Package evaluation to test MendelIHT on Julia 1.14.0-DEV.2071 (559ec66647*) started at 2026-04-24T01:54:50.553 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.14` Set-up completed after 13.56s ################################################################################ # 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 v4.5.2 [66dad0bd] + AliasTables v1.1.3 [4fba245c] + ArrayInterface v7.24.0 [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 v1.4.0 [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 v1.7.1 [b964fa9f] + LaTeXStrings v1.4.0 [10f19ff3] + LayoutPointers v0.1.17 [2ab3a3ac] + LogExpFunctions v0.3.29 [bdcacae8] + LoopVectorization v0.12.173 [1914dd2f] + MacroTools v0.5.16 [d125e4d3] + ManualMemory v0.1.8 [921c7187] + MendelIHT v1.4.11 [e1d29d7a] + Missings v1.2.0 [6fe1bfb0] + OffsetArrays v1.17.0 [bac558e1] + OrderedCollections v1.8.1 [90014a1f] + PDMats v0.11.37 [69de0a69] + Parsers v2.8.3 [1d0040c9] + PolyesterWeave v0.2.2 [2dfb63ee] + PooledArrays v1.4.3 [aea7be01] + PrecompileTools v1.3.3 [21216c6a] + Preferences v1.5.2 [08abe8d2] + PrettyTables v3.3.2 [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 v1.3.1 [0d7ed370] + StaticArrayInterface v1.9.0 [10745b16] + Statistics v1.11.1 [82ae8749] + StatsAPI v1.8.0 [2913bbd2] + StatsBase v0.34.10 [4c63d2b9] + StatsFuns v1.5.2 [3eaba693] + StatsModels v0.7.9 [892a3eda] + StringManipulation v0.4.4 [3783bdb8] + TableTraits v1.0.1 [bd369af6] + Tables v1.12.1 [8290d209] + ThreadingUtilities v0.5.5 ⌅ [3bb67fe8] + TranscodingStreams v0.9.13 [3a884ed6] + UnPack v1.0.2 [a620830f] + VCFTools v0.2.10 [28eba6e3] + VariantCallFormat v0.5.9 [3d5dd08c] + VectorizationBase v0.21.72 [ea10d353] + WeakRefStrings v1.4.2 [76eceee3] + WorkerUtilities v1.6.1 [6e34b625] + Bzip2_jll v1.0.9+0 [efe28fd5] + OpenSpecFun_jll v0.5.6+0 [f50d1b31] + Rmath_jll v0.5.1+0 [76ed43ae] + SQLite_jll v3.51.2+0 [ffd25f8a] + XZ_jll v5.8.3+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 v1.0.0 [9e88b42a] + Serialization v1.11.0 [6462fe0b] + Sockets v1.11.0 [2f01184e] + SparseArrays v1.13.0 [f489334b] + StyledStrings v1.13.0 [4607b0f0] + SuiteSparse [fa267f1f] + TOML v1.0.3 [a4e569a6] + Tar v1.10.0 [8dfed614] + Test v1.11.0 [cf7118a7] + UUIDs v1.11.0 [4ec0a83e] + Unicode v1.11.0 [e66e0078] + CompilerSupportLibraries_jll v1.3.0+1 [deac9b47] + LibCURL_jll v8.19.0+0 [e37daf67] + LibGit2_jll v1.9.2+0 [29816b5a] + LibSSH2_jll v1.11.3+1 [14a3606d] + MozillaCACerts_jll v2026.3.19 [4536629a] + OpenBLAS_jll v0.3.30+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 6.08s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompiling project... 4.9 s ✓ BGEN 7.1 s ✓ VCFTools 27.0 s ✓ SnpArrays WARNING: Constructor for type "MvNormal" was extended in `MendelIHT` without explicit qualification or import.  NOTE: Assumed "MvNormal" refers to `Distributions.MvNormal`. This behavior is deprecated and may differ in future versions.  NOTE: This behavior may have differed in Julia versions prior to 1.12.  Hint: If you intended to create a new generic function of the same name, use `function MvNormal end`.  Hint: To silence the warning, qualify `MvNormal` as `Distributions.MvNormal` in the method signature or explicitly `import Distributions: MvNormal`. 24.7 s ✓ MendelIHT 4 dependencies successfully precompiled in 70 seconds. 170 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 91.38s ################################################################################ # Testing # Testing MendelIHT Status `/tmp/jl_xiSphM/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_xiSphM/Manifest.toml` [7d9f7c33] Accessors v0.1.44 [79e6a3ab] Adapt v4.5.2 [66dad0bd] AliasTables v1.1.3 [4fba245c] ArrayInterface v7.24.0 [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 v1.4.0 [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 v1.7.1 [682c06a0] JSON v1.5.0 [b964fa9f] LaTeXStrings v1.4.0 [10f19ff3] LayoutPointers v0.1.17 [2ab3a3ac] LogExpFunctions v0.3.29 [bdcacae8] LoopVectorization v0.12.173 [1914dd2f] MacroTools v0.5.16 [d125e4d3] ManualMemory v0.1.8 [921c7187] MendelIHT v1.4.11 [e1d29d7a] Missings v1.2.0 [6fe1bfb0] OffsetArrays v1.17.0 [bac558e1] OrderedCollections v1.8.1 [90014a1f] PDMats v0.11.37 [69de0a69] Parsers v2.8.3 [1d0040c9] PolyesterWeave v0.2.2 [2dfb63ee] PooledArrays v1.4.3 [aea7be01] PrecompileTools v1.3.3 [21216c6a] Preferences v1.5.2 [08abe8d2] PrettyTables v3.3.2 [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 v1.3.1 [0d7ed370] StaticArrayInterface v1.9.0 [10745b16] Statistics v1.11.1 [82ae8749] StatsAPI v1.8.0 [2913bbd2] StatsBase v0.34.10 [4c63d2b9] StatsFuns v1.5.2 [3eaba693] StatsModels v0.7.9 [892a3eda] StringManipulation v0.4.4 [ec057cc2] StructUtils v2.8.0 [3783bdb8] TableTraits v1.0.1 [bd369af6] Tables v1.12.1 [8290d209] ThreadingUtilities v0.5.5 ⌅ [3bb67fe8] TranscodingStreams v0.9.13 [3a884ed6] UnPack v1.0.2 [a620830f] VCFTools v0.2.10 [28eba6e3] VariantCallFormat v0.5.9 [3d5dd08c] VectorizationBase v0.21.72 [ea10d353] WeakRefStrings v1.4.2 [76eceee3] WorkerUtilities v1.6.1 [6e34b625] Bzip2_jll v1.0.9+0 [efe28fd5] OpenSpecFun_jll v0.5.6+0 [f50d1b31] Rmath_jll v0.5.1+0 [76ed43ae] SQLite_jll v3.51.2+0 [ffd25f8a] XZ_jll v5.8.3+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 v1.0.0 [9e88b42a] Serialization v1.11.0 [6462fe0b] Sockets v1.11.0 [2f01184e] SparseArrays v1.13.0 [f489334b] StyledStrings v1.13.0 [4607b0f0] SuiteSparse [fa267f1f] TOML v1.0.3 [a4e569a6] Tar v1.10.0 [8dfed614] Test v1.11.0 [cf7118a7] UUIDs v1.11.0 [4ec0a83e] Unicode v1.11.0 [e66e0078] CompilerSupportLibraries_jll v1.3.0+1 [deac9b47] LibCURL_jll v8.19.0+0 [e37daf67] LibGit2_jll v1.9.2+0 [29816b5a] LibSSH2_jll v1.11.3+1 [14a3606d] MozillaCACerts_jll v2026.3.19 [4536629a] OpenBLAS_jll v0.3.30+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:215 └ @ LinearAlgebra ./deprecated.jl:215 Test Summary: | Pass Total Time loglikelihood | 4 4 21.2s Test Summary: | Pass Total Time deviance | 1 1 0.4s Test Summary: | Pass Total Time update_μ! | 4 4 1.5s Test Summary: | Pass Total Time _choose! | 7 7 9.8s Test Summary: | Pass Total Time _iht_backtrack | 7 7 0.0s Test Summary: | Pass Total Time standardize! | 12 12 1.4s Test Summary: | Pass Total Time project_k! | 2 2 1.1s Test Summary: | Pass Total Time project_group_sparse! | 5 5 1.2s Test Summary: | Pass Total Time maf_weights | 6 6 2.1s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse linear regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1522.9962223022756, backtracks = 0, tol = 1.2057814379449925 Iteration 2: loglikelihood = -1391.2826343192148, backtracks = 0, tol = 0.1426020716103911 Iteration 3: loglikelihood = -1380.1169184127793, backtracks = 0, tol = 0.06277123682675885 Iteration 4: loglikelihood = -1379.8068916228706, backtracks = 0, tol = 0.0072110217688192224 Iteration 5: loglikelihood = -1379.803286268984, backtracks = 0, tol = 0.0006949222439372571 Iteration 6: loglikelihood = -1379.8032204078963, backtracks = 0, tol = 0.00012595281384690716 Iteration 7: loglikelihood = -1379.8032191412897, backtracks = 0, tol = 1.2178364667812554e-5 IHT estimated 10 nonzero SNP predictors and 1 non-genetic predictors. Compute time (sec): 0.057932138442993164 Final loglikelihood: -1379.8032191412897 SNP PVE: 0.8690659830220054 Iterations: 7 Selected genetic predictors: 10×2 DataFrame Row │ Position Estimated_β │ Int64 Float64 ─────┼─────────────────────── 1 │ 683 0.483001 2 │ 2015 0.614484 3 │ 2101 1.14044 4 │ 2722 1.40059 5 │ 3311 -0.291404 6 │ 3660 0.119166 7 │ 7396 -1.26316 8 │ 7985 -0.605704 9 │ 8416 -0.116817 10 │ 9982 0.444476 Selected nongenetic predictors: 1×2 DataFrame Row │ Position Estimated_β │ Int64 Float64 ─────┼─────────────────────── 1 │ 1 0.0177229Test Summary: | Pass Total Time fit normal SnpLinAlg | 4 4 24.5s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** 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 = -1748.5172346686593, backtracks = 0, tol = 0.3532580783189319 Iteration 2: loglikelihood = -1487.2401696801066, backtracks = 0, tol = 0.04801282123987328 Iteration 3: loglikelihood = -1381.6283897357555, backtracks = 0, tol = 0.043910538049253524 Iteration 4: loglikelihood = -1345.6455793333566, backtracks = 0, tol = 0.03409135764128692 Iteration 5: loglikelihood = -1323.201927641055, backtracks = 0, tol = 0.07302573033280799 Iteration 6: loglikelihood = -1313.768526514958, backtracks = 0, tol = 0.04188591787411596 Iteration 7: loglikelihood = -1310.2943242870308, backtracks = 0, tol = 