Package evaluation to test MendelIHT on Julia 1.14.0-DEV.2468 (92be8bc088*) started at 2026-07-03T00:34:53.228 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.14` Set-up completed after 14.23s ################################################################################ # 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 v7.27.0 [67c07d97] + Automa v1.2.0 ⌅ [6db4b851] + BGEN v0.1.17 [28d598bf] + BGZFStreams v0.3.2 [47718e42] + BioGenerics v0.1.5 [62783981] + BitTwiddlingConvenienceFunctions v0.1.6 [e1450e63] + BufferedStreams v1.2.2 [2a0fbf3d] + CPUSummary v0.2.7 [336ed68f] + CSV v0.10.16 [fb6a15b2] + CloseOpenIntervals v0.1.13 [523fee87] + CodecBzip2 v0.8.5 [ba30903b] + CodecXz v0.7.4 [944b1d66] + CodecZlib v0.7.8 [6b39b394] + CodecZstd v0.8.7 [861a8166] + Combinatorics v1.1.0 [38540f10] + CommonSolve v0.2.9 [f70d9fcc] + CommonWorldInvalidations v1.1.0 [34da2185] + Compat v4.18.1 [a33af91c] + CompositionsBase v0.1.2 [187b0558] + ConstructionBase v1.6.0 [adafc99b] + CpuId v0.3.1 [a8cc5b0e] + Crayons v4.1.1 [a10d1c49] + DBInterface v2.6.1 [9a962f9c] + DataAPI v1.16.0 [a93c6f00] + DataFrames v1.8.2 [864edb3b] + DataStructures v0.19.5 [e2d170a0] + DataValueInterfaces v1.0.0 [8bb1440f] + DelimitedFiles v1.9.1 [b4f34e82] + Distances v0.10.12 [31c24e10] + Distributions v0.25.129 [ffbed154] + DocStringExtensions v0.9.5 [48062228] + FilePathsBase v0.9.24 [1a297f60] + FillArrays v1.16.0 [38e38edf] + GLM v1.9.5 [c27321d9] + Glob v1.5.0 [3e5b6fbb] + HostCPUFeatures v0.1.18 [34004b35] + HypergeometricFunctions v0.3.28 [09f84164] + HypothesisTests v0.11.8 [615f187c] + IfElse v0.1.1 [842dd82b] + InlineStrings v1.4.5 [3587e190] + InverseFunctions v0.1.17 [41ab1584] + InvertedIndices v1.3.1 [92d709cd] + IrrationalConstants v0.2.6 [82899510] + IteratorInterfaceExtensions v1.0.0 [692b3bcd] + JLLWrappers v1.8.0 [b964fa9f] + LaTeXStrings v1.4.0 [10f19ff3] + LayoutPointers v0.1.17 [2ab3a3ac] + LogExpFunctions v1.0.1 [bdcacae8] + LoopVectorization v0.12.174 [1914dd2f] + MacroTools v0.5.16 [d125e4d3] + ManualMemory v0.1.8 [921c7187] + MendelIHT v1.4.11 [e1d29d7a] + Missings v1.2.0 [6fe1bfb0] + OffsetArrays v1.17.0 ⌅ [bac558e1] + OrderedCollections v1.8.2 [90014a1f] + PDMats v0.11.40 [69de0a69] + Parsers v2.8.6 [1d0040c9] + PolyesterWeave v0.2.2 [2dfb63ee] + PooledArrays v1.4.3 [aea7be01] + PrecompileTools v1.3.4 [21216c6a] + Preferences v1.5.2 [08abe8d2] + PrettyTables v3.3.2 [92933f4c] + ProgressMeter v1.11.0 [43287f4e] + PtrArrays v1.4.0 [1fd47b50] + QuadGK v2.11.3 [189a3867] + Reexport v1.2.2 [ae029012] + Requires v1.3.1 [79098fc4] + Rmath v0.9.0 [f2b01f46] + Roots v3.0.0 [fdea26ae] + SIMD v3.7.2 [94e857df] + SIMDTypes v0.1.0 [476501e8] + SLEEFPirates v0.6.46 [0aa819cd] + SQLite v1.8.1 [431bcebd] + SciMLPublic v1.2.1 [91c51154] + SentinelArrays v1.4.10 [1277b4bf] + ShiftedArrays v2.0.0 [4e780e97] + SnpArrays v0.3.23 [a2af1166] + SortingAlgorithms v1.2.3 [276daf66] + SpecialFunctions v2.8.0 [aedffcd0] + Static v1.4.2 [0d7ed370] + StaticArrayInterface v1.10.0 [10745b16] + Statistics v1.11.1 [82ae8749] + StatsAPI v1.8.0 [2913bbd2] + StatsBase v0.34.12 [4c63d2b9] + StatsFuns v2.2.0 [3eaba693] + StatsModels v0.7.10 [892a3eda] + StringManipulation v0.4.4 [3783bdb8] + TableTraits v1.0.1 [bd369af6] + Tables v1.13.0 [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 v0.5.1+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 v1.11.0 [f43a241f] + Downloads v1.7.0 [7b1f6079] + FileWatching v1.11.0 [9fa8497b] + Future v1.11.0 [b77e0a4c] + InteractiveUtils v1.11.0 [ac6e5ff7] + JuliaSyntaxHighlighting v1.13.0 [b27032c2] + LibCURL v1.0.0 [76f85450] + LibGit2 v1.11.0 [8f399da3] + Libdl v1.11.0 [37e2e46d] + LinearAlgebra v1.14.0 [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 v1.5.5+2 [deac9b47] + LibCURL_jll v8.20.0+1 [e37daf67] + LibGit2_jll v1.9.4+0 [29816b5a] + LibSSH2_jll v1.11.101+0 [14a3606d] + MozillaCACerts_jll v2026.5.14 [4536629a] + OpenBLAS_jll v0.3.33+0 [05823500] + OpenLibm_jll v0.8.7+0 [458c3c95] + OpenSSL_jll v3.5.7+0 [efcefdf7] + PCRE2_jll v10.47.0+0 [bea87d4a] + SuiteSparse_jll v7.10.1+0 [83775a58] + Zlib_jll v1.3.2+0 [3161d3a3] + Zstd_jll v1.5.7+1 [8e850b90] + libblastrampoline_jll v5.15.0+0 [8e850ede] + nghttp2_jll v1.69.0+0 [3f19e933] + p7zip_jll v17.8.0+0 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. To see why use `status --outdated -m` Installation completed after 5.82s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompiling project... 4.7 s ✓ BGEN 7.6 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`. 23.4 s ✓ MendelIHT 3 dependencies successfully precompiled in 43 seconds. 172 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 65.08s ################################################################################ # Testing # Testing MendelIHT Status `/tmp/jl_NyIcB6/Project.toml` ⌅ [6db4b851] BGEN v0.1.17 [6e4b80f9] BenchmarkTools v1.8.0 [336ed68f] CSV v0.10.16 [a93c6f00] DataFrames v1.8.2 [8bb1440f] DelimitedFiles v1.9.1 [b4f34e82] Distances v0.10.12 [31c24e10] Distributions v0.25.129 [38e38edf] GLM v1.9.5 [921c7187] MendelIHT v1.4.11 [92933f4c] ProgressMeter v1.11.0 [189a3867] Reexport v1.2.2 [4e780e97] SnpArrays v0.3.23 [276daf66] SpecialFunctions v2.8.0 [2913bbd2] StatsBase v0.34.12 [a620830f] VCFTools v0.2.10 [37e2e46d] LinearAlgebra v1.14.0 [44cfe95a] Pkg v1.14.0 [9a3f8284] Random v1.11.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_NyIcB6/Manifest.toml` [7d9f7c33] Accessors v0.1.45 [79e6a3ab] Adapt v4.7.0 [66dad0bd] AliasTables v1.1.3 [4fba245c] ArrayInterface v7.27.0 [67c07d97] Automa v1.2.0 ⌅ [6db4b851] BGEN v0.1.17 [28d598bf] BGZFStreams v0.3.2 [6e4b80f9] BenchmarkTools v1.8.0 [47718e42] BioGenerics v0.1.5 [62783981] BitTwiddlingConvenienceFunctions v0.1.6 [e1450e63] BufferedStreams v1.2.2 [2a0fbf3d] CPUSummary v0.2.7 [336ed68f] CSV v0.10.16 [fb6a15b2] CloseOpenIntervals v0.1.13 [523fee87] CodecBzip2 v0.8.5 [ba30903b] CodecXz v0.7.4 [944b1d66] CodecZlib v0.7.8 [6b39b394] CodecZstd v0.8.7 [861a8166] Combinatorics v1.1.0 [38540f10] CommonSolve v0.2.9 [f70d9fcc] CommonWorldInvalidations v1.1.0 [34da2185] Compat v4.18.1 [a33af91c] CompositionsBase v0.1.2 [187b0558] ConstructionBase v1.6.0 [adafc99b] CpuId v0.3.1 [a8cc5b0e] Crayons v4.1.1 [a10d1c49] DBInterface v2.6.1 [9a962f9c] DataAPI v1.16.0 [a93c6f00] DataFrames v1.8.2 [864edb3b] DataStructures v0.19.5 [e2d170a0] DataValueInterfaces v1.0.0 [8bb1440f] DelimitedFiles v1.9.1 [b4f34e82] Distances v0.10.12 [31c24e10] Distributions v0.25.129 [ffbed154] DocStringExtensions v0.9.5 [48062228] FilePathsBase v0.9.24 [1a297f60] FillArrays v1.16.0 [38e38edf] GLM v1.9.5 [c27321d9] Glob v1.5.0 [3e5b6fbb] HostCPUFeatures v0.1.18 [34004b35] HypergeometricFunctions v0.3.28 [09f84164] HypothesisTests v0.11.8 [615f187c] IfElse v0.1.1 [842dd82b] InlineStrings v1.4.5 [3587e190] InverseFunctions v0.1.17 [41ab1584] InvertedIndices v1.3.1 [92d709cd] IrrationalConstants v0.2.6 [82899510] IteratorInterfaceExtensions v1.0.0 [692b3bcd] JLLWrappers v1.8.0 [682c06a0] JSON v1.6.1 [b964fa9f] LaTeXStrings v1.4.0 [10f19ff3] LayoutPointers v0.1.17 [2ab3a3ac] LogExpFunctions v1.0.1 [bdcacae8] LoopVectorization v0.12.174 [1914dd2f] MacroTools v0.5.16 [d125e4d3] ManualMemory v0.1.8 [921c7187] MendelIHT v1.4.11 [e1d29d7a] Missings v1.2.0 [6fe1bfb0] OffsetArrays v1.17.0 ⌅ [bac558e1] OrderedCollections v1.8.2 [90014a1f] PDMats v0.11.40 [69de0a69] Parsers v2.8.6 [1d0040c9] PolyesterWeave v0.2.2 [2dfb63ee] PooledArrays v1.4.3 [aea7be01] PrecompileTools v1.3.4 [21216c6a] Preferences v1.5.2 [08abe8d2] PrettyTables v3.3.2 [92933f4c] ProgressMeter v1.11.0 [43287f4e] PtrArrays v1.4.0 [1fd47b50] QuadGK v2.11.3 [189a3867] Reexport v1.2.2 [ae029012] Requires v1.3.1 [79098fc4] Rmath v0.9.0 [f2b01f46] Roots v3.0.0 [fdea26ae] SIMD v3.7.2 [94e857df] SIMDTypes v0.1.0 [476501e8] SLEEFPirates v0.6.46 [0aa819cd] SQLite v1.8.1 [431bcebd] SciMLPublic v1.2.1 [91c51154] SentinelArrays v1.4.10 [1277b4bf] ShiftedArrays v2.0.0 [4e780e97] SnpArrays v0.3.23 [a2af1166] SortingAlgorithms v1.2.3 [276daf66] SpecialFunctions v2.8.0 [aedffcd0] Static v1.4.2 [0d7ed370] StaticArrayInterface v1.10.0 [10745b16] Statistics v1.11.1 [82ae8749] StatsAPI v1.8.0 [2913bbd2] StatsBase v0.34.12 [4c63d2b9] StatsFuns v2.2.0 [3eaba693] StatsModels v0.7.10 [892a3eda] StringManipulation v0.4.4 [ec057cc2] StructUtils v2.8.2 [3783bdb8] TableTraits v1.0.1 [bd369af6] Tables v1.13.0 [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 v0.5.1+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 v1.11.0 [f43a241f] Downloads v1.7.0 [7b1f6079] FileWatching v1.11.0 [9fa8497b] Future v1.11.0 [b77e0a4c] InteractiveUtils v1.11.0 [ac6e5ff7] JuliaSyntaxHighlighting v1.13.0 [b27032c2] LibCURL v1.0.0 [76f85450] LibGit2 v1.11.0 [8f399da3] Libdl v1.11.0 [37e2e46d] LinearAlgebra v1.14.0 [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 v1.5.5+2 [deac9b47] LibCURL_jll v8.20.0+1 [e37daf67] LibGit2_jll v1.9.4+0 [29816b5a] LibSSH2_jll v1.11.101+0 [14a3606d] MozillaCACerts_jll v2026.5.14 [4536629a] OpenBLAS_jll v0.3.33+0 [05823500] OpenLibm_jll v0.8.7+0 [458c3c95] OpenSSL_jll v3.5.7+0 [efcefdf7] PCRE2_jll v10.47.0+0 [bea87d4a] SuiteSparse_jll v7.10.1+0 [83775a58] Zlib_jll v1.3.2+0 [3161d3a3] Zstd_jll v1.5.7+1 [8e850b90] libblastrampoline_jll v5.15.0+0 [8e850ede] nghttp2_jll v1.69.0+0 [3f19e933] p7zip_jll v17.8.0+0 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. Testing Running tests... ┌ Warning: 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/XAng5/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 15.8s Test Summary: | Pass Total Time deviance | 1 1 0.4s Test Summary: | Pass Total Time update_μ! | 4 4 1.5s Test Summary: | Pass Total Time _choose! | 7 7 9.9s Test Summary: | Pass Total Time _iht_backtrack | 7 7 0.0s Test Summary: | Pass Total Time standardize! | 12 12 1.3s Test Summary: | Pass Total Time project_k! | 2 2 1.0s Test Summary: | Pass Total Time project_group_sparse! | 5 5 1.1s Test Summary: | Pass Total Time maf_weights | 6 6 2.1s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse linear regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1790.3379386681602, backtracks = 0, tol = 1.8958887859222564 Iteration 2: loglikelihood = -1462.4436225160148, backtracks = 0, tol = 0.17553300472420347 Iteration 3: loglikelihood = -1419.714244427062, backtracks = 0, tol = 0.05987147755904731 Iteration 4: loglikelihood = -1418.6355077633607, backtracks = 0, tol = 0.006844371518018372 Iteration 5: loglikelihood = -1418.6190144146922, backtracks = 0, tol = 0.0008612471775229349 Iteration 6: loglikelihood = -1418.6187031035074, backtracks = 0, tol = 0.00012465469702944496 Iteration 7: loglikelihood = -1418.6186970125586, backtracks = 0, tol = 1.845063138694471e-5 IHT estimated 10 nonzero SNP predictors and 1 non-genetic predictors. Compute time (sec): 0.06287097930908203 Final loglikelihood: -1418.6186970125586 SNP PVE: 0.9460374895654483 Iterations: 7 Selected genetic predictors: 10×2 DataFrame Row │ Position Estimated_β │ Int64 Float64 ─────┼─────────────────────── 1 │ 960 0.577266 2 │ 2727 -0.520246 3 │ 3443 2.26182 4 │ 3693 -0.326591 5 │ 4260 1.09474 6 │ 5912 -1.83056 7 │ 7918 -1.77105 8 │ 8188 1.70186 9 │ 8518 -0.719651 10 │ 9790 0.185525 Selected nongenetic predictors: 1×2 DataFrame Row │ Position Estimated_β │ Int64 Float64 ─────┼─────────────────────── 1 │ 1 -0.00651875Test Summary: | Pass Total Time fit normal SnpLinAlg | 4 4 22.7s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse logistic regression Number of threads = 1 Link functin = LogitLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -379.72375963518977, backtracks = 0, tol = 0.6062552017348442 Iteration 2: loglikelihood = -294.14222098196217, backtracks = 0, tol = 0.39035964909167 Iteration 3: loglikelihood = -258.44215825745147, backtracks = 0, tol = 0.18072720194601524 Iteration 4: loglikelihood = -248.39092317275637, backtracks = 1, tol = 0.0581811999889429 Iteration 5: loglikelihood = -241.2861695402178, backtracks = 2, tol = 0.10199490430383734 Iteration 6: loglikelihood = -236.0344401262056, backtracks = 2, tol = 0.10444957184614982 Iteration 7: loglikelihood = -232.75639772007577, backtracks = 2, tol = 0.03618239958756675 Iteration 8: loglikelihood = -230.9028935826695, backtracks = 3, tol = 0.022566251649321353 Iteration 9: loglikelihood = -229.2332883500926, backtracks = 3, tol = 0.02394599965909332 Iteration 10: loglikelihood = -227.8109863155336, backtracks = 3, tol = 0.02260237147851236 Iteration 11: loglikelihood = -226.61429831284372, backtracks = 3, tol = 0.02153016573221634 Iteration 12: loglikelihood = -225.614543213995, backtracks = 3, tol = 0.020073248773013197 Iteration 13: loglikelihood = -225.15228734295533, backtracks = 3, tol = 0.10266272165892033 Iteration 14: loglikelihood = -224.5524858306654, backtracks = 2, tol = 0.010910053499902256 Iteration 15: loglikelihood = -223.90430308527087, backtracks = 3, tol = 0.10669566586572145 Iteration 16: loglikelihood = -223.43342440058004, backtracks = 1, tol = 0.009912340440473734 Iteration 17: loglikelihood = -223.19474883510568, backtracks = 3, tol = 0.10429355504005154 Iteration 18: loglikelihood = -222.7530868660152, backtracks = 1, tol = 0.010133510239484585 Iteration 19: loglikelihood = -222.4546375562022, backtracks = 3, tol = 0.009382230171462355 Iteration 20: loglikelihood = -225.04961416047087, backtracks = 3, tol = 0.13141028198780508 Iteration 21: loglikelihood = -221.57583298738808, backtracks = 0, tol = 0.12983606150115481 Iteration 22: loglikelihood = -220.9953587123894, backtracks = 0, tol = 0.018278220962270587 Iteration 23: loglikelihood = -220.46528702030645, backtracks = 0, tol = 0.10912949798131547 Iteration 24: loglikelihood = -220.22939682199817, backtracks = 1, tol = 0.006133557493960293 Iteration 25: loglikelihood = -220.1149031779291, backtracks = 3, tol = 0.005637364497494655 Iteration 26: loglikelihood = -237.91408320706802, backtracks = 3, tol = 0.1311916630585333 Iteration 27: loglikelihood = -222.6667401701631, backtracks = 0, tol = 0.13008576394077564 Iteration 28: loglikelihood = -220.0179912284672, backtracks = 0, tol = 0.10981267805412102 Iteration 29: loglikelihood = -219.80873468505163, backtracks = 1, tol = 0.006242686572879014 Iteration 30: loglikelihood = -219.71412932030552, backtracks = 1, tol = 0.0052581541847830735 Iteration 31: loglikelihood = -219.67346582214395, backtracks = 3, tol = 0.002736072071808146 Iteration 32: loglikelihood = -236.63118723570068, backtracks = 3, tol = 0.12536959025201838 Iteration 33: loglikelihood = -222.42522446507616, backtracks = 0, tol = 0.12480632457239557 Iteration 34: loglikelihood = -219.76952387571325, backtracks = 0, tol = 0.10782393864869841 Iteration 35: loglikelihood = -219.54239052596037, backtracks = 0, tol = 0.010969385336776636 Iteration 36: loglikelihood = -219.51051719556185, backtracks = 0, tol = 0.0038143069815270263 Iteration 37: loglikelihood = -219.49562270628724, backtracks = 1, tol = 0.0015360028505860806 Iteration 38: loglikelihood = -222.2776344615594, backtracks = 3, tol = 0.10706948875570901 Iteration 39: loglikelihood = -219.86344247649652, backtracks = 0, tol = 0.10682440099239575 Iteration 40: loglikelihood = -219.50637292175287, backtracks = 0, tol = 0.010145149683589566 Iteration 41: loglikelihood = -219.45601478260392, backtracks = 0, tol = 0.004786594360325445 Iteration 42: loglikelihood = -219.44279315931445, backtracks = 0, tol = 0.0023300326568676676 Iteration 43: loglikelihood = -219.434262597912, backtracks = 0, tol = 0.002159682320412748 Iteration 44: loglikelihood = -219.42706752504972, backtracks = 0, tol = 0.0019986878272562235 Iteration 45: loglikelihood = -219.4208881668612, backtracks = 0, tol = 0.001781315196828412 Iteration 46: loglikelihood = -219.41556755717227, backtracks = 0, tol = 0.0017266268818688624 Iteration 47: loglikelihood = -219.41098445944962, backtracks = 0, tol = 0.001504993867218278 Iteration 48: loglikelihood = -219.4070309112888, backtracks = 0, tol = 0.001495426527055874 Iteration 49: loglikelihood = -219.40362030781677, backtracks = 0, tol = 0.001286324051089446 Iteration 50: loglikelihood = -219.4006747755802, backtracks = 0, tol = 0.001295957349435961 Iteration 51: loglikelihood = -219.39813103252988, backtracks = 0, tol = 0.0011058748112207813 Iteration 52: loglikelihood = -219.3959322024177, backtracks = 0, tol = 0.0011233728145861855 Iteration 53: loglikelihood = -219.39403166729804, backtracks = 0, tol = 0.0009536994758608786 Iteration 54: loglikelihood = -219.39238763268273, backtracks = 0, tol = 0.0009739180646352119 Iteration 55: loglikelihood = -219.39096560226784, backtracks = 0, tol = 0.0008239389039648708 Iteration 56: loglikelihood = -219.38973473800374, backtracks = 0, tol = 0.0008444580901064712 Iteration 57: loglikelihood = -219.3886694316569, backtracks = 0, tol = 0.0007126409505425607 Iteration 58: loglikelihood = -219.38774685610232, backtracks = 0, tol = 0.0007323063866727435 Iteration 59: loglikelihood = -219.3869479529937, backtracks = 0, tol = 0.00061686194275372 Iteration 60: loglikelihood = -219.3862557798823, backtracks = 0, tol = 0.0006351404346176769 Iteration 61: loglikelihood = -219.3856561234815, backtracks = 0, tol = 0.000534269842115572 Iteration 62: loglikelihood = -219.38513638040487, backtracks = 0, tol = 0.0005509480422217535 Iteration 63: loglikelihood = -219.38468593224545, backtracks = 0, tol = 0.0004629512780606966 Iteration 64: loglikelihood = -219.38429538513583, backtracks = 0, tol = 0.0004779860767529819 Iteration 65: loglikelihood = -219.38395679466737, backtracks = 0, tol = 0.0004013057505476397 Iteration 66: loglikelihood = -219.38366314739872, backtracks = 0, tol = 0.0004147454994836376 Iteration 67: loglikelihood = -219.38340849212824, backtracks = 0, tol = 0.00034797985178746597 Iteration 68: loglikelihood = -219.38318758502183, backtracks = 0, tol = 0.0003599207374415984 Iteration 69: loglikelihood = -219.38299596326374, backtracks = 0, tol = 0.0003018217223394219 Iteration 70: loglikelihood = -219.3828297011887, backtracks = 0, tol = 0.00031238270039476616 Iteration 71: loglikelihood = -219.38268544908368, backtracks = 0, tol = 0.00026184698528793125 Iteration 72: loglikelihood = -219.3825602648841, backtracks = 0, tol = 0.0002711550905775348 Iteration 73: loglikelihood = -219.38245163239276, backtracks = 0, tol = 0.00022721198022395564 Iteration 74: loglikelihood = -219.38235734460943, backtracks = 0, tol = 0.00023539371282360467 Iteration 75: loglikelihood = -219.38227551018164, backtracks = 0, tol = 0.0001971920991460162 Iteration 76: loglikelihood = -219.382204472153, backtracks = 0, tol = 0.00020436848993624394 Iteration 77: loglikelihood = -219.3821428080304, backtracks = 0, tol = 0.00017116393516432852 Iteration 78: loglikelihood = -219.38208927292968, backtracks = 0, tol = 0.00017744788492952903 Iteration 79: loglikelihood = -219.38204279645043, backtracks = 0, tol = 0.00014859040670150365 Iteration 80: loglikelihood = -219.38200244272016, backtracks = 0, tol = 0.00015408544066832546 Iteration 81: loglikelihood = -219.38196740593906, backtracks = 0, tol = 0.00012900826739905896 Iteration 82: loglikelihood = -219.38193698216227, backtracks = 0, tol = 0.00013380816660865064 Iteration 83: loglikelihood = -219.38191056455443, backtracks = 0, tol = 0.00011201756190578927 Iteration 84: loglikelihood = -219.3818876233726, backtracks = 0, tol = 0.000116206527337935 Iteration 85: loglikelihood = -219.38186770147453, backtracks = 0, tol = 9.727268703830643e-5 Test Summary: | Pass Total Time fit Bernoulli SnpLinAlg | 4 4 4.1s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse Poisson regression Number of threads = 1 Link functin = LogLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -4879.307009926062, backtracks = 0, tol = 0.5000752565458498 Iteration 2: loglikelihood = -2398.9095436070775, backtracks = 0, tol = 0.09337636312444622 Iteration 3: loglikelihood = -1675.8561362655269, backtracks = 0, tol = 0.08582220388365895 Iteration 4: loglikelihood = -1547.379471145526, backtracks = 0, tol = 0.0515712710849079 Iteration 5: loglikelihood = -1492.9095008670747, backtracks = 0, tol = 0.08912006017595733 Iteration 6: loglikelihood = -1437.9550168189403, backtracks = 0, tol = 0.09350470353549765 Iteration 7: loglikelihood = -1409.0927302317837, backtracks = 0, tol = 0.03179690280754624 Iteration 8: loglikelihood = -1377.611334017694, backtracks = 1, tol = 0.05720541599876541 Iteration 9: loglikelihood = -1365.5893818702625, backtracks = 0, tol = 0.05502095084422332 Iteration 10: loglikelihood = -1359.4364918687365, backtracks = 0, tol = 0.02360209506195738 Iteration 11: loglikelihood = -1356.4659123727367, backtracks = 0, tol = 0.02296814501446394 Iteration 12: loglikelihood = -1354.3724898675252, backtracks = 0, tol = 0.013237250560035559 Iteration 13: loglikelihood = -1352.9474455352542, backtracks = 0, tol = 0.013962730794714679 Iteration 14: loglikelihood = -1351.8854974188598, backtracks = 0, tol = 0.00938701859057263 Iteration 15: loglikelihood = -1351.1131970090073, backtracks = 0, tol = 0.009565522930360271 Iteration 16: loglikelihood = -1350.5250571355523, backtracks = 0, tol = 0.006978766246480297 Iteration 17: loglikelihood = -1350.0861108236081, backtracks = 0, tol = 0.006850903723071448 Iteration 18: loglikelihood = -1349.7488025396635, backtracks = 0, tol = 0.0052859893088598 Iteration 19: loglikelihood = -1349.4941721734656, backtracks = 0, tol = 0.005022669303817889 Iteration 20: loglikelihood = -1349.297934426469, backtracks = 0, tol = 0.004034294076137686 Iteration 21: loglikelihood = -1349.1490577222603, backtracks = 0, tol = 0.0037311450378601867 Iteration 22: loglikelihood = -1349.034345567781, backtracks = 0, tol = 0.0030867055459242137 Iteration 23: loglikelihood = -1348.9471536879919, backtracks = 0, tol = 0.002793032907627109 Iteration 24: loglikelihood = -1348.8800841443335, backtracks = 0, tol = 0.00236187098068721 Iteration 25: loglikelihood = -1348.8290846693124, backtracks = 0, tol = 0.0021002430181549987 Iteration 26: loglikelihood = -1348.7899438258044, backtracks = 0, tol = 0.0018054061443100223 Iteration 27: loglikelihood = -1348.7601898555538, backtracks = 0, tol = 0.0015835158379538473 Iteration 28: loglikelihood = -1348.7374080201341, backtracks = 0, tol = 0.0013780863549322537 Iteration 29: loglikelihood = -1348.7200995577025, backtracks = 0, tol = 0.0011958076883465869 Iteration 30: loglikelihood = -1348.7068757659604, backtracks = 0, tol = 0.001050363368995777 Iteration 31: loglikelihood = -1348.6968353326754, backtracks = 0, tol = 0.0009038695373239541 Iteration 32: loglikelihood = -1348.6891789103831, backtracks = 0, tol = 0.0007994960046667786 Iteration 33: loglikelihood = -1348.6833690744538, backtracks = 0, tol = 0.000683580273536794 Iteration 34: loglikelihood = -1348.678945762205, backtracks = 0, tol = 0.0006078374519838613 Iteration 35: loglikelihood = -1348.6755910153818, backtracks = 0, tol = 0.0005171476727740183 Iteration 36: loglikelihood = -1348.6730401845061, backtracks = 0, tol = 0.0004616781858378682 Iteration 37: loglikelihood = -1348.6711064125814, backtracks = 0, tol = 0.0003913119808849324 Iteration 38: loglikelihood = -1348.6696375600711, backtracks = 0, tol = 0.00035039056397096076 Iteration 39: loglikelihood = -1348.66852442263, backtracks = 0, tol = 0.0002961292236784147 Iteration 40: loglikelihood = -1348.6676795954818, backtracks = 0, tol = 0.0002657641613221232 Iteration 41: loglikelihood = -1348.6670395413319, backtracks = 0, tol = 0.00022411399460311242 Iteration 42: loglikelihood = -1348.6665540743484, backtracks = 0, tol = 0.00020147887397833713 Iteration 43: loglikelihood = -1348.6661863579764, backtracks = 0, tol = 0.00016961900520601504 Iteration 44: loglikelihood = -1348.6659075904556, backtracks = 0, tol = 0.0001526858447502832 Iteration 45: loglikelihood = -1348.6656964744864, backtracks = 0, tol = 0.00012837809375750166 Iteration 46: loglikelihood = -1348.6655364871203, backtracks = 0, tol = 0.00011567556264654733 Iteration 47: loglikelihood = -1348.6654153416484, backtracks = 0, tol = 9.716594380562891e-5 Test Summary: | Pass Total Time fit Poisson SnpLinAlg | 4 4 3.3s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse NegativeBinomial regression Number of threads = 1 Link functin = LogLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1739.246224460148, backtracks = 0, tol = 0.48328079096773124 Iteration 2: loglikelihood = -1620.356422924068, backtracks = 0, tol = 0.172808650070122 Iteration 3: loglikelihood = -1562.5180500114895, backtracks = 0, tol = 0.11406787121606292 Iteration 4: loglikelihood = -1542.2716924735678, backtracks = 0, tol = 0.09767910070033277 Iteration 5: loglikelihood = -1540.535651053808, backtracks = 1, tol = 0.016081963536110914 Iteration 6: loglikelihood = -1539.8484812034292, backtracks = 1, tol = 0.014870731049877921 Iteration 7: loglikelihood = -1539.6122792256365, backtracks = 1, tol = 0.00945746764592976 Iteration 8: loglikelihood = -1539.547512587664, backtracks = 1, tol = 0.005005902432924898 Iteration 9: loglikelihood = -1539.5305516696149, backtracks = 1, tol = 0.0025835079642868015 Iteration 10: loglikelihood = -1539.5261867244392, backtracks = 1, tol = 0.0013039224697697 Iteration 11: loglikelihood = -1539.5250689256166, backtracks = 1, tol = 0.0006641270345994375 Iteration 12: loglikelihood = -1539.524784375863, backtracks = 1, tol = 0.0003329601509241211 Iteration 13: loglikelihood = -1539.5247118746972, backtracks = 1, tol = 0.00016919024362392515 Iteration 14: loglikelihood = -1539.5246934644576, backtracks = 1, tol = 8.466503708332886e-5 Test Summary: | Pass Total Time fit NegativeBinomial SnpLinAlg | 4 4 1.3s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse linear regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1806.5594034441697, backtracks = 0, tol = 0.7871638435915012 Iteration 2: loglikelihood = -1443.727919892139, backtracks = 0, tol = 0.1135020613774078 Iteration 3: loglikelihood = -1408.159345910739, backtracks = 0, tol = 0.04523602887109763 Iteration 4: loglikelihood = -1407.58147521395, backtracks = 0, tol = 0.02921969164918464 Iteration 5: loglikelihood = -1407.2201567412253, backtracks = 0, tol = 0.0030985861481926343 Iteration 6: loglikelihood = -1407.2103328050266, backtracks = 0, tol = 0.0005269329187552569 Iteration 7: loglikelihood = -1407.2100388656065, backtracks = 0, tol = 8.720858465618742e-5 Test Summary: | Pass Total Time fit with >1 non-genetic covariates SnpLinAlg | 5 5 1.7s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse linear regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1602.9396723137477, backtracks = 0, tol = 0.4152530240199067 Iteration 2: loglikelihood = -1435.638266488519, backtracks = 0, tol = 0.10597805366263197 Iteration 3: loglikelihood = -1410.7390425074552, backtracks = 0, tol = 0.04039956575844047 Iteration 4: loglikelihood = -1408.036561862484, backtracks = 0, tol = 0.030008601296655696 Iteration 5: loglikelihood = -1407.8845276654397, backtracks = 0, tol = 0.0023876154251211983 Iteration 6: loglikelihood = -1407.883201305375, backtracks = 0, tol = 0.00024093388947179866 Iteration 7: loglikelihood = -1407.8831822565676, backtracks = 1, tol = 2.1986953482083855e-5 Test Summary: | Pass Total Time model selection on non-genetic covariates | 5 5 0.8s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse linear regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 15 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1473.12410014528, backtracks = 0, tol = 0.11162633196865429 Iteration 2: loglikelihood = -1448.37403799896, backtracks = 0, tol = 0.07736217654955346 Iteration 3: loglikelihood = -1429.8981769610311, backtracks = 1, tol = 0.056531823476744666 Iteration 4: loglikelihood = -1404.7133956159753, backtracks = 0, tol = 0.10125409614175711 Iteration 5: loglikelihood = -1397.466171579031, backtracks = 0, tol = 0.05343369325195712 Iteration 6: loglikelihood = -1395.7490747391416, backtracks = 0, tol = 0.08843871418165569 Iteration 7: loglikelihood = -1395.4877576477586, backtracks = 0, tol = 0.0089247040684952 Iteration 8: loglikelihood = -1395.442237061722, backtracks = 0, tol = 0.005277867116132827 Iteration 9: loglikelihood = -1395.4302205892106, backtracks = 0, tol = 0.0027680467744013336 Iteration 10: loglikelihood = -1395.1973617039414, backtracks = 0, tol = 0.0905690065560604 Iteration 11: loglikelihood = -1395.0048067729406, backtracks = 0, tol = 0.007650485819168939 Iteration 12: loglikelihood = -1394.9835209063683, backtracks = 0, tol = 0.0035232591741737973 Iteration 13: loglikelihood = -1394.9793628241396, backtracks = 0, tol = 0.001852195878065177 Iteration 14: loglikelihood = -1394.9779889816232, backtracks = 0, tol = 0.0012530451800711444 Iteration 15: loglikelihood = -1394.977503420045, backtracks = 0, tol = 0.0006829444661300923 Iteration 16: loglikelihood = -1394.9773714862843, backtracks = 1, tol = 0.00022881022816864142 Iteration 17: loglikelihood = -1394.977310220191, backtracks = 2, tol = 0.0001217788197399568 Iteration 18: loglikelihood = -1394.977273607278, backtracks = 2, tol = 8.822469907087602e-5 **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse linear regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 3 Prior weight scaling = off Doubly sparse projection = on Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1535.4672180567934, backtracks = 0, tol = 0.17016419679985048 Iteration 2: loglikelihood = -1508.04343741211, backtracks = 0, tol = 0.21718489399873087 Iteration 3: loglikelihood = -1448.2717322168082, backtracks = 0, tol = 0.15334504607402907 Iteration 4: loglikelihood = -1437.5669418734744, backtracks = 0, tol = 0.08425396177776269 Iteration 5: loglikelihood = -1434.3602241747528, backtracks = 0, tol = 0.03199716666887782 Iteration 6: loglikelihood = -1434.239273652971, backtracks = 2, tol = 0.003498168340088273 Iteration 7: loglikelihood = -1434.1475478538455, backtracks = 2, tol = 0.0030522911015526556 Iteration 8: loglikelihood = -1434.0913475157126, backtracks = 2, tol = 0.0021931576818355514 Iteration 9: loglikelihood = -1434.0584761985995, backtracks = 2, tol = 0.0016688209654910561 Iteration 10: loglikelihood = -1434.0393127719108, backtracks = 2, tol = 0.001317554485128468 Iteration 11: loglikelihood = -1434.0281644425422, backtracks = 2, tol = 0.0010393713220469248 Iteration 12: loglikelihood = -1434.0216963632631, backtracks = 2, tol = 0.0008158673348111212 Iteration 13: loglikelihood = -1434.0179556115852, backtracks = 2, tol = 0.0006363671566384319 Iteration 14: loglikelihood = -1433.8972844529703, backtracks = 2, tol = 0.02105646084267335 Iteration 15: loglikelihood = -1433.6170929347984, backtracks = 1, tol = 0.011448126839540936 Iteration 16: loglikelihood = -1433.5408744767515, backtracks = 2, tol = 0.0040324300639331045 Iteration 17: loglikelihood = -1433.4945867179188, backtracks = 2, tol = 0.003005268578298657 Iteration 18: loglikelihood = -1433.467626121943, backtracks = 2, tol = 0.002187229771831438 Iteration 19: loglikelihood = -1433.4521439235273, backtracks = 2, tol = 0.0016467936133078437 Iteration 20: loglikelihood = -1433.4432822302874, backtracks = 2, tol = 0.0012631945762950846 Iteration 21: loglikelihood = -1433.4382075829426, backtracks = 2, tol = 0.0009580287583338291 Iteration 22: loglikelihood = -1433.4352962137846, backtracks = 2, tol = 0.0007222437442123496 Iteration 23: loglikelihood = -1433.4336216439426, backtracks = 2, tol = 0.0005424739396431532 Iteration 24: loglikelihood = -1433.43265547142, backtracks = 2, tol = 0.00040628145880685523 Iteration 25: loglikelihood = -1433.4320960523787, backtracks = 2, tol = 0.0003034179918772475 Iteration 26: loglikelihood = -1433.4317709097872, backtracks = 2, tol = 0.00022583740291084404 Iteration 27: loglikelihood = -1433.4315812027676, backtracks = 2, tol = 0.0001673653861249394 Iteration 28: loglikelihood = -1432.5898379532837, backtracks = 2, tol = 0.025080215054031605 Iteration 29: loglikelihood = -1431.7678006470733, backtracks = 1, tol = 0.017181190475547538 Iteration 30: loglikelihood = -1430.3157393955933, backtracks = 1, tol = 0.07333968264200234 Iteration 31: loglikelihood = -1429.706868513855, backtracks = 0, tol = 0.020015111727945754 Iteration 32: loglikelihood = -1429.5802551945537, backtracks = 1, tol = 0.00756937670420323 Iteration 33: loglikelihood = -1429.5139450553559, backtracks = 2, tol = 0.003906515984506227 Iteration 34: loglikelihood = -1429.4691972325213, backtracks = 2, tol = 0.003683664863256486 Iteration 35: loglikelihood = -1428.8607526222902, backtracks = 2, tol = 0.08711763846658777 Iteration 36: loglikelihood = -1428.6178427111051, backtracks = 1, tol = 0.006558345246943271 Iteration 37: loglikelihood = -1428.5424083746184, backtracks = 2, tol = 0.0033912200662443866 Iteration 38: loglikelihood = -1428.4933608487952, backtracks = 2, tol = 0.0030098214824111793 Iteration 39: loglikelihood = -1428.4620745885088, backtracks = 2, tol = 0.0025951371119133128 Iteration 40: loglikelihood = -1428.4427329028306, backtracks = 2, tol = 0.002148184701148465 Iteration 41: loglikelihood = -1428.4311433050725, backtracks = 2, tol = 0.0017160493175770867 Iteration 42: loglikelihood = -1428.4243474878394, backtracks = 2, tol = 0.0013407892924840973 Iteration 43: loglikelihood = -1428.420413936832, backtracks = 2, tol = 0.0010343694042998534 Iteration 44: loglikelihood = -1428.4181556141762, backtracks = 2, tol = 0.0007948565534422845 Iteration 45: loglikelihood = -1428.4168664091337, backtracks = 2, tol = 0.000608309643427293 Iteration 46: loglikelihood = -1428.4161334920516, backtracks = 2, tol = 0.0004622621654004415 Iteration 47: loglikelihood = -1428.4157180925672, backtracks = 2, tol = 0.00034956951660978575 Iteration 48: loglikelihood = -1428.4154831711999, backtracks = 2, tol = 0.00026348047442121094 Iteration 49: loglikelihood = -1428.4153505233908, backtracks = 2, tol = 0.00019816133989405092 Iteration 50: loglikelihood = -1428.4152757065372, backtracks = 2, tol = 0.00014882628973647444 Iteration 51: loglikelihood = -1428.4152335404317, backtracks = 2, tol = 0.00011167501044822909 Iteration 52: loglikelihood = -1428.4152097888611, backtracks = 2, tol = 8.375238803842589e-5 Test Summary: | Pass Total Time Correlated predictors and double sparsity Float64 matrix | 2 2 10.3s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse NegativeBinomial regression Number of threads = 1 Link functin = LogLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1489.6794871417972, backtracks = 0, tol = 0.20419386234428719 Iteration 2: loglikelihood = -1422.6635740910274, backtracks = 0, tol = 0.10038930711889289 Iteration 3: loglikelihood = -1418.0584113995642, backtracks = 0, tol = 0.1591805283970545 Iteration 4: loglikelihood = -1378.277828826064, backtracks = 0, tol = 0.15587526142699165 Iteration 5: loglikelihood = -1372.0811904399443, backtracks = 0, tol = 0.038235310548756105 Iteration 6: loglikelihood = -1367.7572222244412, backtracks = 0, tol = 0.07097743986829955 Iteration 7: loglikelihood = -1365.2832292425123, backtracks = 0, tol = 0.07383143580099277 Iteration 8: loglikelihood = -1365.0263237084673, backtracks = 0, tol = 0.008135039010336288 Iteration 9: loglikelihood = -1364.9829587635716, backtracks = 0, tol = 0.0036298043604373158 Iteration 10: loglikelihood = -1364.9702751622567, backtracks = 0, tol = 0.0017331889539182411 Iteration 11: loglikelihood = -1364.966099891954, backtracks = 0, tol = 0.0013476985857203653 Iteration 12: loglikelihood = -1364.964462759818, backtracks = 0, tol = 0.0005175660031302506 Iteration 13: loglikelihood = -1364.9638272405055, backtracks = 0, tol = 0.0005373993187340497 Iteration 14: loglikelihood = -1364.9635696266619, backtracks = 0, tol = 0.00018871868323870107 Iteration 15: loglikelihood = -1364.9634672055668, backtracks = 0, tol = 0.00021817368256078003 Iteration 16: loglikelihood = -1364.963425257382, backtracks = 0, tol = 7.363433002110828e-5 0.977538 seconds (1.55 M allocations: 33.432 MiB, 8.61% gc time, 63.46% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** 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 = -1543.1290890486503, backtracks = 0, tol = 0.20419386234428719 Iteration 2: loglikelihood = -1500.5221904499456, backtracks = 0, tol = 0.1300373495530621 Iteration 3: loglikelihood = -1470.3217261203843, backtracks = 0, tol = 0.0984286044390257 Iteration 4: loglikelihood = -1451.0770169983368, backtracks = 0, tol = 0.09628641939825179 Iteration 5: loglikelihood = -1437.8420179540785, backtracks = 0, tol = 0.07234282352839781 Iteration 6: loglikelihood = -1428.0376222391005, backtracks = 0, tol = 0.01636161442324196 Iteration 7: loglikelihood = -1420.5461884987837, backtracks = 0, tol = 0.0029797521171192436 Iteration 8: loglikelihood = -1414.2564533048817, backtracks = 0, tol = 0.0023186691096463256 Iteration 9: loglikelihood = -1409.0684639418455, backtracks = 0, tol = 0.0008643641121547912 Iteration 10: loglikelihood = -1404.6798134635214, backtracks = 0, tol = 0.000501061271629025 Iteration 11: loglikelihood = -1400.953183963542, backtracks = 0, tol = 0.0006042891282359605 Iteration 12: loglikelihood = -1397.7494062476226, backtracks = 0, tol = 0.0005221893635871229 Iteration 13: loglikelihood = -1394.9774392574795, backtracks = 0, tol = 0.0004920458265641868 Iteration 14: loglikelihood = -1392.5564833555447, backtracks = 0, tol = 0.0004410836011781933 Iteration 15: loglikelihood = -1390.4297847601301, backtracks = 0, tol = 0.0004082503238676747 Iteration 16: loglikelihood = -1388.547871282671, backtracks = 0, tol = 0.0003707039455016335 Iteration 17: loglikelihood = -1386.8743115978727, backtracks = 0, tol = 0.0003450329982758773 Iteration 18: loglikelihood = -1385.3773797533581, backtracks = 0, tol = 0.00031704303630871735 Iteration 19: loglikelihood = -1384.0327817883174, backtracks = 0, tol = 0.00029647758543328184 Iteration 20: loglikelihood = -1382.8193100741232, backtracks = 0, tol = 0.0002748126227434683 Iteration 21: loglikelihood = -1381.7202043854913, backtracks = 0, tol = 0.0002580239197383651 Iteration 22: loglikelihood = -1380.7207872138335, backtracks = 0, tol = 0.00024083414543491774 Iteration 23: loglikelihood = -1379.8091585904303, backtracks = 0, tol = 0.0002269515410333709 Iteration 24: loglikelihood = -1378.9748602350387, backtracks = 0, tol = 0.00021304117846841322 Iteration 25: loglikelihood = -1378.2092333289788, backtracks = 0, tol = 0.00020143362746406193 Iteration 26: loglikelihood = -1377.5046392219926, backtracks = 0, tol = 0.00018998866991287692 Iteration 27: loglikelihood = -1376.854642745781, backtracks = 0, tol = 0.0001801864275448546 Iteration 28: loglikelihood = -1376.253544630079, backtracks = 0, tol = 0.00017063531079251055 Iteration 29: loglikelihood = -1375.6964732331435, backtracks = 0, tol = 0.00016228289058187534 Iteration 30: loglikelihood = -1375.1790968378873, backtracks = 0, tol = 0.00015421391398132953 Iteration 31: loglikelihood = -1374.6976670500144, backtracks = 0, tol = 0.00014703851070048968 Iteration 32: loglikelihood = -1374.2488376600224, backtracks = 0, tol = 0.00014014849359973976 Iteration 33: loglikelihood = -1373.8296826644153, backtracks = 0, tol = 0.00013393812297037843 Iteration 34: loglikelihood = -1373.437579757827, backtracks = 0, tol = 0.00012799941186519384 Iteration 35: loglikelihood = -1373.0702152887923, backtracks = 0, tol = 0.0001225874711481076 Iteration 36: loglikelihood = -1372.7255077926727, backtracks = 0, tol = 0.00011742614576359309 Iteration 37: loglikelihood = -1372.4016065080475, backtracks = 0, tol = 0.00011268032965053816 Iteration 38: loglikelihood = -1372.0968402093547, backtracks = 0, tol = 0.0001081614547159368 Iteration 39: loglikelihood = -1371.8097128326083, backtracks = 0, tol = 0.00010397568281095297 Iteration 40: loglikelihood = -1371.5388685916073, backtracks = 0, tol = 9.999311053104772e-5 0.413257 seconds (1.46 M allocations: 26.501 MiB) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse NegativeBinomial regression Number of threads = 1 Link functin = LogLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -3698.1042, backtracks = 0, tol = 0.09974119604721794 Iteration 2: loglikelihood = -3650.1765, backtracks = 0, tol = 0.04571088131787758 Iteration 3: loglikelihood = -3644.7695, backtracks = 1, tol = 0.014762190379926434 Iteration 4: loglikelihood = -3643.255, backtracks = 1, tol = 0.008422493825660847 Iteration 5: loglikelihood = -3642.8586, backtracks = 1, tol = 0.004376664758600034 Iteration 6: loglikelihood = -3642.7517, backtracks = 1, tol = 0.0022771615680007903 Iteration 7: loglikelihood = -3642.7258, backtracks = 1, tol = 0.0011503784474139233 Iteration 8: loglikelihood = -3642.717, backtracks = 1, tol = 0.00058534035808742 Iteration 9: loglikelihood = -3642.7239, backtracks = 3, tol = 7.349662130558706e-5 25.715957 seconds (12.84 M allocations: 633.178 MiB, 0.70% gc time, 98.45% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** 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 = -3579.5557, backtracks = 0, tol = 0.09974119604721794 Iteration 2: loglikelihood = -3454.348, backtracks = 0, tol = 0.04738640845553645 Iteration 3: loglikelihood = -3240.5332, backtracks = 1, tol = 0.013923189482398308 Iteration 4: loglikelihood = -2999.1785, backtracks = 1, tol = 0.00804807065447854 Iteration 5: loglikelihood = -2981.2603, backtracks = 0, tol = 0.10281688833626178 Iteration 6: loglikelihood = -2731.2595, backtracks = 0, tol = 0.09910994731334732 Iteration 7: loglikelihood = -2612.7712, backtracks = 0, tol = 0.09255299308165095 Iteration 8: loglikelihood = -2489.344, backtracks = 0, tol = 0.093167319367277 Iteration 9: loglikelihood = -2398.6206, backtracks = 0, tol = 0.01777878307264915 Iteration 10: loglikelihood = -2350.1, backtracks = 0, tol = 0.09270975796139144 Iteration 11: loglikelihood = -2279.601, backtracks = 0, tol = 0.10824572732403645 Iteration 12: loglikelihood = -2241.0256, backtracks = 0, tol = 0.016320615555182674 Iteration 13: loglikelihood = -2216.9302, backtracks = 0, tol = 0.004771650092248574 Iteration 14: loglikelihood = -2206.665, backtracks = 0, tol = 0.09503695504889713 Iteration 15: loglikelihood = -2198.8042, backtracks = 0, tol = 0.09509202585954703 Iteration 16: loglikelihood = -2193.692, backtracks = 0, tol = 0.10168897650796967 Iteration 17: loglikelihood = -2190.434, backtracks = 0, tol = 0.10063865699791683 Iteration 18: loglikelihood = -2189.51, backtracks = 0, tol = 0.10175545559647661 Iteration 19: loglikelihood = -2188.128, backtracks = 0, tol = 0.10072259423695479 Iteration 20: loglikelihood = -2186.2524, backtracks = 1, tol = 0.013074314590241764 Iteration 21: loglikelihood = -2185.9019, backtracks = 1, tol = 0.005366937583436936 Iteration 22: loglikelihood = -2185.8396, backtracks = 1, tol = 0.0024607821012779954 Iteration 23: loglikelihood = -2185.8318, backtracks = 1, tol = 0.0012566471107374009 Iteration 24: loglikelihood = -2185.831, backtracks = 2, tol = 0.00032381851757743335 Iteration 25: loglikelihood = -2185.8298, backtracks = 2, tol = 0.0002610381222117113 Iteration 26: loglikelihood = -2185.8284, backtracks = 2, tol = 0.0002090677340878471 Iteration 27: loglikelihood = -2185.828, backtracks = 2, tol = 0.0001665864335117666 Iteration 28: loglikelihood = -2185.8274, backtracks = 2, tol = 0.00013219013914140876 Iteration 29: loglikelihood = -2185.8235, backtracks = 3, tol = 5.226318448126889e-5 0.278761 seconds (1.82 M allocations: 30.208 MiB, 15.12% gc time) Test Summary: | Pass Total Time Negative binomial nuisance parameter Float32 matrix | 12 12 30.0s **** 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 **** ┌ 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 = 1.0257704354307222 Iteration 2: loglikelihood = -1753.4720992614753, backtracks = 0, tol = 0.28706825512903816 Iteration 3: loglikelihood = -1460.3823326395225, backtracks = 0, tol = 0.1059822007319242 Iteration 4: loglikelihood = -1438.5292259047123, backtracks = 0, tol = 0.028655431669451118 Iteration 5: loglikelihood = -1438.0856032112097, backtracks = 0, tol = 0.0034955373515602557 Iteration 6: loglikelihood = -1438.0744350329464, backtracks = 0, tol = 0.0005882060650840543 Iteration 7: loglikelihood = -1438.0741395461057, backtracks = 0, tol = 8.427264473927088e-5 4.822052 seconds (1.02 M allocations: 132.842 MiB, 0.58% gc time, 90.83% compilation time) Test Summary: | Pass Total Time initialze beta | 1 1 5.3s 10.128310 seconds (4.00 M allocations: 82.389 MiB, 0.24% gc time, 0.63% compilation time) 5.341843 seconds (3.98 M allocations: 91.678 MiB, 0.40% gc time) 10.834127 seconds (20.38 M allocations: 438.642 MiB, 0.64% gc time, 16.85% compilation time: 79% of which was recompilation) 8.651042 seconds (20.18 M allocations: 434.190 MiB, 0.92% gc time) 36.872568 seconds (3.36 M allocations: 4.228 GiB, 6.85% gc time, 30.14% compilation time) 54.504913 seconds (72.50 k allocations: 183.674 MiB, 0.21% gc time) Test Summary: | Pass Total Time memory_efficient keyword | 7 7 2m24.6s Test Summary: | Pass Total Time update_support! | 10 10 0.6s 15.089 ms (78 allocations: 4.56 KiB) 4.476 μs (0 allocations: 0 bytes) 140.098 μs (4 allocations: 288 bytes) 6.820 μs (0 allocations: 0 bytes) 47.419 μs (2 allocations: 64 bytes) 30.630 μs (0 allocations: 0 bytes) 25.440 μs (0 allocations: 0 bytes) 28.430 μs (0 allocations: 0 bytes) 104.029 μs (0 allocations: 0 bytes) 39.776 ms (78 allocations: 4.56 KiB) 18.589 μs (0 allocations: 0 bytes) 172.879 μs (4 allocations: 288 bytes) 33.400 μs (0 allocations: 0 bytes) 246.357 μs (2 allocations: 64 bytes) 86.729 μs (0 allocations: 0 bytes) 130.169 μs (0 allocations: 0 bytes) 146.848 μs (0 allocations: 0 bytes) 219.718 μs (0 allocations: 0 bytes) Test Summary: | Total Time benchmarks for multivariate function | 0 2m10.9s **** 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 **** **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse Multivariate Gaussian regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 12 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -2900.9186300194497, backtracks = 0, tol = 0.1480224208200413 Iteration 2: loglikelihood = -2869.406464695619, backtracks = 0, tol = 0.035126790460779864 Iteration 3: loglikelihood = -2868.084702693443, backtracks = 0, tol = 0.0055693496163324524 Iteration 4: loglikelihood = -2868.034423817725, backtracks = 0, tol = 0.001118951762895177 Iteration 5: loglikelihood = -2868.030857635375, backtracks = 0, tol = 0.00031182601179138955 Iteration 6: loglikelihood = -2868.0305288614227, backtracks = 0, tol = 0.00010393305949947338 Iteration 7: loglikelihood = -2868.0304966516946, backtracks = 0, tol = 3.100862049859014e-5 0.415551 seconds (43.83 k allocations: 5.328 MiB, 62.60% compilation time) Test Summary: | Pass Total Time multivariate fit_iht SnpLinAlg | 7 7 12.7s **** 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 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 1.919042 seconds (256.77 k allocations: 167.476 MiB, 54.96% compilation time) Test Summary: | Pass Total Time initialze beta | 5 5 2.5s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** ┌ 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: 0:03:41 Cross validating... 11%|███▌ | ETA: 0:01:02 Cross validating... 14%|████▋ | ETA: 0:00:47 Cross validating... 17%|█████▋ | ETA: 0:00:38 Cross validating... 21%|██████▋ | ETA: 0:00:31 Cross validating... 24%|███████▋ | ETA: 0:00:26 Cross validating... 27%|████████▋ | ETA: 0:00:23 Cross validating... 30%|█████████▋ | ETA: 0:00:20 Cross validating... 33%|██████████▋ | ETA: 0:00:18 Cross validating... 37%|███████████▋ | ETA: 0:00:16 Cross validating... 40%|████████████▊ | ETA: 0:00:14 Cross validating... 43%|█████████████▊ | ETA: 0:00:12 Cross validating... 46%|██████████████▊ | ETA: 0:00:11 Cross validating... 49%|███████████████▊ | ETA: 0:00:10 Cross validating... 52%|████████████████▊ | ETA: 0:00:09 Cross validating... 54%|█████████████████▎ | ETA: 0:00:08 Cross validating... 57%|██████████████████▎ | ETA: 0:00:08 Cross validating... 60%|███████████████████▎ | ETA: 0:00:07 Cross validating... 63%|████████████████████▍ | ETA: 0:00:06 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:05 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:05 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:04 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:03 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:03 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:02 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:02 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:01 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:01 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:01 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:12 Crossvalidation Results: k MSE 0 6192.041142601398 1 4483.428559469334 2 3323.932378620779 3 2225.075025088614 4 1170.0594963848735 5 772.4095540611734 6 597.0169763412761 7 477.74256219017184 8 382.49152334321144 9 347.63669857059 10 336.29960006955014 11 339.6752995818841 12 341.62455487082474 13 342.06213447209194 14 341.5279105153546 15 344.8313526419141 16 347.4960567402104 17 343.8214112146821 18 351.42557493376586 19 371.3593557010364 20 370.95093095696905 Best k = 10 12.200222 seconds (11.23 M allocations: 300.516 MiB, 1.83% gc time, 60.98% 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: 0:00:03 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... 40%|████████████▊ | ETA: 0:00:03 Cross validating... 43%|█████████████▊ | ETA: 0:00:03 Cross validating... 46%|██████████████▊ | ETA: 0:00:02 Cross validating... 49%|███████████████▊ | ETA: 0:00:02 Cross validating... 52%|████████████████▊ | ETA: 0:00:02 Cross validating... 54%|█████████████████▎ | ETA: 0:00:02 Cross validating... 57%|██████████████████▎ | ETA: 0:00:02 Cross validating... 60%|███████████████████▎ | ETA: 0:00:02 Cross validating... 63%|████████████████████▍ | ETA: 0:00:02 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:02 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:01 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:01 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:01 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:01 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:01 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:01 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:01 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:00 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:04 Crossvalidation Results: k MSE 0 6192.041142601398 1 4483.639261464304 2 3334.05500193839 3 2241.518610965358 4 1177.9528924085455 5 781.4790656068265 6 608.2613592796404 7 484.8477119536583 8 391.29362450178326 9 356.75783856410715 10 346.15296200419164 11 354.72266107891886 12 359.89240338718264 13 361.63573096732637 14 367.0263881690058 15 374.31879351126827 16 377.6137397948041 17 381.71843126857664 18 397.80562892258985 19 400.36173618824057 20 407.751298166041 Best k = 10 4.932559 seconds (10.64 M allocations: 223.567 MiB, 0.95% gc time, 0.97% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, normal model | 3 3 18.0s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:06:11 Cross validating... 