Package evaluation to test MendelIHT on Julia 1.14.0-DEV.3106 (9d314127b9*) started at 2026-09-04T02:32:47.235 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.14` Set-up completed after 15.49s ################################################################################ # Installation # Installing MendelIHT... Resolving package versions... Updating `~/.julia/environments/v1.14/Project.toml` [921c7187] + MendelIHT v1.4.11 Updating `~/.julia/environments/v1.14/Manifest.toml` [7d9f7c33] + Accessors v0.1.45 [79e6a3ab] + Adapt v4.7.0 [66dad0bd] + AliasTables v1.1.3 [4fba245c] + ArrayInterface v7.30.1 [67c07d97] + Automa v1.2.0 ⌅ [6db4b851] + BGEN v0.1.17 [28d598bf] + BGZFStreams v0.3.2 [47718e42] + BioGenerics v0.1.5 [62783981] + BitTwiddlingConvenienceFunctions v0.1.6 [e1450e63] + BufferedStreams v1.2.2 [2a0fbf3d] + CPUSummary v0.2.7 [336ed68f] + CSV v0.10.17 [fb6a15b2] + CloseOpenIntervals v0.1.13 [523fee87] + CodecBzip2 v0.8.5 [ba30903b] + CodecXz v0.7.4 [944b1d66] + CodecZlib v0.7.9 [6b39b394] + CodecZstd v0.8.7 [861a8166] + Combinatorics v1.1.0 [38540f10] + CommonSolve v0.2.14 [f70d9fcc] + CommonWorldInvalidations v1.2.0 [34da2185] + Compat v4.18.1 [a33af91c] + CompositionsBase v0.1.2 [187b0558] + ConstructionBase v1.6.0 [adafc99b] + CpuId v0.3.1 [a8cc5b0e] + Crayons v4.2.0 [a10d1c49] + DBInterface v2.7.0 [9a962f9c] + 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To see why use `status --outdated -m` Installation completed after 5.39s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompiling project... 5.1 s ✓ BGEN 6.2 s ✓ VCFTools WARNING: Constructor for type "MvNormal" was extended in `MendelIHT` without explicit qualification or import. NOTE: Assumed "MvNormal" refers to `Distributions.MvNormal`. This behavior is deprecated and may differ in future versions. NOTE: This behavior may have differed in Julia versions prior to 1.12. Hint: If you intended to create a new generic function of the same name, use `function MvNormal end`. Hint: To silence the warning, qualify `MvNormal` as `Distributions.MvNormal` in the method signature or explicitly `import Distributions: MvNormal`. 23.4 s ✓ MendelIHT 3 dependencies successfully precompiled in 36 seconds. 173 already precompiled. 1 dependency had output during precompilation: ┌ MendelIHT │ WARNING: Constructor for type "MvNormal" was extended in `MendelIHT` without explicit qualification or import. │ NOTE: Assumed "MvNormal" refers to `Distributions.MvNormal`. This behavior is deprecated and may differ in future versions. │ NOTE: This behavior may have differed in Julia versions prior to 1.12. │ Hint: If you intended to create a new generic function of the same name, use `function MvNormal end`. │ Hint: To silence the warning, qualify `MvNormal` as `Distributions.MvNormal` in the method signature or explicitly `import Distributions: MvNormal`. └ Precompilation completed after 55.23s ################################################################################ # Testing # Testing MendelIHT Status `/tmp/jl_OlDsCl/Project.toml` ⌅ [6db4b851] BGEN v0.1.17 [6e4b80f9] BenchmarkTools v1.8.0 [336ed68f] CSV v0.10.17 [a93c6f00] DataFrames v1.8.2 [8bb1440f] DelimitedFiles v1.9.1 [b4f34e82] Distances v0.10.12 [31c24e10] Distributions v0.25.131 [38e38edf] GLM v1.9.5 [921c7187] MendelIHT v1.4.11 [92933f4c] ProgressMeter v1.11.0 [189a3867] Reexport v1.2.2 [4e780e97] SnpArrays v0.3.23 [276daf66] SpecialFunctions v2.9.0 [2913bbd2] StatsBase v0.34.13 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libblastrampoline_jll v5.15.0+0 [8e850ede] nghttp2_jll v1.70.0+0 [3f19e933] p7zip_jll v17.8.2+0 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. Testing Running tests... ┌ Warning: accessing `Type.name` is deprecated without replacement. If for detection, use `Base.isType(x)`. │ caller = Distributions.MvNormal(σ::Vector{Float64}) at mvnormal.jl:207 └ @ Distributions ~/.julia/packages/Distributions/RTt4y/src/multivariate/mvnormal.jl:207 ┌ Warning: `MvNormal(σ::AbstractVector{<:Real})` is deprecated, use `MvNormal(LinearAlgebra.Diagonal(map(abs2, σ)))` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `cholesky!(A::RealHermSymComplexHerm{<:Real}, ::Val{true}; kwargs...)` is deprecated, use `cholesky!(A, RowMaximum(); kwargs...)` instead. │ caller = iht_stepsize!(v::MendelIHT.mIHTVariable{Float64, LinearAlgebra.Transpose{Float64, SnpArrays.SnpLinAlg{Float64}}}) at multivariate.jl:241 └ @ MendelIHT ~/.julia/packages/MendelIHT/ZcxZT/src/multivariate.jl:241 Test Summary: | Pass Total Time loglikelihood | 4 4 12.3s Test Summary: | Pass Total Time deviance | 1 1 0.3s Test Summary: | Pass Total Time update_μ! | 4 4 1.2s Test Summary: | Pass Total Time _choose! | 7 7 7.5s Test Summary: | Pass Total Time _iht_backtrack | 7 7 0.0s Test Summary: | Pass Total Time standardize! | 12 12 0.9s Test Summary: | Pass Total Time project_k! | 2 2 0.8s Test Summary: | Pass Total Time project_group_sparse! | 5 5 1.2s Test Summary: | Pass Total Time maf_weights | 6 6 2.0s **** 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 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 = -1423.615191511412, backtracks = 0, tol = 1.4814608881495546 Iteration 2: loglikelihood = -1364.9588299965737, backtracks = 0, tol = 0.13703532019282638 Iteration 3: loglikelihood = -1362.0195751923661, backtracks = 0, tol = 0.04971451590044465 Iteration 4: loglikelihood = -1361.933288914344, backtracks = 0, tol = 0.0027197596709489244 Iteration 5: loglikelihood = -1361.9324424362485, backtracks = 0, tol = 0.0003428339739889938 Iteration 6: loglikelihood = -1361.9324263865644, backtracks = 0, tol = 4.035639216007232e-5 IHT estimated 10 nonzero SNP predictors and 1 non-genetic predictors. Compute time (sec): 0.05384087562561035 Final loglikelihood: -1361.9324263865644 SNP PVE: 0.9120698390568205 Iterations: 6 Selected genetic predictors: 10×2 DataFrame Row │ Position Estimated_β │ Int64 Float64 ─────┼─────────────────────── 1 │ 241 -0.975769 2 │ 913 1.54798 3 │ 1428 0.849238 4 │ 2959 0.434145 5 │ 3010 0.659975 6 │ 3814 -0.846361 7 │ 6440 -1.00828 8 │ 9252 1.46959 9 │ 9560 -0.678923 10 │ 9895 0.113153 Selected nongenetic predictors: 1×2 DataFrame Row │ Position Estimated_β │ Int64 Float64 ─────┼─────────────────────── 1 │ 1 -0.0151317Test Summary: | Pass Total Time fit normal SnpLinAlg | 4 4 23.1s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse logistic regression Number of threads = 1 Link functin = LogitLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -379.72375963518977, backtracks = 0, tol = 0.6062552017348442 Iteration 2: loglikelihood = -294.14222098196217, backtracks = 0, tol = 0.39035964909167 Iteration 3: loglikelihood = -258.44215825745147, backtracks = 0, tol = 0.18072720194601524 Iteration 4: loglikelihood = -248.39092317275637, backtracks = 1, tol = 0.0581811999889429 Iteration 5: loglikelihood = -241.2861695402178, backtracks = 2, tol = 0.10199490430383734 Iteration 6: loglikelihood = -236.0344401262056, backtracks = 2, tol = 0.10444957184614982 Iteration 7: loglikelihood = -232.75639772007577, backtracks = 2, tol = 0.03618239958756675 Iteration 8: loglikelihood = -230.9028935826695, backtracks = 3, tol = 0.022566251649321353 Iteration 9: loglikelihood = -229.2332883500926, backtracks = 3, tol = 0.02394599965909332 Iteration 10: loglikelihood = -227.8109863155336, backtracks = 3, tol = 0.02260237147851236 Iteration 11: loglikelihood = -226.61429831284372, backtracks = 3, tol = 0.02153016573221634 Iteration 12: loglikelihood = -225.614543213995, backtracks = 3, tol = 0.020073248773013197 Iteration 13: loglikelihood = -225.15228734295533, backtracks = 3, tol = 0.10266272165892033 Iteration 14: loglikelihood = -224.5524858306654, backtracks = 2, tol = 0.010910053499902256 Iteration 15: loglikelihood = -223.90430308527087, backtracks = 3, tol = 0.10669566586572145 Iteration 16: loglikelihood = -223.43342440058004, backtracks = 1, tol = 0.009912340440473734 Iteration 17: loglikelihood = -223.19474883510568, backtracks = 3, tol = 0.10429355504005154 Iteration 18: loglikelihood = -222.7530868660152, backtracks = 1, tol = 0.010133510239484585 Iteration 19: loglikelihood = -222.4546375562022, backtracks = 3, tol = 0.009382230171462355 Iteration 20: loglikelihood = -225.04961416047087, backtracks = 3, tol = 0.13141028198780508 Iteration 21: loglikelihood = -221.57583298738808, backtracks = 0, tol = 0.12983606150115481 Iteration 22: loglikelihood = -220.9953587123894, backtracks = 0, tol = 0.018278220962270587 Iteration 23: loglikelihood = -220.46528702030645, backtracks = 0, tol = 0.10912949798131547 Iteration 24: loglikelihood = -220.22939682199817, backtracks = 1, tol = 0.006133557493960293 Iteration 25: loglikelihood = -220.1149031779291, backtracks = 3, tol = 0.005637364497494655 Iteration 26: loglikelihood = -237.91408320706802, backtracks = 3, tol = 0.1311916630585333 Iteration 27: loglikelihood = -222.6667401701631, backtracks = 0, tol = 0.13008576394077564 Iteration 28: loglikelihood = -220.0179912284672, backtracks = 0, tol = 0.10981267805412102 Iteration 29: loglikelihood = -219.80873468505163, backtracks = 1, tol = 0.006242686572879014 Iteration 30: loglikelihood = -219.71412932030552, backtracks = 1, tol = 0.0052581541847830735 Iteration 31: loglikelihood = -219.67346582214395, backtracks = 3, tol = 0.002736072071808146 Iteration 32: loglikelihood = -236.63118723570068, backtracks = 3, tol = 0.12536959025201838 Iteration 33: loglikelihood = -222.42522446507616, backtracks = 0, tol = 0.12480632457239557 Iteration 34: loglikelihood = -219.76952387571325, backtracks = 0, tol = 0.10782393864869841 Iteration 35: loglikelihood = -219.54239052596037, backtracks = 0, tol = 0.010969385336776636 Iteration 36: loglikelihood = -219.51051719556185, backtracks = 0, tol = 0.0038143069815270263 Iteration 37: loglikelihood = -219.49562270628724, backtracks = 1, tol = 0.0015360028505860806 Iteration 38: loglikelihood = -222.2776344615594, backtracks = 3, tol = 0.10706948875570901 Iteration 39: loglikelihood = -219.86344247649652, backtracks = 0, tol = 0.10682440099239575 Iteration 40: loglikelihood = -219.50637292175287, backtracks = 0, tol = 0.010145149683589566 Iteration 41: loglikelihood = -219.45601478260392, backtracks = 0, tol = 0.004786594360325445 Iteration 42: loglikelihood = -219.44279315931445, backtracks = 0, tol = 0.0023300326568676676 Iteration 43: loglikelihood = -219.434262597912, backtracks = 0, tol = 0.002159682320412748 Iteration 44: loglikelihood = -219.42706752504972, backtracks = 0, tol = 0.0019986878272562235 Iteration 45: loglikelihood = -219.4208881668612, backtracks = 0, tol = 0.001781315196828412 Iteration 46: loglikelihood = -219.41556755717227, backtracks = 0, tol = 0.0017266268818688624 Iteration 47: loglikelihood = -219.41098445944962, backtracks = 0, tol = 0.001504993867218278 Iteration 48: loglikelihood = -219.4070309112888, backtracks = 0, tol = 0.001495426527055874 Iteration 49: loglikelihood = -219.40362030781677, backtracks = 0, tol = 0.001286324051089446 Iteration 50: loglikelihood = -219.4006747755802, backtracks = 0, tol = 0.001295957349435961 Iteration 51: loglikelihood = -219.39813103252988, backtracks = 0, tol = 0.0011058748112207813 Iteration 52: loglikelihood = -219.3959322024177, backtracks = 0, tol = 0.0011233728145861855 Iteration 53: loglikelihood = -219.39403166729804, backtracks = 0, tol = 0.0009536994758608786 Iteration 54: loglikelihood = -219.39238763268273, backtracks = 0, tol = 0.0009739180646352119 Iteration 55: loglikelihood = -219.39096560226784, backtracks = 0, tol = 0.0008239389039648708 Iteration 56: loglikelihood = -219.38973473800374, backtracks = 0, tol = 0.0008444580901064712 Iteration 57: loglikelihood = -219.3886694316569, backtracks = 0, tol = 0.0007126409505425607 Iteration 58: loglikelihood = -219.38774685610232, backtracks = 0, tol = 0.0007323063866727435 Iteration 59: loglikelihood = -219.3869479529937, backtracks = 0, tol = 0.00061686194275372 Iteration 60: loglikelihood = -219.3862557798823, backtracks = 0, tol = 0.0006351404346176769 Iteration 61: loglikelihood = -219.3856561234815, backtracks = 0, tol = 0.000534269842115572 Iteration 62: loglikelihood = -219.38513638040487, backtracks = 0, tol = 0.0005509480422217535 Iteration 63: loglikelihood = -219.38468593224545, backtracks = 0, tol = 0.0004629512780606966 Iteration 64: loglikelihood = -219.38429538513583, backtracks = 0, tol = 0.0004779860767529819 Iteration 65: loglikelihood = -219.38395679466737, backtracks = 0, tol = 0.0004013057505476397 Iteration 66: loglikelihood = -219.38366314739872, backtracks = 0, tol = 0.0004147454994836376 Iteration 67: loglikelihood = -219.38340849212824, backtracks = 0, tol = 0.00034797985178746597 Iteration 68: loglikelihood = -219.38318758502183, backtracks = 0, tol = 0.0003599207374415984 Iteration 69: loglikelihood = -219.38299596326374, backtracks = 0, tol = 0.0003018217223394219 Iteration 70: loglikelihood = -219.3828297011887, backtracks = 0, tol = 0.00031238270039476616 Iteration 71: loglikelihood = -219.38268544908368, backtracks = 0, tol = 0.00026184698528793125 Iteration 72: loglikelihood = -219.3825602648841, backtracks = 0, tol = 0.0002711550905775348 Iteration 73: loglikelihood = -219.38245163239276, backtracks = 0, tol = 0.00022721198022395564 Iteration 74: loglikelihood = -219.38235734460943, backtracks = 0, tol = 0.00023539371282360467 Iteration 75: loglikelihood = -219.38227551018164, backtracks = 0, tol = 0.0001971920991460162 Iteration 76: loglikelihood = -219.382204472153, backtracks = 0, tol = 0.00020436848993624394 Iteration 77: loglikelihood = -219.3821428080304, backtracks = 0, tol = 0.00017116393516432852 Iteration 78: loglikelihood = -219.38208927292968, backtracks = 0, tol = 0.00017744788492952903 Iteration 79: loglikelihood = -219.38204279645043, backtracks = 0, tol = 0.00014859040670150365 Iteration 80: loglikelihood = -219.38200244272016, backtracks = 0, tol = 0.00015408544066832546 Iteration 81: loglikelihood = -219.38196740593906, backtracks = 0, tol = 0.00012900826739905896 Iteration 82: loglikelihood = -219.38193698216227, backtracks = 0, tol = 0.00013380816660865064 Iteration 83: loglikelihood = -219.38191056455443, backtracks = 0, tol = 0.00011201756190578927 Iteration 84: loglikelihood = -219.3818876233726, backtracks = 0, tol = 0.000116206527337935 Iteration 85: loglikelihood = -219.38186770147453, backtracks = 0, tol = 9.727268703830643e-5 Test Summary: | Pass Total Time fit Bernoulli SnpLinAlg | 4 4 3.0s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse Poisson regression Number of threads = 1 Link functin = LogLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1891.2462919926966, backtracks = 0, tol = 0.3948130123537378 Iteration 2: loglikelihood = -1467.2620684102772, backtracks = 0, tol = 0.07108294821749922 Iteration 3: loglikelihood = -1400.9097959476123, backtracks = 0, tol = 0.05112809688328976 Iteration 4: loglikelihood = -1340.7153723519223, backtracks = 0, tol = 0.10966099509565545 Iteration 5: loglikelihood = -1330.4988249096198, backtracks = 0, tol = 0.03955004878144754 Iteration 6: loglikelihood = -1325.8510096265939, backtracks = 0, tol = 0.029746628821870187 Iteration 7: loglikelihood = -1323.0731316704967, backtracks = 0, tol = 0.017971138887671576 Iteration 8: loglikelihood = -1321.5292002129565, backtracks = 0, tol = 0.01564680652078499 Iteration 9: loglikelihood = -1320.5961944527446, backtracks = 0, tol = 0.010399296092828154 Iteration 10: loglikelihood = -1320.0848251225123, backtracks = 0, tol = 0.008379814514665268 Iteration 11: loglikelihood = -1319.3904720034207, backtracks = 0, tol = 0.06455734598191896 Iteration 12: loglikelihood = -1318.927321701051, backtracks = 0, tol = 0.06419422893463922 Iteration 13: loglikelihood = -1318.544271692106, backtracks = 0, tol = 0.008968398229859025 Iteration 14: loglikelihood = -1318.451005675695, backtracks = 0, tol = 0.002455345421709794 Iteration 15: loglikelihood = -1318.40665222923, backtracks = 0, tol = 0.003152738343786405 Iteration 16: loglikelihood = -1318.382802504812, backtracks = 0, tol = 0.001473894804451892 Iteration 17: loglikelihood = -1318.3688992860464, backtracks = 0, tol = 0.001994905078402034 Iteration 18: loglikelihood = -1318.3605558880997, backtracks = 0, tol = 0.0009009937918582453 Iteration 19: loglikelihood = -1318.3554798314453, backtracks = 0, tol = 0.0012183428992871594 Iteration 20: loglikelihood = -1318.3523589402844, backtracks = 0, tol = 0.0005547759608586257 Iteration 21: loglikelihood = -1318.3504337740787, backtracks = 0, tol = 0.0007433012157903311 Iteration 22: loglikelihood = -1318.3492399486965, backtracks = 0, tol = 0.00034297841547989845 Iteration 23: loglikelihood = -1318.3484987296983, backtracks = 0, tol = 0.00045543639435083685 Iteration 24: loglikelihood = -1318.3480371258902, backtracks = 0, tol = 0.00021278740866164343 Iteration 25: loglikelihood = -1318.3477494735946, backtracks = 0, tol = 0.000280337776399097 Iteration 26: loglikelihood = -1318.3475698894276, backtracks = 0, tol = 0.0001323864824795809 Iteration 27: loglikelihood = -1318.3474577302134, backtracks = 0, tol = 0.00017323360967062213 Iteration 28: loglikelihood = -1318.3473876008873, backtracks = 0, tol = 8.253779631103168e-5 Test Summary: | Pass Total Time fit Poisson SnpLinAlg | 4 4 2.3s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse 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 = -1575.3247099117325, backtracks = 0, tol = 0.4502611218995794 Iteration 2: loglikelihood = -1491.656151013635, backtracks = 0, tol = 0.1485259572284597 Iteration 3: loglikelihood = -1460.081192170207, backtracks = 0, tol = 0.10456264599431606 Iteration 4: loglikelihood = -1452.455048660343, backtracks = 0, tol = 0.10429539501928074 Iteration 5: loglikelihood = -1449.0709234614344, backtracks = 0, tol = 0.0963686011231672 Iteration 6: loglikelihood = -1448.7977843284139, backtracks = 1, tol = 0.007731837885237061 Iteration 7: loglikelihood = -1448.6631124080902, backtracks = 1, tol = 0.008419838509628467 Iteration 8: loglikelihood = -1448.6148121569618, backtracks = 1, tol = 0.005867988448693003 Iteration 9: loglikelihood = -1448.6073417943978, backtracks = 2, tol = 0.0015927759733974085 Iteration 10: loglikelihood = -1448.6030352017453, backtracks = 2, tol = 0.0012343037574012825 Iteration 11: loglikelihood = -1448.6006395182458, backtracks = 2, tol = 0.0009269932810607964 Iteration 12: loglikelihood = -1448.5993176319205, backtracks = 2, tol = 0.0006919432198472932 Iteration 13: loglikelihood = -1448.5985907782367, backtracks = 2, tol = 0.0005150764006069789 Iteration 14: loglikelihood = -1448.5981919763901, backtracks = 2, tol = 0.00038270764422268825 Iteration 15: loglikelihood = -1448.5979734997356, backtracks = 2, tol = 0.00028396801365971025 Iteration 16: loglikelihood = -1448.5978539445896, backtracks = 2, tol = 0.0002104860050208621 Iteration 17: loglikelihood = -1448.5977885756995, backtracks = 2, tol = 0.00015589541698260632 Iteration 18: loglikelihood = -1448.5977528563228, backtracks = 2, tol = 0.00011539254586060155 Iteration 19: loglikelihood = -1448.5977333474025, backtracks = 2, tol = 8.537197476379275e-5 Test Summary: | Pass Total Time fit NegativeBinomial SnpLinAlg | 4 4 1.2s **** 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 = -2006.1474746909182, backtracks = 0, tol = 0.7502058379642909 Iteration 2: loglikelihood = -1477.6356937971484, backtracks = 0, tol = 0.15375950288625023 Iteration 3: loglikelihood = -1368.9139336175126, backtracks = 0, tol = 0.06573833026855154 Iteration 4: loglikelihood = -1353.6240640283415, backtracks = 0, tol = 0.02990708201413829 Iteration 5: loglikelihood = -1352.4204772662436, backtracks = 0, tol = 0.023001478893907554 Iteration 6: loglikelihood = -1352.0831203899866, backtracks = 0, tol = 0.022891371648470996 Iteration 7: loglikelihood = -1351.9769019132573, backtracks = 0, tol = 0.0015733019493324293 Iteration 8: loglikelihood = -1351.9758090667654, backtracks = 1, tol = 0.0001160567825174929 Iteration 9: loglikelihood = -1351.9755113626143, backtracks = 1, tol = 6.0160936258846825e-5 Test Summary: | Pass Total Time fit with >1 non-genetic covariates SnpLinAlg | 5 5 1.4s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse linear regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1671.1996178556979, backtracks = 0, tol = 0.4926913473016392 Iteration 2: loglikelihood = -1409.8062200490954, backtracks = 0, tol = 0.10463076203187707 Iteration 3: loglikelihood = -1358.2092813458328, backtracks = 0, tol = 0.04988606948920034 Iteration 4: loglikelihood = -1353.632772518429, backtracks = 0, tol = 0.02776600204578528 Iteration 5: loglikelihood = -1353.2593932014836, backtracks = 0, tol = 0.003808353797098955 Iteration 6: loglikelihood = -1352.2985549879174, backtracks = 0, tol = 0.02578054806979083 Iteration 7: loglikelihood = -1352.1912589501906, backtracks = 0, tol = 0.0023011297101424937 Iteration 8: loglikelihood = -1352.1903363397957, backtracks = 0, tol = 0.0002276236081815952 Iteration 9: loglikelihood = -1352.1903245765836, backtracks = 0, tol = 1.7893834148710438e-5 Test Summary: | Pass Total Time model selection on non-genetic covariates | 5 5 0.7s **** 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) = 15 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1473.1241001452804, backtracks = 0, tol = 0.11162633196865432 Iteration 2: loglikelihood = -1448.37403799896, backtracks = 0, tol = 0.07736217654955346 Iteration 3: loglikelihood = -1429.8981769610311, backtracks = 1, tol = 0.056531823476744666 Iteration 4: loglikelihood = -1404.7133956159753, backtracks = 0, tol = 0.10125409614175712 Iteration 5: loglikelihood = -1397.466171579031, backtracks = 0, tol = 0.05343369325195713 Iteration 6: loglikelihood = -1395.7490747391416, backtracks = 0, tol = 0.08843871418165582 Iteration 7: loglikelihood = -1395.4877576477586, backtracks = 0, tol = 0.008924704068495177 Iteration 8: loglikelihood = -1395.442237061722, backtracks = 0, tol = 0.005277867116132827 Iteration 9: loglikelihood = -1395.4302205892106, backtracks = 0, tol = 0.0027680467744013336 Iteration 10: loglikelihood = -1395.1973617039412, backtracks = 0, tol = 0.09056900655606137 Iteration 11: loglikelihood = -1395.0048067729406, backtracks = 0, tol = 0.007650485819168892 Iteration 12: loglikelihood = -1394.9835209063683, backtracks = 0, tol = 0.0035232591741737973 Iteration 13: loglikelihood = -1394.9793628241396, backtracks = 0, tol = 0.001852195878065177 Iteration 14: loglikelihood = -1394.9779889816232, backtracks = 0, tol = 0.0012530451800711446 Iteration 15: loglikelihood = -1394.977503420045, backtracks = 0, tol = 0.0006829444661300694 Iteration 16: loglikelihood = -1394.9773714862843, backtracks = 1, tol = 0.00022881022816864148 Iteration 17: loglikelihood = -1394.9773102201912, backtracks = 2, tol = 0.0001217788197399568 Iteration 18: loglikelihood = -1394.977273607278, backtracks = 2, tol = 8.822469907087602e-5 **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse linear regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 3 Prior weight scaling = off Doubly sparse projection = on Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1535.4672180567934, backtracks = 0, tol = 0.17016419679985048 Iteration 2: loglikelihood = -1508.04343741211, backtracks = 0, tol = 0.21718489399873087 Iteration 3: loglikelihood = -1448.2717322168082, backtracks = 0, tol = 0.15334504607402907 Iteration 4: loglikelihood = -1437.5669418734744, backtracks = 0, tol = 0.08425396177776269 Iteration 5: loglikelihood = -1434.3602241747526, backtracks = 0, tol = 0.03199716666887782 Iteration 6: loglikelihood = -1434.239273652971, backtracks = 2, tol = 0.003498168340088284 Iteration 7: loglikelihood = -1434.1475478538455, backtracks = 2, tol = 0.003052291101552644 Iteration 8: loglikelihood = -1434.0913475157126, backtracks = 2, tol = 0.002193157681835551 Iteration 9: loglikelihood = -1434.0584761985995, backtracks = 2, tol = 0.0016688209654910676 Iteration 10: loglikelihood = -1434.0393127719108, backtracks = 2, tol = 0.001317554485128468 Iteration 11: loglikelihood = -1434.0281644425422, backtracks = 2, tol = 0.0010393713220469133 Iteration 12: loglikelihood = -1434.0216963632631, backtracks = 2, tol = 0.0008158673348111326 Iteration 13: loglikelihood = -1434.0179556115856, backtracks = 2, tol = 0.0006363671566384205 Iteration 14: loglikelihood = -1433.8972844529703, backtracks = 2, tol = 0.021056460842673336 Iteration 15: loglikelihood = -1433.6170929347984, backtracks = 1, tol = 0.011448126839540959 Iteration 16: loglikelihood = -1433.5408744767517, backtracks = 2, tol = 0.0040324300639331045 Iteration 17: loglikelihood = -1433.4945867179188, backtracks = 2, tol = 0.003005268578298657 Iteration 18: loglikelihood = -1433.467626121943, backtracks = 2, tol = 0.002187229771831415 Iteration 19: loglikelihood = -1433.4521439235273, backtracks = 2, tol = 0.0016467936133078437 Iteration 20: loglikelihood = -1433.4432822302874, backtracks = 2, tol = 0.0012631945762950846 Iteration 21: loglikelihood = -1433.4382075829426, backtracks = 2, tol = 0.0009580287583338233 Iteration 22: loglikelihood = -1433.4352962137846, backtracks = 2, tol = 0.0007222437442123496 Iteration 23: loglikelihood = -1433.4336216439426, backtracks = 2, tol = 0.0005424739396431646 Iteration 24: loglikelihood = -1433.43265547142, backtracks = 2, tol = 0.0004062814588068666 Iteration 25: loglikelihood = -1433.4320960523787, backtracks = 2, tol = 0.00030341799187724174 Iteration 26: loglikelihood = -1433.4317709097872, backtracks = 2, tol = 0.00022583740291083832 Iteration 27: loglikelihood = -1433.4315812027676, backtracks = 2, tol = 0.0001673653861249394 Iteration 28: loglikelihood = -1432.5898379532828, backtracks = 2, tol = 0.0250802150540324 Iteration 29: loglikelihood = -1431.7678006470733, backtracks = 1, tol = 0.017181190475547 Iteration 30: loglikelihood = -1430.3157393955933, backtracks = 1, tol = 0.07333968264200223 Iteration 31: loglikelihood = -1429.706868513855, backtracks = 0, tol = 0.02001511172794573 Iteration 32: loglikelihood = -1429.5802551945537, backtracks = 1, tol = 0.00756937670420323 Iteration 33: loglikelihood = -1429.513945055356, backtracks = 2, tol = 0.003906515984506249 Iteration 34: loglikelihood = -1429.469197232521, backtracks = 2, tol = 0.003683664863256532 Iteration 35: loglikelihood = -1428.86075262229, backtracks = 2, tol = 0.08711763846658718 Iteration 36: loglikelihood = -1428.6178427111051, backtracks = 1, tol = 0.006558345246943248 Iteration 37: loglikelihood = -1428.5424083746184, backtracks = 2, tol = 0.0033912200662443866 Iteration 38: loglikelihood = -1428.4933608487952, backtracks = 2, tol = 0.0030098214824111564 Iteration 39: loglikelihood = -1428.4620745885084, backtracks = 2, tol = 0.002595137111913267 Iteration 40: loglikelihood = -1428.4427329028306, backtracks = 2, tol = 0.002148184701148499 Iteration 41: loglikelihood = -1428.4311433050725, backtracks = 2, tol = 0.0017160493175770867 Iteration 42: loglikelihood = -1428.4243474878394, backtracks = 2, tol = 0.0013407892924840858 Iteration 43: loglikelihood = -1428.420413936832, backtracks = 2, tol = 0.0010343694042998762 Iteration 44: loglikelihood = -1428.4181556141764, backtracks = 2, tol = 0.0007948565534422845 Iteration 45: loglikelihood = -1428.4168664091337, backtracks = 2, tol = 0.000608309643427293 Iteration 46: loglikelihood = -1428.4161334920516, backtracks = 2, tol = 0.0004622621654004415 Iteration 47: loglikelihood = -1428.4157180925672, backtracks = 2, tol = 0.00034956951660976293 Iteration 48: loglikelihood = -1428.4154831711999, backtracks = 2, tol = 0.00026348047442121094 Iteration 49: loglikelihood = -1428.415350523391, backtracks = 2, tol = 0.00019816133989405092 Iteration 50: loglikelihood = -1428.4152757065372, backtracks = 2, tol = 0.00014882628973649723 Iteration 51: loglikelihood = -1428.4152335404317, backtracks = 2, tol = 0.00011167501044822909 Iteration 52: loglikelihood = -1428.4152097888611, backtracks = 2, tol = 8.375238803842589e-5 Test Summary: | Pass Total Time Correlated predictors and double sparsity Float64 matrix | 2 2 7.6s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse NegativeBinomial regression Number of threads = 1 Link functin = LogLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1594.374547132283, backtracks = 0, tol = 0.278496374393472 Iteration 2: loglikelihood = -1520.506316347317, backtracks = 0, tol = 0.09793016236461001 Iteration 3: loglikelihood = -1470.2106947937762, backtracks = 0, tol = 0.16298558038416547 Iteration 4: loglikelihood = -1438.0627182353871, backtracks = 0, tol = 0.1316504952781841 Iteration 5: loglikelihood = -1426.0542214063184, backtracks = 0, tol = 0.029622165386953864 Iteration 6: loglikelihood = -1416.369315520832, backtracks = 1, tol = 0.0763598839677371 Iteration 7: loglikelihood = -1413.6232885170261, backtracks = 0, tol = 0.03843969076024097 Iteration 8: loglikelihood = -1412.2027496035712, backtracks = 0, tol = 0.01543531471817483 Iteration 9: loglikelihood = -1398.7118700320132, backtracks = 0, tol = 0.07268715230220726 Iteration 10: loglikelihood = -1396.1717725644562, backtracks = 0, tol = 0.029326113195154758 Iteration 11: loglikelihood = -1395.656628558943, backtracks = 0, tol = 0.012378151133782074 Iteration 12: loglikelihood = -1395.4628472145034, backtracks = 0, tol = 0.007716272180103701 Iteration 13: loglikelihood = -1395.3800488102315, backtracks = 0, tol = 0.005064255700169723 Iteration 14: loglikelihood = -1393.1530297491145, backtracks = 0, tol = 0.058058890009728935 Iteration 15: loglikelihood = -1392.6898032287436, backtracks = 0, tol = 0.007488758071122666 Iteration 16: loglikelihood = -1392.665552735253, backtracks = 0, tol = 0.002649732991456561 Iteration 17: loglikelihood = -1392.6562381502881, backtracks = 0, tol = 0.001672197475121591 Iteration 18: loglikelihood = -1392.6521461578338, backtracks = 0, tol = 0.0011311758626373321 Iteration 19: loglikelihood = -1392.6503384875746, backtracks = 0, tol = 0.0007194959452702394 Iteration 20: loglikelihood = -1392.6495285394997, backtracks = 0, tol = 0.0004992746021279855 Iteration 21: loglikelihood = -1392.6491718319717, backtracks = 0, tol = 0.00032131978138568676 Iteration 22: loglikelihood = -1392.6490124045424, backtracks = 0, tol = 0.00021929513018895192 Iteration 23: loglikelihood = -1392.6489426230635, backtracks = 0, tol = 0.0001426563164020173 Iteration 24: loglikelihood = -1392.6489115631964, backtracks = 0, tol = 9.586392700116097e-5 1.101539 seconds (2.34 M allocations: 46.802 MiB, 9.64% gc time, 56.94% 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 = -1610.4408842460336, backtracks = 0, tol = 0.278496374393472 Iteration 2: loglikelihood = -1564.9698234188975, backtracks = 0, tol = 0.10979536489144945 Iteration 3: loglikelihood = -1511.7896183415708, backtracks = 0, tol = 0.17541005455678801 Iteration 4: loglikelihood = -1495.7766492716821, backtracks = 0, tol = 0.12320330846235351 Iteration 5: loglikelihood = -1480.4970362169888, backtracks = 0, tol = 0.02778660615929167 Iteration 6: loglikelihood = -1461.1032471336866, backtracks = 1, tol = 0.09714321214610627 Iteration 7: loglikelihood = -1447.2399313614592, backtracks = 0, tol = 0.08762143049274228 Iteration 8: loglikelihood = -1439.8850866654948, backtracks = 0, tol = 0.019708785915818188 Iteration 9: loglikelihood = -1435.483327185277, backtracks = 0, tol = 0.08174288077191885 Iteration 10: loglikelihood = -1428.9727372820037, backtracks = 0, tol = 0.07373927863963826 Iteration 11: loglikelihood = -1424.908076684328, backtracks = 0, tol = 0.0048391509822891445 Iteration 12: loglikelihood = -1421.7218893665336, backtracks = 0, tol = 0.0023009111993167125 Iteration 13: loglikelihood = -1418.9662071327489, backtracks = 0, tol = 0.0005390578080929335 Iteration 14: loglikelihood = -1416.6077527913017, backtracks = 0, tol = 0.0004017148477837029 Iteration 15: loglikelihood = -1414.5530325631844, backtracks = 0, tol = 0.0004034761254740277 Iteration 16: loglikelihood = -1412.7632880177664, backtracks = 0, tol = 0.0003771666923892348 Iteration 17: loglikelihood = -1411.188105722855, backtracks = 0, tol = 0.0003386463377499005 Iteration 18: loglikelihood = -1409.7987986172477, backtracks = 0, tol = 0.0003103665769308151 Iteration 19: loglikelihood = -1408.564296445665, backtracks = 0, tol = 0.00028469468648667875 Iteration 20: loglikelihood = -1407.4644161611438, backtracks = 0, tol = 0.00026237578580464436 Iteration 21: loglikelihood = -1406.4789459684375, backtracks = 0, tol = 0.0002432824945696868 Iteration 22: loglikelihood = -1405.5935954847396, backtracks = 0, tol = 0.00022557387621645322 Iteration 23: loglikelihood = -1404.7946610315018, backtracks = 0, tol = 0.0002105842433238752 Iteration 24: loglikelihood = -1404.071860281936, backtracks = 0, tol = 0.00019633657304960327 Iteration 25: loglikelihood = -1403.4155838932058, backtracks = 0, tol = 0.00018420829930362672 Iteration 26: loglikelihood = -1402.8183020365861, backtracks = 0, tol = 0.0001725869506752331 Iteration 27: loglikelihood = -1402.273085770529, backtracks = 0, tol = 0.00016257955293213374 Iteration 28: loglikelihood = -1401.7743266052462, backtracks = 0, tol = 0.00015297733424587194 Iteration 29: loglikelihood = -1401.316909982806, backtracks = 0, tol = 0.0001446000441737635 Iteration 30: loglikelihood = -1400.8965922096004, backtracks = 0, tol = 0.00013657103684640306 Iteration 31: loglikelihood = -1400.5095221254012, backtracks = 0, tol = 0.00012947717865140283 Iteration 32: loglikelihood = -1400.1524420859032, backtracks = 0, tol = 0.00012269042001257442 Iteration 33: loglikelihood = -1399.8224021587523, backtracks = 0, tol = 0.00011662500955012105 Iteration 34: loglikelihood = -1399.5168685538424, backtracks = 0, tol = 0.00011083189775300376 Iteration 35: loglikelihood = -1399.2335477346685, backtracks = 0, tol = 0.00010560213483620684 Iteration 36: loglikelihood = -1398.9704452003932, backtracks = 0, tol = 0.00010061352492219456 Iteration 37: loglikelihood = -1398.7257542303205, backtracks = 0, tol = 9.607063309581218e-5 0.373332 seconds (1.40 M allocations: 25.380 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 = -3545.0027, backtracks = 0, tol = 0.08412858512528902 Iteration 2: loglikelihood = -3497.2783, backtracks = 0, tol = 0.04301747997136826 Iteration 3: loglikelihood = -3492.7239, backtracks = 1, tol = 0.015278101432228602 Iteration 4: loglikelihood = -3476.7625, backtracks = 1, tol = 0.06203722497829146 Iteration 5: loglikelihood = -3472.8616, backtracks = 0, tol = 0.0170597921204366 Iteration 6: loglikelihood = -3472.3152, backtracks = 0, tol = 0.007048615767907882 Iteration 7: loglikelihood = -3472.2288, backtracks = 1, tol = 0.0008934896869521434 Iteration 8: loglikelihood = -3472.1895, backtracks = 1, tol = 0.0013721947415121015 Iteration 9: loglikelihood = -3472.178, backtracks = 1, tol = 0.0008026527871976451 Iteration 10: loglikelihood = -3472.176, backtracks = 1, tol = 0.0003733378493415462 Iteration 11: loglikelihood = -3472.1758, backtracks = 2, tol = 0.00010148776946377345 Iteration 12: loglikelihood = -3472.181, backtracks = 3, tol = 3.751762755706975e-5 19.639645 seconds (14.51 M allocations: 688.379 MiB, 1.11% gc time, 97.49% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** 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 = -3439.8523, backtracks = 0, tol = 0.08412858512528902 Iteration 2: loglikelihood = -3324.0825, backtracks = 0, tol = 0.0443195006088721 Iteration 3: loglikelihood = -3152.0833, backtracks = 1, tol = 0.014475322960679361 Iteration 4: loglikelihood = -2953.7314, backtracks = 1, tol = 0.007446186445372689 Iteration 5: loglikelihood = -2746.3062, backtracks = 1, tol = 0.003446997225879207 Iteration 6: loglikelihood = -2727.2285, backtracks = 0, tol = 0.08312875367147429 Iteration 7: loglikelihood = -2579.245, backtracks = 0, tol = 0.11319490486469197 Iteration 8: loglikelihood = -2424.7834, backtracks = 0, tol = 0.09216249168599464 Iteration 9: loglikelihood = -2343.459, backtracks = 0, tol = 0.08501483522379015 Iteration 10: loglikelihood = -2285.655, backtracks = 0, tol = 0.08438654691549347 Iteration 11: loglikelihood = -2249.8403, backtracks = 0, tol = 0.08127994390273628 Iteration 12: loglikelihood = -2215.1335, backtracks = 0, tol = 0.08860587139574776 Iteration 13: loglikelihood = -2195.7012, backtracks = 0, tol = 0.015182912741496333 Iteration 14: loglikelihood = -2184.646, backtracks = 0, tol = 0.0029707646576222968 Iteration 15: loglikelihood = -2177.7563, backtracks = 0, tol = 0.07777515124910245 Iteration 16: loglikelihood = -2175.033, backtracks = 0, tol = 0.08265407039846434 Iteration 17: loglikelihood = -2172.5967, backtracks = 0, tol = 0.08402642856631824 Iteration 18: loglikelihood = -2170.201, backtracks = 1, tol = 0.013848907017501686 Iteration 19: loglikelihood = -2169.6104, backtracks = 1, tol = 0.005949293088362851 Iteration 20: loglikelihood = -2169.4778, backtracks = 1, tol = 0.0024140703833515718 Iteration 21: loglikelihood = -2169.445, backtracks = 1, tol = 0.0011688021718387254 Iteration 22: loglikelihood = -2169.4346, backtracks = 1, tol = 0.0006325732910621367 Iteration 23: loglikelihood = -2169.4316, backtracks = 1, tol = 0.00033934068408715085 Iteration 24: loglikelihood = -2169.4297, backtracks = 1, tol = 0.00018163982286098946 Iteration 25: loglikelihood = -2169.4282, backtracks = 2, tol = 4.8425038471401816e-5 0.307674 seconds (1.42 M allocations: 23.690 MiB, 40.62% gc time) Test Summary: | Pass Total Time Negative binomial nuisance parameter Float32 matrix | 12 12 23.8s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** ┌ Warning: accessing `Type.name` is deprecated without replacement. If for detection, use `Base.isType(x)`. │ caller = ProgressMeter.Progress(n::Int64, dt::Int64, desc::String, barlen::Nothing, color::Symbol, output::Base.PipeEndpoint; offset::Int64) at deprecated.jl:1 └ @ ProgressMeter ~/.julia/packages/ProgressMeter/N660J/src/deprecated.jl:1 Running sparse linear regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -2896.6116813943763, backtracks = 0, tol = 1.0257704354307224 Iteration 2: loglikelihood = -1753.4720992614753, backtracks = 0, tol = 0.2870682551290383 Iteration 3: loglikelihood = -1460.3823326395222, backtracks = 0, tol = 0.1059822007319242 Iteration 4: loglikelihood = -1438.5292259047123, backtracks = 0, tol = 0.028655431669451118 Iteration 5: loglikelihood = -1438.0856032112097, backtracks = 0, tol = 0.0034955373515602557 Iteration 6: loglikelihood = -1438.074435032946, backtracks = 0, tol = 0.0005882060650840543 Iteration 7: loglikelihood = -1438.0741395461055, backtracks = 0, tol = 8.427264473930937e-5 4.450936 seconds (956.65 k allocations: 129.027 MiB, 3.59% gc time, 89.13% compilation time) Test Summary: | Pass Total Time initialze beta | 1 1 4.8s 7.536539 seconds (4.01 M allocations: 82.742 MiB, 4.97% gc time, 0.97% compilation time) 4.022215 seconds (3.98 M allocations: 91.814 MiB, 0.79% gc time) 10.315922 seconds (20.65 M allocations: 454.865 MiB, 0.89% gc time, 18.48% compilation time: 57% of which was recompilation) 8.090150 seconds (20.19 M allocations: 434.819 MiB, 1.14% gc time) 27.024498 seconds (3.45 M allocations: 4.232 GiB, 6.48% gc time, 28.39% compilation time) 37.738547 seconds (84.77 k allocations: 183.943 MiB, 0.93% gc time) Test Summary: | Pass Total Time memory_efficient keyword | 7 7 1m51.3s Test Summary: | Pass Total Time update_support! | 10 10 0.4s 15.134 ms (89 allocations: 5.19 KiB) 4.583 μs (0 allocations: 0 bytes) 99.219 μs (4 allocations: 288 bytes) 491.490 ns (0 allocations: 0 bytes) 35.080 μs (2 allocations: 64 bytes) 20.820 μs (0 allocations: 0 bytes) 3.578 μs (0 allocations: 0 bytes) 3.764 μs (0 allocations: 0 bytes) 67.430 μs (0 allocations: 0 bytes) 35.133 ms (89 allocations: 5.19 KiB) 18.489 μs (0 allocations: 0 bytes) 121.779 μs (4 allocations: 288 bytes) 2.793 μs (0 allocations: 0 bytes) 154.268 μs (2 allocations: 64 bytes) 44.979 μs (0 allocations: 0 bytes) 23.890 μs (0 allocations: 0 bytes) 24.390 μs (0 allocations: 0 bytes) 159.469 μs (0 allocations: 0 bytes) Test Summary: | Total Time benchmarks for multivariate function | 0 1m51.5s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse Multivariate Gaussian regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 12 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -2900.918630019449, backtracks = 0, tol = 0.14802242082004138 Iteration 2: loglikelihood = -2869.406464695619, backtracks = 0, tol = 0.03512679046077988 Iteration 3: loglikelihood = -2868.084702693443, backtracks = 0, tol = 0.005569349616332472 Iteration 4: loglikelihood = -2868.034423817725, backtracks = 0, tol = 0.0011189517628951667 Iteration 5: loglikelihood = -2868.0308576353746, backtracks = 0, tol = 0.00031182601179140966 Iteration 6: loglikelihood = -2868.0305288614227, backtracks = 0, tol = 0.00010393305949948345 Iteration 7: loglikelihood = -2868.0304966516946, backtracks = 0, tol = 3.100862049858006e-5 0.429125 seconds (46.08 k allocations: 5.433 MiB, 59.27% compilation time) Test Summary: | Pass Total Time multivariate fit_iht SnpLinAlg | 7 7 10.0s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** 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 1.473704 seconds (235.79 k allocations: 166.099 MiB, 57.39% compilation time) Test Summary: | Pass Total Time initialze beta | 5 5 1.9s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** ┌ Warning: accessing `Type.name` is deprecated without replacement. If for detection, use `Base.isType(x)`. │ caller = ProgressMeter.Progress(n::Int64, desc::String, offset::Int64; kwargs::Base.Pairs{Symbol, Union{}, Nothing, @NamedTuple{}}) at deprecated.jl:5 └ @ ProgressMeter ~/.julia/packages/ProgressMeter/N660J/src/deprecated.jl:5 Cross validating... 3%|█ | ETA: 0:02:37 Cross validating... 14%|████▋ | ETA: 0:00:35 Cross validating... 17%|█████▋ | ETA: 0:00:28 Cross validating... 21%|██████▋ | ETA: 0:00:24 Cross validating... 24%|███████▋ | ETA: 0:00:20 Cross validating... 27%|████████▋ | ETA: 0:00:17 Cross validating... 30%|█████████▋ | ETA: 0:00:15 Cross validating... 33%|██████████▋ | ETA: 0:00:14 Cross validating... 37%|███████████▋ | ETA: 0:00:12 Cross validating... 40%|████████████▊ | ETA: 0:00:11 Cross validating... 43%|█████████████▊ | ETA: 0:00:09 Cross validating... 46%|██████████████▊ | ETA: 0:00:08 Cross validating... 49%|███████████████▊ | ETA: 0:00:08 Cross validating... 52%|████████████████▊ | ETA: 0:00:07 Cross validating... 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3393.1594054465068 1 2604.182973311049 2 1840.8074025052974 3 1479.7855350243012 4 1253.3423813309064 5 945.9197827091082 6 680.3673889774309 7 505.6981080421183 8 367.63407508247565 9 303.70238252366323 10 307.9808011423255 11 307.8562834559516 12 315.0443313562669 13 315.4379490045193 14 317.73877705453606 15 330.599995902558 16 323.4296741293551 17 323.2370562267774 18 333.8146626901464 19 352.98781364192683 20 361.84011863568037 Best k = 9 9.764367 seconds (11.81 M allocations: 318.619 MiB, 1.72% gc time, 55.33% 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: 0:00:03 Cross validating... 11%|███▌ | ETA: 0:00:03 Cross validating... 16%|█████▏ | ETA: 0:00:03 Cross validating... 19%|██████▏ | ETA: 0:00:03 Cross validating... 22%|███████▏ | ETA: 0:00:03 Cross validating... 25%|████████▏ | ETA: 0:00:03 Cross validating... 29%|█████████▏ | ETA: 0:00:03 Cross validating... 32%|██████████▏ | ETA: 0:00:03 Cross validating... 35%|███████████▏ | ETA: 0:00:03 Cross validating... 38%|████████████▎ | ETA: 0:00:03 Cross validating... 41%|█████████████▎ | ETA: 0:00:02 Cross validating... 44%|██████████████▎ | ETA: 0:00:02 Cross validating... 48%|███████████████▎ | ETA: 0:00:02 Cross validating... 51%|████████████████▎ | ETA: 0:00:02 Cross validating... 54%|█████████████████▎ | ETA: 0:00:02 Cross validating... 57%|██████████████████▎ | ETA: 0:00:02 Cross validating... 60%|███████████████████▎ | ETA: 0:00:02 Cross validating... 