Package evaluation to test MendelIHT on Julia 1.12.7-DEV.42 (6f510b6086*) started at 2026-06-20T03:55:26.859 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.12` Set-up completed after 9.34s ################################################################################ # Installation # Installing MendelIHT... Resolving package versions... Installed Crayons ────────────────────────── v4.1.1 Installed SIMDTypes ──────────────────────── v0.1.0 Installed BitTwiddlingConvenienceFunctions ─ v0.1.6 Installed CodecXz ────────────────────────── v0.7.4 Installed BioGenerics ────────────────────── v0.1.5 Installed Adapt ──────────────────────────── v4.6.1 Installed IrrationalConstants ────────────── v0.2.6 Installed SIMD ───────────────────────────── v3.7.2 Installed SQLite ─────────────────────────── v1.8.1 Installed OffsetArrays ───────────────────── v1.17.0 Installed LayoutPointers ─────────────────── v0.1.17 Installed CSV ────────────────────────────── v0.10.16 Installed SciMLPublic ────────────────────── v1.0.1 Installed CpuId ──────────────────────────── v0.3.1 Installed VectorizationBase ──────────────── v0.21.74 Installed dlfcn_win32_jll ────────────────── v1.4.2+0 Installed Rmath ──────────────────────────── v0.9.0 Installed HypergeometricFunctions ────────── v0.3.28 Installed StatsFuns ──────────────────────── v2.2.0 Installed Preferences ────────────────────── v1.5.2 Installed TableTraits ────────────────────── v1.0.1 Installed Zstd_jll ───────────────────────── v1.5.7+1 Installed Accessors ──────────────────────── v0.1.44 Installed PtrArrays ──────────────────────── v1.4.0 Installed SpecialFunctions ───────────────── v2.8.0 Installed Bzip2_jll ──────────────────────── v1.0.9+0 Installed CodecBzip2 ─────────────────────── v0.8.5 Installed SQLite_jll ─────────────────────── v3.53.2+0 Installed Parsers ────────────────────────── v2.8.6 Installed SentinelArrays ─────────────────── v1.4.10 Installed CPUSummary ─────────────────────── v0.2.7 Installed XZ_jll ─────────────────────────── v5.8.3+0 Installed Tables ─────────────────────────── v1.12.1 Installed PDMats ─────────────────────────── v0.11.37 Installed PrettyTables ───────────────────── v3.3.2 Installed DataAPI ────────────────────────── v1.16.0 Installed IfElse ─────────────────────────── v0.1.1 Installed PooledArrays ───────────────────── v1.4.3 Installed IteratorInterfaceExtensions ────── v1.0.0 Installed ConstructionBase ───────────────── v1.6.0 Installed InlineStrings ──────────────────── v1.4.5 Installed JLLWrappers ────────────────────── v1.8.0 Installed HostCPUFeatures ────────────────── v0.1.18 Installed ProgressMeter ──────────────────── v1.11.0 Installed LoopVectorization ──────────────── v0.12.174 Installed BGZFStreams ────────────────────── v0.3.2 Installed Roots ──────────────────────────── v3.0.0 Installed PrecompileTools ────────────────── v1.3.4 Installed DataValueInterfaces ────────────── v1.0.0 Installed LaTeXStrings ───────────────────── v1.4.0 Installed ManualMemory ───────────────────── v0.1.8 Installed ThreadingUtilities ─────────────── v0.5.6 Installed OrderedCollections ─────────────── v1.8.2 Installed WorkerUtilities ────────────────── v1.6.1 Installed InvertedIndices ────────────────── v1.3.1 Installed TranscodingStreams ─────────────── v0.9.13 Installed DelimitedFiles ─────────────────── v1.9.1 Installed Combinatorics ──────────────────── v1.1.0 Installed PolyesterWeave ─────────────────── v0.2.2 Installed HypothesisTests ────────────────── v0.11.8 Installed VCFTools ───────────────────────── v0.2.10 Installed Reexport ───────────────────────── v1.2.2 Installed Rmath_jll ──────────────────────── v0.5.1+0 Installed FillArrays ─────────────────────── v1.16.0 Installed FilePathsBase ──────────────────── v0.9.24 Installed Statistics ─────────────────────── v1.11.1 Installed ArrayInterface ─────────────────── v7.25.0 Installed StatsModels ────────────────────── v0.7.10 Installed QuadGK ─────────────────────────── v2.11.3 Installed DBInterface ────────────────────── v2.6.1 Installed VariantCallFormat ──────────────── v0.5.9 Installed GLM ────────────────────────────── v1.9.5 Installed CodecZstd ──────────────────────── v0.8.7 Installed LogExpFunctions ────────────────── v1.0.1 Installed WeakRefStrings ─────────────────── v1.4.3 Installed ShiftedArrays ──────────────────── v2.0.0 Installed DataStructures ─────────────────── v0.19.5 Installed DataFrames ─────────────────────── v1.8.2 Installed AliasTables ────────────────────── v1.1.3 Installed CloseOpenIntervals ─────────────── v0.1.13 Installed SnpArrays ──────────────────────── v0.3.23 Installed BufferedStreams ────────────────── v1.2.2 Installed Requires ───────────────────────── v1.3.1 Installed MacroTools ─────────────────────── v0.5.16 Installed SLEEFPirates ───────────────────── v0.6.46 Installed StatsAPI ───────────────────────── v1.8.0 Installed OpenSpecFun_jll ────────────────── v0.5.6+0 Installed CompositionsBase ───────────────── v0.1.2 Installed Static ─────────────────────────── v1.4.0 Installed UnPack ─────────────────────────── v1.0.2 Installed Compat ─────────────────────────── v4.18.1 Installed Automa ─────────────────────────── v1.2.0 Installed CommonWorldInvalidations ───────── v1.0.0 Installed InverseFunctions ───────────────── v0.1.17 Installed CommonSolve ────────────────────── v0.2.7 Installed Distributions ──────────────────── v0.25.127 Installed Distances ──────────────────────── v0.10.12 Installed CodecZlib ──────────────────────── v0.7.8 Installed StaticArrayInterface ───────────── v1.10.0 Installed Glob ───────────────────────────── v1.5.0 Installed StringManipulation ─────────────── v0.4.4 Installed SortingAlgorithms ──────────────── v1.2.2 Installed Missings ───────────────────────── v1.2.0 Installed DocStringExtensions ────────────── v0.9.5 Installed BGEN ───────────────────────────── v0.1.17 Installed StatsBase ──────────────────────── v0.34.12 Installed MendelIHT ──────────────────────── v1.4.11 Installing 7 artifacts Installed artifact Rmath 121.9 KiB Installed artifact OpenSpecFun 194.9 KiB Installed artifact Bzip2 503.5 KiB Installed artifact SQLite 1.8 MiB Installed artifact Zstd 646.0 KiB Installed artifact XZ 1.6 MiB Installed artifact testfiles 6.2 MiB Updating `~/.julia/environments/v1.12/Project.toml` [921c7187] + MendelIHT v1.4.11 Updating `~/.julia/environments/v1.12/Manifest.toml` [7d9f7c33] + Accessors v0.1.44 [79e6a3ab] + Adapt v4.6.1 [66dad0bd] + AliasTables v1.1.3 [4fba245c] + ArrayInterface v7.25.0 [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 v0.10.16 [fb6a15b2] + CloseOpenIntervals v0.1.13 [523fee87] + CodecBzip2 v0.8.5 [ba30903b] + CodecXz v0.7.4 [944b1d66] + CodecZlib v0.7.8 [6b39b394] + CodecZstd v0.8.7 [861a8166] + Combinatorics v1.1.0 [38540f10] + CommonSolve v0.2.7 [f70d9fcc] + CommonWorldInvalidations v1.0.0 [34da2185] + Compat v4.18.1 [a33af91c] + CompositionsBase v0.1.2 [187b0558] + ConstructionBase v1.6.0 [adafc99b] + CpuId v0.3.1 [a8cc5b0e] + Crayons v4.1.1 [a10d1c49] + DBInterface v2.6.1 [9a962f9c] + DataAPI v1.16.0 [a93c6f00] + DataFrames v1.8.2 [864edb3b] + DataStructures v0.19.5 [e2d170a0] + DataValueInterfaces v1.0.0 [8bb1440f] + DelimitedFiles v1.9.1 [b4f34e82] + Distances v0.10.12 [31c24e10] + Distributions v0.25.127 [ffbed154] + DocStringExtensions v0.9.5 [48062228] + FilePathsBase v0.9.24 [1a297f60] + FillArrays v1.16.0 [38e38edf] + GLM v1.9.5 [c27321d9] + Glob v1.5.0 [3e5b6fbb] + HostCPUFeatures v0.1.18 [34004b35] + HypergeometricFunctions v0.3.28 [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 v1.4.0 [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 v1.8.2 [90014a1f] + PDMats v0.11.37 [69de0a69] + Parsers v2.8.6 [1d0040c9] + PolyesterWeave v0.2.2 [2dfb63ee] + PooledArrays v1.4.3 [aea7be01] + PrecompileTools v1.3.4 [21216c6a] + Preferences v1.5.2 [08abe8d2] + PrettyTables v3.3.2 [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 v3.0.0 [fdea26ae] + SIMD v3.7.2 [94e857df] + SIMDTypes v0.1.0 [476501e8] + SLEEFPirates v0.6.46 [0aa819cd] + SQLite v1.8.1 [431bcebd] + SciMLPublic v1.0.1 [91c51154] + SentinelArrays v1.4.10 [1277b4bf] + ShiftedArrays v2.0.0 [4e780e97] + SnpArrays v0.3.23 [a2af1166] + SortingAlgorithms v1.2.2 [276daf66] + SpecialFunctions v2.8.0 [aedffcd0] + Static v1.4.0 [0d7ed370] + StaticArrayInterface v1.10.0 [10745b16] + Statistics v1.11.1 [82ae8749] + StatsAPI v1.8.0 [2913bbd2] + StatsBase v0.34.12 [4c63d2b9] + StatsFuns v2.2.0 [3eaba693] + StatsModels v0.7.10 [892a3eda] + StringManipulation v0.4.4 [3783bdb8] + TableTraits v1.0.1 [bd369af6] + Tables v1.12.1 [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 v0.5.1+0 [76ed43ae] + SQLite_jll v3.53.2+0 [ffd25f8a] + XZ_jll v5.8.3+0 [3161d3a3] + Zstd_jll v1.5.7+1 [c4b69c83] + dlfcn_win32_jll v1.4.2+0 [0dad84c5] + ArgTools v1.1.2 [56f22d72] + Artifacts v1.11.0 [2a0f44e3] + Base64 v1.11.0 [ade2ca70] + Dates v1.11.0 [8ba89e20] + Distributed v1.11.0 [f43a241f] + Downloads v1.7.0 [7b1f6079] + FileWatching v1.11.0 [9fa8497b] + Future v1.11.0 [b77e0a4c] + InteractiveUtils v1.11.0 [ac6e5ff7] + JuliaSyntaxHighlighting v1.12.0 [b27032c2] + LibCURL v0.6.4 [76f85450] + LibGit2 v1.11.0 [8f399da3] + Libdl v1.11.0 [37e2e46d] + LinearAlgebra v1.12.0 [56ddb016] + Logging v1.11.0 [d6f4376e] + Markdown v1.11.0 [a63ad114] + Mmap v1.11.0 [ca575930] + NetworkOptions v1.3.0 [44cfe95a] + Pkg v1.12.1 [de0858da] + Printf v1.11.0 [3fa0cd96] + REPL v1.11.0 [9a3f8284] + Random v1.11.0 [ea8e919c] + SHA v0.7.0 [9e88b42a] + Serialization v1.11.0 [6462fe0b] + Sockets v1.11.0 [2f01184e] + SparseArrays v1.12.0 [f489334b] + StyledStrings v1.11.0 [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 v1.3.0+1 [deac9b47] + LibCURL_jll v8.15.0+0 [e37daf67] + LibGit2_jll v1.9.0+0 [29816b5a] + LibSSH2_jll v1.11.3+1 [14a3606d] + MozillaCACerts_jll v2025.11.4 [4536629a] + OpenBLAS_jll v0.3.29+0 [05823500] + OpenLibm_jll v0.8.7+0 [458c3c95] + OpenSSL_jll v3.5.6+0 [bea87d4a] + SuiteSparse_jll v7.8.3+2 [83775a58] + Zlib_jll v1.3.1+2 [8e850b90] + libblastrampoline_jll v5.15.0+0 [8e850ede] + nghttp2_jll v1.64.0+1 [3f19e933] + p7zip_jll v17.7.0+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 17.86s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling packages... 4666.8 ms ✓ TestEnv 1 dependency successfully precompiled in 5 seconds. 26 already precompiled. 