Package evaluation to test MendelIHT on Julia 1.14.0-DEV.2043 (b936235316*) started at 2026-04-17T03:39:43.893 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.14` Set-up completed after 14.83s ################################################################################ # Installation # Installing MendelIHT... Resolving package versions... Updating `~/.julia/environments/v1.14/Project.toml` [921c7187] + MendelIHT v1.4.11 Updating `~/.julia/environments/v1.14/Manifest.toml` [7d9f7c33] + Accessors v0.1.44 [79e6a3ab] + Adapt v4.5.2 [66dad0bd] + AliasTables v1.1.3 [4fba245c] + ArrayInterface v7.24.0 [67c07d97] + Automa v1.1.0 ⌅ [6db4b851] + BGEN v0.1.17 [28d598bf] + BGZFStreams v0.3.2 [47718e42] + BioGenerics v0.1.5 [62783981] + BitTwiddlingConvenienceFunctions v0.1.6 [e1450e63] + BufferedStreams v1.2.2 [2a0fbf3d] + CPUSummary v0.2.7 [336ed68f] + CSV v0.10.16 [fb6a15b2] + CloseOpenIntervals v0.1.13 [523fee87] + CodecBzip2 v0.8.5 [ba30903b] + CodecXz v0.7.4 [944b1d66] + CodecZlib v0.7.8 [6b39b394] + CodecZstd v0.8.7 [861a8166] + Combinatorics v1.1.0 [38540f10] + CommonSolve v0.2.6 [f70d9fcc] + CommonWorldInvalidations v1.0.0 [34da2185] + Compat v4.18.1 [a33af91c] + CompositionsBase v0.1.2 [187b0558] + ConstructionBase v1.6.0 [adafc99b] + CpuId v0.3.1 [a8cc5b0e] + Crayons v4.1.1 [a10d1c49] + DBInterface v2.6.1 [9a962f9c] + 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[bea87d4a] + SuiteSparse_jll v7.10.1+0 [83775a58] + Zlib_jll v1.3.2+0 [3161d3a3] + Zstd_jll v1.5.7+1 [8e850b90] + libblastrampoline_jll v5.15.0+0 [8e850ede] + nghttp2_jll v1.68.1+0 [3f19e933] + p7zip_jll v17.8.0+0 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. To see why use `status --outdated -m` Installation completed after 6.39s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompiling project... 4.9 s ✓ BGEN 7.6 s ✓ VCFTools 28.5 s ✓ SnpArrays WARNING: Constructor for type "MvNormal" was extended in `MendelIHT` without explicit qualification or import.  NOTE: Assumed "MvNormal" refers to `Distributions.MvNormal`. This behavior is deprecated and may differ in future versions.  NOTE: This behavior may have differed in Julia versions prior to 1.12.  Hint: If you intended to create a new generic function of the same name, use `function MvNormal end`.  Hint: To silence the warning, qualify `MvNormal` as `Distributions.MvNormal` in the method signature or explicitly `import Distributions: MvNormal`. 26.0 s ✓ MendelIHT 4 dependencies successfully precompiled in 72 seconds. 170 already precompiled. 1 dependency had output during precompilation: ┌ MendelIHT │ WARNING: Constructor for type "MvNormal" was extended in `MendelIHT` without explicit qualification or import. │ NOTE: Assumed "MvNormal" refers to `Distributions.MvNormal`. This behavior is deprecated and may differ in future versions. │ NOTE: This behavior may have differed in Julia versions prior to 1.12. │ Hint: If you intended to create a new generic function of the same name, use `function MvNormal end`. │ Hint: To silence the warning, qualify `MvNormal` as `Distributions.MvNormal` in the method signature or explicitly `import Distributions: MvNormal`. └ Precompilation completed after 95.91s ################################################################################ # Testing # Testing MendelIHT Status `/tmp/jl_a0ZNvV/Project.toml` ⌅ [6db4b851] BGEN v0.1.17 [6e4b80f9] BenchmarkTools v1.8.0 [336ed68f] CSV v0.10.16 [a93c6f00] DataFrames v1.8.2 [8bb1440f] DelimitedFiles v1.9.1 [b4f34e82] Distances v0.10.12 [31c24e10] Distributions v0.25.124 [38e38edf] GLM v1.9.3 [921c7187] MendelIHT v1.4.11 [92933f4c] ProgressMeter v1.11.0 [189a3867] Reexport v1.2.2 [4e780e97] SnpArrays v0.3.23 [276daf66] SpecialFunctions v2.7.2 [2913bbd2] StatsBase v0.34.10 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v1.68.1+0 [3f19e933] p7zip_jll v17.8.0+0 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. Testing Running tests... ┌ Warning: `MvNormal(σ::AbstractVector{<:Real})` is deprecated, use `MvNormal(LinearAlgebra.Diagonal(map(abs2, σ)))` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `cholesky!(A::RealHermSymComplexHerm{<:Real}, ::Val{true}; kwargs...)` is deprecated, use `cholesky!(A, RowMaximum(); kwargs...)` instead. │ caller = iht_stepsize!(v::MendelIHT.mIHTVariable{Float64, LinearAlgebra.Transpose{Float64, SnpArrays.SnpLinAlg{Float64}}}) at multivariate.jl:241 └ @ Core ~/.julia/packages/MendelIHT/ZcxZT/src/multivariate.jl:241 Test Summary: | Pass Total Time loglikelihood | 4 4 16.6s Test Summary: | Pass Total Time deviance | 1 1 0.4s Test Summary: | Pass Total Time update_μ! | 4 4 1.5s Test Summary: | Pass Total Time _choose! | 7 7 10.0s Test Summary: | Pass Total Time _iht_backtrack | 7 7 0.0s Test Summary: | Pass Total Time standardize! | 12 12 1.5s Test Summary: | Pass Total Time project_k! | 2 2 1.1s Test Summary: | Pass Total Time project_group_sparse! | 5 5 1.2s Test Summary: | Pass Total Time maf_weights | 6 6 2.1s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse linear regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1585.8177611589615, backtracks = 0, tol = 1.4442486598199764 Iteration 2: loglikelihood = -1427.689560377828, backtracks = 0, tol = 0.12875922724162786 Iteration 3: loglikelihood = -1415.6251867525532, backtracks = 0, tol = 0.055774459284637604 Iteration 4: loglikelihood = -1413.3981273097172, backtracks = 0, tol = 0.042089070504641835 Iteration 5: loglikelihood = -1413.2033183714257, backtracks = 0, tol = 0.04114283361147167 Iteration 6: loglikelihood = -1413.1366017207736, backtracks = 0, tol = 0.0024544243176808783 Iteration 7: loglikelihood = -1413.1355538787968, backtracks = 0, tol = 0.00028528309752155886 Iteration 8: loglikelihood = -1413.1355371500197, backtracks = 1, tol = 2.1174657043166315e-5 IHT estimated 10 nonzero SNP predictors and 1 non-genetic predictors. Compute time (sec): 0.07120513916015625 Final loglikelihood: -1413.1355371500197 SNP PVE: 0.8462361915344982 Iterations: 8 Selected genetic predictors: 10×2 DataFrame Row │ Position Estimated_β │ Int64 Float64 ─────┼─────────────────────── 1 │ 2884 -0.75205 2 │ 4438 0.537736 3 │ 4576 0.113462 4 │ 4766 0.230998 5 │ 5017 -0.514058 6 │ 6884 0.788244 7 │ 8237 0.325925 8 │ 8571 -0.969808 9 │ 9286 -1.68092 10 │ 9561 -0.220653 Selected nongenetic predictors: 1×2 DataFrame Row │ Position Estimated_β │ Int64 Float64 ─────┼─────────────────────── 1 │ 1 0.0270515Test Summary: | Pass Total Time fit normal SnpLinAlg | 4 4 23.8s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse logistic regression Number of threads = 1 Link functin = LogitLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -379.72375963518977, backtracks = 0, tol = 0.6062552017348442 Iteration 2: loglikelihood = -294.14222098196217, backtracks = 0, tol = 0.39035964909167 Iteration 3: loglikelihood = -258.44215825745147, backtracks = 0, tol = 0.18072720194601524 Iteration 4: loglikelihood = -248.39092317275637, backtracks = 1, tol = 0.0581811999889429 Iteration 5: loglikelihood = -241.2861695402178, backtracks = 2, tol = 0.10199490430383734 Iteration 6: loglikelihood = -236.0344401262056, backtracks = 2, tol = 0.10444957184614982 Iteration 7: loglikelihood = -232.75639772007577, backtracks = 2, tol = 0.03618239958756675 Iteration 8: loglikelihood = -230.9028935826695, backtracks = 3, tol = 0.022566251649321353 Iteration 9: loglikelihood = -229.2332883500926, backtracks = 3, tol = 0.02394599965909332 Iteration 10: loglikelihood = -227.8109863155336, backtracks = 3, tol = 0.02260237147851236 Iteration 11: loglikelihood = -226.61429831284372, backtracks = 3, tol = 0.02153016573221634 Iteration 12: loglikelihood = -225.614543213995, backtracks = 3, tol = 0.020073248773013197 Iteration 13: loglikelihood = -225.15228734295533, backtracks = 3, tol = 0.10266272165892033 Iteration 14: loglikelihood = -224.5524858306654, backtracks = 2, tol = 0.010910053499902256 Iteration 15: loglikelihood = -223.90430308527087, backtracks = 3, tol = 0.10669566586572145 Iteration 16: loglikelihood = -223.43342440058004, backtracks = 1, tol = 0.009912340440473734 Iteration 17: loglikelihood = -223.19474883510568, backtracks = 3, tol = 0.10429355504005154 Iteration 18: loglikelihood = -222.7530868660152, backtracks = 1, tol = 0.010133510239484585 Iteration 19: loglikelihood = -222.4546375562022, backtracks = 3, tol = 0.009382230171462355 Iteration 20: loglikelihood = -225.04961416047087, backtracks = 3, tol = 0.13141028198780508 Iteration 21: loglikelihood = -221.57583298738808, backtracks = 0, tol = 0.12983606150115481 Iteration 22: loglikelihood = -220.9953587123894, backtracks = 0, tol = 0.018278220962270587 Iteration 23: loglikelihood = -220.46528702030645, backtracks = 0, tol = 0.10912949798131547 Iteration 24: loglikelihood = -220.22939682199817, backtracks = 1, tol = 0.006133557493960293 Iteration 25: loglikelihood = -220.1149031779291, backtracks = 3, tol = 0.005637364497494655 Iteration 26: loglikelihood = -237.91408320706802, backtracks = 3, tol = 0.1311916630585333 Iteration 27: loglikelihood = -222.6667401701631, backtracks = 0, tol = 0.13008576394077564 Iteration 28: loglikelihood = -220.0179912284672, backtracks = 0, tol = 0.10981267805412102 Iteration 29: loglikelihood = -219.80873468505163, backtracks = 1, tol = 0.006242686572879014 Iteration 30: loglikelihood = -219.71412932030552, backtracks = 1, tol = 0.0052581541847830735 Iteration 31: loglikelihood = -219.67346582214395, backtracks = 3, tol = 0.002736072071808146 Iteration 