org.hammerlab.guacamole.reference.ContigNotFound: Contig 19 does not exist in the current reference. Available contigs are chr11,chr1_gl000191_random,chr5,chr22,chr1_gl000192_random,chrUn_gl000221,chrUn_gl000234,chr18_gl000207_random,chrUn_gl000232,chrUn_gl000224,chr8,chrUn_gl000248,chrUn_gl000243,chrUn_gl000238,chrUn_gl000249,chrUn_gl000228,chr21_gl000210_random,chrUn_gl000217,chr19,chrY,chr9_gl000198_random,chr6_mann_hap4,chr1,chr4_gl000193_random,chr15,chrUn_gl000213,chr17_gl000204_random,chr19_gl000208_random,chrUn_gl000212,chr17_gl000206_random,chrUn_gl000219,chr12,chr18,chr20,chr8_gl000197_random,chr6_cox_hap2,chr2,chrUn_gl000223,chrUn_gl000237,chr9_gl000200_random,chr7_gl000195_random,chr13,chr6_apd_hap1,chrUn_gl000233,chrUn_gl000227,chrUn_gl000222,chrUn_gl000211,chr9_gl000199_random,chrUn_gl000245,chrUn_gl000242,chrUn_gl000216,chr7,chr19_gl000209_random,chrUn_gl000230,chr14,chrUn_gl000215,chrUn_gl000236,chr6_mcf_hap5,chr3,chrUn_gl000226,chr17_gl000203_random,chrM,chr17,chr6_dbb_hap3,chrUn_gl000246,chr4_gl000194_random,chr11_gl000202_random,chr17_ctg5_hap1,chrUn_gl000241,chr6_qbl_hap6,chr4,chrUn_gl000225,chrUn_gl000231,chrUn_gl000240,chr6,chr9,chr9_gl000201_random,chr4_ctg9_hap1,chrUn_gl000235,chrUn_gl000244,chrUn_gl000220,chrUn_gl000214,chr17_gl000205_random,chrX,chrUn_gl000239,chr6_ssto_hap7,chrUn_gl000218,chrUn_gl000229,chr10,chr21,chr16,chrUn_gl000247,chr8_gl000196_random

GitHub | car2008 | 8 months ago
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    GitHub comment 572#246216026

    GitHub | 8 months ago | car2008
    org.hammerlab.guacamole.reference.ContigNotFound: Contig 19 does not exist in the current reference. Available contigs are chr11,chr1_gl000191_random,chr5,chr22,chr1_gl000192_random,chrUn_gl000221,chrUn_gl000234,chr18_gl000207_random,chrUn_gl000232,chrUn_gl000224,chr8,chrUn_gl000248,chrUn_gl000243,chrUn_gl000238,chrUn_gl000249,chrUn_gl000228,chr21_gl000210_random,chrUn_gl000217,chr19,chrY,chr9_gl000198_random,chr6_mann_hap4,chr1,chr4_gl000193_random,chr15,chrUn_gl000213,chr17_gl000204_random,chr19_gl000208_random,chrUn_gl000212,chr17_gl000206_random,chrUn_gl000219,chr12,chr18,chr20,chr8_gl000197_random,chr6_cox_hap2,chr2,chrUn_gl000223,chrUn_gl000237,chr9_gl000200_random,chr7_gl000195_random,chr13,chr6_apd_hap1,chrUn_gl000233,chrUn_gl000227,chrUn_gl000222,chrUn_gl000211,chr9_gl000199_random,chrUn_gl000245,chrUn_gl000242,chrUn_gl000216,chr7,chr19_gl000209_random,chrUn_gl000230,chr14,chrUn_gl000215,chrUn_gl000236,chr6_mcf_hap5,chr3,chrUn_gl000226,chr17_gl000203_random,chrM,chr17,chr6_dbb_hap3,chrUn_gl000246,chr4_gl000194_random,chr11_gl000202_random,chr17_ctg5_hap1,chrUn_gl000241,chr6_qbl_hap6,chr4,chrUn_gl000225,chrUn_gl000231,chrUn_gl000240,chr6,chr9,chr9_gl000201_random,chr4_ctg9_hap1,chrUn_gl000235,chrUn_gl000244,chrUn_gl000220,chrUn_gl000214,chr17_gl000205_random,chrX,chrUn_gl000239,chr6_ssto_hap7,chrUn_gl000218,chrUn_gl000229,chr10,chr21,chr16,chrUn_gl000247,chr8_gl000196_random