24 dependencies precompiled but different versions are currently loaded (ArgTools, Base64, Dates, Downloads, JuliaSyntaxHighlighting, LibCURL, LibCURL_jll, LibGit2, LibGit2_jll, LibSSH2_jll, Logging, Markdown, MozillaCACerts_jll, NetworkOptions, OpenSSL_jll, Pkg, Printf, StyledStrings, TOML, Tar, UUIDs, Zlib_jll, nghttp2_jll and p7zip_jll). Restart julia to access the new versions. Otherwise, 1 dependent of these packages may trigger further precompilation to work with the unexpected versions. Precompiling package dependencies... Precompiling packages... 2265.0 ms ✓ Combinatorics 798.3 ms ✓ LaTeXStrings 957.0 ms ✓ Glob 719.5 ms ✓ IteratorInterfaceExtensions 1034.0 ms ✓ WorkerUtilities 853.4 ms ✓ StatsAPI 1658.1 ms ✓ OffsetArrays 762.0 ms ✓ UnPack 1938.3 ms ✓ FillArrays 931.8 ms ✓ InverseFunctions 1016.1 ms ✓ BufferedStreams 1102.5 ms ✓ Statistics 761.5 ms ✓ CommonSolve 7988.8 ms ✓ MacroTools 928.4 ms ✓ ManualMemory 877.4 ms ✓ ShiftedArrays 4137.6 ms ✓ OrderedCollections 742.1 ms ✓ DataValueInterfaces 769.4 ms ✓ Reexport 756.8 ms ✓ SIMDTypes 1135.5 ms ✓ DocStringExtensions 1806.6 ms ✓ InlineStrings 5287.4 ms ✓ IrrationalConstants 821.9 ms ✓ CompositionsBase 843.7 ms ✓ PtrArrays 986.4 ms ✓ DBInterface 996.9 ms ✓ DelimitedFiles 842.3 ms ✓ InvertedIndices 785.7 ms ✓ IfElse 3903.8 ms ✓ ConstructionBase 1000.0 ms ✓ Adapt 836.9 ms ✓ CommonWorldInvalidations 790.1 ms ✓ DataAPI 4682.7 ms ✓ Crayons 857.4 ms ✓ SciMLPublic 1859.4 ms ✓ PDMats 1161.8 ms ✓ Requires 1821.7 ms ✓ ProgressMeter 2014.0 ms ✓ SentinelArrays 4214.4 ms ✓ StructUtils 1930.5 ms ✓ CpuId 1149.5 ms ✓ Preferences 3874.7 ms ✓ Compat 2312.9 ms ✓ TranscodingStreams 714.6 ms ✓ TableTraits 1503.5 ms ✓ FillArrays → FillArraysSparseArraysExt 1735.8 ms ✓ InverseFunctions → InverseFunctionsTestExt 868.4 ms ✓ InverseFunctions → InverseFunctionsDatesExt 4492.7 ms ✓ Distances 1379.1 ms ✓ Statistics → SparseArraysExt 859.7 ms ✓ FillArrays → FillArraysStatisticsExt 4874.0 ms ✓ ThreadingUtilities 3466.4 ms ✓ DataStructures 1305.1 ms ✓ LogExpFunctions 811.9 ms ✓ CompositionsBase → CompositionsBaseInverseFunctionsExt 949.3 ms ✓ AliasTables 836.5 ms ✓ ConstructionBase → ConstructionBaseLinearAlgebraExt 1286.3 ms ✓ Adapt → AdaptSparseArraysExt 3844.9 ms ✓ ArrayInterface 827.0 ms ✓ OffsetArrays → OffsetArraysAdaptExt 999.5 ms ✓ PooledArrays 3692.4 ms ✓ Missings 1390.1 ms ✓ FillArrays → FillArraysPDMatsExt 1316.9 ms ✓ JLLWrappers 1019.5 ms ✓ PrecompileTools 852.3 ms ✓ Compat → CompatLinearAlgebraExt 4693.1 ms ✓ BioGenerics 1663.1 ms ✓ CodecZlib 4765.7 ms ✓ Tables 1347.7 ms ✓ Distances → DistancesSparseArraysExt 1086.0 ms ✓ SortingAlgorithms 5132.2 ms ✓ QuadGK 833.4 ms ✓ LogExpFunctions → LogExpFunctionsInverseFunctionsExt 7945.0 ms ✓ Accessors 1319.9 ms ✓ ArrayInterface → ArrayInterfaceSparseArraysExt 1094.0 ms ✓ dlfcn_win32_jll 1390.8 ms ✓ Bzip2_jll 1403.0 ms ✓ Rmath_jll 1399.9 ms ✓ XZ_jll 1409.8 ms ✓ Zstd_jll 1370.2 ms ✓ OpenSpecFun_jll 3397.5 ms ✓ StringManipulation 21689.3 ms ✓ Automa 18334.0 ms ✓ SIMD 15679.4 ms ✓ Parsers 4569.6 ms ✓ Static 2346.3 ms ✓ FilePathsBase 1709.8 ms ✓ BGZFStreams 851.6 ms ✓ StructUtils → StructUtilsTablesExt 7551.9 ms ✓ StatsBase 2140.0 ms ✓ Accessors → LinearAlgebraExt 1871.7 ms ✓ Accessors → TestExt 1428.4 ms ✓ SQLite_jll 1657.7 ms ✓ CodecBzip2 1556.4 ms ✓ Rmath 1552.9 ms ✓ CodecXz 2789.0 ms ✓ CodecZstd 5686.2 ms ✓ SpecialFunctions 49001.0 ms ✓ PrettyTables 10333.6 ms ✓ JSON 923.2 ms ✓ InlineStrings → ParsersExt 930.1 ms ✓ BitTwiddlingConvenienceFunctions 2793.6 ms ✓ CPUSummary 9103.4 ms ✓ StaticArrayInterface 1342.1 ms ✓ FilePathsBase → FilePathsBaseMmapExt 3316.9 ms ✓ FilePathsBase → FilePathsBaseTestExt 16094.5 ms ✓ VariantCallFormat 1497.7 ms ✓ PDMats → StatsBaseExt 9518.2 ms ✓ Roots 2175.9 ms ✓ HypergeometricFunctions 90413.7 ms ✓ DataFrames 11869.1 ms ✓ BenchmarkTools 2278.9 ms ✓ WeakRefStrings 1807.4 ms ✓ HostCPUFeatures 1761.6 ms ✓ PolyesterWeave 1056.2 ms ✓ StaticArrayInterface → StaticArrayInterfaceOffsetArraysExt 1103.8 ms ✓ CloseOpenIntervals 1273.9 ms ✓ LayoutPointers 4962.7 ms ✓ StatsFuns 30882.1 ms ✓ CSV 3995.9 ms ✓ SQLite 20097.4 ms ✓ VectorizationBase 959.6 ms ✓ StatsFuns → StatsFunsInverseFunctionsExt 4969.4 ms ✓ StatsModels 9743.2 ms ✓ Distributions 8490.1 ms ✓ BGEN 5956.1 ms ✓ SLEEFPirates 3447.4 ms ✓ Distributions → DistributionsTestExt 5450.8 ms ✓ GLM 4382.6 ms ✓ HypothesisTests 51229.6 ms ✓ LoopVectorization 5143.4 ms ✓ VCFTools 5161.6 ms ✓ LoopVectorization → SpecialFunctionsExt 28100.4 ms ✓ SnpArrays 44403.2 ms ✓ MendelIHT 135 dependencies successfully precompiled in 704 seconds. 39 already precompiled. 24 dependencies precompiled but different versions are currently loaded (ArgTools, Base64, Dates, Downloads, JuliaSyntaxHighlighting, LibCURL, LibCURL_jll, LibGit2, LibGit2_jll, LibSSH2_jll, Logging, Markdown, MozillaCACerts_jll, NetworkOptions, OpenSSL_jll, Pkg, Printf, StyledStrings, TOML, Tar, UUIDs, Zlib_jll, nghttp2_jll and p7zip_jll). Restart julia to access the new versions. Otherwise, 81 dependents of these packages may trigger further precompilation to work with the unexpected versions. 2 dependencies had output during precompilation: ┌ VariantCallFormat │ [ Info: Compiling VCF parser... └ ┌ 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`. └ Precompilation completed after 725.39s ################################################################################ # Testing # Testing MendelIHT Status `/tmp/jl_kBXMsX/Project.toml` ⌅ [6db4b851] BGEN v0.1.17 [6e4b80f9] BenchmarkTools v1.8.0 [336ed68f] CSV v0.10.16 [a93c6f00] DataFrames v1.8.2 [8bb1440f] DelimitedFiles v1.9.1 [b4f34e82] Distances v0.10.12 [31c24e10] Distributions v0.25.127 [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 v2.8.0 [2913bbd2] StatsBase v0.34.12 [a620830f] VCFTools v0.2.10 [37e2e46d] LinearAlgebra v1.12.0 [44cfe95a] Pkg v1.12.1 [9a3f8284] Random v1.11.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_kBXMsX/Manifest.toml` [7d9f7c33] Accessors v0.1.44 [79e6a3ab] Adapt v4.6.1 [66dad0bd] AliasTables v1.1.3 [4fba245c] ArrayInterface v7.25.0 [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 v0.10.16 [fb6a15b2] CloseOpenIntervals v0.1.13 [523fee87] CodecBzip2 v0.8.5 [ba30903b] CodecXz v0.7.4 [944b1d66] CodecZlib v0.7.8 [6b39b394] CodecZstd v0.8.7 [861a8166] Combinatorics v1.1.0 [38540f10] CommonSolve v0.2.7 [f70d9fcc] CommonWorldInvalidations v1.0.0 [34da2185] Compat v4.18.1 [a33af91c] CompositionsBase v0.1.2 [187b0558] ConstructionBase v1.6.0 [adafc99b] CpuId v0.3.1 [a8cc5b0e] Crayons v4.1.1 [a10d1c49] DBInterface v2.6.1 [9a962f9c] DataAPI v1.16.0 [a93c6f00] DataFrames v1.8.2 [864edb3b] DataStructures v0.19.5 [e2d170a0] DataValueInterfaces v1.0.0 [8bb1440f] DelimitedFiles v1.9.1 [b4f34e82] Distances v0.10.12 [31c24e10] Distributions v0.25.127 [ffbed154] DocStringExtensions v0.9.5 [48062228] FilePathsBase v0.9.24 [1a297f60] FillArrays v1.16.0 [38e38edf] GLM v1.9.5 [c27321d9] Glob v1.5.0 [3e5b6fbb] HostCPUFeatures v0.1.18 [34004b35] HypergeometricFunctions v0.3.28 [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 v1.6.1 [b964fa9f] LaTeXStrings v1.4.0 [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 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[3f19e933] p7zip_jll v17.7.0+0 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. Testing Running tests... ┌ 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 └ @ Core ~/.julia/packages/MendelIHT/ZcxZT/src/multivariate.jl:241 Test Summary: | Pass Total Time loglikelihood | 4 4 16.4s Test Summary: | Pass Total Time deviance | 1 1 0.5s Test Summary: | Pass Total Time update_μ! | 4 4 1.5s Test Summary: | Pass Total Time _choose! | 7 7 9.0s Test Summary: | Pass Total Time _iht_backtrack | 7 7 0.0s Test Summary: | Pass Total Time standardize! | 12 12 2.1s Test Summary: | Pass Total Time project_k! | 2 2 1.0s Test Summary: | Pass Total Time project_group_sparse! | 5 5 1.3s Test Summary: | Pass Total Time maf_weights | 6 6 2.4s **** 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 **** 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 = -1852.6387939759097, backtracks = 0, tol = 2.166372088671523 Iteration 2: loglikelihood = -1440.361650755496, backtracks = 0, tol = 0.170977332200978 Iteration 3: loglikelihood = -1380.3355415821927, backtracks = 0, tol = 0.06113459156226441 Iteration 4: loglikelihood = -1373.2903655269536, backtracks = 0, tol = 0.035377601125619704 Iteration 5: loglikelihood = -1373.0101982853962, backtracks = 1, tol = 0.0020631941650929406 Iteration 6: loglikelihood = -1372.9371930919042, backtracks = 1, tol = 0.001033274621692094 Iteration 7: loglikelihood = -1372.9182610279825, backtracks = 1, tol = 0.0005074261769117227 Iteration 8: loglikelihood = -1372.9133838178195, backtracks = 1, tol = 0.0002448259094919046 Iteration 9: loglikelihood = -1372.9121361480682, backtracks = 1, tol = 0.0001285386707092206 Iteration 10: loglikelihood = -1372.911818958794, backtracks = 1, tol = 6.891654750022139e-5 IHT estimated 10 nonzero SNP predictors and 1 non-genetic predictors. Compute time (sec): 0.0952601432800293 Final loglikelihood: -1372.911818958794 SNP PVE: 0.9507369065095351 Iterations: 10 Selected genetic predictors: 10×2 DataFrame Row │ Position Estimated_β │ Int64 Float64 ─────┼─────────────────────── 1 │ 1070 0.338453 2 │ 1909 -0.952087 3 │ 2192 -0.555007 4 │ 2927 -0.399196 5 │ 3174 -0.138831 6 │ 3452 2.66375 7 │ 4152 0.128127 8 │ 4165 -0.815628 9 │ 6020 2.53882 10 │ 8410 1.55159 Selected nongenetic predictors: 1×2 DataFrame Row │ Position Estimated_β │ Int64 Float64 ─────┼─────────────────────── 1 │ 1 -0.0644931Test Summary: | Pass Total Time fit normal SnpLinAlg | 4 4 23.4s **** 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 **** 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 = -357.05406929589384, backtracks = 0, tol = 0.8380082173781972 Iteration 2: loglikelihood = -253.69247673658248, backtracks = 0, tol = 0.38139022833574177 Iteration 3: loglikelihood = -242.78890265594725, backtracks = 0, tol = 0.21772646553308606 Iteration 4: loglikelihood = -211.3640910919962, backtracks = 0, tol = 0.18632794312765352 Iteration 5: loglikelihood = -206.07758041780974, backtracks = 1, tol = 0.051383518206643046 Iteration 6: loglikelihood = -204.018617087407, backtracks = 3, tol = 0.020052933740041072 Iteration 7: loglikelihood = -202.12440666162166, backtracks = 3, tol = 0.022394307327778626 Iteration 8: loglikelihood = -200.51339216597611, backtracks = 3, tol = 0.021600855513207017 Iteration 9: loglikelihood = -199.1607521139652, backtracks = 3, tol = 0.020205916063858787 Iteration 10: loglikelihood = -198.03368293305746, backtracks = 3, tol = 0.018747980180644195 Iteration 11: loglikelihood = -197.1010787346633, backtracks = 3, tol = 0.01730311555883611 Iteration 12: loglikelihood = -199.1081399043643, backtracks = 3, tol = 0.10742989707378812 Iteration 13: loglikelihood = -196.35077450026276, backtracks = 0, tol = 0.10574886891481221 Iteration 14: loglikelihood = -195.5179886251886, backtracks = 1, tol = 0.016488769010944707 Iteration 15: loglikelihood = -195.26353610431914, backtracks = 3, tol = 0.005398010607219295 Iteration 16: loglikelihood = -194.94618143558304, backtracks = 3, tol = 0.008296620982687967 Iteration 17: loglikelihood = -198.1603861597454, backtracks = 3, tol = 0.1191184942601117 Iteration 18: loglikelihood = -196.08507656080548, backtracks = 0, tol = 0.04091866505365408 Iteration 19: loglikelihood = -194.68771845520706, backtracks = 2, tol = 0.08627046961582337 Iteration 20: loglikelihood = -194.18573370488792, backtracks = 1, tol = 0.012532615214018756 Iteration 21: loglikelihood = -194.04409249060237, backtracks = 2, tol = 0.0045289192218591345 Iteration 22: loglikelihood = -193.89081161879778, backtracks = 2, tol = 0.005408550068552711 Iteration 23: loglikelihood = -197.78991514558754, backtracks = 3, tol = 0.12418846818411548 Iteration 24: loglikelihood = -195.3458651891717, backtracks = 0, tol = 0.04474686356665713 Iteration 25: loglikelihood = -193.85329270192864, backtracks = 1, tol = 0.11642705219079118 Iteration 26: loglikelihood = -193.5872888252266, backtracks = 1, tol = 0.005994529796500222 Iteration 27: loglikelihood = -193.49244103087173, backtracks = 1, tol = 0.003977497505879251 Iteration 28: loglikelihood = -193.43959542357507, backtracks = 2, tol = 0.00330084983993103 Iteration 29: loglikelihood = -197.2834449493823, backtracks = 3, tol = 0.14332949891400917 Iteration 30: loglikelihood = -191.1561814374434, backtracks = 0, tol = 0.14271551862933007 Iteration 31: loglikelihood = -190.2589777412173, backtracks = 1, tol = 0.018296148237923138 Iteration 32: loglikelihood = -189.9878891870221, backtracks = 1, tol = 0.010701165536450384 Iteration 33: loglikelihood = -189.867470684632, backtracks = 1, tol = 0.007473112269951343 Iteration 34: loglikelihood = -193.0058316555954, backtracks = 3, tol = 0.1141647124557401 Iteration 35: loglikelihood = -191.61778833782117, backtracks = 0, tol = 0.033257092226161265 Iteration 36: loglikelihood = -190.26592749131268, backtracks = 0, tol = 0.12758732776034531 Iteration 37: loglikelihood = -189.83372327320802, backtracks = 1, tol = 0.008553392013129577 Iteration 38: loglikelihood = -189.70612855593623, backtracks = 1, tol = 0.0044027459232161385 Iteration 39: loglikelihood = -189.65408637483733, backtracks = 1, tol = 0.003586549894028387 Iteration 40: loglikelihood = -189.6305816735391, backtracks = 3, tol = 0.0019965524261909384 Iteration 41: loglikelihood = -200.89359611814402, backtracks = 3, tol = 0.14583347899126511 Iteration 42: loglikelihood = -193.27097139861027, backtracks = 0, tol = 0.14535809468532176 Iteration 43: loglikelihood = -192.2935217503592, backtracks = 1, tol = 0.015904619777886927 Iteration 44: loglikelihood = -192.0507085557377, backtracks = 1, tol = 0.008141180826631752 Iteration 45: loglikelihood = -191.98876965234143, backtracks = 1, tol = 0.0042025046810855214 Iteration 46: loglikelihood = -191.9726936044892, backtracks = 1, tol = 0.0021655324830217207 Iteration 47: loglikelihood = -191.96846706923031, backtracks = 1, tol = 0.0011055332529237927 Iteration 48: loglikelihood = -191.96734266484526, backtracks = 1, tol = 0.0005555964548322557 Iteration 49: loglikelihood = -191.9670386960076, backtracks = 1, tol = 0.0002733997501911196 Iteration 50: loglikelihood = -191.96695335555074, backtracks = 1, tol = 0.00013154922168130258 Iteration 51: loglikelihood = -191.96692620413978, backtracks = 1, tol = 7.105685194739283e-5 Test Summary: | Pass Total Time fit Bernoulli SnpLinAlg | 4 4 3.1s **** 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 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 = -7686.9827725201685, backtracks = 0, tol = 0.37177508546612004 Iteration 2: loglikelihood = -4746.608022562504, backtracks = 0, tol = 0.03925240224861428 Iteration 3: loglikelihood = -2383.5688511123626, backtracks = 0, tol = 0.06565385075113153 Iteration 4: loglikelihood = -1767.3586369885072, backtracks = 0, tol = 0.0583036293674399 Iteration 5: loglikelihood = -1635.9887685375488, backtracks = 0, tol = 0.04211545788624573 Iteration 6: loglikelihood = -1502.6695060691377, backtracks = 0, tol = 0.10985727868258642 Iteration 7: loglikelihood = -1472.0868338527216, backtracks = 0, tol = 0.07464893770011326 Iteration 8: loglikelihood = -1432.7468065709456, backtracks = 0, tol = 0.04951327847303346 Iteration 9: loglikelihood = -1415.7110080656387, backtracks = 0, tol = 0.03988479661448988 Iteration 10: loglikelihood = -1407.8109706338328, backtracks = 0, tol = 0.024684345971493295 Iteration 11: loglikelihood = -1403.5773036576418, backtracks = 0, tol = 0.01824011778519789 Iteration 12: loglikelihood = -1400.4199943619828, backtracks = 0, tol = 0.01377750723184159 Iteration 13: loglikelihood = -1398.1673740184324, backtracks = 0, tol = 0.011382976433070641 Iteration 14: loglikelihood = -1396.388678363378, backtracks = 0, tol = 0.010295660170060025 Iteration 15: loglikelihood = -1395.0950819680072, backtracks = 0, tol = 0.007641399509499618 Iteration 16: loglikelihood = -1394.065900972146, backtracks = 0, tol = 0.008978230533531407 Iteration 17: loglikelihood = -1393.3347670334813, backtracks = 0, tol = 0.005194740190268204 Iteration 18: loglikelihood = -1392.7659443786617, backtracks = 0, tol = 0.007782576561044449 Iteration 19: loglikelihood = -1392.3792011924793, backtracks = 0, tol = 0.0037225301029825976 Iteration 20: loglikelihood = -1392.1625217514645, backtracks = 1, tol = 0.0031193878785951284 Iteration 21: loglikelihood = -1392.004505763805, backtracks = 0, tol = 0.004750033462085798 Iteration 22: loglikelihood = -1391.8899451599664, backtracks = 0, tol = 0.0024608494652815006 Iteration 23: loglikelihood = -1391.8084350643257, backtracks = 0, tol = 0.0032898835995988146 Iteration 24: loglikelihood = -1391.7484224005914, backtracks = 0, tol = 0.001777509708441895 Iteration 25: loglikelihood = -1391.7047834518216, backtracks = 0, tol = 0.0023445519411919055 Iteration 26: loglikelihood = -1391.6723520795247, backtracks = 0, tol = 0.0013057240157294302 Iteration 27: loglikelihood = -1391.6484572307909, backtracks = 0, tol = 0.0017024659608939933 Iteration 28: loglikelihood = -1391.6305920817383, backtracks = 0, tol = 0.0009684667425032838 Iteration 29: loglikelihood = -1391.6173173987697, backtracks = 0, tol = 0.0012515167620561522 Iteration 30: loglikelihood = -1391.6073524782812, backtracks = 0, tol = 0.0007229423474478623 Iteration 31: loglikelihood = -1391.5999057376077, backtracks = 0, tol = 0.0009278350778825776 Iteration 32: loglikelihood = -1391.594300170416, backtracks = 0, tol = 0.0005420252463343417 Iteration 33: loglikelihood = -1391.5900945637609, backtracks = 0, tol = 0.0006919871574778407 Iteration 34: loglikelihood = -1391.5869225901174, backtracks = 0, tol = 0.0004076228133501562 Iteration 35: loglikelihood = -1391.5845361188865, backtracks = 0, tol = 0.0005183097283052485 Iteration 36: loglikelihood = -1391.5827336649415, backtracks = 0, tol = 0.00030721279317497737 Iteration 37: loglikelihood = -1391.5813748238597, backtracks = 0, tol = 0.0003894385270759325 Iteration 38: loglikelihood = -1391.5803474768254, backtracks = 0, tol = 0.00023190011629351328 Iteration 39: loglikelihood = -1391.5795718328031, backtracks = 0, tol = 0.00029328376945507103 Iteration 40: loglikelihood = -1391.578984973619, backtracks = 0, tol = 0.00017525102005471512 Iteration 41: loglikelihood = -1391.5785414147456, backtracks = 0, tol = 0.00022124742205821476 Iteration 42: loglikelihood = -1391.5782056296944, backtracks = 0, tol = 0.00013255236535894132 Iteration 43: loglikelihood = -1391.5779516324699, backtracks = 0, tol = 0.00016711709910522958 Iteration 44: loglikelihood = -1391.5777592717184, backtracks = 0, tol = 0.00010031992981746184 Iteration 45: loglikelihood = -1391.5776136771103, backtracks = 0, tol = 0.00012635055429248497 Iteration 46: loglikelihood = -1391.5775033797065, backtracks = 0, tol = 7.596098480427114e-5 Test Summary: | Pass Total Time fit Poisson SnpLinAlg | 4 4 2.9s **** 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 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 = -1743.9818150428302, backtracks = 0, tol = 0.39442342766812266 Iteration 2: loglikelihood = -1602.2453635185832, backtracks = 0, tol = 0.19158559023485747 Iteration 3: loglikelihood = -1545.7640927157236, backtracks = 0, tol = 0.12722648517341212 Iteration 4: loglikelihood = -1523.0271259934052, backtracks = 0, tol = 0.09901554518370051 Iteration 5: loglikelihood = -1520.126789658429, backtracks = 0, tol = 0.04271821642728502 Iteration 6: loglikelihood = -1519.377619426839, backtracks = 0, tol = 0.019299330794680956 Iteration 7: loglikelihood = -1519.2062540101117, backtracks = 0, tol = 0.00979491506947032 Iteration 8: loglikelihood = -1519.1656443034653, backtracks = 0, tol = 0.004370191278220429 Iteration 9: loglikelihood = -1519.155892379003, backtracks = 0, tol = 0.0024027478439342816 Iteration 10: loglikelihood = -1519.1534905187334, backtracks = 0, tol = 0.0010951149684893249 Iteration 11: loglikelihood = -1519.1528888767714, backtracks = 0, tol = 0.000612142807201065 Iteration 12: loglikelihood = -1519.152735967082, backtracks = 0, tol = 0.00029053163426686767 Iteration 13: loglikelihood = -1519.152696975164, backtracks = 0, tol = 0.00015883046217543507 Iteration 14: loglikelihood = -1519.1526869856432, backtracks = 0, tol = 7.821682027941178e-5 Test Summary: | Pass Total Time fit NegativeBinomial SnpLinAlg | 4 4 1.3s **** 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 **** 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 = -1823.305004524486, backtracks = 0, tol = 0.7982115173165009 Iteration 2: loglikelihood = -1430.8735483038945, backtracks = 0, tol = 0.11266666909600485 Iteration 3: loglikelihood = -1371.252692538536, backtracks = 0, tol = 0.04716972688325889 Iteration 4: loglikelihood = -1369.4700844397632, backtracks = 0, tol = 0.02538320192236595 Iteration 5: loglikelihood = -1369.3794111305344, backtracks = 0, tol = 0.023567400681682296 Iteration 6: loglikelihood = -1369.3310745183974, backtracks = 0, tol = 0.0015101304013800765 Iteration 7: loglikelihood = -1369.3308620520663, backtracks = 1, tol = 