Package evaluation to test MendelIHT on Julia 1.14.0-DEV.2207 (8c4818189c*) started at 2026-05-18T00:08:51.954 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.14` Set-up completed after 14.75s ################################################################################ # 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 v0.1.44 [79e6a3ab] + Adapt v4.6.0 [66dad0bd] + AliasTables v1.1.3 [4fba245c] + ArrayInterface v7.25.0 [67c07d97] + Automa v1.1.0 ⌅ [6db4b851] + BGEN v0.1.17 [28d598bf] + BGZFStreams v0.3.2 [47718e42] + BioGenerics v0.1.5 [62783981] + BitTwiddlingConvenienceFunctions v0.1.6 [e1450e63] + BufferedStreams v1.2.2 [2a0fbf3d] + CPUSummary v0.2.7 [336ed68f] + CSV v0.10.16 [fb6a15b2] + CloseOpenIntervals v0.1.13 [523fee87] + CodecBzip2 v0.8.5 [ba30903b] + CodecXz v0.7.4 [944b1d66] + CodecZlib v0.7.8 [6b39b394] + CodecZstd v0.8.7 [861a8166] + Combinatorics v1.1.0 [38540f10] + CommonSolve v0.2.6 [f70d9fcc] + CommonWorldInvalidations v1.0.0 [34da2185] + Compat v4.18.1 [a33af91c] + CompositionsBase v0.1.2 [187b0558] + ConstructionBase v1.6.0 [adafc99b] + CpuId v0.3.1 [a8cc5b0e] + Crayons v4.1.1 [a10d1c49] + DBInterface v2.6.1 [9a962f9c] + DataAPI v1.16.0 [a93c6f00] + DataFrames v1.8.2 [864edb3b] + DataStructures v0.19.4 [e2d170a0] + DataValueInterfaces v1.0.0 [8bb1440f] + DelimitedFiles v1.9.1 [b4f34e82] + Distances v0.10.12 [31c24e10] + Distributions v0.25.125 [ffbed154] + DocStringExtensions v0.9.5 [48062228] + FilePathsBase v0.9.24 [1a297f60] + FillArrays v1.16.0 [38e38edf] + GLM v1.9.4 [c27321d9] + Glob v1.5.0 [3e5b6fbb] + HostCPUFeatures v0.1.18 [34004b35] + HypergeometricFunctions v0.3.28 [09f84164] + HypothesisTests v0.11.7 [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 v0.3.29 [bdcacae8] + LoopVectorization v0.12.173 [1914dd2f] + MacroTools v0.5.16 [d125e4d3] + ManualMemory v0.1.8 [921c7187] + MendelIHT v1.4.11 [e1d29d7a] + Missings v1.2.0 [6fe1bfb0] + OffsetArrays v1.17.0 [bac558e1] + OrderedCollections v1.8.1 [90014a1f] + PDMats v0.11.37 [69de0a69] + Parsers v2.8.4 [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 v0.6.43 [0aa819cd] + SQLite v1.8.0 [431bcebd] + SciMLPublic v1.0.1 [91c51154] + SentinelArrays v1.4.9 [1277b4bf] + ShiftedArrays v2.0.0 [4e780e97] + SnpArrays v0.3.23 [a2af1166] + SortingAlgorithms v1.2.2 [276daf66] + SpecialFunctions v2.7.2 [aedffcd0] + Static v1.4.0 [0d7ed370] + StaticArrayInterface v1.10.0 [10745b16] + Statistics v1.11.1 [82ae8749] + StatsAPI v1.8.0 [2913bbd2] + StatsBase v0.34.10 [4c63d2b9] + StatsFuns v1.5.2 [3eaba693] + StatsModels v0.7.9 [892a3eda] + StringManipulation v0.4.4 [3783bdb8] + TableTraits v1.0.1 [bd369af6] + Tables v1.12.1 [8290d209] + ThreadingUtilities v0.5.5 ⌅ [3bb67fe8] + TranscodingStreams v0.9.13 [3a884ed6] + UnPack v1.0.2 [a620830f] + VCFTools v0.2.10 [28eba6e3] + VariantCallFormat v0.5.9 [3d5dd08c] + VectorizationBase v0.21.72 [ea10d353] + WeakRefStrings v1.4.3 [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 v3.51.2+0 [ffd25f8a] + XZ_jll v5.8.3+0 [c4b69c83] + dlfcn_win32_jll v1.4.2+0 [0dad84c5] + ArgTools v1.1.2 [56f22d72] + Artifacts v1.11.0 [2a0f44e3] + Base64 v1.11.0 [ade2ca70] + Dates v1.11.0 [8ba89e20] + Distributed v1.11.0 [f43a241f] + Downloads v1.7.0 [7b1f6079] + FileWatching v1.11.0 [9fa8497b] + Future v1.11.0 [b77e0a4c] + InteractiveUtils v1.11.0 [ac6e5ff7] + JuliaSyntaxHighlighting v1.13.0 [b27032c2] + LibCURL v1.0.0 [76f85450] + LibGit2 v1.11.0 [8f399da3] + Libdl v1.11.0 [37e2e46d] + LinearAlgebra v1.13.0 [56ddb016] + Logging v1.11.0 [d6f4376e] + Markdown v1.11.0 [a63ad114] + Mmap v1.11.0 [ca575930] + NetworkOptions v1.3.0 [44cfe95a] + Pkg v1.14.0 [de0858da] + Printf v1.11.0 [3fa0cd96] + REPL v1.11.0 [9a3f8284] + Random v1.11.0 [ea8e919c] + SHA v1.13.0 [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 v1.5.1+0 [deac9b47] + LibCURL_jll v8.20.0+1 [e37daf67] + LibGit2_jll v1.9.3+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 v3.5.6+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 6.02s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompiling project... 5.1 s ✓ BGEN 7.5 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`. 25.0 s ✓ MendelIHT 3 dependencies successfully precompiled in 46 seconds. 171 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 67.23s ################################################################################ # Testing # Testing MendelIHT Status `/tmp/jl_g5cokX/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 v0.25.125 [38e38edf] GLM v1.9.4 [921c7187] MendelIHT v1.4.11 [92933f4c] ProgressMeter v1.11.0 [189a3867] Reexport v1.2.2 [4e780e97] SnpArrays v0.3.23 [276daf66] SpecialFunctions v2.7.2 [2913bbd2] StatsBase v0.34.10 [a620830f] VCFTools v0.2.10 [37e2e46d] LinearAlgebra v1.13.0 [44cfe95a] Pkg v1.14.0 [9a3f8284] Random v1.11.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_g5cokX/Manifest.toml` [7d9f7c33] Accessors v0.1.44 [79e6a3ab] Adapt v4.6.0 [66dad0bd] AliasTables v1.1.3 [4fba245c] ArrayInterface v7.25.0 [67c07d97] Automa v1.1.0 ⌅ [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 v0.2.6 [f70d9fcc] CommonWorldInvalidations v1.0.0 [34da2185] Compat v4.18.1 [a33af91c] CompositionsBase v0.1.2 [187b0558] ConstructionBase v1.6.0 [adafc99b] CpuId v0.3.1 [a8cc5b0e] Crayons v4.1.1 [a10d1c49] DBInterface v2.6.1 [9a962f9c] DataAPI v1.16.0 [a93c6f00] DataFrames v1.8.2 [864edb3b] DataStructures v0.19.4 [e2d170a0] DataValueInterfaces v1.0.0 [8bb1440f] DelimitedFiles v1.9.1 [b4f34e82] Distances v0.10.12 [31c24e10] Distributions v0.25.125 [ffbed154] DocStringExtensions v0.9.5 [48062228] FilePathsBase v0.9.24 [1a297f60] FillArrays v1.16.0 [38e38edf] GLM v1.9.4 [c27321d9] Glob v1.5.0 [3e5b6fbb] HostCPUFeatures v0.1.18 [34004b35] HypergeometricFunctions v0.3.28 [09f84164] HypothesisTests v0.11.7 [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 v1.6.0 [b964fa9f] LaTeXStrings v1.4.0 [10f19ff3] LayoutPointers v0.1.17 [2ab3a3ac] LogExpFunctions v0.3.29 [bdcacae8] LoopVectorization v0.12.173 [1914dd2f] MacroTools v0.5.16 [d125e4d3] ManualMemory v0.1.8 [921c7187] MendelIHT v1.4.11 [e1d29d7a] Missings v1.2.0 [6fe1bfb0] OffsetArrays v1.17.0 [bac558e1] OrderedCollections v1.8.1 [90014a1f] PDMats v0.11.37 [69de0a69] Parsers v2.8.4 [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 v0.6.43 [0aa819cd] SQLite v1.8.0 [431bcebd] SciMLPublic v1.0.1 [91c51154] SentinelArrays v1.4.9 [1277b4bf] ShiftedArrays v2.0.0 [4e780e97] SnpArrays v0.3.23 [a2af1166] SortingAlgorithms v1.2.2 [276daf66] SpecialFunctions v2.7.2 [aedffcd0] Static v1.4.0 [0d7ed370] StaticArrayInterface v1.10.0 [10745b16] Statistics v1.11.1 [82ae8749] StatsAPI v1.8.0 [2913bbd2] StatsBase v0.34.10 [4c63d2b9] StatsFuns v1.5.2 [3eaba693] StatsModels v0.7.9 [892a3eda] StringManipulation v0.4.4 [ec057cc2] StructUtils v2.8.2 [3783bdb8] TableTraits v1.0.1 [bd369af6] Tables v1.12.1 [8290d209] ThreadingUtilities v0.5.5 ⌅ [3bb67fe8] TranscodingStreams v0.9.13 [3a884ed6] UnPack v1.0.2 [a620830f] VCFTools v0.2.10 [28eba6e3] VariantCallFormat v0.5.9 [3d5dd08c] VectorizationBase v0.21.72 [ea10d353] WeakRefStrings v1.4.3 [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 v3.51.2+0 [ffd25f8a] XZ_jll v5.8.3+0 [c4b69c83] dlfcn_win32_jll v1.4.2+0 [0dad84c5] ArgTools v1.1.2 [56f22d72] Artifacts v1.11.0 [2a0f44e3] Base64 v1.11.0 [ade2ca70] Dates v1.11.0 [8ba89e20] Distributed v1.11.0 [f43a241f] Downloads v1.7.0 [7b1f6079] FileWatching v1.11.0 [9fa8497b] Future v1.11.0 [b77e0a4c] InteractiveUtils v1.11.0 [ac6e5ff7] JuliaSyntaxHighlighting v1.13.0 [b27032c2] LibCURL v1.0.0 [76f85450] LibGit2 v1.11.0 [8f399da3] Libdl v1.11.0 [37e2e46d] LinearAlgebra v1.13.0 [56ddb016] Logging v1.11.0 [d6f4376e] Markdown v1.11.0 [a63ad114] Mmap v1.11.0 [ca575930] NetworkOptions v1.3.0 [44cfe95a] Pkg v1.14.0 [de0858da] Printf v1.11.0 [9abbd945] Profile v1.11.0 [3fa0cd96] REPL v1.11.0 [9a3f8284] Random v1.11.0 [ea8e919c] SHA v1.13.0 [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 v1.5.1+0 [deac9b47] LibCURL_jll v8.20.0+1 [e37daf67] LibGit2_jll v1.9.3+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 v3.5.6+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: `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 = cholesky!