Package evaluation to test MendelIHT on Julia 1.14.0-DEV.2637 (b1f508acef*) started at 2026-07-13T01:33:27.530 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.14` Set-up completed after 14.04s ################################################################################ # Installation # Installing MendelIHT... Resolving package versions... Updating `~/.julia/environments/v1.14/Project.toml` [921c7187] + MendelIHT v1.4.11 Updating `~/.julia/environments/v1.14/Manifest.toml` [7d9f7c33] + Accessors v0.1.45 [79e6a3ab] + Adapt v4.7.0 [66dad0bd] + AliasTables v1.1.3 [4fba245c] + ArrayInterface v7.27.0 [67c07d97] + Automa v1.2.0 ⌅ [6db4b851] + BGEN v0.1.17 [28d598bf] + BGZFStreams v0.3.2 [47718e42] + BioGenerics v0.1.5 [62783981] + BitTwiddlingConvenienceFunctions v0.1.6 [e1450e63] + BufferedStreams v1.2.2 [2a0fbf3d] + CPUSummary v0.2.7 [336ed68f] + CSV v0.10.16 [fb6a15b2] + CloseOpenIntervals v0.1.13 [523fee87] + CodecBzip2 v0.8.5 [ba30903b] + CodecXz v0.7.4 [944b1d66] + CodecZlib v0.7.8 [6b39b394] + CodecZstd v0.8.7 [861a8166] + Combinatorics v1.1.0 [38540f10] + CommonSolve v0.2.11 [f70d9fcc] + CommonWorldInvalidations v1.1.1 [34da2185] + Compat v4.18.1 [a33af91c] + CompositionsBase v0.1.2 [187b0558] + ConstructionBase v1.6.0 [adafc99b] + CpuId v0.3.1 [a8cc5b0e] + Crayons v4.1.1 [a10d1c49] + DBInterface v2.6.1 [9a962f9c] + 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[efcefdf7] + PCRE2_jll v10.47.0+0 [bea87d4a] + SuiteSparse_jll v7.10.1+0 [83775a58] + Zlib_jll v1.3.2+0 [3161d3a3] + Zstd_jll v1.5.7+1 [8e850b90] + libblastrampoline_jll v5.15.0+0 [8e850ede] + nghttp2_jll v1.69.0+0 [3f19e933] + p7zip_jll v17.8.0+0 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. To see why use `status --outdated -m` Installation completed after 5.4s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompiling project... 4.5 s ✓ BGEN 6.9 s ✓ VCFTools WARNING: Constructor for type "MvNormal" was extended in `MendelIHT` without explicit qualification or import. NOTE: Assumed "MvNormal" refers to `Distributions.MvNormal`. This behavior is deprecated and may differ in future versions. NOTE: This behavior may have differed in Julia versions prior to 1.12. Hint: If you intended to create a new generic function of the same name, use `function MvNormal end`. Hint: To silence the warning, qualify `MvNormal` as `Distributions.MvNormal` in the method signature or explicitly `import Distributions: MvNormal`. 21.1 s ✓ MendelIHT 3 dependencies successfully precompiled in 36 seconds. 173 already precompiled. 1 dependency had output during precompilation: ┌ MendelIHT │ WARNING: Constructor for type "MvNormal" was extended in `MendelIHT` without explicit qualification or import. │ NOTE: Assumed "MvNormal" refers to `Distributions.MvNormal`. This behavior is deprecated and may differ in future versions. │ NOTE: This behavior may have differed in Julia versions prior to 1.12. │ Hint: If you intended to create a new generic function of the same name, use `function MvNormal end`. │ Hint: To silence the warning, qualify `MvNormal` as `Distributions.MvNormal` in the method signature or explicitly `import Distributions: MvNormal`. └ Precompilation completed after 62.11s ################################################################################ # Testing # Testing MendelIHT Status `/tmp/jl_mvC0PW/Project.toml` ⌅ [6db4b851] BGEN v0.1.17 [6e4b80f9] BenchmarkTools v1.8.0 [336ed68f] CSV v0.10.16 [a93c6f00] DataFrames v1.8.2 [8bb1440f] DelimitedFiles v1.9.1 [b4f34e82] Distances v0.10.12 [31c24e10] Distributions v0.25.129 [38e38edf] GLM v1.9.5 [921c7187] MendelIHT v1.4.11 [92933f4c] ProgressMeter v1.11.0 [189a3867] Reexport v1.2.2 [4e780e97] SnpArrays v0.3.23 [276daf66] SpecialFunctions v2.8.0 [2913bbd2] StatsBase v0.34.12 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libblastrampoline_jll v5.15.0+0 [8e850ede] nghttp2_jll v1.69.0+0 [3f19e933] p7zip_jll v17.8.0+0 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. Testing Running tests... ┌ Warning: accessing `Type.name` is deprecated without replacement. If for detection, use `Base.isType(x)`. │ caller = Distributions.MvNormal(σ::Vector{Float64}) at mvnormal.jl:207 └ @ Distributions ~/.julia/packages/Distributions/XAng5/src/multivariate/mvnormal.jl:207 ┌ Warning: `MvNormal(σ::AbstractVector{<:Real})` is deprecated, use `MvNormal(LinearAlgebra.Diagonal(map(abs2, σ)))` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `cholesky!(A::RealHermSymComplexHerm{<:Real}, ::Val{true}; kwargs...)` is deprecated, use `cholesky!(A, RowMaximum(); kwargs...)` instead. │ caller = 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 16.3s Test Summary: | Pass Total Time deviance | 1 1 0.4s Test Summary: | Pass Total Time update_μ! | 4 4 1.6s Test Summary: | Pass Total Time _choose! | 7 7 10.1s Test Summary: | Pass Total Time _iht_backtrack | 7 7 0.0s Test Summary: | Pass Total Time standardize! | 12 12 1.4s Test Summary: | Pass Total Time project_k! | 2 2 1.1s Test Summary: | Pass Total Time project_group_sparse! | 5 5 1.2s Test Summary: | Pass Total Time maf_weights | 6 6 2.1s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse linear regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1702.1869764607368, backtracks = 0, tol = 2.177862028568369 Iteration 2: loglikelihood = -1433.9500621413895, backtracks = 0, tol = 0.14264221899272728 Iteration 3: loglikelihood = -1421.5939280179966, backtracks = 0, tol = 0.031843100024129045 Iteration 4: loglikelihood = -1421.4479237107323, backtracks = 0, tol = 0.0038722471963393546 Iteration 5: loglikelihood = -1421.4455813076775, backtracks = 0, tol = 0.0003364279144083857 Iteration 6: loglikelihood = -1421.4455336494134, backtracks = 0, tol = 5.148141699182046e-5 IHT estimated 10 nonzero SNP predictors and 1 non-genetic predictors. Compute time (sec): 0.049855947494506836 Final loglikelihood: -1421.4455336494134 SNP PVE: 0.9343990503261269 Iterations: 6 Selected genetic predictors: 10×2 DataFrame Row │ Position Estimated_β │ Int64 Float64 ─────┼─────────────────────── 1 │ 1879 -0.969942 2 │ 3087 2.02778 3 │ 3607 2.38007 4 │ 3941 0.326184 5 │ 4060 0.349059 6 │ 5017 1.11697 7 │ 5657 0.88941 8 │ 5804 1.21517 9 │ 5990 -0.441522 10 │ 8988 0.397281 Selected nongenetic predictors: 1×2 DataFrame Row │ Position Estimated_β │ Int64 Float64 ─────┼─────────────────────── 1 │ 1 0.0206738Test Summary: | Pass Total Time fit normal SnpLinAlg | 4 4 23.3s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse logistic regression Number of threads = 1 Link functin = LogitLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -379.72375963518977, backtracks = 0, tol = 0.6062552017348442 Iteration 2: loglikelihood = -294.14222098196217, backtracks = 0, tol = 0.39035964909167 Iteration 3: loglikelihood = -258.44215825745147, backtracks = 0, tol = 0.18072720194601524 Iteration 4: loglikelihood = -248.39092317275637, backtracks = 1, tol = 0.0581811999889429 Iteration 5: loglikelihood = -241.2861695402178, backtracks = 2, tol = 0.10199490430383734 Iteration 6: loglikelihood = -236.0344401262056, backtracks = 2, tol = 0.10444957184614982 Iteration 7: loglikelihood = -232.75639772007577, backtracks = 2, tol = 0.03618239958756675 Iteration 8: loglikelihood = -230.9028935826695, backtracks = 3, tol = 0.022566251649321353 Iteration 9: loglikelihood = -229.2332883500926, backtracks = 3, tol = 0.02394599965909332 Iteration 10: loglikelihood = -227.8109863155336, backtracks = 3, tol = 0.02260237147851236 Iteration 11: loglikelihood = -226.61429831284372, backtracks = 3, tol = 0.02153016573221634 Iteration 12: loglikelihood = -225.614543213995, backtracks = 3, tol = 0.020073248773013197 Iteration 13: loglikelihood = -225.15228734295533, backtracks = 3, tol = 0.10266272165892033 Iteration 14: loglikelihood = -224.5524858306654, backtracks = 2, tol = 0.010910053499902256 Iteration 15: loglikelihood = -223.90430308527087, backtracks = 3, tol = 0.10669566586572145 Iteration 16: loglikelihood = -223.43342440058004, backtracks = 1, tol = 0.009912340440473734 Iteration 17: loglikelihood = -223.19474883510568, backtracks = 3, tol = 0.10429355504005154 Iteration 18: loglikelihood = -222.7530868660152, backtracks = 1, tol = 0.010133510239484585 Iteration 19: loglikelihood = -222.4546375562022, backtracks = 3, tol = 0.009382230171462355 Iteration 20: loglikelihood = -225.04961416047087, backtracks = 3, tol = 0.13141028198780508 Iteration 21: loglikelihood = -221.57583298738808, backtracks = 0, tol = 0.12983606150115481 Iteration 22: loglikelihood = -220.9953587123894, backtracks = 0, tol = 0.018278220962270587 Iteration 23: loglikelihood = -220.46528702030645, backtracks = 0, tol = 0.10912949798131547 Iteration 24: loglikelihood = -220.22939682199817, backtracks = 1, tol = 0.006133557493960293 Iteration 25: loglikelihood = -220.1149031779291, backtracks = 3, tol = 0.005637364497494655 Iteration 26: loglikelihood = -237.91408320706802, backtracks = 3, tol = 0.1311916630585333 Iteration 27: loglikelihood = -222.6667401701631, backtracks = 0, tol = 0.13008576394077564 Iteration 28: loglikelihood = -220.0179912284672, backtracks = 0, tol = 0.10981267805412102 Iteration 29: loglikelihood = -219.80873468505163, backtracks = 1, tol = 0.006242686572879014 Iteration 30: loglikelihood = -219.71412932030552, backtracks = 1, tol = 0.0052581541847830735 Iteration 31: loglikelihood = -219.67346582214395, backtracks = 3, tol = 0.002736072071808146 Iteration 32: loglikelihood = -236.63118723570068, backtracks = 3, tol = 0.12536959025201838 Iteration 33: loglikelihood = -222.42522446507616, backtracks = 0, tol = 0.12480632457239557 Iteration 34: loglikelihood = -219.76952387571325, backtracks = 0, tol = 0.10782393864869841 Iteration 35: loglikelihood = -219.54239052596037, backtracks = 0, tol = 0.010969385336776636 Iteration 36: loglikelihood = -219.51051719556185, backtracks = 0, tol = 0.0038143069815270263 Iteration 37: loglikelihood = -219.49562270628724, backtracks = 1, tol = 0.0015360028505860806 Iteration 38: loglikelihood = -222.2776344615594, backtracks = 3, tol = 0.10706948875570901 Iteration 39: loglikelihood = -219.86344247649652, backtracks = 0, tol = 0.10682440099239575 Iteration 40: loglikelihood = -219.50637292175287, backtracks = 0, tol = 0.010145149683589566 Iteration 41: loglikelihood = -219.45601478260392, backtracks = 0, tol = 0.004786594360325445 Iteration 42: loglikelihood = -219.44279315931445, backtracks = 0, tol = 0.0023300326568676676 Iteration 43: loglikelihood = -219.434262597912, backtracks = 0, tol = 0.002159682320412748 Iteration 44: loglikelihood = -219.42706752504972, backtracks = 0, tol = 