Started by upstream project "avocado" build number 5162 originally caused by: Started by upstream project "ADAM" build number 4453 originally caused by: Started by timer [EnvInject] - Loading node environment variables. Building remotely on research-jenkins-worker-07 (research-07 ubuntu) in workspace /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.2.0/label/ubuntu > git rev-parse --is-inside-work-tree # timeout=10 Fetching changes from the remote Git repository > git config remote.origin.url https://github.com/bigdatagenomics/avocado.git # timeout=10 Fetching upstream changes from https://github.com/bigdatagenomics/avocado.git > git --version # timeout=10 > git fetch --tags --progress https://github.com/bigdatagenomics/avocado.git +refs/heads/*:refs/remotes/origin/* Checking out Revision 4cea7777bfa76a940ad875157b92f6de7cead980 (refs/remotes/origin/master) > git config core.sparsecheckout # timeout=10 > git checkout -f 4cea7777bfa76a940ad875157b92f6de7cead980 > git rev-list 4cea7777bfa76a940ad875157b92f6de7cead980 # timeout=10 [ubuntu] $ /bin/bash /tmp/hudson1990500776021953538.sh + set -e + export JAVA_HOME=/usr/lib/jvm/java-8-oracle + JAVA_HOME=/usr/lib/jvm/java-8-oracle + export PATH=/usr/lib/jvm/java-8-oracle/bin/::/home/jenkins/gems/bin:/usr/local/go/bin:/home/jenkins/go-projects/bin:/home/jenkins/anaconda2/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games + PATH=/usr/lib/jvm/java-8-oracle/bin/::/home/jenkins/gems/bin:/usr/local/go/bin:/home/jenkins/go-projects/bin:/home/jenkins/anaconda2/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games + set +x + /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.2.0/label/ubuntu/scripts/jenkins-test # make a tempdir for writing maven cruft to AVOCADO_MVN_TMP_DIR=$(mktemp -d -t avocadoTestMvnXXXXXXX) mktemp -d -t avocadoTestMvnXXXXXXX ++ mktemp -d -t avocadoTestMvnXXXXXXX + AVOCADO_MVN_TMP_DIR=/tmp/avocadoTestMvn5WTHD9Q # add this tempdir to the poms... find . -name pom.xml \ -exec sed -i.bak \ -e "s:sun.io.serialization.extendedDebugInfo=true:sun.io.serialization.extendedDebugInfo=true -Djava.io.tmpdir=${AVOCADO_MVN_TMP_DIR}:g" \ {} \; + find . -name pom.xml -exec sed -i.bak -e 's:sun.io.serialization.extendedDebugInfo=true:sun.io.serialization.extendedDebugInfo=true -Djava.io.tmpdir=/tmp/avocadoTestMvn5WTHD9Q:g' '{}' ';' find . -name "*.bak" -exec rm -f {} \; + find . -name '*.bak' -exec rm -f '{}' ';' # variable declarations export PATH=${JAVA_HOME}/bin/:${PATH} + export PATH=/usr/lib/jvm/java-8-oracle/bin/:/usr/lib/jvm/java-8-oracle/bin/::/home/jenkins/gems/bin:/usr/local/go/bin:/home/jenkins/go-projects/bin:/home/jenkins/anaconda2/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games + PATH=/usr/lib/jvm/java-8-oracle/bin/:/usr/lib/jvm/java-8-oracle/bin/::/home/jenkins/gems/bin:/usr/local/go/bin:/home/jenkins/go-projects/bin:/home/jenkins/anaconda2/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games export MAVEN_OPTS="-Xmx1536m -XX:MaxPermSize=1g -Dfile.encoding=utf-8" + export 'MAVEN_OPTS=-Xmx1536m -XX:MaxPermSize=1g -Dfile.encoding=utf-8' + MAVEN_OPTS='-Xmx1536m -XX:MaxPermSize=1g -Dfile.encoding=utf-8' DIR=$( cd $( dirname ${BASH_SOURCE[0]} ) && pwd ) cd $( dirname ${BASH_SOURCE[0]} ) && pwd dirname ${BASH_SOURCE[0]} +++ dirname /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.2.0/label/ubuntu/scripts/jenkins-test ++ cd /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.2.0/label/ubuntu/scripts ++ pwd + DIR=/home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.2.0/label/ubuntu/scripts PROJECT_ROOT=${DIR}/.. + PROJECT_ROOT=/home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.2.0/label/ubuntu/scripts/.. VERSION=$(grep "<version>" ${PROJECT_ROOT}/pom.xml | head -2 | tail -1 | sed 's/ *<version>//g' | sed 's/<\/version>//g') grep "<version>" ${PROJECT_ROOT}/pom.xml | head -2 | tail -1 | sed 's/ *<version>//g' | sed 's/<\/version>//g' ++ grep '<version>' /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.2.0/label/ubuntu/scripts/../pom.xml ++ head -2 ++ tail -1 ++ sed 's/ *<version>//g' ++ sed 's/<\/version>//g' + VERSION=0.1.1-SNAPSHOT # is the hadoop version set? if ! [[ ${HADOOP_VERSION} ]]; then echo "HADOOP_VERSION environment variable is not set." echo "Please set this variable before running." exit 1 fi + [[ -n 2.3.0 ]] # is the spark version set? if ! [[ ${SPARK_VERSION} ]]; then echo "SPARK_VERSION environment variable is not set." echo "Please set this variable before running." exit 1 fi + [[ -n 2.2.0 ]] # print versions echo "Testing AVOCADO version ${VERSION} on Spark ${SPARK_VERSION} and Hadoop ${HADOOP_VERSION}" + echo 'Testing AVOCADO version 0.1.1-SNAPSHOT on Spark 2.2.0 and Hadoop 2.3.0' Testing AVOCADO version 0.1.1-SNAPSHOT on Spark 2.2.0 and Hadoop 2.3.0 # first, build the sources, run the unit tests, and generate a coverage report mvn clean \ -Dhadoop.version=${HADOOP_VERSION} \ -Dspark.version=${SPARK_VERSION} + mvn clean -Dhadoop.version=2.3.0 -Dspark.version=2.2.0 Java HotSpot(TM) 64-Bit Server VM warning: ignoring option MaxPermSize=1g; support was removed in 8.0 [INFO] Scanning for projects... [WARNING] [WARNING] Some problems were encountered while building the effective model for org.bdgenomics.avocado:avocado-core_2.11:jar:0.1.1-SNAPSHOT [WARNING] 'build.plugins.plugin.version' for org.apache.maven.plugins:maven-jar-plugin is missing. @ line 66, column 15 [WARNING] [WARNING] It is highly recommended to fix these problems because they threaten the stability of your build. [WARNING] [WARNING] For this reason, future Maven versions might no longer support building such malformed projects. [WARNING] [INFO] ------------------------------------------------------------------------ [INFO] Reactor Build Order: [INFO] [INFO] avocado: A Variant Caller, Distributed [INFO] avocado-core: Core variant calling algorithms [INFO] avocado-cli: Command line interface for a distributed variant caller [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building avocado: A Variant Caller, Distributed 0.1.1-SNAPSHOT [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-clean-plugin:2.5:clean (default-clean) @ avocado-parent_2.11 --- [INFO] Deleting /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.2.0/label/ubuntu/target [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building avocado-core: Core variant calling algorithms 0.1.1-SNAPSHOT [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-clean-plugin:2.5:clean (default-clean) @ avocado-core_2.11 --- [INFO] Deleting /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.2.0/label/ubuntu/avocado-core/target [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building avocado-cli: Command line interface for a distributed variant caller 0.1.1-SNAPSHOT [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-clean-plugin:2.5:clean (default-clean) @ avocado-cli_2.11 --- [INFO] Deleting /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.2.0/label/ubuntu/avocado-cli/target [INFO] ------------------------------------------------------------------------ [INFO] Reactor Summary: [INFO] [INFO] avocado: A Variant Caller, Distributed ............. SUCCESS [ 0.198 s] [INFO] avocado-core: Core variant calling algorithms ...... SUCCESS [ 0.077 s] [INFO] avocado-cli: Command line interface for a distributed variant caller SUCCESS [ 0.038 s] [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ [INFO] Total time: 0.486 s [INFO] Finished at: 2019-12-03T04:34:21-08:00 [INFO] Final Memory: 22M/1472M [INFO] ------------------------------------------------------------------------ # if this is a pull request, we need to set the coveralls pr id if [[ ! -z $ghprbPullId ]]; then COVERALLS_PRB_OPTION="-DpullRequest=${ghprbPullId}" fi + [[ ! -z '' ]] # coveralls token should not be visible set +x +v + set +x +v Java HotSpot(TM) 64-Bit Server VM warning: ignoring option MaxPermSize=1g; support was removed in 8.0 [INFO] Scanning for projects... [WARNING] [WARNING] Some problems were encountered while building the effective model for org.bdgenomics.avocado:avocado-core_2.11:jar:0.1.1-SNAPSHOT [WARNING] 'build.plugins.plugin.version' for org.apache.maven.plugins:maven-jar-plugin is missing. @ line 66, column 15 [WARNING] [WARNING] It is highly recommended to fix these problems because they threaten the stability of your build. [WARNING] [WARNING] For this reason, future Maven versions might no longer support building such malformed projects. [WARNING] [INFO] ------------------------------------------------------------------------ [INFO] Reactor Build Order: [INFO] [INFO] avocado: A Variant Caller, Distributed [INFO] avocado-core: Core variant calling algorithms [INFO] avocado-cli: Command line interface for a distributed variant caller [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building avocado: A Variant Caller, Distributed 0.1.1-SNAPSHOT [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ avocado-parent_2.11 --- [INFO] [INFO] --- build-helper-maven-plugin:1.10:add-source (add-source) @ avocado-parent_2.11 --- [INFO] Source directory: /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.2.0/label/ubuntu/src/main/scala added. [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ avocado-parent_2.11 --- [INFO] Modified 0 of 58 .scala files [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ avocado-parent_2.11 --- [INFO] No sources to compile [INFO] [INFO] --- build-helper-maven-plugin:1.10:add-test-source (add-test-source) @ avocado-parent_2.11 --- [INFO] Test Source directory: /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.2.0/label/ubuntu/src/test/scala added. [INFO] [INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ avocado-parent_2.11 --- [INFO] No sources to compile [INFO] [INFO] >>> scoverage-maven-plugin:1.1.1:report (default-cli) > [scoverage]test @ avocado-parent_2.11 >>> [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ avocado-parent_2.11 --- [INFO] [INFO] --- build-helper-maven-plugin:1.10:add-source (add-source) @ avocado-parent_2.11 --- [INFO] Source directory: /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.2.0/label/ubuntu/src/main/scala added. [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ avocado-parent_2.11 --- [INFO] Modified 0 of 58 .scala files [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:pre-compile (default-cli) @ avocado-parent_2.11 --- [INFO] Skipping SCoverage execution for project with packaging type 'pom' [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ avocado-parent_2.11 --- [INFO] No sources to compile [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:post-compile (default-cli) @ avocado-parent_2.11 --- [INFO] [INFO] --- build-helper-maven-plugin:1.10:add-test-source (add-test-source) @ avocado-parent_2.11 --- [INFO] Test Source directory: /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.2.0/label/ubuntu/src/test/scala added. [INFO] [INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ avocado-parent_2.11 --- [INFO] No sources to compile [INFO] [INFO] <<< scoverage-maven-plugin:1.1.1:report (default-cli) < [scoverage]test @ avocado-parent_2.11 <<< [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:report (default-cli) @ avocado-parent_2.11 --- [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building avocado-core: Core variant calling algorithms 0.1.1-SNAPSHOT [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ avocado-core_2.11 --- [INFO] [INFO] --- build-helper-maven-plugin:1.10:add-source (add-source) @ avocado-core_2.11 --- [INFO] Source directory: /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.2.0/label/ubuntu/avocado-core/src/main/scala added. [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ avocado-core_2.11 --- [INFO] Modified 0 of 49 .scala files [INFO] [INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ avocado-core_2.11 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.2.0/label/ubuntu/avocado-core/src/main/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ avocado-core_2.11 --- [WARNING] Expected all dependencies to require Scala version: 2.11.4 [WARNING] org.bdgenomics.utils:utils-misc-spark2_2.11:0.2.11 requires scala version: 2.11.4 [WARNING] org.bdgenomics.utils:utils-metrics-spark2_2.11:0.2.11 requires scala version: 2.11.4 [WARNING] org.bdgenomics.utils:utils-serialization-spark2_2.11:0.2.11 requires scala version: 2.11.4 [WARNING] org.bdgenomics.utils:utils-misc-spark2_2.11:0.2.11 requires scala version: 2.11.4 [WARNING] org.bdgenomics.utils:utils-io-spark2_2.11:0.2.13 requires scala version: 2.11.8 [WARNING] Multiple versions of scala libraries detected! [INFO] /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.2.0/label/ubuntu/avocado-core/src/main/scala:-1: info: compiling [INFO] Compiling 26 source files to /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.2.0/label/ubuntu/avocado-core/target/scala-2.11.4/classes at 1575376470559 [WARNING] warning: there were three deprecation warnings; re-run with -deprecation for details [WARNING] one warning found [INFO] prepare-compile in 0 s [INFO] compile in 11 s [INFO] [INFO] --- maven-compiler-plugin:3.5.1:compile (default-compile) @ avocado-core_2.11 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- build-helper-maven-plugin:1.10:add-test-source (add-test-source) @ avocado-core_2.11 --- [INFO] Test Source directory: /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.2.0/label/ubuntu/avocado-core/src/test/scala added. [INFO] [INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ avocado-core_2.11 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 26 resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ avocado-core_2.11 --- [WARNING] Expected all dependencies to require Scala version: 2.11.4 [WARNING] org.bdgenomics.utils:utils-misc-spark2_2.11:0.2.11 requires scala version: 2.11.4 [WARNING] org.bdgenomics.utils:utils-metrics-spark2_2.11:0.2.11 requires scala version: 2.11.4 [WARNING] org.bdgenomics.utils:utils-serialization-spark2_2.11:0.2.11 requires scala version: 2.11.4 [WARNING] org.bdgenomics.utils:utils-misc-spark2_2.11:0.2.11 requires scala version: 2.11.4 [WARNING] org.bdgenomics.utils:utils-io-spark2_2.11:0.2.13 requires scala version: 2.11.8 [WARNING] Multiple versions of scala libraries detected! [INFO] /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.2.0/label/ubuntu/avocado-core/src/test/scala:-1: info: compiling [INFO] Compiling 23 source files to /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.2.0/label/ubuntu/avocado-core/target/scala-2.11.4/test-classes at 1575376482735 [INFO] prepare-compile in 0 s [INFO] compile in 18 s [INFO] [INFO] --- maven-compiler-plugin:3.5.1:testCompile (default-testCompile) @ avocado-core_2.11 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-surefire-plugin:2.7:test (default-test) @ avocado-core_2.11 --- [INFO] Tests are skipped. [INFO] [INFO] --- scalatest-maven-plugin:1.0:test (test) @ avocado-core_2.11 --- Discovery starting. Discovery completed in 703 milliseconds. Run starting. Expected test count is: 282 LogPhredSuite: - convert log error probabilities to phred scores TreeRegionJoinSuite: - build a forest with a single item and retrieve data - build a forest with data from a single contig and retrieve data - build a forest with data from multiple contigs and retrieve data 2019-12-03 04:35:02 WARN NativeCodeLoader:62 - Unable to load native-hadoop library for your platform... using builtin-java classes where applicable 2019-12-03 04:35:03 WARN Utils:66 - Your hostname, research-jenkins-worker-07 resolves to a loopback address: 127.0.1.1; using 192.168.10.27 instead (on interface eth0) 2019-12-03 04:35:03 WARN Utils:66 - Set SPARK_LOCAL_IP if you need to bind to another address - build a forest out of data on a single contig and retrieve data - run a join between data on a single contig HardLimiterSuite: - add a read to an empty buffer - add a read to a non-empty buffer, without moving forward - add a read to a non-empty buffer, and move forward - trying to add a read to a full buffer—without moving forward—drops the read - add a read to a full buffer, while moving forward and keeping buffer full - add a read to a full buffer, while moving forward and emptying buffer - adding an out of order read should fire an assert - adding a read that is on the wrong contig should fire an assert - apply hard limiting to an iterator that is wholly under the coverage limit - apply hard limiting to an iterator that is partially under the coverage limit - apply hard limiting to an iterator that is wholly over the coverage limit - apply hard limiting on a file that is wholly under the coverage limit - apply hard limiting on a file with sections over the coverage limit VariantSummarySuite: - create from genotype without strand bias components - create from genotype with strand bias components - invalid strand bias causes exception - merge two fully populated summaries - merge two partially populated summaries - populating an annotation should carry old fields RewriteHetsSuite: - should rewrite a bad het snp - should not rewrite het snp if snp filtering is disabled - should rewrite a bad het indel - should not rewrite het indel if indel filtering is disabled - don't rewrite good het calls - don't rewrite homozygous calls - rewrite a het call as a hom alt snp - processing a valid call should not change the call - if processing is disabled, don't rewrite bad calls - process a bad het snp call - process a bad het indel call - disable processing for a whole rdd - process a whole rdd RealignerSuite: - realignment candidate code needs at least one block - read is not a realignment candidate if it is canonical - read is not a realignment candidate if it is canonical and clipped - read is a realignment candidate if there is at least one non-canonical block - realign an indel that is not left normalized - realign a mnp expressed as a complex indel - realign two snps expressed as a complex indel - align sequence with a complex deletion - realign a read with a complex deletion - realign a read with a snp and deletion separated by a flank - realigning a repetative read will fire an assert - realign a set of reads around an insert - realign a set of reads around a deletion 2019-12-03 04:35:08 WARN Realigner:101 - Realigning A_READ failed with exception java.lang.AssertionError: assertion failed: Input sequence contains a repeat.. - realigning a read with a repeat will return the original read - one sample read should fail due to a repeat, all others should realign HardFilterGenotypesSuite: - filter out reference calls - filter out low quality calls - filter out genotypes for emission - filter out genotypes with a low quality per depth - filter out genotypes with a low depth - filter out genotypes with a high depth - filter out genotypes with a low RMS mapping quality - filter out genotypes with a high strand bias - update genotype where no filters were applied - update genotype where filters were applied and passed - update genotype where filters were applied and failed - discard a ref genotype call - keep a ref genotype call - discard a genotype whose quality is too low - build filters and apply to snp - build filters and apply to indel - test adding filters - filter out genotypes with a low allelic fraction - filter out genotypes with a high allelic fraction TrioCallerSuite: - cannot have a sample with no record groups - cannot have a sample with discordant sample ids - extract id from a single read group - extract id from multiple read groups - filter an empty site - filter a site with only ref calls - keep a site with a non-ref call - fill in no-calls for site with missing parents - pass through site with odd copy number - confirm call at site where proband and parents are consistent and phase - confirm call at site where proband and parents are consistent but cannot phase - invalidate call at site where proband and parents are inconsistent - end-to-end trio call test BlockSuite: - folding over a match block returns a match operator - an unknown block must have mismatching input sequences - folding over an unknown block returns our function's result AlignerSuite: - aligning a repetative sequence will fire an assert - align a minimally flanked sequence with a snp - align a minimally flanked sequence with a 3 bp mnp - align a minimally flanked sequence with 2 snps separated by 1bp - align a minimally flanked sequence with 2 snps separated by 3bp - align a minimally flanked sequence with a simple insert - align a minimally flanked sequence with a complex insert - align a minimally flanked sequence with a simple deletion - align a minimally flanked sequence that contains a discordant k-mer pair - align a minimally flanked sequence with a complex deletion - align a minimally flanked sequence with 2 snps separated by two matching k-mers - align a minimally flanked sequence with a snp and an indel separated by one matching k-mer - zip and trim short insert - zip and trim short deletion - cut up a sequence that is longer than the k-mer length - cutting up a sequence that is shorter than the k-mer length yields an empty map - cutting up a repeated sequence throws an assert - get no indices if we have no intersection - get correct index for a single intersection - get correct indices for two k-mers in a row - get correct indices for two k-mers separated by a snp - get correct indices for two k-mers separated by an indel - get correct indices for two k-mers whose positions are flipped - fire assert when cutting up repeatitive reads - fire assert when checking negative index pair - a set of a single index pair is concordant - a set with a pair of index pairs is concordant - a set with multiple good index pairs is concordant - a set with a pair of swapped index pairs is discordant - a set with a pair of both con/discordant index pairs is discordant - making blocks from no indices returns a single unknown block - make blocks from a single match between two snps - make blocks from three matches between two snps - make blocks from three matches between two indels, opposite events - make blocks from three matches between two indels, same events - make blocks from matches between snp/indel/snp BiallelicGenotyperSuite: - properly handle haploid genotype state - properly handle diploid genotype state with het call - properly handle triploid genotype state with hom alt call - scoring read that overlaps no variants should return empty observations in variant only mode - scoring read that overlaps no variants should return empty observations 2019-12-03 04:35:14 WARN TaskSetManager:66 - Stage 5 contains a task of very large size (4472 KB). The maximum recommended task size is 100 KB. 2019-12-03 04:35:14 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. - score snps in a read overlapping a copy number dup boundary 2019-12-03 04:35:31 WARN TaskSetManager:66 - Stage 5 contains a task of very large size (4060 KB). The maximum recommended task size is 100 KB. - score snps in a read overlapping a copy number del boundary - score snp in a read with no evidence of the snp - score snp in a read with evidence of the snp - score snp in a read with evidence of the snp, and non-variant bases - build genotype for het snp - force call possible STR/indel !!! IGNORED !!! - log space factorial - fisher test for strand bias 2019-12-03 04:35:45 WARN BiallelicGenotyper:170 - Input RDD is not persisted. Performance may be degraded. 2019-12-03 04:35:51 WARN TaskSetManager:66 - Stage 5 contains a task of very large size (10813 KB). The maximum recommended task size is 100 KB. - discover and call simple SNP 2019-12-03 04:37:03 WARN BiallelicGenotyper:170 - Input RDD is not persisted. Performance may be degraded. 2019-12-03 04:37:09 WARN TaskSetManager:66 - Stage 5 contains a task of very large size (10813 KB). The maximum recommended task size is 100 KB. - discover and call simple SNP and score all sites 2019-12-03 04:38:21 WARN BiallelicGenotyper:170 - Input RDD is not persisted. Performance may be degraded. 2019-12-03 04:38:28 WARN TaskSetManager:66 - Stage 5 contains a task of very large size (10813 KB). The maximum recommended task size is 100 KB. - discover and call short indel 2019-12-03 04:39:41 WARN BiallelicGenotyper:170 - Input RDD is not persisted. Performance may be degraded. 2019-12-03 04:39:48 WARN TaskSetManager:66 - Stage 5 contains a task of very large size (10813 KB). The maximum recommended task size is 100 KB. 2019-12-03 04:40:00 ERROR BiallelicGenotyper:387 - Processing read H06JUADXX130110:1:1109:10925:52628 failed with exception java.lang.StringIndexOutOfBoundsException: String index out of range: 0. Skipping... 2019-12-03 04:40:00 ERROR BiallelicGenotyper:387 - Processing read H06JUADXX130110:1:1116:7369:15293 failed with exception java.lang.StringIndexOutOfBoundsException: String index out of range: 0. Skipping... 2019-12-03 04:40:00 ERROR BiallelicGenotyper:387 - Processing read H06HDADXX130110:2:1115:12347:40533 failed with exception java.lang.StringIndexOutOfBoundsException: String index out of range: 0. Skipping... 2019-12-03 04:40:00 ERROR BiallelicGenotyper:387 - Processing read H06HDADXX130110:1:2110:7844:95190 failed with exception java.lang.StringIndexOutOfBoundsException: String index out of range: 0. Skipping... 2019-12-03 04:40:00 ERROR BiallelicGenotyper:387 - Processing read H06HDADXX130110:1:2203:13041:33390 failed with exception java.lang.StringIndexOutOfBoundsException: String index out of range: 0. Skipping... - discover and call het and hom snps - score a single read covering a deletion 2019-12-03 04:41:10 WARN TaskSetManager:66 - Stage 7 contains a task of very large size (10813 KB). The maximum recommended task size is 100 KB. - discover and force call hom alt deletion 2019-12-03 04:42:26 WARN TaskSetManager:66 - Stage 7 contains a task of very large size (10813 KB). The maximum recommended task size is 100 KB. - call hom alt AGCCAGTGGACGCCGACCT->A deletion at 1/875159 2019-12-03 04:43:36 WARN BiallelicGenotyper:170 - Input RDD is not persisted. Performance may be degraded. 2019-12-03 04:43:43 WARN TaskSetManager:66 - Stage 5 contains a task of very large size (10813 KB). The maximum recommended task size is 100 KB. - call hom alt TACACACACACACACACACACACACACACAC->T deletion at 1/1777263 2019-12-03 04:44:52 WARN BiallelicGenotyper:170 - Input RDD is not persisted. Performance may be degraded. 2019-12-03 04:45:00 WARN TaskSetManager:66 - Stage 5 contains a task of very large size (10813 KB). The maximum recommended task size is 100 KB. - call hom alt CAG->C deletion at 1/1067596 2019-12-03 04:46:13 WARN BiallelicGenotyper:170 - Input RDD is not persisted. Performance may be degraded. 