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2021-07-29 13:36:32 Hail: INFO: Running Hail version 0.2.61-3c86d3ba497a
2021-07-29 13:36:32 SparkContext: WARN: Using an existing SparkContext; some configuration may not take effect.
2021-07-29 13:36:33 root: INFO: RegionPool: initialized for thread 17: Thread-5
2021-07-29 13:36:33 MemoryStore: INFO: Block broadcast_0 stored as values in memory (estimated size 34.9 KB, free 366.3 MB)
2021-07-29 13:36:33 MemoryStore: INFO: Block broadcast_0_piece0 stored as bytes in memory (estimated size 3.2 KB, free 366.3 MB)
2021-07-29 13:36:33 BlockManagerInfo: INFO: Added broadcast_0_piece0 in memory on c20n02.ruddle.hpc.yale.internal:39864 (size: 3.2 KB, free: 366.3 MB)
2021-07-29 13:36:33 SparkContext: INFO: Created broadcast 0 from broadcast at SparkBackend.scala:250
2021-07-29 13:36:33 root: INFO: timing SparkBackend.parse_matrix_ir total 589.772ms self 589.772ms children 0.000ms %children 0.00%
2021-07-29 13:36:33 root: INFO: timing SparkBackend.parse_value_ir total 138.222ms self 138.222ms children 0.000ms %children 0.00%
2021-07-29 13:36:33 root: INFO: starting execution of query hail_query_1 of initial size 4
2021-07-29 13:36:34 root: INFO: optimize optimize: relationalLowerer, initial IR: before: IR size 4:
(MakeArray Array[Interval[Locus(GRCh37)]]
(ApplySpecial LocusInterval ()
Interval[Locus(GRCh37)]
(Str "MT:5592-5655")
(False)))
2021-07-29 13:36:34 root: INFO: instruction count: 3: __C1Compiled.<init>
2021-07-29 13:36:34 root: INFO: instruction count: 319: __C1Compiled.apply
2021-07-29 13:36:34 root: INFO: instruction count: 10: __C1Compiled.__m15addIRIntermediate
2021-07-29 13:36:34 root: INFO: instruction count: 9: __C1Compiled.setPartitionIndex
2021-07-29 13:36:34 root: INFO: instruction count: 4: __C1Compiled.addPartitionRegion
2021-07-29 13:36:34 root: INFO: instruction count: 3: __C4RGContainer_GRCh37.<init>
2021-07-29 13:36:34 root: INFO: instruction count: 7: __C4RGContainer_GRCh37.<clinit>
2021-07-29 13:36:34 MemoryStore: INFO: Block broadcast_1 stored as values in memory (estimated size 34.9 KB, free 366.2 MB)
2021-07-29 13:36:34 MemoryStore: INFO: Block broadcast_1_piece0 stored as bytes in memory (estimated size 3.2 KB, free 366.2 MB)
2021-07-29 13:36:34 BlockManagerInfo: INFO: Added broadcast_1_piece0 in memory on c20n02.ruddle.hpc.yale.internal:39864 (size: 3.2 KB, free: 366.3 MB)
2021-07-29 13:36:34 SparkContext: INFO: Created broadcast 1 from broadcast at SparkBackend.scala:250
2021-07-29 13:36:34 root: INFO: optimize optimize: relationalLowerer, initial IR: after: IR size 1:
(Literal Array[Interval[Locus(GRCh37)]]
<literal value>)
2021-07-29 13:36:34 root: INFO: optimize optimize: relationalLowerer, after LowerMatrixToTable: before: IR size 1:
(Literal Array[Interval[Locus(GRCh37)]]
<literal value>)
2021-07-29 13:36:34 root: INFO: optimize optimize: relationalLowerer, after LowerMatrixToTable: after: IR size 1:
(Literal Array[Interval[Locus(GRCh37)]]
<literal value>)
2021-07-29 13:36:34 root: INFO: optimize optimize: relationalLowerer, after InterpretNonCompilable: before: IR size 1:
(Literal Array[Interval[Locus(GRCh37)]]
<literal value>)
2021-07-29 13:36:34 root: INFO: optimize optimize: relationalLowerer, after InterpretNonCompilable: after: IR size 1:
(Literal Array[Interval[Locus(GRCh37)]]
<literal value>)
2021-07-29 13:36:34 root: INFO: optimize optimize: compileLowerer, initial IR: before: IR size 2:
(MakeTuple (0)
(Literal Array[Interval[Locus(GRCh37)]]
<literal value>))
2021-07-29 13:36:34 root: INFO: optimize optimize: compileLowerer, initial IR: after: IR size 1:
(Literal Tuple[Array[Interval[Locus(GRCh37)]]]
<literal value>)
2021-07-29 13:36:34 root: INFO: optimize optimize: compileLowerer, after InlineApplyIR: before: IR size 1:
(Literal Tuple[Array[Interval[Locus(GRCh37)]]]
<literal value>)
2021-07-29 13:36:34 root: INFO: optimize optimize: compileLowerer, after InlineApplyIR: after: IR size 1:
(Literal Tuple[Array[Interval[Locus(GRCh37)]]]
<literal value>)
2021-07-29 13:36:34 root: INFO: optimize optimize: compileLowerer, after LowerArrayAggsToRunAggs: before: IR size 1:
(Literal Tuple[Array[Interval[Locus(GRCh37)]]]
<literal value>)
2021-07-29 13:36:34 root: INFO: optimize optimize: compileLowerer, after LowerArrayAggsToRunAggs: after: IR size 1:
(Literal Tuple[Array[Interval[Locus(GRCh37)]]]
<literal value>)
2021-07-29 13:36:34 root: INFO: encoder cache miss (0 hits, 1 misses, 0.000)
2021-07-29 13:36:34 root: INFO: instruction count: 3: __C30etypeEncode.<init>
2021-07-29 13:36:34 root: INFO: instruction count: 5: __C30etypeEncode.apply
2021-07-29 13:36:34 root: INFO: instruction count: 9: __C30etypeEncode.__m31ENCODE_r_tuple_of_r_tuple_of_r_array_of_r_interval_of_r_locusENDEND_TO_r_struct_of_r_struct_of_r_array_of_r_struct_of_r_struct_of_r_binaryANDr_int32ENDANDr_struct_of_r_binaryANDr_int32ENDANDr_boolANDr_boolENDENDEND
2021-07-29 13:36:34 root: INFO: instruction count: 13: __C30etypeEncode.__m32ENCODE_r_tuple_of_r_array_of_r_tuple_of_r_tuple_of_r_binaryANDr_int32ENDANDr_tuple_of_r_binaryANDr_int32ENDANDr_boolANDr_boolENDEND_TO_r_struct_of_r_array_of_r_struct_of_r_struct_of_r_binaryANDr_int32ENDANDr_struct_of_r_binaryANDr_int32ENDANDr_boolANDr_boolENDEND
2021-07-29 13:36:34 root: INFO: instruction count: 49: __C30etypeEncode.__m33ENCODE_r_array_of_r_tuple_of_r_tuple_of_r_binaryANDr_int32ENDANDr_tuple_of_r_binaryANDr_int32ENDANDr_boolANDr_boolEND_TO_r_array_of_r_struct_of_r_struct_of_r_binaryANDr_int32ENDANDr_struct_of_r_binaryANDr_int32ENDANDr_boolANDr_boolEND
2021-07-29 13:36:34 root: INFO: instruction count: 35: __C30etypeEncode.__m34ENCODE_r_tuple_of_r_tuple_of_r_binaryANDr_int32ENDANDr_tuple_of_r_binaryANDr_int32ENDANDr_boolANDr_boolEND_TO_r_struct_of_r_struct_of_r_binaryANDr_int32ENDANDr_struct_of_r_binaryANDr_int32ENDANDr_boolANDr_boolEND
2021-07-29 13:36:34 root: INFO: instruction count: 23: __C30etypeEncode.__m35ENCODE_r_tuple_of_r_binaryANDr_int32END_TO_r_struct_of_r_binaryANDr_int32END
2021-07-29 13:36:34 root: INFO: instruction count: 16: __C30etypeEncode.__m36ENCODE_r_binary_TO_r_binary
2021-07-29 13:36:34 root: INFO: instruction count: 4: __C30etypeEncode.__m37ENCODE_r_int32_TO_r_int32
2021-07-29 13:36:34 root: INFO: instruction count: 4: __C30etypeEncode.__m38ENCODE_r_bool_TO_r_bool
2021-07-29 13:36:34 MemoryStore: INFO: Block broadcast_2 stored as values in memory (estimated size 104.0 B, free 366.2 MB)
2021-07-29 13:36:34 MemoryStore: INFO: Block broadcast_2_piece0 stored as bytes in memory (estimated size 82.0 B, free 366.2 MB)
2021-07-29 13:36:34 BlockManagerInfo: INFO: Added broadcast_2_piece0 in memory on c20n02.ruddle.hpc.yale.internal:39864 (size: 82.0 B, free: 366.3 MB)
2021-07-29 13:36:34 SparkContext: INFO: Created broadcast 2 from broadcast at SparkBackend.scala:250
2021-07-29 13:36:34 root: INFO: instruction count: 3: __C18Compiled.<init>
2021-07-29 13:36:34 root: INFO: instruction count: 3: __C18Compiled.apply
2021-07-29 13:36:34 root: INFO: instruction count: 9: __C18Compiled.setPartitionIndex
2021-07-29 13:36:34 root: INFO: instruction count: 4: __C18Compiled.addPartitionRegion
2021-07-29 13:36:34 root: INFO: instruction count: 23: __C18Compiled.__m22DECODE_r_struct_of_r_struct_of_r_array_of_r_struct_of_r_struct_of_r_binaryANDr_int32ENDANDr_struct_of_r_binaryANDr_int32ENDANDr_boolANDr_boolENDENDEND_TO_r_tuple_of_r_tuple_of_r_array_of_r_interval_of_r_locusENDEND
