Package evaluation of MendelIHT on Julia 1.10.8 (92f03a4775*) started at 2025-02-25T13:46:07.468 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 5.18s ################################################################################ # 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 v0.1.41 [79e6a3ab] + Adapt v4.2.0 [66dad0bd] + AliasTables v1.1.3 [4fba245c] + ArrayInterface v7.18.0 ⌅ [67c07d97] + Automa v0.8.4 ⌅ [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 v0.2.6 [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 v0.8.6 [861a8166] + Combinatorics v1.0.2 [38540f10] + CommonSolve v0.2.4 [f70d9fcc] + CommonWorldInvalidations v1.0.0 [34da2185] + Compat v4.16.0 [a33af91c] + CompositionsBase v0.1.2 [187b0558] + ConstructionBase v1.5.8 [adafc99b] + CpuId v0.3.1 [a8cc5b0e] + Crayons v4.1.1 [a10d1c49] + DBInterface v2.6.1 [9a962f9c] + DataAPI v1.16.0 [a93c6f00] + DataFrames v1.7.0 [864edb3b] + DataStructures v0.18.20 [e2d170a0] + DataValueInterfaces v1.0.0 [8bb1440f] + DelimitedFiles v1.9.1 [b4f34e82] + Distances v0.10.12 [31c24e10] + Distributions v0.25.117 [ffbed154] + DocStringExtensions v0.9.3 [48062228] + FilePathsBase v0.9.23 [1a297f60] + FillArrays v1.13.0 [38e38edf] + GLM v1.9.0 [c27321d9] + Glob v1.3.1 [3e5b6fbb] + HostCPUFeatures v0.1.17 [34004b35] + HypergeometricFunctions v0.3.27 [09f84164] + HypothesisTests v0.11.3 [615f187c] + IfElse v0.1.1 [842dd82b] + InlineStrings v1.4.3 [3587e190] + InverseFunctions v0.1.17 [41ab1584] + InvertedIndices v1.3.1 [92d709cd] + IrrationalConstants v0.2.4 [82899510] + IteratorInterfaceExtensions v1.0.0 [692b3bcd] + JLLWrappers v1.7.0 [b964fa9f] + LaTeXStrings v1.4.0 [10f19ff3] + LayoutPointers v0.1.17 [2ab3a3ac] + LogExpFunctions v0.3.29 [bdcacae8] + LoopVectorization v0.12.171 [1914dd2f] + MacroTools v0.5.15 [d125e4d3] + ManualMemory v0.1.8 [921c7187] + MendelIHT v1.4.11 [e1d29d7a] + Missings v1.2.0 [6fe1bfb0] + OffsetArrays v1.15.0 [bac558e1] + OrderedCollections v1.8.0 [90014a1f] + PDMats v0.11.32 [69de0a69] + Parsers v2.8.1 [1d0040c9] + PolyesterWeave v0.2.2 [2dfb63ee] + PooledArrays v1.4.3 [aea7be01] + PrecompileTools v1.2.1 [21216c6a] + Preferences v1.4.3 [08abe8d2] + PrettyTables v2.4.0 [92933f4c] + ProgressMeter v1.10.2 [43287f4e] + PtrArrays v1.3.0 [1fd47b50] + QuadGK v2.11.2 [189a3867] + Reexport v1.2.2 [ae029012] + Requires v1.3.0 [79098fc4] + Rmath v0.8.0 [f2b01f46] + Roots v2.2.5 [fdea26ae] + SIMD v3.7.1 [94e857df] + SIMDTypes v0.1.0 [476501e8] + SLEEFPirates v0.6.43 [0aa819cd] + SQLite v1.6.1 [91c51154] + SentinelArrays v1.4.8 [1277b4bf] + ShiftedArrays v2.0.0 [4e780e97] + SnpArrays v0.3.22 [a2af1166] + SortingAlgorithms v1.2.1 [276daf66] + SpecialFunctions v2.5.0 [aedffcd0] + Static v1.1.1 [0d7ed370] + StaticArrayInterface v1.8.0 [82ae8749] + StatsAPI v1.7.0 [2913bbd2] + StatsBase v0.34.4 [4c63d2b9] + StatsFuns v1.3.2 [3eaba693] + StatsModels v0.7.4 [892a3eda] + StringManipulation v0.4.1 [3783bdb8] + TableTraits v1.0.1 [bd369af6] + Tables v1.12.0 [8290d209] + ThreadingUtilities v0.5.2 ⌅ [3bb67fe8] + TranscodingStreams v0.9.13 [3a884ed6] + UnPack v1.0.2 [a620830f] + VCFTools v0.2.10 [28eba6e3] + VariantCallFormat v0.5.6 [3d5dd08c] + VectorizationBase v0.21.71 [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 v3.48.0+0 [ffd25f8a] + XZ_jll v5.6.4+1 [3161d3a3] + Zstd_jll v1.5.7+1 [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 v2.28.2+1 [14a3606d] + MozillaCACerts_jll v2023.1.10 [4536629a] + OpenBLAS_jll v0.3.23+4 [05823500] + OpenLibm_jll v0.8.1+4 [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 7.59s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompilation completed after 95.63s ################################################################################ # Testing # Testing MendelIHT Status `/tmp/jl_qNBa9n/Project.toml` ⌅ [6db4b851] BGEN v0.1.17 [6e4b80f9] BenchmarkTools v1.6.0 [336ed68f] CSV v0.10.15 [a93c6f00] DataFrames v1.7.0 [8bb1440f] DelimitedFiles v1.9.1 [b4f34e82] Distances v0.10.12 [31c24e10] Distributions v0.25.117 [38e38edf] GLM v1.9.0 [921c7187] MendelIHT v1.4.11 [92933f4c] ProgressMeter v1.10.2 [189a3867] Reexport v1.2.2 [4e780e97] SnpArrays v0.3.22 [276daf66] SpecialFunctions v2.5.0 [2913bbd2] StatsBase v0.34.4 [a620830f] VCFTools v0.2.10 [37e2e46d] LinearAlgebra [44cfe95a] Pkg v1.10.0 [9a3f8284] Random [8dfed614] Test Status `/tmp/jl_qNBa9n/Manifest.toml` [7d9f7c33] Accessors v0.1.41 [79e6a3ab] Adapt v4.2.0 [66dad0bd] AliasTables v1.1.3 [4fba245c] ArrayInterface v7.18.0 ⌅ [67c07d97] Automa v0.8.4 ⌅ [6db4b851] BGEN v0.1.17 [28d598bf] BGZFStreams v0.3.2 [6e4b80f9] BenchmarkTools v1.6.0 [47718e42] 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[34004b35] HypergeometricFunctions v0.3.27 [09f84164] HypothesisTests v0.11.3 [615f187c] IfElse v0.1.1 [842dd82b] InlineStrings v1.4.3 [3587e190] InverseFunctions v0.1.17 [41ab1584] InvertedIndices v1.3.1 [92d709cd] IrrationalConstants v0.2.4 [82899510] IteratorInterfaceExtensions v1.0.0 [692b3bcd] JLLWrappers v1.7.0 [682c06a0] JSON v0.21.4 [b964fa9f] LaTeXStrings v1.4.0 [10f19ff3] LayoutPointers v0.1.17 [2ab3a3ac] LogExpFunctions v0.3.29 [bdcacae8] LoopVectorization v0.12.171 [1914dd2f] MacroTools v0.5.15 [d125e4d3] ManualMemory v0.1.8 [921c7187] MendelIHT v1.4.11 [e1d29d7a] Missings v1.2.0 [6fe1bfb0] OffsetArrays v1.15.0 [bac558e1] OrderedCollections v1.8.0 [90014a1f] PDMats v0.11.32 [69de0a69] Parsers v2.8.1 [1d0040c9] PolyesterWeave v0.2.2 [2dfb63ee] PooledArrays v1.4.3 [aea7be01] PrecompileTools v1.2.1 [21216c6a] Preferences v1.4.3 [08abe8d2] PrettyTables v2.4.0 [92933f4c] ProgressMeter v1.10.2 [43287f4e] PtrArrays v1.3.0 [1fd47b50] QuadGK v2.11.2 [189a3867] Reexport v1.2.2 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MozillaCACerts_jll v2023.1.10 [4536629a] OpenBLAS_jll v0.3.23+4 [05823500] OpenLibm_jll v0.8.1+4 [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 10.1s Test Summary: | Pass Total Time deviance | 1 1 0.2s Test Summary: | Pass Total Time update_μ! | 4 4 0.6s Test Summary: | Pass Total Time _choose! | 7 7 3.3s 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 1.2s Test Summary: | Pass Total Time maf_weights | 6 6 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 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 = -1941.2118451725744, backtracks = 0, tol = 2.0916791361707885 Iteration 2: loglikelihood = -1445.6972781027728, backtracks = 0, tol = 0.1808961117397348 Iteration 3: loglikelihood = -1398.5783699711824, backtracks = 0, tol = 0.05251238609432768 Iteration 4: loglikelihood = -1398.1015101489497, backtracks = 0, tol = 