2019-12-03 04:46:20 WARN TaskSetManager:66 - Stage 5 contains a task of very large size (10813 KB). The maximum recommended task size is 100 KB. - call hom alt C->G snp at 1/877715 2019-12-03 04:47:33 WARN BiallelicGenotyper:170 - Input RDD is not persisted. Performance may be degraded. 2019-12-03 04:47:41 WARN TaskSetManager:66 - Stage 5 contains a task of very large size (10813 KB). The maximum recommended task size is 100 KB. - call hom alt ACAG->A deletion at 1/886049 2019-12-03 04:48:53 WARN BiallelicGenotyper:170 - Input RDD is not persisted. Performance may be degraded. 2019-12-03 04:49:00 WARN TaskSetManager:66 - Stage 5 contains a task of very large size (10813 KB). The maximum recommended task size is 100 KB. - call hom alt GA->CC mnp at 1/889158–9 2019-12-03 04:50:11 WARN BiallelicGenotyper:170 - Input RDD is not persisted. Performance may be degraded. 2019-12-03 04:50:17 WARN TaskSetManager:66 - Stage 14 contains a task of very large size (10813 KB). The maximum recommended task size is 100 KB. - call hom alt C->CCCCT insertion at 1/866511 2019-12-03 04:50:23 WARN BiallelicGenotyper:170 - Input RDD is not persisted. Performance may be degraded. 2019-12-03 04:50:28 WARN TaskSetManager:66 - Stage 5 contains a task of very large size (10813 KB). The maximum recommended task size is 100 KB. - call het ATG->A deletion at 1/905130 2019-12-03 04:51:39 WARN BiallelicGenotyper:170 - Input RDD is not persisted. Performance may be degraded. 2019-12-03 04:51:46 WARN TaskSetManager:66 - Stage 5 contains a task of very large size (10813 KB). The maximum recommended task size is 100 KB. - call het ATG->A deletion at 1/905130 while scoring all sites 2019-12-03 04:52:59 WARN BiallelicGenotyper:170 - Input RDD is not persisted. Performance may be degraded. 2019-12-03 04:53:06 WARN TaskSetManager:66 - Stage 5 contains a task of very large size (10813 KB). The maximum recommended task size is 100 KB. - call het AG->A deletion at 1/907170 2019-12-03 04:54:17 WARN BiallelicGenotyper:170 - Input RDD is not persisted. Performance may be degraded. 2019-12-03 04:54:24 WARN TaskSetManager:66 - Stage 5 contains a task of very large size (10813 KB). The maximum recommended task size is 100 KB. - call het T->G snp at 1/240898 2019-12-03 04:55:37 WARN BiallelicGenotyper:170 - Input RDD is not persisted. Performance may be degraded. 2019-12-03 04:55:44 WARN TaskSetManager:66 - Stage 5 contains a task of very large size (10813 KB). The maximum recommended task size is 100 KB. - make het alt calls at biallelic snp locus 2019-12-03 04:56:56 WARN BiallelicGenotyper:170 - Input RDD is not persisted. Performance may be degraded. 2019-12-03 04:57:02 WARN TaskSetManager:66 - Stage 5 contains a task of very large size (10813 KB). The maximum recommended task size is 100 KB. - call hom alt T->TAAA insertion at 1/4120185 2019-12-03 04:58:13 WARN BiallelicGenotyper:170 - Input RDD is not persisted. Performance may be degraded. 2019-12-03 04:58:19 WARN TaskSetManager:66 - Stage 5 contains a task of very large size (10813 KB). The maximum recommended task size is 100 KB. - call het alt TTATA,TTA->T insertion at 1/5274547 ObserverSuite: - a fully clipped read will not generate any observations - generate observations for a sequence match under diploid model - generate observations for a read with an insertion under diploid model - generate observations for a read with a deletion under diploid model DiscoveredVariantSuite: - round trip conversion to/from variant SquareOffReferenceModelSuite: - don't trim a snp - trim a mnp - trim an insertion - don't trim a deletion - extract variants finds sites with a called alt - find genotype if variant is present - don't find genotype if variant is not present - excise a genotype from a reference block - square off a site with data from multiple samples DiscoverVariantsSuite: - no variants in unaligned read - no variants in rdd with unaligned read - no variants in read that is a perfect sequence match - no variants in rdd with sequence match reads - find snp in read with a 1bp sequence mismatch - find one snp in reads with 1bp sequence mismatch - find insertion in read - find insertion in reads - find deletion in read - find deletion in reads - find variants in alignment record rdd - break TT->CA mnp into two snps ObservationOperatorSuite: - zero operators are empty - non-zero operators are non-empty - cannot build mismatch with wrong ref length - collapsing a non repeated set of operators should eliminate 0 ops - collapsing a repeated set of operators with mixed match/mismatch - collapse a set of operators with repeats - collapse a set of operators with repeats and clips - make a cigar and md tag from a single sequence match - make a cigar and md tag from a single sequence mismatch - make a cigar and md tag from a single multi-base sequence match - make a cigar and md tag from a single deletion - make a cigar and md tag from a single insertion - make a cigar for a match followed by a deletion - make a cigar for an insertion flanked by matches - make a cigar for a match followed by a mismatch - make a cigar for a multi-base mismatch flanked by matches - make a cigar for a match after a clip - make a cigar for a mismatch after a clip - extract reference from a single snp - extract reference from a single deletion - extract reference from a single insertion - extract reference from a soft clipped sequence - extract reference from a hard clipped sequence - extract reference from a match flanked deletion - extract reference from a match flanked insertion - read must be mapped to extract alignment operators - extracting alignment operators will fail if cigar is unset - extracting alignment operators will fail if cigar is * - extracting alignment operators will fail if MD tag is unset - extract alignment operators from a perfect read - extract alignment operators from a read with a single mismatch - extract alignment operators from a read with a single deletion - extract alignment operators from a read with a single insertion LogUtilsSuite: - test our nifty log summer - can we compute the sum of logs correctly? - can we compute the additive inverse of logs correctly? ObservationSuite: - cannot create an observation with empty likelihoods - cannot create an observation with 1-length likelihoods - cannot create an observation with mismatching likelihood lengths - forward strand must be >= 0 - forward strand cannot exceed coverage - square map-q must be >= 0 - coverage is strictly positive - invert an observation - null an observation RealignmentBlockSuite: - folding over a clip returns the clip operator, soft clip - folding over a clip returns the clip operator, hard clip - folding over a canonical block returns the original alignment - violate an invariant of the fold function, part 1 - violate an invariant of the fold function, part 2 - apply the fold function on a realignable block - having a clip in the middle of a read is illegal - can't have two soft clips back to back - a read that is an exact sequence match is canonical - hard clip before soft clip is ok at start of read - hard clip after soft clip is ok at end of read - a read with a single snp is canonical - a read containing an indel with exact flanks is wholly realignable - a read containing an indel with exact flanks is wholly realignable, with soft clipped bases - a read containing an indel with longer flanks can be split into multiple blocks - a read containing an indel with longer flanks on both sides can be split into multiple blocks - properly handle a read that starts with a long soft clip JointAnnotatorCallerSuite: - discard reference site - calculate MAF for all called genotypes - calculate MAF ignoring uncalled genotypes - roll up variant annotations from a single genotype - roll up variant annotations across multiple genotypes - recalling genotypes is a no-op for no calls and complex hets - recall a genotype so that the state changes - allele frequency being outside of (0.0, 1.0) just computes posteriors - compute variant quality from a single genotype - compute variant quality from multiple genotypes CopyNumberMapSuite: - create an empty map - create a map with only diploid features - create a map with a mix of features PrefilterReadsSuite: - filter on read uniqueness - filter unmapped reads - filter autosomal chromosomes with grc names - filter sex chromosomes with grc names - filter mitochondrial chromosome with a grc names - filter autosomal chromosomes with hg names - filter sex chromosomes with hg names - filter mitochondrial chromosome with a hg names - filter autosomal chromosomes from generator - filter autosomal + sex chromosomes from generator - filter all chromosomes from generator - update a read whose mate is mapped to a filtered contig - filter reads mapped to autosomal chromosomes from generator - filter reads mapped to autosomal + sex chromosomes from generator - filter reads mapped to all chromosomes from generator - filter reads uniquely mapped to autosomal chromosomes from generator - filter reads uniquely mapped to autosomal + sex chromosomes from generator - filter reads uniquely mapped to all chromosomes from generator - filter rdd of reads mapped to autosomal chromosomes from generator - filter rdd of reads mapped to autosomal + sex chromosomes from generator - filter rdd of reads mapped to all chromosomes from generator - filter rdd of reads uniquely mapped to autosomal chromosomes from generator - filter rdd of reads uniquely mapped to autosomal + sex chromosomes from generator - filter rdd of reads uniquely mapped to all chromosomes from generator Run completed in 24 minutes, 39 seconds. Total number of tests run: 282 Suites: completed 23, aborted 0 Tests: succeeded 282, failed 0, canceled 0, ignored 1, pending 0 All tests passed. [INFO] [INFO] >>> scoverage-maven-plugin:1.1.1:report (default-cli) > [scoverage]test @ avocado-core_2.11 >>> [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ avocado-core_2.11 --- [INFO] [INFO] --- build-helper-maven-plugin:1.10:add-source (add-source) @ avocado-core_2.11 --- [INFO] Source directory: /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.2.0/label/ubuntu/avocado-core/src/main/scala added. [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ avocado-core_2.11 --- [INFO] Modified 0 of 49 .scala files [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:pre-compile (default-cli) @ avocado-core_2.11 --- [INFO] [INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ avocado-core_2.11 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.2.0/label/ubuntu/avocado-core/src/main/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ avocado-core_2.11 --- [WARNING] Expected all dependencies to require Scala version: 2.11.4 [WARNING] org.bdgenomics.utils:utils-misc-spark2_2.11:0.2.11 requires scala version: 2.11.4 [WARNING] org.bdgenomics.utils:utils-metrics-spark2_2.11:0.2.11 requires scala version: 2.11.4 [WARNING] org.bdgenomics.utils:utils-serialization-spark2_2.11:0.2.11 requires scala version: 2.11.4 [WARNING] org.bdgenomics.utils:utils-misc-spark2_2.11:0.2.11 requires scala version: 2.11.4 [WARNING] org.bdgenomics.utils:utils-io-spark2_2.11:0.2.13 requires scala version: 2.11.8 [WARNING] Multiple versions of scala libraries detected! [INFO] /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.2.0/label/ubuntu/avocado-core/src/main/scala:-1: info: compiling [INFO] Compiling 26 source files to /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.2.0/label/ubuntu/avocado-core/target/scala-2.11.4/scoverage-classes at 1575377983424 [INFO] [info] Cleaning datadir [/home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.2.0/label/ubuntu/avocado-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. [INFO] [info] Instrumentation completed [2625 statements] [INFO] [info] Wrote instrumentation file [/home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.2.0/label/ubuntu/avocado-core/target/scoverage-data/scoverage.coverage.xml] [INFO] [info] Will write measurement data to [/home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.2.0/label/ubuntu/avocado-core/target/scoverage-data] [WARNING] warning: there were three deprecation warnings; re-run with -deprecation for details [WARNING] one warning found [INFO] prepare-compile in 0 s [INFO] compile in 13 s [INFO] [INFO] --- maven-compiler-plugin:3.5.1:compile (default-compile) @ avocado-core_2.11 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:post-compile (default-cli) @ avocado-core_2.11 --- [INFO] [INFO] --- build-helper-maven-plugin:1.10:add-test-source (add-test-source) @ avocado-core_2.11 --- [INFO] Test Source directory: /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.2.0/label/ubuntu/avocado-core/src/test/scala added. [INFO] [INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ avocado-core_2.11 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 26 resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ avocado-core_2.11 --- [WARNING] Expected all dependencies to require Scala version: 2.11.4 [WARNING] org.bdgenomics.utils:utils-misc-spark2_2.11:0.2.11 requires scala version: 2.11.4 [WARNING] org.bdgenomics.utils:utils-metrics-spark2_2.11:0.2.11 requires scala version: 2.11.4 [WARNING] org.bdgenomics.utils:utils-serialization-spark2_2.11:0.2.11 