{"action":"created","issue":{"url":"https://api.github.com/repos/broadinstitute/gatk/issues/4458","repository_url":"https://api.github.com/repos/broadinstitute/gatk","labels_url":"https://api.github.com/repos/broadinstitute/gatk/issues/4458/labels{/name}","comments_url":"https://api.github.com/repos/broadinstitute/gatk/issues/4458/comments","events_url":"https://api.github.com/repos/broadinstitute/gatk/issues/4458/events","html_url":"https://github.com/broadinstitute/gatk/issues/4458","id":299951531,"number":4458,"title":" StructuralVariationDiscoveryPipelineSpark: Invalid interval exception ","user":{"login":"jjfarrell","id":1960717,"avatar_url":"https://avatars0.githubusercontent.com/u/1960717?v=4","gravatar_id":"","url":"https://api.github.com/users/jjfarrell","html_url":"https://github.com/jjfarrell","followers_url":"https://api.github.com/users/jjfarrell/followers","following_url":"https://api.github.com/users/jjfarrell/following{/other_user}","gists_url":"https://api.github.com/users/jjfarrell/gists{/gist_id}","starred_url":"https://api.github.com/users/jjfarrell/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jjfarrell/subscriptions","organizations_url":"https://api.github.com/users/jjfarrell/orgs","repos_url":"https://api.github.com/users/jjfarrell/repos","events_url":"https://api.github.com/users/jjfarrell/events{/privacy}","received_events_url":"https://api.github.com/users/jjfarrell/received_events","type":"User","site_admin":false},"labels":[{"id":284415544,"url":"https://api.github.com/repos/broadinstitute/gatk/labels/SV","name":"SV","color":"207de5","default":false},{"id":153552584,"url":"https://api.github.com/repos/broadinstitute/gatk/labels/bug","name":"bug","color":"fc2929","default":true}],"state":"closed","locked":false,"assignee":{"login":"SHuang-Broad","id":16310888,"avatar_url":"https://avatars3.githubusercontent.com/u/16310888?v=4","gravatar_id":"","url":"https://api.github.com/users/SHuang-Broad","html_url":"https://github.com/SHuang-Broad","followers_url":"https://api.github.com/users/SHuang-Broad/followers","following_url":"https://api.github.com/users/SHuang-Broad/following{/other_user}","gists_url":"https://api.github.com/users/SHuang-Broad/gists{/gist_id}","starred_url":"https://api.github.com/users/SHuang-Broad/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/SHuang-Broad/subscriptions","organizations_url":"https://api.github.com/users/SHuang-Broad/orgs","repos_url":"https://api.github.com/users/SHuang-Broad/repos","events_url":"https://api.github.com/users/SHuang-Broad/events{/privacy}","received_events_url":"https://api.github.com/users/SHuang-Broad/received_events","type":"User","site_admin":false},"assignees":[{"login":"SHuang-Broad","id":16310888,"avatar_url":"https://avatars3.githubusercontent.com/u/16310888?v=4","gravatar_id":"","url":"https://api.github.com/users/SHuang-Broad","html_url":"https://github.com/SHuang-Broad","followers_url":"https://api.github.com/users/SHuang-Broad/followers","following_url":"https://api.github.com/users/SHuang-Broad/following{/other_user}","gists_url":"https://api.github.com/users/SHuang-Broad/gists{/gist_id}","starred_url":"https://api.github.com/users/SHuang-Broad/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/SHuang-Broad/subscriptions","organizations_url":"https://api.github.com/users/SHuang-Broad/orgs","repos_url":"https://api.github.com/users/SHuang-Broad/repos","events_url":"https://api.github.com/users/SHuang-Broad/events{/privacy}","received_events_url":"https://api.github.com/users/SHuang-Broad/received_events","type":"User","site_admin":false}],"milestone":null,"comments":5,"created_at":"2018-02-24T16:09:44Z","updated_at":"2018-03-06T19:21:31Z","closed_at":"2018-03-06T19:21:31Z","author_association":"NONE","body":"When running  StructuralVariationDiscoveryPipelineSpark (GATK 4.0.1.1) on a hadoop cluster, the following exception occurs. The pipeline has been running fine on other cram files.