AbortedConsole Output

Skipping 15 KB.. Full Log
piling 17 source files to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/target/scala-2.11.12/classes at 1576363433570
[WARNING] /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/src/main/scala/org/bdgenomics/mango/models/AlignmentRecordMaterialization.scala:57: warning: no valid targets for annotation on value sc - it is discarded unused. You may specify targets with meta-annotations, e.g. @(transient @param)
[WARNING] class AlignmentRecordMaterialization(@transient sc: SparkContext,
[WARNING]                                       ^
[WARNING] /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/src/main/scala/org/bdgenomics/mango/models/FeatureMaterialization.scala:43: warning: no valid targets for annotation on value sc - it is discarded unused. You may specify targets with meta-annotations, e.g. @(transient @param)
[WARNING] class FeatureMaterialization(@transient sc: SparkContext,
[WARNING]                               ^
[WARNING] /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/src/main/scala/org/bdgenomics/mango/models/LazyMaterialization.scala:51: warning: no valid targets for annotation on value sc - it is discarded unused. You may specify targets with meta-annotations, e.g. @(transient @param)
[WARNING]                                                              @transient sc: SparkContext,
[WARNING]                                                               ^
[WARNING] /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/src/main/scala/org/bdgenomics/mango/models/VariantContextMaterialization.scala:40: warning: no valid targets for annotation on value sc - it is discarded unused. You may specify targets with meta-annotations, e.g. @(transient @param)
[WARNING] class VariantContextMaterialization(@transient sc: SparkContext,
[WARNING]                                      ^
[WARNING] /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/src/main/scala/org/bdgenomics/mango/util/GenomeConfig.scala:89: warning: A try without a catch or finally is equivalent to putting its body in a block; no exceptions are handled.
[WARNING]     try {
[WARNING]     ^
[WARNING] /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/src/main/scala/org/bdgenomics/mango/converters/SAMRecordConverter.scala:145: warning: method getNotPrimaryAlignmentFlag in class SAMRecord is deprecated: see corresponding Javadoc for more information.
[WARNING]       builder.setPrimaryAlignment(!samRecord.getNotPrimaryAlignmentFlag)
[WARNING]                                              ^
[WARNING] warning: there were four feature warnings; re-run with -feature for details
[WARNING] 7 warnings found
[INFO] prepare-compile in 0 s
[INFO] compile in 12 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ mango-core ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-test-source (add-test-source) @ mango-core ---
[INFO] Test Source directory: /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/src/test/scala added.
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ mango-core ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 24 resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ mango-core ---
[WARNING]  Expected all dependencies to require Scala version: 2.11.12
[WARNING]  net.liftweb:lift-json_2.11:3.3.0 requires scala version: 2.11.11
[WARNING] Multiple versions of scala libraries detected!
[INFO] /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/src/test/scala:-1: info: compiling
[INFO] Compiling 13 source files to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/target/scala-2.11.12/test-classes at 1576363448653
[WARNING] /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/src/test/scala/org/bdgenomics/mango/models/LazyMaterializationSuite.scala:77: warning: no valid targets for annotation on value sc - it is discarded unused. You may specify targets with meta-annotations, e.g. @(transient @param)
[WARNING] class LazyDummy(@transient sc: SparkContext,
[WARNING]                  ^
[WARNING] one warning found
[INFO] prepare-compile in 0 s
[INFO] compile in 12 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ mango-core ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ mango-core ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ mango-core ---
Discovery starting.
Discovery completed in 630 milliseconds.
Run starting. Expected test count is: 72
DiscoverySuite:
2019-12-14 14:44:22 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)
2019-12-14 14:44:22 WARN  Utils:66 - Set SPARK_LOCAL_IP if you need to bind to another address
2019-12-14 14:44:23 WARN  NativeCodeLoader:62 - Unable to load native-hadoop library for your platform... using builtin-java classes where applicable
2019-12-14 14:44:26 WARN  BedReader:158 - No index file for /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/target/scala-2.11.12/test-classes/smalltest.bed found. Generating /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/target/scala-2.11.12/test-classes/smalltest.bed.idx...
