Package evaluation to test MendelIHT on Julia 1.14.0-DEV.2705 (2f35a920f0*) started at 2026-07-20T01:58:34.800 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.14` Set-up completed after 14.36s ################################################################################ # Installation # Installing MendelIHT... Resolving package versions... Updating `~/.julia/environments/v1.14/Project.toml` [921c7187] + MendelIHT v1.4.11 Updating `~/.julia/environments/v1.14/Manifest.toml` [7d9f7c33] + Accessors v0.1.45 [79e6a3ab] + Adapt v4.7.0 [66dad0bd] + AliasTables v1.1.3 [4fba245c] + ArrayInterface v7.27.0 [67c07d97] + Automa v1.2.0 ⌅ [6db4b851] + BGEN v0.1.17 [28d598bf] + BGZFStreams v0.3.2 [47718e42] + BioGenerics v0.1.5 [62783981] + BitTwiddlingConvenienceFunctions v0.1.6 [e1450e63] + BufferedStreams v1.2.2 [2a0fbf3d] + CPUSummary v0.2.7 [336ed68f] + CSV v0.10.16 [fb6a15b2] + CloseOpenIntervals v0.1.13 [523fee87] + CodecBzip2 v0.8.5 [ba30903b] + CodecXz v0.7.4 [944b1d66] + CodecZlib v0.7.8 [6b39b394] + CodecZstd v0.8.7 [861a8166] + Combinatorics v1.1.0 [38540f10] + CommonSolve v0.2.11 [f70d9fcc] + CommonWorldInvalidations v1.1.1 [34da2185] + Compat v4.18.1 [a33af91c] + CompositionsBase v0.1.2 [187b0558] + ConstructionBase v1.6.0 [adafc99b] + CpuId v0.3.1 [a8cc5b0e] + Crayons v4.2.0 [a10d1c49] + DBInterface v2.6.1 [9a962f9c] + 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[efcefdf7] + PCRE2_jll v10.47.0+0 [bea87d4a] + SuiteSparse_jll v7.10.1+0 [83775a58] + Zlib_jll v1.3.2+0 [3161d3a3] + Zstd_jll v1.5.7+1 [8e850b90] + libblastrampoline_jll v5.15.0+0 [8e850ede] + nghttp2_jll v1.69.0+0 [3f19e933] + p7zip_jll v17.8.0+0 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. To see why use `status --outdated -m` Installation completed after 5.79s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompiling project... 4.6 s ✓ BGEN 7.0 s ✓ VCFTools WARNING: Constructor for type "MvNormal" was extended in `MendelIHT` without explicit qualification or import. NOTE: Assumed "MvNormal" refers to `Distributions.MvNormal`. This behavior is deprecated and may differ in future versions. NOTE: This behavior may have differed in Julia versions prior to 1.12. Hint: If you intended to create a new generic function of the same name, use `function MvNormal end`. Hint: To silence the warning, qualify `MvNormal` as `Distributions.MvNormal` in the method signature or explicitly `import Distributions: MvNormal`. 21.2 s ✓ MendelIHT 3 dependencies successfully precompiled in 35 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 63.42s ################################################################################ # Testing # Testing MendelIHT Status `/tmp/jl_CC1GHG/Project.toml` ⌅ [6db4b851] BGEN v0.1.17 [6e4b80f9] BenchmarkTools v1.8.0 [336ed68f] CSV v0.10.16 [a93c6f00] DataFrames v1.8.2 [8bb1440f] DelimitedFiles v1.9.1 [b4f34e82] Distances v0.10.12 [31c24e10] Distributions v0.25.129 [38e38edf] GLM v1.9.5 [921c7187] MendelIHT v1.4.11 [92933f4c] ProgressMeter v1.11.0 [189a3867] Reexport v1.2.2 [4e780e97] SnpArrays v0.3.23 [276daf66] SpecialFunctions v2.8.0 [2913bbd2] StatsBase v0.34.12 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libblastrampoline_jll v5.15.0+0 [8e850ede] nghttp2_jll v1.69.0+0 [3f19e933] p7zip_jll v17.8.0+0 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. Testing Running tests... ┌ Warning: accessing `Type.name` is deprecated without replacement. If for detection, use `Base.isType(x)`. │ caller = Distributions.MvNormal(σ::Vector{Float64}) at mvnormal.jl:207 └ @ Distributions ~/.julia/packages/Distributions/XAng5/src/multivariate/mvnormal.jl:207 ┌ Warning: `MvNormal(σ::AbstractVector{<:Real})` is deprecated, use `MvNormal(LinearAlgebra.Diagonal(map(abs2, σ)))` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `cholesky!(A::RealHermSymComplexHerm{<:Real}, ::Val{true}; kwargs...)` is deprecated, use `cholesky!(A, RowMaximum(); kwargs...)` instead. │ caller = iht_stepsize!(v::MendelIHT.mIHTVariable{Float64, LinearAlgebra.Transpose{Float64, SnpArrays.SnpLinAlg{Float64}}}) at multivariate.jl:241 └ @ MendelIHT ~/.julia/packages/MendelIHT/ZcxZT/src/multivariate.jl:241 Test Summary: | Pass Total Time loglikelihood | 4 4 16.1s Test Summary: | Pass Total Time deviance | 1 1 0.4s Test Summary: | Pass Total Time update_μ! | 4 4 1.8s Test Summary: | Pass Total Time _choose! | 7 7 9.8s Test Summary: | Pass Total Time _iht_backtrack | 7 7 0.0s Test Summary: | Pass Total Time standardize! | 12 12 1.4s Test Summary: | Pass Total Time project_k! | 2 2 1.0s Test Summary: | Pass Total Time project_group_sparse! | 5 5 1.1s Test Summary: | Pass Total Time maf_weights | 6 6 2.3s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** 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 = -1544.9516847482219, backtracks = 0, tol = 1.3286631860817242 Iteration 2: loglikelihood = -1410.3422847371799, backtracks = 0, tol = 0.14090192183275982 Iteration 3: loglikelihood = -1400.067795300239, backtracks = 0, tol = 0.03337593473455892 Iteration 4: loglikelihood = -1399.9811342321366, backtracks = 0, tol = 0.003022378835786979 Iteration 5: loglikelihood = -1399.980201518473, backtracks = 0, tol = 0.0003082940877743266 Iteration 6: loglikelihood = -1399.9801898229505, backtracks = 0, tol = 3.568248641642513e-5 IHT estimated 10 nonzero SNP predictors and 1 non-genetic predictors. Compute time (sec): 0.05425405502319336 Final loglikelihood: -1399.9801898229505 SNP PVE: 0.8322492206731956 Iterations: 6 Selected genetic predictors: 10×2 DataFrame Row │ Position Estimated_β │ Int64 Float64 ─────┼─────────────────────── 1 │ 201 -0.307695 2 │ 3435 -0.127288 3 │ 3438 0.724413 4 │ 3794 -0.673711 5 │ 5807 0.590027 6 │ 6016 0.317696 7 │ 7407 -1.01026 8 │ 7744 0.177886 9 │ 9147 -1.52087 10 │ 9239 0.118107 Selected nongenetic predictors: 1×2 DataFrame Row │ Position Estimated_β │ Int64 Float64 ─────┼─────────────────────── 1 │ 1 0.0327515Test Summary: | Pass Total Time fit normal SnpLinAlg | 4 4 23.4s **** 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 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 3.8s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse 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 = -1336.044771046596, backtracks = 0, tol = 0.31268457312052944 Iteration 2: loglikelihood = -1299.7902737250754, backtracks = 0, tol = 0.054333890877959465 Iteration 3: loglikelihood = -1283.8976279250771, backtracks = 1, tol = 0.06514798590236597 Iteration 4: loglikelihood = -1276.8754203662832, backtracks = 0, tol = 0.08474022614987767 Iteration 5: loglikelihood = -1274.3013841464247, backtracks = 1, tol = 0.015700033571015112 Iteration 6: loglikelihood = -1269.670247990847, backtracks = 1, tol = 0.06685693513202759 Iteration 7: loglikelihood = -1269.0644768109685, backtracks = 1, tol = 0.010872400616969142 Iteration 8: loglikelihood = -1268.8840193164083, backtracks = 2, tol = 0.004446285742954841 Iteration 9: loglikelihood = -1268.7192210535852, backtracks = 2, tol = 0.005391450828055778 Iteration 10: loglikelihood = -1268.6180461651622, backtracks = 2, tol = 0.004638757078764096 Iteration 11: loglikelihood = -1268.5852660679404, backtracks = 3, tol = 0.001946142696251692 Iteration 12: loglikelihood = -1268.5594985511104, backtracks = 3, tol = 0.0017782883033549343 Iteration 13: loglikelihood = -1268.539294975106, backtracks = 3, tol = 0.0016173632750448033 Iteration 14: loglikelihood = -1268.5234841311024, backtracks = 3, tol = 0.001465996690513354 Iteration 15: loglikelihood = -1268.511134726056, backtracks = 3, tol = 0.0013244145718966397 Iteration 16: loglikelihood = -1268.5015074410228, backtracks = 3, tol = 0.0011926503826222353 Iteration 17: loglikelihood = -1268.4940163059766, backtracks = 3, tol = 0.0010706674258683425 Iteration 18: loglikelihood = -1268.4881977943026, backtracks = 3, tol = 0.0009583478825463273 Iteration 19: loglikelihood = -1268.4836860586206, backtracks = 3, tol = 0.0008554796594634837 Iteration 20: loglikelihood = -1268.4801930576466, backtracks = 3, tol = 0.0007617541530386587 Iteration 21: loglikelihood = -1268.4774925952472, backtracks = 3, tol = 0.0006767742669691497 Iteration 22: loglikelihood = -1268.4754075052501, backtracks = 3, tol = 0.0006000697130782751 Iteration 23: loglikelihood = -1268.4737993770825, backtracks = 3, tol = 0.000531116237682995 Iteration 24: loglikelihood = -1268.4725603389056, backtracks = 3, tol = 0.0004693557980647699 Iteration 25: loglikelihood = -1268.4716065075663, backtracks = 3, tol = 0.00041421547675793755 Iteration 26: loglikelihood = -1268.4708727864177, backtracks = 3, tol = 0.0003651237699483042 Iteration 27: loglikelihood = -1268.4703087496762, backtracks = 3, tol = 0.00032152362791134563 Iteration 28: loglikelihood = -1268.4698753986622, backtracks = 3, tol = 0.0002828821739628066 Iteration 29: loglikelihood = -1268.469542614652, backtracks = 3, tol = 0.0002486973753123041 Iteration 30: loglikelihood = -1268.4692871652157, backtracks = 3, tol = 0.00021850211796083948 Iteration 31: loglikelihood = -1268.469091148629, backtracks = 3, tol = 0.00019186619593790548 Iteration 32: loglikelihood = -1268.468940783199, backtracks = 3, tol = 0.00016839670775148363 Iteration 33: loglikelihood = -1268.4688254672812, backtracks = 3, tol = 0.00014773729524586858 Iteration 34: loglikelihood = -1268.4687370509143, backtracks = 3, tol = 0.00012956658643642182 Iteration 35: loglikelihood = -1268.46866927242, backtracks = 3, tol = 0.00011359612921523183 Iteration 36: loglikelihood = -1268.468617323235, backtracks = 3, tol = 9.956803506460428e-5 Test Summary: | Pass Total Time fit Poisson SnpLinAlg | 4 4 3.2s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse NegativeBinomial regression Number of threads = 1 Link functin = LogLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1466.515140075726, backtracks = 0, tol = 0.25155696696214175 Iteration 2: loglikelihood = -1442.9174766751328, backtracks = 0, tol = 0.10304286898519825 Iteration 3: loglikelihood = -1433.5490947446058, backtracks = 0, tol = 0.11880050478810955 Iteration 4: loglikelihood = -1430.2845529117483, backtracks = 0, tol = 0.0962626827616588 Iteration 5: loglikelihood = -1430.0755639432214, backtracks = 1, tol = 0.006412988203435648 Iteration 6: loglikelihood = -1429.9999501485443, backtracks = 1, tol = 0.004467445654845212 Iteration 7: loglikelihood = -1429.974634215004, backtracks = 1, tol = 0.003008065188653803 Iteration 8: loglikelihood = -1429.9675281801674, backtracks = 1, tol = 0.0018772405988770956 Iteration 9: loglikelihood = -1429.435838552676, backtracks = 1, tol = 0.07582320269739506 Iteration 10: loglikelihood = -1429.4024464298932, backtracks = 1, tol = 0.0022778339427059666 Iteration 11: loglikelihood = -1429.3924392155875, backtracks = 1, tol = 0.0012053357904048025 Iteration 12: loglikelihood = -1429.3893545592184, backtracks = 1, tol = 0.0007382832469681833 Iteration 13: loglikelihood = -1429.3883772862646, backtracks = 1, tol = 0.00048408568231576615 Iteration 14: loglikelihood = -1429.3880708148197, backtracks = 1, tol = 0.00029024346042915653 Iteration 15: loglikelihood = -1429.3879811997247, backtracks = 1, tol = 0.00017215420333204743 Iteration 16: loglikelihood = -1429.387957036188, backtracks = 1, tol = 0.000100845359002185 Iteration 17: loglikelihood = -1429.387950811737, backtracks = 1, tol = 5.8046841277040394e-5 Test Summary: | Pass Total Time fit NegativeBinomial SnpLinAlg | 4 4 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 = -1791.0047404823881, backtracks = 0, tol = 0.786821785946614 Iteration 2: loglikelihood = -1458.5102379665263, backtracks = 0, tol = 0.13378173589661033 Iteration 3: loglikelihood = -1391.406885086843, backtracks = 0, tol = 0.04495001421171432 Iteration 4: loglikelihood = -1388.611207982109, backtracks = 0, tol = 0.00951634066205647 Iteration 5: loglikelihood = -1387.780275341217, backtracks = 0, tol = 0.0271123830142177 Iteration 6: loglikelihood = -1387.6920033653387, backtracks = 0, tol = 0.0014406580556265863 Iteration 7: loglikelihood = -1387.6913974413612, backtracks = 1, tol = 9.71252101280397e-5 Test Summary: | Pass Total Time fit with >1 non-genetic covariates SnpLinAlg | 5 5 1.7s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse linear regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1575.4664248683684, backtracks = 0, tol = 0.4643948216848974 Iteration 2: loglikelihood = -1422.1620553433945, backtracks = 0, tol = 0.0797319184436589 Iteration 3: loglikelihood = -1398.54054574219, backtracks = 0, tol = 0.042247137438405497 Iteration 4: loglikelihood = -1392.1466357924776, backtracks = 0, tol = 0.028663007054121902 Iteration 5: loglikelihood = -1390.5267657152833, backtracks = 0, tol = 0.02783998451522653 Iteration 6: loglikelihood = -1390.0966907318978, backtracks = 0, tol = 0.027375534441332165 Iteration 7: loglikelihood = -1389.9668279138211, backtracks = 0, tol = 0.002369585882544791 Iteration 8: loglikelihood = -1389.965720111143, backtracks = 0, tol = 0.00022797668876612396 Iteration 9: loglikelihood = -1389.9657040447319, backtracks = 0, tol = 2.1227293800806555e-5 Test Summary: | Pass Total Time model selection on non-genetic covariates | 5 5 0.8s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse linear regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 15 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1473.12410014528, backtracks = 0, tol = 0.11162633196865429 Iteration 2: loglikelihood = -1448.37403799896, backtracks = 0, tol = 0.07736217654955346 Iteration 3: loglikelihood = -1429.8981769610311, backtracks = 1, tol = 0.056531823476744666 Iteration 4: loglikelihood = -1404.7133956159753, backtracks = 0, tol = 0.10125409614175711 Iteration 5: loglikelihood = -1397.466171579031, backtracks = 0, tol = 0.05343369325195712 Iteration 6: loglikelihood = -1395.7490747391416, backtracks = 0, tol = 0.08843871418165569 Iteration 7: loglikelihood = -1395.4877576477586, backtracks = 0, tol = 0.0089247040684952 Iteration 8: loglikelihood = -1395.442237061722, backtracks = 0, tol = 0.005277867116132827 Iteration 9: loglikelihood = -1395.4302205892106, backtracks = 0, tol = 0.0027680467744013336 Iteration 10: loglikelihood = -1395.1973617039414, backtracks = 0, tol = 0.0905690065560604 Iteration 11: loglikelihood = -1395.0048067729406, backtracks = 0, tol = 0.007650485819168939 Iteration 12: loglikelihood = -1394.9835209063683, backtracks = 0, tol = 0.0035232591741737973 Iteration 13: loglikelihood = -1394.9793628241396, backtracks = 0, tol = 0.001852195878065177 Iteration 14: loglikelihood = -1394.9779889816232, backtracks = 0, tol = 0.0012530451800711444 Iteration 15: loglikelihood = -1394.977503420045, backtracks = 0, tol = 0.0006829444661300923 Iteration 16: loglikelihood = -1394.9773714862843, backtracks = 1, tol = 0.00022881022816864142 Iteration 17: loglikelihood = -1394.977310220191, backtracks = 2, tol = 0.0001217788197399568 Iteration 18: loglikelihood = -1394.977273607278, backtracks = 2, tol = 8.822469907087602e-5 **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse linear regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 3 Prior weight scaling = off Doubly sparse projection = on Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1535.4672180567934, backtracks = 0, tol = 0.17016419679985048 Iteration 2: loglikelihood = -1508.04343741211, backtracks = 0, tol = 0.21718489399873087 Iteration 3: loglikelihood = -1448.2717322168082, backtracks = 0, tol = 0.15334504607402907 Iteration 4: loglikelihood = -1437.5669418734744, backtracks = 0, tol = 0.08425396177776269 Iteration 5: loglikelihood = -1434.3602241747528, backtracks = 0, tol = 0.03199716666887782 Iteration 6: loglikelihood = -1434.239273652971, backtracks = 2, tol = 0.003498168340088273 Iteration 7: loglikelihood = -1434.1475478538455, backtracks = 2, tol = 0.0030522911015526556 Iteration 8: loglikelihood = -1434.0913475157126, backtracks = 2, tol = 0.0021931576818355514 Iteration 9: loglikelihood = -1434.0584761985995, backtracks = 2, tol = 0.0016688209654910561 Iteration 10: loglikelihood = -1434.0393127719108, backtracks = 2, tol = 0.001317554485128468 Iteration 11: loglikelihood = -1434.0281644425422, backtracks = 2, tol = 0.0010393713220469248 Iteration 12: loglikelihood = -1434.0216963632631, backtracks = 2, tol = 0.0008158673348111212 Iteration 13: loglikelihood = -1434.0179556115852, backtracks = 2, tol = 0.0006363671566384319 Iteration 14: loglikelihood = -1433.8972844529703, backtracks = 2, tol = 0.02105646084267335 Iteration 15: loglikelihood = -1433.6170929347984, backtracks = 1, tol = 0.011448126839540936 Iteration 16: loglikelihood = -1433.5408744767515, backtracks = 2, tol = 0.0040324300639331045 Iteration 17: loglikelihood = -1433.4945867179188, backtracks = 2, tol = 0.003005268578298657 Iteration 18: loglikelihood = -1433.467626121943, backtracks = 2, tol = 0.002187229771831438 Iteration 19: loglikelihood = -1433.4521439235273, backtracks = 2, tol = 0.0016467936133078437 Iteration 