Package evaluation to test MendelIHT on Julia 1.14.0-DEV.3055 (7e75a8061a*) started at 2026-08-28T03:29:47.115 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.14` Set-up completed after 15.15s ################################################################################ # Installation # Installing MendelIHT... Resolving package versions... Installed CommonSolve ────────────────────── v0.2.14 Installed CommonWorldInvalidations ───────── v1.2.0 Installed CompositionsBase ───────────────── v0.1.2 Installed Glob ───────────────────────────── v1.5.0 Installed MacroTools ─────────────────────── v0.5.16 Installed DataStructures ─────────────────── v0.19.6 Installed CodecZstd ──────────────────────── v0.8.7 Installed FilePathsBase ──────────────────── v0.9.24 Installed GLM ────────────────────────────── v1.9.5 Installed Rmath_jll ──────────────────────── v0.5.2+0 Installed FillArrays ─────────────────────── v1.17.0 Installed Adapt ──────────────────────────── v4.7.0 Installed Bzip2_jll ──────────────────────── v1.0.9+0 Installed VectorizationBase ──────────────── v0.21.74 Installed ManualMemory ───────────────────── v0.1.8 Installed InlineStrings ──────────────────── v1.4.5 Installed StatsModels ────────────────────── v0.7.10 Installed VCFTools ───────────────────────── v0.2.10 Installed HypergeometricFunctions ────────── v0.3.30 Installed SLEEFPirates ───────────────────── v0.6.46 Installed CSV ────────────────────────────── v0.10.17 Installed StatsBase ──────────────────────── v0.34.13 Installed AliasTables ────────────────────── v1.1.3 Installed ConstructionBase ───────────────── v1.6.0 Installed DelimitedFiles ─────────────────── v1.9.1 Installed BitTwiddlingConvenienceFunctions ─ v0.1.6 Installed CodecZlib ──────────────────────── v0.7.9 Installed ArrayInterface ─────────────────── v7.30.0 Installed OrderedCollections ─────────────── v2.0.1 Installed SIMDTypes ──────────────────────── v0.1.0 Installed ShiftedArrays ──────────────────── v2.0.0 Installed TranscodingStreams ─────────────── v0.9.13 Installed HypothesisTests ────────────────── v0.11.8 Installed Compat ─────────────────────────── v4.18.1 Installed LoopVectorization ──────────────── v0.12.174 Installed IteratorInterfaceExtensions ────── v1.0.0 Installed Combinatorics ──────────────────── v1.1.0 Installed HostCPUFeatures ────────────────── v0.1.18 Installed DataAPI ────────────────────────── v1.16.0 Installed InvertedIndices ────────────────── v1.3.1 Installed SIMD ───────────────────────────── v3.7.2 Installed Statistics ─────────────────────── v1.11.1 Installed PrecompileTools ────────────────── v1.3.4 Installed SentinelArrays ─────────────────── v1.4.10 Installed StatsAPI ───────────────────────── v1.8.0 Installed ProgressMeter ──────────────────── v1.11.0 Installed DataValueInterfaces ────────────── v1.0.0 Installed CpuId ──────────────────────────── v0.3.1 Installed dlfcn_win32_jll ────────────────── v1.4.2+0 (no artifacts on this platform) Installed OffsetArrays ───────────────────── v1.17.0 Installed LayoutPointers ─────────────────── v0.1.17 Installed IrrationalConstants ────────────── v0.2.6 Installed StringManipulation ─────────────── v0.5.0 Installed SciMLPublic ────────────────────── v1.3.0 Installed Distances ──────────────────────── v0.10.12 Installed StaticArrayInterface ───────────── v1.10.0 Installed QuadGK ─────────────────────────── v2.11.3 Installed CodecBzip2 ─────────────────────── v0.8.5 Installed CPUSummary ─────────────────────── v0.2.7 Installed Requires ───────────────────────── v1.3.1 Installed LogExpFunctions ────────────────── v1.0.1 Installed OpenSpecFun_jll ────────────────── v0.5.6+0 Installed Parsers ────────────────────────── v2.8.7 Installed PrettyTables ───────────────────── v3.4.8 Installed Gamma ──────────────────────────── v1.2.0 Installed Rmath ──────────────────────────── v0.9.0 Installed Roots ──────────────────────────── v3.0.7 Installed BufferedStreams ────────────────── v1.2.2 Installed IfElse ─────────────────────────── v0.1.1 Installed Distributions ──────────────────── v0.25.131 Installed StatsFuns ──────────────────────── v2.2.1 Installed Tables ─────────────────────────── v1.14.0 Installed SpecialFunctions ───────────────── v2.9.0 Installed CloseOpenIntervals ─────────────── v0.1.13 Installed PtrArrays ──────────────────────── v1.4.0 Installed BioGenerics ────────────────────── v0.1.5 Installed DataFrames ─────────────────────── v1.8.2 Installed Reexport ───────────────────────── v1.2.2 Installed InverseFunctions ───────────────── v0.1.17 Installed Preferences ────────────────────── v1.5.2 Installed Static ─────────────────────────── v1.4.6 Installed DBInterface ────────────────────── v2.7.0 Installed Missings ───────────────────────── v1.2.0 Installed SortingAlgorithms ──────────────── v1.2.3 Installed LaTeXStrings ───────────────────── v1.4.1 Installed WeakRefStrings ─────────────────── v1.4.3 Installed PooledArrays ───────────────────── v1.4.3 Installed JLLWrappers ────────────────────── v1.8.0 Installed TableTraits ────────────────────── v1.0.1 Installed BGEN ───────────────────────────── v0.1.17 Installed SnpArrays ──────────────────────── v0.3.23 Installed Crayons ────────────────────────── v4.2.0 Installed PDMats ─────────────────────────── v0.11.41 Installed XZ_jll ─────────────────────────── v5.8.3+0 Installed Automa ─────────────────────────── v1.2.0 Installed SQLite ─────────────────────────── v1.8.2 Installed BGZFStreams ────────────────────── v0.3.2 Installed SQLite_jll ─────────────────────── v3.53.2+0 Installed ThreadingUtilities ─────────────── v0.5.6 Installed Accessors ──────────────────────── v0.1.45 Installed CodecXz ────────────────────────── v0.7.4 Installed VariantCallFormat ──────────────── v0.5.9 Installed PolyesterWeave ─────────────────── v0.2.2 Installed UnPack ─────────────────────────── v1.0.2 Installed WorkerUtilities ────────────────── v1.6.1 Installed DocStringExtensions ────────────── v0.9.5 Installed MendelIHT ──────────────────────── v1.4.11 Installing 5 artifacts Installed artifact Rmath 111.3 KiB Installed artifact SQLite 1.2 MiB Installed artifact OpenSpecFun 105.4 KiB Installed artifact Bzip2 152.8 KiB Installed artifact XZ 1018.2 KiB Updating `~/.julia/environments/v1.14/Project.toml` [921c7187] + MendelIHT v1.4.11 Updating `~/.julia/environments/v1.14/Manifest.toml` [7d9f7c33] + Accessors v0.1.45 [79e6a3ab] + Adapt v4.7.0 [66dad0bd] + AliasTables v1.1.3 [4fba245c] + ArrayInterface v7.30.0 [67c07d97] + Automa v1.2.0 ⌅ [6db4b851] + BGEN v0.1.17 [28d598bf] + BGZFStreams v0.3.2 [47718e42] + BioGenerics v0.1.5 [62783981] + BitTwiddlingConvenienceFunctions v0.1.6 [e1450e63] + BufferedStreams v1.2.2 [2a0fbf3d] + CPUSummary v0.2.7 [336ed68f] + CSV v0.10.17 [fb6a15b2] + CloseOpenIntervals v0.1.13 [523fee87] + CodecBzip2 v0.8.5 [ba30903b] + CodecXz v0.7.4 [944b1d66] + CodecZlib v0.7.9 [6b39b394] + CodecZstd v0.8.7 [861a8166] + Combinatorics v1.1.0 [38540f10] + CommonSolve v0.2.14 [f70d9fcc] + CommonWorldInvalidations v1.2.0 [34da2185] + Compat v4.18.1 [a33af91c] + CompositionsBase v0.1.2 [187b0558] + ConstructionBase v1.6.0 [adafc99b] + CpuId v0.3.1 [a8cc5b0e] + Crayons v4.2.0 [a10d1c49] + DBInterface v2.7.0 [9a962f9c] + DataAPI v1.16.0 [a93c6f00] + DataFrames v1.8.2 [864edb3b] + DataStructures v0.19.6 [e2d170a0] + DataValueInterfaces v1.0.0 [8bb1440f] + DelimitedFiles v1.9.1 [b4f34e82] + Distances v0.10.12 [31c24e10] + Distributions v0.25.131 [ffbed154] + DocStringExtensions v0.9.5 [48062228] + FilePathsBase v0.9.24 [1a297f60] + FillArrays v1.17.0 [38e38edf] + GLM v1.9.5 [a0844989] + Gamma v1.2.0 [c27321d9] + Glob v1.5.0 [3e5b6fbb] + HostCPUFeatures v0.1.18 [34004b35] + HypergeometricFunctions v0.3.30 [09f84164] + HypothesisTests v0.11.8 [615f187c] + IfElse v0.1.1 [842dd82b] + InlineStrings v1.4.5 [3587e190] + InverseFunctions v0.1.17 [41ab1584] + InvertedIndices v1.3.1 [92d709cd] + IrrationalConstants v0.2.6 [82899510] + IteratorInterfaceExtensions v1.0.0 [692b3bcd] + JLLWrappers v1.8.0 [b964fa9f] + LaTeXStrings v1.4.1 [10f19ff3] + LayoutPointers v0.1.17 [2ab3a3ac] + LogExpFunctions v1.0.1 [bdcacae8] + LoopVectorization v0.12.174 [1914dd2f] + MacroTools v0.5.16 [d125e4d3] + ManualMemory v0.1.8 [921c7187] + MendelIHT v1.4.11 [e1d29d7a] + Missings v1.2.0 [6fe1bfb0] + OffsetArrays v1.17.0 [bac558e1] + OrderedCollections v2.0.1 [90014a1f] + PDMats v0.11.41 ⌅ [69de0a69] + Parsers v2.8.7 [1d0040c9] + PolyesterWeave v0.2.2 [2dfb63ee] + PooledArrays v1.4.3 [aea7be01] + PrecompileTools v1.3.4 [21216c6a] + Preferences v1.5.2 [08abe8d2] + PrettyTables v3.4.8 [92933f4c] + ProgressMeter v1.11.0 [43287f4e] + PtrArrays v1.4.0 [1fd47b50] + QuadGK v2.11.3 [189a3867] + Reexport v1.2.2 [ae029012] + Requires v1.3.1 [79098fc4] + Rmath v0.9.0 [f2b01f46] + Roots v3.0.7 [fdea26ae] + SIMD v3.7.2 [94e857df] + SIMDTypes v0.1.0 [476501e8] + SLEEFPirates v0.6.46 [0aa819cd] + SQLite v1.8.2 [431bcebd] + SciMLPublic v1.3.0 [91c51154] + SentinelArrays v1.4.10 [1277b4bf] + ShiftedArrays v2.0.0 [4e780e97] + SnpArrays v0.3.23 [a2af1166] + SortingAlgorithms v1.2.3 [276daf66] + SpecialFunctions v2.9.0 [aedffcd0] + Static v1.4.6 [0d7ed370] + StaticArrayInterface v1.10.0 [10745b16] + Statistics v1.11.1 [82ae8749] + StatsAPI v1.8.0 [2913bbd2] + StatsBase v0.34.13 [4c63d2b9] + StatsFuns v2.2.1 [3eaba693] + StatsModels v0.7.10 [892a3eda] + StringManipulation v0.5.0 [3783bdb8] + TableTraits v1.0.1 [bd369af6] + Tables v1.14.0 [8290d209] + ThreadingUtilities v0.5.6 ⌅ [3bb67fe8] + TranscodingStreams v0.9.13 [3a884ed6] + UnPack v1.0.2 [a620830f] + VCFTools v0.2.10 [28eba6e3] + VariantCallFormat v0.5.9 [3d5dd08c] + VectorizationBase v0.21.74 [ea10d353] + WeakRefStrings v1.4.3 [76eceee3] + WorkerUtilities v1.6.1 [6e34b625] + Bzip2_jll v1.0.9+0 [efe28fd5] + OpenSpecFun_jll v0.5.6+0 [f50d1b31] + Rmath_jll v0.5.2+0 [76ed43ae] + SQLite_jll v3.53.2+0 [ffd25f8a] + XZ_jll v5.8.3+0 [c4b69c83] + dlfcn_win32_jll v1.4.2+0 [0dad84c5] + ArgTools v1.2.0 [56f22d72] + Artifacts v1.11.0 [2a0f44e3] + Base64 v1.11.0 [ade2ca70] + Dates v1.11.0 [8ba89e20] + Distributed v1.12.0 [f43a241f] + Downloads v1.7.0 [7b1f6079] + FileWatching v1.11.0 [9fa8497b] + Future v1.11.0 [b77e0a4c] + InteractiveUtils v1.11.0 [ac6e5ff7] + JuliaSyntaxHighlighting v1.13.0 [b27032c2] + LibCURL v1.0.0 [76f85450] + LibGit2 v1.11.0 [8f399da3] + Libdl v1.11.0 [37e2e46d] + LinearAlgebra v1.14.0 [56ddb016] + Logging v1.11.0 [d6f4376e] + Markdown v1.11.0 [a63ad114] + Mmap v1.11.0 [ca575930] + NetworkOptions v1.3.0 [44cfe95a] + Pkg v1.14.0 [de0858da] + Printf v1.11.0 [3fa0cd96] + REPL v1.11.0 [9a3f8284] + Random v1.11.0 [ea8e919c] + SHA v1.13.0 [9e88b42a] + Serialization v1.11.0 [6462fe0b] + Sockets v1.11.0 [2f01184e] + SparseArrays v1.13.0 [f489334b] + StyledStrings v1.13.0 [4607b0f0] + SuiteSparse [fa267f1f] + TOML v1.0.3 [a4e569a6] + Tar v1.10.0 [8dfed614] + Test v1.11.0 [cf7118a7] + UUIDs v1.11.0 [4ec0a83e] + Unicode v1.11.0 [e66e0078] + CompilerSupportLibraries_jll v1.5.7+0 [deac9b47] + LibCURL_jll v8.21.0+0 [e37daf67] + LibGit2_jll v1.9.7+0 [29816b5a] + LibSSH2_jll v1.11.104+0 [14a3606d] + MozillaCACerts_jll v2026.8.13 [4536629a] + OpenBLAS_jll v0.3.34+0 [05823500] + OpenLibm_jll v0.8.7+0 [458c3c95] + OpenSSL_jll v3.5.8+0 [efcefdf7] + PCRE2_jll v10.47.0+0 [bea87d4a] + SuiteSparse_jll v7.10.1+0 [83775a58] + Zlib_jll v1.3.2+0 [3161d3a3] + Zstd_jll v1.5.7+1 [8e850b90] + libblastrampoline_jll v5.15.0+0 [8e850ede] + nghttp2_jll v1.70.0+0 [3f19e933] + p7zip_jll v17.8.2+0 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. To see why use `status --outdated -m` Installation completed after 13.73s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling project... 