Package evaluation to test MendelIHT on Julia 1.14.0-DEV.3081 (21a70e450d*) started at 2026-09-02T07:27:07.943 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.14` Set-up completed after 27.06s ################################################################################ # Installation # Installing MendelIHT... Resolving package versions... Updating `~/.julia/environments/v1.14/Project.toml` [921c7187] + MendelIHT v1.4.11 Updating `~/.julia/environments/v1.14/Manifest.toml` [7d9f7c33] + Accessors v0.1.45 [79e6a3ab] + Adapt v4.7.0 [66dad0bd] + AliasTables v1.1.3 [4fba245c] + ArrayInterface v7.30.1 [67c07d97] + Automa v1.2.0 ⌅ [6db4b851] + BGEN v0.1.17 [28d598bf] + BGZFStreams v0.3.2 [47718e42] + BioGenerics v0.1.5 [62783981] + BitTwiddlingConvenienceFunctions v0.1.6 [e1450e63] + BufferedStreams v1.2.2 [2a0fbf3d] + CPUSummary v0.2.7 [336ed68f] + CSV v0.10.17 [fb6a15b2] + CloseOpenIntervals v0.1.13 [523fee87] + CodecBzip2 v0.8.5 [ba30903b] + CodecXz v0.7.4 [944b1d66] + CodecZlib v0.7.9 [6b39b394] + CodecZstd v0.8.7 [861a8166] + Combinatorics v1.1.0 [38540f10] + CommonSolve v0.2.14 [f70d9fcc] + CommonWorldInvalidations v1.2.0 [34da2185] + Compat v4.18.1 [a33af91c] + CompositionsBase v0.1.2 [187b0558] + ConstructionBase v1.6.0 [adafc99b] + CpuId v0.3.1 [a8cc5b0e] + Crayons v4.2.0 [a10d1c49] + DBInterface v2.7.0 [9a962f9c] + 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To see why use `status --outdated -m` Installation completed after 4.79s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompiling project... 7.1 s ✓ BGEN 9.2 s ✓ VCFTools WARNING: Constructor for type "MvNormal" was extended in `MendelIHT` without explicit qualification or import. NOTE: Assumed "MvNormal" refers to `Distributions.MvNormal`. This behavior is deprecated and may differ in future versions. NOTE: This behavior may have differed in Julia versions prior to 1.12. Hint: If you intended to create a new generic function of the same name, use `function MvNormal end`. Hint: To silence the warning, qualify `MvNormal` as `Distributions.MvNormal` in the method signature or explicitly `import Distributions: MvNormal`. 28.4 s ✓ MendelIHT 3 dependencies successfully precompiled in 52 seconds. 173 already precompiled. 1 dependency had output during precompilation: ┌ MendelIHT │ WARNING: Constructor for type "MvNormal" was extended in `MendelIHT` without explicit qualification or import. │ NOTE: Assumed "MvNormal" refers to `Distributions.MvNormal`. This behavior is deprecated and may differ in future versions. │ NOTE: This behavior may have differed in Julia versions prior to 1.12. │ Hint: If you intended to create a new generic function of the same name, use `function MvNormal end`. │ Hint: To silence the warning, qualify `MvNormal` as `Distributions.MvNormal` in the method signature or explicitly `import Distributions: MvNormal`. └ Precompilation completed after 72.64s ################################################################################ # Testing # Testing MendelIHT Status `/tmp/jl_taCflI/Project.toml` ⌅ [6db4b851] BGEN v0.1.17 [6e4b80f9] BenchmarkTools v1.8.0 [336ed68f] CSV v0.10.17 [a93c6f00] DataFrames v1.8.2 [8bb1440f] DelimitedFiles v1.9.1 [b4f34e82] Distances v0.10.12 [31c24e10] Distributions v0.25.131 [38e38edf] GLM v1.9.5 [921c7187] MendelIHT v1.4.11 [92933f4c] ProgressMeter v1.11.0 [189a3867] Reexport v1.2.2 [4e780e97] SnpArrays v0.3.23 [276daf66] SpecialFunctions v2.9.0 [2913bbd2] StatsBase v0.34.13 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libblastrampoline_jll v5.15.0+0 [8e850ede] nghttp2_jll v1.70.0+0 [3f19e933] p7zip_jll v17.8.2+0 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. Testing Running tests... ┌ Warning: accessing `Type.name` is deprecated without replacement. If for detection, use `Base.isType(x)`. │ caller = Distributions.MvNormal(σ::Vector{Float64}) at mvnormal.jl:207 └ @ Distributions ~/.julia/packages/Distributions/RTt4y/src/multivariate/mvnormal.jl:207 ┌ Warning: `MvNormal(σ::AbstractVector{<:Real})` is deprecated, use `MvNormal(LinearAlgebra.Diagonal(map(abs2, σ)))` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `cholesky!(A::RealHermSymComplexHerm{<:Real}, ::Val{true}; kwargs...)` is deprecated, use `cholesky!(A, RowMaximum(); kwargs...)` instead. │ caller = iht_stepsize!(v::MendelIHT.mIHTVariable{Float64, LinearAlgebra.Transpose{Float64, SnpArrays.SnpLinAlg{Float64}}}) at multivariate.jl:241 └ @ MendelIHT ~/.julia/packages/MendelIHT/ZcxZT/src/multivariate.jl:241 Test Summary: | Pass Total Time loglikelihood | 4 4 12.2s Test Summary: | Pass Total Time deviance | 1 1 0.3s Test Summary: | Pass Total Time update_μ! | 4 4 1.1s Test Summary: | Pass Total Time _choose! | 7 7 7.6s Test Summary: | Pass Total Time _iht_backtrack | 7 7 0.0s Test Summary: | Pass Total Time standardize! | 12 12 0.9s Test Summary: | Pass Total Time project_k! | 2 2 0.9s Test Summary: | Pass Total Time project_group_sparse! | 5 5 1.2s 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 = -1734.9455657516673, backtracks = 0, tol = 2.4931869756907754 Iteration 2: loglikelihood = -1472.2189936040716, backtracks = 0, tol = 0.14338377962737592 Iteration 3: loglikelihood = -1442.5207867317333, backtracks = 0, tol = 0.048892512635956856 Iteration 4: loglikelihood = -1441.2763696296274, backtracks = 0, tol = 0.032642187738262184 Iteration 5: loglikelihood = -1441.1371681964063, backtracks = 0, tol = 0.0021744769230657205 Iteration 6: loglikelihood = -1440.7829676724807, backtracks = 0, tol = 0.0302525793667539 Iteration 7: loglikelihood = -1440.7380042466673, backtracks = 1, tol = 0.0010295676632636455 Iteration 8: loglikelihood = -1440.7266483483907, backtracks = 1, tol = 0.0005212358274374356 Iteration 9: loglikelihood = -1440.7237818222945, backtracks = 1, tol = 0.00026320922757855006 Iteration 10: loglikelihood = -1440.7230582934326, backtracks = 1, tol = 0.00013261057805856192 Iteration 11: loglikelihood = -1440.7228756434836, backtracks = 1, tol = 6.665569501192838e-5 IHT estimated 10 nonzero SNP predictors and 1 non-genetic predictors. Compute time (sec): 0.14268183708190918 Final loglikelihood: -1440.7228756434836 SNP PVE: 0.9420827951886716 Iterations: 11 Selected genetic predictors: 10×2 DataFrame Row │ Position Estimated_β │ Int64 Float64 ─────┼─────────────────────── 1 │ 422 -0.125085 2 │ 1083 -1.2021 3 │ 1163 2.73613 4 │ 3865 -0.518025 5 │ 5326 -0.115939 6 │ 6358 0.821114 7 │ 7353 -1.9372 8 │ 7399 0.805277 9 │ 7819 0.880216 10 │ 8904 -0.86153 Selected nongenetic predictors: 1×2 DataFrame Row │ Position Estimated_β │ Int64 Float64 ─────┼─────────────────────── 1 │ 1 0.00358738Test Summary: | Pass Total Time fit normal SnpLinAlg | 4 4 25.0s **** 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 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 3.9s **** 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 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 = -2546.8035843858106, backtracks = 0, tol = 0.4138820173361715 Iteration 2: loglikelihood = -1851.074130590618, backtracks = 0, tol = 0.05816328101459853 Iteration 3: loglikelihood = -1546.2331519201166, backtracks = 0, tol = 0.056314657482643526 Iteration 4: loglikelihood = -1447.347684201399, backtracks = 0, tol = 0.07695503621019731 Iteration 5: loglikelihood = -1399.5038182285539, backtracks = 0, tol = 0.17242375406857222 Iteration 6: loglikelihood = -1337.3729301080687, backtracks = 0, tol = 0.033348316374824875 Iteration 7: loglikelihood = -1319.2268416040451, backtracks = 0, tol = 0.0715799722324529 Iteration 8: loglikelihood = -1308.240770452349, backtracks = 0, tol = 0.05234338476189334 Iteration 9: loglikelihood = -1305.6311090090974, backtracks = 0, tol = 0.04222185433960991 Iteration 10: loglikelihood = -1302.9139331916424, backtracks = 0, tol = 0.0126318473774065 Iteration 11: loglikelihood = -1301.8793707323482, backtracks = 1, tol = 0.005833964857090832 Iteration 12: loglikelihood = -1301.1953932402532, backtracks = 1, tol = 0.043641639933217506 Iteration 13: loglikelihood = -1299.7072567605517, backtracks = 0, tol = 0.013062125281133931 Iteration 14: loglikelihood = -1299.148523912281, backtracks = 1, tol = 0.03385185354196752 Iteration 15: loglikelihood = -1298.689623293428, backtracks = 1, tol = 0.003316835993889749 Iteration 16: loglikelihood = -1298.5590032192756, backtracks = 2, tol = 0.0024191037838073555 Iteration 17: loglikelihood = -1298.411123451798, backtracks = 2, tol = 0.0028470284538928145 Iteration 18: loglikelihood = -1298.3190160563845, backtracks = 2, tol = 0.002837876180044016 Iteration 19: loglikelihood = -1298.2677084989339, backtracks = 2, tol = 0.0015527628344246098 Iteration 20: loglikelihood = -1298.2320358055176, backtracks = 2, tol = 0.0017283147546676015 Iteration 21: loglikelihood = -1298.2066749291605, backtracks = 2, tol = 0.0011040563801628337 Iteration 22: loglikelihood = -1298.1887822471206, backtracks = 2, tol = 0.001236511597862263 Iteration 23: loglikelihood = -1298.1759795593023, backtracks = 2, tol = 0.0007880995942622606 Iteration 24: loglikelihood = -1298.166895790182, backtracks = 2, tol = 0.0008847099188572707 Iteration 25: loglikelihood = -1298.160381067889, backtracks = 2, tol = 0.0005630970603777602 Iteration 26: loglikelihood = -1298.1557441938662, backtracks = 2, tol = 0.0006332717482049094 Iteration 27: loglikelihood = -1298.15241599441, backtracks = 2, tol = 0.00040264027486343215 Iteration 28: loglikelihood = -1298.1500422242464, backtracks = 2, tol = 0.0004535148993258798 Iteration 29: loglikelihood = -1298.1483380688926, backtracks = 2, tol = 0.0002881036229978765 Iteration 30: loglikelihood = -1298.147120823914, backtracks = 2, tol = 0.00032491604154923597 Iteration 31: loglikelihood = -1298.1462469968073, backtracks = 2, tol = 0.00020626575822445652 Iteration 32: loglikelihood = -1298.1456221658757, backtracks = 2, tol = 0.00023285446670765319 Iteration 33: loglikelihood = -1298.1451736803106, backtracks = 2, tol = 0.00014774054412512673 Iteration 34: loglikelihood = -1298.1448527345476, backtracks = 2, tol = 0.00016691444780279405 Iteration 35: loglikelihood = -1298.1446224053382, backtracks = 2, tol = 0.00010585717981033792 Iteration 36: loglikelihood = -1298.1444574796224, backtracks = 2, tol = 0.00011966599884428657 Iteration 37: loglikelihood = -1298.1443391364498, backtracks = 2, tol = 7.586682926334032e-5 Test Summary: | Pass Total Time fit Poisson SnpLinAlg | 4 4 2.4s **** 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 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 = -1651.5218404569991, backtracks = 0, tol = 0.42254425788644207 Iteration 2: loglikelihood = -1544.3152885344616, backtracks = 0, tol = 0.22833579011087657 Iteration 3: loglikelihood = -1508.151871250215, backtracks = 0, tol = 0.14244094786828912 Iteration 4: loglikelihood = -1498.1799732479694, backtracks = 0, tol = 0.08988306421087197 Iteration 5: loglikelihood = -1495.9387292026615, backtracks = 0, tol = 0.034236081159295065 Iteration 6: loglikelihood = -1495.6468150472804, backtracks = 1, tol = 0.0070695565840010995 Iteration 7: loglikelihood = -1495.325937600917, backtracks = 1, tol = 0.05828868388124526 Iteration 8: loglikelihood = -1495.2607374043293, backtracks = 1, tol = 0.0031881662091026897 Iteration 9: loglikelihood = -1495.237578636996, backtracks = 1, tol = 0.002667749084158329 Iteration 10: loglikelihood = -1495.2303160697973, backtracks = 1, tol = 0.001586650181376044 Iteration 11: loglikelihood = -1495.2282844123317, backtracks = 1, tol = 0.0008993030647213208 Iteration 12: loglikelihood = -1495.2277501493913, backtracks = 1, tol = 0.0004467512525134136 Iteration 13: loglikelihood = -1495.2276695919952, backtracks = 2, tol = 0.00011870817949475629 Iteration 14: loglikelihood = -1495.2276238379445, backtracks = 2, tol = 8.805545089637236e-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 = -1693.082645656323, backtracks = 0, tol = 0.8313591290448643 Iteration 2: loglikelihood = -1470.4001257373548, backtracks = 0, tol = 0.11881992722638358 Iteration 3: loglikelihood = -1442.1433100809945, backtracks = 0, tol = 0.03985451444600237 Iteration 4: loglikelihood = -1437.6876594227551, backtracks = 0, tol = 0.02775898877397945 Iteration 5: loglikelihood = -1436.1019105333105, backtracks = 0, tol = 0.02655261631165667 Iteration 6: loglikelihood = -1435.970083389175, backtracks = 1, tol = 0.0011042861983869784 Iteration 7: loglikelihood = -1435.9365709549074, backtracks = 1, tol = 0.0005575988259661472 Iteration 8: loglikelihood = -1435.9280736335215, backtracks = 1, tol = 0.00029975346948469427 Iteration 9: loglikelihood = -1435.9259237228423, backtracks = 1, tol = 0.00015892734419688468 Iteration 10: loglikelihood = -1435.9253807189266, backtracks = 1, tol = 8.331853998425648e-5 Test Summary: | Pass Total Time fit with >1 non-genetic covariates SnpLinAlg | 5 5 1.4s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse linear regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1571.1494611312867, backtracks = 0, tol = 0.3411877876916434 Iteration 2: loglikelihood = -1459.5130703463274, backtracks = 0, tol = 0.09593599781571245 Iteration 3: loglikelihood = -1441.769623522284, backtracks = 0, tol = 0.04066865422224797 Iteration 4: loglikelihood = -1436.8522485675733, backtracks = 0, tol = 0.031599317302456666 Iteration 5: loglikelihood = -1436.6301984977504, backtracks = 1, tol = 0.0015806780173001106 Iteration 6: loglikelihood = -1436.5731023634844, backtracks = 1, tol = 0.0007767044173407731 Iteration 7: loglikelihood = -1436.5584735899904, backtracks = 1, tol = 0.00039702638659682083 Iteration 8: loglikelihood = -1436.554739386893, backtracks = 1, tol = 0.00021615129029871439 Iteration 9: loglikelihood = -1436.553789424111, backtracks = 1, tol = 0.00011492946988861144 Iteration 10: loglikelihood = -1436.5535484496397, backtracks = 1, tol = 5.993649303784207e-5 Test Summary: | Pass Total Time model selection on non-genetic covariates | 5 5 0.7s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse linear regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 15 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1473.1241001452804, backtracks = 0, tol = 0.11162633196865432 Iteration 2: loglikelihood = -1448.37403799896, backtracks = 0, tol = 0.07736217654955346 Iteration 3: loglikelihood = -1429.8981769610311, backtracks = 1, tol = 0.056531823476744666 Iteration 4: loglikelihood = -1404.7133956159753, backtracks = 0, tol = 0.10125409614175712 Iteration 5: loglikelihood = -1397.466171579031, backtracks = 0, tol = 0.05343369325195713 Iteration 6: loglikelihood = -1395.7490747391416, backtracks = 0, tol = 0.08843871418165582 Iteration 7: loglikelihood = -1395.4877576477586, backtracks = 0, tol = 0.008924704068495177 Iteration 8: loglikelihood = -1395.442237061722, backtracks = 0, tol = 0.005277867116132827 Iteration 9: loglikelihood = -1395.4302205892106, backtracks = 0, tol = 0.0027680467744013336 Iteration 10: loglikelihood = -1395.1973617039412, backtracks = 0, tol = 0.09056900655606137 Iteration 11: loglikelihood = -1395.0048067729406, backtracks = 0, tol = 0.007650485819168892 Iteration 12: loglikelihood = -1394.9835209063683, backtracks = 0, tol = 0.0035232591741737973 Iteration 13: loglikelihood = -1394.9793628241396, backtracks = 0, tol = 0.001852195878065177 Iteration 14: loglikelihood = -1394.9779889816232, backtracks = 0, tol = 0.0012530451800711446 Iteration 15: loglikelihood = -1394.977503420045, backtracks = 0, tol = 0.0006829444661300694 Iteration 16: loglikelihood = -1394.9773714862843, backtracks = 1, tol = 0.00022881022816864148 Iteration 17: loglikelihood = -1394.9773102201912, backtracks = 2, tol = 0.0001217788197399568 Iteration 18: loglikelihood = -1394.977273607278, backtracks = 2, tol = 8.822469907087602e-5 **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse linear regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 3 Prior weight scaling = off Doubly sparse projection = on Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1535.4672180567934, backtracks = 0, tol = 0.17016419679985048 Iteration 2: loglikelihood = -1508.04343741211, backtracks = 0, tol = 0.21718489399873087 Iteration 3: loglikelihood = -1448.2717322168082, backtracks = 0, tol = 0.15334504607402907 Iteration 4: loglikelihood = -1437.5669418734744, backtracks = 0, tol = 0.08425396177776269 Iteration 5: loglikelihood = -1434.3602241747526, backtracks = 0, tol = 0.03199716666887782 Iteration 6: loglikelihood = -1434.239273652971, backtracks = 2, tol = 0.003498168340088284 Iteration 7: loglikelihood = -1434.1475478538455, backtracks = 2, tol = 0.003052291101552644 Iteration 8: loglikelihood = -1434.0913475157126, backtracks = 2, tol = 0.002193157681835551 Iteration 9: loglikelihood = -1434.0584761985995, backtracks = 2, tol = 0.0016688209654910676 Iteration 10: loglikelihood = -1434.0393127719108, backtracks = 2, tol = 0.001317554485128468 Iteration 11: loglikelihood = -1434.0281644425422, backtracks = 2, tol = 0.0010393713220469133 Iteration 12: loglikelihood = -1434.0216963632631, backtracks = 2, tol = 0.0008158673348111326 Iteration 13: loglikelihood = -1434.0179556115856, backtracks = 2, tol = 0.0006363671566384205 Iteration 14: loglikelihood = -1433.8972844529703, backtracks = 2, tol = 0.021056460842673336 Iteration 15: loglikelihood = -1433.6170929347984, backtracks = 1, tol = 0.011448126839540959 Iteration 16: loglikelihood = -1433.5408744767517, backtracks = 2, tol = 0.0040324300639331045 Iteration 17: loglikelihood = -1433.4945867179188, backtracks = 2, tol = 0.003005268578298657 Iteration 18: loglikelihood = -1433.467626121943, backtracks = 2, tol = 0.002187229771831415 Iteration 19: loglikelihood = -1433.4521439235273, backtracks = 2, tol = 0.0016467936133078437 Iteration 20: loglikelihood = -1433.4432822302874, backtracks = 2, tol = 0.0012631945762950846 Iteration 21: loglikelihood = -1433.4382075829426, backtracks = 2, tol = 0.0009580287583338233 Iteration 22: loglikelihood = -1433.4352962137846, backtracks = 2, tol = 0.0007222437442123496 Iteration 23: loglikelihood = -1433.4336216439426, backtracks = 2, tol = 0.0005424739396431646 Iteration 24: loglikelihood = -1433.43265547142, backtracks = 2, tol = 0.0004062814588068666 Iteration 25: loglikelihood = -1433.4320960523787, backtracks = 2, tol = 0.00030341799187724174 Iteration 26: loglikelihood = -1433.4317709097872, backtracks = 2, tol = 0.00022583740291083832 Iteration 27: loglikelihood = -1433.4315812027676, backtracks = 2, tol = 0.0001673653861249394 Iteration 28: loglikelihood = -1432.5898379532828, backtracks = 2, tol = 0.0250802150540324 Iteration 29: loglikelihood = -1431.7678006470733, backtracks = 1, tol = 0.017181190475547 Iteration 30: loglikelihood = -1430.3157393955933, backtracks = 1, tol = 0.07333968264200223 Iteration 31: loglikelihood = -1429.706868513855, backtracks = 0, tol = 0.02001511172794573 Iteration 32: loglikelihood = -1429.5802551945537, backtracks = 1, tol = 0.00756937670420323 Iteration 33: loglikelihood = -1429.513945055356, backtracks = 2, tol = 0.003906515984506249 Iteration 34: loglikelihood = -1429.469197232521, backtracks = 2, tol = 0.003683664863256532 Iteration 35: loglikelihood = -1428.86075262229, backtracks = 2, tol = 0.08711763846658718 Iteration 36: loglikelihood = -1428.6178427111051, backtracks = 1, tol = 0.006558345246943248 Iteration 37: loglikelihood = -1428.5424083746184, backtracks = 2, tol = 0.0033912200662443866 Iteration 38: loglikelihood = -1428.4933608487952, backtracks = 2, tol = 0.0030098214824111564 Iteration 39: loglikelihood = -1428.4620745885084, backtracks = 2, tol = 0.002595137111913267 Iteration 40: loglikelihood = -1428.4427329028306, backtracks = 2, tol = 0.002148184701148499 Iteration 41: loglikelihood = -1428.4311433050725, backtracks = 2, tol = 0.0017160493175770867 Iteration 42: loglikelihood = -1428.4243474878394, backtracks = 2, tol = 0.0013407892924840858 Iteration 43: loglikelihood = -1428.420413936832, backtracks = 2, tol = 0.0010343694042998762 Iteration 44: loglikelihood = -1428.4181556141764, backtracks = 2, tol = 0.0007948565534422845 Iteration 45: loglikelihood = -1428.4168664091337, backtracks = 2, tol = 0.000608309643427293 Iteration 46: loglikelihood = -1428.4161334920516, backtracks = 2, tol = 0.0004622621654004415 Iteration 47: loglikelihood = -1428.4157180925672, backtracks = 2, tol = 0.00034956951660976293 Iteration 48: loglikelihood = -1428.4154831711999, backtracks = 2, tol = 0.00026348047442121094 Iteration 49: loglikelihood = -1428.415350523391, backtracks = 2, tol = 0.00019816133989405092 Iteration 50: loglikelihood = -1428.4152757065372, backtracks = 2, tol = 0.00014882628973649723 Iteration 51: loglikelihood = -1428.4152335404317, backtracks = 2, tol = 0.00011167501044822909 Iteration 52: loglikelihood = -1428.4152097888611, backtracks = 2, tol = 8.375238803842589e-5 Test Summary: | Pass Total Time Correlated predictors and double sparsity Float64 matrix | 2 2 9.2s **** 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 = -1519.81328517319, backtracks = 0, tol = 0.21378296456440468 Iteration 2: loglikelihood = -1454.0125836730288, backtracks = 0, tol = 0.10259310249769055 Iteration 3: loglikelihood = -1390.6819375171506, backtracks = 0, tol = 0.12249025556453846 Iteration 4: loglikelihood = -1364.6280327582701, backtracks = 0, tol = 0.08926300309389562 Iteration 5: loglikelihood = -1359.7321951223203, backtracks = 0, tol = 0.08050858505070209 Iteration 6: loglikelihood = -1357.9030470886373, backtracks = 0, tol = 0.02069306749288666 Iteration 7: loglikelihood = -1357.5165554257646, backtracks = 1, tol = 0.006789373978610176 Iteration 8: loglikelihood = -1356.1727133538789, backtracks = 1, tol = 0.06547916930008174 Iteration 9: loglikelihood = -1355.8774483337106, backtracks = 0, tol = 0.00753659113415703 Iteration 10: loglikelihood = -1355.7891439289194, backtracks = 0, tol = 0.006934869208082046 Iteration 11: loglikelihood = -1355.7547178525517, backtracks = 0, tol = 0.002291071755131109 Iteration 12: loglikelihood = -1355.740076123157, backtracks = 0, tol = 0.002908147745287474 Iteration 13: loglikelihood = -1355.7336812509163, backtracks = 0, tol = 0.0009535872543355612 Iteration 14: loglikelihood = -1355.7308757159701, backtracks = 0, tol = 0.0012645915442599765 Iteration 15: loglikelihood = -1355.729637821948, backtracks = 0, tol = 0.00041543159234517363 Iteration 16: loglikelihood = -1355.7290917242037, backtracks = 0, tol = 0.0005551627653542384 Iteration 17: loglikelihood = -1355.7288503121792, backtracks = 0, tol = 0.00018286818946934024 Iteration 18: loglikelihood = -1355.7287436322267, backtracks = 0, tol = 0.00024452501402465437 Iteration 19: loglikelihood = -1355.7286964483012, backtracks = 0, tol = 8.080268751573141e-5 0.994511 seconds (1.70 M allocations: 36.712 MiB, 11.19% gc time, 61.02% 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 = -1549.4438957411348, backtracks = 0, tol = 0.21378296456440468 Iteration 2: loglikelihood = -1501.9136656734097, backtracks = 0, tol = 0.1145107663888247 Iteration 3: loglikelihood = -1461.259502171479, backtracks = 0, tol = 0.14840370258233082 Iteration 4: loglikelihood = -1438.9547594851117, backtracks = 0, tol = 0.09185007857728807 Iteration 5: loglikelihood = -1425.7437225593662, backtracks = 0, tol = 0.08930112150569652 Iteration 6: loglikelihood = -1416.1487739165966, backtracks = 0, tol = 0.07237950813611656 Iteration 7: loglikelihood = -1408.5558827563523, backtracks = 0, tol = 0.009267074568084675 Iteration 8: loglikelihood = -1401.7822917356364, backtracks = 0, tol = 0.07606603071069248 Iteration 9: loglikelihood = -1396.462418228166, backtracks = 0, tol = 0.005010615424153374 Iteration 10: loglikelihood = -1392.2638316478567, backtracks = 0, tol = 0.0021056959353015895 Iteration 11: loglikelihood = -1388.6767874821708, backtracks = 0, tol = 0.0007191878669662739 Iteration 12: loglikelihood = -1385.6324209918164, backtracks = 0, tol = 0.0004410692875867155 Iteration 13: loglikelihood = -1383.1398259805678, backtracks = 0, tol = 0.07575489896841262 Iteration 14: loglikelihood = -1380.899752467324, backtracks = 0, tol = 0.00609733243990014 Iteration 15: loglikelihood = -1378.8940003671867, backtracks = 0, tol = 0.003272655164218143 Iteration 16: loglikelihood = -1377.4583032950825, backtracks = 0, tol = 0.07333977413028984 Iteration 17: loglikelihood = -1375.5272040641348, backtracks = 0, tol = 0.005434551311160335 Iteration 18: loglikelihood = -1374.1168591840315, backtracks = 0, tol = 0.0030882961525628386 Iteration 19: loglikelihood = -1372.8316882065967, backtracks = 0, tol = 0.000852804253633774 Iteration 20: loglikelihood = -1371.713449760642, backtracks = 0, tol = 0.0008549388159243503 Iteration 21: loglikelihood = -1370.6935071748287, backtracks = 0, tol = 0.0003841754260027961 Iteration 22: loglikelihood = -1369.782551436594, backtracks = 0, tol = 0.0003116148096470475 Iteration 23: loglikelihood = -1369.175297858124, backtracks = 0, tol = 0.07300679389368958 Iteration 24: loglikelihood = -1368.3643122270473, backtracks = 0, tol = 0.006229455582045242 Iteration 25: loglikelihood = -1367.662095089504, backtracks = 0, tol = 0.0034435920090846793 Iteration 26: loglikelihood = -1367.0616160017378, backtracks = 0, tol = 0.0011599351068832268 Iteration 27: loglikelihood = -1366.4802121687487, backtracks = 0, tol = 0.0009802504990713006 Iteration 28: loglikelihood = -1365.953545553026, backtracks = 0, tol = 0.0003628317361463319 Iteration 29: loglikelihood = -1365.4567682170098, backtracks = 0, tol = 0.00036048320324423414 Iteration 30: loglikelihood = -1365.0009945799638, backtracks = 0, tol = 0.00017239589013787098 Iteration 31: loglikelihood = -1364.9147874772682, backtracks = 0, tol = 0.07761869031008987 Iteration 32: loglikelihood = -1364.087032770301, backtracks = 0, tol = 0.00638336890175218 Iteration 33: loglikelihood = -1363.682965687681, backtracks = 0, tol = 0.003826782276447738 Iteration 34: loglikelihood = -1363.300824037126, backtracks = 0, tol = 0.0009930671450134021 Iteration 35: loglikelihood = -1362.9744571423848, backtracks = 0, tol = 0.0011329838382553039 Iteration 36: loglikelihood = -1362.6614369040756, backtracks = 0, tol = 0.00031726012876162526 Iteration 37: loglikelihood = -1362.378283719694, backtracks = 0, tol = 