0.0019986878272562235 Iteration 45: loglikelihood = -219.4208881668612, backtracks = 0, tol = 0.001781315196828412 Iteration 46: loglikelihood = -219.41556755717227, backtracks = 0, tol = 0.0017266268818688624 Iteration 47: loglikelihood = -219.41098445944962, backtracks = 0, tol = 0.001504993867218278 Iteration 48: loglikelihood = -219.4070309112888, backtracks = 0, tol = 0.001495426527055874 Iteration 49: loglikelihood = -219.40362030781677, backtracks = 0, tol = 0.001286324051089446 Iteration 50: loglikelihood = -219.4006747755802, backtracks = 0, tol = 0.001295957349435961 Iteration 51: loglikelihood = -219.39813103252988, backtracks = 0, tol = 0.0011058748112207813 Iteration 52: loglikelihood = -219.3959322024177, backtracks = 0, tol = 0.0011233728145861855 Iteration 53: loglikelihood = -219.39403166729804, backtracks = 0, tol = 0.0009536994758608786 Iteration 54: loglikelihood = -219.39238763268273, backtracks = 0, tol = 0.0009739180646352119 Iteration 55: loglikelihood = -219.39096560226784, backtracks = 0, tol = 0.0008239389039648708 Iteration 56: loglikelihood = -219.38973473800374, backtracks = 0, tol = 0.0008444580901064712 Iteration 57: loglikelihood = -219.3886694316569, backtracks = 0, tol = 0.0007126409505425607 Iteration 58: loglikelihood = -219.38774685610232, backtracks = 0, tol = 0.0007323063866727435 Iteration 59: loglikelihood = -219.3869479529937, backtracks = 0, tol = 0.00061686194275372 Iteration 60: loglikelihood = -219.3862557798823, backtracks = 0, tol = 0.0006351404346176769 Iteration 61: loglikelihood = -219.3856561234815, backtracks = 0, tol = 0.000534269842115572 Iteration 62: loglikelihood = -219.38513638040487, backtracks = 0, tol = 0.0005509480422217535 Iteration 63: loglikelihood = -219.38468593224545, backtracks = 0, tol = 0.0004629512780606966 Iteration 64: loglikelihood = -219.38429538513583, backtracks = 0, tol = 0.0004779860767529819 Iteration 65: loglikelihood = -219.38395679466737, backtracks = 0, tol = 0.0004013057505476397 Iteration 66: loglikelihood = -219.38366314739872, backtracks = 0, tol = 0.0004147454994836376 Iteration 67: loglikelihood = -219.38340849212824, backtracks = 0, tol = 0.00034797985178746597 Iteration 68: loglikelihood = -219.38318758502183, backtracks = 0, tol = 0.0003599207374415984 Iteration 69: loglikelihood = -219.38299596326374, backtracks = 0, tol = 0.0003018217223394219 Iteration 70: loglikelihood = -219.3828297011887, backtracks = 0, tol = 0.00031238270039476616 Iteration 71: loglikelihood = -219.38268544908368, backtracks = 0, tol = 0.00026184698528793125 Iteration 72: loglikelihood = -219.3825602648841, backtracks = 0, tol = 0.0002711550905775348 Iteration 73: loglikelihood = -219.38245163239276, backtracks = 0, tol = 0.00022721198022395564 Iteration 74: loglikelihood = -219.38235734460943, backtracks = 0, tol = 0.00023539371282360467 Iteration 75: loglikelihood = -219.38227551018164, backtracks = 0, tol = 0.0001971920991460162 Iteration 76: loglikelihood = -219.382204472153, backtracks = 0, tol = 0.00020436848993624394 Iteration 77: loglikelihood = -219.3821428080304, backtracks = 0, tol = 0.00017116393516432852 Iteration 78: loglikelihood = -219.38208927292968, backtracks = 0, tol = 0.00017744788492952903 Iteration 79: loglikelihood = -219.38204279645043, backtracks = 0, tol = 0.00014859040670150365 Iteration 80: loglikelihood = -219.38200244272016, backtracks = 0, tol = 0.00015408544066832546 Iteration 81: loglikelihood = -219.38196740593906, backtracks = 0, tol = 0.00012900826739905896 Iteration 82: loglikelihood = -219.38193698216227, backtracks = 0, tol = 0.00013380816660865064 Iteration 83: loglikelihood = -219.38191056455443, backtracks = 0, tol = 0.00011201756190578927 Iteration 84: loglikelihood = -219.3818876233726, backtracks = 0, tol = 0.000116206527337935 Iteration 85: loglikelihood = -219.38186770147453, backtracks = 0, tol = 9.727268703830643e-5 Test Summary: | Pass Total Time fit Bernoulli SnpLinAlg | 4 4 3.9s **** 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 = -3650.3068190911317, backtracks = 0, tol = 0.48964414856210126 Iteration 2: loglikelihood = -2294.7353028151183, backtracks = 0, tol = 0.055733146270062914 Iteration 3: loglikelihood = -1548.0450785096075, backtracks = 0, tol = 0.06867164248056604 Iteration 4: loglikelihood = -1422.2925286950176, backtracks = 0, tol = 0.04948729296437088 Iteration 5: loglikelihood = -1396.8577254746385, backtracks = 0, tol = 0.09159966733874067 Iteration 6: loglikelihood = -1367.487804923534, backtracks = 0, tol = 0.05966309033070909 Iteration 7: loglikelihood = -1354.3921457734716, backtracks = 0, tol = 0.03000524254175405 Iteration 8: loglikelihood = -1349.8676909576395, backtracks = 0, tol = 0.07876945027809841 Iteration 9: loglikelihood = -1334.8267806957972, backtracks = 0, tol = 0.031259568516149326 Iteration 10: loglikelihood = -1332.1455984210404, backtracks = 0, tol = 0.013313152730817554 Iteration 11: loglikelihood = -1324.3993131561367, backtracks = 0, tol = 0.04256313600211219 Iteration 12: loglikelihood = -1321.7780084964463, backtracks = 0, tol = 0.017504663366325845 Iteration 13: loglikelihood = -1320.9555950126016, backtracks = 0, tol = 0.0073759232809306905 Iteration 14: loglikelihood = -1320.4309532105212, backtracks = 0, tol = 0.006844112707609296 Iteration 15: loglikelihood = -1320.106481880919, backtracks = 0, tol = 0.004561400996887293 Iteration 16: loglikelihood = -1319.8906881881308, backtracks = 0, tol = 0.004935591345352128 Iteration 17: loglikelihood = -1319.75733563383, backtracks = 0, tol = 0.0028362963590809107 Iteration 18: loglikelihood = -1319.6929161071023, backtracks = 1, tol = 0.001574439979295898 Iteration 19: loglikelihood = -1319.638256030334, backtracks = 0, tol = 0.003790676066978358 Iteration 20: loglikelihood = -1319.603454442235, backtracks = 0, tol = 0.0015853287225222714 Iteration 21: loglikelihood = -1319.581519621177, backtracks = 0, tol = 0.0023584796955079534 Iteration 22: loglikelihood = -1319.5673265406306, backtracks = 0, tol = 0.0010124338455782202 Iteration 23: loglikelihood = -1319.5581994503796, backtracks = 0, tol = 0.0015048703670264446 Iteration 24: loglikelihood = -1319.5522372477017, backtracks = 0, tol = 0.0006559715876202527 Iteration 25: loglikelihood = -1319.5483576461395, backtracks = 0, tol = 0.000974017859939923 Iteration 26: loglikelihood = -1319.5458084312643, backtracks = 0, tol = 0.00042887039960766654 Iteration 27: loglikelihood = -1319.544137580046, backtracks = 0, tol = 0.0006361549250345107 Iteration 28: loglikelihood = -1319.5430356152126, backtracks = 0, tol = 0.0002819325342787273 Iteration 29: loglikelihood = -1319.542310026256, backtracks = 0, tol = 0.0004178815624662886 Iteration 30: loglikelihood = -1319.5418303400022, backtracks = 0, tol = 0.00018599422063309882 Iteration 31: loglikelihood = -1319.5415135576625, backtracks = 0, tol = 0.0002755258291731993 Iteration 32: loglikelihood = -1319.5413038076347, backtracks = 0, tol = 0.000122981694372289 Iteration 33: loglikelihood = -1319.5411650239157, backtracks = 0, tol = 0.00018210885453904388 Iteration 34: loglikelihood = -1319.5410730379633, backtracks = 0, tol = 8.14381612980065e-5 Test Summary: | Pass Total Time fit Poisson SnpLinAlg | 4 4 3.2s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse NegativeBinomial regression Number of threads = 1 Link functin = LogLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1653.2829615712883, backtracks = 0, tol = 0.4510035235810109 Iteration 2: loglikelihood = -1552.9435754763026, backtracks = 0, tol = 0.17292473724319024 Iteration 3: loglikelihood = -1513.465806538822, backtracks = 0, tol = 0.10512979250224214 Iteration 4: loglikelihood = -1508.0387506535606, backtracks = 0, tol = 0.08691684569452911 Iteration 5: loglikelihood = -1502.311302568779, backtracks = 0, tol = 0.08604183820149847 Iteration 6: loglikelihood = -1501.7965369397639, backtracks = 0, tol = 0.01051247806181127 Iteration 7: loglikelihood = -1501.767449328131, backtracks = 1, tol = 0.002238406524451426 Iteration 8: loglikelihood = -1501.755542089638, backtracks = 1, tol = 0.0015922675255543846 Iteration 9: loglikelihood = -1501.7519724264637, backtracks = 1, tol = 0.001082855670726536 Iteration 10: loglikelihood = -1501.7510215860211, backtracks = 1, tol = 0.0005747895767143187 Iteration 11: loglikelihood = -1501.7507729783047, backtracks = 1, tol = 0.000304405026714723 Iteration 12: loglikelihood = -1501.7507085912, backtracks = 1, tol = 0.0001549136754946659 Iteration 13: loglikelihood = -1501.750691904616, backtracks = 1, tol = 7.961953436281639e-5 Test Summary: | Pass Total Time fit NegativeBinomial SnpLinAlg | 4 4 1.3s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse linear regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1882.3195973187806, backtracks = 0, tol = 0.7543325216816787 Iteration 2: loglikelihood = -1523.3627847443577, backtracks = 0, tol = 0.13955106046857776 Iteration 3: loglikelihood = -1440.0857065684768, backtracks = 0, tol = 0.056828143715971856 Iteration 4: loglikelihood = -1424.273906878735, backtracks = 0, tol = 0.030587622848685478 Iteration 5: loglikelihood = -1423.264218292827, backtracks = 0, tol = 0.006651553103700038 Iteration 6: loglikelihood = -1423.1839126211187, backtracks = 0, tol = 0.026049016872104792 Iteration 7: loglikelihood = -1423.1514758093433, backtracks = 1, tol = 0.0006392351096039447 Iteration 8: loglikelihood = -1423.142969592208, backtracks = 1, tol = 0.00033706180647973357 Iteration 9: loglikelihood = -1423.1407502626234, backtracks = 1, tol = 0.00017622425456697243 Iteration 10: loglikelihood = -1423.140175500161, backtracks = 1, tol = 9.140419679457427e-5 Test Summary: | Pass Total Time fit with >1 non-genetic covariates SnpLinAlg | 5 5 1.7s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse linear regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1709.6653307049953, backtracks = 0, tol = 0.4354176139411981 Iteration 2: loglikelihood = -1474.0209151333308, backtracks = 0, tol = 0.09119795642290826 Iteration 3: loglikelihood = -1426.9440561117783, backtracks = 0, tol = 0.04550185106713162 Iteration 4: loglikelihood = -1423.3261120302536, backtracks = 0, tol = 0.0319110174524781 Iteration 5: loglikelihood = -1423.2212807259734, backtracks = 1, tol = 0.0015019030933387995 Iteration 6: loglikelihood = -1423.1946038577405, backtracks = 1, tol = 0.0007314212073613095 Iteration 7: loglikelihood = -1423.1878270453533, backtracks = 1, tol = 0.0003532482132529153 Iteration 8: loglikelihood = -1423.1861071160954, backtracks = 1, tol = 0.00016935085621302748 Iteration 9: loglikelihood = -1423.185670775244, backtracks = 1, tol = 8.061662119238018e-5 Test Summary: | Pass Total Time model selection on non-genetic covariates | 5 5 0.8s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse linear regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 15 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1473.12410014528, backtracks = 0, tol = 0.11162633196865429 Iteration 2: loglikelihood = -1448.37403799896, backtracks = 0, tol = 0.07736217654955346 Iteration 3: loglikelihood = -1429.8981769610311, backtracks = 1, tol = 0.056531823476744666 Iteration 4: loglikelihood = -1404.7133956159753, backtracks = 0, tol = 0.10125409614175711 Iteration 5: loglikelihood = -1397.466171579031, backtracks = 0, tol = 0.05343369325195712 Iteration 6: loglikelihood = -1395.7490747391416, backtracks = 0, tol = 0.08843871418165569 Iteration 7: loglikelihood = -1395.4877576477586, backtracks = 0, tol = 0.0089247040684952 Iteration 8: loglikelihood = -1395.442237061722, backtracks = 0, tol = 0.005277867116132827 Iteration 9: loglikelihood = -1395.4302205892106, backtracks = 0, tol = 0.0027680467744013336 Iteration 10: loglikelihood = -1395.1973617039414, backtracks = 0, tol = 0.0905690065560604 Iteration 11: loglikelihood = -1395.0048067729406, backtracks = 0, tol = 0.007650485819168939 Iteration 12: loglikelihood = -1394.9835209063683, backtracks = 0, tol = 0.0035232591741737973 Iteration 13: loglikelihood = -1394.9793628241396, backtracks = 0, tol = 0.001852195878065177 Iteration 14: loglikelihood = -1394.9779889816232, backtracks = 0, tol = 0.0012530451800711444 Iteration 15: loglikelihood = -1394.977503420045, backtracks = 0, tol = 0.0006829444661300923 Iteration 16: loglikelihood = -1394.9773714862843, backtracks = 1, tol = 0.00022881022816864142 Iteration 17: loglikelihood = -1394.977310220191, backtracks = 2, tol = 0.0001217788197399568 Iteration 18: loglikelihood = -1394.977273607278, backtracks = 2, tol = 8.822469907087602e-5 **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse linear regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 3 Prior weight scaling = off Doubly sparse projection = on Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1535.4672180567934, backtracks = 0, tol = 0.17016419679985048 Iteration 2: loglikelihood = -1508.04343741211, backtracks = 0, tol = 0.21718489399873087 Iteration 3: loglikelihood = -1448.2717322168082, backtracks = 0, tol = 0.15334504607402907 Iteration 4: loglikelihood = -1437.5669418734744, backtracks = 0, tol = 0.08425396177776269 Iteration 5: loglikelihood = -1434.3602241747528, backtracks = 0, tol = 0.03199716666887782 Iteration 6: loglikelihood = -1434.239273652971, backtracks = 2, tol = 0.003498168340088273 Iteration 7: loglikelihood = -1434.1475478538455, backtracks = 2, tol = 0.0030522911015526556 Iteration 8: loglikelihood = -1434.0913475157126, backtracks = 2, tol = 0.0021931576818355514 Iteration 9: loglikelihood = -1434.0584761985995, backtracks = 2, tol = 0.0016688209654910561 Iteration 10: loglikelihood = -1434.0393127719108, backtracks = 2, tol = 0.001317554485128468 Iteration 11: loglikelihood = -1434.0281644425422, backtracks = 2, tol = 0.0010393713220469248 Iteration 12: loglikelihood = -1434.0216963632631, backtracks = 2, tol = 0.0008158673348111212 Iteration 13: loglikelihood = -1434.0179556115852, backtracks = 2, tol = 0.0006363671566384319 Iteration 14: loglikelihood = -1433.8972844529703, backtracks = 2, tol = 0.02105646084267335 Iteration 15: loglikelihood = -1433.6170929347984, backtracks = 1, tol = 0.011448126839540936 Iteration 16: loglikelihood = -1433.5408744767515, backtracks = 2, tol = 0.0040324300639331045 Iteration 17: loglikelihood = -1433.4945867179188, backtracks = 2, tol = 0.003005268578298657 Iteration 18: loglikelihood = -1433.467626121943, backtracks = 2, tol = 0.002187229771831438 Iteration 19: loglikelihood = -1433.4521439235273, backtracks = 2, tol = 0.0016467936133078437 Iteration 20: loglikelihood = -1433.4432822302874, backtracks = 2, tol = 0.0012631945762950846 Iteration 21: loglikelihood = -1433.4382075829426, backtracks = 2, tol = 0.0009580287583338291 Iteration 22: loglikelihood = -1433.4352962137846, backtracks = 2, tol = 0.0007222437442123496 Iteration 23: loglikelihood = -1433.4336216439426, backtracks = 2, tol = 0.0005424739396431532 Iteration 24: loglikelihood = -1433.43265547142, backtracks = 2, tol = 0.00040628145880685523 Iteration 25: loglikelihood = -1433.4320960523787, backtracks = 2, tol = 0.0003034179918772475 Iteration 26: loglikelihood = -1433.4317709097872, backtracks = 2, tol = 0.00022583740291084404 Iteration 27: loglikelihood = -1433.4315812027676, backtracks = 2, tol = 0.0001673653861249394 Iteration 28: loglikelihood = -1432.5898379532837, backtracks = 2, tol = 0.025080215054031605 Iteration 29: loglikelihood = -1431.7678006470733, backtracks = 1, tol = 0.017181190475547538 Iteration 30: loglikelihood = -1430.3157393955933, backtracks = 1, tol = 0.07333968264200234 Iteration 31: loglikelihood = -1429.706868513855, backtracks = 0, tol = 0.020015111727945754 Iteration 32: loglikelihood = -1429.5802551945537, backtracks = 1, tol = 0.00756937670420323 Iteration 33: loglikelihood = -1429.5139450553559, backtracks = 2, tol = 0.003906515984506227 Iteration 34: loglikelihood = -1429.4691972325213, backtracks = 2, tol = 0.003683664863256486 Iteration 35: loglikelihood = -1428.8607526222902, backtracks = 2, tol = 0.08711763846658777 Iteration 36: loglikelihood = -1428.6178427111051, backtracks = 1, tol = 0.006558345246943271 Iteration 37: loglikelihood = -1428.5424083746184, backtracks = 2, tol = 0.0033912200662443866 Iteration 38: loglikelihood = -1428.4933608487952, backtracks = 2, tol = 0.0030098214824111793 Iteration 39: loglikelihood = -1428.4620745885088, backtracks = 2, tol = 0.0025951371119133128 Iteration 40: loglikelihood = -1428.4427329028306, backtracks = 2, tol = 0.002148184701148465 Iteration 41: loglikelihood = -1428.4311433050725, backtracks = 2, tol = 0.0017160493175770867 Iteration 42: loglikelihood = -1428.4243474878394, backtracks = 2, tol = 0.0013407892924840973 Iteration 43: loglikelihood = -1428.420413936832, backtracks = 2, tol = 0.0010343694042998534 Iteration 44: loglikelihood = -1428.4181556141762, backtracks = 2, tol = 0.0007948565534422845 Iteration 45: loglikelihood = -1428.4168664091337, backtracks = 2, tol = 0.000608309643427293 Iteration 46: loglikelihood = -1428.4161334920516, backtracks = 2, tol = 0.0004622621654004415 Iteration 47: loglikelihood = -1428.4157180925672, backtracks = 2, tol = 0.00034956951660978575 Iteration 48: loglikelihood = -1428.4154831711999, backtracks = 2, tol = 0.00026348047442121094 Iteration 49: loglikelihood = -1428.4153505233908, backtracks = 2, tol = 0.00019816133989405092 Iteration 50: loglikelihood = -1428.4152757065372, backtracks = 2, tol = 0.00014882628973647444 Iteration 51: loglikelihood = -1428.4152335404317, backtracks = 2, tol = 0.00011167501044822909 Iteration 52: loglikelihood = -1428.4152097888611, backtracks = 2, tol = 8.375238803842589e-5 Test Summary: | Pass Total Time Correlated predictors and double sparsity Float64 matrix | 2 2 10.2s **** 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 = -1488.249831071512, backtracks = 0, tol = 0.2295750006348372 Iteration 2: loglikelihood = -1452.844048344371, backtracks = 0, tol = 0.1262697041303048 Iteration 3: loglikelihood = -1411.366562024868, backtracks = 0, tol = 0.10512980235567423 Iteration 4: loglikelihood = -1402.441423153626, backtracks = 0, tol = 0.0960327029577774 Iteration 5: loglikelihood = -1389.5892455461913, backtracks = 0, tol = 0.08304774104252727 Iteration 6: loglikelihood = -1381.4331951270735, backtracks = 0, tol = 0.07766233249706603 Iteration 7: loglikelihood = -1367.5299954673765, backtracks = 0, tol = 0.057066278562998625 Iteration 8: loglikelihood = -1355.9098461411313, backtracks = 0, tol = 0.05461392263368783 Iteration 9: loglikelihood = -1348.2794049681722, backtracks = 0, tol = 0.06487985042168781 Iteration 10: loglikelihood = -1347.0805140606517, backtracks = 0, tol = 0.021182230359000295 Iteration 11: loglikelihood = -1346.72536060745, backtracks = 0, tol = 0.00742417920017284 Iteration 12: loglikelihood = -1346.5918768299075, backtracks = 0, tol = 0.008486943512840624 Iteration 13: loglikelihood = -1344.535439781296, backtracks = 0, tol = 0.07080350037587207 Iteration 14: loglikelihood = -1344.4177046705556, backtracks = 0, tol = 0.08782197433000437 Iteration 15: loglikelihood = -1343.9954035983203, backtracks = 0, tol = 0.010192192487368511 Iteration 16: loglikelihood = -1343.9677328828325, backtracks = 0, tol = 0.0030724697467601355 Iteration 17: loglikelihood = -1343.962159407594, backtracks = 1, tol = 0.0007602946487427799 Iteration 18: loglikelihood = -1343.9580062784844, backtracks = 1, tol = 0.0012484754888863706 Iteration 19: loglikelihood = -1343.9568150195978, backtracks = 1, tol = 0.0005269647116882477 Iteration 20: loglikelihood = -1343.9564657374422, backtracks = 1, tol = 0.0003704886288905051 Iteration 21: loglikelihood = -1343.9563258395635, backtracks = 1, tol = 0.00012812782187684985 Iteration 22: loglikelihood = -1343.956260177714, backtracks = 1, tol = 0.00016167479694641982 Iteration 23: loglikelihood = -1343.956235211672, backtracks = 1, tol = 5.284255223693115e-5 1.099630 seconds (2.95 M allocations: 56.603 MiB, 7.87% gc time, 62.75% 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 = -1525.0886690461844, backtracks = 0, tol = 0.2295750006348372 Iteration 2: loglikelihood = -1500.5237613874885, backtracks = 0, tol = 0.1262697041303048 Iteration 3: loglikelihood = -1470.2415967573252, backtracks = 0, tol = 0.10794715004837172 Iteration 4: loglikelihood = -1456.2932466037792, backtracks = 0, tol = 0.0990143303330282 Iteration 5: loglikelihood = -1441.2999194817367, backtracks = 0, tol = 0.08748249034791768 Iteration 6: loglikelihood = -1430.7162063333956, backtracks = 0, tol = 0.08228785537183082 Iteration 7: loglikelihood = -1416.2849316971044, backtracks = 0, tol = 0.06273142941317571 Iteration 8: loglikelihood = -1403.0639644208081, backtracks = 0, tol = 0.06049167679552569 Iteration 9: loglikelihood = -1394.8131222582708, backtracks = 0, tol = 0.06036786746804488 Iteration 10: loglikelihood = -1384.3824373029597, backtracks = 1, tol = 0.060808072231822406 Iteration 11: loglikelihood = -1379.9230308229614, backtracks = 0, tol = 0.08287650090618963 Iteration 12: loglikelihood = -1376.585871587062, backtracks = 0, tol = 0.08227115889192987 Iteration 13: loglikelihood = -1373.3721379445192, backtracks = 0, tol = 0.00852391781162884 Iteration 