8%|██▌ | ETA: 0:02:22 Cross validating... 13%|████▏ | ETA: 0:01:25 Cross validating... 19%|██████▏ | ETA: 0:00:53 Cross validating... 22%|███████▏ | ETA: 0:00:44 Cross validating... 27%|████████▋ | ETA: 0:00:35 Cross validating... 32%|██████████▏ | ETA: 0:00:28 Cross validating... 37%|███████████▋ | ETA: 0:00:23 Cross validating... 41%|█████████████▎ | ETA: 0:00:19 Cross validating... 48%|███████████████▎ | ETA: 0:00:15 Cross validating... 52%|████████████████▊ | ETA: 0:00:12 Cross validating... 56%|█████████████████▊ | ETA: 0:00:11 Cross validating... 60%|███████████████████▎ | ETA: 0:00:09 Cross validating... 65%|████████████████████▉ | ETA: 0:00:07 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:06 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:05 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:04 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:03 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:02 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:01 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:14 Crossvalidation Results: k MSE 0 1563.5326257324218 1 1187.3038452148437 2 1001.0063936767579 3 778.156437438965 4 625.7663770751954 5 507.21044616699226 6 430.80180972290043 7 376.95135104370115 8 340.3469920959473 9 337.01260015869144 10 331.5040731201172 11 334.0047990112305 12 335.3887189636231 13 330.14586758422854 14 331.47249105834965 15 345.6781077270508 16 341.09862609863285 17 357.02054663085937 18 363.38468676757816 19 373.3471754150391 20 353.10131890869144 Best k = 13 15.892573 seconds (12.44 M allocations: 310.939 MiB, 0.81% gc time, 83.69% 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... 17%|█████▋ | ETA: 0:00:02 Cross validating... 22%|███████▏ | ETA: 0:00:02 Cross validating... 25%|████████▏ | ETA: 0:00:02 Cross validating... 30%|█████████▋ | ETA: 0:00:02 Cross validating... 35%|███████████▏ | ETA: 0:00:02 Cross validating... 41%|█████████████▎ | ETA: 0:00:01 Cross validating... 48%|███████████████▎ | ETA: 0:00:01 Cross validating... 52%|████████████████▊ | ETA: 0:00:01 Cross validating... 57%|██████████████████▎ | ETA: 0:00:01 Cross validating... 62%|███████████████████▊ | ETA: 0:00:01 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:01 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:01 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:01 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:00 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:00 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:02 Crossvalidation Results: k MSE 0 1563.5326257324218 1 1187.3038452148437 2 1001.0063936767579 3 779.2294666137695 4 627.3796798706055 5 507.8150288391114 6 432.2114934997559 7 378.46715634155277 8 345.03989541625975 9 343.2909024963379 10 339.49409280395514 11 345.2717667541504 12 351.3631402587891 13 347.22551806640627 14 356.04766329956055 15 368.0203000488281 16 376.9856129455567 17 375.3812997436524 18 378.86562689208984 19 393.89742819213865 20 407.38040652465816 Best k = 10 2.616240 seconds (10.60 M allocations: 194.457 MiB, 2.11% gc time, 1.67% compilation time) Test Summary: | Pass Total Time Cross validation on Float32 matrix, normal model | 2 2 19.9s **** 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: 0:01:01 Cross validating... 6%|██ | ETA: 0:00:33 Cross validating... 10%|███ | ETA: 0:00:23 Cross validating... 13%|████▏ | ETA: 0:00:18 Cross validating... 16%|█████▏ | ETA: 0:00:15 Cross validating... 19%|██████▏ | ETA: 0:00:13 Cross validating... 22%|███████▏ | ETA: 0:00:11 Cross validating... 25%|████████▏ | ETA: 0:00:10 Cross validating... 29%|█████████▏ | ETA: 0:00:09 Cross validating... 32%|██████████▏ | ETA: 0:00:08 Cross validating... 33%|██████████▋ | ETA: 0:00:08 Cross validating... 37%|███████████▋ | ETA: 0:00:07 Cross validating... 40%|████████████▊ | ETA: 0:00:06 Cross validating... 43%|█████████████▊ | ETA: 0:00:06 Cross validating... 46%|██████████████▊ | ETA: 0:00:05 Cross validating... 49%|███████████████▊ | ETA: 0:00:05 Cross validating... 52%|████████████████▊ | ETA: 0:00:04 Cross validating... 56%|█████████████████▊ | ETA: 0:00:04 Cross validating... 59%|██████████████████▊ | ETA: 0:00:04 Cross validating... 62%|███████████████████▊ | ETA: 0:00:03 Cross validating... 65%|████████████████████▉ | ETA: 0:00:03 Cross validating... 68%|█████████████████████▉ | ETA: 0:00:03 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:02 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:02 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:02 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:02 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:01 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:01 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:01 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:01 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:07 Crossvalidation Results: k MSE 0 462.9549876390355 1 404.2687482301888 2 370.8888772422244 3 325.8341501138365 4 259.6814900151442 5 234.77508514895413 6 221.11283349934536 7 210.57184957307638 8 212.05252991670991 9 220.65863741469573 10 216.88513228686904 11 232.87748536152475 12 226.95835764215576 13 228.09624630546813 14 252.89360035465893 15 233.45268861480372 16 228.12638925009875 17 251.2890969032589 18 258.1058593557729 19 240.18272458979004 20 250.26422758048915 Best k = 7 8.337758 seconds (17.38 M allocations: 403.395 MiB, 1.07% gc time, 31.30% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:04 Cross validating... 6%|██ | ETA: 0:00:05 Cross validating... 10%|███ | ETA: 0:00:05 Cross validating... 13%|████▏ | ETA: 0:00:05 Cross validating... 14%|████▋ | ETA: 0:00:05 Cross validating... 17%|█████▋ | ETA: 0:00:05 Cross validating... 21%|██████▋ | ETA: 0:00:05 Cross validating... 24%|███████▋ | ETA: 0:00:04 Cross validating... 27%|████████▋ | 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... 38%|████████████▎ | ETA: 0:00:04 Cross validating... 41%|█████████████▎ | ETA: 0:00:03 Cross validating... 44%|██████████████▎ | ETA: 0:00:03 Cross validating... 48%|███████████████▎ | ETA: 0:00:03 Cross validating... 51%|████████████████▎ | ETA: 0:00:03 Cross validating... 54%|█████████████████▎ | ETA: 0:00:03 Cross validating... 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... 67%|█████████████████████▍ | ETA: 0:00:02 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:02 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:02 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:01 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:01 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:01 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:01 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:01 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:00 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:05 Crossvalidation Results: k MSE 0 462.9549876390355 1 404.4190067805547 2 371.9235398477282 3 327.6453291900323 4 264.0185113711856 5 238.52313794274428 6 223.76970425839488 7 213.88848693177258 8 220.742548585171 9 227.90314321860146 10 232.13308644926298 11 236.42567841840278 12 240.4434020459037 13 249.5295411980719 14 270.02391708890104 15 270.5269006896684 16 272.9882286276087 17 282.1160808856617 18 273.1774651568283 19 277.93769124092705 20 289.38614349666784 Best k = 7 5.948739 seconds (17.43 M allocations: 361.409 MiB, 1.23% gc time, 1.10% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, logistic model | 2 2 14.7s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:44 Cross validating... 8%|██▌ | ETA: 0:00:19 Cross validating... 11%|███▌ | ETA: 0:00:14 Cross validating... 14%|████▋ | ETA: 0:00:11 Cross validating... 17%|█████▋ | ETA: 0:00:09 Cross validating... 21%|██████▋ | ETA: 0:00:08 Cross validating... 24%|███████▋ | ETA: 0:00:07 Cross validating... 27%|████████▋ | ETA: 0:00:07 Cross validating... 30%|█████████▋ | ETA: 0:00:06 Cross validating... 33%|██████████▋ | ETA: 0:00:06 Cross validating... 38%|████████████▎ | ETA: 0:00:05 Cross validating... 41%|█████████████▎ | ETA: 0:00:04 Cross validating... 44%|██████████████▎ | ETA: 0:00:04 Cross validating... 48%|███████████████▎ | ETA: 0:00:04 Cross validating... 51%|████████████████▎ | ETA: 0:00:04 Cross validating... 54%|█████████████████▎ | ETA: 0:00:03 Cross validating... 57%|██████████████████▎ | ETA: 0:00:03 Cross validating... 60%|███████████████████▎ | ETA: 0:00:03 Cross validating... 63%|████████████████████▍ | ETA: 0:00:03 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:02 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:02 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:02 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:01 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:01 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:01 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:01 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:00 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 0 464.7601457457694 1 446.48502694416175 2 412.0955042355373 3 388.45798335182 4 352.2323075294449 5 342.8426793846327 6 342.31197704924307 7 325.52826038764226 8 327.6263867774695 9 336.2783168450837 10 331.77316235424877 11 332.96520441391414 12 352.8100548593304 13 352.4842396739857 14 353.6398982028512 15 364.84612668685344 16 351.4775633636365 17 345.61816048544983 18 347.63754474699755 19 388.309267806159 20 436.97781399050405 Best k = 7 6.970238 seconds (16.75 M allocations: 399.216 MiB, 6.93% gc time, 35.93% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 5%|█▌ | ETA: 0:00:03 Cross validating... 8%|██▌ | ETA: 0:00:03 Cross validating... 11%|███▌ | ETA: 0:00:03 Cross validating... 14%|████▋ | ETA: 0:00:03 Cross validating... 17%|█████▋ | ETA: 0:00:03 Cross validating... 21%|██████▋ | ETA: 0:00:03 Cross validating... 24%|███████▋ | ETA: 0:00:03 Cross validating... 27%|████████▋ | ETA: 0:00:03 Cross validating... 30%|█████████▋ | ETA: 0:00:03 Cross validating... 33%|██████████▋ | ETA: 0:00:03 Cross validating... 38%|████████████▎ | ETA: 0:00:03 Cross validating... 41%|█████████████▎ | ETA: 0:00:02 Cross validating... 44%|██████████████▎ | ETA: 0:00:02 Cross validating... 48%|███████████████▎ | ETA: 0:00:02 Cross validating... 51%|████████████████▎ | ETA: 0:00:02 Cross validating... 54%|█████████████████▎ | ETA: 0:00:02 Cross validating... 57%|██████████████████▎ | ETA: 0:00:02 Cross validating... 60%|███████████████████▎ | ETA: 0:00:02 Cross validating... 63%|████████████████████▍ | ETA: 0:00:02 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:01 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:01 Cross validating... 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 0 464.7601457457694 1 448.9539457817626 2 416.17947231108894 3 394.28213980192965 4 360.0446597461776 5 349.3184099313172 6 350.5335666360155 7 333.84856028225767 8 343.83665387705605 9 359.0260697619401 10 358.39320769005604 11 360.23101014024996 12 386.8906717694715 13 398.760356174434 14 401.70002101966617 15 407.8949759068869 16 411.4374793487503 17 418.3603915255718 18 426.1323307427699 19 425.3465919109973 20 465.14461261867524 Best k = 7 4.262890 seconds (17.41 M allocations: 359.763 MiB, 1.55% gc time, 1.06% compilation time) Test Summary: | Pass Total Time Cross validation on Float64 matrix, logistic model | 2 2 12.1s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:01:01 Cross validating... 6%|██ | ETA: 0:00:32 Cross validating... 10%|███ | ETA: 0:00:23 Cross validating... 13%|████▏ | ETA: 0:00:18 Cross validating... 16%|█████▏ | ETA: 0:00:14 Cross validating... 19%|██████▏ | ETA: 0:00:12 Cross validating... 22%|███████▏ | ETA: 0:00:11 Cross validating... 24%|███████▋ | ETA: 0:00:10 Cross validating... 27%|████████▋ | ETA: 0:00:09 Cross validating... 30%|█████████▋ | ETA: 0:00:08 Cross validating... 33%|██████████▋ | ETA: 0:00:07 Cross validating... 37%|███████████▋ | ETA: 0:00:07 Cross validating... 40%|████████████▊ | ETA: 0:00:06 Cross validating... 43%|█████████████▊ | ETA: 0:00:06 Cross validating... 46%|██████████████▊ | ETA: 0:00:05 Cross validating... 49%|███████████████▊ | ETA: 0:00:05 Cross validating... 52%|████████████████▊ | ETA: 0:00:04 Cross validating... 56%|█████████████████▊ | ETA: 0:00:04 Cross validating... 59%|██████████████████▊ | ETA: 0:00:04 Cross validating... 