4.663716342280236e-5 Test Summary: | Pass Total Time fit with >1 non-genetic covariates SnpLinAlg | 5 5 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 = -1462.859151664566, backtracks = 0, tol = 0.34296813082539157 Iteration 2: loglikelihood = -1379.3656466141917, backtracks = 0, tol = 0.07223977259068157 Iteration 3: loglikelihood = -1370.7071795213992, backtracks = 0, tol = 0.033663927500042636 Iteration 4: loglikelihood = -1370.3727742132178, backtracks = 0, tol = 0.0263087371526322 Iteration 5: loglikelihood = -1369.627057469172, backtracks = 0, tol = 0.0263087371526322 Iteration 6: loglikelihood = -1369.5266237472015, backtracks = 0, tol = 0.0019287982379442177 Iteration 7: loglikelihood = -1369.525964357122, backtracks = 1, tol = 0.00010557820391836514 Iteration 8: loglikelihood = -1369.525790355861, backtracks = 1, tol = 5.29831736316823e-5 Test Summary: | Pass Total Time model selection on non-genetic covariates | 5 5 1.0s **** 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 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 = -1523.5958299921442, backtracks = 0, tol = 0.129071945392328 Iteration 2: loglikelihood = -1477.249859294593, backtracks = 0, tol = 0.08696841134209665 Iteration 3: loglikelihood = -1476.0121270981692, backtracks = 0, tol = 0.1343225194224959 Iteration 4: loglikelihood = -1447.8443838957955, backtracks = 0, tol = 0.11013528966572202 Iteration 5: loglikelihood = -1427.8242345986778, backtracks = 0, tol = 0.08209060918136464 Iteration 6: loglikelihood = -1414.2794725041153, backtracks = 0, tol = 0.10123294488164228 Iteration 7: loglikelihood = -1411.2564308202386, backtracks = 0, tol = 0.048387448547542636 Iteration 8: loglikelihood = -1411.050772541226, backtracks = 0, tol = 0.009770585645740737 Iteration 9: loglikelihood = -1411.015046678896, backtracks = 0, tol = 0.0044797142739283246 Iteration 10: loglikelihood = -1411.0073439042797, backtracks = 0, tol = 0.001416636381297378 Iteration 11: loglikelihood = -1411.005269199528, backtracks = 0, tol = 0.0009276879819342229 Iteration 12: loglikelihood = -1411.0045554592828, backtracks = 0, tol = 0.0004610425460981298 Iteration 13: loglikelihood = -1411.0042923301237, backtracks = 0, tol = 0.0003630593339154695 Iteration 14: loglikelihood = -1411.0041913953814, backtracks = 0, tol = 0.00018097289114187264 Iteration 15: loglikelihood = -1411.004151515616, backtracks = 0, tol = 0.0001478056297443225 Iteration 16: loglikelihood = -1411.0041354814252, backtracks = 0, tol = 7.383869781080513e-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 = -1576.5944043258398, backtracks = 0, tol = 0.2463131288927061 Iteration 2: loglikelihood = -1505.7732565165654, backtracks = 0, tol = 0.2064188478236517 Iteration 3: loglikelihood = -1447.9586527011343, backtracks = 0, tol = 0.12175655579203716 Iteration 4: loglikelihood = -1435.2881744666033, backtracks = 0, tol = 0.10768352613090407 Iteration 5: loglikelihood = -1429.51454262393, backtracks = 0, tol = 0.07586033223139907 Iteration 6: loglikelihood = -1427.7139178076804, backtracks = 0, tol = 0.04177042151609518 Iteration 7: loglikelihood = -1427.4217897418478, backtracks = 0, tol = 0.012310297064338293 Iteration 8: loglikelihood = -1427.3437566906503, backtracks = 0, tol = 0.004079249115440825 Iteration 9: loglikelihood = -1427.318944353514, backtracks = 0, tol = 0.0023015635627460663 Iteration 10: loglikelihood = -1427.3106426516142, backtracks = 0, tol = 0.001486332592774629 Iteration 11: loglikelihood = -1427.307785188213, backtracks = 0, tol = 0.0008216441158313917 Iteration 12: loglikelihood = -1427.3067826218225, backtracks = 0, tol = 0.0005535056526890428 Iteration 13: loglikelihood = -1427.3064222471853, backtracks = 0, tol = 0.00030122218778151324 Iteration 14: loglikelihood = -1427.306290594537, backtracks = 0, tol = 0.000210435184027697 Iteration 15: loglikelihood = -1427.3062415375573, backtracks = 0, tol = 0.00011334289016943538 Iteration 16: loglikelihood = -1427.3062230242942, backtracks = 0, tol = 8.120447775564562e-5 Test Summary: | Pass Total Time Correlated predictors and double sparsity Float64 matrix | 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 **** 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 = -1706.7962154664776, backtracks = 0, tol = 0.18918175370077445 Iteration 2: loglikelihood = -1601.3298937132615, backtracks = 0, tol = 0.11353412716942468 Iteration 3: loglikelihood = -1508.1335679439414, backtracks = 0, tol = 0.16005880659277733 Iteration 4: loglikelihood = -1476.5007563649053, backtracks = 0, tol = 0.11766555760828631 Iteration 5: loglikelihood = -1449.7793973587777, backtracks = 0, tol = 0.0867924558785441 Iteration 6: loglikelihood = -1428.448222905083, backtracks = 0, tol = 0.05218781559679651 Iteration 7: loglikelihood = -1419.1021667213383, backtracks = 0, tol = 0.03458581349703423 Iteration 8: loglikelihood = -1413.0023806645622, backtracks = 0, tol = 0.022272207409501327 Iteration 9: loglikelihood = -1405.5060964058048, backtracks = 0, tol = 0.04522478285724582 Iteration 10: loglikelihood = -1398.2282340751547, backtracks = 0, tol = 0.05651812575279578 Iteration 11: loglikelihood = -1391.7056105906179, backtracks = 0, tol = 0.027564717378679382 Iteration 12: loglikelihood = -1388.4573250397198, backtracks = 0, tol = 0.05300837636500707 Iteration 13: loglikelihood = -1387.385759438297, backtracks = 0, tol = 0.01145516135972126 Iteration 14: loglikelihood = -1386.9553762120797, backtracks = 0, tol = 0.010926337984974352 Iteration 15: loglikelihood = -1386.737126954723, backtracks = 0, tol = 0.0053160250982798776 Iteration 16: loglikelihood = -1386.6192358192332, backtracks = 0, tol = 0.005785298362235795 Iteration 17: loglikelihood = -1386.5538371759362, backtracks = 0, tol = 0.002917157358930424 Iteration 18: loglikelihood = -1386.5173800969656, backtracks = 0, tol = 0.0031664599543625755 Iteration 19: loglikelihood = -1386.4969429599416, backtracks = 0, tol = 0.0016269140378884985 Iteration 20: loglikelihood = -1386.4854806789804, backtracks = 0, tol = 0.0017571745873781574 Iteration 21: loglikelihood = -1386.4790415970697, backtracks = 0, tol = 0.0009124731387791867 Iteration 22: loglikelihood = -1386.475423720264, backtracks = 0, tol = 0.0009809798794796674 Iteration 23: loglikelihood = -1386.4733901544816, backtracks = 0, tol = 0.0005129576395549715 Iteration 24: loglikelihood = -1386.47224686109, backtracks = 0, tol = 0.0005491337842384761 Iteration 25: loglikelihood = -1386.4716041637503, backtracks = 0, tol = 0.0002886121636556679 Iteration 26: loglikelihood = -1386.471242774815, backtracks = 0, tol = 0.000307767162683271 Iteration 27: loglikelihood = -1386.4710396432092, backtracks = 0, tol = 0.00016242038566386646 Iteration 28: loglikelihood = -1386.470925429338, backtracks = 0, tol = 0.00017257498789011307 Iteration 29: loglikelihood = -1386.4708612450218, backtracks = 0, tol = 9.139781392229764e-5 1.121674 seconds (2.49 M allocations: 50.499 MiB, 8.70% gc time, 53.44% 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 = -1717.941245684496, backtracks = 0, tol = 0.18918175370077445 Iteration 2: loglikelihood = -1649.4601387555902, backtracks = 0, tol = 0.12517865663025715 Iteration 3: loglikelihood = -1574.8032255988667, backtracks = 0, tol = 0.1662023823562924 Iteration 4: loglikelihood = -1553.3726612668274, backtracks = 0, tol = 0.10277491515415342 Iteration 5: loglikelihood = -1522.6710996340921, backtracks = 0, tol = 0.045476628612339066 Iteration 6: loglikelihood = -1505.5920175426245, backtracks = 0, tol = 0.08447132474840419 Iteration 7: loglikelihood = -1484.9487858525288, backtracks = 0, tol = 0.07984925715675906 Iteration 8: loglikelihood = -1481.4578545077636, backtracks = 0, tol = 0.08107048205793432 Iteration 9: loglikelihood = -1460.6281391691655, backtracks = 0, tol = 0.08007216755502548 Iteration 10: loglikelihood = -1456.6844347710103, backtracks = 0, tol = 0.06752035122903417 Iteration 11: loglikelihood = -1445.180166689552, backtracks = 0, tol = 0.06547243217222494 Iteration 12: loglikelihood = -1438.5467631003926, backtracks = 0, tol = 0.024204452027987423 Iteration 13: loglikelihood = -1434.4508810817006, backtracks = 0, tol = 0.06185417247764139 Iteration 14: loglikelihood = -1429.4869500046602, backtracks = 0, tol = 0.06181466009381881 Iteration 15: loglikelihood = -1425.5349924191216, backtracks = 0, tol = 0.0056415625372591574 Iteration 16: loglikelihood = -1422.228426880207, backtracks = 0, tol = 0.0008418229128283894 Iteration 17: loglikelihood = -1419.2720318490422, backtracks = 0, tol = 0.0004754379544903809 Iteration 18: loglikelihood = -1416.6604384909463, backtracks = 0, tol = 0.00043477134941380407 Iteration 19: loglikelihood = -1414.3118782777658, backtracks = 0, tol = 0.00028529530455515955 Iteration 20: loglikelihood = -1412.2089653899575, backtracks = 0, tol = 0.0003332107910935434 Iteration 21: loglikelihood = -1410.3037495131582, backtracks = 0, tol = 0.00023694840970437856 Iteration 22: loglikelihood = -1408.5816089244988, backtracks = 0, tol = 0.0002774449954017832 Iteration 23: loglikelihood = -1407.0105916634284, backtracks = 0, tol = 0.0002102941528991456 Iteration 24: loglikelihood = -1405.57984802651, backtracks = 0, tol = 0.0002415645509482788 Iteration 25: loglikelihood = -1404.2667262227178, backtracks = 0, tol = 0.0001910911079382489 Iteration 26: loglikelihood = -1403.0634195688183, backtracks = 0, tol = 0.0002148671343636389 Iteration 27: loglikelihood = -1401.9531529334465, backtracks = 0, tol = 0.00017577557569052702 Iteration 28: loglikelihood = -1400.9304006313562, backtracks = 0, tol = 0.00019375304766120141 Iteration 29: loglikelihood = -1399.9822917699823, backtracks = 0, tol = 0.00016296445901615742 Iteration 30: loglikelihood = -1399.1049948541659, backtracks = 0, tol = 0.00017651049370292745 Iteration 31: loglikelihood = -1398.2883236314144, backtracks = 0, tol = 0.00015196311543328817 Iteration 32: loglikelihood = -1397.5297161923258, backtracks = 0, tol = 0.00016214873518633686 Iteration 33: loglikelihood = -1396.8208796785784, backtracks = 0, tol = 0.00014235667691529124 Iteration 34: loglikelihood = -1396.1602179572662, backtracks = 0, tol = 0.00015002470491067786 Iteration 35: loglikelihood = -1395.5408000341542, backtracks = 0, tol = 0.00013386733922104752 Iteration 36: loglikelihood = -1394.9617763143174, backtracks = 0, tol = 0.0001396862041153787 Iteration 37: loglikelihood = -1394.4172118505167, backtracks = 0, tol = 0.00012629390697449638 