Package evaluation to test MendelIHT on Julia 1.14.0-DEV.2028 (45a2de3f7a*) started at 2026-04-13T02:10:38.239 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.14` Set-up completed after 14.67s ################################################################################ # Installation # Installing MendelIHT... Resolving package versions... Updating `~/.julia/environments/v1.14/Project.toml` [921c7187] + MendelIHT v1.4.11 Updating `~/.julia/environments/v1.14/Manifest.toml` [7d9f7c33] + Accessors v0.1.44 [79e6a3ab] + Adapt v4.5.2 [66dad0bd] + AliasTables v1.1.3 [4fba245c] + ArrayInterface v7.23.0 [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 v1.68.1+0 [3f19e933] + p7zip_jll v17.8.0+0 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. To see why use `status --outdated -m` Installation completed after 6.23s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompiling project... 4981.7 ms ✓ BGEN 6743.9 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`. 25579.4 ms ✓ MendelIHT 3 dependencies successfully precompiled in 40 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 67.09s ################################################################################ # Testing # Testing MendelIHT Status `/tmp/jl_oT9PD8/Project.toml` ⌅ [6db4b851] BGEN v0.1.17 [6e4b80f9] BenchmarkTools v1.7.0 [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 v2.7.2 [2913bbd2] StatsBase v0.34.10 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v1.68.1+0 [3f19e933] p7zip_jll v17.8.0+0 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. Testing Running tests... ┌ Warning: `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 0.4s Test Summary: | Pass Total Time update_μ! | 4 4 1.5s Test Summary: | Pass Total Time _choose! | 7 7 9.4s Test Summary: | Pass Total Time _iht_backtrack | 7 7 0.0s Test Summary: | Pass Total Time standardize! | 12 12 1.8s Test Summary: | Pass Total Time project_k! | 2 2 0.9s Test Summary: | Pass Total Time project_group_sparse! | 5 5 1.3s Test Summary: | Pass Total Time maf_weights | 6 6 2.0s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse linear regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1614.382229364343, backtracks = 0, tol = 2.1307334211626907 Iteration 2: loglikelihood = -1441.4814467694862, backtracks = 0, tol = 0.12726397628015443 Iteration 3: loglikelihood = -1423.30269215381, backtracks = 0, tol = 0.06348794159137267 Iteration 4: loglikelihood = -1423.085239745613, backtracks = 0, tol = 0.034660416818623405 Iteration 5: loglikelihood = -1422.970895194958, backtracks = 0, tol = 0.0030266932935378056 Iteration 6: loglikelihood = -1421.678500813841, backtracks = 0, tol = 0.03605325429099969 Iteration 7: loglikelihood = -1421.5966181089123, backtracks = 0, tol = 0.002258638044541858 Iteration 8: loglikelihood = -1421.5955125013504, backtracks = 1, tol = 0.0001744420173221144 Iteration 9: loglikelihood = -1421.5952148180709, backtracks = 1, tol = 9.28108842545522e-5 IHT estimated 10 nonzero SNP predictors and 1 non-genetic predictors. Compute time (sec): 0.07212305068969727 Final loglikelihood: -1421.5952148180709 SNP PVE: 0.916404975433477 Iterations: 9 Selected genetic predictors: 10×2 DataFrame Row │ Position Estimated_β │ Int64 Float64 ─────┼─────────────────────── 1 │ 359 -0.493828 2 │ 919 -0.743548 3 │ 1584 -0.127745 4 │ 2341 0.605118 5 │ 2580 -1.67038 6 │ 2866 -0.650298 7 │ 3042 0.219727 8 │ 3831 0.679288 9 │ 6409 -2.36394 10 │ 6801 -0.12306 Selected nongenetic predictors: 1×2 DataFrame Row │ Position Estimated_β │ Int64 Float64 ─────┼─────────────────────── 1 │ 1 -0.042489Test Summary: | Pass Total Time fit normal SnpLinAlg | 4 4 22.9s **** 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 logistic regression Number of threads = 1 Link functin = LogitLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -379.72375963518977, backtracks = 0, tol = 0.6062552017348442 Iteration 2: loglikelihood = -294.14222098196217, backtracks = 0, tol = 0.39035964909167 Iteration 3: loglikelihood = -258.44215825745147, backtracks = 0, tol = 0.18072720194601524 Iteration 4: loglikelihood = -248.39092317275637, backtracks = 1, tol = 0.0581811999889429 Iteration 5: loglikelihood = -241.2861695402178, backtracks = 2, tol = 0.10199490430383734 Iteration 6: loglikelihood = -236.0344401262056, backtracks = 2, tol = 0.10444957184614982 Iteration 7: loglikelihood = -232.75639772007577, backtracks = 2, tol = 0.03618239958756675 Iteration 8: loglikelihood = -230.9028935826695, backtracks = 3, tol = 0.022566251649321353 Iteration 9: loglikelihood = -229.2332883500926, backtracks = 3, tol = 0.02394599965909332 Iteration 10: loglikelihood = -227.8109863155336, backtracks = 3, tol = 0.02260237147851236 Iteration 11: loglikelihood = -226.61429831284372, backtracks = 3, tol = 0.02153016573221634 Iteration 12: loglikelihood = -225.614543213995, backtracks = 3, tol = 0.020073248773013197 Iteration 13: loglikelihood = -225.15228734295533, backtracks = 3, tol = 0.10266272165892033 Iteration 14: loglikelihood = -224.5524858306654, backtracks = 2, tol = 0.010910053499902256 Iteration 15: loglikelihood = -223.90430308527087, backtracks = 3, tol = 0.10669566586572145 Iteration 16: loglikelihood = -223.43342440058004, backtracks = 1, tol = 0.009912340440473734 Iteration 17: loglikelihood = -223.19474883510568, backtracks = 3, tol = 0.10429355504005154 Iteration 18: loglikelihood = -222.7530868660152, backtracks = 1, tol = 0.010133510239484585 Iteration 19: loglikelihood = -222.4546375562022, backtracks = 3, tol = 0.009382230171462355 Iteration 20: loglikelihood = -225.04961416047087, backtracks = 3, tol = 0.13141028198780508 Iteration 21: loglikelihood = -221.57583298738808, backtracks = 0, tol = 0.12983606150115481 Iteration 22: loglikelihood = -220.9953587123894, backtracks = 0, tol = 0.018278220962270587 Iteration 23: loglikelihood = -220.46528702030645, backtracks = 0, tol = 0.10912949798131547 Iteration 24: loglikelihood = -220.22939682199817, backtracks = 1, tol = 0.006133557493960293 Iteration 25: loglikelihood = -220.1149031779291, backtracks = 3, tol = 0.005637364497494655 Iteration 26: loglikelihood = -237.91408320706802, backtracks = 3, tol = 0.1311916630585333 Iteration 27: loglikelihood = -222.6667401701631, backtracks = 0, tol = 0.13008576394077564 Iteration 28: loglikelihood = -220.0179912284672, backtracks = 0, tol = 0.10981267805412102 Iteration 29: loglikelihood = -219.80873468505163, backtracks = 1, tol = 0.006242686572879014 Iteration 30: loglikelihood = -219.71412932030552, backtracks = 1, tol = 0.0052581541847830735 Iteration 31: loglikelihood = -219.67346582214395, backtracks = 3, tol = 0.002736072071808146 Iteration 32: loglikelihood = -236.63118723570068, backtracks = 3, tol = 0.12536959025201838 Iteration 33: loglikelihood = -222.42522446507616, backtracks = 0, tol = 0.12480632457239557 Iteration 34: loglikelihood = -219.76952387571325, backtracks = 0, tol = 0.10782393864869841 Iteration 