62%|███████████████████▊ | ETA: 0:00:03 Cross validating... 65%|████████████████████▉ | ETA: 0:00:03 Cross validating... 68%|█████████████████████▉ | ETA: 0:00:03 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:02 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:02 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:02 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:01 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:01 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:01 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:01 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:07 Crossvalidation Results: k MSE 0 1366.4767869494303 1 955.9233764322779 2 833.605399928816 3 662.0480633160777 4 559.5818345076273 5 484.2198197483613 6 486.3197825476617 7 477.3117780166293 8 454.9924466428619 9 445.37725219759994 10 430.6757443430436 11 432.20854173292 12 421.82678243247875 13 476.372967157845 14 441.69663824861254 15 431.837491684676 16 451.9077609574465 17 467.43184168844147 18 434.59620198069655 19 436.9738444475995 20 448.73839708501026 Best k = 12 8.050088 seconds (15.34 M allocations: 351.959 MiB, 0.94% gc time, 32.21% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:04 Cross validating... 6%|██ | ETA: 0:00:04 Cross validating... 8%|██▌ | ETA: 0:00:05 Cross validating... 11%|███▌ | ETA: 0:00:05 Cross validating... 14%|████▋ | ETA: 0:00:05 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... 29%|█████████▏ | ETA: 0:00:04 Cross validating... 32%|██████████▏ | ETA: 0:00:04 Cross validating... 35%|███████████▏ | ETA: 0:00:04 Cross validating... 38%|████████████▎ | ETA: 0:00:03 Cross validating... 41%|█████████████▎ | ETA: 0:00:03 Cross validating... 44%|██████████████▎ | ETA: 0:00:03 Cross validating... 48%|███████████████▎ | ETA: 0:00:03 Cross validating... 51%|████████████████▎ | ETA: 0:00:03 Cross validating... 54%|█████████████████▎ | ETA: 0:00:03 Cross validating... 57%|██████████████████▎ | ETA: 0:00:02 Cross validating... 59%|██████████████████▊ | ETA: 0:00:02 Cross validating... 60%|███████████████████▎ | ETA: 0:00:02 Cross validating... 63%|████████████████████▍ | ETA: 0:00:02 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:02 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:02 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:02 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:01 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:01 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:01 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:01 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:01 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:00 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:05 Crossvalidation Results: k MSE 0 1366.4767869494303 1 887.9404093355716 2 752.8372703300395 3 615.102086293535 4 527.7060763619488 5 454.3403693750033 6 508.69708236417483 7 452.6144678486559 8 447.1279555358474 9 445.2829901661097 10 432.3707728791915 11 422.64100088867224 12 426.9888997963576 13 443.5305822830864 14 440.751999596367 15 458.7124767217963 16 451.5349481332507 17 458.5471802479143 18 454.0969046452205 19 469.7056151442434 20 473.5811304264538 Best k = 11 5.635909 seconds (14.30 M allocations: 287.494 MiB, 1.06% gc time, 1.03% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, Poisson model | 2 2 14.1s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:01:00 Cross validating... 5%|█▌ | ETA: 0:01:00 Cross validating... 6%|██ | ETA: 0:01:00 Cross validating... 8%|██▌ | ETA: 0:00:59 Cross validating... 10%|███ | ETA: 0:00:58 Cross validating... 11%|███▌ | ETA: 0:00:57 Cross validating... 13%|████▏ | ETA: 0:00:56 Cross validating... 14%|████▋ | ETA: 0:00:55 Cross validating... 16%|█████▏ | ETA: 0:00:54 Cross validating... 17%|█████▋ | ETA: 0:00:49 Cross validating... 19%|██████▏ | ETA: 0:00:44 Cross validating... 21%|██████▋ | ETA: 0:00:44 Cross validating... 22%|███████▏ | ETA: 0:00:44 Cross validating... 24%|███████▋ | ETA: 0:00:44 Cross validating... 25%|████████▏ | ETA: 0:00:43 Cross validating... 27%|████████▋ | ETA: 0:00:42 Cross validating... 29%|█████████▏ | ETA: 0:00:41 Cross validating... 30%|█████████▋ | ETA: 0:00:39 Cross validating... 32%|██████████▏ | ETA: 0:00:38 Cross validating... 33%|██████████▋ | ETA: 0:00:37 Cross validating... 37%|███████████▋ | ETA: 0:00:33 Cross validating... 40%|████████████▊ | ETA: 0:00:32 Cross validating... 41%|█████████████▎ | ETA: 0:00:31 Cross validating... 43%|█████████████▊ | ETA: 0:00:30 Cross validating... 44%|██████████████▎ | ETA: 0:00:29 Cross validating... 46%|██████████████▊ | ETA: 0:00:28 Cross validating... 48%|███████████████▎ | ETA: 0:00:27 Cross validating... 49%|███████████████▊ | ETA: 0:00:26 Cross validating... 51%|████████████████▎ | ETA: 0:00:25 Cross validating... 52%|████████████████▊ | ETA: 0:00:23 Cross validating... 54%|█████████████████▎ | ETA: 0:00:23 Cross validating... 56%|█████████████████▊ | ETA: 0:00:21 Cross validating... 57%|██████████████████▎ | ETA: 0:00:21 Cross validating... 59%|██████████████████▊ | ETA: 0:00:20 Cross validating... 60%|███████████████████▎ | ETA: 0:00:19 Cross validating... 62%|███████████████████▊ | ETA: 0:00:18 Cross validating... 63%|████████████████████▍ | ETA: 0:00:17 Cross validating... 65%|████████████████████▉ | ETA: 0:00:17 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:16 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:14 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:13 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:12 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:11 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:11 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:10 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:09 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:08 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:07 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:07 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:06 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:05 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 0 491.1243635781275 1 351.8620337777008 2 304.4542608058353 3 266.2194531405337 4 219.72597434923134 5 208.52633175947363 6 202.08822910516346 7 196.17032724563825 8 199.40421828302843 9 196.76888107064514 10 197.59539824280682 11 198.95141061629354 12 199.5836816065788 13 199.59301139401734 14 200.67225470024562 15 202.47917366532988 16 202.5872051633902 17 204.12283381385367 18 204.02566435696374 19 207.37597090648856 20 208.5373289867268 Best k = 7 41.552393 seconds (128.04 M allocations: 3.168 GiB, 1.31% gc time, 5.38% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:04 Cross validating... 5%|█▌ | ETA: 0:00:05 Cross validating... 6%|██ | ETA: 0:00:05 Cross validating... 8%|██▌ | ETA: 0:00:05 Cross validating... 10%|███ | ETA: 0:00:06 Cross validating... 11%|███▌ | ETA: 0:00:06 Cross validating... 13%|████▏ | ETA: 0:00:06 Cross validating... 14%|████▋ | ETA: 0:00:06 Cross validating... 16%|█████▏ | ETA: 0:00:06 Cross validating... 17%|█████▋ | ETA: 0:00:06 Cross validating... 19%|██████▏ | ETA: 0:00:07 Cross validating... 21%|██████▋ | ETA: 0:00:07 Cross validating... 22%|███████▏ | ETA: 0:00:07 Cross validating... 24%|███████▋ | ETA: 0:00:07 Cross validating... 25%|████████▏ | ETA: 0:00:08 Cross validating... 27%|████████▋ | ETA: 0:00:08 Cross validating... 29%|█████████▏ | ETA: 0:00:08 Cross validating... 30%|█████████▋ | ETA: 0:00:08 Cross validating... 32%|██████████▏ | ETA: 0:00:08 Cross validating... 33%|██████████▋ | ETA: 0:00:08 Cross validating... 37%|███████████▋ | ETA: 0:00:07 Cross validating... 40%|████████████▊ | ETA: 0:00:07 Cross validating... 41%|█████████████▎ | ETA: 0:00:06 Cross validating... 43%|█████████████▊ | ETA: 0:00:06 Cross validating... 44%|██████████████▎ | ETA: 0:00:06 Cross validating... 46%|██████████████▊ | ETA: 0:00:06 Cross validating... 48%|███████████████▎ | ETA: 0:00:05 Cross validating... 49%|███████████████▊ | ETA: 0:00:05 Cross validating... 51%|████████████████▎ | ETA: 0:00:05 Cross validating... 52%|████████████████▊ | ETA: 0:00:05 Cross validating... 54%|█████████████████▎ | ETA: 0:00:05 Cross validating... 56%|█████████████████▊ | ETA: 0:00:05 Cross validating... 57%|██████████████████▎ | ETA: 0:00:05 Cross validating... 59%|██████████████████▊ | ETA: 0:00:05 Cross validating... 60%|███████████████████▎ | ETA: 0:00:05 Cross validating... 62%|███████████████████▊ | ETA: 0:00:04 Cross validating... 63%|████████████████████▍ | ETA: 0:00:04 Cross validating... 65%|████████████████████▉ | ETA: 0:00:04 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:04 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:04 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:03 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:03 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:03 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:03 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: 0:00:02 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:02 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:01 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:01 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:01 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:01 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:01 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:01 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:11 Crossvalidation Results: k MSE 0 491.1243635781275 1 350.1248600800765 2 299.66622974931147 3 257.05227660802234 4 221.1130200132547 5 210.8455809578871 6 205.09368290924533 7 199.2114881365406 8 205.6259859115284 9 206.34019237440512 10 206.34480290957535 11 212.17882688062775 12 216.90838964119382 13 220.77940350271595 14 221.93052890322633 15 227.47630070778155 16 226.22241718910237 17 230.68779077308142 18 235.77407751365723 19 232.53282295272112 20 237.79648569316163 Best k = 7 12.087887 seconds (35.83 M allocations: 741.277 MiB, 1.50% gc time, 0.56% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, NegativeBinomial model | 2 2 54.1s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:01:06 Cross validating... 6%|██ | ETA: 0:00:34 Cross validating... 10%|███ | ETA: 0:00:23 Cross validating... 13%|████▏ | ETA: 0:00:17 Cross validating... 16%|█████▏ | ETA: 0:00:14 Cross validating... 19%|██████▏ | ETA: 0:00:12 Cross validating... 22%|███████▏ | ETA: 0:00:10 Cross validating... 25%|████████▏ | ETA: 0:00:09 Cross validating... 29%|█████████▏ | ETA: 0:00:08 Cross validating... 32%|██████████▏ | ETA: 0:00:07 Cross validating... 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... 67%|█████████████████████▍ | ETA: 0:00:02 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:02 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... 95%|██████████████████████████████▌ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:05 Crossvalidation Results: k MSE 0 708.7406597900391 1 594.0547950439453 2 472.60887115478516 3 391.07051165771486 4 322.2429605712891 5 274.1304553527832 6 242.98796069335935 7 231.75397763061522 8 211.04413333129884 9 208.82878451538085 10 210.9139321594238 11 206.8662128601074 12 209.29315435791017 13 216.44690969848637 14 210.83974066162108 15 223.69269552612303 16 223.5122525024414 17 217.3672544555664 18 230.29235778808595 19 245.48900619506838 20 214.24631561279296 Best k = 11 6.224734 seconds (17.19 M allocations: 341.580 MiB, 1.48% gc time, 44.74% 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: 0:00:02 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... 52%|████████████████▊ | ETA: 0:00:02 Cross validating... 56%|█████████████████▊ | ETA: 0:00:01 Cross validating... 59%|██████████████████▊ | ETA: 0:00:01 Cross validating... 62%|███████████████████▊ | ETA: 0:00:01 Cross validating... 65%|████████████████████▉ | ETA: 0:00:01 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:01 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:01 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:01 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:01 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:01 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:00 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:00 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:00 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:03 Crossvalidation Results: k MSE 0 708.7406597900391 1 575.6241903076173 2 458.4867525024414 3 380.67050573730467 4 317.43561486816407 5 274.8225385131836 6 243.94065100097657 7 233.23877688598634 8 212.74209445190428 9 214.86823376464844 10 213.80905279541014 11 216.52949041748047 12 220.7860779724121 13 222.78791012573242 14 231.40656030273436 15 233.06280703735348 16 243.6403890075684 17 242.80908297729493 18 238.556499420166 19 251.23290313720705 20 244.79654568481442 Best k = 8 3.409325 seconds (16.26 M allocations: 288.184 MiB, 1.75% gc time, 1.75% compilation time) Test Summary: | Pass Total Time Cross validation on floating point matrices, NegativeBinomial model | 2 2 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 **** Cross validating... 