14: loglikelihood = -1370.799493662931, backtracks = 0, tol = 0.0012521597538649688 Iteration 15: loglikelihood = -1368.529982155065, backtracks = 0, tol = 0.0005394401683950669 Iteration 16: loglikelihood = -1366.5493251320734, backtracks = 0, tol = 0.0003815285273096272 Iteration 17: loglikelihood = -1364.7936911186189, backtracks = 0, tol = 0.00032904573119098957 Iteration 18: loglikelihood = -1363.2388616943904, backtracks = 0, tol = 0.0002826474615632969 Iteration 19: loglikelihood = -1361.8491240303717, backtracks = 0, tol = 0.0002798147878982188 Iteration 20: loglikelihood = -1360.605132694125, backtracks = 0, tol = 0.00024989546540262923 Iteration 21: loglikelihood = -1359.484109079527, backtracks = 0, tol = 0.00024175185511109506 Iteration 22: loglikelihood = -1358.4718455609252, backtracks = 0, tol = 0.00022061185945630377 Iteration 23: loglikelihood = -1357.5530168641421, backtracks = 0, tol = 0.00021186416626944526 Iteration 24: loglikelihood = -1356.7172416279338, backtracks = 0, tol = 0.00019618701906908579 Iteration 25: loglikelihood = -1355.9538165272093, backtracks = 0, tol = 0.00018998329724045955 Iteration 26: loglikelihood = -1355.2550700385102, backtracks = 0, tol = 0.0001780082916598727 Iteration 27: loglikelihood = -1354.6132983287057, backtracks = 0, tol = 0.00017239881219670528 Iteration 28: loglikelihood = -1354.0227484886377, backtracks = 0, tol = 0.00016280521224341368 Iteration 29: loglikelihood = -1353.4777350323131, backtracks = 0, tol = 0.00015746260071086108 Iteration 30: loglikelihood = -1352.9738797150746, backtracks = 0, tol = 0.00014956163526635028 Iteration 31: loglikelihood = -1352.5068969007868, backtracks = 0, tol = 0.00014461603169526384 Iteration 32: loglikelihood = -1352.0734078862138, backtracks = 0, tol = 0.00013796556733970005 Iteration 33: loglikelihood = -1351.6701230931158, backtracks = 0, tol = 0.00013344697586035494 Iteration 34: loglikelihood = -1351.2944015147953, backtracks = 0, tol = 0.0001277524843413395 Iteration 35: loglikelihood = -1350.9436780104907, backtracks = 0, tol = 0.00012364805889946966 Iteration 36: loglikelihood = -1350.615863839171, backtracks = 0, tol = 0.0001187053808888221 Iteration 37: loglikelihood = -1350.308930831063, backtracks = 0, tol = 0.00011498484512982803 Iteration 38: loglikelihood = -1350.021209254477, backtracks = 0, tol = 0.00011064720409676995 Iteration 39: loglikelihood = -1349.7510756115103, backtracks = 0, tol = 0.00010727465078766478 Iteration 40: loglikelihood = -1349.497182052605, backtracks = 0, tol = 0.00010343313332207008 Iteration 41: loglikelihood = -1349.2582145466292, backtracks = 0, tol = 0.00010037250551658918 Iteration 42: loglikelihood = -1349.0330753790065, backtracks = 0, tol = 9.694409539198801e-5 0.411419 seconds (1.54 M allocations: 27.948 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 = -3600.5193, backtracks = 0, tol = 0.08376917405852745 Iteration 2: loglikelihood = -3564.2036, backtracks = 0, tol = 0.042797926385113996 Iteration 3: loglikelihood = -3559.7976, backtracks = 1, tol = 0.011076809390739142 Iteration 4: loglikelihood = -3548.6118, backtracks = 1, tol = 0.05675250488180527 Iteration 5: loglikelihood = -3545.8125, backtracks = 1, tol = 0.008521333248501115 Iteration 6: loglikelihood = -3544.8696, backtracks = 1, tol = 0.005029793604583996 Iteration 7: loglikelihood = -3544.5974, backtracks = 1, tol = 0.0029024714842857337 Iteration 8: loglikelihood = -3544.5195, backtracks = 1, tol = 0.0017100875976360042 Iteration 9: loglikelihood = -3544.5002, backtracks = 1, tol = 0.0009325134338714631 Iteration 10: loglikelihood = -3544.4966, backtracks = 1, tol = 0.0004770404695671339 Iteration 11: loglikelihood = -3544.4956, backtracks = 2, tol = 0.00012032440354633514 Iteration 12: loglikelihood = -3544.5024, backtracks = 3, tol = 4.505711675200093e-5 25.685788 seconds (14.71 M allocations: 666.502 MiB, 0.99% gc time, 97.58% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** 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 = -3501.8906, backtracks = 0, tol = 0.08376917405852745 Iteration 2: loglikelihood = -3400.4204, backtracks = 0, tol = 0.0440123980779864 Iteration 3: loglikelihood = -3218.2725, backtracks = 1, tol = 0.01064929880942198 Iteration 4: loglikelihood = -3013.3342, backtracks = 1, tol = 0.007078186833611861 Iteration 5: loglikelihood = -2786.7305, backtracks = 1, tol = 0.003352500244495182 Iteration 6: loglikelihood = -2703.092, backtracks = 0, tol = 0.08570766295107793 Iteration 7: loglikelihood = -2583.0085, backtracks = 0, tol = 0.09919544714761169 Iteration 8: loglikelihood = -2476.393, backtracks = 0, tol = 0.08316940343104601 Iteration 9: loglikelihood = -2410.3906, backtracks = 0, tol = 0.08427542229751293 Iteration 10: loglikelihood = -2338.382, backtracks = 0, tol = 0.09431031598790963 Iteration 11: loglikelihood = -2302.8088, backtracks = 0, tol = 0.09457743003543949 Iteration 12: loglikelihood = -2265.1829, backtracks = 0, tol = 0.10236550016472865 Iteration 13: loglikelihood = -2246.7756, backtracks = 0, tol = 0.10218502122619935 Iteration 14: loglikelihood = -2229.3325, backtracks = 0, tol = 0.09954355242001611 Iteration 15: loglikelihood = -2221.5544, backtracks = 0, tol = 0.09963280370419335 Iteration 16: loglikelihood = -2218.3584, backtracks = 0, tol = 0.08877735781426302 Iteration 17: loglikelihood = -2215.2712, backtracks = 0, tol = 0.08875698712341692 Iteration 18: loglikelihood = -2215.0078, backtracks = 0, tol = 0.08510285692184764 Iteration 19: loglikelihood = -2213.9297, backtracks = 0, tol = 0.09006409456803217 Iteration 20: loglikelihood = -2212.9539, backtracks = 1, tol = 0.008357861985714454 Iteration 21: loglikelihood = -2212.7224, backtracks = 1, tol = 0.003996418229301922 Iteration 22: loglikelihood = -2212.6646, backtracks = 1, tol = 0.0018698524878063918 Iteration 23: loglikelihood = -2212.6492, backtracks = 1, tol = 0.0008605689130707664 Iteration 24: loglikelihood = -2212.6448, backtracks = 1, tol = 0.0003987896504999909 Iteration 25: loglikelihood = -2212.642, backtracks = 1, tol = 0.0002216263709455537 Iteration 26: loglikelihood = -2212.6414, backtracks = 1, tol = 0.0001229696936885323 Iteration 27: loglikelihood = -2212.639, backtracks = 2, tol = 3.399511635381831e-5 0.204963 seconds (1.54 M allocations: 25.471 MiB) Test Summary: | Pass Total Time Negative binomial nuisance parameter Float32 matrix | 12 12 30.3s **** 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 **** ┌ Warning: accessing `Type.name` is deprecated without replacement. If for detection, use `Base.isType(x)`. │ caller = ProgressMeter.Progress(n::Int64, dt::Int64, desc::String, barlen::Nothing, color::Symbol, output::Base.PipeEndpoint; offset::Int64) at deprecated.jl:1 └ @ ProgressMeter ~/.julia/packages/ProgressMeter/N660J/src/deprecated.jl:1 Running sparse linear regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -2896.6116813943763, backtracks = 0, tol = 1.0257704354307222 Iteration 2: loglikelihood = -1753.4720992614753, backtracks = 0, tol = 0.28706825512903816 Iteration 3: loglikelihood = -1460.3823326395225, backtracks = 0, tol = 0.1059822007319242 Iteration 4: loglikelihood = -1438.5292259047123, backtracks = 0, tol = 0.028655431669451118 Iteration 5: loglikelihood = -1438.0856032112097, backtracks = 0, tol = 0.0034955373515602557 Iteration 6: loglikelihood = -1438.0744350329464, backtracks = 0, tol = 0.0005882060650840543 Iteration 7: loglikelihood = -1438.0741395461057, backtracks = 0, tol = 8.427264473927088e-5 5.230566 seconds (1.03 M allocations: 133.641 MiB, 0.55% gc time, 91.46% compilation time) Test Summary: | Pass Total Time initialze beta | 1 1 5.6s 10.217538 seconds (4.00 M allocations: 82.398 MiB, 0.26% gc time, 0.74% compilation time) 5.659857 seconds (3.98 M allocations: 91.674 MiB, 0.36% gc time) 9.883636 seconds (20.38 M allocations: 438.611 MiB, 1.18% gc time, 16.57% compilation time: 77% of which was recompilation) 7.623609 seconds (20.18 M allocations: 434.186 MiB, 1.01% gc time) 38.336980 seconds (3.40 M allocations: 4.230 GiB, 6.79% gc time, 28.51% compilation time) 54.274670 seconds (72.53 k allocations: 183.670 MiB, 0.15% gc time) Test Summary: | Pass Total Time memory_efficient keyword | 7 7 2m24.2s Test Summary: | Pass Total Time update_support! | 10 10 0.6s 14.571 ms (78 allocations: 4.56 KiB) 4.449 μs (0 allocations: 0 bytes) 157.709 μs (4 allocations: 288 bytes) 5.687 μs (0 allocations: 0 bytes) 51.850 μs (2 allocations: 64 bytes) 30.230 μs (0 allocations: 0 bytes) 26.880 μs (0 allocations: 0 bytes) 27.990 μs (0 allocations: 0 bytes) 106.009 μs (0 allocations: 0 bytes) 30.194 ms (78 allocations: 4.56 KiB) 18.269 μs (0 allocations: 0 bytes) 177.118 μs (4 allocations: 288 bytes) 38.599 μs (0 allocations: 0 bytes) 198.158 μs (2 allocations: 64 bytes) 71.279 μs (0 allocations: 0 bytes) 113.929 μs (0 allocations: 0 bytes) 140.618 μs (0 allocations: 0 bytes) 215.478 μs (0 allocations: 0 bytes) Test Summary: | Total Time benchmarks for multivariate function | 0 2m11.8s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse Multivariate Gaussian regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 12 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -2900.9186300194497, backtracks = 0, tol = 0.1480224208200413 Iteration 2: loglikelihood = -2869.406464695619, backtracks = 0, tol = 0.035126790460779864 Iteration 3: loglikelihood = -2868.084702693443, backtracks = 0, tol = 0.0055693496163324524 Iteration 4: loglikelihood = -2868.034423817725, backtracks = 0, tol = 0.001118951762895177 Iteration 5: loglikelihood = -2868.030857635375, backtracks = 0, tol = 0.00031182601179138955 Iteration 6: loglikelihood = -2868.0305288614227, backtracks = 0, tol = 0.00010393305949947338 Iteration 7: loglikelihood = -2868.0304966516946, backtracks = 0, tol = 3.100862049859014e-5 0.439969 seconds (44.31 k allocations: 5.347 MiB, 64.82% compilation time) Test Summary: | Pass Total Time multivariate fit_iht SnpLinAlg | 7 7 13.2s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse Multivariate Gaussian regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 12 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -2878.028812628852, backtracks = 0, tol = 2.5661768673084553 Iteration 2: loglikelihood = -2868.563037890196, backtracks = 0, tol = 0.024335274263285057 Iteration 3: loglikelihood = -2868.0815051475474, backtracks = 0, tol = 0.004072558228741048 Iteration 4: loglikelihood = -2868.0352100240902, backtracks = 0, tol = 0.0013135682973484317 Iteration 5: loglikelihood = -2868.0309297231934, backtracks = 0, tol = 0.000386434110747091 Iteration 6: loglikelihood = -2868.0305335492912, backtracks = 0, tol = 0.00011924564415557833 Iteration 7: loglikelihood = -2868.0304968517494, backtracks = 0, tol = 3.603726989721193e-5 1.858802 seconds (258.63 k allocations: 167.568 MiB, 60.12% compilation time) Test Summary: | Pass Total Time initialze beta | 5 5 2.3s **** 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 **** ┌ Warning: accessing `Type.name` is deprecated without replacement. If for detection, use `Base.isType(x)`. │ caller = ProgressMeter.Progress(n::Int64, desc::String, offset::Int64; kwargs::Base.Pairs{Symbol, Union{}, Nothing, @NamedTuple{}}) at deprecated.jl:5 └ @ ProgressMeter ~/.julia/packages/ProgressMeter/N660J/src/deprecated.jl:5 Cross validating... 