2021-04-09 20:37:05 Hail: INFO: Running Hail version 0.2.64-1ef70187dc78 2021-04-09 20:37:06 SparkContext: WARN: Using an existing SparkContext; some configuration may not take effect. 2021-04-09 20:37:07 Hail: INFO: Using 2586 intervals with default whole-genome size 1200000 as partitioning for GVCF import 2021-04-09 20:37:07 Hail: INFO: GVCF combiner plan: Branch factor: 100 Batch size: 100 Combining 2 input files in 1 phases with 1 total jobs. Phase 1: 1 job corresponding to 1 final output file. 2021-04-09 20:37:07 Hail: INFO: Starting phase 1/1, merging 2 input GVCFs in 1 job. 2021-04-09 20:37:07 Hail: INFO: Starting phase 1/1, job 1/1 to create 1 merged file, corresponding to ~100.0% of total I/O. 2021-04-09 20:37:07 root: INFO: RegionPool: initialized for thread 17: Thread-5 2021-04-09 20:37:07 YarnSchedulerBackend$YarnDriverEndpoint: INFO: Registered executor NettyRpcEndpointRef(spark-client://Executor) (10.128.0.6:45196) with ID 1 2021-04-09 20:37:07 ExecutorAllocationManager: INFO: New executor 1 has registered (new total is 1) 2021-04-09 20:37:07 MemoryStore: INFO: Block broadcast_0 stored as values in memory (estimated size 2.3 MB, free 21.7 GB) 2021-04-09 20:37:07 YarnSchedulerBackend$YarnDriverEndpoint: INFO: Registered executor NettyRpcEndpointRef(spark-client://Executor) (10.128.0.8:48668) with ID 2 2021-04-09 20:37:07 ExecutorAllocationManager: INFO: New executor 2 has registered (new total is 2) 2021-04-09 20:37:07 BlockManagerMasterEndpoint: INFO: Registering block manager answer-w-1.us-central1-b.c.human-genetics-001.internal:45783 with 9.5 GB RAM, BlockManagerId(1, answer-w-1.us-central1-b.c.human-genetics-001.internal, 45783, None) 2021-04-09 20:37:07 BlockManagerMasterEndpoint: INFO: Registering block manager answer-w-0.us-central1-b.c.human-genetics-001.internal:39767 with 9.5 GB RAM, BlockManagerId(2, answer-w-0.us-central1-b.c.human-genetics-001.internal, 39767, None) 2021-04-09 20:37:08 MemoryStore: INFO: Block broadcast_0_piece0 stored as bytes in memory (estimated size 123.7 KB, free 21.7 GB) 2021-04-09 20:37:08 BlockManagerInfo: INFO: Added broadcast_0_piece0 in memory on answer-m.us-central1-b.c.human-genetics-001.internal:42437 (size: 123.7 KB, free: 21.7 GB) 2021-04-09 20:37:08 SparkContext: INFO: Created broadcast 0 from broadcast at SparkBackend.scala:259 2021-04-09 20:37:08 root: INFO: RegionPool: FREE: 64.0K allocated (64.0K blocks / 0 chunks), regions.size = 1, 0 current java objects, 0 max java objects, thread 17: Thread-5 2021-04-09 20:37:08 root: INFO: timing SparkBackend.parse_value_ir total 1.252s self 1.252s children 0.000ms %children 0.00% 2021-04-09 20:37:08 root: INFO: RegionPool: initialized for thread 17: Thread-5 2021-04-09 20:37:08 root: INFO: starting execution of query hail_query_1 of initial size 15 2021-04-09 20:37:08 root: INFO: optimize optimize: relationalLowerer, initial IR: before: IR size 15: (ToArray (StreamMap __uid_3 (ToStream False (Literal Array[Interval[Locus(GRCh38)]] )) (ApplySpecial Interval () Interval[Struct{locus:Locus(GRCh38)}] (MakeStruct (locus (ApplySpecial start () Locus(GRCh38) (Ref __uid_3)))) (MakeStruct (locus (ApplySpecial end () Locus(GRCh38) (Ref __uid_3)))) (Apply includesStart () Boolean (Ref __uid_3)) (Apply includesEnd () Boolean (Ref __uid_3))))) 2021-04-09 20:37:08 root: INFO: optimize optimize: relationalLowerer, initial IR: after: IR size 15: (ToArray (StreamMap __iruid_2 (ToStream False (Literal Array[Interval[Locus(GRCh38)]] )) (ApplySpecial Interval () Interval[Struct{locus:Locus(GRCh38)}] (MakeStruct (locus (ApplySpecial start () Locus(GRCh38) (Ref __iruid_2)))) (MakeStruct (locus (ApplySpecial end () Locus(GRCh38) (Ref __iruid_2)))) (Apply includesStart () Boolean (Ref __iruid_2)) (Apply includesEnd () Boolean (Ref __iruid_2))))) 2021-04-09 20:37:08 root: INFO: optimize optimize: relationalLowerer, after LowerMatrixToTable: before: IR size 15: (ToArray (StreamMap __iruid_2 (ToStream False (Literal Array[Interval[Locus(GRCh38)]] )) (ApplySpecial Interval () Interval[Struct{locus:Locus(GRCh38)}] (MakeStruct (locus (ApplySpecial start () Locus(GRCh38) (Ref __iruid_2)))) (MakeStruct (locus (ApplySpecial end () Locus(GRCh38) (Ref __iruid_2)))) (Apply includesStart () Boolean (Ref __iruid_2)) (Apply includesEnd () Boolean (Ref __iruid_2))))) 2021-04-09 20:37:08 root: INFO: optimize optimize: relationalLowerer, after LowerMatrixToTable: after: IR size 15: (ToArray (StreamMap __iruid_5 (ToStream False (Literal Array[Interval[Locus(GRCh38)]] )) (ApplySpecial Interval () Interval[Struct{locus:Locus(GRCh38)}] (MakeStruct (locus (ApplySpecial start () Locus(GRCh38) (Ref __iruid_5)))) (MakeStruct (locus (ApplySpecial end () Locus(GRCh38) (Ref __iruid_5)))) (Apply includesStart () Boolean (Ref __iruid_5)) (Apply includesEnd () Boolean (Ref __iruid_5))))) 2021-04-09 20:37:08 root: INFO: optimize optimize: relationalLowerer, after InterpretNonCompilable: before: IR size 15: (ToArray (StreamMap __iruid_5 (ToStream False (Literal Array[Interval[Locus(GRCh38)]] )) (ApplySpecial Interval () Interval[Struct{locus:Locus(GRCh38)}] (MakeStruct (locus (ApplySpecial start () Locus(GRCh38) (Ref __iruid_5)))) (MakeStruct (locus (ApplySpecial end () Locus(GRCh38) (Ref __iruid_5)))) (Apply includesStart () Boolean (Ref __iruid_5)) (Apply includesEnd () Boolean (Ref __iruid_5))))) 2021-04-09 20:37:08 root: INFO: optimize optimize: relationalLowerer, after InterpretNonCompilable: after: IR size 15: (ToArray (StreamMap __iruid_8 (ToStream False (Literal Array[Interval[Locus(GRCh38)]] )) (ApplySpecial Interval () Interval[Struct{locus:Locus(GRCh38)}] (MakeStruct (locus (ApplySpecial start () Locus(GRCh38) (Ref __iruid_8)))) (MakeStruct (locus (ApplySpecial end () Locus(GRCh38) (Ref __iruid_8)))) (Apply includesStart () Boolean (Ref __iruid_8)) (Apply includesEnd () Boolean (Ref __iruid_8))))) 2021-04-09 20:37:08 root: INFO: optimize optimize: compileLowerer, initial IR: before: IR size 16: (MakeTuple (0) (ToArray (StreamMap __iruid_8 (ToStream False (Literal Array[Interval[Locus(GRCh38)]] )) (ApplySpecial Interval () Interval[Struct{locus:Locus(GRCh38)}] (MakeStruct (locus (ApplySpecial start () Locus(GRCh38) (Ref __iruid_8)))) (MakeStruct (locus (ApplySpecial end () Locus(GRCh38) (Ref __iruid_8)))) (Apply includesStart () Boolean (Ref __iruid_8)) (Apply includesEnd () Boolean (Ref __iruid_8)))))) 2021-04-09 20:37:09 root: INFO: optimize optimize: compileLowerer, initial IR: after: IR size 16: (MakeTuple (0) (ToArray (StreamMap __iruid_11 (ToStream False (Literal Array[Interval[Locus(GRCh38)]] )) (ApplySpecial Interval () Interval[Struct{locus:Locus(GRCh38)}] (MakeStruct (locus (ApplySpecial start () Locus(GRCh38) (Ref __iruid_11)))) (MakeStruct (locus (ApplySpecial end () Locus(GRCh38) (Ref __iruid_11)))) (Apply includesStart () Boolean (Ref __iruid_11)) (Apply includesEnd () Boolean (Ref __iruid_11)))))) 2021-04-09 20:37:09 root: INFO: optimize optimize: compileLowerer, after InlineApplyIR: before: IR size 16: (MakeTuple (0) (ToArray (StreamMap __iruid_11 (ToStream False (Literal Array[Interval[Locus(GRCh38)]] )) (ApplySpecial Interval () Interval[Struct{locus:Locus(GRCh38)}] (MakeStruct (locus (ApplySpecial start () Locus(GRCh38) (Ref __iruid_11)))) (MakeStruct (locus (ApplySpecial end () Locus(GRCh38) (Ref __iruid_11)))) (Apply includesStart () Boolean (Ref __iruid_11)) (Apply includesEnd () Boolean (Ref __iruid_11)))))) 2021-04-09 20:37:09 root: INFO: optimize optimize: compileLowerer, after InlineApplyIR: after: IR size 16: (MakeTuple (0) (ToArray (StreamMap __iruid_14 (ToStream False (Literal Array[Interval[Locus(GRCh38)]] )) (ApplySpecial Interval () Interval[Struct{locus:Locus(GRCh38)}] (MakeStruct (locus (ApplySpecial start () Locus(GRCh38) (Ref __iruid_14)))) (MakeStruct (locus (ApplySpecial end () Locus(GRCh38) (Ref __iruid_14)))) (Apply includesStart () Boolean (Ref __iruid_14)) (Apply includesEnd () Boolean (Ref __iruid_14)))))) 2021-04-09 20:37:09 root: INFO: optimize optimize: compileLowerer, after LowerArrayAggsToRunAggs: before: IR size 16: (MakeTuple (0) (ToArray (StreamMap __iruid_14 (ToStream False (Literal Array[Interval[Locus(GRCh38)]] )) (ApplySpecial Interval () Interval[Struct{locus:Locus(GRCh38)}] (MakeStruct (locus (ApplySpecial start () Locus(GRCh38) (Ref __iruid_14)))) (MakeStruct (locus (ApplySpecial end () Locus(GRCh38) (Ref __iruid_14)))) (Apply includesStart () Boolean (Ref __iruid_14)) (Apply includesEnd () Boolean (Ref __iruid_14)))))) 2021-04-09 20:37:09 root: INFO: optimize optimize: compileLowerer, after LowerArrayAggsToRunAggs: after: IR size 16: (MakeTuple (0) (ToArray (StreamMap __iruid_17 (ToStream False (Literal Array[Interval[Locus(GRCh38)]] )) (ApplySpecial Interval () Interval[Struct{locus:Locus(GRCh38)}] (MakeStruct (locus (ApplySpecial start () Locus(GRCh38) (Ref __iruid_17)))) (MakeStruct (locus (ApplySpecial end () Locus(GRCh38) (Ref __iruid_17)))) (Apply includesStart () Boolean (Ref __iruid_17)) (Apply includesEnd () Boolean (Ref __iruid_17)))))) 2021-04-09 20:37:09 root: INFO: encoder cache miss (0 hits, 1 misses, 0.000) 2021-04-09 20:37:09 root: INFO: instruction count: 3: __C26etypeEncode. 2021-04-09 20:37:09 root: INFO: instruction count: 5: __C26etypeEncode.apply 2021-04-09 20:37:09 root: INFO: instruction count: 13: __C26etypeEncode.__m27ENCODE_r_tuple_of_r_array_of_r_interval_of_r_locusEND_TO_r_struct_of_r_array_of_r_struct_of_r_struct_of_r_binaryANDr_int32ENDANDr_struct_of_r_binaryANDr_int32ENDANDr_boolANDr_boolENDEND 2021-04-09 20:37:09 root: INFO: instruction count: 45: __C26etypeEncode.__m28ENCODE_r_array_of_r_interval_of_r_locus_TO_r_array_of_r_struct_of_r_struct_of_r_binaryANDr_int32ENDANDr_struct_of_r_binaryANDr_int32ENDANDr_boolANDr_boolEND 2021-04-09 20:37:09 root: INFO: instruction count: 51: __C26etypeEncode.__m29ENCODE_r_interval_of_r_locus_TO_r_struct_of_r_struct_of_r_binaryANDr_int32ENDANDr_struct_of_r_binaryANDr_int32ENDANDr_boolANDr_boolEND 2021-04-09 20:37:09 root: INFO: instruction count: 39: __C26etypeEncode.__m30ENCODE_r_locus_TO_r_struct_of_r_binaryANDr_int32END 2021-04-09 20:37:09 root: INFO: instruction count: 18: __C26etypeEncode.__m31ENCODE_r_string_TO_r_binary 2021-04-09 20:37:09 root: INFO: instruction count: 6: __C26etypeEncode.__m32ENCODE_r_int32_TO_r_int32 2021-04-09 20:37:09 root: INFO: instruction count: 6: __C26etypeEncode.__m33ENCODE_r_bool_TO_r_bool 2021-04-09 20:37:09 MemoryStore: INFO: Block broadcast_1 stored as values in memory (estimated size 67.7 KB, free 21.7 GB) 2021-04-09 20:37:09 MemoryStore: INFO: Block broadcast_1_piece0 stored as bytes in memory (estimated size 31.0 KB, free 21.7 GB) 2021-04-09 20:37:09 BlockManagerInfo: INFO: Added broadcast_1_piece0 in memory on answer-m.us-central1-b.c.human-genetics-001.internal:42437 (size: 31.0 KB, free: 21.7 GB) 2021-04-09 20:37:09 SparkContext: INFO: Created broadcast 1 from broadcast at SparkBackend.scala:259 2021-04-09 20:37:09 root: INFO: instruction count: 3: __C1Compiled. 2021-04-09 20:37:09 root: INFO: instruction count: 297: __C1Compiled.apply 2021-04-09 20:37:09 root: INFO: instruction count: 8: __C1Compiled.__m15includesStart 2021-04-09 20:37:09 root: INFO: instruction count: 8: __C1Compiled.__m16includesEnd 2021-04-09 20:37:09 root: INFO: instruction count: 9: __C1Compiled.setPartitionIndex 2021-04-09 20:37:09 root: INFO: instruction count: 4: __C1Compiled.addPartitionRegion 2021-04-09 20:37:09 root: INFO: instruction count: 4: __C1Compiled.setPool 2021-04-09 20:37:09 root: INFO: instruction count: 50: __C1Compiled.addLiterals 2021-04-09 20:37:09 root: INFO: instruction count: 23: __C1Compiled.__m19DECODE_r_struct_of_r_array_of_r_struct_of_r_struct_of_r_binaryANDr_int32ENDANDr_struct_of_r_binaryANDr_int32ENDANDr_boolANDr_boolENDEND_TO_r_tuple_of_r_array_of_r_interval_of_r_locusEND 2021-04-09 20:37:09 root: INFO: instruction count: 64: __C1Compiled.__m20INPLACE_DECODE_r_array_of_r_struct_of_r_struct_of_r_binaryANDr_int32ENDANDr_struct_of_r_binaryANDr_int32ENDANDr_boolANDr_boolEND_TO_r_array_of_r_interval_of_r_locus 2021-04-09 20:37:09 root: INFO: instruction count: 36: __C1Compiled.__m21INPLACE_DECODE_r_struct_of_r_struct_of_r_binaryANDr_int32ENDANDr_struct_of_r_binaryANDr_int32ENDANDr_boolANDr_boolEND_TO_r_interval_of_r_locus 2021-04-09 20:37:09 root: INFO: instruction count: 22: __C1Compiled.__m22INPLACE_DECODE_r_struct_of_r_binaryANDr_int32END_TO_r_locus 2021-04-09 20:37:09 root: INFO: instruction count: 33: __C1Compiled.__m23INPLACE_DECODE_r_binary_TO_r_string 2021-04-09 20:37:09 root: INFO: instruction count: 10: __C1Compiled.__m24INPLACE_DECODE_r_int32_TO_r_int32 2021-04-09 20:37:09 root: INFO: instruction count: 10: __C1Compiled.__m25INPLACE_DECODE_r_bool_TO_r_bool 2021-04-09 20:37:09 root: INFO: RegionPool: REPORT_THRESHOLD: 289.6K allocated (128.0K blocks / 161.6K chunks), regions.size = 2, 0 current java objects, 0 max java objects, thread 17: Thread-5 2021-04-09 20:37:09 root: INFO: finished execution of query hail_query_1 2021-04-09 20:37:09 root: INFO: RegionPool: FREE: 417.6K allocated (256.0K blocks / 161.6K chunks), regions.size = 2, 0 current java objects, 0 max java objects, thread 17: Thread-5 2021-04-09 20:37:09 root: INFO: timing SparkBackend.executeJSON total 1.162s self 114.823ms children 1.047s %children 90.12% 2021-04-09 20:37:09 root: INFO: timing SparkBackend.executeJSON/optimize: relationalLowerer, initial IR total 216.751ms self 24.382ms children 192.368ms %children 88.75% 2021-04-09 20:37:09 root: INFO: timing SparkBackend.executeJSON/optimize: relationalLowerer, initial IR/Verify total 1.001ms self 1.001ms children 0.000ms %children 0.00% 2021-04-09 20:37:09 root: INFO: timing SparkBackend.executeJSON/optimize: relationalLowerer, initial IR/LoweringTransformation total 191.326ms self 89.311ms children 102.015ms %children 53.32% 2021-04-09 20:37:09 root: INFO: timing SparkBackend.executeJSON/optimize: relationalLowerer, initial IR/LoweringTransformation/Optimize total 102.015ms self 3.656ms children 98.359ms %children 96.42% 2021-04-09 20:37:09 root: INFO: timing SparkBackend.executeJSON/optimize: relationalLowerer, initial IR/LoweringTransformation/Optimize/FoldConstants total 11.006ms self 11.006ms children 0.000ms %children 0.00% 2021-04-09 20:37:09 root: INFO: timing SparkBackend.executeJSON/optimize: relationalLowerer, initial IR/LoweringTransformation/Optimize/ExtractIntervalFilters total 12.292ms self 12.292ms children 0.000ms %children 0.00% 2021-04-09 20:37:09 root: INFO: timing SparkBackend.executeJSON/optimize: relationalLowerer, initial IR/LoweringTransformation/Optimize/Simplify total 11.524ms self 11.524ms children 0.000ms %children 0.00% 2021-04-09 20:37:09 root: INFO: timing SparkBackend.executeJSON/optimize: relationalLowerer, initial IR/LoweringTransformation/Optimize/ForwardLets total 23.024ms self 23.024ms children 0.000ms %children 0.00% 2021-04-09 20:37:09 root: INFO: timing SparkBackend.executeJSON/optimize: relationalLowerer, initial IR/LoweringTransformation/Optimize/ForwardRelationalLets total 2.481ms self 2.481ms children 0.000ms %children 0.00% 2021-04-09 20:37:09 root: INFO: timing SparkBackend.executeJSON/optimize: relationalLowerer, initial IR/LoweringTransformation/Optimize/PruneDeadFields total 29.362ms self 29.362ms children 0.000ms %children 0.00% 2021-04-09 20:37:09 root: INFO: timing SparkBackend.executeJSON/optimize: relationalLowerer, initial IR/LoweringTransformation/Optimize/FoldConstants total 1.080ms self 1.080ms children 0.000ms %children 0.00% 2021-04-09 20:37:09 root: INFO: timing SparkBackend.executeJSON/optimize: relationalLowerer, initial IR/LoweringTransformation/Optimize/ExtractIntervalFilters total 0.083ms self 0.083ms children 0.000ms %children 0.00% 2021-04-09 20:37:09 root: INFO: timing SparkBackend.executeJSON/optimize: relationalLowerer, initial IR/LoweringTransformation/Optimize/Simplify total 0.211ms self 0.211ms children 0.000ms %children 0.00% 2021-04-09 20:37:09 root: INFO: timing SparkBackend.executeJSON/optimize: relationalLowerer, initial IR/LoweringTransformation/Optimize/ForwardLets total 1.562ms self 1.562ms children 0.000ms %children 0.00% 2021-04-09 20:37:09 root: INFO: timing SparkBackend.executeJSON/optimize: relationalLowerer, initial IR/LoweringTransformation/Optimize/ForwardRelationalLets total 0.167ms self 0.167ms children 0.000ms %children 0.00% 2021-04-09 20:37:09 root: INFO: timing SparkBackend.executeJSON/optimize: relationalLowerer, initial IR/LoweringTransformation/Optimize/PruneDeadFields total 1.126ms self 1.126ms children 0.000ms %children 0.00% 2021-04-09 20:37:09 root: INFO: timing SparkBackend.executeJSON/optimize: relationalLowerer, initial IR/LoweringTransformation/Optimize/FoldConstants total 0.831ms self 0.831ms children 0.000ms %children 0.00% 2021-04-09 20:37:09 root: INFO: timing SparkBackend.executeJSON/optimize: relationalLowerer, initial IR/LoweringTransformation/Optimize/ExtractIntervalFilters total 0.120ms self 0.120ms children 0.000ms %children 0.00% 2021-04-09 20:37:09 root: INFO: timing SparkBackend.executeJSON/optimize: relationalLowerer, initial IR/LoweringTransformation/Optimize/Simplify total 0.187ms self 0.187ms children 0.000ms %children 0.00% 2021-04-09 20:37:09 root: INFO: timing SparkBackend.executeJSON/optimize: relationalLowerer, initial IR/LoweringTransformation/Optimize/ForwardLets total 1.953ms self 1.953ms children 0.000ms %children 0.00% 2021-04-09 20:37:09 root: INFO: timing SparkBackend.executeJSON/optimize: relationalLowerer, initial IR/LoweringTransformation/Optimize/ForwardRelationalLets total 0.109ms self 0.109ms children 0.000ms %children 0.00% 2021-04-09 20:37:09 root: INFO: timing SparkBackend.executeJSON/optimize: relationalLowerer, initial IR/LoweringTransformation/Optimize/PruneDeadFields total 1.239ms self 1.239ms children 0.000ms %children 0.00% 2021-04-09 20:37:09 root: INFO: timing SparkBackend.executeJSON/optimize: relationalLowerer, initial IR/Verify total 0.042ms self 0.042ms children 0.000ms %children 0.00% 2021-04-09 20:37:09 root: INFO: timing SparkBackend.executeJSON/LowerMatrixToTable total 13.076ms self 0.023ms children 13.053ms %children 99.82% 2021-04-09 20:37:09 root: INFO: timing SparkBackend.executeJSON/LowerMatrixToTable/Verify total 0.020ms self 0.020ms children 0.000ms %children 0.00% 2021-04-09 20:37:09 root: INFO: timing SparkBackend.executeJSON/LowerMatrixToTable/LoweringTransformation total 12.951ms self 12.951ms children 0.000ms %children 0.00% 2021-04-09 20:37:09 root: INFO: timing SparkBackend.executeJSON/LowerMatrixToTable/Verify total 0.082ms self 0.082ms children 0.000ms %children 0.00% 2021-04-09 20:37:09 root: INFO: timing SparkBackend.executeJSON/optimize: relationalLowerer, after LowerMatrixToTable total 25.362ms self 0.018ms children 25.344ms %children 99.93% 2021-04-09 20:37:09 root: INFO: timing SparkBackend.executeJSON/optimize: relationalLowerer, after LowerMatrixToTable/Verify total 0.019ms self 0.019ms children 0.000ms %children 0.00% 2021-04-09 20:37:09 root: INFO: timing SparkBackend.executeJSON/optimize: relationalLowerer, after LowerMatrixToTable/LoweringTransformation total 25.299ms self 7.256ms children 18.043ms %children 71.32% 2021-04-09 20:37:09 root: INFO: timing SparkBackend.executeJSON/optimize: relationalLowerer, after LowerMatrixToTable/LoweringTransformation/Optimize total 18.043ms self 0.141ms children 17.903ms %children 99.22% 2021-04-09 20:37:09 root: INFO: timing SparkBackend.executeJSON/optimize: relationalLowerer, after LowerMatrixToTable/LoweringTransformation/Optimize/FoldConstants total 0.376ms self 0.376ms children 0.000ms %children 0.00% 2021-04-09 20:37:09 root: INFO: timing SparkBackend.executeJSON/optimize: relationalLowerer, after LowerMatrixToTable/LoweringTransformation/Optimize/ExtractIntervalFilters total 0.130ms self 0.130ms children 0.000ms %children 0.00% 2021-04-09 20:37:09 root: INFO: timing SparkBackend.executeJSON/optimize: relationalLowerer, after LowerMatrixToTable/LoweringTransformation/Optimize/Simplify total 0.212ms self 0.212ms children 0.000ms %children 0.00% 2021-04-09 20:37:09 root: INFO: timing SparkBackend.executeJSON/optimize: relationalLowerer, after LowerMatrixToTable/LoweringTransformation/Optimize/ForwardLets total 3.198ms self 3.198ms children 0.000ms %children 0.00% 2021-04-09 20:37:09 root: INFO: timing SparkBackend.executeJSON/optimize: relationalLowerer, after LowerMatrixToTable/LoweringTransformation/Optimize/ForwardRelationalLets total 0.141ms self 0.141ms children 0.000ms %children 0.00% 2021-04-09 20:37:09 root: INFO: timing SparkBackend.executeJSON/optimize: relationalLowerer, after LowerMatrixToTable/LoweringTransformation/Optimize/PruneDeadFields total 1.156ms self 1.156ms children 0.000ms %children 0.00% 2021-04-09 20:37:09 root: INFO: timing SparkBackend.executeJSON/optimize: relationalLowerer, after LowerMatrixToTable/LoweringTransformation/Optimize/FoldConstants total 0.791ms self 0.791ms children 0.000ms %children 0.00% 2021-04-09 20:37:09 root: INFO: timing SparkBackend.executeJSON/optimize: relationalLowerer, after LowerMatrixToTable/LoweringTransformation/Optimize/ExtractIntervalFilters total 0.082ms self 0.082ms children 0.000ms %children 0.00% 2021-04-09 20:37:09 root: INFO: timing SparkBackend.executeJSON/optimize: relationalLowerer, after LowerMatrixToTable/LoweringTransformation/Optimize/Simplify total 0.214ms self 0.214ms children 0.000ms %children 0.00% 2021-04-09 20:37:09 root: INFO: timing SparkBackend.executeJSON/optimize: relationalLowerer, after LowerMatrixToTable/LoweringTransformation/Optimize/ForwardLets total 1.208ms self 1.208ms children 0.000ms %children 0.00% 2021-04-09 20:37:09 root: INFO: timing SparkBackend.executeJSON/optimize: relationalLowerer, after LowerMatrixToTable/LoweringTransformation/Optimize/ForwardRelationalLets total 0.160ms self 0.160ms children 0.000ms %children 0.00% 2021-04-09 20:37:09 root: INFO: timing SparkBackend.executeJSON/optimize: relationalLowerer, after LowerMatrixToTable/LoweringTransformation/Optimize/PruneDeadFields total 2.728ms self 2.728ms children 0.000ms %children 0.00% 2021-04-09 20:37:09 root: INFO: timing SparkBackend.executeJSON/optimize: relationalLowerer, after LowerMatrixToTable/LoweringTransformation/Optimize/FoldConstants total 1.339ms self 1.339ms children 0.000ms %children 0.00% 2021-04-09 20:37:09 root: INFO: timing SparkBackend.executeJSON/optimize: relationalLowerer, after LowerMatrixToTable/LoweringTransformation/Optimize/ExtractIntervalFilters total 0.094ms self 0.094ms children 0.000ms %children 0.00% 2021-04-09 20:37:09 root: INFO: timing SparkBackend.executeJSON/optimize: relationalLowerer, after LowerMatrixToTable/LoweringTransformation/Optimize/Simplify total 0.189ms self 0.189ms children 0.000ms %children 0.00% 2021-04-09 20:37:09 root: INFO: timing SparkBackend.executeJSON/optimize: relationalLowerer, after LowerMatrixToTable/LoweringTransformation/Optimize/ForwardLets total 1.497ms self 1.497ms children 0.000ms %children 0.00% 2021-04-09 20:37:09 root: INFO: timing SparkBackend.executeJSON/optimize: relationalLowerer, after LowerMatrixToTable/LoweringTransformation/Optimize/ForwardRelationalLets total 0.229ms self 0.229ms children 0.000ms %children 0.00% 2021-04-09 20:37:09 root: INFO: timing SparkBackend.executeJSON/optimize: relationalLowerer, after LowerMatrixToTable/LoweringTransformation/Optimize/PruneDeadFields total 4.160ms self 4.160ms children 0.000ms %children 0.00% 2021-04-09 20:37:09 root: INFO: timing SparkBackend.executeJSON/optimize: relationalLowerer, after LowerMatrixToTable/Verify total 0.025ms self 0.025ms children 0.000ms %children 0.00% 2021-04-09 20:37:09 root: INFO: timing SparkBackend.executeJSON/InterpretNonCompilable total 4.044ms self 0.023ms children 4.021ms %children 99.43% 2021-04-09 20:37:09 root: INFO: timing SparkBackend.executeJSON/InterpretNonCompilable/Verify total 0.066ms self 0.066ms children 0.000ms %children 0.00% 2021-04-09 20:37:09 root: INFO: timing SparkBackend.executeJSON/InterpretNonCompilable/LoweringTransformation total 3.385ms self 3.385ms children 0.000ms %children 0.00% 2021-04-09 20:37:09 root: INFO: timing SparkBackend.executeJSON/InterpretNonCompilable/Verify total 0.569ms self 0.569ms children 0.000ms %children 0.00% 2021-04-09 20:37:09 root: INFO: timing SparkBackend.executeJSON/optimize: relationalLowerer, after InterpretNonCompilable total 22.524ms self 0.021ms children 22.503ms %children 99.90% 2021-04-09 20:37:09 root: INFO: timing SparkBackend.executeJSON/optimize: relationalLowerer, after InterpretNonCompilable/Verify total 0.020ms self 0.020ms children 0.000ms %children 0.00% 2021-04-09 20:37:09 root: INFO: timing SparkBackend.executeJSON/optimize: relationalLowerer, after InterpretNonCompilable/LoweringTransformation total 22.450ms self 6.235ms children 16.215ms %children 72.23% 2021-04-09 20:37:09 root: INFO: timing SparkBackend.executeJSON/optimize: relationalLowerer, after InterpretNonCompilable/LoweringTransformation/Optimize total 16.215ms self 0.130ms children 16.086ms %children 99.20% 2021-04-09 20:37:09 root: INFO: timing SparkBackend.executeJSON/optimize: relationalLowerer, after InterpretNonCompilable/LoweringTransformation/Optimize/FoldConstants total 0.374ms self 0.374ms children 0.000ms %children 0.00% 2021-04-09 20:37:09 root: INFO: timing SparkBackend.executeJSON/optimize: relationalLowerer, after InterpretNonCompilable/LoweringTransformation/Optimize/ExtractIntervalFilters total 0.155ms self 0.155ms children 0.000ms %children 0.00% 2021-04-09 20:37:09 root: INFO: timing SparkBackend.executeJSON/optimize: relationalLowerer, after InterpretNonCompilable/LoweringTransformation/Optimize/Simplify total 0.230ms self 0.230ms children 0.000ms %children 0.00% 2021-04-09 20:37:09 root: INFO: timing SparkBackend.executeJSON/optimize: relationalLowerer, after InterpretNonCompilable/LoweringTransformation/Optimize/ForwardLets total 1.491ms self 1.491ms children 0.000ms %children 0.00% 2021-04-09 20:37:09 root: INFO: timing SparkBackend.executeJSON/optimize: relationalLowerer, after InterpretNonCompilable/LoweringTransformation/Optimize/ForwardRelationalLets total 0.104ms self 0.104ms children 0.000ms %children 0.00% 2021-04-09 20:37:09 root: INFO: timing SparkBackend.executeJSON/optimize: relationalLowerer, after InterpretNonCompilable/LoweringTransformation/Optimize/PruneDeadFields total 2.227ms self 2.227ms children 0.000ms %children 0.00% 2021-04-09 20:37:09 root: INFO: timing SparkBackend.executeJSON/optimize: relationalLowerer, after InterpretNonCompilable/LoweringTransformation/Optimize/FoldConstants total 0.968ms self 0.968ms children 0.000ms %children 0.00% 2021-04-09 20:37:09 root: INFO: timing SparkBackend.executeJSON/optimize: relationalLowerer, after InterpretNonCompilable/LoweringTransformation/Optimize/ExtractIntervalFilters total 0.109ms self 0.109ms children 0.000ms %children 0.00% 2021-04-09 20:37:09 root: INFO: timing SparkBackend.executeJSON/optimize: relationalLowerer, after InterpretNonCompilable/LoweringTransformation/Optimize/Simplify total 0.201ms self 0.201ms children 0.000ms %children 0.00% 2021-04-09 20:37:09 root: INFO: timing SparkBackend.executeJSON/optimize: relationalLowerer, after InterpretNonCompilable/LoweringTransformation/Optimize/ForwardLets total 0.975ms self 0.975ms children 0.000ms %children 0.00% 2021-04-09 20:37:09 root: INFO: timing SparkBackend.executeJSON/optimize: relationalLowerer, after InterpretNonCompilable/LoweringTransformation/Optimize/ForwardRelationalLets total 0.173ms self 0.173ms children 0.000ms %children 0.00% 2021-04-09 20:37:09 root: INFO: timing SparkBackend.executeJSON/optimize: relationalLowerer, after InterpretNonCompilable/LoweringTransformation/Optimize/PruneDeadFields total 0.920ms self 0.920ms children 0.000ms %children 0.00% 2021-04-09 20:37:09 root: INFO: timing SparkBackend.executeJSON/optimize: relationalLowerer, after InterpretNonCompilable/LoweringTransformation/Optimize/FoldConstants total 0.647ms self 0.647ms children 0.000ms %children 0.00% 2021-04-09 20:37:09 root: INFO: timing SparkBackend.executeJSON/optimize: relationalLowerer, after InterpretNonCompilable/LoweringTransformation/Optimize/ExtractIntervalFilters total 0.099ms self 0.099ms children 0.000ms %children 0.00% 2021-04-09 20:37:09 root: INFO: timing SparkBackend.executeJSON/optimize: relationalLowerer, after InterpretNonCompilable/LoweringTransformation/Optimize/Simplify total 0.279ms self 0.279ms children 0.000ms %children 0.00% 2021-04-09 20:37:09 root: INFO: timing SparkBackend.executeJSON/optimize: relationalLowerer, after InterpretNonCompilable/LoweringTransformation/Optimize/ForwardLets total 1.090ms self 1.090ms children 0.000ms %children 0.00% 2021-04-09 20:37:09 root: INFO: timing SparkBackend.executeJSON/optimize: relationalLowerer, after InterpretNonCompilable/LoweringTransformation/Optimize/ForwardRelationalLets total 0.107ms self 0.107ms children 0.000ms %children 0.00% 2021-04-09 20:37:09 root: INFO: timing SparkBackend.executeJSON/optimize: relationalLowerer, after InterpretNonCompilable/LoweringTransformation/Optimize/PruneDeadFields total 5.939ms self 5.939ms children 0.000ms %children 0.00% 2021-04-09 20:37:09 root: INFO: timing SparkBackend.executeJSON/optimize: relationalLowerer, after InterpretNonCompilable/Verify total 0.033ms self 0.033ms children 0.000ms %children 0.00% 2021-04-09 20:37:09 root: INFO: timing SparkBackend.executeJSON/Compile total 714.772ms self 566.091ms children 148.682ms %children 20.80% 2021-04-09 20:37:09 root: INFO: timing SparkBackend.executeJSON/Compile/optimize: compileLowerer, initial IR total 34.024ms self 0.022ms children 34.002ms %children 99.93% 2021-04-09 20:37:09 root: INFO: timing SparkBackend.executeJSON/Compile/optimize: compileLowerer, initial IR/Verify total 0.032ms self 0.032ms children 0.000ms %children 0.00% 2021-04-09 20:37:09 root: INFO: timing SparkBackend.executeJSON/Compile/optimize: compileLowerer, initial IR/LoweringTransformation total 33.932ms self 15.191ms children 18.741ms %children 55.23% 2021-04-09 20:37:09 root: INFO: timing SparkBackend.executeJSON/Compile/optimize: compileLowerer, initial IR/LoweringTransformation/Optimize total 18.741ms self 0.181ms children 18.560ms %children 99.03% 2021-04-09 20:37:09 root: INFO: timing SparkBackend.executeJSON/Compile/optimize: compileLowerer, initial IR/LoweringTransformation/Optimize/FoldConstants total 1.395ms self 1.395ms children 0.000ms %children 0.00% 2021-04-09 20:37:09 root: INFO: timing SparkBackend.executeJSON/Compile/optimize: compileLowerer, initial IR/LoweringTransformation/Optimize/ExtractIntervalFilters total 0.136ms self 0.136ms children 0.000ms %children 0.00% 2021-04-09 20:37:09 root: INFO: timing