Package evaluation to test MendelIHT on Julia 1.14.0-DEV.1840 (ab7ba34e40*) started at 2026-03-03T23:26:27.090 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.14` Set-up completed after 13.87s ################################################################################ # 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 v0.1.43 [79e6a3ab] + Adapt v4.5.0 [66dad0bd] + AliasTables v1.1.3 [4fba245c] + ArrayInterface v7.22.0 [67c07d97] + Automa v1.1.0 ⌅ [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 v0.2.6 [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 v1.68.0+1 [3f19e933] + p7zip_jll v17.7.0+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 To see why use `status --outdated -m` Installation completed after 5.96s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompiling packages... 4659.7 ms ✓ BGEN 6804.8 ms ✓ 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`. 25216.8 ms ✓ MendelIHT 3 dependencies successfully precompiled in 39 seconds. 171 already precompiled. 1 dependency had output during precompilation: ┌ MendelIHT │ WARNING: Constructor for type "MvNormal" was extended in `MendelIHT` without explicit qualification or import. │ NOTE: Assumed "MvNormal" refers to `Distributions.MvNormal`. This behavior is deprecated and may differ in future versions. │ NOTE: This behavior may have differed in Julia versions prior to 1.12. │ Hint: If you intended to create a new generic function of the same name, use `function MvNormal end`. │ Hint: To silence the warning, qualify `MvNormal` as `Distributions.MvNormal` in the method signature or explicitly `import Distributions: MvNormal`. └ Precompilation completed after 63.34s ################################################################################ # Testing # Testing MendelIHT Status `/tmp/jl_DdW2FP/Project.toml` ⌅ [6db4b851] BGEN v0.1.17 [6e4b80f9] BenchmarkTools v1.6.3 [336ed68f] CSV v0.10.16 [a93c6f00] DataFrames v1.8.1 [8bb1440f] DelimitedFiles v1.9.1 [b4f34e82] Distances v0.10.12 [31c24e10] Distributions v0.25.123 [38e38edf] GLM v1.9.3 [921c7187] MendelIHT v1.4.11 [92933f4c] ProgressMeter v1.11.0 [189a3867] Reexport v1.2.2 [4e780e97] SnpArrays v0.3.23 [276daf66] SpecialFunctions v2.7.1 [2913bbd2] StatsBase v0.34.10 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v1.68.0+1 [3f19e933] p7zip_jll v17.7.0+0 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. Testing Running tests... ┌ 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 └ @ Core ~/.julia/packages/MendelIHT/ZcxZT/src/multivariate.jl:241 Test Summary: | Pass Total Time loglikelihood | 4 4 16.1s Test Summary: | Pass Total Time deviance | 1 1 0.5s Test Summary: | Pass Total Time update_μ! | 4 4 1.6s Test Summary: | Pass Total Time _choose! | 7 7 10.4s Test Summary: | Pass Total Time _iht_backtrack | 7 7 0.0s Test Summary: | Pass Total Time standardize! | 12 12 1.5s Test Summary: | Pass Total Time project_k! | 2 2 1.0s Test Summary: | Pass Total Time project_group_sparse! | 5 5 1.1s Test Summary: | Pass Total Time maf_weights | 6 6 1.8s **** 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) = 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 = -1652.9906166690391, backtracks = 0, tol = 1.5702381596067423 Iteration 2: loglikelihood = -1440.1821232782077, backtracks = 0, tol = 0.14751778400255444 Iteration 3: loglikelihood = -1413.6516091196454, backtracks = 0, tol = 0.07522496300720302 Iteration 4: loglikelihood = -1411.0490449938345, backtracks = 0, tol = 0.017316264969873738 Iteration 5: loglikelihood = -1410.9456491109395, backtracks = 1, tol = 0.002559247728125104 Iteration 6: loglikelihood = -1410.9137499982148, backtracks = 1, tol = 0.0014170707733377128 Iteration 7: loglikelihood = -1410.9047203247608, backtracks = 1, tol = 0.0006959613872825053 Iteration 8: loglikelihood = -1410.9023981650626, backtracks = 1, tol = 0.0003379787293558267 Iteration 9: loglikelihood = -1410.901815494313, backtracks = 1, tol = 0.00017389984083528514 Iteration 10: loglikelihood = -1410.9016697186041, backtracks = 1, tol = 8.753602219664797e-5 IHT estimated 10 nonzero SNP predictors and 1 non-genetic predictors. Compute time (sec): 0.09137296676635742 Final loglikelihood: -1410.9016697186041 SNP PVE: 0.8950686050562865 Iterations: 10 Selected genetic predictors: 10×2 DataFrame Row │ Position Estimated_β │ Int64 Float64 ─────┼─────────────────────── 1 │ 1001 1.13296 2 │ 1905 -1.87187 3 │ 3542 0.28158 4 │ 6236 -0.289035 5 │ 6480 0.962446 6 │ 6766 1.53806 7 │ 8285 0.327942 8 │ 9104 0.1222 9 │ 9739 0.117757 10 │ 9885 -1.26698 Selected nongenetic predictors: 1×2 DataFrame Row │ Position Estimated_β │ Int64 Float64 ─────┼─────────────────────── 1 │ 1 0.00828269Test Summary: | Pass Total Time fit normal SnpLinAlg | 4 4 23.4s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse logistic regression Number of threads = 1 Link functin = LogitLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -379.72375963518977, backtracks = 0, tol = 0.6062552017348442 Iteration 2: loglikelihood = -294.14222098196217, backtracks = 0, tol = 0.39035964909167 Iteration 3: loglikelihood = -258.44215825745147, backtracks = 0, tol = 0.18072720194601524 Iteration 4: loglikelihood = -248.39092317275637, backtracks = 1, tol = 0.0581811999889429 Iteration 5: loglikelihood = -241.2861695402178, backtracks = 2, tol = 0.10199490430383734 Iteration 6: loglikelihood = -236.0344401262056, backtracks = 2, tol = 0.10444957184614982 Iteration 7: loglikelihood = -232.75639772007577, backtracks = 2, tol = 0.03618239958756675 Iteration 8: loglikelihood = -230.9028935826695, backtracks = 3, tol = 0.022566251649321353 Iteration 9: loglikelihood = -229.2332883500926, backtracks = 3, tol = 0.02394599965909332 Iteration 10: loglikelihood = -227.8109863155336, backtracks = 3, tol = 0.02260237147851236 Iteration 11: loglikelihood = -226.61429831284372, backtracks = 3, tol = 0.02153016573221634 Iteration 12: loglikelihood = -225.614543213995, backtracks = 3, tol = 0.020073248773013197 Iteration 13: loglikelihood = -225.15228734295533, backtracks = 3, tol = 0.10266272165892033 Iteration 14: loglikelihood = -224.5524858306654, backtracks = 2, tol = 0.010910053499902256 Iteration 15: loglikelihood = -223.90430308527087, backtracks = 3, tol = 0.10669566586572145 Iteration 16: loglikelihood = -223.43342440058004, backtracks = 1, tol = 0.009912340440473734 Iteration 17: loglikelihood = -223.19474883510568, backtracks = 3, tol = 0.10429355504005154 Iteration 18: loglikelihood = -222.7530868660152, backtracks = 1, tol = 0.010133510239484585 Iteration 19: loglikelihood = -222.4546375562022, backtracks = 3, tol = 0.009382230171462355 Iteration 20: loglikelihood = -225.04961416047087, backtracks = 3, tol = 0.13141028198780508 Iteration 21: loglikelihood = -221.57583298738808, backtracks = 0, tol = 0.12983606150115481 Iteration 22: loglikelihood = -220.9953587123894, backtracks = 0, tol = 0.018278220962270587 Iteration 23: loglikelihood = -220.46528702030645, backtracks = 0, tol = 0.10912949798131547 Iteration 24: loglikelihood = -220.22939682199817, backtracks = 1, tol = 0.006133557493960293 Iteration 25: loglikelihood = -220.1149031779291, backtracks = 3, tol = 0.005637364497494655 Iteration 26: loglikelihood = -237.91408320706802, backtracks = 3, tol = 0.1311916630585333 Iteration 27: loglikelihood = -222.6667401701631, backtracks = 0, tol = 0.13008576394077564 Iteration 28: loglikelihood = -220.0179912284672, backtracks = 0, tol = 0.10981267805412102 Iteration 29: loglikelihood = -219.80873468505163, backtracks = 1, tol = 0.006242686572879014 Iteration 30: loglikelihood = -219.71412932030552, backtracks = 1, tol = 0.0052581541847830735 Iteration 31: loglikelihood = -219.67346582214395, backtracks = 3, tol = 0.002736072071808146 Iteration 32: loglikelihood = -236.63118723570068, backtracks = 3, tol = 0.12536959025201838 Iteration 33: loglikelihood = -222.42522446507616, backtracks = 0, tol = 0.12480632457239557 Iteration 34: loglikelihood = -219.76952387571325, backtracks = 0, tol = 0.10782393864869841 Iteration 35: loglikelihood = -219.54239052596037, backtracks = 0, tol = 0.010969385336776636 Iteration 36: loglikelihood = -219.51051719556185, backtracks = 0, tol = 0.0038143069815270263 Iteration 37: loglikelihood = -219.49562270628724, backtracks = 1, tol = 0.0015360028505860806 Iteration 38: loglikelihood = -222.2776344615594, backtracks = 3, tol = 0.10706948875570901 Iteration 39: loglikelihood = -219.86344247649652, backtracks = 0, tol = 0.10682440099239575 Iteration 40: loglikelihood = -219.50637292175287, backtracks = 0, tol = 0.010145149683589566 Iteration 41: loglikelihood = -219.45601478260392, backtracks = 0, tol = 0.004786594360325445 Iteration 42: loglikelihood = -219.44279315931445, backtracks = 0, tol = 0.0023300326568676676 Iteration 43: loglikelihood = -219.434262597912, backtracks = 0, tol = 0.002159682320412748 Iteration 44: loglikelihood = -219.42706752504972, backtracks = 0, tol = 0.0019986878272562235 Iteration 45: loglikelihood = -219.4208881668612, backtracks = 0, tol = 0.001781315196828412 Iteration 46: loglikelihood = -219.41556755717227, backtracks = 0, tol = 0.0017266268818688624 Iteration 47: loglikelihood = -219.41098445944962, backtracks = 0, tol = 0.001504993867218278 Iteration 48: loglikelihood = -219.4070309112888, backtracks = 0, tol = 0.001495426527055874 Iteration 49: loglikelihood = -219.40362030781677, backtracks = 0, tol = 0.001286324051089446 Iteration 50: loglikelihood = -219.4006747755802, backtracks = 0, tol = 0.001295957349435961 Iteration 51: loglikelihood = -219.39813103252988, backtracks = 0, tol = 0.0011058748112207813 Iteration 52: loglikelihood = -219.3959322024177, backtracks = 0, tol = 0.0011233728145861855 Iteration 53: loglikelihood = -219.39403166729804, backtracks = 0, tol = 0.0009536994758608786 Iteration 54: loglikelihood = -219.39238763268273, backtracks = 0, tol = 0.0009739180646352119 Iteration 55: loglikelihood = -219.39096560226784, backtracks = 0, tol = 0.0008239389039648708 Iteration 56: loglikelihood = -219.38973473800374, backtracks = 0, tol = 0.0008444580901064712 Iteration 57: loglikelihood = -219.3886694316569, backtracks = 0, tol = 0.0007126409505425607 Iteration 58: loglikelihood = -219.38774685610232, backtracks = 0, tol = 0.0007323063866727435 Iteration 59: loglikelihood = -219.3869479529937, backtracks = 0, tol = 0.00061686194275372 Iteration 60: loglikelihood = -219.3862557798823, backtracks = 0, tol = 0.0006351404346176769 Iteration 61: loglikelihood = -219.3856561234815, backtracks = 0, tol = 0.000534269842115572 Iteration 62: loglikelihood = -219.38513638040487, backtracks = 0, tol = 0.0005509480422217535 Iteration 63: loglikelihood = -219.38468593224545, backtracks = 0, tol = 0.0004629512780606966 Iteration 64: loglikelihood = -219.38429538513583, backtracks = 0, tol = 0.0004779860767529819 Iteration 65: loglikelihood = -219.38395679466737, backtracks = 0, tol = 0.0004013057505476397 Iteration 66: loglikelihood = -219.38366314739872, backtracks = 0, tol = 0.0004147454994836376 Iteration 67: loglikelihood = -219.38340849212824, backtracks = 0, tol = 0.00034797985178746597 Iteration 68: loglikelihood = -219.38318758502183, backtracks = 0, tol = 0.0003599207374415984 Iteration 69: loglikelihood = -219.38299596326374, backtracks = 0, tol = 0.0003018217223394219 Iteration 70: loglikelihood = -219.3828297011887, backtracks = 0, tol = 0.00031238270039476616 Iteration 71: loglikelihood = -219.38268544908368, backtracks = 0, tol = 0.00026184698528793125 Iteration 72: loglikelihood = -219.3825602648841, backtracks = 0, tol = 0.0002711550905775348 Iteration 73: loglikelihood = -219.38245163239276, backtracks = 0, tol = 0.00022721198022395564 Iteration 74: loglikelihood = -219.38235734460943, backtracks = 0, tol = 0.00023539371282360467 Iteration 75: loglikelihood = -219.38227551018164, backtracks = 0, tol = 0.0001971920991460162 Iteration 76: loglikelihood = -219.382204472153, backtracks = 0, tol = 0.00020436848993624394 Iteration 77: loglikelihood = -219.3821428080304, backtracks = 0, tol = 0.00017116393516432852 Iteration 78: loglikelihood = -219.38208927292968, backtracks = 0, tol = 0.00017744788492952903 Iteration 79: loglikelihood = -219.38204279645043, backtracks = 0, tol = 0.00014859040670150365 Iteration 80: loglikelihood = -219.38200244272016, backtracks = 0, tol = 0.00015408544066832546 Iteration 81: loglikelihood = -219.38196740593906, backtracks = 0, tol = 0.00012900826739905896 Iteration 82: loglikelihood = -219.38193698216227, backtracks = 0, tol = 0.00013380816660865064 Iteration 83: loglikelihood = -219.38191056455443, backtracks = 0, tol = 0.00011201756190578927 Iteration 84: loglikelihood = -219.3818876233726, backtracks = 0, tol = 0.000116206527337935 Iteration 85: loglikelihood = -219.38186770147453, backtracks = 0, tol = 9.727268703830643e-5 Test Summary: | Pass Total Time fit Bernoulli SnpLinAlg | 4 4 3.5s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse 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 = -10029.32818679162, backtracks = 0, tol = 0.5525830488752057 Iteration 2: loglikelihood = -4453.557134777549, backtracks = 0, tol = 0.06091286576949484 Iteration 3: loglikelihood = -2305.8695817395806, backtracks = 0, tol = 0.07071144784897776 Iteration 4: loglikelihood = -1600.0219651849009, backtracks = 0, tol = 0.07326555937093993 Iteration 5: loglikelihood = -1443.2331846287161, backtracks = 0, tol = 0.05731168362104709 Iteration 6: loglikelihood = -1413.954104276937, backtracks = 0, tol = 0.030704091961585654 Iteration 7: loglikelihood = -1363.5189101322817, backtracks = 0, tol = 0.06909214652594234 Iteration 8: loglikelihood = -1354.2944647403338, backtracks = 0, tol = 0.02963611016664303 Iteration 9: loglikelihood = -1348.7791299708726, backtracks = 0, tol = 0.01590487138063002 Iteration 10: loglikelihood = -1346.5005901845745, backtracks = 0, tol = 0.052120310705112666 Iteration 11: loglikelihood = -1340.8720968652988, backtracks = 0, tol = 0.015249825889697824 Iteration 12: loglikelihood = -1337.2151199353016, backtracks = 1, tol = 0.04388658345728945 Iteration 13: loglikelihood = -1334.4166939833015, backtracks = 0, tol = 0.06513430858140487 Iteration 14: loglikelihood = -1333.20261641667, backtracks = 0, tol = 0.010797158587555965 Iteration 15: loglikelihood = -1332.7094763163643, backtracks = 0, tol = 0.006305801298567975 Iteration 16: loglikelihood = -1332.4219440741858, backtracks = 0, tol = 0.005542742490948696 Iteration 17: loglikelihood = -1332.214025170957, backtracks = 0, tol = 0.005073687201804401 Iteration 18: loglikelihood = -1332.0548775888922, backtracks = 0, tol = 0.003988169722719564 Iteration 19: loglikelihood = -1331.928238901251, backtracks = 0, tol = 0.004399634987907333 Iteration 20: loglikelihood = -1331.824244370127, backtracks = 0, tol = 0.0029591944848171257 Iteration 21: loglikelihood = -1331.7373307102039, backtracks = 0, tol = 0.00385643096483921 Iteration 22: loglikelihood = -1331.663525248862, backtracks = 0, tol = 0.00243546705882481 Iteration 23: loglikelihood = -1331.601711516101, backtracks = 0, tol = 0.0032819480912673385 Iteration 24: loglikelihood = -1331.5487823588219, backtracks = 0, tol = 0.00235711325501278 Iteration 25: loglikelihood = -1331.504319277447, backtracks = 0, tol = 0.002700072836012948 Iteration 26: loglikelihood = -1331.4645042974328, backtracks = 0, tol = 0.0019092183209561988 Iteration 27: loglikelihood = -1331.4282601846726, backtracks = 0, tol = 0.0024791793207064685 Iteration 28: loglikelihood = -1331.3948220980435, backtracks = 0, tol = 0.0015743514596171112 Iteration 29: loglikelihood = -1331.3635074497463, backtracks = 0, tol = 0.002373149220814654 Iteration 30: loglikelihood = -1331.3343698982044, backtracks = 0, tol = 0.0014111463350529312 Iteration 31: loglikelihood = -1331.3068771934145, backtracks = 0, tol = 0.002286056767018427 Iteration 32: loglikelihood = -1331.281166270486, backtracks = 0, tol = 0.001312780452531504 Iteration 33: loglikelihood = -1331.2567975273553, backtracks = 0, tol = 0.002207553890125414 Iteration 34: loglikelihood = -1331.2339160856695, backtracks = 0, tol = 0.001237793899432853 Iteration 35: loglikelihood = -1331.212150167352, backtracks = 0, tol = 0.0021360130149285115 Iteration 36: loglikelihood = -1331.1916430544477, backtracks = 0, tol = 0.0011736677824017733 Iteration 37: loglikelihood = -1331.1720747214313, backtracks = 0, tol = 0.00207059214876742 Iteration 38: loglikelihood = -1331.153583800559, backtracks = 0, tol = 0.0011164537945754715 Iteration 39: loglikelihood = -1331.1358908983475, backtracks = 0, tol = 0.0020105967026272566 Iteration 40: loglikelihood = -1331.1191288749424, backtracks = 0, tol = 0.001064613770214911 Iteration 41: loglikelihood = -1331.103050988857, backtracks = 0, tol = 0.0019554231750566384 Iteration 42: loglikelihood = -1331.0877839287357, backtracks = 0, tol = 0.0010173175092896077 Iteration 43: loglikelihood = -1331.0731076922052, backtracks = 0, tol = 0.001904546017856335 Iteration 44: loglikelihood = -1331.0591427657714, backtracks = 0, tol = 0.0009739800518443053 Iteration 45: loglikelihood = -1331.045691383712, backtracks = 0, tol = 0.0018575078146060783 Iteration 46: loglikelihood = -1331.0328679933111, backtracks = 0, tol = 0.0009341316632543742 Iteration 47: loglikelihood = -1331.0204935587894, backtracks = 0, tol = 0.0018139103167185873 Iteration 48: loglikelihood = -1331.0086767505832, backtracks = 0, tol = 0.0008973762992292003 Iteration 49: loglikelihood = -1330.9972544805717, backtracks = 0, tol = 0.0017734063830312837 Iteration 50: loglikelihood = -1330.986329951775, backtracks = 0, tol = 0.0008633741896685747 Iteration 51: loglikelihood = -1330.9757537820726, backtracks = 0, tol = 0.001735692889583316 Iteration 52: loglikelihood = -1330.96562403377, backtracks = 0, tol = 0.0008318317071108681 Iteration 53: loglikelihood = -1330.9558032011048, backtracks = 0, tol = 0.001700504582286751 Iteration 54: loglikelihood = -1330.9463845325827, backtracks = 0, tol = 0.0008024940218799414 Iteration 55: loglikelihood = -1330.937240888685, backtracks = 0, tol = 0.0016676087921075463 Iteration 56: loglikelihood = -1330.9284610215566, backtracks = 0, tol = 0.0007751392330692314 Iteration 57: loglikelihood = -1330.9199268992936, backtracks = 0, tol = 0.0016368009127532507 Iteration 58: loglikelihood = -1330.9117230802995, backtracks = 0, tol = 0.0007495735078659384 Iteration 59: loglikelihood = -1330.9037395820972, backtracks = 0, tol = 0.001607900539817054 Iteration 60: loglikelihood = -1330.8960570544928, backtracks = 0, tol = 0.0007256270038893913 Iteration 61: loglikelihood = -1330.8885726676808, backtracks = 0, tol = 0.0015807481777992045 Iteration 62: loglikelihood = -1330.8813634295332, backtracks = 0, tol = 0.0007031504317343224 Iteration 63: loglikelihood = -1330.8743328975029, backtracks = 0, tol = 0.0015552024319237803 Iteration 64: loglikelihood = -1330.8675546855957, backtracks = 0, tol = 0.0006820121511944629 Iteration 65: loglikelihood = -1330.8609380808866, backtracks = 0, tol = 0.0015311376125780717 Iteration 66: loglikelihood = -1330.8545535335636, backtracks = 0, tol = 0.0006620957154118754 Iteration 67: loglikelihood = -1330.8483154918088, backtracks = 0, tol = 0.0015084416903341248 Iteration 68: loglikelihood = -1330.8422914548366, backtracks = 0, tol = 0.0006432977916574498 Iteration 69: loglikelihood = -1330.8364005377216, backtracks = 0, tol = 0.0014870145485474655 Iteration 70: loglikelihood = -1330.8307074853956, backtracks = 0, tol = 0.000625526398782945 Iteration 71: loglikelihood = -1330.8251356478875, backtracks = 0, tol = 0.0014667664883906747 Iteration 72: loglikelihood = -1330.8197471975222, backtracks = 0, tol = 0.0006086994107632218 Iteration 73: loglikelihood = -1330.8144693399177, backtracks = 0, tol = 0.0014476169479556095 Iteration 74: loglikelihood = -1330.8093618425567, backtracks = 0, tol = 0.0005927432837231161 Iteration 75: loglikelihood = -1330.804355431937, backtracks = 0, tol = 0.001429493402907018 Iteration 76: loglikelihood = -1330.7995076256568, backtracks = 0, tol = 0.0005775919706470877 Iteration 77: loglikelihood = -1330.794752374492, backtracks = 0, tol = 0.0014123304211300367 Iteration 78: loglikelihood = -1330.7901450893326, backtracks = 0, tol = 0.0005631859937725703 Iteration 79: loglikelihood = -1330.7856226813399, backtracks = 0, tol = 0.001396068848123036 Iteration 80: loglikelihood = -1330.7812385871132, backtracks = 0, tol = 0.0005494716495975536 Iteration 81: loglikelihood = -1330.7769324424992, backtracks = 0, tol = 0.0013806551034681838 Iteration 82: loglikelihood = -1330.7727558323263, backtracks = 0, tol = 0.0005364003255703428 Iteration 83: loglikelihood = -1330.7696738383822, backtracks = 1, tol = 0.0006830202859221554 Iteration 84: loglikelihood = -1330.7668797390818, backtracks = 0, tol = 0.0007349303836117274 Iteration 85: loglikelihood = -1330.764146914095, backtracks = 0, tol = 0.0004373128257211231 Iteration 86: loglikelihood = -1330.761482362315, backtracks = 0, tol = 0.0007121769264188737 Iteration 87: loglikelihood = -1330.7588746892588, backtracks = 0, tol = 0.000427181864143675 Iteration 88: loglikelihood = -1330.756330340582, backtracks = 0, tol = 0.0006907261933166356 Iteration 89: loglikelihood = -1330.7538389001647, backtracks = 0, tol = 0.0004175289727271952 Iteration 90: loglikelihood = -1330.751406318244, backtracks = 0, tol = 0.0006704690234256045 Iteration 91: loglikelihood = -1330.7490230478618, backtracks = 0, tol = 0.0004083363274632127 Iteration 92: loglikelihood = -1330.7466945942808, backtracks = 0, tol = 0.0006513087955029177 Iteration 93: loglikelihood = -1330.7444121852905, backtracks = 0, tol = 0.00039957457429271357 Iteration 94: loglikelihood = -1330.742180925384, backtracks = 0, tol = 0.000633159107534627 Iteration 95: loglikelihood = -1330.7399927351057, backtracks = 0, tol = 0.0003929116929909575 Iteration 96: loglikelihood = -1330.7378523569946, backtracks = 0, tol = 0.0006159424140137354 Iteration 97: loglikelihood = -1330.7357523329079, backtracks = 0, tol = 0.00038746191309820547 Iteration 98: loglikelihood = -1330.7336970776826, backtracks = 0, tol = 0.00059958891295452 Iteration 99: loglikelihood = -1330.73167969194, backtracks = 0, tol = 0.00038221510161241503 Iteration 100: loglikelihood = -1330.729704293091, backtracks = 0, tol = 0.0005840356003726861 Iteration 101: loglikelihood = -1330.7277644856606, backtracks = 0, tol = 0.00037715911165177773 Iteration 102: loglikelihood = -1330.7258641164894, backtracks = 0, tol = 0.0005692254607668191 Iteration 103: loglikelihood = -1330.7239972456503, backtracks = 0, tol = 0.00037228278988035756 Iteration 104: loglikelihood = -1330.7221674733348, backtracks = 0, tol = 0.0005551067709399708 Iteration 105: loglikelihood = -1330.7203692724415, backtracks = 0, tol = 0.00036757587418498046 Iteration 106: loglikelihood = -1330.7186060178128, backtracks = 0, tol = 0.0005416324989668155 Iteration 107: loglikelihood = -1330.7168725573533, backtracks = 0, tol = 0.0003630289039923987 Iteration 108: loglikelihood = -1330.7151720596137, backtracks = 0, tol = 0.0005287597834167481 Iteration 109: loglikelihood = -1330.7134997138787, backtracks = 0, tol = 0.00035863314141315215 Iteration 110: loglikelihood = -1330.7118584994937, backtracks = 0, tol = 0.0005164494805706721 Iteration 111: loglikelihood = -1330.7102439171717, backtracks = 0, tol = 0.00035438050169166033 Iteration 112: loglikelihood = -1330.7086587723898, backtracks = 0, tol = 0.0005046657694680239 Iteration 113: loglikelihood = -1330.7070988505607, backtracks = 0, tol = 0.00035026349168656594 Iteration 114: loglikelihood = -1330.7055667970837, backtracks = 0, tol = 0.0004933758063301809 Iteration 115: loglikelihood = -1330.7040586581304, backtracks = 0, tol = 0.0003462751553021245 Iteration 116: loglikelihood = -1330.702576931511, backtracks = 0, tol = 0.0004825494212924039 Iteration 117: loglikelihood = -1330.7011179026617, backtracks = 0, tol = 0.0003424090249601675 Iteration 118: loglikelihood = -1330.699683933055, backtracks = 0, tol = 0.0004721588515109261 Iteration 119: loglikelihood = -1330.698271528069, backtracks = 0, tol = 0.0003386590783334284 Iteration 120: loglikelihood = -1330.6968829230614, backtracks = 0, tol = 0.0004621785056491499 Iteration 121: loglikelihood = -1330.6955148259344, backtracks = 0, tol = 0.0003350196996796438 Iteration 122: loglikelihood = -1330.694169355187, backtracks = 0, tol = 0.0004525847555157266 Iteration 123: loglikelihood = -1330.6928434055233, backtracks = 0, tol = 0.0003314856452054803 Iteration 124: loglikelihood = -1330.6915389870062, backtracks = 0, tol = 0.0004433557512642939 Iteration 125: loglikelihood = -1330.690253166901, backtracks = 0, tol = 0.00032805201197578203 Iteration 126: loglikelihood = -1330.688987854516, backtracks = 0, tol = 0.0004344712571040293 Iteration 127: loglikelihood = -1330.6877402767825, backtracks = 0, tol = 0.0003247142099421096 Iteration 128: loglikelihood = -1330.6865122492452, backtracks = 0, tol = 0.0004259125049086961 Iteration 129: loglikelihood = -1330.6853011467697, backtracks = 0, tol = 0.0003214679367302218 Iteration 130: loglikelihood = -1330.6841086975455, backtracks = 0, tol = 0.0004176620634860388 Iteration 131: loglikelihood = -1330.6829324137168, backtracks = 0, tol = 0.0003183091548697756 Iteration 132: loglikelihood = -1330.6817739419625, backtracks = 0, tol = 0.0004097037215886438 Iteration 133: loglikelihood = -1330.6806309219846, backtracks = 0, tol = 0.0003152340711879527 Iteration 134: loglikelihood = -1330.6795049243253, backtracks = 0, tol = 0.00040202238300656557 Iteration 135: loglikelihood = -1330.6783937073728, backtracks = 0, tol = 0.00031223911813302644 Iteration 136: loglikelihood = -1330.6772987704517, backtracks = 0, tol = 0.00039460397230941006 Iteration 137: loglikelihood = -1330.6762179825316, backtracks = 0, tol = 0.0003093209368127437 Iteration 138: loglikelihood = -1330.6751527762551, backtracks = 0, tol = 0.00038743534999753594 Iteration 139: loglikelihood = -1330.6741011237175, backtracks = 0, tol = 0.00030647636156794195 Iteration 140: loglikelihood = -1330.6730643950793, backtracks = 0, tol = 0.0003805042359825682 Iteration 141: loglikelihood = -1330.6720406587428, backtracks = 0, tol = 0.0003037024059168592 Iteration 142: loglikelihood = -1330.6710312262119, backtracks = 0, tol = 0.0003737991404592197 Iteration 143: loglikelihood = -1330.670034255948, backtracks = 0, tol = 0.00030099624973108855 Iteration 144: loglikelihood = -1330.6690510043577, backtracks = 0, tol = 0.00036730930134667826 Iteration 145: loglikelihood = -1330.6680797142008, backtracks = 0, tol = 0.0002983552275148568 Iteration 146: loglikelihood = -1330.6671215900622, backtracks = 0, tol = 0.0003610246275833962 Iteration 147: loglikelihood = -1330.6661749536963, backtracks = 0, tol = 0.0002957768176796895 Iteration 148: loglikelihood = -1330.6652409609094, backtracks = 0, tol = 0.0003549356476440135 Iteration 149: loglikelihood = -1330.6643180075525, backtracks = 0, tol = 0.0002932586327137591 Iteration 150: loglikelihood = -1330.6634072034856, backtracks = 0, tol = 0.0003490334627283324 Iteration 151: loglikelihood = -1330.6625070141254, backtracks = 0, tol = 0.0002907984101600268 Iteration 152: loglikelihood = -1330.6616185059897, backtracks = 0, tol = 0.0003433097041302738 Iteration 153: loglikelihood = -1330.660740209903, backtracks = 0, tol = 0.0002883940043266604 Iteration 154: loglikelihood = -1330.6598731514507, backtracks = 0, tol = 0.00033775649436287354 Iteration 155: loglikelihood = -1330.6590159230102, backtracks = 0, tol = 0.00028604337865771547 Iteration 156: loglikelihood = -1330.658169511508, backtracks = 0, tol = 0.0003323664116539346 Iteration 157: loglikelihood = -1330.65733256726, backtracks = 0, tol = 0.0002837445987057568 Iteration 158: loglikelihood = -1330.6565060406256, backtracks = 0, tol = 0.00032713245747892003 Iteration 159: loglikelihood = -1330.655688636564, backtracks = 0, tol = 0.0002814958256490372 Iteration 160: loglikelihood = -1330.654881270825, backtracks = 0, tol = 0.0003220480268310214 Iteration 161: loglikelihood = -1330.6540826999048, backtracks = 0, tol = 0.00027929531030551413 Iteration 162: loglikelihood = -1330.653293806774, backtracks = 0, tol = 0.00031710688096265037 Iteration 163: loglikelihood = -1330.6525133965988, backtracks = 0, tol = 0.00027714138759764534 Iteration 164: loglikelihood = -1330.651742321272, backtracks = 0, tol = 0.000312303122362394 Iteration 165: loglikelihood = -1330.6509794319652, backtracks = 0, tol = 0.0002750324714296534 Iteration 166: loglikelihood = -1330.650225551072, backtracks = 0, tol = 0.00030763117175613286 Iteration 167: loglikelihood = -1330.6494795732867, backtracks = 0, tol = 0.00027296704994121684 Iteration 168: loglikelihood = -1330.6487422929993, backtracks = 0, tol = 0.00030308574694338716 Iteration 169: loglikelihood = -1330.648012646087, backtracks = 0, tol = 0.00027094368110527103 Iteration 170: loglikelihood = -1330.6472914003398, backtracks = 0, tol = 0.00029866184330055507 Iteration 171: loglikelihood = -1330.6465775306633, backtracks = 0, tol = 0.00026896098863967707 Iteration 172: loglikelihood = -1330.6458717795454, backtracks = 0, tol = 0.00029435471580021016 Iteration 173: loglikelihood = -1330.6451731588847, backtracks = 0, tol = 0.00026701765820864995 Iteration 174: loglikelihood = -1330.6444823870966, backtracks = 0, tol = 0.0002901598624091396 Iteration 175: loglikelihood = -1330.6437985111806, backtracks = 0, tol = 0.0002651124338889662 Iteration 176: loglikelihood = -1330.6431222266363, backtracks = 0, tol = 0.000286073008745652 Iteration 177: loglikelihood = -1330.6424526137966, backtracks = 0, tol = 0.0002632441148784611 Iteration 178: loglikelihood = -1330.6417903462984, backtracks = 0, tol = 0.0002820900938842629 Iteration 179: loglikelihood = -1330.6411345361628, backtracks = 0, tol = 0.00026141155242946564 Iteration 180: loglikelihood = -1330.6404858361948, backtracks = 0, tol = 0.0002782072572090802 Iteration 181: loglikelihood = -1330.639843388524, backtracks = 0, tol = 0.00025961364698711786 Iteration 182: loglikelihood = -1330.639207826082, backtracks = 0, tol = 0.0002744208262262454 Iteration 183: loglikelihood = -1330.6385783196545, backtracks = 0, tol = 0.0002578493455186889 Iteration 184: loglikelihood = -1330.6379554831979, backtracks = 0, tol = 0.00027072730525789043 Iteration 185: loglikelihood = -1330.637338514779, backtracks = 0, tol = 0.00025611763901677676 Iteration 186: loglikelihood = -1330.6367280102245, backtracks = 0, tol = 0.00026712336493868916 Iteration 187: loglikelihood = -1330.6361231936003, backtracks = 0, tol = 0.0002544175601650811 Iteration 188: loglikelihood = -1330.6355246433934, backtracks = 0, tol = 0.00026360583245369694 Iteration 189: loglikelihood = -1330.6349316084595, backtracks = 0, tol = 0.0002527481811534847 Iteration 190: loglikelihood = -1330.6343446507083, backtracks = 0, tol = 0.0002601716824556766 Iteration 191: loglikelihood = -1330.6337630426265, backtracks = 0, tol = 0.0002511086116310067 Iteration 192: loglikelihood = -1330.633187330267, backtracks = 0, tol = 0.0002568180286067304 Iteration 193: loglikelihood = -1330.6326168086764, backtracks = 0, tol = 0.0002494979967872262 Iteration 194: loglikelihood = -1330.6320520087204, backtracks = 0, tol = 0.0002535421156962968 Iteration 195: loglikelihood = -1330.631492246996, backtracks = 0, tol = 0.00024791551555235344 Iteration 196: loglikelihood = -1330.6309380398122, backtracks = 0, tol = 0.0002503413122878003 Iteration 197: loglikelihood = -1330.630388724358, backtracks = 0, tol = 0.0002463603789075071 Iteration 198: loglikelihood = -1330.629844802992, backtracks = 0, tol = 0.00024721310385573947 Iteration 199: loglikelihood = -1330.6293056325917, backtracks = 0, tol = 0.00024483182829656755 Did not converge after 200 iterations! IHT run time was 1.7531180381774902 seconds Test Summary: | Pass Total Time fit Poisson SnpLinAlg | 4 4 4.5s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse 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 = -1621.009254912503, backtracks = 0, tol = 0.5779307908336948 Iteration 2: loglikelihood = -1529.6801699904618, backtracks = 0, tol = 0.08469287942662429 Iteration 3: loglikelihood = -1474.7037981468836, backtracks = 0, tol = 0.07879498662568507 Iteration 4: loglikelihood = -1452.511685797454, backtracks = 0, tol = 0.0713203555510474 Iteration 5: loglikelihood = -1447.5452746828153, backtracks = 0, tol = 0.05671706645038795 Iteration 6: loglikelihood = -1443.4850711802749, backtracks = 0, tol = 0.08132497716250878 Iteration 7: loglikelihood = -1441.6239342870401, backtracks = 0, tol = 0.07778677360230003 Iteration 8: loglikelihood = -1440.915469020583, backtracks = 0, tol = 0.020457395055130802 Iteration 9: loglikelihood = -1440.668441483451, backtracks = 1, tol = 0.009786072514898875 Iteration 10: loglikelihood = -1440.4704842398396, backtracks = 2, tol = 0.012958405804829723 Iteration 11: loglikelihood = -1440.3837229568303, backtracks = 3, tol = 0.006694263585263717 Iteration 12: loglikelihood = -1440.3054859607757, backtracks = 3, tol = 0.006743231460523276 Iteration 13: loglikelihood = -1440.2354948239795, backtracks = 3, tol = 0.006743687071493418 Iteration 14: loglikelihood = -1440.1729693205175, backtracks = 3, tol = 0.0067415480397535425 Iteration 15: loglikelihood = -1440.1171904057244, backtracks = 3, tol = 0.006737074515256253 Iteration 16: loglikelihood = -1440.0674920513509, backtracks = 3, tol = 0.006730978326705228 Iteration 17: loglikelihood = -1441.6174489704806, backtracks = 3, tol = 0.08011739407921141 Iteration 18: loglikelihood = -1440.987576975023, backtracks = 0, tol = 0.020456762152175966 Iteration 19: loglikelihood = -1439.9881746550002, backtracks = 1, tol = 0.060693293498136514 Iteration 20: loglikelihood = -1439.8627679763608, backtracks = 1, tol = 0.007017798236090959 Iteration 21: loglikelihood = -1439.820528754141, backtracks = 1, tol = 0.0040505776855718715 Iteration 22: loglikelihood = -1439.8013288084385, backtracks = 2, tol = 0.0033426444228029798 Iteration 23: loglikelihood = -1440.3473590255394, backtracks = 3, tol = 0.08759716928700718 Iteration 24: loglikelihood = -1439.0900811533668, backtracks = 0, tol = 0.08757634310756034 Iteration 25: loglikelihood = -1438.968198925618, backtracks = 0, tol = 0.008323857629063073 Iteration 26: loglikelihood = -1438.952056415228, backtracks = 1, tol = 0.002602859017260664 Iteration 27: loglikelihood = -1444.2532792256875, backtracks = 3, tol = 0.09517720347630296 Iteration 28: loglikelihood = -1440.1989279942495, backtracks = 0, tol = 0.09620273396709607 Iteration 29: loglikelihood = -1439.1279017313916, backtracks = 0, tol = 0.07713878862151156 Iteration 30: loglikelihood = -1438.797194781761, backtracks = 0, tol = 0.07979253532865385 Iteration 31: loglikelihood = -1438.7067944476325, backtracks = 0, tol = 0.00824973865508571 Iteration 32: loglikelihood = -1438.5732438686873, backtracks = 0, tol = 0.07838611540003246 Iteration 33: loglikelihood = -1438.5283302566763, backtracks = 1, tol = 0.0036518743643503826 Iteration 34: loglikelihood = -1438.510689073711, backtracks = 1, tol = 0.00236958938469691 Iteration 35: loglikelihood = -1438.5035920328921, backtracks = 3, tol = 0.0019325479288636576 Iteration 36: loglikelihood = -1447.4559548333946, backtracks = 3, tol = 0.11417873327959668 Iteration 37: loglikelihood = -1440.3260729710112, backtracks = 0, tol = 0.10426404699486835 Iteration 38: loglikelihood = -1440.0618692711437, backtracks = 0, tol = 0.014338474696112869 Iteration 39: loglikelihood = -1440.0404836964444, backtracks = 0, tol = 0.004211448608128858 Iteration 40: loglikelihood = -1440.03651151803, backtracks = 0, tol = 0.0020079325285558797 Iteration 41: loglikelihood = -1440.0343743283372, backtracks = 1, tol = 0.0010189603739048719 Iteration 42: loglikelihood = -1450.8244104075263, backtracks = 3, tol = 0.12372656916264638 Iteration 43: loglikelihood = -1439.7354319924782, backtracks = 0, tol = 0.11921147488600937 Iteration 44: loglikelihood = -1439.032955671432, backtracks = 0, tol = 0.01809251353873421 Iteration 45: loglikelihood = -1438.98077646886, backtracks = 0, tol = 0.005599900758283102 Iteration 46: loglikelihood = -1438.97406324075, backtracks = 1, tol = 0.0010472038236111626 Iteration 47: loglikelihood = -1438.9705239424907, backtracks = 2, tol = 0.001274176112361502 Iteration 48: loglikelihood = -1438.728606458568, backtracks = 3, tol = 0.0804836213524557 Iteration 49: loglikelihood = -1438.5932131288175, backtracks = 0, tol = 0.009141363124590145 Iteration 50: loglikelihood = -1438.5819274004823, backtracks = 0, tol = 0.002192050474683372 Iteration 51: loglikelihood = -1438.5788489970014, backtracks = 1, tol = 0.0011878132425062102 Iteration 52: loglikelihood = -1438.5402128405228, backtracks = 3, tol = 0.07850179566854489 Iteration 53: loglikelihood = -1438.4362554516727, backtracks = 0, tol = 0.00892454256190928 Iteration 54: loglikelihood = -1438.4303633109557, backtracks = 0, tol = 0.0017275230481118458 Iteration 55: loglikelihood = -1438.4276992842333, backtracks = 1, tol = 0.0010761317405978941 Iteration 56: loglikelihood = -1470.1341121188589, backtracks = 3, tol = 0.1792426721915138 Iteration 57: loglikelihood = -1440.4819259012586, backtracks = 0, tol = 0.162909332861328 Iteration 58: loglikelihood = -1440.0606913203058, backtracks = 0, tol = 0.016172448580496487 Iteration 59: loglikelihood = -1440.0105707186017, backtracks = 0, tol = 0.0065481684671108995 Iteration 60: loglikelihood = -1440.0023128515631, backtracks = 0, tol = 0.001903243977730778 Iteration 61: loglikelihood = -1440.0002594979303, backtracks = 0, tol = 0.001447852998764792 Iteration 62: loglikelihood = -1439.9994461459787, backtracks = 1, tol = 0.0005738688383112359 Iteration 63: loglikelihood = -1446.171802326308, backtracks = 3, tol = 0.1023072414532658 Iteration 64: loglikelihood = -1439.5928828218564, backtracks = 0, tol = 0.09860145034989118 Iteration 65: loglikelihood = -1438.977367324092, backtracks = 0, tol = 0.01804774069333908 Iteration 66: loglikelihood = -1438.9390048125829, backtracks = 0, tol = 0.0055717520365927385 Iteration 67: loglikelihood = -1438.9346815256995, backtracks = 1, tol = 0.0008059970287016513 Iteration 68: loglikelihood = -1438.6839411982362, backtracks = 1, tol = 0.07617783713670746 Iteration 69: loglikelihood = -1438.5603502664035, backtracks = 0, tol = 0.008831268930958444 Iteration 70: loglikelihood = -1438.5499971482207, backtracks = 0, tol = 0.0019362583325451363 Iteration 71: loglikelihood = -1438.5482832938685, backtracks = 1, tol = 0.0006616311215351468 Iteration 72: loglikelihood = -1438.5473982982269, backtracks = 3, tol = 0.0006007519263420456 Iteration 73: loglikelihood = -1441.9485468618195, backtracks = 3, tol = 0.10025521159960268 Iteration 74: loglikelihood = -1439.4653381096605, backtracks = 0, tol = 0.10012312687463801 Iteration 75: loglikelihood = -1439.3611666357024, backtracks = 0, tol = 0.006153419983826316 Iteration 76: loglikelihood = -1439.1285731763141, backtracks = 0, tol = 0.07369598319123857 Iteration 77: loglikelihood = -1439.081072822807, backtracks = 0, tol = 0.0058036371684038746 Iteration 78: loglikelihood = -1439.049812778358, backtracks = 0, tol = 0.07437133614429962 Iteration 79: loglikelihood = -1438.985302804085, backtracks = 0, tol = 0.004349363572374469 Iteration 80: loglikelihood = -1438.9801582490238, backtracks = 0, tol = 0.0013408624438226635 Iteration 81: loglikelihood = -1438.9794032141283, backtracks = 0, tol = 0.0006916445105474711 Iteration 82: loglikelihood = -1438.978966808915, backtracks = 1, tol = 0.0005236540623503392 Iteration 83: loglikelihood = -1438.9786163241524, backtracks = 3, tol = 0.000474138023626318 Iteration 84: loglikelihood = -1933.2302946658572, backtracks = 3, tol = 0.3209939130715012 Iteration 85: loglikelihood = -1681.2235270089816, backtracks = 0, tol = 0.8551064543042985 Iteration 86: loglikelihood = -1588.8279864569006, backtracks = 0, tol = 0.07762624113669758 Iteration 87: loglikelihood = -1526.9289967534773, backtracks = 0, tol = 0.07661489882872033 Iteration 88: loglikelihood = -1487.004688423583, backtracks = 0, tol = 0.07958611773145101 Iteration 89: loglikelihood = -1457.8663448123534, backtracks = 0, tol = 0.0857449188655459 Iteration 90: loglikelihood = -1444.0726878420385, backtracks = 0, tol = 0.07701404989420128 Iteration 91: loglikelihood = -1440.5146983217564, backtracks = 0, tol = 0.04884442011945108 Iteration 92: loglikelihood = -1440.2402786204789, backtracks = 0, tol = 0.014307067514319908 Iteration 93: loglikelihood = -1440.2197468717302, backtracks = 0, tol = 0.003936955894170735 Iteration 94: loglikelihood = -1440.2175721958024, backtracks = 0, tol = 0.0014416991197780957 Iteration 95: loglikelihood = -1440.2167895071634, backtracks = 1, tol = 0.0006198364336596935 Iteration 96: loglikelihood = -1439.312492075002, backtracks = 3, tol = 0.06489685107541958 Iteration 97: loglikelihood = -1439.1048802013875, backtracks = 0, tol = 0.009758570998835687 Iteration 98: loglikelihood = -1439.0887806697729, backtracks = 0, tol = 0.0031332142645054853 Iteration 99: loglikelihood = -1438.6213970005363, backtracks = 0, tol = 0.06519818454893782 Iteration 100: loglikelihood = -1438.443599374123, backtracks = 0, tol = 0.07143635215185562 Iteration 101: loglikelihood = -1438.3817731851746, backtracks = 0, tol = 0.006924965862928608 Iteration 102: loglikelihood = -1438.3788270316682, backtracks = 0, tol = 0.0014245952704119561 Iteration 103: loglikelihood = -1438.3780915221678, backtracks = 1, tol = 0.0005441164742320913 Iteration 104: loglikelihood = -1453.9812699835354, backtracks = 3, tol = 0.13391194169226991 Iteration 105: loglikelihood = -1440.2536500582635, backtracks = 0, tol = 0.12204843478408742 Iteration 106: loglikelihood = -1439.9940800311376, backtracks = 0, tol = 0.014023141101143473 Iteration 107: loglikelihood = -1439.9781212359044, backtracks = 0, tol = 0.003079507451618604 Iteration 108: loglikelihood = -1439.976666037235, backtracks = 0, tol = 0.0009748350062591908 Iteration 109: loglikelihood = -1439.9763858354472, backtracks = 1, tol = 0.000268751304157964 Iteration 110: loglikelihood = -1439.9761930443674, backtracks = 3, tol = 0.00033148230521277364 Iteration 111: loglikelihood = -1510.5681663830233, backtracks = 3, tol = 0.21599376136829912 Iteration 112: loglikelihood = -1447.578348491883, backtracks = 0, tol = 0.12359104145928786 Iteration 113: loglikelihood = -1439.7391975791274, backtracks = 0, tol = 0.08469275832592953 Iteration 114: loglikelihood = -1438.953663348492, backtracks = 0, tol = 0.019319748379104683 Iteration 115: loglikelihood = -1438.9085864521126, backtracks = 0, tol = 0.006006431930690548 Iteration 116: loglikelihood = -1438.9035892707427, backtracks = 0, tol = 0.0014107158677011033 Iteration 117: loglikelihood = -1438.9027214606144, backtracks = 0, tol = 0.0008350919188557148 Iteration 118: loglikelihood = -1438.9023880684704, backtracks = 1, tol = 0.0003361914886775712 Iteration 119: loglikelihood = -1588.6216846291811, backtracks = 3, tol = 0.26562351594553324 Iteration 120: loglikelihood = -1447.8577530015198, backtracks = 0, tol = 0.26508705199452476 Iteration 121: loglikelihood = -1440.3600183222252, backtracks = 0, tol = 0.12409804349625074 Iteration 122: loglikelihood = -1439.2702669256232, backtracks = 0, tol = 0.0717771462607223 Iteration 123: loglikelihood = -1439.1342564523939, backtracks = 0, tol = 0.009517518077447502 Iteration 124: loglikelihood = -1439.127167217542, backtracks = 0, tol = 0.0016976564706128701 Iteration 125: loglikelihood = -1439.1264060449607, backtracks = 0, tol = 0.0006480447872304601 Iteration 126: loglikelihood = -1439.1262353547918, backtracks = 1, tol = 0.00019396765117618968 Iteration 127: loglikelihood = -1439.1260758573355, backtracks = 3, tol = 0.00034387494211986875 Iteration 128: loglikelihood = -1915.2919763549678, backtracks = 3, tol = 0.2944233923724166 Iteration 129: loglikelihood = -1769.4418026103724, backtracks = 0, tol = 0.8980009776309885 Iteration 130: loglikelihood = -1617.6637910348884, backtracks = 0, tol = 0.11746382799823174 Iteration 131: loglikelihood = -1542.0668731465462, backtracks = 0, tol = 0.08332211873219465 Iteration 132: loglikelihood = -1493.7779558490643, backtracks = 0, tol = 0.0838358609853505 Iteration 133: loglikelihood = -1463.6688071450278, backtracks = 0, tol = 0.08656180377622251 Iteration 134: loglikelihood = -1446.712830459689, backtracks = 0, tol = 0.07968726455680823 Iteration 135: loglikelihood = -1440.8087507044684, backtracks = 0, tol = 0.058214809909044145 Iteration 136: loglikelihood = -1440.1199021496568, backtracks = 0, tol = 0.022720514373533028 Iteration 137: loglikelihood = -1439.2337798019564, backtracks = 0, tol = 0.06961664983600106 Iteration 138: loglikelihood = -1439.1788176499747, backtracks = 0, tol = 0.005684731187553666 Iteration 139: loglikelihood = -1439.1743284260224, backtracks = 0, tol = 0.001629174632926673 Iteration 140: loglikelihood = -1439.1737083031328, backtracks = 0, tol = 0.0005238223475048983 Iteration 141: loglikelihood = -1439.1735026472768, backtracks = 1, tol = 0.0002511188969922627 Iteration 142: loglikelihood = -1503.3459339429892, backtracks = 3, tol = 0.21022314670326683 Iteration 143: loglikelihood = -1447.4682371465574, backtracks = 0, tol = 0.11787014003914566 Iteration 144: loglikelihood = -1440.267893094428, backtracks = 0, tol = 0.09059274741075472 Iteration 145: loglikelihood = -1439.7860820086837, backtracks = 0, tol = 0.01343981851350935 Iteration 146: loglikelihood = -1439.7566105535761, backtracks = 0, tol = 0.0033801038363917256 Iteration 147: loglikelihood = -1439.7537770611818, backtracks = 0, tol = 