3%|█ | ETA: 0:03:48 Cross validating... 19%|██████▏ | ETA: 0:00:35 Cross validating... 24%|███████▋ | ETA: 0:00:27 Cross validating... 27%|████████▋ | ETA: 0:00:24 Cross validating... 30%|█████████▋ | ETA: 0:00:20 Cross validating... 33%|██████████▋ | ETA: 0:00:18 Cross validating... 37%|███████████▋ | ETA: 0:00:16 Cross validating... 40%|████████████▊ | ETA: 0:00:14 Cross validating... 43%|█████████████▊ | ETA: 0:00:13 Cross validating... 46%|██████████████▊ | ETA: 0:00:11 Cross validating... 49%|███████████████▊ | ETA: 0:00:10 Cross validating... 52%|████████████████▊ | ETA: 0:00:09 Cross validating... 56%|█████████████████▊ | ETA: 0:00:08 Cross validating... 59%|██████████████████▊ | ETA: 0:00:07 Cross validating... 62%|███████████████████▊ | ETA: 0:00:06 Cross validating... 65%|████████████████████▉ | ETA: 0:00:06 Cross validating... 68%|█████████████████████▉ | ETA: 0:00:05 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:04 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:04 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:03 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:03 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:02 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:02 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:01 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:01 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:12 Crossvalidation Results: k MSE 0 5133.022283723454 1 3386.9492555487195 2 2122.7373096793403 3 1587.768147645449 4 1165.289320853601 5 867.5322172298872 6 536.2105481133374 7 479.37597869976815 8 432.17765233682815 9 370.5352541219394 10 336.3109411272014 11 337.1114765927122 12 333.8551923099805 13 338.1402335963653 14 340.24332802119534 15 351.15515805914026 16 347.7407199951429 17 348.9717917714993 18 362.0162291102238 19 348.8637335907945 20 380.95038815910175 Best k = 12 12.214191 seconds (11.14 M allocations: 294.847 MiB, 0.61% gc time, 63.20% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 5%|█▌ | ETA: 0:00:03 Cross validating... 8%|██▌ | ETA: 0:00:03 Cross validating... 11%|███▌ | ETA: 0:00:04 Cross validating... 14%|████▋ | ETA: 0:00:03 Cross validating... 17%|█████▋ | ETA: 0:00:03 Cross 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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 5133.022283723454 1 3388.2556551189864 2 2133.411643063526 3 1595.916033366273 4 1173.4667948001857 5 878.5651885281218 6 541.8447870537332 7 487.76593164461553 8 441.23431167882006 9 379.8766774860547 10 344.20001250366 11 350.5906778341084 12 348.5753409002898 13 360.12685076875846 14 362.42823633833774 15 370.71376152237934 16 361.72085092270873 17 372.62719859921145 18 382.5253522704419 19 390.0321747589899 20 396.73102704507505 Best k = 10 4.846778 seconds (10.24 M allocations: 214.441 MiB, 2.36% gc time, 1.55% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, normal model | 3 3 17.9s **** 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: 0:06:18 Cross validating... 8%|██▌ | ETA: 0:02:25 Cross validating... 13%|████▏ | ETA: 0:01:27 Cross validating... 17%|█████▋ | ETA: 0:01:00 Cross validating... 22%|███████▏ | ETA: 0:00:45 Cross validating... 25%|████████▏ | ETA: 0:00:38 Cross validating... 30%|█████████▋ | ETA: 0:00:30 Cross validating... 35%|███████████▏ | ETA: 0:00:25 Cross validating... 40%|████████████▊ | ETA: 0:00:20 Cross validating... 44%|██████████████▎ | ETA: 0:00:17 Cross validating... 51%|████████████████▎ | ETA: 0:00:13 Cross validating... 54%|█████████████████▎ | ETA: 0:00:12 Cross validating... 59%|██████████████████▊ | ETA: 0:00:10 Cross validating... 63%|████████████████████▍ | ETA: 0:00:08 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:07 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:06 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:04 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:03 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:02 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:02 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:01 Cross validating... 100%|████████████████████████████████| Time: 0:00:15 Crossvalidation Results: k MSE 0 1576.1355906982421 1 1287.8385965576172 2 1072.8139190673828 3 808.2483344726562 4 704.1174799804687 5 537.4622648925781 6 461.8336713867187 7 400.2431428833008 8 357.4667705078125 9 338.86715682983396 10 343.0309079284668 11 345.1859893493653 12 356.09987411499026 13 346.94391354370117 14 367.12915939331054 15 350.964075012207 16 363.9322653503418 17 367.1186653137207 18 369.297725982666 19 390.4121877746582 20 406.0082275695801 Best k = 9 16.327455 seconds (12.75 M allocations: 317.503 MiB, 0.98% gc time, 83.43% 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... 13%|████▏ | ETA: 0:00:02 Cross validating... 19%|██████▏ | ETA: 0:00:02 Cross validating... 24%|███████▋ | ETA: 0:00:02 Cross validating... 29%|█████████▏ | ETA: 0:00:02 Cross validating... 33%|██████████▋ | ETA: 0:00:02 Cross validating... 40%|████████████▊ | ETA: 0:00:01 Cross validating... 44%|██████████████▎ | ETA: 0:00:01 Cross validating... 51%|████████████████▎ | ETA: 0:00:01 Cross validating... 56%|█████████████████▊ | ETA: 0:00:01 Cross validating... 60%|███████████████████▎ | ETA: 0:00:01 Cross validating... 65%|████████████████████▉ | ETA: 0:00:01 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:01 Cross validating... 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... 94%|██████████████████████████████ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:02 Crossvalidation Results: k MSE 0 1576.1355906982421 1 1287.8385965576172 2 1075.4456470947266 3 855.8252520751953 4 708.2145882568359 5 539.8899476928711 6 461.8171331176758 7 406.9593230285644 8 364.6911296691894 9 348.16974826049807 10 357.2234653930664 11 363.41848568725584 12 370.89801699829104 13 371.7728518371582 14 375.95571197509764 15 386.79625558471685 16 390.20471542358393 17 387.42507138061524 18 410.57951568603517 19 416.9278205871582 20 416.55534286499017 Best k = 9 2.672318 seconds (10.65 M allocations: 195.305 MiB, 2.37% gc time, 2.13% compilation time) Test Summary: | Pass Total Time Cross validation on Float32 matrix, normal model | 2 2 20.6s **** 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: 0:01:03 Cross validating... 6%|██ | ETA: 0:00:33 Cross validating... 10%|███ | ETA: 0:00:23 Cross validating... 11%|███▌ | ETA: 0:00:20 Cross validating... 14%|████▋ | ETA: 0:00:16 Cross validating... 16%|█████▏ | ETA: 0:00:15 Cross validating... 19%|██████▏ | ETA: 0:00:13 Cross 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validating... 75%|███████████████████████▉ | ETA: 0:00:02 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:02 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:02 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:01 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:01 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:01 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:07 Crossvalidation Results: k MSE 0 463.09503845427344 1 388.4141774807879 2 308.6649261384138 3 270.40987301912804 4 247.50444489546084 5 222.37172444768777 6 188.13548996806242 7 183.76935942395835 8 185.05515598250582 9 190.98498844214132 10 200.50218889512124 11 200.86629590324617 12 195.34653837543914 13 216.61008424393896 14 205.37748321867304 15 210.89283409804972 16 237.64252049465364 17 221.00015507408324 18 211.93276892571936 19 214.22473313111612 20 228.36796110672032 Best k = 7 8.420520 seconds (17.45 M allocations: 406.776 MiB, 1.08% gc time, 32.45% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:04 Cross validating... 6%|██ | ETA: 0:00:05 Cross validating... 10%|███ | ETA: 0:00:05 Cross validating... 13%|████▏ | ETA: 0:00:05 Cross validating... 16%|█████▏ | ETA: 0:00:05 Cross validating... 19%|██████▏ | ETA: 0:00:05 Cross validating... 22%|███████▏ | ETA: 0:00:04 Cross validating... 25%|████████▏ | ETA: 0:00:04 Cross validating... 29%|█████████▏ | ETA: 0:00:04 Cross validating... 32%|██████████▏ | ETA: 0:00:04 Cross 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validating... 84%|██████████████████████████▉ | ETA: 0:00:01 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:01 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:01 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:00 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:05 Crossvalidation Results: k MSE 0 463.09503845427344 1 389.1069951864338 2 310.6310171745436 3 271.70004794312797 4 249.42273726962807 5 233.74238064952578 6 194.0757256503531 7 199.54541729460857 8 192.2313446152132 9 208.5636228217794 10 204.34084496954367 11 218.70994701053473 12 226.68626675299853 13 223.11118596597208 14 228.57815048227528 15 233.51487606400832 16 259.58209986450896 17 244.1239560692975 18 240.4931737258433 19 255.37970528401638 20 264.0923656775517 Best k = 8 5.890371 seconds (17.57 M allocations: 363.506 MiB, 1.70% gc time, 1.42% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, logistic model | 2 2 14.7s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:48 Cross validating... 6%|██ | ETA: 0:00:25 Cross validating... 10%|███ | ETA: 0:00:18 Cross validating... 13%|████▏ | ETA: 0:00:14 Cross validating... 16%|█████▏ | ETA: 0:00:12 Cross validating... 19%|██████▏ | ETA: 0:00:10 Cross validating... 22%|███████▏ | ETA: 0:00:09 Cross validating... 25%|████████▏ | ETA: 0:00:08 Cross validating... 29%|█████████▏ | ETA: 0:00:07 Cross validating... 32%|██████████▏ | ETA: 0:00:06 Cross validating... 35%|███████████▏ | ETA: 0:00:06 Cross validating... 38%|████████████▎ | ETA: 0:00:05 Cross validating... 41%|█████████████▎ | ETA: 0:00:05 Cross validating... 44%|██████████████▎ | ETA: 0:00:04 Cross validating... 48%|███████████████▎ | ETA: 0:00:04 Cross validating... 51%|████████████████▎ | ETA: 0:00:04 Cross validating... 52%|████████████████▊ | ETA: 0:00:04 Cross validating... 