Package evaluation to test MendelIHT on Julia 1.14.0-DEV.1871 (50d44f5be7*) started at 2026-03-08T23:34:24.636 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.14` Set-up completed after 15.03s ################################################################################ # Installation # Installing MendelIHT... Resolving package versions... Installed Glob ───────────────────────────── v1.4.0 Installed CompositionsBase ───────────────── v0.1.2 Installed CommonWorldInvalidations ───────── v1.0.0 Installed MacroTools ─────────────────────── v0.5.16 Installed CommonSolve ────────────────────── v0.2.6 Installed CodecZstd ──────────────────────── v0.8.7 Installed DataStructures ─────────────────── v0.19.3 Installed FilePathsBase ──────────────────── v0.9.24 Installed Rmath_jll ──────────────────────── v0.5.1+0 Installed Bzip2_jll ──────────────────────── v1.0.9+0 Installed ManualMemory ───────────────────── v0.1.8 Installed GLM ────────────────────────────── v1.9.3 Installed FillArrays ─────────────────────── v1.16.0 Installed VCFTools ───────────────────────── v0.2.10 Installed VectorizationBase ──────────────── v0.21.72 Installed InlineStrings ──────────────────── v1.4.5 Installed Adapt ──────────────────────────── v4.5.0 Installed HypergeometricFunctions ────────── v0.3.28 Installed ConstructionBase ───────────────── v1.6.0 Installed SLEEFPirates ───────────────────── v0.6.43 Installed StatsModels ────────────────────── v0.7.9 Installed AliasTables ────────────────────── v1.1.3 Installed DelimitedFiles ─────────────────── v1.9.1 Installed BitTwiddlingConvenienceFunctions ─ v0.1.6 Installed SIMDTypes ──────────────────────── v0.1.0 Installed StatsBase ──────────────────────── v0.34.10 Installed CodecZlib ──────────────────────── v0.7.8 Installed TranscodingStreams ─────────────── v0.9.13 Installed CSV ────────────────────────────── v0.10.16 Installed ShiftedArrays ──────────────────── v2.0.0 Installed ArrayInterface ─────────────────── v7.23.0 Installed OrderedCollections ─────────────── v1.8.1 Installed Compat ─────────────────────────── v4.18.1 Installed IteratorInterfaceExtensions ────── v1.0.0 Installed Combinatorics ──────────────────── v1.1.0 Installed HypothesisTests ────────────────── v0.11.6 Installed HostCPUFeatures ────────────────── v0.1.18 Installed LoopVectorization ──────────────── v0.12.173 Installed SIMD ───────────────────────────── v3.7.2 Installed DataAPI ────────────────────────── v1.16.0 Installed dlfcn_win32_jll ────────────────── v1.4.2+0 Installed InvertedIndices ────────────────── v1.3.1 Installed StatsAPI ───────────────────────── v1.8.0 Installed Statistics ─────────────────────── v1.11.1 Installed DataValueInterfaces ────────────── v1.0.0 Installed PrecompileTools ────────────────── v1.3.3 Installed CpuId ──────────────────────────── v0.3.1 Installed OffsetArrays ───────────────────── v1.17.0 Installed IrrationalConstants ────────────── v0.2.6 Installed SentinelArrays ─────────────────── v1.4.9 Installed Distances ──────────────────────── v0.10.12 Installed LayoutPointers ─────────────────── v0.1.17 Installed StaticArrayInterface ───────────── v1.9.0 Installed ProgressMeter ──────────────────── v1.11.0 Installed CodecBzip2 ─────────────────────── v0.8.5 Installed SciMLPublic ────────────────────── v1.0.1 Installed QuadGK ─────────────────────────── v2.11.2 Installed CPUSummary ─────────────────────── v0.2.7 Installed OpenSpecFun_jll ────────────────── v0.5.6+0 Installed Requires ───────────────────────── v1.3.1 Installed StringManipulation ─────────────── v0.4.4 Installed LogExpFunctions ────────────────── v0.3.29 Installed Parsers ────────────────────────── v2.8.3 Installed BufferedStreams ────────────────── v1.2.2 Installed Roots ──────────────────────────── v2.2.13 Installed Rmath ──────────────────────────── v0.9.0 Installed IfElse ─────────────────────────── v0.1.1 Installed PrettyTables ───────────────────── v3.2.3 Installed BioGenerics ────────────────────── v0.1.5 Installed CloseOpenIntervals ─────────────── v0.1.13 Installed StatsFuns ──────────────────────── v1.5.2 Installed Distributions ──────────────────── v0.25.123 Installed Tables ─────────────────────────── v1.12.1 Installed PtrArrays ──────────────────────── v1.4.0 Installed Reexport ───────────────────────── v1.2.2 Installed SpecialFunctions ───────────────── v2.7.1 Installed InverseFunctions ───────────────── v0.1.17 Installed Missings ───────────────────────── v1.2.0 Installed DataFrames ─────────────────────── v1.8.1 Installed Preferences ────────────────────── v1.5.2 Installed Static ─────────────────────────── v1.3.1 Installed DBInterface ────────────────────── v2.6.1 Installed WeakRefStrings ─────────────────── v1.4.2 Installed PooledArrays ───────────────────── v1.4.3 Installed JLLWrappers ────────────────────── v1.7.1 Installed TableTraits ────────────────────── v1.0.1 Installed LaTeXStrings ───────────────────── v1.4.0 Installed XZ_jll ─────────────────────────── v5.8.2+0 Installed SortingAlgorithms ──────────────── v1.2.2 Installed Automa ─────────────────────────── v1.1.0 Installed PDMats ─────────────────────────── v0.11.37 Installed Crayons ────────────────────────── v4.1.1 Installed BGZFStreams ────────────────────── v0.3.2 Installed SQLite ─────────────────────────── v1.8.0 Installed SQLite_jll ─────────────────────── v3.51.2+0 Installed VariantCallFormat ──────────────── v0.5.9 Installed CodecXz ────────────────────────── v0.7.4 Installed ThreadingUtilities ─────────────── v0.5.5 Installed PolyesterWeave ─────────────────── v0.2.2 Installed UnPack ─────────────────────────── v1.0.2 Installed WorkerUtilities ────────────────── v1.6.1 Installed SnpArrays ──────────────────────── v0.3.23 Installed DocStringExtensions ────────────── v0.9.5 Installed Accessors ──────────────────────── v0.1.43 Installed BGEN ───────────────────────────── v0.1.17 Installed MendelIHT ──────────────────────── v1.4.11 Installing 6 artifacts Installed artifact Rmath 121.9 KiB Installed artifact OpenSpecFun 194.9 KiB Installed artifact Bzip2 503.5 KiB Installed artifact SQLite 1.7 MiB Installed artifact XZ 1.5 MiB Installed artifact testfiles 6.2 MiB Updating `~/.julia/environments/v1.14/Project.toml` [921c7187] + MendelIHT v1.4.11 Updating `~/.julia/environments/v1.14/Manifest.toml` [7d9f7c33] + Accessors v0.1.43 [79e6a3ab] + Adapt v4.5.0 [66dad0bd] + AliasTables v1.1.3 [4fba245c] + ArrayInterface v7.23.0 [67c07d97] + Automa v1.1.0 ⌅ [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 v0.2.6 [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 v1.8.1 [864edb3b] + DataStructures v0.19.3 [e2d170a0] + DataValueInterfaces v1.0.0 [8bb1440f] + DelimitedFiles v1.9.1 [b4f34e82] + Distances v0.10.12 [31c24e10] + Distributions v0.25.123 [ffbed154] + DocStringExtensions v0.9.5 [48062228] + FilePathsBase v0.9.24 [1a297f60] + FillArrays v1.16.0 [38e38edf] + GLM v1.9.3 [c27321d9] + Glob v1.4.0 [3e5b6fbb] + HostCPUFeatures v0.1.18 [34004b35] + HypergeometricFunctions v0.3.28 [09f84164] + HypothesisTests v0.11.6 [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 v1.7.1 [b964fa9f] + LaTeXStrings v1.4.0 [10f19ff3] + LayoutPointers v0.1.17 [2ab3a3ac] + LogExpFunctions v0.3.29 [bdcacae8] + LoopVectorization v0.12.173 [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 v1.8.1 [90014a1f] + PDMats v0.11.37 [69de0a69] + Parsers v2.8.3 [1d0040c9] + PolyesterWeave v0.2.2 [2dfb63ee] + PooledArrays v1.4.3 [aea7be01] + PrecompileTools v1.3.3 [21216c6a] + Preferences v1.5.2 [08abe8d2] + PrettyTables v3.2.3 [92933f4c] + ProgressMeter v1.11.0 [43287f4e] + PtrArrays v1.4.0 [1fd47b50] + QuadGK v2.11.2 [189a3867] + Reexport v1.2.2 [ae029012] + Requires v1.3.1 [79098fc4] + Rmath v0.9.0 [f2b01f46] + Roots v2.2.13 [fdea26ae] + SIMD v3.7.2 [94e857df] + SIMDTypes v0.1.0 [476501e8] + SLEEFPirates v0.6.43 [0aa819cd] + SQLite v1.8.0 [431bcebd] + SciMLPublic v1.0.1 [91c51154] + SentinelArrays v1.4.9 [1277b4bf] + ShiftedArrays v2.0.0 [4e780e97] + SnpArrays v0.3.23 [a2af1166] + SortingAlgorithms v1.2.2 [276daf66] + SpecialFunctions v2.7.1 [aedffcd0] + Static v1.3.1 [0d7ed370] + StaticArrayInterface v1.9.0 [10745b16] + Statistics v1.11.1 [82ae8749] + StatsAPI v1.8.0 [2913bbd2] + StatsBase v0.34.10 [4c63d2b9] + StatsFuns v1.5.2 [3eaba693] + StatsModels v0.7.9 [892a3eda] + StringManipulation v0.4.4 [3783bdb8] + TableTraits v1.0.1 [bd369af6] + Tables v1.12.1 [8290d209] + ThreadingUtilities v0.5.5 ⌅ [3bb67fe8] + TranscodingStreams v0.9.13 [3a884ed6] + UnPack v1.0.2 [a620830f] + VCFTools v0.2.10 [28eba6e3] + VariantCallFormat v0.5.9 [3d5dd08c] + VectorizationBase v0.21.72 [ea10d353] + WeakRefStrings v1.4.2 [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 v3.51.2+0 [ffd25f8a] + XZ_jll v5.8.2+0 [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 v1.13.0 [b27032c2] + LibCURL v1.0.0 [76f85450] + LibGit2 v1.11.0 [8f399da3] + Libdl v1.11.0 [37e2e46d] + LinearAlgebra v1.13.0 [56ddb016] + Logging v1.11.0 [d6f4376e] + Markdown v1.11.0 [a63ad114] + Mmap v1.11.0 [ca575930] + NetworkOptions v1.3.0 [44cfe95a] + Pkg v1.14.0 [de0858da] + Printf v1.11.0 [3fa0cd96] + REPL v1.11.0 [9a3f8284] + Random v1.11.0 [ea8e919c] + SHA v1.0.0 [9e88b42a] + Serialization v1.11.0 [6462fe0b] + Sockets v1.11.0 [2f01184e] + SparseArrays v1.13.0 [f489334b] + StyledStrings v1.13.0 [4607b0f0] + SuiteSparse [fa267f1f] + TOML v1.0.3 [a4e569a6] + Tar v1.10.0 [8dfed614] + Test v1.11.0 [cf7118a7] + UUIDs v1.11.0 [4ec0a83e] + Unicode v1.11.0 [e66e0078] + CompilerSupportLibraries_jll v1.3.0+1 [deac9b47] + LibCURL_jll v8.18.0+0 [e37daf67] + LibGit2_jll v1.9.2+0 [29816b5a] + LibSSH2_jll v1.11.3+1 [14a3606d] + MozillaCACerts_jll v2025.12.2 [4536629a] + OpenBLAS_jll v0.3.30+0 [05823500] + OpenLibm_jll v0.8.7+0 [458c3c95] + OpenSSL_jll v3.5.5+0 [efcefdf7] + PCRE2_jll v10.47.0+0 [bea87d4a] + SuiteSparse_jll v7.10.1+0 [83775a58] + Zlib_jll v1.3.2+0 [3161d3a3] + Zstd_jll v1.5.7+1 [8e850b90] + libblastrampoline_jll v5.15.0+0 [8e850ede] + nghttp2_jll v1.68.0+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 18.07s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling packages... 4812.0 ms ✓ TestEnv 1 dependency successfully precompiled in 5 seconds. 27 already precompiled. Precompiling package dependencies... Precompiling packages... 