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- ---------------------------------------------------------------------------
- FatalError Traceback (most recent call last)
- <ipython-input-15-1d5c931eefbd> in <module>
- 3 gwas = hl.linear_regression_rows(y=chr16_qc9.phenotype.BMI,
- 4 x=hl.gp_dosage(chr16_qc9.GP),
- ----> 5 covariates=[1.0])
- 6 gwas.row.describe()
- </home/ch283/chloe/lib/python3.7/site-packages/decorator.py:decorator-gen-1525> in linear_regression_rows(y, x, covariates, block_size, pass_through)
- ~/chloe/lib/python3.7/site-packages/hail/typecheck/check.py in wrapper(__original_func, *args, **kwargs)
- 583 def wrapper(__original_func, *args, **kwargs):
- 584 args_, kwargs_ = check_all(__original_func, args, kwargs, checkers, is_method=is_method)
- --> 585 return __original_func(*args_, **kwargs_)
- 586
- 587 return wrapper
- ~/chloe/lib/python3.7/site-packages/hail/methods/statgen.py in linear_regression_rows(y, x, covariates, block_size, pass_through)
- 445 ht_result = ht_result.annotate(**{f: ht_result[f][0] for f in fields})
- 446
- --> 447 return ht_result.persist()
- 448
- 449
- </home/ch283/chloe/lib/python3.7/site-packages/decorator.py:decorator-gen-1085> in persist(self, storage_level)
- ~/chloe/lib/python3.7/site-packages/hail/typecheck/check.py in wrapper(__original_func, *args, **kwargs)
- 583 def wrapper(__original_func, *args, **kwargs):
- 584 args_, kwargs_ = check_all(__original_func, args, kwargs, checkers, is_method=is_method)
- --> 585 return __original_func(*args_, **kwargs_)
- 586
- 587 return wrapper
- ~/chloe/lib/python3.7/site-packages/hail/table.py in persist(self, storage_level)
- 1789 Persisted table.
- 1790 """
- -> 1791 return Env.backend().persist_table(self, storage_level)
- 1792
- 1793 def unpersist(self) -> 'Table':
- ~/chloe/lib/python3.7/site-packages/hail/backend/backend.py in persist_table(self, t, storage_level)
- 126
- 127 def persist_table(self, t, storage_level):
- --> 128 return Table._from_java(self._to_java_ir(t._tir).pyPersist(storage_level))
- 129
- 130 def unpersist_table(self, t):
- ~/chloe/lib/python3.7/site-packages/py4j/java_gateway.py in __call__(self, *args)
- 1255 answer = self.gateway_client.send_command(command)
- 1256 return_value = get_return_value(
- -> 1257 answer, self.gateway_client, self.target_id, self.name)
- 1258
- 1259 for temp_arg in temp_args:
- ~/chloe/lib/python3.7/site-packages/hail/utils/java.py in deco(*args, **kwargs)
- 223 raise FatalError('%s\n\nJava stack trace:\n%s\n'
- 224 'Hail version: %s\n'
- --> 225 'Error summary: %s' % (deepest, full, hail.__version__, deepest)) from None
- 226 except pyspark.sql.utils.CapturedException as e:
- 227 raise FatalError('%s\n\nJava stack trace:\n%s\n'
- FatalError: AssertionError: assertion failed
- Java stack trace:
- is.hail.utils.HailException: error trying to rebuild IR:
- (TableMapRows
- (MatrixToTableApply "{\"name\":\"LinearRegressionRowsSingle\",\"yFields\":[\"__y_0\"],\"xField\":\"__uid_42\",\"covFields\":[\"__cov0\"],\"rowBlockSize\":16,\"passThrough\":[]}"
- (MatrixRename () () ("__uid_43" "__uid_44") ("__y_0" "__cov0") () () ("__uid_45") ("__uid_42")
- (MatrixMapEntries
- (MatrixMapCols None
- (MatrixMapRows
- (MatrixMapCols ()
- (MatrixMapEntries
- (MatrixMapCols None
- (MatrixAnnotateColsTable "__uid_41"
- (MatrixFilterRows
- (MatrixMapRows
- (MatrixAnnotateRowsTable "__uid_37" False
- (MatrixFilterRows
- (MatrixMapRows
- (MatrixUnionRows
- (MatrixFilterRows
- (MatrixMapRows
- (MatrixFilterCols
- (MatrixMapCols None
- (MatrixAnnotateColsTable "__uid_7"
- (MatrixFilterCols
- (MatrixMapCols None
- (MatrixAnnotateColsTable "__uid_4"
- (MatrixMapCols None
- (MatrixAnnotateColsTable "__uid_3"
- (MatrixMapRows
- (MatrixRead None False False "{\"name\":\"MatrixBGENReader\",\"files\":[\"ukb_imp_chr16_v3.bgen\"],\"sampleFile\":\"ukb52480_imp_chr16_v3_s487314.sample\",\"indexFileMap\":{},\"blockSizeInMB\":128}")
- (MakeStruct
- (locus
- (GetField locus
- (Ref va)))
- (alleles
- (GetField alleles
- (Ref va)))
- (rsid
- (GetField rsid
- (Ref va)))
- (varid
- (GetField varid
- (Ref va)))))
- (TableFilter
- (TableLiteral)
- (Coalesce
- (ApplyUnaryPrimOp Bang
- (Apply isnan Boolean
- (GetField BMI
- (Ref row))))
- (False))))
- (InsertFields
- (SelectFields (s)
- (Ref sa))
- None
- (phenotype
- (GetField __uid_3
- (Ref sa)))))
- (TableFilter
- (TableLiteral)
- (ApplySpecial `&&` Boolean
- (Coalesce
- (ApplyUnaryPrimOp Bang
- (Apply isnan Boolean
- (GetField sex
- (Ref row))))
- (False))
- (Coalesce
- (ApplyUnaryPrimOp Bang
- (Apply isnan Boolean
- (GetField ethnic_group
- (Ref row))))
- (False)))))
- (InsertFields
- (SelectFields (s phenotype)
- (Ref sa))
- None
- (ukbb
- (GetField __uid_4
- (Ref sa)))))
- (ApplySpecial `&&` Boolean
- (Coalesce
- (ApplyComparisonOp EQ
- (GetField ethnic_group
- (GetField ukbb
- (Ref sa)))
- (F64 1.0))
- (False))
- (Coalesce
- (ApplyIR contains Boolean
- (Literal Set[String] <literal value>)
- (GetField s
- (Ref sa)))
- (False))))
- (TableLiteral))
- (InsertFields
- (SelectFields (s phenotype ukbb)
- (Ref sa))
- None
- (ukbb2
- (GetField __uid_7
- (Ref sa)))))
- (ApplySpecial `&&` Boolean
- (ApplySpecial `&&` Boolean
- (Coalesce
- (ApplyUnaryPrimOp Bang
- (ApplyIR contains Boolean
- (Literal Set[String] <literal value>)
- (GetField s
- (Ref sa))))
- (False))
- (Coalesce
- (ApplyUnaryPrimOp Bang
- (ApplyIR contains Boolean
- (Literal Set[String] <literal value>)
- (GetField s
- (Ref sa))))
- (False)))
- (Coalesce
- (ApplyUnaryPrimOp Bang
- (ApplyIR contains Boolean
- (Literal Set[String] <literal value>)
- (GetField s
- (Ref sa))))
- (False))))
- (Let __iruid_41770
- (MakeStruct
- (n_called
- (ApplyAggOp Sum
- ()
- (
- (Apply toInt64 Int64
- (ApplyUnaryPrimOp Bang
- (IsNA
- (GetField GT
- (Ref g))))))))
- (n_not_called
- (ApplyAggOp Sum
- ()
- (
- (Apply toInt64 Int64
- (IsNA
- (GetField GT
- (Ref g)))))))
- (n_filtered
- (ApplyBinaryPrimOp Subtract
- (Cast Int64
- (Ref n_cols))
- (ApplyAggOp Count
- ()
- ())))
- (call_stats
- (ApplyAggOp CallStats
- (
- (ArrayLen
- (GetField alleles
- (Ref va))))
- (
- (GetField GT
- (Ref g))))))
- (Let __iruid_41771
- (If
- (ApplyComparisonOp EQ
- (ArrayLen
- (GetField alleles
- (Ref va)))
- (I32 2))
- (Apply hardy_weinberg_test Struct{het_freq_hwe:Float64,p_value:Float64}
- (ApplyIR indexArray Int32
- (GetField homozygote_count
- (GetField call_stats
- (Ref __iruid_41770)))
- (I32 0)
- (Str " File \"<i..."))