2021-07-29 13:36:34 root: INFO: instruction count: 15: __C18Compiled.__m23INPLACE_DECODE_r_struct_of_r_array_of_r_struct_of_r_struct_of_r_binaryANDr_int32ENDANDr_struct_of_r_binaryANDr_int32ENDANDr_boolANDr_boolENDEND_TO_r_tuple_of_r_array_of_r_tuple_of_r_tuple_of_r_binaryANDr_int32ENDANDr_tuple_of_r_binaryANDr_int32ENDANDr_boolANDr_boolENDEND
2021-07-29 13:36:34 root: INFO: instruction count: 52: __C18Compiled.__m24INPLACE_DECODE_r_array_of_r_struct_of_r_struct_of_r_binaryANDr_int32ENDANDr_struct_of_r_binaryANDr_int32ENDANDr_boolANDr_boolEND_TO_r_array_of_r_tuple_of_r_tuple_of_r_binaryANDr_int32ENDANDr_tuple_of_r_binaryANDr_int32ENDANDr_boolANDr_boolEND
2021-07-29 13:36:34 root: INFO: instruction count: 36: __C18Compiled.__m25INPLACE_DECODE_r_struct_of_r_struct_of_r_binaryANDr_int32ENDANDr_struct_of_r_binaryANDr_int32ENDANDr_boolANDr_boolEND_TO_r_tuple_of_r_tuple_of_r_binaryANDr_int32ENDANDr_tuple_of_r_binaryANDr_int32ENDANDr_boolANDr_boolEND
2021-07-29 13:36:34 root: INFO: instruction count: 22: __C18Compiled.__m26INPLACE_DECODE_r_struct_of_r_binaryANDr_int32END_TO_r_tuple_of_r_binaryANDr_int32END
2021-07-29 13:36:34 root: INFO: instruction count: 31: __C18Compiled.__m27INPLACE_DECODE_r_binary_TO_r_binary
2021-07-29 13:36:34 root: INFO: instruction count: 8: __C18Compiled.__m28INPLACE_DECODE_r_int32_TO_r_int32
2021-07-29 13:36:34 root: INFO: instruction count: 8: __C18Compiled.__m29INPLACE_DECODE_r_bool_TO_r_bool
2021-07-29 13:36:34 root: INFO: instruction count: 32: __C18Compiled.addLiterals
2021-07-29 13:36:34 root: INFO: finished execution of query hail_query_1
2021-07-29 13:36:34 root: INFO: timing SparkBackend.executeJSON total 516.430ms self 41.971ms children 474.460ms %children 91.87%
2021-07-29 13:36:34 root: INFO: timing SparkBackend.executeJSON/optimize: relationalLowerer, initial IR total 377.892ms self 0.321ms children 377.571ms %children 99.91%
2021-07-29 13:36:34 root: INFO: timing SparkBackend.executeJSON/optimize: relationalLowerer, initial IR/Verify total 0.320ms self 0.320ms children 0.000ms %children 0.00%
2021-07-29 13:36:34 root: INFO: timing SparkBackend.executeJSON/optimize: relationalLowerer, initial IR/LoweringTransformation total 377.243ms self 111.065ms children 266.178ms %children 70.56%
2021-07-29 13:36:34 root: INFO: timing SparkBackend.executeJSON/optimize: relationalLowerer, initial IR/LoweringTransformation/Optimize total 266.178ms self 1.286ms children 264.892ms %children 99.52%
2021-07-29 13:36:34 root: INFO: timing SparkBackend.executeJSON/optimize: relationalLowerer, initial IR/LoweringTransformation/Optimize/FoldConstants total 243.047ms self 226.654ms children 16.393ms %children 6.74%
2021-07-29 13:36:34 root: INFO: timing SparkBackend.executeJSON/optimize: relationalLowerer, initial IR/LoweringTransformation/Optimize/FoldConstants/InlineApplyIR total 0.780ms self 0.235ms children 0.546ms %children 69.91%
2021-07-29 13:36:34 root: INFO: timing SparkBackend.executeJSON/optimize: relationalLowerer, initial IR/LoweringTransformation/Optimize/FoldConstants/InlineApplyIR/Verify total 0.240ms self 0.240ms children 0.000ms %children 0.00%
2021-07-29 13:36:34 root: INFO: timing SparkBackend.executeJSON/optimize: relationalLowerer, initial IR/LoweringTransformation/Optimize/FoldConstants/InlineApplyIR/LoweringTransformation total 0.271ms self 0.271ms children 0.000ms %children 0.00%
2021-07-29 13:36:34 root: INFO: timing SparkBackend.executeJSON/optimize: relationalLowerer, initial IR/LoweringTransformation/Optimize/FoldConstants/InlineApplyIR/Verify total 0.034ms self 0.034ms children 0.000ms %children 0.00%
2021-07-29 13:36:34 root: INFO: timing SparkBackend.executeJSON/optimize: relationalLowerer, initial IR/LoweringTransformation/Optimize/FoldConstants/LowerArrayAggsToRunAggs total 15.613ms self 0.014ms children 15.599ms %children 99.91%
2021-07-29 13:36:34 root: INFO: timing SparkBackend.executeJSON/optimize: relationalLowerer, initial IR/LoweringTransformation/Optimize/FoldConstants/LowerArrayAggsToRunAggs/Verify total 0.017ms self 0.017ms children 0.000ms %children 0.00%
2021-07-29 13:36:34 root: INFO: timing SparkBackend.executeJSON/optimize: relationalLowerer, initial IR/LoweringTransformation/Optimize/FoldConstants/LowerArrayAggsToRunAggs/LoweringTransformation total 15.393ms self 15.393ms children 0.000ms %children 0.00%
2021-07-29 13:36:34 root: INFO: timing SparkBackend.executeJSON/optimize: relationalLowerer, initial IR/LoweringTransformation/Optimize/FoldConstants/LowerArrayAggsToRunAggs/Verify total 0.189ms self 0.189ms children 0.000ms %children 0.00%
2021-07-29 13:36:34 root: INFO: timing SparkBackend.executeJSON/optimize: relationalLowerer, initial IR/LoweringTransformation/Optimize/ExtractIntervalFilters total 1.946ms self 1.946ms children 0.000ms %children 0.00%
2021-07-29 13:36:34 root: INFO: timing SparkBackend.executeJSON/optimize: relationalLowerer, initial IR/LoweringTransformation/Optimize/Simplify total 5.912ms self 5.912ms children 0.000ms %children 0.00%
2021-07-29 13:36:34 root: INFO: timing SparkBackend.executeJSON/optimize: relationalLowerer, initial IR/LoweringTransformation/Optimize/ForwardLets total 2.052ms self 2.052ms children 0.000ms %children 0.00%
2021-07-29 13:36:34 root: INFO: timing SparkBackend.executeJSON/optimize: relationalLowerer, initial IR/LoweringTransformation/Optimize/ForwardRelationalLets total 1.396ms self 1.396ms children 0.000ms %children 0.00%
2021-07-29 13:36:34 root: INFO: timing SparkBackend.executeJSON/optimize: relationalLowerer, initial IR/LoweringTransformation/Optimize/PruneDeadFields total 10.348ms self 10.348ms children 0.000ms %children 0.00%
2021-07-29 13:36:34 root: INFO: timing SparkBackend.executeJSON/optimize: relationalLowerer, initial IR/LoweringTransformation/Optimize/FoldConstants total 0.048ms self 0.048ms children 0.000ms %children 0.00%
2021-07-29 13:36:34 root: INFO: timing SparkBackend.executeJSON/optimize: relationalLowerer, initial IR/LoweringTransformation/Optimize/ExtractIntervalFilters total 0.006ms self 0.006ms children 0.000ms %children 0.00%
2021-07-29 13:36:34 root: INFO: timing SparkBackend.executeJSON/optimize: relationalLowerer, initial IR/LoweringTransformation/Optimize/Simplify total 0.014ms self 0.014ms children 0.000ms %children 0.00%
2021-07-29 13:36:34 root: INFO: timing SparkBackend.executeJSON/optimize: relationalLowerer, initial IR/LoweringTransformation/Optimize/ForwardLets total 0.078ms self 0.078ms children 0.000ms %children 0.00%
2021-07-29 13:36:34 root: INFO: timing SparkBackend.executeJSON/optimize: relationalLowerer, initial IR/LoweringTransformation/Optimize/ForwardRelationalLets total 0.017ms self 0.017ms children 0.000ms %children 0.00%
2021-07-29 13:36:34 root: INFO: timing SparkBackend.executeJSON/optimize: relationalLowerer, initial IR/LoweringTransformation/Optimize/PruneDeadFields total 0.028ms self 0.028ms children 0.000ms %children 0.00%
2021-07-29 13:36:34 root: INFO: timing SparkBackend.executeJSON/optimize: relationalLowerer, initial IR/Verify total 0.007ms self 0.007ms children 0.000ms %children 0.00%
2021-07-29 13:36:34 root: INFO: timing SparkBackend.executeJSON/LowerMatrixToTable total 6.340ms self 0.013ms children 6.326ms %children 99.79%
2021-07-29 13:36:34 root: INFO: timing SparkBackend.executeJSON/LowerMatrixToTable/Verify total 0.003ms self 0.003ms children 0.000ms %children 0.00%
2021-07-29 13:36:34 root: INFO: timing SparkBackend.executeJSON/LowerMatrixToTable/LoweringTransformation total 6.313ms self 6.313ms children 0.000ms %children 0.00%
