Package evaluation to test MendelIHT on Julia 1.10.10 (c8be17dcfd*) started at 2026-02-03T00:42:40.586 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.10` Set-up completed after 5.41s ################################################################################ # Installation # Installing MendelIHT... Resolving package versions... Updating `~/.julia/environments/v1.10/Project.toml` [921c7187] + MendelIHT v1.4.11 Updating `~/.julia/environments/v1.10/Manifest.toml` [7d9f7c33] + Accessors v0.1.43 [79e6a3ab] + Adapt v4.4.0 [66dad0bd] + AliasTables v1.1.3 [4fba245c] + ArrayInterface v7.22.0 [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 v0.10.15 [fb6a15b2] + CloseOpenIntervals v0.1.13 [523fee87] + CodecBzip2 v0.8.5 [ba30903b] + CodecXz v0.7.4 [944b1d66] + CodecZlib v0.7.8 [6b39b394] + CodecZstd v0.8.7 [861a8166] + Combinatorics v1.1.0 [38540f10] + CommonSolve v0.2.6 [f70d9fcc] + CommonWorldInvalidations v1.0.0 [34da2185] + Compat v4.18.1 [a33af91c] + CompositionsBase v0.1.2 [187b0558] + ConstructionBase v1.6.0 [adafc99b] + CpuId v0.3.1 [a8cc5b0e] + Crayons v4.1.1 [a10d1c49] + DBInterface v2.6.1 [9a962f9c] + DataAPI v1.16.0 [a93c6f00] + DataFrames v1.8.1 [864edb3b] + DataStructures v0.19.3 [e2d170a0] + DataValueInterfaces v1.0.0 [8bb1440f] + DelimitedFiles v1.9.1 [b4f34e82] + Distances v0.10.12 [31c24e10] + Distributions v0.25.123 [ffbed154] + DocStringExtensions v0.9.5 [48062228] + FilePathsBase v0.9.24 [1a297f60] + FillArrays v1.16.0 [38e38edf] + GLM v1.9.2 [c27321d9] + Glob v1.4.0 [3e5b6fbb] + HostCPUFeatures v0.1.18 [34004b35] + HypergeometricFunctions v0.3.28 [09f84164] + HypothesisTests v0.11.6 [615f187c] + IfElse v0.1.1 [842dd82b] + InlineStrings v1.4.5 [3587e190] + InverseFunctions v0.1.17 [41ab1584] + InvertedIndices v1.3.1 [92d709cd] + IrrationalConstants v0.2.6 [82899510] + IteratorInterfaceExtensions v1.0.0 [692b3bcd] + JLLWrappers v1.7.1 [b964fa9f] + LaTeXStrings v1.4.0 [10f19ff3] + LayoutPointers v0.1.17 [2ab3a3ac] + LogExpFunctions v0.3.29 [bdcacae8] + LoopVectorization v0.12.173 [1914dd2f] + MacroTools v0.5.16 [d125e4d3] + ManualMemory v0.1.8 [921c7187] + MendelIHT v1.4.11 [e1d29d7a] + Missings v1.2.0 [6fe1bfb0] + OffsetArrays v1.17.0 [bac558e1] + OrderedCollections v1.8.1 [90014a1f] + PDMats v0.11.37 [69de0a69] + Parsers v2.8.3 [1d0040c9] + PolyesterWeave v0.2.2 [2dfb63ee] + PooledArrays v1.4.3 ⌅ [aea7be01] + PrecompileTools v1.2.1 [21216c6a] + Preferences v1.5.1 [08abe8d2] + PrettyTables v3.1.2 [92933f4c] + ProgressMeter v1.11.0 [43287f4e] + PtrArrays v1.3.0 [1fd47b50] + QuadGK v2.11.2 [189a3867] + Reexport v1.2.2 [ae029012] + Requires v1.3.1 [79098fc4] + Rmath v0.9.0 [f2b01f46] + Roots v2.2.10 [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 v0.3.22 [a2af1166] + SortingAlgorithms v1.2.2 [276daf66] + SpecialFunctions v2.6.1 [aedffcd0] + Static v1.3.1 [0d7ed370] + StaticArrayInterface v1.8.0 [82ae8749] + StatsAPI v1.8.0 [2913bbd2] + StatsBase v0.34.10 [4c63d2b9] + StatsFuns v1.5.2 [3eaba693] + StatsModels v0.7.8 [892a3eda] + StringManipulation v0.4.2 [3783bdb8] + TableTraits v1.0.1 [bd369af6] + Tables v1.12.1 [8290d209] + ThreadingUtilities v0.5.5 ⌅ [3bb67fe8] + TranscodingStreams v0.9.13 [3a884ed6] + UnPack v1.0.2 [a620830f] + VCFTools v0.2.10 [28eba6e3] + VariantCallFormat v0.5.9 [3d5dd08c] + VectorizationBase v0.21.72 [ea10d353] + WeakRefStrings v1.4.2 [76eceee3] + WorkerUtilities v1.6.1 [6e34b625] + Bzip2_jll v1.0.9+0 [efe28fd5] + OpenSpecFun_jll v0.5.6+0 [f50d1b31] + Rmath_jll v0.5.1+0 [76ed43ae] + SQLite_jll v3.51.2+0 [ffd25f8a] + XZ_jll v5.8.2+0 [3161d3a3] + Zstd_jll v1.5.7+1 [c4b69c83] + dlfcn_win32_jll v1.4.2+0 [0dad84c5] + ArgTools v1.1.1 [56f22d72] + Artifacts [2a0f44e3] + Base64 [ade2ca70] + Dates [8ba89e20] + Distributed [f43a241f] + Downloads v1.6.0 [7b1f6079] + FileWatching [9fa8497b] + Future [b77e0a4c] + InteractiveUtils [b27032c2] + LibCURL v0.6.4 [76f85450] + LibGit2 [8f399da3] + Libdl [37e2e46d] + LinearAlgebra [56ddb016] + Logging [d6f4376e] + Markdown [a63ad114] + Mmap [ca575930] + NetworkOptions v1.2.0 [44cfe95a] + Pkg v1.10.0 [de0858da] + Printf [3fa0cd96] + REPL [9a3f8284] + Random [ea8e919c] + SHA v0.7.0 [9e88b42a] + Serialization [6462fe0b] + Sockets [2f01184e] + SparseArrays v1.10.0 [10745b16] + Statistics v1.10.0 [4607b0f0] + SuiteSparse [fa267f1f] + TOML v1.0.3 [a4e569a6] + Tar v1.10.0 [8dfed614] + Test [cf7118a7] + UUIDs [4ec0a83e] + Unicode [e66e0078] + CompilerSupportLibraries_jll v1.1.1+0 [deac9b47] + LibCURL_jll v8.4.0+0 [e37daf67] + LibGit2_jll v1.6.4+0 [29816b5a] + LibSSH2_jll v1.11.0+1 [c8ffd9c3] + MbedTLS_jll v2.28.1010+0 [14a3606d] + MozillaCACerts_jll v2025.12.2 [4536629a] + OpenBLAS_jll v0.3.23+5 [05823500] + OpenLibm_jll v0.8.5+0 [bea87d4a] + SuiteSparse_jll v7.2.1+1 [83775a58] + Zlib_jll v1.2.13+1 [8e850b90] + libblastrampoline_jll v5.11.0+0 [8e850ede] + nghttp2_jll v1.52.0+1 [3f19e933] + p7zip_jll v17.4.0+2 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 10.42s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompiling packages... 7817.2 ms ✓ BGEN 23297.7 ms ✓ VCFTools 146977.2 ms ✓ MendelIHT 3 dependencies successfully precompiled in 182 seconds. 140 already precompiled. 1 dependency had output during precompilation: ┌ VCFTools │ [ Info: Compiling VCF parser... └ Precompilation completed after 194.53s ################################################################################ # Testing # Testing MendelIHT Status `/tmp/jl_M2ZWy6/Project.toml` ⌅ [6db4b851] BGEN v0.1.17 [6e4b80f9] BenchmarkTools v1.6.3 [336ed68f] CSV v0.10.15 [a93c6f00] DataFrames v1.8.1 [8bb1440f] DelimitedFiles v1.9.1 [b4f34e82] Distances v0.10.12 [31c24e10] Distributions v0.25.123 [38e38edf] GLM v1.9.2 [921c7187] MendelIHT v1.4.11 [92933f4c] ProgressMeter v1.11.0 [189a3867] Reexport v1.2.2 [4e780e97] SnpArrays v0.3.22 [276daf66] SpecialFunctions v2.6.1 [2913bbd2] StatsBase v0.34.10 [a620830f] VCFTools v0.2.10 [37e2e46d] LinearAlgebra [44cfe95a] Pkg v1.10.0 [9a3f8284] Random [8dfed614] Test Status `/tmp/jl_M2ZWy6/Manifest.toml` [7d9f7c33] Accessors v0.1.43 [79e6a3ab] Adapt v4.4.0 [66dad0bd] AliasTables v1.1.3 [4fba245c] ArrayInterface v7.22.0 [67c07d97] Automa v1.1.0 ⌅ [6db4b851] BGEN v0.1.17 [28d598bf] BGZFStreams v0.3.2 [6e4b80f9] BenchmarkTools v1.6.3 [47718e42] BioGenerics v0.1.5 [62783981] BitTwiddlingConvenienceFunctions v0.1.6 [e1450e63] BufferedStreams v1.2.2 [2a0fbf3d] CPUSummary v0.2.7 [336ed68f] CSV v0.10.15 [fb6a15b2] CloseOpenIntervals v0.1.13 [523fee87] CodecBzip2 v0.8.5 [ba30903b] CodecXz v0.7.4 [944b1d66] CodecZlib v0.7.8 [6b39b394] CodecZstd v0.8.7 [861a8166] Combinatorics v1.1.0 [38540f10] CommonSolve v0.2.6 [f70d9fcc] CommonWorldInvalidations v1.0.0 [34da2185] Compat v4.18.1 [a33af91c] CompositionsBase v0.1.2 [187b0558] ConstructionBase v1.6.0 [adafc99b] CpuId v0.3.1 [a8cc5b0e] Crayons v4.1.1 [a10d1c49] DBInterface v2.6.1 [9a962f9c] DataAPI v1.16.0 [a93c6f00] DataFrames v1.8.1 [864edb3b] DataStructures v0.19.3 [e2d170a0] DataValueInterfaces v1.0.0 [8bb1440f] DelimitedFiles v1.9.1 [b4f34e82] Distances v0.10.12 [31c24e10] Distributions v0.25.123 [ffbed154] DocStringExtensions v0.9.5 [48062228] FilePathsBase v0.9.24 [1a297f60] FillArrays v1.16.0 [38e38edf] GLM v1.9.2 [c27321d9] Glob v1.4.0 [3e5b6fbb] HostCPUFeatures v0.1.18 [34004b35] HypergeometricFunctions v0.3.28 [09f84164] HypothesisTests v0.11.6 [615f187c] IfElse v0.1.1 [842dd82b] InlineStrings v1.4.5 [3587e190] InverseFunctions v0.1.17 [41ab1584] InvertedIndices v1.3.1 [92d709cd] IrrationalConstants v0.2.6 [82899510] IteratorInterfaceExtensions v1.0.0 [692b3bcd] JLLWrappers v1.7.1 [682c06a0] JSON v1.4.0 [b964fa9f] LaTeXStrings v1.4.0 [10f19ff3] LayoutPointers v0.1.17 [2ab3a3ac] LogExpFunctions v0.3.29 [bdcacae8] LoopVectorization v0.12.173 [1914dd2f] MacroTools v0.5.16 [d125e4d3] ManualMemory v0.1.8 [921c7187] MendelIHT v1.4.11 [e1d29d7a] Missings v1.2.0 [6fe1bfb0] OffsetArrays v1.17.0 [bac558e1] OrderedCollections v1.8.1 [90014a1f] PDMats v0.11.37 [69de0a69] Parsers v2.8.3 [1d0040c9] PolyesterWeave v0.2.2 [2dfb63ee] PooledArrays v1.4.3 ⌅ [aea7be01] PrecompileTools v1.2.1 [21216c6a] Preferences v1.5.1 [08abe8d2] PrettyTables v3.1.2 [92933f4c] ProgressMeter v1.11.0 [43287f4e] PtrArrays v1.3.0 [1fd47b50] QuadGK v2.11.2 [189a3867] Reexport v1.2.2 [ae029012] Requires v1.3.1 [79098fc4] Rmath v0.9.0 [f2b01f46] Roots v2.2.10 [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 v0.3.22 [a2af1166] SortingAlgorithms v1.2.2 [276daf66] SpecialFunctions v2.6.1 [aedffcd0] Static v1.3.1 [0d7ed370] StaticArrayInterface v1.8.0 [82ae8749] StatsAPI v1.8.0 [2913bbd2] StatsBase v0.34.10 [4c63d2b9] StatsFuns v1.5.2 [3eaba693] StatsModels v0.7.8 [892a3eda] StringManipulation v0.4.2 [ec057cc2] StructUtils v2.6.2 [3783bdb8] TableTraits v1.0.1 [bd369af6] Tables v1.12.1 [8290d209] ThreadingUtilities v0.5.5 ⌅ [3bb67fe8] 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SparseArrays v1.10.0 [10745b16] Statistics v1.10.0 [4607b0f0] SuiteSparse [fa267f1f] TOML v1.0.3 [a4e569a6] Tar v1.10.0 [8dfed614] Test [cf7118a7] UUIDs [4ec0a83e] Unicode [e66e0078] CompilerSupportLibraries_jll v1.1.1+0 [deac9b47] LibCURL_jll v8.4.0+0 [e37daf67] LibGit2_jll v1.6.4+0 [29816b5a] LibSSH2_jll v1.11.0+1 [c8ffd9c3] MbedTLS_jll v2.28.1010+0 [14a3606d] MozillaCACerts_jll v2025.12.2 [4536629a] OpenBLAS_jll v0.3.23+5 [05823500] OpenLibm_jll v0.8.5+0 [bea87d4a] SuiteSparse_jll v7.2.1+1 [83775a58] Zlib_jll v1.2.13+1 [8e850b90] libblastrampoline_jll v5.11.0+0 [8e850ede] nghttp2_jll v1.52.0+1 [3f19e933] p7zip_jll v17.4.0+2 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: using deprecated binding Distributions.MatrixReshaped in MendelIHT. , use Distributions.ReshapedDistribution{2, S, D} where D<:Distributions.Distribution{Distributions.ArrayLikeVariate{1}, S} where S<:Distributions.ValueSupport instead. WARNING: both BGEN and SnpArrays export "maf"; uses of it in module MendelIHT must be qualified ┌ Warning: `cholesky!