0.029522228804655583 Iteration 8: loglikelihood = -1307.1514640056, backtracks = 0, tol = 0.06732832452546281 Iteration 9: loglikelihood = -1305.9515756338012, backtracks = 0, tol = 0.012669310050064879 Iteration 10: loglikelihood = -1305.2581683710505, backtracks = 0, tol = 0.06218468643334743 Iteration 11: loglikelihood = -1305.015203544992, backtracks = 1, tol = 0.006070472344991351 Iteration 12: loglikelihood = -1304.9534098659312, backtracks = 2, tol = 0.002637801797724609 Iteration 13: loglikelihood = -1304.9149406970826, backtracks = 2, tol = 0.0021338251525253845 Iteration 14: loglikelihood = -1304.8922980661412, backtracks = 2, tol = 0.0017222470866318084 Iteration 15: loglikelihood = -1304.8792929248214, backtracks = 2, tol = 0.0013098869379673782 Iteration 16: loglikelihood = -1304.8719002938894, backtracks = 2, tol = 0.00099310120734539 Iteration 17: loglikelihood = -1304.8677160997822, backtracks = 2, tol = 0.0007438301796338686 Iteration 18: loglikelihood = -1304.8653526153362, backtracks = 2, tol = 0.0005575409297938459 Iteration 19: loglikelihood = -1304.8640190550707, backtracks = 2, tol = 0.0004166503511645494 Iteration 20: loglikelihood = -1304.8632671530327, backtracks = 2, tol = 0.0003115217486307417 Iteration 21: loglikelihood = -1304.8628434252491, backtracks = 2, tol = 0.00023272309989506374 Iteration 22: loglikelihood = -1304.862604730009, backtracks = 2, tol = 0.00017390333450657426 Iteration 23: loglikelihood = -1304.8624703083115, backtracks = 2, tol = 0.00012992692377953146 Iteration 24: loglikelihood = -1304.8623946264456, backtracks = 2, tol = 9.709095245847459e-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 = -1437.6668117244578, backtracks = 0, tol = 0.4208194227394864 Iteration 2: loglikelihood = -1403.126245836408, backtracks = 0, tol = 0.12690852531684743 Iteration 3: loglikelihood = -1393.8041383390564, backtracks = 0, tol = 0.07138482905600041 Iteration 4: loglikelihood = -1392.5886858018084, backtracks = 1, tol = 0.016365582321700194 Iteration 5: loglikelihood = -1392.152623508063, backtracks = 1, tol = 0.011387460317885767 Iteration 6: loglikelihood = -1392.0231470525296, backtracks = 1, tol = 0.007780251764599955 Iteration 7: loglikelihood = -1391.9882865858897, backtracks = 1, tol = 0.004116248182203826 Iteration 8: loglikelihood = -1391.9791527241732, backtracks = 1, tol = 0.002116082232332855 Iteration 9: loglikelihood = -1391.9767972035488, backtracks = 1, tol = 0.0010754930417496051 Iteration 10: loglikelihood = -1391.9761952100419, backtracks = 1, tol = 0.0005428636511310276 Iteration 11: loglikelihood = -1391.97604213846, backtracks = 1, tol = 0.0002730311569688844 Iteration 12: loglikelihood = -1391.9760033264815, backtracks = 1, tol = 0.0001370697855899855 Iteration 13: loglikelihood = -1391.975993501134, backtracks = 1, tol = 6.875597480831685e-5 Test Summary: | Pass Total Time fit NegativeBinomial SnpLinAlg | 4 4 1.2s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse linear regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1781.0990695956596, backtracks = 0, tol = 0.7761579268666009 Iteration 2: loglikelihood = -1455.6494473161897, backtracks = 0, tol = 0.12861134288389223 Iteration 3: loglikelihood = -1382.053718133737, backtracks = 0, tol = 0.051867935446897086 Iteration 4: loglikelihood = -1369.375046205875, backtracks = 0, tol = 0.02753089193238787 Iteration 5: loglikelihood = -1369.2861391465835, backtracks = 0, tol = 0.02490573530990919 Iteration 6: loglikelihood = -1367.0646199772486, backtracks = 0, tol = 0.024748355264856324 Iteration 7: loglikelihood = -1366.8091858420933, backtracks = 0, tol = 0.002335755552092338 Iteration 8: loglikelihood = -1366.80685175463, backtracks = 0, tol = 0.0002911574675753002 Iteration 9: loglikelihood = -1366.8068124548367, backtracks = 0, tol = 3.3161162876103145e-5 Test Summary: | Pass Total Time fit with >1 non-genetic covariates SnpLinAlg | 5 5 1.6s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse linear regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1494.027322958704, backtracks = 0, tol = 0.25035927202447134 Iteration 2: loglikelihood = -1400.9836740930637, backtracks = 0, tol = 0.0538580784039427 Iteration 3: loglikelihood = -1371.2572095406742, backtracks = 0, tol = 0.03349841047280561 Iteration 4: loglikelihood = -1368.688980467863, backtracks = 0, tol = 0.029674415589323676 Iteration 5: loglikelihood = -1368.3563604038843, backtracks = 0, tol = 0.002973809943816927 Iteration 6: loglikelihood = -1368.3542694540672, backtracks = 1, tol = 0.00018727537456768133 Iteration 7: loglikelihood = -1368.3537253769148, backtracks = 1, tol = 9.610160453316134e-5 Test Summary: | Pass Total Time model selection on non-genetic covariates | 5 5 0.7s **** 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) = 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 = -1491.2018278181201, backtracks = 0, tol = 0.2160127077743468 Iteration 2: loglikelihood = -1422.903531926732, backtracks = 0, tol = 0.09466561822519946 Iteration 3: loglikelihood = -1382.326879766878, backtracks = 1, tol = 0.1013174729094685 Iteration 4: loglikelihood = -1370.883657950086, backtracks = 0, tol = 0.09619808215793964 Iteration 5: loglikelihood = -1346.171980919778, backtracks = 0, tol = 0.07907421142951604 Iteration 6: loglikelihood = -1338.2946693010506, backtracks = 0, tol = 0.06949356143246885 Iteration 7: loglikelihood = -1333.9017608285424, backtracks = 0, tol = 0.06827056165304622 Iteration 8: loglikelihood = -1333.250737744614, backtracks = 0, tol = 0.012071558291246962 Iteration 9: loglikelihood = -1333.1399391649659, backtracks = 0, tol = 0.0032979065433609163 Iteration 10: loglikelihood = -1333.093859199042, backtracks = 0, tol = 0.00493545651625627 Iteration 11: loglikelihood = -1333.0730780304239, backtracks = 0, tol = 0.0016292225632576914 Iteration 12: loglikelihood = -1333.0635355515678, backtracks = 0, tol = 0.0022709970654243143 Iteration 13: loglikelihood = -1333.0591979705562, backtracks = 0, tol = 0.0007433195086644306 Iteration 14: loglikelihood = -1333.0572028018194, backtracks = 0, tol = 0.001054419938674006 Iteration 15: loglikelihood = -1333.0563008590382, backtracks = 0, tol = 0.0003356075154995504 Iteration 16: loglikelihood = -1333.0558876318248, backtracks = 0, tol = 0.0004883779209770591 Iteration 17: loglikelihood = -1333.0557027004893, backtracks = 0, tol = 0.0001500476336787829 Iteration 18: loglikelihood = -1333.0556186494139, backtracks = 0, tol = 0.00022451734111943555 Iteration 19: loglikelihood = -1333.0555815613684, backtracks = 0, tol = 6.626405743535573e-5 0.966020 seconds (2.37 M allocations: 46.851 MiB, 64.33% 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 = -1538.8870365375883, backtracks = 0, tol = 0.2160127077743468 Iteration 2: loglikelihood = -1494.5364362187072, backtracks = 0, tol = 0.12033369030352825 Iteration 3: loglikelihood = -1464.1560179512503, backtracks = 0, tol = 0.1449619723958867 Iteration 4: loglikelihood = -1433.1970599725512, backtracks = 0, tol = 0.10438651374256674 Iteration 5: loglikelihood = -1417.2796023390688, backtracks = 0, tol = 0.07736804713189559 Iteration 6: loglikelihood = -1408.3245935367352, backtracks = 0, tol = 0.08809149798472309 Iteration 7: loglikelihood = -1397.9578450375188, backtracks = 0, tol = 0.07910137456350314 Iteration 8: loglikelihood = -1391.8950083550471, backtracks = 0, tol = 0.0761547238242144 Iteration 9: loglikelihood = -1385.3951137669449, backtracks = 0, tol = 0.0759509607690661 Iteration 10: loglikelihood = -1380.6752640449886, backtracks = 0, tol = 0.00756183645442089 Iteration 11: loglikelihood = -1376.630132940337, backtracks = 0, tol = 0.001414185948772097 Iteration 12: loglikelihood = -1373.1771959520236, backtracks = 0, tol = 0.0004934105774865029 Iteration 13: loglikelihood = -1370.1629582514395, backtracks = 0, tol = 0.00028831944718849824 Iteration 14: loglikelihood = -1367.53174208691, backtracks = 0, tol = 0.0002732820453999128 Iteration 15: loglikelihood = -1365.2115643184488, backtracks = 0, tol = 0.0002441094579269645 Iteration 16: loglikelihood = -1364.1171903984189, backtracks = 0, tol = 0.07129315932410601 Iteration 17: loglikelihood = -1362.0202173139578, backtracks = 0, tol = 0.006877255982811071 Iteration 18: loglikelihood = -1360.3788301542122, backtracks = 0, tol = 0.002088449878845704 Iteration 19: loglikelihood = -1358.2100736399532, backtracks = 0, tol = 0.06920305071548517 Iteration 