Package evaluation to test MendelIHT on Julia 1.14.0-DEV.2386 (9e0b0ca1f2*) started at 2026-06-17T01:35:12.106 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.14` Set-up completed after 14.36s ################################################################################ # Installation # Installing MendelIHT... Resolving package versions... Updating `~/.julia/environments/v1.14/Project.toml` [921c7187] + MendelIHT v1.4.11 Updating `~/.julia/environments/v1.14/Manifest.toml` [7d9f7c33] + Accessors v0.1.44 [79e6a3ab] + Adapt v4.6.1 [66dad0bd] + AliasTables v1.1.3 [4fba245c] + ArrayInterface v7.25.0 [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 v0.2.7 [f70d9fcc] + CommonWorldInvalidations v1.0.0 [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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[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 To see why use `status --outdated -m` Installation completed after 5.55s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompiling project... 4.3 s ✓ BGEN 7.8 s ✓ VCFTools 26.8 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`. 24.5 s ✓ MendelIHT 4 dependencies successfully precompiled in 66 seconds. 170 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 93.08s ################################################################################ # Testing # Testing MendelIHT Status `/tmp/jl_wa7PRc/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 v0.25.126 [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 v0.34.11 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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:219 └ @ Distributions ~/.julia/packages/Distributions/nfRUl/src/multivariate/mvnormal.jl:219 ┌ 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 15.9s 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 9.9s Test Summary: | Pass Total Time _iht_backtrack | 7 7 0.0s Test Summary: | Pass Total Time standardize! | 12 12 1.4s Test Summary: | Pass Total Time project_k! | 2 2 1.0s Test Summary: | Pass Total Time project_group_sparse! | 5 5 1.2s Test Summary: | Pass Total Time maf_weights | 6 6 2.1s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse linear regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1770.8690617353657, backtracks = 0, tol = 2.386235889201217 Iteration 2: loglikelihood = -1411.5615341231412, backtracks = 0, tol = 0.14858768243616227 Iteration 3: loglikelihood = -1385.2385642811194, backtracks = 0, tol = 0.032259363617324815 Iteration 4: loglikelihood = -1385.1447352730552, backtracks = 0, tol = 0.0016884261569556668 Iteration 5: loglikelihood = -1385.1437688729075, backtracks = 0, tol = 0.00022362739800642952 Iteration 6: loglikelihood = -1385.1437559320975, backtracks = 0, tol = 2.1350939048607483e-5 IHT estimated 10 nonzero SNP predictors and 1 non-genetic predictors. Compute time (sec): 0.05300784111022949 Final loglikelihood: -1385.1437559320975 SNP PVE: 0.9535864613816503 Iterations: 6 Selected genetic predictors: 10×2 DataFrame Row │ Position Estimated_β │ Int64 Float64 ─────┼─────────────────────── 1 │ 815 1.93855 2 │ 3274 -2.8582 3 │ 3412 1.56786 4 │ 3479 0.233513 5 │ 3552 -0.827153 6 │ 6683 1.63772 7 │ 7084 -0.234826 8 │ 7115 -0.1631 9 │ 8066 -0.809265 10 │ 9534 -0.220653 Selected nongenetic predictors: 1×2 DataFrame Row │ Position Estimated_β │ Int64 Float64 ─────┼─────────────────────── 1 │ 1 0.0246358Test Summary: | Pass Total Time fit normal SnpLinAlg | 4 4 22.3s **** 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 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 4.3s **** 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 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 = -3179.8231427921573, backtracks = 0, tol = 0.3212496248916375 Iteration 2: loglikelihood = -1875.5281722305388, backtracks = 0, tol = 0.07426850308861377 Iteration 3: loglikelihood = -1571.1492205362792, backtracks = 0, tol = 0.05309304800803685 Iteration 4: loglikelihood = -1509.154908840506, backtracks = 0, tol = 0.060604946590302 Iteration 5: loglikelihood = -1440.1093105175237, backtracks = 0, tol = 0.06420890527907147 Iteration 6: loglikelihood = -1408.9641166206154, backtracks = 0, tol = 0.042373044210143 Iteration 7: loglikelihood = -1382.9629159233646, backtracks = 0, tol = 0.06922347157073137 Iteration 8: loglikelihood = -1365.8329278144402, backtracks = 0, tol = 0.028511350655702414 Iteration 9: loglikelihood = -1355.9476508251691, backtracks = 0, tol = 0.0439954949137728 Iteration 10: loglikelihood = -1350.408845774263, backtracks = 0, tol = 0.016334490951167725 Iteration 11: loglikelihood = -1346.0566621571302, backtracks = 0, tol = 0.048231793212712495 Iteration 12: loglikelihood = -1344.1043481207441, backtracks = 0, tol = 0.0471723545544954 Iteration 13: loglikelihood = -1342.7878160447867, backtracks = 1, tol = 0.004557361737564422 Iteration 14: loglikelihood = -1341.9815929483439, backtracks = 1, tol = 0.005915936263935445 Iteration 15: loglikelihood = -1341.5141318520948, backtracks = 1, tol = 0.04573045350615605 Iteration 16: loglikelihood = -1338.6826119576065, backtracks = 0, tol = 0.010004650195339571 Iteration 17: loglikelihood = -1338.1076569161519, backtracks = 0, tol = 0.007767301061059107 Iteration 18: loglikelihood = -1337.8282321318547, backtracks = 0, tol = 0.003376128766634918 Iteration 19: loglikelihood = -1337.6384573412738, backtracks = 0, tol = 0.004795916699544384 Iteration 20: loglikelihood = -1337.5028082506467, backtracks = 0, tol = 0.0023714121350066042 Iteration 21: loglikelihood = -1337.405260803971, backtracks = 