35: loglikelihood = -219.54239052596037, backtracks = 0, tol = 0.010969385336776636 Iteration 36: loglikelihood = -219.51051719556185, backtracks = 0, tol = 0.0038143069815270263 Iteration 37: loglikelihood = -219.49562270628724, backtracks = 1, tol = 0.0015360028505860806 Iteration 38: loglikelihood = -222.2776344615594, backtracks = 3, tol = 0.10706948875570901 Iteration 39: loglikelihood = -219.86344247649652, backtracks = 0, tol = 0.10682440099239575 Iteration 40: loglikelihood = -219.50637292175287, backtracks = 0, tol = 0.010145149683589566 Iteration 41: loglikelihood = -219.45601478260392, backtracks = 0, tol = 0.004786594360325445 Iteration 42: loglikelihood = -219.44279315931445, backtracks = 0, tol = 0.0023300326568676676 Iteration 43: loglikelihood = -219.434262597912, backtracks = 0, tol = 0.002159682320412748 Iteration 44: loglikelihood = -219.42706752504972, backtracks = 0, tol = 0.0019986878272562235 Iteration 45: loglikelihood = -219.4208881668612, backtracks = 0, tol = 0.001781315196828412 Iteration 46: loglikelihood = -219.41556755717227, backtracks = 0, tol = 0.0017266268818688624 Iteration 47: loglikelihood = -219.41098445944962, backtracks = 0, tol = 0.001504993867218278 Iteration 48: loglikelihood = -219.4070309112888, backtracks = 0, tol = 0.001495426527055874 Iteration 49: loglikelihood = -219.40362030781677, backtracks = 0, tol = 0.001286324051089446 Iteration 50: loglikelihood = -219.4006747755802, backtracks = 0, tol = 0.001295957349435961 Iteration 51: loglikelihood = -219.39813103252988, backtracks = 0, tol = 0.0011058748112207813 Iteration 52: loglikelihood = -219.3959322024177, backtracks = 0, tol = 0.0011233728145861855 Iteration 53: loglikelihood = -219.39403166729804, backtracks = 0, tol = 0.0009536994758608786 Iteration 54: loglikelihood = -219.39238763268273, backtracks = 0, tol = 0.0009739180646352119 Iteration 55: loglikelihood = -219.39096560226784, backtracks = 0, tol = 0.0008239389039648708 Iteration 56: loglikelihood = -219.38973473800374, backtracks = 0, tol = 0.0008444580901064712 Iteration 57: loglikelihood = -219.3886694316569, backtracks = 0, tol = 0.0007126409505425607 Iteration 58: loglikelihood = -219.38774685610232, backtracks = 0, tol = 0.0007323063866727435 Iteration 59: loglikelihood = -219.3869479529937, backtracks = 0, tol = 0.00061686194275372 Iteration 60: loglikelihood = -219.3862557798823, backtracks = 0, tol = 0.0006351404346176769 Iteration 61: loglikelihood = -219.3856561234815, backtracks = 0, tol = 0.000534269842115572 Iteration 62: loglikelihood = -219.38513638040487, backtracks = 0, tol = 0.0005509480422217535 Iteration 63: loglikelihood = -219.38468593224545, backtracks = 0, tol = 0.0004629512780606966 Iteration 64: loglikelihood = -219.38429538513583, backtracks = 0, tol = 0.0004779860767529819 Iteration 65: loglikelihood = -219.38395679466737, backtracks = 0, tol = 0.0004013057505476397 Iteration 66: loglikelihood = -219.38366314739872, backtracks = 0, tol = 0.0004147454994836376 Iteration 67: loglikelihood = -219.38340849212824, backtracks = 0, tol = 0.00034797985178746597 Iteration 68: loglikelihood = -219.38318758502183, backtracks = 0, tol = 0.0003599207374415984 Iteration 69: loglikelihood = -219.38299596326374, backtracks = 0, tol = 0.0003018217223394219 Iteration 70: loglikelihood = -219.3828297011887, backtracks = 0, tol = 0.00031238270039476616 Iteration 71: loglikelihood = -219.38268544908368, backtracks = 0, tol = 0.00026184698528793125 Iteration 72: loglikelihood = -219.3825602648841, backtracks = 0, tol = 0.0002711550905775348 Iteration 73: loglikelihood = -219.38245163239276, backtracks = 0, tol = 0.00022721198022395564 Iteration 74: loglikelihood = -219.38235734460943, backtracks = 0, tol = 0.00023539371282360467 Iteration 75: loglikelihood = -219.38227551018164, backtracks = 0, tol = 0.0001971920991460162 Iteration 76: loglikelihood = -219.382204472153, backtracks = 0, tol = 0.00020436848993624394 Iteration 77: loglikelihood = -219.3821428080304, backtracks = 0, tol = 0.00017116393516432852 Iteration 78: loglikelihood = -219.38208927292968, backtracks = 0, tol = 0.00017744788492952903 Iteration 79: loglikelihood = -219.38204279645043, backtracks = 0, tol = 0.00014859040670150365 Iteration 80: loglikelihood = -219.38200244272016, backtracks = 0, tol = 0.00015408544066832546 Iteration 81: loglikelihood = -219.38196740593906, backtracks = 0, tol = 0.00012900826739905896 Iteration 82: loglikelihood = -219.38193698216227, backtracks = 0, tol = 0.00013380816660865064 Iteration 83: loglikelihood = -219.38191056455443, backtracks = 0, tol = 0.00011201756190578927 Iteration 84: loglikelihood = -219.3818876233726, backtracks = 0, tol = 0.000116206527337935 Iteration 85: loglikelihood = -219.38186770147453, backtracks = 0, tol = 9.727268703830643e-5 Test Summary: | Pass Total Time fit Bernoulli SnpLinAlg | 4 4 3.8s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse Poisson regression Number of threads = 1 Link functin = LogLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1351.4606699951187, backtracks = 0, tol = 0.2959188842160037 Iteration 2: loglikelihood = -1311.054721936645, backtracks = 0, tol = 0.095035566143976 Iteration 3: loglikelihood = -1292.4523058162479, backtracks = 1, tol = 0.07036778578264449 Iteration 4: loglikelihood = -1288.5030359688908, backtracks = 1, tol = 0.06693853736787446 Iteration 5: loglikelihood = -1281.704940922149, backtracks = 1, tol = 0.06227632988736849 Iteration 6: loglikelihood = -1279.6826051928501, backtracks = 1, tol = 0.01955410167367815 Iteration 7: loglikelihood = -1278.7958233690074, backtracks = 1, tol = 0.06273148147851505 Iteration 8: loglikelihood = -1278.1023620810554, backtracks = 1, tol = 0.009651906022142828 Iteration 9: loglikelihood = -1277.7796559813514, backtracks = 2, tol = 0.005202592286360246 Iteration 10: loglikelihood = -1277.473802604536, backtracks = 2, tol = 0.006455529720198194 Iteration 11: loglikelihood = -1277.0352158453975, backtracks = 2, tol = 0.0574236747470361 Iteration 12: loglikelihood = -1276.9472918026415, backtracks = 2, tol = 0.0021787399596155917 Iteration 13: loglikelihood = -1276.8626577728746, backtracks = 2, tol = 0.0027089789209496684 Iteration 14: loglikelihood = -1276.8280321985967, backtracks = 3, tol = 0.001380871705474872 Iteration 15: loglikelihood = -1276.8007819621419, backtracks = 3, tol = 0.0012453173946164763 Iteration 16: loglikelihood = -1276.7796171711889, backtracks = 3, tol = 0.0011110239253700315 Iteration 17: loglikelihood = -1276.763275237185, backtracks = 3, tol = 0.000983057057497755 Iteration 18: loglikelihood = -1276.7506919248535, backtracks = 3, tol = 0.0008661510499934799 Iteration 19: loglikelihood = -1276.7410163525685, backtracks = 3, tol = 0.000761444122644067 Iteration 20: loglikelihood = -1276.7335826574003, backtracks = 3, tol = 0.0006685396789966559 Iteration 21: loglikelihood = -1276.727874493406, backtracks = 3, tol = 0.0005865037086098876 