Package evaluation to test MendelIHT on Julia 1.14.0-DEV.3141 (fbd24f51d0*) started at 2026-09-09T02:37:19.658 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.14` Set-up completed after 15.73s ################################################################################ # 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 v0.1.45 [79e6a3ab] + Adapt v4.7.0 [66dad0bd] + AliasTables v1.1.3 [4fba245c] + ArrayInterface v7.30.1 [67c07d97] + Automa v1.2.0 ⌅ [6db4b851] + BGEN v0.1.17 [28d598bf] + BGZFStreams v0.3.2 [47718e42] + BioGenerics v0.1.5 [62783981] + BitTwiddlingConvenienceFunctions v0.1.6 [e1450e63] + BufferedStreams v1.2.2 [2a0fbf3d] + CPUSummary v0.2.7 [336ed68f] + CSV v0.10.17 [fb6a15b2] + CloseOpenIntervals v0.1.13 [523fee87] + CodecBzip2 v0.8.5 [ba30903b] + CodecXz v0.7.4 [944b1d66] + CodecZlib v0.7.9 [6b39b394] + CodecZstd v0.8.7 [861a8166] + Combinatorics v1.1.0 [38540f10] + CommonSolve v0.2.14 [f70d9fcc] + CommonWorldInvalidations v1.2.2 [34da2185] + Compat v4.18.1 [a33af91c] + CompositionsBase v0.1.2 [187b0558] + ConstructionBase v1.6.0 [adafc99b] + CpuId v0.3.1 [a8cc5b0e] + Crayons v4.2.0 [a10d1c49] + DBInterface v2.7.0 [9a962f9c] + DataAPI v1.16.0 [a93c6f00] + DataFrames v1.8.2 [864edb3b] + DataStructures v0.19.6 [e2d170a0] + DataValueInterfaces v1.0.0 [8bb1440f] + DelimitedFiles v1.9.1 [b4f34e82] + Distances v0.10.12 [31c24e10] + Distributions v0.25.131 [ffbed154] + DocStringExtensions v0.9.5 [48062228] + FilePathsBase v0.9.24 [1a297f60] + FillArrays v1.17.0 [38e38edf] + GLM v1.9.5 [a0844989] + Gamma v1.2.0 [c27321d9] + Glob v1.5.0 [3e5b6fbb] + HostCPUFeatures v0.1.18 [34004b35] + HypergeometricFunctions v0.3.30 ⌅ [09f84164] + HypothesisTests v0.11.8 [615f187c] + IfElse v0.1.1 ⌅ [842dd82b] + InlineStrings v1.4.6 [3587e190] + InverseFunctions v0.1.17 [41ab1584] + InvertedIndices v1.3.1 [92d709cd] + IrrationalConstants v0.2.6 [82899510] + IteratorInterfaceExtensions v1.0.0 [692b3bcd] + JLLWrappers v1.8.0 [b964fa9f] + LaTeXStrings v1.4.1 [10f19ff3] + LayoutPointers v0.1.17 [2ab3a3ac] + LogExpFunctions v1.0.1 [bdcacae8] + LoopVectorization v0.12.174 [1914dd2f] + MacroTools v0.5.16 [d125e4d3] + ManualMemory v0.1.8 [921c7187] + MendelIHT v1.4.11 [e1d29d7a] + Missings v1.2.0 [6fe1bfb0] + OffsetArrays v1.17.0 [bac558e1] + OrderedCollections v2.0.1 [90014a1f] + PDMats v0.11.41 ⌅ [69de0a69] + Parsers v2.8.8 [1d0040c9] + PolyesterWeave v0.2.2 [2dfb63ee] + PooledArrays v1.4.3 [aea7be01] + PrecompileTools v1.3.4 [21216c6a] + Preferences v1.5.2 [08abe8d2] + PrettyTables v3.4.8 [92933f4c] + ProgressMeter v1.11.0 [43287f4e] + PtrArrays v1.4.0 [1fd47b50] + QuadGK v2.11.3 [189a3867] + Reexport v1.2.2 [ae029012] + Requires v1.3.1 [79098fc4] + Rmath v0.9.0 [f2b01f46] + Roots v3.0.8 [fdea26ae] + SIMD v3.7.2 [94e857df] + SIMDTypes v0.1.0 [476501e8] + SLEEFPirates v0.6.46 [0aa819cd] + SQLite v1.8.2 [431bcebd] + SciMLPublic v1.3.0 [91c51154] + SentinelArrays v1.4.10 [1277b4bf] + ShiftedArrays v2.0.0 [4e780e97] + SnpArrays v0.3.23 [a2af1166] + SortingAlgorithms v1.2.3 [276daf66] + SpecialFunctions v2.9.0 [aedffcd0] + Static v1.4.6 [0d7ed370] + StaticArrayInterface v1.10.0 [10745b16] + Statistics v1.11.5 [82ae8749] + StatsAPI v1.8.0 [2913bbd2] + StatsBase v0.34.13 [4c63d2b9] + StatsFuns v2.2.1 [3eaba693] + StatsModels v0.7.10 ⌅ [892a3eda] + StringManipulation v0.5.0 [3783bdb8] + TableTraits v1.0.1 [bd369af6] + Tables v1.14.0 [8290d209] + ThreadingUtilities v0.5.6 ⌅ [3bb67fe8] + TranscodingStreams v0.9.13 [3a884ed6] + UnPack v1.0.2 [a620830f] + VCFTools v0.2.10 [28eba6e3] + VariantCallFormat v0.5.9 [3d5dd08c] + VectorizationBase v0.21.74 [ea10d353] + WeakRefStrings v1.4.3 [76eceee3] + WorkerUtilities v1.6.1 [6e34b625] + Bzip2_jll v1.0.9+0 [efe28fd5] + OpenSpecFun_jll v0.5.6+0 [f50d1b31] + Rmath_jll v0.5.2+0 [76ed43ae] + SQLite_jll v3.53.2+0 [ffd25f8a] + XZ_jll v5.8.3+0 [c4b69c83] + dlfcn_win32_jll v1.4.2+0 [0dad84c5] + ArgTools v1.2.0 [56f22d72] + Artifacts v1.11.0 [2a0f44e3] + Base64 v1.11.0 [ade2ca70] + Dates v1.11.0 [8ba89e20] + Distributed v1.12.0 [f43a241f] + Downloads v1.7.0 [7b1f6079] + FileWatching v1.11.0 [9fa8497b] + Future v1.11.0 [b77e0a4c] + InteractiveUtils v1.11.0 [ac6e5ff7] + JuliaSyntaxHighlighting v1.13.0 [b27032c2] + LibCURL v1.0.0 [76f85450] + LibGit2 v1.11.0 [8f399da3] + Libdl v1.11.0 [37e2e46d] + LinearAlgebra v1.14.0 [56ddb016] + Logging v1.11.0 [d6f4376e] + Markdown v1.11.0 [a63ad114] + Mmap v1.11.0 [ca575930] + NetworkOptions v1.3.0 [44cfe95a] + Pkg v1.14.0 [de0858da] + Printf v1.11.0 [3fa0cd96] + REPL v1.11.0 [9a3f8284] + Random v1.11.0 [ea8e919c] + SHA v1.13.0 [9e88b42a] + Serialization v1.11.0 [6462fe0b] + Sockets v1.11.0 [2f01184e] + SparseArrays v1.13.0 [f489334b] + StyledStrings v1.13.0 [4607b0f0] + SuiteSparse [fa267f1f] + TOML v1.0.3 [a4e569a6] + Tar v1.10.0 [8dfed614] + Test v1.11.0 [cf7118a7] + UUIDs v1.11.0 [4ec0a83e] + Unicode v1.11.0 [e66e0078] + CompilerSupportLibraries_jll v1.5.7+0 [deac9b47] + LibCURL_jll v8.22.0+0 [e37daf67] + LibGit2_jll v1.9.7+0 [29816b5a] + LibSSH2_jll v1.11.104+0 [14a3606d] + MozillaCACerts_jll v2026.8.13 [4536629a] + OpenBLAS_jll v0.3.34+0 [05823500] + OpenLibm_jll v0.8.8+0 [458c3c95] + OpenSSL_jll v3.5.8+0 [efcefdf7] + PCRE2_jll v10.48.0+0 [bea87d4a] + SuiteSparse_jll v7.10.1+0 [83775a58] + Zlib_jll v1.3.2+0 [3161d3a3] + Zstd_jll v1.5.7+1 [8e850b90] + libblastrampoline_jll v5.15.0+0 [8e850ede] + nghttp2_jll v1.70.0+0 [3f19e933] + p7zip_jll v17.8.2+0 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. To see why use `status --outdated -m` Installation completed after 5.31s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompiling project... 5.2 s ✓ BGEN 6.4 s ✓ VCFTools 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`. 21.3 s ✓ MendelIHT 3 dependencies successfully precompiled in 34 seconds. 173 already precompiled. 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 53.26s ################################################################################ # Testing # Testing MendelIHT Status `/tmp/jl_kmTGFk/Project.toml` ⌅ [6db4b851] BGEN v0.1.17 [6e4b80f9] BenchmarkTools v1.8.0 [336ed68f] CSV v0.10.17 [a93c6f00] DataFrames v1.8.2 [8bb1440f] DelimitedFiles v1.9.1 [b4f34e82] Distances v0.10.12 [31c24e10] Distributions v0.25.131 [38e38edf] GLM v1.9.5 [921c7187] MendelIHT v1.4.11 [92933f4c] ProgressMeter v1.11.0 [189a3867] Reexport v1.2.2 [4e780e97] SnpArrays v0.3.23 [276daf66] SpecialFunctions v2.9.0 [2913bbd2] StatsBase v0.34.13 [a620830f] VCFTools v0.2.10 [37e2e46d] LinearAlgebra v1.14.0 [44cfe95a] Pkg v1.14.0 [9a3f8284] Random v1.11.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_kmTGFk/Manifest.toml` [7d9f7c33] Accessors v0.1.45 [79e6a3ab] Adapt v4.7.0 [66dad0bd] AliasTables v1.1.3 [4fba245c] ArrayInterface v7.30.1 [67c07d97] Automa v1.2.0 ⌅ [6db4b851] BGEN v0.1.17 [28d598bf] BGZFStreams v0.3.2 [6e4b80f9] BenchmarkTools v1.8.0 [47718e42] BioGenerics v0.1.5 [62783981] BitTwiddlingConvenienceFunctions v0.1.6 [e1450e63] BufferedStreams v1.2.2 [2a0fbf3d] CPUSummary v0.2.7 [336ed68f] CSV v0.10.17 [fb6a15b2] CloseOpenIntervals v0.1.13 [523fee87] CodecBzip2 v0.8.5 [ba30903b] CodecXz v0.7.4 [944b1d66] CodecZlib v0.7.9 [6b39b394] CodecZstd v0.8.7 [861a8166] Combinatorics v1.1.0 [38540f10] CommonSolve v0.2.14 [f70d9fcc] CommonWorldInvalidations v1.2.2 [34da2185] Compat v4.18.1 [a33af91c] CompositionsBase v0.1.2 [187b0558] ConstructionBase v1.6.0 [adafc99b] CpuId v0.3.1 [a8cc5b0e] Crayons v4.2.0 [a10d1c49] DBInterface v2.7.0 [9a962f9c] DataAPI v1.16.0 [a93c6f00] DataFrames v1.8.2 [864edb3b] DataStructures v0.19.6 [e2d170a0] DataValueInterfaces v1.0.0 [8bb1440f] DelimitedFiles v1.9.1 [b4f34e82] Distances v0.10.12 [31c24e10] Distributions v0.25.131 [ffbed154] DocStringExtensions v0.9.5 [48062228] FilePathsBase v0.9.24 [1a297f60] FillArrays v1.17.0 [38e38edf] GLM v1.9.5 [a0844989] Gamma v1.2.0 [c27321d9] Glob v1.5.0 [3e5b6fbb] HostCPUFeatures v0.1.18 [34004b35] HypergeometricFunctions v0.3.30 ⌅ [09f84164] HypothesisTests v0.11.8 [615f187c] IfElse v0.1.1 ⌅ [842dd82b] InlineStrings v1.4.6 [3587e190] InverseFunctions v0.1.17 [41ab1584] InvertedIndices v1.3.1 [92d709cd] IrrationalConstants v0.2.6 [82899510] IteratorInterfaceExtensions v1.0.0 [692b3bcd] JLLWrappers v1.8.0 [682c06a0] JSON v1.8.0 [b964fa9f] LaTeXStrings v1.4.1 [10f19ff3] LayoutPointers v0.1.17 [2ab3a3ac] LogExpFunctions v1.0.1 [bdcacae8] LoopVectorization v0.12.174 [1914dd2f] MacroTools v0.5.16 [d125e4d3] ManualMemory v0.1.8 [921c7187] MendelIHT v1.4.11 [e1d29d7a] Missings v1.2.0 [6fe1bfb0] OffsetArrays v1.17.0 [bac558e1] OrderedCollections v2.0.1 [90014a1f] PDMats v0.11.41 ⌅ [69de0a69] Parsers v2.8.8 [1d0040c9] PolyesterWeave v0.2.2 [2dfb63ee] PooledArrays v1.4.3 [aea7be01] PrecompileTools v1.3.4 [21216c6a] Preferences v1.5.2 [08abe8d2] PrettyTables v3.4.8 [92933f4c] ProgressMeter v1.11.0 [43287f4e] PtrArrays v1.4.0 [1fd47b50] QuadGK v2.11.3 [189a3867] Reexport v1.2.2 [ae029012] Requires v1.3.1 [79098fc4] Rmath v0.9.0 [f2b01f46] Roots v3.0.8 [fdea26ae] SIMD v3.7.2 [94e857df] SIMDTypes v0.1.0 [476501e8] SLEEFPirates v0.6.46 [0aa819cd] SQLite v1.8.2 [431bcebd] SciMLPublic v1.3.0 [91c51154] SentinelArrays v1.4.10 [1277b4bf] ShiftedArrays v2.0.0 [4e780e97] SnpArrays v0.3.23 [a2af1166] SortingAlgorithms v1.2.3 [276daf66] SpecialFunctions v2.9.0 [aedffcd0] Static v1.4.6 [0d7ed370] StaticArrayInterface v1.10.0 [10745b16] Statistics v1.11.5 [82ae8749] StatsAPI v1.8.0 [2913bbd2] StatsBase v0.34.13 [4c63d2b9] StatsFuns v2.2.1 [3eaba693] StatsModels v0.7.10 ⌅ [892a3eda] StringManipulation v0.5.0 [ec057cc2] StructUtils v2.8.5 [3783bdb8] TableTraits v1.0.1 [bd369af6] Tables v1.14.0 [8290d209] ThreadingUtilities v0.5.6 ⌅ [3bb67fe8] TranscodingStreams v0.9.13 [3a884ed6] UnPack v1.0.2 [a620830f] VCFTools v0.2.10 [28eba6e3] VariantCallFormat v0.5.9 [3d5dd08c] VectorizationBase v0.21.74 [ea10d353] WeakRefStrings v1.4.3 [76eceee3] WorkerUtilities v1.6.1 [6e34b625] Bzip2_jll v1.0.9+0 [efe28fd5] OpenSpecFun_jll v0.5.6+0 [f50d1b31] Rmath_jll v0.5.2+0 [76ed43ae] SQLite_jll v3.53.2+0 [ffd25f8a] XZ_jll v5.8.3+0 [c4b69c83] dlfcn_win32_jll v1.4.2+0 [0dad84c5] ArgTools v1.2.0 [56f22d72] Artifacts v1.11.0 [2a0f44e3] Base64 v1.11.0 [ade2ca70] Dates v1.11.0 [8ba89e20] Distributed v1.12.0 [f43a241f] Downloads v1.7.0 [7b1f6079] FileWatching v1.11.0 [9fa8497b] Future v1.11.0 [b77e0a4c] InteractiveUtils v1.11.0 [ac6e5ff7] JuliaSyntaxHighlighting v1.13.0 [b27032c2] LibCURL v1.0.0 [76f85450] LibGit2 v1.11.0 [8f399da3] Libdl v1.11.0 [37e2e46d] LinearAlgebra v1.14.0 [56ddb016] Logging v1.11.0 [d6f4376e] Markdown v1.11.0 [a63ad114] Mmap v1.11.0 [ca575930] NetworkOptions v1.3.0 [44cfe95a] Pkg v1.14.0 [de0858da] Printf v1.11.0 [9abbd945] Profile v1.11.0 [3fa0cd96] REPL v1.11.0 [9a3f8284] Random v1.11.0 [ea8e919c] SHA v1.13.0 [9e88b42a] Serialization v1.11.0 [6462fe0b] Sockets v1.11.0 [2f01184e] SparseArrays v1.13.0 [f489334b] StyledStrings v1.13.0 [4607b0f0] SuiteSparse [fa267f1f] TOML v1.0.3 [a4e569a6] Tar v1.10.0 [8dfed614] Test v1.11.0 [cf7118a7] UUIDs v1.11.0 [4ec0a83e] Unicode v1.11.0 [e66e0078] CompilerSupportLibraries_jll v1.5.7+0 [deac9b47] LibCURL_jll v8.22.0+0 [e37daf67] LibGit2_jll v1.9.7+0 [29816b5a] LibSSH2_jll v1.11.104+0 [14a3606d] MozillaCACerts_jll v2026.8.13 [4536629a] OpenBLAS_jll v0.3.34+0 [05823500] OpenLibm_jll v0.8.8+0 [458c3c95] OpenSSL_jll v3.5.8+0 [efcefdf7] PCRE2_jll v10.48.0+0 [bea87d4a] SuiteSparse_jll v7.10.1+0 [83775a58] Zlib_jll v1.3.2+0 [3161d3a3] Zstd_jll v1.5.7+1 [8e850b90] libblastrampoline_jll v5.15.0+0 [8e850ede] nghttp2_jll v1.70.0+0 [3f19e933] p7zip_jll v17.8.2+0 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. Testing Running tests... ┌ Warning: accessing `Type.name` is deprecated without replacement. If for detection, use `Base.isType(x)`. │ caller = Distributions.MvNormal(σ::Vector{Float64}) at mvnormal.jl:207 └ @ Distributions ~/.julia/packages/Distributions/RTt4y/src/multivariate/mvnormal.jl:207 ┌ Warning: `MvNormal(σ::AbstractVector{<:Real})` is deprecated, use `MvNormal(LinearAlgebra.Diagonal(map(abs2, σ)))` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `cholesky!(A::RealHermSymComplexHerm{<:Real}, ::Val{true}; kwargs...)