\r\n\r\n**Caused by: java.lang.IllegalArgumentException: Invalid interval. Contig:chrUn_JTFH01000312v1_decoy start:0 end:0**\r\n\r\n Below is the stack and other details. \r\n\r\nThe pipeline looks like it is running through all the contigs and is not limited to  chr1-chr22, ChrY, ChrX and ChrM. Would it help running the software if the extra 3000+ contig names in the GRCh38 reference are excluded? If so, what is the best way to exclude processing the extra contigs?\r\n\r\n```\r\n18/02/23 23:06:22 INFO scheduler.TaskSetManager: Finished task 24.0 in stage 15.0 (TID 29435) in 2906 ms on scc-q04.scc.bu.edu (executor 1) (48/70)\r\n18/02/23 23:06:23 INFO scheduler.TaskSetManager: Finished task 52.0 in stage 15.0 (TID 29463) in 2354 ms on scc-q04.scc.bu.edu (executor 1) (49/70)\r\n18/02/23 23:06:23 INFO scheduler.TaskSetManager: Finished task 37.0 in stage 15.0 (TID 29448) in 2653 ms on scc-q03.scc.bu.edu (executor 6) (50/70)\r\n18/02/23 23:06:23 WARN scheduler.TaskSetManager: Lost task 27.0 in stage 15.0 (TID 29438, scc-q13.scc.bu.edu, executor 7): org.broadinstitute.hellbender.exceptions.GATKException: Erred when inferring breakpoint location and event type                                                                                 from chimeric alignment:\r\nasm010450:tig00000      1_189_chrUn_JTFH01000312v1_decoy:663-851_-_189M512H_60_8_149_O  153_701_chrUn_JTFH01000312v1_decoy:1-549_+_152S549M_60_0_549_O\r\n        at org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.NovelAdjacencyReferenceLocations.<init>(NovelAdjacencyReferenceLocations.java:51)\r\n        at org.broadinstitute.hellbender.tools.spark.sv.discovery.DiscoverVariantsFromContigAlignmentsSAMSpark.lambda$null$0(DiscoverVariantsFromContigAlignmentsSAMSpark.java:175)\r\n        at java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:193)\r\n        at java.util.ArrayList$ArrayListSpliterator.tryAdvance(ArrayList.java:1351)\r\n        at java.util.stream.StreamSpliterators$WrappingSpliterator.lambda$initPartialTraversalState$0(StreamSpliterators.java:294)\r\n        at java.util.stream.StreamSpliterators$AbstractWrappingSpliterator.fillBuffer(StreamSpliterators.java:206)\r\n        at java.util.stream.StreamSpliterators$AbstractWrappingSpliterator.doAdvance(StreamSpliterators.java:161)\r\n        at java.util.stream.StreamSpliterators$WrappingSpliterator.tryAdvance(StreamSpliterators.java:300)\r\n        at java.util.Spliterators$1Adapter.hasNext(Spliterators.java:681)\r\n        at scala.collection.convert.Wrappers$JIteratorWrapper.hasNext(Wrappers.scala:42)\r\n        at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:438)\r\n        at org.apache.spark.shuffle.sort.BypassMergeSortShuffleWriter.write(BypassMergeSortShuffleWriter.java:149)\r\n        at org.apache.spark.scheduler.ShuffleMapTask.runTask(ShuffleMapTask.scala:96)\r\n        at org.apache.spark.scheduler.ShuffleMapTask.runTask(ShuffleMapTask.scala:53)\r\n        at org.apache.spark.scheduler.Task.run(Task.scala:99)\r\n        at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:282)\r\n        at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)\r\n        at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)\r\n        at java.lang.Thread.run(Thread.java:745)\r\nCaused by: java.lang.IllegalArgumentException: Invalid interval. Contig:chrUn_JTFH01000312v1_decoy start:0 end:0\r\n        at org.broadinstitute.hellbender.utils.Utils.validateArg(Utils.java:687)\r\n        at org.broadinstitute.hellbender.utils.SimpleInterval.validatePositions(SimpleInterval.java:61)\r\n        at org.broadinstitute.hellbender.utils.SimpleInterval.