20: loglikelihood = -1433.4432822302874, backtracks = 2, tol = 0.0012631945762950846 Iteration 21: loglikelihood = -1433.4382075829426, backtracks = 2, tol = 0.0009580287583338291 Iteration 22: loglikelihood = -1433.4352962137846, backtracks = 2, tol = 0.0007222437442123496 Iteration 23: loglikelihood = -1433.4336216439426, backtracks = 2, tol = 0.0005424739396431532 Iteration 24: loglikelihood = -1433.43265547142, backtracks = 2, tol = 0.00040628145880685523 Iteration 25: loglikelihood = -1433.4320960523787, backtracks = 2, tol = 0.0003034179918772475 Iteration 26: loglikelihood = -1433.4317709097872, backtracks = 2, tol = 0.00022583740291084404 Iteration 27: loglikelihood = -1433.4315812027676, backtracks = 2, tol = 0.0001673653861249394 Iteration 28: loglikelihood = -1432.5898379532837, backtracks = 2, tol = 0.025080215054031605 Iteration 29: loglikelihood = -1431.7678006470733, backtracks = 1, tol = 0.017181190475547538 Iteration 30: loglikelihood = -1430.3157393955933, backtracks = 1, tol = 0.07333968264200234 Iteration 31: loglikelihood = -1429.706868513855, backtracks = 0, tol = 0.020015111727945754 Iteration 32: loglikelihood = -1429.5802551945537, backtracks = 1, tol = 0.00756937670420323 Iteration 33: loglikelihood = -1429.5139450553559, backtracks = 2, tol = 0.003906515984506227 Iteration 34: loglikelihood = -1429.4691972325213, backtracks = 2, tol = 0.003683664863256486 Iteration 35: loglikelihood = -1428.8607526222902, backtracks = 2, tol = 0.08711763846658777 Iteration 36: loglikelihood = -1428.6178427111051, backtracks = 1, tol = 0.006558345246943271 Iteration 37: loglikelihood = -1428.5424083746184, backtracks = 2, tol = 0.0033912200662443866 Iteration 38: loglikelihood = -1428.4933608487952, backtracks = 2, tol = 0.0030098214824111793 Iteration 39: loglikelihood = -1428.4620745885088, backtracks = 2, tol = 0.0025951371119133128 Iteration 40: loglikelihood = -1428.4427329028306, backtracks = 2, tol = 0.002148184701148465 Iteration 41: loglikelihood = -1428.4311433050725, backtracks = 2, tol = 0.0017160493175770867 Iteration 42: loglikelihood = -1428.4243474878394, backtracks = 2, tol = 0.0013407892924840973 Iteration 43: loglikelihood = -1428.420413936832, backtracks = 2, tol = 0.0010343694042998534 Iteration 44: loglikelihood = -1428.4181556141762, backtracks = 2, tol = 0.0007948565534422845 Iteration 45: loglikelihood = -1428.4168664091337, backtracks = 2, tol = 0.000608309643427293 Iteration 46: loglikelihood = -1428.4161334920516, backtracks = 2, tol = 0.0004622621654004415 Iteration 47: loglikelihood = -1428.4157180925672, backtracks = 2, tol = 0.00034956951660978575 Iteration 48: loglikelihood = -1428.4154831711999, backtracks = 2, tol = 0.00026348047442121094 Iteration 49: loglikelihood = -1428.4153505233908, backtracks = 2, tol = 0.00019816133989405092 Iteration 50: loglikelihood = -1428.4152757065372, backtracks = 2, tol = 0.00014882628973647444 Iteration 51: loglikelihood = -1428.4152335404317, backtracks = 2, tol = 0.00011167501044822909 Iteration 52: loglikelihood = -1428.4152097888611, backtracks = 2, tol = 8.375238803842589e-5 Test Summary: | Pass Total Time Correlated predictors and double sparsity Float64 matrix | 2 2 10.7s **** 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 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 = -1659.5897821727315, backtracks = 0, tol = 0.13112558121335754 Iteration 2: loglikelihood = -1578.6334058352847, backtracks = 0, tol = 0.07344092812299824 Iteration 3: loglikelihood = -1507.5685483549846, backtracks = 0, tol = 0.1001486547228284 Iteration 4: loglikelihood = -1468.428858834313, backtracks = 0, tol = 0.06999756781648067 Iteration 5: loglikelihood = -1438.3679818444948, backtracks = 0, tol = 0.06914817250611735 Iteration 6: loglikelihood = -1424.0233664672182, backtracks = 0, tol = 0.04029768586002624 Iteration 7: loglikelihood = -1413.3901444074722, backtracks = 0, tol = 0.07233965005776323 Iteration 8: loglikelihood = -1392.7945738013611, backtracks = 0, tol = 0.06614251630682512 Iteration 9: loglikelihood = -1390.5698542898404, backtracks = 1, tol = 0.013370324571360278 Iteration 10: loglikelihood = -1389.5882663602085, backtracks = 2, tol = 0.009419037245797589 Iteration 11: loglikelihood = -1388.8171552147196, backtracks = 2, tol = 0.008084335462922681 Iteration 12: loglikelihood = -1388.3522874890555, backtracks = 2, tol = 0.006841429484260647 Iteration 13: loglikelihood = -1383.7622589769176, backtracks = 2, tol = 0.04122532410005536 Iteration 14: loglikelihood = -1382.172466614417, backtracks = 0, tol = 0.016175945869942393 Iteration 15: loglikelihood = -1381.8373461138367, backtracks = 0, tol = 0.008375872482958758 Iteration 16: loglikelihood = -1381.720355967443, backtracks = 0, tol = 0.004080637996430795 Iteration 17: loglikelihood = -1381.6696651780192, backtracks = 0, tol = 0.0038180066286127275 Iteration 18: loglikelihood = -1381.6442004788605, backtracks = 0, tol = 0.0018685157573951263 Iteration 19: loglikelihood = -1381.6312904132703, backtracks = 0, tol = 0.0019502632616223703 Iteration 20: loglikelihood = -1381.6246102522143, backtracks = 0, tol = 0.0010182511772139488 Iteration 21: loglikelihood = -1381.6211718381246, backtracks = 0, tol = 0.0010179103646157362 Iteration 22: loglikelihood = -1381.6193822612286, backtracks = 0, tol = 0.00052785591420729 Iteration 23: loglikelihood = -1381.6184547217438, backtracks = 0, tol = 0.0005368452631438564 Iteration 24: loglikelihood = -1381.6179702196416, backtracks = 0, tol = 0.000271329092941127 Iteration 25: loglikelihood = -1381.6177176936894, backtracks = 0, tol = 0.0002850416177467121 Iteration 26: loglikelihood = -1381.61758549281, backtracks = 0, tol = 0.0001394563150757921 Iteration 27: loglikelihood = -1381.6175162899615, backtracks = 0, tol = 0.00015203534002688872 Iteration 28: loglikelihood = -1381.6174800367696, backtracks = 0, tol = 7.174357873418839e-5 1.300598 seconds (4.83 M allocations: 85.913 MiB, 4.64% gc time, 46.59% 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 = -1673.3420780675256, backtracks = 0, tol = 0.13112558121335754 Iteration 2: loglikelihood = -1618.513771944383, backtracks = 0, tol = 0.07922699697635463 Iteration 3: loglikelihood = -1572.2530878151604, backtracks = 0, tol = 0.09968403558871831 Iteration 4: loglikelihood = -1539.4143204634554, backtracks = 0, tol = 0.08532452198984257 Iteration 5: loglikelihood = -1524.4701465713733, backtracks = 0, tol = 0.11537742174982424 Iteration 6: loglikelihood = -1488.545714938724, backtracks = 0, tol = 0.06755177005532258 Iteration 7: loglikelihood = -1473.6480483637756, backtracks = 0, tol = 0.03408256311867063 Iteration 8: loglikelihood = -1458.75342510062, backtracks = 0, tol = 0.06084126850874633 Iteration 9: loglikelihood = -1449.1159686987717, backtracks = 0, tol = 0.0325997394314315 Iteration 10: loglikelihood = -1441.0619650054844, backtracks = 0, tol = 0.013446902353222765 Iteration 11: loglikelihood = -1434.7715362574816, backtracks = 0, tol = 0.004501860753221512 Iteration 12: loglikelihood = -1429.2575464863562, backtracks = 0, tol = 0.0038233840491566752 Iteration 13: loglikelihood = -1424.6570995578015, backtracks = 0, tol = 0.0015154972850281916 Iteration 14: loglikelihood = -1420.6516331243167, backtracks = 0, tol = 0.0011941189908187904 Iteration 15: loglikelihood = -1417.2166796764866, backtracks = 0, tol = 0.0004922358914931138 Iteration 16: loglikelihood = -1414.2118254839775, backtracks = 0, tol = 0.00043859914990246183 Iteration 17: loglikelihood = -1411.5915151777863, backtracks = 0, tol = 0.00048139015469940476 Iteration 18: loglikelihood = -1409.2779461048367, backtracks = 0, tol = 0.00044328421178808664 Iteration 19: loglikelihood = -1402.8392935591717, backtracks = 0, tol = 0.06029276127034701 Iteration 20: loglikelihood = -1400.7433143474937, backtracks = 0, tol = 0.003634255559927862 Iteration 21: loglikelihood = -1399.0079424146688, backtracks = 0, tol = 0.0009947837068287968 Iteration 22: loglikelihood = -1397.4254556065443, backtracks = 0, tol = 0.0004431448567928047 Iteration 23: loglikelihood = -1396.0056496074417, backtracks = 0, tol = 0.00017021055163961814 Iteration 24: loglikelihood = -1393.4674569357996, backtracks = 1, tol = 8.339923858036848e-5 0.241336 seconds (929.12 k allocations: 17.001 MiB) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse NegativeBinomial regression Number of threads = 1 Link functin = LogLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -3674.3894, backtracks = 0, tol = 0.09143474490683817 Iteration 2: loglikelihood = -3639.3823, backtracks = 0, tol = 0.041791459549224655 Iteration 3: loglikelihood = -3635.8237, backtracks = 1, tol = 0.009649254630001127 Iteration 4: loglikelihood = -3618.9963, backtracks = 1, tol = 0.059593530985294234 Iteration 5: loglikelihood = -3608.2708, backtracks = 0, tol = 0.07920926509994833 Iteration 6: loglikelihood = -3606.4524, backtracks = 1, tol = 0.006379219394561886 Iteration 7: loglikelihood = -3605.8262, backtracks = 1, tol = 0.004341600425384717 Iteration 8: loglikelihood = -3605.6375, backtracks = 1, tol = 0.0029461929202558644 Iteration 9: loglikelihood = -3605.586, backtracks = 1, tol = 0.001518486433505439 Iteration 10: loglikelihood = -3605.5737, backtracks = 1, tol = 0.0007762553928295507 Iteration 11: loglikelihood = -3605.5737, backtracks = 3, tol = 9.697293385840538e-5 26.969571 seconds (13.75 M allocations: 652.439 MiB, 2.06% gc time, 96.97% 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 = -3568.7588, backtracks = 0, tol = 0.09143474490683817 Iteration 2: loglikelihood = -3460.1482, backtracks = 0, tol = 0.04277530465170926 Iteration 3: loglikelihood = -3235.7183, backtracks = 1, tol = 0.009497146696841107 Iteration 4: loglikelihood = -2978.689, backtracks = 1, tol = 0.005763929500916326 Iteration 5: loglikelihood = -2876.925, backtracks = 0, tol = 0.08900329372792458 Iteration 6: loglikelihood = -2714.4426, backtracks = 0, tol = 0.09170817023353978 Iteration 7: loglikelihood = -2580.6404, backtracks = 0, tol = 0.09198198485741539 Iteration 8: loglikelihood = -2460.2, backtracks = 0, tol = 0.0884541671354828 Iteration 9: loglikelihood = -2362.058, backtracks = 0, tol = 0.08273284717573073 Iteration 10: loglikelihood = -2288.0269, backtracks = 0, tol = 0.08294773799061672 Iteration 11: loglikelihood = -2230.126, backtracks = 0, tol = 0.08368290368620626 Iteration 12: loglikelihood = -2193.099, backtracks = 0, tol = 0.0833469070138125 Iteration 13: loglikelihood = -2166.6392, backtracks = 0, tol = 0.08272587941167812 Iteration 14: loglikelihood = -2152.7957, backtracks = 0, tol = 0.08222082864933303 Iteration 15: loglikelihood = -2144.636, backtracks = 0, tol = 0.08281997047178369 Iteration 16: loglikelihood = -2139.8223, backtracks = 0, tol = 0.09046009862614493 Iteration 17: loglikelihood = -2139.686, backtracks = 0, tol = 0.09041295510792155 Iteration 18: loglikelihood = -2136.1675, backtracks = 0, tol = 0.09858983524262648 Iteration 19: loglikelihood = -2134.7974, backtracks = 1, tol = 0.012075917667428724 Iteration 20: loglikelihood = -2134.5225, backtracks = 1, tol = 0.0054326203370447315 Iteration 21: loglikelihood = -2134.4722, backtracks = 1, tol = 0.00248590520963781 Iteration 22: loglikelihood = -2134.462, backtracks = 1, tol = 0.0011542721811870942 Iteration 23: loglikelihood = -2134.4626, backtracks = 3, tol = 0.0001360205288882382 Iteration 24: loglikelihood = -2134.462, backtracks = 2, tol = 0.0002352539247768304 Iteration 25: loglikelihood = -2134.4622, backtracks = 3, tol = 8.676446942606932e-5 0.192408 seconds (1.48 M allocations: 24.674 MiB) Test Summary: | Pass Total Time Negative binomial nuisance parameter Float32 matrix | 12 12 31.7s **** 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 **** ┌ Warning: accessing `Type.name` is deprecated without replacement. If for detection, use `Base.isType(x)`. │ caller = ProgressMeter.Progress(n::Int64, dt::Int64, desc::String, barlen::Nothing, color::Symbol, output::Base.PipeEndpoint; offset::Int64) at deprecated.jl:1 └ @ ProgressMeter ~/.julia/packages/ProgressMeter/N660J/src/deprecated.jl:1 Running sparse linear regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -2896.6116813943763, backtracks = 0, tol = 1.0257704354307222 Iteration 2: loglikelihood = -1753.4720992614753, backtracks = 0, tol = 0.28706825512903816 Iteration 3: loglikelihood = -1460.3823326395225, backtracks = 0, tol = 0.1059822007319242 Iteration 4: loglikelihood = -1438.5292259047123, backtracks = 0, tol = 0.028655431669451118 Iteration 5: loglikelihood = -1438.0856032112097, backtracks = 0, tol = 0.0034955373515602557 Iteration 6: loglikelihood = -1438.0744350329464, backtracks = 0, tol = 0.0005882060650840543 Iteration 7: loglikelihood = -1438.0741395461057, backtracks = 0, tol = 8.427264473927088e-5 5.388892 seconds (1.04 M allocations: 134.315 MiB, 1.21% gc time, 92.21% compilation time) Test Summary: | Pass Total Time initialze beta | 1 1 5.8s 10.230391 seconds (4.00 M allocations: 82.395 MiB, 0.68% gc time, 0.72% compilation time) 5.235848 seconds (3.98 M allocations: 91.674 MiB, 0.11% gc time) 10.806288 seconds (20.38 M allocations: 438.607 MiB, 1.32% gc time, 16.71% compilation time: 77% of which was recompilation) 8.418949 seconds (20.18 M allocations: 434.191 MiB, 1.28% gc time) 36.674085 seconds (3.41 M allocations: 4.230 GiB, 6.10% gc time, 30.66% compilation time) 53.368548 seconds (72.53 k allocations: 183.670 MiB, 0.99% gc time) Test Summary: | Pass Total Time memory_efficient keyword | 7 7 2m21.7s Test Summary: | Pass Total Time update_support! | 10 10 0.6s 14.137 ms (78 allocations: 4.56 KiB) 3.721 μs (0 allocations: 0 bytes) 165.228 μs (4 allocations: 288 bytes) 5.617 μs (0 allocations: 0 bytes) 56.700 μs (2 allocations: 64 bytes) 34.439 μs (0 allocations: 0 bytes) 29.170 μs (0 allocations: 0 bytes) 28.620 μs (0 allocations: 0 bytes) 103.699 μs (0 allocations: 0 bytes) 38.934 ms (78 allocations: 4.56 KiB) 18.760 μs (0 allocations: 0 bytes) 197.348 μs (4 allocations: 288 bytes) 39.249 μs (0 allocations: 0 bytes) 323.217 μs (2 allocations: 64 bytes) 102.659 μs (0 allocations: 0 bytes) 148.929 μs (0 allocations: 0 bytes) 176.619 μs (0 allocations: 0 bytes) 270.717 μs (0 allocations: 0 bytes) Test Summary: | Total Time benchmarks for multivariate function | 0 2m12.2s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse Multivariate Gaussian regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 12 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -2900.9186300194497, backtracks = 0, tol = 0.1480224208200413 Iteration 2: loglikelihood = -2869.406464695619, backtracks = 0, tol = 0.035126790460779864 Iteration 3: loglikelihood = -2868.084702693443, backtracks = 0, tol = 0.0055693496163324524 Iteration 4: loglikelihood = -2868.034423817725, backtracks = 0, tol = 0.001118951762895177 Iteration 5: loglikelihood = -2868.030857635375, backtracks = 0, tol = 0.00031182601179138955 Iteration 6: loglikelihood = -2868.0305288614227, backtracks = 0, tol = 0.00010393305949947338 Iteration 7: loglikelihood = -2868.0304966516946, backtracks = 0, tol = 3.100862049859014e-5 0.436529 seconds (44.21 k allocations: 5.347 MiB, 64.63% compilation time) Test Summary: | Pass Total Time multivariate fit_iht SnpLinAlg | 7 7 12.1s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse Multivariate Gaussian regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 12 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -2878.028812628852, backtracks = 0, tol = 2.5661768673084553 Iteration 2: loglikelihood = -2868.563037890196, backtracks = 0, tol = 0.024335274263285057 Iteration 3: loglikelihood = -2868.0815051475474, backtracks = 0, tol = 0.004072558228741048 Iteration 4: loglikelihood = -2868.0352100240902, backtracks = 0, tol = 0.0013135682973484317 Iteration 5: loglikelihood = -2868.0309297231934, 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 1.962024 seconds (258.54 k allocations: 167.592 MiB, 4.44% gc time, 55.78% compilation time) Test Summary: | Pass Total Time initialze beta | 5 5 2.5s **** 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, desc::String, offset::Int64; kwargs::Base.Pairs{Symbol, Union{}, Nothing, @NamedTuple{}}) at deprecated.jl:5 └ @ ProgressMeter ~/.julia/packages/ProgressMeter/N660J/src/deprecated.jl:5 Cross validating... 3%|█ | ETA: 0:03:39 Cross validating... 13%|████▏ | ETA: 0:00:54 Cross validating... 16%|█████▏ | ETA: 0:00:42 Cross validating... 19%|██████▏ | ETA: 0:00:34 Cross validating... 22%|███████▏ | ETA: 0:00:29 Cross validating... 25%|████████▏ | ETA: 0:00:25 Cross validating... 29%|█████████▏ | ETA: 0:00:22 Cross validating... 32%|██████████▏ | ETA: 0:00:19 Cross validating... 35%|███████████▏ | ETA: 0:00:17 Cross validating... 38%|████████████▎ | ETA: 0:00:15 Cross validating... 41%|█████████████▎ | ETA: 0:00:13 Cross validating... 44%|██████████████▎ | ETA: 0:00:12 Cross validating... 48%|███████████████▎ | ETA: 0:00:10 Cross validating... 