Iteration 38: loglikelihood = -1393.90684177267, backtracks = 0, tol = 0.00013079298113656922 Iteration 39: loglikelihood = -1393.4254721111408, backtracks = 0, tol = 0.00011948238533516974 Iteration 40: loglikelihood = -1392.9732988273909, backtracks = 0, tol = 0.0001230727161526675 Iteration 41: loglikelihood = -1392.5456911093604, backtracks = 0, tol = 0.00011331034634767092 Iteration 42: loglikelihood = -1392.1432062290403, backtracks = 0, tol = 0.00011629646048914966 Iteration 43: loglikelihood = -1391.7616543429974, backtracks = 0, tol = 0.00010767814532538242 Iteration 44: loglikelihood = -1391.401870222233, backtracks = 0, tol = 0.00011026737937912453 Iteration 45: loglikelihood = -1391.0600231285441, backtracks = 0, tol = 0.00010250372765091029 Iteration 46: loglikelihood = -1390.7371526824081, backtracks = 0, tol = 0.00010481899808364321 Iteration 47: loglikelihood = -1390.429733683694, backtracks = 0, tol = 9.77195163329523e-5 0.506205 seconds (1.82 M allocations: 32.572 MiB, 3.93% gc 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 = -3492.6863, backtracks = 0, tol = 0.08788410390695592 Iteration 2: loglikelihood = -3452.4795, backtracks = 0, tol = 0.045202108060694524 Iteration 3: loglikelihood = -3448.4802, backtracks = 1, tol = 0.012989568257852704 Iteration 4: loglikelihood = -3447.4053, backtracks = 1, tol = 0.007516000325780011 Iteration 5: loglikelihood = -3447.126, backtracks = 1, tol = 0.00380758682503546 Iteration 6: loglikelihood = -3447.058, backtracks = 1, tol = 0.0019677495329581754 Iteration 7: loglikelihood = -3447.041, backtracks = 1, tol = 0.0009749317501952326 Iteration 8: loglikelihood = -3447.0366, backtracks = 1, tol = 0.0004908369552697376 Iteration 9: loglikelihood = -3447.0366, backtracks = 1, tol = 0.00024247011829696606 Iteration 10: loglikelihood = -3447.0369, backtracks = 3, tol = 3.0294599488468803e-5 24.165313 seconds (19.89 M allocations: 872.624 MiB, 1.63% gc time, 97.68% 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 **** 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 = -3399.7695, backtracks = 0, tol = 0.08788410390695592 Iteration 2: loglikelihood = -3300.0615, backtracks = 0, tol = 0.046272234784237185 Iteration 3: loglikelihood = -3138.767, backtracks = 1, tol = 0.012501341753157853 Iteration 4: loglikelihood = -2954.609, backtracks = 1, tol = 0.0065490382134024226 Iteration 5: loglikelihood = -2758.2993, backtracks = 1, tol = 0.0027840091849987312 Iteration 6: loglikelihood = -2678.0957, backtracks = 0, tol = 0.08037815698119498 Iteration 7: loglikelihood = -2565.5515, backtracks = 0, tol = 0.09332711182299476 Iteration 8: loglikelihood = -2449.6272, backtracks = 0, tol = 0.09236584405183987 Iteration 9: loglikelihood = -2366.3755, backtracks = 0, tol = 0.08542057477853825 Iteration 10: loglikelihood = -2306.223, backtracks = 0, tol = 0.08498986755738916 Iteration 11: loglikelihood = -2255.7664, backtracks = 0, tol = 0.08745444585827808 Iteration 12: loglikelihood = -2223.1091, backtracks = 0, tol = 0.08689856230545623 Iteration 13: loglikelihood = -2198.7952, backtracks = 0, tol = 0.08578267598134266 Iteration 14: loglikelihood = -2185.2703, backtracks = 0, tol = 0.08526410870830799 Iteration 15: loglikelihood = -2175.808, backtracks = 0, tol = 0.0846127398399434 Iteration 16: loglikelihood = -2171.4097, backtracks = 0, tol = 0.08412474279539733 Iteration 17: loglikelihood = -2168.1814, backtracks = 0, tol = 0.0840292309215808 Iteration 18: loglikelihood = -2167.0671, backtracks = 0, tol = 0.08355694079753286 Iteration 19: loglikelihood = -2165.9714, backtracks = 0, tol = 0.083748846404563 Iteration 20: loglikelihood = -2165.8293, backtracks = 0, tol = 0.08328362954777421 Iteration 21: loglikelihood = -2165.3882, backtracks = 0, tol = 0.08361342380862692 Iteration 22: loglikelihood = -2164.99, backtracks = 1, tol = 0.005311747301726886 Iteration 23: loglikelihood = -2164.8943, backtracks = 1, tol = 0.002311483782342685 Iteration 24: loglikelihood = -2164.8706, backtracks = 1, tol = 0.0010855091285464137 Iteration 25: loglikelihood = -2164.0847, backtracks = 0, tol = 0.0797735565052517 Iteration 26: loglikelihood = -2163.821, backtracks = 0, tol = 0.010070578792278177 Iteration 27: loglikelihood = -2163.804, backtracks = 1, tol = 0.001376979637440744 Iteration 28: loglikelihood = -2163.8064, backtracks = 3, tol = 0.0002030211534846525 Iteration 29: loglikelihood = -2163.806, backtracks = 3, tol = 0.00018178304179602793 Iteration 30: loglikelihood = -2163.8066, backtracks = 3, tol = 0.00016205067428186372 Iteration 31: loglikelihood = -2163.8066, backtracks = 3, tol = 0.00014428403184725376 Iteration 32: loglikelihood = -2163.805, backtracks = 1, tol = 0.0005136469253356396 Iteration 33: loglikelihood = -2163.804, backtracks = 1, tol = 0.0002862188393258108 Iteration 34: loglikelihood = -2163.8013, backtracks = 2, tol = 8.045585475926718e-5 0.288487 seconds (2.10 M allocations: 34.859 MiB) Test Summary: | Pass Total Time Negative binomial nuisance parameter Float32 matrix | 12 12 29.2s **** 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 = -2973.20721158067, backtracks = 0, tol = 0.9753037901485436 Iteration 2: loglikelihood = -1640.6694321323835, backtracks = 0, tol = 0.2999151154493682 Iteration 3: loglikelihood = -1418.3315050219228, backtracks = 0, tol = 0.10707075072938249 Iteration 4: loglikelihood = -1411.8219428589443, backtracks = 0, tol = 0.038898114770295936 Iteration 5: loglikelihood = -1410.7307354136753, backtracks = 0, tol = 0.03138838740051226 Iteration 6: loglikelihood = -1410.653861909991, backtracks = 0, tol = 0.001736989736614678 Iteration 7: loglikelihood = -1410.6533631901768, backtracks = 1, tol = 8.130020517735094e-5 5.366131 seconds (1.60 M allocations: 154.243 MiB, 0.94% gc time, 90.99% compilation time: 3% of which was recompilation) Test Summary: | Pass Total Time initialze beta | 1 1 5.9s 9.971568 seconds (3.69 M allocations: 76.569 MiB, 0.58% gc time, 0.66% compilation time) 5.800758 seconds (3.66 M allocations: 85.269 MiB, 0.37% gc time) 10.420587 seconds (20.79 M allocations: 446.953 MiB, 0.92% gc time, 14.18% compilation time: 77% of which was recompilation) 8.527484 seconds (20.48 M allocations: 439.087 MiB, 0.92% gc time) 44.437946 seconds (6.31 M allocations: 4.345 GiB, 13.14% gc time, 29.52% compilation time) 61.323346 seconds (81.26 k allocations: 183.405 MiB, 0.16% gc time) Test Summary: | Pass Total Time memory_efficient keyword | 7 7 2m38.6s Test Summary: | Pass Total Time update_support! | 10 10 0.5s 11.012 ms (78 allocations: 4.56 KiB) 5.120 μs (0 allocations: 0 bytes) 164.000 μs (4 allocations: 288 bytes) 15.230 μs (0 allocations: 0 bytes) 49.150 μs (2 allocations: 64 bytes) 32.460 μs (0 allocations: 0 bytes) 42.710 μs (0 allocations: 0 bytes) 41.580 μs (0 allocations: 0 bytes) 76.760 μs (0 allocations: 0 bytes) 31.169 ms (78 allocations: 4.56 KiB) 27.850 μs (0 allocations: 0 bytes) 207.810 μs (4 allocations: 288 bytes) 78.150 μs (0 allocations: 0 bytes) 248.950 μs (2 allocations: 64 bytes) 113.130 μs (0 allocations: 0 bytes) 201.940 μs (0 allocations: 0 bytes) 180.100 μs (0 allocations: 0 bytes) 258.730 μs (0 allocations: 0 bytes) Test Summary: | Total Time benchmarks for multivariate function | 0 2m23.7s **** 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 **** **** 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 = -2900.9186300194497, backtracks = 0, tol = 0.14802242082004133 Iteration 2: loglikelihood = -2869.406464695619, backtracks = 0, tol = 0.03512679046077987 Iteration 3: loglikelihood = -2868.084702693443, backtracks = 0, tol = 0.0055693496163324524 Iteration 4: loglikelihood = -2868.034423817725, backtracks = 0, tol = 0.001118951762895177 Iteration 5: loglikelihood = -2868.0308576353746, backtracks = 0, tol = 0.00031182601179140966 Iteration 6: loglikelihood = -2868.0305288614227, backtracks = 0, tol = 0.0001039330594994784 Iteration 7: loglikelihood = -2868.0304966516946, backtracks = 0, tol = 3.10086204985851e-5 0.359590 seconds (62.60 k allocations: 6.018 MiB, 65.95% 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 = 0.02433527426328489 Iteration 3: loglikelihood = -2868.0815051475474, backtracks = 0, tol = 0.004072558228741211 Iteration 4: loglikelihood = -2868.0352100240902, backtracks = 0, tol = 0.0013135682973484518 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 2.119929 seconds (389.59 k allocations: 172.927 MiB, 3.59% gc time, 56.14% compilation time) Test Summary: | Pass Total Time initialze beta | 5 5 2.7s **** 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 **** Cross validating... 3%|█ | ETA: 0:03:49 Cross validating... 13%|████▏ | ETA: 0:00:56 Cross validating... 16%|█████▏ | ETA: 0:00:44 Cross validating... 19%|██████▏ | ETA: 0:00:36 Cross validating... 22%|███████▏ | ETA: 0:00:30 Cross validating... 25%|████████▏ | ETA: 0:00:26 Cross validating... 29%|█████████▏ | ETA: 0:00:22 Cross validating... 32%|██████████▏ | ETA: 0:00:20 Cross validating... 35%|███████████▏ | ETA: 0:00:17 Cross validating... 38%|████████████▎ | ETA: 0:00:15 Cross validating... 41%|█████████████▎ | ETA: 0:00:13 Cross validating... 44%|██████████████▎ | ETA: 0:00:12 Cross validating... 48%|███████████████▎ | ETA: 0:00:11 Cross validating... 51%|████████████████▎ | ETA: 0:00:10 Cross validating... 54%|█████████████████▎ | ETA: 0:00:09 Cross validating... 57%|██████████████████▎ | ETA: 0:00:08 Cross validating... 60%|███████████████████▎ | ETA: 0:00:07 Cross validating... 63%|████████████████████▍ | ETA: 0:00:06 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:05 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:05 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:04 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:03 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:03 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:02 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:02 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:01 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:01 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:01 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:12 Crossvalidation Results: k MSE 0 6201.179669454221 1 4335.198594124064 2 1900.3274465180134 3 1008.31451158603 4 720.3267954595996 5 507.73961725036133 6 409.5029172991385 7 356.3134842327928 8 316.69809888504665 9 318.40850076093295 10 319.6821124187953 11 320.5107426576112 12 330.777633239775 13 323.14704231852573 14 325.86742672583426 15 337.7341756468765 16 331.8850954902432 17 362.3523894101513 18 349.75948633137386 19 359.05837517535633 20 373.22109558785473 Best k = 8 12.347820 seconds (12.04 M allocations: 318.563 MiB, 0.60% gc time, 63.08% 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... 