2020-10-01 13:22:17 Hail: INFO: Running Hail version 0.2.49-11ae8408bad0 2020-10-01 13:22:17 SparkContext: WARN: Using an existing SparkContext; some configuration may not take effect. 2020-10-01 13:22:18 root: INFO: RegionPool: initialized for thread 31: Thread-5 2020-10-01 13:22:18 MemoryStore: INFO: Block broadcast_0 stored as values in memory (estimated size 34.8 KB, free 366.3 MB) 2020-10-01 13:22:19 MemoryStore: INFO: Block broadcast_0_piece0 stored as bytes in memory (estimated size 3.2 KB, free 366.3 MB) 2020-10-01 13:22:19 BlockManagerInfo: INFO: Added broadcast_0_piece0 in memory on qlu-1:28416 (size: 3.2 KB, free: 366.3 MB) 2020-10-01 13:22:19 SparkContext: INFO: Created broadcast 0 from broadcast at SparkBackend.scala:233 2020-10-01 13:22:19 Hail: INFO: Found 37652 samples in fam file. 2020-10-01 13:22:19 Hail: INFO: Found 2302 variants in bim file. 2020-10-01 13:22:20 root: INFO: globbing path /z/Comp/lu_group/Members/xiaoyuan/software/hail/test/logistic/covar_l1.txt returned 1 files: covar_l1.txt 2020-10-01 13:22:20 Hail: INFO: Reading table to impute column types 2020-10-01 13:22:20 MemoryStore: INFO: Block broadcast_1 stored as values in memory (estimated size 237.3 KB, free 366.0 MB) 2020-10-01 13:22:20 MemoryStore: INFO: Block broadcast_1_piece0 stored as bytes in memory (estimated size 23.0 KB, free 366.0 MB) 2020-10-01 13:22:20 BlockManagerInfo: INFO: Added broadcast_1_piece0 in memory on qlu-1:28416 (size: 23.0 KB, free: 366.3 MB) 2020-10-01 13:22:20 SparkContext: INFO: Created broadcast 1 from broadcast at SparkBackend.scala:233 2020-10-01 13:22:20 SparkContext: INFO: Starting job: reduce at TextTableReader.scala:226 2020-10-01 13:22:20 DAGScheduler: INFO: Got job 0 (reduce at TextTableReader.scala:226) with 1 output partitions 2020-10-01 13:22:20 DAGScheduler: INFO: Final stage: ResultStage 0 (reduce at TextTableReader.scala:226) 2020-10-01 13:22:20 DAGScheduler: INFO: Parents of final stage: List() 2020-10-01 13:22:20 DAGScheduler: INFO: Missing parents: List() 2020-10-01 13:22:20 DAGScheduler: INFO: Submitting ResultStage 0 (MapPartitionsRDD[1] at mapPartitions at TextTableReader.scala:185), which has no missing parents 2020-10-01 13:22:20 MemoryStore: INFO: Block broadcast_2 stored as values in memory (estimated size 4.2 KB, free 366.0 MB) 2020-10-01 13:22:20 MemoryStore: INFO: Block broadcast_2_piece0 stored as bytes in memory (estimated size 2.5 KB, free 366.0 MB) 2020-10-01 13:22:20 BlockManagerInfo: INFO: Added broadcast_2_piece0 in memory on qlu-1:28416 (size: 2.5 KB, free: 366.3 MB) 2020-10-01 13:22:20 SparkContext: INFO: Created broadcast 2 from broadcast at DAGScheduler.scala:1161 2020-10-01 13:22:20 DAGScheduler: INFO: Submitting 1 missing tasks from ResultStage 0 (MapPartitionsRDD[1] at mapPartitions at TextTableReader.scala:185) (first 15 tasks are for partitions Vector(0)) 2020-10-01 13:22:20 TaskSchedulerImpl: INFO: Adding task set 0.0 with 1 tasks 2020-10-01 13:22:20 TaskSetManager: INFO: Starting task 0.0 in stage 0.0 (TID 0, localhost, executor driver, partition 0, PROCESS_LOCAL, 8001 bytes) 2020-10-01 13:22:20 Executor: INFO: Running task 0.0 in stage 0.0 (TID 0) 2020-10-01 13:22:21 Executor: INFO: Finished task 0.0 in stage 0.0 (TID 0). 891 bytes result sent to driver 2020-10-01 13:22:22 TaskSetManager: INFO: Finished task 0.0 in stage 0.0 (TID 0) in 1333 ms on localhost (executor driver) (1/1) 2020-10-01 13:22:22 TaskSchedulerImpl: INFO: Removed TaskSet 0.0, whose tasks have all completed, from pool 2020-10-01 13:22:22 DAGScheduler: INFO: ResultStage 0 (reduce at TextTableReader.scala:226) finished in 1.502 s 2020-10-01 13:22:22 DAGScheduler: INFO: Job 0 finished: reduce at TextTableReader.scala:226, took 1.609855 s 2020-10-01 13:22:22 Hail: INFO: Finished type imputation Loading column 'IID' as type 'str' (user-specified) Loading column 'isMale' as type 'int32' (imputed) Loading column 'isAxiom' as type 'bool' (imputed) Loading column 'PC1' as type 'float64' (imputed) Loading column 'PC2' as type 'float64' (imputed) Loading column 'PC3' as type 'float64' (imputed) Loading column 'PC4' as type 'float64' (imputed) Loading column 'PC5' as type 'float64' (imputed) Loading column 'PC6' as type 'float64' (imputed) Loading column 'PC7' as type 'float64' (imputed) Loading column 'PC8' as type 'float64' (imputed) Loading column 'PC9' as type 'float64' (imputed) Loading column 'PC10' as type 'float64' (imputed) Loading column 'PC11' as type 'float64' (imputed) Loading column 'PC12' as type 'float64' (imputed) Loading column 'PC13' as type 'float64' (imputed) Loading column 'PC14' as type 'float64' (imputed) Loading column 'PC15' as type 'float64' (imputed) Loading column 'PC16' as type 'float64' (imputed) Loading column 'PC17' as type 'float64' (imputed) Loading column 'PC18' as type 'float64' (imputed) Loading column 'PC19' as type 'float64' (imputed) Loading column 'PC20' as type 'float64' (imputed) Loading column 'pheno' as type 'bool' (imputed) 2020-10-01 13:22:22 root: INFO: Timer: Time taken for legacyRelationalLowerer, initial IR -- Verify : 2.139ms, total 23.004ms 2020-10-01 13:22:22 root: INFO: optimize legacyRelationalLowerer, initial IR: before: IR size 82: (TableMapRows (MatrixToTableApply "{\"name\":\"LogisticRegression\",\"test\":\"wald\",\"yFields\":[\"__y_0\"],\"xField\":\"__uid_4\",\"covFields\":[\"__cov0\",\"__cov1\"],\"passThrough\":[]}" (MatrixRename () () ("__uid_5" "__uid_6" "__uid_7") ("__y_0" "__cov0" "__cov1") () () ("__uid_8") ("__uid_4") (MatrixMapEntries (MatrixMapCols None (MatrixMapRows (MatrixMapCols None (MatrixMapCols () (MatrixMapEntries (MatrixMapCols None (MatrixMapCols None (MatrixAnnotateColsTable "__uid_3" (MatrixRead None False False "{\"bed\":\"/z/Comp/lu_group/Members/xiaoyuan/UKB_participation/23_check_weight/subgroup_test/condor_geno/chr22_sexl1_40_40.bed\",\"bim\":\"/z/Comp/lu_group/Members/xiaoyuan/UKB_participation/23_check_weight/subgroup_test/condor_geno/chr22_sexl1_40_40.bim\",\"fam\":\"/z/Comp/lu_group/Members/xiaoyuan/UKB_participation/23_check_weight/subgroup_test/condor_geno/chr22_sexl1_40_40.fam\",\"delimiter\":\"\\\\\\\\s+\",\"missing\":\"NA\",\"quantPheno\":true,\"a2Reference\":true,\"rg\":\"GRCh37\",\"contigRecoding\":{\"23\":\"X\",\"24\":\"Y\",\"25\":\"X\",\"26\":\"MT\"},\"skipInvalidLoci\":false,\"name\":\"MatrixPLINKReader\"}") (TableKeyBy (IID) False (TableRead None False "{\"files\":[\"/z/Comp/lu_group/Members/xiaoyuan/software/hail/test/logistic/covar_l1.txt\"],\"typeMapStr\":{\"IID\":\"String\"},\"comment\":[],\"separator\":\"\\t\",\"missing\":[\"NA\"],\"hasHeader\":true,\"impute\":true,\"quoteStr\":null,\"skipBlankLines\":false,\"forceBGZ\":false,\"filterAndReplace\":{},\"forceGZ\":false,\"name\":\"TextTableReader\"}"))) (InsertFields (SelectFields (s fam_id pat_id mat_id is_female quant_pheno) (Ref sa)) None (covar (GetField __uid_3 (Ref sa))))) (Let __cse_1 (GetField covar (Ref sa)) (InsertFields (SelectFields (s fam_id pat_id mat_id is_female quant_pheno covar) (Ref sa)) None (__uid_5 (Apply toFloat64 () Float64 (GetField pheno (Ref __cse_1)))) (__uid_6 (ApplyIR toFloat64 () Float64 (I32 1))) (__uid_7 (Apply toFloat64 () Float64 (GetField isAxiom (Ref __cse_1))))))) (InsertFields (SelectFields (GT) (Ref g)) None (__uid_8 (ApplyIR toFloat64 () Float64 (Apply nNonRefAlleles () Int32 (GetField GT (Ref g))))))) (SelectFields (s fam_id pat_id mat_id is_female quant_pheno covar __uid_5 __uid_6 __uid_7) (Ref sa))) (SelectFields (fam_id pat_id mat_id is_female quant_pheno covar __uid_5 __uid_6 __uid_7) (SelectFields (s fam_id pat_id mat_id is_female quant_pheno covar __uid_5 __uid_6 __uid_7) (Ref sa)))) (SelectFields (locus alleles) (MakeStruct (locus (GetField locus (Ref va))) (alleles (GetField alleles (Ref va))) (rsid (GetField rsid (Ref va))) (cm_position (GetField cm_position (Ref va)))))) (SelectFields (__uid_5 __uid_6 __uid_7) (SelectFields (fam_id pat_id mat_id is_female quant_pheno covar __uid_5 __uid_6 __uid_7) (Ref sa)))) (SelectFields (__uid_8) (SelectFields (GT __uid_8) (Ref g)))))) (SelectFields (locus alleles beta standard_error z_stat p_value fit) (Let __uid_9 (ApplyIR indexArray () Struct{beta:Float64,standard_error:Float64,z_stat:Float64,p_value:Float64,fit:Struct{n_iterations:Int32,converged:Boolean,exploded:Boolean}} (GetField logistic_regression (Ref row)) (I32 0) (Str " File \"te...")) (InsertFields (SelectFields (locus alleles logistic_regression) (Ref row)) None (beta (GetField beta (Ref __uid_9))) (standard_error (GetField standard_error (Ref __uid_9))) (z_stat (GetField z_stat (Ref __uid_9))) (p_value (GetField p_value (Ref __uid_9))) (fit (GetField fit (Ref __uid_9))))))) 2020-10-01 13:22:23 root: INFO: Timer: Time taken for legacyRelationalLowerer, initial IR -- LoweringTransformation -- Optimize -- FoldConstants : 13.323ms, total 86.143ms 2020-10-01 13:22:23 root: INFO: Timer: Time taken for legacyRelationalLowerer, initial IR -- LoweringTransformation -- Optimize -- ExtractIntervalFilters : 10.483ms, total 97.652ms 2020-10-01 13:22:23 root: INFO: Timer: Time taken for legacyRelationalLowerer, initial IR -- LoweringTransformation -- Optimize -- Simplify : 95.615ms, total 194.273ms 2020-10-01 13:22:23 root: INFO: Timer: Time taken for legacyRelationalLowerer, initial IR -- LoweringTransformation -- Optimize -- ForwardLets : 38.986ms, total 234.930ms 2020-10-01 13:22:23 root: INFO: Timer: Time taken for legacyRelationalLowerer, initial IR -- LoweringTransformation -- Optimize -- ForwardRelationalLets : 4.910ms, total 241.722ms 2020-10-01 13:22:23 root: INFO: Prune: InsertFields: eliminating field 'covar' 2020-10-01 13:22:23 root: INFO: Timer: Time taken for legacyRelationalLowerer, initial IR -- LoweringTransformation -- Optimize -- PruneDeadFields : 78.246ms, total 320.979ms 2020-10-01 13:22:23 root: INFO: Timer: Time taken for legacyRelationalLowerer, initial IR -- LoweringTransformation -- Optimize -- FoldConstants : 1.458ms, total 323.272ms 2020-10-01 13:22:23 root: INFO: Timer: Time taken for legacyRelationalLowerer, initial IR -- LoweringTransformation -- Optimize -- ExtractIntervalFilters : 2.145ms, total 325.610ms 2020-10-01 13:22:23 root: INFO: Timer: Time taken for legacyRelationalLowerer, initial IR -- LoweringTransformation -- Optimize -- Simplify : 3.193ms, total 328.998ms 2020-10-01 13:22:23 root: INFO: Timer: Time taken for legacyRelationalLowerer, initial IR -- LoweringTransformation -- Optimize -- ForwardLets : 13.182ms, total 342.429ms 2020-10-01 13:22:23 root: INFO: Timer: Time taken for legacyRelationalLowerer, initial IR -- LoweringTransformation -- Optimize -- ForwardRelationalLets : 0.760ms, total 343.775ms 2020-10-01 13:22:23 root: INFO: Timer: Time taken for legacyRelationalLowerer, initial IR -- LoweringTransformation -- Optimize -- PruneDeadFields : 13.765ms, total 357.777ms 2020-10-01 13:22:23 root: INFO: Timer: Time taken for legacyRelationalLowerer, initial IR -- LoweringTransformation -- Optimize -- FoldConstants : 4.108ms, total 362.540ms 2020-10-01 13:22:23 root: INFO: Timer: Time taken for legacyRelationalLowerer, initial IR -- LoweringTransformation -- Optimize -- ExtractIntervalFilters : 2.087ms, total 364.850ms 2020-10-01 13:22:23 root: INFO: Timer: Time taken for legacyRelationalLowerer, initial IR -- LoweringTransformation -- Optimize -- Simplify : 2.690ms, total 367.756ms 2020-10-01 13:22:23 root: INFO: Timer: Time taken for legacyRelationalLowerer, initial IR -- LoweringTransformation -- Optimize -- ForwardLets : 11.524ms, total 379.521ms 2020-10-01 13:22:23 root: INFO: Timer: Time taken for legacyRelationalLowerer, initial IR -- LoweringTransformation -- Optimize -- ForwardRelationalLets : 3.642ms, total 385.292ms 2020-10-01 13:22:23 root: INFO: Timer: Time taken for legacyRelationalLowerer, initial IR -- LoweringTransformation -- Optimize -- PruneDeadFields : 13.493ms, total 400.192ms 2020-10-01 13:22:23 root: INFO: Timer: Time taken for legacyRelationalLowerer, initial IR -- LoweringTransformation -- Optimize : 329.016ms, total 401.025ms, tagged coverage 95.3 2020-10-01 13:22:23 root: INFO: optimize legacyRelationalLowerer, initial IR: after: IR size 58: (TableMapRows (MatrixToTableApply "{\"name\":\"LogisticRegression\",\"test\":\"wald\",\"yFields\":[\"__y_0\"],\"xField\":\"__uid_4\",\"covFields\":[\"__cov0\",\"__cov1\"],\"passThrough\":[]}" (MatrixRename () () ("__uid_5" "__uid_6" "__uid_7") ("__y_0" "__cov0" "__cov1") () () ("__uid_8") ("__uid_4") (MatrixMapEntries (MatrixMapRows (MatrixMapCols () (MatrixMapEntries (MatrixMapCols () (MatrixAnnotateColsTable "__uid_3" (MatrixRead Matrix{global:Struct{},col_key:[s],col:Struct{s:String},row_key:[[locus,alleles]],row:Struct{locus:Locus(GRCh37),alleles:Array[String]},entry:Struct{GT:Call}} False False "{\"bed\":\"/z/Comp/lu_group/Members/xiaoyuan/UKB_participation/23_check_weight/subgroup_test/condor_geno/chr22_sexl1_40_40.bed\",\"bim\":\"/z/Comp/lu_group/Members/xiaoyuan/UKB_participation/23_check_weight/subgroup_test/condor_geno/chr22_sexl1_40_40.bim\",\"fam\":\"/z/Comp/lu_group/Members/xiaoyuan/UKB_participation/23_check_weight/subgroup_test/condor_geno/chr22_sexl1_40_40.fam\",\"delimiter\":\"\\\\\\\\s+\",\"missing\":\"NA\",\"quantPheno\":true,\"a2Reference\":true,\"rg\":\"GRCh37\",\"contigRecoding\":{\"23\":\"X\",\"24\":\"Y\",\"25\":\"X\",\"26\":\"MT\"},\"skipInvalidLoci\":false,\"name\":\"MatrixPLINKReader\"}") (TableKeyBy (IID) False (TableRead Table{global:Struct{},key:[],row:Struct{IID:String,isAxiom:Boolean,pheno:Boolean}} False "{\"files\":[\"/z/Comp/lu_group/Members/xiaoyuan/software/hail/test/logistic/covar_l1.txt\"],\"typeMapStr\":{\"IID\":\"String\"},\"comment\":[],\"separator\":\"\\t\",\"missing\":[\"NA\"],\"hasHeader\":true,\"impute\":true,\"quoteStr\":null,\"skipBlankLines\":false,\"forceBGZ\":false,\"filterAndReplace\":{},\"forceGZ\":false,\"name\":\"TextTableReader\"}"))) (Let __iruid_45 (GetField __uid_3 (Ref sa)) (InsertFields (SelectFields () (Ref sa)) ("__uid_5" "__uid_6" "__uid_7") (__uid_5 (Apply toFloat64 () Float64 (GetField pheno (Ref __iruid_45)))) (__uid_6 (F64 1.0)) (__uid_7 (Apply toFloat64 () Float64 (GetField isAxiom (Ref __iruid_45))))))) (InsertFields (Ref g) None (__uid_8 (Cast Float64 (Apply nNonRefAlleles () Int32 (GetField GT (Ref g))))))) (Ref sa)) (MakeStruct (locus (GetField locus (Ref va))) (alleles (GetField alleles (Ref va))))) (SelectFields (__uid_8) (Ref g))))) (SelectFields (locus alleles beta standard_error z_stat p_value fit) (Let __iruid_46 (ApplyIR indexArray () Struct{beta:Float64,standard_error:Float64,z_stat:Float64,p_value:Float64,fit:Struct{n_iterations:Int32,converged:Boolean,exploded:Boolean}} (GetField logistic_regression (Ref row)) (I32 0) (Str " File \"te...")) (InsertFields (Ref row) None (beta (GetField beta (Ref __iruid_46))) (standard_error (GetField standard_error (Ref __iruid_46))) (z_stat (GetField z_stat (Ref __iruid_46))) (p_value (GetField p_value (Ref __iruid_46))) (fit (GetField fit (Ref __iruid_46))))))) 2020-10-01 13:22:23 root: INFO: Timer: Time taken for legacyRelationalLowerer, initial IR -- LoweringTransformation : 390.162ms, total 415.757ms, tagged coverage 80.4 2020-10-01 13:22:23 root: INFO: Timer: Time taken for legacyRelationalLowerer, initial IR -- Verify : 0.165ms, total 417.055ms 2020-10-01 13:22:23 root: INFO: Timer: Time taken for legacyRelationalLowerer, initial IR : 396.860ms, total 417.374ms, tagged coverage 79.6 2020-10-01 13:22:23 root: INFO: Timer: Time taken for LowerMatrixToTable -- Verify : 0.109ms, total 417.741ms 2020-10-01 13:22:23 root: INFO: Timer: Time taken for LowerMatrixToTable -- LoweringTransformation : 61.771ms, total 479.765ms 2020-10-01 13:22:23 root: INFO: Timer: Time taken for LowerMatrixToTable -- Verify : 2.138ms, total 483.140ms 2020-10-01 13:22:23 root: INFO: Timer: Time taken for LowerMatrixToTable : 66.409ms, total 484.033ms, tagged coverage 96.4 2020-10-01 13:22:23 root: INFO: Timer: Time taken for legacyRelationalLowerer, after LowerMatrixToTable -- Verify : 0.206ms, total 485.795ms 2020-10-01 13:22:23 root: INFO: optimize legacyRelationalLowerer, after LowerMatrixToTable: before: IR size 163: (TableMapRows (TableToTableApply "{\"name\":\"WrappedMatrixToTableFunction\",\"function\":{\"name\":\"LogisticRegression\",\"test\":\"wald\",\"yFields\":[\"__y_0\"],\"xField\":\"__uid_4\",\"covFields\":[\"__cov0\",\"__cov1\"],\"passThrough\":[]},\"colsFieldName\":\"__cols\",\"entriesFieldName\":\"the entries! [877f12a8827e18f61222c6c8c5fb04a8]\",\"colKey\":[]}" (TableMapRows (TableMapGlobals (TableRename () () () () (TableMapRows (TableMapRows (TableMapGlobals (TableMapRows (TableMapGlobals (TableMapGlobals (TableRead Table{global:Struct{__cols:Array[Struct{s:String}]},key:[locus,alleles],row:Struct{locus:Locus(GRCh37),alleles:Array[String],`the entries! [877f12a8827e18f61222c6c8c5fb04a8]`:Array[Struct{GT:Call}]}} False "{\"bed\":\"/z/Comp/lu_group/Members/xiaoyuan/UKB_participation/23_check_weight/subgroup_test/condor_geno/chr22_sexl1_40_40.bed\",\"bim\":\"/z/Comp/lu_group/Members/xiaoyuan/UKB_participation/23_check_weight/subgroup_test/condor_geno/chr22_sexl1_40_40.bim\",\"fam\":\"/z/Comp/lu_group/Members/xiaoyuan/UKB_participation/23_check_weight/subgroup_test/condor_geno/chr22_sexl1_40_40.fam\",\"delimiter\":\"\\\\\\\\s+\",\"missing\":\"NA\",\"quantPheno\":true,\"a2Reference\":true,\"rg\":\"GRCh37\",\"contigRecoding\":{\"23\":\"X\",\"24\":\"Y\",\"25\":\"X\",\"26\":\"MT\"},\"skipInvalidLoci\":false,\"name\":\"MatrixPLINKReader\"}") (Let __dictfield (ToDict (ToStream (ToArray (StreamMap __iruid_57 (ToStream (GetField rows (TableCollect (TableKeyBy () False (TableKeyBy (IID) False (TableRead Table{global:Struct{},key:[],row:Struct{IID:String,isAxiom:Boolean,pheno:Boolean}} False "{\"files\":[\"/z/Comp/lu_group/Members/xiaoyuan/software/hail/test/logistic/covar_l1.txt\"],\"typeMapStr\":{\"IID\":\"String\"},\"comment\":[],\"separator\":\"\\t\",\"missing\":[\"NA\"],\"hasHeader\":true,\"impute\":true,\"quoteStr\":null,\"skipBlankLines\":false,\"forceBGZ\":false,\"filterAndReplace\":{},\"forceGZ\":false,\"name\":\"TextTableReader\"}")))))) (MakeTuple (0 1) (SelectFields (IID) (Ref __iruid_57)) (SelectFields (isAxiom pheno) (Ref __iruid_57))))))) (InsertFields (Ref global) None (__cols (ToArray (StreamMap __iruid_56 (ToStream (GetField __cols (Ref global))) (InsertFields (Ref __iruid_56) None (__uid_3 (ApplyIR get () Struct{isAxiom:Boolean,pheno:Boolean} (Ref __dictfield) (MakeStruct (IID (GetField s (Ref __iruid_56))))))))))))) (InsertFields (Ref global) None (__cols (ToArray (StreamMap __iruid_61 (ToStream (ToArray (StreamRange (I32 0) (ArrayLen (GetField __cols (Ref global))) (I32 1)))) (Let __cols_array (GetField __cols (Ref global)) (Let sa (ArrayRef (Ref __cols_array) (Ref __iruid_61) (Str "")) (Let __iruid_45 (GetField __uid_3 (Ref sa)) (InsertFields (SelectFields () (Ref