` is deprecated, use `cholesky!(A, RowMaximum(); kwargs...)` instead. │ caller = iht_stepsize!(v::MendelIHT.mIHTVariable{Float64, LinearAlgebra.Transpose{Float64, SnpArrays.SnpLinAlg{Float64}}}) at multivariate.jl:241 └ @ MendelIHT ~/.julia/packages/MendelIHT/ZcxZT/src/multivariate.jl:241 Test Summary: | Pass Total Time loglikelihood | 4 4 12.4s Test Summary: | Pass Total Time deviance | 1 1 0.3s Test Summary: | Pass Total Time update_μ! | 4 4 1.3s Test Summary: | Pass Total Time _choose! | 7 7 7.2s Test Summary: | Pass Total Time _iht_backtrack | 7 7 0.0s Test Summary: | Pass Total Time standardize! | 12 12 1.0s Test Summary: | Pass Total Time project_k! | 2 2 1.2s Test Summary: | Pass Total Time project_group_sparse! | 5 5 1.1s Test Summary: | Pass Total Time maf_weights | 6 6 1.9s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse linear regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1502.1643204858658, backtracks = 0, tol = 0.9589920436377886 Iteration 2: loglikelihood = -1402.5879607698023, backtracks = 0, tol = 0.11693999089475798 Iteration 3: loglikelihood = -1395.1441893080257, backtracks = 0, tol = 0.06001890274089784 Iteration 4: loglikelihood = -1393.6630362803203, backtracks = 0, tol = 0.05249110330204436 Iteration 5: loglikelihood = -1393.3165245420962, backtracks = 0, tol = 0.007736181461229842 Iteration 6: loglikelihood = -1392.9918015179705, backtracks = 0, tol = 0.05146101195314806 Iteration 7: loglikelihood = -1392.9003987777207, backtracks = 0, tol = 0.0033892201582335657 Iteration 8: loglikelihood = -1392.899083965668, backtracks = 0, tol = 0.0004148329952196032 Iteration 9: loglikelihood = -1392.8990559157244, backtracks = 0, tol = 5.54031437067904e-5 IHT estimated 10 nonzero SNP predictors and 1 non-genetic predictors. Compute time (sec): 0.07965087890625 Final loglikelihood: -1392.8990559157244 SNP PVE: 0.7779149474758742 Iterations: 9 Selected genetic predictors: 10×2 DataFrame Row │ Position Estimated_β │ Int64 Float64 ─────┼─────────────────────── 1 │ 1812 -1.06352 2 │ 2394 0.23535 3 │ 2508 0.662978 4 │ 4370 0.106829 5 │ 7210 -0.381722 6 │ 7559 0.117039 7 │ 7946 0.924232 8 │ 8655 -0.634532 9 │ 9151 0.523048 10 │ 9332 0.262909 Selected nongenetic predictors: 1×2 DataFrame Row │ Position Estimated_β │ Int64 Float64 ─────┼─────────────────────── 1 │ 1 -0.0144878Test Summary: | Pass Total Time fit normal SnpLinAlg | 4 4 23.2s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse 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 3.7s **** 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 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 = -1484.3412358635196, backtracks = 0, tol = 0.42745893680377206 Iteration 2: loglikelihood = -1299.3853265258006, backtracks = 0, tol = 0.07909225466068746 Iteration 3: loglikelihood = -1262.7648197070919, backtracks = 0, tol = 0.05784522696445497 Iteration 4: loglikelihood = -1258.6031286144384, backtracks = 0, tol = 0.022885318975868544 Iteration 5: loglikelihood = -1248.1888295460249, backtracks = 0, tol = 0.07154278112919928 Iteration 6: loglikelihood = -1245.8460406354066, backtracks = 0, tol = 0.08915855041827919 Iteration 7: loglikelihood = -1244.4558192295715, backtracks = 0, tol = 0.0825101062649035 Iteration 8: loglikelihood = -1243.97707056958, backtracks = 0, tol = 0.009613604802687279 Iteration 9: loglikelihood = -1243.8907799370415, backtracks = 0, tol = 0.0042786881045777025 Iteration 10: loglikelihood = -1243.8525768214581, backtracks = 0, tol = 0.0035764161403260882 Iteration 11: loglikelihood = -1243.8349139903928, backtracks = 0, tol = 0.0020871117650836093 Iteration 12: loglikelihood = -1243.8258302116442, backtracks = 0, tol = 0.001699476526218604 Iteration 13: loglikelihood = -1243.8211551228721, backtracks = 0, tol = 0.0011009106345818932 Iteration 14: loglikelihood = -1243.818607813428, backtracks = 0, tol = 0.0008825546094802867 Iteration 15: loglikelihood = -1243.8172177828928, backtracks = 0, tol = 0.0006138072025669208 Iteration 16: loglikelihood = -1243.8164324413178, backtracks = 0, tol = 0.0005526602019921307 Iteration 17: loglikelihood = -1243.8159879968798, backtracks = 0, tol = 0.00035226150799146837 Iteration 18: loglikelihood = -1243.8157310827175, backtracks = 0, tol = 0.0003481751229464698 Iteration 19: loglikelihood = -1243.8155823969123, backtracks = 0, tol = 0.00020586453282198504 Iteration 20: loglikelihood = -1243.815495262699, backtracks = 0, tol = 0.0002149888492499333 Iteration 21: loglikelihood = -1243.8154441688666, backtracks = 0, tol = 0.0001215359511060445 Iteration 22: loglikelihood = -1243.8154139948979, backtracks = 0, tol = 0.00013107672294901423 Iteration 23: loglikelihood = -1243.8153961716173, backtracks = 0, tol = 7.21297868735794e-5 Test Summary: | Pass Total Time fit Poisson SnpLinAlg | 4 4 2.2s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse 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 = -1374.608876464765, backtracks = 0, tol = 0.37873357818498365 Iteration 2: loglikelihood = -1351.6422853529994, backtracks = 0, tol = 0.08983574664654893 Iteration 3: loglikelihood = -1341.931649887667, backtracks = 0, tol = 0.07964705105460537 Iteration 4: loglikelihood = -1340.206955963839, backtracks = 0, tol = 0.0999988364346257 Iteration 5: loglikelihood = -1339.4588538063254, backtracks = 0, tol = 0.02440731297773652 Iteration 6: loglikelihood = -1339.4051440922542, backtracks = 1, tol = 0.00493982930977389 Iteration 7: loglikelihood = -1339.3900128093646, backtracks = 1, tol = 0.0025917001890380046 Iteration 8: loglikelihood = -1339.3859539159287, backtracks = 1, tol = 0.0013248209608427179 Iteration 9: loglikelihood = -1339.3848833543016, backtracks = 1, tol = 0.0006807544138110446 Iteration 10: loglikelihood = -1339.3846026608846, backtracks = 1, tol = 0.000348644267061181 Iteration 11: loglikelihood = -1339.3845293653483, backtracks = 1, tol = 0.00017837639407844468 Iteration 12: loglikelihood = -1339.3845102779242, backtracks = 1, tol = 9.108123895122676e-5 Test Summary: | Pass Total Time fit NegativeBinomial SnpLinAlg | 4 4 1.1s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse linear regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 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 = -1840.616602962211, backtracks = 0, tol = 0.8224174645636793 Iteration 2: loglikelihood = -1450.1804444019538, backtracks = 0, tol = 0.1524040820369703 Iteration 3: loglikelihood = -1392.6964761573515, backtracks = 0, tol = 0.04561218304787145 Iteration 4: loglikelihood = -1389.2211434513517, backtracks = 0, tol = 0.030110500141393142 Iteration 5: loglikelihood = -1388.4982998237435, backtracks = 0, tol = 0.02538885353147593 Iteration 6: loglikelihood = -1388.4131013022206, backtracks = 1, tol = 0.000913248385359093 Iteration 7: loglikelihood = -1388.3911332940743, backtracks = 1, tol = 0.00046965019431938237 Iteration 8: loglikelihood = -1388.385508131747, backtracks = 1, tol = 0.0002375211358875265 Iteration 9: loglikelihood = -1388.3840773098639, backtracks = 1, tol = 0.00011860415454147572 Iteration 10: loglikelihood = -1388.3837153321645, backtracks = 1, tol = 5.873655853000916e-5 Test Summary: | Pass Total Time fit with >1 non-genetic covariates SnpLinAlg | 5 5 1.6s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse linear regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1745.2212239242929, backtracks = 0, tol = 0.7517436270776945 Iteration 2: loglikelihood = -1455.3781940591143, backtracks = 0, tol = 0.1384202427224909 Iteration 3: loglikelihood = -1393.1174463091593, backtracks = 0, tol = 0.042258297530054195 Iteration 4: loglikelihood = -1388.8757249567714, backtracks = 0, tol = 0.03018822873984506 Iteration 5: loglikelihood = -1388.7182287461294, backtracks = 0, tol = 0.002219554301058312 Iteration 6: loglikelihood = -1388.7158129881284, backtracks = 0, tol = 0.00038439726190120295 Iteration 7: loglikelihood = -1388.7157633906945, backtracks = 0, tol = 3.879525426191157e-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 = -1473.1241001452804, backtracks = 0, tol = 0.11162633196865432 Iteration 2: loglikelihood = -1448.37403799896, backtracks = 0, tol = 0.07736217654955346 Iteration 3: loglikelihood = -1429.8981769610311, backtracks = 1, tol = 0.056531823476744666 Iteration 4: loglikelihood = -1404.7133956159753, backtracks = 0, tol = 0.10125409614175712 Iteration 5: loglikelihood = -1397.466171579031, backtracks = 0, tol = 0.05343369325195713 Iteration 6: loglikelihood = -1395.7490747391416, backtracks = 0, tol = 0.08843871418165582 Iteration 7: loglikelihood = -1395.4877576477586, backtracks = 0, tol = 0.008924704068495177 Iteration 8: loglikelihood = -1395.442237061722, backtracks = 0, tol = 0.005277867116132827 Iteration 9: loglikelihood = -1395.4302205892106, backtracks = 0, tol = 0.0027680467744013336 Iteration 10: loglikelihood = -1395.1973617039412, backtracks = 0, tol = 0.09056900655606137 Iteration 11: loglikelihood = -1395.0048067729406, backtracks = 0, tol = 0.007650485819168892 Iteration 12: loglikelihood = -1394.9835209063683, backtracks = 0, tol = 0.0035232591741737973 Iteration 13: loglikelihood = -1394.9793628241396, backtracks = 0, tol = 0.001852195878065177 Iteration 14: loglikelihood = -1394.9779889816232, backtracks = 0, tol = 0.0012530451800711446 Iteration 15: loglikelihood = -1394.977503420045, backtracks = 0, tol = 0.0006829444661300694 Iteration 16: loglikelihood = -1394.9773714862843, backtracks = 1, tol = 0.00022881022816864148 Iteration 17: loglikelihood = -1394.9773102201912, backtracks = 2, tol = 0.0001217788197399568 Iteration 18: loglikelihood = -1394.977273607278, backtracks = 2, tol = 8.822469907087602e-5 **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse linear regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 3 Prior weight scaling = off Doubly sparse projection = on Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1535.4672180567934, backtracks = 0, tol = 0.17016419679985048 Iteration 2: loglikelihood = -1508.04343741211, backtracks = 0, tol = 0.21718489399873087 Iteration 3: loglikelihood = -1448.2717322168082, backtracks = 0, tol = 0.15334504607402907 Iteration 4: loglikelihood = -1437.5669418734744, backtracks = 0, tol = 0.08425396177776269 Iteration 5: loglikelihood = -1434.3602241747526, backtracks = 0, tol = 0.03199716666887782 Iteration 6: loglikelihood = -1434.239273652971, backtracks = 2, tol = 0.003498168340088284 Iteration 7: loglikelihood = -1434.1475478538455, backtracks = 2, tol = 0.003052291101552644 Iteration 8: loglikelihood = -1434.0913475157126, backtracks = 2, tol = 0.002193157681835551 Iteration 9: loglikelihood = -1434.0584761985995, backtracks = 2, tol = 0.0016688209654910676 Iteration 10: loglikelihood = -1434.0393127719108, backtracks = 2, tol = 0.001317554485128468 Iteration 11: loglikelihood = -1434.0281644425422, backtracks = 2, tol = 0.0010393713220469133 Iteration 12: loglikelihood = -1434.0216963632631, backtracks = 2, tol = 0.0008158673348111326 Iteration 13: loglikelihood = -1434.0179556115856, backtracks = 2, tol = 0.0006363671566384205 Iteration 14: loglikelihood = -1433.8972844529703, backtracks = 2, tol = 0.021056460842673336 Iteration 15: loglikelihood = -1433.6170929347984, backtracks = 1, tol = 0.011448126839540959 Iteration 16: loglikelihood = -1433.5408744767517, backtracks = 2, tol = 0.0040324300639331045 Iteration 17: loglikelihood = -1433.4945867179188, backtracks = 2, tol = 0.003005268578298657 Iteration 18: loglikelihood = -1433.467626121943, backtracks = 2, tol = 0.002187229771831415 Iteration 19: loglikelihood = -1433.4521439235273, backtracks = 2, tol = 0.0016467936133078437 Iteration 20: loglikelihood = -1433.4432822302874, backtracks = 2, tol = 0.0012631945762950846 Iteration 21: loglikelihood = -1433.4382075829426, backtracks = 2, tol = 0.0009580287583338233 Iteration 22: loglikelihood = -1433.4352962137846, backtracks = 2, tol = 0.0007222437442123496 Iteration 23: loglikelihood = -1433.4336216439426, backtracks = 2, tol = 0.0005424739396431646 Iteration 24: loglikelihood = -1433.43265547142, backtracks = 2, tol = 0.0004062814588068666 Iteration 25: loglikelihood = -1433.4320960523787, backtracks = 2, tol = 0.00030341799187724174 Iteration 26: loglikelihood = -1433.4317709097872, backtracks = 2, tol = 0.00022583740291083832 Iteration 27: loglikelihood = -1433.4315812027676, backtracks = 2, tol = 0.0001673653861249394 Iteration 28: loglikelihood = -1432.5898379532828, backtracks = 2, tol = 0.0250802150540324 Iteration 29: loglikelihood = -1431.7678006470733, backtracks = 1, tol = 0.017181190475547 Iteration 30: loglikelihood = -1430.3157393955933, backtracks = 1, tol = 0.07333968264200223 Iteration 31: loglikelihood = -1429.706868513855, backtracks = 0, tol = 0.02001511172794573 Iteration 32: loglikelihood = -1429.5802551945537, backtracks = 1, tol = 0.00756937670420323 Iteration 33: loglikelihood = -1429.513945055356, backtracks = 2, tol = 0.003906515984506249 Iteration 34: loglikelihood = -1429.469197232521, backtracks = 2, tol = 0.003683664863256532 Iteration 35: loglikelihood = -1428.86075262229, backtracks = 2, tol = 0.08711763846658718 Iteration 36: loglikelihood = -1428.6178427111051, backtracks = 1, tol = 0.006558345246943248 Iteration 37: loglikelihood = -1428.5424083746184, backtracks = 2, tol = 0.0033912200662443866 Iteration 38: loglikelihood = -1428.4933608487952, backtracks = 2, tol = 0.0030098214824111564 Iteration 39: loglikelihood = -1428.4620745885084, backtracks = 2, tol = 0.002595137111913267 Iteration 40: loglikelihood = -1428.4427329028306, backtracks = 2, tol = 0.002148184701148499 Iteration 41: loglikelihood = -1428.4311433050725, backtracks = 2, tol = 0.0017160493175770867 Iteration 42: loglikelihood = -1428.4243474878394, backtracks = 2, tol = 0.0013407892924840858 Iteration 43: loglikelihood = -1428.420413936832, backtracks = 2, tol = 0.0010343694042998762 Iteration 44: loglikelihood = -1428.4181556141764, backtracks = 2, tol = 0.0007948565534422845 Iteration 45: loglikelihood = -1428.4168664091337, backtracks = 2, tol = 0.000608309643427293 Iteration 46: loglikelihood = -1428.4161334920516, backtracks = 2, tol = 0.0004622621654004415 Iteration 47: loglikelihood = -1428.4157180925672, backtracks = 2, tol = 0.00034956951660976293 Iteration 48: loglikelihood = -1428.4154831711999, backtracks = 2, tol = 0.00026348047442121094 Iteration 49: loglikelihood = -1428.415350523391, backtracks = 2, tol = 0.00019816133989405092 Iteration 50: loglikelihood = -1428.4152757065372, backtracks = 2, tol = 0.00014882628973649723 Iteration 51: loglikelihood = -1428.4152335404317, backtracks = 2, tol = 0.00011167501044822909 Iteration 52: loglikelihood = -1428.4152097888611, backtracks = 2, tol = 8.375238803842589e-5 Test Summary: | Pass Total Time Correlated predictors and double sparsity Float64 matrix | 2 2 8.0s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse 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 = -1521.7049649089258, backtracks = 0, tol = 0.19103184291298617 Iteration 2: loglikelihood = -1452.3000973975265, backtracks = 0, tol = 0.0983547913906988 Iteration 3: loglikelihood = -1405.1336757006416, backtracks = 0, tol = 0.13375043563528483 Iteration 4: loglikelihood = -1381.0391528184516, backtracks = 0, tol = 0.04688946191973199 Iteration 5: loglikelihood = -1351.5379362626124, backtracks = 1, tol = 0.05384952112251694 Iteration 6: loglikelihood = -1344.9335360232192, backtracks = 1, tol = 0.021778443852180116 Iteration 7: loglikelihood = -1342.1860860812697, backtracks = 2, tol = 0.0143071196404827 Iteration 8: loglikelihood = -1335.197747292335, backtracks = 2, tol = 0.045182630758872584 Iteration 9: loglikelihood = -1327.9478868801498, backtracks = 0, tol = 0.05514148692510442 Iteration 10: loglikelihood = -1326.3563990570033, backtracks = 0, tol = 0.01744130554099187 Iteration 11: loglikelihood = -1324.544808928848, backtracks = 0, tol = 0.05414201657996152 Iteration 12: loglikelihood = -1324.067991878226, backtracks = 0, tol = 0.008932949439014926 Iteration 13: loglikelihood = -1323.926883697193, backtracks = 0, tol = 0.004565384180464308 Iteration 14: loglikelihood = -1323.8579650150416, backtracks = 0, tol = 0.004706482490995183 Iteration 15: loglikelihood = -1323.8212723757365, backtracks = 0, tol = 0.0022091197543407186 Iteration 16: loglikelihood = -1323.8013802099267, backtracks = 0, tol = 0.0025245226423488104 Iteration 17: loglikelihood = -1323.7904281512192, backtracks = 0, tol = 0.0012806933856678415 Iteration 18: loglikelihood = -1323.7843932155229, backtracks = 0, tol = 0.001377729370755343 Iteration 19: loglikelihood = -1323.7810507320924, backtracks = 0, tol = 0.0007271908769486632 Iteration 20: loglikelihood = -1323.7792007088603, backtracks = 0, tol = 0.000758367566057291 Iteration 21: loglikelihood = -1323.7781744627048, backtracks = 0, tol = 0.0004079971250048963 Iteration 22: loglikelihood = -1323.7776054741248, backtracks = 0, tol = 0.00041929640064190983 Iteration 23: loglikelihood = -1323.7772896635904, backtracks = 0, tol = 0.00022762290684381385 Iteration 24: loglikelihood = -1323.7771144235192, backtracks = 0, tol = 0.00023236659670292288 Iteration 25: loglikelihood = -1323.7770171320435, backtracks = 0, tol = 0.00012665616138521417 Iteration 26: loglikelihood = -1323.7769631224076, backtracks = 0, tol = 0.00012893254934533412 Iteration 27: loglikelihood = -1323.7769331321872, backtracks = 0, tol = 7.038927775216516e-5 1.249652 seconds (4.07 M allocations: 73.951 MiB, 6.36% gc time, 48.48% 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 = -1559.4374979301365, backtracks = 0, tol = 0.19103184291298617 Iteration 2: loglikelihood = -1513.1989571728884, backtracks = 0, tol = 0.1233547054281014 Iteration 3: loglikelihood = -1481.1377950066303, backtracks = 0, tol = 0.13527655633168 Iteration 4: loglikelihood = -1452.5092358436252, backtracks = 0, tol = 0.08181456552517381 Iteration 5: loglikelihood = -1432.8789216856035, backtracks = 0, tol = 0.05651394112843964 Iteration 6: loglikelihood = -1412.0829575886964, backtracks = 0, tol = 0.06301828539916282 Iteration 7: loglikelihood = -1404.3903775596802, backtracks = 0, tol = 0.06291938599242065 Iteration 8: loglikelihood = -1393.70880380776, backtracks = 0, tol = 0.0578238080495508 Iteration 9: loglikelihood = -1386.0582250863074, backtracks = 0, tol = 0.06385869123064886 Iteration 10: loglikelihood = -1376.245472446153, backtracks = 1, tol = 0.004147077974627478 Iteration 11: loglikelihood = -1369.7216560389234, backtracks = 1, tol = 0.003329444619583966 Iteration 12: loglikelihood = -1364.885475927212, backtracks = 1, tol = 0.0024841006501738795 Iteration 13: loglikelihood = -1361.1481893381042, backtracks = 1, tol = 0.001436755358054263 Iteration 14: loglikelihood = -1357.7818464855677, backtracks = 1, tol = 0.0007339637926329995 Iteration 15: loglikelihood = -1354.439929815369, backtracks = 1, tol = 0.0003862151324363641 Iteration 16: loglikelihood = -1354.1296840895734, backtracks = 0, tol = 0.067618563729358 Iteration 17: loglikelihood = -1349.5948907120876, backtracks = 0, tol = 0.06758447550969288 Iteration 18: loglikelihood = -1348.119969058364, backtracks = 0, tol = 0.004070200884703302 Iteration 19: loglikelihood = -1346.7540583585937, backtracks = 0, tol = 0.0019103067417000205 Iteration 20: loglikelihood = -1345.5582358545435, backtracks = 0, tol = 0.0006927979187821956 Iteration 21: loglikelihood = -1344.4404543890314, backtracks = 0, tol = 0.0004291150848757398 Iteration 22: loglikelihood = -1343.4182803997778, backtracks = 0, tol = 0.00027352223004073456 Iteration 23: loglikelihood = -1342.4672620658007, backtracks = 0, tol = 0.0001642967226331957 Iteration 24: loglikelihood = -1341.590240517645, backtracks = 0, tol = 0.00018555461950805113 Iteration 25: loglikelihood = -1340.7729871967322, backtracks = 0, tol = 0.00010752838710879775 Iteration 26: loglikelihood = -1340.015083931907, backtracks = 0, tol = 0.00015099284261096288 Iteration 27: loglikelihood = -1339.306660864452, backtracks = 0, tol = 0.00010224109225303816 Iteration 28: loglikelihood = -1338.646593597804, backtracks = 0, tol = 0.00013097042656918547 Iteration 29: loglikelihood = -1338.4273803743279, backtracks = 0, tol = 0.056453796659668744 Iteration 30: loglikelihood = -1337.8652261696434, backtracks = 0, tol = 0.004511155702888668 Iteration 31: loglikelihood = -1337.3289802198613, backtracks = 0, tol = 0.0017535335178109626 Iteration 32: loglikelihood = -1336.8592806411248, backtracks = 0, tol = 0.001174666161243459 Iteration 33: loglikelihood = -1336.3904282678727, backtracks = 0, tol = 0.0007600561185333877 Iteration 34: loglikelihood = -1335.9585728401992, backtracks = 0, tol = 0.0003863365772850979 Iteration 35: loglikelihood = -1335.5391738457706, backtracks = 0, tol = 0.00035050031993828746 Iteration 36: loglikelihood = -1335.1469401050354, backtracks = 0, tol = 0.00016813226352716898 Iteration 37: loglikelihood = -1334.5076482449501, backtracks = 0, tol = 0.05678503611136772 Iteration 38: loglikelihood = -1333.9859279370764, backtracks = 0, tol = 0.004238815998797936 Iteration 39: loglikelihood = -1333.6220241593319, backtracks = 0, tol = 0.0017166172762632314 Iteration 40: loglikelihood = -1333.257959535669, backtracks = 0, tol = 0.0011184383562994303 Iteration 41: loglikelihood = -1332.9382579505734, backtracks = 0, tol = 0.0007736486401626245 Iteration 42: loglikelihood = -1332.624772168061, backtracks = 0, tol = 0.000409740600648843 Iteration 43: loglikelihood = -1332.3367049194155, backtracks = 0, tol = 0.0003358426924115387 Iteration 44: loglikelihood = -1332.0578980267333, backtracks = 0, tol = 0.00017041915515584262 Iteration 45: loglikelihood = -1331.7962813059382, backtracks = 0, tol = 0.00014540168150448885 Iteration 46: loglikelihood = -1331.5443650578904, backtracks = 0, tol = 8.748223878306228e-5 0.529181 seconds (1.80 M allocations: 32.663 MiB, 15.45% gc time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse NegativeBinomial regression Number of threads = 1 Link functin = LogLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -3688.5784, backtracks = 0, tol = 0.08991984465525915 Iteration 2: loglikelihood = -3646.773, backtracks = 0, tol = 0.04368573308663559 Iteration 3: loglikelihood = -3642.6853, backtracks = 1, tol = 0.012030094827939864 Iteration 4: loglikelihood = -3641.541, backtracks = 1, tol = 0.007063990826795202 Iteration 5: loglikelihood = -3641.2375, backtracks = 1, tol = 0.0036049636862996574 Iteration 6: loglikelihood = -3631.8481, backtracks = 1, tol = 0.06786230046796343 Iteration 7: loglikelihood = -3619.6914, backtracks = 0, tol = 0.07466572769478412 Iteration 8: loglikelihood = -3617.4502, backtracks = 1, tol = 0.00834999662706185 Iteration 9: loglikelihood = -3616.7417, backtracks = 1, tol = 0.004765261591218497 Iteration 10: loglikelihood = -3616.5278, backtracks = 1, tol = 0.0024556889347032095 Iteration 11: loglikelihood = -3616.4688, backtracks = 1, tol = 0.0015329781013500193 Iteration 12: loglikelihood = -3616.452, backtracks = 1, tol = 0.0008467285419505666 Iteration 13: loglikelihood = -3616.452, backtracks = 1, tol = 0.00043575904562499095 Iteration 14: loglikelihood = -3616.4502, backtracks = 1, tol = 0.00022060677897356968 Iteration 15: loglikelihood = -3616.45, backtracks = 1, tol = 0.00011074786458846833 Iteration 16: loglikelihood = -3616.4504, backtracks = 3, tol = 1.389403768186273e-5 20.354762 seconds (16.45 M allocations: 717.165 MiB, 1.27% gc time, 96.75% 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 **** 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 = -3579.558, backtracks = 0, tol = 0.08991984465525915 Iteration 2: loglikelihood = -3465.265, backtracks = 0, tol = 0.04483300093125789 Iteration 3: loglikelihood = -3251.037, backtracks = 1, tol = 0.011472661160382534 Iteration 4: loglikelihood = -3018.0862, backtracks = 1, tol = 0.006250106002610148 Iteration 5: loglikelihood = -2776.7158, backtracks = 1, tol = 0.002728193466331798 Iteration 6: loglikelihood = -2668.179, backtracks = 0, tol = 0.08294399718159884 Iteration 7: loglikelihood = -2536.5796, backtracks = 0, tol = 0.08068702448785534 Iteration 8: loglikelihood = -2440.0225, backtracks = 0, tol = 0.07566272271999284 Iteration 9: loglikelihood = -2366.3342, backtracks = 0, tol = 0.07526159549043647 Iteration 10: loglikelihood = -2318.14, backtracks = 0, tol = 0.09489123730208986 Iteration 11: loglikelihood = -2271.1113, backtracks = 0, tol = 0.10702623435232868 Iteration 12: loglikelihood = -2238.522, backtracks = 0, tol = 0.09021078844858717 Iteration 13: loglikelihood = -2220.9924, backtracks = 0, tol = 0.07818016247402933 Iteration 14: loglikelihood = -2212.2695, backtracks = 0, tol = 0.07882304305113763 Iteration 15: loglikelihood = -2206.7144, backtracks = 0, tol = 0.0785015589648936 Iteration 16: loglikelihood = -2204.7292, backtracks = 0, tol = 0.08050885869806718 Iteration 17: loglikelihood = -2202.5825, backtracks = 0, tol = 0.08003760258661417 Iteration 18: loglikelihood = -2201.1125, backtracks = 1, tol = 0.0053537635403291635 Iteration 19: loglikelihood = -2200.776, backtracks = 1, tol = 0.0029843485487629985 Iteration 20: loglikelihood = -2200.7112, backtracks = 1, tol = 0.001692896651343484 Iteration 21: loglikelihood = -2200.698, backtracks = 1, tol = 0.0009645176155473854 Iteration 22: loglikelihood = -2200.6958, backtracks = 1, tol = 0.0005547830169785985 Iteration 23: loglikelihood = -2200.6982, backtracks = 3, tol = 8.061216233203327e-5 0.131565 seconds (1.33 M allocations: 22.217 MiB) Test Summary: | Pass Total Time Negative binomial nuisance parameter Float32 matrix | 12 12 24.7s **** 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 **** ┌ Warning: accessing `Type.name` is deprecated without replacement. If for detection, use `Base.isType(x)`. │ caller = ProgressMeter.Progress(n::Int64, dt::Int64, desc::String, barlen::Nothing, color::Symbol, output::Base.PipeEndpoint; offset::Int64) at deprecated.jl:1 └ @ ProgressMeter ~/.julia/packages/ProgressMeter/N660J/src/deprecated.jl:1 Running sparse linear regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -2896.6116813943763, backtracks = 0, tol = 1.0257704354307224 Iteration 2: loglikelihood = -1753.4720992614753, backtracks = 0, tol = 0.2870682551290383 Iteration 3: loglikelihood = -1460.3823326395222, backtracks = 0, tol = 0.1059822007319242 Iteration 4: loglikelihood = -1438.5292259047123, backtracks = 0, tol = 0.028655431669451118 Iteration 5: loglikelihood = -1438.0856032112097, backtracks = 0, tol = 0.0034955373515602557 Iteration 6: loglikelihood = -1438.074435032946, backtracks = 0, tol = 0.0005882060650840543 Iteration 7: loglikelihood = -1438.0741395461055, backtracks = 0, tol = 8.427264473930937e-5 3.637008 seconds (897.01 k allocations: 128.123 MiB, 1.30% gc time, 91.97% compilation time) Test Summary: | Pass Total Time initialze beta | 1 1 3.9s 6.160782 seconds (4.01 M allocations: 82.752 MiB, 0.47% gc time, 1.10% compilation time) 3.334892 seconds (3.98 M allocations: 91.817 MiB, 0.70% gc time) 10.201229 seconds (20.65 M allocations: 454.916 MiB, 1.04% gc time, 18.28% compilation time: 58% of which was recompilation) 8.115270 seconds (20.19 M allocations: 434.834 MiB, 1.29% gc time) 27.933932 seconds (3.45 M allocations: 4.231 GiB, 7.95% gc time, 29.83% compilation time) 39.835516 seconds (82.96 k allocations: 183.862 MiB, 0.23% gc time) Test Summary: | Pass Total Time memory_efficient keyword | 7 7 1m53.0s Test Summary: | Pass Total Time update_support! | 10 10 0.4s 14.988 ms (89 allocations: 5.20 KiB) 4.381 μs (0 allocations: 0 bytes) 88.799 μs (4 allocations: 288 bytes) 536.339 ns (0 allocations: 0 bytes) 34.960 μs (2 allocations: 64 bytes) 20.440 μs (0 allocations: 0 bytes) 3.812 μs (0 allocations: 0 bytes) 3.645 μs (0 allocations: 0 bytes) 76.889 μs (0 allocations: 0 bytes) 39.226 ms (89 allocations: 5.20 KiB) 18.780 μs (0 allocations: 0 bytes) 142.539 μs (4 allocations: 288 bytes) 2.846 μs (0 allocations: 0 bytes) 175.348 μs (2 allocations: 64 bytes) 42.780 μs (0 allocations: 0 bytes) 25.069 μs (0 allocations: 0 bytes) 24.710 μs (0 allocations: 0 bytes) 127.939 μs (0 allocations: 0 bytes) Test Summary: | Total Time benchmarks for multivariate function | 0 1m52.7s **** 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 = -2900.918630019449, backtracks = 0, tol = 0.14802242082004138 Iteration 2: loglikelihood = -2869.406464695619, backtracks = 0, tol = 0.03512679046077988 Iteration 3: loglikelihood = -2868.084702693443, backtracks = 0, tol = 0.005569349616332472 Iteration 4: loglikelihood = -2868.034423817725, backtracks = 0, tol = 0.0011189517628951667 Iteration 5: loglikelihood = -2868.0308576353746, backtracks = 0, tol = 0.00031182601179140966 Iteration 6: loglikelihood = -2868.0305288614227, backtracks = 0, tol = 0.00010393305949948345 Iteration 7: loglikelihood = -2868.0304966516946, backtracks = 0, tol = 3.100862049858006e-5 0.424018 seconds (46.02 k allocations: 5.430 MiB, 63.83% compilation time) Test Summary: | Pass Total Time multivariate fit_iht SnpLinAlg | 7 7 10.1s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse Multivariate Gaussian regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 12 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -2878.028812628852, backtracks = 0, tol = 2.5661768673084553 Iteration 2: loglikelihood = -2868.563037890196, backtracks = 0, tol = 0.024335274263285057 Iteration 3: loglikelihood = -2868.0815051475474, backtracks = 0, tol = 0.004072558228741048 Iteration 4: loglikelihood = -2868.0352100240902, backtracks = 0, tol = 0.0013135682973484317 Iteration 5: loglikelihood = -2868.0309297231934, backtracks = 0, tol = 0.000386434110747091 Iteration 6: loglikelihood = -2868.0305335492912, backtracks = 0, tol = 0.00011924564415557833 Iteration 7: loglikelihood = -2868.0304968517494, backtracks = 0, tol = 3.603726989721193e-5 1.495896 seconds (235.74 k allocations: 166.240 MiB, 59.04% compilation time) Test Summary: | Pass Total Time initialze beta | 5 5 1.9s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** ┌ Warning: accessing `Type.name` is deprecated without replacement. If for detection, use `Base.isType(x)`. │ caller = ProgressMeter.Progress(n::Int64, desc::String, offset::Int64; kwargs::Base.Pairs{Symbol, Union{}, Nothing, @NamedTuple{}}) at deprecated.jl:5 └ @ ProgressMeter ~/.julia/packages/ProgressMeter/N660J/src/deprecated.jl:5 Cross validating... 3%|█ | ETA: 0:02:44 Cross validating... 16%|█████▏ | ETA: 0:00:33 Cross validating... 24%|███████▋ | ETA: 0:00:21 Cross validating... 27%|████████▋ | ETA: 0:00:18 Cross validating... 30%|█████████▋ | ETA: 0:00:16 Cross validating... 33%|██████████▋ | ETA: 0:00:14 Cross validating... 37%|███████████▋ | ETA: 0:00:12 Cross validating... 40%|████████████▊ | ETA: 0:00:11 Cross validating... 43%|█████████████▊ | ETA: 0:00:10 Cross validating... 46%|██████████████▊ | ETA: 0:00:09 Cross validating... 49%|███████████████▊ | ETA: 0:00:08 Cross validating... 52%|████████████████▊ | ETA: 0:00:07 Cross validating... 56%|█████████████████▊ | ETA: 0:00:06 Cross validating... 59%|██████████████████▊ | ETA: 0:00:06 Cross validating... 62%|███████████████████▊ | ETA: 0:00:05 Cross validating... 65%|████████████████████▉ | ETA: 0:00:05 Cross validating... 68%|█████████████████████▉ | ETA: 0:00:04 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:04 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:03 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:03 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:02 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:02 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:02 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:01 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:01 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:10 Crossvalidation Results: k MSE 0 1428.1468914860743 1 1053.2583800557022 2 794.1177838105751 3 641.4232001312147 4 510.82840242299244 5 420.1415561581483 6 366.7277332901373 7 351.45275397420505 8 325.87443244661375 9 329.1781661765606 10 332.3984985115271 11 335.81158404649443 12 336.4271083652865 13 337.22320261792066 14 348.411144842869 15 337.0745011423653 16 343.0943933451256 17 376.50349791159385 18 360.0479910966285 19 358.90558238044787 20 359.284660477396 Best k = 8 10.204633 seconds (11.43 M allocations: 308.902 MiB, 1.69% gc time, 56.06% 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... 38%|████████████▎ | ETA: 0:00:03 Cross validating... 41%|█████████████▎ | 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... 56%|█████████████████▊ | ETA: 0:00:02 Cross validating... 59%|██████████████████▊ | ETA: 0:00:02 Cross validating... 62%|███████████████████▊ | ETA: 0:00:02 Cross validating... 65%|████████████████████▉ | ETA: 0:00:02 Cross validating... 68%|█████████████████████▉ | ETA: 0:00:01 Cross validating... 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 1428.1468914860743 1 1053.669920480605 2 800.8500752182624 3 646.1358556550077 4 519.3038766199968 5 426.1101003615603 6 371.70246091949656 7 357.3034225114665 8 332.2465134051479 9 341.5694149517338 10 350.60187319015427 11 355.95383319949235 12 362.31921733087586 13 363.4824100091318 14 372.1774699059447 15 369.8729720981093 16 382.7441261233745 17 390.3343953380491 18 387.8851957925551 19 387.0162018036426 20 400.9639144207815 Best k = 8 4.752147 seconds (10.71 M allocations: 226.809 MiB, 1.34% gc time, 1.35% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, normal model | 3 3 15.6s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:04:37 Cross validating... 10%|███ | ETA: 0:01:28 Cross validating... 14%|████▋ | ETA: 0:00:56 Cross validating... 19%|██████▏ | ETA: 0:00:40 Cross validating... 24%|███████▋ | ETA: 0:00:31 Cross validating... 29%|█████████▏ | ETA: 0:00:24 Cross validating... 30%|█████████▋ | ETA: 0:00:23 Cross validating... 35%|███████████▏ | ETA: 0:00:19 Cross validating... 41%|█████████████▎ | ETA: 0:00:14 Cross validating... 46%|██████████████▊ | ETA: 0:00:12 Cross validating... 51%|████████████████▎ | ETA: 0:00:10 Cross validating... 56%|█████████████████▊ | ETA: 0:00:08 Cross validating... 60%|███████████████████▎ | ETA: 0:00:07 Cross validating... 65%|████████████████████▉ | ETA: 0:00:06 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:05 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:04 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:03 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:02 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:01 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:01 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:11 Crossvalidation Results: k MSE 0 1547.8928676757814 1 1247.9250421142578 2 991.5188731079102 3 794.824564819336 4 644.6919350585938 5 510.7913133544922 6 432.8374747009277 7 369.09640643310547 8 346.05519018554685 9 330.49054010009763 10 317.8953649291992 11 321.6140262145996 12 323.3386647644043 13 324.5714104003906 14 327.4715975341797 15 341.540522064209 16 329.05077975463865 17 345.01929638671874 18 334.82026168823245 19 352.4836667785645 20 351.1074663696289 Best k = 10 12.838633 seconds (13.04 M allocations: 334.543 MiB, 1.44% gc time, 79.80% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 6%|██ | ETA: 0:00:02 Cross validating... 11%|███▌ | ETA: 0:00:02 Cross validating... 16%|█████▏ | ETA: 0:00:02 Cross validating... 21%|██████▋ | ETA: 0:00:02 Cross validating... 25%|████████▏ | ETA: 0:00:02 Cross validating... 29%|█████████▏ | ETA: 0:00:02 Cross validating... 33%|██████████▋ | ETA: 0:00:02 Cross validating... 38%|████████████▎ | ETA: 0:00:02 Cross validating... 44%|██████████████▎ | ETA: 0:00:01 Cross validating... 49%|███████████████▊ | ETA: 0:00:01 Cross validating... 54%|█████████████████▎ | 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... 71%|██████████████████████▉ | ETA: 0:00:01 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:01 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:01 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:00 Cross validating... 