56%|█████████████████▊ | ETA: 0:00:03 Cross validating... 59%|██████████████████▊ | ETA: 0:00:03 Cross validating... 62%|███████████████████▊ | ETA: 0:00:03 Cross validating... 65%|████████████████████▉ | ETA: 0:00:02 Cross validating... 68%|█████████████████████▉ | ETA: 0:00:02 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:02 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:02 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:01 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:01 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:01 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:01 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:00 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:06 Crossvalidation Results: k MSE 0 465.5669577331759 1 440.05442564820817 2 412.8328011454871 3 372.7216028818834 4 352.304526614056 5 351.35221176768755 6 345.6062059462705 7 339.40831300244145 8 339.92179958644203 9 342.30053730250006 10 347.7706937336862 11 342.253918551492 12 336.9401685842072 13 380.3679941917113 14 333.5535683429787 15 344.71194785956345 16 375.22369720966515 17 391.2789816769018 18 375.29791374159583 19 380.11076897284204 20 381.0268650627755 Best k = 14 7.422311 seconds (16.94 M allocations: 402.267 MiB, 7.19% gc time, 37.63% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:03 Cross validating... 6%|██ | ETA: 0:00:04 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: 0:00:03 Cross validating... 48%|███████████████▎ | ETA: 0:00:02 Cross validating... 51%|████████████████▎ | ETA: 0:00:02 Cross validating... 54%|█████████████████▎ | ETA: 0:00:02 Cross validating... 57%|██████████████████▎ | ETA: 0:00:02 Cross validating... 60%|███████████████████▎ | ETA: 0:00:02 Cross validating... 63%|████████████████████▍ | ETA: 0:00:02 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:02 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:01 Cross validating... 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 0 465.5669577331759 1 440.33093589422253 2 415.45552001759415 3 378.1578171990544 4 358.7132429104769 5 362.69501951894256 6 365.60407544193856 7 360.12318163015993 8 365.00550736002333 9 373.1895263402415 10 383.74035077857275 11 390.2976729194907 12 385.0002908869292 13 394.07180722022724 14 389.353624178203 15 403.0599387051999 16 420.44304922590715 17 421.6580570781534 18 437.69642473384033 19 438.48766459349486 20 430.6831671808329 Best k = 4 4.637917 seconds (17.65 M allocations: 364.262 MiB, 1.39% gc time, 1.26% compilation time) Test Summary: | Pass Total Time Cross validation on Float64 matrix, logistic model | 2 2 13.1s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:01:03 Cross validating... 6%|██ | ETA: 0:00:33 Cross validating... 10%|███ | ETA: 0:00:23 Cross validating... 13%|████▏ | ETA: 0:00:18 Cross validating... 16%|█████▏ | ETA: 0:00:15 Cross validating... 19%|██████▏ | ETA: 0:00:13 Cross validating... 22%|███████▏ | ETA: 0:00:11 Cross validating... 25%|████████▏ | ETA: 0:00:10 Cross validating... 29%|█████████▏ | ETA: 0:00:09 Cross validating... 32%|██████████▏ | ETA: 0:00:08 Cross validating... 35%|███████████▏ | ETA: 0:00:07 Cross validating... 37%|███████████▋ | ETA: 0:00:07 Cross validating... 40%|████████████▊ | ETA: 0:00:06 Cross validating... 43%|█████████████▊ | ETA: 0:00:06 Cross validating... 46%|██████████████▊ | ETA: 0:00:05 Cross validating... 49%|███████████████▊ | ETA: 0:00:05 Cross validating... 52%|████████████████▊ | ETA: 0:00:04 Cross validating... 56%|█████████████████▊ | ETA: 0:00:04 Cross validating... 59%|██████████████████▊ | ETA: 0:00:04 Cross validating... 62%|███████████████████▊ | ETA: 0:00:03 Cross validating... 65%|████████████████████▉ | ETA: 0:00:03 Cross validating... 68%|█████████████████████▉ | ETA: 0:00:03 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:02 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:02 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:02 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:01 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:01 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:01 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:01 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:07 Crossvalidation Results: k MSE 0 1170.215721309809 1 874.7982301508471 2 647.1848137499783 3 534.6162264827682 4 502.8633132774871 5 456.0291015173468 6 393.3854089804767 7 395.1710025260783 8 396.5445303845022 9 389.08165917578174 10 395.82520938898847 11 392.2001994340907 12 413.32527789119746 13 393.22069947586203 14 410.4394125672161 15 395.40504904622395 16 402.85210033393406 17 432.68977836274513 18 417.52526852239765 19 409.50802706809736 20 408.959388584547 Best k = 9 8.344552 seconds (15.11 M allocations: 350.023 MiB, 0.93% gc time, 34.06% 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: 0:00:04 Cross validating... 6%|██ | ETA: 0:00:04 Cross validating... 10%|███ | ETA: 0:00:04 Cross validating... 11%|███▌ | ETA: 0:00:05 Cross validating... 14%|████▋ | ETA: 0:00:04 Cross validating... 17%|█████▋ | ETA: 0:00:04 Cross validating... 21%|██████▋ | ETA: 0:00:04 Cross validating... 24%|███████▋ | ETA: 0:00:04 Cross validating... 27%|████████▋ | ETA: 0:00:04 Cross validating... 30%|█████████▋ | ETA: 0:00:04 Cross validating... 33%|██████████▋ | ETA: 0:00:04 Cross validating... 37%|███████████▋ | ETA: 0:00:03 Cross validating... 40%|████████████▊ | ETA: 0:00:03 Cross validating... 43%|█████████████▊ | ETA: 0:00:03 Cross validating... 46%|██████████████▊ | ETA: 0:00:03 Cross validating... 49%|███████████████▊ | ETA: 0:00:03 Cross validating... 52%|████████████████▊ | ETA: 0:00:03 Cross validating... 56%|█████████████████▊ | ETA: 0:00:02 Cross validating... 59%|██████████████████▊ | ETA: 0:00:02 Cross validating... 62%|███████████████████▊ | ETA: 0:00:02 Cross validating... 65%|████████████████████▉ | ETA: 0:00:02 Cross validating... 68%|█████████████████████▉ | ETA: 0:00:02 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:02 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:01 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:01 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:01 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:01 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:01 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:01 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:05 Crossvalidation Results: k MSE 0 1170.215721309809 1 831.6919196122902 2 630.5760786480738 3 529.7004135887533 4 506.1387984543602 5 451.2849208187868 6 392.4673464607936 7 391.25492992136196 8 401.03903957466224 9 400.51125473743804 10 397.949198050261 11 422.2195035714433 12 418.5262641028866 13 419.7400811268168 14 424.35737996169667 15 440.41736498803675 16 447.2307311149307 17 453.40170792270607 18 452.6895936336448 19 443.83097245427723 20 445.01631095509646 Best k = 7 5.557909 seconds (14.04 M allocations: 280.693 MiB, 1.55% gc time, 0.54% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, Poisson model | 2 2 14.3s **** 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: 0:01:31 Cross validating... 5%|█▌ | ETA: 0:01:20 Cross validating... 6%|██ | ETA: 0:01:14 Cross validating... 8%|██▌ | ETA: 0:01:10 Cross validating... 11%|███▌ | ETA: 0:00:57 Cross validating... 13%|████▏ | ETA: 0:00:56 Cross validating... 14%|████▋ | ETA: 0:00:50 Cross validating... 16%|█████▏ | ETA: 0:00:45 Cross validating... 17%|█████▋ | ETA: 0:00:41 Cross validating... 19%|██████▏ | ETA: 0:00:37 Cross validating... 21%|██████▋ | ETA: 0:00:38 Cross validating... 22%|███████▏ | ETA: 0:00:38 Cross validating... 24%|███████▋ | ETA: 0:00:38 Cross validating... 25%|████████▏ | ETA: 0:00:38 Cross validating... 27%|████████▋ | ETA: 0:00:36 Cross validating... 29%|█████████▏ | ETA: 0:00:33 Cross validating... 30%|█████████▋ | ETA: 0:00:31 Cross validating... 32%|██████████▏ | ETA: 0:00:31 Cross validating... 33%|██████████▋ | ETA: 0:00:29 Cross validating... 37%|███████████▋ | ETA: 0:00:26 Cross validating... 40%|████████████▊ | ETA: 0:00:26 Cross validating... 41%|█████████████▎ | ETA: 0:00:25 Cross validating... 44%|██████████████▎ | ETA: 0:00:23 Cross validating... 48%|███████████████▎ | ETA: 0:00:20 Cross validating... 49%|███████████████▊ | ETA: 0:00:19 Cross validating... 51%|████████████████▎ | ETA: 0:00:19 Cross validating... 52%|████████████████▊ | ETA: 0:00:18 Cross validating... 54%|█████████████████▎ | ETA: 0:00:17 Cross validating... 57%|██████████████████▎ | ETA: 0:00:15 Cross validating... 59%|██████████████████▊ | ETA: 0:00:14 Cross validating... 60%|███████████████████▎ | ETA: 0:00:13 Cross validating... 62%|███████████████████▊ | ETA: 0:00:13 Cross validating... 63%|████████████████████▍ | ETA: 0:00:13 Cross validating... 65%|████████████████████▉ | ETA: 0:00:12 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:12 Cross 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validating... 95%|██████████████████████████████▌ | ETA: 0:00:02 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:01 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:01 Cross validating... 100%|████████████████████████████████| Time: 0:00:37 Crossvalidation Results: k MSE 0 455.9173475953578 1 361.331004227515 2 282.71392324400045 3 249.42522543126313 4 231.12129767915155 5 213.41030415363377 6 203.305897099201 7 204.62356491168052 8 206.23189696346645 9 205.97228219536322 10 207.23590355368958 11 208.6210762442032 12 209.04486577408156 13 206.86257778131352 14 211.63888119252567 15 211.83416468771435 16 210.26561612315945 17 211.69539485921663 18 213.13106992597557 19 214.88516537899872 20 216.71153365606307 Best k = 6 37.703679 seconds (116.73 M allocations: 2.930 GiB, 1.29% gc time, 6.16% 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: 0:00:07 Cross validating... 6%|██ | ETA: 0:00:06 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: 0:00:06 Cross validating... 17%|█████▋ | ETA: 0:00:06 Cross validating... 19%|██████▏ | ETA: 0:00:07 Cross validating... 21%|██████▋ | ETA: 0:00:07 Cross validating... 22%|███████▏ | ETA: 0:00:07 Cross validating... 24%|███████▋ | ETA: 0:00:07 Cross validating... 25%|████████▏ | ETA: 0:00:07 Cross validating... 27%|████████▋ | ETA: 0:00:07 Cross validating... 29%|█████████▏ | ETA: 0:00:07 Cross validating... 30%|█████████▋ | ETA: 0:00:07 Cross validating... 32%|██████████▏ | ETA: 0:00:07 Cross validating... 