(A::LinearAlgebra.Symmetric{Float64, Matrix{Float64}}, ::Val{true}; kwargs::Base.Pairs{Symbol, Union{}, Nothing, @NamedTuple{}}) at deprecated.jl:216 └ @ LinearAlgebra ./deprecated.jl:216 Test Summary: | Pass Total Time loglikelihood | 4 4 27.7s Test Summary: | Pass Total Time deviance | 1 1 0.4s Test Summary: | Pass Total Time update_μ! | 4 4 1.4s Test Summary: | Pass Total Time _choose! | 7 7 9.4s Test Summary: | Pass Total Time _iht_backtrack | 7 7 0.0s Test Summary: | Pass Total Time standardize! | 12 12 1.6s Test Summary: | Pass Total Time project_k! | 2 2 0.9s Test Summary: | Pass Total Time project_group_sparse! | 5 5 1.3s 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 = -1507.7457421661427, backtracks = 0, tol = 1.3141334262806794 Iteration 2: loglikelihood = -1432.7142467407946, backtracks = 0, tol = 0.1194343063900404 Iteration 3: loglikelihood = -1429.9781342447077, backtracks = 0, tol = 0.020758330704329038 Iteration 4: loglikelihood = -1429.9483020495247, backtracks = 0, tol = 0.0018065831896519559 Iteration 5: loglikelihood = -1429.9475864482536, backtracks = 0, tol = 0.0002775611979197525 Iteration 6: loglikelihood = -1429.9475646178057, backtracks = 0, tol = 5.848574166150798e-5 IHT estimated 10 nonzero SNP predictors and 1 non-genetic predictors. Compute time (sec): 0.053932905197143555 Final loglikelihood: -1429.9475646178057 SNP PVE: 0.852891695951092 Iterations: 6 Selected genetic predictors: 10×2 DataFrame Row │ Position Estimated_β │ Int64 Float64 ─────┼─────────────────────── 1 │ 133 0.301889 2 │ 887 -1.43773 3 │ 1367 -0.563038 4 │ 1594 -1.08673 5 │ 2599 1.12215 6 │ 3248 -0.320087 7 │ 4282 -0.170654 8 │ 6412 0.722844 9 │ 7852 -0.354086 10 │ 9265 0.238727 Selected nongenetic predictors: 1×2 DataFrame Row │ Position Estimated_β │ Int64 Float64 ─────┼─────────────────────── 1 │ 1 -0.0418439Test Summary: | Pass Total Time fit normal SnpLinAlg | 4 4 22.2s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse logistic regression Number of threads = 1 Link functin = LogitLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -379.72375963518977, backtracks = 0, tol = 0.6062552017348442 Iteration 2: loglikelihood = -294.14222098196217, backtracks = 0, tol = 0.39035964909167 Iteration 3: loglikelihood = -258.44215825745147, backtracks = 0, tol = 0.18072720194601524 Iteration 4: loglikelihood = -248.39092317275637, backtracks = 1, tol = 0.0581811999889429 Iteration 5: loglikelihood = -241.2861695402178, backtracks = 2, tol = 0.10199490430383734 Iteration 6: loglikelihood = -236.0344401262056, backtracks = 2, tol = 0.10444957184614982 Iteration 7: loglikelihood = -232.75639772007577, backtracks = 2, tol = 0.03618239958756675 Iteration 8: loglikelihood = -230.9028935826695, backtracks = 3, tol = 0.022566251649321353 Iteration 9: loglikelihood = -229.2332883500926, backtracks = 3, tol = 0.02394599965909332 Iteration 10: loglikelihood = -227.8109863155336, backtracks = 3, tol = 0.02260237147851236 Iteration 11: loglikelihood = -226.61429831284372, backtracks = 3, tol = 0.02153016573221634 Iteration 12: loglikelihood = -225.614543213995, backtracks = 3, tol = 0.020073248773013197 Iteration 13: loglikelihood = -225.15228734295533, backtracks = 3, tol = 0.10266272165892033 Iteration 14: loglikelihood = -224.5524858306654, backtracks = 2, tol = 0.010910053499902256 Iteration 15: loglikelihood = -223.90430308527087, backtracks = 3, tol = 0.10669566586572145 Iteration 16: loglikelihood = -223.43342440058004, backtracks = 1, tol = 0.009912340440473734 Iteration 17: loglikelihood = -223.19474883510568, backtracks = 3, tol = 0.10429355504005154 Iteration 18: loglikelihood = -222.7530868660152, backtracks = 1, tol = 0.010133510239484585 Iteration 19: loglikelihood = -222.4546375562022, backtracks = 3, tol = 0.009382230171462355 Iteration 20: loglikelihood = -225.04961416047087, backtracks = 3, tol = 0.13141028198780508 Iteration 21: loglikelihood = -221.57583298738808, backtracks = 0, tol = 0.12983606150115481 Iteration 22: loglikelihood = -220.9953587123894, backtracks = 0, tol = 0.018278220962270587 Iteration 23: loglikelihood = -220.46528702030645, backtracks = 0, tol = 0.10912949798131547 Iteration 24: loglikelihood = -220.22939682199817, backtracks = 1, tol = 0.006133557493960293 Iteration 25: loglikelihood = -220.1149031779291, backtracks = 3, tol = 0.005637364497494655 Iteration 26: loglikelihood = -237.91408320706802, backtracks = 3, tol = 0.1311916630585333 Iteration 27: loglikelihood = -222.6667401701631, backtracks = 0, tol = 0.13008576394077564 Iteration 28: loglikelihood = -220.0179912284672, backtracks = 0, tol = 0.10981267805412102 Iteration 29: loglikelihood = -219.80873468505163, backtracks = 1, tol = 0.006242686572879014 Iteration 30: loglikelihood = -219.71412932030552, backtracks = 1, tol = 0.0052581541847830735 Iteration 31: loglikelihood = -219.67346582214395, backtracks = 3, tol = 0.002736072071808146 Iteration 32: loglikelihood = -236.63118723570068, backtracks = 3, tol = 0.12536959025201838 Iteration 33: loglikelihood = -222.42522446507616, backtracks = 0, tol = 0.12480632457239557 Iteration 34: loglikelihood = -219.76952387571325, backtracks = 0, tol = 0.10782393864869841 Iteration 35: loglikelihood = -219.54239052596037, backtracks = 0, tol = 0.010969385336776636 Iteration 36: loglikelihood = -219.51051719556185, backtracks = 0, tol = 0.0038143069815270263 Iteration 37: loglikelihood = -219.49562270628724, backtracks = 1, tol = 0.0015360028505860806 Iteration 38: loglikelihood = -222.2776344615594, backtracks = 3, tol = 0.10706948875570901 Iteration 39: loglikelihood = -219.86344247649652, backtracks = 0, tol = 0.10682440099239575 Iteration 40: loglikelihood = -219.50637292175287, backtracks = 0, tol = 0.010145149683589566 Iteration 41: loglikelihood = -219.45601478260392, backtracks = 0, tol = 0.004786594360325445 Iteration 42: loglikelihood = -219.44279315931445, backtracks = 0, tol = 0.0023300326568676676 Iteration 43: loglikelihood = -219.434262597912, backtracks = 0, tol = 0.002159682320412748 Iteration 44: loglikelihood = -219.42706752504972, backtracks = 0, tol = 0.0019986878272562235 Iteration 45: loglikelihood = -219.4208881668612, backtracks = 0, tol = 0.001781315196828412 Iteration 46: loglikelihood = -219.41556755717227, backtracks = 0, tol = 0.0017266268818688624 Iteration 47: loglikelihood = -219.41098445944962, backtracks = 0, tol = 0.001504993867218278 Iteration 48: loglikelihood = -219.4070309112888, backtracks = 0, tol = 0.001495426527055874 Iteration 49: loglikelihood = -219.40362030781677, backtracks = 0, tol = 0.001286324051089446 Iteration 50: loglikelihood = -219.4006747755802, backtracks = 0, tol = 0.001295957349435961 Iteration 51: loglikelihood = -219.39813103252988, backtracks = 0, tol = 0.0011058748112207813 Iteration 52: loglikelihood = -219.3959322024177, backtracks = 0, tol = 0.0011233728145861855 Iteration 53: loglikelihood = -219.39403166729804, backtracks = 0, tol = 0.0009536994758608786 Iteration 54: loglikelihood = -219.39238763268273, backtracks = 0, tol = 0.0009739180646352119 Iteration 55: loglikelihood = -219.39096560226784, backtracks = 0, tol = 0.0008239389039648708 Iteration 56: loglikelihood = -219.38973473800374, backtracks = 0, tol = 0.0008444580901064712 Iteration 57: loglikelihood = -219.3886694316569, backtracks = 0, tol = 0.0007126409505425607 Iteration 58: loglikelihood = -219.38774685610232, backtracks = 0, tol = 0.0007323063866727435 Iteration 59: loglikelihood = -219.3869479529937, backtracks = 0, tol = 0.00061686194275372 Iteration 60: loglikelihood = -219.3862557798823, backtracks = 0, tol = 0.0006351404346176769 Iteration 61: loglikelihood = -219.3856561234815, backtracks = 0, tol = 0.000534269842115572 Iteration 62: loglikelihood = -219.38513638040487, backtracks = 0, tol = 0.0005509480422217535 Iteration 63: loglikelihood = -219.38468593224545, backtracks = 0, tol = 0.0004629512780606966 Iteration 64: loglikelihood = -219.38429538513583, backtracks = 0, tol = 0.0004779860767529819 Iteration 65: loglikelihood = -219.38395679466737, backtracks = 0, tol = 0.0004013057505476397 Iteration 66: loglikelihood = -219.38366314739872, backtracks = 0, tol = 0.0004147454994836376 Iteration 67: loglikelihood = -219.38340849212824, backtracks = 0, tol = 0.00034797985178746597 Iteration 68: loglikelihood = -219.38318758502183, backtracks = 0, tol = 0.0003599207374415984 Iteration 69: loglikelihood = -219.38299596326374, backtracks = 0, tol = 0.0003018217223394219 Iteration 70: loglikelihood = -219.3828297011887, backtracks = 0, tol = 0.00031238270039476616 Iteration 71: loglikelihood = -219.38268544908368, backtracks = 0, tol = 0.00026184698528793125 Iteration 72: loglikelihood = -219.3825602648841, backtracks = 0, tol = 0.0002711550905775348 Iteration 73: loglikelihood = -219.38245163239276, backtracks = 0, tol = 0.00022721198022395564 Iteration 74: loglikelihood = -219.38235734460943, backtracks = 0, tol = 0.00023539371282360467 Iteration 75: loglikelihood = -219.38227551018164, backtracks = 0, tol = 0.0001971920991460162 Iteration 76: loglikelihood = -219.382204472153, backtracks = 0, tol = 0.00020436848993624394 Iteration 77: loglikelihood = -219.3821428080304, backtracks = 0, tol = 0.00017116393516432852 Iteration 78: loglikelihood = -219.38208927292968, backtracks = 0, tol = 0.00017744788492952903 Iteration 79: loglikelihood = -219.38204279645043, backtracks = 0, tol = 0.00014859040670150365 Iteration 80: loglikelihood = -219.38200244272016, backtracks = 0, tol = 0.00015408544066832546 Iteration 81: loglikelihood = -219.38196740593906, backtracks = 0, tol = 0.00012900826739905896 Iteration 82: loglikelihood = -219.38193698216227, backtracks = 0, tol = 0.00013380816660865064 Iteration 83: loglikelihood = -219.38191056455443, backtracks = 0, tol = 0.00011201756190578927 Iteration 84: loglikelihood = -219.3818876233726, backtracks = 0, tol = 0.000116206527337935 Iteration 85: loglikelihood = -219.38186770147453, backtracks = 0, tol = 9.727268703830643e-5 Test Summary: | Pass Total Time fit Bernoulli SnpLinAlg | 4 4 4.0s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse 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 = -1351.6583505211129, backtracks = 0, tol = 0.3245584100636996 Iteration 2: loglikelihood = -1304.3253762119675, backtracks = 0, tol = 0.06975502719426246 Iteration 3: loglikelihood = -1293.5808966429188, backtracks = 0, tol = 0.06903443863801738 Iteration 4: loglikelihood = -1289.1191998409454, backtracks = 0, tol = 0.03982093980528248 Iteration 5: loglikelihood = -1287.4734277996322, backtracks = 0, tol = 0.024347205575979747 Iteration 6: loglikelihood = -1286.6477638300335, backtracks = 0, tol = 0.016085793556931214 Iteration 7: loglikelihood = -1286.230117354096, backtracks = 0, tol = 0.01080378187404553 Iteration 8: loglikelihood = -1285.9043681246615, backtracks = 0, tol = 0.0682141619586807 Iteration 9: loglikelihood = -1285.7570613923338, backtracks = 1, tol = 0.005139586048626907 Iteration 10: loglikelihood = -1285.7109424439554, backtracks = 2, tol = 0.002891154026997874 Iteration 11: loglikelihood = -1285.6641927310397, backtracks = 2, tol = 0.0037714664981649544 Iteration 12: loglikelihood = -1285.6351414090834, backtracks = 2, tol = 0.003218320411080163 Iteration 13: loglikelihood = -1285.6180500025753, backtracks = 2, tol = 0.0025029494947296995 Iteration 14: loglikelihood = -1285.60815665698, backtracks = 2, tol = 0.001957823133402266 Iteration 15: loglikelihood = -1285.6024564049387, backtracks = 2, tol = 0.0014456175595743454 Iteration 16: loglikelihood = -1285.5991334239895, backtracks = 2, tol = 0.0011205145146626712 Iteration 17: loglikelihood = -1285.5971419461207, backtracks = 2, tol = 0.0008297859165592434 Iteration 18: loglikelihood = -1285.5959122787785, backtracks = 2, tol = 0.0006725844566112759 Iteration 19: loglikelihood = -1285.5951413954326, backtracks = 2, tol = 0.0005131189674461289 Iteration 20: loglikelihood = -1285.5946550178187, backtracks = 2, tol = 0.00042333706838313333 Iteration 21: loglikelihood = -1285.594347499926, backtracks = 2, tol = 0.0003244650994793926 Iteration 22: loglikelihood = -1285.594152711383, backtracks = 2, tol = 0.0002683163022729617 Iteration 23: loglikelihood = -1285.59402923097, backtracks = 2, tol = 0.00020581226737600983 Iteration 24: loglikelihood = -1285.593950874302, backtracks = 2, tol = 0.0001703489672627879 Iteration 25: loglikelihood = -1285.5939011303199, backtracks = 2, tol = 0.0001307173854701111 Iteration 26: loglikelihood = -1285.5938695314123, backtracks = 2, tol = 0.00010824763479099445 Iteration 27: loglikelihood = -1285.5938494538211, backtracks = 2, tol = 8.308271630607687e-5 Test Summary: | Pass Total Time fit Poisson SnpLinAlg | 4 4 3.2s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse NegativeBinomial regression Number of threads = 1 Link functin = LogLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1456.3658438845828, backtracks = 0, tol = 0.32442179966843016 Iteration 2: loglikelihood = -1427.3741751765772, backtracks = 0, tol = 0.0914958894830873 Iteration 3: loglikelihood = -1423.0504779268012, backtracks = 0, tol = 0.11802511690390088 Iteration 4: loglikelihood = -1416.984105490722, backtracks = 0, tol = 0.11344549593622304 Iteration 5: loglikelihood = -1416.6527054488204, backtracks = 1, tol = 0.00712255110356705 Iteration 6: loglikelihood = -1416.5149923840117, backtracks = 1, tol = 0.0070663958143853565 Iteration 7: loglikelihood = -1416.4807567788127, backtracks = 2, tol = 0.003205133202036598 Iteration 8: loglikelihood = -1416.4596258550366, backtracks = 2, tol = 0.0027668738268642676 Iteration 9: loglikelihood = -1416.446897364514, backtracks = 2, tol = 0.0023081493290616935 Iteration 10: loglikelihood = -1416.4393710785137, backtracks = 2, tol = 0.0018756591817560085 Iteration 11: loglikelihood = -1416.4349784488477, backtracks = 2, tol = 0.0014953363064538051 Iteration 12: loglikelihood = -1416.4324384151546, backtracks = 2, tol = 0.0011753204996156966 Iteration 13: loglikelihood = -1416.4309798216057, backtracks = 2, tol = 0.0009137574898433008 Iteration 14: loglikelihood = -1416.430146763278, backtracks = 2, tol = 0.0007043476459319266 Iteration 15: loglikelihood = -1416.429673004227, backtracks = 2, tol = 0.0005392911238191321 Iteration 16: loglikelihood = -1416.4294044845701, backtracks = 2, tol = 0.0004107562532471336 Iteration 17: loglikelihood = -1416.429252690949, backtracks = 2, tol = 0.0003115942687003598 Iteration 18: loglikelihood = -1416.429167056138, backtracks = 2, tol = 0.00023564133098842328 Iteration 19: loglikelihood = -1416.429118819911, backtracks = 2, tol = 0.00017778356912495714 Iteration 20: loglikelihood = -1416.4290916815464, backtracks = 2, tol = 0.00013389263904081794 Iteration 21: loglikelihood = -1416.4290764267726, backtracks = 2, tol = 0.00010070107832749875 Iteration 22: loglikelihood = -1416.4290678577079, backtracks = 2, tol = 7.565980630567658e-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 = -1934.5756707115384, backtracks = 0, tol = 0.7246882185033121 Iteration 2: loglikelihood = -1487.267811504296, backtracks = 0, tol = 0.15502544365765653 Iteration 3: loglikelihood = -1412.218505224893, backtracks = 0, tol = 0.055892536702728875 Iteration 4: loglikelihood = -1406.9268534790078, backtracks = 0, tol = 0.032165936490256966 Iteration 5: loglikelihood = -1405.456365961489, backtracks = 0, tol = 0.027857535234857234 Iteration 6: loglikelihood = -1405.4410824136264, backtracks = 0, tol = 0.028497706182716614 Iteration 7: loglikelihood = -1405.3299422395366, backtracks = 0, tol = 0.001831230313812285 Iteration 8: loglikelihood = -1405.329254802445, backtracks = 0, tol = 0.00012265751875025578 Iteration 9: loglikelihood = -1405.3292419612967, backtracks = 0, tol = 2.0200612086639128e-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 = -1689.3270884307412, backtracks = 0, tol = 0.5449541725006347 Iteration 2: loglikelihood = -1441.7379308318116, backtracks = 0, tol = 0.09995522649357891 Iteration 3: loglikelihood = -1407.4453771406952, backtracks = 0, tol = 0.04396958848025447 Iteration 4: loglikelihood = -1405.3129024467385, backtracks = 0, tol = 0.03270655243444163 Iteration 5: loglikelihood = -1405.1925741357336, backtracks = 0, tol = 0.0023236641750295547 Iteration 6: loglikelihood = -1405.1920167715634, backtracks = 1, tol = 9.954532635011979e-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 12.0s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse NegativeBinomial regression Number of threads = 1 Link functin = LogLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1583.120223754502, backtracks = 0, tol = 0.19797562702835875 Iteration 2: loglikelihood = -1507.9226677956283, backtracks = 0, tol = 0.09853851822475779 Iteration 3: loglikelihood = -1452.6962597544464, backtracks = 0, tol = 0.1291198710167294 Iteration 4: loglikelihood = -1450.9520104649303, backtracks = 0, tol = 0.11217323913971496 Iteration 5: loglikelihood = -1425.0773108974624, backtracks = 1, tol = 0.0337021328262484 Iteration 6: loglikelihood = -1410.718914128168, backtracks = 0, tol = 0.08290843669210182 Iteration 7: loglikelihood = -1397.2504743795887, backtracks = 1, tol = 0.029989665323606626 Iteration 8: loglikelihood = -1378.6977605632653, backtracks = 0, tol = 0.05551441131871894 Iteration 9: loglikelihood = -1377.3128461453477, backtracks = 1, tol = 0.012124318729062885 Iteration 10: loglikelihood = -1374.071057378459, backtracks = 1, tol = 0.053337589371614716 Iteration 11: loglikelihood = -1373.359085409526, backtracks = 1, tol = 0.010745688714817504 Iteration 12: loglikelihood = -1373.0363034619854, backtracks = 1, tol = 0.0065750557304301085 Iteration 13: loglikelihood = -1372.9107551480324, backtracks = 1, tol = 0.004694776317496513 Iteration 14: loglikelihood = -1372.8734082040912, backtracks = 1, tol = 0.003012697765970453 Iteration 15: loglikelihood = -1372.8568731216255, backtracks = 1, tol = 0.001319667911206589 Iteration 16: loglikelihood = -1372.8486526575584, backtracks = 1, tol = 0.0014248607496067816 Iteration 17: loglikelihood = -1372.8447276039492, backtracks = 1, tol = 0.0006188754785396384 Iteration 18: loglikelihood = -1372.8428393955214, backtracks = 1, tol = 0.0006801971165697614 Iteration 19: loglikelihood = -1372.8418992644529, backtracks = 1, tol = 0.00029925203404593313 Iteration 20: loglikelihood = -1372.8414613464768, backtracks = 1, tol = 0.00032576666932667325 Iteration 21: loglikelihood = -1372.841236018812, backtracks = 1, tol = 0.00014619862078128876 Iteration 22: loglikelihood = -1372.8411341325857, backtracks = 1, tol = 0.00015629800685726202 Iteration 23: loglikelihood = -1372.8410802307505, backtracks = 1, tol = 7.159877804584509e-5 1.247410 seconds (4.91 M allocations: 87.227 MiB, 1.84% gc time, 52.09% 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 = -1603.4513882074605, backtracks = 0, tol = 0.19797562702835875 Iteration 2: loglikelihood = -1554.3817646713294, backtracks = 0, tol = 0.09853851822475779 Iteration 3: loglikelihood = -1528.425167061551, backtracks = 0, tol = 0.13724024124413925 Iteration 4: loglikelihood = -1514.1045176971274, backtracks = 0, tol = 0.1172508310791844 Iteration 5: loglikelihood = -1498.639171869928, backtracks = 0, tol = 0.10046996290215011 Iteration 6: loglikelihood = -1483.3716895267899, backtracks = 0, tol = 0.08147254582711885 Iteration 7: loglikelihood = -1467.4016672181833, backtracks = 0, tol = 0.0681502736694814 Iteration 8: loglikelihood = -1453.8551866669677, backtracks = 0, tol = 0.05390620330561597 Iteration 9: loglikelihood = -1439.8133598107147, backtracks = 0, tol = 0.051230368719210176 