Package evaluation to test MendelIHT on Julia 1.14.0-DEV.1893 (b4aba01002*) started at 2026-03-15T23:33:20.464 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.14` Set-up completed after 13.47s ################################################################################ # Installation # Installing MendelIHT... Resolving package versions... 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+1 [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 v17.8.0+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 5.91s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompiling packages... 2346.3 ms ✓ CodecBzip2 2055.5 ms ✓ CodecXz 4858.6 ms ✓ BGEN 7123.6 ms ✓ VCFTools 28259.2 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`. 25800.6 ms ✓ MendelIHT 6 dependencies successfully precompiled in 75 seconds. 168 already precompiled. 26 dependencies precompiled but different versions are currently loaded (ArgTools, Base64, Dates, Downloads, JuliaSyntaxHighlighting, LibCURL, LibCURL_jll, LibGit2, LibGit2_jll, LibSSH2_jll, Logging, Markdown, MozillaCACerts_jll, NetworkOptions, OpenSSL_jll, PCRE2_jll, Pkg, Printf, StyledStrings, TOML, Tar, UUIDs, Zlib_jll, Zstd_jll, nghttp2_jll and p7zip_jll). Restart julia to access the new versions. Otherwise, 85 dependents of these packages may trigger further precompilation to work with the unexpected versions. 1 dependency had output during precompilation: ┌ MendelIHT │ WARNING: Constructor for type "MvNormal" was extended in `MendelIHT` without explicit qualification or import. │ NOTE: Assumed "MvNormal" refers to `Distributions.MvNormal`. This behavior is deprecated and may differ in future versions. │ NOTE: This behavior may have differed in Julia versions prior to 1.12. │ Hint: If you intended to create a new generic function of the same name, use `function MvNormal end`. │ Hint: To silence the warning, qualify `MvNormal` as `Distributions.MvNormal` in the method signature or explicitly `import Distributions: MvNormal`. └ Precompilation completed after 97.69s ################################################################################ # Testing # Testing MendelIHT Status `/tmp/jl_UqeO0B/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_UqeO0B/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 [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 [682c06a0] JSON v1.4.0 [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 [ec057cc2] StructUtils v2.6.3 [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 [9abbd945] Profile 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+1 [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 v17.8.0+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 15.8s Test Summary: | Pass Total Time deviance | 1 1 0.5s Test Summary: | Pass Total Time update_μ! | 4 4 1.4s Test Summary: | Pass Total Time _choose! | 7 7 9.8s Test Summary: | Pass Total Time _iht_backtrack | 7 7 0.0s Test Summary: | Pass Total Time standardize! | 12 12 1.5s Test Summary: | Pass Total Time project_k! | 2 2 1.0s Test Summary: | Pass Total Time project_group_sparse! | 5 5 1.2s Test Summary: | Pass Total Time maf_weights | 6 6 2.1s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse linear regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 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 = -1642.2873618528702, backtracks = 0, tol = 1.5009173688880304 Iteration 2: loglikelihood = -1469.850921261597, backtracks = 0, tol = 0.1651769681554293 Iteration 3: loglikelihood = -1438.680977203135, backtracks = 0, tol = 0.05687964943228356 Iteration 4: loglikelihood = -1438.246071741775, backtracks = 0, tol = 0.04809772658780401 Iteration 5: loglikelihood = -1437.845091310305, backtracks = 0, tol = 0.005372991687349329 Iteration 6: loglikelihood = -1437.8441911442453, backtracks = 1, tol = 0.00019092859667304267 Iteration 7: loglikelihood = -1437.843961041486, backtracks = 1, tol = 9.319917908778441e-5 IHT estimated 10 nonzero SNP predictors and 1 non-genetic predictors. Compute time (sec): 0.06980705261230469 Final loglikelihood: -1437.843961041486 SNP PVE: 0.8953131603377504 Iterations: 7 Selected genetic predictors: 10×2 DataFrame Row │ Position Estimated_β │ Int64 Float64 ─────┼─────────────────────── 1 │ 122 0.585033 2 │ 712 1.05298 3 │ 853 0.142468 4 │ 1181 1.74595 5 │ 1464 -1.33803 6 │ 3653 -0.154113 7 │ 5350 0.324076 8 │ 6828 1.26662 9 │ 8392 -0.122274 10 │ 9207 -0.907529 Selected nongenetic predictors: 1×2 DataFrame Row │ Position Estimated_β │ Int64 Float64 ─────┼─────────────────────── 1 │ 1 -0.0335028Test Summary: | Pass Total Time fit normal SnpLinAlg | 4 4 23.9s **** 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 3.9s **** 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 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 = -2084.8073636539784, backtracks = 0, tol = 0.37710991598392596 Iteration 2: loglikelihood = -1523.8408109772415, backtracks = 0, tol = 0.0600949421016996 Iteration 3: loglikelihood = -1345.6072179435328, backtracks = 0, tol = 0.05347204283462253 Iteration 4: loglikelihood = -1312.810811782877, backtracks = 0, tol = 0.05490058431392483 Iteration 5: loglikelihood = -1284.0232955002677, backtracks = 0, tol = 0.08678787676405614 Iteration 6: loglikelihood = -1272.1516702150952, backtracks = 0, tol = 0.030356260158968786 Iteration 7: loglikelihood = -1267.517958076909, backtracks = 1, tol = 0.06200808784947693 Iteration 8: loglikelihood = -1263.2098801583816, backtracks = 0, tol = 0.023356217979530178 Iteration 9: loglikelihood = -1261.5300209294035, backtracks = 0, tol = 0.014379626454532031 Iteration 10: loglikelihood = -1260.706273978488, backtracks = 0, tol = 0.04410142487206504 Iteration 11: loglikelihood = -1259.1426733359763, backtracks = 0, tol = 0.0130369818891131 Iteration 12: loglikelihood = -1258.6526211912053, backtracks = 1, tol = 0.005531458749650361 Iteration 13: loglikelihood = -1258.3586487161972, backtracks = 1, tol = 0.005972440572837377 Iteration 14: loglikelihood = -1256.9480172115677, backtracks = 0, tol = 0.0642944659831692 Iteration 15: loglikelihood = -1256.09377559032, backtracks = 0, tol = 0.00903049554012696 Iteration 16: loglikelihood = -1255.9445137526968, backtracks = 0, tol = 0.005082136348842657 Iteration 17: loglikelihood = -1255.8977846729902, backtracks = 0, tol = 0.002315822527241583 Iteration 18: loglikelihood = -1255.8718762664864, backtracks = 0, tol = 0.0021548038946666115 Iteration 19: loglikelihood = -1255.8558187396159, backtracks = 0, tol = 0.0012331620585030979 Iteration 20: loglikelihood = -1255.8454345814082, backtracks = 0, tol = 0.0013446436955868659 Iteration 21: loglikelihood = -1255.8387219116032, backtracks = 0, tol = 0.0008334899131780727 Iteration 22: loglikelihood = -1255.8343250418138, backtracks = 0, tol = 0.0008569580444436285 Iteration 23: loglikelihood = -1255.831456951821, backtracks = 0, tol = 0.0005574277333085701 Iteration 24: loglikelihood = -1255.8295756446282, backtracks = 0, tol = 0.0005511141513941419 Iteration 25: loglikelihood = -1255.8283460414466, backtracks = 0, tol = 0.00036887694003152714 Iteration 26: loglikelihood = -1255.82754003753, backtracks = 0, tol = 0.00035653592196991995 Iteration 27: loglikelihood = -1255.8270130721132, backtracks = 0, tol = 0.00024283611085148106 Iteration 28: loglikelihood = -1255.8266679457777, backtracks = 0, tol = 0.00023148787500928766 Iteration 29: loglikelihood = -1255.826442312133, backtracks = 0, tol = 0.00015939753708301677 Iteration 30: loglikelihood = -1255.8262946397126, backtracks = 0, tol = 0.00015063352850954972 Iteration 31: loglikelihood = -1255.8261981058965, backtracks = 0, tol = 0.00010445365228043371 Iteration 32: loglikelihood = -1255.8261349578565, backtracks = 0, tol = 9.815898721080002e-5 Test Summary: | Pass Total Time fit Poisson SnpLinAlg | 4 4 3.3s **** 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 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 = -1477.4673644356576, backtracks = 0, tol = 0.38365440875333434 Iteration 2: loglikelihood = -1426.9067940394891, backtracks = 0, tol = 0.15991446770840123 Iteration 3: loglikelihood = -1414.2406598172895, backtracks = 0, tol = 0.08446809014228235 Iteration 4: loglikelihood = -1413.1376230293454, backtracks = 0, tol = 0.07629701052777266 Iteration 5: loglikelihood = -1412.5152110077872, backtracks = 0, tol = 0.019362777838345772 Iteration 6: loglikelihood = -1412.4500843854114, backtracks = 1, tol = 0.005654051966709954 Iteration 7: loglikelihood = -1411.7537117671689, backtracks = 1, tol = 0.06870325972538108 Iteration 8: loglikelihood = -1411.6753284600147, backtracks = 0, tol = 0.07092667923862418 Iteration 9: loglikelihood = -1411.5372292999725, backtracks = 0, tol = 0.007794820981279877 Iteration 10: loglikelihood = -1411.5341111988591, backtracks = 1, tol = 0.0006197706629270814 Iteration 11: loglikelihood = -1411.5331999439968, backtracks = 1, tol = 0.0004003409692663539 Iteration 12: loglikelihood = -1411.5329531896757, backtracks = 1, tol = 0.00022193152847710046 Iteration 13: loglikelihood = -1411.5328896066585, backtracks = 1, tol = 0.000120325411634749 Iteration 14: loglikelihood = -1411.5328732542876, backtracks = 1, tol = 6.978854087580771e-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 = -1861.1766154791044, backtracks = 0, tol = 0.7683402749477479 Iteration 2: loglikelihood = -1513.2652415192092, backtracks = 0, tol = 0.12344569778063769 Iteration 3: loglikelihood = -1438.1665398786956, backtracks = 0, tol = 0.05769340339189632 Iteration 4: loglikelihood = -1433.3234653715706, backtracks = 0, tol = 0.03181896274150099 Iteration 5: loglikelihood = -1430.4798696871314, backtracks = 0, tol = 0.027057430629452615 Iteration 6: loglikelihood = -1429.9415975442778, backtracks = 0, tol = 0.024966580560736227 Iteration 7: loglikelihood = -1429.8063306677159, backtracks = 0, tol = 0.0025226943321929344 Iteration 8: loglikelihood = -1429.8055860163956, backtracks = 0, tol = 0.00015958371366102408 Iteration 9: loglikelihood = -1429.805573181898, backtracks = 0, tol = 2.8453027887456914e-5 Test Summary: | Pass Total Time fit with >1 non-genetic covariates SnpLinAlg | 5 5 1.7s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse 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 = -1594.3824156745397, backtracks = 0, tol = 0.4057705720105265 Iteration 2: loglikelihood = -1456.1071576386812, backtracks = 0, tol = 0.08662916814301669 Iteration 3: loglikelihood = -1434.5242585547217, backtracks = 0, tol = 0.035200752348133656 Iteration 4: loglikelihood = -1431.0819942837265, backtracks = 0, tol = 0.031189362582253716 Iteration 5: loglikelihood = -1429.9749374144483, backtracks = 0, tol = 0.02782351333827074 Iteration 6: loglikelihood = -1429.8761681237193, backtracks = 0, tol = 0.0018848744354837852 Iteration 7: loglikelihood = -1429.8758424781618, backtracks = 0, tol = 9.16791253150964e-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 10.6s **** 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 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 = -1502.4523809172883, backtracks = 0, tol = 0.22886213502485298 Iteration 2: loglikelihood = -1443.5260716366856, backtracks = 0, tol = 0.10014668621050128 Iteration 3: loglikelihood = -1422.6349264157893, backtracks = 0, tol = 0.13817021853505831 Iteration 4: loglikelihood = -1385.2408955861133, backtracks = 0, tol = 0.10328476146492428 Iteration 5: loglikelihood = -1366.9146554830672, backtracks = 0, tol = 0.06086542405767059 Iteration 6: loglikelihood = -1360.226910844108, backtracks = 0, tol = 0.0686527961908119 Iteration 7: loglikelihood = -1356.546553588798, backtracks = 0, tol = 0.03085976926753042 Iteration 8: loglikelihood = -1355.617751959814, backtracks = 0, tol = 0.01849023049694834 Iteration 9: loglikelihood = -1355.2830866999757, backtracks = 0, tol = 0.008627871481997684 Iteration 10: loglikelihood = -1355.1549163961638, backtracks = 0, tol = 0.007019833071799472 Iteration 11: loglikelihood = -1354.6069223377872, backtracks = 0, tol = 0.07599618886604417 Iteration 12: loglikelihood = -1354.2924725331516, backtracks = 0, tol = 0.007378183375099326 Iteration 13: loglikelihood = -1354.2824389537038, backtracks = 1, tol = 0.00093281216683989 Iteration 14: loglikelihood = -1354.2781146485263, backtracks = 1, tol = 0.0008317061290553008 Iteration 15: loglikelihood = -1354.276624077903, backtracks = 1, tol = 0.0005457284816365479 Iteration 16: loglikelihood = -1354.2762424936534, backtracks = 1, tol = 0.0003498340201565669 Iteration 17: loglikelihood = -1354.2761110205647, backtracks = 1, tol = 0.00011630651085498377 Iteration 18: loglikelihood = -1354.2760510956837, backtracks = 1, tol = 0.0001366707705635293 Iteration 19: loglikelihood = -1354.2760259034014, backtracks = 1, tol = 5.139729973457398e-5 1.114181 seconds (3.29 M allocations: 61.331 MiB, 6.14% gc time, 54.36% 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 = -1530.7148808739732, backtracks = 0, tol = 0.22886213502485298 Iteration 2: loglikelihood = -1490.6742091338526, backtracks = 0, tol = 0.11897555343148426 Iteration 3: loglikelihood = -1460.9831648403713, backtracks = 0, tol = 0.11687065099175604 Iteration 4: loglikelihood = -1438.4593465282273, backtracks = 0, tol = 0.10528407964973452 Iteration 5: loglikelihood = -1429.9806651168672, backtracks = 0, tol = 0.11707617037355782 Iteration 6: loglikelihood = -1411.6706719460547, backtracks = 0, tol = 0.09064660194817387 Iteration 7: loglikelihood = -1403.1420644375976, backtracks = 0, tol = 0.08295682722205189 Iteration 8: loglikelihood = -1397.0631508954777, backtracks = 0, tol = 0.013016898093751988 Iteration 9: loglikelihood = -1392.3985989456783, backtracks = 0, tol = 0.002830474275573753 Iteration 10: loglikelihood = -1388.380701372604, backtracks = 0, tol = 0.0020357047570286587 Iteration 11: loglikelihood = -1385.009279480327, backtracks = 0, tol = 0.0008380158137915615 Iteration 12: loglikelihood = -1382.1166369752273, backtracks = 0, tol = 0.00031014315996609406 Iteration 13: loglikelihood = -1379.6294396667613, backtracks = 0, tol = 0.00042943655810525293 Iteration 14: loglikelihood = -1377.46904146673, backtracks = 0, tol = 0.00035227276150747334 Iteration 15: loglikelihood = -1375.5825239985973, backtracks = 0, tol = 0.00035796920619096613 Iteration 16: loglikelihood = -1373.9224753416004, backtracks = 0, tol = 0.00031682970890293275 Iteration 17: loglikelihood = -1372.4540671020693, backtracks = 0, tol = 0.0003015131764042932 Iteration 18: loglikelihood = -1371.1471762558028, backtracks = 0, tol = 0.00027330439878937857 Iteration 19: loglikelihood = -1369.9786570417675, backtracks = 0, tol = 0.00025837217708403026 Iteration 20: loglikelihood = -1368.9286794813886, backtracks = 0, tol = 0.00023854255569388745 Iteration 21: loglikelihood = -1367.9814461877409, backtracks = 0, tol = 0.00022538100914395973 Iteration 22: loglikelihood = -1367.1234248816406, backtracks = 0, tol = 0.00021045759871941074 Iteration 23: loglikelihood = -1366.343524914306, backtracks = 0, tol = 0.00019910092238039422 Iteration 24: loglikelihood = -1365.632214080125, backtracks = 0, tol = 0.0001873509306342658 Iteration 25: loglikelihood = -1364.9815087474983, backtracks = 0, tol = 0.00017764485170189341 Iteration 26: loglikelihood = -1364.3845116628208, backtracks = 0, tol = 0.00016809668372685225 Iteration 27: loglikelihood = -1363.8353486065291, backtracks = 0, tol = 0.00015980914553641608 Iteration 28: loglikelihood = -1363.3289137162267, backtracks = 0, tol = 0.00015186943267480517 Iteration 29: loglikelihood = -1362.8608007782032, backtracks = 0, tol = 0.00014476722347090518 Iteration 30: loglikelihood = -1362.4271552295234, backtracks = 0, tol = 0.00013805041778899808 Iteration 31: loglikelihood = -1362.0246151139322, backtracks = 0, tol = 0.00013192864378372662 Iteration 32: loglikelihood = -1361.65022053418, backtracks = 0, tol = 0.00012617045835077025 Iteration 33: loglikelihood = -1361.3013670129603, backtracks = 0, tol = 0.00012085882120028476 Iteration 34: loglikelihood = -1360.9757474307823, backtracks = 0, tol = 0.00011586975470991967 Iteration 35: loglikelihood = -1360.6713164778994, backtracks = 0, tol = 0.00011122999840834358 Iteration 36: loglikelihood = -1360.3862518721135, backtracks = 0, tol = 0.00010686916674389335 Iteration 37: loglikelihood = -1360.1189276451191, backtracks = 0, tol = 0.00010278996138906621 Iteration 38: loglikelihood = -1359.8678873346757, backtracks = 0, tol = 9.894961125290255e-5 0.406547 seconds (1.38 M allocations: 25.052 MiB) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse NegativeBinomial regression Number of threads = 1 Link functin = LogLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -4004.481, backtracks = 0, tol = 0.0689512396020298 Iteration 2: loglikelihood = -3980.1167, backtracks = 0, tol = 0.03415876794550282 Iteration 3: loglikelihood = -3977.933, backtracks = 1, tol = 0.006309571285218824 Iteration 4: loglikelihood = -3977.294, backtracks = 1, tol = 0.004667637663902353 Iteration 5: loglikelihood = -3977.1267, backtracks = 1, tol = 0.0023658180158383168 Iteration 6: loglikelihood = -3977.0857, backtracks = 1, tol = 0.0012056723766529468 Iteration 7: loglikelihood = -3977.077, backtracks = 1, tol = 0.0006050508204602863 Iteration 8: loglikelihood = -3977.077, backtracks = 1, tol = 0.0003031523036756029 Iteration 9: loglikelihood = -3977.0747, backtracks = 1, tol = 0.000151439344808641 Iteration 10: loglikelihood = -3977.0776, backtracks = 3, tol = 1.89066710830979e-5 24.129442 seconds (14.46 M allocations: 659.655 