- (ApplyBinaryPrimOp Subtract
- (ApplyIR indexArray Int32
- (GetField AC
- (GetField call_stats
- (Ref __iruid_41770)))
- (I32 1)
- (Str " File \"<i..."))
- (ApplyBinaryPrimOp Multiply
- (I32 2)
- (ApplyIR indexArray Int32
- (GetField homozygote_count
- (GetField call_stats
- (Ref __iruid_41770)))
- (I32 1)
- (Str " File \"<i..."))))
- (ApplyIR indexArray Int32
- (GetField homozygote_count
- (GetField call_stats
- (Ref __iruid_41770)))
- (I32 1)
- (Str " File \"<i...")))
- (NA Struct{het_freq_hwe:Float64,p_value:Float64}))
- (Let __iruid_41776
- (ArrayMap __iruid_41777
- (ToArray
- (StreamRange
- (I32 0)
- (ArrayLen
- (GetField alleles
- (Ref va)))
- (I32 1)))
- (ApplySpecial `||` Boolean
- (ApplyComparisonOp EQ
- (Ref __iruid_41777)
- (I32 0))
- (ApplyComparisonOp EQ
- (ApplyIR __uid_1 Int32
- (ApplyIR indexArray String
- (GetField alleles
- (Ref va))
- (I32 0)
- (Str " File \"<i..."))
- (ApplyIR indexArray String
- (GetField alleles
- (Ref va))
- (Ref __iruid_41777)
- (Str " File \"<i...")))
- (I32 1))))
- (Let __iruid_41778
- (ArrayMap __iruid_41779
- (ArrayFilter __iruid_41780
- (ArrayMap __iruid_41781
- (ToArray
- (StreamRange
- (I32 0)
- (ArrayLen
- (Ref __iruid_41776))
- (I32 1)))
- (MakeTuple (0 1)
- (Ref __iruid_41781)
- (ApplyIR indexArray Boolean
- (Ref __iruid_41776)
- (Ref __iruid_41781)
- (Str " File \"<i..."))))
- (GetTupleElement 1
- (Ref __iruid_41780)))
- (GetTupleElement 0
- (Ref __iruid_41779)))
- (Let __iruid_41782
- (Apply min_rep Struct{locus:Locus(GRCh37),alleles:Array[String]}
- (GetField locus
- (Ref va))
- (ArrayMap __iruid_41783
- (Ref __iruid_41778)
- (ApplyIR indexArray String
- (GetField alleles
- (Ref va))
- (Ref __iruid_41783)
- (Str " File \"<i..."))))
- (InsertFields
- (Ref va)
- ("locus" "alleles" "rsid" "varid" "variant_qc" "__allele_inclusion" "old_locus" "old_alleles" "old_to_new" "new_to_old" "__new_locus" "__new_alleles")
- (variant_qc
- (MakeStruct
- (AC
- (GetField AC
- (GetField call_stats
- (Ref __iruid_41770))))
- (AF
- (GetField AF
- (GetField call_stats
- (Ref __iruid_41770))))
- (AN
- (GetField AN
- (GetField call_stats
- (Ref __iruid_41770))))
- (homozygote_count
- (GetField homozygote_count
- (GetField call_stats
- (Ref __iruid_41770))))
- (call_rate
- (ApplyBinaryPrimOp FloatingPointDivide
- (Cast Float64
- (GetField n_called
- (Ref __iruid_41770)))
- (Cast Float64
- (ApplyBinaryPrimOp Add
- (ApplyBinaryPrimOp Add
- (GetField n_called
- (Ref __iruid_41770))
- (GetField n_not_called
- (Ref __iruid_41770)))
- (GetField n_filtered
- (Ref __iruid_41770))))))
- (n_called
- (GetField n_called
- (Ref __iruid_41770)))
- (n_not_called
- (GetField n_not_called
- (Ref __iruid_41770)))
- (n_filtered
- (GetField n_filtered
- (Ref __iruid_41770)))
- (n_het
- (ApplyBinaryPrimOp Subtract
- (GetField n_called
- (Ref __iruid_41770))
- (Cast Int64
- (ArrayFold __iruid_41773 __iruid_41774
- (ArrayFilter __iruid_41775
- (GetField homozygote_count
- (GetField call_stats
- (Ref __iruid_41770)))
- (ApplyUnaryPrimOp Bang
- (IsNA
- (Ref __iruid_41775))))
- (I32 0)
- (ApplyBinaryPrimOp Add
- (Ref __iruid_41773)
- (Ref __iruid_41774))))))
- (n_non_ref
- (ApplyBinaryPrimOp Subtract
- (GetField n_called
- (Ref __iruid_41770))
- (Cast Int64
- (ApplyIR indexArray Int32
- (GetField homozygote_count
- (GetField call_stats
- (Ref __iruid_41770)))
- (I32 0)
- (Str " File \"<i...")))))
- (het_freq_hwe
- (GetField het_freq_hwe
- (Ref __iruid_41771)))
- (p_value_hwe
- (GetField p_value
- (Ref __iruid_41771)))))
- (__allele_inclusion
- (Ref __iruid_41776))
- (old_locus
- (GetField locus
- (Ref va)))
- (old_alleles
- (GetField alleles
- (Ref va)))
- (old_to_new
- (Let __iruid_41784
- (ToDict
- (ArrayMap __iruid_41785
- (Let __iruid_41786
- (ArrayFilter __iruid_41787
- (Let __iruid_41788
- (GetField alleles
- (Ref va))
- (ArrayMap __iruid_41789
- (ToArray
- (StreamRange
- (I32 0)
- (ArrayLen
- (Ref __iruid_41788))
- (I32 1)))
- (MakeTuple (0 1)
- (Ref __iruid_41789)
- (ApplyIR indexArray String
- (Ref __iruid_41788)
- (Ref __iruid_41789)
- (Str " File \"<i...")))))
- (ApplyIR indexArray Boolean
- (Ref __iruid_41776)
- (GetTupleElement 0
- (Ref __iruid_41787))
- (Str " File \"<i...")))
- (ArrayMap __iruid_41790
- (ToArray
- (StreamRange
- (I32 0)
- (ArrayLen
- (Ref __iruid_41786))
- (I32 1)))
- (MakeTuple (0 1)
- (Ref __iruid_41790)
- (ApplyIR indexArray Tuple[Int32,String]
- (Ref __iruid_41786)
- (Ref __iruid_41790)
- (Str " File \"<i...")))))