5.0 s ✓ TestEnv 1 dependency successfully precompiled in 5 seconds. 27 already precompiled. Precompiling package dependencies... Precompiling project... 3.6 s ✓ MacroTools 1.4 s ✓ InlineStrings 0.5 s ✓ Reexport 0.7 s ✓ ConstructionBase 2.1 s ✓ IrrationalConstants 0.5 s ✓ DataValueInterfaces 0.6 s ✓ StatsAPI 1.9 s ✓ Combinatorics 0.5 s ✓ LaTeXStrings 0.7 s ✓ Glob 0.9 s ✓ Statistics 0.7 s ✓ IfElse 0.5 s ✓ PtrArrays 0.6 s ✓ ManualMemory 0.6 s ✓ Adapt 0.6 s ✓ DataAPI 0.6 s ✓ InvertedIndices 0.6 s ✓ InverseFunctions 0.5 s ✓ CompositionsBase 0.6 s ✓ ShiftedArrays 0.7 s ✓ WorkerUtilities 2.2 s ✓ FillArrays 0.5 s ✓ UnPack 0.6 s ✓ DBInterface 1.0 s ✓ OrderedCollections 0.9 s ✓ DocStringExtensions 1.3 s ✓ OffsetArrays 0.7 s ✓ BufferedStreams 0.5 s ✓ SIMDTypes 0.5 s ✓ IteratorInterfaceExtensions 2.1 s ✓ Crayons 0.8 s ✓ Requires 2.2 s ✓ ProgressMeter 0.7 s ✓ DelimitedFiles 1.9 s ✓ SentinelArrays 1.7 s ✓ StructUtils 1.6 s ✓ CpuId 2.2 s ✓ PDMats 0.8 s ✓ Compat 1.3 s ✓ Preferences 2.3 s ✓ TranscodingStreams 0.5 s ✓ ConstructionBase → ConstructionBaseLinearAlgebraExt 1.5 s ✓ Statistics → SparseArraysExt 1.1 s ✓ Distances 0.7 s ✓ AliasTables 1.3 s ✓ ThreadingUtilities 0.9 s ✓ ArrayInterface 1.5 s ✓ Adapt → AdaptSparseArraysExt 1.0 s ✓ Missings 0.8 s ✓ PooledArrays 1.0 s ✓ InverseFunctions → InverseFunctionsDatesExt 1.6 s ✓ InverseFunctions → InverseFunctionsTestExt 0.6 s ✓ CompositionsBase → CompositionsBaseInverseFunctionsExt 1.9 s ✓ FillArrays → FillArraysSparseArraysExt 0.9 s ✓ FillArrays → FillArraysStatisticsExt 3.3 s ✓ DataStructures 1.1 s ✓ LogExpFunctions 0.5 s ✓ OffsetArrays → OffsetArraysAdaptExt 0.5 s ✓ TableTraits 2.0 s ✓ FillArrays → FillArraysPDMatsExt 0.5 s ✓ Compat → CompatLinearAlgebraExt 1.5 s ✓ PrecompileTools 1.3 s ✓ JLLWrappers 1.6 s ✓ BioGenerics 1.9 s ✓ CodecZstd 1.6 s ✓ CodecZlib 1.5 s ✓ Distances → DistancesSparseArraysExt 0.9 s ✓ ArrayInterface → ArrayInterfaceFillArraysExt 1.4 s ✓ ArrayInterface → ArrayInterfaceSparseArraysExt 4.2 s ✓ Accessors 0.8 s ✓ SortingAlgorithms 1.7 s ✓ QuadGK 0.6 s ✓ LogExpFunctions → LogExpFunctionsInverseFunctionsExt 1.5 s ✓ Gamma 1.7 s ✓ Tables 1.9 s ✓ FilePathsBase 6.0 s ✓ StringManipulation 13.0 s ✓ SIMD 1.5 s ✓ CommonSolve 1.6 s ✓ SciMLPublic 1.4 s ✓ CommonWorldInvalidations 17.7 s ✓ Automa 10.8 s ✓ Parsers 1.8 s ✓ Bzip2_jll 1.2 s ✓ XZ_jll 1.2 s ✓ Rmath_jll 1.1 s ✓ OpenSpecFun_jll 0.9 s ✓ dlfcn_win32_jll 1.5 s ✓ BGZFStreams 1.8 s ✓ Accessors → TestExt 2.3 s ✓ Accessors → LinearAlgebraExt 4.7 s ✓ StatsBase 2.0 s ✓ HypergeometricFunctions 0.8 s ✓ StructUtils → StructUtilsTablesExt 2.4 s ✓ FilePathsBase → FilePathsBaseTestExt 0.9 s ✓ FilePathsBase → FilePathsBaseMmapExt 42.8 s ✓ PrettyTables 1.8 s ✓ Static 9.6 s ✓ JSON 0.9 s ✓ InlineStrings → ParsersExt 1.8 s ✓ CodecBzip2 1.7 s ✓ CodecXz 1.7 s ✓ Rmath 5.4 s ✓ SpecialFunctions 1.3 s ✓ SQLite_jll [ Info: Compiling VCF parser... 13.9 s ✓ VariantCallFormat 5.3 s ✓ Roots 1.8 s ✓ PDMats → StatsBaseExt 79.1 s ✓ DataFrames 0.9 s ✓ BitTwiddlingConvenienceFunctions 2.6 s ✓ CPUSummary 2.8 s ✓ StaticArrayInterface 10.0 s ✓ BenchmarkTools 2.5 s ✓ WeakRefStrings 2.2 s ✓ StatsFuns 1.9 s ✓ HostCPUFeatures 1.8 s ✓ PolyesterWeave 0.9 s ✓ StaticArrayInterface → StaticArrayInterfaceOffsetArraysExt 1.0 s ✓ CloseOpenIntervals 1.2 s ✓ LayoutPointers 27.2 s ✓ CSV 4.6 s ✓ SQLite 1.0 s ✓ StatsFuns → StatsFunsInverseFunctionsExt 5.6 s ✓ StatsModels 17.5 s ✓ VectorizationBase 3.9 s ✓ BGEN 10.4 s ✓ Distributions 3.0 s ✓ SLEEFPirates 6.5 s ✓ GLM 4.5 s ✓ Distributions → DistributionsTestExt 4.6 s ✓ HypothesisTests 34.6 s ✓ LoopVectorization 6.3 s ✓ VCFTools 2.9 s ✓ LoopVectorization → SpecialFunctionsExt 23.6 s ✓ SnpArrays WARNING: Constructor for type "MvNormal" was extended in `MendelIHT` without explicit qualification or import. NOTE: Assumed "MvNormal" refers to `Distributions.MvNormal`. This behavior is deprecated and may differ in future versions. NOTE: This behavior may have differed in Julia versions prior to 1.12. Hint: If you intended to create a new generic function of the same name, use `function MvNormal end`. Hint: To silence the warning, qualify `MvNormal` as `Distributions.MvNormal` in the method signature or explicitly `import Distributions: MvNormal`. 22.3 s ✓ MendelIHT 136 dependencies successfully precompiled in 541 seconds. 40 already precompiled. 2 dependencies had output during precompilation: ┌ MendelIHT │ WARNING: Constructor for type "MvNormal" was extended in `MendelIHT` without explicit qualification or import. │ NOTE: Assumed "MvNormal" refers to `Distributions.MvNormal`. This behavior is deprecated and may differ in future versions. │ NOTE: This behavior may have differed in Julia versions prior to 1.12. │ Hint: If you intended to create a new generic function of the same name, use `function MvNormal end`. │ Hint: To silence the warning, qualify `MvNormal` as `Distributions.MvNormal` in the method signature or explicitly `import Distributions: MvNormal`. └ ┌ VariantCallFormat │ [ Info: Compiling VCF parser... └ Precompilation completed after 556.15s ################################################################################ # Testing # Testing MendelIHT Status `/tmp/jl_xNRMGS/Project.toml` ⌅ [6db4b851] BGEN v0.1.17 [6e4b80f9] BenchmarkTools v1.8.0 [336ed68f] CSV v0.10.17 [a93c6f00] DataFrames v1.8.2 [8bb1440f] DelimitedFiles v1.9.1 [b4f34e82] Distances v0.10.12 [31c24e10] Distributions v0.25.131 [38e38edf] GLM v1.9.5 [921c7187] MendelIHT v1.4.11 [92933f4c] ProgressMeter v1.11.0 [189a3867] Reexport v1.2.2 [4e780e97] SnpArrays v0.3.23 [276daf66] SpecialFunctions v2.9.0 [2913bbd2] StatsBase v0.34.13 [a620830f] VCFTools v0.2.10 [37e2e46d] LinearAlgebra v1.14.0 [44cfe95a] Pkg v1.14.0 [9a3f8284] Random v1.11.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_xNRMGS/Manifest.toml` [7d9f7c33] Accessors v0.1.45 [79e6a3ab] Adapt v4.7.0 [66dad0bd] AliasTables v1.1.3 [4fba245c] ArrayInterface v7.30.0 [67c07d97] Automa v1.2.0 ⌅ [6db4b851] BGEN v0.1.17 [28d598bf] BGZFStreams v0.3.2 [6e4b80f9] BenchmarkTools v1.8.0 [47718e42] BioGenerics v0.1.5 [62783981] BitTwiddlingConvenienceFunctions v0.1.6 [e1450e63] BufferedStreams v1.2.2 [2a0fbf3d] CPUSummary v0.2.7 [336ed68f] CSV v0.10.17 [fb6a15b2] CloseOpenIntervals v0.1.13 [523fee87] CodecBzip2 v0.8.5 [ba30903b] CodecXz v0.7.4 [944b1d66] CodecZlib v0.7.9 [6b39b394] CodecZstd v0.8.7 [861a8166] Combinatorics v1.1.0 [38540f10] CommonSolve v0.2.14 [f70d9fcc] CommonWorldInvalidations v1.2.0 [34da2185] Compat v4.18.1 [a33af91c] CompositionsBase v0.1.2 [187b0558] ConstructionBase v1.6.0 [adafc99b] CpuId v0.3.1 [a8cc5b0e] Crayons v4.2.0 [a10d1c49] DBInterface v2.7.0 [9a962f9c] DataAPI v1.16.0 [a93c6f00] DataFrames v1.8.2 [864edb3b] DataStructures v0.19.6 [e2d170a0] DataValueInterfaces v1.0.0 [8bb1440f] DelimitedFiles v1.9.1 [b4f34e82] Distances v0.10.12 [31c24e10] Distributions v0.25.131 [ffbed154] DocStringExtensions v0.9.5 [48062228] FilePathsBase v0.9.24 [1a297f60] FillArrays v1.17.0 [38e38edf] GLM v1.9.5 [a0844989] Gamma v1.2.0 [c27321d9] Glob v1.5.0 [3e5b6fbb] HostCPUFeatures v0.1.18 [34004b35] HypergeometricFunctions v0.3.30 [09f84164] HypothesisTests v0.11.8 [615f187c] IfElse v0.1.1 [842dd82b] InlineStrings v1.4.5 [3587e190] InverseFunctions v0.1.17 [41ab1584] InvertedIndices v1.3.1 [92d709cd] IrrationalConstants v0.2.6 [82899510] IteratorInterfaceExtensions v1.0.0 [692b3bcd] JLLWrappers v1.8.0 [682c06a0] JSON v1.7.1 [b964fa9f] LaTeXStrings v1.4.1 [10f19ff3] LayoutPointers v0.1.17 [2ab3a3ac] LogExpFunctions v1.0.1 [bdcacae8] LoopVectorization v0.12.174 [1914dd2f] MacroTools v0.5.16 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Testing Running tests... ┌ Warning: accessing `Type.name` is deprecated without replacement. If for detection, use `Base.isType(x)`. │ caller = Distributions.MvNormal(σ::Vector{Float64}) at mvnormal.jl:207 └ @ Distributions ~/.julia/packages/Distributions/RTt4y/src/multivariate/mvnormal.jl:207 ┌ Warning: `MvNormal(σ::AbstractVector{<:Real})` is deprecated, use `MvNormal(LinearAlgebra.Diagonal(map(abs2, σ)))` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `cholesky!(A::RealHermSymComplexHerm{<:Real}, ::Val{true}; kwargs...)` is deprecated, use `cholesky!(A, RowMaximum(); kwargs...)` instead. │ caller = iht_stepsize!(v::MendelIHT.mIHTVariable{Float64, LinearAlgebra.Transpose{Float64, SnpArrays.SnpLinAlg{Float64}}}) at multivariate.jl:241 └ @ MendelIHT ~/.julia/packages/MendelIHT/ZcxZT/src/multivariate.jl:241 Test Summary: | Pass Total Time loglikelihood | 4 4 11.0s Test Summary: | Pass Total Time deviance | 1 1 0.3s Test Summary: | Pass Total Time update_μ! | 4 4 1.1s Test Summary: | Pass Total Time _choose! | 7 7 6.4s Test Summary: | Pass Total Time _iht_backtrack | 7 7 0.0s Test Summary: | Pass Total Time standardize! | 12 12 1.1s Test Summary: | Pass Total Time project_k! | 2 2 0.9s Test Summary: | Pass Total Time project_group_sparse! | 5 5 1.0s Test Summary: | Pass Total Time maf_weights | 6 6 1.9s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse linear regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1555.6524613747974, backtracks = 0, tol = 1.5200103175337956 Iteration 2: loglikelihood = -1396.634865524987, backtracks = 0, tol = 0.14914713679813002 Iteration 3: loglikelihood = -1388.172645306194, backtracks = 0, tol = 0.06295088334791751 Iteration 4: loglikelihood = -1387.9011890727902, backtracks = 0, tol = 0.006235660343191222 Iteration 5: loglikelihood = -1387.89766659018, backtracks = 0, tol = 0.0006415053931136559 Iteration 6: loglikelihood = -1387.897586216152, backtracks = 0, tol = 8.358769110960486e-5 IHT estimated 10 nonzero SNP predictors and 1 non-genetic predictors. Compute time (sec): 0.05129814147949219 Final loglikelihood: -1387.897586216152 SNP PVE: 0.9172739207398073 Iterations: 6 Selected genetic predictors: 10×2 DataFrame Row │ Position Estimated_β │ Int64 Float64 ─────┼─────────────────────── 1 │ 1138 1.22043 2 │ 1446 -0.914761 3 │ 1831 -1.65364 4 │ 1832 1.21917 5 │ 2571 -0.783382 6 │ 4720 0.199127 7 │ 4753 -0.565942 8 │ 6481 -0.622385 9 │ 8531 -0.147402 10 │ 9841 -1.48681 Selected nongenetic predictors: 1×2 DataFrame Row │ Position Estimated_β │ Int64 Float64 ─────┼─────────────────────── 1 │ 1 0.0177718Test Summary: | Pass Total Time fit normal SnpLinAlg | 4 4 21.7s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse logistic regression Number of threads = 1 Link functin = LogitLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -379.72375963518977, backtracks = 0, tol = 0.6062552017348442 Iteration 2: loglikelihood = -294.14222098196217, backtracks = 0, tol = 0.39035964909167 Iteration 3: loglikelihood = -258.44215825745147, backtracks = 0, tol = 0.18072720194601524 Iteration 4: loglikelihood = -248.39092317275637, backtracks = 1, tol = 0.0581811999889429 Iteration 5: loglikelihood = -241.2861695402178, backtracks = 2, tol = 0.10199490430383734 Iteration 6: loglikelihood = -236.0344401262056, backtracks = 2, tol = 0.10444957184614982 Iteration 7: loglikelihood = -232.75639772007577, backtracks = 2, tol = 0.03618239958756675 Iteration 8: loglikelihood = -230.9028935826695, backtracks = 3, tol = 0.022566251649321353 Iteration 9: loglikelihood = -229.2332883500926, backtracks = 3, tol = 0.02394599965909332 Iteration 10: loglikelihood = -227.8109863155336, backtracks = 3, tol = 0.02260237147851236 Iteration 11: loglikelihood = -226.61429831284372, backtracks = 3, tol = 0.02153016573221634 Iteration 12: loglikelihood = -225.614543213995, backtracks = 3, tol = 0.020073248773013197 Iteration 13: loglikelihood = -225.15228734295533, backtracks = 3, tol = 0.10266272165892033 Iteration 14: loglikelihood = -224.5524858306654, backtracks = 2, tol = 0.010910053499902256 Iteration 15: loglikelihood = -223.90430308527087, backtracks = 3, tol = 0.10669566586572145 Iteration 16: loglikelihood = -223.43342440058004, backtracks = 1, tol = 0.009912340440473734 Iteration 17: loglikelihood = -223.19474883510568, backtracks = 3, tol = 0.10429355504005154 Iteration 18: loglikelihood = -222.7530868660152, backtracks = 1, tol = 0.010133510239484585 Iteration 19: loglikelihood = -222.4546375562022, backtracks = 3, tol = 0.009382230171462355 Iteration 20: loglikelihood = -225.04961416047087, backtracks = 3, tol = 0.13141028198780508 Iteration 21: loglikelihood = -221.57583298738808, backtracks = 0, tol = 0.12983606150115481 Iteration 22: loglikelihood = -220.9953587123894, backtracks = 0, tol = 0.018278220962270587 Iteration 23: loglikelihood = -220.46528702030645, backtracks = 0, tol = 0.10912949798131547 Iteration 24: loglikelihood = -220.22939682199817, backtracks = 1, tol = 0.006133557493960293 Iteration 25: loglikelihood = -220.1149031779291, backtracks = 3, tol = 0.005637364497494655 Iteration 26: loglikelihood = -237.91408320706802, backtracks = 3, tol = 0.1311916630585333 Iteration 27: loglikelihood = -222.6667401701631, backtracks = 0, tol = 0.13008576394077564 Iteration 28: loglikelihood = -220.0179912284672, backtracks = 0, tol = 0.10981267805412102 Iteration 29: loglikelihood = -219.80873468505163, backtracks = 1, tol = 0.006242686572879014 Iteration 30: loglikelihood = -219.71412932030552, backtracks = 1, tol = 0.0052581541847830735 Iteration 31: loglikelihood = -219.67346582214395, backtracks = 3, tol = 0.002736072071808146 Iteration 32: loglikelihood = -236.63118723570068, backtracks = 3, tol = 0.12536959025201838 Iteration 33: loglikelihood = -222.42522446507616, backtracks = 0, tol = 0.12480632457239557 Iteration 34: loglikelihood = -219.76952387571325, backtracks = 0, tol = 0.10782393864869841 Iteration 35: loglikelihood = -219.54239052596037, backtracks = 0, tol = 0.010969385336776636 Iteration 36: loglikelihood = -219.51051719556185, backtracks = 0, tol = 0.0038143069815270263 Iteration 37: loglikelihood = -219.49562270628724, backtracks = 1, tol = 0.0015360028505860806 Iteration 38: loglikelihood = -222.2776344615594, backtracks = 3, tol = 0.10706948875570901 Iteration 39: loglikelihood = -219.86344247649652, backtracks = 0, tol = 0.10682440099239575 Iteration 40: loglikelihood = -219.50637292175287, backtracks = 0, tol = 0.010145149683589566 Iteration 41: loglikelihood = -219.45601478260392, backtracks = 0, tol = 0.004786594360325445 Iteration 42: loglikelihood = -219.44279315931445, backtracks = 0, tol = 0.0023300326568676676 Iteration 43: loglikelihood = -219.434262597912, backtracks = 0, tol = 0.002159682320412748 Iteration 44: loglikelihood = -219.42706752504972, backtracks = 0, tol = 0.0019986878272562235 Iteration 45: loglikelihood = -219.4208881668612, backtracks = 0, tol = 0.001781315196828412 Iteration 46: loglikelihood = -219.41556755717227, backtracks = 0, tol = 0.0017266268818688624 Iteration 47: loglikelihood = -219.41098445944962, backtracks = 0, tol = 0.001504993867218278 Iteration 48: loglikelihood = -219.4070309112888, backtracks = 0, tol = 0.001495426527055874 Iteration 49: loglikelihood = -219.40362030781677, backtracks = 0, tol = 0.001286324051089446 Iteration 50: loglikelihood = -219.4006747755802, backtracks = 0, tol = 0.001295957349435961 Iteration 51: loglikelihood = -219.39813103252988, backtracks = 0, tol = 0.0011058748112207813 Iteration 52: loglikelihood = -219.3959322024177, backtracks = 0, tol = 0.0011233728145861855 Iteration 53: loglikelihood = -219.39403166729804, backtracks = 0, tol = 0.0009536994758608786 Iteration 54: loglikelihood = -219.39238763268273, backtracks = 0, tol = 0.0009739180646352119 Iteration 55: loglikelihood = -219.39096560226784, backtracks = 0, tol = 0.0008239389039648708 Iteration 56: loglikelihood = -219.38973473800374, backtracks = 0, tol = 0.0008444580901064712 Iteration 57: loglikelihood = -219.3886694316569, backtracks = 0, tol = 0.0007126409505425607 Iteration 58: loglikelihood = -219.38774685610232, backtracks = 0, tol = 0.0007323063866727435 Iteration 59: loglikelihood = -219.3869479529937, backtracks = 0, tol = 0.00061686194275372 Iteration 60: loglikelihood = -219.3862557798823, backtracks = 0, tol = 0.0006351404346176769 Iteration 61: loglikelihood = -219.3856561234815, backtracks = 0, tol = 0.000534269842115572 Iteration 62: loglikelihood = -219.38513638040487, backtracks = 0, tol = 0.0005509480422217535 Iteration 63: loglikelihood = -219.38468593224545, backtracks = 0, tol = 0.0004629512780606966 Iteration 64: loglikelihood = -219.38429538513583, backtracks = 0, tol = 0.0004779860767529819 Iteration 65: loglikelihood = -219.38395679466737, backtracks = 0, tol = 0.0004013057505476397 Iteration 66: loglikelihood = -219.38366314739872, backtracks = 0, tol = 0.0004147454994836376 Iteration 67: loglikelihood = -219.38340849212824, backtracks = 0, tol = 0.00034797985178746597 Iteration 68: loglikelihood = -219.38318758502183, backtracks = 0, tol = 0.0003599207374415984 Iteration 69: loglikelihood = -219.38299596326374, backtracks = 0, tol = 0.0003018217223394219 Iteration 70: loglikelihood = -219.3828297011887, backtracks = 0, tol = 0.00031238270039476616 Iteration 71: loglikelihood = -219.38268544908368, backtracks = 0, tol = 0.00026184698528793125 Iteration 72: loglikelihood = -219.3825602648841, backtracks = 0, tol = 0.0002711550905775348 Iteration 73: loglikelihood = -219.38245163239276, backtracks = 0, tol = 0.00022721198022395564 Iteration 74: loglikelihood = -219.38235734460943, backtracks = 0, tol = 0.00023539371282360467 Iteration 75: loglikelihood = -219.38227551018164, backtracks = 0, tol = 0.0001971920991460162 Iteration 76: loglikelihood = -219.382204472153, backtracks = 0, tol = 0.00020436848993624394 Iteration 77: loglikelihood = -219.3821428080304, backtracks = 0, tol = 0.00017116393516432852 Iteration 78: loglikelihood = -219.38208927292968, backtracks = 0, tol = 0.00017744788492952903 Iteration 79: loglikelihood = -219.38204279645043, backtracks = 0, tol = 0.00014859040670150365 Iteration 80: loglikelihood = -219.38200244272016, backtracks = 0, tol = 0.00015408544066832546 Iteration 81: loglikelihood = -219.38196740593906, backtracks = 0, tol = 0.00012900826739905896 Iteration 82: loglikelihood = -219.38193698216227, backtracks = 0, tol = 0.00013380816660865064 Iteration 83: loglikelihood = -219.38191056455443, backtracks = 0, tol = 0.00011201756190578927 Iteration 84: loglikelihood = -219.3818876233726, backtracks = 0, tol = 0.000116206527337935 Iteration 85: loglikelihood = -219.38186770147453, backtracks = 0, tol = 9.727268703830643e-5 Test Summary: | Pass Total Time fit Bernoulli SnpLinAlg | 4 4 3.0s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse Poisson regression Number of threads = 1 Link functin = LogLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1508.961871158932, backtracks = 0, tol = 0.24274291620983157 Iteration 2: loglikelihood = -1411.6812865196564, backtracks = 0, tol = 0.054771544561095925 Iteration 3: loglikelihood = -1374.6259625878, backtracks = 0, tol = 0.07471791304915551 Iteration 4: loglikelihood = -1346.969723368328, backtracks = 0, tol = 0.10223062807206443 Iteration 5: loglikelihood = -1337.6820136185283, backtracks = 0, tol = 0.043760096351953506 Iteration 6: loglikelihood = -1335.3710181359609, backtracks = 1, tol = 0.011871188262876272 Iteration 7: loglikelihood = -1334.1189071710044, backtracks = 2, tol = 0.012244668894139454 Iteration 8: loglikelihood = -1333.3085633660567, backtracks = 2, tol = 0.00973577359885583 Iteration 9: loglikelihood = -1333.0509026442949, backtracks = 3, tol = 0.003971644652559567 Iteration 10: loglikelihood = -1332.8510061675236, backtracks = 3, tol = 0.0034833092450562986 Iteration 11: loglikelihood = -1332.696413033785, backtracks = 3, tol = 0.003063882269365831 Iteration 12: loglikelihood = -1332.5770538075185, backtracks = 3, tol = 0.002695717461149161 Iteration 13: loglikelihood = -1332.485012812384, backtracks = 3, tol = 0.0023703971939278926 Iteration 14: loglikelihood = -1332.4141091193096, backtracks = 3, tol = 0.0020828356419437533 Iteration 15: loglikelihood = -1332.359534206839, backtracks = 3, tol = 0.0018289717099348084 Iteration 16: loglikelihood = -1332.3175572408343, backtracks = 3, tol = 0.0016051745691467731 Iteration 17: loglikelihood = -1332.2852895268634, backtracks = 3, tol = 0.001408125843721966 Iteration 18: loglikelihood = -1332.2604981079587, backtracks = 3, tol = 0.001234803234821923 Iteration 19: loglikelihood = -1332.2414592374964, backtracks = 3, tol = 0.001082474716376387 Iteration 20: loglikelihood = -1332.2268437495609, backtracks = 3, tol = 0.0009486870093960777 Iteration 21: loglikelihood = -1332.2156277056395, backtracks = 3, tol = 0.0008312484563020771 Iteration 22: loglikelihood = -1332.2070229387166, backtracks = 3, tol = 0.0007282087641020328 Iteration 23: loglikelihood = -1332.2004231846242, backtracks = 3, tol = 0.0006378376241162303 Iteration 24: loglikelihood = -1332.1953623788208, backtracks = 3, tol = 0.0005586034938744975 Iteration 25: loglikelihood = -1332.1914824204357, backtracks = 3, tol = 0.0004891532900538192 Iteration 26: loglikelihood = -1332.1885082862132, backtracks = 3, tol = 0.000428293394287069 Iteration 27: loglikelihood = -1332.18622883957, backtracks = 3, tol = 0.0003749721584201088 Iteration 28: loglikelihood = -1332.1844820453143, backtracks = 3, tol = 0.00032826396447496433 Iteration 29: loglikelihood = -1332.1831435877357, backtracks = 3, tol = 0.0002873548157563465 Iteration 30: loglikelihood = -1332.182118114865, backtracks = 3, tol = 0.0002515293896293603 Iteration 31: loglikelihood = -1332.1813325069386, backtracks = 3, tol = 0.0002201594573512746 Iteration 32: loglikelihood = -1332.1807307038907, backtracks = 3, tol = 0.0001926935643532154 Iteration 33: loglikelihood = -1332.1802697325925, backtracks = 3, tol = 0.0001686478606871642 Iteration 34: loglikelihood = -1332.1799166567507, backtracks = 3, tol = 0.00014759797285401047 Iteration 35: loglikelihood = -1332.1796462360785, backtracks = 3, tol = 0.00012917181286822905 Iteration 36: loglikelihood = -1332.1794391302506, backtracks = 3, tol = 0.00011304322684439123 Iteration 37: loglikelihood = -1332.1792805212901, backtracks = 3, tol = 9.89263927354963e-5 Test Summary: | Pass Total Time fit Poisson SnpLinAlg | 4 4 2.5s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse NegativeBinomial regression Number of threads = 1 Link functin = LogLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1515.8754528726029, backtracks = 0, tol = 0.29932089633362446 Iteration 2: loglikelihood = -1461.2277857468594, backtracks = 0, tol = 0.16710452493013384 Iteration 3: loglikelihood = -1443.4829236863377, backtracks = 0, tol = 0.12933153728340352 Iteration 4: loglikelihood = -1442.3724610657166, backtracks = 0, tol = 0.0969169387327912 Iteration 5: loglikelihood = -1441.4065226512964, backtracks = 0, tol = 0.08684739000422424 Iteration 6: loglikelihood = -1441.3536979303854, backtracks = 1, tol = 0.003990399795718662 Iteration 7: loglikelihood = -1441.3368130275553, backtracks = 1, tol = 0.0024651805842828074 Iteration 8: loglikelihood = -1441.3308457296264, backtracks = 1, tol = 0.0015650546178115764 Iteration 9: loglikelihood = -1441.3288723648636, backtracks = 1, tol = 0.0009254568447217263 Iteration 10: loglikelihood = -1441.3283169641186, backtracks = 1, tol = 0.0005040722920246094 Iteration 11: loglikelihood = -1441.3281694934233, backtracks = 1, tol = 0.0002553000754417679 Iteration 12: loglikelihood = -1441.3281305259372, backtracks = 1, tol = 0.00013182722418254422 Iteration 13: loglikelihood = -1441.3281202604694, backtracks = 1, tol = 6.720948709401658e-5 Test Summary: | Pass Total Time fit NegativeBinomial SnpLinAlg | 4 4 1.2s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse linear regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1838.5998105284161, backtracks = 0, tol = 0.7665574539665566 Iteration 2: loglikelihood = -1486.0344607673119, backtracks = 0, tol = 0.1220259091957632 Iteration 3: loglikelihood = -1381.9581097728408, backtracks = 0, tol = 0.05395340565842351 Iteration 4: loglikelihood = -1371.0054335320751, backtracks = 0, tol = 0.03091280982049791 Iteration 5: loglikelihood = -1368.7502507890265, backtracks = 0, tol = 0.025888209026709613 Iteration 6: loglikelihood = -1368.570473718789, backtracks = 0, tol = 0.0022653528794173766 Iteration 7: loglikelihood = -1368.4742023599242, backtracks = 0, tol = 0.02498551188686455 Iteration 8: loglikelihood = -1368.3205303796094, backtracks = 0, tol = 0.0020768078214670935 Iteration 9: loglikelihood = -1368.3180398790414, backtracks = 0, tol = 0.00034370110881049585 Iteration 10: loglikelihood = -1368.3179797426365, backtracks = 0, tol = 3.585037605187182e-5 Test Summary: | Pass Total Time fit with >1 non-genetic covariates SnpLinAlg | 5 5 1.5s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse linear regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1527.7982072884276, backtracks = 0, tol = 0.31984347714055267 Iteration 2: loglikelihood = -1394.0769862895322, backtracks = 0, tol = 0.08312466921495311 Iteration 3: loglikelihood = -1372.7641851701899, backtracks = 0, tol = 0.03476534159334489 Iteration 4: loglikelihood = -1370.2253552733614, backtracks = 0, tol = 0.030667930336920234 Iteration 5: loglikelihood = -1370.0145928570382, backtracks = 1, tol = 0.0014633596357759731 Iteration 6: loglikelihood = -1369.9599473923445, backtracks = 1, tol = 0.0007375089023016231 Iteration 7: loglikelihood = -1369.945882992751, backtracks = 1, tol = 0.0003646308442790052 Iteration 8: loglikelihood = -1369.9422898857447, backtracks = 1, tol = 0.0001932027862884596 Iteration 9: loglikelihood = -1369.941377608369, backtracks = 1, tol = 0.00010016587445106316 Iteration 10: loglikelihood = -1369.9411470450673, backtracks = 1, tol = 5.085090652913003e-5 Test Summary: | Pass Total Time model selection on non-genetic covariates | 5 5 1.1s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse linear regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 15 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1473.1241001452804, backtracks = 0, tol = 0.11162633196865432 Iteration 2: loglikelihood = -1448.37403799896, backtracks = 0, tol = 0.07736217654955346 Iteration 3: loglikelihood = -1429.8981769610311, backtracks = 1, tol = 0.056531823476744666 Iteration 4: loglikelihood = -1404.7133956159753, backtracks = 0, tol = 0.10125409614175712 Iteration 5: loglikelihood = -1397.466171579031, backtracks = 0, tol = 0.05343369325195713 Iteration 6: loglikelihood = -1395.7490747391416, backtracks = 0, tol = 0.08843871418165582 Iteration 7: loglikelihood = -1395.4877576477586, backtracks = 0, tol = 0.008924704068495177 Iteration 8: loglikelihood = -1395.442237061722, backtracks = 0, tol = 0.005277867116132827 Iteration 9: loglikelihood = -1395.4302205892106, backtracks = 0, tol = 0.0027680467744013336 Iteration 10: loglikelihood = -1395.1973617039412, backtracks = 0, tol = 0.09056900655606137 Iteration 11: loglikelihood = -1395.0048067729406, backtracks = 0, tol = 0.007650485819168892 Iteration 12: loglikelihood = -1394.9835209063683, backtracks = 0, tol = 0.0035232591741737973 Iteration 13: loglikelihood = -1394.9793628241396, backtracks = 0, tol = 0.001852195878065177 Iteration 14: loglikelihood = -1394.9779889816232, backtracks = 0, tol = 0.0012530451800711446 Iteration 15: loglikelihood = -1394.977503420045, backtracks = 0, tol = 0.0006829444661300694 Iteration 16: loglikelihood = -1394.9773714862843, backtracks = 1, tol = 0.00022881022816864148 Iteration 17: loglikelihood = -1394.9773102201912, backtracks = 2, tol = 0.0001217788197399568 Iteration 18: loglikelihood = -1394.977273607278, backtracks = 2, tol = 8.822469907087602e-5 **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse linear regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 3 Prior weight scaling = off Doubly sparse projection = on Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1535.4672180567934, backtracks = 0, tol = 0.17016419679985048 Iteration 2: loglikelihood = -1508.04343741211, backtracks = 0, tol = 0.21718489399873087 Iteration 3: loglikelihood = -1448.2717322168082, backtracks = 0, tol = 0.15334504607402907 Iteration 4: loglikelihood = -1437.5669418734744, backtracks = 0, tol = 0.08425396177776269 Iteration 5: loglikelihood = -1434.3602241747526, backtracks = 0, tol = 0.03199716666887782 Iteration 6: loglikelihood = -1434.239273652971, backtracks = 2, tol = 0.003498168340088284 Iteration 7: loglikelihood = -1434.1475478538455, backtracks = 2, tol = 0.003052291101552644 Iteration 8: loglikelihood = -1434.0913475157126, backtracks = 2, tol = 0.002193157681835551 Iteration 9: loglikelihood = -1434.0584761985995, backtracks = 2, tol = 0.0016688209654910676 Iteration 10: loglikelihood = -1434.0393127719108, backtracks = 2, tol = 0.001317554485128468 Iteration 11: loglikelihood = -1434.0281644425422, backtracks = 2, tol = 0.0010393713220469133 Iteration 12: loglikelihood = -1434.0216963632631, backtracks = 2, tol = 0.0008158673348111326 Iteration 13: loglikelihood = -1434.0179556115856, backtracks = 2, tol = 0.0006363671566384205 Iteration 14: loglikelihood = -1433.8972844529703, backtracks = 2, tol = 0.021056460842673336 Iteration 15: loglikelihood = -1433.6170929347984, backtracks = 1, tol = 0.011448126839540959 Iteration 16: loglikelihood = -1433.5408744767517, backtracks = 2, tol = 0.0040324300639331045 Iteration 17: loglikelihood = -1433.4945867179188, backtracks = 2, tol = 0.003005268578298657 Iteration 18: loglikelihood = -1433.467626121943, backtracks = 2, tol = 0.002187229771831415 Iteration 19: loglikelihood = -1433.4521439235273, backtracks = 2, tol = 0.0016467936133078437 Iteration 20: loglikelihood = -1433.4432822302874, backtracks = 2, tol = 0.0012631945762950846 Iteration 21: loglikelihood = -1433.4382075829426, backtracks = 2, tol = 0.0009580287583338233 Iteration 22: loglikelihood = -1433.4352962137846, backtracks = 2, tol = 0.0007222437442123496 Iteration 23: loglikelihood = -1433.4336216439426, backtracks = 2, tol = 0.0005424739396431646 Iteration 24: loglikelihood = -1433.43265547142, backtracks = 2, tol = 0.0004062814588068666 Iteration 25: loglikelihood = -1433.4320960523787, backtracks = 2, tol = 0.00030341799187724174 Iteration 26: loglikelihood = -1433.4317709097872, backtracks = 2, tol = 0.00022583740291083832 Iteration 27: loglikelihood = -1433.4315812027676, backtracks = 2, tol = 0.0001673653861249394 Iteration 28: loglikelihood = -1432.5898379532828, backtracks = 2, tol = 0.0250802150540324 Iteration 29: loglikelihood = -1431.7678006470733, backtracks = 1, tol = 0.017181190475547 Iteration 30: loglikelihood = -1430.3157393955933, backtracks = 1, tol = 0.07333968264200223 Iteration 31: loglikelihood = -1429.706868513855, backtracks = 0, tol = 0.02001511172794573 Iteration 32: loglikelihood = -1429.5802551945537, backtracks = 1, tol = 0.00756937670420323 Iteration 33: loglikelihood = -1429.513945055356, backtracks = 2, tol = 0.003906515984506249 Iteration 34: loglikelihood = -1429.469197232521, backtracks = 2, tol = 0.003683664863256532 Iteration 35: loglikelihood = -1428.86075262229, backtracks = 2, tol = 0.08711763846658718 Iteration 36: loglikelihood = -1428.6178427111051, backtracks = 1, tol = 0.006558345246943248 Iteration 37: loglikelihood = -1428.5424083746184, backtracks = 2, tol = 0.0033912200662443866 Iteration 38: loglikelihood = -1428.4933608487952, backtracks = 2, tol = 0.0030098214824111564 Iteration 39: loglikelihood = -1428.4620745885084, backtracks = 2, tol = 0.002595137111913267 Iteration 40: loglikelihood = -1428.4427329028306, backtracks = 2, tol = 0.002148184701148499 Iteration 41: loglikelihood = -1428.4311433050725, backtracks = 2, tol = 0.0017160493175770867 Iteration 42: loglikelihood = -1428.4243474878394, backtracks = 2, tol = 0.0013407892924840858 Iteration 43: loglikelihood = -1428.420413936832, backtracks = 2, tol = 0.0010343694042998762 Iteration 44: loglikelihood = -1428.4181556141764, backtracks = 2, tol = 0.0007948565534422845 Iteration 45: loglikelihood = -1428.4168664091337, backtracks = 2, tol = 0.000608309643427293 Iteration 46: loglikelihood = -1428.4161334920516, backtracks = 2, tol = 0.0004622621654004415 Iteration 47: loglikelihood = -1428.4157180925672, backtracks = 2, tol = 0.00034956951660976293 Iteration 48: loglikelihood = -1428.4154831711999, backtracks = 2, tol = 0.00026348047442121094 Iteration 49: loglikelihood = -1428.415350523391, backtracks = 2, tol = 0.00019816133989405092 Iteration 50: loglikelihood = -1428.4152757065372, backtracks = 2, tol = 0.00014882628973649723 Iteration 51: loglikelihood = -1428.4152335404317, backtracks = 2, tol = 0.00011167501044822909 Iteration 52: loglikelihood = -1428.4152097888611, backtracks = 2, tol = 8.375238803842589e-5 Test Summary: | Pass Total Time Correlated predictors and double sparsity Float64 matrix | 2 2 7.5s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse NegativeBinomial regression Number of threads = 1 Link functin = LogLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1352.1211026320173, backtracks = 0, tol = 0.19521846088028466 Iteration 2: loglikelihood = -1326.019415932778, backtracks = 0, tol = 0.07732430408846168 Iteration 3: loglikelihood = -1299.9360192144761, backtracks = 0, tol = 0.06865802702341454 Iteration 4: loglikelihood = -1283.6838219246786, backtracks = 0, tol = 0.06918873287675839 Iteration 5: loglikelihood = -1275.1123147351298, backtracks = 0, tol = 0.04955726209912235 Iteration 6: loglikelihood = -1272.7446710851052, backtracks = 0, tol = 0.024696434564030673 Iteration 7: loglikelihood = -1271.7282140814264, backtracks = 0, tol = 0.021188702052702447 Iteration 8: loglikelihood = -1271.2556897332438, backtracks = 0, tol = 0.010732498620479439 Iteration 9: loglikelihood = -1271.0015053060636, backtracks = 0, tol = 0.01232700071732641 Iteration 10: loglikelihood = -1270.8634942772171, backtracks = 0, tol = 0.006358812267602384 Iteration 11: loglikelihood = -1267.163206565297, backtracks = 0, tol = 0.07443531360981445 Iteration 12: loglikelihood = -1264.5534305789306, backtracks = 0, tol = 0.03680168413273232 Iteration 13: loglikelihood = -1264.1899533015821, backtracks = 0, tol = 0.010404596332515717 Iteration 14: loglikelihood = -1264.1097217621443, backtracks = 0, tol = 