20: loglikelihood = -1356.8700652291138, backtracks = 0, tol = 0.006703041480013251 Iteration 21: loglikelihood = -1355.6671064401958, backtracks = 0, tol = 0.0014742043853303078 Iteration 22: loglikelihood = -1354.5907388280843, backtracks = 0, tol = 0.00039741077868391835 Iteration 23: loglikelihood = -1353.59143120119, backtracks = 0, tol = 0.00033026249401925037 Iteration 24: loglikelihood = -1352.676310169498, backtracks = 0, tol = 0.00019251130474183076 Iteration 25: loglikelihood = -1351.831450808057, backtracks = 0, tol = 0.00010932659442690248 Iteration 26: loglikelihood = -1351.0531116446682, backtracks = 0, tol = 0.00011984369844274808 Iteration 27: loglikelihood = -1349.7084467346187, backtracks = 1, tol = 6.392528251555459e-5 0.304022 seconds (1.01 M allocations: 18.459 MiB, 7.64% 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 = -3664.841, backtracks = 0, tol = 0.0810293627309861 Iteration 2: loglikelihood = -3618.1824, backtracks = 0, tol = 0.0427693628147275 Iteration 3: loglikelihood = -3613.296, backtracks = 1, tol = 0.014469882750187511 Iteration 4: loglikelihood = -3611.9727, backtracks = 1, tol = 0.007943637666112705 Iteration 5: loglikelihood = -3611.6265, backtracks = 1, tol = 0.004133758696023544 Iteration 6: loglikelihood = -3611.5403, backtracks = 1, tol = 0.002104829677880896 Iteration 7: loglikelihood = -3611.5203, backtracks = 1, tol = 0.0010565074097791363 Iteration 8: loglikelihood = -3611.5156, backtracks = 1, tol = 0.0005279449889603871 Iteration 9: loglikelihood = -3611.5151, backtracks = 1, tol = 0.00026271214341529815 Iteration 10: loglikelihood = -3611.5205, backtracks = 3, tol = 3.265162563651068e-5 26.743854 seconds (14.63 M allocations: 676.489 MiB, 4.17% gc time, 95.24% 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 = -3551.7458, backtracks = 0, tol = 0.0810293627309861 Iteration 2: loglikelihood = -3430.5945, backtracks = 0, tol = 0.044117221941923725 Iteration 3: loglikelihood = -3239.7195, backtracks = 1, tol = 0.013723136500277374 Iteration 4: loglikelihood = -3020.7236, backtracks = 1, tol = 0.0071781612802285025 Iteration 5: loglikelihood = -2791.1511, backtracks = 1, tol = 0.0032819924411521323 Iteration 6: loglikelihood = -2690.9214, backtracks = 0, tol = 0.0815527106213735 Iteration 7: loglikelihood = -2566.7324, backtracks = 0, tol = 0.08448558312427136 Iteration 8: loglikelihood = -2460.7107, backtracks = 0, tol = 0.08360789651939893 Iteration 9: loglikelihood = -2369.9421, backtracks = 0, tol = 0.08657566170345068 Iteration 10: loglikelihood = -2305.704, backtracks = 0, tol = 0.08037832916036854 Iteration 11: loglikelihood = -2261.8162, backtracks = 0, tol = 0.08521239128310588 Iteration 12: loglikelihood = -2233.102, backtracks = 0, tol = 0.09276794947542627 Iteration 13: loglikelihood = -2215.3486, backtracks = 0, tol = 0.09350703240038138 Iteration 14: loglikelihood = -2203.2344, backtracks = 0, tol = 0.09320423399816291 Iteration 15: loglikelihood = -2197.9365, backtracks = 0, tol = 0.09385997408888282 Iteration 16: loglikelihood = -2193.2322, backtracks = 0, tol = 0.09463839376964091 Iteration 17: loglikelihood = -2192.5256, backtracks = 0, tol = 0.09524185625138908 Iteration 18: loglikelihood = -2190.2737, backtracks = 0, tol = 0.09517834172095085 Iteration 19: loglikelihood = -2188.6873, backtracks = 1, tol = 0.010517010428069367 Iteration 20: loglikelihood = -2188.364, backtracks = 1, tol = 0.004003687993373144 Iteration 21: loglikelihood = -2188.302, backtracks = 1, tol = 0.0015014742637076656 Iteration 22: loglikelihood = -2188.294, backtracks = 1, tol = 0.0006883208900652886 Iteration 23: loglikelihood = -2188.296, backtracks = 3, tol = 9.696891395041264e-5 0.214299 seconds (1.30 M allocations: 21.664 MiB) Test Summary: | Pass Total Time Negative binomial nuisance parameter Float32 matrix | 12 12 31.4s **** 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 **** 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 4.765403 seconds (1.15 M allocations: 137.114 MiB, 0.92% gc time, 91.36% compilation time) Test Summary: | Pass Total Time initialze beta | 1 1 5.2s 9.860649 seconds (4.00 M allocations: 82.500 MiB, 0.59% gc time, 0.63% compilation time) 5.277336 seconds (3.98 M allocations: 91.679 MiB, 0.44% gc time) 10.328910 seconds (20.41 M allocations: 439.470 MiB, 0.83% gc time, 18.68% compilation time: 79% of which was recompilation) 8.035490 seconds (20.18 M allocations: 434.189 MiB, 1.21% gc time) 52.290470 seconds (3.85 M allocations: 4.245 GiB, 8.65% gc time, 21.40% compilation time) 54.593372 seconds (70.38 k allocations: 183.442 MiB, 0.18% gc time) Test Summary: | Pass Total Time memory_efficient keyword | 7 7 2m38.6s Test Summary: | Pass Total Time update_support! | 10 10 0.6s 14.473 ms (78 allocations: 4.56 KiB) 4.860 μs (0 allocations: 0 bytes) 128.579 μs (4 allocations: 288 bytes) 7.125 μs (0 allocations: 0 bytes) 47.269 μs (2 allocations: 64 bytes) 29.549 μs (0 allocations: 0 bytes) 25.360 μs (0 allocations: 0 bytes) 27.360 μs (0 allocations: 0 bytes) 100.979 μs (0 allocations: 0 bytes) 37.172 ms (78 allocations: 4.56 KiB) 21.439 μs (0 allocations: 0 bytes) 163.718 μs (4 allocations: 288 bytes) 32.339 μs (0 allocations: 0 bytes) 229.518 μs (2 allocations: 64 bytes) 87.969 μs (0 allocations: 0 bytes) 121.169 μs (0 allocations: 0 bytes) 137.979 μs (0 allocations: 0 bytes) 196.248 μs (0 allocations: 0 bytes) Test Summary: | Total Time benchmarks for multivariate function | 0 2m18.4s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse Multivariate Gaussian regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 12 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -2900.9186300194497, backtracks = 0, tol = 0.1480224208200413 Iteration 2: loglikelihood = -2869.406464695619, backtracks = 0, tol = 0.035126790460779864 Iteration 3: loglikelihood = -2868.084702693443, backtracks = 0, tol = 0.0055693496163324524 Iteration 4: loglikelihood = -2868.034423817725, backtracks = 0, tol = 0.001118951762895177 Iteration 5: loglikelihood = -2868.030857635375, backtracks = 0, tol = 0.00031182601179138955 Iteration 6: loglikelihood = -2868.0305288614227, backtracks = 0, tol = 0.00010393305949947338 Iteration 7: loglikelihood = -2868.0304966516946, backtracks = 0, tol = 3.100862049859014e-5 0.431041 seconds (49.46 k allocations: 5.502 MiB, 63.70% compilation time) Test Summary: | Pass Total Time multivariate fit_iht SnpLinAlg | 7 7 11.4s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** 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 1.869478 seconds (282.41 k allocations: 168.158 MiB, 55.45% 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: 0:03:21 Cross validating... 19%|██████▏ | ETA: 0:00:31 Cross validating... 22%|███████▏ | ETA: 0:00:26 Cross validating... 25%|████████▏ | ETA: 0:00:22 Cross validating... 29%|█████████▏ | ETA: 0:00:19 Cross validating... 32%|██████████▏ | ETA: 0:00:17 Cross validating... 35%|███████████▏ | ETA: 0:00:15 Cross validating... 38%|████████████▎ | ETA: 0:00:13 Cross validating... 41%|█████████████▎ | ETA: 0:00:12 Cross validating... 44%|██████████████▎ | ETA: 0:00:10 Cross validating... 48%|███████████████▎ | ETA: 0:00:09 Cross validating... 51%|████████████████▎ | ETA: 0:00:08 Cross validating... 54%|█████████████████▎ | ETA: 0:00:08 Cross validating... 57%|██████████████████▎ | ETA: 0:00:07 Cross validating... 60%|███████████████████▎ | ETA: 0:00:06 Cross validating... 63%|████████████████████▍ | ETA: 0:00:05 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:05 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:04 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:03 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:03 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:02 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:02 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:01 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:01 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:01 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:10 Crossvalidation Results: k MSE 0 2368.71686343986 1 1738.6693984705944 2 1136.8693949405433 3 722.9282893017371 4 611.4901368404456 5 474.8124601799246 6 410.09927100343367 7 346.6030205911477 8 319.37396761195066 9 323.75579199115765 10 327.75300773534104 11 329.7523931347572 12 334.39016747281005 13 334.0834404952134 14 337.84309308590076 15 338.46789832866784 16 356.7985999667445 17 387.2298670554265 18 342.8919803760851 19 385.5126689399068 20 351.2376386921761 Best k = 8 10.886538 seconds (11.50 M allocations: 304.392 MiB, 1.65% gc time, 61.79% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:03 Cross validating... 