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

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Solutions on the web1

  • via GitHub by car2008
    , 10 months ago
    ,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
  • Stack trace

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

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