Package evaluation of MendelIHT on Julia 1.10.9 (96dc2d8c45*) started at 2025-06-06T21:39:05.576 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 5.15s ################################################################################ # 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 v0.1.42 [79e6a3ab] + Adapt v4.3.0 [66dad0bd] + AliasTables v1.1.3 [4fba245c] + ArrayInterface v7.19.0 ⌅ [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 v1.0.3 [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 v0.18.22 [e2d170a0] + DataValueInterfaces v1.0.0 [8bb1440f] + DelimitedFiles v1.9.1 [b4f34e82] + Distances v0.10.12 [31c24e10] + Distributions v0.25.120 [ffbed154] + DocStringExtensions v0.9.4 [48062228] + FilePathsBase v0.9.24 [1a297f60] + FillArrays v1.13.0 [38e38edf] + GLM v1.9.0 [c27321d9] + Glob v1.3.1 [3e5b6fbb] + HostCPUFeatures v0.1.17 [34004b35] + HypergeometricFunctions v0.3.28 [09f84164] + HypothesisTests v0.11.5 [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 v0.12.172 [1914dd2f] + MacroTools v0.5.16 [d125e4d3] + ManualMemory v0.1.8 [921c7187] + MendelIHT v1.4.11 [e1d29d7a] + Missings v1.2.0 [6fe1bfb0] + OffsetArrays v1.17.0 [bac558e1] + OrderedCollections v1.8.1 [90014a1f] + PDMats v0.11.35 [69de0a69] + Parsers v2.8.3 [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 v1.10.4 [43287f4e] + PtrArrays v1.3.0 [1fd47b50] + QuadGK v2.11.2 [189a3867] + Reexport v1.2.2 [ae029012] + Requires v1.3.1 [79098fc4] + Rmath v0.8.0 [f2b01f46] + Roots v2.2.7 [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 v2.5.1 [aedffcd0] + Static v1.2.0 [0d7ed370] + StaticArrayInterface v1.8.0 [82ae8749] + StatsAPI v1.7.1 [2913bbd2] + StatsBase v0.34.5 [4c63d2b9] + StatsFuns v1.5.0 [3eaba693] + StatsModels v0.7.4 [892a3eda] + StringManipulation v0.4.1 [3783bdb8] + TableTraits v1.0.1 [bd369af6] + Tables v1.12.1 [8290d209] + ThreadingUtilities v0.5.4 ⌅ [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 v5.8.1+0 [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 v0.8.5+0 [bea87d4a] + SuiteSparse_jll v7.2.1+1 [83775a58] + Zlib_jll v1.2.13+1 [8e850b90] + libblastrampoline_jll v5.11.0+0 [8e850ede] + nghttp2_jll v1.52.0+1 [3f19e933] + p7zip_jll v17.4.0+2 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. To see why use `status --outdated -m` Installation completed after 8.7s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompilation completed after 99.86s ################################################################################ # Testing # Testing MendelIHT Status `/tmp/jl_BLPDno/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 v0.25.120 [38e38edf] GLM v1.9.0 [921c7187] MendelIHT v1.4.11 [92933f4c] ProgressMeter v1.10.4 [189a3867] Reexport v1.2.2 [4e780e97] SnpArrays v0.3.22 [276daf66] SpecialFunctions v2.5.1 [2913bbd2] StatsBase v0.34.5 [a620830f] VCFTools v0.2.10 [37e2e46d] LinearAlgebra [44cfe95a] Pkg v1.10.0 [9a3f8284] Random [8dfed614] Test Status `/tmp/jl_BLPDno/Manifest.toml` [7d9f7c33] Accessors v0.1.42 [79e6a3ab] Adapt v4.3.0 [66dad0bd] AliasTables v1.1.3 [4fba245c] ArrayInterface v7.19.0 ⌅ [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 v0.3.28 [09f84164] HypothesisTests v0.11.5 [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 v0.12.172 [1914dd2f] MacroTools v0.5.16 [d125e4d3] ManualMemory v0.1.8 [921c7187] MendelIHT v1.4.11 [e1d29d7a] Missings v1.2.0 [6fe1bfb0] OffsetArrays v1.17.0 [bac558e1] OrderedCollections v1.8.1 [90014a1f] PDMats v0.11.35 [69de0a69] Parsers v2.8.3 [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 v1.10.4 [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 v0.8.5+0 [bea87d4a] SuiteSparse_jll v7.2.1+1 [83775a58] Zlib_jll v1.2.13+1 [8e850b90] libblastrampoline_jll v5.11.0+0 [8e850ede] nghttp2_jll v1.52.0+1 [3f19e933] p7zip_jll v17.4.0+2 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. Testing Running tests... ┌ Warning: `MvNormal(σ::AbstractVector{<:Real})` is deprecated, use `MvNormal(LinearAlgebra.Diagonal(map(abs2, σ)))` instead. │ caller = ip:0x0 └ @ Core :-1 WARNING: using deprecated binding Distributions.MatrixReshaped in MendelIHT. , use Distributions.ReshapedDistribution{2, S, D} where D<:Distributions.Distribution{Distributions.ArrayLikeVariate{1}, S} where S<:Distributions.ValueSupport instead. WARNING: both BGEN and SnpArrays export "maf"; uses of it in module MendelIHT must be qualified ┌ Warning: `cholesky!(A::RealHermSymComplexHerm{<:BlasReal, <:StridedMatrix}, ::Val{true}; kwargs...)` is deprecated, use `cholesky!(A, RowMaximum(); kwargs...)` instead. │ caller = iht_stepsize!(v::MendelIHT.mIHTVariable{Float64, LinearAlgebra.Transpose{Float64, SnpArrays.SnpLinAlg{Float64}}}) at multivariate.jl:241 └ @ MendelIHT ~/.julia/packages/MendelIHT/ZcxZT/src/multivariate.jl:241 Test Summary: | Pass Total Time loglikelihood | 4 4 6.9s Test Summary: | Pass Total Time deviance | 1 1 0.2s Test Summary: | Pass Total Time update_μ! | 4 4 0.5s Test Summary: | Pass Total Time _choose! | 7 7 2.8s Test Summary: | Pass Total Time _iht_backtrack | 7 7 0.0s Test Summary: | Pass Total Time standardize! | 12 12 0.7s Test Summary: | Pass Total Time project_k! | 2 2 0.6s Test Summary: | Pass Total Time project_group_sparse! | 5 5 1.0s Test Summary: | Pass Total Time maf_weights | 6 6 1.6s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse linear regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1727.4260342557327, backtracks = 0, tol = 1.5784725145251073 Iteration 2: loglikelihood = -1444.6450334640026, backtracks = 0, tol = 0.1555962364906338 Iteration 3: loglikelihood = -1402.2492715228439, backtracks = 0, tol = 0.06508899440971888 Iteration 4: loglikelihood = -1401.4533644760231, backtracks = 0, tol = 0.009069782499489136 Iteration 5: loglikelihood = -1401.4435025251948, backtracks = 0, tol = 0.0008995607736184987 Iteration 6: loglikelihood = -1401.4433353511574, backtracks = 0, tol = 0.00013759406894533682 Iteration 7: loglikelihood = -1401.4433321365923, backtracks = 0, tol = 1.802174141553453e-5 IHT estimated 10 nonzero SNP predictors and 1 non-genetic predictors. Compute time (sec): 0.046221017837524414 Final loglikelihood: -1401.4433321365923 SNP PVE: 0.889040448779381 Iterations: 7 Selected genetic predictors: 10×2 DataFrame Row │ Position Estimated_β │ Int64 Float64 ─────┼─────────────────────── 1 │ 1647 0.310187 2 │ 1966 1.95984 3 │ 2047 -0.378905 4 │ 2692 0.939015 5 │ 3295 0.352162 6 │ 4372 -1.03904 7 │ 5125 0.152782 8 │ 5150 0.226072 9 │ 6681 0.384774 10 │ 7248 1.36032 Selected nongenetic predictors: 1×2 DataFrame Row │ Position Estimated_β │ Int64 Float64 ─────┼─────────────────────── 1 │ 1 0.0165646Test Summary: | Pass Total Time fit normal SnpLinAlg | 4 4 7.7s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse logistic regression Number of threads = 1 Link functin = LogitLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -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 = -11693.457729703192, backtracks = 0, tol = 0.7243868485698881 Iteration 2: loglikelihood = -5606.914050700375, backtracks = 0, tol = 0.04053862974794624 Iteration 3: loglikelihood = -2818.634355264302, backtracks = 0, tol = 0.05871665878934485 Iteration 4: loglikelihood = -1698.9531268747116, backtracks = 0, tol = 0.07601868271083181 Iteration 5: loglikelihood = -1403.083988245291, backtracks = 0, tol = 0.07129244590783984 Iteration 6: loglikelihood = -1364.2566445492816, backtracks = 0, tol = 0.039374060981093514 Iteration 7: loglikelihood = -1312.049221132526, backtracks = 0, tol = 0.07661625104825381 Iteration 8: loglikelihood = -1297.372576123991, backtracks = 0, tol = 0.026945785177025228 Iteration 9: loglikelihood = -1292.4648021717264, backtracks = 0, tol = 0.026410879440483183 Iteration 10: loglikelihood = -1290.5000440605625, backtracks = 0, tol = 0.010522193992066482 Iteration 11: loglikelihood = -1289.0852430927637, backtracks = 0, tol = 0.013065314694138117 Iteration 12: loglikelihood = -1288.1628603123822, backtracks = 0, tol = 0.007082593587754833 Iteration 13: loglikelihood = -1287.5771146705258, backtracks = 0, tol = 0.04260737499363845 Iteration 14: loglikelihood = -1286.6021598023806, backtracks = 1, tol = 0.007937899757075194 Iteration 15: loglikelihood = -1286.2823222515715, backtracks = 1, tol = 0.003615952349568246 Iteration 16: loglikelihood = -1286.1275361962619, backtracks = 0, tol = 0.004750082311273666 Iteration 17: loglikelihood = -1286.028696679052, backtracks = 0, tol = 0.003238313598686461 Iteration 18: loglikelihood = -1285.9637165970428, backtracks = 0, tol = 0.003206853419987305 Iteration 19: loglikelihood = -1285.91934856428, backtracks = 0, tol = 0.00217040835745799 Iteration 20: loglikelihood = -1285.888886157908, backtracks = 0, tol = 0.002193966209220428 Iteration 21: loglikelihood = -1285.8675362023614, backtracks = 0, tol = 0.001501601910018545 Iteration 22: loglikelihood = -1285.8525762942413, backtracks = 0, tol = 0.0015222538625867248 Iteration 23: loglikelihood = -1285.8419622721008, backtracks = 0, tol = 0.00105554551135492 Iteration 24: loglikelihood = -1285.8344428949279, backtracks = 0, tol = 0.0010677365884694129 Iteration 25: loglikelihood = -1285.8290727882058, backtracks = 0, tol = 0.0007487882159610865 Iteration 26: loglikelihood = -1285.825243556208, backtracks = 0, tol = 0.0007548844412509926 Iteration 27: loglikelihood = -1285.8224982746729, backtracks = 0, tol = 0.0005342023867072114 Iteration 28: loglikelihood = -1285.8205326668526, backtracks = 0, tol = 0.0005367632220319869 Iteration 29: loglikelihood = -1285.8191200715412, backtracks = 0, tol = 0.0003825319809895298 Iteration 30: loglikelihood = -1285.818105935543, backtracks = 0, tol = 0.00038325548493541365 Iteration 31: loglikelihood = -1285.8173759781507, backtracks = 0, tol = 0.0002746144198939866 Iteration 32: loglikelihood = -1285.8168509732548, backtracks = 0, tol = 0.00027447911526855913 Iteration 33: loglikelihood = -1285.8164726875996, backtracks = 0, tol = 0.00019748572646148806 Iteration 34: loglikelihood = -1285.8162002756108, backtracks = 0, tol = 0.00019701261969238217 Iteration 35: loglikelihood = -1285.816003852218, backtracks = 0, tol = 0.00014219343829553454 Iteration 36: loglikelihood = -1285.8158622808596, backtracks = 0, tol = 0.00014164051703479224 Iteration 37: loglikelihood = -1285.8157601499734, backtracks = 0, tol = 0.00010247089862844512 Iteration 38: loglikelihood = -1285.8156864948285, backtracks = 0, tol = 0.0001019537888557441 Iteration 39: loglikelihood = -1285.8156333409793, backtracks = 0, tol = 7.389094093142887e-5 Test Summary: | Pass Total Time fit Poisson SnpLinAlg | 4 4 1.5s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse NegativeBinomial regression Number of threads = 1 Link functin = LogLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1644.8279628820655, backtracks = 0, tol = 0.6345348650382708 Iteration 2: loglikelihood = -1551.8238591737663, backtracks = 0, tol = 0.09631704976019462 Iteration 3: loglikelihood = -1501.9967661741434, backtracks = 0, tol = 0.08478146181816136 Iteration 4: loglikelihood = -1489.5889115659984, backtracks = 0, tol = 0.058405932567831984 Iteration 5: loglikelihood = -1481.527394618542, backtracks = 0, tol = 0.0738629885401546 Iteration 6: loglikelihood = -1480.0981067018206, backtracks = 0, tol = 0.02878323265217605 Iteration 7: loglikelihood = -1479.9612619297197, backtracks = 1, tol = 0.005857122562280235 Iteration 8: loglikelihood = -1479.9169709219816, backtracks = 1, tol = 0.003641752063237332 Iteration 9: loglikelihood = -1479.9049980122873, backtracks = 1, tol = 0.0019092618391609811 Iteration 10: loglikelihood = -1479.9018523082593, backtracks = 1, tol = 0.0010238732621727976 Iteration 11: loglikelihood = -1479.9010408019615, backtracks = 1, tol = 0.0005344924392196904 Iteration 12: loglikelihood = -1479.9008313749516, backtracks = 1, tol = 0.0002765928222153255 Iteration 13: loglikelihood = -1479.9007776716433, backtracks = 1, tol = 0.00014176393403802937 Iteration 14: loglikelihood = -1479.9007638713856, backtracks = 1, tol = 7.254026411150394e-5 Test Summary: | Pass Total Time fit NegativeBinomial SnpLinAlg | 4 4 0.9s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse linear regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1934.7058692291926, backtracks = 0, tol = 0.7284921889028015 Iteration 2: loglikelihood = -1511.9910894701702, backtracks = 0, tol = 0.14725521633732996 Iteration 3: loglikelihood = -1402.976319324934, backtracks = 0, tol = 0.06309543852193972 Iteration 4: loglikelihood = -1388.3448769935915, backtracks = 0, tol = 0.027025083903825645 Iteration 5: loglikelihood = -1386.6295735272483, backtracks = 0, tol = 0.024897226767833406 Iteration 6: loglikelihood = -1386.5622552564414, backtracks = 0, tol = 0.0012537082591914193 Iteration 7: loglikelihood = -1384.9505638078006, backtracks = 0, tol = 0.0235815790945603 Iteration 8: loglikelihood = -1384.7777793459056, backtracks = 0, tol = 0.00233529837531626 Iteration 9: loglikelihood = -1384.7769114472574, backtracks = 0, tol = 0.00015104938967376406 Iteration 10: loglikelihood = -1384.7768968784455, backtracks = 0, tol = 2.9208319276002706e-5 Test