- correctly gathers regions of occupancy from Feature file
- does not fail when no regions discovered
VariantContextMaterializationSuite:
2019-12-14 14:44:26 WARN  VcfReader:205 - No index file for /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/target/scala-2.11.12/test-classes/truetest.genotypes.vcf found. Generating /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/target/scala-2.11.12/test-classes/truetest.genotypes.vcf.idx...
- Fetch from 1 vcf file with genotypes
- gets sample information
- Can extract json
2019-12-14 14:44:33 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.
- Can read Partitioned Parquet Genotypes
- correctly reassigns referenceName
2019-12-14 14:44:43 WARN  VcfReader:205 - No index file for /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/target/scala-2.11.12/test-classes/bqsr1.vcf found. Generating /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/target/scala-2.11.12/test-classes/bqsr1.vcf.idx...
- returns from file without genotypes
- more than 1 vcf file
- Should handle chromosomes with different prefixes
- fetches multiple regions from load
GenomeConfigSuite:
- Should read in genome path
- Should parse chrom sizes file
- Should parse refSeq.txt file
- Should fail when genome file does not exist
- should build genome
BamReaderSuite:
- Should load local bam file
- Gets file header
- loads all data when region is not specified
- Fails on files that are not bam or sam
- Should return empty on invalid chromosome
- Should return no data on empty dictionary
- Should load local sam file
- Should load local bam files with incorrect prefixes file
- Should load data from HDFS using Spark
- Should load http bam file
RefSeqSuite:
- Should convert refseq file to GA4GH genes
GA4GHutilSuite:
- create JSON from AlignmentRecordDataset
- create JSON from AlignmentRecordDataset with 1 sample
- create JSON from AlignmentRecordDataset with more than 1 sample
- create JSON with genotypes from VCF using GenotypeDataset
- create JSON without genotypes from VCF using VariantDataset
- create JSON from FeatureDataset
LazyMaterializationSuite:
- Should correctly reassigns chr prefix
2019-12-14 14:45:03 WARN  Bookkeep:66 - bookkeeping queue is empty
2019-12-14 14:45:03 WARN  LazyDummy:247 - memory limit exceeded. Dropping null from cache
2019-12-14 14:45:03 WARN  LazyDummy:247 - memory limit exceeded. Dropping chrM from cache
- Should check and clear memory
FeatureMaterializationSuite:
- assert raw data returns from one block
2019-12-14 14:45:03 WARN  BedReader:158 - No index file for /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/target/scala-2.11.12/test-classes/smalltest2.bed found. Generating /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/target/scala-2.11.12/test-classes/smalltest2.bed.idx...
- can fetch multiple files
- Should handle chromosomes with different prefixes
- fetches multiple regions from load
BookkeepSuite:
- remembers new regions
- adds new regions to existing chromosomes
- adds new chromosome
- merges regions
- saves sequence dictionary
- get and put region where region equals chunk size
AlignmentRecordMaterializationSuite:
- create new AlignmentRecordMaterialization
- return raw data from AlignmentRecordMaterialization
- can process stringified data
- Read Partitioned Data
- fetches multiple regions from load
- Should handle chromosomes with different prefixes
- should get data from unindexed file when referenceName predicates do not match
2019-12-14 14:45:34 WARN  BedReader:158 - No index file for /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/target/scala-2.11.12/test-classes/small.1.sorted.narrowPeak found. Generating /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/target/scala-2.11.12/test-classes/small.1.sorted.narrowPeak.idx...