sa)) ("__uid_5" "__uid_6" "__uid_7") (__uid_5 (Apply toFloat64 () Float64 (GetField pheno (Ref __iruid_45)))) (__uid_6 (F64 1.0)) (__uid_7 (Apply toFloat64 () Float64 (GetField isAxiom (Ref __iruid_45))))))))))))) (InsertFields (Ref row) None (`the entries! [877f12a8827e18f61222c6c8c5fb04a8]` (ToArray (StreamZip AssumeSameLength (g sa) (ToStream (GetField `the entries! [877f12a8827e18f61222c6c8c5fb04a8]` (Ref row))) (ToStream (GetField __cols (Ref global))) (InsertFields (Ref g) None (__uid_8 (Cast Float64 (Apply nNonRefAlleles () Int32 (GetField GT (Ref g))))))))))) (InsertFields (Ref global) None (__cols (ToArray (StreamMap __iruid_62 (ToStream (ToArray (StreamRange (I32 0) (ArrayLen (GetField __cols (Ref global))) (I32 1)))) (Let __cols_array (GetField __cols (Ref global)) (Let sa (ArrayRef (Ref __cols_array) (Ref __iruid_62) (Str "")) (Ref sa)))))))) (Let n_cols (ArrayLen (GetField __cols (Ref global))) (InsertFields (Let __iruid_63 (MakeStruct) (MakeStruct (locus (GetField locus (SelectFields (locus alleles) (Ref row)))) (alleles (GetField alleles (SelectFields (locus alleles) (Ref row)))))) None (`the entries! [877f12a8827e18f61222c6c8c5fb04a8]` (GetField `the entries! [877f12a8827e18f61222c6c8c5fb04a8]` (Ref row)))))) (InsertFields (Ref row) None (`the entries! [877f12a8827e18f61222c6c8c5fb04a8]` (ToArray (StreamZip AssumeSameLength (g sa) (ToStream (GetField `the entries! [877f12a8827e18f61222c6c8c5fb04a8]` (Ref row))) (ToStream (GetField __cols (Ref global))) (SelectFields (__uid_8) (Ref g)))))))) (CastRename Struct{__cols:Array[Struct{__y_0:Float64,__cov0:Float64,__cov1:Float64}]} (Ref global))) (CastRename Struct{locus:Locus(GRCh37),alleles:Array[String],`the entries! [877f12a8827e18f61222c6c8c5fb04a8]`:Array[Struct{__uid_4:Float64}]} (Ref row)))) (SelectFields (locus alleles beta standard_error z_stat p_value fit) (Let __iruid_46 (ApplyIR indexArray () Struct{beta:Float64,standard_error:Float64,z_stat:Float64,p_value:Float64,fit:Struct{n_iterations:Int32,converged:Boolean,exploded:Boolean}} (GetField logistic_regression (Ref row)) (I32 0) (Str " File \"te...")) (InsertFields (Ref row) None (beta (GetField beta (Ref __iruid_46))) (standard_error (GetField standard_error (Ref __iruid_46))) (z_stat (GetField z_stat (Ref __iruid_46))) (p_value (GetField p_value (Ref __iruid_46))) (fit (GetField fit (Ref __iruid_46))))))) 2020-10-01 13:22:23 root: INFO: Timer: Time taken for legacyRelationalLowerer, after LowerMatrixToTable -- LoweringTransformation -- Optimize -- FoldConstants : 6.294ms, total 507.384ms 2020-10-01 13:22:23 root: INFO: Timer: Time taken for legacyRelationalLowerer, after LowerMatrixToTable -- LoweringTransformation -- Optimize -- ExtractIntervalFilters : 3.956ms, total 511.781ms 2020-10-01 13:22:23 root: INFO: Timer: Time taken for legacyRelationalLowerer, after LowerMatrixToTable -- LoweringTransformation -- Optimize -- Simplify : 39.403ms, total 551.465ms 2020-10-01 13:22:23 root: INFO: Timer: Time taken for legacyRelationalLowerer, after LowerMatrixToTable -- LoweringTransformation -- Optimize -- ForwardLets : 27.649ms, total 579.940ms 2020-10-01 13:22:23 root: INFO: Timer: Time taken for legacyRelationalLowerer, after LowerMatrixToTable -- LoweringTransformation -- Optimize -- ForwardRelationalLets : 1.900ms, total 582.867ms 2020-10-01 13:22:23 root: INFO: Timer: Time taken for legacyRelationalLowerer, after LowerMatrixToTable -- LoweringTransformation -- Optimize -- PruneDeadFields : 44.857ms, total 627.911ms 2020-10-01 13:22:23 root: INFO: Timer: Time taken for legacyRelationalLowerer, after LowerMatrixToTable -- LoweringTransformation -- Optimize -- FoldConstants : 2.827ms, total 631.594ms 2020-10-01 13:22:23 root: INFO: Timer: Time taken for legacyRelationalLowerer, after LowerMatrixToTable -- LoweringTransformation -- Optimize -- ExtractIntervalFilters : 2.409ms, total 634.308ms 2020-10-01 13:22:23 root: INFO: Timer: Time taken for legacyRelationalLowerer, after LowerMatrixToTable -- LoweringTransformation -- Optimize -- Simplify : 6.196ms, total 640.808ms 2020-10-01 13:22:23 root: INFO: Timer: Time taken for legacyRelationalLowerer, after LowerMatrixToTable -- LoweringTransformation -- Optimize -- ForwardLets : 20.946ms, total 662.251ms 2020-10-01 13:22:23 root: INFO: Timer: Time taken for legacyRelationalLowerer, after LowerMatrixToTable -- LoweringTransformation -- Optimize -- ForwardRelationalLets : 1.153ms, total 664.041ms 2020-10-01 13:22:23 root: INFO: Timer: Time taken for legacyRelationalLowerer, after LowerMatrixToTable -- LoweringTransformation -- Optimize -- PruneDeadFields : 24.031ms, total 689.953ms 2020-10-01 13:22:23 root: INFO: Timer: Time taken for legacyRelationalLowerer, after LowerMatrixToTable -- LoweringTransformation -- Optimize -- FoldConstants : 1.658ms, total 692.574ms 2020-10-01 13:22:23 root: INFO: Timer: Time taken for legacyRelationalLowerer, after LowerMatrixToTable -- LoweringTransformation -- Optimize -- ExtractIntervalFilters : 1.938ms, total 694.771ms 2020-10-01 13:22:23 root: INFO: Timer: Time taken for legacyRelationalLowerer, after LowerMatrixToTable -- LoweringTransformation -- Optimize -- Simplify : 3.155ms, total 698.209ms 2020-10-01 13:22:23 root: INFO: Timer: Time taken for legacyRelationalLowerer, after LowerMatrixToTable -- LoweringTransformation -- Optimize -- ForwardLets : 20.030ms, total 718.528ms 2020-10-01 13:22:23 root: INFO: Timer: Time taken for legacyRelationalLowerer, after LowerMatrixToTable -- LoweringTransformation -- Optimize -- ForwardRelationalLets : 2.691ms, total 721.561ms 2020-10-01 13:22:23 root: INFO: Timer: Time taken for legacyRelationalLowerer, after LowerMatrixToTable -- LoweringTransformation -- Optimize -- PruneDeadFields : 16.178ms, total 738.054ms 2020-10-01 13:22:23 root: INFO: Timer: Time taken for legacyRelationalLowerer, after LowerMatrixToTable -- LoweringTransformation -- Optimize : 237.609ms, total 738.686ms, tagged coverage 95.6 2020-10-01 13:22:23 root: INFO: optimize legacyRelationalLowerer, after LowerMatrixToTable: after: IR size 124: (TableMapRows (TableToTableApply "{\"name\":\"WrappedMatrixToTableFunction\",\"function\":{\"name\":\"LogisticRegression\",\"test\":\"wald\",\"yFields\":[\"__y_0\"],\"xField\":\"__uid_4\",\"covFields\":[\"__cov0\",\"__cov1\"],\"passThrough\":[]},\"colsFieldName\":\"__cols\",\"entriesFieldName\":\"the entries! [877f12a8827e18f61222c6c8c5fb04a8]\",\"colKey\":[]}" (TableMapRows (TableMapGlobals (TableMapRows (TableMapGlobals (TableMapRows (TableMapGlobals (TableRead Table{global:Struct{__cols:Array[Struct{s:String}]},key:[locus,alleles],row:Struct{locus:Locus(GRCh37),alleles:Array[String],`the entries! [877f12a8827e18f61222c6c8c5fb04a8]`:Array[Struct{GT:Call}]}} False "{\"bed\":\"/z/Comp/lu_group/Members/xiaoyuan/UKB_participation/23_check_weight/subgroup_test/condor_geno/chr22_sexl1_40_40.bed\",\"bim\":\"/z/Comp/lu_group/Members/xiaoyuan/UKB_participation/23_check_weight/subgroup_test/condor_geno/chr22_sexl1_40_40.bim\",\"fam\":\"/z/Comp/lu_group/Members/xiaoyuan/UKB_participation/23_check_weight/subgroup_test/condor_geno/chr22_sexl1_40_40.fam\",\"delimiter\":\"\\\\\\\\s+\",\"missing\":\"NA\",\"quantPheno\":true,\"a2Reference\":true,\"rg\":\"GRCh37\",\"contigRecoding\":{\"23\":\"X\",\"24\":\"Y\",\"25\":\"X\",\"26\":\"MT\"},\"skipInvalidLoci\":false,\"name\":\"MatrixPLINKReader\"}") (Let __iruid_166 (ToDict (StreamMap __iruid_167 (ToStream (GetField rows (TableCollect (TableRead Table{global:Struct{},key:[],row:Struct{IID:String,isAxiom:Boolean,pheno:Boolean}} False "{\"files\":[\"/z/Comp/lu_group/Members/xiaoyuan/software/hail/test/logistic/covar_l1.txt\"],\"typeMapStr\":{\"IID\":\"String\"},\"comment\":[],\"separator\":\"\\t\",\"missing\":[\"NA\"],\"hasHeader\":true,\"impute\":true,\"quoteStr\":null,\"skipBlankLines\":false,\"forceBGZ\":false,\"filterAndReplace\":{},\"forceGZ\":false,\"name\":\"TextTableReader\"}")))) (MakeTuple (0 1) (SelectFields (IID) (Ref __iruid_167)) (SelectFields (isAxiom pheno) (Ref __iruid_167))))) (Let __iruid_168 (ToArray (StreamMap __iruid_169 (ToStream (GetField __cols (Ref global))) (InsertFields (Ref __iruid_169) None (__uid_3 (ApplyIR get () Struct{isAxiom:Boolean,pheno:Boolean} (Ref __iruid_166) (MakeStruct (IID (GetField s (Ref __iruid_169))))))))) (InsertFields (Ref global) ("__cols") (__cols (ToArray (StreamMap __iruid_170 (StreamRange (I32 0) (ArrayLen (Ref __iruid_168)) (I32 1)) (Let __iruid_171 (ArrayRef (Ref __iruid_168) (Ref __iruid_170) (Str "")) (Let __iruid_172 (GetField __uid_3 (Ref __iruid_171)) (InsertFields (SelectFields () (Ref __iruid_171)) ("__uid_5" "__uid_6" "__uid_7") (__uid_5 (Apply toFloat64 () Float64 (GetField pheno (Ref __iruid_172)))) (__uid_6 (F64 1.0)) (__uid_7 (Apply toFloat64 () Float64 (GetField isAxiom (Ref __iruid_172)))))))))))))) (InsertFields (Ref row) None (`the entries! [877f12a8827e18f61222c6c8c5fb04a8]` (ToArray (StreamMap __iruid_173 (ToStream (GetField `the entries! [877f12a8827e18f61222c6c8c5fb04a8]` (Ref row))) (InsertFields (Ref __iruid_173) None (__uid_8 (Cast Float64 (Apply nNonRefAlleles () Int32 (GetField GT (Ref __iruid_173))))))))))) (InsertFields (Ref global) None (__cols (ToArray (StreamMap __iruid_174 (StreamRange (I32 0) (ArrayLen (GetField __cols (Ref global))) (I32 1)) (ArrayRef (GetField __cols (Ref global)) (Ref __iruid_174) (Str ""))))))) (MakeStruct (locus (GetField locus (Ref row))) (alleles (GetField alleles (Ref row))) (the entries! [877f12a8827e18f61222c6c8c5fb04a8] (ToArray (StreamMap __iruid_175 (ToStream (GetField `the entries! [877f12a8827e18f61222c6c8c5fb04a8]` (Ref row))) (SelectFields (__uid_8) (Ref __iruid_175))))))) (CastRename Struct{__cols:Array[Struct{__y_0:Float64,__cov0:Float64,__cov1:Float64}]} (Ref global))) (CastRename Struct{locus:Locus(GRCh37),alleles:Array[String],`the entries! [877f12a8827e18f61222c6c8c5fb04a8]`:Array[Struct{__uid_4:Float64}]} (Ref row)))) (SelectFields (locus alleles beta standard_error z_stat p_value fit) (Let __iruid_176 (ApplyIR indexArray () Struct{beta:Float64,standard_error:Float64,z_stat:Float64,p_value:Float64,fit:Struct{n_iterations:Int32,converged:Boolean,exploded:Boolean}} (GetField logistic_regression (Ref row)) (I32 0) (Str " File \"te...")) (InsertFields (Ref row) None (beta (GetField beta (Ref __iruid_176))) (standard_error (GetField standard_error (Ref __iruid_176))) (z_stat (GetField z_stat (Ref __iruid_176))) (p_value (GetField p_value (Ref __iruid_176))) (fit (GetField fit (Ref __iruid_176))))))) 2020-10-01 13:22:23 root: INFO: Timer: Time taken for legacyRelationalLowerer, after LowerMatrixToTable -- LoweringTransformation : 259.397ms, total 745.358ms, tagged coverage 87.6 2020-10-01 13:22:23 root: INFO: Timer: Time taken for legacyRelationalLowerer, after LowerMatrixToTable -- Verify : 0.139ms, total 745.783ms 2020-10-01 13:22:23 root: INFO: Timer: Time taken for legacyRelationalLowerer, after LowerMatrixToTable : 260.385ms, total 745.969ms, tagged coverage 87.4 2020-10-01 13:22:23 root: INFO: Timer: Time taken for InterpretNonCompilable -- Verify : 0.183ms, total 746.429ms 2020-10-01 13:22:23 root: INFO: interpreting non compilable node: TableCollect 2020-10-01 13:22:23 root: INFO: encoder cache miss (0 hits, 1 misses, 0.000) 2020-10-01 13:22:23 root: INFO: instruction count: 6: __C1etypeEncode. 2020-10-01 13:22:23 root: INFO: instruction count: 8: __C1etypeEncode.apply 2020-10-01 13:22:23 root: INFO: instruction count: 8: __C1etypeEncode.__m2ENCODE_r_tuple_of_r_stringANDr_boolANDr_boolEND_TO_r_struct_of_r_binaryANDr_boolANDr_boolEND 2020-10-01 13:22:23 root: INFO: instruction count: 34: __C1etypeEncode.__m3write_fields_group_0 2020-10-01 13:22:23 root: INFO: instruction count: 19: __C1etypeEncode.__m4ENCODE_r_binary_TO_r_binary 2020-10-01 13:22:23 root: INFO: instruction count: 7: __C1etypeEncode.__m5ENCODE_r_bool_TO_r_bool 2020-10-01 13:22:24 SparkContext: INFO: Starting job: collect at RVD.scala:761 2020-10-01 13:22:24 DAGScheduler: INFO: Got job 1 (collect at RVD.scala:761) with 1 output partitions 2020-10-01 13:22:24 DAGScheduler: INFO: Final stage: ResultStage 1 (collect at RVD.scala:761) 2020-10-01 13:22:24 DAGScheduler: INFO: Parents of final stage: List() 2020-10-01 13:22:24 DAGScheduler: INFO: Missing parents: List() 2020-10-01 13:22:24 DAGScheduler: INFO: Submitting ResultStage 1 (MapPartitionsRDD[5] at mapPartitions at ContextRDD.scala:160), which has no missing parents 2020-10-01 13:22:24 MemoryStore: INFO: Block broadcast_3 stored as values in memory (estimated size 15.0 KB, free 366.0 MB) 2020-10-01 13:22:24 MemoryStore: INFO: Block broadcast_3_piece0 stored as bytes in memory (estimated size 7.9 KB, free 366.0 MB) 2020-10-01 13:22:24 BlockManagerInfo: INFO: Added broadcast_3_piece0 in memory on qlu-1:28416 (size: 7.9 KB, free: 366.3 MB) 2020-10-01 13:22:24 SparkContext: INFO: Created broadcast 3 from broadcast at DAGScheduler.scala:1161 2020-10-01 13:22:24 DAGScheduler: INFO: Submitting 1 missing tasks from ResultStage 1 (MapPartitionsRDD[5] at mapPartitions at ContextRDD.scala:160) (first 15 tasks are for partitions Vector(0)) 2020-10-01 13:22:24 TaskSchedulerImpl: INFO: Adding task set 1.0 with 1 tasks 2020-10-01 13:22:24 TaskSetManager: INFO: Starting task 0.0 in stage 1.0 (TID 1, localhost, executor driver, partition 0, PROCESS_LOCAL, 8011 bytes) 2020-10-01 13:22:24 Executor: INFO: Running task 0.0 in stage 1.0 (TID 1) 2020-10-01 13:22:24 root: INFO: RegionPool: initialized for thread 130: Executor task launch worker for task 1 2020-10-01 13:22:24 Executor: INFO: Finished task 0.0 in stage 1.0 (TID 1). 795268 bytes result sent to driver 2020-10-01 13:22:24 TaskSetManager: INFO: Finished task 0.0 in stage 1.0 (TID 1) in 614 ms on localhost (executor driver) (1/1) 2020-10-01 13:22:24 TaskSchedulerImpl: INFO: Removed TaskSet 1.0, whose tasks have all completed, from pool 2020-10-01 13:22:24 DAGScheduler: INFO: ResultStage 1 (collect at RVD.scala:761) finished in 0.656 s 2020-10-01 13:22:24 DAGScheduler: INFO: Job 1 finished: collect at RVD.scala:761, took 0.666916 s 2020-10-01 13:22:24 root: INFO: decoder cache miss (0 hits, 1 misses, 0.000 2020-10-01 13:22:24 root: INFO: instruction count: 6: __C6etypeDecode. 2020-10-01 13:22:24 root: INFO: instruction count: 8: __C6etypeDecode.apply 2020-10-01 13:22:24 root: INFO: instruction count: 25: __C6etypeDecode.__m7DECODE_r_struct_of_r_binaryANDr_boolANDr_boolEND_TO_r_tuple_of_r_stringANDr_boolANDr_boolEND 2020-10-01 13:22:24 root: INFO: instruction count: 25: __C6etypeDecode.__m8read_fields_group_0 2020-10-01 13:22:24 root: INFO: instruction count: 34: __C6etypeDecode.__m9INPLACE_DECODE_r_binary_TO_r_binary 2020-10-01 13:22:24 root: INFO: instruction count: 11: __C6etypeDecode.__m10INPLACE_DECODE_r_bool_TO_r_bool 2020-10-01 13:22:24 root: INFO: took 1.266s 2020-10-01 13:22:24 root: INFO: Timer: Time taken for InterpretNonCompilable -- LoweringTransformation : 1.271s, total 2.018s 2020-10-01 13:22:24 root: INFO: Timer: Time taken for InterpretNonCompilable -- Verify : 1.064ms, total 2.019s 2020-10-01 13:22:24 root: INFO: Timer: Time taken for InterpretNonCompilable : 1.274s, total 2.021s, tagged coverage 99.8 2020-10-01 13:22:24 root: INFO: Timer: Time taken for legacyRelationalLowerer, after LegacyInterpretNonCompilable -- Verify : 0.051ms, total 2.021s 2020-10-01 13:22:24 root: INFO: optimize legacyRelationalLowerer, after LegacyInterpretNonCompilable: before: IR size 123: (TableMapRows (TableToTableApply "{\"name\":\"WrappedMatrixToTableFunction\",\"function\":{\"name\":\"LogisticRegression\",\"test\":\"wald\",\"yFields\":[\"__y_0\"],\"xField\":\"__uid_4\",\"covFields\":[\"__cov0\",\"__cov1\"],\"passThrough\":[]},\"colsFieldName\":\"__cols\",\"entriesFieldName\":\"the entries! [877f12a8827e18f61222c6c8c5fb04a8]\",\"colKey\":[]}" (TableMapRows (TableMapGlobals (TableMapRows (TableMapGlobals (TableMapRows (TableMapGlobals (TableRead Table{global:Struct{__cols:Array[Struct{s:String}]},key:[locus,alleles],row:Struct{locus:Locus(GRCh37),alleles:Array[String],`the entries! [877f12a8827e18f61222c6c8c5fb04a8]`:Array[Struct{GT:Call}]}} False "{\"bed\":\"/z/Comp/lu_group/Members/xiaoyuan/UKB_participation/23_check_weight/subgroup_test/condor_geno/chr22_sexl1_40_40.bed\",\"bim\":\"/z/Comp/lu_group/Members/xiaoyuan/UKB_participation/23_check_weight/subgroup_test/condor_geno/chr22_sexl1_40_40.bim\",\"fam\":\"/z/Comp/lu_group/Members/xiaoyuan/UKB_participation/23_check_weight/subgroup_test/condor_geno/chr22_sexl1_40_40.fam\",\"delimiter\":\"\\\\\\\\s+\",\"missing\":\"NA\",\"quantPheno\":true,\"a2Reference\":true,\"rg\":\"GRCh37\",\"contigRecoding\":{\"23\":\"X\",\"24\":\"Y\",\"25\":\"X\",\"26\":\"MT\"},\"skipInvalidLoci\":false,\"name\":\"MatrixPLINKReader\"}") (Let __iruid_166 (ToDict (StreamMap __iruid_167 (ToStream (GetField rows (Literal Struct{rows:Array[Struct{IID:String,isAxiom:Boolean,pheno:Boolean}],global:Struct{}} ))) (MakeTuple (0 1) (SelectFields (IID) (Ref __iruid_167)) (SelectFields (isAxiom pheno) (Ref __iruid_167))))) (Let __iruid_168 (ToArray (StreamMap __iruid_169 (ToStream (GetField __cols (Ref global))) (InsertFields (Ref __iruid_169) None (__uid_3 (ApplyIR get () Struct{isAxiom:Boolean,pheno:Boolean} (Ref __iruid_166) (MakeStruct (IID (GetField s (Ref __iruid_169))))))))) (InsertFields (Ref global) ("__cols") (__cols (ToArray (StreamMap __iruid_170 (StreamRange (I32 0) (ArrayLen (Ref __iruid_168)) (I32 1)) (Let __iruid_171 (ArrayRef (Ref __iruid_168) (Ref __iruid_170) (Str "")) (Let __iruid_172 (GetField __uid_3 (Ref __iruid_171)) (InsertFields (SelectFields () (Ref __iruid_171)) ("__uid_5" "__uid_6" "__uid_7") (__uid_5 (Apply toFloat64 () Float64 (GetField pheno (Ref __iruid_172)))) (__uid_6 (F64 1.0)) (__uid_7 (Apply toFloat64 () Float64 (GetField isAxiom (Ref __iruid_172)))))))))))))) (InsertFields (Ref row) None (`the entries! [877f12a8827e18f61222c6c8c5fb04a8]` (ToArray (StreamMap __iruid_173 (ToStream (GetField `the entries! [877f12a8827e18f61222c6c8c5fb04a8]` (Ref row))) (InsertFields (Ref __iruid_173) None (__uid_8 (Cast Float64 (Apply nNonRefAlleles () Int32 (GetField GT (Ref __iruid_173))))))))))) (InsertFields (Ref global) None (__cols (ToArray (StreamMap __iruid_174 (StreamRange (I32 0) (ArrayLen (GetField __cols (Ref global))) (I32 1)) (ArrayRef (GetField __cols (Ref global)) (Ref __iruid_174) (Str ""))))))) (MakeStruct (locus (GetField locus (Ref row))) (alleles (GetField alleles (Ref row))) (the entries! [877f12a8827e18f61222c6c8c5fb04a8] (ToArray (StreamMap __iruid_175 (ToStream (GetField `the entries! [877f12a8827e18f61222c6c8c5fb04a8]` (Ref row))) (SelectFields (__uid_8) (Ref __iruid_175))))))) (CastRename Struct{__cols:Array[Struct{__y_0:Float64,__cov0:Float64,__cov1:Float64}]} (Ref global))) (CastRename Struct{locus:Locus(GRCh37),alleles:Array[String],`the entries! [877f12a8827e18f61222c6c8c5fb04a8]`:Array[Struct{__uid_4:Float64}]} (Ref