2021-07-29 13:36:34 root: INFO: timing SparkBackend.executeJSON/LowerMatrixToTable/Verify total 0.010ms self 0.010ms children 0.000ms %children 0.00%
2021-07-29 13:36:34 root: INFO: timing SparkBackend.executeJSON/optimize: relationalLowerer, after LowerMatrixToTable total 0.619ms self 0.011ms children 0.608ms %children 98.20%
2021-07-29 13:36:34 root: INFO: timing SparkBackend.executeJSON/optimize: relationalLowerer, after LowerMatrixToTable/Verify total 0.002ms self 0.002ms children 0.000ms %children 0.00%
2021-07-29 13:36:34 root: INFO: timing SparkBackend.executeJSON/optimize: relationalLowerer, after LowerMatrixToTable/LoweringTransformation total 0.602ms self 0.385ms children 0.217ms %children 36.04%
2021-07-29 13:36:34 root: INFO: timing SparkBackend.executeJSON/optimize: relationalLowerer, after LowerMatrixToTable/LoweringTransformation/Optimize total 0.217ms self 0.034ms children 0.183ms %children 84.55%
2021-07-29 13:36:34 root: INFO: timing SparkBackend.executeJSON/optimize: relationalLowerer, after LowerMatrixToTable/LoweringTransformation/Optimize/FoldConstants total 0.041ms self 0.041ms children 0.000ms %children 0.00%
2021-07-29 13:36:34 root: INFO: timing SparkBackend.executeJSON/optimize: relationalLowerer, after LowerMatrixToTable/LoweringTransformation/Optimize/ExtractIntervalFilters total 0.007ms self 0.007ms children 0.000ms %children 0.00%
2021-07-29 13:36:34 root: INFO: timing SparkBackend.executeJSON/optimize: relationalLowerer, after LowerMatrixToTable/LoweringTransformation/Optimize/Simplify total 0.015ms self 0.015ms children 0.000ms %children 0.00%
2021-07-29 13:36:34 root: INFO: timing SparkBackend.executeJSON/optimize: relationalLowerer, after LowerMatrixToTable/LoweringTransformation/Optimize/ForwardLets total 0.072ms self 0.072ms children 0.000ms %children 0.00%
2021-07-29 13:36:34 root: INFO: timing SparkBackend.executeJSON/optimize: relationalLowerer, after LowerMatrixToTable/LoweringTransformation/Optimize/ForwardRelationalLets total 0.013ms self 0.013ms children 0.000ms %children 0.00%
2021-07-29 13:36:34 root: INFO: timing SparkBackend.executeJSON/optimize: relationalLowerer, after LowerMatrixToTable/LoweringTransformation/Optimize/PruneDeadFields total 0.035ms self 0.035ms children 0.000ms %children 0.00%
2021-07-29 13:36:34 root: INFO: timing SparkBackend.executeJSON/optimize: relationalLowerer, after LowerMatrixToTable/Verify total 0.003ms self 0.003ms children 0.000ms %children 0.00%
2021-07-29 13:36:34 root: INFO: timing SparkBackend.executeJSON/InterpretNonCompilable total 1.034ms self 0.012ms children 1.022ms %children 98.85%
2021-07-29 13:36:34 root: INFO: timing SparkBackend.executeJSON/InterpretNonCompilable/Verify total 0.003ms self 0.003ms children 0.000ms %children 0.00%
2021-07-29 13:36:34 root: INFO: timing SparkBackend.executeJSON/InterpretNonCompilable/LoweringTransformation total 1.011ms self 1.011ms children 0.000ms %children 0.00%
2021-07-29 13:36:34 root: INFO: timing SparkBackend.executeJSON/InterpretNonCompilable/Verify total 0.008ms self 0.008ms children 0.000ms %children 0.00%
2021-07-29 13:36:34 root: INFO: timing SparkBackend.executeJSON/optimize: relationalLowerer, after InterpretNonCompilable total 0.649ms self 0.011ms children 0.638ms %children 98.33%
2021-07-29 13:36:34 root: INFO: timing SparkBackend.executeJSON/optimize: relationalLowerer, after InterpretNonCompilable/Verify total 0.002ms self 0.002ms children 0.000ms %children 0.00%
2021-07-29 13:36:34 root: INFO: timing SparkBackend.executeJSON/optimize: relationalLowerer, after InterpretNonCompilable/LoweringTransformation total 0.633ms self 0.422ms children 0.211ms %children 33.28%
2021-07-29 13:36:34 root: INFO: timing SparkBackend.executeJSON/optimize: relationalLowerer, after InterpretNonCompilable/LoweringTransformation/Optimize total 0.211ms self 0.024ms children 0.187ms %children 88.75%
2021-07-29 13:36:34 root: INFO: timing SparkBackend.executeJSON/optimize: relationalLowerer, after InterpretNonCompilable/LoweringTransformation/Optimize/FoldConstants total 0.041ms self 0.041ms children 0.000ms %children 0.00%
2021-07-29 13:36:34 root: INFO: timing SparkBackend.executeJSON/optimize: relationalLowerer, after InterpretNonCompilable/LoweringTransformation/Optimize/ExtractIntervalFilters total 0.007ms self 0.007ms children 0.000ms %children 0.00%
2021-07-29 13:36:34 root: INFO: timing SparkBackend.executeJSON/optimize: relationalLowerer, after InterpretNonCompilable/LoweringTransformation/Optimize/Simplify total 0.014ms self 0.014ms children 0.000ms %children 0.00%
2021-07-29 13:36:34 root: INFO: timing SparkBackend.executeJSON/optimize: relationalLowerer, after InterpretNonCompilable/LoweringTransformation/Optimize/ForwardLets total 0.083ms self 0.083ms children 0.000ms %children 0.00%
2021-07-29 13:36:34 root: INFO: timing SparkBackend.executeJSON/optimize: relationalLowerer, after InterpretNonCompilable/LoweringTransformation/Optimize/ForwardRelationalLets total 0.014ms self 0.014ms children 0.000ms %children 0.00%
2021-07-29 13:36:34 root: INFO: timing SparkBackend.executeJSON/optimize: relationalLowerer, after InterpretNonCompilable/LoweringTransformation/Optimize/PruneDeadFields total 0.027ms self 0.027ms children 0.000ms %children 0.00%
2021-07-29 13:36:34 root: INFO: timing SparkBackend.executeJSON/optimize: relationalLowerer, after InterpretNonCompilable/Verify total 0.003ms self 0.003ms children 0.000ms %children 0.00%
2021-07-29 13:36:34 root: INFO: timing SparkBackend.executeJSON/Compile total 79.120ms self 69.325ms children 9.795ms %children 12.38%
2021-07-29 13:36:34 root: INFO: timing SparkBackend.executeJSON/Compile/optimize: compileLowerer, initial IR total 7.552ms self 0.034ms children 7.517ms %children 99.55%
2021-07-29 13:36:34 root: INFO: timing SparkBackend.executeJSON/Compile/optimize: compileLowerer, initial IR/Verify total 0.005ms self 0.005ms children 0.000ms %children 0.00%
2021-07-29 13:36:34 root: INFO: timing SparkBackend.executeJSON/Compile/optimize: compileLowerer, initial IR/LoweringTransformation total 7.509ms self 6.793ms children 0.716ms %children 9.53%
2021-07-29 13:36:34 root: INFO: timing SparkBackend.executeJSON/Compile/optimize: compileLowerer, initial IR/LoweringTransformation/Optimize total 0.716ms self 0.059ms children 0.657ms %children 91.80%
2021-07-29 13:36:34 root: INFO: timing SparkBackend.executeJSON/Compile/optimize: compileLowerer, initial IR/LoweringTransformation/Optimize/FoldConstants total 0.360ms self 0.360ms children 0.000ms %children 0.00%
2021-07-29 13:36:34 root: INFO: timing SparkBackend.executeJSON/Compile/optimize: compileLowerer, initial IR/LoweringTransformation/Optimize/ExtractIntervalFilters total 0.007ms self 0.007ms children 0.000ms %children 0.00%
2021-07-29 13:36:34 root: INFO: timing SparkBackend.executeJSON/Compile/optimize: compileLowerer, initial IR/LoweringTransformation/Optimize/Simplify total 0.015ms self 0.015ms children 0.000ms %children 0.00%
2021-07-29 13:36:34 root: INFO: timing SparkBackend.executeJSON/Compile/optimize: compileLowerer, initial IR/LoweringTransformation/Optimize/ForwardLets total 0.071ms self 0.071ms children 0.000ms %children 0.00%
2021-07-29 13:36:34 root: INFO: timing SparkBackend.executeJSON/Compile/optimize: compileLowerer, initial IR/LoweringTransformation/Optimize/ForwardRelationalLets total 0.013ms self 0.013ms children 0.000ms %children 0.00%
2021-07-29 13:36:34 root: INFO: timing SparkBackend.executeJSON/Compile/optimize: compileLowerer, initial IR/LoweringTransformation/Optimize/PruneDeadFields total 0.028ms self 0.028ms children 0.000ms %children 0.00%