0, tol = 0.003419170120036208 Iteration 22: loglikelihood = -1337.3336589349997, backtracks = 0, tol = 0.0017076289693778001 Iteration 23: loglikelihood = -1337.2813576869291, backtracks = 0, tol = 0.0024658005780436735 Iteration 24: loglikelihood = -1337.2426969081246, backtracks = 0, tol = 0.0012484278955868255 Iteration 25: loglikelihood = -1337.2142612202622, backtracks = 0, tol = 0.001794940347708018 Iteration 26: loglikelihood = -1337.1931788277752, backtracks = 0, tol = 0.0009191890433733238 Iteration 27: loglikelihood = -1337.1776100326001, backtracks = 0, tol = 0.0013151433766006861 Iteration 28: loglikelihood = -1337.1660481443753, backtracks = 0, tol = 0.0006794653387128923 Iteration 29: loglikelihood = -1337.1574878139447, backtracks = 0, tol = 0.0009680340813810449 Iteration 30: loglikelihood = -1337.151124161084, backtracks = 0, tol = 0.0005056939180389085 Iteration 31: loglikelihood = -1337.1464042651053, backtracks = 0, tol = 0.0007148718584765849 Iteration 32: loglikelihood = -1337.1428932348529, backtracks = 0, tol = 0.0003770793429692471 Iteration 33: loglikelihood = -1337.1402859256432, backtracks = 0, tol = 0.0005291590636321885 Iteration 34: loglikelihood = -1337.1383455514006, backtracks = 0, tol = 0.0002811163309500573 Iteration 35: loglikelihood = -1337.1369033686005, backtracks = 0, tol = 0.0003923586808327752 Iteration 36: loglikelihood = -1337.1358297664356, backtracks = 0, tol = 0.00020953900976004882 Iteration 37: loglikelihood = -1337.1350313150424, backtracks = 0, tol = 0.00029128540753905883 Iteration 38: loglikelihood = -1337.1344368013072, backtracks = 0, tol = 0.00015616546970988461 Iteration 39: loglikelihood = -1337.1339944547012, backtracks = 0, tol = 0.00021644543381984222 Iteration 40: loglikelihood = -1337.1336650424148, backtracks = 0, tol = 0.0001163751030201275 Iteration 41: loglikelihood = -1337.1334198633945, backtracks = 0, tol = 0.00016094144829464633 Iteration 42: loglikelihood = -1337.133237261264, backtracks = 0, tol = 8.671638576680717e-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 = -1709.046398443543, backtracks = 0, tol = 0.3550012958814253 Iteration 2: loglikelihood = -1573.5332388025824, backtracks = 0, tol = 0.2164036285663452 Iteration 3: loglikelihood = -1528.859675973972, backtracks = 0, tol = 0.1549397239997772 Iteration 4: loglikelihood = -1516.1108421004549, backtracks = 0, tol = 0.0902224030880512 Iteration 5: loglikelihood = -1512.184875533241, backtracks = 0, tol = 0.040748262978145385 Iteration 6: loglikelihood = -1510.6176676190055, backtracks = 1, tol = 0.04390117752497699 Iteration 7: loglikelihood = -1510.2387138441275, backtracks = 1, tol = 0.008142895968370431 Iteration 8: loglikelihood = -1510.0931043649134, backtracks = 1, tol = 0.005723849273032034 Iteration 9: loglikelihood = -1509.5645692485398, backtracks = 1, tol = 0.053108326773814746 Iteration 10: loglikelihood = -1509.5000185933375, backtracks = 0, tol = 0.004536012026900973 Iteration 11: loglikelihood = -1509.4930795577277, backtracks = 0, tol = 0.0017959237698135686 Iteration 12: loglikelihood = -1509.4918896143297, backtracks = 1, tol = 0.0005445169271582236 Iteration 13: loglikelihood = -1509.4912501599367, backtracks = 1, tol = 0.0004076331210930639 Iteration 14: loglikelihood = -1509.491067668251, backtracks = 1, tol = 0.00021853254375422642 Iteration 15: loglikelihood = -1509.4910160472473, backtracks = 1, tol = 0.0001333159403085089 Iteration 16: loglikelihood = -1509.4910024465614, backtracks = 1, tol = 6.147714779010948e-5 Test Summary: | Pass Total Time fit NegativeBinomial SnpLinAlg | 4 4 1.3s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse linear regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1873.0652940553148, backtracks = 0, tol = 0.7951493577139694 Iteration 2: loglikelihood = -1442.05905655971, backtracks = 0, tol = 0.14003277492664293 Iteration 3: loglikelihood = -1387.686208070192, backtracks = 0, tol = 0.04651945123851264 Iteration 4: loglikelihood = -1383.716116890118, backtracks = 0, tol = 0.025873363948477144 Iteration 5: loglikelihood = -1382.361544899726, backtracks = 0, tol = 0.024191015230240365 Iteration 6: loglikelihood = -1382.233569057952, backtracks = 0, tol = 0.002249725269344456 Iteration 7: loglikelihood = -1382.2329083727666, backtracks = 1, tol = 8.794584796325987e-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 = -1550.3893737337937, backtracks = 0, tol = 0.5152084512804859 Iteration 2: loglikelihood = -1396.9552309030596, backtracks = 0, tol = 0.10246385696275145 Iteration 3: loglikelihood = -1383.613667450807, backtracks = 0, tol = 0.03725745483001101 Iteration 4: loglikelihood = -1383.3366113893792, backtracks = 1, tol = 0.0018000220580671477 Iteration 5: loglikelihood = -1383.2642157852813, backtracks = 1, tol = 0.000877732771596435 Iteration 6: loglikelihood = -1383.2453115386986, backtracks = 1, tol = 0.00041712917668429683 Iteration 7: loglikelihood = -1383.2403972205395, backtracks = 1, tol = 0.0002011058663302175 Iteration 8: loglikelihood = -1383.2391290179091, backtracks = 1, tol = 0.00011106508987502891 Iteration 9: loglikelihood = -1383.238804402223, backtracks = 1, tol = 5.957466696092576e-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 10.1s **** 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 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 = -1520.1482685265933, backtracks = 0, tol = 0.2046022773014874 Iteration 2: loglikelihood = -1468.8763002682467, backtracks = 0, tol = 0.08619061056848121 Iteration 3: loglikelihood = -1426.7268306689673, backtracks = 0, tol = 0.11475455331266475 Iteration 4: loglikelihood = -1405.9947829384257, backtracks = 0, tol = 0.08859301312716879 Iteration 5: loglikelihood = -1401.0684144461002, backtracks = 1, tol = 0.029418683941463516 Iteration 6: loglikelihood = -1393.109665828018, backtracks = 2, tol = 0.07350522703555934 Iteration 7: loglikelihood = -1388.2098926833867, backtracks = 0, tol = 0.07230946288407264 Iteration 8: loglikelihood = -1377.058433162432, backtracks = 0, tol = 0.08275421173536254 Iteration 9: loglikelihood = -1376.7226804361585, backtracks = 0, tol = 0.08355428476329053 Iteration 10: loglikelihood = -1371.595195863841, backtracks = 0, tol = 0.0707660355725659 Iteration 11: loglikelihood = -1370.6156621295036, backtracks = 0, tol = 0.013051664886351724 Iteration 12: loglikelihood = -1370.4999444338214, backtracks = 1, tol = 0.0035290267021644995 Iteration 13: loglikelihood = -1370.4575075861162, backtracks = 2, tol = 0.0025102819483426675 Iteration 14: loglikelihood = -1370.4311183205702, backtracks = 2, tol = 0.0018647290657268305 Iteration 15: loglikelihood = -1370.415995640632, backtracks = 2, tol = 0.0014472712406783843 Iteration 16: loglikelihood = -1370.4073940127357, backtracks = 2, tol = 0.0010848122793414331 Iteration 17: loglikelihood = -1370.4025153895313, backtracks = 2, tol = 0.0008168040375271832 Iteration 18: loglikelihood = -1370.3997507318134, backtracks = 2, tol = 0.0006123630343447224 Iteration 19: loglikelihood = -1370.3981842943751, backtracks = 2, tol = 0.00045895896016914605 Iteration 20: loglikelihood = -1370.3972965002058, backtracks = 2, tol = 0.000343527956178237 Iteration 21: loglikelihood = -1370.3967930508825, backtracks = 2, tol = 0.0002568880958173264 Iteration 22: loglikelihood = -1370.3965073357099, backtracks = 2, tol = 0.00019186537117845632 Iteration 23: loglikelihood = -1370.3963450380822, backtracks = 2, tol = 0.000143107146738099 Iteration 24: loglikelihood = -1370.3962527504173, backtracks = 2, tol = 0.00010656673130130312 Iteration 25: loglikelihood = -1370.396200214216, backtracks = 2, tol = 7.920544272800993e-5 1.724374 seconds (9.13 M allocations: 152.452 MiB, 2.64% gc time, 37.40% 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 = -1547.5303449818025, backtracks = 0, tol = 0.2046022773014874 Iteration 2: loglikelihood = -1512.943579619022, backtracks = 0, tol = 0.0960985082503267 Iteration 3: loglikelihood = -1480.9811787474307, backtracks = 0, tol = 0.10867802171741776 Iteration 4: loglikelihood = -1461.3994844002605, backtracks = 0, tol = 0.08729402425314546 Iteration 5: loglikelihood = -1456.6940838983435, backtracks = 0, tol = 0.1227466886262713 Iteration 6: loglikelihood = -1437.1177772404046, backtracks = 0, tol = 0.11951888900752834 Iteration 7: loglikelihood = -1422.407852468426, backtracks = 0, tol = 0.06824625316647126 Iteration 8: loglikelihood = -1417.5739802624887, backtracks = 0, tol = 0.07162557441570482 Iteration 9: loglikelihood = -1410.1753847963932, backtracks = 1, tol = 0.004781444184744319 Iteration 10: loglikelihood = -1403.7549099241837, backtracks = 1, tol = 0.06416988999870248 Iteration 11: loglikelihood = -1400.3188800740195, backtracks = 0, tol = 0.008834537009557119 Iteration 12: loglikelihood = -1395.2558386399455, backtracks = 1, tol = 0.0016366865601896026 Iteration 13: loglikelihood = -1391.6938822654827, backtracks = 1, tol = 0.001436905266713182 Iteration 14: loglikelihood = -1388.8985880801429, backtracks = 1, tol = 0.0010249375139861358 Iteration 15: loglikelihood = -1386.6258657182118, backtracks = 1, tol = 0.0007636427561010103 Iteration 16: loglikelihood = -1384.6494366330392, backtracks = 1, tol = 0.0006004036830281543 Iteration 17: loglikelihood = -1382.9906511468796, backtracks = 1, tol = 0.000503450766486587 Iteration 18: loglikelihood = -1381.5922718644647, backtracks = 1, tol = 0.0004561563963490861 Iteration 19: loglikelihood = -1380.4073893140633, backtracks = 1, tol = 0.00041972839196711574 Iteration 20: loglikelihood = -1379.4622800913864, backtracks = 1, tol = 0.0003859221728327162 Iteration 21: loglikelihood = -1378.6538844063484, backtracks = 1, tol = 0.0003436899702443698 Iteration 22: loglikelihood = -1377.9561152332212, backtracks = 1, tol = 0.00030810353284719427 Iteration 23: loglikelihood = -1377.3495477212728, backtracks = 1, tol = 0.0002786168122284726 Iteration 24: loglikelihood = -1376.818991519878, backtracks = 1, tol = 0.0002536741413418131 Iteration 25: loglikelihood = -1376.3523924448625, backtracks = 1, tol = 0.0002322300679010218 Iteration 26: loglikelihood = -1375.8887365982512, backtracks = 1, tol = 0.00021354415568544758 Iteration 27: loglikelihood = -1375.5236875659202, backtracks = 1, tol = 0.000208406346592278 Iteration 28: loglikelihood = -1375.2018527118387, backtracks = 1, tol = 0.000189487495573193 Iteration 29: loglikelihood = -1374.9029735730592, backtracks = 1, tol = 0.00017236115407322087 Iteration 30: loglikelihood = -1374.6339162330212, backtracks = 1, tol = 0.00016126747954243008 Iteration 31: loglikelihood = -1374.3915558718268, backtracks = 1, tol = 0.00015140215898459407 Iteration 32: loglikelihood = -1374.1476987154954, backtracks = 1, tol = 0.00014216005875392467 Iteration 33: loglikelihood = -1373.9718796245995, backtracks = 1, tol = 0.00014067795348323241 Iteration 34: loglikelihood = -1373.772878142399, backtracks = 1, tol = 0.00012350909362976453 Iteration 35: loglikelihood = -1373.6312093264542, backtracks = 1, tol = 0.0001224970252590746 Iteration 36: loglikelihood = -1373.465841880693, backtracks = 1, tol = 0.00010746567490447229 