2020-09-03 16:50:39 Hail: INFO: Running Hail version 0.2.56-87d89a1d8159
2020-09-03 16:50:40 SparkContext: WARN: Using an existing SparkContext; some configuration may not take effect.
2020-09-03 16:50:41 YarnSchedulerBackend$YarnDriverEndpoint: INFO: Registered executor NettyRpcEndpointRef(spark-client://Executor) (10.128.0.63:37516) with ID 1
2020-09-03 16:50:41 ExecutorAllocationManager: INFO: New executor 1 has registered (new total is 1)
2020-09-03 16:50:41 BlockManagerMasterEndpoint: INFO: Registering block manager jg3-w-0.c.maclab-ukbb.internal:45095 with 5.6 GB RAM, BlockManagerId(1, jg3-w-0.c.maclab-ukbb.internal, 45095, None)
2020-09-03 16:50:41 YarnSchedulerBackend$YarnDriverEndpoint: INFO: Registered executor NettyRpcEndpointRef(spark-client://Executor) (10.128.0.68:46456) with ID 2
2020-09-03 16:50:41 ExecutorAllocationManager: INFO: New executor 2 has registered (new total is 2)
2020-09-03 16:50:41 BlockManagerMasterEndpoint: INFO: Registering block manager jg3-w-1.c.maclab-ukbb.internal:42241 with 5.6 GB RAM, BlockManagerId(2, jg3-w-1.c.maclab-ukbb.internal, 42241, None)
2020-09-03 16:50:41 root: INFO: RegionPool: initialized for thread 17: Thread-5
2020-09-03 16:50:42 MemoryStore: INFO: Block broadcast_0 stored as values in memory (estimated size 2.3 MB, free 21.7 GB)
2020-09-03 16:50:42 MemoryStore: INFO: Block broadcast_0_piece0 stored as bytes in memory (estimated size 123.7 KB, free 21.7 GB)
2020-09-03 16:50:42 BlockManagerInfo: INFO: Added broadcast_0_piece0 in memory on jg3-m.c.maclab-ukbb.internal:36967 (size: 123.7 KB, free: 21.7 GB)
2020-09-03 16:50:42 SparkContext: INFO: Created broadcast 0 from broadcast at SparkBackend.scala:233
2020-09-03 16:50:55 root: INFO: globbing path gs://gnomad-tmp/duplicate_1kg.txt returned 1 files: duplicate_1kg.txt
2020-09-03 16:50:56 Hail: INFO: Reading table without type imputation
  Loading field 's' as type str (not specified)
  Loading field 's_new' as type str (not specified)
2020-09-03 16:50:57 MemoryStore: INFO: Block broadcast_1 stored as values in memory (estimated size 401.3 KB, free 21.7 GB)
2020-09-03 16:50:57 MemoryStore: INFO: Block broadcast_1_piece0 stored as bytes in memory (estimated size 28.5 KB, free 21.7 GB)
2020-09-03 16:50:57 BlockManagerInfo: INFO: Added broadcast_1_piece0 in memory on jg3-m.c.maclab-ukbb.internal:36967 (size: 28.5 KB, free: 21.7 GB)
2020-09-03 16:50:57 SparkContext: INFO: Created broadcast 1 from broadcast at SparkBackend.scala:233
2020-09-03 16:51:20 root: INFO: Timer: Time taken for optimize: relationalLowerer, initial IR -- Verify : 1.158ms, total 58.367ms
2020-09-03 16:51:20 root: INFO: optimize optimize: relationalLowerer, initial IR: before: IR size 41: 
(TableCount
  (TableMapRows
    (TableFilter
      (TableIntervalJoin __uid_4 False
        (TableKeyBy (locus) False
          (TableFilter
            (TableMapRows
              (TableRange 64444167 128)
              (InsertFields
                (SelectFields (idx)
                  (Ref row))
                None
                (locus
                  (Apply Locus () Locus(GRCh38)
                    (Str "chr20")
                    (ApplyBinaryPrimOp Add
                      (GetField idx
                        (Ref row))
                      (I32 1))))))
            (Let __cse_1
              (GetField locus
                (Ref row))
              (Coalesce
                (ApplyComparisonOp NEQ
                  (Apply lower () String
                    (ApplyIR getReferenceSequence (Locus(GRCh38)) String
                      (Apply contig () String
                        (Ref __cse_1))
                      (Apply position () Int32
                        (Ref __cse_1))
                      (I32 0)
                      (I32 0)))
                  (Str "n"))
                (False)))))
        (TableRead None False "{\"path\":\"gs://gnomad-public/resources/grch38/telomeres_and_centromeres/hg38.telomeresAndMergedCentromeres.ht\",\"name\":\"TableNativeReader\"}"))
      (Coalesce
        (IsNA
          (GetField __uid_4
            (Ref row)))
        (False)))
    (SelectFields (idx locus)
      (SelectFields (idx locus __uid_4)
        (Ref row)))))
2020-09-03 16:51:20 root: INFO: Timer: Time taken for optimize: relationalLowerer, initial IR -- LoweringTransformation -- Optimize -- FoldConstants : 17.035ms, total 99.499ms
2020-09-03 16:51:20 root: INFO: Timer: Time taken for optimize: relationalLowerer, initial IR -- LoweringTransformation -- Optimize -- ExtractIntervalFilters : 13.653ms, total 113.930ms
2020-09-03 16:51:20 root: INFO: Timer: Time taken for optimize: relationalLowerer, initial IR -- LoweringTransformation -- Optimize -- Simplify : 23.880ms, total 138.557ms
2020-09-03 16:51:20 root: INFO: Timer: Time taken for optimize: relationalLowerer, initial IR -- LoweringTransformation -- Optimize -- ForwardLets : 28.734ms, total 168.049ms
2020-09-03 16:51:20 root: INFO: Timer: Time taken for optimize: relationalLowerer, initial IR -- LoweringTransformation -- Optimize -- ForwardRelationalLets : 2.518ms, total 171.330ms
2020-09-03 16:51:20 root: INFO: Timer: Time taken for optimize: relationalLowerer, initial IR -- LoweringTransformation -- Optimize -- PruneDeadFields : 150.897ms, total 322.962ms
2020-09-03 16:51:20 root: INFO: Timer: Time taken for optimize: relationalLowerer, initial IR -- LoweringTransformation -- Optimize -- FoldConstants : 1.750ms, total 324.986ms
2020-09-03 16:51:20 root: INFO: Timer: Time taken for optimize: relationalLowerer, initial IR -- LoweringTransformation -- Optimize -- ExtractIntervalFilters : 1.866ms, total 327.125ms
2020-09-03 16:51:20 root: INFO: Timer: Time taken for optimize: relationalLowerer, initial IR -- LoweringTransformation -- Optimize -- Simplify : 1.778ms, total 329.190ms
2020-09-03 16:51:20 root: INFO: Timer: Time taken for optimize: relationalLowerer, initial IR -- LoweringTransformation -- Optimize -- ForwardLets : 6.226ms, total 335.668ms
2020-09-03 16:51:20 root: INFO: Timer: Time taken for optimize: relationalLowerer, initial IR -- LoweringTransformation -- Optimize -- ForwardRelationalLets : 0.653ms, total 336.626ms
2020-09-03 16:51:20 root: INFO: Timer: Time taken for optimize: relationalLowerer, initial IR -- LoweringTransformation -- Optimize -- PruneDeadFields : 10.277ms, total 347.175ms
2020-09-03 16:51:20 root: INFO: Timer: Time taken for optimize: relationalLowerer, initial IR -- LoweringTransformation -- Optimize -- FoldConstants : 0.860ms, total 348.551ms
2020-09-03 16:51:20 root: INFO: Timer: Time taken for optimize: relationalLowerer, initial IR -- LoweringTransformation -- Optimize -- ExtractIntervalFilters : 0.992ms, total 349.801ms
2020-09-03 16:51:20 root: INFO: Timer: Time taken for optimize: relationalLowerer, initial IR -- LoweringTransformation -- Optimize -- Simplify : 1.590ms, total 351.636ms
2020-09-03 16:51:20 root: INFO: Timer: Time taken for optimize: relationalLowerer, initial IR -- LoweringTransformation -- Optimize -- ForwardLets : 5.190ms, total 357.061ms
2020-09-03 16:51:20 root: INFO: Timer: Time taken for optimize: relationalLowerer, initial IR -- LoweringTransformation -- Optimize -- ForwardRelationalLets : 0.399ms, total 357.716ms
2020-09-03 16:51:20 root: INFO: Timer: Time taken for optimize: relationalLowerer, initial IR -- LoweringTransformation -- Optimize -- PruneDeadFields : 3.968ms, total 361.835ms
2020-09-03 16:51:20 root: INFO: Timer: Time taken for optimize: relationalLowerer, initial IR -- LoweringTransformation -- Optimize : 280.650ms, total 362.115ms, tagged coverage 97.0
2020-09-03 16:51:20 root: INFO: optimize optimize: relationalLowerer, initial IR: after: IR size 43:
(TableCount
  (TableFilter
    (TableIntervalJoin __uid_4 False
      (TableKeyBy (locus) False
        (TableMapRows
          (TableKeyBy () False
            (TableFilter
              (TableMapRows
                (TableRange 64444167 128)
                (InsertFields
                  (Ref row)
                  None
                  (locus
                    (Apply Locus () Locus(GRCh38)
                      (Str "chr20")
                      (ApplyBinaryPrimOp Add
                        (GetField idx
                          (Ref row))
                        (I32 1))))))
              (Let __iruid_36
                (GetField locus
                  (Ref row))
                (Coalesce
                  (ApplyComparisonOp NEQ
                    (Apply lower () String
                      (ApplyIR getReferenceSequence (Locus(GRCh38)) String
                        (Apply contig () String
                          (Ref __iruid_36))
                        (Apply position () Int32
                          (Ref __iruid_36))
                        (I32 0)
                        (I32 0)))
                    (Str "n"))
                  (False)))))
          (If
            (IsNA
              (Ref row))
            (NA Struct{locus:Locus(GRCh38)})
            (MakeStruct
              (locus
                (GetField locus
                  (Ref row)))))))
      (TableRead Table{global:Struct{},key:[interval],row:Struct{interval:Interval[Locus(GRCh38)]}} False "{\"path\":\"gs://gnomad-public/resources/grch38/telomeres_and_centromeres/hg38.telomeresAndMergedCentromeres.ht\",\"name\":\"TableNativeReader\"}"))
    (IsNA
      (GetField __uid_4
        (Ref row)))))
2020-09-03 16:51:20 root: INFO: Timer: Time taken for optimize: relationalLowerer, initial IR -- LoweringTransformation : 307.831ms, total 370.186ms, tagged coverage 88.4
2020-09-03 16:51:20 root: INFO: Timer: Time taken for optimize: relationalLowerer, initial IR -- Verify : 0.094ms, total 371.173ms
2020-09-03 16:51:20 root: INFO: Timer: Time taken for optimize: relationalLowerer, initial IR : 314.740ms, total 371.381ms, tagged coverage 86.9
2020-09-03 16:51:20 root: INFO: Timer: Time taken for LowerMatrixToTable -- Verify : 0.063ms, total 373.302ms
2020-09-03 16:51:20 root: INFO: Timer: Time taken for LowerMatrixToTable -- LoweringTransformation : 12.726ms, total 386.212ms
2020-09-03 16:51:20 root: INFO: Timer: Time taken for LowerMatrixToTable -- Verify : 0.102ms, total 386.603ms
2020-09-03 16:51:20 root: INFO: Timer: Time taken for LowerMatrixToTable : 13.481ms, total 386.714ms, tagged coverage 95.6
2020-09-03 16:51:20 root: INFO: Timer: Time taken for optimize: relationalLowerer, after LowerMatrixToTable -- Verify : 0.121ms, total 390.537ms
2020-09-03 16:51:20 root: INFO: optimize optimize: relationalLowerer, after LowerMatrixToTable: before: IR size 43: 
(TableCount
  (TableFilter
    (TableIntervalJoin __uid_4 False
      (TableKeyBy (locus) False
        (TableMapRows
          (TableKeyBy () False
            (TableFilter
              (TableMapRows
                (TableRange 64444167 128)
                (InsertFields
                  (Ref row)
                  None
                  (locus
                    (Apply Locus () Locus(GRCh38)
                      (Str "chr20")
                      (ApplyBinaryPrimOp Add
                        (GetField idx
                          (Ref row))
                        (I32 1))))))
              (Let __iruid_36
                (GetField locus
                  (Ref row))
                (Coalesce
                  (ApplyComparisonOp NEQ
                    (Apply lower () String
                      (ApplyIR getReferenceSequence (Locus(GRCh38)) String
                        (Apply contig () String
                          (Ref __iruid_36))
                        (Apply position () Int32
                          (Ref __iruid_36))
                        (I32 0)
                        (I32 0)))
                    (Str "n"))
                  (False)))))
          (If
            (IsNA
              (Ref row))
            (NA Struct{locus:Locus(GRCh38)})
            (MakeStruct
              (locus
                (GetField locus
                  (Ref row)))))))
      (TableRead Table{global:Struct{},key:[interval],row:Struct{interval:Interval[Locus(GRCh38)]}} False "{\"path\":\"gs://gnomad-public/resources/grch38/telomeres_and_centromeres/hg38.telomeresAndMergedCentromeres.ht\",\"name\":\"TableNativeReader\"}"))
    (IsNA
      (GetField __uid_4
        (Ref row)))))
2020-09-03 16:51:20 root: INFO: Timer: Time taken for optimize: relationalLowerer, after LowerMatrixToTable -- LoweringTransformation -- Optimize -- FoldConstants : 0.655ms, total 393.902ms
2020-09-03 16:51:20 root: INFO: Timer: Time taken for optimize: relationalLowerer, after LowerMatrixToTable -- LoweringTransformation -- Optimize -- ExtractIntervalFilters : 5.226ms, total 399.335ms
2020-09-03 16:51:20 root: INFO: Timer: Time taken for optimize: relationalLowerer, after LowerMatrixToTable -- LoweringTransformation -- Optimize -- Simplify : 1.570ms, total 401.171ms
2020-09-03 16:51:20 root: INFO: Timer: Time taken for optimize: relationalLowerer, after LowerMatrixToTable -- LoweringTransformation -- Optimize -- ForwardLets : 4.589ms, total 406.156ms
2020-09-03 16:51:20 root: INFO: Timer: Time taken for optimize: relationalLowerer, after LowerMatrixToTable -- LoweringTransformation -- Optimize -- ForwardRelationalLets : 0.308ms, total 406.757ms
2020-09-03 16:51:20 root: INFO: Timer: Time taken for optimize: relationalLowerer, after LowerMatrixToTable -- LoweringTransformation -- Optimize -- PruneDeadFields : 4.037ms, total 410.962ms
2020-09-03 16:51:20 root: INFO: Timer: Time taken for optimize: relationalLowerer, after LowerMatrixToTable -- LoweringTransformation -- Optimize -- FoldConstants : 0.502ms, total 411.719ms
2020-09-03 16:51:20 root: INFO: Timer: Time taken for optimize: relationalLowerer, after LowerMatrixToTable -- LoweringTransformation -- Optimize -- ExtractIntervalFilters : 0.703ms, total 412.576ms
2020-09-03 16:51:20 root: INFO: Timer: Time taken for optimize: relationalLowerer, after LowerMatrixToTable -- LoweringTransformation -- Optimize -- Simplify : 1.076ms, total 413.816ms
2020-09-03 16:51:20 root: INFO: Timer: Time taken for optimize: relationalLowerer, after LowerMatrixToTable -- LoweringTransformation -- Optimize -- ForwardLets : 4.904ms, total 418.892ms
2020-09-03 16:51:20 root: INFO: Timer: Time taken for optimize: relationalLowerer, after LowerMatrixToTable -- LoweringTransformation -- Optimize -- ForwardRelationalLets : 0.374ms, total 419.503ms
2020-09-03 16:51:20 root: INFO: Timer: Time taken for optimize: relationalLowerer, after LowerMatrixToTable -- LoweringTransformation -- Optimize -- PruneDeadFields : 5.728ms, total 425.392ms
2020-09-03 16:51:20 root: INFO: Timer: Time taken for optimize: relationalLowerer, after LowerMatrixToTable -- LoweringTransformation -- Optimize -- FoldConstants : 0.592ms, total 426.302ms
2020-09-03 16:51:20 root: INFO: Timer: Time taken for optimize: relationalLowerer, after LowerMatrixToTable -- LoweringTransformation -- Optimize -- ExtractIntervalFilters : 0.652ms, total 427.145ms
2020-09-03 16:51:20 root: INFO: Timer: Time taken for optimize: relationalLowerer, after LowerMatrixToTable -- LoweringTransformation -- Optimize -- Simplify : 0.910ms, total 428.213ms
2020-09-03 16:51:20 root: INFO: Timer: Time taken for optimize: relationalLowerer, after LowerMatrixToTable -- LoweringTransformation -- Optimize -- ForwardLets : 4.238ms, total 432.607ms
2020-09-03 16:51:20 root: INFO: Timer: Time taken for optimize: relationalLowerer, after LowerMatrixToTable -- LoweringTransformation -- Optimize -- ForwardRelationalLets : 0.228ms, total 433.066ms
2020-09-03 16:51:20 root: INFO: Timer: Time taken for optimize: relationalLowerer, after LowerMatrixToTable -- LoweringTransformation -- Optimize -- PruneDeadFields : 3.798ms, total 437.009ms
2020-09-03 16:51:20 root: INFO: Timer: Time taken for optimize: relationalLowerer, after LowerMatrixToTable -- LoweringTransformation -- Optimize : 43.982ms, total 437.223ms, tagged coverage 91.2
2020-09-03 16:51:20 root: INFO: optimize optimize: relationalLowerer, after LowerMatrixToTable: after: IR size 43:
(TableCount
  (TableFilter
    (TableIntervalJoin __uid_4 False
      (TableKeyBy (locus) False
        (TableMapRows
          (TableKeyBy () False
            (TableFilter
              (TableMapRows
                (TableRange 64444167 128)
                (InsertFields
                  (Ref row)
                  None
                  (locus
                    (Apply Locus () Locus(GRCh38)
                      (Str "chr20")
                      (ApplyBinaryPrimOp Add
                        (GetField idx
                          (Ref row))
                        (I32 1))))))
              (Let __iruid_75
                (GetField locus
                  (Ref row))
                (Coalesce
                  (ApplyComparisonOp NEQ
                    (Apply lower () String
                      (ApplyIR getReferenceSequence (Locus(GRCh38)) String
                        (Apply contig () String
                          (Ref __iruid_75))
                        (Apply position () Int32
                          (Ref __iruid_75))
                        (I32 0)
                        (I32 0)))
                    (Str "n"))
                  (False)))))
          (If
            (IsNA
              (Ref row))
            (NA Struct{locus:Locus(GRCh38)})
            (MakeStruct
              (locus
                (GetField locus
                  (Ref row)))))))
      (TableRead Table{global:Struct{},key:[interval],row:Struct{interval:Interval[Locus(GRCh38)]}} False "{\"path\":\"gs://gnomad-public/resources/grch38/telomeres_and_centromeres/hg38.telomeresAndMergedCentromeres.ht\",\"name\":\"TableNativeReader\"}"))
    (IsNA
      (GetField __uid_4
        (Ref row)))))
2020-09-03 16:51:20 root: INFO: Timer: Time taken for optimize: relationalLowerer, after LowerMatrixToTable -- LoweringTransformation : 48.647ms, total 439.505ms, tagged coverage 82.4
2020-09-03 16:51:20 root: INFO: Timer: Time taken for optimize: relationalLowerer, after LowerMatrixToTable -- Verify : 0.051ms, total 439.728ms
2020-09-03 16:51:20 root: INFO: Timer: Time taken for optimize: relationalLowerer, after LowerMatrixToTable : 49.418ms, total 439.822ms, tagged coverage 81.5
2020-09-03 16:51:20 root: INFO: Timer: Time taken for InterpretNonCompilable -- Verify : 0.058ms, total 440.741ms
2020-09-03 16:51:20 root: INFO: interpreting non compilable node: TableCount
2020-09-03 16:51:21 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, initial IR -- Verify : 0.128ms, total 840.456ms
2020-09-03 16:51:21 root: INFO: optimize optimize: compileLowerer, initial IR: before: IR size 11: 
(Coalesce
  (InsertFields
    (In +PCStruct{idx:+PInt32} 1)
    None
    (locus
      (Apply Locus () Locus(GRCh38)
        (Str "chr20")
        (ApplyBinaryPrimOp Add
          (GetField idx
            (In +PCStruct{idx:+PInt32} 1))
          (I32 1)))))
  (Die Struct{idx:Int32,locus:Locus(GRCh38)}
    (Str "Internal e...")))
2020-09-03 16:51:21 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, initial IR -- LoweringTransformation -- Optimize -- FoldConstants : 0.712ms, total 843.415ms
2020-09-03 16:51:21 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, initial IR -- LoweringTransformation -- Optimize -- ExtractIntervalFilters : 0.098ms, total 843.740ms
2020-09-03 16:51:21 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, initial IR -- LoweringTransformation -- Optimize -- Simplify : 0.190ms, total 844.039ms
2020-09-03 16:51:21 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, initial IR -- LoweringTransformation -- Optimize -- ForwardLets : 1.918ms, total 846.116ms
2020-09-03 16:51:21 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, initial IR -- LoweringTransformation -- Optimize -- ForwardRelationalLets : 0.083ms, total 846.390ms
2020-09-03 16:51:21 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, initial IR -- LoweringTransformation -- Optimize -- PruneDeadFields : 0.865ms, total 847.394ms
2020-09-03 16:51:21 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, initial IR -- LoweringTransformation -- Optimize : 4.916ms, total 847.611ms, tagged coverage 78.6
2020-09-03 16:51:21 root: INFO: optimize optimize: compileLowerer, initial IR: after: IR size 11:
(Coalesce
  (InsertFields
    (In +PCStruct{idx:+PInt32} 1)
    None
    (locus
      (Apply Locus () Locus(GRCh38)
        (Str "chr20")
        (ApplyBinaryPrimOp Add
          (GetField idx
            (In +PCStruct{idx:+PInt32} 1))
          (I32 1)))))
  (Die Struct{idx:Int32,locus:Locus(GRCh38)}
    (Str "Internal e...")))
2020-09-03 16:51:21 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, initial IR -- LoweringTransformation : 7.690ms, total 848.417ms, tagged coverage 50.3
2020-09-03 16:51:21 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, initial IR -- Verify : 0.019ms, total 848.629ms
2020-09-03 16:51:21 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, initial IR : 8.395ms, total 848.716ms, tagged coverage 47.8
2020-09-03 16:51:21 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- InlineApplyIR -- Verify : 0.860ms, total 849.909ms
2020-09-03 16:51:21 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- InlineApplyIR -- LoweringTransformation : 0.952ms, total 851.023ms
2020-09-03 16:51:21 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- InlineApplyIR -- Verify : 0.040ms, total 851.219ms
2020-09-03 16:51:21 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- InlineApplyIR : 2.288ms, total 851.314ms, tagged coverage 81.0
2020-09-03 16:51:21 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, after InlineApplyIR -- Verify : 0.014ms, total 851.611ms
2020-09-03 16:51:21 root: INFO: optimize optimize: compileLowerer, after InlineApplyIR: before: IR size 11: 
(Coalesce
  (InsertFields
    (In +PCStruct{idx:+PInt32} 1)
    None
    (locus
      (Apply Locus () Locus(GRCh38)
        (Str "chr20")
        (ApplyBinaryPrimOp Add
          (GetField idx
            (In +PCStruct{idx:+PInt32} 1))
          (I32 1)))))
  (Die Struct{idx:Int32,locus:Locus(GRCh38)}
    (Str "Internal e...")))
2020-09-03 16:51:21 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, after InlineApplyIR -- LoweringTransformation -- Optimize -- FoldConstants : 0.164ms, total 852.333ms
2020-09-03 16:51:21 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, after InlineApplyIR -- LoweringTransformation -- Optimize -- ExtractIntervalFilters : 0.076ms, total 852.531ms
2020-09-03 16:51:21 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, after InlineApplyIR -- LoweringTransformation -- Optimize -- Simplify : 0.176ms, total 852.803ms
2020-09-03 16:51:21 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, after InlineApplyIR -- LoweringTransformation -- Optimize -- ForwardLets : 0.953ms, total 853.862ms
2020-09-03 16:51:21 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, after InlineApplyIR -- LoweringTransformation -- Optimize -- ForwardRelationalLets : 0.081ms, total 854.092ms
2020-09-03 16:51:21 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, after InlineApplyIR -- LoweringTransformation -- Optimize -- PruneDeadFields : 0.620ms, total 854.820ms
2020-09-03 16:51:21 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, after InlineApplyIR -- LoweringTransformation -- Optimize : 2.840ms, total 855.003ms, tagged coverage 72.9
2020-09-03 16:51:21 root: INFO: optimize optimize: compileLowerer, after InlineApplyIR: after: IR size 11:
(Coalesce
  (InsertFields
    (In +PCStruct{idx:+PInt32} 1)
    None
    (locus
      (Apply Locus () Locus(GRCh38)
        (Str "chr20")
        (ApplyBinaryPrimOp Add
          (GetField idx
            (In +PCStruct{idx:+PInt32} 1))
          (I32 1)))))
  (Die Struct{idx:Int32,locus:Locus(GRCh38)}
    (Str "Internal e...")))
2020-09-03 16:51:21 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, after InlineApplyIR -- LoweringTransformation : 3.840ms, total 855.561ms, tagged coverage 53.9
2020-09-03 16:51:21 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, after InlineApplyIR -- Verify : 0.017ms, total 855.705ms
2020-09-03 16:51:21 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, after InlineApplyIR : 4.194ms, total 855.788ms, tagged coverage 50.1
2020-09-03 16:51:21 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- LowerArrayAggsToRunAggs -- Verify : 0.050ms, total 856.115ms
2020-09-03 16:51:21 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- LowerArrayAggsToRunAggs -- LoweringTransformation : 5.634ms, total 861.874ms
2020-09-03 16:51:21 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- LowerArrayAggsToRunAggs -- Verify : 0.519ms, total 862.652ms
2020-09-03 16:51:21 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- LowerArrayAggsToRunAggs : 6.834ms, total 862.897ms, tagged coverage 90.8
2020-09-03 16:51:21 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, after LowerArrayAggsToRunAggs -- Verify : 0.021ms, total 863.393ms
2020-09-03 16:51:21 root: INFO: optimize optimize: compileLowerer, after LowerArrayAggsToRunAggs: before: IR size 11: 
(Coalesce
  (InsertFields
    (In +PCStruct{idx:+PInt32} 1)
    None
    (locus
      (Apply Locus () Locus(GRCh38)
        (Str "chr20")
        (ApplyBinaryPrimOp Add
          (GetField idx
            (In +PCStruct{idx:+PInt32} 1))
          (I32 1)))))
  (Die Struct{idx:Int32,locus:Locus(GRCh38)}
    (Str "Internal e...")))
2020-09-03 16:51:21 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, after LowerArrayAggsToRunAggs -- LoweringTransformation -- Optimize -- FoldConstants : 0.181ms, total 864.176ms
2020-09-03 16:51:21 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, after LowerArrayAggsToRunAggs -- LoweringTransformation -- Optimize -- ExtractIntervalFilters : 0.099ms, total 866.219ms
2020-09-03 16:51:21 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, after LowerArrayAggsToRunAggs -- LoweringTransformation -- Optimize -- Simplify : 0.164ms, total 866.518ms
2020-09-03 16:51:21 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, after LowerArrayAggsToRunAggs -- LoweringTransformation -- Optimize -- ForwardLets : 1.875ms, total 868.498ms
2020-09-03 16:51:21 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, after LowerArrayAggsToRunAggs -- LoweringTransformation -- Optimize -- ForwardRelationalLets : 0.079ms, total 868.754ms
2020-09-03 16:51:21 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, after LowerArrayAggsToRunAggs -- LoweringTransformation -- Optimize -- PruneDeadFields : 0.832ms, total 869.820ms
2020-09-03 16:51:21 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, after LowerArrayAggsToRunAggs -- LoweringTransformation -- Optimize : 6.008ms, total 869.997ms, tagged coverage 53.7
2020-09-03 16:51:21 root: INFO: optimize optimize: compileLowerer, after LowerArrayAggsToRunAggs: after: IR size 11:
(Coalesce
  (InsertFields
    (In +PCStruct{idx:+PInt32} 1)
    None
    (locus
      (Apply Locus () Locus(GRCh38)
        (Str "chr20")
        (ApplyBinaryPrimOp Add
          (GetField idx
            (In +PCStruct{idx:+PInt32} 1))
          (I32 1)))))
  (Die Struct{idx:Int32,locus:Locus(GRCh38)}
    (Str "Internal e...")))
2020-09-03 16:51:21 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, after LowerArrayAggsToRunAggs -- LoweringTransformation : 7.051ms, total 870.611ms, tagged coverage 45.8
2020-09-03 16:51:21 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, after LowerArrayAggsToRunAggs -- Verify : 0.019ms, total 870.792ms
2020-09-03 16:51:21 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, after LowerArrayAggsToRunAggs : 7.510ms, total 870.876ms, tagged coverage 43.5
2020-09-03 16:51:22 root: INFO: encoder cache miss (0 hits, 1 misses, 0.000)
2020-09-03 16:51:22 root: INFO: instruction count: 6: __C20etypeEncode.<init>
2020-09-03 16:51:22 root: INFO: instruction count: 8: __C20etypeEncode.apply
2020-09-03 16:51:22 root: INFO: instruction count: 8: __C20etypeEncode.__m21ENCODE_r_tuple_of_r_stringANDr_stringEND_TO_r_struct_of_r_binaryANDr_binaryEND
2020-09-03 16:51:22 root: INFO: instruction count: 24: __C20etypeEncode.__m22write_fields_group_0
2020-09-03 16:51:22 root: INFO: instruction count: 19: __C20etypeEncode.__m23ENCODE_r_binary_TO_r_binary
2020-09-03 16:51:22 MemoryStore: INFO: Block broadcast_2 stored as values in memory (estimated size 136.0 B, free 21.7 GB)
2020-09-03 16:51:22 MemoryStore: INFO: Block broadcast_2_piece0 stored as bytes in memory (estimated size 118.0 B, free 21.7 GB)
2020-09-03 16:51:22 BlockManagerInfo: INFO: Added broadcast_2_piece0 in memory on jg3-m.c.maclab-ukbb.internal:36967 (size: 118.0 B, free: 21.7 GB)
2020-09-03 16:51:22 SparkContext: INFO: Created broadcast 2 from broadcast at SparkBackend.scala:233
2020-09-03 16:51:22 root: INFO: instruction count: 6: __C1Compiled.<init>
2020-09-03 16:51:22 root: INFO: instruction count: 82: __C1Compiled.apply
2020-09-03 16:51:22 root: INFO: instruction count: 63: __C1Compiled.__m5Locus
2020-09-03 16:51:22 root: INFO: instruction count: 8: __C1Compiled.__m10addIRIntermediate
2020-09-03 16:51:22 root: INFO: instruction count: 11: __C1Compiled.__m12addIRIntermediate
2020-09-03 16:51:22 root: INFO: instruction count: 14: __C1Compiled.setPartitionIndex
2020-09-03 16:51:22 root: INFO: instruction count: 7: __C1Compiled.addPartitionRegion
2020-09-03 16:51:22 root: INFO: instruction count: 25: __C1Compiled.__m16DECODE_r_struct_of_r_binaryANDr_binaryEND_TO_r_tuple_of_r_stringANDr_stringEND
2020-09-03 16:51:22 root: INFO: instruction count: 18: __C1Compiled.__m17read_fields_group_0
2020-09-03 16:51:22 root: INFO: instruction count: 34: __C1Compiled.__m18INPLACE_DECODE_r_binary_TO_r_binary
2020-09-03 16:51:22 root: INFO: instruction count: 50: __C1Compiled.addLiterals
2020-09-03 16:51:22 root: INFO: instruction count: 6: __C8RGContainer_GRCh38.<init>
2020-09-03 16:51:22 root: INFO: instruction count: 27: __C8RGContainer_GRCh38.<clinit>
2020-09-03 16:51:22 root: INFO: instruction count: 6: __C9FSContainer.<init>
2020-09-03 16:51:22 root: INFO: instruction count: 31: __C9FSContainer.init_filesystem
2020-09-03 16:51:22 root: INFO: instruction count: 6: __C9FSContainer.<clinit>
2020-09-03 16:51:22 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, initial IR -- Verify : 0.162ms, total 1.979s
2020-09-03 16:51:22 root: INFO: optimize optimize: compileLowerer, initial IR: before: IR size 17: 
(Coalesce
  (Let __iruid_75
    (GetField locus
      (In +PCStruct{idx:+PInt32,locus:+PCLocus(GRCh38)} 0))
    (Coalesce
      (ApplyComparisonOp NEQ
        (Apply lower () String
          (ApplyIR getReferenceSequence (Locus(GRCh38)) String
            (Apply contig () String
              (Ref __iruid_75))
            (Apply position () Int32
              (Ref __iruid_75))
            (I32 0)
            (I32 0)))
        (Str "n"))
      (False)))
  (False))
2020-09-03 16:51:22 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, initial IR -- LoweringTransformation -- Optimize -- FoldConstants : 0.726ms, total 1.982s
2020-09-03 16:51:22 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, initial IR -- LoweringTransformation -- Optimize -- ExtractIntervalFilters : 0.090ms, total 1.982s
2020-09-03 16:51:22 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, initial IR -- LoweringTransformation -- Optimize -- Simplify : 0.586ms, total 1.983s
2020-09-03 16:51:22 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, initial IR -- LoweringTransformation -- Optimize -- ForwardLets : 1.823ms, total 1.985s
2020-09-03 16:51:22 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, initial IR -- LoweringTransformation -- Optimize -- ForwardRelationalLets : 0.306ms, total 1.986s
2020-09-03 16:51:22 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, initial IR -- LoweringTransformation -- Optimize -- PruneDeadFields : 2.324ms, total 1.988s
2020-09-03 16:51:22 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, initial IR -- LoweringTransformation -- Optimize -- FoldConstants : 0.237ms, total 1.989s
2020-09-03 16:51:22 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, initial IR -- LoweringTransformation -- Optimize -- ExtractIntervalFilters : 0.080ms, total 1.989s
2020-09-03 16:51:22 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, initial IR -- LoweringTransformation -- Optimize -- Simplify : 0.758ms, total 1.990s
2020-09-03 16:51:22 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, initial IR -- LoweringTransformation -- Optimize -- ForwardLets : 1.753ms, total 1.992s
2020-09-03 16:51:22 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, initial IR -- LoweringTransformation -- Optimize -- ForwardRelationalLets : 0.219ms, total 1.992s
2020-09-03 16:51:22 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, initial IR -- LoweringTransformation -- Optimize -- PruneDeadFields : 1.618ms, total 1.994s
2020-09-03 16:51:22 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, initial IR -- LoweringTransformation -- Optimize -- FoldConstants : 0.206ms, total 1.994s
2020-09-03 16:51:22 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, initial IR -- LoweringTransformation -- Optimize -- ExtractIntervalFilters : 0.187ms, total 1.995s
2020-09-03 16:51:22 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, initial IR -- LoweringTransformation -- Optimize -- Simplify : 0.459ms, total 1.995s
2020-09-03 16:51:22 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, initial IR -- LoweringTransformation -- Optimize -- ForwardLets : 1.983ms, total 1.997s
2020-09-03 16:51:22 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, initial IR -- LoweringTransformation -- Optimize -- ForwardRelationalLets : 0.149ms, total 1.998s
2020-09-03 16:51:22 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, initial IR -- LoweringTransformation -- Optimize -- PruneDeadFields : 1.493ms, total 1.999s
2020-09-03 16:51:22 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, initial IR -- LoweringTransformation -- Optimize : 18.072ms, total 2.000s, tagged coverage 83.0
2020-09-03 16:51:22 root: INFO: optimize optimize: compileLowerer, initial IR: after: IR size 17:
(Coalesce
  (Let __iruid_119
    (GetField locus
      (In +PCStruct{idx:+PInt32,locus:+PCLocus(GRCh38)} 0))
    (Coalesce
      (ApplyComparisonOp NEQ
        (Apply lower () String
          (ApplyIR getReferenceSequence (Locus(GRCh38)) String
            (Apply contig () String
              (Ref __iruid_119))
            (Apply position () Int32
              (Ref __iruid_119))
            (I32 0)
            (I32 0)))
        (Str "n"))
      (False)))
  (False))
2020-09-03 16:51:22 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, initial IR -- LoweringTransformation : 20.671ms, total 2.000s, tagged coverage 72.6
2020-09-03 16:51:22 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, initial IR -- Verify : 0.025ms, total 2.001s
2020-09-03 16:51:22 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, initial IR : 21.366ms, total 2.001s, tagged coverage 71.1
2020-09-03 16:51:22 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- InlineApplyIR -- Verify : 0.039ms, total 2.001s
2020-09-03 16:51:22 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- InlineApplyIR -- LoweringTransformation : 1.436ms, total 2.003s
2020-09-03 16:51:22 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- InlineApplyIR -- Verify : 0.092ms, total 2.003s
2020-09-03 16:51:22 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- InlineApplyIR : 2.030ms, total 2.003s, tagged coverage 77.2
2020-09-03 16:51:22 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, after InlineApplyIR -- Verify : 0.054ms, total 2.004s
2020-09-03 16:51:22 root: INFO: optimize optimize: compileLowerer, after InlineApplyIR: before: IR size 30: 
(Coalesce
  (Let __iruid_119
    (GetField locus
      (In +PCStruct{idx:+PInt32,locus:+PCLocus(GRCh38)} 0))
    (Coalesce
      (ApplyComparisonOp NEQ
        (Apply lower () String
          (Let __iruid_124
            (Apply contig () String
              (Ref __iruid_119))
            (Let __iruid_125
              (Apply position () Int32
                (Ref __iruid_119))
              (Let __iruid_126
                (I32 0)
                (Let __iruid_127
                  (I32 0)
                  (If
                    (Apply isValidLocus (Locus(GRCh38)) Boolean
                      (Ref __iruid_124)
                      (Ref __iruid_125))
                    (Apply getReferenceSequenceFromValidLocus (Locus(GRCh38)) String
                      (Ref __iruid_124)
                      (Ref __iruid_125)
                      (Ref __iruid_126)
                      (Ref __iruid_127))
                    (NA String)))))))
        (Str "n"))
      (False)))
  (False))
2020-09-03 16:51:22 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, after InlineApplyIR -- LoweringTransformation -- Optimize -- FoldConstants : 0.288ms, total 2.005s
2020-09-03 16:51:22 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, after InlineApplyIR -- LoweringTransformation -- Optimize -- ExtractIntervalFilters : 0.265ms, total 2.006s
2020-09-03 16:51:22 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, after InlineApplyIR -- LoweringTransformation -- Optimize -- Simplify : 0.409ms, total 2.006s
2020-09-03 16:51:22 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, after InlineApplyIR -- LoweringTransformation -- Optimize -- ForwardLets : 2.575ms, total 2.009s
2020-09-03 16:51:22 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, after InlineApplyIR -- LoweringTransformation -- Optimize -- ForwardRelationalLets : 0.232ms, total 2.010s
2020-09-03 16:51:22 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, after InlineApplyIR -- LoweringTransformation -- Optimize -- PruneDeadFields : 1.416ms, total 2.011s
2020-09-03 16:51:22 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, after InlineApplyIR -- LoweringTransformation -- Optimize -- FoldConstants : 0.283ms, total 2.012s
2020-09-03 16:51:22 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, after InlineApplyIR -- LoweringTransformation -- Optimize -- ExtractIntervalFilters : 0.159ms, total 2.012s
2020-09-03 16:51:22 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, after InlineApplyIR -- LoweringTransformation -- Optimize -- Simplify : 0.298ms, total 2.012s
2020-09-03 16:51:22 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, after InlineApplyIR -- LoweringTransformation -- Optimize -- ForwardLets : 2.935ms, total 2.016s
2020-09-03 16:51:22 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, after InlineApplyIR -- LoweringTransformation -- Optimize -- ForwardRelationalLets : 0.170ms, total 2.016s
2020-09-03 16:51:22 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, after InlineApplyIR -- LoweringTransformation -- Optimize -- PruneDeadFields : 1.437ms, total 2.018s
2020-09-03 16:51:22 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, after InlineApplyIR -- LoweringTransformation -- Optimize -- FoldConstants : 0.259ms, total 2.018s
2020-09-03 16:51:22 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, after InlineApplyIR -- LoweringTransformation -- Optimize -- ExtractIntervalFilters : 0.114ms, total 2.018s
2020-09-03 16:51:22 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, after InlineApplyIR -- LoweringTransformation -- Optimize -- Simplify : 0.319ms, total 2.019s
2020-09-03 16:51:22 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, after InlineApplyIR -- LoweringTransformation -- Optimize -- ForwardLets : 2.661ms, total 2.022s
2020-09-03 16:51:22 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, after InlineApplyIR -- LoweringTransformation -- Optimize -- ForwardRelationalLets : 0.165ms, total 2.022s
2020-09-03 16:51:22 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, after InlineApplyIR -- LoweringTransformation -- Optimize -- PruneDeadFields : 1.142ms, total 2.023s
2020-09-03 16:51:22 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, after InlineApplyIR -- LoweringTransformation -- Optimize : 18.283ms, total 2.023s, tagged coverage 82.7
2020-09-03 16:51:22 root: INFO: optimize optimize: compileLowerer, after InlineApplyIR: after: IR size 26:
(Coalesce
  (Let __iruid_136
    (GetField locus
      (In +PCStruct{idx:+PInt32,locus:+PCLocus(GRCh38)} 0))
    (Coalesce
      (ApplyComparisonOp NEQ
        (Apply lower () String
          (Let __iruid_137
            (Apply contig () String
              (Ref __iruid_136))
            (Let __iruid_138
              (Apply position () Int32
                (Ref __iruid_136))
              (If
                (Apply isValidLocus (Locus(GRCh38)) Boolean
                  (Ref __iruid_137)
                  (Ref __iruid_138))
                (Apply getReferenceSequenceFromValidLocus (Locus(GRCh38)) String
                  (Ref __iruid_137)
                  (Ref __iruid_138)
                  (I32 0)
                  (I32 0))
                (NA String)))))
        (Str "n"))
      (False)))
  (False))
2020-09-03 16:51:22 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, after InlineApplyIR -- LoweringTransformation : 20.891ms, total 2.025s, tagged coverage 72.4
2020-09-03 16:51:22 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, after InlineApplyIR -- Verify : 0.064ms, total 2.025s
2020-09-03 16:51:22 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, after InlineApplyIR : 21.794ms, total 2.025s, tagged coverage 70.0
2020-09-03 16:51:22 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- LowerArrayAggsToRunAggs -- Verify : 0.065ms, total 2.026s
2020-09-03 16:51:22 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- LowerArrayAggsToRunAggs -- LoweringTransformation : 10.003ms, total 2.036s
2020-09-03 16:51:22 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- LowerArrayAggsToRunAggs -- Verify : 0.086ms, total 2.037s
2020-09-03 16:51:22 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- LowerArrayAggsToRunAggs : 10.780ms, total 2.037s, tagged coverage 94.2
2020-09-03 16:51:22 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, after LowerArrayAggsToRunAggs -- Verify : 0.048ms, total 2.037s
2020-09-03 16:51:22 root: INFO: optimize optimize: compileLowerer, after LowerArrayAggsToRunAggs: before: IR size 26: 
(Coalesce
  (Let __iruid_136
    (GetField locus
      (In +PCStruct{idx:+PInt32,locus:+PCLocus(GRCh38)} 0))
    (Coalesce
      (ApplyComparisonOp NEQ
        (Apply lower () String
          (Let __iruid_137
            (Apply contig () String
              (Ref __iruid_136))
            (Let __iruid_138
              (Apply position () Int32
                (Ref __iruid_136))
              (If
                (Apply isValidLocus (Locus(GRCh38)) Boolean
                  (Ref __iruid_137)
                  (Ref __iruid_138))
                (Apply getReferenceSequenceFromValidLocus (Locus(GRCh38)) String
                  (Ref __iruid_137)
                  (Ref __iruid_138)
                  (I32 0)
                  (I32 0))
                (NA String)))))
        (Str "n"))
      (False)))
  (False))
2020-09-03 16:51:22 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, after LowerArrayAggsToRunAggs -- LoweringTransformation -- Optimize -- FoldConstants : 0.460ms, total 2.039s
2020-09-03 16:51:22 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, after LowerArrayAggsToRunAggs -- LoweringTransformation -- Optimize -- ExtractIntervalFilters : 0.131ms, total 2.040s
2020-09-03 16:51:22 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, after LowerArrayAggsToRunAggs -- LoweringTransformation -- Optimize -- Simplify : 0.308ms, total 2.040s
2020-09-03 16:51:22 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, after LowerArrayAggsToRunAggs -- LoweringTransformation -- Optimize -- ForwardLets : 3.179ms, total 2.043s
2020-09-03 16:51:22 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, after LowerArrayAggsToRunAggs -- LoweringTransformation -- Optimize -- ForwardRelationalLets : 0.191ms, total 2.044s
2020-09-03 16:51:22 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, after LowerArrayAggsToRunAggs -- LoweringTransformation -- Optimize -- PruneDeadFields : 1.898ms, total 2.046s
2020-09-03 16:51:22 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, after LowerArrayAggsToRunAggs -- LoweringTransformation -- Optimize -- FoldConstants : 0.269ms, total 2.046s
2020-09-03 16:51:22 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, after LowerArrayAggsToRunAggs -- LoweringTransformation -- Optimize -- ExtractIntervalFilters : 0.105ms, total 2.047s
2020-09-03 16:51:22 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, after LowerArrayAggsToRunAggs -- LoweringTransformation -- Optimize -- Simplify : 0.333ms, total 2.047s
2020-09-03 16:51:22 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, after LowerArrayAggsToRunAggs -- LoweringTransformation -- Optimize -- ForwardLets : 1.710ms, total 2.049s
2020-09-03 16:51:22 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, after LowerArrayAggsToRunAggs -- LoweringTransformation -- Optimize -- ForwardRelationalLets : 0.115ms, total 2.049s
2020-09-03 16:51:22 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, after LowerArrayAggsToRunAggs -- LoweringTransformation -- Optimize -- PruneDeadFields : 1.063ms, total 2.050s
2020-09-03 16:51:22 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, after LowerArrayAggsToRunAggs -- LoweringTransformation -- Optimize -- FoldConstants : 0.318ms, total 2.051s
2020-09-03 16:51:22 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, after LowerArrayAggsToRunAggs -- LoweringTransformation -- Optimize -- ExtractIntervalFilters : 0.116ms, total 2.051s
2020-09-03 16:51:22 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, after LowerArrayAggsToRunAggs -- LoweringTransformation -- Optimize -- Simplify : 0.450ms, total 2.052s
2020-09-03 16:51:22 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, after LowerArrayAggsToRunAggs -- LoweringTransformation -- Optimize -- ForwardLets : 2.715ms, total 2.055s
2020-09-03 16:51:22 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, after LowerArrayAggsToRunAggs -- LoweringTransformation -- Optimize -- ForwardRelationalLets : 0.123ms, total 2.055s
2020-09-03 16:51:22 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, after LowerArrayAggsToRunAggs -- LoweringTransformation -- Optimize -- PruneDeadFields : 1.099ms, total 2.056s
2020-09-03 16:51:22 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, after LowerArrayAggsToRunAggs -- LoweringTransformation -- Optimize : 17.532ms, total 2.056s, tagged coverage 83.2
2020-09-03 16:51:22 root: INFO: optimize optimize: compileLowerer, after LowerArrayAggsToRunAggs: after: IR size 26:
(Coalesce
  (Let __iruid_145
    (GetField locus
      (In +PCStruct{idx:+PInt32,locus:+PCLocus(GRCh38)} 0))
    (Coalesce
      (ApplyComparisonOp NEQ
        (Apply lower () String
          (Let __iruid_146
            (Apply contig () String
              (Ref __iruid_145))
            (Let __iruid_147
              (Apply position () Int32
                (Ref __iruid_145))
              (If
                (Apply isValidLocus (Locus(GRCh38)) Boolean
                  (Ref __iruid_146)
                  (Ref __iruid_147))
                (Apply getReferenceSequenceFromValidLocus (Locus(GRCh38)) String
                  (Ref __iruid_146)
                  (Ref __iruid_147)
                  (I32 0)
                  (I32 0))
                (NA String)))))
        (Str "n"))
      (False)))
  (False))
2020-09-03 16:51:22 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, after LowerArrayAggsToRunAggs -- LoweringTransformation : 19.662ms, total 2.057s, tagged coverage 74.2
2020-09-03 16:51:22 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, after LowerArrayAggsToRunAggs -- Verify : 0.035ms, total 2.058s
2020-09-03 16:51:22 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, after LowerArrayAggsToRunAggs : 20.269ms, total 2.058s, tagged coverage 72.4
2020-09-03 16:51:22 root: INFO: encoder cache miss (0 hits, 2 misses, 0.000)
2020-09-03 16:51:22 root: INFO: instruction count: 6: __C52etypeEncode.<init>
2020-09-03 16:51:22 root: INFO: instruction count: 8: __C52etypeEncode.apply
2020-09-03 16:51:22 root: INFO: instruction count: 8: __C52etypeEncode.__m53ENCODE_r_tuple_of_r_stringEND_TO_r_struct_of_r_binaryEND
2020-09-03 16:51:22 root: INFO: instruction count: 14: __C52etypeEncode.__m54write_fields_group_0
2020-09-03 16:51:22 root: INFO: instruction count: 19: __C52etypeEncode.__m55ENCODE_r_binary_TO_r_binary
2020-09-03 16:51:22 MemoryStore: INFO: Block broadcast_3 stored as values in memory (estimated size 72.0 B, free 21.7 GB)
2020-09-03 16:51:22 MemoryStore: INFO: Block broadcast_3_piece0 stored as bytes in memory (estimated size 58.0 B, free 21.7 GB)
2020-09-03 16:51:22 BlockManagerInfo: INFO: Added broadcast_3_piece0 in memory on jg3-m.c.maclab-ukbb.internal:36967 (size: 58.0 B, free: 21.7 GB)
2020-09-03 16:51:22 SparkContext: INFO: Created broadcast 3 from broadcast at SparkBackend.scala:233
2020-09-03 16:51:22 root: INFO: instruction count: 6: __C24Compiled.<init>
2020-09-03 16:51:22 root: INFO: instruction count: 193: __C24Compiled.apply
2020-09-03 16:51:22 root: INFO: instruction count: 147: __C24Compiled.__m29cord
2020-09-03 16:51:22 root: INFO: instruction count: 64: __C24Compiled.__m30lower
2020-09-03 16:51:22 root: INFO: instruction count: 11: __C24Compiled.__m35contig
2020-09-03 16:51:22 root: INFO: instruction count: 11: __C24Compiled.__m38position
2020-09-03 16:51:22 root: INFO: instruction count: 28: __C24Compiled.__m39isValidLocus
2020-09-03 16:51:22 root: INFO: instruction count: 67: __C24Compiled.__m42getReferenceSequenceFromValidLocus
2020-09-03 16:51:22 root: INFO: instruction count: 14: __C24Compiled.setPartitionIndex
2020-09-03 16:51:22 root: INFO: instruction count: 7: __C24Compiled.addPartitionRegion
2020-09-03 16:51:22 root: INFO: instruction count: 25: __C24Compiled.__m48DECODE_r_struct_of_r_binaryEND_TO_r_tuple_of_r_stringEND
2020-09-03 16:51:22 root: INFO: instruction count: 11: __C24Compiled.__m49read_fields_group_0
2020-09-03 16:51:22 root: INFO: instruction count: 34: __C24Compiled.__m50INPLACE_DECODE_r_binary_TO_r_binary
2020-09-03 16:51:22 root: INFO: instruction count: 41: __C24Compiled.addLiterals
2020-09-03 16:51:22 root: INFO: instruction count: 6: __C40RGContainer_GRCh38.<init>
2020-09-03 16:51:22 root: INFO: instruction count: 27: __C40RGContainer_GRCh38.<clinit>
2020-09-03 16:51:22 root: INFO: instruction count: 6: __C41FSContainer.<init>
2020-09-03 16:51:22 root: INFO: instruction count: 31: __C41FSContainer.init_filesystem
2020-09-03 16:51:22 root: INFO: instruction count: 6: __C41FSContainer.<clinit>
2020-09-03 16:51:22 root: INFO: encoder cache miss (0 hits, 3 misses, 0.000)
2020-09-03 16:51:22 root: INFO: instruction count: 6: __C56etypeEncode.<init>
2020-09-03 16:51:22 root: INFO: instruction count: 8: __C56etypeEncode.apply
2020-09-03 16:51:22 root: INFO: instruction count: 4: __C56etypeEncode.__m57ENCODE_r_tuple_of_END_TO_r_struct_of_END
2020-09-03 16:51:22 root: INFO: decoder cache miss (0 hits, 1 misses, 0.000
2020-09-03 16:51:22 root: INFO: instruction count: 6: __C58etypeDecode.<init>
2020-09-03 16:51:22 root: INFO: instruction count: 8: __C58etypeDecode.apply
2020-09-03 16:51:22 root: INFO: instruction count: 19: __C58etypeDecode.__m59DECODE_r_struct_of_END_TO_r_tuple_of_END
2020-09-03 16:51:22 MemoryStore: INFO: Block broadcast_4 stored as values in memory (estimated size 2.5 KB, free 21.7 GB)
2020-09-03 16:51:22 MemoryStore: INFO: Block broadcast_4_piece0 stored as bytes in memory (estimated size 944.0 B, free 21.7 GB)
2020-09-03 16:51:22 BlockManagerInfo: INFO: Added broadcast_4_piece0 in memory on jg3-m.c.maclab-ukbb.internal:36967 (size: 944.0 B, free: 21.7 GB)
2020-09-03 16:51:22 SparkContext: INFO: Created broadcast 4 from broadcast at SparkBackend.scala:233
2020-09-03 16:51:22 root: INFO: keysIfOneToOne struct{idx: int32} RVDPartitioner(struct{idx: int32}, [[[0]-[503471]),
[[503471]-[1006942]),
[[1006942]-[1510413]),
[[1510413]-[2013884]),
[[2013884]-[2517355]),
[[2517355]-[3020826]),
[[3020826]-[3524297]),
[[3524297]-[4027767]),
[[4027767]-[4531237]),
[[4531237]-[5034707]),
[[5034707]-[5538177]),
[[5538177]-[6041647]),
[[6041647]-[6545117]),
[[6545117]-[7048587]),
[[7048587]-[7552057]),
[[7552057]-[8055527]),
[[8055527]-[8558997]),
[[8558997]-[9062467]),
[[9062467]-[9565937]),
[[9565937]-[10069407]),
[[10069407]-[10572877]),
[[10572877]-[11076347]),
[[11076347]-[11579817]),
[[11579817]-[12083287]),
[[12083287]-[12586757]),
[[12586757]-[13090227]),
[[13090227]-[13593697]),
[[13593697]-[14097167]),
[[14097167]-[14600637]),
[[14600637]-[15104107]),
[[15104107]-[15607577]),
[[15607577]-[16111047]),
[[16111047]-[16614517]),
[[16614517]-[17117987]),
[[17117987]-[17621457]),
[[17621457]-[18124927]),
[[18124927]-[18628397]),
[[18628397]-[19131867]),
[[19131867]-[19635337]),
[[19635337]-[20138807]),
[[20138807]-[20642277]),
[[20642277]-[21145747]),
[[21145747]-[21649217]),
[[21649217]-[22152687]),
[[22152687]-[22656157]),
[[22656157]-[23159627]),
[[23159627]-[23663097]),
[[23663097]-[24166567]),
[[24166567]-[24670037]),
[[24670037]-[25173507]),
[[25173507]-[25676977]),
[[25676977]-[26180447]),
[[26180447]-[26683917]),
[[26683917]-[27187387]),
[[27187387]-[27690857]),
[[27690857]-[28194327]),
[[28194327]-[28697797]),
[[28697797]-[29201267]),
[[29201267]-[29704737]),
[[29704737]-[30208207]),
[[30208207]-[30711677]),
[[30711677]-[31215147]),
[[31215147]-[31718617]),
[[31718617]-[32222087]),
[[32222087]-[32725557]),
[[32725557]-[33229027]),
[[33229027]-[33732497]),
[[33732497]-[34235967]),
[[34235967]-[34739437]),
[[34739437]-[35242907]),
[[35242907]-[35746377]),
[[35746377]-[36249847]),
[[36249847]-[36753317]),
[[36753317]-[37256787]),
[[37256787]-[37760257]),
[[37760257]-[38263727]),
[[38263727]-[38767197]),
[[38767197]-[39270667]),
[[39270667]-[39774137]),
[[39774137]-[40277607]),
[[40277607]-[40781077]),
[[40781077]-[41284547]),
[[41284547]-[41788017]),
[[41788017]-[42291487]),
[[42291487]-[42794957]),
[[42794957]-[43298427]),
[[43298427]-[43801897]),
[[43801897]-[44305367]),
[[44305367]-[44808837]),
[[44808837]-[45312307]),
[[45312307]-[45815777]),
[[45815777]-[46319247]),
[[46319247]-[46822717]),
[[46822717]-[47326187]),
[[47326187]-[47829657]),
[[47829657]-[48333127]),
[[48333127]-[48836597]),
[[48836597]-[49340067]),
[[49340067]-[49843537]),
[[49843537]-[50347007]),
[[50347007]-[50850477]),
[[50850477]-[51353947]),
[[51353947]-[51857417]),
[[51857417]-[52360887]),
[[52360887]-[52864357]),
[[52864357]-[53367827]),
[[53367827]-[53871297]),
[[53871297]-[54374767]),
[[54374767]-[54878237]),
[[54878237]-[55381707]),
[[55381707]-[55885177]),
[[55885177]-[56388647]),
[[56388647]-[56892117]),
[[56892117]-[57395587]),
[[57395587]-[57899057]),
[[57899057]-[58402527]),
[[58402527]-[58905997]),
[[58905997]-[59409467]),
[[59409467]-[59912937]),
[[59912937]-[60416407]),
[[60416407]-[60919877]),
[[60919877]-[61423347]),
[[61423347]-[61926817]),
[[61926817]-[62430287]),
[[62430287]-[62933757]),
[[62933757]-[63437227]),
[[63437227]-[63940697]),
[[63940697]-[64444167])])
2020-09-03 16:51:22 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, initial IR -- Verify : 0.049ms, total 2.269s
2020-09-03 16:51:22 root: INFO: optimize optimize: compileLowerer, initial IR: before: IR size 10: 
(Coalesce
  (If
    (IsNA
      (In +PCStruct{idx:+PInt32,locus:+PCLocus(GRCh38)} 1))
    (NA Struct{locus:Locus(GRCh38)})
    (MakeStruct
      (locus
        (GetField locus
          (In +PCStruct{idx:+PInt32,locus:+PCLocus(GRCh38)} 1)))))
  (Die Struct{locus:Locus(GRCh38)}
    (Str "Internal e...")))
2020-09-03 16:51:22 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, initial IR -- LoweringTransformation -- Optimize -- FoldConstants : 0.443ms, total 2.270s
2020-09-03 16:51:22 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, initial IR -- LoweringTransformation -- Optimize -- ExtractIntervalFilters : 0.444ms, total 2.271s
2020-09-03 16:51:22 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, initial IR -- LoweringTransformation -- Optimize -- Simplify : 0.214ms, total 2.272s
2020-09-03 16:51:22 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, initial IR -- LoweringTransformation -- Optimize -- ForwardLets : 8.069ms, total 2.280s
2020-09-03 16:51:22 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, initial IR -- LoweringTransformation -- Optimize -- ForwardRelationalLets : 0.127ms, total 2.280s
2020-09-03 16:51:22 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, initial IR -- LoweringTransformation -- Optimize -- PruneDeadFields : 0.692ms, total 2.281s
2020-09-03 16:51:22 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, initial IR -- LoweringTransformation -- Optimize : 11.460ms, total 2.281s, tagged coverage 87.2
2020-09-03 16:51:22 root: INFO: optimize optimize: compileLowerer, initial IR: after: IR size 10:
(Coalesce
  (If
    (IsNA
      (In +PCStruct{idx:+PInt32,locus:+PCLocus(GRCh38)} 1))
    (NA Struct{locus:Locus(GRCh38)})
    (MakeStruct
      (locus
        (GetField locus
          (In +PCStruct{idx:+PInt32,locus:+PCLocus(GRCh38)} 1)))))
  (Die Struct{locus:Locus(GRCh38)}
    (Str "Internal e...")))
2020-09-03 16:51:22 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, initial IR -- LoweringTransformation : 13.166ms, total 2.282s, tagged coverage 75.9
2020-09-03 16:51:22 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, initial IR -- Verify : 0.046ms, total 2.283s
2020-09-03 16:51:22 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, initial IR : 13.987ms, total 2.283s, tagged coverage 72.1
2020-09-03 16:51:22 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- InlineApplyIR -- Verify : 0.052ms, total 2.283s
2020-09-03 16:51:22 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- InlineApplyIR -- LoweringTransformation : 0.258ms, total 2.284s
2020-09-03 16:51:22 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- InlineApplyIR -- Verify : 0.062ms, total 2.284s
2020-09-03 16:51:22 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- InlineApplyIR : 1.015ms, total 2.284s, tagged coverage 36.6
2020-09-03 16:51:22 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, after InlineApplyIR -- Verify : 0.019ms, total 2.285s
2020-09-03 16:51:22 root: INFO: optimize optimize: compileLowerer, after InlineApplyIR: before: IR size 10: 
(Coalesce
  (If
    (IsNA
      (In +PCStruct{idx:+PInt32,locus:+PCLocus(GRCh38)} 1))
    (NA Struct{locus:Locus(GRCh38)})
    (MakeStruct
      (locus
        (GetField locus
          (In +PCStruct{idx:+PInt32,locus:+PCLocus(GRCh38)} 1)))))
  (Die Struct{locus:Locus(GRCh38)}
    (Str "Internal e...")))
2020-09-03 16:51:22 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, after InlineApplyIR -- LoweringTransformation -- Optimize -- FoldConstants : 0.297ms, total 2.286s
2020-09-03 16:51:22 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, after InlineApplyIR -- LoweringTransformation -- Optimize -- ExtractIntervalFilters : 0.184ms, total 2.286s
2020-09-03 16:51:22 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, after InlineApplyIR -- LoweringTransformation -- Optimize -- Simplify : 0.198ms, total 2.287s
2020-09-03 16:51:22 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, after InlineApplyIR -- LoweringTransformation -- Optimize -- ForwardLets : 1.341ms, total 2.288s
2020-09-03 16:51:22 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, after InlineApplyIR -- LoweringTransformation -- Optimize -- ForwardRelationalLets : 0.120ms, total 2.289s
2020-09-03 16:51:22 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, after InlineApplyIR -- LoweringTransformation -- Optimize -- PruneDeadFields : 0.640ms, total 2.289s
2020-09-03 16:51:22 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, after InlineApplyIR -- LoweringTransformation -- Optimize : 4.035ms, total 2.290s, tagged coverage 68.9
2020-09-03 16:51:22 root: INFO: optimize optimize: compileLowerer, after InlineApplyIR: after: IR size 10:
(Coalesce
  (If
    (IsNA
      (In +PCStruct{idx:+PInt32,locus:+PCLocus(GRCh38)} 1))
    (NA Struct{locus:Locus(GRCh38)})
    (MakeStruct
      (locus
        (GetField locus
          (In +PCStruct{idx:+PInt32,locus:+PCLocus(GRCh38)} 1)))))
  (Die Struct{locus:Locus(GRCh38)}
    (Str "Internal e...")))
2020-09-03 16:51:22 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, after InlineApplyIR -- LoweringTransformation : 5.472ms, total 2.290s, tagged coverage 50.8
2020-09-03 16:51:22 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, after InlineApplyIR -- Verify : 0.036ms, total 2.291s
2020-09-03 16:51:22 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, after InlineApplyIR : 6.152ms, total 2.291s, tagged coverage 46.1
2020-09-03 16:51:22 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- LowerArrayAggsToRunAggs -- Verify : 0.062ms, total 2.291s
2020-09-03 16:51:22 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- LowerArrayAggsToRunAggs -- LoweringTransformation : 1.522ms, total 2.293s
2020-09-03 16:51:22 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- LowerArrayAggsToRunAggs -- Verify : 0.050ms, total 2.293s
2020-09-03 16:51:22 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- LowerArrayAggsToRunAggs : 2.297ms, total 2.293s, tagged coverage 71.2
2020-09-03 16:51:22 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, after LowerArrayAggsToRunAggs -- Verify : 0.019ms, total 2.294s
2020-09-03 16:51:22 root: INFO: optimize optimize: compileLowerer, after LowerArrayAggsToRunAggs: before: IR size 10: 
(Coalesce
  (If
    (IsNA
      (In +PCStruct{idx:+PInt32,locus:+PCLocus(GRCh38)} 1))
    (NA Struct{locus:Locus(GRCh38)})
    (MakeStruct
      (locus
        (GetField locus
          (In +PCStruct{idx:+PInt32,locus:+PCLocus(GRCh38)} 1)))))
  (Die Struct{locus:Locus(GRCh38)}
    (Str "Internal e...")))
2020-09-03 16:51:22 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, after LowerArrayAggsToRunAggs -- LoweringTransformation -- Optimize -- FoldConstants : 0.383ms, total 2.295s
2020-09-03 16:51:22 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, after LowerArrayAggsToRunAggs -- LoweringTransformation -- Optimize -- ExtractIntervalFilters : 0.126ms, total 2.295s
2020-09-03 16:51:22 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, after LowerArrayAggsToRunAggs -- LoweringTransformation -- Optimize -- Simplify : 0.182ms, total 2.295s
2020-09-03 16:51:22 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, after LowerArrayAggsToRunAggs -- LoweringTransformation -- Optimize -- ForwardLets : 1.387ms, total 2.297s
2020-09-03 16:51:22 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, after LowerArrayAggsToRunAggs -- LoweringTransformation -- Optimize -- ForwardRelationalLets : 0.325ms, total 2.298s
2020-09-03 16:51:22 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, after LowerArrayAggsToRunAggs -- LoweringTransformation -- Optimize -- PruneDeadFields : 0.575ms, total 2.298s
2020-09-03 16:51:22 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, after LowerArrayAggsToRunAggs -- LoweringTransformation -- Optimize : 4.070ms, total 2.299s, tagged coverage 73.2
2020-09-03 16:51:22 root: INFO: optimize optimize: compileLowerer, after LowerArrayAggsToRunAggs: after: IR size 10:
(Coalesce
  (If
    (IsNA
      (In +PCStruct{idx:+PInt32,locus:+PCLocus(GRCh38)} 1))
    (NA Struct{locus:Locus(GRCh38)})
    (MakeStruct
      (locus
        (GetField locus
          (In +PCStruct{idx:+PInt32,locus:+PCLocus(GRCh38)} 1)))))
  (Die Struct{locus:Locus(GRCh38)}
    (Str "Internal e...")))
2020-09-03 16:51:22 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, after LowerArrayAggsToRunAggs -- LoweringTransformation : 5.540ms, total 2.299s, tagged coverage 53.8
2020-09-03 16:51:22 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, after LowerArrayAggsToRunAggs -- Verify : 0.032ms, total 2.300s
2020-09-03 16:51:22 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, after LowerArrayAggsToRunAggs : 6.116ms, total 2.300s, tagged coverage 49.5
2020-09-03 16:51:22 root: INFO: encoder cache hit
2020-09-03 16:51:22 MemoryStore: INFO: Block broadcast_5 stored as values in memory (estimated size 120.0 B, free 21.7 GB)
2020-09-03 16:51:22 MemoryStore: INFO: Block broadcast_5_piece0 stored as bytes in memory (estimated size 109.0 B, free 21.7 GB)
2020-09-03 16:51:22 BlockManagerInfo: INFO: Added broadcast_5_piece0 in memory on jg3-m.c.maclab-ukbb.internal:36967 (size: 109.0 B, free: 21.7 GB)
2020-09-03 16:51:22 SparkContext: INFO: Created broadcast 5 from broadcast at SparkBackend.scala:233
2020-09-03 16:51:22 root: INFO: instruction count: 6: __C60Compiled.<init>
2020-09-03 16:51:22 root: INFO: instruction count: 189: __C60Compiled.apply
2020-09-03 16:51:22 root: INFO: instruction count: 11: __C60Compiled.__m63addIRIntermediate
2020-09-03 16:51:22 root: INFO: instruction count: 14: __C60Compiled.setPartitionIndex
2020-09-03 16:51:22 root: INFO: instruction count: 7: __C60Compiled.addPartitionRegion
2020-09-03 16:51:22 root: INFO: instruction count: 25: __C60Compiled.__m67DECODE_r_struct_of_r_binaryEND_TO_r_tuple_of_r_stringEND
2020-09-03 16:51:22 root: INFO: instruction count: 11: __C60Compiled.__m68read_fields_group_0
2020-09-03 16:51:22 root: INFO: instruction count: 34: __C60Compiled.__m69INPLACE_DECODE_r_binary_TO_r_binary
2020-09-03 16:51:22 root: INFO: instruction count: 41: __C60Compiled.addLiterals
2020-09-03 16:51:22 SparkContext: INFO: Starting job: runJob at ContextRDD.scala:228
2020-09-03 16:51:22 DAGScheduler: INFO: Got job 0 (runJob at ContextRDD.scala:228) with 128 output partitions
2020-09-03 16:51:22 DAGScheduler: INFO: Final stage: ResultStage 0 (runJob at ContextRDD.scala:228)
2020-09-03 16:51:22 DAGScheduler: INFO: Parents of final stage: List()
2020-09-03 16:51:22 DAGScheduler: INFO: Missing parents: List()
2020-09-03 16:51:22 DAGScheduler: INFO: Submitting ResultStage 0 (MapPartitionsRDD[6] at mapPartitions at ContextRDD.scala:212), which has no missing parents
2020-09-03 16:51:23 MemoryStore: INFO: Block broadcast_6 stored as values in memory (estimated size 572.0 KB, free 21.7 GB)
2020-09-03 16:51:23 MemoryStore: INFO: Block broadcast_6_piece0 stored as bytes in memory (estimated size 179.3 KB, free 21.7 GB)
2020-09-03 16:51:23 BlockManagerInfo: INFO: Added broadcast_6_piece0 in memory on jg3-m.c.maclab-ukbb.internal:36967 (size: 179.3 KB, free: 21.7 GB)
2020-09-03 16:51:23 SparkContext: INFO: Created broadcast 6 from broadcast at DAGScheduler.scala:1163
2020-09-03 16:51:23 DAGScheduler: INFO: Submitting 128 missing tasks from ResultStage 0 (MapPartitionsRDD[6] at mapPartitions at ContextRDD.scala:212) (first 15 tasks are for partitions Vector(0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14))
2020-09-03 16:51:23 YarnScheduler: INFO: Adding task set 0.0 with 128 tasks
2020-09-03 16:51:23 FairSchedulableBuilder: INFO: Added task set TaskSet_0.0 tasks to pool default
2020-09-03 16:51:23 TaskSetManager: INFO: Starting task 0.0 in stage 0.0 (TID 0, jg3-w-1.c.maclab-ukbb.internal, executor 2, partition 0, PROCESS_LOCAL, 7733 bytes)
2020-09-03 16:51:23 TaskSetManager: INFO: Starting task 1.0 in stage 0.0 (TID 1, jg3-w-0.c.maclab-ukbb.internal, executor 1, partition 1, PROCESS_LOCAL, 7733 bytes)
2020-09-03 16:51:23 TaskSetManager: INFO: Starting task 2.0 in stage 0.0 (TID 2, jg3-w-1.c.maclab-ukbb.internal, executor 2, partition 2, PROCESS_LOCAL, 7733 bytes)
2020-09-03 16:51:23 TaskSetManager: INFO: Starting task 3.0 in stage 0.0 (TID 3, jg3-w-0.c.maclab-ukbb.internal, executor 1, partition 3, PROCESS_LOCAL, 7733 bytes)
2020-09-03 16:51:23 TaskSetManager: INFO: Starting task 4.0 in stage 0.0 (TID 4, jg3-w-1.c.maclab-ukbb.internal, executor 2, partition 4, PROCESS_LOCAL, 7733 bytes)
2020-09-03 16:51:23 TaskSetManager: INFO: Starting task 5.0 in stage 0.0 (TID 5, jg3-w-0.c.maclab-ukbb.internal, executor 1, partition 5, PROCESS_LOCAL, 7733 bytes)
2020-09-03 16:51:23 TaskSetManager: INFO: Starting task 6.0 in stage 0.0 (TID 6, jg3-w-1.c.maclab-ukbb.internal, executor 2, partition 6, PROCESS_LOCAL, 7733 bytes)
2020-09-03 16:51:23 TaskSetManager: INFO: Starting task 7.0 in stage 0.0 (TID 7, jg3-w-0.c.maclab-ukbb.internal, executor 1, partition 7, PROCESS_LOCAL, 7733 bytes)
2020-09-03 16:51:23 BlockManagerInfo: INFO: Added broadcast_6_piece0 in memory on jg3-w-0.c.maclab-ukbb.internal:45095 (size: 179.3 KB, free: 5.6 GB)
2020-09-03 16:51:23 BlockManagerInfo: INFO: Added broadcast_6_piece0 in memory on jg3-w-1.c.maclab-ukbb.internal:42241 (size: 179.3 KB, free: 5.6 GB)
2020-09-03 16:51:24 ExecutorAllocationManager: INFO: Requesting 1 new executor because tasks are backlogged (new desired total will be 3)
2020-09-03 16:51:24 BlockManagerInfo: INFO: Added broadcast_5_piece0 in memory on jg3-w-0.c.maclab-ukbb.internal:45095 (size: 109.0 B, free: 5.6 GB)
2020-09-03 16:51:24 BlockManagerInfo: INFO: Added broadcast_3_piece0 in memory on jg3-w-0.c.maclab-ukbb.internal:45095 (size: 58.0 B, free: 5.6 GB)
2020-09-03 16:51:24 BlockManagerInfo: INFO: Added broadcast_4_piece0 in memory on jg3-w-0.c.maclab-ukbb.internal:45095 (size: 944.0 B, free: 5.6 GB)
2020-09-03 16:51:24 BlockManagerInfo: INFO: Added broadcast_2_piece0 in memory on jg3-w-0.c.maclab-ukbb.internal:45095 (size: 118.0 B, free: 5.6 GB)
2020-09-03 16:51:24 BlockManagerInfo: INFO: Added broadcast_5_piece0 in memory on jg3-w-1.c.maclab-ukbb.internal:42241 (size: 109.0 B, free: 5.6 GB)
2020-09-03 16:51:24 BlockManagerInfo: INFO: Added broadcast_3_piece0 in memory on jg3-w-1.c.maclab-ukbb.internal:42241 (size: 58.0 B, free: 5.6 GB)
2020-09-03 16:51:24 BlockManagerInfo: INFO: Added broadcast_4_piece0 in memory on jg3-w-1.c.maclab-ukbb.internal:42241 (size: 944.0 B, free: 5.6 GB)
2020-09-03 16:51:24 BlockManagerInfo: INFO: Added broadcast_2_piece0 in memory on jg3-w-1.c.maclab-ukbb.internal:42241 (size: 118.0 B, free: 5.6 GB)
2020-09-03 16:51:24 BlockManagerInfo: INFO: Added broadcast_1_piece0 in memory on jg3-w-0.c.maclab-ukbb.internal:45095 (size: 28.5 KB, free: 5.6 GB)
2020-09-03 16:51:24 BlockManagerInfo: INFO: Added broadcast_1_piece0 in memory on jg3-w-1.c.maclab-ukbb.internal:42241 (size: 28.5 KB, free: 5.6 GB)
2020-09-03 16:51:25 ExecutorAllocationManager: INFO: Requesting 2 new executors because tasks are backlogged (new desired total will be 5)
2020-09-03 16:51:26 ExecutorAllocationManager: INFO: Requesting 4 new executors because tasks are backlogged (new desired total will be 9)
2020-09-03 16:51:27 ExecutorAllocationManager: INFO: Requesting 8 new executors because tasks are backlogged (new desired total will be 17)
2020-09-03 16:51:27 YarnSchedulerBackend$YarnDriverEndpoint: INFO: Registered executor NettyRpcEndpointRef(spark-client://Executor) (10.128.0.68:46474) with ID 3
2020-09-03 16:51:27 ExecutorAllocationManager: INFO: New executor 3 has registered (new total is 3)
2020-09-03 16:51:27 TaskSetManager: INFO: Starting task 8.0 in stage 0.0 (TID 8, jg3-w-1.c.maclab-ukbb.internal, executor 3, partition 8, PROCESS_LOCAL, 7733 bytes)
2020-09-03 16:51:27 TaskSetManager: INFO: Starting task 9.0 in stage 0.0 (TID 9, jg3-w-1.c.maclab-ukbb.internal, executor 3, partition 9, PROCESS_LOCAL, 7733 bytes)
2020-09-03 16:51:27 TaskSetManager: INFO: Starting task 10.0 in stage 0.0 (TID 10, jg3-w-1.c.maclab-ukbb.internal, executor 3, partition 10, PROCESS_LOCAL, 7733 bytes)
2020-09-03 16:51:27 TaskSetManager: INFO: Starting task 11.0 in stage 0.0 (TID 11, jg3-w-1.c.maclab-ukbb.internal, executor 3, partition 11, PROCESS_LOCAL, 7733 bytes)
2020-09-03 16:51:27 BlockManagerMasterEndpoint: INFO: Registering block manager jg3-w-1.c.maclab-ukbb.internal:37701 with 5.6 GB RAM, BlockManagerId(3, jg3-w-1.c.maclab-ukbb.internal, 37701, None)
2020-09-03 16:51:28 ExecutorAllocationManager: INFO: Requesting 15 new executors because tasks are backlogged (new desired total will be 32)
2020-09-03 16:51:28 BlockManagerInfo: INFO: Added broadcast_6_piece0 in memory on jg3-w-1.c.maclab-ukbb.internal:37701 (size: 179.3 KB, free: 5.6 GB)
2020-09-03 16:51:28 BlockManagerInfo: INFO: Added broadcast_5_piece0 in memory on jg3-w-1.c.maclab-ukbb.internal:37701 (size: 109.0 B, free: 5.6 GB)
2020-09-03 16:51:28 BlockManagerInfo: INFO: Added broadcast_3_piece0 in memory on jg3-w-1.c.maclab-ukbb.internal:37701 (size: 58.0 B, free: 5.6 GB)
2020-09-03 16:51:28 BlockManagerInfo: INFO: Added broadcast_4_piece0 in memory on jg3-w-1.c.maclab-ukbb.internal:37701 (size: 944.0 B, free: 5.6 GB)
2020-09-03 16:51:28 BlockManagerInfo: INFO: Added broadcast_2_piece0 in memory on jg3-w-1.c.maclab-ukbb.internal:37701 (size: 118.0 B, free: 5.6 GB)
2020-09-03 16:51:28 BlockManagerInfo: INFO: Added broadcast_1_piece0 in memory on jg3-w-1.c.maclab-ukbb.internal:37701 (size: 28.5 KB, free: 5.6 GB)
2020-09-03 16:51:50 TaskSetManager: INFO: Starting task 12.0 in stage 0.0 (TID 12, jg3-w-0.c.maclab-ukbb.internal, executor 1, partition 12, PROCESS_LOCAL, 7733 bytes)
2020-09-03 16:51:50 TaskSetManager: INFO: Starting task 13.0 in stage 0.0 (TID 13, jg3-w-0.c.maclab-ukbb.internal, executor 1, partition 13, PROCESS_LOCAL, 7733 bytes)
2020-09-03 16:51:50 TaskSetManager: INFO: Starting task 14.0 in stage 0.0 (TID 14, jg3-w-0.c.maclab-ukbb.internal, executor 1, partition 14, PROCESS_LOCAL, 7733 bytes)
2020-09-03 16:51:50 TaskSetManager: INFO: Starting task 15.0 in stage 0.0 (TID 15, jg3-w-0.c.maclab-ukbb.internal, executor 1, partition 15, PROCESS_LOCAL, 7733 bytes)
2020-09-03 16:51:50 TaskSetManager: INFO: Finished task 7.0 in stage 0.0 (TID 7) in 27181 ms on jg3-w-0.c.maclab-ukbb.internal (executor 1) (1/128)
2020-09-03 16:51:50 TaskSetManager: INFO: Finished task 5.0 in stage 0.0 (TID 5) in 27214 ms on jg3-w-0.c.maclab-ukbb.internal (executor 1) (2/128)
2020-09-03 16:51:50 TaskSetManager: INFO: Finished task 3.0 in stage 0.0 (TID 3) in 27222 ms on jg3-w-0.c.maclab-ukbb.internal (executor 1) (3/128)
2020-09-03 16:51:50 TaskSetManager: INFO: Finished task 1.0 in stage 0.0 (TID 1) in 27231 ms on jg3-w-0.c.maclab-ukbb.internal (executor 1) (4/128)
2020-09-03 16:51:51 TaskSetManager: INFO: Starting task 16.0 in stage 0.0 (TID 16, jg3-w-0.c.maclab-ukbb.internal, executor 1, partition 16, PROCESS_LOCAL, 7733 bytes)
2020-09-03 16:51:51 TaskSetManager: INFO: Finished task 12.0 in stage 0.0 (TID 12) in 1323 ms on jg3-w-0.c.maclab-ukbb.internal (executor 1) (5/128)
2020-09-03 16:51:51 TaskSetManager: INFO: Starting task 17.0 in stage 0.0 (TID 17, jg3-w-0.c.maclab-ukbb.internal, executor 1, partition 17, PROCESS_LOCAL, 7733 bytes)
2020-09-03 16:51:51 TaskSetManager: INFO: Finished task 15.0 in stage 0.0 (TID 15) in 1317 ms on jg3-w-0.c.maclab-ukbb.internal (executor 1) (6/128)
2020-09-03 16:51:51 TaskSetManager: INFO: Starting task 18.0 in stage 0.0 (TID 18, jg3-w-0.c.maclab-ukbb.internal, executor 1, partition 18, PROCESS_LOCAL, 7733 bytes)
2020-09-03 16:51:51 TaskSetManager: INFO: Finished task 13.0 in stage 0.0 (TID 13) in 1344 ms on jg3-w-0.c.maclab-ukbb.internal (executor 1) (7/128)
2020-09-03 16:51:51 TaskSetManager: INFO: Starting task 19.0 in stage 0.0 (TID 19, jg3-w-0.c.maclab-ukbb.internal, executor 1, partition 19, PROCESS_LOCAL, 7733 bytes)
2020-09-03 16:51:51 TaskSetManager: INFO: Finished task 14.0 in stage 0.0 (TID 14) in 1370 ms on jg3-w-0.c.maclab-ukbb.internal (executor 1) (8/128)
2020-09-03 16:51:52 TaskSetManager: INFO: Starting task 20.0 in stage 0.0 (TID 20, jg3-w-0.c.maclab-ukbb.internal, executor 1, partition 20, PROCESS_LOCAL, 7733 bytes)
2020-09-03 16:51:52 TaskSetManager: INFO: Finished task 16.0 in stage 0.0 (TID 16) in 1177 ms on jg3-w-0.c.maclab-ukbb.internal (executor 1) (9/128)
2020-09-03 16:51:52 TaskSetManager: INFO: Starting task 21.0 in stage 0.0 (TID 21, jg3-w-0.c.maclab-ukbb.internal, executor 1, partition 21, PROCESS_LOCAL, 7733 bytes)
2020-09-03 16:51:52 TaskSetManager: INFO: Starting task 22.0 in stage 0.0 (TID 22, jg3-w-0.c.maclab-ukbb.internal, executor 1, partition 22, PROCESS_LOCAL, 7733 bytes)
2020-09-03 16:51:52 TaskSetManager: INFO: Finished task 19.0 in stage 0.0 (TID 19) in 1227 ms on jg3-w-0.c.maclab-ukbb.internal (executor 1) (10/128)
2020-09-03 16:51:52 TaskSetManager: INFO: Finished task 18.0 in stage 0.0 (TID 18) in 1256 ms on jg3-w-0.c.maclab-ukbb.internal (executor 1) (11/128)
2020-09-03 16:51:52 TaskSetManager: INFO: Starting task 23.0 in stage 0.0 (TID 23, jg3-w-0.c.maclab-ukbb.internal, executor 1, partition 23, PROCESS_LOCAL, 7733 bytes)
2020-09-03 16:51:52 TaskSetManager: INFO: Finished task 17.0 in stage 0.0 (TID 17) in 1287 ms on jg3-w-0.c.maclab-ukbb.internal (executor 1) (12/128)
2020-09-03 16:51:53 TaskSetManager: INFO: Starting task 24.0 in stage 0.0 (TID 24, jg3-w-0.c.maclab-ukbb.internal, executor 1, partition 24, PROCESS_LOCAL, 7733 bytes)
2020-09-03 16:51:53 TaskSetManager: INFO: Finished task 20.0 in stage 0.0 (TID 20) in 1141 ms on jg3-w-0.c.maclab-ukbb.internal (executor 1) (13/128)
2020-09-03 16:51:53 TaskSetManager: INFO: Starting task 25.0 in stage 0.0 (TID 25, jg3-w-0.c.maclab-ukbb.internal, executor 1, partition 25, PROCESS_LOCAL, 7733 bytes)
2020-09-03 16:51:53 TaskSetManager: INFO: Starting task 26.0 in stage 0.0 (TID 26, jg3-w-0.c.maclab-ukbb.internal, executor 1, partition 26, PROCESS_LOCAL, 7733 bytes)
2020-09-03 16:51:53 TaskSetManager: INFO: Finished task 22.0 in stage 0.0 (TID 22) in 1161 ms on jg3-w-0.c.maclab-ukbb.internal (executor 1) (14/128)
2020-09-03 16:51:53 TaskSetManager: INFO: Finished task 21.0 in stage 0.0 (TID 21) in 1165 ms on jg3-w-0.c.maclab-ukbb.internal (executor 1) (15/128)
2020-09-03 16:51:53 TaskSetManager: INFO: Starting task 27.0 in stage 0.0 (TID 27, jg3-w-0.c.maclab-ukbb.internal, executor 1, partition 27, PROCESS_LOCAL, 7733 bytes)
2020-09-03 16:51:53 TaskSetManager: INFO: Finished task 23.0 in stage 0.0 (TID 23) in 1173 ms on jg3-w-0.c.maclab-ukbb.internal (executor 1) (16/128)
2020-09-03 16:51:54 TaskSetManager: INFO: Starting task 28.0 in stage 0.0 (TID 28, jg3-w-0.c.maclab-ukbb.internal, executor 1, partition 28, PROCESS_LOCAL, 7733 bytes)
2020-09-03 16:51:54 TaskSetManager: INFO: Finished task 24.0 in stage 0.0 (TID 24) in 1093 ms on jg3-w-0.c.maclab-ukbb.internal (executor 1) (17/128)
2020-09-03 16:51:54 TaskSetManager: INFO: Starting task 29.0 in stage 0.0 (TID 29, jg3-w-0.c.maclab-ukbb.internal, executor 1, partition 29, PROCESS_LOCAL, 7733 bytes)
2020-09-03 16:51:54 TaskSetManager: INFO: Finished task 26.0 in stage 0.0 (TID 26) in 1131 ms on jg3-w-0.c.maclab-ukbb.internal (executor 1) (18/128)
2020-09-03 16:51:54 TaskSetManager: INFO: Starting task 30.0 in stage 0.0 (TID 30, jg3-w-0.c.maclab-ukbb.internal, executor 1, partition 30, PROCESS_LOCAL, 7733 bytes)
2020-09-03 16:51:54 TaskSetManager: INFO: Finished task 25.0 in stage 0.0 (TID 25) in 1149 ms on jg3-w-0.c.maclab-ukbb.internal (executor 1) (19/128)
2020-09-03 16:51:55 TaskSetManager: INFO: Starting task 31.0 in stage 0.0 (TID 31, jg3-w-0.c.maclab-ukbb.internal, executor 1, partition 31, PROCESS_LOCAL, 7733 bytes)
2020-09-03 16:51:55 TaskSetManager: INFO: Finished task 27.0 in stage 0.0 (TID 27) in 1147 ms on jg3-w-0.c.maclab-ukbb.internal (executor 1) (20/128)
2020-09-03 16:51:55 TaskSetManager: INFO: Starting task 32.0 in stage 0.0 (TID 32, jg3-w-1.c.maclab-ukbb.internal, executor 2, partition 32, PROCESS_LOCAL, 7733 bytes)
2020-09-03 16:51:55 TaskSetManager: INFO: Finished task 4.0 in stage 0.0 (TID 4) in 32031 ms on jg3-w-1.c.maclab-ukbb.internal (executor 2) (21/128)
2020-09-03 16:51:55 TaskSetManager: INFO: Starting task 33.0 in stage 0.0 (TID 33, jg3-w-1.c.maclab-ukbb.internal, executor 2, partition 33, PROCESS_LOCAL, 7733 bytes)
2020-09-03 16:51:55 TaskSetManager: INFO: Finished task 2.0 in stage 0.0 (TID 2) in 32114 ms on jg3-w-1.c.maclab-ukbb.internal (executor 2) (22/128)
2020-09-03 16:51:55 TaskSetManager: INFO: Starting task 34.0 in stage 0.0 (TID 34, jg3-w-1.c.maclab-ukbb.internal, executor 2, partition 34, PROCESS_LOCAL, 7733 bytes)
2020-09-03 16:51:55 TaskSetManager: INFO: Finished task 6.0 in stage 0.0 (TID 6) in 32179 ms on jg3-w-1.c.maclab-ukbb.internal (executor 2) (23/128)
2020-09-03 16:51:55 TaskSetManager: INFO: Starting task 35.0 in stage 0.0 (TID 35, jg3-w-1.c.maclab-ukbb.internal, executor 2, partition 35, PROCESS_LOCAL, 7733 bytes)
2020-09-03 16:51:55 TaskSetManager: INFO: Finished task 0.0 in stage 0.0 (TID 0) in 32307 ms on jg3-w-1.c.maclab-ukbb.internal (executor 2) (24/128)
2020-09-03 16:51:56 TaskSetManager: INFO: Starting task 36.0 in stage 0.0 (TID 36, jg3-w-0.c.maclab-ukbb.internal, executor 1, partition 36, PROCESS_LOCAL, 7733 bytes)
2020-09-03 16:51:56 TaskSetManager: INFO: Finished task 28.0 in stage 0.0 (TID 28) in 1245 ms on jg3-w-0.c.maclab-ukbb.internal (executor 1) (25/128)
2020-09-03 16:51:56 TaskSetManager: INFO: Starting task 37.0 in stage 0.0 (TID 37, jg3-w-0.c.maclab-ukbb.internal, executor 1, partition 37, PROCESS_LOCAL, 7733 bytes)
2020-09-03 16:51:56 TaskSetManager: INFO: Finished task 30.0 in stage 0.0 (TID 30) in 1144 ms on jg3-w-0.c.maclab-ukbb.internal (executor 1) (26/128)
2020-09-03 16:51:56 TaskSetManager: INFO: Starting task 38.0 in stage 0.0 (TID 38, jg3-w-0.c.maclab-ukbb.internal, executor 1, partition 38, PROCESS_LOCAL, 7733 bytes)
2020-09-03 16:51:56 TaskSetManager: INFO: Finished task 29.0 in stage 0.0 (TID 29) in 1177 ms on jg3-w-0.c.maclab-ukbb.internal (executor 1) (27/128)
2020-09-03 16:51:56 TaskSetManager: INFO: Starting task 39.0 in stage 0.0 (TID 39, jg3-w-0.c.maclab-ukbb.internal, executor 1, partition 39, PROCESS_LOCAL, 7733 bytes)
2020-09-03 16:51:56 TaskSetManager: INFO: Finished task 31.0 in stage 0.0 (TID 31) in 1190 ms on jg3-w-0.c.maclab-ukbb.internal (executor 1) (28/128)
2020-09-03 16:51:56 TaskSetManager: INFO: Starting task 40.0 in stage 0.0 (TID 40, jg3-w-1.c.maclab-ukbb.internal, executor 2, partition 40, PROCESS_LOCAL, 7733 bytes)
2020-09-03 16:51:56 TaskSetManager: INFO: Finished task 33.0 in stage 0.0 (TID 33) in 1290 ms on jg3-w-1.c.maclab-ukbb.internal (executor 2) (29/128)
2020-09-03 16:51:56 TaskSetManager: INFO: Starting task 41.0 in stage 0.0 (TID 41, jg3-w-1.c.maclab-ukbb.internal, executor 2, partition 41, PROCESS_LOCAL, 7733 bytes)
2020-09-03 16:51:56 TaskSetManager: INFO: Finished task 35.0 in stage 0.0 (TID 35) in 1270 ms on jg3-w-1.c.maclab-ukbb.internal (executor 2) (30/128)
2020-09-03 16:51:56 TaskSetManager: INFO: Starting task 42.0 in stage 0.0 (TID 42, jg3-w-1.c.maclab-ukbb.internal, executor 2, partition 42, PROCESS_LOCAL, 7733 bytes)
2020-09-03 16:51:56 TaskSetManager: INFO: Finished task 34.0 in stage 0.0 (TID 34) in 1413 ms on jg3-w-1.c.maclab-ukbb.internal (executor 2) (31/128)
2020-09-03 16:51:56 TaskSetManager: INFO: Starting task 43.0 in stage 0.0 (TID 43, jg3-w-1.c.maclab-ukbb.internal, executor 2, partition 43, PROCESS_LOCAL, 7733 bytes)
2020-09-03 16:51:56 TaskSetManager: INFO: Finished task 32.0 in stage 0.0 (TID 32) in 1850 ms on jg3-w-1.c.maclab-ukbb.internal (executor 2) (32/128)
2020-09-03 16:51:57 TaskSetManager: INFO: Starting task 44.0 in stage 0.0 (TID 44, jg3-w-0.c.maclab-ukbb.internal, executor 1, partition 44, PROCESS_LOCAL, 7733 bytes)
2020-09-03 16:51:57 TaskSetManager: INFO: Finished task 36.0 in stage 0.0 (TID 36) in 1138 ms on jg3-w-0.c.maclab-ukbb.internal (executor 1) (33/128)
2020-09-03 16:51:57 TaskSetManager: INFO: Starting task 45.0 in stage 0.0 (TID 45, jg3-w-0.c.maclab-ukbb.internal, executor 1, partition 45, PROCESS_LOCAL, 7733 bytes)
2020-09-03 16:51:57 TaskSetManager: INFO: Finished task 38.0 in stage 0.0 (TID 38) in 1108 ms on jg3-w-0.c.maclab-ukbb.internal (executor 1) (34/128)
2020-09-03 16:51:57 TaskSetManager: INFO: Starting task 46.0 in stage 0.0 (TID 46, jg3-w-0.c.maclab-ukbb.internal, executor 1, partition 46, PROCESS_LOCAL, 7733 bytes)
2020-09-03 16:51:57 TaskSetManager: INFO: Finished task 37.0 in stage 0.0 (TID 37) in 1184 ms on jg3-w-0.c.maclab-ukbb.internal (executor 1) (35/128)
2020-09-03 16:51:57 TaskSetManager: INFO: Starting task 47.0 in stage 0.0 (TID 47, jg3-w-0.c.maclab-ukbb.internal, executor 1, partition 47, PROCESS_LOCAL, 7733 bytes)
2020-09-03 16:51:57 TaskSetManager: INFO: Finished task 39.0 in stage 0.0 (TID 39) in 1154 ms on jg3-w-0.c.maclab-ukbb.internal (executor 1) (36/128)
2020-09-03 16:51:57 TaskSetManager: INFO: Starting task 48.0 in stage 0.0 (TID 48, jg3-w-1.c.maclab-ukbb.internal, executor 3, partition 48, PROCESS_LOCAL, 7733 bytes)
2020-09-03 16:51:57 TaskSetManager: WARN: Lost task 9.0 in stage 0.0 (TID 9, jg3-w-1.c.maclab-ukbb.internal, executor 3): java.lang.NullPointerException
	at scala.collection.immutable.StringOps$.apply$extension(StringOps.scala:37)
	at is.hail.io.reference.FASTAReader.readBlock(FASTAReader.scala:99)
	at is.hail.io.reference.FASTAReader.lookupGlobalPos(FASTAReader.scala:138)
	at is.hail.io.reference.FASTAReader.lookup(FASTAReader.scala:110)
	at is.hail.variant.ReferenceGenome.getSequence(ReferenceGenome.scala:357)
	at __C24Compiled.__m42getReferenceSequenceFromValidLocus(Unknown Source)
	at __C24Compiled.apply(Unknown Source)
	at is.hail.expr.ir.TableFilter$$anonfun$execute$2.apply(TableIR.scala:946)
	at is.hail.expr.ir.TableFilter$$anonfun$execute$2.apply(TableIR.scala:946)
	at is.hail.expr.ir.TableValue$$anonfun$3.apply(TableValue.scala:65)
	at is.hail.expr.ir.TableValue$$anonfun$3.apply(TableValue.scala:65)
	at is.hail.rvd.RVD$$anonfun$17$$anonfun$apply$2.apply$mcZJ$sp(RVD.scala:605)
	at is.hail.rvd.RVD$$anonfun$17$$anonfun$apply$2.apply(RVD.scala:604)
	at is.hail.rvd.RVD$$anonfun$17$$anonfun$apply$2.apply(RVD.scala:604)
	at scala.collection.Iterator$$anon$13.hasNext(Iterator.scala:464)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
	at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:409)
	at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:409)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
	at is.hail.rvd.RVD$$anonfun$32.apply(RVD.scala:1222)
	at is.hail.rvd.RVD$$anonfun$32.apply(RVD.scala:1221)
	at is.hail.sparkextras.ContextRDD$$anonfun$crunJobWithIndex$1.apply(ContextRDD.scala:232)
	at is.hail.sparkextras.ContextRDD$$anonfun$crunJobWithIndex$1.apply(ContextRDD.scala:230)
	at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:90)
	at org.apache.spark.scheduler.Task.run(Task.scala:123)
	at org.apache.spark.executor.Executor$TaskRunner$$anonfun$10.apply(Executor.scala:408)
	at org.apache.spark.util.Utils$.tryWithSafeFinally(Utils.scala:1360)
	at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:414)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
	at java.lang.Thread.run(Thread.java:748)