Iteration 22: loglikelihood = -1276.723493116295, backtracks = 3, tol = 0.0005142597727773818 Iteration 23: loglikelihood = -1276.7201312444115, backtracks = 3, tol = 0.0004507431039720322 Iteration 24: loglikelihood = -1276.717552368245, backtracks = 3, tol = 0.0003949590203637449 Iteration 25: loglikelihood = -1276.7155745998095, backtracks = 3, tol = 0.0003460023653809524 Iteration 26: loglikelihood = -1276.7140581444887, backtracks = 3, tol = 0.00030306061355757325 Iteration 27: loglikelihood = -1276.7128956136105, backtracks = 3, tol = 0.0002654100566855562 Iteration 28: loglikelihood = -1276.7120045474283, backtracks = 3, tol = 0.00023240917881980027 Iteration 29: loglikelihood = -1276.7113216513312, backtracks = 3, tol = 0.0002034910959576374 Iteration 30: loglikelihood = -1276.710798357001, backtracks = 3, tol = 0.00017815594204839458 Iteration 31: loglikelihood = -1276.7103974065037, backtracks = 3, tol = 0.00015596361471647134 Iteration 32: loglikelihood = -1276.7100902253349, backtracks = 3, tol = 0.00013652706286999556 Iteration 33: loglikelihood = -1276.709854903296, backtracks = 3, tol = 0.00011950618060570635 Iteration 34: loglikelihood = -1276.7096746433447, backtracks = 3, tol = 0.00010460231124893658 Iteration 35: loglikelihood = -1276.7095365704542, backtracks = 3, tol = 9.155333478852818e-5 Test Summary: | Pass Total Time fit Poisson 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 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 = -1495.9882302882302, backtracks = 0, tol = 0.2635160741524356 Iteration 2: loglikelihood = -1458.6319590503015, backtracks = 0, tol = 0.19207891668493432 Iteration 3: loglikelihood = -1452.1768010509936, backtracks = 0, tol = 0.10591044512504248 Iteration 4: loglikelihood = -1448.7058239713356, backtracks = 0, tol = 0.04327886942513317 Iteration 5: loglikelihood = -1447.0610377742485, backtracks = 1, tol = 0.06740484950013877 Iteration 6: loglikelihood = -1446.8547756735657, backtracks = 1, tol = 0.0058675485119509 Iteration 7: loglikelihood = -1446.7643905602104, backtracks = 1, tol = 0.00508604081189252 Iteration 8: loglikelihood = -1446.7466845925803, backtracks = 2, tol = 0.0017219401079998258 Iteration 9: loglikelihood = -1446.7365326944148, backtracks = 2, tol = 0.0013257550852506614 Iteration 10: loglikelihood = -1446.7307430312333, backtracks = 2, tol = 0.0010125163761978639 Iteration 11: loglikelihood = -1446.7274526568426, backtracks = 2, tol = 0.0007695500907368756 Iteration 12: loglikelihood = -1446.7255870866968, backtracks = 2, tol = 0.0005830532117414406 Iteration 13: loglikelihood = -1446.7245310863543, backtracks = 2, tol = 0.0004408034661572806 Iteration 14: loglikelihood = -1446.723934037477, backtracks = 2, tol = 0.00033274790504867375 Iteration 15: loglikelihood = -1446.7235967572115, backtracks = 2, tol = 0.0002508974830661088 Iteration 16: loglikelihood = -1446.7234063397746, backtracks = 2, tol = 0.00018902092255022412 Iteration 17: loglikelihood = -1446.7232988843614, backtracks = 2, tol = 0.0001423123401364174 Iteration 18: loglikelihood = -1446.7232382655998, backtracks = 2, tol = 0.00010709202038733831 Iteration 19: loglikelihood = -1446.7232040770675, backtracks = 2, tol = 8.055637126790458e-5 Test Summary: | Pass Total Time fit NegativeBinomial SnpLinAlg | 4 4 1.2s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse linear regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1932.296202316908, backtracks = 0, tol = 0.7983823027990606 Iteration 2: loglikelihood = -1494.6944667502366, backtracks = 0, tol = 0.13396553294311606 Iteration 3: loglikelihood = -1415.9230432512388, backtracks = 0, tol = 0.049576512360347935 Iteration 4: loglikelihood = -1412.316583088362, backtracks = 0, tol = 0.03286554874328582 Iteration 5: loglikelihood = -1410.2824670572559, backtracks = 0, tol = 0.027375338214955715 Iteration 6: loglikelihood = -1410.1932101895914, backtracks = 0, tol = 0.0016515336134344466 Iteration 7: loglikelihood = -1410.1924509964085, backtracks = 0, tol = 0.00015929980767197095 Iteration 8: loglikelihood = -1410.192440458769, backtracks = 0, tol = 1.8554719750788367e-5 Test Summary: | Pass Total Time fit with >1 non-genetic covariates SnpLinAlg | 5 5 1.6s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse 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 = -1789.882579844242, backtracks = 0, tol = 0.5275928040566606 Iteration 2: loglikelihood = -1457.0666205028303, backtracks = 0, tol = 0.14706705779257073 Iteration 3: loglikelihood = -1411.2811589623539, backtracks = 0, tol = 0.0476363637690342 Iteration 4: loglikelihood = -1410.3115027683793, backtracks = 0, tol = 0.00729913204004829 Iteration 5: loglikelihood = -1410.2989075589285, backtracks = 0, tol = 0.0006489614660434092 Iteration 6: loglikelihood = -1410.298659284219, backtracks = 0, tol = 0.00010553120027222315 Iteration 7: loglikelihood = -1410.2986536009578, backtracks = 0, tol = 1.7909149196961647e-5 Test Summary: | Pass Total Time model selection on non-genetic covariates | 5 5 0.7s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse linear regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 15 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1473.12410014528, 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 11.2s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse NegativeBinomial regression Number of threads = 1 Link functin = LogLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1480.6916720337729, backtracks = 0, tol = 0.1891404174178382 Iteration 2: loglikelihood = -1430.8848257602467, backtracks = 0, tol = 0.09069250398605026 Iteration 3: loglikelihood = -1428.5439636074223, backtracks = 0, tol = 0.1382202430315452 Iteration 4: loglikelihood = -1391.1158092034361, backtracks = 0, tol = 0.09236237263855258 Iteration 5: loglikelihood = -1385.681186990552, backtracks = 0, tol = 0.056065932643486145 Iteration 6: loglikelihood = -1373.1076052347423, backtracks = 0, tol = 0.04240339368751657 Iteration 7: loglikelihood = -1361.5836675729145, backtracks = 0, tol = 0.045897107137588794 Iteration 8: loglikelihood = -1358.5847926110512, backtracks = 0, tol = 0.062425593753535596 Iteration 9: loglikelihood = -1357.16440208441, backtracks = 0, tol = 0.06007609093068151 Iteration 10: loglikelihood = -1356.5883249663948, backtracks = 0, tol = 0.011333304724661057 Iteration 11: loglikelihood = -1356.4670972454694, backtracks = 1, tol = 0.0036689158023789055 Iteration 12: loglikelihood = -1356.4040727170002, backtracks = 2, tol = 0.0025407696486013935 Iteration 13: loglikelihood = -1356.3650434737012, backtracks = 2, tol = 0.002045757270700206 Iteration 14: loglikelihood = -1356.3422782664256, backtracks = 2, tol = 0.001588813788489915 Iteration 15: loglikelihood = -1356.329282643484, backtracks = 2, tol = 0.0012183409783476321 Iteration 16: loglikelihood = -1356.3219220689077, backtracks = 2, tol = 0.0009206557822426874 Iteration 17: loglikelihood = -1356.3177660507263, backtracks = 2, tol = 0.0006940288785633206 Iteration 18: loglikelihood = -1356.3154228113592, backtracks = 2, tol = 0.0005219137682602494 Iteration 19: loglikelihood = -1356.3141027396664, backtracks = 2, tol = 0.0003921618234858222 Iteration 20: loglikelihood = -1356.3133594726623, backtracks = 2, tol = 0.0002944539513677771 Iteration 21: loglikelihood = -1356.3129411349148, backtracks = 2, tol = 0.00022100274071474573 Iteration 22: loglikelihood = -1356.3127057449262, backtracks = 2, tol = 0.0001658237414905932 Iteration 23: loglikelihood = -1356.3125733226723, backtracks = 2, tol = 0.0001243961978627457 Iteration 24: loglikelihood = -1356.3124988382042, backtracks = 2, tol = 9.330607506982167e-5 1.571176 seconds (8.46 M allocations: 142.426 MiB, 2.76% gc time, 39.04% 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 = -1521.0228996356498, backtracks = 0, tol = 0.1891404174178382 Iteration 2: loglikelihood = -1491.1290795132234, backtracks = 0, tol = 0.11074119731142856 Iteration 3: loglikelihood = -1471.4602451777089, backtracks = 0, tol = 0.10175777230146726 Iteration 4: loglikelihood = -1453.1604197354493, backtracks = 0, tol = 0.08209501572527597 Iteration 5: loglikelihood = -1442.4220605393598, backtracks = 0, tol = 0.06505513934868529 Iteration 6: loglikelihood = -1427.8627545220302, backtracks = 0, tol = 0.046790431110656144 Iteration 7: loglikelihood = -1414.42230554719, backtracks = 0, tol = 0.04417267838377016 Iteration 8: loglikelihood = -1406.2538755815528, backtracks = 0, tol = 0.07759422740780778 Iteration 9: loglikelihood = -1403.1764839977332, backtracks = 0, tol = 0.07670520685807011 Iteration 10: loglikelihood = -1396.6746010031918, backtracks = 0, tol = 0.07625537029402768 Iteration 11: loglikelihood = -1392.8674231258938, backtracks = 0, tol = 0.008883052975088037 Iteration 12: loglikelihood = -1389.589804668713, backtracks = 0, tol = 0.002600835384330592 Iteration 13: loglikelihood = -1386.3705260144482, backtracks = 0, tol = 0.07724926904174773 Iteration 14: loglikelihood = -1384.498747429304, backtracks = 0, tol = 0.07626110919920148 Iteration 15: loglikelihood = -1384.4437560261106, backtracks = 0, tol = 0.07609557673750365 Iteration 16: loglikelihood = -1380.5379050697936, backtracks = 0, tol = 0.07376197033488836 Iteration 17: loglikelihood = -1378.7775237162, backtracks = 0, tol = 0.007860545232966466 Iteration 18: loglikelihood = -1377.2592951130364, backtracks = 0, tol = 0.0015787284561437276 Iteration 19: loglikelihood = -1375.9310237558373, backtracks = 0, tol = 0.0005002966534707425 Iteration 20: loglikelihood = -1374.72831259921, backtracks = 0, tol = 0.00023204552373015612 Iteration 21: loglikelihood = -1373.1009424691829, backtracks = 0, tol = 0.07266499474826195 Iteration 22: loglikelihood = -1372.8589712575463, backtracks = 0, tol = 0.07388460562126545 Iteration 23: loglikelihood = -1371.1056815643408, backtracks = 1, tol = 0.004584372386013491 Iteration 24: loglikelihood = -1369.7562708943158, backtracks = 1, tol = 0.002437389544735192 Iteration 25: loglikelihood = -1368.6434460128153, backtracks = 1, tol = 0.0013126489506091335 Iteration 26: loglikelihood = -1367.7115638271664, backtracks = 1, tol = 0.0007258114715179252 Iteration 27: loglikelihood = -1366.909910745208, backtracks = 1, tol = 0.0004183608580237633 Iteration 28: loglikelihood = -1366.2132037962253, backtracks = 1, tol = 0.000255999995866279 Iteration 29: loglikelihood = -1365.601514297488, backtracks = 1, tol = 0.00017523060361473926 Iteration 30: loglikelihood = -1365.0581683032517, backtracks = 1, tol = 0.00014787794886374797 Iteration 31: loglikelihood = -1364.5704167884885, backtracks = 1, tol = 0.00012948787311153486 Iteration 32: loglikelihood = -1364.1291674491572, backtracks = 1, tol = 0.00011631465971188068 Iteration 33: loglikelihood = -1363.7279164130102, backtracks = 1, tol = 0.00010633060555246233 Iteration 34: loglikelihood = -1363.361776268829, backtracks = 1, tol = 9.833386466793302e-5 0.340444 seconds (1.44 M allocations: 26.583 MiB) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse NegativeBinomial regression Number of threads = 1 Link functin = LogLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -3774.762, backtracks = 0, tol = 0.08341253579874071 Iteration 2: loglikelihood = -3740.308, backtracks = 0, tol = 0.03909101022812322 Iteration 3: loglikelihood = -3718.8374, backtracks = 1, tol = 0.053261626614722245 Iteration 4: loglikelihood = -3713.1724, backtracks = 1, tol = 0.013858081090246385 Iteration 5: loglikelihood = -3711.414, backtracks = 1, tol = 0.006973911007587473 Iteration 6: loglikelihood = -3693.7876, backtracks = 1, tol = 0.058991282332476365 Iteration 7: loglikelihood = -3689.9038, backtracks = 1, tol = 0.012681541795213521 Iteration 8: loglikelihood = -3688.7207, backtracks = 1, tol = 0.006776991324079732 Iteration 9: loglikelihood = -3688.3652, backtracks = 1, tol = 0.003383913711758953 Iteration 10: loglikelihood = -3688.2625, backtracks = 1, tol = 0.001869547488923737 Iteration 11: loglikelihood = -3688.2349, backtracks = 1, tol = 0.0010906447259326395 Iteration 12: loglikelihood = -3688.2302, backtracks = 1, tol = 0.0005819258188390235 Iteration 13: loglikelihood = -3688.2312, backtracks = 3, tol = 7.451202847787263e-5 25.142609 seconds (16.13 M allocations: 699.592 MiB, 1.20% gc time, 97.30% 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 = -3667.467, backtracks = 0, tol = 0.08341253579874071 Iteration 2: loglikelihood = -3557.5103, backtracks = 0, tol = 0.04008690467146134 Iteration 3: loglikelihood = -3310.0798, backtracks = 1, tol = 0.05311621101872554 Iteration 4: loglikelihood = -3293.1238, backtracks = 0, tol = 0.09236369668495863 Iteration 5: loglikelihood = -3051.0935, backtracks = 0, tol = 0.09347588228039806 Iteration 6: loglikelihood = -2920.9172, backtracks = 0, tol = 0.08215215513423507 Iteration 7: loglikelihood = -2793.825, backtracks = 0, tol = 0.07932881541757862 Iteration 8: loglikelihood = -2663.5818, backtracks = 0, tol = 0.08077311950112058 Iteration 9: loglikelihood = -2554.0837, backtracks = 0, tol = 0.08426153908900796 Iteration 10: loglikelihood = -2450.128, backtracks = 0, tol = 0.08402627410324046 Iteration 11: loglikelihood = -2373.518, backtracks = 0, tol = 0.09547270817474267 Iteration 12: loglikelihood = -2303.6582, backtracks = 0, tol = 0.09490629983773453 Iteration 13: loglikelihood = -2264.624, backtracks = 0, tol = 0.09524454018030991 Iteration 14: loglikelihood = -2231.9944, backtracks = 0, tol = 0.09479899601324948 Iteration 15: loglikelihood = -2219.1655, backtracks = 0, tol = 0.09612420777216467 Iteration 16: loglikelihood = -2205.8767, backtracks = 0, tol = 0.09570816930725527 Iteration 17: loglikelihood = -2204.4922, backtracks = 0, tol = 0.09674041949391192 Iteration 18: loglikelihood = -2198.3325, backtracks = 0, tol = 0.09634734334107 Iteration 19: loglikelihood = -2194.6438, backtracks = 1, tol = 