{"action":"created","issue":{"url":"https://api.github.com/repos/broadinstitute/gatk-protected/issues/826","repository_url":"https://api.github.com/repos/broadinstitute/gatk-protected","labels_url":"https://api.github.com/repos/broadinstitute/gatk-protected/issues/826/labels{/name}","comments_url":"https://api.github.com/repos/broadinstitute/gatk-protected/issues/826/comments","events_url":"https://api.github.com/repos/broadinstitute/gatk-protected/issues/826/events","html_url":"https://github.com/broadinstitute/gatk-protected/pull/826","id":195653418,"number":826,"title":"Rev gatk public to 4.alpha.2-110-ga71331d-20161129.223512-1","user":{"login":"droazen","id":798637,"avatar_url":"https://avatars.githubusercontent.com/u/798637?v=3","gravatar_id":"","url":"https://api.github.com/users/droazen","html_url":"https://github.com/droazen","followers_url":"https://api.github.com/users/droazen/followers","following_url":"https://api.github.com/users/droazen/following{/other_user}","gists_url":"https://api.github.com/users/droazen/gists{/gist_id}","starred_url":"https://api.github.com/users/droazen/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/droazen/subscriptions","organizations_url":"https://api.github.com/users/droazen/orgs","repos_url":"https://api.github.com/users/droazen/repos","events_url":"https://api.github.com/users/droazen/events{/privacy}","received_events_url":"https://api.github.com/users/droazen/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":{"login":"droazen","id":798637,"avatar_url":"https://avatars.githubusercontent.com/u/798637?v=3","gravatar_id":"","url":"https://api.github.com/users/droazen","html_url":"https://github.com/droazen","followers_url":"https://api.github.com/users/droazen/followers","following_url":"https://api.github.com/users/droazen/following{/other_user}","gists_url":"https://api.github.com/users/droazen/gists{/gist_id}","starred_url":"https://api.github.com/users/droazen/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/droazen/subscriptions","organizations_url":"https://api.github.com/users/droazen/orgs","repos_url":"https://api.github.com/users/droazen/repos","events_url":"https://api.github.com/users/droazen/events{/privacy}","received_events_url":"https://api.github.com/users/droazen/received_events","type":"User","site_admin":false},"assignees":[{"login":"droazen","id":798637,"avatar_url":"https://avatars.githubusercontent.com/u/798637?v=3","gravatar_id":"","url":"https://api.github.com/users/droazen","html_url":"https://github.com/droazen","followers_url":"https://api.github.com/users/droazen/followers","following_url":"https://api.github.com/users/droazen/following{/other_user}","gists_url":"https://api.github.com/users/droazen/gists{/gist_id}","starred_url":"https://api.github.com/users/droazen/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/droazen/subscriptions","organizations_url":"https://api.github.com/users/droazen/orgs","repos_url":"https://api.github.com/users/droazen/repos","events_url":"https://api.github.com/users/droazen/events{/privacy}","received_events_url":"https://api.github.com/users/droazen/received_events","type":"User","site_admin":false}],"milestone":null,"comments":9,"created_at":"2016-12-14T21:40:56Z","updated_at":"2016-12-16T16:46:24Z","closed_at":null,"pull_request":{"url":"https://api.github.com/repos/broadinstitute/gatk-protected/pulls/826","html_url":"https://github.com/broadinstitute/gatk-protected/pull/826","diff_url":"https://github.com/broadinstitute/gatk-protected/pull/826.diff","patch_url":"https://github.com/broadinstitute/gatk-protected/pull/826.patch"},"body":"-Fix failing HaplotypeCallerIntegrationTest by adjusting command lines\r\n to account for the change in public in commit:\r\n 50cb7f70a28e1b7f8821ecfd2d2665aefaaae54d \"Change list argument behavior to replace\"\r\n\r\n-Add a temporary shim in PairHMMLikelihoodCalculationEngine to allow\r\n us to compile pending the merge of