63%|████████████████████▍ | ETA: 0:00:02 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:01 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:01 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:01 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:01 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:01 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:01 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:00 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:00 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:04 Crossvalidation Results: k MSE 0 3393.1594054465068 1 2606.781290056814 2 1842.4333011669505 3 1486.8358292844855 4 1262.7023950924017 5 956.3178129691114 6 684.1994268680517 7 512.0249148351206 8 377.11501521269076 9 310.07097937177446 10 319.95829052232205 11 325.6400060121168 12 337.01071800807296 13 344.4587205166562 14 347.2441044506071 15 352.32695524418193 16 363.0575456735204 17 359.3420785346466 18 374.2135926213888 19 368.7674811566158 20 383.2690250704047 Best k = 9 4.458719 seconds (10.68 M allocations: 226.452 MiB, 1.88% gc time, 1.36% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, normal model | 3 3 14.9s **** 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: 0:04:21 Cross validating... 10%|███ | ETA: 0:01:23 Cross validating... 16%|█████▏ | ETA: 0:00:47 Cross validating... 21%|██████▋ | ETA: 0:00:34 Cross validating... 25%|████████▏ | ETA: 0:00:27 Cross validating... 30%|█████████▋ | ETA: 0:00:21 Cross validating... 35%|███████████▏ | ETA: 0:00:17 Cross validating... 41%|█████████████▎ | ETA: 0:00:13 Cross validating... 48%|███████████████▎ | ETA: 0:00:11 Cross validating... 52%|████████████████▊ | ETA: 0:00:09 Cross validating... 57%|██████████████████▎ | ETA: 0:00:07 Cross validating... 60%|███████████████████▎ | ETA: 0:00:07 Cross validating... 65%|████████████████████▉ | ETA: 0:00:05 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:04 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:03 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:02 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:01 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:01 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:10 Crossvalidation Results: k MSE 0 1550.2008327636718 1 1247.7656075439454 2 1011.6363612060546 3 796.0564381713867 4 634.8659105224609 5 516.1655781860352 6 454.4057174377441 7 375.787559173584 8 342.37153982543947 9 325.2862705383301 10 326.9348967590332 11 323.59544506835937 12 326.0145776672363 13 329.9478915710449 14 343.65410372924805 15 333.28846347045896 16 345.14634912109375 17 354.33269934082034 18 369.8271376342774 19 373.81982324218745 20 354.71919845581056 Best k = 11 12.186286 seconds (12.82 M allocations: 331.267 MiB, 0.77% gc time, 80.07% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 6%|██ | ETA: 0:00:02 Cross validating... 13%|████▏ | ETA: 0:00:02 Cross validating... 17%|█████▋ | ETA: 0:00:02 Cross validating... 22%|███████▏ | ETA: 0:00:02 Cross validating... 27%|████████▋ | ETA: 0:00:02 Cross validating... 30%|█████████▋ | ETA: 0:00:02 Cross validating... 35%|███████████▏ | ETA: 0:00:02 Cross validating... 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... 63%|████████████████████▍ | ETA: 0:00:01 Cross validating... 68%|█████████████████████▉ | ETA: 0:00:01 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:01 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:00 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:00 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:00 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:02 Crossvalidation Results: k MSE 0 1550.2008327636718 1 1253.738734741211 2 1013.2882860107421 3 796.0564381713867 4 635.3580806884765 5 524.0411033935546 6 461.34528958129886 7 381.48445996093756 8 350.3345552978516 9 345.4775199890137 10 343.30173101806645 11 345.72218676757814 12 346.0591227416992 13 359.4401893005371 14 364.20566857910154 15 368.3957327575684 16 375.5240364990234 17 389.1651905822754 18 395.0085117797852 19 387.24706115722654 20 401.3108792419434 Best k = 10 2.480857 seconds (11.05 M allocations: 203.956 MiB, 2.64% gc time, 1.74% compilation time) Test Summary: | Pass Total Time Cross validation on Float32 matrix, normal model | 2 2 16.0s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:42 Cross validating... 6%|██ | ETA: 0:00:23 Cross validating... 10%|███ | ETA: 0:00:16 Cross validating... 13%|████▏ | ETA: 0:00:13 Cross validating... 14%|████▋ | ETA: 0:00:12 Cross validating... 17%|█████▋ | ETA: 0:00:10 Cross validating... 21%|██████▋ | ETA: 0:00:09 Cross validating... 24%|███████▋ | ETA: 0:00:08 Cross validating... 27%|████████▋ | ETA: 0:00:07 Cross validating... 30%|█████████▋ | ETA: 0:00:07 Cross 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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: 0:00:06 Crossvalidation Results: k MSE 0 463.34744346965437 1 428.9275660183579 2 378.872545617867 3 350.5968959021418 4 337.92487286987193 5 310.9941777183019 6 287.41994296672436 7 259.98660600753414 8 243.1007036316392 9 249.56318684508636 10 256.0057248471991 11 254.25261005567538 12 262.70199404279595 13 270.35148922842836 14 257.42031125981464 15 272.88204027822235 16 309.04513733911745 17 265.19304896992236 18 276.7283930211854 19 322.308414686925 20 268.88573785886507 Best k = 8 7.397362 seconds (17.74 M allocations: 420.088 MiB, 1.66% gc time, 25.81% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:04 Cross validating... 6%|██ | ETA: 0:00:05 Cross validating... 10%|███ | ETA: 0:00:05 Cross validating... 13%|████▏ | ETA: 0:00:05 Cross validating... 16%|█████▏ | ETA: 0:00:05 Cross validating... 19%|██████▏ | ETA: 0:00:04 Cross validating... 22%|███████▏ | ETA: 0:00:04 Cross validating... 25%|████████▏ | ETA: 0:00:04 Cross validating... 29%|█████████▏ | ETA: 0:00:04 Cross validating... 32%|██████████▏ | ETA: 0:00:04 Cross validating... 35%|███████████▏ | ETA: 0:00:04 Cross validating... 38%|████████████▎ | ETA: 0:00:03 Cross validating... 41%|█████████████▎ | ETA: 0:00:03 Cross validating... 44%|██████████████▎ | ETA: 0:00:03 Cross validating... 48%|███████████████▎ | ETA: 0:00:03 Cross 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98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:05 Crossvalidation Results: k MSE 0 463.34744346965437 1 429.26197547783846 2 380.10705020082844 3 352.89701744867114 4 341.09294923578085 5 313.7982094898939 6 292.82381865003225 7 265.72644373626605 8 249.10980376894304 9 256.4924295345213 10 265.19428258172104 11 274.8296197213064 12 281.3776962033345 13 284.9322774699266 14 287.5593364093252 15 301.4258585702882 16 305.1005655411112 17 314.2820043185567 18 319.0989462172805 19 318.96145802457227 20 322.5772962295331 Best k = 8 5.596852 seconds (17.71 M allocations: 367.919 MiB, 1.87% gc time, 1.30% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, logistic model | 2 2 13.3s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:38 Cross validating... 8%|██▌ | ETA: 0:00:17 Cross validating... 13%|████▏ | ETA: 0:00:11 Cross validating... 16%|█████▏ | ETA: 0:00:09 Cross validating... 19%|██████▏ | ETA: 0:00:08 Cross validating... 22%|███████▏ | ETA: 0:00:07 Cross validating... 25%|████████▏ | ETA: 0:00:06 Cross validating... 29%|█████████▏ | ETA: 0:00:06 Cross validating... 32%|██████████▏ | ETA: 0:00:05 Cross validating... 35%|███████████▏ | ETA: 0:00:05 Cross validating... 40%|████████████▊ | ETA: 0:00:04 Cross validating... 43%|█████████████▊ | ETA: 0:00:04 Cross validating... 46%|██████████████▊ | ETA: 0:00:03 Cross validating... 49%|███████████████▊ | ETA: 0:00:03 Cross validating... 52%|████████████████▊ | ETA: 0:00:03 Cross validating... 56%|█████████████████▊ | ETA: 0:00:03 Cross validating... 59%|██████████████████▊ | ETA: 0:00:02 Cross validating... 62%|███████████████████▊ | ETA: 0:00:02 Cross validating... 65%|████████████████████▉ | ETA: 0:00:02 Cross validating... 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: 0:00:04 Crossvalidation Results: k MSE 0 464.3707911381221 1 438.8928617166121 2 400.2340141464298 3 389.348194347961 4 374.3762388849184 5 355.7641612198631 6 327.2180441996325 7 323.46183431369957 8 321.2581144353673 9 323.46103532468146 10 326.6769831351263 11 328.2582454752774 12 336.6687203374819 13 341.3187012293811 14 339.19866447740543 15 348.33302149269525 16 342.04163782040314 17 341.6211963385961 18 345.57290052297026 19 346.67745100630924 20 346.2380734955136 Best k = 8 6.188438 seconds (16.57 M allocations: 400.300 MiB, 1.92% gc time, 38.19% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 5%|█▌ | ETA: 0:00:04 Cross validating... 8%|██▌ | ETA: 0:00:04 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: 0:00:02 Cross validating... 41%|█████████████▎ | ETA: 0:00:02 Cross validating... 