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 1547.8928676757814 1 1251.7826882324218 2 994.140007385254 3 795.571121459961 4 648.6114697265625 5 514.5500109863282 6 439.87074719238274 7 381.8760782165527 8 353.88890509033206 9 343.245719543457 10 330.44078811645505 11 340.80658343505854 12 344.2451328430176 13 344.6587396850586 14 354.8452206726074 15 365.1702082824707 16 364.06843658447264 17 370.6635815429688 18 382.0989446105957 19 382.31831536865235 20 383.97771844482423 Best k = 10 2.740178 seconds (11.15 M allocations: 205.333 MiB, 2.12% gc time, 1.77% compilation time) Test Summary: | Pass Total Time Cross validation on Float32 matrix, normal model | 2 2 16.9s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:41 Cross validating... 6%|██ | ETA: 0:00:22 Cross validating... 10%|███ | ETA: 0:00:16 Cross validating... 13%|████▏ | ETA: 0:00:13 Cross validating... 16%|█████▏ | ETA: 0:00:11 Cross validating... 19%|██████▏ | ETA: 0:00:09 Cross validating... 21%|██████▋ | ETA: 0:00:09 Cross validating... 24%|███████▋ | ETA: 0:00:08 Cross validating... 27%|████████▋ | ETA: 0:00:07 Cross validating... 30%|█████████▋ | ETA: 0:00:07 Cross validating... 33%|██████████▋ | ETA: 0:00:06 Cross validating... 37%|███████████▋ | ETA: 0:00:06 Cross validating... 40%|████████████▊ | ETA: 0:00:05 Cross validating... 43%|█████████████▊ | ETA: 0:00:05 Cross validating... 46%|██████████████▊ | ETA: 0:00:04 Cross validating... 49%|███████████████▊ | ETA: 0:00:04 Cross validating... 52%|████████████████▊ | ETA: 0:00:04 Cross validating... 56%|█████████████████▊ | ETA: 0:00:03 Cross validating... 59%|██████████████████▊ | ETA: 0:00:03 Cross validating... 62%|███████████████████▊ | ETA: 0:00:03 Cross validating... 65%|████████████████████▉ | ETA: 0:00:03 Cross validating... 68%|█████████████████████▉ | ETA: 0:00:02 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:02 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:02 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:02 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:01 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:01 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:01 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:01 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:01 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:06 Crossvalidation Results: k MSE 0 463.90367542866693 1 424.8854051618205 2 410.48559224095516 3 383.33673529756504 4 370.99393071326887 5 357.495059952568 6 348.1728318162043 7 346.9206154907354 8 349.0713366497837 9 341.3822131497875 10 356.1249931341471 11 350.3409960129865 12 350.30022268669984 13 341.6514477489794 14 344.1030093536127 15 349.7188716653204 16 346.85444384327906 17 374.9344424905512 18 342.6483981960083 19 406.85014067258555 20 359.65197985226615 Best k = 9 7.417755 seconds (18.32 M allocations: 442.244 MiB, 2.18% gc time, 23.89% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:03 Cross validating... 6%|██ | ETA: 0:00:04 Cross validating... 10%|███ | ETA: 0:00:04 Cross validating... 11%|███▌ | ETA: 0:00:05 Cross validating... 14%|████▋ | ETA: 0:00:05 Cross validating... 17%|█████▋ | ETA: 0:00:04 Cross validating... 21%|██████▋ | ETA: 0:00:04 Cross validating... 24%|███████▋ | ETA: 0:00:04 Cross validating... 27%|████████▋ | ETA: 0:00:04 Cross validating... 30%|█████████▋ | ETA: 0:00:04 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: 0:00:02 Cross validating... 59%|██████████████████▊ | ETA: 0:00:02 Cross validating... 62%|███████████████████▊ | ETA: 0:00:02 Cross validating... 65%|████████████████████▉ | ETA: 0:00:02 Cross validating... 68%|█████████████████████▉ | ETA: 0:00:02 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:02 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... 86%|███████████████████████████▍ | ETA: 0:00:01 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:01 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:00 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:05 Crossvalidation Results: k MSE 0 463.90367542866693 1 428.81660882391486 2 414.8884427192911 3 394.29514517657947 4 378.8974851851699 5 366.2673768136772 6 359.35565990592625 7 363.745369566067 8 366.362737124734 9 359.6527890367338 10 372.6675215833655 11 380.1210834519288 12 386.28326608237 13 391.2691963295838 14 386.45257557643635 15 399.3520512361031 16 405.3112883430904 17 421.80031116490477 18 412.51321810890136 19 430.2464468639838 20 415.389604407006 Best k = 6 5.601908 seconds (18.19 M allocations: 381.837 MiB, 1.60% gc time, 1.19% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, logistic model | 2 2 13.3s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:34 Cross validating... 6%|██ | ETA: 0:00:19 Cross validating... 10%|███ | ETA: 0:00:13 Cross validating... 13%|████▏ | ETA: 0:00:10 Cross validating... 16%|█████▏ | ETA: 0:00:09 Cross validating... 19%|██████▏ | ETA: 0:00:08 Cross validating... 22%|███████▏ | ETA: 0:00:07 Cross validating... 25%|████████▏ | ETA: 0:00:06 Cross validating... 29%|█████████▏ | ETA: 0:00:06 Cross validating... 32%|██████████▏ | ETA: 0:00:05 Cross validating... 37%|███████████▋ | ETA: 0:00:04 Cross validating... 40%|████████████▊ | ETA: 0:00:04 Cross validating... 43%|█████████████▊ | ETA: 0:00:04 Cross validating... 46%|██████████████▊ | ETA: 0:00:03 Cross validating... 49%|███████████████▊ | ETA: 0:00:03 Cross validating... 52%|████████████████▊ | ETA: 0:00:03 Cross validating... 56%|█████████████████▊ | ETA: 0:00:03 Cross validating... 59%|██████████████████▊ | ETA: 0:00:02 Cross validating... 62%|███████████████████▊ | ETA: 0:00:02 Cross validating... 65%|████████████████████▉ | ETA: 0:00:02 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:02 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:01 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:01 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:01 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:01 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:01 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:00 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:05 Crossvalidation Results: k MSE 0 463.9689909242685 1 433.9654764737469 2 405.7932103046754 3 392.6901476909168 4 369.31811339719064 5 343.33077379895684 6 318.72201060381985 7 319.5187801899455 8 322.20552933089857 9 320.3805844901485 10 321.3521423590751 11 321.91430120634755 12 327.34522277402544 13 343.72180757895217 14 346.68982789467896 15 354.4954329937585 16 344.5067852514766 17 334.5793412605298 18 366.1592050410133 19 336.2400524167856 20 340.4092186285701 Best k = 6 6.358616 seconds (16.89 M allocations: 408.280 MiB, 2.27% gc time, 35.29% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 5%|█▌ | ETA: 0:00:03 Cross validating... 8%|██▌ | ETA: 0:00:03 Cross validating... 11%|███▌ | ETA: 0:00:03 Cross validating... 14%|████▋ | ETA: 0:00:03 Cross validating... 17%|█████▋ | ETA: 0:00:03 Cross validating... 21%|██████▋ | ETA: 0:00:03 Cross validating... 24%|███████▋ | ETA: 0:00:03 Cross validating... 27%|████████▋ | ETA: 0:00:03 Cross validating... 30%|█████████▋ | ETA: 0:00:03 Cross validating... 33%|██████████▋ | ETA: 0:00:03 Cross validating... 37%|███████████▋ | ETA: 0:00:03 Cross validating... 40%|████████████▊ | ETA: 0:00:03 Cross validating... 43%|█████████████▊ | ETA: 0:00:02 Cross validating... 46%|██████████████▊ | ETA: 0:00:02 Cross validating... 49%|███████████████▊ | ETA: 0:00:02 Cross validating... 52%|████████████████▊ | ETA: 0:00:02 Cross validating... 56%|█████████████████▊ | ETA: 0:00:02 Cross validating... 59%|██████████████████▊ | ETA: 0:00:02 Cross validating... 62%|███████████████████▊ | ETA: 0:00:02 Cross validating... 65%|████████████████████▉ | ETA: 0:00:02 Cross validating... 68%|█████████████████████▉ | ETA: 0:00:01 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:01 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:01 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:01 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:01 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:01 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:01 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:00 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:04 Crossvalidation Results: k MSE 0 463.9689909242685 1 433.98827258175146 2 406.3506101472456 3 395.13254000232973 4 373.1877384662856 5 347.10062103928703 6 322.8228810932305 7 326.4050876286936 8 335.1361143532863 9 338.08837083446593 10 335.6977424397177 11 341.11175840832436 12 358.04350747440407 13 362.4074026423866 14 373.83051748902136 15 380.07946734127137 16 386.3068819292439 17 383.589672634033 18 400.61705949788484 19 412.28526681474796 20 429.3331913548395 Best k = 6 4.342973 seconds (17.37 M allocations: 358.158 MiB, 1.50% gc time, 1.11% compilation time) Test Summary: | Pass Total Time Cross validation on Float64 matrix, logistic model | 2 2 11.4s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:39 Cross validating... 6%|██ | ETA: 0:00:21 Cross validating... 10%|███ | ETA: 0:00:15 Cross validating... 13%|████▏ | ETA: 0:00:12 Cross validating... 16%|█████▏ | ETA: 0:00:10 Cross validating... 19%|██████▏ | ETA: 0:00:09 Cross validating... 21%|██████▋ | ETA: 0:00:09 Cross validating... 24%|███████▋ | ETA: 0:00:08 Cross validating... 27%|████████▋ | ETA: 0:00:07 Cross validating... 30%|█████████▋ | ETA: 0:00:06 Cross validating... 33%|██████████▋ | ETA: 0:00:06 Cross validating... 37%|███████████▋ | ETA: 0:00:05 Cross validating... 40%|████████████▊ | ETA: 0:00:05 Cross validating... 43%|█████████████▊ | ETA: 0:00:05 Cross validating... 46%|██████████████▊ | ETA: 0:00:04 Cross validating... 49%|███████████████▊ | ETA: 0:00:04 Cross validating... 52%|████████████████▊ | ETA: 0:00:04 Cross validating... 56%|█████████████████▊ | ETA: 0:00:03 Cross validating... 59%|██████████████████▊ | ETA: 0:00:03 Cross validating... 62%|███████████████████▊ | ETA: 0:00:03 Cross validating... 65%|████████████████████▉ | ETA: 0:00:03 Cross validating... 68%|█████████████████████▉ | ETA: 0:00:02 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:02 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:02 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:02 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:01 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:01 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:01 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:01 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:06 Crossvalidation Results: k MSE 0 491.0720509492853 1 434.43285600149 2 410.73429779143623 3 404.664744525595 4 399.42141370342983 5 391.7745782982796 6 396.0075515867219 7 393.441645392958 8 394.8235530909277 9 399.2371039703137 10 392.5787380031015 11 399.0692244554231 12 397.5960166739068 13 397.74508737983297 14 401.470695565014 15 409.9651057689198 16 411.9705083488405 17 405.67903924429834 18 401.5593529628726 19 400.28910313459824 20 404.92403581717224 Best k = 5 7.181945 seconds (15.87 M allocations: 390.921 MiB, 1.13% gc time, 24.56% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:03 Cross validating... 6%|██ | ETA: 0:00:04 Cross validating... 10%|███ | ETA: 0:00:04 Cross validating... 13%|████▏ | ETA: 0:00:04 Cross validating... 16%|█████▏ | ETA: 0:00:04 Cross validating... 19%|██████▏ | ETA: 0:00:04 Cross validating... 22%|███████▏ | ETA: 0:00:04 Cross validating... 25%|████████▏ | ETA: 0:00:04 Cross validating... 29%|█████████▏ | ETA: 0:00:04 Cross validating... 30%|█████████▋ | ETA: 0:00:04 Cross validating... 33%|██████████▋ | ETA: 0:00:04 Cross validating... 37%|███████████▋ | ETA: 0:00:03 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: 0:00:02 Cross validating... 59%|██████████████████▊ | ETA: 0:00:02 Cross validating... 62%|███████████████████▊ | ETA: 0:00:02 Cross validating... 65%|████████████████████▉ | ETA: 0:00:02 Cross validating... 