2020-09-03 16:51:58 TaskSetManager: INFO: Starting task 9.1 in stage 0.0 (TID 49, jg3-w-1.c.maclab-ukbb.internal, executor 2, partition 9, PROCESS_LOCAL, 7733 bytes)
2020-09-03 16:51:58 TaskSetManager: INFO: Finished task 40.0 in stage 0.0 (TID 40) in 1798 ms on jg3-w-1.c.maclab-ukbb.internal (executor 2) (37/128)
2020-09-03 16:51:58 TaskSetManager: INFO: Starting task 49.0 in stage 0.0 (TID 50, jg3-w-0.c.maclab-ukbb.internal, executor 1, partition 49, PROCESS_LOCAL, 7733 bytes)
2020-09-03 16:51:58 TaskSetManager: INFO: Finished task 44.0 in stage 0.0 (TID 44) in 1187 ms on jg3-w-0.c.maclab-ukbb.internal (executor 1) (38/128)
2020-09-03 16:51:58 TaskSetManager: INFO: Starting task 50.0 in stage 0.0 (TID 51, jg3-w-0.c.maclab-ukbb.internal, executor 1, partition 50, PROCESS_LOCAL, 7733 bytes)
2020-09-03 16:51:58 TaskSetManager: INFO: Finished task 45.0 in stage 0.0 (TID 45) in 1144 ms on jg3-w-0.c.maclab-ukbb.internal (executor 1) (39/128)
2020-09-03 16:51:58 TaskSetManager: INFO: Starting task 51.0 in stage 0.0 (TID 52, jg3-w-1.c.maclab-ukbb.internal, executor 2, partition 51, PROCESS_LOCAL, 7733 bytes)
2020-09-03 16:51:58 TaskSetManager: INFO: Finished task 41.0 in stage 0.0 (TID 41) in 1839 ms on jg3-w-1.c.maclab-ukbb.internal (executor 2) (40/128)
2020-09-03 16:51:58 TaskSetManager: INFO: Starting task 52.0 in stage 0.0 (TID 53, jg3-w-0.c.maclab-ukbb.internal, executor 1, partition 52, PROCESS_LOCAL, 7733 bytes)
2020-09-03 16:51:58 TaskSetManager: INFO: Finished task 46.0 in stage 0.0 (TID 46) in 1171 ms on jg3-w-0.c.maclab-ukbb.internal (executor 1) (41/128)
2020-09-03 16:51:58 TaskSetManager: INFO: Starting task 53.0 in stage 0.0 (TID 54, jg3-w-0.c.maclab-ukbb.internal, executor 1, partition 53, PROCESS_LOCAL, 7733 bytes)
2020-09-03 16:51:58 TaskSetManager: INFO: Finished task 47.0 in stage 0.0 (TID 47) in 1162 ms on jg3-w-0.c.maclab-ukbb.internal (executor 1) (42/128)
2020-09-03 16:51:58 TaskSetManager: INFO: Starting task 54.0 in stage 0.0 (TID 55, jg3-w-1.c.maclab-ukbb.internal, executor 2, partition 54, PROCESS_LOCAL, 7733 bytes)
2020-09-03 16:51:58 TaskSetManager: INFO: Finished task 42.0 in stage 0.0 (TID 42) in 2142 ms on jg3-w-1.c.maclab-ukbb.internal (executor 2) (43/128)
2020-09-03 16:51:58 TaskSetManager: INFO: Starting task 55.0 in stage 0.0 (TID 56, jg3-w-1.c.maclab-ukbb.internal, executor 2, partition 55, PROCESS_LOCAL, 7733 bytes)
2020-09-03 16:51:58 TaskSetManager: INFO: Finished task 43.0 in stage 0.0 (TID 43) in 1911 ms on jg3-w-1.c.maclab-ukbb.internal (executor 2) (44/128)
2020-09-03 16:51:58 TaskSetManager: INFO: Starting task 56.0 in stage 0.0 (TID 57, jg3-w-1.c.maclab-ukbb.internal, executor 3, partition 56, PROCESS_LOCAL, 7733 bytes)
2020-09-03 16:51:58 TaskSetManager: INFO: Lost task 8.0 in stage 0.0 (TID 8) on jg3-w-1.c.maclab-ukbb.internal, executor 3: java.lang.NullPointerException (null) [duplicate 1]
2020-09-03 16:51:59 TaskSetManager: INFO: Starting task 8.1 in stage 0.0 (TID 58, jg3-w-0.c.maclab-ukbb.internal, executor 1, partition 8, PROCESS_LOCAL, 7733 bytes)
2020-09-03 16:51:59 TaskSetManager: INFO: Finished task 52.0 in stage 0.0 (TID 53) in 1091 ms on jg3-w-0.c.maclab-ukbb.internal (executor 1) (45/128)
2020-09-03 16:51:59 TaskSetManager: INFO: Starting task 57.0 in stage 0.0 (TID 59, jg3-w-0.c.maclab-ukbb.internal, executor 1, partition 57, PROCESS_LOCAL, 7733 bytes)
2020-09-03 16:51:59 TaskSetManager: INFO: Finished task 50.0 in stage 0.0 (TID 51) in 1192 ms on jg3-w-0.c.maclab-ukbb.internal (executor 1) (46/128)
2020-09-03 16:51:59 TaskSetManager: INFO: Starting task 58.0 in stage 0.0 (TID 60, jg3-w-0.c.maclab-ukbb.internal, executor 1, partition 58, PROCESS_LOCAL, 7733 bytes)
2020-09-03 16:51:59 TaskSetManager: INFO: Finished task 49.0 in stage 0.0 (TID 50) in 1260 ms on jg3-w-0.c.maclab-ukbb.internal (executor 1) (47/128)
2020-09-03 16:51:59 TaskSetManager: INFO: Starting task 59.0 in stage 0.0 (TID 61, jg3-w-0.c.maclab-ukbb.internal, executor 1, partition 59, PROCESS_LOCAL, 7733 bytes)
2020-09-03 16:51:59 TaskSetManager: INFO: Finished task 53.0 in stage 0.0 (TID 54) in 1251 ms on jg3-w-0.c.maclab-ukbb.internal (executor 1) (48/128)
2020-09-03 16:52:00 TaskSetManager: INFO: Starting task 60.0 in stage 0.0 (TID 62, jg3-w-1.c.maclab-ukbb.internal, executor 2, partition 60, PROCESS_LOCAL, 7733 bytes)
2020-09-03 16:52:00 TaskSetManager: INFO: Finished task 9.1 in stage 0.0 (TID 49) in 1865 ms on jg3-w-1.c.maclab-ukbb.internal (executor 2) (49/128)
2020-09-03 16:52:00 TaskSetManager: INFO: Starting task 61.0 in stage 0.0 (TID 63, jg3-w-1.c.maclab-ukbb.internal, executor 3, partition 61, PROCESS_LOCAL, 7733 bytes)
2020-09-03 16:52:00 TaskSetManager: INFO: Finished task 11.0 in stage 0.0 (TID 11) in 32873 ms on jg3-w-1.c.maclab-ukbb.internal (executor 3) (50/128)
2020-09-03 16:52:00 TaskSetManager: INFO: Starting task 62.0 in stage 0.0 (TID 64, jg3-w-1.c.maclab-ukbb.internal, executor 3, partition 62, PROCESS_LOCAL, 7733 bytes)
2020-09-03 16:52:00 TaskSetManager: INFO: Finished task 48.0 in stage 0.0 (TID 48) in 2856 ms on jg3-w-1.c.maclab-ukbb.internal (executor 3) (51/128)
2020-09-03 16:52:00 TaskSetManager: INFO: Starting task 63.0 in stage 0.0 (TID 65, jg3-w-1.c.maclab-ukbb.internal, executor 3, partition 63, PROCESS_LOCAL, 7735 bytes)
2020-09-03 16:52:00 TaskSetManager: INFO: Finished task 10.0 in stage 0.0 (TID 10) in 32908 ms on jg3-w-1.c.maclab-ukbb.internal (executor 3) (52/128)
2020-09-03 16:52:00 TaskSetManager: INFO: Starting task 64.0 in stage 0.0 (TID 66, jg3-w-1.c.maclab-ukbb.internal, executor 2, partition 64, PROCESS_LOCAL, 7737 bytes)
2020-09-03 16:52:00 TaskSetManager: INFO: Finished task 51.0 in stage 0.0 (TID 52) in 1897 ms on jg3-w-1.c.maclab-ukbb.internal (executor 2) (53/128)
2020-09-03 16:52:00 TaskSetManager: INFO: Starting task 65.0 in stage 0.0 (TID 67, jg3-w-1.c.maclab-ukbb.internal, executor 2, partition 65, PROCESS_LOCAL, 7737 bytes)
2020-09-03 16:52:00 TaskSetManager: INFO: Finished task 54.0 in stage 0.0 (TID 55) in 1904 ms on jg3-w-1.c.maclab-ukbb.internal (executor 2) (54/128)
2020-09-03 16:52:00 TaskSetManager: INFO: Starting task 66.0 in stage 0.0 (TID 68, jg3-w-0.c.maclab-ukbb.internal, executor 1, partition 66, PROCESS_LOCAL, 7737 bytes)
2020-09-03 16:52:00 TaskSetManager: INFO: Finished task 57.0 in stage 0.0 (TID 59) in 1158 ms on jg3-w-0.c.maclab-ukbb.internal (executor 1) (55/128)
2020-09-03 16:52:00 TaskSetManager: INFO: Starting task 67.0 in stage 0.0 (TID 69, jg3-w-0.c.maclab-ukbb.internal, executor 1, partition 67, PROCESS_LOCAL, 7737 bytes)
2020-09-03 16:52:00 TaskSetManager: INFO: Finished task 58.0 in stage 0.0 (TID 60) in 1148 ms on jg3-w-0.c.maclab-ukbb.internal (executor 1) (56/128)
2020-09-03 16:52:00 TaskSetManager: INFO: Starting task 68.0 in stage 0.0 (TID 70, jg3-w-0.c.maclab-ukbb.internal, executor 1, partition 68, PROCESS_LOCAL, 7737 bytes)
2020-09-03 16:52:00 TaskSetManager: INFO: Finished task 8.1 in stage 0.0 (TID 58) in 1211 ms on jg3-w-0.c.maclab-ukbb.internal (executor 1) (57/128)
2020-09-03 16:52:00 TaskSetManager: INFO: Starting task 69.0 in stage 0.0 (TID 71, jg3-w-1.c.maclab-ukbb.internal, executor 2, partition 69, PROCESS_LOCAL, 7737 bytes)
2020-09-03 16:52:00 TaskSetManager: INFO: Finished task 55.0 in stage 0.0 (TID 56) in 1942 ms on jg3-w-1.c.maclab-ukbb.internal (executor 2) (58/128)
2020-09-03 16:52:00 TaskSetManager: INFO: Starting task 70.0 in stage 0.0 (TID 72, jg3-w-0.c.maclab-ukbb.internal, executor 1, partition 70, PROCESS_LOCAL, 7737 bytes)
2020-09-03 16:52:00 TaskSetManager: INFO: Finished task 59.0 in stage 0.0 (TID 61) in 1161 ms on jg3-w-0.c.maclab-ukbb.internal (executor 1) (59/128)
2020-09-03 16:52:01 TaskSetManager: INFO: Starting task 71.0 in stage 0.0 (TID 73, jg3-w-1.c.maclab-ukbb.internal, executor 3, partition 71, PROCESS_LOCAL, 7737 bytes)
2020-09-03 16:52:01 TaskSetManager: INFO: Finished task 56.0 in stage 0.0 (TID 57) in 2191 ms on jg3-w-1.c.maclab-ukbb.internal (executor 3) (60/128)
2020-09-03 16:52:01 TaskSetManager: INFO: Starting task 72.0 in stage 0.0 (TID 74, jg3-w-0.c.maclab-ukbb.internal, executor 1, partition 72, PROCESS_LOCAL, 7737 bytes)
2020-09-03 16:52:01 TaskSetManager: INFO: Starting task 73.0 in stage 0.0 (TID 75, jg3-w-0.c.maclab-ukbb.internal, executor 1, partition 73, PROCESS_LOCAL, 7737 bytes)
2020-09-03 16:52:01 TaskSetManager: INFO: Finished task 67.0 in stage 0.0 (TID 69) in 1089 ms on jg3-w-0.c.maclab-ukbb.internal (executor 1) (61/128)
2020-09-03 16:52:01 TaskSetManager: INFO: Finished task 66.0 in stage 0.0 (TID 68) in 1127 ms on jg3-w-0.c.maclab-ukbb.internal (executor 1) (62/128)
2020-09-03 16:52:01 TaskSetManager: INFO: Starting task 74.0 in stage 0.0 (TID 76, jg3-w-0.c.maclab-ukbb.internal, executor 1, partition 74, PROCESS_LOCAL, 7737 bytes)
2020-09-03 16:52:01 TaskSetManager: INFO: Finished task 68.0 in stage 0.0 (TID 70) in 1101 ms on jg3-w-0.c.maclab-ukbb.internal (executor 1) (63/128)
2020-09-03 16:52:01 TaskSetManager: INFO: Starting task 75.0 in stage 0.0 (TID 77, jg3-w-1.c.maclab-ukbb.internal, executor 2, partition 75, PROCESS_LOCAL, 7737 bytes)
2020-09-03 16:52:01 TaskSetManager: INFO: Finished task 60.0 in stage 0.0 (TID 62) in 1801 ms on jg3-w-1.c.maclab-ukbb.internal (executor 2) (64/128)
2020-09-03 16:52:01 TaskSetManager: INFO: Starting task 76.0 in stage 0.0 (TID 78, jg3-w-1.c.maclab-ukbb.internal, executor 3, partition 76, PROCESS_LOCAL, 7737 bytes)
2020-09-03 16:52:01 TaskSetManager: INFO: Finished task 61.0 in stage 0.0 (TID 63) in 1710 ms on jg3-w-1.c.maclab-ukbb.internal (executor 3) (65/128)
2020-09-03 16:52:02 TaskSetManager: INFO: Starting task 77.0 in stage 0.0 (TID 79, jg3-w-0.c.maclab-ukbb.internal, executor 1, partition 77, PROCESS_LOCAL, 7737 bytes)
2020-09-03 16:52:02 TaskSetManager: INFO: Finished task 70.0 in stage 0.0 (TID 72) in 1165 ms on jg3-w-0.c.maclab-ukbb.internal (executor 1) (66/128)
2020-09-03 16:52:02 TaskSetManager: INFO: Starting task 78.0 in stage 0.0 (TID 80, jg3-w-1.c.maclab-ukbb.internal, executor 2, partition 78, PROCESS_LOCAL, 7737 bytes)
2020-09-03 16:52:02 TaskSetManager: INFO: Finished task 64.0 in stage 0.0 (TID 66) in 1852 ms on jg3-w-1.c.maclab-ukbb.internal (executor 2) (67/128)
2020-09-03 16:52:02 TaskSetManager: INFO: Starting task 79.0 in stage 0.0 (TID 81, jg3-w-1.c.maclab-ukbb.internal, executor 3, partition 79, PROCESS_LOCAL, 7737 bytes)
2020-09-03 16:52:02 TaskSetManager: INFO: Finished task 62.0 in stage 0.0 (TID 64) in 2147 ms on jg3-w-1.c.maclab-ukbb.internal (executor 3) (68/128)
2020-09-03 16:52:02 TaskSetManager: INFO: Starting task 80.0 in stage 0.0 (TID 82, jg3-w-1.c.maclab-ukbb.internal, executor 3, partition 80, PROCESS_LOCAL, 7737 bytes)
2020-09-03 16:52:02 TaskSetManager: INFO: Finished task 63.0 in stage 0.0 (TID 65) in 2128 ms on jg3-w-1.c.maclab-ukbb.internal (executor 3) (69/128)
2020-09-03 16:52:02 TaskSetManager: INFO: Starting task 81.0 in stage 0.0 (TID 83, jg3-w-0.c.maclab-ukbb.internal, executor 1, partition 81, PROCESS_LOCAL, 7737 bytes)
2020-09-03 16:52:02 TaskSetManager: INFO: Finished task 73.0 in stage 0.0 (TID 75) in 1106 ms on jg3-w-0.c.maclab-ukbb.internal (executor 1) (70/128)
2020-09-03 16:52:02 TaskSetManager: INFO: Starting task 82.0 in stage 0.0 (TID 84, jg3-w-0.c.maclab-ukbb.internal, executor 1, partition 82, PROCESS_LOCAL, 7737 bytes)
2020-09-03 16:52:02 TaskSetManager: INFO: Finished task 72.0 in stage 0.0 (TID 74) in 1117 ms on jg3-w-0.c.maclab-ukbb.internal (executor 1) (71/128)
2020-09-03 16:52:02 TaskSetManager: INFO: Starting task 83.0 in stage 0.0 (TID 85, jg3-w-0.c.maclab-ukbb.internal, executor 1, partition 83, PROCESS_LOCAL, 7737 bytes)
2020-09-03 16:52:02 TaskSetManager: INFO: Finished task 74.0 in stage 0.0 (TID 76) in 1113 ms on jg3-w-0.c.maclab-ukbb.internal (executor 1) (72/128)
2020-09-03 16:52:03 TaskSetManager: INFO: Starting task 84.0 in stage 0.0 (TID 86, jg3-w-1.c.maclab-ukbb.internal, executor 2, partition 84, PROCESS_LOCAL, 7737 bytes)
2020-09-03 16:52:03 TaskSetManager: INFO: Finished task 65.0 in stage 0.0 (TID 67) in 2308 ms on jg3-w-1.c.maclab-ukbb.internal (executor 2) (73/128)
2020-09-03 16:52:03 TaskSetManager: INFO: Starting task 85.0 in stage 0.0 (TID 87, jg3-w-1.c.maclab-ukbb.internal, executor 2, partition 85, PROCESS_LOCAL, 7737 bytes)
2020-09-03 16:52:03 TaskSetManager: INFO: Finished task 69.0 in stage 0.0 (TID 71) in 2299 ms on jg3-w-1.c.maclab-ukbb.internal (executor 2) (74/128)
2020-09-03 16:52:03 TaskSetManager: INFO: Starting task 86.0 in stage 0.0 (TID 88, jg3-w-0.c.maclab-ukbb.internal, executor 1, partition 86, PROCESS_LOCAL, 7737 bytes)
2020-09-03 16:52:03 TaskSetManager: INFO: Finished task 77.0 in stage 0.0 (TID 79) in 1134 ms on jg3-w-0.c.maclab-ukbb.internal (executor 1) (75/128)
2020-09-03 16:52:03 TaskSetManager: INFO: Starting task 87.0 in stage 0.0 (TID 89, jg3-w-1.c.maclab-ukbb.internal, executor 3, partition 87, PROCESS_LOCAL, 7737 bytes)
2020-09-03 16:52:03 TaskSetManager: INFO: Finished task 71.0 in stage 0.0 (TID 73) in 2521 ms on jg3-w-1.c.maclab-ukbb.internal (executor 3) (76/128)
2020-09-03 16:52:03 TaskSetManager: INFO: Starting task 88.0 in stage 0.0 (TID 90, jg3-w-1.c.maclab-ukbb.internal, executor 3, partition 88, PROCESS_LOCAL, 7737 bytes)
2020-09-03 16:52:03 TaskSetManager: INFO: Finished task 76.0 in stage 0.0 (TID 78) in 1852 ms on jg3-w-1.c.maclab-ukbb.internal (executor 3) (77/128)
2020-09-03 16:52:03 TaskSetManager: INFO: Starting task 89.0 in stage 0.0 (TID 91, jg3-w-1.c.maclab-ukbb.internal, executor 2, partition 89, PROCESS_LOCAL, 7737 bytes)
2020-09-03 16:52:03 TaskSetManager: INFO: Finished task 75.0 in stage 0.0 (TID 77) in 1988 ms on jg3-w-1.c.maclab-ukbb.internal (executor 2) (78/128)
2020-09-03 16:52:04 TaskSetManager: INFO: Starting task 90.0 in stage 0.0 (TID 92, jg3-w-0.c.maclab-ukbb.internal, executor 1, partition 90, PROCESS_LOCAL, 7737 bytes)
2020-09-03 16:52:04 TaskSetManager: INFO: Finished task 81.0 in stage 0.0 (TID 83) in 1174 ms on jg3-w-0.c.maclab-ukbb.internal (executor 1) (79/128)
2020-09-03 16:52:04 TaskSetManager: INFO: Starting task 91.0 in stage 0.0 (TID 93, jg3-w-0.c.maclab-ukbb.internal, executor 1, partition 91, PROCESS_LOCAL, 7737 bytes)
2020-09-03 16:52:04 TaskSetManager: INFO: Finished task 82.0 in stage 0.0 (TID 84) in 1170 ms on jg3-w-0.c.maclab-ukbb.internal (executor 1) (80/128)
2020-09-03 16:52:04 TaskSetManager: INFO: Starting task 92.0 in stage 0.0 (TID 94, jg3-w-0.c.maclab-ukbb.internal, executor 1, partition 92, PROCESS_LOCAL, 7737 bytes)
2020-09-03 16:52:04 TaskSetManager: INFO: Finished task 83.0 in stage 0.0 (TID 85) in 1191 ms on jg3-w-0.c.maclab-ukbb.internal (executor 1) (81/128)
2020-09-03 16:52:04 TaskSetManager: INFO: Starting task 93.0 in stage 0.0 (TID 95, jg3-w-1.c.maclab-ukbb.internal, executor 2, partition 93, PROCESS_LOCAL, 7737 bytes)
2020-09-03 16:52:04 TaskSetManager: INFO: Finished task 78.0 in stage 0.0 (TID 80) in 1981 ms on jg3-w-1.c.maclab-ukbb.internal (executor 2) (82/128)
2020-09-03 16:52:04 TaskSetManager: INFO: Starting task 94.0 in stage 0.0 (TID 96, jg3-w-1.c.maclab-ukbb.internal, executor 3, partition 94, PROCESS_LOCAL, 7737 bytes)
2020-09-03 16:52:04 TaskSetManager: INFO: Finished task 79.0 in stage 0.0 (TID 81) in 1899 ms on jg3-w-1.c.maclab-ukbb.internal (executor 3) (83/128)
2020-09-03 16:52:04 TaskSetManager: INFO: Starting task 95.0 in stage 0.0 (TID 97, jg3-w-0.c.maclab-ukbb.internal, executor 1, partition 95, PROCESS_LOCAL, 7737 bytes)
2020-09-03 16:52:04 TaskSetManager: INFO: Finished task 86.0 in stage 0.0 (TID 88) in 1152 ms on jg3-w-0.c.maclab-ukbb.internal (executor 1) (84/128)
2020-09-03 16:52:04 TaskSetManager: INFO: Starting task 96.0 in stage 0.0 (TID 98, jg3-w-1.c.maclab-ukbb.internal, executor 3, partition 96, PROCESS_LOCAL, 7737 bytes)
2020-09-03 16:52:04 TaskSetManager: INFO: Finished task 80.0 in stage 0.0 (TID 82) in 2102 ms on jg3-w-1.c.maclab-ukbb.internal (executor 3) (85/128)
2020-09-03 16:52:05 TaskSetManager: INFO: Starting task 97.0 in stage 0.0 (TID 99, jg3-w-1.c.maclab-ukbb.internal, executor 2, partition 97, PROCESS_LOCAL, 7737 bytes)
2020-09-03 16:52:05 TaskSetManager: INFO: Finished task 84.0 in stage 0.0 (TID 86) in 1971 ms on jg3-w-1.c.maclab-ukbb.internal (executor 2) (86/128)
2020-09-03 16:52:05 TaskSetManager: INFO: Starting task 98.0 in stage 0.0 (TID 100, jg3-w-0.c.maclab-ukbb.internal, executor 1, partition 98, PROCESS_LOCAL, 7737 bytes)
2020-09-03 16:52:05 TaskSetManager: INFO: Finished task 91.0 in stage 0.0 (TID 93) in 1065 ms on jg3-w-0.c.maclab-ukbb.internal (executor 1) (87/128)
2020-09-03 16:52:05 TaskSetManager: INFO: Starting task 99.0 in stage 0.0 (TID 101, jg3-w-0.c.maclab-ukbb.internal, executor 1, partition 99, PROCESS_LOCAL, 7737 bytes)
2020-09-03 16:52:05 TaskSetManager: INFO: Finished task 90.0 in stage 0.0 (TID 92) in 1126 ms on jg3-w-0.c.maclab-ukbb.internal (executor 1) (88/128)
2020-09-03 16:52:05 TaskSetManager: INFO: Starting task 100.0 in stage 0.0 (TID 102, jg3-w-0.c.maclab-ukbb.internal, executor 1, partition 100, PROCESS_LOCAL, 7737 bytes)
2020-09-03 16:52:05 TaskSetManager: INFO: Finished task 92.0 in stage 0.0 (TID 94) in 1125 ms on jg3-w-0.c.maclab-ukbb.internal (executor 1) (89/128)
2020-09-03 16:52:05 TaskSetManager: INFO: Starting task 101.0 in stage 0.0 (TID 103, jg3-w-1.c.maclab-ukbb.internal, executor 2, partition 101, PROCESS_LOCAL, 7737 bytes)
2020-09-03 16:52:05 TaskSetManager: INFO: Finished task 85.0 in stage 0.0 (TID 87) in 2200 ms on jg3-w-1.c.maclab-ukbb.internal (executor 2) (90/128)
2020-09-03 16:52:05 TaskSetManager: INFO: Starting task 102.0 in stage 0.0 (TID 104, jg3-w-0.c.maclab-ukbb.internal, executor 1, partition 102, PROCESS_LOCAL, 7737 bytes)
2020-09-03 16:52:05 TaskSetManager: INFO: Finished task 95.0 in stage 0.0 (TID 97) in 1124 ms on jg3-w-0.c.maclab-ukbb.internal (executor 1) (91/128)
2020-09-03 16:52:05 TaskSetManager: INFO: Starting task 103.0 in stage 0.0 (TID 105, jg3-w-1.c.maclab-ukbb.internal, executor 3, partition 103, PROCESS_LOCAL, 7737 bytes)
2020-09-03 16:52:05 TaskSetManager: INFO: Finished task 87.0 in stage 0.0 (TID 89) in 2165 ms on jg3-w-1.c.maclab-ukbb.internal (executor 3) (92/128)
2020-09-03 16:52:05 TaskSetManager: INFO: Starting task 104.0 in stage 0.0 (TID 106, jg3-w-1.c.maclab-ukbb.internal, executor 2, partition 104, PROCESS_LOCAL, 7737 bytes)
2020-09-03 16:52:05 TaskSetManager: INFO: Finished task 89.0 in stage 0.0 (TID 91) in 1856 ms on jg3-w-1.c.maclab-ukbb.internal (executor 2) (93/128)
2020-09-03 16:52:05 TaskSetManager: INFO: Starting task 105.0 in stage 0.0 (TID 107, jg3-w-1.c.maclab-ukbb.internal, executor 3, partition 105, PROCESS_LOCAL, 7737 bytes)
2020-09-03 16:52:05 TaskSetManager: INFO: Finished task 88.0 in stage 0.0 (TID 90) in 2079 ms on jg3-w-1.c.maclab-ukbb.internal (executor 3) (94/128)
2020-09-03 16:52:06 TaskSetManager: INFO: Starting task 106.0 in stage 0.0 (TID 108, jg3-w-1.c.maclab-ukbb.internal, executor 2, partition 106, PROCESS_LOCAL, 7737 bytes)
2020-09-03 16:52:06 TaskSetManager: INFO: Finished task 93.0 in stage 0.0 (TID 95) in 2011 ms on jg3-w-1.c.maclab-ukbb.internal (executor 2) (95/128)
2020-09-03 16:52:06 TaskSetManager: INFO: Starting task 107.0 in stage 0.0 (TID 109, jg3-w-0.c.maclab-ukbb.internal, executor 1, partition 107, PROCESS_LOCAL, 7737 bytes)
2020-09-03 16:52:06 TaskSetManager: INFO: Finished task 98.0 in stage 0.0 (TID 100) in 1110 ms on jg3-w-0.c.maclab-ukbb.internal (executor 1) (96/128)
2020-09-03 16:52:06 TaskSetManager: INFO: Starting task 108.0 in stage 0.0 (TID 110, jg3-w-1.c.maclab-ukbb.internal, executor 3, partition 108, PROCESS_LOCAL, 7737 bytes)
2020-09-03 16:52:06 TaskSetManager: INFO: Finished task 94.0 in stage 0.0 (TID 96) in 2050 ms on jg3-w-1.c.maclab-ukbb.internal (executor 3) (97/128)
2020-09-03 16:52:06 TaskSetManager: INFO: Starting task 109.0 in stage 0.0 (TID 111, jg3-w-0.c.maclab-ukbb.internal, executor 1, partition 109, PROCESS_LOCAL, 7737 bytes)
2020-09-03 16:52:06 TaskSetManager: INFO: Finished task 99.0 in stage 0.0 (TID 101) in 1108 ms on jg3-w-0.c.maclab-ukbb.internal (executor 1) (98/128)
2020-09-03 16:52:06 TaskSetManager: INFO: Starting task 110.0 in stage 0.0 (TID 112, jg3-w-0.c.maclab-ukbb.internal, executor 1, partition 110, PROCESS_LOCAL, 7737 bytes)
2020-09-03 16:52:06 TaskSetManager: INFO: Finished task 100.0 in stage 0.0 (TID 102) in 1129 ms on jg3-w-0.c.maclab-ukbb.internal (executor 1) (99/128)
2020-09-03 16:52:06 TaskSetManager: INFO: Marking task 96 in stage 0.0 (on jg3-w-1.c.maclab-ukbb.internal) as speculatable because it ran more than 1890 ms
2020-09-03 16:52:06 TaskSetManager: INFO: Starting task 111.0 in stage 0.0 (TID 113, jg3-w-1.c.maclab-ukbb.internal, executor 3, partition 111, PROCESS_LOCAL, 7737 bytes)
2020-09-03 16:52:06 TaskSetManager: INFO: Finished task 96.0 in stage 0.0 (TID 98) in 2023 ms on jg3-w-1.c.maclab-ukbb.internal (executor 3) (100/128)
2020-09-03 16:52:06 TaskSetManager: INFO: Starting task 112.0 in stage 0.0 (TID 114, jg3-w-0.c.maclab-ukbb.internal, executor 1, partition 112, PROCESS_LOCAL, 7737 bytes)
2020-09-03 16:52:06 TaskSetManager: INFO: Finished task 102.0 in stage 0.0 (TID 104) in 1131 ms on jg3-w-0.c.maclab-ukbb.internal (executor 1) (101/128)
2020-09-03 16:52:06 TaskSetManager: INFO: Starting task 113.0 in stage 0.0 (TID 115, jg3-w-1.c.maclab-ukbb.internal, executor 2, partition 113, PROCESS_LOCAL, 7737 bytes)
2020-09-03 16:52:06 TaskSetManager: INFO: Finished task 97.0 in stage 0.0 (TID 99) in 1896 ms on jg3-w-1.c.maclab-ukbb.internal (executor 2) (102/128)
2020-09-03 16:52:07 TaskSetManager: INFO: Starting task 114.0 in stage 0.0 (TID 116, jg3-w-1.c.maclab-ukbb.internal, executor 2, partition 114, PROCESS_LOCAL, 7737 bytes)
2020-09-03 16:52:07 TaskSetManager: INFO: Finished task 101.0 in stage 0.0 (TID 103) in 1913 ms on jg3-w-1.c.maclab-ukbb.internal (executor 2) (103/128)
2020-09-03 16:52:07 TaskSetManager: INFO: Starting task 115.0 in stage 0.0 (TID 117, jg3-w-0.c.maclab-ukbb.internal, executor 1, partition 115, PROCESS_LOCAL, 7737 bytes)
2020-09-03 16:52:07 TaskSetManager: INFO: Finished task 107.0 in stage 0.0 (TID 109) in 1119 ms on jg3-w-0.c.maclab-ukbb.internal (executor 1) (104/128)
2020-09-03 16:52:07 TaskSetManager: INFO: Starting task 116.0 in stage 0.0 (TID 118, jg3-w-0.c.maclab-ukbb.internal, executor 1, partition 116, PROCESS_LOCAL, 7737 bytes)
2020-09-03 16:52:07 TaskSetManager: INFO: Finished task 109.0 in stage 0.0 (TID 111) in 1093 ms on jg3-w-0.c.maclab-ukbb.internal (executor 1) (105/128)
2020-09-03 16:52:07 TaskSetManager: INFO: Starting task 117.0 in stage 0.0 (TID 119, jg3-w-0.c.maclab-ukbb.internal, executor 1, partition 117, PROCESS_LOCAL, 7737 bytes)
2020-09-03 16:52:07 TaskSetManager: INFO: Finished task 110.0 in stage 0.0 (TID 112) in 1102 ms on jg3-w-0.c.maclab-ukbb.internal (executor 1) (106/128)
2020-09-03 16:52:07 TaskSetManager: INFO: Marking task 103 in stage 0.0 (on jg3-w-1.c.maclab-ukbb.internal) as speculatable because it ran more than 1887 ms
2020-09-03 16:52:07 TaskSetManager: INFO: Marking task 104 in stage 0.0 (on jg3-w-1.c.maclab-ukbb.internal) as speculatable because it ran more than 1887 ms
2020-09-03 16:52:07 TaskSetManager: INFO: Starting task 118.0 in stage 0.0 (TID 120, jg3-w-1.c.maclab-ukbb.internal, executor 2, partition 118, PROCESS_LOCAL, 7737 bytes)
2020-09-03 16:52:07 TaskSetManager: INFO: Finished task 104.0 in stage 0.0 (TID 106) in 1984 ms on jg3-w-1.c.maclab-ukbb.internal (executor 2) (107/128)
2020-09-03 16:52:07 TaskSetManager: INFO: Marking task 105 in stage 0.0 (on jg3-w-1.c.maclab-ukbb.internal) as speculatable because it ran more than 1890 ms
2020-09-03 16:52:07 TaskSetManager: INFO: Starting task 119.0 in stage 0.0 (TID 121, jg3-w-0.c.maclab-ukbb.internal, executor 1, partition 119, PROCESS_LOCAL, 7737 bytes)
2020-09-03 16:52:07 TaskSetManager: INFO: Finished task 112.0 in stage 0.0 (TID 114) in 1231 ms on jg3-w-0.c.maclab-ukbb.internal (executor 1) (108/128)
2020-09-03 16:52:07 TaskSetManager: INFO: Starting task 120.0 in stage 0.0 (TID 122, jg3-w-1.c.maclab-ukbb.internal, executor 3, partition 120, PROCESS_LOCAL, 7737 bytes)
2020-09-03 16:52:07 TaskSetManager: INFO: Finished task 103.0 in stage 0.0 (TID 105) in 2103 ms on jg3-w-1.c.maclab-ukbb.internal (executor 3) (109/128)
2020-09-03 16:52:07 TaskSetManager: INFO: Starting task 121.0 in stage 0.0 (TID 123, jg3-w-1.c.maclab-ukbb.internal, executor 3, partition 121, PROCESS_LOCAL, 7737 bytes)
2020-09-03 16:52:07 TaskSetManager: INFO: Finished task 105.0 in stage 0.0 (TID 107) in 2085 ms on jg3-w-1.c.maclab-ukbb.internal (executor 3) (110/128)
2020-09-03 16:52:08 TaskSetManager: INFO: Starting task 122.0 in stage 0.0 (TID 124, jg3-w-1.c.maclab-ukbb.internal, executor 2, partition 122, PROCESS_LOCAL, 7737 bytes)
2020-09-03 16:52:08 TaskSetManager: INFO: Finished task 106.0 in stage 0.0 (TID 108) in 1904 ms on jg3-w-1.c.maclab-ukbb.internal (executor 2) (111/128)
2020-09-03 16:52:08 TaskSetManager: INFO: Starting task 123.0 in stage 0.0 (TID 125, jg3-w-1.c.maclab-ukbb.internal, executor 3, partition 123, PROCESS_LOCAL, 7737 bytes)
2020-09-03 16:52:08 TaskSetManager: INFO: Finished task 108.0 in stage 0.0 (TID 110) in 1844 ms on jg3-w-1.c.maclab-ukbb.internal (executor 3) (112/128)
2020-09-03 16:52:08 TaskSetManager: INFO: Starting task 124.0 in stage 0.0 (TID 126, jg3-w-1.c.maclab-ukbb.internal, executor 3, partition 124, PROCESS_LOCAL, 7737 bytes)
2020-09-03 16:52:08 TaskSetManager: INFO: Finished task 111.0 in stage 0.0 (TID 113) in 1918 ms on jg3-w-1.c.maclab-ukbb.internal (executor 3) (113/128)
2020-09-03 16:52:08 TaskSetManager: INFO: Starting task 125.0 in stage 0.0 (TID 127, jg3-w-0.c.maclab-ukbb.internal, executor 1, partition 125, PROCESS_LOCAL, 7737 bytes)
2020-09-03 16:52:08 TaskSetManager: INFO: Finished task 115.0 in stage 0.0 (TID 117) in 1161 ms on jg3-w-0.c.maclab-ukbb.internal (executor 1) (114/128)
2020-09-03 16:52:08 TaskSetManager: INFO: Starting task 126.0 in stage 0.0 (TID 128, jg3-w-0.c.maclab-ukbb.internal, executor 1, partition 126, PROCESS_LOCAL, 7737 bytes)
2020-09-03 16:52:08 TaskSetManager: INFO: Finished task 116.0 in stage 0.0 (TID 118) in 1138 ms on jg3-w-0.c.maclab-ukbb.internal (executor 1) (115/128)
2020-09-03 16:52:08 TaskSetManager: INFO: Starting task 127.0 in stage 0.0 (TID 129, jg3-w-0.c.maclab-ukbb.internal, executor 1, partition 127, PROCESS_LOCAL, 7737 bytes)
2020-09-03 16:52:08 TaskSetManager: INFO: Finished task 117.0 in stage 0.0 (TID 119) in 1156 ms on jg3-w-0.c.maclab-ukbb.internal (executor 1) (116/128)
2020-09-03 16:52:08 TaskSetManager: INFO: Marking task 113 in stage 0.0 (on jg3-w-1.c.maclab-ukbb.internal) as speculatable because it ran more than 1898 ms
2020-09-03 16:52:08 TaskSetManager: INFO: Finished task 113.0 in stage 0.0 (TID 115) in 2007 ms on jg3-w-1.c.maclab-ukbb.internal (executor 2) (117/128)
2020-09-03 16:52:08 TaskSetManager: INFO: Finished task 119.0 in stage 0.0 (TID 121) in 1107 ms on jg3-w-0.c.maclab-ukbb.internal (executor 1) (118/128)
2020-09-03 16:52:09 TaskSetManager: INFO: Marking task 114 in stage 0.0 (on jg3-w-1.c.maclab-ukbb.internal) as speculatable because it ran more than 1898 ms
2020-09-03 16:52:09 TaskSetManager: INFO: Starting task 114.1 in stage 0.0 (TID 130, jg3-w-0.c.maclab-ukbb.internal, executor 1, partition 114, PROCESS_LOCAL, 7737 bytes)
2020-09-03 16:52:09 TaskSetManager: INFO: Killing attempt 1 for task 114.1 in stage 0.0 (TID 130) on jg3-w-0.c.maclab-ukbb.internal as the attempt 0 succeeded on jg3-w-1.c.maclab-ukbb.internal
2020-09-03 16:52:09 TaskSetManager: INFO: Finished task 114.0 in stage 0.0 (TID 116) in 2043 ms on jg3-w-1.c.maclab-ukbb.internal (executor 2) (119/128)
2020-09-03 16:52:09 TaskSetManager: WARN: Lost task 114.1 in stage 0.0 (TID 130, jg3-w-0.c.maclab-ukbb.internal, executor 1): TaskKilled (another attempt succeeded)
2020-09-03 16:52:09 TaskSetManager: INFO: Task 114.1 in stage 0.0 (TID 130) failed, but the task will not be re-executed (either because the task failed with a shuffle data fetch failure, so the previous stage needs to be re-run, or because a different copy of the task has already succeeded).
2020-09-03 16:52:09 TaskSetManager: WARN: Lost task 126.0 in stage 0.0 (TID 128, jg3-w-0.c.maclab-ukbb.internal, executor 1): htsjdk.samtools.SAMException: Unable to load chr20(63780569, 63784665) from /tmp/fasta-reader-FcVGkbAEQi5MCYD6x7hi1B.fasta
	at htsjdk.samtools.reference.AbstractIndexedFastaSequenceFile.getSubsequenceAt(AbstractIndexedFastaSequenceFile.java:207)
	at htsjdk.samtools.reference.IndexedFastaSequenceFile.getSubsequenceAt(IndexedFastaSequenceFile.java:49)
	at is.hail.io.reference.FASTAReader.getSequence(FASTAReader.scala:73)
	at is.hail.io.reference.FASTAReader.fillBlock(FASTAReader.scala:83)
	at is.hail.io.reference.FASTAReader.readBlock(FASTAReader.scala:93)
	at is.hail.io.reference.FASTAReader.readBlock(FASTAReader.scala:99)
	at is.hail.io.reference.FASTAReader.lookupGlobalPos(FASTAReader.scala:138)
	at is.hail.io.reference.FASTAReader.lookup(FASTAReader.scala:110)
	at is.hail.variant.ReferenceGenome.getSequence(ReferenceGenome.scala:357)
	at __C24Compiled.__m42getReferenceSequenceFromValidLocus(Unknown Source)
	at __C24Compiled.apply(Unknown Source)
	at is.hail.expr.ir.TableFilter$$anonfun$execute$2.apply(TableIR.scala:946)
	at is.hail.expr.ir.TableFilter$$anonfun$execute$2.apply(TableIR.scala:946)
	at is.hail.expr.ir.TableValue$$anonfun$3.apply(TableValue.scala:65)
	at is.hail.expr.ir.TableValue$$anonfun$3.apply(TableValue.scala:65)
	at is.hail.rvd.RVD$$anonfun$17$$anonfun$apply$2.apply$mcZJ$sp(RVD.scala:605)
	at is.hail.rvd.RVD$$anonfun$17$$anonfun$apply$2.apply(RVD.scala:604)
	at is.hail.rvd.RVD$$anonfun$17$$anonfun$apply$2.apply(RVD.scala:604)
	at scala.collection.Iterator$$anon$13.hasNext(Iterator.scala:464)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
	at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:409)
	at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:409)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
	at is.hail.rvd.RVDPartitionInfo$$anonfun$apply$1.apply(RVDPartitionInfo.scala:66)
	at is.hail.rvd.RVDPartitionInfo$$anonfun$apply$1.apply(RVDPartitionInfo.scala:38)
	at is.hail.utils.package$.using(package.scala:609)
	at is.hail.rvd.RVDPartitionInfo$.apply(RVDPartitionInfo.scala:38)
	at is.hail.rvd.RVD$$anonfun$32.apply(RVD.scala:1223)
	at is.hail.rvd.RVD$$anonfun$32.apply(RVD.scala:1221)
	at is.hail.sparkextras.ContextRDD$$anonfun$crunJobWithIndex$1.apply(ContextRDD.scala:232)
	at is.hail.sparkextras.ContextRDD$$anonfun$crunJobWithIndex$1.apply(ContextRDD.scala:230)
	at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:90)
	at org.apache.spark.scheduler.Task.run(Task.scala:123)
	at org.apache.spark.executor.Executor$TaskRunner$$anonfun$10.apply(Executor.scala:408)
	at org.apache.spark.util.Utils$.tryWithSafeFinally(Utils.scala:1360)
	at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:414)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
	at java.lang.Thread.run(Thread.java:748)
Caused by: java.nio.channels.ClosedChannelException
	at sun.nio.ch.FileChannelImpl.ensureOpen(FileChannelImpl.java:110)
	at sun.nio.ch.FileChannelImpl.read(FileChannelImpl.java:715)
	at htsjdk.samtools.reference.IndexedFastaSequenceFile.readFromPosition(IndexedFastaSequenceFile.java:148)
	at htsjdk.samtools.reference.AbstractIndexedFastaSequenceFile.getSubsequenceAt(AbstractIndexedFastaSequenceFile.java:204)
	... 38 more