0.005425455775451148 Iteration 5: loglikelihood = -1398.0918343938063, backtracks = 0, tol = 0.0006790046165418766 Iteration 6: loglikelihood = -1398.0916028154143, backtracks = 0, tol = 0.00013903844563055028 Iteration 7: loglikelihood = -1398.0915963382263, backtracks = 0, tol = 1.7407826086848427e-5 IHT estimated 10 nonzero SNP predictors and 1 non-genetic predictors. Compute time (sec): 0.0629880428314209 Final loglikelihood: -1398.0915963382263 SNP PVE: 0.9498077068040098 Iterations: 7 Selected genetic predictors: 10×2 DataFrame Row │ Position Estimated_β │ Int64 Float64 ─────┼─────────────────────── 1 │ 44 -1.23973 2 │ 3476 1.66416 3 │ 5520 -1.81242 4 │ 5811 0.55403 5 │ 6001 0.455946 6 │ 7440 1.72346 7 │ 7609 -0.450165 8 │ 7628 -2.49942 9 │ 8624 -1.24154 10 │ 9767 -0.327881 Selected nongenetic predictors: 1×2 DataFrame Row │ Position Estimated_β │ Int64 Float64 ─────┼─────────────────────── 1 │ 1 0.0215726Test Summary: | Pass Total Time fit normal SnpLinAlg | 4 4 10.3s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse 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 = -2987.5072579956113, backtracks = 0, tol = 0.32328447895212004 Iteration 2: loglikelihood = -2200.8560382383625, backtracks = 0, tol = 0.04580053368428095 Iteration 3: loglikelihood = -1831.0225090302392, backtracks = 0, tol = 0.04694182300831291 Iteration 4: loglikelihood = -1593.7342999073103, backtracks = 0, tol = 0.06273103139253437 Iteration 5: loglikelihood = -1491.5005860202934, backtracks = 0, tol = 0.10749909897157366 Iteration 6: loglikelihood = -1440.7553647060822, backtracks = 0, tol = 0.07153845004659207 Iteration 7: loglikelihood = -1411.9827423161753, backtracks = 0, tol = 0.05485727316172249 Iteration 8: loglikelihood = -1372.691149495042, backtracks = 0, tol = 0.09244037479949986 Iteration 9: loglikelihood = -1359.9508282354939, backtracks = 0, tol = 0.038854193084251615 Iteration 10: loglikelihood = -1348.1943354101106, backtracks = 0, tol = 0.052170342822141585 Iteration 11: loglikelihood = -1343.193051325501, backtracks = 0, tol = 0.025622897806501663 Iteration 12: loglikelihood = -1340.070900237143, backtracks = 0, tol = 0.015253583710069638 Iteration 13: loglikelihood = -1338.071743437447, backtracks = 0, tol = 0.016351662012729667 Iteration 14: loglikelihood = -1336.6876144600335, backtracks = 0, tol = 0.0104795725469362 Iteration 15: loglikelihood = -1335.7698365985127, backtracks = 0, tol = 0.0105820535034471 Iteration 16: loglikelihood = -1335.1382695244201, backtracks = 0, tol = 0.007179754082903604 Iteration 17: loglikelihood = -1334.7225220886235, backtracks = 0, tol = 0.006864661602858823 Iteration 18: loglikelihood = -1334.4414865042127, backtracks = 0, tol = 0.0048485526457085195 Iteration 19: loglikelihood = -1334.2585727593919, backtracks = 0, tol = 0.004436227183601783 Iteration 20: loglikelihood = -1334.1371909558602, backtracks = 0, tol = 0.003219229809664083 Iteration 21: loglikelihood = -1334.0589827640667, backtracks = 0, tol = 0.0028497852875863173 Iteration 22: loglikelihood = -1334.0078977838346, backtracks = 0, tol = 0.0021042501997192782 Iteration 23: loglikelihood = -1333.975238911465, backtracks = 0, tol = 0.0018199555459560974 Iteration 24: loglikelihood = -1333.9541642737686, backtracks = 0, tol = 0.001358563906824122 Iteration 25: loglikelihood = -1333.9407663157085, backtracks = 0, tol = 0.0011567183274273985 Iteration 26: loglikelihood = -1333.9321958009893, backtracks = 0, tol = 0.0008693402957841064 Iteration 27: loglikelihood = -1333.9267679879413, backtracks = 0, tol = 0.0007325824333620594 Iteration 28: loglikelihood = -1333.9233165834555, backtracks = 0, tol = 0.0005529003299143231 Iteration 29: loglikelihood = -1333.9211363016443, backtracks = 0, tol = 0.0004628235587541728 Iteration 30: loglikelihood = -1333.9197554165155, backtracks = 0, tol = 0.00035022232014583505 Iteration 31: loglikelihood = -1333.9188845370443, backtracks = 0, tol = 0.00029191563183376983 Iteration 32: loglikelihood = -1333.9183343902769, backtracks = 0, tol = 0.00022125650931213202 Iteration 33: loglikelihood = -1333.91798779798, backtracks = 0, tol = 0.00018392037351381486 Iteration 34: loglikelihood = -1333.9177692150238, backtracks = 0, tol = 0.0001395445720745179 Iteration 35: loglikelihood = -1333.917631600795, backtracks = 0, tol = 0.00011579760321801179 Iteration 36: loglikelihood = -1333.9175449047063, backtracks = 0, tol = 8.791463748456188e-5 Test Summary: | Pass Total Time fit Poisson SnpLinAlg | 4 4 1.6s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse 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 = -1687.2742339336523, backtracks = 0, tol = 0.32814121989999867 Iteration 2: loglikelihood = -1581.564224299248, backtracks = 0, tol = 0.21455475234388194 Iteration 3: loglikelihood = -1545.7575678526161, backtracks = 0, tol = 0.15130690136205352 Iteration 4: loglikelihood = -1542.5259906111228, backtracks = 0, tol = 0.08421375433138932 Iteration 5: loglikelihood = -1538.700164606461, backtracks = 0, tol = 0.08066960858075746 Iteration 6: loglikelihood = -1538.4516389119633, backtracks = 1, tol = 0.00832323076109721 Iteration 7: loglikelihood = -1538.3644880374986, backtracks = 1, tol = 0.004200242644022148 Iteration 8: loglikelihood = -1538.3469120811058, backtracks = 2, tol = 0.0015945884863727232 Iteration 9: loglikelihood = -1538.3366263385165, backtracks = 2, tol = 0.0012560438826384691 Iteration 10: loglikelihood = -1538.3307052704074, backtracks = 2, tol = 0.0009680511228813363 Iteration 11: loglikelihood = -1538.327332560136, backtracks = 2, tol = 0.0007360609706336963 Iteration 12: loglikelihood = -1538.3254228343235, backtracks = 2, tol = 0.0005555241896579401 Iteration 13: loglikelihood = -1538.3243448456326, backtracks = 2, tol = 0.00041770624875520264 Iteration 14: loglikelihood = -1538.3237372880635, backtracks = 2, tol = 0.00031353352080617093 Iteration 15: loglikelihood = -1538.323395120144, backtracks = 2, tol = 0.0002351679177513713 Iteration 16: loglikelihood = -1538.3232024820325, backtracks = 2, tol = 0.00017634437806160553 Iteration 17: loglikelihood = -1538.3230940445328, backtracks = 2, tol = 0.0001322295408673703 Iteration 18: loglikelihood = -1538.3230330079423, backtracks = 2, tol = 9.915554672800646e-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 = -1859.4478353671236, backtracks = 0, tol = 0.8775734538239128 Iteration 2: loglikelihood = -1434.4692063937307, backtracks = 0, tol = 0.13738320529802645 Iteration 3: loglikelihood = -1383.0805216821739, backtracks = 