68%|█████████████████████▉ | ETA: 0:00:02 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:02 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 0 491.0720509492853 1 437.04212298539005 2 413.0252346186153 3 408.0508530098441 4 407.56379533701636 5 400.671642020054 6 416.0795929286486 7 419.46107141744517 8 410.26664887475965 9 421.4842761236423 10 429.7987012055154 11 425.2658148750989 12 437.0986430715128 13 448.97485420469627 14 442.41444905553124 15 446.62318109462865 16 460.9773560958895 17 467.6545460441794 18 469.2454981349425 19 473.9414640237957 20 462.0715249476155 Best k = 5 5.361934 seconds (14.30 M allocations: 287.953 MiB, 1.28% gc time, 0.52% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, Poisson model | 2 2 12.9s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:38 Cross validating... 6%|██ | ETA: 0:00:33 Cross validating... 10%|███ | ETA: 0:00:24 Cross validating... 11%|███▌ | ETA: 0:00:21 Cross validating... 14%|████▋ | ETA: 0:00:21 Cross validating... 16%|█████▏ | ETA: 0:00:24 Cross validating... 19%|██████▏ | ETA: 0:00:21 Cross validating... 21%|██████▋ | ETA: 0:00:19 Cross validating... 22%|███████▏ | ETA: 0:00:21 Cross validating... 24%|███████▋ | ETA: 0:00:22 Cross validating... 25%|████████▏ | ETA: 0:00:23 Cross validating... 27%|████████▋ | ETA: 0:00:22 Cross validating... 29%|█████████▏ | ETA: 0:00:23 Cross validating... 30%|█████████▋ | ETA: 0:00:24 Cross validating... 32%|██████████▏ | ETA: 0:00:24 Cross validating... 33%|██████████▋ | ETA: 0:00:24 Cross validating... 37%|███████████▋ | ETA: 0:00:23 Cross validating... 38%|████████████▎ | ETA: 0:00:23 Cross validating... 40%|████████████▊ | ETA: 0:00:23 Cross validating... 41%|█████████████▎ | ETA: 0:00:23 Cross validating... 43%|█████████████▊ | ETA: 0:00:23 Cross validating... 44%|██████████████▎ | ETA: 0:00:22 Cross validating... 46%|██████████████▊ | ETA: 0:00:22 Cross validating... 48%|███████████████▎ | ETA: 0:00:22 Cross validating... 49%|███████████████▊ | ETA: 0:00:21 Cross validating... 51%|████████████████▎ | ETA: 0:00:21 Cross validating... 52%|████████████████▊ | ETA: 0:00:21 Cross validating... 54%|█████████████████▎ | ETA: 0:00:20 Cross validating... 56%|█████████████████▊ | ETA: 0:00:20 Cross validating... 57%|██████████████████▎ | ETA: 0:00:19 Cross validating... 59%|██████████████████▊ | ETA: 0:00:19 Cross validating... 60%|███████████████████▎ | ETA: 0:00:18 Cross validating... 62%|███████████████████▊ | ETA: 0:00:17 Cross validating... 63%|████████████████████▍ | ETA: 0:00:16 Cross validating... 65%|████████████████████▉ | ETA: 0:00:16 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:15 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:12 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:11 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:10 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:08 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:08 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:07 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:06 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:06 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:05 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:04 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:04 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:03 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:03 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: 0:00:41 Crossvalidation Results: k MSE 0 296.2569722403895 1 284.67887894012256 2 267.9095177887233 3 252.6117335310725 4 252.3217739356802 5 253.63610249347838 6 256.7966176634602 7 256.5503152597629 8 254.74800286075134 9 255.74385638368585 10 257.7565149237922 11 260.31028048263397 12 261.08094551765726 13 262.4318764208239 14 263.51225567506026 15 264.1059846331633 16 260.07887121872335 17 266.8188415121385 18 262.5916256300585 19 269.84159779069967 20 268.69338350350085 Best k = 4 41.975294 seconds (138.90 M allocations: 3.459 GiB, 1.34% gc time, 3.47% 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... 8%|██▌ | ETA: 0:00:04 Cross validating... 10%|███ | ETA: 0:00:05 Cross validating... 11%|███▌ | ETA: 0:00:05 Cross validating... 13%|████▏ | ETA: 0:00:05 Cross validating... 14%|████▋ | ETA: 0:00:06 Cross validating... 16%|█████▏ | ETA: 0:00:06 Cross validating... 17%|█████▋ | ETA: 0:00:06 Cross validating... 19%|██████▏ | ETA: 0:00:06 Cross validating... 21%|██████▋ | ETA: 0:00:06 Cross validating... 22%|███████▏ | ETA: 0:00:06 Cross validating... 24%|███████▋ | ETA: 0:00:06 Cross validating... 25%|████████▏ | ETA: 0:00:06 Cross validating... 27%|████████▋ | ETA: 0:00:06 Cross validating... 29%|█████████▏ | ETA: 0:00:06 Cross validating... 30%|█████████▋ | ETA: 0:00:06 Cross validating... 32%|██████████▏ | ETA: 0:00:06 Cross validating... 33%|██████████▋ | ETA: 0:00:06 Cross validating... 37%|███████████▋ | ETA: 0:00:06 Cross validating... 38%|████████████▎ | ETA: 0:00:06 Cross validating... 41%|█████████████▎ | ETA: 0:00:05 Cross validating... 43%|█████████████▊ | ETA: 0:00:05 Cross validating... 44%|██████████████▎ | ETA: 0:00:05 Cross validating... 46%|██████████████▊ | ETA: 0:00:05 Cross validating... 48%|███████████████▎ | ETA: 0:00:04 Cross validating... 49%|███████████████▊ | ETA: 0:00:04 Cross validating... 51%|████████████████▎ | ETA: 0:00:04 Cross validating... 52%|████████████████▊ | ETA: 0:00:04 Cross validating... 54%|█████████████████▎ | ETA: 0:00:04 Cross validating... 56%|█████████████████▊ | ETA: 0:00:04 Cross validating... 57%|██████████████████▎ | ETA: 0:00:04 Cross validating... 59%|██████████████████▊ | ETA: 0:00:04 Cross validating... 60%|███████████████████▎ | ETA: 0:00:04 Cross validating... 62%|███████████████████▊ | ETA: 0:00:04 Cross validating... 63%|████████████████████▍ | ETA: 0:00:04 Cross validating... 65%|████████████████████▉ | ETA: 0:00:03 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:03 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:03 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:02 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:02 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:02 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:02 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:02 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:02 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:02 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:01 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:01 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:01 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:01 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:01 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:01 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:01 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:09 Crossvalidation Results: k MSE 0 296.2569722403895 1 287.72970170593584 2 272.2231475013184 3 258.8679468473384 4 259.5122761075656 5 267.7432165051385 6 273.63053125604597 7 275.604276675791 8 279.18158390453937 9 284.9671130591708 10 286.04988002979604 11 289.6112283866062 12 298.9779738006807 13 300.5141480858805 14 321.9868249199409 15 314.7232686172188 16 315.8490327630241 17 313.8298480169989 18 330.24929085501844 19 343.39765430875127 20 324.728782920621 Best k = 3 9.179739 seconds (28.90 M allocations: 590.775 MiB, 1.12% gc time, 0.82% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, NegativeBinomial model | 2 2 51.5s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:46 Cross validating... 6%|██ | ETA: 0:00:24 Cross validating... 10%|███ | ETA: 0:00:16 Cross validating... 13%|████▏ | ETA: 0:00:12 Cross validating... 16%|█████▏ | ETA: 0:00:10 Cross validating... 21%|██████▋ | ETA: 0:00:08 Cross validating... 25%|████████▏ | ETA: 0:00:06 Cross validating... 30%|█████████▋ | ETA: 0:00:05 Cross validating... 33%|██████████▋ | ETA: 0:00:05 Cross validating... 38%|████████████▎ | ETA: 0:00:04 Cross validating... 41%|█████████████▎ | ETA: 0:00:04 Cross validating... 44%|██████████████▎ | ETA: 0:00:04 Cross validating... 49%|███████████████▊ | ETA: 0:00:03 Cross validating... 52%|████████████████▊ | ETA: 0:00:03 Cross validating... 56%|█████████████████▊ | ETA: 0:00:03 Cross validating... 60%|███████████████████▎ | ETA: 0:00:02 Cross validating... 65%|████████████████████▉ | ETA: 0:00:02 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:02 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:01 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:01 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:01 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:01 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:01 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:05 Crossvalidation Results: k MSE 0 708.7406597900391 1 594.0547950439453 2 472.60887115478516 3 391.07051165771486 4 322.2429605712891 5 274.1304553527832 6 242.98796069335935 7 231.75397763061522 8 211.04413333129884 9 208.82878451538085 10 210.9139321594238 11 206.8662128601074 12 209.29315435791017 13 216.44690969848637 14 210.83974066162108 15 223.69269552612303 16 223.5122525024414 17 217.3672544555664 18 230.29235778808595 19 245.48900619506838 20 214.24631561279296 Best k = 11 5.739247 seconds (17.23 M allocations: 344.124 MiB, 11.60% gc time, 34.47% 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: 0:00:03 Cross validating... 14%|████▋ | ETA: 0:00:02 Cross validating... 17%|█████▋ | 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... 33%|██████████▋ | ETA: 0:00:02 Cross validating... 38%|████████████▎ | ETA: 0:00:02 Cross validating... 41%|█████████████▎ | ETA: 0:00:02 Cross validating... 44%|██████████████▎ | ETA: 0:00:02 Cross validating... 49%|███████████████▊ | ETA: 0:00:02 Cross validating... 54%|█████████████████▎ | ETA: 0:00:01 Cross validating... 59%|██████████████████▊ | ETA: 0:00:01 Cross validating... 62%|███████████████████▊ | ETA: 0:00:01 Cross validating... 65%|████████████████████▉ | ETA: 0:00:01 Cross validating... 68%|█████████████████████▉ | ETA: 0:00:01 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:01 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:01 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:01 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:01 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:01 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:00 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:00 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:03 Crossvalidation Results: k MSE 0 708.7406597900391 1 575.6241903076173 2 458.4867525024414 3 380.67050573730467 4 317.43561486816407 5 274.8225385131836 6 243.94065100097657 7 233.23877688598634 8 212.74209445190428 9 214.86823376464844 10 213.80905279541014 11 216.52949041748047 12 220.7860779724121 13 222.78791012573242 14 231.40656030273436 15 233.06280703735348 16 243.6403890075684 17 242.80908297729493 18 238.556499420166 19 251.23290313720705 20 244.79654568481442 Best k = 8 3.441742 seconds (16.27 M allocations: 288.805 MiB, 2.53% gc time, 1.25% compilation time) Test Summary: | Pass Total Time Cross validation on floating point matrices, NegativeBinomial model | 2 2 9.7s **** 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: 0:01:07 Cross validating... 3%|█ | ETA: 0:00:49 Cross validating... 4%|█▎ | ETA: 0:00:40 Cross validating... 5%|█▋ | ETA: 0:00:35 Cross validating... 6%|█▉ | ETA: 0:00:32 Cross validating... 7%|██▎ | ETA: 0:00:30 Cross validating... 8%|██▌ | ETA: 0:00:28 Cross validating... 9%|██▉ | ETA: 0:00:26 Cross validating... 10%|███▎ | ETA: 0:00:25 Cross validating... 11%|███▌ | ETA: 0:00:24 Cross validating... 12%|███▉ | ETA: 0:00:23 Cross validating... 13%|████▏ | ETA: 0:00:22 Cross validating... 14%|████▌ | ETA: 0:00:22 Cross validating... 15%|████▊ | ETA: 0:00:21 Cross validating... 16%|█████▏ | ETA: 0:00:20 Cross validating... 17%|█████▌ | ETA: 0:00:20 Cross validating... 18%|█████▊ | ETA: 0:00:19 Cross validating... 19%|██████▏ | ETA: 0:00:19 Cross validating... 20%|██████▍ | ETA: 0:00:19 Cross validating... 21%|██████▊ | ETA: 0:00:18 Cross validating... 22%|███████ | ETA: 0:00:17 Cross validating... 23%|███████▍ | ETA: 0:00:17 Cross validating... 24%|███████▋ | ETA: 0:00:17 Cross validating... 25%|████████ | ETA: 0:00:16 Cross validating... 