2021-07-29 13:36:34 root: INFO: timing SparkBackend.executeJSON/Compile/optimize: compileLowerer, initial IR/LoweringTransformation/Optimize/FoldConstants total 0.039ms self 0.039ms children 0.000ms %children 0.00%
2021-07-29 13:36:34 root: INFO: timing SparkBackend.executeJSON/Compile/optimize: compileLowerer, initial IR/LoweringTransformation/Optimize/ExtractIntervalFilters total 0.006ms self 0.006ms children 0.000ms %children 0.00%
2021-07-29 13:36:34 root: INFO: timing SparkBackend.executeJSON/Compile/optimize: compileLowerer, initial IR/LoweringTransformation/Optimize/Simplify total 0.015ms self 0.015ms children 0.000ms %children 0.00%
2021-07-29 13:36:34 root: INFO: timing SparkBackend.executeJSON/Compile/optimize: compileLowerer, initial IR/LoweringTransformation/Optimize/ForwardLets total 0.063ms self 0.063ms children 0.000ms %children 0.00%
2021-07-29 13:36:34 root: INFO: timing SparkBackend.executeJSON/Compile/optimize: compileLowerer, initial IR/LoweringTransformation/Optimize/ForwardRelationalLets total 0.013ms self 0.013ms children 0.000ms %children 0.00%
2021-07-29 13:36:34 root: INFO: timing SparkBackend.executeJSON/Compile/optimize: compileLowerer, initial IR/LoweringTransformation/Optimize/PruneDeadFields total 0.028ms self 0.028ms children 0.000ms %children 0.00%
2021-07-29 13:36:34 root: INFO: timing SparkBackend.executeJSON/Compile/optimize: compileLowerer, initial IR/Verify total 0.004ms self 0.004ms children 0.000ms %children 0.00%
2021-07-29 13:36:34 root: INFO: timing SparkBackend.executeJSON/Compile/InlineApplyIR total 0.036ms self 0.006ms children 0.030ms %children 82.79%
2021-07-29 13:36:34 root: INFO: timing SparkBackend.executeJSON/Compile/InlineApplyIR/Verify total 0.005ms self 0.005ms children 0.000ms %children 0.00%
2021-07-29 13:36:34 root: INFO: timing SparkBackend.executeJSON/Compile/InlineApplyIR/LoweringTransformation total 0.020ms self 0.020ms children 0.000ms %children 0.00%
2021-07-29 13:36:34 root: INFO: timing SparkBackend.executeJSON/Compile/InlineApplyIR/Verify total 0.005ms self 0.005ms children 0.000ms %children 0.00%
2021-07-29 13:36:34 root: INFO: timing SparkBackend.executeJSON/Compile/optimize: compileLowerer, after InlineApplyIR total 0.626ms self 0.009ms children 0.617ms %children 98.55%
2021-07-29 13:36:34 root: INFO: timing SparkBackend.executeJSON/Compile/optimize: compileLowerer, after InlineApplyIR/Verify total 0.002ms self 0.002ms children 0.000ms %children 0.00%
2021-07-29 13:36:34 root: INFO: timing SparkBackend.executeJSON/Compile/optimize: compileLowerer, after InlineApplyIR/LoweringTransformation total 0.612ms self 0.414ms children 0.198ms %children 32.32%
2021-07-29 13:36:34 root: INFO: timing SparkBackend.executeJSON/Compile/optimize: compileLowerer, after InlineApplyIR/LoweringTransformation/Optimize total 0.198ms self 0.020ms children 0.178ms %children 90.06%
2021-07-29 13:36:34 root: INFO: timing SparkBackend.executeJSON/Compile/optimize: compileLowerer, after InlineApplyIR/LoweringTransformation/Optimize/FoldConstants total 0.043ms self 0.043ms children 0.000ms %children 0.00%
2021-07-29 13:36:34 root: INFO: timing SparkBackend.executeJSON/Compile/optimize: compileLowerer, after InlineApplyIR/LoweringTransformation/Optimize/ExtractIntervalFilters total 0.008ms self 0.008ms children 0.000ms %children 0.00%
2021-07-29 13:36:34 root: INFO: timing SparkBackend.executeJSON/Compile/optimize: compileLowerer, after InlineApplyIR/LoweringTransformation/Optimize/Simplify total 0.015ms self 0.015ms children 0.000ms %children 0.00%
2021-07-29 13:36:34 root: INFO: timing SparkBackend.executeJSON/Compile/optimize: compileLowerer, after InlineApplyIR/LoweringTransformation/Optimize/ForwardLets total 0.072ms self 0.072ms children 0.000ms %children 0.00%
2021-07-29 13:36:34 root: INFO: timing SparkBackend.executeJSON/Compile/optimize: compileLowerer, after InlineApplyIR/LoweringTransformation/Optimize/ForwardRelationalLets total 0.013ms self 0.013ms children 0.000ms %children 0.00%
2021-07-29 13:36:34 root: INFO: timing SparkBackend.executeJSON/Compile/optimize: compileLowerer, after InlineApplyIR/LoweringTransformation/Optimize/PruneDeadFields total 0.027ms self 0.027ms children 0.000ms %children 0.00%
2021-07-29 13:36:34 root: INFO: timing SparkBackend.executeJSON/Compile/optimize: compileLowerer, after InlineApplyIR/Verify total 0.003ms self 0.003ms children 0.000ms %children 0.00%
2021-07-29 13:36:34 root: INFO: timing SparkBackend.executeJSON/Compile/LowerArrayAggsToRunAggs total 0.945ms self 0.009ms children 0.936ms %children 99.04%
2021-07-29 13:36:34 root: INFO: timing SparkBackend.executeJSON/Compile/LowerArrayAggsToRunAggs/Verify total 0.005ms self 0.005ms children 0.000ms %children 0.00%
2021-07-29 13:36:34 root: INFO: timing SparkBackend.executeJSON/Compile/LowerArrayAggsToRunAggs/LoweringTransformation total 0.924ms self 0.924ms children 0.000ms %children 0.00%
2021-07-29 13:36:34 root: INFO: timing SparkBackend.executeJSON/Compile/LowerArrayAggsToRunAggs/Verify total 0.007ms self 0.007ms children 0.000ms %children 0.00%
2021-07-29 13:36:34 root: INFO: timing SparkBackend.executeJSON/Compile/optimize: compileLowerer, after LowerArrayAggsToRunAggs total 0.636ms self 0.009ms children 0.627ms %children 98.53%
2021-07-29 13:36:34 root: INFO: timing SparkBackend.executeJSON/Compile/optimize: compileLowerer, after LowerArrayAggsToRunAggs/Verify total 0.002ms self 0.002ms children 0.000ms %children 0.00%
2021-07-29 13:36:34 root: INFO: timing SparkBackend.executeJSON/Compile/optimize: compileLowerer, after LowerArrayAggsToRunAggs/LoweringTransformation total 0.621ms self 0.428ms children 0.194ms %children 31.20%
2021-07-29 13:36:34 root: INFO: timing SparkBackend.executeJSON/Compile/optimize: compileLowerer, after LowerArrayAggsToRunAggs/LoweringTransformation/Optimize total 0.194ms self 0.020ms children 0.173ms %children 89.47%
2021-07-29 13:36:34 root: INFO: timing SparkBackend.executeJSON/Compile/optimize: compileLowerer, after LowerArrayAggsToRunAggs/LoweringTransformation/Optimize/FoldConstants total 0.040ms self 0.040ms children 0.000ms %children 0.00%
2021-07-29 13:36:34 root: INFO: timing SparkBackend.executeJSON/Compile/optimize: compileLowerer, after LowerArrayAggsToRunAggs/LoweringTransformation/Optimize/ExtractIntervalFilters total 0.008ms self 0.008ms children 0.000ms %children 0.00%
2021-07-29 13:36:34 root: INFO: timing SparkBackend.executeJSON/Compile/optimize: compileLowerer, after LowerArrayAggsToRunAggs/LoweringTransformation/Optimize/Simplify total 0.014ms self 0.014ms children 0.000ms %children 0.00%
2021-07-29 13:36:34 root: INFO: timing SparkBackend.executeJSON/Compile/optimize: compileLowerer, after LowerArrayAggsToRunAggs/LoweringTransformation/Optimize/ForwardLets total 0.072ms self 0.072ms children 0.000ms %children 0.00%
2021-07-29 13:36:34 root: INFO: timing SparkBackend.executeJSON/Compile/optimize: compileLowerer, after LowerArrayAggsToRunAggs/LoweringTransformation/Optimize/ForwardRelationalLets total 0.013ms self 0.013ms children 0.000ms %children 0.00%
2021-07-29 13:36:34 root: INFO: timing SparkBackend.executeJSON/Compile/optimize: compileLowerer, after LowerArrayAggsToRunAggs/LoweringTransformation/Optimize/PruneDeadFields total 0.027ms self 0.027ms children 0.000ms %children 0.00%