51%|████████████████▎ | ETA: 0:00:09 Cross validating... 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100%|████████████████████████████████| Time: 0:00:12 Crossvalidation Results: k MSE 0 1919.7533563272498 1 1165.83533058306 2 841.8459271864665 3 659.8432416639378 4 515.0824012520845 5 406.8228479895976 6 379.24291362894184 7 341.8584421340801 8 338.77816573293467 9 340.36472087042455 10 343.0552755918591 11 345.82012250333526 12 348.70270411769843 13 342.6209551286764 14 350.6955294692357 15 360.17276675768926 16 363.1285995422441 17 365.4028603500368 18 356.11224497428015 19 395.88001424174377 20 411.80848773615435 Best k = 8 12.224567 seconds (11.33 M allocations: 295.166 MiB, 1.08% gc time, 61.10% 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: 0:00:03 Cross validating... 10%|███ | ETA: 0:00:03 Cross validating... 13%|████▏ | ETA: 0:00:03 Cross validating... 16%|█████▏ | ETA: 0:00:03 Cross validating... 19%|██████▏ | ETA: 0:00:03 Cross validating... 22%|███████▏ | ETA: 0:00:03 Cross validating... 25%|████████▏ | ETA: 0:00:03 Cross validating... 27%|████████▋ | ETA: 0:00:03 Cross validating... 30%|█████████▋ | ETA: 0:00:03 Cross validating... 33%|██████████▋ | ETA: 0:00:03 Cross validating... 37%|███████████▋ | ETA: 0:00:03 Cross validating... 40%|████████████▊ | ETA: 0:00:03 Cross validating... 43%|█████████████▊ | ETA: 0:00:03 Cross validating... 46%|██████████████▊ | ETA: 0:00:02 Cross validating... 49%|███████████████▊ | ETA: 0:00:02 Cross validating... 52%|████████████████▊ | ETA: 0:00:02 Cross validating... 56%|█████████████████▊ | ETA: 0:00:02 Cross validating... 59%|██████████████████▊ | ETA: 0:00:02 Cross validating... 62%|███████████████████▊ | ETA: 0:00:02 Cross validating... 65%|████████████████████▉ | ETA: 0:00:02 Cross validating... 68%|█████████████████████▉ | ETA: 0:00:02 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:01 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:01 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:01 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:01 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:01 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:01 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:00 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:04 Crossvalidation Results: k MSE 0 1919.7533563272498 1 1165.8989104498696 2 843.7162546558824 3 665.9809856985315 4 521.4698867958788 5 414.2403795202649 6 386.4481775989933 7 348.71116990591315 8 348.27687407850374 9 355.19432913790064 10 360.3546359445968 11 368.3002686378167 12 378.092257088536 13 374.1715111142113 14 389.7602757792082 15 384.2304001237146 16 392.7448673087571 17 391.6273808803415 18 398.27518183193274 19 415.223522219047 20 411.8084877361544 Best k = 8 4.860892 seconds (10.25 M allocations: 214.533 MiB, 1.11% gc time, 1.22% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, normal model | 3 3 17.9s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:05:50 Cross validating... 10%|███ | ETA: 0:01:50 Cross validating... 16%|█████▏ | ETA: 0:01:02 Cross validating... 21%|██████▋ | ETA: 0:00:46 Cross validating... 25%|████████▏ | ETA: 0:00:35 Cross validating... 30%|█████████▋ | ETA: 0:00:28 Cross validating... 35%|███████████▏ | ETA: 0:00:23 Cross validating... 40%|████████████▊ | ETA: 0:00:19 Cross validating... 46%|██████████████▊ | ETA: 0:00:15 Cross validating... 51%|████████████████▎ | ETA: 0:00:12 Cross validating... 56%|█████████████████▊ | ETA: 0:00:10 Cross validating... 60%|███████████████████▎ | ETA: 0:00:08 Cross validating... 65%|████████████████████▉ | ETA: 0:00:07 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:05 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:04 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:03 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:02 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:01 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:13 Crossvalidation Results: k MSE 0 1677.781792480469 1 1342.7467126464844 2 1023.0786236572267 3 823.3037357788087 4 629.8395372314453 5 524.0557829284669 6 433.3870585632325 7 374.5667884216309 8 351.4425375366211 9 335.2664613647461 10 336.21998046875 11 337.4250549011231 12 335.6000659179688 13 346.8114622802734 14 338.58934594726566 15 357.346246673584 16 356.53492312622075 17 347.86153262329105 18 353.2945281677246 19 357.2325453491211 20 350.92904519653325 Best k = 9 15.121497 seconds (12.41 M allocations: 310.550 MiB, 0.52% gc time, 83.76% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 5%|█▌ | ETA: 0:00:02 Cross validating... 11%|███▌ | ETA: 0:00:02 Cross validating... 17%|█████▋ | ETA: 0:00:02 Cross validating... 22%|███████▏ | ETA: 0:00:02 Cross validating... 27%|████████▋ | ETA: 0:00:02 Cross validating... 32%|██████████▏ | ETA: 0:00:02 Cross validating... 37%|███████████▋ | ETA: 0:00:02 Cross validating... 43%|█████████████▊ | ETA: 0:00:01 Cross validating... 49%|███████████████▊ | ETA: 0:00:01 Cross validating... 54%|█████████████████▎ | ETA: 0:00:01 Cross validating... 59%|██████████████████▊ | ETA: 0:00:01 Cross validating... 63%|████████████████████▍ | ETA: 0:00:01 Cross validating... 68%|█████████████████████▉ | ETA: 0:00:01 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:01 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:00 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:00 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:00 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:02 Crossvalidation Results: k MSE 0 1677.781792480469 1 1342.895514404297 2 1023.681679992676 3 824.1892035522462 4 631.0092314453125 5 525.3615757141114 6 435.0555234985352 7 376.33686297607426 8 354.25026571655275 9 339.8354993896485 10 343.4532875976563 11 348.08195104980473 12 349.09619610595706 13 362.23457650756836 14 356.9373083496094 15 376.95027801513675 16 378.1985601501465 17 380.10958609008793 18 390.00063073730473 19 392.65938146972655 20 390.97461901855473 Best k = 9 2.590380 seconds (10.86 M allocations: 199.489 MiB, 1.90% gc time, 1.82% compilation time) Test Summary: | Pass Total Time Cross validation on Float32 matrix, normal model | 2 2 19.1s **** 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: 0:00:59 Cross validating... 6%|██ | ETA: 0:00:31 Cross validating... 10%|███ | ETA: 0:00:21 Cross validating... 13%|████▏ | ETA: 0:00:17 Cross validating... 14%|████▋ | ETA: 0:00:15 Cross validating... 17%|█████▋ | ETA: 0:00:13 Cross validating... 21%|██████▋ | ETA: 0:00:11 Cross validating... 24%|███████▋ | ETA: 0:00:10 Cross validating... 27%|████████▋ | ETA: 0:00:09 Cross validating... 30%|█████████▋ | ETA: 0:00:08 Cross validating... 33%|██████████▋ | ETA: 0:00:07 Cross validating... 37%|███████████▋ | ETA: 0:00:07 Cross validating... 40%|████████████▊ | ETA: 0:00:06 Cross validating... 43%|█████████████▊ | ETA: 0:00:06 Cross validating... 46%|██████████████▊ | ETA: 0:00:05 Cross validating... 49%|███████████████▊ | ETA: 0:00:05 Cross validating... 52%|████████████████▊ | ETA: 0:00:04 Cross validating... 56%|█████████████████▊ | ETA: 0:00:04 Cross validating... 59%|██████████████████▊ | ETA: 0:00:04 Cross validating... 62%|███████████████████▊ | ETA: 0:00:03 Cross validating... 65%|████████████████████▉ | ETA: 0:00:03 Cross validating... 68%|█████████████████████▉ | ETA: 0:00:03 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:02 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:02 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:02 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:01 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:01 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:01 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:01 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:07 Crossvalidation Results: k MSE 0 463.67414218474244 1 392.9799734565893 2 350.10446235329886 3 326.6428223435793 4 308.87143096655643 5 307.31610941880024 6 299.7522491078746 7 294.72021071123845 8 303.5400260932095 9 303.7859712034749 10 297.9605195625713 11 307.98693949214356 12 301.31832009040613 13 305.46928091691893 14 326.24430463238207 15 317.95806299902415 16 318.8074558084246 17 319.70451312686663 18 343.1011215877161 19 328.61041446385696 20 336.31745230658214 Best k = 7 8.125929 seconds (16.89 M allocations: 393.822 MiB, 1.18% gc time, 31.50% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:03 Cross validating... 6%|██ | ETA: 0:00:04 Cross validating... 10%|███ | ETA: 0:00:04 Cross validating... 