row)))) (SelectFields (locus alleles beta standard_error z_stat p_value fit) (Let __iruid_176 (ApplyIR indexArray () Struct{beta:Float64,standard_error:Float64,z_stat:Float64,p_value:Float64,fit:Struct{n_iterations:Int32,converged:Boolean,exploded:Boolean}} (GetField logistic_regression (Ref row)) (I32 0) (Str " File \"te...")) (InsertFields (Ref row) None (beta (GetField beta (Ref __iruid_176))) (standard_error (GetField standard_error (Ref __iruid_176))) (z_stat (GetField z_stat (Ref __iruid_176))) (p_value (GetField p_value (Ref __iruid_176))) (fit (GetField fit (Ref __iruid_176))))))) 2020-10-01 13:22:24 root: INFO: Timer: Time taken for legacyRelationalLowerer, after LegacyInterpretNonCompilable -- LoweringTransformation -- Optimize -- FoldConstants : 1.732ms, total 2.028s 2020-10-01 13:22:24 root: INFO: Timer: Time taken for legacyRelationalLowerer, after LegacyInterpretNonCompilable -- LoweringTransformation -- Optimize -- ExtractIntervalFilters : 2.156ms, total 2.030s 2020-10-01 13:22:24 root: INFO: Timer: Time taken for legacyRelationalLowerer, after LegacyInterpretNonCompilable -- LoweringTransformation -- Optimize -- Simplify : 3.191ms, total 2.034s 2020-10-01 13:22:24 root: INFO: Timer: Time taken for legacyRelationalLowerer, after LegacyInterpretNonCompilable -- LoweringTransformation -- Optimize -- ForwardLets : 18.808ms, total 2.053s 2020-10-01 13:22:24 root: INFO: Timer: Time taken for legacyRelationalLowerer, after LegacyInterpretNonCompilable -- LoweringTransformation -- Optimize -- ForwardRelationalLets : 0.982ms, total 2.054s 2020-10-01 13:22:24 root: INFO: Timer: Time taken for legacyRelationalLowerer, after LegacyInterpretNonCompilable -- LoweringTransformation -- Optimize -- PruneDeadFields : 16.626ms, total 2.071s 2020-10-01 13:22:24 root: INFO: Timer: Time taken for legacyRelationalLowerer, after LegacyInterpretNonCompilable -- LoweringTransformation -- Optimize -- FoldConstants : 0.837ms, total 2.072s 2020-10-01 13:22:24 root: INFO: Timer: Time taken for legacyRelationalLowerer, after LegacyInterpretNonCompilable -- LoweringTransformation -- Optimize -- ExtractIntervalFilters : 1.105ms, total 2.073s 2020-10-01 13:22:24 root: INFO: Timer: Time taken for legacyRelationalLowerer, after LegacyInterpretNonCompilable -- LoweringTransformation -- Optimize -- Simplify : 1.899ms, total 2.075s 2020-10-01 13:22:25 root: INFO: Timer: Time taken for legacyRelationalLowerer, after LegacyInterpretNonCompilable -- LoweringTransformation -- Optimize -- ForwardLets : 12.127ms, total 2.088s 2020-10-01 13:22:25 root: INFO: Timer: Time taken for legacyRelationalLowerer, after LegacyInterpretNonCompilable -- LoweringTransformation -- Optimize -- ForwardRelationalLets : 1.574ms, total 2.089s 2020-10-01 13:22:25 root: INFO: Timer: Time taken for legacyRelationalLowerer, after LegacyInterpretNonCompilable -- LoweringTransformation -- Optimize -- PruneDeadFields : 15.246ms, total 2.105s 2020-10-01 13:22:25 root: INFO: Timer: Time taken for legacyRelationalLowerer, after LegacyInterpretNonCompilable -- LoweringTransformation -- Optimize -- FoldConstants : 0.873ms, total 2.106s 2020-10-01 13:22:25 root: INFO: Timer: Time taken for legacyRelationalLowerer, after LegacyInterpretNonCompilable -- LoweringTransformation -- Optimize -- ExtractIntervalFilters : 2.693ms, total 2.109s 2020-10-01 13:22:25 root: INFO: Timer: Time taken for legacyRelationalLowerer, after LegacyInterpretNonCompilable -- LoweringTransformation -- Optimize -- Simplify : 2.351ms, total 2.111s 2020-10-01 13:22:25 root: INFO: Timer: Time taken for legacyRelationalLowerer, after LegacyInterpretNonCompilable -- LoweringTransformation -- Optimize -- ForwardLets : 12.222ms, total 2.124s 2020-10-01 13:22:25 root: INFO: Timer: Time taken for legacyRelationalLowerer, after LegacyInterpretNonCompilable -- LoweringTransformation -- Optimize -- ForwardRelationalLets : 1.573ms, total 2.126s 2020-10-01 13:22:25 root: INFO: Timer: Time taken for legacyRelationalLowerer, after LegacyInterpretNonCompilable -- LoweringTransformation -- Optimize -- PruneDeadFields : 10.406ms, total 2.136s 2020-10-01 13:22:25 root: INFO: Timer: Time taken for legacyRelationalLowerer, after LegacyInterpretNonCompilable -- LoweringTransformation -- Optimize : 110.053ms, total 2.136s, tagged coverage 96.7 2020-10-01 13:22:25 root: INFO: optimize legacyRelationalLowerer, after LegacyInterpretNonCompilable: after: IR size 122: (TableMapRows (TableToTableApply "{\"name\":\"WrappedMatrixToTableFunction\",\"function\":{\"name\":\"LogisticRegression\",\"test\":\"wald\",\"yFields\":[\"__y_0\"],\"xField\":\"__uid_4\",\"covFields\":[\"__cov0\",\"__cov1\"],\"passThrough\":[]},\"colsFieldName\":\"__cols\",\"entriesFieldName\":\"the entries! [877f12a8827e18f61222c6c8c5fb04a8]\",\"colKey\":[]}" (TableMapRows (TableMapGlobals (TableMapRows (TableMapGlobals (TableMapRows (TableMapGlobals (TableRead Table{global:Struct{__cols:Array[Struct{s:String}]},key:[locus,alleles],row:Struct{locus:Locus(GRCh37),alleles:Array[String],`the entries! [877f12a8827e18f61222c6c8c5fb04a8]`:Array[Struct{GT:Call}]}} False "{\"bed\":\"/z/Comp/lu_group/Members/xiaoyuan/UKB_participation/23_check_weight/subgroup_test/condor_geno/chr22_sexl1_40_40.bed\",\"bim\":\"/z/Comp/lu_group/Members/xiaoyuan/UKB_participation/23_check_weight/subgroup_test/condor_geno/chr22_sexl1_40_40.bim\",\"fam\":\"/z/Comp/lu_group/Members/xiaoyuan/UKB_participation/23_check_weight/subgroup_test/condor_geno/chr22_sexl1_40_40.fam\",\"delimiter\":\"\\\\\\\\s+\",\"missing\":\"NA\",\"quantPheno\":true,\"a2Reference\":true,\"rg\":\"GRCh37\",\"contigRecoding\":{\"23\":\"X\",\"24\":\"Y\",\"25\":\"X\",\"26\":\"MT\"},\"skipInvalidLoci\":false,\"name\":\"MatrixPLINKReader\"}") (Let __iruid_271 (ToDict (StreamMap __iruid_272 (ToStream (Literal Array[Struct{IID:String,isAxiom:Boolean,pheno:Boolean}] )) (MakeTuple (0 1) (SelectFields (IID) (Ref __iruid_272)) (SelectFields (isAxiom pheno) (Ref __iruid_272))))) (Let __iruid_273 (ToArray (StreamMap __iruid_274 (ToStream (GetField __cols (Ref global))) (InsertFields (Ref __iruid_274) None (__uid_3 (ApplyIR get () Struct{isAxiom:Boolean,pheno:Boolean} (Ref __iruid_271) (MakeStruct (IID (GetField s (Ref __iruid_274))))))))) (InsertFields (Ref global) ("__cols") (__cols (ToArray (StreamMap __iruid_275 (StreamRange (I32 0) (ArrayLen (Ref __iruid_273)) (I32 1)) (Let __iruid_276 (ArrayRef (Ref __iruid_273) (Ref __iruid_275) (Str "")) (Let __iruid_277 (GetField __uid_3 (Ref __iruid_276)) (InsertFields (SelectFields () (Ref __iruid_276)) ("__uid_5" "__uid_6" "__uid_7") (__uid_5 (Apply toFloat64 () Float64 (GetField pheno (Ref __iruid_277)))) (__uid_6 (F64 1.0)) (__uid_7 (Apply toFloat64 () Float64 (GetField isAxiom (Ref __iruid_277)))))))))))))) (InsertFields (Ref row) None (`the entries! [877f12a8827e18f61222c6c8c5fb04a8]` (ToArray (StreamMap __iruid_278 (ToStream (GetField `the entries! [877f12a8827e18f61222c6c8c5fb04a8]` (Ref row))) (InsertFields (Ref __iruid_278) None (__uid_8 (Cast Float64 (Apply nNonRefAlleles () Int32 (GetField GT (Ref __iruid_278))))))))))) (InsertFields (Ref global) None (__cols (ToArray (StreamMap __iruid_279 (StreamRange (I32 0) (ArrayLen (GetField __cols (Ref global))) (I32 1)) (ArrayRef (GetField __cols (Ref global)) (Ref __iruid_279) (Str ""))))))) (MakeStruct (locus (GetField locus (Ref row))) (alleles (GetField alleles (Ref row))) (the entries! [877f12a8827e18f61222c6c8c5fb04a8] (ToArray (StreamMap __iruid_280 (ToStream (GetField `the entries! [877f12a8827e18f61222c6c8c5fb04a8]` (Ref row))) (SelectFields (__uid_8) (Ref __iruid_280))))))) (CastRename Struct{__cols:Array[Struct{__y_0:Float64,__cov0:Float64,__cov1:Float64}]} (Ref global))) (CastRename Struct{locus:Locus(GRCh37),alleles:Array[String],`the entries! [877f12a8827e18f61222c6c8c5fb04a8]`:Array[Struct{__uid_4:Float64}]} (Ref row)))) (SelectFields (locus alleles beta standard_error z_stat p_value fit) (Let __iruid_281 (ApplyIR indexArray () Struct{beta:Float64,standard_error:Float64,z_stat:Float64,p_value:Float64,fit:Struct{n_iterations:Int32,converged:Boolean,exploded:Boolean}} (GetField logistic_regression (Ref row)) (I32 0) (Str " File \"te...")) (InsertFields (Ref row) None (beta (GetField beta (Ref __iruid_281))) (standard_error (GetField standard_error (Ref __iruid_281))) (z_stat (GetField z_stat (Ref __iruid_281))) (p_value (GetField p_value (Ref __iruid_281))) (fit (GetField fit (Ref __iruid_281))))))) 2020-10-01 13:22:25 root: INFO: Timer: Time taken for legacyRelationalLowerer, after LegacyInterpretNonCompilable -- LoweringTransformation : 118.710ms, total 2.140s, tagged coverage 89.6 2020-10-01 13:22:25 root: INFO: Timer: Time taken for legacyRelationalLowerer, after LegacyInterpretNonCompilable -- Verify : 0.058ms, total 2.140s 2020-10-01 13:22:25 root: INFO: Timer: Time taken for legacyRelationalLowerer, after LegacyInterpretNonCompilable : 119.737ms, total 2.141s, tagged coverage 89.0 2020-10-01 13:22:25 MemoryStore: INFO: Block broadcast_4 stored as values in memory (estimated size 798.6 KB, free 365.2 MB) 2020-10-01 13:22:25 MemoryStore: INFO: Block broadcast_4_piece0 stored as bytes in memory (estimated size 43.8 KB, free 365.2 MB) 2020-10-01 13:22:25 BlockManagerInfo: INFO: Added broadcast_4_piece0 in memory on qlu-1:28416 (size: 43.8 KB, free: 366.2 MB) 2020-10-01 13:22:25 SparkContext: INFO: Created broadcast 4 from broadcast at SparkBackend.scala:233 2020-10-01 13:22:25 root: INFO: RegionPool: REPORT_THRESHOLD: 422.2K allocated (128.0K blocks / 294.2K chunks), regions.size = 2, 0 current java objects, 0 max java objects, thread 31: Thread-5 2020-10-01 13:22:25 root: INFO: RegionPool: REPORT_THRESHOLD: 550.2K allocated (256.0K blocks / 294.2K chunks), regions.size = 2, 0 current java objects, 0 max java objects, thread 31: Thread-5 2020-10-01 13:22:25 root: INFO: Timer: Time taken for compileLowerer, initial IR -- Verify : 0.371ms, total 2.335s 2020-10-01 13:22:25 root: INFO: optimize compileLowerer, initial IR: before: IR size 53: (Coalesce (Let __iruid_271 (ToDict (StreamMap __iruid_272 (ToStream (Literal Array[Struct{IID:String,isAxiom:Boolean,pheno:Boolean}] )) (MakeTuple (0 1) (SelectFields (IID) (Ref __iruid_272)) (SelectFields (isAxiom pheno) (Ref __iruid_272))))) (Let __iruid_273 (ToArray (StreamMap __iruid_274 (ToStream (GetField __cols (In +PCStruct{__cols:+PCArray[+PCStruct{s:+PCString}]} 0))) (InsertFields (Ref __iruid_274) None (__uid_3 (ApplyIR get () Struct{isAxiom:Boolean,pheno:Boolean} (Ref __iruid_271) (MakeStruct (IID (GetField s (Ref __iruid_274))))))))) (InsertFields (In +PCStruct{__cols:+PCArray[+PCStruct{s:+PCString}]} 0) ("__cols") (__cols (ToArray (StreamMap __iruid_275 (StreamRange (I32 0) (ArrayLen (Ref __iruid_273)) (I32 1)) (Let __iruid_276 (ArrayRef (Ref __iruid_273) (Ref __iruid_275) (Str "")) (Let __iruid_277 (GetField __uid_3 (Ref __iruid_276)) (InsertFields (SelectFields () (Ref __iruid_276)) ("__uid_5" "__uid_6" "__uid_7") (__uid_5 (Apply toFloat64 () Float64 (GetField pheno (Ref __iruid_277)))) (__uid_6 (F64 1.0)) (__uid_7 (Apply toFloat64 () Float64 (GetField isAxiom (Ref __iruid_277))))))))))))) (Die Struct{__cols:Array[Struct{__uid_5:Float64,__uid_6:Float64,__uid_7:Float64}]} (Str "Internal e..."))) 2020-10-01 13:22:25 root: INFO: Timer: Time taken for compileLowerer, initial IR -- LoweringTransformation -- Optimize -- FoldConstants : 1.479ms, total 2.340s 2020-10-01 13:22:25 root: INFO: Timer: Time taken for compileLowerer, initial IR -- LoweringTransformation -- Optimize -- ExtractIntervalFilters : 0.266ms, total 2.341s 2020-10-01 13:22:25 root: INFO: Timer: Time taken for compileLowerer, initial IR -- LoweringTransformation -- Optimize -- Simplify : 1.447ms, total 2.342s 2020-10-01 13:22:25 root: INFO: Timer: Time taken for compileLowerer, initial IR -- LoweringTransformation -- Optimize -- ForwardLets : 6.012ms, total 2.349s 2020-10-01 13:22:25 root: INFO: Timer: Time taken for compileLowerer, initial IR -- LoweringTransformation -- Optimize -- ForwardRelationalLets : 0.303ms, total 2.349s 2020-10-01 13:22:25 root: INFO: Timer: Time taken for compileLowerer, initial IR -- LoweringTransformation -- Optimize -- PruneDeadFields : 5.184ms, total 2.354s 2020-10-01 13:22:25 root: INFO: Timer: Time taken for compileLowerer, initial IR -- LoweringTransformation -- Optimize -- FoldConstants : 0.415ms, total 2.355s 2020-10-01 13:22:25 root: INFO: Timer: Time taken for compileLowerer, initial IR -- LoweringTransformation -- Optimize -- ExtractIntervalFilters : 0.231ms, total 2.355s 2020-10-01 13:22:25 root: INFO: Timer: Time taken for compileLowerer, initial IR -- LoweringTransformation -- Optimize -- Simplify : 0.873ms, total 2.356s 2020-10-01 13:22:25 root: INFO: Timer: Time taken for compileLowerer, initial IR -- LoweringTransformation -- Optimize -- ForwardLets : 5.175ms, total 2.362s 2020-10-01 13:22:25 root: INFO: Timer: Time taken for compileLowerer, initial IR -- LoweringTransformation -- Optimize -- ForwardRelationalLets : 0.970ms, total 2.363s 2020-10-01 13:22:25 root: INFO: Timer: Time taken for compileLowerer, initial IR -- LoweringTransformation -- Optimize -- PruneDeadFields : 6.591ms, total 2.370s 2020-10-01 13:22:25 root: INFO: Timer: Time taken for compileLowerer, initial IR -- LoweringTransformation -- Optimize -- FoldConstants : 0.437ms, total 2.370s 2020-10-01 13:22:25 root: INFO: Timer: Time taken for compileLowerer, initial IR -- LoweringTransformation -- Optimize -- ExtractIntervalFilters : 0.222ms, total 2.371s 2020-10-01 13:22:25 root: INFO: Timer: Time taken for compileLowerer, initial IR -- LoweringTransformation -- Optimize -- Simplify : 0.861ms, total 2.372s 2020-10-01 13:22:25 root: INFO: Timer: Time taken for compileLowerer, initial IR -- LoweringTransformation -- Optimize -- ForwardLets : 7.323ms, total 2.379s 2020-10-01 13:22:25 root: INFO: Timer: Time taken for compileLowerer, initial IR -- LoweringTransformation -- Optimize -- ForwardRelationalLets : 0.280ms, total 2.379s 2020-10-01 13:22:25 root: INFO: Timer: Time taken for compileLowerer, initial IR -- LoweringTransformation -- Optimize -- PruneDeadFields : 3.370ms, total 2.383s 2020-10-01 13:22:25 root: INFO: Timer: Time taken for compileLowerer, initial IR -- LoweringTransformation -- Optimize : 44.454ms, total 2.383s, tagged coverage 93.2 2020-10-01 13:22:25 root: INFO: optimize compileLowerer, initial IR: after: IR size 53: (Coalesce (Let __iruid_344 (ToDict (StreamMap __iruid_345 (ToStream (Literal Array[Struct{IID:String,isAxiom:Boolean,pheno:Boolean}] )) (MakeTuple (0 1) (SelectFields (IID) (Ref __iruid_345)) (SelectFields (isAxiom pheno) (Ref __iruid_345))))) (Let __iruid_346 (ToArray (StreamMap __iruid_347 (ToStream (GetField __cols (In +PCStruct{__cols:+PCArray[+PCStruct{s:+PCString}]} 0))) (InsertFields (Ref __iruid_347) None (__uid_3 (ApplyIR get () Struct{isAxiom:Boolean,pheno:Boolean} (Ref __iruid_344) (MakeStruct (IID (GetField s (Ref __iruid_347))))))))) (InsertFields (In +PCStruct{__cols:+PCArray[+PCStruct{s:+PCString}]} 0) ("__cols") (__cols (ToArray (StreamMap __iruid_348 (StreamRange (I32 0) (ArrayLen (Ref __iruid_346)) (I32 1)) (Let __iruid_349 (ArrayRef (Ref __iruid_346) (Ref __iruid_348) (Str "")) (Let __iruid_350 (GetField __uid_3 (Ref __iruid_349)) (InsertFields (SelectFields () (Ref __iruid_349)) ("__uid_5" "__uid_6" "__uid_7") (__uid_5 (Apply toFloat64 () Float64 (GetField pheno (Ref __iruid_350)))) (__uid_6 (F64 1.0)) (__uid_7 (Apply toFloat64 () Float64 (GetField isAxiom (Ref __iruid_350))))))))))))) (Die Struct{__cols:Array[Struct{__uid_5:Float64,__uid_6:Float64,__uid_7:Float64}]} (Str "Internal e..."))) 2020-10-01 13:22:25 root: INFO: Timer: Time taken for compileLowerer, initial IR -- LoweringTransformation : 49.784ms, total 2.385s, tagged coverage 83.2 2020-10-01 13:22:25 root: INFO: Timer: Time taken for compileLowerer, initial IR -- Verify : 0.043ms, total 2.386s 2020-10-01 13:22:25 root: INFO: Timer: Time taken for compileLowerer, initial IR : 51.101ms, total 2.386s, tagged coverage 81.9 2020-10-01 13:22:25 root: INFO: Timer: Time taken for InlineApplyIR -- Verify : 0.102ms, total 2.386s 2020-10-01 13:22:25 root: INFO: Timer: Time taken for InlineApplyIR -- LoweringTransformation : 0.791ms, total 2.387s 2020-10-01 13:22:25 root: INFO: Timer: Time taken for InlineApplyIR -- Verify : 0.178ms, total 2.388s 2020-10-01 13:22:25 root: INFO: Timer: Time taken for InlineApplyIR : 1.883ms, total 2.388s, tagged coverage 56.9 2020-10-01 13:22:25 root: INFO: Timer: Time taken for compileLowerer, after InlineApplyIR -- Verify : 0.034ms, total 2.388s 2020-10-01 13:22:25 root: INFO: optimize compileLowerer, after InlineApplyIR: before: IR size 85: (Coalesce (Let __iruid_344 (ToDict (StreamMap __iruid_345 (ToStream (Literal Array[Struct{IID:String,isAxiom:Boolean,pheno:Boolean}] )) (MakeTuple (0 1) (SelectFields (IID) (Ref __iruid_345)) (SelectFields (isAxiom pheno) (Ref __iruid_345))))) (Let __iruid_346 (ToArray (StreamMap __iruid_347 (ToStream (GetField __cols (In +PCStruct{__cols:+PCArray[+PCStruct{s:+PCString}]} 0))) (InsertFields (Ref __iruid_347) None (__uid_3 (Let __iruid_357 (Ref __iruid_344) (Let __iruid_358 (MakeStruct (IID (GetField s (Ref __iruid_347)))) (If (IsNA (Ref __iruid_357)) (NA Struct{isAxiom:Boolean,pheno:Boolean}) (Let __iruid_359 (LowerBoundOnOrderedCollection True (Ref __iruid_357) (Ref __iruid_358)) (If (ApplyComparisonOp EQWithNA (Ref __iruid_359) (ArrayLen (CastToArray (Ref __iruid_357)))) (NA Struct{isAxiom:Boolean,pheno:Boolean}) (If (ApplyComparisonOp EQWithNA (GetField key (ArrayRef (CastToArray (Ref __iruid_357)) (Ref __iruid_359) (Str ""))) (Ref __iruid_358)) (GetField value (ArrayRef (CastToArray (Ref __iruid_357)) (Ref __iruid_359) (Str ""))) (NA Struct{isAxiom:Boolean,pheno:Boolean}))))))))))) (InsertFields (In +PCStruct{__cols:+PCArray[+PCStruct{s:+PCString}]} 0) ("__cols") (__cols (ToArray (StreamMap __iruid_348 (StreamRange (I32 0) (ArrayLen (Ref __iruid_346)) (I32 1)) (Let __iruid_349 (ArrayRef (Ref __iruid_346) (Ref __iruid_348) (Str "")) (Let __iruid_350 (GetField __uid_3 (Ref __iruid_349)) (InsertFields (SelectFields () (Ref __iruid_349)) ("__uid_5" "__uid_6" "__uid_7") (__uid_5 (Apply toFloat64 () Float64 (GetField pheno (Ref __iruid_350)))) (__uid_6 (F64 1.0)) (__uid_7 (Apply toFloat64 () Float64 (GetField isAxiom (Ref __iruid_350))))))))))))) (Die Struct{__cols:Array[Struct{__uid_5:Float64,__uid_6:Float64,__uid_7:Float64}]} (Str "Internal e..."))) 2020-10-01 13:22:25 root: INFO: Timer: Time taken for compileLowerer, after InlineApplyIR -- LoweringTransformation -- Optimize -- FoldConstants : 0.648ms, total 2.390s 2020-10-01 13:22:25 root: INFO: Timer: Time taken for compileLowerer, after InlineApplyIR -- LoweringTransformation -- Optimize -- ExtractIntervalFilters : 0.307ms, total 2.391s 2020-10-01 13:22:25 