Iteration 37: loglikelihood = -1373.308849739096, backtracks = 1, tol = 0.00010787343505179753 Iteration 38: loglikelihood = -1373.20382808805, backtracks = 1, tol = 0.00010863956151265895 Iteration 39: loglikelihood = -1373.0767052617161, backtracks = 1, tol = 9.279916251720013e-5 0.449134 seconds (1.96 M allocations: 36.527 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 = -3849.3772, backtracks = 0, tol = 0.08890090679022933 Iteration 2: loglikelihood = -3783.025, backtracks = 0, tol = 0.053608355231201325 Iteration 3: loglikelihood = -3774.1519, backtracks = 1, tol = 0.01811140235575063 Iteration 4: loglikelihood = -3771.6772, backtracks = 1, tol = 0.010855434980687289 Iteration 5: loglikelihood = -3771.023, backtracks = 1, tol = 0.005501684361827698 Iteration 6: loglikelihood = -3770.8545, backtracks = 1, tol = 0.0029526932417716758 Iteration 7: loglikelihood = -3770.813, backtracks = 1, tol = 0.001429474060081589 Iteration 8: loglikelihood = -3770.8015, backtracks = 1, tol = 0.0007508696032530911 Iteration 9: loglikelihood = -3770.8008, backtracks = 1, tol = 0.00035752407357463246 Iteration 10: loglikelihood = -3770.8035, backtracks = 3, tol = 4.695709938272809e-5 24.298065 seconds (13.27 M allocations: 639.037 MiB, 1.05% gc time, 98.41% 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 = -3707.303, backtracks = 0, tol = 0.08890090679022933 Iteration 2: loglikelihood = -3552.5745, backtracks = 0, tol = 0.05541072047879858 Iteration 3: loglikelihood = -3328.5964, backtracks = 1, tol = 0.017384530676609413 Iteration 4: loglikelihood = -3069.0557, backtracks = 1, tol = 0.009765649662999334 Iteration 5: loglikelihood = -3068.4485, backtracks = 0, tol = 0.09855795775387599 Iteration 6: loglikelihood = -2819.1516, backtracks = 0, tol = 0.11361465938198595 Iteration 7: loglikelihood = -2658.171, backtracks = 0, tol = 0.0854394100365711 Iteration 8: loglikelihood = -2538.7295, backtracks = 0, tol = 0.07732597107641948 Iteration 9: loglikelihood = -2438.82, backtracks = 0, tol = 0.09042255863719859 Iteration 10: loglikelihood = -2363.4, backtracks = 0, tol = 0.009637516872807311 Iteration 11: loglikelihood = -2309.7036, backtracks = 0, tol = 0.08602117777790995 Iteration 12: loglikelihood = -2272.7227, backtracks = 0, tol = 0.08607502077200616 Iteration 13: loglikelihood = -2249.4915, backtracks = 0, tol = 0.08689853185747562 Iteration 14: loglikelihood = -2236.0088, backtracks = 0, tol = 0.08689733137706251 Iteration 15: loglikelihood = -2228.1418, backtracks = 0, tol = 0.08862193058442913 Iteration 16: loglikelihood = -2221.1404, backtracks = 1, tol = 0.006875977698447716 Iteration 17: loglikelihood = -2219.5269, backtracks = 1, tol = 0.0034812759243729448 Iteration 18: loglikelihood = -2219.2063, backtracks = 1, tol = 0.0019111040943798326 Iteration 19: loglikelihood = -2219.1382, backtracks = 1, tol = 0.0010621181613360417 Iteration 20: loglikelihood = -2219.124, backtracks = 1, tol = 0.0005697033595638791 Iteration 21: loglikelihood = -2219.1228, backtracks = 1, tol = 0.00030170691919746364 Iteration 22: loglikelihood = -2219.1223, backtracks = 2, tol = 8.104893093597902e-5 0.121505 seconds (1.29 M allocations: 21.432 MiB) Test Summary: | Pass Total Time Negative binomial nuisance parameter Float32 matrix | 12 12 29.5s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** ┌ Warning: accessing `Type.name` is deprecated without replacement. If for detection, use `Base.isType(x)`. │ caller = ProgressMeter.Progress(n::Int64, dt::Int64, desc::String, barlen::Nothing, color::Symbol, output::Base.PipeEndpoint; offset::Int64) at deprecated.jl:1 └ @ ProgressMeter ~/.julia/packages/ProgressMeter/N660J/src/deprecated.jl:1 Running sparse linear regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -2896.6116813943763, backtracks = 0, tol = 1.0257704354307222 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 4.525691 seconds (1.02 M allocations: 132.824 MiB, 0.62% gc time, 91.09% compilation time) Test Summary: | Pass Total Time initialze beta | 1 1 4.8s 9.902289 seconds (4.00 M allocations: 82.388 MiB, 0.63% gc time, 0.94% compilation time) 5.434482 seconds (3.98 M allocations: 91.678 MiB, 1.27% gc time) 10.667699 seconds (20.38 M allocations: 438.624 MiB, 0.78% gc time, 16.07% compilation time: 79% of which was recompilation) 8.507410 seconds (20.18 M allocations: 434.187 MiB, 0.70% gc time) 37.561674 seconds (3.35 M allocations: 4.228 GiB, 6.77% gc time, 30.05% compilation time) 55.537239 seconds (72.50 k allocations: 183.675 MiB, 0.21% gc time) Test Summary: | Pass Total Time memory_efficient keyword | 7 7 2m25.8s Test Summary: | Pass Total Time update_support! | 10 10 0.7s 15.328 ms (78 allocations: 4.56 KiB) 4.546 μs (0 allocations: 0 bytes) 131.600 μs (4 allocations: 288 bytes) 6.620 μs (0 allocations: 0 bytes) 52.660 μs (2 allocations: 64 bytes) 30.590 μs (0 allocations: 0 bytes) 25.530 μs (0 allocations: 0 bytes) 24.630 μs (0 allocations: 0 bytes) 101.600 μs (0 allocations: 0 bytes) 39.444 ms (78 allocations: 4.56 KiB) 18.500 μs (0 allocations: 0 bytes) 163.040 μs (4 allocations: 288 bytes) 33.880 μs (0 allocations: 0 bytes) 255.850 μs (2 allocations: 64 bytes) 85.030 μs (0 allocations: 0 bytes) 116.340 μs (0 allocations: 0 bytes) 146.720 μs (0 allocations: 0 bytes) 227.440 μs (0 allocations: 0 bytes) Test Summary: | Total Time benchmarks for multivariate function | 0 2m10.8s **** 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 **** **** 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 0.433782 seconds (43.84 k allocations: 5.329 MiB, 62.59% compilation time) Test Summary: | Pass Total Time multivariate fit_iht SnpLinAlg | 7 7 13.2s **** 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 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 2.050868 seconds (256.73 k allocations: 167.470 MiB, 59.23% compilation time) Test Summary: | Pass Total Time initialze beta | 5 5 2.6s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** ┌ 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: 0:03:58 Cross validating... 