BedReaderSuite:
- Should load local bed file
- Should load all records when region is not specified
- Fails on files that are not bed format
- Should return empty on invalid chromosome
- Should load local narrowPeak file
- Should load local bed files with incorrect prefixes file
- Should load data from HDFS using Spark
- Should load remote bed file
VcfReaderSuite:
- Should load local vcf file
2019-12-14 14:45:35 WARN  VcfReader:205 - No index file for /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/target/scala-2.11.12/test-classes/small.vcf.gz found. Generating /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/target/scala-2.11.12/test-classes/small.vcf.gz.tbi...
- Gets file header
2019-12-14 14:45:35 WARN  VcfReader:205 - No index file for /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/target/scala-2.11.12/test-classes/test.vcf.bgz found. Generating /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/target/scala-2.11.12/test-classes/test.vcf.bgz.tbi...
2019-12-14 14:45:35 WARN  VcfReader:205 - No index file for /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/target/scala-2.11.12/test-classes/test.vcf found. Generating /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/target/scala-2.11.12/test-classes/test.vcf.idx...
- Should load bgz file
2019-12-14 14:45:35 WARN  VcfReader:205 - No index file for /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/target/scala-2.11.12/test-classes/test.vcf.bgzf.gz found. Generating /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/target/scala-2.11.12/test-classes/test.vcf.bgzf.gz.tbi...
- Should load compressed bgz file
- Should load all records when region is not defined
- Fails on files that are not vcf or vcf.gz
- Should return empty on invalid chromosome
- Should load local vcf files with incorrect prefixes file
- Should load genotypes
- loads gzipped vcfs
2019-12-14 14:45:35 WARN  VCFInputFormat:410 - No tabix index file found for file:/home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/target/scala-2.11.12/test-classes/truetest.genotypes.vcf.tbi, splits will not be filtered, which may be very inefficient
- Should load data from HDFS using Spark
- Should load http vcf file
Run completed in 1 minute, 20 seconds.
Total number of tests run: 72
Suites: completed 13, aborted 0
Tests: succeeded 72, failed 0, canceled 0, ignored 0, pending 0
All tests passed.
[INFO] 
[INFO] >>> scoverage-maven-plugin:1.1.1:report (default-cli) > [scoverage]test @ mango-core >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ mango-core ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ mango-core ---
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-source (add-source) @ mango-core ---
[INFO] Source directory: /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/src/main/scala added.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default) @ mango-core ---
[INFO] Modified 0 of 30 .scala files
[INFO] 
[INFO] --- scoverage-maven-plugin:1.1.1:pre-compile (default-cli) @ mango-core ---
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ mango-core ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ mango-core ---
[WARNING]  Expected all dependencies to require Scala version: 2.11.12
[WARNING]  net.liftweb:lift-json_2.11:3.3.0 requires scala version: 2.11.11
[WARNING] Multiple versions of scala libraries detected!
[INFO] /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/src/main/scala:-1: info: compiling
[INFO] Compiling 17 source files to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/target/scala-2.11.12/scoverage-classes at 1576363544592
[WARNING] /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/src/main/scala/org/bdgenomics/mango/models/AlignmentRecordMaterialization.scala:57: warning: no valid targets for annotation on value sc - it is discarded unused. You may specify targets with meta-annotations, e.g. @(transient @param)
[WARNING] class AlignmentRecordMaterialization(@transient sc: SparkContext,
[WARNING]                                       ^
[WARNING] /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/src/main/scala/org/bdgenomics/mango/models/FeatureMaterialization.scala:43: warning: no valid targets for annotation on value sc - it is discarded unused. You may specify targets with meta-annotations, e.g. @(transient @param)
[WARNING] class FeatureMaterialization(@transient sc: SparkContext,
[WARNING]                               ^
[WARNING] /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/src/main/scala/org/bdgenomics/mango/models/LazyMaterialization.scala:51: warning: no valid targets for annotation on value sc - it is discarded unused. You may specify targets with meta-annotations, e.g. @(transient @param)
[WARNING]                                                              @transient sc: SparkContext,
[WARNING]                                                               ^
[WARNING] /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/src/main/scala/org/bdgenomics/mango/models/VariantContextMaterialization.scala:40: warning: no valid targets for annotation on value sc - it is discarded unused. You may specify targets with meta-annotations, e.g. @(transient @param)
[WARNING] class VariantContextMaterialization(@transient sc: SparkContext,
[WARNING]                                      ^
[WARNING] /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/src/main/scala/org/bdgenomics/mango/util/GenomeConfig.scala:89: warning: A try without a catch or finally is equivalent to putting its body in a block; no exceptions are handled.