4675.0 ms ✓ MacroTools 1761.2 ms ✓ InlineStrings 890.2 ms ✓ Reexport 1247.2 ms ✓ ConstructionBase 2264.4 ms ✓ IrrationalConstants 861.0 ms ✓ DataValueInterfaces 991.9 ms ✓ StatsAPI 2341.9 ms ✓ Combinatorics 863.6 ms ✓ CommonSolve 941.2 ms ✓ LaTeXStrings 1404.3 ms ✓ Glob 1268.2 ms ✓ Statistics 1224.5 ms ✓ IfElse 981.4 ms ✓ PtrArrays 1056.3 ms ✓ ManualMemory 989.9 ms ✓ DataAPI 869.4 ms ✓ SciMLPublic 857.9 ms ✓ CommonWorldInvalidations 953.7 ms ✓ InvertedIndices 970.6 ms ✓ InverseFunctions 905.9 ms ✓ CompositionsBase 925.4 ms ✓ ShiftedArrays 1047.3 ms ✓ WorkerUtilities 2252.4 ms ✓ FillArrays 824.7 ms ✓ UnPack 863.4 ms ✓ DBInterface 1415.4 ms ✓ OrderedCollections 1191.4 ms ✓ DocStringExtensions 1702.5 ms ✓ OffsetArrays 1080.8 ms ✓ BufferedStreams 818.1 ms ✓ SIMDTypes 733.9 ms ✓ IteratorInterfaceExtensions 1956.5 ms ✓ Crayons 1044.5 ms ✓ DelimitedFiles 1289.7 ms ✓ Requires 1849.4 ms ✓ CpuId 2057.9 ms ✓ PDMats 2483.5 ms ✓ SentinelArrays 1837.6 ms ✓ StructUtils 1885.8 ms ✓ ProgressMeter 1225.1 ms ✓ Compat 1483.2 ms ✓ Preferences 2375.7 ms ✓ TranscodingStreams 852.8 ms ✓ ConstructionBase → ConstructionBaseLinearAlgebraExt 1501.5 ms ✓ Statistics → SparseArraysExt 1551.6 ms ✓ Distances 1064.7 ms ✓ AliasTables 1892.4 ms ✓ ThreadingUtilities 1019.4 ms ✓ Missings 1062.9 ms ✓ PooledArrays 1227.5 ms ✓ InverseFunctions → InverseFunctionsDatesExt 1669.9 ms ✓ InverseFunctions → InverseFunctionsTestExt 914.8 ms ✓ CompositionsBase → CompositionsBaseInverseFunctionsExt 1714.9 ms ✓ FillArrays → FillArraysSparseArraysExt 1096.7 ms ✓ FillArrays → FillArraysStatisticsExt 3779.0 ms ✓ DataStructures 1428.2 ms ✓ LogExpFunctions 837.5 ms ✓ TableTraits 1017.8 ms ✓ Adapt 1628.1 ms ✓ FillArrays → FillArraysPDMatsExt 892.8 ms ✓ Compat → CompatLinearAlgebraExt 1330.1 ms ✓ PrecompileTools 1536.3 ms ✓ JLLWrappers 1665.1 ms ✓ BioGenerics 2522.1 ms ✓ CodecZstd 1656.8 ms ✓ CodecZlib 1496.7 ms ✓ Distances → DistancesSparseArraysExt 5450.8 ms ✓ Accessors 1218.0 ms ✓ SortingAlgorithms 2471.9 ms ✓ QuadGK 853.5 ms ✓ LogExpFunctions → LogExpFunctionsInverseFunctionsExt 1954.8 ms ✓ Tables 1172.5 ms ✓ ArrayInterface 1447.3 ms ✓ Adapt → AdaptSparseArraysExt 878.8 ms ✓ OffsetArrays → OffsetArraysAdaptExt 2537.4 ms ✓ FilePathsBase 3972.5 ms ✓ StringManipulation 15044.7 ms ✓ SIMD 16889.3 ms ✓ Parsers 7962.0 ms ✓ Static 2290.4 ms ✓ Bzip2_jll 2343.8 ms ✓ XZ_jll 2450.3 ms ✓ Rmath_jll 2226.8 ms ✓ OpenSpecFun_jll 1555.6 ms ✓ dlfcn_win32_jll 1819.0 ms ✓ BGZFStreams 2425.9 ms ✓ Accessors → TestExt 2713.8 ms ✓ Accessors → LinearAlgebraExt 4791.6 ms ✓ StatsBase 1287.0 ms ✓ StructUtils → StructUtilsTablesExt 1506.4 ms ✓ ArrayInterface → ArrayInterfaceSparseArraysExt 3206.3 ms ✓ FilePathsBase → FilePathsBaseTestExt 1314.9 ms ✓ FilePathsBase → FilePathsBaseMmapExt 41100.9 ms ✓ PrettyTables 19052.0 ms ✓ Automa 8036.0 ms ✓ JSON 1295.7 ms ✓ InlineStrings → ParsersExt 1319.2 ms ✓ BitTwiddlingConvenienceFunctions 3117.5 ms ✓ CPUSummary 8918.9 ms ✓ StaticArrayInterface 2046.8 ms ✓ CodecBzip2 1979.8 ms ✓ CodecXz 1979.3 ms ✓ Rmath 5552.7 ms ✓ SpecialFunctions 2399.1 ms ✓ SQLite_jll 7681.8 ms ✓ Roots 1706.4 ms ✓ PDMats → StatsBaseExt 82527.9 ms ✓ DataFrames [ Info: Compiling VCF parser... 16078.1 ms ✓ VariantCallFormat 3492.0 ms ✓ BenchmarkTools 2802.5 ms ✓ WeakRefStrings 3000.9 ms ✓ HostCPUFeatures 2353.3 ms ✓ PolyesterWeave 1687.6 ms ✓ StaticArrayInterface → StaticArrayInterfaceOffsetArraysExt 1808.1 ms ✓ CloseOpenIntervals 1862.6 ms ✓ LayoutPointers 2802.0 ms ✓ HypergeometricFunctions 28732.6 ms ✓ CSV 4808.7 ms ✓ SQLite 16696.9 ms ✓ VectorizationBase 3376.2 ms ✓ StatsFuns 4911.6 ms ✓ BGEN 4010.1 ms ✓ SLEEFPirates 1554.2 ms ✓ StatsFuns → StatsFunsInverseFunctionsExt 5793.0 ms ✓ StatsModels 10399.2 ms ✓ Distributions 40753.7 ms ✓ LoopVectorization 5963.2 ms ✓ GLM 3893.0 ms ✓ Distributions → DistributionsTestExt 4618.0 ms ✓ HypothesisTests 3732.3 ms ✓ LoopVectorization → SpecialFunctionsExt 6291.7 ms ✓ VCFTools 24914.4 ms ✓ SnpArrays WARNING: Constructor for type "MvNormal" was extended in `MendelIHT` without explicit qualification or import.  NOTE: Assumed "MvNormal" refers to `Distributions.MvNormal`. This behavior is deprecated and may differ in future versions.  NOTE: This behavior may have differed in Julia versions prior to 1.12.  Hint: If you intended to create a new generic function of the same name, use `function MvNormal end`.  Hint: To silence the warning, qualify `MvNormal` as `Distributions.MvNormal` in the method signature or explicitly `import Distributions: MvNormal`. 24070.9 ms ✓ MendelIHT 134 dependencies successfully precompiled in 608 seconds. 40 already precompiled. 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 632.16s ################################################################################ # Testing # Testing MendelIHT Status `/tmp/jl_KAZCHV/Project.toml` ⌅ [6db4b851] BGEN v0.1.17 [6e4b80f9] BenchmarkTools v1.6.3 [336ed68f] CSV v0.10.16 [a93c6f00] DataFrames v1.8.1 [8bb1440f] DelimitedFiles v1.9.1 [b4f34e82] Distances v0.10.12 [31c24e10] Distributions v0.25.123 [38e38edf] GLM v1.9.3 [921c7187] MendelIHT v1.4.11 [92933f4c] ProgressMeter v1.11.0 [189a3867] Reexport v1.2.2 [4e780e97] SnpArrays v0.3.23 [276daf66] SpecialFunctions v2.7.1 [2913bbd2] StatsBase v0.34.10 [a620830f] VCFTools v0.2.10 [37e2e46d] LinearAlgebra v1.13.0 [44cfe95a] Pkg v1.14.0 [9a3f8284] Random v1.11.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_KAZCHV/Manifest.toml` [7d9f7c33] Accessors v0.1.43 [79e6a3ab] Adapt v4.5.0 [66dad0bd] AliasTables v1.1.3 [4fba245c] ArrayInterface v7.23.0 [67c07d97] Automa v1.1.0 ⌅ [6db4b851] BGEN v0.1.17 [28d598bf] BGZFStreams v0.3.2 [6e4b80f9] BenchmarkTools v1.6.3 [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 v0.2.6 [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 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v1.68.0+1 [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 16.9s 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 10.8s Test Summary: | Pass Total Time _iht_backtrack | 7 7 0.0s Test Summary: | Pass Total Time standardize! | 12 12 1.6s Test Summary: | Pass Total Time project_k! | 2 2 1.0s Test Summary: | Pass Total Time project_group_sparse! | 5 5 1.5s Test Summary: | Pass Total Time maf_weights | 6 6 2.2s **** 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 = -1486.189137223143, backtracks = 0, tol = 0.8135872348563492 Iteration 2: loglikelihood = -1368.5441339551699, backtracks = 0, tol = 0.13737112808675692 Iteration 3: loglikelihood = -1363.0629966324832, backtracks = 0, tol = 0.023380643686040696 Iteration 4: loglikelihood = -1361.8018991640392, backtracks = 0, tol = 0.06507444055913464 Iteration 5: loglikelihood = -1361.5412386557898, backtracks = 0, tol = 0.007588237792380612 Iteration 6: loglikelihood = -1361.5397049491576, backtracks = 0, tol = 0.000717766529442934 Iteration 7: loglikelihood = -1361.5396870898326, backtracks = 0, tol = 5.468692599362343e-5 IHT estimated 10 nonzero SNP predictors and 1 non-genetic predictors. Compute time (sec): 0.064971923828125 Final loglikelihood: -1361.5396870898326 SNP PVE: 0.8037255479918245 Iterations: 7 Selected genetic predictors: 10×2 DataFrame Row │ Position Estimated_β │ Int64 Float64 ─────┼─────────────────────── 1 │ 2742 0.128339 2 │ 3037 -0.407964 3 │ 4608 -0.630515 4 │ 4718 0.476002 5 │ 5621 -0.286867 6 │ 6020 -0.23909 7 │ 6425 0.882876 8 │ 6520 -0.914077 9 │ 6868 -0.799675 10 │ 9699 0.577692 Selected nongenetic predictors: 1×2 DataFrame Row │ Position Estimated_β │ Int64 Float64 ─────┼─────────────────────── 1 │ 1 -0.00729136Test Summary: | Pass Total Time fit normal SnpLinAlg | 4 4 25.9s **** 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 logistic regression Number of threads = 1 Link functin = LogitLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -379.72375963518977, backtracks = 0, tol = 0.6062552017348442 Iteration 2: loglikelihood = -294.14222098196217, backtracks = 0, tol = 0.39035964909167 Iteration 3: loglikelihood = -258.44215825745147, backtracks = 0, tol = 0.18072720194601524 Iteration 4: loglikelihood = -248.39092317275637, backtracks = 1, tol = 0.0581811999889429 Iteration 5: loglikelihood = -241.2861695402178, backtracks = 2, tol = 0.10199490430383734 Iteration 6: loglikelihood = -236.0344401262056, backtracks = 2, tol = 0.10444957184614982 Iteration 7: loglikelihood = -232.75639772007577, backtracks = 2, tol = 0.03618239958756675 Iteration 8: loglikelihood = -230.9028935826695, backtracks = 3, tol = 0.022566251649321353 Iteration 9: loglikelihood = -229.2332883500926, backtracks = 3, tol = 0.02394599965909332 Iteration 10: loglikelihood = -227.8109863155336, backtracks = 3, tol = 0.02260237147851236 Iteration 11: loglikelihood = -226.61429831284372, backtracks = 3, tol = 0.02153016573221634 Iteration 12: loglikelihood = -225.614543213995, backtracks = 3, tol = 0.020073248773013197 Iteration 13: loglikelihood = -225.15228734295533, backtracks = 3, tol = 0.10266272165892033 Iteration 14: loglikelihood = -224.5524858306654, backtracks = 2, tol = 0.010910053499902256 Iteration 15: loglikelihood = -223.90430308527087, backtracks = 3, tol = 0.10669566586572145 Iteration 16: loglikelihood = -223.43342440058004, backtracks = 1, tol = 0.009912340440473734 Iteration 17: loglikelihood = -223.19474883510568, backtracks = 3, tol = 0.10429355504005154 Iteration 18: loglikelihood = -222.7530868660152, backtracks = 1, tol = 0.010133510239484585 Iteration 19: loglikelihood = -222.4546375562022, backtracks = 3, tol = 0.009382230171462355 Iteration 20: loglikelihood = -225.04961416047087, backtracks = 3, tol = 0.13141028198780508 Iteration 21: loglikelihood = -221.57583298738808, backtracks = 0, tol = 0.12983606150115481 Iteration 22: loglikelihood = -220.9953587123894, backtracks = 0, tol = 0.018278220962270587 Iteration 23: loglikelihood = -220.46528702030645, backtracks = 0, tol = 0.10912949798131547 Iteration 24: loglikelihood = -220.22939682199817, backtracks = 1, tol = 0.006133557493960293 Iteration 25: loglikelihood = -220.1149031779291, backtracks = 3, tol = 0.005637364497494655 Iteration 26: loglikelihood = -237.91408320706802, backtracks = 3, tol = 0.1311916630585333 Iteration 27: loglikelihood = -222.6667401701631, backtracks = 0, tol = 0.13008576394077564 Iteration 28: loglikelihood = -220.0179912284672, backtracks = 0, tol = 0.10981267805412102 Iteration 29: loglikelihood = -219.80873468505163, backtracks = 1, tol = 0.006242686572879014 Iteration 30: loglikelihood = -219.71412932030552, backtracks = 1, tol = 0.0052581541847830735 Iteration 31: loglikelihood = -219.67346582214395, backtracks = 3, tol = 0.002736072071808146 Iteration 32: loglikelihood = -236.63118723570068, backtracks = 3, tol = 0.12536959025201838 Iteration 33: loglikelihood = -222.42522446507616, backtracks = 0, tol = 0.12480632457239557 Iteration 34: loglikelihood = -219.76952387571325, backtracks = 0, tol = 0.10782393864869841 Iteration 35: loglikelihood = -219.54239052596037, backtracks = 0, tol = 0.010969385336776636 