11%|███▌ | ETA: 0:01:06 Cross validating... 14%|████▋ | ETA: 0:00:51 Cross validating... 17%|█████▋ | ETA: 0:00:40 Cross validating... 21%|██████▋ | ETA: 0:00:34 Cross validating... 24%|███████▋ | ETA: 0:00:28 Cross validating... 27%|████████▋ | ETA: 0:00:25 Cross validating... 30%|█████████▋ | ETA: 0:00:21 Cross validating... 33%|██████████▋ | ETA: 0:00:19 Cross validating... 37%|███████████▋ | ETA: 0:00:17 Cross validating... 40%|████████████▊ | ETA: 0:00:15 Cross validating... 43%|█████████████▊ | ETA: 0:00:13 Cross validating... 46%|██████████████▊ | ETA: 0:00:12 Cross validating... 49%|███████████████▊ | ETA: 0:00:10 Cross validating... 52%|████████████████▊ 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Crossvalidation Results: k MSE 0 6732.160349392532 1 4043.0018821728327 2 2551.6418442349623 3 1738.3818570647998 4 784.9719270037422 5 597.9537600399894 6 372.36239837078676 7 356.7025328970596 8 340.43693045341337 9 321.4712378994826 10 317.4926457047108 11 316.15486923838836 12 326.791827678549 13 327.962748832124 14 338.70434954419466 15 330.7605469506027 16 327.42587884147247 17 336.8958397894202 18 351.2528312223178 19 351.55689599913586 20 369.86502298353696 Best k = 11 12.648848 seconds (11.32 M allocations: 297.405 MiB, 1.47% gc time, 63.14% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 5%|█▌ | ETA: 0:00:03 Cross validating... 10%|███ | ETA: 0:00:03 Cross validating... 13%|████▏ | ETA: 0:00:03 Cross validating... 16%|█████▏ | ETA: 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0:00:01 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:01 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:01 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:01 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:00 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:00 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:04 Crossvalidation Results: k MSE 0 6732.160349392532 1 4045.561867127023 2 2597.185790813455 3 1770.7696101904685 4 799.1690036943374 5 594.3495187805718 6 380.0849938214666 7 364.98457704836915 8 347.982542399258 9 328.9932269870652 10 325.9484936199301 11 335.06071303761905 12 349.53480014707566 13 349.6086808376208 14 363.54697601652197 15 348.39466065587567 16 365.0573164478788 17 365.5675571277445 18 382.83408033256717 19 391.1299065113468 20 389.24650431902137 Best k = 10 4.573300 seconds (10.20 M allocations: 214.519 MiB, 1.25% gc time, 1.10% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, normal model | 3 3 18.0s **** 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: 0:06:22 Cross validating... 8%|██▌ | ETA: 0:02:26 Cross validating... 14%|████▋ | ETA: 0:01:16 Cross validating... 19%|██████▏ | ETA: 0:00:55 Cross validating... 24%|███████▋ | ETA: 0:00:42 Cross validating... 29%|█████████▏ | ETA: 0:00:33 Cross validating... 35%|███████████▏ | ETA: 0:00:25 Cross validating... 41%|█████████████▎ | ETA: 0:00:19 Cross validating... 48%|███████████████▎ | ETA: 0:00:15 Cross validating... 54%|█████████████████▎ | ETA: 0:00:12 Cross validating... 60%|███████████████████▎ | ETA: 0:00:09 Cross validating... 65%|████████████████████▉ | ETA: 0:00:07 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:06 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:05 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:04 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:03 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:02 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:01 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:14 Crossvalidation Results: k MSE 0 1542.9236721191405 1 1217.7150583496093 2 1015.4249404296875 3 818.4349271240235 4 655.7763096923828 5 573.7256522216796 6 457.97862612915037 7 394.75362322998046 8 365.0583411560059 9 349.5608575134277 10 351.63280752563475 11 354.0384528198242 12 356.76555786132815 13 354.75764178466795 14 356.1433544921875 15 358.3429885559082 16 367.0376889343262 17 362.1269257507324 18 385.82693807983395 19 386.59162161254886 20 366.2580078735352 Best k = 9 16.067884 seconds (12.26 M allocations: 303.799 MiB, 0.64% gc time, 85.28% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 6%|██ | ETA: 0:00:02 Cross validating... 11%|███▌ | ETA: 0:00:02 Cross validating... 16%|█████▏ | ETA: 0:00:02 Cross validating... 21%|██████▋ | ETA: 0:00:02 Cross validating... 24%|███████▋ | ETA: 0:00:02 Cross validating... 29%|█████████▏ | ETA: 0:00:02 Cross validating... 33%|██████████▋ | ETA: 0:00:02 Cross validating... 40%|████████████▊ | ETA: 0:00:01 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... 75%|███████████████████████▉ | ETA: 0:00:01 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:01 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:00 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:00 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:02 Crossvalidation Results: k MSE 0 1542.9236721191405 1 1218.221272216797 2 1016.6631884765625 3 820.2177264404297 4 658.10112890625 5 577.2349686279297 6 461.98128707885746 7 397.36022326660157 8 369.80282757568364 9 354.13301690673825 10 358.47952758789063 11 361.30016326904297 12 370.9387496337891 13 374.5223900756836 14 378.1068264465332 15 387.52433941650395 16 394.8737167663574 17 392.60858828735354 18 393.5792116088867 19 407.21460021972655 20 412.00999563598634 Best k = 9 2.677088 seconds (11.08 M allocations: 202.626 MiB, 2.10% gc time, 1.70% compilation time) Test Summary: | Pass Total Time Cross validation on Float32 matrix, normal model | 2 2 20.2s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:01:03 Cross validating... 