11%|███▌ | ETA: 0:00:05 Cross validating... 14%|████▋ | ETA: 0:00:05 Cross validating... 17%|█████▋ | ETA: 0:00:05 Cross validating... 21%|██████▋ | ETA: 0:00:04 Cross validating... 22%|███████▏ | ETA: 0:00:04 Cross validating... 24%|███████▋ | ETA: 0:00:04 Cross validating... 27%|████████▋ | ETA: 0:00:04 Cross validating... 30%|█████████▋ | ETA: 0:00:04 Cross validating... 33%|██████████▋ | ETA: 0:00:04 Cross validating... 37%|███████████▋ | ETA: 0:00:04 Cross validating... 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| ETA: 0:00:01 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:01 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:00 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:05 Crossvalidation Results: k MSE 0 463.67414218474244 1 394.44095659896834 2 352.65568914491035 3 330.19181387225956 4 313.1819062548317 5 313.458119345338 6 307.38265984242526 7 301.486491201245 8 313.26401177418967 9 312.2040629781171 10 318.66398725157075 11 323.2324963234816 12 325.76232070729026 13 341.75180872720955 14 342.8314750463696 15 348.3147977629741 16 349.5204461776479 17 358.22422351459335 18 360.21384022856193 19 381.84304320109874 20 374.9206449103908 Best k = 7 5.894274 seconds (16.89 M allocations: 346.624 MiB, 1.13% gc time, 1.17% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, logistic model | 2 2 14.5s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:44 Cross validating... 8%|██▌ | ETA: 0:00:19 Cross validating... 11%|███▌ | ETA: 0:00:14 Cross validating... 14%|████▋ | ETA: 0:00:11 Cross validating... 17%|█████▋ | ETA: 0:00:10 Cross validating... 21%|██████▋ | ETA: 0:00:08 Cross validating... 24%|███████▋ | ETA: 0:00:07 Cross validating... 27%|████████▋ | ETA: 0:00:07 Cross validating... 30%|█████████▋ | ETA: 0:00:06 Cross validating... 33%|██████████▋ | ETA: 0:00:06 Cross validating... 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: 0:00:04 Cross validating... 54%|█████████████████▎ | ETA: 0:00:03 Cross validating... 57%|██████████████████▎ | ETA: 0:00:03 Cross validating... 60%|███████████████████▎ | ETA: 0:00:03 Cross validating... 63%|████████████████████▍ | ETA: 0:00:02 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:02 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:02 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:02 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:01 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:01 Cross validating... 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 0 465.69976170829926 1 428.4858383285557 2 397.04764884685767 3 375.4033583515645 4 362.43346106951196 5 345.815808348288 6 334.7873522271582 7 329.04750383484486 8 333.17176599638685 9 329.1302680508875 10 326.3490317930758 11 334.6284465689526 12 332.47715900200524 13 340.2670894739905 14 354.74756457621226 15 339.0848478018656 16 351.6263245078935 17 343.00990129989907 18 348.0543716596609 19 421.7980169933345 20 366.578270584552 Best k = 10 6.916867 seconds (17.00 M allocations: 397.302 MiB, 6.46% gc time, 36.49% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:03 Cross validating... 6%|██ | ETA: 0:00:03 Cross validating... 10%|███ | ETA: 0:00:03 Cross validating... 13%|████▏ | ETA: 0:00:03 Cross validating... 16%|█████▏ | ETA: 0:00:03 Cross validating... 19%|██████▏ | ETA: 0:00:03 Cross validating... 22%|███████▏ | ETA: 0:00:03 Cross validating... 25%|████████▏ | ETA: 0:00:03 Cross validating... 29%|█████████▏ | ETA: 0:00:03 Cross validating... 32%|██████████▏ | ETA: 0:00:03 Cross validating... 35%|███████████▏ | ETA: 0:00:03 Cross validating... 38%|████████████▎ | ETA: 0:00:02 Cross validating... 41%|█████████████▎ | ETA: 0:00:02 Cross validating... 44%|██████████████▎ | ETA: 0:00:02 Cross validating... 48%|███████████████▎ | ETA: 0:00:02 Cross validating... 51%|████████████████▎ | ETA: 0:00:02 Cross validating... 54%|█████████████████▎ | ETA: 0:00:02 Cross validating... 57%|██████████████████▎ | ETA: 0:00:02 Cross validating... 60%|███████████████████▎ | ETA: 0:00:02 Cross validating... 63%|████████████████████▍ | ETA: 0:00:02 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:01 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:01 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:01 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:01 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:01 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:01 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:01 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:00 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:04 Crossvalidation Results: k MSE 0 465.69976170829926 1 428.78311693327123 2 399.31716348914347 3 377.08689384778427 4 364.93657156641245 5 348.4878579773326 6 339.0151624374286 7 338.5710737203895 8 350.99174106787075 9 349.7798369216147 10 358.93330735353953 11 363.48745121475974 12 371.3225751634452 13 376.2191096091548 14 391.4061302922597 15 392.78487464616614 16 396.699766262798 17 418.99205352194673 18 422.7123680676824 19 426.1569355534734 20 426.1765995981355 Best k = 7 4.197234 seconds (16.84 M allocations: 343.028 MiB, 1.49% gc time, 1.15% compilation time) Test Summary: | Pass Total Time Cross validation on Float64 matrix, logistic model | 2 2 12.0s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:58 Cross validating... 6%|██ | ETA: 0:00:31 Cross validating... 10%|███ | ETA: 0:00:21 Cross validating... 13%|████▏ | ETA: 0:00:17 Cross validating... 16%|█████▏ | ETA: 0:00:14 Cross validating... 17%|█████▋ | ETA: 0:00:13 Cross validating... 21%|██████▋ | ETA: 0:00:11 Cross validating... 22%|███████▏ | ETA: 0:00:11 Cross validating... 25%|████████▏ | ETA: 0:00:10 Cross validating... 29%|█████████▏ | ETA: 0:00:09 Cross validating... 32%|██████████▏ | ETA: 0:00:08 Cross validating... 33%|██████████▋ | ETA: 0:00:08 Cross validating... 37%|███████████▋ | ETA: 0:00:07 Cross validating... 40%|████████████▊ | ETA: 0:00:06 Cross validating... 43%|█████████████▊ | ETA: 0:00:06 Cross validating... 46%|██████████████▊ | ETA: 0:00:05 Cross validating... 49%|███████████████▊ | ETA: 0:00:05 Cross validating... 52%|████████████████▊ | ETA: 0:00:04 Cross validating... 56%|█████████████████▊ | ETA: 0:00:04 Cross validating... 59%|██████████████████▊ | ETA: 0:00:04 Cross validating... 62%|███████████████████▊ | ETA: 0:00:03 Cross validating... 65%|████████████████████▉ | ETA: 0:00:03 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:03 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:03 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:02 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:02 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:02 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:01 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:01 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:01 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:01 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:07 Crossvalidation Results: k MSE 0 541.0567600336295 1 464.0029606904823 2 423.84356122234516 3 400.074563728789 4 391.77697182596245 5 388.8216434394652 6 380.9418306137028 7 386.87188094106614 8 384.6654329269445 9 387.3282332425623 10 395.99049150283685 11 387.21547371969393 12 374.7196351321223 13 383.2820941881167 14 378.1411136219976 15 380.3278086723293 16 377.1053441236518 17 375.7313698805027 18 390.412558671187 19 382.2366149790453 20 386.97358498189675 Best k = 12 8.376740 seconds (16.66 M allocations: 410.837 MiB, 1.19% gc time, 29.57% 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: 0:00:05 Cross validating... 10%|███ | ETA: 0:00:05 Cross validating... 13%|████▏ | ETA: 0:00:05 Cross validating... 16%|█████▏ | ETA: 0:00:05 Cross validating... 19%|██████▏ | ETA: 0:00:05 Cross validating... 21%|██████▋ | ETA: 0:00:05 Cross validating... 24%|███████▋ | ETA: 0:00:05 Cross validating... 27%|████████▋ | 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%|████████████▎ | ETA: 0:00:04 Cross validating... 41%|█████████████▎ | ETA: 0:00:03 Cross validating... 44%|██████████████▎ | ETA: 0:00:03 Cross validating... 48%|███████████████▎ | ETA: 0:00:03 Cross validating... 51%|████████████████▎ | ETA: 0:00:03 Cross validating... 52%|████████████████▊ | ETA: 0:00:03 Cross validating... 56%|█████████████████▊ | ETA: 0:00:03 Cross validating... 59%|██████████████████▊ | ETA: 0:00:02 Cross validating... 62%|███████████████████▊ | ETA: 0:00:02 Cross validating... 63%|████████████████████▍ | ETA: 0:00:02 Cross validating... 