0.0004145178921627323 Iteration 38: loglikelihood = -1362.109222139211, backtracks = 0, tol = 0.0001873026469038884 Iteration 39: loglikelihood = -1361.8605518025283, backtracks = 0, tol = 0.00016777862466863625 Iteration 40: loglikelihood = -1361.6247968140344, backtracks = 0, tol = 0.00014600436382885027 Iteration 41: loglikelihood = -1361.404865370546, backtracks = 0, tol = 0.0001019625173279293 Iteration 42: loglikelihood = -1360.9183280313541, backtracks = 1, tol = 6.0824110944061384e-5 0.399460 seconds (1.56 M allocations: 28.229 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 = -3773.084, backtracks = 0, tol = 0.08213695401489376 Iteration 2: loglikelihood = -3713.506, backtracks = 0, tol = 0.04622369290689827 Iteration 3: loglikelihood = -3689.6099, backtracks = 1, tol = 0.05658498986373856 Iteration 4: loglikelihood = -3684.8127, backtracks = 1, tol = 0.010996870864205036 Iteration 5: loglikelihood = -3682.9858, backtracks = 1, tol = 0.006708656731358647 Iteration 6: loglikelihood = -3682.4043, backtracks = 1, tol = 0.005030700780256702 Iteration 7: loglikelihood = -3682.2449, backtracks = 1, tol = 0.002780204560635184 Iteration 8: loglikelihood = -3682.2024, backtracks = 1, tol = 0.001468760844235563 Iteration 9: loglikelihood = -3682.1934, backtracks = 1, tol = 0.0007308217418685742 Iteration 10: loglikelihood = -3682.1914, backtracks = 1, tol = 0.0003749626938966544 Iteration 11: loglikelihood = -3682.1895, backtracks = 1, tol = 0.00018536953722184498 Iteration 12: loglikelihood = -3682.1965, backtracks = 3, tol = 2.3672155752711594e-5 21.435048 seconds (14.90 M allocations: 693.928 MiB, 1.21% gc time, 97.16% 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 = -3643.9841, backtracks = 0, tol = 0.08213695401489376 Iteration 2: loglikelihood = -3501.4521, backtracks = 0, tol = 0.047680480576524104 Iteration 3: loglikelihood = -3289.342, backtracks = 1, tol = 0.015361899652798125 Iteration 4: loglikelihood = -3043.339, backtracks = 1, tol = 0.007888848969828863 Iteration 5: loglikelihood = -2961.5012, backtracks = 0, tol = 0.0915558329945515 Iteration 6: loglikelihood = -2848.4102, backtracks = 0, tol = 0.12178414517191352 Iteration 7: loglikelihood = -2642.7668, backtracks = 0, tol = 0.09336627002996527 Iteration 8: loglikelihood = -2534.5083, backtracks = 0, tol = 0.08594178173553312 Iteration 9: loglikelihood = -2465.9727, backtracks = 0, tol = 0.10720630575726378 Iteration 10: loglikelihood = -2362.8435, backtracks = 0, tol = 0.1060900678665769 Iteration 11: loglikelihood = -2315.407, backtracks = 0, tol = 0.08958762136102179 Iteration 12: loglikelihood = -2266.7625, backtracks = 0, tol = 0.08893927518827305 Iteration 13: loglikelihood = -2244.7537, backtracks = 0, tol = 0.08656419843138523 Iteration 14: loglikelihood = -2229.5088, backtracks = 0, tol = 0.08463174873364723 Iteration 15: loglikelihood = -2229.4414, backtracks = 0, tol = 0.09145188191502211 Iteration 16: loglikelihood = -2218.6162, backtracks = 0, tol = 0.0952608589332661 Iteration 17: loglikelihood = -2218.255, backtracks = 0, tol = 0.0994849581056361 Iteration 18: loglikelihood = -2211.9343, backtracks = 0, tol = 0.10278330941169792 Iteration 19: loglikelihood = -2208.5671, backtracks = 1, tol = 0.01792419590240867 Iteration 20: loglikelihood = -2207.772, backtracks = 1, tol = 0.009890685158888069 Iteration 21: loglikelihood = -2207.5596, backtracks = 1, tol = 0.005439386939875873 Iteration 22: loglikelihood = -2207.5159, backtracks = 1, tol = 0.0029467005384184917 Iteration 23: loglikelihood = -2207.5037, backtracks = 2, tol = 0.0007842704706764892 Iteration 24: loglikelihood = -2207.4963, backtracks = 2, tol = 0.0005991313166146118 Iteration 25: loglikelihood = -2207.493, backtracks = 2, tol = 0.0004570191055330468 Iteration 26: loglikelihood = -2207.491, backtracks = 2, tol = 0.0003482183585120662 Iteration 27: loglikelihood = -2207.4905, backtracks = 2, tol = 0.0002650873574587175 Iteration 28: loglikelihood = -2207.4905, backtracks = 2, tol = 0.00020166525015473334 Iteration 29: loglikelihood = -2207.489, backtracks = 2, tol = 0.00015334164950843587 Iteration 30: loglikelihood = -2207.483, backtracks = 3, tol = 5.826689760503806e-5 0.377561 seconds (1.98 M allocations: 32.897 MiB, 11.03% gc time) Test Summary: | Pass Total Time Negative binomial nuisance parameter Float32 matrix | 12 12 25.8s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** ┌ Warning: accessing `Type.name` is deprecated without replacement. If for detection, use `Base.isType(x)`. │ caller = ProgressMeter.Progress(n::Int64, dt::Int64, desc::String, barlen::Nothing, color::Symbol, output::Base.PipeEndpoint; offset::Int64) at deprecated.jl:1 └ @ ProgressMeter ~/.julia/packages/ProgressMeter/N660J/src/deprecated.jl:1 Running sparse linear regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -2896.6116813943763, backtracks = 0, tol = 1.0257704354307224 Iteration 2: loglikelihood = -1753.4720992614753, backtracks = 0, tol = 0.2870682551290383 Iteration 3: loglikelihood = -1460.3823326395222, backtracks = 0, tol = 0.1059822007319242 Iteration 4: loglikelihood = -1438.5292259047123, backtracks = 0, tol = 0.028655431669451118 Iteration 5: loglikelihood = -1438.0856032112097, backtracks = 0, tol = 0.0034955373515602557 Iteration 6: loglikelihood = -1438.074435032946, backtracks = 0, tol = 0.0005882060650840543 Iteration 7: loglikelihood = -1438.0741395461055, backtracks = 0, tol = 8.427264473930937e-5 4.571426 seconds (956.65 k allocations: 129.065 MiB, 0.61% gc time, 92.13% compilation time) Test Summary: | Pass Total Time initialze beta | 1 1 4.9s 7.025321 seconds (4.01 M allocations: 82.751 MiB, 0.35% gc time, 1.06% compilation time) 4.835187 seconds (3.98 M allocations: 91.817 MiB, 0.42% gc time) 11.085515 seconds (20.65 M allocations: 454.873 MiB, 1.11% gc time, 20.40% compilation time: 51% of which was recompilation) 7.792634 seconds (20.19 M allocations: 434.834 MiB, 0.99% gc time) 31.467584 seconds (3.45 M allocations: 4.232 GiB, 7.18% gc time, 25.58% compilation time) 46.078488 seconds (84.77 k allocations: 183.946 MiB, 0.16% gc time) Test Summary: | Pass Total Time memory_efficient keyword | 7 7 2m06.0s Test Summary: | Pass Total Time update_support! | 10 10 0.8s 13.682 ms (89 allocations: 5.20 KiB) 4.154 μs (0 allocations: 0 bytes) 91.479 μs (4 allocations: 288 bytes) 451.276 ns (0 allocations: 0 bytes) 31.819 μs (2 allocations: 64 bytes) 19.030 μs (0 allocations: 0 bytes) 3.801 μs (0 allocations: 0 bytes) 3.825 μs (0 allocations: 0 bytes) 59.790 μs (0 allocations: 0 bytes) 35.795 ms (89 allocations: 5.20 KiB) 17.820 μs (0 allocations: 0 bytes) 131.019 μs (4 allocations: 288 bytes) 2.693 μs (0 allocations: 0 bytes) 138.238 μs (2 allocations: 64 bytes) 39.480 μs (0 allocations: 0 bytes) 22.259 μs (0 allocations: 0 bytes) 22.420 μs (0 allocations: 0 bytes) 159.829 μs (0 allocations: 0 bytes) Test Summary: | Total Time benchmarks for multivariate function | 0 1m57.3s **** 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 **** **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse Multivariate Gaussian regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 12 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -2900.918630019449, backtracks = 0, tol = 0.14802242082004138 Iteration 2: loglikelihood = -2869.406464695619, backtracks = 0, tol = 0.03512679046077988 Iteration 3: loglikelihood = -2868.084702693443, backtracks = 0, tol = 0.005569349616332472 Iteration 4: loglikelihood = -2868.034423817725, backtracks = 0, tol = 0.0011189517628951667 Iteration 5: loglikelihood = -2868.0308576353746, backtracks = 0, tol = 0.00031182601179140966 Iteration 6: loglikelihood = -2868.0305288614227, backtracks = 0, tol = 0.00010393305949948345 Iteration 7: loglikelihood = -2868.0304966516946, backtracks = 0, tol = 3.100862049858006e-5 0.483895 seconds (46.08 k allocations: 5.433 MiB, 67.75% compilation time) Test Summary: | Pass Total Time multivariate fit_iht SnpLinAlg | 7 7 13.4s **** 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 1.551303 seconds (235.79 k allocations: 166.105 MiB, 62.96% compilation time) Test Summary: | Pass Total Time initialze beta | 5 5 1.9s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** ┌ Warning: accessing `Type.name` is deprecated without replacement. If for detection, use `Base.isType(x)`. │ caller = ProgressMeter.Progress(n::Int64, desc::String, offset::Int64; kwargs::Base.Pairs{Symbol, Union{}, Nothing, @NamedTuple{}}) at deprecated.jl:5 └ @ ProgressMeter ~/.julia/packages/ProgressMeter/N660J/src/deprecated.jl:5 Cross validating... 3%|█ | ETA: 0:03:20 Cross validating... 10%|███ | ETA: 0:01:10 Cross validating... 11%|███▌ | ETA: 0:01:00 Cross validating... 13%|████▏ | ETA: 0:00:53 Cross validating... 