2%|▋ | ETA: 0:01:21 Cross validating... 3%|█ | ETA: 0:00:58 Cross validating... 4%|█▎ | ETA: 0:00:46 Cross validating... 5%|█▋ | ETA: 0:00:39 Cross validating... 6%|█▉ | ETA: 0:00:34 Cross validating... 7%|██▎ | ETA: 0:00:30 Cross validating... 8%|██▌ | ETA: 0:00:28 Cross validating... 9%|██▉ | ETA: 0:00:25 Cross validating... 10%|███▎ | ETA: 0:00:24 Cross validating... 11%|███▌ | ETA: 0:00:23 Cross validating... 12%|███▉ | ETA: 0:00:22 Cross validating... 13%|████▏ | ETA: 0:00:21 Cross validating... 14%|████▌ | ETA: 0:00:21 Cross validating... 15%|████▊ | ETA: 0:00:20 Cross validating... 16%|█████▏ | ETA: 0:00:20 Cross validating... 17%|█████▌ | ETA: 0:00:19 Cross validating... 18%|█████▊ | ETA: 0:00:19 Cross validating... 19%|██████▏ | ETA: 0:00:19 Cross validating... 20%|██████▍ | ETA: 0:00:18 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: 0:00:16 Cross validating... 25%|████████ | ETA: 0:00:16 Cross validating... 26%|████████▍ | ETA: 0:00:15 Cross validating... 27%|████████▋ | ETA: 0:00:15 Cross validating... 28%|█████████ | ETA: 0:00:14 Cross validating... 29%|█████████▎ | ETA: 0:00:14 Cross validating... 30%|█████████▋ | ETA: 0:00:13 Cross validating... 31%|█████████▉ | ETA: 0:00:13 Cross validating... 32%|██████████▎ | ETA: 0:00:13 Cross validating... 33%|██████████▌ | ETA: 0:00:13 Cross validating... 34%|██████████▉ | ETA: 0:00:12 Cross validating... 35%|███████████▎ | ETA: 0:00:12 Cross validating... 36%|███████████▌ | ETA: 0:00:12 Cross validating... 37%|███████████▉ | ETA: 0:00:12 Cross validating... 38%|████████████▏ | ETA: 0:00:12 Cross validating... 39%|████████████▌ | ETA: 0:00:12 Cross validating... 40%|████████████▊ | ETA: 0:00:11 Cross validating... 41%|█████████████▏ | ETA: 0:00:11 Cross validating... 42%|█████████████▌ | ETA: 0:00:11 Cross validating... 43%|█████████████▊ | ETA: 0:00:10 Cross validating... 44%|██████████████▏ | ETA: 0:00:10 Cross validating... 45%|██████████████▍ | ETA: 0:00:10 Cross validating... 46%|██████████████▊ | ETA: 0:00:10 Cross validating... 47%|███████████████ | ETA: 0:00:09 Cross validating... 48%|███████████████▍ | ETA: 0:00:09 Cross validating... 49%|███████████████▋ | ETA: 0:00:09 Cross validating... 50%|████████████████ | ETA: 0:00:09 Cross validating... 51%|████████████████▍ | ETA: 0:00:08 Cross validating... 52%|████████████████▋ | ETA: 0:00:08 Cross validating... 53%|█████████████████ | ETA: 0:00:08 Cross validating... 54%|█████████████████▎ | ETA: 0:00:08 Cross validating... 55%|█████████████████▋ | ETA: 0:00:08 Cross validating... 56%|█████████████████▉ | ETA: 0:00:08 Cross validating... 57%|██████████████████▎ | ETA: 0:00:08 Cross validating... 58%|██████████████████▌ | ETA: 0:00:07 Cross validating... 59%|██████████████████▉ | ETA: 0:00:07 Cross validating... 60%|███████████████████▎ | ETA: 0:00:07 Cross validating... 61%|███████████████████▌ | ETA: 0:00:07 Cross validating... 62%|███████████████████▉ | ETA: 0:00:07 Cross validating... 63%|████████████████████▏ | ETA: 0:00:06 Cross validating... 64%|████████████████████▌ | ETA: 0:00:06 Cross validating... 65%|████████████████████▊ | ETA: 0:00:06 Cross validating... 66%|█████████████████████▏ | ETA: 0:00:06 Cross validating... 67%|█████████████████████▌ | ETA: 0:00:06 Cross validating... 68%|█████████████████████▊ | ETA: 0:00:05 Cross validating... 69%|██████████████████████▏ | ETA: 0:00:05 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:05 Cross validating... 71%|██████████████████████▊ | ETA: 0:00:05 Cross validating... 72%|███████████████████████ | ETA: 0:00:05 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:05 Cross validating... 74%|███████████████████████▋ | ETA: 0:00:04 Cross validating... 75%|████████████████████████ | ETA: 0:00:04 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:04 Cross validating... 77%|████████████████████████▋ | ETA: 0:00:04 Cross validating... 78%|█████████████████████████ | ETA: 0:00:04 Cross validating... 79%|█████████████████████████▎ | ETA: 0:00:04 Cross validating... 80%|█████████████████████████▋ | ETA: 0:00:03 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:03 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: 0:00:02 Cross validating... 86%|███████████████████████████▌ | ETA: 0:00:02 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:02 Cross validating... 88%|████████████████████████████▏ | ETA: 0:00:02 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:02 Cross validating... 90%|████████████████████████████▊ | ETA: 0:00:02 Cross validating... 91%|█████████████████████████████▏ | ETA: 0:00:01 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:01 Cross validating... 93%|█████████████████████████████▊ | ETA: 0:00:01 Cross validating... 94%|██████████████████████████████▏ | ETA: 0:00:01 Cross validating... 95%|██████████████████████████████▍ | ETA: 0:00:01 Cross validating... 96%|██████████████████████████████▊ | ETA: 0:00:01 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▍| ETA: 0:00:00 Cross validating... 99%|███████████████████████████████▋| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:16 Crossvalidation Results: k MSE 1 3552.190393956106 2 3109.0800924945484 3 2596.3736370993097 4 2341.8391570794647 5 2230.9196528790008 6 2052.193696032125 7 2008.7748716077165 8 1899.7541899206012 9 1857.821223705183 10 1889.4158099500812 11 1918.6787962767432 12 1934.6759498391134 13 1938.0794289582286 14 1954.0612944535826 15 1965.2982841287974 16 1970.6869130441426 17 2001.6820805777238 18 2014.3986107560272 19 1993.7081184786111 20 2011.1316440873911 Best k = 9 16.719646 seconds (299.42 k allocations: 203.855 MiB, 0.38% gc time, 10.10% compilation time) Test Summary: | Pass Total Time multivariate cross validation SnpLinAlg | 3 3 21.4s Test Summary: | Pass Total Time wrapper univariate | 20 20 2m03.0s **** 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: 0:00:11 Cross validating... 3%|█ | ETA: 0:00:10 Cross validating... 4%|█▎ | ETA: 0:00:11 Cross validating... 5%|█▋ | ETA: 0:00:11 Cross validating... 6%|█▉ | ETA: 0:00:12 Cross validating... 7%|██▎ | ETA: 0:00:12 Cross validating... 8%|██▌ | ETA: 0:00:12 Cross validating... 9%|██▉ | ETA: 0:00:13 Cross validating... 10%|███▎ | ETA: 0:00:14 Cross validating... 11%|███▌ | ETA: 0:00:15 Cross validating... 12%|███▉ | ETA: 0:00:15 Cross validating... 13%|████▏ | ETA: 0:00:16 Cross validating... 14%|████▌ | ETA: 0:00:16 Cross validating... 15%|████▊ | ETA: 0:00:19 Cross validating... 16%|█████▏ | ETA: 0:00:20 Cross validating... 17%|█████▌ | ETA: 0:00:21 Cross validating... 18%|█████▊ | ETA: 0:00:20 Cross validating... 19%|██████▏ | ETA: 0:00:20 Cross validating... 20%|██████▍ | ETA: 0:00:20 Cross validating... 21%|██████▊ | ETA: 0:00:20 Cross validating... 22%|███████ | ETA: 0:00:19 Cross validating... 23%|███████▍ | ETA: 0:00:18 Cross validating... 24%|███████▋ | ETA: 0:00:18 Cross validating... 25%|████████ | ETA: 0:00:17 Cross validating... 26%|████████▍ | ETA: 0:00:17 Cross validating... 27%|████████▋ | ETA: 0:00:17 Cross validating... 28%|█████████ | ETA: 0:00:17 Cross validating... 29%|█████████▎ | ETA: 0:00:17 Cross validating... 30%|█████████▋ | ETA: 0:00:17 Cross validating... 31%|█████████▉ | ETA: 0:00:16 Cross validating... 32%|██████████▎ | ETA: 0:00:16 Cross validating... 33%|██████████▌ | ETA: 0:00:16 Cross validating... 34%|██████████▉ | ETA: 0:00:16 Cross validating... 35%|███████████▎ | ETA: 0:00:16 Cross validating... 36%|███████████▌ | ETA: 0:00:16 Cross validating... 37%|███████████▉ | ETA: 0:00:16 Cross validating... 38%|████████████▏ | ETA: 0:00:15 Cross validating... 39%|████████████▌ | ETA: 0:00:15 Cross validating... 40%|████████████▊ | ETA: 0:00:15 Cross validating... 41%|█████████████▏ | ETA: 0:00:15 Cross validating... 42%|█████████████▌ | ETA: 0:00:14 Cross validating... 43%|█████████████▊ | ETA: 0:00:14 Cross validating... 44%|██████████████▏ | ETA: 0:00:13 Cross validating... 45%|██████████████▍ | ETA: 0:00:13 Cross validating... 46%|██████████████▊ | ETA: 0:00:13 Cross validating... 47%|███████████████ | ETA: 0:00:12 Cross validating... 48%|███████████████▍ | ETA: 0:00:12 Cross validating... 49%|███████████████▋ | ETA: 0:00:12 Cross validating... 50%|████████████████ | ETA: 0:00:12 Cross validating... 51%|████████████████▍ | ETA: 0:00:11 Cross validating... 52%|████████████████▋ | ETA: 0:00:11 Cross validating... 53%|█████████████████ | ETA: 0:00:11 Cross validating... 54%|█████████████████▎ | ETA: 0:00:11 Cross validating... 55%|█████████████████▋ | ETA: 0:00:11 Cross validating... 56%|█████████████████▉ | ETA: 0:00:10 Cross validating... 57%|██████████████████▎ | ETA: 0:00:10 Cross validating... 58%|██████████████████▌ | ETA: 0:00:10 Cross validating... 59%|██████████████████▉ | ETA: 0:00:10 Cross validating... 60%|███████████████████▎ | ETA: 0:00:10 Cross validating... 61%|███████████████████▌ | ETA: 0:00:09 Cross validating... 62%|███████████████████▉ | ETA: 0:00:09 Cross validating... 63%|████████████████████▏ | ETA: 0:00:09 Cross validating... 64%|████████████████████▌ | ETA: 0:00:09 Cross validating... 65%|████████████████████▊ | ETA: 0:00:08 Cross validating... 66%|█████████████████████▏ | ETA: 0:00:08 Cross validating... 67%|█████████████████████▌ | ETA: 0:00:08 Cross validating... 68%|█████████████████████▊ | ETA: 0:00:07 Cross validating... 69%|██████████████████████▏ | ETA: 0:00:07 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:07 Cross validating... 71%|██████████████████████▊ | ETA: 0:00:07 Cross validating... 72%|███████████████████████ | ETA: 0:00:07 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:06 Cross validating... 74%|███████████████████████▋ | ETA: 0:00:06 Cross validating... 75%|████████████████████████ | ETA: 0:00:06 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:06 Cross validating... 77%|████████████████████████▋ | ETA: 0:00:05 Cross validating... 78%|█████████████████████████ | ETA: 0:00:05 Cross validating... 79%|█████████████████████████▎ | ETA: 0:00:05 Cross validating... 80%|█████████████████████████▋ | ETA: 0:00:05 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:05 Cross validating... 82%|██████████████████████████▎ | ETA: 0:00:04 Cross validating... 83%|██████████████████████████▌ | ETA: 0:00:04 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:04 Cross validating... 85%|███████████████████████████▎ | ETA: 0:00:04 Cross validating... 86%|███████████████████████████▌ | ETA: 0:00:03 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:03 Cross validating... 88%|████████████████████████████▏ | ETA: 0:00:03 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:03 Cross validating... 90%|████████████████████████████▊ | ETA: 0:00:02 Cross validating... 91%|█████████████████████████████▏ | ETA: 0:00:02 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:02 Cross validating... 93%|█████████████████████████████▊ | ETA: 0:00:02 Cross validating... 94%|██████████████████████████████▏ | ETA: 0:00:01 Cross validating... 95%|██████████████████████████████▍ | ETA: 0:00:01 Cross validating... 96%|██████████████████████████████▊ | ETA: 0:00:01 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:01 Cross validating... 98%|███████████████████████████████▍| ETA: 0:00:00 Cross validating... 99%|███████████████████████████████▋| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:24 Crossvalidation Results: k MSE 1 2838.788679198002 2 2514.3973428708136 3 2305.6176519676274 4 2222.025304867614 5 2075.1670384588365 6 2067.7948989723845 7 2053.427506114907 8 2086.405384830965 9 2080.984460901671 10 2105.131199502364 11 2132.407165368786 12 2138.267187460652 13 2166.002210829576 14 2194.9918295115804 15 2189.890403738045 16 2191.181293229578 17 2209.4669750564362 18 2221.2595493644303 19 2238.7425945763257 20 2253.9559571797727 Best k = 7 **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 2%|▋ | ETA: 0:00:10 Cross validating... 3%|█ | ETA: 0:00:10 Cross validating... 4%|█▎ | ETA: 0:00:11 Cross validating... 5%|█▋ | ETA: 0:00:11 Cross validating... 6%|█▉ | ETA: 0:00:12 Cross validating... 7%|██▎ | ETA: 0:00:13 Cross validating... 8%|██▌ | ETA: 0:00:13 Cross validating... 9%|██▉ | ETA: 0:00:14 Cross validating... 10%|███▎ | ETA: 0:00:14 Cross validating... 11%|███▌ | ETA: 0:00:15 Cross validating... 12%|███▉ | ETA: 0:00:16 Cross validating... 