8%|██▌ | ETA: 0:00:03 Cross validating... 13%|████▏ | ETA: 0:00:03 Cross validating... 16%|█████▏ | ETA: 0:00:03 Cross validating... 19%|██████▏ | ETA: 0:00:03 Cross validating... 22%|███████▏ | ETA: 0:00:03 Cross validating... 25%|████████▏ | ETA: 0:00:03 Cross validating... 29%|█████████▏ | ETA: 0:00:03 Cross validating... 32%|██████████▏ | ETA: 0:00:03 Cross validating... 35%|███████████▏ | ETA: 0:00:03 Cross validating... 40%|████████████▊ | ETA: 0:00:02 Cross validating... 44%|██████████████▎ | ETA: 0:00:02 Cross validating... 49%|███████████████▊ | ETA: 0:00:02 Cross validating... 52%|████████████████▊ | ETA: 0:00:02 Cross validating... 56%|█████████████████▊ | ETA: 0:00:02 Cross validating... 59%|██████████████████▊ | ETA: 0:00:02 Cross validating... 62%|███████████████████▊ | ETA: 0:00:02 Cross validating... 65%|████████████████████▉ | ETA: 0:00:01 Cross validating... 68%|█████████████████████▉ | ETA: 0:00:01 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:01 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:01 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:01 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:01 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:01 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:00 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:00 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:04 Crossvalidation Results: k MSE 0 2368.71686343986 1 1742.8017655325693 2 1137.9581091382145 3 724.5644280206363 4 616.4930049718756 5 482.23493418662997 6 418.35529062873053 7 353.60617703762153 8 327.23060068009784 9 334.61370374883313 10 347.2086936850284 11 351.88515359542714 12 363.52894448289504 13 364.14405381352606 14 375.37734657005944 15 381.1249863863627 16 376.8628332905803 17 399.5481979373159 18 395.7904376726449 19 397.7787772776483 20 388.83357750606285 Best k = 8 4.480145 seconds (10.63 M allocations: 224.336 MiB, 1.11% gc time, 0.90% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, normal model | 3 3 16.2s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:05:50 Cross validating... 8%|██▌ | ETA: 0:02:15 Cross validating... 13%|████▏ | ETA: 0:01:21 Cross validating... 17%|█████▋ | ETA: 0:00:56 Cross validating... 21%|██████▋ | ETA: 0:00:46 Cross validating... 24%|███████▋ | ETA: 0:00:39 Cross validating... 27%|████████▋ | ETA: 0:00:33 Cross validating... 30%|█████████▋ | ETA: 0:00:29 Cross validating... 33%|██████████▋ | ETA: 0:00:25 Cross validating... 38%|████████████▎ | ETA: 0:00:21 Cross validating... 43%|█████████████▊ | ETA: 0:00:17 Cross validating... 48%|███████████████▎ | ETA: 0:00:14 Cross validating... 51%|████████████████▎ | ETA: 0:00:13 Cross validating... 56%|█████████████████▊ | ETA: 0:00:11 Cross validating... 59%|██████████████████▊ | ETA: 0:00:09 Cross validating... 62%|███████████████████▊ | ETA: 0:00:08 Cross validating... 65%|████████████████████▉ | ETA: 0:00:07 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:06 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:05 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:04 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:03 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:02 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:01 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:01 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:14 Crossvalidation Results: k MSE 0 1582.969313354492 1 1213.4170982666014 2 957.9066713867187 3 771.5791979980469 4 618.172206237793 5 510.28427615356446 6 428.3794743041992 7 395.89360623168943 8 346.9263112792969 9 335.2981706542969 10 337.21222854614257 11 341.18662298583985 12 345.90683975219724 13 346.3930420227051 14 349.1304961853027 15 353.56707022094724 16 349.5195448303223 17 365.4365697937012 18 366.6188124389648 19 370.469891418457 20 381.0977964172363 Best k = 9 15.891720 seconds (12.38 M allocations: 307.389 MiB, 0.71% gc time, 79.51% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 5%|█▌ | ETA: 0:00:02 Cross validating... 10%|███ | ETA: 0:00:02 Cross validating... 14%|████▋ | ETA: 0:00:02 Cross validating... 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... 48%|███████████████▎ | ETA: 0:00:02 Cross validating... 52%|████████████████▊ | ETA: 0:00:01 Cross validating... 56%|█████████████████▊ | ETA: 0:00:01 Cross validating... 59%|██████████████████▊ | ETA: 0:00:01 Cross validating... 62%|███████████████████▊ | ETA: 0:00:01 Cross validating... 65%|████████████████████▉ | ETA: 0:00:01 Cross validating... 68%|█████████████████████▉ | ETA: 0:00:01 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:01 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:01 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:01 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:00 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:00 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:00 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:03 Crossvalidation Results: k MSE 0 1582.969313354492 1 1215.9176116943358 2 957.9066713867187 3 774.7195088500977 4 623.2587725830078 5 513.8975246276855 6 434.22246685791015 7 398.31924575805664 8 351.9471718139648 9 341.2296653137207 10 348.1152310791016 11 356.6596444396973 12 363.9631592407227 13 375.77208209228513 14 380.6957851257324 15 377.7333825378418 16 382.7971255187988 17 394.3611206665039 18 390.2436770629883 19 409.040515045166 20 411.30434072875977 Best k = 9 3.263600 seconds (10.45 M allocations: 191.700 MiB, 1.51% gc time, 1.14% compilation time) Test Summary: | Pass Total Time Cross validation on Float32 matrix, normal model | 2 2 21.2s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:01:02 Cross validating... 6%|██ | ETA: 0:00:33 Cross validating... 10%|███ | ETA: 0:00:23 Cross validating... 13%|████▏ | ETA: 0:00:18 Cross validating... 16%|█████▏ | ETA: 0:00:15 Cross validating... 19%|██████▏ | ETA: 0:00:13 Cross validating... 22%|███████▏ | ETA: 0:00:11 Cross validating... 25%|████████▏ | ETA: 0:00:10 Cross validating... 29%|█████████▏ | ETA: 0:00:09 Cross validating... 32%|██████████▏ | ETA: 0:00:08 Cross validating... 35%|███████████▏ | ETA: 0:00:07 Cross validating... 38%|████████████▎ | ETA: 0:00:06 Cross validating... 41%|█████████████▎ | ETA: 0:00:06 Cross validating... 44%|██████████████▎ | ETA: 0:00:05 Cross validating... 48%|███████████████▎ | ETA: 0:00:05 Cross validating... 51%|████████████████▎ | ETA: 0:00:04 Cross validating... 54%|█████████████████▎ | ETA: 0:00:04 Cross validating... 57%|██████████████████▎ | ETA: 0:00:04 Cross validating... 60%|███████████████████▎ | ETA: 0:00:03 Cross validating... 63%|████████████████████▍ | ETA: 0:00:03 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:03 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:02 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:02 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:02 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:02 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:01 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:01 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:01 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:01 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:07 Crossvalidation Results: k MSE 0 463.4198975060679 1 424.77031885665303 2 381.682724330552 3 318.0469791347272 4 308.11121623722977 5 289.6027235819919 6 284.8439272412229 7 281.696349847935 8 286.25291810339195 9 288.4600612084919 10 291.1442211254647 11 303.0147314856809 12 304.88823204169273 13 303.2104727828271 14 300.4803870005455 15 308.9957000434481 16 311.674097050674 17 353.0533652298292 18 348.06724989253735 19 328.22037022320876 20 359.2303504578899 Best k = 7 7.961597 seconds (17.10 M allocations: 406.745 MiB, 1.13% gc time, 33.95% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:04 Cross validating... 6%|██ | ETA: 0:00:05 Cross validating... 10%|███ | ETA: 0:00:05 Cross validating... 13%|████▏ | ETA: 0:00:04 Cross validating... 16%|█████▏ | ETA: 0:00:04 Cross validating... 19%|██████▏ | ETA: 0:00:04 Cross validating... 22%|███████▏ | ETA: 0:00:04 Cross validating... 25%|████████▏ | ETA: 0:00:04 Cross validating... 29%|█████████▏ | ETA: 0:00:04 Cross validating... 32%|██████████▏ | ETA: 0:00:04 Cross validating... 