Package evaluation to test MendelIHT on Julia 1.14.0-DEV.2621 (b841d233e9*) started at 2026-07-10T02:12:15.237 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.14` Set-up completed after 15.03s ################################################################################ # 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 v0.2.9 [f70d9fcc] + CommonWorldInvalidations v1.1.0 [34da2185] + Compat v4.18.1 [a33af91c] + CompositionsBase v0.1.2 [187b0558] + ConstructionBase v1.6.0 [adafc99b] + CpuId v0.3.1 [a8cc5b0e] + Crayons v4.1.1 [a10d1c49] + DBInterface v2.6.1 [9a962f9c] + 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[efcefdf7] + PCRE2_jll v10.47.0+0 [bea87d4a] + SuiteSparse_jll v7.10.1+0 [83775a58] + Zlib_jll v1.3.2+0 [3161d3a3] + Zstd_jll v1.5.7+1 [8e850b90] + libblastrampoline_jll v5.15.0+0 [8e850ede] + nghttp2_jll v1.69.0+0 [3f19e933] + p7zip_jll v17.8.0+0 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. To see why use `status --outdated -m` Installation completed after 5.66s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompiling project... 4.4 s ✓ BGEN 7.2 s ✓ VCFTools 26.4 s ✓ SnpArrays 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`. 22.3 s ✓ MendelIHT 4 dependencies successfully precompiled in 63 seconds. 172 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 91.15s ################################################################################ # Testing # Testing MendelIHT Status `/tmp/jl_bqeIu4/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 16.4s Test Summary: | Pass Total Time deviance | 1 1 0.4s Test Summary: | Pass Total Time update_μ! | 4 4 1.5s Test Summary: | Pass Total Time _choose! | 7 7 10.1s Test Summary: | Pass Total Time _iht_backtrack | 7 7 0.0s Test Summary: | Pass Total Time standardize! | 12 12 1.3s Test Summary: | Pass Total Time project_k! | 2 2 1.0s Test Summary: | Pass Total Time project_group_sparse! | 5 5 1.2s Test Summary: | Pass Total Time maf_weights | 6 6 2.2s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse 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 = -1825.9263832880054, backtracks = 0, tol = 2.074836226943322 Iteration 2: loglikelihood = -1475.6902822776897, backtracks = 0, tol = 0.15796737376821088 Iteration 3: loglikelihood = -1414.269081415918, backtracks = 0, tol = 0.05786452662642087 Iteration 4: loglikelihood = -1409.18071811543, backtracks = 0, tol = 0.03253570299174362 Iteration 5: loglikelihood = -1409.0236160991371, backtracks = 0, tol = 0.0027796305459736443 Iteration 6: loglikelihood = -1408.5939073751147, backtracks = 0, tol = 0.032199687208337165 Iteration 7: loglikelihood = -1408.5406650137668, backtracks = 0, tol = 0.0014965988509836115 Iteration 8: loglikelihood = -1408.540081140762, backtracks = 0, tol = 0.0001511204641473127 Iteration 9: loglikelihood = -1408.5400727106796, backtracks = 0, tol = 1.946103366696256e-5 IHT estimated 10 nonzero SNP predictors and 1 non-genetic predictors. Compute time (sec): 0.07480192184448242 Final loglikelihood: -1408.5400727106796 SNP PVE: 0.9448736144041078 Iterations: 9 Selected genetic predictors: 10×2 DataFrame Row │ Position Estimated_β │ Int64 Float64 ─────┼─────────────────────── 1 │ 4041 1.1753 2 │ 5471 0.930095 3 │ 5801 -0.119767 4 │ 6860 -0.706145 5 │ 7833 0.157248 6 │ 8737 -0.337288 7 │ 8917 1.96124 8 │ 9204 2.55034 9 │ 9440 -0.436316 10 │ 9878 1.88287 Selected nongenetic predictors: 1×2 DataFrame Row │ Position Estimated_β │ Int64 Float64 ─────┼─────────────────────── 1 │ 1 0.0448776Test Summary: | Pass Total Time fit normal SnpLinAlg | 4 4 24.2s **** 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 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 4.0s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse Poisson regression Number of threads = 1 Link functin = LogLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -3156.488075063946, backtracks = 0, tol = 0.35936258328828374 Iteration 2: loglikelihood = -2155.5650059242294, backtracks = 0, tol = 0.05321291178140196 Iteration 3: loglikelihood = -1623.076470299319, backtracks = 0, tol = 0.04886567771468436 Iteration 4: loglikelihood = -1478.9985790519734, backtracks = 0, tol = 0.0614709501634984 Iteration 5: loglikelihood = -1380.4932347543975, backtracks = 0, tol = 0.1435158843930312 Iteration 6: loglikelihood = -1369.1596351611204, backtracks = 0, tol = 0.0669089913747691 Iteration 7: loglikelihood = -1352.908210457403, backtracks = 0, tol = 0.02589009205896323 Iteration 8: loglikelihood = -1345.197717071163, backtracks = 0, tol = 0.05697430822312238 Iteration 9: loglikelihood = -1336.8283796098617, backtracks = 0, tol = 0.056302974785446644 Iteration 10: loglikelihood = -1333.672727939807, backtracks = 0, tol = 0.014889623371858809 Iteration 11: loglikelihood = -1332.2375600362554, backtracks = 0, tol = 0.012899398000842595 Iteration 12: loglikelihood = -1331.3351874707514, backtracks = 0, tol = 0.00799695553012234 Iteration 13: loglikelihood = -1330.7713442872073, backtracks = 0, tol = 0.007995318493812026 Iteration 14: loglikelihood = -1330.4930409071249, backtracks = 1, tol = 0.002584491139221689 Iteration 15: loglikelihood = -1330.2551872974332, backtracks = 2, tol = 0.0046858068260417175 Iteration 16: loglikelihood = -1330.0888445481908, backtracks = 2, tol = 0.0032471381226942247 Iteration 17: loglikelihood = -1329.980584023167, backtracks = 2, tol = 0.003200418414618757 Iteration 18: loglikelihood = -1329.9083370227631, backtracks = 2, tol = 0.0021132430485622587 Iteration 19: loglikelihood = -1329.8604347832445, backtracks = 2, tol = 0.0021273160686868576 Iteration 20: loglikelihood = -1329.8284229547983, backtracks = 2, tol = 0.0014011389091327818 Iteration 21: loglikelihood = -1329.8070999194451, backtracks = 2, tol = 0.001418155420036804 Iteration 22: loglikelihood = -1329.7928239450923, backtracks = 2, tol = 0.000933360782019526 Iteration 23: loglikelihood = -1329.783287939223, backtracks = 2, tol = 0.0009478498985267736 Iteration 24: loglikelihood = -1329.7768958236777, backtracks = 2, tol = 0.0006235209013188224 Iteration 25: loglikelihood = -1329.7726180207646, backtracks = 2, tol = 0.0006346072104139709 Iteration 26: loglikelihood = -1329.769748343615, backtracks = 2, tol = 