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: 0:00:04 Cross validating... 24%|███████▋ | ETA: 0:00:03 Cross validating... 27%|████████▋ | ETA: 0:00:03 Cross 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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 6201.179669454221 1 4347.46063372641 2 1904.7813561467444 3 1017.3450567024911 4 729.7973333110942 5 511.9792954232663 6 412.3890289469368 7 359.0471600448409 8 320.7461644299759 9 325.4875834666342 10 330.3379426039211 11 332.1346912249218 12 335.0335208893323 13 333.9080018254259 14 353.5194117122921 15 351.40716711495725 16 356.26386074938273 17 358.0806543721394 18 376.7439067384588 19 371.2566451257781 20 375.4471364473832 Best k = 8 4.850599 seconds (10.79 M allocations: 227.421 MiB, 1.78% gc time, 1.14% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, normal model | 3 3 18.1s **** 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: 0:04:06 Cross validating... 10%|███ | ETA: 0:01:19 Cross validating... 16%|█████▏ | ETA: 0:00:44 Cross validating... 22%|███████▏ | ETA: 0:00:30 Cross validating... 27%|████████▋ | ETA: 0:00:23 Cross validating... 32%|██████████▏ | ETA: 0:00:19 Cross validating... 38%|████████████▎ | ETA: 0:00:14 Cross validating... 44%|██████████████▎ | ETA: 0:00:11 Cross validating... 51%|████████████████▎ | ETA: 0:00:09 Cross validating... 56%|█████████████████▊ | ETA: 0:00:07 Cross validating... 60%|███████████████████▎ | ETA: 0:00:06 Cross validating... 65%|████████████████████▉ | ETA: 0:00:05 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:04 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:03 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:02 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:01 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:01 Cross validating... 100%|████████████████████████████████| Time: 0:00:10 Crossvalidation Results: k MSE 0 1601.319770751953 1 1352.1641228027345 2 1036.2262430419923 3 828.1546306152344 4 661.6884172363282 5 570.5495653076172 6 460.35190362548826 7 388.105234375 8 354.9005658569336 9 352.063778503418 10 354.10029589843754 11 351.4441131591797 12 352.9461133422852 13 370.7975758666993 14 358.7430003051758 15 362.88428021240236 16 376.52443182373054 17 392.1751675415039 18 398.91678985595706 19 361.98406878662115 20 369.7349998168945 Best k = 11 11.185081 seconds (13.43 M allocations: 336.020 MiB, 1.02% gc time, 80.88% 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... 8%|██▌ | ETA: 0:00:01 Cross validating... 13%|████▏ | ETA: 0:00:02 Cross validating... 19%|██████▏ | ETA: 0:00:02 Cross validating... 24%|███████▋ | ETA: 0:00:02 Cross validating... 29%|█████████▏ | ETA: 0:00:02 Cross validating... 33%|██████████▋ | ETA: 0:00:02 Cross validating... 41%|█████████████▎ | ETA: 0:00:01 Cross validating... 49%|███████████████▊ | 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... 83%|██████████████████████████▍ | ETA: 0:00:00 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:00 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:02 Crossvalidation Results: k MSE 0 1601.319770751953 1 1355.897981201172 2 1041.9411818847657 3 832.0292741699219 4 665.7275910644531 5 580.6403720703125 6 467.47843902587897 7 394.12614605712895 8 360.3324585571289 9 357.86692669677734 10 361.2504040527344 11 373.42214349365236 12 394.5946166381836 13 392.8648052978516 14 403.63599127197267 15 408.2000222778321 16 397.96788830566413 17 410.9911950073242 18 413.4033491210938 19 408.2929742431641 20 428.4565200195313 Best k = 9 2.172534 seconds (10.67 M allocations: 196.407 MiB, 1.82% gc time, 1.40% compilation time) Test Summary: | Pass Total Time Cross validation on Float32 matrix, normal model | 2 2 14.7s **** 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 **** Cross validating... 3%|█ | ETA: 0:00:38 Cross validating... 6%|██ | ETA: 0:00:21 Cross validating... 10%|███ | ETA: 0:00:15 Cross validating... 13%|████▏ | ETA: 0:00:12 Cross validating... 16%|█████▏ | ETA: 0:00:10 Cross validating... 19%|██████▏ | ETA: 0:00:09 Cross validating... 22%|███████▏ | ETA: 0:00:08 Cross validating... 25%|████████▏ | ETA: 0:00:07 Cross validating... 29%|█████████▏ | ETA: 0:00:06 Cross validating... 32%|██████████▏ | ETA: 0:00:06 Cross validating... 35%|███████████▏ | ETA: 0:00:05 Cross validating... 38%|████████████▎ | ETA: 0:00:05 Cross validating... 41%|█████████████▎ | ETA: 0:00:04 Cross validating... 44%|██████████████▎ | ETA: 0:00:04 Cross validating... 48%|███████████████▎ | ETA: 0:00:04 Cross validating... 51%|████████████████▎ | ETA: 0:00:03 Cross validating... 54%|█████████████████▎ | ETA: 0:00:03 Cross validating... 57%|██████████████████▎ | ETA: 0:00:03 Cross validating... 60%|███████████████████▎ | ETA: 0:00:03 Cross validating... 63%|████████████████████▍ | ETA: 0:00:02 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:02 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:02 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: 0:00:01 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 0 462.5814529957379 1 378.4023925305369 2 276.3699966432012 3 235.98855865995444 4 219.95978214329824 5 203.81158499157866 6 201.07212758895218 7 197.81832738394615 8 199.66452960744752 9 212.83297473376192 10 201.671880001926 11 229.9366965638066 12 207.61929175606633 13 239.384509661442 14 219.10590765862864 15 228.62856775229037 16 236.6354805486667 17 262.9134928285276 18 222.3775204578829 19 237.73593951656093 20 218.87613854152562 Best k = 7 6.317332 seconds (17.87 M allocations: 416.079 MiB, 1.11% 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... 3%|█ | ETA: 0:00:04 Cross validating... 6%|██ | ETA: 0:00:04 Cross validating... 8%|██▌ | ETA: 0:00:05 Cross validating... 11%|███▌ | ETA: 0:00:05 Cross validating... 14%|████▋ | ETA: 0:00:04 Cross validating... 17%|█████▋ | ETA: 0:00:04 Cross 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validating... 75%|███████████████████████▉ | ETA: 0:00:01 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:01 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:01 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:01 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:01 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:01 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:01 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 0 462.5814529957379 1 378.9620844917171 2 278.8791661766743 3 237.16081538898703 4 223.0072254102206 5 206.59631056074807 6 206.64033859031028 7 199.54842792086504 8 213.62437898830618 9 211.55631381441148 10 230.81922150705284 11 232.24045309187528 12 230.66893791806683 13 231.6506016523189 14 242.3612720600894 15 231.85775732552557 16 267.55017210933096 17 262.9134928285276 18 250.82301717661346 19 272.200940559164 20 263.60580943895445 Best k = 7 5.911456 seconds (18.02 M allocations: 376.273 MiB, 1.06% gc time, 1.05% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, logistic model | 2 2 12.6s **** 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: 0:00:15 Cross validating... 13%|████▏ | ETA: 0:00:12 Cross validating... 16%|█████▏ | ETA: 0:00:10 Cross validating... 19%|██████▏ | ETA: 0:00:09 Cross validating... 22%|███████▏ | ETA: 0:00:08 Cross validating... 25%|████████▏ | ETA: 0:00:07 Cross validating... 27%|████████▋ | ETA: 0:00:07 Cross validating... 30%|█████████▋ | ETA: 0:00:06 Cross validating... 33%|██████████▋ | 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: 0:00:05 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: 0:00:03 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... 84%|██████████████████████████▉ | ETA: 0:00:01 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:01 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:01 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:06 Crossvalidation Results: k MSE 0 462.98670425378816 1 434.7206840034346 2 399.84261841938917 3 365.6033776357125 4 354.8826694157098 5 340.52169303156796 6 331.21804814033476 7 322.5104203180018 8 324.1457688429359 9 329.02765395318147 10 326.39016840284836 11 333.05897268656696 12 339.43884328466214 13 330.77660930464083 14 345.31387842158057 15 333.46872993037454 16 334.76146630128443 17 338.2734933475128 18 337.99545231344115 19 335.5191123286819 20 342.21795920830857 Best k = 7 7.830953 seconds (16.39 M allocations: 395.061 MiB, 11.32% gc time, 29.46% 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: 0:00:04 Cross validating... 10%|███ | ETA: 0:00:04 Cross validating... 13%|████▏ | ETA: 0:00:04 Cross validating... 16%|█████▏ | 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... 27%|████████▋ | ETA: 0:00:04 Cross validating... 30%|█████████▋ | ETA: 0:00:03 Cross validating... 33%|██████████▋ | 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... 48%|███████████████▎ | ETA: 0:00:03 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: 0:00:02 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: 0:00:04 Crossvalidation Results: k MSE 0 462.98670425378816 1 435.4006566893378 2 400.82446758350085 3 367.0722940563493 4 357.4277841889991 5 342.4301253070882 6 334.4673919181985 7 328.4901761544481 8 333.8326097801186 9 343.9277663121418 10 346.9202297995043 11 358.36540314822605 12 365.1748287043213 13 363.1221774209504 14 375.17953602249725 15 374.0704760614605 16 384.43922893858974 17 391.5220647966407 18 398.9259942101669 19 398.93137909443027 20 418.6801124646345 Best k = 7 5.018081 seconds (17.39 M allocations: 359.354 MiB, 1.12% gc time, 0.80% compilation time) Test Summary: | Pass Total Time Cross validation on Float64 matrix, logistic model | 2 2 13.8s **** 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: 0:00:54 Cross validating... 5%|█▌ | ETA: 0:00:38 Cross validating... 8%|██▌ | ETA: 0:00:24 Cross validating... 11%|███▌ | ETA: 0:00:18 Cross validating... 14%|████▋ | ETA: 0:00:14 Cross validating... 17%|█████▋ | ETA: 0:00:12 Cross validating... 21%|██████▋ | ETA: 0:00:11 Cross validating... 24%|███████▋ | ETA: 0:00:09 Cross validating... 27%|████████▋ | ETA: 0:00:08 Cross validating... 30%|█████████▋ | ETA: 0:00:08 Cross validating... 33%|██████████▋ | ETA: 0:00:07 Cross validating... 37%|███████████▋ | ETA: 0:00:06 Cross validating... 