[WARNING]     try {
[WARNING]     ^
[INFO] [info] Cleaning datadir [/home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/target/scoverage-data]
[INFO] [info] Beginning coverage instrumentation
[WARNING] [warn] Could not instrument [EmptyTree$/null]. No pos.
[WARNING] [warn] Could not instrument [EmptyTree$/null]. No pos.
[WARNING] [warn] Could not instrument [EmptyTree$/null]. No pos.
[WARNING] [warn] Could not instrument [EmptyTree$/null]. No pos.
[WARNING] [warn] Could not instrument [EmptyTree$/null]. No pos.
[WARNING] [warn] Could not instrument [EmptyTree$/null]. No pos.
[WARNING] [warn] Could not instrument [EmptyTree$/null]. No pos.
[WARNING] [warn] Could not instrument [EmptyTree$/null]. No pos.
[WARNING] [warn] Could not instrument [EmptyTree$/null]. No pos.
[WARNING] [warn] Could not instrument [EmptyTree$/null]. No pos.
[WARNING] [warn] Could not instrument [EmptyTree$/null]. No pos.
[INFO] [info] Instrumentation completed [1611 statements]
[INFO] [info] Wrote instrumentation file [/home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/target/scoverage-data/scoverage.coverage.xml]
[INFO] [info] Will write measurement data to [/home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/target/scoverage-data]
[WARNING] /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/src/main/scala/org/bdgenomics/mango/converters/SAMRecordConverter.scala:145: warning: method getNotPrimaryAlignmentFlag in class SAMRecord is deprecated: see corresponding Javadoc for more information.
[WARNING]       builder.setPrimaryAlignment(!samRecord.getNotPrimaryAlignmentFlag)
[WARNING]                                              ^
[WARNING] warning: there were four feature warnings; re-run with -feature for details
[WARNING] 7 warnings found
[INFO] prepare-compile in 0 s
[INFO] compile in 13 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ mango-core ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- scoverage-maven-plugin:1.1.1:post-compile (default-cli) @ mango-core ---
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-test-source (add-test-source) @ mango-core ---
[INFO] Test Source directory: /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/src/test/scala added.
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ mango-core ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 24 resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ mango-core ---
[WARNING]  Expected all dependencies to require Scala version: 2.11.12
[WARNING]  net.liftweb:lift-json_2.11:3.3.0 requires scala version: 2.11.11
[WARNING] Multiple versions of scala libraries detected!
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ mango-core ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ mango-core ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ mango-core ---
Discovery starting.
Discovery completed in 621 milliseconds.
Run starting. Expected test count is: 72
DiscoverySuite:
2019-12-14 14:46:01 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)
2019-12-14 14:46:01 WARN  Utils:66 - Set SPARK_LOCAL_IP if you need to bind to another address
2019-12-14 14:46:02 WARN  NativeCodeLoader:62 - Unable to load native-hadoop library for your platform... using builtin-java classes where applicable
2019-12-14 14:46:03 WARN  BedReader:158 - No index file for /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/target/scala-2.11.12/test-classes/smalltest.bed found. Generating /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/target/scala-2.11.12/test-classes/smalltest.bed.idx...
- correctly gathers regions of occupancy from Feature file
- does not fail when no regions discovered
VariantContextMaterializationSuite:
2019-12-14 14:46:04 WARN  VcfReader:205 - No index file for /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/target/scala-2.11.12/test-classes/truetest.genotypes.vcf found. Generating /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/target/scala-2.11.12/test-classes/truetest.genotypes.vcf.idx...