https://github.com/broadinstitute/gatk-protected/pull/813"},"comment":{"url":"https://api.github.com/repos/broadinstitute/gatk-protected/issues/comments/267637792","html_url":"https://github.com/broadinstitute/gatk-protected/pull/826#issuecomment-267637792","issue_url":"https://api.github.com/repos/broadinstitute/gatk-protected/issues/826","id":267637792,"user":{"login":"lbergelson","id":4700332,"avatar_url":"https://avatars.githubusercontent.com/u/4700332?v=3","gravatar_id":"","url":"https://api.github.com/users/lbergelson","html_url":"https://github.com/lbergelson","followers_url":"https://api.github.com/users/lbergelson/followers","following_url":"https://api.github.com/users/lbergelson/following{/other_user}","gists_url":"https://api.github.com/users/lbergelson/gists{/gist_id}","starred_url":"https://api.github.com/users/lbergelson/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/lbergelson/subscriptions","organizations_url":"https://api.github.com/users/lbergelson/orgs","repos_url":"https://api.github.com/users/lbergelson/repos","events_url":"https://api.github.com/users/lbergelson/events{/privacy}","received_events_url":"https://api.github.com/users/lbergelson/received_events","type":"User","site_admin":false},"created_at":"2016-12-16T16:46:24Z","updated_at":"2016-12-16T16:46:24Z","body":"@gspowley I was able to recreate a SIGSEV by running the gatk-protected tests in this branch within a docker image of ubuntu 14.04.  \r\n\r\nthis is the stdout/sdterr leading up to the error:\r\n\r\n```\r\nGradle suite > Gradle test > org.broadinstitute.hellbender.tools.HaplotypeCallerSparkIntegrationTest.testVCFModeIsConcordantWithGATK3_5Results STANDARD_ERROR\r\n    [December 15, 2016 10:21:40 PM UTC] org.broadinstitute.hellbender.tools.HaplotypeCallerSpark  --output /tmp/testVCFModeIsConcordantWithGATK3Results2104641340351559111.vcf --pair_hmm_implementation AVX_LOGLESS_CACHING --reference /gatk-protected/src/test/resources/large/human_g1k_v37.20.21.2bit --input /gatk-protected/src/test/resources/large/CEUTrio.HiSeq.WGS.b37.NA12878.20.21.bam --intervals 20:10000000-10100000 --verbosity ERROR  --readShardSize 5000 --readShardPadding 100 --minAssemblyRegionSize 50 --maxAssemblyRegionSize 300 --assemblyRegionPadding 100 --activeProbabilityThreshold 0.002 --maxProbPropagationDistance 50 --GVCFGQBands 1 --GVCFGQBands 2 --GVCFGQBands 3 --GVCFGQBands 4 --GVCFGQBands 5 --GVCFGQBands 6 --GVCFGQBands 7 --GVCFGQBands 8 --GVCFGQBands 9 --GVCFGQBands 10 --GVCFGQBands 11 --GVCFGQBands 12 --GVCFGQBands 13 --GVCFGQBands 14 --GVCFGQBands 15 --GVCFGQBands 16 --GVCFGQBands 17 --GVCFGQBands 18 --GVCFGQBands 19 --GVCFGQBands 20 --GVCFGQBands 21 --GVCFGQBands 22 --GVCFGQBands 23 --GVCFGQBands 24 --GVCFGQBands 25 --GVCFGQBands 26 --GVCFGQBands 27 --GVCFGQBands 28 --GVCFGQBands 29 --GVCFGQBands 30 --GVCFGQBands 31 --GVCFGQBands 32 --GVCFGQBands 33 --GVCFGQBands 34 --GVCFGQBands 35 --GVCFGQBands 36 --GVCFGQBands 37 --GVCFGQBands 38 --GVCFGQBands 39 --GVCFGQBands 40 --GVCFGQBands 41 --GVCFGQBands 42 --GVCFGQBands 43 --GVCFGQBands 44 --GVCFGQBands 45 --GVCFGQBands 46 --GVCFGQBands 47 --GVCFGQBands 48 --GVCFGQBands 49 --GVCFGQBands 50 --GVCFGQBands 51 --GVCFGQBands 52 --GVCFGQBands 53 --GVCFGQBands 54 --GVCFGQBands 55 --GVCFGQBands 56 --GVCFGQBands 57 --GVCFGQBands 58 --GVCFGQBands 59 --GVCFGQBands 60 --GVCFGQBands 70 --GVCFGQBands 80 --GVCFGQBands 90 --GVCFGQBands 99 --indelSizeToEliminateInRefModel 10 --useAllelesTrigger false --dontTrimActiveRegions false --maxDiscARExtension 25 --maxGGAARExtension 300 --paddingAroundIndels 150 --paddingAroundSNPs 20 --kmerSize 10 --kmerSize 25 --dontIncreaseKmerSizesForCycles false --allowNonUniqueKmersInRef false --numPruningSamples 1 --recoverDanglingHeads false --doNotRecoverDanglingBranches false --minDanglingBranchLength 4 --consensus false --maxNumHaplotypesInPopulation 128 --errorCorrectKmers false --minPruning 2 --debugGraphTransformations false --kmerLengthForReadErrorCorrection 25 --minObservationsForKmerToBeSolid 20 --likelihoodCalculationEngine PairHMM --base_quality_score_threshold 18 --gcpHMM 10 --pcr_indel_model CONSERVATIVE --phredScaledGlobalReadMismappingRate 45 --debug