Package evaluation to test MendelIHT on Julia 1.14.0-DEV.3071 (c76331c927*) started at 2026-08-31T01:06:45.156 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.14` Set-up completed after 14.8s ################################################################################ # 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 v7.30.0 [67c07d97] + Automa v1.2.0 ⌅ [6db4b851] + BGEN v0.1.17 [28d598bf] + BGZFStreams v0.3.2 [47718e42] + BioGenerics v0.1.5 [62783981] + BitTwiddlingConvenienceFunctions v0.1.6 [e1450e63] + BufferedStreams v1.2.2 [2a0fbf3d] + CPUSummary v0.2.7 [336ed68f] + CSV v0.10.17 [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 v1.2.0 [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 v10.47.0+0 [bea87d4a] + SuiteSparse_jll v7.10.1+0 [83775a58] + Zlib_jll v1.3.2+0 [3161d3a3] + Zstd_jll v1.5.7+1 [8e850b90] + libblastrampoline_jll v5.15.0+0 [8e850ede] + nghttp2_jll v1.70.0+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 To see why use `status --outdated -m` Installation completed after 4.92s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompiling project... 4.7 s ✓ BGEN 7.7 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`. 24.3 s ✓ MendelIHT 3 dependencies successfully precompiled in 39 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 64.91s ################################################################################ # Testing # Testing MendelIHT Status `/tmp/jl_WGHwK2/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 12.5s 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 7.6s 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 = -1677.7143346023133, backtracks = 0, tol = 2.018497561514066 Iteration 2: loglikelihood = -1429.885260236055, backtracks = 0, tol = 0.13846913826829876 Iteration 3: loglikelihood = -1404.0538394555115, backtracks = 0, tol = 0.048802189298038846 Iteration 4: loglikelihood = -1403.8998447811027, backtracks = 0, tol = 0.0028874941760517045 Iteration 5: loglikelihood = -1403.8986263562201, backtracks = 1, tol = 0.00017924727402804857 Iteration 6: loglikelihood = -1403.8983056233196, backtracks = 1, tol = 8.957810840264639e-5 IHT estimated 10 nonzero SNP predictors and 1 non-genetic predictors. Compute time (sec): 0.05173206329345703 Final loglikelihood: -1403.8983056233196 SNP PVE: 0.9203961019721367 Iterations: 6 Selected genetic predictors: 10×2 DataFrame Row │ Position Estimated_β │ Int64 Float64 ─────┼─────────────────────── 1 │ 989 1.93142 2 │ 3694 2.27969 3 │ 5124 -0.123112 4 │ 6673 0.113775 5 │ 7950 0.352463 6 │ 8120 -0.468828 7 │ 8168 -0.833653 8 │ 9370 0.710532 9 │ 9385 -0.605437 10 │ 9995 0.23143 Selected nongenetic predictors: 1×2 DataFrame Row │ Position Estimated_β │ Int64 Float64 ─────┼─────────────────────── 1 │ 1 -0.015791Test Summary: | Pass Total Time fit normal SnpLinAlg | 4 4 22.5s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse logistic regression Number of threads = 1 Link functin = LogitLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -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 3.1s **** 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 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 = -1908.7904671836159, backtracks = 0, tol = 0.39604752654255154 Iteration 2: loglikelihood = -1460.284518461925, backtracks = 0, tol = 0.06008987610887883 Iteration 3: loglikelihood = -1383.2481328380727, backtracks = 0, tol = 0.05722248427147627 Iteration 4: loglikelihood = -1341.9760189780782, backtracks = 0, tol = 0.15546020638475774 Iteration 5: loglikelihood = -1306.5493064535922, backtracks = 0, tol = 0.09019040413184957 Iteration 6: loglikelihood = -1298.4266850224324, backtracks = 0, tol = 0.061635720399542196 Iteration 7: loglikelihood = -1295.2472434034817, backtracks = 0, tol = 0.014931410638413623 Iteration 8: loglikelihood = -1292.116665715338, backtracks = 0, tol = 0.05610363314407874 Iteration 9: loglikelihood = -1291.2323464223307, backtracks = 0, tol = 0.01192343739225276 Iteration 10: loglikelihood = -1290.922169412343, backtracks = 0, tol = 0.005505902309675441 Iteration 11: loglikelihood = -1290.7597734415806, backtracks = 0, tol = 0.007087385683438791 Iteration 12: loglikelihood = -1290.66866509408, backtracks = 0, tol = 0.0028508437854916145 Iteration 13: loglikelihood = -1290.6167278737023, backtracks = 0, tol = 0.004041855756106123 Iteration 14: loglikelihood = -1290.5864028301658, backtracks = 0, tol = 0.0016292325126097138 Iteration 15: loglikelihood = -1290.5686797377502, backtracks = 0, tol = 0.0023456903957828215 Iteration 16: loglikelihood = -1290.5581992054251, backtracks = 0, tol = 0.0009549317762052312 Iteration 17: loglikelihood = -1290.5520058749041, backtracks = 0, tol = 0.0013788093387440805 Iteration 18: loglikelihood = -1290.5483228093783, backtracks = 0, tol = 0.0005659871095005718 Iteration 19: loglikelihood = -1290.546134200045, backtracks = 0, tol = 0.0008165581637273447 Iteration 20: loglikelihood = -1290.544829013699, backtracks = 0, tol = 0.00033783694841359033 Iteration 21: loglikelihood = -1290.5440510868075, backtracks = 0, tol = 0.00048568252126302334 Iteration 22: loglikelihood = -1290.5435864662145, backtracks = 0, tol = 0.00020186241899995783 Iteration 23: loglikelihood = -1290.5433090687297, backtracks = 0, tol = 0.0002896116233066274 Iteration 24: loglikelihood = -1290.543143251091, backtracks = 0, tol = 0.0001206906640420652 Iteration 25: loglikelihood = -1290.5430441538329, backtracks = 0, tol = 0.0001729516820004577 Iteration 26: loglikelihood = -1290.5429848882331, backtracks = 0, tol = 7.218665608169439e-5 Test Summary: | Pass Total Time fit Poisson SnpLinAlg | 4 4 2.6s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse NegativeBinomial regression Number of threads = 1 Link functin = LogLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1591.9271428460454, backtracks = 0, tol = 0.3834233916003413 Iteration 2: loglikelihood = -1521.038785527169, backtracks = 0, tol = 0.1674582314078805 Iteration 3: loglikelihood = -1490.5193826991826, backtracks = 0, tol = 0.09282978721638116 