0.013704697717800687 Iteration 20: loglikelihood = -2193.932, backtracks = 1, tol = 0.005739391943038162 Iteration 21: loglikelihood = -2193.8015, backtracks = 1, tol = 0.002656875618313004 Iteration 22: loglikelihood = -2193.7822, backtracks = 1, tol = 0.0013250929415671686 Iteration 23: loglikelihood = -2193.78, backtracks = 1, tol = 0.0006614828202510662 Iteration 24: loglikelihood = -2193.7795, backtracks = 1, tol = 0.00034986862690039713 Iteration 25: loglikelihood = -2193.7783, backtracks = 2, tol = 9.540631809887103e-5 0.976834 seconds (1.38 M allocations: 22.803 MiB, 76.29% gc time) Test Summary: | Pass Total Time Negative binomial nuisance parameter Float32 matrix | 12 12 31.3s **** 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 4.626005 seconds (1.15 M allocations: 137.116 MiB, 0.49% gc time, 91.43% compilation time) Test Summary: | Pass Total Time initialze beta | 1 1 5.2s 9.911898 seconds (4.00 M allocations: 82.499 MiB, 0.45% gc time, 0.65% compilation time) 5.208171 seconds (3.98 M allocations: 91.678 MiB, 1.03% gc time) 10.385053 seconds (20.41 M allocations: 439.459 MiB, 1.08% gc time, 17.78% compilation time: 78% of which was recompilation) 8.210259 seconds (20.18 M allocations: 434.189 MiB, 1.32% gc time) 39.191713 seconds (3.85 M allocations: 4.245 GiB, 11.46% gc time, 27.27% compilation time) 55.033826 seconds (71.97 k allocations: 183.461 MiB) Test Summary: | Pass Total Time memory_efficient keyword | 7 7 2m25.9s Test Summary: | Pass Total Time update_support! | 10 10 0.6s 14.766 ms (78 allocations: 4.56 KiB) 5.027 μs (0 allocations: 0 bytes) 132.338 μs (4 allocations: 288 bytes) 6.638 μs (0 allocations: 0 bytes) 55.440 μs (2 allocations: 64 bytes) 32.200 μs (0 allocations: 0 bytes) 24.949 μs (0 allocations: 0 bytes) 29.239 μs (0 allocations: 0 bytes) 106.379 μs (0 allocations: 0 bytes) 38.319 ms (78 allocations: 4.56 KiB) 27.530 μs (0 allocations: 0 bytes) 179.358 μs (4 allocations: 288 bytes) 32.960 μs (0 allocations: 0 bytes) 243.768 μs (2 allocations: 64 bytes) 88.089 μs (0 allocations: 0 bytes) 127.128 μs (0 allocations: 0 bytes) 161.019 μs (0 allocations: 0 bytes) 196.458 μs (0 allocations: 0 bytes) Test Summary: | Total Time benchmarks for multivariate function | 0 3m33.5s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse Multivariate Gaussian regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 12 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -2900.9186300194497, 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 0.418310 seconds (49.51 k allocations: 5.501 MiB, 62.27% compilation time) Test Summary: | Pass Total Time multivariate fit_iht SnpLinAlg | 7 7 12.0s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse Multivariate Gaussian regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 12 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -2878.028812628852, backtracks = 0, tol = 2.5661768673084553 Iteration 2: loglikelihood = -2868.563037890196, backtracks = 0, tol = 0.024335274263285057 Iteration 3: loglikelihood = -2868.0815051475474, backtracks = 0, tol = 0.004072558228741048 Iteration 4: loglikelihood = -2868.0352100240902, backtracks = 0, tol = 0.0013135682973484317 Iteration 5: loglikelihood = -2868.0309297231934, backtracks = 0, tol = 0.000386434110747091 Iteration 6: loglikelihood = -2868.0305335492912, backtracks = 0, tol = 0.00011924564415557833 Iteration 7: loglikelihood = -2868.0304968517494, backtracks = 0, tol = 3.603726989721193e-5 1.800595 seconds (282.58 k allocations: 168.153 MiB, 58.94% compilation time) Test Summary: | Pass Total Time initialze beta | 5 5 2.3s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:03:30 Cross validating... 11%|███▌ | ETA: 0:00:59 Cross validating... 14%|████▋ | ETA: 0:00:45 Cross validating... 17%|█████▋ | ETA: 0:00:36 Cross validating... 21%|██████▋ | ETA: 0:00:30 Cross validating... 24%|███████▋ | ETA: 0:00:25 Cross validating... 27%|████████▋ | ETA: 0:00:22 Cross validating... 30%|█████████▋ | ETA: 0:00:19 Cross validating... 33%|██████████▋ | ETA: 0:00:17 Cross validating... 35%|███████████▏ | ETA: 0:00:16 Cross validating... 38%|████████████▎ | ETA: 0:00:14 Cross validating... 41%|█████████████▎ | ETA: 0:00:13 Cross validating... 44%|██████████████▎ | ETA: 0:00:11 Cross validating... 48%|███████████████▎ | ETA: 0:00:10 Cross validating... 51%|████████████████▎ | ETA: 0:00:09 Cross validating... 54%|█████████████████▎ | ETA: 0:00:08 Cross validating... 57%|██████████████████▎ | ETA: 0:00:07 Cross validating... 60%|███████████████████▎ | ETA: 0:00:06 Cross validating... 63%|████████████████████▍ | ETA: 0:00:06 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:05 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:04 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:04 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:03 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:03 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:02 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:02 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:01 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: 0:00:11 Crossvalidation Results: k MSE 0 4050.975590943737 1 1922.9593142619233 2 1025.3390886346929 3 836.7555668430641 4 676.8055769312346 5 555.198743334949 6 447.3502082368715 7 365.4388334180476 8 348.7862541434712 9 351.20651902788484 10 354.92611799724546 11 358.2021793185288 12 362.6861025712269 13 364.2340331903252 14 366.9626721204651 15 369.33046466489066 16 367.62338231550757 17 386.7815405459467 18 405.27412122064516 19 376.8818626765733 20 380.0613938364097 Best k = 8 11.832012 seconds (11.36 M allocations: 300.230 MiB, 1.00% gc time, 59.67% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 5%|█▌ | ETA: 0:00:03 Cross validating... 8%|██▌ | ETA: 0:00:03 Cross validating... 11%|███▌ | ETA: 0:00:03 Cross validating... 14%|████▋ | ETA: 0:00:03 Cross validating... 17%|█████▋ | ETA: 0:00:03 Cross validating... 21%|██████▋ | ETA: 0:00:03 Cross validating... 24%|███████▋ | ETA: 0:00:03 Cross validating... 27%|████████▋ | ETA: 0:00:03 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: 0:00:02 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: 0:00:02 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:01 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:01 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:01 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:01 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:01 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:01 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:00 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:00 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:04 Crossvalidation Results: k MSE 0 4050.975590943737 1 1924.354903516099 2 1030.859707445632 3 840.4151092462005 4 683.0715211333213 5 561.9402097686798 6 454.76189929774694 7 370.85106177940395 8 355.08425520995274 9 361.4372127745373 10 370.9412966306323 11 379.2788809065339 12 389.88908972355046 13 397.96693416139726 14 403.3394726542757 15 409.3727980890935 16 414.2144675236051 17 423.7343615883829 18 420.7376787915696 19 436.2663427673049 20 448.0217775550806 Best k = 8 4.637927 seconds (10.34 M allocations: 216.798 MiB, 1.60% gc time, 1.03% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, normal model | 3 3 17.3s **** 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: 0:05:47 Cross validating... 