Iteration 10: loglikelihood = -1426.6710120494984, backtracks = 0, tol = 0.061236927850611016 Iteration 11: loglikelihood = -1420.8136859730296, backtracks = 0, tol = 0.0410259886051929 Iteration 12: loglikelihood = -1416.172856781416, backtracks = 0, tol = 0.012726927575264106 Iteration 13: loglikelihood = -1412.9761125646396, backtracks = 0, tol = 0.06288207374906163 Iteration 14: loglikelihood = -1409.5493443388775, backtracks = 0, tol = 0.06253305104707244 Iteration 15: loglikelihood = -1406.4774989050388, backtracks = 0, tol = 0.006044817260145455 Iteration 16: loglikelihood = -1403.987504157678, backtracks = 0, tol = 0.0007404960828692928 Iteration 17: loglikelihood = -1401.7786299841493, backtracks = 0, tol = 0.0004158662673359156 Iteration 18: loglikelihood = -1398.256097172948, backtracks = 1, tol = 0.0002467686688118109 Iteration 19: loglikelihood = -1397.8716799796812, backtracks = 0, tol = 0.06426431114229737 Iteration 20: loglikelihood = -1394.8069539984265, backtracks = 0, tol = 0.06219519821222205 Iteration 21: loglikelihood = -1393.4487657246752, backtracks = 0, tol = 0.005476637348467857 Iteration 22: loglikelihood = -1392.2302003260322, backtracks = 0, tol = 0.001068177966945656 Iteration 23: loglikelihood = -1391.1412705777084, backtracks = 0, tol = 0.0005384772636922273 Iteration 24: loglikelihood = -1390.1378231607493, backtracks = 0, tol = 0.0001469217983954429 Iteration 25: loglikelihood = -1389.9742986118333, backtracks = 0, tol = 0.06312431449263195 Iteration 26: loglikelihood = -1388.91631015625, backtracks = 0, tol = 0.06294878602708504 Iteration 27: loglikelihood = -1387.5695291797706, backtracks = 0, tol = 0.008267082180343817 Iteration 28: loglikelihood = -1386.827172101323, backtracks = 0, tol = 0.0022310595091444515 Iteration 29: loglikelihood = -1386.1267421812747, backtracks = 0, tol = 0.0009242589024000817 Iteration 30: loglikelihood = -1385.499794551844, backtracks = 0, tol = 0.0003272586833198675 Iteration 31: loglikelihood = -1384.911355115671, backtracks = 0, tol = 0.00019362705679121643 Iteration 32: loglikelihood = -1384.249437606639, backtracks = 0, tol = 0.05983147321417971 Iteration 33: loglikelihood = -1384.1214034391971, backtracks = 0, tol = 0.059829806754507775 Iteration 34: loglikelihood = -1383.4241873881713, backtracks = 0, tol = 0.004708708877346254 Iteration 35: loglikelihood = -1382.9761611947647, backtracks = 0, tol = 0.001835861345787576 Iteration 36: loglikelihood = -1382.5460381430735, backtracks = 0, tol = 0.0005050795184529151 Iteration 37: loglikelihood = -1382.1532806951914, backtracks = 0, tol = 0.00023059543220075858 Iteration 38: loglikelihood = -1381.7802990639477, backtracks = 0, tol = 0.0001607278958820629 Iteration 39: loglikelihood = -1381.3033579716073, backtracks = 0, tol = 0.05931140467903689 Iteration 40: loglikelihood = -1380.6450499560945, backtracks = 1, tol = 0.0036382374532173897 Iteration 41: loglikelihood = -1380.1257899218967, backtracks = 1, tol = 0.0023867752468494504 Iteration 42: loglikelihood = -1379.6787458608094, backtracks = 1, tol = 0.0013252882714198976 Iteration 43: loglikelihood = -1379.2654004375534, backtracks = 1, tol = 0.0007133342261697813 Iteration 44: loglikelihood = -1378.9038853276934, backtracks = 1, tol = 0.0003813458058352925 Iteration 45: loglikelihood = -1378.581431981726, backtracks = 1, tol = 0.00020307484514377576 Iteration 46: loglikelihood = -1378.2836538285055, backtracks = 1, tol = 0.00014425764366944195 Iteration 47: loglikelihood = -1378.0020538585072, backtracks = 1, tol = 0.00011302272994232108 Iteration 48: loglikelihood = -1377.735203986253, backtracks = 1, tol = 9.542488155011111e-5 0.498079 seconds (1.96 M allocations: 35.612 MiB, 3.21% gc time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse NegativeBinomial regression Number of threads = 1 Link functin = LogLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -3443.819, backtracks = 0, tol = 0.08825200852869804 Iteration 2: loglikelihood = -3401.9468, backtracks = 0, tol = 0.04543932482577365 Iteration 3: loglikelihood = -3379.6958, backtracks = 1, tol = 0.06192798323297979 Iteration 4: loglikelihood = -3374.66, backtracks = 1, tol = 0.013146305604897927 Iteration 5: loglikelihood = -3372.866, backtracks = 1, tol = 0.00764054538627671 Iteration 6: loglikelihood = -3347.2837, backtracks = 1, tol = 0.07172867021762225 Iteration 7: loglikelihood = -3341.1265, backtracks = 1, tol = 0.016036378143873858 Iteration 8: loglikelihood = -3338.8013, backtracks = 1, tol = 0.011299379086361227 Iteration 9: loglikelihood = -3338.078, backtracks = 1, tol = 0.005752431671441618 Iteration 10: loglikelihood = -3337.8635, backtracks = 1, tol = 0.0027415876046715374 Iteration 11: loglikelihood = -3337.8591, backtracks = 1, tol = 0.0770629805800471 Iteration 12: loglikelihood = -3336.4348, backtracks = 1, tol = 0.007906031431996939 Iteration 13: loglikelihood = -3336.0476, backtracks = 1, tol = 0.00419930369979985 Iteration 14: loglikelihood = -3335.9465, backtracks = 1, tol = 0.0021300782500248325 Iteration 15: loglikelihood = -3335.923, backtracks = 1, tol = 0.001045667807726179 Iteration 16: loglikelihood = -3335.9167, backtracks = 1, tol = 0.0005005018602051371 Iteration 17: loglikelihood = -3335.9155, backtracks = 3, tol = 5.954834072086143e-5 26.504892 seconds (17.91 M allocations: 724.100 MiB, 4.46% gc time, 93.62% 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 = -3346.57, backtracks = 0, tol = 0.08825200852869804 Iteration 2: loglikelihood = -3241.3801, backtracks = 0, tol = 0.04683156917021988 Iteration 3: loglikelihood = -3068.4778, backtracks = 1, tol = 0.06037878572785042 Iteration 4: loglikelihood = -3055.253, backtracks = 0, tol = 0.10454758030555832 Iteration 5: loglikelihood = -2874.0789, backtracks = 0, tol = 0.10245742925692264 Iteration 6: loglikelihood = -2775.7097, backtracks = 0, tol = 0.07524912451347072 Iteration 7: loglikelihood = -2680.8545, backtracks = 0, tol = 0.08549962062091435 Iteration 8: loglikelihood = -2583.3906, backtracks = 0, tol = 0.011908710503405752 Iteration 9: loglikelihood = -2507.192, backtracks = 0, tol = 0.09443518355823526 Iteration 10: loglikelihood = -2409.1663, backtracks = 0, tol = 0.09484170510177797 Iteration 11: loglikelihood = -2328.3237, backtracks = 0, tol = 0.08738640306224689 Iteration 12: loglikelihood = -2263.27, backtracks = 0, tol = 0.08693978437796027 Iteration 13: loglikelihood = -2216.3604, backtracks = 0, tol = 0.09367942482891795 Iteration 14: loglikelihood = -2178.9805, backtracks = 0, tol = 0.09393470865809768 Iteration 15: loglikelihood = -2156.182, backtracks = 0, tol = 0.09598792293142434 Iteration 16: loglikelihood = -2138.8325, backtracks = 0, tol = 0.09632142950662137 Iteration 17: loglikelihood = -2130.3748, backtracks = 0, tol = 0.09738039425733733 Iteration 18: loglikelihood = -2123.35, backtracks = 0, tol = 0.09769013794423075 Iteration 19: loglikelihood = -2121.2092, backtracks = 0, tol = 0.09826128980711397 Iteration 20: loglikelihood = -2118.2942, backtracks = 0, tol = 0.09857552096671096 Iteration 21: loglikelihood = -2116.5996, backtracks = 1, tol = 0.006997564001957186 Iteration 22: loglikelihood = -2116.1685, backtracks = 1, tol = 0.0033100354731567623 Iteration 23: loglikelihood = -2116.0518, backtracks = 1, tol = 0.0015697160301277133 Iteration 24: loglikelihood = -2116.0205, backtracks = 1, tol = 0.0007518787606198862 Iteration 25: loglikelihood = -2116.0122, backtracks = 1, tol = 0.0003635964185024217 Iteration 26: loglikelihood = -2116.0083, backtracks = 1, tol = 0.00017680600312301747 Iteration 27: loglikelihood = -2116.0054, backtracks = 1, tol = 9.014240715332063e-5 0.195316 seconds (1.39 M allocations: 22.999 MiB) Test Summary: | Pass Total Time Negative binomial nuisance parameter Float32 matrix | 12 12 31.3s **** 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 = -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 4.932342 seconds (1.14 M allocations: 136.668 MiB, 1.84% gc time, 89.50% compilation time) Test Summary: | Pass Total Time initialze beta | 1 1 5.4s 10.004645 seconds (4.00 M allocations: 82.494 MiB, 0.34% gc time, 0.62% compilation time) 5.331679 seconds (3.98 M allocations: 91.675 MiB, 0.16% gc time) 10.322616 seconds (20.41 M allocations: 439.376 MiB, 0.77% gc time, 17.24% compilation time: 77% of which was recompilation) 8.411661 seconds (20.18 M allocations: 434.191 MiB, 0.94% gc time) 47.754270 seconds (3.77 M allocations: 4.239 GiB, 8.94% gc time, 22.30% compilation time) 53.049797 seconds (70.38 k allocations: 183.440 MiB, 0.26% gc time) Test Summary: | Pass Total Time memory_efficient keyword | 7 7 2m31.2s Test Summary: | Pass Total Time update_support! | 10 10 0.7s 13.692 ms (78 allocations: 4.56 KiB) 4.240 μs (0 allocations: 0 bytes) 127.168 μs (4 allocations: 288 bytes) 6.117 μs (0 allocations: 0 bytes) 40.320 μs (2 allocations: 64 bytes) 31.209 μs (0 allocations: 0 bytes) 24.810 μs (0 allocations: 0 bytes) 28.040 μs (0 allocations: 0 bytes) 101.439 μs (0 allocations: 0 bytes) 34.451 ms (78 allocations: 4.56 KiB) 18.269 μs (0 allocations: 0 bytes) 167.298 μs (4 allocations: 288 bytes) 34.310 μs (0 allocations: 0 bytes) 206.688 μs (2 allocations: 64 bytes) 82.339 μs (0 allocations: 0 bytes) 124.049 μs (0 allocations: 0 bytes) 146.549 μs (0 allocations: 0 bytes) 181.428 μs (0 allocations: 0 bytes) Test Summary: | Total Time benchmarks for multivariate function | 0 2m18.2s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** **** 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 0.428950 seconds (49.39 k allocations: 5.493 MiB, 64.31% compilation time) Test Summary: | Pass Total Time multivariate fit_iht SnpLinAlg | 7 7 12.2s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse 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 1.950017 seconds (282.12 k allocations: 168.121 MiB, 57.67% 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 **** Cross validating... 