root: INFO: Timer: Time taken for compileLowerer, after InlineApplyIR -- LoweringTransformation -- Optimize -- Simplify : 1.665ms, total 2.393s 2020-10-01 13:22:25 root: INFO: Timer: Time taken for compileLowerer, after InlineApplyIR -- LoweringTransformation -- Optimize -- ForwardLets : 7.771ms, total 2.402s 2020-10-01 13:22:25 root: INFO: Timer: Time taken for compileLowerer, after InlineApplyIR -- LoweringTransformation -- Optimize -- ForwardRelationalLets : 0.366ms, total 2.402s 2020-10-01 13:22:25 root: INFO: Timer: Time taken for compileLowerer, after InlineApplyIR -- LoweringTransformation -- Optimize -- PruneDeadFields : 4.961ms, total 2.407s 2020-10-01 13:22:25 root: INFO: Timer: Time taken for compileLowerer, after InlineApplyIR -- LoweringTransformation -- Optimize -- FoldConstants : 0.472ms, total 2.408s 2020-10-01 13:22:25 root: INFO: Timer: Time taken for compileLowerer, after InlineApplyIR -- LoweringTransformation -- Optimize -- ExtractIntervalFilters : 0.671ms, total 2.409s 2020-10-01 13:22:25 root: INFO: Timer: Time taken for compileLowerer, after InlineApplyIR -- LoweringTransformation -- Optimize -- Simplify : 0.880ms, total 2.410s 2020-10-01 13:22:25 root: INFO: Timer: Time taken for compileLowerer, after InlineApplyIR -- LoweringTransformation -- Optimize -- ForwardLets : 8.339ms, total 2.419s 2020-10-01 13:22:25 root: INFO: Timer: Time taken for compileLowerer, after InlineApplyIR -- LoweringTransformation -- Optimize -- ForwardRelationalLets : 0.724ms, total 2.420s 2020-10-01 13:22:25 root: INFO: Timer: Time taken for compileLowerer, after InlineApplyIR -- LoweringTransformation -- Optimize -- PruneDeadFields : 4.857ms, total 2.425s 2020-10-01 13:22:25 root: INFO: Timer: Time taken for compileLowerer, after InlineApplyIR -- LoweringTransformation -- Optimize -- FoldConstants : 0.506ms, total 2.426s 2020-10-01 13:22:25 root: INFO: Timer: Time taken for compileLowerer, after InlineApplyIR -- LoweringTransformation -- Optimize -- ExtractIntervalFilters : 0.315ms, total 2.426s 2020-10-01 13:22:25 root: INFO: Timer: Time taken for compileLowerer, after InlineApplyIR -- LoweringTransformation -- Optimize -- Simplify : 1.343ms, total 2.427s 2020-10-01 13:22:25 root: INFO: Timer: Time taken for compileLowerer, after InlineApplyIR -- LoweringTransformation -- Optimize -- ForwardLets : 9.235ms, total 2.437s 2020-10-01 13:22:25 root: INFO: Timer: Time taken for compileLowerer, after InlineApplyIR -- LoweringTransformation -- Optimize -- ForwardRelationalLets : 1.657ms, total 2.439s 2020-10-01 13:22:25 root: INFO: Timer: Time taken for compileLowerer, after InlineApplyIR -- LoweringTransformation -- Optimize -- PruneDeadFields : 4.142ms, total 2.443s 2020-10-01 13:22:25 root: INFO: Timer: Time taken for compileLowerer, after InlineApplyIR -- LoweringTransformation -- Optimize : 55.213ms, total 2.445s, tagged coverage 88.5 2020-10-01 13:22:25 root: INFO: optimize compileLowerer, after InlineApplyIR: after: IR size 83: (Coalesce (Let __iruid_379 (ToDict (StreamMap __iruid_380 (ToStream (Literal Array[Struct{IID:String,isAxiom:Boolean,pheno:Boolean}] )) (MakeTuple (0 1) (SelectFields (IID) (Ref __iruid_380)) (SelectFields (isAxiom pheno) (Ref __iruid_380))))) (Let __iruid_381 (ToArray (StreamMap __iruid_382 (ToStream (GetField __cols (In +PCStruct{__cols:+PCArray[+PCStruct{s:+PCString}]} 0))) (InsertFields (Ref __iruid_382) None (__uid_3 (Let __iruid_383 (MakeStruct (IID (GetField s (Ref __iruid_382)))) (If (IsNA (Ref __iruid_379)) (NA Struct{isAxiom:Boolean,pheno:Boolean}) (Let __iruid_384 (LowerBoundOnOrderedCollection True (Ref __iruid_379) (Ref __iruid_383)) (If (ApplyComparisonOp EQWithNA (Ref __iruid_384) (ArrayLen (CastToArray (Ref __iruid_379)))) (NA Struct{isAxiom:Boolean,pheno:Boolean}) (If (ApplyComparisonOp EQWithNA (GetField key (ArrayRef (CastToArray (Ref __iruid_379)) (Ref __iruid_384) (Str ""))) (Ref __iruid_383)) (GetField value (ArrayRef (CastToArray (Ref __iruid_379)) (Ref __iruid_384) (Str ""))) (NA Struct{isAxiom:Boolean,pheno:Boolean})))))))))) (InsertFields (In +PCStruct{__cols:+PCArray[+PCStruct{s:+PCString}]} 0) ("__cols") (__cols (ToArray (StreamMap __iruid_385 (StreamRange (I32 0) (ArrayLen (Ref __iruid_381)) (I32 1)) (Let __iruid_386 (ArrayRef (Ref __iruid_381) (Ref __iruid_385) (Str "")) (Let __iruid_387 (GetField __uid_3 (Ref __iruid_386)) (InsertFields (SelectFields () (Ref __iruid_386)) ("__uid_5" "__uid_6" "__uid_7") (__uid_5 (Apply toFloat64 () Float64 (GetField pheno (Ref __iruid_387)))) (__uid_6 (F64 1.0)) (__uid_7 (Apply toFloat64 () Float64 (GetField isAxiom (Ref __iruid_387))))))))))))) (Die Struct{__cols:Array[Struct{__uid_5:Float64,__uid_6:Float64,__uid_7:Float64}]} (Str "Internal e..."))) 2020-10-01 13:22:25 root: INFO: Timer: Time taken for compileLowerer, after InlineApplyIR -- LoweringTransformation : 58.242ms, total 2.446s, tagged coverage 83.9 2020-10-01 13:22:25 root: INFO: Timer: Time taken for compileLowerer, after InlineApplyIR -- Verify : 0.046ms, total 2.447s 2020-10-01 13:22:25 root: INFO: Timer: Time taken for compileLowerer, after InlineApplyIR : 58.724ms, total 2.447s, tagged coverage 83.3 2020-10-01 13:22:25 root: INFO: Timer: Time taken for LowerArrayAggsToRunAggs -- Verify : 0.161ms, total 2.447s 2020-10-01 13:22:25 ContextCleaner: INFO: Cleaned accumulator 28 2020-10-01 13:22:25 ContextCleaner: INFO: Cleaned accumulator 38 2020-10-01 13:22:25 ContextCleaner: INFO: Cleaned accumulator 47 2020-10-01 13:22:25 ContextCleaner: INFO: Cleaned accumulator 37 2020-10-01 13:22:25 ContextCleaner: INFO: Cleaned accumulator 39 2020-10-01 13:22:25 ContextCleaner: INFO: Cleaned accumulator 27 2020-10-01 13:22:25 ContextCleaner: INFO: Cleaned accumulator 32 2020-10-01 13:22:25 ContextCleaner: INFO: Cleaned accumulator 45 2020-10-01 13:22:25 ContextCleaner: INFO: Cleaned accumulator 26 2020-10-01 13:22:25 ContextCleaner: INFO: Cleaned accumulator 44 2020-10-01 13:22:25 ContextCleaner: INFO: Cleaned accumulator 31 2020-10-01 13:22:25 ContextCleaner: INFO: Cleaned accumulator 35 2020-10-01 13:22:25 ContextCleaner: INFO: Cleaned accumulator 36 2020-10-01 13:22:25 BlockManagerInfo: INFO: Removed broadcast_3_piece0 on qlu-1:28416 in memory (size: 7.9 KB, free: 366.2 MB) 2020-10-01 13:22:25 ContextCleaner: INFO: Cleaned accumulator 49 2020-10-01 13:22:25 ContextCleaner: INFO: Cleaned accumulator 40 2020-10-01 13:22:25 ContextCleaner: INFO: Cleaned accumulator 34 2020-10-01 13:22:25 ContextCleaner: INFO: Cleaned accumulator 33 2020-10-01 13:22:25 ContextCleaner: INFO: Cleaned accumulator 43 2020-10-01 13:22:25 ContextCleaner: INFO: Cleaned accumulator 46 2020-10-01 13:22:25 ContextCleaner: INFO: Cleaned accumulator 50 2020-10-01 13:22:25 ContextCleaner: INFO: Cleaned accumulator 29 2020-10-01 13:22:25 ContextCleaner: INFO: Cleaned accumulator 48 2020-10-01 13:22:25 ContextCleaner: INFO: Cleaned accumulator 30 2020-10-01 13:22:25 ContextCleaner: INFO: Cleaned accumulator 41 2020-10-01 13:22:25 ContextCleaner: INFO: Cleaned accumulator 42 2020-10-01 13:22:25 root: INFO: Timer: Time taken for LowerArrayAggsToRunAggs -- LoweringTransformation : 184.854ms, total 2.633s 2020-10-01 13:22:25 root: INFO: Timer: Time taken for LowerArrayAggsToRunAggs -- Verify : 0.663ms, total 2.634s 2020-10-01 13:22:25 root: INFO: Timer: Time taken for LowerArrayAggsToRunAggs : 187.597ms, total 2.634s, tagged coverage 99.0 2020-10-01 13:22:25 root: INFO: Timer: Time taken for compileLowerer, after LowerArrayAggsToRunAggs -- Verify : 0.053ms, total 2.635s 2020-10-01 13:22:25 root: INFO: optimize compileLowerer, after LowerArrayAggsToRunAggs: before: IR size 83: (Coalesce (Let __iruid_379 (ToDict (StreamMap __iruid_380 (ToStream (Literal Array[Struct{IID:String,isAxiom:Boolean,pheno:Boolean}] )) (MakeTuple (0 1) (SelectFields (IID) (Ref __iruid_380)) (SelectFields (isAxiom pheno) (Ref __iruid_380))))) (Let __iruid_381 (ToArray (StreamMap __iruid_382 (ToStream (GetField __cols (In +PCStruct{__cols:+PCArray[+PCStruct{s:+PCString}]} 0))) (InsertFields (Ref __iruid_382) None (__uid_3 (Let __iruid_383 (MakeStruct (IID (GetField s (Ref __iruid_382)))) (If (IsNA (Ref __iruid_379)) (NA Struct{isAxiom:Boolean,pheno:Boolean}) (Let __iruid_384 (LowerBoundOnOrderedCollection True (Ref __iruid_379) (Ref __iruid_383)) (If (ApplyComparisonOp EQWithNA (Ref __iruid_384) (ArrayLen (CastToArray (Ref __iruid_379)))) (NA Struct{isAxiom:Boolean,pheno:Boolean}) (If (ApplyComparisonOp EQWithNA (GetField key (ArrayRef (CastToArray (Ref __iruid_379)) (Ref __iruid_384) (Str ""))) (Ref __iruid_383)) (GetField value (ArrayRef (CastToArray (Ref __iruid_379)) (Ref __iruid_384) (Str ""))) (NA Struct{isAxiom:Boolean,pheno:Boolean})))))))))) (InsertFields (In +PCStruct{__cols:+PCArray[+PCStruct{s:+PCString}]} 0) ("__cols") (__cols (ToArray (StreamMap __iruid_385 (StreamRange (I32 0) (ArrayLen (Ref __iruid_381)) (I32 1)) (Let __iruid_386 (ArrayRef (Ref __iruid_381) (Ref __iruid_385) (Str "")) (Let __iruid_387 (GetField __uid_3 (Ref __iruid_386)) (InsertFields (SelectFields () (Ref __iruid_386)) ("__uid_5" "__uid_6" "__uid_7") (__uid_5 (Apply toFloat64 () Float64 (GetField pheno (Ref __iruid_387)))) (__uid_6 (F64 1.0)) (__uid_7 (Apply toFloat64 () Float64 (GetField isAxiom (Ref __iruid_387))))))))))))) (Die Struct{__cols:Array[Struct{__uid_5:Float64,__uid_6:Float64,__uid_7:Float64}]} (Str "Internal e..."))) 2020-10-01 13:22:25 root: INFO: Timer: Time taken for compileLowerer, after LowerArrayAggsToRunAggs -- LoweringTransformation -- Optimize -- FoldConstants : 0.396ms, total 2.637s 2020-10-01 13:22:25 root: INFO: Timer: Time taken for compileLowerer, after LowerArrayAggsToRunAggs -- LoweringTransformation -- Optimize -- ExtractIntervalFilters : 0.550ms, total 2.637s 2020-10-01 13:22:25 root: INFO: Timer: Time taken for compileLowerer, after LowerArrayAggsToRunAggs -- LoweringTransformation -- Optimize -- Simplify : 1.066ms, total 2.638s 2020-10-01 13:22:25 root: INFO: Timer: Time taken for compileLowerer, after LowerArrayAggsToRunAggs -- LoweringTransformation -- Optimize -- ForwardLets : 4.901ms, total 2.643s 2020-10-01 13:22:25 root: INFO: Timer: Time taken for compileLowerer, after LowerArrayAggsToRunAggs -- LoweringTransformation -- Optimize -- ForwardRelationalLets : 0.362ms, total 2.644s 2020-10-01 13:22:25 root: INFO: Timer: Time taken for compileLowerer, after LowerArrayAggsToRunAggs -- LoweringTransformation -- Optimize -- PruneDeadFields : 6.607ms, total 2.651s 2020-10-01 13:22:25 root: INFO: Timer: Time taken for compileLowerer, after LowerArrayAggsToRunAggs -- LoweringTransformation -- Optimize -- FoldConstants : 0.421ms, total 2.652s 2020-10-01 13:22:25 root: INFO: Timer: Time taken for compileLowerer, after LowerArrayAggsToRunAggs -- LoweringTransformation -- Optimize -- ExtractIntervalFilters : 0.684ms, total 2.653s 2020-10-01 13:22:25 root: INFO: Timer: Time taken for compileLowerer, after LowerArrayAggsToRunAggs -- LoweringTransformation -- Optimize -- Simplify : 1.471ms, total 2.654s 2020-10-01 13:22:25 root: INFO: Timer: Time taken for compileLowerer, after LowerArrayAggsToRunAggs -- LoweringTransformation -- Optimize -- ForwardLets : 5.873ms, total 2.660s 2020-10-01 13:22:25 root: INFO: Timer: Time taken for compileLowerer, after LowerArrayAggsToRunAggs -- LoweringTransformation -- Optimize -- ForwardRelationalLets : 0.355ms, total 2.661s 2020-10-01 13:22:25 root: INFO: Timer: Time taken for compileLowerer, after LowerArrayAggsToRunAggs -- LoweringTransformation -- Optimize -- PruneDeadFields : 3.461ms, total 2.665s 2020-10-01 13:22:25 root: INFO: Timer: Time taken for compileLowerer, after LowerArrayAggsToRunAggs -- LoweringTransformation -- Optimize -- FoldConstants : 0.424ms, total 2.665s 2020-10-01 13:22:25 root: INFO: Timer: Time taken for compileLowerer, after LowerArrayAggsToRunAggs -- LoweringTransformation -- Optimize -- ExtractIntervalFilters : 0.270ms, total 2.665s 2020-10-01 13:22:25 root: INFO: Timer: Time taken for compileLowerer, after LowerArrayAggsToRunAggs -- LoweringTransformation -- Optimize -- Simplify : 1.089ms, total 2.667s 2020-10-01 13:22:25 root: INFO: Timer: Time taken for compileLowerer, after LowerArrayAggsToRunAggs -- LoweringTransformation -- Optimize -- ForwardLets : 10.677ms, total 2.677s 2020-10-01 13:22:25 root: INFO: Timer: Time taken for compileLowerer, after LowerArrayAggsToRunAggs -- LoweringTransformation -- Optimize -- ForwardRelationalLets : 0.304ms, total 2.678s 2020-10-01 13:22:25 root: INFO: Timer: Time taken for compileLowerer, after LowerArrayAggsToRunAggs -- LoweringTransformation -- Optimize -- PruneDeadFields : 3.753ms, total 2.682s 2020-10-01 13:22:25 root: INFO: Timer: Time taken for compileLowerer, after LowerArrayAggsToRunAggs -- LoweringTransformation -- Optimize : 45.739ms, total 2.682s, tagged coverage 93.3 2020-10-01 13:22:25 root: INFO: optimize compileLowerer, after LowerArrayAggsToRunAggs: after: IR size 83: (Coalesce (Let __iruid_406 (ToDict (StreamMap __iruid_407 (ToStream (Literal Array[Struct{IID:String,isAxiom:Boolean,pheno:Boolean}] )) (MakeTuple (0 1) (SelectFields (IID) (Ref __iruid_407)) (SelectFields (isAxiom pheno) (Ref __iruid_407))))) (Let __iruid_408 (ToArray (StreamMap __iruid_409 (ToStream (GetField __cols (In +PCStruct{__cols:+PCArray[+PCStruct{s:+PCString}]} 0))) (InsertFields (Ref __iruid_409) None (__uid_3 (Let __iruid_410 (MakeStruct (IID (GetField s (Ref __iruid_409)))) (If (IsNA (Ref __iruid_406)) (NA Struct{isAxiom:Boolean,pheno:Boolean}) (Let __iruid_411 (LowerBoundOnOrderedCollection True (Ref __iruid_406) (Ref __iruid_410)) (If (ApplyComparisonOp EQWithNA (Ref __iruid_411) (ArrayLen (CastToArray (Ref __iruid_406)))) (NA Struct{isAxiom:Boolean,pheno:Boolean}) (If (ApplyComparisonOp EQWithNA (GetField key (ArrayRef (CastToArray (Ref __iruid_406)) (Ref __iruid_411) (Str ""))) (Ref __iruid_410)) (GetField value (ArrayRef (CastToArray (Ref __iruid_406)) (Ref __iruid_411) (Str ""))) (NA Struct{isAxiom:Boolean,pheno:Boolean})))))))))) (InsertFields (In +PCStruct{__cols:+PCArray[+PCStruct{s:+PCString}]} 0) ("__cols") (__cols (ToArray (StreamMap __iruid_412 (StreamRange (I32 0) (ArrayLen (Ref __iruid_408)) (I32 1)) (Let __iruid_413 (ArrayRef (Ref __iruid_408) (Ref __iruid_412) (Str "")) (Let __iruid_414 (GetField __uid_3 (Ref __iruid_413)) (InsertFields (SelectFields () (Ref __iruid_413)) ("__uid_5" "__uid_6" "__uid_7") (__uid_5 (Apply toFloat64 () Float64 (GetField pheno (Ref __iruid_414)))) (__uid_6 (F64 1.0)) (__uid_7 (Apply toFloat64 () Float64 (GetField isAxiom (Ref __iruid_414))))))))))))) (Die Struct{__cols:Array[Struct{__uid_5:Float64,__uid_6:Float64,__uid_7:Float64}]} (Str "Internal e..."))) 2020-10-01 13:22:25 root: INFO: Timer: Time taken for compileLowerer, after LowerArrayAggsToRunAggs -- LoweringTransformation : 48.697ms, total 2.683s, tagged coverage 87.6 2020-10-01 13:22:25 root: INFO: Timer: Time taken for compileLowerer, after LowerArrayAggsToRunAggs -- Verify : 0.033ms, total 2.684s 2020-10-01 13:22:25 root: INFO: Timer: Time taken for compileLowerer, after LowerArrayAggsToRunAggs : 49.111ms, total 2.684s, tagged coverage 87.1 2020-10-01 13:22:25 root: INFO: encoder cache miss (0 hits, 2 misses, 0.000) 2020-10-01 13:22:25 root: INFO: instruction count: 6: __C114etypeEncode. 2020-10-01 13:22:25 root: INFO: instruction count: 8: __C114etypeEncode.apply 2020-10-01 13:22:25 root: INFO: instruction count: 8: __C114etypeEncode.__m115ENCODE_r_tuple_of_r_stringANDr_array_of_r_tuple_of_r_stringANDr_boolANDr_boolENDEND_TO_r_struct_of_r_binaryANDr_array_of_r_struct_of_r_binaryANDr_boolANDr_boolENDEND 2020-10-01 13:22:25 root: INFO: instruction count: 24: __C114etypeEncode.__m116write_fields_group_0 2020-10-01 13:22:25 root: INFO: instruction count: 19: __C114etypeEncode.__m117ENCODE_r_binary_TO_r_binary 2020-10-01 13:22:25 root: INFO: instruction count: 45: __C114etypeEncode.__m118ENCODE_r_array_of_r_tuple_of_r_binaryANDr_boolANDr_boolEND_TO_r_array_of_r_struct_of_r_binaryANDr_boolANDr_boolEND 2020-10-01 13:22:25 root: INFO: instruction count: 8: __C114etypeEncode.__m119ENCODE_r_tuple_of_r_binaryANDr_boolANDr_boolEND_TO_r_struct_of_r_binaryANDr_boolANDr_boolEND 2020-10-01 13:22:25 root: INFO: instruction count: 34: __C114etypeEncode.__m120write_fields_group_0 2020-10-01 13:22:25 root: INFO: instruction count: 7: __C114etypeEncode.__m121ENCODE_r_bool_TO_r_bool 2020-10-01 13:22:25 root: INFO: RegionPool: REPORT_THRESHOLD: 1.4M allocated (512.0K blocks / 882.5K chunks), regions.size = 2, 0 current java objects, 0 max java objects, thread 31: Thread-5 2020-10-01 13:22:25 MemoryStore: INFO: Block broadcast_5 stored as values in memory (estimated size 478.2 KB, free 364.7 MB) 2020-10-01 13:22:25 MemoryStore: INFO: Block broadcast_5_piece0 stored as bytes in memory (estimated size 268.8 KB, free 364.4 MB) 2020-10-01 13:22:25 BlockManagerInfo: INFO: Added broadcast_5_piece0 in memory on qlu-1:28416 (size: 268.8 KB, free: 366.0 MB) 2020-10-01 13:22:25 SparkContext: INFO: Created broadcast 5 from broadcast at SparkBackend.scala:233 2020-10-01 13:22:26 root: INFO: instruction count: 6: __C11Compiled. 2020-10-01 13:22:26 root: INFO: instruction count: 51: __C11Compiled.apply 2020-10-01 13:22:26 root: INFO: instruction count: 707: __C11Compiled.__m16wrapped 2020-10-01 13:22:26 root: INFO: instruction count: 15: __C11Compiled.__m19setup_jab 2020-10-01 13:22:26 root: INFO: instruction count: 62: __C11Compiled.__m20discardNext 2020-10-01 13:22:26 root: INFO: instruction count: 102: __C11Compiled.__m21cord 2020-10-01 13:22:26 root: INFO: instruction count: 135: __C11Compiled.__m22cord 2020-10-01 13:22:26 root: INFO: instruction count: 8: __C11Compiled.__m40addIRIntermediate 2020-10-01 13:22:26 root: INFO: instruction count: 11: __C11Compiled.__m41addIRIntermediate 2020-10-01 13:22:26 root: INFO: instruction count: 11: __C11Compiled.__m45addIRIntermediate 2020-10-01 13:22:26 root: INFO: instruction count: 11: __C11Compiled.__m49addIRIntermediate 2020-10-01 13:22:26 root: INFO: instruction count: 146: __C11Compiled.__m54wrapped 2020-10-01 13:22:26 root: INFO: instruction count: 442: __C11Compiled.__m63wrapped 2020-10-01 13:22:26 root: INFO: instruction count: 77: __C11Compiled.__m70findElt 2020-10-01 13:22:26 root: INFO: instruction count: 115: __C11Compiled.__m71cord 2020-10-01 13:22:26 root: INFO: instruction count: 142: __C11Compiled.__m72cord 2020-10-01 13:22:26 root: INFO: instruction count: 38: __C11Compiled.__m73cord 2020-10-01 13:22:26 root: INFO: instruction count: 11: __C11Compiled.__m74addIRIntermediate 2020-10-01 13:22:26 root: INFO: instruction count: 11: __C11Compiled.__m75addIRIntermediate 2020-10-01 13:22:26 root: INFO: instruction count: 368: __C11Compiled.__m79wrapped 2020-10-01 13:22:26 root: INFO: instruction count: 87: __C11Compiled.__m99wrapped 2020-10-01 13:22:26 root: INFO: instruction count: 6: __C11Compiled.