false --useFilteredReadsForAnnotations false --emitRefConfidence NONE --bamWriterType CALLED_HAPLOTYPES --disableOptimizations false --justDetermineActiveRegions false --dontGenotype false --dontUseSoftClippedBases false --captureAssemblyFailureBAM false --errorCorrectReads false --doNotRunPhysicalPhasing false --min_base_quality_score 10 --group StandardAnnotation --group StandardHCAnnotation --useNewAFCalculator false --annotateNDA false --heterozygosity 0.001 --indel_heterozygosity 1.25E-4 --heterozygosity_stdev 0.01 --standard_min_confidence_threshold_for_calling 30.0 --standard_min_confidence_threshold_for_emitting 30.0 --max_alternate_alleles 6 --max_genotype_count 1024 --sample_ploidy 2 --genotyping_mode DISCOVERY --contamination_fraction_to_filter 0.0 --output_mode EMIT_VARIANTS_ONLY --allSitePLs false --readValidationStringency SILENT --interval_set_rule UNION --interval_padding 0 --interval_exclusion_padding 0 --bamPartitionSize 0 --disableSequenceDictionaryValidation false --shardedOutput false --numReducers 0 --sparkMaster local[*] --help false --version false --QUIET false --use_jdk_deflater false --disableAllReadFilters false --mappingQuality 20\r\nTest: Test method testVCFModeIsConcordantWithGATK3_5Results(org.broadinstitute.hellbender.tools.HaplotypeCallerSparkIntegrationTest) produced standard out/err: [December 15, 2016 10:21:40 PM UTC] Executing as root@cf09b9cdcb5d on Linux 4.4.38-boot2docker amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_111-b14; Version: Version:null\r\n\r\n    [December 15, 2016 10:21:40 PM UTC] Executing as root@cf09b9cdcb5d on Linux 4.4.38-boot2docker amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_111-b14; Version: Version:null\r\n#\r\n# A fatal error has been detected by the Java Runtime Environment:\r\n#\r\n#  SIGSEGV (0xb) at pc=0x00007f5f3ddf2f60, pid=248, tid=0x00007f5f27623700\r\n#\r\n# JRE version: Java(TM) SE Runtime Environment (8.0_111-b14) (build 1.8.0_111-b14)\r\n# Java VM: Java HotSpot(TM) 64-Bit Server VM (25.111-b14 mixed mode linux-amd64 compressed oops)\r\n# Problematic frame:\r\n# V  [libjvm.so+0x98ff60]  PSRootsClosure<false>::do_oop(oopDesc**)+0x20\r\n#\r\n# Failed to write core dump. Core dumps have been disabled. To enable core dumping, try \"ulimit -c unlimited\" before starting Java again\r\n#\r\n# An error report file with more information is saved as:\r\n# /gatk-protected/hs_err_pid248.log\r\n#\r\n# If you would like to submit a bug report, please visit:\r\n#   http://bugreport.java.com/bugreport/crash.jsp\r\n#\r\n\r\n4157 tests completed, 17 failed, 6 skipped\r\n:test FAILED\r\n\r\nFAILURE: Build failed with an exception.\r\n\r\n* What went wrong:\r\nExecution failed for task ':test'.\r\n> Process 'Gradle Test Executor 1' finished with non-zero exit value 134\r\n\r\n* Try:\r\nRun with --stacktrace option to get the stack trace. Run with --info or --debug option to get more log output.\r\n\r\nBUILD FAILED\r\n```\r\n\r\nHere's the hs_err file:\r\n[hs_err_pid248.log.txt](https://github.com/broadinstitute/gatk-protected/files/657704/hs_err_pid248.log.txt)\r\n\r\nI also produce a a different libjvm error when running again:\r\n\r\n```\r\nGradle suite > Gradle test > org.broadinstitute.hellbender.tools.HaplotypeCallerSparkIntegrationTest.testVCFModeIsConcordantWithGATK3_5ResultsAlleleSpecificAnnotations STANDARD_ERROR\r\n    [December 16, 2016 4:40:26 PM UTC] org.broadinstitute.hellbender.tools.HaplotypeCallerSpark done. Elapsed time: 0.03 minutes.\r\nTest: Test method testVCFModeIsConcordantWithGATK3_5ResultsAlleleSpecificAnnotations(org.broadinstitute.hellbender.tools.HaplotypeCallerSparkIntegrationTest) produced standard out/err: Runtime.totalMemory()=2253914112\r\n\r\n    Runtime.totalMemory()=2253914112\r\n> Building 85% > :test > 82 tests completed*** Error in `/usr/lib/jvm/java-8-oracle/bin/java': double free or corruption (out): 0x00007f4a953824e0 ***\r\n:test FAILED\r\n```\r\n\r\nThat didn't produce a hs_err file or any sort of dump though."}}
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