35%|███████████▏ | ETA: 0:00:03 Cross validating... 38%|████████████▎ | ETA: 0:00:03 Cross validating... 41%|█████████████▎ | ETA: 0:00:03 Cross validating... 44%|██████████████▎ | ETA: 0:00:03 Cross validating... 48%|███████████████▎ | ETA: 0:00:03 Cross validating... 51%|████████████████▎ | ETA: 0:00:03 Cross validating... 54%|█████████████████▎ | ETA: 0:00:02 Cross validating... 57%|██████████████████▎ | ETA: 0:00:02 Cross validating... 60%|███████████████████▎ | ETA: 0:00:02 Cross validating... 63%|████████████████████▍ | ETA: 0:00:02 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:02 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:02 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:01 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:01 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:01 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:01 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:01 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:01 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:00 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:05 Crossvalidation Results: k MSE 0 463.4198975060679 1 426.791414460889 2 385.4603563827312 3 324.69555652467164 4 315.1856098855447 5 297.01538194918356 6 293.9526450799683 7 292.52821954903214 8 307.89459152260247 9 314.04427214052856 10 328.05090425118993 11 331.85646383934693 12 335.0912960071025 13 360.55093356436555 14 360.84501925852754 15 371.19331966604926 16 371.769308054669 17 386.6761448047587 18 382.12845822066663 19 400.96082996148834 20 397.2018228953231 Best k = 7 5.297377 seconds (17.64 M allocations: 364.750 MiB, 1.23% gc time, 1.03% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, logistic 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: 0:00:43 Cross validating... 6%|██ | ETA: 0:00:23 Cross validating... 10%|███ | ETA: 0:00:16 Cross validating... 13%|████▏ | ETA: 0:00:13 Cross validating... 14%|████▋ | ETA: 0:00:12 Cross validating... 17%|█████▋ | ETA: 0:00:10 Cross validating... 19%|██████▏ | ETA: 0:00:10 Cross validating... 22%|███████▏ | ETA: 0:00:09 Cross validating... 25%|████████▏ | ETA: 0:00:08 Cross validating... 27%|████████▋ | ETA: 0:00:08 Cross validating... 30%|█████████▋ | ETA: 0:00:07 Cross validating... 33%|██████████▋ | ETA: 0:00:07 Cross validating... 37%|███████████▋ | ETA: 0:00:06 Cross validating... 40%|████████████▊ | ETA: 0:00:05 Cross validating... 43%|█████████████▊ | ETA: 0:00:06 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... 67%|█████████████████████▍ | ETA: 0:00:03 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:03 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:02 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:02 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:02 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:02 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:01 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:01 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:01 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:01 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:01 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:07 Crossvalidation Results: k MSE 0 462.85646298664346 1 442.6462917179392 2 406.25601543870846 3 362.42788187871986 4 349.81858523340395 5 330.01225611585556 6 328.2399493222215 7 323.4551075294274 8 327.22682667421975 9 341.3782663144251 10 331.1622574446408 11 328.756118866564 12 330.25978839495184 13 337.05704980863504 14 342.7040756951261 15 376.02078612268275 16 345.0700889639059 17 345.0128993448018 18 358.63897529012365 19 369.7920841326301 20 426.3568715132682 Best k = 7 8.762269 seconds (16.47 M allocations: 389.779 MiB, 10.44% gc time, 26.67% 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: 0:00:05 Cross validating... 6%|██ | ETA: 0:00:05 Cross validating... 10%|███ | ETA: 0:00:05 Cross validating... 13%|████▏ | ETA: 0:00:05 Cross validating... 16%|█████▏ | ETA: 0:00:05 Cross validating... 17%|█████▋ | ETA: 0:00:05 Cross validating... 21%|██████▋ | ETA: 0:00:05 Cross validating... 24%|███████▋ | ETA: 0:00:05 Cross validating... 27%|████████▋ | ETA: 0:00:04 Cross validating... 30%|█████████▋ | 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: 0:00:04 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: 0:00:03 Cross validating... 60%|███████████████████▎ | ETA: 0:00:02 Cross validating... 63%|████████████████████▍ | ETA: 0:00:02 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:02 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:02 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:02 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:01 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:01 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:01 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:01 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:01 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:00 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:05 Crossvalidation Results: k MSE 0 462.85646298664346 1 445.3402964888139 2 409.77601562406 3 366.95611732780407 4 354.9389474506427 5 335.09227411461285 6 335.8756711764797 7 332.3872786500058 8 343.0393018199344 9 355.7138240973156 10 357.07185810682586 11 357.4743808315339 12 374.60387308778354 13 380.0264607302078 14 400.17143224900065 15 402.41214146296454 16 413.7571280525216 17 417.99563673785445 18 420.56382491824536 19 436.40447815353355 20 465.7429566999142 Best k = 7 5.941566 seconds (17.49 M allocations: 359.905 MiB, 1.03% gc time, 0.62% compilation time) Test Summary: | Pass Total Time Cross validation on Float64 matrix, logistic model | 2 2 16.3s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:55 Cross validating... 6%|██ | ETA: 0:00:29 Cross validating... 10%|███ | ETA: 0:00:20 Cross validating... 13%|████▏ | ETA: 0:00:16 Cross validating... 16%|█████▏ | ETA: 0:00:13 Cross validating... 19%|██████▏ | ETA: 0:00:11 Cross validating... 22%|███████▏ | ETA: 0:00:10 Cross validating... 25%|████████▏ | ETA: 0:00:09 Cross validating... 29%|█████████▏ | ETA: 0:00:08 Cross validating... 32%|██████████▏ | ETA: 0:00:07 Cross validating... 35%|███████████▏ | ETA: 0:00:06 Cross validating... 38%|████████████▎ | ETA: 0:00:06 Cross validating... 41%|█████████████▎ | ETA: 0:00:05 Cross validating... 44%|██████████████▎ | ETA: 0:00:05 Cross validating... 48%|███████████████▎ | ETA: 0:00:04 Cross validating... 51%|████████████████▎ | ETA: 0:00:04 Cross validating... 54%|█████████████████▎ | ETA: 0:00:04 Cross validating... 57%|██████████████████▎ | ETA: 0:00:03 Cross validating... 60%|███████████████████▎ | ETA: 0:00:03 Cross validating... 63%|████████████████████▍ | ETA: 0:00:03 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:03 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: 0:00:06 Crossvalidation Results: k MSE 0 649.5458637051561 1 548.9912241333449 2 493.77684830446356 3 427.7214709537133 4 410.09686755126756 5 395.28056989826416 6 395.3098494675771 7 389.0345757811215 8 391.5354620164676 9 399.1000898612085 10 406.6960711363445 11 389.8367896298801 12 413.63828479835934 13 426.713438264626 14 414.7097902444302 15 405.52345288443934 16 430.0876998764918 17 404.6344269444002 18 411.5578555699783 19 429.17489852923944 20 412.84636431696106 Best k = 7 7.314347 seconds (15.19 M allocations: 356.248 MiB, 1.11% gc time, 32.58% 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... 16%|█████▏ | ETA: 0:00:04 Cross validating... 19%|██████▏ | ETA: 0:00:04 Cross validating... 22%|███████▏ | ETA: 0:00:04 Cross validating... 25%|████████▏ | ETA: 0:00:04 Cross validating... 29%|█████████▏ | ETA: 0:00:04 Cross validating... 32%|██████████▏ | ETA: 0:00:03 Cross validating... 35%|███████████▏ | ETA: 0:00:03 Cross validating... 38%|████████████▎ | ETA: 0:00:03 Cross validating... 41%|█████████████▎ | ETA: 0:00:03 Cross validating... 44%|██████████████▎ | ETA: 0:00:03 Cross validating... 48%|███████████████▎ | ETA: 0:00:03 Cross validating... 51%|████████████████▎ | ETA: 0:00:02 Cross validating... 54%|█████████████████▎ | ETA: 0:00:02 Cross validating... 57%|██████████████████▎ | ETA: 0:00:02 Cross validating... 60%|███████████████████▎ | ETA: 0:00:02 Cross validating... 