__m100toFloat64 2020-10-01 13:22:26 root: INFO: instruction count: 11: __C11Compiled.__m101addIRIntermediate 2020-10-01 13:22:26 root: INFO: instruction count: 8: __C11Compiled.__m102addIRIntermediate 2020-10-01 13:22:26 root: INFO: instruction count: 14: __C11Compiled.setPartitionIndex 2020-10-01 13:22:26 root: INFO: instruction count: 7: __C11Compiled.addPartitionRegion 2020-10-01 13:22:26 root: INFO: instruction count: 25: __C11Compiled.__m106DECODE_r_struct_of_r_binaryANDr_array_of_r_struct_of_r_binaryANDr_boolANDr_boolENDEND_TO_r_tuple_of_r_stringANDr_array_of_r_tuple_of_r_stringANDr_boolANDr_boolENDEND 2020-10-01 13:22:26 root: INFO: instruction count: 18: __C11Compiled.__m107read_fields_group_0 2020-10-01 13:22:26 root: INFO: instruction count: 34: __C11Compiled.__m108INPLACE_DECODE_r_binary_TO_r_binary 2020-10-01 13:22:26 root: INFO: instruction count: 58: __C11Compiled.__m109INPLACE_DECODE_r_array_of_r_struct_of_r_binaryANDr_boolANDr_boolEND_TO_r_array_of_r_tuple_of_r_binaryANDr_boolANDr_boolEND 2020-10-01 13:22:26 root: INFO: instruction count: 17: __C11Compiled.__m110INPLACE_DECODE_r_struct_of_r_binaryANDr_boolANDr_boolEND_TO_r_tuple_of_r_binaryANDr_boolANDr_boolEND 2020-10-01 13:22:26 root: INFO: instruction count: 25: __C11Compiled.__m111read_fields_group_0 2020-10-01 13:22:26 root: INFO: instruction count: 11: __C11Compiled.__m112INPLACE_DECODE_r_bool_TO_r_bool 2020-10-01 13:22:26 root: INFO: instruction count: 64: __C11Compiled.addLiterals 2020-10-01 13:22:26 root: INFO: instruction count: 6: __C23sort_compare. 2020-10-01 13:22:26 root: INFO: instruction count: 10: __C23sort_compare.apply 2020-10-01 13:22:26 root: INFO: instruction count: 21: __C23sort_compare.apply 2020-10-01 13:22:26 root: INFO: instruction count: 57: __C23sort_compare.__m25sort 2020-10-01 13:22:26 root: INFO: instruction count: 26: __C23sort_compare.__m26cord 2020-10-01 13:22:26 root: INFO: instruction count: 115: __C23sort_compare.__m27cord 2020-10-01 13:22:26 root: INFO: instruction count: 142: __C23sort_compare.__m28cord 2020-10-01 13:22:26 root: INFO: RegionPool: REPORT_THRESHOLD: 2.0M allocated (1.2M blocks / 882.5K chunks), regions.size = 2, 0 current java objects, 0 max java objects, thread 31: Thread-5 2020-10-01 13:22:26 root: INFO: RegionPool: REPORT_THRESHOLD: 4.1M allocated (2.1M blocks / 2.0M chunks), regions.size = 2, 0 current java objects, 0 max java objects, thread 31: Thread-5 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, initial IR -- Verify : 0.062ms, total 3.476s 2020-10-01 13:22:26 root: INFO: optimize compileLowerer, initial IR: before: IR size 16: (Coalesce (InsertFields (In +PCStruct{locus:+PCLocus(GRCh37),alleles:+PCArray[+PCString],`the entries! [877f12a8827e18f61222c6c8c5fb04a8]`:+PCArray[+PCStruct{GT:PCCall}]} 1) None (`the entries! [877f12a8827e18f61222c6c8c5fb04a8]` (ToArray (StreamMap __iruid_278 (ToStream (GetField `the entries! [877f12a8827e18f61222c6c8c5fb04a8]` (In +PCStruct{locus:+PCLocus(GRCh37),alleles:+PCArray[+PCString],`the entries! [877f12a8827e18f61222c6c8c5fb04a8]`:+PCArray[+PCStruct{GT:PCCall}]} 1))) (InsertFields (Ref __iruid_278) None (__uid_8 (Cast Float64 (Apply nNonRefAlleles () Int32 (GetField GT (Ref __iruid_278)))))))))) (Die Struct{locus:Locus(GRCh37),alleles:Array[String],`the entries! [877f12a8827e18f61222c6c8c5fb04a8]`:Array[Struct{GT:Call,__uid_8:Float64}]} (Str "Internal e..."))) 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, initial IR -- LoweringTransformation -- Optimize -- FoldConstants : 0.681ms, total 3.478s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, initial IR -- LoweringTransformation -- Optimize -- ExtractIntervalFilters : 0.102ms, total 3.478s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, initial IR -- LoweringTransformation -- Optimize -- Simplify : 0.322ms, total 3.478s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, initial IR -- LoweringTransformation -- Optimize -- ForwardLets : 0.919ms, total 3.479s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, initial IR -- LoweringTransformation -- Optimize -- ForwardRelationalLets : 0.108ms, total 3.480s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, initial IR -- LoweringTransformation -- Optimize -- PruneDeadFields : 1.360ms, total 3.481s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, initial IR -- LoweringTransformation -- Optimize -- FoldConstants : 0.229ms, total 3.482s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, initial IR -- LoweringTransformation -- Optimize -- ExtractIntervalFilters : 0.070ms, total 3.482s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, initial IR -- LoweringTransformation -- Optimize -- Simplify : 0.251ms, total 3.482s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, initial IR -- LoweringTransformation -- Optimize -- ForwardLets : 2.343ms, total 3.486s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, initial IR -- LoweringTransformation -- Optimize -- ForwardRelationalLets : 0.085ms, total 3.486s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, initial IR -- LoweringTransformation -- Optimize -- PruneDeadFields : 1.007ms, total 3.488s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, initial IR -- LoweringTransformation -- Optimize -- FoldConstants : 0.237ms, total 3.488s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, initial IR -- LoweringTransformation -- Optimize -- ExtractIntervalFilters : 0.078ms, total 3.489s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, initial IR -- LoweringTransformation -- Optimize -- Simplify : 0.259ms, total 3.489s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, initial IR -- LoweringTransformation -- Optimize -- ForwardLets : 0.754ms, total 3.490s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, initial IR -- LoweringTransformation -- Optimize -- ForwardRelationalLets : 0.086ms, total 3.490s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, initial IR -- LoweringTransformation -- Optimize -- PruneDeadFields : 0.905ms, total 3.491s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, initial IR -- LoweringTransformation -- Optimize : 14.236ms, total 3.491s, tagged coverage 68.8 2020-10-01 13:22:26 root: INFO: optimize compileLowerer, initial IR: after: IR size 16: (Coalesce (InsertFields (In +PCStruct{locus:+PCLocus(GRCh37),alleles:+PCArray[+PCString],`the entries! [877f12a8827e18f61222c6c8c5fb04a8]`:+PCArray[+PCStruct{GT:PCCall}]} 1) None (`the entries! [877f12a8827e18f61222c6c8c5fb04a8]` (ToArray (StreamMap __iruid_418 (ToStream (GetField `the entries! [877f12a8827e18f61222c6c8c5fb04a8]` (In +PCStruct{locus:+PCLocus(GRCh37),alleles:+PCArray[+PCString],`the entries! [877f12a8827e18f61222c6c8c5fb04a8]`:+PCArray[+PCStruct{GT:PCCall}]} 1))) (InsertFields (Ref __iruid_418) None (__uid_8 (Cast Float64 (Apply nNonRefAlleles () Int32 (GetField GT (Ref __iruid_418)))))))))) (Die Struct{locus:Locus(GRCh37),alleles:Array[String],`the entries! [877f12a8827e18f61222c6c8c5fb04a8]`:Array[Struct{GT:Call,__uid_8:Float64}]} (Str "Internal e..."))) 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, initial IR -- LoweringTransformation : 15.495ms, total 3.492s, tagged coverage 63.2 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, initial IR -- Verify : 0.013ms, total 3.492s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, initial IR : 16.338ms, total 3.492s, tagged coverage 60.4 2020-10-01 13:22:26 root: INFO: Timer: Time taken for InlineApplyIR -- Verify : 0.040ms, total 3.492s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for InlineApplyIR -- LoweringTransformation : 0.037ms, total 3.492s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for InlineApplyIR -- Verify : 0.026ms, total 3.492s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for InlineApplyIR : 0.322ms, total 3.492s, tagged coverage 31.9 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after InlineApplyIR -- Verify : 0.009ms, total 3.493s 2020-10-01 13:22:26 root: INFO: optimize compileLowerer, after InlineApplyIR: before: IR size 16: (Coalesce (InsertFields (In +PCStruct{locus:+PCLocus(GRCh37),alleles:+PCArray[+PCString],`the entries! [877f12a8827e18f61222c6c8c5fb04a8]`:+PCArray[+PCStruct{GT:PCCall}]} 1) None (`the entries! [877f12a8827e18f61222c6c8c5fb04a8]` (ToArray (StreamMap __iruid_418 (ToStream (GetField `the entries! [877f12a8827e18f61222c6c8c5fb04a8]` (In +PCStruct{locus:+PCLocus(GRCh37),alleles:+PCArray[+PCString],`the entries! [877f12a8827e18f61222c6c8c5fb04a8]`:+PCArray[+PCStruct{GT:PCCall}]} 1))) (InsertFields (Ref __iruid_418) None (__uid_8 (Cast Float64 (Apply nNonRefAlleles () Int32 (GetField GT (Ref __iruid_418)))))))))) (Die Struct{locus:Locus(GRCh37),alleles:Array[String],`the entries! [877f12a8827e18f61222c6c8c5fb04a8]`:Array[Struct{GT:Call,__uid_8:Float64}]} (Str "Internal e..."))) 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after InlineApplyIR -- LoweringTransformation -- Optimize -- FoldConstants : 0.153ms, total 3.493s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after InlineApplyIR -- LoweringTransformation -- Optimize -- ExtractIntervalFilters : 0.079ms, total 3.493s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after InlineApplyIR -- LoweringTransformation -- Optimize -- Simplify : 0.242ms, total 3.494s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after InlineApplyIR -- LoweringTransformation -- Optimize -- ForwardLets : 0.646ms, total 3.494s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after InlineApplyIR -- LoweringTransformation -- Optimize -- ForwardRelationalLets : 0.085ms, total 3.495s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after InlineApplyIR -- LoweringTransformation -- Optimize -- PruneDeadFields : 0.812ms, total 3.495s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after InlineApplyIR -- LoweringTransformation -- Optimize -- FoldConstants : 0.180ms, total 3.496s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after InlineApplyIR -- LoweringTransformation -- Optimize -- ExtractIntervalFilters : 0.068ms, total 3.496s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after InlineApplyIR -- LoweringTransformation -- Optimize -- Simplify : 0.588ms, total 3.497s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after InlineApplyIR -- LoweringTransformation -- Optimize -- ForwardLets : 0.829ms, total 3.497s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after InlineApplyIR -- LoweringTransformation -- Optimize -- ForwardRelationalLets : 0.086ms, total 3.498s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after InlineApplyIR -- LoweringTransformation -- Optimize -- PruneDeadFields : 0.855ms, total 3.499s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after InlineApplyIR -- LoweringTransformation -- Optimize -- FoldConstants : 0.178ms, total 3.499s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after InlineApplyIR -- LoweringTransformation -- Optimize -- ExtractIntervalFilters : 0.069ms, total 3.499s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after InlineApplyIR -- LoweringTransformation -- Optimize -- Simplify : 0.233ms, total 3.499s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after InlineApplyIR -- LoweringTransformation -- Optimize -- ForwardLets : 0.733ms, total 3.500s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after InlineApplyIR -- LoweringTransformation -- Optimize -- ForwardRelationalLets : 0.135ms, total 3.500s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after InlineApplyIR -- LoweringTransformation -- Optimize -- PruneDeadFields : 1.120ms, total 3.502s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after InlineApplyIR -- LoweringTransformation -- Optimize : 8.726ms, total 3.502s, tagged coverage 81.2 2020-10-01 13:22:26 root: INFO: optimize compileLowerer, after InlineApplyIR: after: IR size 16: (Coalesce (InsertFields (In +PCStruct{locus:+PCLocus(GRCh37),alleles:+PCArray[+PCString],`the entries! [877f12a8827e18f61222c6c8c5fb04a8]`:+PCArray[+PCStruct{GT:PCCall}]} 1) None (`the entries! [877f12a8827e18f61222c6c8c5fb04a8]` (ToArray (StreamMap __iruid_421 (ToStream (GetField `the entries! [877f12a8827e18f61222c6c8c5fb04a8]` (In +PCStruct{locus:+PCLocus(GRCh37),alleles:+PCArray[+PCString],`the entries! [877f12a8827e18f61222c6c8c5fb04a8]`:+PCArray[+PCStruct{GT:PCCall}]} 1))) (InsertFields (Ref __iruid_421) None (__uid_8 (Cast Float64 (Apply nNonRefAlleles () Int32 (GetField GT (Ref __iruid_421)))))))))) (Die Struct{locus:Locus(GRCh37),alleles:Array[String],`the entries! [877f12a8827e18f61222c6c8c5fb04a8]`:Array[Struct{GT:Call,__uid_8:Float64}]} (Str "Internal e..."))) 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after InlineApplyIR -- LoweringTransformation : 9.995ms, total 3.503s, tagged coverage 70.9 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after InlineApplyIR -- Verify : 0.010ms, total 3.503s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after InlineApplyIR : 10.295ms, total 3.503s, tagged coverage 69.0 2020-10-01 13:22:26 root: INFO: Timer: Time taken for LowerArrayAggsToRunAggs -- Verify : 0.022ms, total 3.503s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for LowerArrayAggsToRunAggs -- LoweringTransformation : 5.741ms, total 3.509s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for LowerArrayAggsToRunAggs -- Verify : 0.033ms, total 3.509s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for LowerArrayAggsToRunAggs : 6.131ms, total 3.509s, tagged coverage 94.5 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after LowerArrayAggsToRunAggs -- Verify : 0.009ms, total 3.510s 2020-10-01 13:22:26 root: INFO: optimize compileLowerer, after LowerArrayAggsToRunAggs: before: IR size 16: (Coalesce (InsertFields (In +PCStruct{locus:+PCLocus(GRCh37),alleles:+PCArray[+PCString],`the entries! [877f12a8827e18f61222c6c8c5fb04a8]`:+PCArray[+PCStruct{GT:PCCall}]} 1) None (`the entries! [877f12a8827e18f61222c6c8c5fb04a8]` (ToArray (StreamMap __iruid_421 (ToStream (GetField `the entries! [877f12a8827e18f61222c6c8c5fb04a8]` (In +PCStruct{locus:+PCLocus(GRCh37),alleles:+PCArray[+PCString],`the entries! [877f12a8827e18f61222c6c8c5fb04a8]`:+PCArray[+PCStruct{GT:PCCall}]} 1))) (InsertFields (Ref __iruid_421) None (__uid_8 (Cast Float64 (Apply nNonRefAlleles () Int32 (GetField GT (Ref __iruid_421)))))))))) (Die Struct{locus:Locus(GRCh37),alleles:Array[String],`the entries! [877f12a8827e18f61222c6c8c5fb04a8]`:Array[Struct{GT:Call,__uid_8:Float64}]} (Str "Internal e..."))) 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after LowerArrayAggsToRunAggs -- LoweringTransformation -- Optimize -- FoldConstants : 0.086ms, total 3.510s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after LowerArrayAggsToRunAggs -- LoweringTransformation -- Optimize -- ExtractIntervalFilters : 0.076ms, total 3.510s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after LowerArrayAggsToRunAggs -- LoweringTransformation -- Optimize -- Simplify : 0.263ms, total 3.511s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after LowerArrayAggsToRunAggs -- LoweringTransformation -- Optimize -- ForwardLets : 0.634ms, total 3.511s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after LowerArrayAggsToRunAggs -- LoweringTransformation -- Optimize -- ForwardRelationalLets : 0.083ms, total 3.511s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after LowerArrayAggsToRunAggs -- LoweringTransformation -- Optimize -- PruneDeadFields : 1.173ms, total 3.513s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after LowerArrayAggsToRunAggs -- LoweringTransformation -- Optimize -- FoldConstants : 0.191ms, total 3.513s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after LowerArrayAggsToRunAggs -- LoweringTransformation -- Optimize -- ExtractIntervalFilters : 0.088ms, total 3.513s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after LowerArrayAggsToRunAggs -- LoweringTransformation -- Optimize -- Simplify : 0.254ms, total 3.514s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after LowerArrayAggsToRunAggs -- LoweringTransformation -- Optimize -- ForwardLets : 3.252ms, total 3.517s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after LowerArrayAggsToRunAggs -- LoweringTransformation -- Optimize -- ForwardRelationalLets : 0.081ms, total 3.517s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after LowerArrayAggsToRunAggs -- LoweringTransformation -- Optimize -- PruneDeadFields : 1.216ms, total 3.519s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after LowerArrayAggsToRunAggs -- LoweringTransformation -- Optimize -- FoldConstants : 0.176ms, total 3.519s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after LowerArrayAggsToRunAggs -- LoweringTransformation -- Optimize -- ExtractIntervalFilters : 0.081ms, total 3.519s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after LowerArrayAggsToRunAggs -- LoweringTransformation -- Optimize -- Simplify : 0.232ms, total 3.519s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after LowerArrayAggsToRunAggs -- LoweringTransformation -- Optimize -- ForwardLets : 1.353ms, total 3.521s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after LowerArrayAggsToRunAggs -- LoweringTransformation -- Optimize -- ForwardRelationalLets : 0.083ms, total 3.521s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after LowerArrayAggsToRunAggs -- LoweringTransformation -- Optimize -- PruneDeadFields : 0.763ms, total 3.522s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after LowerArrayAggsToRunAggs -- LoweringTransformation -- Optimize : 12.049ms, total 3.522s, tagged coverage 83.7 2020-10-01 13:22:26 root: INFO: optimize compileLowerer, after LowerArrayAggsToRunAggs: after: IR size 16: (Coalesce (InsertFields (In +PCStruct{locus:+PCLocus(GRCh37),alleles:+PCArray[+PCString],`the entries! [877f12a8827e18f61222c6c8c5fb04a8]`:+PCArray[+PCStruct{GT:PCCall}]} 1) None (`the entries! [877f12a8827e18f61222c6c8c5fb04a8]` (ToArray (StreamMap __iruid_424 (ToStream (GetField `the entries! [877f12a8827e18f61222c6c8c5fb04a8]` (In +PCStruct{locus:+PCLocus(GRCh37),alleles:+PCArray[+PCString],`the entries! [877f12a8827e18f61222c6c8c5fb04a8]`:+PCArray[+PCStruct{GT:PCCall}]} 1))) (InsertFields (Ref __iruid_424) None (__uid_8 (Cast Float64 (Apply nNonRefAlleles () Int32 (GetField GT (Ref __iruid_424)))))))))) (Die Struct{locus:Locus(GRCh37),alleles:Array[String],`the entries! [877f12a8827e18f61222c6c8c5fb04a8]`:Array[Struct{GT:Call,__uid_8:Float64}]} (Str "Internal e..."))) 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after LowerArrayAggsToRunAggs -- LoweringTransformation : 12.911ms, total 3.523s, tagged coverage 78.1 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after LowerArrayAggsToRunAggs -- Verify : 0.011ms, total 3.523s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after LowerArrayAggsToRunAggs : 13.172ms, total 3.523s, tagged coverage 76.7 2020-10-01 13:22:26 root: INFO: encoder cache miss (0 hits, 3 misses, 0.000) 2020-10-01 13:22:26 root: INFO: instruction count: 6: __C148etypeEncode. 