14%|████▋ | ETA: 0:00:47 Cross validating... 16%|█████▏ | ETA: 0:00:42 Cross validating... 17%|█████▋ | ETA: 0:00:39 Cross validating... 19%|██████▏ | ETA: 0:00:36 Cross validating... 21%|██████▋ | ETA: 0:00:33 Cross validating... 22%|███████▏ | ETA: 0:00:31 Cross validating... 24%|███████▋ | ETA: 0:00:29 Cross validating... 25%|████████▏ | ETA: 0:00:27 Cross validating... 27%|████████▋ | ETA: 0:00:25 Cross validating... 30%|█████████▋ | ETA: 0:00:22 Cross validating... 32%|██████████▏ | ETA: 0:00:21 Cross validating... 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81%|█████████████████████████▉ | ETA: 0:00:03 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:02 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:02 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:01 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:01 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:13 Crossvalidation Results: k MSE 0 6011.379324554545 1 3154.067015861416 2 1897.5940504307448 3 1426.089631265701 4 1102.7325540617212 5 867.8102868083156 6 673.156165715801 7 448.27478166934793 8 358.19571591572776 9 360.74694380488484 10 362.10102210921775 11 363.79757803246605 12 362.49113868128313 13 366.49942771731867 14 368.21350350236344 15 389.81812437476117 16 388.03749902202526 17 375.2130212702149 18 385.91099940265167 19 404.8131324106996 20 423.2923825958982 Best k = 8 13.688732 seconds (11.67 M allocations: 311.212 MiB, 1.33% gc time, 49.64% 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... 43%|█████████████▊ | ETA: 0:00:02 Cross validating... 46%|██████████████▊ | ETA: 0:00:02 Cross validating... 49%|███████████████▊ | ETA: 0:00:02 Cross validating... 51%|████████████████▎ | ETA: 0:00:02 Cross validating... 54%|█████████████████▎ | ETA: 0:00:02 Cross validating... 56%|█████████████████▊ | ETA: 0:00:02 Cross validating... 57%|██████████████████▎ | ETA: 0:00:02 Cross validating... 59%|██████████████████▊ | ETA: 0:00:02 Cross validating... 60%|███████████████████▎ | ETA: 0:00:02 Cross validating... 62%|███████████████████▊ | ETA: 0:00:02 Cross validating... 63%|████████████████████▍ | ETA: 0:00:02 Cross validating... 65%|████████████████████▉ | 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... 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... 89%|████████████████████████████▌ | ETA: 0:00:01 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:01 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:00 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:00 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:06 Crossvalidation Results: k MSE 0 6011.379324554545 1 3160.3478092832192 2 1913.9692190600153 3 1455.1983759753361 4 1120.8138959740052 5 885.6804191781914 6 687.4705523388391 7 457.1519193350292 8 367.47915691091725 9 371.4176641484901 10 373.67925079563065 11 381.16397816905976 12 390.77352877268953 13 394.0614656262738 14 390.65129967126563 15 410.63287802389294 16 399.51309010671184 17 423.50581301975205 18 427.26970758657535 19 427.165145247194 20 448.3215850662957 Best k = 8 6.922158 seconds (10.73 M allocations: 226.411 MiB, 0.75% gc time, 0.80% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, normal model | 3 3 21.8s **** 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: 0:05:27 Cross validating... 8%|██▌ | ETA: 0:02:06 Cross validating... 14%|████▋ | ETA: 0:01:06 Cross validating... 17%|█████▋ | ETA: 0:00:53 Cross validating... 21%|██████▋ | ETA: 0:00:44 Cross validating... 22%|███████▏ | ETA: 0:00:40 Cross validating... 24%|███████▋ | ETA: 0:00:37 Cross validating... 29%|█████████▏ | ETA: 0:00:30 Cross validating... 33%|██████████▋ | ETA: 0:00:24 Cross validating... 40%|████████████▊ | ETA: 0:00:18 Cross validating... 46%|██████████████▊ | ETA: 0:00:14 Cross validating... 52%|████████████████▊ | ETA: 0:00:11 Cross validating... 57%|██████████████████▎ | ETA: 0:00:09 Cross validating... 62%|███████████████████▊ | ETA: 0:00:08 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:06 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:05 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:03 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:02 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:01 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:13 Crossvalidation Results: k MSE 0 1544.0529052734375 1 1239.913590942383 2 957.7792881469727 3 805.6280180664063 4 598.6312597045899 5 485.24149707031256 6 399.78798672485357 7 355.9213971862793 8 342.2218901977539 9 320.63990716552735 10 323.9029462890625 11 324.7440964965821 12 327.66069833374024 13 331.73056167602545 14 333.83265130615234 15 336.81647332763674 16 334.4730061645508 17 347.438958190918 18 353.3963372497559 19 358.30821801757816 20 371.10644790649417 Best k = 9 14.840352 seconds (12.81 M allocations: 329.004 MiB, 0.85% gc time, 79.71% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:04 Cross validating... 8%|██▌ | ETA: 0:00:03 Cross validating... 14%|████▋ | ETA: 0:00:02 Cross validating... 21%|██████▋ | ETA: 0:00:02 Cross validating... 25%|████████▏ | ETA: 0:00:02 Cross validating... 30%|█████████▋ | ETA: 0:00:02 Cross validating... 35%|███████████▏ | ETA: 0:00:02 Cross validating... 43%|█████████████▊ | ETA: 0:00:01 Cross validating... 49%|███████████████▊ | ETA: 0:00:01 Cross validating... 56%|█████████████████▊ | ETA: 0:00:01 Cross validating... 60%|███████████████████▎ | ETA: 0:00:01 Cross validating... 63%|████████████████████▍ | ETA: 0:00:01 Cross validating... 68%|█████████████████████▉ | ETA: 0:00:01 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:01 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:00 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:00 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:02 Crossvalidation Results: k MSE 0 1544.0529052734375 1 1239.913590942383 2 957.7792881469727 3 809.5669071044922 4 601.0986207275391 5 485.5889067687989 6 400.4566880493164 7 358.4832772216797 8 344.2510969543457 9 323.07897689819333 10 330.8042514648438 11 334.9042581176758 12 341.28528192138674 13 354.3492573852539 14 359.81172869873046 15 367.7408224487305 16 365.1044697265625 17 378.7296849975586 18 391.0007423706055 19 391.6685395202637 20 395.81488760375976 Best k = 9 2.552783 seconds (10.51 M allocations: 193.418 MiB, 2.18% gc time, 5.74% compilation time) Test Summary: | Pass Total Time Cross validation on Float32 matrix, normal model | 2 2 19.5s **** 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: 0:00:40 Cross validating... 5%|█▌ | ETA: 0:00:28 Cross validating... 8%|██▌ | ETA: 0:00:18 Cross validating... 11%|███▌ | ETA: 0:00:14 Cross validating... 14%|████▋ | ETA: 0:00:12 Cross validating... 16%|█████▏ | ETA: 0:00:11 Cross validating... 17%|█████▋ | ETA: 0:00:11 Cross validating... 19%|██████▏ | ETA: 0:00:10 Cross validating... 21%|██████▋ | ETA: 0:00:10 Cross validating... 22%|███████▏ | ETA: 0:00:09 Cross validating... 24%|███████▋ | ETA: 0:00:09 Cross 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62%|███████████████████▊ | ETA: 0:00:04 Cross validating... 65%|████████████████████▉ | ETA: 0:00:03 Cross validating... 68%|█████████████████████▉ | ETA: 0:00:03 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:03 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:03 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:02 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:02 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:02 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:02 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: 0:00:08 Crossvalidation Results: k MSE 0 462.33779326824276 1 340.8114978583461 2 277.79339874033224 3 247.09705771644693 4 232.9934673370519 5 207.86831500713677 6 187.83199632570128 7 167.66679531313707 8 160.40926841114535 9 160.38574407686735 10 161.6296826643807 11 175.72398235947796 12 184.71040943292638 13 173.54472779926226 14 173.69525757034805 15 180.16908347046396 16 175.67918043552814 17 207.69636715401128 18 189.3336136989393 19 207.72065989694968 20 226.8620871570435 Best k = 9 9.223359 seconds (17.39 M allocations: 406.067 MiB, 1.70% gc time, 21.42% 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... 8%|██▌ | ETA: 0:00:05 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: 0:00:04 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... 54%|█████████████████▎ | ETA: 0:00:02 Cross validating... 56%|█████████████████▊ | ETA: 0:00:02 Cross validating... 59%|██████████████████▊ | ETA: 0:00:02 Cross validating... 60%|███████████████████▎ | ETA: 0:00:02 Cross validating... 62%|███████████████████▊ | ETA: 0:00:02 Cross validating... 