SparkBackend.executeJSON/Compile/optimize: compileLowerer, initial IR/LoweringTransformation/Optimize/Simplify total 0.617ms self 0.617ms children 0.000ms %children 0.00% 2021-04-09 20:37:09 root: INFO: timing SparkBackend.executeJSON/Compile/optimize: compileLowerer, initial IR/LoweringTransformation/Optimize/ForwardLets total 2.095ms self 2.095ms children 0.000ms %children 0.00% 2021-04-09 20:37:09 root: INFO: timing SparkBackend.executeJSON/Compile/optimize: compileLowerer, initial IR/LoweringTransformation/Optimize/ForwardRelationalLets total 0.224ms self 0.224ms children 0.000ms %children 0.00% 2021-04-09 20:37:09 root: INFO: timing SparkBackend.executeJSON/Compile/optimize: compileLowerer, initial IR/LoweringTransformation/Optimize/PruneDeadFields total 5.876ms self 5.876ms children 0.000ms %children 0.00% 2021-04-09 20:37:09 root: INFO: timing SparkBackend.executeJSON/Compile/optimize: compileLowerer, initial IR/LoweringTransformation/Optimize/FoldConstants total 0.739ms self 0.739ms children 0.000ms %children 0.00% 2021-04-09 20:37:09 root: INFO: timing SparkBackend.executeJSON/Compile/optimize: compileLowerer, initial IR/LoweringTransformation/Optimize/ExtractIntervalFilters total 0.092ms self 0.092ms children 0.000ms %children 0.00% 2021-04-09 20:37:09 root: INFO: timing SparkBackend.executeJSON/Compile/optimize: compileLowerer, initial IR/LoweringTransformation/Optimize/Simplify total 0.189ms self 0.189ms children 0.000ms %children 0.00% 2021-04-09 20:37:09 root: INFO: timing SparkBackend.executeJSON/Compile/optimize: compileLowerer, initial IR/LoweringTransformation/Optimize/ForwardLets total 1.265ms self 1.265ms children 0.000ms %children 0.00% 2021-04-09 20:37:09 root: INFO: timing SparkBackend.executeJSON/Compile/optimize: compileLowerer, initial IR/LoweringTransformation/Optimize/ForwardRelationalLets total 0.098ms self 0.098ms children 0.000ms %children 0.00% 2021-04-09 20:37:09 root: INFO: timing SparkBackend.executeJSON/Compile/optimize: compileLowerer, initial IR/LoweringTransformation/Optimize/PruneDeadFields total 1.032ms self 1.032ms children 0.000ms %children 0.00% 2021-04-09 20:37:09 root: INFO: timing SparkBackend.executeJSON/Compile/optimize: compileLowerer, initial IR/LoweringTransformation/Optimize/FoldConstants total 0.689ms self 0.689ms children 0.000ms %children 0.00% 2021-04-09 20:37:09 root: INFO: timing SparkBackend.executeJSON/Compile/optimize: compileLowerer, initial IR/LoweringTransformation/Optimize/ExtractIntervalFilters total 0.087ms self 0.087ms children 0.000ms %children 0.00% 2021-04-09 20:37:09 root: INFO: timing SparkBackend.executeJSON/Compile/optimize: compileLowerer, initial IR/LoweringTransformation/Optimize/Simplify total 0.197ms self 0.197ms children 0.000ms %children 0.00% 2021-04-09 20:37:09 root: INFO: timing SparkBackend.executeJSON/Compile/optimize: compileLowerer, initial IR/LoweringTransformation/Optimize/ForwardLets total 1.742ms self 1.742ms children 0.000ms %children 0.00% 2021-04-09 20:37:09 root: INFO: timing SparkBackend.executeJSON/Compile/optimize: compileLowerer, initial IR/LoweringTransformation/Optimize/ForwardRelationalLets total 0.175ms self 0.175ms children 0.000ms %children 0.00% 2021-04-09 20:37:09 root: INFO: timing SparkBackend.executeJSON/Compile/optimize: compileLowerer, initial IR/LoweringTransformation/Optimize/PruneDeadFields total 1.912ms self 1.912ms children 0.000ms %children 0.00% 2021-04-09 20:37:09 root: INFO: timing SparkBackend.executeJSON/Compile/optimize: compileLowerer, initial IR/Verify total 0.038ms self 0.038ms children 0.000ms %children 0.00% 2021-04-09 20:37:09 root: INFO: timing SparkBackend.executeJSON/Compile/InlineApplyIR total 0.896ms self 0.031ms children 0.865ms %children 96.55% 2021-04-09 20:37:09 root: INFO: timing SparkBackend.executeJSON/Compile/InlineApplyIR/Verify total 0.044ms self 0.044ms children 0.000ms %children 0.00% 2021-04-09 20:37:09 root: INFO: timing SparkBackend.executeJSON/Compile/InlineApplyIR/LoweringTransformation total 0.726ms self 0.726ms children 0.000ms %children 0.00% 2021-04-09 20:37:09 root: INFO: timing SparkBackend.executeJSON/Compile/InlineApplyIR/Verify total 0.095ms self 0.095ms children 0.000ms %children 0.00% 2021-04-09 20:37:09 root: INFO: timing SparkBackend.executeJSON/Compile/optimize: compileLowerer, after InlineApplyIR total 14.231ms self 0.065ms children 14.165ms %children 99.54% 2021-04-09 20:37:09 root: INFO: timing SparkBackend.executeJSON/Compile/optimize: compileLowerer, after InlineApplyIR/Verify total 0.017ms self 0.017ms children 0.000ms %children 0.00% 2021-04-09 20:37:09 root: INFO: timing SparkBackend.executeJSON/Compile/optimize: compileLowerer, after InlineApplyIR/LoweringTransformation total 14.120ms self 4.458ms children 9.661ms %children 68.42% 2021-04-09 20:37:09 root: INFO: timing SparkBackend.executeJSON/Compile/optimize: compileLowerer, after InlineApplyIR/LoweringTransformation/Optimize total 9.661ms self 0.117ms children 9.544ms %children 98.79% 2021-04-09 20:37:09 root: INFO: timing SparkBackend.executeJSON/Compile/optimize: compileLowerer, after InlineApplyIR/LoweringTransformation/Optimize/FoldConstants total 0.246ms self 0.246ms children 0.000ms %children 0.00% 2021-04-09 20:37:09 root: INFO: timing SparkBackend.executeJSON/Compile/optimize: compileLowerer, after InlineApplyIR/LoweringTransformation/Optimize/ExtractIntervalFilters total 0.109ms self 0.109ms children 0.000ms %children 0.00% 2021-04-09 20:37:09 root: INFO: timing SparkBackend.executeJSON/Compile/optimize: compileLowerer, after InlineApplyIR/LoweringTransformation/Optimize/Simplify total 0.271ms self 0.271ms children 0.000ms %children 0.00% 2021-04-09 20:37:09 root: INFO: timing SparkBackend.executeJSON/Compile/optimize: compileLowerer, after InlineApplyIR/LoweringTransformation/Optimize/ForwardLets total 1.327ms self 1.327ms children 0.000ms %children 0.00% 2021-04-09 20:37:09 root: INFO: timing SparkBackend.executeJSON/Compile/optimize: compileLowerer, after InlineApplyIR/LoweringTransformation/Optimize/ForwardRelationalLets total 0.135ms self 0.135ms children 0.000ms %children 0.00% 2021-04-09 20:37:09 root: INFO: timing SparkBackend.executeJSON/Compile/optimize: compileLowerer, after InlineApplyIR/LoweringTransformation/Optimize/PruneDeadFields total 1.078ms self 1.078ms children 0.000ms %children 0.00% 2021-04-09 20:37:09 root: INFO: timing SparkBackend.executeJSON/Compile/optimize: compileLowerer, after InlineApplyIR/LoweringTransformation/Optimize/FoldConstants total 0.782ms self 0.782ms children 0.000ms %children 0.00% 2021-04-09 20:37:09 root: INFO: timing SparkBackend.executeJSON/Compile/optimize: compileLowerer, after InlineApplyIR/LoweringTransformation/Optimize/ExtractIntervalFilters total 0.098ms self 0.098ms children 0.000ms %children 0.00% 2021-04-09 20:37:09 root: INFO: timing SparkBackend.executeJSON/Compile/optimize: compileLowerer, after InlineApplyIR/LoweringTransformation/Optimize/Simplify total 0.158ms self 0.158ms children 0.000ms %children 0.00% 2021-04-09 20:37:09 root: INFO: timing SparkBackend.executeJSON/Compile/optimize: compileLowerer, after InlineApplyIR/LoweringTransformation/Optimize/ForwardLets total 0.989ms self 0.989ms children 0.000ms %children 0.00% 2021-04-09 20:37:09 root: INFO: timing SparkBackend.executeJSON/Compile/optimize: compileLowerer, after InlineApplyIR/LoweringTransformation/Optimize/ForwardRelationalLets total 0.106ms self 0.106ms children 0.000ms %children 0.00% 2021-04-09 20:37:09 root: INFO: timing SparkBackend.executeJSON/Compile/optimize: compileLowerer, after InlineApplyIR/LoweringTransformation/Optimize/PruneDeadFields total 0.860ms self 0.860ms children 0.000ms %children 0.00% 2021-04-09 20:37:09 root: INFO: timing SparkBackend.executeJSON/Compile/optimize: compileLowerer, after InlineApplyIR/LoweringTransformation/Optimize/FoldConstants total 0.558ms self 0.558ms children 0.000ms %children 0.00% 2021-04-09 20:37:09 root: INFO: timing SparkBackend.executeJSON/Compile/optimize: compileLowerer, after InlineApplyIR/LoweringTransformation/Optimize/ExtractIntervalFilters total 0.095ms self 0.095ms children 0.000ms %children 0.00% 2021-04-09 20:37:09 root: INFO: timing SparkBackend.executeJSON/Compile/optimize: compileLowerer, after InlineApplyIR/LoweringTransformation/Optimize/Simplify total 0.173ms self 0.173ms children 0.000ms %children 0.00% 2021-04-09 20:37:09 root: INFO: timing SparkBackend.executeJSON/Compile/optimize: compileLowerer, after InlineApplyIR/LoweringTransformation/Optimize/ForwardLets total 1.725ms self 1.725ms children 0.000ms %children 0.00% 2021-04-09 20:37:09 root: INFO: timing SparkBackend.executeJSON/Compile/optimize: compileLowerer, after InlineApplyIR/LoweringTransformation/Optimize/ForwardRelationalLets total 0.080ms self 0.080ms children 0.000ms %children 0.00% 2021-04-09 20:37:09 root: INFO: timing SparkBackend.executeJSON/Compile/optimize: compileLowerer, after InlineApplyIR/LoweringTransformation/Optimize/PruneDeadFields total 0.755ms self 0.755ms children 0.000ms %children 0.00% 2021-04-09 20:37:09 root: INFO: timing SparkBackend.executeJSON/Compile/optimize: compileLowerer, after InlineApplyIR/Verify total 0.028ms self 0.028ms children 0.000ms %children 0.00% 2021-04-09 20:37:09 root: INFO: timing SparkBackend.executeJSON/Compile/LowerArrayAggsToRunAggs total 85.721ms self 0.021ms children 85.700ms %children 99.98% 2021-04-09 20:37:09 root: INFO: timing SparkBackend.executeJSON/Compile/LowerArrayAggsToRunAggs/Verify total 0.042ms self 0.042ms children 0.000ms %children 0.00% 2021-04-09 20:37:09 root: INFO: timing SparkBackend.executeJSON/Compile/LowerArrayAggsToRunAggs/LoweringTransformation total 85.049ms self 85.049ms children 0.000ms %children 0.00% 2021-04-09 20:37:09 root: INFO: timing SparkBackend.executeJSON/Compile/LowerArrayAggsToRunAggs/Verify total 0.609ms self 0.609ms children 0.000ms %children 0.00% 2021-04-09 20:37:09 root: INFO: timing SparkBackend.executeJSON/Compile/optimize: compileLowerer, after LowerArrayAggsToRunAggs total 13.811ms self 0.017ms children 13.794ms %children 99.88% 2021-04-09 20:37:09 root: INFO: timing SparkBackend.executeJSON/Compile/optimize: compileLowerer, after LowerArrayAggsToRunAggs/Verify total 0.017ms self 0.017ms children 0.000ms %children 0.00% 2021-04-09 20:37:09 root: INFO: timing SparkBackend.executeJSON/Compile/optimize: compileLowerer, after LowerArrayAggsToRunAggs/LoweringTransformation total 13.740ms self 4.101ms children 9.638ms %children 70.15% 2021-04-09 20:37:09 root: INFO: timing SparkBackend.executeJSON/Compile/optimize: compileLowerer, after LowerArrayAggsToRunAggs/LoweringTransformation/Optimize total 9.638ms self 0.117ms children 9.521ms %children 98.78% 2021-04-09 20:37:09 root: INFO: timing SparkBackend.executeJSON/Compile/optimize: compileLowerer, after LowerArrayAggsToRunAggs/LoweringTransformation/Optimize/FoldConstants total 0.260ms self 0.260ms children 0.000ms %children 0.00% 2021-04-09 20:37:09 root: INFO: timing SparkBackend.executeJSON/Compile/optimize: compileLowerer, after LowerArrayAggsToRunAggs/LoweringTransformation/Optimize/ExtractIntervalFilters total 0.118ms self 0.118ms children 0.000ms %children 0.00% 2021-04-09 20:37:09 root: INFO: timing SparkBackend.executeJSON/Compile/optimize: compileLowerer, after LowerArrayAggsToRunAggs/LoweringTransformation/Optimize/Simplify total 0.206ms self 0.206ms children 0.000ms %children 0.00% 2021-04-09 20:37:09 root: INFO: timing SparkBackend.executeJSON/Compile/optimize: compileLowerer, after LowerArrayAggsToRunAggs/LoweringTransformation/Optimize/ForwardLets total 1.172ms self 1.172ms children 0.000ms %children 0.00% 2021-04-09 20:37:09 root: INFO: timing SparkBackend.executeJSON/Compile/optimize: compileLowerer, after LowerArrayAggsToRunAggs/LoweringTransformation/Optimize/ForwardRelationalLets total 0.095ms self 0.095ms children 0.000ms %children 0.00% 2021-04-09 20:37:09 root: INFO: timing SparkBackend.executeJSON/Compile/optimize: compileLowerer, after LowerArrayAggsToRunAggs/LoweringTransformation/Optimize/PruneDeadFields total 1.746ms self 1.746ms children 0.000ms %children 0.00% 2021-04-09 20:37:09 root: INFO: timing SparkBackend.executeJSON/Compile/optimize: compileLowerer, after LowerArrayAggsToRunAggs/LoweringTransformation/Optimize/FoldConstants total 0.898ms self 0.898ms children 0.000ms %children 0.00% 2021-04-09 20:37:09 root: INFO: timing SparkBackend.executeJSON/Compile/optimize: compileLowerer, after LowerArrayAggsToRunAggs/LoweringTransformation/Optimize/ExtractIntervalFilters total 0.105ms self 0.105ms children 0.000ms %children 0.00% 2021-04-09 20:37:09 root: INFO: timing SparkBackend.executeJSON/Compile/optimize: compileLowerer, after LowerArrayAggsToRunAggs/LoweringTransformation/Optimize/Simplify total 0.161ms self 0.161ms children 0.000ms %children 0.00% 2021-04-09 20:37:09 root: INFO: timing SparkBackend.executeJSON/Compile/optimize: compileLowerer, after LowerArrayAggsToRunAggs/LoweringTransformation/Optimize/ForwardLets total 1.144ms self 1.144ms children 0.000ms %children 0.00% 2021-04-09 20:37:09 root: INFO: timing SparkBackend.executeJSON/Compile/optimize: compileLowerer, after LowerArrayAggsToRunAggs/LoweringTransformation/Optimize/ForwardRelationalLets total 0.083ms self 0.083ms children 0.000ms %children 0.00% 2021-04-09 20:37:09 root: INFO: timing SparkBackend.executeJSON/Compile/optimize: compileLowerer, after LowerArrayAggsToRunAggs/LoweringTransformation/Optimize/PruneDeadFields total 0.856ms self 0.856ms children 0.000ms %children 0.00% 2021-04-09 20:37:09 root: INFO: timing SparkBackend.executeJSON/Compile/optimize: compileLowerer, after LowerArrayAggsToRunAggs/LoweringTransformation/Optimize/FoldConstants total 0.556ms self 0.556ms children 0.000ms %children 0.00% 2021-04-09 20:37:09 root: INFO: timing SparkBackend.executeJSON/Compile/optimize: compileLowerer, after LowerArrayAggsToRunAggs/LoweringTransformation/Optimize/ExtractIntervalFilters total 0.087ms self 0.087ms children 0.000ms %children 0.00% 2021-04-09 20:37:09 root: INFO: timing SparkBackend.executeJSON/Compile/optimize: compileLowerer, after LowerArrayAggsToRunAggs/LoweringTransformation/Optimize/Simplify total 0.172ms self 0.172ms children 0.000ms %children 0.00% 2021-04-09 20:37:09 root: INFO: timing SparkBackend.executeJSON/Compile/optimize: compileLowerer, after LowerArrayAggsToRunAggs/LoweringTransformation/Optimize/ForwardLets total 0.976ms self 0.976ms children 0.000ms %children 0.00% 2021-04-09 20:37:09 root: INFO: timing SparkBackend.executeJSON/Compile/optimize: compileLowerer, after LowerArrayAggsToRunAggs/LoweringTransformation/Optimize/ForwardRelationalLets total 0.172ms self 0.172ms children 0.000ms %children 0.00% 2021-04-09 20:37:09 root: INFO: timing SparkBackend.executeJSON/Compile/optimize: compileLowerer, after LowerArrayAggsToRunAggs/LoweringTransformation/Optimize/PruneDeadFields total 0.715ms self 0.715ms children 0.000ms %children 0.00% 2021-04-09 20:37:09 root: INFO: timing SparkBackend.executeJSON/Compile/optimize: compileLowerer, after LowerArrayAggsToRunAggs/Verify total 0.038ms self 0.038ms children 0.000ms %children 0.00% 2021-04-09 20:37:09 root: INFO: timing SparkBackend.executeJSON/InitializeCompiledFunction total 16.623ms self 16.623ms children 0.000ms %children 0.00% 2021-04-09 20:37:09 root: INFO: timing SparkBackend.executeJSON/RunCompiledFunction total 2.693ms self 2.693ms children 0.000ms %children 0.00% 2021-04-09 20:37:09 root: INFO: timing SparkBackend.executeJSON/convertRegionValueToAnnotation total 31.168ms self 31.168ms children 0.000ms %children 0.00% 2021-04-09 20:37:10 root: INFO: RegionPool: initialized for thread 17: Thread-5 2021-04-09 20:37:10 MemoryStore: INFO: Block broadcast_2 stored as values in memory (estimated size 402.0 KB, free 21.7 GB) 2021-04-09 20:37:10 MemoryStore: INFO: Block broadcast_2_piece0 stored as bytes in memory (estimated size 28.4 KB, free 21.7 GB) 2021-04-09 20:37:10 BlockManagerInfo: INFO: Added broadcast_2_piece0 in memory on answer-m.us-central1-b.c.human-genetics-001.internal:42437 (size: 28.4 KB, free: 21.7 GB) 2021-04-09 20:37:10 SparkContext: INFO: Created broadcast 2 from broadcast at SparkBackend.scala:259 2021-04-09 20:37:11 MemoryStore: INFO: Block broadcast_3 stored as values in memory (estimated size 555.2 KB, free 21.7 GB) 2021-04-09 20:37:11 MemoryStore: INFO: Block broadcast_3_piece0 stored as bytes in memory (estimated size 40.7 KB, free 21.7 GB) 2021-04-09 20:37:11 BlockManagerInfo: INFO: Added broadcast_3_piece0 in memory on answer-m.us-central1-b.c.human-genetics-001.internal:42437 (size: 40.7 KB, free: 21.7 GB) 2021-04-09 20:37:11 SparkContext: INFO: Created broadcast 3 from broadcast at SparkBackend.scala:259 2021-04-09 20:37:12 SparkContext: INFO: Starting job: collect at LoadVCF.scala:1915 2021-04-09 20:37:12 DAGScheduler: INFO: Got job 0 (collect at LoadVCF.scala:1915) with 2 output partitions 2021-04-09 20:37:12 DAGScheduler: INFO: Final stage: ResultStage 0 (collect at LoadVCF.scala:1915) 2021-04-09 20:37:12 DAGScheduler: INFO: Parents of final stage: List() 2021-04-09 20:37:12 DAGScheduler: INFO: Missing parents: List() 2021-04-09 20:37:12 DAGScheduler: INFO: Submitting ResultStage 0 (MapPartitionsRDD[1] at map at LoadVCF.scala:1894), which has no missing parents 2021-04-09 20:37:12 MemoryStore: INFO: Block broadcast_4 stored as values in memory (estimated size 11.6 KB, free 21.7 GB) 2021-04-09 20:37:12 MemoryStore: INFO: Block broadcast_4_piece0 stored as bytes in memory (estimated size 6.0 KB, free 21.7 GB) 2021-04-09 20:37:12 BlockManagerInfo: INFO: Added broadcast_4_piece0 in memory on answer-m.us-central1-b.c.human-genetics-001.internal:42437 (size: 6.0 KB, free: 21.7 GB) 2021-04-09 20:37:12 SparkContext: INFO: Created broadcast 4 from broadcast at DAGScheduler.scala:1163 2021-04-09 20:37:12 DAGScheduler: INFO: Submitting 2 missing tasks from ResultStage 0 (MapPartitionsRDD[1] at map at LoadVCF.scala:1894) (first 15 tasks are for partitions Vector(0, 1)) 2021-04-09 20:37:12 YarnScheduler: INFO: Adding task set 0.0 with 2 tasks 2021-04-09 20:37:12 FairSchedulableBuilder: INFO: Added task set TaskSet_0.0 tasks to pool default 2021-04-09 20:37:12 TaskSetManager: INFO: Starting task 0.0 in stage 0.0 (TID 0, answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1, partition 0, PROCESS_LOCAL, 7888 bytes) 2021-04-09 20:37:12 TaskSetManager: INFO: Starting task 1.0 in stage 0.0 (TID 1, answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2, partition 1, PROCESS_LOCAL, 7888 bytes) 2021-04-09 20:37:12 BlockManagerInfo: INFO: Added broadcast_4_piece0 in memory on answer-w-1.us-central1-b.c.human-genetics-001.internal:45783 (size: 6.0 KB, free: 9.5 GB) 2021-04-09 20:37:12 BlockManagerInfo: INFO: Added broadcast_4_piece0 in memory on answer-w-0.us-central1-b.c.human-genetics-001.internal:39767 (size: 6.0 KB, free: 9.5 GB) 2021-04-09 20:37:12 BlockManagerInfo: INFO: Added broadcast_2_piece0 in memory on answer-w-1.us-central1-b.c.human-genetics-001.internal:45783 (size: 28.4 KB, free: 9.5 GB) 2021-04-09 20:37:13 BlockManagerInfo: INFO: Added broadcast_2_piece0 in memory on answer-w-0.us-central1-b.c.human-genetics-001.internal:39767 (size: 28.4 KB, free: 9.5 GB) 2021-04-09 20:37:14 TaskSetManager: INFO: Finished task 0.0 in stage 0.0 (TID 0) in 2163 ms on answer-w-1.us-central1-b.c.human-genetics-001.internal (executor 1) (1/2) 2021-04-09 20:37:14 TaskSetManager: INFO: Finished task 1.0 in stage 0.0 (TID 1) in 2284 ms on answer-w-0.us-central1-b.c.human-genetics-001.internal (executor 2) (2/2) 2021-04-09 20:37:14 YarnScheduler: INFO: Removed TaskSet 0.0, whose tasks have all completed, from pool default 2021-04-09 20:37:14 DAGScheduler: INFO: ResultStage 0 (collect at LoadVCF.scala:1915) finished in 2.359 s 2021-04-09 20:37:14 DAGScheduler: INFO: Job 0 finished: collect at LoadVCF.scala:1915, took 2.411422 s 2021-04-09 20:37:14 root: INFO: encoder cache miss (0 hits, 2 misses, 0.000) 2021-04-09 20:37:14 root: INFO: instruction count: 3: __C34etypeEncode. 2021-04-09 20:37:14 root: INFO: instruction count: 5: __C34etypeEncode.apply 2021-04-09 20:37:14 root: INFO: instruction count: 13: __C34etypeEncode.__m35ENCODE_r_tuple_of_r_array_of_r_tuple_of_r_stringENDEND_TO_r_struct_of_r_array_of_r_struct_of_r_binaryENDEND 2021-04-09 20:37:14 root: INFO: instruction count: 45: __C34etypeEncode.__m36ENCODE_r_array_of_r_tuple_of_r_stringEND_TO_r_array_of_r_struct_of_r_binaryEND 2021-04-09 20:37:14 root: INFO: instruction count: 13: __C34etypeEncode.__m37ENCODE_r_tuple_of_r_stringEND_TO_r_struct_of_r_binaryEND 2021-04-09 20:37:14 root: INFO: instruction count: 18: __C34etypeEncode.__m38ENCODE_r_string_TO_r_binary 2021-04-09 20:37:14 root: INFO: encoder cache hit 2021-04-09 20:37:14 root: INFO: RegionPool: FREE: 64.0K allocated (64.0K blocks / 0 chunks), regions.size = 1, 0 current java objects, 0 max java objects, thread 17: Thread-5 2021-04-09 20:37:14 root: INFO: timing SparkBackend.pyImportVCFs total 3.940s self 3.940s children 0.000ms %children 0.00% 2021-04-09 20:37:14 root: INFO: RegionPool: initialized for thread 17: Thread-5 2021-04-09 20:37:14 root: INFO: RegionPool: FREE: 64.0K allocated (64.0K blocks / 0 chunks), regions.size = 1, 0 current java objects, 0 max java objects, thread 17: Thread-5 2021-04-09 20:37:14 root: INFO: timing SparkBackend.parse_value_ir total 90.785ms self 90.785ms children 0.000ms %children 0.00% 2021-04-09 20:37:14 root: INFO: RegionPool: initialized for thread 17: Thread-5 2021-04-09 20:37:14 root: INFO: RegionPool: FREE: 64.0K allocated (64.0K blocks / 0 chunks), regions.size = 1, 0 current java objects, 0 max java objects, thread 17: Thread-5 2021-04-09 20:37:14 root: INFO: timing SparkBackend.parse_value_ir total 27.872ms self 27.872ms children 0.000ms %children 0.00% 2021-04-09 20:37:15 root: INFO: RegionPool: initialized for thread 17: Thread-5 2021-04-09 20:37:15 root: INFO: RegionPool: FREE: 64.0K allocated (64.0K blocks / 0 chunks), regions.size = 1, 0 current java objects, 0 max java objects, thread 17: Thread-5 2021-04-09 20:37:15 root: INFO: timing SparkBackend.parse_value_ir total 70.268ms self 70.268ms children 0.000ms %children 0.00% 2021-04-09 20:37:15 root: INFO: RegionPool: initialized for thread 17: Thread-5 2021-04-09 20:37:15 root: INFO: RegionPool: FREE: 64.0K allocated (64.0K blocks / 0 chunks), regions.size = 1, 0 current java objects, 0 max java objects, thread 17: Thread-5 2021-04-09 20:37:15 root: INFO: timing SparkBackend.parse_value_ir total 71.059ms self 71.059ms children 0.000ms %children 0.00% 2021-04-09 20:37:15 root: INFO: RegionPool: initialized for thread 17: Thread-5 2021-04-09 20:37:15 root: INFO: starting execution of query hail_query_2 of initial size 34 2021-04-09 20:37:15 root: INFO: optimize optimize: relationalLowerer, initial IR: before: IR size 34: (MatrixWrite "{\"name\":\"MatrixNativeWriter\",\"path\":\"gs://human-genetics-berylc/ALS/answer_als_hail/tmp/output.mt\",\"overwrite\":false,\"stageLocally\":false,\"codecSpecJSONStr\":null,\"partitions\":null,\"partitionsTypeStr\":null}" (CastTableToMatrix __entries __cols (s) (TableMapGlobals (TableMapRows (TableMultiWayZipJoin "data" "g" (TableMapRows (CastMatrixToTable "__entries" "__cols" (MatrixLiteral)) (ApplyIR __uid_4 () Struct{locus:Locus(GRCh38),alleles:Array[String],rsid:String,__entries:Array[Struct{LA:Array[Int32],LGT:Call,LAD:Array[Int32],LPGT:Call,LPL:Array[Int32],RGQ:Int32,END:Int32,gvcf_info:Struct{BaseQRankSum:Float64,ClippingRankSum:Float64,DS:Boolean,ExcessHet:Float64,HaplotypeScore:Float64,InbreedingCoeff:Float64,MLEAC:Array[Int32],MLEAF:Array[Float64],MQ:Float64,MQ0:Int32,MQRankSum:Float64,RAW_MQ:Float64,ReadPosRankSum:Float64,VariantType:String},AB:Float64,DP:Int32,GQ:Int32,MIN_DP:Int32,MQ0:Int32,PID:String,SB:Array[Int32]}]} (Ref row))) (TableMapRows (CastMatrixToTable "__entries" "__cols" (MatrixLiteral)) (ApplyIR __uid_4 () Struct{locus:Locus(GRCh38),alleles:Array[String],rsid:String,__entries:Array[Struct{LA:Array[Int32],LGT:Call,LAD:Array[Int32],LPGT:Call,LPL:Array[Int32],RGQ:Int32,END:Int32,gvcf_info:Struct{BaseQRankSum:Float64,ClippingRankSum:Float64,DS:Boolean,ExcessHet:Float64,HaplotypeScore:Float64,InbreedingCoeff:Float64,MLEAC:Array[Int32],MLEAF:Array[Float64],MQ:Float64,MQ0:Int32,MQRankSum:Float64,RAW_MQ:Float64,ReadPosRankSum:Float64,VariantType:String},AB:Float64,DP:Int32,GQ:Int32,MIN_DP:Int32,MQ0:Int32,PID:String,SB:Array[Int32]}]} (Ref row)))) (ApplyIR __uid_9 () Struct{locus:Locus(GRCh38),alleles:Array[String],rsid:String,__entries:Array[Struct{LA:Array[Int32],LGT:Call,LAD:Array[Int32],LPGT:Call,LPL:Array[Int32],RGQ:Int32,END:Int32,gvcf_info:Struct{BaseQRankSum:Float64,ClippingRankSum:Float64,DS:Boolean,ExcessHet:Float64,HaplotypeScore:Float64,InbreedingCoeff:Float64,MLEAC:Array[Int32],MLEAF:Array[Float64],MQ:Float64,MQ0:Int32,MQRankSum:Float64,RAW_MQ:Float64,ReadPosRankSum:Float64,VariantType:String},AB:Float64,DP:Int32,GQ:Int32,MIN_DP:Int32,MQ0:Int32,PID:String,SB:Array[Int32]}]} (Ref row) (Ref global))) (SelectFields (__cols) (InsertFields (SelectFields (g) (Ref global)) None (__cols (ToArray (StreamFlatMap __uid_48 (ToStream False (ToArray (StreamMap __uid_46 (ToStream False (GetField g (Ref global))) (GetField __cols (Ref __uid_46))))) (ToStream False (Ref __uid_48)))))))))) 2021-04-09 20:37:15 root: INFO: optimize optimize: relationalLowerer, initial IR: after: IR size 29: (MatrixWrite "{\"name\":\"MatrixNativeWriter\",\"path\":\"gs://human-genetics-berylc/ALS/answer_als_hail/tmp/output.mt\",\"overwrite\":false,\"stageLocally\":false,\"codecSpecJSONStr\":null,\"partitions\":null,\"partitionsTypeStr\":null}" (CastTableToMatrix __entries __cols (s) (TableMapGlobals (TableMapRows (TableMultiWayZipJoin "data" "g" (TableMapRows (CastMatrixToTable "__entries" "__cols" (MatrixLiteral)) (ApplyIR __uid_4 () Struct{locus:Locus(GRCh38),alleles:Array[String],rsid:String,__entries:Array[Struct{LA:Array[Int32],LGT:Call,LAD:Array[Int32],LPGT:Call,LPL:Array[Int32],RGQ:Int32,END:Int32,gvcf_info:Struct{BaseQRankSum:Float64,ClippingRankSum:Float64,DS:Boolean,ExcessHet:Float64,HaplotypeScore:Float64,InbreedingCoeff:Float64,MLEAC:Array[Int32],MLEAF:Array[Float64],MQ:Float64,MQ0:Int32,MQRankSum:Float64,RAW_MQ:Float64,ReadPosRankSum:Float64,VariantType:String},AB:Float64,DP:Int32,GQ:Int32,MIN_DP:Int32,MQ0:Int32,PID:String,SB:Array[Int32]}]} (Ref row))) (TableMapRows (CastMatrixToTable "__entries" "__cols" (MatrixLiteral)) (ApplyIR __uid_4 () Struct{locus:Locus(GRCh38),alleles:Array[String],rsid:String,__entries:Array[Struct{LA:Array[Int32],LGT:Call,LAD:Array[Int32],LPGT:Call,LPL:Array[Int32],RGQ:Int32,END:Int32,gvcf_info:Struct{BaseQRankSum:Float64,ClippingRankSum:Float64,DS:Boolean,ExcessHet:Float64,HaplotypeScore:Float64,InbreedingCoeff:Float64,MLEAC:Array[Int32],MLEAF:Array[Float64],MQ:Float64,MQ0:Int32,MQRankSum:Float64,RAW_MQ:Float64,ReadPosRankSum:Float64,VariantType:String},AB:Float64,DP:Int32,GQ:Int32,MIN_DP:Int32,MQ0:Int32,PID:String,SB:Array[Int32]}]} (Ref row)))) (ApplyIR __uid_9 () Struct{locus:Locus(GRCh38),alleles:Array[String],rsid:String,__entries:Array[Struct{LA:Array[Int32],LGT:Call,LAD:Array[Int32],LPGT:Call,LPL:Array[Int32],RGQ:Int32,END:Int32,gvcf_info:Struct{BaseQRankSum:Float64,ClippingRankSum:Float64,DS:Boolean,ExcessHet:Float64,HaplotypeScore:Float64,InbreedingCoeff:Float64,MLEAC:Array[Int32],MLEAF:Array[Float64],MQ:Float64,MQ0:Int32,MQRankSum:Float64,RAW_MQ:Float64,ReadPosRankSum:Float64,VariantType:String},AB:Float64,DP:Int32,GQ:Int32,MIN_DP:Int32,MQ0:Int32,PID:String,SB:Array[Int32]}]} (Ref row) (Ref global))) (InsertFields (SelectFields () (Ref global)) ("__cols") (__cols (ToArray (StreamFlatMap __iruid_781 (ToStream False (GetField g (Ref global))) (ToStream False (GetField __cols (Ref __iruid_781)))))))))) 2021-04-09 20:37:15 root: INFO: optimize optimize: relationalLowerer, after LowerMatrixToTable: before: IR size 53: (TableWrite "{\"writer\":{\"path\":\"gs://human-genetics-berylc/ALS/answer_als_hail/tmp/output.mt\",\"overwrite\":false,\"stageLocally\":false,\"codecSpecJSONStr\":null,\"partitions\":null,\"partitionsTypeStr\":null},\"colsFieldName\":\"__cols\",\"entriesFieldName\":\"the entries! [877f12a8827e18f61222c6c8c5fb04a8]\",\"colKey\":[\"s\"]}" (TableRename ("__entries") ( "the entries! [877f12a8827e18f61222c6c8c5fb04a8]") ("__cols") ("__cols") (TableMapRows (TableMapGlobals (TableMapRows (TableMultiWayZipJoin "data" "g" (TableMapRows (TableRename ( "the entries! [877f12a8827e18f61222c6c8c5fb04a8]") ("__entries") ("__cols") ("__cols") (TableMapRows (TableLiteral) (SelectFields (locus alleles rsid qual filters info `the entries! [877f12a8827e18f61222c6c8c5fb04a8]`) (Ref row)))) (ApplyIR __uid_4 () Struct{locus:Locus(GRCh38),alleles:Array[String],rsid:String,__entries:Array[Struct{LA:Array[Int32],LGT:Call,LAD:Array[Int32],LPGT:Call,LPL:Array[Int32],RGQ:Int32,END:Int32,gvcf_info:Struct{BaseQRankSum:Float64,ClippingRankSum:Float64,DS:Boolean,ExcessHet:Float64,HaplotypeScore:Float64,InbreedingCoeff:Float64,MLEAC:Array[Int32],MLEAF:Array[Float64],MQ:Float64,MQ0:Int32,MQRankSum:Float64,RAW_MQ:Float64,ReadPosRankSum:Float64,VariantType:String},AB:Float64,DP:Int32,GQ:Int32,MIN_DP:Int32,MQ0:Int32,PID:String,SB:Array[Int32]}]} (Ref row))) (TableMapRows (TableRename ( "the entries! [877f12a8827e18f61222c6c8c5fb04a8]") ("__entries") ("__cols") ("__cols") (TableMapRows (TableLiteral) (SelectFields (locus alleles rsid qual filters info `the entries! [877f12a8827e18f61222c6c8c5fb04a8]`) (Ref row)))) (ApplyIR __uid_4 () Struct{locus:Locus(GRCh38),alleles:Array[String],rsid:String,__entries:Array[Struct{LA:Array[Int32],LGT:Call,LAD:Array[Int32],LPGT:Call,LPL:Array[Int32],RGQ:Int32,END:Int32,gvcf_info:Struct{BaseQRankSum:Float64,ClippingRankSum:Float64,DS:Boolean,ExcessHet:Float64,HaplotypeScore:Float64,InbreedingCoeff:Float64,MLEAC:Array[Int32],MLEAF:Array[Float64],MQ:Float64,MQ0:Int32,MQRankSum:Float64,RAW_MQ:Float64,ReadPosRankSum:Float64,VariantType:String},AB:Float64,DP:Int32,GQ:Int32,MIN_DP:Int32,MQ0:Int32,PID:String,SB:Array[Int32]}]} (Ref row)))) (ApplyIR __uid_9 () Struct{locus:Locus(GRCh38),alleles:Array[String],rsid:String,__entries:Array[Struct{LA:Array[Int32],LGT:Call,LAD:Array[Int32],LPGT:Call,LPL:Array[Int32],RGQ:Int32,END:Int32,gvcf_info:Struct{BaseQRankSum:Float64,ClippingRankSum:Float64,DS:Boolean,ExcessHet:Float64,HaplotypeScore:Float64,InbreedingCoeff:Float64,MLEAC:Array[Int32],MLEAF:Array[Float64],MQ:Float64,MQ0:Int32,MQRankSum:Float64,RAW_MQ:Float64,ReadPosRankSum:Float64,VariantType:String},AB:Float64,DP:Int32,GQ:Int32,MIN_DP:Int32,MQ0:Int32,PID:String,SB:Array[Int32]}]} (Ref row) (Ref global))) (InsertFields (SelectFields () (Ref global)) ("__cols") (__cols (ToArray (StreamFlatMap __iruid_781 (ToStream False (GetField g (Ref global))) (ToStream False (GetField __cols (Ref __iruid_781)))))))) (If (IsNA (GetField __entries (Ref row))) (Die Struct{locus:Locus(GRCh38),alleles:Array[String],rsid:String,__entries:Array[Struct{LA:Array[Int32],LGT:Call,LAD:Array[Int32],LPGT:Call,LPL:Array[Int32],RGQ:Int32,END:Int32,gvcf_info:Struct{BaseQRankSum:Float64,ClippingRankSum:Float64,DS:Boolean,ExcessHet:Float64,HaplotypeScore:Float64,InbreedingCoeff:Float64,MLEAC:Array[Int32],MLEAF:Array[Float64],MQ:Float64,MQ0:Int32,MQRankSum:Float64,RAW_MQ:Float64,ReadPosRankSum:Float64,VariantType:String},AB:Float64,DP:Int32,GQ:Int32,MIN_DP:Int32,MQ0:Int32,PID:String,SB:Array[Int32]}]} -1 (Str "missing en...")) (If (ApplyComparisonOp NEQWithNA (ArrayLen (GetField __entries (Ref row))) (ArrayLen (GetField __cols (Ref global)))) (Die Struct{locus:Locus(GRCh38),alleles:Array[String],rsid:String,__entries:Array[Struct{LA:Array[Int32],LGT:Call,LAD:Array[Int32],LPGT:Call,LPL:Array[Int32],RGQ:Int32,END:Int32,gvcf_info:Struct{BaseQRankSum:Float64,ClippingRankSum:Float64,DS:Boolean,ExcessHet:Float64,HaplotypeScore:Float64,InbreedingCoeff:Float64,MLEAC:Array[Int32],MLEAF:Array[Float64],MQ:Float64,MQ0:Int32,MQRankSum:Float64,RAW_MQ:Float64,ReadPosRankSum:Float64,VariantType:String},AB:Float64,DP:Int32,GQ:Int32,MIN_DP:Int32,MQ0:Int32,PID:String,SB:Array[Int32]}]} -1 (Str "length mis...")) (Ref row)))))) 2021-04-09 20:37:15 root: INFO: optimize optimize: relationalLowerer, after LowerMatrixToTable: after: IR size 47: (TableWrite "{\"writer\":{\"path\":\"gs://human-genetics-berylc/ALS/answer_als_hail/tmp/output.mt\",\"overwrite\":false,\"stageLocally\":false,\"codecSpecJSONStr\":null,\"partitions\":null,\"partitionsTypeStr\":null},\"colsFieldName\":\"__cols\",\"entriesFieldName\":\"the entries! [877f12a8827e18f61222c6c8c5fb04a8]\",\"colKey\":[\"s\"]}" (TableRename ("__entries") ( "the entries! [877f12a8827e18f61222c6c8c5fb04a8]") ("__cols") ("__cols") (TableMapRows (TableMapGlobals (TableMapRows (TableMultiWayZipJoin "data" "g" (TableMapRows (TableRename ( "the entries! [877f12a8827e18f61222c6c8c5fb04a8]") ("__entries") ("__cols") ("__cols") (TableLiteral)) (ApplyIR __uid_4 () Struct{locus:Locus(GRCh38),alleles:Array[String],rsid:String,__entries:Array[Struct{LA:Array[Int32],LGT:Call,LAD:Array[Int32],LPGT:Call,LPL:Array[Int32],RGQ:Int32,END:Int32,gvcf_info:Struct{BaseQRankSum:Float64,ClippingRankSum:Float64,DS:Boolean,ExcessHet:Float64,HaplotypeScore:Float64,InbreedingCoeff:Float64,MLEAC:Array[Int32],MLEAF:Array[Float64],MQ:Float64,MQ0:Int32,MQRankSum:Float64,RAW_MQ:Float64,ReadPosRankSum:Float64,VariantType:String},AB:Float64,DP:Int32,GQ:Int32,MIN_DP:Int32,MQ0:Int32,PID:String,SB:Array[Int32]}]} (Ref row))) (TableMapRows (TableRename ( "the entries! [877f12a8827e18f61222c6c8c5fb04a8]") ("__entries") ("__cols") ("__cols") (TableLiteral)) (ApplyIR __uid_4 () Struct{locus:Locus(GRCh38),alleles:Array[String],rsid:String,__entries:Array[Struct{LA:Array[Int32],LGT:Call,LAD:Array[Int32],LPGT:Call,LPL:Array[Int32],RGQ:Int32,END:Int32,gvcf_info:Struct{BaseQRankSum:Float64,ClippingRankSum:Float64,DS:Boolean,ExcessHet:Float64,HaplotypeScore:Float64,InbreedingCoeff:Float64,MLEAC:Array[Int32],MLEAF:Array[Float64],MQ:Float64,MQ0:Int32,MQRankSum:Float64,RAW_MQ:Float64,ReadPosRankSum:Float64,VariantType:String},AB:Float64,DP:Int32,GQ:Int32,MIN_DP:Int32,MQ0:Int32,PID:String,SB:Array[Int32]}]} (Ref row)))) (ApplyIR __uid_9 () Struct{locus:Locus(GRCh38),alleles:Array[String],rsid:String,__entries:Array[Struct{LA:Array[Int32],LGT:Call,LAD:Array[Int32],LPGT:Call,LPL:Array[Int32],RGQ:Int32,END:Int32,gvcf_info:Struct{BaseQRankSum:Float64,ClippingRankSum:Float64,DS:Boolean,ExcessHet:Float64,HaplotypeScore:Float64,InbreedingCoeff:Float64,MLEAC:Array[Int32],MLEAF:Array[Float64],MQ:Float64,MQ0:Int32,MQRankSum:Float64,RAW_MQ:Float64,ReadPosRankSum:Float64,VariantType:String},AB:Float64,DP:Int32,GQ:Int32,MIN_DP:Int32,MQ0:Int32,PID:String,SB:Array[Int32]}]} (Ref row) (Ref global))) (InsertFields (SelectFields () (Ref global)) ("__cols") (__cols (ToArray (StreamFlatMap __iruid_1447 (ToStream False (GetField g (Ref global))) (ToStream False (GetField __cols (Ref __iruid_1447)))))))) (If (IsNA (GetField __entries (Ref row))) (Die Struct{locus:Locus(GRCh38),alleles:Array[String],rsid:String,__entries:Array[Struct{LA:Array[Int32],LGT:Call,LAD:Array[Int32],LPGT:Call,LPL:Array[Int32],RGQ:Int32,END:Int32,gvcf_info:Struct{BaseQRankSum:Float64,ClippingRankSum:Float64,DS:Boolean,ExcessHet:Float64,HaplotypeScore:Float64,InbreedingCoeff:Float64,MLEAC:Array[Int32],MLEAF:Array[Float64],MQ:Float64,MQ0:Int32,MQRankSum:Float64,RAW_MQ:Float64,ReadPosRankSum:Float64,VariantType:String},AB:Float64,DP:Int32,GQ:Int32,MIN_DP:Int32,MQ0:Int32,PID:String,SB:Array[Int32]}]} -1 (Str "missing en...")) (If (ApplyComparisonOp NEQWithNA (ArrayLen (GetField __entries (Ref row))) (ArrayLen (GetField __cols (Ref global)))) (Die Struct{locus:Locus(GRCh38),alleles:Array[String],rsid:String,__entries:Array[Struct{LA:Array[Int32],LGT:Call,LAD:Array[Int32],LPGT:Call,LPL:Array[Int32],RGQ:Int32,END:Int32,gvcf_info:Struct{BaseQRankSum:Float64,ClippingRankSum:Float64,DS:Boolean,ExcessHet:Float64,HaplotypeScore:Float64,InbreedingCoeff:Float64,MLEAC:Array[Int32],MLEAF:Array[Float64],MQ:Float64,MQ0:Int32,MQRankSum:Float64,RAW_MQ:Float64,ReadPosRankSum:Float64,VariantType:String},AB:Float64,DP:Int32,GQ:Int32,MIN_DP:Int32,MQ0:Int32,PID:String,SB:Array[Int32]}]} -1 (Str "length mis...")) (Ref row)))))) 2021-04-09 20:37:15 root: INFO: interpreting non compilable node: TableWrite 2021-04-09 20:37:15 root: INFO: decoder cache miss (0 hits, 1 misses, 0.000 2021-04-09 20:37:15 root: INFO: instruction count: 3: __C39etypeDecode. 2021-04-09 20:37:15 root: INFO: instruction count: 5: __C39etypeDecode.apply 2021-04-09 20:37:15 root: INFO: instruction count: 23: __C39etypeDecode.__m40DECODE_r_struct_of_r_array_of_r_struct_of_r_binaryENDEND_TO_r_tuple_of_r_array_of_r_tuple_of_r_stringENDEND 2021-04-09 20:37:15 root: INFO: instruction count: 64: __C39etypeDecode.__m41INPLACE_DECODE_r_array_of_r_struct_of_r_binaryEND_TO_r_array_of_r_tuple_of_r_stringEND 2021-04-09 20:37:15 root: INFO: instruction count: 15: __C39etypeDecode.__m42INPLACE_DECODE_r_struct_of_r_binaryEND_TO_r_tuple_of_r_stringEND 2021-04-09 20:37:15 root: INFO: instruction count: 33: __C39etypeDecode.__m43INPLACE_DECODE_r_binary_TO_r_string 2021-04-09 20:37:15 root: INFO: optimize optimize: compileLowerer, initial IR: before: IR size 5: (Coalesce (ApplyIR __uid_4 () Struct{locus:Locus(GRCh38),alleles:Array[String],rsid:String,__entries:Array[Struct{LA:Array[Int32],LGT:Call,LAD:Array[Int32],LPGT:Call,LPL:Array[Int32],RGQ:Int32,END:Int32,gvcf_info:Struct{BaseQRankSum:Float64,ClippingRankSum:Float64,DS:Boolean,ExcessHet:Float64,HaplotypeScore:Float64,InbreedingCoeff:Float64,MLEAC:Array[Int32],MLEAF:Array[Float64],MQ:Float64,MQ0:Int32,MQRankSum:Float64,RAW_MQ:Float64,ReadPosRankSum:Float64,VariantType:String},AB:Float64,DP:Int32,GQ:Int32,MIN_DP:Int32,MQ0:Int32,PID:String,SB:Array[Int32]}]} (In +PCStruct{locus:+PCLocus(GRCh38),alleles:+PCArray[+PCString],rsid:PCString,qual:PFloat64,filters:PCSet[+PCString],info:+PCStruct{BaseQRankSum:PFloat64,ClippingRankSum:PFloat64,DP:PInt32,DS:+PBoolean,END:PInt32,ExcessHet:PFloat64,HaplotypeScore:PFloat64,InbreedingCoeff:PFloat64,MLEAC:PCArray[PInt32],MLEAF:PCArray[PFloat64],MQ:PFloat64,MQ0:PInt32,MQRankSum:PFloat64,RAW_MQ:PFloat64,ReadPosRankSum:PFloat64,VariantType:PCString},__entries:+PCArray[+PCStruct{AB:PFloat64,AD:PCArray[PInt32],DP:PInt32,GQ:PInt32,GT:PCCall,MIN_DP:PInt32,MQ0:PInt32,PGT:PCCall,PID:PCString,PL:PCArray[PInt32],SB:PCArray[PInt32]}]} 1)) (Die Struct{locus:Locus(GRCh38),alleles:Array[String],rsid:String,__entries:Array[Struct{LA:Array[Int32],LGT:Call,LAD:Array[Int32],LPGT:Call,LPL:Array[Int32],RGQ:Int32,END:Int32,gvcf_info:Struct{BaseQRankSum:Float64,ClippingRankSum:Float64,DS:Boolean,ExcessHet:Float64,HaplotypeScore:Float64,InbreedingCoeff:Float64,MLEAC:Array[Int32],MLEAF:Array[Float64],MQ:Float64,MQ0:Int32,MQRankSum:Float64,RAW_MQ:Float64,ReadPosRankSum:Float64,VariantType:String},AB:Float64,DP:Int32,GQ:Int32,MIN_DP:Int32,MQ0:Int32,PID:String,SB:Array[Int32]}]} -1 (Str "Internal e..."))) 2021-04-09 20:37:15 root: INFO: optimize optimize: compileLowerer, initial IR: after: IR size 5: (Coalesce (ApplyIR __uid_4 () Struct{locus:Locus(GRCh38),alleles:Array[String],rsid:String,__entries:Array[Struct{LA:Array[Int32],LGT:Call,LAD:Array[Int32],LPGT:Call,LPL:Array[Int32],RGQ:Int32,END:Int32,gvcf_info:Struct{BaseQRankSum:Float64,ClippingRankSum:Float64,DS:Boolean,ExcessHet:Float64,HaplotypeScore:Float64,InbreedingCoeff:Float64,MLEAC:Array[Int32],MLEAF:Array[Float64],MQ:Float64,MQ0:Int32,MQRankSum:Float64,RAW_MQ:Float64,ReadPosRankSum:Float64,VariantType:String},AB:Float64,DP:Int32,GQ:Int32,MIN_DP:Int32,MQ0:Int32,PID:String,SB:Array[Int32]}]} (In +PCStruct{locus:+PCLocus(GRCh38),alleles:+PCArray[+PCString],rsid:PCString,qual:PFloat64,filters:PCSet[+PCString],info:+PCStruct{BaseQRankSum:PFloat64,ClippingRankSum:PFloat64,DP:PInt32,DS:+PBoolean,END:PInt32,ExcessHet:PFloat64,HaplotypeScore:PFloat64,InbreedingCoeff:PFloat64,MLEAC:PCArray[PInt32],MLEAF:PCArray[PFloat64],MQ:PFloat64,MQ0:PInt32,MQRankSum:PFloat64,RAW_MQ:PFloat64,ReadPosRankSum:PFloat64,VariantType:PCString},__entries:+PCArray[+PCStruct{AB:PFloat64,AD:PCArray[PInt32],DP:PInt32,GQ:PInt32,GT:PCCall,MIN_DP:PInt32,MQ0:PInt32,PGT:PCCall,PID:PCString,PL:PCArray[PInt32],SB:PCArray[PInt32]}]} 1)) (Die Struct{locus:Locus(GRCh38),alleles:Array[String],rsid:String,__entries:Array[Struct{LA:Array[Int32],LGT:Call,LAD:Array[Int32],LPGT:Call,LPL:Array[Int32],RGQ:Int32,END:Int32,gvcf_info:Struct{BaseQRankSum:Float64,ClippingRankSum:Float64,DS:Boolean,ExcessHet:Float64,HaplotypeScore:Float64,InbreedingCoeff:Float64,MLEAC:Array[Int32],MLEAF:Array[Float64],MQ:Float64,MQ0:Int32,MQRankSum:Float64,RAW_MQ:Float64,ReadPosRankSum:Float64,VariantType:String},AB:Float64,DP:Int32,GQ:Int32,MIN_DP:Int32,MQ0:Int32,PID:String,SB:Array[Int32]}]} -1 (Str "Internal e..."))) 2021-04-09 20:37:15 root: INFO: optimize optimize: compileLowerer, after InlineApplyIR: before: IR size 296: (Coalesce (Let __iruid_1557 (In +PCStruct{locus:+PCLocus(GRCh38),alleles:+PCArray[+PCString],rsid:PCString,qual:PFloat64,filters:PCSet[+PCString],info:+PCStruct{BaseQRankSum:PFloat64,ClippingRankSum:PFloat64,DP:PInt32,DS:+PBoolean,END:PInt32,ExcessHet:PFloat64,HaplotypeScore:PFloat64,InbreedingCoeff:PFloat64,MLEAC:PCArray[PInt32],MLEAF:PCArray[PFloat64],MQ:PFloat64,MQ0:PInt32,MQRankSum:PFloat64,RAW_MQ:PFloat64,ReadPosRankSum:PFloat64,VariantType:PCString},__entries:+PCArray[+PCStruct{AB:PFloat64,AD:PCArray[PInt32],DP:PInt32,GQ:PInt32,GT:PCCall,MIN_DP:PInt32,MQ0:PInt32,PGT:PCCall,PID:PCString,PL:PCArray[PInt32],SB:PCArray[PInt32]}]} 1) (Let __cse_1 (GetField alleles (Ref __iruid_1557)) (Let __cse_2 (GetField END (GetField info (Ref __iruid_1557))) (Let __uid_7 (ApplyComparisonOp EQ (Let __iruid_1570 (Ref __cse_1) (Let __iruid_1571 (I32 -1) (Let __iruid_1572 (Str " File \"")) (Let __uid_6 (ArrayLen (CastToArray (Ref __cse_1))) (MakeStruct (locus (GetField locus (Ref __iruid_1557))) (alleles (If (Ref __uid_7) (Let __iruid_1558 (GetField alleles (Ref __iruid_1557)) (Let __iruid_1559 (I32 -1) (If (IsNA (Ref __iruid_1558)) (Ref __iruid_1558) (ToArray (StreamMap __iruid_1560 (StreamRange False (I32 0) (If (ApplyComparisonOp LT (Ref __iruid_1559) (I32 0)) (ApplyBinaryPrimOp Add (ArrayLen (Ref __iruid_1558)) (Ref __iruid_1559)) (If (ApplyComparisonOp LT (Ref __iruid_1559) (ArrayLen (Ref __iruid_1558))) (Ref __iruid_1559) (ArrayLen (Ref __iruid_1558)))) (I32 1)) (ArrayRef (Ref __iruid_1558) (Ref __iruid_1560) (Str ""))))))) (GetField alleles (Ref __iruid_1557)))) (rsid (GetField rsid (Ref __iruid_1557))) (__entries (ToArray (StreamMap __uid_8 (ToStream False (GetField __entries (Ref __iruid_1557))) (MakeStruct (LA (ToArray (StreamRange False (I32 0) (ApplyBinaryPrimOp Subtract (Ref __uid_6) (If (Ref __uid_7) (I32 1) (I32 0))) (I32 1)))) (LGT (If (ApplyComparisonOp LT (Apply unphasedDiploidGtIndex () Int32 (GetField GT (Ref __uid_8))) (Apply triangle () Int32 (ApplyBinaryPrimOp Subtract (Ref __uid_6) (Apply toInt32 () Int32 (Ref __uid_7))))) (GetField GT (Ref __uid_8)) (If (ApplyComparisonOp LT (Apply unphasedDiploidGtIndex () Int32 (GetField GT (Ref __uid_8))) (Apply triangle () Int32 (Ref __uid_6))) (NA Call) (Die Call 1 (Apply concat () String (Apply concat () String (Apply concat () String (Str "invalid GT ") (Apply str () String (GetField GT (Ref __uid_8)))) (Str " at site ")) (Apply str () String (GetField locus (Ref __iruid_1557)))))))) (LAD (If (Ref __uid_7) (Let __iruid_1561 (GetField AD (Ref __uid_8)) (Let __iruid_1562 (I32 -1) (If (IsNA (Ref __iruid_1561)) (Ref __iruid_1561) (ToArray (StreamMap __iruid_1563 (StreamRange False (I32 0) (If (ApplyComparisonOp LT (Ref __iruid_1562) (I32 0)) (ApplyBinaryPrimOp Add (ArrayLen (Ref __iruid_1561)) (Ref __iruid_1562)) (If (ApplyComparisonOp LT (Ref __iruid_1562) (ArrayLen (Ref __iruid_1561))) (Ref __iruid_1562) (ArrayLen (Ref __iruid_1561)))) (I32 1)) (ArrayRef (Ref __iruid_1561) (Ref __iruid_1563) (Str ""))))))) (GetField AD (Ref __uid_8)))) (LPGT (GetField PGT (Ref __uid_8))) (LPL (If (Ref __uid_7) (If (ApplyComparisonOp GT (Ref __uid_6) (I32 2)) (Let __iruid_1564 (GetField PL (Ref __uid_8)) (Let __iruid_1565 (ApplyUnaryPrimOp Negate (Ref __uid_6)) (If (IsNA (Ref __iruid_1564)) (Ref __iruid_1564) (ToArray (StreamMap __iruid_1566 (StreamRange False (I32 0) (If (ApplyComparisonOp LT (Ref __iruid_1565) (I32 0)) (ApplyBinaryPrimOp Add (ArrayLen (Ref __iruid_1564)) (Ref __iruid_1565)) (If (ApplyComparisonOp LT (Ref __iruid_1565) (ArrayLen (Ref __iruid_1564))) (Ref __iruid_1565) (ArrayLen (Ref __iruid_1564)))) (I32 1)) (ArrayRef (Ref __iruid_1564) (Ref __iruid_1566) (Str ""))))))) (NA Array[Int32])) (If (ApplyComparisonOp GT (Ref __uid_6) (I32 1)) (GetField PL (Ref __uid_8)) (NA Array[Int32])))) (RGQ (If (Ref __uid_7) (Let __iruid_1567 (GetField PL (Ref __uid_8)) (Let __iruid_1568 (Apply unphasedDiploidGtIndex () Int32 (Apply Call () Call (I32 0) (ApplyBinaryPrimOp Subtract (Ref __uid_6) (I32 1)) (False))) (Let __iruid_1569 (Str " File \"")) (Let __iruid_1613 (ArrayLen (Ref __iruid_1610)) (MakeStruct (locus (GetField locus (In +PCStruct{locus:+PCLocus(GRCh38),alleles:+PCArray[+PCString],rsid:PCString,qual:PFloat64,filters:PCSet[+PCString],info:+PCStruct{BaseQRankSum:PFloat64,ClippingRankSum:PFloat64,DP:PInt32,DS:+PBoolean,END:PInt32,ExcessHet:PFloat64,HaplotypeScore:PFloat64,InbreedingCoeff:PFloat64,MLEAC:PCArray[PInt32],MLEAF:PCArray[PFloat64],MQ:PFloat64,MQ0:PInt32,MQRankSum:PFloat64,RAW_MQ:PFloat64,ReadPosRankSum:PFloat64,VariantType:PCString},__entries:+PCArray[+PCStruct{AB:PFloat64,AD:PCArray[PInt32],DP:PInt32,GQ:PInt32,GT:PCCall,MIN_DP:PInt32,MQ0:PInt32,PGT:PCCall,PID:PCString,PL:PCArray[PInt32],SB:PCArray[PInt32]}]} 1))) (alleles (If (Ref __iruid_1612) (Let __iruid_1614 (GetField alleles (In +PCStruct{locus:+PCLocus(GRCh38),alleles:+PCArray[+PCString],rsid:PCString,qual:PFloat64,filters:PCSet[+PCString],info:+PCStruct{BaseQRankSum:PFloat64,ClippingRankSum:PFloat64,DP:PInt32,DS:+PBoolean,END:PInt32,ExcessHet:PFloat64,HaplotypeScore:PFloat64,InbreedingCoeff:PFloat64,MLEAC:PCArray[PInt32],MLEAF:PCArray[PFloat64],MQ:PFloat64,MQ0:PInt32,MQRankSum:PFloat64,RAW_MQ:PFloat64,ReadPosRankSum:PFloat64,VariantType:PCString},__entries:+PCArray[+PCStruct{AB:PFloat64,AD:PCArray[PInt32],DP:PInt32,GQ:PInt32,GT:PCCall,MIN_DP:PInt32,MQ0:PInt32,PGT:PCCall,PID:PCString,PL:PCArray[PInt32],SB:PCArray[PInt32]}]} 1)) (If (IsNA (Ref __iruid_1614)) (Ref __iruid_1614) (ToArray (StreamMap __iruid_1615 (StreamRange False (I32 0) (ApplyBinaryPrimOp Add (ArrayLen (Ref __iruid_1614)) (I32 -1)) (I32 1)) (ArrayRef (Ref __iruid_1614) (Ref __iruid_1615) (Str "")))))) (GetField alleles (In +PCStruct{locus:+PCLocus(GRCh38),alleles:+PCArray[+PCString],rsid:PCString,qual:PFloat64,filters:PCSet[+PCString],info:+PCStruct{BaseQRankSum:PFloat64,ClippingRankSum:PFloat64,DP:PInt32,DS:+PBoolean,END:PInt32,ExcessHet:PFloat64,HaplotypeScore:PFloat64,InbreedingCoeff:PFloat64,MLEAC:PCArray[PInt32],MLEAF:PCArray[PFloat64],MQ:PFloat64,MQ0:PInt32,MQRankSum:PFloat64,RAW_MQ:PFloat64,ReadPosRankSum:PFloat64,VariantType:PCString},__entries:+PCArray[+PCStruct{AB:PFloat64,AD:PCArray[PInt32],DP:PInt32,GQ:PInt32,GT:PCCall,MIN_DP:PInt32,MQ0:PInt32,PGT:PCCall,PID:PCString,PL:PCArray[PInt32],SB:PCArray[PInt32]}]} 1)))) (rsid (GetField rsid (In +PCStruct{locus:+PCLocus(GRCh38),alleles:+PCArray[+PCString],rsid:PCString,qual:PFloat64,filters:PCSet[+PCString],info:+PCStruct{BaseQRankSum:PFloat64,ClippingRankSum:PFloat64,DP:PInt32,DS:+PBoolean,END:PInt32,ExcessHet:PFloat64,HaplotypeScore:PFloat64,InbreedingCoeff:PFloat64,MLEAC:PCArray[PInt32],MLEAF:PCArray[PFloat64],MQ:PFloat64,MQ0:PInt32,MQRankSum:PFloat64,RAW_MQ:PFloat64,ReadPosRankSum:PFloat64,VariantType:PCString},__entries:+PCArray[+PCStruct{AB:PFloat64,AD:PCArray[PInt32],DP:PInt32,GQ:PInt32,GT:PCCall,MIN_DP:PInt32,MQ0:PInt32,PGT:PCCall,PID:PCString,PL:PCArray[PInt32],SB:PCArray[PInt32]}]} 1))) (__entries (ToArray (StreamMap __iruid_1616 (ToStream False (GetField __entries (In +PCStruct{locus:+PCLocus(GRCh38),alleles:+PCArray[+PCString],rsid:PCString,qual:PFloat64,filters:PCSet[+PCString],info:+PCStruct{BaseQRankSum:PFloat64,ClippingRankSum:PFloat64,DP:PInt32,DS:+PBoolean,END:PInt32,ExcessHet:PFloat64,HaplotypeScore:PFloat64,InbreedingCoeff:PFloat64,MLEAC:PCArray[PInt32],MLEAF:PCArray[PFloat64],MQ:PFloat64,MQ0:PInt32,MQRankSum:PFloat64,RAW_MQ:PFloat64,ReadPosRankSum:PFloat64,VariantType:PCString},__entries:+PCArray[+PCStruct{AB:PFloat64,AD:PCArray[PInt32],DP:PInt32,GQ:PInt32,GT:PCCall,MIN_DP:PInt32,MQ0:PInt32,PGT:PCCall,PID:PCString,PL:PCArray[PInt32],SB:PCArray[PInt32]}]} 1))) (MakeStruct (LA (ToArray (StreamRange False (I32 0) (ApplyBinaryPrimOp Subtract (Ref __iruid_1613) (If (Ref __iruid_1612) (I32 1) (I32 0))) (I32 1)))) (LGT (If (ApplyComparisonOp LT (Apply unphasedDiploidGtIndex () Int32 (GetField GT (Ref __iruid_1616))) (Apply triangle () Int32 (ApplyBinaryPrimOp Subtract (Ref __iruid_1613) (Apply toInt32 () Int32 (Ref __iruid_1612))))) (GetField GT (Ref __iruid_1616)) (If (ApplyComparisonOp LT (Apply unphasedDiploidGtIndex () Int32 (GetField GT (Ref __iruid_1616))) (Apply triangle () Int32 (Ref __iruid_1613))) (NA Call) (Die Call 1 (Apply concat () String (Apply concat () String (Apply concat () String (Str "invalid GT ") (Apply str () String (GetField GT (Ref __iruid_1616)))) (Str " at site ")) (Apply str () String (GetField locus (In +PCStruct{locus:+PCLocus(GRCh38),alleles:+PCArray[+PCString],rsid:PCString,qual:PFloat64,filters:PCSet[+PCString],info:+PCStruct{BaseQRankSum:PFloat64,ClippingRankSum:PFloat64,DP:PInt32,DS:+PBoolean,END:PInt32,ExcessHet:PFloat64,HaplotypeScore:PFloat64,InbreedingCoeff:PFloat64,MLEAC:PCArray[PInt32],MLEAF:PCArray[PFloat64],MQ:PFloat64,MQ0:PInt32,MQRankSum:PFloat64,RAW_MQ:PFloat64,ReadPosRankSum:PFloat64,VariantType:PCString},__entries:+PCArray[+PCStruct{AB:PFloat64,AD:PCArray[PInt32],DP:PInt32,GQ:PInt32,GT:PCCall,MIN_DP:PInt32,MQ0:PInt32,PGT:PCCall,PID:PCString,PL:PCArray[PInt32],SB:PCArray[PInt32]}]} 1)))))))) (LAD (If (Ref __iruid_1612) (Let __iruid_1617 (GetField AD (Ref __iruid_1616)) (If (IsNA (Ref __iruid_1617)) (Ref __iruid_1617) (ToArray (StreamMap __iruid_1618 (StreamRange False (I32 0) (ApplyBinaryPrimOp Add (ArrayLen (Ref __iruid_1617)) (I32 -1)) (I32 1)) (ArrayRef (Ref __iruid_1617) (Ref __iruid_1618) (Str "")))))) (GetField AD (Ref __iruid_1616)))) (LPGT (GetField PGT (Ref __iruid_1616))) (LPL (If (Ref __iruid_1612) (If (ApplyComparisonOp GT (Ref __iruid_1613) (I32 2)) (Let __iruid_1619 (GetField PL (Ref __iruid_1616)) (Let __iruid_1620 (ApplyUnaryPrimOp Negate (Ref __iruid_1613)) (If (IsNA (Ref __iruid_1619)) (Ref __iruid_1619) (ToArray (StreamMap __iruid_1621 (StreamRange False (I32 0) (If (ApplyComparisonOp LT (Ref __iruid_1620) (I32 0)) (ApplyBinaryPrimOp Add (ArrayLen (Ref __iruid_1619)) (Ref __iruid_1620)) (If (ApplyComparisonOp LT (Ref __iruid_1620) (ArrayLen (Ref __iruid_1619))) (Ref __iruid_1620) (ArrayLen (Ref __iruid_1619)))) (I32 1)) (ArrayRef (Ref __iruid_1619) (Ref __iruid_1621) (Str ""))))))) (NA Array[Int32])) (If (ApplyComparisonOp GT (Ref __iruid_1613) (I32 1)) (GetField PL (Ref __iruid_1616)) (NA Array[Int32])))) (RGQ (If (Ref __iruid_1612) (Let __iruid_1622 (GetField PL (Ref __iruid_1616)) (Let __iruid_1623 (Apply unphasedDiploidGtIndex () Int32 (Apply Call () Call (I32 0) (ApplyBinaryPrimOp Subtract (Ref __iruid_1613) (I32 1)) (False))) (ArrayRef (Ref __iruid_1622) (If (ApplyComparisonOp LT (Ref __iruid_1623) (I32 0)) (ApplyBinaryPrimOp Add (ArrayLen (Ref __iruid_1622)) (Ref __iruid_1623)) (Ref __iruid_1623)) (Str " File \"")) (Let __iruid_1613 (ArrayLen (Ref __iruid_1610)) (MakeStruct (locus (GetField locus (In +PCStruct{locus:+PCLocus(GRCh38),alleles:+PCArray[+PCString],rsid:PCString,qual:PFloat64,filters:PCSet[+PCString],info:+PCStruct{BaseQRankSum:PFloat64,ClippingRankSum:PFloat64,DP:PInt32,DS:+PBoolean,END:PInt32,ExcessHet:PFloat64,HaplotypeScore:PFloat64,InbreedingCoeff:PFloat64,MLEAC:PCArray[PInt32],MLEAF:PCArray[PFloat64],MQ:PFloat64,MQ0:PInt32,MQRankSum:PFloat64,RAW_MQ:PFloat64,ReadPosRankSum:PFloat64,VariantType:PCString},__entries:+PCArray[+PCStruct{AB:PFloat64,AD:PCArray[PInt32],DP:PInt32,GQ:PInt32,GT:PCCall,MIN_DP:PInt32,MQ0:PInt32,PGT:PCCall,PID:PCString,PL:PCArray[PInt32],SB:PCArray[PInt32]}]} 1))) (alleles (If (Ref __iruid_1612) (Let __iruid_1614 (GetField alleles (In +PCStruct{locus:+PCLocus(GRCh38),alleles:+PCArray[+PCString],rsid:PCString,qual:PFloat64,filters:PCSet[+PCString],info:+PCStruct{BaseQRankSum:PFloat64,ClippingRankSum:PFloat64,DP:PInt32,DS:+PBoolean,END:PInt32,ExcessHet:PFloat64,HaplotypeScore:PFloat64,InbreedingCoeff:PFloat64,MLEAC:PCArray[PInt32],MLEAF:PCArray[PFloat64],MQ:PFloat64,MQ0:PInt32,MQRankSum:PFloat64,RAW_MQ:PFloat64,ReadPosRankSum:PFloat64,VariantType:PCString},__entries:+PCArray[+PCStruct{AB:PFloat64,AD:PCArray[PInt32],DP:PInt32,GQ:PInt32,GT:PCCall,MIN_DP:PInt32,MQ0:PInt32,PGT:PCCall,PID:PCString,PL:PCArray[PInt32],SB:PCArray[PInt32]}]} 1)) (If (IsNA (Ref __iruid_1614)) (Ref __iruid_1614) (ToArray (StreamMap __iruid_1615 (StreamRange False (I32 0) (ApplyBinaryPrimOp Add (ArrayLen (Ref __iruid_1614)) (I32 -1)) (I32 1)) (ArrayRef (Ref __iruid_1614) (Ref __iruid_1615) (Str "")))))) (GetField alleles (In +PCStruct{locus:+PCLocus(GRCh38),alleles:+PCArray[+PCString],rsid:PCString,qual:PFloat64,filters:PCSet[+PCString],info:+PCStruct{BaseQRankSum:PFloat64,ClippingRankSum:PFloat64,DP:PInt32,DS:+PBoolean,END:PInt32,ExcessHet:PFloat64,HaplotypeScore:PFloat64,InbreedingCoeff:PFloat64,MLEAC:PCArray[PInt32],MLEAF:PCArray[PFloat64],MQ:PFloat64,MQ0:PInt32,MQRankSum:PFloat64,RAW_MQ:PFloat64,ReadPosRankSum:PFloat64,VariantType:PCString},__entries:+PCArray[+PCStruct{AB:PFloat64,AD:PCArray[PInt32],DP:PInt32,GQ:PInt32,GT:PCCall,MIN_DP:PInt32,MQ0:PInt32,PGT:PCCall,PID:PCString,PL:PCArray[PInt32],SB:PCArray[PInt32]}]} 1)))) (rsid (GetField rsid (In +PCStruct{locus:+PCLocus(GRCh38),alleles:+PCArray[+PCString],rsid:PCString,qual:PFloat64,filters:PCSet[+PCString],info:+PCStruct{BaseQRankSum:PFloat64,ClippingRankSum:PFloat64,DP:PInt32,DS:+PBoolean,END:PInt32,ExcessHet:PFloat64,HaplotypeScore:PFloat64,InbreedingCoeff:PFloat64,MLEAC:PCArray[PInt32],MLEAF:PCArray[PFloat64],MQ:PFloat64,MQ0:PInt32,MQRankSum:PFloat64,RAW_MQ:PFloat64,ReadPosRankSum:PFloat64,VariantType:PCString},__entries:+PCArray[+PCStruct{AB:PFloat64,AD:PCArray[PInt32],DP:PInt32,GQ:PInt32,GT:PCCall,MIN_DP:PInt32,MQ0:PInt32,PGT:PCCall,PID:PCString,PL:PCArray[PInt32],SB:PCArray[PInt32]}]} 1))) (__entries (ToArray (StreamMap __iruid_1616 (ToStream False (GetField __entries (In +PCStruct{locus:+PCLocus(GRCh38),alleles:+PCArray[+PCString],rsid:PCString,qual:PFloat64,filters:PCSet[+PCString],info:+PCStruct{BaseQRankSum:PFloat64,ClippingRankSum:PFloat64,DP:PInt32,DS:+PBoolean,END:PInt32,ExcessHet:PFloat64,HaplotypeScore:PFloat64,InbreedingCoeff:PFloat64,MLEAC:PCArray[PInt32],MLEAF:PCArray[PFloat64],MQ:PFloat64,MQ0:PInt32,MQRankSum:PFloat64,RAW_MQ:PFloat64,ReadPosRankSum:PFloat64,VariantType:PCString},__entries:+PCArray[+PCStruct{AB:PFloat64,AD:PCArray[PInt32],DP:PInt32,GQ:PInt32,GT:PCCall,MIN_DP:PInt32,MQ0:PInt32,PGT:PCCall,PID:PCString,PL:PCArray[PInt32],SB:PCArray[PInt32]}]} 1))) (MakeStruct (LA (ToArray (StreamRange False (I32 0) (ApplyBinaryPrimOp Subtract (Ref __iruid_1613) (If (Ref __iruid_1612) (I32 1) (I32 0))) (I32 1)))) (LGT (If (ApplyComparisonOp LT (Apply unphasedDiploidGtIndex () Int32 (GetField GT (Ref __iruid_1616))) (Apply triangle () Int32 (ApplyBinaryPrimOp Subtract (Ref __iruid_1613) (Apply toInt32 () Int32 (Ref __iruid_1612))))) (GetField GT (Ref __iruid_1616)) (If (ApplyComparisonOp LT (Apply unphasedDiploidGtIndex () Int32 (GetField GT (Ref __iruid_1616))) (Apply triangle () Int32 (Ref __iruid_1613))) (NA Call) (Die Call 1 (Apply concat () String (Apply concat () String (Apply concat () String (Str "invalid GT ") (Apply str () String (GetField GT (Ref __iruid_1616)))) (Str " at site ")) (Apply str () String (GetField locus (In +PCStruct{locus:+PCLocus(GRCh38),alleles:+PCArray[+PCString],rsid:PCString,qual:PFloat64,filters:PCSet[+PCString],info:+PCStruct{BaseQRankSum:PFloat64,ClippingRankSum:PFloat64,DP:PInt32,DS:+PBoolean,END:PInt32,ExcessHet:PFloat64,HaplotypeScore:PFloat64,InbreedingCoeff:PFloat64,MLEAC:PCArray[PInt32],MLEAF:PCArray[PFloat64],MQ:PFloat64,MQ0:PInt32,MQRankSum:PFloat64,RAW_MQ:PFloat64,ReadPosRankSum:PFloat64,VariantType:PCString},__entries:+PCArray[+PCStruct{AB:PFloat64,AD:PCArray[PInt32],DP:PInt32,GQ:PInt32,GT:PCCall,MIN_DP:PInt32,MQ0:PInt32,PGT:PCCall,PID:PCString,PL:PCArray[PInt32],SB:PCArray[PInt32]}]} 1)))))))) (LAD (If (Ref __iruid_1612) (Let __iruid_1617 (GetField AD (Ref __iruid_1616)) (If (IsNA (Ref __iruid_1617)) (Ref __iruid_1617) (ToArray (StreamMap __iruid_1618 (StreamRange False (I32 0) (ApplyBinaryPrimOp Add (ArrayLen (Ref __iruid_1617)) (I32 -1)) (I32 1)) (ArrayRef (Ref __iruid_1617) (Ref __iruid_1618) (Str "")))))) (GetField AD (Ref __iruid_1616)))) (LPGT (GetField PGT (Ref __iruid_1616))) (LPL (If (Ref __iruid_1612) (If (ApplyComparisonOp GT (Ref __iruid_1613) (I32 2)) (Let __iruid_1619 (GetField PL (Ref __iruid_1616)) (Let __iruid_1620 (ApplyUnaryPrimOp Negate (Ref __iruid_1613)) (If (IsNA (Ref __iruid_1619)) (Ref __iruid_1619) (ToArray (StreamMap __iruid_1621 (StreamRange False (I32 0) (If (ApplyComparisonOp LT (Ref __iruid_1620) (I32 0)) (ApplyBinaryPrimOp Add (ArrayLen (Ref __iruid_1619)) (Ref __iruid_1620)) (If (ApplyComparisonOp LT (Ref __iruid_1620) (ArrayLen (Ref __iruid_1619))) (Ref __iruid_1620) (ArrayLen (Ref __iruid_1619)))) (I32 1)) (ArrayRef (Ref __iruid_1619) (Ref __iruid_1621) (Str ""))))))) (NA Array[Int32])) (If (ApplyComparisonOp GT (Ref __iruid_1613) (I32 1)) (GetField PL (Ref __iruid_1616)) (NA Array[Int32])))) (RGQ (If (Ref __iruid_1612) (Let __iruid_1622 (GetField PL (Ref __iruid_1616)) (Let __iruid_1623 (Apply unphasedDiploidGtIndex () Int32 (Apply Call () Call (I32 0) (ApplyBinaryPrimOp Subtract (Ref __iruid_1613) (I32 1)) (False))) (ArrayRef (Ref __iruid_1622) (If (ApplyComparisonOp LT (Ref __iruid_1623) (I32 0)) (ApplyBinaryPrimOp Add (ArrayLen (Ref __iruid_1622)) (Ref __iruid_1623)) (Ref __iruid_1623)) (Str " File \"")) (Let __iruid_1658 (ArrayLen (Ref __iruid_1655)) (MakeStruct (locus (GetField locus (In +PCStruct{locus:+PCLocus(GRCh38),alleles:+PCArray[+PCString],rsid:PCString,qual:PFloat64,filters:PCSet[+PCString],info:+PCStruct{BaseQRankSum:PFloat64,ClippingRankSum:PFloat64,DP:PInt32,DS:+PBoolean,END:PInt32,ExcessHet:PFloat64,HaplotypeScore:PFloat64,InbreedingCoeff:PFloat64,MLEAC:PCArray[PInt32],MLEAF:PCArray[PFloat64],MQ:PFloat64,MQ0:PInt32,MQRankSum:PFloat64,RAW_MQ:PFloat64,ReadPosRankSum:PFloat64,VariantType:PCString},__entries:+PCArray[+PCStruct{AB:PFloat64,AD:PCArray[PInt32],DP:PInt32,GQ:PInt32,GT:PCCall,MIN_DP:PInt32,MQ0:PInt32,PGT:PCCall,PID:PCString,PL:PCArray[PInt32],SB:PCArray[PInt32]}]} 1))) (alleles (If (Ref __iruid_1657) (Let __iruid_1659 (GetField alleles (In +PCStruct{locus:+PCLocus(GRCh38),alleles:+PCArray[+PCString],rsid:PCString,qual:PFloat64,filters:PCSet[+PCString],info:+PCStruct{BaseQRankSum:PFloat64,ClippingRankSum:PFloat64,DP:PInt32,DS:+PBoolean,END:PInt32,ExcessHet:PFloat64,HaplotypeScore:PFloat64,InbreedingCoeff:PFloat64,MLEAC:PCArray[PInt32],MLEAF:PCArray[PFloat64],MQ:PFloat64,MQ0:PInt32,MQRankSum:PFloat64,RAW_MQ:PFloat64,ReadPosRankSum:PFloat64,VariantType:PCString},__entries:+PCArray[+PCStruct{AB:PFloat64,AD:PCArray[PInt32],DP:PInt32,GQ:PInt32,GT:PCCall,MIN_DP:PInt32,MQ0:PInt32,PGT:PCCall,PID:PCString,PL:PCArray[PInt32],SB:PCArray[PInt32]}]} 1)) (If (IsNA (Ref __iruid_1659)) (Ref __iruid_1659) (ToArray (StreamMap __iruid_1660 (StreamRange False (I32 0) (ApplyBinaryPrimOp Add (ArrayLen (Ref __iruid_1659)) (I32 -1)) (I32 1)) (ArrayRef (Ref __iruid_1659) (Ref __iruid_1660) (Str "")))))) (GetField alleles (In +PCStruct{locus:+PCLocus(GRCh38),alleles:+PCArray[+PCString],rsid:PCString,qual:PFloat64,filters:PCSet[+PCString],info:+PCStruct{BaseQRankSum:PFloat64,ClippingRankSum:PFloat64,DP:PInt32,DS:+PBoolean,END:PInt32,ExcessHet:PFloat64,HaplotypeScore:PFloat64,InbreedingCoeff:PFloat64,MLEAC:PCArray[PInt32],MLEAF:PCArray[PFloat64],MQ:PFloat64,MQ0:PInt32,MQRankSum:PFloat64,RAW_MQ:PFloat64,ReadPosRankSum:PFloat64,VariantType:PCString},__entries:+PCArray[+PCStruct{AB:PFloat64,AD:PCArray[PInt32],DP:PInt32,GQ:PInt32,GT:PCCall,MIN_DP:PInt32,MQ0:PInt32,PGT:PCCall,PID:PCString,PL:PCArray[PInt32],SB:PCArray[PInt32]}]} 1)))) (rsid (GetField rsid (In +PCStruct{locus:+PCLocus(GRCh38),alleles:+PCArray[+PCString],rsid:PCString,qual:PFloat64,filters:PCSet[+PCString],info:+PCStruct{BaseQRankSum:PFloat64,ClippingRankSum:PFloat64,DP:PInt32,DS:+PBoolean,END:PInt32,ExcessHet:PFloat64,HaplotypeScore:PFloat64,InbreedingCoeff:PFloat64,MLEAC:PCArray[PInt32],MLEAF:PCArray[PFloat64],MQ:PFloat64,MQ0:PInt32,MQRankSum:PFloat64,RAW_MQ:PFloat64,ReadPosRankSum:PFloat64,VariantType:PCString},__entries:+PCArray[+PCStruct{AB:PFloat64,AD:PCArray[PInt32],DP:PInt32,GQ:PInt32,GT:PCCall,MIN_DP:PInt32,MQ0:PInt32,PGT:PCCall,PID:PCString,PL:PCArray[PInt32],SB:PCArray[PInt32]}]} 1))) (__entries (ToArray (StreamMap __iruid_1661 (ToStream False (GetField __entries (In +PCStruct{locus:+PCLocus(GRCh38),alleles:+PCArray[+PCString],rsid:PCString,qual:PFloat64,filters:PCSet[+PCString],info:+PCStruct{BaseQRankSum:PFloat64,ClippingRankSum:PFloat64,DP:PInt32,DS:+PBoolean,END:PInt32,ExcessHet:PFloat64,HaplotypeScore:PFloat64,InbreedingCoeff:PFloat64,MLEAC:PCArray[PInt32],MLEAF:PCArray[PFloat64],MQ:PFloat64,MQ0:PInt32,MQRankSum:PFloat64,RAW_MQ:PFloat64,ReadPosRankSum:PFloat64,VariantType:PCString},__entries:+PCArray[+PCStruct{AB:PFloat64,AD:PCArray[PInt32],DP:PInt32,GQ:PInt32,GT:PCCall,MIN_DP:PInt32,MQ0:PInt32,PGT:PCCall,PID:PCString,PL:PCArray[PInt32],SB:PCArray[PInt32]}]} 1))) (MakeStruct (LA (ToArray (StreamRange False (I32 0) (ApplyBinaryPrimOp Subtract (Ref __iruid_1658) (If (Ref __iruid_1657) (I32 1) (I32 0))) (I32 1)))) (LGT (If (ApplyComparisonOp LT (Apply unphasedDiploidGtIndex () Int32 (GetField GT (Ref __iruid_1661))) (Apply triangle () Int32 (ApplyBinaryPrimOp Subtract (Ref __iruid_1658) (Apply toInt32 () Int32 (Ref __iruid_1657))))) (GetField GT (Ref __iruid_1661)) (If (ApplyComparisonOp LT (Apply unphasedDiploidGtIndex () Int32 (GetField GT (Ref __iruid_1661))) (Apply triangle () Int32 (Ref __iruid_1658))) (NA Call) (Die Call 1 (Apply concat () String (Apply concat () String (Apply concat () String (Str "invalid GT ") (Apply str () String (GetField GT (Ref __iruid_1661)))) (Str " at site ")) (Apply str () String (GetField locus (In +PCStruct{locus:+PCLocus(GRCh38),alleles:+PCArray[+PCString],rsid:PCString,qual:PFloat64,filters:PCSet[+PCString],info:+PCStruct{BaseQRankSum:PFloat64,ClippingRankSum:PFloat64,DP:PInt32,DS:+PBoolean,END:PInt32,ExcessHet:PFloat64,HaplotypeScore:PFloat64,InbreedingCoeff:PFloat64,MLEAC:PCArray[PInt32],MLEAF:PCArray[PFloat64],MQ:PFloat64,MQ0:PInt32,MQRankSum:PFloat64,RAW_MQ:PFloat64,ReadPosRankSum:PFloat64,VariantType:PCString},__entries:+PCArray[+PCStruct{AB:PFloat64,AD:PCArray[PInt32],DP:PInt32,GQ:PInt32,GT:PCCall,MIN_DP:PInt32,MQ0:PInt32,PGT:PCCall,PID:PCString,PL:PCArray[PInt32],SB:PCArray[PInt32]}]} 1)))))))) (LAD (If (Ref __iruid_1657) (Let __iruid_1662 (GetField AD (Ref __iruid_1661)) (If (IsNA (Ref __iruid_1662)) (Ref __iruid_1662) (ToArray (StreamMap __iruid_1663 (StreamRange False (I32 0) (ApplyBinaryPrimOp Add (ArrayLen (Ref __iruid_1662)) (I32 -1)) (I32 1)) (ArrayRef (Ref __iruid_1662) (Ref __iruid_1663) (Str "")))))) (GetField AD (Ref __iruid_1661)))) (LPGT (GetField PGT (Ref __iruid_1661))) (LPL (If (Ref __iruid_1657) (If (ApplyComparisonOp GT (Ref __iruid_1658) (I32 2)) (Let __iruid_1664 (GetField PL (Ref __iruid_1661)) (Let __iruid_1665 (ApplyUnaryPrimOp Negate (Ref __iruid_1658)) (If (IsNA (Ref __iruid_1664)) (Ref __iruid_1664) (ToArray (StreamMap __iruid_1666 (StreamRange False (I32 0) (If (ApplyComparisonOp LT (Ref __iruid_1665) (I32 0)) (ApplyBinaryPrimOp Add (ArrayLen (Ref __iruid_1664)) (Ref __iruid_1665)) (If (ApplyComparisonOp LT (Ref __iruid_1665) (ArrayLen (Ref __iruid_1664))) (Ref __iruid_1665) (ArrayLen (Ref __iruid_1664)))) (I32 1)) (ArrayRef (Ref __iruid_1664) (Ref __iruid_1666) (Str ""))))))) (NA Array[Int32])) (If (ApplyComparisonOp GT (Ref __iruid_1658) (I32 1)) (GetField PL (Ref __iruid_1661)) (NA Array[Int32])))) (RGQ (If (Ref __iruid_1657) (Let __iruid_1667 (GetField PL (Ref __iruid_1661)) (Let __iruid_1668 (Apply unphasedDiploidGtIndex () Int32 (Apply Call () Call (I32 0) (ApplyBinaryPrimOp Subtract (Ref __iruid_1658) (I32 1)) (False))) (ArrayRef (Ref __iruid_1667) (If (ApplyComparisonOp LT (Ref __iruid_1668) (I32 0)) (ApplyBinaryPrimOp Add (ArrayLen (Ref __iruid_1667)) (Ref __iruid_1668)) (Ref __iruid_1668)) (Str " File \" 2021-04-09 20:37:16 root: INFO: instruction count: 5: __C171etypeEncode.apply 2021-04-09 20:37:16 root: INFO: instruction count: 43: __C171etypeEncode.