Iteration 4: loglikelihood = -1485.2811031168026, backtracks = 0, tol = 0.09988755923279481 Iteration 5: loglikelihood = -1480.537446285171, backtracks = 0, tol = 0.0765979851789199 Iteration 6: loglikelihood = -1479.999294466316, backtracks = 1, tol = 0.014380348972788887 Iteration 7: loglikelihood = -1479.8332114747, backtracks = 1, tol = 0.007650487593244974 Iteration 8: loglikelihood = -1479.781551066552, backtracks = 1, tol = 0.0037921620123402898 Iteration 9: loglikelihood = -1478.7683218614604, backtracks = 1, tol = 0.05984015346535933 Iteration 10: loglikelihood = -1478.6896912375646, backtracks = 0, tol = 0.07565906489234497 Iteration 11: loglikelihood = -1478.5925179207388, backtracks = 0, tol = 0.006119449646652971 Iteration 12: loglikelihood = -1478.591657325766, backtracks = 1, tol = 0.00047868472985349714 Iteration 13: loglikelihood = -1478.5913607472262, backtracks = 1, tol = 0.000263022271969337 Iteration 14: loglikelihood = -1478.5912610753696, backtracks = 1, tol = 0.00013616778544668553 Iteration 15: loglikelihood = -1478.5912291024845, backtracks = 1, tol = 7.585965572491892e-5 Test Summary: | Pass Total Time fit NegativeBinomial SnpLinAlg | 4 4 1.1s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse linear regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1814.8192646122516, backtracks = 0, tol = 0.7763199567671034 Iteration 2: loglikelihood = -1443.1414076875906, backtracks = 0, tol = 0.1080742725288692 Iteration 3: loglikelihood = -1399.9297616882552, backtracks = 0, tol = 0.039570636523437265 Iteration 4: loglikelihood = -1398.8607493277905, backtracks = 0, tol = 0.005263248688541866 Iteration 5: loglikelihood = -1398.8508842292176, backtracks = 0, tol = 0.0007046758566736572 Iteration 6: loglikelihood = -1398.8507718157005, backtracks = 0, tol = 5.179378546655164e-5 Test Summary: | Pass Total Time fit with >1 non-genetic covariates SnpLinAlg | 5 5 1.4s **** 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 **** 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 = -1463.3612005518753, backtracks = 0, tol = 0.25082805481481896 Iteration 2: loglikelihood = -1405.939260527421, backtracks = 0, tol = 0.06546054872847301 Iteration 3: loglikelihood = -1399.2127031510265, backtracks = 0, tol = 0.03412934289908886 Iteration 4: loglikelihood = -1399.059555406593, backtracks = 1, tol = 0.0015799383359872017 Iteration 5: loglikelihood = -1399.0203495840133, backtracks = 1, tol = 0.0007913265143844264 Iteration 6: loglikelihood = -1399.010342770494, backtracks = 1, tol = 0.00039322278976916227 Iteration 7: loglikelihood = -1399.0077973154046, backtracks = 1, tol = 0.00019415247908522498 Iteration 8: loglikelihood = -1399.0071520090187, backtracks = 1, tol = 9.543948461513756e-5 Test Summary: | Pass Total Time model selection on non-genetic covariates | 5 5 0.6s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse linear regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 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 7.6s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse NegativeBinomial regression Number of threads = 1 Link functin = LogLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1729.774044085064, backtracks = 0, tol = 0.20624654787576255 Iteration 2: loglikelihood = -1625.1046395319102, backtracks = 0, tol = 0.10224711023192383 Iteration 3: loglikelihood = -1531.8617716467943, backtracks = 0, tol = 0.17371692054612978 Iteration 4: loglikelihood = -1492.8139362620898, backtracks = 0, tol = 0.12404358814918764 Iteration 5: loglikelihood = -1479.4907006206377, backtracks = 0, tol = 0.05209172543617479 Iteration 6: loglikelihood = -1471.3311320300077, backtracks = 0, tol = 0.05678897284753298 Iteration 7: loglikelihood = -1466.0973179397995, backtracks = 0, tol = 0.027201672349771566 Iteration 8: loglikelihood = -1453.1281978882882, backtracks = 0, tol = 0.07396529747154937 Iteration 9: loglikelihood = -1449.593967931279, backtracks = 0, tol = 0.022821032440499628 Iteration 10: loglikelihood = -1448.1354187391787, backtracks = 0, tol = 0.017373122814756687 Iteration 11: loglikelihood = -1447.265257460677, backtracks = 0, tol = 0.012136133874391915 Iteration 12: loglikelihood = -1446.6963268880456, backtracks = 0, tol = 0.01226489795187078 Iteration 13: loglikelihood = -1446.3151068190143, backtracks = 0, tol = 0.008073761271072274 Iteration 14: loglikelihood = -1446.0556447804377, backtracks = 0, tol = 0.008484339631446665 Iteration 15: loglikelihood = -1445.8787521527233, backtracks = 0, tol = 0.0055544792893927825 Iteration 16: loglikelihood = -1441.4134882714334, backtracks = 0, tol = 0.04656327954113831 Iteration 17: loglikelihood = -1438.7177543632827, backtracks = 0, tol = 0.026138504411053216 Iteration 18: loglikelihood = -1438.2119149231514, backtracks = 0, tol = 0.008524511175450975 Iteration 19: loglikelihood = -1438.0502027624896, backtracks = 0, tol = 0.005317728907821664 Iteration 20: loglikelihood = -1437.9840431259931, backtracks = 0, tol = 0.00387243806626043 Iteration 21: loglikelihood = -1437.9510733647437, backtracks = 0, tol = 0.0021091603748454374 Iteration 22: loglikelihood = -1437.9341723007244, backtracks = 0, tol = 0.0020210032046677107 Iteration 23: loglikelihood = -1437.925164602916, backtracks = 0, tol = 0.001088780235589177 Iteration 24: loglikelihood = -1437.9203646343888, backtracks = 0, tol = 0.0010782736335297762 Iteration 25: loglikelihood = -1437.9177506664005, backtracks = 0, tol = 0.0005790613554815249 Iteration 26: loglikelihood = -1437.916328950698, backtracks = 0, tol = 0.0005843651767489389 Iteration 27: loglikelihood = -1437.9155414556858, backtracks = 0, tol = 0.00033123819907005653 Iteration 28: loglikelihood = -1437.9151052491789, backtracks = 0, tol = 0.0003211829490815359 Iteration 29: loglikelihood = -1437.91486001121, backtracks = 0, tol = 0.00019051753787048103 Iteration 30: loglikelihood = -1437.9147219553183, backtracks = 0, tol = 0.00017871266035334398 Iteration 31: loglikelihood = -1437.9146433663966, backtracks = 0, tol = 0.000110121383911176 Iteration 32: loglikelihood = -1437.9145985191242, backtracks = 0, tol = 0.00010046757835922234 Iteration 33: loglikelihood = -1437.9145727370683, backtracks = 0, tol = 6.389206325132223e-5 1.048334 seconds (2.92 M allocations: 56.244 MiB, 4.40% gc time, 53.23% 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 = -1738.3234096550457, backtracks = 0, tol = 0.20624654787576255 Iteration 2: loglikelihood = -1674.6435378338679, backtracks = 0, tol = 0.10848658549930172 Iteration 3: loglikelihood = -1599.9856314957153, backtracks = 0, tol = 0.19726250641023235 Iteration 4: loglikelihood = -1573.7079177234448, backtracks = 0, tol = 0.11986602030234905 Iteration 5: loglikelihood = -1548.7712346431717, backtracks = 0, tol = 0.08768525081655788 Iteration 6: loglikelihood = -1533.6404637521207, backtracks = 0, tol = 0.05476935444276092 Iteration 7: loglikelihood = -1521.0194573361698, backtracks = 0, tol = 0.030570133026894358 Iteration 8: loglikelihood = -1512.2637131749177, backtracks = 0, tol = 0.03018216095660325 Iteration 9: loglikelihood = -1504.1115243752415, backtracks = 0, tol = 0.016812283479390556 Iteration 10: loglikelihood = -1494.4850788251356, backtracks = 0, tol = 0.06665800687295774 Iteration 11: loglikelihood = -1487.951792728785, backtracks = 0, tol = 0.04130308493159544 Iteration 12: loglikelihood = -1482.9324417138077, backtracks = 0, tol = 0.010960640966137409 Iteration 13: loglikelihood = -1478.9756451079577, backtracks = 0, tol = 0.004538492753018212 Iteration 14: loglikelihood = -1475.2970779032191, backtracks = 0, tol = 0.0033212217162540436 Iteration 15: loglikelihood = -1472.1942206164374, backtracks = 0, tol = 0.0021078288898771567 Iteration 16: loglikelihood = -1469.3770318595957, backtracks = 0, tol = 0.001293077977576519 Iteration 17: loglikelihood = -1466.9357841168267, backtracks = 0, tol = 0.0009778194708159973 Iteration 18: loglikelihood = -1463.9477606953592, backtracks = 0, tol = 0.06312929809653016 Iteration 19: loglikelihood = -1460.5474697991303, backtracks = 0, tol = 0.03414980336237759 Iteration 20: loglikelihood = -1458.732924902716, backtracks = 0, tol = 0.0031376233832399215 Iteration 21: loglikelihood = -1457.173322441227, backtracks = 0, tol = 0.0011618893425311698 Iteration 22: loglikelihood = -1455.7116939093817, backtracks = 0, tol = 0.0009257201753848318 Iteration 23: loglikelihood = -1454.3999635880891, backtracks = 0, tol = 0.00040786971244722057 Iteration 24: loglikelihood = -1453.1883542761816, backtracks = 0, tol = 0.0002964020964117083 Iteration 25: loglikelihood = -1452.08600981801, backtracks = 0, tol = 0.00023190928680184237 Iteration 26: loglikelihood = -1451.0701250106538, backtracks = 0, tol = 0.00019784137985912991 Iteration 27: loglikelihood = -1450.1391024699935, backtracks = 0, tol = 0.00020078618194754584 Iteration 28: loglikelihood = -1449.2792154510425, backtracks = 0, tol = 0.00018905048894776876 Iteration 29: loglikelihood = -1448.486961802357, backtracks = 0, tol = 0.00018459158254197758 Iteration 30: loglikelihood = -1447.7527840857763, backtracks = 0, tol = 0.00017345432707191886 Iteration 31: loglikelihood = -1447.0733190001797, backtracks = 0, tol = 0.00016811669838556344 Iteration 32: loglikelihood = -1446.4414599309412, backtracks = 0, tol = 0.00015843825577119383 Iteration 33: loglikelihood = -1446.3758867548213, backtracks = 0, tol = 0.05775474081815951 Iteration 34: loglikelihood = -1445.540576719136, backtracks = 0, tol = 0.06063346477617954 Iteration 35: loglikelihood = -1444.844111052823, backtracks = 0, tol = 0.004260601635921153 Iteration 36: loglikelihood = -1444.3523427053774, backtracks = 0, tol = 0.001323795432528918 Iteration 37: loglikelihood = -1443.8838842620673, backtracks = 0, tol = 0.0004518776403747456 Iteration 38: loglikelihood = -1443.4632534434545, backtracks = 0, tol = 0.0005118788225603428 Iteration 39: loglikelihood = -1443.0617222645135, backtracks = 0, tol = 0.0002262867415459436 Iteration 40: loglikelihood = -1442.3436919431667, backtracks = 1, tol = 0.00014172028576304335 Iteration 41: loglikelihood = -1441.7062436350066, backtracks = 1, tol = 0.00015766567591199212 Iteration 42: loglikelihood = -1441.1343797990621, backtracks = 1, tol = 0.00017781156932448973 Iteration 43: loglikelihood = -1440.6220427185765, backtracks = 1, tol = 0.00018509822211718683 Iteration 44: loglikelihood = -1440.1621930768285, backtracks = 1, tol = 0.000184218299577635 Iteration 45: loglikelihood = -1439.7500013364013, backtracks = 1, tol = 0.00017888134417042782 Iteration 46: loglikelihood = -1439.3782316154523, backtracks = 1, tol = 0.00017111503773175287 Iteration 47: loglikelihood = -1439.041977101571, backtracks = 1, tol = 0.0001638085005648343 Iteration 48: loglikelihood = -1438.7370223471612, backtracks = 1, tol = 0.00015619066505214593 Iteration 49: loglikelihood = -1438.459742022543, backtracks = 1, tol = 0.00014865633530715844 Iteration 50: loglikelihood = -1438.2264810964707, backtracks = 1, tol = 0.00014144449992402103 Iteration 51: loglikelihood = -1438.0151759315065, backtracks = 1, tol = 0.00013055476704657037 Iteration 52: loglikelihood = -1437.8224501365576, backtracks = 1, tol = 0.00012091392145931632 Iteration 53: loglikelihood = -1437.645738524625, backtracks = 1, tol = 0.00011283356482641215 Iteration 54: loglikelihood = -1437.4830120890604, backtracks = 1, tol = 0.00010609074301499737 Iteration 55: loglikelihood = -1437.3326631156358, backtracks = 1, tol = 0.00010042476745128094 Iteration 56: loglikelihood = -1437.1933990559207, backtracks = 1, tol = 9.558244352426942e-5 0.592793 seconds (2.53 M allocations: 45.603 MiB, 5.47% gc time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse NegativeBinomial regression Number of threads = 1 Link functin = LogLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -3806.8926, backtracks = 0, tol = 0.0766555191906392 Iteration 2: loglikelihood = -3779.251, backtracks = 0, tol = 0.040632175255773215 Iteration 3: loglikelihood = -3776.2136, backtracks = 1, tol = 0.006920521392204418 Iteration 4: loglikelihood = -3775.2104, backtracks = 1, tol = 0.006182032068740111 Iteration 5: loglikelihood = -3774.9426, backtracks = 1, tol = 0.003193119366099431 Iteration 6: loglikelihood = -3774.875, backtracks = 1, tol = 0.0016513614735635554 Iteration 7: loglikelihood = -3774.8616, backtracks = 1, tol = 0.0008366853525327381 Iteration 8: loglikelihood = -3774.8562, backtracks = 1, tol = 0.000423289313916967 Iteration 9: loglikelihood = -3774.855, backtracks = 1, tol = 0.00021312445639495544 Iteration 10: loglikelihood = -3774.8599, backtracks = 3, tol = 2.6793305053650518e-5 19.209689 seconds (13.85 M allocations: 677.839 MiB, 1.67% gc time, 97.26% 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 = -3698.9294, backtracks = 0, tol = 0.0766555191906392 Iteration 2: loglikelihood = -3595.6726, backtracks = 0, tol = 0.04160189144975188 Iteration 3: loglikelihood = -3378.8672, backtracks = 1, tol = 0.006849453873893229 Iteration 4: loglikelihood = -3115.8896, backtracks = 1, tol = 0.005582344484242521 Iteration 5: loglikelihood = -3010.9814, backtracks = 0, tol = 0.08608680131656975 Iteration 6: loglikelihood = -2866.3083, backtracks = 0, tol = 0.0818005369942359 Iteration 7: loglikelihood = -2709.981, backtracks = 0, tol = 0.08028806703505062 Iteration 8: loglikelihood = -2594.8945, backtracks = 0, tol = 0.08112763198112005 Iteration 9: loglikelihood = -2495.5254, backtracks = 0, tol = 0.08207129799458175 Iteration 10: loglikelihood = -2420.6536, backtracks = 0, tol = 0.09065155471128311 Iteration 11: loglikelihood = -2358.9404, backtracks = 0, tol = 0.09042335949590197 Iteration 12: loglikelihood = -2319.7979, backtracks = 0, tol = 0.10120957602365717 Iteration 13: loglikelihood = -2285.519, backtracks = 0, tol = 0.10020839714921685 Iteration 14: loglikelihood = -2268.381, backtracks = 0, tol = 0.09317698029051923 Iteration 15: loglikelihood = -2256.6484, backtracks = 0, tol = 0.09298362703955734 Iteration 16: loglikelihood = -2251.1633, backtracks = 0, tol = 0.014758242448631208 Iteration 17: loglikelihood = -2248.6387, backtracks = 0, tol = 0.003480064501127744 Iteration 18: loglikelihood = -2247.328, backtracks = 0, tol = 0.0008217014903563149 Iteration 19: loglikelihood = -2246.2644, backtracks = 1, tol = 0.00011685289674230195 Iteration 20: loglikelihood = -2246.1223, backtracks = 0, tol = 0.00032731269812539746 Iteration 21: loglikelihood = -2246.0027, backtracks = 1, tol = 5.03234955594901e-5 0.145289 seconds (1.08 M allocations: 17.967 MiB) Test Summary: | Pass Total Time Negative binomial nuisance parameter Float32 matrix | 12 12 23.5s **** 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 **** ┌ 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 4.426588 seconds (956.64 k allocations: 129.035 MiB, 1.75% gc time, 90.87% compilation time) Test Summary: | Pass Total Time initialze beta | 1 1 4.8s 7.132885 seconds (4.01 M allocations: 82.752 MiB, 0.43% gc time, 1.11% compilation time) 4.171309 seconds (3.98 M allocations: 91.817 MiB, 1.91% gc time) 10.586411 seconds (20.65 M allocations: 454.876 MiB, 6.12% gc time, 17.96% compilation time: 51% of which was recompilation) 7.723019 seconds (20.19 M allocations: 434.834 MiB, 1.17% gc time) 28.554136 seconds (3.45 M allocations: 4.232 GiB, 6.88% gc time, 26.93% compilation time) 41.219823 seconds (84.77 k allocations: 183.946 MiB, 0.21% gc time) Test Summary: | Pass Total Time memory_efficient keyword | 7 7 1m55.6s Test Summary: | Pass Total Time update_support! | 10 10 0.4s 14.862 ms (89 allocations: 5.20 KiB) 4.310 μs (0 allocations: 0 bytes) 91.939 μs (4 allocations: 288 bytes) 523.626 ns (0 allocations: 0 bytes) 34.050 μs (2 allocations: 64 bytes) 20.339 μs (0 allocations: 0 bytes) 4.579 μs (0 allocations: 0 bytes) 3.704 μs (0 allocations: 0 bytes) 65.409 μs (0 allocations: 0 bytes) 33.858 ms (89 allocations: 5.20 KiB) 18.500 μs (0 allocations: 0 bytes) 111.769 μs (4 allocations: 288 bytes) 2.660 μs (0 allocations: 0 bytes) 122.419 μs (2 allocations: 64 bytes) 41.470 μs (0 allocations: 0 bytes) 23.780 μs (0 allocations: 0 bytes) 24.520 μs (0 allocations: 0 bytes) 147.798 μs (0 allocations: 0 bytes) Test Summary: | Total Time benchmarks for multivariate function | 0 1m51.1s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse Multivariate Gaussian regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 12 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -2900.918630019449, 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 0.403626 seconds (46.08 k allocations: 5.433 MiB, 62.41% compilation time) Test Summary: | Pass Total Time multivariate fit_iht SnpLinAlg | 7 7 9.7s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse 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 1.504013 seconds (235.79 k allocations: 166.147 MiB, 55.28% compilation time) Test Summary: | Pass Total Time initialze beta | 5 5 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 **** ┌ 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: 0:02:42 Cross validating... 14%|████▋ | ETA: 0:00:36 Cross validating... 17%|█████▋ | ETA: 0:00:29 Cross validating... 21%|██████▋ | ETA: 0:00:24 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... 56%|█████████████████▊ | ETA: 0:00:06 Cross validating... 59%|██████████████████▊ | ETA: 0:00:06 Cross validating... 62%|███████████████████▊ | ETA: 0:00:05 Cross validating... 65%|████████████████████▉ | ETA: 0:00:04 Cross validating... 68%|█████████████████████▉ | ETA: 0:00:04 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:04 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:03 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:03 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:02 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:02 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:01 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: 0:00:10 Crossvalidation Results: k MSE 0 4096.198971817863 1 2248.069349404819 2 978.8961395776029 3 739.7466773946925 4 584.1646378402075 5 474.9028936456954 6 397.906983266024 7 355.8176711704938 8 336.0291316258557 9 340.32285235340737 10 342.05956636943563 11 348.20148910438036 12 348.0251227399522 13 349.1811116143889 14 355.0548409310293 15 376.53077611127065 16 357.0643748128558 17 386.63686480173067 18 363.84915175522633 19 368.5865016932561 20 372.91475206683515 Best k = 8 10.159668 seconds (11.62 M allocations: 312.014 MiB, 1.66% gc time, 55.39% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 5%|█▌ | ETA: 0:00:04 Cross validating... 