MiB, 1.26% gc time, 97.66% 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 = -3888.5059, backtracks = 0, tol = 0.0689512396020298 Iteration 2: loglikelihood = -3776.5557, backtracks = 0, tol = 0.03485159349877252 Iteration 3: loglikelihood = -3516.54, backtracks = 1, tol = 0.0062321333444681154 Iteration 4: loglikelihood = -3216.8877, backtracks = 1, tol = 0.003903802308419022 Iteration 5: loglikelihood = -3064.7422, backtracks = 0, tol = 0.07541859552319197 Iteration 6: loglikelihood = -2921.891, backtracks = 0, tol = 0.08201028492214923 Iteration 7: loglikelihood = -2798.7886, backtracks = 0, tol = 0.08527398893709173 Iteration 8: loglikelihood = -2651.6301, backtracks = 0, tol = 0.08789303762561756 Iteration 9: loglikelihood = -2564.2314, backtracks = 0, tol = 0.09346732486676372 Iteration 10: loglikelihood = -2497.9585, backtracks = 0, tol = 0.10286377668677983 Iteration 11: loglikelihood = -2438.9675, backtracks = 0, tol = 0.12018361267910789 Iteration 12: loglikelihood = -2310.944, backtracks = 1, tol = 0.09701308154136855 Iteration 13: loglikelihood = -2290.166, backtracks = 1, tol = 0.018062304687190434 Iteration 14: loglikelihood = -2285.8696, backtracks = 1, tol = 0.008087454190211592 Iteration 15: loglikelihood = -2285.115, backtracks = 1, tol = 0.0039043902576492598 Iteration 16: loglikelihood = -2281.6345, backtracks = 1, tol = 0.044656852589095665 Iteration 17: loglikelihood = -2280.2053, backtracks = 1, tol = 0.022011834545199477 Iteration 18: loglikelihood = -2279.8945, backtracks = 1, tol = 0.009399498501825799 Iteration 19: loglikelihood = -2279.8167, backtracks = 1, tol = 0.004074092201803703 Iteration 20: loglikelihood = -2279.8052, backtracks = 1, tol = 0.001831561075961538 Iteration 21: loglikelihood = -2279.803, backtracks = 1, tol = 0.0008555814150118669 Iteration 22: loglikelihood = -2279.8022, backtracks = 1, tol = 0.0004130962702709664 Iteration 23: loglikelihood = -2279.8005, backtracks = 1, tol = 0.00020396090737205655 Iteration 24: loglikelihood = -2279.7812, backtracks = 2, tol = 5.107003689768135e-5 0.192369 seconds (1.57 M allocations: 26.096 MiB) Test Summary: | Pass Total Time Negative binomial nuisance parameter Float32 matrix | 12 12 28.7s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Initializing β to univariate regression values... 80%|█▋| ETA: 0:00:01Running 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 6.118194 seconds (1.23 M allocations: 141.498 MiB, 13.07% gc time, 80.27% compilation time) Test Summary: | Pass Total Time initialze beta | 1 1 6.6s 10.621704 seconds (4.00 M allocations: 82.490 MiB, 0.20% gc time, 0.59% compilation time) 6.094170 seconds (3.98 M allocations: 91.674 MiB, 1.11% gc time) 11.587484 seconds (20.41 M allocations: 439.525 MiB, 0.88% gc time, 17.10% compilation time: 80% of which was recompilation) 9.182538 seconds (20.18 M allocations: 434.189 MiB, 1.07% gc time) 41.443992 seconds (3.76 M allocations: 4.239 GiB, 11.59% gc time, 30.20% compilation time) 53.107663 seconds (71.97 k allocations: 183.460 MiB) Test Summary: | Pass Total Time memory_efficient keyword | 7 7 2m31.7s Test Summary: | Pass Total Time update_support! | 10 10 0.8s 15.039 ms (78 allocations: 4.56 KiB) 5.143 μs (0 allocations: 0 bytes) 141.229 μs (4 allocations: 288 bytes) 6.598 μs (0 allocations: 0 bytes) 60.590 μs (2 allocations: 64 bytes) 39.959 μs (0 allocations: 0 bytes) 25.350 μs (0 allocations: 0 bytes) 28.370 μs (0 allocations: 0 bytes) 76.939 μs (0 allocations: 0 bytes) 34.483 ms (78 allocations: 4.56 KiB) 27.790 μs (0 allocations: 0 bytes) 198.628 μs (4 allocations: 288 bytes) 33.760 μs (0 allocations: 0 bytes) 288.598 μs (2 allocations: 64 bytes) 92.599 μs (0 allocations: 0 bytes) 122.419 μs (0 allocations: 0 bytes) 124.659 μs (0 allocations: 0 bytes) 216.028 μs (0 allocations: 0 bytes) Test Summary: | Total Time benchmarks for multivariate function | 0 3m40.7s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse Multivariate Gaussian regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 12 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -2900.9186300194497, backtracks = 0, tol = 0.1480224208200413 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 0.444684 seconds (49.19 k allocations: 5.483 MiB, 62.57% compilation time) Test Summary: | Pass Total Time multivariate fit_iht SnpLinAlg | 7 7 13.5s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse 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 2.197208 seconds (312.23 k allocations: 169.921 MiB, 63.80% compilation time) Test Summary: | Pass Total Time initialze beta | 5 5 2.7s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:03:58 Cross validating... 6%|██ | ETA: 0:01:57 Cross validating... 10%|███ | ETA: 0:01:16 Cross validating... 13%|████▏ | ETA: 0:00:56 Cross validating... 16%|█████▏ | ETA: 0:00:44 Cross validating... 19%|██████▏ | ETA: 0:00:36 Cross validating... 22%|███████▏ | ETA: 0:00:30 Cross validating... 25%|████████▏ | ETA: 0:00:26 Cross validating... 29%|█████████▏ | ETA: 0:00:22 Cross validating... 32%|██████████▏ | ETA: 0:00:20 Cross validating... 35%|███████████▏ | ETA: 0:00:17 Cross validating... 38%|████████████▎ | ETA: 0:00:15 Cross validating... 41%|█████████████▎ | ETA: 0:00:14 Cross validating... 44%|██████████████▎ | ETA: 0:00:12 Cross validating... 48%|███████████████▎ | ETA: 0:00:11 Cross validating... 51%|████████████████▎ | ETA: 0:00:10 Cross validating... 54%|█████████████████▎ | ETA: 0:00:09 Cross validating... 57%|██████████████████▎ | ETA: 0:00:08 Cross validating... 60%|███████████████████▎ | ETA: 0:00:07 Cross validating... 63%|████████████████████▍ | ETA: 0:00:06 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:05 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:04 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:04 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:03 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:03 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:02 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:02 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:01 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:01 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:01 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:12 Crossvalidation Results: k MSE 0 3326.685370768072 1 2305.679654285475 2 1817.7736504801803 3 1143.3664114720261 4 791.8288847381176 5 516.6100248832314 6 401.6397353842724 7 367.18835748170517 8 369.65976107490127 9 364.47821090590367 10 374.2477992940748 11 369.5549663095936 12 371.583292642508 13 383.15780369370793 14 373.18731302520666 15 378.8261878317584 16 390.94043535427323 17 391.8012517529555 18 406.0918302663135 19 399.5603805272806 20 436.08554876564483 Best k = 9 12.509003 seconds (11.65 M allocations: 301.128 MiB, 2.00% gc time, 62.36% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 5%|█▌ | ETA: 0:00:03 Cross validating... 10%|███ | ETA: 0:00:03 Cross validating... 13%|████▏ | ETA: 0:00:03 Cross validating... 16%|█████▏ | ETA: 0:00:03 Cross validating... 19%|██████▏ | ETA: 0:00:03 Cross validating... 22%|███████▏ | ETA: 0:00:03 Cross validating... 25%|████████▏ | ETA: 0:00:03 Cross validating... 29%|█████████▏ | ETA: 0:00:03 Cross validating... 32%|██████████▏ | ETA: 0:00:03 Cross validating... 35%|███████████▏ | ETA: 0:00:03 Cross validating... 40%|████████████▊ | ETA: 0:00:03 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... 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... 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: 0:00:00 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 3326.685370768072 1 2306.591629103157 2 1823.351529285268 3 1163.2394898584407 4 801.1517131635712 5 522.4236032044566 6 406.18435433183566 7 371.61850318212 8 377.9711784639959 9 373.30413321274455 10 391.4820880494335 11 387.4659051570037 12 392.5896994169873 13 401.1875936467786 14 403.85252195203105 15 416.73042791949695 16 413.0257720571175 17 418.3799194561064 18 416.5538186500911 19 424.87398352539606 20 436.08554876564483 Best k = 7 4.658820 seconds (10.45 M allocations: 220.225 MiB, 0.85% gc time, 1.03% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, normal model | 3 3 18.2s **** 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 **** Cross validating... 3%|█ | ETA: 0:08:09 Cross validating... 8%|██▌ | ETA: 0:03:07 Cross validating... 13%|████▏ | ETA: 0:01:52 Cross validating... 17%|█████▋ | ETA: 0:01:18 Cross validating... 21%|██████▋ | ETA: 0:01:03 Cross validating... 25%|████████▏ | ETA: 0:00:49 Cross validating... 29%|█████████▏ | ETA: 0:00:42 Cross validating... 32%|██████████▏ | ETA: 0:00:36 Cross validating... 37%|███████████▋ | ETA: 0:00:30 Cross validating... 41%|█████████████▎ | ETA: 0:00:24 Cross validating... 