0, tol = 0.046476498474094685 Iteration 4: loglikelihood = -1381.503009879947, backtracks = 0, tol = 0.02654499809653186 Iteration 5: loglikelihood = -1381.204977840103, backtracks = 0, tol = 0.003024855777909187 Iteration 6: loglikelihood = -1380.7001764054983, backtracks = 0, tol = 0.02734438948225774 Iteration 7: loglikelihood = -1380.452105966716, backtracks = 0, tol = 0.0023422951090211397 Iteration 8: loglikelihood = -1380.450089269163, backtracks = 1, tol = 0.00013565704078993119 Iteration 9: loglikelihood = -1380.4495524833378, backtracks = 1, tol = 6.673811511276762e-5 Test Summary: | Pass Total Time fit with >1 non-genetic covariates SnpLinAlg | 5 5 1.2s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse linear regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1603.5918501890287, backtracks = 0, tol = 0.4407707596037506 Iteration 2: loglikelihood = -1405.014053881761, backtracks = 0, tol = 0.10763375407887524 Iteration 3: loglikelihood = -1384.190245384787, backtracks = 0, tol = 0.03653698711656954 Iteration 4: loglikelihood = -1383.1636965842508, backtracks = 0, tol = 0.004850706818045008 Iteration 5: loglikelihood = -1382.8666244439332, backtracks = 0, tol = 0.02969291527677356 Iteration 6: loglikelihood = -1382.5408953414524, backtracks = 0, tol = 0.003332444796492627 Iteration 7: loglikelihood = -1382.538334183823, backtracks = 1, tol = 0.00019992514067338935 Iteration 8: loglikelihood = -1382.537660293881, backtracks = 1, tol = 9.466920350064336e-5 Test Summary: | Pass Total Time model selection on non-genetic covariates | 5 5 0.8s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse linear regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 15 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -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 4.9s **** 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 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 = -1366.5596481757862, backtracks = 0, tol = 0.16768686253242943 Iteration 2: loglikelihood = -1340.7513984386871, backtracks = 0, tol = 0.07865167018025121 Iteration 3: loglikelihood = -1310.6647555371267, backtracks = 0, tol = 0.10085486801471222 Iteration 4: loglikelihood = -1303.33568200531, backtracks = 1, tol = 0.029141518177380796 Iteration 5: loglikelihood = -1299.8501524210621, backtracks = 1, tol = 0.023513700008306118 Iteration 6: loglikelihood = -1293.6060642572104, backtracks = 1, tol = 0.08942256108982304 Iteration 7: loglikelihood = -1288.5883225413477, backtracks = 0, tol = 0.06209315270864074 Iteration 8: loglikelihood = -1288.066287061872, backtracks = 0, tol = 0.01762028584366617 Iteration 9: loglikelihood = -1287.754637780227, backtracks = 0, tol = 0.08941885338578096 Iteration 10: loglikelihood = -1287.0837215838358, backtracks = 0, tol = 0.014039320472856135 Iteration 11: loglikelihood = -1287.0126024972826, backtracks = 0, tol = 0.08528036401067093 Iteration 12: loglikelihood = -1286.7170332473781, backtracks = 0, tol = 0.00954792060185618 Iteration 13: loglikelihood = -1286.7145443931217, backtracks = 1, tol = 0.0007128850818483489 Iteration 14: loglikelihood = -1286.7134773010573, backtracks = 1, tol = 0.00043890516576666825 Iteration 15: loglikelihood = -1286.7131247190446, backtracks = 1, tol = 0.00030383659205756317 Iteration 16: loglikelihood = -1286.71306744025, backtracks = 2, tol = 9.560314642094546e-5 0.574197 seconds (3.26 M allocations: 58.994 MiB, 44.48% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse NegativeBinomial regression Number of threads = 1 Link functin = LogLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1416.0897942609593, backtracks = 0, tol = 0.16768686253242943 Iteration 2: loglikelihood = -1391.1155052778117, backtracks = 0, tol = 0.11919879295717063 Iteration 3: loglikelihood = -1386.1151704099673, backtracks = 0, tol = 0.14009790390510996 Iteration 4: loglikelihood = -1362.0242330067422, backtracks = 0, tol = 0.08185397717027652 Iteration 5: loglikelihood = -1346.9889931423245, backtracks = 0, tol = 0.09391516375289863 Iteration 6: loglikelihood = -1337.3625596929649, backtracks = 0, tol = 0.08960404357354172 Iteration 7: loglikelihood = -1333.0397375603704, backtracks = 0, tol = 0.08735705234336329 Iteration 8: loglikelihood = -1327.3769193451144, backtracks = 0, tol = 0.08660948583542002 Iteration 9: loglikelihood = -1323.4012363875613, backtracks = 0, tol = 0.009632030684900835 Iteration 10: loglikelihood = -1320.216274913422, backtracks = 0, tol = 0.001353113702989281 Iteration 11: loglikelihood = -1317.474112496789, backtracks = 0, tol = 0.0005484397815387147 Iteration 12: loglikelihood = -1314.8091099332726, backtracks = 0, tol = 0.08134000369212052 Iteration 13: loglikelihood = -1312.6267463400338, backtracks = 0, tol = 0.0058368513558719306 Iteration 14: loglikelihood = -1311.1584863516737, backtracks = 0, tol = 0.08074707249005497 Iteration 15: loglikelihood = -1309.397788681803, backtracks = 0, tol = 0.08073522913764106 Iteration 16: loglikelihood = -1307.6759318571226, backtracks = 0, tol = 0.008950848889245955 Iteration 17: loglikelihood = -1306.3816113046157, backtracks = 0, tol = 0.0017620449386577994 Iteration 18: loglikelihood = -1305.2068626639252, backtracks = 0, tol = 0.0004732240204407197 Iteration 19: loglikelihood = -1303.2593853373764, backtracks = 1, tol = 0.00018092821303865287 Iteration 20: loglikelihood = -1301.6566557140131, backtracks = 1, tol = 0.0003373920460805325 Iteration 21: loglikelihood = -1300.3118373854954, backtracks = 1, tol = 0.0003793399887365651 Iteration 22: loglikelihood = -1299.1720305846184, backtracks = 1, tol = 0.00038054925122101414 Iteration 23: loglikelihood = -1298.1956747968952, backtracks = 1, tol = 0.00036238758089913206 Iteration 24: loglikelihood = -1297.3511417623608, backtracks = 1, tol = 0.00033672624613784137 Iteration 25: loglikelihood = -1296.614206043023, backtracks = 1, tol = 0.00030950526940588113 Iteration 26: loglikelihood = -1295.9417469031375, backtracks = 1, tol = 0.0002834453646156283 Iteration 27: loglikelihood = -1295.3466775399386, backtracks = 1, tol = 0.0002637400724331874 Iteration 28: loglikelihood = -1294.8171185870865, backtracks = 1, tol = 0.0002444582195780332 Iteration 29: loglikelihood = -1294.3432303422223, backtracks = 1, tol = 0.0002263606520777925 Iteration 30: loglikelihood = -1293.9169566982737, backtracks = 1, tol = 0.0002097895154245768 Iteration 31: loglikelihood = -1293.531690754648, backtracks = 1, tol = 0.00019481209314328255 Iteration 32: loglikelihood = -1293.1819828829416, backtracks = 1, tol = 0.0001813507258914562 Iteration 33: loglikelihood = -1292.8633048629047, backtracks = 1, tol = 0.0001692651556642212 Iteration 34: loglikelihood = -1292.5718644371332, backtracks = 1, tol = 0.00015839823029643768 Iteration 35: loglikelihood = -1292.3044609674125, backtracks = 1, tol = 0.00014859854918341427 Iteration 36: loglikelihood = -1292.0583732371533, backtracks = 1, tol = 0.00013972996747552366 Iteration 37: loglikelihood = -1291.8312719062465, backtracks = 1, tol = 0.00013167420541965947 Iteration 38: loglikelihood = -1291.6211507217802, backtracks = 1, tol = 0.00012433018685938687 Iteration 39: loglikelihood = -1291.426271992102, backtracks = 1, tol = 0.00011761207139989625 Iteration 40: loglikelihood = -1291.2451229571293, backtracks = 1, tol = 0.00011144696799962466 Iteration 41: loglikelihood = -1291.07638054727, backtracks = 1, tol = 0.0001057727761929695 Iteration 42: loglikelihood = -1290.9188826625013, backtracks = 1, tol = 0.00010053631912450936 Iteration 43: loglikelihood = -1290.7716045712884, backtracks = 1, tol = 9.56917970161648e-5 0.439079 seconds (2.00 M allocations: 42.108 MiB, 8.77% gc time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse NegativeBinomial regression Number of threads = 1 Link functin = LogLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -3565.5066, backtracks = 0, tol = 0.08167578982336135 Iteration 2: loglikelihood = -3537.181, backtracks = 0, tol = 0.039983405137619686 Iteration 3: loglikelihood = -3534.0425, backtracks = 1, tol = 0.007556685049578356 Iteration 4: loglikelihood = -3513.649, backtracks = 1, tol = 0.06205446789655416 Iteration 5: loglikelihood = -3510.6392, backtracks = 1, tol = 0.010403465259181646 Iteration 6: loglikelihood = -3509.6375, backtracks = 1, tol = 0.0051769396234882656 Iteration 7: loglikelihood = -3509.3357, backtracks = 1, tol = 0.003468327298666964 Iteration 8: loglikelihood = -3495.7832, backtracks = 1, tol = 0.06674748525746999 Iteration 9: loglikelihood = -3494.3345, backtracks = 1, tol = 0.0068050600356122865 Iteration 10: loglikelihood = -3493.8545, backtracks = 1, tol = 0.003961023419523851 Iteration 11: loglikelihood = -3493.7124, backtracks = 1, tol = 0.0019920344202356897 Iteration 12: loglikelihood = -3493.6646, backtracks = 1, tol = 0.0012305017271558468 Iteration 13: loglikelihood = -3493.6558, backtracks = 1, tol = 0.0007280804534317883 Iteration 14: loglikelihood = -3493.6514, backtracks = 1, tol = 0.0003938915595937445 Iteration 15: loglikelihood = -3483.8005, backtracks = 1, tol = 0.07242762180529135 Iteration 16: loglikelihood = -3482.6384, backtracks = 1, tol = 0.006030178038884804 Iteration 17: loglikelihood = -3482.3025, backtracks = 1, tol = 0.003205328312204899 Iteration 18: loglikelihood = -3482.2146, backtracks = 1, tol = 0.0015407501647463977 Iteration 19: loglikelihood = -3482.198, backtracks = 1, tol = 0.0007502852960622527 Iteration 20: loglikelihood = -3482.1885, backtracks = 1, tol = 0.00036987541882228255 Iteration 21: loglikelihood = -3482.1877, backtracks = 1, tol = 0.00018340937960573852 Iteration 22: loglikelihood = -3482.1873, backtracks = 1, tol = 9.123737740298368e-5 13.786800 seconds (16.22 M allocations: 573.876 MiB, 1.37% gc time, 93.09% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse NegativeBinomial regression Number of threads = 1 Link functin = LogLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -3476.9563, backtracks = 0, tol = 0.08167578982336135 Iteration 2: loglikelihood = -3387.3918, backtracks = 0, tol = 0.04062416178552938 Iteration 3: loglikelihood = -3213.1055, backtracks = 1, tol = 0.007703509043282089 Iteration 4: loglikelihood = -3010.2144, backtracks = 1, tol = 0.005295745578539992 Iteration 5: loglikelihood = -2886.691, backtracks = 0, tol = 0.08575777156877248 Iteration 6: loglikelihood = -2759.3599, backtracks = 0, tol = 0.08537171772425817 Iteration 7: loglikelihood = -2653.6152, backtracks = 0, tol = 0.08633394043755845 Iteration 8: loglikelihood = -2553.551, backtracks = 0, tol = 0.08784187184729739 Iteration 9: loglikelihood = -2458.547, backtracks = 0, tol = 0.08737940528406062 Iteration 10: loglikelihood = -2380.374, backtracks = 0, tol = 0.08641034031953543 Iteration 11: loglikelihood = -2313.3994, backtracks = 0, tol = 0.08851793004736368 Iteration 12: loglikelihood = -2265.6714, backtracks = 0, tol = 0.08855247779339459 Iteration 13: loglikelihood = -2228.8384, backtracks = 0, tol = 0.08928087084152896 Iteration 14: loglikelihood = -2206.9202, backtracks = 0, tol = 0.08925590136970062 Iteration 15: loglikelihood = -2194.081, backtracks = 0, tol = 0.09442928589131801 Iteration 16: loglikelihood = -2192.76, backtracks = 0, tol = 0.10126467437166327 Iteration 17: loglikelihood = -2183.963, backtracks = 0, tol = 0.10046297191968617 Iteration 18: loglikelihood = -2183.4902, backtracks = 0, tol = 0.10024311950184561 Iteration 19: loglikelihood = -2179.4758, backtracks = 0, tol = 0.10051383636350694 Iteration 20: loglikelihood = -2175.2483, backtracks = 1, tol = 0.016983327438887853 Iteration 21: loglikelihood = -2174.4253, backtracks = 1, tol = 0.007815279413979614 Iteration 22: loglikelihood = -2174.2598, backtracks = 1, tol = 0.0037139461134196756 Iteration 23: loglikelihood = -2174.2273, backtracks = 1, tol = 0.0017670669773149751 Iteration 24: loglikelihood = -2174.2212, backtracks = 1, tol = 0.0008318955992083552 Iteration 25: loglikelihood = -2174.2212, backtracks = 1, tol = 0.0004351648799876274 Iteration 26: loglikelihood = -2174.22, backtracks = 3, tol = 6.0805006439877004e-5 0.203758 seconds (1.49 M allocations: 26.088 MiB) Test Summary: | Pass Total Time Negative binomial nuisance parameter Float32 matrix | 12 12 17.0s **** 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 = -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 5.872803 seconds (804.67 k allocations: 119.359 MiB, 1.10% gc time, 89.64% compilation time) Test Summary: | Pass Total Time initialze beta | 1 1 6.2s 6.063494 seconds (3.93 M allocations: 93.412 MiB, 0.89% gc time, 0.68% compilation time) 3.919820 seconds (3.90 M allocations: 101.152 MiB) 9.503409 seconds (22.46 M allocations: 558.959 MiB, 1.30% gc time, 2.18% compilation time) 9.109273 seconds (22.37 M allocations: 560.640 MiB, 1.12% gc time) 27.843291 seconds (1.83 M allocations: 3.478 GiB, 0.59% gc time, 13.85% compilation time) 22.051533 seconds (57.83 k allocations: 319.311 MiB, 0.08% gc time) Test Summary: | Pass Total Time memory_efficient keyword | 7 7 1m26.2s Test Summary: | Pass Total