基因数据处理31之avocado运行avocado-cli中的avocado问题3-变异

读入的read为：

val fqFile = "hs38DHSE1L100F1.sam"

读取结果：

cleanedReads.count:1
{"readNum": 0,"contig": {"contigName": "chrUn_KN707963v1_decoy","contigLength": 62955,"contigMD5": null,"referenceURL": null,"assembly": null,"species": null,"referenceIndex": 357},"start": 44526,"oldPosition": null,"end": 44596,"mapq": 0,"readName": "chrUn_KN707963v1_decoy_44034_44596_0:0:0_3:0:0_0","sequence": "GTGAGATACATTTCCACTGATCAAACACGTGATGTAACCCTTGTCATGGTTCTGCTTACAGGGGATTTGT","qual": "2222222222222222222222222222222222222222222222222222222222222222222222","cigar": "70M","oldCigar": null,"basesTrimmedFromStart": 0,"basesTrimmedFromEnd": 0,"readPaired": false,"properPair": false,"readMapped": true,"mateMapped": false,"failedVendorQualityChecks": false,"duplicateRead": false,"readNegativeStrand": true,"mateNegativeStrand": false,"primaryAlignment": true,"secondaryAlignment": false,"supplementaryAlignment": false,"mismatchingPositions": "4T22G18A23","origQual": null,"attributes": "XT:A:RtXO:i:0tXM:i:3tNM:i:3tXG:i:0tX1:i:3tX0:i:3","recordGroupName": null,"recordGroupSequencingCenter": null,"recordGroupDescription": null,"recordGroupRunDateEpoch": null,"recordGroupFlowOrder": null,"recordGroupKeySequence": null,"recordGroupLibrary": null,"recordGroupPredictedMedianInsertSize": null,"recordGroupPlatform": null,"recordGroupPlatformUnit": null,"recordGroupSample": null,"mateAlignmentStart": null,"mateAlignmentEnd": null,"mateContig": null,"inferredInsertSize": null}

变异识别时报错：getRecordGroupSample

2016-05-28 15:47:18 ERROR Executor:96 - Exception in task 0.0 in stage 16.0 (TID 14)
java.lang.NullPointerException
    at org.bdgenomics.avocado.discovery.ReadExplorer$$anonfun$readToObservations$1.apply(ReadExplorer.scala:54)
	at org.bdgenomics.avocado.discovery.ReadExplorer$$anonfun$readToObservations$1.apply(ReadExplorer.scala:46)
    at org.apache.spark.rdd.Timer.time(Timer.scala:57)
    at org.bdgenomics.avocado.discovery.ReadExplorer.readToObservations(ReadExplorer.scala:46)
    at org.bdgenomics.avocado.discovery.ReadExplorer$$anonfun$discover$1$$anonfun$apply$3.apply(ReadExplorer.scala:177)
    at org.bdgenomics.avocado.discovery.ReadExplorer$$anonfun$discover$1$$anonfun$apply$3.apply(ReadExplorer.scala:177)
    at scala.collection.Iterator$$anon$13.hasNext(Iterator.scala:371)
	at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:327)
    at org.apache.spark.util.collection.ExternalSorter.insertAll(ExternalSorter.scala:207)
    at org.apache.spark.shuffle.sort.SortShuffleWriter.write(SortShuffleWriter.scala:62)
    at org.apache.spark.scheduler.ShuffleMapTask.runTask(ShuffleMapTask.scala:70)
    at org.apache.spark.scheduler.ShuffleMapTask.runTask(ShuffleMapTask.scala:41)
    at org.apache.spark.scheduler.Task.run(Task.scala:70)
    at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:213)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
    at java.lang.Thread.run(Unknown Source)
2016-05-28 15:47:18 WARN  TaskSetManager:71 - Lost task 0.0 in stage 16.0 (TID 14,localhost): java.lang.NullPointerException
    at org.bdgenomics.avocado.discovery.ReadExplorer$$anonfun$readToObservations$1.apply(ReadExplorer.scala:54)
	at org.bdgenomics.avocado.discovery.ReadExplorer$$anonfun$readToObservations$1.apply(ReadExplorer.scala:46)
    at org.apache.spark.rdd.Timer.time(Timer.scala:57)
    at org.bdgenomics.avocado.discovery.ReadExplorer.readToObservations(ReadExplorer.scala:46)
    at org.bdgenomics.avocado.discovery.ReadExplorer$$anonfun$discover$1$$anonfun$apply$3.apply(ReadExplorer.scala:177)
    at org.bdgenomics.avocado.discovery.ReadExplorer$$anonfun$discover$1$$anonfun$apply$3.apply(ReadExplorer.scala:177)
    at scala.collection.Iterator$$anon$13.hasNext(Iterator.scala:371)
	at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:327)
    at org.apache.spark.util.collection.ExternalSorter.insertAll(ExternalSorter.scala:207)
    at org.apache.spark.shuffle.sort.SortShuffleWriter.write(SortShuffleWriter.scala:62)
    at org.apache.spark.scheduler.ShuffleMapTask.runTask(ShuffleMapTask.scala:70)
    at org.apache.spark.scheduler.ShuffleMapTask.runTask(ShuffleMapTask.scala:41)
    at org.apache.spark.scheduler.Task.run(Task.scala:70)
    at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:213)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
    at java.lang.Thread.run(Unknown Source)