32: loglikelihood = -236.63118723570068, backtracks = 3, tol = 0.12536959025201838 Iteration 33: loglikelihood = -222.42522446507616, backtracks = 0, tol = 0.12480632457239557 Iteration 34: loglikelihood = -219.76952387571325, backtracks = 0, tol = 0.10782393864869841 Iteration 35: loglikelihood = -219.54239052596037, backtracks = 0, tol = 0.010969385336776636 Iteration 36: loglikelihood = -219.51051719556185, backtracks = 0, tol = 0.0038143069815270263 Iteration 37: loglikelihood = -219.49562270628724, backtracks = 1, tol = 0.0015360028505860806 Iteration 38: loglikelihood = -222.2776344615594, backtracks = 3, tol = 0.10706948875570901 Iteration 39: loglikelihood = -219.86344247649652, backtracks = 0, tol = 0.10682440099239575 Iteration 40: loglikelihood = -219.50637292175287, backtracks = 0, tol = 0.010145149683589566 Iteration 41: loglikelihood = -219.45601478260392, backtracks = 0, tol = 0.004786594360325445 Iteration 42: loglikelihood = -219.44279315931445, backtracks = 0, tol = 0.0023300326568676676 Iteration 43: loglikelihood = -219.434262597912, backtracks = 0, tol = 0.002159682320412748 Iteration 44: loglikelihood = -219.42706752504972, backtracks = 0, tol = 0.0019986878272562235 Iteration 45: loglikelihood = -219.4208881668612, backtracks = 0, tol = 0.001781315196828412 Iteration 46: loglikelihood = -219.41556755717227, backtracks = 0, tol = 0.0017266268818688624 Iteration 47: loglikelihood = -219.41098445944962, backtracks = 0, tol = 0.001504993867218278 Iteration 48: loglikelihood = -219.4070309112888, backtracks = 0, tol = 0.001495426527055874 Iteration 49: loglikelihood = -219.40362030781677, backtracks = 0, tol = 0.001286324051089446 Iteration 50: loglikelihood = -219.4006747755802, backtracks = 0, tol = 0.001295957349435961 Iteration 51: loglikelihood = -219.39813103252988, backtracks = 0, tol = 0.0011058748112207813 Iteration 52: loglikelihood = -219.3959322024177, backtracks = 0, tol = 0.0011233728145861855 Iteration 53: loglikelihood = -219.39403166729804, backtracks = 0, tol = 0.0009536994758608786 Iteration 54: loglikelihood = -219.39238763268273, backtracks = 0, tol = 0.0009739180646352119 Iteration 55: loglikelihood = -219.39096560226784, backtracks = 0, tol = 0.0008239389039648708 Iteration 56: loglikelihood = -219.38973473800374, backtracks = 0, tol = 0.0008444580901064712 Iteration 57: loglikelihood = -219.3886694316569, backtracks = 0, tol = 0.0007126409505425607 Iteration 58: loglikelihood = -219.38774685610232, backtracks = 0, tol = 0.0007323063866727435 Iteration 59: loglikelihood = -219.3869479529937, backtracks = 0, tol = 0.00061686194275372 Iteration 60: loglikelihood = -219.3862557798823, backtracks = 0, tol = 0.0006351404346176769 Iteration 61: loglikelihood = -219.3856561234815, backtracks = 0, tol = 0.000534269842115572 Iteration 62: loglikelihood = -219.38513638040487, backtracks = 0, tol = 0.0005509480422217535 Iteration 63: loglikelihood = -219.38468593224545, backtracks = 0, tol = 0.0004629512780606966 Iteration 64: loglikelihood = -219.38429538513583, backtracks = 0, tol = 0.0004779860767529819 Iteration 65: loglikelihood = -219.38395679466737, backtracks = 0, tol = 0.0004013057505476397 Iteration 66: loglikelihood = -219.38366314739872, backtracks = 0, tol = 0.0004147454994836376 Iteration 67: loglikelihood = -219.38340849212824, backtracks = 0, tol = 0.00034797985178746597 Iteration 68: loglikelihood = -219.38318758502183, backtracks = 0, tol = 0.0003599207374415984 Iteration 69: loglikelihood = -219.38299596326374, backtracks = 0, tol = 0.0003018217223394219 Iteration 70: loglikelihood = -219.3828297011887, backtracks = 0, tol = 0.00031238270039476616 Iteration 71: loglikelihood = -219.38268544908368, backtracks = 0, tol = 0.00026184698528793125 Iteration 72: loglikelihood = -219.3825602648841, backtracks = 0, tol = 0.0002711550905775348 Iteration 73: loglikelihood = -219.38245163239276, backtracks = 0, tol = 0.00022721198022395564 Iteration 74: loglikelihood = -219.38235734460943, backtracks = 0, tol = 0.00023539371282360467 Iteration 75: loglikelihood = -219.38227551018164, backtracks = 0, tol = 0.0001971920991460162 Iteration 76: loglikelihood = -219.382204472153, backtracks = 0, tol = 0.00020436848993624394 Iteration 77: loglikelihood = -219.3821428080304, backtracks = 0, tol = 0.00017116393516432852 Iteration 78: loglikelihood = -219.38208927292968, backtracks = 0, tol = 0.00017744788492952903 Iteration 79: loglikelihood = -219.38204279645043, backtracks = 0, tol = 0.00014859040670150365 Iteration 80: loglikelihood = -219.38200244272016, backtracks = 0, tol = 0.00015408544066832546 Iteration 81: loglikelihood = -219.38196740593906, backtracks = 0, tol = 0.00012900826739905896 Iteration 82: loglikelihood = -219.38193698216227, backtracks = 0, tol = 0.00013380816660865064 Iteration 83: loglikelihood = -219.38191056455443, backtracks = 0, tol = 0.00011201756190578927 Iteration 84: loglikelihood = -219.3818876233726, backtracks = 0, tol = 0.000116206527337935 Iteration 85: loglikelihood = -219.38186770147453, backtracks = 0, tol = 9.727268703830643e-5 Test Summary: | Pass Total Time fit Bernoulli SnpLinAlg | 4 4 3.8s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse Poisson regression Number of threads = 1 Link functin = LogLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1346.6757466528434, backtracks = 0, tol = 0.20967802383359654 Iteration 2: loglikelihood = -1324.5940327067347, backtracks = 0, tol = 0.06315960959736804 Iteration 3: loglikelihood = -1315.7744255805105, backtracks = 1, tol = 0.08220641347257548 Iteration 4: loglikelihood = -1310.9685319878167, backtracks = 1, tol = 0.07100625121871013 Iteration 5: loglikelihood = -1310.0283365823577, backtracks = 2, tol = 0.011908323927885217 Iteration 6: loglikelihood = -1309.247877363674, backtracks = 2, tol = 0.014091891616389107 Iteration 7: loglikelihood = -1308.742949851054, backtracks = 2, tol = 0.012378106064823315 Iteration 8: loglikelihood = -1308.284045773678, backtracks = 2, tol = 0.05923339581679422 Iteration 9: loglikelihood = -1306.9434884181867, backtracks = 1, tol = 0.06490817117003317 Iteration 10: loglikelihood = -1306.6747602155458, backtracks = 0, tol = 0.006787120769292247 Iteration 11: loglikelihood = -1306.6285363288775, backtracks = 1, tol = 0.0023094379988941316 Iteration 12: loglikelihood = -1306.6010382757781, backtracks = 2, tol = 0.0024121474030182515 Iteration 13: loglikelihood = -1306.5788099270467, backtracks = 2, tol = 0.0026693793957082287 Iteration 14: loglikelihood = -1306.570901206303, backtracks = 3, tol = 0.0012197042935652986 Iteration 15: loglikelihood = -1306.5647049183315, backtracks = 3, tol = 0.0010917005585251596 Iteration 16: loglikelihood = -1306.559908508387, backtracks = 3, tol = 0.0009681860392853813 Iteration 17: loglikelihood = -1306.5562079507044, backtracks = 3, tol = 0.0008551726450191214 Iteration 18: loglikelihood = -1306.553358162137, backtracks = 3, tol = 0.0007534629971008929 Iteration 19: loglikelihood = -1306.5511660601633, backtracks = 3, tol = 0.0006628022240437354 Iteration 20: loglikelihood = -1306.5494811767371, backtracks = 3, tol = 0.0005824253143940892 Iteration 21: loglikelihood = -1306.5481869001503, backtracks = 3, tol = 0.0005113984141145331 Iteration 22: loglikelihood = -1306.5471931320862, backtracks = 3, tol = 0.00044876845465652765 Iteration 23: loglikelihood = -1306.5464303883157, backtracks = 3, tol = 0.00039362602820329663 Iteration 24: loglikelihood = -1306.5458451491033, backtracks = 3, tol = 0.00034513027835329524 Iteration 25: loglikelihood = -1306.5453962290378, backtracks = 3, tol = 0.0003025167771958288 Iteration 26: loglikelihood = -1306.5450519571841, backtracks = 3, tol = 0.00026509757200916903 Iteration 27: loglikelihood = -1306.544787993402, backtracks = 3, tol = 0.00023225759269183749 Iteration 28: loglikelihood = -1306.544585640721, backtracks = 3, tol = 0.00020344943307072134 Iteration 29: loglikelihood = -1306.544430543074, backtracks = 3, tol = 0.00017818752203820531 Iteration 30: loglikelihood = -1306.5443116814404, backtracks = 3, tol = 0.00015604221601944624 Iteration 31: loglikelihood = -1306.544220600858, backtracks = 3, tol = 0.00013663409407999372 Iteration 32: loglikelihood = -1306.54415081553, backtracks = 3, tol = 0.00011962860061386771 Iteration 33: loglikelihood = -1306.5440973514244, backtracks = 3, tol = 0.00010473110317209703 Iteration 34: loglikelihood = -1306.544056394681, backtracks = 3, tol = 9.168238805270864e-5 Test Summary: | Pass Total Time fit Poisson SnpLinAlg | 4 4 3.1s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse NegativeBinomial regression Number of threads = 1 Link functin = LogLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1445.5726911927993, backtracks = 0, tol = 0.19238657742210466 Iteration 2: loglikelihood = -1433.2867089872784, backtracks = 0, tol = 0.1329908219433721 Iteration 3: loglikelihood = -1433.1190863782388, backtracks = 0, tol = 0.12253545329680689 Iteration 4: loglikelihood = -1430.1821018809053, backtracks = 0, tol = 0.102107280457239 Iteration 5: loglikelihood = -1430.0073554364146, backtracks = 1, tol = 0.010079962963087132 Iteration 6: loglikelihood = -1429.9643694167694, backtracks = 2, tol = 0.004588507183297651 Iteration 7: loglikelihood = -1429.9375305898932, backtracks = 2, tol = 0.003878003488931927 Iteration 8: loglikelihood = -1429.9214444832937, backtracks = 2, tol = 0.0031063694760448493 Iteration 9: loglikelihood = -1429.9120967087551, backtracks = 2, tol = 0.0024001524513766175 Iteration 10: loglikelihood = -1429.9067602271634, backtracks = 2, tol = 0.0018209487064104353 Iteration 11: loglikelihood = -1429.9037418852988, backtracks = 2, tol = 0.0013705063118022002 Iteration 12: loglikelihood = -1429.9020433279109, backtracks = 2, tol = 0.0010279234944505153 Iteration 13: loglikelihood = -1429.901090387252, backtracks = 2, tol = 0.0007697112626351729 Iteration 14: loglikelihood = -1429.9005568372806, backtracks = 2, tol = 0.0005758354423128562 Iteration 15: loglikelihood = -1429.9002585274259, backtracks = 2, tol = 0.00043053575124364136 Iteration 16: loglikelihood = -1429.9000919138257, backtracks = 2, tol = 0.0003217583707356433 Iteration 17: loglikelihood = -1429.8999989273743, backtracks = 2, tol = 0.0002403828056612684 Iteration 18: loglikelihood = -1429.8999470617794, backtracks = 2, tol = 0.00017953992857124812 Iteration 19: loglikelihood = -1429.8999181448632, backtracks = 2, tol = 0.00013406864673504648 Iteration 20: loglikelihood = -1429.8999020278675, backtracks = 2, tol = 0.00010009711803309854 Iteration 21: loglikelihood = -1429.8998930471516, backtracks = 2, tol = 7.472396453371995e-5 Test Summary: | Pass Total Time fit NegativeBinomial SnpLinAlg | 4 4 1.3s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse linear regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1719.8834334827131, backtracks = 0, tol = 0.7482510650615045 Iteration 2: loglikelihood = -1457.5078832673241, backtracks = 0, tol = 0.11101466624275239 Iteration 3: loglikelihood = -1406.8093241896984, backtracks = 0, tol = 0.03755361101996953 Iteration 4: loglikelihood = -1405.870609897732, backtracks = 0, tol = 0.02620999117307883 Iteration 5: loglikelihood = -1405.6880550076662, backtracks = 0, tol = 0.0028494001153871362 Iteration 6: loglikelihood = -1405.6864854692672, backtracks = 1, tol = 9.414541328361198e-5 Test Summary: | Pass Total Time fit with >1 non-genetic covariates SnpLinAlg | 5 5 1.6s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse linear regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1506.5483905403487, backtracks = 0, tol = 0.2370582394433339 Iteration 2: loglikelihood = -1414.40398613282, backtracks = 0, tol = 0.05803753487643197 Iteration 3: loglikelihood = -1405.6406773008202, backtracks = 0, tol = 0.03374460520340846 Iteration 4: loglikelihood = -1405.4708630569994, backtracks = 1, tol = 0.0020892903391052015 Iteration 5: loglikelihood = -1405.4264545239982, backtracks = 1, tol = 0.0010477320810894529 Iteration 6: loglikelihood = -1405.414856838977, backtracks = 1, tol = 0.0005168468742437329 Iteration 7: loglikelihood = -1405.411837717244, backtracks = 1, tol = 0.0002510023934349695 Iteration 8: loglikelihood = -1405.4110550044009, backtracks = 1, tol = 0.0001203567502719193 Iteration 9: loglikelihood = -1405.4108529365396, backtracks = 1, tol = 5.7209997392654504e-5 Test Summary: | Pass Total Time model selection on non-genetic covariates | 5 5 0.8s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse linear regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 15 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1473.12410014528, backtracks = 0, tol = 0.11162633196865429 Iteration 2: loglikelihood = -1448.37403799896, backtracks = 0, tol = 0.07736217654955346 Iteration 3: loglikelihood = -1429.8981769610311, backtracks = 1, tol = 0.056531823476744666 Iteration 4: loglikelihood = -1404.7133956159753, backtracks = 0, tol = 0.10125409614175711 Iteration 5: loglikelihood = -1397.466171579031, backtracks = 0, tol = 0.05343369325195712 Iteration 6: loglikelihood = -1395.7490747391416, backtracks = 0, tol = 0.08843871418165569 Iteration 7: loglikelihood = -1395.4877576477586, backtracks = 0, tol = 0.0089247040684952 Iteration 8: loglikelihood = -1395.442237061722, backtracks = 0, tol = 0.005277867116132827 Iteration 9: loglikelihood = -1395.4302205892106, backtracks = 0, tol = 0.0027680467744013336 Iteration 10: loglikelihood = -1395.1973617039414, backtracks = 0, tol = 0.0905690065560604 Iteration 11: loglikelihood = -1395.0048067729406, backtracks = 0, tol = 0.007650485819168939 Iteration 12: loglikelihood = -1394.9835209063683, backtracks = 0, tol = 0.0035232591741737973 Iteration 13: loglikelihood = -1394.9793628241396, backtracks = 0, tol = 0.001852195878065177 Iteration 14: loglikelihood = -1394.9779889816232, backtracks = 0, tol = 0.0012530451800711444 Iteration 15: loglikelihood = -1394.977503420045, backtracks = 0, tol = 0.0006829444661300923 Iteration 16: loglikelihood = -1394.9773714862843, backtracks = 1, tol = 0.00022881022816864142 Iteration 17: loglikelihood = -1394.977310220191, backtracks = 2, tol = 0.0001217788197399568 Iteration 18: loglikelihood = -1394.977273607278, backtracks = 2, tol = 8.822469907087602e-5 **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse linear regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 3 Prior weight scaling = off Doubly sparse projection = on Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1535.4672180567934, backtracks = 0, tol = 0.17016419679985048 Iteration 2: loglikelihood = -1508.04343741211, backtracks = 0, tol = 0.21718489399873087 Iteration 3: loglikelihood = -1448.2717322168082, backtracks = 0, tol = 0.15334504607402907 Iteration 4: loglikelihood = -1437.5669418734744, backtracks = 0, tol = 0.08425396177776269 Iteration 5: loglikelihood = -1434.3602241747528, backtracks = 0, tol = 0.03199716666887782 Iteration 6: loglikelihood = -1434.239273652971, backtracks = 2, tol = 0.003498168340088273 Iteration 7: loglikelihood = -1434.1475478538455, backtracks = 2, tol = 0.0030522911015526556 Iteration 8: loglikelihood = -1434.0913475157126, backtracks = 2, tol = 0.0021931576818355514 Iteration 9: loglikelihood = -1434.0584761985995, backtracks = 2, tol = 0.0016688209654910561 Iteration 10: loglikelihood = -1434.0393127719108, backtracks = 2, tol = 0.001317554485128468 Iteration 11: loglikelihood = -1434.0281644425422, backtracks = 2, tol = 0.0010393713220469248 Iteration 12: loglikelihood = -1434.0216963632631, backtracks = 2, tol = 0.0008158673348111212 Iteration 13: loglikelihood = -1434.0179556115852, backtracks = 2, tol = 0.0006363671566384319 Iteration 14: loglikelihood = -1433.8972844529703, backtracks = 2, tol = 0.02105646084267335 Iteration 15: loglikelihood = -1433.6170929347984, backtracks = 1, tol = 0.011448126839540936 Iteration 16: loglikelihood = -1433.5408744767515, backtracks = 2, tol = 0.0040324300639331045 Iteration 17: loglikelihood = -1433.4945867179188, backtracks = 2, tol = 0.003005268578298657 Iteration 18: loglikelihood = -1433.467626121943, backtracks = 2, tol = 0.002187229771831438 Iteration 19: loglikelihood = -1433.4521439235273, backtracks = 2, tol = 0.0016467936133078437 Iteration 20: loglikelihood = -1433.4432822302874, backtracks = 2, tol = 0.0012631945762950846 Iteration 21: loglikelihood = -1433.4382075829426, backtracks = 2, tol = 0.0009580287583338291 Iteration 22: loglikelihood = -1433.4352962137846, backtracks = 2, tol = 0.0007222437442123496 Iteration 23: loglikelihood = -1433.4336216439426, backtracks = 2, tol = 0.0005424739396431532 Iteration 24: loglikelihood = -1433.43265547142, backtracks = 2, tol = 0.00040628145880685523 Iteration 25: loglikelihood = -1433.4320960523787, backtracks = 2, tol = 0.0003034179918772475 Iteration 26: loglikelihood = -1433.4317709097872, backtracks = 2, tol = 0.00022583740291084404 Iteration 27: loglikelihood = -1433.4315812027676, backtracks = 2, tol = 0.0001673653861249394 Iteration 28: loglikelihood = -1432.5898379532837, backtracks = 2, tol = 0.025080215054031605 Iteration 29: loglikelihood = -1431.7678006470733, backtracks = 1, tol = 0.017181190475547538 Iteration 30: loglikelihood = -1430.3157393955933, backtracks = 1, tol = 0.07333968264200234 Iteration 31: loglikelihood = -1429.706868513855, backtracks = 0, tol = 0.020015111727945754 Iteration 32: loglikelihood = -1429.5802551945537, backtracks = 1, tol = 0.00756937670420323 Iteration 33: loglikelihood = -1429.5139450553559, backtracks = 2, tol = 0.003906515984506227 Iteration 34: loglikelihood = -1429.4691972325213, backtracks = 2, tol = 0.003683664863256486 Iteration 35: loglikelihood = -1428.8607526222902, backtracks = 2, tol = 0.08711763846658777 Iteration 36: loglikelihood = -1428.6178427111051, backtracks = 1, tol = 0.006558345246943271 Iteration 37: loglikelihood = -1428.5424083746184, backtracks = 2, tol = 0.0033912200662443866 Iteration 38: loglikelihood = -1428.4933608487952, backtracks = 2, tol = 0.0030098214824111793 Iteration 39: loglikelihood = -1428.4620745885088, backtracks = 2, tol = 0.0025951371119133128 Iteration 40: loglikelihood = -1428.4427329028306, backtracks = 2, tol = 0.002148184701148465 Iteration 41: loglikelihood = -1428.4311433050725, backtracks = 2, tol = 0.0017160493175770867 Iteration 42: loglikelihood = -1428.4243474878394, backtracks = 2, tol = 0.0013407892924840973 Iteration 43: loglikelihood = -1428.420413936832, backtracks = 2, tol = 0.0010343694042998534 Iteration 44: loglikelihood = -1428.4181556141762, backtracks = 2, tol = 0.0007948565534422845 Iteration 45: loglikelihood = -1428.4168664091337, backtracks = 2, tol = 0.000608309643427293 Iteration 46: loglikelihood = -1428.4161334920516, backtracks = 2, tol = 0.0004622621654004415 Iteration 47: loglikelihood = -1428.4157180925672, backtracks = 2, tol = 0.00034956951660978575 Iteration 48: loglikelihood = -1428.4154831711999, backtracks = 2, tol = 0.00026348047442121094 Iteration 49: loglikelihood = -1428.4153505233908, backtracks = 2, tol = 0.00019816133989405092 Iteration 50: loglikelihood = -1428.4152757065372, backtracks = 2, tol = 0.00014882628973647444 Iteration 51: loglikelihood = -1428.4152335404317, backtracks = 2, tol = 0.00011167501044822909 Iteration 52: loglikelihood = -1428.4152097888611, backtracks = 2, tol = 8.375238803842589e-5 Test Summary: | Pass Total Time Correlated predictors and double sparsity Float64 matrix | 2 2 11.5s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse NegativeBinomial regression Number of threads = 1 Link functin = LogLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1468.4149026644245, backtracks = 0, tol = 0.28822081086215096 Iteration 2: loglikelihood = -1405.6908916955415, backtracks = 0, tol = 0.12010247003841744 Iteration 3: loglikelihood = -1373.012799074145, backtracks = 0, tol = 0.10665018355027024 Iteration 4: loglikelihood = -1352.5164532683293, backtracks = 0, tol = 0.057590395471246454 Iteration 5: loglikelihood = -1336.1198293867865, backtracks = 0, tol = 0.057798237620715606 Iteration 6: loglikelihood = -1331.8663991066473, backtracks = 0, tol = 0.03717502176775622 Iteration 7: loglikelihood = -1329.8824855076277, backtracks = 0, tol = 0.019106177016382047 Iteration 8: loglikelihood = -1328.8902629019024, backtracks = 0, tol = 0.017462969528120192 Iteration 9: loglikelihood = -1328.3412723672907, backtracks = 0, tol = 0.01072003827560655 Iteration 10: loglikelihood = -1328.0373054820216, backtracks = 0, tol = 0.009166835605377463 Iteration 11: loglikelihood = -1327.8604878512185, backtracks = 0, tol = 0.006494858141489911 Iteration 12: loglikelihood = -1327.7567996770747, backtracks = 0, tol = 0.005068125909615018 Iteration 13: loglikelihood = -1327.6934627786186, backtracks = 0, tol = 0.004112493121265622 Iteration 14: loglikelihood = -1327.654114117507, backtracks = 0, tol = 0.0029150612503846826 Iteration 15: loglikelihood = -1327.6286839212696, backtracks = 0, tol = 0.0027115600835065923 Iteration 16: loglikelihood = -1327.6119091041876, backtracks = 0, tol = 0.0017452349234992185 Iteration 17: loglikelihood = -1327.6004550762445, backtracks = 0, tol = 0.001853671145564522 Iteration 18: loglikelihood = -1327.5924965752183, backtracks = 0, tol = 0.0010898381709082024 Iteration 19: loglikelihood = -1327.5868269168263, backtracks = 0, tol = 0.0013039914601233756 Iteration 20: loglikelihood = -1327.582741397785, backtracks = 0, tol = 0.0007256582880223158 Iteration 21: loglikelihood = -1327.5797520426452, backtracks = 0, tol = 0.000936622306083662 Iteration 22: loglikelihood = -1327.577550990165, backtracks = 0, tol = 0.0005497106826310023 Iteration 23: loglikelihood = -1327.5759167464587, backtracks = 0, tol = 0.0006826238679386409 Iteration 24: loglikelihood = -1327.5746995790828, backtracks = 0, tol = 0.00041671746535400765 Iteration 25: loglikelihood = -1327.5737891434796, backtracks = 0, tol = 0.0005025073883982907 Iteration 26: loglikelihood = -1327.5731071263024, backtracks = 0, tol = 0.00031571721481887495 Iteration 27: loglikelihood = -1327.572595137671, backtracks = 0, tol = 0.00037244647450761735 Iteration 28: loglikelihood = -1327.5722104922243, backtracks = 0, tol = 0.00023899953858549843 Iteration 29: loglikelihood = -1327.5719212305894, backtracks = 0, tol = 0.0002773359703464836 Iteration 30: loglikelihood = -1327.5717035921405, backtracks = 0, tol = 0.00018079601578212926 Iteration 31: loglikelihood = -1327.5715397753274, backtracks = 0, tol = 0.0002071760198130959 Iteration 32: loglikelihood = -1327.5714164192511, backtracks = 0, tol = 0.000136699594640867 Iteration 33: loglikelihood = -1327.5713235208977, backtracks = 0, tol = 0.00015511098763435163 Iteration 34: loglikelihood = -1327.5712535312755, backtracks = 0, tol = 0.00010332835432660626 Iteration 35: loglikelihood = -1327.571200804198, backtracks = 0, tol = 0.00011631484600927222 Iteration 36: loglikelihood = -1327.5711610648366, backtracks = 0, tol = 7.809356799159955e-5 1.142446 seconds (3.28 M allocations: 62.164 MiB, 2.28% gc time, 50.73% 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 = -1528.319701334009, backtracks = 0, tol = 0.28822081086215096 Iteration 2: loglikelihood = -1510.8852027866428, backtracks = 0, tol = 0.1797556688283638 Iteration 3: loglikelihood = -1485.028325237688, backtracks = 0, tol = 0.10292774816787865 Iteration 4: loglikelihood = -1464.258380692393, backtracks = 0, tol = 0.09525423260241027 Iteration 5: loglikelihood = -1442.3804766114556, backtracks = 0, tol = 0.06649225615118216 Iteration 6: loglikelihood = -1421.833159596674, backtracks = 0, tol = 0.06202819957566343 Iteration 7: loglikelihood = -1411.9562422699184, backtracks = 0, tol = 0.08053590337955682 Iteration 8: loglikelihood = -1394.7640719124745, backtracks = 0, tol = 0.07615095535792642 Iteration 9: loglikelihood = -1385.9324642919962, backtracks = 0, tol = 0.05078968598922973 Iteration 10: loglikelihood = -1379.3391738164114, backtracks = 0, tol = 0.014760128230445277 Iteration 11: loglikelihood = -1376.2132474544653, backtracks = 0, tol = 0.059670730340701986 Iteration 12: loglikelihood = -1369.0686414878342, backtracks = 0, tol = 0.06435810615691896 Iteration 13: loglikelihood = -1364.9748529800377, backtracks = 0, tol = 0.055541211753811756 Iteration 14: loglikelihood = -1361.2430246183915, backtracks = 0, tol = 0.005979489884060162 Iteration 15: loglikelihood = -1358.172010008485, backtracks = 0, tol = 0.0010840599020143526 Iteration 16: loglikelihood = -1355.4286634063576, backtracks = 0, tol = 0.00047809202528588987 Iteration 17: loglikelihood = -1353.863149474323, backtracks = 0, tol = 0.057421233208439844 Iteration 18: loglikelihood = -1351.1910535017191, backtracks = 0, tol = 0.058893169406146174 Iteration 19: loglikelihood = -1348.9099532361406, backtracks = 0, tol = 0.007380696090919729 Iteration 20: loglikelihood = -1347.1779589467944, backtracks = 0, tol = 0.0011339238420445185 Iteration 21: loglikelihood = -1345.5862382337464, backtracks = 0, tol = 0.0004448117602783022 Iteration 22: loglikelihood = -1343.077099172677, backtracks = 1, tol = 0.000223913272696048 Iteration 23: loglikelihood = -1342.5654194666804, backtracks = 0, tol = 0.0541262841932651 Iteration 24: loglikelihood = -1341.1549206884674, backtracks = 0, tol = 0.059099067475805234 Iteration 25: loglikelihood = -1339.7139342479932, backtracks = 0, tol = 0.007283904830388935 Iteration 26: loglikelihood = -1338.7689728202013, backtracks = 0, tol = 0.0014793102719284695 Iteration 27: loglikelihood = -1337.8771261757067, backtracks = 0, tol = 0.0005825894400605029 Iteration 28: loglikelihood = -1336.4785982554054, backtracks = 1, tol = 0.0002244979310345413 Iteration 29: loglikelihood = -1335.0774637596646, backtracks = 1, tol = 0.00022022104582247382 Iteration 30: loglikelihood = -1333.843427957405, backtracks = 1, tol = 0.00026477116986002445 Iteration 31: loglikelihood = -1332.7587436294314, backtracks = 1, tol = 0.0002800341417859197 Iteration 32: loglikelihood = -1331.8017470667642, backtracks = 1, tol = 0.00027627310604754965 Iteration 33: loglikelihood = -1330.9534618149785, backtracks = 1, tol = 0.0002629155665231355 Iteration 34: loglikelihood = -1330.3101741979183, backtracks = 1, tol = 0.00024570022320294333 Iteration 35: loglikelihood = -1329.7477164144, backtracks = 1, tol = 0.00021513969112441707 Iteration 36: loglikelihood = -1329.2500815902422, backtracks = 1, tol = 0.0001875368610363833 Iteration 37: loglikelihood = -1328.8053830623605, backtracks = 1, tol = 0.00016515005659057348 Iteration 38: loglikelihood = -1328.4034301192096, backtracks = 1, tol = 0.0001471436998533807 Iteration 39: loglikelihood = -1328.035558008293, backtracks = 1, tol = 0.00013276854062338597 Iteration 40: loglikelihood = -1327.6947829665298, backtracks = 1, tol = 0.00012146604396455469 Iteration 41: loglikelihood = -1327.3759219490742, backtracks = 1, tol = 0.00011273608536675766 Iteration 42: loglikelihood = -1327.0755372591834, backtracks = 1, tol = 0.0001060680870486886 Iteration 43: loglikelihood = -1326.7916430812359, backtracks = 1, tol = 0.00010093084706247164 Iteration 44: loglikelihood = -1326.5232413775818, backtracks = 1, tol = 9.680726044889808e-5 0.481744 seconds (1.93 M allocations: 35.425 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 = -3551.7349, backtracks = 0, tol = 0.08013555563538065 Iteration 2: loglikelihood = -3492.4797, backtracks = 0, tol = 0.04896589649747134 Iteration 3: loglikelihood = -3485.867, backtracks = 1, tol = 0.018932079456006622 Iteration 4: loglikelihood = -3484.003, backtracks = 1, tol = 0.01008862413182005 Iteration 5: loglikelihood = -3483.513, backtracks = 1, tol = 0.005553987867655961 Iteration 6: loglikelihood = -3483.3884, backtracks = 1, tol = 0.0027562998254031575 Iteration 7: loglikelihood = -3483.359, backtracks = 1, tol = 0.0014512740210470571 Iteration 8: loglikelihood = -3483.3486, backtracks = 1, tol = 0.0007028527687432901 Iteration 9: loglikelihood = -3483.3467, backtracks = 1, tol = 0.0003674994532474764 Iteration 10: loglikelihood = -3483.3494, backtracks = 3, tol = 4.404838031067778e-5 25.481490 seconds (14.70 M allocations: 677.614 MiB, 4.17% gc time, 95.03% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** 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 = -3437.0144, backtracks = 0, tol = 0.08013555563538065 Iteration 2: loglikelihood = -3306.3503, backtracks = 