- (MakeTuple (0 1)
- (GetTupleElement 1
- (GetTupleElement 1
- (Ref __iruid_41785)))
- (GetTupleElement 0
- (Ref __iruid_41785)))))
- (ArrayMap __iruid_41791
- (GetField alleles
- (Ref va))
- (ApplyIR get Int32
- (Ref __iruid_41784)
- (Ref __iruid_41791)))))
- (new_to_old
- (Ref __iruid_41778))
- (__new_locus
- (GetField locus
- (Ref __iruid_41782)))
- (__new_alleles
- (GetField alleles
- (Ref __iruid_41782))))))))))
- (ApplySpecial `&&` Boolean
- (Coalesce
- (ApplyComparisonOp GT
- (ArrayLen
- (GetField __new_alleles
- (Ref va)))
- (I32 1))
- (False))
- (Coalesce
- (ApplySpecial `&&` Boolean
- (ApplyComparisonOp EQ
- (GetField locus
- (Ref va))
- (GetField __new_locus
- (Ref va)))
- (ApplyComparisonOp EQ
- (GetField alleles
- (Ref va))
- (GetField __new_alleles
- (Ref va))))
- (False))))
- (MatrixKeyRowsBy (locus alleles) False
- (MatrixMapRows
- (MatrixKeyRowsBy () False
- (MatrixFilterRows
- (MatrixMapRows
- (MatrixFilterCols
- (MatrixMapCols None
- (MatrixAnnotateColsTable "__uid_7"
- (MatrixFilterCols
- (MatrixMapCols None
- (MatrixAnnotateColsTable "__uid_4"
- (MatrixMapCols None
- (MatrixAnnotateColsTable "__uid_3"
- (MatrixMapRows
- (MatrixRead None False False "{\"name\":\"MatrixBGENReader\",\"files\":[\"ukb_imp_chr16_v3.bgen\"],\"sampleFile\":\"ukb52480_imp_chr16_v3_s487314.sample\",\"indexFileMap\":{},\"blockSizeInMB\":128}")
- (MakeStruct
- (locus
- (GetField locus
- (Ref va)))
- (alleles
- (GetField alleles
- (Ref va)))
- (rsid
- (GetField rsid
- (Ref va)))
- (varid
- (GetField varid
- (Ref va)))))
- (TableFilter
- (TableLiteral)
- (Coalesce
- (ApplyUnaryPrimOp Bang
- (Apply isnan Boolean
- (GetField BMI
- (Ref row))))
- (False))))
- (InsertFields
- (SelectFields (s)
- (Ref sa))
- None
- (phenotype
- (GetField __uid_3
- (Ref sa)))))
- (TableFilter
- (TableLiteral)
- (ApplySpecial `&&` Boolean
- (Coalesce
- (ApplyUnaryPrimOp Bang
- (Apply isnan Boolean
- (GetField sex
- (Ref row))))
- (False))
- (Coalesce
- (ApplyUnaryPrimOp Bang
- (Apply isnan Boolean
- (GetField ethnic_group
- (Ref row))))
- (False)))))
- (InsertFields
- (SelectFields (s phenotype)
- (Ref sa))
- None
- (ukbb
- (GetField __uid_4
- (Ref sa)))))
- (ApplySpecial `&&` Boolean
- (Coalesce
- (ApplyComparisonOp EQ
- (GetField ethnic_group
- (GetField ukbb
- (Ref sa)))
- (F64 1.0))
- (False))
- (Coalesce
- (ApplyIR contains Boolean
- (Literal Set[String] <literal value>)
- (GetField s
- (Ref sa)))
- (False))))
- (TableLiteral))
- (InsertFields
- (SelectFields (s phenotype ukbb)
- (Ref sa))
- None
- (ukbb2
- (GetField __uid_7
- (Ref sa)))))
- (ApplySpecial `&&` Boolean
- (ApplySpecial `&&` Boolean
- (Coalesce
- (ApplyUnaryPrimOp Bang
- (ApplyIR contains Boolean
- (Literal Set[String] <literal value>)
- (GetField s
- (Ref sa))))
- (False))
- (Coalesce
- (ApplyUnaryPrimOp Bang
- (ApplyIR contains Boolean
- (Literal Set[String] <literal value>)
- (GetField s
- (Ref sa))))
- (False)))
- (Coalesce
- (ApplyUnaryPrimOp Bang
- (ApplyIR contains Boolean
- (Literal Set[String] <literal value>)
- (GetField s
- (Ref sa))))
- (False))))
- (Let __iruid_41795
- (MakeStruct
- (n_called
- (ApplyAggOp Sum
- ()
- (
- (Apply toInt64 Int64
- (ApplyUnaryPrimOp Bang
- (IsNA
- (GetField GT
- (Ref g))))))))
- (n_not_called
- (ApplyAggOp Sum
- ()
- (
- (Apply toInt64 Int64
- (IsNA
- (GetField GT
- (Ref g)))))))
- (n_filtered
- (ApplyBinaryPrimOp Subtract
- (Cast Int64
- (Ref n_cols))
- (ApplyAggOp Count
- ()
- ())))
- (call_stats
- (ApplyAggOp CallStats
- (
- (ArrayLen
- (GetField alleles
- (Ref va))))
- (
- (GetField GT
- (Ref g))))))
- (Let __iruid_41796
- (If
- (ApplyComparisonOp EQ
- (ArrayLen
- (GetField alleles
- (Ref va)))
- (I32 2))
- (Apply hardy_weinberg_test Struct{het_freq_hwe:Float64,p_value:Float64}
- (ApplyIR indexArray Int32
- (GetField homozygote_count
- (GetField call_stats
- (Ref __iruid_41795)))
- (I32 0)
- (Str " File \"<i..."))
- (ApplyBinaryPrimOp Subtract
- (ApplyIR indexArray Int32
- (GetField AC
- (GetField call_stats
- (Ref __iruid_41795)))
- (I32 1)
- (Str " File \"<i..."))
- (ApplyBinaryPrimOp Multiply
- (I32 2)
- (ApplyIR indexArray Int32
- (GetField homozygote_count
- (GetField call_stats
- (Ref __iruid_41795)))
- (I32 1)
- (Str " File \"<i..."))))
- (ApplyIR indexArray Int32
- (GetField homozygote_count
- (GetField call_stats
- (Ref __iruid_41795)))
- (I32 1)
- (Str " File \"<i...")))
- (NA Struct{het_freq_hwe:Float64,p_value:Float64}))
- (Let __iruid_41801
- (ArrayMap __iruid_41802
- (ToArray
- (StreamRange
- (I32 0)
- (ArrayLen
- (GetField alleles
- (Ref va)))
- (I32 1)))
- (ApplySpecial `||` Boolean
- (ApplyComparisonOp EQ
- (Ref __iruid_41802)
- (I32 0))
- (ApplyComparisonOp EQ
- (ApplyIR __uid_1 Int32
- (ApplyIR indexArray String
- (GetField alleles
- (Ref va))
- (I32 0)
- (Str " File \"<i..."))
- (ApplyIR indexArray String
- (GetField alleles
- (Ref va))
- (Ref __iruid_41802)
- (Str " File \"<i...")))
- (I32 1))))
- (Let __iruid_41803
- (ArrayMap __iruid_41804
- (ArrayFilter __iruid_41805
- (ArrayMap __iruid_41806
- (ToArray
- (StreamRange
- (I32 0)
- (ArrayLen
- (Ref __iruid_41801))
- (I32 1)))
- (MakeTuple (0 1)
- (Ref __iruid_41806)
- (ApplyIR indexArray Boolean
- (Ref __iruid_41801)
- (Ref __iruid_41806)
- (Str " File \"<i..."))))
- (GetTupleElement 1
- (Ref __iruid_41805)))
- (GetTupleElement 0
- (Ref __iruid_41804)))
- (Let __iruid_41807
- (Apply min_rep Struct{locus:Locus(GRCh37),alleles:Array[String]}
- (GetField locus
- (Ref va))
- (ArrayMap __iruid_41808
- (Ref __iruid_41803)
- (ApplyIR indexArray String
- (GetField alleles
- (Ref va))
- (Ref __iruid_41808)
- (Str " File \"<i..."))))
- (InsertFields
- (Ref va)
- ("locus" "alleles" "rsid" "varid" "variant_qc" "__allele_inclusion" "old_locus" "old_alleles" "old_to_new" "new_to_old" "__new_locus" "__new_alleles")
- (variant_qc
- (MakeStruct
- (AC
- (GetField AC
- (GetField call_stats
- (Ref __iruid_41795))))
- (AF
- (GetField AF
- (GetField call_stats
- (Ref __iruid_41795))))
- (AN
- (GetField AN
- (GetField call_stats
- (Ref __iruid_41795))))
- (homozygote_count
- (GetField homozygote_count
- (GetField call_stats
- (Ref __iruid_41795))))
- (call_rate
- (ApplyBinaryPrimOp FloatingPointDivide
- (Cast Float64
- (GetField n_called
- (Ref __iruid_41795)))
- (Cast Float64
- (ApplyBinaryPrimOp Add
- (ApplyBinaryPrimOp Add
- (GetField n_called
- (Ref __iruid_41795))
- (GetField n_not_called
- (Ref __iruid_41795)))
- (GetField n_filtered
- (Ref __iruid_41795))))))
- (n_called
- (GetField n_called
- (Ref __iruid_41795)))
- (n_not_called
- (GetField n_not_called
- (Ref __iruid_41795)))
- (n_filtered
- (GetField n_filtered
- (Ref __iruid_41795)))
- (n_het
- (ApplyBinaryPrimOp Subtract
- (GetField n_called
- (Ref __iruid_41795))
- (Cast Int64
- (ArrayFold __iruid_41798 __iruid_41799
- (ArrayFilter __iruid_41800
- (GetField homozygote_count
- (GetField call_stats
- (Ref __iruid_41795)))
- (ApplyUnaryPrimOp Bang
- (IsNA
- (Ref __iruid_41800))))
- (I32 0)
- (ApplyBinaryPrimOp Add
- (Ref __iruid_41798)
- (Ref __iruid_41799))))))
- (n_non_ref
- (ApplyBinaryPrimOp Subtract
- (GetField n_called
- (Ref __iruid_41795))
- (Cast Int64
- (ApplyIR indexArray Int32
- (GetField homozygote_count
- (GetField call_stats
- (Ref __iruid_41795)))
- (I32 0)
- (Str " File \"<i...")))))
- (het_freq_hwe
- (GetField het_freq_hwe
- (Ref __iruid_41796)))
- (p_value_hwe
- (GetField p_value
- (Ref __iruid_41796)))))
- (__allele_inclusion
- (Ref __iruid_41801))
- (old_locus
- (GetField locus
- (Ref va)))
- (old_alleles
- (GetField alleles
- (Ref va)))
- (old_to_new
- (Let __iruid_41809
- (ToDict
- (ArrayMap __iruid_41810
- (Let __iruid_41811
- (ArrayFilter __iruid_41812
- (Let __iruid_41813
- (GetField alleles
- (Ref va))
- (ArrayMap __iruid_41814
- (ToArray
- (StreamRange
- (I32 0)
- (ArrayLen
- (Ref __iruid_41813))
- (I32 1)))
- (MakeTuple (0 1)
- (Ref __iruid_41814)
- (ApplyIR indexArray String
- (Ref __iruid_41813)
- (Ref __iruid_41814)
- (Str " File \"<i...")))))