__m172ENCODE_r_tuple_of_r_stringANDr_stringANDr_stringANDr_stringEND_TO_r_struct_of_r_binaryANDr_binaryANDr_binaryANDr_binaryEND 2021-04-09 20:37:16 root: INFO: instruction count: 18: __C171etypeEncode.__m173ENCODE_r_string_TO_r_binary 2021-04-09 20:37:16 MemoryStore: INFO: Block broadcast_5 stored as values in memory (estimated size 200.0 B, free 21.7 GB) 2021-04-09 20:37:16 MemoryStore: INFO: Block broadcast_5_piece0 stored as bytes in memory (estimated size 156.0 B, free 21.7 GB) 2021-04-09 20:37:16 BlockManagerInfo: INFO: Added broadcast_5_piece0 in memory on answer-m.us-central1-b.c.human-genetics-001.internal:42437 (size: 156.0 B, free: 21.7 GB) 2021-04-09 20:37:16 SparkContext: INFO: Created broadcast 5 from broadcast at SparkBackend.scala:259 2021-04-09 20:37:16 root: INFO: instruction count: 3: __C44Compiled. 2021-04-09 20:37:16 root: INFO: instruction count: 112: __C44Compiled.apply 2021-04-09 20:37:16 root: INFO: instruction count: 34: __C44Compiled.__m54ord_equiv 2021-04-09 20:37:16 root: INFO: instruction count: 15: __C44Compiled.__m55ord_equivNonnull 2021-04-09 20:37:16 root: INFO: instruction count: 5: __C44Compiled.__m56ord_compareNonnull 2021-04-09 20:37:16 root: INFO: instruction count: 92: __C44Compiled.__m57ord_compareNonnull 2021-04-09 20:37:16 root: INFO: instruction count: 6: __C44Compiled.__m92unphasedDiploidGtIndex 2021-04-09 20:37:16 root: INFO: instruction count: 10: __C44Compiled.__m93triangle 2021-04-09 20:37:16 root: INFO: instruction count: 2: __C44Compiled.__m94toInt32 2021-04-09 20:37:16 root: INFO: instruction count: 14: __C44Compiled.__m95ord_lt 2021-04-09 20:37:16 root: INFO: instruction count: 12: __C44Compiled.__m96ord_ltNonnull 2021-04-09 20:37:16 root: INFO: instruction count: 80: __C44Compiled.__m97concat 2021-04-09 20:37:16 root: INFO: instruction count: 80: __C44Compiled.__m100concat 2021-04-09 20:37:16 root: INFO: instruction count: 56: __C44Compiled.__m104str 2021-04-09 20:37:16 root: INFO: instruction count: 12: __C44Compiled.__m107setup_null 2021-04-09 20:37:16 root: INFO: instruction count: 93: __C44Compiled.__m111str 2021-04-09 20:37:16 root: INFO: instruction count: 23: __C44Compiled.__m115setup_null 2021-04-09 20:37:16 root: INFO: instruction count: 7: __C44Compiled.__m133ord_gt 2021-04-09 20:37:16 root: INFO: instruction count: 12: __C44Compiled.__m134ord_gtNonnull 2021-04-09 20:37:16 root: INFO: instruction count: 7: __C44Compiled.__m143ord_lt 2021-04-09 20:37:16 root: INFO: instruction count: 12: __C44Compiled.__m144ord_ltNonnull 2021-04-09 20:37:16 root: INFO: instruction count: 14: __C44Compiled.__m145ord_lt 2021-04-09 20:37:16 root: INFO: instruction count: 12: __C44Compiled.__m146ord_ltNonnull 2021-04-09 20:37:16 root: INFO: instruction count: 6: __C44Compiled.__m162unphasedDiploidGtIndex 2021-04-09 20:37:16 root: INFO: instruction count: 8: __C44Compiled.__m163Call 2021-04-09 20:37:16 root: INFO: instruction count: 9: __C44Compiled.setPartitionIndex 2021-04-09 20:37:16 root: INFO: instruction count: 4: __C44Compiled.addPartitionRegion 2021-04-09 20:37:16 root: INFO: instruction count: 4: __C44Compiled.setPool 2021-04-09 20:37:16 root: INFO: instruction count: 63: __C44Compiled.addLiterals 2021-04-09 20:37:16 root: INFO: instruction count: 44: __C44Compiled.__m169DECODE_r_struct_of_r_binaryANDr_binaryANDr_binaryANDr_binaryEND_TO_r_tuple_of_r_stringANDr_stringANDr_stringANDr_stringEND 2021-04-09 20:37:16 root: INFO: instruction count: 33: __C44Compiled.__m170INPLACE_DECODE_r_binary_TO_r_string 2021-04-09 20:37:16 root: INFO: instruction count: 472: __C44Compiled.applyregion198_256 2021-04-09 20:37:16 root: INFO: instruction count: 751: __C44Compiled.applyregion121_177 2021-04-09 20:37:16 root: INFO: instruction count: 643: __C44Compiled.applyregion74_120 2021-04-09 20:37:16 root: INFO: instruction count: 236: __C44Compiled.applyregion56_73 2021-04-09 20:37:16 root: INFO: instruction count: 146: __C44Compiled.applyregion39_49 2021-04-09 20:37:16 root: INFO: instruction count: 259: __C44Compiled.applyregion178_197 2021-04-09 20:37:16 root: INFO: instruction count: 497: __C44Compiled.applyregion34_289 2021-04-09 20:37:16 root: INFO: instruction count: 642: __C44Compiled.applyregion4_292 2021-04-09 20:37:16 root: INFO: instruction count: 3: __C174applySpills. 2021-04-09 20:37:16 root: INFO: instruction count: 3: __C112RGContainer_GRCh38. 2021-04-09 20:37:16 root: INFO: instruction count: 15: __C112RGContainer_GRCh38. 2021-04-09 20:37:16 root: INFO: decoder cache hit 2021-04-09 20:37:16 root: INFO: optimize optimize: compileLowerer, initial IR: before: IR size 6: (Coalesce (ApplyIR __uid_9 () Struct{locus:Locus(GRCh38),alleles:Array[String],rsid:String,__entries:Array[Struct{LA:Array[Int32],LGT:Call,LAD:Array[Int32],LPGT:Call,LPL:Array[Int32],RGQ:Int32,END:Int32,gvcf_info:Struct{BaseQRankSum:Float64,ClippingRankSum:Float64,DS:Boolean,ExcessHet:Float64,HaplotypeScore:Float64,InbreedingCoeff:Float64,MLEAC:Array[Int32],MLEAF:Array[Float64],MQ:Float64,MQ0:Int32,MQRankSum:Float64,RAW_MQ:Float64,ReadPosRankSum:Float64,VariantType:String},AB:Float64,DP:Int32,GQ:Int32,MIN_DP:Int32,MQ0:Int32,PID:String,SB:Array[Int32]}]} (In +PCStruct{locus:+PCLocus(GRCh38),data:+PCArray[PCStruct{alleles:+PCArray[+PCString],rsid:PCString,__entries:+PCArray[+PCStruct{LA:+PCArray[+PInt32],LGT:PCCall,LAD:PCArray[PInt32],LPGT:PCCall,LPL:PCArray[PInt32],RGQ:PInt32,END:PInt32,gvcf_info:PCStruct{BaseQRankSum:PFloat64,ClippingRankSum:PFloat64,DS:+PBoolean,ExcessHet:PFloat64,HaplotypeScore:PFloat64,InbreedingCoeff:PFloat64,MLEAC:PCArray[PInt32],MLEAF:PCArray[PFloat64],MQ:PFloat64,MQ0:PInt32,MQRankSum:PFloat64,RAW_MQ:PFloat64,ReadPosRankSum:PFloat64,VariantType:PCString},AB:PFloat64,DP:PInt32,GQ:PInt32,MIN_DP:PInt32,MQ0:PInt32,PID:PCString,SB:PCArray[PInt32]}]}]} 1) (In +PCStruct{g:+PCArray[+PCStruct{__cols:+PCArray[+PCStruct{s:+PCString}]}]} 0)) (Die Struct{locus:Locus(GRCh38),alleles:Array[String],rsid:String,__entries:Array[Struct{LA:Array[Int32],LGT:Call,LAD:Array[Int32],LPGT:Call,LPL:Array[Int32],RGQ:Int32,END:Int32,gvcf_info:Struct{BaseQRankSum:Float64,ClippingRankSum:Float64,DS:Boolean,ExcessHet:Float64,HaplotypeScore:Float64,InbreedingCoeff:Float64,MLEAC:Array[Int32],MLEAF:Array[Float64],MQ:Float64,MQ0:Int32,MQRankSum:Float64,RAW_MQ:Float64,ReadPosRankSum:Float64,VariantType:String},AB:Float64,DP:Int32,GQ:Int32,MIN_DP:Int32,MQ0:Int32,PID:String,SB:Array[Int32]}]} -1 (Str "Internal e..."))) 2021-04-09 20:37:16 root: INFO: optimize optimize: compileLowerer, initial IR: after: IR size 6: (Coalesce (ApplyIR __uid_9 () Struct{locus:Locus(GRCh38),alleles:Array[String],rsid:String,__entries:Array[Struct{LA:Array[Int32],LGT:Call,LAD:Array[Int32],LPGT:Call,LPL:Array[Int32],RGQ:Int32,END:Int32,gvcf_info:Struct{BaseQRankSum:Float64,ClippingRankSum:Float64,DS:Boolean,ExcessHet:Float64,HaplotypeScore:Float64,InbreedingCoeff:Float64,MLEAC:Array[Int32],MLEAF:Array[Float64],MQ:Float64,MQ0:Int32,MQRankSum:Float64,RAW_MQ:Float64,ReadPosRankSum:Float64,VariantType:String},AB:Float64,DP:Int32,GQ:Int32,MIN_DP:Int32,MQ0:Int32,PID:String,SB:Array[Int32]}]} (In +PCStruct{locus:+PCLocus(GRCh38),data:+PCArray[PCStruct{alleles:+PCArray[+PCString],rsid:PCString,__entries:+PCArray[+PCStruct{LA:+PCArray[+PInt32],LGT:PCCall,LAD:PCArray[PInt32],LPGT:PCCall,LPL:PCArray[PInt32],RGQ:PInt32,END:PInt32,gvcf_info:PCStruct{BaseQRankSum:PFloat64,ClippingRankSum:PFloat64,DS:+PBoolean,ExcessHet:PFloat64,HaplotypeScore:PFloat64,InbreedingCoeff:PFloat64,MLEAC:PCArray[PInt32],MLEAF:PCArray[PFloat64],MQ:PFloat64,MQ0:PInt32,MQRankSum:PFloat64,RAW_MQ:PFloat64,ReadPosRankSum:PFloat64,VariantType:PCString},AB:PFloat64,DP:PInt32,GQ:PInt32,MIN_DP:PInt32,MQ0:PInt32,PID:PCString,SB:PCArray[PInt32]}]}]} 1) (In +PCStruct{g:+PCArray[+PCStruct{__cols:+PCArray[+PCStruct{s:+PCString}]}]} 0)) (Die Struct{locus:Locus(GRCh38),alleles:Array[String],rsid:String,__entries:Array[Struct{LA:Array[Int32],LGT:Call,LAD:Array[Int32],LPGT:Call,LPL:Array[Int32],RGQ:Int32,END:Int32,gvcf_info:Struct{BaseQRankSum:Float64,ClippingRankSum:Float64,DS:Boolean,ExcessHet:Float64,HaplotypeScore:Float64,InbreedingCoeff:Float64,MLEAC:Array[Int32],MLEAF:Array[Float64],MQ:Float64,MQ0:Int32,MQRankSum:Float64,RAW_MQ:Float64,ReadPosRankSum:Float64,VariantType:String},AB:Float64,DP:Int32,GQ:Int32,MIN_DP:Int32,MQ0:Int32,PID:String,SB:Array[Int32]}]} -1 (Str "Internal e..."))) 2021-04-09 20:37:16 root: INFO: optimize optimize: compileLowerer, after InlineApplyIR: before: IR size 923: (Coalesce (Let __iruid_1887 (In +PCStruct{locus:+PCLocus(GRCh38),data:+PCArray[PCStruct{alleles:+PCArray[+PCString],rsid:PCString,__entries:+PCArray[+PCStruct{LA:+PCArray[+PInt32],LGT:PCCall,LAD:PCArray[PInt32],LPGT:PCCall,LPL:PCArray[PInt32],RGQ:PInt32,END:PInt32,gvcf_info:PCStruct{BaseQRankSum:PFloat64,ClippingRankSum:PFloat64,DS:+PBoolean,ExcessHet:PFloat64,HaplotypeScore:PFloat64,InbreedingCoeff:PFloat64,MLEAC:PCArray[PInt32],MLEAF:PCArray[PFloat64],MQ:PFloat64,MQ0:PInt32,MQRankSum:PFloat64,RAW_MQ:PFloat64,ReadPosRankSum:PFloat64,VariantType:PCString},AB:PFloat64,DP:PInt32,GQ:PInt32,MIN_DP:PInt32,MQ0:PInt32,PID:PCString,SB:PCArray[PInt32]}]}]} 1) (Let __iruid_1888 (In +PCStruct{g:+PCArray[+PCStruct{__cols:+PCArray[+PCStruct{s:+PCString}]}]} 0) (Let __cse_2 (GetField data (Ref __iruid_1887)) (Let __cse_1 (ToArray (StreamMap __uid_12 (ToStream False (Ref __cse_2)) (GetField alleles (Ref __uid_12)))) (Let __uid_28 (Let __uid_16 (StreamFold __uid_14 __uid_15 (ToStream False (ToArray (StreamMap __uid_13 (ToStream False (Ref __cse_1)) (Coalesce (Let __iruid_1892 (Ref __uid_13) (Let __iruid_1893 (I32 0) (Let __iruid_1894 (Str " File \" 2021-04-09 20:37:16 root: INFO: instruction count: 47: __C195Compiled.apply 2021-04-09 20:37:16 root: INFO: instruction count: 56: __C195Compiled.__m196str 2021-04-09 20:37:16 root: INFO: instruction count: 12: __C195Compiled.__m199setup_null 2021-04-09 20:37:16 root: INFO: instruction count: 9: __C195Compiled.setPartitionIndex 2021-04-09 20:37:16 root: INFO: instruction count: 4: __C195Compiled.addPartitionRegion 2021-04-09 20:37:16 root: INFO: instruction count: 4: __C195Compiled.setPool 2021-04-09 20:37:16 root: INFO: optimize optimize: compileLowerer, after InlineApplyIR: after: IR size 703: (Coalesce (Let __iruid_2169 (GetField data (In +PCStruct{locus:+PCLocus(GRCh38),data:+PCArray[PCStruct{alleles:+PCArray[+PCString],rsid:PCString,__entries:+PCArray[+PCStruct{LA:+PCArray[+PInt32],LGT:PCCall,LAD:PCArray[PInt32],LPGT:PCCall,LPL:PCArray[PInt32],RGQ:PInt32,END:PInt32,gvcf_info:PCStruct{BaseQRankSum:PFloat64,ClippingRankSum:PFloat64,DS:+PBoolean,ExcessHet:PFloat64,HaplotypeScore:PFloat64,InbreedingCoeff:PFloat64,MLEAC:PCArray[PInt32],MLEAF:PCArray[PFloat64],MQ:PFloat64,MQ0:PInt32,MQRankSum:PFloat64,RAW_MQ:PFloat64,ReadPosRankSum:PFloat64,VariantType:PCString},AB:PFloat64,DP:PInt32,GQ:PInt32,MIN_DP:PInt32,MQ0:PInt32,PID:PCString,SB:PCArray[PInt32]}]}]} 1)) (Let __iruid_2170 (ToArray (StreamMap __iruid_2171 (ToStream False (Ref __iruid_2169)) (GetField alleles (Ref __iruid_2171)))) (Let __iruid_2172 (StreamFold __iruid_2173 __iruid_2174 (ToStream False (Ref __iruid_2170)) (Str "") (Let __iruid_2175 (Coalesce (ArrayRef (Ref __iruid_2174) (I32 0) (Str " File \" 2021-04-09 20:37:17 root: INFO: instruction count: 5: __C636etypeEncode.apply 2021-04-09 20:37:17 root: INFO: instruction count: 103: __C636etypeEncode.__m637ENCODE_r_tuple_of_r_stringANDr_stringANDr_stringANDr_stringANDr_stringANDr_stringANDr_stringANDr_stringANDr_stringANDr_stringEND_TO_r_struct_of_r_binaryANDr_binaryANDr_binaryANDr_binaryANDr_binaryANDr_binaryANDr_binaryANDr_binaryANDr_binaryANDr_binaryEND 2021-04-09 20:37:17 root: INFO: instruction count: 18: __C636etypeEncode.__m638ENCODE_r_string_TO_r_binary 2021-04-09 20:37:17 MemoryStore: INFO: Block broadcast_6 stored as values in memory (estimated size 312.0 B, free 21.7 GB) 2021-04-09 20:37:17 MemoryStore: INFO: Block broadcast_6_piece0 stored as bytes in memory (estimated size 270.0 B, free 21.7 GB) 2021-04-09 20:37:17 BlockManagerInfo: INFO: Added broadcast_6_piece0 in memory on answer-m.us-central1-b.c.human-genetics-001.internal:42437 (size: 270.0 B, free: 21.7 GB) 2021-04-09 20:37:17 SparkContext: INFO: Created broadcast 6 from broadcast at SparkBackend.scala:259 2021-04-09 20:37:17 root: INFO: instruction count: 3: __C205Compiled. 2021-04-09 20:37:17 root: INFO: instruction count: 159: __C205Compiled.apply 2021-04-09 20:37:17 root: INFO: instruction count: 23: __C205Compiled.__m238length 2021-04-09 20:37:17 root: INFO: instruction count: 7: __C205Compiled.__m239ord_gt 2021-04-09 20:37:17 root: INFO: instruction count: 12: __C205Compiled.__m240ord_gtNonnull 2021-04-09 20:37:17 root: INFO: instruction count: 43: __C205Compiled.__m279regexMatch 2021-04-09 20:37:17 root: INFO: instruction count: 23: __C205Compiled.__m281length 2021-04-09 20:37:17 root: INFO: instruction count: 48: __C205Compiled.__m282ord_equiv 2021-04-09 20:37:17 root: INFO: instruction count: 12: __C205Compiled.__m283ord_equivNonnull 2021-04-09 20:37:17 root: INFO: instruction count: 41: __C205Compiled.__m284ord_equiv 2021-04-09 20:37:17 root: INFO: instruction count: 12: __C205Compiled.__m285ord_equivNonnull 2021-04-09 20:37:17 root: INFO: instruction count: 48: __C205Compiled.__m286ord_equiv 2021-04-09 20:37:17 root: INFO: instruction count: 15: __C205Compiled.__m287ord_equivNonnull 2021-04-09 20:37:17 root: INFO: instruction count: 5: __C205Compiled.__m288ord_compareNonnull 2021-04-09 20:37:17 root: INFO: instruction count: 92: __C205Compiled.__m289ord_compareNonnull 2021-04-09 20:37:17 root: INFO: instruction count: 20: __C205Compiled.__m290ord_lt 2021-04-09 20:37:17 root: INFO: instruction count: 12: __C205Compiled.__m291ord_ltNonnull 2021-04-09 20:37:17 root: INFO: instruction count: 14: __C205Compiled.__m296ord_lt 2021-04-09 20:37:17 root: INFO: instruction count: 12: __C205Compiled.__m297ord_ltNonnull 2021-04-09 20:37:17 root: INFO: instruction count: 14: __C205Compiled.__m298ord_gteq 2021-04-09 20:37:17 root: INFO: instruction count: 12: __C205Compiled.__m299ord_gteqNonnull 2021-04-09 20:37:17 root: INFO: instruction count: 80: __C205Compiled.__m300concat 2021-04-09 20:37:17 root: INFO: instruction count: 56: __C205Compiled.__m306str 2021-04-09 20:37:17 root: INFO: instruction count: 12: __C205Compiled.__m309setup_null 2021-04-09 20:37:17 root: INFO: instruction count: 62: __C205Compiled.__m312substring 2021-04-09 20:37:17 root: INFO: instruction count: 14: __C205Compiled.__m319ord_lt 2021-04-09 20:37:17 root: INFO: instruction count: 43: __C205Compiled.__m320endswith 2021-04-09 20:37:17 root: INFO: instruction count: 14: __C205Compiled.__m329ord_lt 2021-04-09 20:37:17 root: INFO: instruction count: 12: __C205Compiled.__m330ord_ltNonnull 2021-04-09 20:37:17 root: INFO: instruction count: 20: __C205Compiled.__m331ord_gteq 2021-04-09 20:37:17 root: INFO: instruction count: 12: __C205Compiled.__m332ord_gteqNonnull 2021-04-09 20:37:17 root: INFO: instruction count: 41: __C205Compiled.__m350ord_equiv 2021-04-09 20:37:17 root: INFO: instruction count: 15: __C205Compiled.__m351ord_equivNonnull 2021-04-09 20:37:17 root: INFO: instruction count: 5: __C205Compiled.__m352ord_compareNonnull 2021-04-09 20:37:17 root: INFO: instruction count: 92: __C205Compiled.__m353ord_compareNonnull 2021-04-09 20:37:17 root: INFO: instruction count: 80: __C205Compiled.__m355concat 2021-04-09 20:37:17 root: INFO: instruction count: 14: __C205Compiled.__m366ord_gteq 2021-04-09 20:37:17 root: INFO: instruction count: 12: __C205Compiled.__m367ord_gteqNonnull 2021-04-09 20:37:17 root: INFO: instruction count: 7: __C205Compiled.__m370ord_lt 2021-04-09 20:37:17 root: INFO: instruction count: 12: __C205Compiled.__m371ord_ltNonnull 2021-04-09 20:37:17 root: INFO: instruction count: 7: __C205Compiled.__m372ord_gteq 2021-04-09 20:37:17 root: INFO: instruction count: 12: __C205Compiled.__m373ord_gteqNonnull 2021-04-09 20:37:17 root: INFO: instruction count: 62: __C205Compiled.__m374substring 2021-04-09 20:37:17 root: INFO: instruction count: 12: __C205Compiled.__m379setup_jab 2021-04-09 20:37:17 root: INFO: instruction count: 12: __C205Compiled.__m408setup_jab 2021-04-09 20:37:17 root: INFO: instruction count: 86: __C205Compiled.__m409discardNext 2021-04-09 20:37:17 root: INFO: instruction count: 12: __C205Compiled.__m421setup_jab 2021-04-09 20:37:17 root: INFO: instruction count: 86: __C205Compiled.__m422discardNext 2021-04-09 20:37:17 root: INFO: instruction count: 12: __C205Compiled.__m457setup_jab 2021-04-09 20:37:17 root: INFO: instruction count: 12: __C205Compiled.__m495setup_jab 2021-04-09 20:37:17 root: INFO: instruction count: 112: __C205Compiled.__m496discardNext 2021-04-09 20:37:17 root: INFO: instruction count: 12: __C205Compiled.__m524setup_jab 2021-04-09 20:37:17 root: INFO: instruction count: 118: __C205Compiled.__m575findElt 2021-04-09 20:37:17 root: INFO: instruction count: 48: __C205Compiled.__m576ord_compare 2021-04-09 20:37:17 root: INFO: instruction count: 69: __C205Compiled.__m578str 2021-04-09 20:37:17 root: INFO: instruction count: 12: __C205Compiled.__m581setup_null 2021-04-09 20:37:17 root: INFO: instruction count: 65: __C205Compiled.__m585str 2021-04-09 20:37:17 root: INFO: instruction count: 12: __C205Compiled.__m588setup_null 2021-04-09 20:37:17 root: INFO: instruction count: 12: __C205Compiled.__m591setup_null 2021-04-09 20:37:17 root: INFO: instruction count: 9: __C205Compiled.setPartitionIndex 2021-04-09 20:37:17 root: INFO: instruction count: 4: __C205Compiled.addPartitionRegion 2021-04-09 20:37:17 root: INFO: instruction count: 4: __C205Compiled.setPool 2021-04-09 20:37:17 root: INFO: instruction count: 117: __C205Compiled.addLiterals 2021-04-09 20:37:17 root: INFO: instruction count: 86: __C205Compiled.__m634DECODE_r_struct_of_r_binaryANDr_binaryANDr_binaryANDr_binaryANDr_binaryANDr_binaryANDr_binaryANDr_binaryANDr_binaryANDr_binaryEND_TO_r_tuple_of_r_stringANDr_stringANDr_stringANDr_stringANDr_stringANDr_stringANDr_stringANDr_stringANDr_stringANDr_stringEND 2021-04-09 20:37:17 root: INFO: instruction count: 33: __C205Compiled.__m635INPLACE_DECODE_r_binary_TO_r_string 2021-04-09 20:37:17 root: INFO: instruction count: 553: __C205Compiled.applyregion495_495 2021-04-09 20:37:17 root: INFO: instruction count: 209: __C205Compiled.applyregion591_602 2021-04-09 20:37:17 root: INFO: instruction count: 132: __C205Compiled.applyregion531_531 2021-04-09 20:37:17 root: INFO: instruction count: 273: __C205Compiled.applyregion729_741 2021-04-09 20:37:17 root: INFO: instruction count: 526: __C205Compiled.applyregion530_603 2021-04-09 20:37:17 root: INFO: instruction count: 500: __C205Compiled.applyregion493_497 2021-04-09 20:37:17 root: INFO: instruction count: 757: __C205Compiled.applyregion634_743 2021-04-09 20:37:17 root: INFO: instruction count: 219: __C205Compiled.applyregion618_633 2021-04-09 20:37:17 root: INFO: instruction count: 173: __C205Compiled.applyregion476_486 2021-04-09 20:37:17 root: INFO: instruction count: 163: __C205Compiled.applyregion501_508 2021-04-09 20:37:17 root: INFO: instruction count: 154: __C205Compiled.applyregion604_606 2021-04-09 20:37:17 root: INFO: instruction count: 124: __C205Compiled.applyregion610_617 2021-04-09 20:37:17 root: INFO: instruction count: 120: __C205Compiled.applyregion488_490 2021-04-09 20:37:17 root: INFO: instruction count: 1112: __C205Compiled.applyregion457_756 2021-04-09 20:37:17 root: INFO: instruction count: 244: __C205Compiled.applyregion380_431 2021-04-09 20:37:17 root: INFO: instruction count: 189: __C205Compiled.applyregion780_794 2021-04-09 20:37:17 root: INFO: instruction count: 112: __C205Compiled.applyregion336_346 2021-04-09 20:37:17 root: INFO: instruction count: 102: __C205Compiled.applyregion437_447 2021-04-09 20:37:17 root: INFO: instruction count: 121: __C205Compiled.applyregion357_379 2021-04-09 20:37:17 root: INFO: instruction count: 515: __C205Compiled.applyregion330_795 2021-04-09 20:37:17 root: INFO: instruction count: 695: __C205Compiled.applyregion241_285 2021-04-09 20:37:17 root: INFO: instruction count: 361: __C205Compiled.applyregion229_796 2021-04-09 20:37:17 root: INFO: instruction count: 271: __C205Compiled.applyregion63_119 2021-04-09 20:37:17 root: INFO: instruction count: 272: __C205Compiled.applyregion168_225 2021-04-09 20:37:17 root: INFO: instruction count: 262: __C205Compiled.applyregion41_62 2021-04-09 20:37:17 root: INFO: instruction count: 176: __C205Compiled.applyregion140_167 2021-04-09 20:37:17 root: INFO: instruction count: 162: __C205Compiled.applyregion967_987 2021-04-09 20:37:17 root: INFO: instruction count: 473: __C205Compiled.applyregion935_1041 2021-04-09 20:37:17 root: INFO: instruction count: 466: __C205Compiled.applyregion1042_1135 2021-04-09 20:37:17 root: INFO: instruction count: 437: __C205Compiled.applyregion1223_1309 2021-04-09 20:37:17 root: INFO: instruction count: 321: __C205Compiled.applyregion1168_1222 2021-04-09 20:37:17 root: INFO: instruction count: 67: __C205Compiled.applyregion1138_1152 2021-04-09 20:37:17 root: INFO: instruction count: 571: __C205Compiled.applyregion30_798 2021-04-09 20:37:17 root: INFO: instruction count: 568: __C205Compiled.applyregion886_1336 2021-04-09 20:37:17 root: INFO: instruction count: 633: __C205Compiled.applyregion827_877 2021-04-09 20:37:17 root: INFO: instruction count: 374: __C205Compiled.applyregion1417_1473 2021-04-09 20:37:17 root: INFO: instruction count: 102: __C205Compiled.applyregion810_820 2021-04-09 20:37:17 root: INFO: instruction count: 102: __C205Compiled.applyregion821_823 2021-04-09 20:37:17 root: INFO: instruction count: 97: __C205Compiled.applyregion1337_1359 2021-04-09 20:37:17 root: INFO: instruction count: 684: __C205Compiled.applyregion30_1475 2021-04-09 20:37:17 root: INFO: instruction count: 545: __C205Compiled.applyregion1_1476 2021-04-09 20:37:17 root: INFO: instruction count: 3: __C640applySpills. 2021-04-09 20:37:17 root: INFO: instruction count: 3: __C410sort_compare. 2021-04-09 20:37:17 root: INFO: instruction count: 35: __C410sort_compare.apply 2021-04-09 20:37:17 root: INFO: instruction count: 18: __C410sort_compare.apply 2021-04-09 20:37:17 root: INFO: instruction count: 86: __C410sort_compare.__m412sort 2021-04-09 20:37:17 root: INFO: instruction count: 48: __C410sort_compare.__m413ord_compare 2021-04-09 20:37:17 root: INFO: instruction count: 5: __C410sort_compare.__m414ord_compareNonnull 2021-04-09 20:37:17 root: INFO: instruction count: 92: __C410sort_compare.__m415ord_compareNonnull 2021-04-09 20:37:17 root: INFO: instruction count: 7: __C410sort_compare.__m416ord_lt 2021-04-09 20:37:17 root: INFO: instruction count: 12: __C410sort_compare.__m417ord_ltNonnull 2021-04-09 20:37:17 root: INFO: instruction count: 3: __C423sort_compare. 2021-04-09 20:37:17 root: INFO: instruction count: 35: __C423sort_compare.apply 2021-04-09 20:37:17 root: INFO: instruction count: 18: __C423sort_compare.apply 2021-04-09 20:37:17 root: INFO: instruction count: 86: __C423sort_compare.__m425sort 2021-04-09 20:37:17 root: INFO: instruction count: 48: __C423sort_compare.__m426ord_compare 2021-04-09 20:37:17 root: INFO: instruction count: 5: __C423sort_compare.__m427ord_compareNonnull 2021-04-09 20:37:17 root: INFO: instruction count: 92: __C423sort_compare.__m428ord_compareNonnull 2021-04-09 20:37:17 root: INFO: instruction count: 7: __C423sort_compare.__m429ord_lt 2021-04-09 20:37:17 root: INFO: instruction count: 12: __C423sort_compare.__m430ord_ltNonnull 2021-04-09 20:37:17 root: INFO: instruction count: 3: __C497sort_compare. 2021-04-09 20:37:17 root: INFO: instruction count: 11: __C497sort_compare.apply 2021-04-09 20:37:17 root: INFO: instruction count: 18: __C497sort_compare.apply 2021-04-09 20:37:17 root: INFO: instruction count: 112: __C497sort_compare.__m499sort 2021-04-09 20:37:17 root: INFO: instruction count: 48: __C497sort_compare.__m500ord_compare 2021-04-09 20:37:17 root: INFO: instruction count: 5: __C497sort_compare.__m501ord_compareNonnull 2021-04-09 20:37:17 root: INFO: instruction count: 92: __C497sort_compare.__m502ord_compareNonnull 2021-04-09 20:37:17 root: INFO: instruction count: 7: __C497sort_compare.__m503ord_lt 2021-04-09 20:37:17 root: INFO: instruction count: 12: __C497sort_compare.__m504ord_ltNonnull 2021-04-09 20:37:17 root: INFO: encoder cache miss (1 hits, 5 misses, 0.167) 2021-04-09 20:37:17 root: INFO: instruction count: 3: __C727etypeEncode. 2021-04-09 20:37:17 root: INFO: instruction count: 5: __C727etypeEncode.apply 2021-04-09 20:37:17 root: INFO: instruction count: 13: __C727etypeEncode.__m728ENCODE_r_tuple_of_r_array_of_r_tuple_of_r_array_of_r_tuple_of_r_stringENDENDEND_TO_r_struct_of_r_array_of_r_struct_of_r_array_of_r_struct_of_r_binaryENDENDEND 2021-04-09 20:37:17 root: INFO: instruction count: 45: __C727etypeEncode.__m729ENCODE_r_array_of_r_tuple_of_r_array_of_r_tuple_of_r_stringENDEND_TO_r_array_of_r_struct_of_r_array_of_r_struct_of_r_binaryENDEND 2021-04-09 20:37:17 root: INFO: instruction count: 13: __C727etypeEncode.__m730ENCODE_r_tuple_of_r_array_of_r_tuple_of_r_stringENDEND_TO_r_struct_of_r_array_of_r_struct_of_r_binaryENDEND 2021-04-09 20:37:17 root: INFO: instruction count: 45: __C727etypeEncode.__m731ENCODE_r_array_of_r_tuple_of_r_stringEND_TO_r_array_of_r_struct_of_r_binaryEND 2021-04-09 20:37:17 root: INFO: instruction count: 13: __C727etypeEncode.__m732ENCODE_r_tuple_of_r_stringEND_TO_r_struct_of_r_binaryEND 2021-04-09 20:37:17 root: INFO: instruction count: 18: __C727etypeEncode.__m733ENCODE_r_string_TO_r_binary 2021-04-09 20:37:17 root: INFO: decoder cache miss (1 hits, 2 misses, 0.333 2021-04-09 20:37:17 root: INFO: instruction count: 3: __C734etypeDecode. 2021-04-09 20:37:17 root: INFO: instruction count: 5: __C734etypeDecode.apply 2021-04-09 20:37:17 root: INFO: instruction count: 23: __C734etypeDecode.__m735DECODE_r_struct_of_r_array_of_r_struct_of_r_array_of_r_struct_of_r_binaryENDENDEND_TO_r_tuple_of_r_array_of_r_tuple_of_r_array_of_r_tuple_of_r_stringENDENDEND 2021-04-09 20:37:17 root: INFO: instruction count: 64: __C734etypeDecode.__m736INPLACE_DECODE_r_array_of_r_struct_of_r_array_of_r_struct_of_r_binaryENDEND_TO_r_array_of_r_tuple_of_r_array_of_r_tuple_of_r_stringENDEND 2021-04-09 20:37:17 root: INFO: instruction count: 15: __C734etypeDecode.__m737INPLACE_DECODE_r_struct_of_r_array_of_r_struct_of_r_binaryENDEND_TO_r_tuple_of_r_array_of_r_tuple_of_r_stringENDEND 2021-04-09 20:37:17 root: INFO: instruction count: 64: __C734etypeDecode.__m738INPLACE_DECODE_r_array_of_r_struct_of_r_binaryEND_TO_r_array_of_r_tuple_of_r_stringEND 2021-04-09 20:37:17 root: INFO: instruction count: 15: __C734etypeDecode.__m739INPLACE_DECODE_r_struct_of_r_binaryEND_TO_r_tuple_of_r_stringEND 2021-04-09 20:37:17 root: INFO: instruction count: 33: __C734etypeDecode.