2020-09-03 16:52:09 TaskSetManager: WARN: Lost task 125.0 in stage 0.0 (TID 127, jg3-w-0.c.maclab-ukbb.internal, executor 1): htsjdk.samtools.SAMException: Unable to load chr20(63280857, 63284953) from /tmp/fasta-reader-FcVGkbAEQi5MCYD6x7hi1B.fasta
	at htsjdk.samtools.reference.AbstractIndexedFastaSequenceFile.getSubsequenceAt(AbstractIndexedFastaSequenceFile.java:207)
	at htsjdk.samtools.reference.IndexedFastaSequenceFile.getSubsequenceAt(IndexedFastaSequenceFile.java:49)
	at is.hail.io.reference.FASTAReader.getSequence(FASTAReader.scala:73)
	at is.hail.io.reference.FASTAReader.fillBlock(FASTAReader.scala:83)
	at is.hail.io.reference.FASTAReader.readBlock(FASTAReader.scala:93)
	at is.hail.io.reference.FASTAReader.readBlock(FASTAReader.scala:99)
	at is.hail.io.reference.FASTAReader.lookupGlobalPos(FASTAReader.scala:138)
	at is.hail.io.reference.FASTAReader.lookup(FASTAReader.scala:110)
	at is.hail.variant.ReferenceGenome.getSequence(ReferenceGenome.scala:357)
	at __C24Compiled.__m42getReferenceSequenceFromValidLocus(Unknown Source)
	at __C24Compiled.apply(Unknown Source)
	at is.hail.expr.ir.TableFilter$$anonfun$execute$2.apply(TableIR.scala:946)
	at is.hail.expr.ir.TableFilter$$anonfun$execute$2.apply(TableIR.scala:946)
	at is.hail.expr.ir.TableValue$$anonfun$3.apply(TableValue.scala:65)
	at is.hail.expr.ir.TableValue$$anonfun$3.apply(TableValue.scala:65)
	at is.hail.rvd.RVD$$anonfun$17$$anonfun$apply$2.apply$mcZJ$sp(RVD.scala:605)
	at is.hail.rvd.RVD$$anonfun$17$$anonfun$apply$2.apply(RVD.scala:604)
	at is.hail.rvd.RVD$$anonfun$17$$anonfun$apply$2.apply(RVD.scala:604)
	at scala.collection.Iterator$$anon$13.hasNext(Iterator.scala:464)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
	at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:409)
	at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:409)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
	at is.hail.rvd.RVDPartitionInfo$$anonfun$apply$1.apply(RVDPartitionInfo.scala:66)
	at is.hail.rvd.RVDPartitionInfo$$anonfun$apply$1.apply(RVDPartitionInfo.scala:38)
	at is.hail.utils.package$.using(package.scala:609)
	at is.hail.rvd.RVDPartitionInfo$.apply(RVDPartitionInfo.scala:38)
	at is.hail.rvd.RVD$$anonfun$32.apply(RVD.scala:1223)
	at is.hail.rvd.RVD$$anonfun$32.apply(RVD.scala:1221)
	at is.hail.sparkextras.ContextRDD$$anonfun$crunJobWithIndex$1.apply(ContextRDD.scala:232)
	at is.hail.sparkextras.ContextRDD$$anonfun$crunJobWithIndex$1.apply(ContextRDD.scala:230)
	at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:90)
	at org.apache.spark.scheduler.Task.run(Task.scala:123)
	at org.apache.spark.executor.Executor$TaskRunner$$anonfun$10.apply(Executor.scala:408)
	at org.apache.spark.util.Utils$.tryWithSafeFinally(Utils.scala:1360)
	at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:414)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
	at java.lang.Thread.run(Thread.java:748)
Caused by: java.nio.channels.ClosedChannelException
	at sun.nio.ch.FileChannelImpl.ensureOpen(FileChannelImpl.java:110)
	at sun.nio.ch.FileChannelImpl.read(FileChannelImpl.java:715)
	at htsjdk.samtools.reference.IndexedFastaSequenceFile.readFromPosition(IndexedFastaSequenceFile.java:148)
	at htsjdk.samtools.reference.AbstractIndexedFastaSequenceFile.getSubsequenceAt(AbstractIndexedFastaSequenceFile.java:204)
	... 38 more