8%|██▌ | ETA: 0:02:13 Cross validating... 14%|████▋ | ETA: 0:01:10 Cross validating... 21%|██████▋ | ETA: 0:00:45 Cross validating... 24%|███████▋ | ETA: 0:00:38 Cross validating... 29%|█████████▏ | ETA: 0:00:30 Cross validating... 33%|██████████▋ | ETA: 0:00:24 Cross validating... 38%|████████████▎ | ETA: 0:00:20 Cross validating... 43%|█████████████▊ | ETA: 0:00:17 Cross validating... 48%|███████████████▎ | ETA: 0:00:14 Cross validating... 52%|████████████████▊ | ETA: 0:00:12 Cross validating... 57%|██████████████████▎ | ETA: 0:00:10 Cross validating... 62%|███████████████████▊ | ETA: 0:00:08 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:07 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:05 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:04 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:03 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:02 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:01 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:13 Crossvalidation Results: k MSE 0 1626.5185961914062 1 1319.5070190429688 2 1050.3265170898437 3 852.68006640625 4 635.9205598144531 5 537.705501953125 6 425.64002709960937 7 377.5232763671875 8 337.7181768798828 9 335.5172020263672 10 337.25238830566406 11 339.750138671875 12 341.7765025634766 13 341.31099353027344 14 344.3516495361328 15 346.5185588378906 16 350.2226956787109 17 353.0842761230469 18 362.9807567138672 19 353.65432421875 20 381.65293957519526 Best k = 9 15.178864 seconds (12.89 M allocations: 320.128 MiB, 1.05% gc time, 82.82% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 6%|██ | ETA: 0:00:02 Cross validating... 11%|███▌ | ETA: 0:00:02 Cross validating... 17%|█████▋ | ETA: 0:00:02 Cross validating... 22%|███████▏ | ETA: 0:00:02 Cross validating... 27%|████████▋ | ETA: 0:00:02 Cross validating... 30%|█████████▋ | ETA: 0:00:02 Cross validating... 35%|███████████▏ | ETA: 0:00:02 Cross validating... 40%|████████████▊ | ETA: 0:00:02 Cross validating... 44%|██████████████▎ | ETA: 0:00:01 Cross validating... 51%|████████████████▎ | ETA: 0:00:01 Cross validating... 56%|█████████████████▊ | ETA: 0:00:01 Cross validating... 60%|███████████████████▎ | ETA: 0:00:01 Cross validating... 65%|████████████████████▉ | ETA: 0:00:01 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:01 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:01 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:00 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:00 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:00 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:02 Crossvalidation Results: k MSE 0 1626.5185961914062 1 1319.8910849609374 2 1050.3265170898437 3 865.2069248046876 4 635.9206564941406 5 541.6314487304687 6 431.37908569335934 7 381.4962491455078 8 343.8475262451172 9 343.4234611816406 10 349.06797021484374 11 355.4681672363281 12 366.30321655273434 13 364.8156268310547 14 374.2770827636719 15 380.5968267822266 16 390.7023012695313 17 397.1755072021484 18 399.06380651855466 19 392.24885388183594 20 407.1717907714844 Best k = 9 2.632843 seconds (11.01 M allocations: 203.434 MiB, 1.98% gc time, 1.51% compilation time) Test Summary: | Pass Total Time Cross validation on Float32 matrix, normal model | 2 2 19.1s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:57 Cross validating... 6%|██ | ETA: 0:00:30 Cross validating... 10%|███ | ETA: 0:00:21 Cross validating... 13%|████▏ | ETA: 0:00:16 Cross validating... 16%|█████▏ | ETA: 0:00:13 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... 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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 0 462.0733923140245 1 343.51141663996 2 268.00158603039586 3 248.92123793415885 4 232.80029611186688 5 231.87188617107256 6 231.3065666452343 7 234.32774708376297 8 235.77118525353055 9 228.5135326944519 10 248.11558433395714 11 243.31120076608323 12 237.63881119393204 13 268.03333569648356 14 252.83722572445694 15 277.3535927715751 16 265.9667121250826 17 264.50358063174554 18 251.5310049213365 19 279.6990308205134 20 290.56371819660603 Best k = 9 7.693197 seconds (17.79 M allocations: 417.341 MiB, 1.47% gc time, 31.15% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:04 Cross validating... 6%|██ | ETA: 0:00:05 Cross validating... 10%|███ | ETA: 0:00:05 Cross validating... 13%|████▏ | ETA: 0:00:05 Cross validating... 14%|████▋ | ETA: 0:00:05 Cross validating... 17%|█████▋ | ETA: 0:00:05 Cross validating... 21%|██████▋ | ETA: 0:00:04 Cross validating... 24%|███████▋ | ETA: 0:00:04 Cross validating... 27%|████████▋ | ETA: 0:00:04 Cross validating... 30%|█████████▋ | ETA: 0:00:04 Cross validating... 33%|██████████▋ | ETA: 0:00:04 Cross validating... 37%|███████████▋ | ETA: 0:00:03 Cross validating... 40%|████████████▊ | ETA: 0:00:03 Cross validating... 43%|█████████████▊ | ETA: 0:00:03 Cross validating... 46%|██████████████▊ | ETA: 0:00:03 Cross validating... 49%|███████████████▊ | ETA: 0:00:03 Cross validating... 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ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:05 Crossvalidation Results: k MSE 0 462.0733923140245 1 343.6262370894103 2 269.5900637140322 3 250.0640298285485 4 234.9945915835567 5 230.75025328643025 6 239.1776013303969 7 244.30360337995285 8 242.7991320539254 9 241.857281041482 10 245.80336280022442 11 262.5458233413978 12 265.18823779427186 13 262.8026935556293 14 266.215730202494 15 294.0119715542298 16 281.47360423869816 17 303.7606757243161 18 299.38741732772417 19 303.65795927053085 20 323.81921417753676 Best k = 5 5.530582 seconds (17.93 M allocations: 373.612 MiB, 1.26% gc time, 1.15% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, logistic 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: 0:00:48 Cross validating... 8%|██▌ | ETA: 0:00:20 Cross validating... 11%|███▌ | ETA: 0:00:15 Cross validating... 14%|████▋ | ETA: 0:00:12 Cross validating... 17%|█████▋ | ETA: 0:00:10 Cross validating... 21%|██████▋ | ETA: 0:00:09 Cross validating... 24%|███████▋ | ETA: 0:00:08 Cross validating... 27%|████████▋ | ETA: 0:00:07 Cross validating... 30%|█████████▋ | ETA: 0:00:06 Cross validating... 32%|██████████▏ | ETA: 0:00:06 Cross validating... 35%|███████████▏ | ETA: 0:00:06 Cross validating... 40%|████████████▊ | ETA: 0:00:05 Cross validating... 43%|█████████████▊ | ETA: 0:00:04 Cross validating... 46%|██████████████▊ | ETA: 0:00:04 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... 