65%|████████████████████▉ | ETA: 0:00:02 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:02 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:02 Cross validating... 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... 90%|█████████████████████████████ | ETA: 0:00:01 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:05 Crossvalidation Results: k MSE 0 541.0567600336295 1 464.32031040789195 2 424.95267033822074 3 402.28783923192 4 395.9186894855181 5 390.4752010755692 6 388.53276669679735 7 395.9102791861029 8 402.96926356219905 9 400.821070784265 10 415.58576887486527 11 412.11075290322657 12 416.83922287974275 13 423.0296632842175 14 402.95663821911864 15 409.6379957858216 16 403.04282598593807 17 406.44508149960916 18 440.69420565868876 19 420.1611252638205 20 434.2859866107863 Best k = 6 5.976594 seconds (16.25 M allocations: 340.757 MiB, 1.26% gc time, 0.41% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, Poisson model | 2 2 14.8s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:59 Cross validating... 6%|██ | ETA: 0:00:45 Cross validating... 8%|██▌ | ETA: 0:00:47 Cross validating... 10%|███ | ETA: 0:00:49 Cross validating... 11%|███▌ | ETA: 0:00:42 Cross validating... 13%|████▏ | ETA: 0:00:43 Cross validating... 14%|████▋ | ETA: 0:00:44 Cross validating... 16%|█████▏ | ETA: 0:00:45 Cross validating... 17%|█████▋ | ETA: 0:00:45 Cross validating... 19%|██████▏ | ETA: 0:00:45 Cross validating... 21%|██████▋ | ETA: 0:00:45 Cross validating... 22%|███████▏ | ETA: 0:00:45 Cross validating... 24%|███████▋ | ETA: 0:00:42 Cross validating... 25%|████████▏ | ETA: 0:00:41 Cross validating... 27%|████████▋ | ETA: 0:00:41 Cross validating... 29%|█████████▏ | ETA: 0:00:40 Cross validating... 30%|█████████▋ | ETA: 0:00:40 Cross validating... 32%|██████████▏ | ETA: 0:00:39 Cross validating... 33%|██████████▋ | ETA: 0:00:39 Cross validating... 37%|███████████▋ | ETA: 0:00:34 Cross validating... 40%|████████████▊ | ETA: 0:00:30 Cross validating... 43%|█████████████▊ | ETA: 0:00:28 Cross validating... 44%|██████████████▎ | ETA: 0:00:27 Cross validating... 46%|██████████████▊ | ETA: 0:00:27 Cross validating... 48%|███████████████▎ | ETA: 0:00:25 Cross validating... 49%|███████████████▊ | ETA: 0:00:25 Cross validating... 51%|████████████████▎ | ETA: 0:00:25 Cross validating... 52%|████████████████▊ | ETA: 0:00:24 Cross validating... 54%|█████████████████▎ | ETA: 0:00:23 Cross validating... 56%|█████████████████▊ | ETA: 0:00:23 Cross validating... 57%|██████████████████▎ | ETA: 0:00:22 Cross validating... 59%|██████████████████▊ | ETA: 0:00:22 Cross validating... 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92%|█████████████████████████████▌ | ETA: 0:00:04 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:03 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:02 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:02 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:01 Cross validating... 100%|████████████████████████████████| Time: 0:00:49 Crossvalidation Results: k MSE 0 302.01736473505645 1 271.4198488541168 2 251.3465260654839 3 246.07420382309218 4 239.08515531303863 5 239.31745824710347 6 238.22022225338355 7 236.2549255352872 8 235.75028509720073 9 236.91810338678692 10 239.39221314010723 11 238.11964531134595 12 239.85730287471335 13 241.60350621476948 14 242.9422801864347 15 240.5121194780492 16 244.92264368188995 17 240.76002240464857 18 241.72031651050975 19 244.6821385106319 20 242.04797003555984 Best k = 8 49.812219 seconds (151.61 M allocations: 3.874 GiB, 1.27% gc time, 4.49% 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: 0:00:06 Cross validating... 8%|██▌ | ETA: 0:00:07 Cross validating... 10%|███ | ETA: 0:00:07 Cross validating... 11%|███▌ | ETA: 0:00:08 Cross validating... 13%|████▏ | ETA: 0:00:08 Cross validating... 14%|████▋ | ETA: 0:00:09 Cross validating... 16%|█████▏ | ETA: 0:00:09 Cross validating... 17%|█████▋ | ETA: 0:00:10 Cross validating... 19%|██████▏ | ETA: 0:00:10 Cross validating... 21%|██████▋ | ETA: 0:00:10 Cross validating... 22%|███████▏ | ETA: 0:00:10 Cross validating... 24%|███████▋ | ETA: 0:00:10 Cross validating... 25%|████████▏ | ETA: 0:00:10 Cross validating... 27%|████████▋ | ETA: 0:00:10 Cross validating... 29%|█████████▏ | ETA: 0:00:10 Cross validating... 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62%|███████████████████▊ | ETA: 0:00:05 Cross validating... 63%|████████████████████▍ | ETA: 0:00:04 Cross validating... 65%|████████████████████▉ | ETA: 0:00:04 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:04 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:04 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:03 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:03 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:02 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:02 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:02 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:02 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:02 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:02 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:01 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:01 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:01 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:01 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:01 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:01 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:11 Crossvalidation Results: k MSE 0 302.01736473505645 1 271.381116082719 2 251.66127395208736 3 247.50029513833096 4 241.3419374973706 5 244.6527190500264 6 241.7040269206377 7 238.63326619041723 8 239.6812317752704 9 247.20976795872946 10 248.82734252245774 11 250.1278779759907 12 251.73191039471806 13 254.71928203641775 14 260.1372283799118 15 261.984085441303 16 266.60824500132185 17 276.5907323235424 18 275.3374236677757 19 278.8497627742048 20 274.081898079835 Best k = 7 11.931115 seconds (35.26 M allocations: 733.605 MiB, 1.14% gc time, 0.71% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, NegativeBinomial model | 2 2 1m02.2s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:01:09 Cross validating... 6%|██ | ETA: 0:00:35 Cross validating... 10%|███ | ETA: 0:00:23 Cross validating... 14%|████▋ | ETA: 0:00:16 Cross validating... 17%|█████▋ | ETA: 0:00:13 Cross validating... 22%|███████▏ | ETA: 0:00:10 Cross validating... 25%|████████▏ | ETA: 0:00:09 Cross validating... 29%|█████████▏ | ETA: 0:00:08 Cross validating... 32%|██████████▏ | ETA: 0:00:07 Cross validating... 37%|███████████▋ | ETA: 0:00:06 Cross validating... 40%|████████████▊ | ETA: 0:00:05 Cross validating... 43%|█████████████▊ | ETA: 0:00:05 Cross validating... 48%|███████████████▎ | 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... 67%|█████████████████████▍ | ETA: 0:00:02 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:02 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:01 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:01 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:01 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:01 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:05 Crossvalidation Results: k MSE 0 708.7406597900391 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 6.137034 seconds (17.22 M allocations: 343.612 MiB, 1.32% gc time, 46.80% 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... 19%|██████▏ | ETA: 0:00:03 Cross validating... 22%|███████▏ | ETA: 0:00:02 Cross 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validating... 89%|████████████████████████████▌ | ETA: 0:00:00 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:03 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 3.301469 seconds (16.26 M allocations: 288.221 MiB, 2.66% gc time, 1.06% compilation time) Test Summary: | Pass Total Time Cross validation on floating point matrices, NegativeBinomial model | 2 2 10.0s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 2%|▋ | ETA: 0:01:14 Cross validating... 3%|█ | ETA: 0:00:52 Cross validating... 4%|█▎ | ETA: 0:00:41 Cross validating... 5%|█▋ | ETA: 0:00:35 Cross validating... 6%|█▉ | ETA: 0:00:31 Cross validating... 7%|██▎ | ETA: 0:00:28 Cross validating... 8%|██▌ | ETA: 0:00:27 Cross validating... 9%|██▉ | ETA: 0:00:26 Cross validating... 10%|███▎ | ETA: 0:00:24 Cross validating... 11%|███▌ | ETA: 0:00:23 Cross validating... 12%|███▉ | ETA: 0:00:23 Cross validating... 