2020-09-03 16:52:09 TaskSetManager: WARN: Lost task 127.0 in stage 0.0 (TID 129, jg3-w-0.c.maclab-ukbb.internal, executor 1): htsjdk.samtools.SAMException: Unable to load chr20(64239321, 64243417) from /tmp/fasta-reader-FcVGkbAEQi5MCYD6x7hi1B.fasta
	at htsjdk.samtools.reference.AbstractIndexedFastaSequenceFile.getSubsequenceAt(AbstractIndexedFastaSequenceFile.java:207)
	at htsjdk.samtools.reference.IndexedFastaSequenceFile.getSubsequenceAt(IndexedFastaSequenceFile.java:49)
	at is.hail.io.reference.FASTAReader.getSequence(FASTAReader.scala:73)
	at is.hail.io.reference.FASTAReader.fillBlock(FASTAReader.scala:83)
	at is.hail.io.reference.FASTAReader.readBlock(FASTAReader.scala:93)
	at is.hail.io.reference.FASTAReader.readBlock(FASTAReader.scala:99)
	at is.hail.io.reference.FASTAReader.lookupGlobalPos(FASTAReader.scala:138)
	at is.hail.io.reference.FASTAReader.lookup(FASTAReader.scala:110)
	at is.hail.variant.ReferenceGenome.getSequence(ReferenceGenome.scala:357)
	at __C24Compiled.__m42getReferenceSequenceFromValidLocus(Unknown Source)
	at __C24Compiled.apply(Unknown Source)
	at is.hail.expr.ir.TableFilter$$anonfun$execute$2.apply(TableIR.scala:946)
	at is.hail.expr.ir.TableFilter$$anonfun$execute$2.apply(TableIR.scala:946)
	at is.hail.expr.ir.TableValue$$anonfun$3.apply(TableValue.scala:65)
	at is.hail.expr.ir.TableValue$$anonfun$3.apply(TableValue.scala:65)
	at is.hail.rvd.RVD$$anonfun$17$$anonfun$apply$2.apply$mcZJ$sp(RVD.scala:605)
	at is.hail.rvd.RVD$$anonfun$17$$anonfun$apply$2.apply(RVD.scala:604)
	at is.hail.rvd.RVD$$anonfun$17$$anonfun$apply$2.apply(RVD.scala:604)
	at scala.collection.Iterator$$anon$13.hasNext(Iterator.scala:464)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
	at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:409)
	at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:409)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
	at is.hail.rvd.RVDPartitionInfo$$anonfun$apply$1.apply(RVDPartitionInfo.scala:66)
	at is.hail.rvd.RVDPartitionInfo$$anonfun$apply$1.apply(RVDPartitionInfo.scala:38)
	at is.hail.utils.package$.using(package.scala:609)
	at is.hail.rvd.RVDPartitionInfo$.apply(RVDPartitionInfo.scala:38)
	at is.hail.rvd.RVD$$anonfun$32.apply(RVD.scala:1223)
	at is.hail.rvd.RVD$$anonfun$32.apply(RVD.scala:1221)
	at is.hail.sparkextras.ContextRDD$$anonfun$crunJobWithIndex$1.apply(ContextRDD.scala:232)
	at is.hail.sparkextras.ContextRDD$$anonfun$crunJobWithIndex$1.apply(ContextRDD.scala:230)
	at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:90)
	at org.apache.spark.scheduler.Task.run(Task.scala:123)
	at org.apache.spark.executor.Executor$TaskRunner$$anonfun$10.apply(Executor.scala:408)
	at org.apache.spark.util.Utils$.tryWithSafeFinally(Utils.scala:1360)
	at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:414)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
	at java.lang.Thread.run(Thread.java:748)
Caused by: java.nio.channels.ClosedChannelException
	at sun.nio.ch.FileChannelImpl.ensureOpen(FileChannelImpl.java:110)
	at sun.nio.ch.FileChannelImpl.read(FileChannelImpl.java:715)
	at htsjdk.samtools.reference.IndexedFastaSequenceFile.readFromPosition(IndexedFastaSequenceFile.java:148)
	at htsjdk.samtools.reference.AbstractIndexedFastaSequenceFile.getSubsequenceAt(AbstractIndexedFastaSequenceFile.java:204)
	... 38 more

2020-09-03 16:52:09 TaskSetManager: INFO: Starting task 127.1 in stage 0.0 (TID 131, jg3-w-1.c.maclab-ukbb.internal, executor 2, partition 127, PROCESS_LOCAL, 7737 bytes)
2020-09-03 16:52:09 TaskSetManager: INFO: Starting task 125.1 in stage 0.0 (TID 132, jg3-w-0.c.maclab-ukbb.internal, executor 1, partition 125, PROCESS_LOCAL, 7737 bytes)
2020-09-03 16:52:09 TaskSetManager: INFO: Starting task 126.1 in stage 0.0 (TID 133, jg3-w-1.c.maclab-ukbb.internal, executor 2, partition 126, PROCESS_LOCAL, 7737 bytes)
2020-09-03 16:52:09 ExecutorAllocationManager: INFO: Requesting 0 new executor because tasks are backlogged (new desired total will be 5)
2020-09-03 16:52:09 TaskSetManager: INFO: Marking task 118 in stage 0.0 (on jg3-w-1.c.maclab-ukbb.internal) as speculatable because it ran more than 1905 ms
2020-09-03 16:52:09 TaskSetManager: INFO: Starting task 118.1 in stage 0.0 (TID 134, jg3-w-0.c.maclab-ukbb.internal, executor 1, partition 118, PROCESS_LOCAL, 7737 bytes)
2020-09-03 16:52:09 TaskSetManager: WARN: Lost task 118.1 in stage 0.0 (TID 134, jg3-w-0.c.maclab-ukbb.internal, executor 1): htsjdk.samtools.SAMException: Unable to load chr20(59410137, 59414233) from /tmp/fasta-reader-FcVGkbAEQi5MCYD6x7hi1B.fasta
	at htsjdk.samtools.reference.AbstractIndexedFastaSequenceFile.getSubsequenceAt(AbstractIndexedFastaSequenceFile.java:207)
	at htsjdk.samtools.reference.IndexedFastaSequenceFile.getSubsequenceAt(IndexedFastaSequenceFile.java:49)
	at is.hail.io.reference.FASTAReader.getSequence(FASTAReader.scala:73)
	at is.hail.io.reference.FASTAReader.fillBlock(FASTAReader.scala:83)
	at is.hail.io.reference.FASTAReader.readBlock(FASTAReader.scala:93)
	at is.hail.io.reference.FASTAReader.readBlock(FASTAReader.scala:99)
	at is.hail.io.reference.FASTAReader.lookupGlobalPos(FASTAReader.scala:138)
	at is.hail.io.reference.FASTAReader.lookup(FASTAReader.scala:110)
	at is.hail.variant.ReferenceGenome.getSequence(ReferenceGenome.scala:357)
	at __C24Compiled.__m42getReferenceSequenceFromValidLocus(Unknown Source)
	at __C24Compiled.apply(Unknown Source)
	at is.hail.expr.ir.TableFilter$$anonfun$execute$2.apply(TableIR.scala:946)
	at is.hail.expr.ir.TableFilter$$anonfun$execute$2.apply(TableIR.scala:946)
	at is.hail.expr.ir.TableValue$$anonfun$3.apply(TableValue.scala:65)
	at is.hail.expr.ir.TableValue$$anonfun$3.apply(TableValue.scala:65)
	at is.hail.rvd.RVD$$anonfun$17$$anonfun$apply$2.apply$mcZJ$sp(RVD.scala:605)
	at is.hail.rvd.RVD$$anonfun$17$$anonfun$apply$2.apply(RVD.scala:604)
	at is.hail.rvd.RVD$$anonfun$17$$anonfun$apply$2.apply(RVD.scala:604)
	at scala.collection.Iterator$$anon$13.hasNext(Iterator.scala:464)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
	at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:409)
	at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:409)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
	at is.hail.rvd.RVDPartitionInfo$$anonfun$apply$1.apply(RVDPartitionInfo.scala:66)
	at is.hail.rvd.RVDPartitionInfo$$anonfun$apply$1.apply(RVDPartitionInfo.scala:38)
	at is.hail.utils.package$.using(package.scala:609)
	at is.hail.rvd.RVDPartitionInfo$.apply(RVDPartitionInfo.scala:38)
	at is.hail.rvd.RVD$$anonfun$32.apply(RVD.scala:1223)
	at is.hail.rvd.RVD$$anonfun$32.apply(RVD.scala:1221)
	at is.hail.sparkextras.ContextRDD$$anonfun$crunJobWithIndex$1.apply(ContextRDD.scala:232)
	at is.hail.sparkextras.ContextRDD$$anonfun$crunJobWithIndex$1.apply(ContextRDD.scala:230)
	at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:90)
	at org.apache.spark.scheduler.Task.run(Task.scala:123)
	at org.apache.spark.executor.Executor$TaskRunner$$anonfun$10.apply(Executor.scala:408)
	at org.apache.spark.util.Utils$.tryWithSafeFinally(Utils.scala:1360)
	at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:414)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
	at java.lang.Thread.run(Thread.java:748)
Caused by: java.nio.channels.ClosedChannelException
	at sun.nio.ch.FileChannelImpl.ensureOpen(FileChannelImpl.java:110)
	at sun.nio.ch.FileChannelImpl.read(FileChannelImpl.java:715)
	at htsjdk.samtools.reference.IndexedFastaSequenceFile.readFromPosition(IndexedFastaSequenceFile.java:148)
	at htsjdk.samtools.reference.AbstractIndexedFastaSequenceFile.getSubsequenceAt(AbstractIndexedFastaSequenceFile.java:204)
	... 38 more