__m740INPLACE_DECODE_r_binary_TO_r_string 2021-04-09 20:37:17 MemoryStore: INFO: Block broadcast_7 stored as values in memory (estimated size 10.1 KB, free 21.7 GB) 2021-04-09 20:37:17 MemoryStore: INFO: Block broadcast_7_piece0 stored as bytes in memory (estimated size 2.6 KB, free 21.7 GB) 2021-04-09 20:37:17 BlockManagerInfo: INFO: Added broadcast_7_piece0 in memory on answer-m.us-central1-b.c.human-genetics-001.internal:42437 (size: 2.6 KB, free: 21.7 GB) 2021-04-09 20:37:17 SparkContext: INFO: Created broadcast 7 from broadcast at SparkBackend.scala:259 2021-04-09 20:37:17 root: INFO: optimize optimize: compileLowerer, initial IR: before: IR size 14: (Coalesce (InsertFields (SelectFields () (In +PCStruct{g:+PCArray[+PCStruct{__cols:+PCArray[+PCStruct{s:+PCString}]}]} 0)) ("__cols") (__cols (ToArray (StreamFlatMap __iruid_1447 (ToStream False (GetField g (In +PCStruct{g:+PCArray[+PCStruct{__cols:+PCArray[+PCStruct{s:+PCString}]}]} 0))) (ToStream False (GetField __cols (Ref __iruid_1447))))))) (Die Struct{__cols:Array[Struct{s:String}]} -1 (Str "Internal e..."))) 2021-04-09 20:37:17 root: INFO: optimize optimize: compileLowerer, initial IR: after: IR size 14: (Coalesce (InsertFields (SelectFields () (In +PCStruct{g:+PCArray[+PCStruct{__cols:+PCArray[+PCStruct{s:+PCString}]}]} 0)) ("__cols") (__cols (ToArray (StreamFlatMap __iruid_2423 (ToStream False (GetField g (In +PCStruct{g:+PCArray[+PCStruct{__cols:+PCArray[+PCStruct{s:+PCString}]}]} 0))) (ToStream False (GetField __cols (Ref __iruid_2423))))))) (Die Struct{__cols:Array[Struct{s:String}]} -1 (Str "Internal e..."))) 2021-04-09 20:37:17 root: INFO: optimize optimize: compileLowerer, after InlineApplyIR: before: IR size 14: (Coalesce (InsertFields (SelectFields () (In +PCStruct{g:+PCArray[+PCStruct{__cols:+PCArray[+PCStruct{s:+PCString}]}]} 0)) ("__cols") (__cols (ToArray (StreamFlatMap __iruid_2423 (ToStream False (GetField g (In +PCStruct{g:+PCArray[+PCStruct{__cols:+PCArray[+PCStruct{s:+PCString}]}]} 0))) (ToStream False (GetField __cols (Ref __iruid_2423))))))) (Die Struct{__cols:Array[Struct{s:String}]} -1 (Str "Internal e..."))) 2021-04-09 20:37:17 root: INFO: optimize optimize: compileLowerer, after InlineApplyIR: after: IR size 14: (Coalesce (InsertFields (SelectFields () (In +PCStruct{g:+PCArray[+PCStruct{__cols:+PCArray[+PCStruct{s:+PCString}]}]} 0)) ("__cols") (__cols (ToArray (StreamFlatMap __iruid_2426 (ToStream False (GetField g (In +PCStruct{g:+PCArray[+PCStruct{__cols:+PCArray[+PCStruct{s:+PCString}]}]} 0))) (ToStream False (GetField __cols (Ref __iruid_2426))))))) (Die Struct{__cols:Array[Struct{s:String}]} -1 (Str "Internal e..."))) 2021-04-09 20:37:17 root: INFO: optimize optimize: compileLowerer, after LowerArrayAggsToRunAggs: before: IR size 14: (Coalesce (InsertFields (SelectFields () (In +PCStruct{g:+PCArray[+PCStruct{__cols:+PCArray[+PCStruct{s:+PCString}]}]} 0)) ("__cols") (__cols (ToArray (StreamFlatMap __iruid_2426 (ToStream False (GetField g (In +PCStruct{g:+PCArray[+PCStruct{__cols:+PCArray[+PCStruct{s:+PCString}]}]} 0))) (ToStream False (GetField __cols (Ref __iruid_2426))))))) (Die Struct{__cols:Array[Struct{s:String}]} -1 (Str "Internal e..."))) 2021-04-09 20:37:17 root: INFO: optimize optimize: compileLowerer, after LowerArrayAggsToRunAggs: after: IR size 14: (Coalesce (InsertFields (SelectFields () (In +PCStruct{g:+PCArray[+PCStruct{__cols:+PCArray[+PCStruct{s:+PCString}]}]} 0)) ("__cols") (__cols (ToArray (StreamFlatMap __iruid_2429 (ToStream False (GetField g (In +PCStruct{g:+PCArray[+PCStruct{__cols:+PCArray[+PCStruct{s:+PCString}]}]} 0))) (ToStream False (GetField __cols (Ref __iruid_2429))))))) (Die Struct{__cols:Array[Struct{s:String}]} -1 (Str "Internal e..."))) 2021-04-09 20:37:17 root: INFO: encoder cache miss (1 hits, 6 misses, 0.143) 2021-04-09 20:37:17 root: INFO: instruction count: 3: __C765etypeEncode. 2021-04-09 20:37:17 root: INFO: instruction count: 5: __C765etypeEncode.apply 2021-04-09 20:37:17 root: INFO: instruction count: 13: __C765etypeEncode.__m766ENCODE_r_tuple_of_r_stringEND_TO_r_struct_of_r_binaryEND 2021-04-09 20:37:17 root: INFO: instruction count: 18: __C765etypeEncode.__m767ENCODE_r_string_TO_r_binary 2021-04-09 20:37:17 MemoryStore: INFO: Block broadcast_8 stored as values in memory (estimated size 152.0 B, free 21.7 GB) 2021-04-09 20:37:17 MemoryStore: INFO: Block broadcast_8_piece0 stored as bytes in memory (estimated size 110.0 B, free 21.7 GB) 2021-04-09 20:37:17 BlockManagerInfo: INFO: Added broadcast_8_piece0 in memory on answer-m.us-central1-b.c.human-genetics-001.internal:42437 (size: 110.0 B, free: 21.7 GB) 2021-04-09 20:37:17 SparkContext: INFO: Created broadcast 8 from broadcast at SparkBackend.scala:259 2021-04-09 20:37:17 root: INFO: instruction count: 3: __C741Compiled. 2021-04-09 20:37:17 root: INFO: instruction count: 308: __C741Compiled.apply 2021-04-09 20:37:17 root: INFO: instruction count: 12: __C741Compiled.__m749setup_jab 2021-04-09 20:37:17 root: INFO: instruction count: 9: __C741Compiled.setPartitionIndex 2021-04-09 20:37:17 root: INFO: instruction count: 4: __C741Compiled.addPartitionRegion 2021-04-09 20:37:17 root: INFO: instruction count: 4: __C741Compiled.setPool 2021-04-09 20:37:17 root: INFO: instruction count: 36: __C741Compiled.addLiterals 2021-04-09 20:37:17 root: INFO: instruction count: 23: __C741Compiled.__m763DECODE_r_struct_of_r_binaryEND_TO_r_tuple_of_r_stringEND 2021-04-09 20:37:17 root: INFO: instruction count: 33: __C741Compiled.__m764INPLACE_DECODE_r_binary_TO_r_string 2021-04-09 20:37:17 root: INFO: optimize optimize: compileLowerer, initial IR: before: IR size 20: (Coalesce (If (IsNA (GetField __entries (In +PCStruct{locus:+PCLocus(GRCh38),alleles:PCArray[PCString],rsid:PCString,__entries:+PCArray[PCStruct{LA:+PCArray[PInt32],LGT:PCCall,LAD:PCArray[PInt32],LPGT:PCCall,LPL:PCArray[PInt32],RGQ:PInt32,END:PInt32,gvcf_info:PCStruct{BaseQRankSum:PFloat64,ClippingRankSum:PFloat64,DS:+PBoolean,ExcessHet:PFloat64,HaplotypeScore:PFloat64,InbreedingCoeff:PFloat64,MLEAC:PCArray[PInt32],MLEAF:PCArray[PFloat64],MQ:PFloat64,MQ0:PInt32,MQRankSum:PFloat64,RAW_MQ:PFloat64,ReadPosRankSum:PFloat64,VariantType:PCString},AB:PFloat64,DP:PInt32,GQ:PInt32,MIN_DP:PInt32,MQ0:PInt32,PID:PCString,SB:PCArray[PInt32]}]} 1))) (Die Struct{locus:Locus(GRCh38),alleles:Array[String],rsid:String,__entries:Array[Struct{LA:Array[Int32],LGT:Call,LAD:Array[Int32],LPGT:Call,LPL:Array[Int32],RGQ:Int32,END:Int32,gvcf_info:Struct{BaseQRankSum:Float64,ClippingRankSum:Float64,DS:Boolean,ExcessHet:Float64,HaplotypeScore:Float64,InbreedingCoeff:Float64,MLEAC:Array[Int32],MLEAF:Array[Float64],MQ:Float64,MQ0:Int32,MQRankSum:Float64,RAW_MQ:Float64,ReadPosRankSum:Float64,VariantType:String},AB:Float64,DP:Int32,GQ:Int32,MIN_DP:Int32,MQ0:Int32,PID:String,SB:Array[Int32]}]} -1 (Str "missing en...")) (If (ApplyComparisonOp NEQWithNA (ArrayLen (GetField __entries (In +PCStruct{locus:+PCLocus(GRCh38),alleles:PCArray[PCString],rsid:PCString,__entries:+PCArray[PCStruct{LA:+PCArray[PInt32],LGT:PCCall,LAD:PCArray[PInt32],LPGT:PCCall,LPL:PCArray[PInt32],RGQ:PInt32,END:PInt32,gvcf_info:PCStruct{BaseQRankSum:PFloat64,ClippingRankSum:PFloat64,DS:+PBoolean,ExcessHet:PFloat64,HaplotypeScore:PFloat64,InbreedingCoeff:PFloat64,MLEAC:PCArray[PInt32],MLEAF:PCArray[PFloat64],MQ:PFloat64,MQ0:PInt32,MQRankSum:PFloat64,RAW_MQ:PFloat64,ReadPosRankSum:PFloat64,VariantType:PCString},AB:PFloat64,DP:PInt32,GQ:PInt32,MIN_DP:PInt32,MQ0:PInt32,PID:PCString,SB:PCArray[PInt32]}]} 1))) (ArrayLen (GetField __cols (In +PCStruct{__cols:+PCArray[+PCStruct{s:+PCString}]} 0)))) (Die Struct{locus:Locus(GRCh38),alleles:Array[String],rsid:String,__entries:Array[Struct{LA:Array[Int32],LGT:Call,LAD:Array[Int32],LPGT:Call,LPL:Array[Int32],RGQ:Int32,END:Int32,gvcf_info:Struct{BaseQRankSum:Float64,ClippingRankSum:Float64,DS:Boolean,ExcessHet:Float64,HaplotypeScore:Float64,InbreedingCoeff:Float64,MLEAC:Array[Int32],MLEAF:Array[Float64],MQ:Float64,MQ0:Int32,MQRankSum:Float64,RAW_MQ:Float64,ReadPosRankSum:Float64,VariantType:String},AB:Float64,DP:Int32,GQ:Int32,MIN_DP:Int32,MQ0:Int32,PID:String,SB:Array[Int32]}]} -1 (Str "length mis...")) (In +PCStruct{locus:+PCLocus(GRCh38),alleles:PCArray[PCString],rsid:PCString,__entries:+PCArray[PCStruct{LA:+PCArray[PInt32],LGT:PCCall,LAD:PCArray[PInt32],LPGT:PCCall,LPL:PCArray[PInt32],RGQ:PInt32,END:PInt32,gvcf_info:PCStruct{BaseQRankSum:PFloat64,ClippingRankSum:PFloat64,DS:+PBoolean,ExcessHet:PFloat64,HaplotypeScore:PFloat64,InbreedingCoeff:PFloat64,MLEAC:PCArray[PInt32],MLEAF:PCArray[PFloat64],MQ:PFloat64,MQ0:PInt32,MQRankSum:PFloat64,RAW_MQ:PFloat64,ReadPosRankSum:PFloat64,VariantType:PCString},AB:PFloat64,DP:PInt32,GQ:PInt32,MIN_DP:PInt32,MQ0:PInt32,PID:PCString,SB:PCArray[PInt32]}]} 1))) (Die Struct{locus:Locus(GRCh38),alleles:Array[String],rsid:String,__entries:Array[Struct{LA:Array[Int32],LGT:Call,LAD:Array[Int32],LPGT:Call,LPL:Array[Int32],RGQ:Int32,END:Int32,gvcf_info:Struct{BaseQRankSum:Float64,ClippingRankSum:Float64,DS:Boolean,ExcessHet:Float64,HaplotypeScore:Float64,InbreedingCoeff:Float64,MLEAC:Array[Int32],MLEAF:Array[Float64],MQ:Float64,MQ0:Int32,MQRankSum:Float64,RAW_MQ:Float64,ReadPosRankSum:Float64,VariantType:String},AB:Float64,DP:Int32,GQ:Int32,MIN_DP:Int32,MQ0:Int32,PID:String,SB:Array[Int32]}]} -1 (Str "Internal e..."))) 2021-04-09 20:37:17 root: INFO: optimize optimize: compileLowerer, initial IR: after: IR size 20: (Coalesce (If (IsNA (GetField __entries (In +PCStruct{locus:+PCLocus(GRCh38),alleles:PCArray[PCString],rsid:PCString,__entries:+PCArray[PCStruct{LA:+PCArray[PInt32],LGT:PCCall,LAD:PCArray[PInt32],LPGT:PCCall,LPL:PCArray[PInt32],RGQ:PInt32,END:PInt32,gvcf_info:PCStruct{BaseQRankSum:PFloat64,ClippingRankSum:PFloat64,DS:+PBoolean,ExcessHet:PFloat64,HaplotypeScore:PFloat64,InbreedingCoeff:PFloat64,MLEAC:PCArray[PInt32],MLEAF:PCArray[PFloat64],MQ:PFloat64,MQ0:PInt32,MQRankSum:PFloat64,RAW_MQ:PFloat64,ReadPosRankSum:PFloat64,VariantType:PCString},AB:PFloat64,DP:PInt32,GQ:PInt32,MIN_DP:PInt32,MQ0:PInt32,PID:PCString,SB:PCArray[PInt32]}]} 1))) (Die Struct{locus:Locus(GRCh38),alleles:Array[String],rsid:String,__entries:Array[Struct{LA:Array[Int32],LGT:Call,LAD:Array[Int32],LPGT:Call,LPL:Array[Int32],RGQ:Int32,END:Int32,gvcf_info:Struct{BaseQRankSum:Float64,ClippingRankSum:Float64,DS:Boolean,ExcessHet:Float64,HaplotypeScore:Float64,InbreedingCoeff:Float64,MLEAC:Array[Int32],MLEAF:Array[Float64],MQ:Float64,MQ0:Int32,MQRankSum:Float64,RAW_MQ:Float64,ReadPosRankSum:Float64,VariantType:String},AB:Float64,DP:Int32,GQ:Int32,MIN_DP:Int32,MQ0:Int32,PID:String,SB:Array[Int32]}]} -1 (Str "missing en...")) (If (ApplyComparisonOp NEQWithNA (ArrayLen (GetField __entries (In +PCStruct{locus:+PCLocus(GRCh38),alleles:PCArray[PCString],rsid:PCString,__entries:+PCArray[PCStruct{LA:+PCArray[PInt32],LGT:PCCall,LAD:PCArray[PInt32],LPGT:PCCall,LPL:PCArray[PInt32],RGQ:PInt32,END:PInt32,gvcf_info:PCStruct{BaseQRankSum:PFloat64,ClippingRankSum:PFloat64,DS:+PBoolean,ExcessHet:PFloat64,HaplotypeScore:PFloat64,InbreedingCoeff:PFloat64,MLEAC:PCArray[PInt32],MLEAF:PCArray[PFloat64],MQ:PFloat64,MQ0:PInt32,MQRankSum:PFloat64,RAW_MQ:PFloat64,ReadPosRankSum:PFloat64,VariantType:PCString},AB:PFloat64,DP:PInt32,GQ:PInt32,MIN_DP:PInt32,MQ0:PInt32,PID:PCString,SB:PCArray[PInt32]}]} 1))) (ArrayLen (GetField __cols (In +PCStruct{__cols:+PCArray[+PCStruct{s:+PCString}]} 0)))) (Die Struct{locus:Locus(GRCh38),alleles:Array[String],rsid:String,__entries:Array[Struct{LA:Array[Int32],LGT:Call,LAD:Array[Int32],LPGT:Call,LPL:Array[Int32],RGQ:Int32,END:Int32,gvcf_info:Struct{BaseQRankSum:Float64,ClippingRankSum:Float64,DS:Boolean,ExcessHet:Float64,HaplotypeScore:Float64,InbreedingCoeff:Float64,MLEAC:Array[Int32],MLEAF:Array[Float64],MQ:Float64,MQ0:Int32,MQRankSum:Float64,RAW_MQ:Float64,ReadPosRankSum:Float64,VariantType:String},AB:Float64,DP:Int32,GQ:Int32,MIN_DP:Int32,MQ0:Int32,PID:String,SB:Array[Int32]}]} -1 (Str "length mis...")) (In +PCStruct{locus:+PCLocus(GRCh38),alleles:PCArray[PCString],rsid:PCString,__entries:+PCArray[PCStruct{LA:+PCArray[PInt32],LGT:PCCall,LAD:PCArray[PInt32],LPGT:PCCall,LPL:PCArray[PInt32],RGQ:PInt32,END:PInt32,gvcf_info:PCStruct{BaseQRankSum:PFloat64,ClippingRankSum:PFloat64,DS:+PBoolean,ExcessHet:PFloat64,HaplotypeScore:PFloat64,InbreedingCoeff:PFloat64,MLEAC:PCArray[PInt32],MLEAF:PCArray[PFloat64],MQ:PFloat64,MQ0:PInt32,MQRankSum:PFloat64,RAW_MQ:PFloat64,ReadPosRankSum:PFloat64,VariantType:PCString},AB:PFloat64,DP:PInt32,GQ:PInt32,MIN_DP:PInt32,MQ0:PInt32,PID:PCString,SB:PCArray[PInt32]}]} 1))) (Die Struct{locus:Locus(GRCh38),alleles:Array[String],rsid:String,__entries:Array[Struct{LA:Array[Int32],LGT:Call,LAD:Array[Int32],LPGT:Call,LPL:Array[Int32],RGQ:Int32,END:Int32,gvcf_info:Struct{BaseQRankSum:Float64,ClippingRankSum:Float64,DS:Boolean,ExcessHet:Float64,HaplotypeScore:Float64,InbreedingCoeff:Float64,MLEAC:Array[Int32],MLEAF:Array[Float64],MQ:Float64,MQ0:Int32,MQRankSum:Float64,RAW_MQ:Float64,ReadPosRankSum:Float64,VariantType:String},AB:Float64,DP:Int32,GQ:Int32,MIN_DP:Int32,MQ0:Int32,PID:String,SB:Array[Int32]}]} -1 (Str "Internal e..."))) 2021-04-09 20:37:17 root: INFO: optimize optimize: compileLowerer, after InlineApplyIR: before: IR size 20: (Coalesce (If (IsNA (GetField __entries (In +PCStruct{locus:+PCLocus(GRCh38),alleles:PCArray[PCString],rsid:PCString,__entries:+PCArray[PCStruct{LA:+PCArray[PInt32],LGT:PCCall,LAD:PCArray[PInt32],LPGT:PCCall,LPL:PCArray[PInt32],RGQ:PInt32,END:PInt32,gvcf_info:PCStruct{BaseQRankSum:PFloat64,ClippingRankSum:PFloat64,DS:+PBoolean,ExcessHet:PFloat64,HaplotypeScore:PFloat64,InbreedingCoeff:PFloat64,MLEAC:PCArray[PInt32],MLEAF:PCArray[PFloat64],MQ:PFloat64,MQ0:PInt32,MQRankSum:PFloat64,RAW_MQ:PFloat64,ReadPosRankSum:PFloat64,VariantType:PCString},AB:PFloat64,DP:PInt32,GQ:PInt32,MIN_DP:PInt32,MQ0:PInt32,PID:PCString,SB:PCArray[PInt32]}]} 1))) (Die Struct{locus:Locus(GRCh38),alleles:Array[String],rsid:String,__entries:Array[Struct{LA:Array[Int32],LGT:Call,LAD:Array[Int32],LPGT:Call,LPL:Array[Int32],RGQ:Int32,END:Int32,gvcf_info:Struct{BaseQRankSum:Float64,ClippingRankSum:Float64,DS:Boolean,ExcessHet:Float64,HaplotypeScore:Float64,InbreedingCoeff:Float64,MLEAC:Array[Int32],MLEAF:Array[Float64],MQ:Float64,MQ0:Int32,MQRankSum:Float64,RAW_MQ:Float64,ReadPosRankSum:Float64,VariantType:String},AB:Float64,DP:Int32,GQ:Int32,MIN_DP:Int32,MQ0:Int32,PID:String,SB:Array[Int32]}]} -1 (Str "missing en...")) (If (ApplyComparisonOp NEQWithNA (ArrayLen (GetField __entries (In +PCStruct{locus:+PCLocus(GRCh38),alleles:PCArray[PCString],rsid:PCString,__entries:+PCArray[PCStruct{LA:+PCArray[PInt32],LGT:PCCall,LAD:PCArray[PInt32],LPGT:PCCall,LPL:PCArray[PInt32],RGQ:PInt32,END:PInt32,gvcf_info:PCStruct{BaseQRankSum:PFloat64,ClippingRankSum:PFloat64,DS:+PBoolean,ExcessHet:PFloat64,HaplotypeScore:PFloat64,InbreedingCoeff:PFloat64,MLEAC:PCArray[PInt32],MLEAF:PCArray[PFloat64],MQ:PFloat64,MQ0:PInt32,MQRankSum:PFloat64,RAW_MQ:PFloat64,ReadPosRankSum:PFloat64,VariantType:PCString},AB:PFloat64,DP:PInt32,GQ:PInt32,MIN_DP:PInt32,MQ0:PInt32,PID:PCString,SB:PCArray[PInt32]}]} 1))) (ArrayLen (GetField __cols (In +PCStruct{__cols:+PCArray[+PCStruct{s:+PCString}]} 0)))) (Die Struct{locus:Locus(GRCh38),alleles:Array[String],rsid:String,__entries:Array[Struct{LA:Array[Int32],LGT:Call,LAD:Array[Int32],LPGT:Call,LPL:Array[Int32],RGQ:Int32,END:Int32,gvcf_info:Struct{BaseQRankSum:Float64,ClippingRankSum:Float64,DS:Boolean,ExcessHet:Float64,HaplotypeScore:Float64,InbreedingCoeff:Float64,MLEAC:Array[Int32],MLEAF:Array[Float64],MQ:Float64,MQ0:Int32,MQRankSum:Float64,RAW_MQ:Float64,ReadPosRankSum:Float64,VariantType:String},AB:Float64,DP:Int32,GQ:Int32,MIN_DP:Int32,MQ0:Int32,PID:String,SB:Array[Int32]}]} -1 (Str "length mis...")) (In +PCStruct{locus:+PCLocus(GRCh38),alleles:PCArray[PCString],rsid:PCString,__entries:+PCArray[PCStruct{LA:+PCArray[PInt32],LGT:PCCall,LAD:PCArray[PInt32],LPGT:PCCall,LPL:PCArray[PInt32],RGQ:PInt32,END:PInt32,gvcf_info:PCStruct{BaseQRankSum:PFloat64,ClippingRankSum:PFloat64,DS:+PBoolean,ExcessHet:PFloat64,HaplotypeScore:PFloat64,InbreedingCoeff:PFloat64,MLEAC:PCArray[PInt32],MLEAF:PCArray[PFloat64],MQ:PFloat64,MQ0:PInt32,MQRankSum:PFloat64,RAW_MQ:PFloat64,ReadPosRankSum:PFloat64,VariantType:PCString},AB:PFloat64,DP:PInt32,GQ:PInt32,MIN_DP:PInt32,MQ0:PInt32,PID:PCString,SB:PCArray[PInt32]}]} 1))) (Die Struct{locus:Locus(GRCh38),alleles:Array[String],rsid:String,__entries:Array[Struct{LA:Array[Int32],LGT:Call,LAD:Array[Int32],LPGT:Call,LPL:Array[Int32],RGQ:Int32,END:Int32,gvcf_info:Struct{BaseQRankSum:Float64,ClippingRankSum:Float64,DS:Boolean,ExcessHet:Float64,HaplotypeScore:Float64,InbreedingCoeff:Float64,MLEAC:Array[Int32],MLEAF:Array[Float64],MQ:Float64,MQ0:Int32,MQRankSum:Float64,RAW_MQ:Float64,ReadPosRankSum:Float64,VariantType:String},AB:Float64,DP:Int32,GQ:Int32,MIN_DP:Int32,MQ0:Int32,PID:String,SB:Array[Int32]}]} -1 (Str "Internal e..."))) 2021-04-09 20:37:17 root: INFO: optimize optimize: compileLowerer, after InlineApplyIR: after: IR size 20: (Coalesce (If (IsNA (GetField __entries (In +PCStruct{locus:+PCLocus(GRCh38),alleles:PCArray[PCString],rsid:PCString,__entries:+PCArray[PCStruct{LA:+PCArray[PInt32],LGT:PCCall,LAD:PCArray[PInt32],LPGT:PCCall,LPL:PCArray[PInt32],RGQ:PInt32,END:PInt32,gvcf_info:PCStruct{BaseQRankSum:PFloat64,ClippingRankSum:PFloat64,DS:+PBoolean,ExcessHet:PFloat64,HaplotypeScore:PFloat64,InbreedingCoeff:PFloat64,MLEAC:PCArray[PInt32],MLEAF:PCArray[PFloat64],MQ:PFloat64,MQ0:PInt32,MQRankSum:PFloat64,RAW_MQ:PFloat64,ReadPosRankSum:PFloat64,VariantType:PCString},AB:PFloat64,DP:PInt32,GQ:PInt32,MIN_DP:PInt32,MQ0:PInt32,PID:PCString,SB:PCArray[PInt32]}]} 1))) (Die Struct{locus:Locus(GRCh38),alleles:Array[String],rsid:String,__entries:Array[Struct{LA:Array[Int32],LGT:Call,LAD:Array[Int32],LPGT:Call,LPL:Array[Int32],RGQ:Int32,END:Int32,gvcf_info:Struct{BaseQRankSum:Float64,ClippingRankSum:Float64,DS:Boolean,ExcessHet:Float64,HaplotypeScore:Float64,InbreedingCoeff:Float64,MLEAC:Array[Int32],MLEAF:Array[Float64],MQ:Float64,MQ0:Int32,MQRankSum:Float64,RAW_MQ:Float64,ReadPosRankSum:Float64,VariantType:String},AB:Float64,DP:Int32,GQ:Int32,MIN_DP:Int32,MQ0:Int32,PID:String,SB:Array[Int32]}]} -1 (Str "missing en...")) (If (ApplyComparisonOp NEQWithNA (ArrayLen (GetField __entries (In +PCStruct{locus:+PCLocus(GRCh38),alleles:PCArray[PCString],rsid:PCString,__entries:+PCArray[PCStruct{LA:+PCArray[PInt32],LGT:PCCall,LAD:PCArray[PInt32],LPGT:PCCall,LPL:PCArray[PInt32],RGQ:PInt32,END:PInt32,gvcf_info:PCStruct{BaseQRankSum:PFloat64,ClippingRankSum:PFloat64,DS:+PBoolean,ExcessHet:PFloat64,HaplotypeScore:PFloat64,InbreedingCoeff:PFloat64,MLEAC:PCArray[PInt32],MLEAF:PCArray[PFloat64],MQ:PFloat64,MQ0:PInt32,MQRankSum:PFloat64,RAW_MQ:PFloat64,ReadPosRankSum:PFloat64,VariantType:PCString},AB:PFloat64,DP:PInt32,GQ:PInt32,MIN_DP:PInt32,MQ0:PInt32,PID:PCString,SB:PCArray[PInt32]}]} 1))) (ArrayLen (GetField __cols (In +PCStruct{__cols:+PCArray[+PCStruct{s:+PCString}]} 0)))) (Die Struct{locus:Locus(GRCh38),alleles:Array[String],rsid:String,__entries:Array[Struct{LA:Array[Int32],LGT:Call,LAD:Array[Int32],LPGT:Call,LPL:Array[Int32],RGQ:Int32,END:Int32,gvcf_info:Struct{BaseQRankSum:Float64,ClippingRankSum:Float64,DS:Boolean,ExcessHet:Float64,HaplotypeScore:Float64,InbreedingCoeff:Float64,MLEAC:Array[Int32],MLEAF:Array[Float64],MQ:Float64,MQ0:Int32,MQRankSum:Float64,RAW_MQ:Float64,ReadPosRankSum:Float64,VariantType:String},AB:Float64,DP:Int32,GQ:Int32,MIN_DP:Int32,MQ0:Int32,PID:String,SB:Array[Int32]}]} -1 (Str "length mis...")) (In +PCStruct{locus:+PCLocus(GRCh38),alleles:PCArray[PCString],rsid:PCString,__entries:+PCArray[PCStruct{LA:+PCArray[PInt32],LGT:PCCall,LAD:PCArray[PInt32],LPGT:PCCall,LPL:PCArray[PInt32],RGQ:PInt32,END:PInt32,gvcf_info:PCStruct{BaseQRankSum:PFloat64,ClippingRankSum:PFloat64,DS:+PBoolean,ExcessHet:PFloat64,HaplotypeScore:PFloat64,InbreedingCoeff:PFloat64,MLEAC:PCArray[PInt32],MLEAF:PCArray[PFloat64],MQ:PFloat64,MQ0:PInt32,MQRankSum:PFloat64,RAW_MQ:PFloat64,ReadPosRankSum:PFloat64,VariantType:PCString},AB:PFloat64,DP:PInt32,GQ:PInt32,MIN_DP:PInt32,MQ0:PInt32,PID:PCString,SB:PCArray[PInt32]}]} 1))) (Die Struct{locus:Locus(GRCh38),alleles:Array[String],rsid:String,__entries:Array[Struct{LA:Array[Int32],LGT:Call,LAD:Array[Int32],LPGT:Call,LPL:Array[Int32],RGQ:Int32,END:Int32,gvcf_info:Struct{BaseQRankSum:Float64,ClippingRankSum:Float64,DS:Boolean,ExcessHet:Float64,HaplotypeScore:Float64,InbreedingCoeff:Float64,MLEAC:Array[Int32],MLEAF:Array[Float64],MQ:Float64,MQ0:Int32,MQRankSum:Float64,RAW_MQ:Float64,ReadPosRankSum:Float64,VariantType:String},AB:Float64,DP:Int32,GQ:Int32,MIN_DP:Int32,MQ0:Int32,PID:String,SB:Array[Int32]}]} -1 (Str "Internal e..."))) 2021-04-09 20:37:17 root: INFO: optimize optimize: compileLowerer, after LowerArrayAggsToRunAggs: before: IR size 20: (Coalesce (If (IsNA (GetField __entries (In +PCStruct{locus:+PCLocus(GRCh38),alleles:PCArray[PCString],rsid:PCString,__entries:+PCArray[PCStruct{LA:+PCArray[PInt32],LGT:PCCall,LAD:PCArray[PInt32],LPGT:PCCall,LPL:PCArray[PInt32],RGQ:PInt32,END:PInt32,gvcf_info:PCStruct{BaseQRankSum:PFloat64,ClippingRankSum:PFloat64,DS:+PBoolean,ExcessHet:PFloat64,HaplotypeScore:PFloat64,InbreedingCoeff:PFloat64,MLEAC:PCArray[PInt32],MLEAF:PCArray[PFloat64],MQ:PFloat64,MQ0:PInt32,MQRankSum:PFloat64,RAW_MQ:PFloat64,ReadPosRankSum:PFloat64,VariantType:PCString},AB:PFloat64,DP:PInt32,GQ:PInt32,MIN_DP:PInt32,MQ0:PInt32,PID:PCString,SB:PCArray[PInt32]}]} 1))) (Die Struct{locus:Locus(GRCh38),alleles:Array[String],rsid:String,__entries:Array[Struct{LA:Array[Int32],LGT:Call,LAD:Array[Int32],LPGT:Call,LPL:Array[Int32],RGQ:Int32,END:Int32,gvcf_info:Struct{BaseQRankSum:Float64,ClippingRankSum:Float64,DS:Boolean,ExcessHet:Float64,HaplotypeScore:Float64,InbreedingCoeff:Float64,MLEAC:Array[Int32],MLEAF:Array[Float64],MQ:Float64,MQ0:Int32,MQRankSum:Float64,RAW_MQ:Float64,ReadPosRankSum:Float64,VariantType:String},AB:Float64,DP:Int32,GQ:Int32,MIN_DP:Int32,MQ0:Int32,PID:String,SB:Array[Int32]}]} -1 (Str "missing en...")) (If (ApplyComparisonOp NEQWithNA (ArrayLen (GetField __entries (In +PCStruct{locus:+PCLocus(GRCh38),alleles:PCArray[PCString],rsid:PCString,__entries:+PCArray[PCStruct{LA:+PCArray[PInt32],LGT:PCCall,LAD:PCArray[PInt32],LPGT:PCCall,LPL:PCArray[PInt32],RGQ:PInt32,END:PInt32,gvcf_info:PCStruct{BaseQRankSum:PFloat64,ClippingRankSum:PFloat64,DS:+PBoolean,ExcessHet:PFloat64,HaplotypeScore:PFloat64,InbreedingCoeff:PFloat64,MLEAC:PCArray[PInt32],MLEAF:PCArray[PFloat64],MQ:PFloat64,MQ0:PInt32,MQRankSum:PFloat64,RAW_MQ:PFloat64,ReadPosRankSum:PFloat64,VariantType:PCString},AB:PFloat64,DP:PInt32,GQ:PInt32,MIN_DP:PInt32,MQ0:PInt32,PID:PCString,SB:PCArray[PInt32]}]} 1))) (ArrayLen (GetField __cols (In +PCStruct{__cols:+PCArray[+PCStruct{s:+PCString}]} 0)))) (Die Struct{locus:Locus(GRCh38),alleles:Array[String],rsid:String,__entries:Array[Struct{LA:Array[Int32],LGT:Call,LAD:Array[Int32],LPGT:Call,LPL:Array[Int32],RGQ:Int32,END:Int32,gvcf_info:Struct{BaseQRankSum:Float64,ClippingRankSum:Float64,DS:Boolean,ExcessHet:Float64,HaplotypeScore:Float64,InbreedingCoeff:Float64,MLEAC:Array[Int32],MLEAF:Array[Float64],MQ:Float64,MQ0:Int32,MQRankSum:Float64,RAW_MQ:Float64,ReadPosRankSum:Float64,VariantType:String},AB:Float64,DP:Int32,GQ:Int32,MIN_DP:Int32,MQ0:Int32,PID:String,SB:Array[Int32]}]} -1 (Str "length mis...")) (In +PCStruct{locus:+PCLocus(GRCh38),alleles:PCArray[PCString],rsid:PCString,__entries:+PCArray[PCStruct{LA:+PCArray[PInt32],LGT:PCCall,LAD:PCArray[PInt32],LPGT:PCCall,LPL:PCArray[PInt32],RGQ:PInt32,END:PInt32,gvcf_info:PCStruct{BaseQRankSum:PFloat64,ClippingRankSum:PFloat64,DS:+PBoolean,ExcessHet:PFloat64,HaplotypeScore:PFloat64,InbreedingCoeff:PFloat64,MLEAC:PCArray[PInt32],MLEAF:PCArray[PFloat64],MQ:PFloat64,MQ0:PInt32,MQRankSum:PFloat64,RAW_MQ:PFloat64,ReadPosRankSum:PFloat64,VariantType:PCString},AB:PFloat64,DP:PInt32,GQ:PInt32,MIN_DP:PInt32,MQ0:PInt32,PID:PCString,SB:PCArray[PInt32]}]} 1))) (Die Struct{locus:Locus(GRCh38),alleles:Array[String],rsid:String,__entries:Array[Struct{LA:Array[Int32],LGT:Call,LAD:Array[Int32],LPGT:Call,LPL:Array[Int32],RGQ:Int32,END:Int32,gvcf_info:Struct{BaseQRankSum:Float64,ClippingRankSum:Float64,DS:Boolean,ExcessHet:Float64,HaplotypeScore:Float64,InbreedingCoeff:Float64,MLEAC:Array[Int32],MLEAF:Array[Float64],MQ:Float64,MQ0:Int32,MQRankSum:Float64,RAW_MQ:Float64,ReadPosRankSum:Float64,VariantType:String},AB:Float64,DP:Int32,GQ:Int32,MIN_DP:Int32,MQ0:Int32,PID:String,SB:Array[Int32]}]} -1 (Str "Internal e..."))) 2021-04-09 20:37:17 root: INFO: optimize optimize: compileLowerer, after LowerArrayAggsToRunAggs: after: IR size 20: (Coalesce (If (IsNA (GetField __entries (In +PCStruct{locus:+PCLocus(GRCh38),alleles:PCArray[PCString],rsid:PCString,__entries:+PCArray[PCStruct{LA:+PCArray[PInt32],LGT:PCCall,LAD:PCArray[PInt32],LPGT:PCCall,LPL:PCArray[PInt32],RGQ:PInt32,END:PInt32,gvcf_info:PCStruct{BaseQRankSum:PFloat64,ClippingRankSum:PFloat64,DS:+PBoolean,ExcessHet:PFloat64,HaplotypeScore:PFloat64,InbreedingCoeff:PFloat64,MLEAC:PCArray[PInt32],MLEAF:PCArray[PFloat64],MQ:PFloat64,MQ0:PInt32,MQRankSum:PFloat64,RAW_MQ:PFloat64,ReadPosRankSum:PFloat64,VariantType:PCString},AB:PFloat64,DP:PInt32,GQ:PInt32,MIN_DP:PInt32,MQ0:PInt32,PID:PCString,SB:PCArray[PInt32]}]} 1))) (Die Struct{locus:Locus(GRCh38),alleles:Array[String],rsid:String,__entries:Array[Struct{LA:Array[Int32],LGT:Call,LAD:Array[Int32],LPGT:Call,LPL:Array[Int32],RGQ:Int32,END:Int32,gvcf_info:Struct{BaseQRankSum:Float64,ClippingRankSum:Float64,DS:Boolean,ExcessHet:Float64,HaplotypeScore:Float64,InbreedingCoeff:Float64,MLEAC:Array[Int32],MLEAF:Array[Float64],MQ:Float64,MQ0:Int32,MQRankSum:Float64,RAW_MQ:Float64,ReadPosRankSum:Float64,VariantType:String},AB:Float64,DP:Int32,GQ:Int32,MIN_DP:Int32,MQ0:Int32,PID:String,SB:Array[Int32]}]} -1 (Str "missing en...")) (If (ApplyComparisonOp NEQWithNA (ArrayLen (GetField __entries (In +PCStruct{locus:+PCLocus(GRCh38),alleles:PCArray[PCString],rsid:PCString,__entries:+PCArray[PCStruct{LA:+PCArray[PInt32],LGT:PCCall,LAD:PCArray[PInt32],LPGT:PCCall,LPL:PCArray[PInt32],RGQ:PInt32,END:PInt32,gvcf_info:PCStruct{BaseQRankSum:PFloat64,ClippingRankSum:PFloat64,DS:+PBoolean,ExcessHet:PFloat64,HaplotypeScore:PFloat64,InbreedingCoeff:PFloat64,MLEAC:PCArray[PInt32],MLEAF:PCArray[PFloat64],MQ:PFloat64,MQ0:PInt32,MQRankSum:PFloat64,RAW_MQ:PFloat64,ReadPosRankSum:PFloat64,VariantType:PCString},AB:PFloat64,DP:PInt32,GQ:PInt32,MIN_DP:PInt32,MQ0:PInt32,PID:PCString,SB:PCArray[PInt32]}]} 1))) (ArrayLen (GetField __cols (In +PCStruct{__cols:+PCArray[+PCStruct{s:+PCString}]} 0)))) (Die Struct{locus:Locus(GRCh38),alleles:Array[String],rsid:String,__entries:Array[Struct{LA:Array[Int32],LGT:Call,LAD:Array[Int32],LPGT:Call,LPL:Array[Int32],RGQ:Int32,END:Int32,gvcf_info:Struct{BaseQRankSum:Float64,ClippingRankSum:Float64,DS:Boolean,ExcessHet:Float64,HaplotypeScore:Float64,InbreedingCoeff:Float64,MLEAC:Array[Int32],MLEAF:Array[Float64],MQ:Float64,MQ0:Int32,MQRankSum:Float64,RAW_MQ:Float64,ReadPosRankSum:Float64,VariantType:String},AB:Float64,DP:Int32,GQ:Int32,MIN_DP:Int32,MQ0:Int32,PID:String,SB:Array[Int32]}]} -1 (Str "length mis...")) (In +PCStruct{locus:+PCLocus(GRCh38),alleles:PCArray[PCString],rsid:PCString,__entries:+PCArray[PCStruct{LA:+PCArray[PInt32],LGT:PCCall,LAD:PCArray[PInt32],LPGT:PCCall,LPL:PCArray[PInt32],RGQ:PInt32,END:PInt32,gvcf_info:PCStruct{BaseQRankSum:PFloat64,ClippingRankSum:PFloat64,DS:+PBoolean,ExcessHet:PFloat64,HaplotypeScore:PFloat64,InbreedingCoeff:PFloat64,MLEAC:PCArray[PInt32],MLEAF:PCArray[PFloat64],MQ:PFloat64,MQ0:PInt32,MQRankSum:PFloat64,RAW_MQ:PFloat64,ReadPosRankSum:PFloat64,VariantType:PCString},AB:PFloat64,DP:PInt32,GQ:PInt32,MIN_DP:PInt32,MQ0:PInt32,PID:PCString,SB:PCArray[PInt32]}]} 1))) (Die Struct{locus:Locus(GRCh38),alleles:Array[String],rsid:String,__entries:Array[Struct{LA:Array[Int32],LGT:Call,LAD:Array[Int32],LPGT:Call,LPL:Array[Int32],RGQ:Int32,END:Int32,gvcf_info:Struct{BaseQRankSum:Float64,ClippingRankSum:Float64,DS:Boolean,ExcessHet:Float64,HaplotypeScore:Float64,InbreedingCoeff:Float64,MLEAC:Array[Int32],MLEAF:Array[Float64],MQ:Float64,MQ0:Int32,MQRankSum:Float64,RAW_MQ:Float64,ReadPosRankSum:Float64,VariantType:String},AB:Float64,DP:Int32,GQ:Int32,MIN_DP:Int32,MQ0:Int32,PID:String,SB:Array[Int32]}]} -1 (Str "Internal e..."))) 2021-04-09 20:37:17 root: INFO: encoder cache miss (1 hits, 7 misses, 0.125) 2021-04-09 20:37:17 root: INFO: instruction count: 3: __C779etypeEncode. 2021-04-09 20:37:17 root: INFO: instruction count: 5: __C779etypeEncode.apply 2021-04-09 20:37:17 root: INFO: instruction count: 33: __C779etypeEncode.__m780ENCODE_r_tuple_of_r_stringANDr_stringANDr_stringEND_TO_r_struct_of_r_binaryANDr_binaryANDr_binaryEND 2021-04-09 20:37:17 root: INFO: instruction count: 18: __C779etypeEncode.__m781ENCODE_r_string_TO_r_binary 2021-04-09 20:37:17 MemoryStore: INFO: Block broadcast_9 stored as values in memory (estimated size 312.0 B, free 21.7 GB) 2021-04-09 20:37:17 MemoryStore: INFO: Block broadcast_9_piece0 stored as bytes in memory (estimated size 228.0 B, free 21.7 GB) 2021-04-09 20:37:17 BlockManagerInfo: INFO: Added broadcast_9_piece0 in memory on answer-m.us-central1-b.c.human-genetics-001.internal:42437 (size: 228.0 B, free: 21.7 GB) 2021-04-09 20:37:17 SparkContext: INFO: Created broadcast 9 from broadcast at SparkBackend.scala:259 2021-04-09 20:37:17 root: INFO: instruction count: 3: __C768Compiled. 2021-04-09 20:37:17 root: INFO: instruction count: 111: __C768Compiled.apply 2021-04-09 20:37:17 root: INFO: instruction count: 34: __C768Compiled.__m770ord_equiv 2021-04-09 20:37:17 root: INFO: instruction count: 12: __C768Compiled.__m771ord_equivNonnull 2021-04-09 20:37:17 root: INFO: instruction count: 9: __C768Compiled.setPartitionIndex 2021-04-09 20:37:17 root: INFO: instruction count: 4: __C768Compiled.addPartitionRegion 2021-04-09 20:37:17 root: INFO: instruction count: 4: __C768Compiled.setPool 2021-04-09 20:37:17 root: INFO: instruction count: 54: __C768Compiled.addLiterals 2021-04-09 20:37:17 root: INFO: instruction count: 37: __C768Compiled.__m777DECODE_r_struct_of_r_binaryANDr_binaryANDr_binaryEND_TO_r_tuple_of_r_stringANDr_stringANDr_stringEND 2021-04-09 20:37:17 root: INFO: instruction count: 33: __C768Compiled.__m778INPLACE_DECODE_r_binary_TO_r_string 2021-04-09 20:37:17 root: INFO: encoder cache hit 2021-04-09 20:37:17 root: INFO: decoder cache hit 2021-04-09 20:37:17 MemoryStore: INFO: Block broadcast_10 stored as values in memory (estimated size 7.2 KB, free 21.7 GB) 2021-04-09 20:37:17 MemoryStore: INFO: Block broadcast_10_piece0 stored as bytes in memory (estimated size 2.3 KB, free 21.7 GB) 2021-04-09 20:37:17 BlockManagerInfo: INFO: Added broadcast_10_piece0 in memory on answer-m.us-central1-b.c.human-genetics-001.internal:42437 (size: 2.3 KB, free: 21.7 GB) 2021-04-09 20:37:17 SparkContext: INFO: Created broadcast 10 from broadcast at SparkBackend.scala:259 2021-04-09 20:37:19 root: INFO: encoder cache miss (2 hits, 8 misses, 0.200) 2021-04-09 20:37:19 root: INFO: instruction count: 3: __C782etypeEncode. 2021-04-09 20:37:19 root: INFO: instruction count: 5: __C782etypeEncode.apply 2021-04-09 20:37:19 root: INFO: instruction count: 69: __C782etypeEncode.__m783ENCODE_r_tuple_of_r_locusANDo_array_of_o_stringANDo_stringANDr_array_of_o_tuple_of_r_array_of_o_int32ANDo_callANDo_array_of_o_int32ANDo_callANDo_array_of_o_int32ANDo_int32ANDo_int32ANDo_tuple_of_o_float64ANDo_float64ANDr_boolANDo_float64ANDo_float64ANDo_float64ANDo_array_of_o_int32ANDo_array_of_o_float64ANDo_float64ANDo_int32ANDo_float64ANDo_float64ANDo_float64ANDo_stringENDANDo_float64ANDo_int32ANDo_int32ANDo_int32ANDo_int32ANDo_stringANDo_array_of_o_int32ENDEND_TO_r_struct_of_r_struct_of_r_binaryANDr_int32ENDANDo_array_of_o_binaryANDo_binaryEND 2021-04-09 20:37:19 root: INFO: instruction count: 39: __C782etypeEncode.