0.0011373004894627906 Iteration 148: loglikelihood = -1439.7533797508859, backtracks = 1, tol = 0.0003040007426788635 Iteration 149: loglikelihood = -1439.7531651297472, backtracks = 2, tol = 0.00027136801703968284 Iteration 150: loglikelihood = -1439.7529798992653, backtracks = 3, tol = 0.00033494517148721404 Iteration 151: loglikelihood = -1597.2830349882072, backtracks = 3, tol = 0.26956937538115544 Iteration 152: loglikelihood = -1456.2555900450423, backtracks = 0, tol = 0.24597409776515247 Iteration 153: loglikelihood = -1441.4536156769684, backtracks = 0, tol = 0.11147893928696044 Iteration 154: loglikelihood = -1439.1542112324341, backtracks = 0, tol = 0.0825858589271028 Iteration 155: loglikelihood = -1438.8105539021633, backtracks = 0, tol = 0.013237915957240496 Iteration 156: loglikelihood = -1438.7936587094273, backtracks = 0, tol = 0.0026454713213495736 Iteration 157: loglikelihood = -1438.7926029405567, backtracks = 0, tol = 0.0007759521443883674 Iteration 158: loglikelihood = -1438.7924132362514, backtracks = 1, tol = 0.00027051998644889955 Iteration 159: loglikelihood = -1441.4216439624533, backtracks = 3, tol = 0.07699146428379389 Iteration 160: loglikelihood = -1439.2583018987903, backtracks = 0, tol = 0.07348902313934288 Iteration 161: loglikelihood = -1439.114398331042, backtracks = 0, tol = 0.011402714456246547 Iteration 162: loglikelihood = -1439.107244282158, backtracks = 0, tol = 0.0020141302181614987 Iteration 163: loglikelihood = -1438.5841448285676, backtracks = 0, tol = 0.06771694376064676 Iteration 164: loglikelihood = -1438.5433992850667, backtracks = 0, tol = 0.004349481566181843 Iteration 165: loglikelihood = -1438.5388846680087, backtracks = 0, tol = 0.0015268618202451218 Iteration 166: loglikelihood = -1438.5380832571009, backtracks = 0, tol = 0.0008195808455405498 Iteration 167: loglikelihood = -1438.5378481792095, backtracks = 1, tol = 0.000236045513254772 Iteration 168: loglikelihood = -1438.5376972405788, backtracks = 3, tol = 0.0002611290536787896 Iteration 169: loglikelihood = -1459.82414089413, backtracks = 3, tol = 0.1511801774044756 Iteration 170: loglikelihood = -1441.3871033854875, backtracks = 0, tol = 0.1417033977645 Iteration 171: loglikelihood = -1440.1057734532199, backtracks = 0, tol = 0.09037352529760727 Iteration 172: loglikelihood = -1439.0096257063294, backtracks = 0, tol = 0.07866095202101642 Iteration 173: loglikelihood = -1438.80136146111, backtracks = 0, tol = 0.009697458476783813 Iteration 174: loglikelihood = -1438.790941910853, backtracks = 0, tol = 0.0020325155186750113 Iteration 175: loglikelihood = -1438.790149384587, backtracks = 0, tol = 0.0007197065863946933 Iteration 176: loglikelihood = -1438.7899883992236, backtracks = 1, tol = 0.00021392592781111793 Iteration 177: loglikelihood = -1438.7898751097287, backtracks = 3, tol = 0.00025000356893781103 Iteration 178: loglikelihood = -1589.1634661003507, backtracks = 3, tol = 0.2556265293707785 Iteration 179: loglikelihood = -1452.552560665693, backtracks = 0, tol = 0.24405354021303613 Iteration 180: loglikelihood = -1441.3771371636599, backtracks = 0, tol = 0.10646440120950824 Iteration 181: loglikelihood = -1438.4531807393812, backtracks = 0, tol = 0.0819908574084704 Iteration 182: loglikelihood = -1438.357695238986, backtracks = 0, tol = 0.006302470145176044 Iteration 183: loglikelihood = -1438.3548722494077, backtracks = 0, tol = 0.0011097689972640644 Iteration 184: loglikelihood = -1438.3544388667954, backtracks = 0, tol = 0.0004441345169501309 Iteration 185: loglikelihood = -1438.3542757432801, backtracks = 1, tol = 0.00023528880456641837 Iteration 186: loglikelihood = -1451.2719605264715, backtracks = 3, tol = 0.1205150198482431 Iteration 187: loglikelihood = -1440.2308861032345, backtracks = 0, tol = 0.10992199368702625 Iteration 188: loglikelihood = -1439.9790406864265, backtracks = 0, tol = 0.013261658987995882 Iteration 189: loglikelihood = -1439.9646386929162, backtracks = 0, tol = 0.0028714448411979896 Iteration 190: loglikelihood = -1439.9635950551992, backtracks = 0, tol = 0.0008481420202499352 Iteration 191: loglikelihood = -1439.9634964407712, backtracks = 1, tol = 0.00015781645537964984 Iteration 192: loglikelihood = -1439.9634442803242, backtracks = 2, tol = 0.00014644992573932853 Iteration 193: loglikelihood = -1459.9292877332641, backtracks = 3, tol = 0.13510831112088198 Iteration 194: loglikelihood = -1440.7884301220222, backtracks = 0, tol = 0.12311290249210505 Iteration 195: loglikelihood = -1439.73401200827, backtracks = 0, tol = 0.018372651083735644 Iteration 196: loglikelihood = -1439.6594202975841, backtracks = 0, tol = 0.004668235276630553 Iteration 197: loglikelihood = -1439.6512495553804, backtracks = 0, tol = 0.00229496038073228 Iteration 198: loglikelihood = -1439.6501532830382, backtracks = 0, tol = 0.0006379491729720532 Iteration 199: loglikelihood = -1439.455070640733, backtracks = 0, tol = 0.06647010207300362 Did not converge after 200 iterations! IHT run time was 1.889503002166748 seconds Test Summary: | Pass Total Time fit NegativeBinomial 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 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 = -1895.6817530117432, backtracks = 0, tol = 0.7487457255335821 Iteration 2: loglikelihood = -1468.5921142063191, backtracks = 0, tol = 0.12673584810478897 Iteration 3: loglikelihood = -1385.048709677313, backtracks = 0, tol = 0.049200727128063414 Iteration 4: loglikelihood = -1381.4933634067318, backtracks = 0, tol = 0.027984086728747897 Iteration 5: loglikelihood = -1381.1288775321932, backtracks = 0, tol = 0.0032267542080228503 Iteration 6: loglikelihood = -1381.1228316901081, backtracks = 0, tol = 0.00036881777484580543 Iteration 7: loglikelihood = -1381.1227233735872, backtracks = 0, tol = 5.1487880608376086e-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 = -1621.7760455891369, backtracks = 0, tol = 0.43325890443617193 Iteration 2: loglikelihood = -1426.5215245153813, backtracks = 0, tol = 0.11902517277432047 Iteration 3: loglikelihood = -1390.88112368643, backtracks = 0, tol = 0.04186108429001714 Iteration 4: loglikelihood = -1383.1988871112108, backtracks = 0, tol = 0.031596342174109074 Iteration 5: loglikelihood = -1381.9339831297987, backtracks = 0, tol = 0.02899661429692843 Iteration 6: loglikelihood = -1381.768553227728, backtracks = 0, tol = 0.0021837955959562285 Iteration 7: loglikelihood = -1381.7675291796452, backtracks = 0, tol = 0.00018799886093269253 Iteration 8: loglikelihood = -1381.767516448331, backtracks = 0, tol = 2.4091892215040324e-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 11.9s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse 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 = -1350.5328538988588, backtracks = 0, tol = 0.19655646203292798 Iteration 2: loglikelihood = -1326.8114145242373, backtracks = 0, tol = 0.09766417642560901 Iteration 3: loglikelihood = -1315.6275705816824, backtracks = 0, tol = 0.12281344826154843 Iteration 4: loglikelihood = -1302.7927671831987, backtracks = 0, tol = 0.035616609202826714 Iteration 5: loglikelihood = -1289.4669013612895, backtracks = 1, tol = 0.07525534074187919 Iteration 6: loglikelihood = -1282.5751491505864, backtracks = 0, tol = 0.07532396218740547 Iteration 7: loglikelihood = -1281.4613227320885, backtracks = 0, tol = 0.02499414705107195 Iteration 8: loglikelihood = -1281.2019784200613, backtracks = 1, tol = 0.006397266862268846 Iteration 9: loglikelihood = -1281.099196301906, backtracks = 2, tol = 0.0032982562717557623 Iteration 10: loglikelihood = -1281.0324230257381, backtracks = 2, tol = 0.002770720701853799 Iteration 11: loglikelihood = -1280.994108777983, backtracks = 2, tol = 0.0022005069330303696 Iteration 12: loglikelihood = -1280.9723593916951, backtracks = 2, tol = 0.0016708215532854722 Iteration 13: loglikelihood = -1280.9600447805424, backtracks = 2, tol = 0.0012613426694823896 Iteration 14: loglikelihood = -1280.95308399353, backtracks = 2, tol = 0.0009502357805015958 Iteration 15: loglikelihood = -1280.9491540604947, backtracks = 2, tol = 0.0007149516088363981 Iteration 16: loglikelihood = -1280.9469371436717, backtracks = 2, tol = 0.0005374645388919969 Iteration 17: loglikelihood = -1280.9456873108406, backtracks = 2, tol = 0.00040379979664385054 Iteration 18: loglikelihood = -1280.9449830018114, backtracks = 2, tol = 0.00030325098027566763 Iteration 19: loglikelihood = -1280.9445862368154, backtracks = 2, tol = 0.00022767270621490537 Iteration 20: loglikelihood = -1280.944362777223, backtracks = 2, tol = 0.00017089447737912461 Iteration 21: loglikelihood = -1280.9442369464603, backtracks = 2, tol = 0.00012825658535666897 Iteration 22: loglikelihood = -1280.944166100261, backtracks = 2, tol = 9.624628300019553e-5 1.279937 seconds (5.45 M allocations: 96.496 MiB, 3.99% gc time, 50.39% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** 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 = -1413.445451967821, backtracks = 0, tol = 0.19655646203292798 Iteration 2: loglikelihood = -1389.7215639923602, backtracks = 0, tol = 0.13544629245117334 Iteration 3: loglikelihood = -1372.019132495297, backtracks = 0, tol = 0.10090723869117378 Iteration 4: loglikelihood = -1357.191491154092, backtracks = 0, tol = 0.06893763151764766 Iteration 5: loglikelihood = -1346.6681610666778, backtracks = 0, tol = 0.08611088176172507 Iteration 6: loglikelihood = -1335.1106815311828, backtracks = 0, tol = 0.08277448286790634 Iteration 7: loglikelihood = -1326.266412520209, backtracks = 1, tol = 0.009321937073574886 Iteration 8: loglikelihood = -1320.2073712005736, backtracks = 1, tol = 0.005439745261880203 Iteration 9: loglikelihood = -1316.6195943777814, backtracks = 1, tol = 0.0039757217488584845 Iteration 10: loglikelihood = -1314.3351400168951, backtracks = 1, tol = 0.002358185415017401 Iteration 11: loglikelihood = -1312.7272330697626, backtracks = 1, tol = 0.0012189186520850353 Iteration 12: loglikelihood = -1311.3545213953455, backtracks = 1, tol = 0.0005802874419540479 Iteration 13: loglikelihood = -1309.6022911349066, backtracks = 1, tol = 0.00025064529148187116 Iteration 14: loglikelihood = -1309.1242423267524, backtracks = 0, tol = 0.08152420530165164 Iteration 15: loglikelihood = -1305.874788290834, backtracks = 0, tol = 0.07583634084232979 Iteration 16: loglikelihood = -1304.4268183218323, backtracks = 0, tol = 0.007875125024219406 Iteration 17: loglikelihood = -1303.1561180446618, backtracks = 0, tol = 0.0019534089179020753 Iteration 18: loglikelihood = -1301.9202247822334, backtracks = 0, tol = 0.07423978742053193 Iteration 19: loglikelihood = -1300.8774168091213, backtracks = 0, tol = 0.003713764451535184 Iteration 20: loglikelihood = -1299.9325348338389, backtracks = 0, tol = 0.000809763131225246 Iteration 21: loglikelihood = -1298.4612505479047, backtracks = 1, tol = 0.00012273022163246605 Iteration 22: loglikelihood = -1297.7150953537293, backtracks = 0, tol = 0.00017700136920920066 Iteration 23: loglikelihood = -1296.5513763850884, backtracks = 1, tol = 3.2944248741792444e-5 0.264575 seconds (962.02 k allocations: 18.109 MiB, 5.66% gc time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse NegativeBinomial regression Number of threads = 1 Link functin = LogLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -3712.9985, backtracks = 0, tol = 0.0884837004056088 Iteration 2: loglikelihood = -3669.8262, backtracks = 0, tol = 0.042376821403982634 Iteration 3: loglikelihood = -3665.1506, backtracks = 1, tol = 0.01141573440127078 Iteration 4: loglikelihood = -3663.7952, backtracks = 1, tol = 0.0075379227925213435 Iteration 5: loglikelihood = -3663.4336, backtracks = 1, tol = 0.0038583913365421232 Iteration 6: loglikelihood = -3649.9067, backtracks = 1, tol = 0.06025971605202465 Iteration 7: loglikelihood = -3631.755, backtracks = 0, tol = 0.07360390346264022 Iteration 8: loglikelihood = -3621.238, backtracks = 0, tol = 0.079828129543511 Iteration 9: loglikelihood = -3619.5198, backtracks = 0, tol = 0.00836644781298298 Iteration 10: loglikelihood = -3619.312, backtracks = 0, tol = 0.004601940634399198 Iteration 11: loglikelihood = -3619.274, backtracks = 0, tol = 0.0011145622554858071 Iteration 12: loglikelihood = -3619.2688, backtracks = 0, tol = 0.000959980673118487 Iteration 13: loglikelihood = -3619.268, backtracks = 0, tol = 0.0002135324749831627 Iteration 14: loglikelihood = -3619.2666, backtracks = 1, tol = 0.00010024296906487447 Iteration 15: loglikelihood = -3619.2693, backtracks = 3, tol = 1.9838250639587995e-5 23.905677 seconds (15.38 M allocations: 673.782 MiB, 4.49% gc time, 97.50% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** 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 = -3598.7883, backtracks = 0, tol = 0.0884837004056088 Iteration 2: loglikelihood = -3478.0327, backtracks = 0, tol = 0.04357461525452655 Iteration 3: loglikelihood = -3267.5938, backtracks = 1, tol = 0.011096246881160149 Iteration 4: loglikelihood = -3035.1758, backtracks = 1, tol = 0.006816611754920409 Iteration 5: loglikelihood = -2970.0955, backtracks = 0, tol = 0.09246755104297756 Iteration 6: loglikelihood = -2789.7053, backtracks = 0, tol = 0.09306511532648759 Iteration 7: loglikelihood = -2650.8262, backtracks = 0, tol = 0.09003951385381426 Iteration 8: loglikelihood = -2539.5312, backtracks = 0, tol = 0.08318249214553167 Iteration 9: loglikelihood = -2436.8357, backtracks = 0, tol = 0.08845478335631474 Iteration 10: loglikelihood = -2366.896, backtracks = 0, tol = 0.08933520877676224 Iteration 11: loglikelihood = -2321.8816, backtracks = 0, tol = 0.10250667614015793 Iteration 12: loglikelihood = -2271.4094, backtracks = 0, tol = 0.10378172511882001 Iteration 13: loglikelihood = -2246.067, backtracks = 0, tol = 0.10741013095136234 Iteration 14: loglikelihood = -2225.0815, backtracks = 0, tol = 0.1076120872241131 Iteration 15: loglikelihood = -2214.363, backtracks = 0, tol = 0.10732536680846083 Iteration 16: loglikelihood = -2202.978, backtracks = 1, tol = 0.02194995041341831 Iteration 17: loglikelihood = -2200.4714, backtracks = 1, tol = 0.009542686983335229 Iteration 18: loglikelihood = -2199.9583, backtracks = 1, tol = 0.004195046076437805 Iteration 19: loglikelihood = -2199.8738, backtracks = 1, tol = 0.0018381390079287327 Iteration 20: loglikelihood = -2199.8728, backtracks = 2, tol = 0.000395880460805355 Iteration 21: loglikelihood = -2199.871, backtracks = 3, tol = 0.00014037763133964413 Iteration 22: loglikelihood = -2199.8706, backtracks = 3, tol = 0.00011986765491919794 Iteration 23: loglikelihood = -2199.8691, backtracks = 3, tol = 0.00010232375885393401 Iteration 24: loglikelihood = -2199.8704, backtracks = 3, tol = 8.72813113638301e-5 0.189316 seconds (1.63 M allocations: 27.008 MiB) Test Summary: | Pass Total Time Negative binomial nuisance parameter Float32 matrix | 12 12 28.3s **** 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 = -2896.6116813943763, backtracks = 0, tol = 1.0257704354307222 Iteration 2: loglikelihood = -1753.4720992614753, backtracks = 0, tol = 0.28706825512903816 Iteration 3: loglikelihood = -1460.3823326395225, backtracks = 0, tol = 0.1059822007319242 Iteration 4: loglikelihood = -1438.5292259047123, backtracks = 0, tol = 0.028655431669451118 Iteration 5: loglikelihood = -1438.0856032112097, backtracks = 0, tol = 0.0034955373515602557 Iteration 6: loglikelihood = -1438.0744350329464, backtracks = 0, tol = 0.0005882060650840543 Iteration 7: loglikelihood = -1438.0741395461057, backtracks = 0, tol = 8.427264473927088e-5 5.281362 seconds (1.18 M allocations: 138.741 MiB, 1.39% gc time, 92.56% compilation time) Test Summary: | Pass Total Time initialze beta | 1 1 5.7s 9.616756 seconds (4.00 M allocations: 82.521 MiB, 0.46% gc time, 0.67% compilation time) 5.226553 seconds (3.98 M allocations: 91.706 MiB, 0.19% gc time) 10.930746 seconds (20.41 M allocations: 439.524 MiB, 0.92% gc time, 19.92% compilation time: 80% of which was recompilation) 8.199637 seconds (20.18 M allocations: 434.188 MiB, 1.18% gc time) 41.521945 seconds (3.77 M allocations: 4.240 GiB, 10.46% gc time, 31.02% compilation time) 50.893911 seconds (71.97 k allocations: 183.458 MiB, 0.27% gc time) Test Summary: | Pass Total Time memory_efficient keyword | 7 7 2m26.9s Test Summary: | Pass Total Time update_support! | 10 10 0.7s 14.798 ms (78 allocations: 4.56 KiB) 5.002 μs (0 allocations: 0 bytes) 166.948 μs (4 allocations: 288 bytes) 6.624 μs (0 allocations: 0 bytes) 52.850 μs (2 allocations: 64 bytes) 37.580 μs (0 allocations: 0 bytes) 22.390 μs (0 allocations: 0 bytes) 28.689 μs (0 allocations: 0 bytes) 85.959 μs (0 allocations: 0 bytes) 33.683 ms (78 allocations: 4.56 KiB) 26.869 μs (0 allocations: 0 bytes) 179.239 μs (4 allocations: 288 bytes) 34.980 μs (0 allocations: 0 bytes) 224.678 μs (2 allocations: 64 bytes) 77.589 μs (0 allocations: 0 bytes) 127.779 μs (0 allocations: 0 bytes) 152.959 μs (0 allocations: 0 bytes) 184.538 μs (0 allocations: 0 bytes) Test Summary: | Total Time benchmarks for multivariate function | 0 3m33.1s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse Multivariate Gaussian regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 12 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -2900.9186300194497, 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 0.463620 seconds (49.19 k allocations: 5.483 MiB, 64.79% compilation time) Test Summary: | Pass Total Time multivariate fit_iht SnpLinAlg | 7 7 11.4s **** 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 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 2.192947 seconds (312.40 k allocations: 169.941 MiB, 64.57% compilation time) Test Summary: | Pass Total Time initialze beta | 5 5 2.7s **** 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: 0:03:56 Cross validating... 13%|████▏ | ETA: 0:00:57 Cross validating... 16%|█████▏ | ETA: 0:00:45 Cross validating... 19%|██████▏ | ETA: 0:00:36 Cross validating... 22%|███████▏ | ETA: 0:00:31 Cross validating... 25%|████████▏ | ETA: 0:00:26 Cross validating... 29%|█████████▏ | ETA: 0:00:23 Cross validating... 32%|██████████▏ | ETA: 0:00:20 Cross validating... 35%|███████████▏ | ETA: 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89%|████████████████████████████▌ | ETA: 0:00:02 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:01 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:01 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:12 Crossvalidation Results: k MSE 0 3158.2635924441456 1 3062.1866208107026 2 2725.0386829927947 3 2300.940707954077 4 1606.9935623594297 5 423.66887740751156 6 399.7449457482302 7 375.01315616829163 8 339.155736828813 9 349.7847017637204 10 345.29025919035604 11 352.6692864580783 12 353.9460593585227 13 350.68979788479004 14 350.1670581797054 15 365.60367825464124 16 376.30159908153087 17 514.7951033824525 18 527.7273640631115 19 358.84889144376604 20 398.1744901931125 Best k = 8 12.786131 seconds (12.27 M allocations: 319.787 MiB, 1.26% gc time, 61.99% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:04 Cross validating... 6%|██ | ETA: 0:00:04 Cross validating... 10%|███ | ETA: 0:00:04 Cross validating... 13%|████▏ | ETA: 0:00:04 Cross validating... 16%|█████▏ | ETA: 0:00:04 Cross validating... 19%|██████▏ | ETA: 0:00:04 Cross validating... 21%|██████▋ | ETA: 0:00:04 Cross validating... 24%|███████▋ | ETA: 0:00:04 Cross validating... 27%|████████▋ | ETA: 0:00:04 Cross validating... 30%|█████████▋ | ETA: 0:00:04 Cross validating... 33%|██████████▋ | ETA: 0:00:03 Cross validating... 38%|████████████▎ | ETA: 0:00:03 Cross validating... 41%|█████████████▎ | ETA: 0:00:03 Cross validating... 44%|██████████████▎ | ETA: 0:00:03 Cross validating... 46%|██████████████▊ | ETA: 0:00:03 Cross validating... 49%|███████████████▊ | ETA: 0:00:03 Cross validating... 52%|████████████████▊ | ETA: 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Crossvalidation Results: k MSE 0 3158.2635924441456 1 3114.3315654088387 2 2778.0398569411313 3 2355.6389188560556 4 1666.3305000637763 5 430.5478094761613 6 413.2137326278057 7 393.1466647016724 8 365.3979103663717 9 372.55840089944616 10 396.73697588023094 11 422.4684632726862 12 433.2392457450274 13 512.1904992152708 14 515.9994881512577 15 528.0496547937541 16 555.8282143683734 17 541.3018842364254 18 557.9263855792943 19 572.0575652575658 20 573.5279409849005 Best k = 8 5.166155 seconds (11.97 M allocations: 253.905 MiB, 0.92% gc time, 0.99% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, normal model | 3 3 18.8s **** 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: 0:07:13 Cross validating... 8%|██▌ | ETA: 0:02:47 Cross validating... 13%|████▏ | ETA: 0:01:40 Cross validating... 17%|█████▋ | ETA: 0:01:09 Cross validating... 22%|███████▏ | ETA: 0:00:52 Cross validating... 25%|████████▏ | ETA: 0:00:44 Cross validating... 29%|█████████▏ | ETA: 0:00:38 Cross validating... 32%|██████████▏ | ETA: 0:00:33 Cross validating... 35%|███████████▏ | ETA: 0:00:29 Cross validating... 40%|████████████▊ | ETA: 0:00:23 Cross validating... 44%|██████████████▎ | ETA: 0:00:19 Cross validating... 49%|███████████████▊ | ETA: 0:00:16 Cross validating... 54%|█████████████████▎ | ETA: 0:00:14 Cross validating... 59%|██████████████████▊ | ETA: 0:00:11 Cross validating... 62%|███████████████████▊ | ETA: 0:00:10 Cross validating... 65%|████████████████████▉ | ETA: 0:00:09 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:07 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:06 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:04 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:03 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:02 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:02 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:01 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:01 Cross validating... 100%|████████████████████████████████| Time: 0:00:17 Crossvalidation Results: k MSE 0 1715.2939133300779 1 1363.4845240478517 2 1130.7440638427734 3 851.0205718994141 4 727.765517578125 5 574.1274478149414 6 469.45411145019534 7 400.85074136352534 8 362.95117321777343 9 345.7822051696777 10 348.20294714355464 11 353.0211907348633 12 352.9628870544434 13 357.6599117126465 14 360.3943276672363 15 358.78429934692383 16 361.74861184692384 17 362.130903503418 18 370.33030340576175 19 395.13050936889647 20 365.2190402832031 Best k = 9 18.620362 seconds (12.17 M allocations: 303.422 MiB, 0.41% gc time, 82.55% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 5%|█▌ | ETA: 0:00:02 Cross validating... 8%|██▌ | ETA: 0:00:03 Cross validating... 13%|████▏ | ETA: 0:00:02 Cross validating... 17%|█████▋ | ETA: 0:00:02 Cross validating... 21%|██████▋ | ETA: 0:00:02 Cross validating... 24%|███████▋ | ETA: 0:00:02 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... 43%|█████████████▊ | ETA: 0:00:02 Cross validating... 48%|███████████████▎ | ETA: 0:00:02 Cross validating... 