Package evaluation to test MendelIHT on Julia 1.14.0-DEV.3128 (f573e2bf71*) started at 2026-09-07T02:26:30.814 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.14` Set-up completed after 15.94s ################################################################################ # 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 v7.30.1 [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 v0.10.17 [fb6a15b2] + CloseOpenIntervals v0.1.13 [523fee87] + CodecBzip2 v0.8.5 [ba30903b] + CodecXz v0.7.4 [944b1d66] + CodecZlib v0.7.9 [6b39b394] + CodecZstd v0.8.7 [861a8166] + Combinatorics v1.1.0 [38540f10] + CommonSolve v0.2.14 [f70d9fcc] + CommonWorldInvalidations v1.2.1 [34da2185] + Compat v4.18.1 [a33af91c] + CompositionsBase v0.1.2 [187b0558] + ConstructionBase v1.6.0 [adafc99b] + CpuId v0.3.1 [a8cc5b0e] + Crayons v4.2.0 [a10d1c49] + DBInterface v2.7.0 [9a962f9c] + 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[efcefdf7] + PCRE2_jll v10.48.0+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 v1.70.0+0 [3f19e933] + p7zip_jll v17.8.2+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 To see why use `status --outdated -m` Installation completed after 5.38s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompiling project... 5.0 s ✓ BGEN 6.4 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`. 20.6 s ✓ MendelIHT 3 dependencies successfully precompiled in 33 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 52.14s ################################################################################ # Testing # Testing MendelIHT Status `/tmp/jl_v5XJ5b/Project.toml` ⌅ [6db4b851] BGEN v0.1.17 [6e4b80f9] BenchmarkTools v1.8.0 [336ed68f] CSV v0.10.17 [a93c6f00] DataFrames v1.8.2 [8bb1440f] DelimitedFiles v1.9.1 [b4f34e82] Distances v0.10.12 [31c24e10] Distributions v0.25.131 [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 v2.9.0 [2913bbd2] StatsBase v0.34.13 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libblastrampoline_jll v5.15.0+0 [8e850ede] nghttp2_jll v1.70.0+0 [3f19e933] p7zip_jll v17.8.2+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/RTt4y/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 13.7s Test Summary: | Pass Total Time deviance | 1 1 0.3s Test Summary: | Pass Total Time update_μ! | 4 4 1.2s Test Summary: | Pass Total Time _choose! | 7 7 7.0s Test Summary: | Pass Total Time _iht_backtrack | 7 7 0.0s Test Summary: | Pass Total Time standardize! | 12 12 0.9s Test Summary: | Pass Total Time project_k! | 2 2 0.9s Test Summary: | Pass Total Time project_group_sparse! | 5 5 1.1s Test Summary: | Pass Total Time maf_weights | 6 6 1.9s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse linear regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1806.421450649008, backtracks = 0, tol = 2.143676279169666 Iteration 2: loglikelihood = -1458.280695538129, backtracks = 0, tol = 0.1526882166152866 Iteration 3: loglikelihood = -1430.0397939854831, backtracks = 0, tol = 0.037151578545670715 Iteration 4: loglikelihood = -1429.6255455459811, backtracks = 0, tol = 0.004198945817974805 Iteration 5: loglikelihood = -1429.6175825012017, backtracks = 0, tol = 0.0006180607971158955 Iteration 6: loglikelihood = -1429.6173961277632, backtracks = 0, tol = 9.057032921908385e-5 IHT estimated 10 nonzero SNP predictors and 1 non-genetic predictors. Compute time (sec): 0.04724693298339844 Final loglikelihood: -1429.6173961277632 SNP PVE: 0.9374926132920052 Iterations: 6 Selected genetic predictors: 10×2 DataFrame Row │ Position Estimated_β │ Int64 Float64 ─────┼─────────────────────── 1 │ 1338 0.930432 2 │ 2777 2.01748 3 │ 2849 0.468395 4 │ 3097 -1.11987 5 │ 6314 -0.921081 6 │ 6605 -2.40736 7 │ 6972 1.28452 8 │ 7640 0.403418 9 │ 9568 0.377536 10 │ 9766 1.01469 Selected nongenetic predictors: 1×2 DataFrame Row │ Position Estimated_β │ Int64 Float64 ─────┼─────────────────────── 1 │ 1 -0.0660037Test Summary: | Pass Total Time fit normal SnpLinAlg | 4 4 22.1s **** 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 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 3.0s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse Poisson regression Number of threads = 1 Link functin = LogLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -3590.0769292885057, backtracks = 0, tol = 0.3437215689065142 Iteration 2: loglikelihood = -2150.228879445285, backtracks = 0, tol = 0.05872925394322736 Iteration 3: loglikelihood = -1616.9448523784524, backtracks = 0, tol = 0.06203633371171278 Iteration 4: loglikelihood = -1493.0360846752274, backtracks = 0, tol = 0.04894059049287387 Iteration 5: loglikelihood = -1396.0337470041638, backtracks = 0, tol = 0.12792228702727967 Iteration 6: loglikelihood = -1368.5622440353836, backtracks = 0, tol = 0.0621796044713289 Iteration 7: loglikelihood = -1357.8032010143334, backtracks = 0, tol = 0.030808648826998186 Iteration 8: loglikelihood = -1346.7618023743441, backtracks = 0, tol = 0.04390903359199243 Iteration 9: loglikelihood = -1342.1338523302684, backtracks = 0, tol = 0.016791545502282533 Iteration 10: loglikelihood = -1338.750455444608, backtracks = 0, tol = 0.01618443914343601 Iteration 11: loglikelihood = -1336.684256068342, backtracks = 0, tol = 0.010336337617053055 Iteration 12: loglikelihood = -1333.1742233957502, backtracks = 0, tol = 0.06317027581965774 Iteration 13: loglikelihood = -1330.1567225126075, backtracks = 0, tol = 0.013410367807609382 Iteration 14: loglikelihood = -1329.3022834612957, backtracks = 0, tol = 0.010126786993245826 Iteration 15: loglikelihood = -1328.896144929486, backtracks = 0, tol = 0.006154557277143851 Iteration 16: loglikelihood = -1328.6786480324981, backtracks = 0, tol = 0.003670559345678271 Iteration 17: loglikelihood = -1328.52533623282, backtracks = 0, tol = 0.0036423223192521693 Iteration 18: loglikelihood = -1328.4144312291978, backtracks = 0, tol = 0.0025905783413288776 Iteration 19: loglikelihood = -1328.3356865408155, backtracks = 0, tol = 0.002552010253487486 Iteration 20: loglikelihood = -1328.2788545111098, backtracks = 0, tol = 0.0018787079298598689 Iteration 21: loglikelihood = -1328.2384989810605, backtracks = 0, tol = 0.0017989885255885124 Iteration 22: loglikelihood = -1328.209509297131, backtracks = 0, tol = 0.0013563776649163281 Iteration 23: loglikelihood = -1328.188955455233, backtracks = 0, tol = 0.0012683697258636785 Iteration 24: loglikelihood = -1328.1742610518727, backtracks = 0, tol = 0.0009742620678059584 Iteration 25: loglikelihood = -1328.163861734711, backtracks = 0, tol = 0.0008939109014345565 Iteration 26: loglikelihood = -1328.1564579593226, backtracks = 0, tol = 0.0006964060605544132 Iteration 27: loglikelihood = -1328.1512269654174, backtracks = 0, tol = 0.0006296611143025758 Iteration 28: loglikelihood = -1328.1475152270152, backtracks = 0, tol = 0.000495738138157349 Iteration 29: loglikelihood = -1328.144896309498, backtracks = 0, tol = 0.00044329908640501907 Iteration 30: loglikelihood = -1328.1430427893724, backtracks = 0, tol = 0.00035172545095387103 Iteration 31: loglikelihood = -1328.1417363453522, backtracks = 0, tol = 0.0003119630406173856 Iteration 32: loglikelihood = -1328.1408134932074, backtracks = 0, tol = 0.00024891444575825733 Iteration 33: loglikelihood = -1328.1401635286038, backtracks = 0, tol = 0.00021946632149416192 Iteration 34: loglikelihood = -1328.139705048964, backtracks = 0, tol = 0.00017582086470979772 Iteration 35: loglikelihood = -1328.1393823242379, backtracks = 0, tol = 0.00015435746290505957 Iteration 36: loglikelihood = -1328.1391549083849, backtracks = 0, tol = 0.0001240180918186021 Iteration 37: loglikelihood = -1328.1389948951555, backtracks = 0, tol = 0.00010854537611961814 Iteration 38: loglikelihood = -1328.1388822201448, backtracks = 0, tol = 8.738993724604274e-5 Test Summary: | Pass Total Time fit Poisson SnpLinAlg | 4 4 2.2s **** 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 = -1678.3453469268657, backtracks = 0, tol = 0.347576231446983 Iteration 2: loglikelihood = -1584.2803974603444, backtracks = 0, tol = 0.18427838733146193 Iteration 3: loglikelihood = -1549.7802780844036, backtracks = 0, tol = 0.10128618361594276 Iteration 4: loglikelihood = -1536.5903885183088, backtracks = 0, tol = 0.10239949727780708 Iteration 5: loglikelihood = -1535.2575451099103, backtracks = 0, tol = 0.07523938818878656 Iteration 6: loglikelihood = -1534.654940304101, backtracks = 0, tol = 0.0162590029451093 Iteration 7: loglikelihood = -1534.5835007792123, backtracks = 1, tol = 0.00362738812143804 Iteration 8: loglikelihood = -1534.5461295212258, backtracks = 1, tol = 0.003196864351137912 Iteration 9: loglikelihood = -1534.5349048389062, backtracks = 1, tol = 0.0019145986873627605 Iteration 10: loglikelihood = -1534.5317589593262, backtracks = 1, tol = 0.0009442573980178538 Iteration 11: loglikelihood = -1534.5308959731983, backtracks = 1, tol = 0.0005399250553985416 Iteration 12: loglikelihood = -1534.530662353161, backtracks = 1, tol = 0.0002625522739900544 Iteration 13: loglikelihood = -1534.5305992582685, backtracks = 1, tol = 0.00014559880719366495 Iteration 14: loglikelihood = -1534.5305823308445, backtracks = 1, tol = 7.142688795360777e-5 Test Summary: | Pass Total Time fit NegativeBinomial SnpLinAlg | 4 4 0.9s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse linear regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1893.8244900054185, backtracks = 0, tol = 0.7601640402095994 Iteration 2: loglikelihood = -1476.535239374326, backtracks = 0, tol = 0.12169972100248337 Iteration 3: loglikelihood = -1426.055932677944, backtracks = 0, tol = 0.046549920651892 Iteration 4: loglikelihood = -1422.387413001786, backtracks = 0, tol = 0.031620542431811054 Iteration 5: loglikelihood = -1422.1186242574222, backtracks = 1, tol = 0.0021895447636910872 Iteration 6: loglikelihood = -1422.0477680870395, backtracks = 1, tol = 0.0011099873719449573 Iteration 7: loglikelihood = -1422.029228841483, backtracks = 1, tol = 0.000555123425617637 Iteration 8: loglikelihood = -1422.0244292399334, backtracks = 1, tol = 0.000274881829356608 Iteration 9: loglikelihood = -1422.0231991202456, backtracks = 1, tol = 0.00013566829709791095 Iteration 10: loglikelihood = -1422.0228861925311, backtracks = 1, tol = 6.71128943211664e-5 Test Summary: | Pass Total Time fit with >1 non-genetic covariates SnpLinAlg | 5 5 1.3s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse linear regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1665.3633406983417, backtracks = 0, tol = 0.44964381891839084 Iteration 2: loglikelihood = -1443.5582025115893, backtracks = 0, tol = 0.09595038335488223 Iteration 3: loglikelihood = -1422.4034404944923, backtracks = 0, tol = 0.038526718460395556 Iteration 4: loglikelihood = -1422.1311640612128, backtracks = 1, tol = 0.0018185738755528492 Iteration 5: loglikelihood = -1422.060862582771, backtracks = 1, tol = 0.0009125072042682459 Iteration 6: loglikelihood = -1422.042815550857, backtracks = 1, tol = 0.0004504627156612613 Iteration 7: loglikelihood = -1422.0382106138168, backtracks = 1, tol = 0.00021909909478508546 Iteration 8: loglikelihood = -1422.0370417930487, backtracks = 1, tol = 0.00010632620268942995 Iteration 9: loglikelihood = -1422.0367463247644, backtracks = 1, tol = 5.641103445643535e-5 Test Summary: | Pass Total Time model selection on non-genetic covariates | 5 5 0.5s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse linear regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 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 = -1473.1241001452804, backtracks = 0, tol = 0.11162633196865432 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 = 0.10125409614175712 Iteration 5: loglikelihood = -1397.466171579031, backtracks = 0, tol = 0.05343369325195713 Iteration 6: loglikelihood = -1395.7490747391416, backtracks = 0, tol = 0.08843871418165582 Iteration 7: loglikelihood = -1395.4877576477586, backtracks = 0, tol = 0.008924704068495177 Iteration 8: loglikelihood = -1395.442237061722, backtracks = 0, tol = 0.005277867116132827 Iteration 9: loglikelihood = -1395.4302205892106, backtracks = 0, tol = 0.0027680467744013336 Iteration 10: loglikelihood = -1395.1973617039412, backtracks = 0, tol = 0.09056900655606137 Iteration 11: loglikelihood = -1395.0048067729406, backtracks = 0, tol = 0.007650485819168892 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 = 0.0012530451800711446 Iteration 15: loglikelihood = -1394.977503420045, backtracks = 0, tol = 0.0006829444661300694 Iteration 16: loglikelihood = -1394.9773714862843, backtracks = 1, tol = 0.00022881022816864148 Iteration 17: loglikelihood = -1394.9773102201912, 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 = -1434.3602241747526, backtracks = 0, tol = 0.03199716666887782 Iteration 6: loglikelihood = -1434.239273652971, backtracks = 2, tol = 0.003498168340088284 Iteration 7: loglikelihood = -1434.1475478538455, backtracks = 2, tol = 0.003052291101552644 Iteration 8: loglikelihood = -1434.0913475157126, backtracks = 2, tol = 0.002193157681835551 Iteration 9: loglikelihood = -1434.0584761985995, backtracks = 2, tol = 0.0016688209654910676 Iteration 10: loglikelihood = -1434.0393127719108, backtracks = 2, tol = 0.001317554485128468 Iteration 11: loglikelihood = -1434.0281644425422, backtracks = 2, tol = 0.0010393713220469133 Iteration 12: loglikelihood = -1434.0216963632631, backtracks = 2, tol = 0.0008158673348111326 Iteration 13: loglikelihood = -1434.0179556115856, backtracks = 2, tol = 0.0006363671566384205 Iteration 14: loglikelihood = -1433.8972844529703, backtracks = 2, tol = 0.021056460842673336 Iteration 15: loglikelihood = -1433.6170929347984, backtracks = 1, tol = 0.011448126839540959 Iteration 16: loglikelihood = -1433.5408744767517, backtracks = 2, tol = 0.0040324300639331045 Iteration 17: loglikelihood = -1433.4945867179188, backtracks = 2, tol = 0.003005268578298657 Iteration 18: loglikelihood = -1433.467626121943, backtracks = 2, tol = 0.002187229771831415 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 = 0.0009580287583338233 Iteration 22: loglikelihood = -1433.4352962137846, backtracks = 2, tol = 0.0007222437442123496 Iteration 23: loglikelihood = -1433.4336216439426, backtracks = 2, tol = 0.0005424739396431646 Iteration 24: loglikelihood = -1433.43265547142, backtracks = 2, tol = 0.0004062814588068666 Iteration 25: loglikelihood = -1433.4320960523787, backtracks = 2, tol = 0.00030341799187724174 Iteration 26: loglikelihood = -1433.4317709097872, backtracks = 2, tol = 0.00022583740291083832 Iteration 27: loglikelihood = -1433.4315812027676, backtracks = 2, tol = 0.0001673653861249394 Iteration 28: loglikelihood = -1432.5898379532828, backtracks = 2, tol = 0.0250802150540324 Iteration 29: loglikelihood = -1431.7678006470733, backtracks = 1, tol = 0.017181190475547 Iteration 30: loglikelihood = -1430.3157393955933, backtracks = 1, tol = 0.07333968264200223 Iteration 31: loglikelihood = -1429.706868513855, backtracks = 0, tol = 0.02001511172794573 Iteration 32: loglikelihood = -1429.5802551945537, backtracks = 1, tol = 0.00756937670420323 Iteration 33: loglikelihood = -1429.513945055356, backtracks = 2, tol = 0.003906515984506249 Iteration 34: loglikelihood = -1429.469197232521, backtracks = 2, tol = 0.003683664863256532 Iteration 35: loglikelihood = -1428.86075262229, backtracks = 2, tol = 0.08711763846658718 Iteration 36: loglikelihood = -1428.6178427111051, backtracks = 1, tol = 0.006558345246943248 Iteration 37: loglikelihood = -1428.5424083746184, backtracks = 2, tol = 0.0033912200662443866 Iteration 38: loglikelihood = -1428.4933608487952, backtracks = 2, tol = 0.0030098214824111564 Iteration 39: loglikelihood = -1428.4620745885084, backtracks = 2, tol = 0.002595137111913267 Iteration 40: loglikelihood = -1428.4427329028306, backtracks = 2, tol = 0.002148184701148499 Iteration 41: loglikelihood = -1428.4311433050725, backtracks = 2, tol = 0.0017160493175770867 Iteration 42: loglikelihood = -1428.4243474878394, backtracks = 2, tol = 0.0013407892924840858 Iteration 43: loglikelihood = -1428.420413936832, backtracks = 2, tol = 0.0010343694042998762 Iteration 44: loglikelihood = -1428.4181556141764, 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 = 0.00034956951660976293 Iteration 48: loglikelihood = -1428.4154831711999, backtracks = 2, tol = 0.00026348047442121094 Iteration 49: loglikelihood = -1428.415350523391, backtracks = 2, tol = 0.00019816133989405092 Iteration 50: loglikelihood = -1428.4152757065372, backtracks = 2, tol = 0.00014882628973649723 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 6.2s **** 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 = -1549.8161173741325, backtracks = 0, tol = 0.23676456625057019 Iteration 2: loglikelihood = -1466.5489412147283, backtracks = 0, tol = 0.14649547508501956 Iteration 3: loglikelihood = -1414.720425536786, backtracks = 1, tol = 0.07895881692272465 Iteration 4: loglikelihood = -1389.26684481544, backtracks = 0, tol = 0.12176741612678235 Iteration 5: loglikelihood = -1358.6873673108485, backtracks = 1, tol = 0.040970412988712436 Iteration 6: loglikelihood = -1348.491792848529, backtracks = 1, tol = 0.05864815175238717 Iteration 7: loglikelihood = -1337.5957274599743, backtracks = 0, tol = 0.056490902490358895 Iteration 8: loglikelihood = -1327.25974515391, backtracks = 1, tol = 0.052158685899166515 Iteration 9: loglikelihood = -1319.594397908708, backtracks = 1, tol = 0.04571546941826928 Iteration 10: loglikelihood = -1316.2184407146472, backtracks = 1, tol = 0.019829344083368568 Iteration 11: loglikelihood = -1314.806990669207, backtracks = 1, tol = 0.011937851070645556 Iteration 12: loglikelihood = -1308.5472668658433, backtracks = 1, tol = 0.04772134246313636 Iteration 13: loglikelihood = -1306.2515940996095, backtracks = 0, tol = 0.02403465058398759 Iteration 14: loglikelihood = -1305.4535168891882, backtracks = 0, tol = 0.011694368601364897 Iteration 15: loglikelihood = -1305.090058052454, backtracks = 0, tol = 0.009581961931110761 Iteration 16: loglikelihood = -1304.9058974272493, backtracks = 0, tol = 0.006422753068905882 Iteration 17: loglikelihood = -1304.8040289275993, backtracks = 0, tol = 0.004668345347764374 Iteration 18: loglikelihood = -1304.7473054141612, backtracks = 0, tol = 0.0036202914311134365 Iteration 19: loglikelihood = -1304.714978286756, backtracks = 0, tol = 0.0025007232444204854 Iteration 20: loglikelihood = -1304.696732163173, backtracks = 0, tol = 0.0020533560166706576 Iteration 21: loglikelihood = -1304.6862863615588, backtracks = 0, tol = 0.001388039618377117 Iteration 22: loglikelihood = -1304.6803776414706, backtracks = 0, tol = 0.001168511098019486 Iteration 23: loglikelihood = -1304.6769904992802, backtracks = 0, tol = 0.0007811936727822007 Iteration 24: loglikelihood = -1304.6750724788847, backtracks = 0, tol = 0.0006666138326442492 Iteration 25: loglikelihood = -1304.6739718278136, backtracks = 0, tol = 0.00044240799645619075 Iteration 26: loglikelihood = -1304.673347782746, backtracks = 0, tol = 0.00038110451709064423 Iteration 27: loglikelihood = -1304.672989263916, backtracks = 0, tol = 0.0002513902686924313 Iteration 28: loglikelihood = -1304.6727856878413, backtracks = 0, tol = 0.0002183090448840405 Iteration 29: loglikelihood = -1304.6726685865876, backtracks = 0, tol = 0.00014316801482994442 Iteration 30: loglikelihood = -1304.6726019837758, backtracks = 0, tol = 0.00012529022623278423 Iteration 31: loglikelihood = -1304.6725636233766, backtracks = 0, tol = 8.168052228901659e-5 0.956056 seconds (4.85 M allocations: 86.373 MiB, 6.63% gc time, 47.89% 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 = -1577.638980350186, backtracks = 0, tol = 0.23676456625057019 Iteration 2: loglikelihood = -1512.4148903842174, backtracks = 0, tol = 0.18810645941396376 Iteration 3: loglikelihood = -1476.4170650902204, backtracks = 1, tol = 0.08285419933059818 Iteration 4: loglikelihood = -1462.608038792955, backtracks = 0, tol = 0.15287092610720282 Iteration 5: loglikelihood = -1433.9754758422591, backtracks = 0, tol = 0.11510225251509039 Iteration 6: loglikelihood = -1410.091777755258, backtracks = 0, tol = 0.059543065277151995 Iteration 7: loglikelihood = -1390.587855447727, backtracks = 1, tol = 0.020377415921472138 Iteration 8: loglikelihood = -1374.4211565313365, backtracks = 2, tol = 0.012082181928907225 Iteration 9: loglikelihood = -1367.3403148554603, backtracks = 2, tol = 0.056344653202415246 Iteration 10: loglikelihood = -1358.2050519038924, backtracks = 0, tol = 0.06684349087527632 Iteration 11: loglikelihood = -1354.376382199277, backtracks = 0, tol = 0.07146989688199316 Iteration 12: loglikelihood = -1348.5633953193465, backtracks = 0, tol = 0.06033906269818074 Iteration 13: loglikelihood = -1344.8498481484385, backtracks = 0, tol = 0.008160477600453407 Iteration 14: loglikelihood = -1342.1314280192346, backtracks = 0, tol = 0.0031351636505387837 Iteration 15: loglikelihood = -1339.5699056362591, backtracks = 0, tol = 0.0022599068489614254 Iteration 16: loglikelihood = -1337.3438053051011, backtracks = 0, tol = 0.0010240558824421767 Iteration 17: loglikelihood = -1335.3055206455476, backtracks = 0, tol = 0.0005777970101811842 Iteration 18: loglikelihood = -1333.4666484765548, backtracks = 0, tol = 0.00029229728319496223 Iteration 19: loglikelihood = -1331.8012220510207, backtracks = 0, tol = 0.00017295585240263155 Iteration 20: loglikelihood = -1330.2887638340283, backtracks = 0, tol = 0.00023196538905012536 Iteration 21: loglikelihood = -1330.2720358825204, backtracks = 0, tol = 0.06406521998632538 Iteration 22: loglikelihood = -1327.7083886263244, backtracks = 0, tol = 0.0640667864425867 Iteration 23: loglikelihood = -1326.5579876612155, backtracks = 0, tol = 0.004800416258071449 Iteration 24: loglikelihood = -1325.4691585410367, backtracks = 0, tol = 0.0015507418810009276 Iteration 25: loglikelihood = -1324.5100107895737, backtracks = 0, tol = 0.0009940716234760401 Iteration 26: loglikelihood = -1323.60793810693, backtracks = 0, tol = 0.00024061652956747063 Iteration 27: loglikelihood = -1322.7712058249256, backtracks = 0, tol = 0.00021038497800398274 Iteration 28: loglikelihood = -1321.0870038376295, backtracks = 1, tol = 9.548582165999084e-5 0.247090 seconds (1.18 M allocations: 21.737 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 = -3579.508, backtracks = 0, tol = 0.06773551685099492 Iteration 2: loglikelihood = -3553.3987, backtracks = 0, tol = 0.03528814126953867 Iteration 3: loglikelihood = -3550.4617, backtracks = 1, tol = 0.008690845298857316 Iteration 4: loglikelihood = -3528.8777, backtracks = 1, tol = 0.0582863346545783 Iteration 5: loglikelihood = -3524.1726, backtracks = 1, tol = 0.013544152016705157 Iteration 6: loglikelihood = -3522.6807, backtracks = 1, tol = 0.008252869589713576 Iteration 7: loglikelihood = -3522.2463, backtracks = 1, tol = 0.004146527957261172 Iteration 8: loglikelihood = -3522.1208, backtracks = 1, tol = 0.0019271832074341147 Iteration 9: loglikelihood = -3508.9678, backtracks = 1, tol = 0.061163266909480506 Iteration 10: loglikelihood = -3507.5623, backtracks = 1, tol = 0.007116075328529947 Iteration 11: loglikelihood = -3507.137, backtracks = 1, tol = 0.0041412075593537075 Iteration 12: loglikelihood = -3507.003, backtracks = 1, tol = 0.002091428147750291 Iteration 13: loglikelihood = -3506.9663, backtracks = 1, tol = 0.0010085126503467786 Iteration 14: loglikelihood = -3506.9553, backtracks = 1, tol = 0.0006266595440035097 Iteration 15: loglikelihood = -3506.9543, backtracks = 1, tol = 0.0003391007248875201 Iteration 16: loglikelihood = -3506.9534, backtracks = 1, tol = 0.00017345940636624696 Iteration 17: loglikelihood = -3506.9575, backtracks = 3, tol = 2.1875985544078818e-5 14.726335 seconds (17.16 M allocations: 728.413 MiB, 1.30% gc time, 96.37% 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 = -3492.686, backtracks = 0, tol = 0.06773551685099492 Iteration 2: loglikelihood = -3404.9802, backtracks = 0, tol = 0.03593997926722049 Iteration 3: loglikelihood = -3214.8154, backtracks = 1, tol = 0.008573583544438705 Iteration 4: loglikelihood = -2995.7102, backtracks = 1, tol = 0.005622975881111042 Iteration 5: loglikelihood = -2933.7756, backtracks = 0, tol = 0.08878970409948417 Iteration 6: loglikelihood = -2747.32, backtracks = 0, tol = 0.08810499566784231 Iteration 7: loglikelihood = -2645.1648, backtracks = 0, tol = 0.08041381514087736 Iteration 8: loglikelihood = -2543.692, backtracks = 0, tol = 0.08591144811888388 Iteration 9: loglikelihood = -2465.6353, backtracks = 0, tol = 0.08584415889493763 Iteration 10: loglikelihood = -2380.2317, backtracks = 0, tol = 0.07927339739960097 Iteration 11: loglikelihood = -2331.2874, backtracks = 0, tol = 0.08502276211764521 Iteration 12: loglikelihood = -2276.0164, backtracks = 0, tol = 0.08530352487469033 Iteration 13: loglikelihood = -2254.3284, backtracks = 0, tol = 0.08744786767485992 Iteration 14: loglikelihood = -2224.523, backtracks = 0, tol = 0.0877724226435094 Iteration 15: loglikelihood = -2220.0042, backtracks = 0, tol = 0.08854694092620423 Iteration 16: loglikelihood = -2204.5378, backtracks = 0, tol = 0.08896454975829061 Iteration 17: loglikelihood = -2197.1934, backtracks = 1, tol = 0.009883360540031295 Iteration 18: loglikelihood = -2195.2212, backtracks = 1, tol = 0.005584730605425068 Iteration 19: loglikelihood = -2194.7063, backtracks = 1, tol = 0.003137207053855777 Iteration 20: loglikelihood = -2194.5789, backtracks = 1, tol = 0.001737507967432186 Iteration 21: loglikelihood = -2194.544, backtracks = 1, tol = 0.0009464493944964308 Iteration 22: loglikelihood = -2194.5308, backtracks = 1, tol = 0.0005080319572379144 Iteration 23: loglikelihood = -2194.5283, backtracks = 2, tol = 0.0001350238257356128 Iteration 24: loglikelihood = -2194.5273, backtracks = 1, tol = 0.00020754203356126435 Iteration 25: loglikelihood = -2194.5254, backtracks = 2, tol = 5.433254646011774e-5 0.166116 seconds (1.46 M allocations: 24.232 MiB) Test Summary: | Pass Total Time Negative binomial nuisance parameter Float32 matrix | 12 12 18.4s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** ┌ 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 = 1.0257704354307224 Iteration 2: loglikelihood = -1753.4720992614753, backtracks = 0, tol = 0.2870682551290383 Iteration 3: loglikelihood = -1460.3823326395222, 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 = -1438.074435032946, backtracks = 0, tol = 0.0005882060650840543 Iteration 7: loglikelihood = -1438.0741395461055, backtracks = 0, tol = 8.427264473930937e-5 3.167023 seconds (896.97 k allocations: 128.125 MiB, 0.68% gc time, 91.92% compilation time) Test Summary: | Pass Total Time initialze beta | 1 1 3.4s 6.107948 seconds (4.01 M allocations: 82.752 MiB, 0.74% gc time, 0.94% compilation time) 4.003705 seconds (3.98 M allocations: 91.817 MiB, 0.65% gc time) 10.304256 seconds (20.65 M allocations: 454.914 MiB, 0.74% gc time, 19.33% compilation time: 55% of which was recompilation) 8.226671 seconds (20.19 M allocations: 434.834 MiB, 1.33% gc time) 28.683693 seconds (3.45 M allocations: 4.231 GiB, 8.18% gc time, 28.75% compilation time) 40.202904 seconds (82.96 k allocations: 183.863 MiB) Test Summary: | Pass Total Time memory_efficient keyword | 7 7 1m53.5s Test Summary: | Pass Total Time update_support! | 10 10 0.4s 14.746 ms (89 allocations: 5.20 KiB) 3.771 μs (0 allocations: 0 bytes) 85.729 μs (4 allocations: 288 bytes) 480.562 ns (0 allocations: 0 bytes) 28.410 μs (2 allocations: 64 bytes) 19.900 μs (0 allocations: 0 bytes) 3.596 μs (0 allocations: 0 bytes) 3.584 μs (0 allocations: 0 bytes) 59.760 μs (0 allocations: 0 bytes) 35.032 ms (89 allocations: 5.20 KiB) 15.650 μs (0 allocations: 0 bytes) 133.948 μs (4 allocations: 288 bytes) 2.725 μs (0 allocations: 0 bytes) 136.969 μs (2 allocations: 64 bytes) 42.500 μs (0 allocations: 0 bytes) 24.440 μs (0 allocations: 0 bytes) 24.100 μs (0 allocations: 0 bytes) 120.539 μs (0 allocations: 0 bytes) Test Summary: | Total Time benchmarks for multivariate function | 0 1m51.3s **** 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 **** **** 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 = -2900.918630019449, backtracks = 0, tol = 0.14802242082004138 Iteration 2: loglikelihood = -2869.406464695619, backtracks = 0, tol = 0.03512679046077988 Iteration 3: loglikelihood = -2868.084702693443, backtracks = 0, tol = 0.005569349616332472 Iteration 4: loglikelihood = -2868.034423817725, backtracks = 0, tol = 0.0011189517628951667 Iteration 5: loglikelihood = -2868.0308576353746, backtracks = 0, tol = 0.00031182601179140966 Iteration 6: loglikelihood = -2868.0305288614227, backtracks = 0, tol = 0.00010393305949948345 Iteration 7: loglikelihood = -2868.0304966516946, backtracks = 0, tol = 3.100862049858006e-5 0.415449 seconds (46.02 k allocations: 5.430 MiB, 62.77% compilation time) Test Summary: | Pass Total Time multivariate fit_iht SnpLinAlg | 7 7 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 **** 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 1.489240 seconds (235.74 k allocations: 166.205 MiB, 60.02% compilation time) Test Summary: | Pass Total Time initialze beta | 5 5 1.8s **** 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 **** ┌ 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: 0:02:45 Cross validating... 14%|████▋ | ETA: 0:00:37 Cross validating... 17%|█████▋ | ETA: 0:00:30 Cross validating... 21%|██████▋ | ETA: 0:00:25 Cross validating... 24%|███████▋ | ETA: 0:00:21 Cross validating... 27%|████████▋ | ETA: 0:00:18 Cross validating... 30%|█████████▋ | ETA: 0:00:16 Cross validating... 33%|██████████▋ | ETA: 0:00:14 Cross validating... 37%|███████████▋ | ETA: 0:00:12 Cross validating... 40%|████████████▊ | ETA: 0:00:11 Cross validating... 43%|█████████████▊ | ETA: 0:00:10 Cross validating... 46%|██████████████▊ | ETA: 0:00:09 Cross validating... 49%|███████████████▊ | ETA: 0:00:08 Cross validating... 52%|████████████████▊ | ETA: 0:00:07 Cross validating... 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5457.078174245791 1 3470.6494628084347 2 2345.0659157724313 3 1795.6703986152875 4 1339.7530421800882 5 1112.2132257346104 6 781.3905312843352 7 512.8618445746574 8 439.19629383931516 9 388.4364612886137 10 340.65811650591274 11 343.3590837173504 12 347.303144454817 13 348.8844956334735 14 350.92429081316226 15 352.3194170834364 16 355.205039028665 17 359.0932789637791 18 359.1790974571366 19 363.8699506771447 20 396.762429243711 Best k = 10 10.045156 seconds (11.25 M allocations: 304.726 MiB, 1.16% gc time, 57.29% 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... 10%|███ | ETA: 0:00:03 Cross validating... 13%|████▏ | ETA: 0:00:03 Cross validating... 16%|█████▏ | ETA: 0:00:03 Cross validating... 19%|██████▏ | ETA: 0:00:03 Cross validating... 22%|███████▏ | ETA: 0:00:03 Cross validating... 25%|████████▏ | ETA: 0:00:03 Cross validating... 29%|█████████▏ | ETA: 0:00:03 Cross validating... 32%|██████████▏ | ETA: 0:00:03 Cross validating... 35%|███████████▏ | ETA: 0:00:03 Cross validating... 40%|████████████▊ | ETA: 0:00:03 Cross validating... 43%|█████████████▊ | ETA: 0:00:03 Cross validating... 46%|██████████████▊ | ETA: 0:00:02 Cross validating... 49%|███████████████▊ | ETA: 0:00:02 Cross validating... 52%|████████████████▊ | ETA: 0:00:02 Cross validating... 56%|█████████████████▊ | ETA: 0:00:02 Cross validating... 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... 95%|██████████████████████████████▌ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:04 Crossvalidation Results: k MSE 0 5457.078174245791 1 3474.329260152516 2 2358.623845100152 3 1808.3245070804492 4 1349.6315889339164 5 1118.3031131510693 6 786.0159613848398 7 518.8948090126062 8 444.6349418267953 9 396.02023726777804 10 349.4673876494609 11 355.6036706909059 12 370.08534575867776 13 373.8306762102332 14 374.074573898224 15 381.5047139178023 16 390.29951364113595 17 396.80551982335294 18 402.16928451509773 19 407.8792338377448 20 410.70068468512426 Best k = 10 4.842855 seconds (10.73 M allocations: 225.785 MiB, 2.30% gc time, 1.43% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, normal model | 3 3 15.5s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:04:36 Cross validating... 