40%|████████████▊ | ETA: 0:00:06 Cross validating... 43%|█████████████▊ | ETA: 0:00:05 Cross validating... 46%|██████████████▊ | ETA: 0:00:05 Cross validating... 49%|███████████████▊ | ETA: 0:00:04 Cross validating... 52%|████████████████▊ | ETA: 0:00:04 Cross validating... 56%|█████████████████▊ | ETA: 0:00:04 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... 84%|██████████████████████████▉ | ETA: 0:00:01 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:01 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:01 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:06 Crossvalidation Results: k MSE 0 1561.9207378735864 1 1380.8405062786892 2 946.3847791656754 3 565.8001034032482 4 555.8320803898182 5 571.4271064597192 6 532.6942596254606 7 515.8412898635445 8 505.4336539927453 9 501.2577732444993 10 492.9555599415905 11 490.5018713161064 12 492.6575443384052 13 536.8755663349327 14 578.6334538954061 15 516.1785373609455 16 531.6629100699465 17 521.5155558218612 18 507.66171261039716 19 503.5137453089304 20 501.68089246278623 Best k = 11 7.592052 seconds (15.44 M allocations: 358.920 MiB, 0.94% gc time, 29.82% 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: 0:00:02 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: 0:00:02 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... 94%|██████████████████████████████ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:05 Crossvalidation Results: k MSE 0 1561.9207378735864 1 1246.6313062492895 2 779.2554331345142 3 520.0330693708111 4 506.16652175070317 5 507.1931819337857 6 499.25223143886035 7 490.9428447287972 8 509.5947033742606 9 504.6462314156828 10 525.9974749650346 11 538.9539127702913 12 500.6793229174535 13 567.9435540179727 14 526.2882761310591 15 548.4907845703276 16 533.5314703196386 17 582.0632854506753 18 558.7251179150624 19 613.9834149783458 20 604.8971962244505 Best k = 7 5.604819 seconds (14.13 M allocations: 283.486 MiB, 1.09% gc time, 1.27% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, Poisson model | 2 2 13.8s **** 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: 0:00:56 Cross validating... 5%|█▌ | ETA: 0:00:39 Cross validating... 8%|██▌ | ETA: 0:00:36 Cross validating... 10%|███ | ETA: 0:00:39 Cross validating... 13%|████▏ | ETA: 0:00:30 Cross validating... 14%|████▋ | ETA: 0:00:27 Cross validating... 16%|█████▏ | ETA: 0:00:25 Cross validating... 17%|█████▋ | ETA: 0:00:23 Cross validating... 19%|██████▏ | ETA: 0:00:21 Cross validating... 21%|██████▋ | ETA: 0:00:20 Cross validating... 22%|███████▏ | ETA: 0:00:19 Cross validating... 24%|███████▋ | ETA: 0:00:18 Cross validating... 25%|████████▏ | ETA: 0:00:17 Cross validating... 27%|████████▋ | ETA: 0:00:16 Cross validating... 29%|█████████▏ | ETA: 0:00:15 Cross validating... 30%|█████████▋ | ETA: 0:00:15 Cross validating... 32%|██████████▏ | ETA: 0:00:16 Cross validating... 33%|██████████▋ | ETA: 0:00:17 Cross validating... 37%|███████████▋ | ETA: 0:00:17 Cross validating... 38%|████████████▎ | ETA: 0:00:16 Cross validating... 40%|████████████▊ | ETA: 0:00:16 Cross validating... 41%|█████████████▎ | ETA: 0:00:15 Cross validating... 43%|█████████████▊ | ETA: 0:00:16 Cross validating... 44%|██████████████▎ | ETA: 0:00:16 Cross validating... 48%|███████████████▎ | ETA: 0:00:14 Cross validating... 49%|███████████████▊ | ETA: 0:00:14 Cross validating... 51%|████████████████▎ | ETA: 0:00:14 Cross validating... 52%|████████████████▊ | ETA: 0:00:14 Cross validating... 54%|█████████████████▎ | ETA: 0:00:14 Cross validating... 56%|█████████████████▊ | ETA: 0:00:14 Cross validating... 57%|██████████████████▎ | ETA: 0:00:14 Cross validating... 59%|██████████████████▊ | ETA: 0:00:13 Cross validating... 60%|███████████████████▎ | ETA: 0:00:13 Cross validating... 62%|███████████████████▊ | ETA: 0:00:13 Cross validating... 63%|████████████████████▍ | ETA: 0:00:13 Cross validating... 65%|████████████████████▉ | ETA: 0:00:12 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:12 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:10 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:10 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:09 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:09 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:08 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:07 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:07 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:06 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:06 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:05 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:04 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:04 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:03 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: 0:00:35 Crossvalidation Results: k MSE 0 531.3030704208727 1 422.89379461201383 2 317.367342853419 3 234.60268108122636 4 222.50321585181322 5 208.7867770840599 6 208.15334815371637 7 208.76273375306693 8 209.12930192980923 9 210.48576931058832 10 211.83119510619318 11 212.46314488129988 12 214.05403662223677 13 212.90039230041106 14 216.91709992579894 15 216.67382968048898 16 218.10282982142166 17 218.12643266610513 18 219.26396308690602 19 220.38372280633297 20 219.25024459335626 Best k = 6 35.982194 seconds (109.99 M allocations: 2.852 GiB, 1.23% gc time, 5.56% 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: 0:00:08 Cross validating... 5%|█▌ | ETA: 0:00:10 Cross validating... 6%|██ | ETA: 0:00:09 Cross validating... 8%|██▌ | ETA: 0:00:09 Cross validating... 10%|███ | ETA: 0:00:08 Cross validating... 11%|███▌ | ETA: 0:00:08 Cross validating... 13%|████▏ | ETA: 0:00:08 Cross validating... 14%|████▋ | ETA: 0:00:08 Cross validating... 16%|█████▏ | ETA: 0:00:08 Cross validating... 17%|█████▋ | ETA: 0:00:08 Cross validating... 19%|██████▏ | ETA: 0:00:08 Cross validating... 21%|██████▋ | ETA: 0:00:08 Cross validating... 22%|███████▏ | ETA: 0:00:08 Cross validating... 24%|███████▋ | ETA: 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validating... 84%|██████████████████████████▉ | ETA: 0:00:02 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:02 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:01 Cross validating... 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: 0:00:01 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:12 Crossvalidation Results: k MSE 0 531.3030704208727 1 423.0907340472829 2 316.57183204900855 3 235.0032731242224 4 220.0320952883519 5 209.9908618551882 6 210.1490948736963 7 212.91880886872636 8 214.41457992003296 9 219.18111794541352 10 225.14401797600112 11 223.70140914842972 12 227.57599415663782 13 233.58416617810678 14 237.81260519621878 15 250.20889634687273 16 244.53917941754338 17 252.92310663867755 18 260.3141523999408 19 265.9120137550543 20 268.04938843358076 Best k = 5 12.095541 seconds (33.88 M allocations: 686.936 MiB, 1.32% gc time, 0.56% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, NegativeBinomial model | 2 2 48.5s **** 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: 0:00:59 Cross validating... 6%|██ | ETA: 0:00:30 Cross validating... 10%|███ | ETA: 0:00:21 Cross validating... 13%|████▏ | ETA: 0:00:16 Cross validating... 16%|█████▏ | ETA: 0:00:13 Cross validating... 19%|██████▏ | ETA: 0:00:11 Cross validating... 22%|███████▏ | ETA: 0:00:09 Cross validating... 25%|████████▏ | ETA: 0:00:08 Cross validating... 29%|█████████▏ | ETA: 0:00:07 Cross validating... 32%|██████████▏ | 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: 0:00:03 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: 0:00:02 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:02 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:02 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 0 691.7500225830079 1 622.5072396240234 2 512.5984967346192 3 404.1873347473144 4 329.1224825439453 5 269.25713952636715 6 254.24000593566893 7 224.95246855163572 8 210.14389988708496 9 203.5730756072998 10 206.3555386505127 11 208.19131018066406 12 216.8473366241455 13 229.8447658843994 14 213.42113655090333 15 214.1879868621826 16 224.7288980255127 17 218.40956840515133 18 214.59177186584472 19 217.02808283996583 20 229.5842406768799 Best k = 9 6.207507 seconds (17.22 M allocations: 345.447 MiB, 1.45% gc time, 39.45% 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... 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Time: 0:00:04 Crossvalidation Results: k MSE 0 691.7500225830079 1 601.5035169677735 2 491.64564691162104 3 387.2143143005371 4 320.7548650817871 5 268.1246952209473 6 254.63632737731933 7 227.02002976989746 8 212.62741166687013 9 212.0953056640625 10 212.51340118408203 11 214.56212982177735 12 220.0984645233154 13 226.74450151062013 14 231.7223010253906 15 222.91655926513673 16 236.85316429138186 17 238.8029296417236 18 236.3234663696289 19 245.07382664489745 20 246.47416119384764 Best k = 9 4.182118 seconds (16.42 M allocations: 292.700 MiB, 3.98% gc time, 1.36% compilation time) Test Summary: | Pass Total Time Cross validation on floating point matrices, NegativeBinomial model | 2 2 11.0s **** 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... 2%|▋ | ETA: 0:01:08 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ETA: 0:00:05 Cross validating... 69%|██████████████████████▏ | ETA: 0:00:05 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:04 Cross validating... 71%|██████████████████████▊ | ETA: 0:00:04 Cross validating... 72%|███████████████████████ | ETA: 0:00:04 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:04 Cross validating... 74%|███████████████████████▋ | ETA: 0:00:04 Cross validating... 75%|████████████████████████ | ETA: 0:00:04 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:04 Cross validating... 77%|████████████████████████▋ | ETA: 0:00:03 Cross validating... 78%|█████████████████████████ | ETA: 0:00:03 Cross validating... 79%|█████████████████████████▎ | ETA: 0:00:03 Cross validating... 80%|█████████████████████████▋ | ETA: 0:00:03 Cross validating... 82%|██████████████████████████▎ | ETA: 0:00:03 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:02 Cross validating... 86%|███████████████████████████▌ | ETA: 0:00:02 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:02 Cross validating... 88%|████████████████████████████▏ | ETA: 0:00:02 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:02 Cross validating... 90%|████████████████████████████▊ | ETA: 0:00:01 Cross validating... 