0, tol = 0.05064869954519803 Iteration 3: loglikelihood = -3125.5032, backtracks = 1, tol = 0.017869468629632963 Iteration 4: loglikelihood = -2914.5974, backtracks = 1, tol = 0.009209184362750913 Iteration 5: loglikelihood = -2702.9988, backtracks = 1, tol = 0.004141375529704105 Iteration 6: loglikelihood = -2596.0034, backtracks = 0, tol = 0.08327663546586936 Iteration 7: loglikelihood = -2479.6016, backtracks = 0, tol = 0.09423794676287983 Iteration 8: loglikelihood = -2394.5334, backtracks = 0, tol = 0.09647551640691741 Iteration 9: loglikelihood = -2342.6396, backtracks = 0, tol = 0.09973255975720162 Iteration 10: loglikelihood = -2292.2004, backtracks = 0, tol = 0.12771523788176253 Iteration 11: loglikelihood = -2236.2563, backtracks = 0, tol = 0.12715577290179908 Iteration 12: loglikelihood = -2218.6824, backtracks = 0, tol = 0.13017584390653655 Iteration 13: loglikelihood = -2214.8809, backtracks = 0, tol = 0.12992230909945593 Iteration 14: loglikelihood = -2189.5925, backtracks = 0, tol = 0.1341728310537206 Iteration 15: loglikelihood = -2163.123, backtracks = 0, tol = 0.12566448600082517 Iteration 16: loglikelihood = -2145.948, backtracks = 1, tol = 0.0818015669668136 Iteration 17: loglikelihood = -2143.8418, backtracks = 1, tol = 0.0234619925520713 Iteration 18: loglikelihood = -2143.2761, backtracks = 1, tol = 0.013112231914229807 Iteration 19: loglikelihood = -2143.1035, backtracks = 1, tol = 0.007159773655789318 Iteration 20: loglikelihood = -2143.048, backtracks = 1, tol = 0.003803781212118962 Iteration 21: loglikelihood = -2143.0234, backtracks = 1, tol = 0.002008770129703277 Iteration 22: loglikelihood = -2143.0164, backtracks = 1, tol = 0.001069862280477717 Iteration 23: loglikelihood = -2143.0142, backtracks = 1, tol = 0.0005784789858422336 Iteration 24: loglikelihood = -2143.0127, backtracks = 1, tol = 0.00031602480805303836 Iteration 25: loglikelihood = -2143.0117, backtracks = 1, tol = 0.00017395064758098528 Iteration 26: loglikelihood = -2143.0, backtracks = 2, tol = 4.810609025579705e-5 0.213215 seconds (1.54 M allocations: 25.560 MiB) Test Summary: | Pass Total Time Negative binomial nuisance parameter Float32 matrix | 12 12 30.2s **** 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 = -2896.6116813943763, backtracks = 0, tol = 1.0257704354307222 Iteration 2: loglikelihood = -1753.4720992614753, backtracks = 0, tol = 0.28706825512903816 Iteration 3: loglikelihood = -1460.3823326395225, backtracks = 0, tol = 0.1059822007319242 Iteration 4: loglikelihood = -1438.5292259047123, backtracks = 0, tol = 0.028655431669451118 Iteration 5: loglikelihood = -1438.0856032112097, backtracks = 0, tol = 0.0034955373515602557 Iteration 6: loglikelihood = -1438.0744350329464, backtracks = 0, tol = 0.0005882060650840543 Iteration 7: loglikelihood = -1438.0741395461057, backtracks = 0, tol = 8.427264473927088e-5 4.690985 seconds (1.15 M allocations: 137.102 MiB, 1.55% gc time, 91.46% compilation time) Test Summary: | Pass Total Time initialze beta | 1 1 5.1s 10.071826 seconds (4.00 M allocations: 82.500 MiB, 0.52% gc time, 0.59% compilation time) 5.416525 seconds (3.98 M allocations: 91.678 MiB, 0.51% gc time) 10.341501 seconds (20.41 M allocations: 439.457 MiB, 1.00% gc time, 16.60% compilation time: 78% of which was recompilation) 8.029156 seconds (20.18 M allocations: 434.188 MiB, 0.84% gc time) 38.835797 seconds (3.85 M allocations: 4.244 GiB, 11.82% gc time, 25.87% compilation time) 55.380774 seconds (71.97 k allocations: 183.461 MiB) Test Summary: | Pass Total Time memory_efficient keyword | 7 7 2m25.8s Test Summary: | Pass Total Time update_support! | 10 10 0.6s 14.536 ms (78 allocations: 4.56 KiB) 4.837 μs (0 allocations: 0 bytes) 121.509 μs (4 allocations: 288 bytes) 6.407 μs (0 allocations: 0 bytes) 46.120 μs (2 allocations: 64 bytes) 29.930 μs (0 allocations: 0 bytes) 24.519 μs (0 allocations: 0 bytes) 27.950 μs (0 allocations: 0 bytes) 103.419 μs (0 allocations: 0 bytes) 37.431 ms (78 allocations: 4.56 KiB) 26.359 μs (0 allocations: 0 bytes) 166.659 μs (4 allocations: 288 bytes) 33.800 μs (0 allocations: 0 bytes) 194.288 μs (2 allocations: 64 bytes) 90.529 μs (0 allocations: 0 bytes) 120.979 μs (0 allocations: 0 bytes) 137.619 μs (0 allocations: 0 bytes) 185.088 μs (0 allocations: 0 bytes) Test Summary: | Total Time benchmarks for multivariate function | 0 2m16.3s **** 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 = -2900.9186300194497, backtracks = 0, tol = 0.1480224208200413 Iteration 2: loglikelihood = -2869.406464695619, backtracks = 0, tol = 0.035126790460779864 Iteration 3: loglikelihood = -2868.084702693443, backtracks = 0, tol = 0.0055693496163324524 Iteration 4: loglikelihood = -2868.034423817725, backtracks = 0, tol = 0.001118951762895177 Iteration 5: loglikelihood = -2868.030857635375, backtracks = 0, tol = 0.00031182601179138955 Iteration 6: loglikelihood = -2868.0305288614227, backtracks = 0, tol = 0.00010393305949947338 Iteration 7: loglikelihood = -2868.0304966516946, backtracks = 0, tol = 3.100862049859014e-5 0.437943 seconds (49.51 k allocations: 5.501 MiB, 63.24% compilation time) Test Summary: | Pass Total Time multivariate fit_iht SnpLinAlg | 7 7 11.9s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse 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 1.855927 seconds (282.43 k allocations: 168.145 MiB, 57.33% compilation time) Test Summary: | Pass Total Time initialze beta | 5 5 2.5s **** 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: 0:03:13 Cross validating... 16%|█████▏ | ETA: 0:00:36 Cross validating... 22%|███████▏ | ETA: 0:00:25 Cross validating... 25%|████████▏ | ETA: 0:00:21 Cross validating... 29%|█████████▏ | ETA: 0:00:18 Cross validating... 32%|██████████▏ | ETA: 0:00:16 Cross validating... 37%|███████████▋ | ETA: 0:00:13 Cross validating... 40%|████████████▊ | ETA: 0:00:12 Cross validating... 43%|█████████████▊ | ETA: 0:00:10 Cross validating... 46%|██████████████▊ | ETA: 0:00:09 Cross validating... 51%|████████████████▎ | ETA: 0:00:08 Cross validating... 54%|█████████████████▎ | ETA: 0:00:07 Cross validating... 57%|██████████████████▎ | ETA: 0:00:06 Cross validating... 60%|███████████████████▎ | ETA: 0:00:06 Cross validating... 63%|████████████████████▍ | ETA: 0:00:05 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:04 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:04 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:03 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:03 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:02 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:02 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:02 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:01 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:01 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:01 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:10 Crossvalidation Results: k MSE 0 2173.773617011234 1 1285.38898840821 2 994.6235285037935 3 820.9346009270387 4 605.4916381513165 5 538.6898777084601 6 456.7440803313051 7 385.05727500191193 8 357.53747476691336 9 338.35119733648105 10 342.8258256000903 11 344.7699867844324 12 347.4020989783097 13 348.6846570699492 14 350.0834768804574 15 365.59126934288355 16 373.3633772942357 17 357.1264994102638 18 357.4978380835702 19 358.0740464767962 20 370.4638093394942 Best k = 9 10.721836 seconds (11.94 M allocations: 320.051 MiB, 1.29% gc time, 60.55% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:03 Cross validating... 6%|██ | ETA: 0:00:03 Cross validating... 10%|███ | ETA: 0:00:03 Cross validating... 13%|████▏ | ETA: 0:00:03 Cross validating... 16%|█████▏ | ETA: 0:00:03 Cross validating... 19%|██████▏ | ETA: 0:00:03 Cross validating... 22%|███████▏ | ETA: 0:00:03 Cross validating... 25%|████████▏ | ETA: 0:00:03 Cross validating... 29%|█████████▏ | ETA: 0:00:03 Cross validating... 32%|██████████▏ | ETA: 0:00:03 Cross validating... 35%|███████████▏ | ETA: 0:00:03 Cross validating... 38%|████████████▎ | ETA: 0:00:03 Cross validating... 41%|█████████████▎ | ETA: 0:00:03 Cross validating... 44%|██████████████▎ | ETA: 0:00:03 Cross validating... 48%|███████████████▎ | ETA: 0:00:02 Cross validating... 51%|████████████████▎ | ETA: 0:00:02 Cross validating... 54%|█████████████████▎ | ETA: 0:00:02 Cross validating... 57%|██████████████████▎ | ETA: 0:00:02 Cross validating... 60%|███████████████████▎ | ETA: 0:00:02 Cross validating... 63%|████████████████████▍ | ETA: 0:00:02 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:02 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:01 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:01 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:01 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:01 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:01 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:00 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:00 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:04 Crossvalidation Results: k MSE 0 2173.773617011234 1 1285.5780897367142 2 999.2756079725986 3 824.5040626136462 4 608.5121493533074 5 543.398320337813 6 463.1860696413578 7 391.7171308620438 8 364.80954785233473 9 345.00019601325846 10 356.13085153556585 11 359.7405153124955 12 368.3609751178618 13 373.2683150772066 14 378.3334291539556 15 380.77326401756886 16 385.70525994340073 17 398.97341440933775 18 398.405457516488 19 400.53985843897954 20 408.8525922899811 Best k = 9 4.463502 seconds (11.09 M allocations: 234.663 MiB, 1.56% gc time, 0.94% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, normal model | 3 3 15.9s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:05:16 Cross validating... 