0.00041731580604238727 Iteration 27: loglikelihood = -1329.7678254386685, backtracks = 2, tol = 0.00042536919903454805 Iteration 28: loglikelihood = -1329.7665348529817, backtracks = 2, tol = 0.000279653192353537 Iteration 29: loglikelihood = -1329.7656693252507, backtracks = 2, tol = 0.00028533563625367356 Iteration 30: loglikelihood = -1329.7650882236164, backtracks = 2, tol = 0.00018755836777185488 Iteration 31: loglikelihood = -1329.7646982862657, backtracks = 2, tol = 0.00019149838636103267 Iteration 32: loglikelihood = -1329.76443643192, backtracks = 2, tol = 0.00012586220678170197 Iteration 33: loglikelihood = -1329.7642606517952, backtracks = 2, tol = 0.00012856435903655272 Iteration 34: loglikelihood = -1329.7641425933612, backtracks = 2, tol = 8.449220473413599e-5 Test Summary: | Pass Total Time fit Poisson SnpLinAlg | 4 4 3.3s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** 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 = -1661.6259769937549, backtracks = 0, tol = 0.35346051873351103 Iteration 2: loglikelihood = -1545.8240064969386, backtracks = 0, tol = 0.21798833967029382 Iteration 3: loglikelihood = -1513.2146274711029, backtracks = 0, tol = 0.14144791916352215 Iteration 4: loglikelihood = -1506.6233036872986, backtracks = 0, tol = 0.07372237304209783 Iteration 5: loglikelihood = -1502.3412401997693, backtracks = 0, tol = 0.06816217418925753 Iteration 6: loglikelihood = -1499.7002466998842, backtracks = 0, tol = 0.07477714476637078 Iteration 7: loglikelihood = -1499.3128769067853, backtracks = 0, tol = 0.012487563207221039 Iteration 8: loglikelihood = -1499.2789794541557, backtracks = 1, tol = 0.0024036530064313246 Iteration 9: loglikelihood = -1499.264259391416, backtracks = 1, tol = 0.00207835205389891 Iteration 10: loglikelihood = -1499.2595955599622, backtracks = 1, tol = 0.0013449882435216777 Iteration 11: loglikelihood = -1499.258327555009, backtracks = 1, tol = 0.0006779742586526691 Iteration 12: loglikelihood = -1499.2579844726938, backtracks = 1, tol = 0.00036791827957101506 Iteration 13: loglikelihood = -1499.2578926963454, backtracks = 1, tol = 0.00018425348980616172 Iteration 14: loglikelihood = -1499.2578679986761, backtracks = 1, tol = 9.819304002193576e-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 = -1773.0454916109732, backtracks = 0, tol = 0.8638940808373208 Iteration 2: loglikelihood = -1446.6181488375066, backtracks = 0, tol = 0.11962824194705125 Iteration 3: loglikelihood = -1391.9691555128004, backtracks = 0, tol = 0.040635393852470766 Iteration 4: loglikelihood = -1389.1780654194822, backtracks = 0, tol = 0.027487284483873792 Iteration 5: loglikelihood = -1389.095998587373, backtracks = 1, tol = 0.0009313893442603021 Iteration 6: loglikelihood = -1389.0750263658153, backtracks = 1, tol = 0.00043657085753491683 Iteration 7: loglikelihood = -1389.0696841532085, backtracks = 1, tol = 0.0002043503444164925 Iteration 8: loglikelihood = -1389.0683275107713, backtracks = 1, tol = 9.95289228693836e-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 = -1624.7807113803399, backtracks = 0, tol = 0.48126746864006914 Iteration 2: loglikelihood = -1423.0638312628594, backtracks = 0, tol = 0.09622739051650409 Iteration 3: loglikelihood = -1390.4718545260666, backtracks = 0, tol = 0.038780804747421516 Iteration 4: loglikelihood = -1390.1744679278277, backtracks = 0, tol = 0.003148849795007747 Iteration 5: loglikelihood = -1390.173336805657, backtracks = 0, tol = 0.0001869365518598562 Iteration 6: loglikelihood = -1390.1733296813916, backtracks = 0, tol = 1.5580570438400922e-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 = -1555.3223644139696, backtracks = 0, tol = 0.21433253596041632 Iteration 2: loglikelihood = -1484.424708949294, backtracks = 0, tol = 0.11572418520433408 Iteration 3: loglikelihood = -1448.6870854449057, backtracks = 0, tol = 0.21702508823537656 Iteration 4: loglikelihood = -1389.5607702247923, backtracks = 0, tol = 0.14121118338808833 Iteration 5: loglikelihood = -1368.5804268837805, backtracks = 0, tol = 0.08341345859511787 Iteration 6: loglikelihood = -1351.3035814455918, backtracks = 0, tol = 0.05678493481791416 Iteration 7: loglikelihood = -1341.309920018483, backtracks = 0, tol = 0.06497332433809391 Iteration 8: loglikelihood = -1340.5070732046233, backtracks = 0, tol = 0.01376929166399182 Iteration 9: loglikelihood = -1340.188207178899, backtracks = 0, tol = 0.00620370411936553 Iteration 10: loglikelihood = -1340.0431056777957, backtracks = 0, tol = 0.006801371429965065 Iteration 11: loglikelihood = -1339.9710079900217, backtracks = 0, tol = 0.0029532770183780246 Iteration 12: loglikelihood = -1339.9348009484677, backtracks = 0, tol = 0.003418672576509613 Iteration 13: loglikelihood = -1339.9164254101154, backtracks = 0, tol = 0.0014933552366894573 Iteration 14: loglikelihood = -1339.9071082718888, backtracks = 0, tol = 0.0017214474047052113 Iteration 15: loglikelihood = -1339.9023833629547, backtracks = 0, tol = 0.0007561379852389101 Iteration 16: loglikelihood = -1339.8999888842654, backtracks = 0, tol = 0.0008671595084108633 Iteration 17: loglikelihood = -1339.8987776594192, backtracks = 0, tol = 0.00038752475127075994 Iteration 18: loglikelihood = -1339.8981648707531, backtracks = 0, tol = 0.0004365468051273734 Iteration 19: loglikelihood = -1339.8978556243858, backtracks = 0, tol = 0.00019710983218152714 Iteration 20: loglikelihood = -1339.8976994488098, backtracks = 0, tol = 0.00021950657957977746 Iteration 21: loglikelihood = -1339.8976208000731, backtracks = 0, tol = 9.978540995783997e-5 1.035806 seconds (1.76 M allocations: 37.653 MiB, 8.58% gc time, 71.05% 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 = -1578.4371904008901, backtracks = 0, tol = 0.21433253596041632 Iteration 2: loglikelihood = -1526.313680038939, backtracks = 0, tol = 0.13397461491234647 Iteration 3: loglikelihood = -1474.1629318492805, backtracks = 0, tol = 0.1628589378293295 Iteration 4: loglikelihood = -1458.169715010266, backtracks = 0, tol = 0.11162176616100497 Iteration 5: loglikelihood = -1432.071776231883, backtracks = 0, tol = 0.07794854849649083 Iteration 6: loglikelihood = -1415.9674283693344, backtracks = 0, tol = 0.06972736107341128 Iteration 7: loglikelihood = -1405.840901733289, backtracks = 0, tol = 0.07508334809179185 Iteration 8: loglikelihood = -1398.1581924709483, backtracks = 0, tol = 0.0840511349182097 Iteration 9: loglikelihood = -1391.7445468818057, backtracks = 0, tol = 0.010050647967268955 Iteration 10: loglikelihood = -1386.4176977820387, backtracks = 0, tol = 0.0017006637702913292 Iteration 11: loglikelihood = -1381.9683817292882, backtracks = 0, tol = 0.0007276245894591596 Iteration 12: loglikelihood = -1378.1408059879716, backtracks = 0, tol = 0.0006545924859238451 Iteration 13: loglikelihood = -1375.2204776999495, backtracks = 0, tol = 0.07447466056539735 Iteration 14: loglikelihood = -1372.1106564638449, backtracks = 0, tol = 0.07447171946117218 Iteration 15: loglikelihood = -1369.516615916089, backtracks = 0, tol = 0.004485721689652526 Iteration 16: loglikelihood = -1367.3306253142534, backtracks = 0, tol = 0.0004952024139924284 Iteration 17: loglikelihood = -1365.3709498175008, backtracks = 0, tol = 0.0005484309238355396 Iteration 18: loglikelihood = -1363.63504238527, backtracks = 0, tol = 0.0005421076631903349 Iteration 19: loglikelihood = -1362.0705811835624, backtracks = 0, tol = 0.00037239425134601205 Iteration 20: loglikelihood = -1361.2534205729241, backtracks = 0, tol = 0.07244483258168913 Iteration 21: loglikelihood = -1359.483968046555, backtracks = 0, tol = 0.07244506237077754 Iteration 22: loglikelihood = -1358.2594975202232, backtracks = 0, tol = 0.004620811180908753 Iteration 23: loglikelihood = -1357.2220354194092, backtracks = 0, tol = 0.0004450466881043897 Iteration 24: loglikelihood = -1356.2621838794873, backtracks = 0, tol = 0.00026289680054717823 Iteration 25: loglikelihood = -1355.3866167839167, backtracks = 0, tol = 0.0003342080063410898 Iteration 26: loglikelihood = -1354.576934559941, backtracks = 0, tol = 0.000227201456747473 Iteration 27: loglikelihood = -1353.8345694749892, backtracks = 0, tol = 0.0002507031646840018 Iteration 28: loglikelihood = -1353.145283100281, backtracks = 0, tol = 0.00020749908015977252 Iteration 29: loglikelihood = -1352.5103702296742, backtracks = 0, tol = 0.0002213927843200231 Iteration 30: loglikelihood = -1351.9183561378575, backtracks = 0, tol = 0.000187796541077937 Iteration 31: loglikelihood = -1351.3708122616022, backtracks = 0, tol = 0.00019851087789994856 Iteration 32: loglikelihood = -1350.8582313606828, backtracks = 0, tol = 0.0001703811361000259 Iteration 33: loglikelihood = -1350.3824445820417, backtracks = 0, tol = 0.0001794500032776215 Iteration 34: loglikelihood = -1349.935422800395, backtracks = 0, tol = 0.00015531556695529196 Iteration 35: loglikelihood = -1349.5191605302741, backtracks = 0, tol = 0.00016322003386318992 Iteration 36: loglikelihood = -1349.126781190468, backtracks = 0, tol = 0.00014227928250574786 Iteration 37: loglikelihood = -1348.7603536994352, backtracks = 0, tol = 0.0001492043009651128 Iteration 38: loglikelihood = -1348.4139248397285, backtracks = 0, tol = 0.00013093618655230952 Iteration 39: loglikelihood = -1348.0895717297235, backtracks = 0, tol = 0.00013697579365481137 Iteration 40: loglikelihood = -1347.782095785963, backtracks = 0, tol = 0.00012100027401887081 Iteration 41: loglikelihood = -1347.4935372691668, backtracks = 0, tol = 0.0001262215115481038 Iteration 42: loglikelihood = -1347.2193236278338, backtracks = 0, tol = 0.00011223960524081596 Iteration 43: loglikelihood = -1346.961429466782, backtracks = 0, tol = 0.0001167027262250369 Iteration 44: loglikelihood = -1346.7158076957223, backtracks = 0, tol = 0.00010446789443495309 Iteration 45: loglikelihood = -1346.484350083971, backtracks = 0, tol = 0.00010823165675751689 Iteration 46: loglikelihood = -1346.2634548444541, backtracks = 0, tol = 9.753500260743004e-5 0.439274 seconds (1.70 M allocations: 30.641 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 = -3776.302, backtracks = 0, tol = 0.09173687406348396 Iteration 2: loglikelihood = -3727.789, backtracks = 0, tol = 0.04035899276466378 Iteration 3: loglikelihood = -3724.6392, backtracks = 1, tol = 0.012430228558142678 Iteration 4: loglikelihood = -3687.5457, backtracks = 1, tol = 0.06511851782734454 Iteration 5: loglikelihood = -3680.9329, backtracks = 0, tol = 0.013723127650402912 Iteration 6: loglikelihood = -3679.8374, backtracks = 0, tol = 0.010930800559713098 Iteration 7: loglikelihood = -3679.6738, backtracks = 1, tol = 0.0010920915198735321 Iteration 8: loglikelihood = -3679.595, backtracks = 1, tol = 0.0015399594564346499 Iteration 9: loglikelihood = -3679.574, backtracks = 1, tol = 0.0011459153312743222 Iteration 10: loglikelihood = -3679.5735, backtracks = 1, tol = 0.0005295430408369001 Iteration 11: loglikelihood = -3679.5696, backtracks = 1, tol = 0.00028979333478730654 Iteration 12: loglikelihood = -3679.5688, backtracks = 2, tol = 6.950706395301867e-5 25.715867 seconds (13.73 M allocations: 651.684 MiB, 0.89% gc time, 98.17% 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 = -3652.8462, backtracks = 0, tol = 0.09173687406348396 Iteration 2: loglikelihood = -3520.1846, backtracks = 0, tol = 0.04176201303985401 Iteration 3: loglikelihood = -3290.2717, backtracks = 1, tol = 0.011889198860456746 Iteration 4: loglikelihood = -3005.205, backtracks = 1, tol = 0.006079690734218737 Iteration 5: loglikelihood = -2924.9026, backtracks = 0, tol = 0.09619763271180115 Iteration 6: loglikelihood = -2725.998, backtracks = 0, tol = 0.0967559088707616 Iteration 7: loglikelihood = -2570.4927, backtracks = 0, tol = 0.09668655495573661 Iteration 8: loglikelihood = -2463.2715, backtracks = 0, tol = 0.10676733475961958 Iteration 9: loglikelihood = -2355.3584, backtracks = 0, tol = 0.10566145816262804 Iteration 10: loglikelihood = -2287.1812, backtracks = 0, tol = 0.11855826520508025 Iteration 11: loglikelihood = -2240.895, backtracks = 0, tol = 0.11832706822957315 Iteration 12: loglikelihood = -2205.0564, backtracks = 0, tol = 0.12694697215345246 Iteration 13: loglikelihood = -2185.2417, backtracks = 0, tol = 0.12578303980725927 Iteration 14: loglikelihood = -2172.6824, backtracks = 0, tol = 0.12531833458136618 Iteration 15: loglikelihood = -2168.6907, backtracks = 0, tol = 0.12477049150008716 Iteration 16: loglikelihood = -2154.7754, backtracks = 1, tol = 0.04280944486685696 Iteration 17: loglikelihood = -2151.9055, backtracks = 0, tol = 0.1149200736156058 Iteration 18: loglikelihood = -2144.2275, backtracks = 1, tol = 0.028299975462696098 Iteration 19: loglikelihood = -2142.8467, backtracks = 1, tol = 0.011284125741128121 Iteration 20: loglikelihood = -2142.5566, backtracks = 1, tol = 0.005814698462859038 Iteration 21: loglikelihood = -2142.4873, backtracks = 1, tol = 0.0030083300103026555 Iteration 22: loglikelihood = -2142.4697, backtracks = 1, tol = 0.0015621065807465415 Iteration 23: loglikelihood = -2142.4646, backtracks = 1, tol = 0.0008055604740122179 Iteration 24: loglikelihood = -2142.4631, backtracks = 1, tol = 0.00040906933091652343 Iteration 25: loglikelihood = -2142.463, backtracks = 1, tol = 0.00022259219404760776 Iteration 26: loglikelihood = -2142.4612, backtracks = 2, tol = 6.338690480397571e-5 0.200937 seconds (1.51 M allocations: 25.013 MiB) Test Summary: | Pass Total Time Negative binomial nuisance parameter Float32 matrix | 12 12 30.3s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** ┌ Warning: accessing `Type.name` is deprecated without replacement. If for detection, use `Base.isType(x)`. │ caller = ProgressMeter.Progress(n::Int64, dt::Int64, desc::String, barlen::Nothing, color::Symbol, output::Base.PipeEndpoint; offset::Int64) at deprecated.jl:1 └ @ ProgressMeter ~/.julia/packages/ProgressMeter/N660J/src/deprecated.jl:1 Running sparse linear regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -2896.6116813943763, backtracks = 0, tol = 1.0257704354307222 Iteration 2: loglikelihood = -1753.4720992614753, backtracks = 0, tol = 0.28706825512903816 Iteration 3: loglikelihood = -1460.3823326395225, backtracks = 0, tol = 0.1059822007319242 Iteration 4: loglikelihood = -1438.5292259047123, backtracks = 0, tol = 0.028655431669451118 Iteration 5: loglikelihood = -1438.0856032112097, backtracks = 0, tol = 0.0034955373515602557 Iteration 6: loglikelihood = -1438.0744350329464, backtracks = 0, tol = 0.0005882060650840543 Iteration 7: loglikelihood = -1438.0741395461057, backtracks = 0, tol = 8.427264473927088e-5 5.248056 seconds (1.03 M allocations: 133.633 MiB, 0.99% gc time, 90.80% compilation time) Test Summary: | Pass Total Time initialze beta | 1 1 5.7s 9.769473 seconds (4.00 M allocations: 82.396 MiB, 0.23% gc time, 0.82% compilation time) 5.220002 seconds (3.98 M allocations: 91.674 MiB, 0.41% gc time) 10.303188 seconds (20.38 M allocations: 438.613 MiB, 0.69% gc time, 17.90% compilation time: 78% of which was recompilation) 8.152087 seconds (20.18 M allocations: 434.187 MiB, 0.77% gc time) 35.769842 seconds (3.40 M allocations: 4.230 GiB, 6.57% gc time, 31.30% compilation time) 50.434274 seconds (72.53 k allocations: 183.668 MiB, 0.12% gc time) Test Summary: | Pass Total Time memory_efficient keyword | 7 7 2m18.3s Test Summary: | Pass Total Time update_support! | 10 10 0.7s 14.935 ms (78 allocations: 4.56 KiB) 4.407 μs (0 allocations: 0 bytes) 143.899 μs (4 allocations: 288 bytes) 6.605 μs (0 allocations: 0 bytes) 45.680 μs (2 allocations: 64 bytes) 29.710 μs (0 allocations: 0 bytes) 25.170 μs (0 allocations: 0 bytes) 29.000 μs (0 allocations: 0 bytes) 102.089 μs (0 allocations: 0 bytes) 37.170 ms (78 allocations: 4.56 KiB) 18.450 μs (0 allocations: 0 bytes) 182.459 μs (4 allocations: 288 bytes) 33.219 μs (0 allocations: 0 bytes) 197.918 μs (2 allocations: 64 bytes) 80.609 μs (0 allocations: 0 bytes) 113.659 μs (0 allocations: 0 bytes) 142.049 μs (0 allocations: 0 bytes) 216.168 μs (0 allocations: 0 bytes) Test Summary: | Total Time benchmarks for multivariate function | 0 2m11.7s **** 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 **** **** 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 0.448763 seconds (44.31 k allocations: 5.347 MiB, 65.93% compilation time) Test Summary: | Pass Total Time multivariate fit_iht SnpLinAlg | 7 7 12.7s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse Multivariate Gaussian regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 12 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -2878.028812628852, backtracks = 0, tol = 2.5661768673084553 Iteration 2: loglikelihood = -2868.563037890196, backtracks = 0, tol = 0.024335274263285057 Iteration 3: loglikelihood = -2868.0815051475474, backtracks = 0, tol = 0.004072558228741048 Iteration 4: loglikelihood = -2868.0352100240902, backtracks = 0, tol = 0.0013135682973484317 Iteration 5: loglikelihood = -2868.0309297231934, backtracks = 0, tol = 0.000386434110747091 Iteration 6: loglikelihood = -2868.0305335492912, backtracks = 0, tol = 0.00011924564415557833 Iteration 7: loglikelihood = -2868.0304968517494, backtracks = 0, tol = 3.603726989721193e-5 1.880238 seconds (258.77 k allocations: 167.607 MiB, 60.52% compilation time) Test Summary: | Pass Total Time initialze beta | 5 5 2.3s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** ┌ Warning: accessing `Type.name` is deprecated without replacement. If for detection, use `Base.isType(x)`. │ caller = ProgressMeter.Progress(n::Int64, desc::String, offset::Int64; kwargs::Base.Pairs{Symbol, Union{}, Nothing, @NamedTuple{}}) at deprecated.jl:5 └ @ ProgressMeter ~/.julia/packages/ProgressMeter/N660J/src/deprecated.jl:5 Cross validating... 3%|█ | ETA: 0:03:40 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: 0:00:21 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 5914.448442276206 1 3768.5676779139358 2 2445.718069310908 3 1383.5697381993211 4 913.0263108417423 5 602.0692443720835 6 440.3283222165825 7 376.6014286746247 8 339.2405942486503 9 340.24533363479964 10 341.0078694044625 11 340.3247989138129 12 343.66079545741354 13 355.1294118019571 14 352.1774075294366 15 350.5483932443214 16 361.66789946494197 17 353.1737925489588 18 382.4690941296978 19 412.1894675865839 20 370.7093866872123 Best k = 8 12.198679 seconds (11.31 M allocations: 294.187 MiB, 1.13% gc time, 61.39% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:04 Cross validating... 8%|██▌ | ETA: 0:00:04 Cross validating... 11%|███▌ | ETA: 0:00:03 Cross validating... 14%|████▋ | ETA: 0:00:03 Cross validating... 17%|█████▋ | ETA: 0:00:03 Cross validating... 21%|██████▋ | ETA: 0:00:03 Cross validating... 