(A::RealHermSymComplexHerm{<:BlasReal, <:StridedMatrix}, ::Val{true}; kwargs...)` is deprecated, use `cholesky!(A, RowMaximum(); kwargs...)` instead. │ caller = iht_stepsize!(v::MendelIHT.mIHTVariable{Float64, LinearAlgebra.Transpose{Float64, SnpArrays.SnpLinAlg{Float64}}}) at multivariate.jl:241 └ @ MendelIHT ~/.julia/packages/MendelIHT/ZcxZT/src/multivariate.jl:241 Test Summary: | Pass Total Time loglikelihood | 4 4 10.8s Test Summary: | Pass Total Time deviance | 1 1 0.3s Test Summary: | Pass Total Time update_μ! | 4 4 0.7s Test Summary: | Pass Total Time _choose! | 7 7 6.1s Test Summary: | Pass Total Time _iht_backtrack | 7 7 0.0s Test Summary: | Pass Total Time standardize! | 12 12 0.9s Test Summary: | Pass Total Time project_k! | 2 2 0.7s Test Summary: | Pass Total Time project_group_sparse! | 5 5 1.3s Test Summary: | Pass Total Time maf_weights | 6 6 1.7s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse linear regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1564.3992155594028, backtracks = 0, tol = 1.3673939943735551 Iteration 2: loglikelihood = -1452.3116384469317, backtracks = 0, tol = 0.17004119275971813 Iteration 3: loglikelihood = -1445.7570720930094, backtracks = 0, tol = 0.03332226020876874 Iteration 4: loglikelihood = -1445.6871335522244, backtracks = 0, tol = 0.002540685370328147 Iteration 5: loglikelihood = -1445.6858677214782, backtracks = 0, tol = 0.00039526321341443 Iteration 6: loglikelihood = -1445.6858412964516, backtracks = 0, tol = 5.869650810102198e-5 IHT estimated 10 nonzero SNP predictors and 1 non-genetic predictors. Compute time (sec): 0.05672407150268555 Final loglikelihood: -1445.6858412964516 SNP PVE: 0.8703593191239238 Iterations: 6 Selected genetic predictors: 10×2 DataFrame Row │ Position Estimated_β │ Int64 Float64 ─────┼─────────────────────── 1 │ 61 1.144 2 │ 2431 1.49952 3 │ 4443 -0.308667 4 │ 4683 0.668886 5 │ 5491 0.696805 6 │ 5534 -0.211859 7 │ 5606 0.974476 8 │ 7093 0.183335 9 │ 7353 0.416477 10 │ 9597 1.19034 Selected nongenetic predictors: 1×2 DataFrame Row │ Position Estimated_β │ Int64 Float64 ─────┼─────────────────────── 1 │ 1 0.0117418Test Summary: | Pass Total Time fit normal SnpLinAlg | 4 4 14.5s **** 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 = -392.0613389694829, backtracks = 0, tol = 0.8730901958956809 Iteration 2: loglikelihood = -324.9035992953096, backtracks = 0, tol = 0.37468033381473603 Iteration 3: loglikelihood = -314.4576180510749, backtracks = 0, tol = 0.18117469195974145 Iteration 4: loglikelihood = -307.17120238234924, backtracks = 0, tol = 0.20765797375681136 Iteration 5: loglikelihood = -284.2750391567721, backtracks = 0, tol = 0.15301986546015767 Iteration 6: loglikelihood = -277.27663868321736, backtracks = 0, tol = 0.12366590377744598 Iteration 7: loglikelihood = -275.33174540792857, backtracks = 0, tol = 0.11995781851207363 Iteration 8: loglikelihood = -274.00227689291256, backtracks = 0, tol = 0.13425705096802434 Iteration 9: loglikelihood = -272.42570707066176, backtracks = 0, tol = 0.13062487689506594 Iteration 10: loglikelihood = -271.6127494701915, backtracks = 1, tol = 0.014084709740603905 Iteration 11: loglikelihood = -271.21244333942826, backtracks = 2, tol = 0.1201985684325286 Iteration 12: loglikelihood = -271.0103441232668, backtracks = 0, tol = 0.11857285013443566 Iteration 13: loglikelihood = -270.8337543576222, backtracks = 0, tol = 0.12346613175215097 Iteration 14: loglikelihood = -269.5247497681469, backtracks = 0, tol = 0.028384798131160908 Iteration 15: loglikelihood = -269.35970760524765, backtracks = 2, tol = 0.008731708473894107 Iteration 16: loglikelihood = -270.40635199002895, backtracks = 3, tol = 0.1133956208994299 Iteration 17: loglikelihood = -269.413508000131, backtracks = 0, tol = 0.11291168071728155 Iteration 18: loglikelihood = -269.10999497936746, backtracks = 1, tol = 0.008293583210477146 Iteration 19: loglikelihood = -268.9857927598226, backtracks = 1, tol = 0.005539259461288692 Iteration 20: loglikelihood = -268.92614341521636, backtracks = 3, tol = 0.005010218979297465 Iteration 21: loglikelihood = -274.2463794266506, backtracks = 3, tol = 0.1336018966074166 Iteration 22: loglikelihood = -269.6121854296775, backtracks = 0, tol = 0.13324484663524946 Iteration 23: loglikelihood = -269.3000631274804, backtracks = 1, tol = 0.009051334941603338 Iteration 24: loglikelihood = -269.18717049214536, backtracks = 1, tol = 0.005046890912954357 Iteration 25: loglikelihood = -269.12255664581176, backtracks = 2, tol = 0.006498455684112915 Iteration 26: loglikelihood = -271.01095696096377, backtracks = 3, tol = 0.13318047795315832 Iteration 27: loglikelihood = -269.19410610687686, backtracks = 0, tol = 0.037734492538885445 Iteration 28: loglikelihood = -269.1621756728032, backtracks = 1, tol = 0.0029267014522422145 Iteration 29: loglikelihood = -269.14177450859614, backtracks = 2, tol = 0.11416186270993073 Iteration 30: loglikelihood = -268.56190907682867, backtracks = 0, tol = 0.017423581291083783 Iteration 31: loglikelihood = -268.54780892627923, backtracks = 2, tol = 0.0018004181004697385 Iteration 32: loglikelihood = -268.5345394093837, backtracks = 3, tol = 0.0023437740398678355 Iteration 33: loglikelihood = -295.5848019755624, backtracks = 3, tol = 0.17203631799093508 Iteration 34: loglikelihood = -271.52260706621433, backtracks = 0, tol = 0.172159043855635 Iteration 35: loglikelihood = -268.08728889244776, backtracks = 0, tol = 0.10451214438980992 Iteration 36: loglikelihood = -267.81029095979324, backtracks = 0, tol = 0.008333121656828098 Iteration 37: loglikelihood = -267.78973102642817, backtracks = 2, tol = 0.0021358438624526793 Iteration 38: loglikelihood = -267.77289093967966, backtracks = 3, tol = 0.0024380312396850767 Iteration 39: loglikelihood = -273.45748034770054, backtracks = 3, tol = 0.11275475852841757 Iteration 40: loglikelihood = -272.0941923199055, backtracks = 0, tol = 0.1191579214744465 Iteration 41: loglikelihood = -270.43033036539066, backtracks = 0, tol = 0.1143167312562471 Iteration 42: loglikelihood = -266.73818541682306, backtracks = 0, tol = 0.09250576621603741 Iteration 43: loglikelihood = -266.49996496220683, backtracks = 1, tol = 0.008842127485972916 Iteration 44: loglikelihood = -266.4341007458304, backtracks = 1, tol = 0.005021939169150144 Iteration 45: loglikelihood = -266.4136101111252, backtracks = 1, tol = 0.0029116911062026583 Iteration 46: loglikelihood = -266.40683025124895, backtracks = 2, tol = 0.001379268417436446 Iteration 47: loglikelihood = -266.40057428246746, backtracks = 3, tol = 0.0018555584112598426 Iteration 48: loglikelihood = -415.65070261240936, backtracks = 3, tol = 0.26230292903751057 Iteration 49: loglikelihood = -290.6111737479507, backtracks = 0, tol = 0.26227803202765265 Iteration 50: loglikelihood = -284.18177476353924, backtracks = 0, tol = 0.1976236921412461 Iteration 51: loglikelihood = -274.4079828777766, backtracks = 0, tol = 0.14002543988681554 Iteration 52: loglikelihood = -271.4130772812644, backtracks = 0, tol = 0.14348717399842917 Iteration 53: loglikelihood = -270.8615733053613, backtracks = 1, tol = 0.011861864942256743 Iteration 54: loglikelihood = -270.70563690014967, backtracks = 2, tol = 0.005243107039436466 Iteration 55: loglikelihood = -270.60970051237746, backtracks = 3, tol = 0.004478487165980047 Iteration 56: loglikelihood = -268.95598422583896, backtracks = 3, tol = 0.07293571197699035 Iteration 57: loglikelihood = -268.49843001758177, backtracks = 1, tol = 0.01170177764941356 Iteration 58: loglikelihood = -268.3688291681088, backtracks = 1, tol = 0.005938252431770799 Iteration 59: loglikelihood = -268.31811089863953, backtracks = 1, tol = 0.0032877124172649213 Iteration 60: loglikelihood = -268.3001600817185, backtracks = 3, tol = 0.0020358182654901967 Iteration 61: loglikelihood = -268.2818493208017, backtracks = 3, tol = 0.0024172246961868113 Iteration 62: loglikelihood = -268.2664279649848, backtracks = 3, tol = 0.0023219746243507405 Iteration 63: loglikelihood = -270.90074173218886, backtracks = 3, tol = 0.09553303409909164 Iteration 64: loglikelihood = -270.8476408273805, backtracks = 0, tol = 0.10599717839548882 Iteration 65: loglikelihood = -269.99911535939725, backtracks = 0, tol = 0.10647406546176132 Iteration 66: loglikelihood = -268.52569957774267, backtracks = 0, tol = 0.11383951050445491 Iteration 67: loglikelihood = -267.2840412368419, backtracks = 0, tol = 0.022526980702438307 Iteration 68: loglikelihood = -267.24334324780307, backtracks = 1, tol = 0.003242906584439214 Iteration 69: loglikelihood = -267.2277357986281, backtracks = 3, tol = 0.0019683833156607603 Iteration 70: loglikelihood = -267.2120636581105, backtracks = 3, tol = 0.0022401884546430035 Iteration 71: loglikelihood = -267.19852423968126, backtracks = 3, tol = 0.002158039853960769 Iteration 72: loglikelihood = -267.18776935319676, backtracks = 3, tol = 0.0019131127224676402 Iteration 73: loglikelihood = -267.17930075841264, backtracks = 3, tol = 0.0016843377892314952 Iteration 74: loglikelihood = -267.1725754250023, backtracks = 3, tol = 0.0014905090311857516 Iteration 75: loglikelihood = -267.98415648876295, backtracks = 3, tol = 0.09839839608794078 Iteration 76: loglikelihood = -267.55005175289057, backtracks = 0, tol = 0.09852912837408959 Iteration 77: loglikelihood = -267.26597514986105, backtracks = 1, tol = 0.007470480836812042 Iteration 78: loglikelihood = -267.18899868411665, backtracks = 1, tol = 0.00365388727225263 Iteration 79: loglikelihood = -267.1670743812828, backtracks = 1, tol = 0.0020458345327274414 Iteration 80: loglikelihood = -267.15976240842065, backtracks = 1, tol = 0.0012348532370538236 Iteration 81: loglikelihood = -267.1571567456466, backtracks = 2, tol = 0.0006491297767733038 Iteration 82: loglikelihood = -267.15519379007725, backtracks = 3, tol = 0.00066773174394343 Iteration 83: loglikelihood = -277.69187205253513, backtracks = 3, tol = 0.12867378741127675 Iteration 84: loglikelihood = -267.3056391467074, backtracks = 0, tol = 0.12697554121158497 Iteration 85: loglikelihood = -266.3289353104731, backtracks = 0, tol = 0.020124164069145366 Iteration 86: loglikelihood = -266.29542211393215, backtracks = 0, tol = 0.004676101948649591 Iteration 87: loglikelihood = -266.2938110669265, backtracks = 1, tol = 0.0004983277490446857 Iteration 88: loglikelihood = -266.29317963468174, backtracks = 2, tol = 0.0003919505705957704 Iteration 89: loglikelihood = -266.29248030391125, backtracks = 3, tol = 0.0006270189288869327 Iteration 90: loglikelihood = -1365.2179935426598, backtracks = 3, tol = 0.6006368982257869 Iteration 91: loglikelihood = -604.3666806008217, backtracks = 0, tol = 0.9689056229699662 Iteration 92: loglikelihood = -413.8736133305052, backtracks = 1, tol = 0.23289988873959666 Iteration 93: loglikelihood = -365.0937120169318, backtracks = 2, tol = 0.1273402600759157 Iteration 94: loglikelihood = -329.7125243957955, backtracks = 1, tol = 0.15261390690265253 Iteration 95: loglikelihood = -318.24269817731727, backtracks = 0, tol = 0.13490733316488954 Iteration 96: loglikelihood = -298.81451391888214, backtracks = 1, tol = 0.12163996060528931 Iteration 97: loglikelihood = -287.6458167318868, backtracks = 1, tol = 0.10520757539969099 Iteration 98: loglikelihood = -283.5916126905397, backtracks = 2, tol = 0.0298417006421918 Iteration 99: loglikelihood = -278.687667247772, backtracks = 3, tol = 0.10048639819408357 Iteration 100: loglikelihood = -276.1119956737588, backtracks = 2, tol = 0.025136305543493134 Iteration 101: loglikelihood = -283.8416383672816, backtracks = 3, tol = 0.11518402854290014 Iteration 102: loglikelihood = -280.2516153295548, backtracks = 1, tol = 0.028653355499222363 Iteration 103: loglikelihood = -273.7123220352219, backtracks = 2, tol = 0.10369495935538557 Iteration 104: loglikelihood = -272.1265589917195, backtracks = 1, tol = 0.01571737335408097 Iteration 105: loglikelihood = -269.7629289176443, backtracks = 2, tol = 0.09557817381565424 Iteration 106: loglikelihood = -268.8448002571265, backtracks = 1, tol = 0.013541099846406312 Iteration 107: loglikelihood = -268.2864006304056, backtracks = 3, tol = 0.01395692926886281 Iteration 108: loglikelihood = -270.53685230005937, backtracks = 3, tol = 0.09406505137232392 Iteration 109: loglikelihood = -267.5783246180018, backtracks = 1, tol = 0.09777168918953937 Iteration 110: loglikelihood = -267.19317136773793, backtracks = 1, tol = 0.0069869957534714425 Iteration 111: loglikelihood = -267.02580840797526, backtracks = 3, tol = 0.0058388011794597815 Iteration 112: loglikelihood = -266.8439605208202, backtracks = 3, tol = 0.00788422653593289 Iteration 113: loglikelihood = -266.69444541342114, backtracks = 3, tol = 0.007770933043114403 Iteration 114: loglikelihood = -266.5824697998546, backtracks = 3, tol = 0.006739030539089166 Iteration 115: loglikelihood = -266.49887965417196, backtracks = 3, tol = 0.005764075784342567 Iteration 116: loglikelihood = -266.4362787191651, backtracks = 3, tol = 0.004940809903286242 Iteration 117: loglikelihood = -266.3892537671587, backtracks = 3, tol = 0.004246418361434426 Iteration 118: loglikelihood = -266.35383704678173, backtracks = 3, tol = 0.003658466582615637 Iteration 119: loglikelihood = -266.3271035961275, backtracks = 3, tol = 0.0031584998984640097 Iteration 120: loglikelihood = -266.30688600928994, backtracks = 3, tol = 0.0027317496047756314 Iteration 121: loglikelihood = -266.29157110291254, backtracks = 3, tol = 0.002366300148902215 Iteration 122: loglikelihood = -266.2799536363677, backtracks = 3, tol = 0.002052461267444272 Iteration 123: loglikelihood = -266.27113021650587, backtracks = 3, tol = 0.001782286377196141 Iteration 124: loglikelihood = -266.26442180322596, backtracks = 3, tol = 0.0015492098215234872 Iteration 125: loglikelihood = -266.25931675933714, backtracks = 3, tol = 0.0013477703647973287 Iteration 126: loglikelihood = -266.25542877648263, backtracks = 3, tol = 0.0011733982472657792 Iteration 127: loglikelihood = -266.2524656484708, backtracks = 3, tol = 0.001022249388966114 Iteration 128: loglikelihood = -266.2502060029224, backtracks = 3, tol = 0.0008910749736433335 Iteration 129: loglikelihood = -266.2484819028848, backtracks = 3, tol = 0.0007771178744830548 Iteration 130: loglikelihood = -266.24716579834814, backtracks = 3, tol = 0.0006780296613032269 Iteration 131: loglikelihood = -266.24616071442364, backtracks = 3, tol = 0.0005918035482891417 Iteration 132: loglikelihood = -266.2453928564611, backtracks = 3, tol = 0.0005167198055694955 Iteration 133: loglikelihood = -266.24480602563284, backtracks = 3, tol = 0.0004513010039524991 Iteration 134: loglikelihood = -266.24435739440304, backtracks = 3, tol = 0.0003942750833118048 Iteration 135: loglikelihood = -266.24401430588614, backtracks = 3, tol = 0.0003445446957139589 Iteration 136: loglikelihood = -266.24375184572466, backtracks = 3, tol = 0.00030116161912389065 Iteration 137: loglikelihood = -266.2435509979024, backtracks = 3, tol = 0.00026330529787236406 Iteration 138: loglikelihood = -266.24339724264445, backtracks = 3, tol = 0.00023026476440154482 Iteration 139: loglikelihood = -266.24327948949445, backtracks = 3, tol = 0.0002014233491772845 Iteration 140: loglikelihood = -266.24318926480316, backtracks = 3, tol = 0.00017624570374245814 Iteration 141: loglikelihood = -266.24312009256204, backtracks = 3, tol = 0.00015426675423134076 Iteration 142: loglikelihood = -266.2430670222733, backtracks = 3, tol = 0.000135082275646778 Iteration 143: loglikelihood = -266.2430262687634, backtracks = 3, tol = 0.00011834083563469558 Iteration 144: loglikelihood = -266.2429949372632, backtracks = 3, tol = 0.00010373690418656192 Iteration 145: loglikelihood = -266.2429708134703, backtracks = 3, tol = 9.100496580258867e-5 Test Summary: | Pass Total Time fit Bernoulli SnpLinAlg | 4 4 2.9s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse Poisson regression Number of threads = 1 Link functin = LogLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -2744.3597381634627, backtracks = 0, tol = 0.5663130340353787 Iteration 2: loglikelihood = -1760.2360659571814, backtracks = 0, tol = 0.0635012065767357 Iteration 3: loglikelihood = -1366.3100880811016, backtracks = 0, tol = 0.08323811079815084 Iteration 4: loglikelihood = -1295.2065048176828, backtracks = 0, tol = 0.06130091214013117 Iteration 5: loglikelihood = -1269.7438934603858, backtracks = 0, tol = 0.05360750476497757 Iteration 6: loglikelihood = -1260.269338945676, backtracks = 0, tol = 0.04178174625603973 Iteration 7: loglikelihood = -1255.8265222956818, backtracks = 0, tol = 0.022610902128585353 Iteration 8: loglikelihood = -1253.2118740174044, backtracks = 0, tol = 0.021089845520301104 Iteration 9: loglikelihood = -1251.840051357329, backtracks = 0, tol = 0.012113599303305356 Iteration 10: loglikelihood = -1245.5978618504193, backtracks = 0, tol = 0.057113473385880714 Iteration 11: loglikelihood = -1244.580479190058, backtracks = 0, tol = 0.013125995690587634 Iteration 12: loglikelihood = -1244.166984570316, backtracks = 0, tol = 0.007621611543335286 Iteration 13: loglikelihood = -1243.9794444247714, backtracks = 0, tol = 0.006951300499749036 Iteration 14: loglikelihood = -1243.8819121055437, backtracks = 0, tol = 0.0036929980357152453 Iteration 15: loglikelihood = -1243.8297393312548, backtracks = 0, tol = 0.003947435896913094 Iteration 16: loglikelihood = -1243.800406948408, backtracks = 0, tol = 0.002032124708815571 Iteration 17: loglikelihood = -1243.783794592032, backtracks = 0, tol = 0.002288565589027969 Iteration 18: loglikelihood = -1243.7741675584107, backtracks = 0, tol = 0.0011654339208557482 Iteration 19: loglikelihood = -1243.7685817370213, backtracks = 0, tol = 0.0013401732624759586 Iteration 20: loglikelihood = -1243.7653023779192, backtracks = 0, tol = 0.0006803066386904824 Iteration 21: loglikelihood = -1243.76337768945, backtracks = 0, tol = 0.0007896376693605383 Iteration 22: loglikelihood = -1243.7622408340867, backtracks = 0, tol = 0.00040049554033395657 Iteration 23: loglikelihood = -1243.7615696829844, backtracks = 0, tol = 0.000466992333102015 Iteration 24: loglikelihood = -1243.7611720380066, backtracks = 0, tol = 0.00023681008526501576 Iteration 25: loglikelihood = -1243.760936543637, backtracks = 0, tol = 0.00027679878554917684 Iteration 26: loglikelihood = -1243.7607967902975, backtracks = 0, tol = 0.0001403621692660967 Iteration 27: loglikelihood = -1243.760713879462, backtracks = 0, tol = 0.00016428656433057197 Iteration 28: loglikelihood = -1243.7606646321535, backtracks = 0, tol = 8.330960497649561e-5 Test Summary: | Pass Total Time fit Poisson SnpLinAlg | 4 4 1.5s **** 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 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 = -1544.5636982714564, backtracks = 0, tol = 0.5482810993440485 Iteration 2: loglikelihood = -1466.283021512827, backtracks = 0, tol = 0.11084383229101219 Iteration 3: loglikelihood = -1436.159986880084, backtracks = 0, tol = 0.08115302427586692 Iteration 4: loglikelihood = -1424.1577922831873, backtracks = 0, tol = 0.06458685436639923 Iteration 5: loglikelihood = -1419.5180377133838, backtracks = 0, tol = 0.0968448093029104 Iteration 6: loglikelihood = -1419.160275445878, backtracks = 1, tol = 0.008098854574837338 Iteration 