requires scala version: 2.11.4 [WARNING] org.bdgenomics.utils:utils-misc-spark2_2.11:0.2.11 requires scala version: 2.11.4 [WARNING] org.bdgenomics.utils:utils-io-spark2_2.11:0.2.13 requires scala version: 2.11.8 [WARNING] Multiple versions of scala libraries detected! [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-compiler-plugin:3.5.1:testCompile (default-testCompile) @ avocado-core_2.11 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-surefire-plugin:2.7:test (default-test) @ avocado-core_2.11 --- [INFO] Tests are skipped. [INFO] [INFO] --- scalatest-maven-plugin:1.0:test (test) @ avocado-core_2.11 --- Discovery starting. Discovery completed in 709 milliseconds. Run starting. Expected test count is: 282 LogPhredSuite: - convert log error probabilities to phred scores TreeRegionJoinSuite: - build a forest with a single item and retrieve data - build a forest with data from a single contig and retrieve data - build a forest with data from multiple contigs and retrieve data 2019-12-03 04:59:59 WARN NativeCodeLoader:62 - Unable to load native-hadoop library for your platform... using builtin-java classes where applicable 2019-12-03 04:59:59 WARN Utils:66 - Your hostname, research-jenkins-worker-07 resolves to a loopback address: 127.0.1.1; using 192.168.10.27 instead (on interface eth0) 2019-12-03 04:59:59 WARN Utils:66 - Set SPARK_LOCAL_IP if you need to bind to another address - build a forest out of data on a single contig and retrieve data - run a join between data on a single contig HardLimiterSuite: - add a read to an empty buffer - add a read to a non-empty buffer, without moving forward - add a read to a non-empty buffer, and move forward - trying to add a read to a full buffer—without moving forward—drops the read - add a read to a full buffer, while moving forward and keeping buffer full - add a read to a full buffer, while moving forward and emptying buffer - adding an out of order read should fire an assert - adding a read that is on the wrong contig should fire an assert - apply hard limiting to an iterator that is wholly under the coverage limit - apply hard limiting to an iterator that is partially under the coverage limit - apply hard limiting to an iterator that is wholly over the coverage limit - apply hard limiting on a file that is wholly under the coverage limit - apply hard limiting on a file with sections over the coverage limit VariantSummarySuite: - create from genotype without strand bias components - create from genotype with strand bias components - invalid strand bias causes exception - merge two fully populated summaries - merge two partially populated summaries - populating an annotation should carry old fields RewriteHetsSuite: - should rewrite a bad het snp - should not rewrite het snp if snp filtering is disabled - should rewrite a bad het indel - should not rewrite het indel if indel filtering is disabled - don't rewrite good het calls - don't rewrite homozygous calls - rewrite a het call as a hom alt snp - processing a valid call should not change the call - if processing is disabled, don't rewrite bad calls - process a bad het snp call - process a bad het indel call - disable processing for a whole rdd - process a whole rdd RealignerSuite: - realignment candidate code needs at least one block - read is not a realignment candidate if it is canonical - read is not a realignment candidate if it is canonical and clipped - read is a realignment candidate if there is at least one non-canonical block - realign an indel that is not left normalized - realign a mnp expressed as a complex indel - realign two snps expressed as a complex indel - align sequence with a complex deletion - realign a read with a complex deletion - realign a read with a snp and deletion separated by a flank - realigning a repetative read will fire an assert - realign a set of reads around an insert - realign a set of reads around a deletion 2019-12-03 05:00:05 WARN Realigner:101 - Realigning A_READ failed with exception java.lang.AssertionError: assertion failed: Input sequence contains a repeat.. - realigning a read with a repeat will return the original read - one sample read should fail due to a repeat, all others should realign HardFilterGenotypesSuite: - filter out reference calls - filter out low quality calls - filter out genotypes for emission - filter out genotypes with a low quality per depth - filter out genotypes with a low depth - filter out genotypes with a high depth - filter out genotypes with a low RMS mapping quality - filter out genotypes with a high strand bias - update genotype where no filters were applied - update genotype where filters were applied and passed - update genotype where filters were applied and failed - discard a ref genotype call - keep a ref genotype call - discard a genotype whose quality is too low - build filters and apply to snp - build filters and apply to indel - test adding filters - filter out genotypes with a low allelic fraction - filter out genotypes with a high allelic fraction TrioCallerSuite: - cannot have a sample with no record groups - cannot have a sample with discordant sample ids - extract id from a single read group - extract id from multiple read groups - filter an empty site - filter a site with only ref calls - keep a site with a non-ref call - fill in no-calls for site with missing parents - pass through site with odd copy number - confirm call at site where proband and parents are consistent and phase - confirm call at site where proband and parents are consistent but cannot phase - invalidate call at site where proband and parents are inconsistent - end-to-end trio call test BlockSuite: - folding over a match block returns a match operator - an unknown block must have mismatching input sequences - folding over an unknown block returns our function's result AlignerSuite: - aligning a repetative sequence will fire an assert - align a minimally flanked sequence with a snp - align a minimally flanked sequence with a 3 bp mnp - align a minimally flanked sequence with 2 snps separated by 1bp - align a minimally flanked sequence with 2 snps separated by 3bp - align a minimally flanked sequence with a simple insert - align a minimally flanked sequence with a complex insert - align a minimally flanked sequence with a simple deletion - align a minimally flanked sequence that contains a discordant k-mer pair - align a minimally flanked sequence with a complex deletion - align a minimally flanked sequence with 2 snps separated by two matching k-mers - align a minimally flanked sequence with a snp and an indel separated by one matching k-mer - zip and trim short insert - zip and trim short deletion - cut up a sequence that is longer than the k-mer length - cutting up a sequence that is shorter than the k-mer length yields an empty map - cutting up a repeated sequence throws an assert - get no indices if we have no intersection - get correct index for a single intersection - get correct indices for two k-mers in a row - get correct indices for two k-mers separated by a snp - get correct indices for two k-mers separated by an indel - get correct indices for two k-mers whose positions are flipped - fire assert when cutting up repeatitive reads - fire assert when checking negative index pair - a set of a single index pair is concordant - a set with a pair of index pairs is concordant - a set with multiple good index pairs is concordant - a set with a pair of swapped index pairs is discordant - a set with a pair of both con/discordant index pairs is discordant - making blocks from no indices returns a single unknown block - make blocks from a single match between two snps - make blocks from three matches between two snps - make blocks from three matches between two indels, opposite events - make blocks from three matches between two indels, same events - make blocks from matches between snp/indel/snp BiallelicGenotyperSuite: - properly handle haploid genotype state - properly handle diploid genotype state with het call - properly handle triploid genotype state with hom alt call - scoring read that overlaps no variants should return empty observations in variant only mode - scoring read that overlaps no variants should return empty observations 2019-12-03 05:00:11 WARN TaskSetManager:66 - Stage 5 contains a task of very large size (4472 KB). The maximum recommended task size is 100 KB. 2019-12-03 05:00:11 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. - score snps in a read overlapping a copy number dup boundary 2019-12-03 05:00:29 WARN TaskSetManager:66 - Stage 5 contains a task of very large size (4060 KB). The maximum recommended task size is 100 KB. - score snps in a read overlapping a copy number del boundary - score snp in a read with no evidence of the snp - score snp in a read with evidence of the snp - score snp in a read with evidence of the snp, and non-variant bases - build genotype for het snp - force call possible STR/indel !!! IGNORED !!! - log space factorial - fisher test for strand bias 2019-12-03 05:00:47 WARN BiallelicGenotyper:170 - Input RDD is not persisted. Performance may be degraded. 2019-12-03 05:00:54 WARN TaskSetManager:66 - Stage 5 contains a task of very large size (10813 KB). The maximum recommended task size is 100 KB. - discover and call simple SNP 2019-12-03 05:02:06 WARN BiallelicGenotyper:170 - Input RDD is not persisted. Performance may be degraded. 2019-12-03 05:02:14 WARN TaskSetManager:66 - Stage 5 contains a task of very large size (10813 KB). The maximum recommended task size is 100 KB. - discover and call simple SNP and score all sites 2019-12-03 05:03:27 WARN BiallelicGenotyper:170 - Input RDD is not persisted. Performance may be degraded. 2019-12-03 05:03:36 WARN TaskSetManager:66 - Stage 5 contains a task of very large size (10813 KB). The maximum recommended task size is 100 KB. - discover and call short indel 2019-12-03 05:04:47 WARN BiallelicGenotyper:170 - Input RDD is not persisted. Performance may be degraded. 2019-12-03 05:04:56 WARN TaskSetManager:66 - Stage 5 contains a task of very large size (10813 KB). The maximum recommended task size is 100 KB. 2019-12-03 05:05:08 ERROR BiallelicGenotyper:387 - Processing read H06JUADXX130110:1:1109:10925:52628 failed with exception java.lang.StringIndexOutOfBoundsException: String index out of range: 0. Skipping... 2019-12-03 05:05:08 ERROR BiallelicGenotyper:387 - Processing read H06JUADXX130110:1:1116:7369:15293 failed with exception java.lang.StringIndexOutOfBoundsException: String index out of range: 0. Skipping... 2019-12-03 05:05:08 ERROR BiallelicGenotyper:387 - Processing read H06HDADXX130110:2:1115:12347:40533 failed with exception java.lang.StringIndexOutOfBoundsException: String index out of range: 0. Skipping... 2019-12-03 05:05:08 ERROR BiallelicGenotyper:387 - Processing read H06HDADXX130110:1:2110:7844:95190 failed with exception java.lang.StringIndexOutOfBoundsException: String index out of range: 0. Skipping... 2019-12-03 05:05:08 ERROR BiallelicGenotyper:387 - Processing read H06HDADXX130110:1:2203:13041:33390 failed with exception java.lang.StringIndexOutOfBoundsException: String index out of range: 0. Skipping... - discover and call het and hom snps - score a single read covering a deletion 2019-12-03 05:06:18 WARN TaskSetManager:66 - Stage 7 contains a task of very large size (10813 KB). The maximum recommended task size is 100 KB. - discover and force call hom alt deletion 2019-12-03 05:07:37 WARN TaskSetManager:66 - Stage 7 contains a task of very large size (10813 KB). The maximum recommended task size is 100 KB. - call hom alt AGCCAGTGGACGCCGACCT->A deletion at 1/875159 2019-12-03 05:08:49 WARN BiallelicGenotyper:170 - Input RDD is not persisted. Performance may be degraded. 2019-12-03 05:08:57 WARN TaskSetManager:66 - Stage 5 contains a task of very large size (10813 KB). The maximum recommended task size is 100 KB. - call hom alt TACACACACACACACACACACACACACACAC->T deletion at 1/1777263 2019-12-03 05:10:09 WARN BiallelicGenotyper:170 - Input RDD is not persisted. Performance may be degraded. 2019-12-03 05:10:18 WARN TaskSetManager:66 - Stage 5 contains a task of very large size (10813 KB). The maximum recommended task size is 100 KB. - call hom alt CAG->C deletion at 1/1067596 2019-12-03 05:11:31 WARN BiallelicGenotyper:170 - Input RDD is not persisted. Performance may be degraded. 2019-12-03 05:11:39 WARN TaskSetManager:66 - Stage 5 contains a task of very large size (10813 KB). The maximum recommended task size is 100 KB. - call hom alt C->G snp at 1/877715 2019-12-03 05:12:54 WARN BiallelicGenotyper:170 - Input RDD is not persisted. Performance may be degraded. 2019-12-03 05:13:03 WARN TaskSetManager:66 - Stage 5 contains a task of very large size (10813 KB). The maximum recommended task size is 100 KB. - call hom alt ACAG->A deletion at 1/886049 2019-12-03 05:14:17 WARN BiallelicGenotyper:170 - Input RDD is not persisted. Performance may be degraded. 2019-12-03 05:14:25 WARN TaskSetManager:66 - Stage 5 contains a task of very large size (10813 KB). The maximum recommended task size is 100 KB. - call hom alt GA->CC mnp at 1/889158–9 2019-12-03 05:15:37 WARN BiallelicGenotyper:170 - Input RDD is not persisted. Performance may be degraded. 