33%|██████████▋ | ETA: 0:00:08 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90%|█████████████████████████████ | ETA: 0:00:01 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:01 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:01 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:01 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:10 Crossvalidation Results: k MSE 0 455.9173475953578 1 362.31046388038226 2 283.40428638694397 3 250.18013962306838 4 231.63357085998382 5 222.59350814754112 6 205.13882765054035 7 208.9732148654172 8 213.429959560106 9 211.3094435790561 10 213.54793660699625 11 221.52169373307936 12 220.75810297397084 13 222.0886429804473 14 238.44354045899394 15 229.4289380812596 16 225.7679094450708 17 244.61161960134513 18 241.17948955676485 19 247.74792879120446 20 258.0008683753815 Best k = 6 11.038687 seconds (32.22 M allocations: 650.344 MiB, 1.59% gc time, 0.77% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, NegativeBinomial model | 2 2 49.2s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:01:11 Cross validating... 6%|██ | ETA: 0:00:36 Cross validating... 10%|███ | ETA: 0:00:24 Cross validating... 13%|████▏ | ETA: 0:00:18 Cross validating... 16%|█████▏ | ETA: 0:00:15 Cross validating... 19%|██████▏ | ETA: 0:00:12 Cross validating... 22%|███████▏ | ETA: 0:00:11 Cross validating... 25%|████████▏ | ETA: 0:00:09 Cross validating... 29%|█████████▏ | ETA: 0:00:08 Cross validating... 32%|██████████▏ | ETA: 0:00:07 Cross validating... 37%|███████████▋ | ETA: 0:00:06 Cross validating... 40%|████████████▊ | ETA: 0:00:06 Cross validating... 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98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:05 Crossvalidation Results: k MSE 0 708.7406597900391 1 594.0547950439453 2 472.60887115478516 3 391.07051165771486 4 322.2429605712891 5 274.1304553527832 6 242.98796069335935 7 231.75397763061522 8 211.04413333129884 9 208.82878451538085 10 210.9139321594238 11 206.8662128601074 12 209.29315435791017 13 216.44690969848637 14 210.83974066162108 15 223.69269552612303 16 223.5122525024414 17 217.3672544555664 18 230.29235778808595 19 245.48900619506838 20 214.24631561279296 Best k = 11 6.492086 seconds (17.22 M allocations: 343.618 MiB, 1.50% gc time, 46.28% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 5%|█▌ | ETA: 0:00:03 Cross validating... 8%|██▌ | ETA: 0:00:03 Cross validating... 11%|███▌ | ETA: 0:00:03 Cross validating... 14%|████▋ | ETA: 0:00:03 Cross validating... 17%|█████▋ | ETA: 0:00:03 Cross validating... 21%|██████▋ | ETA: 0:00:03 Cross validating... 24%|███████▋ | ETA: 0:00:03 Cross validating... 27%|████████▋ | ETA: 0:00:02 Cross validating... 30%|█████████▋ | ETA: 0:00:02 Cross validating... 33%|██████████▋ | ETA: 0:00:02 Cross validating... 38%|████████████▎ | ETA: 0:00:02 Cross validating... 41%|█████████████▎ | ETA: 0:00:02 Cross validating... 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: 0:00:01 Cross validating... 60%|███████████████████▎ | ETA: 0:00:01 Cross validating... 63%|████████████████████▍ | ETA: 0:00:01 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:01 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14 231.40656030273436 15 233.06280703735348 16 243.6403890075684 17 242.80908297729493 18 238.556499420166 19 251.23290313720705 20 244.79654568481442 Best k = 8 3.423666 seconds (16.26 M allocations: 288.225 MiB, 1.65% gc time, 1.18% compilation time) Test Summary: | Pass Total Time Cross validation on floating point matrices, NegativeBinomial model | 2 2 10.5s **** 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: 0:01:22 Cross validating... 3%|█ | ETA: 0:00:58 Cross validating... 4%|█▎ | ETA: 0:00:45 Cross validating... 5%|█▋ | ETA: 0:00:39 Cross validating... 6%|█▉ | ETA: 0:00:34 Cross validating... 7%|██▎ | ETA: 0:00:30 Cross validating... 8%|██▌ | ETA: 0:00:28 Cross validating... 9%|██▉ | ETA: 0:00:26 Cross validating... 10%|███▎ | ETA: 0:00:24 Cross 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97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▍| ETA: 0:00:00 Cross validating... 99%|███████████████████████████████▋| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:16 Crossvalidation Results: k MSE 1 3130.5167255589895 2 2522.7040637681216 3 2376.4933115510885 4 2320.948752429626 5 2250.225874650594 6 2139.042427120781 7 2154.948735015062 8 2169.899436484573 9 2175.223366720778 10 2204.429785396296 11 2195.341384117982 12 2215.4793430461023 13 2206.287312094592 14 2217.1433384862407 15 2272.6594360230506 16 2259.053427659046 17 2256.356416319903 18 2294.9210730748546 19 2300.454135738318 20 2345.25047128734 Best k = 6 16.927562 seconds (301.82 k allocations: 213.421 MiB, 0.73% gc time, 10.46% compilation time) Test Summary: | Pass Total Time multivariate cross validation SnpLinAlg | 3 3 21.8s Test Summary: | Pass Total Time wrapper univariate | 20 20 2m00.8s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 2%|▋ | ETA: 0:00:10 Cross validating... 3%|█ | ETA: 0:00:10 Cross validating... 4%|█▎ | ETA: 0:00:11 Cross validating... 5%|█▋ | ETA: 0:00:11 Cross validating... 6%|█▉ | ETA: 0:00:12 Cross validating... 7%|██▎ | ETA: 0:00:12 Cross validating... 8%|██▌ | ETA: 0:00:12 Cross validating... 9%|██▉ | ETA: 0:00:13 Cross validating... 10%|███▎ | ETA: 0:00:14 Cross validating... 11%|███▌ | ETA: 0:00:15 Cross validating... 12%|███▉ | ETA: 0:00:15 Cross validating... 13%|████▏ | ETA: 0:00:16 Cross validating... 14%|████▌ | ETA: 0:00:16 Cross validating... 15%|████▊ | ETA: 0:00:16 Cross validating... 16%|█████▏ | ETA: 0:00:18 Cross validating... 17%|█████▌ | ETA: 0:00:18 Cross validating... 18%|█████▊ | ETA: 0:00:18 Cross validating... 19%|██████▏ | ETA: 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| ETA: 0:00:10 Cross validating... 58%|██████████████████▌ | ETA: 0:00:10 Cross validating... 59%|██████████████████▉ | ETA: 0:00:09 Cross validating... 60%|███████████████████▎ | ETA: 0:00:09 Cross validating... 61%|███████████████████▌ | ETA: 0:00:09 Cross validating... 62%|███████████████████▉ | ETA: 0:00:09 Cross validating... 63%|████████████████████▏ | ETA: 0:00:08 Cross validating... 64%|████████████████████▌ | ETA: 0:00:08 Cross validating... 65%|████████████████████▊ | ETA: 0:00:08 Cross validating... 66%|█████████████████████▏ | ETA: 0:00:08 Cross validating... 67%|█████████████████████▌ | ETA: 0:00:07 Cross validating... 68%|█████████████████████▊ | ETA: 0:00:07 Cross validating... 69%|██████████████████████▏ | ETA: 0:00:07 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:07 Cross validating... 71%|██████████████████████▊ | ETA: 0:00:07 Cross validating... 72%|███████████████████████ | ETA: 0:00:06 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:06 Cross validating... 74%|███████████████████████▋ | ETA: 0:00:06 Cross validating... 75%|████████████████████████ | ETA: 0:00:06 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:05 Cross validating... 77%|████████████████████████▋ | ETA: 0:00:05 Cross validating... 78%|█████████████████████████ | ETA: 0:00:05 Cross validating... 79%|█████████████████████████▎ | ETA: 0:00:05 Cross validating... 80%|█████████████████████████▋ | ETA: 0:00:05 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:04 Cross validating... 82%|██████████████████████████▎ | ETA: 0:00:04 Cross validating... 83%|██████████████████████████▌ | ETA: 0:00:04 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:04 Cross validating... 85%|███████████████████████████▎ | ETA: 0:00:03 Cross validating... 86%|███████████████████████████▌ | ETA: 0:00:03 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:03 Cross validating... 88%|████████████████████████████▏ | ETA: 0:00:03 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:02 Cross validating... 90%|████████████████████████████▊ | ETA: 0:00:02 Cross validating... 91%|█████████████████████████████▏ | ETA: 0:00:02 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:02 Cross validating... 93%|█████████████████████████████▊ | ETA: 0:00:02 Cross validating... 94%|██████████████████████████████▏ | ETA: 0:00:01 Cross validating... 95%|██████████████████████████████▍ | ETA: 0:00:01 Cross validating... 96%|██████████████████████████████▊ | ETA: 0:00:01 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:01 Cross validating... 98%|███████████████████████████████▍| ETA: 0:00:00 Cross validating... 99%|███████████████████████████████▋| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:23 Crossvalidation Results: k MSE 1 2838.788679198002 2 2514.3973428708136 3 2305.6176519676274 4 2222.025304867614 5 2075.1670384588365 6 2067.7948989723845 7 2053.427506114907 8 2086.405384830965 9 2080.984460901671 10 2105.131199502364 11 2132.407165368786 12 2138.267187460652 13 2166.002210829576 14 2194.9918295115804 15 2189.890403738045 16 2191.181293229578 17 2209.4669750564362 18 2221.2595493644303 19 2238.7425945763257 20 2253.9559571797727 Best k = 7 **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 2%|▋ | ETA: 0:00:10 Cross validating... 3%|█ | ETA: 0:00:10 Cross validating... 4%|█▎ | ETA: 0:00:11 Cross validating... 5%|█▋ | ETA: 0:00:11 Cross validating... 6%|█▉ | ETA: 0:00:12 Cross validating... 7%|██▎ | ETA: 0:00:12 Cross validating... 8%|██▌ | ETA: 0:00:12 Cross validating... 9%|██▉ | ETA: 0:00:13 Cross validating... 10%|███▎ | ETA: 0:00:14 Cross validating... 11%|███▌ | ETA: 0:00:15 Cross validating... 12%|███▉ | ETA: 0:00:15 Cross validating... 13%|████▏ | ETA: 0:00:16 Cross validating... 14%|████▌ | ETA: 0:00:16 Cross validating... 15%|████▊ | ETA: 0:00:17 Cross validating... 16%|█████▏ | ETA: 0:00:18 Cross validating... 17%|█████▌ | ETA: 0:00:18 Cross validating... 18%|█████▊ | ETA: 0:00:18 Cross validating... 19%|██████▏ | ETA: 0:00:18 Cross validating... 20%|██████▍ | ETA: 0:00:18 Cross validating... 21%|██████▊ | ETA: 0:00:18 Cross validating... 22%|███████ | ETA: 0:00:17 Cross validating... 23%|███████▍ | ETA: 0:00:16 Cross validating... 24%|███████▋ | ETA: 0:00:16 Cross validating... 25%|████████ | ETA: 0:00:16 Cross validating... 26%|████████▍ | ETA: 0:00:15 Cross validating... 27%|████████▋ | ETA: 0:00:15 Cross validating... 28%|█████████ | ETA: 0:00:15 Cross validating... 29%|█████████▎ | ETA: 0:00:15 Cross validating... 30%|█████████▋ | ETA: 0:00:15 Cross validating... 31%|█████████▉ | ETA: 0:00:15 Cross validating... 32%|██████████▎ | ETA: 0:00:15 Cross validating... 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0:00:11 Cross validating... 52%|████████████████▋ | ETA: 0:00:11 Cross validating... 53%|█████████████████ | ETA: 0:00:10 Cross validating... 54%|█████████████████▎ | ETA: 0:00:10 Cross validating... 55%|█████████████████▋ | ETA: 0:00:10 Cross validating... 56%|█████████████████▉ | ETA: 0:00:10 Cross validating... 57%|██████████████████▎ | ETA: 0:00:10 Cross validating... 