24%|███████▋ | ETA: 0:00:03 Cross validating... 27%|████████▋ | ETA: 0:00:03 Cross validating... 30%|█████████▋ | ETA: 0:00:03 Cross validating... 33%|██████████▋ | ETA: 0:00:03 Cross validating... 38%|████████████▎ | ETA: 0:00:03 Cross validating... 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 5914.448442276206 1 3807.027949925776 2 2489.4174367569262 3 1396.303305059786 4 920.9098601997756 5 605.1935746043357 6 442.91655088614414 7 379.8989182603252 8 343.71722875095395 9 348.7753039026811 10 356.6723706497577 11 354.415721059499 12 365.2550365112505 13 371.4024163630737 14 387.34905258760716 15 388.35076346125413 16 385.67751693760505 17 405.39159655146244 18 396.0699660372106 19 412.189467586584 20 402.9985488171143 Best k = 8 4.880791 seconds (10.35 M allocations: 217.041 MiB, 1.96% gc time, 1.39% 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: 0:05:54 Cross validating... 8%|██▌ | ETA: 0:02:16 Cross validating... 14%|████▋ | ETA: 0:01:11 Cross validating... 19%|██████▏ | ETA: 0:00:51 Cross validating... 24%|███████▋ | ETA: 0:00:39 Cross validating... 29%|█████████▏ | ETA: 0:00:31 Cross validating... 33%|██████████▋ | ETA: 0:00:25 Cross validating... 40%|████████████▊ | ETA: 0:00:19 Cross validating... 44%|██████████████▎ | ETA: 0:00:16 Cross validating... 49%|███████████████▊ | ETA: 0:00:13 Cross validating... 54%|█████████████████▎ | ETA: 0:00:11 Cross validating... 59%|██████████████████▊ | ETA: 0:00:09 Cross validating... 63%|████████████████████▍ | ETA: 0:00:08 Cross validating... 68%|█████████████████████▉ | ETA: 0:00:06 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:05 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:04 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:03 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:01 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:01 Cross validating... 100%|████████████████████████████████| Time: 0:00:14 Crossvalidation Results: k MSE 0 1598.5593342285156 1 1242.535166381836 2 963.7644469604492 3 800.2175325927735 4 601.5266961975098 5 487.97642984008786 6 406.9708630981445 7 353.7594619140625 8 322.8741271057129 9 310.70403375244143 10 308.00287188720705 11 307.2668201904297 12 309.508706451416 13 311.6720624694824 14 319.66481484985354 15 314.0128040771484 16 332.6364479675293 17 323.4441027832031 18 315.5245186462402 19 320.3903332824707 20 327.17407943725584 Best k = 11 15.287409 seconds (12.20 M allocations: 307.264 MiB, 0.60% gc time, 83.62% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 5%|█▌ | ETA: 0:00:02 Cross validating... 11%|███▌ | ETA: 0:00:02 Cross validating... 16%|█████▏ | ETA: 0:00:02 Cross validating... 21%|██████▋ | ETA: 0:00:02 Cross validating... 25%|████████▏ | ETA: 0:00:02 Cross validating... 30%|█████████▋ | ETA: 0:00:02 Cross validating... 35%|███████████▏ | ETA: 0:00:02 Cross validating... 41%|█████████████▎ | ETA: 0:00:01 Cross validating... 46%|██████████████▊ | ETA: 0:00:01 Cross validating... 51%|████████████████▎ | ETA: 0:00:01 Cross validating... 56%|█████████████████▊ | ETA: 0:00:01 Cross validating... 60%|███████████████████▎ | ETA: 0:00:01 Cross validating... 65%|████████████████████▉ | ETA: 0:00:01 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:01 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:01 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:00 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:00 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:02 Crossvalidation Results: k MSE 0 1598.5593342285156 1 1247.707955444336 2 963.7644469604492 3 800.8833439331056 4 605.0832391662598 5 493.7672334289551 6 435.5551303710937 7 356.77548696899413 8 325.9573108825683 9 320.24154504394534 10 322.78617807006833 11 322.96201541137697 12 325.920759399414 13 336.4256134643555 14 338.88452416992186 15 343.46257028198244 16 344.49931875610355 17 349.068649017334 18 347.46991885375974 19 359.51994049072266 20 369.9626592712402 Best k = 9 2.591166 seconds (10.50 M allocations: 193.337 MiB, 2.07% gc time, 2.18% compilation time) Test Summary: | Pass Total Time Cross validation on Float32 matrix, normal model | 2 2 19.4s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:01:02 Cross validating... 6%|██ | ETA: 0:00:33 Cross validating... 8%|██▌ | ETA: 0:00:27 Cross validating... 11%|███▌ | ETA: 0:00:20 Cross validating... 14%|████▋ | ETA: 0:00:16 Cross validating... 17%|█████▋ | ETA: 0:00:13 Cross validating... 21%|██████▋ | ETA: 0:00:12 Cross validating... 24%|███████▋ | ETA: 0:00:10 Cross validating... 25%|████████▏ | ETA: 0:00:10 Cross validating... 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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... 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 0 462.70495432090684 1 398.19247335175436 2 334.1118151778883 3 273.4614069573168 4 255.33502458108643 5 221.72556363867614 6 216.68674376535805 7 210.03717594812647 8 222.55694989876872 9 210.03349414183904 10 242.42373368938604 11 217.1094161459461 12 215.48713141373145 13 231.57467207811362 14 253.50279120679988 15 248.83060797027792 16 219.5005242243157 17 243.27310595573152 18 224.41827886459882 19 247.8985400074149 20 225.37735654593072 Best k = 9 8.287417 seconds (17.26 M allocations: 402.829 MiB, 0.96% gc time, 32.88% 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... 5%|█▌ | ETA: 0:00:05 Cross validating... 8%|██▌ | ETA: 0:00:05 Cross validating... 11%|███▌ | ETA: 0:00:05 Cross validating... 14%|████▋ | ETA: 0:00:05 Cross validating... 17%|█████▋ | ETA: 0:00:05 Cross validating... 21%|██████▋ | ETA: 0:00:05 Cross validating... 24%|███████▋ | ETA: 0:00:04 Cross validating... 27%|████████▋ | ETA: 0:00:04 Cross validating... 29%|█████████▏ | ETA: 0:00:04 Cross validating... 32%|██████████▏ | ETA: 0:00:04 Cross validating... 33%|██████████▋ | ETA: 0:00:04 Cross validating... 