Iteration 36: loglikelihood = -219.51051719556185, backtracks = 0, tol = 0.0038143069815270263 Iteration 37: loglikelihood = -219.49562270628724, backtracks = 1, tol = 0.0015360028505860806 Iteration 38: loglikelihood = -222.2776344615594, backtracks = 3, tol = 0.10706948875570901 Iteration 39: loglikelihood = -219.86344247649652, backtracks = 0, tol = 0.10682440099239575 Iteration 40: loglikelihood = -219.50637292175287, backtracks = 0, tol = 0.010145149683589566 Iteration 41: loglikelihood = -219.45601478260392, backtracks = 0, tol = 0.004786594360325445 Iteration 42: loglikelihood = -219.44279315931445, backtracks = 0, tol = 0.0023300326568676676 Iteration 43: loglikelihood = -219.434262597912, backtracks = 0, tol = 0.002159682320412748 Iteration 44: loglikelihood = -219.42706752504972, backtracks = 0, tol = 0.0019986878272562235 Iteration 45: loglikelihood = -219.4208881668612, backtracks = 0, tol = 0.001781315196828412 Iteration 46: loglikelihood = -219.41556755717227, backtracks = 0, tol = 0.0017266268818688624 Iteration 47: loglikelihood = -219.41098445944962, backtracks = 0, tol = 0.001504993867218278 Iteration 48: loglikelihood = -219.4070309112888, backtracks = 0, tol = 0.001495426527055874 Iteration 49: loglikelihood = -219.40362030781677, backtracks = 0, tol = 0.001286324051089446 Iteration 50: loglikelihood = -219.4006747755802, backtracks = 0, tol = 0.001295957349435961 Iteration 51: loglikelihood = -219.39813103252988, backtracks = 0, tol = 0.0011058748112207813 Iteration 52: loglikelihood = -219.3959322024177, backtracks = 0, tol = 0.0011233728145861855 Iteration 53: loglikelihood = -219.39403166729804, backtracks = 0, tol = 0.0009536994758608786 Iteration 54: loglikelihood = -219.39238763268273, backtracks = 0, tol = 0.0009739180646352119 Iteration 55: loglikelihood = -219.39096560226784, backtracks = 0, tol = 0.0008239389039648708 Iteration 56: loglikelihood = -219.38973473800374, backtracks = 0, tol = 0.0008444580901064712 Iteration 57: loglikelihood = -219.3886694316569, backtracks = 0, tol = 0.0007126409505425607 Iteration 58: loglikelihood = -219.38774685610232, backtracks = 0, tol = 0.0007323063866727435 Iteration 59: loglikelihood = -219.3869479529937, backtracks = 0, tol = 0.00061686194275372 Iteration 60: loglikelihood = -219.3862557798823, backtracks = 0, tol = 0.0006351404346176769 Iteration 61: loglikelihood = -219.3856561234815, backtracks = 0, tol = 0.000534269842115572 Iteration 62: loglikelihood = -219.38513638040487, backtracks = 0, tol = 0.0005509480422217535 Iteration 63: loglikelihood = -219.38468593224545, backtracks = 0, tol = 0.0004629512780606966 Iteration 64: loglikelihood = -219.38429538513583, backtracks = 0, tol = 0.0004779860767529819 Iteration 65: loglikelihood = -219.38395679466737, backtracks = 0, tol = 0.0004013057505476397 Iteration 66: loglikelihood = -219.38366314739872, backtracks = 0, tol = 0.0004147454994836376 Iteration 67: loglikelihood = -219.38340849212824, backtracks = 0, tol = 0.00034797985178746597 Iteration 68: loglikelihood = -219.38318758502183, backtracks = 0, tol = 0.0003599207374415984 Iteration 69: loglikelihood = -219.38299596326374, backtracks = 0, tol = 0.0003018217223394219 Iteration 70: loglikelihood = -219.3828297011887, backtracks = 0, tol = 0.00031238270039476616 Iteration 71: loglikelihood = -219.38268544908368, backtracks = 0, tol = 0.00026184698528793125 Iteration 72: loglikelihood = -219.3825602648841, backtracks = 0, tol = 0.0002711550905775348 Iteration 73: loglikelihood = -219.38245163239276, backtracks = 0, tol = 0.00022721198022395564 Iteration 74: loglikelihood = -219.38235734460943, backtracks = 0, tol = 0.00023539371282360467 Iteration 75: loglikelihood = -219.38227551018164, backtracks = 0, tol = 0.0001971920991460162 Iteration 76: loglikelihood = -219.382204472153, backtracks = 0, tol = 0.00020436848993624394 Iteration 77: loglikelihood = -219.3821428080304, backtracks = 0, tol = 0.00017116393516432852 Iteration 78: loglikelihood = -219.38208927292968, backtracks = 0, tol = 0.00017744788492952903 Iteration 79: loglikelihood = -219.38204279645043, backtracks = 0, tol = 0.00014859040670150365 Iteration 80: loglikelihood = -219.38200244272016, backtracks = 0, tol = 0.00015408544066832546 Iteration 81: loglikelihood = -219.38196740593906, backtracks = 0, tol = 0.00012900826739905896 Iteration 82: loglikelihood = -219.38193698216227, backtracks = 0, tol = 0.00013380816660865064 Iteration 83: loglikelihood = -219.38191056455443, backtracks = 0, tol = 0.00011201756190578927 Iteration 84: loglikelihood = -219.3818876233726, backtracks = 0, tol = 0.000116206527337935 Iteration 85: loglikelihood = -219.38186770147453, backtracks = 0, tol = 9.727268703830643e-5 Test Summary: | Pass Total Time fit Bernoulli SnpLinAlg | 4 4 4.2s **** 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 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 = -1321.2463522095577, backtracks = 0, tol = 0.19889739805369192 Iteration 2: loglikelihood = -1305.681752124262, backtracks = 0, tol = 0.048726819031126266 Iteration 3: loglikelihood = -1300.4895811465803, backtracks = 1, tol = 0.07436184374867508 Iteration 4: loglikelihood = -1299.2902957006913, backtracks = 1, tol = 0.011433614482637737 Iteration 5: loglikelihood = -1298.6289323053336, backtracks = 1, tol = 0.01426333816330487 Iteration 6: loglikelihood = -1298.4108488013273, backtracks = 1, tol = 0.009454202106188362 Iteration 7: loglikelihood = -1298.3440507226983, backtracks = 1, tol = 0.005335808286024753 Iteration 8: loglikelihood = -1298.3180932703813, backtracks = 1, tol = 0.003410286353290892 Iteration 9: loglikelihood = -1298.3047281527433, backtracks = 1, tol = 0.002469255080521498 Iteration 10: loglikelihood = -1298.2986406294503, backtracks = 1, tol = 0.0017331884991112537 Iteration 11: loglikelihood = -1298.2954631248654, backtracks = 1, tol = 0.0012254672398063352 Iteration 12: loglikelihood = -1298.2939607466737, backtracks = 1, tol = 0.000876490114205403 Iteration 13: loglikelihood = -1298.293171082887, backtracks = 1, tol = 0.0006157768142759087 Iteration 14: loglikelihood = -1298.292792746639, backtracks = 1, tol = 0.00044296933558276083 Iteration 15: loglikelihood = -1298.2925930972056, backtracks = 1, tol = 0.00031083997768870174 Iteration 16: loglikelihood = -1298.2924970005354, backtracks = 1, tol = 0.00022387830434372137 Iteration 17: loglikelihood = -1298.292446143129, backtracks = 1, tol = 0.00015723895109745695 Iteration 18: loglikelihood = -1298.2924216405006, backtracks = 1, tol = 0.00011315530079775927 Iteration 19: loglikelihood = -1298.2924086401674, backtracks = 1, tol = 7.962182231316097e-5 Test Summary: | Pass Total Time fit Poisson SnpLinAlg | 4 4 3.2s **** 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 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 = -1427.0592848894069, backtracks = 0, tol = 0.20359113727378242 Iteration 2: loglikelihood = -1416.9671000195606, backtracks = 0, tol = 0.0725349164655579 Iteration 3: loglikelihood = -1410.526747694798, backtracks = 0, tol = 0.09178004635887457 Iteration 4: loglikelihood = -1408.8327495424855, backtracks = 0, tol = 0.09587245176318177 Iteration 5: loglikelihood = -1406.7021614634027, backtracks = 0, tol = 0.09251513072945285 Iteration 6: loglikelihood = -1406.4710295741936, backtracks = 0, tol = 0.015409636193895722 Iteration 7: loglikelihood = -1406.4440824388666, backtracks = 0, tol = 0.0048115011107518835 Iteration 8: loglikelihood = -1406.4403118995654, backtracks = 0, tol = 0.002396479123737075 Iteration 9: loglikelihood = -1406.4397696507385, backtracks = 0, tol = 0.0007161576225088039 Iteration 10: loglikelihood = -1406.4396908250192, backtracks = 0, tol = 0.0003645010483275717 Iteration 11: loglikelihood = -1406.4396793716196, backtracks = 0, tol = 0.00010469197150018739 Iteration 12: loglikelihood = -1406.4396777167806, backtracks = 0, tol = 5.392768837120423e-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 = -1975.4171730676978, backtracks = 0, tol = 0.7001976239084349 Iteration 2: loglikelihood = -1495.2379671429587, backtracks = 0, tol = 0.16148727926735984 Iteration 3: loglikelihood = -1370.4401418416514, backtracks = 0, tol = 0.07175911785474819 Iteration 4: loglikelihood = -1356.7938600042921, backtracks = 0, tol = 0.026926893123744265 Iteration 5: loglikelihood = -1356.2918411528635, backtracks = 1, tol = 0.0026054735636148333 Iteration 6: loglikelihood = -1356.1596990553403, backtracks = 1, tol = 0.0014806874352245802 Iteration 7: loglikelihood = -1356.1248819589557, backtracks = 1, tol = 0.0008259531962176216 Iteration 8: loglikelihood = -1356.1157510627816, backtracks = 1, tol = 0.0004493307153357644 Iteration 9: loglikelihood = -1356.113378775269, backtracks = 1, tol = 0.00023794231058746102 Iteration 10: loglikelihood = -1356.1127690435883, backtracks = 1, tol = 0.000123079316742799 Iteration 11: loglikelihood = -1356.1126137677666, backtracks = 1, tol = 6.259635407982316e-5 Test Summary: | Pass Total Time fit with >1 non-genetic covariates SnpLinAlg | 5 5 1.8s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** 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 = -1538.8226012475607, backtracks = 0, tol = 0.34591069728106577 Iteration 2: loglikelihood = -1378.9289368119796, backtracks = 0, tol = 0.08789355064640204 Iteration 3: loglikelihood = -1360.0479164748908, backtracks = 0, tol = 0.03984805921240669 Iteration 4: loglikelihood = -1354.7733551099866, backtracks = 0, tol = 0.0316663893570711 Iteration 5: loglikelihood = -1353.9609902212296, backtracks = 0, tol = 0.027312096315884913 Iteration 6: loglikelihood = -1353.8867549696783, backtracks = 1, tol = 0.001139629438093782 Iteration 7: loglikelihood = -1353.867770928115, backtracks = 1, tol = 0.0005609895228936993 Iteration 8: loglikelihood = -1353.8629295305373, backtracks = 1, tol = 0.000274403345793276 Iteration 9: loglikelihood = -1353.8616984653754, backtracks = 1, tol = 0.0001336237818821619 Iteration 10: loglikelihood = -1353.8613862849384, backtracks = 1, tol = 6.491281972292819e-5 Test Summary: | Pass Total Time model selection on non-genetic covariates | 5 5 0.8s **** 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 **** Running sparse linear regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 15 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1473.12410014528, backtracks = 0, tol = 0.11162633196865429 Iteration 2: loglikelihood = -1448.37403799896, backtracks = 0, tol = 0.07736217654955346 Iteration 3: loglikelihood = -1429.8981769610311, backtracks = 1, tol = 0.056531823476744666 