7: loglikelihood = -1419.0438297425562, backtracks = 1, tol = 0.004998123329653479 Iteration 8: loglikelihood = -1419.0070378964863, backtracks = 1, tol = 0.0031751077385943874 Iteration 9: loglikelihood = -1418.9957880314903, backtracks = 1, tol = 0.001963701079718174 Iteration 10: loglikelihood = -1418.9925047443771, backtracks = 1, tol = 0.0011410599623664114 Iteration 11: loglikelihood = -1418.9915924168342, backtracks = 1, tol = 0.0006214612109788576 Iteration 12: loglikelihood = -1418.9913457562434, backtracks = 1, tol = 0.0003282218511776227 Iteration 13: loglikelihood = -1418.9912798362018, backtracks = 1, tol = 0.00017131460605336203 Iteration 14: loglikelihood = -1418.9912623104176, backtracks = 1, tol = 8.885832808533048e-5 Test Summary: | Pass Total Time fit NegativeBinomial SnpLinAlg | 4 4 1.0s **** 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 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 = -1851.9723598146345, backtracks = 0, tol = 0.770729574805905 Iteration 2: loglikelihood = -1509.7955119434546, backtracks = 0, tol = 0.13026901578742164 Iteration 3: loglikelihood = -1437.669962030035, backtracks = 0, tol = 0.0535246979954356 Iteration 4: loglikelihood = -1432.766152493088, backtracks = 0, tol = 0.02915945873447629 Iteration 5: loglikelihood = -1432.583714146459, backtracks = 1, tol = 0.0015720135166242537 Iteration 6: loglikelihood = -1432.5368164721242, backtracks = 1, tol = 0.0007956019542386402 Iteration 7: loglikelihood = -1432.524831529285, backtracks = 1, tol = 0.0004000495470405744 Iteration 8: loglikelihood = -1432.5217850209, backtracks = 1, tol = 0.0002003654893460441 Iteration 9: loglikelihood = -1432.5210138720263, backtracks = 1, tol = 0.00010019704337242294 Iteration 10: loglikelihood = -1432.5208192622486, backtracks = 1, tol = 5.0105672171141456e-5 Test Summary: | Pass Total Time fit with >1 non-genetic covariates SnpLinAlg | 5 5 1.3s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse linear regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1606.6641825470604, backtracks = 0, tol = 0.3453824308115848 Iteration 2: loglikelihood = -1453.1616585045042, backtracks = 0, tol = 0.09732750876494278 Iteration 3: loglikelihood = -1436.7601911560628, backtracks = 0, tol = 0.04111637712580123 Iteration 4: loglikelihood = -1434.158027493463, backtracks = 0, tol = 0.029204573732192086 Iteration 5: loglikelihood = -1433.3526376147895, backtracks = 0, tol = 0.03126568232215824 Iteration 6: loglikelihood = -1433.238866899064, backtracks = 0, tol = 0.0030470434575719605 Iteration 7: loglikelihood = -1433.237713255994, backtracks = 0, tol = 0.000334539128202527 Iteration 8: loglikelihood = -1433.2376972494883, backtracks = 0, tol = 3.311060620672562e-5 Test Summary: | Pass Total Time model selection on non-genetic covariates | 5 5 0.9s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse linear regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 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 = -1521.3614838029296, backtracks = 0, tol = 0.12907962854042923 Iteration 2: loglikelihood = -1474.6943473131034, backtracks = 0, tol = 0.08649046940236123 Iteration 3: loglikelihood = -1473.7241783459324, backtracks = 0, tol = 0.13441890656327116 Iteration 4: loglikelihood = -1445.2935874280492, backtracks = 0, tol = 0.10965284430523985 Iteration 5: loglikelihood = -1425.2270300644025, backtracks = 0, tol = 0.0816389234422241 Iteration 6: loglikelihood = -1411.5063823214248, backtracks = 0, tol = 0.10118405976438942 Iteration 7: loglikelihood = -1408.4868672816774, backtracks = 0, tol = 0.048113453188792864 Iteration 8: loglikelihood = -1408.280048752867, backtracks = 0, tol = 0.00978060185428834 Iteration 9: loglikelihood = -1408.2440432669837, backtracks = 0, tol = 0.004479894390213807 Iteration 10: loglikelihood = -1408.2362603709748, backtracks = 0, tol = 0.0014165205138653683 Iteration 11: loglikelihood = -1408.2341564813737, backtracks = 0, tol = 0.0009271672261786421 Iteration 12: loglikelihood = -1408.233431241675, backtracks = 0, tol = 0.0004618705207559795 Iteration 13: loglikelihood = -1408.2331634555173, backtracks = 0, tol = 0.0003631795597290925 Iteration 14: loglikelihood = -1408.2330605988539, backtracks = 0, tol = 0.00018152275395087088 Iteration 15: loglikelihood = -1408.2330199122043, backtracks = 0, tol = 0.00014797476270119196 Iteration 16: loglikelihood = -1408.2330035363016, backtracks = 0, tol = 7.413728328656441e-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 = -1574.3954333498655, backtracks = 0, tol = 0.24636950238645036 Iteration 2: loglikelihood = -1504.3092998298516, backtracks = 0, tol = 0.2052942773177233 Iteration 3: loglikelihood = -1445.5384865999365, backtracks = 0, tol = 0.12171159189399039 Iteration 4: loglikelihood = -1440.284438118203, backtracks = 1, tol = 0.03476266101636157 Iteration 5: loglikelihood = -1433.1386150336928, backtracks = 1, tol = 0.059389962723894886 Iteration 6: loglikelihood = -1427.674880993642, backtracks = 1, tol = 0.044298861408494705 Iteration 7: loglikelihood = -1426.04168583884, backtracks = 1, tol = 0.02212759125755032 Iteration 8: loglikelihood = -1425.6080062358958, backtracks = 1, tol = 0.01144320384441705 Iteration 9: loglikelihood = -1425.494315732238, backtracks = 1, tol = 0.005874078649513755 Iteration 10: loglikelihood = -1425.4642792256793, backtracks = 1, tol = 0.0029057611979618862 Iteration 11: loglikelihood = -1425.456175024548, backtracks = 1, tol = 0.0014553924462932812 Iteration 12: loglikelihood = -1425.4539135256236, backtracks = 1, tol = 0.0006979037936934472 Iteration 13: loglikelihood = -1425.4532488752498, backtracks = 1, tol = 0.0003481264326759868 Iteration 14: loglikelihood = -1425.453037780787, backtracks = 1, tol = 0.00016782378895479223 Iteration 15: loglikelihood = -1425.4529646838891, backtracks = 1, tol = 0.0001417924122155212 Iteration 16: loglikelihood = -1425.452937896266, backtracks = 1, tol = 6.036136995848839e-5 Test Summary: | Pass Total Time Correlated predictors and double sparsity Float64 matrix | 2 2 6.1s **** 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 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 = -1526.0023930116256, backtracks = 0, tol = 0.20488913645641643 Iteration 2: loglikelihood = -1473.5739085771106, backtracks = 0, tol = 0.09888699396918385 Iteration 3: loglikelihood = -1413.7016368832362, backtracks = 0, tol = 0.09360722027256105 Iteration 4: loglikelihood = -1394.5406644977522, backtracks = 0, tol = 0.08113647447535799 Iteration 5: loglikelihood = -1386.01490830659, backtracks = 0, tol = 0.06022903535447882 Iteration 6: loglikelihood = -1380.8772794354702, backtracks = 0, tol = 0.031046864330412212 Iteration 7: loglikelihood = -1367.611331590696, backtracks = 0, tol = 0.07645236466558811 Iteration 8: loglikelihood = -1358.4754421506984, backtracks = 0, tol = 0.062284277470870376 Iteration 9: loglikelihood = -1357.0137492483955, backtracks = 0, tol = 0.024985387421438417 Iteration 10: loglikelihood = -1356.0933064296555, backtracks = 0, tol = 0.014838803161089029 Iteration 11: loglikelihood = -1349.7954835006024, backtracks = 0, tol = 0.06197600504571301 Iteration 12: loglikelihood = -1346.6436839122937, backtracks = 0, tol = 0.03796356232003585 Iteration 13: loglikelihood = -1345.9999712747526, backtracks = 0, tol = 0.01412003274233954 Iteration 14: loglikelihood = -1345.769342386157, backtracks = 0, tol = 0.009326997010935537 Iteration 15: loglikelihood = -1345.6766196520832, backtracks = 0, tol = 0.006020808457933139 Iteration 16: loglikelihood = -1345.6365578675482, backtracks = 0, tol = 0.0032603874567089823 Iteration 17: loglikelihood = -1345.619570649613, backtracks = 0, tol = 0.002611389161587769 Iteration 18: loglikelihood = -1345.61214928464, backtracks = 0, tol = 0.001359258764512488 Iteration 19: loglikelihood = -1345.6089574844102, backtracks = 0, tol = 0.001153626030614498 Iteration 20: loglikelihood = -1345.6075505593485, backtracks = 0, tol = 0.0005800242491092911 Iteration 21: loglikelihood = -1345.6069365166609, backtracks = 0, tol = 0.000517595483160235 Iteration 22: loglikelihood = -1345.6066640933539, backtracks = 0, tol = 0.0002501849303506902 Iteration 23: loglikelihood = -1345.6065436671008, backtracks = 0, tol = 0.0002350646695576753 Iteration 24: loglikelihood = -1345.606490092036, backtracks = 0, tol = 0.00010861391843052756 Iteration 25: loglikelihood = -1345.606466186036, backtracks = 0, tol = 0.00010762220878305669 Iteration 26: loglikelihood = -1345.6064555721907, backtracks = 0, tol = 4.7254213384318785e-5 0.741941 seconds (2.02 M allocations: 40.492 MiB, 15.17% gc time, 37.80% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** 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 = -1552.6643494859704, backtracks = 0, tol = 0.20488913645641643 Iteration 2: loglikelihood = -1504.016331235133, backtracks = 0, tol = 0.12293679850304728 Iteration 3: loglikelihood = -1469.1107750885021, backtracks = 0, tol = 0.12186853178201384 Iteration 4: loglikelihood = -1446.497565904897, backtracks = 0, tol = 0.07443094162652206 Iteration 5: loglikelihood = -1432.4332702491479, backtracks = 0, tol = 0.10811839330736361 Iteration 6: loglikelihood = -1416.117759900142, backtracks = 0, tol = 0.06520807400996428 Iteration 7: loglikelihood = -1408.104833877445, backtracks = 0, tol = 0.08607741335302671 Iteration 8: loglikelihood = -1399.961502323573, backtracks = 0, tol = 0.020869492877543257 Iteration 9: loglikelihood = -1392.6871827902698, backtracks = 0, tol = 0.09144959485100247 Iteration 10: loglikelihood = -1383.4521072336515, backtracks = 1, tol = 0.02009469601835133 Iteration 11: loglikelihood = -1377.39598498753, backtracks = 1, tol = 