6%|██ | ETA: 0:00:33 Cross validating... 10%|███ | ETA: 0:00:24 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 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78%|████████████████████████▉ | ETA: 0:00:02 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:02 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:01 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:01 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:01 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:01 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:07 Crossvalidation Results: k MSE 0 464.27363377974564 1 376.990220444971 2 301.4392556653039 3 270.03659072222825 4 221.12758790416672 5 211.38797565739793 6 191.84499097291368 7 195.25287871572192 8 201.9141296628133 9 207.4977530981731 10 216.60112869893834 11 214.1587995694818 12 215.73765609085106 13 235.1915375339405 14 204.70649631512202 15 229.7026272055645 16 222.40476856253366 17 210.13932407697396 18 249.55956468646102 19 213.41828383619637 20 237.4893117200371 Best k = 6 8.635053 seconds (17.35 M allocations: 401.050 MiB, 1.36% gc time, 32.18% 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... 11%|███▌ | ETA: 0:00:05 Cross validating... 14%|████▋ | ETA: 0:00:05 Cross validating... 17%|█████▋ | ETA: 0:00:05 Cross validating... 19%|██████▏ | ETA: 0:00:05 Cross validating... 22%|███████▏ | ETA: 0:00:05 Cross validating... 25%|████████▏ | 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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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... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:05 Crossvalidation Results: k MSE 0 464.27363377974564 1 377.1749750890799 2 302.1626691699275 3 270.7979576374413 4 222.8441246514151 5 214.12424217252303 6 196.0694945112016 7 204.28747237785615 8 210.06214706953722 9 213.7744285702179 10 221.30974712401562 11 224.149566559352 12 233.5479830362638 13 227.03505133444946 14 242.73745498415505 15 233.26908020664112 16 254.8764125978547 17 249.7696949094053 18 261.9796380792329 19 258.43187367763187 20 274.83208309150325 Best k = 6 6.069005 seconds (17.99 M allocations: 374.531 MiB, 1.27% gc time, 1.20% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, logistic model | 2 2 15.1s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:48 Cross validating... 6%|██ | ETA: 0:00:25 Cross validating... 10%|███ | ETA: 0:00:17 Cross validating... 13%|████▏ | ETA: 0:00:13 Cross validating... 16%|█████▏ | ETA: 0:00:11 Cross validating... 19%|██████▏ | ETA: 0:00:09 Cross validating... 22%|███████▏ | ETA: 0:00:08 Cross validating... 25%|████████▏ | ETA: 0:00:07 Cross validating... 29%|█████████▏ | ETA: 0:00:07 Cross validating... 32%|██████████▏ | ETA: 0:00:06 Cross validating... 35%|███████████▏ | ETA: 0:00:06 Cross validating... 38%|████████████▎ | ETA: 0:00:05 Cross validating... 41%|█████████████▎ | ETA: 0:00:05 Cross 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0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:05 Crossvalidation Results: k MSE 0 463.36806735946834 1 438.783536957805 2 400.95703207358406 3 380.01243337594445 4 352.4087641159059 5 344.2841942546943 6 329.6399951055664 7 312.9223312985969 8 315.5754641528075 9 318.95512460048997 10 323.63048204676613 11 324.0875977878215 12 333.12334856696305 13 328.8745083840125 14 371.8149481674658 15 345.0447224795672 16 358.8515270138523 17 337.62252361452516 18 386.06997219959027 19 371.02084869815604 20 343.53056875426915 Best k = 7 6.964017 seconds (16.83 M allocations: 393.837 MiB, 6.64% gc time, 39.03% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:03 Cross validating... 6%|██ | ETA: 0:00:03 Cross validating... 10%|███ | ETA: 0:00:03 Cross validating... 13%|████▏ | ETA: 0:00:03 Cross validating... 16%|█████▏ | ETA: 0:00:03 Cross validating... 19%|██████▏ | ETA: 0:00:03 Cross validating... 22%|███████▏ | ETA: 0:00:03 Cross validating... 25%|████████▏ | ETA: 0:00:03 Cross validating... 29%|█████████▏ | ETA: 0:00:03 Cross validating... 32%|██████████▏ | ETA: 0:00:02 Cross validating... 37%|███████████▋ | ETA: 0:00:02 Cross validating... 40%|████████████▊ | ETA: 0:00:02 Cross validating... 43%|█████████████▊ | ETA: 0:00:02 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: 0:00:01 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... 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: 0:00:00 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 0 463.36806735946834 1 440.0934912790858 2 402.36880840586275 3 381.9410542739232 4 354.8255991541398 5 348.0927020430628 6 333.9483615891495 7 317.902345253258 8 325.5761360677159 9 337.26207801509787 10 343.0079552337604 11 349.6840921372308 12 362.545008823876 13 369.61815356169484 14 380.08921437776917 15 383.94811502454127 16 391.95108936716383 17 380.3410230416489 18 430.017245727391 19 421.7616486479432 20 424.8341330380791 Best k = 7 3.837290 seconds (17.13 M allocations: 352.036 MiB, 1.67% gc time, 0.88% compilation time) Test Summary: | Pass Total Time Cross validation on Float64 matrix, logistic model | 2 2 11.7s **** 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: 0:01:03 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... 