Summary: | Pass Total Time fit with >1 non-genetic covariates SnpLinAlg | 5 5 1.1s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse linear regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1490.3341750525394, backtracks = 0, tol = 0.40502157047925846 Iteration 2: loglikelihood = -1402.8275197220837, backtracks = 0, tol = 0.07235576513949929 Iteration 3: loglikelihood = -1394.5361372859463, backtracks = 0, tol = 0.034898329132782326 Iteration 4: loglikelihood = -1385.1265677213987, backtracks = 0, tol = 0.0331996526833453 Iteration 5: loglikelihood = -1384.7800425020014, backtracks = 0, tol = 0.0034116549494267482 Iteration 6: loglikelihood = -1384.7774877365846, backtracks = 0, tol = 0.00030214843169651287 Iteration 7: loglikelihood = -1384.777459015231, backtracks = 0, tol = 2.9742650968227684e-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 5.2s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse NegativeBinomial regression Number of threads = 1 Link functin = LogLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1532.1059484191142, backtracks = 0, tol = 0.24209471058885657 Iteration 2: loglikelihood = -1427.6083074616765, backtracks = 0, tol = 0.1428220558247263 Iteration 3: loglikelihood = -1387.880868940681, backtracks = 0, tol = 0.16808576363966335 Iteration 4: loglikelihood = -1363.134355468146, backtracks = 0, tol = 0.08154237485766093 Iteration 5: loglikelihood = -1358.2071356885465, backtracks = 0, tol = 0.031114606372187232 Iteration 6: loglikelihood = -1357.1633806358427, backtracks = 1, tol = 0.010992331889385913 Iteration 7: loglikelihood = -1356.600277753973, backtracks = 1, tol = 0.012240634253152685 Iteration 8: loglikelihood = -1356.3962281500962, backtracks = 1, tol = 0.004818264950504001 Iteration 9: loglikelihood = -1356.3122380809675, backtracks = 1, tol = 0.004943060578596497 Iteration 10: loglikelihood = -1356.2673161982545, backtracks = 1, tol = 0.0021895417885073078 Iteration 11: loglikelihood = -1356.2475330320635, backtracks = 1, tol = 0.0023991720738597232 Iteration 12: loglikelihood = -1356.236838530942, backtracks = 1, tol = 0.0010556062593660048 Iteration 13: loglikelihood = -1356.2320571167822, backtracks = 1, tol = 0.001178893643826298 Iteration 14: loglikelihood = -1356.2294817775485, backtracks = 1, tol = 0.0005132624874293473 Iteration 15: loglikelihood = -1356.2283162268884, backtracks = 1, tol = 0.0005826038008080966 Iteration 16: loglikelihood = -1356.2276935081843, backtracks = 1, tol = 0.00025032069369071013 Iteration 17: loglikelihood = -1356.2274082472961, backtracks = 1, tol = 0.0002886952923365878 Iteration 18: loglikelihood = -1356.227257301142, backtracks = 1, tol = 0.0001223035198785354 Iteration 19: loglikelihood = -1356.2271873364289, backtracks = 1, tol = 0.00014324181935678216 Iteration 20: loglikelihood = -1356.2271506833663, backtracks = 1, tol = 5.983553941413932e-5 1.571259 seconds (6.47 M allocations: 109.777 MiB, 33.50% gc time, 17.01% 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 = -1571.2816148326278, backtracks = 0, tol = 0.24209471058885657 Iteration 2: loglikelihood = -1509.2707307267597, backtracks = 0, tol = 0.17167852000537648 Iteration 3: loglikelihood = -1468.6497571009475, backtracks = 0, tol = 0.15682734808123444 Iteration 4: loglikelihood = -1451.0888364298378, backtracks = 0, tol = 0.06942407196199503 Iteration 5: loglikelihood = -1437.9734119961247, backtracks = 0, tol = 0.023074484253336802 Iteration 6: loglikelihood = -1428.430264085155, backtracks = 0, tol = 0.013578469565003692 Iteration 7: loglikelihood = -1420.1644023315514, backtracks = 0, tol = 0.008698617991176416 Iteration 8: loglikelihood = -1413.7832611518036, backtracks = 0, tol = 0.009431547896221497 Iteration 9: loglikelihood = -1408.1474486371753, backtracks = 0, tol = 0.006131962191917335 Iteration 10: loglikelihood = -1402.5628106797485, backtracks = 0, tol = 0.07227876774506362 Iteration 11: loglikelihood = -1396.9826757710327, backtracks = 0, tol = 0.04969551042906009 Iteration 12: loglikelihood = -1393.2953713170227, backtracks = 0, tol = 0.007216830666541637 Iteration 13: loglikelihood = -1390.6692333121566, backtracks = 0, tol = 0.07411329008841822 Iteration 14: loglikelihood = -1387.9040962371807, backtracks = 0, tol = 0.012065393532367567 Iteration 15: loglikelihood = -1385.5324411975232, backtracks = 0, tol = 0.0022737514421628463 Iteration 16: loglikelihood = -1383.4504800100765, backtracks = 0, tol = 0.0711814106085089 Iteration 17: loglikelihood = -1381.2649414900504, backtracks = 0, tol = 0.004592023889353508 Iteration 18: loglikelihood = -1379.5451443257912, backtracks = 0, tol = 0.0018315336872085691 Iteration 19: loglikelihood = -1377.9775000984432, backtracks = 0, tol = 0.0007035876901012334 Iteration 20: loglikelihood = -1376.5932561258962, backtracks = 0, tol = 0.0005345154036135946 Iteration 21: loglikelihood = -1375.3298290695898, backtracks = 0, tol = 0.00030562013573320163 Iteration 22: loglikelihood = -1374.1922884331145, backtracks = 0, tol = 0.0002531756814905989 Iteration 23: loglikelihood = -1373.1486959438707, backtracks = 0, tol = 0.00022392253781555385 Iteration 24: loglikelihood = -1372.1995097238007, backtracks = 0, tol = 0.0002229077421995324 Iteration 25: loglikelihood = -1371.3238564895269, backtracks = 0, tol = 0.00018272529706439604 Iteration 26: loglikelihood = -1370.5219814613608, backtracks = 0, tol = 0.0001994105511673202 Iteration 27: loglikelihood = -1369.7784549684873, backtracks = 0, tol = 0.00016294728488680987 Iteration 28: loglikelihood = -1369.0940066948535, backtracks = 0, tol = 0.00017950006570022876 Iteration 29: loglikelihood = -1368.4564566078109, backtracks = 0, tol = 0.00014858911196212511 Iteration 30: loglikelihood = -1367.8670233499452, backtracks = 0, tol = 0.00016411900875903623 Iteration 31: loglikelihood = -1367.3157145314926, backtracks = 0, tol = 0.00013555035616792796 Iteration 32: loglikelihood = -1366.8041225846437, backtracks = 0, tol = 0.00015213998073810195 Iteration 33: loglikelihood = -1366.3238395289845, backtracks = 0, tol = 0.00012403010484410458 Iteration 34: loglikelihood = -1365.8767096972317, backtracks = 0, tol = 0.00014181742190174285 Iteration 35: loglikelihood = -1365.45553083489, backtracks = 0, tol = 0.00011390366370221195 Iteration 36: loglikelihood = -1365.0622957304422, backtracks = 0, tol = 0.00013272583214802433 Iteration 37: loglikelihood = -1364.690754027944, backtracks = 0, tol = 0.00010498791616743744 Iteration 38: loglikelihood = -1364.3429664268176, backtracks = 0, tol = 0.00012459860992198937 