0.010802480482557985 Iteration 12: loglikelihood = -1373.0526041182761, backtracks = 1, tol = 0.00624318617259823 Iteration 13: loglikelihood = -1370.051012220124, backtracks = 1, tol = 0.0037747047092147753 Iteration 14: loglikelihood = -1365.612762742557, backtracks = 1, tol = 0.064292357982115 Iteration 15: loglikelihood = -1362.3168066636888, backtracks = 1, tol = 0.006522452233514655 Iteration 16: loglikelihood = -1359.7733421934993, backtracks = 1, tol = 0.0033697413805022793 Iteration 17: loglikelihood = -1357.7211644549427, backtracks = 1, tol = 0.001668001623234549 Iteration 18: loglikelihood = -1356.0143520444053, backtracks = 1, tol = 0.0007674389102498477 Iteration 19: loglikelihood = -1355.96957853663, backtracks = 0, tol = 0.07804292218984321 Iteration 20: loglikelihood = -1354.715649556565, backtracks = 0, tol = 0.013670470674409428 Iteration 21: loglikelihood = -1353.9885109276825, backtracks = 0, tol = 0.0008599778979942496 Iteration 22: loglikelihood = -1353.3105348232114, backtracks = 0, tol = 0.00019838457753043669 Iteration 23: loglikelihood = -1352.5842712716512, backtracks = 0, tol = 0.0649773260586303 Iteration 24: loglikelihood = -1352.4552066088297, backtracks = 0, tol = 0.07454323329583452 Iteration 25: loglikelihood = -1351.585467982756, backtracks = 0, tol = 0.010311987151716518 Iteration 26: loglikelihood = -1351.0892882486569, backtracks = 0, tol = 0.000618183931156932 Iteration 27: loglikelihood = -1350.6239791711005, backtracks = 0, tol = 0.00018582414350208282 Iteration 28: loglikelihood = -1350.1590129948795, backtracks = 0, tol = 0.07042070701432593 Iteration 29: loglikelihood = -1349.5676310886258, backtracks = 0, tol = 0.008485879803050805 Iteration 30: loglikelihood = -1349.2086353238985, backtracks = 0, tol = 0.000955231191694096 Iteration 31: loglikelihood = -1348.8661800778332, backtracks = 0, tol = 0.00041249286943055303 Iteration 32: loglikelihood = -1348.3947122572893, backtracks = 1, tol = 0.00019446805817574224 Iteration 33: loglikelihood = -1347.9756240351564, backtracks = 1, tol = 0.0001219485864016202 Iteration 34: loglikelihood = -1347.630992559427, backtracks = 1, tol = 0.0001104283116149333 Iteration 35: loglikelihood = -1347.3469480698016, backtracks = 1, tol = 0.00010132530937036096 Iteration 36: loglikelihood = -1347.1192677821703, backtracks = 1, tol = 9.20178855833793e-5 0.388857 seconds (1.63 M allocations: 33.584 MiB) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse NegativeBinomial regression Number of threads = 1 Link functin = LogLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -3671.6968, backtracks = 0, tol = 0.09517660215143353 Iteration 2: loglikelihood = -3614.5203, backtracks = 0, tol = 0.04836228607779133 Iteration 3: loglikelihood = -3587.3508, backtracks = 1, tol = 0.06433871852269185 Iteration 4: loglikelihood = -3582.5144, backtracks = 1, tol = 0.010743665311432555 Iteration 5: loglikelihood = -3580.5925, backtracks = 1, tol = 0.007095109215822986 Iteration 6: loglikelihood = -3579.992, backtracks = 1, tol = 0.005094234701577118 Iteration 7: loglikelihood = -3579.8232, backtracks = 1, tol = 0.002816710001246968 Iteration 8: loglikelihood = -3568.1497, backtracks = 1, tol = 0.06814549212823923 Iteration 9: loglikelihood = -3557.7915, backtracks = 0, tol = 0.08873097124397056 Iteration 10: loglikelihood = -3552.721, backtracks = 0, tol = 0.01730624110261502 Iteration 11: loglikelihood = -3552.3694, backtracks = 1, tol = 0.004194912731173898 Iteration 12: loglikelihood = -3552.1833, backtracks = 1, tol = 0.0033026234456481405 Iteration 13: loglikelihood = -3552.1287, backtracks = 1, tol = 0.0015427331578654556 Iteration 14: loglikelihood = -3552.1147, backtracks = 1, tol = 0.000961490297323268 Iteration 15: loglikelihood = -3552.1128, backtracks = 1, tol = 0.0004078967992348514 Iteration 16: loglikelihood = -3552.1113, backtracks = 2, tol = 0.00012637650881011656 Iteration 17: loglikelihood = -3552.1106, backtracks = 2, tol = 9.158708744029797e-5 15.344698 seconds (13.60 M allocations: 525.714 MiB, 6.71% gc time, 95.68% 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 = -3553.6267, backtracks = 0, tol = 0.09517660215143353 Iteration 2: loglikelihood = -3422.3738, backtracks = 0, tol = 0.04991710875676883 Iteration 3: loglikelihood = -3215.3647, backtracks = 1, tol = 0.06315094924640285 Iteration 4: loglikelihood = -3160.6519, backtracks = 0, tol = 0.08637006305327125 Iteration 5: loglikelihood = -2991.7195, backtracks = 0, tol = 0.09703545117909972 Iteration 6: loglikelihood = -2882.2861, backtracks = 0, tol = 0.011816449876553278 Iteration 7: loglikelihood = -2819.9104, backtracks = 0, tol = 0.09713506584701767 Iteration 8: loglikelihood = -2649.1555, backtracks = 0, tol = 0.10756746276642631 Iteration 9: loglikelihood = -2542.3733, backtracks = 0, tol = 0.012213728691650796 Iteration 10: loglikelihood = -2449.941, backtracks = 0, tol = 0.08240264320431157 Iteration 11: loglikelihood = -2368.5757, backtracks = 0, tol = 0.012547038565005737 Iteration 12: loglikelihood = -2305.5093, backtracks = 0, tol = 0.08425323002787703 Iteration 13: loglikelihood = -2258.6448, backtracks = 0, tol = 0.08441790351548006 Iteration 14: loglikelihood = -2226.8032, backtracks = 0, tol = 0.010119059540884627 Iteration 15: loglikelihood = -2207.136, backtracks = 0, tol = 0.0029088242325653077 Iteration 16: loglikelihood = -2189.4158, backtracks = 1, tol = 0.00040045294632575683 Iteration 17: loglikelihood = -2183.3184, backtracks = 1, tol = 0.0003072498921874691 Iteration 18: loglikelihood = -2181.337, backtracks = 1, tol = 0.00024700403233021917 Iteration 19: loglikelihood = -2180.6873, backtracks = 1, tol = 0.0001743678548453821 Iteration 20: loglikelihood = -2180.4585, backtracks = 1, tol = 0.00011944379189812558 Iteration 21: loglikelihood = -2180.3706, backtracks = 1, tol = 7.66741540390517e-5 0.164604 seconds (1.17 M allocations: 20.465 MiB, 5.84% gc time) Test Summary: | Pass Total Time Negative binomial nuisance parameter Float32 matrix | 12 12 19.6s **** 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 = -2940.629877504658, backtracks = 0, tol = 1.0120831316661991 Iteration 2: loglikelihood = -1611.3018786628645, backtracks = 0, tol = 0.2701768857908283 Iteration 3: loglikelihood = -1426.8961669494083, backtracks = 0, tol = 0.10621330484015029 Iteration 4: loglikelihood = -1415.5993528550066, backtracks = 0, tol = 0.03380877787297415 Iteration 5: loglikelihood = -1415.4728162418598, backtracks = 0, tol = 0.0023147521282136743 Iteration 6: loglikelihood = -1415.472201570803, backtracks = 0, tol = 0.0001809219245981915 Iteration 7: loglikelihood = -1415.472196844447, backtracks = 0, tol = 1.294077221849416e-5 5.801861 seconds (728.49 k allocations: 114.247 MiB, 0.54% gc time, 90.52% compilation time) Test Summary: | Pass Total Time initialze beta | 1 1 6.2s 5.977973 seconds (3.93 M allocations: 93.411 MiB, 1.44% gc time, 0.65% compilation time) 3.997696 seconds (3.90 M allocations: 101.152 MiB, 0.73% gc time) 10.262686 seconds (22.59 M allocations: 566.742 MiB, 0.68% gc time, 10.94% compilation time: 62% of which was recompilation) 8.774478 seconds (22.37 M allocations: 560.635 MiB, 0.23% gc time) 28.662510 seconds (1.86 M allocations: 3.479 GiB, 0.60% gc time, 19.03% compilation time) 23.757867 seconds (57.83 k allocations: 319.311 MiB, 0.12% gc time) Test Summary: | Pass Total Time memory_efficient keyword | 7 7 1m30.3s Test Summary: | Pass Total Time update_support! | 10 10 0.5s 12.039 ms (76 allocations: 5.30 KiB) 5.186 μs (2 allocations: 176 bytes) 113.459 μs (2 allocations: 288 bytes) 2.726 μs (0 allocations: 0 bytes) 23.780 μs (2 allocations: 128 bytes) 13.430 μs (0 allocations: 0 bytes) 3.784 μs (0 allocations: 0 bytes) 4.146 μs (0 allocations: 0 bytes) 29.530 μs (0 allocations: 0 bytes) 30.645 ms (76 allocations: 5.30 KiB) 28.420 μs (2 allocations: 1.02 KiB) 117.279 μs (2 allocations: 288 bytes) 13.489 μs (0 allocations: 0 bytes) 119.759 μs (2 allocations: 128 bytes) 40.850 μs (0 allocations: 0 bytes) 24.250 μs (0 allocations: 0 bytes) 23.830 μs (0 allocations: 0 bytes) 89.639 μs (0 allocations: 0 bytes) Test Summary: | Time benchmarks for multivariate function | None 2m31.1s **** 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 **** **** 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 = 0.14802242082004133 Iteration 2: loglikelihood = -2869.406464695619, backtracks = 0, tol = 0.03512679046077987 Iteration 3: loglikelihood = -2868.084702693443, backtracks = 0, tol = 0.0055693496163324524 Iteration 4: loglikelihood = -2868.034423817725, backtracks = 0, tol = 0.001118951762895177 Iteration 5: loglikelihood = -2868.0308576353746, backtracks = 0, tol = 0.00031182601179140966 Iteration 6: loglikelihood = -2868.0305288614227, backtracks = 0, tol = 0.00010393305949948345 Iteration 7: loglikelihood = -2868.0304966516946, backtracks = 0, tol = 3.1008620498575026e-5 0.684076 seconds (28.61 k allocations: 6.026 MiB, 24.57% compilation time) Test Summary: | Pass Total Time multivariate fit_iht SnpLinAlg | 7 7 10.1s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse Multivariate Gaussian regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 12 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -2878.028812628852, backtracks = 0, tol = 2.5661768673084553 Iteration 2: loglikelihood = -2868.563037890196, backtracks = 0, tol = 0.024335274263285057 Iteration 3: loglikelihood = -2868.0815051475474, backtracks = 0, tol = 0.004072558228741048 Iteration 4: loglikelihood = -2868.0352100240902, backtracks = 0, tol = 0.0013135682973484317 Iteration 5: loglikelihood = -2868.030929723194, backtracks = 0, tol = 0.000386434110747091 Iteration 6: loglikelihood = -2868.0305335492912, backtracks = 0, tol = 0.00011924564415557833 Iteration 7: loglikelihood = -2868.0304968517494, backtracks = 0, tol = 3.603726989721193e-5 2.378370 seconds (253.57 k allocations: 173.027 MiB, 1.96% gc time, 52.09% compilation time) Test Summary: | Pass Total Time initialze beta | 5 5 2.9s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:02:15 Cross validating... 