3%|█ | ETA: 0:03:50 Cross validating... 13%|████▏ | ETA: 0:00:56 Cross validating... 16%|█████▏ | ETA: 0:00:43 Cross validating... 19%|██████▏ | ETA: 0:00:35 Cross validating... 22%|███████▏ | ETA: 0:00:30 Cross validating... 25%|████████▏ | ETA: 0:00:25 Cross validating... 29%|█████████▏ | ETA: 0:00:22 Cross validating... 32%|██████████▏ | ETA: 0:00:19 Cross validating... 35%|███████████▏ | ETA: 0:00:17 Cross validating... 38%|████████████▎ | ETA: 0:00:15 Cross validating... 41%|█████████████▎ | ETA: 0:00:13 Cross validating... 44%|██████████████▎ | ETA: 0:00:12 Cross validating... 48%|███████████████▎ | ETA: 0:00:11 Cross validating... 51%|████████████████▎ | ETA: 0:00:10 Cross validating... 54%|█████████████████▎ | ETA: 0:00:09 Cross validating... 57%|██████████████████▎ | ETA: 0:00:08 Cross validating... 60%|███████████████████▎ | ETA: 0:00:07 Cross validating... 63%|████████████████████▍ | ETA: 0:00:06 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:05 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:05 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:04 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:03 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:03 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:02 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:02 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:01 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:01 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:01 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:12 Crossvalidation Results: k MSE 0 2324.3166186788044 1 1574.9313793794156 2 1201.581110585151 3 765.1418173019131 4 577.1786755494066 5 473.56732779396975 6 450.27298040309705 7 425.17802979949374 8 370.12939473640756 9 353.3609538056834 10 342.81575280450323 11 345.77478210076265 12 348.5291883160312 13 360.7901252627416 14 350.81839142757786 15 351.2652124045826 16 364.87754938143553 17 350.8875937593425 18 363.01342625853556 19 362.98216354331464 20 391.9074654923804 Best k = 10 12.234130 seconds (11.41 M allocations: 300.744 MiB, 1.32% gc time, 63.18% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 5%|█▌ | ETA: 0:00:03 Cross validating... 10%|███ | ETA: 0:00:03 Cross validating... 13%|████▏ | ETA: 0:00:03 Cross validating... 16%|█████▏ | ETA: 0:00:03 Cross validating... 19%|██████▏ | ETA: 0:00:03 Cross validating... 22%|███████▏ | ETA: 0:00:03 Cross validating... 25%|████████▏ | ETA: 0:00:03 Cross validating... 29%|█████████▏ | ETA: 0:00:03 Cross validating... 30%|█████████▋ | ETA: 0:00:03 Cross validating... 33%|██████████▋ | ETA: 0:00:03 Cross validating... 37%|███████████▋ | ETA: 0:00:03 Cross validating... 40%|████████████▊ | ETA: 0:00:03 Cross validating... 44%|██████████████▎ | ETA: 0:00:03 Cross validating... 48%|███████████████▎ | ETA: 0:00:02 Cross validating... 51%|████████████████▎ | ETA: 0:00:02 Cross validating... 54%|█████████████████▎ | ETA: 0:00:02 Cross validating... 57%|██████████████████▎ | ETA: 0:00:02 Cross validating... 60%|███████████████████▎ | ETA: 0:00:02 Cross validating... 63%|████████████████████▍ | ETA: 0:00:02 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:02 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:01 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:01 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:01 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:01 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:01 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:01 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 2324.3166186788044 1 1577.639091007334 2 1216.9593052324049 3 772.7871911880552 4 584.9336692975164 5 478.31545548883145 6 457.3695437113272 7 434.4380718506658 8 384.6912767622889 9 369.93877833665454 10 359.16470044699076 11 365.2996934984167 12 373.99368900990567 13 377.5026383518742 14 378.20551320220807 15 377.14819511893415 16 388.70167475982157 17 386.4022135534272 18 396.1993215717497 19 392.7058383506835 20 391.9074654923804 Best k = 10 4.751587 seconds (10.53 M allocations: 222.770 MiB, 1.68% gc time, 1.05% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, normal model | 3 3 17.8s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:06:05 Cross validating... 10%|███ | ETA: 0:01:55 Cross validating... 14%|████▋ | ETA: 0:01:14 Cross validating... 19%|██████▏ | ETA: 0:00:53 Cross validating... 24%|███████▋ | ETA: 0:00:40 Cross validating... 29%|█████████▏ | ETA: 0:00:32 Cross validating... 33%|██████████▋ | ETA: 0:00:26 Cross validating... 40%|████████████▊ | ETA: 0:00:20 Cross validating... 46%|██████████████▊ | ETA: 0:00:15 Cross validating... 52%|████████████████▊ | ETA: 0:00:12 Cross validating... 57%|██████████████████▎ | ETA: 0:00:10 Cross validating... 62%|███████████████████▊ | ETA: 0:00:08 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:07 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:05 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:04 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:03 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:02 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:01 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:01 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:14 Crossvalidation Results: k MSE 0 1521.5961071777344 1 1266.6909759521486 2 941.9244219970703 3 751.9563745117188 4 627.7997390747071 5 519.6525157165528 6 433.9156575012207 7 397.22232421875003 8 349.68844558715824 9 337.0042922973633 10 338.5606999206543 11 340.3861851501465 12 343.6156552124024 13 346.66157730102543 14 348.2998506164551 15 348.4530387878418 16 351.5399729919434 17 360.52782135009767 18 379.90017852783205 19 379.1922953796387 20 372.5833146667481 Best k = 9 15.836869 seconds (12.61 M allocations: 311.446 MiB, 0.61% gc time, 83.00% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 5%|█▌ | ETA: 0:00:03 Cross validating... 10%|███ | ETA: 0:00:02 Cross validating... 14%|████▋ | ETA: 0:00:02 Cross validating... 17%|█████▋ | ETA: 0:00:02 Cross validating... 21%|██████▋ | ETA: 0:00:02 Cross validating... 24%|███████▋ | ETA: 0:00:02 Cross validating... 27%|████████▋ | ETA: 0:00:02 Cross validating... 30%|█████████▋ | ETA: 0:00:02 Cross validating... 33%|██████████▋ | ETA: 0:00:02 Cross validating... 38%|████████████▎ | ETA: 0:00:02 Cross validating... 43%|█████████████▊ | ETA: 0:00:02 Cross validating... 46%|██████████████▊ | ETA: 0:00:02 Cross validating... 51%|████████████████▎ | ETA: 0:00:02 Cross validating... 54%|█████████████████▎ | ETA: 0:00:02 Cross validating... 57%|██████████████████▎ | ETA: 0:00:01 Cross validating... 60%|███████████████████▎ | ETA: 0:00:01 Cross validating... 63%|████████████████████▍ | ETA: 0:00:01 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:01 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:01 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:01 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:01 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:01 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:00 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:00 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:03 Crossvalidation Results: k MSE 0 1521.5961071777344 1 1267.9187231445312 2 943.9184872436524 3 753.831258544922 4 631.1272302246094 5 521.9711811828613 6 437.23626541137696 7 405.4242584228516 8 360.11040481567386 9 348.4395643615723 10 352.6568414306641 11 357.36922164916996 12 364.0823295593262 13 372.07056808471685 14 366.4748931884766 15 386.75953735351567 16 388.0295855712891 17 380.4302249145508 18 398.1733934020997 19 392.10565383911137 20 389.99595657348635 Best k = 9 3.420874 seconds (10.84 M allocations: 199.089 MiB, 1.31% gc time, 1.31% compilation time) Test Summary: | Pass Total Time Cross validation on Float32 matrix, normal model | 2 2 21.4s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:58 Cross validating... 6%|██ | ETA: 0:00:31 Cross validating... 10%|███ | ETA: 0:00:22 Cross validating... 13%|████▏ | ETA: 0:00:17 Cross validating... 16%|█████▏ | ETA: 0:00:14 Cross validating... 17%|█████▋ | ETA: 0:00:13 Cross validating... 21%|██████▋ | ETA: 0:00:11 Cross validating... 24%|███████▋ | ETA: 0:00:10 Cross validating... 27%|████████▋ | ETA: 0:00:09 Cross validating... 30%|█████████▋ | ETA: 0:00:08 Cross validating... 33%|██████████▋ | ETA: 0:00:07 Cross validating... 