- (ApplyIR indexArray Boolean
- (Ref __iruid_41801)
- (GetTupleElement 0
- (Ref __iruid_41812))
- (Str " File \"<i...")))
- (ArrayMap __iruid_41815
- (ToArray
- (StreamRange
- (I32 0)
- (ArrayLen
- (Ref __iruid_41811))
- (I32 1)))
- (MakeTuple (0 1)
- (Ref __iruid_41815)
- (ApplyIR indexArray Tuple[Int32,String]
- (Ref __iruid_41811)
- (Ref __iruid_41815)
- (Str " File \"<i...")))))
- (MakeTuple (0 1)
- (GetTupleElement 1
- (GetTupleElement 1
- (Ref __iruid_41810)))
- (GetTupleElement 0
- (Ref __iruid_41810)))))
- (ArrayMap __iruid_41816
- (GetField alleles
- (Ref va))
- (ApplyIR get Int32
- (Ref __iruid_41809)
- (Ref __iruid_41816)))))
- (new_to_old
- (Ref __iruid_41803))
- (__new_locus
- (GetField locus
- (Ref __iruid_41807)))
- (__new_alleles
- (GetField alleles
- (Ref __iruid_41807))))))))))
- (ApplySpecial `&&` Boolean
- (Coalesce
- (ApplyComparisonOp GT
- (ArrayLen
- (GetField __new_alleles
- (Ref va)))
- (I32 1))
- (False))
- (Coalesce
- (ApplySpecial `||` Boolean
- (ApplyComparisonOp NEQ
- (GetField locus
- (Ref va))
- (GetField __new_locus
- (Ref va)))
- (ApplyComparisonOp NEQ
- (GetField alleles
- (Ref va))
- (GetField __new_alleles
- (Ref va))))
- (False)))))
- (InsertFields
- (Ref va)
- None
- (locus
- (GetField __new_locus
- (Ref va)))
- (alleles
- (GetField __new_alleles
- (Ref va)))))))
- (MakeStruct
- (locus
- (GetField locus
- (Ref va)))
- (alleles
- (GetField alleles
- (Ref va)))
- (rsid
- (GetField rsid
- (Ref va)))
- (varid
- (GetField varid
- (Ref va)))
- (variant_qc
- (GetField variant_qc
- (Ref va)))
- (old_locus
- (GetField old_locus
- (Ref va)))
- (old_alleles
- (GetField old_alleles
- (Ref va)))
- (old_to_new
- (GetField old_to_new
- (Ref va)))
- (new_to_old
- (GetField new_to_old
- (Ref va)))))
- (Coalesce
- (ApplyComparisonOp GT
- (GetField p_value_hwe
- (GetField variant_qc
- (Ref va)))
- (F64 1.0E-10))
- (False)))
- (TableKeyByAndAggregate None 50
- (TableMapRows
- (TableLeftJoinRightDistinct __uid_40
- (TableKeyBy (__uid_38) False
- (MatrixRowsTable
- (MatrixMapRows
- (MatrixFilterRows
- (MatrixMapRows
- (MatrixUnionRows
- (MatrixFilterRows
- (MatrixMapRows
- (MatrixFilterCols
- (MatrixMapCols None
- (MatrixAnnotateColsTable "__uid_7"
- (MatrixFilterCols
- (MatrixMapCols None
- (MatrixAnnotateColsTable "__uid_4"
- (MatrixMapCols None
- (MatrixAnnotateColsTable "__uid_3"
- (MatrixMapRows
- (MatrixRead None False False "{\"name\":\"MatrixBGENReader\",\"files\":[\"ukb_imp_chr16_v3.bgen\"],\"sampleFile\":\"ukb52480_imp_chr16_v3_s487314.sample\",\"indexFileMap\":{},\"blockSizeInMB\":128}")
- (MakeStruct
- (locus
- (GetField locus
- (Ref va)))
- (alleles
- (GetField alleles
- (Ref va)))
- (rsid
- (GetField rsid
- (Ref va)))
- (varid
- (GetField varid
- (Ref va)))))
- (TableFilter
- (TableLiteral)
- (Coalesce
- (ApplyUnaryPrimOp Bang
- (Apply isnan Boolean
- (GetField BMI
- (Ref row))))
- (False))))
- (InsertFields
- (SelectFields (s)
- (Ref sa))
- None
- (phenotype
- (GetField __uid_3
- (Ref sa)))))
- (TableFilter
- (TableLiteral)
- (ApplySpecial `&&` Boolean
- (Coalesce
- (ApplyUnaryPrimOp Bang
- (Apply isnan Boolean
- (GetField sex
- (Ref row))))
- (False))
- (Coalesce
- (ApplyUnaryPrimOp Bang
- (Apply isnan Boolean
- (GetField ethnic_group
- (Ref row))))
- (False)))))
- (InsertFields
- (SelectFields (s phenotype)
- (Ref sa))
- None
- (ukbb
- (GetField __uid_4
- (Ref sa)))))
- (ApplySpecial `&&` Boolean
- (Coalesce
- (ApplyComparisonOp EQ
- (GetField ethnic_group
- (GetField ukbb
- (Ref sa)))
- (F64 1.0))
- (False))
- (Coalesce
- (ApplyIR contains Boolean
- (Literal Set[String] <literal value>)
- (GetField s
- (Ref sa)))
- (False))))
- (TableLiteral))
- (InsertFields
- (SelectFields (s phenotype ukbb)
- (Ref sa))
- None
- (ukbb2
- (GetField __uid_7
- (Ref sa)))))
- (ApplySpecial `&&` Boolean
- (ApplySpecial `&&` Boolean
- (Coalesce
- (ApplyUnaryPrimOp Bang
- (ApplyIR contains Boolean
- (Literal Set[String] <literal value>)
- (GetField s
- (Ref sa))))
- (False))
- (Coalesce
- (ApplyUnaryPrimOp Bang
- (ApplyIR contains Boolean
- (Literal Set[String] <literal value>)
- (GetField s
- (Ref sa))))
- (False)))
- (Coalesce
- (ApplyUnaryPrimOp Bang
- (ApplyIR contains Boolean
- (Literal Set[String] <literal value>)
- (GetField s
- (Ref sa))))
- (False))))
- (Let __iruid_41820
- (MakeStruct
- (n_called
- (ApplyAggOp Sum
- ()
- (
- (Apply toInt64 Int64
- (ApplyUnaryPrimOp Bang
- (IsNA
- (GetField GT
- (Ref g))))))))
- (n_not_called
- (ApplyAggOp Sum
- ()
- (
- (Apply toInt64 Int64
- (IsNA
- (GetField GT
- (Ref g)))))))
- (n_filtered
- (ApplyBinaryPrimOp Subtract
- (Cast Int64
- (Ref n_cols))
- (ApplyAggOp Count
- ()
- ())))
- (call_stats
- (ApplyAggOp CallStats
- (
- (ArrayLen
- (GetField alleles
- (Ref va))))
- (
- (GetField GT
- (Ref g))))))
- (Let __iruid_41821
- (If
- (ApplyComparisonOp EQ
- (ArrayLen
- (GetField alleles
- (Ref va)))
- (I32 2))
- (Apply hardy_weinberg_test Struct{het_freq_hwe:Float64,p_value:Float64}
- (ApplyIR indexArray Int32
- (GetField homozygote_count
- (GetField call_stats
- (Ref __iruid_41820)))
- (I32 0)
- (Str " File \"<i..."))
- (ApplyBinaryPrimOp Subtract
- (ApplyIR indexArray Int32
- (GetField AC
- (GetField call_stats
- (Ref __iruid_41820)))
- (I32 1)
- (Str " File \"<i..."))
- (ApplyBinaryPrimOp Multiply
- (I32 2)
- (ApplyIR indexArray Int32
- (GetField homozygote_count
- (GetField call_stats
- (Ref __iruid_41820)))
- (I32 1)
- (Str " File \"<i..."))))
- (ApplyIR indexArray Int32
- (GetField homozygote_count
- (GetField call_stats
- (Ref __iruid_41820)))
- (I32 1)
- (Str " File \"<i...")))