26%|████████▍ | ETA: 0:00:16 Cross validating... 27%|████████▋ | ETA: 0:00:16 Cross validating... 28%|█████████ | ETA: 0:00:15 Cross validating... 29%|█████████▎ | ETA: 0:00:15 Cross validating... 30%|█████████▋ | ETA: 0:00:15 Cross validating... 31%|█████████▉ | ETA: 0:00:14 Cross validating... 32%|██████████▎ | ETA: 0:00:14 Cross validating... 33%|██████████▌ | ETA: 0:00:14 Cross validating... 34%|██████████▉ | ETA: 0:00:14 Cross validating... 35%|███████████▎ | ETA: 0:00:13 Cross validating... 36%|███████████▌ | ETA: 0:00:13 Cross validating... 37%|███████████▉ | ETA: 0:00:13 Cross validating... 38%|████████████▏ | ETA: 0:00:13 Cross validating... 39%|████████████▌ | ETA: 0:00:13 Cross validating... 40%|████████████▊ | ETA: 0:00:12 Cross validating... 41%|█████████████▏ | ETA: 0:00:12 Cross validating... 42%|█████████████▌ | ETA: 0:00:12 Cross validating... 43%|█████████████▊ | ETA: 0:00:11 Cross validating... 44%|██████████████▏ | ETA: 0:00:11 Cross validating... 45%|██████████████▍ | ETA: 0:00:11 Cross validating... 46%|██████████████▊ | ETA: 0:00:11 Cross validating... 47%|███████████████ | ETA: 0:00:11 Cross validating... 48%|███████████████▍ | ETA: 0:00:10 Cross validating... 49%|███████████████▋ | ETA: 0:00:10 Cross validating... 50%|████████████████ | ETA: 0:00:10 Cross validating... 51%|████████████████▍ | ETA: 0:00:10 Cross validating... 52%|████████████████▋ | ETA: 0:00:09 Cross validating... 53%|█████████████████ | ETA: 0:00:09 Cross validating... 54%|█████████████████▎ | ETA: 0:00:09 Cross validating... 55%|█████████████████▋ | ETA: 0:00:09 Cross validating... 56%|█████████████████▉ | ETA: 0:00:09 Cross validating... 57%|██████████████████▎ | ETA: 0:00:08 Cross validating... 58%|██████████████████▌ | ETA: 0:00:08 Cross validating... 59%|██████████████████▉ | ETA: 0:00:08 Cross validating... 60%|███████████████████▎ | ETA: 0:00:08 Cross validating... 61%|███████████████████▌ | ETA: 0:00:08 Cross validating... 62%|███████████████████▉ | ETA: 0:00:07 Cross validating... 63%|████████████████████▏ | ETA: 0:00:07 Cross validating... 64%|████████████████████▌ | ETA: 0:00:07 Cross validating... 65%|████████████████████▊ | ETA: 0:00:07 Cross validating... 66%|█████████████████████▏ | ETA: 0:00:07 Cross validating... 67%|█████████████████████▌ | ETA: 0:00:06 Cross validating... 68%|█████████████████████▊ | ETA: 0:00:06 Cross validating... 69%|██████████████████████▏ | ETA: 0:00:06 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:06 Cross validating... 71%|██████████████████████▊ | ETA: 0:00:06 Cross validating... 72%|███████████████████████ | ETA: 0:00:05 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:05 Cross validating... 74%|███████████████████████▋ | ETA: 0:00:05 Cross validating... 75%|████████████████████████ | ETA: 0:00:05 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:05 Cross validating... 77%|████████████████████████▋ | ETA: 0:00:04 Cross validating... 78%|█████████████████████████ | ETA: 0:00:04 Cross validating... 79%|█████████████████████████▎ | ETA: 0:00:04 Cross validating... 80%|█████████████████████████▋ | ETA: 0:00:04 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:04 Cross validating... 82%|██████████████████████████▎ | ETA: 0:00:03 Cross validating... 83%|██████████████████████████▌ | ETA: 0:00:03 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:03 Cross validating... 85%|███████████████████████████▎ | ETA: 0:00:03 Cross validating... 86%|███████████████████████████▌ | ETA: 0:00:03 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: 0:00:02 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:02 Cross validating... 93%|█████████████████████████████▊ | ETA: 0:00:01 Cross validating... 94%|██████████████████████████████▏ | ETA: 0:00:01 Cross validating... 95%|██████████████████████████████▍ | ETA: 0:00:01 Cross validating... 96%|██████████████████████████████▊ | ETA: 0:00:01 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:01 Cross validating... 98%|███████████████████████████████▍| ETA: 0:00:00 Cross validating... 99%|███████████████████████████████▋| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:19 Crossvalidation Results: k MSE 1 3631.7034725233943 2 3225.7920069739066 3 3005.846319416403 4 2786.595084370308 5 2565.6580152730903 6 2456.4707741928596 7 2360.4687637293287 8 2338.3909223345645 9 2346.0394716757637 10 2359.7043996595135 11 2360.585567246783 12 2381.9742287897166 13 2383.373206664033 14 2400.8616169261477 15 2404.8988256170055 16 2434.1370247366035 17 2460.41627432999 18 2469.695789335173 19 2484.128127750697 20 2494.810504060706 Best k = 8 19.378378 seconds (357.26 k allocations: 314.522 MiB, 0.69% gc time, 6.81% compilation time) Test Summary: | Pass Total Time multivariate cross validation SnpLinAlg | 3 3 23.7s Test Summary: | Pass Total Time wrapper univariate | 20 20 2m02.0s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 2%|▋ | ETA: 0:00:10 Cross validating... 3%|█ | ETA: 0:00:10 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: 0:00:14 Cross validating... 8%|██▌ | ETA: 0:00:14 Cross validating... 9%|██▉ | ETA: 0:00:15 Cross validating... 10%|███▎ | ETA: 0:00:16 Cross validating... 11%|███▌ | ETA: 0:00:17 Cross validating... 12%|███▉ | ETA: 0:00:18 Cross validating... 13%|████▏ | ETA: 0:00:18 Cross validating... 14%|████▌ | ETA: 0:00:19 Cross validating... 15%|████▊ | ETA: 0:00:19 Cross validating... 16%|█████▏ | ETA: 0:00:21 Cross validating... 17%|█████▌ | ETA: 0:00:21 Cross validating... 18%|█████▊ | ETA: 0:00:21 Cross validating... 19%|██████▏ | ETA: 0:00:22 Cross validating... 20%|██████▍ | ETA: 0:00:22 Cross validating... 21%|██████▊ | ETA: 0:00:21 Cross validating... 22%|███████ | ETA: 0:00:20 Cross validating... 23%|███████▍ | ETA: 0:00:20 Cross validating... 24%|███████▋ | ETA: 0:00:19 Cross validating... 25%|████████ | ETA: 0:00:19 Cross validating... 26%|████████▍ | ETA: 0:00:18 Cross validating... 27%|████████▋ | ETA: 0:00:18 Cross validating... 28%|█████████ | ETA: 0:00:18 Cross validating... 29%|█████████▎ | ETA: 0:00:19 Cross validating... 30%|█████████▋ | ETA: 0:00:18 Cross validating... 31%|█████████▉ | ETA: 0:00:18 Cross validating... 32%|██████████▎ | ETA: 0:00:18 Cross validating... 33%|██████████▌ | ETA: 0:00:18 Cross validating... 34%|██████████▉ | ETA: 0:00:18 Cross validating... 35%|███████████▎ | ETA: 0:00:18 Cross validating... 36%|███████████▌ | ETA: 0:00:17 Cross validating... 37%|███████████▉ | ETA: 0:00:17 Cross validating... 38%|████████████▏ | ETA: 0:00:17 Cross validating... 39%|████████████▌ | ETA: 0:00:17 Cross validating... 40%|████████████▊ | ETA: 0:00:17 Cross validating... 41%|█████████████▏ | ETA: 0:00:16 Cross validating... 42%|█████████████▌ | ETA: 0:00:16 Cross validating... 43%|█████████████▊ | ETA: 0:00:15 Cross validating... 44%|██████████████▏ | ETA: 0:00:15 Cross validating... 45%|██████████████▍ | ETA: 0:00:14 Cross validating... 46%|██████████████▊ | ETA: 0:00:14 Cross validating... 47%|███████████████ | ETA: 0:00:14 Cross validating... 48%|███████████████▍ | ETA: 0:00:14 Cross validating... 49%|███████████████▋ | ETA: 0:00:13 Cross validating... 50%|████████████████ | ETA: 0:00:13 Cross validating... 51%|████████████████▍ | ETA: 0:00:13 Cross validating... 52%|████████████████▋ | ETA: 0:00:13 Cross validating... 53%|█████████████████ | ETA: 0:00:12 Cross validating... 54%|█████████████████▎ | ETA: 0:00:12 Cross validating... 55%|█████████████████▋ | ETA: 0:00:12 Cross validating... 56%|█████████████████▉ | ETA: 0:00:12 Cross validating... 57%|██████████████████▎ | ETA: 0:00:12 Cross validating... 58%|██████████████████▌ | ETA: 0:00:11 Cross validating... 59%|██████████████████▉ | ETA: 0:00:11 Cross validating... 60%|███████████████████▎ | ETA: 0:00:11 Cross validating... 61%|███████████████████▌ | ETA: 0:00:11 Cross validating... 62%|███████████████████▉ | ETA: 0:00:10 Cross validating... 63%|████████████████████▏ | ETA: 0:00:10 Cross validating... 64%|████████████████████▌ | ETA: 0:00:10 Cross validating... 65%|████████████████████▊ | ETA: 0:00:09 Cross validating... 66%|█████████████████████▏ | ETA: 0:00:09 Cross validating... 67%|█████████████████████▌ | ETA: 0:00:09 Cross validating... 68%|█████████████████████▊ | ETA: 0:00:09 Cross validating... 69%|██████████████████████▏ | ETA: 0:00:08 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:08 Cross validating... 71%|██████████████████████▊ | ETA: 0:00:08 Cross validating... 72%|███████████████████████ | ETA: 0:00:07 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:07 Cross validating... 74%|███████████████████████▋ | ETA: 0:00:07 Cross validating... 75%|████████████████████████ | ETA: 0:00:07 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:06 Cross validating... 77%|████████████████████████▋ | ETA: 0:00:06 Cross validating... 78%|█████████████████████████ | ETA: 0:00:06 Cross validating... 79%|█████████████████████████▎ | ETA: 0:00:06 Cross validating... 80%|█████████████████████████▋ | ETA: 0:00:05 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:05 Cross validating... 82%|██████████████████████████▎ | ETA: 0:00:05 Cross validating... 83%|██████████████████████████▌ | ETA: 0:00:05 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:04 Cross validating... 85%|███████████████████████████▎ | ETA: 0:00:04 Cross validating... 86%|███████████████████████████▌ | ETA: 0:00:04 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: 0:00:03 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: 0:00:02 Cross validating... 95%|██████████████████████████████▍ | ETA: 0:00:01 Cross validating... 96%|██████████████████████████████▊ | ETA: 0:00:01 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:01 Cross validating... 98%|███████████████████████████████▍| ETA: 0:00:01 Cross validating... 99%|███████████████████████████████▋| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:27 Crossvalidation Results: k MSE 1 2838.788679198002 2 2514.397342870813 3 2305.6176519676274 4 2222.025304867614 5 2075.167038458837 6 2067.794898972384 7 2053.427506114907 8 2086.405384830965 9 2080.984460901671 10 2105.1311995023634 11 2132.407165368786 12 2138.267187460652 13 2166.002210829576 14 2194.9918295115804 15 2189.890403738045 16 2191.1812932295775 17 2209.4669750564367 18 2221.2595493644303 19 2238.742594576326 20 2253.9559571797727 Best k = 7 **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 2%|▋ | ETA: 0:00:12 Cross validating... 3%|█ | ETA: 0:00:12 Cross validating... 4%|█▎ | ETA: 0:00:14 Cross validating... 5%|█▋ | ETA: 0:00:13 Cross validating... 6%|█▉ | ETA: 0:00:14 Cross validating... 7%|██▎ | ETA: 0:00:15 Cross validating... 8%|██▌ | ETA: 0:00:15 Cross validating... 9%|██▉ | ETA: 0:00:16 Cross validating... 10%|███▎ | ETA: 0:00:17 Cross validating... 11%|███▌ | ETA: 0:00:17 Cross validating... 12%|███▉ | ETA: 0:00:18 Cross validating... 13%|████▏ | ETA: 0:00:18 Cross validating... 14%|████▌ | ETA: 0:00:19 Cross validating... 15%|████▊ | ETA: 0:00:19 Cross validating... 16%|█████▏ | ETA: 0:00:21 Cross validating... 17%|█████▌ | ETA: 0:00:21 Cross validating... 18%|█████▊ | ETA: 0:00:21 Cross validating... 19%|██████▏ | ETA: 0:00:21 Cross validating... 20%|██████▍ | ETA: 0:00:21 Cross validating... 21%|██████▊ | ETA: 0:00:21 Cross validating... 22%|███████ | ETA: 0:00:20 Cross validating... 23%|███████▍ | ETA: 0:00:19 Cross validating... 24%|███████▋ | ETA: 0:00:19 Cross validating... 25%|████████ | ETA: 0:00:18 Cross validating... 26%|████████▍ | ETA: 0:00:18 Cross validating... 27%|████████▋ | ETA: 0:00:18 Cross validating... 28%|█████████ | ETA: 0:00:18 Cross validating... 29%|█████████▎ | ETA: 0:00:18 Cross validating... 30%|█████████▋ | ETA: 0:00:18 Cross validating... 31%|█████████▉ | ETA: 0:00:18 Cross validating... 32%|██████████▎ | ETA: 0:00:18 Cross validating... 33%|██████████▌ | ETA: 0:00:18 Cross validating... 34%|██████████▉ | ETA: 0:00:18 Cross validating... 35%|███████████▎ | ETA: 0:00:18 Cross validating... 36%|███████████▌ | ETA: 0:00:17 Cross validating... 37%|███████████▉ | ETA: 0:00:17 Cross validating... 