37%|███████████▋ | ETA: 0:00:07 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 0 461.61574390996736 1 426.5700152201929 2 388.6243615982047 3 343.7351396805759 4 328.0764819462957 5 304.8103028711344 6 301.70407824650084 7 297.48762108442895 8 298.90166034859175 9 306.6926375431155 10 307.95979586831464 11 319.90531662634993 12 313.2881460374544 13 314.5390335734362 14 325.7269782054607 15 337.29976890689545 16 353.1765277365272 17 351.82733635226083 18 350.66860146068643 19 369.891669796424 20 356.1154514141434 Best k = 7 8.136179 seconds (18.38 M allocations: 433.973 MiB, 0.94% gc time, 30.72% 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... 8%|██▌ | ETA: 0:00:05 Cross validating... 11%|███▌ | ETA: 0:00:05 Cross validating... 14%|████▋ | ETA: 0:00:05 Cross validating... 16%|█████▏ | ETA: 0:00:05 Cross validating... 19%|██████▏ | ETA: 0:00:05 Cross validating... 22%|███████▏ | ETA: 0:00:05 Cross validating... 25%|████████▏ | ETA: 0:00:04 Cross validating... 29%|█████████▏ | ETA: 0:00:04 Cross validating... 32%|██████████▏ | ETA: 0:00:04 Cross validating... 35%|███████████▏ | ETA: 0:00:04 Cross validating... 38%|████████████▎ | ETA: 0:00:04 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... 57%|██████████████████▎ | ETA: 0:00:02 Cross validating... 60%|███████████████████▎ | ETA: 0:00:02 Cross validating... 63%|████████████████████▍ | ETA: 0:00:02 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:02 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:02 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:02 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... 90%|█████████████████████████████ | ETA: 0:00:01 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:05 Crossvalidation Results: k MSE 0 461.61574390996736 1 426.6511875722693 2 389.1597202229883 3 344.6235438966214 4 329.92028645084736 5 307.53609946154717 6 297.80334984098636 7 313.9799496570565 8 312.5807024809556 9 327.8941017779776 10 333.0924528550293 11 338.72231817760746 12 345.9640750528274 13 356.12530177635324 14 366.4639956623532 15 379.22533813097476 16 384.3968475826837 17 380.18629350534053 18 417.4502576074706 19 414.40984344414113 20 440.72814278052846 Best k = 6 5.785794 seconds (19.07 M allocations: 403.643 MiB, 1.14% gc time, 1.04% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, logistic model | 2 2 14.4s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:48 Cross validating... 6%|██ | ETA: 0:00:26 Cross validating... 10%|███ | ETA: 0:00:18 Cross validating... 13%|████▏ | ETA: 0:00:15 Cross validating... 16%|█████▏ | ETA: 0:00:12 Cross validating... 19%|██████▏ | ETA: 0:00:11 Cross validating... 22%|███████▏ | ETA: 0:00:09 Cross validating... 24%|███████▋ | ETA: 0:00:09 Cross validating... 25%|████████▏ | ETA: 0:00:09 Cross validating... 29%|█████████▏ | ETA: 0:00:08 Cross validating... 32%|██████████▏ | ETA: 0:00:07 Cross validating... 33%|██████████▋ | ETA: 0:00:07 Cross validating... 37%|███████████▋ | ETA: 0:00:06 Cross validating... 40%|████████████▊ | ETA: 0:00:06 Cross validating... 43%|█████████████▊ | ETA: 0:00:06 Cross validating... 46%|██████████████▊ | ETA: 0:00:06 Cross validating... 49%|███████████████▊ | ETA: 0:00:05 Cross validating... 52%|████████████████▊ | ETA: 0:00:05 Cross validating... 56%|█████████████████▊ | ETA: 0:00:04 Cross validating... 59%|██████████████████▊ | ETA: 0:00:04 Cross validating... 62%|███████████████████▊ | ETA: 0:00:04 Cross validating... 65%|████████████████████▉ | ETA: 0:00:03 Cross validating... 68%|█████████████████████▉ | ETA: 0:00:03 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:02 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:02 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:02 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:02 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:01 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:01 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:01 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:01 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:01 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:07 Crossvalidation Results: k MSE 0 462.4597731632043 1 418.55335609707225 2 386.4260714929876 3 363.18348998154227 4 351.32765479095275 5 339.2582700348334 6 332.28353184712614 7 320.10925544563116 8 317.2479227578013 9 314.5231641589521 10 325.69426476276055 11 325.29422225080316 12 330.1882903361309 13 329.75081297624143 14 327.2249210497421 15 323.0622777874197 16 357.4916678401007 17 341.8640973098653 18 327.44113573258744 19 335.68490890508997 20 357.2523451884207 Best k = 9 8.956468 seconds (16.56 M allocations: 391.090 MiB, 11.37% gc time, 28.99% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:03 Cross validating... 6%|██ | ETA: 0:00:04 Cross validating... 10%|███ | ETA: 0:00:04 Cross validating... 13%|████▏ | ETA: 0:00:04 Cross validating... 16%|█████▏ | ETA: 0:00:04 Cross validating... 19%|██████▏ | ETA: 0:00:04 Cross validating... 22%|███████▏ | ETA: 0:00:04 Cross validating... 25%|████████▏ | ETA: 0:00:04 Cross validating... 29%|█████████▏ | ETA: 0:00:04 Cross validating... 32%|██████████▏ | ETA: 0:00:04 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... 49%|███████████████▊ | ETA: 0:00:03 Cross validating... 52%|████████████████▊ | ETA: 0:00:03 Cross validating... 56%|█████████████████▊ | ETA: 0:00:03 Cross validating... 59%|██████████████████▊ | ETA: 0:00:02 Cross validating... 62%|███████████████████▊ | ETA: 0:00:02 Cross validating... 65%|████████████████████▉ | ETA: 0:00:02 Cross validating... 68%|█████████████████████▉ | ETA: 0:00:02 Cross validating... 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 0 462.4597731632043 1 419.412066580298 2 389.86524864242836 3 366.73228204131595 4 356.2475232507443 5 346.88842044493924 6 343.8292172387979 7 331.1997489969669 8 331.08761507997036 9 336.3000934699134 10 340.77979345319534 11 345.6257762091625 12 356.70649888990897 13 370.1418315653159 14 376.2807693688626 15 371.3770914193912 16 387.05963066431127 17 393.7087822449157 18 401.9618103964531 19 407.3824783813021 20 430.02061067924967 Best k = 8 5.790475 seconds (17.09 M allocations: 349.757 MiB, 0.89% gc time, 0.81% compilation time) Test Summary: | Pass Total Time Cross validation on Float64 matrix, logistic model | 2 2 16.4s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:01:00 Cross validating... 6%|██ | ETA: 0:00:32 Cross validating... 10%|███ | ETA: 0:00:22 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: 0:00:11 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: 0:00:05 Cross validating... 46%|██████████████▊ | ETA: 0:00:05 Cross validating... 49%|███████████████▊ | ETA: 0:00:04 Cross validating... 52%|████████████████▊ | ETA: 0:00:04 Cross validating... 56%|█████████████████▊ | ETA: 0:00:04 Cross validating... 59%|██████████████████▊ | ETA: 0:00:03 Cross validating... 62%|███████████████████▊ | ETA: 0:00:03 Cross validating... 65%|████████████████████▉ | ETA: 0:00:03 Cross validating... 68%|█████████████████████▉ | ETA: 0:00:03 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 0 518.3759469353428 1 462.48632360256045 2 446.67813526581057 3 416.1857703621045 4 393.235152269696 5 383.02636163080297 6 376.3351248472831 7 389.44294123065123 8 382.5925878969151 9 385.7305415461696 10 385.74419879052033 11 386.58206146250876 12 391.08268422095324 13 394.3155173201576 14 402.0446296854225 15 420.79784249863377 16 395.0036168088635 17 396.474956171289 18 401.76292307257495 19 396.4893016102375 20 396.6509470758223 Best k = 6 7.843859 seconds (15.58 M allocations: 384.808 MiB, 0.83% gc time, 33.41% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:04 Cross validating... 6%|██ | ETA: 0:00:04 Cross validating... 10%|███ | ETA: 0:00:04 Cross validating... 13%|████▏ | ETA: 0:00:04 Cross validating... 14%|████▋ | ETA: 0:00:04 Cross validating... 17%|█████▋ | ETA: 0:00:04 Cross validating... 21%|██████▋ | ETA: 0:00:04 Cross validating... 24%|███████▋ | ETA: 0:00:04 Cross validating... 27%|████████▋ | ETA: 0:00:04 Cross validating... 30%|█████████▋ | ETA: 0:00:04 Cross validating... 33%|██████████▋ | ETA: 0:00:04 Cross validating... 37%|███████████▋ | ETA: 0:00:03 Cross validating... 40%|████████████▊ | ETA: 0:00:03 Cross validating... 43%|█████████████▊ | ETA: 0:00:03 Cross validating... 46%|██████████████▊ | ETA: 0:00:03 Cross validating... 49%|███████████████▊ | ETA: 0:00:03 Cross validating... 52%|████████████████▊ | ETA: 0:00:02 Cross validating... 56%|█████████████████▊ | ETA: 0:00:02 Cross validating... 59%|██████████████████▊ | ETA: 0:00:02 Cross validating... 62%|███████████████████▊ | ETA: 0:00:02 Cross validating... 65%|████████████████████▉ | ETA: 0:00:02 Cross validating... 68%|█████████████████████▉ | ETA: 0:00:02 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:02 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:01 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:01 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:01 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:01 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:01 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:01 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:05 Crossvalidation Results: k MSE 0 518.3759469353428 1 463.8923732756404 2 447.7750133342154 3 417.9541834763581 4 397.178436977156 5 390.24777861056236 6 387.8914796158723 7 405.55853177833274 8 400.30977312248825 9 409.3213096100028 10 420.9188418537099 11 428.86299954160603 12 432.92254499536125 13 440.728051226715 14 444.3672661286281 15 448.68445954759994 16 449.0795068165355 17 448.4330672530805 18 447.5407224685814 19 448.40951847023564 20 464.6648434604711 Best k = 6 5.433316 seconds (14.83 M allocations: 302.992 MiB, 1.32% gc time, 0.93% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, Poisson model | 2 2 13.7s **** 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: 0:00:50 Cross validating... 