91%|█████████████████████████████▏ | ETA: 0:00:01 Cross validating... 93%|█████████████████████████████▊ | ETA: 0:00:01 Cross validating... 94%|██████████████████████████████▏ | ETA: 0:00:01 Cross validating... 95%|██████████████████████████████▍ | ETA: 0:00:01 Cross validating... 96%|██████████████████████████████▊ | ETA: 0:00:01 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▍| ETA: 0:00:00 Cross validating... 99%|███████████████████████████████▋| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:14 Crossvalidation Results: k MSE 1 3045.053719360797 2 2554.9998083481396 3 2290.4451136455627 4 2234.7554482052074 5 2207.8712904727977 6 2200.6322468390877 7 2185.412646913357 8 2180.1490383350715 9 2186.496013065014 10 2187.1727227306355 11 2190.7240552789995 12 2210.8391871788617 13 2222.2323887380235 14 2239.4921443613675 15 2259.566733060493 16 2269.5358825103212 17 2283.0231520054213 18 2308.327980095557 19 2336.083811004401 20 2391.414811946462 Best k = 8 14.417834 seconds (435.57 k allocations: 254.086 MiB, 0.45% gc time, 10.22% compilation time) Test Summary: | Pass Total Time multivariate cross validation SnpLinAlg | 3 3 19.4s Test Summary: | Pass Total Time wrapper univariate | 20 20 1m52.5s **** 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: 0:00:08 Cross validating... 4%|█▎ | ETA: 0:00:08 Cross validating... 6%|█▉ | ETA: 0:00:09 Cross validating... 7%|██▎ | ETA: 0:00:09 Cross validating... 8%|██▌ | ETA: 0:00:09 Cross validating... 9%|██▉ | ETA: 0:00:10 Cross validating... 10%|███▎ | ETA: 0:00:11 Cross validating... 11%|███▌ | ETA: 0:00:12 Cross validating... 12%|███▉ | ETA: 0:00:12 Cross validating... 13%|████▏ | ETA: 0:00:12 Cross validating... 14%|████▌ | ETA: 0:00:13 Cross validating... 15%|████▊ | ETA: 0:00:13 Cross validating... 16%|█████▏ | ETA: 0:00:14 Cross validating... 17%|█████▌ | ETA: 0:00:14 Cross validating... 18%|█████▊ | ETA: 0:00:14 Cross validating... 19%|██████▏ | ETA: 0:00:14 Cross validating... 20%|██████▍ | ETA: 0:00:15 Cross validating... 22%|███████ | ETA: 0:00:13 Cross validating... 24%|███████▋ | ETA: 0:00:13 Cross validating... 26%|████████▍ | ETA: 0:00:12 Cross validating... 27%|████████▋ | ETA: 0:00:12 Cross validating... 28%|█████████ | ETA: 0:00:12 Cross validating... 29%|█████████▎ | ETA: 0:00:12 Cross validating... 30%|█████████▋ | ETA: 0:00:12 Cross validating... 31%|█████████▉ | ETA: 0:00:12 Cross validating... 32%|██████████▎ | ETA: 0:00:12 Cross validating... 33%|██████████▌ | ETA: 0:00:12 Cross validating... 34%|██████████▉ | ETA: 0:00:12 Cross validating... 35%|███████████▎ | ETA: 0:00:12 Cross validating... 36%|███████████▌ | ETA: 0:00:12 Cross validating... 37%|███████████▉ | ETA: 0:00:12 Cross validating... 38%|████████████▏ | ETA: 0:00:12 Cross validating... 39%|████████████▌ | ETA: 0:00:11 Cross validating... 40%|████████████▊ | ETA: 0:00:11 Cross validating... 42%|█████████████▌ | ETA: 0:00:11 Cross validating... 44%|██████████████▏ | ETA: 0:00:10 Cross validating... 46%|██████████████▊ | ETA: 0:00:09 Cross validating... 47%|███████████████ | ETA: 0:00:09 Cross validating... 48%|███████████████▍ | ETA: 0:00:09 Cross validating... 49%|███████████████▋ | ETA: 0:00:09 Cross validating... 50%|████████████████ | ETA: 0:00:09 Cross validating... 51%|████████████████▍ | ETA: 0:00:09 Cross validating... 52%|████████████████▋ | ETA: 0:00:08 Cross 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89%|████████████████████████████▌ | ETA: 0:00:02 Cross validating... 90%|████████████████████████████▊ | ETA: 0:00:02 Cross validating... 91%|█████████████████████████████▏ | ETA: 0:00:02 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:01 Cross validating... 93%|█████████████████████████████▊ | ETA: 0:00:01 Cross validating... 94%|██████████████████████████████▏ | ETA: 0:00:01 Cross validating... 95%|██████████████████████████████▍ | ETA: 0:00:01 Cross validating... 96%|██████████████████████████████▊ | ETA: 0:00:01 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:01 Cross validating... 98%|███████████████████████████████▍| ETA: 0:00:00 Cross validating... 99%|███████████████████████████████▋| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:18 Crossvalidation Results: k MSE 1 2838.788679198002 2 2514.397342870813 3 2305.6176519676274 4 2222.025304867614 5 2075.167038458837 6 2067.794898972384 7 2053.427506114907 8 2086.405384830965 9 2080.984460901671 10 2105.1311995023634 11 2132.407165368786 12 2138.2671874606517 13 2166.002210829576 14 2194.991829511581 15 2189.890403738045 16 2191.1812932295775 17 2209.4669750564362 18 2221.2595493644303 19 2238.7425945763257 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: 0:00:08 Cross validating... 4%|█▎ | ETA: 0:00:08 Cross validating... 6%|█▉ | ETA: 0:00:09 Cross validating... 7%|██▎ | ETA: 0:00:10 Cross validating... 8%|██▌ | ETA: 0:00:10 Cross validating... 9%|██▉ | ETA: 0:00:11 Cross validating... 10%|███▎ | ETA: 0:00:11 Cross validating... 11%|███▌ | ETA: 0:00:12 Cross validating... 12%|███▉ | ETA: 0:00:12 Cross validating... 13%|████▏ | ETA: 0:00:13 Cross validating... 14%|████▌ | 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94%|██████████████████████████████▏ | ETA: 0:00:01 Cross validating... 95%|██████████████████████████████▍ | ETA: 0:00:01 Cross validating... 96%|██████████████████████████████▊ | ETA: 0:00:01 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:01 Cross validating... 98%|███████████████████████████████▍| ETA: 0:00:00 Cross validating... 99%|███████████████████████████████▋| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:19 Crossvalidation Results: k MSE 1 2838.788679198002 2 2514.397342870813 3 2305.6176519676274 4 2222.025304867614 5 2075.167038458837 6 2067.794898972384 7 2053.427506114907 8 2086.405384830965 9 2080.984460901671 10 2105.1311995023634 11 2132.407165368786 12 2138.2671874606517 13 2166.002210829576 14 2194.991829511581 15 2189.890403738045 16 2191.1812932295775 17 2209.4669750564362 18 2221.2595493644303 19 2238.7425945763257 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: 0:00:08 Cross validating... 4%|█▎ | ETA: 0:00:08 Cross validating... 6%|█▉ | ETA: 0:00:09 Cross validating... 7%|██▎ | ETA: 0:00:09 Cross validating... 8%|██▌ | ETA: 0:00:09 Cross validating... 9%|██▉ | ETA: 0:00:10 Cross validating... 10%|███▎ | ETA: 0:00:11 Cross validating... 11%|███▌ | ETA: 0:00:12 Cross validating... 12%|███▉ | ETA: 0:00:12 Cross validating... 13%|████▏ | ETA: 0:00:12 Cross validating... 14%|████▌ | ETA: 0:00:13 Cross validating... 15%|████▊ | ETA: 0:00:13 Cross validating... 16%|█████▏ | ETA: 0:00:14 Cross validating... 17%|█████▌ | ETA: 0:00:14 Cross validating... 18%|█████▊ | ETA: 0:00:14 Cross validating... 19%|██████▏ | ETA: 0:00:15 Cross validating... 20%|██████▍ | ETA: 0:00:15 Cross validating... 22%|███████ | ETA: 0:00:14 Cross 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validating... 99%|███████████████████████████████▋| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:18 Crossvalidation Results: k MSE 1 2838.788679198002 2 2514.397342870813 3 2305.6176519676274 4 2222.025304867614 5 2075.167038458837 6 2067.794898972384 7 2053.427506114907 8 2086.405384830965 9 2080.984460901671 10 2105.1311995023634 11 2132.407165368786 12 2138.2671874606517 13 2166.002210829576 14 2194.991829511581 15 2189.890403738045 16 2191.1812932295775 17 2209.4669750564362 18 2221.2595493644303 19 2238.7425945763257 20 2253.9559571797727 Best k = 7 Test Summary: | Pass Total Time wrapper multivariate | 8 8 1m11.5s 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:44 [2] process(codec::CodecZlib.ZlibDecompressor, input::TranscodingStreams.Memory, output::TranscodingStreams.Memory, error_ref::TranscodingStreams.Error) @ CodecZlib ~/.julia/packages/CodecZlib/lEc2s/src/decompression.jl:186 [3] decompress(io::IOStream, v::Variant, h::BGEN.Header; decompressed::Nothing) @ BGEN ~/.julia/packages/BGEN/dfgRU/src/genotypes.jl:72 [4] decompress @ ~/.julia/packages/BGEN/dfgRU/src/genotypes.jl:42 [inlined] [5] first_allele_dosage!(b::Bgen, v::Variant; T::Type, mean_impute::Bool, clear_decompressed::Bool, data::Nothing, decompressed::Nothing, is_decompressed::Bool) @ BGEN ~/.julia/packages/BGEN/dfgRU/src/genotypes.jl:571 [6] first_allele_dosage! @ ~/.julia/packages/BGEN/dfgRU/src/genotypes.jl:549 [inlined] [7] convert_bgen_gt(t::Type{Float64}, b::Bgen) @ MendelIHT ~/.julia/packages/MendelIHT/ZcxZT/src/wrapper.jl:380 [8] macro expansion @ ./timing.jl:697 [inlined] [9] macro expansion @ ~/.julia/packages/MendelIHT/ZcxZT/test/wrapper_test.jl:187 [inlined] [10] macro expansion @ /opt/julia/share/julia/stdlib/v1.12/Test/src/Test.jl:1777 [inlined] [11] top-level scope @ ~/.julia/packages/MendelIHT/ZcxZT/test/wrapper_test.jl:185 [12] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:307 [13] top-level scope @ ~/.julia/packages/MendelIHT/ZcxZT/test/runtests.jl:20 [14] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:307 [15] top-level scope @ none:6 [16] eval(m::Module, e::Any) @ Core ./boot.jl:489 [17] exec_options(opts::Base.JLOptions) @ Base ./client.jl:283 [18] _start() @ Base ./client.jl:550 Test Summary: | Error Total Time read BGEN and VCF | 1 1 2.7s RNG of the outermost testset: Xoshiro(0xbd720837d8d5195d, 0x5532a11579621f21, 0xc533de05c1b52992, 0x54bcf844d7741369, 0xe8380b76f1b1ce79) 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 1027.55s ERROR: LoadError: Package MendelIHT errored during testing Stacktrace: [1] pkgerror(msg::String) @ Pkg.Types /opt/julia/share/julia/stdlib/v1.12/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/v1.12/Pkg/src/Operations.jl:2538 [3] test @ /opt/julia/share/julia/stdlib/v1.12/Pkg/src/Operations.jl:2387 [inlined] [4] 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/v1.12/Pkg/src/API.jl:552 [5] test(pkgs::Vector{PackageSpec}; io::IOContext{IO}, kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.12/Pkg/src/API.jl:169 [6] test(pkgs::Vector{String}; kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.12/Pkg/src/API.jl:157 [7] test @ /opt/julia/share/julia/stdlib/v1.12/Pkg/src/API.jl:157 [inlined] [8] #test#81 @ /opt/julia/share/julia/stdlib/v1.12/Pkg/src/API.jl:156 [inlined] [9] top-level scope @ /PkgEval.jl/scripts/evaluate.jl:223 [10] include(mod::Module, _path::String) @ Base ./Base.jl:306 [11] exec_options(opts::Base.JLOptions) @ Base ./client.jl:317 [12] _start() @ Base ./client.jl:550 in expression starting at /PkgEval.jl/scripts/evaluate.jl:214 PkgEval failed after 1802.46s: package tests unexpectedly errored