37%|███████████▋ | ETA: 0:00:04 Cross 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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 0 462.70495432090684 1 399.0234943779268 2 336.2799846764399 3 276.52843775679656 4 259.1011330785668 5 228.30027885235864 6 223.17892081845247 7 221.4412070205533 8 226.75417996719477 9 224.73769403262457 10 235.58846515295377 11 245.443221014288 12 242.51847533307117 13 247.28549949033845 14 262.290577726029 15 259.52605966096394 16 275.26821680983056 17 270.43999675010235 18 278.0316128552279 19 266.3387079245144 20 278.07137570757203 Best k = 7 5.944357 seconds (17.88 M allocations: 371.112 MiB, 1.62% gc time, 1.37% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, logistic model | 2 2 14.7s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:45 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: 0:00:09 Cross validating... 21%|██████▋ | ETA: 0:00:08 Cross validating... 24%|███████▋ | ETA: 0:00:07 Cross validating... 27%|████████▋ | ETA: 0:00:06 Cross validating... 30%|█████████▋ | ETA: 0:00:06 Cross validating... 33%|██████████▋ | ETA: 0:00:05 Cross validating... 38%|████████████▎ | ETA: 0:00:05 Cross validating... 41%|█████████████▎ | ETA: 0:00:04 Cross validating... 44%|██████████████▎ | ETA: 0:00:04 Cross validating... 48%|███████████████▎ | ETA: 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100%|████████████████████████████████| Time: 0:00:05 Crossvalidation Results: k MSE 0 463.3070367855024 1 433.9629733566845 2 414.95986909750695 3 387.29415803175795 4 359.12680259966515 5 340.82158217264174 6 334.0338219618679 7 329.5924355510302 8 333.08524338217364 9 348.8364230253419 10 336.06656380114856 11 348.4093913812998 12 352.4130028244023 13 348.56413367054995 14 371.6583950786868 15 358.62304525988725 16 356.39907422362324 17 379.545223912536 18 346.095522411256 19 356.655449338055 20 374.3992938541698 Best k = 7 6.977227 seconds (16.52 M allocations: 391.975 MiB, 7.22% gc time, 36.99% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:03 Cross validating... 6%|██ | ETA: 0:00:04 Cross validating... 10%|███ | ETA: 0:00:04 Cross validating... 13%|████▏ | ETA: 0:00:04 Cross validating... 16%|█████▏ | ETA: 0:00:04 Cross validating... 19%|██████▏ | ETA: 0:00:03 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: 0:00:03 Cross validating... 41%|█████████████▎ | ETA: 0:00:03 Cross validating... 44%|██████████████▎ | ETA: 0:00:02 Cross validating... 48%|███████████████▎ | ETA: 0:00:02 Cross validating... 51%|████████████████▎ | ETA: 0:00:02 Cross validating... 54%|█████████████████▎ | ETA: 0:00:02 Cross validating... 57%|██████████████████▎ | ETA: 0:00:02 Cross validating... 60%|███████████████████▎ | ETA: 0:00:02 Cross validating... 63%|████████████████████▍ | ETA: 0:00:02 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:01 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:01 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:01 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:01 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:01 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:01 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:01 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:00 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:04 Crossvalidation Results: k MSE 0 463.3070367855024 1 434.1120705493179 2 416.2698031809313 3 388.4461763430073 4 360.34585244275627 5 343.48084550702674 6 337.6843937432593 7 335.526722756601 8 344.05072272338 9 351.58589071148515 10 363.89508183258505 11 360.36738910241064 12 365.74069091220815 13 375.6602757583923 14 384.3137615319024 15 383.94533793601283 16 405.1533195074319 17 401.47650727079315 18 405.43058399191995 19 396.54181895954696 20 426.88586813888753 Best k = 7 4.411455 seconds (17.75 M allocations: 366.206 MiB, 2.34% gc time, 1.27% compilation time) Test Summary: | Pass Total Time Cross validation on Float64 matrix, logistic model | 2 2 12.4s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:01:03 Cross validating... 6%|██ | ETA: 0:00:33 Cross validating... 10%|███ | ETA: 0:00:23 Cross validating... 13%|████▏ | ETA: 0:00:18 Cross validating... 16%|█████▏ | ETA: 0:00:15 Cross validating... 19%|██████▏ | ETA: 0:00:13 Cross validating... 22%|███████▏ | ETA: 0:00:11 Cross validating... 25%|████████▏ | ETA: 0:00:10 Cross validating... 29%|█████████▏ | ETA: 0:00:09 Cross validating... 30%|█████████▋ | 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... 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... 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 1322.639097755958 1 1100.9025086920474 2 721.0311282077778 3 561.6574056770111 4 470.4123625264979 5 414.86106333831367 6 391.8111468509268 7 372.5393295805434 8 362.2170501519507 9 378.84181918518664 10 433.0353660491169 11 429.02864759860074 12 416.1307052608257 13 391.5180505212992 14 396.27789208770935 15 418.72434253570356 16 415.6043303586612 17 415.77443116476854 18 421.2478878662151 19 429.618929951184 20 437.178962966852 Best k = 8 8.328048 seconds (15.21 M allocations: 349.363 MiB, 1.01% gc time, 33.22% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:04 Cross validating... 6%|██ | ETA: 0:00:05 Cross validating... 10%|███ | ETA: 0:00:05 Cross validating... 13%|████▏ | ETA: 0:00:04 Cross validating... 14%|████▋ | ETA: 0:00:05 Cross validating... 17%|█████▋ | ETA: 0:00:04 Cross validating... 21%|██████▋ | ETA: 0:00:04 Cross validating... 24%|███████▋ | ETA: 0:00:04 Cross validating... 27%|████████▋ | ETA: 0:00:04 Cross validating... 30%|█████████▋ | ETA: 0:00:04 Cross validating... 33%|██████████▋ | ETA: 0:00:04 Cross validating... 37%|███████████▋ | ETA: 0:00:03 Cross validating... 40%|████████████▊ | ETA: 0:00:03 Cross validating... 41%|█████████████▎ | ETA: 0:00:03 Cross validating... 44%|██████████████▎ | ETA: 0:00:03 Cross validating... 48%|███████████████▎ | ETA: 0:00:03 Cross validating... 51%|████████████████▎ | ETA: 0:00:03 Cross validating... 54%|█████████████████▎ | ETA: 0:00:03 Cross validating... 57%|██████████████████▎ | ETA: 0:00:02 Cross validating... 60%|███████████████████▎ | ETA: 0:00:02 Cross validating... 