2019-12-03 05:15:45 WARN TaskSetManager:66 - Stage 14 contains a task of very large size (10813 KB). The maximum recommended task size is 100 KB. - call hom alt C->CCCCT insertion at 1/866511 2019-12-03 05:15:50 WARN BiallelicGenotyper:170 - Input RDD is not persisted. Performance may be degraded. 2019-12-03 05:15:58 WARN TaskSetManager:66 - Stage 5 contains a task of very large size (10813 KB). The maximum recommended task size is 100 KB. - call het ATG->A deletion at 1/905130 2019-12-03 05:17:10 WARN BiallelicGenotyper:170 - Input RDD is not persisted. Performance may be degraded. 2019-12-03 05:17:18 WARN TaskSetManager:66 - Stage 5 contains a task of very large size (10813 KB). The maximum recommended task size is 100 KB. - call het ATG->A deletion at 1/905130 while scoring all sites 2019-12-03 05:18:32 WARN BiallelicGenotyper:170 - Input RDD is not persisted. Performance may be degraded. 2019-12-03 05:18:40 WARN TaskSetManager:66 - Stage 5 contains a task of very large size (10813 KB). The maximum recommended task size is 100 KB. - call het AG->A deletion at 1/907170 2019-12-03 05:19:55 WARN BiallelicGenotyper:170 - Input RDD is not persisted. Performance may be degraded. 2019-12-03 05:20:03 WARN TaskSetManager:66 - Stage 5 contains a task of very large size (10813 KB). The maximum recommended task size is 100 KB. - call het T->G snp at 1/240898 2019-12-03 05:21:19 WARN BiallelicGenotyper:170 - Input RDD is not persisted. Performance may be degraded. 2019-12-03 05:21:27 WARN TaskSetManager:66 - Stage 5 contains a task of very large size (10813 KB). The maximum recommended task size is 100 KB. - make het alt calls at biallelic snp locus 2019-12-03 05:22:40 WARN BiallelicGenotyper:170 - Input RDD is not persisted. Performance may be degraded. 2019-12-03 05:22:48 WARN TaskSetManager:66 - Stage 5 contains a task of very large size (10813 KB). The maximum recommended task size is 100 KB. - call hom alt T->TAAA insertion at 1/4120185 2019-12-03 05:24:01 WARN BiallelicGenotyper:170 - Input RDD is not persisted. Performance may be degraded. 2019-12-03 05:24:10 WARN TaskSetManager:66 - Stage 5 contains a task of very large size (10813 KB). The maximum recommended task size is 100 KB. - call het alt TTATA,TTA->T insertion at 1/5274547 ObserverSuite: - a fully clipped read will not generate any observations - generate observations for a sequence match under diploid model - generate observations for a read with an insertion under diploid model - generate observations for a read with a deletion under diploid model DiscoveredVariantSuite: - round trip conversion to/from variant SquareOffReferenceModelSuite: - don't trim a snp - trim a mnp - trim an insertion - don't trim a deletion - extract variants finds sites with a called alt - find genotype if variant is present - don't find genotype if variant is not present - excise a genotype from a reference block - square off a site with data from multiple samples DiscoverVariantsSuite: - no variants in unaligned read - no variants in rdd with unaligned read - no variants in read that is a perfect sequence match - no variants in rdd with sequence match reads - find snp in read with a 1bp sequence mismatch - find one snp in reads with 1bp sequence mismatch - find insertion in read - find insertion in reads - find deletion in read - find deletion in reads - find variants in alignment record rdd - break TT->CA mnp into two snps ObservationOperatorSuite: - zero operators are empty - non-zero operators are non-empty - cannot build mismatch with wrong ref length - collapsing a non repeated set of operators should eliminate 0 ops - collapsing a repeated set of operators with mixed match/mismatch - collapse a set of operators with repeats - collapse a set of operators with repeats and clips - make a cigar and md tag from a single sequence match - make a cigar and md tag from a single sequence mismatch - make a cigar and md tag from a single multi-base sequence match - make a cigar and md tag from a single deletion - make a cigar and md tag from a single insertion - make a cigar for a match followed by a deletion - make a cigar for an insertion flanked by matches - make a cigar for a match followed by a mismatch - make a cigar for a multi-base mismatch flanked by matches - make a cigar for a match after a clip - make a cigar for a mismatch after a clip - extract reference from a single snp - extract reference from a single deletion - extract reference from a single insertion - extract reference from a soft clipped sequence - extract reference from a hard clipped sequence - extract reference from a match flanked deletion - extract reference from a match flanked insertion - read must be mapped to extract alignment operators - extracting alignment operators will fail if cigar is unset - extracting alignment operators will fail if cigar is * - extracting alignment operators will fail if MD tag is unset - extract alignment operators from a perfect read - extract alignment operators from a read with a single mismatch - extract alignment operators from a read with a single deletion - extract alignment operators from a read with a single insertion LogUtilsSuite: - test our nifty log summer - can we compute the sum of logs correctly? - can we compute the additive inverse of logs correctly? ObservationSuite: - cannot create an observation with empty likelihoods - cannot create an observation with 1-length likelihoods - cannot create an observation with mismatching likelihood lengths - forward strand must be >= 0 - forward strand cannot exceed coverage - square map-q must be >= 0 - coverage is strictly positive - invert an observation - null an observation RealignmentBlockSuite: - folding over a clip returns the clip operator, soft clip - folding over a clip returns the clip operator, hard clip - folding over a canonical block returns the original alignment - violate an invariant of the fold function, part 1 - violate an invariant of the fold function, part 2 - apply the fold function on a realignable block - having a clip in the middle of a read is illegal - can't have two soft clips back to back - a read that is an exact sequence match is canonical - hard clip before soft clip is ok at start of read - hard clip after soft clip is ok at end of read - a read with a single snp is canonical - a read containing an indel with exact flanks is wholly realignable - a read containing an indel with exact flanks is wholly realignable, with soft clipped bases - a read containing an indel with longer flanks can be split into multiple blocks - a read containing an indel with longer flanks on both sides can be split into multiple blocks - properly handle a read that starts with a long soft clip JointAnnotatorCallerSuite: - discard reference site - calculate MAF for all called genotypes - calculate MAF ignoring uncalled genotypes - roll up variant annotations from a single genotype - roll up variant annotations across multiple genotypes - recalling genotypes is a no-op for no calls and complex hets - recall a genotype so that the state changes - allele frequency being outside of (0.0, 1.0) just computes posteriors - compute variant quality from a single genotype - compute variant quality from multiple genotypes CopyNumberMapSuite: - create an empty map - create a map with only diploid features - create a map with a mix of features PrefilterReadsSuite: - filter on read uniqueness - filter unmapped reads - filter autosomal chromosomes with grc names - filter sex chromosomes with grc names - filter mitochondrial chromosome with a grc names - filter autosomal chromosomes with hg names - filter sex chromosomes with hg names - filter mitochondrial chromosome with a hg names - filter autosomal chromosomes from generator - filter autosomal + sex chromosomes from generator - filter all chromosomes from generator - update a read whose mate is mapped to a filtered contig - filter reads mapped to autosomal chromosomes from generator - filter reads mapped to autosomal + sex chromosomes from generator - filter reads mapped to all chromosomes from generator - filter reads uniquely mapped to autosomal chromosomes from generator - filter reads uniquely mapped to autosomal + sex chromosomes from generator - filter reads uniquely mapped to all chromosomes from generator - filter rdd of reads mapped to autosomal chromosomes from generator - filter rdd of reads mapped to autosomal + sex chromosomes from generator - filter rdd of reads mapped to all chromosomes from generator - filter rdd of reads uniquely mapped to autosomal chromosomes from generator - filter rdd of reads uniquely mapped to autosomal + sex chromosomes from generator - filter rdd of reads uniquely mapped to all chromosomes from generator Run completed in 25 minutes, 35 seconds. Total number of tests run: 282 Suites: completed 23, aborted 0 Tests: succeeded 282, failed 0, canceled 0, ignored 1, pending 0 All tests passed. [INFO] [INFO] <<< scoverage-maven-plugin:1.1.1:report (default-cli) < [scoverage]test @ avocado-core_2.11 <<< [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:report (default-cli) @ avocado-core_2.11 --- [INFO] [scoverage] Generating cobertura XML report... [INFO] [scoverage] Generating scoverage XML report... [INFO] [scoverage] Generating scoverage HTML report... [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building avocado-cli: Command line interface for a distributed variant caller 0.1.1-SNAPSHOT [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ avocado-cli_2.11 --- [INFO] [INFO] --- git-commit-id-plugin:2.2.1:revision (default) @ avocado-cli_2.11 --- [INFO] [INFO] --- build-helper-maven-plugin:1.10:add-source (add-source) @ avocado-cli_2.11 --- [INFO] Source directory: /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.2.0/label/ubuntu/avocado-cli/src/main/scala added. [INFO] [INFO] --- templating-maven-plugin:1.0.0:filter-sources (filter-src) @ avocado-cli_2.11 --- [INFO] Coping files with filtering to temporary directory. [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 1 resource [INFO] Copied 1 files to output directory: /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.2.0/label/ubuntu/avocado-cli/target/generated-sources/java-templates [INFO] Source directory: /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.2.0/label/ubuntu/avocado-cli/target/generated-sources/java-templates added. [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ avocado-cli_2.11 --- [INFO] Modified 0 of 9 .scala files [INFO] [INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ avocado-cli_2.11 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.2.0/label/ubuntu/avocado-cli/src/main/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ avocado-cli_2.11 --- [WARNING] Expected all dependencies to require Scala version: 2.11.4 [WARNING] org.bdgenomics.utils:utils-misc-spark2_2.11:0.2.11 requires scala version: 2.11.4 [WARNING] org.bdgenomics.utils:utils-metrics-spark2_2.11:0.2.11 requires scala version: 2.11.4 [WARNING] org.bdgenomics.utils:utils-cli-spark2_2.11:0.2.11 requires scala version: 2.11.4 [WARNING] org.bdgenomics.utils:utils-misc-spark2_2.11:0.2.11 requires scala version: 2.11.4 [WARNING] org.bdgenomics.utils:utils-serialization-spark2_2.11:0.2.11 requires scala version: 2.11.4 [WARNING] org.bdgenomics.utils:utils-io-spark2_2.11:0.2.13 requires scala version: 2.11.8 [WARNING] Multiple versions of scala libraries detected! [INFO] /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.2.0/label/ubuntu/avocado-cli/src/main/scala:-1: info: compiling [INFO] /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.2.0/label/ubuntu/avocado-cli/target/generated-sources/java-templates:-1: info: compiling [INFO] Compiling 8 source files to /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.2.0/label/ubuntu/avocado-cli/target/scala-2.11.4/classes at 1575379537389 [INFO] prepare-compile in 0 s [INFO] compile in 4 s [INFO] [INFO] --- maven-compiler-plugin:3.5.1:compile (default-compile) @ avocado-cli_2.11 --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 1 source file to /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.2.0/label/ubuntu/avocado-cli/target/scala-2.11.4/classes [INFO] [INFO] --- build-helper-maven-plugin:1.10:add-test-source (add-test-source) @ avocado-cli_2.11 --- [INFO] Test Source directory: /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.2.0/label/ubuntu/avocado-cli/src/test/scala added. [INFO] [INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ avocado-cli_2.11 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 2 resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ avocado-cli_2.11 --- [WARNING] Expected all dependencies to require Scala version: 2.11.4 [WARNING] org.bdgenomics.utils:utils-misc-spark2_2.11:0.2.11 requires scala version: 2.11.4 [WARNING] org.bdgenomics.utils:utils-metrics-spark2_2.11:0.2.11 requires scala version: 2.11.4 [WARNING] org.bdgenomics.utils:utils-cli-spark2_2.11:0.2.11 requires scala version: 2.11.4 [WARNING] org.bdgenomics.utils:utils-misc-spark2_2.11:0.2.11 requires scala version: 2.11.4 [WARNING] org.bdgenomics.utils:utils-serialization-spark2_2.11:0.2.11 requires scala version: 2.11.4 [WARNING] org.bdgenomics.utils:utils-io-spark2_2.11:0.2.13 requires scala version: 2.11.8 [WARNING] Multiple versions of scala libraries detected! [INFO] /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.2.0/label/ubuntu/avocado-cli/src/test/scala:-1: info: compiling [INFO] Compiling 2 source files to /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.2.0/label/ubuntu/avocado-cli/target/scala-2.11.4/test-classes at 1575379542743 [INFO] prepare-compile in 0 s [INFO] compile in 3 s [INFO] [INFO] --- maven-compiler-plugin:3.5.1:testCompile (default-testCompile) @ avocado-cli_2.11 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-surefire-plugin:2.7:test (default-test) @ avocado-cli_2.11 --- [INFO] Tests are skipped. [INFO] [INFO] --- scalatest-maven-plugin:1.0:test (test) @ avocado-cli_2.11 --- Discovery starting. Discovery completed in 118 milliseconds. Run starting. Expected test count is: 2 ReassembleSuite: - k-mer length must be positive MergeDiscoveredSuite: 2019-12-03 05:25:47 WARN NativeCodeLoader:62 - Unable to load native-hadoop library for your platform... using builtin-java classes where applicable 2019-12-03 05:25:47 WARN Utils:66 - Your hostname, research-jenkins-worker-07 resolves to a loopback address: 127.0.1.1; using 192.168.10.27 instead (on interface eth0) 2019-12-03 05:25:47 WARN Utils:66 - Set SPARK_LOCAL_IP if you need to bind to another address 2019-12-03 05:25:52 WARN DatasetBoundVariantRDD:154 - Saving directly as Parquet from SQL. Options other than compression codec are ignored. 