46%|██████████████▊ | ETA: 0:00:20 Cross validating... 51%|████████████████▎ | ETA: 0:00:17 Cross validating... 56%|█████████████████▊ | ETA: 0:00:14 Cross validating... 59%|██████████████████▊ | ETA: 0:00:12 Cross validating... 62%|███████████████████▊ | ETA: 0:00:11 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:09 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:07 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:06 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:04 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:03 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:02 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:01 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:18 Crossvalidation Results: k MSE 0 1752.3331866455078 1 1401.816566040039 2 1089.8367017211913 3 817.3222497558593 4 652.7391810913086 5 539.913961517334 6 448.9732565612793 7 413.1792781677246 8 361.48577929687497 9 347.9011190795899 10 352.87135360717775 11 355.5398712768555 12 358.48959219360347 13 369.30885455322266 14 372.9455140380859 15 377.8767771911621 16 376.101680847168 17 369.5544602661133 18 406.9828894042969 19 372.2411091003418 20 436.93415560913087 Best k = 9 20.191198 seconds (12.82 M allocations: 315.583 MiB, 0.40% gc time, 85.75% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 5%|█▌ | ETA: 0:00:02 Cross validating... 10%|███ | ETA: 0:00:02 Cross validating... 16%|█████▏ | ETA: 0:00:02 Cross validating... 21%|██████▋ | ETA: 0:00:02 Cross validating... 24%|███████▋ | ETA: 0:00:02 Cross validating... 27%|████████▋ | ETA: 0:00:02 Cross validating... 30%|█████████▋ | ETA: 0:00:02 Cross validating... 35%|███████████▏ | ETA: 0:00:02 Cross validating... 40%|████████████▊ | ETA: 0:00:02 Cross validating... 46%|██████████████▊ | ETA: 0:00:01 Cross validating... 51%|████████████████▎ | ETA: 0:00:01 Cross validating... 56%|█████████████████▊ | ETA: 0:00:01 Cross validating... 60%|███████████████████▎ | ETA: 0:00:01 Cross validating... 65%|████████████████████▉ | ETA: 0:00:01 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:01 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:01 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:00 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:00 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:00 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:02 Crossvalidation Results: k MSE 0 1752.3331866455078 1 1402.3565119628906 2 1090.1556606445313 3 817.4814610595703 4 654.9793535766602 5 543.1384981689454 6 449.48754238891604 7 416.1638479309082 8 365.2951543884277 9 352.2011081848144 10 362.90116427612304 11 369.6968338317871 12 378.99143557739256 13 387.1557993469238 14 400.2932322998047 15 413.1506379699707 16 407.14725109863275 17 417.5710469055176 18 409.7067335510254 19 429.6794506835937 20 436.9341960144043 Best k = 9 2.741465 seconds (10.77 M allocations: 197.773 MiB, 1.91% gc time, 1.75% compilation time) Test Summary: | Pass Total Time Cross validation on Float32 matrix, normal model | 2 2 24.5s **** 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: 0:01:08 Cross validating... 6%|██ | ETA: 0:00:35 Cross validating... 10%|███ | ETA: 0:00:24 Cross validating... 13%|████▏ | ETA: 0:00:19 Cross validating... 14%|████▋ | ETA: 0:00:17 Cross validating... 17%|█████▋ | ETA: 0:00:14 Cross validating... 21%|██████▋ | ETA: 0:00:12 Cross validating... 24%|███████▋ | ETA: 0:00:11 Cross validating... 25%|████████▏ | ETA: 0:00:10 Cross validating... 29%|█████████▏ | ETA: 0:00:09 Cross validating... 32%|██████████▏ | ETA: 0:00:08 Cross validating... 35%|███████████▏ | ETA: 0:00:07 Cross validating... 38%|████████████▎ | ETA: 0:00:07 Cross validating... 41%|█████████████▎ | ETA: 0:00:06 Cross validating... 44%|██████████████▎ | ETA: 0:00:05 Cross validating... 48%|███████████████▎ | ETA: 0:00:05 Cross validating... 51%|████████████████▎ | ETA: 0:00:05 Cross validating... 54%|█████████████████▎ | ETA: 0:00:04 Cross validating... 57%|██████████████████▎ | ETA: 0:00:04 Cross validating... 60%|███████████████████▎ | ETA: 0:00:03 Cross validating... 63%|████████████████████▍ | ETA: 0:00:03 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:03 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:02 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:02 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:02 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:02 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:01 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:01 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:01 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:01 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:07 Crossvalidation Results: k MSE 0 461.51076100057287 1 407.703625081502 2 371.3489475787444 3 330.12968553934417 4 296.68880638854444 5 267.53682635520704 6 252.35660404127344 7 255.03979981497525 8 261.1627382359886 9 260.5064269006827 10 261.11213420547296 11 284.31106588212003 12 273.70221614949355 13 282.75516413655714 14 282.444091842584 15 272.3900621046528 16 286.7765217314158 17 284.50619267206383 18 288.84451352884565 19 271.5034382047409 20 300.09281875034435 Best k = 6 8.388400 seconds (17.51 M allocations: 414.361 MiB, 1.17% gc time, 36.56% 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... 5%|█▌ | ETA: 0:00:04 Cross validating... 8%|██▌ | ETA: 0:00:04 Cross validating... 11%|███▌ | ETA: 0:00:04 Cross validating... 14%|████▋ | ETA: 0:00:04 Cross validating... 17%|█████▋ | ETA: 0:00:04 Cross validating... 19%|██████▏ | ETA: 0:00:04 Cross validating... 22%|███████▏ | ETA: 0:00:04 Cross validating... 25%|████████▏ | ETA: 0:00:04 Cross validating... 29%|█████████▏ | ETA: 0:00:04 Cross validating... 32%|██████████▏ | ETA: 0:00:04 Cross validating... 35%|███████████▏ | ETA: 0:00:04 Cross validating... 38%|████████████▎ | ETA: 0:00:03 Cross validating... 41%|█████████████▎ | ETA: 0:00:03 Cross validating... 44%|██████████████▎ | ETA: 0:00:03 Cross validating... 48%|███████████████▎ | ETA: 0:00:03 Cross validating... 51%|████████████████▎ | ETA: 0:00:03 Cross validating... 54%|█████████████████▎ | ETA: 0:00:03 Cross validating... 57%|██████████████████▎ | ETA: 0:00:02 Cross validating... 60%|███████████████████▎ | ETA: 0:00:02 Cross validating... 63%|████████████████████▍ | ETA: 0:00:02 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:02 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:02 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:01 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:01 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:01 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:01 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:01 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:01 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:05 Crossvalidation Results: k MSE 0 461.51076100057287 1 408.4972300146841 2 372.4973533097121 3 331.09717698290046 4 297.3754960720778 5 271.3047138599746 6 256.8852215245756 7 263.43358973486573 8 273.139657090028 9 272.68783175156346 10 285.10808635998274 11 292.80325167515355 12 295.31678190288744 13 298.8516670586805 14 318.1233838799674 15 315.2145088281078 16 310.6682834771924 17 330.95782427708525 18 333.90680715501605 19 323.73977642955657 20 324.74818896680745 Best k = 6 5.391661 seconds (17.61 M allocations: 365.857 MiB, 1.26% gc time, 1.13% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, logistic model | 2 2 14.2s **** 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 **** Cross validating... 3%|█ | ETA: 0:00:58 Cross validating... 6%|██ | ETA: 0:00:30 Cross validating... 10%|███ | ETA: 0:00:21 Cross validating... 13%|████▏ | ETA: 0:00:16 Cross validating... 16%|█████▏ | ETA: 0:00:14 Cross validating... 19%|██████▏ | ETA: 0:00:11 Cross validating... 22%|███████▏ | ETA: 0:00:10 Cross validating... 25%|████████▏ | ETA: 0:00:09 Cross validating... 29%|█████████▏ | ETA: 0:00:08 Cross validating... 32%|██████████▏ | ETA: 0:00:07 Cross validating... 35%|███████████▏ | ETA: 0:00:07 Cross validating... 38%|████████████▎ | ETA: 0:00:06 Cross validating... 41%|█████████████▎ | ETA: 0:00:05 Cross validating... 44%|██████████████▎ | ETA: 0:00:05 Cross validating... 46%|██████████████▊ | ETA: 0:00:06 Cross validating... 49%|███████████████▊ | ETA: 0:00:05 Cross validating... 52%|████████████████▊ | ETA: 0:00:05 Cross validating... 56%|█████████████████▊ | ETA: 0:00:04 Cross validating... 59%|██████████████████▊ | ETA: 0:00:04 Cross validating... 62%|███████████████████▊ | ETA: 0:00:03 Cross validating... 65%|████████████████████▉ | ETA: 0:00:03 Cross validating... 68%|█████████████████████▉ | ETA: 0:00:03 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:02 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:02 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:02 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:02 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... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:07 Crossvalidation Results: k MSE 0 463.9305118760668 1 423.55638332462945 2 397.14881825374937 3 378.8202324294624 4 357.801284500955 5 337.2307196983808 6 316.0413564515139 7 320.36775351524216 8 319.0726932113846 9 332.7428450157535 10 319.5984925422285 11 328.6377702740455 12 328.5693666232972 13 321.09022853101044 14 314.93759529168005 15 326.39914854467287 16 326.7892524538677 17 344.4982165191671 18 357.4972022927187 19 333.0810549858602 20 345.8570580004265 Best k = 14 8.649363 seconds (16.93 M allocations: 398.954 MiB, 12.87% gc time, 35.21% 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: 0:00:04 Cross validating... 8%|██▌ | ETA: 0:00:04 Cross validating... 11%|███▌ | ETA: 0:00:04 Cross validating... 14%|████▋ | ETA: 0:00:04 Cross validating... 17%|█████▋ | ETA: 0:00:04 Cross validating... 21%|██████▋ | ETA: 0:00:03 Cross validating... 24%|███████▋ | ETA: 0:00:03 Cross validating... 27%|████████▋ | ETA: 0:00:03 Cross validating... 30%|█████████▋ | 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: 0:00:02 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 0 463.9305118760668 1 424.23862280557455 2 398.22792851201285 3 380.681566059579 4 358.00877578271025 5 340.8463729051931 6 321.45557134329977 7 330.81116435171833 8 342.769995347655 9 335.65199151444403 10 346.6170356717879 11 340.8166974179485 12 356.70860730526897 13 348.7750758224029 14 350.1960163419434 15 369.4794899561365 16 377.4859465292099 17 402.46404749035133 18 379.97638885326734 19 398.76214063086843 20 392.59861433954507 Best k = 6 4.737506 seconds (17.29 M allocations: 355.873 MiB, 1.91% gc time, 0.93% compilation time) Test Summary: | Pass Total Time Cross validation on Float64 matrix, logistic model | 2 2 14.4s **** 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: 0:01:07 Cross validating... 6%|██ | ETA: 0:00:35 Cross validating... 10%|███ | ETA: 0:00:24 Cross validating... 13%|████▏ | ETA: 0:00:19 Cross validating... 14%|████▋ | ETA: 0:00:17 Cross validating... 17%|█████▋ | ETA: 0:00:14 Cross validating... 21%|██████▋ | ETA: 0:00:12 Cross validating... 24%|███████▋ | ETA: 0:00:11 Cross validating... 27%|████████▋ | ETA: 0:00:10 Cross validating... 29%|█████████▏ | ETA: 0:00:09 Cross validating... 30%|█████████▋ | ETA: 0:00:09 Cross validating... 32%|██████████▏ | ETA: 0:00:08 Cross validating... 35%|███████████▏ | ETA: 0:00:08 Cross validating... 38%|████████████▎ | ETA: 0:00:07 Cross validating... 41%|█████████████▎ | ETA: 0:00:06 Cross validating... 44%|██████████████▎ | ETA: 0:00:06 Cross validating... 48%|███████████████▎ | ETA: 0:00:05 Cross validating... 51%|████████████████▎ | ETA: 0:00:05 Cross validating... 54%|█████████████████▎ | ETA: 0:00:04 Cross validating... 56%|█████████████████▊ | ETA: 0:00:04 Cross validating... 59%|██████████████████▊ | ETA: 0:00:04 Cross validating... 62%|███████████████████▊ | ETA: 0:00:03 Cross validating... 65%|████████████████████▉ | ETA: 0:00:03 Cross validating... 68%|█████████████████████▉ | ETA: 0:00:03 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:02 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:02 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:02 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:02 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: 0:00:01 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:07 Crossvalidation Results: k MSE 0 800.2503267764425 1 696.8822852336314 2 518.7927047114238 3 428.6834014553617 4 392.5579680560708 5 355.2939344191701 6 346.6404231254819 7 340.9766898039385 8 342.4550117661739 9 351.6791887280425 10 353.2808968469863 11 364.30957914795994 12 345.5245703881695 13 348.6581209044151 14 376.59575279370495 15 360.92286185304636 16 346.63866656174235 17 351.4536001884022 18 353.0687142653187 19 361.3854236891434 20 360.76204389406854 Best k = 7 8.696093 seconds (15.23 M allocations: 359.274 MiB, 1.05% gc time, 33.91% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:04 Cross validating... 6%|██ | ETA: 0:00:05 Cross validating... 10%|███ | ETA: 0:00:05 Cross validating... 13%|████▏ | ETA: 0:00:05 Cross validating... 14%|████▋ | ETA: 0:00:05 Cross validating... 17%|█████▋ | ETA: 0:00:05 Cross validating... 21%|██████▋ | ETA: 0:00:04 Cross validating... 24%|███████▋ | ETA: 0:00:04 Cross validating... 27%|████████▋ | ETA: 0:00:04 Cross validating... 30%|█████████▋ | ETA: 0:00:04 Cross validating... 33%|██████████▋ | ETA: 0:00:04 Cross validating... 37%|███████████▋ | ETA: 0:00:04 Cross validating... 40%|████████████▊ | ETA: 0:00:03 Cross validating... 43%|█████████████▊ | ETA: 0:00:03 Cross validating... 46%|██████████████▊ | ETA: 0:00:03 Cross validating... 49%|███████████████▊ | ETA: 0:00:03 Cross validating... 52%|████████████████▊ | ETA: 0:00:03 Cross validating... 56%|█████████████████▊ | ETA: 0:00:03 Cross validating... 59%|██████████████████▊ | ETA: 0:00:02 Cross validating... 62%|███████████████████▊ | ETA: 0:00:02 Cross validating... 65%|████████████████████▉ | ETA: 0:00:02 Cross validating... 68%|█████████████████████▉ | ETA: 0:00:02 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:02 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:01 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:01 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:01 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:01 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:01 Cross validating... 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 0 800.2503267764425 1 691.9698747650141 2 526.9800919859616 3 430.7801038749062 4 382.5243564369187 5 359.55943429221463 6 357.7705114723241 7 350.36644743515177 8 351.1590681756367 9 369.6235656388055 10 374.0287520352714 11 374.7253969842051 12 379.2423349655653 13 375.97075525420536 14 383.966173666395 15 374.6256643688806 16 384.05124530169996 17 395.5009490430938 18 384.0902987407413 19 386.17424472975847 20 396.1732303196111 Best k = 7 5.856211 seconds (14.36 M allocations: 289.627 MiB, 1.25% gc time, 1.18% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, Poisson model | 2 2 15.0s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:01:39 Cross validating... 5%|█▌ | ETA: 0:01:26 Cross validating... 6%|██ | ETA: 0:01:19 Cross validating... 8%|██▌ | ETA: 0:01:03 Cross validating... 10%|███ | ETA: 0:00:53 Cross validating... 13%|████▏ | ETA: 0:00:39 Cross validating... 14%|████▋ | ETA: 0:00:35 Cross validating... 16%|█████▏ | ETA: 0:00:36 Cross validating... 17%|█████▋ | ETA: 0:00:33 Cross validating... 19%|██████▏ | ETA: 0:00:34 Cross validating... 21%|██████▋ | ETA: 0:00:31 Cross validating... 22%|███████▏ | ETA: 0:00:29 Cross validating... 24%|███████▋ | ETA: 0:00:27 Cross validating... 25%|████████▏ | ETA: 0:00:28 Cross validating... 27%|████████▋ | ETA: 0:00:29 Cross validating... 29%|█████████▏ | ETA: 0:00:29 Cross validating... 30%|█████████▋ | ETA: 0:00:28 Cross validating... 32%|██████████▏ | ETA: 0:00:26 Cross validating... 33%|██████████▋ | ETA: 0:00:27 Cross validating... 37%|███████████▋ | ETA: 0:00:23 Cross validating... 40%|████████████▊ | ETA: 0:00:23 Cross validating... 44%|██████████████▎ | ETA: 0:00:19 Cross validating... 48%|███████████████▎ | ETA: 0:00:17 Cross validating... 49%|███████████████▊ | ETA: 0:00:17 Cross validating... 52%|████████████████▊ | ETA: 0:00:15 Cross validating... 56%|█████████████████▊ | ETA: 0:00:14 Cross validating... 57%|██████████████████▎ | ETA: 0:00:13 Cross validating... 59%|██████████████████▊ | ETA: 0:00:13 Cross validating... 60%|███████████████████▎ | ETA: 0:00:12 Cross validating... 62%|███████████████████▊ | ETA: 0:00:12 Cross validating... 63%|████████████████████▍ | ETA: 0:00:12 Cross validating... 65%|████████████████████▉ | ETA: 0:00:11 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:11 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:09 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:08 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:06 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:06 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:05 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:05 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:05 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:04 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:04 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:03 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:03 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:02 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:02 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:01 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:01 Cross validating... 