63%|████████████████████▍ | ETA: 0:00:02 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:02 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:01 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:01 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:01 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:01 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:01 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:01 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:01 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:00 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:04 Crossvalidation Results: k MSE 0 649.5458637051561 1 551.2339403430997 2 495.3927161685158 3 432.0867274977414 4 413.93526434759053 5 398.90627807894657 6 402.3464827207064 7 419.2848198525263 8 409.56564517040977 9 420.1224504695472 10 420.7367333294987 11 422.939644386381 12 432.3088210043253 13 433.7363873140148 14 441.82369460923064 15 431.8786336125041 16 447.27863556153466 17 459.42391659195357 18 445.3202974274862 19 444.52586756409556 20 458.00098260197467 Best k = 5 5.025619 seconds (14.38 M allocations: 289.697 MiB, 1.16% gc time, 1.00% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, Poisson model | 2 2 12.8s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:01:02 Cross validating... 5%|█▌ | ETA: 0:01:02 Cross validating... 8%|██▌ | ETA: 0:00:37 Cross validating... 11%|███▌ | ETA: 0:00:42 Cross validating... 13%|████▏ | ETA: 0:00:43 Cross validating... 14%|████▋ | ETA: 0:00:43 Cross validating... 16%|█████▏ | ETA: 0:00:39 Cross validating... 17%|█████▋ | ETA: 0:00:39 Cross validating... 19%|██████▏ | ETA: 0:00:39 Cross validating... 21%|██████▋ | ETA: 0:00:39 Cross validating... 22%|███████▏ | ETA: 0:00:39 Cross validating... 25%|████████▏ | ETA: 0:00:34 Cross validating... 27%|████████▋ | ETA: 0:00:31 Cross validating... 29%|█████████▏ | ETA: 0:00:29 Cross validating... 30%|█████████▋ | ETA: 0:00:30 Cross validating... 32%|██████████▏ | ETA: 0:00:30 Cross validating... 33%|██████████▋ | ETA: 0:00:30 Cross validating... 37%|███████████▋ | ETA: 0:00:26 Cross validating... 40%|████████████▊ | ETA: 0:00:23 Cross validating... 43%|█████████████▊ | ETA: 0:00:23 Cross validating... 46%|██████████████▊ | ETA: 0:00:20 Cross validating... 48%|███████████████▎ | ETA: 0:00:19 Cross validating... 49%|███████████████▊ | ETA: 0:00:18 Cross validating... 51%|████████████████▎ | ETA: 0:00:17 Cross validating... 52%|████████████████▊ | ETA: 0:00:17 Cross validating... 54%|█████████████████▎ | ETA: 0:00:16 Cross validating... 56%|█████████████████▊ | ETA: 0:00:16 Cross validating... 57%|██████████████████▎ | ETA: 0:00:16 Cross validating... 59%|██████████████████▊ | ETA: 0:00:15 Cross validating... 60%|███████████████████▎ | ETA: 0:00:15 Cross validating... 62%|███████████████████▊ | ETA: 0:00:15 Cross validating... 63%|████████████████████▍ | ETA: 0:00:15 Cross validating... 65%|████████████████████▉ | ETA: 0:00:14 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:14 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:12 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:10 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:09 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:08 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:07 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:06 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:06 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:05 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:05 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:04 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:04 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:03 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:02 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: 0:00:38 Crossvalidation Results: k MSE 0 331.5314121137414 1 280.1540158195797 2 256.62192747843403 3 232.05008982981147 4 228.557289063604 5 225.2405938284628 6 225.77616032237978 7 226.17622693501045 8 227.22243514144537 9 229.37316576349062 10 229.26010899042797 11 230.81202883924172 12 229.51988234340945 13 234.8854313956375 14 234.24521754001736 15 235.0848946267193 16 237.30008176997828 17 237.69133329354116 18 238.59700779150282 19 239.09950773072563 20 237.01169235855033 Best k = 5 39.378174 seconds (125.23 M allocations: 3.192 GiB, 1.24% gc time, 5.90% 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... 3%|█ | ETA: 0:00:05 Cross validating... 6%|██ | ETA: 0:00:04 Cross validating... 10%|███ | ETA: 0:00:04 Cross validating... 11%|███▌ | ETA: 0:00:04 Cross validating... 14%|████▋ | ETA: 0:00:05 Cross validating... 16%|█████▏ | ETA: 0:00:05 Cross validating... 17%|█████▋ | ETA: 0:00:05 Cross validating... 19%|██████▏ | ETA: 0:00:05 Cross validating... 21%|██████▋ | ETA: 0:00:05 Cross validating... 22%|███████▏ | ETA: 0:00:05 Cross validating... 24%|███████▋ | ETA: 0:00:05 Cross validating... 25%|████████▏ | ETA: 0:00:05 Cross validating... 27%|████████▋ | ETA: 0:00:05 Cross validating... 29%|█████████▏ | ETA: 0:00:05 Cross validating... 30%|█████████▋ | ETA: 0:00:06 Cross validating... 32%|██████████▏ | ETA: 0:00:06 Cross validating... 33%|██████████▋ | ETA: 0:00:06 Cross validating... 37%|███████████▋ | ETA: 0:00:05 Cross validating... 40%|████████████▊ | ETA: 0:00:05 Cross validating... 41%|█████████████▎ | ETA: 0:00:04 Cross validating... 43%|█████████████▊ | ETA: 0:00:04 Cross validating... 44%|██████████████▎ | ETA: 0:00:04 Cross validating... 46%|██████████████▊ | ETA: 0:00:04 Cross validating... 48%|███████████████▎ | ETA: 0:00:04 Cross validating... 49%|███████████████▊ | ETA: 0:00:04 Cross validating... 51%|████████████████▎ | ETA: 0:00:04 Cross validating... 52%|████████████████▊ | ETA: 0:00:04 Cross validating... 54%|█████████████████▎ | ETA: 0:00:04 Cross validating... 56%|█████████████████▊ | ETA: 0:00:04 Cross validating... 57%|██████████████████▎ | ETA: 0:00:04 Cross validating... 59%|██████████████████▊ | ETA: 0:00:04 Cross validating... 60%|███████████████████▎ | ETA: 0:00:04 Cross validating... 62%|███████████████████▊ | ETA: 0:00:03 Cross validating... 63%|████████████████████▍ | ETA: 0:00:03 Cross validating... 65%|████████████████████▉ | ETA: 0:00:03 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:03 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:03 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:02 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:02 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:02 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:02 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:02 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:01 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:01 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:01 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:01 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:01 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:01 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:01 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:09 Crossvalidation Results: k MSE 0 331.5314121137414 1 281.72565169650267 2 257.841329010918 3 233.66565237731362 4 230.4246723897727 5 229.16829343618252 6 232.89596351610248 7 234.3085087876815 8 235.9513854742241 9 245.16817331247952 10 240.3805756470196 11 252.85229938170855 12 250.3863692064129 13 249.58677269081696 14 259.65839703668405 15 257.80112516942097 16 268.0336530994566 17 262.20529041221795 18 267.27192490685803 19 275.8820516195693 20 260.20928170734885 Best k = 5 10.022245 seconds (31.21 M allocations: 639.378 MiB, 1.58% gc time, 0.55% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, NegativeBinomial model | 2 2 49.8s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:01:03 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: 0:00:13 Cross validating... 19%|██████▏ | ETA: 0:00:11 Cross validating... 22%|███████▏ | ETA: 0:00:10 Cross validating... 27%|████████▋ | ETA: 0:00:08 Cross validating... 30%|█████████▋ | ETA: 0:00:07 Cross validating... 33%|██████████▋ | ETA: 0:00:06 Cross validating... 38%|████████████▎ | ETA: 0:00:05 Cross validating... 41%|█████████████▎ | ETA: 0:00:05 Cross validating... 46%|██████████████▊ | ETA: 0:00:04 Cross validating... 49%|███████████████▊ | ETA: 0:00:04 Cross validating... 54%|█████████████████▎ | ETA: 0:00:03 Cross validating... 59%|██████████████████▊ | ETA: 0:00:03 Cross validating... 62%|███████████████████▊ | ETA: 0:00:02 Cross validating... 