    Root Cause Analysis

    1. org.hammerlab.guacamole.reference.ContigNotFound

      Contig 19 does not exist in the current reference. Available contigs are chr11,chr1_gl000191_random,chr5,chr22,chr1_gl000192_random,chrUn_gl000221,chrUn_gl000234,chr18_gl000207_random,chrUn_gl000232,chrUn_gl000224,chr8,chrUn_gl000248,chrUn_gl000243,chrUn_gl000238,chrUn_gl000249,chrUn_gl000228,chr21_gl000210_random,chrUn_gl000217,chr19,chrY,chr9_gl000198_random,chr6_mann_hap4,chr1,chr4_gl000193_random,chr15,chrUn_gl000213,chr17_gl000204_random,chr19_gl000208_random,chrUn_gl000212,chr17_gl000206_random,chrUn_gl000219,chr12,chr18,chr20,chr8_gl000197_random,chr6_cox_hap2,chr2,chrUn_gl000223,chrUn_gl000237,chr9_gl000200_random,chr7_gl000195_random,chr13,chr6_apd_hap1,chrUn_gl000233,chrUn_gl000227,chrUn_gl000222,chrUn_gl000211,chr9_gl000199_random,chrUn_gl000245,chrUn_gl000242,chrUn_gl000216,chr7,chr19_gl000209_random,chrUn_gl000230,chr14,chrUn_gl000215,chrUn_gl000236,chr6_mcf_hap5,chr3,chrUn_gl000226,chr17_gl000203_random,chrM,chr17,chr6_dbb_hap3,chrUn_gl000246,chr4_gl000194_random,chr11_gl000202_random,chr17_ctg5_hap1,chrUn_gl000241,chr6_qbl_hap6,chr4,chrUn_gl000225,chrUn_gl000231,chrUn_gl000240,chr6,chr9,chr9_gl000201_random,chr4_ctg9_hap1,chrUn_gl000235,chrUn_gl000244,chrUn_gl000220,chrUn_gl000214,chr17_gl000205_random,chrX,chrUn_gl000239,chr6_ssto_hap7,chrUn_gl000218,chrUn_gl000229,chr10,chr21,chr16,chrUn_gl000247,chr8_gl000196_random

      at org.hammerlab.guacamole.reference.ReferenceBroadcast.getContig()
    2. org.hammerlab.guacamole
      PileupFlatMapUtils$$anonfun$pileupFlatMapMultipleSamples$1$$anonfun$7.apply
      1. org.hammerlab.guacamole.reference.ReferenceBroadcast.getContig(ReferenceBroadcast.scala:18)
      2. org.hammerlab.guacamole.distributed.PileupFlatMapUtils$$anonfun$pileupFlatMapMultipleSamples$1$$anonfun$7.apply(PileupFlatMapUtils.scala:123)
      3. org.hammerlab.guacamole.distributed.PileupFlatMapUtils$$anonfun$pileupFlatMapMultipleSamples$1$$anonfun$7.apply(PileupFlatMapUtils.scala:116)
      3 frames
    3. Scala
      AbstractTraversable.map
      1. scala.collection.TraversableLike$$anonfun$map$1.apply(TraversableLike.scala:244)
      2. scala.collection.TraversableLike$$anonfun$map$1.apply(TraversableLike.scala:244)
      3. scala.collection.Iterator$class.foreach(Iterator.scala:727)
      4. scala.collection.AbstractIterator.foreach(Iterator.scala:1157)
      5. scala.collection.IterableLike$class.foreach(IterableLike.scala:72)
      6. scala.collection.AbstractIterable.foreach(Iterable.scala:54)
      7. scala.collection.TraversableLike$class.map(TraversableLike.scala:244)
      8. scala.collection.AbstractTraversable.map(Traversable.scala:105)
      8 frames
    4. org.hammerlab.guacamole
      WindowFlatMapUtils$$anonfun$splitPartitionByContigAndMap$2.apply
      1. org.hammerlab.guacamole.distributed.PileupFlatMapUtils$$anonfun$pileupFlatMapMultipleSamples$1.apply(PileupFlatMapUtils.scala:116)
      2. org.hammerlab.guacamole.distributed.PileupFlatMapUtils$$anonfun$pileupFlatMapMultipleSamples$1.apply(PileupFlatMapUtils.scala:104)
      3. org.hammerlab.guacamole.distributed.WindowFlatMapUtils$$anonfun$windowFlatMapWithState$1$$anonfun$apply$1.apply(WindowFlatMapUtils.scala:65)
      4. org.hammerlab.guacamole.distributed.WindowFlatMapUtils$$anonfun$windowFlatMapWithState$1$$anonfun$apply$1.apply(WindowFlatMapUtils.scala:55)
      5. org.hammerlab.guacamole.distributed.WindowFlatMapUtils$$anonfun$splitPartitionByContigAndMap$2.apply(WindowFlatMapUtils.scala:141)
      6. org.hammerlab.guacamole.distributed.WindowFlatMapUtils$$anonfun$splitPartitionByContigAndMap$2.apply(WindowFlatMapUtils.scala:131)
      6 frames
    5. Scala
      Iterator$$anon$13.hasNext
      1. scala.collection.Iterator$$anon$13.hasNext(Iterator.scala:371)
      1 frame
    6. Spark
      Executor$TaskRunner.run
      1. org.apache.spark.storage.MemoryStore.unrollSafely(MemoryStore.scala:284)
      2. org.apache.spark.CacheManager.putInBlockManager(CacheManager.scala:171)
      3. org.apache.spark.CacheManager.getOrCompute(CacheManager.scala:78)
      4. org.apache.spark.rdd.RDD.iterator(RDD.scala:268)
      5. org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:66)
      6. org.apache.spark.scheduler.Task.run(Task.scala:89)
      7. org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:214)
      7 frames
    7. Java RT
      Thread.run
      1. java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
      2. java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
      3. java.lang.Thread.run(Thread.java:745)
      3 frames