65%|████████████████████▉ | ETA: 0:00:02 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:02 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:02 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:02 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:02 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 0 462.33779326824276 1 342.9307385066081 2 280.5249274288269 3 249.11372172239732 4 236.32179231726485 5 216.6989189598255 6 194.28152193414675 7 173.9633650183211 8 170.9118111489164 9 167.87082721144884 10 175.459819274624 11 184.48985715478796 12 187.0740336339469 13 182.82403496579855 14 198.47729882381023 15 209.86195379300432 16 200.3259637884507 17 213.53447276388042 18 217.39281061696033 19 219.91725834367918 20 239.13610707283027 Best k = 9 5.993552 seconds (18.28 M allocations: 382.542 MiB, 1.92% gc time, 1.08% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, logistic model | 2 2 15.5s **** 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: 0:00:36 Cross validating... 8%|██▌ | ETA: 0:00:15 Cross validating... 11%|███▌ | ETA: 0:00:12 Cross validating... 16%|█████▏ | ETA: 0:00:09 Cross validating... 19%|██████▏ | ETA: 0:00:08 Cross validating... 21%|██████▋ | ETA: 0:00:08 Cross validating... 22%|███████▏ | ETA: 0:00:07 Cross validating... 25%|████████▏ | ETA: 0:00:07 Cross validating... 29%|█████████▏ | ETA: 0:00:06 Cross validating... 32%|██████████▏ | ETA: 0:00:05 Cross validating... 37%|███████████▋ | ETA: 0:00:05 Cross validating... 40%|████████████▊ | ETA: 0:00:04 Cross validating... 44%|██████████████▎ | ETA: 0:00:04 Cross validating... 48%|███████████████▎ | ETA: 0:00:03 Cross validating... 51%|████████████████▎ | ETA: 0:00:03 Cross validating... 52%|████████████████▊ | ETA: 0:00:03 Cross validating... 56%|█████████████████▊ | ETA: 0:00:03 Cross validating... 59%|██████████████████▊ | ETA: 0:00:03 Cross validating... 62%|███████████████████▊ | ETA: 0:00:02 Cross validating... 65%|████████████████████▉ | ETA: 0:00:02 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:02 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:02 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 0 465.1302796091852 1 431.15609360985945 2 402.3995488515509 3 363.8149470907571 4 341.73888031758713 5 320.91384941275453 6 318.6088036947327 7 312.77655035236023 8 314.5918287530929 9 320.8140754579217 10 319.4076704157532 11 330.79585849623845 12 319.5464666621462 13 332.44389015681054 14 325.88303591953843 15 356.09575048847444 16 334.03508808141936 17 360.93924479719055 18 331.9654530662413 19 377.3829072277084 20 328.7987258042558 Best k = 7 6.486973 seconds (16.64 M allocations: 399.896 MiB, 1.67% gc time, 35.23% 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: 0:00:02 Cross validating... 41%|█████████████▎ | ETA: 0:00:02 Cross validating... 44%|██████████████▎ | ETA: 0:00:02 Cross validating... 48%|███████████████▎ | ETA: 0:00:02 Cross validating... 51%|████████████████▎ | ETA: 0:00:02 Cross validating... 54%|█████████████████▎ | ETA: 0:00:02 Cross validating... 57%|██████████████████▎ | ETA: 0:00:02 Cross validating... 60%|███████████████████▎ | ETA: 0:00:02 Cross validating... 63%|████████████████████▍ | ETA: 0:00:01 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:01 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:01 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:01 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:01 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:01 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:01 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:01 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:00 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:00 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:03 Crossvalidation Results: k MSE 0 465.1302796091852 1 431.36352937214883 2 403.2710735782731 3 365.03361775005163 4 343.2354991334353 5 322.62933378366614 6 324.8631067861574 7 322.0112774566577 8 327.07251664156604 9 344.99218676117414 10 351.5931349945958 11 363.8998782159613 12 347.0456250625126 13 355.1627691674946 14 379.46792742434496 15 381.858666673692 16 393.5000484333449 17 396.7540366011299 18 392.223459022627 19 389.8615271896409 20 408.59169097356425 Best k = 7 3.934539 seconds (17.35 M allocations: 356.433 MiB, 1.95% gc time, 1.01% compilation time) Test Summary: | Pass Total Time Cross validation on Float64 matrix, logistic model | 2 2 11.1s **** 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: 0:00:38 Cross validating... 6%|██ | ETA: 0:00:21 Cross validating... 10%|███ | ETA: 0:00:15 Cross validating... 13%|████▏ | ETA: 0:00:12 Cross validating... 16%|█████▏ | ETA: 0:00:10 Cross validating... 19%|██████▏ | ETA: 0:00:09 Cross validating... 22%|███████▏ | ETA: 0:00:08 Cross validating... 25%|████████▏ | ETA: 0:00:07 Cross validating... 29%|█████████▏ | ETA: 0:00:07 Cross validating... 32%|██████████▏ | ETA: 0:00:06 Cross validating... 33%|██████████▋ | ETA: 0:00:06 Cross validating... 37%|███████████▋ | ETA: 0:00:05 Cross validating... 40%|████████████▊ | ETA: 0:00:05 Cross validating... 43%|█████████████▊ | ETA: 0:00:04 Cross validating... 46%|██████████████▊ | ETA: 0:00:04 Cross validating... 49%|███████████████▊ | ETA: 0:00:04 Cross validating... 52%|████████████████▊ | ETA: 0:00:03 Cross validating... 56%|█████████████████▊ | ETA: 0:00:03 Cross validating... 59%|██████████████████▊ | ETA: 0:00:03 Cross validating... 62%|███████████████████▊ | ETA: 0:00:03 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: 0:00:02 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: 0:00:06 Crossvalidation Results: k MSE 0 1260.5105700576034 1 825.3346483431967 2 608.2615526538368 3 545.7014912026051 4 466.56934998088855 5 414.03922787632894 6 384.83632918681076 7 350.46741865635744 8 355.5496370845241 9 351.5790615636571 10 363.18903397687524 11 354.01933420961603 12 356.19757931389745 13 365.72099931270157 14 370.6476015681103 15 367.0775951591638 16 377.7153225358777 17 367.31515179136227 18 364.947007672386 19 383.2518805462751 20 382.90751407341736 Best k = 7 6.896801 seconds (15.36 M allocations: 363.229 MiB, 1.55% gc time, 25.02% 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... 14%|████▋ | 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... 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... 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... 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: 0:00:05 Crossvalidation Results: k MSE 0 1260.5105700576034 1 792.5685269808251 2 606.5220000714511 3 550.4408212243632 4 494.2867662733172 5 423.4438569112741 6 392.28237958963035 7 354.57561997254766 8 353.6239109638485 9 366.44310838708645 10 372.17202681751513 11 370.03300654387255 12 382.85495759651764 13 391.951483128537 14 399.68708864204433 15 410.8035503528647 16 415.0288964300022 17 416.68262556963475 18 415.1603367224063 19 424.0950042849306 20 446.29734685438814 Best k = 8 5.258565 seconds (14.24 M allocations: 287.005 MiB, 1.62% gc time, 0.56% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, Poisson model | 2 2 12.5s **** 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: 0:00:38 Cross validating... 6%|██ | ETA: 0:00:33 Cross validating... 8%|██▌ | ETA: 0:00:37 Cross validating... 10%|███ | ETA: 0:00:40 Cross validating... 11%|███▌ | ETA: 0:00:41 Cross validating... 13%|████▏ | ETA: 0:00:42 Cross validating... 14%|████▋ | ETA: 0:00:42 Cross validating... 16%|█████▏ | ETA: 0:00:42 Cross validating... 17%|█████▋ | ETA: 0:00:43 Cross validating... 19%|██████▏ | ETA: 0:00:42 Cross validating... 21%|██████▋ | ETA: 0:00:42 Cross validating... 22%|███████▏ | ETA: 0:00:42 Cross validating... 24%|███████▋ | ETA: 0:00:41 Cross validating... 25%|████████▏ | ETA: 0:00:41 Cross validating... 27%|████████▋ | ETA: 0:00:40 Cross validating... 29%|█████████▏ | ETA: 0:00:40 Cross validating... 30%|█████████▋ | ETA: 0:00:39 Cross validating... 32%|██████████▏ | ETA: 0:00:38 Cross validating... 33%|██████████▋ | ETA: 0:00:38 Cross validating... 37%|███████████▋ | ETA: 0:00:33 Cross validating... 38%|████████████▎ | ETA: 0:00:33 Cross validating... 40%|████████████▊ | ETA: 0:00:32 Cross validating... 41%|█████████████▎ | ETA: 0:00:31 Cross validating... 43%|█████████████▊ | ETA: 0:00:31 Cross validating... 44%|██████████████▎ | ETA: 0:00:30 Cross validating... 46%|██████████████▊ | ETA: 0:00:29 Cross validating... 48%|███████████████▎ | ETA: 0:00:29 Cross validating... 49%|███████████████▊ | ETA: 0:00:27 Cross validating... 51%|████████████████▎ | ETA: 0:00:25 Cross validating... 52%|████████████████▊ | ETA: 0:00:24 Cross validating... 54%|█████████████████▎ | ETA: 0:00:23 Cross validating... 56%|█████████████████▊ | ETA: 0:00:22 Cross validating... 57%|██████████████████▎ | ETA: 0:00:21 Cross validating... 59%|██████████████████▊ | ETA: 0:00:20 Cross validating... 60%|███████████████████▎ | ETA: 0:00:19 Cross validating... 