8%|██▌ | ETA: 0:00:03 Cross validating... 11%|███▌ | ETA: 0:00:03 Cross validating... 14%|████▋ | ETA: 0:00:03 Cross validating... 17%|█████▋ | ETA: 0:00:03 Cross validating... 21%|██████▋ | ETA: 0:00:03 Cross validating... 24%|███████▋ | ETA: 0:00:03 Cross validating... 27%|████████▋ | ETA: 0:00:03 Cross validating... 30%|█████████▋ | ETA: 0:00:03 Cross validating... 33%|██████████▋ | ETA: 0:00:03 Cross validating... 38%|████████████▎ | ETA: 0:00:03 Cross validating... 41%|█████████████▎ | ETA: 0:00:03 Cross validating... 44%|██████████████▎ | ETA: 0:00:02 Cross validating... 48%|███████████████▎ | ETA: 0:00:02 Cross validating... 51%|████████████████▎ | ETA: 0:00:02 Cross validating... 54%|█████████████████▎ | ETA: 0:00:02 Cross validating... 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: 0:00:01 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:01 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:01 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:01 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:01 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:01 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:01 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:00 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:04 Crossvalidation Results: k MSE 0 4096.198971817863 1 2255.8525484859656 2 980.3370349959023 3 745.1333421963486 4 590.8501508332678 5 484.515193010953 6 405.87203076998094 7 361.2804236221531 8 343.1677661172097 9 353.26079642225676 10 362.34009857564695 11 376.7678326272868 12 376.81000185237394 13 382.4252359419546 14 396.3212801448375 15 391.6464493617176 16 409.02624034611955 17 409.9114599662681 18 433.8905620480719 19 413.18885435050106 20 409.2629880774458 Best k = 8 4.682319 seconds (10.46 M allocations: 219.746 MiB, 1.31% gc time, 0.95% 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: 0:04:43 Cross validating... 8%|██▌ | ETA: 0:01:49 Cross validating... 14%|████▋ | ETA: 0:00:57 Cross validating... 17%|█████▋ | ETA: 0:00:45 Cross validating... 22%|███████▏ | ETA: 0:00:34 Cross validating... 27%|████████▋ | ETA: 0:00:27 Cross validating... 32%|██████████▏ | ETA: 0:00:22 Cross validating... 37%|███████████▋ | ETA: 0:00:18 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... 62%|███████████████████▊ | ETA: 0:00:07 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:05 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:04 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:03 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:02 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:02 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:01 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:11 Crossvalidation Results: k MSE 0 1519.7457419433595 1 1209.9372127685547 2 976.311528564453 3 800.2070340576172 4 642.731263671875 5 527.1324346313477 6 447.8128699645996 7 420.13293734741205 8 365.53379785156244 9 364.27128192138673 10 367.63670391845704 11 370.496095703125 12 375.58921279907224 13 380.2947402648926 14 375.4775405578613 15 386.12777651977535 16 400.73007138061524 17 383.4809407043457 18 407.4930953063965 19 423.55860974121094 20 397.3136956176758 Best k = 9 13.072408 seconds (12.74 M allocations: 328.040 MiB, 1.24% gc time, 79.66% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 6%|██ | ETA: 0:00:02 Cross validating... 11%|███▌ | ETA: 0:00:02 Cross validating... 16%|█████▏ | ETA: 0:00:02 Cross validating... 21%|██████▋ | ETA: 0:00:02 Cross validating... 24%|███████▋ | ETA: 0:00:02 Cross validating... 29%|█████████▏ | ETA: 0:00:02 Cross validating... 33%|██████████▋ | ETA: 0:00:02 Cross validating... 40%|████████████▊ | ETA: 0:00:02 Cross validating... 46%|██████████████▊ | ETA: 0:00:01 Cross validating... 52%|████████████████▊ | ETA: 0:00:01 Cross validating... 57%|██████████████████▎ | ETA: 0:00:01 Cross validating... 60%|███████████████████▎ | ETA: 0:00:01 Cross validating... 65%|████████████████████▉ | ETA: 0:00:01 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:01 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:01 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:00 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:00 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:00 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:02 Crossvalidation Results: k MSE 0 1519.7457419433595 1 1210.0102601318358 2 976.311528564453 3 802.7500639648438 4 643.6320291137695 5 529.4801156616211 6 450.505522064209 7 424.1191551513672 8 371.8088298339843 9 373.1507911987305 10 382.7615528869629 11 391.13102920532225 12 404.9111556396484 13 404.9790015869141 14 410.7600235900879 15 412.3039179382324 16 434.0408796691895 17 430.5802153930664 18 427.6822685546875 19 435.8282141418457 20 437.81005865478517 Best k = 8 2.635196 seconds (10.82 M allocations: 199.330 MiB, 2.48% gc time, 1.73% compilation time) Test Summary: | Pass Total Time Cross validation on Float32 matrix, normal model | 2 2 17.1s **** 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: 0:00:40 Cross validating... 6%|██ | ETA: 0:00:21 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 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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... 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 0 465.5619531123536 1 362.55694019953853 2 286.2330037888587 3 272.80477033907033 4 247.58902834920616 5 242.80750593525778 6 235.01794040334977 7 236.54576530661757 8 246.6144691597371 9 245.3254037318315 10 254.19008264343654 11 251.709701245102 12 261.4378315681838 13 260.45129983381435 14 270.34644739704686 15 265.0863256309516 16 267.82155829101237 17 263.3160864118139 18 256.86360194245 19 253.48508816824926 20 290.52799778224 Best k = 6 7.127169 seconds (16.94 M allocations: 395.370 MiB, 1.82% gc time, 25.04% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:04 Cross validating... 