63%|████████████████████▍ | ETA: 0:00:02 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:02 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:02 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:01 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:01 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:01 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:01 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:01 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:01 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:00 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:05 Crossvalidation Results: k MSE 0 1322.639097755958 1 1031.0024608322096 2 696.7954532113905 3 543.917113873674 4 465.3768100475878 5 395.1673228791852 6 386.09410246404906 7 367.88373189338256 8 373.39154354804083 9 390.0948366220033 10 409.8318675651964 11 419.44696450605767 12 426.31026473277063 13 442.9164977277893 14 458.87524328618713 15 465.0728711731878 16 476.9717349040567 17 529.0948533721645 18 534.0779591359121 19 527.5000063296944 20 544.2858213951458 Best k = 7 5.560768 seconds (14.15 M allocations: 283.824 MiB, 1.28% gc time, 0.55% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, Poisson model | 2 2 14.3s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:01:29 Cross validating... 5%|█▌ | ETA: 0:01:19 Cross validating... 6%|██ | ETA: 0:01:00 Cross validating... 8%|██▌ | ETA: 0:00:59 Cross validating... 10%|███ | ETA: 0:00:50 Cross validating... 13%|████▏ | ETA: 0:00:37 Cross validating... 16%|█████▏ | ETA: 0:00:30 Cross validating... 17%|█████▋ | ETA: 0:00:27 Cross validating... 19%|██████▏ | ETA: 0:00:29 Cross validating... 21%|██████▋ | ETA: 0:00:31 Cross validating... 22%|███████▏ | ETA: 0:00:28 Cross validating... 24%|███████▋ | ETA: 0:00:30 Cross validating... 25%|████████▏ | ETA: 0:00:31 Cross validating... 27%|████████▋ | ETA: 0:00:31 Cross validating... 29%|█████████▏ | ETA: 0:00:29 Cross validating... 30%|█████████▋ | ETA: 0:00:30 Cross validating... 32%|██████████▏ | ETA: 0:00:30 Cross validating... 33%|██████████▋ | ETA: 0:00:30 Cross validating... 37%|███████████▋ | ETA: 0:00:28 Cross 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validating... 97%|███████████████████████████████ | ETA: 0:00:01 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:01 Cross validating... 100%|████████████████████████████████| Time: 0:00:41 Crossvalidation Results: k MSE 0 490.6942251877331 1 388.90658195252456 2 311.709257395113 3 258.0696028832048 4 231.76609150757287 5 220.06577920997194 6 207.92922287125003 7 200.68298663776062 8 201.61428882063754 9 202.98090544284298 10 203.80734738710595 11 205.92555388192994 12 207.51971386599075 13 208.26747211174444 14 210.60133990521348 15 211.5894237668591 16 211.41024402884307 17 213.33332821389553 18 211.0496908631811 19 213.33869768986034 20 215.08823091763986 Best k = 7 42.114073 seconds (130.43 M allocations: 3.345 GiB, 1.21% gc time, 5.32% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:05 Cross validating... 5%|█▌ | ETA: 0:00:06 Cross validating... 6%|██ | ETA: 0:00:06 Cross validating... 8%|██▌ | ETA: 0:00:06 Cross validating... 10%|███ | ETA: 0:00:06 Cross validating... 11%|███▌ | ETA: 0:00:06 Cross validating... 13%|████▏ | ETA: 0:00:06 Cross validating... 14%|████▋ | ETA: 0:00:06 Cross validating... 16%|█████▏ | ETA: 0:00:06 Cross validating... 17%|█████▋ | ETA: 0:00:07 Cross validating... 19%|██████▏ | ETA: 0:00:07 Cross validating... 21%|██████▋ | ETA: 0:00:07 Cross validating... 22%|███████▏ | ETA: 0:00:07 Cross validating... 24%|███████▋ | ETA: 0:00:07 Cross validating... 25%|████████▏ | ETA: 0:00:07 Cross validating... 27%|████████▋ | ETA: 0:00:07 Cross validating... 29%|█████████▏ | ETA: 0:00:07 Cross validating... 30%|█████████▋ | ETA: 0:00:07 Cross validating... 32%|██████████▏ | ETA: 0:00:07 Cross validating... 33%|██████████▋ | ETA: 0:00:07 Cross validating... 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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 0 490.6942251877331 1 385.26059595962124 2 312.0140775939105 3 260.9772279976078 4 233.33317714944727 5 222.0678819757424 6 209.73109538436222 7 203.68623976019595 8 206.81706467570123 9 210.49402700367926 10 212.80821629863848 11 216.13854710610167 12 217.8732349778516 13 224.5928625085882 14 234.8286905165711 15 237.67577227237868 16 239.70467714693444 17 241.76192046628466 18 238.16759290719943 19 244.834659504833 20 252.19924120822674 Best k = 7 11.708345 seconds (34.77 M allocations: 715.729 MiB, 1.37% gc time, 0.87% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, NegativeBinomial model | 2 2 54.3s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:01:02 Cross validating... 8%|██▌ | ETA: 0:00:25 Cross validating... 11%|███▌ | ETA: 0:00:18 Cross validating... 14%|████▋ | ETA: 0:00:14 Cross validating... 17%|█████▋ | ETA: 0:00:12 Cross validating... 21%|██████▋ | ETA: 0:00:10 Cross validating... 24%|███████▋ | ETA: 0:00:09 Cross validating... 27%|████████▋ | ETA: 0:00:08 Cross validating... 30%|█████████▋ | ETA: 0:00:07 Cross validating... 33%|██████████▋ | ETA: 0:00:06 Cross validating... 38%|████████████▎ | ETA: 0:00:05 Cross validating... 41%|█████████████▎ | ETA: 0:00:05 Cross validating... 44%|██████████████▎ | ETA: 0:00:04 Cross validating... 48%|███████████████▎ | ETA: 0:00:04 Cross validating... 51%|████████████████▎ | ETA: 0:00:04 Cross validating... 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... 79%|█████████████████████████▍ | ETA: 0:00:01 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:01 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:01 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:05 Crossvalidation Results: k MSE 0 708.7406597900391 1 594.0547950439453 2 472.60887115478516 3 391.07051165771486 4 322.2429605712891 5 274.1304553527832 6 242.98796069335935 7 231.75397763061522 8 211.04413333129884 9 208.82878451538085 10 210.9139321594238 11 206.8662128601074 12 209.29315435791017 13 216.44690969848637 14 210.83974066162108 15 223.69269552612303 16 223.5122525024414 17 217.3672544555664 18 230.29235778808595 19 245.48900619506838 20 214.24631561279296 Best k = 11 6.086318 seconds (17.22 M allocations: 343.612 MiB, 1.42% gc time, 45.39% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 6%|██ | ETA: 0:00:02 Cross validating... 11%|███▌ | ETA: 0:00:02 Cross validating... 16%|█████▏ | ETA: 0:00:02 Cross validating... 21%|██████▋ | ETA: 0:00:02 Cross validating... 