Time update_support! | 10 10 0.6s 10.584 ms (76 allocations: 5.30 KiB) 5.308 μs (2 allocations: 176 bytes) 99.069 μs (2 allocations: 288 bytes) 2.741 μs (0 allocations: 0 bytes) 19.809 μs (2 allocations: 128 bytes) 11.359 μs (0 allocations: 0 bytes) 3.895 μs (0 allocations: 0 bytes) 3.860 μs (0 allocations: 0 bytes) 28.959 μs (0 allocations: 0 bytes) 26.784 ms (76 allocations: 5.30 KiB) 28.049 μs (2 allocations: 1.02 KiB) 148.958 μs (2 allocations: 288 bytes) 13.069 μs (0 allocations: 0 bytes) 98.369 μs (2 allocations: 128 bytes) 43.570 μs (0 allocations: 0 bytes) 23.870 μs (0 allocations: 0 bytes) 22.790 μs (0 allocations: 0 bytes) 93.999 μs (0 allocations: 0 bytes) Test Summary: | Time benchmarks for multivariate function | None 2m24.8s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** **** 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 0.567992 seconds (28.60 k allocations: 6.024 MiB, 23.32% compilation time) Test Summary: | Pass Total Time multivariate fit_iht SnpLinAlg | 7 7 7.9s **** 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 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 2.891116 seconds (466.64 k allocations: 187.457 MiB, 2.63% gc time, 58.25% compilation time) Test Summary: | Pass Total Time initialze beta | 5 5 3.3s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:01:58 Cross validating... 30%|█████████▋ | ETA: 0:00:14 Cross validating... 33%|██████████▋ | ETA: 0:00:13 Cross validating... 37%|███████████▋ | ETA: 0:00:11 Cross validating... 40%|████████████▊ | ETA: 0:00:10 Cross validating... 43%|█████████████▊ | ETA: 0:00:09 Cross validating... 48%|███████████████▎ | ETA: 0:00:08 Cross validating... 51%|████████████████▎ | ETA: 0:00:07 Cross validating... 54%|█████████████████▎ | ETA: 0:00:06 Cross validating... 57%|██████████████████▎ | ETA: 0:00:06 Cross validating... 60%|███████████████████▎ | ETA: 0:00:05 Cross validating... 63%|████████████████████▍ | ETA: 0:00:04 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:04 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:03 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:03 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:03 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:02 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:02 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:01 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: 0:00:09 Crossvalidation Results: k MSE 0 6429.581095208203 1 4534.896629858961 2 3649.5811272972664 3 2903.031671965898 4 1675.688638106323 5 1122.1474668357478 6 596.1693097697503 7 494.1673288771947 8 439.2509233191122 9 356.6566225912975 10 321.2906950772116 11 324.51438809971864 12 326.79029110708734 13 327.3136595139753 14 332.97866473996237 15 332.8291448356643 16 334.72990595927297 17 363.8273880910979 18 356.28854123432836 19 358.7230737329404 20 363.90955714474126 Best k = 10 9.668612 seconds (12.57 M allocations: 386.089 MiB, 0.78% gc time, 50.77% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:03 Cross validating... 6%|██ | ETA: 0:00:04 Cross validating... 10%|███ | ETA: 0:00:04 Cross validating... 13%|████▏ | ETA: 0:00:04 Cross validating... 16%|█████▏ | ETA: 0:00:04 Cross validating... 19%|██████▏ | ETA: 0:00:04 Cross validating... 22%|███████▏ | ETA: 0:00:04 Cross validating... 25%|████████▏ | ETA: 0:00:04 Cross validating... 29%|█████████▏ | ETA: 0:00:04 Cross validating... 32%|██████████▏ | ETA: 0:00:03 Cross 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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 6429.581095208203 1 4547.1837909785545 2 3669.6910673325515 3 2925.3061370634937 4 1706.0680442719713 5 1139.0747209046517 6 602.6021373951125 7 501.14806332798764 8 445.94183846986937 9 363.9779349540945 10 330.1891674883915 11 338.59241749506793 12 345.5611401235767 13 352.93111503987427 14 362.12277956133056 15 368.1513668846157 16 374.31049582868013 17 385.52397806210445 18 370.9781247440318 19 377.09317731085923 20 373.20745000186446 Best k = 10 5.088941 seconds (11.66 M allocations: 282.043 MiB, 0.61% gc time, 0.34% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, normal model | 3 3 15.5s **** 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: 0:05:51 Cross validating... 8%|██▌ | ETA: 0:02:15 Cross validating... 13%|████▏ | ETA: 0:01:21 Cross validating... 17%|█████▋ | ETA: 0:00:56 Cross validating... 22%|███████▏ | ETA: 0:00:42 Cross validating... 27%|████████▋ | ETA: 0:00:33 Cross validating... 32%|██████████▏ | ETA: 0:00:26 Cross validating... 37%|███████████▋ | ETA: 0:00:22 Cross validating... 41%|█████████████▎ | ETA: 0:00:18 Cross validating... 48%|███████████████▎ | ETA: 0:00:14 Cross validating... 52%|████████████████▊ | ETA: 0:00:12 Cross validating... 57%|██████████████████▎ | ETA: 0:00:10 Cross validating... 62%|███████████████████▊ | ETA: 0:00:08 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:07 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:05 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:04 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:03 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:02 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:01 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:14 Crossvalidation Results: k MSE 0 1646.1499067382813 1 1254.2493027343749 2 1006.0279254150389 3 774.7572395019531 4 645.0644654541015 5 535.7557746582031 6 434.68934490966797 7 379.30763134765624 8 352.7495122680664 9 345.0803101196289 10 345.58518646240236 11 343.2411979980469 12 352.49476293945315 13 346.781087097168 14 353.01334967041015 15 363.6602379760742 16 359.810455871582 17 354.8134966430664 18 360.1002752685547 19 366.2531710205078 20 353.69340759277344 Best k = 11 14.666181 seconds (13.45 M allocations: 348.732 MiB, 0.52% gc time, 80.42% 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... 6%|██ | ETA: 0:00:02 Cross validating... 11%|███▌ | ETA: 0:00:02 Cross validating... 16%|█████▏ | ETA: 0:00:02 Cross validating... 21%|██████▋ | ETA: 0:00:02 Cross validating... 25%|████████▏ | ETA: 0:00:02 Cross validating... 30%|█████████▋ | ETA: 0:00:02 Cross validating... 37%|███████████▋ | ETA: 0:00:02 Cross validating... 41%|█████████████▎ | ETA: 0:00:02 Cross validating... 46%|██████████████▊ | ETA: 0:00:01 Cross validating... 51%|████████████████▎ | ETA: 0:00:01 Cross validating... 56%|█████████████████▊ | ETA: 0:00:01 Cross validating... 60%|███████████████████▎ | ETA: 0:00:01 Cross validating... 