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 0 462.2899777536257 1 405.56704941107455 2 389.119912495986 3 367.32254531855114 4 332.8406958438479 5 313.92984646908275 6 309.4021691349439 7 307.19354024290817 8 308.8709168595424 9 311.75572796959204 10 311.6928968659363 11 313.501791486378 12 318.0116554041448 13 342.42769782075914 14 356.8865526712306 15 366.7041219296007 16 333.1315706690642 17 324.1284574343435 18 329.71542466268284 19 366.6671223230402 20 332.0057693750002 Best k = 7 7.876309 seconds (16.32 M allocations: 382.815 MiB, 12.60% gc time, 34.75% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 5%|█▌ | ETA: 0:00:04 Cross validating... 8%|██▌ | ETA: 0:00:04 Cross validating... 11%|███▌ | ETA: 0:00:04 Cross validating... 14%|████▋ | ETA: 0:00:04 Cross validating... 17%|█████▋ | ETA: 0:00:04 Cross validating... 21%|██████▋ | ETA: 0:00:03 Cross validating... 24%|███████▋ | ETA: 0:00:03 Cross validating... 27%|████████▋ | ETA: 0:00:03 Cross validating... 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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 0 462.2899777536257 1 405.9567414209734 2 392.38957795763196 3 371.0629284476307 4 338.43044265507217 5 319.2659765346038 6 318.3277547474234 7 323.4964062414077 8 327.4203560916063 9 336.16146160518036 10 342.05354514874597 11 349.6397876539346 12 356.2768127114672 13 358.7036904464964 14 383.8968450856712 15 372.0887968154598 16 381.053142772968 17 395.5532868244439 18 372.56525666709075 19 391.5724874190517 20 409.1782504249408 Best k = 6 4.465622 seconds (16.99 M allocations: 348.607 MiB, 2.18% 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: 0:01:00 Cross validating... 5%|█▌ | ETA: 0:00:42 Cross validating... 8%|██▌ | ETA: 0:00:26 Cross validating... 11%|███▌ | ETA: 0:00:19 Cross validating... 14%|████▋ | ETA: 0:00:16 Cross validating... 17%|█████▋ | ETA: 0:00:13 Cross validating... 21%|██████▋ | ETA: 0:00:11 Cross validating... 24%|███████▋ | ETA: 0:00:10 Cross validating... 27%|████████▋ | ETA: 0:00:09 Cross validating... 30%|█████████▋ | ETA: 0:00:08 Cross validating... 33%|██████████▋ | ETA: 0:00:07 Cross validating... 37%|███████████▋ | ETA: 0:00:07 Cross validating... 40%|████████████▊ | ETA: 0:00:06 Cross validating... 43%|█████████████▊ | ETA: 0:00:06 Cross validating... 46%|██████████████▊ | ETA: 0:00:05 Cross validating... 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Cross validating... 100%|████████████████████████████████| Time: 0:00:07 Crossvalidation Results: k MSE 0 602.4775368585493 1 505.58824399376726 2 436.33365358336556 3 416.59992857029425 4 393.4525683531559 5 391.07348338064355 6 359.09896754828856 7 352.73919965650055 8 347.4841609329146 9 364.62918974661045 10 357.35156991147414 11 372.00904782894287 12 364.4881519039227 13 357.93404818822125 14 376.2607144643474 15 364.6004454577843 16 402.2074393735663 17 379.5327478938498 18 380.77921395791265 19 373.0935947413855 20 368.1829016815333 Best k = 8 8.089213 seconds (16.36 M allocations: 389.017 MiB, 0.93% 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: 0:00:05 Cross validating... 10%|███ | ETA: 0:00:05 Cross validating... 13%|████▏ | ETA: 0:00:04 Cross validating... 16%|█████▏ | ETA: 0:00:04 Cross validating... 17%|█████▋ | ETA: 0:00:04 Cross validating... 21%|██████▋ | ETA: 0:00:04 Cross validating... 24%|███████▋ | ETA: 0:00:04 Cross validating... 27%|████████▋ | ETA: 0:00:04 Cross validating... 30%|█████████▋ | ETA: 0:00:04 Cross validating... 33%|██████████▋ | ETA: 0:00:04 Cross validating... 37%|███████████▋ | ETA: 0:00:03 Cross validating... 40%|████████████▊ | ETA: 0:00:03 Cross validating... 43%|█████████████▊ | ETA: 0:00:03 Cross validating... 46%|██████████████▊ | ETA: 0:00:03 Cross validating... 49%|███████████████▊ | ETA: 0:00:03 Cross validating... 52%|████████████████▊ | ETA: 0:00:03 Cross validating... 56%|█████████████████▊ | ETA: 0:00:02 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: 0:00:02 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:01 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:01 Cross validating... 81%|█████████████████████████▉ | 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... 94%|██████████████████████████████ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:05 Crossvalidation Results: k MSE 0 602.4775368585493 1 503.16529043261113 2 437.6156286110244 3 420.02813489699656 4 399.47607242035065 5 399.9358457081219 6 379.9665507901625 7 368.7479481507006 8 363.0433790892597 9 379.06433669981425 10 373.51810517493317 11 383.9346820391929 12 382.0728981244606 13 393.4119692128394 14 400.4668083603738 15 404.2006520797356 16 408.44835805244617 17 399.45380439409655 18 411.91169757004565 19 404.5008412285026 20 392.39970849001804 Best k = 8 5.548339 seconds (16.38 M allocations: 344.250 MiB, 1.13% gc time, 1.05% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, Poisson model | 2 2 14.1s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:01:00 Cross validating... 5%|█▌ | ETA: 0:00:59 Cross validating... 6%|██ | ETA: 0:00:59 Cross validating... 10%|███ | ETA: 0:00:48 Cross validating... 11%|███▌ | ETA: 0:00:49 Cross validating... 13%|████▏ | ETA: 0:00:48 Cross validating... 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0:00:01 Cross validating... 100%|████████████████████████████████| Time: 0:00:50 Crossvalidation Results: k MSE 0 315.11471029221906 1 261.73773599685757 2 230.3640001528928 3 220.6682426175683 4 213.34134219278727 5 211.13265309681879 6 208.68550894085996 7 210.2125234027531 8 209.2868799544019 9 206.07136494911816 10 207.8366454019416 11 206.60244235767345 12 207.95717601506138 13 207.9288383716774 14 208.02753422741915 15 209.37729926850642 16 211.60919799780288 17 213.61129857207453 18 213.6276935788128 19 214.46411276233658 20 216.45880155095088 Best k = 9 50.440961 seconds (163.35 M allocations: 4.106 GiB, 1.29% gc time, 4.41% 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: 0:00:07 Cross validating... 6%|██ | ETA: 0:00:07 Cross 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0:00:04 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:03 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:03 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:03 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:03 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:02 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:02 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:02 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:02 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:02 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:01 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:01 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:01 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:01 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:01 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:13 Crossvalidation Results: k MSE 0 315.11471029221906 1 261.248617902262 2 233.77689199285138 3 223.82687808257276 4 218.42763356719774 5 215.98395682792597 6 219.40135401794834 7 217.5925655017317 8 217.31638866061695 9 221.435266269286 10 225.58900172843556 11 216.98823656436213 12 218.92657827919163 13 229.59398874016472 14 233.10920836507069 15 232.4103647958994 16 249.18933261245115 17 245.85952669869732 18 236.9119638955823 19 247.82857852550893 20 243.2414367081483 Best k = 5 13.679932 seconds (44.21 M allocations: 938.257 MiB, 1.53% gc time, 0.47% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, NegativeBinomial model | 2 2 1m04.5s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:01:09 Cross validating... 