25%|████████▏ | ETA: 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ETA: 0:00:00 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: 0:00:03 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 3.089229 seconds (16.26 M allocations: 288.219 MiB, 1.91% gc time, 0.95% compilation time) Test Summary: | Pass Total Time Cross validation on floating point matrices, NegativeBinomial model | 2 2 9.7s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 2%|▋ | ETA: 0:01:27 Cross validating... 3%|█ | ETA: 0:01:03 Cross validating... 4%|█▎ | ETA: 0:00:54 Cross validating... 5%|█▋ | ETA: 0:00:46 Cross validating... 6%|█▉ | ETA: 0:00:40 Cross validating... 7%|██▎ | ETA: 0:00:36 Cross validating... 8%|██▌ | ETA: 0:00:33 Cross validating... 9%|██▉ | ETA: 0:00:31 Cross validating... 10%|███▎ | ETA: 0:00:29 Cross validating... 11%|███▌ | ETA: 0:00:28 Cross validating... 12%|███▉ | ETA: 0:00:27 Cross validating... 13%|████▏ | ETA: 0:00:26 Cross validating... 14%|████▌ | ETA: 0:00:25 Cross validating... 15%|████▊ | ETA: 0:00:24 Cross validating... 16%|█████▏ | ETA: 0:00:23 Cross validating... 17%|█████▌ | ETA: 0:00:23 Cross validating... 18%|█████▊ | ETA: 0:00:22 Cross validating... 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88%|████████████████████████████▏ | ETA: 0:00:02 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:02 Cross validating... 90%|████████████████████████████▊ | ETA: 0:00:02 Cross validating... 91%|█████████████████████████████▏ | ETA: 0:00:02 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:02 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: 0:00:19 Crossvalidation Results: k MSE 1 3909.0290282106857 2 3508.223765702376 3 3368.4754684449094 4 3087.857270275935 5 2862.878106886741 6 2734.767185940414 7 2584.8074343341887 8 2500.482322423992 9 2486.1632567052584 10 2503.3620576671765 11 2525.0141682432595 12 2534.5925536089176 13 2535.3293121826005 14 2537.164049956151 15 2561.2306490400924 16 2573.133860845237 17 2592.8357758541997 18 2616.9378228515793 19 2620.5966363620128 20 2666.358107843999 Best k = 9 19.634174 seconds (333.22 k allocations: 266.491 MiB, 0.73% gc time, 8.92% compilation time) Test Summary: | Pass Total Time multivariate cross validation SnpLinAlg | 3 3 24.5s Test Summary: | Pass Total Time wrapper univariate | 20 20 2m01.6s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 2%|▋ | ETA: 0:00:10 Cross validating... 3%|█ | ETA: 0:00:10 Cross validating... 4%|█▎ | ETA: 0:00:11 Cross 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ETA: 0:00:02 Cross validating... 94%|██████████████████████████████▏ | ETA: 0:00:01 Cross validating... 95%|██████████████████████████████▍ | ETA: 0:00:01 Cross validating... 96%|██████████████████████████████▊ | ETA: 0:00:01 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:01 Cross validating... 98%|███████████████████████████████▍| ETA: 0:00:00 Cross validating... 99%|███████████████████████████████▋| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:23 Crossvalidation Results: k MSE 1 2838.788679198002 2 2514.3973428708136 3 2305.6176519676274 4 2222.025304867614 5 2075.1670384588365 6 2067.7948989723845 7 2053.427506114907 8 2086.405384830965 9 2080.984460901671 10 2105.131199502364 11 2132.407165368786 12 2138.267187460652 13 2166.002210829576 14 2194.9918295115804 15 2189.890403738045 16 2191.181293229578 17 2209.4669750564362 18 2221.2595493644303 19 2238.7425945763257 20 2253.9559571797727 Best k = 7 **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 2%|▋ | ETA: 0:00:10 Cross validating... 3%|█ | ETA: 0:00:11 Cross validating... 4%|█▎ | ETA: 0:00:11 Cross validating... 5%|█▋ | ETA: 0:00:11 Cross validating... 6%|█▉ | ETA: 0:00:13 Cross validating... 7%|██▎ | ETA: 0:00:13 Cross validating... 8%|██▌ | ETA: 0:00:13 Cross validating... 9%|██▉ | ETA: 0:00:14 Cross validating... 10%|███▎ | ETA: 0:00:15 Cross validating... 11%|███▌ | ETA: 0:00:15 Cross validating... 12%|███▉ | ETA: 0:00:16 Cross validating... 13%|████▏ | ETA: 0:00:16 Cross validating... 14%|████▌ | ETA: 0:00:16 Cross validating... 15%|████▊ | ETA: 0:00:17 Cross validating... 16%|█████▏ | ETA: 0:00:18 Cross validating... 17%|█████▌ | ETA: 0:00:18 Cross validating... 18%|█████▊ | ETA: 0:00:18 Cross validating... 19%|██████▏ | 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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 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0:00:04 Cross validating... 83%|██████████████████████████▌ | ETA: 0:00:04 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:04 Cross validating... 85%|███████████████████████████▎ | ETA: 0:00:03 Cross validating... 86%|███████████████████████████▌ | ETA: 0:00:03 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:03 Cross validating... 88%|████████████████████████████▏ | ETA: 0:00:03 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:02 Cross validating... 90%|████████████████████████████▊ | ETA: 0:00:02 Cross validating... 91%|█████████████████████████████▏ | ETA: 0:00:02 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:02 Cross validating... 93%|█████████████████████████████▊ | ETA: 0:00:02 Cross validating... 94%|██████████████████████████████▏ | ETA: 0:00:01 Cross validating... 95%|██████████████████████████████▍ | ETA: 0:00:01 Cross validating... 96%|██████████████████████████████▊ | ETA: 0:00:01 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:01 Cross validating... 98%|███████████████████████████████▍| ETA: 0:00:00 Cross validating... 99%|███████████████████████████████▋| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:23 Crossvalidation Results: k MSE 1 2838.788679198002 2 2514.3973428708136 3 2305.6176519676274 4 2222.025304867614 5 2075.1670384588365 6 2067.7948989723845 7 2053.427506114907 8 2086.405384830965 9 2080.984460901671 10 2105.131199502364 11 2132.407165368786 12 2138.267187460652 13 2166.002210829576 14 2194.9918295115804 15 2189.890403738045 16 2191.181293229578 17 2209.4669750564362 18 2221.2595493644303 19 2238.7425945763257 20 2253.9559571797727 Best k = 7 Test Summary: | Pass Total Time wrapper multivariate | 8 8 1m26.0s 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(0x5cf9306ba8a4170e, 0x6e3b6087ad4cd764, 0x88ff806658c6a70a, 0x7bf63adbf56b60e8, 0xb8647006225b86c4) 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 1095.0s 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 1241.5s: package tests unexpectedly errored