44%|██████████████▎ | ETA: 0:00:02 Cross validating... 48%|███████████████▎ | ETA: 0:00:02 Cross validating... 51%|████████████████▎ | ETA: 0:00:02 Cross validating... 54%|█████████████████▎ | ETA: 0:00:02 Cross validating... 57%|██████████████████▎ | ETA: 0:00:02 Cross validating... 60%|███████████████████▎ | ETA: 0:00:02 Cross validating... 63%|████████████████████▍ | ETA: 0:00:01 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:01 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:01 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:01 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:01 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:01 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:01 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:01 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:00 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:00 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:03 Crossvalidation Results: k MSE 0 464.3707911381221 1 441.6654988700243 2 403.5653395965501 3 392.9107426425899 4 377.9397840087287 5 360.1070437021019 6 332.513648695603 7 329.28849295300233 8 329.0472816539118 9 337.0821379462981 10 346.1697383053272 11 349.5748449498236 12 356.0947919052944 13 363.43333894404805 14 380.2586828126007 15 368.6257443922823 16 399.46963406643647 17 398.0697959024037 18 403.4055029825986 19 398.3323916137277 20 391.44479686210383 Best k = 8 4.050222 seconds (16.97 M allocations: 346.788 MiB, 1.83% gc time, 1.12% compilation time) Test Summary: | Pass Total Time Cross validation on Float64 matrix, logistic model | 2 2 10.8s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:41 Cross validating... 6%|██ | ETA: 0:00:22 Cross validating... 8%|██▌ | ETA: 0:00:19 Cross validating... 11%|███▌ | ETA: 0:00:15 Cross validating... 14%|████▋ | ETA: 0:00:12 Cross validating... 17%|█████▋ | ETA: 0:00:10 Cross validating... 21%|██████▋ | ETA: 0:00:09 Cross validating... 24%|███████▋ | ETA: 0:00:08 Cross validating... 27%|████████▋ | ETA: 0:00:07 Cross validating... 30%|█████████▋ | ETA: 0:00:07 Cross validating... 33%|██████████▋ | ETA: 0:00:06 Cross validating... 37%|███████████▋ | ETA: 0:00:06 Cross validating... 40%|████████████▊ | ETA: 0:00:05 Cross validating... 43%|█████████████▊ | ETA: 0:00:05 Cross validating... 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97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:06 Crossvalidation Results: k MSE 0 858.7182404741206 1 702.9526392128141 2 557.7882249608379 3 499.5481910125708 4 468.36614757286094 5 430.43813922109916 6 415.7524704479309 7 396.76412127043136 8 386.8716747048718 9 365.2343613812755 10 369.6590663312607 11 375.280862155177 12 370.93121909093406 13 371.2732379201622 14 375.47455431680515 15 389.3682125017117 16 393.2720345639103 17 400.58761135930956 18 416.34371704402326 19 389.2964239214959 20 386.12991775373433 Best k = 9 7.228297 seconds (15.21 M allocations: 361.900 MiB, 1.43% gc time, 25.85% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:04 Cross validating... 6%|██ | ETA: 0:00:05 Cross validating... 10%|███ | ETA: 0:00:05 Cross validating... 13%|████▏ | ETA: 0:00:05 Cross validating... 16%|█████▏ | ETA: 0:00:05 Cross validating... 19%|██████▏ | ETA: 0:00:04 Cross validating... 22%|███████▏ | ETA: 0:00:04 Cross validating... 25%|████████▏ | ETA: 0:00:04 Cross validating... 29%|█████████▏ | ETA: 0:00:04 Cross validating... 32%|██████████▏ | ETA: 0:00:04 Cross validating... 35%|███████████▏ | ETA: 0:00:03 Cross validating... 38%|████████████▎ | ETA: 0:00:03 Cross validating... 41%|█████████████▎ | ETA: 0:00:03 Cross validating... 44%|██████████████▎ | ETA: 0:00:03 Cross validating... 48%|███████████████▎ | ETA: 0:00:03 Cross validating... 51%|████████████████▎ | ETA: 0:00:03 Cross validating... 54%|█████████████████▎ | ETA: 0:00:02 Cross validating... 57%|██████████████████▎ | ETA: 0:00:02 Cross validating... 60%|███████████████████▎ | ETA: 0:00:02 Cross validating... 63%|████████████████████▍ | ETA: 0:00:02 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:02 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:02 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:01 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:01 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:01 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:01 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:01 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:01 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:00 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:05 Crossvalidation Results: k MSE 0 858.7182404741206 1 691.5518309421525 2 552.7427705555019 3 499.2734473662513 4 468.5548566860356 5 431.9047367041023 6 416.3650179616926 7 397.43302742580875 8 387.4776839680023 9 367.910845286506 10 387.41412429610625 11 382.28204748100245 12 388.88781387604706 13 390.5985578440595 14 392.96927800668624 15 408.1073869301672 16 410.8366630128042 17 406.63358071978894 18 422.4636464919556 19 424.9587044069704 20 430.8052180062448 Best k = 9 5.393699 seconds (14.23 M allocations: 286.084 MiB, 1.96% gc time, 0.55% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, Poisson model | 2 2 12.9s **** 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: 0:01:10 Cross validating... 5%|█▌ | ETA: 0:01:06 Cross validating... 6%|██ | ETA: 0:01:02 Cross validating... 10%|███ | ETA: 0:00:42 Cross validating... 11%|███▌ | ETA: 0:00:43 Cross validating... 13%|████▏ | ETA: 0:00:44 Cross validating... 14%|████▋ | ETA: 0:00:44 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51%|████████████████▎ | ETA: 0:00:23 Cross validating... 52%|████████████████▊ | ETA: 0:00:23 Cross validating... 54%|█████████████████▎ | ETA: 0:00:22 Cross validating... 56%|█████████████████▊ | ETA: 0:00:21 Cross validating... 57%|██████████████████▎ | ETA: 0:00:20 Cross validating... 59%|██████████████████▊ | ETA: 0:00:20 Cross validating... 60%|███████████████████▎ | ETA: 0:00:19 Cross validating... 62%|███████████████████▊ | ETA: 0:00:18 Cross validating... 63%|████████████████████▍ | ETA: 0:00:17 Cross validating... 65%|████████████████████▉ | ETA: 0:00:16 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:15 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:14 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:13 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:11 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:09 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:08 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:07 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:06 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:06 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:05 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:04 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:04 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:03 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:03 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:02 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:01 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:01 Cross validating... 100%|████████████████████████████████| Time: 0:00:39 Crossvalidation Results: k MSE 0 421.172644103455 1 337.0045163422653 2 292.93472834599964 3 284.0673193471309 4 255.65299076613215 5 244.54217522960425 6 237.00534490123871 7 229.87621999279355 8 226.6281457751139 9 227.2397134616956 10 227.07881785705513 11 229.7645648728929 12 227.9167642989887 13 228.18097275398566 14 233.10384271821977 15 231.818353802501 16 234.18309205370977 17 234.54561885701338 18 234.7026397732935 19 235.97528413287588 20 235.34289994625368 Best k = 8 39.677225 seconds (132.80 M allocations: 3.332 GiB, 1.40% gc time, 3.92% 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... 10%|███ | ETA: 0:00:06 Cross validating... 11%|███▌ | ETA: 0:00:07 Cross validating... 13%|████▏ | ETA: 0:00:07 Cross validating... 14%|████▋ | ETA: 0:00:07 Cross validating... 16%|█████▏ | ETA: 0:00:07 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81%|█████████████████████████▉ | ETA: 0:00:02 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:02 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:02 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:02 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:01 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:01 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:01 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:01 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:01 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:01 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:11 Crossvalidation Results: k MSE 0 421.172644103455 1 336.69421702088425 2 293.11829436242624 3 285.1099140605431 4 259.0657496397566 5 253.30505136063803 6 243.26988755968677 7 236.19086846314713 8 234.54818972876106 9 236.45370237274147 10 242.01121047668585 11 243.52857732692564 12 244.42320495791068 13 248.3212481822996 14 251.92723088817624 15 259.7851739033417 16 260.1427890710282 17 260.5391729638213 18 266.3019460994228 19 263.09046387448063 20 268.5474317870739 Best k = 8 12.057134 seconds (39.54 M allocations: 827.805 MiB, 1.63% gc time, 0.76% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, NegativeBinomial model | 2 2 52.0s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:48 Cross validating... 