- (NA Struct{het_freq_hwe:Float64,p_value:Float64}))
- (Let __iruid_41826
- (ArrayMap __iruid_41827
- (ToArray
- (StreamRange
- (I32 0)
- (ArrayLen
- (GetField alleles
- (Ref va)))
- (I32 1)))
- (ApplySpecial `||` Boolean
- (ApplyComparisonOp EQ
- (Ref __iruid_41827)
- (I32 0))
- (ApplyComparisonOp EQ
- (ApplyIR __uid_1 Int32
- (ApplyIR indexArray String
- (GetField alleles
- (Ref va))
- (I32 0)
- (Str " File \"<i..."))
- (ApplyIR indexArray String
- (GetField alleles
- (Ref va))
- (Ref __iruid_41827)
- (Str " File \"<i...")))
- (I32 1))))
- (Let __iruid_41828
- (ArrayMap __iruid_41829
- (ArrayFilter __iruid_41830
- (ArrayMap __iruid_41831
- (ToArray
- (StreamRange
- (I32 0)
- (ArrayLen
- (Ref __iruid_41826))
- (I32 1)))
- (MakeTuple (0 1)
- (Ref __iruid_41831)
- (ApplyIR indexArray Boolean
- (Ref __iruid_41826)
- (Ref __iruid_41831)
- (Str " File \"<i..."))))
- (GetTupleElement 1
- (Ref __iruid_41830)))
- (GetTupleElement 0
- (Ref __iruid_41829)))
- (Let __iruid_41832
- (Apply min_rep Struct{locus:Locus(GRCh37),alleles:Array[String]}
- (GetField locus
- (Ref va))
- (ArrayMap __iruid_41833
- (Ref __iruid_41828)
- (ApplyIR indexArray String
- (GetField alleles
- (Ref va))
- (Ref __iruid_41833)
- (Str " File \"<i..."))))
- (InsertFields
- (Ref va)
- ("locus" "alleles" "rsid" "varid" "variant_qc" "__allele_inclusion" "old_locus" "old_alleles" "old_to_new" "new_to_old" "__new_locus" "__new_alleles")
- (variant_qc
- (MakeStruct
- (AC
- (GetField AC
- (GetField call_stats
- (Ref __iruid_41820))))
- (AF
- (GetField AF
- (GetField call_stats
- (Ref __iruid_41820))))
- (AN
- (GetField AN
- (GetField call_stats
- (Ref __iruid_41820))))
- (homozygote_count
- (GetField homozygote_count
- (GetField call_stats
- (Ref __iruid_41820))))
- (call_rate
- (ApplyBinaryPrimOp FloatingPointDivide
- (Cast Float64
- (GetField n_called
- (Ref __iruid_41820)))
- (Cast Float64
- (ApplyBinaryPrimOp Add
- (ApplyBinaryPrimOp Add
- (GetField n_called
- (Ref __iruid_41820))
- (GetField n_not_called
- (Ref __iruid_41820)))
- (GetField n_filtered
- (Ref __iruid_41820))))))
- (n_called
- (GetField n_called
- (Ref __iruid_41820)))
- (n_not_called
- (GetField n_not_called
- (Ref __iruid_41820)))
- (n_filtered
- (GetField n_filtered
- (Ref __iruid_41820)))
- (n_het
- (ApplyBinaryPrimOp Subtract
- (GetField n_called
- (Ref __iruid_41820))
- (Cast Int64
- (ArrayFold __iruid_41823 __iruid_41824
- (ArrayFilter __iruid_41825
- (GetField homozygote_count
- (GetField call_stats
- (Ref __iruid_41820)))
- (ApplyUnaryPrimOp Bang
- (IsNA
- (Ref __iruid_41825))))
- (I32 0)
- (ApplyBinaryPrimOp Add
- (Ref __iruid_41823)
- (Ref __iruid_41824))))))
- (n_non_ref
- (ApplyBinaryPrimOp Subtract
- (GetField n_called
- (Ref __iruid_41820))
- (Cast Int64
- (ApplyIR indexArray Int32
- (GetField homozygote_count
- (GetField call_stats
- (Ref __iruid_41820)))
- (I32 0)
- (Str " File \"<i...")))))
- (het_freq_hwe
- (GetField het_freq_hwe
- (Ref __iruid_41821)))
- (p_value_hwe
- (GetField p_value
- (Ref __iruid_41821)))))
- (__allele_inclusion
- (Ref __iruid_41826))
- (old_locus
- (GetField locus
- (Ref va)))
- (old_alleles
- (GetField alleles
- (Ref va)))
- (old_to_new
- (Let __iruid_41834
- (ToDict
- (ArrayMap __iruid_41835
- (Let __iruid_41836
- (ArrayFilter __iruid_41837
- (Let __iruid_41838
- (GetField alleles
- (Ref va))
- (ArrayMap __iruid_41839
- (ToArray
- (StreamRange
- (I32 0)
- (ArrayLen
- (Ref __iruid_41838))
- (I32 1)))
- (MakeTuple (0 1)
- (Ref __iruid_41839)
- (ApplyIR indexArray String
- (Ref __iruid_41838)
- (Ref __iruid_41839)
- (Str " File \"<i...")))))
- (ApplyIR indexArray Boolean
- (Ref __iruid_41826)
- (GetTupleElement 0
- (Ref __iruid_41837))
- (Str " File \"<i...")))
- (ArrayMap __iruid_41840
- (ToArray
- (StreamRange
- (I32 0)
- (ArrayLen
- (Ref __iruid_41836))
- (I32 1)))
- (MakeTuple (0 1)
- (Ref __iruid_41840)
- (ApplyIR indexArray Tuple[Int32,String]
- (Ref __iruid_41836)
- (Ref __iruid_41840)
- (Str " File \"<i...")))))
- (MakeTuple (0 1)
- (GetTupleElement 1
- (GetTupleElement 1
- (Ref __iruid_41835)))
- (GetTupleElement 0
- (Ref __iruid_41835)))))
- (ArrayMap __iruid_41841
- (GetField alleles
- (Ref va))
- (ApplyIR get Int32
- (Ref __iruid_41834)
- (Ref __iruid_41841)))))
- (new_to_old
- (Ref __iruid_41828))
- (__new_locus
- (GetField locus
- (Ref __iruid_41832)))
- (__new_alleles
- (GetField alleles
- (Ref __iruid_41832))))))))))
- (ApplySpecial `&&` Boolean
- (Coalesce
- (ApplyComparisonOp GT
- (ArrayLen
- (GetField __new_alleles
- (Ref va)))
- (I32 1))
- (False))
- (Coalesce
- (ApplySpecial `&&` Boolean
- (ApplyComparisonOp EQ
- (GetField locus
- (Ref va))
- (GetField __new_locus
- (Ref va)))
- (ApplyComparisonOp EQ
- (GetField alleles
- (Ref va))
- (GetField __new_alleles
- (Ref va))))
- (False))))
- (MatrixKeyRowsBy (locus alleles) False
- (MatrixMapRows
- (MatrixKeyRowsBy () False
- (MatrixFilterRows
- (MatrixMapRows
- (MatrixFilterCols
- (MatrixMapCols None
- (MatrixAnnotateColsTable "__uid_7"
- (MatrixFilterCols
- (MatrixMapCols None
- (MatrixAnnotateColsTable "__uid_4"
- (MatrixMapCols None
- (MatrixAnnotateColsTable "__uid_3"
- (MatrixMapRows
- (MatrixRead None False False "{\"name\":\"MatrixBGENReader\",\"files\":[\"ukb_imp_chr16_v3.bgen\"],\"sampleFile\":\"ukb52480_imp_chr16_v3_s487314.sample\",\"indexFileMap\":{},\"blockSizeInMB\":128}")
- (MakeStruct
- (locus
- (GetField locus
- (Ref va)))
- (alleles
- (GetField alleles
- (Ref va)))
- (rsid
- (GetField rsid
- (Ref va)))
- (varid
- (GetField varid
- (Ref va)))))
- (TableFilter
- (TableLiteral)
- (Coalesce
- (ApplyUnaryPrimOp Bang
- (Apply isnan Boolean
- (GetField BMI
- (Ref row))))
- (False))))
- (InsertFields
- (SelectFields (s)
- (Ref sa))
- None
- (phenotype
- (GetField __uid_3
- (Ref sa)))))
- (TableFilter
- (TableLiteral)
- (ApplySpecial `&&` Boolean
- (Coalesce
- (ApplyUnaryPrimOp Bang
- (Apply isnan Boolean
- (GetField sex
- (Ref row))))
- (False))
- (Coalesce
- (ApplyUnaryPrimOp Bang
- (Apply isnan Boolean