2021-07-29 13:36:34 root: INFO: timing SparkBackend.executeJSON/Compile/optimize: compileLowerer, after LowerArrayAggsToRunAggs/Verify total 0.003ms self 0.003ms children 0.000ms %children 0.00%
2021-07-29 13:36:34 root: INFO: timing SparkBackend.executeJSON/InitializeCompiledFunction total 7.592ms self 7.592ms children 0.000ms %children 0.00%
2021-07-29 13:36:34 root: INFO: timing SparkBackend.executeJSON/RunCompiledFunction total 0.011ms self 0.011ms children 0.000ms %children 0.00%
2021-07-29 13:36:34 root: INFO: timing SparkBackend.executeJSON/convertRegionValueToAnnotation total 1.204ms self 1.204ms children 0.000ms %children 0.00%
2021-07-29 13:36:34 root: INFO: timing SparkBackend.parse_value_ir total 60.413ms self 60.413ms children 0.000ms %children 0.00%
2021-07-29 13:36:34 root: INFO: starting execution of query hail_query_2 of initial size 120
2021-07-29 13:36:34 root: INFO: optimize optimize: relationalLowerer, initial IR: before: IR size 120:
(TableWrite
"{\"name\":\"TableNativeWriter\",\"path\":\"/home/ml2529/scratch60/SFARI/finalized_callsets/read_viz_mito_variants.ht\",\"overwrite\":true,\"stageLocally\":false,\"codecSpecJSONStr\":null}"
(TableMapRows
(MatrixRowsTable
(MatrixMapRows
(MatrixMapEntries
(MatrixFilterIntervals
"[{\"start\":{\"locus\":{\"contig\":\"MT\",\"position\":5592}},\"end\":{\"locus\":{\"contig\":\"MT\",\"position\":5655}},\"includeStart\":true,\"includeEnd\":false}]"
True
(MatrixMapEntries
(MatrixMapEntries
(MatrixMapRows
(MatrixRead None False False
"{\"path\":\"/home/ml2529/scratch60/SFARI/finalized_callsets/combined_SPARK1_mito_callset.mt\",\"name\":\"MatrixNativeReader\"}")
(InsertFields
(SelectFields (locus alleles filters) (Ref va))
None
(filters
(ToSet
(ToStream False
(ToArray
(StreamMap __uid_3
(ToStream False
(CastToArray (GetField filters (Ref va))))
(Apply replace () String
(Ref __uid_3)
(Str "-")
(Str "_")))))))))
(InsertFields
(SelectFields (DP HL MQ TLOD FT) (Ref g))
None
(FT
(Apply split () Array[String]
(ApplyIR slice () String
(Apply str () String (GetField FT (Ref g)))
(I32 2)
(I32 -2))
(Str ";")))))
(Let __cse_1
(GetField HL (Ref g))
(InsertFields
(SelectFields (DP HL MQ TLOD FT) (Ref g))
None
(GT
(If
(ApplySpecial land () Boolean
(ApplyComparisonOp LT (Ref __cse_1) (F64 0.95))
(ApplyComparisonOp GT (Ref __cse_1) (F64 0.0)))
(Apply Call () Call (Str "0/1"))
(If
(ApplyComparisonOp GTEQ
(GetField HL (Ref g))
(F64 0.95))
(Apply Call () Call (Str "1/1"))
(If
(ApplyComparisonOp EQ
(GetField HL (Ref g))
(ApplyIR toFloat64 () Float64 (I32 0)))
(Apply Call () Call (Str "0/0"))
(NA Call)))))))))
(InsertFields
(SelectFields (GT HL DP)
(SelectFields (DP HL MQ TLOD FT GT) (Ref g)))
None))
(AggLet __cse_3 False
(GetField GT (Ref g))
(AggLet __cse_4 False
(GetField s (Ref sa))
(AggLet __cse_2 False
(GetField HL (Ref g))
(InsertFields
(SelectFields (locus alleles filters) (Ref va))
None
(samples_w_het_var
(AggFilter False
(Apply isHet () Boolean (Ref __cse_3))
(ApplyAggOp TakeBy
((I32 3))
((MakeStruct (S (Ref __cse_4)) (HL (Ref __cse_2)))
(MakeTuple (0 1)
(ApplyUnaryPrimOp Negate (Ref __cse_2))
(ApplySeeded rand_unif 1 Float64
(ApplyIR toFloat64 () Float64 (I32 0))
(ApplyIR toFloat64 () Float64 (I32 1))))))))
(samples_w_hom_var
(AggFilter False
(Apply isHomVar () Boolean (Ref __cse_3))
(ApplyAggOp TakeBy
((I32 3))
((MakeStruct (S (Ref __cse_4)) (HL (Ref __cse_2)))
(MakeTuple (0 1)
(ApplyUnaryPrimOp Negate (Ref __cse_2))
(ApplySeeded rand_unif 1 Float64
(ApplyIR toFloat64 () Float64 (I32 0))
(ApplyIR toFloat64 () Float64 (I32 1))))))))))))))
(InsertFields
(SelectFields
(locus alleles samples_w_het_var
samples_w_hom_var)
(SelectFields
(locus alleles filters samples_w_het_var
samples_w_hom_var)
(Ref row)))
None)))
2021-07-29 13:36:34 root: INFO: instruction count: 3: __C39Compiled.<init>
2021-07-29 13:36:34 root: INFO: instruction count: 57: __C39Compiled.apply
2021-07-29 13:36:34 root: INFO: instruction count: 24: __C39Compiled.__m42Call
2021-07-29 13:36:34 root: INFO: instruction count: 5: __C39Compiled.__m43addIRIntermediate
2021-07-29 13:36:34 root: INFO: instruction count: 9: __C39Compiled.setPartitionIndex
2021-07-29 13:36:34 root: INFO: instruction count: 4: __C39Compiled.addPartitionRegion
2021-07-29 13:36:34 root: INFO: Prune: InsertFields: eliminating field 'filters'
2021-07-29 13:36:34 root: INFO: Prune: InsertFields: eliminating field 'FT'
2021-07-29 13:36:34 root: INFO: optimize optimize: relationalLowerer, initial IR: after: IR size 75:
(TableWrite
"{\"name\":\"TableNativeWriter\",\"path\":\"/home/ml2529/scratch60/SFARI/finalized_callsets/read_viz_mito_variants.ht\",\"overwrite\":true,\"stageLocally\":false,\"codecSpecJSONStr\":null}"
(MatrixRowsTable
(MatrixMapRows
(MatrixMapEntries
(MatrixFilterIntervals
"[{\"start\":{\"locus\":{\"contig\":\"MT\",\"position\":5592}},\"end\":{\"locus\":{\"contig\":\"MT\",\"position\":5655}},\"includeStart\":true,\"includeEnd\":false}]"
True
(MatrixMapEntries
(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{HL:Float64}}
False False
"{\"path\":\"/home/ml2529/scratch60/SFARI/finalized_callsets/combined_SPARK1_mito_callset.mt\",\"name\":\"MatrixNativeReader\"}")
(Let __iruid_55
(GetField HL (Ref g))
(InsertFields
(Ref g)
("HL" "GT")
(GT
(If
(ApplySpecial land () Boolean
(ApplyComparisonOp LT (Ref __iruid_55) (F64 0.95))
(ApplyComparisonOp GT (Ref __iruid_55) (F64 0.0)))
(Literal Call <literal value>)
(If
(ApplyComparisonOp GTEQ
(GetField HL (Ref g))
(F64 0.95))
(Literal Call <literal value>)
(If
(ApplyComparisonOp EQ
(GetField HL (Ref g))
(F64 0.0))
(Literal Call <literal value>)
(NA Call)))))))))
(SelectFields (GT HL) (Ref g)))
(AggLet __iruid_56 False
(GetField GT (Ref g))
(AggLet __iruid_57 False
(GetField s (Ref sa))
(AggLet __iruid_58 False
(GetField HL (Ref g))
(InsertFields
(Ref va)
None
(samples_w_het_var
(AggFilter False
(Apply isHet () Boolean (Ref __iruid_56))
(ApplyAggOp TakeBy
((I32 3))
((MakeStruct
(S (Ref __iruid_57))
(HL (Ref __iruid_58)))
(MakeTuple (0 1)
(ApplyUnaryPrimOp Negate (Ref __iruid_58))
(ApplySeeded rand_unif 1 Float64
(F64 0.0)
(F64 1.0)))))))
(samples_w_hom_var
(AggFilter False
(Apply isHomVar () Boolean (Ref __iruid_56))
(ApplyAggOp TakeBy
((I32 3))
((MakeStruct
(S (Ref __iruid_57))
(HL (Ref __iruid_58)))
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2021-07-29 13:36:34 root: INFO: Prune: InsertFields: eliminating field 'the entries! [877f12a8827e18f61222c6c8c5fb04a8]'
2021-07-29 13:36:34 root: INFO: optimize optimize: relationalLowerer, after LowerMatrixToTable: after: IR size 108:
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(InsertFields
(Ref global)
None
(__cols
(ToArray
(ReadPartition Struct{s:String}
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(Str "/home/ml25..."))))))
(Let __iruid_107
(ToArray
(StreamMap __iruid_108
(ToStream False
(GetField
`the entries! [877f12a8827e18f61222c6c8c5fb04a8]`
(Ref row)))
(Let __iruid_109
(GetField HL (Ref __iruid_108))
(InsertFields
(Ref __iruid_108)
("GT" "HL")
(GT
(If
(ApplySpecial land () Boolean
(ApplyComparisonOp LT
(Ref __iruid_109)
(F64 0.95))
(ApplyComparisonOp GT
(Ref __iruid_109)
(F64 0.0)))
(Literal Call <literal value>)
(If
(ApplyComparisonOp GTEQ
(GetField HL (Ref __iruid_108))
(F64 0.95))
(Literal Call <literal value>)
(If
(ApplyComparisonOp EQ
(GetField HL (Ref __iruid_108))
(F64 0.0))
(Literal Call <literal value>)
(NA Call)))))))))
(StreamAgg __iruid_110
(StreamFilter __iruid_111
(StreamRange False
(I32 0)
(ArrayLen (Ref __iruid_107))
(I32 1))
(ApplyUnaryPrimOp Bang
(IsNA
(ArrayRef
(Ref __iruid_107)
(Ref __iruid_111)
(Str "")))))