2019-12-03 05:25:53 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. SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. - merge variants discovered from two samples Run completed in 11 seconds, 409 milliseconds. Total number of tests run: 2 Suites: completed 3, aborted 0 Tests: succeeded 2, failed 0, canceled 0, ignored 0, pending 0 All tests passed. [INFO] [INFO] >>> scoverage-maven-plugin:1.1.1:report (default-cli) > [scoverage]test @ avocado-cli_2.11 >>> [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ avocado-cli_2.11 --- [INFO] [INFO] --- git-commit-id-plugin:2.2.1:revision (default) @ avocado-cli_2.11 --- [INFO] [INFO] --- build-helper-maven-plugin:1.10:add-source (add-source) @ avocado-cli_2.11 --- [INFO] Source directory: /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.2.0/label/ubuntu/avocado-cli/src/main/scala added. [INFO] [INFO] --- templating-maven-plugin:1.0.0:filter-sources (filter-src) @ avocado-cli_2.11 --- [INFO] Coping files with filtering to temporary directory. [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 1 resource [INFO] No files needs to be copied to output directory. Up to date: /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.2.0/label/ubuntu/avocado-cli/target/generated-sources/java-templates [INFO] Source directory: /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.2.0/label/ubuntu/avocado-cli/target/generated-sources/java-templates added. [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ avocado-cli_2.11 --- [INFO] Modified 0 of 9 .scala files [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:pre-compile (default-cli) @ avocado-cli_2.11 --- [INFO] [INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ avocado-cli_2.11 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.2.0/label/ubuntu/avocado-cli/src/main/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ avocado-cli_2.11 --- [WARNING] Expected all dependencies to require Scala version: 2.11.4 [WARNING] org.bdgenomics.utils:utils-misc-spark2_2.11:0.2.11 requires scala version: 2.11.4 [WARNING] org.bdgenomics.utils:utils-metrics-spark2_2.11:0.2.11 requires scala version: 2.11.4 [WARNING] org.bdgenomics.utils:utils-cli-spark2_2.11:0.2.11 requires scala version: 2.11.4 [WARNING] org.bdgenomics.utils:utils-misc-spark2_2.11:0.2.11 requires scala version: 2.11.4 [WARNING] org.bdgenomics.utils:utils-serialization-spark2_2.11:0.2.11 requires scala version: 2.11.4 [WARNING] org.bdgenomics.utils:utils-io-spark2_2.11:0.2.13 requires scala version: 2.11.8 [WARNING] Multiple versions of scala libraries detected! [INFO] /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.2.0/label/ubuntu/avocado-cli/src/main/scala:-1: info: compiling [INFO] /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.2.0/label/ubuntu/avocado-cli/target/generated-sources/java-templates:-1: info: compiling [INFO] /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.2.0/label/ubuntu/avocado-cli/target/generated-sources/annotations:-1: info: compiling [INFO] Compiling 8 source files to /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.2.0/label/ubuntu/avocado-cli/target/scala-2.11.4/scoverage-classes at 1575379558661 [INFO] [info] Cleaning datadir [/home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.2.0/label/ubuntu/avocado-cli/target/scoverage-data] [INFO] [info] Beginning coverage instrumentation [INFO] [info] Instrumentation completed [457 statements] [INFO] [info] Wrote instrumentation file [/home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.2.0/label/ubuntu/avocado-cli/target/scoverage-data/scoverage.coverage.xml] [INFO] [info] Will write measurement data to [/home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.2.0/label/ubuntu/avocado-cli/target/scoverage-data] [INFO] prepare-compile in 0 s [INFO] compile in 5 s [INFO] [INFO] --- maven-compiler-plugin:3.5.1:compile (default-compile) @ avocado-cli_2.11 --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 1 source file to /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.2.0/label/ubuntu/avocado-cli/target/scala-2.11.4/scoverage-classes [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:post-compile (default-cli) @ avocado-cli_2.11 --- [INFO] [INFO] --- build-helper-maven-plugin:1.10:add-test-source (add-test-source) @ avocado-cli_2.11 --- [INFO] Test Source directory: /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.2.0/label/ubuntu/avocado-cli/src/test/scala added. [INFO] [INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ avocado-cli_2.11 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 2 resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ avocado-cli_2.11 --- [WARNING] Expected all dependencies to require Scala version: 2.11.4 [WARNING] org.bdgenomics.utils:utils-misc-spark2_2.11:0.2.11 requires scala version: 2.11.4 [WARNING] org.bdgenomics.utils:utils-metrics-spark2_2.11:0.2.11 requires scala version: 2.11.4 [WARNING] org.bdgenomics.utils:utils-cli-spark2_2.11:0.2.11 requires scala version: 2.11.4 [WARNING] org.bdgenomics.utils:utils-misc-spark2_2.11:0.2.11 requires scala version: 2.11.4 [WARNING] org.bdgenomics.utils:utils-serialization-spark2_2.11:0.2.11 requires scala version: 2.11.4 [WARNING] org.bdgenomics.utils:utils-io-spark2_2.11:0.2.13 requires scala version: 2.11.8 [WARNING] Multiple versions of scala libraries detected! [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-compiler-plugin:3.5.1:testCompile (default-testCompile) @ avocado-cli_2.11 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-surefire-plugin:2.7:test (default-test) @ avocado-cli_2.11 --- [INFO] Tests are skipped. [INFO] [INFO] --- scalatest-maven-plugin:1.0:test (test) @ avocado-cli_2.11 --- Discovery starting. Discovery completed in 117 milliseconds. Run starting. Expected test count is: 2 ReassembleSuite: - k-mer length must be positive MergeDiscoveredSuite: 2019-12-03 05:26:05 WARN NativeCodeLoader:62 - Unable to load native-hadoop library for your platform... using builtin-java classes where applicable 2019-12-03 05:26:05 WARN Utils:66 - Your hostname, research-jenkins-worker-07 resolves to a loopback address: 127.0.1.1; using 192.168.10.27 instead (on interface eth0) 2019-12-03 05:26:05 WARN Utils:66 - Set SPARK_LOCAL_IP if you need to bind to another address 2019-12-03 05:26:10 WARN DatasetBoundVariantRDD:154 - Saving directly as Parquet from SQL. Options other than compression codec are ignored. 2019-12-03 05:26:10 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. SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. - merge variants discovered from two samples Run completed in 10 seconds, 840 milliseconds. Total number of tests run: 2 Suites: completed 3, aborted 0 Tests: succeeded 2, failed 0, canceled 0, ignored 0, pending 0 All tests passed. [INFO] [INFO] <<< scoverage-maven-plugin:1.1.1:report (default-cli) < [scoverage]test @ avocado-cli_2.11 <<< [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:report (default-cli) @ avocado-cli_2.11 --- [INFO] [scoverage] Generating cobertura XML report... [INFO] [scoverage] Generating scoverage XML report... [INFO] [scoverage] Generating scoverage HTML report... [INFO] [scoverage] Generating aggregated cobertura XML report... [INFO] [scoverage] Generating aggregated scoverage XML report... [INFO] [scoverage] Generating aggregated scoverage HTML report... [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building avocado: A Variant Caller, Distributed 0.1.1-SNAPSHOT [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- coveralls-maven-plugin:3.0.1:report (default-cli) @ avocado-parent_2.11 --- [INFO] Starting Coveralls job for jenkins (5162 / https://amplab.cs.berkeley.edu/jenkins/job/avocado/HADOOP_VERSION=2.3.0,SCALAVER=2.11,SPARK_VERSION=2.2.0,label=ubuntu/5162/) [INFO] Using repository token <secret> [INFO] Git commit 4cea777 in master [INFO] Writing Coveralls data to /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.2.0/label/ubuntu/target/coveralls.json... [INFO] Processing coverage report from /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.2.0/label/ubuntu/target/cobertura.xml [INFO] Successfully wrote Coveralls data in 157ms [INFO] Gathered code coverage metrics for 45 source files with 10503 lines of code: [INFO] - 1687 relevant lines [INFO] - 1346 covered lines [INFO] - 341 missed lines [INFO] Submitting Coveralls data to API [INFO] Successfully submitted Coveralls data in 1129ms for Job #5162.2 [INFO] https://coveralls.io/jobs/56407956 [INFO] *** It might take hours for Coveralls to update the actual coverage numbers for a job [INFO] If you see question marks in the report, please be patient [INFO] ------------------------------------------------------------------------ [INFO] Reactor Summary: [INFO] [INFO] avocado: A Variant Caller, Distributed ............. SUCCESS [ 1.608 s] [INFO] avocado-core: Core variant calling algorithms ...... SUCCESS [51:08 min] [INFO] avocado-cli: Command line interface for a distributed variant caller SUCCESS [ 41.585 s] [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ [INFO] Total time: 51:56 min [INFO] Finished at: 2019-12-03T05:26:18-08:00 [INFO] Final Memory: 73M/1475M [INFO] ------------------------------------------------------------------------ # if those pass, build the distribution package mvn -U \ -P distribution \ package \ -DskipTests \ -Dhadoop.version=${HADOOP_VERSION} \ -Dspark.version=${SPARK_VERSION} \ -DargLine=${AVOCADO_MVN_TMP_DIR} + mvn -U -P distribution package -DskipTests -Dhadoop.version=2.3.0 -Dspark.version=2.2.0 -DargLine=/tmp/avocadoTestMvn5WTHD9Q Java HotSpot(TM) 64-Bit Server VM warning: ignoring option MaxPermSize=1g; support was removed in 8.0 [INFO] Scanning for projects... [WARNING] [WARNING] Some problems were encountered while building the effective model for org.bdgenomics.avocado:avocado-core_2.11:jar:0.1.1-SNAPSHOT [WARNING] 'build.plugins.plugin.version' for org.apache.maven.plugins:maven-jar-plugin is missing. @ line 66, column 15 [WARNING] [WARNING] It is highly recommended to fix these problems because they threaten the stability of your build. [WARNING] [WARNING] For this reason, future Maven versions might no longer support building such malformed projects. [WARNING] [INFO] ------------------------------------------------------------------------ [INFO] Reactor Build Order: [INFO] [INFO] avocado: A Variant Caller, Distributed [INFO] avocado-core: Core variant calling algorithms [INFO] avocado-cli: Command line interface for a distributed variant caller [INFO] avocado: distribution [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building avocado: A Variant Caller, Distributed 0.1.1-SNAPSHOT [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ avocado-parent_2.11 --- [INFO] [INFO] --- build-helper-maven-plugin:1.10:add-source (add-source) @ avocado-parent_2.11 --- [INFO] Source directory: /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.2.0/label/ubuntu/src/main/scala added. [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ avocado-parent_2.11 --- [INFO] Modified 0 of 58 .scala files [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ avocado-parent_2.11 --- [INFO] No sources to compile [INFO] [INFO] --- build-helper-maven-plugin:1.10:add-test-source (add-test-source) @ avocado-parent_2.11 --- [INFO] Test Source directory: /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.2.0/label/ubuntu/src/test/scala added. [INFO] [INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ avocado-parent_2.11 --- [INFO] No sources to compile [INFO] [INFO] --- maven-source-plugin:2.2.1:jar-no-fork (attach-sources) @ avocado-parent_2.11 --- [INFO] [INFO] --- maven-javadoc-plugin:2.9.1:jar (attach-javadocs) @ avocado-parent_2.11 --- [INFO] Not executing Javadoc as the project is not a Java classpath-capable package [INFO] [INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) > generate-sources @ avocado-parent_2.11 >>> [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ avocado-parent_2.11 --- [INFO] [INFO] --- build-helper-maven-plugin:1.10:add-source (add-source) @ avocado-parent_2.11 --- [INFO] Source directory: /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.2.0/label/ubuntu/src/main/scala added. [INFO] [INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) < generate-sources @ avocado-parent_2.11 <<< [INFO] [INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ avocado-parent_2.11 --- [INFO] No source files found [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building avocado-core: Core variant calling algorithms 0.1.1-SNAPSHOT [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ avocado-core_2.11 --- [INFO] [INFO] --- build-helper-maven-plugin:1.10:add-source (add-source) @ avocado-core_2.11 --- [INFO] Source directory: /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.2.0/label/ubuntu/avocado-core/src/main/scala added. [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ avocado-core_2.11 --- [INFO] Modified 0 of 49 .scala files [INFO] [INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ avocado-core_2.11 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.2.0/label/ubuntu/avocado-core/src/main/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ avocado-core_2.11 --- [WARNING] Expected all dependencies to require Scala version: 2.11.4 [WARNING] org.bdgenomics.utils:utils-misc-spark2_2.11:0.2.11 requires scala version: 2.11.4 [WARNING] org.bdgenomics.utils:utils-metrics-spark2_2.11:0.2.11 requires scala version: 2.11.4 [WARNING] org.bdgenomics.utils:utils-serialization-spark2_2.11:0.2.11 requires scala version: 2.11.4 [WARNING] org.bdgenomics.utils:utils-misc-spark2_2.11:0.2.11 requires scala version: 2.11.4 [WARNING] org.bdgenomics.utils:utils-io-spark2_2.11:0.2.13 requires scala version: 2.11.8 [WARNING] Multiple versions of scala libraries detected! [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-compiler-plugin:3.5.1:compile (default-compile) @ avocado-core_2.11 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- build-helper-maven-plugin:1.10:add-test-source (add-test-source) @ avocado-core_2.11 --- [INFO] Test Source directory: /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.2.0/label/ubuntu/avocado-core/src/test/scala added. [INFO] [INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ avocado-core_2.11 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 26 resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ avocado-core_2.11 --- [WARNING] Expected all dependencies to require Scala version: 2.11.4 [WARNING] org.bdgenomics.utils:utils-misc-spark2_2.11:0.2.11 requires scala version: 2.11.4 [WARNING] org.bdgenomics.utils:utils-metrics-spark2_2.11:0.2.11 requires scala version: 2.11.4 [WARNING] org.bdgenomics.utils:utils-serialization-spark2_2.11:0.2.11 requires scala version: 2.11.4 [WARNING] org.bdgenomics.utils:utils-misc-spark2_2.11:0.2.11 requires scala version: 2.11.4 [WARNING] org.bdgenomics.utils:utils-io-spark2_2.11:0.2.13 requires scala version: 2.11.8 [WARNING] Multiple versions of scala libraries detected! [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-compiler-plugin:3.5.1:testCompile (default-testCompile) @ avocado-core_2.11 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-surefire-plugin:2.7:test (default-test) @ avocado-core_2.11 --- [INFO] Tests are skipped. [INFO] [INFO] --- scalatest-maven-plugin:1.0:test (test) @ avocado-core_2.11 --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:2.4:jar (default-jar) @ avocado-core_2.11 --- [INFO] Building jar: /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.2.0/label/ubuntu/avocado-core/target/avocado-core_2.11-0.1.1-SNAPSHOT.jar [INFO] [INFO] --- maven-source-plugin:2.2.1:jar-no-fork (attach-sources) @ avocado-core_2.11 --- [INFO] Building jar: /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.2.0/label/ubuntu/avocado-core/target/avocado-core_2.11-0.1.1-SNAPSHOT-sources.jar [INFO] [INFO] --- maven-javadoc-plugin:2.9.1:jar (attach-javadocs) @ avocado-core_2.11 --- [INFO] [INFO] --- maven-jar-plugin:2.4:test-jar (default) @ avocado-core_2.11 --- [INFO] Building jar: /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.2.0/label/ubuntu/avocado-core/target/avocado-core_2.11-0.1.1-SNAPSHOT-tests.jar [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building avocado-cli: Command line interface for a distributed variant caller 0.1.1-SNAPSHOT [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ avocado-cli_2.11 --- [INFO] [INFO] --- git-commit-id-plugin:2.2.1:revision (default) @ avocado-cli_2.11 --- [INFO] [INFO] --- build-helper-maven-plugin:1.10:add-source (add-source) @ avocado-cli_2.11 --- [INFO] Source directory: /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.2.0/label/ubuntu/avocado-cli/src/main/scala added. [INFO] [INFO] --- templating-maven-plugin:1.0.0:filter-sources (filter-src) @ avocado-cli_2.11 --- [INFO] Coping files with filtering to temporary directory. [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 1 resource [INFO] Copied 1 files to output directory: /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.2.0/label/ubuntu/avocado-cli/target/generated-sources/java-templates [INFO] Source directory: /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.2.0/label/ubuntu/avocado-cli/target/generated-sources/java-templates added. [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ avocado-cli_2.11 --- [INFO] Modified 0 of 9 .scala files [INFO] [INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ avocado-cli_2.11 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.2.0/label/ubuntu/avocado-cli/src/main/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ avocado-cli_2.11 --- [WARNING] Expected all dependencies to require Scala version: 2.11.4 [WARNING] org.bdgenomics.utils:utils-misc-spark2_2.11:0.2.11 requires scala version: 2.11.4 [WARNING] org.bdgenomics.utils:utils-metrics-spark2_2.11:0.2.11 requires scala version: 2.11.4 [WARNING] org.bdgenomics.utils:utils-cli-spark2_2.11:0.2.11 requires scala version: 2.11.4 [WARNING] org.bdgenomics.utils:utils-misc-spark2_2.11:0.2.11 requires scala version: 2.11.4 [WARNING] org.bdgenomics.utils:utils-serialization-spark2_2.11:0.2.11 requires scala version: 2.11.4 [WARNING] org.bdgenomics.utils:utils-io-spark2_2.11:0.2.13 requires scala version: 2.11.8 [WARNING] Multiple versions of scala libraries detected! [INFO] /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.2.0/label/ubuntu/avocado-cli/src/main/scala:-1: info: compiling [INFO] /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.2.0/label/ubuntu/avocado-cli/target/generated-sources/java-templates:-1: info: compiling [INFO] Compiling 8 source files to /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.2.0/label/ubuntu/avocado-cli/target/scala-2.11.4/classes at 1575379591054 [INFO] prepare-compile in 0 s [INFO] compile in 4 s [INFO] [INFO] --- maven-compiler-plugin:3.5.1:compile (default-compile) @ avocado-cli_2.11 --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 1 source file to /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.2.0/label/ubuntu/avocado-cli/target/scala-2.11.4/classes [INFO] [INFO] --- build-helper-maven-plugin:1.10:add-test-source (add-test-source) @ avocado-cli_2.11 --- [INFO] Test Source directory: /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.2.0/label/ubuntu/avocado-cli/src/test/scala added. [INFO] [INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ avocado-cli_2.11 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 2 resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ avocado-cli_2.11 --- [WARNING] Expected all dependencies to require Scala version: 2.11.4 [WARNING] org.bdgenomics.utils:utils-misc-spark2_2.11:0.2.11 requires scala version: 2.11.4 [WARNING] org.bdgenomics.utils:utils-metrics-spark2_2.11:0.2.11 requires scala version: 2.11.4 [WARNING] org.bdgenomics.utils:utils-cli-spark2_2.11:0.2.11 requires scala version: 2.11.4 [WARNING] org.bdgenomics.utils:utils-misc-spark2_2.11:0.2.11 requires scala version: 2.11.4 [WARNING] org.bdgenomics.utils:utils-serialization-spark2_2.11:0.2.11 requires scala version: 2.11.4 [WARNING] org.bdgenomics.utils:utils-io-spark2_2.11:0.2.13 requires scala version: 2.11.8 [WARNING] Multiple versions of scala libraries detected! [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-compiler-plugin:3.5.1:testCompile (default-testCompile) @ avocado-cli_2.11 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-surefire-plugin:2.7:test (default-test) @ avocado-cli_2.11 --- [INFO] Tests are skipped. [INFO] [INFO] --- scalatest-maven-plugin:1.0:test (test) @ avocado-cli_2.11 --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:2.4:jar (default-jar) @ avocado-cli_2.11 --- [INFO] Building jar: /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.2.0/label/ubuntu/avocado-cli/target/avocado-cli_2.11-0.1.1-SNAPSHOT.jar [INFO] [INFO] --- maven-source-plugin:2.2.1:jar-no-fork (attach-sources) @ avocado-cli_2.11 --- [INFO] Building jar: /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.2.0/label/ubuntu/avocado-cli/target/avocado-cli_2.11-0.1.1-SNAPSHOT-sources.jar [INFO] [INFO] --- maven-javadoc-plugin:2.9.1:jar (attach-javadocs) @ avocado-cli_2.11 --- [INFO] The goal 'org.apache.maven.plugins:maven-javadoc-plugin:2.9.1:javadoc' has not been previously called for the module: 'org.bdgenomics.avocado:avocado-core_2.11:jar:0.1.1-SNAPSHOT'. Trying to invoke it... Java HotSpot(TM) 64-Bit Server VM warning: ignoring option MaxPermSize=1g; support was removed in 8.0 [WARNING] Creating fake javadoc directory to prevent repeated invocations: /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.2.0/label/ubuntu/avocado-core/target/apidocs [ERROR] Error fetching link: /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.2.0/label/ubuntu/avocado-core/target/apidocs/package-list. Ignored it. [INFO] Loading source files for package org.bdgenomics.avocado.cli... Constructing Javadoc information... Standard Doclet version 1.8.0_191 Building tree for all the packages and classes... Generating /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.2.0/label/ubuntu/avocado-cli/target/apidocs/org/bdgenomics/avocado/cli/About.html... Generating /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.2.0/label/ubuntu/avocado-cli/target/apidocs/org/bdgenomics/avocado/cli/package-frame.html... Generating /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.2.0/label/ubuntu/avocado-cli/target/apidocs/org/bdgenomics/avocado/cli/package-summary.html... Generating /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.2.0/label/ubuntu/avocado-cli/target/apidocs/org/bdgenomics/avocado/cli/package-tree.html... Generating /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.2.0/label/ubuntu/avocado-cli/target/apidocs/constant-values.html... Generating /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.2.0/label/ubuntu/avocado-cli/target/apidocs/org/bdgenomics/avocado/cli/class-use/About.html... Generating /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.2.0/label/ubuntu/avocado-cli/target/apidocs/org/bdgenomics/avocado/cli/package-use.html... Building index for all the packages and classes... Generating /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.2.0/label/ubuntu/avocado-cli/target/apidocs/overview-tree.html... Generating /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.2.0/label/ubuntu/avocado-cli/target/apidocs/index-all.html... Generating /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.2.0/label/ubuntu/avocado-cli/target/apidocs/deprecated-list.html... Building index for all classes... Generating /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.2.0/label/ubuntu/avocado-cli/target/apidocs/allclasses-frame.html... Generating /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.2.0/label/ubuntu/avocado-cli/target/apidocs/allclasses-noframe.html... Generating /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.2.0/label/ubuntu/avocado-cli/target/apidocs/index.html... Generating /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.2.0/label/ubuntu/avocado-cli/target/apidocs/help-doc.html... [INFO] Building jar: /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.2.0/label/ubuntu/avocado-cli/target/avocado-cli_2.11-0.1.1-SNAPSHOT-javadoc.jar [INFO] [INFO] --- maven-shade-plugin:2.4.3:shade (default) @ avocado-cli_2.11 --- [INFO] Including org.bdgenomics.utils:utils-cli-spark2_2.11:jar:0.2.11 in the shaded jar. [INFO] Including org.apache.parquet:parquet-avro:jar:1.8.1 in the shaded jar. [INFO] Including org.apache.parquet:parquet-format:jar:2.3.0-incubating in the shaded jar. [INFO] Including org.bdgenomics.utils:utils-misc-spark2_2.11:jar:0.2.11 in the shaded jar. [INFO] Including org.bdgenomics.utils:utils-metrics-spark2_2.11:jar:0.2.11 in the shaded jar. [INFO] Including com.netflix.servo:servo-core:jar:0.5.5 in the shaded jar. [INFO] Including com.google.code.findbugs:annotations:jar:2.0.0 in the shaded jar. [INFO] Including org.scala-lang:scala-library:jar:2.11.4 in the shaded jar. [INFO] Including args4j:args4j:jar:2.0.23 in the shaded jar. [INFO] Including org.bdgenomics.utils:utils-serialization-spark2_2.11:jar:0.2.11 in the shaded jar. [INFO] Including org.bdgenomics.avocado:avocado-core_2.11:jar:0.1.1-SNAPSHOT in the shaded jar. [INFO] Including