0.0064985151859834386 Iteration 15: loglikelihood = -1264.0870589865074, backtracks = 0, tol = 0.00334669482222611 Iteration 16: loglikelihood = -1264.0796782279936, backtracks = 0, tol = 0.001702601525524262 Iteration 17: loglikelihood = -1264.0771942163608, backtracks = 0, tol = 0.0011490532827230643 Iteration 18: loglikelihood = -1264.0763415754077, backtracks = 0, tol = 0.0005389135427883253 Iteration 19: loglikelihood = -1264.0760428700846, backtracks = 0, tol = 0.00039697934260789214 Iteration 20: loglikelihood = -1264.0759456608089, backtracks = 0, tol = 0.00018165045472578784 Iteration 21: loglikelihood = -1264.0759097476625, backtracks = 0, tol = 0.0001372983298118342 Iteration 22: loglikelihood = -1264.0758894254193, backtracks = 0, tol = 6.23389149544416e-5 1.030292 seconds (3.70 M allocations: 67.293 MiB, 4.10% gc time, 53.18% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse NegativeBinomial regression Number of threads = 1 Link functin = LogLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1415.1474288431502, backtracks = 0, tol = 0.19521846088028466 Iteration 2: loglikelihood = -1388.5667694987073, backtracks = 0, tol = 0.09079923676850919 Iteration 3: loglikelihood = -1365.976501305746, backtracks = 0, tol = 0.09700413940070886 Iteration 4: loglikelihood = -1351.331569840099, backtracks = 0, tol = 0.04823619482047593 Iteration 5: loglikelihood = -1342.6781276930312, backtracks = 0, tol = 0.03302856002556825 Iteration 6: loglikelihood = -1335.0518314782043, backtracks = 0, tol = 0.018458043666661584 Iteration 7: loglikelihood = -1326.3440341059681, backtracks = 0, tol = 0.08492579929310054 Iteration 8: loglikelihood = -1319.0480677706144, backtracks = 0, tol = 0.08295609787028799 Iteration 9: loglikelihood = -1314.2703437562348, backtracks = 0, tol = 0.011691948250994573 Iteration 10: loglikelihood = -1310.593215701649, backtracks = 0, tol = 0.0039065692067013075 Iteration 11: loglikelihood = -1307.3262871924762, backtracks = 0, tol = 0.0019391477515388357 Iteration 12: loglikelihood = -1304.5058199511025, backtracks = 0, tol = 0.000487720979286677 Iteration 13: loglikelihood = -1302.0215330031565, backtracks = 0, tol = 0.0002414953725043872 Iteration 14: loglikelihood = -1299.8310021072034, backtracks = 0, tol = 0.0003073349235383617 Iteration 15: loglikelihood = -1297.884646646697, backtracks = 0, tol = 0.00022085360754353715 Iteration 16: loglikelihood = -1296.1462933389976, backtracks = 0, tol = 0.0002177025063375361 Iteration 17: loglikelihood = -1294.5844290867708, backtracks = 0, tol = 0.00019606297666290124 Iteration 18: loglikelihood = -1293.1742893687126, backtracks = 0, tol = 0.0001864480671192226 Iteration 19: loglikelihood = -1291.8950249714694, backtracks = 0, tol = 0.0001726969684849791 Iteration 20: loglikelihood = -1290.7296094779065, backtracks = 0, tol = 0.0001630995280281683 Iteration 21: loglikelihood = -1289.6637049880335, backtracks = 0, tol = 0.0001529964036507306 Iteration 22: loglikelihood = -1288.6853170255476, backtracks = 0, tol = 0.00014462954159529765 Iteration 23: loglikelihood = -1287.7842560681418, backtracks = 0, tol = 0.00013659934553002535 Iteration 24: loglikelihood = -1286.951855346876, backtracks = 0, tol = 0.00012950048546271528 Iteration 25: loglikelihood = -1286.1806761197802, backtracks = 0, tol = 0.00012287512106728306 Iteration 26: loglikelihood = -1285.4643106754058, backtracks = 0, tol = 0.00011685831872704367 Iteration 27: loglikelihood = -1284.7972045939619, backtracks = 0, tol = 0.00011127841749229911 Iteration 28: loglikelihood = -1284.1745234377274, backtracks = 0, tol = 0.00010614566082509418 Iteration 29: loglikelihood = -1283.5920387230067, backtracks = 0, tol = 0.00010138183126898145 Iteration 30: loglikelihood = -1283.0460373813344, backtracks = 0, tol = 9.696711470697652e-5 0.314796 seconds (1.05 M allocations: 19.379 MiB) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse NegativeBinomial regression Number of threads = 1 Link functin = LogLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -3675.9265, backtracks = 0, tol = 0.07721570382883446 Iteration 2: loglikelihood = -3624.5425, backtracks = 0, tol = 0.06389251405268948 Iteration 3: loglikelihood = -3614.8286, backtracks = 1, tol = 0.016557965722775295 Iteration 4: loglikelihood = -3611.7197, backtracks = 1, tol = 0.009541578431635512 Iteration 5: loglikelihood = -3610.8171, backtracks = 1, tol = 0.00565779760084043 Iteration 6: loglikelihood = -3610.5752, backtracks = 1, tol = 0.0032290205549344473 Iteration 7: loglikelihood = -3610.5154, backtracks = 1, tol = 0.0016987385556107536 Iteration 8: loglikelihood = -3610.501, backtracks = 1, tol = 0.0008575302211826922 Iteration 9: loglikelihood = -3610.4958, backtracks = 1, tol = 0.0004292731342736006 Iteration 10: loglikelihood = -3597.7224, backtracks = 1, tol = 0.06598512190927475 Iteration 11: loglikelihood = -3583.5344, backtracks = 0, tol = 0.07760325843179647 Iteration 12: loglikelihood = -3582.7651, backtracks = 0, tol = 0.006387479029048874 Iteration 13: loglikelihood = -3582.6743, backtracks = 0, tol = 0.0029188860542389895 Iteration 14: loglikelihood = -3582.662, backtracks = 0, tol = 0.0007174532241551656 Iteration 15: loglikelihood = -3582.661, backtracks = 0, tol = 0.0005533941338877802 Iteration 16: loglikelihood = -3582.6604, backtracks = 1, tol = 5.7621109247886165e-5 18.442888 seconds (15.02 M allocations: 695.902 MiB, 1.65% gc time, 96.16% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse NegativeBinomial regression Number of threads = 1 Link functin = LogLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -3578.3364, backtracks = 0, tol = 0.07721570382883446 Iteration 2: loglikelihood = -3462.1548, backtracks = 0, tol = 0.06389251405268948 Iteration 3: loglikelihood = -3388.8164, backtracks = 0, tol = 0.08985714205947715 Iteration 4: loglikelihood = -3268.2449, backtracks = 0, tol = 0.0830202561060533 Iteration 5: loglikelihood = -3166.5586, backtracks = 0, tol = 0.07347294742050899 Iteration 6: loglikelihood = -3063.7593, backtracks = 0, tol = 0.011956126792607718 Iteration 7: loglikelihood = -2958.0303, backtracks = 0, tol = 0.00501843615319968 Iteration 8: loglikelihood = -2888.441, backtracks = 0, tol = 0.0954677995695163 Iteration 9: loglikelihood = -2731.9111, backtracks = 0, tol = 0.09389580703956725 Iteration 10: loglikelihood = -2615.0513, backtracks = 0, tol = 0.08678482999731754 Iteration 11: loglikelihood = -2501.084, backtracks = 0, tol = 0.08475872577406089 Iteration 12: loglikelihood = -2404.065, backtracks = 0, tol = 0.08363676037218767 Iteration 13: loglikelihood = -2327.349, backtracks = 0, tol = 0.08330274137288463 Iteration 14: loglikelihood = -2267.294, backtracks = 0, tol = 0.0814674520078109 Iteration 15: loglikelihood = -2227.072, backtracks = 0, tol = 0.08116470096510867 Iteration 16: loglikelihood = -2198.7476, backtracks = 0, tol = 0.08123018559259092 Iteration 17: loglikelihood = -2181.8384, backtracks = 0, tol = 0.011802189879209937 Iteration 18: loglikelihood = -2173.7544, backtracks = 0, tol = 0.08622235154797973 Iteration 19: loglikelihood = -2167.3645, backtracks = 0, tol = 0.08626831790745011 Iteration 20: loglikelihood = -2164.2747, backtracks = 0, tol = 0.013041158103712987 Iteration 21: loglikelihood = -2162.8545, backtracks = 0, tol = 0.002448936563697025 Iteration 22: loglikelihood = -2162.1482, backtracks = 0, tol = 0.0007396244502086387 Iteration 23: loglikelihood = -2161.636, backtracks = 1, tol = 9.52454970664387e-5 0.162182 seconds (1.06 M allocations: 17.483 MiB) Test Summary: | Pass Total Time Negative binomial nuisance parameter Float32 matrix | 12 12 22.4s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** ┌ Warning: accessing `Type.name` is deprecated without replacement. If for detection, use `Base.isType(x)`. │ caller = ProgressMeter.Progress(n::Int64, dt::Int64, desc::String, barlen::Nothing, color::Symbol, output::Base.PipeEndpoint; offset::Int64) at deprecated.jl:1 └ @ ProgressMeter ~/.julia/packages/ProgressMeter/N660J/src/deprecated.jl:1 Running sparse linear regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -2896.6116813943763, backtracks = 0, tol = 1.0257704354307224 Iteration 2: loglikelihood = -1753.4720992614753, backtracks = 0, tol = 0.2870682551290383 Iteration 3: loglikelihood = -1460.3823326395222, backtracks = 0, tol = 0.1059822007319242 Iteration 4: loglikelihood = -1438.5292259047123, backtracks = 0, tol = 0.028655431669451118 Iteration 5: loglikelihood = -1438.0856032112097, backtracks = 0, tol = 0.0034955373515602557 Iteration 6: loglikelihood = -1438.074435032946, backtracks = 0, tol = 0.0005882060650840543 Iteration 7: loglikelihood = -1438.0741395461055, backtracks = 0, tol = 8.427264473930937e-5 4.552146 seconds (956.65 k allocations: 129.037 MiB, 2.74% gc time, 89.81% compilation time) Test Summary: | Pass Total Time initialze beta | 1 1 4.9s 7.559067 seconds (4.01 M allocations: 82.751 MiB, 0.41% gc time, 1.04% compilation time) 4.145391 seconds (3.98 M allocations: 91.817 MiB, 0.74% gc time) 10.303386 seconds (20.65 M allocations: 454.870 MiB, 1.09% gc time, 18.00% compilation time: 55% of which was recompilation) 8.375494 seconds (20.19 M allocations: 434.834 MiB, 1.19% gc time) 28.035954 seconds (3.45 M allocations: 4.231 GiB, 8.45% gc time, 25.54% compilation time) 42.124580 seconds (84.77 k allocations: 183.946 MiB, 0.10% gc time) Test Summary: | Pass Total Time memory_efficient keyword | 7 7 1m56.1s Test Summary: | Pass Total Time update_support! | 10 10 0.4s 13.613 ms (89 allocations: 5.20 KiB) 4.496 μs (0 allocations: 0 bytes) 89.959 μs (4 allocations: 288 bytes) 483.104 ns (0 allocations: 0 bytes) 33.579 μs (2 allocations: 64 bytes) 21.510 μs (0 allocations: 0 bytes) 3.749 μs (0 allocations: 0 bytes) 3.801 μs (0 allocations: 0 bytes) 71.890 μs (0 allocations: 0 bytes) 39.312 ms (89 allocations: 5.20 KiB) 18.320 μs (0 allocations: 0 bytes) 133.199 μs (4 allocations: 288 bytes) 2.724 μs (0 allocations: 0 bytes) 179.329 μs (2 allocations: 64 bytes) 43.499 μs (0 allocations: 0 bytes) 22.869 μs (0 allocations: 0 bytes) 24.229 μs (0 allocations: 0 bytes) 152.659 μs (0 allocations: 0 bytes) Test Summary: | Total Time benchmarks for multivariate function | 0 1m53.4s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse Multivariate Gaussian regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 12 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -2900.918630019449, backtracks = 0, tol = 0.14802242082004138 Iteration 2: loglikelihood = -2869.406464695619, backtracks = 0, tol = 0.03512679046077988 Iteration 3: loglikelihood = -2868.084702693443, backtracks = 0, tol = 0.005569349616332472 Iteration 4: loglikelihood = -2868.034423817725, backtracks = 0, tol = 0.0011189517628951667 Iteration 5: loglikelihood = -2868.0308576353746, backtracks = 0, tol = 0.00031182601179140966 Iteration 6: loglikelihood = -2868.0305288614227, backtracks = 0, tol = 0.00010393305949948345 Iteration 7: loglikelihood = -2868.0304966516946, backtracks = 0, tol = 3.100862049858006e-5 0.424445 seconds (46.08 k allocations: 5.432 MiB, 63.20% compilation time) Test Summary: | Pass Total Time multivariate fit_iht SnpLinAlg | 7 7 10.1s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse Multivariate Gaussian regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 12 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -2878.028812628852, backtracks = 0, tol = 2.5661768673084553 Iteration 2: loglikelihood = -2868.563037890196, backtracks = 0, tol = 0.024335274263285057 Iteration 3: loglikelihood = -2868.0815051475474, backtracks = 0, tol = 0.004072558228741048 Iteration 4: loglikelihood = -2868.0352100240902, backtracks = 0, tol = 0.0013135682973484317 Iteration 5: loglikelihood = -2868.0309297231934, backtracks = 0, tol = 0.000386434110747091 Iteration 6: loglikelihood = -2868.0305335492912, backtracks = 0, tol = 0.00011924564415557833 Iteration 7: loglikelihood = -2868.0304968517494, backtracks = 0, tol = 3.603726989721193e-5 1.466424 seconds (235.92 k allocations: 166.272 MiB, 58.15% compilation time) Test Summary: | Pass Total Time initialze beta | 5 5 1.8s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** ┌ Warning: accessing `Type.name` is deprecated without replacement. If for detection, use `Base.isType(x)`. │ caller = ProgressMeter.Progress(n::Int64, desc::String, offset::Int64; kwargs::Base.Pairs{Symbol, Union{}, Nothing, @NamedTuple{}}) at deprecated.jl:5 └ @ ProgressMeter ~/.julia/packages/ProgressMeter/N660J/src/deprecated.jl:5 Cross validating... 