Iteration 39: loglikelihood = -1364.0134553142482, backtracks = 0, tol = 9.710685753145325e-5 0.424966 seconds (1.51 M allocations: 29.947 MiB) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse NegativeBinomial regression Number of threads = 1 Link functin = LogLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -3600.3948, backtracks = 0, tol = 0.0835394934670704 Iteration 2: loglikelihood = -3548.529, backtracks = 0, tol = 0.047742335854912485 Iteration 3: loglikelihood = -3520.9312, backtracks = 1, tol = 0.061987151238616964 Iteration 4: loglikelihood = -3513.9941, backtracks = 1, tol = 0.014461161871245892 Iteration 5: loglikelihood = -3511.411, backtracks = 1, tol = 0.008800520631577977 Iteration 6: loglikelihood = -3510.6426, backtracks = 1, tol = 0.005394055750906609 Iteration 7: loglikelihood = -3497.0955, backtracks = 1, tol = 0.07027677687290942 Iteration 8: loglikelihood = -3495.728, backtracks = 1, tol = 0.005870727156059559 Iteration 9: loglikelihood = -3495.167, backtracks = 1, tol = 0.003988327433876259 Iteration 10: loglikelihood = -3494.9702, backtracks = 1, tol = 0.0028131953521635215 Iteration 11: loglikelihood = -3487.1807, backtracks = 1, tol = 0.07872619802906787 Iteration 12: loglikelihood = -3475.7456, backtracks = 0, tol = 0.08659579297820823 Iteration 13: loglikelihood = -3474.031, backtracks = 0, tol = 0.006705112239839922 Iteration 14: loglikelihood = -3473.8691, backtracks = 0, tol = 0.0049675015969173385 Iteration 15: loglikelihood = -3473.8257, backtracks = 0, tol = 0.001189347254000493 Iteration 16: loglikelihood = -3473.823, backtracks = 0, tol = 0.0012235046782128277 Iteration 17: loglikelihood = -3473.8167, backtracks = 1, tol = 0.0001494197828365114 Iteration 18: loglikelihood = -3473.8184, backtracks = 3, tol = 4.423465435392622e-5 12.943859 seconds (13.56 M allocations: 531.392 MiB, 4.77% gc time, 94.96% 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 = -3489.5505, backtracks = 0, tol = 0.0835394934670704 Iteration 2: loglikelihood = -3366.6711, backtracks = 0, tol = 0.04915387643077777 Iteration 3: loglikelihood = -3146.967, backtracks = 1, tol = 0.06063911984179207 Iteration 4: loglikelihood = -3138.3503, backtracks = 0, tol = 0.1016932833427035 Iteration 5: loglikelihood = -2916.8389, backtracks = 0, tol = 0.10288012262307704 Iteration 6: loglikelihood = -2793.5679, backtracks = 0, tol = 0.08896049919938945 Iteration 7: loglikelihood = -2685.7893, backtracks = 0, tol = 0.08543169355162665 Iteration 8: loglikelihood = -2582.5034, backtracks = 0, tol = 0.08729200195884565 Iteration 9: loglikelihood = -2483.2756, backtracks = 0, tol = 0.08758974431903982 Iteration 10: loglikelihood = -2393.8142, backtracks = 0, tol = 0.08672773168291134 Iteration 11: loglikelihood = -2328.7214, backtracks = 0, tol = 0.10063818316396288 Iteration 12: loglikelihood = -2271.0374, backtracks = 0, tol = 0.10043668566936316 Iteration 13: loglikelihood = -2224.0933, backtracks = 0, tol = 0.10853916995226909 Iteration 14: loglikelihood = -2192.3203, backtracks = 0, tol = 0.10788348883651355 Iteration 15: loglikelihood = -2172.9714, backtracks = 0, tol = 0.10385222374448592 Iteration 16: loglikelihood = -2161.05, backtracks = 0, tol = 0.10350009724856342 Iteration 17: loglikelihood = -2154.7979, backtracks = 0, tol = 0.10503144542699978 Iteration 18: loglikelihood = -2150.8193, backtracks = 0, tol = 0.10471686078025948 Iteration 19: loglikelihood = -2149.3152, backtracks = 0, tol = 0.1059088863979579 Iteration 20: loglikelihood = -2147.936, backtracks = 0, tol = 0.1056064585208745 Iteration 21: loglikelihood = -2147.8616, backtracks = 0, tol = 0.1064054222400746 Iteration 22: loglikelihood = -2147.2048, backtracks = 0, tol = 0.10611115627354555 Iteration 23: loglikelihood = -2144.924, backtracks = 1, tol = 0.018078818594395814 Iteration 24: loglikelihood = -2144.5796, backtracks = 1, tol = 0.006931729402215928 Iteration 25: loglikelihood = -2142.8896, backtracks = 0, tol = 0.09908843589148716 Iteration 26: loglikelihood = -2141.9963, backtracks = 1, tol = 0.011076282896478478 Iteration 27: loglikelihood = -2141.8386, backtracks = 1, tol = 0.005305734454840627 Iteration 28: loglikelihood = -2141.7996, backtracks = 1, tol = 0.0025489182526283252 Iteration 29: loglikelihood = -2141.788, backtracks = 1, tol = 0.001209453742946308 Iteration 30: loglikelihood = -2141.7869, backtracks = 1, tol = 0.0006134757881829597 Iteration 31: loglikelihood = -2141.7834, backtracks = 1, tol = 0.00032531378142402226 Iteration 32: loglikelihood = -2141.7837, backtracks = 3, tol = 4.5480430156331106e-5 0.215211 seconds (1.78 M allocations: 31.172 MiB) Test Summary: | Pass Total Time Negative binomial nuisance parameter Float32 matrix | 12 12 17.7s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse linear regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -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 5.461678 seconds (777.09 k allocations: 117.353 MiB, 0.60% gc time, 90.67% compilation time) Test Summary: | Pass Total Time initialze beta | 1 1 5.9s 6.170797 seconds (3.93 M allocations: 93.411 MiB, 0.60% gc time, 0.66% compilation time) 3.957074 seconds (3.90 M allocations: 101.152 MiB, 0.64% gc time) 7.045649 seconds (22.46 M allocations: 558.961 MiB, 0.42% gc time, 2.22% compilation time) 7.439442 seconds (22.37 M allocations: 560.640 MiB, 0.30% gc time) 27.451737 seconds (1.83 M allocations: 3.478 GiB, 0.61% gc time, 13.44% compilation time) 23.792620 seconds (57.83 k allocations: 319.311 MiB, 0.06% gc time) Test Summary: | Pass Total Time memory_efficient keyword | 7 7 1m24.0s Test Summary: | Pass Total Time update_support! | 10 10 0.5s 10.084 ms (76 allocations: 5.30 KiB) 5.116 μs (2 allocations: 176 bytes) 99.099 μs (2 allocations: 288 bytes) 2.716 μs (0 allocations: 0 bytes) 22.669 μs (2 allocations: 128 bytes) 11.340 μs (0 allocations: 0 bytes) 3.695 μs (0 allocations: 0 bytes) 3.859 μs (0 allocations: 0 bytes) 29.469 μs (0 allocations: 0 bytes) 30.291 ms (76 allocations: 5.30 KiB) 28.700 μs (2 allocations: 1.02 KiB) 148.728 μs (2 allocations: 288 bytes) 14.780 μs (0 allocations: 0 bytes) 100.789 μs (2 allocations: 128 bytes) 44.539 μs (0 allocations: 0 bytes) 28.900 μs (0 allocations: 0 bytes) 23.589 μs (0 allocations: 0 bytes) 88.350 μs (0 allocations: 0 bytes) Test Summary: | Time benchmarks for multivariate function | None 2m27.1s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse Multivariate Gaussian regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 12 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -2900.9186300194497, backtracks = 0, tol = 0.14802242082004133 Iteration 2: loglikelihood = -2869.406464695619, backtracks = 0, tol = 0.03512679046077987 Iteration 3: loglikelihood = -2868.084702693443, backtracks = 0, tol = 0.0055693496163324524 Iteration 4: loglikelihood = -2868.034423817725, backtracks = 0, tol = 0.001118951762895177 Iteration 5: loglikelihood = -2868.0308576353746, backtracks = 0, tol = 0.00031182601179140966 Iteration 6: loglikelihood = -2868.0305288614227, backtracks = 0, tol = 0.00010393305949948345 Iteration 7: loglikelihood = -2868.0304966516946, backtracks = 0, tol = 3.1008620498575026e-5 0.650314 seconds (36.10 k allocations: 6.535 MiB, 21.14% compilation time) Test Summary: | Pass Total Time multivariate fit_iht SnpLinAlg | 7 7 8.1s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse Multivariate Gaussian regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 12 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -2878.028812628852, backtracks = 0, tol = 2.5661768673084553 Iteration 2: loglikelihood = -2868.563037890196, backtracks = 0, tol = 0.024335274263285057 Iteration 3: loglikelihood = -2868.0815051475474, backtracks = 0, tol = 0.004072558228741048 Iteration 4: loglikelihood = -2868.0352100240902, backtracks = 0, tol = 0.0013135682973484317 Iteration 5: loglikelihood = -2868.030929723194, backtracks = 0, tol = 0.000386434110747091 Iteration 6: loglikelihood = -2868.0305335492912, backtracks = 0, tol = 0.00011924564415557833 Iteration 7: loglikelihood = -2868.0304968517494, backtracks = 0, tol = 3.603726989721193e-5 2.865360 seconds (466.60 k allocations: 187.469 MiB, 2.71% gc time, 59.87% 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: 0:01:56 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... 46%|██████████████▊ | ETA: 0:00:08 Cross validating... 49%|███████████████▊ | ETA: 0:00:07 Cross validating... 52%|████████████████▊ | ETA: 0:00:06 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 2924.439383216143 1 1796.7909783882228 2 1166.7979266048164 3 813.3714738774627 4 524.1309387603607 5 486.00294675599025 6 440.30358751013745 7 394.6465642415813 8 346.8147223696517 9 330.8512767163221 10 329.37779222683486 11 331.994720907021 12 339.7192745355306 13 337.78912592571254 14 338.8939905013351 15 340.52749943231345 16 352.50736577343287 17 340.16818084889854 18 344.6735554397102 19 357.47239389193135 20 362.7460669887353 Best k = 10 9.686282 seconds (12.71 M allocations: 392.819 MiB, 0.78% gc time, 50.06% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:03 Cross validating... 6%|██ | ETA: 0:00:03 Cross validating... 10%|███ | ETA: 0:00:03 Cross validating... 13%|████▏ | ETA: 0:00:03 Cross validating... 16%|█████▏ | ETA: 0:00:03 Cross validating... 19%|██████▏ | ETA: 0:00:03 Cross validating... 22%|███████▏ | ETA: 0:00:03 Cross validating... 25%|████████▏ | ETA: 0:00:03 Cross validating... 29%|█████████▏ | ETA: 0:00:03 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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... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:04 Crossvalidation Results: k MSE 0 2924.439383216143 1 1797.284998978033 2 1173.325205361976 3 820.6252572199603 4 528.509837628223 5 493.9756403938841 6 450.20789908830017 7 403.4650315939738 8 356.64454836215987 9 340.97707735857466 10 341.7327826091168 11 347.9684109411479 12 358.74893575074765 13 363.1788243581899 14 368.4159415990953 15 371.50614697914864 16 373.0925399151115 17 371.1741862953833 18 384.7708490680077 19 389.504209468545 20 394.13523210335745 Best k = 9 5.022741 seconds (11.65 M allocations: 285.076 MiB, 0.65% gc time, 0.33% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, normal model | 3 3 15.4s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:05:50 Cross validating... 8%|██▌ | ETA: 0:02:15 Cross validating... 13%|████▏ | ETA: 0:01:21 Cross validating... 17%|█████▋ | ETA: 0:00:56 Cross validating... 22%|███████▏ | ETA: 0:00:42 Cross validating... 27%|████████▋ | ETA: 0:00:33 Cross validating... 30%|█████████▋ | ETA: 0:00:28 Cross validating... 33%|██████████▋ | ETA: 0:00:25 Cross validating... 38%|████████████▎ | ETA: 0:00:20 Cross validating... 43%|█████████████▊ | ETA: 0:00:17 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... 65%|████████████████████▉ | ETA: 0:00:07 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:06 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:05 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:03 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:03 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:02 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:01 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:14 Crossvalidation Results: k MSE 0 1560.05594921875 1 1279.5736118164061 2 1022.8045040283205 3 796.6607552490235 4 636.0837203369141 5 524.4077139892578 6 464.16578198242183 7 393.98951257324217 8 366.7139546508789 9 349.4809404907227 10 352.09354846191405 11 357.0707883911133 12 366.4817882690429 13 372.4817534790039 14 367.7080319213867 15 367.3106452026367 16 364.3014705810547 17 381.3570414428711 18 387.0271789550781 19 387.6978104858398 20 375.2228884887695 Best k = 9 14.582750 seconds (12.99 M allocations: 337.746 MiB, 0.57% gc time, 80.48% 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 **** 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... 35%|███████████▏ | ETA: 0:00:02 Cross validating... 41%|█████████████▎ | ETA: 0:00:01 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... 68%|█████████████████████▉ | ETA: 0:00:01 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:01 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:01 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:00 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:00 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:00 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:02 Crossvalidation Results: k MSE 0 1560.05594921875 1 1279.8906040039062 2 1023.2460660400391 3 802.0525571289063 4 639.0639427490235 5 527.5768243408203 6 470.9269691772461 7 401.0749921875 8 373.5683501586914 9 356.5201115112304 10 362.78783471679685 11 370.721507446289 12 373.1470818481445 13 385.88944104003906 14 408.270043762207 15 401.9248783569336 16 411.05925 17 407.491010131836 18 421.82722399902343 19 425.5785975952149 20 433.7098634643554 Best k = 9 2.993396 seconds (11.57 M allocations: 233.243 MiB, 1.22% gc time, 1.00% compilation time) Test Summary: | Pass Total Time Cross validation on Float32 matrix, normal model | 2 2 18.6s **** 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 **** Cross validating... 