100%|████████████████████████████████| Time: 0:00:34 Crossvalidation Results: k MSE 0 355.8085315071269 1 299.0939168504748 2 269.95964702573235 3 251.5435413736813 4 236.76651206741383 5 217.44936206988206 6 208.84869648802427 7 210.31801557717048 8 212.78234698951545 9 213.90715039515968 10 215.77873448391992 11 215.72693356325192 12 216.54376754313847 13 218.17951065829567 14 220.3575356020698 15 219.87578251317916 16 220.46321000299395 17 222.98971203736258 18 222.0878515737446 19 225.4707150170836 20 224.53363874430687 Best k = 6 34.858562 seconds (124.15 M allocations: 3.182 GiB, 1.39% gc time, 7.54% 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: 0:00:05 Cross validating... 13%|████▏ | ETA: 0:00:05 Cross validating... 16%|█████▏ | ETA: 0:00:04 Cross validating... 17%|█████▋ | ETA: 0:00:05 Cross validating... 19%|██████▏ | ETA: 0:00:05 Cross validating... 21%|██████▋ | ETA: 0:00:05 Cross validating... 24%|███████▋ | ETA: 0:00:04 Cross validating... 25%|████████▏ | ETA: 0:00:05 Cross validating... 27%|████████▋ | ETA: 0:00:05 Cross validating... 29%|█████████▏ | ETA: 0:00:05 Cross validating... 30%|█████████▋ | ETA: 0:00:05 Cross validating... 32%|██████████▏ | ETA: 0:00:05 Cross validating... 33%|██████████▋ | ETA: 0:00:05 Cross validating... 38%|████████████▎ | ETA: 0:00:04 Cross validating... 41%|█████████████▎ | ETA: 0:00:04 Cross validating... 44%|██████████████▎ | ETA: 0:00:04 Cross validating... 48%|███████████████▎ | ETA: 0:00:03 Cross validating... 49%|███████████████▊ | ETA: 0:00:03 Cross validating... 51%|████████████████▎ | ETA: 0:00:03 Cross validating... 52%|████████████████▊ | ETA: 0:00:03 Cross validating... 54%|█████████████████▎ | ETA: 0:00:03 Cross validating... 56%|█████████████████▊ | ETA: 0:00:03 Cross validating... 57%|██████████████████▎ | ETA: 0:00:03 Cross validating... 59%|██████████████████▊ | ETA: 0:00:03 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: 0:00:01 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:01 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: 0:00:00 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: 0:00:07 Crossvalidation Results: k MSE 0 355.8085315071269 1 299.21265219790155 2 270.1782862459462 3 252.76020422573438 4 238.14699924274493 5 219.66827854179672 6 210.7380848851418 7 215.23656754401188 8 217.76945123340752 9 223.35303644799558 10 228.39166085628966 11 232.31540922154755 12 233.25159974952504 13 238.04152057552625 14 245.54894031409304 15 245.20873898411014 16 246.4714117735365 17 251.51903911655734 18 257.27078781054547 19 254.58796320667898 20 268.1007720599821 Best k = 6 7.990878 seconds (32.04 M allocations: 658.472 MiB, 1.12% gc time, 0.63% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, NegativeBinomial model | 2 2 43.3s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:01:03 Cross validating... 8%|██▌ | ETA: 0:00:25 Cross validating... 13%|████▏ | ETA: 0:00:16 Cross validating... 17%|█████▋ | ETA: 0:00:12 Cross validating... 21%|██████▋ | ETA: 0:00:10 Cross validating... 24%|███████▋ | ETA: 0:00:09 Cross validating... 27%|████████▋ | ETA: 0:00:08 Cross validating... 30%|█████████▋ | ETA: 0:00:07 Cross validating... 33%|██████████▋ | ETA: 0:00:06 Cross validating... 37%|███████████▋ | ETA: 0:00:05 Cross validating... 40%|████████████▊ | ETA: 0:00:05 Cross validating... 44%|██████████████▎ | ETA: 0:00:04 Cross validating... 48%|███████████████▎ | ETA: 0:00:04 Cross validating... 52%|████████████████▊ | ETA: 0:00:03 Cross validating... 56%|█████████████████▊ | ETA: 0:00:03 Cross validating... 59%|██████████████████▊ | ETA: 0:00:03 Cross validating... 63%|████████████████████▍ | ETA: 0:00:02 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:02 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:01 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:01 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:01 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:01 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 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 5.444967 seconds (17.00 M allocations: 337.849 MiB, 1.64% gc time, 46.42% 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... 29%|█████████▏ | ETA: 0:00:02 Cross validating... 33%|██████████▋ | ETA: 0:00:02 Cross validating... 38%|████████████▎ | ETA: 0:00:02 Cross validating... 43%|█████████████▊ | ETA: 0:00:01 Cross validating... 48%|███████████████▎ | ETA: 0:00:01 Cross validating... 52%|████████████████▊ | ETA: 0:00:01 Cross validating... 57%|██████████████████▎ | ETA: 0:00:01 Cross validating... 62%|███████████████████▊ | ETA: 0:00:01 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:01 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:01 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:01 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:00 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:00 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:02 Crossvalidation Results: k MSE 0 709.7238911132813 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 2.665577 seconds (16.17 M allocations: 286.691 MiB, 1.73% gc time, 1.86% 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: 0:01:11 Cross validating... 3%|█ | ETA: 0:00:50 Cross validating... 5%|█▋ | ETA: 0:00:35 Cross validating... 6%|█▉ | ETA: 0:00:31 Cross validating... 7%|██▎ | ETA: 0:00:28 Cross validating... 8%|██▌ | ETA: 0:00:26 Cross validating... 9%|██▉ | ETA: 0:00:25 Cross validating... 10%|███▎ | ETA: 0:00:24 Cross validating... 11%|███▌ | ETA: 0:00:22 Cross validating... 12%|███▉ | ETA: 0:00:21 Cross validating... 13%|████▏ | ETA: 0:00:21 Cross validating... 14%|████▌ | ETA: 0:00:20 Cross validating... 15%|████▊ | ETA: 0:00:20 Cross validating... 16%|█████▏ | ETA: 0:00:19 Cross validating... 17%|█████▌ | ETA: 0:00:19 Cross validating... 18%|█████▊ | ETA: 0:00:18 Cross validating... 19%|██████▏ | ETA: 0:00:18 Cross validating... 20%|██████▍ | ETA: 0:00:17 Cross validating... 22%|███████ | ETA: 0:00:16 Cross validating... 24%|███████▋ | ETA: 0:00:15 Cross validating... 26%|████████▍ | ETA: 0:00:14 Cross validating... 28%|█████████ | ETA: 0:00:13 Cross validating... 30%|█████████▋ | ETA: 0:00:13 Cross validating... 31%|█████████▉ | ETA: 0:00:12 Cross validating... 32%|██████████▎ | ETA: 0:00:12 Cross validating... 33%|██████████▌ | ETA: 0:00:12 Cross validating... 34%|██████████▉ | ETA: 0:00:12 Cross validating... 35%|███████████▎ | ETA: 0:00:12 Cross validating... 36%|███████████▌ | ETA: 0:00:11 Cross validating... 37%|███████████▉ | ETA: 0:00:11 Cross validating... 38%|████████████▏ | ETA: 0:00:11 Cross validating... 39%|████████████▌ | ETA: 0:00:11 Cross validating... 40%|████████████▊ | ETA: 0:00:11 Cross validating... 42%|█████████████▌ | ETA: 0:00:10 Cross validating... 44%|██████████████▏ | ETA: 0:00:10 Cross validating... 46%|██████████████▊ | ETA: 0:00:09 Cross validating... 47%|███████████████ | ETA: 0:00:09 Cross validating... 48%|███████████████▍ | ETA: 0:00:09 Cross validating... 49%|███████████████▋ | ETA: 0:00:09 Cross validating... 50%|████████████████ | ETA: 0:00:08 Cross validating... 51%|████████████████▍ | ETA: 0:00:08 Cross validating... 52%|████████████████▋ | ETA: 0:00:08 Cross validating... 53%|█████████████████ | ETA: 0:00:08 Cross validating... 54%|█████████████████▎ | ETA: 0:00:08 Cross validating... 55%|█████████████████▋ | ETA: 0:00:08 Cross validating... 56%|█████████████████▉ | ETA: 0:00:07 Cross validating... 57%|██████████████████▎ | ETA: 0:00:07 Cross validating... 58%|██████████████████▌ | ETA: 0:00:07 Cross validating... 59%|██████████████████▉ | ETA: 0:00:07 Cross validating... 60%|███████████████████▎ | ETA: 0:00:07 Cross validating... 62%|███████████████████▉ | ETA: 0:00:06 Cross validating... 63%|████████████████████▏ | ETA: 0:00:06 Cross validating... 65%|████████████████████▊ | ETA: 0:00:06 Cross validating... 66%|█████████████████████▏ | ETA: 0:00:06 Cross validating... 67%|█████████████████████▌ | ETA: 0:00:05 Cross validating... 68%|█████████████████████▊ | ETA: 0:00:05 Cross validating... 69%|██████████████████████▏ | ETA: 0:00:05 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:05 Cross validating... 71%|██████████████████████▊ | ETA: 0:00:05 Cross validating... 72%|███████████████████████ | ETA: 0:00:05 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:04 Cross validating... 74%|███████████████████████▋ | ETA: 0:00:04 Cross validating... 75%|████████████████████████ | ETA: 0:00:04 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:04 Cross validating... 77%|████████████████████████▋ | ETA: 0:00:04 Cross validating... 78%|█████████████████████████ | ETA: 0:00:04 Cross validating... 79%|█████████████████████████▎ | ETA: 0:00:03 Cross validating... 