- Fetch from 1 vcf file with genotypes
- gets sample information
- Can extract json
2019-12-14 14:46:12 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.
- Can read Partitioned Parquet Genotypes
- correctly reassigns referenceName
2019-12-14 14:46:23 WARN  VcfReader:205 - No index file for /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/target/scala-2.11.12/test-classes/bqsr1.vcf found. Generating /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/target/scala-2.11.12/test-classes/bqsr1.vcf.idx...
- returns from file without genotypes
- more than 1 vcf file
- Should handle chromosomes with different prefixes
- fetches multiple regions from load
GenomeConfigSuite:
- Should read in genome path
- Should parse chrom sizes file
- Should parse refSeq.txt file
- Should fail when genome file does not exist
- should build genome
BamReaderSuite:
- Should load local bam file
- Gets file header
- loads all data when region is not specified
- Fails on files that are not bam or sam
- Should return empty on invalid chromosome
- Should return no data on empty dictionary
- Should load local sam file
- Should load local bam files with incorrect prefixes file
- Should load data from HDFS using Spark
- Should load http bam file
RefSeqSuite:
- Should convert refseq file to GA4GH genes
GA4GHutilSuite:
- create JSON from AlignmentRecordDataset
- create JSON from AlignmentRecordDataset with 1 sample
- create JSON from AlignmentRecordDataset with more than 1 sample
- create JSON with genotypes from VCF using GenotypeDataset
- create JSON without genotypes from VCF using VariantDataset
- create JSON from FeatureDataset
LazyMaterializationSuite:
- Should correctly reassigns chr prefix
2019-12-14 14:46:50 WARN  Bookkeep:66 - bookkeeping queue is empty
2019-12-14 14:46:50 WARN  LazyDummy:247 - memory limit exceeded. Dropping null from cache
2019-12-14 14:46:50 WARN  LazyDummy:247 - memory limit exceeded. Dropping chrM from cache
- Should check and clear memory
FeatureMaterializationSuite:
- assert raw data returns from one block
2019-12-14 14:46:51 WARN  BedReader:158 - No index file for /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/target/scala-2.11.12/test-classes/smalltest2.bed found. Generating /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/target/scala-2.11.12/test-classes/smalltest2.bed.idx...
- can fetch multiple files
- Should handle chromosomes with different prefixes
- fetches multiple regions from load
BookkeepSuite:
- remembers new regions
- adds new regions to existing chromosomes
- adds new chromosome
- merges regions
- saves sequence dictionary
- get and put region where region equals chunk size
AlignmentRecordMaterializationSuite:
- create new AlignmentRecordMaterialization
- return raw data from AlignmentRecordMaterialization
- can process stringified data
- Read Partitioned Data
- fetches multiple regions from load
- Should handle chromosomes with different prefixes
- should get data from unindexed file when referenceName predicates do not match
2019-12-14 14:47:38 WARN  BedReader:158 - No index file for /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/target/scala-2.11.12/test-classes/small.1.sorted.narrowPeak found. Generating /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/target/scala-2.11.12/test-classes/small.1.sorted.narrowPeak.idx...
BedReaderSuite:
- Should load local bed file
- Should load all records when region is not specified
- Fails on files that are not bed format
- Should return empty on invalid chromosome
- Should load local narrowPeak file
- Should load local bed files with incorrect prefixes file
- Should load data from HDFS using Spark
- Should load remote bed file
2019-12-14 14:47:39 WARN  VcfReader:205 - No index file for /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/target/scala-2.11.12/test-classes/small.vcf.gz found. Generating /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/target/scala-2.11.12/test-classes/small.vcf.gz.tbi...