76%|████████████████████████▍ | ETA: 0:00:02 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:02 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:01 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:01 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:01 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:01 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:07 Crossvalidation Results: k MSE 0 1376.5585959026457 1 1157.6685042203223 2 915.8682813507412 3 567.8117697299826 4 399.082462787201 5 380.53699844152675 6 369.5715023859748 7 367.4559246459024 8 355.7701051756631 9 369.2471189829264 10 365.6921246969396 11 385.8145467673636 12 376.93501024609344 13 385.1994915203934 14 393.3526939391502 15 382.6723612975712 16 373.0576404944861 17 409.70122359055244 18 408.9636941176943 19 393.7233674234046 20 447.45341285741017 Best k = 8 8.305728 seconds (15.66 M allocations: 359.907 MiB, 0.91% gc time, 32.56% 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 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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 1376.5585959026457 1 1012.7335401334321 2 836.556650706554 3 537.8729620398772 4 376.578467753881 5 350.6484461511585 6 357.1657057203371 7 368.79229145892197 8 370.8283891294558 9 382.7048062522753 10 386.22317566725525 11 383.77429658570475 12 398.29768641414137 13 396.93013310591164 14 393.3827407966404 15 394.2979822336646 16 389.9579609684131 17 409.0058869652576 18 417.7687517022319 19 419.9962700005145 20 438.383059226077 Best k = 5 5.796911 seconds (14.53 M allocations: 294.332 MiB, 1.07% gc time, 1.15% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, Poisson model | 2 2 14.5s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:01:34 Cross validating... 5%|█▌ | ETA: 0:01:23 Cross validating... 6%|██ | ETA: 0:01:17 Cross validating... 10%|███ | ETA: 0:00:51 Cross validating... 11%|███▌ | ETA: 0:00:52 Cross validating... 14%|████▋ | ETA: 0:00:46 Cross validating... 16%|█████▏ | ETA: 0:00:41 Cross validating... 17%|█████▋ | ETA: 0:00:37 Cross validating... 19%|██████▏ | ETA: 0:00:34 Cross validating... 21%|██████▋ | ETA: 0:00:31 Cross validating... 22%|███████▏ | ETA: 0:00:29 Cross validating... 24%|███████▋ | ETA: 0:00:30 Cross validating... 25%|████████▏ | ETA: 0:00:28 Cross validating... 27%|████████▋ | ETA: 0:00:29 Cross validating... 29%|█████████▏ | ETA: 0:00:27 Cross validating... 30%|█████████▋ | ETA: 0:00:28 Cross validating... 32%|██████████▏ | ETA: 0:00:26 Cross validating... 33%|██████████▋ | ETA: 0:00:24 Cross validating... 37%|███████████▋ 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90%|█████████████████████████████ | ETA: 0:00:04 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:04 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:03 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:02 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:01 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:01 Cross validating... 100%|████████████████████████████████| Time: 0:00:45 Crossvalidation Results: k MSE 0 513.2929107996897 1 387.93009980154994 2 352.0937612246993 3 234.12694614708118 4 193.89664916486504 5 186.39373293452724 6 186.1347139243827 7 188.3942721697046 8 188.14748177087415 9 188.92723864687537 10 190.1427579896002 11 191.4385535825353 12 190.9559375142112 13 191.78405360598515 14 192.32878072378242 15 192.1547359354048 16 194.54506301196827 17 195.853242691547 18 189.59682571822955 19 189.6631679179718 20 194.56941879290042 Best k = 6 46.239552 seconds (142.29 M allocations: 3.596 GiB, 1.26% gc time, 5.01% 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: 0:00:06 Cross validating... 5%|█▌ | ETA: 0:00:06 Cross validating... 6%|██ | ETA: 0:00:08 Cross validating... 10%|███ | ETA: 0:00:08 Cross validating... 11%|███▌ | ETA: 0:00:07 Cross validating... 13%|████▏ | ETA: 0:00:08 Cross validating... 14%|████▋ | ETA: 0:00:08 Cross validating... 16%|█████▏ | ETA: 0:00:08 Cross validating... 17%|█████▋ | ETA: 0:00:08 Cross validating... 19%|██████▏ | ETA: 0:00:08 Cross validating... 21%|██████▋ | ETA: 0:00:08 Cross validating... 22%|███████▏ | ETA: 0:00:08 Cross validating... 24%|███████▋ | ETA: 0:00:08 Cross validating... 25%|████████▏ | ETA: 0:00:08 Cross validating... 27%|████████▋ | ETA: 0:00:08 Cross 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0:00:02 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:02 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: 0:00:12 Crossvalidation Results: k MSE 0 513.2929107996897 1 382.8901744491676 2 350.7329055045026 3 235.47718879377646 4 194.92256905945905 5 187.47857159335587 6 188.0428362049535 7 195.82284530041343 8 197.3034792328343 9 205.00210857226767 10 205.05374166827988 11 205.4507919711224 12 209.255461418747 13 212.66722662159003 14 221.911351822974 15 216.2319594167742 16 229.25660757764422 17 223.8146788064478 18 228.35583026891243 19 217.1955570067478 20 231.8465792847893 Best k = 5 12.896629 seconds (38.22 M allocations: 786.286 MiB, 1.36% gc time, 0.60% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, NegativeBinomial model | 2 2 59.6s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:01:09 Cross validating... 6%|██ | ETA: 0:00:35 Cross validating... 10%|███ | ETA: 0:00:23 Cross validating... 14%|████▋ | ETA: 0:00:16 Cross validating... 16%|█████▏ | ETA: 0:00:14 Cross validating... 19%|██████▏ | ETA: 0:00:12 Cross validating... 