2020-09-03 16:52:09 TaskSetManager: INFO: Marking task 120 in stage 0.0 (on jg3-w-1.c.maclab-ukbb.internal) as speculatable because it ran more than 1905 ms
2020-09-03 16:52:09 TaskSetManager: INFO: Marking task 118 in stage 0.0 (on jg3-w-1.c.maclab-ukbb.internal) as speculatable because it ran more than 1905 ms
2020-09-03 16:52:09 TaskSetManager: INFO: Starting task 120.1 in stage 0.0 (TID 135, jg3-w-0.c.maclab-ukbb.internal, executor 1, partition 120, PROCESS_LOCAL, 7737 bytes)
2020-09-03 16:52:09 TaskSetManager: INFO: Finished task 122.0 in stage 0.0 (TID 124) in 1723 ms on jg3-w-1.c.maclab-ukbb.internal (executor 2) (120/128)
2020-09-03 16:52:09 TaskSetManager: WARN: Lost task 120.1 in stage 0.0 (TID 135, jg3-w-0.c.maclab-ukbb.internal, executor 1): htsjdk.samtools.SAMException: Unable to load chr20(60417753, 60421849) from /tmp/fasta-reader-FcVGkbAEQi5MCYD6x7hi1B.fasta
	at htsjdk.samtools.reference.AbstractIndexedFastaSequenceFile.getSubsequenceAt(AbstractIndexedFastaSequenceFile.java:207)
	at htsjdk.samtools.reference.IndexedFastaSequenceFile.getSubsequenceAt(IndexedFastaSequenceFile.java:49)
	at is.hail.io.reference.FASTAReader.getSequence(FASTAReader.scala:73)
	at is.hail.io.reference.FASTAReader.fillBlock(FASTAReader.scala:83)
	at is.hail.io.reference.FASTAReader.readBlock(FASTAReader.scala:93)
	at is.hail.io.reference.FASTAReader.readBlock(FASTAReader.scala:99)
	at is.hail.io.reference.FASTAReader.lookupGlobalPos(FASTAReader.scala:138)
	at is.hail.io.reference.FASTAReader.lookup(FASTAReader.scala:110)
	at is.hail.variant.ReferenceGenome.getSequence(ReferenceGenome.scala:357)
	at __C24Compiled.__m42getReferenceSequenceFromValidLocus(Unknown Source)
	at __C24Compiled.apply(Unknown Source)
	at is.hail.expr.ir.TableFilter$$anonfun$execute$2.apply(TableIR.scala:946)
	at is.hail.expr.ir.TableFilter$$anonfun$execute$2.apply(TableIR.scala:946)
	at is.hail.expr.ir.TableValue$$anonfun$3.apply(TableValue.scala:65)
	at is.hail.expr.ir.TableValue$$anonfun$3.apply(TableValue.scala:65)
	at is.hail.rvd.RVD$$anonfun$17$$anonfun$apply$2.apply$mcZJ$sp(RVD.scala:605)
	at is.hail.rvd.RVD$$anonfun$17$$anonfun$apply$2.apply(RVD.scala:604)
	at is.hail.rvd.RVD$$anonfun$17$$anonfun$apply$2.apply(RVD.scala:604)
	at scala.collection.Iterator$$anon$13.hasNext(Iterator.scala:464)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
	at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:409)
	at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:409)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
	at is.hail.rvd.RVDPartitionInfo$$anonfun$apply$1.apply(RVDPartitionInfo.scala:66)
	at is.hail.rvd.RVDPartitionInfo$$anonfun$apply$1.apply(RVDPartitionInfo.scala:38)
	at is.hail.utils.package$.using(package.scala:609)
	at is.hail.rvd.RVDPartitionInfo$.apply(RVDPartitionInfo.scala:38)
	at is.hail.rvd.RVD$$anonfun$32.apply(RVD.scala:1223)
	at is.hail.rvd.RVD$$anonfun$32.apply(RVD.scala:1221)
	at is.hail.sparkextras.ContextRDD$$anonfun$crunJobWithIndex$1.apply(ContextRDD.scala:232)
	at is.hail.sparkextras.ContextRDD$$anonfun$crunJobWithIndex$1.apply(ContextRDD.scala:230)
	at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:90)
	at org.apache.spark.scheduler.Task.run(Task.scala:123)
	at org.apache.spark.executor.Executor$TaskRunner$$anonfun$10.apply(Executor.scala:408)
	at org.apache.spark.util.Utils$.tryWithSafeFinally(Utils.scala:1360)
	at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:414)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
	at java.lang.Thread.run(Thread.java:748)
Caused by: java.nio.channels.ClosedChannelException
	at sun.nio.ch.FileChannelImpl.ensureOpen(FileChannelImpl.java:110)
	at sun.nio.ch.FileChannelImpl.read(FileChannelImpl.java:715)
	at htsjdk.samtools.reference.IndexedFastaSequenceFile.readFromPosition(IndexedFastaSequenceFile.java:148)
	at htsjdk.samtools.reference.AbstractIndexedFastaSequenceFile.getSubsequenceAt(AbstractIndexedFastaSequenceFile.java:204)
	... 38 more

2020-09-03 16:52:09 TaskSetManager: INFO: Finished task 120.0 in stage 0.0 (TID 122) in 1984 ms on jg3-w-1.c.maclab-ukbb.internal (executor 3) (121/128)
2020-09-03 16:52:09 TaskSetManager: INFO: Finished task 121.0 in stage 0.0 (TID 123) in 1908 ms on jg3-w-1.c.maclab-ukbb.internal (executor 3) (122/128)
2020-09-03 16:52:09 TaskSetManager: INFO: Finished task 118.0 in stage 0.0 (TID 120) in 2138 ms on jg3-w-1.c.maclab-ukbb.internal (executor 2) (123/128)
2020-09-03 16:52:09 TaskSetManager: INFO: Finished task 123.0 in stage 0.0 (TID 125) in 1758 ms on jg3-w-1.c.maclab-ukbb.internal (executor 3) (124/128)
2020-09-03 16:52:10 TaskSetManager: INFO: Lost task 125.1 in stage 0.0 (TID 132) on jg3-w-0.c.maclab-ukbb.internal, executor 1: htsjdk.samtools.SAMException (Unable to load chr20(63280857, 63284953) from /tmp/fasta-reader-FcVGkbAEQi5MCYD6x7hi1B.fasta) [duplicate 1]
2020-09-03 16:52:10 TaskSetManager: INFO: Starting task 125.2 in stage 0.0 (TID 136, jg3-w-1.c.maclab-ukbb.internal, executor 3, partition 125, PROCESS_LOCAL, 7737 bytes)
2020-09-03 16:52:10 TaskSetManager: INFO: Finished task 124.0 in stage 0.0 (TID 126) in 1604 ms on jg3-w-1.c.maclab-ukbb.internal (executor 3) (125/128)
2020-09-03 16:52:10 ExecutorAllocationManager: INFO: Requesting 0 new executor because tasks are backlogged (new desired total will be 4)
2020-09-03 16:52:10 TaskSetManager: INFO: Finished task 127.1 in stage 0.0 (TID 131) in 1204 ms on jg3-w-1.c.maclab-ukbb.internal (executor 2) (126/128)
2020-09-03 16:52:10 TaskSetManager: INFO: Finished task 126.1 in stage 0.0 (TID 133) in 1265 ms on jg3-w-1.c.maclab-ukbb.internal (executor 2) (127/128)
2020-09-03 16:52:11 TaskSetManager: INFO: Finished task 125.2 in stage 0.0 (TID 136) in 990 ms on jg3-w-1.c.maclab-ukbb.internal (executor 3) (128/128)
2020-09-03 16:52:11 DAGScheduler: INFO: ResultStage 0 (runJob at ContextRDD.scala:228) finished in 48.044 s
2020-09-03 16:52:11 YarnScheduler: INFO: Removed TaskSet 0.0, whose tasks have all completed, from pool default
2020-09-03 16:52:11 DAGScheduler: INFO: Job 0 finished: runJob at ContextRDD.scala:228, took 48.129611 s
2020-09-03 16:52:11 Hail: INFO: Coerced sorted dataset
2020-09-03 16:52:11 root: INFO: decoder cache hit
2020-09-03 16:52:11 root: INFO: decoder cache miss (1 hits, 2 misses, 0.333
2020-09-03 16:52:11 root: INFO: instruction count: 6: __C71etypeDecode.<init>
2020-09-03 16:52:11 root: INFO: instruction count: 8: __C71etypeDecode.apply
2020-09-03 16:52:11 root: INFO: instruction count: 38: __C71etypeDecode.__m72DECODE_r_struct_of_o_struct_of_o_struct_of_r_binaryANDr_int32ENDANDo_struct_of_r_binaryANDr_int32ENDANDr_boolANDr_boolENDANDo_binaryEND_TO_r_tuple_of_o_interval_of_o_locusEND
2020-09-03 16:52:11 root: INFO: instruction count: 47: __C71etypeDecode.__m73read_fields_group_0
2020-09-03 16:52:11 root: INFO: instruction count: 30: __C71etypeDecode.__m74INPLACE_DECODE_o_struct_of_o_struct_of_r_binaryANDr_int32ENDANDo_struct_of_r_binaryANDr_int32ENDANDr_boolANDr_boolEND_TO_o_tuple_of_o_tuple_of_r_binaryANDr_int32ENDANDo_tuple_of_r_binaryANDr_int32ENDANDr_boolANDr_boolEND
2020-09-03 16:52:11 root: INFO: instruction count: 74: __C71etypeDecode.__m75read_fields_group_0
2020-09-03 16:52:11 root: INFO: instruction count: 17: __C71etypeDecode.__m76INPLACE_DECODE_o_struct_of_r_binaryANDr_int32END_TO_o_tuple_of_r_binaryANDr_int32END
2020-09-03 16:52:11 root: INFO: instruction count: 18: __C71etypeDecode.__m77read_fields_group_0
2020-09-03 16:52:11 root: INFO: instruction count: 34: __C71etypeDecode.__m78INPLACE_DECODE_r_binary_TO_r_binary
2020-09-03 16:52:11 root: INFO: instruction count: 11: __C71etypeDecode.__m79INPLACE_DECODE_r_int32_TO_r_int32
2020-09-03 16:52:11 root: INFO: instruction count: 11: __C71etypeDecode.__m80INPLACE_DECODE_r_bool_TO_r_bool
2020-09-03 16:52:11 root: INFO: instruction count: 12: __C71etypeDecode.__m81SKIP_o_binary
2020-09-03 16:52:11 MemoryStore: INFO: Block broadcast_7 stored as values in memory (estimated size 3.5 MB, free 21.7 GB)
2020-09-03 16:52:11 MemoryStore: INFO: Block broadcast_7_piece0 stored as bytes in memory (estimated size 37.0 KB, free 21.7 GB)
2020-09-03 16:52:11 BlockManagerInfo: INFO: Added broadcast_7_piece0 in memory on jg3-m.c.maclab-ukbb.internal:36967 (size: 37.0 KB, free: 21.7 GB)
2020-09-03 16:52:11 SparkContext: INFO: Created broadcast 7 from broadcast at RVDPartitioner.scala:93
2020-09-03 16:52:11 root: INFO: encoder cache miss (1 hits, 4 misses, 0.200)
2020-09-03 16:52:11 root: INFO: instruction count: 6: __C82etypeEncode.<init>
2020-09-03 16:52:11 root: INFO: instruction count: 8: __C82etypeEncode.apply
2020-09-03 16:52:11 root: INFO: instruction count: 20: __C82etypeEncode.__m83ENCODE_r_tuple_of_o_interval_of_o_locusEND_TO_r_struct_of_o_struct_of_o_struct_of_r_binaryANDr_int32ENDANDo_struct_of_r_binaryANDr_int32ENDANDr_boolANDr_boolENDEND
2020-09-03 16:52:11 root: INFO: instruction count: 21: __C82etypeEncode.__m84write_fields_group_0
2020-09-03 16:52:11 root: INFO: instruction count: 20: __C82etypeEncode.__m85ENCODE_o_tuple_of_o_tuple_of_r_binaryANDr_int32ENDANDo_tuple_of_r_binaryANDr_int32ENDANDr_boolANDr_boolEND_TO_o_struct_of_o_struct_of_r_binaryANDr_int32ENDANDo_struct_of_r_binaryANDr_int32ENDANDr_boolANDr_boolEND
2020-09-03 16:52:11 root: INFO: instruction count: 58: __C82etypeEncode.__m86write_fields_group_0
2020-09-03 16:52:11 root: INFO: instruction count: 8: __C82etypeEncode.__m87ENCODE_o_tuple_of_r_binaryANDr_int32END_TO_o_struct_of_r_binaryANDr_int32END
2020-09-03 16:52:11 root: INFO: instruction count: 24: __C82etypeEncode.__m88write_fields_group_0
2020-09-03 16:52:11 root: INFO: instruction count: 19: __C82etypeEncode.__m89ENCODE_r_binary_TO_r_binary
2020-09-03 16:52:11 root: INFO: instruction count: 7: __C82etypeEncode.__m90ENCODE_r_int32_TO_r_int32
2020-09-03 16:52:11 root: INFO: instruction count: 7: __C82etypeEncode.__m91ENCODE_r_bool_TO_r_bool
2020-09-03 16:52:11 root: INFO: decoder cache miss (1 hits, 3 misses, 0.250
2020-09-03 16:52:11 root: INFO: instruction count: 6: __C92etypeDecode.<init>
2020-09-03 16:52:11 root: INFO: instruction count: 8: __C92etypeDecode.apply
2020-09-03 16:52:11 root: INFO: instruction count: 38: __C92etypeDecode.__m93DECODE_r_struct_of_o_struct_of_o_struct_of_r_binaryANDr_int32ENDANDo_struct_of_r_binaryANDr_int32ENDANDr_boolANDr_boolENDEND_TO_r_tuple_of_o_interval_of_o_locusEND
2020-09-03 16:52:11 root: INFO: instruction count: 32: __C92etypeDecode.__m94read_fields_group_0
2020-09-03 16:52:11 root: INFO: instruction count: 30: __C92etypeDecode.__m95INPLACE_DECODE_o_struct_of_o_struct_of_r_binaryANDr_int32ENDANDo_struct_of_r_binaryANDr_int32ENDANDr_boolANDr_boolEND_TO_o_tuple_of_o_tuple_of_r_binaryANDr_int32ENDANDo_tuple_of_r_binaryANDr_int32ENDANDr_boolANDr_boolEND
2020-09-03 16:52:11 root: INFO: instruction count: 74: __C92etypeDecode.__m96read_fields_group_0
2020-09-03 16:52:11 root: INFO: instruction count: 17: __C92etypeDecode.__m97INPLACE_DECODE_o_struct_of_r_binaryANDr_int32END_TO_o_tuple_of_r_binaryANDr_int32END
2020-09-03 16:52:11 root: INFO: instruction count: 18: __C92etypeDecode.__m98read_fields_group_0
2020-09-03 16:52:11 root: INFO: instruction count: 34: __C92etypeDecode.__m99INPLACE_DECODE_r_binary_TO_r_binary
2020-09-03 16:52:11 root: INFO: instruction count: 11: __C92etypeDecode.__m100INPLACE_DECODE_r_int32_TO_r_int32
2020-09-03 16:52:11 root: INFO: instruction count: 11: __C92etypeDecode.__m101INPLACE_DECODE_r_bool_TO_r_bool
2020-09-03 16:52:11 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, initial IR -- Verify : 0.059ms, total 51.244s
2020-09-03 16:52:11 root: INFO: optimize optimize: compileLowerer, initial IR: before: IR size 5: 
(Coalesce
  (IsNA
    (GetField __uid_4
      (In +PCStruct{locus:+PCLocus(GRCh38),__uid_4:PCStruct{}} 0)))
  (False))
2020-09-03 16:52:11 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, initial IR -- LoweringTransformation -- Optimize -- FoldConstants : 0.399ms, total 51.245s
2020-09-03 16:52:11 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, initial IR -- LoweringTransformation -- Optimize -- ExtractIntervalFilters : 0.205ms, total 51.246s
2020-09-03 16:52:11 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, initial IR -- LoweringTransformation -- Optimize -- Simplify : 5.336ms, total 51.251s
2020-09-03 16:52:11 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, initial IR -- LoweringTransformation -- Optimize -- ForwardLets : 0.527ms, total 51.252s
2020-09-03 16:52:11 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, initial IR -- LoweringTransformation -- Optimize -- ForwardRelationalLets : 0.065ms, total 51.252s
2020-09-03 16:52:11 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, initial IR -- LoweringTransformation -- Optimize -- PruneDeadFields : 0.239ms, total 51.253s
2020-09-03 16:52:11 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, initial IR -- LoweringTransformation -- Optimize -- FoldConstants : 0.265ms, total 51.253s
2020-09-03 16:52:11 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, initial IR -- LoweringTransformation -- Optimize -- ExtractIntervalFilters : 0.035ms, total 51.253s
2020-09-03 16:52:11 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, initial IR -- LoweringTransformation -- Optimize -- Simplify : 0.108ms, total 51.254s
2020-09-03 16:52:11 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, initial IR -- LoweringTransformation -- Optimize -- ForwardLets : 0.398ms, total 51.254s
2020-09-03 16:52:11 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, initial IR -- LoweringTransformation -- Optimize -- ForwardRelationalLets : 0.053ms, total 51.255s
2020-09-03 16:52:11 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, initial IR -- LoweringTransformation -- Optimize -- PruneDeadFields : 0.169ms, total 51.255s
2020-09-03 16:52:11 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, initial IR -- LoweringTransformation -- Optimize : 10.264ms, total 51.255s, tagged coverage 76.0
2020-09-03 16:52:11 root: INFO: optimize optimize: compileLowerer, initial IR: after: IR size 3:
(IsNA
  (GetField __uid_4
    (In +PCStruct{locus:+PCLocus(GRCh38),__uid_4:PCStruct{}} 0)))
2020-09-03 16:52:11 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, initial IR -- LoweringTransformation : 11.187ms, total 51.256s, tagged coverage 69.7
2020-09-03 16:52:11 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, initial IR -- Verify : 0.018ms, total 51.256s
2020-09-03 16:52:11 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, initial IR : 12.277ms, total 51.256s, tagged coverage 64.2
2020-09-03 16:52:11 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- InlineApplyIR -- Verify : 0.024ms, total 51.256s
2020-09-03 16:52:11 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- InlineApplyIR -- LoweringTransformation : 0.055ms, total 51.257s
2020-09-03 16:52:11 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- InlineApplyIR -- Verify : 0.023ms, total 51.257s
2020-09-03 16:52:11 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- InlineApplyIR : 0.580ms, total 51.257s, tagged coverage 17.4
2020-09-03 16:52:11 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, after InlineApplyIR -- Verify : 0.011ms, total 51.257s
2020-09-03 16:52:11 root: INFO: optimize optimize: compileLowerer, after InlineApplyIR: before: IR size 3: 
(IsNA
  (GetField __uid_4
    (In +PCStruct{locus:+PCLocus(GRCh38),__uid_4:PCStruct{}} 0)))
2020-09-03 16:52:11 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, after InlineApplyIR -- LoweringTransformation -- Optimize -- FoldConstants : 0.128ms, total 51.258s
2020-09-03 16:52:11 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, after InlineApplyIR -- LoweringTransformation -- Optimize -- ExtractIntervalFilters : 0.035ms, total 51.258s
2020-09-03 16:52:11 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, after InlineApplyIR -- LoweringTransformation -- Optimize -- Simplify : 0.106ms, total 51.258s
2020-09-03 16:52:11 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, after InlineApplyIR -- LoweringTransformation -- Optimize -- ForwardLets : 1.322ms, total 51.260s
2020-09-03 16:52:11 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, after InlineApplyIR -- LoweringTransformation -- Optimize -- ForwardRelationalLets : 0.097ms, total 51.260s
2020-09-03 16:52:11 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, after InlineApplyIR -- LoweringTransformation -- Optimize -- PruneDeadFields : 0.215ms, total 51.260s
2020-09-03 16:52:11 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, after InlineApplyIR -- LoweringTransformation -- Optimize : 2.849ms, total 51.260s, tagged coverage 66.8
2020-09-03 16:52:11 root: INFO: optimize optimize: compileLowerer, after InlineApplyIR: after: IR size 3:
(IsNA
  (GetField __uid_4
    (In +PCStruct{locus:+PCLocus(GRCh38),__uid_4:PCStruct{}} 0)))
2020-09-03 16:52:11 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, after InlineApplyIR -- LoweringTransformation : 3.559ms, total 51.261s, tagged coverage 53.5
2020-09-03 16:52:11 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, after InlineApplyIR -- Verify : 0.044ms, total 51.261s
2020-09-03 16:52:11 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, after InlineApplyIR : 3.982ms, total 51.261s, tagged coverage 49.2
2020-09-03 16:52:11 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- LowerArrayAggsToRunAggs -- Verify : 0.022ms, total 51.261s
2020-09-03 16:52:11 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- LowerArrayAggsToRunAggs -- LoweringTransformation : 0.597ms, total 51.262s
2020-09-03 16:52:11 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- LowerArrayAggsToRunAggs -- Verify : 0.025ms, total 51.262s
2020-09-03 16:52:11 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- LowerArrayAggsToRunAggs : 1.102ms, total 51.262s, tagged coverage 58.4
2020-09-03 16:52:11 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, after LowerArrayAggsToRunAggs -- Verify : 0.009ms, total 51.263s
2020-09-03 16:52:11 root: INFO: optimize optimize: compileLowerer, after LowerArrayAggsToRunAggs: before: IR size 3: 
(IsNA
  (GetField __uid_4
    (In +PCStruct{locus:+PCLocus(GRCh38),__uid_4:PCStruct{}} 0)))
2020-09-03 16:52:11 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, after LowerArrayAggsToRunAggs -- LoweringTransformation -- Optimize -- FoldConstants : 0.129ms, total 51.263s
2020-09-03 16:52:11 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, after LowerArrayAggsToRunAggs -- LoweringTransformation -- Optimize -- ExtractIntervalFilters : 0.035ms, total 51.263s
2020-09-03 16:52:11 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, after LowerArrayAggsToRunAggs -- LoweringTransformation -- Optimize -- Simplify : 0.099ms, total 51.263s
2020-09-03 16:52:11 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, after LowerArrayAggsToRunAggs -- LoweringTransformation -- Optimize -- ForwardLets : 0.547ms, total 51.264s
2020-09-03 16:52:11 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, after LowerArrayAggsToRunAggs -- LoweringTransformation -- Optimize -- ForwardRelationalLets : 0.060ms, total 51.264s
2020-09-03 16:52:11 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, after LowerArrayAggsToRunAggs -- LoweringTransformation -- Optimize -- PruneDeadFields : 0.170ms, total 51.265s
2020-09-03 16:52:11 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, after LowerArrayAggsToRunAggs -- LoweringTransformation -- Optimize : 1.735ms, total 51.265s, tagged coverage 60.0
2020-09-03 16:52:11 root: INFO: optimize optimize: compileLowerer, after LowerArrayAggsToRunAggs: after: IR size 3:
(IsNA
  (GetField __uid_4
    (In +PCStruct{locus:+PCLocus(GRCh38),__uid_4:PCStruct{}} 0)))
2020-09-03 16:52:11 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, after LowerArrayAggsToRunAggs -- LoweringTransformation : 2.429ms, total 51.265s, tagged coverage 42.8
2020-09-03 16:52:11 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, after LowerArrayAggsToRunAggs -- Verify : 0.081ms, total 51.265s
2020-09-03 16:52:11 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation -- optimize: compileLowerer, after LowerArrayAggsToRunAggs : 2.834ms, total 51.265s, tagged coverage 39.9
2020-09-03 16:52:11 root: INFO: instruction count: 6: __C102Compiled.<init>
2020-09-03 16:52:11 root: INFO: instruction count: 24: __C102Compiled.apply
2020-09-03 16:52:11 root: INFO: instruction count: 14: __C102Compiled.setPartitionIndex
2020-09-03 16:52:11 root: INFO: instruction count: 7: __C102Compiled.addPartitionRegion
2020-09-03 16:52:11 SparkContext: INFO: Starting job: fold at RVD.scala:735
2020-09-03 16:52:11 DAGScheduler: INFO: Registering RDD 12 (mapPartitions at ContextRDD.scala:160) as input to shuffle 0
2020-09-03 16:52:11 DAGScheduler: INFO: Got job 1 (fold at RVD.scala:735) with 128 output partitions
2020-09-03 16:52:11 DAGScheduler: INFO: Final stage: ResultStage 2 (fold at RVD.scala:735)
2020-09-03 16:52:11 DAGScheduler: INFO: Parents of final stage: List(ShuffleMapStage 1)
2020-09-03 16:52:11 DAGScheduler: INFO: Missing parents: List(ShuffleMapStage 1)
2020-09-03 16:52:11 DAGScheduler: INFO: Submitting ShuffleMapStage 1 (MapPartitionsRDD[12] at mapPartitions at ContextRDD.scala:160), which has no missing parents
2020-09-03 16:52:11 MemoryStore: INFO: Block broadcast_8 stored as values in memory (estimated size 143.4 KB, free 21.7 GB)
2020-09-03 16:52:11 MemoryStore: INFO: Block broadcast_8_piece0 stored as bytes in memory (estimated size 49.5 KB, free 21.7 GB)
2020-09-03 16:52:11 BlockManagerInfo: INFO: Added broadcast_8_piece0 in memory on jg3-m.c.maclab-ukbb.internal:36967 (size: 49.5 KB, free: 21.7 GB)
2020-09-03 16:52:11 SparkContext: INFO: Created broadcast 8 from broadcast at DAGScheduler.scala:1163
2020-09-03 16:52:11 DAGScheduler: INFO: Submitting 12 missing tasks from ShuffleMapStage 1 (MapPartitionsRDD[12] at mapPartitions at ContextRDD.scala:160) (first 15 tasks are for partitions Vector(0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11))
2020-09-03 16:52:11 YarnScheduler: INFO: Adding task set 1.0 with 12 tasks
2020-09-03 16:52:11 FairSchedulableBuilder: INFO: Added task set TaskSet_1.0 tasks to pool default
2020-09-03 16:52:11 TaskSetManager: INFO: Starting task 0.0 in stage 1.0 (TID 137, jg3-w-1.c.maclab-ukbb.internal, executor 2, partition 0, PROCESS_LOCAL, 7697 bytes)
2020-09-03 16:52:11 TaskSetManager: INFO: Starting task 1.0 in stage 1.0 (TID 138, jg3-w-1.c.maclab-ukbb.internal, executor 3, partition 1, PROCESS_LOCAL, 7697 bytes)
2020-09-03 16:52:11 TaskSetManager: INFO: Starting task 2.0 in stage 1.0 (TID 139, jg3-w-0.c.maclab-ukbb.internal, executor 1, partition 2, PROCESS_LOCAL, 7697 bytes)
2020-09-03 16:52:11 TaskSetManager: INFO: Starting task 3.0 in stage 1.0 (TID 140, jg3-w-1.c.maclab-ukbb.internal, executor 2, partition 3, PROCESS_LOCAL, 7697 bytes)
2020-09-03 16:52:11 TaskSetManager: INFO: Starting task 4.0 in stage 1.0 (TID 141, jg3-w-1.c.maclab-ukbb.internal, executor 3, partition 4, PROCESS_LOCAL, 7697 bytes)
2020-09-03 16:52:11 TaskSetManager: INFO: Starting task 5.0 in stage 1.0 (TID 142, jg3-w-0.c.maclab-ukbb.internal, executor 1, partition 5, PROCESS_LOCAL, 7697 bytes)
2020-09-03 16:52:11 TaskSetManager: INFO: Starting task 6.0 in stage 1.0 (TID 143, jg3-w-1.c.maclab-ukbb.internal, executor 2, partition 6, PROCESS_LOCAL, 7697 bytes)
2020-09-03 16:52:11 TaskSetManager: INFO: Starting task 7.0 in stage 1.0 (TID 144, jg3-w-1.c.maclab-ukbb.internal, executor 3, partition 7, PROCESS_LOCAL, 7697 bytes)
2020-09-03 16:52:11 TaskSetManager: INFO: Starting task 8.0 in stage 1.0 (TID 145, jg3-w-0.c.maclab-ukbb.internal, executor 1, partition 8, PROCESS_LOCAL, 7697 bytes)
2020-09-03 16:52:11 TaskSetManager: INFO: Starting task 9.0 in stage 1.0 (TID 146, jg3-w-1.c.maclab-ukbb.internal, executor 2, partition 9, PROCESS_LOCAL, 7697 bytes)
2020-09-03 16:52:11 TaskSetManager: INFO: Starting task 10.0 in stage 1.0 (TID 147, jg3-w-1.c.maclab-ukbb.internal, executor 3, partition 10, PROCESS_LOCAL, 7698 bytes)
2020-09-03 16:52:11 TaskSetManager: INFO: Starting task 11.0 in stage 1.0 (TID 148, jg3-w-0.c.maclab-ukbb.internal, executor 1, partition 11, PROCESS_LOCAL, 7698 bytes)
2020-09-03 16:52:11 BlockManagerInfo: INFO: Added broadcast_8_piece0 in memory on jg3-w-0.c.maclab-ukbb.internal:45095 (size: 49.5 KB, free: 5.6 GB)
2020-09-03 16:52:11 BlockManagerInfo: INFO: Added broadcast_8_piece0 in memory on jg3-w-1.c.maclab-ukbb.internal:42241 (size: 49.5 KB, free: 5.6 GB)
2020-09-03 16:52:11 BlockManagerInfo: INFO: Added broadcast_8_piece0 in memory on jg3-w-1.c.maclab-ukbb.internal:37701 (size: 49.5 KB, free: 5.6 GB)
2020-09-03 16:52:12 BlockManagerInfo: INFO: Added broadcast_7_piece0 in memory on jg3-w-1.c.maclab-ukbb.internal:42241 (size: 37.0 KB, free: 5.6 GB)
2020-09-03 16:52:12 BlockManagerInfo: INFO: Added broadcast_7_piece0 in memory on jg3-w-1.c.maclab-ukbb.internal:37701 (size: 37.0 KB, free: 5.6 GB)
2020-09-03 16:52:12 BlockManagerInfo: INFO: Added broadcast_7_piece0 in memory on jg3-w-0.c.maclab-ukbb.internal:45095 (size: 37.0 KB, free: 5.6 GB)
2020-09-03 16:52:12 TaskSetManager: INFO: Finished task 0.0 in stage 1.0 (TID 137) in 493 ms on jg3-w-1.c.maclab-ukbb.internal (executor 2) (1/12)
2020-09-03 16:52:12 TaskSetManager: INFO: Finished task 6.0 in stage 1.0 (TID 143) in 490 ms on jg3-w-1.c.maclab-ukbb.internal (executor 2) (2/12)
2020-09-03 16:52:12 TaskSetManager: INFO: Finished task 3.0 in stage 1.0 (TID 140) in 491 ms on jg3-w-1.c.maclab-ukbb.internal (executor 2) (3/12)
2020-09-03 16:52:12 TaskSetManager: INFO: Finished task 1.0 in stage 1.0 (TID 138) in 494 ms on jg3-w-1.c.maclab-ukbb.internal (executor 3) (4/12)
2020-09-03 16:52:12 TaskSetManager: INFO: Finished task 4.0 in stage 1.0 (TID 141) in 493 ms on jg3-w-1.c.maclab-ukbb.internal (executor 3) (5/12)
2020-09-03 16:52:12 TaskSetManager: INFO: Finished task 7.0 in stage 1.0 (TID 144) in 494 ms on jg3-w-1.c.maclab-ukbb.internal (executor 3) (6/12)
2020-09-03 16:52:12 TaskSetManager: INFO: Finished task 10.0 in stage 1.0 (TID 147) in 501 ms on jg3-w-1.c.maclab-ukbb.internal (executor 3) (7/12)
2020-09-03 16:52:12 TaskSetManager: INFO: Finished task 5.0 in stage 1.0 (TID 142) in 523 ms on jg3-w-0.c.maclab-ukbb.internal (executor 1) (8/12)
2020-09-03 16:52:12 TaskSetManager: INFO: Finished task 8.0 in stage 1.0 (TID 145) in 523 ms on jg3-w-0.c.maclab-ukbb.internal (executor 1) (9/12)
2020-09-03 16:52:12 TaskSetManager: INFO: Finished task 11.0 in stage 1.0 (TID 148) in 523 ms on jg3-w-0.c.maclab-ukbb.internal (executor 1) (10/12)
2020-09-03 16:52:12 TaskSetManager: INFO: Finished task 2.0 in stage 1.0 (TID 139) in 525 ms on jg3-w-0.c.maclab-ukbb.internal (executor 1) (11/12)
2020-09-03 16:52:12 TaskSetManager: INFO: Finished task 9.0 in stage 1.0 (TID 146) in 535 ms on jg3-w-1.c.maclab-ukbb.internal (executor 2) (12/12)
2020-09-03 16:52:12 YarnScheduler: INFO: Removed TaskSet 1.0, whose tasks have all completed, from pool default
2020-09-03 16:52:12 DAGScheduler: INFO: ShuffleMapStage 1 (mapPartitions at ContextRDD.scala:160) finished in 0.560 s
2020-09-03 16:52:12 DAGScheduler: INFO: looking for newly runnable stages
2020-09-03 16:52:12 DAGScheduler: INFO: running: Set()
2020-09-03 16:52:12 DAGScheduler: INFO: waiting: Set(ResultStage 2)
2020-09-03 16:52:12 DAGScheduler: INFO: failed: Set()
2020-09-03 16:52:12 DAGScheduler: INFO: Submitting ResultStage 2 (MapPartitionsRDD[27] at mapPartitions at ContextRDD.scala:160), which has no missing parents
2020-09-03 16:52:12 MemoryStore: INFO: Block broadcast_9 stored as values in memory (estimated size 708.6 KB, free 21.7 GB)
2020-09-03 16:52:12 MemoryStore: INFO: Block broadcast_9_piece0 stored as bytes in memory (estimated size 223.6 KB, free 21.7 GB)
2020-09-03 16:52:12 BlockManagerInfo: INFO: Added broadcast_9_piece0 in memory on jg3-m.c.maclab-ukbb.internal:36967 (size: 223.6 KB, free: 21.7 GB)
2020-09-03 16:52:12 SparkContext: INFO: Created broadcast 9 from broadcast at DAGScheduler.scala:1163
2020-09-03 16:52:12 DAGScheduler: INFO: Submitting 128 missing tasks from ResultStage 2 (MapPartitionsRDD[27] at mapPartitions at ContextRDD.scala:160) (first 15 tasks are for partitions Vector(0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14))
2020-09-03 16:52:12 YarnScheduler: INFO: Adding task set 2.0 with 128 tasks
2020-09-03 16:52:12 FairSchedulableBuilder: INFO: Added task set TaskSet_2.0 tasks to pool default
2020-09-03 16:52:12 TaskSetManager: INFO: Starting task 52.0 in stage 2.0 (TID 149, jg3-w-1.c.maclab-ukbb.internal, executor 3, partition 52, NODE_LOCAL, 8099 bytes)
2020-09-03 16:52:12 TaskSetManager: INFO: Starting task 53.0 in stage 2.0 (TID 150, jg3-w-1.c.maclab-ukbb.internal, executor 2, partition 53, NODE_LOCAL, 8099 bytes)
2020-09-03 16:52:12 TaskSetManager: INFO: Starting task 54.0 in stage 2.0 (TID 151, jg3-w-1.c.maclab-ukbb.internal, executor 3, partition 54, NODE_LOCAL, 8099 bytes)
2020-09-03 16:52:12 TaskSetManager: INFO: Starting task 55.0 in stage 2.0 (TID 152, jg3-w-1.c.maclab-ukbb.internal, executor 2, partition 55, NODE_LOCAL, 8099 bytes)
2020-09-03 16:52:12 TaskSetManager: INFO: Starting task 56.0 in stage 2.0 (TID 153, jg3-w-1.c.maclab-ukbb.internal, executor 3, partition 56, NODE_LOCAL, 8099 bytes)
2020-09-03 16:52:12 TaskSetManager: INFO: Starting task 57.0 in stage 2.0 (TID 154, jg3-w-1.c.maclab-ukbb.internal, executor 2, partition 57, NODE_LOCAL, 8099 bytes)
2020-09-03 16:52:12 TaskSetManager: INFO: Starting task 58.0 in stage 2.0 (TID 155, jg3-w-1.c.maclab-ukbb.internal, executor 3, partition 58, NODE_LOCAL, 8099 bytes)
2020-09-03 16:52:12 TaskSetManager: INFO: Starting task 59.0 in stage 2.0 (TID 156, jg3-w-1.c.maclab-ukbb.internal, executor 2, partition 59, NODE_LOCAL, 8099 bytes)
2020-09-03 16:52:12 TaskSetManager: INFO: Starting task 0.0 in stage 2.0 (TID 157, jg3-w-0.c.maclab-ukbb.internal, executor 1, partition 0, PROCESS_LOCAL, 8099 bytes)
2020-09-03 16:52:12 TaskSetManager: INFO: Starting task 1.0 in stage 2.0 (TID 158, jg3-w-0.c.maclab-ukbb.internal, executor 1, partition 1, PROCESS_LOCAL, 8099 bytes)
2020-09-03 16:52:12 TaskSetManager: INFO: Starting task 2.0 in stage 2.0 (TID 159, jg3-w-0.c.maclab-ukbb.internal, executor 1, partition 2, PROCESS_LOCAL, 8099 bytes)
2020-09-03 16:52:12 TaskSetManager: INFO: Starting task 3.0 in stage 2.0 (TID 160, jg3-w-0.c.maclab-ukbb.internal, executor 1, partition 3, PROCESS_LOCAL, 8099 bytes)
2020-09-03 16:52:12 BlockManagerInfo: INFO: Added broadcast_9_piece0 in memory on jg3-w-0.c.maclab-ukbb.internal:45095 (size: 223.6 KB, free: 5.6 GB)
2020-09-03 16:52:12 BlockManagerInfo: INFO: Added broadcast_9_piece0 in memory on jg3-w-1.c.maclab-ukbb.internal:42241 (size: 223.6 KB, free: 5.6 GB)
2020-09-03 16:52:12 BlockManagerInfo: INFO: Added broadcast_9_piece0 in memory on jg3-w-1.c.maclab-ukbb.internal:37701 (size: 223.6 KB, free: 5.6 GB)
2020-09-03 16:52:12 MapOutputTrackerMasterEndpoint: INFO: Asked to send map output locations for shuffle 0 to 10.128.0.63:37516
2020-09-03 16:52:12 MapOutputTrackerMasterEndpoint: INFO: Asked to send map output locations for shuffle 0 to 10.128.0.68:46474
2020-09-03 16:52:12 MapOutputTrackerMasterEndpoint: INFO: Asked to send map output locations for shuffle 0 to 10.128.0.68:46456
2020-09-03 16:52:13 TaskSetManager: INFO: Starting task 4.0 in stage 2.0 (TID 161, jg3-w-0.c.maclab-ukbb.internal, executor 1, partition 4, PROCESS_LOCAL, 8099 bytes)
2020-09-03 16:52:13 TaskSetManager: WARN: Lost task 1.0 in stage 2.0 (TID 158, jg3-w-0.c.maclab-ukbb.internal, executor 1): htsjdk.samtools.SAMException: Unable to load chr20(501465, 505561) from /tmp/fasta-reader-FcVGkbAEQi5MCYD6x7hi1B.fasta
	at htsjdk.samtools.reference.AbstractIndexedFastaSequenceFile.getSubsequenceAt(AbstractIndexedFastaSequenceFile.java:207)
	at htsjdk.samtools.reference.IndexedFastaSequenceFile.getSubsequenceAt(IndexedFastaSequenceFile.java:49)
	at is.hail.io.reference.FASTAReader.getSequence(FASTAReader.scala:73)
	at is.hail.io.reference.FASTAReader.fillBlock(FASTAReader.scala:83)
	at is.hail.io.reference.FASTAReader.readBlock(FASTAReader.scala:93)
	at is.hail.io.reference.FASTAReader.readBlock(FASTAReader.scala:99)
	at is.hail.io.reference.FASTAReader.lookupGlobalPos(FASTAReader.scala:138)
	at is.hail.io.reference.FASTAReader.lookup(FASTAReader.scala:110)
	at is.hail.variant.ReferenceGenome.getSequence(ReferenceGenome.scala:357)
	at __C24Compiled.__m42getReferenceSequenceFromValidLocus(Unknown Source)
	at __C24Compiled.apply(Unknown Source)
	at is.hail.expr.ir.TableFilter$$anonfun$execute$2.apply(TableIR.scala:946)
	at is.hail.expr.ir.TableFilter$$anonfun$execute$2.apply(TableIR.scala:946)
	at is.hail.expr.ir.TableValue$$anonfun$3.apply(TableValue.scala:65)
	at is.hail.expr.ir.TableValue$$anonfun$3.apply(TableValue.scala:65)
	at is.hail.rvd.RVD$$anonfun$17$$anonfun$apply$2.apply$mcZJ$sp(RVD.scala:605)
	at is.hail.rvd.RVD$$anonfun$17$$anonfun$apply$2.apply(RVD.scala:604)
	at is.hail.rvd.RVD$$anonfun$17$$anonfun$apply$2.apply(RVD.scala:604)
	at scala.collection.Iterator$$anon$13.hasNext(Iterator.scala:464)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
	at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:409)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
	at is.hail.io.RichContextRDDLong$$anonfun$boundary$extension$2$$anon$1.hasNext(RichContextRDDRegionValue.scala:188)
	at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:409)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
	at scala.collection.Iterator$$anon$1.hasNext(Iterator.scala:1002)
	at is.hail.utils.richUtils.RichIterator$$anon$5.isValid(RichIterator.scala:30)
	at is.hail.utils.StagingIterator.isValid(FlipbookIterator.scala:48)
	at is.hail.utils.FlipbookIterator$$anon$9.setValue(FlipbookIterator.scala:327)
	at is.hail.utils.FlipbookIterator$$anon$9.<init>(FlipbookIterator.scala:344)
	at is.hail.utils.FlipbookIterator.leftJoinDistinct(FlipbookIterator.scala:323)
	at is.hail.annotations.OrderedRVIterator.leftIntervalJoinDistinct(OrderedRVIterator.scala:51)
	at is.hail.rvd.KeyedRVD$$anonfun$orderedLeftIntervalJoinDistinct$1$$anonfun$apply$2.apply(KeyedRVD.scala:131)
	at is.hail.rvd.KeyedRVD$$anonfun$orderedLeftIntervalJoinDistinct$1$$anonfun$apply$2.apply(KeyedRVD.scala:127)
	at is.hail.sparkextras.ContextRDD$$anonfun$czipPartitions$1$$anonfun$apply$24.apply(ContextRDD.scala:305)
	at is.hail.sparkextras.ContextRDD$$anonfun$czipPartitions$1$$anonfun$apply$24.apply(ContextRDD.scala:305)
	at is.hail.sparkextras.ContextRDD$$anonfun$cmapPartitions$1$$anonfun$apply$9$$anonfun$apply$10.apply(ContextRDD.scala:208)
	at is.hail.sparkextras.ContextRDD$$anonfun$cmapPartitions$1$$anonfun$apply$9$$anonfun$apply$10.apply(ContextRDD.scala:208)
	at scala.collection.Iterator$$anon$12.nextCur(Iterator.scala:435)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:441)
	at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:409)
	at scala.collection.Iterator$$anon$13.hasNext(Iterator.scala:462)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
	at is.hail.io.RichContextRDDLong$$anonfun$boundary$extension$2$$anon$1.hasNext(RichContextRDDRegionValue.scala:188)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
	at scala.collection.Iterator$class.foreach(Iterator.scala:891)
	at scala.collection.AbstractIterator.foreach(Iterator.scala:1334)
	at is.hail.rvd.RVD$$anonfun$23.apply(RVD.scala:731)
	at is.hail.rvd.RVD$$anonfun$23.apply(RVD.scala:729)
	at is.hail.sparkextras.ContextRDD$$anonfun$cmapPartitions$1$$anonfun$apply$9.apply(ContextRDD.scala:208)
	at is.hail.sparkextras.ContextRDD$$anonfun$cmapPartitions$1$$anonfun$apply$9.apply(ContextRDD.scala:208)
	at is.hail.utils.richUtils.RichContextRDD$$anonfun$cleanupRegions$1$$anonfun$2.apply(RichContextRDD.scala:57)
	at is.hail.utils.richUtils.RichContextRDD$$anonfun$cleanupRegions$1$$anonfun$2.apply(RichContextRDD.scala:57)
	at scala.collection.Iterator$$anon$12.nextCur(Iterator.scala:435)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:441)
	at is.hail.utils.richUtils.RichContextRDD$$anonfun$cleanupRegions$1$$anon$1.hasNext(RichContextRDD.scala:66)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
	at scala.collection.Iterator$class.foreach(Iterator.scala:891)
	at scala.collection.AbstractIterator.foreach(Iterator.scala:1334)
	at scala.collection.TraversableOnce$class.foldLeft(TraversableOnce.scala:157)
	at scala.collection.AbstractIterator.foldLeft(Iterator.scala:1334)
	at scala.collection.TraversableOnce$class.fold(TraversableOnce.scala:212)
	at scala.collection.AbstractIterator.fold(Iterator.scala:1334)
	at org.apache.spark.rdd.RDD$$anonfun$fold$1$$anonfun$22.apply(RDD.scala:1141)
	at org.apache.spark.rdd.RDD$$anonfun$fold$1$$anonfun$22.apply(RDD.scala:1141)
	at org.apache.spark.SparkContext$$anonfun$36.apply(SparkContext.scala:2157)
	at org.apache.spark.SparkContext$$anonfun$36.apply(SparkContext.scala:2157)
	at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:90)
	at org.apache.spark.scheduler.Task.run(Task.scala:123)
	at org.apache.spark.executor.Executor$TaskRunner$$anonfun$10.apply(Executor.scala:408)
	at org.apache.spark.util.Utils$.tryWithSafeFinally(Utils.scala:1360)
	at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:414)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
	at java.lang.Thread.run(Thread.java:748)
Caused by: java.nio.channels.ClosedChannelException
	at sun.nio.ch.FileChannelImpl.ensureOpen(FileChannelImpl.java:110)
	at sun.nio.ch.FileChannelImpl.read(FileChannelImpl.java:715)
	at htsjdk.samtools.reference.IndexedFastaSequenceFile.readFromPosition(IndexedFastaSequenceFile.java:148)
	at htsjdk.samtools.reference.AbstractIndexedFastaSequenceFile.getSubsequenceAt(AbstractIndexedFastaSequenceFile.java:204)
	... 74 more