3%|█ | ETA: 0:00:31 Cross validating... 6%|██ | ETA: 0:00:18 Cross validating... 8%|██▌ | ETA: 0:00:15 Cross validating... 11%|███▌ | ETA: 0:00:12 Cross validating... 13%|████▏ | ETA: 0:00:11 Cross validating... 16%|█████▏ | ETA: 0:00:10 Cross validating... 19%|██████▏ | ETA: 0:00:08 Cross validating... 22%|███████▏ | ETA: 0:00:08 Cross validating... 25%|████████▏ | ETA: 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validating... 92%|█████████████████████████████▌ | ETA: 0:00:01 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:00 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: 0:00:07 Crossvalidation Results: k MSE 0 464.2087914607164 1 412.1338105476094 2 360.3764046688082 3 334.14029901005046 4 294.0242352941087 5 291.5359311522119 6 299.0157543628116 7 296.7574871141057 8 298.14593308606146 9 303.84389578041146 10 308.8053783410718 11 328.5679413694409 12 300.1409291563822 13 332.7360211771641 14 337.8831791929507 15 307.03020012262044 16 321.3730454140282 17 354.82551193576876 18 315.4198499937413 19 328.4602629594609 20 315.411145062785 Best k = 5 7.878895 seconds (18.91 M allocations: 507.319 MiB, 0.61% gc time, 15.66% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:05 Cross validating... 5%|█▌ | ETA: 0:00:05 Cross validating... 6%|██ | ETA: 0:00:05 Cross validating... 8%|██▌ | ETA: 0:00:06 Cross validating... 10%|███ | ETA: 0:00:06 Cross validating... 11%|███▌ | ETA: 0:00:06 Cross validating... 13%|████▏ | ETA: 0:00:06 Cross validating... 14%|████▋ | ETA: 0:00:06 Cross validating... 16%|█████▏ | ETA: 0:00:05 Cross validating... 17%|█████▋ | ETA: 0:00:05 Cross validating... 19%|██████▏ | ETA: 0:00:05 Cross validating... 21%|██████▋ | ETA: 0:00:05 Cross validating... 22%|███████▏ | ETA: 0:00:05 Cross validating... 24%|███████▋ | ETA: 0:00:05 Cross validating... 25%|████████▏ | ETA: 0:00:05 Cross validating... 27%|████████▋ | ETA: 0:00:05 Cross validating... 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62%|███████████████████▊ | ETA: 0:00:02 Cross validating... 63%|████████████████████▍ | ETA: 0:00:02 Cross validating... 65%|████████████████████▉ | ETA: 0:00:02 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:02 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:02 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:02 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:02 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:02 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:02 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:01 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:01 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:01 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:01 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:01 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:01 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:01 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:01 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:01 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:06 Crossvalidation Results: k MSE 0 464.2087914607164 1 412.70387848454806 2 361.21961395559777 3 336.6019870746053 4 297.17503418791557 5 297.36100638871767 6 311.8935025704076 7 312.41948908030577 8 317.35001643268066 9 317.33056396562574 10 325.33621197132334 11 334.78917664442304 12 327.8200322783647 13 343.0845307614665 14 348.04458206673263 15 357.1788038376821 16 374.15072842992515 17 377.5440158662726 18 382.4241581826373 19 376.46175217389055 20 383.57783997433637 Best k = 4 6.673468 seconds (19.70 M allocations: 489.444 MiB, 0.52% gc time, 0.25% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, logistic model | 2 2 14.9s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:27 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: 0:00:06 Cross validating... 25%|████████▏ | ETA: 0:00:06 Cross validating... 29%|█████████▏ | ETA: 0:00:05 Cross validating... 32%|██████████▏ | ETA: 0:00:05 Cross validating... 33%|██████████▋ | ETA: 0:00:05 Cross validating... 38%|████████████▎ | ETA: 0:00:04 Cross validating... 41%|█████████████▎ | ETA: 0:00:04 Cross validating... 44%|██████████████▎ | ETA: 0:00:04 Cross validating... 48%|███████████████▎ | ETA: 0:00:03 Cross validating... 51%|████████████████▎ | ETA: 0:00:03 Cross validating... 54%|█████████████████▎ | ETA: 0:00:03 Cross validating... 57%|██████████████████▎ | ETA: 0:00:03 Cross validating... 59%|██████████████████▊ | ETA: 0:00:03 Cross validating... 62%|███████████████████▊ | ETA: 0:00:02 Cross validating... 65%|████████████████████▉ | ETA: 0:00:02 Cross validating... 68%|█████████████████████▉ | ETA: 0:00:02 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:02 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:02 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:01 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:01 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:01 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:01 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:01 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:00 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:06 Crossvalidation Results: k MSE 0 463.7040558365505 1 439.13649981827314 2 388.049055507512 3 371.12146845836435 4 348.00156840428804 5 323.4305664592427 6 300.6676375727924 7 301.9611165804304 8 305.5707479451649 9 310.4968468226131 10 309.0405027461776 11 313.2651515177211 12 312.3317072880577 13 310.4289064331332 14 337.4946894277383 15 342.0020991767999 16 355.3242319283728 17 336.25410914641975 18 317.91686545803236 19 315.6149290025652 20 313.78338078050365 Best k = 6 6.676585 seconds (17.80 M allocations: 478.164 MiB, 12.83% gc time, 16.33% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** 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: 0:00:03 Cross validating... 25%|████████▏ | ETA: 0:00:03 Cross validating... 27%|████████▋ | ETA: 0:00:03 Cross validating... 30%|█████████▋ | ETA: 0:00:03 Cross validating... 33%|██████████▋ | ETA: 0:00:03 Cross validating... 38%|████████████▎ | ETA: 0:00:03 Cross validating... 41%|█████████████▎ | ETA: 0:00:03 Cross validating... 44%|██████████████▎ | ETA: 0:00:02 Cross validating... 48%|███████████████▎ | ETA: 0:00:02 Cross validating... 51%|████████████████▎ | ETA: 0:00:02 Cross validating... 54%|█████████████████▎ | ETA: 0:00:02 Cross validating... 57%|██████████████████▎ | ETA: 0:00:02 Cross validating... 60%|███████████████████▎ | ETA: 0:00:02 Cross validating... 