62%|███████████████████▊ | ETA: 0:00:18 Cross validating... 63%|████████████████████▍ | ETA: 0:00:17 Cross validating... 65%|████████████████████▉ | ETA: 0:00:16 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:16 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:14 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:12 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:11 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:11 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:10 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:09 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:09 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:08 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:07 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:06 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:06 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:05 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:04 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:03 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:03 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:02 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:01 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:01 Cross validating... 100%|████████████████████████████████| Time: 0:00:42 Crossvalidation Results: k MSE 0 486.5547996494571 1 322.17094338269845 2 265.8197342746273 3 249.03705387222092 4 232.9397570767171 5 211.5174502544653 6 204.35581332875032 7 190.96047380882106 8 192.91410091331818 9 194.17083933706817 10 195.50474299895717 11 195.95114461189522 12 196.92956142392774 13 194.29902717631288 14 196.9997022921362 15 195.30228480494205 16 198.39882159229083 17 196.1831329654675 18 197.6957991798702 19 201.55728852927643 20 197.96535678821124 Best k = 7 42.864309 seconds (144.10 M allocations: 3.681 GiB, 1.39% gc time, 3.34% 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... 8%|██▌ | ETA: 0:00:05 Cross validating... 10%|███ | ETA: 0:00:06 Cross validating... 11%|███▌ | ETA: 0:00:06 Cross validating... 13%|████▏ | ETA: 0:00:06 Cross validating... 14%|████▋ | ETA: 0:00:06 Cross validating... 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79%|█████████████████████████▍ | ETA: 0:00:02 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: 0:00:01 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:01 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:01 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:01 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:01 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:01 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:11 Crossvalidation Results: k MSE 0 486.5547996494571 1 321.74509076558536 2 266.65871428681754 3 250.99059910868198 4 235.2854322532774 5 214.73159634453273 6 208.36536459563973 7 195.01838421524974 8 199.73377036833364 9 199.7423134497759 10 205.44106261304933 11 209.07087484310904 12 213.8268377240293 13 214.80550856472985 14 221.80136812146065 15 222.157967102339 16 223.9384613766062 17 223.99587877525715 18 228.68632146215765 19 242.28792503169694 20 229.23559844079477 Best k = 7 11.463547 seconds (35.47 M allocations: 734.822 MiB, 6.91% gc time, 0.76% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, NegativeBinomial model | 2 2 54.7s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:45 Cross validating... 6%|██ | ETA: 0:00:23 Cross validating... 10%|███ | ETA: 0:00:16 Cross validating... 14%|████▋ | ETA: 0:00:11 Cross validating... 17%|█████▋ | ETA: 0:00:09 Cross validating... 22%|███████▏ | ETA: 0:00:07 Cross validating... 24%|███████▋ | ETA: 0:00:07 Cross validating... 29%|█████████▏ | ETA: 0:00:06 Cross validating... 32%|██████████▏ | ETA: 0:00:05 Cross validating... 37%|███████████▋ | ETA: 0:00:05 Cross validating... 40%|████████████▊ | ETA: 0:00:04 Cross validating... 43%|█████████████▊ | ETA: 0:00:04 Cross validating... 48%|███████████████▎ | ETA: 0:00:03 Cross validating... 52%|████████████████▊ | ETA: 0:00:03 Cross validating... 56%|█████████████████▊ | ETA: 0:00:03 Cross validating... 59%|██████████████████▊ | ETA: 0:00:02 Cross validating... 62%|███████████████████▊ | ETA: 0:00:02 Cross validating... 65%|████████████████████▉ | ETA: 0:00:02 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:02 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:01 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:01 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:01 Cross validating... 86%|███████████████████████████▍ | 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 0 708.7406597900391 1 594.0547950439453 2 472.60887115478516 3 391.07051165771486 4 322.2429605712891 5 274.1304553527832 6 242.98796069335935 7 231.75397763061522 8 211.04413333129884 9 208.82878451538085 10 210.9139321594238 11 206.8662128601074 12 209.29315435791017 13 216.44690969848637 14 210.83974066162108 15 223.69269552612303 16 223.5122525024414 17 217.3672544555664 18 230.29235778808595 19 245.48900619506838 20 214.24631561279296 Best k = 11 5.189664 seconds (17.23 M allocations: 344.251 MiB, 2.49% gc time, 37.51% 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... 10%|███ | ETA: 0:00:02 Cross validating... 14%|████▋ | 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... 32%|██████████▏ | ETA: 0:00:02 Cross validating... 37%|███████████▋ | ETA: 0:00:02 Cross validating... 41%|█████████████▎ | ETA: 0:00:02 Cross validating... 46%|██████████████▊ | ETA: 0:00:02 Cross validating... 51%|████████████████▎ | ETA: 0:00:01 Cross validating... 56%|█████████████████▊ | ETA: 0:00:01 Cross validating... 60%|███████████████████▎ | ETA: 0:00:01 Cross validating... 63%|████████████████████▍ | ETA: 0:00:01 Cross validating... 68%|█████████████████████▉ | ETA: 0:00:01 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:01 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:01 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:01 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:00 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:00 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:02 Crossvalidation Results: k MSE 0 708.7406597900391 1 575.6241903076173 2 458.4867525024414 3 380.67050573730467 4 317.43561486816407 5 274.8225385131836 6 243.94065100097657 7 233.23877688598634 8 212.74209445190428 9 214.86823376464844 10 213.80905279541014 11 216.52949041748047 12 220.7860779724121 13 222.78791012573242 14 231.40656030273436 15 233.06280703735348 16 243.6403890075684 17 242.80908297729493 18 238.556499420166 19 251.23290313720705 20 244.79654568481442 Best k = 8 2.984118 seconds (16.27 M allocations: 288.799 MiB, 2.20% gc time, 1.37% compilation time) Test Summary: | Pass Total Time Cross validation on floating point matrices, NegativeBinomial model | 2 2 8.6s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 2%|▋ | ETA: 0:01:06 Cross validating... 3%|█ | ETA: 0:00:47 Cross validating... 4%|█▎ | ETA: 0:00:37 Cross validating... 5%|█▋ | ETA: 0:00:31 Cross validating... 6%|█▉ | ETA: 0:00:28 Cross validating... 7%|██▎ | ETA: 0:00:25 Cross validating... 8%|██▌ | ETA: 0:00:23 Cross validating... 9%|██▉ | ETA: 0:00:21 Cross validating... 10%|███▎ | ETA: 0:00:20 Cross validating... 11%|███▌ | ETA: 0:00:19 Cross validating... 12%|███▉ | ETA: 0:00:18 Cross 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87%|███████████████████████████▉ | ETA: 0:00:02 Cross validating... 88%|████████████████████████████▏ | ETA: 0:00:02 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:02 Cross validating... 90%|████████████████████████████▊ | ETA: 0:00:01 Cross validating... 91%|█████████████████████████████▏ | ETA: 0:00:01 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:01 Cross validating... 93%|█████████████████████████████▊ | ETA: 0:00:01 Cross validating... 94%|██████████████████████████████▏ | ETA: 0:00:01 Cross validating... 95%|██████████████████████████████▍ | ETA: 0:00:01 Cross validating... 96%|██████████████████████████████▊ | ETA: 0:00:01 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▍| ETA: 0:00:00 Cross validating... 99%|███████████████████████████████▋| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:15 Crossvalidation Results: k MSE 1 3821.786812425349 2 3414.6471849095974 3 3130.8489281229326 4 3002.552535316641 5 2792.429449979641 6 2622.8531774496755 7 2552.0543645305097 8 2537.4790267061153 9 2553.0543736836134 10 2561.095402427057 11 2567.5463306726265 12 2546.840620708477 13 2586.781036834275 14 2595.152687654449 15 2613.256248910856 16 2605.045715710481 17 2631.5581419349355 18 2659.578771814199 19 2666.744648758519 20 2707.406128362077 Best k = 8 15.422338 seconds (314.33 k allocations: 198.116 MiB, 0.69% gc time, 8.61% compilation time) Test Summary: | Pass Total Time multivariate cross validation SnpLinAlg | 3 3 19.7s Test Summary: | Pass Total Time wrapper univariate | 20 20 1m33.4s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 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: 0:00:15 Cross validating... 