33%|██████████▋ | ETA: 0:00:14 Cross validating... 38%|████████████▎ | ETA: 0:00:12 Cross validating... 41%|█████████████▎ | ETA: 0:00:11 Cross validating... 44%|██████████████▎ | ETA: 0:00:09 Cross validating... 48%|███████████████▎ | ETA: 0:00:08 Cross validating... 51%|████████████████▎ | ETA: 0:00:08 Cross validating... 54%|█████████████████▎ | ETA: 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Crossvalidation Results: k MSE 0 2720.186405495873 1 1956.2598953911838 2 1537.6020126929106 3 1064.110504731509 4 781.6471368888213 5 614.665568216025 6 469.3063234305213 7 412.0046515011516 8 377.31414240562856 9 367.2151214056838 10 351.7293716295932 11 355.27815287663 12 357.9628146221903 13 362.1545134516431 14 362.70213292608616 15 367.2649648729805 16 383.0134835055884 17 371.30865024876584 18 368.8860172495407 19 390.66521610700966 20 370.7267550383665 Best k = 10 10.380970 seconds (12.29 M allocations: 379.373 MiB, 0.89% gc time, 54.63% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:03 Cross validating... 6%|██ | ETA: 0:00:03 Cross validating... 10%|███ | ETA: 0:00:03 Cross validating... 13%|████▏ | ETA: 0:00:03 Cross validating... 16%|█████▏ | ETA: 0:00:03 Cross validating... 19%|██████▏ | ETA: 0:00:03 Cross validating... 22%|███████▏ | ETA: 0:00:03 Cross validating... 25%|████████▏ | ETA: 0:00:03 Cross validating... 29%|█████████▏ | ETA: 0:00:03 Cross validating... 32%|██████████▏ | ETA: 0:00:03 Cross validating... 33%|██████████▋ | ETA: 0:00:03 Cross validating... 37%|███████████▋ | ETA: 0:00:03 Cross validating... 41%|█████████████▎ | ETA: 0:00:02 Cross validating... 44%|██████████████▎ | ETA: 0:00:02 Cross validating... 48%|███████████████▎ | ETA: 0:00:02 Cross validating... 51%|████████████████▎ | ETA: 0:00:02 Cross validating... 54%|█████████████████▎ | ETA: 0:00:02 Cross validating... 57%|██████████████████▎ | ETA: 0:00:02 Cross validating... 60%|███████████████████▎ | ETA: 0:00:02 Cross validating... 63%|████████████████████▍ | ETA: 0:00:02 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:02 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:01 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:01 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:01 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:01 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:01 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:01 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:00 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:04 Crossvalidation Results: k MSE 0 2720.186405495873 1 1957.340312139823 2 1546.2914950469908 3 1077.0150046104964 4 787.078577003416 5 620.6098492998593 6 472.5081508446257 7 416.6788088867303 8 382.6116983004333 9 372.81176849709925 10 358.8031384980317 11 366.4717237142997 12 375.5462895581778 13 384.668662021273 14 389.593779035112 15 399.6527122165061 16 410.7874443759725 17 415.70471662382874 18 414.7984387616285 19 412.53693228570694 20 422.10338339840496 Best k = 10 4.901194 seconds (11.04 M allocations: 265.596 MiB, 0.64% gc time, 0.44% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, normal model | 3 3 16.1s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:06:19 Cross validating... 8%|██▌ | ETA: 0:02:26 Cross validating... 11%|███▌ | ETA: 0:01:41 Cross validating... 16%|█████▏ | ETA: 0:01:08 Cross validating... 21%|██████▋ | ETA: 0:00:50 Cross validating... 25%|████████▏ | ETA: 0:00:38 Cross validating... 29%|█████████▏ | ETA: 0:00:33 Cross validating... 32%|██████████▏ | ETA: 0:00:29 Cross validating... 37%|███████████▋ | ETA: 0:00:23 Cross validating... 41%|█████████████▎ | ETA: 0:00:19 Cross validating... 46%|██████████████▊ | ETA: 0:00:16 Cross validating... 51%|████████████████▎ | ETA: 0:00:13 Cross validating... 56%|█████████████████▊ | ETA: 0:00:11 Cross validating... 60%|███████████████████▎ | ETA: 0:00:09 Cross validating... 63%|████████████████████▍ | ETA: 0:00:08 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:07 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:06 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:05 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:03 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:02 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:02 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:01 Cross validating... 100%|████████████████████████████████| Time: 0:00:15 Crossvalidation Results: k MSE 0 1586.7791516113282 1 1257.4022875976561 2 983.1075610351561 3 790.7971337890625 4 648.8489813232422 5 521.6927101135254 6 452.8347903442383 7 366.1281819152832 8 333.3414418029785 9 325.6749143981934 10 320.1107600402832 11 323.60072586059573 12 326.0043437194824 13 327.47797958374025 14 330.84032485961916 15 340.16357879638673 16 345.10634384155276 17 336.8177458190918 18 366.10614624023435 19 354.6035865783691 20 363.93460723876956 Best k = 10 15.793829 seconds (13.49 M allocations: 349.450 MiB, 0.55% gc time, 80.59% 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... 6%|██ | ETA: 0:00:02 Cross validating... 11%|███▌ | ETA: 0:00:02 Cross validating... 16%|█████▏ | ETA: 0:00:02 Cross validating... 19%|██████▏ | 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 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0:00:02 Crossvalidation Results: k MSE 0 1586.7791516113282 1 1307.8691052246093 2 985.6224771118164 3 820.456676940918 4 656.8826132202149 5 521.713705291748 6 461.5891972351074 7 372.445339050293 8 342.0770704650879 9 334.3616665649414 10 330.5085078430176 11 340.0372415161133 12 350.0385090637207 13 351.37051986694337 14 360.09341293334955 15 363.01993972778325 16 371.75573272705077 17 363.48218231201173 18 383.0709933471679 19 393.5946241760254 20 398.67035522460935 Best k = 10 3.107791 seconds (11.74 M allocations: 237.543 MiB, 1.32% gc time, 1.08% compilation time) Test Summary: | Pass Total Time Cross validation on Float32 matrix, normal model | 2 2 20.0s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:36 Cross validating... 6%|██ | ETA: 0:00:20 Cross validating... 8%|██▌ | ETA: 0:00:17 Cross validating... 11%|███▌ | ETA: 0:00:14 Cross validating... 14%|████▋ | ETA: 0:00:11 Cross validating... 17%|█████▋ | ETA: 0:00:10 Cross validating... 19%|██████▏ | ETA: 0:00:09 Cross validating... 22%|███████▏ | ETA: 0:00:08 Cross validating... 25%|████████▏ | ETA: 0:00:07 Cross validating... 29%|█████████▏ | ETA: 0:00:07 Cross validating... 32%|██████████▏ | ETA: 0:00:06 Cross validating... 100%|████████████████████████████████| Time: 0:00:18 Crossvalidation Results: k MSE 0 459.0066651071316 1 416.0378809604273 2 384.44130850116505 3 336.25575423141356 4 311.67389422681606 5 281.80622314150315 6 276.66854851553865 7 272.1808181901199 8 273.77855851639447 9 276.20139302837373 10 277.19624591010256 11 283.6505982634772 12 300.3037858601026 13 293.5765023119455 14 301.50901032292376 15 317.9239768632724 16 306.94002003852427 17 316.8004696205541 18 338.6791104596174 19 328.3813105585096 20 339.72556902822214 Best k = 7 18.992871 seconds (18.88 M allocations: 508.629 MiB, 0.29% gc time, 7.70% 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: 0:00:05 Cross validating... 11%|███▌ | ETA: 0:00:05 Cross validating... 14%|████▋ | ETA: 0:00:05 Cross validating... 17%|█████▋ | ETA: 0:00:05 Cross validating... 21%|██████▋ | ETA: 0:00:04 Cross validating... 24%|███████▋ | ETA: 0:00:04 Cross validating... 25%|████████▏ | ETA: 0:00:04 Cross validating... 29%|█████████▏ | ETA: 0:00:04 Cross validating... 32%|██████████▏ | ETA: 0:00:04 Cross validating... 35%|███████████▏ | ETA: 0:00:04 Cross validating... 38%|████████████▎ | ETA: 0:00:04 Cross validating... 41%|█████████████▎ | ETA: 0:00:03 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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 0 459.0066651071316 1 416.4513910954694 2 386.3251462429434 3 337.2776584080729 4 312.9654032148231 5 283.7729743420137 6 285.5738715638028 7 283.01547545955464 8 286.31283983445445 9 296.66903667659926 10 297.3250047023612 11 319.0119695743417 12 318.75383181386957 13 317.2747011778586 14 328.66162030724286 15 337.60125946460556 16 336.84216095221 17 344.021088062127 18 358.1041018453801 19 354.331821140738 20 375.8303084126951 Best k = 7 6.085647 seconds (19.20 M allocations: 470.937 MiB, 0.65% gc time, 0.40% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, logistic model | 2 2 25.5s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:31 Cross validating... 6%|██ | ETA: 0:00:17 Cross validating... 10%|███ | ETA: 0:00:12 Cross validating... 13%|████▏ | ETA: 0:00:10 Cross validating... 14%|████▋ | ETA: 0:00:09 Cross validating... 17%|█████▋ | ETA: 0:00:08 Cross validating... 21%|██████▋ | ETA: 0:00:07 Cross validating... 24%|███████▋ | ETA: 0:00:06 Cross validating... 27%|████████▋ | ETA: 0:00:06 Cross validating... 30%|█████████▋ | ETA: 0:00:05 Cross validating... 33%|██████████▋ | ETA: 0:00:05 Cross validating... 38%|████████████▎ | ETA: 0:00:04 Cross validating... 40%|████████████▊ | ETA: 0:00:04 Cross validating... 43%|█████████████▊ | ETA: 0:00:04 Cross validating... 46%|██████████████▊ | ETA: 0:00:03 Cross validating... 49%|███████████████▊ | ETA: 0:00:03 Cross validating... 