65%|████████████████████▉ | ETA: 0:00:01 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:01 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:01 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:00 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:00 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:00 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:02 Crossvalidation Results: k MSE 0 1646.1499067382813 1 1254.5785397949219 2 1009.4697105712889 3 774.7572395019531 4 647.9888244628906 5 538.4611126708984 6 437.19260839843747 7 381.8244813842773 8 357.1045568237305 9 349.89101556396486 10 352.2469564819336 11 354.6123079833984 12 358.68817700195314 13 367.8412661743164 14 379.3946574707031 15 370.45772778320315 16 384.54262084960936 17 395.48464874267574 18 391.19342364501955 19 394.31042700195314 20 392.69243475341796 Best k = 9 2.976477 seconds (12.03 M allocations: 243.627 MiB, 1.28% gc time, 1.02% compilation time) Test Summary: | Pass Total Time Cross validation on Float32 matrix, normal model | 2 2 18.7s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:31 Cross validating... 6%|██ | ETA: 0:00:18 Cross validating... 10%|███ | ETA: 0:00:13 Cross validating... 13%|████▏ | ETA: 0:00:11 Cross validating... 16%|█████▏ | ETA: 0:00:09 Cross validating... 19%|██████▏ | ETA: 0:00:08 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: 0:00:06 Cross validating... 33%|██████████▋ | ETA: 0:00:06 Cross validating... 37%|███████████▋ | ETA: 0:00:05 Cross validating... 40%|████████████▊ | 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Cross validating... 94%|██████████████████████████████ | ETA: 0:00:00 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 0 462.4338985945287 1 393.7446872943649 2 369.61396774693765 3 318.76894737715173 4 280.5126167729633 5 228.0910964334624 6 201.31153935686055 7 190.25321121250875 8 165.68217186566199 9 173.46666658255867 10 178.02155719761538 11 195.46032434605667 12 190.51524628102277 13 190.1349344112666 14 210.0060567272149 15 192.93062585066463 16 196.47388140980252 17 219.1957833262673 18 189.61848204556588 19 206.49199318981334 20 196.6076131096599 Best k = 8 6.964288 seconds (17.64 M allocations: 458.045 MiB, 0.72% gc time, 17.63% 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... 5%|█▌ | ETA: 0:00:04 Cross validating... 8%|██▌ | ETA: 0:00:04 Cross validating... 11%|███▌ | ETA: 0:00:04 Cross validating... 14%|████▋ | ETA: 0:00:04 Cross validating... 16%|█████▏ | ETA: 0:00:04 Cross validating... 19%|██████▏ | ETA: 0:00:04 Cross validating... 22%|███████▏ | ETA: 0:00:04 Cross validating... 25%|████████▏ | ETA: 0:00:04 Cross validating... 29%|█████████▏ | ETA: 0:00:04 Cross validating... 32%|██████████▏ | ETA: 0:00:04 Cross validating... 35%|███████████▏ | ETA: 0:00:04 Cross validating... 38%|████████████▎ | ETA: 0:00:03 Cross validating... 41%|█████████████▎ | ETA: 0:00:03 Cross validating... 44%|██████████████▎ | ETA: 0:00:03 Cross validating... 48%|███████████████▎ | ETA: 0:00:03 Cross validating... 51%|████████████████▎ | ETA: 0:00:03 Cross validating... 54%|█████████████████▎ | ETA: 0:00:03 Cross validating... 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100%|████████████████████████████████| Time: 0:00:05 Crossvalidation Results: k MSE 0 462.4338985945287 1 394.76428215655847 2 371.592014422399 3 322.3848190665207 4 283.8784089963957 5 234.2239385397528 6 209.28225864118502 7 197.52884184112963 8 173.19958348450714 9 183.2632859500447 10 184.82766581964384 11 189.59550471462808 12 201.182764257945 13 201.63732669045106 14 216.3402515376507 15 226.48492344850538 16 218.23251095935186 17 230.69213066685887 18 242.24739714497994 19 241.7297409127625 20 250.6585144167065 Best k = 8 5.850183 seconds (18.53 M allocations: 448.762 MiB, 0.60% gc time, 0.38% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, logistic model | 2 2 13.2s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:27 Cross validating... 6%|██ | ETA: 0:00:15 Cross validating... 10%|███ | ETA: 0:00:11 Cross validating... 13%|████▏ | ETA: 0:00:09 Cross validating... 16%|█████▏ | ETA: 0:00:08 Cross validating... 19%|██████▏ | ETA: 0:00:07 Cross validating... 22%|███████▏ | ETA: 0:00:07 Cross validating... 25%|████████▏ | ETA: 0:00:06 Cross validating... 29%|█████████▏ | ETA: 0:00:06 Cross validating... 32%|██████████▏ | ETA: 0:00:05 Cross validating... 33%|██████████▋ | ETA: 0:00:05 Cross validating... 37%|███████████▋ | ETA: 0:00:05 Cross validating... 40%|████████████▊ | ETA: 0:00:04 Cross validating... 43%|█████████████▊ | ETA: 0:00:04 Cross validating... 46%|██████████████▊ | ETA: 0:00:04 Cross validating... 49%|███████████████▊ | ETA: 0:00:03 Cross validating... 52%|████████████████▊ | ETA: 0:00:03 Cross validating... 56%|█████████████████▊ | ETA: 0:00:03 Cross validating... 57%|██████████████████▎ | ETA: 0:00:03 Cross validating... 60%|███████████████████▎ | ETA: 0:00:03 Cross validating... 63%|████████████████████▍ | ETA: 0:00:03 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:02 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:02 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:02 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:01 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:01 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:01 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:01 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:01 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:06 Crossvalidation Results: k MSE 0 463.4270934941942 1 447.6334239003502 2 424.9045915759725 3 383.5114958944686 4 360.5846660936337 5 352.6381897836199 6 337.41540367520383 7 338.09821805961684 8 336.55160650876223 9 334.10565973388776 10 345.77847357633004 11 331.8638356172101 12 342.41745510090016 13 353.63647766788256 14 365.65862945959975 15 354.757880020435 16 340.6709597211075 17 343.16621300589486 18 395.362934396136 19 396.48720741402684 20 371.8098393036708 Best k = 11 7.165714 seconds (18.14 M allocations: 487.609 MiB, 11.50% gc time, 15.56% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:04 Cross validating... 6%|██ | ETA: 0:00:04 Cross validating... 10%|███ | ETA: 0:00:04 Cross validating... 13%|████▏ | ETA: 0:00:04 Cross validating... 16%|█████▏ | ETA: 0:00:04 Cross validating... 19%|██████▏ | ETA: 0:00:04 Cross validating... 22%|███████▏ | ETA: 0:00:04 Cross validating... 