5%|█▌ | ETA: 0:00:49 Cross validating... 8%|██▌ | ETA: 0:00:39 Cross validating... 10%|███ | ETA: 0:00:33 Cross validating... 13%|████▏ | ETA: 0:00:25 Cross validating... 14%|████▋ | ETA: 0:00:23 Cross validating... 16%|█████▏ | ETA: 0:00:21 Cross validating... 17%|█████▋ | ETA: 0:00:19 Cross validating... 21%|██████▋ | ETA: 0:00:16 Cross validating... 22%|███████▏ | ETA: 0:00:15 Cross validating... 24%|███████▋ | ETA: 0:00:15 Cross validating... 25%|████████▏ | ETA: 0:00:14 Cross validating... 27%|████████▋ | ETA: 0:00:13 Cross validating... 29%|█████████▏ | ETA: 0:00:12 Cross validating... 30%|█████████▋ | ETA: 0:00:13 Cross validating... 32%|██████████▏ | ETA: 0:00:14 Cross validating... 33%|██████████▋ | ETA: 0:00:14 Cross validating... 38%|████████████▎ | ETA: 0:00:13 Cross validating... 40%|████████████▊ | ETA: 0:00:13 Cross validating... 41%|█████████████▎ | ETA: 0:00:13 Cross validating... 44%|██████████████▎ | ETA: 0:00:12 Cross validating... 48%|███████████████▎ | ETA: 0:00:11 Cross validating... 49%|███████████████▊ | ETA: 0:00:11 Cross validating... 51%|████████████████▎ | ETA: 0:00:11 Cross validating... 52%|████████████████▊ | ETA: 0:00:11 Cross validating... 56%|█████████████████▊ | ETA: 0:00:10 Cross validating... 57%|██████████████████▎ | ETA: 0:00:10 Cross validating... 59%|██████████████████▊ | ETA: 0:00:09 Cross validating... 60%|███████████████████▎ | ETA: 0:00:09 Cross validating... 62%|███████████████████▊ | ETA: 0:00:09 Cross validating... 63%|████████████████████▍ | ETA: 0:00:09 Cross validating... 65%|████████████████████▉ | ETA: 0:00:09 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:09 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:08 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:07 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:07 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:06 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:06 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:05 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:05 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:04 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:04 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:04 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:03 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:03 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:02 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:02 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:02 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:01 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:01 Cross validating... 100%|████████████████████████████████| Time: 0:00:33 Crossvalidation Results: k MSE 0 296.02950660759416 1 268.388402081982 2 249.1796542776122 3 236.97490196042224 4 223.8199233491427 5 222.2701261608947 6 220.11969879430032 7 220.89029593127538 8 222.8597861320792 9 224.01205303981592 10 227.3465344231847 11 226.03660154860972 12 226.12411471542578 13 228.10562237225173 14 232.52963593352408 15 227.28457727755085 16 233.1719218170979 17 233.77805229408955 18 236.95585259565647 19 234.83447446088246 20 231.66354142384012 Best k = 6 33.654212 seconds (122.55 M allocations: 3.030 GiB, 1.20% gc time, 5.66% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 5%|█▌ | ETA: 0:00:04 Cross validating... 6%|██ | ETA: 0:00:05 Cross validating... 8%|██▌ | ETA: 0:00:06 Cross validating... 10%|███ | ETA: 0:00:06 Cross validating... 11%|███▌ | ETA: 0:00:07 Cross validating... 13%|████▏ | ETA: 0:00:07 Cross validating... 14%|████▋ | ETA: 0:00:08 Cross validating... 16%|█████▏ | ETA: 0:00:08 Cross validating... 17%|█████▋ | ETA: 0:00:08 Cross validating... 19%|██████▏ | ETA: 0:00:09 Cross validating... 21%|██████▋ | ETA: 0:00:09 Cross validating... 22%|███████▏ | ETA: 0:00:09 Cross validating... 24%|███████▋ | ETA: 0:00:09 Cross validating... 25%|████████▏ | ETA: 0:00:09 Cross validating... 27%|████████▋ | ETA: 0:00:09 Cross validating... 29%|█████████▏ | ETA: 0:00:09 Cross validating... 30%|█████████▋ | ETA: 0:00:09 Cross validating... 32%|██████████▏ | ETA: 0:00:09 Cross validating... 33%|██████████▋ | ETA: 0:00:09 Cross validating... 37%|███████████▋ | ETA: 0:00:08 Cross validating... 40%|████████████▊ | ETA: 0:00:07 Cross validating... 41%|█████████████▎ | ETA: 0:00:07 Cross validating... 43%|█████████████▊ | ETA: 0:00:07 Cross validating... 44%|██████████████▎ | ETA: 0:00:07 Cross validating... 46%|██████████████▊ | ETA: 0:00:07 Cross validating... 48%|███████████████▎ | ETA: 0:00:06 Cross validating... 49%|███████████████▊ | ETA: 0:00:06 Cross validating... 51%|████████████████▎ | ETA: 0:00:06 Cross validating... 52%|████████████████▊ | ETA: 0:00:06 Cross validating... 54%|█████████████████▎ | ETA: 0:00:06 Cross validating... 56%|█████████████████▊ | ETA: 0:00:06 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: 0:00:05 Cross validating... 63%|████████████████████▍ | ETA: 0:00:05 Cross validating... 65%|████████████████████▉ | ETA: 0:00:05 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:04 Cross validating... 71%|██████████████████████▉ | 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: 0:00:03 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: 0:00:02 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: 0:00:13 Crossvalidation Results: k MSE 0 296.02950660759416 1 269.15608544601685 2 250.5747994005245 3 238.25813690480993 4 225.0579477240043 5 224.32743924376825 6 223.8025356830563 7 233.63620713317576 8 232.426416618154 9 235.31836410701465 10 242.4603308348224 11 242.6952462863083 12 248.2561405920994 13 254.04811416089427 14 258.3580139322045 15 263.8056779645105 16 265.2774709544059 17 275.41200394050446 18 273.79372236753 19 274.4880246182819 20 276.44077511242847 Best k = 6 13.915307 seconds (44.98 M allocations: 953.777 MiB, 1.44% gc time, 0.46% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, NegativeBinomial model | 2 2 48.1s **** 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: 0:00:33 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... 57%|██████████████████▎ | ETA: 0:00:03 Cross validating... 60%|███████████████████▎ | ETA: 0:00:03 Cross validating... 63%|████████████████████▍ | ETA: 0:00:02 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:02 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:02 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:02 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:01 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:01 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:01 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:01 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:05 Crossvalidation Results: k MSE 0 709.7238911132813 1 600.8470166015625 2 478.37098138427734 3 399.75837347412113 4 316.3170971069336 5 274.59901690673826 6 232.61785809326173 7 221.00282696533208 8 205.62119918823245 9 198.3431817626953 10 200.94596459960937 11 201.86666357421876 12 202.35683154296873 13 208.02664166259768 14 206.9071481628418 15 209.87240182495117 16 216.0480528869629 17 212.0296098022461 18 217.49209603881837 19 225.60646734619144 20 213.36869631958012 Best k = 9 6.095448 seconds (17.00 M allocations: 337.707 MiB, 1.42% gc time, 44.90% 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... 13%|████▏ | ETA: 0:00:03 Cross validating... 17%|█████▋ | ETA: 0:00:03 Cross validating... 22%|███████▏ | ETA: 0:00:02 Cross validating... 25%|████████▏ | ETA: 0:00:02 Cross validating... 29%|█████████▏ | ETA: 0:00:02 Cross validating... 32%|██████████▏ | ETA: 0:00:02 Cross validating... 37%|███████████▋ | ETA: 0:00:02 Cross validating... 40%|████████████▊ | ETA: 0:00:02 Cross validating... 43%|█████████████▊ | ETA: 0:00:02 Cross validating... 48%|███████████████▎ | ETA: 0:00:02 Cross validating... 51%|████████████████▎ | ETA: 0:00:02 Cross validating... 54%|█████████████████▎ | ETA: 0:00:01 Cross validating... 57%|██████████████████▎ | ETA: 0:00:01 Cross validating... 60%|███████████████████▎ | ETA: 0:00:01 Cross validating... 63%|████████████████████▍ | ETA: 0:00:01 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:01 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:01 Cross validating... 75%|███████████████████████▉ | 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... 90%|█████████████████████████████ | ETA: 0:00:00 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:03 Crossvalidation Results: k MSE 0 709.7238911132813 1 580.5206424560547 2 462.45179821777344 3 375.725685546875 4 311.8335130615235 5 265.69685809326177 6 235.52074707031255 7 221.8731430358887 8 209.48005477905275 9 202.0256286010742 10 206.40357376098632 11 209.8904744873047 12 212.83695938110353 13 217.36745034790042 14 219.17275009155276 15 218.94907879638671 16 225.10276358032226 17 228.24513723754882 18 225.50167910766604 19 235.0626920776367 20 227.98946899414062 Best k = 9 3.275272 seconds (16.17 M allocations: 286.701 MiB, 1.55% gc time, 1.87% compilation time) Test Summary: | Pass Total Time Cross validation on floating point matrices, NegativeBinomial model | 2 2 9.9s **** 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... 