65%|████████████████████▉ | ETA: 0:00:02 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:02 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:02 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:01 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:01 Cross validating... 86%|███████████████████████████▍ | 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 0 709.7238911132813 1 600.8470166015625 2 478.37098138427734 3 399.75837347412113 4 316.3170971069336 5 274.59901690673826 6 232.61785809326173 7 221.00282696533208 8 205.62119918823245 9 198.3431817626953 10 200.94596459960937 11 201.86666357421876 12 202.35683154296873 13 208.02664166259768 14 206.9071481628418 15 209.87240182495117 16 216.0480528869629 17 212.0296098022461 18 217.49209603881837 19 225.60646734619144 20 213.36869631958012 Best k = 9 5.899081 seconds (17.01 M allocations: 337.892 MiB, 1.67% gc time, 43.59% 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... 16%|█████▏ | ETA: 0:00:03 Cross validating... 21%|██████▋ | ETA: 0:00:02 Cross validating... 24%|███████▋ | ETA: 0:00:02 Cross validating... 27%|████████▋ | ETA: 0:00:02 Cross validating... 32%|██████████▏ | ETA: 0:00:02 Cross validating... 37%|███████████▋ | ETA: 0:00:02 Cross validating... 41%|█████████████▎ | ETA: 0:00:02 Cross validating... 46%|██████████████▊ | ETA: 0:00:02 Cross validating... 49%|███████████████▊ | ETA: 0:00:02 Cross validating... 54%|█████████████████▎ | ETA: 0:00:01 Cross validating... 59%|██████████████████▊ | ETA: 0:00:01 Cross validating... 62%|███████████████████▊ | ETA: 0:00:01 Cross validating... 65%|████████████████████▉ | ETA: 0:00:01 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:01 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:01 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:01 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:01 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:00 Cross validating... 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 3.218648 seconds (16.17 M allocations: 286.707 MiB, 1.58% gc time, 1.55% compilation time) Test Summary: | Pass Total Time Cross validation on floating point matrices, NegativeBinomial model | 2 2 9.8s **** 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... 2%|▋ | ETA: 0:01:30 Cross validating... 3%|█ | ETA: 0:01:05 Cross validating... 4%|█▎ | ETA: 0:00:53 Cross validating... 5%|█▋ | ETA: 0:00:45 Cross validating... 6%|█▉ | ETA: 0:00:40 Cross validating... 7%|██▎ | ETA: 0:00:36 Cross validating... 8%|██▌ | ETA: 0:00:34 Cross validating... 9%|██▉ | ETA: 0:00:31 Cross validating... 10%|███▎ | ETA: 0:00:30 Cross validating... 11%|███▌ | ETA: 0:00:28 Cross validating... 12%|███▉ | ETA: 0:00:27 Cross validating... 13%|████▏ | ETA: 0:00:26 Cross validating... 14%|████▌ | ETA: 0:00:25 Cross validating... 15%|████▊ | ETA: 0:00:24 Cross validating... 16%|█████▏ | ETA: 0:00:23 Cross validating... 17%|█████▌ | ETA: 0:00:22 Cross validating... 18%|█████▊ | ETA: 0:00:22 Cross validating... 19%|██████▏ | ETA: 0:00:21 Cross validating... 20%|██████▍ | ETA: 0:00:21 Cross validating... 21%|██████▊ | ETA: 0:00:20 Cross validating... 22%|███████ | ETA: 0:00:20 Cross validating... 23%|███████▍ | ETA: 0:00:19 Cross validating... 24%|███████▋ | ETA: 0:00:19 Cross validating... 25%|████████ | ETA: 0:00:18 Cross validating... 26%|████████▍ | ETA: 0:00:18 Cross validating... 27%|████████▋ | ETA: 0:00:17 Cross validating... 28%|█████████ | ETA: 0:00:17 Cross validating... 29%|█████████▎ | ETA: 0:00:17 Cross validating... 30%|█████████▋ | ETA: 0:00:16 Cross validating... 31%|█████████▉ | ETA: 0:00:16 Cross validating... 32%|██████████▎ | ETA: 0:00:16 Cross validating... 33%|██████████▌ | ETA: 0:00:15 Cross validating... 34%|██████████▉ | ETA: 0:00:15 Cross validating... 35%|███████████▎ | ETA: 0:00:15 Cross validating... 36%|███████████▌ | ETA: 0:00:14 Cross validating... 37%|███████████▉ | ETA: 0:00:14 Cross validating... 38%|████████████▏ | ETA: 0:00:14 Cross validating... 39%|████████████▌ | ETA: 0:00:14 Cross validating... 40%|████████████▊ | ETA: 0:00:13 Cross validating... 41%|█████████████▏ | ETA: 0:00:13 Cross validating... 42%|█████████████▌ | ETA: 0:00:13 Cross validating... 43%|█████████████▊ | ETA: 0:00:12 Cross validating... 44%|██████████████▏ | ETA: 0:00:12 Cross validating... 45%|██████████████▍ | ETA: 0:00:12 Cross validating... 46%|██████████████▊ | ETA: 0:00:12 Cross validating... 47%|███████████████ | ETA: 0:00:11 Cross validating... 48%|███████████████▍ | ETA: 0:00:11 Cross validating... 49%|███████████████▋ | ETA: 0:00:11 Cross validating... 50%|████████████████ | ETA: 0:00:11 Cross validating... 51%|████████████████▍ | ETA: 0:00:10 Cross validating... 52%|████████████████▋ | ETA: 0:00:10 Cross validating... 53%|█████████████████ | ETA: 0:00:10 Cross validating... 54%|█████████████████▎ | ETA: 0:00:10 Cross validating... 55%|█████████████████▋ | ETA: 0:00:10 Cross validating... 56%|█████████████████▉ | ETA: 0:00:09 Cross validating... 57%|██████████████████▎ | ETA: 0:00:09 Cross validating... 58%|██████████████████▌ | ETA: 0:00:09 Cross validating... 59%|██████████████████▉ | ETA: 0:00:09 Cross validating... 60%|███████████████████▎ | ETA: 0:00:08 Cross validating... 61%|███████████████████▌ | ETA: 0:00:08 Cross validating... 62%|███████████████████▉ | ETA: 0:00:08 Cross validating... 63%|████████████████████▏ | ETA: 0:00:08 Cross validating... 64%|████████████████████▌ | ETA: 0:00:07 Cross validating... 65%|████████████████████▊ | ETA: 0:00:07 Cross validating... 66%|█████████████████████▏ | ETA: 0:00:07 Cross validating... 67%|█████████████████████▌ | ETA: 0:00:07 Cross validating... 68%|█████████████████████▊ | ETA: 0:00:07 Cross validating... 69%|██████████████████████▏ | ETA: 0:00:06 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:06 Cross validating... 71%|██████████████████████▊ | ETA: 0:00:06 Cross validating... 72%|███████████████████████ | ETA: 0:00:06 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:06 Cross validating... 74%|███████████████████████▋ | ETA: 0:00:05 Cross validating... 75%|████████████████████████ | ETA: 0:00:05 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:05 Cross validating... 77%|████████████████████████▋ | ETA: 0:00:05 Cross validating... 78%|█████████████████████████ | ETA: 0:00:04 Cross validating... 79%|█████████████████████████▎ | ETA: 0:00:04 Cross validating... 80%|█████████████████████████▋ | ETA: 0:00:04 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:04 Cross validating... 82%|██████████████████████████▎ | ETA: 0:00:04 Cross validating... 83%|██████████████████████████▌ | ETA: 0:00:03 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:03 Cross validating... 85%|███████████████████████████▎ | ETA: 0:00:03 Cross validating... 86%|███████████████████████████▌ | ETA: 0:00:03 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:03 Cross validating... 88%|████████████████████████████▏ | ETA: 0:00:02 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:02 Cross validating... 90%|████████████████████████████▊ | ETA: 0:00:02 Cross validating... 91%|█████████████████████████████▏ | ETA: 0:00:02 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:02 Cross validating... 93%|█████████████████████████████▊ | ETA: 0:00:01 Cross validating... 94%|██████████████████████████████▏ | ETA: 0:00:01 Cross validating... 95%|██████████████████████████████▍ | ETA: 0:00:01 Cross validating... 96%|██████████████████████████████▊ | ETA: 0:00:01 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:01 Cross validating... 98%|███████████████████████████████▍| ETA: 0:00:00 Cross validating... 99%|███████████████████████████████▋| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:19 Crossvalidation Results: k MSE 1 3335.7345964159726 2 2930.402921781947 3 2686.265003274224 4 2552.4700605614657 5 2481.475328534019 6 2441.9536320616826 7 2309.3983615955444 8 2282.3212675100353 9 2287.6933637401376 10 2292.650178746854 11 2316.7231187704556 12 2312.495859825697 13 2316.7594942715077 14 2331.6719567900145 15 2341.601094591691 16 2322.6564881798076 17 2341.1233560656638 18 2342.000783480458 19 2349.0425550499576 20 2351.5857049312267 Best k = 8 20.247939 seconds (345.76 k allocations: 221.953 MiB, 0.34% gc time, 8.48% compilation time) Test Summary: | Pass Total Time multivariate cross validation SnpLinAlg | 3 3 25.2s Test Summary: | Pass Total Time wrapper univariate | 20 20 1m45.4s **** 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... 2%|▋ | ETA: 0:00:10 Cross validating... 3%|█ | ETA: 0:00:10 Cross validating... 