8%|██▌ | ETA: 0:01:47 Cross validating... 13%|████▏ | ETA: 0:01:04 Cross validating... 17%|█████▋ | ETA: 0:00:45 Cross validating... 21%|██████▋ | ETA: 0:00:37 Cross validating... 25%|████████▏ | ETA: 0:00:28 Cross validating... 29%|█████████▏ | ETA: 0:00:25 Cross validating... 32%|██████████▏ | ETA: 0:00:21 Cross validating... 37%|███████████▋ | ETA: 0:00:17 Cross validating... 41%|█████████████▎ | ETA: 0:00:15 Cross validating... 43%|█████████████▊ | ETA: 0:00:14 Cross validating... 48%|███████████████▎ | ETA: 0:00:11 Cross validating... 52%|████████████████▊ | ETA: 0:00:10 Cross validating... 57%|██████████████████▎ | ETA: 0:00:08 Cross validating... 60%|███████████████████▎ | ETA: 0:00:07 Cross validating... 63%|████████████████████▍ | ETA: 0:00:06 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:06 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:04 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: 0:00:01 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:01 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:12 Crossvalidation Results: k MSE 0 1737.5192940673828 1 1389.3400091552735 2 1159.8234946289062 3 871.193081604004 4 693.8547092895508 5 568.4866885986328 6 485.12064877319335 7 418.3615153808594 8 389.5727936706543 9 362.86755703735355 10 366.0834526672363 11 368.20186389160153 12 367.87247491455076 13 369.8876986083984 14 380.5658739013672 15 374.71095278930665 16 381.68543630981446 17 375.4939732055664 18 391.40845391845704 19 375.61922775268556 20 379.52256307983396 Best k = 9 13.299764 seconds (12.26 M allocations: 318.888 MiB, 1.10% gc time, 76.78% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 5%|█▌ | ETA: 0:00:02 Cross validating... 10%|███ | ETA: 0:00:02 Cross validating... 14%|████▋ | ETA: 0:00:02 Cross validating... 19%|██████▏ | ETA: 0:00:02 Cross validating... 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90%|█████████████████████████████ | ETA: 0:00:00 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:03 Crossvalidation Results: k MSE 0 1737.5192940673828 1 1389.3400091552735 2 1164.0430511474608 3 877.2232872924806 4 700.2760359497071 5 581.6288023681641 6 496.26624124145513 7 427.9456856689453 8 393.49537893676757 9 372.302532043457 10 380.50259619140627 11 386.4164265136719 12 387.73028723144535 13 395.5814549255371 14 406.604217956543 15 413.95987353515625 16 412.71489782714843 17 425.00932791137694 18 419.4981799316406 19 421.3277059631348 20 427.0461432495117 Best k = 9 3.275156 seconds (10.34 M allocations: 189.934 MiB, 2.83% gc time, 1.34% compilation time) Test Summary: | Pass Total Time Cross validation on Float32 matrix, normal model | 2 2 18.1s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:42 Cross validating... 6%|██ | ETA: 0:00:22 Cross validating... 10%|███ | ETA: 0:00:16 Cross validating... 13%|████▏ | ETA: 0:00:13 Cross validating... 16%|█████▏ | ETA: 0:00:11 Cross validating... 17%|█████▋ | ETA: 0:00:10 Cross validating... 21%|██████▋ | ETA: 0:00:09 Cross validating... 24%|███████▋ | ETA: 0:00:08 Cross validating... 27%|████████▋ | ETA: 0:00:07 Cross validating... 30%|█████████▋ | ETA: 0:00:07 Cross validating... 33%|██████████▋ | ETA: 0:00:06 Cross validating... 37%|███████████▋ | ETA: 0:00:06 Cross validating... 40%|████████████▊ | ETA: 0:00:05 Cross validating... 43%|█████████████▊ | ETA: 0:00:05 Cross validating... 46%|██████████████▊ | ETA: 0:00:04 Cross validating... 49%|███████████████▊ | ETA: 0:00:04 Cross validating... 52%|████████████████▊ 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Crossvalidation Results: k MSE 0 462.5430150988632 1 381.95734533411974 2 325.6943373020925 3 290.1366792604207 4 272.60795716309894 5 256.76680346238817 6 241.71607511480926 7 210.32630231288076 8 214.70051257230918 9 220.0425163457629 10 210.3149965472877 11 231.24746681398076 12 213.2466107040927 13 223.63020504535606 14 236.35274256905643 15 229.66597207413704 16 228.57423438774808 17 229.72026604026325 18 241.3593153651529 19 226.5387779401014 20 254.91056484179603 Best k = 10 7.208943 seconds (17.23 M allocations: 400.770 MiB, 1.53% gc time, 25.85% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:04 Cross validating... 6%|██ | ETA: 0:00:04 Cross validating... 10%|███ | ETA: 0:00:04 Cross validating... 13%|████▏ | ETA: 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validating... 73%|███████████████████████▍ | ETA: 0:00:01 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:01 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:01 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:01 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:01 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:01 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:00 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:05 Crossvalidation Results: k MSE 0 462.5430150988632 1 382.91965407303377 2 329.1235199420471 3 292.6949596282816 4 282.2273720770726 5 259.7151712821766 6 246.8506373002186 7 218.17973225957377 8 225.82560529525995 9 217.91177607055806 10 227.5607482472987 11 232.4151323097584 12 224.5048566646289 13 234.86677857578135 14 241.05912847214557 15 245.31411967247374 16 244.86775168662012 17 252.79148432438978 18 247.51280462582446 19 261.5955041369858 20 257.4481556428159 Best k = 9 5.626469 seconds (17.87 M allocations: 373.853 MiB, 1.77% gc time, 1.39% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, logistic model | 2 2 13.1s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:35 Cross validating... 6%|██ | ETA: 0:00:19 Cross validating... 10%|███ | ETA: 0:00:14 Cross validating... 13%|████▏ | ETA: 0:00:11 Cross validating... 16%|█████▏ | ETA: 0:00:10 Cross validating... 19%|██████▏ | ETA: 0:00:09 Cross validating... 22%|███████▏ | ETA: 0:00:08 Cross validating... 25%|████████▏ | ETA: 0:00:07 Cross validating... 29%|█████████▏ | ETA: 0:00:06 Cross validating... 30%|█████████▋ | ETA: 0:00:06 Cross validating... 33%|██████████▋ | ETA: 0:00:06 Cross validating... 37%|███████████▋ | ETA: 0:00:05 Cross validating... 40%|████████████▊ | ETA: 0:00:05 Cross validating... 43%|█████████████▊ | ETA: 0:00:04 Cross validating... 46%|██████████████▊ | ETA: 0:00:04 Cross validating... 49%|███████████████▊ | ETA: 0:00:04 Cross validating... 52%|████████████████▊ | ETA: 0:00:03 Cross validating... 56%|█████████████████▊ | ETA: 0:00:03 Cross validating... 59%|██████████████████▊ | ETA: 0:00:03 Cross validating... 60%|███████████████████▎ | 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... 75%|███████████████████████▉ | 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: 0:00:01 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:06 Crossvalidation Results: k MSE 0 464.84977819295966 1 445.9213651947231 2 426.2646739931099 3 395.4700192305886 4 366.4816383167976 5 340.0940402613557 6 338.45388187979626 7 332.38143445194714 8 332.4029775235699 9 331.8148170232447 10 334.3051825842649 11 331.9490789032187 12 339.87256399057617 13 339.18391859112285 14 340.48092754017813 15 344.1432966335866 16 359.0329884526698 17 341.43592806799836 18 341.19881173406407 19 351.6810819892449 20 374.8423987335816 Best k = 9 7.724551 seconds (16.90 M allocations: 410.224 MiB, 1.22% gc time, 29.32% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:04 Cross validating... 6%|██ | ETA: 0:00:05 Cross validating... 8%|██▌ | ETA: 0:00:05 Cross validating... 11%|███▌ | ETA: 0:00:05 Cross validating... 14%|████▋ | ETA: 0:00:05 Cross validating... 17%|█████▋ | ETA: 0:00:05 Cross validating... 21%|██████▋ | ETA: 0:00:05 Cross validating... 24%|███████▋ | ETA: 0:00:04 Cross validating... 27%|████████▋ | ETA: 0:00:04 Cross validating... 30%|█████████▋ | ETA: 0:00:04 Cross validating... 33%|██████████▋ | ETA: 0:00:04 Cross validating... 37%|███████████▋ | ETA: 0:00:04 Cross validating... 40%|████████████▊ | ETA: 0:00:03 Cross validating... 43%|█████████████▊ | ETA: 0:00:03 Cross validating... 46%|██████████████▊ | ETA: 0:00:03 Cross validating... 49%|███████████████▊ | ETA: 0:00:03 Cross validating... 52%|████████████████▊ | ETA: 0:00:03 Cross validating... 