VcfReaderSuite:
- Should load local vcf file
- Gets file header
2019-12-14 14:47:39 WARN  VcfReader:205 - No index file for /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/target/scala-2.11.12/test-classes/test.vcf.bgz found. Generating /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/target/scala-2.11.12/test-classes/test.vcf.bgz.tbi...
2019-12-14 14:47:39 WARN  VcfReader:205 - No index file for /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/target/scala-2.11.12/test-classes/test.vcf found. Generating /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/target/scala-2.11.12/test-classes/test.vcf.idx...
- Should load bgz file
2019-12-14 14:47:39 WARN  VcfReader:205 - No index file for /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/target/scala-2.11.12/test-classes/test.vcf.bgzf.gz found. Generating /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/target/scala-2.11.12/test-classes/test.vcf.bgzf.gz.tbi...
- Should load compressed bgz file
- Should load all records when region is not defined
- Fails on files that are not vcf or vcf.gz
- Should return empty on invalid chromosome
- Should load local vcf files with incorrect prefixes file
- Should load genotypes
- loads gzipped vcfs
2019-12-14 14:47:39 WARN  VCFInputFormat:410 - No tabix index file found for file:/home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/target/scala-2.11.12/test-classes/truetest.genotypes.vcf.tbi, splits will not be filtered, which may be very inefficient
- Should load data from HDFS using Spark
- Should load http vcf file
Run completed in 1 minute, 44 seconds.
Total number of tests run: 72
Suites: completed 13, aborted 0
Tests: succeeded 72, failed 0, canceled 0, ignored 0, pending 0
All tests passed.
[INFO] 
[INFO] <<< scoverage-maven-plugin:1.1.1:report (default-cli) < [scoverage]test @ mango-core <<<
[INFO] 
[INFO] --- scoverage-maven-plugin:1.1.1:report (default-cli) @ mango-core ---
[INFO] [scoverage] Generating cobertura XML report...
[INFO] [scoverage] Generating scoverage XML report...
[INFO] [scoverage] Generating scoverage HTML report...
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building mango: CLI 0.0.4-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ mango-cli ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ mango-cli ---
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-source (add-source) @ mango-cli ---
[INFO] Source directory: /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/src/main/scala added.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default) @ mango-cli ---
[INFO] Modified 0 of 8 .scala files
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ mango-cli ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ mango-cli ---
[WARNING]  Expected all dependencies to require Scala version: 2.11.12
[WARNING]  net.liftweb:lift-json_2.11:3.3.0 requires scala version: 2.11.11
[WARNING] Multiple versions of scala libraries detected!
[INFO] /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/src/main/scala:-1: info: compiling
[INFO] Compiling 4 source files to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/scala-2.11.12/classes at 1576363668445
[INFO] prepare-compile in 0 s
[INFO] compile in 11 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ mango-cli ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-test-source (add-test-source) @ mango-cli ---
[INFO] Test Source directory: /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/src/test/scala added.
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ mango-cli ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 8 resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ mango-cli ---
[WARNING]  Expected all dependencies to require Scala version: 2.11.12
[WARNING]  net.liftweb:lift-json_2.11:3.3.0 requires scala version: 2.11.11
[WARNING] Multiple versions of scala libraries detected!
[INFO] /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/src/test/scala:-1: info: compiling
[INFO] Compiling 4 source files to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/scala-2.11.12/test-classes at 1576363680541
[INFO] prepare-compile in 0 s
[INFO] compile in 10 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ mango-cli ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ mango-cli ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ mango-cli ---
Discovery starting.
Discovery completed in 1 second, 115 milliseconds.