3%|█ | ETA: 0:02:18 Cross validating... 17%|█████▋ | ETA: 0:00:25 Cross validating... 22%|███████▏ | ETA: 0:00:19 Cross validating... 25%|████████▏ | ETA: 0:00:17 Cross validating... 29%|█████████▏ | ETA: 0:00:15 Cross validating... 32%|██████████▏ | ETA: 0:00:13 Cross validating... 35%|███████████▏ | ETA: 0:00:11 Cross validating... 38%|████████████▎ | ETA: 0:00:10 Cross validating... 41%|█████████████▎ | ETA: 0:00:09 Cross validating... 44%|██████████████▎ | ETA: 0:00:08 Cross validating... 48%|███████████████▎ | ETA: 0:00:07 Cross validating... 51%|████████████████▎ | ETA: 0:00:07 Cross validating... 54%|█████████████████▎ | ETA: 0:00:06 Cross validating... 57%|██████████████████▎ | ETA: 0:00:05 Cross validating... 60%|███████████████████▎ | ETA: 0:00:05 Cross validating... 63%|████████████████████▍ | ETA: 0:00:04 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:04 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:03 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:03 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:03 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:02 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:02 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:01 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:01 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:01 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:09 Crossvalidation Results: k MSE 0 3791.5420216307543 1 2822.5975789366967 2 2110.4738483537376 3 1499.9003085107558 4 1045.3892500129803 5 767.7499054874406 6 558.8607613472576 7 440.1356750842431 8 332.41831273908855 9 320.7417716115063 10 321.25021088336894 11 324.97175593829763 12 324.7588141836613 13 325.53697316951224 14 330.37405319647803 15 331.2733505887616 16 345.14284751588974 17 335.75130546296316 18 350.70793746919435 19 366.76035516647426 20 362.77160783258154 Best k = 9 9.157899 seconds (11.60 M allocations: 314.050 MiB, 1.89% gc time, 53.75% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 5%|█▌ | ETA: 0:00:03 Cross validating... 10%|███ | ETA: 0:00:03 Cross validating... 14%|████▋ | ETA: 0:00:02 Cross validating... 17%|█████▋ | ETA: 0:00:02 Cross validating... 21%|██████▋ | ETA: 0:00:03 Cross validating... 24%|███████▋ | ETA: 0:00:03 Cross validating... 27%|████████▋ | ETA: 0:00:03 Cross validating... 30%|█████████▋ | ETA: 0:00:03 Cross validating... 33%|██████████▋ | ETA: 0:00:03 Cross validating... 38%|████████████▎ | ETA: 0:00:02 Cross validating... 41%|█████████████▎ | ETA: 0:00:02 Cross validating... 44%|██████████████▎ | ETA: 0:00:02 Cross validating... 48%|███████████████▎ | ETA: 0:00:02 Cross validating... 51%|████████████████▎ | ETA: 0:00:02 Cross validating... 54%|█████████████████▎ | ETA: 0:00:02 Cross validating... 57%|██████████████████▎ | ETA: 0:00:02 Cross validating... 60%|███████████████████▎ | ETA: 0:00:02 Cross validating... 63%|████████████████████▍ | ETA: 0:00:02 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:01 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:01 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:01 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:01 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:01 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:01 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:00 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:04 Crossvalidation Results: k MSE 0 3791.5420216307543 1 2824.5249418891817 2 2118.505050613342 3 1509.605222881618 4 1057.0988879361473 5 781.5347074301087 6 569.6869629543273 7 450.1962646774232 8 339.1497507893263 9 328.21134390614384 10 332.0563543456621 11 340.6552681002727 12 350.07022069072093 13 343.1081006384015 14 350.3695179776443 15 361.1066274541305 16 370.6289460290285 17 373.45703797238207 18 378.13397238618984 19 386.19608850831213 20 395.2830267659394 Best k = 9 4.252608 seconds (10.17 M allocations: 215.028 MiB, 2.41% gc time, 1.49% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, normal model | 3 3 14.0s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:04:49 Cross validating... 8%|██▌ | ETA: 0:01:51 Cross validating... 13%|████▏ | ETA: 0:01:07 Cross validating... 17%|█████▋ | ETA: 0:00:46 Cross validating... 22%|███████▏ | ETA: 0:00:35 Cross validating... 27%|████████▋ | ETA: 0:00:27 Cross validating... 29%|█████████▏ | ETA: 0:00:26 Cross validating... 33%|██████████▋ | ETA: 0:00:21 Cross validating... 41%|█████████████▎ | ETA: 0:00:15 Cross validating... 48%|███████████████▎ | ETA: 0:00:12 Cross validating... 52%|████████████████▊ | ETA: 0:00:10 Cross validating... 57%|██████████████████▎ | ETA: 0:00:08 Cross validating... 62%|███████████████████▊ | ETA: 0:00:07 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:06 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:04 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:04 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:02 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:01 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:01 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:11 Crossvalidation Results: k MSE 0 1661.14301940918 1 1280.9779263916016 2 1020.0119146118165 3 838.6720261230469 4 720.3996900024415 5 592.0781802368165 6 453.7593829956055 7 398.8666525573731 8 364.1266454162598 9 359.48616387939455 10 353.8710353393555 11 355.91809860229495 12 358.377379486084 13 360.17291210937503 14 372.87344607543946 15 380.1742243652344 16 368.5943120117188 17 364.4454892883301 18 390.81140747070316 19 411.221867767334 20 404.5169579162598 Best k = 10 13.212701 seconds (12.72 M allocations: 327.624 MiB, 1.29% gc time, 80.85% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 6%|██ | ETA: 0:00:02 Cross validating... 11%|███▌ | ETA: 0:00:02 Cross validating... 16%|█████▏ | ETA: 0:00:02 Cross validating... 21%|██████▋ | ETA: 0:00:02 Cross validating... 25%|████████▏ | ETA: 0:00:02 Cross validating... 30%|█████████▋ | ETA: 0:00:02 Cross validating... 35%|███████████▏ | ETA: 0:00:02 Cross validating... 41%|█████████████▎ | ETA: 0:00:01 Cross validating... 46%|██████████████▊ | ETA: 0:00:01 Cross validating... 51%|████████████████▎ | ETA: 0:00:01 Cross validating... 54%|█████████████████▎ | ETA: 0:00:01 Cross validating... 59%|██████████████████▊ | ETA: 0:00:01 Cross validating... 63%|████████████████████▍ | ETA: 0:00:01 Cross validating... 68%|█████████████████████▉ | ETA: 0:00:01 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:01 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:01 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:00 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:00 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:02 Crossvalidation Results: k MSE 0 1661.14301940918 1 1280.9779263916016 2 1021.665348449707 3 842.237451171875 4 731.0948333740234 5 599.3919526977539 6 463.3057256469727 7 408.1014371032715 8 375.78066540527345 9 372.45576245117195 10 369.54464453125 11 377.71555517578133 12 383.64710629272463 13 388.4876700744629 14 402.33807241821296 15 402.3691662597656 16 414.3969948120117 17 407.4568319091797 18 434.789603515625 19 430.8916892700196 20 423.19626828002936 Best k = 10 2.599516 seconds (11.12 M allocations: 204.321 MiB, 2.52% gc time, 1.54% compilation time) Test Summary: | Pass Total Time Cross validation on Float32 matrix, normal model | 2 2 17.1s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:41 Cross validating... 6%|██ | ETA: 0:00:22 Cross validating... 10%|███ | ETA: 0:00:16 Cross validating... 13%|████▏ | ETA: 0:00:13 Cross validating... 14%|████▋ | ETA: 0:00:12 Cross validating... 17%|█████▋ | ETA: 0:00:10 Cross validating... 21%|██████▋ | ETA: 0:00:09 Cross validating... 24%|███████▋ | ETA: 0:00:08 Cross validating... 27%|████████▋ | ETA: 0:00:07 Cross validating... 30%|█████████▋ | ETA: 0:00:07 Cross validating... 33%|██████████▋ | ETA: 0:00:06 Cross validating... 37%|███████████▋ | ETA: 0:00:06 Cross validating... 40%|████████████▊ | ETA: 0:00:05 Cross validating... 43%|█████████████▊ | ETA: 0:00:05 Cross validating... 46%|██████████████▊ | ETA: 0:00:04 Cross validating... 49%|███████████████▊ | ETA: 0:00:04 Cross validating... 52%|████████████████▊ | ETA: 0:00:04 Cross validating... 56%|█████████████████▊ | ETA: 0:00:03 Cross validating... 59%|██████████████████▊ | ETA: 0:00:03 Cross validating... 62%|███████████████████▊ | ETA: 0:00:03 Cross validating... 65%|████████████████████▉ | ETA: 0:00:03 Cross validating... 68%|█████████████████████▉ | ETA: 0:00:02 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:02 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:02 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:02 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:01 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:01 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:01 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:01 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:01 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:06 Crossvalidation Results: k MSE 0 462.01820012835464 1 430.16068948365273 2 392.88544974828665 3 346.8425896824656 4 302.19193507390065 5 270.6338715996571 6 252.21827574968245 7 230.11117459053924 8 227.06194739627364 9 231.73910295544138 10 231.42597551572624 11 238.6603739232034 12 242.6771413493724 13 238.44729835697115 14 250.3782053342166 15 261.38399827989196 16 251.99716239169783 17 276.86812916086166 18 272.4660934688935 19 274.71802381047496 20 295.053337278186 Best k = 8 7.241959 seconds (17.40 M allocations: 411.838 MiB, 1.83% gc time, 26.20% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 5%|█▌ | ETA: 0:00:03 Cross validating... 8%|██▌ | ETA: 0:00:04 Cross validating... 11%|███▌ | ETA: 0:00:04 Cross validating... 14%|████▋ | ETA: 0:00:04 Cross validating... 17%|█████▋ | ETA: 0:00:04 Cross validating... 21%|██████▋ | ETA: 0:00:04 Cross validating... 24%|███████▋ | ETA: 0:00:04 Cross validating... 25%|████████▏ | ETA: 0:00:04 Cross validating... 29%|█████████▏ | ETA: 0:00:04 Cross validating... 32%|██████████▏ | ETA: 0:00:03 Cross validating... 35%|███████████▏ | ETA: 0:00:03 Cross validating... 38%|████████████▎ | ETA: 0:00:03 Cross validating... 41%|█████████████▎ | ETA: 0:00:03 Cross validating... 44%|██████████████▎ | ETA: 0:00:03 Cross validating... 