<init>(SimpleInterval.java:37)\r\n        at org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.NovelAdjacencyReferenceLocations$BreakpointsInference.getLeftJustifiedBreakpoints(NovelAdjacencyReferenceLocations.java:86)\r\n        at org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.NovelAdjacencyReferenceLocations.leftJustifyBreakpoints(NovelAdjacencyReferenceLocations.java:301)\r\n        at org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.NovelAdjacencyReferenceLocations.<init>(NovelAdjacencyReferenceLocations.java:46)\r\n        ... 18 more\r\n\r\n\r\n8/02/23 23:06:24 INFO storage.BlockManagerMaster: BlockManagerMaster stopped\r\n18/02/23 23:06:24 INFO scheduler.OutputCommitCoordinator$OutputCommitCoordinatorEndpoint: OutputCommitCoordinator stopped!\r\n18/02/23 23:06:24 INFO spark.SparkContext: Successfully stopped SparkContext\r\n23:06:24.240 INFO  StructuralVariationDiscoveryPipelineSpark - Shutting down engine\r\n[February 23, 2018 11:06:24 PM EST] org.broadinstitute.hellbender.tools.spark.sv.StructuralVariationDiscoveryPipelineSpark done. Elapsed time: 73.92 minutes.\r\nRuntime.totalMemory()=10458497024\r\norg.apache.spark.SparkException: Job aborted due to stage failure: Task 27 in stage 15.0 failed 4 times, most recent failure: Lost task 27.3 in stage 15.0 (TID 29483, scc-q15.scc.bu.edu, executor 13): org.broadinstitute.hellbender.exc                                                                                eptions.GATKException: Erred when inferring breakpoint location and event type from chimeric alignment:\r\nasm010450:tig00000      1_189_chrUn_JTFH01000312v1_decoy:663-851_-_189M512H_60_8_149_O  153_701_chrUn_JTFH01000312v1_decoy:1-549_+_152S549M_60_0_549_O\r\n        at org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.NovelAdjacencyReferenceLocations.<init>(NovelAdjacencyReferenceLocations.java:51)\r\n        at org.broadinstitute.hellbender.tools.spark.sv.discovery.DiscoverVariantsFromContigAlignmentsSAMSpark.lambda$null$0(DiscoverVariantsFromContigAlignmentsSAMSpark.java:175)\r\n        at java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:193)\r\n        at java.util.ArrayList$ArrayListSpliterator.tryAdvance(ArrayList.java:1351)\r\n        at java.util.stream.StreamSpliterators$WrappingSpliterator.lambda$initPartialTraversalState$0(StreamSpliterators.java:294)\r\n        at java.util.stream.StreamSpliterators$AbstractWrappingSpliterator.fillBuffer(StreamSpliterators.java:206)\r\n        at java.util.stream.StreamSpliterators$AbstractWrappingSpliterator.doAdvance(StreamSpliterators.java:161)\r\n        at java.util.stream.StreamSpliterators$WrappingSpliterator.tryAdvance(StreamSpliterators.java:300)\r\n        at java.util.Spliterators$1Adapter.hasNext(Spliterators.java:681)\r\n        at scala.collection.convert.Wrappers$JIteratorWrapper.hasNext(Wrappers.scala:42)\r\n        at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:438)\r\n        at org.apache.spark.shuffle.sort.BypassMergeSortShuffleWriter.write(BypassMergeSortShuffleWriter.java:149)\r\n        at org.apache.spark.scheduler.ShuffleMapTask.runTask(ShuffleMapTask.scala:96)\r\n        