63%|████████████████████▍ | ETA: 0:00:02 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:01 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:01 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:01 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:01 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:01 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:01 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:01 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:00 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:04 Crossvalidation Results: k MSE 0 463.7040558365505 1 441.5127394630992 2 391.61466646416955 3 379.8087295362778 4 353.070724899924 5 328.25332860789695 6 305.3538235103994 7 309.65793092279046 8 317.26387031100415 9 323.5972842642434 10 328.0191857775831 11 345.00660736614367 12 336.697969789608 13 342.75724715917545 14 348.9888208113502 15 362.7299417024641 16 371.7281401948378 17 374.17313357937337 18 368.5331377107957 19 387.29244186856494 20 381.0421658273304 Best k = 6 4.391793 seconds (18.70 M allocations: 450.585 MiB, 0.65% gc time, 1.18% compilation time) Test Summary: | Pass Total Time Cross validation on Float64 matrix, logistic model | 2 2 11.5s **** 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: 0:00:21 Cross validating... 6%|██ | ETA: 0:00:12 Cross validating... 10%|███ | ETA: 0:00:09 Cross validating... 13%|████▏ | ETA: 0:00:08 Cross validating... 16%|█████▏ | ETA: 0:00:07 Cross validating... 19%|██████▏ | ETA: 0:00:06 Cross validating... 22%|███████▏ | ETA: 0:00:05 Cross validating... 25%|████████▏ | ETA: 0:00:05 Cross validating... 29%|█████████▏ | ETA: 0:00:05 Cross validating... 32%|██████████▏ | ETA: 0:00:04 Cross validating... 35%|███████████▏ | ETA: 0:00:04 Cross validating... 38%|████████████▎ | ETA: 0:00:04 Cross validating... 41%|█████████████▎ | ETA: 0:00:03 Cross validating... 44%|██████████████▎ | ETA: 0:00:03 Cross validating... 48%|███████████████▎ | ETA: 0:00:03 Cross validating... 51%|████████████████▎ | ETA: 0:00:03 Cross validating... 54%|█████████████████▎ | ETA: 0:00:02 Cross validating... 57%|██████████████████▎ | ETA: 0:00:02 Cross validating... 60%|███████████████████▎ | ETA: 0:00:02 Cross validating... 63%|████████████████████▍ | ETA: 0:00:02 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:02 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:01 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:01 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:01 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:01 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:01 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:01 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:00 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:04 Crossvalidation Results: k MSE 0 979.4076273706539 1 545.1293174281603 2 447.0447174032404 3 413.8146863263328 4 377.46259161716796 5 377.5683857531058 6 376.9983175103074 7 373.9920355851187 8 380.6698740861152 9 378.8216367971424 10 381.3104454606487 11 380.93276798111026 12 402.80523475601274 13 407.7057397350509 14 406.01495258312013 15 397.6169697170216 16 399.44871870809095 17 386.1019453887 18 393.36184607709527 19 409.3466448799629 20 404.88135236630717 Best k = 7 5.344319 seconds (15.66 M allocations: 401.264 MiB, 0.58% gc time, 15.93% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 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: 0:00:03 Cross validating... 25%|████████▏ | ETA: 0:00:03 Cross validating... 29%|█████████▏ | ETA: 0:00:03 Cross validating... 32%|██████████▏ | ETA: 0:00:03 Cross validating... 35%|███████████▏ | ETA: 0:00:03 Cross validating... 38%|████████████▎ | ETA: 0:00:03 Cross validating... 41%|█████████████▎ | ETA: 0:00:03 Cross validating... 44%|██████████████▎ | ETA: 0:00:02 Cross validating... 48%|███████████████▎ | ETA: 0:00:02 Cross validating... 51%|████████████████▎ | ETA: 0:00:02 Cross validating... 54%|█████████████████▎ | ETA: 0:00:02 Cross validating... 57%|██████████████████▎ | ETA: 0:00:02 Cross validating... 60%|███████████████████▎ | ETA: 0:00:02 Cross validating... 63%|████████████████████▍ | ETA: 0:00:02 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:02 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:01 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:01 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:01 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:01 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:01 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:01 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:01 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:00 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:04 Crossvalidation Results: k MSE 0 979.4076273706539 1 537.562558966097 2 441.2780580262471 3 420.3837971708632 4 377.30572563055034 5 398.1248208556866 6 390.1600970202477 7 388.53790122193175 8 392.3032911772551 9 412.0567560727526 10 412.7180635842219 11 417.83005098024796 12 414.8473341903052 13 421.69175016576247 14 411.702235383602 15 422.8624465821649 16 423.97567886064917 17 428.18108419148905 18 441.0294862289405 19 451.02861339515425 20 453.9870449114017 Best k = 4 5.139054 seconds (14.76 M allocations: 333.510 MiB, 0.53% gc time, 0.25% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, Poisson model | 2 2 10.8s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:59 Cross validating... 5%|█▌ | ETA: 0:00:59 Cross validating... 6%|██ | ETA: 0:00:58 Cross validating... 8%|██▌ | ETA: 0:00:47 Cross validating... 10%|███ | ETA: 0:00:40 Cross validating... 11%|███▌ | ETA: 0:00:35 Cross validating... 13%|████▏ | ETA: 0:00:31 Cross validating... 14%|████▋ | ETA: 0:00:28 Cross validating... 16%|█████▏ | ETA: 0:00:26 Cross validating... 17%|█████▋ | ETA: 0:00:24 Cross validating... 19%|██████▏ | ETA: 0:00:22 Cross validating... 21%|██████▋ | ETA: 0:00:20 Cross validating... 22%|███████▏ | ETA: 0:00:22 Cross validating... 24%|███████▋ | ETA: 0:00:24 Cross validating... 25%|████████▏ | ETA: 0:00:25 Cross validating... 27%|████████▋ | ETA: 0:00:26 Cross validating... 29%|█████████▏ | ETA: 0:00:27 Cross validating... 30%|█████████▋ | ETA: 0:00:25 Cross validating... 32%|██████████▏ | ETA: 0:00:26 Cross validating... 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ETA: 0:00:01 Cross validating... 