(AggLet __iruid_112 False
(ArrayRef
(Ref __iruid_107)
(Ref __iruid_110)
(Str ""))
(AggLet __iruid_113 False
(GetField GT (Ref __iruid_112))
(AggLet __iruid_114 False
(GetField s
(ArrayRef
(GetField __cols (Ref global))
(Ref __iruid_110)
(Str "")))
(AggLet __iruid_115 False
(GetField HL (Ref __iruid_112))
(InsertFields
(SelectFields (locus alleles) (Ref row))
None
(samples_w_het_var
(AggFilter False
(Apply isHet () Boolean (Ref __iruid_113))
(ApplyAggOp TakeBy
((I32 3))
((MakeStruct
(S (Ref __iruid_114))
(HL (Ref __iruid_115)))
(MakeTuple (0 1)
(ApplyUnaryPrimOp Negate (Ref __iruid_115))
(ApplySeeded rand_unif 1 Float64
(F64 0.0)
(F64 1.0)))))))
(samples_w_hom_var
(AggFilter False
(Apply isHomVar () Boolean (Ref __iruid_113))
(ApplyAggOp TakeBy
((I32 3))
((MakeStruct
(S (Ref __iruid_114))
(HL (Ref __iruid_115)))
(MakeTuple (0 1)
(ApplyUnaryPrimOp Negate (Ref __iruid_115))
(ApplySeeded rand_unif 1 Float64
(F64 0.0)
(F64 1.0)))))))))))))))
(SelectFields () (Ref global))))
2021-07-29 13:36:34 root: INFO: interpreting non compilable node: TableWrite
2021-07-29 13:36:34 root: INFO: decoder cache miss (0 hits, 1 misses, 0.000
2021-07-29 13:36:34 root: INFO: instruction count: 3: __C46etypeDecode.<init>
2021-07-29 13:36:34 root: INFO: instruction count: 5: __C46etypeDecode.apply
2021-07-29 13:36:34 root: INFO: instruction count: 16: __C46etypeDecode.__m47DECODE_r_struct_of_END_TO_r_tuple_of_END
2021-07-29 13:36:34 root: INFO: decoder cache miss (0 hits, 2 misses, 0.000
2021-07-29 13:36:34 root: INFO: instruction count: 3: __C48etypeDecode.<init>
2021-07-29 13:36:34 root: INFO: instruction count: 5: __C48etypeDecode.apply
2021-07-29 13:36:34 root: INFO: instruction count: 34: __C48etypeDecode.__m49DECODE_r_struct_of_r_struct_of_r_binaryANDr_int32ENDANDr_array_of_r_binaryANDr_array_of_r_binaryEND_TO_r_tuple_of_r_locusANDr_array_of_r_stringEND
2021-07-29 13:36:34 root: INFO: instruction count: 22: __C48etypeDecode.__m50INPLACE_DECODE_r_struct_of_r_binaryANDr_int32END_TO_r_tuple_of_r_binaryANDr_int32END
2021-07-29 13:36:34 root: INFO: instruction count: 31: __C48etypeDecode.__m51INPLACE_DECODE_r_binary_TO_r_binary
2021-07-29 13:36:34 root: INFO: instruction count: 8: __C48etypeDecode.__m52INPLACE_DECODE_r_int32_TO_r_int32
2021-07-29 13:36:34 root: INFO: instruction count: 52: __C48etypeDecode.__m53INPLACE_DECODE_r_array_of_r_binary_TO_r_array_of_r_binary
2021-07-29 13:36:34 root: INFO: instruction count: 22: __C48etypeDecode.__m54SKIP_r_array_of_r_binary
2021-07-29 13:36:34 root: INFO: instruction count: 7: __C48etypeDecode.__m55SKIP_r_binary
2021-07-29 13:36:34 root: INFO: decoder cache miss (0 hits, 3 misses, 0.000
2021-07-29 13:36:34 root: INFO: instruction count: 3: __C56etypeDecode.<init>
2021-07-29 13:36:34 root: INFO: instruction count: 5: __C56etypeDecode.apply
2021-07-29 13:36:34 root: INFO: instruction count: 23: __C56etypeDecode.__m57DECODE_r_struct_of_r_array_of_o_struct_of_o_int32ANDo_float64ANDo_float64ANDo_float64ANDo_array_of_r_binaryENDEND_TO_r_tuple_of_r_array_of_o_tuple_of_o_float64ENDEND
2021-07-29 13:36:34 root: INFO: instruction count: 97: __C56etypeDecode.__m58INPLACE_DECODE_r_array_of_o_struct_of_o_int32ANDo_float64ANDo_float64ANDo_float64ANDo_array_of_r_binaryEND_TO_r_array_of_o_tuple_of_o_float64END
2021-07-29 13:36:34 root: INFO: instruction count: 98: __C56etypeDecode.__m59INPLACE_DECODE_o_struct_of_o_int32ANDo_float64ANDo_float64ANDo_float64ANDo_array_of_r_binaryEND_TO_o_tuple_of_o_float64END
2021-07-29 13:36:34 root: INFO: instruction count: 3: __C56etypeDecode.__m60SKIP_o_int32
2021-07-29 13:36:34 root: INFO: instruction count: 8: __C56etypeDecode.__m61INPLACE_DECODE_o_float64_TO_o_float64
2021-07-29 13:36:34 root: INFO: instruction count: 3: __C56etypeDecode.__m62SKIP_o_float64
2021-07-29 13:36:34 root: INFO: instruction count: 22: __C56etypeDecode.__m63SKIP_o_array_of_r_binary
2021-07-29 13:36:34 root: INFO: instruction count: 7: __C56etypeDecode.__m64SKIP_r_binary
2021-07-29 13:36:35 root: INFO: optimize optimize: compileLowerer, initial IR: before: IR size 4:
(InsertFields
(In
+PCStruct{locus:+PCLocus(GRCh37),alleles:+PCArray[+PCString]}
0)
None
(`the entries! [877f12a8827e18f61222c6c8c5fb04a8]`
(GetField
`the entries! [877f12a8827e18f61222c6c8c5fb04a8]`
(In
+PCStruct{`the entries! [877f12a8827e18f61222c6c8c5fb04a8]`:+PCArray[PCStruct{HL:PFloat64}]}
1))))
2021-07-29 13:36:35 root: INFO: optimize optimize: compileLowerer, initial IR: after: IR size 4:
(InsertFields
(In
+PCStruct{locus:+PCLocus(GRCh37),alleles:+PCArray[+PCString]}
0)
None
(`the entries! [877f12a8827e18f61222c6c8c5fb04a8]`
(GetField
`the entries! [877f12a8827e18f61222c6c8c5fb04a8]`
(In
+PCStruct{`the entries! [877f12a8827e18f61222c6c8c5fb04a8]`:+PCArray[PCStruct{HL:PFloat64}]}
1))))
2021-07-29 13:36:35 root: INFO: optimize optimize: compileLowerer, after InlineApplyIR: before: IR size 4:
(InsertFields
(In
+PCStruct{locus:+PCLocus(GRCh37),alleles:+PCArray[+PCString]}
0)
None
(`the entries! [877f12a8827e18f61222c6c8c5fb04a8]`
(GetField
`the entries! [877f12a8827e18f61222c6c8c5fb04a8]`
(In
+PCStruct{`the entries! [877f12a8827e18f61222c6c8c5fb04a8]`:+PCArray[PCStruct{HL:PFloat64}]}
1))))
2021-07-29 13:36:35 root: INFO: optimize optimize: compileLowerer, after InlineApplyIR: after: IR size 4:
(InsertFields
(In
+PCStruct{locus:+PCLocus(GRCh37),alleles:+PCArray[+PCString]}
0)
None
(`the entries! [877f12a8827e18f61222c6c8c5fb04a8]`
(GetField
`the entries! [877f12a8827e18f61222c6c8c5fb04a8]`
(In
+PCStruct{`the entries! [877f12a8827e18f61222c6c8c5fb04a8]`:+PCArray[PCStruct{HL:PFloat64}]}
1))))
2021-07-29 13:36:35 root: INFO: optimize optimize: compileLowerer, after LowerArrayAggsToRunAggs: before: IR size 4:
(InsertFields
(In
+PCStruct{locus:+PCLocus(GRCh37),alleles:+PCArray[+PCString]}
0)
None
(`the entries! [877f12a8827e18f61222c6c8c5fb04a8]`
(GetField
`the entries! [877f12a8827e18f61222c6c8c5fb04a8]`
(In
+PCStruct{`the entries! [877f12a8827e18f61222c6c8c5fb04a8]`:+PCArray[PCStruct{HL:PFloat64}]}
1))))
2021-07-29 13:36:35 root: INFO: optimize optimize: compileLowerer, after LowerArrayAggsToRunAggs: after: IR size 4:
(InsertFields
(In
+PCStruct{locus:+PCLocus(GRCh37),alleles:+PCArray[+PCString]}
0)
None
(`the entries! [877f12a8827e18f61222c6c8c5fb04a8]`
(GetField
`the entries! [877f12a8827e18f61222c6c8c5fb04a8]`
(In
+PCStruct{`the entries! [877f12a8827e18f61222c6c8c5fb04a8]`:+PCArray[PCStruct{HL:PFloat64}]}
1))))
2021-07-29 13:36:35 root: INFO: instruction count: 3: __C65Compiled.<init>
2021-07-29 13:36:35 root: INFO: instruction count: 68: __C65Compiled.apply
2021-07-29 13:36:35 root: INFO: instruction count: 10: __C65Compiled.__m69addIRIntermediate
2021-07-29 13:36:35 root: INFO: instruction count: 5: __C65Compiled.__m70addIRIntermediate
2021-07-29 13:36:35 root: INFO: instruction count: 5: __C65Compiled.__m71addIRIntermediate
2021-07-29 13:36:35 root: INFO: instruction count: 9: __C65Compiled.setPartitionIndex
2021-07-29 13:36:35 root: INFO: instruction count: 4: __C65Compiled.addPartitionRegion
2021-07-29 13:36:35 MemoryStore: INFO: Block broadcast_3 stored as values in memory (estimated size 237.3 KB, free 366.0 MB)
2021-07-29 13:36:35 MemoryStore: INFO: Block broadcast_3_piece0 stored as bytes in memory (estimated size 23.0 KB, free 366.0 MB)
2021-07-29 13:36:35 BlockManagerInfo: INFO: Added broadcast_3_piece0 in memory on c20n02.ruddle.hpc.yale.internal:39864 (size: 23.0 KB, free: 366.3 MB)
2021-07-29 13:36:35 SparkContext: INFO: Created broadcast 3 from broadcast at SparkBackend.scala:250