13%|████▏ | ETA: 0:00:22 Cross validating... 14%|████▌ | ETA: 0:00:21 Cross validating... 15%|████▊ | ETA: 0:00:21 Cross validating... 16%|█████▏ | ETA: 0:00:20 Cross validating... 17%|█████▌ | ETA: 0:00:20 Cross validating... 18%|█████▊ | ETA: 0:00:19 Cross validating... 19%|██████▏ | ETA: 0:00:19 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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 4287.860446754629 2 4042.395160337511 3 3768.060553039619 4 3625.9647707414833 5 3669.250267137992 6 3675.7509882323643 7 3701.2297882960074 8 3726.465631115726 9 3707.2358990959206 10 3754.9694037440577 11 3774.071206674641 12 3808.471799971858 13 3833.404197767929 14 3857.98598758415 15 3938.6994965720414 16 3946.3953144758852 17 4015.821858672148 18 4065.345312250066 19 4061.254203634858 20 4087.83087022796 Best k = 4 17.452486 seconds (312.00 k allocations: 217.881 MiB, 0.57% gc time, 9.17% compilation time) Test Summary: | Pass Total Time multivariate cross validation SnpLinAlg | 3 3 22.0s Test Summary: | Pass Total Time wrapper univariate | 20 20 1m59.0s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 2%|▋ | ETA: 0:00:10 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: 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94%|██████████████████████████████▏ | ETA: 0:00:01 Cross validating... 95%|██████████████████████████████▍ | ETA: 0:00:01 Cross validating... 96%|██████████████████████████████▊ | ETA: 0:00:01 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:01 Cross validating... 98%|███████████████████████████████▍| ETA: 0:00:00 Cross validating... 99%|███████████████████████████████▋| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:23 Crossvalidation Results: k MSE 1 2838.788679198002 2 2514.3973428708136 3 2305.6176519676274 4 2222.025304867614 5 2075.1670384588365 6 2067.7948989723845 7 2053.427506114907 8 2086.405384830965 9 2080.984460901671 10 2105.131199502364 11 2132.407165368786 12 2138.267187460652 13 2166.002210829576 14 2194.9918295115804 15 2189.890403738045 16 2191.181293229578 17 2209.4669750564362 18 2221.2595493644303 19 2238.7425945763257 20 2253.9559571797727 Best k = 7 **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 2%|▋ | ETA: 0:00:10 Cross validating... 3%|█ | ETA: 0:00:10 Cross validating... 4%|█▎ | ETA: 0:00:11 Cross validating... 5%|█▋ | ETA: 0:00:10 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: 0:00:15 Cross validating... 12%|███▉ | ETA: 0:00:16 Cross validating... 13%|████▏ | ETA: 0:00:16 Cross validating... 14%|████▌ | ETA: 0:00:16 Cross validating... 15%|████▊ | ETA: 0:00:17 Cross validating... 16%|█████▏ | ETA: 0:00:18 Cross validating... 17%|█████▌ | ETA: 0:00:18 Cross validating... 18%|█████▊ | ETA: 0:00:18 Cross validating... 19%|██████▏ | ETA: 0:00:18 Cross validating... 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2053.427506114907 8 2086.405384830965 9 2080.984460901671 10 2105.131199502364 11 2132.407165368786 12 2138.267187460652 13 2166.002210829576 14 2194.9918295115804 15 2189.890403738045 16 2191.181293229578 17 2209.4669750564362 18 2221.2595493644303 19 2238.7425945763257 20 2253.9559571797727 Best k = 7 **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 2%|▋ | ETA: 0:00:10 Cross validating... 3%|█ | ETA: 0:00:10 Cross validating... 4%|█▎ | ETA: 0:00:11 Cross validating... 5%|█▋ | ETA: 0:00:10 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: 0:00:15 Cross validating... 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ETA: 0:00:04 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:04 Cross validating... 85%|███████████████████████████▎ | ETA: 0:00:03 Cross validating... 86%|███████████████████████████▌ | ETA: 0:00:03 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:03 Cross validating... 88%|████████████████████████████▏ | ETA: 0:00:03 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:02 Cross validating... 90%|████████████████████████████▊ | ETA: 0:00:02 Cross validating... 91%|█████████████████████████████▏ | ETA: 0:00:02 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:02 Cross validating... 93%|█████████████████████████████▊ | ETA: 0:00:02 Cross validating... 94%|██████████████████████████████▏ | ETA: 0:00:01 Cross validating... 95%|██████████████████████████████▍ | ETA: 0:00:01 Cross validating... 96%|██████████████████████████████▊ | ETA: 0:00:01 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:01 Cross validating... 98%|███████████████████████████████▍| ETA: 0:00:00 Cross validating... 99%|███████████████████████████████▋| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:23 Crossvalidation Results: k MSE 1 2838.788679198002 2 2514.3973428708136 3 2305.6176519676274 4 2222.025304867614 5 2075.1670384588365 6 2067.7948989723845 7 2053.427506114907 8 2086.405384830965 9 2080.984460901671 10 2105.131199502364 11 2132.407165368786 12 2138.267187460652 13 2166.002210829576 14 2194.9918295115804 15 2189.890403738045 16 2191.181293229578 17 2209.4669750564362 18 2221.2595493644303 19 2238.7425945763257 20 2253.9559571797727 Best k = 7 Test Summary: | Pass Total Time wrapper multivariate | 8 8 1m24.9s read BGEN and VCF: Error During Test at /home/pkgeval/.julia/packages/MendelIHT/ZcxZT/test/wrapper_test.jl:184 Got exception outside of a @test startproc must be called before process Stacktrace: [1] error(s::String) @ Base error.jl:56 [2] process(codec::CodecZlib.ZlibDecompressor, input::TranscodingStreams.Memory, output::TranscodingStreams.Memory, error_ref::TranscodingStreams.Error) @ CodecZlib ~/.julia/packages/CodecZlib/lEc2s/src/decompression.jl:186 [3] decompress(io::IOStream, v::Variant, h::BGEN.Header; decompressed::Nothing) @ BGEN ~/.julia/packages/BGEN/dfgRU/src/genotypes.jl:72 [4] first_allele_dosage!(b::Bgen, v::Variant; T::Core.TypeEgal{Float64}, mean_impute::Bool, clear_decompressed::Bool, data::Nothing, decompressed::Nothing, is_decompressed::Bool) @ BGEN ~/.julia/packages/BGEN/dfgRU/src/genotypes.jl:571 [5] convert_bgen_gt(t::Core.TypeEgal{Float64}, b::Bgen) @ MendelIHT ~/.julia/packages/MendelIHT/ZcxZT/src/wrapper.jl:380 [6] macro expansion @ ./timing.jl:741 [inlined] [7] macro expansion @ ~/.julia/packages/MendelIHT/ZcxZT/test/wrapper_test.jl:187 [inlined] [8] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:2246 [inlined] [9] top-level scope @ ~/.julia/packages/MendelIHT/ZcxZT/test/wrapper_test.jl:185 [10] include(mapexpr::Function, mod::Module, _path::String) @ Base Base.jl:326 [11] top-level scope @ ~/.julia/packages/MendelIHT/ZcxZT/test/runtests.jl:20 [12] include(mapexpr::Function, mod::Module, _path::String) @ Base Base.jl:326 [13] top-level scope @ none:6 [14] eval(m::Module, e::Any) @ Core boot.jl:545 [15] exec_options(opts::Base.JLOptions) @ Base client.jl:321 [16] _start() @ Base client.jl:596 Test Summary: | Error Total Time read BGEN and VCF | 1 1 3.4s RNG of the outermost testset: Xoshiro(0x46b7f733f5ef7c1d, 0x2a2d1748a75e81e5, 0x21d353cd6b26248b, 0x0333d34f2bdc52b7, 0x84caa73b36cffb84) 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 1088.51s ERROR: LoadError: Package MendelIHT errored during testing Stacktrace: [1] pkgerror(msg::String) @ Pkg.Types /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Types.jl:68 [2] test(ctx::Pkg.Types.Context, pkgs::Vector{PackageSpec}; coverage::Bool, julia_args::Cmd, test_args::Cmd, test_fn::Nothing, force_latest_compatible_version::Bool, allow_earlier_backwards_compatible_versions::Bool, allow_reresolve::Bool) @ Pkg.Operations /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Operations.jl:3247 [3] test(ctx::Pkg.Types.Context, pkgs::Vector{PackageSpec}; coverage::Bool, test_fn::Nothing, julia_args::Cmd, test_args::Cmd, force_latest_compatible_version::Bool, allow_earlier_backwards_compatible_versions::Bool, allow_reresolve::Bool, kwargs::@Kwargs{io::IOContext{IO}}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:587 [4] test(pkgs::Vector{PackageSpec}; io::IOContext{IO}, kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:172 [5] test(pkgs::Vector{String}; kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:160 [6] test(pkg::String; kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:159 [inlined] [7] top-level scope @ /PkgEval.jl/scripts/evaluate.jl:223 [8] include(mod::Module, _path::String) @ Base Base.jl:325 [9] exec_options(opts::Base.JLOptions) @ Base client.jl:355 [10] _start() @ Base client.jl:596 in expression starting at /PkgEval.jl/scripts/evaluate.jl:214 PkgEval failed after 1207.25s: package tests unexpectedly errored