6%|██ | ETA: 0:00:25 Cross validating... 10%|███ | ETA: 0:00:17 Cross validating... 13%|████▏ | ETA: 0:00:13 Cross 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validating... 81%|█████████████████████████▉ | ETA: 0:00:01 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:01 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:01 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:05 Crossvalidation Results: k MSE 0 708.7406597900391 1 594.0547950439453 2 472.60887115478516 3 391.07051165771486 4 322.2429605712891 5 274.1304553527832 6 242.98796069335935 7 231.75397763061522 8 211.04413333129884 9 208.82878451538085 10 210.9139321594238 11 206.8662128601074 12 209.29315435791017 13 216.44690969848637 14 210.83974066162108 15 223.69269552612303 16 223.5122525024414 17 217.3672544555664 18 230.29235778808595 19 245.48900619506838 20 214.24631561279296 Best k = 11 5.690035 seconds (17.23 M allocations: 344.123 MiB, 7.13% gc time, 36.83% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 5%|█▌ | ETA: 0:00:03 Cross validating... 8%|██▌ | ETA: 0:00:08 Cross validating... 13%|████▏ | ETA: 0:00:06 Cross validating... 17%|█████▋ | ETA: 0:00:05 Cross validating... 22%|███████▏ | ETA: 0:00:04 Cross validating... 27%|████████▋ | ETA: 0:00:03 Cross validating... 30%|█████████▋ | ETA: 0:00:03 Cross validating... 35%|███████████▏ | ETA: 0:00:03 Cross validating... 38%|████████████▎ | ETA: 0:00:03 Cross validating... 41%|█████████████▎ | ETA: 0:00:02 Cross validating... 44%|██████████████▎ | 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: 0:00:01 Cross validating... 65%|████████████████████▉ | ETA: 0:00:01 Cross validating... 68%|█████████████████████▉ | ETA: 0:00:01 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:01 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:01 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:01 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:01 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:00 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:03 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 3.663463 seconds (16.27 M allocations: 288.782 MiB, 12.84% gc time, 1.11% compilation time) Test Summary: | Pass Total Time Cross validation on floating point matrices, NegativeBinomial model | 2 2 9.8s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 2%|▋ | ETA: 0:01:03 Cross validating... 3%|█ | ETA: 0:00:45 Cross validating... 4%|█▎ | ETA: 0:00:36 Cross validating... 5%|█▋ | ETA: 0:00:30 Cross validating... 6%|█▉ | ETA: 0:00:27 Cross validating... 7%|██▎ | ETA: 0:00:24 Cross validating... 8%|██▌ | ETA: 0:00:22 Cross 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ETA: 0:00:01 Cross validating... 96%|██████████████████████████████▊ | ETA: 0:00:01 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▍| ETA: 0:00:00 Cross validating... 99%|███████████████████████████████▋| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:16 Crossvalidation Results: k MSE 1 4352.61939613173 2 4036.838761067405 3 3838.7866942398264 4 3727.5435499393243 5 3611.114044953881 6 3425.0207174537113 7 3413.349602868825 8 3449.3996479761167 9 3442.9223077862794 10 3479.8564148745154 11 3500.551977836358 12 3546.234983154765 13 3634.2785446589996 14 3647.7059871168285 15 3699.322062434556 16 3689.570302766239 17 3702.7884210826915 18 3718.416899218296 19 3753.338704020542 20 3806.946075032376 Best k = 7 16.266161 seconds (319.56 k allocations: 199.407 MiB, 0.63% gc time, 8.02% compilation time) Test Summary: | Pass Total Time multivariate cross validation SnpLinAlg | 3 3 20.6s Test Summary: | Pass Total Time wrapper univariate | 20 20 1m34.6s **** 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 validating... 5%|█▋ | ETA: 0:00:11 Cross validating... 6%|█▉ | ETA: 0:00:12 Cross validating... 7%|██▎ | ETA: 0:00:12 Cross validating... 8%|██▌ | ETA: 0:00:12 Cross validating... 9%|██▉ | ETA: 0:00:13 Cross validating... 10%|███▎ | ETA: 0:00:14 Cross validating... 11%|███▌ | ETA: 0:00:15 Cross validating... 12%|███▉ | ETA: 0:00:15 Cross validating... 13%|████▏ | ETA: 0:00:16 Cross validating... 14%|████▌ | ETA: 0:00:16 Cross validating... 15%|████▊ | ETA: 0:00:16 Cross validating... 16%|█████▏ | ETA: 0:00:18 Cross validating... 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2838.788679198002 2 2514.397342870813 3 2305.6176519676274 4 2222.025304867614 5 2075.167038458837 6 2067.794898972384 7 2053.427506114907 8 2086.405384830965 9 2080.984460901671 10 2105.1311995023634 11 2132.407165368786 12 2138.267187460652 13 2166.002210829576 14 2194.9918295115804 15 2189.890403738045 16 2191.1812932295775 17 2209.4669750564367 18 2221.2595493644303 19 2238.742594576326 20 2253.9559571797727 Best k = 7 **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 2%|▋ | ETA: 0:00:10 Cross validating... 3%|█ | ETA: 0:00:10 Cross validating... 4%|█▎ | ETA: 0:00:11 Cross validating... 5%|█▋ | ETA: 0:00:11 Cross validating... 6%|█▉ | ETA: 0:00:12 Cross validating... 7%|██▎ | ETA: 0:00:12 Cross validating... 8%|██▌ | ETA: 0:00:12 Cross validating... 9%|██▉ | 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14 2194.9918295115804 15 2189.890403738045 16 2191.1812932295775 17 2209.4669750564367 18 2221.2595493644303 19 2238.742594576326 20 2253.9559571797727 Best k = 7 Test Summary: | Pass Total Time wrapper multivariate | 8 8 1m23.6s read BGEN and VCF: Error During Test at /home/pkgeval/.julia/packages/MendelIHT/ZcxZT/test/wrapper_test.jl:184 Got exception outside of a @test startproc must be called before process Stacktrace: [1] error(s::String) @ Base error.jl:56 [2] process(codec::CodecZlib.ZlibDecompressor, input::TranscodingStreams.Memory, output::TranscodingStreams.Memory, error_ref::TranscodingStreams.Error) @ CodecZlib ~/.julia/packages/CodecZlib/BjTS1/src/decompression.jl:199 [3] decompress(io::IOStream, v::Variant, h::BGEN.Header; decompressed::Nothing) @ BGEN ~/.julia/packages/BGEN/dfgRU/src/genotypes.jl:72 [4] first_allele_dosage!(b::Bgen, v::Variant; T::Core.TypeEgal{Float64}, mean_impute::Bool, clear_decompressed::Bool, data::Nothing, decompressed::Nothing, is_decompressed::Bool) @ BGEN ~/.julia/packages/BGEN/dfgRU/src/genotypes.jl:571 [5] convert_bgen_gt(t::Core.TypeEgal{Float64}, b::Bgen) @ MendelIHT ~/.julia/packages/MendelIHT/ZcxZT/src/wrapper.jl:380 [6] macro expansion @ ./timing.jl:741 [inlined] [7] macro expansion @ ~/.julia/packages/MendelIHT/ZcxZT/test/wrapper_test.jl:187 [inlined] [8] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:2247 [inlined] [9] top-level scope @ ~/.julia/packages/MendelIHT/ZcxZT/test/wrapper_test.jl:185 Test Summary: | Error Total Time read BGEN and VCF | 1 1 3.2s RNG of the outermost testset: Xoshiro(0x89791cd94cdc4426, 0xc6f0521fe51100ea, 0xaa55d336141082d6, 0xb505013cf9d9eeeb, 0x251a3bf235575d7f) 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 975.25s ERROR: LoadError: Package MendelIHT errored during testing Stacktrace: [1] pkgerror(msg::String) @ Pkg.Types /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Types.jl:68 [2] test(ctx::Pkg.Types.Context, pkgs::Vector{PackageSpec}; coverage::Bool, julia_args::Cmd, test_args::Cmd, test_fn::Nothing, force_latest_compatible_version::Bool, allow_earlier_backwards_compatible_versions::Bool, allow_reresolve::Bool) @ Pkg.Operations /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Operations.jl:3298 [3] test(ctx::Pkg.Types.Context, pkgs::Vector{PackageSpec}; coverage::Bool, test_fn::Nothing, julia_args::Cmd, test_args::Cmd, force_latest_compatible_version::Bool, allow_earlier_backwards_compatible_versions::Bool, allow_reresolve::Bool, kwargs::@Kwargs{io::IOContext{IO}}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:587 [4] test(pkgs::Vector{PackageSpec}; io::IOContext{IO}, kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:172 [5] test(pkgs::Vector{String}; kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:160 [6] test(pkg::String; kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:159 [inlined] [7] top-level scope @ /PkgEval.jl/scripts/evaluate.jl:223 in expression starting at /PkgEval.jl/scripts/evaluate.jl:214 PkgEval failed after 1089.85s: package tests unexpectedly errored