56%|█████████████████▊ | ETA: 0:00:03 Cross validating... 59%|██████████████████▊ | ETA: 0:00:02 Cross validating... 62%|███████████████████▊ | ETA: 0:00:02 Cross validating... 65%|████████████████████▉ | ETA: 0:00:02 Cross validating... 68%|█████████████████████▉ | ETA: 0:00:02 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:02 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:01 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:01 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:01 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:01 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:01 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:01 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:05 Crossvalidation Results: k MSE 0 464.84977819295966 1 447.27930774888364 2 428.49396966577945 3 397.95699000395194 4 370.351227053537 5 345.44479823955845 6 346.8384888252089 7 349.4056186564959 8 343.7845259606279 9 348.90638495840955 10 351.8772635699997 11 352.17709483955264 12 354.5832332312189 13 371.0046475201865 14 373.84644216690594 15 389.57543231976217 16 394.3870951673096 17 396.0695180355411 18 402.21726660437565 19 402.8981575166705 20 416.6396650038097 Best k = 8 5.724593 seconds (17.13 M allocations: 352.113 MiB, 1.17% gc time, 0.84% compilation time) Test Summary: | Pass Total Time Cross validation on Float64 matrix, logistic model | 2 2 14.4s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:41 Cross validating... 6%|██ | ETA: 0:00:23 Cross validating... 10%|███ | ETA: 0:00:16 Cross validating... 13%|████▏ | ETA: 0:00:13 Cross validating... 16%|█████▏ | ETA: 0:00:11 Cross validating... 19%|██████▏ | ETA: 0:00:09 Cross validating... 21%|██████▋ | ETA: 0:00:09 Cross validating... 24%|███████▋ | ETA: 0:00:08 Cross validating... 27%|████████▋ | ETA: 0:00:07 Cross validating... 30%|█████████▋ | ETA: 0:00:06 Cross validating... 33%|██████████▋ | ETA: 0:00:06 Cross validating... 37%|███████████▋ | ETA: 0:00:05 Cross validating... 40%|████████████▊ | ETA: 0:00:05 Cross validating... 43%|█████████████▊ | ETA: 0:00:05 Cross validating... 46%|██████████████▊ | ETA: 0:00:04 Cross validating... 49%|███████████████▊ | 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... 75%|███████████████████████▉ | ETA: 0:00:02 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:02 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:01 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:01 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:01 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:01 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:06 Crossvalidation Results: k MSE 0 1244.5129346454723 1 1019.7815380677387 2 723.1093407084676 3 582.2761184008285 4 508.9065587705795 5 425.0176310599612 6 408.7485511095859 7 388.16610548190397 8 386.9205930773935 9 385.6431813572439 10 377.96935817914175 11 381.7590857707151 12 390.00417178397583 13 393.85386668534136 14 392.71589689513036 15 402.2964690019008 16 398.4455569483141 17 392.46766381259494 18 388.4629812911845 19 399.9408806941632 20 393.4054103781681 Best k = 10 7.180191 seconds (15.82 M allocations: 371.693 MiB, 1.09% gc time, 25.91% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:04 Cross validating... 6%|██ | ETA: 0:00:04 Cross validating... 10%|███ | ETA: 0:00:04 Cross validating... 13%|████▏ | ETA: 0:00:04 Cross validating... 16%|█████▏ | ETA: 0:00:04 Cross validating... 19%|██████▏ | ETA: 0:00:04 Cross validating... 22%|███████▏ | ETA: 0:00:04 Cross validating... 25%|████████▏ | ETA: 0:00:04 Cross validating... 29%|█████████▏ | ETA: 0:00:04 Cross validating... 32%|██████████▏ | ETA: 0:00:03 Cross validating... 35%|███████████▏ | ETA: 0:00:03 Cross validating... 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: 0:00:02 Cross validating... 56%|█████████████████▊ | ETA: 0:00:02 Cross validating... 59%|██████████████████▊ | ETA: 0:00:02 Cross validating... 62%|███████████████████▊ | ETA: 0:00:02 Cross validating... 65%|████████████████████▉ | ETA: 0:00:02 Cross validating... 68%|█████████████████████▉ | 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: 0:00:05 Crossvalidation Results: k MSE 0 1244.5129346454723 1 950.5755657420813 2 705.7744055531869 3 573.0414212035643 4 503.5543081287498 5 422.7144324720497 6 398.2953994012388 7 364.33529118327635 8 390.9509085013995 9 395.76333194647646 10 369.0324481271349 11 384.68882291880163 12 397.44284865874755 13 408.4108315168796 14 408.76113066572395 15 413.59621986078685 16 406.0365989839456 17 424.71892103498556 18 442.03447316332176 19 437.71776745391355 20 445.84515894632506 Best k = 7 5.079555 seconds (14.41 M allocations: 290.949 MiB, 1.35% gc time, 0.58% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, Poisson model | 2 2 12.6s **** 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: 0:01:05 Cross validating... 5%|█▌ | ETA: 0:01:03 Cross validating... 6%|██ | ETA: 0:00:48 Cross validating... 10%|███ | ETA: 0:00:33 Cross validating... 13%|████▏ | ETA: 0:00:32 Cross validating... 14%|████▋ | ETA: 0:00:34 Cross validating... 16%|█████▏ | ETA: 0:00:35 Cross validating... 17%|█████▋ | ETA: 0:00:35 Cross validating... 19%|██████▏ | ETA: 0:00:36 Cross validating... 21%|██████▋ | ETA: 0:00:33 Cross validating... 22%|███████▏ | ETA: 0:00:31 Cross validating... 24%|███████▋ | ETA: 0:00:31 Cross validating... 25%|████████▏ | ETA: 0:00:29 Cross validating... 27%|████████▋ | ETA: 0:00:30 Cross validating... 29%|█████████▏ | ETA: 0:00:28 Cross validating... 30%|█████████▋ | ETA: 0:00:28 Cross validating... 32%|██████████▏ | ETA: 0:00:28 Cross validating... 33%|██████████▋ | ETA: 0:00:26 Cross validating... 38%|████████████▎ | ETA: 0:00:23 Cross validating... 40%|████████████▊ | ETA: 0:00:23 Cross validating... 41%|█████████████▎ | ETA: 0:00:22 Cross validating... 43%|█████████████▊ | ETA: 0:00:22 Cross validating... 44%|██████████████▎ | ETA: 0:00:22 Cross validating... 46%|██████████████▊ | ETA: 0:00:21 Cross validating... 48%|███████████████▎ | ETA: 0:00:21 Cross validating... 49%|███████████████▊ | ETA: 0:00:21 Cross validating... 51%|████████████████▎ | ETA: 0:00:21 Cross validating... 52%|████████████████▊ | ETA: 0:00:21 Cross validating... 54%|█████████████████▎ | ETA: 0:00:19 Cross validating... 56%|█████████████████▊ | ETA: 0:00:18 Cross validating... 57%|██████████████████▎ | ETA: 0:00:17 Cross validating... 59%|██████████████████▊ | ETA: 0:00:16 Cross validating... 60%|███████████████████▎ | ETA: 0:00:15 Cross validating... 62%|███████████████████▊ | ETA: 0:00:15 Cross validating... 63%|████████████████████▍ | ETA: 0:00:14 Cross validating... 65%|████████████████████▉ | ETA: 0:00:13 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:13 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:11 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:10 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:09 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:09 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:08 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:08 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:07 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:07 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:06 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:06 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:05 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:05 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:04 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:03 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:03 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:02 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:01 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:01 Cross validating... 