25%|████████▏ | ETA: 0:00:04 Cross 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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: 0:00:05 Crossvalidation Results: k MSE 0 463.4270934941942 1 448.77292866204573 2 426.59485241660343 3 386.5407169033926 4 364.6522539124437 5 357.72603121171244 6 345.8795155640807 7 351.91856994063585 8 345.7181549584508 9 353.4522543870055 10 367.90999598129923 11 363.79560766450254 12 385.03211722140577 13 388.4232445643902 14 389.53075723231706 15 414.6024966047876 16 422.39546324171926 17 409.9303858065217 18 413.90030770143414 19 451.730068877756 20 460.151712028616 Best k = 8 5.415751 seconds (18.32 M allocations: 436.475 MiB, 0.63% gc time, 0.57% compilation time) Test Summary: | Pass Total Time Cross validation on Float64 matrix, logistic model | 2 2 13.1s **** 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: 0:00:32 Cross validating... 6%|██ | ETA: 0:00:18 Cross validating... 10%|███ | ETA: 0:00:13 Cross validating... 11%|███▌ | ETA: 0:00:12 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: 0:00:07 Cross validating... 30%|█████████▋ | ETA: 0:00:06 Cross validating... 33%|██████████▋ | ETA: 0:00:06 Cross validating... 37%|███████████▋ | ETA: 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90%|█████████████████████████████ | ETA: 0:00:01 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:06 Crossvalidation Results: k MSE 0 1421.6277507485493 1 1215.668996460619 2 1064.2620586242442 3 852.2585606925643 4 704.0863781207986 5 525.8656480545254 6 430.20062467296106 7 418.23642836941264 8 423.64077340755 9 434.7967364028773 10 406.00002854988526 11 391.8446208198601 12 404.3430198894608 13 442.6347458092674 14 422.40757539356485 15 443.61739726164996 16 434.50884357177665 17 417.09117550912697 18 436.4543163003619 19 460.8455798211728 20 469.75787096779567 Best k = 11 7.233324 seconds (17.01 M allocations: 456.457 MiB, 0.77% gc time, 17.20% 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... 8%|██▌ | ETA: 0:00:05 Cross validating... 11%|███▌ | ETA: 0:00:05 Cross validating... 14%|████▋ | ETA: 0:00:05 Cross validating... 17%|█████▋ | ETA: 0:00:05 Cross validating... 21%|██████▋ | ETA: 0:00:05 Cross validating... 24%|███████▋ | ETA: 0:00:04 Cross validating... 27%|████████▋ | ETA: 0:00:04 Cross validating... 30%|█████████▋ | ETA: 0:00:04 Cross validating... 33%|██████████▋ | ETA: 0:00:04 Cross validating... 37%|███████████▋ | ETA: 0:00:04 Cross validating... 40%|████████████▊ | ETA: 0:00:03 Cross validating... 43%|█████████████▊ | ETA: 0:00:03 Cross validating... 46%|██████████████▊ | ETA: 0:00:03 Cross validating... 49%|███████████████▊ | ETA: 0:00:03 Cross validating... 52%|████████████████▊ | ETA: 0:00:03 Cross validating... 56%|█████████████████▊ | ETA: 0:00:03 Cross validating... 59%|██████████████████▊ | ETA: 0:00:02 Cross validating... 62%|███████████████████▊ | ETA: 0:00:02 Cross validating... 65%|████████████████████▉ | ETA: 0:00:02 Cross validating... 68%|█████████████████████▉ | ETA: 0:00:02 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:02 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:01 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:01 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:01 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:01 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:01 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:01 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:05 Crossvalidation Results: k MSE 0 1421.6277507485493 1 1112.7849312757276 2 975.6815934575492 3 810.3473469249091 4 676.5228412012364 5 507.7696053243801 6 424.51442149571716 7 394.67019148820344 8 418.4317970108191 9 400.93267717511776 10 420.04545130290336 11 424.77301197865734 12 441.0819438226573 13 443.350995188492 14 449.46719790624877 15 457.7244835662033 16 487.35203419867605 17 490.7756592331559 18 499.79669272960103 19 498.88444690194683 20 513.65012468345 Best k = 7 6.042392 seconds (15.86 M allocations: 373.200 MiB, 0.56% gc time, 0.30% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, Poisson model | 2 2 13.7s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:30 Cross validating... 6%|██ | ETA: 0:00:33 Cross validating... 8%|██▌ | ETA: 0:00:38 Cross validating... 10%|███ | ETA: 0:00:41 Cross 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| ETA: 0:00:09 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:08 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:07 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:07 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:06 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:05 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:05 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:04 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:03 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:03 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:02 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:01 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:01 Cross validating... 100%|████████████████████████████████| Time: 0:00:40 Crossvalidation Results: k MSE 0 469.1255069883922 1 376.7678090906883 2 341.82460634901196 3 301.54696730639876 4 240.3299971600574 5 213.9913524116513 6 199.59123247386117 7 196.7172395747733 8 192.98807679587364 9 194.59743790298518 10 195.25573674516585 11 196.08714597335987 12 197.97144878833038 13 198.20648056862154 14 199.30297016542008 15 199.65537368518653 16 202.036077826805 17 202.07864570605432 18 202.82431682239087 19 200.25781466049384 20 204.69857616648414 Best k = 8 41.296790 seconds (138.09 M allocations: 4.028 GiB, 0.50% gc time, 2.68% 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 **** Cross validating... 3%|█ | ETA: 0:00:04 Cross validating... 5%|█▌ | ETA: 0:00:05 Cross validating... 6%|██ | ETA: 0:00:06 Cross validating... 8%|██▌ | ETA: 0:00:06 Cross validating... 11%|███▌ | ETA: 0:00:06 Cross validating... 13%|████▏ | 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Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:02 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:02 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:02 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:02 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:01 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:01 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:01 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:01 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:01 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:01 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:10 Crossvalidation Results: k MSE 0 469.1255069883922 1 376.84696788380745 2 342.77684313640015 3 304.9370045657406 4 243.62028253243682 5 217.61778874592207 6 202.57911822626704 7 200.25430453436317 8 199.6512218225929 9 202.6460636508297 10 206.66543813183227 11 213.06002351564774 12 214.71033957397356 13 214.68027428087942 14 215.87263843694666 15 220.74904811392088 16 223.15760683509316 17 226.84234481163787 18 233.04869863737952 19 230.34620153363596 20 237.5153461358949 Best k = 8 10.819608 seconds (38.26 M allocations: 938.687 MiB, 0.56% gc time, 0.20% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, NegativeBinomial model | 2 2 52.5s **** 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: 0:00:37 Cross validating... 