2020-09-03 16:52:13 TaskSetManager: INFO: Starting task 1.1 in stage 2.0 (TID 162, jg3-w-0.c.maclab-ukbb.internal, executor 1, partition 1, PROCESS_LOCAL, 8099 bytes)
2020-09-03 16:52:13 TaskSetManager: WARN: Lost task 0.0 in stage 2.0 (TID 157, jg3-w-0.c.maclab-ukbb.internal, executor 1): htsjdk.samtools.SAMException: Unable to load chr19(58615273, 58617616) from /tmp/fasta-reader-FcVGkbAEQi5MCYD6x7hi1B.fasta
	at htsjdk.samtools.reference.AbstractIndexedFastaSequenceFile.getSubsequenceAt(AbstractIndexedFastaSequenceFile.java:207)
	at htsjdk.samtools.reference.IndexedFastaSequenceFile.getSubsequenceAt(IndexedFastaSequenceFile.java:49)
	at is.hail.io.reference.FASTAReader.getSequence(FASTAReader.scala:73)
	at is.hail.io.reference.FASTAReader.fillBlock(FASTAReader.scala:83)
	at is.hail.io.reference.FASTAReader.readBlock(FASTAReader.scala:93)
	at is.hail.io.reference.FASTAReader.readBlock(FASTAReader.scala:99)
	at is.hail.io.reference.FASTAReader.lookupGlobalPos(FASTAReader.scala:138)
	at is.hail.io.reference.FASTAReader.lookup(FASTAReader.scala:110)
	at is.hail.variant.ReferenceGenome.getSequence(ReferenceGenome.scala:357)
	at __C24Compiled.__m42getReferenceSequenceFromValidLocus(Unknown Source)
	at __C24Compiled.apply(Unknown Source)
	at is.hail.expr.ir.TableFilter$$anonfun$execute$2.apply(TableIR.scala:946)
	at is.hail.expr.ir.TableFilter$$anonfun$execute$2.apply(TableIR.scala:946)
	at is.hail.expr.ir.TableValue$$anonfun$3.apply(TableValue.scala:65)
	at is.hail.expr.ir.TableValue$$anonfun$3.apply(TableValue.scala:65)
	at is.hail.rvd.RVD$$anonfun$17$$anonfun$apply$2.apply$mcZJ$sp(RVD.scala:605)
	at is.hail.rvd.RVD$$anonfun$17$$anonfun$apply$2.apply(RVD.scala:604)
	at is.hail.rvd.RVD$$anonfun$17$$anonfun$apply$2.apply(RVD.scala:604)
	at scala.collection.Iterator$$anon$13.hasNext(Iterator.scala:464)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
	at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:409)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
	at is.hail.io.RichContextRDDLong$$anonfun$boundary$extension$2$$anon$1.hasNext(RichContextRDDRegionValue.scala:188)
	at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:409)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
	at scala.collection.Iterator$$anon$1.hasNext(Iterator.scala:1002)
	at is.hail.utils.richUtils.RichIterator$$anon$5.isValid(RichIterator.scala:30)
	at is.hail.utils.StagingIterator.isValid(FlipbookIterator.scala:48)
	at is.hail.utils.FlipbookIterator$$anon$9.setValue(FlipbookIterator.scala:327)
	at is.hail.utils.FlipbookIterator$$anon$9.<init>(FlipbookIterator.scala:344)
	at is.hail.utils.FlipbookIterator.leftJoinDistinct(FlipbookIterator.scala:323)
	at is.hail.annotations.OrderedRVIterator.leftIntervalJoinDistinct(OrderedRVIterator.scala:51)
	at is.hail.rvd.KeyedRVD$$anonfun$orderedLeftIntervalJoinDistinct$1$$anonfun$apply$2.apply(KeyedRVD.scala:131)
	at is.hail.rvd.KeyedRVD$$anonfun$orderedLeftIntervalJoinDistinct$1$$anonfun$apply$2.apply(KeyedRVD.scala:127)
	at is.hail.sparkextras.ContextRDD$$anonfun$czipPartitions$1$$anonfun$apply$24.apply(ContextRDD.scala:305)
	at is.hail.sparkextras.ContextRDD$$anonfun$czipPartitions$1$$anonfun$apply$24.apply(ContextRDD.scala:305)
	at is.hail.sparkextras.ContextRDD$$anonfun$cmapPartitions$1$$anonfun$apply$9$$anonfun$apply$10.apply(ContextRDD.scala:208)
	at is.hail.sparkextras.ContextRDD$$anonfun$cmapPartitions$1$$anonfun$apply$9$$anonfun$apply$10.apply(ContextRDD.scala:208)
	at scala.collection.Iterator$$anon$12.nextCur(Iterator.scala:435)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:441)
	at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:409)
	at scala.collection.Iterator$$anon$13.hasNext(Iterator.scala:462)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
	at is.hail.io.RichContextRDDLong$$anonfun$boundary$extension$2$$anon$1.hasNext(RichContextRDDRegionValue.scala:188)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
	at scala.collection.Iterator$class.foreach(Iterator.scala:891)
	at scala.collection.AbstractIterator.foreach(Iterator.scala:1334)
	at is.hail.rvd.RVD$$anonfun$23.apply(RVD.scala:731)
	at is.hail.rvd.RVD$$anonfun$23.apply(RVD.scala:729)
	at is.hail.sparkextras.ContextRDD$$anonfun$cmapPartitions$1$$anonfun$apply$9.apply(ContextRDD.scala:208)
	at is.hail.sparkextras.ContextRDD$$anonfun$cmapPartitions$1$$anonfun$apply$9.apply(ContextRDD.scala:208)
	at is.hail.utils.richUtils.RichContextRDD$$anonfun$cleanupRegions$1$$anonfun$2.apply(RichContextRDD.scala:57)
	at is.hail.utils.richUtils.RichContextRDD$$anonfun$cleanupRegions$1$$anonfun$2.apply(RichContextRDD.scala:57)
	at scala.collection.Iterator$$anon$12.nextCur(Iterator.scala:435)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:441)
	at is.hail.utils.richUtils.RichContextRDD$$anonfun$cleanupRegions$1$$anon$1.hasNext(RichContextRDD.scala:66)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
	at scala.collection.Iterator$class.foreach(Iterator.scala:891)
	at scala.collection.AbstractIterator.foreach(Iterator.scala:1334)
	at scala.collection.TraversableOnce$class.foldLeft(TraversableOnce.scala:157)
	at scala.collection.AbstractIterator.foldLeft(Iterator.scala:1334)
	at scala.collection.TraversableOnce$class.fold(TraversableOnce.scala:212)
	at scala.collection.AbstractIterator.fold(Iterator.scala:1334)
	at org.apache.spark.rdd.RDD$$anonfun$fold$1$$anonfun$22.apply(RDD.scala:1141)
	at org.apache.spark.rdd.RDD$$anonfun$fold$1$$anonfun$22.apply(RDD.scala:1141)
	at org.apache.spark.SparkContext$$anonfun$36.apply(SparkContext.scala:2157)
	at org.apache.spark.SparkContext$$anonfun$36.apply(SparkContext.scala:2157)
	at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:90)
	at org.apache.spark.scheduler.Task.run(Task.scala:123)
	at org.apache.spark.executor.Executor$TaskRunner$$anonfun$10.apply(Executor.scala:408)
	at org.apache.spark.util.Utils$.tryWithSafeFinally(Utils.scala:1360)
	at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:414)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
	at java.lang.Thread.run(Thread.java:748)
Caused by: java.nio.channels.ClosedChannelException
	at sun.nio.ch.FileChannelImpl.ensureOpen(FileChannelImpl.java:110)
	at sun.nio.ch.FileChannelImpl.read(FileChannelImpl.java:715)
	at htsjdk.samtools.reference.IndexedFastaSequenceFile.readFromPosition(IndexedFastaSequenceFile.java:148)
	at htsjdk.samtools.reference.AbstractIndexedFastaSequenceFile.getSubsequenceAt(AbstractIndexedFastaSequenceFile.java:204)
	... 74 more

2020-09-03 16:52:13 TaskSetManager: INFO: Starting task 0.1 in stage 2.0 (TID 163, jg3-w-0.c.maclab-ukbb.internal, executor 1, partition 0, PROCESS_LOCAL, 8099 bytes)
2020-09-03 16:52:13 TaskSetManager: WARN: Lost task 2.0 in stage 2.0 (TID 159, jg3-w-0.c.maclab-ukbb.internal, executor 1): htsjdk.samtools.SAMException: Unable to load chr20(1009369, 1013465) from /tmp/fasta-reader-FcVGkbAEQi5MCYD6x7hi1B.fasta
	at htsjdk.samtools.reference.AbstractIndexedFastaSequenceFile.getSubsequenceAt(AbstractIndexedFastaSequenceFile.java:207)
	at htsjdk.samtools.reference.IndexedFastaSequenceFile.getSubsequenceAt(IndexedFastaSequenceFile.java:49)
	at is.hail.io.reference.FASTAReader.getSequence(FASTAReader.scala:73)
	at is.hail.io.reference.FASTAReader.fillBlock(FASTAReader.scala:83)
	at is.hail.io.reference.FASTAReader.readBlock(FASTAReader.scala:93)
	at is.hail.io.reference.FASTAReader.readBlock(FASTAReader.scala:99)
	at is.hail.io.reference.FASTAReader.lookupGlobalPos(FASTAReader.scala:138)
	at is.hail.io.reference.FASTAReader.lookup(FASTAReader.scala:110)
	at is.hail.variant.ReferenceGenome.getSequence(ReferenceGenome.scala:357)
	at __C24Compiled.__m42getReferenceSequenceFromValidLocus(Unknown Source)
	at __C24Compiled.apply(Unknown Source)
	at is.hail.expr.ir.TableFilter$$anonfun$execute$2.apply(TableIR.scala:946)
	at is.hail.expr.ir.TableFilter$$anonfun$execute$2.apply(TableIR.scala:946)
	at is.hail.expr.ir.TableValue$$anonfun$3.apply(TableValue.scala:65)
	at is.hail.expr.ir.TableValue$$anonfun$3.apply(TableValue.scala:65)
	at is.hail.rvd.RVD$$anonfun$17$$anonfun$apply$2.apply$mcZJ$sp(RVD.scala:605)
	at is.hail.rvd.RVD$$anonfun$17$$anonfun$apply$2.apply(RVD.scala:604)
	at is.hail.rvd.RVD$$anonfun$17$$anonfun$apply$2.apply(RVD.scala:604)
	at scala.collection.Iterator$$anon$13.hasNext(Iterator.scala:464)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
	at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:409)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
	at is.hail.io.RichContextRDDLong$$anonfun$boundary$extension$2$$anon$1.hasNext(RichContextRDDRegionValue.scala:188)
	at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:409)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
	at scala.collection.Iterator$$anon$1.hasNext(Iterator.scala:1002)
	at is.hail.utils.richUtils.RichIterator$$anon$5.isValid(RichIterator.scala:30)
	at is.hail.utils.StagingIterator.isValid(FlipbookIterator.scala:48)
	at is.hail.utils.FlipbookIterator$$anon$9.setValue(FlipbookIterator.scala:327)
	at is.hail.utils.FlipbookIterator$$anon$9.advance(FlipbookIterator.scala:341)
	at is.hail.utils.StagingIterator.advance(FlipbookIterator.scala:53)
	at is.hail.utils.FlipbookIterator$$anon$5.advance(FlipbookIterator.scala:179)
	at is.hail.utils.StagingIterator.stage(FlipbookIterator.scala:61)
	at is.hail.utils.StagingIterator.hasNext(FlipbookIterator.scala:71)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
	at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:409)
	at scala.collection.Iterator$$anon$13.hasNext(Iterator.scala:462)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
	at is.hail.io.RichContextRDDLong$$anonfun$boundary$extension$2$$anon$1.hasNext(RichContextRDDRegionValue.scala:188)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
	at scala.collection.Iterator$class.foreach(Iterator.scala:891)
	at scala.collection.AbstractIterator.foreach(Iterator.scala:1334)
	at is.hail.rvd.RVD$$anonfun$23.apply(RVD.scala:731)
	at is.hail.rvd.RVD$$anonfun$23.apply(RVD.scala:729)
	at is.hail.sparkextras.ContextRDD$$anonfun$cmapPartitions$1$$anonfun$apply$9.apply(ContextRDD.scala:208)
	at is.hail.sparkextras.ContextRDD$$anonfun$cmapPartitions$1$$anonfun$apply$9.apply(ContextRDD.scala:208)
	at is.hail.utils.richUtils.RichContextRDD$$anonfun$cleanupRegions$1$$anonfun$2.apply(RichContextRDD.scala:57)
	at is.hail.utils.richUtils.RichContextRDD$$anonfun$cleanupRegions$1$$anonfun$2.apply(RichContextRDD.scala:57)
	at scala.collection.Iterator$$anon$12.nextCur(Iterator.scala:435)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:441)
	at is.hail.utils.richUtils.RichContextRDD$$anonfun$cleanupRegions$1$$anon$1.hasNext(RichContextRDD.scala:66)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
	at scala.collection.Iterator$class.foreach(Iterator.scala:891)
	at scala.collection.AbstractIterator.foreach(Iterator.scala:1334)
	at scala.collection.TraversableOnce$class.foldLeft(TraversableOnce.scala:157)
	at scala.collection.AbstractIterator.foldLeft(Iterator.scala:1334)
	at scala.collection.TraversableOnce$class.fold(TraversableOnce.scala:212)
	at scala.collection.AbstractIterator.fold(Iterator.scala:1334)
	at org.apache.spark.rdd.RDD$$anonfun$fold$1$$anonfun$22.apply(RDD.scala:1141)
	at org.apache.spark.rdd.RDD$$anonfun$fold$1$$anonfun$22.apply(RDD.scala:1141)
	at org.apache.spark.SparkContext$$anonfun$36.apply(SparkContext.scala:2157)
	at org.apache.spark.SparkContext$$anonfun$36.apply(SparkContext.scala:2157)
	at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:90)
	at org.apache.spark.scheduler.Task.run(Task.scala:123)
	at org.apache.spark.executor.Executor$TaskRunner$$anonfun$10.apply(Executor.scala:408)
	at org.apache.spark.util.Utils$.tryWithSafeFinally(Utils.scala:1360)
	at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:414)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
	at java.lang.Thread.run(Thread.java:748)
Caused by: java.nio.channels.ClosedChannelException
	at sun.nio.ch.FileChannelImpl.ensureOpen(FileChannelImpl.java:110)
	at sun.nio.ch.FileChannelImpl.read(FileChannelImpl.java:715)
	at htsjdk.samtools.reference.IndexedFastaSequenceFile.readFromPosition(IndexedFastaSequenceFile.java:148)
	at htsjdk.samtools.reference.AbstractIndexedFastaSequenceFile.getSubsequenceAt(AbstractIndexedFastaSequenceFile.java:204)
	... 69 more

2020-09-03 16:52:13 TaskSetManager: INFO: Starting task 2.1 in stage 2.0 (TID 164, jg3-w-0.c.maclab-ukbb.internal, executor 1, partition 2, PROCESS_LOCAL, 8099 bytes)
2020-09-03 16:52:13 TaskSetManager: INFO: Lost task 1.1 in stage 2.0 (TID 162) on jg3-w-0.c.maclab-ukbb.internal, executor 1: htsjdk.samtools.SAMException (Unable to load chr20(501465, 505561) from /tmp/fasta-reader-FcVGkbAEQi5MCYD6x7hi1B.fasta) [duplicate 1]
2020-09-03 16:52:13 TaskSetManager: INFO: Starting task 1.2 in stage 2.0 (TID 165, jg3-w-0.c.maclab-ukbb.internal, executor 1, partition 1, PROCESS_LOCAL, 8099 bytes)
2020-09-03 16:52:13 TaskSetManager: INFO: Lost task 0.1 in stage 2.0 (TID 163) on jg3-w-0.c.maclab-ukbb.internal, executor 1: htsjdk.samtools.SAMException (Unable to load chr19(58615273, 58617616) from /tmp/fasta-reader-FcVGkbAEQi5MCYD6x7hi1B.fasta) [duplicate 1]
2020-09-03 16:52:13 TaskSetManager: INFO: Starting task 0.2 in stage 2.0 (TID 166, jg3-w-0.c.maclab-ukbb.internal, executor 1, partition 0, PROCESS_LOCAL, 8099 bytes)
2020-09-03 16:52:13 TaskSetManager: WARN: Lost task 4.0 in stage 2.0 (TID 161, jg3-w-0.c.maclab-ukbb.internal, executor 1): htsjdk.samtools.SAMException: Unable to load chr20(2016985, 2021081) from /tmp/fasta-reader-FcVGkbAEQi5MCYD6x7hi1B.fasta
	at htsjdk.samtools.reference.AbstractIndexedFastaSequenceFile.getSubsequenceAt(AbstractIndexedFastaSequenceFile.java:207)
	at htsjdk.samtools.reference.IndexedFastaSequenceFile.getSubsequenceAt(IndexedFastaSequenceFile.java:49)
	at is.hail.io.reference.FASTAReader.getSequence(FASTAReader.scala:73)
	at is.hail.io.reference.FASTAReader.fillBlock(FASTAReader.scala:83)
	at is.hail.io.reference.FASTAReader.readBlock(FASTAReader.scala:93)
	at is.hail.io.reference.FASTAReader.readBlock(FASTAReader.scala:99)
	at is.hail.io.reference.FASTAReader.lookupGlobalPos(FASTAReader.scala:138)
	at is.hail.io.reference.FASTAReader.lookup(FASTAReader.scala:110)
	at is.hail.variant.ReferenceGenome.getSequence(ReferenceGenome.scala:357)
	at __C24Compiled.__m42getReferenceSequenceFromValidLocus(Unknown Source)
	at __C24Compiled.apply(Unknown Source)
	at is.hail.expr.ir.TableFilter$$anonfun$execute$2.apply(TableIR.scala:946)
	at is.hail.expr.ir.TableFilter$$anonfun$execute$2.apply(TableIR.scala:946)
	at is.hail.expr.ir.TableValue$$anonfun$3.apply(TableValue.scala:65)
	at is.hail.expr.ir.TableValue$$anonfun$3.apply(TableValue.scala:65)
	at is.hail.rvd.RVD$$anonfun$17$$anonfun$apply$2.apply$mcZJ$sp(RVD.scala:605)
	at is.hail.rvd.RVD$$anonfun$17$$anonfun$apply$2.apply(RVD.scala:604)
	at is.hail.rvd.RVD$$anonfun$17$$anonfun$apply$2.apply(RVD.scala:604)
	at scala.collection.Iterator$$anon$13.hasNext(Iterator.scala:464)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
	at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:409)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
	at is.hail.io.RichContextRDDLong$$anonfun$boundary$extension$2$$anon$1.hasNext(RichContextRDDRegionValue.scala:188)
	at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:409)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
	at scala.collection.Iterator$$anon$1.hasNext(Iterator.scala:1002)
	at is.hail.utils.richUtils.RichIterator$$anon$5.isValid(RichIterator.scala:30)
	at is.hail.utils.StagingIterator.isValid(FlipbookIterator.scala:48)
	at is.hail.utils.FlipbookIterator$$anon$9.setValue(FlipbookIterator.scala:327)
	at is.hail.utils.FlipbookIterator$$anon$9.advance(FlipbookIterator.scala:341)
	at is.hail.utils.StagingIterator.advance(FlipbookIterator.scala:53)
	at is.hail.utils.FlipbookIterator$$anon$5.advance(FlipbookIterator.scala:179)
	at is.hail.utils.StagingIterator.stage(FlipbookIterator.scala:61)
	at is.hail.utils.StagingIterator.hasNext(FlipbookIterator.scala:71)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
	at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:409)
	at scala.collection.Iterator$$anon$13.hasNext(Iterator.scala:462)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
	at is.hail.io.RichContextRDDLong$$anonfun$boundary$extension$2$$anon$1.hasNext(RichContextRDDRegionValue.scala:188)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
	at scala.collection.Iterator$class.foreach(Iterator.scala:891)
	at scala.collection.AbstractIterator.foreach(Iterator.scala:1334)
	at is.hail.rvd.RVD$$anonfun$23.apply(RVD.scala:731)
	at is.hail.rvd.RVD$$anonfun$23.apply(RVD.scala:729)
	at is.hail.sparkextras.ContextRDD$$anonfun$cmapPartitions$1$$anonfun$apply$9.apply(ContextRDD.scala:208)
	at is.hail.sparkextras.ContextRDD$$anonfun$cmapPartitions$1$$anonfun$apply$9.apply(ContextRDD.scala:208)
	at is.hail.utils.richUtils.RichContextRDD$$anonfun$cleanupRegions$1$$anonfun$2.apply(RichContextRDD.scala:57)
	at is.hail.utils.richUtils.RichContextRDD$$anonfun$cleanupRegions$1$$anonfun$2.apply(RichContextRDD.scala:57)
	at scala.collection.Iterator$$anon$12.nextCur(Iterator.scala:435)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:441)
	at is.hail.utils.richUtils.RichContextRDD$$anonfun$cleanupRegions$1$$anon$1.hasNext(RichContextRDD.scala:66)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
	at scala.collection.Iterator$class.foreach(Iterator.scala:891)
	at scala.collection.AbstractIterator.foreach(Iterator.scala:1334)
	at scala.collection.TraversableOnce$class.foldLeft(TraversableOnce.scala:157)
	at scala.collection.AbstractIterator.foldLeft(Iterator.scala:1334)
	at scala.collection.TraversableOnce$class.fold(TraversableOnce.scala:212)
	at scala.collection.AbstractIterator.fold(Iterator.scala:1334)
	at org.apache.spark.rdd.RDD$$anonfun$fold$1$$anonfun$22.apply(RDD.scala:1141)
	at org.apache.spark.rdd.RDD$$anonfun$fold$1$$anonfun$22.apply(RDD.scala:1141)
	at org.apache.spark.SparkContext$$anonfun$36.apply(SparkContext.scala:2157)
	at org.apache.spark.SparkContext$$anonfun$36.apply(SparkContext.scala:2157)
	at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:90)
	at org.apache.spark.scheduler.Task.run(Task.scala:123)
	at org.apache.spark.executor.Executor$TaskRunner$$anonfun$10.apply(Executor.scala:408)
	at org.apache.spark.util.Utils$.tryWithSafeFinally(Utils.scala:1360)
	at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:414)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
	at java.lang.Thread.run(Thread.java:748)
Caused by: java.nio.channels.ClosedChannelException
	at sun.nio.ch.FileChannelImpl.ensureOpen(FileChannelImpl.java:110)
	at sun.nio.ch.FileChannelImpl.read(FileChannelImpl.java:715)
	at htsjdk.samtools.reference.IndexedFastaSequenceFile.readFromPosition(IndexedFastaSequenceFile.java:148)
	at htsjdk.samtools.reference.AbstractIndexedFastaSequenceFile.getSubsequenceAt(AbstractIndexedFastaSequenceFile.java:204)
	... 69 more