2020-10-01 13:22:26 root: INFO: instruction count: 8: __C148etypeEncode.apply 2020-10-01 13:22:26 root: INFO: instruction count: 8: __C148etypeEncode.__m149ENCODE_r_tuple_of_r_stringEND_TO_r_struct_of_r_binaryEND 2020-10-01 13:22:26 root: INFO: instruction count: 14: __C148etypeEncode.__m150write_fields_group_0 2020-10-01 13:22:26 root: INFO: instruction count: 19: __C148etypeEncode.__m151ENCODE_r_binary_TO_r_binary 2020-10-01 13:22:26 MemoryStore: INFO: Block broadcast_6 stored as values in memory (estimated size 104.0 B, free 364.4 MB) 2020-10-01 13:22:26 MemoryStore: INFO: Block broadcast_6_piece0 stored as bytes in memory (estimated size 109.0 B, free 364.4 MB) 2020-10-01 13:22:26 BlockManagerInfo: INFO: Added broadcast_6_piece0 in memory on qlu-1:28416 (size: 109.0 B, free: 366.0 MB) 2020-10-01 13:22:26 SparkContext: INFO: Created broadcast 6 from broadcast at SparkBackend.scala:233 2020-10-01 13:22:26 root: INFO: instruction count: 6: __C122Compiled. 2020-10-01 13:22:26 root: INFO: instruction count: 44: __C122Compiled.apply 2020-10-01 13:22:26 root: INFO: instruction count: 170: __C122Compiled.__m126wrapped 2020-10-01 13:22:26 root: INFO: instruction count: 11: __C122Compiled.__m127addIRIntermediate 2020-10-01 13:22:26 root: INFO: instruction count: 8: __C122Compiled.__m128addIRIntermediate 2020-10-01 13:22:26 root: INFO: instruction count: 79: __C122Compiled.__m137wrapped 2020-10-01 13:22:26 root: INFO: instruction count: 9: __C122Compiled.__m138nNonRefAlleles 2020-10-01 13:22:26 root: INFO: instruction count: 11: __C122Compiled.__m139addIRIntermediate 2020-10-01 13:22:26 root: INFO: instruction count: 8: __C122Compiled.__m140addIRIntermediate 2020-10-01 13:22:26 root: INFO: instruction count: 14: __C122Compiled.setPartitionIndex 2020-10-01 13:22:26 root: INFO: instruction count: 7: __C122Compiled.addPartitionRegion 2020-10-01 13:22:26 root: INFO: instruction count: 25: __C122Compiled.__m144DECODE_r_struct_of_r_binaryEND_TO_r_tuple_of_r_stringEND 2020-10-01 13:22:26 root: INFO: instruction count: 11: __C122Compiled.__m145read_fields_group_0 2020-10-01 13:22:26 root: INFO: instruction count: 34: __C122Compiled.__m146INPLACE_DECODE_r_binary_TO_r_binary 2020-10-01 13:22:26 root: INFO: instruction count: 41: __C122Compiled.addLiterals 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, initial IR -- Verify : 0.097ms, total 3.609s 2020-10-01 13:22:26 root: INFO: optimize compileLowerer, initial IR: before: IR size 18: (Coalesce (InsertFields (In +PCStruct{__cols:+PCArray[+PCStruct{__uid_5:PFloat64,__uid_6:+PFloat64,__uid_7:PFloat64}]} 0) None (__cols (ToArray (StreamMap __iruid_279 (StreamRange (I32 0) (ArrayLen (GetField __cols (In +PCStruct{__cols:+PCArray[+PCStruct{__uid_5:PFloat64,__uid_6:+PFloat64,__uid_7:PFloat64}]} 0))) (I32 1)) (ArrayRef (GetField __cols (In +PCStruct{__cols:+PCArray[+PCStruct{__uid_5:PFloat64,__uid_6:+PFloat64,__uid_7:PFloat64}]} 0)) (Ref __iruid_279) (Str "")))))) (Die Struct{__cols:Array[Struct{__uid_5:Float64,__uid_6:Float64,__uid_7:Float64}]} (Str "Internal e..."))) 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, initial IR -- LoweringTransformation -- Optimize -- FoldConstants : 0.303ms, total 3.610s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, initial IR -- LoweringTransformation -- Optimize -- ExtractIntervalFilters : 0.098ms, total 3.610s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, initial IR -- LoweringTransformation -- Optimize -- Simplify : 0.254ms, total 3.611s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, initial IR -- LoweringTransformation -- Optimize -- ForwardLets : 0.916ms, total 3.612s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, initial IR -- LoweringTransformation -- Optimize -- ForwardRelationalLets : 0.103ms, total 3.612s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, initial IR -- LoweringTransformation -- Optimize -- PruneDeadFields : 0.888ms, total 3.613s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, initial IR -- LoweringTransformation -- Optimize -- FoldConstants : 0.167ms, total 3.613s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, initial IR -- LoweringTransformation -- Optimize -- ExtractIntervalFilters : 0.068ms, total 3.613s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, initial IR -- LoweringTransformation -- Optimize -- Simplify : 0.187ms, total 3.614s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, initial IR -- LoweringTransformation -- Optimize -- ForwardLets : 0.693ms, total 3.614s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, initial IR -- LoweringTransformation -- Optimize -- ForwardRelationalLets : 0.077ms, total 3.615s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, initial IR -- LoweringTransformation -- Optimize -- PruneDeadFields : 0.530ms, total 3.615s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, initial IR -- LoweringTransformation -- Optimize -- FoldConstants : 0.166ms, total 3.615s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, initial IR -- LoweringTransformation -- Optimize -- ExtractIntervalFilters : 0.084ms, total 3.616s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, initial IR -- LoweringTransformation -- Optimize -- Simplify : 0.189ms, total 3.616s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, initial IR -- LoweringTransformation -- Optimize -- ForwardLets : 0.642ms, total 3.617s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, initial IR -- LoweringTransformation -- Optimize -- ForwardRelationalLets : 0.076ms, total 3.617s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, initial IR -- LoweringTransformation -- Optimize -- PruneDeadFields : 0.544ms, total 3.617s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, initial IR -- LoweringTransformation -- Optimize : 7.468ms, total 3.617s, tagged coverage 80.2 2020-10-01 13:22:26 root: INFO: optimize compileLowerer, initial IR: after: IR size 18: (Coalesce (InsertFields (In +PCStruct{__cols:+PCArray[+PCStruct{__uid_5:PFloat64,__uid_6:+PFloat64,__uid_7:PFloat64}]} 0) None (__cols (ToArray (StreamMap __iruid_427 (StreamRange (I32 0) (ArrayLen (GetField __cols (In +PCStruct{__cols:+PCArray[+PCStruct{__uid_5:PFloat64,__uid_6:+PFloat64,__uid_7:PFloat64}]} 0))) (I32 1)) (ArrayRef (GetField __cols (In +PCStruct{__cols:+PCArray[+PCStruct{__uid_5:PFloat64,__uid_6:+PFloat64,__uid_7:PFloat64}]} 0)) (Ref __iruid_427) (Str "")))))) (Die Struct{__cols:Array[Struct{__uid_5:Float64,__uid_6:Float64,__uid_7:Float64}]} (Str "Internal e..."))) 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, initial IR -- LoweringTransformation : 8.380ms, total 3.618s, tagged coverage 71.4 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, initial IR -- Verify : 0.013ms, total 3.618s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, initial IR : 8.875ms, total 3.618s, tagged coverage 68.7 2020-10-01 13:22:26 root: INFO: Timer: Time taken for InlineApplyIR -- Verify : 0.036ms, total 3.622s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for InlineApplyIR -- LoweringTransformation : 0.047ms, total 3.622s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for InlineApplyIR -- Verify : 0.027ms, total 3.622s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for InlineApplyIR : 3.846ms, total 3.622s, tagged coverage 2.8 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after InlineApplyIR -- Verify : 0.009ms, total 3.622s 2020-10-01 13:22:26 root: INFO: optimize compileLowerer, after InlineApplyIR: before: IR size 18: (Coalesce (InsertFields (In +PCStruct{__cols:+PCArray[+PCStruct{__uid_5:PFloat64,__uid_6:+PFloat64,__uid_7:PFloat64}]} 0) None (__cols (ToArray (StreamMap __iruid_427 (StreamRange (I32 0) (ArrayLen (GetField __cols (In +PCStruct{__cols:+PCArray[+PCStruct{__uid_5:PFloat64,__uid_6:+PFloat64,__uid_7:PFloat64}]} 0))) (I32 1)) (ArrayRef (GetField __cols (In +PCStruct{__cols:+PCArray[+PCStruct{__uid_5:PFloat64,__uid_6:+PFloat64,__uid_7:PFloat64}]} 0)) (Ref __iruid_427) (Str "")))))) (Die Struct{__cols:Array[Struct{__uid_5:Float64,__uid_6:Float64,__uid_7:Float64}]} (Str "Internal e..."))) 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after InlineApplyIR -- LoweringTransformation -- Optimize -- FoldConstants : 0.096ms, total 3.622s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after InlineApplyIR -- LoweringTransformation -- Optimize -- ExtractIntervalFilters : 0.071ms, total 3.623s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after InlineApplyIR -- LoweringTransformation -- Optimize -- Simplify : 0.197ms, total 3.623s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after InlineApplyIR -- LoweringTransformation -- Optimize -- ForwardLets : 0.693ms, total 3.624s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after InlineApplyIR -- LoweringTransformation -- Optimize -- ForwardRelationalLets : 0.082ms, total 3.624s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after InlineApplyIR -- LoweringTransformation -- Optimize -- PruneDeadFields : 0.928ms, total 3.625s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after InlineApplyIR -- LoweringTransformation -- Optimize -- FoldConstants : 0.506ms, total 3.626s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after InlineApplyIR -- LoweringTransformation -- Optimize -- ExtractIntervalFilters : 0.068ms, total 3.626s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after InlineApplyIR -- LoweringTransformation -- Optimize -- Simplify : 0.181ms, total 3.626s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after InlineApplyIR -- LoweringTransformation -- Optimize -- ForwardLets : 0.712ms, total 3.627s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after InlineApplyIR -- LoweringTransformation -- Optimize -- ForwardRelationalLets : 0.110ms, total 3.627s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after InlineApplyIR -- LoweringTransformation -- Optimize -- PruneDeadFields : 0.892ms, total 3.628s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after InlineApplyIR -- LoweringTransformation -- Optimize -- FoldConstants : 0.162ms, total 3.628s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after InlineApplyIR -- LoweringTransformation -- Optimize -- ExtractIntervalFilters : 0.074ms, total 3.628s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after InlineApplyIR -- LoweringTransformation -- Optimize -- Simplify : 0.195ms, total 3.629s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after InlineApplyIR -- LoweringTransformation -- Optimize -- ForwardLets : 0.619ms, total 3.629s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after InlineApplyIR -- LoweringTransformation -- Optimize -- ForwardRelationalLets : 0.077ms, total 3.629s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after InlineApplyIR -- LoweringTransformation -- Optimize -- PruneDeadFields : 0.507ms, total 3.630s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after InlineApplyIR -- LoweringTransformation -- Optimize : 7.710ms, total 3.630s, tagged coverage 80.0 2020-10-01 13:22:26 root: INFO: optimize compileLowerer, after InlineApplyIR: after: IR size 18: (Coalesce (InsertFields (In +PCStruct{__cols:+PCArray[+PCStruct{__uid_5:PFloat64,__uid_6:+PFloat64,__uid_7:PFloat64}]} 0) None (__cols (ToArray (StreamMap __iruid_430 (StreamRange (I32 0) (ArrayLen (GetField __cols (In +PCStruct{__cols:+PCArray[+PCStruct{__uid_5:PFloat64,__uid_6:+PFloat64,__uid_7:PFloat64}]} 0))) (I32 1)) (ArrayRef (GetField __cols (In +PCStruct{__cols:+PCArray[+PCStruct{__uid_5:PFloat64,__uid_6:+PFloat64,__uid_7:PFloat64}]} 0)) (Ref __iruid_430) (Str "")))))) (Die Struct{__cols:Array[Struct{__uid_5:Float64,__uid_6:Float64,__uid_7:Float64}]} (Str "Internal e..."))) 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after InlineApplyIR -- LoweringTransformation : 8.479ms, total 3.631s, tagged coverage 72.8 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after InlineApplyIR -- Verify : 0.029ms, total 3.631s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after InlineApplyIR : 8.749ms, total 3.631s, tagged coverage 70.9 2020-10-01 13:22:26 root: INFO: Timer: Time taken for LowerArrayAggsToRunAggs -- Verify : 0.025ms, total 3.631s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for LowerArrayAggsToRunAggs -- LoweringTransformation : 3.044ms, total 3.634s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for LowerArrayAggsToRunAggs -- Verify : 0.387ms, total 3.634s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for LowerArrayAggsToRunAggs : 3.694ms, total 3.635s, tagged coverage 93.6 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after LowerArrayAggsToRunAggs -- Verify : 0.009ms, total 3.635s 2020-10-01 13:22:26 root: INFO: optimize compileLowerer, after LowerArrayAggsToRunAggs: before: IR size 18: (Coalesce (InsertFields (In +PCStruct{__cols:+PCArray[+PCStruct{__uid_5:PFloat64,__uid_6:+PFloat64,__uid_7:PFloat64}]} 0) None (__cols (ToArray (StreamMap __iruid_430 (StreamRange (I32 0) (ArrayLen (GetField __cols (In +PCStruct{__cols:+PCArray[+PCStruct{__uid_5:PFloat64,__uid_6:+PFloat64,__uid_7:PFloat64}]} 0))) (I32 1)) (ArrayRef (GetField __cols (In +PCStruct{__cols:+PCArray[+PCStruct{__uid_5:PFloat64,__uid_6:+PFloat64,__uid_7:PFloat64}]} 0)) (Ref __iruid_430) (Str "")))))) (Die Struct{__cols:Array[Struct{__uid_5:Float64,__uid_6:Float64,__uid_7:Float64}]} (Str "Internal e..."))) 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after LowerArrayAggsToRunAggs -- LoweringTransformation -- Optimize -- FoldConstants : 0.101ms, total 3.635s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after LowerArrayAggsToRunAggs -- LoweringTransformation -- Optimize -- ExtractIntervalFilters : 0.076ms, total 3.635s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after LowerArrayAggsToRunAggs -- LoweringTransformation -- Optimize -- Simplify : 0.187ms, total 3.636s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after LowerArrayAggsToRunAggs -- LoweringTransformation -- Optimize -- ForwardLets : 2.039ms, total 3.638s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after LowerArrayAggsToRunAggs -- LoweringTransformation -- Optimize -- ForwardRelationalLets : 0.079ms, total 3.638s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after LowerArrayAggsToRunAggs -- LoweringTransformation -- Optimize -- PruneDeadFields : 0.574ms, total 3.638s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after LowerArrayAggsToRunAggs -- LoweringTransformation -- Optimize -- FoldConstants : 0.141ms, total 3.639s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after LowerArrayAggsToRunAggs -- LoweringTransformation -- Optimize -- ExtractIntervalFilters : 0.066ms, total 3.639s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after LowerArrayAggsToRunAggs -- LoweringTransformation -- Optimize -- Simplify : 0.190ms, total 3.639s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after LowerArrayAggsToRunAggs -- LoweringTransformation -- Optimize -- ForwardLets : 0.614ms, total 3.640s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after LowerArrayAggsToRunAggs -- LoweringTransformation -- Optimize -- ForwardRelationalLets : 0.077ms, total 3.640s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after LowerArrayAggsToRunAggs -- LoweringTransformation -- Optimize -- PruneDeadFields : 0.892ms, total 3.641s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after LowerArrayAggsToRunAggs -- LoweringTransformation -- Optimize -- FoldConstants : 0.149ms, total 3.641s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after LowerArrayAggsToRunAggs -- LoweringTransformation -- Optimize -- ExtractIntervalFilters : 0.071ms, total 3.641s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after LowerArrayAggsToRunAggs -- LoweringTransformation -- Optimize -- Simplify : 0.185ms, total 3.642s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after LowerArrayAggsToRunAggs -- LoweringTransformation -- Optimize -- ForwardLets : 0.655ms, total 3.642s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after LowerArrayAggsToRunAggs -- LoweringTransformation -- Optimize -- ForwardRelationalLets : 0.077ms, total 3.642s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after LowerArrayAggsToRunAggs -- LoweringTransformation -- Optimize -- PruneDeadFields : 0.552ms, total 3.643s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after LowerArrayAggsToRunAggs -- LoweringTransformation -- Optimize : 8.104ms, total 3.643s, tagged coverage 83.0 2020-10-01 13:22:26 root: INFO: optimize compileLowerer, after LowerArrayAggsToRunAggs: after: IR size 18: (Coalesce (InsertFields (In +PCStruct{__cols:+PCArray[+PCStruct{__uid_5:PFloat64,__uid_6:+PFloat64,__uid_7:PFloat64}]} 0) None (__cols (ToArray (StreamMap __iruid_433 (StreamRange (I32 0) (ArrayLen (GetField __cols (In +PCStruct{__cols:+PCArray[+PCStruct{__uid_5:PFloat64,__uid_6:+PFloat64,__uid_7:PFloat64}]} 0))) (I32 1)) (ArrayRef (GetField __cols (In +PCStruct{__cols:+PCArray[+PCStruct{__uid_5:PFloat64,__uid_6:+PFloat64,__uid_7:PFloat64}]} 0)) (Ref __iruid_433) (Str "")))))) (Die Struct{__cols:Array[Struct{__uid_5:Float64,__uid_6:Float64,__uid_7:Float64}]} (Str "Internal e..."))) 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after LowerArrayAggsToRunAggs -- LoweringTransformation : 8.915ms, total 3.644s, tagged coverage 75.4 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after LowerArrayAggsToRunAggs -- Verify : 0.011ms, total 3.644s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after LowerArrayAggsToRunAggs : 9.167ms, total 3.644s, tagged coverage 73.6 2020-10-01 13:22:26 root: INFO: encoder cache hit 2020-10-01 13:22:26 MemoryStore: INFO: Block broadcast_7 stored as values in memory (estimated size 104.0 B, free 364.4 MB) 2020-10-01 13:22:26 MemoryStore: INFO: Block broadcast_7_piece0 stored as bytes in memory (estimated size 104.0 B, free 364.4 MB) 2020-10-01 13:22:26 BlockManagerInfo: INFO: Added broadcast_7_piece0 in memory on qlu-1:28416 (size: 104.0 B, free: 366.0 MB) 2020-10-01 13:22:26 SparkContext: INFO: Created broadcast 7 from broadcast at SparkBackend.scala:233 2020-10-01 13:22:26 root: INFO: instruction count: 6: __C152Compiled. 2020-10-01 13:22:26 root: INFO: instruction count: 43: __C152Compiled.apply 2020-10-01 13:22:26 root: INFO: instruction count: 311: __C152Compiled.__m156wrapped 2020-10-01 13:22:26 root: INFO: instruction count: 11: __C152Compiled.__m166addIRIntermediate 2020-10-01 13:22:26 root: INFO: instruction count: 8: __C152Compiled.__m167addIRIntermediate 2020-10-01 13:22:26 root: INFO: instruction count: 14: __C152Compiled.setPartitionIndex 2020-10-01 13:22:26 root: INFO: instruction count: 7: __C152Compiled.addPartitionRegion 2020-10-01 13:22:26 root: INFO: instruction count: 25: __C152Compiled.