基因数据处理30之avocado运行avocado-cli中的avocado问题1和2

问题1：

avocado中的run方法中：

println("stats.coverage:" + stats.coverage)

调用的是：

lazy val coverage = ComputingCoverage.time {
    ScoreCoverage(inputDataset)
  }

然后报错：

Exception in thread "main" java.lang.UnsupportedOperationException: empty collection
    at org.apache.spark.rdd.RDD$$anonfun$reduce$1$$anonfun$apply$36.apply(RDD.scala:985)
    at org.apache.spark.rdd.RDD$$anonfun$reduce$1$$anonfun$apply$36.apply(RDD.scala:985)
    at scala.Option.getOrElse(Option.scala:120)
    at org.apache.spark.rdd.RDD$$anonfun$reduce$1.apply(RDD.scala:985)
	at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:147)
	at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:108)
	at org.apache.spark.rdd.RDD.withScope(RDD.scala:286)
	at org.apache.spark.rdd.RDD.reduce(RDD.scala:965)
	at org.bdgenomics.avocado.stats.ScoreCoverage$.apply(ScoreCoverage.scala:44)
	at org.bdgenomics.avocado.stats.AvocadoConfigAndStats$$anonfun$coverage$1.apply(AvocadoConfigAndStats.scala:33)
    at org.bdgenomics.avocado.stats.AvocadoConfigAndStats$$anonfun$coverage$1.apply(AvocadoConfigAndStats.scala:33)
    at org.apache.spark.rdd.Timer.time(Timer.scala:57)
    at org.bdgenomics.avocado.stats.AvocadoConfigAndStats.coverage$lzycompute(AvocadoConfigAndStats.scala:32)
    at org.bdgenomics.avocado.stats.AvocadoConfigAndStats.coverage(AvocadoConfigAndStats.scala:32)
    at org.bdgenomics.avocado.cli.Avocado.run(Avocado.scala:263)
    at org.bdgenomics.avocado.cli.AvocadoSuite$.main(AvocadoSuite.scala:60)
    at org.bdgenomics.avocado.cli.AvocadoSuite.main(AvocadoSuite.scala)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
    at java.lang.reflect.Method.invoke(Unknown Source)
    at com.intellij.rt.execution.application.AppMain.main(AppMain.java:144)

问题2：

println("stats.referenceSeq:" + stats.referenceSeq)

调用的是:

println("stats.referenceSeq:" + stats.referenceSeq)

报错:

stats.referenceObservations:MapPartitionsRDD[26] at flatMap at SliceReference.scala:28
2016-05-28 15:16:50 ERROR Executor:96 - Exception in task 0.0 in stage 10.0 (TID 9)
java.io.NotSerializableException: org.bdgenomics.formats.avro.NucleotideContigFragment
Serialization stack:
    - object not serializable (class: org.bdgenomics.formats.avro.NucleotideContigFragment,value: {"contig": {"contigName": "chrUn_KN707606v1_decoy","contigLength": 2200,"contigMD5": null,"referenceURL": null,"assembly": null,"species": null,"referenceIndex": null},"description": "AC:KN707606.1 gi:734691250 LN:2200 rl:unplaced M5:20c768ac79ca38077e5012ee0e5f8333 AS:hs38d1","fragmentSequence": "ctagtagctgggactacaagcgcccgccaccacacccggctaatttttttgtatttttagtggagacaggtttcaccgtgttggccaggatggtctcgatctcctgaccttgtgatctgcccaccttgccctcccaaagtgctgggattacaggcatgagccaccatacccggcagTGTCCTATCCATTTTTAAGGCAGCCACTTGGAGTTGGAGCATGTCTTTCTCTCATAATCTCTTACCAGATGTCTCAGAGCAGCCTGTGCACTTTAACTCCAGACATTCTGCCACTGAGCCCCCTAGAGCTCCAGCTTTTAAAGCACTTGGGGTGAGCCTCGAGAGATGACAGACGGAGCTGCCCAAGAGCTGCCAGCTGCCAACCCTGCCTGGGGCTTCACGGCCCGCGCCCTACTTCCTCTCAGCTGGCTCCACACCCTGGGGCGTGTAATTTCCAAATTCTCACTCCCAGGGCTAATTTGGGGGATAAGACATTTGATTAGAAGTATCAgaaaccagctgggcatggtggctcacacctgtaatcccagcactttgggaggttatgactagaggatcatttgaactcaggaattcaagaccagcctggataacagtgagaccccatctctacaaaatataaacaattatgtgagcatggtggtgcacacctgtagtccctgttccttgggaggctgaggccggaggatcccttgagcccaggagttcaaggctgcagagagctgcgattgtgccactgcacactaacctgggagatagagcaagaacttgtctcagaaaaaaaaagtatcaggaaCTAATCTCCAGTCCTATCAAGTTAGGCATAAGGTCAATGTGTGATAGCTGAGTGTCACAGAAACCAAGGACAGGAATGCAACTGCCACTGGGGATGAACTGGAAGTGGGGAGTTAAACCACCTCAGAATGTccccatttttgtttcttctccagATGTGCTGCTTTGCTTTTCCGTATGTTTCTCTACGGACCAGCTACCTCTCCTCTGCCAACAGATCCAAGTTGTGCATGTTATGGGTCCAAACACCACGTGACAAGCCCATTCTTCCAGTTTCTCAGACCAGAAACTGCACTGTCCTCTAACTGCTTCTTCTCCCTCTTGCATCTGGTCCTTGGGGAAATCCTGTTTGCCCGGCCTTCAGCATATATCCACAGTTTAACCTTAACCACTCCTCGCCACCACTCGCGGGGGCGAGCAGCCTTCGCCCCCTGCCTAGATTACTACAGTAACTTCATTGTTCTTTCTACTTCTCTCTTTGCCCCTCTGCTATCTCAAAACAGCATCCAAAATGCACCTAGCAAGAGCATGTCATTCCTCTGCACAAAACTCTccaacttctctctttttttttttttttttttttttgagacggagtctcactctgtcacccaggctggagtgcaatagtgtgatcttggctcactgcaacctccacctcccagattcaagcgattctcctgcctcagcctcctgagtagctgagattacaggttcatgtcaccatgcccggctaatttttgtatttttagtagagacagggtttcaccatgttagtcaggctggtctcgaactcctgaccttgtgatccacccgcctcagcctcccaaagtgctgggattataggcatgagccaccgtgcatgacCAACTTCTCTTTTTGTTCAGAGTAAAAGCCAACGGCCCATGAGGCTTTCCATGGTCACGCCTCCGCTCATTCGCTCTGTGGCTTTGTCTTACACGGGTTCACTCCTCACTGGCCGCCTTGCTGACCCCATAGCTCACGGGCCTTACTCTGCTctcggggcctttgcacttgctccaCTGCAAATGCTCCTCCCCCAGAGGCCTTTGTGGCCCATTCCCTCGGTTCCTTAGGAACAATCCCTTCCCTGGTCAAACCTCCACTGACATCTGTCTCCTtcccttctgaattttttttctccgGTAGTATTTATCACTCTGCTATCCTTAGGATTTCCTTATCTTGTTTATCATCATCTCCTCATCCAGAGcttaagtcctttttttttttttgagatagagtctcgctctgtcgcccaggctggagtgcagtggcgcgatctcgtctcgctgaaagctccacctcccgggttcacgccattctcccgcctcagcctcccgagtagctgggactacaggcactcg","fragmentNumber": 0,"fragmentStartPosition": 0,"fragmentLength": 2200,"numberOfFragmentsInContig": 1})
    - element of array (index: 0)
    - array (class [Lorg.bdgenomics.formats.avro.NucleotideContigFragment;,size 1)
    at org.apache.spark.serializer.SerializationDebugger$.improveException(SerializationDebugger.scala:40)
    at org.apache.spark.serializer.JavaSerializationStream.writeObject(JavaSerializer.scala:47)
    at org.apache.spark.serializer.JavaSerializerInstance.serialize(JavaSerializer.scala:81)
    at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:236)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
    at java.lang.Thread.run(Unknown Source)
2016-05-28 15:16:50 ERROR TaskSetManager:75 - Task 0.0 in stage 10.0 (TID 9) had a not serializable result: org.bdgenomics.formats.avro.NucleotideContigFragment
Serialization stack:
    - object not serializable (class: org.bdgenomics.formats.avro.NucleotideContigFragment,size 1); not retrying
Exception in thread "main" org.apache.spark.SparkException: Job aborted due to stage failure: Task 0.0 in stage 10.0 (TID 9) had a not serializable result: org.bdgenomics.formats.avro.NucleotideContigFragment
Serialization stack:
    - object not serializable (class: org.bdgenomics.formats.avro.NucleotideContigFragment,size 1)
    at org.apache.spark.scheduler.DAGScheduler.org$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)

Process finished with exit code 1

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