58%|██████████████████▌ | ETA: 0:00:10 Cross validating... 59%|██████████████████▉ | ETA: 0:00:09 Cross validating... 60%|███████████████████▎ | ETA: 0:00:09 Cross validating... 61%|███████████████████▌ | ETA: 0:00:09 Cross validating... 62%|███████████████████▉ | ETA: 0:00:09 Cross validating... 63%|████████████████████▏ | ETA: 0:00:08 Cross validating... 64%|████████████████████▌ | ETA: 0:00:08 Cross validating... 65%|████████████████████▊ | ETA: 0:00:08 Cross validating... 66%|█████████████████████▏ | ETA: 0:00:08 Cross validating... 67%|█████████████████████▌ | ETA: 0:00:07 Cross validating... 68%|█████████████████████▊ | ETA: 0:00:07 Cross validating... 69%|██████████████████████▏ | ETA: 0:00:07 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:07 Cross validating... 71%|██████████████████████▊ | ETA: 0:00:06 Cross validating... 72%|███████████████████████ | ETA: 0:00:06 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:06 Cross validating... 74%|███████████████████████▋ | ETA: 0:00:06 Cross validating... 75%|████████████████████████ | ETA: 0:00:06 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:05 Cross validating... 77%|████████████████████████▋ | ETA: 0:00:05 Cross validating... 78%|█████████████████████████ | ETA: 0:00:05 Cross validating... 79%|█████████████████████████▎ | ETA: 0:00:05 Cross validating... 80%|█████████████████████████▋ | ETA: 0:00:05 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:04 Cross validating... 82%|██████████████████████████▎ | ETA: 0:00:04 Cross validating... 83%|██████████████████████████▌ | ETA: 0:00:04 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:04 Cross validating... 85%|███████████████████████████▎ | ETA: 0:00:03 Cross validating... 86%|███████████████████████████▌ | ETA: 0:00:03 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:03 Cross validating... 88%|████████████████████████████▏ | ETA: 0:00:03 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:02 Cross validating... 90%|████████████████████████████▊ | ETA: 0:00:02 Cross validating... 91%|█████████████████████████████▏ | ETA: 0:00:02 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:02 Cross validating... 93%|█████████████████████████████▊ | ETA: 0:00:02 Cross validating... 94%|██████████████████████████████▏ | ETA: 0:00:01 Cross validating... 95%|██████████████████████████████▍ | ETA: 0:00:01 Cross validating... 96%|██████████████████████████████▊ | ETA: 0:00:01 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:01 Cross validating... 98%|███████████████████████████████▍| ETA: 0:00:00 Cross validating... 99%|███████████████████████████████▋| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:23 Crossvalidation Results: k MSE 1 2838.788679198002 2 2514.3973428708136 3 2305.6176519676274 4 2222.025304867614 5 2075.1670384588365 6 2067.7948989723845 7 2053.427506114907 8 2086.405384830965 9 2080.984460901671 10 2105.131199502364 11 2132.407165368786 12 2138.267187460652 13 2166.002210829576 14 2194.9918295115804 15 2189.890403738045 16 2191.181293229578 17 2209.4669750564362 18 2221.2595493644303 19 2238.7425945763257 20 2253.9559571797727 Best k = 7 **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 2%|▋ | ETA: 0:00:10 Cross validating... 3%|█ | ETA: 0:00:10 Cross validating... 4%|█▎ | ETA: 0:00:11 Cross validating... 5%|█▋ | ETA: 0:00:11 Cross validating... 6%|█▉ | ETA: 0:00:12 Cross validating... 7%|██▎ | ETA: 0:00:13 Cross validating... 8%|██▌ | ETA: 0:00:13 Cross validating... 9%|██▉ | ETA: 0:00:14 Cross validating... 10%|███▎ | ETA: 0:00:15 Cross validating... 11%|███▌ | ETA: 0:00:15 Cross validating... 12%|███▉ | ETA: 0:00:16 Cross validating... 13%|████▏ | ETA: 0:00:16 Cross validating... 14%|████▌ | ETA: 0:00:16 Cross validating... 15%|████▊ | ETA: 0:00:17 Cross validating... 16%|█████▏ | ETA: 0:00:18 Cross validating... 17%|█████▌ | ETA: 0:00:18 Cross validating... 18%|█████▊ | ETA: 0:00:18 Cross validating... 19%|██████▏ | ETA: 0:00:19 Cross validating... 20%|██████▍ | ETA: 0:00:19 Cross validating... 21%|██████▊ | ETA: 0:00:18 Cross validating... 22%|███████ | ETA: 0:00:17 Cross validating... 23%|███████▍ | ETA: 0:00:17 Cross validating... 24%|███████▋ | ETA: 0:00:16 Cross validating... 25%|████████ | ETA: 0:00:16 Cross 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| ETA: 0:00:09 Cross validating... 63%|████████████████████▏ | ETA: 0:00:08 Cross validating... 64%|████████████████████▌ | ETA: 0:00:08 Cross validating... 65%|████████████████████▊ | ETA: 0:00:08 Cross validating... 66%|█████████████████████▏ | ETA: 0:00:08 Cross validating... 67%|█████████████████████▌ | ETA: 0:00:07 Cross validating... 68%|█████████████████████▊ | ETA: 0:00:07 Cross validating... 69%|██████████████████████▏ | ETA: 0:00:07 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:07 Cross validating... 71%|██████████████████████▊ | ETA: 0:00:07 Cross validating... 72%|███████████████████████ | ETA: 0:00:06 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:06 Cross validating... 74%|███████████████████████▋ | ETA: 0:00:06 Cross validating... 75%|████████████████████████ | ETA: 0:00:06 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:05 Cross validating... 77%|████████████████████████▋ | ETA: 0:00:05 Cross validating... 78%|█████████████████████████ | ETA: 0:00:05 Cross validating... 79%|█████████████████████████▎ | ETA: 0:00:05 Cross validating... 80%|█████████████████████████▋ | ETA: 0:00:05 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:04 Cross validating... 82%|██████████████████████████▎ | ETA: 0:00:04 Cross validating... 83%|██████████████████████████▌ | ETA: 0:00:04 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:04 Cross validating... 85%|███████████████████████████▎ | ETA: 0:00:03 Cross validating... 86%|███████████████████████████▌ | ETA: 0:00:03 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:03 Cross validating... 88%|████████████████████████████▏ | ETA: 0:00:03 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:02 Cross validating... 90%|████████████████████████████▊ | ETA: 0:00:02 Cross validating... 91%|█████████████████████████████▏ | ETA: 0:00:02 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:02 Cross validating... 93%|█████████████████████████████▊ | ETA: 0:00:02 Cross validating... 94%|██████████████████████████████▏ | ETA: 0:00:01 Cross validating... 95%|██████████████████████████████▍ | ETA: 0:00:01 Cross validating... 96%|██████████████████████████████▊ | ETA: 0:00:01 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:01 Cross validating... 98%|███████████████████████████████▍| ETA: 0:00:00 Cross validating... 99%|███████████████████████████████▋| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:23 Crossvalidation Results: k MSE 1 2838.788679198002 2 2514.3973428708136 3 2305.6176519676274 4 2222.025304867614 5 2075.1670384588365 6 2067.7948989723845 7 2053.427506114907 8 2086.405384830965 9 2080.984460901671 10 2105.131199502364 11 2132.407165368786 12 2138.267187460652 13 2166.002210829576 14 2194.9918295115804 15 2189.890403738045 16 2191.181293229578 17 2209.4669750564362 18 2221.2595493644303 19 2238.7425945763257 20 2253.9559571797727 Best k = 7 Test Summary: | Pass Total Time wrapper multivariate | 8 8 1m26.2s read BGEN and VCF: Error During Test at /home/pkgeval/.julia/packages/MendelIHT/ZcxZT/test/wrapper_test.jl:184 Got exception outside of a @test startproc must be called before process Stacktrace: [1] error(s::String) @ Base error.jl:56 [2] process(codec::CodecZlib.ZlibDecompressor, input::TranscodingStreams.Memory, output::TranscodingStreams.Memory, error_ref::TranscodingStreams.Error) @ CodecZlib ~/.julia/packages/CodecZlib/lEc2s/src/decompression.jl:186 [3] decompress(io::IOStream, v::Variant, h::BGEN.Header; decompressed::Nothing) @ BGEN ~/.julia/packages/BGEN/dfgRU/src/genotypes.jl:72 [4] first_allele_dosage!(b::Bgen, v::Variant; T::Core.TypeEgal{Float64}, mean_impute::Bool, clear_decompressed::Bool, data::Nothing, decompressed::Nothing, is_decompressed::Bool) @ BGEN ~/.julia/packages/BGEN/dfgRU/src/genotypes.jl:571 [5] convert_bgen_gt(t::Core.TypeEgal{Float64}, b::Bgen) @ MendelIHT ~/.julia/packages/MendelIHT/ZcxZT/src/wrapper.jl:380 [6] macro expansion @ ./timing.jl:741 [inlined] [7] macro expansion @ ~/.julia/packages/MendelIHT/ZcxZT/test/wrapper_test.jl:187 [inlined] [8] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:2246 [inlined] [9] top-level scope @ ~/.julia/packages/MendelIHT/ZcxZT/test/wrapper_test.jl:185 [10] include(mapexpr::Function, mod::Module, _path::String) @ Base Base.jl:326 [11] top-level scope @ ~/.julia/packages/MendelIHT/ZcxZT/test/runtests.jl:20 [12] include(mapexpr::Function, mod::Module, _path::String) @ Base Base.jl:326 [13] top-level scope @ none:6 [14] eval(m::Module, e::Any) @ Core boot.jl:545 [15] exec_options(opts::Base.JLOptions) @ Base client.jl:321 [16] _start() @ Base client.jl:596 Test Summary: | Error Total Time read BGEN and VCF | 1 1 3.6s RNG of the outermost testset: Xoshiro(0x09beec275eb843d8, 0x46a24b9f420a2c17, 0x7918ab5c77c6504e, 0x2dae529c55302938, 0x7ae56a19d0077a2b) 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 1085.85s ERROR: LoadError: Package MendelIHT errored during testing Stacktrace: [1] pkgerror(msg::String) @ Pkg.Types /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Types.jl:68 [2] test(ctx::Pkg.Types.Context, pkgs::Vector{PackageSpec}; coverage::Bool, julia_args::Cmd, test_args::Cmd, test_fn::Nothing, force_latest_compatible_version::Bool, allow_earlier_backwards_compatible_versions::Bool, allow_reresolve::Bool) @ Pkg.Operations /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Operations.jl:3247 [3] test(ctx::Pkg.Types.Context, pkgs::Vector{PackageSpec}; coverage::Bool, test_fn::Nothing, julia_args::Cmd, test_args::Cmd, force_latest_compatible_version::Bool, allow_earlier_backwards_compatible_versions::Bool, allow_reresolve::Bool, kwargs::@Kwargs{io::IOContext{IO}}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:587 [4] test(pkgs::Vector{PackageSpec}; io::IOContext{IO}, kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:172 [5] test(pkgs::Vector{String}; kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:160 [6] test(pkg::String; kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:159 [inlined] [7] top-level scope @ /PkgEval.jl/scripts/evaluate.jl:223 [8] include(mod::Module, _path::String) @ Base Base.jl:325 [9] exec_options(opts::Base.JLOptions) @ Base client.jl:355 [10] _start() @ Base client.jl:596 in expression starting at /PkgEval.jl/scripts/evaluate.jl:214 PkgEval failed after 1210.24s: package tests unexpectedly errored