- (GetField ethnic_group
- (Ref row))))
- (False)))))
- (InsertFields
- (SelectFields (s phenotype)
- (Ref sa))
- None
- (ukbb
- (GetField __uid_4
- (Ref sa)))))
- (ApplySpecial `&&` Boolean
- (Coalesce
- (ApplyComparisonOp EQ
- (GetField ethnic_group
- (GetField ukbb
- (Ref sa)))
- (F64 1.0))
- (False))
- (Coalesce
- (ApplyIR contains Boolean
- (Literal Set[String] <literal value>)
- (GetField s
- (Ref sa)))
- (False))))
- (TableLiteral))
- (InsertFields
- (SelectFields (s phenotype ukbb)
- (Ref sa))
- None
- (ukbb2
- (GetField __uid_7
- (Ref sa)))))
- (ApplySpecial `&&` Boolean
- (ApplySpecial `&&` Boolean
- (Coalesce
- (ApplyUnaryPrimOp Bang
- (ApplyIR contains Boolean
- (Literal Set[String] <literal value>)
- (GetField s
- (Ref sa))))
- (False))
- (Coalesce
- (ApplyUnaryPrimOp Bang
- (ApplyIR contains Boolean
- (Literal Set[String] <literal value>)
- (GetField s
- (Ref sa))))
- (False)))
- (Coalesce
- (ApplyUnaryPrimOp Bang
- (ApplyIR contains Boolean
- (Literal Set[String] <literal value>)
- (GetField s
- (Ref sa))))
- (False))))
- (Let __iruid_41845
- (AggLet __iruid_41846 False
- (GetField GT
- (Ref g))
- (InsertFields
- (Ref va)
- None
- (variant_qc
- (Let __iruid_41847
- (MakeStruct
- (n_called
- (ApplyAggOp Sum
- ()
- (
- (Apply toInt64 Int64
- (ApplyUnaryPrimOp Bang
- (IsNA
- (Ref __iruid_41846)))))))
- (n_not_called
- (ApplyAggOp Sum
- ()
- (
- (Apply toInt64 Int64
- (IsNA
- (Ref __iruid_41846))))))
- (n_filtered
- (ApplyBinaryPrimOp Subtract
- (Cast Int64
- (Ref n_cols))
- (ApplyAggOp Count
- ()
- ())))
- (call_stats
- (ApplyAggOp CallStats
- (
- (ArrayLen
- (GetField alleles
- (Ref va))))
- (
- (Ref __iruid_41846)))))
- (Let __iruid_41849
- (GetField call_stats
- (Ref __iruid_41847))
- (Let __iruid_41850
- (GetField homozygote_count
- (Ref __iruid_41849))
- (Let __iruid_41851
- (GetField n_called
- (Ref __iruid_41847))
- (Let __iruid_41852
- (GetField n_not_called
- (Ref __iruid_41847))
- (Let __iruid_41853
- (GetField n_filtered
- (Ref __iruid_41847))
- (Let __iruid_41854
- (If
- (ApplyComparisonOp EQ
- (ArrayLen
- (GetField alleles
- (Ref va)))
- (I32 2))
- (Let __iruid_41855
- (GetField call_stats
- (Ref __iruid_41847))
- (Let __iruid_41856
- (GetField homozygote_count
- (Ref __iruid_41855))
- (Apply hardy_weinberg_test Struct{het_freq_hwe:Float64,p_value:Float64}
- (ApplyIR indexArray Int32
- (Ref __iruid_41856)
- (I32 0)
- (Str " File \"<i..."))
- (ApplyBinaryPrimOp Subtract
- (ApplyIR indexArray Int32
- (GetField AC
- (Ref __iruid_41855))
- (I32 1)
- (Str " File \"<i..."))
- (ApplyBinaryPrimOp Multiply
- (I32 2)
- (ApplyIR indexArray Int32
- (Ref __iruid_41856)
- (I32 1)
- (Str " File \"<i..."))))
- (ApplyIR indexArray Int32
- (Ref __iruid_41856)
- (I32 1)
- (Str " File \"<i...")))))
- (NA Struct{het_freq_hwe:Float64,p_value:Float64}))
- (MakeStruct
- (AC
- (GetField AC
- (Ref __iruid_41849)))
- (AF
- (GetField AF
- (Ref __iruid_41849)))
- (AN
- (GetField AN
- (Ref __iruid_41849)))
- (homozygote_count
- (Ref __iruid_41850))
- (call_rate
- (ApplyBinaryPrimOp FloatingPointDivide
- (Cast Float64
- (Ref __iruid_41851))
- (Cast Float64
- (ApplyBinaryPrimOp Add
- (ApplyBinaryPrimOp Add
- (Ref __iruid_41851)
- (Ref __iruid_41852))
- (Ref __iruid_41853)))))
- (n_called
- (Ref __iruid_41851))
- (n_not_called
- (Ref __iruid_41852))
- (n_filtered
- (Ref __iruid_41853))
- (n_het
- (ApplyBinaryPrimOp Subtract
- (Ref __iruid_41851)
- (Cast Int64
- (ArrayFold __iruid_41862 __iruid_41863
- (ArrayFilter __iruid_41860
- (Ref __iruid_41850)
- (ApplyUnaryPrimOp Bang
- (IsNA
- (Ref __iruid_41860))))
- (Cast Int32
- (I64 0))
- (ApplyBinaryPrimOp Add
- (Ref __iruid_41862)
- (Ref __iruid_41863))))))
- (n_non_ref
- (ApplyBinaryPrimOp Subtract
- (Ref __iruid_41851)
- (Cast Int64
- (ApplyIR indexArray Int32
- (Ref __iruid_41850)
- (I32 0)
- (Str " File \"<i...")))))
- (het_freq_hwe
- (GetField het_freq_hwe
- (Ref __iruid_41854)))
- (p_value_hwe
- (GetField p_value
- (Ref __iruid_41854))))))))))))))
- (Let __iruid_41865
- (GetField alleles
- (Ref __iruid_41845))
- (Let __iruid_41866
- (ArrayMap __iruid_41867
- (ToArray
- (StreamRange
- (I32 0)
- (ArrayLen
- (Ref __iruid_41865))
- (I32 1)))
- (ApplySpecial `||` Boolean
- (ApplyComparisonOp EQ
- (Ref __iruid_41867)
- (I32 0))
- (ApplyComparisonOp EQ
- (ApplyIR __uid_1 Int32
- (ApplyIR indexArray String
- (Ref __iruid_41865)
- (I32 0)
- (Str " File \"<i..."))
- (ApplyIR indexArray String
- (Ref __iruid_41865)
- (Ref __iruid_41867)
- (Str " File \"<i...")))
- (I32 1))))
- (Let __iruid_41868
- (GetField alleles
- (Ref __iruid_41845))
- (Let __iruid_41869
- (ArrayMap __iruid_41870
- (ArrayFilter __iruid_41871
- (ArrayMap __iruid_41872
- (ToArray
- (StreamRange
- (I32 0)
- (ArrayLen
- (Ref __iruid_41866))
- (I32 1)))
- (MakeTuple (0 1)
- (Ref __iruid_41872)
- (ApplyIR indexArray Boolean
- (Ref __iruid_41866)
- (Ref __iruid_41872)
- (Str " File \"<i..."))))
- (GetTupleElement 1
- (Ref __iruid_41871)))
- (GetTupleElement 0
- (Ref __iruid_41870)))
- (Let __iruid_41873
- (Apply min_rep Struct{locus:Locus(GRCh37),alleles:Array[String]}
- (GetField locus
- (Ref __iruid_41845))
- (ArrayMap __iruid_41874
- (Ref __iruid_41869)
- (ApplyIR indexArray String
- (GetField alleles
- (Ref __iruid_41845))
- (Ref __iruid_41874)
- (Str " File \"<i..."))))
- (InsertFields
- (Ref __iruid_41845)
- ("locus" "alleles" "rsid" "varid" "variant_qc" "__allele_inclusion" "old_locus" "old_alleles" "old_to_new" "new_to_old" "__new_locus" "__new_alleles")
- (__allele_inclusion
- (Ref __iruid_41866))
- (old_locus
- (GetField locus
- (Ref __iruid_41845)))
- (old_alleles
- (Ref __iruid_41865))
- (old_to_new
- (Let __iruid_41875
- (ToDict
- (ArrayMap __iruid_41876
- (Let __iruid_41877
- (ArrayFilter __iruid_41878
- (ArrayMap __iruid_41879
- (ToArray
- (StreamRange
- (I32 0)
- (ArrayLen
- (Ref __iruid_41868))
- (I32 1)))
- (MakeTuple (0 1)
- (Ref __iruid_41879)
- (ApplyIR indexArray String
- (Ref __iruid_41868)
- (Ref __iruid_41879)
- (Str " File \"<i..."))))