13%|████▏ | ETA: 0:00:16 Cross validating... 14%|████▌ | ETA: 0:00:16 Cross validating... 15%|████▊ | ETA: 0:00:17 Cross validating... 16%|█████▏ | ETA: 0:00:18 Cross validating... 17%|█████▌ | ETA: 0:00:18 Cross validating... 18%|█████▊ | ETA: 0:00:18 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: 0:00:16 Cross validating... 25%|████████ | ETA: 0:00:16 Cross validating... 26%|████████▍ | ETA: 0:00:15 Cross validating... 27%|████████▋ | ETA: 0:00:16 Cross validating... 28%|█████████ | ETA: 0:00:16 Cross validating... 29%|█████████▎ | ETA: 0:00:16 Cross validating... 30%|█████████▋ | ETA: 0:00:16 Cross validating... 31%|█████████▉ | ETA: 0:00:16 Cross validating... 32%|██████████▎ | ETA: 0:00:15 Cross validating... 33%|██████████▌ | ETA: 0:00:15 Cross validating... 34%|██████████▉ | ETA: 0:00:15 Cross validating... 35%|███████████▎ | ETA: 0:00:15 Cross validating... 36%|███████████▌ | ETA: 0:00:15 Cross validating... 37%|███████████▉ | ETA: 0:00:15 Cross validating... 38%|████████████▏ | ETA: 0:00:15 Cross validating... 39%|████████████▌ | ETA: 0:00:15 Cross validating... 40%|████████████▊ | ETA: 0:00:14 Cross validating... 41%|█████████████▏ | ETA: 0:00:14 Cross validating... 42%|█████████████▌ | ETA: 0:00:14 Cross validating... 43%|█████████████▊ | ETA: 0:00:13 Cross validating... 44%|██████████████▏ | ETA: 0:00:13 Cross validating... 45%|██████████████▍ | ETA: 0:00:12 Cross validating... 46%|██████████████▊ | ETA: 0:00:12 Cross validating... 47%|███████████████ | ETA: 0:00:12 Cross validating... 48%|███████████████▍ | ETA: 0:00:12 Cross validating... 49%|███████████████▋ | ETA: 0:00:11 Cross validating... 50%|████████████████ | ETA: 0:00:11 Cross validating... 51%|████████████████▍ | ETA: 0:00:11 Cross validating... 52%|████████████████▋ | ETA: 0:00:11 Cross validating... 53%|█████████████████ | ETA: 0:00:11 Cross validating... 54%|█████████████████▎ | ETA: 0:00:10 Cross validating... 55%|█████████████████▋ | ETA: 0:00:10 Cross validating... 56%|█████████████████▉ | ETA: 0:00:10 Cross validating... 57%|██████████████████▎ | ETA: 0:00:10 Cross validating... 58%|██████████████████▌ | ETA: 0:00:10 Cross validating... 59%|██████████████████▉ | ETA: 0:00:10 Cross validating... 60%|███████████████████▎ | ETA: 0:00:09 Cross validating... 61%|███████████████████▌ | ETA: 0:00:09 Cross validating... 62%|███████████████████▉ | ETA: 0:00:09 Cross validating... 63%|████████████████████▏ | ETA: 0:00:09 Cross validating... 64%|████████████████████▌ | ETA: 0:00:08 Cross validating... 65%|████████████████████▊ | ETA: 0:00:08 Cross validating... 66%|█████████████████████▏ | ETA: 0:00:08 Cross validating... 67%|█████████████████████▌ | ETA: 0:00:07 Cross validating... 68%|█████████████████████▊ | ETA: 0:00:07 Cross validating... 69%|██████████████████████▏ | ETA: 0:00:07 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:07 Cross validating... 71%|██████████████████████▊ | ETA: 0:00:07 Cross validating... 72%|███████████████████████ | ETA: 0:00:06 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:06 Cross validating... 74%|███████████████████████▋ | ETA: 0:00:06 Cross validating... 75%|████████████████████████ | ETA: 0:00:06 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:05 Cross validating... 77%|████████████████████████▋ | ETA: 0:00:05 Cross validating... 78%|█████████████████████████ | ETA: 0:00:05 Cross validating... 79%|█████████████████████████▎ | ETA: 0:00:05 Cross validating... 80%|█████████████████████████▋ | ETA: 0:00:05 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:04 Cross validating... 82%|██████████████████████████▎ | ETA: 0:00:04 Cross validating... 83%|██████████████████████████▌ | ETA: 0:00:04 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:04 Cross validating... 85%|███████████████████████████▎ | ETA: 0:00:03 Cross validating... 86%|███████████████████████████▌ | ETA: 0:00:03 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:03 Cross validating... 88%|████████████████████████████▏ | ETA: 0:00:03 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:02 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: 0:00:02 Cross validating... 94%|██████████████████████████████▏ | ETA: 0:00:01 Cross validating... 95%|██████████████████████████████▍ | ETA: 0:00:01 Cross validating... 96%|██████████████████████████████▊ | ETA: 0:00:01 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:01 Cross validating... 98%|███████████████████████████████▍| ETA: 0:00:00 Cross validating... 99%|███████████████████████████████▋| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:23 Crossvalidation Results: k MSE 1 2838.788679198002 2 2514.3973428708136 3 2305.6176519676274 4 2222.025304867614 5 2075.1670384588365 6 2067.7948989723845 7 2053.427506114907 8 2086.405384830965 9 2080.984460901671 10 2105.131199502364 11 2132.407165368786 12 2138.267187460652 13 2166.002210829576 14 2194.9918295115804 15 2189.890403738045 16 2191.181293229578 17 2209.4669750564362 18 2221.2595493644303 19 2238.7425945763257 20 2253.9559571797727 Best k = 7 **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 2%|▋ | ETA: 0:00:10 Cross validating... 3%|█ | ETA: 0:00:10 Cross validating... 4%|█▎ | ETA: 0:00:11 Cross validating... 5%|█▋ | ETA: 0:00:11 Cross validating... 6%|█▉ | ETA: 0:00:12 Cross validating... 7%|██▎ | ETA: 0:00:12 Cross validating... 8%|██▌ | ETA: 0:00:12 Cross validating... 9%|██▉ | ETA: 0:00:13 Cross validating... 10%|███▎ | ETA: 0:00:14 Cross validating... 11%|███▌ | ETA: 0:00:15 Cross validating... 12%|███▉ | ETA: 0:00:16 Cross validating... 13%|████▏ | ETA: 0:00:16 Cross validating... 14%|████▌ | ETA: 0:00:17 Cross validating... 15%|████▊ | ETA: 0:00:17 Cross validating... 16%|█████▏ | ETA: 0:00:18 Cross validating... 17%|█████▌ | ETA: 0:00:18 Cross validating... 18%|█████▊ | ETA: 0:00:18 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: 0:00:16 Cross validating... 25%|████████ | ETA: 0:00:16 Cross validating... 26%|████████▍ | ETA: 0:00:15 Cross validating... 27%|████████▋ | ETA: 0:00:16 Cross validating... 28%|█████████ | ETA: 0:00:16 Cross validating... 29%|█████████▎ | ETA: 0:00:16 Cross validating... 30%|█████████▋ | ETA: 0:00:16 Cross validating... 31%|█████████▉ | ETA: 0:00:16 Cross validating... 32%|██████████▎ | ETA: 0:00:16 Cross validating... 33%|██████████▌ | ETA: 0:00:15 Cross validating... 34%|██████████▉ | ETA: 0:00:15 Cross validating... 35%|███████████▎ | ETA: 0:00:15 Cross validating... 36%|███████████▌ | ETA: 0:00:15 Cross validating... 37%|███████████▉ | ETA: 0:00:15 Cross validating... 38%|████████████▏ | ETA: 0:00:15 Cross validating... 39%|████████████▌ | ETA: 0:00:15 Cross validating... 40%|████████████▊ | ETA: 0:00:15 Cross validating... 41%|█████████████▏ | ETA: 0:00:14 Cross validating... 42%|█████████████▌ | ETA: 0:00:14 Cross validating... 43%|█████████████▊ | ETA: 0:00:13 Cross validating... 44%|██████████████▏ | ETA: 0:00:13 Cross validating... 45%|██████████████▍ | ETA: 0:00:13 Cross validating... 46%|██████████████▊ | ETA: 0:00:12 Cross validating... 47%|███████████████ | ETA: 0:00:12 Cross validating... 48%|███████████████▍ | ETA: 0:00:12 Cross validating... 49%|███████████████▋ | ETA: 0:00:11 Cross validating... 50%|████████████████ | ETA: 0:00:11 Cross validating... 51%|████████████████▍ | ETA: 0:00:11 Cross validating... 52%|████████████████▋ | ETA: 0:00:11 Cross validating... 53%|█████████████████ | ETA: 0:00:11 Cross validating... 54%|█████████████████▎ | ETA: 0:00:10 Cross validating... 55%|█████████████████▋ | ETA: 0:00:10 Cross validating... 56%|█████████████████▉ | ETA: 0:00:10 Cross validating... 57%|██████████████████▎ | ETA: 0:00:10 Cross validating... 58%|██████████████████▌ | ETA: 0:00:10 Cross validating... 59%|██████████████████▉ | ETA: 0:00:10 Cross validating... 60%|███████████████████▎ | ETA: 0:00:09 Cross validating... 61%|███████████████████▌ | ETA: 0:00:09 Cross validating... 62%|███████████████████▉ | ETA: 0:00:09 Cross validating... 63%|████████████████████▏ | ETA: 0:00:09 Cross validating... 64%|████████████████████▌ | ETA: 0:00:08 Cross validating... 65%|████████████████████▊ | ETA: 0:00:08 Cross validating... 66%|█████████████████████▏ | ETA: 0:00:08 Cross validating... 67%|█████████████████████▌ | ETA: 0:00:08 Cross validating... 68%|█████████████████████▊ | ETA: 0:00:07 Cross validating... 69%|██████████████████████▏ | ETA: 0:00:07 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:07 Cross validating... 71%|██████████████████████▊ | ETA: 0:00:07 Cross validating... 72%|███████████████████████ | ETA: 0:00:06 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:06 Cross validating... 74%|███████████████████████▋ | ETA: 0:00:06 Cross validating... 75%|████████████████████████ | ETA: 0:00:06 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:05 Cross validating... 77%|████████████████████████▋ | ETA: 0:00:05 Cross validating... 78%|█████████████████████████ | ETA: 0:00:05 Cross validating... 79%|█████████████████████████▎ | ETA: 0:00:05 Cross validating... 80%|█████████████████████████▋ | ETA: 0:00:05 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:04 Cross validating... 82%|██████████████████████████▎ | ETA: 0:00:04 Cross validating... 83%|██████████████████████████▌ | ETA: 0:00:04 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:04 Cross validating... 85%|███████████████████████████▎ | ETA: 0:00:03 Cross validating... 86%|███████████████████████████▌ | ETA: 0:00:03 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:03 Cross validating... 88%|████████████████████████████▏ | ETA: 0:00:03 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:02 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: 0:00:02 Cross validating... 94%|██████████████████████████████▏ | ETA: 0:00:01 Cross validating... 95%|██████████████████████████████▍ | ETA: 0:00:01 Cross validating... 96%|██████████████████████████████▊ | ETA: 0:00:01 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:01 Cross validating... 98%|███████████████████████████████▍| ETA: 0:00:00 Cross validating... 99%|███████████████████████████████▋| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:23 Crossvalidation Results: k MSE 1 2838.788679198002 2 2514.3973428708136 3 2305.6176519676274 4 2222.025304867614 5 2075.1670384588365 6 2067.7948989723845 7 2053.427506114907 8 2086.405384830965 9 2080.984460901671 10 2105.131199502364 11 2132.407165368786 12 2138.267187460652 13 2166.002210829576 14 2194.9918295115804 15 2189.890403738045 16 2191.181293229578 17 2209.4669750564362 18 2221.2595493644303 19 2238.7425945763257 20 2253.9559571797727 Best k = 7 Test Summary: | Pass Total Time wrapper multivariate | 8 8 1m27.0s read BGEN and VCF: Error During Test at /home/pkgeval/.julia/packages/MendelIHT/ZcxZT/test/wrapper_test.jl:184 Got exception outside of a @test startproc must be called before process Stacktrace: [1] error(s::String) @ Base error.jl:56 [2] process(codec::CodecZlib.ZlibDecompressor, input::TranscodingStreams.Memory, output::TranscodingStreams.Memory, error_ref::TranscodingStreams.Error) @ CodecZlib ~/.julia/packages/CodecZlib/lEc2s/src/decompression.jl:186 [3] decompress(io::IOStream, v::Variant, h::BGEN.Header; decompressed::Nothing) @ BGEN ~/.julia/packages/BGEN/dfgRU/src/genotypes.jl:72 [4] first_allele_dosage!(b::Bgen, v::Variant; T::Type, mean_impute::Bool, clear_decompressed::Bool, data::Nothing, decompressed::Nothing, is_decompressed::Bool) @ BGEN ~/.julia/packages/BGEN/dfgRU/src/genotypes.jl:571 [5] convert_bgen_gt(t::Type{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:2246 [inlined] [9] top-level scope @ ~/.julia/packages/MendelIHT/ZcxZT/test/wrapper_test.jl:185 [10] include(mapexpr::Function, mod::Module, _path::String) @ Base Base.jl:326 [11] top-level scope @ ~/.julia/packages/MendelIHT/ZcxZT/test/runtests.jl:20 [12] include(mapexpr::Function, mod::Module, _path::String) @ Base Base.jl:326 [13] top-level scope @ none:6 [14] eval(m::Module, e::Any) @ Core boot.jl:522 [15] exec_options(opts::Base.JLOptions) @ Base client.jl:321 [16] _start() @ Base client.jl:596 Test Summary: | Error Total Time read BGEN and VCF | 1 1 4.2s RNG of the outermost testset: Xoshiro(0xe9794cef373a4966, 0x0b15899fc4fd1352, 0x00901e76595d9702, 0x8f510a0a2a1cc00e, 0xf8c1c8656bceb6c8) 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 1082.91s 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:3247 [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 [8] include(mod::Module, _path::String) @ Base Base.jl:325 [9] exec_options(opts::Base.JLOptions) @ Base client.jl:355 [10] _start() @ Base client.jl:596 in expression starting at /PkgEval.jl/scripts/evaluate.jl:214 PkgEval failed after 1193.38s: package tests unexpectedly errored