__m784ENCODE_r_locus_TO_r_struct_of_r_binaryANDr_int32END 2021-04-09 20:37:19 root: INFO: instruction count: 18: __C782etypeEncode.__m785ENCODE_r_string_TO_r_binary 2021-04-09 20:37:19 root: INFO: instruction count: 6: __C782etypeEncode.__m786ENCODE_r_int32_TO_r_int32 2021-04-09 20:37:19 root: INFO: instruction count: 125: __C782etypeEncode.__m787ENCODE_o_array_of_o_string_TO_o_array_of_o_binary 2021-04-09 20:37:19 root: INFO: instruction count: 18: __C782etypeEncode.__m788ENCODE_o_string_TO_o_binary 2021-04-09 20:37:19 root: INFO: encoder cache miss (2 hits, 9 misses, 0.182) 2021-04-09 20:37:19 root: INFO: instruction count: 3: __C789etypeEncode. 2021-04-09 20:37:19 root: INFO: instruction count: 5: __C789etypeEncode.apply 2021-04-09 20:37:19 root: INFO: instruction count: 13: __C789etypeEncode.__m790ENCODE_r_tuple_of_r_locusANDo_array_of_o_stringANDo_stringANDr_array_of_o_tuple_of_r_array_of_o_int32ANDo_callANDo_array_of_o_int32ANDo_callANDo_array_of_o_int32ANDo_int32ANDo_int32ANDo_tuple_of_o_float64ANDo_float64ANDr_boolANDo_float64ANDo_float64ANDo_float64ANDo_array_of_o_int32ANDo_array_of_o_float64ANDo_float64ANDo_int32ANDo_float64ANDo_float64ANDo_float64ANDo_stringENDANDo_float64ANDo_int32ANDo_int32ANDo_int32ANDo_int32ANDo_stringANDo_array_of_o_int32ENDEND_TO_r_struct_of_r_array_of_o_struct_of_r_array_of_o_int32ANDo_int32ANDo_array_of_o_int32ANDo_int32ANDo_array_of_o_int32ANDo_int32ANDo_int32ANDo_struct_of_o_float64ANDo_float64ANDr_boolANDo_float64ANDo_float64ANDo_float64ANDo_array_of_o_int32ANDo_array_of_o_float64ANDo_float64ANDo_int32ANDo_float64ANDo_float64ANDo_float64ANDo_binaryENDANDo_float64ANDo_int32ANDo_int32ANDo_int32ANDo_int32ANDo_binaryANDo_array_of_o_int32ENDEND 2021-04-09 20:37:19 root: INFO: instruction count: 121: __C789etypeEncode.__m791ENCODE_r_array_of_o_tuple_of_r_array_of_o_int32ANDo_callANDo_array_of_o_int32ANDo_callANDo_array_of_o_int32ANDo_int32ANDo_int32ANDo_tuple_of_o_float64ANDo_float64ANDr_boolANDo_float64ANDo_float64ANDo_float64ANDo_array_of_o_int32ANDo_array_of_o_float64ANDo_float64ANDo_int32ANDo_float64ANDo_float64ANDo_float64ANDo_stringENDANDo_float64ANDo_int32ANDo_int32ANDo_int32ANDo_int32ANDo_stringANDo_array_of_o_int32END_TO_r_array_of_o_struct_of_r_array_of_o_int32ANDo_int32ANDo_array_of_o_int32ANDo_int32ANDo_array_of_o_int32ANDo_int32ANDo_int32ANDo_struct_of_o_float64ANDo_float64ANDr_boolANDo_float64ANDo_float64ANDo_float64ANDo_array_of_o_int32ANDo_array_of_o_float64ANDo_float64ANDo_int32ANDo_float64ANDo_float64ANDo_float64ANDo_binaryENDANDo_float64ANDo_int32ANDo_int32ANDo_int32ANDo_int32ANDo_binaryANDo_array_of_o_int32END 2021-04-09 20:37:19 root: INFO: instruction count: 291: __C789etypeEncode.__m792ENCODE_o_tuple_of_r_array_of_o_int32ANDo_callANDo_array_of_o_int32ANDo_callANDo_array_of_o_int32ANDo_int32ANDo_int32ANDo_tuple_of_o_float64ANDo_float64ANDr_boolANDo_float64ANDo_float64ANDo_float64ANDo_array_of_o_int32ANDo_array_of_o_float64ANDo_float64ANDo_int32ANDo_float64ANDo_float64ANDo_float64ANDo_stringENDANDo_float64ANDo_int32ANDo_int32ANDo_int32ANDo_int32ANDo_stringANDo_array_of_o_int32END_TO_o_struct_of_r_array_of_o_int32ANDo_int32ANDo_array_of_o_int32ANDo_int32ANDo_array_of_o_int32ANDo_int32ANDo_int32ANDo_struct_of_o_float64ANDo_float64ANDr_boolANDo_float64ANDo_float64ANDo_float64ANDo_array_of_o_int32ANDo_array_of_o_float64ANDo_float64ANDo_int32ANDo_float64ANDo_float64ANDo_float64ANDo_binaryENDANDo_float64ANDo_int32ANDo_int32ANDo_int32ANDo_int32ANDo_binaryANDo_array_of_o_int32END 2021-04-09 20:37:19 root: INFO: instruction count: 125: __C789etypeEncode.__m793ENCODE_r_array_of_o_int32_TO_r_array_of_o_int32 2021-04-09 20:37:19 root: INFO: instruction count: 6: __C789etypeEncode.__m794ENCODE_o_int32_TO_o_int32 2021-04-09 20:37:19 root: INFO: instruction count: 6: __C789etypeEncode.__m795ENCODE_o_call_TO_o_int32 2021-04-09 20:37:19 root: INFO: instruction count: 125: __C789etypeEncode.__m796ENCODE_o_array_of_o_int32_TO_o_array_of_o_int32 2021-04-09 20:37:19 root: INFO: instruction count: 276: __C789etypeEncode.__m797ENCODE_o_tuple_of_o_float64ANDo_float64ANDr_boolANDo_float64ANDo_float64ANDo_float64ANDo_array_of_o_int32ANDo_array_of_o_float64ANDo_float64ANDo_int32ANDo_float64ANDo_float64ANDo_float64ANDo_stringEND_TO_o_struct_of_o_float64ANDo_float64ANDr_boolANDo_float64ANDo_float64ANDo_float64ANDo_array_of_o_int32ANDo_array_of_o_float64ANDo_float64ANDo_int32ANDo_float64ANDo_float64ANDo_float64ANDo_binaryEND 2021-04-09 20:37:19 root: INFO: instruction count: 6: __C789etypeEncode.__m798ENCODE_o_float64_TO_o_float64 2021-04-09 20:37:19 root: INFO: instruction count: 6: __C789etypeEncode.__m799ENCODE_r_bool_TO_r_bool 2021-04-09 20:37:19 root: INFO: instruction count: 125: __C789etypeEncode.__m800ENCODE_o_array_of_o_float64_TO_o_array_of_o_float64 2021-04-09 20:37:19 root: INFO: instruction count: 18: __C789etypeEncode.__m801ENCODE_o_string_TO_o_binary 2021-04-09 20:37:20 root: INFO: instruction count: 3: __C802indexwriter. 2021-04-09 20:37:20 root: INFO: instruction count: 130: __C802indexwriter.apply 2021-04-09 20:37:20 root: INFO: instruction count: 344: __C802indexwriter.__m811writeInternalNode 2021-04-09 20:37:20 root: INFO: instruction count: 13: __C802indexwriter.__m812ENCODE_o_tuple_of_r_array_of_r_tuple_of_r_int64ANDr_int64ANDr_tuple_of_r_locusENDANDr_int64ANDr_tuple_of_o_int64ENDENDEND_TO_o_struct_of_r_array_of_r_struct_of_r_int64ANDr_int64ANDr_struct_of_r_struct_of_r_binaryANDr_int32ENDENDANDr_int64ANDr_struct_of_o_int64ENDENDEND 2021-04-09 20:37:20 root: INFO: instruction count: 45: __C802indexwriter.__m813ENCODE_r_array_of_r_tuple_of_r_int64ANDr_int64ANDr_tuple_of_r_locusENDANDr_int64ANDr_tuple_of_o_int64ENDEND_TO_r_array_of_r_struct_of_r_int64ANDr_int64ANDr_struct_of_r_struct_of_r_binaryANDr_int32ENDENDANDr_int64ANDr_struct_of_o_int64ENDEND 2021-04-09 20:37:20 root: INFO: instruction count: 45: __C802indexwriter.__m814ENCODE_r_tuple_of_r_int64ANDr_int64ANDr_tuple_of_r_locusENDANDr_int64ANDr_tuple_of_o_int64ENDEND_TO_r_struct_of_r_int64ANDr_int64ANDr_struct_of_r_struct_of_r_binaryANDr_int32ENDENDANDr_int64ANDr_struct_of_o_int64ENDEND 2021-04-09 20:37:20 root: INFO: instruction count: 6: __C802indexwriter.__m815ENCODE_r_int64_TO_r_int64 2021-04-09 20:37:20 root: INFO: instruction count: 9: __C802indexwriter.__m816ENCODE_r_tuple_of_r_locusEND_TO_r_struct_of_r_struct_of_r_binaryANDr_int32ENDEND 2021-04-09 20:37:20 root: INFO: instruction count: 39: __C802indexwriter.__m817ENCODE_r_locus_TO_r_struct_of_r_binaryANDr_int32END 2021-04-09 20:37:20 root: INFO: instruction count: 18: __C802indexwriter.__m818ENCODE_r_string_TO_r_binary 2021-04-09 20:37:20 root: INFO: instruction count: 6: __C802indexwriter.__m819ENCODE_r_int32_TO_r_int32 2021-04-09 20:37:20 root: INFO: instruction count: 34: __C802indexwriter.__m820ENCODE_r_tuple_of_o_int64END_TO_r_struct_of_o_int64END 2021-04-09 20:37:20 root: INFO: instruction count: 6: __C802indexwriter.__m821ENCODE_o_int64_TO_o_int64 2021-04-09 20:37:20 root: INFO: instruction count: 277: __C802indexwriter.__m823writeLeafNode 2021-04-09 20:37:20 root: INFO: instruction count: 23: __C802indexwriter.__m824ENCODE_o_tuple_of_r_int64ANDr_array_of_r_tuple_of_r_tuple_of_r_locusENDANDr_int64ANDr_tuple_of_o_int64ENDENDEND_TO_o_struct_of_r_int64ANDr_array_of_r_struct_of_r_struct_of_r_struct_of_r_binaryANDr_int32ENDENDANDr_int64ANDr_struct_of_o_int64ENDENDEND 2021-04-09 20:37:20 root: INFO: instruction count: 45: __C802indexwriter.__m825ENCODE_r_array_of_r_tuple_of_r_tuple_of_r_locusENDANDr_int64ANDr_tuple_of_o_int64ENDEND_TO_r_array_of_r_struct_of_r_struct_of_r_struct_of_r_binaryANDr_int32ENDENDANDr_int64ANDr_struct_of_o_int64ENDEND 2021-04-09 20:37:20 root: INFO: instruction count: 25: __C802indexwriter.__m826ENCODE_r_tuple_of_r_tuple_of_r_locusENDANDr_int64ANDr_tuple_of_o_int64ENDEND_TO_r_struct_of_r_struct_of_r_struct_of_r_binaryANDr_int32ENDENDANDr_int64ANDr_struct_of_o_int64ENDEND 2021-04-09 20:37:20 root: INFO: instruction count: 52: __C802indexwriter.__m827flush 2021-04-09 20:37:20 root: INFO: instruction count: 152: __C802indexwriter.init 2021-04-09 20:37:20 root: INFO: instruction count: 4: __C802indexwriter.setObjects 2021-04-09 20:37:20 root: INFO: instruction count: 28: __C802indexwriter.close 2021-04-09 20:37:20 root: INFO: instruction count: 7: __C802indexwriter.trackedOS 2021-04-09 20:37:20 root: INFO: instruction count: 9: __C802indexwriter.setPartitionIndex 2021-04-09 20:37:20 root: INFO: instruction count: 4: __C802indexwriter.addPartitionRegion 2021-04-09 20:37:20 root: INFO: instruction count: 4: __C802indexwriter.setPool 2021-04-09 20:37:20 root: INFO: instruction count: 3: __C829FSContainer. 2021-04-09 20:37:20 root: INFO: instruction count: 28: __C829FSContainer.init_filesystem 2021-04-09 20:37:20 root: INFO: instruction count: 3: __C829FSContainer. 2021-04-09 20:37:20 SparkContext: INFO: Starting job: collect at ContextRDD.scala:176 2021-04-09 20:37:20 DAGScheduler: INFO: Got job 1 (collect at ContextRDD.scala:176) with 2586 output partitions 2021-04-09 20:37:20 DAGScheduler: INFO: Final stage: ResultStage 1 (collect at ContextRDD.scala:176) 2021-04-09 20:37:20 DAGScheduler: INFO: Parents of final stage: List() 2021-04-09 20:37:20 DAGScheduler: INFO: Missing parents: List() 2021-04-09 20:37:20 DAGScheduler: INFO: Submitting ResultStage 1 (MapPartitionsRDD[22] at mapPartitions at ContextRDD.scala:168), which has no missing parents 2021-04-09 20:37:20 MemoryStore: INFO: Block broadcast_11 stored as values in memory (estimated size 622.5 KB, free 21.7 GB) 2021-04-09 20:37:20 MemoryStore: INFO: Block broadcast_11_piece0 stored as bytes in memory (estimated size 234.4 KB, free 21.7 GB) 2021-04-09 20:37:20 BlockManagerInfo: INFO: Added broadcast_11_piece0 in memory on answer-m.us-central1-b.c.human-genetics-001.internal:42437 (size: 234.4 KB, free: 21.7 GB) 2021-04-09 20:37:20 SparkContext: INFO: Created broadcast 11 from broadcast at DAGScheduler.scala:1163 2021-04-09 20:37:20 DAGScheduler: INFO: Submitting 2586 missing tasks from ResultStage 1 (MapPartitionsRDD[22] at mapPartitions at ContextRDD.scala:168) (first 15 tasks are for partitions Vector(0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14)) 2021-04-09 20:37:20 YarnScheduler: INFO: Adding task set 1.0 with 2586 tasks 2021-04-09 20:37:20 FairSchedulableBuilder: INFO: Added task set TaskSet_1.0 tasks to pool default 2021-04-09 20:37:20 TaskSetManager: INFO: Starting task 0.0 in stage 1.0 (TID 2, answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1, partition 0, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:20 TaskSetManager: INFO: Starting task 1.0 in stage 1.0 (TID 3, answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2, partition 1, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:20 TaskSetManager: INFO: Starting task 2.0 in stage 1.0 (TID 4, answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1, partition 2, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:20 TaskSetManager: INFO: Starting task 3.0 in stage 1.0 (TID 5, answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2, partition 3, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:20 TaskSetManager: INFO: Starting task 4.0 in stage 1.0 (TID 6, answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1, partition 4, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:20 TaskSetManager: INFO: Starting task 5.0 in stage 1.0 (TID 7, answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2, partition 5, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:20 TaskSetManager: INFO: Starting task 6.0 in stage 1.0 (TID 8, answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1, partition 6, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:20 TaskSetManager: INFO: Starting task 7.0 in stage 1.0 (TID 9, answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2, partition 7, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:20 BlockManagerInfo: INFO: Added broadcast_11_piece0 in memory on answer-w-0.us-central1-b.c.human-genetics-001.internal:39767 (size: 234.4 KB, free: 9.5 GB) 2021-04-09 20:37:20 BlockManagerInfo: INFO: Added broadcast_11_piece0 in memory on answer-w-1.us-central1-b.c.human-genetics-001.internal:45783 (size: 234.4 KB, free: 9.5 GB) 2021-04-09 20:37:20 TaskSetManager: INFO: Starting task 8.0 in stage 1.0 (TID 10, answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1, partition 8, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:20 TaskSetManager: INFO: Starting task 9.0 in stage 1.0 (TID 11, answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1, partition 9, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:20 TaskSetManager: INFO: Starting task 10.0 in stage 1.0 (TID 12, answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1, partition 10, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:20 TaskSetManager: INFO: Starting task 11.0 in stage 1.0 (TID 13, answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2, partition 11, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:20 TaskSetManager: INFO: Starting task 12.0 in stage 1.0 (TID 14, answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2, partition 12, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:20 TaskSetManager: INFO: Starting task 13.0 in stage 1.0 (TID 15, answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2, partition 13, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:20 TaskSetManager: WARN: Lost task 4.0 in stage 1.0 (TID 6, answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1): java.lang.ArrayIndexOutOfBoundsException: 3366 at is.hail.io.tabix.TabixReader$$anonfun$1.apply(TabixReader.scala:116) at is.hail.io.tabix.TabixReader$$anonfun$1.apply(TabixReader.scala:86) at is.hail.utils.package$.using(package.scala:618) at is.hail.io.tabix.TabixReader.(TabixReader.scala:86) at is.hail.io.vcf.PartitionedVCFRDD.compute(LoadVCF.scala:1486) at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:346) at org.apache.spark.rdd.RDD.iterator(RDD.scala:310) at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:52) at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:346) at org.apache.spark.rdd.RDD.iterator(RDD.scala:310) at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:52) at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:346) at org.apache.spark.rdd.RDD.iterator(RDD.scala:310) at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:52) at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:346) at org.apache.spark.rdd.RDD.iterator(RDD.scala:310) at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:52) at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:346) at org.apache.spark.rdd.RDD.iterator(RDD.scala:310) at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:52) at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:346) at org.apache.spark.rdd.RDD.iterator(RDD.scala:310) at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:52) at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:346) at org.apache.spark.rdd.RDD.iterator(RDD.scala:310) at is.hail.sparkextras.MultiWayZipPartitionsRDD$$anonfun$2.apply(MultiWayZipPartitionsRDD.scala:38) at is.hail.sparkextras.MultiWayZipPartitionsRDD$$anonfun$2.apply(MultiWayZipPartitionsRDD.scala:38) at scala.Array$.tabulate(Array.scala:331) at is.hail.sparkextras.MultiWayZipPartitionsRDD.compute(MultiWayZipPartitionsRDD.scala:38) at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:346) at org.apache.spark.rdd.RDD.iterator(RDD.scala:310) at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:52) at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:346) at org.apache.spark.rdd.RDD.iterator(RDD.scala:310) at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:52) at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:346) at org.apache.spark.rdd.RDD.iterator(RDD.scala:310) at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:52) at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:346) at org.apache.spark.rdd.RDD.iterator(RDD.scala:310) at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:52) at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:346) at org.apache.spark.rdd.RDD.iterator(RDD.scala:310) at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:52) at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:346) at org.apache.spark.rdd.RDD.iterator(RDD.scala:310) at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:52) at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:346) at org.apache.spark.rdd.RDD.iterator(RDD.scala:310) 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) 2021-04-09 20:37:20 TaskSetManager: INFO: Lost task 6.0 in stage 1.0 (TID 8) on answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1: java.lang.ArrayIndexOutOfBoundsException (3366) [duplicate 1] 2021-04-09 20:37:20 TaskSetManager: INFO: Lost task 3.0 in stage 1.0 (TID 5) on answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2: java.lang.ArrayIndexOutOfBoundsException (3366) [duplicate 2] 2021-04-09 20:37:20 TaskSetManager: INFO: Lost task 0.0 in stage 1.0 (TID 2) on answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1: java.lang.ArrayIndexOutOfBoundsException (3366) [duplicate 3] 2021-04-09 20:37:20 TaskSetManager: INFO: Lost task 7.0 in stage 1.0 (TID 9) on answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2: java.lang.ArrayIndexOutOfBoundsException (3366) [duplicate 4] 2021-04-09 20:37:20 TaskSetManager: INFO: Starting task 7.1 in stage 1.0 (TID 16, answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2, partition 7, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:20 TaskSetManager: INFO: Lost task 5.0 in stage 1.0 (TID 7) on answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2: java.lang.ArrayIndexOutOfBoundsException (3366) [duplicate 5] 2021-04-09 20:37:20 TaskSetManager: INFO: Lost task 1.0 in stage 1.0 (TID 3) on answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2: java.lang.ArrayIndexOutOfBoundsException (3366) [duplicate 6] 2021-04-09 20:37:20 TaskSetManager: INFO: Starting task 1.1 in stage 1.0 (TID 17, answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1, partition 1, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:20 TaskSetManager: INFO: Lost task 2.0 in stage 1.0 (TID 4) on answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1: java.lang.ArrayIndexOutOfBoundsException (3366) [duplicate 7] 2021-04-09 20:37:20 TaskSetManager: INFO: Starting task 2.1 in stage 1.0 (TID 18, answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1, partition 2, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:20 TaskSetManager: INFO: Lost task 9.0 in stage 1.0 (TID 11) on answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1: java.lang.ArrayIndexOutOfBoundsException (3366) [duplicate 8] 2021-04-09 20:37:20 TaskSetManager: INFO: Starting task 9.1 in stage 1.0 (TID 19, answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2, partition 9, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:20 TaskSetManager: INFO: Lost task 11.0 in stage 1.0 (TID 13) on answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2: java.lang.ArrayIndexOutOfBoundsException (3366) [duplicate 9] 2021-04-09 20:37:20 TaskSetManager: INFO: Starting task 11.1 in stage 1.0 (TID 20, answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2, partition 11, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:20 TaskSetManager: INFO: Lost task 12.0 in stage 1.0 (TID 14) on answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2: java.lang.ArrayIndexOutOfBoundsException (3366) [duplicate 10] 2021-04-09 20:37:20 TaskSetManager: INFO: Starting task 12.1 in stage 1.0 (TID 21, answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1, partition 12, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:20 TaskSetManager: INFO: Lost task 8.0 in stage 1.0 (TID 10) on answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1: java.lang.ArrayIndexOutOfBoundsException (3366) [duplicate 11] 2021-04-09 20:37:20 TaskSetManager: INFO: Starting task 8.1 in stage 1.0 (TID 22, answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2, partition 8, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:20 TaskSetManager: INFO: Lost task 13.0 in stage 1.0 (TID 15) on answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2: java.lang.ArrayIndexOutOfBoundsException (3366) [duplicate 12] 2021-04-09 20:37:20 TaskSetManager: INFO: Starting task 13.1 in stage 1.0 (TID 23, answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1, partition 13, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:20 TaskSetManager: WARN: Lost task 10.0 in stage 1.0 (TID 12, answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1): java.lang.ArrayIndexOutOfBoundsException 2021-04-09 20:37:20 TaskSetManager: INFO: Starting task 10.1 in stage 1.0 (TID 24, answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1, partition 10, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:20 TaskSetManager: INFO: Lost task 1.1 in stage 1.0 (TID 17) on answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1: java.lang.ArrayIndexOutOfBoundsException (null) [duplicate 1] 2021-04-09 20:37:20 TaskSetManager: INFO: Starting task 1.2 in stage 1.0 (TID 25, answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2, partition 1, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:20 TaskSetManager: INFO: Lost task 7.1 in stage 1.0 (TID 16) on answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2: java.lang.ArrayIndexOutOfBoundsException (null) [duplicate 2] 2021-04-09 20:37:20 TaskSetManager: INFO: Starting task 7.2 in stage 1.0 (TID 26, answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1, partition 7, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:20 TaskSetManager: INFO: Lost task 12.1 in stage 1.0 (TID 21) on answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1: java.lang.ArrayIndexOutOfBoundsException (null) [duplicate 3] 2021-04-09 20:37:20 TaskSetManager: INFO: Starting task 12.2 in stage 1.0 (TID 27, answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2, partition 12, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:20 TaskSetManager: INFO: Lost task 9.1 in stage 1.0 (TID 19) on answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2: java.lang.ArrayIndexOutOfBoundsException (null) [duplicate 4] 2021-04-09 20:37:20 TaskSetManager: INFO: Starting task 9.2 in stage 1.0 (TID 28, answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2, partition 9, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:20 TaskSetManager: INFO: Lost task 8.1 in stage 1.0 (TID 22) on answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2: java.lang.ArrayIndexOutOfBoundsException (null) [duplicate 5] 2021-04-09 20:37:20 TaskSetManager: INFO: Starting task 8.2 in stage 1.0 (TID 29, answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1, partition 8, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:20 TaskSetManager: INFO: Lost task 2.1 in stage 1.0 (TID 18) on answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1: java.lang.ArrayIndexOutOfBoundsException (null) [duplicate 6] 2021-04-09 20:37:20 TaskSetManager: INFO: Starting task 2.2 in stage 1.0 (TID 30, answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2, partition 2, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:20 TaskSetManager: INFO: Lost task 11.1 in stage 1.0 (TID 20) on answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2: java.lang.ArrayIndexOutOfBoundsException (null) [duplicate 7] 2021-04-09 20:37:20 TaskSetManager: INFO: Starting task 11.2 in stage 1.0 (TID 31, answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1, partition 11, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:20 TaskSetManager: INFO: Lost task 13.1 in stage 1.0 (TID 23) on answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1: java.lang.ArrayIndexOutOfBoundsException (null) [duplicate 8] 2021-04-09 20:37:20 TaskSetManager: INFO: Starting task 13.2 in stage 1.0 (TID 32, answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2, partition 13, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:20 TaskSetManager: INFO: Lost task 1.2 in stage 1.0 (TID 25) on answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2: java.lang.ArrayIndexOutOfBoundsException (null) [duplicate 9] 2021-04-09 20:37:20 TaskSetManager: INFO: Starting task 1.3 in stage 1.0 (TID 33, answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1, partition 1, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:20 TaskSetManager: INFO: Lost task 10.1 in stage 1.0 (TID 24) on answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1: java.lang.ArrayIndexOutOfBoundsException (null) [duplicate 10] 2021-04-09 20:37:20 TaskSetManager: INFO: Starting task 10.2 in stage 1.0 (TID 34, answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2, partition 10, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:20 TaskSetManager: INFO: Lost task 12.2 in stage 1.0 (TID 27) on answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2: java.lang.ArrayIndexOutOfBoundsException (null) [duplicate 11] 2021-04-09 20:37:20 TaskSetManager: INFO: Starting task 12.3 in stage 1.0 (TID 35, answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2, partition 12, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:20 TaskSetManager: INFO: Lost task 9.2 in stage 1.0 (TID 28) on answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2: java.lang.ArrayIndexOutOfBoundsException (null) [duplicate 12] 2021-04-09 20:37:20 TaskSetManager: INFO: Starting task 9.3 in stage 1.0 (TID 36, answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1, partition 9, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:20 TaskSetManager: INFO: Lost task 7.2 in stage 1.0 (TID 26) on answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1: java.lang.ArrayIndexOutOfBoundsException (null) [duplicate 13] 2021-04-09 20:37:21 TaskSetManager: INFO: Starting task 7.3 in stage 1.0 (TID 37, answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2, partition 7, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:21 TaskSetManager: INFO: Lost task 2.2 in stage 1.0 (TID 30) on answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2: java.lang.ArrayIndexOutOfBoundsException (null) [duplicate 14] 2021-04-09 20:37:21 TaskSetManager: INFO: Starting task 2.3 in stage 1.0 (TID 38, answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1, partition 2, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:21 TaskSetManager: INFO: Lost task 8.2 in stage 1.0 (TID 29) on answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1: java.lang.ArrayIndexOutOfBoundsException (null) [duplicate 15] 2021-04-09 20:37:21 TaskSetManager: INFO: Starting task 8.3 in stage 1.0 (TID 39, answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1, partition 8, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:21 TaskSetManager: INFO: Lost task 11.2 in stage 1.0 (TID 31) on answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1: java.lang.ArrayIndexOutOfBoundsException (null) [duplicate 16] 2021-04-09 20:37:21 TaskSetManager: INFO: Starting task 11.3 in stage 1.0 (TID 40, answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2, partition 11, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:21 TaskSetManager: INFO: Lost task 13.2 in stage 1.0 (TID 32) on answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2: java.lang.ArrayIndexOutOfBoundsException (null) [duplicate 17] 2021-04-09 20:37:21 TaskSetManager: INFO: Starting task 13.3 in stage 1.0 (TID 41, answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1, partition 13, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:21 TaskSetManager: INFO: Lost task 1.3 in stage 1.0 (TID 33) on answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1: java.lang.ArrayIndexOutOfBoundsException (null) [duplicate 18] 2021-04-09 20:37:21 TaskSetManager: INFO: Starting task 1.4 in stage 1.0 (TID 42, answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2, partition 1, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:21 TaskSetManager: INFO: Lost task 10.2 in stage 1.0 (TID 34) on answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2: java.lang.ArrayIndexOutOfBoundsException (null) [duplicate 19] 2021-04-09 20:37:21 TaskSetManager: INFO: Starting task 10.3 in stage 1.0 (TID 43, answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2, partition 10, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:21 TaskSetManager: INFO: Lost task 12.3 in stage 1.0 (TID 35) on answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2: java.lang.ArrayIndexOutOfBoundsException (null) [duplicate 20] 2021-04-09 20:37:21 TaskSetManager: INFO: Starting task 12.4 in stage 1.0 (TID 44, answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2, partition 12, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:21 TaskSetManager: INFO: Lost task 7.3 in stage 1.0 (TID 37) on answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2: java.lang.ArrayIndexOutOfBoundsException (null) [duplicate 21] 2021-04-09 20:37:21 TaskSetManager: INFO: Starting task 7.4 in stage 1.0 (TID 45, answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1, partition 7, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:21 TaskSetManager: INFO: Lost task 9.3 in stage 1.0 (TID 36) on answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1: java.lang.ArrayIndexOutOfBoundsException (null) [duplicate 22] 2021-04-09 20:37:21 TaskSetManager: INFO: Starting task 9.4 in stage 1.0 (TID 46, answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1, partition 9, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:21 TaskSetManager: INFO: Lost task 8.3 in stage 1.0 (TID 39) on answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1: java.lang.ArrayIndexOutOfBoundsException (null) [duplicate 23] 2021-04-09 20:37:21 TaskSetManager: INFO: Starting task 8.4 in stage 1.0 (TID 47, answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2, partition 8, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:21 TaskSetManager: INFO: Lost task 11.3 in stage 1.0 (TID 40) on answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2: java.lang.ArrayIndexOutOfBoundsException (null) [duplicate 24] 2021-04-09 20:37:21 TaskSetManager: INFO: Starting task 11.4 in stage 1.0 (TID 48, answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1, partition 11, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:21 TaskSetManager: INFO: Lost task 2.3 in stage 1.0 (TID 38) on answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1: java.lang.ArrayIndexOutOfBoundsException (null) [duplicate 25] 2021-04-09 20:37:21 TaskSetManager: INFO: Starting task 2.4 in stage 1.0 (TID 49, answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2, partition 2, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:21 TaskSetManager: INFO: Lost task 10.3 in stage 1.0 (TID 43) on answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2: java.lang.ArrayIndexOutOfBoundsException (null) [duplicate 26] 2021-04-09 20:37:21 TaskSetManager: INFO: Starting task 10.4 in stage 1.0 (TID 50, answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2, partition 10, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:21 TaskSetManager: INFO: Lost task 12.4 in stage 1.0 (TID 44) on answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2: java.lang.ArrayIndexOutOfBoundsException (null) [duplicate 27] 2021-04-09 20:37:21 TaskSetManager: INFO: Starting task 12.5 in stage 1.0 (TID 51, answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1, partition 12, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:21 TaskSetManager: INFO: Lost task 13.3 in stage 1.0 (TID 41) on answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1: java.lang.ArrayIndexOutOfBoundsException (null) [duplicate 28] 2021-04-09 20:37:21 TaskSetManager: INFO: Starting task 13.4 in stage 1.0 (TID 52, answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2, partition 13, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:21 TaskSetManager: INFO: Lost task 1.4 in stage 1.0 (TID 42) on answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2: java.lang.ArrayIndexOutOfBoundsException (null) [duplicate 29] 2021-04-09 20:37:21 TaskSetManager: INFO: Starting task 1.5 in stage 1.0 (TID 53, answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1, partition 1, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:21 TaskSetManager: INFO: Lost task 9.4 in stage 1.0 (TID 46) on answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1: java.lang.ArrayIndexOutOfBoundsException (null) [duplicate 30] 2021-04-09 20:37:21 TaskSetManager: INFO: Starting task 9.5 in stage 1.0 (TID 54, answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2, partition 9, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:21 TaskSetManager: INFO: Lost task 8.4 in stage 1.0 (TID 47) on answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2: java.lang.ArrayIndexOutOfBoundsException (null) [duplicate 31] 2021-04-09 20:37:21 TaskSetManager: INFO: Starting task 8.5 in stage 1.0 (TID 55, answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1, partition 8, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:21 TaskSetManager: INFO: Lost task 11.4 in stage 1.0 (TID 48) on answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1: java.lang.ArrayIndexOutOfBoundsException (null) [duplicate 32] 2021-04-09 20:37:21 TaskSetManager: INFO: Starting task 11.5 in stage 1.0 (TID 56, answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1, partition 11, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:21 TaskSetManager: INFO: Lost task 12.5 in stage 1.0 (TID 51) on answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1: java.lang.ArrayIndexOutOfBoundsException (null) [duplicate 33] 2021-04-09 20:37:21 TaskSetManager: INFO: Starting task 12.6 in stage 1.0 (TID 57, answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2, partition 12, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:21 TaskSetManager: INFO: Lost task 10.4 in stage 1.0 (TID 50) on answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2: java.lang.ArrayIndexOutOfBoundsException (null) [duplicate 34] 2021-04-09 20:37:21 TaskSetManager: INFO: Starting task 10.5 in stage 1.0 (TID 58, answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1, partition 10, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:21 TaskSetManager: INFO: Lost task 7.4 in stage 1.0 (TID 45) on answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1: java.lang.ArrayIndexOutOfBoundsException (null) [duplicate 35] 2021-04-09 20:37:21 TaskSetManager: INFO: Starting task 7.5 in stage 1.0 (TID 59, answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2, partition 7, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:21 TaskSetManager: INFO: Lost task 2.4 in stage 1.0 (TID 49) on answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2: java.lang.ArrayIndexOutOfBoundsException (null) [duplicate 36] 2021-04-09 20:37:21 TaskSetManager: INFO: Starting task 2.5 in stage 1.0 (TID 60, answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2, partition 2, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:21 TaskSetManager: INFO: Lost task 9.5 in stage 1.0 (TID 54) on answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2: java.lang.ArrayIndexOutOfBoundsException (null) [duplicate 37] 2021-04-09 20:37:21 TaskSetManager: INFO: Starting task 9.6 in stage 1.0 (TID 61, answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1, partition 9, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:21 TaskSetManager: INFO: Lost task 1.5 in stage 1.0 (TID 53) on answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1: java.lang.ArrayIndexOutOfBoundsException (null) [duplicate 38] 2021-04-09 20:37:21 TaskSetManager: INFO: Starting task 1.6 in stage 1.0 (TID 62, answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1, partition 1, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:21 TaskSetManager: INFO: Lost task 8.5 in stage 1.0 (TID 55) on answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1: java.lang.ArrayIndexOutOfBoundsException (null) [duplicate 39] 2021-04-09 20:37:21 ExecutorAllocationManager: INFO: Requesting 2 new executors because tasks are backlogged (new desired total will be 3) 2021-04-09 20:37:21 TaskSetManager: INFO: Starting task 8.6 in stage 1.0 (TID 63, answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2, partition 8, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:21 TaskSetManager: INFO: Lost task 13.4 in stage 1.0 (TID 52) on answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2: java.lang.ArrayIndexOutOfBoundsException (null) [duplicate 40] 2021-04-09 20:37:21 TaskSetManager: INFO: Starting task 13.5 in stage 1.0 (TID 64, answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2, partition 13, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:21 TaskSetManager: INFO: Lost task 7.5 in stage 1.0 (TID 59) on answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2: java.lang.ArrayIndexOutOfBoundsException (null) [duplicate 41] 2021-04-09 20:37:21 TaskSetManager: INFO: Starting task 7.6 in stage 1.0 (TID 65, answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2, partition 7, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:21 TaskSetManager: INFO: Lost task 12.6 in stage 1.0 (TID 57) on answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2: java.lang.ArrayIndexOutOfBoundsException (null) [duplicate 42] 2021-04-09 20:37:21 TaskSetManager: INFO: Starting task 12.7 in stage 1.0 (TID 66, answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1, partition 12, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:21 TaskSetManager: INFO: Lost task 10.5 in stage 1.0 (TID 58) on answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1: java.lang.ArrayIndexOutOfBoundsException (null) [duplicate 43] 2021-04-09 20:37:21 TaskSetManager: INFO: Starting task 10.6 in stage 1.0 (TID 67, answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1, partition 10, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:21 TaskSetManager: INFO: Lost task 11.5 in stage 1.0 (TID 56) on answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1: java.lang.ArrayIndexOutOfBoundsException (null) [duplicate 44] 2021-04-09 20:37:21 TaskSetManager: INFO: Starting task 11.6 in stage 1.0 (TID 68, answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2, partition 11, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:21 TaskSetManager: INFO: Lost task 2.5 in stage 1.0 (TID 60) on answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2: java.lang.ArrayIndexOutOfBoundsException (null) [duplicate 45] 2021-04-09 20:37:21 TaskSetManager: INFO: Starting task 2.6 in stage 1.0 (TID 69, answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1, partition 2, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:21 TaskSetManager: INFO: Lost task 9.6 in stage 1.0 (TID 61) on answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1: java.lang.ArrayIndexOutOfBoundsException (null) [duplicate 46] 2021-04-09 20:37:21 TaskSetManager: INFO: Starting task 9.7 in stage 1.0 (TID 70, answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2, partition 9, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:21 TaskSetManager: INFO: Lost task 8.6 in stage 1.0 (TID 63) on answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2: java.lang.ArrayIndexOutOfBoundsException (null) [duplicate 47] 2021-04-09 20:37:21 TaskSetManager: INFO: Starting task 8.7 in stage 1.0 (TID 71, answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1, partition 8, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:21 TaskSetManager: INFO: Lost task 1.6 in stage 1.0 (TID 62) on answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1: java.lang.ArrayIndexOutOfBoundsException (null) [duplicate 48] 2021-04-09 20:37:21 TaskSetManager: INFO: Starting task 1.7 in stage 1.0 (TID 72, answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2, partition 1, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:21 TaskSetManager: INFO: Lost task 13.5 in stage 1.0 (TID 64) on answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2: java.lang.ArrayIndexOutOfBoundsException (null) [duplicate 49] 2021-04-09 20:37:21 TaskSetManager: INFO: Starting task 13.6 in stage 1.0 (TID 73, answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2, partition 13, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:21 TaskSetManager: INFO: Lost task 11.6 in stage 1.0 (TID 68) on answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2: java.lang.ArrayIndexOutOfBoundsException (null) [duplicate 50] 2021-04-09 20:37:21 TaskSetManager: INFO: Starting task 11.7 in stage 1.0 (TID 74, answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2, partition 11, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:21 TaskSetManager: INFO: Lost task 7.6 in stage 1.0 (TID 65) on answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2: java.lang.ArrayIndexOutOfBoundsException (null) [duplicate 51] 2021-04-09 20:37:21 TaskSetManager: INFO: Starting task 7.7 in stage 1.0 (TID 75, answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1, partition 7, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:21 TaskSetManager: INFO: Lost task 12.7 in stage 1.0 (TID 66) on answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1: java.lang.ArrayIndexOutOfBoundsException (null) [duplicate 52] 2021-04-09 20:37:21 TaskSetManager: INFO: Starting task 12.8 in stage 1.0 (TID 76, answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1, partition 12, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:21 TaskSetManager: INFO: Lost task 10.6 in stage 1.0 (TID 67) on answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1: java.lang.ArrayIndexOutOfBoundsException (null) [duplicate 53] 2021-04-09 20:37:21 TaskSetManager: INFO: Starting task 10.7 in stage 1.0 (TID 77, answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1, partition 10, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:21 TaskSetManager: INFO: Lost task 2.6 in stage 1.0 (TID 69) on answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1: java.lang.ArrayIndexOutOfBoundsException (null) [duplicate 54] 2021-04-09 20:37:21 TaskSetManager: INFO: Starting task 2.7 in stage 1.0 (TID 78, answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2, partition 2, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:21 TaskSetManager: INFO: Lost task 9.7 in stage 1.0 (TID 70) on answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2: java.lang.ArrayIndexOutOfBoundsException (null) [duplicate 55] 2021-04-09 20:37:21 TaskSetManager: INFO: Starting task 9.8 in stage 1.0 (TID 79, answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2, partition 9, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:21 TaskSetManager: INFO: Lost task 13.6 in stage 1.0 (TID 73) on answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2: java.lang.ArrayIndexOutOfBoundsException (null) [duplicate 56] 2021-04-09 20:37:21 TaskSetManager: INFO: Starting task 13.7 in stage 1.0 (TID 80, answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1, partition 13, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:21 TaskSetManager: INFO: Lost task 8.7 in stage 1.0 (TID 71) on answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1: java.lang.ArrayIndexOutOfBoundsException (null) [duplicate 57] 2021-04-09 20:37:21 TaskSetManager: INFO: Starting task 8.8 in stage 1.0 (TID 81, answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1, partition 8, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:21 TaskSetManager: INFO: Lost task 7.7 in stage 1.0 (TID 75) on answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1: java.lang.ArrayIndexOutOfBoundsException (null) [duplicate 58] 2021-04-09 20:37:21 TaskSetManager: INFO: Starting task 7.8 in stage 1.0 (TID 82, answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2, partition 7, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:21 TaskSetManager: INFO: Lost task 1.7 in stage 1.0 (TID 72) on answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2: java.lang.ArrayIndexOutOfBoundsException (null) [duplicate 59] 2021-04-09 20:37:21 TaskSetManager: INFO: Starting task 1.8 in stage 1.0 (TID 83, answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2, partition 1, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:21 TaskSetManager: INFO: Lost task 11.7 in stage 1.0 (TID 74) on answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2: java.lang.ArrayIndexOutOfBoundsException (null) [duplicate 60] 2021-04-09 20:37:21 TaskSetManager: INFO: Starting task 11.8 in stage 1.0 (TID 84, answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1, partition 11, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:21 TaskSetManager: INFO: Lost task 12.8 in stage 1.0 (TID 76) on answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1: java.lang.ArrayIndexOutOfBoundsException (null) [duplicate 61] 2021-04-09 20:37:21 TaskSetManager: INFO: Starting task 12.9 in stage 1.0 (TID 85, answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1, partition 12, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:21 TaskSetManager: INFO: Lost task 10.7 in stage 1.0 (TID 77) on answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1: java.lang.ArrayIndexOutOfBoundsException (null) [duplicate 62] 2021-04-09 20:37:21 TaskSetManager: INFO: Starting task 10.8 in stage 1.0 (TID 86, answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2, partition 10, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:21 TaskSetManager: INFO: Lost task 2.7 in stage 1.0 (TID 78) on answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2: java.lang.ArrayIndexOutOfBoundsException (null) [duplicate 63] 2021-04-09 20:37:21 TaskSetManager: INFO: Starting task 2.8 in stage 1.0 (TID 87, answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2, partition 2, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:21 TaskSetManager: INFO: Lost task 9.8 in stage 1.0 (TID 79) on answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2: java.lang.ArrayIndexOutOfBoundsException (null) [duplicate 64] 2021-04-09 20:37:21 TaskSetManager: INFO: Starting task 9.9 in stage 1.0 (TID 88, answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2, partition 9, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:21 TaskSetManager: INFO: Lost task 7.8 in stage 1.0 (TID 82) on answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2: java.lang.ArrayIndexOutOfBoundsException (null) [duplicate 65] 2021-04-09 20:37:21 TaskSetManager: INFO: Starting task 7.9 in stage 1.0 (TID 89, answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2, partition 7, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:21 TaskSetManager: INFO: Lost task 1.8 in stage 1.0 (TID 83) on answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2: java.lang.ArrayIndexOutOfBoundsException (null) [duplicate 66] 2021-04-09 20:37:21 TaskSetManager: INFO: Starting task 1.9 in stage 1.0 (TID 90, answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1, partition 1, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:21 TaskSetManager: INFO: Lost task 8.8 in stage 1.0 (TID 81) on answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1: java.lang.ArrayIndexOutOfBoundsException (null) [duplicate 67] 2021-04-09 20:37:21 TaskSetManager: INFO: Starting task 8.9 in stage 1.0 (TID 91, answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1, partition 8, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:21 TaskSetManager: INFO: Lost task 11.8 in stage 1.0 (TID 84) on answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1: java.lang.ArrayIndexOutOfBoundsException (null) [duplicate 68] 2021-04-09 20:37:21 TaskSetManager: INFO: Starting task 11.9 in stage 1.0 (TID 92, answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2, partition 11, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:21 TaskSetManager: INFO: Lost task 2.8 in stage 1.0 (TID 87) on answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2: java.lang.ArrayIndexOutOfBoundsException (null) [duplicate 69] 2021-04-09 20:37:21 TaskSetManager: INFO: Starting task 2.9 in stage 1.0 (TID 93, answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1, partition 2, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:21 TaskSetManager: INFO: Lost task 12.9 in stage 1.0 (TID 85) on answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1: java.lang.ArrayIndexOutOfBoundsException (null) [duplicate 70] 2021-04-09 20:37:21 TaskSetManager: INFO: Starting task 12.10 in stage 1.0 (TID 94, answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2, partition 12, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:21 TaskSetManager: INFO: Lost task 9.9 in stage 1.0 (TID 88) on answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2: java.lang.ArrayIndexOutOfBoundsException (null) [duplicate 71] 2021-04-09 20:37:21 TaskSetManager: INFO: Starting task 9.10 in stage 1.0 (TID 95, answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2, partition 9, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:21 TaskSetManager: INFO: Lost task 10.8 in stage 1.0 (TID 86) on answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2: java.lang.ArrayIndexOutOfBoundsException (null) [duplicate 72] 2021-04-09 20:37:21 TaskSetManager: INFO: Starting task 10.9 in stage 1.0 (TID 96, answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1, partition 10, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:21 TaskSetManager: INFO: Lost task 13.7 in stage 1.0 (TID 80) on answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1: java.lang.ArrayIndexOutOfBoundsException (null) [duplicate 73] 2021-04-09 20:37:21 TaskSetManager: INFO: Starting task 13.8 in stage 1.0 (TID 97, answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2, partition 13, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:21 TaskSetManager: INFO: Lost task 7.9 in stage 1.0 (TID 89) on answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2: java.lang.ArrayIndexOutOfBoundsException (null) [duplicate 74] 2021-04-09 20:37:21 TaskSetManager: INFO: Starting task 7.10 in stage 1.0 (TID 98, answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1, partition 7, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:21 TaskSetManager: INFO: Lost task 8.9 in stage 1.0 (TID 91) on answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1: java.lang.ArrayIndexOutOfBoundsException (null) [duplicate 75] 2021-04-09 20:37:21 TaskSetManager: INFO: Starting task 8.10 in stage 1.0 (TID 99, answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1, partition 8, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:21 TaskSetManager: INFO: Lost task 1.9 in stage 1.0 (TID 90) on answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1: java.lang.ArrayIndexOutOfBoundsException (null) [duplicate 76] 2021-04-09 20:37:21 TaskSetManager: INFO: Starting task 1.10 in stage 1.0 (TID 100, answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1, partition 1, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:21 TaskSetManager: INFO: Lost task 10.9 in stage 1.0 (TID 96) on answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1: java.lang.ArrayIndexOutOfBoundsException (null) [duplicate 77] 2021-04-09 20:37:21 TaskSetManager: INFO: Starting task 10.10 in stage 1.0 (TID 101, answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2, partition 10, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:21 TaskSetManager: INFO: Lost task 12.10 in stage 1.0 (TID 94) on answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2: java.lang.ArrayIndexOutOfBoundsException (null) [duplicate 78] 2021-04-09 20:37:21 TaskSetManager: INFO: Starting task 12.11 in stage 1.0 (TID 102, answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2, partition 12, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:21 TaskSetManager: INFO: Lost task 9.10 in stage 1.0 (TID 95) on answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2: java.lang.ArrayIndexOutOfBoundsException (null) [duplicate 79] 2021-04-09 20:37:21 TaskSetManager: INFO: Starting task 9.11 in stage 1.0 (TID 103, answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1, partition 9, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:21 TaskSetManager: INFO: Lost task 2.9 in stage 1.0 (TID 93) on answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1: java.lang.ArrayIndexOutOfBoundsException (null) [duplicate 80] 2021-04-09 20:37:21 TaskSetManager: INFO: Starting task 2.10 in stage 1.0 (TID 104, answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2, partition 2, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:21 TaskSetManager: INFO: Lost task 11.9 in stage 1.0 (TID 92) on answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2: java.lang.ArrayIndexOutOfBoundsException (null) [duplicate 81] 2021-04-09 20:37:21 TaskSetManager: INFO: Starting task 11.10 in stage 1.0 (TID 105, answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2, partition 11, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:21 TaskSetManager: INFO: Lost task 13.8 in stage 1.0 (TID 97) on answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2: java.lang.ArrayIndexOutOfBoundsException (null) [duplicate 82] 2021-04-09 20:37:21 TaskSetManager: INFO: Starting task 13.9 in stage 1.0 (TID 106, answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1, partition 13, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:21 TaskSetManager: INFO: Lost task 7.10 in stage 1.0 (TID 98) on answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1: java.lang.ArrayIndexOutOfBoundsException (null) [duplicate 83] 2021-04-09 20:37:21 TaskSetManager: INFO: Starting task 7.11 in stage 1.0 (TID 107, answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2, partition 7, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:21 TaskSetManager: INFO: Lost task 10.10 in stage 1.0 (TID 101) on answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2: java.lang.ArrayIndexOutOfBoundsException (null) [duplicate 84] 2021-04-09 20:37:21 TaskSetManager: INFO: Starting task 10.11 in stage 1.0 (TID 108, answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1, partition 10, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:21 TaskSetManager: INFO: Lost task 1.10 in stage 1.0 (TID 100) on answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1: java.lang.ArrayIndexOutOfBoundsException (null) [duplicate 85] 2021-04-09 20:37:21 TaskSetManager: INFO: Starting task 1.11 in stage 1.0 (TID 109, answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1, partition 1, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:21 TaskSetManager: INFO: Lost task 8.10 in stage 1.0 (TID 99) on answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1: java.lang.ArrayIndexOutOfBoundsException (null) [duplicate 86] 2021-04-09 20:37:21 TaskSetManager: INFO: Starting task 8.11 in stage 1.0 (TID 110, answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2, partition 8, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:21 TaskSetManager: INFO: Lost task 2.10 in stage 1.0 (TID 104) on answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2: java.lang.ArrayIndexOutOfBoundsException (null) [duplicate 87] 2021-04-09 20:37:21 TaskSetManager: INFO: Starting task 2.11 in stage 1.0 (TID 111, answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2, partition 2, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:21 TaskSetManager: INFO: Lost task 11.10 in stage 1.0 (TID 105) on answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2: java.lang.ArrayIndexOutOfBoundsException (null) [duplicate 88] 2021-04-09 20:37:21 TaskSetManager: INFO: Starting task 11.11 in stage 1.0 (TID 112, answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1, partition 11, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:21 TaskSetManager: INFO: Lost task 9.11 in stage 1.0 (TID 103) on answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1: java.lang.ArrayIndexOutOfBoundsException (null) [duplicate 89] 2021-04-09 20:37:21 TaskSetManager: INFO: Starting task 9.12 in stage 1.0 (TID 113, answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1, partition 9, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:21 TaskSetManager: INFO: Lost task 13.9 in stage 1.0 (TID 106) on answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1: java.lang.ArrayIndexOutOfBoundsException (null) [duplicate 90] 2021-04-09 20:37:21 TaskSetManager: INFO: Starting task 13.10 in stage 1.0 (TID 114, answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2, partition 13, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:21 TaskSetManager: INFO: Lost task 7.11 in stage 1.0 (TID 107) on answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2: java.lang.ArrayIndexOutOfBoundsException (null) [duplicate 91] 2021-04-09 20:37:21 TaskSetManager: INFO: Starting task 7.12 in stage 1.0 (TID 115, answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2, partition 7, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:21 TaskSetManager: INFO: Lost task 12.11 in stage 1.0 (TID 102) on answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2: java.lang.ArrayIndexOutOfBoundsException (null) [duplicate 92] 2021-04-09 20:37:21 TaskSetManager: INFO: Starting task 12.12 in stage 1.0 (TID 116, answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1, partition 12, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:21 TaskSetManager: INFO: Lost task 1.11 in stage 1.0 (TID 109) on answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1: java.lang.ArrayIndexOutOfBoundsException (null) [duplicate 93] 2021-04-09 20:37:22 TaskSetManager: INFO: Starting task 1.12 in stage 1.0 (TID 117, answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2, partition 1, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:22 TaskSetManager: INFO: Lost task 2.11 in stage 1.0 (TID 111) on answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2: java.lang.ArrayIndexOutOfBoundsException (null) [duplicate 94] 2021-04-09 20:37:22 TaskSetManager: INFO: Starting task 2.12 in stage 1.0 (TID 118, answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1, partition 2, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:22 TaskSetManager: INFO: Lost task 11.11 in stage 1.0 (TID 112) on answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1: java.lang.ArrayIndexOutOfBoundsException (null) [duplicate 95] 2021-04-09 20:37:22 TaskSetManager: INFO: Starting task 11.12 in stage 1.0 (TID 119, answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2, partition 11, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:22 TaskSetManager: INFO: Lost task 8.11 in stage 1.0 (TID 110) on answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2: java.lang.ArrayIndexOutOfBoundsException (null) [duplicate 96] 2021-04-09 20:37:22 TaskSetManager: INFO: Starting task 8.12 in stage 1.0 (TID 120, answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1, partition 8, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:22 TaskSetManager: INFO: Lost task 10.11 in stage 1.0 (TID 108) on answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1: java.lang.ArrayIndexOutOfBoundsException (null) [duplicate 97] 2021-04-09 20:37:22 TaskSetManager: INFO: Starting task 10.12 in stage 1.0 (TID 121, answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1, partition 10, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:22 TaskSetManager: INFO: Lost task 9.12 in stage 1.0 (TID 113) on answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1: java.lang.ArrayIndexOutOfBoundsException (null) [duplicate 98] 2021-04-09 20:37:22 TaskSetManager: INFO: Starting task 9.13 in stage 1.0 (TID 122, answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2, partition 9, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:22 TaskSetManager: INFO: Lost task 7.12 in stage 1.0 (TID 115) on answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2: java.lang.ArrayIndexOutOfBoundsException (null) [duplicate 99] 2021-04-09 20:37:22 TaskSetManager: INFO: Starting task 7.13 in stage 1.0 (TID 123, answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2, partition 7, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:22 TaskSetManager: INFO: Lost task 13.10 in stage 1.0 (TID 114) on answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2: java.lang.ArrayIndexOutOfBoundsException (null) [duplicate 100] 2021-04-09 20:37:22 TaskSetManager: INFO: Starting task 13.11 in stage 1.0 (TID 124, answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1, partition 13, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:22 TaskSetManager: INFO: Lost task 12.12 in stage 1.0 (TID 116) on answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1: java.lang.ArrayIndexOutOfBoundsException (null) [duplicate 101] 2021-04-09 20:37:22 TaskSetManager: INFO: Starting task 12.13 in stage 1.0 (TID 125, answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1, partition 12, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:22 TaskSetManager: INFO: Lost task 2.12 in stage 1.0 (TID 118) on answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1: java.lang.ArrayIndexOutOfBoundsException (null) [duplicate 102] 2021-04-09 20:37:22 TaskSetManager: INFO: Starting task 2.13 in stage 1.0 (TID 126, answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1, partition 2, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:22 TaskSetManager: INFO: Lost task 10.12 in stage 1.0 (TID 121) on answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1: java.lang.ArrayIndexOutOfBoundsException (null) [duplicate 103] 2021-04-09 20:37:22 TaskSetManager: INFO: Starting task 10.13 in stage 1.0 (TID 127, answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2, partition 10, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:22 TaskSetManager: INFO: Lost task 9.13 in stage 1.0 (TID 122) on answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2: java.lang.ArrayIndexOutOfBoundsException (null) [duplicate 104] 2021-04-09 20:37:22 TaskSetManager: INFO: Starting task 9.14 in stage 1.0 (TID 128, answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2, partition 9, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:22 TaskSetManager: INFO: Lost task 1.12 in stage 1.0 (TID 117) on answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2: java.lang.ArrayIndexOutOfBoundsException (null) [duplicate 105] 2021-04-09 20:37:22 TaskSetManager: INFO: Starting task 1.13 in stage 1.0 (TID 129, answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2, partition 1, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:22 TaskSetManager: INFO: Lost task 11.12 in stage 1.0 (TID 119) on answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2: java.lang.ArrayIndexOutOfBoundsException (null) [duplicate 106] 2021-04-09 20:37:22 TaskSetManager: INFO: Starting task 11.13 in stage 1.0 (TID 130, answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2, partition 11, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:22 TaskSetManager: INFO: Lost task 7.13 in stage 1.0 (TID 123) on answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2: java.lang.ArrayIndexOutOfBoundsException (null) [duplicate 107] 2021-04-09 20:37:22 TaskSetManager: INFO: Starting task 7.14 in stage 1.0 (TID 131, answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1, partition 7, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:22 TaskSetManager: INFO: Lost task 8.12 in stage 1.0 (TID 120) on answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1: java.lang.ArrayIndexOutOfBoundsException (null) [duplicate 108] 2021-04-09 20:37:22 TaskSetManager: INFO: Starting task 8.13 in stage 1.0 (TID 132, answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1, partition 8, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:22 TaskSetManager: INFO: Lost task 12.13 in stage 1.0 (TID 125) on answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1: java.lang.ArrayIndexOutOfBoundsException (null) [duplicate 109] 2021-04-09 20:37:22 TaskSetManager: INFO: Starting task 12.14 in stage 1.0 (TID 133, answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1, partition 12, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:22 TaskSetManager: INFO: Lost task 13.11 in stage 1.0 (TID 124) on answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1: java.lang.ArrayIndexOutOfBoundsException (null) [duplicate 110] 2021-04-09 20:37:22 TaskSetManager: INFO: Starting task 13.12 in stage 1.0 (TID 134, answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2, partition 13, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:22 TaskSetManager: INFO: Lost task 9.14 in stage 1.0 (TID 128) on answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2: java.lang.ArrayIndexOutOfBoundsException (null) [duplicate 111] 2021-04-09 20:37:22 TaskSetManager: INFO: Starting task 9.15 in stage 1.0 (TID 135, answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2, partition 9, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:22 TaskSetManager: INFO: Lost task 1.13 in stage 1.0 (TID 129) on answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2: java.lang.ArrayIndexOutOfBoundsException (null) [duplicate 112] 2021-04-09 20:37:22 TaskSetManager: INFO: Starting task 1.14 in stage 1.0 (TID 136, answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1, partition 1, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:22 TaskSetManager: INFO: Lost task 2.13 in stage 1.0 (TID 126) on answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1: java.lang.ArrayIndexOutOfBoundsException (null) [duplicate 113] 2021-04-09 20:37:22 TaskSetManager: INFO: Starting task 2.14 in stage 1.0 (TID 137, answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2, partition 2, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:22 TaskSetManager: INFO: Lost task 10.13 in stage 1.0 (TID 127) on answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2: java.lang.ArrayIndexOutOfBoundsException (null) [duplicate 114] 2021-04-09 20:37:22 TaskSetManager: INFO: Starting task 10.14 in stage 1.0 (TID 138, answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1, partition 10, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:22 TaskSetManager: INFO: Lost task 7.14 in stage 1.0 (TID 131) on answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1: java.lang.ArrayIndexOutOfBoundsException (null) [duplicate 115] 2021-04-09 20:37:22 TaskSetManager: INFO: Starting task 7.15 in stage 1.0 (TID 139, answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2, partition 7, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:22 TaskSetManager: INFO: Lost task 11.13 in stage 1.0 (TID 130) on answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2: java.lang.ArrayIndexOutOfBoundsException (null) [duplicate 116] 2021-04-09 20:37:22 TaskSetManager: INFO: Starting task 11.14 in stage 1.0 (TID 140, answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1, partition 11, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:22 TaskSetManager: INFO: Lost task 8.13 in stage 1.0 (TID 132) on answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1: java.lang.ArrayIndexOutOfBoundsException (null) [duplicate 117] 2021-04-09 20:37:22 TaskSetManager: INFO: Starting task 8.14 in stage 1.0 (TID 141, answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2, partition 8, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:22 TaskSetManager: INFO: Lost task 9.15 in stage 1.0 (TID 135) on answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2: java.lang.ArrayIndexOutOfBoundsException (null) [duplicate 118] 2021-04-09 20:37:22 TaskSetManager: INFO: Starting task 9.16 in stage 1.0 (TID 142, answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1, partition 9, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:22 TaskSetManager: INFO: Lost task 10.14 in stage 1.0 (TID 138) on answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1: java.lang.ArrayIndexOutOfBoundsException (null) [duplicate 119] 2021-04-09 20:37:22 TaskSetManager: INFO: Starting task 10.15 in stage 1.0 (TID 143, answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1, partition 10, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:22 TaskSetManager: INFO: Lost task 12.14 in stage 1.0 (TID 133) on answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1: java.lang.ArrayIndexOutOfBoundsException (null) [duplicate 120] 2021-04-09 20:37:22 TaskSetManager: INFO: Starting task 12.15 in stage 1.0 (TID 144, answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2, partition 12, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:22 TaskSetManager: INFO: Lost task 2.14 in stage 1.0 (TID 137) on answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2: java.lang.ArrayIndexOutOfBoundsException (null) [duplicate 121] 2021-04-09 20:37:22 TaskSetManager: INFO: Starting task 2.15 in stage 1.0 (TID 145, answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2, partition 2, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:22 TaskSetManager: INFO: Lost task 7.15 in stage 1.0 (TID 139) on answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2: java.lang.ArrayIndexOutOfBoundsException (null) [duplicate 122] 2021-04-09 20:37:22 TaskSetManager: INFO: Starting task 7.16 in stage 1.0 (TID 146, answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2, partition 7, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:22 TaskSetManager: INFO: Lost task 13.12 in stage 1.0 (TID 134) on answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2: java.lang.ArrayIndexOutOfBoundsException (null) [duplicate 123] 2021-04-09 20:37:22 TaskSetManager: INFO: Starting task 13.13 in stage 1.0 (TID 147, answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1, partition 13, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:22 TaskSetManager: INFO: Lost task 1.14 in stage 1.0 (TID 136) on answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1: java.lang.ArrayIndexOutOfBoundsException (null) [duplicate 124] 2021-04-09 20:37:22 ExecutorAllocationManager: INFO: Requesting 1 new executor because tasks are backlogged (new desired total will be 4) 2021-04-09 20:37:22 TaskSetManager: INFO: Starting task 1.15 in stage 1.0 (TID 148, answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1, partition 1, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:22 TaskSetManager: INFO: Lost task 11.14 in stage 1.0 (TID 140) on answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1: java.lang.ArrayIndexOutOfBoundsException (null) [duplicate 125] 2021-04-09 20:37:22 TaskSetManager: INFO: Starting task 11.15 in stage 1.0 (TID 149, answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1, partition 11, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:22 TaskSetManager: INFO: Lost task 10.15 in stage 1.0 (TID 143) on answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1: java.lang.ArrayIndexOutOfBoundsException (null) [duplicate 126] 2021-04-09 20:37:22 TaskSetManager: INFO: Starting task 10.16 in stage 1.0 (TID 150, answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2, partition 10, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:22 TaskSetManager: INFO: Lost task 8.14 in stage 1.0 (TID 141) on answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2: java.lang.ArrayIndexOutOfBoundsException (null) [duplicate 127] 2021-04-09 20:37:22 TaskSetManager: INFO: Starting task 8.15 in stage 1.0 (TID 151, answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1, partition 8, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:22 TaskSetManager: INFO: Lost task 9.16 in stage 1.0 (TID 142) on answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1: java.lang.ArrayIndexOutOfBoundsException (null) [duplicate 128] 2021-04-09 20:37:22 TaskSetManager: INFO: Starting task 9.17 in stage 1.0 (TID 152, answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1, partition 9, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:22 TaskSetManager: INFO: Lost task 13.13 in stage 1.0 (TID 147) on answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1: java.lang.ArrayIndexOutOfBoundsException (null) [duplicate 129] 2021-04-09 20:37:22 TaskSetManager: INFO: Starting task 13.14 in stage 1.0 (TID 153, answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2, partition 13, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:22 TaskSetManager: INFO: Lost task 2.15 in stage 1.0 (TID 145) on answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2: java.lang.ArrayIndexOutOfBoundsException (null) [duplicate 130] 2021-04-09 20:37:22 TaskSetManager: INFO: Starting task 2.16 in stage 1.0 (TID 154, answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2, partition 2, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:22 TaskSetManager: INFO: Lost task 12.15 in stage 1.0 (TID 144) on answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2: java.lang.ArrayIndexOutOfBoundsException (null) [duplicate 131] 2021-04-09 20:37:22 TaskSetManager: INFO: Starting task 12.16 in stage 1.0 (TID 155, answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1, partition 12, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:22 TaskSetManager: INFO: Lost task 1.15 in stage 1.0 (TID 148) on answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1: java.lang.ArrayIndexOutOfBoundsException (null) [duplicate 132] 2021-04-09 20:37:22 TaskSetManager: INFO: Starting task 1.16 in stage 1.0 (TID 156, answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2, partition 1, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:22 TaskSetManager: INFO: Lost task 7.16 in stage 1.0 (TID 146) on answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2: java.lang.ArrayIndexOutOfBoundsException (null) [duplicate 133] 2021-04-09 20:37:22 TaskSetManager: INFO: Starting task 7.17 in stage 1.0 (TID 157, answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1, partition 7, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:22 TaskSetManager: INFO: Lost task 11.15 in stage 1.0 (TID 149) on answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1: java.lang.ArrayIndexOutOfBoundsException (null) [duplicate 134] 2021-04-09 20:37:22 TaskSetManager: INFO: Starting task 11.16 in stage 1.0 (TID 158, answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2, partition 11, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:22 TaskSetManager: INFO: Lost task 2.16 in stage 1.0 (TID 154) on answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2: java.lang.ArrayIndexOutOfBoundsException (null) [duplicate 135] 2021-04-09 20:37:22 TaskSetManager: INFO: Starting task 2.17 in stage 1.0 (TID 159, answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2, partition 2, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:22 TaskSetManager: INFO: Lost task 10.16 in stage 1.0 (TID 150) on answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2: java.lang.ArrayIndexOutOfBoundsException (null) [duplicate 136] 2021-04-09 20:37:22 TaskSetManager: INFO: Starting task 10.17 in stage 1.0 (TID 160, answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2, partition 10, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:22 TaskSetManager: INFO: Lost task 13.14 in stage 1.0 (TID 153) on answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2: java.lang.ArrayIndexOutOfBoundsException (null) [duplicate 137] 2021-04-09 20:37:22 TaskSetManager: INFO: Starting task 13.15 in stage 1.0 (TID 161, answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1, partition 13, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:22 TaskSetManager: INFO: Lost task 8.15 in stage 1.0 (TID 151) on answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1: java.lang.ArrayIndexOutOfBoundsException (null) [duplicate 138] 2021-04-09 20:37:22 TaskSetManager: INFO: Starting task 8.16 in stage 1.0 (TID 162, answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1, partition 8, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:22 TaskSetManager: INFO: Lost task 9.17 in stage 1.0 (TID 152) on answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1: java.lang.ArrayIndexOutOfBoundsException (null) [duplicate 139] 2021-04-09 20:37:22 TaskSetManager: INFO: Starting task 9.18 in stage 1.0 (TID 163, answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1, partition 9, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:22 TaskSetManager: INFO: Lost task 12.16 in stage 1.0 (TID 155) on answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1: java.lang.ArrayIndexOutOfBoundsException (null) [duplicate 140] 2021-04-09 20:37:22 TaskSetManager: INFO: Starting task 12.17 in stage 1.0 (TID 164, answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1, partition 12, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:22 TaskSetManager: INFO: Lost task 7.17 in stage 1.0 (TID 157) on answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1: java.lang.ArrayIndexOutOfBoundsException (null) [duplicate 141] 2021-04-09 20:37:22 TaskSetManager: INFO: Starting task 7.18 in stage 1.0 (TID 165, answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2, partition 7, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:22 TaskSetManager: INFO: Lost task 1.16 in stage 1.0 (TID 156) on answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2: java.lang.ArrayIndexOutOfBoundsException (null) [duplicate 142] 2021-04-09 20:37:22 TaskSetManager: INFO: Starting task 1.17 in stage 1.0 (TID 166, answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2, partition 1, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:22 TaskSetManager: INFO: Lost task 11.16 in stage 1.0 (TID 158) on answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2: java.lang.ArrayIndexOutOfBoundsException (null) [duplicate 143] 2021-04-09 20:37:22 TaskSetManager: INFO: Starting task 11.17 in stage 1.0 (TID 167, answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1, partition 11, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:22 TaskSetManager: INFO: Lost task 13.15 in stage 1.0 (TID 161) on answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1: java.lang.ArrayIndexOutOfBoundsException (null) [duplicate 144] 2021-04-09 20:37:22 TaskSetManager: INFO: Starting task 13.16 in stage 1.0 (TID 168, answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1, partition 13, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:22 TaskSetManager: INFO: Lost task 8.16 in stage 1.0 (TID 162) on answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1: java.lang.ArrayIndexOutOfBoundsException (null) [duplicate 145] 2021-04-09 20:37:22 TaskSetManager: INFO: Starting task 8.17 in stage 1.0 (TID 169, answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2, partition 8, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:22 TaskSetManager: INFO: Lost task 2.17 in stage 1.0 (TID 159) on answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2: java.lang.ArrayIndexOutOfBoundsException (null) [duplicate 146] 2021-04-09 20:37:22 TaskSetManager: INFO: Starting task 2.18 in stage 1.0 (TID 170, answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2, partition 2, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:22 TaskSetManager: INFO: Lost task 10.17 in stage 1.0 (TID 160) on answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2: java.lang.ArrayIndexOutOfBoundsException (null) [duplicate 147] 2021-04-09 20:37:22 TaskSetManager: INFO: Starting task 10.18 in stage 1.0 (TID 171, answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1, partition 10, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:22 TaskSetManager: INFO: Lost task 12.17 in stage 1.0 (TID 164) on answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1: java.lang.ArrayIndexOutOfBoundsException (null) [duplicate 148] 2021-04-09 20:37:22 TaskSetManager: INFO: Starting task 12.18 in stage 1.0 (TID 172, answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2, partition 12, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:22 TaskSetManager: INFO: Lost task 7.18 in stage 1.0 (TID 165) on answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2: java.lang.ArrayIndexOutOfBoundsException (null) [duplicate 149] 2021-04-09 20:37:22 TaskSetManager: INFO: Starting task 7.19 in stage 1.0 (TID 173, answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2, partition 7, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:22 TaskSetManager: INFO: Lost task 1.17 in stage 1.0 (TID 166) on answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2: java.lang.ArrayIndexOutOfBoundsException (null) [duplicate 150] 2021-04-09 20:37:22 TaskSetManager: INFO: Starting task 1.18 in stage 1.0 (TID 174, answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1, partition 1, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:22 TaskSetManager: INFO: Lost task 9.18 in stage 1.0 (TID 163) on answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1: java.lang.ArrayIndexOutOfBoundsException (null) [duplicate 151] 2021-04-09 20:37:22 TaskSetManager: INFO: Starting task 9.19 in stage 1.0 (TID 175, answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1, partition 9, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:22 TaskSetManager: INFO: Lost task 11.17 in stage 1.0 (TID 167) on answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1: java.lang.ArrayIndexOutOfBoundsException (null) [duplicate 152] 2021-04-09 20:37:22 TaskSetManager: INFO: Starting task 11.18 in stage 1.0 (TID 176, answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2, partition 11, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:22 TaskSetManager: INFO: Lost task 8.17 in stage 1.0 (TID 169) on answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2: java.lang.ArrayIndexOutOfBoundsException (null) [duplicate 153] 2021-04-09 20:37:22 TaskSetManager: INFO: Starting task 8.18 in stage 1.0 (TID 177, answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1, partition 8, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:22 TaskSetManager: INFO: Lost task 13.16 in stage 1.0 (TID 168) on answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1: java.lang.ArrayIndexOutOfBoundsException (null) [duplicate 154] 2021-04-09 20:37:22 TaskSetManager: INFO: Starting task 13.17 in stage 1.0 (TID 178, answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2, partition 13, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:22 TaskSetManager: INFO: Lost task 12.18 in stage 1.0 (TID 172) on answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2: java.lang.ArrayIndexOutOfBoundsException (null) [duplicate 155] 2021-04-09 20:37:22 TaskSetManager: INFO: Starting task 12.19 in stage 1.0 (TID 179, answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2, partition 12, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:22 TaskSetManager: INFO: Lost task 2.18 in stage 1.0 (TID 170) on answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2: java.lang.ArrayIndexOutOfBoundsException (null) [duplicate 156] 2021-04-09 20:37:22 TaskSetManager: INFO: Starting task 2.19 in stage 1.0 (TID 180, answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1, partition 2, PROCESS_LOCAL, 7974 bytes) 2021-04-09 20:37:22 TaskSetManager: INFO: Lost task 9.19 in stage 1.0 (TID 175) on answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1: java.lang.ArrayIndexOutOfBoundsException (null) [duplicate 157] 2021-04-09 20:37:22 TaskSetManager: ERROR: Task 9 in stage 1.0 failed 20 times; aborting job 2021-04-09 20:37:22 YarnScheduler: INFO: Cancelling stage 1 2021-04-09 20:37:22 YarnScheduler: INFO: Killing all running tasks in stage 1: Stage cancelled 2021-04-09 20:37:22 YarnScheduler: INFO: Stage 1 was cancelled 2021-04-09 20:37:22 DAGScheduler: INFO: ResultStage 1 (collect at ContextRDD.scala:176) failed in 2.483 s due to Job aborted due to stage failure: Task 9 in stage 1.0 failed 20 times, most recent failure: Lost task 9.19 in stage 1.0 (TID 175, answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1): java.lang.ArrayIndexOutOfBoundsException Driver stacktrace: 2021-04-09 20:37:22 DAGScheduler: INFO: Job 1 failed: collect at ContextRDD.scala:176, took 2.579449 s 2021-04-09 20:37:22 root: ERROR: error while applying lowering 'InterpretNonCompilable' 2021-04-09 20:37:22 root: INFO: RegionPool: FREE: 192.0K allocated (192.0K blocks / 0 chunks), regions.size = 3, 0 current java objects, 0 max java objects, thread 17: Thread-5 2021-04-09 20:37:22 root: ERROR: ArrayIndexOutOfBoundsException: null From org.apache.spark.SparkException: Job aborted due to stage failure: Task 9 in stage 1.0 failed 20 times, most recent failure: Lost task 9.19 in stage 1.0 (TID 175, answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1): java.lang.ArrayIndexOutOfBoundsException 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$$anon$1.run(EventLoop.scala:49) at org.apache.spark.scheduler.DAGScheduler.runJob(DAGScheduler.scala:738) at org.apache.spark.SparkContext.runJob(SparkContext.scala:2061) at org.apache.spark.SparkContext.runJob(SparkContext.scala:2082) at org.apache.spark.SparkContext.runJob(SparkContext.scala:2101) at org.apache.spark.SparkContext.runJob(SparkContext.scala:2126) at org.apache.spark.rdd.RDD$$anonfun$collect$1.apply(RDD.scala:990) at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:151) at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:112) at org.apache.spark.rdd.RDD.withScope(RDD.scala:385) at org.apache.spark.rdd.RDD.collect(RDD.scala:989) at is.hail.sparkextras.ContextRDD.collect(ContextRDD.scala:176) at is.hail.rvd.RVD.writeRowsSplit(RVD.scala:953) at is.hail.expr.ir.MatrixValue.write(MatrixValue.scala:246) at is.hail.expr.ir.MatrixNativeWriter.apply(MatrixWriter.scala:62) at is.hail.expr.ir.WrappedMatrixWriter.apply(MatrixWriter.scala:41) at is.hail.expr.ir.Interpret$.run(Interpret.scala:819) 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$$anonfun$1.apply(LoweringPass.scala:15) at is.hail.utils.ExecutionTimer.time(ExecutionTimer.scala:81) at is.hail.expr.ir.lowering.LoweringPass$$anonfun$apply$3.apply(LoweringPass.scala:15) at is.hail.expr.ir.lowering.LoweringPass$$anonfun$apply$3.apply(LoweringPass.scala:13) at is.hail.utils.ExecutionTimer.time(ExecutionTimer.scala:81) at is.hail.expr.ir.lowering.LoweringPass$class.apply(LoweringPass.scala:13) at is.hail.expr.ir.lowering.InterpretNonCompilablePass$.apply(LoweringPass.scala:62) at is.hail.expr.ir.lowering.LoweringPipeline$$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:362) at is.hail.backend.spark.SparkBackend$$anonfun$execute$1.apply(SparkBackend.scala:346) at is.hail.backend.spark.SparkBackend$$anonfun$execute$1.apply(SparkBackend.scala:343) at is.hail.expr.ir.ExecuteContext$$anonfun$scoped$1$$anonfun$apply$1.apply(ExecuteContext.scala:48) at is.hail.expr.ir.ExecuteContext$$anonfun$scoped$1$$anonfun$apply$1.apply(ExecuteContext.scala:48) at is.hail.utils.package$.using(package.scala:618) at is.hail.expr.ir.ExecuteContext$$anonfun$scoped$1.apply(ExecuteContext.scala:48) at is.hail.expr.ir.ExecuteContext$$anonfun$scoped$1.apply(ExecuteContext.scala:47) at is.hail.utils.package$.using(package.scala:618) at is.hail.annotations.RegionPool$.scoped(RegionPool.scala:13) at is.hail.expr.ir.ExecuteContext$.scoped(ExecuteContext.scala:47) at is.hail.backend.spark.SparkBackend.withExecuteContext(SparkBackend.scala:256) at is.hail.backend.spark.SparkBackend.execute(SparkBackend.scala:343) at is.hail.backend.spark.SparkBackend$$anonfun$7.apply(SparkBackend.scala:387) at is.hail.backend.spark.SparkBackend$$anonfun$7.apply(SparkBackend.scala:385) at is.hail.utils.ExecutionTimer$.time(ExecutionTimer.scala:52) at is.hail.backend.spark.SparkBackend.executeJSON(SparkBackend.scala:385) 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) java.lang.ArrayIndexOutOfBoundsException: null at 2021-04-09 20:37:22 TaskSetManager: WARN: Lost task 8.18 in stage 1.0 (TID 177, answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1): TaskKilled (Stage cancelled) 2021-04-09 20:37:22 TaskSetManager: WARN: Lost task 11.18 in stage 1.0 (TID 176, answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2): TaskKilled (Stage cancelled) 2021-04-09 20:37:22 TaskSetManager: WARN: Lost task 10.18 in stage 1.0 (TID 171, answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1): TaskKilled (Stage cancelled) 2021-04-09 20:37:22 TaskSetManager: WARN: Lost task 7.19 in stage 1.0 (TID 173, answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2): TaskKilled (Stage cancelled) 2021-04-09 20:37:22 TaskSetManager: WARN: Lost task 13.17 in stage 1.0 (TID 178, answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2): TaskKilled (Stage cancelled) 2021-04-09 20:37:22 TaskSetManager: WARN: Lost task 2.19 in stage 1.0 (TID 180, answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1): TaskKilled (Stage cancelled) 2021-04-09 20:37:22 TaskSetManager: WARN: Lost task 12.19 in stage 1.0 (TID 179, answer-w-0.us-central1-b.c.human-genetics-001.internal, executor 2): TaskKilled (Stage cancelled) 2021-04-09 20:37:22 TaskSetManager: WARN: Lost task 1.18 in stage 1.0 (TID 174, answer-w-1.us-central1-b.c.human-genetics-001.internal, executor 1): TaskKilled (Stage cancelled) 2021-04-09 20:37:22 YarnScheduler: INFO: Removed TaskSet 1.0, whose tasks have all completed, from pool default 2021-04-09 20:37:24 YarnSchedulerBackend$YarnDriverEndpoint: INFO: Registered executor NettyRpcEndpointRef(spark-client://Executor) (10.128.0.6:45382) with ID 3 2021-04-09 20:37:24 ExecutorAllocationManager: INFO: New executor 3 has registered (new total is 3) 2021-04-09 20:37:24 BlockManagerMasterEndpoint: INFO: Registering block manager answer-w-1.us-central1-b.c.human-genetics-001.internal:33613 with 9.5 GB RAM, BlockManagerId(3, answer-w-1.us-central1-b.c.human-genetics-001.internal, 33613, None) 2021-04-09 20:38:22 ExecutorAllocationManager: INFO: Request to remove executorIds: 2, 1 2021-04-09 20:38:22 YarnClientSchedulerBackend: INFO: Requesting to kill executor(s) 2, 1 2021-04-09 20:38:22 YarnClientSchedulerBackend: INFO: Actual list of executor(s) to be killed is 2, 1 2021-04-09 20:38:22 ExecutorAllocationManager: INFO: Removing executor 2 because it has been idle for 60 seconds (new desired total will be 2) 2021-04-09 20:38:22 ExecutorAllocationManager: INFO: Removing executor 1 because it has been idle for 60 seconds (new desired total will be 1) 2021-04-09 20:38:24 ExecutorAllocationManager: INFO: Request to remove executorIds: 3 2021-04-09 20:38:26 YarnSchedulerBackend$YarnDriverEndpoint: INFO: Disabling executor 1. 2021-04-09 20:38:26 DAGScheduler: INFO: Executor lost: 1 (epoch 0) 2021-04-09 20:38:26 BlockManagerMasterEndpoint: INFO: Trying to remove executor 1 from BlockManagerMaster. 2021-04-09 20:38:26 BlockManagerMasterEndpoint: INFO: Removing block manager BlockManagerId(1, answer-w-1.us-central1-b.c.human-genetics-001.internal, 45783, None) 2021-04-09 20:38:26 BlockManagerMaster: INFO: Removed 1 successfully in removeExecutor 2021-04-09 20:38:26 YarnScheduler: INFO: Executor 1 on answer-w-1.us-central1-b.c.human-genetics-001.internal killed by driver. 2021-04-09 20:38:26 ExecutorAllocationManager: INFO: Existing executor 1 has been removed (new total is 2) 2021-04-09 20:38:27 YarnSchedulerBackend$YarnDriverEndpoint: INFO: Disabling executor 2. 2021-04-09 20:38:27 DAGScheduler: INFO: Executor lost: 2 (epoch 0) 2021-04-09 20:38:27 BlockManagerMasterEndpoint: INFO: Trying to remove executor 2 from BlockManagerMaster. 2021-04-09 20:38:27 BlockManagerMasterEndpoint: INFO: Removing block manager BlockManagerId(2, answer-w-0.us-central1-b.c.human-genetics-001.internal, 39767, None) 2021-04-09 20:38:27 BlockManagerMaster: INFO: Removed 2 successfully in removeExecutor 2021-04-09 20:38:27 YarnScheduler: INFO: Executor 2 on answer-w-0.us-central1-b.c.human-genetics-001.internal killed by driver. 2021-04-09 20:38:27 ExecutorAllocationManager: INFO: Existing executor 2 has been removed (new total is 1)