__m171DECODE_r_struct_of_r_binaryEND_TO_r_tuple_of_r_stringEND 2020-10-01 13:22:26 root: INFO: instruction count: 11: __C152Compiled.__m172read_fields_group_0 2020-10-01 13:22:26 root: INFO: instruction count: 34: __C152Compiled.__m173INPLACE_DECODE_r_binary_TO_r_binary 2020-10-01 13:22:26 root: INFO: instruction count: 41: __C152Compiled.addLiterals 2020-10-01 13:22:26 root: INFO: RegionPool: REPORT_THRESHOLD: 8.7M allocated (4.4M blocks / 4.3M chunks), regions.size = 2, 0 current java objects, 0 max java objects, thread 31: Thread-5 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, initial IR -- Verify : 0.062ms, total 3.713s 2020-10-01 13:22:26 root: INFO: optimize compileLowerer, initial IR: before: IR size 15: (Coalesce (MakeStruct (locus (GetField locus (In +PCStruct{locus:+PCLocus(GRCh37),alleles:+PCArray[+PCString],`the entries! [877f12a8827e18f61222c6c8c5fb04a8]`:+PCArray[+PCStruct{GT:PCCall,__uid_8:PFloat64}]} 1))) (alleles (GetField alleles (In +PCStruct{locus:+PCLocus(GRCh37),alleles:+PCArray[+PCString],`the entries! [877f12a8827e18f61222c6c8c5fb04a8]`:+PCArray[+PCStruct{GT:PCCall,__uid_8:PFloat64}]} 1))) (the entries! [877f12a8827e18f61222c6c8c5fb04a8] (ToArray (StreamMap __iruid_280 (ToStream (GetField `the entries! [877f12a8827e18f61222c6c8c5fb04a8]` (In +PCStruct{locus:+PCLocus(GRCh37),alleles:+PCArray[+PCString],`the entries! [877f12a8827e18f61222c6c8c5fb04a8]`:+PCArray[+PCStruct{GT:PCCall,__uid_8:PFloat64}]} 1))) (SelectFields (__uid_8) (Ref __iruid_280)))))) (Die Struct{locus:Locus(GRCh37),alleles:Array[String],`the entries! [877f12a8827e18f61222c6c8c5fb04a8]`:Array[Struct{__uid_8:Float64}]} (Str "Internal e..."))) 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, initial IR -- LoweringTransformation -- Optimize -- FoldConstants : 0.314ms, total 3.714s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, initial IR -- LoweringTransformation -- Optimize -- ExtractIntervalFilters : 0.102ms, total 3.715s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, initial IR -- LoweringTransformation -- Optimize -- Simplify : 0.336ms, total 3.715s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, initial IR -- LoweringTransformation -- Optimize -- ForwardLets : 0.902ms, total 3.716s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, initial IR -- LoweringTransformation -- Optimize -- ForwardRelationalLets : 0.088ms, total 3.716s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, initial IR -- LoweringTransformation -- Optimize -- PruneDeadFields : 0.721ms, total 3.717s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, initial IR -- LoweringTransformation -- Optimize -- FoldConstants : 0.537ms, total 3.718s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, initial IR -- LoweringTransformation -- Optimize -- ExtractIntervalFilters : 0.048ms, total 3.718s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, initial IR -- LoweringTransformation -- Optimize -- Simplify : 0.163ms, total 3.718s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, initial IR -- LoweringTransformation -- Optimize -- ForwardLets : 0.366ms, total 3.718s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, initial IR -- LoweringTransformation -- Optimize -- ForwardRelationalLets : 0.056ms, total 3.718s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, initial IR -- LoweringTransformation -- Optimize -- PruneDeadFields : 0.431ms, total 3.719s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, initial IR -- LoweringTransformation -- Optimize -- FoldConstants : 0.214ms, total 3.719s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, initial IR -- LoweringTransformation -- Optimize -- ExtractIntervalFilters : 0.063ms, total 3.719s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, initial IR -- LoweringTransformation -- Optimize -- Simplify : 0.135ms, total 3.720s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, initial IR -- LoweringTransformation -- Optimize -- ForwardLets : 0.374ms, total 3.720s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, initial IR -- LoweringTransformation -- Optimize -- ForwardRelationalLets : 0.061ms, total 3.721s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, initial IR -- LoweringTransformation -- Optimize -- PruneDeadFields : 0.412ms, total 3.721s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, initial IR -- LoweringTransformation -- Optimize : 7.098ms, total 3.721s, tagged coverage 75.0 2020-10-01 13:22:26 root: INFO: optimize compileLowerer, initial IR: after: IR size 12: (MakeStruct (locus (GetField locus (In +PCStruct{locus:+PCLocus(GRCh37),alleles:+PCArray[+PCString],`the entries! [877f12a8827e18f61222c6c8c5fb04a8]`:+PCArray[+PCStruct{GT:PCCall,__uid_8:PFloat64}]} 1))) (alleles (GetField alleles (In +PCStruct{locus:+PCLocus(GRCh37),alleles:+PCArray[+PCString],`the entries! [877f12a8827e18f61222c6c8c5fb04a8]`:+PCArray[+PCStruct{GT:PCCall,__uid_8:PFloat64}]} 1))) (the entries! [877f12a8827e18f61222c6c8c5fb04a8] (ToArray (StreamMap __iruid_437 (ToStream (GetField `the entries! [877f12a8827e18f61222c6c8c5fb04a8]` (In +PCStruct{locus:+PCLocus(GRCh37),alleles:+PCArray[+PCString],`the entries! [877f12a8827e18f61222c6c8c5fb04a8]`:+PCArray[+PCStruct{GT:PCCall,__uid_8:PFloat64}]} 1))) (SelectFields (__uid_8) (Ref __iruid_437)))))) 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, initial IR -- LoweringTransformation : 8.233ms, total 3.722s, tagged coverage 64.7 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, initial IR -- Verify : 0.014ms, total 3.722s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, initial IR : 8.907ms, total 3.722s, tagged coverage 60.6 2020-10-01 13:22:26 root: INFO: Timer: Time taken for InlineApplyIR -- Verify : 0.033ms, total 3.722s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for InlineApplyIR -- LoweringTransformation : 0.073ms, total 3.722s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for InlineApplyIR -- Verify : 0.022ms, total 3.722s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for InlineApplyIR : 0.386ms, total 3.722s, tagged coverage 33.0 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after InlineApplyIR -- Verify : 0.006ms, total 3.722s 2020-10-01 13:22:26 root: INFO: optimize compileLowerer, after InlineApplyIR: before: IR size 12: (MakeStruct (locus (GetField locus (In +PCStruct{locus:+PCLocus(GRCh37),alleles:+PCArray[+PCString],`the entries! [877f12a8827e18f61222c6c8c5fb04a8]`:+PCArray[+PCStruct{GT:PCCall,__uid_8:PFloat64}]} 1))) (alleles (GetField alleles (In +PCStruct{locus:+PCLocus(GRCh37),alleles:+PCArray[+PCString],`the entries! [877f12a8827e18f61222c6c8c5fb04a8]`:+PCArray[+PCStruct{GT:PCCall,__uid_8:PFloat64}]} 1))) (the entries! [877f12a8827e18f61222c6c8c5fb04a8] (ToArray (StreamMap __iruid_437 (ToStream (GetField `the entries! [877f12a8827e18f61222c6c8c5fb04a8]` (In +PCStruct{locus:+PCLocus(GRCh37),alleles:+PCArray[+PCString],`the entries! [877f12a8827e18f61222c6c8c5fb04a8]`:+PCArray[+PCStruct{GT:PCCall,__uid_8:PFloat64}]} 1))) (SelectFields (__uid_8) (Ref __iruid_437)))))) 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after InlineApplyIR -- LoweringTransformation -- Optimize -- FoldConstants : 0.069ms, total 3.723s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after InlineApplyIR -- LoweringTransformation -- Optimize -- ExtractIntervalFilters : 0.051ms, total 3.723s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after InlineApplyIR -- LoweringTransformation -- Optimize -- Simplify : 0.507ms, total 3.724s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after InlineApplyIR -- LoweringTransformation -- Optimize -- ForwardLets : 0.394ms, total 3.724s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after InlineApplyIR -- LoweringTransformation -- Optimize -- ForwardRelationalLets : 0.743ms, total 3.725s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after InlineApplyIR -- LoweringTransformation -- Optimize -- PruneDeadFields : 0.435ms, total 3.725s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after InlineApplyIR -- LoweringTransformation -- Optimize -- FoldConstants : 0.163ms, total 3.726s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after InlineApplyIR -- LoweringTransformation -- Optimize -- ExtractIntervalFilters : 0.049ms, total 3.726s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after InlineApplyIR -- LoweringTransformation -- Optimize -- Simplify : 0.132ms, total 3.726s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after InlineApplyIR -- LoweringTransformation -- Optimize -- ForwardLets : 0.455ms, total 3.726s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after InlineApplyIR -- LoweringTransformation -- Optimize -- ForwardRelationalLets : 0.056ms, total 3.727s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after InlineApplyIR -- LoweringTransformation -- Optimize -- PruneDeadFields : 0.423ms, total 3.727s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after InlineApplyIR -- LoweringTransformation -- Optimize -- FoldConstants : 0.194ms, total 3.727s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after InlineApplyIR -- LoweringTransformation -- Optimize -- ExtractIntervalFilters : 0.051ms, total 3.727s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after InlineApplyIR -- LoweringTransformation -- Optimize -- Simplify : 0.133ms, total 3.728s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after InlineApplyIR -- LoweringTransformation -- Optimize -- ForwardLets : 0.441ms, total 3.728s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after InlineApplyIR -- LoweringTransformation -- Optimize -- ForwardRelationalLets : 0.072ms, total 3.728s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after InlineApplyIR -- LoweringTransformation -- Optimize -- PruneDeadFields : 0.404ms, total 3.729s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after InlineApplyIR -- LoweringTransformation -- Optimize : 6.144ms, total 3.729s, tagged coverage 77.6 2020-10-01 13:22:26 root: INFO: optimize compileLowerer, after InlineApplyIR: after: IR size 12: (MakeStruct (locus (GetField locus (In +PCStruct{locus:+PCLocus(GRCh37),alleles:+PCArray[+PCString],`the entries! [877f12a8827e18f61222c6c8c5fb04a8]`:+PCArray[+PCStruct{GT:PCCall,__uid_8:PFloat64}]} 1))) (alleles (GetField alleles (In +PCStruct{locus:+PCLocus(GRCh37),alleles:+PCArray[+PCString],`the entries! [877f12a8827e18f61222c6c8c5fb04a8]`:+PCArray[+PCStruct{GT:PCCall,__uid_8:PFloat64}]} 1))) (the entries! [877f12a8827e18f61222c6c8c5fb04a8] (ToArray (StreamMap __iruid_440 (ToStream (GetField `the entries! [877f12a8827e18f61222c6c8c5fb04a8]` (In +PCStruct{locus:+PCLocus(GRCh37),alleles:+PCArray[+PCString],`the entries! [877f12a8827e18f61222c6c8c5fb04a8]`:+PCArray[+PCStruct{GT:PCCall,__uid_8:PFloat64}]} 1))) (SelectFields (__uid_8) (Ref __iruid_440)))))) 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after InlineApplyIR -- LoweringTransformation : 6.927ms, total 3.729s, tagged coverage 68.9 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after InlineApplyIR -- Verify : 0.009ms, total 3.729s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after InlineApplyIR : 7.159ms, total 3.730s, tagged coverage 66.8 2020-10-01 13:22:26 root: INFO: Timer: Time taken for LowerArrayAggsToRunAggs -- Verify : 0.046ms, total 3.730s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for LowerArrayAggsToRunAggs -- LoweringTransformation : 1.229ms, total 3.731s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for LowerArrayAggsToRunAggs -- Verify : 0.070ms, total 3.731s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for LowerArrayAggsToRunAggs : 1.595ms, total 3.731s, tagged coverage 84.4 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after LowerArrayAggsToRunAggs -- Verify : 0.006ms, total 3.731s 2020-10-01 13:22:26 root: INFO: optimize compileLowerer, after LowerArrayAggsToRunAggs: before: IR size 12: (MakeStruct (locus (GetField locus (In +PCStruct{locus:+PCLocus(GRCh37),alleles:+PCArray[+PCString],`the entries! [877f12a8827e18f61222c6c8c5fb04a8]`:+PCArray[+PCStruct{GT:PCCall,__uid_8:PFloat64}]} 1))) (alleles (GetField alleles (In +PCStruct{locus:+PCLocus(GRCh37),alleles:+PCArray[+PCString],`the entries! [877f12a8827e18f61222c6c8c5fb04a8]`:+PCArray[+PCStruct{GT:PCCall,__uid_8:PFloat64}]} 1))) (the entries! [877f12a8827e18f61222c6c8c5fb04a8] (ToArray (StreamMap __iruid_440 (ToStream (GetField `the entries! [877f12a8827e18f61222c6c8c5fb04a8]` (In +PCStruct{locus:+PCLocus(GRCh37),alleles:+PCArray[+PCString],`the entries! [877f12a8827e18f61222c6c8c5fb04a8]`:+PCArray[+PCStruct{GT:PCCall,__uid_8:PFloat64}]} 1))) (SelectFields (__uid_8) (Ref __iruid_440)))))) 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after LowerArrayAggsToRunAggs -- LoweringTransformation -- Optimize -- FoldConstants : 0.059ms, total 3.732s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after LowerArrayAggsToRunAggs -- LoweringTransformation -- Optimize -- ExtractIntervalFilters : 0.089ms, total 3.732s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after LowerArrayAggsToRunAggs -- LoweringTransformation -- Optimize -- Simplify : 0.141ms, total 3.732s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after LowerArrayAggsToRunAggs -- LoweringTransformation -- Optimize -- ForwardLets : 0.434ms, total 3.733s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after LowerArrayAggsToRunAggs -- LoweringTransformation -- Optimize -- ForwardRelationalLets : 0.058ms, total 3.733s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after LowerArrayAggsToRunAggs -- LoweringTransformation -- Optimize -- PruneDeadFields : 0.445ms, total 3.734s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after LowerArrayAggsToRunAggs -- LoweringTransformation -- Optimize -- FoldConstants : 0.206ms, total 3.734s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after LowerArrayAggsToRunAggs -- LoweringTransformation -- Optimize -- ExtractIntervalFilters : 0.067ms, total 3.734s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after LowerArrayAggsToRunAggs -- LoweringTransformation -- Optimize -- Simplify : 0.130ms, total 3.734s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after LowerArrayAggsToRunAggs -- LoweringTransformation -- Optimize -- ForwardLets : 0.375ms, total 3.735s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after LowerArrayAggsToRunAggs -- LoweringTransformation -- Optimize -- ForwardRelationalLets : 0.054ms, total 3.735s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after LowerArrayAggsToRunAggs -- LoweringTransformation -- Optimize -- PruneDeadFields : 0.442ms, total 3.735s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after LowerArrayAggsToRunAggs -- LoweringTransformation -- Optimize -- FoldConstants : 0.155ms, total 3.736s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after LowerArrayAggsToRunAggs -- LoweringTransformation -- Optimize -- ExtractIntervalFilters : 0.079ms, total 3.736s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after LowerArrayAggsToRunAggs -- LoweringTransformation -- Optimize -- Simplify : 0.133ms, total 3.736s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after LowerArrayAggsToRunAggs -- LoweringTransformation -- Optimize -- ForwardLets : 0.363ms, total 3.736s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after LowerArrayAggsToRunAggs -- LoweringTransformation -- Optimize -- ForwardRelationalLets : 0.057ms, total 3.737s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after LowerArrayAggsToRunAggs -- LoweringTransformation -- Optimize -- PruneDeadFields : 0.400ms, total 3.737s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after LowerArrayAggsToRunAggs -- LoweringTransformation -- Optimize : 5.417ms, total 3.737s, tagged coverage 68.1 2020-10-01 13:22:26 root: INFO: optimize compileLowerer, after LowerArrayAggsToRunAggs: after: IR size 12: (MakeStruct (locus (GetField locus (In +PCStruct{locus:+PCLocus(GRCh37),alleles:+PCArray[+PCString],`the entries! [877f12a8827e18f61222c6c8c5fb04a8]`:+PCArray[+PCStruct{GT:PCCall,__uid_8:PFloat64}]} 1))) (alleles (GetField alleles (In +PCStruct{locus:+PCLocus(GRCh37),alleles:+PCArray[+PCString],`the entries! [877f12a8827e18f61222c6c8c5fb04a8]`:+PCArray[+PCStruct{GT:PCCall,__uid_8:PFloat64}]} 1))) (the entries! [877f12a8827e18f61222c6c8c5fb04a8] (ToArray (StreamMap __iruid_443 (ToStream (GetField `the entries! [877f12a8827e18f61222c6c8c5fb04a8]` (In +PCStruct{locus:+PCLocus(GRCh37),alleles:+PCArray[+PCString],`the entries! [877f12a8827e18f61222c6c8c5fb04a8]`:+PCArray[+PCStruct{GT:PCCall,__uid_8:PFloat64}]} 1))) (SelectFields (__uid_8) (Ref __iruid_443)))))) 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after LowerArrayAggsToRunAggs -- LoweringTransformation : 6.167ms, total 3.738s, tagged coverage 59.8 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after LowerArrayAggsToRunAggs -- Verify : 0.008ms, total 3.738s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after LowerArrayAggsToRunAggs : 6.422ms, total 3.738s, tagged coverage 57.7 2020-10-01 13:22:26 root: INFO: instruction count: 6: __C175Compiled. 2020-10-01 13:22:26 root: INFO: instruction count: 25: __C175Compiled.apply 2020-10-01 13:22:26 root: INFO: instruction count: 198: __C175Compiled.__m178wrapped 2020-10-01 13:22:26 root: INFO: instruction count: 11: __C175Compiled.__m179addIRIntermediate 2020-10-01 13:22:26 root: INFO: instruction count: 8: __C175Compiled.__m180addIRIntermediate 2020-10-01 13:22:26 root: INFO: instruction count: 11: __C175Compiled.__m189addIRIntermediate 2020-10-01 13:22:26 root: INFO: instruction count: 8: __C175Compiled.__m190addIRIntermediate 2020-10-01 13:22:26 root: INFO: instruction count: 14: __C175Compiled.setPartitionIndex 2020-10-01 13:22:26 root: INFO: instruction count: 7: __C175Compiled.addPartitionRegion 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, initial IR -- Verify : 0.047ms, total 3.761s 2020-10-01 13:22:26 root: INFO: optimize compileLowerer, initial IR: before: IR size 5: (Coalesce (CastRename Struct{__cols:Array[Struct{__y_0:Float64,__cov0:Float64,__cov1:Float64}]} (In +PCStruct{__cols:+PCArray[+PCStruct{__uid_5:PFloat64,__uid_6:+PFloat64,__uid_7:PFloat64}]} 0)) (Die Struct{__cols:Array[Struct{__y_0:Float64,__cov0:Float64,__cov1:Float64}]} (Str "Internal e..."))) 