6%|██ | ETA: 0:00:35 Cross validating... 10%|███ | ETA: 0:00:24 Cross validating... 13%|████▏ | ETA: 0:00:18 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... 33%|██████████▋ | ETA: 0:00:07 Cross validating... 38%|████████████▎ | ETA: 0:00:06 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... 57%|██████████████████▎ | ETA: 0:00:03 Cross validating... 60%|███████████████████▎ | ETA: 0:00:03 Cross validating... 63%|████████████████████▍ | ETA: 0:00:02 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:02 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:02 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:02 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:01 Cross validating... 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 0 709.7238911132813 1 600.8470166015625 2 478.37098138427734 3 399.75837347412113 4 316.3170971069336 5 274.59901690673826 6 232.61785809326173 7 221.00282696533208 8 205.62119918823245 9 198.3431817626953 10 200.94596459960937 11 201.86666357421876 12 202.35683154296873 13 208.02664166259768 14 206.9071481628418 15 209.87240182495117 16 216.0480528869629 17 212.0296098022461 18 217.49209603881837 19 225.60646734619144 20 213.36869631958012 Best k = 9 6.314123 seconds (17.01 M allocations: 337.916 MiB, 1.62% gc time, 46.08% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 5%|█▌ | ETA: 0:00:03 Cross validating... 8%|██▌ | ETA: 0:00:03 Cross validating... 11%|███▌ | ETA: 0:00:03 Cross validating... 14%|████▋ | ETA: 0:00:03 Cross validating... 17%|█████▋ | ETA: 0:00:03 Cross validating... 22%|███████▏ | ETA: 0:00:03 Cross validating... 25%|████████▏ | ETA: 0:00:02 Cross validating... 29%|█████████▏ | ETA: 0:00:02 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94%|██████████████████████████████ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:03 Crossvalidation Results: k MSE 0 709.7238911132813 1 580.5206424560547 2 462.45179821777344 3 375.725685546875 4 311.8335130615235 5 265.69685809326177 6 235.52074707031255 7 221.8731430358887 8 209.48005477905275 9 202.0256286010742 10 206.40357376098632 11 209.8904744873047 12 212.83695938110353 13 217.36745034790042 14 219.17275009155276 15 218.94907879638671 16 225.10276358032226 17 228.24513723754882 18 225.50167910766604 19 235.0626920776367 20 227.98946899414062 Best k = 9 3.366938 seconds (16.17 M allocations: 286.718 MiB, 1.71% gc time, 1.92% compilation time) Test Summary: | Pass Total Time Cross validation on floating point matrices, NegativeBinomial model | 2 2 10.2s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 2%|▋ | ETA: 0:01:24 Cross validating... 3%|█ | ETA: 0:01:00 Cross validating... 4%|█▎ | ETA: 0:00:47 Cross validating... 5%|█▋ | ETA: 0:00:40 Cross validating... 6%|█▉ | ETA: 0:00:35 Cross validating... 7%|██▎ | ETA: 0:00:32 Cross validating... 8%|██▌ | ETA: 0:00:31 Cross validating... 9%|██▉ | ETA: 0:00:29 Cross validating... 10%|███▎ | ETA: 0:00:27 Cross validating... 11%|███▌ | ETA: 0:00:26 Cross validating... 12%|███▉ | ETA: 0:00:25 Cross validating... 13%|████▏ | ETA: 0:00:24 Cross validating... 14%|████▌ | ETA: 0:00:23 Cross validating... 15%|████▊ | ETA: 0:00:22 Cross validating... 16%|█████▏ | ETA: 0:00:22 Cross validating... 17%|█████▌ | ETA: 0:00:21 Cross validating... 18%|█████▊ | ETA: 0:00:21 Cross validating... 19%|██████▏ | ETA: 0:00:20 Cross validating... 20%|██████▍ | ETA: 0:00:20 Cross validating... 21%|██████▊ 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1763.2963379709383 11 1772.9937727268712 12 1773.5673209184079 13 1795.611822488325 14 1807.1281402155425 15 1805.8401266767482 16 1809.926842952397 17 1817.3117226831237 18 1827.473014810471 19 1841.0813294611191 20 1840.3316995411137 Best k = 8 18.708338 seconds (336.60 k allocations: 243.198 MiB, 0.72% gc time, 9.33% compilation time) Test Summary: | Pass Total Time multivariate cross validation SnpLinAlg | 3 3 24.0s Test Summary: | Pass Total Time wrapper univariate | 20 20 1m49.2s **** 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: 0:00:11 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: 0:00:13 Cross validating... 7%|██▎ | ETA: 0:00:13 Cross 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Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 2%|▋ | ETA: 0:00:10 Cross validating... 3%|█ | ETA: 0:00:10 Cross validating... 4%|█▎ | ETA: 0:00:11 Cross validating... 5%|█▋ | ETA: 0:00:11 Cross validating... 6%|█▉ | ETA: 0:00:12 Cross validating... 7%|██▎ | ETA: 0:00:12 Cross validating... 8%|██▌ | ETA: 0:00:12 Cross validating... 9%|██▉ | ETA: 0:00:13 Cross validating... 10%|███▎ | ETA: 0:00:14 Cross validating... 11%|███▌ | ETA: 0:00:15 Cross validating... 12%|███▉ | ETA: 0:00:15 Cross validating... 13%|████▏ | ETA: 0:00:16 Cross validating... 14%|████▌ | ETA: 0:00:16 Cross validating... 15%|████▊ | ETA: 0:00:16 Cross validating... 16%|█████▏ | ETA: 0:00:18 Cross validating... 17%|█████▌ | ETA: 0:00:18 Cross validating... 18%|█████▊ | ETA: 0:00:18 Cross validating... 19%|██████▏ | ETA: 0:00:18 Cross validating... 20%|██████▍ | ETA: 0:00:19 Cross validating... 21%|██████▊ | ETA: 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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: 0:00:11 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: 0:00:15 Cross validating... 11%|███▌ | ETA: 0:00:15 Cross validating... 12%|███▉ | ETA: 0:00:16 Cross validating... 13%|████▏ | ETA: 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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 1m28.5s 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:2246 [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:318 [18] _start() @ Base ./client.jl:593 Test Summary: | Error Total Time read BGEN and VCF | 1 1 3.1s RNG of the outermost testset: Xoshiro(0x900cb06b720f2579, 0x937850f9931584a6, 0x60a88432f8b338d4, 0x41be4fbdd51481aa, 0xf9f46687da5f5b35) 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 1151.61s 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:3160 [3] test @ /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Operations.jl:3025 [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:352 [14] _start() @ Base ./client.jl:593 in expression starting at /PkgEval.jl/scripts/evaluate.jl:214 PkgEval failed after 1269.35s: package tests unexpectedly errored