Iteration 4: loglikelihood = -1404.7133956159753, backtracks = 0, tol = 0.10125409614175711 Iteration 5: loglikelihood = -1397.466171579031, backtracks = 0, tol = 0.05343369325195712 Iteration 6: loglikelihood = -1395.7490747391416, backtracks = 0, tol = 0.08843871418165569 Iteration 7: loglikelihood = -1395.4877576477586, backtracks = 0, tol = 0.0089247040684952 Iteration 8: loglikelihood = -1395.442237061722, backtracks = 0, tol = 0.005277867116132827 Iteration 9: loglikelihood = -1395.4302205892106, backtracks = 0, tol = 0.0027680467744013336 Iteration 10: loglikelihood = -1395.1973617039414, backtracks = 0, tol = 0.0905690065560604 Iteration 11: loglikelihood = -1395.0048067729406, backtracks = 0, tol = 0.007650485819168939 Iteration 12: loglikelihood = -1394.9835209063683, backtracks = 0, tol = 0.0035232591741737973 Iteration 13: loglikelihood = -1394.9793628241396, backtracks = 0, tol = 0.001852195878065177 Iteration 14: loglikelihood = -1394.9779889816232, backtracks = 0, tol = 0.0012530451800711444 Iteration 15: loglikelihood = -1394.977503420045, backtracks = 0, tol = 0.0006829444661300923 Iteration 16: loglikelihood = -1394.9773714862843, backtracks = 1, tol = 0.00022881022816864142 Iteration 17: loglikelihood = -1394.977310220191, backtracks = 2, tol = 0.0001217788197399568 Iteration 18: loglikelihood = -1394.977273607278, backtracks = 2, tol = 8.822469907087602e-5 **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse linear regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 3 Prior weight scaling = off Doubly sparse projection = on Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1535.4672180567934, backtracks = 0, tol = 0.17016419679985048 Iteration 2: loglikelihood = -1508.04343741211, backtracks = 0, tol = 0.21718489399873087 Iteration 3: loglikelihood = -1448.2717322168082, backtracks = 0, tol = 0.15334504607402907 Iteration 4: loglikelihood = -1437.5669418734744, backtracks = 0, tol = 0.08425396177776269 Iteration 5: loglikelihood = -1434.3602241747528, backtracks = 0, tol = 0.03199716666887782 Iteration 6: loglikelihood = -1434.239273652971, backtracks = 2, tol = 0.003498168340088273 Iteration 7: loglikelihood = -1434.1475478538455, backtracks = 2, tol = 0.0030522911015526556 Iteration 8: loglikelihood = -1434.0913475157126, backtracks = 2, tol = 0.0021931576818355514 Iteration 9: loglikelihood = -1434.0584761985995, backtracks = 2, tol = 0.0016688209654910561 Iteration 10: loglikelihood = -1434.0393127719108, backtracks = 2, tol = 0.001317554485128468 Iteration 11: loglikelihood = -1434.0281644425422, backtracks = 2, tol = 0.0010393713220469248 Iteration 12: loglikelihood = -1434.0216963632631, backtracks = 2, tol = 0.0008158673348111212 Iteration 13: loglikelihood = -1434.0179556115852, backtracks = 2, tol = 0.0006363671566384319 Iteration 14: loglikelihood = -1433.8972844529703, backtracks = 2, tol = 0.02105646084267335 Iteration 15: loglikelihood = -1433.6170929347984, backtracks = 1, tol = 0.011448126839540936 Iteration 16: loglikelihood = -1433.5408744767515, backtracks = 2, tol = 0.0040324300639331045 Iteration 17: loglikelihood = -1433.4945867179188, backtracks = 2, tol = 0.003005268578298657 Iteration 18: loglikelihood = -1433.467626121943, backtracks = 2, tol = 0.002187229771831438 Iteration 19: loglikelihood = -1433.4521439235273, backtracks = 2, tol = 0.0016467936133078437 Iteration 20: loglikelihood = -1433.4432822302874, backtracks = 2, tol = 0.0012631945762950846 Iteration 21: loglikelihood = -1433.4382075829426, backtracks = 2, tol = 0.0009580287583338291 Iteration 22: loglikelihood = -1433.4352962137846, backtracks = 2, tol = 0.0007222437442123496 Iteration 23: loglikelihood = -1433.4336216439426, backtracks = 2, tol = 0.0005424739396431532 Iteration 24: loglikelihood = -1433.43265547142, backtracks = 2, tol = 0.00040628145880685523 Iteration 25: loglikelihood = -1433.4320960523787, backtracks = 2, tol = 0.0003034179918772475 Iteration 26: loglikelihood = -1433.4317709097872, backtracks = 2, tol = 0.00022583740291084404 Iteration 27: loglikelihood = -1433.4315812027676, backtracks = 2, tol = 0.0001673653861249394 Iteration 28: loglikelihood = -1432.5898379532837, backtracks = 2, tol = 0.025080215054031605 Iteration 29: loglikelihood = -1431.7678006470733, backtracks = 1, tol = 0.017181190475547538 Iteration 30: loglikelihood = -1430.3157393955933, backtracks = 1, tol = 0.07333968264200234 Iteration 31: loglikelihood = -1429.706868513855, backtracks = 0, tol = 0.020015111727945754 Iteration 32: loglikelihood = -1429.5802551945537, backtracks = 1, tol = 0.00756937670420323 Iteration 33: loglikelihood = -1429.5139450553559, backtracks = 2, tol = 0.003906515984506227 Iteration 34: loglikelihood = -1429.4691972325213, backtracks = 2, tol = 0.003683664863256486 Iteration 35: loglikelihood = -1428.8607526222902, backtracks = 2, tol = 0.08711763846658777 Iteration 36: loglikelihood = -1428.6178427111051, backtracks = 1, tol = 0.006558345246943271 Iteration 37: loglikelihood = -1428.5424083746184, backtracks = 2, tol = 0.0033912200662443866 Iteration 38: loglikelihood = -1428.4933608487952, backtracks = 2, tol = 0.0030098214824111793 Iteration 39: loglikelihood = -1428.4620745885088, backtracks = 2, tol = 0.0025951371119133128 Iteration 40: loglikelihood = -1428.4427329028306, backtracks = 2, tol = 0.002148184701148465 Iteration 41: loglikelihood = -1428.4311433050725, backtracks = 2, tol = 0.0017160493175770867 Iteration 42: loglikelihood = -1428.4243474878394, backtracks = 2, tol = 0.0013407892924840973 Iteration 43: loglikelihood = -1428.420413936832, backtracks = 2, tol = 0.0010343694042998534 Iteration 44: loglikelihood = -1428.4181556141762, backtracks = 2, tol = 0.0007948565534422845 Iteration 45: loglikelihood = -1428.4168664091337, backtracks = 2, tol = 0.000608309643427293 Iteration 46: loglikelihood = -1428.4161334920516, backtracks = 2, tol = 0.0004622621654004415 Iteration 47: loglikelihood = -1428.4157180925672, backtracks = 2, tol = 0.00034956951660978575 Iteration 48: loglikelihood = -1428.4154831711999, backtracks = 2, tol = 0.00026348047442121094 Iteration 49: loglikelihood = -1428.4153505233908, backtracks = 2, tol = 0.00019816133989405092 Iteration 50: loglikelihood = -1428.4152757065372, backtracks = 2, tol = 0.00014882628973647444 Iteration 51: loglikelihood = -1428.4152335404317, backtracks = 2, tol = 0.00011167501044822909 Iteration 52: loglikelihood = -1428.4152097888611, backtracks = 2, tol = 8.375238803842589e-5 Test Summary: | Pass Total Time Correlated predictors and double sparsity Float64 matrix | 2 2 11.1s **** 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 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 = -1788.9795182130729, backtracks = 0, tol = 0.2049759046545593 Iteration 2: loglikelihood = -1633.2259087562775, backtracks = 0, tol = 0.13794679762107898 Iteration 3: loglikelihood = -1496.169162847471, backtracks = 0, tol = 0.15748869645808444 Iteration 4: loglikelihood = -1472.4052138407733, backtracks = 0, tol = 0.06541981903535217 Iteration 5: loglikelihood = -1459.4778762647104, backtracks = 0, tol = 0.06345727189299452 Iteration 6: loglikelihood = -1452.3519561847077, backtracks = 0, tol = 0.029192137667880678 Iteration 7: loglikelihood = -1438.236209574659, backtracks = 0, tol = 0.09535253697944152 Iteration 8: loglikelihood = -1431.3261559260775, backtracks = 0, tol = 0.07572373732439057 Iteration 9: loglikelihood = -1428.0401530951406, backtracks = 0, tol = 0.051293347154821714 Iteration 10: loglikelihood = -1427.3682056998373, backtracks = 0, tol = 0.008583504702897283 Iteration 11: loglikelihood = -1427.1217937787, backtracks = 0, tol = 0.008471280744170258 Iteration 12: loglikelihood = -1426.998097721376, backtracks = 0, tol = 0.004090893266111741 Iteration 13: loglikelihood = -1426.9317286234243, backtracks = 0, tol = 0.004777913224621877 Iteration 14: loglikelihood = -1426.8961160222163, backtracks = 0, tol = 0.0021117566791228654 Iteration 15: loglikelihood = -1426.8765136889776, backtracks = 0, tol = 0.0027217799890706523 Iteration 16: loglikelihood = -1426.8660441130482, backtracks = 0, tol = 0.0011075072513973855 Iteration 17: loglikelihood = -1426.60744626638, backtracks = 0, tol = 0.052421148091673066 Iteration 18: loglikelihood = -1426.5311821081395, backtracks = 0, tol = 0.003650013532771377 Iteration 19: loglikelihood = -1426.5279773760376, backtracks = 0, tol = 0.0006533353178666595 Iteration 20: loglikelihood = -1426.5271630924117, backtracks = 0, tol = 0.0003649421803952299 Iteration 21: loglikelihood = -1426.5268786446206, backtracks = 0, tol = 0.00017696380699662822 Iteration 22: loglikelihood = -1426.526742509287, backtracks = 0, tol = 0.00021159230180570117 Iteration 23: loglikelihood = -1426.526673507093, backtracks = 0, tol = 8.466343121834575e-5 0.980010 seconds (1.84 M allocations: 38.920 MiB, 66.83% 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 = -1793.160476485713, backtracks = 0, tol = 0.2049759046545593 Iteration 2: loglikelihood = -1689.9664738353501, backtracks = 0, tol = 0.1455947243917727 Iteration 3: loglikelihood = -1605.1559444772374, backtracks = 0, tol = 0.187349431017811 Iteration 4: loglikelihood = -1567.4799190045449, backtracks = 0, tol = 0.1216561208278552 Iteration 5: loglikelihood = -1548.4882057784919, backtracks = 0, tol = 0.1050964128039922 Iteration 6: loglikelihood = -1527.3270954573952, backtracks = 0, tol = 0.035879139660654036 Iteration 7: loglikelihood = -1518.27561861483, backtracks = 0, tol = 0.09289545448096916 Iteration 8: loglikelihood = -1500.3296736413, backtracks = 0, tol = 0.09193400976238375 Iteration 9: loglikelihood = -1490.871512036915, backtracks = 0, tol = 0.009408676525725863 Iteration 10: loglikelihood = -1483.6401012501908, backtracks = 0, tol = 0.0024845576617749496 Iteration 11: loglikelihood = -1477.4037747054401, backtracks = 0, tol = 0.002017696534666651 Iteration 12: loglikelihood = -1472.1754162408085, backtracks = 0, tol = 0.0005943194324159857 Iteration 13: loglikelihood = -1467.6649427033071, backtracks = 0, tol = 0.0003401582216801023 Iteration 14: loglikelihood = -1463.7743698334566, backtracks = 0, tol = 0.0002938608906586114 Iteration 15: loglikelihood = -1461.6804880926777, backtracks = 0, tol = 0.06310810686173102 Iteration 16: loglikelihood = -1457.5602681202085, backtracks = 0, tol = 0.06311817124451824 Iteration 17: loglikelihood = -1454.7932577140439, backtracks = 0, tol = 0.005871679741009954 Iteration 18: loglikelihood = -1452.4996556171702, backtracks = 0, tol = 0.0005575782094461663 Iteration 19: loglikelihood = -1450.4353331575116, backtracks = 0, tol = 0.000322909297908159 Iteration 20: loglikelihood = -1447.005227197963, backtracks = 1, tol = 0.00023631600348139606 Iteration 21: loglikelihood = -1446.819719807183, backtracks = 0, tol = 0.0616089289072416 Iteration 22: loglikelihood = -1444.3026766467178, backtracks = 0, tol = 0.06162514640019529 Iteration 23: loglikelihood = -1442.9281700447395, backtracks = 0, tol = 0.005818335644569925 Iteration 24: loglikelihood = -1441.8332168856234, backtracks = 0, tol = 0.0005817755357466324 Iteration 25: loglikelihood = -1440.8196746979077, backtracks = 0, tol = 0.0002636877639140414 Iteration 26: loglikelihood = -1439.102668980237, backtracks = 1, tol = 0.00020041940480078788 Iteration 27: loglikelihood = -1437.6048972898789, backtracks = 1, tol = 0.00018205020525149246 Iteration 28: loglikelihood = -1436.3420033164955, backtracks = 1, tol = 0.00022437025591350514 Iteration 29: loglikelihood = -1435.2706589143877, backtracks = 1, tol = 0.0002454212383377169 Iteration 30: loglikelihood = -1434.3602285439354, backtracks = 1, tol = 0.0002529025965733506 Iteration 31: loglikelihood = -1433.6058521464643, backtracks = 1, tol = 0.0002697471262203497 Iteration 32: loglikelihood = -1432.9750507457188, backtracks = 1, tol = 0.00028328831696050925 Iteration 33: loglikelihood = -1432.4444633794483, backtracks = 1, tol = 0.0002799735686860001 Iteration 34: loglikelihood = -1431.9922656068604, backtracks = 1, tol = 0.0002638097797898838 Iteration 35: loglikelihood = -1431.5982512365906, backtracks = 1, tol = 0.00023895797450572802 Iteration 36: loglikelihood = -1431.2460444796586, backtracks = 1, tol = 0.00021164545244876974 Iteration 37: loglikelihood = -1430.9240606959183, backtracks = 1, tol = 0.00018620658448425907 Iteration 38: loglikelihood = -1430.626148023436, backtracks = 1, tol = 0.00016561831976910513 Iteration 39: loglikelihood = -1430.3503971794357, backtracks = 1, tol = 0.00015068485045679466 Iteration 40: loglikelihood = -1430.0972272310296, backtracks = 1, tol = 0.0001409695784748924 Iteration 41: loglikelihood = -1429.8674789161494, backtracks = 1, tol = 0.00013509326156220845 Iteration 42: loglikelihood = -1429.6614667431095, backtracks = 1, tol = 0.00013147544746880657 Iteration 43: loglikelihood = -1429.4787328200766, backtracks = 1, tol = 0.0001286530054545657 Iteration 44: loglikelihood = -1429.3181487590862, backtracks = 1, tol = 0.00012550971232611158 Iteration 45: loglikelihood = -1429.1780688761492, backtracks = 1, tol = 0.0001213109477827555 Iteration 46: loglikelihood = -1429.056446354572, backtracks = 1, tol = 0.00011569814353233831 Iteration 47: loglikelihood = -1428.9508731243805, backtracks = 1, tol = 0.00010863285969293232 Iteration 48: loglikelihood = -1428.8585097939167, backtracks = 1, tol = 0.00010031798445066021 Iteration 49: loglikelihood = -1428.7758265609582, backtracks = 1, tol = 9.109206399795554e-5 0.557364 seconds (2.49 M allocations: 45.055 MiB, 4.38% 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 = -3642.6863, backtracks = 0, tol = 0.0835442367894988 Iteration 2: loglikelihood = -3588.9321, backtracks = 0, tol = 0.04776107484484006 Iteration 3: loglikelihood = -3583.4822, backtracks = 1, tol = 0.015975281207256473 Iteration 4: loglikelihood = -3581.9688, backtracks = 1, tol = 0.008649889235816303 Iteration 5: loglikelihood = -3581.5708, backtracks = 1, tol = 0.004686811770759876 Iteration 6: loglikelihood = -3581.4707, backtracks = 1, tol = 0.002354497903779603 Iteration 7: loglikelihood = -3581.45, backtracks = 1, tol = 0.0012113311289568282 Iteration 8: loglikelihood = -3581.4429, backtracks = 1, tol = 0.0005977323368027984 Iteration 9: loglikelihood = -3581.4426, backtracks = 1, tol = 0.0003030942145707159 Iteration 10: loglikelihood = -3581.4404, backtracks = 1, tol = 0.0001490937941302549 Iteration 11: loglikelihood = -3581.4438, backtracks = 3, tol = 1.8790343211652357e-5 26.013751 seconds (14.96 M allocations: 666.986 MiB, 0.86% gc time, 98.05% 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 = -3526.6477, backtracks = 0, tol = 0.0835442367894988 Iteration 2: loglikelihood = -3397.986, backtracks = 0, tol = 0.04912451505908135 Iteration 3: loglikelihood = -3214.528, backtracks = 1, tol = 0.015141431050211398 Iteration 4: loglikelihood = -2998.8665, backtracks = 1, tol = 0.00785951393430454 Iteration 5: loglikelihood = -2772.9158, backtracks = 1, tol = 0.003484342571031252 Iteration 6: loglikelihood = -2666.8289, backtracks = 0, tol = 0.08780524916936311 Iteration 7: loglikelihood = -2537.6182, backtracks = 0, tol = 0.08805585800947788 Iteration 8: loglikelihood = -2422.6958, backtracks = 0, tol = 0.0771483965876457 Iteration 9: loglikelihood = -2333.2007, backtracks = 0, tol = 0.01442581584707962 Iteration 10: loglikelihood = -2276.8545, backtracks = 0, tol = 0.08441216487368244 Iteration 11: loglikelihood = -2229.851, backtracks = 0, tol = 0.11221802823007039 Iteration 12: loglikelihood = -2203.8174, backtracks = 0, tol = 0.11223516125010914 Iteration 13: loglikelihood = -2182.8494, backtracks = 0, tol = 0.10999263670324377 Iteration 14: loglikelihood = -2168.6545, backtracks = 0, tol = 0.10906169008975417 Iteration 15: loglikelihood = -2164.0378, backtracks = 0, tol = 0.11097333286897333 Iteration 16: loglikelihood = -2158.5586, backtracks = 0, tol = 0.11030973712664553 Iteration 17: loglikelihood = -2153.419, backtracks = 1, tol = 0.019958353741728104 Iteration 18: loglikelihood = -2152.412, backtracks = 1, tol = 0.009207629076269576 Iteration 19: loglikelihood = -2152.1797, backtracks = 1, tol = 0.004367293463804823 Iteration 20: loglikelihood = -2147.0977, backtracks = 1, tol = 0.061612884793186454 Iteration 21: loglikelihood = -2145.6055, backtracks = 1, tol = 0.02400248507980581 Iteration 22: loglikelihood = -2145.1707, backtracks = 1, tol = 0.011839499502848244 Iteration 23: loglikelihood = -2145.0356, backtracks = 1, tol = 0.0057768428159311125 Iteration 24: loglikelihood = -2144.991, backtracks = 1, tol = 0.0028411062941286 Iteration 25: loglikelihood = -2144.973, backtracks = 1, tol = 0.0014403508422949352 Iteration 26: loglikelihood = -2144.969, backtracks = 1, tol = 0.0007529763899769243 Iteration 27: loglikelihood = -2144.9663, backtracks = 1, tol = 0.00043234421144623995 Iteration 28: loglikelihood = -2144.9658, backtracks = 3, tol = 6.191752395780613e-5 0.215021 seconds (1.69 M allocations: 28.043 MiB) Test Summary: | Pass Total Time Negative binomial nuisance parameter Float32 matrix | 12 12 30.6s **** 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 **** Running sparse linear regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -2896.6116813943763, backtracks = 0, tol = 1.0257704354307222 Iteration 2: loglikelihood = -1753.4720992614753, backtracks = 0, tol = 0.28706825512903816 Iteration 3: loglikelihood = -1460.3823326395225, backtracks = 0, tol = 0.1059822007319242 Iteration 4: loglikelihood = -1438.5292259047123, backtracks = 0, tol = 0.028655431669451118 Iteration 5: loglikelihood = -1438.0856032112097, backtracks = 0, tol = 0.0034955373515602557 Iteration 6: loglikelihood = -1438.0744350329464, backtracks = 0, tol = 0.0005882060650840543 Iteration 7: loglikelihood = -1438.0741395461057, backtracks = 0, tol = 8.427264473927088e-5 5.273875 seconds (1.18 M allocations: 138.716 MiB, 3.20% gc time, 89.86% compilation time) Test Summary: | Pass Total Time initialze beta | 1 1 5.8s 10.508267 seconds (4.00 M allocations: 82.493 MiB, 7.72% gc time, 0.67% compilation time) 5.583789 seconds (3.98 M allocations: 91.679 MiB, 1.22% gc time) 10.769168 seconds (20.41 M allocations: 439.522 MiB, 0.89% gc time, 17.50% compilation time: 79% of which was recompilation) 8.172910 seconds (20.18 M allocations: 434.190 MiB, 1.16% gc time) 41.765274 seconds (3.76 M allocations: 4.239 GiB, 9.39% gc time, 30.48% compilation time) 51.457766 seconds (71.97 k allocations: 183.473 MiB, 0.22% gc time) Test Summary: | Pass Total Time memory_efficient keyword | 7 7 2m28.2s Test Summary: | Pass Total Time update_support! | 10 10 0.6s 14.361 ms (78 allocations: 4.56 KiB) 4.950 μs (0 allocations: 0 bytes) 158.388 μs (4 allocations: 288 bytes) 7.647 μs (0 allocations: 0 bytes) 54.049 μs (2 allocations: 64 bytes) 42.020 μs (0 allocations: 0 bytes) 25.110 μs (0 allocations: 0 bytes) 28.860 μs (0 allocations: 0 bytes) 94.649 μs (0 allocations: 0 bytes) 37.934 ms (78 allocations: 4.56 KiB) 26.419 μs (0 allocations: 0 bytes) 176.288 μs (4 allocations: 288 bytes) 32.539 μs (0 allocations: 0 bytes) 261.488 μs (2 allocations: 64 bytes) 87.019 μs (0 allocations: 0 bytes) 122.759 μs (0 allocations: 0 bytes) 124.809 μs (0 allocations: 0 bytes) 201.358 μs (0 allocations: 0 bytes) Test Summary: | Total Time benchmarks for multivariate function | 0 3m36.4s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse Multivariate Gaussian regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 12 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -2900.9186300194497, backtracks = 0, tol = 0.1480224208200413 Iteration 2: loglikelihood = -2869.406464695619, backtracks = 0, tol = 0.035126790460779864 Iteration 3: loglikelihood = -2868.084702693443, backtracks = 0, tol = 0.0055693496163324524 Iteration 4: loglikelihood = -2868.034423817725, backtracks = 0, tol = 0.001118951762895177 Iteration 5: loglikelihood = -2868.030857635375, backtracks = 0, tol = 0.00031182601179138955 Iteration 6: loglikelihood = -2868.0305288614227, backtracks = 0, tol = 0.00010393305949947338 Iteration 7: loglikelihood = -2868.0304966516946, backtracks = 0, tol = 3.100862049859014e-5 0.412181 seconds (49.20 k allocations: 5.484 MiB, 62.58% compilation time) Test Summary: | Pass Total Time multivariate fit_iht SnpLinAlg | 7 7 11.9s **** 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 Multivariate Gaussian regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 12 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -2878.028812628852, backtracks = 0, tol = 2.5661768673084553 Iteration 2: loglikelihood = -2868.563037890196, backtracks = 0, tol = 0.024335274263285057 Iteration 3: loglikelihood = -2868.0815051475474, backtracks = 0, tol = 0.004072558228741048 Iteration 4: loglikelihood = -2868.0352100240902, backtracks = 0, tol = 0.0013135682973484317 Iteration 5: loglikelihood = -2868.0309297231934, backtracks = 0, tol = 0.000386434110747091 Iteration 6: loglikelihood = -2868.0305335492912, backtracks = 0, tol = 0.00011924564415557833 Iteration 7: loglikelihood = -2868.0304968517494, backtracks = 0, tol = 3.603726989721193e-5 2.086342 seconds (312.10 k allocations: 169.913 MiB, 62.36% compilation time) Test Summary: | Pass Total Time initialze beta | 5 5 2.6s **** 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: 0:03:32 Cross validating... 