6%|██ | ETA: 0:00:05 Cross validating... 10%|███ | ETA: 0:00:05 Cross validating... 13%|████▏ | ETA: 0:00:05 Cross validating... 16%|█████▏ | ETA: 0:00:05 Cross validating... 19%|██████▏ | ETA: 0:00:04 Cross validating... 22%|███████▏ | ETA: 0:00:04 Cross validating... 25%|████████▏ | ETA: 0:00:04 Cross validating... 29%|█████████▏ | ETA: 0:00:04 Cross validating... 30%|█████████▋ | ETA: 0:00:04 Cross validating... 32%|██████████▏ | ETA: 0:00:04 Cross validating... 35%|███████████▏ | ETA: 0:00:04 Cross validating... 38%|████████████▎ | 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validating... 90%|█████████████████████████████ | ETA: 0:00:01 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:00 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:05 Crossvalidation Results: k MSE 0 465.5619531123536 1 364.9034293680959 2 289.44092077251617 3 276.8224077222196 4 252.1062970898485 5 248.31821642597168 6 242.37227653668674 7 250.1431035000122 8 251.75379521624188 9 256.6410649494497 10 272.12553297177527 11 259.54195624007104 12 279.7059233128371 13 283.6775535805997 14 303.6837503978 15 302.8515186534489 16 300.6435559867957 17 293.0701965127199 18 292.881885283663 19 315.41109626067595 20 326.71896730014714 Best k = 6 5.664645 seconds (17.60 M allocations: 364.126 MiB, 2.10% gc time, 1.31% 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: 0:00:41 Cross validating... 6%|██ | ETA: 0:00:23 Cross validating... 10%|███ | ETA: 0:00:16 Cross validating... 11%|███▌ | ETA: 0:00:15 Cross validating... 14%|████▋ | ETA: 0:00:12 Cross validating... 16%|█████▏ | ETA: 0:00:11 Cross validating... 19%|██████▏ | ETA: 0:00:10 Cross validating... 21%|██████▋ | ETA: 0:00:09 Cross validating... 22%|███████▏ | ETA: 0:00:09 Cross validating... 24%|███████▋ | ETA: 0:00:09 Cross validating... 25%|████████▏ | ETA: 0:00:08 Cross validating... 29%|█████████▏ | ETA: 0:00:07 Cross validating... 30%|█████████▋ | ETA: 0:00:07 Cross validating... 32%|██████████▏ | ETA: 0:00:07 Cross validating... 33%|██████████▋ | ETA: 0:00:07 Cross validating... 37%|███████████▋ | 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ETA: 0:00:02 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:02 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:01 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:01 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:01 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:01 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:01 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:07 Crossvalidation Results: k MSE 0 463.16696787141166 1 429.16367609925044 2 398.1329042335092 3 393.599825047168 4 374.36037376746276 5 362.2523905773855 6 356.9428750669565 7 348.5237773827541 8 335.66977713502706 9 345.10410878368924 10 342.6868224820404 11 352.17253342127447 12 345.8234757046232 13 357.01114414953463 14 359.1967290554586 15 350.28809933297816 16 379.33332041297774 17 374.3206197965492 18 403.89009132748487 19 355.92944512820736 20 366.2744434641457 Best k = 8 8.400177 seconds (17.04 M allocations: 408.031 MiB, 1.15% gc time, 28.03% 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... 6%|██ | ETA: 0:00:06 Cross validating... 8%|██▌ | ETA: 0:00:06 Cross validating... 11%|███▌ | ETA: 0:00:06 Cross validating... 13%|████▏ | ETA: 0:00:06 Cross validating... 16%|█████▏ | ETA: 0:00:05 Cross validating... 17%|█████▋ | ETA: 0:00:05 Cross validating... 21%|██████▋ | ETA: 0:00:05 Cross validating... 22%|███████▏ | ETA: 0:00:05 Cross validating... 25%|████████▏ | ETA: 0:00:05 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0:00:02 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:02 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:02 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:01 Cross validating... 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... 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... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:06 Crossvalidation Results: k MSE 0 463.16696787141166 1 429.1944932967341 2 399.32270930145205 3 396.8213862553995 4 378.1563241130367 5 367.12759237536125 6 365.2153774731596 7 358.6306375991044 8 348.4469057145065 9 356.51848936612384 10 365.61600707437344 11 376.8443436370362 12 384.9822518312035 13 387.6271639932977 14 396.55667261802597 15 410.14003889973617 16 419.04002046926234 17 424.70796197311927 18 433.46789131691344 19 442.25532753075345 20 454.2955619169657 Best k = 8 6.299278 seconds (17.27 M allocations: 354.814 MiB, 1.82% gc time, 0.73% compilation time) Test Summary: | Pass Total Time Cross validation on Float64 matrix, logistic model | 2 2 15.3s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:42 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... 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: 0:00:05 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 0 940.4371556446781 1 734.9587783863608 2 455.4256375460574 3 400.2784847856316 4 366.1215483521213 5 358.3874294418547 6 351.3000352728361 7 357.1470680263126 8 360.7906354011627 9 360.4949472767442 10 368.14016288026505 11 367.2307722860803 12 364.37069286223505 13 356.81263248147536 14 367.293691960959 15 370.7686700513502 16 378.78001875453464 17 361.07154386253455 18 373.31477523344273 19 383.9059761274266 20 424.180126541612 Best k = 6 7.217702 seconds (15.37 M allocations: 356.917 MiB, 1.60% gc time, 26.34% 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... 38%|████████████▎ | ETA: 0:00:03 Cross validating... 41%|█████████████▎ | ETA: 0:00:03 Cross validating... 44%|██████████████▎ | ETA: 0:00:03 Cross validating... 48%|███████████████▎ | ETA: 0:00:03 Cross validating... 51%|████████████████▎ | ETA: 0:00:02 Cross validating... 54%|█████████████████▎ | ETA: 0:00:02 Cross validating... 57%|██████████████████▎ | ETA: 0:00:02 Cross validating... 