100%|████████████████████████████████| Time: 0:00:41 Crossvalidation Results: k MSE 0 449.14535476299557 1 350.2538088325411 2 287.17329151967937 3 269.99263015833765 4 247.63374988522352 5 234.750004552439 6 209.83486116681289 7 202.87004373743508 8 201.22691656223117 9 202.9419525983858 10 204.32526988733906 11 203.20110065992998 12 201.78821212577407 13 207.91374623041654 14 209.5985182417263 15 208.7729796615447 16 211.08716378339813 17 214.57610447720432 18 211.9882507441022 19 210.39563293948464 20 214.19459322421858 Best k = 8 41.750936 seconds (143.09 M allocations: 3.600 GiB, 3.19% gc time, 3.28% 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... 3%|█ | ETA: 0:00:05 Cross validating... 5%|█▌ | ETA: 0:00:05 Cross validating... 6%|██ | ETA: 0:00:07 Cross validating... 8%|██▌ | ETA: 0:00:07 Cross validating... 10%|███ | ETA: 0:00:07 Cross validating... 11%|███▌ | ETA: 0:00:07 Cross validating... 13%|████▏ | ETA: 0:00:07 Cross validating... 14%|████▋ | ETA: 0:00:07 Cross validating... 16%|█████▏ | ETA: 0:00:07 Cross validating... 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ETA: 0:00:05 Cross validating... 54%|█████████████████▎ | ETA: 0:00:05 Cross validating... 56%|█████████████████▊ | ETA: 0:00:05 Cross validating... 57%|██████████████████▎ | ETA: 0:00:05 Cross validating... 59%|██████████████████▊ | ETA: 0:00:04 Cross validating... 60%|███████████████████▎ | ETA: 0:00:04 Cross validating... 62%|███████████████████▊ | ETA: 0:00:04 Cross validating... 63%|████████████████████▍ | ETA: 0:00:04 Cross validating... 65%|████████████████████▉ | ETA: 0:00:04 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:04 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:03 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:03 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:03 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:03 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:02 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:02 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:02 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:02 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:02 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:02 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:01 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:01 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:01 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:01 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:01 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:01 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:11 Crossvalidation Results: k MSE 0 449.14535476299557 1 345.98905347179044 2 286.69325365888335 3 270.93385194962366 4 248.25230684634644 5 236.2062369962901 6 213.26342089346943 7 206.35709497667992 8 206.6862332994903 9 212.42194052892592 10 215.14693425519636 11 220.08593024371788 12 220.51517433193806 13 225.90371234697017 14 236.47844155044274 15 233.52504110104087 16 231.60844543290028 17 246.38333568950316 18 240.38266429330304 19 245.9114105811033 20 251.83985505467916 Best k = 7 11.147163 seconds (36.10 M allocations: 742.426 MiB, 1.52% gc time, 0.67% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, NegativeBinomial model | 2 2 53.2s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:47 Cross validating... 6%|██ | ETA: 0:00:24 Cross validating... 10%|███ | ETA: 0:00:17 Cross validating... 14%|████▋ | ETA: 0:00:11 Cross validating... 19%|██████▏ | ETA: 0:00:09 Cross 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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 0 708.7406597900391 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 5.364676 seconds (17.23 M allocations: 344.117 MiB, 2.58% gc time, 38.75% 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 **** Cross validating... 5%|█▌ | ETA: 0:00:02 Cross validating... 10%|███ | ETA: 0:00:03 Cross validating... 14%|████▋ | ETA: 0:00:03 Cross validating... 19%|██████▏ | ETA: 0:00:02 Cross validating... 24%|███████▋ | ETA: 0:00:02 Cross validating... 27%|████████▋ | ETA: 0:00:02 Cross validating... 30%|█████████▋ | ETA: 0:00:02 Cross validating... 35%|███████████▏ | ETA: 0:00:02 Cross validating... 40%|████████████▊ | ETA: 0:00:02 Cross validating... 43%|█████████████▊ | ETA: 0:00:02 Cross validating... 48%|███████████████▎ | ETA: 0:00:02 Cross validating... 52%|████████████████▊ | ETA: 0:00:01 Cross validating... 56%|█████████████████▊ | ETA: 0:00:01 Cross validating... 59%|██████████████████▊ | ETA: 0:00:01 Cross validating... 62%|███████████████████▊ | ETA: 0:00:01 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:01 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:01 Cross 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288.801 MiB, 1.80% gc time, 1.31% compilation time) Test Summary: | Pass Total Time Cross validation on floating point matrices, NegativeBinomial model | 2 2 9.0s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 2%|▋ | ETA: 0:01:08 Cross validating... 3%|█ | ETA: 0:00:50 Cross validating... 4%|█▎ | ETA: 0:00:41 Cross validating... 5%|█▋ | ETA: 0:00:36 Cross validating... 6%|█▉ | ETA: 0:00:32 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: 0:00:25 Cross validating... 11%|███▌ | ETA: 0:00:24 Cross validating... 12%|███▉ | ETA: 0:00:23 Cross validating... 13%|████▏ | ETA: 0:00:22 Cross validating... 14%|████▌ | ETA: 0:00:21 Cross validating... 15%|████▊ | 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100%|████████████████████████████████| Time: 0:00:18 Crossvalidation Results: k MSE 1 3177.6855104304154 2 2661.9630966507775 3 2595.265787841986 4 2400.729116236827 5 2337.9855912415715 6 2296.6992352106395 7 2257.363696046194 8 2277.9894847834153 9 2295.729889021155 10 2300.4822976825317 11 2334.20640246499 12 2326.9328085137945 13 2342.9987487403464 14 2359.462913234066 15 2350.8319323416817 16 2413.58205445909 17 2407.708821159972 18 2417.763202338011 19 2429.7375140367467 20 2423.359965850035 Best k = 7 18.799374 seconds (350.18 k allocations: 248.714 MiB, 0.44% gc time, 6.87% compilation time) Test Summary: | Pass Total Time multivariate cross validation SnpLinAlg | 3 3 23.1s Test Summary: | Pass Total Time wrapper univariate | 20 20 1m32.7s **** 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... 2%|▋ | ETA: 0:00:09 Cross validating... 3%|█ | ETA: 0:00:09 Cross validating... 4%|█▎ | ETA: 0:00:10 Cross validating... 5%|█▋ | ETA: 0:00:10 Cross validating... 6%|█▉ | ETA: 0:00:11 Cross validating... 7%|██▎ | ETA: 0:00:12 Cross validating... 8%|██▌ | ETA: 0:00:12 Cross validating... 9%|██▉ | ETA: 0:00:13 Cross validating... 10%|███▎ | ETA: 0:00:14 Cross validating... 11%|███▌ | ETA: 0:00:14 Cross validating... 12%|███▉ | ETA: 0:00:15 Cross validating... 13%|████▏ | ETA: 0:00:16 Cross validating... 14%|████▌ | ETA: 0:00:16 Cross validating... 15%|████▊ | ETA: 0:00:16 Cross validating... 16%|█████▏ | ETA: 0:00:17 Cross validating... 17%|█████▌ | ETA: 0:00:18 Cross validating... 18%|█████▊ | ETA: 0:00:18 Cross validating... 19%|██████▏ | ETA: 0:00:18 Cross validating... 20%|██████▍ | ETA: 0:00:18 Cross validating... 21%|██████▊ | ETA: 0:00:17 Cross validating... 22%|███████ | ETA: 0:00:17 Cross validating... 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60%|███████████████████▎ | ETA: 0:00:09 Cross validating... 61%|███████████████████▌ | ETA: 0:00:09 Cross validating... 62%|███████████████████▉ | ETA: 0:00:08 Cross validating... 63%|████████████████████▏ | ETA: 0:00:08 Cross validating... 64%|████████████████████▌ | ETA: 0:00:08 Cross validating... 65%|████████████████████▊ | ETA: 0:00:08 Cross validating... 66%|█████████████████████▏ | ETA: 0:00:07 Cross validating... 67%|█████████████████████▌ | ETA: 0:00:07 Cross validating... 68%|█████████████████████▊ | ETA: 0:00:07 Cross validating... 69%|██████████████████████▏ | ETA: 0:00:07 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:07 Cross validating... 71%|██████████████████████▊ | ETA: 0:00:06 Cross validating... 72%|███████████████████████ | ETA: 0:00:06 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:06 Cross validating... 74%|███████████████████████▋ | ETA: 0:00:06 Cross validating... 75%|████████████████████████ | ETA: 0:00:05 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: 0:00:04 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:04 Cross validating... 