2021-07-29 13:36:35 root: INFO: decoder cache miss (0 hits, 4 misses, 0.000
2021-07-29 13:36:35 root: INFO: instruction count: 3: __C74etypeDecode.<init>
2021-07-29 13:36:35 root: INFO: instruction count: 5: __C74etypeDecode.apply
2021-07-29 13:36:35 root: INFO: instruction count: 30: __C74etypeDecode.__m75DECODE_o_struct_of_r_int64ANDr_array_of_r_struct_of_r_struct_of_r_struct_of_r_binaryANDr_int32ENDANDr_array_of_r_binaryENDANDr_int64ANDr_struct_of_o_int64ENDENDEND_TO_o_tuple_of_r_int64ANDr_array_of_r_tuple_of_r_tuple_of_r_locusANDr_array_of_r_stringENDANDr_int64ANDr_tuple_of_o_int64ENDENDEND
2021-07-29 13:36:35 root: INFO: instruction count: 8: __C74etypeDecode.__m76INPLACE_DECODE_r_int64_TO_r_int64
2021-07-29 13:36:35 root: INFO: instruction count: 52: __C74etypeDecode.__m77INPLACE_DECODE_r_array_of_r_struct_of_r_struct_of_r_struct_of_r_binaryANDr_int32ENDANDr_array_of_r_binaryENDANDr_int64ANDr_struct_of_o_int64ENDEND_TO_r_array_of_r_tuple_of_r_tuple_of_r_tuple_of_r_binaryANDr_int32ENDANDr_array_of_r_binaryENDANDr_int64ANDr_tuple_of_o_int64ENDEND
2021-07-29 13:36:35 root: INFO: instruction count: 29: __C74etypeDecode.__m78INPLACE_DECODE_r_struct_of_r_struct_of_r_struct_of_r_binaryANDr_int32ENDANDr_array_of_r_binaryENDANDr_int64ANDr_struct_of_o_int64ENDEND_TO_r_tuple_of_r_tuple_of_r_tuple_of_r_binaryANDr_int32ENDANDr_array_of_r_binaryENDANDr_int64ANDr_tuple_of_o_int64ENDEND
2021-07-29 13:36:35 root: INFO: instruction count: 22: __C74etypeDecode.__m79INPLACE_DECODE_r_struct_of_r_struct_of_r_binaryANDr_int32ENDANDr_array_of_r_binaryEND_TO_r_tuple_of_r_tuple_of_r_binaryANDr_int32ENDANDr_array_of_r_binaryEND
2021-07-29 13:36:35 root: INFO: instruction count: 22: __C74etypeDecode.__m80INPLACE_DECODE_r_struct_of_r_binaryANDr_int32END_TO_r_tuple_of_r_binaryANDr_int32END
2021-07-29 13:36:35 root: INFO: instruction count: 31: __C74etypeDecode.__m81INPLACE_DECODE_r_binary_TO_r_binary
2021-07-29 13:36:35 root: INFO: instruction count: 8: __C74etypeDecode.__m82INPLACE_DECODE_r_int32_TO_r_int32
2021-07-29 13:36:35 root: INFO: instruction count: 52: __C74etypeDecode.__m83INPLACE_DECODE_r_array_of_r_binary_TO_r_array_of_r_binary
2021-07-29 13:36:35 root: INFO: instruction count: 46: __C74etypeDecode.__m84INPLACE_DECODE_r_struct_of_o_int64END_TO_r_tuple_of_o_int64END
2021-07-29 13:36:35 root: INFO: instruction count: 8: __C74etypeDecode.__m85INPLACE_DECODE_o_int64_TO_o_int64
2021-07-29 13:36:35 root: INFO: decoder cache miss (0 hits, 5 misses, 0.000
2021-07-29 13:36:35 root: INFO: instruction count: 3: __C86etypeDecode.<init>
2021-07-29 13:36:35 root: INFO: instruction count: 5: __C86etypeDecode.apply
2021-07-29 13:36:35 root: INFO: instruction count: 23: __C86etypeDecode.__m87DECODE_o_struct_of_r_array_of_r_struct_of_r_int64ANDr_int64ANDr_struct_of_r_struct_of_r_binaryANDr_int32ENDANDr_array_of_r_binaryENDANDr_int64ANDr_struct_of_o_int64ENDENDEND_TO_o_tuple_of_r_array_of_r_tuple_of_r_int64ANDr_int64ANDr_tuple_of_r_locusANDr_array_of_r_stringENDANDr_int64ANDr_tuple_of_o_int64ENDENDEND
2021-07-29 13:36:35 root: INFO: instruction count: 52: __C86etypeDecode.__m88INPLACE_DECODE_r_array_of_r_struct_of_r_int64ANDr_int64ANDr_struct_of_r_struct_of_r_binaryANDr_int32ENDANDr_array_of_r_binaryENDANDr_int64ANDr_struct_of_o_int64ENDEND_TO_r_array_of_r_tuple_of_r_int64ANDr_int64ANDr_tuple_of_r_tuple_of_r_binaryANDr_int32ENDANDr_array_of_r_binaryENDANDr_int64ANDr_tuple_of_o_int64ENDEND
2021-07-29 13:36:35 root: INFO: instruction count: 43: __C86etypeDecode.__m89INPLACE_DECODE_r_struct_of_r_int64ANDr_int64ANDr_struct_of_r_struct_of_r_binaryANDr_int32ENDANDr_array_of_r_binaryENDANDr_int64ANDr_struct_of_o_int64ENDEND_TO_r_tuple_of_r_int64ANDr_int64ANDr_tuple_of_r_tuple_of_r_binaryANDr_int32ENDANDr_array_of_r_binaryENDANDr_int64ANDr_tuple_of_o_int64ENDEND
2021-07-29 13:36:35 root: INFO: instruction count: 8: __C86etypeDecode.__m90INPLACE_DECODE_r_int64_TO_r_int64
2021-07-29 13:36:35 root: INFO: instruction count: 22: __C86etypeDecode.__m91INPLACE_DECODE_r_struct_of_r_struct_of_r_binaryANDr_int32ENDANDr_array_of_r_binaryEND_TO_r_tuple_of_r_tuple_of_r_binaryANDr_int32ENDANDr_array_of_r_binaryEND
2021-07-29 13:36:35 root: INFO: instruction count: 22: __C86etypeDecode.__m92INPLACE_DECODE_r_struct_of_r_binaryANDr_int32END_TO_r_tuple_of_r_binaryANDr_int32END
2021-07-29 13:36:35 root: INFO: instruction count: 31: __C86etypeDecode.__m93INPLACE_DECODE_r_binary_TO_r_binary
2021-07-29 13:36:35 root: INFO: instruction count: 8: __C86etypeDecode.__m94INPLACE_DECODE_r_int32_TO_r_int32
2021-07-29 13:36:35 root: INFO: instruction count: 52: __C86etypeDecode.__m95INPLACE_DECODE_r_array_of_r_binary_TO_r_array_of_r_binary
2021-07-29 13:36:35 root: INFO: instruction count: 46: __C86etypeDecode.__m96INPLACE_DECODE_r_struct_of_o_int64END_TO_r_tuple_of_o_int64END
2021-07-29 13:36:35 root: INFO: instruction count: 8: __C86etypeDecode.__m97INPLACE_DECODE_o_int64_TO_o_int64
2021-07-29 13:36:35 MemoryStore: INFO: Block broadcast_4 stored as values in memory (estimated size 41.9 KB, free 365.9 MB)
2021-07-29 13:36:35 MemoryStore: INFO: Block broadcast_4_piece0 stored as bytes in memory (estimated size 1462.0 B, free 365.9 MB)
2021-07-29 13:36:35 BlockManagerInfo: INFO: Added broadcast_4_piece0 in memory on c20n02.ruddle.hpc.yale.internal:39864 (size: 1462.0 B, free: 366.3 MB)
2021-07-29 13:36:35 SparkContext: INFO: Created broadcast 4 from broadcast at RVDPartitioner.scala:93
2021-07-29 13:36:35 Hail: INFO: reading 1 of 101 data partitions
2021-07-29 13:36:35 root: INFO: optimize optimize: compileLowerer, initial IR: before: IR size 8:
(Coalesce
(InsertFields
(In +PCStruct{} 0)
None
(__cols
(ToArray
(ReadPartition Struct{s:String}
"{\"name\":\"PartitionNativeReader\",\"spec\":{\"name\":\"TypedCodecSpec\",\"_eType\":\"+EBaseStruct{s:+EBinary}\",\"_vType\":\"Struct{s:String}\",\"_bufferSpec\":{\"name\":\"LEB128BufferSpec\",\"child\":{\"name\":\"BlockingBufferSpec\",\"blockSize\":32768,\"child\":{\"name\":\"LZ4HCBlockBufferSpec\",\"blockSize\":32768,\"child\":{\"name\":\"StreamBlockBufferSpec\"}}}}}}"
(Str "/home/ml25...")))))
(Die Struct{__cols:Array[Struct{s:String}]} -1
(Str "Internal e...")))
2021-07-29 13:36:35 root: INFO: optimize optimize: compileLowerer, initial IR: after: IR size 8:
(Coalesce
(InsertFields
(In +PCStruct{} 0)
None
(__cols
(ToArray
(ReadPartition Struct{s:String}
"{\"name\":\"PartitionNativeReader\",\"spec\":{\"name\":\"TypedCodecSpec\",\"_eType\":\"+EBaseStruct{s:+EBinary}\",\"_vType\":\"Struct{s:String}\",\"_bufferSpec\":{\"name\":\"LEB128BufferSpec\",\"child\":{\"name\":\"BlockingBufferSpec\",\"blockSize\":32768,\"child\":{\"name\":\"LZ4HCBlockBufferSpec\",\"blockSize\":32768,\"child\":{\"name\":\"StreamBlockBufferSpec\"}}}}}}"
(Str "/home/ml25...")))))
(Die Struct{__cols:Array[Struct{s:String}]} -1
(Str "Internal e...")))
2021-07-29 13:36:35 root: INFO: optimize optimize: compileLowerer, after InlineApplyIR: before: IR size 8:
(Coalesce
(InsertFields
(In +PCStruct{} 0)
None
(__cols
(ToArray
(ReadPartition Struct{s:String}
"{\"name\":\"PartitionNativeReader\",\"spec\":{\"name\":\"TypedCodecSpec\",\"_eType\":\"+EBaseStruct{s:+EBinary}\",\"_vType\":\"Struct{s:String}\",\"_bufferSpec\":{\"name\":\"LEB128BufferSpec\",\"child\":{\"name\":\"BlockingBufferSpec\",\"blockSize\":32768,\"child\":{\"name\":\"LZ4HCBlockBufferSpec\",\"blockSize\":32768,\"child\":{\"name\":\"StreamBlockBufferSpec\"}}}}}}"
(Str "/home/ml25...")))))
(Die Struct{__cols:Array[Struct{s:String}]} -1
(Str "Internal e...")))