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, initial IR -- LoweringTransformation -- Optimize -- FoldConstants : 0.120ms, total 3.762s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, initial IR -- LoweringTransformation -- Optimize -- ExtractIntervalFilters : 0.035ms, total 3.762s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, initial IR -- LoweringTransformation -- Optimize -- Simplify : 0.135ms, total 3.762s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, initial IR -- LoweringTransformation -- Optimize -- ForwardLets : 0.419ms, total 3.762s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, initial IR -- LoweringTransformation -- Optimize -- ForwardRelationalLets : 0.043ms, total 3.762s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, initial IR -- LoweringTransformation -- Optimize -- PruneDeadFields : 0.358ms, total 3.763s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, initial IR -- LoweringTransformation -- Optimize : 1.644ms, total 3.763s, tagged coverage 67.5 2020-10-01 13:22:26 root: INFO: optimize compileLowerer, initial IR: after: IR size 5: (Coalesce (CastRename Struct{__cols:Array[Struct{__y_0:Float64,__cov0:Float64,__cov1:Float64}]} (In +PCStruct{__cols:+PCArray[+PCStruct{__uid_5:PFloat64,__uid_6:+PFloat64,__uid_7:PFloat64}]} 0)) (Die Struct{__cols:Array[Struct{__y_0:Float64,__cov0:Float64,__cov1:Float64}]} (Str "Internal e..."))) 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, initial IR -- LoweringTransformation : 2.291ms, total 3.763s, tagged coverage 48.5 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, initial IR -- Verify : 0.007ms, total 3.763s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, initial IR : 2.709ms, total 3.764s, tagged coverage 43.0 2020-10-01 13:22:26 root: INFO: Timer: Time taken for InlineApplyIR -- Verify : 0.016ms, total 3.764s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for InlineApplyIR -- LoweringTransformation : 0.017ms, total 3.764s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for InlineApplyIR -- Verify : 0.024ms, total 3.764s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for InlineApplyIR : 0.268ms, total 3.764s, tagged coverage 21.2 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after InlineApplyIR -- Verify : 0.005ms, total 3.764s 2020-10-01 13:22:26 root: INFO: optimize compileLowerer, after InlineApplyIR: before: IR size 5: (Coalesce (CastRename Struct{__cols:Array[Struct{__y_0:Float64,__cov0:Float64,__cov1:Float64}]} (In +PCStruct{__cols:+PCArray[+PCStruct{__uid_5:PFloat64,__uid_6:+PFloat64,__uid_7:PFloat64}]} 0)) (Die Struct{__cols:Array[Struct{__y_0:Float64,__cov0:Float64,__cov1:Float64}]} (Str "Internal e..."))) 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after InlineApplyIR -- LoweringTransformation -- Optimize -- FoldConstants : 0.048ms, total 3.765s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after InlineApplyIR -- LoweringTransformation -- Optimize -- ExtractIntervalFilters : 0.043ms, total 3.765s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after InlineApplyIR -- LoweringTransformation -- Optimize -- Simplify : 0.073ms, total 3.765s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after InlineApplyIR -- LoweringTransformation -- Optimize -- ForwardLets : 0.331ms, total 3.765s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after InlineApplyIR -- LoweringTransformation -- Optimize -- ForwardRelationalLets : 0.047ms, total 3.765s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after InlineApplyIR -- LoweringTransformation -- Optimize -- PruneDeadFields : 0.212ms, total 3.766s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after InlineApplyIR -- LoweringTransformation -- Optimize : 1.186ms, total 3.766s, tagged coverage 63.5 2020-10-01 13:22:26 root: INFO: optimize compileLowerer, after InlineApplyIR: after: IR size 5: (Coalesce (CastRename Struct{__cols:Array[Struct{__y_0:Float64,__cov0:Float64,__cov1:Float64}]} (In +PCStruct{__cols:+PCArray[+PCStruct{__uid_5:PFloat64,__uid_6:+PFloat64,__uid_7:PFloat64}]} 0)) (Die Struct{__cols:Array[Struct{__y_0:Float64,__cov0:Float64,__cov1:Float64}]} (Str "Internal e..."))) 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after InlineApplyIR -- LoweringTransformation : 1.938ms, total 3.766s, tagged coverage 38.9 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after InlineApplyIR -- Verify : 0.005ms, total 3.766s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after InlineApplyIR : 2.172ms, total 3.766s, tagged coverage 35.1 2020-10-01 13:22:26 root: INFO: Timer: Time taken for LowerArrayAggsToRunAggs -- Verify : 0.014ms, total 3.766s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for LowerArrayAggsToRunAggs -- LoweringTransformation : 0.539ms, total 3.767s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for LowerArrayAggsToRunAggs -- Verify : 0.016ms, total 3.767s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for LowerArrayAggsToRunAggs : 0.768ms, total 3.767s, tagged coverage 74.2 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after LowerArrayAggsToRunAggs -- Verify : 0.004ms, total 3.767s 2020-10-01 13:22:26 root: INFO: optimize compileLowerer, after LowerArrayAggsToRunAggs: before: IR size 5: (Coalesce (CastRename Struct{__cols:Array[Struct{__y_0:Float64,__cov0:Float64,__cov1:Float64}]} (In +PCStruct{__cols:+PCArray[+PCStruct{__uid_5:PFloat64,__uid_6:+PFloat64,__uid_7:PFloat64}]} 0)) (Die Struct{__cols:Array[Struct{__y_0:Float64,__cov0:Float64,__cov1:Float64}]} (Str "Internal e..."))) 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after LowerArrayAggsToRunAggs -- LoweringTransformation -- Optimize -- FoldConstants : 0.043ms, total 3.767s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after LowerArrayAggsToRunAggs -- LoweringTransformation -- Optimize -- ExtractIntervalFilters : 0.028ms, total 3.767s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after LowerArrayAggsToRunAggs -- LoweringTransformation -- Optimize -- Simplify : 0.072ms, total 3.768s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after LowerArrayAggsToRunAggs -- LoweringTransformation -- Optimize -- ForwardLets : 0.310ms, total 3.768s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after LowerArrayAggsToRunAggs -- LoweringTransformation -- Optimize -- ForwardRelationalLets : 0.032ms, total 3.768s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after LowerArrayAggsToRunAggs -- LoweringTransformation -- Optimize -- PruneDeadFields : 0.228ms, total 3.768s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after LowerArrayAggsToRunAggs -- LoweringTransformation -- Optimize : 1.133ms, total 3.768s, tagged coverage 62.9 2020-10-01 13:22:26 root: INFO: optimize compileLowerer, after LowerArrayAggsToRunAggs: after: IR size 5: (Coalesce (CastRename Struct{__cols:Array[Struct{__y_0:Float64,__cov0:Float64,__cov1:Float64}]} (In +PCStruct{__cols:+PCArray[+PCStruct{__uid_5:PFloat64,__uid_6:+PFloat64,__uid_7:PFloat64}]} 0)) (Die Struct{__cols:Array[Struct{__y_0:Float64,__cov0:Float64,__cov1:Float64}]} (Str "Internal e..."))) 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after LowerArrayAggsToRunAggs -- LoweringTransformation : 1.553ms, total 3.769s, tagged coverage 45.9 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after LowerArrayAggsToRunAggs -- Verify : 0.006ms, total 3.769s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after LowerArrayAggsToRunAggs : 1.784ms, total 3.769s, tagged coverage 40.5 2020-10-01 13:22:26 root: INFO: encoder cache hit 2020-10-01 13:22:26 MemoryStore: INFO: Block broadcast_8 stored as values in memory (estimated size 104.0 B, free 364.4 MB) 2020-10-01 13:22:26 MemoryStore: INFO: Block broadcast_8_piece0 stored as bytes in memory (estimated size 104.0 B, free 364.4 MB) 2020-10-01 13:22:26 BlockManagerInfo: INFO: Added broadcast_8_piece0 in memory on qlu-1:28416 (size: 104.0 B, free: 366.0 MB) 2020-10-01 13:22:26 SparkContext: INFO: Created broadcast 8 from broadcast at SparkBackend.scala:233 2020-10-01 13:22:26 root: INFO: instruction count: 6: __C193Compiled. 2020-10-01 13:22:26 root: INFO: instruction count: 165: __C193Compiled.apply 2020-10-01 13:22:26 root: INFO: instruction count: 14: __C193Compiled.setPartitionIndex 2020-10-01 13:22:26 root: INFO: instruction count: 7: __C193Compiled.addPartitionRegion 2020-10-01 13:22:26 root: INFO: instruction count: 25: __C193Compiled.__m197DECODE_r_struct_of_r_binaryEND_TO_r_tuple_of_r_stringEND 2020-10-01 13:22:26 root: INFO: instruction count: 11: __C193Compiled.__m198read_fields_group_0 2020-10-01 13:22:26 root: INFO: instruction count: 34: __C193Compiled.__m199INPLACE_DECODE_r_binary_TO_r_binary 2020-10-01 13:22:26 root: INFO: instruction count: 41: __C193Compiled.addLiterals 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, initial IR -- Verify : 0.035ms, total 3.840s 2020-10-01 13:22:26 root: INFO: optimize compileLowerer, initial IR: before: IR size 5: (Coalesce (CastRename Struct{locus:Locus(GRCh37),alleles:Array[String],`the entries! [877f12a8827e18f61222c6c8c5fb04a8]`:Array[Struct{__uid_4:Float64}]} (In +PCStruct{locus:+PCLocus(GRCh37),alleles:+PCArray[+PCString],`the entries! [877f12a8827e18f61222c6c8c5fb04a8]`:+PCArray[+PCStruct{__uid_8:PFloat64}]} 1)) (Die Struct{locus:Locus(GRCh37),alleles:Array[String],`the entries! [877f12a8827e18f61222c6c8c5fb04a8]`:Array[Struct{__uid_4:Float64}]} (Str "Internal e..."))) 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, initial IR -- LoweringTransformation -- Optimize -- FoldConstants : 0.272ms, total 3.841s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, initial IR -- LoweringTransformation -- Optimize -- ExtractIntervalFilters : 0.052ms, total 3.842s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, initial IR -- LoweringTransformation -- Optimize -- Simplify : 0.181ms, total 3.842s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, initial IR -- LoweringTransformation -- Optimize -- ForwardLets : 3.102ms, total 3.845s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, initial IR -- LoweringTransformation -- Optimize -- ForwardRelationalLets : 0.058ms, total 3.846s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, initial IR -- LoweringTransformation -- Optimize -- PruneDeadFields : 0.505ms, total 3.846s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, initial IR -- LoweringTransformation -- Optimize : 5.456ms, total 3.847s, tagged coverage 76.4 2020-10-01 13:22:26 root: INFO: optimize compileLowerer, initial IR: after: IR size 5: (Coalesce (CastRename Struct{locus:Locus(GRCh37),alleles:Array[String],`the entries! [877f12a8827e18f61222c6c8c5fb04a8]`:Array[Struct{__uid_4:Float64}]} (In +PCStruct{locus:+PCLocus(GRCh37),alleles:+PCArray[+PCString],`the entries! [877f12a8827e18f61222c6c8c5fb04a8]`:+PCArray[+PCStruct{__uid_8:PFloat64}]} 1)) (Die Struct{locus:Locus(GRCh37),alleles:Array[String],`the entries! [877f12a8827e18f61222c6c8c5fb04a8]`:Array[Struct{__uid_4:Float64}]} (Str "Internal e..."))) 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, initial IR -- LoweringTransformation : 6.223ms, total 3.847s, tagged coverage 67.0 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, initial IR -- Verify : 0.008ms, total 3.847s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, initial IR : 6.850ms, total 3.847s, tagged coverage 61.5 2020-10-01 13:22:26 root: INFO: Timer: Time taken for InlineApplyIR -- Verify : 0.024ms, total 3.847s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for InlineApplyIR -- LoweringTransformation : 0.019ms, total 3.847s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for InlineApplyIR -- Verify : 0.013ms, total 3.847s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for InlineApplyIR : 0.227ms, total 3.847s, tagged coverage 24.7 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after InlineApplyIR -- Verify : 0.004ms, total 3.848s 2020-10-01 13:22:26 root: INFO: optimize compileLowerer, after InlineApplyIR: before: IR size 5: (Coalesce (CastRename Struct{locus:Locus(GRCh37),alleles:Array[String],`the entries! [877f12a8827e18f61222c6c8c5fb04a8]`:Array[Struct{__uid_4:Float64}]} (In +PCStruct{locus:+PCLocus(GRCh37),alleles:+PCArray[+PCString],`the entries! [877f12a8827e18f61222c6c8c5fb04a8]`:+PCArray[+PCStruct{__uid_8:PFloat64}]} 1)) (Die Struct{locus:Locus(GRCh37),alleles:Array[String],`the entries! [877f12a8827e18f61222c6c8c5fb04a8]`:Array[Struct{__uid_4:Float64}]} (Str "Internal e..."))) 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after InlineApplyIR -- LoweringTransformation -- Optimize -- FoldConstants : 0.043ms, total 3.848s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after InlineApplyIR -- LoweringTransformation -- Optimize -- ExtractIntervalFilters : 0.025ms, total 3.848s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after InlineApplyIR -- LoweringTransformation -- Optimize -- Simplify : 0.078ms, total 3.848s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after InlineApplyIR -- LoweringTransformation -- Optimize -- ForwardLets : 2.284ms, total 3.850s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after InlineApplyIR -- LoweringTransformation -- Optimize -- ForwardRelationalLets : 0.034ms, total 3.851s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after InlineApplyIR -- LoweringTransformation -- Optimize -- PruneDeadFields : 0.292ms, total 3.851s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after InlineApplyIR -- LoweringTransformation -- Optimize : 3.149ms, total 3.851s, tagged coverage 87.5 2020-10-01 13:22:26 root: INFO: optimize compileLowerer, after InlineApplyIR: after: IR size 5: (Coalesce (CastRename Struct{locus:Locus(GRCh37),alleles:Array[String],`the entries! [877f12a8827e18f61222c6c8c5fb04a8]`:Array[Struct{__uid_4:Float64}]} (In +PCStruct{locus:+PCLocus(GRCh37),alleles:+PCArray[+PCString],`the entries! [877f12a8827e18f61222c6c8c5fb04a8]`:+PCArray[+PCStruct{__uid_8:PFloat64}]} 1)) (Die Struct{locus:Locus(GRCh37),alleles:Array[String],`the entries! [877f12a8827e18f61222c6c8c5fb04a8]`:Array[Struct{__uid_4:Float64}]} (Str "Internal e..."))) 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after InlineApplyIR -- LoweringTransformation : 3.708ms, total 3.851s, tagged coverage 74.3 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after InlineApplyIR -- Verify : 0.006ms, total 3.851s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after InlineApplyIR : 3.925ms, total 3.851s, tagged coverage 70.5 2020-10-01 13:22:26 root: INFO: Timer: Time taken for LowerArrayAggsToRunAggs -- Verify : 0.010ms, total 3.852s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for LowerArrayAggsToRunAggs -- LoweringTransformation : 0.433ms, total 3.852s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for LowerArrayAggsToRunAggs -- Verify : 0.034ms, total 3.852s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for LowerArrayAggsToRunAggs : 1.040ms, total 3.853s, tagged coverage 45.9 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after LowerArrayAggsToRunAggs -- Verify : 0.004ms, total 3.853s 2020-10-01 13:22:26 root: INFO: optimize compileLowerer, after LowerArrayAggsToRunAggs: before: IR size 5: (Coalesce (CastRename Struct{locus:Locus(GRCh37),alleles:Array[String],`the entries! [877f12a8827e18f61222c6c8c5fb04a8]`:Array[Struct{__uid_4:Float64}]} (In +PCStruct{locus:+PCLocus(GRCh37),alleles:+PCArray[+PCString],`the entries! [877f12a8827e18f61222c6c8c5fb04a8]`:+PCArray[+PCStruct{__uid_8:PFloat64}]} 1)) (Die Struct{locus:Locus(GRCh37),alleles:Array[String],`the entries! [877f12a8827e18f61222c6c8c5fb04a8]`:Array[Struct{__uid_4:Float64}]} (Str "Internal e..."))) 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after LowerArrayAggsToRunAggs -- LoweringTransformation -- Optimize -- FoldConstants : 0.042ms, total 3.853s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after LowerArrayAggsToRunAggs -- LoweringTransformation -- Optimize -- ExtractIntervalFilters : 0.025ms, total 3.853s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after LowerArrayAggsToRunAggs -- LoweringTransformation -- Optimize -- Simplify : 0.089ms, total 3.853s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after LowerArrayAggsToRunAggs -- LoweringTransformation -- Optimize -- ForwardLets : 0.222ms, total 3.853s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after LowerArrayAggsToRunAggs -- LoweringTransformation -- Optimize -- ForwardRelationalLets : 0.032ms, total 3.854s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after LowerArrayAggsToRunAggs -- LoweringTransformation -- Optimize -- PruneDeadFields : 0.210ms, total 3.854s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after LowerArrayAggsToRunAggs -- LoweringTransformation -- Optimize : 1.006ms, total 3.854s, tagged coverage 61.6 2020-10-01 13:22:26 root: INFO: optimize compileLowerer, after LowerArrayAggsToRunAggs: after: IR size 5: (Coalesce (CastRename Struct{locus:Locus(GRCh37),alleles:Array[String],`the entries! [877f12a8827e18f61222c6c8c5fb04a8]`:Array[Struct{__uid_4:Float64}]} (In +PCStruct{locus:+PCLocus(GRCh37),alleles:+PCArray[+PCString],`the entries! [877f12a8827e18f61222c6c8c5fb04a8]`:+PCArray[+PCStruct{__uid_8:PFloat64}]} 1)) (Die Struct{locus:Locus(GRCh37),alleles:Array[String],`the entries! [877f12a8827e18f61222c6c8c5fb04a8]`:Array[Struct{__uid_4:Float64}]} (Str "Internal e..."))) 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after LowerArrayAggsToRunAggs -- LoweringTransformation : 1.473ms, total 3.854s, tagged coverage 42.1 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after LowerArrayAggsToRunAggs -- Verify : 0.005ms, total 3.854s 2020-10-01 13:22:26 root: INFO: Timer: Time taken for compileLowerer, after LowerArrayAggsToRunAggs : 1.679ms, total 3.854s, tagged coverage 37.5 2020-10-01 13:22:26 root: INFO: encoder cache hit 2020-10-01 13:22:26 MemoryStore: INFO: Block broadcast_9 stored as values in memory (estimated size 104.0 B, free 364.4 MB) 2020-10-01 13:22:26 MemoryStore: INFO: Block broadcast_9_piece0 stored as bytes in memory (estimated size 109.0 B, free 364.4 MB) 2020-10-01 13:22:26 BlockManagerInfo: INFO: Added broadcast_9_piece0 in memory on qlu-1:28416 (size: 109.0 B, free: 366.0 MB) 2020-10-01 13:22:26 SparkContext: INFO: Created broadcast 9 from broadcast at SparkBackend.scala:233 2020-10-01 13:22:26 root: INFO: instruction count: 6: __C201Compiled. 2020-10-01 13:22:26 root: INFO: instruction count: 173: __C201Compiled.apply 2020-10-01 13:22:26 root: INFO: instruction count: 14: __C201Compiled.setPartitionIndex 2020-10-01 13:22:26 root: INFO: instruction count: 7: __C201Compiled.addPartitionRegion 2020-10-01 13:22:26 root: INFO: instruction count: 25: __C201Compiled.__m205DECODE_r_struct_of_r_binaryEND_TO_r_tuple_of_r_stringEND 2020-10-01 13:22:26 root: INFO: instruction count: 11: __C201Compiled.__m206read_fields_group_0 2020-10-01 13:22:26 root: INFO: instruction count: 34: __C201Compiled.__m207INPLACE_DECODE_r_binary_TO_r_binary 2020-10-01 13:22:26 root: INFO: instruction count: 41: __C201Compiled.addLiterals 2020-10-01 13:22:27 Hail: INFO: logistic_regression_rows: running wald on 37652 samples for response variable y, with input variable x, and 2 additional covariates... 2020-10-01 13:22:27 JniLoader: INFO: successfully loaded /tmp/jniloader41302633382189116netlib-native_system-linux-x86_64.so