82%|██████████████████████████▎ | ETA: 0:00:04 Cross validating... 83%|██████████████████████████▌ | ETA: 0:00:04 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:04 Cross validating... 85%|███████████████████████████▎ | ETA: 0:00:03 Cross validating... 86%|███████████████████████████▌ | ETA: 0:00:03 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:03 Cross validating... 88%|████████████████████████████▏ | ETA: 0:00:03 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:02 Cross validating... 90%|████████████████████████████▊ | ETA: 0:00:02 Cross validating... 91%|█████████████████████████████▏ | ETA: 0:00:02 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:02 Cross validating... 93%|█████████████████████████████▊ | ETA: 0:00:02 Cross validating... 94%|██████████████████████████████▏ | ETA: 0:00:01 Cross validating... 95%|██████████████████████████████▍ | ETA: 0:00:01 Cross validating... 96%|██████████████████████████████▊ | ETA: 0:00:01 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:01 Cross validating... 98%|███████████████████████████████▍| ETA: 0:00:00 Cross validating... 99%|███████████████████████████████▋| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:22 Crossvalidation Results: k MSE 1 2838.788679198002 2 2514.397342870813 3 2305.6176519676274 4 2222.025304867614 5 2075.167038458837 6 2067.794898972384 7 2053.427506114907 8 2086.405384830965 9 2080.984460901671 10 2105.1311995023634 11 2132.407165368786 12 2138.267187460652 13 2166.002210829576 14 2194.9918295115804 15 2189.890403738045 16 2191.1812932295775 17 2209.4669750564367 18 2221.2595493644303 19 2238.742594576326 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: 0:00:15 Cross validating... 14%|████▌ | ETA: 0:00:16 Cross validating... 15%|████▊ | 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0:00:06 Cross validating... 71%|██████████████████████▊ | ETA: 0:00:06 Cross validating... 72%|███████████████████████ | ETA: 0:00:06 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:06 Cross validating... 74%|███████████████████████▋ | ETA: 0:00:06 Cross validating... 75%|████████████████████████ | ETA: 0:00:05 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:05 Cross validating... 77%|████████████████████████▋ | ETA: 0:00:05 Cross validating... 78%|█████████████████████████ | ETA: 0:00:05 Cross validating... 79%|█████████████████████████▎ | ETA: 0:00:05 Cross validating... 80%|█████████████████████████▋ | ETA: 0:00:04 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:04 Cross validating... 82%|██████████████████████████▎ | ETA: 0:00:04 Cross validating... 83%|██████████████████████████▌ | ETA: 0:00:04 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:03 Cross validating... 85%|███████████████████████████▎ | ETA: 0:00:03 Cross validating... 86%|███████████████████████████▌ | ETA: 0:00:03 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:03 Cross validating... 88%|████████████████████████████▏ | ETA: 0:00:03 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:02 Cross validating... 90%|████████████████████████████▊ | ETA: 0:00:02 Cross validating... 91%|█████████████████████████████▏ | ETA: 0:00:02 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:02 Cross validating... 93%|█████████████████████████████▊ | ETA: 0:00:02 Cross validating... 94%|██████████████████████████████▏ | ETA: 0:00:01 Cross validating... 95%|██████████████████████████████▍ | ETA: 0:00:01 Cross validating... 96%|██████████████████████████████▊ | ETA: 0:00:01 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:01 Cross validating... 98%|███████████████████████████████▍| ETA: 0:00:00 Cross validating... 99%|███████████████████████████████▋| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:22 Crossvalidation Results: k MSE 1 2838.788679198002 2 2514.397342870813 3 2305.6176519676274 4 2222.025304867614 5 2075.167038458837 6 2067.794898972384 7 2053.427506114907 8 2086.405384830965 9 2080.984460901671 10 2105.1311995023634 11 2132.407165368786 12 2138.267187460652 13 2166.002210829576 14 2194.9918295115804 15 2189.890403738045 16 2191.1812932295775 17 2209.4669750564367 18 2221.2595493644303 19 2238.742594576326 20 2253.9559571797727 Best k = 7 **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 2%|▋ | ETA: 0:00:10 Cross validating... 3%|█ | ETA: 0:00:10 Cross validating... 4%|█▎ | ETA: 0:00:11 Cross validating... 5%|█▋ | ETA: 0:00:10 Cross validating... 6%|█▉ | ETA: 0:00:12 Cross validating... 7%|██▎ | 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validating... 66%|█████████████████████▏ | ETA: 0:00:07 Cross validating... 67%|█████████████████████▌ | ETA: 0:00:07 Cross validating... 68%|█████████████████████▊ | ETA: 0:00:07 Cross validating... 69%|██████████████████████▏ | ETA: 0:00:07 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:06 Cross validating... 71%|██████████████████████▊ | ETA: 0:00:06 Cross validating... 72%|███████████████████████ | ETA: 0:00:06 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:06 Cross validating... 74%|███████████████████████▋ | ETA: 0:00:06 Cross validating... 75%|████████████████████████ | ETA: 0:00:05 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:05 Cross validating... 77%|████████████████████████▋ | ETA: 0:00:05 Cross validating... 78%|█████████████████████████ | ETA: 0:00:05 Cross validating... 79%|█████████████████████████▎ | ETA: 0:00:05 Cross validating... 80%|█████████████████████████▋ | ETA: 0:00:04 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:04 Cross validating... 82%|██████████████████████████▎ | ETA: 0:00:04 Cross validating... 83%|██████████████████████████▌ | ETA: 0:00:04 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:03 Cross validating... 85%|███████████████████████████▎ | ETA: 0:00:03 Cross validating... 86%|███████████████████████████▌ | ETA: 0:00:03 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:03 Cross validating... 88%|████████████████████████████▏ | ETA: 0:00:03 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:02 Cross validating... 90%|████████████████████████████▊ | ETA: 0:00:02 Cross validating... 91%|█████████████████████████████▏ | ETA: 0:00:02 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:02 Cross validating... 93%|█████████████████████████████▊ | ETA: 0:00:02 Cross validating... 94%|██████████████████████████████▏ | ETA: 0:00:01 Cross validating... 95%|██████████████████████████████▍ | ETA: 0:00:01 Cross validating... 96%|██████████████████████████████▊ | ETA: 0:00:01 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:01 Cross validating... 98%|███████████████████████████████▍| ETA: 0:00:00 Cross validating... 99%|███████████████████████████████▋| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:22 Crossvalidation Results: k MSE 1 2838.788679198002 2 2514.397342870813 3 2305.6176519676274 4 2222.025304867614 5 2075.167038458837 6 2067.794898972384 7 2053.427506114907 8 2086.405384830965 9 2080.984460901671 10 2105.1311995023634 11 2132.407165368786 12 2138.267187460652 13 2166.002210829576 14 2194.9918295115804 15 2189.890403738045 16 2191.1812932295775 17 2209.4669750564367 18 2221.2595493644303 19 2238.742594576326 20 2253.9559571797727 Best k = 7 Test Summary: | Pass Total Time wrapper multivariate | 8 8 1m21.1s 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/BjTS1/src/decompression.jl:199 [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:2247 [inlined] [9] top-level scope @ ~/.julia/packages/MendelIHT/ZcxZT/test/wrapper_test.jl:185 Test Summary: | Error Total Time read BGEN and VCF | 1 1 3.1s RNG of the outermost testset: Xoshiro(0x2b2a619002f713b1, 0x35d8c57351e7cfc3, 0x0308cc1042c2be3f, 0x83c68ff8509287be, 0x764e9e057a7df067) 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 958.58s 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:3298 [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 in expression starting at /PkgEval.jl/scripts/evaluate.jl:214 PkgEval failed after 1069.08s: package tests unexpectedly errored