2020-09-03 16:52:13 TaskSetManager: INFO: Starting task 4.1 in stage 2.0 (TID 167, jg3-w-0.c.maclab-ukbb.internal, executor 1, partition 4, PROCESS_LOCAL, 8099 bytes)
2020-09-03 16:52:13 TaskSetManager: INFO: Lost task 1.2 in stage 2.0 (TID 165) on jg3-w-0.c.maclab-ukbb.internal, executor 1: htsjdk.samtools.SAMException (Unable to load chr20(501465, 505561) from /tmp/fasta-reader-FcVGkbAEQi5MCYD6x7hi1B.fasta) [duplicate 2]
2020-09-03 16:52:13 TaskSetManager: INFO: Starting task 1.3 in stage 2.0 (TID 168, jg3-w-0.c.maclab-ukbb.internal, executor 1, partition 1, PROCESS_LOCAL, 8099 bytes)
2020-09-03 16:52:13 TaskSetManager: INFO: Lost task 2.1 in stage 2.0 (TID 164) on jg3-w-0.c.maclab-ukbb.internal, executor 1: htsjdk.samtools.SAMException (Unable to load chr20(1009369, 1013465) from /tmp/fasta-reader-FcVGkbAEQi5MCYD6x7hi1B.fasta) [duplicate 1]
2020-09-03 16:52:13 TaskSetManager: INFO: Starting task 2.2 in stage 2.0 (TID 169, jg3-w-0.c.maclab-ukbb.internal, executor 1, partition 2, PROCESS_LOCAL, 8099 bytes)
2020-09-03 16:52:13 TaskSetManager: INFO: Lost task 0.2 in stage 2.0 (TID 166) on jg3-w-0.c.maclab-ukbb.internal, executor 1: htsjdk.samtools.SAMException (Unable to load chr19(58615273, 58617616) from /tmp/fasta-reader-FcVGkbAEQi5MCYD6x7hi1B.fasta) [duplicate 2]
2020-09-03 16:52:13 TaskSetManager: INFO: Starting task 0.3 in stage 2.0 (TID 170, jg3-w-0.c.maclab-ukbb.internal, executor 1, partition 0, PROCESS_LOCAL, 8099 bytes)
2020-09-03 16:52:13 TaskSetManager: INFO: Lost task 1.3 in stage 2.0 (TID 168) on jg3-w-0.c.maclab-ukbb.internal, executor 1: htsjdk.samtools.SAMException (Unable to load chr20(501465, 505561) from /tmp/fasta-reader-FcVGkbAEQi5MCYD6x7hi1B.fasta) [duplicate 3]
2020-09-03 16:52:13 TaskSetManager: INFO: Starting task 1.4 in stage 2.0 (TID 171, jg3-w-0.c.maclab-ukbb.internal, executor 1, partition 1, PROCESS_LOCAL, 8099 bytes)
2020-09-03 16:52:13 TaskSetManager: INFO: Lost task 0.3 in stage 2.0 (TID 170) on jg3-w-0.c.maclab-ukbb.internal, executor 1: htsjdk.samtools.SAMException (Unable to load chr19(58615273, 58617616) from /tmp/fasta-reader-FcVGkbAEQi5MCYD6x7hi1B.fasta) [duplicate 3]
2020-09-03 16:52:13 TaskSetManager: INFO: Starting task 0.4 in stage 2.0 (TID 172, jg3-w-0.c.maclab-ukbb.internal, executor 1, partition 0, PROCESS_LOCAL, 8099 bytes)
2020-09-03 16:52:13 TaskSetManager: INFO: Lost task 2.2 in stage 2.0 (TID 169) on jg3-w-0.c.maclab-ukbb.internal, executor 1: htsjdk.samtools.SAMException (Unable to load chr20(1009369, 1013465) from /tmp/fasta-reader-FcVGkbAEQi5MCYD6x7hi1B.fasta) [duplicate 2]
2020-09-03 16:52:13 TaskSetManager: INFO: Starting task 2.3 in stage 2.0 (TID 173, jg3-w-0.c.maclab-ukbb.internal, executor 1, partition 2, PROCESS_LOCAL, 8099 bytes)
2020-09-03 16:52:13 TaskSetManager: INFO: Lost task 4.1 in stage 2.0 (TID 167) on jg3-w-0.c.maclab-ukbb.internal, executor 1: htsjdk.samtools.SAMException (Unable to load chr20(2016985, 2021081) from /tmp/fasta-reader-FcVGkbAEQi5MCYD6x7hi1B.fasta) [duplicate 1]
2020-09-03 16:52:13 TaskSetManager: INFO: Starting task 4.2 in stage 2.0 (TID 174, jg3-w-0.c.maclab-ukbb.internal, executor 1, partition 4, PROCESS_LOCAL, 8099 bytes)
2020-09-03 16:52:13 TaskSetManager: INFO: Lost task 1.4 in stage 2.0 (TID 171) on jg3-w-0.c.maclab-ukbb.internal, executor 1: htsjdk.samtools.SAMException (Unable to load chr20(501465, 505561) from /tmp/fasta-reader-FcVGkbAEQi5MCYD6x7hi1B.fasta) [duplicate 4]
2020-09-03 16:52:13 TaskSetManager: INFO: Starting task 1.5 in stage 2.0 (TID 175, jg3-w-0.c.maclab-ukbb.internal, executor 1, partition 1, PROCESS_LOCAL, 8099 bytes)
2020-09-03 16:52:13 TaskSetManager: INFO: Lost task 0.4 in stage 2.0 (TID 172) on jg3-w-0.c.maclab-ukbb.internal, executor 1: htsjdk.samtools.SAMException (Unable to load chr19(58615273, 58617616) from /tmp/fasta-reader-FcVGkbAEQi5MCYD6x7hi1B.fasta) [duplicate 4]
2020-09-03 16:52:13 TaskSetManager: INFO: Starting task 0.5 in stage 2.0 (TID 176, jg3-w-0.c.maclab-ukbb.internal, executor 1, partition 0, PROCESS_LOCAL, 8099 bytes)
2020-09-03 16:52:13 TaskSetManager: INFO: Lost task 1.5 in stage 2.0 (TID 175) on jg3-w-0.c.maclab-ukbb.internal, executor 1: htsjdk.samtools.SAMException (Unable to load chr20(501465, 505561) from /tmp/fasta-reader-FcVGkbAEQi5MCYD6x7hi1B.fasta) [duplicate 5]
2020-09-03 16:52:13 TaskSetManager: INFO: Starting task 1.6 in stage 2.0 (TID 177, jg3-w-0.c.maclab-ukbb.internal, executor 1, partition 1, PROCESS_LOCAL, 8099 bytes)
2020-09-03 16:52:13 TaskSetManager: INFO: Lost task 2.3 in stage 2.0 (TID 173) on jg3-w-0.c.maclab-ukbb.internal, executor 1: htsjdk.samtools.SAMException (Unable to load chr20(1009369, 1013465) from /tmp/fasta-reader-FcVGkbAEQi5MCYD6x7hi1B.fasta) [duplicate 3]
2020-09-03 16:52:13 TaskSetManager: INFO: Starting task 2.4 in stage 2.0 (TID 178, jg3-w-0.c.maclab-ukbb.internal, executor 1, partition 2, PROCESS_LOCAL, 8099 bytes)
2020-09-03 16:52:13 TaskSetManager: INFO: Lost task 4.2 in stage 2.0 (TID 174) on jg3-w-0.c.maclab-ukbb.internal, executor 1: htsjdk.samtools.SAMException (Unable to load chr20(2016985, 2021081) from /tmp/fasta-reader-FcVGkbAEQi5MCYD6x7hi1B.fasta) [duplicate 2]
2020-09-03 16:52:13 TaskSetManager: INFO: Starting task 4.3 in stage 2.0 (TID 179, jg3-w-0.c.maclab-ukbb.internal, executor 1, partition 4, PROCESS_LOCAL, 8099 bytes)
2020-09-03 16:52:13 TaskSetManager: INFO: Lost task 0.5 in stage 2.0 (TID 176) on jg3-w-0.c.maclab-ukbb.internal, executor 1: htsjdk.samtools.SAMException (Unable to load chr19(58615273, 58617616) from /tmp/fasta-reader-FcVGkbAEQi5MCYD6x7hi1B.fasta) [duplicate 5]
2020-09-03 16:52:13 TaskSetManager: INFO: Starting task 0.6 in stage 2.0 (TID 180, jg3-w-0.c.maclab-ukbb.internal, executor 1, partition 0, PROCESS_LOCAL, 8099 bytes)
2020-09-03 16:52:13 TaskSetManager: INFO: Lost task 1.6 in stage 2.0 (TID 177) on jg3-w-0.c.maclab-ukbb.internal, executor 1: htsjdk.samtools.SAMException (Unable to load chr20(501465, 505561) from /tmp/fasta-reader-FcVGkbAEQi5MCYD6x7hi1B.fasta) [duplicate 6]
2020-09-03 16:52:13 TaskSetManager: INFO: Starting task 1.7 in stage 2.0 (TID 181, jg3-w-0.c.maclab-ukbb.internal, executor 1, partition 1, PROCESS_LOCAL, 8099 bytes)
2020-09-03 16:52:13 TaskSetManager: INFO: Lost task 0.6 in stage 2.0 (TID 180) on jg3-w-0.c.maclab-ukbb.internal, executor 1: htsjdk.samtools.SAMException (Unable to load chr19(58615273, 58617616) from /tmp/fasta-reader-FcVGkbAEQi5MCYD6x7hi1B.fasta) [duplicate 6]
2020-09-03 16:52:13 TaskSetManager: INFO: Starting task 0.7 in stage 2.0 (TID 182, jg3-w-0.c.maclab-ukbb.internal, executor 1, partition 0, PROCESS_LOCAL, 8099 bytes)
2020-09-03 16:52:13 TaskSetManager: INFO: Lost task 2.4 in stage 2.0 (TID 178) on jg3-w-0.c.maclab-ukbb.internal, executor 1: htsjdk.samtools.SAMException (Unable to load chr20(1009369, 1013465) from /tmp/fasta-reader-FcVGkbAEQi5MCYD6x7hi1B.fasta) [duplicate 4]
2020-09-03 16:52:13 ExecutorAllocationManager: INFO: Requesting 3 new executors because tasks are backlogged (new desired total will be 4)
2020-09-03 16:52:13 TaskSetManager: INFO: Starting task 2.5 in stage 2.0 (TID 183, jg3-w-0.c.maclab-ukbb.internal, executor 1, partition 2, PROCESS_LOCAL, 8099 bytes)
2020-09-03 16:52:13 TaskSetManager: INFO: Lost task 1.7 in stage 2.0 (TID 181) on jg3-w-0.c.maclab-ukbb.internal, executor 1: htsjdk.samtools.SAMException (Unable to load chr20(501465, 505561) from /tmp/fasta-reader-FcVGkbAEQi5MCYD6x7hi1B.fasta) [duplicate 7]
2020-09-03 16:52:13 TaskSetManager: INFO: Starting task 1.8 in stage 2.0 (TID 184, jg3-w-0.c.maclab-ukbb.internal, executor 1, partition 1, PROCESS_LOCAL, 8099 bytes)
2020-09-03 16:52:13 TaskSetManager: INFO: Lost task 4.3 in stage 2.0 (TID 179) on jg3-w-0.c.maclab-ukbb.internal, executor 1: htsjdk.samtools.SAMException (Unable to load chr20(2016985, 2021081) from /tmp/fasta-reader-FcVGkbAEQi5MCYD6x7hi1B.fasta) [duplicate 3]
2020-09-03 16:52:13 TaskSetManager: INFO: Starting task 4.4 in stage 2.0 (TID 185, jg3-w-0.c.maclab-ukbb.internal, executor 1, partition 4, PROCESS_LOCAL, 8099 bytes)
2020-09-03 16:52:13 TaskSetManager: INFO: Lost task 0.7 in stage 2.0 (TID 182) on jg3-w-0.c.maclab-ukbb.internal, executor 1: htsjdk.samtools.SAMException (Unable to load chr19(58615273, 58617616) from /tmp/fasta-reader-FcVGkbAEQi5MCYD6x7hi1B.fasta) [duplicate 7]
2020-09-03 16:52:13 TaskSetManager: INFO: Starting task 0.8 in stage 2.0 (TID 186, jg3-w-0.c.maclab-ukbb.internal, executor 1, partition 0, PROCESS_LOCAL, 8099 bytes)
2020-09-03 16:52:13 TaskSetManager: INFO: Lost task 1.8 in stage 2.0 (TID 184) on jg3-w-0.c.maclab-ukbb.internal, executor 1: htsjdk.samtools.SAMException (Unable to load chr20(501465, 505561) from /tmp/fasta-reader-FcVGkbAEQi5MCYD6x7hi1B.fasta) [duplicate 8]
2020-09-03 16:52:13 TaskSetManager: INFO: Starting task 1.9 in stage 2.0 (TID 187, jg3-w-0.c.maclab-ukbb.internal, executor 1, partition 1, PROCESS_LOCAL, 8099 bytes)
2020-09-03 16:52:13 TaskSetManager: INFO: Lost task 2.5 in stage 2.0 (TID 183) on jg3-w-0.c.maclab-ukbb.internal, executor 1: htsjdk.samtools.SAMException (Unable to load chr20(1009369, 1013465) from /tmp/fasta-reader-FcVGkbAEQi5MCYD6x7hi1B.fasta) [duplicate 5]
2020-09-03 16:52:13 TaskSetManager: INFO: Starting task 2.6 in stage 2.0 (TID 188, jg3-w-0.c.maclab-ukbb.internal, executor 1, partition 2, PROCESS_LOCAL, 8099 bytes)
2020-09-03 16:52:13 TaskSetManager: INFO: Lost task 0.8 in stage 2.0 (TID 186) on jg3-w-0.c.maclab-ukbb.internal, executor 1: htsjdk.samtools.SAMException (Unable to load chr19(58615273, 58617616) from /tmp/fasta-reader-FcVGkbAEQi5MCYD6x7hi1B.fasta) [duplicate 8]
2020-09-03 16:52:13 TaskSetManager: INFO: Starting task 0.9 in stage 2.0 (TID 189, jg3-w-0.c.maclab-ukbb.internal, executor 1, partition 0, PROCESS_LOCAL, 8099 bytes)
2020-09-03 16:52:13 TaskSetManager: INFO: Lost task 4.4 in stage 2.0 (TID 185) on jg3-w-0.c.maclab-ukbb.internal, executor 1: htsjdk.samtools.SAMException (Unable to load chr20(2016985, 2021081) from /tmp/fasta-reader-FcVGkbAEQi5MCYD6x7hi1B.fasta) [duplicate 4]
2020-09-03 16:52:13 TaskSetManager: INFO: Starting task 4.5 in stage 2.0 (TID 190, jg3-w-0.c.maclab-ukbb.internal, executor 1, partition 4, PROCESS_LOCAL, 8099 bytes)
2020-09-03 16:52:13 TaskSetManager: INFO: Lost task 1.9 in stage 2.0 (TID 187) on jg3-w-0.c.maclab-ukbb.internal, executor 1: htsjdk.samtools.SAMException (Unable to load chr20(501465, 505561) from /tmp/fasta-reader-FcVGkbAEQi5MCYD6x7hi1B.fasta) [duplicate 9]
2020-09-03 16:52:13 TaskSetManager: INFO: Starting task 1.10 in stage 2.0 (TID 191, jg3-w-0.c.maclab-ukbb.internal, executor 1, partition 1, PROCESS_LOCAL, 8099 bytes)
2020-09-03 16:52:13 TaskSetManager: INFO: Lost task 0.9 in stage 2.0 (TID 189) on jg3-w-0.c.maclab-ukbb.internal, executor 1: htsjdk.samtools.SAMException (Unable to load chr19(58615273, 58617616) from /tmp/fasta-reader-FcVGkbAEQi5MCYD6x7hi1B.fasta) [duplicate 9]
2020-09-03 16:52:13 TaskSetManager: INFO: Starting task 0.10 in stage 2.0 (TID 192, jg3-w-0.c.maclab-ukbb.internal, executor 1, partition 0, PROCESS_LOCAL, 8099 bytes)
2020-09-03 16:52:13 TaskSetManager: INFO: Lost task 2.6 in stage 2.0 (TID 188) on jg3-w-0.c.maclab-ukbb.internal, executor 1: htsjdk.samtools.SAMException (Unable to load chr20(1009369, 1013465) from /tmp/fasta-reader-FcVGkbAEQi5MCYD6x7hi1B.fasta) [duplicate 6]
2020-09-03 16:52:13 TaskSetManager: INFO: Starting task 2.7 in stage 2.0 (TID 193, jg3-w-0.c.maclab-ukbb.internal, executor 1, partition 2, PROCESS_LOCAL, 8099 bytes)
2020-09-03 16:52:13 TaskSetManager: INFO: Lost task 1.10 in stage 2.0 (TID 191) on jg3-w-0.c.maclab-ukbb.internal, executor 1: htsjdk.samtools.SAMException (Unable to load chr20(501465, 505561) from /tmp/fasta-reader-FcVGkbAEQi5MCYD6x7hi1B.fasta) [duplicate 10]
2020-09-03 16:52:13 TaskSetManager: INFO: Starting task 1.11 in stage 2.0 (TID 194, jg3-w-0.c.maclab-ukbb.internal, executor 1, partition 1, PROCESS_LOCAL, 8099 bytes)
2020-09-03 16:52:13 TaskSetManager: INFO: Lost task 0.10 in stage 2.0 (TID 192) on jg3-w-0.c.maclab-ukbb.internal, executor 1: htsjdk.samtools.SAMException (Unable to load chr19(58615273, 58617616) from /tmp/fasta-reader-FcVGkbAEQi5MCYD6x7hi1B.fasta) [duplicate 10]
2020-09-03 16:52:13 TaskSetManager: INFO: Starting task 0.11 in stage 2.0 (TID 195, jg3-w-0.c.maclab-ukbb.internal, executor 1, partition 0, PROCESS_LOCAL, 8099 bytes)
2020-09-03 16:52:13 TaskSetManager: INFO: Lost task 4.5 in stage 2.0 (TID 190) on jg3-w-0.c.maclab-ukbb.internal, executor 1: htsjdk.samtools.SAMException (Unable to load chr20(2016985, 2021081) from /tmp/fasta-reader-FcVGkbAEQi5MCYD6x7hi1B.fasta) [duplicate 5]
2020-09-03 16:52:13 TaskSetManager: INFO: Starting task 4.6 in stage 2.0 (TID 196, jg3-w-0.c.maclab-ukbb.internal, executor 1, partition 4, PROCESS_LOCAL, 8099 bytes)
2020-09-03 16:52:13 TaskSetManager: INFO: Lost task 1.11 in stage 2.0 (TID 194) on jg3-w-0.c.maclab-ukbb.internal, executor 1: htsjdk.samtools.SAMException (Unable to load chr20(501465, 505561) from /tmp/fasta-reader-FcVGkbAEQi5MCYD6x7hi1B.fasta) [duplicate 11]
2020-09-03 16:52:13 TaskSetManager: INFO: Starting task 1.12 in stage 2.0 (TID 197, jg3-w-0.c.maclab-ukbb.internal, executor 1, partition 1, PROCESS_LOCAL, 8099 bytes)
2020-09-03 16:52:13 TaskSetManager: INFO: Lost task 0.11 in stage 2.0 (TID 195) on jg3-w-0.c.maclab-ukbb.internal, executor 1: htsjdk.samtools.SAMException (Unable to load chr19(58615273, 58617616) from /tmp/fasta-reader-FcVGkbAEQi5MCYD6x7hi1B.fasta) [duplicate 11]
2020-09-03 16:52:13 TaskSetManager: INFO: Starting task 0.12 in stage 2.0 (TID 198, jg3-w-0.c.maclab-ukbb.internal, executor 1, partition 0, PROCESS_LOCAL, 8099 bytes)
2020-09-03 16:52:13 TaskSetManager: INFO: Lost task 2.7 in stage 2.0 (TID 193) on jg3-w-0.c.maclab-ukbb.internal, executor 1: htsjdk.samtools.SAMException (Unable to load chr20(1009369, 1013465) from /tmp/fasta-reader-FcVGkbAEQi5MCYD6x7hi1B.fasta) [duplicate 7]
2020-09-03 16:52:13 TaskSetManager: INFO: Starting task 2.8 in stage 2.0 (TID 199, jg3-w-0.c.maclab-ukbb.internal, executor 1, partition 2, PROCESS_LOCAL, 8099 bytes)
2020-09-03 16:52:13 TaskSetManager: INFO: Lost task 1.12 in stage 2.0 (TID 197) on jg3-w-0.c.maclab-ukbb.internal, executor 1: htsjdk.samtools.SAMException (Unable to load chr20(501465, 505561) from /tmp/fasta-reader-FcVGkbAEQi5MCYD6x7hi1B.fasta) [duplicate 12]
2020-09-03 16:52:13 TaskSetManager: INFO: Starting task 1.13 in stage 2.0 (TID 200, jg3-w-0.c.maclab-ukbb.internal, executor 1, partition 1, PROCESS_LOCAL, 8099 bytes)
2020-09-03 16:52:13 TaskSetManager: INFO: Lost task 4.6 in stage 2.0 (TID 196) on jg3-w-0.c.maclab-ukbb.internal, executor 1: htsjdk.samtools.SAMException (Unable to load chr20(2016985, 2021081) from /tmp/fasta-reader-FcVGkbAEQi5MCYD6x7hi1B.fasta) [duplicate 6]
2020-09-03 16:52:13 TaskSetManager: INFO: Starting task 4.7 in stage 2.0 (TID 201, jg3-w-0.c.maclab-ukbb.internal, executor 1, partition 4, PROCESS_LOCAL, 8099 bytes)
2020-09-03 16:52:13 TaskSetManager: INFO: Lost task 0.12 in stage 2.0 (TID 198) on jg3-w-0.c.maclab-ukbb.internal, executor 1: htsjdk.samtools.SAMException (Unable to load chr19(58615273, 58617616) from /tmp/fasta-reader-FcVGkbAEQi5MCYD6x7hi1B.fasta) [duplicate 12]
2020-09-03 16:52:13 TaskSetManager: INFO: Starting task 0.13 in stage 2.0 (TID 202, jg3-w-0.c.maclab-ukbb.internal, executor 1, partition 0, PROCESS_LOCAL, 8099 bytes)
2020-09-03 16:52:13 TaskSetManager: INFO: Lost task 1.13 in stage 2.0 (TID 200) on jg3-w-0.c.maclab-ukbb.internal, executor 1: htsjdk.samtools.SAMException (Unable to load chr20(501465, 505561) from /tmp/fasta-reader-FcVGkbAEQi5MCYD6x7hi1B.fasta) [duplicate 13]
2020-09-03 16:52:13 TaskSetManager: INFO: Starting task 1.14 in stage 2.0 (TID 203, jg3-w-0.c.maclab-ukbb.internal, executor 1, partition 1, PROCESS_LOCAL, 8099 bytes)
2020-09-03 16:52:13 TaskSetManager: INFO: Lost task 2.8 in stage 2.0 (TID 199) on jg3-w-0.c.maclab-ukbb.internal, executor 1: htsjdk.samtools.SAMException (Unable to load chr20(1009369, 1013465) from /tmp/fasta-reader-FcVGkbAEQi5MCYD6x7hi1B.fasta) [duplicate 8]
2020-09-03 16:52:13 TaskSetManager: INFO: Starting task 2.9 in stage 2.0 (TID 204, jg3-w-0.c.maclab-ukbb.internal, executor 1, partition 2, PROCESS_LOCAL, 8099 bytes)
2020-09-03 16:52:13 TaskSetManager: INFO: Lost task 0.13 in stage 2.0 (TID 202) on jg3-w-0.c.maclab-ukbb.internal, executor 1: htsjdk.samtools.SAMException (Unable to load chr19(58615273, 58617616) from /tmp/fasta-reader-FcVGkbAEQi5MCYD6x7hi1B.fasta) [duplicate 13]
2020-09-03 16:52:13 TaskSetManager: INFO: Starting task 0.14 in stage 2.0 (TID 205, jg3-w-0.c.maclab-ukbb.internal, executor 1, partition 0, PROCESS_LOCAL, 8099 bytes)
2020-09-03 16:52:13 TaskSetManager: INFO: Lost task 1.14 in stage 2.0 (TID 203) on jg3-w-0.c.maclab-ukbb.internal, executor 1: htsjdk.samtools.SAMException (Unable to load chr20(501465, 505561) from /tmp/fasta-reader-FcVGkbAEQi5MCYD6x7hi1B.fasta) [duplicate 14]
2020-09-03 16:52:13 TaskSetManager: INFO: Starting task 1.15 in stage 2.0 (TID 206, jg3-w-0.c.maclab-ukbb.internal, executor 1, partition 1, PROCESS_LOCAL, 8099 bytes)
2020-09-03 16:52:13 TaskSetManager: INFO: Lost task 4.7 in stage 2.0 (TID 201) on jg3-w-0.c.maclab-ukbb.internal, executor 1: htsjdk.samtools.SAMException (Unable to load chr20(2016985, 2021081) from /tmp/fasta-reader-FcVGkbAEQi5MCYD6x7hi1B.fasta) [duplicate 7]
2020-09-03 16:52:13 TaskSetManager: INFO: Starting task 4.8 in stage 2.0 (TID 207, jg3-w-0.c.maclab-ukbb.internal, executor 1, partition 4, PROCESS_LOCAL, 8099 bytes)
2020-09-03 16:52:13 TaskSetManager: INFO: Lost task 0.14 in stage 2.0 (TID 205) on jg3-w-0.c.maclab-ukbb.internal, executor 1: htsjdk.samtools.SAMException (Unable to load chr19(58615273, 58617616) from /tmp/fasta-reader-FcVGkbAEQi5MCYD6x7hi1B.fasta) [duplicate 14]
2020-09-03 16:52:13 TaskSetManager: INFO: Starting task 0.15 in stage 2.0 (TID 208, jg3-w-0.c.maclab-ukbb.internal, executor 1, partition 0, PROCESS_LOCAL, 8099 bytes)
2020-09-03 16:52:13 TaskSetManager: INFO: Lost task 1.15 in stage 2.0 (TID 206) on jg3-w-0.c.maclab-ukbb.internal, executor 1: htsjdk.samtools.SAMException (Unable to load chr20(501465, 505561) from /tmp/fasta-reader-FcVGkbAEQi5MCYD6x7hi1B.fasta) [duplicate 15]
2020-09-03 16:52:13 TaskSetManager: INFO: Starting task 1.16 in stage 2.0 (TID 209, jg3-w-0.c.maclab-ukbb.internal, executor 1, partition 1, PROCESS_LOCAL, 8099 bytes)
2020-09-03 16:52:13 TaskSetManager: INFO: Lost task 0.15 in stage 2.0 (TID 208) on jg3-w-0.c.maclab-ukbb.internal, executor 1: htsjdk.samtools.SAMException (Unable to load chr19(58615273, 58617616) from /tmp/fasta-reader-FcVGkbAEQi5MCYD6x7hi1B.fasta) [duplicate 15]
2020-09-03 16:52:13 TaskSetManager: INFO: Starting task 0.16 in stage 2.0 (TID 210, jg3-w-0.c.maclab-ukbb.internal, executor 1, partition 0, PROCESS_LOCAL, 8099 bytes)
2020-09-03 16:52:13 TaskSetManager: INFO: Lost task 2.9 in stage 2.0 (TID 204) on jg3-w-0.c.maclab-ukbb.internal, executor 1: htsjdk.samtools.SAMException (Unable to load chr20(1009369, 1013465) from /tmp/fasta-reader-FcVGkbAEQi5MCYD6x7hi1B.fasta) [duplicate 9]
2020-09-03 16:52:13 TaskSetManager: INFO: Starting task 2.10 in stage 2.0 (TID 211, jg3-w-0.c.maclab-ukbb.internal, executor 1, partition 2, PROCESS_LOCAL, 8099 bytes)
2020-09-03 16:52:13 TaskSetManager: INFO: Lost task 1.16 in stage 2.0 (TID 209) on jg3-w-0.c.maclab-ukbb.internal, executor 1: htsjdk.samtools.SAMException (Unable to load chr20(501465, 505561) from /tmp/fasta-reader-FcVGkbAEQi5MCYD6x7hi1B.fasta) [duplicate 16]
2020-09-03 16:52:13 TaskSetManager: INFO: Starting task 1.17 in stage 2.0 (TID 212, jg3-w-0.c.maclab-ukbb.internal, executor 1, partition 1, PROCESS_LOCAL, 8099 bytes)
2020-09-03 16:52:13 TaskSetManager: INFO: Lost task 0.16 in stage 2.0 (TID 210) on jg3-w-0.c.maclab-ukbb.internal, executor 1: htsjdk.samtools.SAMException (Unable to load chr19(58615273, 58617616) from /tmp/fasta-reader-FcVGkbAEQi5MCYD6x7hi1B.fasta) [duplicate 16]
2020-09-03 16:52:13 TaskSetManager: INFO: Starting task 0.17 in stage 2.0 (TID 213, jg3-w-0.c.maclab-ukbb.internal, executor 1, partition 0, PROCESS_LOCAL, 8099 bytes)
2020-09-03 16:52:13 TaskSetManager: INFO: Lost task 4.8 in stage 2.0 (TID 207) on jg3-w-0.c.maclab-ukbb.internal, executor 1: htsjdk.samtools.SAMException (Unable to load chr20(2016985, 2021081) from /tmp/fasta-reader-FcVGkbAEQi5MCYD6x7hi1B.fasta) [duplicate 8]
2020-09-03 16:52:13 TaskSetManager: INFO: Starting task 4.9 in stage 2.0 (TID 214, jg3-w-0.c.maclab-ukbb.internal, executor 1, partition 4, PROCESS_LOCAL, 8099 bytes)
2020-09-03 16:52:13 TaskSetManager: INFO: Lost task 0.17 in stage 2.0 (TID 213) on jg3-w-0.c.maclab-ukbb.internal, executor 1: htsjdk.samtools.SAMException (Unable to load chr19(58615273, 58617616) from /tmp/fasta-reader-FcVGkbAEQi5MCYD6x7hi1B.fasta) [duplicate 17]
2020-09-03 16:52:13 TaskSetManager: INFO: Starting task 0.18 in stage 2.0 (TID 215, jg3-w-0.c.maclab-ukbb.internal, executor 1, partition 0, PROCESS_LOCAL, 8099 bytes)
2020-09-03 16:52:13 TaskSetManager: INFO: Lost task 1.17 in stage 2.0 (TID 212) on jg3-w-0.c.maclab-ukbb.internal, executor 1: htsjdk.samtools.SAMException (Unable to load chr20(501465, 505561) from /tmp/fasta-reader-FcVGkbAEQi5MCYD6x7hi1B.fasta) [duplicate 17]
2020-09-03 16:52:13 TaskSetManager: INFO: Starting task 1.18 in stage 2.0 (TID 216, jg3-w-0.c.maclab-ukbb.internal, executor 1, partition 1, PROCESS_LOCAL, 8099 bytes)
2020-09-03 16:52:13 TaskSetManager: INFO: Lost task 2.10 in stage 2.0 (TID 211) on jg3-w-0.c.maclab-ukbb.internal, executor 1: htsjdk.samtools.SAMException (Unable to load chr20(1009369, 1013465) from /tmp/fasta-reader-FcVGkbAEQi5MCYD6x7hi1B.fasta) [duplicate 10]
2020-09-03 16:52:13 TaskSetManager: INFO: Starting task 2.11 in stage 2.0 (TID 217, jg3-w-0.c.maclab-ukbb.internal, executor 1, partition 2, PROCESS_LOCAL, 8099 bytes)
2020-09-03 16:52:13 TaskSetManager: INFO: Lost task 0.18 in stage 2.0 (TID 215) on jg3-w-0.c.maclab-ukbb.internal, executor 1: htsjdk.samtools.SAMException (Unable to load chr19(58615273, 58617616) from /tmp/fasta-reader-FcVGkbAEQi5MCYD6x7hi1B.fasta) [duplicate 18]
2020-09-03 16:52:13 TaskSetManager: INFO: Starting task 0.19 in stage 2.0 (TID 218, jg3-w-0.c.maclab-ukbb.internal, executor 1, partition 0, PROCESS_LOCAL, 8099 bytes)
2020-09-03 16:52:13 TaskSetManager: INFO: Lost task 1.18 in stage 2.0 (TID 216) on jg3-w-0.c.maclab-ukbb.internal, executor 1: htsjdk.samtools.SAMException (Unable to load chr20(501465, 505561) from /tmp/fasta-reader-FcVGkbAEQi5MCYD6x7hi1B.fasta) [duplicate 18]
2020-09-03 16:52:13 TaskSetManager: INFO: Starting task 1.19 in stage 2.0 (TID 219, jg3-w-0.c.maclab-ukbb.internal, executor 1, partition 1, PROCESS_LOCAL, 8099 bytes)
2020-09-03 16:52:13 TaskSetManager: INFO: Lost task 4.9 in stage 2.0 (TID 214) on jg3-w-0.c.maclab-ukbb.internal, executor 1: htsjdk.samtools.SAMException (Unable to load chr20(2016985, 2021081) from /tmp/fasta-reader-FcVGkbAEQi5MCYD6x7hi1B.fasta) [duplicate 9]
2020-09-03 16:52:13 TaskSetManager: INFO: Starting task 4.10 in stage 2.0 (TID 220, jg3-w-0.c.maclab-ukbb.internal, executor 1, partition 4, PROCESS_LOCAL, 8099 bytes)
2020-09-03 16:52:13 TaskSetManager: INFO: Lost task 2.11 in stage 2.0 (TID 217) on jg3-w-0.c.maclab-ukbb.internal, executor 1: htsjdk.samtools.SAMException (Unable to load chr20(1009369, 1013465) from /tmp/fasta-reader-FcVGkbAEQi5MCYD6x7hi1B.fasta) [duplicate 11]
2020-09-03 16:52:13 TaskSetManager: INFO: Starting task 2.12 in stage 2.0 (TID 221, jg3-w-0.c.maclab-ukbb.internal, executor 1, partition 2, PROCESS_LOCAL, 8099 bytes)
2020-09-03 16:52:13 TaskSetManager: INFO: Lost task 0.19 in stage 2.0 (TID 218) on jg3-w-0.c.maclab-ukbb.internal, executor 1: htsjdk.samtools.SAMException (Unable to load chr19(58615273, 58617616) from /tmp/fasta-reader-FcVGkbAEQi5MCYD6x7hi1B.fasta) [duplicate 19]
2020-09-03 16:52:13 TaskSetManager: ERROR: Task 0 in stage 2.0 failed 20 times; aborting job
2020-09-03 16:52:13 TaskSetManager: INFO: Lost task 1.19 in stage 2.0 (TID 219) on jg3-w-0.c.maclab-ukbb.internal, executor 1: htsjdk.samtools.SAMException (Unable to load chr20(501465, 505561) from /tmp/fasta-reader-FcVGkbAEQi5MCYD6x7hi1B.fasta) [duplicate 19]
2020-09-03 16:52:13 YarnScheduler: INFO: Cancelling stage 2
2020-09-03 16:52:13 YarnScheduler: INFO: Killing all running tasks in stage 2: Stage cancelled
2020-09-03 16:52:13 YarnScheduler: INFO: Stage 2 was cancelled
2020-09-03 16:52:13 DAGScheduler: INFO: ResultStage 2 (fold at RVD.scala:735) failed in 1.447 s due to Job aborted due to stage failure: Task 0 in stage 2.0 failed 20 times, most recent failure: Lost task 0.19 in stage 2.0 (TID 218, jg3-w-0.c.maclab-ukbb.internal, executor 1): htsjdk.samtools.SAMException: Unable to load chr19(58615273, 58617616) from /tmp/fasta-reader-FcVGkbAEQi5MCYD6x7hi1B.fasta
	at htsjdk.samtools.reference.AbstractIndexedFastaSequenceFile.getSubsequenceAt(AbstractIndexedFastaSequenceFile.java:207)
	at htsjdk.samtools.reference.IndexedFastaSequenceFile.getSubsequenceAt(IndexedFastaSequenceFile.java:49)
	at is.hail.io.reference.FASTAReader.getSequence(FASTAReader.scala:73)
	at is.hail.io.reference.FASTAReader.fillBlock(FASTAReader.scala:83)
	at is.hail.io.reference.FASTAReader.readBlock(FASTAReader.scala:93)
	at is.hail.io.reference.FASTAReader.readBlock(FASTAReader.scala:99)
	at is.hail.io.reference.FASTAReader.lookupGlobalPos(FASTAReader.scala:138)
	at is.hail.io.reference.FASTAReader.lookup(FASTAReader.scala:110)
	at is.hail.variant.ReferenceGenome.getSequence(ReferenceGenome.scala:357)
	at __C24Compiled.__m42getReferenceSequenceFromValidLocus(Unknown Source)
	at __C24Compiled.apply(Unknown Source)
	at is.hail.expr.ir.TableFilter$$anonfun$execute$2.apply(TableIR.scala:946)
	at is.hail.expr.ir.TableFilter$$anonfun$execute$2.apply(TableIR.scala:946)
	at is.hail.expr.ir.TableValue$$anonfun$3.apply(TableValue.scala:65)
	at is.hail.expr.ir.TableValue$$anonfun$3.apply(TableValue.scala:65)
	at is.hail.rvd.RVD$$anonfun$17$$anonfun$apply$2.apply$mcZJ$sp(RVD.scala:605)
	at is.hail.rvd.RVD$$anonfun$17$$anonfun$apply$2.apply(RVD.scala:604)
	at is.hail.rvd.RVD$$anonfun$17$$anonfun$apply$2.apply(RVD.scala:604)
	at scala.collection.Iterator$$anon$13.hasNext(Iterator.scala:464)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
	at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:409)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
	at is.hail.io.RichContextRDDLong$$anonfun$boundary$extension$2$$anon$1.hasNext(RichContextRDDRegionValue.scala:188)
	at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:409)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
	at scala.collection.Iterator$$anon$1.hasNext(Iterator.scala:1002)
	at is.hail.utils.richUtils.RichIterator$$anon$5.isValid(RichIterator.scala:30)
	at is.hail.utils.StagingIterator.isValid(FlipbookIterator.scala:48)
	at is.hail.utils.FlipbookIterator$$anon$9.setValue(FlipbookIterator.scala:327)
	at is.hail.utils.FlipbookIterator$$anon$9.<init>(FlipbookIterator.scala:344)
	at is.hail.utils.FlipbookIterator.leftJoinDistinct(FlipbookIterator.scala:323)
	at is.hail.annotations.OrderedRVIterator.leftIntervalJoinDistinct(OrderedRVIterator.scala:51)
	at is.hail.rvd.KeyedRVD$$anonfun$orderedLeftIntervalJoinDistinct$1$$anonfun$apply$2.apply(KeyedRVD.scala:131)
	at is.hail.rvd.KeyedRVD$$anonfun$orderedLeftIntervalJoinDistinct$1$$anonfun$apply$2.apply(KeyedRVD.scala:127)
	at is.hail.sparkextras.ContextRDD$$anonfun$czipPartitions$1$$anonfun$apply$24.apply(ContextRDD.scala:305)
	at is.hail.sparkextras.ContextRDD$$anonfun$czipPartitions$1$$anonfun$apply$24.apply(ContextRDD.scala:305)
	at is.hail.sparkextras.ContextRDD$$anonfun$cmapPartitions$1$$anonfun$apply$9$$anonfun$apply$10.apply(ContextRDD.scala:208)
	at is.hail.sparkextras.ContextRDD$$anonfun$cmapPartitions$1$$anonfun$apply$9$$anonfun$apply$10.apply(ContextRDD.scala:208)
	at scala.collection.Iterator$$anon$12.nextCur(Iterator.scala:435)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:441)
	at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:409)
	at scala.collection.Iterator$$anon$13.hasNext(Iterator.scala:462)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
	at is.hail.io.RichContextRDDLong$$anonfun$boundary$extension$2$$anon$1.hasNext(RichContextRDDRegionValue.scala:188)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
	at scala.collection.Iterator$class.foreach(Iterator.scala:891)
	at scala.collection.AbstractIterator.foreach(Iterator.scala:1334)
	at is.hail.rvd.RVD$$anonfun$23.apply(RVD.scala:731)
	at is.hail.rvd.RVD$$anonfun$23.apply(RVD.scala:729)
	at is.hail.sparkextras.ContextRDD$$anonfun$cmapPartitions$1$$anonfun$apply$9.apply(ContextRDD.scala:208)
	at is.hail.sparkextras.ContextRDD$$anonfun$cmapPartitions$1$$anonfun$apply$9.apply(ContextRDD.scala:208)
	at is.hail.utils.richUtils.RichContextRDD$$anonfun$cleanupRegions$1$$anonfun$2.apply(RichContextRDD.scala:57)
	at is.hail.utils.richUtils.RichContextRDD$$anonfun$cleanupRegions$1$$anonfun$2.apply(RichContextRDD.scala:57)
	at scala.collection.Iterator$$anon$12.nextCur(Iterator.scala:435)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:441)
	at is.hail.utils.richUtils.RichContextRDD$$anonfun$cleanupRegions$1$$anon$1.hasNext(RichContextRDD.scala:66)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
	at scala.collection.Iterator$class.foreach(Iterator.scala:891)
	at scala.collection.AbstractIterator.foreach(Iterator.scala:1334)
	at scala.collection.TraversableOnce$class.foldLeft(TraversableOnce.scala:157)
	at scala.collection.AbstractIterator.foldLeft(Iterator.scala:1334)
	at scala.collection.TraversableOnce$class.fold(TraversableOnce.scala:212)
	at scala.collection.AbstractIterator.fold(Iterator.scala:1334)
	at org.apache.spark.rdd.RDD$$anonfun$fold$1$$anonfun$22.apply(RDD.scala:1141)
	at org.apache.spark.rdd.RDD$$anonfun$fold$1$$anonfun$22.apply(RDD.scala:1141)
	at org.apache.spark.SparkContext$$anonfun$36.apply(SparkContext.scala:2157)
	at org.apache.spark.SparkContext$$anonfun$36.apply(SparkContext.scala:2157)
	at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:90)
	at org.apache.spark.scheduler.Task.run(Task.scala:123)
	at org.apache.spark.executor.Executor$TaskRunner$$anonfun$10.apply(Executor.scala:408)
	at org.apache.spark.util.Utils$.tryWithSafeFinally(Utils.scala:1360)
	at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:414)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
	at java.lang.Thread.run(Thread.java:748)
Caused by: java.nio.channels.ClosedChannelException
	at sun.nio.ch.FileChannelImpl.ensureOpen(FileChannelImpl.java:110)
	at sun.nio.ch.FileChannelImpl.read(FileChannelImpl.java:715)
	at htsjdk.samtools.reference.IndexedFastaSequenceFile.readFromPosition(IndexedFastaSequenceFile.java:148)
	at htsjdk.samtools.reference.AbstractIndexedFastaSequenceFile.getSubsequenceAt(AbstractIndexedFastaSequenceFile.java:204)
	... 74 more