- (ApplyIR indexArray Boolean
- (Ref __iruid_41866)
- (GetTupleElement 0
- (Ref __iruid_41878))
- (Str " File \"<i...")))
- (ArrayMap __iruid_41880
- (ToArray
- (StreamRange
- (I32 0)
- (ArrayLen
- (Ref __iruid_41877))
- (I32 1)))
- (MakeTuple (0 1)
- (Ref __iruid_41880)
- (ApplyIR indexArray Tuple[Int32,String]
- (Ref __iruid_41877)
- (Ref __iruid_41880)
- (Str " File \"<i...")))))
- (MakeTuple (0 1)
- (GetTupleElement 1
- (GetTupleElement 1
- (Ref __iruid_41876)))
- (GetTupleElement 0
- (Ref __iruid_41876)))))
- (ArrayMap __iruid_41881
- (Ref __iruid_41868)
- (ApplyIR get Int32
- (Ref __iruid_41875)
- (Ref __iruid_41881)))))
- (new_to_old
- (Ref __iruid_41869))
- (__new_locus
- (GetField locus
- (Ref __iruid_41873)))
- (__new_alleles
- (GetField alleles
- (Ref __iruid_41873)))))))))))
- (ApplySpecial `&&` Boolean
- (Coalesce
- (ApplyComparisonOp GT
- (ArrayLen
- (GetField __new_alleles
- (Ref va)))
- (I32 1))
- (False))
- (Coalesce
- (ApplySpecial `||` Boolean
- (ApplyComparisonOp NEQ
- (GetField locus
- (Ref va))
- (GetField __new_locus
- (Ref va)))
- (ApplyComparisonOp NEQ
- (GetField alleles
- (Ref va))
- (GetField __new_alleles
- (Ref va))))
- (False)))))
- (InsertFields
- (Ref va)
- None
- (locus
- (GetField __new_locus
- (Ref va)))
- (alleles
- (GetField __new_alleles
- (Ref va)))))))
- (MakeStruct
- (locus
- (GetField locus
- (Ref va)))
- (alleles
- (GetField alleles
- (Ref va)))
- (rsid
- (GetField rsid
- (Ref va)))
- (varid
- (GetField varid
- (Ref va)))
- (variant_qc
- (GetField variant_qc
- (Ref va)))
- (old_locus
- (GetField old_locus
- (Ref va)))
- (old_alleles
- (GetField old_alleles
- (Ref va)))
- (old_to_new
- (GetField old_to_new
- (Ref va)))
- (new_to_old
- (GetField new_to_old
- (Ref va)))))
- (Coalesce
- (ApplyComparisonOp GT
- (GetField p_value_hwe
- (GetField variant_qc
- (Ref va)))
- (F64 1.0E-10))
- (False)))
- (InsertFields
- (SelectFields (locus alleles)
- (Ref va))
- None
- (__uid_38
- (GetField varid
- (Ref va)))))))
- (TableLiteral))
- (InsertFields
- (SelectFields (locus alleles __uid_38)
- (Ref row))
- None
- (__uid_39
- (GetField __uid_40
- (Ref row)))))
- (MakeStruct
- (__uid_37
- (Let __iruid_41885
- (ApplyAggOp Collect
- ()
- (
- (MakeTuple (0 1)
- (MakeTuple (0)
- (GetField __uid_38
- (Ref row)))
- (GetField __uid_39
- (Ref row)))))
- (ToDict
- (Ref __iruid_41885)))))
- (SelectFields (locus alleles)
- (Ref row))))
- (InsertFields
- (SelectFields (locus alleles rsid varid variant_qc old_locus old_alleles old_to_new new_to_old)
- (Ref va))
- None
- (SNP_info
- (ApplyIR get Struct{MAF:Float64,minor_allele:String,info_score:Float64}
- (GetField __uid_37
- (GetField __uid_37
- (Ref va)))
- (MakeTuple (0)
- (GetField varid
- (Ref va)))))))
- (ApplySpecial `&&` Boolean
- (Coalesce
- (ApplyComparisonOp GT
- (GetField info_score
- (GetField SNP_info
- (Ref va)))
- (F64 0.4))
- (False))
- (Coalesce
- (ApplyComparisonOp GT
- (GetField MAF
- (GetField SNP_info
- (Ref va)))
- (F64 0.001))
- (False))))
- (TableLiteral))
- (Let __iruid_41887
- (SelectFields (s phenotype ukbb ukbb2)
- (Ref sa))
- (InsertFields
- (Ref __iruid_41887)
- ("s" "phenotype" "ukbb" "ukbb2" "PCA" "__uid_43" "__uid_44")
- (PCA
- (GetField __uid_41
- (Ref sa)))
- (__uid_43
- (GetField BMI
- (GetField phenotype
- (Ref __iruid_41887))))
- (__uid_44
- (F64 1.0)))))
- (InsertFields
- (Ref g)
- None
- (__uid_45
- (Apply dosage Float64
- (GetField GP
- (Ref g))))))
- (SelectFields (phenotype ukbb ukbb2 PCA __uid_43 __uid_44)
- (Ref sa)))
- (MakeStruct
- (locus
- (GetField locus
- (Ref va)))
- (alleles
- (GetField alleles
- (Ref va)))))
- (SelectFields (__uid_43 __uid_44)
- (Ref sa)))
- (SelectFields (__uid_45)
- (Ref g)))))
- (InsertFields
- (Ref row)
- None
- (y_transpose_x
- (ApplyIR indexArray Float64
- (GetField y_transpose_x
- (Ref row))
- (I32 0)
- (Str " File \"<i...")))
- (beta
- (ApplyIR indexArray Float64
- (GetField beta
- (Ref row))
- (I32 0)
- (Str " File \"<i...")))
- (standard_error
- (ApplyIR indexArray Float64
- (GetField standard_error
- (Ref row))
- (I32 0)
- (Str " File \"<i...")))
- (t_stat
- (ApplyIR indexArray Float64
- (GetField t_stat
- (Ref row))
- (I32 0)
- (Str " File \"<i...")))
- (p_value
- (ApplyIR indexArray Float64
- (GetField p_value
- (Ref row))
- (I32 0)
- (Str " File \"<i...")))))