52%|████████████████▊ | ETA: 0:00:01 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... 75%|███████████████████████▉ | ETA: 0:00:01 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:01 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:00 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 1715.2939133300779 1 1363.5657520751954 2 1130.7440638427734 3 852.8955785522461 4 733.8164234619142 5 575.0331779174804 6 475.12959210205076 7 403.80291680908203 8 367.62459649658206 9 351.1398486633301 10 357.50898739624023 11 370.7891187744141 12 375.33748034667974 13 385.273145690918 14 391.1782518615722 15 393.39548526000976 16 404.6133218078613 17 411.9068720703125 18 413.05191024780277 19 425.6442936706543 20 414.58342492675786 Best k = 9 3.346326 seconds (10.56 M allocations: 194.095 MiB, 1.69% gc time, 1.34% compilation time) Test Summary: | Pass Total Time Cross validation on Float32 matrix, normal model | 2 2 23.9s **** 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: 0:01:00 Cross validating... 6%|██ | ETA: 0:00:31 Cross validating... 10%|███ | ETA: 0:00:22 Cross validating... 11%|███▌ | ETA: 0:00:19 Cross validating... 14%|████▋ | ETA: 0:00:15 Cross validating... 17%|█████▋ | ETA: 0:00:13 Cross validating... 21%|██████▋ | ETA: 0:00:11 Cross validating... 22%|███████▏ | ETA: 0:00:11 Cross validating... 25%|████████▏ | ETA: 0:00:10 Cross validating... 29%|█████████▏ | ETA: 0:00:09 Cross validating... 32%|██████████▏ | ETA: 0:00:08 Cross validating... 35%|███████████▏ | ETA: 0:00:07 Cross validating... 38%|████████████▎ | ETA: 0:00:06 Cross validating... 41%|█████████████▎ | ETA: 0:00:06 Cross validating... 44%|██████████████▎ | ETA: 0:00:05 Cross validating... 48%|███████████████▎ | ETA: 0:00:05 Cross validating... 51%|████████████████▎ | ETA: 0:00:04 Cross validating... 54%|█████████████████▎ | ETA: 0:00:04 Cross validating... 57%|██████████████████▎ | ETA: 0:00:04 Cross validating... 60%|███████████████████▎ | ETA: 0:00:03 Cross validating... 63%|████████████████████▍ | ETA: 0:00:03 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:03 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:02 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:02 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:02 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:02 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:01 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:01 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:01 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:01 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:07 Crossvalidation Results: k MSE 0 462.3188072686215 1 404.5627035047179 2 357.7587820808105 3 346.16056946470337 4 315.3815358995026 5 307.2652201347404 6 310.0178765337029 7 313.8462074528313 8 315.15002575990786 9 315.4371978652666 10 325.21096884688035 11 313.03419530437077 12 318.2522900566134 13 322.3708455885663 14 323.8550886791465 15 313.5573994575592 16 321.46897185256285 17 350.89545202003757 18 341.01009195490195 19 330.32045850824625 20 331.655481118419 Best k = 5 8.093959 seconds (17.19 M allocations: 405.740 MiB, 0.96% gc time, 33.33% 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... 5%|█▌ | ETA: 0:00:03 Cross validating... 8%|██▌ | ETA: 0:00:03 Cross validating... 11%|███▌ | ETA: 0:00:03 Cross validating... 14%|████▋ | ETA: 0:00:04 Cross validating... 17%|█████▋ | ETA: 0:00:03 Cross validating... 21%|██████▋ | ETA: 0:00:04 Cross validating... 24%|███████▋ | ETA: 0:00:04 Cross validating... 27%|████████▋ | ETA: 0:00:04 Cross validating... 30%|█████████▋ | ETA: 0:00:03 Cross validating... 33%|██████████▋ | ETA: 0:00:03 Cross validating... 38%|████████████▎ | ETA: 0:00:03 Cross validating... 41%|█████████████▎ | ETA: 0:00:03 Cross validating... 44%|██████████████▎ | ETA: 0:00:03 Cross validating... 46%|██████████████▊ | ETA: 0:00:03 Cross validating... 49%|███████████████▊ | ETA: 0:00:03 Cross validating... 52%|████████████████▊ | ETA: 0:00:02 Cross validating... 56%|█████████████████▊ | ETA: 0:00:02 Cross validating... 59%|██████████████████▊ | ETA: 0:00:02 Cross validating... 62%|███████████████████▊ | ETA: 0:00:02 Cross validating... 65%|████████████████████▉ | ETA: 0:00:02 Cross validating... 68%|█████████████████████▉ | ETA: 0:00:02 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:01 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:01 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:01 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:01 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:01 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:01 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:01 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 0 462.3188072686215 1 404.73177675592933 2 359.7148913210192 3 350.69366859822304 4 320.129444432241 5 311.74864477695206 6 316.5958173314324 7 329.10086436506214 8 334.2361257540106 9 335.22770024502813 10 349.52808938912233 11 350.0641294430823 12 349.57668951613476 13 359.52654607248627 14 363.0461637748265 15 363.3055802639859 16 367.63357152767026 17 377.43676060734674 18 394.93410176819145 19 397.0257976672175 20 408.01793537790354 Best k = 5 5.425609 seconds (17.52 M allocations: 364.530 MiB, 1.72% gc time, 0.95% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, logistic model | 2 2 13.9s **** 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: 0:00:50 Cross validating... 6%|██ | ETA: 0:00:26 Cross validating... 11%|███▌ | ETA: 0:00:15 Cross validating... 14%|████▋ | ETA: 0:00:13 Cross validating... 17%|█████▋ | ETA: 0:00:11 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... 35%|███████████▏ | ETA: 0:00:06 Cross validating... 38%|████████████▎ | ETA: 0:00:05 Cross validating... 41%|█████████████▎ | ETA: 0:00:05 Cross validating... 46%|██████████████▊ | ETA: 0:00:04 Cross validating... 49%|███████████████▊ | ETA: 0:00:04 Cross validating... 52%|████████████████▊ | ETA: 0:00:04 Cross validating... 56%|█████████████████▊ | ETA: 0:00:04 Cross validating... 59%|██████████████████▊ | ETA: 0:00:03 Cross validating... 62%|███████████████████▊ | ETA: 0:00:03 Cross validating... 65%|████████████████████▉ | ETA: 0:00:03 Cross validating... 68%|█████████████████████▉ | ETA: 0:00:02 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:02 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:02 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:01 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:01 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:01 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:01 Cross validating... 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 0 464.37857734343254 1 425.5644776097341 2 410.9181257969367 3 387.9177918899146 4 356.1849017695748 5 343.5436287705212 6 329.70675929129067 7 328.42324773820826 8 328.0702314253392 9 328.0294038395623 10 332.2706075112627 11 339.2617071417102 12 350.94939593303246 13 338.1034591893925 14 353.05904662429197 15 342.6461544888788 16 360.08634570593574 17 363.1574339566197 18 372.5365331533103 19 366.6304050315728 20 393.56888237217464 Best k = 9 7.944316 seconds (16.46 M allocations: 388.313 MiB, 12.58% gc time, 34.84% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:04 Cross validating... 6%|██ | ETA: 0:00:04 Cross validating... 10%|███ | ETA: 0:00:04 Cross validating... 13%|████▏ | ETA: 0:00:04 Cross validating... 16%|█████▏ | ETA: 0:00:03 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: 0:00:03 Cross validating... 44%|██████████████▎ | ETA: 0:00:02 Cross validating... 48%|███████████████▎ | ETA: 0:00:02 Cross validating... 51%|████████████████▎ | ETA: 0:00:02 Cross validating... 54%|█████████████████▎ | ETA: 0:00:02 Cross validating... 57%|██████████████████▎ | ETA: 0:00:02 Cross validating... 60%|███████████████████▎ | ETA: 0:00:02 Cross validating... 63%|████████████████████▍ | ETA: 0:00:02 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:01 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:01 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:01 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:01 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:01 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:01 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:01 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:00 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:04 Crossvalidation Results: k MSE 0 464.37857734343254 1 425.658024301983 2 411.74803469207353 3 389.00282766617875 4 357.9616508198595 5 344.18053438872516 6 332.2919099404417 7 333.42990274421726 8 336.6502717763079 9 348.9428223837675 10 351.6962579333618 11 346.8037528112772 12 379.5467740059532 13 373.6092304789415 14 377.57058172615905 15 397.37697180090527 16 395.4699468386914 17 407.3520437252837 18 423.60730264284143 19 420.08398771668334 20 436.6838854242808 Best k = 6 4.390878 seconds (16.97 M allocations: 347.986 MiB, 2.01% gc time, 1.02% compilation time) Test Summary: | Pass Total Time Cross validation on Float64 matrix, 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: 0:00:57 Cross validating... 6%|██ | ETA: 0:00:30 Cross validating... 10%|███ | ETA: 0:00:21 Cross validating... 13%|████▏ | ETA: 0:00:17 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 validating... 32%|██████████▏ | ETA: 0:00:07 Cross validating... 35%|███████████▏ | ETA: 0:00:07 Cross validating... 38%|████████████▎ | ETA: 0:00:06 Cross validating... 41%|█████████████▎ | ETA: 0:00:06 Cross validating... 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95%|██████████████████████████████▌ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:07 Crossvalidation Results: k MSE 0 880.9569738841421 1 649.8949800097168 2 534.6607057997899 3 498.32371920227774 4 422.35562947766135 5 408.5019658416977 6 411.6643128760919 7 407.2277233290464 8 415.0108390821971 9 406.3777289226973 10 414.3473712114783 11 413.84742359827146 12 412.74501534136476 13 413.09313759248994 14 411.9826299079673 15 411.7073866312099 16 411.9367929793819 17 413.82053940845117 18 430.91843025511014 19 425.1558405499894 20 417.5764678983013 Best k = 9 7.892295 seconds (14.78 M allocations: 344.279 MiB, 1.20% gc time, 32.31% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:04 Cross validating... 6%|██ | ETA: 0:00:04 Cross validating... 10%|███ | ETA: 0:00:05 Cross validating... 13%|████▏ | ETA: 0:00:04 Cross validating... 16%|█████▏ | ETA: 0:00:04 Cross validating... 19%|██████▏ | ETA: 0:00:04 Cross validating... 22%|███████▏ | ETA: 0:00:04 Cross validating... 25%|████████▏ | ETA: 0:00:04 Cross validating... 29%|█████████▏ | ETA: 0:00:04 Cross validating... 32%|██████████▏ | ETA: 0:00:04 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 0 880.9569738841421 1 640.6939135122507 2 526.6080837909149 3 481.0426993389672 4 415.35995136751103 5 395.08416006774587 6 399.3548126321979 7 400.71583594343645 8 411.84281321564106 9 418.0598269816879 10 412.0334995697967 11 418.4164990442085 12 417.94249736532174 13 423.09694714511676 14 417.58340060127597 15 426.22891664113376 16 422.6220989355294 17 442.0079660247148 18 445.2699991086988 19 450.73405270784957 20 453.291148194692 Best k = 5 5.401287 seconds (13.69 M allocations: 271.015 MiB, 0.94% gc time, 1.12% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, Poisson model | 2 2 13.7s **** 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: 0:01:04 Cross validating... 5%|█▌ | ETA: 0:00:44 Cross validating... 