80%|█████████████████████████▋ | ETA: 0:00:03 Cross validating... 82%|██████████████████████████▎ | ETA: 0:00:03 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:03 Cross validating... 86%|███████████████████████████▌ | ETA: 0:00:02 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:02 Cross validating... 88%|████████████████████████████▏ | ETA: 0:00:02 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:02 Cross validating... 90%|████████████████████████████▊ | ETA: 0:00:02 Cross validating... 91%|█████████████████████████████▏ | ETA: 0:00:01 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:01 Cross validating... 93%|█████████████████████████████▊ | ETA: 0:00:01 Cross validating... 94%|██████████████████████████████▏ | ETA: 0:00:01 Cross validating... 95%|██████████████████████████████▍ | ETA: 0:00:01 Cross validating... 96%|██████████████████████████████▊ | ETA: 0:00:01 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▍| ETA: 0:00:00 Cross validating... 99%|███████████████████████████████▋| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:16 Crossvalidation Results: k MSE 1 2980.365720245539 2 2554.2761564798475 3 2290.357649360491 4 2239.7428610752254 5 2126.960759383692 6 2101.2244989572173 7 2058.9508052586993 8 2090.214567273788 9 2109.206338128974 10 2131.4832365635925 11 2154.54682112848 12 2162.1868488628343 13 2207.6391254628275 14 2208.8779323437366 15 2210.037626863626 16 2244.43540926099 17 2252.3174547705944 18 2252.933875783446 19 2274.0908669579535 20 2300.6276442241297 Best k = 7 16.384738 seconds (334.42 k allocations: 240.174 MiB, 0.56% gc time, 8.79% compilation time) Test Summary: | Pass Total Time multivariate cross validation SnpLinAlg | 3 3 20.4s Test Summary: | Pass Total Time wrapper univariate | 20 20 1m54.7s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 2%|▋ | ETA: 0:00:11 Cross validating... 3%|█ | ETA: 0:00:11 Cross validating... 4%|█▎ | ETA: 0:00:12 Cross validating... 5%|█▋ | ETA: 0:00:11 Cross validating... 6%|█▉ | ETA: 0:00:13 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: 0:00:15 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: 0:00:18 Cross validating... 16%|█████▏ | ETA: 0:00:19 Cross validating... 17%|█████▌ | ETA: 0:00:19 Cross validating... 18%|█████▊ | ETA: 0:00:19 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 Cross validating... 26%|████████▍ | ETA: 0:00:16 Cross validating... 27%|████████▋ | ETA: 0:00:16 Cross validating... 28%|█████████ | ETA: 0:00:16 Cross validating... 29%|█████████▎ | ETA: 0:00:17 Cross validating... 30%|█████████▋ | ETA: 0:00:17 Cross validating... 31%|█████████▉ | ETA: 0:00:16 Cross validating... 32%|██████████▎ | ETA: 0:00:16 Cross validating... 33%|██████████▌ | ETA: 0:00:16 Cross validating... 34%|██████████▉ | ETA: 0:00:16 Cross validating... 35%|███████████▎ | ETA: 0:00:16 Cross validating... 36%|███████████▌ | ETA: 0:00:16 Cross validating... 37%|███████████▉ | ETA: 0:00:16 Cross validating... 38%|████████████▏ | ETA: 0:00:15 Cross validating... 39%|████████████▌ | ETA: 0:00:15 Cross validating... 40%|████████████▊ | ETA: 0:00:15 Cross validating... 41%|█████████████▏ | ETA: 0:00:15 Cross validating... 42%|█████████████▌ | ETA: 0:00:14 Cross validating... 43%|█████████████▊ | ETA: 0:00:14 Cross validating... 44%|██████████████▏ | ETA: 0:00:13 Cross validating... 45%|██████████████▍ | ETA: 0:00:13 Cross validating... 46%|██████████████▊ | ETA: 0:00:13 Cross validating... 47%|███████████████ | ETA: 0:00:12 Cross validating... 48%|███████████████▍ | ETA: 0:00:12 Cross validating... 49%|███████████████▋ | ETA: 0:00:12 Cross validating... 50%|████████████████ | ETA: 0:00:12 Cross validating... 51%|████████████████▍ | ETA: 0:00:12 Cross validating... 52%|████████████████▋ | ETA: 0:00:11 Cross validating... 53%|█████████████████ | ETA: 0:00:11 Cross validating... 54%|█████████████████▎ | ETA: 0:00:11 Cross validating... 55%|█████████████████▋ | ETA: 0:00:11 Cross validating... 56%|█████████████████▉ | ETA: 0:00:11 Cross validating... 57%|██████████████████▎ | ETA: 0:00:10 Cross validating... 58%|██████████████████▌ | ETA: 0:00:10 Cross validating... 59%|██████████████████▉ | ETA: 0:00:10 Cross validating... 60%|███████████████████▎ | ETA: 0:00:10 Cross validating... 61%|███████████████████▌ | ETA: 0:00:10 Cross validating... 62%|███████████████████▉ | ETA: 0:00:09 Cross validating... 63%|████████████████████▏ | ETA: 0:00:09 Cross validating... 64%|████████████████████▌ | ETA: 0:00:09 Cross validating... 65%|████████████████████▊ | ETA: 0:00:08 Cross validating... 66%|█████████████████████▏ | ETA: 0:00:08 Cross validating... 67%|█████████████████████▌ | ETA: 0:00:08 Cross validating... 68%|█████████████████████▊ | ETA: 0:00:08 Cross validating... 69%|██████████████████████▏ | ETA: 0:00:07 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:07 Cross validating... 71%|██████████████████████▊ | ETA: 0:00:07 Cross validating... 72%|███████████████████████ | ETA: 0:00:07 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:06 Cross validating... 74%|███████████████████████▋ | ETA: 0:00:06 Cross validating... 75%|████████████████████████ | ETA: 0:00:06 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:06 Cross validating... 77%|████████████████████████▋ | ETA: 0:00:06 Cross validating... 78%|█████████████████████████ | ETA: 0:00:05 Cross validating... 79%|█████████████████████████▎ | ETA: 0:00:05 Cross validating... 80%|█████████████████████████▋ | ETA: 0:00:05 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:05 Cross validating... 82%|██████████████████████████▎ | ETA: 0:00:04 Cross validating... 83%|██████████████████████████▌ | ETA: 0:00:04 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:04 Cross validating... 85%|███████████████████████████▎ | ETA: 0:00:04 Cross validating... 86%|███████████████████████████▌ | ETA: 0:00:03 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:03 Cross validating... 88%|████████████████████████████▏ | ETA: 0:00:03 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:03 Cross validating... 90%|████████████████████████████▊ | ETA: 0:00:02 Cross validating... 91%|█████████████████████████████▏ | ETA: 0:00:02 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:02 Cross validating... 93%|█████████████████████████████▊ | ETA: 0:00:02 Cross validating... 94%|██████████████████████████████▏ | ETA: 0:00:01 Cross validating... 95%|██████████████████████████████▍ | ETA: 0:00:01 Cross validating... 96%|██████████████████████████████▊ | ETA: 0:00:01 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:01 Cross validating... 98%|███████████████████████████████▍| ETA: 0:00:00 Cross validating... 99%|███████████████████████████████▋| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:25 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: 0:00:11 Cross validating... 3%|█ | ETA: 0:00:11 Cross validating... 4%|█▎ | ETA: 0:00:12 Cross validating... 5%|█▋ | ETA: 0:00:12 Cross validating... 6%|█▉ | ETA: 0:00:13 Cross validating... 7%|██▎ | ETA: 0:00:13 Cross validating... 8%|██▌ | ETA: 0:00:13 Cross validating... 9%|██▉ | ETA: 0:00:15 Cross validating... 10%|███▎ | ETA: 0:00:15 Cross validating... 11%|███▌ | ETA: 0:00:16 Cross validating... 12%|███▉ | ETA: 0:00:17 Cross validating... 13%|████▏ | ETA: 0:00:17 Cross validating... 14%|████▌ | ETA: 0:00:17 Cross validating... 15%|████▊ | ETA: 0:00:18 Cross validating... 16%|█████▏ | ETA: 0:00:19 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 Cross validating... 26%|████████▍ | ETA: 0:00:16 Cross validating... 27%|████████▋ | ETA: 0:00:17 Cross validating... 28%|█████████ | ETA: 0:00:17 Cross validating... 29%|█████████▎ | ETA: 0:00:17 Cross validating... 30%|█████████▋ | ETA: 0:00:17 Cross validating... 31%|█████████▉ | ETA: 0:00:17 Cross validating... 32%|██████████▎ | ETA: 0:00:16 Cross validating... 33%|██████████▌ | ETA: 0:00:16 Cross validating... 34%|██████████▉ | ETA: 0:00:16 Cross validating... 35%|███████████▎ | ETA: 0:00:16 Cross validating... 36%|███████████▌ | ETA: 0:00:16 Cross validating... 37%|███████████▉ | ETA: 0:00:16 Cross validating... 38%|████████████▏ | ETA: 0:00:16 Cross validating... 39%|████████████▌ | ETA: 0:00:15 Cross validating... 40%|████████████▊ | ETA: 0:00:15 Cross validating... 41%|█████████████▏ | ETA: 0:00:15 Cross validating... 42%|█████████████▌ | ETA: 0:00:14 Cross validating... 43%|█████████████▊ | ETA: 0:00:14 Cross validating... 44%|██████████████▏ | ETA: 0:00:13 Cross validating... 45%|██████████████▍ | ETA: 0:00:13 Cross validating... 46%|██████████████▊ | ETA: 0:00:13 Cross validating... 47%|███████████████ | ETA: 0:00:12 Cross validating... 48%|███████████████▍ | ETA: 0:00:12 Cross validating... 49%|███████████████▋ | ETA: 0:00:12 Cross validating... 50%|████████████████ | ETA: 0:00:12 Cross validating... 