100%|████████████████████████████████| Time: 0:00:33 Crossvalidation Results: k MSE 0 398.52055276179703 1 288.24927913484566 2 256.1784244946362 3 242.1589524316933 4 223.02563504253658 5 225.0304449872471 6 224.25064168714505 7 224.0118441443618 8 225.44914561684016 9 226.38409873666126 10 228.4397324229924 11 228.49041405243105 12 229.8178461472991 13 232.12774909234517 14 230.8561864002184 15 232.88995782823417 16 229.5599644385648 17 237.04074259434555 18 234.21379495136858 19 233.14834000579532 20 235.41004390189227 Best k = 4 33.475036 seconds (127.48 M allocations: 3.765 GiB, 0.52% gc time, 3.11% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 5%|█▌ | ETA: 0:00:04 Cross validating... 6%|██ | ETA: 0:00:05 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398.52055276179703 1 287.9818812452623 2 256.06688111942015 3 242.6363858866606 4 224.1255757026576 5 229.02201318553358 6 228.33807971632893 7 232.0620113898472 8 235.7790624366588 9 238.70109492757888 10 244.6024260910872 11 248.72965331286758 12 248.26068363894052 13 252.5322283876418 14 253.0905906549572 15 257.6515137527811 16 261.2489272905749 17 267.6460693351854 18 283.4638609586969 19 276.6604083817823 20 286.78489048531105 Best k = 4 9.378070 seconds (37.38 M allocations: 893.272 MiB, 0.70% gc time, 0.18% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, NegativeBinomial model | 2 2 43.2s **** 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... 8%|██▌ | ETA: 0:00:12 Cross validating... 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97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:03 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 3.642149 seconds (17.77 M allocations: 379.654 MiB, 1.37% gc time, 29.62% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 6%|██ | ETA: 0:00:02 Cross 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94%|██████████████████████████████ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:02 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 2.625306 seconds (17.20 M allocations: 333.508 MiB, 1.51% gc time, 0.82% compilation time) Test Summary: | Pass Total Time Cross validation on floating point matrices, NegativeBinomial model | 2 2 6.5s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, 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1230.1889297644345 11 1230.9577423015944 12 1233.444446708212 13 1246.647385782617 14 1246.7490168491756 15 1242.5675909260074 16 1257.0682582060822 17 1264.437892484379 18 1264.7977816191458 19 1284.843362418993 20 1286.2919895404843 Best k = 8 28.622353 seconds (316.76 k allocations: 404.252 MiB, 0.13% gc time, 2.13% compilation time) Test Summary: | Pass Total Time multivariate cross validation SnpLinAlg | 3 3 30.5s Test Summary: | Pass Total Time wrapper univariate | 20 20 1m07.5s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 2%|▋ | ETA: 0:00:19 Cross validating... 3%|█ | ETA: 0:00:19 Cross validating... 4%|█▎ | ETA: 0:00:20 Cross validating... 5%|█▋ | ETA: 0:00:20 Cross validating... 6%|█▉ | ETA: 0:00:23 Cross validating... 7%|██▎ | ETA: 0:00:23 Cross 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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: 0:00:24 Cross validating... 8%|██▌ | ETA: 0:00:25 Cross validating... 9%|██▉ | ETA: 0:00:26 Cross validating... 10%|███▎ | ETA: 0:00:27 Cross validating... 11%|███▌ | ETA: 0:00:27 Cross validating... 12%|███▉ | ETA: 0:00:27 Cross validating... 13%|████▏ | ETA: 0:00:28 Cross validating... 14%|████▌ | ETA: 0:00:28 Cross validating... 15%|████▊ | ETA: 0:00:29 Cross validating... 16%|█████▏ | ETA: 0:00:29 Cross validating... 17%|█████▌ | ETA: 0:00:30 Cross validating... 18%|█████▊ | ETA: 0:00:31 Cross validating... 19%|██████▏ | ETA: 0:00:32 Cross validating... 20%|██████▍ | ETA: 0:00:32 Cross validating... 21%|██████▊ | ETA: 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2146.932938567968 11 2136.233335135846 12 2157.0997044352102 13 2186.316288272038 14 2203.704554775872 15 2216.007861148507 16 2219.0864904635287 17 2226.9002968977798 18 2213.193277562036 19 2234.064675154158 20 2245.124287391089 Best k = 6 **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 2%|▋ | ETA: 0:00:18 Cross validating... 3%|█ | ETA: 0:00:17 Cross validating... 4%|█▎ | ETA: 0:00:19 Cross validating... 5%|█▋ | ETA: 0:00:18 Cross validating... 6%|█▉ | ETA: 0:00:21 Cross validating... 7%|██▎ | ETA: 0:00:21 Cross validating... 8%|██▌ | ETA: 0:00:22 Cross validating... 9%|██▉ | ETA: 0:00:24 Cross validating... 10%|███▎ | ETA: 0:00:25 Cross validating... 11%|███▌ | ETA: 0:00:25 Cross validating... 12%|███▉ | ETA: 0:00:25 Cross validating... 13%|████▏ | ETA: 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84%|██████████████████████████▉ | ETA: 0:00:06 Cross validating... 85%|███████████████████████████▎ | ETA: 0:00:06 Cross validating... 86%|███████████████████████████▌ | ETA: 0:00:06 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:05 Cross validating... 88%|████████████████████████████▏ | ETA: 0:00:05 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:04 Cross validating... 90%|████████████████████████████▊ | ETA: 0:00:04 Cross validating... 91%|█████████████████████████████▏ | ETA: 0:00:04 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:03 Cross validating... 93%|█████████████████████████████▊ | ETA: 0:00:03 Cross validating... 94%|██████████████████████████████▏ | ETA: 0:00:02 Cross validating... 95%|██████████████████████████████▍ | ETA: 0:00:02 Cross validating... 96%|██████████████████████████████▊ | ETA: 0:00:02 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:01 Cross validating... 98%|███████████████████████████████▍| ETA: 0:00:01 Cross validating... 99%|███████████████████████████████▋| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:41 Crossvalidation Results: k MSE 1 2849.383229379955 2 2524.303106109175 3 2312.799164395459 4 2230.747234917732 5 2083.421861525868 6 2075.7860282241654 7 2080.295568366649 8 2096.5527441552867 9 2103.7789161312476 10 2146.932938567968 11 2136.233335135846 12 2157.0997044352102 13 2186.316288272038 14 2203.704554775872 15 2216.007861148507 16 2219.0864904635287 17 2226.9002968977798 18 2213.193277562036 19 2234.064675154158 20 2245.124287391089 Best k = 6 Test Summary: | Pass Total Time wrapper multivariate | 8 8 2m18.5s 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 4.9s ERROR: LoadError: Some tests did not pass: 0 passed, 0 failed, 1 errored, 0 broken. in expression starting at /home/pkgeval/.julia/packages/MendelIHT/ZcxZT/test/wrapper_test.jl:184 in expression starting at /home/pkgeval/.julia/packages/MendelIHT/ZcxZT/test/runtests.jl:20 Testing failed after 898.71s 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 1023.67s: package tests unexpectedly errored