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0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:06 Crossvalidation Results: k MSE 0 461.4974975306281 1 428.13936935433185 2 409.70782853387726 3 386.10573194982874 4 360.44424403986966 5 349.178859418068 6 344.85244391906167 7 350.9384922163893 8 352.05399738161213 9 355.6590768228396 10 357.51617908997173 11 361.05461051155277 12 350.5073978386567 13 361.38522427059706 14 354.17258242515527 15 361.0499901267581 16 357.9497009701521 17 414.97145622711645 18 360.5063824065604 19 379.69183753120933 20 382.5212578769392 Best k = 6 6.963411 seconds (17.08 M allocations: 457.876 MiB, 15.00% gc time, 17.52% 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 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Cross validating... 71%|██████████████████████▉ | ETA: 0:00:01 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:01 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:01 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:01 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:01 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:01 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:00 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:04 Crossvalidation Results: k MSE 0 461.4974975306281 1 428.13979642393576 2 411.07026896432103 3 388.0906974063854 4 363.0676991248116 5 353.0225071301198 6 350.8144380300655 7 363.0119653367674 8 362.02832763166896 9 379.3564101626469 10 389.64549523767863 11 390.38162242683563 12 381.70299903938275 13 397.03634958675843 14 397.49163016354566 15 420.1227525802311 16 420.5732188432005 17 433.5600491153664 18 441.2137014578956 19 437.86643854071485 20 438.8580010393663 Best k = 6 4.955006 seconds (17.69 M allocations: 419.348 MiB, 0.79% gc time, 0.64% compilation time) Test Summary: | Pass Total Time Cross validation on Float64 matrix, logistic model | 2 2 12.5s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:33 Cross validating... 6%|██ | ETA: 0:00:19 Cross validating... 10%|███ | ETA: 0:00:14 Cross validating... 13%|████▏ | ETA: 0:00:11 Cross validating... 16%|█████▏ | ETA: 0:00:10 Cross validating... 19%|██████▏ | ETA: 0:00:09 Cross validating... 22%|███████▏ | ETA: 0:00:08 Cross validating... 25%|████████▏ | ETA: 0:00:07 Cross validating... 29%|█████████▏ | ETA: 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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: 0:00:06 Crossvalidation Results: k MSE 0 745.6343845824972 1 546.3323345777613 2 503.78739319308943 3 427.9715691256423 4 397.41524551557404 5 363.43040615699397 6 363.33887298061774 7 349.11678574100506 8 352.0011933665812 9 346.2287811204038 10 375.0071015405258 11 367.7959203051827 12 378.32401299581005 13 373.66308346387825 14 383.8794351062282 15 394.2948840292068 16 407.7551885726758 17 401.5616051649285 18 388.8805308516596 19 406.30459730791733 20 393.81906313685147 Best k = 9 7.112087 seconds (15.72 M allocations: 403.978 MiB, 0.67% gc time, 18.22% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:04 Cross validating... 6%|██ | ETA: 0:00:05 Cross validating... 10%|███ | ETA: 0:00:05 Cross validating... 13%|████▏ | ETA: 0:00:05 Cross validating... 16%|█████▏ | ETA: 0:00:05 Cross validating... 19%|██████▏ | ETA: 0:00:04 Cross validating... 21%|██████▋ | ETA: 0:00:04 Cross validating... 24%|███████▋ | ETA: 0:00:04 Cross validating... 27%|████████▋ | ETA: 0:00:04 Cross validating... 30%|█████████▋ | ETA: 0:00:04 Cross validating... 33%|██████████▋ | ETA: 0:00:04 Cross validating... 37%|███████████▋ | ETA: 0:00:04 Cross validating... 40%|████████████▊ | ETA: 0:00:03 Cross validating... 43%|█████████████▊ | ETA: 0:00:03 Cross validating... 46%|██████████████▊ | ETA: 0:00:03 Cross 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ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:05 Crossvalidation Results: k MSE 0 745.6343845824972 1 549.0266181716347 2 505.99613995928735 3 431.40314241863587 4 402.1226372673668 5 368.8246488054964 6 363.09734905213946 7 360.50517058305695 8 367.2477440943575 9 366.69775734153654 10 380.68367838267517 11 376.0820570968034 12 388.00308225445303 13 385.22807619673915 14 394.8679219198742 15 408.62905514457145 16 416.00472797363244 17 426.85549782008377 18 421.2474617737672 19 422.0392539912756 20 425.6930283819676 Best k = 7 5.830465 seconds (14.68 M allocations: 330.510 MiB, 0.85% gc time, 0.40% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, Poisson model | 2 2 13.3s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:33 Cross validating... 6%|██ | ETA: 0:00:18 Cross validating... 8%|██▌ | ETA: 0:00:26 Cross validating... 10%|███ | ETA: 0:00:23 Cross validating... 11%|███▌ | ETA: 0:00:27 Cross validating... 13%|████▏ | ETA: 0:00:31 Cross validating... 14%|████▋ | ETA: 0:00:33 Cross validating... 16%|█████▏ | ETA: 0:00:35 Cross validating... 17%|█████▋ | ETA: 0:00:32 Cross validating... 19%|██████▏ | ETA: 0:00:29 Cross validating... 21%|██████▋ | ETA: 0:00:27 Cross validating... 22%|███████▏ | ETA: 0:00:25 Cross validating... 24%|███████▋ | ETA: 0:00:26 Cross validating... 25%|████████▏ | ETA: 0:00:27 Cross validating... 27%|████████▋ | ETA: 0:00:26 Cross validating... 29%|█████████▏ | ETA: 0:00:26 Cross validating... 30%|█████████▋ | ETA: 0:00:27 Cross validating... 32%|██████████▏ | ETA: 0:00:27 Cross validating... 33%|██████████▋ | ETA: 0:00:26 Cross validating... 37%|███████████▋ | ETA: 0:00:22 Cross validating... 40%|████████████▊ | ETA: 0:00:20 Cross 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validating... 97%|███████████████████████████████ | ETA: 0:00:01 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:01 Cross validating... 100%|████████████████████████████████| Time: 0:00:47 Crossvalidation Results: k MSE 0 382.77007080896493 1 305.9560046222957 2 279.606915685143 3 249.0271982453664 4 234.53474970991536 5 225.91187350575498 6 225.81418362558148 7 227.0282353828673 8 228.25205391878794 9 230.6321422168829 10 231.71044232758817 11 234.4982227120055 12 232.31748370902122 13 235.98868501944594 14 233.16686991049238 15 231.63782767039916 16 234.04233701783193 17 239.26282765941616 18 239.67282074597864 19 235.76688853725955 20 240.528270217545 Best k = 6 48.403589 seconds (159.24 M allocations: 4.628 GiB, 0.42% gc time, 2.42% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:04 Cross validating... 5%|█▌ | ETA: 0:00:04 Cross validating... 8%|██▌ | ETA: 0:00:05 Cross validating... 10%|███ | ETA: 0:00:05 Cross validating... 11%|███▌ | ETA: 0:00:05 Cross validating... 13%|████▏ | ETA: 0:00:05 Cross validating... 14%|████▋ | ETA: 0:00:05 Cross validating... 16%|█████▏ | ETA: 0:00:06 Cross validating... 17%|█████▋ | ETA: 0:00:06 Cross validating... 19%|██████▏ | ETA: 0:00:06 Cross validating... 21%|██████▋ | ETA: 0:00:06 Cross validating... 22%|███████▏ | ETA: 0:00:06 Cross validating... 24%|███████▋ | ETA: 0:00:06 Cross validating... 25%|████████▏ | ETA: 0:00:07 Cross validating... 27%|████████▋ | ETA: 0:00:07 Cross validating... 29%|█████████▏ | ETA: 0:00:07 Cross validating... 30%|█████████▋ | ETA: 0:00:07 Cross validating... 32%|██████████▏ | ETA: 0:00:07 Cross validating... 33%|██████████▋ | ETA: 0:00:07 Cross validating... 37%|███████████▋ | ETA: 0:00:06 Cross 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95%|██████████████████████████████▌ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:10 Crossvalidation Results: k MSE 0 382.77007080896493 1 307.2940344015137 2 283.38563268048813 3 250.4852681434865 4 236.05672099348263 5 228.09660643367062 6 229.15897146911237 7 234.23981110657525 8 236.5085426886501 9 248.3110710139896 10 251.4331536936137 11 255.86758257186105 12 249.4552004853629 13 254.81642757102196 14 257.4743252404544 15 262.5539763585556 16 264.9384416004999 17 266.6211218074451 18 270.6345299852351 19 271.02531340873475 20 278.3984058725224 Best k = 5 10.571482 seconds (31.37 M allocations: 737.493 MiB, 0.58% gc time, 0.23% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, NegativeBinomial model | 2 2 59.4s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:40 Cross validating... 6%|██ | ETA: 0:00:21 Cross validating... 10%|███ | ETA: 0:00:15 Cross validating... 14%|████▋ | ETA: 0:00:10 Cross validating... 17%|█████▋ | ETA: 0:00:09 Cross validating... 21%|██████▋ | ETA: 0:00:08 Cross validating... 24%|███████▋ | ETA: 0:00:07 Cross validating... 27%|████████▋ | ETA: 0:00:06 Cross validating... 30%|█████████▋ | ETA: 0:00:05 Cross validating... 33%|██████████▋ | ETA: 0:00:05 Cross validating... 38%|████████████▎ | ETA: 0:00:04 Cross validating... 41%|█████████████▎ | ETA: 0:00:04 Cross validating... 44%|██████████████▎ | ETA: 0:00:04 Cross validating... 48%|███████████████▎ | ETA: 0:00:03 Cross validating... 51%|████████████████▎ | ETA: 0:00:03 Cross validating... 54%|█████████████████▎ | ETA: 0:00:03 Cross validating... 57%|██████████████████▎ | ETA: 0:00:02 Cross validating... 60%|███████████████████▎ | ETA: 0:00:02 Cross validating... 63%|████████████████████▍ | ETA: 0:00:02 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:02 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:02 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:01 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:01 Cross validating... 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 0 727.2352371826172 1 625.3318281860352 2 555.4637250061035 3 442.782374420166 4 361.465425201416 5 305.9858067932129 6 269.4161679534912 7 234.81090499877928 8 224.14337092590333 9 225.74375103759766 10 227.04923620605467 11 229.9636925354004 12 233.22000840759276 13 234.5388558959961 14 252.85983618164062 15 241.37099768066406 16 250.11475730895998 17 246.87874307250976 18 228.40458023071287 19 252.00773777770996 20 243.57044248962404 Best k = 8 5.407106 seconds (17.77 M allocations: 379.717 MiB, 1.28% gc time, 29.42% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 5%|█▌ | ETA: 0:00:02 Cross validating... 