13%|████▏ | ETA: 0:00:52 Cross validating... 16%|█████▏ | ETA: 0:00:40 Cross validating... 19%|██████▏ | ETA: 0:00:33 Cross validating... 22%|███████▏ | ETA: 0:00:28 Cross validating... 25%|████████▏ | ETA: 0:00:24 Cross validating... 29%|█████████▏ | ETA: 0:00:20 Cross validating... 32%|██████████▏ | ETA: 0:00:18 Cross validating... 35%|███████████▏ | ETA: 0:00:16 Cross validating... 38%|████████████▎ | ETA: 0:00:14 Cross validating... 41%|█████████████▎ | ETA: 0:00:12 Cross validating... 44%|██████████████▎ | ETA: 0:00:11 Cross validating... 48%|███████████████▎ | ETA: 0:00:10 Cross validating... 51%|████████████████▎ | ETA: 0:00:09 Cross validating... 54%|█████████████████▎ | ETA: 0:00:08 Cross validating... 57%|██████████████████▎ | ETA: 0:00:07 Cross validating... 60%|███████████████████▎ | ETA: 0:00:06 Cross validating... 63%|████████████████████▍ | ETA: 0:00:06 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:05 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:04 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:03 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:03 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:02 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:02 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:02 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:01 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:01 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:11 Crossvalidation Results: k MSE 0 1519.0323517533013 1 1262.6874481198263 2 995.6334242226069 3 729.7234537499183 4 622.8868264493897 5 481.784688651126 6 398.16971205419986 7 349.5957318228957 8 323.7560635842498 9 304.67734834261194 10 307.65268753589834 11 305.6342803162262 12 306.89835286314684 13 311.3015798691222 14 312.77815873302086 15 312.3573398803013 16 327.5020672185045 17 333.8732591513992 18 316.9226005550148 19 335.33818559323026 20 323.6866211808998 Best k = 9 11.379671 seconds (11.31 M allocations: 302.775 MiB, 1.98% gc time, 62.63% 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: 0:00:03 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... 37%|███████████▋ | ETA: 0:00:03 Cross validating... 40%|████████████▊ | ETA: 0:00:03 Cross validating... 43%|█████████████▊ | ETA: 0:00:02 Cross validating... 46%|██████████████▊ | ETA: 0:00:02 Cross validating... 49%|███████████████▊ | ETA: 0:00:02 Cross validating... 52%|████████████████▊ | ETA: 0:00:02 Cross validating... 56%|█████████████████▊ | ETA: 0:00:02 Cross validating... 59%|██████████████████▊ | ETA: 0:00:02 Cross validating... 62%|███████████████████▊ | ETA: 0:00:02 Cross validating... 65%|████████████████████▉ | ETA: 0:00:02 Cross validating... 68%|█████████████████████▉ | ETA: 0:00:01 Cross validating... 71%|██████████████████████▉ | 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: 0:00:00 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:00 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:04 Crossvalidation Results: k MSE 0 1519.0323517533013 1 1266.4704457218659 2 1000.3178483319753 3 735.7024436749045 4 628.5885478296652 5 489.14974605297556 6 405.6325777576293 7 357.98093159330676 8 332.71916696359494 9 311.8285518649813 10 319.2896801271909 11 317.9939164897406 12 323.56046734193285 13 333.91879786644466 14 337.5063090590488 15 339.2682823428648 16 340.84643844384095 17 349.3698700739492 18 348.3866914439622 19 360.53557500743227 20 354.50132614312884 Best k = 9 4.380296 seconds (10.74 M allocations: 227.054 MiB, 1.11% gc time, 1.04% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, normal model | 3 3 16.5s **** 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: 0:06:36 Cross validating... 8%|██▌ | ETA: 0:02:32 Cross validating... 13%|████▏ | ETA: 0:01:31 Cross validating... 17%|█████▋ | ETA: 0:01:03 Cross validating... 22%|███████▏ | ETA: 0:00:48 Cross validating... 25%|████████▏ | ETA: 0:00:40 Cross validating... 29%|█████████▏ | ETA: 0:00:35 Cross validating... 32%|██████████▏ | ETA: 0:00:30 Cross validating... 37%|███████████▋ | ETA: 0:00:24 Cross validating... 41%|█████████████▎ | ETA: 0:00:20 Cross validating... 44%|██████████████▎ | ETA: 0:00:18 Cross validating... 49%|███████████████▊ | ETA: 0:00:15 Cross validating... 54%|█████████████████▎ | ETA: 0:00:12 Cross validating... 57%|██████████████████▎ | ETA: 0:00:11 Cross validating... 60%|███████████████████▎ | ETA: 0:00:10 Cross validating... 63%|████████████████████▍ | ETA: 0:00:09 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:08 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:06 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:05 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:04 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:03 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:02 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: 0:00:16 Crossvalidation Results: k MSE 0 1539.4741861572265 1 1285.1393680419922 2 995.7854979858399 3 831.2358716430665 4 627.3484179077149 5 507.88334866333014 6 411.8995897827149 7 375.3060171813965 8 330.1631900634766 9 312.8652543640137 10 312.5296408386231 11 317.1180780944824 12 316.5554684753418 13 320.69296426391605 14 318.5227594299317 15 320.07097521972656 16 336.53783679199216 17 337.60957705688475 18 345.4723744812012 19 342.76020535278326 20 334.7367911682129 Best k = 10 17.380057 seconds (12.59 M allocations: 310.690 MiB, 0.54% gc time, 80.99% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 6%|██ | ETA: 0:00:02 Cross validating... 11%|███▌ | ETA: 0:00:02 Cross validating... 16%|█████▏ | ETA: 0:00:02 Cross validating... 19%|██████▏ | ETA: 0:00:02 Cross validating... 22%|███████▏ | ETA: 0:00:02 Cross validating... 25%|████████▏ | ETA: 0:00:02 Cross validating... 29%|█████████▏ | ETA: 0:00:02 Cross validating... 32%|██████████▏ | ETA: 0:00:02 Cross validating... 35%|███████████▏ | ETA: 0:00:02 Cross validating... 40%|████████████▊ | ETA: 0:00:02 Cross validating... 44%|██████████████▎ | ETA: 0:00:02 Cross validating... 48%|███████████████▎ | ETA: 0:00:02 Cross validating... 51%|████████████████▎ | ETA: 0:00:02 Cross validating... 54%|█████████████████▎ | ETA: 0:00:01 Cross validating... 57%|██████████████████▎ | ETA: 0:00:01 Cross validating... 60%|███████████████████▎ | ETA: 0:00:01 Cross validating... 63%|████████████████████▍ | ETA: 0:00:01 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:01 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:01 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:01 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:01 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:01 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:00 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: 0:00:03 Crossvalidation Results: k MSE 0 1539.4741861572265 1 1285.1393680419922 2 995.7854979858399 3 837.8690919189454 4 632.0293645629883 5 509.2634852905274 6 414.4696273193359 7 378.42675457763676 8 331.74160498046876 9 316.5581356201172 10 314.75104623413085 11 331.32761041259766 12 332.36773052978515 13 342.38070513916017 14 343.25372799682617 15 345.6920503540039 16 346.95757916259765 17 359.16635012817386 18 370.04587567138674 19 380.47828863525393 20 363.8261949768066 Best k = 10 3.362549 seconds (11.01 M allocations: 201.939 MiB, 1.47% gc time, 0.94% compilation time) Test Summary: | Pass Total Time Cross validation on Float32 matrix, normal model | 2 2 22.4s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:55 Cross validating... 6%|██ | ETA: 0:00:29 Cross validating... 8%|██▌ | ETA: 0:00:24 Cross validating... 11%|███▌ | ETA: 0:00:18 Cross validating... 14%|████▋ | ETA: 0:00:15 Cross validating... 17%|█████▋ | ETA: 0:00:13 Cross validating... 21%|██████▋ | ETA: 0:00:11 Cross validating... 24%|███████▋ | ETA: 0:00:10 Cross validating... 27%|████████▋ | ETA: 0:00:09 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: 0:00:07 Crossvalidation Results: k MSE 0 462.41100368051707 1 429.7573485306028 2 401.67470005737266 3 381.35821240396825 4 359.6241910381435 5 347.42208139347326 6 333.5355530977579 7 328.35686921343023 8 337.927699311543 9 335.26461711931734 10 335.12252346162074 11 330.1894710439479 12 342.7312085594199 13 336.05114112539565 14 354.8009631334809 15 334.9549922382446 16 347.85051505123783 17 388.12157301596284 18 351.2133833190124 19 343.0395770765647 20 387.07821816699425 Best k = 7 7.821176 seconds (18.04 M allocations: 432.762 MiB, 1.11% gc time, 30.84% 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: 0:00:04 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: 0:00:03 Cross validating... 32%|██████████▏ | ETA: 0:00:03 Cross validating... 35%|███████████▏ | ETA: 0:00:03 Cross validating... 38%|████████████▎ | ETA: 0:00:03 Cross validating... 41%|█████████████▎ | ETA: 0:00:03 Cross validating... 44%|██████████████▎ | ETA: 0:00:03 Cross validating... 48%|███████████████▎ | ETA: 0:00:02 Cross validating... 51%|████████████████▎ | ETA: 0:00:02 Cross validating... 54%|█████████████████▎ | ETA: 0:00:02 Cross validating... 57%|██████████████████▎ | ETA: 0:00:02 Cross validating... 60%|███████████████████▎ | ETA: 0:00:02 Cross validating... 63%|████████████████████▍ | ETA: 0:00:02 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:01 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:01 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:01 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:01 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:01 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:01 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:01 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:01 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:00 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:04 Crossvalidation Results: k MSE 0 462.41100368051707 1 430.1045937396766 2 402.35289750350216 3 387.36879174055395 4 362.71025135794383 5 351.2045131673366 6 337.6293388505112 7 333.43178425823027 8 342.7781832117981 9 347.28360646061464 10 351.5889095274799 11 351.63169873996304 12 364.04679517965315 13 367.7839878886745 14 370.89568661441604 15 375.845319201202 16 378.50240427014865 17 386.0945075832246 18 402.9903909103097 19 407.11843143164435 20 405.3750948816095 Best k = 7 4.657340 seconds (17.86 M allocations: 370.997 MiB, 1.40% gc time, 1.34% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, logistic model | 2 2 12.9s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:40 Cross validating... 