51%|████████████████▍ | ETA: 0:00:12 Cross validating... 52%|████████████████▋ | ETA: 0:00:11 Cross validating... 53%|█████████████████ | ETA: 0:00:11 Cross validating... 54%|█████████████████▎ | ETA: 0:00:11 Cross validating... 55%|█████████████████▋ | ETA: 0:00:11 Cross validating... 56%|█████████████████▉ | ETA: 0:00:11 Cross validating... 57%|██████████████████▎ | ETA: 0:00:10 Cross validating... 58%|██████████████████▌ | ETA: 0:00:10 Cross validating... 59%|██████████████████▉ | ETA: 0:00:10 Cross validating... 60%|███████████████████▎ | ETA: 0:00:10 Cross validating... 61%|███████████████████▌ | ETA: 0:00:10 Cross validating... 62%|███████████████████▉ | ETA: 0:00:09 Cross validating... 63%|████████████████████▏ | ETA: 0:00:09 Cross validating... 64%|████████████████████▌ | ETA: 0:00:09 Cross validating... 65%|████████████████████▊ | ETA: 0:00:08 Cross validating... 66%|█████████████████████▏ | ETA: 0:00:08 Cross validating... 67%|█████████████████████▌ | ETA: 0:00:08 Cross validating... 68%|█████████████████████▊ | ETA: 0:00:08 Cross validating... 69%|██████████████████████▏ | ETA: 0:00:07 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:07 Cross validating... 71%|██████████████████████▊ | ETA: 0:00:07 Cross validating... 72%|███████████████████████ | ETA: 0:00:07 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:06 Cross validating... 74%|███████████████████████▋ | ETA: 0:00:06 Cross validating... 75%|████████████████████████ | ETA: 0:00:06 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:06 Cross validating... 77%|████████████████████████▋ | ETA: 0:00:06 Cross validating... 78%|█████████████████████████ | ETA: 0:00:05 Cross validating... 79%|█████████████████████████▎ | ETA: 0:00:05 Cross validating... 80%|█████████████████████████▋ | ETA: 0:00:05 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:05 Cross validating... 82%|██████████████████████████▎ | ETA: 0:00:04 Cross validating... 83%|██████████████████████████▌ | ETA: 0:00:04 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:04 Cross validating... 85%|███████████████████████████▎ | ETA: 0:00:04 Cross validating... 86%|███████████████████████████▌ | ETA: 0:00:03 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:03 Cross validating... 88%|████████████████████████████▏ | ETA: 0:00:03 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:03 Cross validating... 90%|████████████████████████████▊ | ETA: 0:00:02 Cross validating... 91%|█████████████████████████████▏ | ETA: 0:00:02 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:02 Cross validating... 93%|█████████████████████████████▊ | ETA: 0:00:02 Cross validating... 94%|██████████████████████████████▏ | ETA: 0:00:01 Cross validating... 95%|██████████████████████████████▍ | ETA: 0:00:01 Cross validating... 96%|██████████████████████████████▊ | ETA: 0:00:01 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:01 Cross validating... 98%|███████████████████████████████▍| ETA: 0:00:00 Cross validating... 99%|███████████████████████████████▋| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:25 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: 0:00:11 Cross validating... 3%|█ | ETA: 0:00:11 Cross validating... 4%|█▎ | ETA: 0:00:13 Cross validating... 5%|█▋ | ETA: 0:00:12 Cross validating... 6%|█▉ | ETA: 0:00:13 Cross validating... 7%|██▎ | ETA: 0:00:14 Cross validating... 8%|██▌ | ETA: 0:00:13 Cross validating... 9%|██▉ | ETA: 0:00:15 Cross validating... 10%|███▎ | ETA: 0:00:15 Cross validating... 11%|███▌ | ETA: 0:00:16 Cross validating... 12%|███▉ | ETA: 0:00:17 Cross validating... 13%|████▏ | ETA: 0:00:17 Cross validating... 14%|████▌ | ETA: 0:00:17 Cross validating... 15%|████▊ | ETA: 0:00:18 Cross validating... 16%|█████▏ | ETA: 0:00:19 Cross validating... 17%|█████▌ | ETA: 0:00:19 Cross validating... 18%|█████▊ | ETA: 0:00:19 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 Cross validating... 26%|████████▍ | ETA: 0:00:16 Cross validating... 27%|████████▋ | ETA: 0:00:16 Cross validating... 28%|█████████ | ETA: 0:00:16 Cross validating... 29%|█████████▎ | ETA: 0:00:16 Cross validating... 30%|█████████▋ | ETA: 0:00:16 Cross validating... 31%|█████████▉ | ETA: 0:00:16 Cross validating... 32%|██████████▎ | ETA: 0:00:16 Cross validating... 33%|██████████▌ | ETA: 0:00:16 Cross validating... 34%|██████████▉ | ETA: 0:00:16 Cross validating... 35%|███████████▎ | ETA: 0:00:16 Cross validating... 36%|███████████▌ | ETA: 0:00:16 Cross validating... 37%|███████████▉ | ETA: 0:00:16 Cross validating... 38%|████████████▏ | ETA: 0:00:15 Cross validating... 39%|████████████▌ | ETA: 0:00:15 Cross validating... 40%|████████████▊ | ETA: 0:00:15 Cross validating... 41%|█████████████▏ | ETA: 0:00:15 Cross validating... 42%|█████████████▌ | ETA: 0:00:14 Cross validating... 43%|█████████████▊ | ETA: 0:00:14 Cross validating... 44%|██████████████▏ | ETA: 0:00:13 Cross validating... 45%|██████████████▍ | ETA: 0:00:13 Cross validating... 46%|██████████████▊ | ETA: 0:00:13 Cross validating... 47%|███████████████ | ETA: 0:00:12 Cross validating... 48%|███████████████▍ | ETA: 0:00:12 Cross validating... 49%|███████████████▋ | ETA: 0:00:12 Cross validating... 50%|████████████████ | ETA: 0:00:12 Cross validating... 51%|████████████████▍ | ETA: 0:00:11 Cross validating... 52%|████████████████▋ | ETA: 0:00:11 Cross validating... 53%|█████████████████ | ETA: 0:00:11 Cross validating... 54%|█████████████████▎ | ETA: 0:00:11 Cross validating... 55%|█████████████████▋ | ETA: 0:00:11 Cross validating... 56%|█████████████████▉ | ETA: 0:00:10 Cross validating... 57%|██████████████████▎ | ETA: 0:00:10 Cross validating... 58%|██████████████████▌ | ETA: 0:00:10 Cross validating... 59%|██████████████████▉ | ETA: 0:00:10 Cross validating... 60%|███████████████████▎ | ETA: 0:00:10 Cross validating... 61%|███████████████████▌ | ETA: 0:00:10 Cross validating... 62%|███████████████████▉ | ETA: 0:00:09 Cross validating... 63%|████████████████████▏ | ETA: 0:00:09 Cross validating... 64%|████████████████████▌ | ETA: 0:00:09 Cross validating... 65%|████████████████████▊ | ETA: 0:00:08 Cross validating... 66%|█████████████████████▏ | ETA: 0:00:08 Cross validating... 67%|█████████████████████▌ | ETA: 0:00:08 Cross validating... 68%|█████████████████████▊ | ETA: 0:00:08 Cross validating... 69%|██████████████████████▏ | ETA: 0:00:07 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:07 Cross validating... 71%|██████████████████████▊ | ETA: 0:00:07 Cross validating... 72%|███████████████████████ | ETA: 0:00:07 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:06 Cross validating... 74%|███████████████████████▋ | ETA: 0:00:06 Cross validating... 75%|████████████████████████ | ETA: 0:00:06 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:06 Cross validating... 77%|████████████████████████▋ | ETA: 0:00:06 Cross validating... 78%|█████████████████████████ | ETA: 0:00:05 Cross validating... 79%|█████████████████████████▎ | ETA: 0:00:05 Cross validating... 80%|█████████████████████████▋ | ETA: 0:00:05 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:05 Cross validating... 82%|██████████████████████████▎ | ETA: 0:00:04 Cross validating... 83%|██████████████████████████▌ | ETA: 0:00:04 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:04 Cross validating... 85%|███████████████████████████▎ | ETA: 0:00:04 Cross validating... 86%|███████████████████████████▌ | ETA: 0:00:03 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:03 Cross validating... 88%|████████████████████████████▏ | ETA: 0:00:03 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:03 Cross validating... 90%|████████████████████████████▊ | ETA: 0:00:02 Cross validating... 91%|█████████████████████████████▏ | ETA: 0:00:02 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:02 Cross validating... 93%|█████████████████████████████▊ | ETA: 0:00:02 Cross validating... 94%|██████████████████████████████▏ | ETA: 0:00:01 Cross validating... 95%|██████████████████████████████▍ | ETA: 0:00:01 Cross validating... 96%|██████████████████████████████▊ | ETA: 0:00:01 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:01 Cross validating... 98%|███████████████████████████████▍| ETA: 0:00:00 Cross validating... 99%|███████████████████████████████▋| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:25 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 Test Summary: | Pass Total Time wrapper multivariate | 8 8 1m30.3s 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 3.3s RNG of the outermost testset: Xoshiro(0x7513aef1f0999b46, 0xcc81dca6b5037409, 0x9d4bd2e547c0b183, 0x8e2eabc4218bcb20, 0xd05b15bd6139fcd0) 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 1171.31s 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 1313.21s: package tests unexpectedly errored