4%|█▎ | ETA: 0:00:11 Cross validating... 5%|█▋ | ETA: 0:00:11 Cross validating... 6%|█▉ | ETA: 0:00:12 Cross validating... 7%|██▎ | ETA: 0:00:13 Cross validating... 8%|██▌ | ETA: 0:00:13 Cross validating... 9%|██▉ | ETA: 0:00:14 Cross validating... 10%|███▎ | ETA: 0:00:15 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: 0:00:19 Cross validating... 18%|█████▊ | ETA: 0:00:19 Cross validating... 19%|██████▏ | ETA: 0:00:19 Cross validating... 20%|██████▍ | ETA: 0:00:19 Cross validating... 21%|██████▊ | ETA: 0:00:18 Cross validating... 22%|███████ | ETA: 0:00:18 Cross validating... 23%|███████▍ | ETA: 0:00:17 Cross validating... 24%|███████▋ | ETA: 0:00:17 Cross validating... 25%|████████ | ETA: 0:00:16 Cross validating... 26%|████████▍ | ETA: 0:00:16 Cross validating... 27%|████████▋ | ETA: 0:00:16 Cross validating... 28%|█████████ | ETA: 0:00:16 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: 0:00:13 Cross validating... 46%|██████████████▊ | ETA: 0:00:12 Cross validating... 47%|███████████████ | ETA: 0:00:12 Cross validating... 48%|███████████████▍ | ETA: 0:00:12 Cross validating... 49%|███████████████▋ | ETA: 0:00:11 Cross validating... 50%|████████████████ | ETA: 0:00:11 Cross validating... 51%|████████████████▍ | ETA: 0:00:11 Cross validating... 52%|████████████████▋ | ETA: 0:00:11 Cross validating... 53%|█████████████████ | ETA: 0:00:11 Cross validating... 54%|█████████████████▎ | ETA: 0:00:11 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: 0:00:10 Cross validating... 61%|███████████████████▌ | ETA: 0:00:09 Cross validating... 62%|███████████████████▉ | ETA: 0:00:09 Cross validating... 63%|████████████████████▏ | ETA: 0:00:09 Cross validating... 64%|████████████████████▌ | ETA: 0:00:08 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: 0:00:06 Cross validating... 77%|████████████████████████▋ | ETA: 0:00:05 Cross validating... 78%|█████████████████████████ | ETA: 0:00:05 Cross validating... 79%|█████████████████████████▎ | ETA: 0:00:05 Cross validating... 80%|█████████████████████████▋ | ETA: 0:00:05 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:04 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: 0:00:03 Cross validating... 90%|████████████████████████████▊ | ETA: 0:00:02 Cross validating... 91%|█████████████████████████████▏ | ETA: 0:00:02 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:02 Cross validating... 93%|█████████████████████████████▊ | ETA: 0:00:02 Cross validating... 94%|██████████████████████████████▏ | ETA: 0:00:01 Cross validating... 95%|██████████████████████████████▍ | ETA: 0:00:01 Cross validating... 96%|██████████████████████████████▊ | ETA: 0:00:01 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:01 Cross validating... 98%|███████████████████████████████▍| ETA: 0:00:00 Cross validating... 99%|███████████████████████████████▋| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:24 Crossvalidation Results: k MSE 1 2838.788679198002 2 2514.3973428708136 3 2305.6176519676274 4 2222.025304867614 5 2075.1670384588365 6 2067.7948989723845 7 2053.427506114907 8 2086.405384830965 9 2080.984460901671 10 2105.131199502364 11 2132.407165368786 12 2138.267187460652 13 2166.002210829576 14 2194.9918295115804 15 2189.890403738045 16 2191.181293229578 17 2209.4669750564362 18 2221.2595493644303 19 2238.7425945763257 20 2253.9559571797727 Best k = 7 **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 2%|▋ | ETA: 0:00:10 Cross validating... 3%|█ | ETA: 0:00:10 Cross validating... 4%|█▎ | ETA: 0:00:11 Cross validating... 5%|█▋ | ETA: 0:00:10 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: 0:00:14 Cross validating... 12%|███▉ | ETA: 0:00:15 Cross validating... 13%|████▏ | ETA: 0:00:15 Cross validating... 14%|████▌ | ETA: 0:00:16 Cross validating... 15%|████▊ | ETA: 0:00:16 Cross validating... 16%|█████▏ | ETA: 0:00:17 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: 0:00:17 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: 0:00:14 Cross validating... 36%|███████████▌ | ETA: 0:00:14 Cross validating... 37%|███████████▉ | ETA: 0:00:14 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: 0:00:12 Cross validating... 45%|██████████████▍ | ETA: 0:00:12 Cross validating... 46%|██████████████▊ | ETA: 0:00:12 Cross validating... 47%|███████████████ | ETA: 0:00:11 Cross validating... 48%|███████████████▍ | ETA: 0:00:11 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: 0:00:10 Cross validating... 53%|█████████████████ | ETA: 0:00:10 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: 0:00:09 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: 0:00:07 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: 0:00:06 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: 0:00:13 Cross validating... 8%|██▌ | ETA: 0:00:13 Cross validating... 9%|██▉ | ETA: 0:00:14 Cross validating... 10%|███▎ | ETA: 0:00:14 Cross validating... 11%|███▌ | ETA: 0:00:15 Cross validating... 12%|███▉ | ETA: 0:00:16 Cross validating... 13%|████▏ | ETA: 0:00:16 Cross validating... 14%|████▌ | ETA: 0:00:17 Cross validating... 15%|████▊ | ETA: 0:00:17 Cross validating... 16%|█████▏ | ETA: 0:00:18 Cross validating... 17%|█████▌ | ETA: 0:00:19 Cross validating... 18%|█████▊ | ETA: 0:00:19 Cross validating... 19%|██████▏ | ETA: 0:00:19 Cross validating... 20%|██████▍ | ETA: 0:00:19 Cross validating... 21%|██████▊ | ETA: 0:00:18 Cross validating... 22%|███████ | ETA: 0:00:18 Cross validating... 23%|███████▍ | ETA: 0:00:17 Cross validating... 24%|███████▋ | ETA: 0:00:17 Cross validating... 25%|████████ | ETA: 0:00:16 Cross validating... 26%|████████▍ | ETA: 0:00:16 Cross validating... 27%|████████▋ | ETA: 0:00:16 Cross validating... 28%|█████████ | ETA: 0:00:16 Cross validating... 29%|█████████▎ | ETA: 0:00:16 Cross validating... 30%|█████████▋ | ETA: 0:00:16 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: 0:00:14 Cross validating... 38%|████████████▏ | ETA: 0:00:14 Cross validating... 39%|████████████▌ | ETA: 0:00:14 Cross validating... 40%|████████████▊ | ETA: 0:00:14 Cross validating... 42%|█████████████▌ | ETA: 0:00:13 Cross validating... 44%|██████████████▏ | ETA: 0:00:12 Cross validating... 45%|██████████████▍ | ETA: 0:00:12 Cross validating... 46%|██████████████▊ | ETA: 0:00:12 Cross validating... 47%|███████████████ | ETA: 0:00:11 Cross validating... 48%|███████████████▍ | ETA: 0:00:11 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: 0:00:10 Cross validating... 53%|█████████████████ | ETA: 0:00:10 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: 0:00:09 Cross validating... 58%|██████████████████▌ | ETA: 0:00:09 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: 0:00:07 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: 0:00:06 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: 0:00:22 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 1m25.8s read BGEN and VCF: Error During Test at /home/pkgeval/.julia/packages/MendelIHT/ZcxZT/test/wrapper_test.jl:184 Got exception outside of a @test startproc must be called before process Stacktrace: [1] error(s::String) @ Base ./error.jl:56 [2] process(codec::CodecZlib.ZlibDecompressor, input::TranscodingStreams.Memory, output::TranscodingStreams.Memory, error_ref::TranscodingStreams.Error) @ CodecZlib ~/.julia/packages/CodecZlib/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] getproperty(x::Nothing, f::Symbol) @ Base ~/.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:318 [18] _start() @ Base ./client.jl:593 Test Summary: | Error Total Time read BGEN and VCF | 1 1 3.2s RNG of the outermost testset: Xoshiro(0x736fc8977184590f, 0x2e42ccded3397da5, 0x4d8831d904785834, 0xf1d2d1ef707c42af, 0x1ea4e5fd14f05dcb) 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 1080.36s 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:3162 [3] Cmd(cmd::Cmd) @ Base /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Operations.jl:3025 [inlined] [4] test(ctx::Pkg.Types.Context, pkgs::Vector{PackageSpec}; coverage::Bool, test_fn::Nothing, julia_args::Cmd, test_args::Cmd, force_latest_compatible_version::Bool, allow_earlier_backwards_compatible_versions::Bool, allow_reresolve::Bool, kwargs::@Kwargs{io::IOContext{IO}}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:586 [5] 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:352 [12] _start() @ Base ./client.jl:593 in expression starting at /PkgEval.jl/scripts/evaluate.jl:214 PkgEval failed after 1221.62s: package tests unexpectedly errored