at org.apache.spark.scheduler.ShuffleMapTask.runTask(ShuffleMapTask.scala:53)\r\n        at org.apache.spark.scheduler.Task.run(Task.scala:99)\r\n        at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:282)\r\n        at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)\r\n        at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)\r\n        at java.lang.Thread.run(Thread.java:745)\r\nCaused by: java.lang.IllegalArgumentException: Invalid interval. Contig:chrUn_JTFH01000312v1_decoy start:0 end:0\r\n        at org.broadinstitute.hellbender.utils.Utils.validateArg(Utils.java:687)\r\n        at org.broadinstitute.hellbender.utils.SimpleInterval.validatePositions(SimpleInterval.java:61)\r\n        at org.broadinstitute.hellbender.utils.SimpleInterval.<init>(SimpleInterval.java:37)\r\n        at org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.NovelAdjacencyReferenceLocations$BreakpointsInference.getLeftJustifiedBreakpoints(NovelAdjacencyReferenceLocations.java:86)\r\n        at org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.NovelAdjacencyReferenceLocations.leftJustifyBreakpoints(NovelAdjacencyReferenceLocations.java:301)\r\n        at org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.NovelAdjacencyReferenceLocations.<init>(NovelAdjacencyReferenceLocations.java:46)\r\n        ... 18 more\r\n\r\nDriver stacktrace:\r\n        at org.apache.spark.scheduler.DAGScheduler.org$apache$spark$scheduler$DAGScheduler$$failJobAndIndependentStages(DAGScheduler.scala:1435)\r\n        at org.apache.spark.scheduler.DAGScheduler$$anonfun$abortStage$1.apply(DAGScheduler.scala:1423)\r\n        at org.apache.spark.scheduler.DAGScheduler$$anonfun$abortStage$1.apply(DAGScheduler.scala:1422)\r\n        at scala.collection.mutable.ResizableArray$class.foreach(ResizableArray.scala:59)\r\n        at scala.collection.mutable.ArrayBuffer.foreach(ArrayBuffer.scala:48)\r\n        at org.apache.spark.scheduler.DAGScheduler.abortStage(DAGScheduler.scala:1422)\r\n        at org.apache.spark.scheduler.DAGScheduler$$anonfun$handleTaskSetFailed$1.apply(DAGScheduler.scala:802)\r\n        at org.apache.spark.scheduler.DAGScheduler$$anonfun$handleTaskSetFailed$1.apply(DAGScheduler.scala:802)\r\n        at scala.Option.foreach(Option.scala:257)\r\n        at org.apache.spark.scheduler.DAGScheduler.handleTaskSetFailed(DAGScheduler.scala:802)\r\n        at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.doOnReceive(DAGScheduler.scala:1650)\r\n        at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:1605)\r\n        at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:1594)\r\n        at org.apache.spark.util.EventLoop$$anon$1.run(EventLoop.scala:48)\r\n        at org.apache.spark.scheduler.DAGScheduler.runJob(DAGScheduler.scala:628)\r\n        at org.apache.spark.SparkContext.runJob(SparkContext.scala:1918)\r\n        at org.apache.spark.SparkContext.runJob(SparkContext.scala:1931)\r\n        at org.apache.spark.SparkContext.runJob(SparkContext.scala:1944)\r\n        at org.apache.spark.SparkContext.runJob(SparkContext.scala:1958)\r\n        at org.apache.spark.rdd.RDD$$anonfun$collect$1.apply(RDD.scala:935)\r\n        at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:151)\r\n        at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:112)\r\n        at org.apache.spark.rdd.RDD.withScope(RDD.scala:362)\r\n        at org.apache.spark.rdd.RDD.collect(RDD.scala:934)\r\n        at org.apache.spark.api.java.JavaRDDLike$class.collect(JavaRDDLike.scala:361)\r\n        at