8%|██▌ | ETA: 0:02:02 Cross validating... 11%|███▌ | ETA: 0:01:25 Cross validating... 17%|█████▋ | ETA: 0:00:51 Cross validating... 22%|███████▏ | ETA: 0:00:38 Cross validating... 27%|████████▋ | ETA: 0:00:30 Cross validating... 32%|██████████▏ | ETA: 0:00:24 Cross validating... 37%|███████████▋ | ETA: 0:00:20 Cross validating... 41%|█████████████▎ | ETA: 0:00:16 Cross validating... 46%|██████████████▊ | ETA: 0:00:14 Cross validating... 51%|████████████████▎ | ETA: 0:00:11 Cross validating... 56%|█████████████████▊ | ETA: 0:00:09 Cross validating... 60%|███████████████████▎ | ETA: 0:00:08 Cross validating... 65%|████████████████████▉ | ETA: 0:00:06 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:05 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:04 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:03 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:02 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:02 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:01 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:12 Crossvalidation Results: k MSE 0 1681.0513663330078 1 1352.1453282470702 2 1088.235284423828 3 844.2218167724609 4 679.3523568725586 5 547.818907043457 6 464.8884279174805 7 412.52451525878905 8 374.425591217041 9 359.17445654296876 10 362.65057211303713 11 365.1328537902832 12 367.57010556030275 13 372.6029356994629 14 370.9617658996582 15 374.808009552002 16 392.3361418762207 17 405.25897406005856 18 379.04033908081055 19 419.5201479797363 20 381.32220501708986 Best k = 9 13.967946 seconds (12.80 M allocations: 317.384 MiB, 0.87% gc time, 81.36% 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... 11%|███▌ | ETA: 0:00:02 Cross validating... 16%|█████▏ | ETA: 0:00:02 Cross validating... 21%|██████▋ | ETA: 0:00:02 Cross validating... 24%|███████▋ | ETA: 0:00:02 Cross validating... 27%|████████▋ | ETA: 0:00:02 Cross validating... 32%|██████████▏ | ETA: 0:00:02 Cross validating... 37%|███████████▋ | ETA: 0:00:02 Cross validating... 41%|█████████████▎ | ETA: 0:00:01 Cross validating... 48%|███████████████▎ | ETA: 0:00:01 Cross validating... 52%|████████████████▊ | ETA: 0:00:01 Cross validating... 57%|██████████████████▎ | ETA: 0:00:01 Cross validating... 60%|███████████████████▎ | ETA: 0:00:01 Cross validating... 65%|████████████████████▉ | ETA: 0:00:01 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:01 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:01 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:01 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:00 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:00 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:02 Crossvalidation Results: k MSE 0 1681.0513663330078 1 1353.130630493164 2 1092.267669189453 3 852.3066616210938 4 738.037489868164 5 554.2463104248047 6 467.4157903137207 7 425.2789981384277 8 385.35423770141597 9 370.1766893920898 10 379.29140274047853 11 386.91568200683594 12 392.3825672302246 13 410.7724143066406 14 411.8826365661621 15 416.5034630737305 16 425.96092510986324 17 427.9775028686523 18 431.04556436157225 19 429.9266233825683 20 429.85924276733397 Best k = 9 2.676926 seconds (10.93 M allocations: 201.035 MiB, 1.88% gc time, 1.65% compilation time) Test Summary: | Pass Total Time Cross validation on Float32 matrix, normal model | 2 2 17.9s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:59 Cross validating... 6%|██ | ETA: 0:00:32 Cross validating... 10%|███ | ETA: 0:00:22 Cross validating... 13%|████▏ | ETA: 0:00:17 Cross validating... 14%|████▋ | ETA: 0:00:16 Cross validating... 17%|█████▋ | ETA: 0:00:13 Cross validating... 21%|██████▋ | ETA: 0:00:11 Cross validating... 24%|███████▋ | ETA: 0:00:10 Cross validating... 27%|████████▋ | ETA: 0:00:09 Cross validating... 30%|█████████▋ | ETA: 0:00:08 Cross validating... 33%|██████████▋ | ETA: 0:00:07 Cross 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ETA: 0:00:01 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:01 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:07 Crossvalidation Results: k MSE 0 465.61232341281607 1 422.7956686031304 2 400.4571057635062 3 365.1739318729876 4 345.080929726764 5 334.87555172882765 6 326.56756092557714 7 323.8166939076491 8 321.0740280590344 9 324.63541776365713 10 326.2536910776058 11 330.08906001593886 12 360.11005230819853 13 336.6639083798528 14 338.4383482570182 15 344.94271268924786 16 361.9011084386007 17 335.8174967731559 18 340.44535658970034 19 373.96311653365774 20 374.5468366852539 Best k = 8 8.194548 seconds (18.21 M allocations: 431.366 MiB, 0.93% gc time, 31.55% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:05 Cross validating... 6%|██ | ETA: 0:00:05 Cross validating... 10%|███ | ETA: 0:00:05 Cross validating... 11%|███▌ | ETA: 0:00:05 Cross validating... 14%|████▋ | ETA: 0:00:05 Cross validating... 17%|█████▋ | ETA: 0:00:05 Cross validating... 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: 0:00:04 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... 51%|████████████████▎ | ETA: 0:00:03 Cross validating... 52%|████████████████▊ 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Crossvalidation Results: k MSE 0 465.61232341281607 1 423.2177589475481 2 401.4409643867795 3 367.17980116119224 4 347.788481542631 5 343.8714427067912 6 330.9752721557704 7 325.2515038739018 8 331.9464718997549 9 340.4626438006695 10 345.53546908881856 11 356.84313237250785 12 370.70311613199976 13 382.24549797954364 14 378.9325908687042 15 395.68712784135545 16 383.80970452969893 17 387.3267252376596 18 400.96344291884384 19 384.31445347199923 20 414.27432196214784 Best k = 7 5.727122 seconds (18.31 M allocations: 383.064 MiB, 1.12% gc time, 1.05% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, logistic model | 2 2 14.3s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:45 Cross validating... 6%|██ | ETA: 0:00:24 Cross validating... 10%|███ | ETA: 0:00:17 Cross validating... 13%|████▏ | ETA: 0:00:13 Cross validating... 16%|█████▏ | ETA: 0:00:11 Cross validating... 19%|██████▏ | ETA: 0:00:09 Cross validating... 22%|███████▏ | ETA: 0:00:08 Cross validating... 25%|████████▏ | ETA: 0:00:07 Cross validating... 29%|█████████▏ | ETA: 0:00:07 Cross validating... 32%|██████████▏ | ETA: 0:00:07 Cross validating... 35%|███████████▏ | ETA: 0:00:06 Cross validating... 38%|████████████▎ | ETA: 0:00:05 Cross validating... 41%|█████████████▎ | ETA: 0:00:05 Cross validating... 44%|██████████████▎ | ETA: 0:00:05 Cross validating... 48%|███████████████▎ | ETA: 0:00:05 Cross validating... 51%|████████████████▎ | ETA: 0:00:04 Cross validating... 54%|█████████████████▎ | ETA: 0:00:04 Cross validating... 57%|██████████████████▎ | ETA: 0:00:04 Cross validating... 60%|███████████████████▎ | ETA: 0:00:03 Cross validating... 63%|████████████████████▍ | ETA: 0:00:03 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:03 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:02 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:02 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:02 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:02 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:01 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:01 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:01 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:01 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:07 Crossvalidation Results: k MSE 0 462.46126192370855 1 436.3788548984383 2 392.55766977634124 3 380.08496935016905 4 360.20786478524616 5 334.2475518045129 6 335.0785642088731 7 333.4773991385122 8 335.17454081963405 9 338.82340861296586 10 335.5635875210826 11 343.20333756056215 12 346.7521237038778 13 351.4847202650563 14 359.7484233586697 15 372.5457802900498 16 393.69243570166833 17 353.02463086919875 18 352.44564117287183 19 402.84082278215726 20 361.4225069300453 Best k = 7 8.462987 seconds (16.15 M allocations: 377.547 MiB, 11.50% gc time, 29.76% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 5%|█▌ | ETA: 0:00:04 Cross validating... 8%|██▌ | ETA: 0:00:04 Cross validating... 11%|███▌ | ETA: 0:00:04 Cross validating... 14%|████▋ | ETA: 0:00:04 Cross validating... 17%|█████▋ | ETA: 0:00:04 Cross validating... 21%|██████▋ | ETA: 0:00:04 Cross validating... 24%|███████▋ | ETA: 0:00:04 Cross validating... 27%|████████▋ | ETA: 0:00:04 Cross validating... 30%|█████████▋ | ETA: 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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 0 462.46126192370855 1 438.35473700100783 2 395.44479278238356 3 384.78313320983483 4 364.23122751439973 5 338.3300732074654 6 342.3369580533078 7 343.5664643514124 8 350.5023078426035 9 360.54665012128675 10 354.95600893988257 11 381.1097765637084 12 388.2933502626226 13 387.96868179443186 14 394.6559919356824 15 390.68531174574184 16 410.0972814474608 17 416.5211273322821 18 400.5283480510846 19 405.1807612564925 20 421.234874842157 Best k = 5 5.327049 seconds (17.09 M allocations: 349.566 MiB, 1.07% gc time, 0.86% compilation time) Test Summary: | Pass Total Time Cross validation on Float64 matrix, logistic model | 2 2 15.1s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:01:01 Cross validating... 6%|██ | ETA: 0:00:32 Cross validating... 10%|███ | ETA: 0:00:22 Cross validating... 