commons-codec:commons-codec:jar:1.4 in the shaded jar. [INFO] Including commons-logging:commons-logging:jar:1.1.3 in the shaded jar. [INFO] Including org.apache.commons:commons-compress:jar:1.4.1 in the shaded jar. [INFO] Including commons-io:commons-io:jar:1.3.2 in the shaded jar. [INFO] Including org.bdgenomics.adam:adam-core-spark2_2.11:jar:0.24.0 in the shaded jar. [INFO] Including org.bdgenomics.utils:utils-io-spark2_2.11:jar:0.2.13 in the shaded jar. [INFO] Including org.bdgenomics.utils:utils-intervalrdd-spark2_2.11:jar:0.2.13 in the shaded jar. [INFO] Including org.hammerlab:genomic-loci_2.11:jar:1.4.4 in the shaded jar. [INFO] Including org.hammerlab:args4s_2.11:jar:1.0.0 in the shaded jar. [INFO] Including org.hammerlab:iterator_2.11:jar:1.0.0 in the shaded jar. [INFO] Including org.spire-math:spire_2.11:jar:0.11.0 in the shaded jar. [INFO] Including org.spire-math:spire-macros_2.11:jar:0.11.0 in the shaded jar. [INFO] Including org.typelevel:machinist_2.11:jar:0.4.1 in the shaded jar. [INFO] Including org.hammerlab:string-utils_2.11:jar:1.0.0 in the shaded jar. [INFO] Including com.esotericsoftware.kryo:kryo:jar:2.24.0 in the shaded jar. [INFO] Including com.esotericsoftware.minlog:minlog:jar:1.2 in the shaded jar. [INFO] Including org.objenesis:objenesis:jar:2.1 in the shaded jar. [INFO] Including org.bdgenomics.bdg-formats:bdg-formats:jar:0.11.3 in the shaded jar. [INFO] Including it.unimi.dsi:fastutil:jar:6.6.5 in the shaded jar. [INFO] Including org.apache.avro:avro:jar:1.8.0 in the shaded jar. [INFO] Including org.codehaus.jackson:jackson-core-asl:jar:1.9.13 in the shaded jar. [INFO] Including org.codehaus.jackson:jackson-mapper-asl:jar:1.9.13 in the shaded jar. [INFO] Including com.thoughtworks.paranamer:paranamer:jar:2.7 in the shaded jar. [INFO] Including org.tukaani:xz:jar:1.5 in the shaded jar. [INFO] Including org.apache.parquet:parquet-scala_2.10:jar:1.8.2 in the shaded jar. [INFO] Including org.seqdoop:hadoop-bam:jar:7.9.2 in the shaded jar. [INFO] Including com.github.jsr203hadoop:jsr203hadoop:jar:1.0.3 in the shaded jar. [INFO] Including com.github.samtools:htsjdk:jar:2.13.2 in the shaded jar. [INFO] Including org.apache.commons:commons-jexl:jar:2.1.1 in the shaded jar. [INFO] Including gov.nih.nlm.ncbi:ngs-java:jar:1.2.4 in the shaded jar. [INFO] Including org.apache.httpcomponents:httpclient:jar:4.5.2 in the shaded jar. [INFO] Including org.apache.httpcomponents:httpcore:jar:4.4.4 in the shaded jar. [INFO] Including com.google.guava:guava:jar:16.0.1 in the shaded jar. [INFO] Including org.bdgenomics.adam:adam-codegen-spark2_2.11:jar:0.24.0 in the shaded jar. [INFO] Including org.bdgenomics.adam:adam-cli-spark2_2.11:jar:0.24.0 in the shaded jar. [INFO] Including org.bdgenomics.adam:adam-apis-spark2_2.11:jar:0.24.0 in the shaded jar. [INFO] Including net.codingwell:scala-guice_2.11:jar:4.1.0 in the shaded jar. [INFO] Including com.google.inject:guice:jar:4.1.0 in the shaded jar. [INFO] Including javax.inject:javax.inject:jar:1 in the shaded jar. [INFO] Including aopalliance:aopalliance:jar:1.0 in the shaded jar. [INFO] Including com.google.inject.extensions:guice-multibindings:jar:4.1.0 in the shaded jar. [INFO] Including org.apache.commons:commons-math3:jar:3.4.1 in the shaded jar. [INFO] Including com.google.code.findbugs:jsr305:jar:1.3.9 in the shaded jar. [INFO] Including org.slf4j:slf4j-api:jar:1.7.16 in the shaded jar. [INFO] Including org.xerial.snappy:snappy-java:jar:1.1.2.6 in the shaded jar. [INFO] Including org.apache.parquet:parquet-column:jar:1.8.2 in the shaded jar. [INFO] Including org.apache.parquet:parquet-common:jar:1.8.2 in the shaded jar. [INFO] Including org.apache.parquet:parquet-encoding:jar:1.8.2 in the shaded jar. [INFO] Including org.apache.parquet:parquet-hadoop:jar:1.8.2 in the shaded jar. [INFO] Including org.apache.parquet:parquet-jackson:jar:1.8.2 in the shaded jar. [INFO] Including org.scala-lang:scala-reflect:jar:2.11.7 in the shaded jar. [WARNING] annotations-2.0.0.jar, jsr305-1.3.9.jar define 34 overlapping classes: [WARNING] - javax.annotation.RegEx [WARNING] - javax.annotation.concurrent.Immutable [WARNING] - javax.annotation.meta.TypeQualifierDefault [WARNING] - javax.annotation.meta.TypeQualifier [WARNING] - javax.annotation.Syntax [WARNING] - javax.annotation.CheckForNull [WARNING] - javax.annotation.Nonnull [WARNING] - javax.annotation.CheckReturnValue [WARNING] - javax.annotation.meta.TypeQualifierNickname [WARNING] - javax.annotation.MatchesPattern [WARNING] - 24 more... [WARNING] maven-shade-plugin has detected that some class files are [WARNING] present in two or more JARs. When this happens, only one [WARNING] single version of the class is copied to the uber jar. [WARNING] Usually this is not harmful and you can skip these warnings, [WARNING] otherwise try to manually exclude artifacts based on [WARNING] mvn dependency:tree -Ddetail=true and the above output. [WARNING] See http://maven.apache.org/plugins/maven-shade-plugin/ [INFO] Replacing original artifact with shaded artifact. [INFO] Replacing /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.2.0/label/ubuntu/avocado-cli/target/avocado-cli_2.11-0.1.1-SNAPSHOT.jar with /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.2.0/label/ubuntu/avocado-cli/target/avocado-cli_2.11-0.1.1-SNAPSHOT-shaded.jar [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building avocado: distribution 0.1.1-SNAPSHOT [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ avocado-distribution_2.11 --- [INFO] [INFO] --- build-helper-maven-plugin:1.10:add-source (add-source) @ avocado-distribution_2.11 --- [INFO] Source directory: /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.2.0/label/ubuntu/avocado-distribution/src/main/scala added. [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ avocado-distribution_2.11 --- [INFO] Modified 0 of 0 .scala files [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ avocado-distribution_2.11 --- [INFO] No sources to compile [INFO] [INFO] --- build-helper-maven-plugin:1.10:add-test-source (add-test-source) @ avocado-distribution_2.11 --- [INFO] Test Source directory: /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.2.0/label/ubuntu/avocado-distribution/src/test/scala added. [INFO] [INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ avocado-distribution_2.11 --- [INFO] No sources to compile [INFO] [INFO] --- maven-source-plugin:2.2.1:jar-no-fork (attach-sources) @ avocado-distribution_2.11 --- [INFO] [INFO] --- maven-javadoc-plugin:2.9.1:jar (attach-javadocs) @ avocado-distribution_2.11 --- [INFO] Not executing Javadoc as the project is not a Java classpath-capable package [INFO] [INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) > generate-sources @ avocado-distribution_2.11 >>> [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ avocado-distribution_2.11 --- [INFO] [INFO] --- build-helper-maven-plugin:1.10:add-source (add-source) @ avocado-distribution_2.11 --- [INFO] Source directory: /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.2.0/label/ubuntu/avocado-distribution/src/main/scala added. [INFO] [INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) < generate-sources @ avocado-distribution_2.11 <<< [INFO] [INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ avocado-distribution_2.11 --- [INFO] No source files found [INFO] [INFO] --- maven-assembly-plugin:2.4.1:single (default) @ avocado-distribution_2.11 --- [INFO] Reading assembly descriptor: src/main/assembly/assembly.xml [INFO] Building tar: /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.2.0/label/ubuntu/avocado-distribution/target/avocado-distribution_2.11-0.1.1-SNAPSHOT-bin.tar.gz [INFO] Building tar: /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.2.0/label/ubuntu/avocado-distribution/target/avocado-distribution_2.11-0.1.1-SNAPSHOT-bin.tar.bz2 [INFO] Building zip: /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.2.0/label/ubuntu/avocado-distribution/target/avocado-distribution_2.11-0.1.1-SNAPSHOT-bin.zip [INFO] ------------------------------------------------------------------------ [INFO] Reactor Summary: [INFO] [INFO] avocado: A Variant Caller, Distributed ............. SUCCESS [ 3.733 s] [INFO] avocado-core: Core variant calling algorithms ...... SUCCESS [ 4.920 s] [INFO] avocado-cli: Command line interface for a distributed variant caller SUCCESS [ 18.456 s] [INFO] avocado: distribution .............................. SUCCESS [ 1.191 s] [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ [INFO] Total time: 28.475 s [INFO] Finished at: 2019-12-03T05:26:48-08:00 [INFO] Final Memory: 88M/1419M [INFO] ------------------------------------------------------------------------ # we are done with maven, so clean up the maven temp dir find ${AVOCADO_MVN_TMP_DIR} + find /tmp/avocadoTestMvn5WTHD9Q /tmp/avocadoTestMvn5WTHD9Q /tmp/avocadoTestMvn5WTHD9Q/64836218219336141 /tmp/avocadoTestMvn5WTHD9Q/64836218219336141/.trio.vcf.crc /tmp/avocadoTestMvn5WTHD9Q/64836218219336141/trio.vcf /tmp/avocadoTestMvn5WTHD9Q/9019294472111348249 /tmp/avocadoTestMvn5WTHD9Q/9019294472111348249/.trio.vcf.crc /tmp/avocadoTestMvn5WTHD9Q/9019294472111348249/trio.vcf rm -rf ${AVOCADO_MVN_TMP_DIR} + rm -rf /tmp/avocadoTestMvn5WTHD9Q find . -name pom.xml \ -exec sed -i.bak \ -e "s:sun.io.serialization.extendedDebugInfo=true -Djava.io.tmpdir=${AVOCADO_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/avocadoTestMvn5WTHD9Q:sun.io.serialization.extendedDebugInfo=true:g' '{}' ';' find . -name "*.bak" -exec rm -f {} \; + find . -name '*.bak' -exec rm -f '{}' ';' if test -n "$(git status --porcelain)" then echo "Applying move_to_xyz script marred a pom.xml file." echo "Exiting..." exit 1 fi git status --porcelain ++ git status --porcelain + test -n '' ./scripts/format-source + ./scripts/format-source +++ dirname ./scripts/format-source ++ cd ./scripts ++ pwd + DIR=/home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.2.0/label/ubuntu/scripts + pushd /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.2.0/label/ubuntu/scripts/.. ~/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.2.0/label/ubuntu ~/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.2.0/label/ubuntu + mvn org.scalariform:scalariform-maven-plugin:format license:format Java HotSpot(TM) 64-Bit Server VM warning: ignoring option MaxPermSize=1g; support was removed in 8.0 [INFO] Scanning for projects... [WARNING] [WARNING] Some problems were encountered while building the effective model for org.bdgenomics.avocado:avocado-core_2.11:jar:0.1.1-SNAPSHOT [WARNING] 'build.plugins.plugin.version' for org.apache.maven.plugins:maven-jar-plugin is missing. @ line 66, column 15 [WARNING] [WARNING] It is highly recommended to fix these problems because they threaten the stability of your build. [WARNING] [WARNING] For this reason, future Maven versions might no longer support building such malformed projects. [WARNING] [INFO] ------------------------------------------------------------------------ [INFO] Reactor Build Order: [INFO] [INFO] avocado: A Variant Caller, Distributed [INFO] avocado-core: Core variant calling algorithms [INFO] avocado-cli: Command line interface for a distributed variant caller [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building avocado: A Variant Caller, Distributed 0.1.1-SNAPSHOT [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ avocado-parent_2.11 --- [INFO] Modified 0 of 58 .scala files [INFO] [INFO] --- maven-license-plugin:1.10.b1:format (default-cli) @ avocado-parent_2.11 --- [INFO] Updating license headers... [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building avocado-core: Core variant calling algorithms 0.1.1-SNAPSHOT [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ avocado-core_2.11 --- [INFO] Modified 0 of 49 .scala files [INFO] [INFO] --- maven-license-plugin:1.10.b1:format (default-cli) @ avocado-core_2.11 --- [INFO] Updating license headers... [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building avocado-cli: Command line interface for a distributed variant caller 0.1.1-SNAPSHOT [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ avocado-cli_2.11 --- [INFO] Modified 0 of 9 .scala files [INFO] [INFO] --- maven-license-plugin:1.10.b1:format (default-cli) @ avocado-cli_2.11 --- [INFO] Updating license headers... [INFO] ------------------------------------------------------------------------ [INFO] Reactor Summary: [INFO] [INFO] avocado: A Variant Caller, Distributed ............. SUCCESS [ 3.005 s] [INFO] avocado-core: Core variant calling algorithms ...... SUCCESS [ 1.138 s] [INFO] avocado-cli: Command line interface for a distributed variant caller SUCCESS [ 0.093 s] [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ [INFO] Total time: 4.594 s [INFO] Finished at: 2019-12-03T05:26:55-08:00 [INFO] Final Memory: 16M/1101M [INFO] ------------------------------------------------------------------------ + popd ~/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.2.0/label/ubuntu if test -n "$(git status --porcelain)" then echo "Please run './scripts/format-source'" exit 1 fi git status --porcelain ++ git status --porcelain + test -n '' echo + echo echo "All the tests passed" + echo 'All the tests passed' All the tests passed echo + echo + '[' 2.2.0 == 2.2.0 ']' + '[' 2.3.0 == 2.6.0 ']' Recording test results Finished: SUCCESS