60%|███████████████████▎ | ETA: 0:00:02 Cross validating... 63%|████████████████████▍ | ETA: 0:00:02 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:02 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:02 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:01 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:01 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:01 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:01 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:01 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:01 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:00 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:05 Crossvalidation Results: k MSE 0 940.4371556446781 1 714.8572388262822 2 459.32681300685437 3 413.1025462930962 4 377.84129650658895 5 362.3997348355315 6 360.0749811327377 7 368.6211560915425 8 372.4490628856766 9 363.36800059840084 10 376.00862576622717 11 386.2738977193521 12 393.7052764171639 13 375.89398433013446 14 398.0080022192522 15 397.2491370664116 16 405.3657867987108 17 401.94558348854866 18 410.68450010344554 19 416.0698051469983 20 424.180126541612 Best k = 6 5.108195 seconds (14.24 M allocations: 286.622 MiB, 1.10% gc time, 0.50% 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: 0:01:07 Cross validating... 6%|██ | ETA: 0:00:47 Cross validating... 10%|███ | ETA: 0:00:40 Cross validating... 11%|███▌ | ETA: 0:00:35 Cross validating... 14%|████▋ | ETA: 0:00:32 Cross validating... 16%|█████▏ | ETA: 0:00:29 Cross validating... 17%|█████▋ | ETA: 0:00:26 Cross validating... 19%|██████▏ | ETA: 0:00:24 Cross validating... 22%|███████▏ | ETA: 0:00:21 Cross validating... 24%|███████▋ | ETA: 0:00:19 Cross validating... 25%|████████▏ | ETA: 0:00:18 Cross validating... 27%|████████▋ | ETA: 0:00:17 Cross validating... 29%|█████████▏ | ETA: 0:00:16 Cross validating... 30%|█████████▋ | ETA: 0:00:16 Cross validating... 32%|██████████▏ | ETA: 0:00:17 Cross validating... 33%|██████████▋ | ETA: 0:00:16 Cross validating... 37%|███████████▋ | ETA: 0:00:16 Cross validating... 38%|████████████▎ | ETA: 0:00:16 Cross validating... 41%|█████████████▎ | ETA: 0:00:14 Cross validating... 44%|██████████████▎ | ETA: 0:00:13 Cross validating... 46%|██████████████▊ | ETA: 0:00:13 Cross validating... 48%|███████████████▎ | ETA: 0:00:13 Cross validating... 49%|███████████████▊ | ETA: 0:00:14 Cross validating... 51%|████████████████▎ | ETA: 0:00:14 Cross validating... 52%|████████████████▊ | ETA: 0:00:14 Cross validating... 54%|█████████████████▎ | ETA: 0:00:14 Cross validating... 57%|██████████████████▎ | ETA: 0:00:13 Cross validating... 59%|██████████████████▊ | ETA: 0:00:13 Cross validating... 60%|███████████████████▎ | ETA: 0:00:13 Cross validating... 62%|███████████████████▊ | ETA: 0:00:12 Cross validating... 63%|████████████████████▍ | ETA: 0:00:12 Cross validating... 65%|████████████████████▉ | ETA: 0:00:11 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:11 Cross validating... 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validating... 98%|███████████████████████████████▌| ETA: 0:00:01 Cross validating... 100%|████████████████████████████████| Time: 0:00:33 Crossvalidation Results: k MSE 0 407.76275575318533 1 325.9683388431331 2 242.1663448810763 3 231.32127238322477 4 216.6290946859839 5 216.77873350806658 6 216.35218243733416 7 217.18929227482664 8 216.0749667260115 9 217.47544683632728 10 217.59364900520404 11 219.25462103446563 12 217.14073372244744 13 219.14929058477713 14 220.8431087765179 15 219.3157796202105 16 219.67105683505787 17 223.83886007448783 18 220.37000022829494 19 221.00131425551274 20 223.56187529984675 Best k = 8 33.945963 seconds (113.57 M allocations: 2.850 GiB, 1.46% gc time, 4.27% 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... 6%|██ | ETA: 0:00:06 Cross validating... 8%|██▌ | ETA: 0:00:06 Cross validating... 10%|███ | ETA: 0:00:06 Cross validating... 11%|███▌ | ETA: 0:00:06 Cross validating... 13%|████▏ | ETA: 0:00:06 Cross validating... 14%|████▋ | ETA: 0:00:06 Cross validating... 16%|█████▏ | ETA: 0:00:07 Cross validating... 17%|█████▋ | ETA: 0:00:07 Cross validating... 19%|██████▏ | ETA: 0:00:07 Cross validating... 21%|██████▋ | ETA: 0:00:08 Cross validating... 22%|███████▏ | ETA: 0:00:08 Cross validating... 24%|███████▋ | ETA: 0:00:08 Cross validating... 25%|████████▏ | ETA: 0:00:08 Cross validating... 27%|████████▋ | ETA: 0:00:08 Cross validating... 29%|█████████▏ | ETA: 0:00:08 Cross validating... 30%|█████████▋ | ETA: 0:00:08 Cross validating... 32%|██████████▏ | ETA: 0:00:08 Cross validating... 33%|██████████▋ | ETA: 0:00:08 Cross validating... 37%|███████████▋ | ETA: 0:00:07 Cross validating... 40%|████████████▊ | ETA: 0:00:07 Cross validating... 43%|█████████████▊ | 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97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:11 Crossvalidation Results: k MSE 0 407.76275575318533 1 324.13093574135195 2 243.01009299462174 3 231.9986770514302 4 217.93124176532373 5 220.2272690294447 6 224.0584545772989 7 225.1355823452995 8 229.72614882456867 9 232.04808561396143 10 232.096178511657 11 235.93355798823666 12 236.76174165783004 13 242.67613582609698 14 239.85081779691888 15 245.56010435334449 16 237.805842025019 17 256.9674437699772 18 254.38078733685072 19 265.8366733592488 20 258.4385138494772 Best k = 4 11.186452 seconds (35.78 M allocations: 739.280 MiB, 1.17% gc time, 0.65% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, NegativeBinomial model | 2 2 45.4s **** 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: 0:00:44 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: 0:00:10 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... 32%|██████████▏ | ETA: 0:00:06 Cross validating... 35%|███████████▏ | ETA: 0:00:05 Cross validating... 38%|████████████▎ | ETA: 0:00:05 Cross validating... 41%|█████████████▎ | ETA: 0:00:04 Cross validating... 44%|██████████████▎ | ETA: 0:00:04 Cross validating... 48%|███████████████▎ | ETA: 0:00:04 Cross validating... 51%|████████████████▎ | ETA: 0:00:03 Cross validating... 