Run starting. Expected test count is: 31
MangoMainSuite:
- default command groups is non empty
- module provides default command groups
- inject default command groups when called via main
- command groups is empty when called via apply
- single command group
- add new command group to default command groups
- module restores default command groups when called via apply
- custom module with single command group
- custom module with new command group added to default command groups
VizReadsSuite:
2019-12-14 14:48:16 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)
2019-12-14 14:48:16 WARN  Utils:66 - Set SPARK_LOCAL_IP if you need to bind to another address
2019-12-14 14:48:17 WARN  NativeCodeLoader:62 - Unable to load native-hadoop library for your platform... using builtin-java classes where applicable
2019-12-14 14:48:21 WARN  VcfReader:205 - No index file for /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/scala-2.11.12/test-classes/truetest.genotypes.vcf found. Generating /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/scala-2.11.12/test-classes/truetest.genotypes.vcf.idx...
2019-12-14 14:48:21 WARN  BedReader:158 - No index file for /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/scala-2.11.12/test-classes/smalltest.bed found. Generating /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/scala-2.11.12/test-classes/smalltest.bed.idx...
2019-12-14 14:48:21 WARN  BedReader:158 - No index file for /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/scala-2.11.12/test-classes/mouse_chrM.coverage.bed found. Generating /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/scala-2.11.12/test-classes/mouse_chrM.coverage.bed.idx...
- Should pass for discovery mode
Could not load resource: [/WEB-INF/layouts/browser.ssp]
Could not load resource: [/WEB-INF/layouts/overall.ssp]
- Should get browser and overall template information
- should return reads
- Should throw error when reads do not exist
- Reads should throw NotFound error on invalid reference
- should not return reads with invalid key
- /variants/:key/:ref
- should not return variants with invalid key
- Should throw error when variants do not exist
- /features/:key/:ref
- should not return features with invalid key
- Should throw error when features do not exist
- Features should throw out of bounds error on invalid reference
- gets coverage from feature endpoint
- should not return coverage with invalid key
- Should return coverage and features
- gets genes
- Coverage should throw out of bounds error on invalid reference
- Should trigger requests for http files
2019-12-14 14:49:17 WARN  VcfReader:205 - No index file for /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/../example-files/ALL.chr17.7500000-7515000.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf found. Generating /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/../example-files/ALL.chr17.7500000-7515000.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.idx...
- should run example files
MakeGenomeSuite:
Exception in thread "Thread-120" java.io.FileNotFoundException: http://hgdownload.soe.ucsc.edu/goldenPath/anoGam1/database/refGene.txt.gz
	at sun.net.www.protocol.http.HttpURLConnection.getInputStream0(HttpURLConnection.java:1896)
	at sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1498)
	at java.net.URL.openStream(URL.java:1057)
	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$1.run(ProcessImpl.scala:23)
Exception in thread "Thread-132" java.io.FileNotFoundException: http://hgdownload.cse.ucsc.edu/goldenpath/anoGam1/database/cytoBand.txt.gz
	at sun.net.www.protocol.http.HttpURLConnection.getInputStream0(HttpURLConnection.java:1896)
	at sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1498)
	at java.net.URL.openStream(URL.java:1057)
	at scala.sys.process.ProcessBuilderImpl$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)
2019-12-14 14:49:26 WARN  GenomeConfig:141 - No refGene file found at http://hgdownload.cse.ucsc.edu/goldenpath/anoGam1/database/cytoBand.txt.gz for genome anoGam1
- creates genome
- fails with invalid genome
Run completed in 1 minute, 18 seconds.
Total number of tests run: 31
Suites: completed 4, aborted 0
Tests: succeeded 31, failed 0, canceled 0, ignored 0, pending 0
All tests passed.
[INFO] 
[INFO] >>> scoverage-maven-plugin:1.1.1:report (default-cli) > [scoverage]test @ mango-cli >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ mango-cli ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ mango-cli ---
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-source (add-source) @ mango-cli ---
[INFO] Source directory: /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/src/main/scala added.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default) @ mango-cli ---
[INFO] Modified 0 of 8 .scala files
[INFO] 
[INFO] --- scoverage-maven-plugin:1.1.1:pre-compile (default-cli) @ mango-cli ---
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ mango-cli ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ mango-cli ---
[WARNING]  Expected all dependencies to require Scala version: 2.11.12
[WARNING]  net.liftweb:lift-json_2.11:3.3.0 requires scala version: 2.11.11
[WARNING] Multiple versions of scala libraries detected!