8%|██▌ | ETA: 0:00:17 Cross validating... 11%|███▌ | ETA: 0:00:13 Cross validating... 14%|████▋ | ETA: 0:00:10 Cross validating... 17%|█████▋ | ETA: 0:00:09 Cross validating... 21%|██████▋ | ETA: 0:00:08 Cross validating... 24%|███████▋ | ETA: 0:00:07 Cross validating... 27%|████████▋ | ETA: 0:00:06 Cross validating... 30%|█████████▋ | ETA: 0:00:06 Cross validating... 33%|██████████▋ | ETA: 0:00:05 Cross validating... 38%|████████████▎ | ETA: 0:00:04 Cross validating... 43%|█████████████▊ | ETA: 0:00:04 Cross validating... 48%|███████████████▎ | ETA: 0:00:04 Cross validating... 51%|████████████████▎ | ETA: 0:00:04 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: 0:00:02 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:01 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:01 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:01 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:01 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:00 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 0 462.3765342961453 1 447.0629110924408 2 414.8152547813896 3 381.13901042854707 4 337.1357691146438 5 327.69487212743627 6 313.00449928643815 7 312.1083898499501 8 303.53756463746527 9 305.5296639287982 10 311.31001482230363 11 312.1721490015766 12 335.00688077414685 13 317.16542880855053 14 332.47945826187885 15 340.0793932058284 16 332.47638463174326 17 353.11294239663596 18 381.40456140685933 19 374.880582535768 20 333.11090041252555 Best k = 8 6.423359 seconds (16.54 M allocations: 388.357 MiB, 12.71% gc time, 33.68% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 5%|█▌ | ETA: 0:00:03 Cross validating... 8%|██▌ | ETA: 0:00:03 Cross validating... 11%|███▌ | ETA: 0:00:03 Cross validating... 14%|████▋ | ETA: 0:00:03 Cross validating... 17%|█████▋ | ETA: 0:00:03 Cross validating... 21%|██████▋ | ETA: 0:00:03 Cross validating... 24%|███████▋ | ETA: 0:00:03 Cross validating... 27%|████████▋ | ETA: 0:00:03 Cross validating... 30%|█████████▋ | ETA: 0:00:03 Cross validating... 33%|██████████▋ | ETA: 0:00:03 Cross validating... 38%|████████████▎ | ETA: 0:00:02 Cross validating... 41%|█████████████▎ | ETA: 0:00:02 Cross validating... 44%|██████████████▎ | ETA: 0:00:02 Cross validating... 48%|███████████████▎ | ETA: 0:00:02 Cross validating... 51%|████████████████▎ | ETA: 0:00:02 Cross validating... 54%|█████████████████▎ | ETA: 0:00:02 Cross validating... 57%|██████████████████▎ | ETA: 0:00:02 Cross validating... 60%|███████████████████▎ | ETA: 0:00:02 Cross validating... 63%|████████████████████▍ | ETA: 0:00:01 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:01 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:01 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:01 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:01 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:01 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:01 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:00 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: 0:00:03 Crossvalidation Results: k MSE 0 462.3765342961453 1 449.5655810853989 2 417.1812467946779 3 383.4204488655755 4 339.78086946135386 5 331.76398034026903 6 318.6088337120267 7 321.5203399238282 8 316.10257030306667 9 321.24787099097716 10 327.54390908557207 11 340.6386537166011 12 348.36670275125596 13 348.5067722383792 14 367.8675903194733 15 383.3983950770809 16 399.2647958344195 17 391.79514472952826 18 407.59890749986175 19 419.2147690100151 20 415.123979482495 Best k = 8 3.792574 seconds (17.65 M allocations: 364.937 MiB, 2.07% gc time, 0.82% compilation time) Test Summary: | Pass Total Time Cross validation on Float64 matrix, logistic model | 2 2 10.9s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:46 Cross validating... 6%|██ | ETA: 0:00:25 Cross validating... 10%|███ | ETA: 0:00:17 Cross validating... 13%|████▏ | ETA: 0:00:14 Cross validating... 16%|█████▏ | ETA: 0:00:11 Cross validating... 19%|██████▏ | ETA: 0:00:10 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... 35%|███████████▏ | ETA: 0:00:06 Cross validating... 38%|████████████▎ | ETA: 0:00:05 Cross validating... 41%|█████████████▎ | ETA: 0:00:05 Cross validating... 44%|██████████████▎ | ETA: 0:00:04 Cross validating... 48%|███████████████▎ | ETA: 0:00:04 Cross validating... 51%|████████████████▎ | ETA: 0:00:04 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: 0:00:03 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:02 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:02 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:02 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: 0:00:06 Crossvalidation Results: k MSE 0 465.0833336924902 1 460.4324796218508 2 442.5063354784987 3 436.39081959439017 4 406.29650758975873 5 401.8635211576203 6 392.6358810882377 7 396.8503761659754 8 400.78644293970325 9 399.94046307674586 10 397.11247821585425 11 397.3793560878073 12 397.1585310462475 13 411.3928542120291 14 396.98206693566743 15 401.8598821031189 16 416.8631561962546 17 406.46886649056364 18 405.4109784578138 19 406.09024405529 20 412.5428941054373 Best k = 6 6.779256 seconds (16.70 M allocations: 423.661 MiB, 1.08% gc time, 29.56% 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: 0:00:03 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... 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: 0:00:03 Cross validating... 35%|███████████▏ | ETA: 0:00:03 Cross validating... 38%|████████████▎ | ETA: 0:00:03 Cross validating... 41%|█████████████▎ | ETA: 0:00:03 Cross validating... 44%|██████████████▎ | ETA: 0:00:03 Cross validating... 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 0 465.0833336924902 1 463.38082320803596 2 447.9191915164921 3 433.9846690499666 4 426.02366553204183 5 411.1853026487262 6 404.1610179062623 7 408.5399633521572 8 421.15327507122197 9 420.4159418344044 10 415.6867807571976 11 411.7181103069378 12 424.40198359400904 13 425.01759851158687 14 426.319176340196 15 438.37599026193277 16 441.61704912348466 17 452.4826031412754 18 459.81117025618175 19 459.53141629659945 20 471.72597095891126 Best k = 6 4.757384 seconds (15.49 M allocations: 322.300 MiB, 1.65% gc time, 1.06% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, Poisson model | 2 2 11.8s **** 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: 0:01:13 Cross validating... 6%|██ | ETA: 0:00:38 Cross validating... 10%|███ | ETA: 0:00:26 Cross validating... 11%|███▌ | ETA: 0:00:28 Cross 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Time: 0:00:44 Crossvalidation Results: k MSE 0 275.89090229028943 1 265.8984981208556 2 256.5620563587315 3 247.40147078566022 4 243.64348966417793 5 241.48404799070687 6 243.55165049903633 7 239.82345890749355 8 239.30305246502178 9 245.38445416796117 10 249.24219021206528 11 247.87483732684188 12 247.86039796918504 13 238.51078516461476 14 247.88497361242588 15 247.50200461250142 16 241.20429876072092 17 245.01814730113924 18 245.12006407196782 19 242.55906074572317 20 253.82324364388347 Best k = 13 44.690453 seconds (150.40 M allocations: 3.899 GiB, 1.28% gc time, 4.14% 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: 0:00:03 Cross validating... 5%|█▌ | 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... 14%|████▋ | ETA: 0:00:05 Cross validating... 16%|█████▏ | ETA: 0:00:05 Cross validating... 17%|█████▋ | ETA: 0:00:05 Cross validating... 19%|██████▏ | ETA: 0:00:05 Cross validating... 21%|██████▋ | ETA: 0:00:05 Cross validating... 22%|███████▏ | ETA: 0:00:05 Cross validating... 24%|███████▋ | ETA: 0:00:05 Cross validating... 25%|████████▏ | ETA: 0:00:06 Cross validating... 27%|████████▋ | ETA: 0:00:06 Cross validating... 29%|█████████▏ | ETA: 0:00:06 Cross validating... 30%|█████████▋ | ETA: 0:00:06 Cross validating... 32%|██████████▏ | ETA: 0:00:07 Cross validating... 33%|██████████▋ | ETA: 0:00:07 Cross validating... 37%|███████████▋ | ETA: 0:00:06 Cross validating... 40%|████████████▊ | ETA: 0:00:05 Cross validating... 43%|█████████████▊ | ETA: 0:00:05 Cross validating... 44%|██████████████▎ | ETA: 0:00:05 Cross validating... 46%|██████████████▊ | ETA: 0:00:05 Cross validating... 49%|███████████████▊ | ETA: 0:00:04 Cross validating... 51%|████████████████▎ | ETA: 0:00:04 Cross validating... 52%|████████████████▊ | ETA: 0:00:04 Cross validating... 54%|█████████████████▎ | ETA: 0:00:04 Cross validating... 56%|█████████████████▊ | ETA: 0:00:04 Cross validating... 57%|██████████████████▎ | ETA: 0:00:04 Cross validating... 59%|██████████████████▊ | ETA: 0:00:04 Cross validating... 60%|███████████████████▎ | ETA: 0:00:03 Cross validating... 62%|███████████████████▊ | ETA: 0:00:03 Cross validating... 63%|████████████████████▍ | ETA: 0:00:03 Cross validating... 65%|████████████████████▉ | 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... 79%|█████████████████████████▍ | ETA: 0:00:02 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:02 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:01 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:01 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:01 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: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:09 Crossvalidation Results: k MSE 0 275.89090229028943 1 266.2805114872394 2 257.39682745175395 3 248.70278744397035 4 244.23777208161664 5 244.92556341408786 6 249.60782020036692 7 248.96782104765387 8 250.82386904727542 9 256.49878801074937 10 266.7073792738038 11 262.92224390889885 12 262.1583606987448 13 261.01317581517003 14 273.97101376932727 15 273.63450773592643 16 262.45404895125205 17 275.45156068221627 18 269.55943945924366 19 273.11507237968596 20 302.32357575954603 Best k = 4 9.374891 seconds (33.88 M allocations: 705.168 MiB, 1.49% gc time, 0.65% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, NegativeBinomial model | 2 2 54.4s **** 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 **** Cross validating... 3%|█ | ETA: 0:00:56 Cross validating... 6%|██ | ETA: 0:00:29 Cross validating... 11%|███▌ | ETA: 0:00:17 Cross validating... 14%|████▋ | ETA: 0:00:13 Cross validating... 19%|██████▏ 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100%|████████████████████████████████| Time: 0:00:04 Crossvalidation Results: k MSE 0 709.7238911132813 1 600.8470166015625 2 478.37098138427734 3 399.75837347412113 4 316.3170971069336 5 274.59901690673826 6 232.61785809326173 7 221.00282696533208 8 205.62119918823245 9 198.3431817626953 10 200.94596459960937 11 201.86666357421876 12 202.35683154296873 13 208.02664166259768 14 206.9071481628418 15 209.87240182495117 16 216.0480528869629 17 212.0296098022461 18 217.49209603881837 19 225.60646734619144 20 213.36869631958012 Best k = 9 4.975123 seconds (17.00 M allocations: 337.831 MiB, 1.79% gc time, 45.79% 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: 0:00:02 Cross validating... 