org.apache.spark.api.java.AbstractJavaRDDLike.collect(JavaRDDLike.scala:45)\r\n        at org.broadinstitute.hellbender.tools.spark.sv.discovery.DiscoverVariantsFromContigAlignmentsSAMSpark.discoverVariantsFromChimeras(DiscoverVariantsFromContigAlignmentsSAMSpark.java:183)\r\n        at org.broadinstitute.hellbender.tools.spark.sv.StructuralVariationDiscoveryPipelineSpark.runTool(StructuralVariationDiscoveryPipelineSpark.java:178)\r\n        at org.broadinstitute.hellbender.engine.spark.GATKSparkTool.runPipeline(GATKSparkTool.java:387)\r\n        at org.broadinstitute.hellbender.engine.spark.SparkCommandLineProgram.doWork(SparkCommandLineProgram.java:30)\r\n        at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:136)\r\n        at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:179)\r\n        at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:198)\r\n        at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:153)\r\n        at org.broadinstitute.hellbender.Main.mainEntry(Main.java:195)\r\n        at org.broadinstitute.hellbender.Main.main(Main.java:277)\r\n        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)\r\n        at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)\r\n        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\r\n        at java.lang.reflect.Method.invoke(Method.java:498)\r\n        at org.apache.spark.deploy.SparkSubmit$.org$apache$spark$deploy$SparkSubmit$$runMain(SparkSubmit.scala:738)\r\n        at org.apache.spark.deploy.SparkSubmit$.doRunMain$1(SparkSubmit.scala:187)\r\n        at org.apache.spark.deploy.SparkSubmit$.submit(SparkSubmit.scala:212)\r\n        at org.apache.spark.deploy.SparkSubmit$.main(SparkSubmit.scala:126)\r\n        at org.apache.spark.deploy.SparkSubmit.main(SparkSubmit.scala)\r\nCaused by: org.broadinstitute.hellbender.exceptions.GATKException: Erred when inferring breakpoint location and event type from chimeric alignment:\r\nasm010450:tig00000      1_189_chrUn_JTFH01000312v1_decoy:663-851_-_189M512H_60_8_149_O  153_701_chrUn_JTFH01000312v1_decoy:1-549_+_152S549M_60_0_549_O\r\n        at org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.NovelAdjacencyReferenceLocations.<init>(NovelAdjacencyReferenceLocations.java:51)\r\n        at org.broadinstitute.hellbender.tools.spark.sv.discovery.DiscoverVariantsFromContigAlignmentsSAMSpark.lambda$null$0(DiscoverVariantsFromContigAlignmentsSAMSpark.java:175)\r\n        at java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:193)\r\n        at java.util.ArrayList$ArrayListSpliterator.tryAdvance(ArrayList.java:1351)\r\n        at java.util.stream.StreamSpliterators$WrappingSpliterator.lambda$initPartialTraversalState$0(StreamSpliterators.java:294)\r\n        at java.util.stream.StreamSpliterators$AbstractWrappingSpliterator.fillBuffer(StreamSpliterators.java:206)\r\n        at java.util.stream.StreamSpliterators$AbstractWrappingSpliterator.doAdvance(StreamSpliterators.java:161)\r\n        at java.util.stream.StreamSpliterators$WrappingSpliterator.tryAdvance(StreamSpliterators.java:300)\r\n        at java.util.Spliterators$1Adapter.hasNext(Spliterators.java:681)\r\n        at scala.collection.convert.Wrappers$JIteratorWrapper.hasNext(Wrappers.scala:42)\r\n        at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:438)\r\n        at org.apache.spark.shuffle.sort.BypassMergeSortShuffleWriter.write(BypassMergeSortShuffleWriter.java:149)\r\n        at org.apache.spark.scheduler.ShuffleMapTask.runTask(ShuffleMapTask.scala:96)\r\n        at org.apache.spark.scheduler.ShuffleMapTask.runTask(ShuffleMapTask.scala:53)\r\n        