6%|██ | ETA: 0:00:20 Cross validating... 10%|███ | ETA: 0:00:14 Cross validating... 14%|████▋ | ETA: 0:00:10 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: 0:00:05 Cross validating... 30%|█████████▋ | ETA: 0:00:05 Cross validating... 35%|███████████▏ | ETA: 0:00:04 Cross validating... 40%|████████████▊ | ETA: 0:00:04 Cross validating... 43%|█████████████▊ | ETA: 0:00:03 Cross validating... 46%|██████████████▊ | ETA: 0:00:03 Cross validating... 49%|███████████████▊ | ETA: 0:00:03 Cross validating... 52%|████████████████▊ | ETA: 0:00:03 Cross validating... 56%|█████████████████▊ | ETA: 0:00:02 Cross validating... 59%|██████████████████▊ | ETA: 0:00:02 Cross validating... 62%|███████████████████▊ | ETA: 0:00:02 Cross validating... 65%|████████████████████▉ | ETA: 0:00:02 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:02 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:01 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:01 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:01 Cross validating... 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 0 727.2352371826172 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 5.101153 seconds (17.78 M allocations: 379.887 MiB, 1.55% gc time, 29.05% 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: 0:00:02 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: 0:00:02 Cross validating... 24%|███████▋ | ETA: 0:00:02 Cross validating... 27%|████████▋ | ETA: 0:00:02 Cross validating... 30%|█████████▋ | ETA: 0:00:02 Cross validating... 33%|██████████▋ | ETA: 0:00:02 Cross validating... 38%|████████████▎ | ETA: 0:00:02 Cross validating... 41%|█████████████▎ | ETA: 0:00:02 Cross validating... 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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 3.512821 seconds (17.20 M allocations: 333.526 MiB, 1.47% gc time, 0.84% compilation time) Test Summary: | Pass Total Time Cross validation on floating point matrices, NegativeBinomial model | 2 2 9.0s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 2%|▋ | ETA: 0:00:56 Cross validating... 3%|█ 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0:00:03 Cross validating... 93%|█████████████████████████████▊ | ETA: 0:00:02 Cross validating... 94%|██████████████████████████████▏ | ETA: 0:00:02 Cross validating... 95%|██████████████████████████████▍ | ETA: 0:00:02 Cross validating... 96%|██████████████████████████████▊ | ETA: 0:00:01 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:01 Cross validating... 98%|███████████████████████████████▍| ETA: 0:00:01 Cross validating... 99%|███████████████████████████████▋| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:33 Crossvalidation Results: k MSE 1 2369.252146642447 2 1797.7919068009041 3 1526.5350804430318 4 1440.8921707166382 5 1388.1634602649337 6 1343.89258296367 7 1308.6765932055355 8 1319.0824776417815 9 1327.86978913953 10 1344.9121835845435 11 1355.2396615571354 12 1354.414158947971 13 1376.851806526074 14 1372.2076565040616 15 1382.7059366774317 16 1391.2660388807512 17 1412.2346946803991 18 1412.4366509757888 19 1412.139189146939 20 1408.7211053862466 Best k = 7 33.590940 seconds (324.78 k allocations: 437.362 MiB, 0.21% gc time, 2.15% compilation time) Test Summary: | Pass Total Time multivariate cross validation SnpLinAlg | 3 3 36.4s Test Summary: | Pass Total Time wrapper univariate | 20 20 1m11.1s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 2%|▋ | ETA: 0:00:21 Cross validating... 3%|█ | ETA: 0:00:20 Cross validating... 4%|█▎ | ETA: 0:00:22 Cross validating... 5%|█▋ | ETA: 0:00:21 Cross validating... 6%|█▉ | ETA: 0:00:24 Cross validating... 7%|██▎ | ETA: 0:00:25 Cross validating... 8%|██▌ | ETA: 0:00:25 Cross validating... 9%|██▉ | ETA: 0:00:27 Cross validating... 10%|███▎ | ETA: 0:00:28 Cross validating... 11%|███▌ | ETA: 0:00:28 Cross validating... 12%|███▉ | 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validating... 98%|███████████████████████████████▍| ETA: 0:00:01 Cross validating... 99%|███████████████████████████████▋| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:45 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: 0:00:19 Cross validating... 3%|█ | ETA: 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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: 0:00:20 Cross validating... 3%|█ | ETA: 0:00:20 Cross validating... 4%|█▎ | ETA: 0:00:22 Cross validating... 5%|█▋ | ETA: 0:00:21 Cross validating... 6%|█▉ | ETA: 0:00:24 Cross validating... 7%|██▎ | ETA: 0:00:25 Cross validating... 8%|██▌ | ETA: 0:00:25 Cross validating... 9%|██▉ | ETA: 0:00:27 Cross validating... 10%|███▎ | ETA: 0:00:28 Cross validating... 11%|███▌ | ETA: 0:00:28 Cross validating... 12%|███▉ | ETA: 0:00:28 Cross validating... 13%|████▏ | ETA: 0:00:29 Cross validating... 14%|████▌ | ETA: 0:00:29 Cross validating... 15%|████▊ | ETA: 0:00:30 Cross validating... 16%|█████▏ | ETA: 0:00:31 Cross validating... 17%|█████▌ | ETA: 0:00:31 Cross validating... 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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 2m29.6s 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:1577 [inlined] [11] top-level scope @ ~/.julia/packages/MendelIHT/ZcxZT/test/wrapper_test.jl:185 [12] include(fname::String) @ Base.MainInclude ./client.jl:494 [13] top-level scope @ ~/.julia/packages/MendelIHT/ZcxZT/test/runtests.jl:20 [14] include(fname::String) @ Base.MainInclude ./client.jl:494 [15] top-level scope @ none:6 [16] eval @ ./boot.jl:385 [inlined] [17] exec_options(opts::Base.JLOptions) @ Base ./client.jl:296 [18] _start() @ Base ./client.jl:557 Test Summary: | Error Total Time read BGEN and VCF | 1 1 5.2s 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 959.24s 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:219 in expression starting at /PkgEval.jl/scripts/evaluate.jl:210 PkgEval failed after 1080.59s: package tests unexpectedly errored