[INFO] /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/src/main/scala:-1: info: compiling
[INFO] Compiling 4 source files to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/scala-2.11.12/scoverage-classes at 1576363772196
[INFO] [info] Cleaning datadir [/home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/scoverage-data]
[INFO] [info] Beginning coverage instrumentation
[WARNING] [warn] Could not instrument [EmptyTree$/null]. No pos.
[WARNING] [warn] Could not instrument [EmptyTree$/null]. No pos.
[WARNING] [warn] Could not instrument [EmptyTree$/null]. No pos.
[WARNING] [warn] Could not instrument [EmptyTree$/null]. No pos.
[WARNING] [warn] Could not instrument [EmptyTree$/null]. No pos.
[WARNING] [warn] Could not instrument [EmptyTree$/null]. No pos.
[WARNING] [warn] Could not instrument [EmptyTree$/null]. No pos.
[WARNING] [warn] Could not instrument [EmptyTree$/null]. No pos.
[WARNING] [warn] Could not instrument [EmptyTree$/null]. No pos.
[WARNING] [warn] Could not instrument [EmptyTree$/null]. No pos.
[WARNING] [warn] Could not instrument [EmptyTree$/null]. No pos.
[WARNING] [warn] Could not instrument [EmptyTree$/null]. No pos.
[INFO] [info] Instrumentation completed [895 statements]
[INFO] [info] Wrote instrumentation file [/home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/scoverage-data/scoverage.coverage.xml]
[INFO] [info] Will write measurement data to [/home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/scoverage-data]
[INFO] prepare-compile in 0 s
[INFO] compile in 21 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ mango-cli ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- scoverage-maven-plugin:1.1.1:post-compile (default-cli) @ mango-cli ---
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-test-source (add-test-source) @ mango-cli ---
[INFO] Test Source directory: /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/src/test/scala added.
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ mango-cli ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 8 resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ mango-cli ---
[WARNING]  Expected all dependencies to require Scala version: 2.11.12
[WARNING]  net.liftweb:lift-json_2.11:3.3.0 requires scala version: 2.11.11
[WARNING] Multiple versions of scala libraries detected!
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ mango-cli ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ mango-cli ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ mango-cli ---
Discovery starting.
Discovery completed in 1 second, 744 milliseconds.
Run starting. Expected test count is: 31
MangoMainSuite:
- default command groups is non empty
- module provides default command groups
- inject default command groups when called via main
- command groups is empty when called via apply
- single command group
- add new command group to default command groups
- module restores default command groups when called via apply
- custom module with single command group
- custom module with new command group added to default command groups
VizReadsSuite:
2019-12-14 14:50:01 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)
2019-12-14 14:50:01 WARN  Utils:66 - Set SPARK_LOCAL_IP if you need to bind to another address
2019-12-14 14:50:02 WARN  NativeCodeLoader:62 - Unable to load native-hadoop library for your platform... using builtin-java classes where applicable
2019-12-14 14:50:09 WARN  VcfReader:205 - No index file for /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/scala-2.11.12/test-classes/truetest.genotypes.vcf found. Generating /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/scala-2.11.12/test-classes/truetest.genotypes.vcf.idx...
2019-12-14 14:50:09 WARN  BedReader:158 - No index file for /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/scala-2.11.12/test-classes/smalltest.bed found. Generating /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/scala-2.11.12/test-classes/smalltest.bed.idx...
2019-12-14 14:50:09 WARN  BedReader:158 - No index file for /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/scala-2.11.12/test-classes/mouse_chrM.coverage.bed found. Generating /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/scala-2.11.12/test-classes/mouse_chrM.coverage.bed.idx...
Build timed out (after 30 minutes). Marking the build as aborted.
Build was aborted
Finished: ABORTED