14%|████▌ | ETA: 0:00:16 Cross validating... 15%|████▊ | ETA: 0:00:16 Cross validating... 16%|█████▏ | ETA: 0:00:17 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: 0:00:18 Cross validating... 21%|██████▊ | ETA: 0:00:17 Cross validating... 22%|███████ | ETA: 0:00:17 Cross validating... 23%|███████▍ | ETA: 0:00:16 Cross validating... 24%|███████▋ | ETA: 0:00:16 Cross validating... 25%|████████ | ETA: 0:00:15 Cross 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78%|█████████████████████████ | ETA: 0:00:05 Cross validating... 79%|█████████████████████████▎ | ETA: 0:00:05 Cross validating... 80%|█████████████████████████▋ | ETA: 0:00:05 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:04 Cross validating... 82%|██████████████████████████▎ | ETA: 0:00:04 Cross validating... 83%|██████████████████████████▌ | ETA: 0:00:04 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:04 Cross validating... 85%|███████████████████████████▎ | ETA: 0:00:03 Cross validating... 86%|███████████████████████████▌ | ETA: 0:00:03 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:03 Cross validating... 88%|████████████████████████████▏ | ETA: 0:00:03 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:02 Cross validating... 90%|████████████████████████████▊ | ETA: 0:00:02 Cross validating... 91%|█████████████████████████████▏ | ETA: 0:00:02 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:02 Cross validating... 93%|█████████████████████████████▊ | ETA: 0:00:02 Cross validating... 94%|██████████████████████████████▏ | ETA: 0:00:01 Cross validating... 95%|██████████████████████████████▍ | ETA: 0:00:01 Cross validating... 96%|██████████████████████████████▊ | ETA: 0:00:01 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:01 Cross validating... 98%|███████████████████████████████▍| ETA: 0:00:00 Cross validating... 99%|███████████████████████████████▋| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:22 Crossvalidation Results: k MSE 1 2838.788679198002 2 2514.397342870813 3 2305.6176519676274 4 2222.025304867614 5 2075.167038458837 6 2067.794898972384 7 2053.427506114907 8 2086.405384830965 9 2080.984460901671 10 2105.1311995023634 11 2132.407165368786 12 2138.267187460652 13 2166.002210829576 14 2194.9918295115804 15 2189.890403738045 16 2191.1812932295775 17 2209.4669750564367 18 2221.2595493644303 19 2238.742594576326 20 2253.9559571797727 Best k = 7 **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 2%|▋ | ETA: 0:00:10 Cross validating... 3%|█ | ETA: 0:00:10 Cross validating... 4%|█▎ | ETA: 0:00:11 Cross validating... 5%|█▋ | ETA: 0:00:12 Cross validating... 6%|█▉ | ETA: 0:00:13 Cross validating... 7%|██▎ | ETA: 0:00:13 Cross validating... 8%|██▌ | ETA: 0:00:13 Cross validating... 9%|██▉ | ETA: 0:00:13 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: 0:00:15 Cross validating... 14%|████▌ | ETA: 0:00:16 Cross validating... 15%|████▊ | ETA: 0:00:16 Cross validating... 16%|█████▏ | ETA: 0:00:17 Cross validating... 17%|█████▌ | ETA: 0:00:17 Cross validating... 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88%|████████████████████████████▏ | ETA: 0:00:03 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:02 Cross validating... 90%|████████████████████████████▊ | ETA: 0:00:02 Cross validating... 91%|█████████████████████████████▏ | ETA: 0:00:02 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:02 Cross validating... 93%|█████████████████████████████▊ | ETA: 0:00:02 Cross validating... 94%|██████████████████████████████▏ | ETA: 0:00:01 Cross validating... 95%|██████████████████████████████▍ | ETA: 0:00:01 Cross validating... 96%|██████████████████████████████▊ | ETA: 0:00:01 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:01 Cross validating... 98%|███████████████████████████████▍| ETA: 0:00:00 Cross validating... 99%|███████████████████████████████▋| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:22 Crossvalidation Results: k MSE 1 2838.788679198002 2 2514.397342870813 3 2305.6176519676274 4 2222.025304867614 5 2075.167038458837 6 2067.794898972384 7 2053.427506114907 8 2086.405384830965 9 2080.984460901671 10 2105.1311995023634 11 2132.407165368786 12 2138.267187460652 13 2166.002210829576 14 2194.9918295115804 15 2189.890403738045 16 2191.1812932295775 17 2209.4669750564367 18 2221.2595493644303 19 2238.742594576326 20 2253.9559571797727 Best k = 7 **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 2%|▋ | ETA: 0:00:10 Cross validating... 3%|█ | ETA: 0:00:10 Cross validating... 4%|█▎ | ETA: 0:00:11 Cross validating... 5%|█▋ | ETA: 0:00:11 Cross validating... 6%|█▉ | ETA: 0:00:12 Cross validating... 7%|██▎ | ETA: 0:00:12 Cross validating... 8%|██▌ | ETA: 0:00:12 Cross validating... 9%|██▉ | ETA: 0:00:13 Cross validating... 10%|███▎ | ETA: 0:00:14 Cross 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83%|██████████████████████████▌ | ETA: 0:00:04 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:04 Cross validating... 85%|███████████████████████████▎ | ETA: 0:00:03 Cross validating... 86%|███████████████████████████▌ | ETA: 0:00:03 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:03 Cross validating... 88%|████████████████████████████▏ | ETA: 0:00:03 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:02 Cross validating... 90%|████████████████████████████▊ | ETA: 0:00:02 Cross validating... 91%|█████████████████████████████▏ | ETA: 0:00:02 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:02 Cross validating... 93%|█████████████████████████████▊ | ETA: 0:00:02 Cross validating... 94%|██████████████████████████████▏ | ETA: 0:00:01 Cross validating... 95%|██████████████████████████████▍ | ETA: 0:00:01 Cross validating... 96%|██████████████████████████████▊ | ETA: 0:00:01 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:01 Cross validating... 98%|███████████████████████████████▍| ETA: 0:00:00 Cross validating... 99%|███████████████████████████████▋| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:23 Crossvalidation Results: k MSE 1 2838.788679198002 2 2514.397342870813 3 2305.6176519676274 4 2222.025304867614 5 2075.167038458837 6 2067.794898972384 7 2053.427506114907 8 2086.405384830965 9 2080.984460901671 10 2105.1311995023634 11 2132.407165368786 12 2138.267187460652 13 2166.002210829576 14 2194.9918295115804 15 2189.890403738045 16 2191.1812932295775 17 2209.4669750564367 18 2221.2595493644303 19 2238.742594576326 20 2253.9559571797727 Best k = 7 Test Summary: | Pass Total Time wrapper multivariate | 8 8 1m23.5s 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/BjTS1/src/decompression.jl:199 [3] decompress(io::IOStream, v::Variant, h::BGEN.Header; decompressed::Nothing) @ BGEN ~/.julia/packages/BGEN/dfgRU/src/genotypes.jl:72 [4] first_allele_dosage!(b::Bgen, v::Variant; T::Core.TypeEgal{Float64}, mean_impute::Bool, clear_decompressed::Bool, data::Nothing, decompressed::Nothing, is_decompressed::Bool) @ BGEN ~/.julia/packages/BGEN/dfgRU/src/genotypes.jl:571 [5] convert_bgen_gt(t::Core.TypeEgal{Float64}, b::Bgen) @ MendelIHT ~/.julia/packages/MendelIHT/ZcxZT/src/wrapper.jl:380 [6] macro expansion @ ./timing.jl:741 [inlined] [7] macro expansion @ ~/.julia/packages/MendelIHT/ZcxZT/test/wrapper_test.jl:187 [inlined] [8] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:2247 [inlined] [9] top-level scope @ ~/.julia/packages/MendelIHT/ZcxZT/test/wrapper_test.jl:185 Test Summary: | Error Total Time read BGEN and VCF | 1 1 3.3s RNG of the outermost testset: Xoshiro(0xf0b011f99e2e6e9f, 0xe28788a41b51508b, 0x39a895d0b08bdb07, 0x4bf10a3543753cd5, 0xcc28e06e3b125136) 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 909.83s 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:3283 [3] test(ctx::Pkg.Types.Context, pkgs::Vector{PackageSpec}; coverage::Bool, test_fn::Nothing, julia_args::Cmd, test_args::Cmd, force_latest_compatible_version::Bool, allow_earlier_backwards_compatible_versions::Bool, allow_reresolve::Bool, kwargs::@Kwargs{io::IOContext{IO}}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:587 [4] test(pkgs::Vector{PackageSpec}; io::IOContext{IO}, kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:172 [5] test(pkgs::Vector{String}; kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:160 [6] test(pkg::String; kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:159 [inlined] [7] top-level scope @ /PkgEval.jl/scripts/evaluate.jl:223 in expression starting at /PkgEval.jl/scripts/evaluate.jl:214 PkgEval failed after 1196.98s: package tests unexpectedly errored