2%|▋ | ETA: 0:00:58 Cross validating... 4%|█▎ | ETA: 0:00:34 Cross validating... 5%|█▋ | ETA: 0:00:30 Cross validating... 6%|█▉ | ETA: 0:00:27 Cross validating... 7%|██▎ | ETA: 0:00:25 Cross validating... 8%|██▌ | ETA: 0:00:23 Cross validating... 9%|██▉ | ETA: 0:00:22 Cross validating... 10%|███▎ | ETA: 0:00:21 Cross validating... 11%|███▌ | ETA: 0:00:20 Cross validating... 12%|███▉ | ETA: 0:00:19 Cross validating... 13%|████▏ | ETA: 0:00:19 Cross validating... 14%|████▌ | ETA: 0:00:18 Cross validating... 15%|████▊ | ETA: 0:00:18 Cross validating... 16%|█████▏ | ETA: 0:00:17 Cross validating... 17%|█████▌ | ETA: 0:00:17 Cross validating... 18%|█████▊ | ETA: 0:00:17 Cross validating... 19%|██████▏ | ETA: 0:00:16 Cross validating... 20%|██████▍ | ETA: 0:00:16 Cross validating... 21%|██████▊ | ETA: 0:00:16 Cross validating... 22%|███████ | ETA: 0:00:15 Cross validating... 23%|███████▍ | ETA: 0:00:15 Cross validating... 24%|███████▋ | ETA: 0:00:15 Cross validating... 25%|████████ | ETA: 0:00:14 Cross validating... 26%|████████▍ | ETA: 0:00:14 Cross validating... 27%|████████▋ | ETA: 0:00:14 Cross validating... 28%|█████████ | ETA: 0:00:13 Cross validating... 29%|█████████▎ | ETA: 0:00:13 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: 0:00:12 Cross validating... 34%|██████████▉ | ETA: 0:00:12 Cross validating... 35%|███████████▎ | ETA: 0:00:12 Cross validating... 36%|███████████▌ | ETA: 0:00:12 Cross validating... 37%|███████████▉ | ETA: 0:00:11 Cross validating... 38%|████████████▏ | ETA: 0:00:11 Cross validating... 39%|████████████▌ | ETA: 0:00:11 Cross validating... 40%|████████████▊ | ETA: 0:00:11 Cross validating... 41%|█████████████▏ | ETA: 0:00:11 Cross validating... 42%|█████████████▌ | ETA: 0:00:10 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: 0:00:09 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: 0:00:06 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: 0:00:05 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... 82%|██████████████████████████▎ | ETA: 0:00:03 Cross validating... 83%|██████████████████████████▌ | ETA: 0:00:03 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:03 Cross validating... 85%|███████████████████████████▎ | ETA: 0:00:03 Cross validating... 86%|███████████████████████████▌ | ETA: 0:00:02 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: 0:00:02 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:01 Cross validating... 93%|█████████████████████████████▊ | ETA: 0:00:01 Cross validating... 94%|██████████████████████████████▏ | ETA: 0:00:01 Cross validating... 95%|██████████████████████████████▍ | ETA: 0:00:01 Cross validating... 96%|██████████████████████████████▊ | ETA: 0:00:01 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:01 Cross validating... 98%|███████████████████████████████▍| ETA: 0:00:00 Cross validating... 99%|███████████████████████████████▋| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:17 Crossvalidation Results: k MSE 1 3587.19185259628 2 3025.5710020801293 3 2744.1257652780414 4 2576.1657202465285 5 2420.036067071612 6 2265.7156915731484 7 2170.900119218417 8 2177.6338859516627 9 2198.1458813668073 10 2230.005537750434 11 2241.0478311989723 12 2255.2398414584304 13 2270.1988680360305 14 2311.939605397712 15 2292.5246315496306 16 2290.358934012797 17 2319.0897152862312 18 2334.8434386830777 19 2353.984443749928 20 2347.9050504074876 Best k = 7 17.598043 seconds (344.06 k allocations: 241.663 MiB, 0.51% gc time, 6.57% compilation time) Test Summary: | Pass Total Time multivariate cross validation SnpLinAlg | 3 3 21.4s Test Summary: | Pass Total Time wrapper univariate | 20 20 1m59.5s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 2%|▋ | ETA: 0:00:10 Cross validating... 3%|█ | ETA: 0:00:10 Cross validating... 4%|█▎ | ETA: 0:00:11 Cross validating... 5%|█▋ | ETA: 0:00:11 Cross validating... 6%|█▉ | ETA: 0:00:12 Cross validating... 7%|██▎ | ETA: 0:00:12 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: 0:00:17 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: 0:00:18 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: 0:00:16 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: 0:00:14 Cross validating... 10%|███▎ | ETA: 0:00:15 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: 0:00:15 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: 0:00:15 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: 0:00:12 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 **** 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: 0:00:15 Cross validating... 13%|████▏ | ETA: 0:00:16 Cross validating... 14%|████▌ | ETA: 0:00:16 Cross validating... 15%|████▊ | ETA: 0:00:16 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: 0:00:18 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: 0:00:16 Cross validating... 24%|███████▋ | ETA: 0:00:16 Cross validating... 25%|████████ | ETA: 0:00:15 Cross validating... 26%|████████▍ | ETA: 0:00:15 Cross validating... 27%|████████▋ | ETA: 0:00:15 Cross validating... 28%|█████████ | ETA: 0:00:15 Cross validating... 29%|█████████▎ | ETA: 0:00:15 Cross validating... 30%|█████████▋ | ETA: 0:00:15 Cross validating... 31%|█████████▉ | ETA: 0:00:15 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: 0:00:14 Cross validating... 39%|████████████▌ | ETA: 0:00:14 Cross validating... 40%|████████████▊ | ETA: 0:00:14 Cross validating... 41%|█████████████▏ | ETA: 0:00:14 Cross validating... 42%|█████████████▌ | ETA: 0:00:13 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: 0:00:09 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: 0:00:08 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 Test Summary: | Pass Total Time wrapper multivariate | 8 8 1m26.9s read BGEN and VCF: Error During Test at /home/pkgeval/.julia/packages/MendelIHT/ZcxZT/test/wrapper_test.jl:184 Got exception outside of a @test startproc must be called before process Stacktrace: [1] error(s::String) @ Base ./error.jl:56 [2] process(codec::CodecZlib.ZlibDecompressor, input::TranscodingStreams.Memory, output::TranscodingStreams.Memory, error_ref::TranscodingStreams.Error) @ CodecZlib ~/.julia/packages/CodecZlib/lEc2s/src/decompression.jl:186 [3] decompress(io::IOStream, v::Variant, h::BGEN.Header; decompressed::Nothing) @ BGEN ~/.julia/packages/BGEN/dfgRU/src/genotypes.jl:72 [4] decompress @ ~/.julia/packages/BGEN/dfgRU/src/genotypes.jl:42 [inlined] [5] first_allele_dosage!(b::Bgen, v::Variant; T::Type, mean_impute::Bool, clear_decompressed::Bool, data::Nothing, decompressed::Nothing, is_decompressed::Bool) @ BGEN ~/.julia/packages/BGEN/dfgRU/src/genotypes.jl:571 [6] collect(itr::Base.Generator{UnitRange{Int64}, MendelIHT.var"#convert_bgen_gt##0#convert_bgen_gt##1"}) @ Base ~/.julia/packages/BGEN/dfgRU/src/genotypes.jl:549 [inlined] [7] convert_bgen_gt(t::Type{Float64}, b::Bgen) @ MendelIHT ~/.julia/packages/MendelIHT/ZcxZT/src/wrapper.jl:380 [8] macro expansion @ ./timing.jl:739 [inlined] [9] macro expansion @ ~/.julia/packages/MendelIHT/ZcxZT/test/wrapper_test.jl:187 [inlined] [10] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:2246 [inlined] [11] top-level scope @ ~/.julia/packages/MendelIHT/ZcxZT/test/wrapper_test.jl:185 [12] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:327 [13] top-level scope @ ~/.julia/packages/MendelIHT/ZcxZT/test/runtests.jl:20 [14] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:327 [15] top-level scope @ none:6 [16] eval(m::Module, e::Any) @ Core ./boot.jl:517 [17] exec_options(opts::Base.JLOptions) @ Base ./client.jl:321 [18] _start() @ Base ./client.jl:596 Test Summary: | Error Total Time read BGEN and VCF | 1 1 2.9s RNG of the outermost testset: Xoshiro(0xb5f252ec2fdbb5c3, 0x6160d6f425f67bf9, 0x5660a23a34faecbd, 0xc86e810e73154eea, 0x04fd8a50d03af1c5) 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 1104.07s 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] Cmd(cmd::Cmd) @ Base /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Operations.jl:3110 [inlined] [4] test(ctx::Pkg.Types.Context, pkgs::Vector{PackageSpec}; coverage::Bool, test_fn::Nothing, julia_args::Cmd, test_args::Cmd, force_latest_compatible_version::Bool, allow_earlier_backwards_compatible_versions::Bool, allow_reresolve::Bool, kwargs::@Kwargs{io::IOContext{IO}}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:587 [5] 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 [6] test(pkgs::Vector{String}; kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:160 [7] test @ /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:160 [inlined] [8] test(pkg::String; kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:159 [inlined] [9] top-level scope @ /PkgEval.jl/scripts/evaluate.jl:223 [10] include(mod::Module, _path::String) @ Base ./Base.jl:326 [11] exec_options(opts::Base.JLOptions) @ Base ./client.jl:355 [12] _start() @ Base ./client.jl:596 in expression starting at /PkgEval.jl/scripts/evaluate.jl:214 PkgEval failed after 1220.37s: package tests unexpectedly errored