8%|██▌ | ETA: 0:00:03 Cross validating... 11%|███▌ | ETA: 0:00:03 Cross validating... 14%|████▋ | ETA: 0:00:03 Cross validating... 17%|█████▋ | ETA: 0:00:03 Cross validating... 21%|██████▋ | ETA: 0:00:03 Cross validating... 24%|███████▋ | ETA: 0:00:03 Cross validating... 27%|████████▋ | ETA: 0:00:03 Cross validating... 30%|█████████▋ | ETA: 0:00:02 Cross validating... 33%|██████████▋ | ETA: 0:00:02 Cross validating... 38%|████████████▎ | ETA: 0:00:02 Cross validating... 41%|█████████████▎ | ETA: 0:00:02 Cross validating... 44%|██████████████▎ | ETA: 0:00:02 Cross validating... 48%|███████████████▎ | ETA: 0:00:02 Cross validating... 51%|████████████████▎ | ETA: 0:00:02 Cross validating... 54%|█████████████████▎ | ETA: 0:00:02 Cross validating... 57%|██████████████████▎ | ETA: 0:00:02 Cross validating... 60%|███████████████████▎ | ETA: 0:00:01 Cross validating... 63%|████████████████████▍ | ETA: 0:00:01 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:01 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:01 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:01 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:01 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:01 Cross validating... 84%|██████████████████████████▉ | 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: 0:00:03 Crossvalidation Results: k MSE 0 727.2352371826172 1 602.3721643371582 2 539.0958049011231 3 427.0158553161621 4 352.6532766723633 5 304.4845976409912 6 268.2629245300293 7 236.68222570800782 8 226.1005362701416 9 232.472183883667 10 235.7863609008789 11 241.0907580871582 12 243.97056771850586 13 247.2414393005371 14 255.25111973571774 15 256.67198440551755 16 259.67903814697263 17 257.49018920898436 18 253.48160185241701 19 264.7414868774414 20 267.0213729400635 Best k = 8 3.756029 seconds (17.20 M allocations: 333.531 MiB, 1.48% gc time, 0.91% compilation time) Test Summary: | Pass Total Time Cross validation on floating point matrices, NegativeBinomial model | 2 2 9.5s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 2%|▋ | ETA: 0:00:59 Cross validating... 3%|█ | ETA: 0:00:45 Cross validating... 4%|█▎ | ETA: 0:00:39 Cross validating... 5%|█▋ | ETA: 0:00:36 Cross validating... 6%|█▉ | ETA: 0:00:34 Cross validating... 7%|██▎ | ETA: 0:00:33 Cross validating... 8%|██▌ | ETA: 0:00:32 Cross validating... 9%|██▉ | ETA: 0:00:32 Cross validating... 10%|███▎ | ETA: 0:00:32 Cross validating... 11%|███▌ | ETA: 0:00:31 Cross validating... 12%|███▉ | ETA: 0:00:31 Cross validating... 13%|████▏ | ETA: 0:00:31 Cross validating... 14%|████▌ | ETA: 0:00:30 Cross validating... 15%|████▊ | 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100%|████████████████████████████████| Time: 0:00:32 Crossvalidation Results: k MSE 1 2923.915298828888 2 2602.202541932896 3 2306.8513107687986 4 2130.006433352069 5 2071.5451762006655 6 1984.6508833096382 7 1937.2650470163585 8 1926.1953797415026 9 1937.568788479048 10 1958.391868278116 11 1971.9516166977298 12 1986.0196232867675 13 1997.0729495357173 14 1977.6584776866173 15 1993.1378520228395 16 2018.7628919933675 17 2039.5432060878006 18 2045.60254949115 19 2065.8681606746018 20 2075.6602382369233 Best k = 8 33.055013 seconds (328.28 k allocations: 474.872 MiB, 0.17% gc time, 2.90% compilation time) Test Summary: | Pass Total Time multivariate cross validation SnpLinAlg | 3 3 36.3s Test Summary: | Pass Total Time wrapper univariate | 20 20 1m19.3s **** 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... 2%|▋ | ETA: 0:00:20 Cross validating... 3%|█ | ETA: 0:00:19 Cross validating... 4%|█▎ | ETA: 0:00:21 Cross validating... 5%|█▋ | ETA: 0:00:20 Cross validating... 6%|█▉ | ETA: 0:00:23 Cross validating... 7%|██▎ | ETA: 0:00:24 Cross validating... 8%|██▌ | ETA: 0:00:24 Cross validating... 9%|██▉ | ETA: 0:00:26 Cross validating... 10%|███▎ | ETA: 0:00:27 Cross validating... 11%|███▌ | ETA: 0:00:27 Cross validating... 12%|███▉ | ETA: 0:00:27 Cross validating... 13%|████▏ | ETA: 0:00:28 Cross validating... 14%|████▌ | ETA: 0:00:28 Cross validating... 15%|████▊ | ETA: 0:00:31 Cross validating... 16%|█████▏ | ETA: 0:00:32 Cross validating... 17%|█████▌ | ETA: 0:00:32 Cross validating... 18%|█████▊ | ETA: 0:00:33 Cross validating... 19%|██████▏ | ETA: 0:00:34 Cross validating... 20%|██████▍ | ETA: 0:00:34 Cross validating... 21%|██████▊ | ETA: 0:00:33 Cross validating... 22%|███████ | ETA: 0:00:32 Cross validating... 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2186.316288272038 14 2203.704554775872 15 2216.007861148507 16 2219.0864904635287 17 2226.9002968977798 18 2213.193277562036 19 2234.064675154158 20 2245.124287391089 Best k = 6 **** 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: 0:00:19 Cross validating... 3%|█ | ETA: 0:00:19 Cross validating... 4%|█▎ | ETA: 0:00:21 Cross validating... 5%|█▋ | ETA: 0:00:20 Cross validating... 6%|█▉ | ETA: 0:00:22 Cross validating... 7%|██▎ | ETA: 0:00:23 Cross validating... 8%|██▌ | ETA: 0:00:24 Cross validating... 9%|██▉ | ETA: 0:00:25 Cross validating... 10%|███▎ | ETA: 0:00:26 Cross validating... 11%|███▌ | ETA: 0:00:26 Cross validating... 12%|███▉ | ETA: 0:00:26 Cross validating... 13%|████▏ | ETA: 0:00:27 Cross validating... 14%|████▌ | ETA: 0:00:27 Cross 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99%|███████████████████████████████▋| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:42 Crossvalidation Results: k MSE 1 2849.383229379955 2 2524.303106109175 3 2312.799164395459 4 2230.747234917732 5 2083.421861525868 6 2075.7860282241654 7 2080.295568366649 8 2096.5527441552867 9 2103.7789161312476 10 2146.932938567968 11 2136.233335135846 12 2157.0997044352102 13 2186.316288272038 14 2203.704554775872 15 2216.007861148507 16 2219.0864904635287 17 2226.9002968977798 18 2213.193277562036 19 2234.064675154158 20 2245.124287391089 Best k = 6 **** 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: 0:00:18 Cross validating... 3%|█ | ETA: 0:00:19 Cross validating... 4%|█▎ | ETA: 0:00:20 Cross validating... 5%|█▋ | ETA: 0:00:21 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94%|██████████████████████████████▏ | ETA: 0:00:02 Cross validating... 95%|██████████████████████████████▍ | ETA: 0:00:02 Cross validating... 96%|██████████████████████████████▊ | ETA: 0:00:02 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:01 Cross validating... 98%|███████████████████████████████▍| ETA: 0:00:01 Cross validating... 99%|███████████████████████████████▋| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:42 Crossvalidation Results: k MSE 1 2849.383229379955 2 2524.303106109175 3 2312.799164395459 4 2230.747234917732 5 2083.421861525868 6 2075.7860282241654 7 2080.295568366649 8 2096.5527441552867 9 2103.7789161312476 10 2146.932938567968 11 2136.233335135846 12 2157.0997044352102 13 2186.316288272038 14 2203.704554775872 15 2216.007861148507 16 2219.0864904635287 17 2226.9002968977798 18 2213.193277562036 19 2234.064675154158 20 2245.124287391089 Best k = 6 Test Summary: | Pass Total Time wrapper multivariate | 8 8 2m24.8s 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:35 [2] process(codec::CodecZlib.ZlibDecompressor, input::TranscodingStreams.Memory, output::TranscodingStreams.Memory, error_ref::TranscodingStreams.Error) @ CodecZlib ~/.julia/packages/CodecZlib/lEc2s/src/decompression.jl:186 [3] decompress(io::IOStream, v::Variant, h::BGEN.Header; decompressed::Nothing) @ BGEN ~/.julia/packages/BGEN/dfgRU/src/genotypes.jl:72 [4] decompress @ ~/.julia/packages/BGEN/dfgRU/src/genotypes.jl:42 [inlined] [5] first_allele_dosage!(b::Bgen, v::Variant; T::Type, mean_impute::Bool, clear_decompressed::Bool, data::Nothing, decompressed::Nothing, is_decompressed::Bool) @ BGEN ~/.julia/packages/BGEN/dfgRU/src/genotypes.jl:571 [6] first_allele_dosage! @ ~/.julia/packages/BGEN/dfgRU/src/genotypes.jl:549 [inlined] [7] convert_bgen_gt(t::Type{Float64}, b::Bgen) @ MendelIHT ~/.julia/packages/MendelIHT/ZcxZT/src/wrapper.jl:380 [8] macro expansion @ ./timing.jl:279 [inlined] [9] macro expansion @ ~/.julia/packages/MendelIHT/ZcxZT/test/wrapper_test.jl:187 [inlined] [10] macro expansion @ /opt/julia/share/julia/stdlib/v1.10/Test/src/Test.jl:1582 [inlined] [11] top-level scope @ ~/.julia/packages/MendelIHT/ZcxZT/test/wrapper_test.jl:185 [12] include(fname::String) @ Base.MainInclude ./client.jl:487 [13] top-level scope @ ~/.julia/packages/MendelIHT/ZcxZT/test/runtests.jl:20 [14] include(fname::String) @ Base.MainInclude ./client.jl:487 [15] top-level scope @ none:6 Test Summary: | Error Total Time read BGEN and VCF | 1 1 5.9s 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 1003.74s ERROR: LoadError: Package MendelIHT errored during testing Stacktrace: [1] pkgerror(msg::String) @ Pkg.Types /opt/julia/share/julia/stdlib/v1.10/Pkg/src/Types.jl:70 [2] test(ctx::Pkg.Types.Context, pkgs::Vector{Pkg.Types.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/v1.10/Pkg/src/Operations.jl:2034 [3] test @ /opt/julia/share/julia/stdlib/v1.10/Pkg/src/Operations.jl:1915 [inlined] [4] test(ctx::Pkg.Types.Context, pkgs::Vector{Pkg.Types.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::Base.PipeEndpoint}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.10/Pkg/src/API.jl:444 [5] test(pkgs::Vector{Pkg.Types.PackageSpec}; io::Base.PipeEndpoint, kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.10/Pkg/src/API.jl:159 [6] test @ /opt/julia/share/julia/stdlib/v1.10/Pkg/src/API.jl:147 [inlined] [7] #test#74 @ /opt/julia/share/julia/stdlib/v1.10/Pkg/src/API.jl:146 [inlined] [8] top-level scope @ /PkgEval.jl/scripts/evaluate.jl:223 in expression starting at /PkgEval.jl/scripts/evaluate.jl:214 PkgEval failed after 1243.11s: package tests unexpectedly errored