- at is.hail.utils.ErrorHandling$class.fatal(ErrorHandling.scala:11)
- at is.hail.utils.package$.fatal(package.scala:74)
- at is.hail.expr.ir.PruneDeadFields$.apply(PruneDeadFields.scala:73)
- at is.hail.expr.ir.Optimize$$anonfun$apply$1$$anonfun$apply$mcV$sp$6.apply(Optimize.scala:28)
- at is.hail.expr.ir.Optimize$$anonfun$apply$1$$anonfun$apply$mcV$sp$6.apply(Optimize.scala:28)
- at is.hail.expr.ir.Optimize$$anonfun$is$hail$expr$ir$Optimize$$runOpt$1$1.apply(Optimize.scala:17)
- at is.hail.expr.ir.Optimize$$anonfun$is$hail$expr$ir$Optimize$$runOpt$1$1.apply(Optimize.scala:17)
- at is.hail.utils.ExecutionTimer.time(ExecutionTimer.scala:69)
- at is.hail.expr.ir.Optimize$.is$hail$expr$ir$Optimize$$runOpt$1(Optimize.scala:17)
- at is.hail.expr.ir.Optimize$$anonfun$apply$1.apply$mcV$sp(Optimize.scala:28)
- at is.hail.expr.ir.Optimize$$anonfun$apply$1.apply(Optimize.scala:21)
- at is.hail.expr.ir.Optimize$$anonfun$apply$1.apply(Optimize.scala:21)
- at is.hail.utils.ExecutionTimer.time(ExecutionTimer.scala:69)
- at is.hail.expr.ir.Optimize$.apply(Optimize.scala:20)
- at is.hail.expr.ir.lowering.LoweringPipeline.apply(LoweringPipeline.scala:16)
- at is.hail.expr.ir.Interpret$.apply(Interpret.scala:23)
- at is.hail.expr.ir.TableIR$$anonfun$persist$1.apply(TableIR.scala:49)
- at is.hail.expr.ir.TableIR$$anonfun$persist$1.apply(TableIR.scala:48)
- at is.hail.utils.package$.using(package.scala:596)
- at is.hail.expr.ir.ExecuteContext$$anonfun$scoped$1.apply(ExecuteContext.scala:10)
- at is.hail.expr.ir.ExecuteContext$$anonfun$scoped$1.apply(ExecuteContext.scala:9)
- at is.hail.utils.package$.using(package.scala:596)
- at is.hail.annotations.Region$.scoped(Region.scala:18)
- at is.hail.expr.ir.ExecuteContext$.scoped(ExecuteContext.scala:9)
- at is.hail.expr.ir.TableIR.persist(TableIR.scala:48)
- at is.hail.expr.ir.TableIR.pyPersist(TableIR.scala:68)
- at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
- at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
- at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
- at java.lang.reflect.Method.invoke(Method.java:498)
- at py4j.reflection.MethodInvoker.invoke(MethodInvoker.java:244)
- at py4j.reflection.ReflectionEngine.invoke(ReflectionEngine.java:357)
- at py4j.Gateway.invoke(Gateway.java:282)
- at py4j.commands.AbstractCommand.invokeMethod(AbstractCommand.java:132)
- at py4j.commands.CallCommand.execute(CallCommand.java:79)
- at py4j.GatewayConnection.run(GatewayConnection.java:238)
- at java.lang.Thread.run(Thread.java:748)
- java.lang.AssertionError: assertion failed
- at scala.Predef$.assert(Predef.scala:156)
- at is.hail.expr.ir.PruneDeadFields$.upcast(PruneDeadFields.scala:1867)
- at is.hail.expr.ir.PruneDeadFields$.upcast(PruneDeadFields.scala:1849)
- at is.hail.expr.ir.PruneDeadFields$$anonfun$175.apply(PruneDeadFields.scala:1841)
- at is.hail.expr.ir.PruneDeadFields$$anonfun$175.apply(PruneDeadFields.scala:1840)
- at scala.collection.TraversableLike$$anonfun$map$1.apply(TraversableLike.scala:234)
- at scala.collection.TraversableLike$$anonfun$map$1.apply(TraversableLike.scala:234)
- at scala.collection.IndexedSeqOptimized$class.foreach(IndexedSeqOptimized.scala:33)
- at scala.collection.mutable.WrappedArray.foreach(WrappedArray.scala:35)
- at scala.collection.TraversableLike$class.map(TraversableLike.scala:234)
- at scala.collection.AbstractTraversable.map(Traversable.scala:104)
- at is.hail.expr.ir.PruneDeadFields$.upcast(PruneDeadFields.scala:1840)
- at is.hail.expr.ir.PruneDeadFields$.upcast(PruneDeadFields.scala:1889)
- at is.hail.expr.ir.PruneDeadFields$$anonfun$rebuild$4.apply(PruneDeadFields.scala:1507)
- at is.hail.expr.ir.PruneDeadFields$$anonfun$rebuild$4.apply(PruneDeadFields.scala:1506)
- at scala.collection.TraversableLike$$anonfun$map$1.apply(TraversableLike.scala:234)
- at scala.collection.TraversableLike$$anonfun$map$1.apply(TraversableLike.scala:234)
- at scala.collection.mutable.ResizableArray$class.foreach(ResizableArray.scala:59)
- at scala.collection.mutable.ArrayBuffer.foreach(ArrayBuffer.scala:48)
- at scala.collection.TraversableLike$class.map(TraversableLike.scala:234)
- at scala.collection.AbstractTraversable.map(Traversable.scala:104)
- at is.hail.expr.ir.PruneDeadFields$.rebuild(PruneDeadFields.scala:1506)
- at is.hail.expr.ir.PruneDeadFields$.rebuild(PruneDeadFields.scala:1465)
- at is.hail.expr.ir.PruneDeadFields$.rebuild(PruneDeadFields.scala:1456)
- at is.hail.expr.ir.PruneDeadFields$.rebuild(PruneDeadFields.scala:1515)
- at is.hail.expr.ir.PruneDeadFields$.rebuild(PruneDeadFields.scala:1465)
- at is.hail.expr.ir.PruneDeadFields$.rebuild(PruneDeadFields.scala:1456)
- at is.hail.expr.ir.PruneDeadFields$.rebuild(PruneDeadFields.scala:1475)
- at is.hail.expr.ir.PruneDeadFields$.rebuild(PruneDeadFields.scala:1462)
- at is.hail.expr.ir.PruneDeadFields$.rebuild(PruneDeadFields.scala:1475)
- at is.hail.expr.ir.PruneDeadFields$.rebuild(PruneDeadFields.scala:1465)
- at is.hail.expr.ir.PruneDeadFields$.rebuild(PruneDeadFields.scala:1475)
- at is.hail.expr.ir.PruneDeadFields$.rebuild(PruneDeadFields.scala:1462)
- at is.hail.expr.ir.PruneDeadFields$.rebuild(PruneDeadFields.scala:1529)
- at is.hail.expr.ir.PruneDeadFields$$anonfun$rebuild$3.apply(PruneDeadFields.scala:1432)
- at is.hail.expr.ir.PruneDeadFields$$anonfun$rebuild$3.apply(PruneDeadFields.scala:1429)
- at scala.collection.TraversableLike$$anonfun$map$1.apply(TraversableLike.scala:234)
- at scala.collection.TraversableLike$$anonfun$map$1.apply(TraversableLike.scala:234)
- at scala.collection.IndexedSeqOptimized$class.foreach(IndexedSeqOptimized.scala:33)
- at scala.collection.mutable.WrappedArray.foreach(WrappedArray.scala:35)
- at scala.collection.TraversableLike$class.map(TraversableLike.scala:234)
- at scala.collection.AbstractTraversable.map(Traversable.scala:104)
- at is.hail.expr.ir.PruneDeadFields$.rebuild(PruneDeadFields.scala:1429)
- at is.hail.expr.ir.PruneDeadFields$.rebuild(PruneDeadFields.scala:1358)
- at is.hail.expr.ir.PruneDeadFields$.apply(PruneDeadFields.scala:82)
- at is.hail.expr.ir.Optimize$$anonfun$apply$1$$anonfun$apply$mcV$sp$6.apply(Optimize.scala:28)
- at is.hail.expr.ir.Optimize$$anonfun$apply$1$$anonfun$apply$mcV$sp$6.apply(Optimize.scala:28)
- at is.hail.expr.ir.Optimize$$anonfun$is$hail$expr$ir$Optimize$$runOpt$1$1.apply(Optimize.scala:17)
- at is.hail.expr.ir.Optimize$$anonfun$is$hail$expr$ir$Optimize$$runOpt$1$1.apply(Optimize.scala:17)
- at is.hail.utils.ExecutionTimer.time(ExecutionTimer.scala:69)
- at is.hail.expr.ir.Optimize$.is$hail$expr$ir$Optimize$$runOpt$1(Optimize.scala:17)
- at is.hail.expr.ir.Optimize$$anonfun$apply$1.apply$mcV$sp(Optimize.scala:28)
- at is.hail.expr.ir.Optimize$$anonfun$apply$1.apply(Optimize.scala:21)
- at is.hail.expr.ir.Optimize$$anonfun$apply$1.apply(Optimize.scala:21)
- at is.hail.utils.ExecutionTimer.time(ExecutionTimer.scala:69)
- at is.hail.expr.ir.Optimize$.apply(Optimize.scala:20)
- at is.hail.expr.ir.lowering.LoweringPipeline.apply(LoweringPipeline.scala:16)
- at is.hail.expr.ir.Interpret$.apply(Interpret.scala:23)
- at is.hail.expr.ir.TableIR$$anonfun$persist$1.apply(TableIR.scala:49)
- at is.hail.expr.ir.TableIR$$anonfun$persist$1.apply(TableIR.scala:48)
- at is.hail.utils.package$.using(package.scala:596)
- at is.hail.expr.ir.ExecuteContext$$anonfun$scoped$1.apply(ExecuteContext.scala:10)
- at is.hail.expr.ir.ExecuteContext$$anonfun$scoped$1.apply(ExecuteContext.scala:9)
- at is.hail.utils.package$.using(package.scala:596)
- at is.hail.annotations.Region$.scoped(Region.scala:18)
- at is.hail.expr.ir.ExecuteContext$.scoped(ExecuteContext.scala:9)
- at is.hail.expr.ir.TableIR.persist(TableIR.scala:48)
- at is.hail.expr.ir.TableIR.pyPersist(TableIR.scala:68)
- at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
- at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
- at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
- at java.lang.reflect.Method.invoke(Method.java:498)
- at py4j.reflection.MethodInvoker.invoke(MethodInvoker.java:244)
- at py4j.reflection.ReflectionEngine.invoke(ReflectionEngine.java:357)
- at py4j.Gateway.invoke(Gateway.java:282)
- at py4j.commands.AbstractCommand.invokeMethod(AbstractCommand.java:132)
- at py4j.commands.CallCommand.execute(CallCommand.java:79)
- at py4j.GatewayConnection.run(GatewayConnection.java:238)
- at java.lang.Thread.run(Thread.java:748)
- Hail version: 0.2.33-5d8cae649505
- Error summary: AssertionError: assertion failed
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