13%|████▏ | ETA: 0:00:17 Cross validating... 16%|█████▏ | ETA: 0:00:14 Cross validating... 19%|██████▏ | ETA: 0:00:12 Cross validating... 22%|███████▏ | ETA: 0:00:10 Cross validating... 25%|████████▏ | ETA: 0:00:09 Cross validating... 29%|█████████▏ | ETA: 0:00:08 Cross validating... 30%|█████████▋ | ETA: 0:00:08 Cross validating... 33%|██████████▋ | ETA: 0:00:07 Cross validating... 37%|███████████▋ | ETA: 0:00:06 Cross validating... 40%|████████████▊ | ETA: 0:00:06 Cross validating... 43%|█████████████▊ | ETA: 0:00:05 Cross validating... 46%|██████████████▊ | ETA: 0:00:05 Cross validating... 49%|███████████████▊ | ETA: 0:00:04 Cross validating... 52%|████████████████▊ | ETA: 0:00:04 Cross validating... 56%|█████████████████▊ | ETA: 0:00:04 Cross validating... 59%|██████████████████▊ | ETA: 0:00:03 Cross validating... 62%|███████████████████▊ | ETA: 0:00:03 Cross validating... 65%|████████████████████▉ | ETA: 0:00:03 Cross validating... 68%|█████████████████████▉ | ETA: 0:00:02 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:02 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:02 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:02 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:01 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:01 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:01 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:01 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:01 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:07 Crossvalidation Results: k MSE 0 495.1245727774985 1 470.1710594253064 2 447.75748603504303 3 406.4487196772552 4 389.3168106023038 5 373.77825915559436 6 377.14333683002303 7 379.1082341542507 8 380.84647264439985 9 382.31325440944863 10 387.3626644984708 11 412.4172142480045 12 388.4453171465107 13 391.1870644326118 14 391.95844580073424 15 393.7689733787068 16 405.8529179251257 17 407.94685557133164 18 410.5289049828823 19 436.9598509240835 20 396.6524035176014 Best k = 5 8.001698 seconds (16.94 M allocations: 417.148 MiB, 0.83% gc time, 33.09% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:04 Cross validating... 6%|██ | ETA: 0:00:05 Cross validating... 10%|███ | ETA: 0:00:04 Cross validating... 13%|████▏ | ETA: 0:00:05 Cross validating... 16%|█████▏ | ETA: 0:00:04 Cross validating... 19%|██████▏ | ETA: 0:00:04 Cross validating... 22%|███████▏ | ETA: 0:00:04 Cross validating... 25%|████████▏ | ETA: 0:00:04 Cross validating... 27%|████████▋ | ETA: 0:00:04 Cross validating... 30%|█████████▋ | ETA: 0:00:04 Cross validating... 33%|██████████▋ | ETA: 0:00:04 Cross validating... 37%|███████████▋ | ETA: 0:00:04 Cross validating... 40%|████████████▊ | ETA: 0:00:03 Cross validating... 43%|█████████████▊ | ETA: 0:00:03 Cross validating... 46%|██████████████▊ | ETA: 0:00:03 Cross validating... 49%|███████████████▊ | ETA: 0:00:03 Cross validating... 52%|████████████████▊ | ETA: 0:00:03 Cross validating... 56%|█████████████████▊ | ETA: 0:00:03 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... 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 0 495.1245727774985 1 469.30771599880353 2 447.33002802638487 3 409.8773723644737 4 391.5589083427511 5 375.56837593949814 6 383.41591414363415 7 389.93740728672225 8 396.7783975982708 9 402.53720580609047 10 413.7737040071166 11 425.86849674267245 12 417.82940263948706 13 422.7695670978603 14 429.4075088758871 15 437.2250169439302 16 428.9011844841722 17 444.0874748057431 18 448.26886373747993 19 451.87009883766603 20 439.4973422368462 Best k = 5 5.804898 seconds (17.07 M allocations: 364.656 MiB, 1.18% gc time, 1.02% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, Poisson model | 2 2 14.2s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:54 Cross validating... 5%|█▌ | ETA: 0:00:54 Cross validating... 6%|██ | ETA: 0:00:51 Cross 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98%|███████████████████████████████▌| ETA: 0:00:01 Cross validating... 100%|████████████████████████████████| Time: 0:00:44 Crossvalidation Results: k MSE 0 299.91952495171006 1 291.13683808226074 2 276.0941476847761 3 264.5918106548072 4 252.9096655305387 5 251.5935291833935 6 244.07199691282418 7 245.9431717307022 8 247.0162914802588 9 249.7781466637761 10 251.09501737166525 11 253.45580965621772 12 253.3942242198539 13 255.29821881548227 14 254.11423031338978 15 255.93730063899355 16 258.05971606896975 17 254.84257061427917 18 260.7236256024744 19 260.33200795312337 20 265.13137333563367 Best k = 6 45.137787 seconds (149.51 M allocations: 3.785 GiB, 1.24% gc time, 4.57% 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: 0:00:05 Cross 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94%|██████████████████████████████ | ETA: 0:00:01 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:01 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:13 Crossvalidation Results: k MSE 0 299.91952495171006 1 292.16613140005626 2 278.1122857630115 3 266.80937675593475 4 263.09466143189707 5 260.9634752480271 6 250.3318144711464 7 254.825118149877 8 255.6687307997368 9 265.57401611264754 10 269.15376616685353 11 273.34438604804035 12 279.3260229716295 13 277.7783093982347 14 290.9839226354886 15 291.3421967125528 16 290.611901776492 17 291.01312132744573 18 302.0307428171568 19 303.725493513021 20 306.6701717470875 Best k = 6 13.470350 seconds (46.47 M allocations: 997.429 MiB, 1.56% gc time, 0.45% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, NegativeBinomial model | 2 2 59.0s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:59 Cross validating... 6%|██ | ETA: 0:00:30 Cross validating... 10%|███ | ETA: 0:00:21 Cross validating... 13%|████▏ | ETA: 0:00:16 Cross validating... 16%|█████▏ | ETA: 0:00:13 Cross validating... 19%|██████▏ | ETA: 0:00:11 Cross validating... 22%|███████▏ | ETA: 0:00:09 Cross validating... 25%|████████▏ | ETA: 0:00:08 Cross validating... 29%|█████████▏ | ETA: 0:00:07 Cross validating... 33%|██████████▋ | ETA: 0:00:06 Cross validating... 38%|████████████▎ | ETA: 0:00:05 Cross validating... 41%|█████████████▎ | ETA: 0:00:05 Cross validating... 46%|██████████████▊ | ETA: 0:00:04 Cross validating... 49%|███████████████▊ | ETA: 0:00:04 Cross validating... 52%|████████████████▊ | ETA: 0:00:03 Cross validating... 57%|██████████████████▎ | ETA: 0:00:03 Cross validating... 60%|███████████████████▎ | ETA: 0:00:03 Cross validating... 63%|████████████████████▍ | 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... 79%|█████████████████████████▍ | ETA: 0:00:01 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:01 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:01 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:01 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:00 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:05 Crossvalidation Results: k MSE 0 709.7238911132813 1 600.8470166015625 2 478.37098138427734 3 399.75837347412113 4 316.3170971069336 5 274.59901690673826 6 232.61785809326173 7 221.00282696533208 8 205.62119918823245 9 198.3431817626953 10 200.94596459960937 11 201.86666357421876 12 202.35683154296873 13 208.02664166259768 14 206.9071481628418 15 209.87240182495117 16 216.0480528869629 17 212.0296098022461 18 217.49209603881837 19 225.60646734619144 20 213.36869631958012 Best k = 9 5.845347 seconds (17.01 M allocations: 337.910 MiB, 1.50% gc time, 43.10% 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: 0:00:02 Cross validating... 33%|██████████▋ | ETA: 0:00:02 Cross validating... 38%|████████████▎ | ETA: 0:00:02 Cross validating... 41%|█████████████▎ | ETA: 0:00:02 Cross validating... 46%|██████████████▊ | ETA: 0:00:02 Cross validating... 49%|███████████████▊ | ETA: 0:00:02 Cross validating... 52%|████████████████▊ | ETA: 0:00:02 Cross validating... 57%|██████████████████▎ | ETA: 0:00:01 Cross validating... 60%|███████████████████▎ | ETA: 0:00:01 Cross validating... 63%|████████████████████▍ | ETA: 0:00:01 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:01 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:01 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:01 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:01 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:01 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:01 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:00 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:00 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:03 Crossvalidation Results: k MSE 0 709.7238911132813 1 580.5206424560547 2 462.45179821777344 3 375.725685546875 4 311.8335130615235 5 265.69685809326177 6 235.52074707031255 7 221.8731430358887 8 209.48005477905275 9 202.0256286010742 10 206.40357376098632 11 209.8904744873047 12 212.83695938110353 13 217.36745034790042 14 219.17275009155276 15 218.94907879638671 16 225.10276358032226 17 228.24513723754882 18 225.50167910766604 19 235.0626920776367 20 227.98946899414062 Best k = 9 3.433085 seconds (16.17 M allocations: 286.711 MiB, 1.67% gc time, 1.69% compilation time) Test Summary: | Pass Total Time Cross validation on floating point matrices, NegativeBinomial model | 2 2 9.8s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 2%|▋ | ETA: 0:01:13 Cross validating... 3%|█ | ETA: 0:00:53 Cross validating... 4%|█▎ | ETA: 0:00:44 Cross validating... 5%|█▋ | ETA: 0:00:38 Cross validating... 6%|█▉ | ETA: 0:00:34 Cross validating... 7%|██▎ | ETA: 0:00:31 Cross validating... 8%|██▌ | ETA: 0:00:29 Cross validating... 9%|██▉ | ETA: 0:00:28 Cross validating... 