54%|█████████████████▎ | ETA: 0:00:03 Cross validating... 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708.7406597900391 1 594.0547950439453 2 472.60887115478516 3 391.07051165771486 4 322.2429605712891 5 274.1304553527832 6 242.98796069335935 7 231.75397763061522 8 211.04413333129884 9 208.82878451538085 10 210.9139321594238 11 206.8662128601074 12 209.29315435791017 13 216.44690969848637 14 210.83974066162108 15 223.69269552612303 16 223.5122525024414 17 217.3672544555664 18 230.29235778808595 19 245.48900619506838 20 214.24631561279296 Best k = 11 6.798700 seconds (17.23 M allocations: 344.260 MiB, 10.95% gc time, 28.27% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 5%|█▌ | ETA: 0:00:03 Cross validating... 8%|██▌ | ETA: 0:00:03 Cross validating... 11%|███▌ | ETA: 0:00:03 Cross validating... 14%|████▋ | ETA: 0:00:03 Cross validating... 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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: 0:00:00 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:00 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:04 Crossvalidation Results: k MSE 0 708.7406597900391 1 575.6241903076173 2 458.4867525024414 3 380.67050573730467 4 317.43561486816407 5 274.8225385131836 6 243.94065100097657 7 233.23877688598634 8 212.74209445190428 9 214.86823376464844 10 213.80905279541014 11 216.52949041748047 12 220.7860779724121 13 222.78791012573242 14 231.40656030273436 15 233.06280703735348 16 243.6403890075684 17 242.80908297729493 18 238.556499420166 19 251.23290313720705 20 244.79654568481442 Best k = 8 4.264617 seconds (16.27 M allocations: 288.814 MiB, 2.04% gc time, 0.89% compilation time) Test Summary: | Pass Total Time Cross validation on floating point matrices, NegativeBinomial model | 2 2 11.6s **** 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... 2%|▋ | ETA: 0:01:02 Cross validating... 3%|█ | ETA: 0:00:45 Cross validating... 4%|█▎ | ETA: 0:00:37 Cross validating... 5%|█▋ | ETA: 0:00:32 Cross validating... 6%|█▉ | ETA: 0:00:28 Cross validating... 7%|██▎ | ETA: 0:00:26 Cross validating... 8%|██▌ | ETA: 0:00:25 Cross validating... 9%|██▉ | ETA: 0:00:24 Cross validating... 10%|███▎ | ETA: 0:00:23 Cross 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0:00:03 Cross validating... 83%|██████████████████████████▌ | ETA: 0:00:03 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:03 Cross validating... 85%|███████████████████████████▎ | ETA: 0:00:03 Cross validating... 86%|███████████████████████████▌ | ETA: 0:00:02 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:02 Cross validating... 88%|████████████████████████████▏ | ETA: 0:00:02 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: 0:00:01 Cross validating... 93%|█████████████████████████████▊ | ETA: 0:00:01 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: 0:00:17 Crossvalidation Results: k MSE 1 2621.7663219292817 2 1950.1487291162107 3 1631.7731134910352 4 1504.3226982758408 5 1428.4054926532574 6 1362.732559377785 7 1378.3921749248907 8 1380.8321481501507 9 1393.1817252330925 10 1387.2260427186948 11 1379.232052230465 12 1406.3308422780667 13 1414.400621590709 14 1423.9757172599561 15 1427.8157542437216 16 1435.256042542295 17 1446.2582310845507 18 1437.2167559064055 19 1450.0619916051232 20 1466.45607623286 Best k = 6 18.127022 seconds (348.80 k allocations: 261.681 MiB, 0.85% gc time, 6.74% compilation time) Test Summary: | Pass Total Time multivariate cross validation SnpLinAlg | 3 3 22.2s Test Summary: | Pass Total Time wrapper univariate | 20 20 1m33.7s **** 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: 0:00:10 Cross validating... 3%|█ | ETA: 0:00:10 Cross validating... 4%|█▎ | 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: 0:00:14 Cross validating... 12%|███▉ | ETA: 0:00:15 Cross validating... 13%|████▏ | ETA: 0:00:15 Cross validating... 14%|████▌ | ETA: 0:00:15 Cross validating... 15%|████▊ | ETA: 0:00:16 Cross validating... 16%|█████▏ | ETA: 0:00:18 Cross validating... 17%|█████▌ | ETA: 0:00:18 Cross validating... 18%|█████▊ | ETA: 0:00:18 Cross validating... 19%|██████▏ | ETA: 0:00:18 Cross validating... 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89%|████████████████████████████▌ | ETA: 0:00:03 Cross validating... 90%|████████████████████████████▊ | ETA: 0:00:02 Cross validating... 91%|█████████████████████████████▏ | ETA: 0:00:02 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:02 Cross validating... 93%|█████████████████████████████▊ | ETA: 0:00:02 Cross validating... 94%|██████████████████████████████▏ | ETA: 0:00:01 Cross validating... 95%|██████████████████████████████▍ | ETA: 0:00:01 Cross validating... 96%|██████████████████████████████▊ | ETA: 0:00:01 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:01 Cross validating... 98%|███████████████████████████████▍| ETA: 0:00:00 Cross validating... 99%|███████████████████████████████▋| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:23 Crossvalidation Results: k MSE 1 2838.788679198002 2 2514.397342870813 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%|██▎ | 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: 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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: 0:00:11 Cross validating... 3%|█ | ETA: 0:00:10 Cross 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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 1m22.6s read BGEN and VCF: Error During Test at /home/pkgeval/.julia/packages/MendelIHT/ZcxZT/test/wrapper_test.jl:184 Got exception outside of a @test startproc must be called before process Stacktrace: [1] error(s::String) @ Base error.jl: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 3.7s RNG of the outermost testset: Xoshiro(0x50abe310665c3617, 0x871058acc8e35677, 0x225c118601345151, 0xdf274ee4fb199d33, 0xabbc6cf7a4bf1c76) 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 970.32s 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:3283 [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 1105.88s: package tests unexpectedly errored