6%|██ | ETA: 0:00:47 Cross validating... 10%|███ | ETA: 0:00:32 Cross validating... 11%|███▌ | 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ETA: 0:00:22 Cross validating... 49%|███████████████▊ | ETA: 0:00:22 Cross validating... 51%|████████████████▎ | ETA: 0:00:22 Cross validating... 52%|████████████████▊ | ETA: 0:00:20 Cross validating... 54%|█████████████████▎ | ETA: 0:00:20 Cross validating... 56%|█████████████████▊ | ETA: 0:00:20 Cross validating... 57%|██████████████████▎ | ETA: 0:00:19 Cross validating... 59%|██████████████████▊ | ETA: 0:00:19 Cross validating... 60%|███████████████████▎ | ETA: 0:00:18 Cross validating... 62%|███████████████████▊ | ETA: 0:00:17 Cross validating... 63%|████████████████████▍ | ETA: 0:00:16 Cross validating... 65%|████████████████████▉ | ETA: 0:00:15 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:15 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:13 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:12 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:11 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:09 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:09 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:08 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: 0:00:05 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:04 Cross validating... 92%|█████████████████████████████▌ | 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: 0:00:41 Crossvalidation Results: k MSE 0 390.4729629888637 1 354.84751649178907 2 276.7253632699868 3 249.07020978616134 4 230.62423172080662 5 230.01527706734385 6 231.18994954661719 7 232.61188468838515 8 233.55507090510497 9 234.73633135375024 10 235.85437166355518 11 234.3226576051867 12 235.95686284983387 13 233.4149073457885 14 234.5628480094387 15 235.84712752542026 16 236.0089927727583 17 234.05911386016385 18 234.76500391280268 19 242.2128262290998 20 239.2507913714379 Best k = 5 41.656744 seconds (133.81 M allocations: 3.403 GiB, 1.21% gc time, 5.52% 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... 6%|██ | ETA: 0:00:05 Cross validating... 8%|██▌ | ETA: 0:00:05 Cross validating... 10%|███ | ETA: 0:00:13 Cross validating... 11%|███▌ | ETA: 0:00:17 Cross 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79%|█████████████████████████▍ | ETA: 0:00:08 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: 0:00:02 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: 0:00:35 Crossvalidation Results: k MSE 0 390.4729629888637 1 355.3600441627876 2 279.154706496747 3 250.78197209042094 4 232.30363212218407 5 233.1682700382397 6 236.29948436303297 7 238.71285518236363 8 241.63840544398528 9 246.43035097783553 10 248.64200055525396 11 250.9158229501887 12 258.17149579253385 13 259.26342047006267 14 257.5723234452135 15 267.85435732289096 16 261.9090654810622 17 264.415130492906 18 275.3002876896171 19 284.8367715605462 20 287.80002793460056 Best k = 4 35.193999 seconds (117.14 M allocations: 2.375 GiB, 1.05% gc time, 0.19% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, NegativeBinomial model | 2 2 1m17.3s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:01:04 Cross validating... 6%|██ | ETA: 0:00:33 Cross validating... 10%|███ | ETA: 0:00:23 Cross validating... 13%|████▏ | ETA: 0:00:17 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 validating... 32%|██████████▏ | ETA: 0:00:07 Cross validating... 35%|███████████▏ | ETA: 0:00:07 Cross validating... 38%|████████████▎ | ETA: 0:00:06 Cross validating... 41%|█████████████▎ | ETA: 0:00:05 Cross validating... 44%|██████████████▎ | ETA: 0:00:05 Cross validating... 48%|███████████████▎ | ETA: 0:00:05 Cross validating... 51%|████████████████▎ | ETA: 0:00:04 Cross validating... 54%|█████████████████▎ | ETA: 0:00:04 Cross validating... 57%|██████████████████▎ | ETA: 0:00:03 Cross validating... 60%|███████████████████▎ | ETA: 0:00:03 Cross validating... 63%|████████████████████▍ | ETA: 0:00:03 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:02 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:02 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:02 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:02 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:01 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:01 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:01 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:01 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:06 Crossvalidation Results: k MSE 0 709.7238911132813 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 7.092429 seconds (17.01 M allocations: 337.900 MiB, 1.68% gc time, 37.41% 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 **** Cross validating... 3%|█ | ETA: 0:00:03 Cross validating... 6%|██ | ETA: 0:00:04 Cross validating... 10%|███ | ETA: 0:00:04 Cross validating... 13%|████▏ | ETA: 0:00:04 Cross validating... 16%|█████▏ | ETA: 0:00:03 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... 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Cross validating... 90%|█████████████████████████████ | ETA: 0:00:00 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:04 Crossvalidation Results: k MSE 0 709.7238911132813 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 4.305450 seconds (16.18 M allocations: 286.715 MiB, 1.21% gc time, 1.35% compilation time) Test Summary: | Pass Total Time Cross validation on floating point matrices, NegativeBinomial model | 2 2 12.2s **** 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: 0:01:38 Cross validating... 3%|█ | ETA: 0:01:11 Cross validating... 4%|█▎ | ETA: 0:00:57 Cross validating... 5%|█▋ | ETA: 0:00:48 Cross validating... 6%|█▉ | ETA: 0:00:43 Cross validating... 7%|██▎ | ETA: 0:00:39 Cross validating... 8%|██▌ | ETA: 0:00:36 Cross validating... 9%|██▉ | ETA: 0:00:34 Cross validating... 10%|███▎ | ETA: 0:00:32 Cross validating... 11%|███▌ | ETA: 0:00:30 Cross validating... 12%|███▉ | ETA: 0:00:29 Cross validating... 13%|████▏ | ETA: 0:00:27 Cross validating... 14%|████▌ | ETA: 0:00:26 Cross validating... 15%|████▊ | ETA: 0:00:25 Cross validating... 16%|█████▏ | ETA: 0:00:25 Cross validating... 17%|█████▌ | ETA: 0:00:24 Cross validating... 18%|█████▊ | ETA: 0:00:23 Cross validating... 19%|██████▏ | ETA: 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2293.091374220803 8 2262.7883504567085 9 2273.5112427153776 10 2291.409450713177 11 2275.281309946654 12 2298.462308860815 13 2313.7169607068035 14 2323.5968222443626 15 2342.978805598088 16 2350.290556812409 17 2364.382309930254 18 2371.5044223862774 19 2372.486673633201 20 2388.3126310091475 Best k = 8 20.639706 seconds (357.84 k allocations: 260.430 MiB, 0.34% gc time, 9.21% compilation time) Test Summary: | Pass Total Time multivariate cross validation SnpLinAlg | 3 3 25.9s Test Summary: | Pass Total Time wrapper univariate | 20 20 1m48.7s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 2%|▋ | ETA: 0:00:11 Cross validating... 3%|█ | ETA: 0:00:11 Cross validating... 4%|█▎ | ETA: 0:00:11 Cross validating... 5%|█▋ | ETA: 0:00:11 Cross validating... 6%|█▉ | ETA: 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94%|██████████████████████████████▏ | ETA: 0:00:01 Cross validating... 95%|██████████████████████████████▍ | ETA: 0:00:01 Cross validating... 96%|██████████████████████████████▊ | ETA: 0:00:01 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:01 Cross validating... 98%|███████████████████████████████▍| ETA: 0:00:00 Cross validating... 99%|███████████████████████████████▋| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:24 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 **** 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%|██▉ | ETA: 0:00:14 Cross validating... 10%|███▎ | ETA: 0:00:14 Cross validating... 11%|███▌ | ETA: 0:00:15 Cross validating... 12%|███▉ | ETA: 0:00:16 Cross validating... 13%|████▏ | ETA: 0:00:16 Cross validating... 14%|████▌ | ETA: 0:00:16 Cross validating... 15%|████▊ | ETA: 0:00:17 Cross validating... 16%|█████▏ | ETA: 0:00:18 Cross validating... 17%|█████▌ | ETA: 0:00:19 Cross validating... 18%|█████▊ | ETA: 0:00:18 Cross validating... 19%|██████▏ | ETA: 0:00:19 Cross validating... 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2053.427506114907 8 2086.405384830965 9 2080.984460901671 10 2105.131199502364 11 2132.407165368786 12 2138.267187460652 13 2166.002210829576 14 2194.9918295115804 15 2189.890403738045 16 2191.181293229578 17 2209.4669750564362 18 2221.2595493644303 19 2238.7425945763257 20 2253.9559571797727 Best k = 7 **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 2%|▋ | ETA: 0:00:11 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%|██▉ | ETA: 0:00:14 Cross validating... 10%|███▎ | ETA: 0:00:14 Cross validating... 11%|███▌ | ETA: 0:00:15 Cross validating... 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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 1m27.2s 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] decompress @ ~/.julia/packages/BGEN/dfgRU/src/genotypes.jl:42 [inlined] [5] 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 [6] first_allele_dosage! @ ~/.julia/packages/BGEN/dfgRU/src/genotypes.jl:549 [inlined] [7] convert_bgen_gt(t::Type{Float64}, b::Bgen) @ MendelIHT ~/.julia/packages/MendelIHT/ZcxZT/src/wrapper.jl:380 [8] macro expansion @ ./timing.jl:739 [inlined] [9] macro expansion @ ~/.julia/packages/MendelIHT/ZcxZT/test/wrapper_test.jl:187 [inlined] [10] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:2243 [inlined] [11] top-level scope @ ~/.julia/packages/MendelIHT/ZcxZT/test/wrapper_test.jl:185 [12] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:324 [13] top-level scope @ ~/.julia/packages/MendelIHT/ZcxZT/test/runtests.jl:20 [14] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:324 [15] top-level scope @ none:6 [16] eval(m::Module, e::Any) @ Core ./boot.jl:517 [17] exec_options(opts::Base.JLOptions) @ Base ./client.jl:310 [18] _start() @ Base ./client.jl:585 Test Summary: | Error Total Time read BGEN and VCF | 1 1 3.4s RNG of the outermost testset: Xoshiro(0x8f57b2dfd22c6230, 0x77ab6ba3f489853c, 0x777d29ba61d2557f, 0x728cd82c585977b5, 0x6da5afa60356e352) 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 1180.54s 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:3138 [3] test @ /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Operations.jl:3003 [inlined] [4] 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:586 [5] kwcall(::@NamedTuple{julia_args::Cmd, io::IOContext{IO}}, ::typeof(Pkg.API.test), ctx::Pkg.Types.Context, pkgs::Vector{PackageSpec}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:562 [6] 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 [7] kwcall(::@NamedTuple{julia_args::Cmd}, ::typeof(Pkg.API.test), pkgs::Vector{PackageSpec}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:161 [8] test(pkgs::Vector{String}; kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:160 [9] test @ /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:160 [inlined] [10] kwcall(::@NamedTuple{julia_args::Cmd}, ::typeof(Pkg.API.test), pkg::String) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:159 [11] top-level scope @ /PkgEval.jl/scripts/evaluate.jl:223 [12] include(mod::Module, _path::String) @ Base ./Base.jl:323 [13] exec_options(opts::Base.JLOptions) @ Base ./client.jl:344 [14] _start() @ Base ./client.jl:585 in expression starting at /PkgEval.jl/scripts/evaluate.jl:214 PkgEval failed after 1285.73s: package tests unexpectedly errored