46%|██████████████▊ | ETA: 0:00:03 Cross validating... 49%|███████████████▊ | ETA: 0:00:03 Cross validating... 52%|████████████████▊ | ETA: 0:00:02 Cross validating... 56%|█████████████████▊ | ETA: 0:00:02 Cross validating... 59%|██████████████████▊ | ETA: 0:00:02 Cross validating... 62%|███████████████████▊ | ETA: 0:00:02 Cross validating... 65%|████████████████████▉ | ETA: 0:00:02 Cross validating... 68%|█████████████████████▉ | ETA: 0:00:02 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:01 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:01 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:01 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:01 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:01 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:01 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:00 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:05 Crossvalidation Results: k MSE 0 462.01820012835464 1 432.3377069412535 2 395.5116314112818 3 349.1767703660119 4 304.2050157180271 5 273.2474619795463 6 254.98650738818156 7 233.85314145917954 8 233.69802043863496 9 244.7951398765304 10 250.01919505568208 11 258.8314764277716 12 259.59955832591004 13 265.3490684684456 14 272.884941708463 15 271.1419335343643 16 270.75907676947725 17 283.84975905423283 18 294.63916228384466 19 302.7460253730305 20 329.9362980082553 Best k = 8 5.278076 seconds (17.65 M allocations: 366.741 MiB, 1.47% gc time, 1.47% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, logistic model | 2 2 12.8s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:36 Cross validating... 6%|██ | ETA: 0:00:19 Cross validating... 10%|███ | ETA: 0:00:13 Cross validating... 13%|████▏ | ETA: 0:00:11 Cross validating... 16%|█████▏ | ETA: 0:00:09 Cross validating... 19%|██████▏ | ETA: 0:00:08 Cross validating... 21%|██████▋ | ETA: 0:00:07 Cross validating... 24%|███████▋ | ETA: 0:00:07 Cross validating... 27%|████████▋ | ETA: 0:00:06 Cross validating... 30%|█████████▋ | ETA: 0:00:05 Cross validating... 33%|██████████▋ | ETA: 0:00:05 Cross validating... 38%|████████████▎ | ETA: 0:00:04 Cross validating... 43%|█████████████▊ | ETA: 0:00:04 Cross validating... 46%|██████████████▊ | ETA: 0:00:03 Cross validating... 49%|███████████████▊ | ETA: 0:00:03 Cross validating... 52%|████████████████▊ | ETA: 0:00:03 Cross validating... 56%|█████████████████▊ | ETA: 0:00:03 Cross validating... 59%|██████████████████▊ | ETA: 0:00:02 Cross validating... 62%|███████████████████▊ | ETA: 0:00:02 Cross validating... 65%|████████████████████▉ | ETA: 0:00:02 Cross validating... 68%|█████████████████████▉ | ETA: 0:00:02 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:01 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:01 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:01 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:01 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:01 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:01 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:00 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:05 Crossvalidation Results: k MSE 0 465.2807970731294 1 437.35959744754757 2 391.97139521804024 3 380.7351416455822 4 367.62113744696364 5 334.9717995105578 6 309.10924758312643 7 309.6197864683191 8 309.06594274736017 9 311.26655761163977 10 308.35058373103976 11 305.4215568940434 12 313.91424650427086 13 316.96704193643154 14 324.83135774538584 15 318.09524957484126 16 330.8369505601018 17 320.7368546128191 18 317.31609903640395 19 344.9524557416688 20 374.43183485745175 Best k = 11 6.179696 seconds (16.72 M allocations: 400.000 MiB, 1.41% gc time, 35.68% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 5%|█▌ | ETA: 0:00:03 Cross validating... 8%|██▌ | ETA: 0:00:03 Cross validating... 11%|███▌ | ETA: 0:00:03 Cross validating... 14%|████▋ | ETA: 0:00:03 Cross validating... 17%|█████▋ | ETA: 0:00:03 Cross validating... 21%|██████▋ | ETA: 0:00:03 Cross validating... 24%|███████▋ | ETA: 0:00:03 Cross validating... 27%|████████▋ | ETA: 0:00:03 Cross validating... 30%|█████████▋ | ETA: 0:00:03 Cross validating... 33%|██████████▋ | ETA: 0:00:03 Cross validating... 38%|████████████▎ | ETA: 0:00:02 Cross validating... 41%|█████████████▎ | ETA: 0:00:02 Cross validating... 44%|██████████████▎ | ETA: 0:00:02 Cross validating... 48%|███████████████▎ | ETA: 0:00:02 Cross validating... 51%|████████████████▎ | ETA: 0:00:02 Cross validating... 54%|█████████████████▎ | ETA: 0:00:02 Cross validating... 57%|██████████████████▎ | ETA: 0:00:02 Cross validating... 60%|███████████████████▎ | ETA: 0:00:02 Cross validating... 63%|████████████████████▍ | ETA: 0:00:01 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:01 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:01 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:01 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:01 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:01 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:01 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:01 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:00 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:04 Crossvalidation Results: k MSE 0 465.2807970731294 1 438.10857990445845 2 393.67989397034717 3 385.6522018607651 4 375.52367653812587 5 345.4578391215338 6 321.14493007550794 7 325.0493780254414 8 326.5970819105777 9 321.80410676599547 10 331.53794198952295 11 333.5314418068949 12 356.1755874738518 13 364.81362708094997 14 351.71061422072296 15 375.5983966849771 16 367.7235930319236 17 392.6803803635778 18 391.5194030950639 19 395.94243923043945 20 404.04933105404916 Best k = 6 4.128884 seconds (17.00 M allocations: 348.721 MiB, 1.70% gc time, 1.09% compilation time) Test Summary: | Pass Total Time Cross validation on Float64 matrix, logistic model | 2 2 10.9s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:43 Cross validating... 6%|██ | ETA: 0:00:23 Cross validating... 8%|██▌ | ETA: 0:00:20 Cross validating... 11%|███▌ | ETA: 0:00:15 Cross validating... 14%|████▋ | ETA: 0:00:12 Cross validating... 17%|█████▋ | ETA: 0:00:11 Cross validating... 21%|██████▋ | ETA: 0:00:09 Cross validating... 24%|███████▋ | ETA: 0:00:08 Cross validating... 27%|████████▋ | ETA: 0:00:07 Cross validating... 29%|█████████▏ | ETA: 0:00:07 Cross validating... 32%|██████████▏ | ETA: 0:00:07 Cross validating... 35%|███████████▏ | ETA: 0:00:06 Cross validating... 38%|████████████▎ | ETA: 0:00:05 Cross validating... 41%|█████████████▎ | ETA: 0:00:05 Cross validating... 44%|██████████████▎ | ETA: 0:00:05 Cross validating... 48%|███████████████▎ | ETA: 0:00:04 Cross validating... 51%|████████████████▎ | ETA: 0:00:04 Cross validating... 54%|█████████████████▎ | ETA: 0:00:04 Cross validating... 57%|██████████████████▎ | ETA: 0:00:03 Cross validating... 60%|███████████████████▎ | ETA: 0:00:03 Cross validating... 63%|████████████████████▍ | ETA: 0:00:03 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:02 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:02 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:02 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:02 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:01 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:01 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:01 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:01 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:01 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:06 Crossvalidation Results: k MSE 0 727.4045976541995 1 683.4309306864159 2 609.1086950473557 3 482.0502689963069 4 432.12067273204434 5 401.37353544657066 6 388.3520752682831 7 367.868039546344 8 371.86936814004514 9 371.7294598693006 10 379.54697199328274 11 377.54825983279443 12 385.9338226843769 13 397.85307435207346 14 387.69075548943806 15 387.2689151381428 16 399.60181226357815 17 383.81437108884194 18 406.7364650244494 19 394.28196652450924 20 390.1974300624926 Best k = 7 7.403423 seconds (16.59 M allocations: 408.069 MiB, 1.34% gc time, 25.94% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:04 Cross validating... 6%|██ | ETA: 0:00:05 Cross validating... 10%|███ | ETA: 0:00:05 Cross validating... 13%|████▏ | ETA: 0:00:05 Cross validating... 16%|█████▏ | ETA: 0:00:04 Cross validating... 19%|██████▏ | ETA: 0:00:04 Cross validating... 22%|███████▏ | ETA: 0:00:04 Cross validating... 25%|████████▏ | ETA: 0:00:04 Cross validating... 29%|█████████▏ | ETA: 0:00:04 Cross validating... 32%|██████████▏ | ETA: 0:00:04 Cross validating... 35%|███████████▏ | ETA: 0:00:04 Cross validating... 38%|████████████▎ | ETA: 0:00:03 Cross validating... 41%|█████████████▎ | ETA: 0:00:03 Cross validating... 44%|██████████████▎ | ETA: 0:00:03 Cross validating... 48%|███████████████▎ | ETA: 0:00:03 Cross validating... 51%|████████████████▎ | ETA: 0:00:03 Cross validating... 54%|█████████████████▎ | ETA: 0:00:03 Cross validating... 57%|██████████████████▎ | ETA: 0:00:02 Cross validating... 60%|███████████████████▎ | ETA: 0:00:02 Cross validating... 63%|████████████████████▍ | ETA: 0:00:02 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:02 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:02 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:01 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:01 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:01 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:01 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:01 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:01 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:00 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:05 Crossvalidation Results: k MSE 0 727.4045976541995 1 666.1847141272862 2 596.4807406147752 3 482.730336136155 4 434.26590595958294 5 407.49895962728556 6 395.19549935586736 7 376.8787261855358 8 385.7900809141828 9 386.70771196341406 10 388.34314701273746 11 395.1408505875757 12 391.36351260264667 13 420.9983063099395 14 417.9680990269487 15 411.47178494388777 16 427.70174982178105 17 415.1827358871914 18 422.76869562251215 19 436.53805945833824 20 434.26619881595394 Best k = 7 5.561371 seconds (16.04 M allocations: 335.990 MiB, 1.28% gc time, 0.55% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, Poisson model | 2 2 13.3s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:40 Cross validating... 6%|██ | ETA: 0:00:35 Cross validating... 8%|██▌ | ETA: 0:00:38 Cross validating... 11%|███▌ | ETA: 0:00:28 Cross validating... 14%|████▋ | ETA: 0:00:23 Cross validating... 17%|█████▋ | ETA: 0:00:23 Cross validating... 19%|██████▏ | ETA: 0:00:24 Cross 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0:00:05 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:04 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:04 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:03 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:02 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:02 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:01 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:01 Cross validating... 100%|████████████████████████████████| Time: 0:00:40 Crossvalidation Results: k MSE 0 351.84301969254574 1 326.6412781496722 2 291.30567534489865 3 247.8702630843846 4 224.28203303873295 5 211.76583605481113 6 202.7174028524198 7 200.5472562467183 8 198.6578295714928 9 195.71085402543127 10 199.15809475295652 11 202.24449746686054 12 202.04171261408615 13 205.73473381283986 14 203.10173635630753 15 203.92271567324264 16 203.34511167015157 17 205.41270715753848 18 204.9649549828721 19 206.59103634720952 20 209.39214438405293 Best k = 9 40.958410 seconds (138.88 M allocations: 3.566 GiB, 1.56% gc time, 3.70% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:07 Cross validating... 