Driver stacktrace:
2020-09-03 16:52:13 DAGScheduler: INFO: Job 1 failed: fold at RVD.scala:735, took 2.048297 s
2020-09-03 16:52:13 root: ERROR: error while applying lowering 'InterpretNonCompilable'
2020-09-03 16:52:13 TaskSetManager: WARN: Lost task 3.0 in stage 2.0 (TID 160, jg3-w-0.c.maclab-ukbb.internal, executor 1): TaskKilled (Stage cancelled)
2020-09-03 16:52:13 root: INFO: The exact same exception object, org.apache.spark.SparkException: Job aborted due to stage failure: Task 0 in stage 2.0 failed 20 times, most recent failure: Lost task 0.19 in stage 2.0 (TID 218, jg3-w-0.c.maclab-ukbb.internal, executor 1): htsjdk.samtools.SAMException: Unable to load chr19(58615273, 58617616) from /tmp/fasta-reader-FcVGkbAEQi5MCYD6x7hi1B.fasta
	at htsjdk.samtools.reference.AbstractIndexedFastaSequenceFile.getSubsequenceAt(AbstractIndexedFastaSequenceFile.java:207)
	at htsjdk.samtools.reference.IndexedFastaSequenceFile.getSubsequenceAt(IndexedFastaSequenceFile.java:49)
	at is.hail.io.reference.FASTAReader.getSequence(FASTAReader.scala:73)
	at is.hail.io.reference.FASTAReader.fillBlock(FASTAReader.scala:83)
	at is.hail.io.reference.FASTAReader.readBlock(FASTAReader.scala:93)
	at is.hail.io.reference.FASTAReader.readBlock(FASTAReader.scala:99)
	at is.hail.io.reference.FASTAReader.lookupGlobalPos(FASTAReader.scala:138)
	at is.hail.io.reference.FASTAReader.lookup(FASTAReader.scala:110)
	at is.hail.variant.ReferenceGenome.getSequence(ReferenceGenome.scala:357)
	at __C24Compiled.__m42getReferenceSequenceFromValidLocus(Unknown Source)
	at __C24Compiled.apply(Unknown Source)
	at is.hail.expr.ir.TableFilter$$anonfun$execute$2.apply(TableIR.scala:946)
	at is.hail.expr.ir.TableFilter$$anonfun$execute$2.apply(TableIR.scala:946)
	at is.hail.expr.ir.TableValue$$anonfun$3.apply(TableValue.scala:65)
	at is.hail.expr.ir.TableValue$$anonfun$3.apply(TableValue.scala:65)
	at is.hail.rvd.RVD$$anonfun$17$$anonfun$apply$2.apply$mcZJ$sp(RVD.scala:605)
	at is.hail.rvd.RVD$$anonfun$17$$anonfun$apply$2.apply(RVD.scala:604)
	at is.hail.rvd.RVD$$anonfun$17$$anonfun$apply$2.apply(RVD.scala:604)
	at scala.collection.Iterator$$anon$13.hasNext(Iterator.scala:464)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
	at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:409)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
	at is.hail.io.RichContextRDDLong$$anonfun$boundary$extension$2$$anon$1.hasNext(RichContextRDDRegionValue.scala:188)
	at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:409)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
	at scala.collection.Iterator$$anon$1.hasNext(Iterator.scala:1002)
	at is.hail.utils.richUtils.RichIterator$$anon$5.isValid(RichIterator.scala:30)
	at is.hail.utils.StagingIterator.isValid(FlipbookIterator.scala:48)
	at is.hail.utils.FlipbookIterator$$anon$9.setValue(FlipbookIterator.scala:327)
	at is.hail.utils.FlipbookIterator$$anon$9.<init>(FlipbookIterator.scala:344)
	at is.hail.utils.FlipbookIterator.leftJoinDistinct(FlipbookIterator.scala:323)
	at is.hail.annotations.OrderedRVIterator.leftIntervalJoinDistinct(OrderedRVIterator.scala:51)
	at is.hail.rvd.KeyedRVD$$anonfun$orderedLeftIntervalJoinDistinct$1$$anonfun$apply$2.apply(KeyedRVD.scala:131)
	at is.hail.rvd.KeyedRVD$$anonfun$orderedLeftIntervalJoinDistinct$1$$anonfun$apply$2.apply(KeyedRVD.scala:127)
	at is.hail.sparkextras.ContextRDD$$anonfun$czipPartitions$1$$anonfun$apply$24.apply(ContextRDD.scala:305)
	at is.hail.sparkextras.ContextRDD$$anonfun$czipPartitions$1$$anonfun$apply$24.apply(ContextRDD.scala:305)
	at is.hail.sparkextras.ContextRDD$$anonfun$cmapPartitions$1$$anonfun$apply$9$$anonfun$apply$10.apply(ContextRDD.scala:208)
	at is.hail.sparkextras.ContextRDD$$anonfun$cmapPartitions$1$$anonfun$apply$9$$anonfun$apply$10.apply(ContextRDD.scala:208)
	at scala.collection.Iterator$$anon$12.nextCur(Iterator.scala:435)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:441)
	at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:409)
	at scala.collection.Iterator$$anon$13.hasNext(Iterator.scala:462)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
	at is.hail.io.RichContextRDDLong$$anonfun$boundary$extension$2$$anon$1.hasNext(RichContextRDDRegionValue.scala:188)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
	at scala.collection.Iterator$class.foreach(Iterator.scala:891)
	at scala.collection.AbstractIterator.foreach(Iterator.scala:1334)
	at is.hail.rvd.RVD$$anonfun$23.apply(RVD.scala:731)
	at is.hail.rvd.RVD$$anonfun$23.apply(RVD.scala:729)
	at is.hail.sparkextras.ContextRDD$$anonfun$cmapPartitions$1$$anonfun$apply$9.apply(ContextRDD.scala:208)
	at is.hail.sparkextras.ContextRDD$$anonfun$cmapPartitions$1$$anonfun$apply$9.apply(ContextRDD.scala:208)
	at is.hail.utils.richUtils.RichContextRDD$$anonfun$cleanupRegions$1$$anonfun$2.apply(RichContextRDD.scala:57)
	at is.hail.utils.richUtils.RichContextRDD$$anonfun$cleanupRegions$1$$anonfun$2.apply(RichContextRDD.scala:57)
	at scala.collection.Iterator$$anon$12.nextCur(Iterator.scala:435)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:441)
	at is.hail.utils.richUtils.RichContextRDD$$anonfun$cleanupRegions$1$$anon$1.hasNext(RichContextRDD.scala:66)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
	at scala.collection.Iterator$class.foreach(Iterator.scala:891)
	at scala.collection.AbstractIterator.foreach(Iterator.scala:1334)
	at scala.collection.TraversableOnce$class.foldLeft(TraversableOnce.scala:157)
	at scala.collection.AbstractIterator.foldLeft(Iterator.scala:1334)
	at scala.collection.TraversableOnce$class.fold(TraversableOnce.scala:212)
	at scala.collection.AbstractIterator.fold(Iterator.scala:1334)
	at org.apache.spark.rdd.RDD$$anonfun$fold$1$$anonfun$22.apply(RDD.scala:1141)
	at org.apache.spark.rdd.RDD$$anonfun$fold$1$$anonfun$22.apply(RDD.scala:1141)
	at org.apache.spark.SparkContext$$anonfun$36.apply(SparkContext.scala:2157)
	at org.apache.spark.SparkContext$$anonfun$36.apply(SparkContext.scala:2157)
	at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:90)
	at org.apache.spark.scheduler.Task.run(Task.scala:123)
	at org.apache.spark.executor.Executor$TaskRunner$$anonfun$10.apply(Executor.scala:408)
	at org.apache.spark.util.Utils$.tryWithSafeFinally(Utils.scala:1360)
	at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:414)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
	at java.lang.Thread.run(Thread.java:748)
Caused by: java.nio.channels.ClosedChannelException
	at sun.nio.ch.FileChannelImpl.ensureOpen(FileChannelImpl.java:110)
	at sun.nio.ch.FileChannelImpl.read(FileChannelImpl.java:715)
	at htsjdk.samtools.reference.IndexedFastaSequenceFile.readFromPosition(IndexedFastaSequenceFile.java:148)
	at htsjdk.samtools.reference.AbstractIndexedFastaSequenceFile.getSubsequenceAt(AbstractIndexedFastaSequenceFile.java:204)
	... 74 more

Driver stacktrace:, was thrown by both
the consumer and the close method. I will throw the original.
2020-09-03 16:52:13 TaskSetManager: WARN: Lost task 4.10 in stage 2.0 (TID 220, jg3-w-0.c.maclab-ukbb.internal, executor 1): TaskKilled (Stage cancelled)
2020-09-03 16:52:13 root: ERROR: ClosedChannelException: null
From org.apache.spark.SparkException: Job aborted due to stage failure: Task 0 in stage 2.0 failed 20 times, most recent failure: Lost task 0.19 in stage 2.0 (TID 218, jg3-w-0.c.maclab-ukbb.internal, executor 1): htsjdk.samtools.SAMException: Unable to load chr19(58615273, 58617616) from /tmp/fasta-reader-FcVGkbAEQi5MCYD6x7hi1B.fasta
	at htsjdk.samtools.reference.AbstractIndexedFastaSequenceFile.getSubsequenceAt(AbstractIndexedFastaSequenceFile.java:207)
	at htsjdk.samtools.reference.IndexedFastaSequenceFile.getSubsequenceAt(IndexedFastaSequenceFile.java:49)
	at is.hail.io.reference.FASTAReader.getSequence(FASTAReader.scala:73)
	at is.hail.io.reference.FASTAReader.fillBlock(FASTAReader.scala:83)
	at is.hail.io.reference.FASTAReader.readBlock(FASTAReader.scala:93)
	at is.hail.io.reference.FASTAReader.readBlock(FASTAReader.scala:99)
	at is.hail.io.reference.FASTAReader.lookupGlobalPos(FASTAReader.scala:138)
	at is.hail.io.reference.FASTAReader.lookup(FASTAReader.scala:110)
	at is.hail.variant.ReferenceGenome.getSequence(ReferenceGenome.scala:357)
	at __C24Compiled.__m42getReferenceSequenceFromValidLocus(Unknown Source)
	at __C24Compiled.apply(Unknown Source)
	at is.hail.expr.ir.TableFilter$$anonfun$execute$2.apply(TableIR.scala:946)
	at is.hail.expr.ir.TableFilter$$anonfun$execute$2.apply(TableIR.scala:946)
	at is.hail.expr.ir.TableValue$$anonfun$3.apply(TableValue.scala:65)
	at is.hail.expr.ir.TableValue$$anonfun$3.apply(TableValue.scala:65)
	at is.hail.rvd.RVD$$anonfun$17$$anonfun$apply$2.apply$mcZJ$sp(RVD.scala:605)
	at is.hail.rvd.RVD$$anonfun$17$$anonfun$apply$2.apply(RVD.scala:604)
	at is.hail.rvd.RVD$$anonfun$17$$anonfun$apply$2.apply(RVD.scala:604)
	at scala.collection.Iterator$$anon$13.hasNext(Iterator.scala:464)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
	at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:409)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
	at is.hail.io.RichContextRDDLong$$anonfun$boundary$extension$2$$anon$1.hasNext(RichContextRDDRegionValue.scala:188)
	at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:409)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
	at scala.collection.Iterator$$anon$1.hasNext(Iterator.scala:1002)
	at is.hail.utils.richUtils.RichIterator$$anon$5.isValid(RichIterator.scala:30)
	at is.hail.utils.StagingIterator.isValid(FlipbookIterator.scala:48)
	at is.hail.utils.FlipbookIterator$$anon$9.setValue(FlipbookIterator.scala:327)
	at is.hail.utils.FlipbookIterator$$anon$9.<init>(FlipbookIterator.scala:344)
	at is.hail.utils.FlipbookIterator.leftJoinDistinct(FlipbookIterator.scala:323)
	at is.hail.annotations.OrderedRVIterator.leftIntervalJoinDistinct(OrderedRVIterator.scala:51)
	at is.hail.rvd.KeyedRVD$$anonfun$orderedLeftIntervalJoinDistinct$1$$anonfun$apply$2.apply(KeyedRVD.scala:131)
	at is.hail.rvd.KeyedRVD$$anonfun$orderedLeftIntervalJoinDistinct$1$$anonfun$apply$2.apply(KeyedRVD.scala:127)
	at is.hail.sparkextras.ContextRDD$$anonfun$czipPartitions$1$$anonfun$apply$24.apply(ContextRDD.scala:305)
	at is.hail.sparkextras.ContextRDD$$anonfun$czipPartitions$1$$anonfun$apply$24.apply(ContextRDD.scala:305)
	at is.hail.sparkextras.ContextRDD$$anonfun$cmapPartitions$1$$anonfun$apply$9$$anonfun$apply$10.apply(ContextRDD.scala:208)
	at is.hail.sparkextras.ContextRDD$$anonfun$cmapPartitions$1$$anonfun$apply$9$$anonfun$apply$10.apply(ContextRDD.scala:208)
	at scala.collection.Iterator$$anon$12.nextCur(Iterator.scala:435)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:441)
	at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:409)
	at scala.collection.Iterator$$anon$13.hasNext(Iterator.scala:462)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
	at is.hail.io.RichContextRDDLong$$anonfun$boundary$extension$2$$anon$1.hasNext(RichContextRDDRegionValue.scala:188)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
	at scala.collection.Iterator$class.foreach(Iterator.scala:891)
	at scala.collection.AbstractIterator.foreach(Iterator.scala:1334)
	at is.hail.rvd.RVD$$anonfun$23.apply(RVD.scala:731)
	at is.hail.rvd.RVD$$anonfun$23.apply(RVD.scala:729)
	at is.hail.sparkextras.ContextRDD$$anonfun$cmapPartitions$1$$anonfun$apply$9.apply(ContextRDD.scala:208)
	at is.hail.sparkextras.ContextRDD$$anonfun$cmapPartitions$1$$anonfun$apply$9.apply(ContextRDD.scala:208)
	at is.hail.utils.richUtils.RichContextRDD$$anonfun$cleanupRegions$1$$anonfun$2.apply(RichContextRDD.scala:57)
	at is.hail.utils.richUtils.RichContextRDD$$anonfun$cleanupRegions$1$$anonfun$2.apply(RichContextRDD.scala:57)
	at scala.collection.Iterator$$anon$12.nextCur(Iterator.scala:435)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:441)
	at is.hail.utils.richUtils.RichContextRDD$$anonfun$cleanupRegions$1$$anon$1.hasNext(RichContextRDD.scala:66)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
	at scala.collection.Iterator$class.foreach(Iterator.scala:891)
	at scala.collection.AbstractIterator.foreach(Iterator.scala:1334)
	at scala.collection.TraversableOnce$class.foldLeft(TraversableOnce.scala:157)
	at scala.collection.AbstractIterator.foldLeft(Iterator.scala:1334)
	at scala.collection.TraversableOnce$class.fold(TraversableOnce.scala:212)
	at scala.collection.AbstractIterator.fold(Iterator.scala:1334)
	at org.apache.spark.rdd.RDD$$anonfun$fold$1$$anonfun$22.apply(RDD.scala:1141)
	at org.apache.spark.rdd.RDD$$anonfun$fold$1$$anonfun$22.apply(RDD.scala:1141)
	at org.apache.spark.SparkContext$$anonfun$36.apply(SparkContext.scala:2157)
	at org.apache.spark.SparkContext$$anonfun$36.apply(SparkContext.scala:2157)
	at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:90)
	at org.apache.spark.scheduler.Task.run(Task.scala:123)
	at org.apache.spark.executor.Executor$TaskRunner$$anonfun$10.apply(Executor.scala:408)
	at org.apache.spark.util.Utils$.tryWithSafeFinally(Utils.scala:1360)
	at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:414)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
	at java.lang.Thread.run(Thread.java:748)
Caused by: java.nio.channels.ClosedChannelException
	at sun.nio.ch.FileChannelImpl.ensureOpen(FileChannelImpl.java:110)
	at sun.nio.ch.FileChannelImpl.read(FileChannelImpl.java:715)
	at htsjdk.samtools.reference.IndexedFastaSequenceFile.readFromPosition(IndexedFastaSequenceFile.java:148)
	at htsjdk.samtools.reference.AbstractIndexedFastaSequenceFile.getSubsequenceAt(AbstractIndexedFastaSequenceFile.java:204)
	... 74 more

Driver stacktrace:
	at org.apache.spark.scheduler.DAGScheduler.org$apache$spark$scheduler$DAGScheduler$$failJobAndIndependentStages(DAGScheduler.scala:1892)
	at org.apache.spark.scheduler.DAGScheduler$$anonfun$abortStage$1.apply(DAGScheduler.scala:1880)
	at org.apache.spark.scheduler.DAGScheduler$$anonfun$abortStage$1.apply(DAGScheduler.scala:1879)
	at scala.collection.mutable.ResizableArray$class.foreach(ResizableArray.scala:59)
	at scala.collection.mutable.ArrayBuffer.foreach(ArrayBuffer.scala:48)
	at org.apache.spark.scheduler.DAGScheduler.abortStage(DAGScheduler.scala:1879)
	at org.apache.spark.scheduler.DAGScheduler$$anonfun$handleTaskSetFailed$1.apply(DAGScheduler.scala:927)
	at org.apache.spark.scheduler.DAGScheduler$$anonfun$handleTaskSetFailed$1.apply(DAGScheduler.scala:927)
	at scala.Option.foreach(Option.scala:257)
	at org.apache.spark.scheduler.DAGScheduler.handleTaskSetFailed(DAGScheduler.scala:927)
	at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.doOnReceive(DAGScheduler.scala:2113)
	at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:2062)
	at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:2051)
	at org.apache.spark.util.EventLoop$$anon$1.run(EventLoop.scala:49)
	at org.apache.spark.scheduler.DAGScheduler.runJob(DAGScheduler.scala:738)
	at org.apache.spark.SparkContext.runJob(SparkContext.scala:2061)
	at org.apache.spark.SparkContext.runJob(SparkContext.scala:2158)
	at org.apache.spark.rdd.RDD$$anonfun$fold$1.apply(RDD.scala:1143)
	at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:151)
	at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:112)
	at org.apache.spark.rdd.RDD.withScope(RDD.scala:385)
	at org.apache.spark.rdd.RDD.fold(RDD.scala:1137)
	at is.hail.rvd.RVD.count(RVD.scala:735)
	at is.hail.expr.ir.Interpret$$anonfun$run$3.apply$mcJ$sp(Interpret.scala:815)
	at is.hail.expr.ir.Interpret$$anonfun$run$3.apply(Interpret.scala:815)
	at is.hail.expr.ir.Interpret$$anonfun$run$3.apply(Interpret.scala:815)
	at scala.Option.getOrElse(Option.scala:121)
	at is.hail.expr.ir.Interpret$.run(Interpret.scala:815)
	at is.hail.expr.ir.Interpret$.alreadyLowered(Interpret.scala:53)
	at is.hail.expr.ir.InterpretNonCompilable$.interpretAndCoerce$1(InterpretNonCompilable.scala:16)
	at is.hail.expr.ir.InterpretNonCompilable$.is$hail$expr$ir$InterpretNonCompilable$$rewrite$1(InterpretNonCompilable.scala:53)
	at is.hail.expr.ir.InterpretNonCompilable$.apply(InterpretNonCompilable.scala:58)
	at is.hail.expr.ir.lowering.InterpretNonCompilablePass$.transform(LoweringPass.scala:67)
	at is.hail.expr.ir.lowering.LoweringPass$$anonfun$apply$3$$anonfun$1.apply(LoweringPass.scala:15)
	at is.hail.expr.ir.lowering.LoweringPass$$anonfun$apply$3$$anonfun$1.apply(LoweringPass.scala:15)
	at is.hail.utils.ExecutionTimer.time(ExecutionTimer.scala:69)
	at is.hail.expr.ir.lowering.LoweringPass$$anonfun$apply$3.apply(LoweringPass.scala:15)
	at is.hail.expr.ir.lowering.LoweringPass$$anonfun$apply$3.apply(LoweringPass.scala:13)
	at is.hail.utils.ExecutionTimer.time(ExecutionTimer.scala:69)
	at is.hail.expr.ir.lowering.LoweringPass$class.apply(LoweringPass.scala:13)
	at is.hail.expr.ir.lowering.InterpretNonCompilablePass$.apply(LoweringPass.scala:62)
	at is.hail.expr.ir.lowering.LoweringPipeline$$anonfun$apply$1.apply(LoweringPipeline.scala:14)
	at is.hail.expr.ir.lowering.LoweringPipeline$$anonfun$apply$1.apply(LoweringPipeline.scala:12)
	at scala.collection.IndexedSeqOptimized$class.foreach(IndexedSeqOptimized.scala:33)
	at scala.collection.mutable.WrappedArray.foreach(WrappedArray.scala:35)
	at is.hail.expr.ir.lowering.LoweringPipeline.apply(LoweringPipeline.scala:12)
	at is.hail.expr.ir.CompileAndEvaluate$._apply(CompileAndEvaluate.scala:28)
	at is.hail.backend.spark.SparkBackend.is$hail$backend$spark$SparkBackend$$_execute(SparkBackend.scala:334)
	at is.hail.backend.spark.SparkBackend$$anonfun$execute$1.apply(SparkBackend.scala:321)
	at is.hail.backend.spark.SparkBackend$$anonfun$execute$1.apply(SparkBackend.scala:320)
	at is.hail.expr.ir.ExecuteContext$$anonfun$scoped$1.apply(ExecuteContext.scala:20)
	at is.hail.expr.ir.ExecuteContext$$anonfun$scoped$1.apply(ExecuteContext.scala:18)
	at is.hail.utils.package$.using(package.scala:609)
	at is.hail.annotations.Region$.scoped(Region.scala:18)
	at is.hail.expr.ir.ExecuteContext$.scoped(ExecuteContext.scala:18)
	at is.hail.backend.spark.SparkBackend.withExecuteContext(SparkBackend.scala:230)
	at is.hail.backend.spark.SparkBackend.execute(SparkBackend.scala:320)
	at is.hail.backend.spark.SparkBackend.executeJSON(SparkBackend.scala:349)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at py4j.reflection.MethodInvoker.invoke(MethodInvoker.java:244)
	at py4j.reflection.ReflectionEngine.invoke(ReflectionEngine.java:357)
	at py4j.Gateway.invoke(Gateway.java:282)
	at py4j.commands.AbstractCommand.invokeMethod(AbstractCommand.java:132)
	at py4j.commands.CallCommand.execute(CallCommand.java:79)
	at py4j.GatewayConnection.run(GatewayConnection.java:238)
	at java.lang.Thread.run(Thread.java:748)

htsjdk.samtools.SAMException: Unable to load chr19(58615273, 58617616) from /tmp/fasta-reader-FcVGkbAEQi5MCYD6x7hi1B.fasta
	at htsjdk.samtools.reference.AbstractIndexedFastaSequenceFile.getSubsequenceAt(AbstractIndexedFastaSequenceFile.java:207)
	at htsjdk.samtools.reference.IndexedFastaSequenceFile.getSubsequenceAt(IndexedFastaSequenceFile.java:49)
	at is.hail.io.reference.FASTAReader.getSequence(FASTAReader.scala:73)
	at is.hail.io.reference.FASTAReader.fillBlock(FASTAReader.scala:83)
	at is.hail.io.reference.FASTAReader.readBlock(FASTAReader.scala:93)
	at is.hail.io.reference.FASTAReader.readBlock(FASTAReader.scala:99)
	at is.hail.io.reference.FASTAReader.lookupGlobalPos(FASTAReader.scala:138)
	at is.hail.io.reference.FASTAReader.lookup(FASTAReader.scala:110)
	at is.hail.variant.ReferenceGenome.getSequence(ReferenceGenome.scala:357)
	at __C24Compiled.__m42getReferenceSequenceFromValidLocus(Unknown Source)
	at __C24Compiled.apply(Unknown Source)
	at is.hail.expr.ir.TableFilter$$anonfun$execute$2.apply(TableIR.scala:946)
	at is.hail.expr.ir.TableFilter$$anonfun$execute$2.apply(TableIR.scala:946)
	at is.hail.expr.ir.TableValue$$anonfun$3.apply(TableValue.scala:65)
	at is.hail.expr.ir.TableValue$$anonfun$3.apply(TableValue.scala:65)
	at is.hail.rvd.RVD$$anonfun$17$$anonfun$apply$2.apply$mcZJ$sp(RVD.scala:605)
	at is.hail.rvd.RVD$$anonfun$17$$anonfun$apply$2.apply(RVD.scala:604)
	at is.hail.rvd.RVD$$anonfun$17$$anonfun$apply$2.apply(RVD.scala:604)
	at scala.collection.Iterator$$anon$13.hasNext(Iterator.scala:464)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
	at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:409)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
	at is.hail.io.RichContextRDDLong$$anonfun$boundary$extension$2$$anon$1.hasNext(RichContextRDDRegionValue.scala:188)
	at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:409)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
	at scala.collection.Iterator$$anon$1.hasNext(Iterator.scala:1002)
	at is.hail.utils.richUtils.RichIterator$$anon$5.isValid(RichIterator.scala:30)
	at is.hail.utils.StagingIterator.isValid(FlipbookIterator.scala:48)
	at is.hail.utils.FlipbookIterator$$anon$9.setValue(FlipbookIterator.scala:327)
	at is.hail.utils.FlipbookIterator$$anon$9.<init>(FlipbookIterator.scala:344)
	at is.hail.utils.FlipbookIterator.leftJoinDistinct(FlipbookIterator.scala:323)
	at is.hail.annotations.OrderedRVIterator.leftIntervalJoinDistinct(OrderedRVIterator.scala:51)
	at is.hail.rvd.KeyedRVD$$anonfun$orderedLeftIntervalJoinDistinct$1$$anonfun$apply$2.apply(KeyedRVD.scala:131)
	at is.hail.rvd.KeyedRVD$$anonfun$orderedLeftIntervalJoinDistinct$1$$anonfun$apply$2.apply(KeyedRVD.scala:127)
	at is.hail.sparkextras.ContextRDD$$anonfun$czipPartitions$1$$anonfun$apply$24.apply(ContextRDD.scala:305)
	at is.hail.sparkextras.ContextRDD$$anonfun$czipPartitions$1$$anonfun$apply$24.apply(ContextRDD.scala:305)
	at is.hail.sparkextras.ContextRDD$$anonfun$cmapPartitions$1$$anonfun$apply$9$$anonfun$apply$10.apply(ContextRDD.scala:208)
	at is.hail.sparkextras.ContextRDD$$anonfun$cmapPartitions$1$$anonfun$apply$9$$anonfun$apply$10.apply(ContextRDD.scala:208)
	at scala.collection.Iterator$$anon$12.nextCur(Iterator.scala:435)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:441)
	at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:409)
	at scala.collection.Iterator$$anon$13.hasNext(Iterator.scala:462)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
	at is.hail.io.RichContextRDDLong$$anonfun$boundary$extension$2$$anon$1.hasNext(RichContextRDDRegionValue.scala:188)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
	at scala.collection.Iterator$class.foreach(Iterator.scala:891)
	at scala.collection.AbstractIterator.foreach(Iterator.scala:1334)
	at is.hail.rvd.RVD$$anonfun$23.apply(RVD.scala:731)
	at is.hail.rvd.RVD$$anonfun$23.apply(RVD.scala:729)
	at is.hail.sparkextras.ContextRDD$$anonfun$cmapPartitions$1$$anonfun$apply$9.apply(ContextRDD.scala:208)
	at is.hail.sparkextras.ContextRDD$$anonfun$cmapPartitions$1$$anonfun$apply$9.apply(ContextRDD.scala:208)
	at is.hail.utils.richUtils.RichContextRDD$$anonfun$cleanupRegions$1$$anonfun$2.apply(RichContextRDD.scala:57)
	at is.hail.utils.richUtils.RichContextRDD$$anonfun$cleanupRegions$1$$anonfun$2.apply(RichContextRDD.scala:57)
	at scala.collection.Iterator$$anon$12.nextCur(Iterator.scala:435)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:441)
	at is.hail.utils.richUtils.RichContextRDD$$anonfun$cleanupRegions$1$$anon$1.hasNext(RichContextRDD.scala:66)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
	at scala.collection.Iterator$class.foreach(Iterator.scala:891)
	at scala.collection.AbstractIterator.foreach(Iterator.scala:1334)
	at scala.collection.TraversableOnce$class.foldLeft(TraversableOnce.scala:157)
	at scala.collection.AbstractIterator.foldLeft(Iterator.scala:1334)
	at scala.collection.TraversableOnce$class.fold(TraversableOnce.scala:212)
	at scala.collection.AbstractIterator.fold(Iterator.scala:1334)
	at org.apache.spark.rdd.RDD$$anonfun$fold$1$$anonfun$22.apply(RDD.scala:1141)
	at org.apache.spark.rdd.RDD$$anonfun$fold$1$$anonfun$22.apply(RDD.scala:1141)
	at org.apache.spark.SparkContext$$anonfun$36.apply(SparkContext.scala:2157)
	at org.apache.spark.SparkContext$$anonfun$36.apply(SparkContext.scala:2157)
	at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:90)
	at org.apache.spark.scheduler.Task.run(Task.scala:123)
	at org.apache.spark.executor.Executor$TaskRunner$$anonfun$10.apply(Executor.scala:408)
	at org.apache.spark.util.Utils$.tryWithSafeFinally(Utils.scala:1360)
	at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:414)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
	at java.lang.Thread.run(Thread.java:748)

java.nio.channels.ClosedChannelException: null
	at sun.nio.ch.FileChannelImpl.ensureOpen(FileChannelImpl.java:110)
	at sun.nio.ch.FileChannelImpl.read(FileChannelImpl.java:715)
	at htsjdk.samtools.reference.IndexedFastaSequenceFile.readFromPosition(IndexedFastaSequenceFile.java:148)
	at htsjdk.samtools.reference.AbstractIndexedFastaSequenceFile.getSubsequenceAt(AbstractIndexedFastaSequenceFile.java:204)
	at htsjdk.samtools.reference.IndexedFastaSequenceFile.getSubsequenceAt(IndexedFastaSequenceFile.java:49)
	at is.hail.io.reference.FASTAReader.getSequence(FASTAReader.scala:73)
	at is.hail.io.reference.FASTAReader.fillBlock(FASTAReader.scala:83)
	at is.hail.io.reference.FASTAReader.readBlock(FASTAReader.scala:93)
	at is.hail.io.reference.FASTAReader.readBlock(FASTAReader.scala:99)
	at is.hail.io.reference.FASTAReader.lookupGlobalPos(FASTAReader.scala:138)
	at is.hail.io.reference.FASTAReader.lookup(FASTAReader.scala:110)
	at is.hail.variant.ReferenceGenome.getSequence(ReferenceGenome.scala:357)
	at __C24Compiled.__m42getReferenceSequenceFromValidLocus(Unknown Source)
	at __C24Compiled.apply(Unknown Source)
	at is.hail.expr.ir.TableFilter$$anonfun$execute$2.apply(TableIR.scala:946)
	at is.hail.expr.ir.TableFilter$$anonfun$execute$2.apply(TableIR.scala:946)
	at is.hail.expr.ir.TableValue$$anonfun$3.apply(TableValue.scala:65)
	at is.hail.expr.ir.TableValue$$anonfun$3.apply(TableValue.scala:65)
	at is.hail.rvd.RVD$$anonfun$17$$anonfun$apply$2.apply$mcZJ$sp(RVD.scala:605)
	at is.hail.rvd.RVD$$anonfun$17$$anonfun$apply$2.apply(RVD.scala:604)
	at is.hail.rvd.RVD$$anonfun$17$$anonfun$apply$2.apply(RVD.scala:604)
	at scala.collection.Iterator$$anon$13.hasNext(Iterator.scala:464)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
	at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:409)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
	at is.hail.io.RichContextRDDLong$$anonfun$boundary$extension$2$$anon$1.hasNext(RichContextRDDRegionValue.scala:188)
	at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:409)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
	at scala.collection.Iterator$$anon$1.hasNext(Iterator.scala:1002)
	at is.hail.utils.richUtils.RichIterator$$anon$5.isValid(RichIterator.scala:30)
	at is.hail.utils.StagingIterator.isValid(FlipbookIterator.scala:48)
	at is.hail.utils.FlipbookIterator$$anon$9.setValue(FlipbookIterator.scala:327)
	at is.hail.utils.FlipbookIterator$$anon$9.<init>(FlipbookIterator.scala:344)
	at is.hail.utils.FlipbookIterator.leftJoinDistinct(FlipbookIterator.scala:323)
	at is.hail.annotations.OrderedRVIterator.leftIntervalJoinDistinct(OrderedRVIterator.scala:51)
	at is.hail.rvd.KeyedRVD$$anonfun$orderedLeftIntervalJoinDistinct$1$$anonfun$apply$2.apply(KeyedRVD.scala:131)
	at is.hail.rvd.KeyedRVD$$anonfun$orderedLeftIntervalJoinDistinct$1$$anonfun$apply$2.apply(KeyedRVD.scala:127)
	at is.hail.sparkextras.ContextRDD$$anonfun$czipPartitions$1$$anonfun$apply$24.apply(ContextRDD.scala:305)
	at is.hail.sparkextras.ContextRDD$$anonfun$czipPartitions$1$$anonfun$apply$24.apply(ContextRDD.scala:305)
	at is.hail.sparkextras.ContextRDD$$anonfun$cmapPartitions$1$$anonfun$apply$9$$anonfun$apply$10.apply(ContextRDD.scala:208)
	at is.hail.sparkextras.ContextRDD$$anonfun$cmapPartitions$1$$anonfun$apply$9$$anonfun$apply$10.apply(ContextRDD.scala:208)
	at scala.collection.Iterator$$anon$12.nextCur(Iterator.scala:435)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:441)
	at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:409)
	at scala.collection.Iterator$$anon$13.hasNext(Iterator.scala:462)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
	at is.hail.io.RichContextRDDLong$$anonfun$boundary$extension$2$$anon$1.hasNext(RichContextRDDRegionValue.scala:188)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
	at scala.collection.Iterator$class.foreach(Iterator.scala:891)
	at scala.collection.AbstractIterator.foreach(Iterator.scala:1334)
	at is.hail.rvd.RVD$$anonfun$23.apply(RVD.scala:731)
	at is.hail.rvd.RVD$$anonfun$23.apply(RVD.scala:729)
	at is.hail.sparkextras.ContextRDD$$anonfun$cmapPartitions$1$$anonfun$apply$9.apply(ContextRDD.scala:208)
	at is.hail.sparkextras.ContextRDD$$anonfun$cmapPartitions$1$$anonfun$apply$9.apply(ContextRDD.scala:208)
	at is.hail.utils.richUtils.RichContextRDD$$anonfun$cleanupRegions$1$$anonfun$2.apply(RichContextRDD.scala:57)
	at is.hail.utils.richUtils.RichContextRDD$$anonfun$cleanupRegions$1$$anonfun$2.apply(RichContextRDD.scala:57)
	at scala.collection.Iterator$$anon$12.nextCur(Iterator.scala:435)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:441)
	at is.hail.utils.richUtils.RichContextRDD$$anonfun$cleanupRegions$1$$anon$1.hasNext(RichContextRDD.scala:66)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
	at scala.collection.Iterator$class.foreach(Iterator.scala:891)
	at scala.collection.AbstractIterator.foreach(Iterator.scala:1334)
	at scala.collection.TraversableOnce$class.foldLeft(TraversableOnce.scala:157)
	at scala.collection.AbstractIterator.foldLeft(Iterator.scala:1334)
	at scala.collection.TraversableOnce$class.fold(TraversableOnce.scala:212)
	at scala.collection.AbstractIterator.fold(Iterator.scala:1334)
	at org.apache.spark.rdd.RDD$$anonfun$fold$1$$anonfun$22.apply(RDD.scala:1141)
	at org.apache.spark.rdd.RDD$$anonfun$fold$1$$anonfun$22.apply(RDD.scala:1141)
	at org.apache.spark.SparkContext$$anonfun$36.apply(SparkContext.scala:2157)
	at org.apache.spark.SparkContext$$anonfun$36.apply(SparkContext.scala:2157)
	at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:90)
	at org.apache.spark.scheduler.Task.run(Task.scala:123)
	at org.apache.spark.executor.Executor$TaskRunner$$anonfun$10.apply(Executor.scala:408)
	at org.apache.spark.util.Utils$.tryWithSafeFinally(Utils.scala:1360)
	at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:414)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
	at java.lang.Thread.run(Thread.java:748)





2020-09-03 16:52:13 TaskSetManager: WARN: Lost task 2.12 in stage 2.0 (TID 221, jg3-w-0.c.maclab-ukbb.internal, executor 1): TaskKilled (Stage cancelled)
2020-09-03 16:52:16 TaskSetManager: WARN: Lost task 52.0 in stage 2.0 (TID 149, jg3-w-1.c.maclab-ukbb.internal, executor 3): TaskKilled (Stage cancelled)
2020-09-03 16:52:17 TaskSetManager: WARN: Lost task 59.0 in stage 2.0 (TID 156, jg3-w-1.c.maclab-ukbb.internal, executor 2): TaskKilled (Stage cancelled)
2020-09-03 16:52:18 TaskSetManager: WARN: Lost task 56.0 in stage 2.0 (TID 153, jg3-w-1.c.maclab-ukbb.internal, executor 3): TaskKilled (Stage cancelled)
2020-09-03 16:52:18 TaskSetManager: WARN: Lost task 54.0 in stage 2.0 (TID 151, jg3-w-1.c.maclab-ukbb.internal, executor 3): TaskKilled (Stage cancelled)
2020-09-03 16:52:18 TaskSetManager: WARN: Lost task 58.0 in stage 2.0 (TID 155, jg3-w-1.c.maclab-ukbb.internal, executor 3): TaskKilled (Stage cancelled)
2020-09-03 16:52:18 TaskSetManager: WARN: Lost task 57.0 in stage 2.0 (TID 154, jg3-w-1.c.maclab-ukbb.internal, executor 2): TaskKilled (Stage cancelled)
2020-09-03 16:52:18 TaskSetManager: WARN: Lost task 53.0 in stage 2.0 (TID 150, jg3-w-1.c.maclab-ukbb.internal, executor 2): TaskKilled (Stage cancelled)
2020-09-03 16:52:18 TaskSetManager: WARN: Lost task 55.0 in stage 2.0 (TID 152, jg3-w-1.c.maclab-ukbb.internal, executor 2): TaskKilled (Stage cancelled)
2020-09-03 16:52:18 YarnScheduler: INFO: Removed TaskSet 2.0, whose tasks have all completed, from pool default
2020-09-03 16:53:14 ExecutorAllocationManager: INFO: Request to remove executorIds: 1
2020-09-03 16:53:14 YarnClientSchedulerBackend: INFO: Requesting to kill executor(s) 1
2020-09-03 16:53:14 YarnClientSchedulerBackend: INFO: Actual list of executor(s) to be killed is 1
2020-09-03 16:53:14 ExecutorAllocationManager: INFO: Removing executor 1 because it has been idle for 60 seconds (new desired total will be 2)
2020-09-03 16:53:18 YarnSchedulerBackend$YarnDriverEndpoint: INFO: Disabling executor 1.
2020-09-03 16:53:18 DAGScheduler: INFO: Executor lost: 1 (epoch 1)
2020-09-03 16:53:18 BlockManagerMasterEndpoint: INFO: Trying to remove executor 1 from BlockManagerMaster.
2020-09-03 16:53:18 BlockManagerMasterEndpoint: INFO: Removing block manager BlockManagerId(1, jg3-w-0.c.maclab-ukbb.internal, 45095, None)
2020-09-03 16:53:18 BlockManagerMaster: INFO: Removed 1 successfully in removeExecutor
2020-09-03 16:53:18 YarnScheduler: INFO: Executor 1 on jg3-w-0.c.maclab-ukbb.internal killed by driver.
2020-09-03 16:53:18 ExecutorAllocationManager: INFO: Existing executor 1 has been removed (new total is 2)
2020-09-03 16:53:18 ExecutorAllocationManager: INFO: Request to remove executorIds: 3
2020-09-03 16:53:18 YarnClientSchedulerBackend: INFO: Requesting to kill executor(s) 3
2020-09-03 16:53:18 YarnClientSchedulerBackend: INFO: Actual list of executor(s) to be killed is 3
2020-09-03 16:53:18 ExecutorAllocationManager: INFO: Removing executor 3 because it has been idle for 60 seconds (new desired total will be 1)
2020-09-03 16:53:18 ExecutorAllocationManager: INFO: Request to remove executorIds: 2
2020-09-03 16:53:22 YarnSchedulerBackend$YarnDriverEndpoint: INFO: Disabling executor 3.
2020-09-03 16:53:22 DAGScheduler: INFO: Executor lost: 3 (epoch 1)
2020-09-03 16:53:22 BlockManagerMasterEndpoint: INFO: Trying to remove executor 3 from BlockManagerMaster.
2020-09-03 16:53:22 BlockManagerMasterEndpoint: INFO: Removing block manager BlockManagerId(3, jg3-w-1.c.maclab-ukbb.internal, 37701, None)
2020-09-03 16:53:22 BlockManagerMaster: INFO: Removed 3 successfully in removeExecutor
2020-09-03 16:53:22 YarnScheduler: INFO: Executor 3 on jg3-w-1.c.maclab-ukbb.internal killed by driver.
2020-09-03 16:53:22 ExecutorAllocationManager: INFO: Existing executor 3 has been removed (new total is 1)