2016-05-28 15:47:18 ERROR TaskSetManager:75 - Task 0 in stage 16.0 failed 1 times; aborting job
Exception in thread "main" org.apache.spark.SparkException: Job aborted due to stage failure: Task 0 in stage 16.0 failed 1 times,most recent failure: Lost task 0.0 in stage 16.0 (TID 14,localhost): java.lang.NullPointerException
    at org.bdgenomics.avocado.discovery.ReadExplorer$$anonfun$readToObservations$1.apply(ReadExplorer.scala:54)
	at org.bdgenomics.avocado.discovery.ReadExplorer$$anonfun$readToObservations$1.apply(ReadExplorer.scala:46)
    at org.apache.spark.rdd.Timer.time(Timer.scala:57)
    at org.bdgenomics.avocado.discovery.ReadExplorer.readToObservations(ReadExplorer.scala:46)
    at org.bdgenomics.avocado.discovery.ReadExplorer$$anonfun$discover$1$$anonfun$apply$3.apply(ReadExplorer.scala:177)
    at org.bdgenomics.avocado.discovery.ReadExplorer$$anonfun$discover$1$$anonfun$apply$3.apply(ReadExplorer.scala:177)
    at scala.collection.Iterator$$anon$13.hasNext(Iterator.scala:371)
	at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:327)
    at org.apache.spark.util.collection.ExternalSorter.insertAll(ExternalSorter.scala:207)
    at org.apache.spark.shuffle.sort.SortShuffleWriter.write(SortShuffleWriter.scala:62)
    at org.apache.spark.scheduler.ShuffleMapTask.runTask(ShuffleMapTask.scala:70)
    at org.apache.spark.scheduler.ShuffleMapTask.runTask(ShuffleMapTask.scala:41)
    at org.apache.spark.scheduler.Task.run(Task.scala:70)
    at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:213)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
    at java.lang.Thread.run(Unknown Source)

Driver stacktrace:
    at org.apache.spark.scheduler.DAGScheduler.org$apache$spark$scheduler$DAGScheduler$$failJobAndIndependentStages(DAGScheduler.scala:1273)
	at org.apache.spark.scheduler.DAGScheduler$$anonfun$abortStage$1.apply(DAGScheduler.scala:1264)
    at org.apache.spark.scheduler.DAGScheduler$$anonfun$abortStage$1.apply(DAGScheduler.scala:1263)
	at scala.collection.mutable.ResizableArray$class.foreach(ResizableArray.scala:59)
	at scala.collection.mutable.ArrayBuffer.foreach(ArrayBuffer.scala:47)
	at org.apache.spark.scheduler.DAGScheduler.abortStage(DAGScheduler.scala:1263)
	at org.apache.spark.scheduler.DAGScheduler$$anonfun$handleTaskSetFailed$1.apply(DAGScheduler.scala:730)
    at org.apache.spark.scheduler.DAGScheduler$$anonfun$handleTaskSetFailed$1.apply(DAGScheduler.scala:730)
	at scala.Option.foreach(Option.scala:236)
	at org.apache.spark.scheduler.DAGScheduler.handleTaskSetFailed(DAGScheduler.scala:730)
	at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:1457)
	at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:1418)
	at org.apache.spark.util.EventLoop$$anon$1.run(EventLoop.scala:48)

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