6%|██ | ETA: 0:00:06 Cross validating... 8%|██▌ | ETA: 0:00:06 Cross validating... 11%|███▌ | ETA: 0:00:06 Cross validating... 13%|████▏ | ETA: 0:00:06 Cross validating... 14%|████▋ | ETA: 0:00:06 Cross validating... 16%|█████▏ | ETA: 0:00:06 Cross validating... 17%|█████▋ | ETA: 0:00:06 Cross validating... 19%|██████▏ | ETA: 0:00:06 Cross validating... 21%|██████▋ | ETA: 0:00:06 Cross validating... 22%|███████▏ | ETA: 0:00:06 Cross validating... 24%|███████▋ | ETA: 0:00:06 Cross validating... 25%|████████▏ | ETA: 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89%|████████████████████████████▌ | ETA: 0:00:01 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:01 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:01 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:01 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:10 Crossvalidation Results: k MSE 0 351.84301969254574 1 325.7975526927775 2 291.6722640390621 3 249.4912491671691 4 234.15115097078188 5 214.78658663526505 6 205.5356430259837 7 204.919663830465 8 203.82597168222532 9 202.39984539544466 10 214.95886905816684 11 216.2002589044892 12 223.30157799982783 13 227.5321496169871 14 222.756138453495 15 227.14535895256466 16 229.03365636730317 17 232.94737693352334 18 238.8268048894577 19 240.193948178496 20 245.30781898421895 Best k = 9 10.190468 seconds (32.50 M allocations: 672.863 MiB, 1.92% gc time, 0.78% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, NegativeBinomial model | 2 2 51.5s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:39 Cross validating... 8%|██▌ | ETA: 0:00:16 Cross validating... 13%|████▏ | ETA: 0:00:10 Cross validating... 17%|█████▋ | ETA: 0:00:08 Cross validating... 21%|██████▋ | ETA: 0:00:07 Cross validating... 24%|███████▋ | ETA: 0:00:06 Cross validating... 27%|████████▋ | ETA: 0:00:06 Cross validating... 30%|█████████▋ | ETA: 0:00:05 Cross validating... 33%|██████████▋ | ETA: 0:00:05 Cross validating... 38%|████████████▎ | ETA: 0:00:04 Cross validating... 41%|█████████████▎ | ETA: 0:00:04 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0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:05 Crossvalidation Results: k MSE 0 708.7406597900391 1 594.0547950439453 2 472.60887115478516 3 391.07051165771486 4 322.2429605712891 5 274.1304553527832 6 242.98796069335935 7 231.75397763061522 8 211.04413333129884 9 208.82878451538085 10 210.9139321594238 11 206.8662128601074 12 209.29315435791017 13 216.44690969848637 14 210.83974066162108 15 223.69269552612303 16 223.5122525024414 17 217.3672544555664 18 230.29235778808595 19 245.48900619506838 20 214.24631561279296 Best k = 11 5.729447 seconds (17.23 M allocations: 344.264 MiB, 13.20% gc time, 31.09% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 5%|█▌ | ETA: 0:00:03 Cross validating... 8%|██▌ | ETA: 0:00:03 Cross validating... 11%|███▌ | ETA: 0:00:03 Cross validating... 14%|████▋ | ETA: 0:00:03 Cross validating... 17%|█████▋ | ETA: 0:00:03 Cross validating... 21%|██████▋ | ETA: 0:00:02 Cross validating... 24%|███████▋ | ETA: 0:00:02 Cross validating... 27%|████████▋ | ETA: 0:00:02 Cross validating... 30%|█████████▋ | ETA: 0:00:02 Cross validating... 33%|██████████▋ | ETA: 0:00:02 Cross validating... 38%|████████████▎ | ETA: 0:00:02 Cross validating... 41%|█████████████▎ | ETA: 0:00:02 Cross validating... 44%|██████████████▎ | ETA: 0:00:02 Cross validating... 48%|███████████████▎ | ETA: 0:00:02 Cross validating... 51%|████████████████▎ | ETA: 0:00:02 Cross validating... 54%|█████████████████▎ | ETA: 0:00:02 Cross validating... 57%|██████████████████▎ | ETA: 0:00:01 Cross validating... 60%|███████████████████▎ | ETA: 0:00:01 Cross validating... 63%|████████████████████▍ | ETA: 0:00:01 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:01 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:01 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:01 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:01 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:01 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:00 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:00 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:03 Crossvalidation Results: k MSE 0 708.7406597900391 1 575.6241903076173 2 458.4867525024414 3 380.67050573730467 4 317.43561486816407 5 274.8225385131836 6 243.94065100097657 7 233.23877688598634 8 212.74209445190428 9 214.86823376464844 10 213.80905279541014 11 216.52949041748047 12 220.7860779724121 13 222.78791012573242 14 231.40656030273436 15 233.06280703735348 16 243.6403890075684 17 242.80908297729493 18 238.556499420166 19 251.23290313720705 20 244.79654568481442 Best k = 8 3.388233 seconds (16.27 M allocations: 288.808 MiB, 1.65% gc time, 1.22% compilation time) Test Summary: | Pass Total Time Cross validation on floating point matrices, NegativeBinomial model | 2 2 9.5s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 2%|▋ | ETA: 0:01:05 Cross validating... 3%|█ | ETA: 0:00:46 Cross validating... 4%|█▎ | ETA: 0:00:37 Cross validating... 5%|█▋ | ETA: 0:00:32 Cross validating... 6%|█▉ | ETA: 0:00:29 Cross validating... 7%|██▎ | ETA: 0:00:27 Cross validating... 8%|██▌ | ETA: 0:00:25 Cross validating... 9%|██▉ | ETA: 0:00:24 Cross validating... 10%|███▎ | ETA: 0:00:23 Cross validating... 11%|███▌ | 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98%|███████████████████████████████▍| ETA: 0:00:00 Cross validating... 99%|███████████████████████████████▋| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:16 Crossvalidation Results: k MSE 1 3203.574200344833 2 2998.687030053236 3 2897.6974965749596 4 2833.8255236292516 5 2843.7772170392304 6 2875.0765181363176 7 2882.259806451971 8 2917.185026921881 9 2916.103665401295 10 2969.4523902727533 11 2970.755265319206 12 3013.1643983666418 13 3047.658635804261 14 3048.8805890908375 15 3082.2155479958615 16 3097.0634745820616 17 3073.1305645612056 18 3138.8297394196716 19 3160.352217861099 20 3226.6037876771975 Best k = 4 16.656211 seconds (327.19 k allocations: 222.640 MiB, 0.48% gc time, 8.15% compilation time) Test Summary: | Pass Total Time multivariate cross validation SnpLinAlg | 3 3 21.0s Test Summary: | Pass Total Time wrapper univariate | 20 20 1m32.8s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 2%|▋ | ETA: 0:00:10 Cross validating... 3%|█ | ETA: 0:00:10 Cross validating... 4%|█▎ | ETA: 0:00:11 Cross validating... 5%|█▋ | ETA: 0:00:11 Cross validating... 6%|█▉ | ETA: 0:00:12 Cross validating... 7%|██▎ | ETA: 0:00:12 Cross validating... 8%|██▌ | ETA: 0:00:12 Cross validating... 9%|██▉ | ETA: 0:00:13 Cross validating... 10%|███▎ | ETA: 0:00:14 Cross validating... 11%|███▌ | ETA: 0:00:14 Cross validating... 12%|███▉ | ETA: 0:00:15 Cross validating... 13%|████▏ | ETA: 0:00:15 Cross validating... 14%|████▌ | ETA: 0:00:16 Cross validating... 15%|████▊ | ETA: 0:00:16 Cross validating... 16%|█████▏ | ETA: 0:00:17 Cross validating... 17%|█████▌ | ETA: 0:00:19 Cross validating... 18%|█████▊ | ETA: 0:00:19 Cross validating... 19%|██████▏ | ETA: 0:00:19 Cross validating... 20%|██████▍ | ETA: 0:00:19 Cross 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2105.1311995023634 11 2132.407165368786 12 2138.267187460652 13 2166.002210829576 14 2194.9918295115804 15 2189.890403738045 16 2191.1812932295775 17 2209.4669750564367 18 2221.2595493644303 19 2238.742594576326 20 2253.9559571797727 Best k = 7 **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 2%|▋ | ETA: 0:00:10 Cross validating... 3%|█ | ETA: 0:00:10 Cross validating... 4%|█▎ | ETA: 0:00:11 Cross validating... 5%|█▋ | ETA: 0:00:11 Cross validating... 6%|█▉ | ETA: 0:00:12 Cross validating... 7%|██▎ | ETA: 0:00:12 Cross validating... 8%|██▌ | ETA: 0:00:12 Cross validating... 9%|██▉ | ETA: 0:00:13 Cross validating... 10%|███▎ | ETA: 0:00:14 Cross validating... 11%|███▌ | ETA: 0:00:15 Cross validating... 12%|███▉ | ETA: 0:00:15 Cross validating... 13%|████▏ | ETA: 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2253.9559571797727 Best k = 7 Test Summary: | Pass Total Time wrapper multivariate | 8 8 1m24.0s read BGEN and VCF: Error During Test at /home/pkgeval/.julia/packages/MendelIHT/ZcxZT/test/wrapper_test.jl:184 Got exception outside of a @test startproc must be called before process Stacktrace: [1] error(s::String) @ Base error.jl:56 [2] process(codec::CodecZlib.ZlibDecompressor, input::TranscodingStreams.Memory, output::TranscodingStreams.Memory, error_ref::TranscodingStreams.Error) @ CodecZlib ~/.julia/packages/CodecZlib/BjTS1/src/decompression.jl:199 [3] decompress(io::IOStream, v::Variant, h::BGEN.Header; decompressed::Nothing) @ BGEN ~/.julia/packages/BGEN/dfgRU/src/genotypes.jl:72 [4] first_allele_dosage!(b::Bgen, v::Variant; T::Core.TypeEgal{Float64}, mean_impute::Bool, clear_decompressed::Bool, data::Nothing, decompressed::Nothing, is_decompressed::Bool) @ BGEN ~/.julia/packages/BGEN/dfgRU/src/genotypes.jl:571 [5] convert_bgen_gt(t::Core.TypeEgal{Float64}, b::Bgen) @ MendelIHT ~/.julia/packages/MendelIHT/ZcxZT/src/wrapper.jl:380 [6] macro expansion @ ./timing.jl:741 [inlined] [7] macro expansion @ ~/.julia/packages/MendelIHT/ZcxZT/test/wrapper_test.jl:187 [inlined] [8] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:2247 [inlined] [9] top-level scope @ ~/.julia/packages/MendelIHT/ZcxZT/test/wrapper_test.jl:185 Test Summary: | Error Total Time read BGEN and VCF | 1 1 3.2s RNG of the outermost testset: Xoshiro(0x2175011f8b58f43a, 0x397a83dff89e355f, 0xa996ebee07ec6cd1, 0x697e7bd61106c738, 0x004c8b40140126f4) ERROR: LoadError: Some tests did not pass: 0 passed, 0 failed, 1 errored, 0 broken. in expression starting at /home/pkgeval/.julia/packages/MendelIHT/ZcxZT/test/wrapper_test.jl:184 in expression starting at /home/pkgeval/.julia/packages/MendelIHT/ZcxZT/test/runtests.jl:20 Testing failed after 974.29s ERROR: LoadError: Package MendelIHT errored during testing Stacktrace: [1] pkgerror(msg::String) @ Pkg.Types /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Types.jl:68 [2] test(ctx::Pkg.Types.Context, pkgs::Vector{PackageSpec}; coverage::Bool, julia_args::Cmd, test_args::Cmd, test_fn::Nothing, force_latest_compatible_version::Bool, allow_earlier_backwards_compatible_versions::Bool, allow_reresolve::Bool) @ Pkg.Operations /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Operations.jl:3283 [3] test(ctx::Pkg.Types.Context, pkgs::Vector{PackageSpec}; coverage::Bool, test_fn::Nothing, julia_args::Cmd, test_args::Cmd, force_latest_compatible_version::Bool, allow_earlier_backwards_compatible_versions::Bool, allow_reresolve::Bool, kwargs::@Kwargs{io::IOContext{IO}}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:587 [4] test(pkgs::Vector{PackageSpec}; io::IOContext{IO}, kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:172 [5] test(pkgs::Vector{String}; kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:160 [6] test(pkg::String; kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:159 [inlined] [7] top-level scope @ /PkgEval.jl/scripts/evaluate.jl:223 in expression starting at /PkgEval.jl/scripts/evaluate.jl:214 PkgEval failed after 1612.94s: package tests unexpectedly errored