at org.apache.spark.scheduler.Task.run(Task.scala:99)\r\n        at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:282)\r\n        at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)\r\n        at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)\r\n        at java.lang.Thread.run(Thread.java:745)\r\nCaused by: java.lang.IllegalArgumentException: Invalid interval. Contig:chrUn_JTFH01000312v1_decoy start:0 end:0\r\n        at org.broadinstitute.hellbender.utils.Utils.validateArg(Utils.java:687)\r\n        at org.broadinstitute.hellbender.utils.SimpleInterval.validatePositions(SimpleInterval.java:61)\r\n        at org.broadinstitute.hellbender.utils.SimpleInterval.<init>(SimpleInterval.java:37)\r\n        at org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.NovelAdjacencyReferenceLocations$BreakpointsInference.getLeftJustifiedBreakpoints(NovelAdjacencyReferenceLocations.java:86)\r\n        at org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.NovelAdjacencyReferenceLocations.leftJustifyBreakpoints(NovelAdjacencyReferenceLocations.java:301)\r\n        at org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.NovelAdjacencyReferenceLocations.<init>(NovelAdjacencyReferenceLocations.java:46)\r\n        ... 18 more\r\n18/02/23 23:06:24 INFO util.ShutdownHookManager: Shutdown hook called\r\n18/02/23 23:06:24 INFO util.ShutdownHookManager: Deleting directory /restricted/projectnb/casa/wgs.hg38/sv/gatk.sv/tmp/farrell/spark-94fa6743-3d29-4748-b8f8-d13a52dfed31\r\n```\r\n\r\nThe command line is:\r\n\r\n ```\r\ngatk --java-options \"-Djava.io.tmpdir=tmp\"   StructuralVariationDiscoveryPipelineSpark \\\r\n     -R $REF \\\r\n     --aligner-index-image GRCh38_full_analysis_set_plus_decoy_hla.fa.img \\\r\n     --kmers-to-ignore GRCh38_ignored_kmers.txt \\\r\n     --contig-sam-file $SAMPLE.contig-sam-file\\\r\n     -I $CRAM_DIR/$SAMPLE.cram \\\r\n     -O hdfs:///user/farrell/$CENTER/sv/$SAMPLE.sv.vcf -- --spark-runner SPARK --spark-master yarn  --executor-memory=20G --driver-memory 16g --driver-cores 4 --executor-cores=5  --num-executors 8  --files $REF.img\r\n\r\n```\r\n"},"comment":{"url":"https://api.github.com/repos/broadinstitute/gatk/issues/comments/370896619","html_url":"https://github.com/broadinstitute/gatk/issues/4458#issuecomment-370896619","issue_url":"https://api.github.com/repos/broadinstitute/gatk/issues/4458","id":370896619,"user":{"login":"SHuang-Broad","id":16310888,"avatar_url":"https://avatars3.githubusercontent.com/u/16310888?v=4","gravatar_id":"","url":"https://api.github.com/users/SHuang-Broad","html_url":"https://github.com/SHuang-Broad","followers_url":"https://api.github.com/users/SHuang-Broad/followers","following_url":"https://api.github.com/users/SHuang-Broad/following{/other_user}","gists_url":"https://api.github.com/users/SHuang-Broad/gists{/gist_id}","starred_url":"https://api.github.com/users/SHuang-Broad/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/SHuang-Broad/subscriptions","organizations_url":"https://api.github.com/users/SHuang-Broad/orgs","repos_url":"https://api.github.com/users/SHuang-Broad/repos","events_url":"https://api.github.com/users/SHuang-Broad/events{/privacy}","received_events_url":"https://api.github.com/users/SHuang-Broad/received_events","type":"User","site_admin":false},"created_at":"2018-03-06T19:21:31Z","updated_at":"2018-03-06T19:21:31Z","author_association":"CONTRIBUTOR","body":"Thanks for using our pipeline and reporting the issue @jjfarrell !"}}
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