10%|███ | ETA: 0:00:02 Cross validating... 14%|████▋ | ETA: 0:00:02 Cross validating... 19%|██████▏ | ETA: 0:00:02 Cross validating... 24%|███████▋ | ETA: 0:00:02 Cross validating... 27%|████████▋ | ETA: 0:00:02 Cross validating... 30%|█████████▋ | ETA: 0:00:02 Cross validating... 33%|██████████▋ | ETA: 0:00:02 Cross validating... 38%|████████████▎ | ETA: 0:00:02 Cross validating... 41%|█████████████▎ | ETA: 0:00:02 Cross validating... 46%|██████████████▊ | ETA: 0:00:02 Cross validating... 49%|███████████████▊ | ETA: 0:00:01 Cross validating... 52%|████████████████▊ | ETA: 0:00:01 Cross validating... 56%|█████████████████▊ | ETA: 0:00:01 Cross validating... 59%|██████████████████▊ | ETA: 0:00:01 Cross validating... 62%|███████████████████▊ | ETA: 0:00:01 Cross validating... 65%|████████████████████▉ | ETA: 0:00:01 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:01 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:01 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:01 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:01 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:00 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:00 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:03 Crossvalidation Results: k MSE 0 709.7238911132813 1 580.5206424560547 2 462.45179821777344 3 375.725685546875 4 311.8335130615235 5 265.69685809326177 6 235.52074707031255 7 221.8731430358887 8 209.48005477905275 9 202.0256286010742 10 206.40357376098632 11 209.8904744873047 12 212.83695938110353 13 217.36745034790042 14 219.17275009155276 15 218.94907879638671 16 225.10276358032226 17 228.24513723754882 18 225.50167910766604 19 235.0626920776367 20 227.98946899414062 Best k = 9 3.123475 seconds (16.17 M allocations: 286.701 MiB, 1.92% gc time, 1.44% compilation time) Test Summary: | Pass Total Time Cross validation on floating point matrices, NegativeBinomial model | 2 2 8.5s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 2%|▋ | ETA: 0:01:37 Cross validating... 3%|█ | ETA: 0:01:07 Cross validating... 4%|█▎ | ETA: 0:00:53 Cross validating... 5%|█▋ | ETA: 0:00:45 Cross validating... 6%|█▉ | ETA: 0:00:39 Cross validating... 7%|██▎ | ETA: 0:00:34 Cross validating... 8%|██▌ | ETA: 0:00:32 Cross validating... 9%|██▉ | ETA: 0:00:29 Cross validating... 10%|███▎ | ETA: 0:00:28 Cross validating... 11%|███▌ | ETA: 0:00:26 Cross validating... 12%|███▉ | ETA: 0:00:25 Cross validating... 13%|████▏ | ETA: 0:00:25 Cross validating... 14%|████▌ | ETA: 0:00:24 Cross validating... 15%|████▊ | ETA: 0:00:23 Cross validating... 16%|█████▏ | ETA: 0:00:23 Cross validating... 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2407.583369907133 2 2147.645944940088 3 1798.6956642938917 4 1503.3227410949069 5 1392.804286057142 6 1247.517383478293 7 1188.5029619111704 8 1142.846551038621 9 1125.2707797958697 10 1133.1745192856508 11 1138.0730543543373 12 1149.8565316622742 13 1152.8782668717895 14 1150.5361921695644 15 1157.1864177638868 16 1155.4054203067435 17 1169.614920392264 18 1174.8169716627249 19 1167.9275725449866 20 1184.4508152775898 Best k = 9 18.769357 seconds (333.16 k allocations: 218.791 MiB, 0.66% gc time, 10.16% compilation time) Test Summary: | Pass Total Time multivariate cross validation SnpLinAlg | 3 3 24.2s Test Summary: | Pass Total Time wrapper univariate | 20 20 1m47.5s **** 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: 0:00:10 Cross validating... 3%|█ | ETA: 0:00:10 Cross validating... 4%|█▎ | ETA: 0:00:11 Cross validating... 5%|█▋ | ETA: 0:00:11 Cross validating... 6%|█▉ | ETA: 0:00:12 Cross validating... 7%|██▎ | ETA: 0:00:13 Cross validating... 8%|██▌ | ETA: 0:00:13 Cross validating... 9%|██▉ | ETA: 0:00:14 Cross validating... 10%|███▎ | ETA: 0:00:14 Cross validating... 11%|███▌ | ETA: 0:00:15 Cross validating... 12%|███▉ | ETA: 0:00:16 Cross validating... 13%|████▏ | ETA: 0:00:18 Cross validating... 14%|████▌ | ETA: 0:00:18 Cross validating... 15%|████▊ | ETA: 0:00:18 Cross validating... 16%|█████▏ | ETA: 0:00:20 Cross validating... 17%|█████▌ | ETA: 0:00:20 Cross validating... 18%|█████▊ | ETA: 0:00:20 Cross validating... 19%|██████▏ | ETA: 0:00:20 Cross validating... 20%|██████▍ | ETA: 0:00:20 Cross validating... 21%|██████▊ | ETA: 0:00:19 Cross validating... 22%|███████ | ETA: 0:00:18 Cross validating... 23%|███████▍ | ETA: 0:00:18 Cross validating... 24%|███████▋ | ETA: 0:00:17 Cross validating... 25%|████████ | ETA: 0:00:17 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0:00:02 Cross validating... 93%|█████████████████████████████▊ | ETA: 0:00:02 Cross validating... 94%|██████████████████████████████▏ | ETA: 0:00:02 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: 0:00:01 Cross validating... 99%|███████████████████████████████▋| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:25 Crossvalidation Results: k MSE 1 2838.788679198002 2 2514.3973428708136 3 2305.6176519676274 4 2222.025304867614 5 2075.1670384588365 6 2067.7948989723845 7 2053.427506114907 8 2086.405384830965 9 2080.984460901671 10 2105.131199502364 11 2132.407165368786 12 2138.267187460652 13 2166.002210829576 14 2194.9918295115804 15 2189.890403738045 16 2191.181293229578 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: 0:00:10 Cross validating... 3%|█ | ETA: 0:00:10 Cross validating... 4%|█▎ | ETA: 0:00:11 Cross validating... 5%|█▋ | ETA: 0:00:11 Cross validating... 6%|█▉ | ETA: 0:00:12 Cross validating... 7%|██▎ | ETA: 0:00:13 Cross validating... 8%|██▌ | ETA: 0:00:13 Cross validating... 9%|██▉ | ETA: 0:00:14 Cross validating... 10%|███▎ | ETA: 0:00:14 Cross validating... 11%|███▌ | ETA: 0:00:16 Cross validating... 12%|███▉ | ETA: 0:00:16 Cross validating... 13%|████▏ | ETA: 0:00:17 Cross validating... 14%|████▌ | ETA: 0:00:17 Cross validating... 15%|████▊ | ETA: 0:00:17 Cross validating... 16%|█████▏ | ETA: 0:00:19 Cross validating... 17%|█████▌ | ETA: 0:00:19 Cross 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2305.6176519676274 4 2222.025304867614 5 2075.1670384588365 6 2067.7948989723845 7 2053.427506114907 8 2086.405384830965 9 2080.984460901671 10 2105.131199502364 11 2132.407165368786 12 2138.267187460652 13 2166.002210829576 14 2194.9918295115804 15 2189.890403738045 16 2191.181293229578 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: 0:00:11 Cross validating... 3%|█ | ETA: 0:00:10 Cross validating... 4%|█▎ | ETA: 0:00:11 Cross validating... 5%|█▋ | ETA: 0:00:11 Cross validating... 6%|█▉ | ETA: 0:00:12 Cross validating... 7%|██▎ | ETA: 0:00:13 Cross validating... 8%|██▌ | ETA: 0:00:13 Cross validating... 9%|██▉ | ETA: 0:00:14 Cross validating... 10%|███▎ 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| 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: 0:00:24 Crossvalidation Results: k MSE 1 2838.788679198002 2 2514.3973428708136 3 2305.6176519676274 4 2222.025304867614 5 2075.1670384588365 6 2067.7948989723845 7 2053.427506114907 8 2086.405384830965 9 2080.984460901671 10 2105.131199502364 11 2132.407165368786 12 2138.267187460652 13 2166.002210829576 14 2194.9918295115804 15 2189.890403738045 16 2191.181293229578 17 2209.4669750564362 18 2221.2595493644303 19 2238.7425945763257 20 2253.9559571797727 Best k = 7 Test Summary: | Pass Total Time wrapper multivariate | 8 8 1m29.9s read BGEN and VCF: Error During Test at /home/pkgeval/.julia/packages/MendelIHT/ZcxZT/test/wrapper_test.jl:184 Got exception outside of a @test startproc must be called before process Stacktrace: [1] error(s::String) @ Base ./error.jl:56 [2] process(codec::CodecZlib.ZlibDecompressor, input::TranscodingStreams.Memory, output::TranscodingStreams.Memory, error_ref::TranscodingStreams.Error) @ CodecZlib ~/.julia/packages/CodecZlib/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:739 [inlined] [9] macro expansion @ ~/.julia/packages/MendelIHT/ZcxZT/test/wrapper_test.jl:187 [inlined] [10] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:2243 [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:324 [13] top-level scope @ ~/.julia/packages/MendelIHT/ZcxZT/test/runtests.jl:20 [14] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:324 [15] top-level scope @ none:6 [16] eval(m::Module, e::Any) @ Core ./boot.jl:517 [17] exec_options(opts::Base.JLOptions) @ Base ./client.jl:310 [18] _start() @ Base ./client.jl:585 Test Summary: | Error Total Time read BGEN and VCF | 1 1 3.1s RNG of the outermost testset: Xoshiro(0x4e3381a217ff58cc, 0xcffe76f305fd668c, 0x3fde3d4066af922e, 0x6b570968e271d890, 0xece75a9b5c825346) 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 1173.47s ERROR: LoadError: Package MendelIHT errored during testing Stacktrace: [1] pkgerror(msg::String) @ Pkg.Types /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Types.jl:68 [2] test(ctx::Pkg.Types.Context, pkgs::Vector{PackageSpec}; coverage::Bool, julia_args::Cmd, test_args::Cmd, test_fn::Nothing, force_latest_compatible_version::Bool, allow_earlier_backwards_compatible_versions::Bool, allow_reresolve::Bool) @ Pkg.Operations /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Operations.jl:3138 [3] test @ /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Operations.jl:3003 [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/v1.14/Pkg/src/API.jl:586 [5] kwcall(::@NamedTuple{julia_args::Cmd, io::IOContext{IO}}, ::typeof(Pkg.API.test), ctx::Pkg.Types.Context, pkgs::Vector{PackageSpec}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:562 [6] test(pkgs::Vector{PackageSpec}; io::IOContext{IO}, kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:172 [7] kwcall(::@NamedTuple{julia_args::Cmd}, ::typeof(Pkg.API.test), pkgs::Vector{PackageSpec}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:161 [8] test(pkgs::Vector{String}; kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:160 [9] test @ /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:160 [inlined] [10] kwcall(::@NamedTuple{julia_args::Cmd}, ::typeof(Pkg.API.test), pkg::String) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:159 [11] top-level scope @ /PkgEval.jl/scripts/evaluate.jl:223 [12] include(mod::Module, _path::String) @ Base ./Base.jl:323 [13] exec_options(opts::Base.JLOptions) @ Base ./client.jl:344 [14] _start() @ Base ./client.jl:585 in expression starting at /PkgEval.jl/scripts/evaluate.jl:214 PkgEval failed after 1893.35s: package tests unexpectedly errored