38%|████████████▏ | ETA: 0:00:17 Cross validating... 39%|████████████▌ | ETA: 0:00:17 Cross validating... 40%|████████████▊ | ETA: 0:00:17 Cross validating... 41%|█████████████▏ | ETA: 0:00:16 Cross validating... 42%|█████████████▌ | ETA: 0:00:16 Cross validating... 43%|█████████████▊ | ETA: 0:00:15 Cross validating... 44%|██████████████▏ | ETA: 0:00:15 Cross validating... 45%|██████████████▍ | ETA: 0:00:14 Cross validating... 46%|██████████████▊ | ETA: 0:00:14 Cross validating... 47%|███████████████ | ETA: 0:00:14 Cross validating... 48%|███████████████▍ | ETA: 0:00:13 Cross validating... 49%|███████████████▋ | ETA: 0:00:13 Cross validating... 50%|████████████████ | ETA: 0:00:13 Cross validating... 51%|████████████████▍ | ETA: 0:00:13 Cross validating... 52%|████████████████▋ | ETA: 0:00:12 Cross validating... 53%|█████████████████ | ETA: 0:00:12 Cross validating... 54%|█████████████████▎ | ETA: 0:00:12 Cross validating... 55%|█████████████████▋ | ETA: 0:00:12 Cross validating... 56%|█████████████████▉ | ETA: 0:00:12 Cross validating... 57%|██████████████████▎ | ETA: 0:00:11 Cross validating... 58%|██████████████████▌ | ETA: 0:00:11 Cross validating... 59%|██████████████████▉ | ETA: 0:00:11 Cross validating... 60%|███████████████████▎ | ETA: 0:00:11 Cross validating... 61%|███████████████████▌ | ETA: 0:00:11 Cross validating... 62%|███████████████████▉ | ETA: 0:00:10 Cross validating... 63%|████████████████████▏ | ETA: 0:00:10 Cross validating... 64%|████████████████████▌ | ETA: 0:00:10 Cross validating... 65%|████████████████████▊ | ETA: 0:00:09 Cross validating... 66%|█████████████████████▏ | ETA: 0:00:09 Cross validating... 67%|█████████████████████▌ | ETA: 0:00:09 Cross validating... 68%|█████████████████████▊ | ETA: 0:00:08 Cross validating... 69%|██████████████████████▏ | ETA: 0:00:08 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:08 Cross validating... 71%|██████████████████████▊ | ETA: 0:00:08 Cross validating... 72%|███████████████████████ | ETA: 0:00:07 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:07 Cross validating... 74%|███████████████████████▋ | ETA: 0:00:07 Cross validating... 75%|████████████████████████ | ETA: 0:00:07 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:06 Cross validating... 77%|████████████████████████▋ | ETA: 0:00:06 Cross validating... 78%|█████████████████████████ | ETA: 0:00:06 Cross validating... 79%|█████████████████████████▎ | ETA: 0:00:06 Cross validating... 80%|█████████████████████████▋ | ETA: 0:00:05 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:05 Cross validating... 82%|██████████████████████████▎ | ETA: 0:00:05 Cross validating... 83%|██████████████████████████▌ | ETA: 0:00:05 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:04 Cross validating... 85%|███████████████████████████▎ | ETA: 0:00:04 Cross validating... 86%|███████████████████████████▌ | ETA: 0:00:04 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: 0:00:03 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: 0:00:02 Cross validating... 95%|██████████████████████████████▍ | ETA: 0:00:01 Cross validating... 96%|██████████████████████████████▊ | ETA: 0:00:01 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:01 Cross validating... 98%|███████████████████████████████▍| ETA: 0:00:01 Cross validating... 99%|███████████████████████████████▋| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:27 Crossvalidation Results: k MSE 1 2838.788679198002 2 2514.397342870813 3 2305.6176519676274 4 2222.025304867614 5 2075.167038458837 6 2067.794898972384 7 2053.427506114907 8 2086.405384830965 9 2080.984460901671 10 2105.1311995023634 11 2132.407165368786 12 2138.267187460652 13 2166.002210829576 14 2194.9918295115804 15 2189.890403738045 16 2191.1812932295775 17 2209.4669750564367 18 2221.2595493644303 19 2238.742594576326 20 2253.9559571797727 Best k = 7 **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 2%|▋ | ETA: 0:00:12 Cross validating... 3%|█ | ETA: 0:00:13 Cross validating... 4%|█▎ | ETA: 0:00:14 Cross validating... 5%|█▋ | ETA: 0:00:14 Cross validating... 6%|█▉ | ETA: 0:00:15 Cross validating... 7%|██▎ | ETA: 0:00:15 Cross validating... 8%|██▌ | ETA: 0:00:15 Cross validating... 9%|██▉ | ETA: 0:00:16 Cross validating... 10%|███▎ | ETA: 0:00:17 Cross validating... 11%|███▌ | ETA: 0:00:18 Cross validating... 12%|███▉ | ETA: 0:00:18 Cross validating... 13%|████▏ | ETA: 0:00:19 Cross validating... 14%|████▌ | ETA: 0:00:19 Cross validating... 15%|████▊ | ETA: 0:00:19 Cross validating... 16%|█████▏ | ETA: 0:00:21 Cross validating... 17%|█████▌ | ETA: 0:00:21 Cross validating... 18%|█████▊ | ETA: 0:00:21 Cross validating... 19%|██████▏ | ETA: 0:00:22 Cross validating... 20%|██████▍ | ETA: 0:00:22 Cross validating... 21%|██████▊ | ETA: 0:00:21 Cross validating... 22%|███████ | ETA: 0:00:20 Cross validating... 23%|███████▍ | ETA: 0:00:20 Cross validating... 24%|███████▋ | ETA: 0:00:19 Cross validating... 25%|████████ | ETA: 0:00:19 Cross validating... 26%|████████▍ | ETA: 0:00:18 Cross validating... 27%|████████▋ | ETA: 0:00:18 Cross validating... 28%|█████████ | ETA: 0:00:18 Cross validating... 29%|█████████▎ | ETA: 0:00:18 Cross validating... 30%|█████████▋ | ETA: 0:00:18 Cross validating... 31%|█████████▉ | ETA: 0:00:18 Cross validating... 32%|██████████▎ | ETA: 0:00:18 Cross validating... 33%|██████████▌ | ETA: 0:00:18 Cross validating... 34%|██████████▉ | ETA: 0:00:18 Cross validating... 35%|███████████▎ | ETA: 0:00:18 Cross validating... 36%|███████████▌ | ETA: 0:00:18 Cross validating... 37%|███████████▉ | ETA: 0:00:18 Cross validating... 38%|████████████▏ | ETA: 0:00:17 Cross validating... 39%|████████████▌ | ETA: 0:00:17 Cross validating... 40%|████████████▊ | ETA: 0:00:17 Cross validating... 41%|█████████████▏ | ETA: 0:00:17 Cross validating... 42%|█████████████▌ | ETA: 0:00:16 Cross validating... 43%|█████████████▊ | ETA: 0:00:16 Cross validating... 44%|██████████████▏ | ETA: 0:00:15 Cross validating... 45%|██████████████▍ | ETA: 0:00:15 Cross validating... 46%|██████████████▊ | ETA: 0:00:14 Cross validating... 47%|███████████████ | ETA: 0:00:14 Cross validating... 48%|███████████████▍ | ETA: 0:00:14 Cross validating... 49%|███████████████▋ | ETA: 0:00:13 Cross validating... 50%|████████████████ | ETA: 0:00:13 Cross validating... 51%|████████████████▍ | ETA: 0:00:13 Cross validating... 52%|████████████████▋ | ETA: 0:00:13 Cross validating... 53%|█████████████████ | ETA: 0:00:12 Cross validating... 54%|█████████████████▎ | ETA: 0:00:12 Cross validating... 55%|█████████████████▋ | ETA: 0:00:12 Cross validating... 56%|█████████████████▉ | ETA: 0:00:12 Cross validating... 57%|██████████████████▎ | ETA: 0:00:12 Cross validating... 58%|██████████████████▌ | ETA: 0:00:11 Cross validating... 59%|██████████████████▉ | ETA: 0:00:11 Cross validating... 60%|███████████████████▎ | ETA: 0:00:11 Cross validating... 61%|███████████████████▌ | ETA: 0:00:11 Cross validating... 62%|███████████████████▉ | ETA: 0:00:10 Cross validating... 63%|████████████████████▏ | ETA: 0:00:10 Cross validating... 64%|████████████████████▌ | ETA: 0:00:10 Cross validating... 65%|████████████████████▊ | ETA: 0:00:09 Cross validating... 66%|█████████████████████▏ | ETA: 0:00:09 Cross validating... 67%|█████████████████████▌ | ETA: 0:00:09 Cross validating... 68%|█████████████████████▊ | ETA: 0:00:09 Cross validating... 69%|██████████████████████▏ | ETA: 0:00:08 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:08 Cross validating... 71%|██████████████████████▊ | ETA: 0:00:08 Cross validating... 72%|███████████████████████ | ETA: 0:00:07 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:07 Cross validating... 74%|███████████████████████▋ | ETA: 0:00:07 Cross validating... 75%|████████████████████████ | ETA: 0:00:07 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:06 Cross validating... 77%|████████████████████████▋ | ETA: 0:00:06 Cross validating... 78%|█████████████████████████ | ETA: 0:00:06 Cross validating... 79%|█████████████████████████▎ | ETA: 0:00:06 Cross validating... 80%|█████████████████████████▋ | ETA: 0:00:06 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:05 Cross validating... 82%|██████████████████████████▎ | ETA: 0:00:05 Cross validating... 83%|██████████████████████████▌ | ETA: 0:00:05 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:04 Cross validating... 85%|███████████████████████████▎ | ETA: 0:00:04 Cross validating... 86%|███████████████████████████▌ | ETA: 0:00:04 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:04 Cross validating... 88%|████████████████████████████▏ | ETA: 0:00:03 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:03 Cross validating... 90%|████████████████████████████▊ | ETA: 0:00:03 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: 0:00:02 Cross validating... 95%|██████████████████████████████▍ | ETA: 0:00:01 Cross validating... 96%|██████████████████████████████▊ | ETA: 0:00:01 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:01 Cross validating... 98%|███████████████████████████████▍| ETA: 0:00:01 Cross validating... 99%|███████████████████████████████▋| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:28 Crossvalidation Results: k MSE 1 2838.788679198002 2 2514.397342870813 3 2305.6176519676274 4 2222.025304867614 5 2075.167038458837 6 2067.794898972384 7 2053.427506114907 8 2086.405384830965 9 2080.984460901671 10 2105.1311995023634 11 2132.407165368786 12 2138.267187460652 13 2166.002210829576 14 2194.9918295115804 15 2189.890403738045 16 2191.1812932295775 17 2209.4669750564367 18 2221.2595493644303 19 2238.742594576326 20 2253.9559571797727 Best k = 7 Test Summary: | Pass Total Time wrapper multivariate | 8 8 1m42.8s read BGEN and VCF: Error During Test at /home/pkgeval/.julia/packages/MendelIHT/ZcxZT/test/wrapper_test.jl:184 Got exception outside of a @test startproc must be called before process Stacktrace: [1] error(s::String) @ Base error.jl:56 [2] process(codec::CodecZlib.ZlibDecompressor, input::TranscodingStreams.Memory, output::TranscodingStreams.Memory, error_ref::TranscodingStreams.Error) @ CodecZlib ~/.julia/packages/CodecZlib/BjTS1/src/decompression.jl:199 [3] decompress(io::IOStream, v::Variant, h::BGEN.Header; decompressed::Nothing) @ BGEN ~/.julia/packages/BGEN/dfgRU/src/genotypes.jl:72 [4] first_allele_dosage!(b::Bgen, v::Variant; T::Core.TypeEgal{Float64}, mean_impute::Bool, clear_decompressed::Bool, data::Nothing, decompressed::Nothing, is_decompressed::Bool) @ BGEN ~/.julia/packages/BGEN/dfgRU/src/genotypes.jl:571 [5] convert_bgen_gt(t::Core.TypeEgal{Float64}, b::Bgen) @ MendelIHT ~/.julia/packages/MendelIHT/ZcxZT/src/wrapper.jl:380 [6] macro expansion @ ./timing.jl:741 [inlined] [7] macro expansion @ ~/.julia/packages/MendelIHT/ZcxZT/test/wrapper_test.jl:187 [inlined] [8] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:2252 [inlined] [9] top-level scope @ ~/.julia/packages/MendelIHT/ZcxZT/test/wrapper_test.jl:185 Test Summary: | Error Total Time read BGEN and VCF | 1 1 4.7s RNG of the outermost testset: Xoshiro(0xcedc5ee9056c2d64, 0xa72989c34829b0b7, 0x70f1f584d6bcca87, 0x87b2d830ce59e87d, 0xaef6b120b40e8f97) 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 1031.71s 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:3298 [3] test(ctx::Pkg.Types.Context, pkgs::Vector{PackageSpec}; coverage::Bool, test_fn::Nothing, julia_args::Cmd, test_args::Cmd, force_latest_compatible_version::Bool, allow_earlier_backwards_compatible_versions::Bool, allow_reresolve::Bool, kwargs::@Kwargs{io::IOContext{IO}}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:587 [4] test(pkgs::Vector{PackageSpec}; io::IOContext{IO}, kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:172 [5] test(pkgs::Vector{String}; kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:160 [6] test(pkg::String; kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:159 [inlined] [7] top-level scope @ /PkgEval.jl/scripts/evaluate.jl:223 in expression starting at /PkgEval.jl/scripts/evaluate.jl:214 PkgEval failed after 1161.29s: package tests unexpectedly errored