10%|███▎ | ETA: 0:00:26 Cross validating... 11%|███▌ | ETA: 0:00:25 Cross validating... 12%|███▉ | ETA: 0:00:24 Cross validating... 13%|████▏ | ETA: 0:00:24 Cross validating... 14%|████▌ | ETA: 0:00:23 Cross validating... 15%|████▊ | ETA: 0:00:22 Cross validating... 16%|█████▏ | ETA: 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100%|████████████████████████████████| Time: 0:00:19 Crossvalidation Results: k MSE 1 3797.4105793809645 2 3336.3094293824565 3 3123.1851948233543 4 3058.877428701601 5 2988.236379873571 6 2992.148791291897 7 3002.0213603764714 8 3022.6019023102685 9 3039.097580530102 10 3066.8145791545653 11 3098.8530344289215 12 3127.722156242134 13 3144.541130879048 14 3103.6927824587565 15 3139.583870209679 16 3161.7296807910407 17 3163.306134525252 18 3169.330681470503 19 3221.132765503533 20 3275.4601854803677 Best k = 5 19.897128 seconds (356.23 k allocations: 288.729 MiB, 0.51% gc time, 7.52% compilation time) Test Summary: | Pass Total Time multivariate cross validation SnpLinAlg | 3 3 24.9s Test Summary: | Pass Total Time wrapper univariate | 20 20 1m46.6s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 2%|▋ | ETA: 0:00:10 Cross validating... 3%|█ | ETA: 0:00:10 Cross validating... 4%|█▎ | ETA: 0:00:11 Cross validating... 5%|█▋ | ETA: 0:00:11 Cross validating... 6%|█▉ | ETA: 0:00:12 Cross validating... 7%|██▎ | ETA: 0:00:12 Cross validating... 8%|██▌ | ETA: 0:00:12 Cross validating... 9%|██▉ | ETA: 0:00:14 Cross validating... 10%|███▎ | ETA: 0:00:14 Cross validating... 11%|███▌ | ETA: 0:00:15 Cross validating... 12%|███▉ | ETA: 0:00:16 Cross validating... 13%|████▏ | ETA: 0:00:16 Cross validating... 14%|████▌ | ETA: 0:00:16 Cross validating... 15%|████▊ | ETA: 0:00:17 Cross validating... 16%|█████▏ | ETA: 0:00:18 Cross validating... 17%|█████▌ | ETA: 0:00:19 Cross validating... 18%|█████▊ | ETA: 0:00:19 Cross validating... 19%|██████▏ | ETA: 0:00:19 Cross validating... 20%|██████▍ | ETA: 0:00:19 Cross validating... 21%|██████▊ | ETA: 0:00:18 Cross validating... 22%|███████ | ETA: 0:00:18 Cross validating... 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60%|███████████████████▎ | ETA: 0:00:10 Cross validating... 61%|███████████████████▌ | ETA: 0:00:09 Cross validating... 62%|███████████████████▉ | ETA: 0:00:09 Cross validating... 63%|████████████████████▏ | ETA: 0:00:09 Cross validating... 64%|████████████████████▌ | ETA: 0:00:08 Cross validating... 65%|████████████████████▊ | ETA: 0:00:08 Cross validating... 66%|█████████████████████▏ | ETA: 0:00:08 Cross validating... 67%|█████████████████████▌ | ETA: 0:00:08 Cross validating... 68%|█████████████████████▊ | ETA: 0:00:07 Cross validating... 69%|██████████████████████▏ | ETA: 0:00:07 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:07 Cross validating... 71%|██████████████████████▊ | ETA: 0:00:07 Cross validating... 72%|███████████████████████ | ETA: 0:00:06 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:06 Cross validating... 74%|███████████████████████▋ | ETA: 0:00:06 Cross validating... 75%|████████████████████████ | ETA: 0:00:06 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:06 Cross validating... 77%|████████████████████████▋ | ETA: 0:00:05 Cross validating... 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: 0:00:03 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: 0:00:24 Crossvalidation Results: k MSE 1 2838.788679198002 2 2514.3973428708136 3 2305.6176519676274 4 2222.025304867614 5 2075.1670384588365 6 2067.7948989723845 7 2053.427506114907 8 2086.405384830965 9 2080.984460901671 10 2105.131199502364 11 2132.407165368786 12 2138.267187460652 13 2166.002210829576 14 2194.9918295115804 15 2189.890403738045 16 2191.181293229578 17 2209.4669750564362 18 2221.2595493644303 19 2238.7425945763257 20 2253.9559571797727 Best k = 7 **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 2%|▋ | ETA: 0:00:14 Cross validating... 3%|█ | ETA: 0:00:13 Cross validating... 4%|█▎ | ETA: 0:00:13 Cross validating... 5%|█▋ | ETA: 0:00:12 Cross validating... 6%|█▉ | ETA: 0:00:13 Cross validating... 7%|██▎ | ETA: 0:00:13 Cross validating... 8%|██▌ | ETA: 0:00:13 Cross validating... 9%|██▉ | ETA: 0:00:14 Cross validating... 10%|███▎ | ETA: 0:00:15 Cross validating... 11%|███▌ | ETA: 0:00:16 Cross validating... 12%|███▉ | ETA: 0:00:16 Cross validating... 13%|████▏ | ETA: 0:00:16 Cross validating... 14%|████▌ | ETA: 0:00:17 Cross 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99%|███████████████████████████████▋| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:23 Crossvalidation Results: k MSE 1 2838.788679198002 2 2514.3973428708136 3 2305.6176519676274 4 2222.025304867614 5 2075.1670384588365 6 2067.7948989723845 7 2053.427506114907 8 2086.405384830965 9 2080.984460901671 10 2105.131199502364 11 2132.407165368786 12 2138.267187460652 13 2166.002210829576 14 2194.9918295115804 15 2189.890403738045 16 2191.181293229578 17 2209.4669750564362 18 2221.2595493644303 19 2238.7425945763257 20 2253.9559571797727 Best k = 7 **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 2%|▋ | ETA: 0:00:10 Cross validating... 4%|█▎ | ETA: 0:00:11 Cross validating... 6%|█▉ | ETA: 0:00:11 Cross validating... 7%|██▎ | ETA: 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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: 0:00:23 Crossvalidation Results: k MSE 1 2838.788679198002 2 2514.3973428708136 3 2305.6176519676274 4 2222.025304867614 5 2075.1670384588365 6 2067.7948989723845 7 2053.427506114907 8 2086.405384830965 9 2080.984460901671 10 2105.131199502364 11 2132.407165368786 12 2138.267187460652 13 2166.002210829576 14 2194.9918295115804 15 2189.890403738045 16 2191.181293229578 17 2209.4669750564362 18 2221.2595493644303 19 2238.7425945763257 20 2253.9559571797727 Best k = 7 Test Summary: | Pass Total Time wrapper multivariate | 8 8 1m25.8s read BGEN and VCF: Error During Test at /home/pkgeval/.julia/packages/MendelIHT/ZcxZT/test/wrapper_test.jl:184 Got exception outside of a @test startproc must be called before process Stacktrace: [1] error(s::String) @ Base ./error.jl:56 [2] process(codec::CodecZlib.ZlibDecompressor, input::TranscodingStreams.Memory, output::TranscodingStreams.Memory, error_ref::TranscodingStreams.Error) @ CodecZlib ~/.julia/packages/CodecZlib/lEc2s/src/decompression.jl:186 [3] decompress(io::IOStream, v::Variant, h::BGEN.Header; decompressed::Nothing) @ BGEN ~/.julia/packages/BGEN/dfgRU/src/genotypes.jl:72 [4] decompress @ ~/.julia/packages/BGEN/dfgRU/src/genotypes.jl:42 [inlined] [5] first_allele_dosage!(b::Bgen, v::Variant; T::Type, mean_impute::Bool, clear_decompressed::Bool, data::Nothing, decompressed::Nothing, is_decompressed::Bool) @ BGEN ~/.julia/packages/BGEN/dfgRU/src/genotypes.jl:571 [6] first_allele_dosage! @ ~/.julia/packages/BGEN/dfgRU/src/genotypes.jl:549 [inlined] [7] convert_bgen_gt(t::Type{Float64}, b::Bgen) @ MendelIHT ~/.julia/packages/MendelIHT/ZcxZT/src/wrapper.jl:380 [8] macro expansion @ ./timing.jl:739 [inlined] [9] macro expansion @ ~/.julia/packages/MendelIHT/ZcxZT/test/wrapper_test.jl:187 [inlined] [10] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:2246 [inlined] [11] top-level scope @ ~/.julia/packages/MendelIHT/ZcxZT/test/wrapper_test.jl:185 [12] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:327 [13] top-level scope @ ~/.julia/packages/MendelIHT/ZcxZT/test/runtests.jl:20 [14] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:327 [15] top-level scope @ none:6 [16] eval(m::Module, e::Any) @ Core ./boot.jl:517 [17] exec_options(opts::Base.JLOptions) @ Base ./client.jl:318 [18] _start() @ Base ./client.jl:593 Test Summary: | Error Total Time read BGEN and VCF | 1 1 3.0s RNG of the outermost testset: Xoshiro(0x7cb3ff61c92169ec, 0x0ca60689a9b2efee, 0x67c2707d0c10f8d9, 0xcaccf55db3510703, 0x350cfaffe9c64708) 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 1068.68s 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:3162 [3] test @ /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Operations.jl:3025 [inlined] [4] test(ctx::Pkg.Types.Context, pkgs::Vector{PackageSpec}; coverage::Bool, test_fn::Nothing, julia_args::Cmd, test_args::Cmd, force_latest_compatible_version::Bool, allow_earlier_backwards_compatible_versions::Bool, allow_reresolve::Bool, kwargs::@Kwargs{io::IOContext{IO}}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:586 [5] kwcall(::@NamedTuple{julia_args::Cmd, io::IOContext{IO}}, ::typeof(Pkg.API.test), ctx::Pkg.Types.Context, pkgs::Vector{PackageSpec}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:562 [6] test(pkgs::Vector{PackageSpec}; io::IOContext{IO}, kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:172 [7] kwcall(::@NamedTuple{julia_args::Cmd}, ::typeof(Pkg.API.test), pkgs::Vector{PackageSpec}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:161 [8] test(pkgs::Vector{String}; kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:160 [9] test @ /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:160 [inlined] [10] kwcall(::@NamedTuple{julia_args::Cmd}, ::typeof(Pkg.API.test), pkg::String) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:159 [11] top-level scope @ /PkgEval.jl/scripts/evaluate.jl:223 [12] include(mod::Module, _path::String) @ Base ./Base.jl:326 [13] exec_options(opts::Base.JLOptions) @ Base ./client.jl:352 [14] _start() @ Base ./client.jl:593 in expression starting at /PkgEval.jl/scripts/evaluate.jl:214 PkgEval failed after 1212.8s: package tests unexpectedly errored