP/1.1,[http/1.1]}{0.0.0.0:4041}
2019-05-22 15:18:12 INFO  SparkUI:54 - Stopped Spark web UI at http://192.168.10.32:4041
2019-05-22 15:18:12 INFO  MapOutputTrackerMasterEndpoint:54 - MapOutputTrackerMasterEndpoint stopped!
2019-05-22 15:18:12 INFO  MemoryStore:54 - MemoryStore cleared
2019-05-22 15:18:12 INFO  BlockManager:54 - BlockManager stopped
2019-05-22 15:18:12 INFO  BlockManagerMaster:54 - BlockManagerMaster stopped
2019-05-22 15:18:12 INFO  OutputCommitCoordinator$OutputCommitCoordinatorEndpoint:54 - OutputCommitCoordinator stopped!
2019-05-22 15:18:12 INFO  SparkContext:54 - Successfully stopped SparkContext
2019-05-22 15:18:12 INFO  ShutdownHookManager:54 - Shutdown hook called
2019-05-22 15:18:12 INFO  ShutdownHookManager:54 - Deleting directory /tmp/spark-40654521-5ee3-4c88-9a6d-43bd1a41c4e2
2019-05-22 15:18:12 INFO  ShutdownHookManager:54 - Deleting directory /tmp/spark-a321034a-0fb6-4713-8735-82ac55388940
/home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/scripts/jenkins-test: line 294: 127302 Terminated              bash -xv ${PROJECT_ROOT}/example-files/browser-scripts/run-example.sh &> ${MANGO_BROWSER_LOGS}
+ unzip /tmp/mangoTestomLifRb/deleteMePleaseThisIsNoLongerNeeded/anoGam1.genome -d /tmp/mangoTestomLifRb/deleteMePleaseThisIsNoLongerNeeded/anoGam1
Archive:  /tmp/mangoTestomLifRb/deleteMePleaseThisIsNoLongerNeeded/anoGam1.genome
  inflating: /tmp/mangoTestomLifRb/deleteMePleaseThisIsNoLongerNeeded/anoGam1/cytoBand.txt.gz  
  inflating: /tmp/mangoTestomLifRb/deleteMePleaseThisIsNoLongerNeeded/anoGam1/refGene.txt.gz  
  inflating: /tmp/mangoTestomLifRb/deleteMePleaseThisIsNoLongerNeeded/anoGam1/anoGam1.chrom.sizes  
  inflating: /tmp/mangoTestomLifRb/deleteMePleaseThisIsNoLongerNeeded/anoGam1/properties.txt  
+ pushd /tmp/mangoTestomLifRb/deleteMePleaseThisIsNoLongerNeeded/anoGam1
/tmp/mangoTestomLifRb/deleteMePleaseThisIsNoLongerNeeded/anoGam1 /tmp/mangoTestomLifRb/deleteMePleaseThisIsNoLongerNeeded ~/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu
+ cat properties.txt
sequenceLocation=http://hgdownload.cse.ucsc.edu/goldenPath/anoGam1/bigZips/anoGam1.2bit
chromSizes=anoGam1.chrom.sizes
refGene=refGene.txt.gz
+ cat anoGam1.chrom.sizes
chr2L	48795086
chr2R	62725911
chr3L	41284009
chr3R	53272125
chrM	15363
chrU	59568033
chrX	22145176
+ popd
/tmp/mangoTestomLifRb/deleteMePleaseThisIsNoLongerNeeded ~/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu
+ rm -rf /tmp/mangoTestomLifRb/deleteMePleaseThisIsNoLongerNeeded/anoGam1 /tmp/mangoTestomLifRb/deleteMePleaseThisIsNoLongerNeeded/anoGam1.genome
+ rm -rf /tmp/mangoTestomLifRb/deleteMePleaseThisIsNoLongerNeeded

echo
+ echo

echo "All the tests passed"
+ echo 'All the tests passed'
All the tests passed
echo
+ echo

Finished: SUCCESS