22%|███████▏ | ETA: 0:00:10 Cross validating... 25%|████████▏ | ETA: 0:00:09 Cross validating... 29%|█████████▏ | ETA: 0:00:08 Cross 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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 0 709.7238911132813 1 600.8470166015625 2 478.37098138427734 3 399.75837347412113 4 316.3170971069336 5 274.59901690673826 6 232.61785809326173 7 221.00282696533208 8 205.62119918823245 9 198.3431817626953 10 200.94596459960937 11 201.86666357421876 12 202.35683154296873 13 208.02664166259768 14 206.9071481628418 15 209.87240182495117 16 216.0480528869629 17 212.0296098022461 18 217.49209603881837 19 225.60646734619144 20 213.36869631958012 Best k = 9 6.303635 seconds (16.96 M allocations: 336.278 MiB, 1.44% gc time, 45.77% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 5%|█▌ | ETA: 0:00:03 Cross validating... 8%|██▌ | ETA: 0:00:03 Cross validating... 11%|███▌ | ETA: 0:00:03 Cross validating... 14%|████▋ | ETA: 0:00:03 Cross validating... 17%|█████▋ | ETA: 0:00:03 Cross validating... 21%|██████▋ | ETA: 0:00:03 Cross validating... 24%|███████▋ | ETA: 0:00:03 Cross validating... 27%|████████▋ | ETA: 0:00:02 Cross validating... 30%|█████████▋ | ETA: 0:00:02 Cross validating... 33%|██████████▋ | ETA: 0:00:02 Cross validating... 38%|████████████▎ | ETA: 0:00:02 Cross validating... 41%|█████████████▎ | ETA: 0:00:02 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: 0:00:01 Cross validating... 59%|██████████████████▊ | ETA: 0:00:01 Cross validating... 62%|███████████████████▊ | ETA: 0:00:01 Cross validating... 65%|████████████████████▉ | 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: 0:00:00 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 0 709.7238911132813 1 580.5206424560547 2 462.45179821777344 3 375.725685546875 4 311.8335130615235 5 265.69685809326177 6 235.52074707031255 7 221.8731430358887 8 209.48005477905275 9 202.0256286010742 10 206.40357376098632 11 209.8904744873047 12 212.83695938110353 13 217.36745034790042 14 219.17275009155276 15 218.94907879638671 16 225.10276358032226 17 228.24513723754882 18 225.50167910766604 19 235.0626920776367 20 227.98946899414062 Best k = 9 3.400289 seconds (16.17 M allocations: 286.688 MiB, 1.68% gc time, 1.95% compilation time) Test Summary: | Pass Total Time Cross validation on floating point matrices, NegativeBinomial model | 2 2 10.2s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 2%|▋ | ETA: 0:01:25 Cross validating... 3%|█ | ETA: 0:01:01 Cross validating... 4%|█▎ | ETA: 0:00:50 Cross validating... 5%|█▋ | ETA: 0:00:44 Cross validating... 6%|█▉ | ETA: 0:00:38 Cross validating... 7%|██▎ | ETA: 0:00:34 Cross validating... 8%|██▌ | 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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 2777.992262375642 2 2539.51769391967 3 2243.4426524278906 4 2165.091451810553 5 2087.8823419120768 6 2094.384255733219 7 2107.755256095819 8 2120.201370103653 9 2131.665254996346 10 2156.6535636230647 11 2150.427051753142 12 2184.1493309215375 13 2185.315783172944 14 2190.788874378509 15 2211.0517437431 16 2233.687628010097 17 2208.7534559418764 18 2215.8419629149253 19 2274.8542767233725 20 2264.634041817239 Best k = 5 19.322443 seconds (320.53 k allocations: 247.921 MiB, 0.58% gc time, 9.28% compilation time) Test Summary: | Pass Total Time multivariate cross validation SnpLinAlg | 3 3 24.2s Test Summary: | Pass Total Time wrapper univariate | 20 20 2m06.1s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 2%|▋ | ETA: 0:00:14 Cross validating... 3%|█ | ETA: 0:00:13 Cross validating... 4%|█▎ | ETA: 0:00:13 Cross validating... 5%|█▋ | ETA: 0:00:12 Cross validating... 6%|█▉ | ETA: 0:00:13 Cross validating... 7%|██▎ | ETA: 0:00:14 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: 0:00:16 Cross validating... 12%|███▉ | ETA: 0:00:16 Cross validating... 13%|████▏ | ETA: 0:00:17 Cross validating... 14%|████▌ | ETA: 0:00:17 Cross validating... 15%|████▊ | ETA: 0:00:17 Cross validating... 16%|█████▏ | ETA: 0:00:19 Cross validating... 17%|█████▌ 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2838.788679198002 2 2514.3973428708136 3 2305.6176519676274 4 2222.025304867614 5 2075.1670384588365 6 2067.7948989723845 7 2053.427506114907 8 2086.405384830965 9 2080.984460901671 10 2105.131199502364 11 2132.407165368786 12 2138.267187460652 13 2166.002210829576 14 2194.9918295115804 15 2189.890403738045 16 2191.181293229578 17 2209.4669750564362 18 2221.2595493644303 19 2238.7425945763257 20 2253.9559571797727 Best k = 7 **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 2%|▋ | ETA: 0:00:10 Cross validating... 3%|█ | ETA: 0:00:10 Cross validating... 4%|█▎ | ETA: 0:00:11 Cross validating... 5%|█▋ | ETA: 0:00:11 Cross validating... 6%|█▉ | ETA: 0:00:12 Cross validating... 7%|██▎ | ETA: 0:00:13 Cross validating... 8%|██▌ | ETA: 0:00:13 Cross validating... 9%|██▉ | 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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: 0:00:24 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 1m27.4s 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::Type, 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::Type{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:522 [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 2.9s RNG of the outermost testset: Xoshiro(0x08ab71567e6d384e, 0xece68542ade64716, 0xb04390fb551d3198, 0xad31d3928e6143b3, 0xfd0d9f09165adf6d) 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 1104.5s 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 1236.01s: package tests unexpectedly errored