2021-07-29 13:36:35 root: INFO: optimize optimize: compileLowerer, after InlineApplyIR: after: IR size 8:
(Coalesce
(InsertFields
(In +PCStruct{} 0)
None
(__cols
(ToArray
(ReadPartition Struct{s:String}
"{\"name\":\"PartitionNativeReader\",\"spec\":{\"name\":\"TypedCodecSpec\",\"_eType\":\"+EBaseStruct{s:+EBinary}\",\"_vType\":\"Struct{s:String}\",\"_bufferSpec\":{\"name\":\"LEB128BufferSpec\",\"child\":{\"name\":\"BlockingBufferSpec\",\"blockSize\":32768,\"child\":{\"name\":\"LZ4HCBlockBufferSpec\",\"blockSize\":32768,\"child\":{\"name\":\"StreamBlockBufferSpec\"}}}}}}"
(Str "/home/ml25...")))))
(Die Struct{__cols:Array[Struct{s:String}]} -1
(Str "Internal e...")))
2021-07-29 13:36:35 root: INFO: optimize optimize: compileLowerer, after LowerArrayAggsToRunAggs: before: IR size 8:
(Coalesce
(InsertFields
(In +PCStruct{} 0)
None
(__cols
(ToArray
(ReadPartition Struct{s:String}
"{\"name\":\"PartitionNativeReader\",\"spec\":{\"name\":\"TypedCodecSpec\",\"_eType\":\"+EBaseStruct{s:+EBinary}\",\"_vType\":\"Struct{s:String}\",\"_bufferSpec\":{\"name\":\"LEB128BufferSpec\",\"child\":{\"name\":\"BlockingBufferSpec\",\"blockSize\":32768,\"child\":{\"name\":\"LZ4HCBlockBufferSpec\",\"blockSize\":32768,\"child\":{\"name\":\"StreamBlockBufferSpec\"}}}}}}"
(Str "/home/ml25...")))))
(Die Struct{__cols:Array[Struct{s:String}]} -1
(Str "Internal e...")))
2021-07-29 13:36:35 root: INFO: optimize optimize: compileLowerer, after LowerArrayAggsToRunAggs: after: IR size 8:
(Coalesce
(InsertFields
(In +PCStruct{} 0)
None
(__cols
(ToArray
(ReadPartition Struct{s:String}
"{\"name\":\"PartitionNativeReader\",\"spec\":{\"name\":\"TypedCodecSpec\",\"_eType\":\"+EBaseStruct{s:+EBinary}\",\"_vType\":\"Struct{s:String}\",\"_bufferSpec\":{\"name\":\"LEB128BufferSpec\",\"child\":{\"name\":\"BlockingBufferSpec\",\"blockSize\":32768,\"child\":{\"name\":\"LZ4HCBlockBufferSpec\",\"blockSize\":32768,\"child\":{\"name\":\"StreamBlockBufferSpec\"}}}}}}"
(Str "/home/ml25...")))))
(Die Struct{__cols:Array[Struct{s:String}]} -1
(Str "Internal e...")))
2021-07-29 13:36:35 root: INFO: encoder cache miss (0 hits, 2 misses, 0.000)
2021-07-29 13:36:35 root: INFO: instruction count: 3: __C119etypeEncode.<init>
2021-07-29 13:36:35 root: INFO: instruction count: 5: __C119etypeEncode.apply
2021-07-29 13:36:35 root: INFO: instruction count: 23: __C119etypeEncode.__m120ENCODE_r_tuple_of_r_stringANDr_stringEND_TO_r_struct_of_r_binaryANDr_binaryEND
2021-07-29 13:36:35 root: INFO: instruction count: 16: __C119etypeEncode.__m121ENCODE_r_binary_TO_r_binary
2021-07-29 13:36:35 MemoryStore: INFO: Block broadcast_5 stored as values in memory (estimated size 232.0 B, free 365.9 MB)
2021-07-29 13:36:35 MemoryStore: INFO: Block broadcast_5_piece0 stored as bytes in memory (estimated size 214.0 B, free 365.9 MB)
2021-07-29 13:36:35 BlockManagerInfo: INFO: Added broadcast_5_piece0 in memory on c20n02.ruddle.hpc.yale.internal:39864 (size: 214.0 B, free: 366.3 MB)
2021-07-29 13:36:35 SparkContext: INFO: Created broadcast 5 from broadcast at SparkBackend.scala:250
2021-07-29 13:36:35 root: INFO: instruction count: 3: __C98Compiled.<init>
2021-07-29 13:36:35 root: INFO: instruction count: 348: __C98Compiled.apply
2021-07-29 13:36:35 root: INFO: instruction count: 23: __C98Compiled.__m102DECODE_r_struct_of_r_binaryEND_TO_r_tuple_of_r_stringEND
2021-07-29 13:36:35 root: INFO: instruction count: 31: __C98Compiled.__m103INPLACE_DECODE_r_binary_TO_r_binary
2021-07-29 13:36:35 root: INFO: instruction count: 12: __C98Compiled.__m110setup_jab
2021-07-29 13:36:35 root: INFO: instruction count: 10: __C98Compiled.__m113addIRIntermediate
2021-07-29 13:36:35 root: INFO: instruction count: 5: __C98Compiled.__m114addIRIntermediate
2021-07-29 13:36:35 root: INFO: instruction count: 9: __C98Compiled.setPartitionIndex
2021-07-29 13:36:35 root: INFO: instruction count: 4: __C98Compiled.addPartitionRegion
2021-07-29 13:36:35 root: INFO: instruction count: 30: __C98Compiled.__m118DECODE_r_struct_of_r_binaryANDr_binaryEND_TO_r_tuple_of_r_stringANDr_stringEND
2021-07-29 13:36:35 root: INFO: instruction count: 45: __C98Compiled.addLiterals
2021-07-29 13:36:35 root: INFO: instruction count: 3: __C112FSContainer.<init>
2021-07-29 13:36:35 root: INFO: instruction count: 28: __C112FSContainer.init_filesystem
2021-07-29 13:36:35 root: INFO: instruction count: 3: __C112FSContainer.<clinit>
2021-07-29 13:36:35 root: INFO: optimize optimize: compileLowerer, initial IR: before: IR size 98:
(Coalesce
(Let __iruid_107
(ToArray
(StreamMap __iruid_108
(ToStream False
(GetField
`the entries! [877f12a8827e18f61222c6c8c5fb04a8]`
(In
+PCStruct{locus:+PCLocus(GRCh37),alleles:+PCArray[+PCString],`the entries! [877f12a8827e18f61222c6c8c5fb04a8]`:+PCArray[PCStruct{HL:PFloat64}]}
1)))
(Let __iruid_109
(GetField HL (Ref __iruid_108))
(InsertFields
(Ref __iruid_108)
("GT" "HL")
(GT
(If
(ApplySpecial land () Boolean
(ApplyComparisonOp LT
(Ref __iruid_109)
(F64 0.95))
(ApplyComparisonOp GT
(Ref __iruid_109)
(F64 0.0)))
(Literal Call <literal value>)
(If
(ApplyComparisonOp GTEQ
(GetField HL (Ref __iruid_108))
(F64 0.95))
(Literal Call <literal value>)
(If
(ApplyComparisonOp EQ
(GetField HL (Ref __iruid_108))
(F64 0.0))
(Literal Call <literal value>)
(NA Call)))))))))
(StreamAgg __iruid_110
(StreamFilter __iruid_111
(StreamRange False
(I32 0)
(ArrayLen (Ref __iruid_107))
(I32 1))
(ApplyUnaryPrimOp Bang
(IsNA
(ArrayRef
(Ref __iruid_107)
(Ref __iruid_111)
(Str "")))))
(AggLet __iruid_112 False
(ArrayRef
(Ref __iruid_107)
(Ref __iruid_110)
(Str ""))
(AggLet __iruid_113 False
(GetField GT (Ref __iruid_112))
(AggLet __iruid_114 False
(GetField s
(ArrayRef
(GetField __cols
(In
+PCStruct{__cols:+PCArray[+PCStruct{s:+PCString}]}
0))
(Ref __iruid_110)
(Str "")))
(AggLet __iruid_115 False
(GetField HL (Ref __iruid_112))
(InsertFields
(SelectFields (locus alleles)
(In
+PCStruct{locus:+PCLocus(GRCh37),alleles:+PCArray[+PCString],`the entries! [877f12a8827e18f61222c6c8c5fb04a8]`:+PCArray[PCStruct{HL:PFloat64}]}
1))
None
(samples_w_het_var
(AggFilter False
(Apply isHet () Boolean (Ref __iruid_113))
(ApplyAggOp TakeBy
((I32 3))
((MakeStruct
(S (Ref __iruid_114))
(HL (Ref __iruid_115)))
(MakeTuple (0 1)
(ApplyUnaryPrimOp Negate (Ref __iruid_115))
(ApplySeeded rand_unif 1 Float64
(F64 0.0)
(F64 1.0)))))))
(samples_w_hom_var
(AggFilter False
(Apply isHomVar () Boolean (Ref __iruid_113))
(ApplyAggOp TakeBy
((I32 3))
((MakeStruct
(S (Ref __iruid_114))
(HL (Ref __iruid_115)))
(MakeTuple (0 1)
(ApplyUnaryPrimOp Negate (Ref __iruid_115))
(ApplySeeded rand_unif 1 Float64
(F64 0.0)
(F64 1.0))))))))))))))
(Die
Struct{locus:Locus(GRCh37),alleles:Array[String],samples_w_het_var:Array[Struct{S:String,HL:Float64}],samples_w_hom_var:Array[Struct{S:String,HL:Float64}]}
-1
(Str "Internal e...")))
2021-07-29 13:36:35 root: INFO: optimize optimize: compileLowerer, initial IR: after: IR size 98:
(Coalesce
(Let __iruid_135
(ToArray
(StreamMap __iruid_136
(ToStream False
(GetField
`the entries! [877f12a8827e18f61222c6c8c5fb04a8]`
(In
+PCStruct{locus:+PCLocus(GRCh37),alleles:+PCArray[+PCString],`the entries! [877f12a8827e18f61222c6c8c5fb04a8]`:+PCArray[PCStruct{HL:PFloat64}]}
1)))
(Let __iruid_137